Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

PubMed

Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J; Waghorn, Garry C; Janssen, Peter H

2013-01-01

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided.

A rapid and efficient DNA extraction protocol from fresh and frozen human blood samples.

PubMed

Guha, Pokhraj; Das, Avishek; Dutta, Somit; Chaudhuri, Tapas Kumar

2018-01-01

Different methods available for extraction of human genomic DNA suffer from one or more drawbacks including low yield, compromised quality, cost, time consumption, use of toxic organic solvents, and many more. Herein, we aimed to develop a method to extract DNA from 500 μL of fresh or frozen human blood. Five hundred microliters of fresh and frozen human blood samples were used for standardization of the extraction procedure. Absorbance at 260 and 280 nm, respectively, (A 260 /A 280 ) were estimated to check the quality and quantity of the extracted DNA sample. Qualitative assessment of the extracted DNA was checked by Polymerase Chain reaction and double digestion of the DNA sample. Our protocol resulted in average yield of 22±2.97 μg and 20.5±3.97 μg from 500 μL of fresh and frozen blood, respectively, which were comparable to many reference protocols and kits. Besides yielding bulk amount of DNA, our protocol is rapid, economical, and avoids toxic organic solvents such as Phenol. Due to unaffected quality, the DNA is suitable for downstream applications. The protocol may also be useful for pursuing basic molecular researches in laboratories having limited funds. © 2017 Wiley Periodicals, Inc.

Sample preservation, transport and processing strategies for honeybee RNA extraction: Influence on RNA yield, quality, target quantification and data normalization.

PubMed

Forsgren, Eva; Locke, Barbara; Semberg, Emilia; Laugen, Ane T; Miranda, Joachim R de

2017-08-01

Viral infections in managed honey bees are numerous, and most of them are caused by viruses with an RNA genome. Since RNA degrades rapidly, appropriate sample management and RNA extraction methods are imperative to get high quality RNA for downstream assays. This study evaluated the effect of various sampling-transport scenarios (combinations of temperature, RNA stabilizers, and duration) of transport on six RNA quality parameters; yield, purity, integrity, cDNA synthesis efficiency, target detection and quantification. The use of water and extraction buffer were also compared for a primary bee tissue homogenate prior to RNA extraction. The strategy least affected by time was preservation of samples at -80°C. All other regimens turned out to be poor alternatives unless the samples were frozen or processed within 24h. Chemical stabilizers have the greatest impact on RNA quality and adding an extra homogenization step (a QIAshredder™ homogenizer) to the extraction protocol significantly improves the RNA yield and chemical purity. This study confirms that RIN values (RNA Integrity Number), should be used cautiously with bee RNA. Using water for the primary homogenate has no negative effect on RNA quality as long as this step is no longer than 15min. Copyright © 2017 Elsevier B.V. All rights reserved.

Extractive sampling and optical remote sensing of F100 aircraft engine emissions.

PubMed

Cowen, Kenneth; Goodwin, Bradley; Joseph, Darrell; Tefend, Matthew; Satola, Jan; Kagann, Robert; Hashmonay, Ram; Spicer, Chester; Holdren, Michael; Mayfield, Howard

2009-05-01

The Strategic Environmental Research and Development Program (SERDP) has initiated several programs to develop and evaluate techniques to characterize emissions from military aircraft to meet increasingly stringent regulatory requirements. This paper describes the results of a recent field study using extractive and optical remote sensing (ORS) techniques to measure emissions from six F-15 fighter aircraft. Testing was performed between November 14 and 16, 2006 on the trim-pad facility at Tyndall Air Force Base in Panama City, FL. Measurements were made on eight different F100 engines, and the engines were tested on-wing of in-use aircraft. A total of 39 test runs were performed at engine power levels that ranged from idle to military power. The approach adopted for these tests involved extractive sampling with collocated ORS measurements at a distance of approximately 20-25 nozzle diameters downstream of the engine exit plane. The emission indices calculated for carbon dioxide, carbon monoxide, nitric oxide, and several volatile organic compounds showed very good agreement when comparing the extractive and ORS sampling methods.

Sources, spatial variation, and speciation of heavy metals in sediments of the Tamagawa River in Central Japan.

PubMed

Shikazono, N; Tatewaki, K; Mohiuddin, K M; Nakano, T; Zakir, H M

2012-01-01

Sediments of the Tamagawa River in central Japan were studied to explain the spatial variation, to identify the sources of heavy metals, and to evaluate the anthropogenic influence on these pollutants in the river. Sediment samples were collected from 20 sites along the river (five upstream, four midstream, and 11 downstream). Heavy metal concentrations, viz. chromium, nickel, copper, zinc, lead, cadmium, and molybdenum, in the samples were measured using inductively coupled plasma-mass spectroscopy. The chemical speciations of heavy metals in the sediments were identified by the widely used five-step Hall method. Lead isotopes were analyzed to identify what portion is contributed by anthropogenic sources. The total heavy metal concentrations were compared with global averages for continental crust (shale) and average values for Japanese river sediments. The mean heavy metal concentrations were higher in downstream sediments than in upstream and midstream samples, and the concentrations in the silt samples were higher than those in the sand samples. Speciation results demonstrate that, for chromium and nickel, the residual fractions were dominant. These findings imply that the influence of anthropogenic chromium and nickel contamination is negligible, while copper, zinc, and lead were mostly extracted in the non-residual fraction (metals in adsorbed/exchangeable/carbonate forms or bound to amorphous Fe oxyhydroxides, crystalline Fe oxides, or organic matter), indicating that these elements have high chemical mobility. The proportion of lead (Pb) isotopes in the downstream silt samples indicates that Pb accumulation is primarily derived from anthropogenic sources.

The LabTube - a novel microfluidic platform for assay automation in laboratory centrifuges.

PubMed

Kloke, A; Fiebach, A R; Zhang, S; Drechsel, L; Niekrawietz, S; Hoehl, M M; Kneusel, R; Panthel, K; Steigert, J; von Stetten, F; Zengerle, R; Paust, N

2014-05-07

Assay automation is the key for successful transformation of modern biotechnology into routine workflows. Yet, it requires considerable investment in processing devices and auxiliary infrastructure, which is not cost-efficient for laboratories with low or medium sample throughput or point-of-care testing. To close this gap, we present the LabTube platform, which is based on assay specific disposable cartridges for processing in laboratory centrifuges. LabTube cartridges comprise interfaces for sample loading and downstream applications and fluidic unit operations for release of prestored reagents, mixing, and solid phase extraction. Process control is achieved by a centrifugally-actuated ballpen mechanism. To demonstrate the workflow and functionality of the LabTube platform, we show two LabTube automated sample preparation assays from laboratory routines: DNA extractions from whole blood and purification of His-tagged proteins. Equal DNA and protein yields were observed compared to manual reference runs, while LabTube automation could significantly reduce the hands-on-time to one minute per extraction.

Successive DNA extractions improve characterization of soil microbial communities

PubMed Central

de Hollander, Mattias; Smidt, Hauke; van Veen, Johannes A.

2017-01-01

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition. PMID:28168105

Successful isolation and PCR amplification of DNA from National Institute of Standards and Technology herbal dietary supplement standard reference material powders and extracts.

PubMed

Cimino, Matthew T

2010-03-01

Twenty-four herbal dietary supplement powder and extract reference standards provided by the National Institute of Standards and Technology (NIST) were investigated using three different commercially available DNA extraction kits to evaluate DNA availability for downstream nucleotide-based applications. The material included samples of Camellia, Citrus, Ephedra, Ginkgo, Hypericum, Serenoa, And Vaccinium. Protocols from Qiagen, MoBio, and Phytopure were used to isolate and purify DNA from the NIST standards. The resulting DNA concentration was quantified using SYBR Green fluorometry. Each of the 24 samples yielded DNA, though the concentration of DNA from each approach was notably different. The Phytopure method consistently yielded more DNA. The average yield ratio was 22 : 3 : 1 (ng/microL; Phytopure : Qiagen : MoBio). Amplification of the internal transcribed spacer II region using PCR was ultimately successful in 22 of the 24 samples. Direct sequencing chromatograms of the amplified material suggested that most of the samples were comprised of mixtures. However, the sequencing chromatograms of 12 of the 24 samples were sufficient to confirm the identity of the target material. The successful extraction, amplification, and sequencing of DNA from these herbal dietary supplement extracts and powders supports a continued effort to explore nucleotide sequence-based tools for the authentication and identification of plants in dietary supplements. (c) Georg Thieme Verlag KG Stuttgart . New York.

EVALUATION OF ANDROSTENEDIONE AS AN ANDROGENIC COMPONENT OF RIVER WATER DOWNSTREAM OF A PULP AND PAPER MILL EFFLUENT

EPA Science Inventory

This study evaluates a recent report indicating that androstenedione contributes to the androgenicity of water downstream of a pulp and paper mill discharge on the Fenholloway River, Florida, USA. Extraction and concentration of Fenholloway water with C18 solid phase extraction c...

Design of the ILC RTML Extraction Lines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seletskiy, S.; Tenenbaum, P.; Walz, D.

2011-10-17

The ILC [1] Damping Ring to the Main Linac beamline (RTML) contains three extraction lines (EL). Each EL can be used both for an emergency abort dumping of the beam and tune-up continual train-by-train extraction. Two of the extraction lines are located downstream of the first and second stages of the RTML bunch compressor, and must accept both compressed and uncompressed beam with energy spreads of 2.5% and 0.15%, respectively. In this paper we report on an optics design that allowed minimizing the length of the extraction lines while offsetting the beam dumps from the main line by the distancemore » required for acceptable radiation levels in the service tunnel. The proposed extraction lines can accommodate beams with different energy spreads while at the same time providing the beam size acceptable for the aluminum dump window. The RTML incorporates three extraction lines, which can be used for either an emergency beam abort or for a train-by-train extraction. The first EL is located downstream of the Damping Ring extraction arc. The other two extraction lines are located downstream of each stage of the two-stage bunch compressor. The first extraction line (EL1) receives 5GeV beam with an 0.15% energy spread. The extraction line located downstream of the first stage of bunch compressor (ELBC1) receives both compressed and uncompressed beam, and therefore must accept beam with both 5 and 4.88GeV energy, and 0.15% and 2.5% energy spread, respectively. The extraction line located after the second stage of the bunch compressor (ELBC2) receives 15GeV beam with either 0.15 or 1.8% energy spread. Each of the three extraction lines is equipped with the 220kW aluminum ball dump, which corresponds to the power of the continuously dumped beam with 5GeV energy, i.e., the beam trains must be delivered to the ELBC2 dump at reduced repetition rate.« less

[Corrected Title: Solid-Phase Extraction of Polar Compounds from Water] Automated Electrostatics Environmental Chamber

NASA Technical Reports Server (NTRS)

Sauer, Richard; Rutz, Jeffrey; Schultz, John

2005-01-01

A solid-phase extraction (SPE) process has been developed for removing alcohols, carboxylic acids, aldehydes, ketones, amines, and other polar organic compounds from water. This process can be either a subprocess of a water-reclamation process or a means of extracting organic compounds from water samples for gas-chromatographic analysis. This SPE process is an attractive alternative to an Environmental Protection Administration liquid-liquid extraction process that generates some pollution and does not work in a microgravitational environment. In this SPE process, one forces a water sample through a resin bed by use of positive pressure on the upstream side and/or suction on the downstream side, thereby causing organic compounds from the water to be adsorbed onto the resin. If gas-chromatographic analysis is to be done, the resin is dried by use of a suitable gas, then the adsorbed compounds are extracted from the resin by use of a solvent. Unlike the liquid-liquid process, the SPE process works in both microgravity and Earth gravity. In comparison with the liquid-liquid process, the SPE process is more efficient, extracts a wider range of organic compounds, generates less pollution, and costs less.

Protocol Improvements for Low Concentration DNA-Based Bioaerosol Sampling and Analysis

PubMed Central

Ng, Chun Kiat; Miller, Dana; Cao, Bin

2015-01-01

Introduction As bioaerosol research attracts increasing attention, there is a need for additional efforts that focus on method development to deal with different environmental samples. Bioaerosol environmental samples typically have very low biomass concentrations in the air, which often leaves researchers with limited options in choosing the downstream analysis steps, especially when culture-independent methods are intended. Objectives This study investigates the impacts of three important factors that can influence the performance of culture-independent DNA-based analysis in dealing with bioaerosol environmental samples engaged in this study. The factors are: 1) enhanced high temperature sonication during DNA extraction; 2) effect of sampling duration on DNA recoverability; and 3) an alternative method for concentrating composite samples. In this study, DNA extracted from samples was analysed using the Qubit fluorometer (for direct total DNA measurement) and quantitative polymerase chain reaction (qPCR). Results and Findings The findings suggest that additional lysis from high temperature sonication is crucial: DNA yields from both high and low biomass samples increased up to 600% when the protocol included 30-min sonication at 65°C. Long air sampling duration on a filter media was shown to have a negative impact on DNA recoverability with up to 98% of DNA lost over a 20-h sampling period. Pooling DNA from separate samples during extraction was proven to be feasible with margins of error below 30%. PMID:26619279

Downstream Effects of Diversion Dams on Riparian Vegetation Communities in the Routt National Forest, Colorado

NASA Astrophysics Data System (ADS)

Caskey, S. T.; Wohl, E. E.; Dwire, K. A.; Merritt, D. M.; Schnackenberg, L.

2012-12-01

The relationship between riparian vegetation and changes in fluvial processes as a response to flow diversion is not well understood. Water extraction affects the hydrologic flow regime (i.e., magnitude, duration, and frequency of flows) reducing peak and base-flows, which could negatively impact riparian vegetation. Vegetation communities are temporally and spatially variable and are strongly interrelated with alluvial landforms and hydrograph variability. This research compares riparian community characteristics on diverted and undiverted pool-riffle channels and low gradient valleys to examine changes associated with flow diversion in the Routt National Forest (RNF). The RNF is the only under-appropriated area in Colorado, making future water extraction proposals likely. Many small extraction canals siphon water from small, headwater streams in the RNF, but the site-specific or cumulative effects of these diversions on riverine ecosystems have not been investigated. Systematic investigation is necessary, however, to determine whether existing flow diversions have influenced riparian communities and, if so, which communities are most sensitive to diversions. A total of 36 sites were sampled with five channel cross sections established per site, extending into the riparian zone at distance of two times the active channel width, and vegetation was sampled using the line-point intercept method. Preliminary results suggest a shift in vegetation communities from typical riparian species composition to more upland vegetation. The relative sensitivity of these responses are different depending on valley type; low- gradient, unconfined areas are less tolerant of diversion than steeper, confined reaches. Additionally, when stratified by plant assemblage, Salix abundance is significantly reduced downstream of diversion. The results of this study contribute to the collective understanding of mountain headwater riparian vegetation community response to changes in flow regimes and fluvial processes related directly to water extraction by diversion dams.

Use of Dimethyl Pimelimidate with Microfluidic System for Nucleic Acids Extraction without Electricity.

PubMed

Jin, Choong Eun; Lee, Tae Yoon; Koo, Bonhan; Choi, Kyung-Chul; Chang, Suhwan; Park, Se Yoon; Kim, Ji Yeun; Kim, Sung-Han; Shin, Yong

2017-07-18

The isolation of nucleic acids in the lab on a chip is crucial to achieve the maximal effectiveness of point-of-care testing for detection in clinical applications. Here, we report on the use of a simple and versatile single-channel microfluidic platform that combines dimethyl pimelimidate (DMP) for nucleic acids (both RNA and DNA) extraction without electricity using a thin-film system. The system is based on the adaption of DMP into nonchaotropic-based nucleic acids and the capture of reagents into a low-cost thin-film platform for use as a microfluidic total analysis system, which can be utilized for sample processing in clinical diagnostics. Moreover, we assessed the use of the DMP system for the extraction of nucleic acids from various samples, including mammalian cells, bacterial cells, and viruses from human disease, and we also confirmed that the quality and quantity of the nucleic acids extracted were sufficient to allow for the robust detection of biomarkers and/or pathogens in downstream analysis. Furthermore, this DMP system does not require any instruments and electricity, and has improved time efficiency, portability, and affordability. Thus, we believe that the DMP system may change the paradigm of sample processing in clinical diagnostics.

Mass spectrometry-based proteomics for translational research: a technical overview.

PubMed

Paulo, Joao A; Kadiyala, Vivek; Banks, Peter A; Steen, Hanno; Conwell, Darwin L

2012-03-01

Mass spectrometry-based investigation of clinical samples enables the high-throughput identification of protein biomarkers. We provide an overview of mass spectrometry-based proteomic techniques that are applicable to the investigation of clinical samples. We address sample collection, protein extraction and fractionation, mass spectrometry modalities, and quantitative proteomics. Finally, we examine the limitations and further potential of such technologies. Liquid chromatography fractionation coupled with tandem mass spectrometry is well suited to handle mixtures of hundreds or thousands of proteins. Mass spectrometry-based proteome elucidation can reveal potential biomarkers and aid in the development of hypotheses for downstream investigation of the molecular mechanisms of disease.

Mass Spectrometry-Based Proteomics for Translational Research: A Technical Overview

PubMed Central

Paulo, Joao A.; Kadiyala, Vivek; Banks, Peter A.; Steen, Hanno; Conwell, Darwin L.

2012-01-01

Mass spectrometry-based investigation of clinical samples enables the high-throughput identification of protein biomarkers. We provide an overview of mass spectrometry-based proteomic techniques that are applicable to the investigation of clinical samples. We address sample collection, protein extraction and fractionation, mass spectrometry modalities, and quantitative proteomics. Finally, we examine the limitations and further potential of such technologies. Liquid chromatography fractionation coupled with tandem mass spectrometry is well suited to handle mixtures of hundreds or thousands of proteins. Mass spectrometry-based proteome elucidation can reveal potential biomarkers and aid in the development of hypotheses for downstream investigation of the molecular mechanisms of disease. PMID:22461744

Invertebrate drift during in-channel gravel mining: the Upper River Cinca (Southern Pyrenees)

NASA Astrophysics Data System (ADS)

Béjar, Maria; Gibbins, Chris; Vericat, Damià; Batalla, Ramon J.; Muñoz, Efrén; Ramos, Ester; Lobera, Gemma; Andrés López-Tarazón, Jose; Piqué, Gemma; Tena, Álvaro; Buendía, Cristina; Rennie, Colin D.

2015-04-01

Invertebrate drift has been widely studied as an important mechanism to structure the benthic assemblages and as a part of invertebrate behavior in fluvial systems. River channel disturbance is considered the main factor affecting the organization of riverine communities and contributes to key ecological processes. However, little is known about involuntary drift associated to bed disturbance due to the difficulties associated with sampling during floods. In-channel gravel mining offers an opportunity to study involuntary drift associated not only to local bed disturbances but also to sudden changes on suspended sediment concentrations and flow. High suspended sediment concentrations and sudden changes in flow also prompt drift due to the limiting conditions (i.e. lack of oxygen, hydric stress). Within this context, invertebrate drift was monitored in the Upper River Cinca (Southern Pyrenees) during two gravel mining activities performed in summer 2014. The data acquisition design includes: drift, suspended sediment, bedload, bed mobility and flow. Data was acquired before, during and after mining at different sampling locations located upstream and downstream the perturbation. Drift and suspended sediment transport were sampled at 5 sections: 1 control site upstream the mining and 4 downstream. Bedload samples were collected just downstream the channel where gravels were extracted. Bed mobility and changes on topography were assessed by means of GPS-aDcp and repeat topographic surveys. Discharge was continuously recorded 2.5 km downstream the mining location. Additionally, two turbidity meters registered water turbidity at 15 minute intervals in two of the four sampling sections located downstream. This experimental design provides data on the spatial and temporal variability of drift associated to a local bed disturbance that (i) changes the distribution of flow across the section where mining was performed, (ii) increase substantially suspended sediment transport, and (iii) generates bed mobility and changes on local morphology and roughness that, ultimately, modify channel topography. Samples are being post-processed. Preliminary results show markedly differences in drift in terms of densities and species at different temporal and spatial scales. These differences can be attributed to the type of disturbance during mining: (i) hydric stress associated to changes on the distribution of flows, (ii) the sudden increase of suspended sediment concentrations, or (iii) high bed mobility just downstream from the mining location. These results will provide: (a) a new framework to understand ecological responses during river disturbances and (b) key information or guidelines for an appropriate management in human stressed fluvial systems.

An integratable microfluidic cartridge for forensic swab samples lysis.

PubMed

Yang, Jianing; Brooks, Carla; Estes, Matthew D; Hurth, Cedric M; Zenhausern, Frederic

2014-01-01

Fully automated rapid forensic DNA analysis requires integrating several multistep processes onto a single microfluidic platform, including substrate lysis, extraction of DNA from the released lysate solution, multiplexed PCR amplification of STR loci, separation of PCR products by capillary electrophoresis, and analysis for allelic peak calling. Over the past several years, most of the rapid DNA analysis systems developed started with the reference swab sample lysate and involved an off-chip lysis of collected substrates. As a result of advancement in technology and chemistry, addition of a microfluidic module for swab sample lysis has been achieved in a few of the rapid DNA analysis systems. However, recent reports on integrated rapid DNA analysis systems with swab-in and answer-out capability lack any quantitative and qualitative characterization of the swab-in sample lysis module, which is important for downstream forensic sample processing. Maximal collection and subsequent recovery of the biological material from the crime scene is one of the first and critical steps in forensic DNA technology. Herein we present the design, fabrication and characterization of an integratable swab lysis cartridge module and the test results obtained from different types of commonly used forensic swab samples, including buccal, saliva, and blood swab samples, demonstrating the compatibility with different downstream DNA extraction chemistries. This swab lysis cartridge module is easy to operate, compatible with both forensic and microfluidic requirements, and ready to be integrated with our existing automated rapid forensic DNA analysis system. Following the characterization of the swab lysis module, an integrated run from buccal swab sample-in to the microchip CE electropherogram-out was demonstrated on the integrated prototype instrument. Therefore, in this study, we demonstrate that this swab lysis cartridge module is: (1) functionally, comparable with routine benchtop lysis, (2) compatible with various types of swab samples and chemistries, and (3) integratable to achieve a micro total analysis system (μTAS) for rapid DNA analysis. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Reliable noninvasive prenatal testing by massively parallel sequencing of circulating cell-free DNA from maternal plasma processed up to 24h after venipuncture.

PubMed

Buysse, Karen; Beulen, Lean; Gomes, Ingrid; Gilissen, Christian; Keesmaat, Chantal; Janssen, Irene M; Derks-Willemen, Judith J H T; de Ligt, Joep; Feenstra, Ilse; Bekker, Mireille N; van Vugt, John M G; Geurts van Kessel, Ad; Vissers, Lisenka E L M; Faas, Brigitte H W

2013-12-01

Circulating cell-free fetal DNA (ccffDNA) in maternal plasma is an attractive source for noninvasive prenatal testing (NIPT). The amount of total cell-free DNA significantly increases 24h after venipuncture, leading to a relative decrease of the ccffDNA fraction in the blood sample. In this study, we evaluated the downstream effects of extended processing times on the reliability of aneuploidy detection by massively parallel sequencing (MPS). Whole blood from pregnant women carrying normal and trisomy 21 (T21) fetuses was collected in regular EDTA anti-coagulated tubes and processed within 6h, 24 and 48h after venipuncture. Samples of all three different time points were further analyzed by MPS using Z-score calculation and the percentage of ccffDNA based on X-chromosome reads. Both T21 samples were correctly identified as such at all time-points. However, after 48h, a higher deviation in Z-scores was noticed. Even though the percentage of ccffDNA in a plasma sample has been shown previously to significantly decrease 24h after venipuncture, the percentages based on MPS results did not show a significant decrease after 6, 24 or 48h. The quality and quantity of ccffDNA extracted from plasma samples processed up to 24h after venipuncture are sufficiently high for reliable downstream NIPT analysis by MPS. Furthermore, we show that it is important to determine the percentage of ccffDNA in the fraction of the sample that is actually used for NIPT, as downstream procedures might influence the fetal or maternal fraction. © 2013.

Probing emissions of military cargo aircraft: description of a joint field measurement Strategic Environmental Research and Development Program.

PubMed

Cheng, Meng-Dawn; Corporan, Edwin; DeWitt, Matthew J; Spicer, Chester W; Holdren, Michael W; Cowen, Kenneth A; Laskin, Alex; Harris, David B; Shores, Richard C; Kagann, Robert; Hashmonay, Ram

2008-06-01

To develop effective air quality control strategies for military air bases, there is a need to accurately quantify these emissions. In support of the Strategic Environmental Research and Development Program project, the particulate matter (PM) and gaseous emissions from two T56 engines on a parked C-130 aircraft were characterized at the Kentucky Air National Guard base in Louisville, KY. Conventional and research-grade instrumentation and methodology were used in the field campaign during the first week of October 2005. Particulate emissions were sampled at the engine exit plane and at 15 m downstream. In addition, remote sensing of the gaseous species was performed via spectroscopic techniques at 5 and 15 m downstream of the engine exit. It was found that PM mass and number concentrations measured at 15-m downstream locations, after dilution-correction generally agreed well with those measured at the engine exhaust plane; however, higher variations were observed in the far-field after natural dilution of the downstream measurements was accounted for. Using carbon dioxide-normalized data we demonstrated that gas species measurements by extractive and remote sensing techniques agreed reasonably well.

An Efficient Method for Genomic DNA Extraction from Different Molluscs Species

PubMed Central

Pereira, Jorge C.; Chaves, Raquel; Bastos, Estela; Leitão, Alexandra; Guedes-Pinto, Henrique

2011-01-01

The selection of a DNA extraction method is a critical step when subsequent analysis depends on the DNA quality and quantity. Unlike mammals, for which several capable DNA extraction methods have been developed, for molluscs the availability of optimized genomic DNA extraction protocols is clearly insufficient. Several aspects such as animal physiology, the type (e.g., adductor muscle or gills) or quantity of tissue, can explain the lack of efficiency (quality and yield) in molluscs genomic DNA extraction procedure. In an attempt to overcome these aspects, this work describes an efficient method for molluscs genomic DNA extraction that was tested in several species from different orders: Veneridae, Ostreidae, Anomiidae, Cardiidae (Bivalvia) and Muricidae (Gastropoda), with different weight sample tissues. The isolated DNA was of high molecular weight with high yield and purity, even with reduced quantities of tissue. Moreover, the genomic DNA isolated, demonstrated to be suitable for several downstream molecular techniques, such as PCR sequencing among others. PMID:22174651

[Spatial distribution characteristics of the physical and chemical properties of water in the Kunes River after the supply of snowmelt during spring].

PubMed

Liu, Xiang; Guo, Ling-Peng; Zhang, Fei-Yun; Ma, Jie; Mu, Shu-Yong; Zhao, Xin; Li, Lan-Hai

2015-02-01

Eight physical and chemical indicators related to water quality were monitored from nineteen sampling sites along the Kunes River at the end of snowmelt season in spring. To investigate the spatial distribution characteristics of water physical and chemical properties, cluster analysis (CA), discriminant analysis (DA) and principal component analysis (PCA) are employed. The result of cluster analysis showed that the Kunes River could be divided into three reaches according to the similarities of water physical and chemical properties among sampling sites, representing the upstream, midstream and downstream of the river, respectively; The result of discriminant analysis demonstrated that the reliability of such a classification was high, and DO, Cl- and BOD5 were the significant indexes leading to this classification; Three principal components were extracted on the basis of the principal component analysis, in which accumulative variance contribution could reach 86.90%. The result of principal component analysis also indicated that water physical and chemical properties were mostly affected by EC, ORP, NO3(-) -N, NH4(+) -N, Cl- and BOD5. The sorted results of principal component scores in each sampling sites showed that the water quality was mainly influenced by DO in upstream, by pH in midstream, and by the rest of indicators in downstream. The order of comprehensive scores for principal components revealed that the water quality degraded from the upstream to downstream, i.e., the upstream had the best water quality, followed by the midstream, while the water quality at downstream was the worst. This result corresponded exactly to the three reaches classified using cluster analysis. Anthropogenic activity and the accumulation of pollutants along the river were probably the main reasons leading to this spatial difference.

Simultaneous extraction of proteins and metabolites from cells in culture

PubMed Central

Sapcariu, Sean C.; Kanashova, Tamara; Weindl, Daniel; Ghelfi, Jenny; Dittmar, Gunnar; Hiller, Karsten

2014-01-01

Proper sample preparation is an integral part of all omics approaches, and can drastically impact the results of a wide number of analyses. As metabolomics and proteomics research approaches often yield complementary information, it is desirable to have a sample preparation procedure which can yield information for both types of analyses from the same cell population. This protocol explains a method for the separation and isolation of metabolites and proteins from the same biological sample, in order for downstream use in metabolomics and proteomics analyses simultaneously. In this way, two different levels of biological regulation can be studied in a single sample, minimizing the variance that would result from multiple experiments. This protocol can be used with both adherent and suspension cell cultures, and the extraction of metabolites from cellular medium is also detailed, so that cellular uptake and secretion of metabolites can be quantified. Advantages of this technique includes:1.Inexpensive and quick to perform; this method does not require any kits.2.Can be used on any cells in culture, including cell lines and primary cells extracted from living organisms.3.A wide variety of different analysis techniques can be used, adding additional value to metabolomics data analyzed from a sample; this is of high value in experimental systems biology. PMID:26150938

Detection of ethene and other hydrocarbons in gas turbine engine exhaust using non-intrusive FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Arrigone, Giovanni M.; Welch, Michael A.; Hilton, Moira; Miller, Michael N.; Wilson, Christopher W.

2003-04-01

As part of the EU funded project AEROJET2, a number of gas turbine engine tests were performed in different facilities around Europe. At Farnborough, UK a Spey engine was used to test a suite of prototype optically based instrumentation designed to measure exhaust gas emissions without using extractive probe systems. In addition to the AEROJET 2 prototype instrumentation, a Bruker Equinox 55 Fourier transform infrared (FTIR) spectrometer was used to obtain infrared spectra of the exhaust plume both in emission and absorption mode. The Bruker FTIR spectrometer was fitted with a periscope system so that different lines of sight could be monitored in the plume in a vertical plane 25 cm downstream from the nozzle exit and 20 cm upstream of the center line of sight of the AEROJET 2 prototype instrumentation. DERA (now QinetiQ) provided exhaust gas analysis data for different engine running conditions using samples extracted from the plume with an intrusive probe. The probe sampled along a horizontal plane across the centerline of the engine 45 cm downstream of the nozzle exit. The Bruker spectrometer used both InSb (indium antimonide) and MCT (mercury-cadmium-telluride) detectors to maximize the sensitivity across the IR range 600-4000 cm-1. Typically, CO2 and H2O IR signatures dominate the observed spectra of the plume. However, the engine tests showed that at low power engine conditions spectral features associated with CO around 2147 cm-1 and with hydrocarbons could be observed at around 3000 cm-1. In particular the presence of ethene (C2H2) was detected from observation of its characteristic in and out of plane vibration mode at 949 cm-1. At high engine powers the presence of NO was detected at 1900.3 cm-1. Species concentrations were calculated using a slab model for each line of sight compared against reference spectra. The engine plume was assumed to be symmetric about the centerline. On this basis, data from the extractive sampling gas analysis that had been obtained by traversing the probe across a horizontal plane through the centerline could be compared with non-intrusive measurements made by scanning vertically. Adjustments have been made to account for the 20 cm downstream offset in measurement planes of the probe and the spectrometer behind the nozzle exit.

Colloidal mode of transport in the Potomac River watershed

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maher, I.L.; Foster, G.D.

1995-12-31

Similarly to the particulate phase the colloidal phase may play an important role in the organic contaminant transport downstream the river. The colloidal phase consisting of microparticles and micromolecules which are small enough to be mobile and large enough to attract pollutants can absorb nonpolar organic compounds similarly as do soil and sediment particles. To test the hypothesis three river water samples have been analyzed for PAH content in the dissolved, the colloidal, and the particulate phase. The first sample was collected at the Blue Ridge province of Potomac River watershed, at Point of Rocks, the second one in themore » Pidmont province, at Riverbend Park, and the third sample at Coastal Plane, at Dyke Marsh (Belle Heven marina). In the laboratory environment each water sample was prefiltered to separate the particulate phase form the dissolved and colloidal phase. One part of the prefiltered water sample was ultrafiltered to separate colloids while the second part of the water was Goulden extracted. The separated colloidal phase was liquid-liquid extracted (LLE) while filters containing the suspended solids were Soxhlet extracted. The extracts of the particulate phase, the colloidal phase, and the dissolved plus colloidal phase were analyzed for selected PAHs via GC/MS. It is planned that concentrations of selected PAHs in three phases will be used for calculations of the partition coefficients, the colloid/dissolved partition coefficient and the particle/dissolved partition coefficient. Both partition coefficients will be compared to define the significance of organic contaminant transport by aquatic colloids.« less

Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods.

PubMed

Gautam, Aarti; Kumar, Raina; Dimitrov, George; Hoke, Allison; Hammamieh, Rasha; Jett, Marti

2016-10-01

miRNAs act as important regulators of gene expression by promoting mRNA degradation or by attenuating protein translation. Since miRNAs are stably expressed in bodily fluids, there is growing interest in profiling these miRNAs, as it is minimally invasive and cost-effective as a diagnostic matrix. A technical hurdle in studying miRNA dynamics is the ability to reliably extract miRNA as small sample volumes and low RNA abundance create challenges for extraction and downstream applications. The purpose of this study was to develop a pipeline for the recovery of miRNA using small volumes of archived serum samples. The RNA was extracted employing several widely utilized RNA isolation kits/methods with and without addition of a carrier. The small RNA library preparation was carried out using Illumina TruSeq small RNA kit and sequencing was carried out using Illumina platform. A fraction of five microliters of total RNA was used for library preparation as quantification is below the detection limit. We were able to profile miRNA levels in serum from all the methods tested. We found out that addition of nucleic acid based carrier molecules had higher numbers of processed reads but it did not enhance the mapping of any miRBase annotated sequences. However, some of the extraction procedures offer certain advantages: RNA extracted by TRIzol seemed to align to the miRBase best; extractions using TRIzol with carrier yielded higher miRNA-to-small RNA ratios. Nuclease free glycogen can be carrier of choice for miRNA sequencing. Our findings illustrate that miRNA extraction and quantification is influenced by the choice of methodologies. Addition of nucleic acid- based carrier molecules during extraction procedure is not a good choice when assaying miRNA using sequencing. The careful selection of an extraction method permits the archived serum samples to become valuable resources for high-throughput applications.

Evaluation of a Freezer Mill for Bone Pulverization prior to DNA Extraction: An Improved Workflow for STR Analysis.

PubMed

Morales Colón, Emely; Hernández, Mireya; Candelario, Mariel; Meléndez, María; Dawson Cruz, Tracey

2018-03-01

Traditional methods for bone pulverization typically generate heat, risking stability of DNA sample. SPEX™ has developed cryogenic grinders which introduce liquid nitrogen to cool the sample and aid in the grinding process. In this study, the Freezer Mill 6970 EFM was used with two DNA extraction methods and routine downstream STR analysis procedures. DNA from as little as 0.1 g of bone powder was used to develop full STR profiles after freezer mill pulverization, and the method was reproducible. Further, no contamination was detected upon cleaning/reuse of the sample vials. There were no significant differences in DNA yield, STR alleles detected, or peak heights using the freezer mill as compared to traditional grinding, and successful DNA profiles were achieved from as low as 0.1 g of bone powder with this method. Overall, this work indicates that this cryogenic mill method may be used as a viable alternative to traditional tissue grinders. © 2017 American Academy of Forensic Sciences.

Extraction and purification methods in downstream processing of plant-based recombinant proteins.

PubMed

Łojewska, Ewelina; Kowalczyk, Tomasz; Olejniczak, Szymon; Sakowicz, Tomasz

2016-04-01

During the last two decades, the production of recombinant proteins in plant systems has been receiving increased attention. Currently, proteins are considered as the most important biopharmaceuticals. However, high costs and problems with scaling up the purification and isolation processes make the production of plant-based recombinant proteins a challenging task. This paper presents a summary of the information regarding the downstream processing in plant systems and provides a comprehensible overview of its key steps, such as extraction and purification. To highlight the recent progress, mainly new developments in the downstream technology have been chosen. Furthermore, besides most popular techniques, alternative methods have been described. Copyright © 2015 Elsevier Inc. All rights reserved.

Application of solid-phase microextraction for in vivo laboratory and field sampling of pharmaceuticals in fish.

PubMed

Zhou, Simon Ningsun; Oakes, Ken D; Servos, Mark R; Pawliszyn, Janusz

2008-08-15

Previous field studies utilizing solid-phase microextraction (SPME) predominantly focused on volatile and semivolatile compounds in air or water. Earlier in vivo sampling studies utilizing SPME were limited to the liquid matrix (blood). The present study has expanded the SPME technique to semisolid tissues under laboratory and field conditions through the investigation of both theoretical and applied experimental approaches. Pre-equilibrium extraction and desorption were performed in vivo in two separate animals. Excellent linearity was found between the amounts extracted by SPME from the muscle of living fish and the waterborne concentrations of pharmaceuticals. A simple SPME method is also described to simultaneously determine free and total analyte concentrations in living tissue. The utility of in vivo SPME sampling was evaluated in wild fish collected from a number of different river locations under varying degrees of influence from municipal wastewater effluents. Diphenhydramine and diltiazem were detected in the muscle of fish downstream of a local wastewater treatment plant. Based on this study, SPME demonstrated several important advantages such as simplicity, sensitivity, and robustness under laboratory and in vivo field sampling conditions.

Occurrence of Organic Wastewater Compounds in the Tinkers Creek Watershed and Two Other Tributaries to the Cuyahoga River, Northeast Ohio

USGS Publications Warehouse

Tertuliani, J.S.; Alvarez, D.A.; Furlong, E.T.; Meyer, M.T.; Zaugg, S.D.; Koltun, G.F.

2008-01-01

The U.S. Geological Survey - in cooperation with the Ohio Water Development Authority; National Park Service; Cities of Aurora, Bedford, Bedford Heights, Solon, and Twinsburg; and Portage and Summit Counties - and in collaboration with the Ohio Environmental Protection Agency, did a study to determine the occurrence and distribution of organic wastewater compounds (OWCs) in the Tinkers Creek watershed in northeastern Ohio. In the context of this report, OWCs refer to a wide range of compounds such as antibiotics, prescription and nonprescription pharmaceuticals, personal-care products, household and industrial compounds (for example, antimicrobials, fragrances, surfactants, fire retardants, and so forth) and a variety of other chemicals. Canisters containing polar organic integrative sampler (POCIS) and semipermeable membrane device (SPMD) media were deployed instream for a 28-day period in Mayand June 2006 at locations upstream and downstream from seven wastewater-treatment-plant (WWTP) outfalls in the Tinkers Creek watershed, at a site on Tinkers Creek downstream from all WWTP discharges, and at one reference site each in two nearby watersheds (Yellow Creek and Furnace Run) that drain to the Cuyahoga River. Streambed-sediment samples also were collected at each site when the canisters were retrieved. POCIS and SPMDs are referred to as 'passive samplers' because they sample compounds that they are exposed to without use of mechanical or moving parts. OWCs detected in POCIS and SPMD extracts are referred to in this report as 'detections in water' because both POCIS and SPMDs provided time-weighted measures of concentration in the stream over the exposure period. Streambed sediments also reflect exposure to OWCs in the stream over a long period of time and provide another OWC exposure pathway for aquatic organisms. Four separate laboratory methods were used to analyze for 32 antibiotic, 20 pharmaceutical, 57 to 66 wastewater, and 33 hydrophobic compounds. POCIS and streambed-sediment extracts were analyzed by both the pharmaceutical and wastewater methods. POCIS extracts also were analyzed by the antibiotic method, and SPMD extracts were analyzed by the hydrophobic-compound method. Analytes associated with a given laboratory method are referred to in aggregate by the method name (for example, antibiotic-method analytes are referred to as 'antibiotic compounds') even though some analytes associated with the method may not be strictly classified as such. In addition, some compounds were included in the analyte list for more than one laboratory method. For a given sample matrix, individual compounds detected by more than one analytical method are included independently in counts for each method. A total of 12 antibiotic, 20 pharmaceutical, 41 wastewater, and 22 hydrophobic compounds were detected in water at one or more sites. Eight pharmaceutical and 37 wastewater compounds were detected in streambed sediments. The numbers of detections at reference sites tended to be in the low range of detection counts observed in the Tinkers Creek watershed for a given analytical method. Also, the total numbers of compounds detected in water and sediment at the reference sites were less than the total numbers of compounds detected at sites in the Tinkers Creek watershed. With the exception of hydrophobic compounds, it was common at most sites to have more compounds detected in samples collected downstream from WWTP outfalls than in corresponding samples collected upstream from the outfalls. This was particularly true for antibiotic, pharmaceutical, and wastewater compounds in water. In contrast, it was common to have more hydrophobic compounds detected in samples collected upstream from WWTP outfalls than downstream. Caffeine, fluoranthene, N,N-diethyl-meta-toluamide (DEET), phenanthrene, and pyrene were detected in water at all sites in the Tinkers Creek watershed, irrespective of whether the site was upstream or downs

Quality of water and bed material in streams of Logan Township, Gloucester County, New Jersey, 1984

USGS Publications Warehouse

Hochreiter, J.J.; Kozinski, Jane

1985-01-01

The surface water and surficial-bed material at seven stations on three streams in Logan Township, Gloucester County, New Jersey, were sampled in the fall of 1984. Samples of water were analyzed for volatile organic compounds, trace metals, and organochlorine and organophosphorous compounds. Surficial-bed material was analyzed for extractable trace metals and organochlorine compounds. Water samples from two closely spaced sampling locations along Raccoon Creek contained elevated concentrations of methylene chloride (455 and 1800 micrograms/L, respectively), a volatile organic solvent. Bed-material samples taken from Little Timber and Birch Creeks contained elevated levels of trace metals and organochlorine compounds, including polychlorinated biphenyls (PCB's). Contaminant concentrations in bed-material samples taken from Raccoon Creek were much lower than those found previously by the U.S. Geological Survey in 1980. Only a trace of PCB 's was detected in any bed material sample taken from Racoon Creek. Gas chromatographic flame-ionization detector scans, performed on solvent extracts of all water and sediment samples, were useful in characterizing the presence or absence of organic contaminants in those samples. Changes in the character of organic contamination along the reaches of two streams were apparent when the fingerprints of chromatograms representing upstream sites were compared to those representing downstream sites. (Author 's abstract)

Development and evaluation of a real-time fluorescent polymerase chain reaction assay for the detection of bovine contaminates in cattle feed.

PubMed

Rensen, Gabriel; Smith, Wayne; Ruzante, Juliana; Sawyer, Mary; Osburn, Bennie; Cullor, James

2005-01-01

A real-time fluorescent polymerase chain reaction assay for detecting prohibited ruminant materials such as bovine meat and bone meal (BMBM) in cattle feed using primers and FRET probes targeting the ruminant specific mitochondrial cytochrome b gene was developed and evaluated on two different types of cattle feed. Common problems involved with PCR based testing of cattle feed include the presence of high levels of PCR inhibitors and the need for certain pre-sample processing techniques in order to perform DNA extractions. We have developed a pre-sample processing technique for extracting DNA from cattle feed which does not require the feed sample to be ground to a fine powder and utilizes materials that are disposed of between samples, thus, reducing the potential of cross contamination. The DNA extraction method utilizes Whatman FTA card technology, is adaptable to high sample throughput analysis and allows for room temperature storage with established archiving of samples of up to 14 years. The Whatman FTA cards are subsequently treated with RNAse and undergo a Chelex-100 extraction (BioRad, Hercules, CA), thus removing potential PCR inhibitors and eluting the DNA from the FTA card for downstream PCR analysis. The detection limit was evaluated over a period of 30 trials on calf starter mix and heifer starter ration feed samples spiked with known concentrations of BMBM. The PCR detection assay detected 0.05% wt/wt BMBM contamination with 100% sensitivity, 100% specificity, and 100% confidence. Concentrations of 0.005% and 0.001% wt/wt BMBM contamination were also detected in both feed types but with varying levels of confidence.

Quality Control of RNA Preservation and Extraction from Paraffin-Embedded Tissue: Implications for RT-PCR and Microarray Analysis

PubMed Central

Pichler, Martin; Zatloukal, Kurt

2013-01-01

Analysis of RNA isolated from fixed and paraffin-embedded tissues is widely used in biomedical research and molecular pathological diagnostics. We have performed a comprehensive and systematic investigation of the impact of factors in the pre-analytical workflow, such as different fixatives, fixation time, RNA extraction method and storage of tissues in paraffin blocks, on several downstream reactions including complementary DNA (cDNA) synthesis, quantitative reverse transcription polymerase chain reaction (qRT-PCR) and microarray hybridization. We compared the effects of routine formalin fixation with the non-crosslinking, alcohol-based Tissue Tek Xpress Molecular Fixative (TTXMF, Sakura Finetek), and cryopreservation as gold standard for molecular analyses. Formalin fixation introduced major changes into microarray gene expression data and led to marked gene-to-gene variations in delta-ct values of qRT-PCR. We found that qRT-PCR efficiency and gene-to-gene variations were mainly attributed to differences in the efficiency of cDNA synthesis as the most sensitive step. These differences could not be reliably detected by quality assessment of total RNA isolated from formalin-fixed tissues by electrophoresis or spectrophotometry. Although RNA from TTXMF fixed samples was as fragmented as RNA from formalin fixed samples, much higher cDNA yield and lower ct-values were obtained in qRT-PCR underlining the negative impact of crosslinking by formalin. In order to better estimate the impact of pre-analytical procedures such as fixation on the reliability of downstream analysis, we applied a qRT-PCR-based assay using amplicons of different length and an assay measuring the efficiency of cDNA generation. Together these two assays allowed better quality assessment of RNA extracted from fixed and paraffin-embedded tissues and should be used to supplement quality scores derived from automated electrophoresis. A better standardization of the pre-analytical workflow, application of additional quality controls and detailed sample information would markedly improve the comparability and reliability of molecular studies based on formalin-fixed and paraffin-embedded tissue samples. PMID:23936242

Downstream processing of hyperforin from Hypericum perforatum root cultures.

PubMed

Haas, Paul; Gaid, Mariam; Zarinwall, Ajmal; Beerhues, Ludger; Scholl, Stephan

2018-05-01

Hyperforin is a major metabolite of the medicinal plant Hypericum perforatum (St. John's Wort) and has recently been found in hormone induced root cultures. The objective of this study is to identify a downstream process for the production of a hyperforin-rich extract with maximum extraction efficiency and minimal decomposition. The maximum extraction time was found to be 60min. The comparison of two equipment concepts for the extraction and solvent evaporation was performed employing two different solvents. While the rotary mixer showed better results for the extraction efficiency than a stirred vessel, the latter set-up was able to handle larger volumes but did not meet all process requirements. For the evaporation the prompt evaporation of the extraction agent using nitrogen stripping led to minor decomposition. In a 5L stirred vessel, the highest specific extraction of hyperforin was 4.3mg hyperforin/g dry weight bio material. Parameters for the equipment design for extraction and solvent evaporation were determined based on the experimental data. Copyright © 2017 Elsevier B.V. All rights reserved.

A Centrifugal Microfluidic Platform That Separates Whole Blood Samples into Multiple Removable Fractions Due to Several Discrete but Continuous Density Gradient Sections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moen, Scott T.; Hatcher, Christopher L.; Singh, Anup K.

We present a miniaturized centrifugal platform that uses density centrifugation for separation and analysis of biological components in small volume samples (~5 μL). We demonstrate the ability to enrich leukocytes for on-disk visualization via microscopy, as well as recovery of viable cells from each of the gradient partitions. In addition, we simplified the traditional Modified Wright-Giemsa staining by decreasing the time, volume, and expertise involved in the procedure. From a whole blood sample, we were able to extract 95.15% of leukocytes while excluding 99.8% of red blood cells. Furthermore, this platform has great potential in both medical diagnostics and researchmore » applications as it offers a simpler, automated, and inexpensive method for biological sample separation, analysis, and downstream culturing.« less

A Centrifugal Microfluidic Platform That Separates Whole Blood Samples into Multiple Removable Fractions Due to Several Discrete but Continuous Density Gradient Sections

DOE PAGES

Moen, Scott T.; Hatcher, Christopher L.; Singh, Anup K.

2016-04-07

We present a miniaturized centrifugal platform that uses density centrifugation for separation and analysis of biological components in small volume samples (~5 μL). We demonstrate the ability to enrich leukocytes for on-disk visualization via microscopy, as well as recovery of viable cells from each of the gradient partitions. In addition, we simplified the traditional Modified Wright-Giemsa staining by decreasing the time, volume, and expertise involved in the procedure. From a whole blood sample, we were able to extract 95.15% of leukocytes while excluding 99.8% of red blood cells. Furthermore, this platform has great potential in both medical diagnostics and researchmore » applications as it offers a simpler, automated, and inexpensive method for biological sample separation, analysis, and downstream culturing.« less

Short Communication An efficient method for simultaneous extraction of high-quality RNA and DNA from various plant tissues.

PubMed

Oliveira, R R; Viana, A J C; Reátegui, A C E; Vincentz, M G A

2015-12-29

Determination of gene expression is an important tool to study biological processes and relies on the quality of the extracted RNA. Changes in gene expression profiles may be directly related to mutations in regulatory DNA sequences or alterations in DNA cytosine methylation, which is an epigenetic mark. Correlation of gene expression with DNA sequence or epigenetic mark polymorphism is often desirable; for this, a robust protocol to isolate high-quality RNA and DNA simultaneously from the same sample is required. Although commercial kits and protocols are available, they are mainly optimized for animal tissues and, in general, restricted to RNA or DNA extraction, not both. In the present study, we describe an efficient and accessible method to extract both RNA and DNA simultaneously from the same sample of various plant tissues, using small amounts of starting material. The protocol was efficient in the extraction of high-quality nucleic acids from several Arabidopsis thaliana tissues (e.g., leaf, inflorescence stem, flower, fruit, cotyledon, seedlings, root, and embryo) and from other tissues of non-model plants, such as Avicennia schaueriana (Acanthaceae), Theobroma cacao (Malvaceae), Paspalum notatum (Poaceae), and Sorghum bicolor (Poaceae). The obtained nucleic acids were used as templates for downstream analyses, such as mRNA sequencing, quantitative real time-polymerase chain reaction, bisulfite treatment, and others; the results were comparable to those obtained with commercial kits. We believe that this protocol could be applied to a broad range of plant species, help avoid technical and sampling biases, and facilitate several RNA- and DNA-dependent analyses.

PMA-Linked Fluorescence for Rapid Detection of Viable Bacterial Endospores

NASA Technical Reports Server (NTRS)

LaDuc, Myron T.; Venkateswaran, Kasthuri; Mohapatra, Bidyut

2012-01-01

The most common approach for assessing the abundance of viable bacterial endospores is the culture-based plating method. However, culture-based approaches are heavily biased and oftentimes incompatible with upstream sample processing strategies, which make viable cells/spores uncultivable. This shortcoming highlights the need for rapid molecular diagnostic tools to assess more accurately the abundance of viable spacecraft-associated microbiota, perhaps most importantly bacterial endospores. Propidium monoazide (PMA) has received a great deal of attention due to its ability to differentiate live, viable bacterial cells from dead ones. PMA gains access to the DNA of dead cells through compromised membranes. Once inside the cell, it intercalates and eventually covalently bonds with the double-helix structures upon photoactivation with visible light. The covalently bound DNA is significantly altered, and unavailable to downstream molecular-based manipulations and analyses. Microbiological samples can be treated with appropriate concentrations of PMA and exposed to visible light prior to undergoing total genomic DNA extraction, resulting in an extract comprised solely of DNA arising from viable cells. This ability to extract DNA selectively from living cells is extremely powerful, and bears great relevance to many microbiological arenas.

High metal reactivity and environmental risks at a site contaminated by glass waste.

PubMed

Augustsson, A; Åström, M; Bergbäck, B; Elert, M; Höglund, L O; Kleja, D B

2016-07-01

This study addresses the reactivity and risks of metals (Ba, Cd, Co, Cr, Cu, Ni, Pb, Zn, As and Sb) at a Swedish site with large glass waste deposits. Old glassworks sites typically have high total metal concentrations, but as the metals are mainly bound within the glass waste and considered relatively inert, environmental investigations at these kinds of sites are limited. In this study, soil and landfill samples were subjected to a sequential chemical extraction procedure. Data from batch leaching tests and groundwater upstream and downstream of the waste deposits were also interpreted. The sequential extraction revealed that metals in <2 mm soil/waste samples were largely associated with geochemically active fractions, indicating that metals are released from pristine glass and subsequently largely retained in the surrounding soil and/or on secondary mineral coatings on fine glass particles. From the approximately 12,000 m(3) of coarse glass waste at the site, almost 4000 kg of Pb is estimated to have been lost through corrosion, which, however, corresponds to only a small portion of the total amount of Pb in the waste. Metal sorption within the waste deposits or in underlying soil layers is supported by fairly low metal concentrations in groundwater. However, elevated concentrations in downstream groundwater and in leachates of batch leaching tests were observed for several metals, indicating on-going leaching. Taken together, the high metal concentrations in geochemically active forms and the high amounts of as yet uncorroded metal-rich glass, indicate considerable risks to human health and the environment. Copyright © 2016. Published by Elsevier Ltd.

Development of a method for bacteria and virus recovery from heating, ventilation, and air conditioning (HVAC) filters.

PubMed

Farnsworth, James E; Goyal, Sagar M; Kim, Seung Won; Kuehn, Thomas H; Raynor, Peter C; Ramakrishnan, M A; Anantharaman, Senthilvelan; Tang, Weihua

2006-10-01

The aim of the work presented here is to study the effectiveness of building air handling units (AHUs) in serving as high volume sampling devices for airborne bacteria and viruses. An HVAC test facility constructed according to ASHRAE Standard 52.2-1999 was used for the controlled loading of HVAC filter media with aerosolized bacteria and virus. Nonpathogenic Bacillus subtilis var. niger was chosen as a surrogate for Bacillus anthracis. Three animal viruses; transmissible gastroenteritis virus (TGEV), avian pneumovirus (APV), and fowlpox virus were chosen as surrogates for three human viruses; SARS coronavirus, respiratory syncytial virus, and smallpox virus; respectively. These bacteria and viruses were nebulized in separate tests and injected into the test duct of the test facility upstream of a MERV 14 filter. SKC Biosamplers upstream and downstream of the test filter served as reference samplers. The collection efficiency of the filter media was calculated to be 96.5 +/- 1.5% for B. subtilis, however no collection efficiency was measured for the viruses as no live virus was ever recovered from the downstream samplers. Filter samples were cut from the test filter and eluted by hand-shaking. An extraction efficiency of 105 +/- 19% was calculated for B. subtilis. The viruses were extracted at much lower efficiencies (0.7-20%). Our results indicate that the airborne concentration of spore-forming bacteria in building AHUs may be determined by analyzing the material collected on HVAC filter media, however culture-based analytical techniques are impractical for virus recovery. Molecular-based identification techniques such as PCR could be used.

An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing.

PubMed

Amini, Parisa; Ettlin, Julia; Opitz, Lennart; Clementi, Elena; Malbon, Alexandra; Markkanen, Enni

2017-08-23

Formalin-fixed paraffin embedded (FFPE) tissue constitutes a vast treasury of samples for biomedical research. Thus far however, extraction of RNA from FFPE tissue has proved challenging due to chemical RNA-protein crosslinking and RNA fragmentation, both of which heavily impact on RNA quantity and quality for downstream analysis. With very small sample sizes, e.g. when performing Laser-capture microdissection (LCM) to isolate specific subpopulations of cells, recovery of sufficient RNA for analysis with reverse-transcription quantitative PCR (RT-qPCR) or next-generation sequencing (NGS) becomes very cumbersome and difficult. We excised matched cancer-associated stroma (CAS) and normal stroma from clinical specimen of FFPE canine mammary tumours using LCM, and compared the commonly used protease-based RNA isolation procedure with an adapted novel technique that additionally incorporates a focused ultrasonication step. We successfully adapted a protocol that uses focused ultrasonication to isolate RNA from small amounts of deparaffinised, stained, clinical LCM samples. Using this approach, we found that total RNA yields could be increased by 8- to 12-fold compared to a commonly used protease-based extraction technique. Surprisingly, RNA extracted using this new approach was qualitatively at least equal if not superior compared to the old approach, as Cq values in RT-qPCR were on average 2.3-fold lower using the new method. Finally, we demonstrate that RNA extracted using the new method performs comparably in NGS as well. We present a successful isolation protocol for extraction of RNA from difficult and limiting FFPE tissue samples that enables successful analysis of small sections of clinically relevant specimen. The possibility to study gene expression signatures in specific small sections of archival FFPE tissue, which often entail large amounts of highly relevant clinical follow-up data, unlocks a new dimension of hitherto difficult-to-analyse samples which now become amenable for investigation.

A modified protocol for RNA extraction from different peach tissues suitable for gene isolation and real-time PCR analysis.

PubMed

Tong, Zhaoguo; Qu, Shenchun; Zhang, Jiyu; Wang, Fei; Tao, Jianmin; Gao, Zhihong; Zhang, Zhen

2012-03-01

RNA extraction is the first step in the study of gene isolation and expression. However, it is difficult to extract high quantity and quality RNA from tissues containing large quantities of polysaccharides and polyphenols. Peach (Prunus persica), in addition to containing high levels of polysaccharides and polyphenols, is a challenging starting material for RNA isolation using a single method because of different amounts of those substances in diverse tissues. Based on three reported methods, we developed a modified RNA isolation protocol to solve this problem, leading to high quality and quantity of total RNA from peach mesocarp tissues of fruits which were sampled from all developmental stages and different storage periods, as well as from other tissues including flowers, leaves, stems, and roots. With our modified method, 28-650 μg of total RNA was routinely obtained from per gram of fresh material, gave at least a 1.16-fold improvement by compared with those isolated by other seven methods. The RNA extracts were successfully used in downstream applications such as RT-PCR, RACE, and real-time PCR.

Comparison of Different Buffers for Protein Extraction from Formalin-Fixed and Paraffin-Embedded Tissue Specimens.

PubMed

Shen, Kaini; Sun, Jian; Cao, Xinxin; Zhou, Daobin; Li, Jian

2015-01-01

We determined the best extraction buffer for proteomic investigation using formalin-fixation and paraffin-embedded (FFPE) specimens. A Zwittergent 3-16 based buffer, sodium dodecyl sulfate (SDS)-containing buffer with/without polyethylene glycol 20000 (PEG20000), urea-containing buffer, and FFPE-FASP protein preparation kit were compared for protein extraction from different types of rat FFPE tissues, including the heart, brain, liver, lung, and kidney. All of the samples were divided into two groups of laser microdissected (LMD) and non-LMD specimens. For both kinds of specimens, Zwittergent was the most efficient buffer for identifying peptides and proteins, was broadly applicable to different tissues without impairing the enzymatic digestion, and was well compatible with mass spectrometry analysis. As a high molecular weight carrier substance, PEG20000 improved the identification of peptides and proteins; however, such an advantage is limited to tissues containing submicrograms to micrograms of protein. Considering its low lytic strength, urea-containing buffer would not be the first alternative for protein recovery. In conclusion, Zwittergent 3-16 is an effective buffer for extracting proteins from FFPE specimens for downstream proteomics analysis.

[Laser microdissection for biology and medicine].

PubMed

Podgornyĭ, O V; Lazarev, V N; Govorun, V M

2012-01-01

For routine extraction of DNA, RNA, proteins and metabolites, small tissue pieces are placed into lysing solution. These tissue pieces in general contain different cell types. For this reason, lysate contains components of different cell types, which complicates the interpretation of molecular analysis results. The laser microdissection allows overcoming this trouble. The laser microdissection is a method to procure tissue samples contained defined cell subpopulations, individual cells and even subsellular components under direct microscopic visualization. Collected samples can be undergone to different downstream molecular assays: DNA analysis, RNA transcript profiling, cDNA library generation and gene expression analysis, proteomic analysis and metabolite profiling. The laser microdissection has wide applications in oncology (research and routine), cellular and molecular biology, biochemistry and forensics. This paper reviews the principles of different laser microdissection instruments, examples of laser microdissection application and problems of sample preparation for laser microdissection.

A floating trap for sampling downstream migrant fishes.

Treesearch

Carl E. McLemore; Fred H. Everest; William R. Humphreys; Mario F. Solazzi

1989-01-01

Fishery scientists and managers are interested in obtaining information about downstream movements of fish species for biological and economic reasons. Different types of nets and traps have been used for this purpose with only partial success. The floating, self-cleaning downstream migrant trap described here proved successful for sampling several salmoniform and...

Effects of small impoundments on downstream crayfish assemblages

Treesearch

Susan B. Adams

2013-01-01

Dams and impoundments, both large and small, affect downstream physicochemical characteristics and up- and downstream biotic communities. I tested whether small dams and their impoundments altered downstream crayfish assemblages in northern Mississippi. I sampled crayfish and measured physicochemical variables at 4 sites downstream of impoundments (outlet sites) and 4...

A novel combination of silane-coated silica colloid with hybrid RNA extraction protocol and RNA enrichment for downstream applications of spermatozoal RNA.

PubMed

Vijayalakshmy, K; Kumar, P; Virmani, M; Pawaria, S; Lalaji, N S; Sharma, P; Rajendran, R; Yadav, P S; Kumar, D

2018-05-14

Spermatozoa are specialised cells with low RNA content as compared to somatic cells. The suitable sperm RNA extraction and enrichment protocols for downstream applications are available for human, cattle, stallion and mouse but not for buffalo spermatozoa. Therefore, the present work was conducted to find out suitable colloidal solution for sperm purification and appropriate protocol for sperm RNA extraction and enrichment/amplification of RNA. For purification, we used PVP-coated silica colloidal solution (PVP-Si), silane-coated silica colloidal solution (Silane-Si) and iodixanol. Sperm recovery rate, total sperm motility and progressive sperm motility were significantly improved after separation by Silane-Si and iodixanol compared to PVA-Si method. The combined guanidinium thiocyanate-phenol-chloroform (GTPC) with silica matrix (SM)-based RNA extraction yielded more quantity of RNA in compared to individual method. The hybrid of SM and GTPC into a single protocol yielded 360-450 ng RNA from 30 million buffalo spermatozoa. For the first time, we adopted new way to enrich sperm RNA that increased the RNA concentration 4-5 times that was sufficient for downstream applications. The linear amplification of sperm RNA increased RNA concentration around 27-45 times. In summary, Silane-Si colloid for sperm separation, hybrid SM and GTPC protocol for sperm RNA extraction followed by enrichment or amplification of RNA was found suitable for high-throughput analyses of buffalo sperm RNA. © 2018 Blackwell Verlag GmbH.

Efficient recovery of proteins from multiple source samples after TRIzol(®) or TRIzol(®)LS RNA extraction and long-term storage.

PubMed

Simões, André E S; Pereira, Diane M; Amaral, Joana D; Nunes, Ana F; Gomes, Sofia E; Rodrigues, Pedro M; Lo, Adrian C; D'Hooge, Rudi; Steer, Clifford J; Thibodeau, Stephen N; Borralho, Pedro M; Rodrigues, Cecília M P

2013-03-15

Simultaneous isolation of nucleic acids and proteins from a single biological sample facilitates meaningful data interpretation and reduces time, cost and sampling errors. This is particularly relevant for rare human and animal specimens, often scarce, and/or irreplaceable. TRIzol(®) and TRIzol(®)LS are suitable for simultaneous isolation of RNA, DNA and proteins from the same biological sample. These reagents are widely used for RNA and/or DNA isolation, while reports on their use for protein extraction are limited, attributable to technical difficulties in protein solubilisation. TRIzol(®)LS was used for RNA isolation from 284 human colon cancer samples, including normal colon mucosa, tubulovillous adenomas, and colon carcinomas with proficient and deficient mismatch repair system. TRIzol(®) was used for RNA isolation from human colon cancer cells, from brains of transgenic Alzheimer's disease mice model, and from cultured mouse cortical neurons. Following RNA extraction, the TRIzol(®)-chloroform fractions from human colon cancer samples and from mouse hippocampus and frontal cortex were stored for 2 years and 3 months, respectively, at -80°C until used for protein isolation.Simple modifications to the TRIzol(®) manufacturer's protocol, including Urea:SDS solubilization and sonication, allowed improved protein recovery yield compared to the TRIzol(®) manufacturer's protocol. Following SDS-PAGE and Ponceau and Coomassie staining, recovered proteins displayed wide molecular weight range and staining pattern comparable to those obtainable with commonly used protein extraction protocols. We also show that nuclear and cytosolic proteins can be easily extracted and detected by immunoblotting, and that posttranslational modifications, such as protein phosphorylation, are detectable in proteins recovered from TRIzol(®)-chloroform fractions stored for up to 2 years at -80°C. We provide a novel approach to improve protein recovery from samples processed for nucleic acid extraction with TRIzol(®) and TRIzol(®)LS compared to the manufacturer`s protocol, allowing downstream immunoblotting and evaluation of steady-state relative protein expression levels. The method was validated in large sets of samples from multiple sources, including human colon cancer and brains of transgenic Alzheimer's disease mice model, stored in TRIzol(®)-chloroform for up to two years. Collectively, we provide a faster and cheaper alternative to the TRIzol(®) manufacturer`s protein extraction protocol, illustrating the high relevance, and wide applicability, of the present protein isolation method for the immunoblot evaluation of steady-state relative protein expression levels in samples from multiple sources, and following prolonged storage.

Lagrangian sampling of wastewater treatment plant effluent in Boulder Creek, Colorado, and Fourmile Creek, Iowa, during the summer of 2003 and spring of 2005--Hydrological and chemical data

USGS Publications Warehouse

Barber, Larry B.; Keefe, Steffanie H.; Kolpin, Dana W.; Schnoebelen, Douglas J.; Flynn, Jennifer L.; Brown, Gregory K.; Furlong, Edward T.; Glassmeyer, Susan T.; Gray, James L.; Meyer, Michael T.; Sandstrom, Mark W.; Taylor, Howard E.; Zaugg, Steven D.

2011-01-01

This report presents methods and data for a Lagrangian sampling investigation into chemical loading and in-stream attenuation of inorganic and organic contaminants in two wastewater treatment-plant effluent-dominated streams: Boulder Creek, Colorado, and Fourmile Creek, Iowa. Water-quality sampling was timed to coincide with low-flow conditions when dilution of the wastewater treatment-plant effluent by stream water was at a minimum. Sample-collection times corresponded to estimated travel times (based on tracer tests) to allow the same "parcel" of water to reach downstream sampling locations. The water-quality data are linked directly to stream discharge using flow- and depth-integrated composite sampling protocols. A range of chemical analyses was made for nutrients, carbon, major elements, trace elements, biological components, acidic and neutral organic wastewater compounds, antibiotic compounds, pharmaceutical compounds, steroid and steroidal-hormone compounds, and pesticide compounds. Physical measurements were made for field conditions, stream discharge, and time-of-travel studies. Two Lagrangian water samplings were conducted in each stream, one in the summer of 2003 and the other in the spring of 2005. Water samples were collected from five sites in Boulder Creek: upstream from the wastewater treatment plant, the treatment-plant effluent, and three downstream sites. Fourmile Creek had seven sampling sites: upstream from the wastewater treatment plant, the treatment-plant effluent, four downstream sites, and a tributary. At each site, stream discharge was measured, and equal width-integrated composite water samples were collected and split for subsequent chemical, physical, and biological analyses. During the summer of 2003 sampling, Boulder Creek downstream from the wastewater treatment plant consisted of 36 percent effluent, and Fourmile Creek downstream from the respective wastewater treatment plant was 81 percent effluent. During the spring of 2005 samplings, Boulder Creek downstream from the wastewater treatment plant was 40 percent effluent, and Fourmile Creek downstream from that wastewater treatment plant was 28 percent effluent. At each site, 300 individual constituents were determined to characterize the water. Most of the inorganic constituents were detected in all of the stream and treatment-plant effluent samples, whereas detection of synthetic organic compounds was more limited and contaminants typically occurred only in wastewater treatment-plant effluents and at downstream sites. Concentrations ranged from nanograms per liter to milligrams per liter.

xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data.

PubMed

Uppal, Karan; Soltow, Quinlyn A; Strobel, Frederick H; Pittard, W Stephen; Gernert, Kim M; Yu, Tianwei; Jones, Dean P

2013-01-16

Detection of low abundance metabolites is important for de novo mapping of metabolic pathways related to diet, microbiome or environmental exposures. Multiple algorithms are available to extract m/z features from liquid chromatography-mass spectral data in a conservative manner, which tends to preclude detection of low abundance chemicals and chemicals found in small subsets of samples. The present study provides software to enhance such algorithms for feature detection, quality assessment, and annotation. xMSanalyzer is a set of utilities for automated processing of metabolomics data. The utilites can be classified into four main modules to: 1) improve feature detection for replicate analyses by systematic re-extraction with multiple parameter settings and data merger to optimize the balance between sensitivity and reliability, 2) evaluate sample quality and feature consistency, 3) detect feature overlap between datasets, and 4) characterize high-resolution m/z matches to small molecule metabolites and biological pathways using multiple chemical databases. The package was tested with plasma samples and shown to more than double the number of features extracted while improving quantitative reliability of detection. MS/MS analysis of a random subset of peaks that were exclusively detected using xMSanalyzer confirmed that the optimization scheme improves detection of real metabolites. xMSanalyzer is a package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. The program was designed to integrate with existing packages such as apLCMS and XCMS, but the framework can also be used to enhance data extraction for other LC/MS data software.

Downstream valorization and comprehensive two-dimensional liquid chromatography-based chemical characterization of bioactives from black chokeberries (Aronia melanocarpa) pomace.

PubMed

Brazdauskas, T; Montero, L; Venskutonis, P R; Ibañez, E; Herrero, M

2016-10-14

In this work, a new alternative for the downstream processing and valorization of black chokeberry pomace (Aronia melanocarpa) which could be potentially coupled to a biorefinery process is proposed. This alternative is based on the application of pressurized liquid extraction (PLE) to the residue obtained after the supercritical fluid extraction of the berry pomace. An experimental design is employed to study and optimize the most relevant extraction conditions in order to attain extracts with high extraction yields, total phenols content and antioxidant activity. Moreover, the PLE extracts were characterized by using a new method based on the application of comprehensive two-dimensional liquid chromatography in order to correlate their activity with their chemical composition. Thanks to the use of this powerful analytical tool, 61 compounds could be separated being possible the tentative identification of different anthocyanins, proanthocyanidins, flavonoids and phenolic acids. By using the optimized PLE approach (using pressurized 46% ethanol in water at 165°C containing 1.8% formic acid), extracts with high total phenols content (236.6mg GAE g -1 extract) and high antioxidant activities (4.35mmol TE g -1 extract and EC 50 5.92μgmL -1 ) could be obtained with high yields (72.5%). Copyright © 2016 Elsevier B.V. All rights reserved.

Aquatic assessment of the Pike Hill Copper Mine Superfund site, Corinth, Vermont

USGS Publications Warehouse

Piatak, Nadine M.; Argue, Denise M.; Seal, Robert R.; Kiah, Richard G.; Besser, John M.; Coles, James F.; Hammarstrom, Jane M.; Levitan, Denise M.; Deacon, Jeffrey R.; Ingersoll, Christopher G.

2013-01-01

The Pike Hill Copper Mine Superfund site in Corinth, Orange County, Vermont, includes the Eureka, Union, and Smith mines along with areas of downstream aquatic ecosystem impairment. The site was placed on the U.S. Environmental Protection Agency (USEPA) National Priorities List in 2004. The mines, which operated from about 1847 to 1919, contain underground workings, foundations from historical structures, several waste-rock piles, and some flotation tailings. The mine site is drained to the northeast by Pike Hill Brook, which includes several wetland areas, and to the southeast by an unnamed tributary that flows to the south and enters Cookville Brook. Both brooks eventually drain into the Waits River, which flows into the Connecticut River. The aquatic ecosystem at the site was assessed using a variety of approaches that investigated surface-water quality, sediment quality, and various ecological indicators of stream-ecosystem health. The degradation of surface-water quality is caused by elevated concentrations of copper, and to a lesser extent cadmium, with localized effects caused by aluminum, iron, and zinc. Copper concentrations in surface waters reached or exceeded the USEPA national recommended chronic water-quality criteria for the protection of aquatic life in all of the Pike Hill Brook sampling locations except for the location farthest downstream, in half of the locations sampled in the tributary to Cookville Brook, and in about half of the locations in one wetland area located in Pike Hill Brook. Most of these same locations also contained concentrations of cadmium that exceeded the chronic water-quality criteria. In contrast, surface waters at background sampling locations were below these criteria for copper and cadmium. Comparison of hardness-based and Biotic Ligand Model (BLM)-based criteria for copper yields similar results with respect to the extent or number of stations impaired for surface waters in the affected area. However, the BLM-based criteria are commonly lower values than the hardness-based criteria and thus suggest a greater degree or magnitude of impairment at the sampling locations. The riffle-habitat benthic invertebrate richness and abundance data correlate strongly with the extent of impact based on water quality for both brooks. Similarly, the fish community assessments document degraded conditions throughout most of Pike Hill Brook, whereas the data for the tributary to Cookville Brook suggest less degradation to this brook. The sediment environment shows similar extents of impairment to the surface-water environment, with most sampling locations in Pike Hill Brook, including the wetland areas, and the tributary to Cookville Brook affected. Sediment impairment is caused by elevated copper concentrations, although localized degradation due to elevated cadmium and zinc concentrations was documented on the basis of exceedances of probable effects concentrations (PECs). In contrast to impairment determined by exceedances of PECs, equilibrium-partitioning sediment benchmarks (based on simultaneously extracted metals, acid volatile sulfides, and total organic carbon) predict no toxic effects in sediments at the background locations and uncertain toxic effects throughout Pike Hill Brook and the tributary to Cookville Brook, with the exception of the most downstream Cookville Brook location, which indicated no toxic effects. Acute laboratory toxicity testing using the amphipod Hyalella azteca and the midge Chironomus dilutus on pore waters extracted from sediment in situ indicate impairment (based on tests with H. azteca) at only one location in Pike Hill Brook and no impairment in the tributary to Cookville Brook. Chronic laboratory sediment toxicity testing using H. azteca and C. dilutus indicated toxicity in Pike Hill Brook at several locations in the lower reach and two locations in the tributary to Cookville Brook. Toxicity was not indicated for either species in sediment from the most acidic metal-rich location, likely due to the low lability of copper in that sediment, as indicated by a low proportion of extractable copper (simultaneously extracted metal (SEM) copper only 5 percent of total copper) and due to the flushing of acidic metal-rich pore water from experimental chambers as overlying test water was introduced before and replaced periodically during the toxicity tests. Depositional habitat invertebrate richness and abundance data generally agreed with the results of toxicity tests and with the extent of impact in the watersheds on the basis of sediment and pore waters. The information was used to develop an overall assessment of the impact of mine drainage on the aquatic system downstream from the Pike Hill copper mines. Most of Pike Hill Brook, including several wetland areas that are all downstream from the Eureka and Union mines, was found to be impaired on the basis of water-quality data and biological assessments of fish or benthic invertebrate communities. In contrast, only one location in the tributary to Cookville Brook, downstream from the Smith mine, is definitively impaired. The biological community begins to recover at the most downstream locations in both brooks due to natural attenuation from mixing with unimpaired streams. On the basis of water quality and biological assessment, the reference locations were of good quality. The sediment toxicity, chemistry, and aquatic community survey data suggest that the sediments could be a source of toxicity in Pike Hill Brook and the tributary to Cookville Brook. On the basis of water quality, sediment quality, and biologic communities, the impacts of mine drainage on the aquatic ecosystem health of the watersheds in the study area are generally consistent with the toxicity suggested from laboratory toxicity testing on pore water and sediments.

Effects of backpacker use, pack stock trail use, and pack stock grazing on water-quality indicators, including nutrients, E. coli, hormones, and pharmaceuticals, in Yosemite National Park, USA

USGS Publications Warehouse

Forrester, Harrison; Clow, David W.; Roche, James W.; Heyvaert, Alan C.; Battaglin, William A.

2017-01-01

We investigated how visitor-use affects water quality in wilderness in Yosemite National Park. During the summers of 2012–2014, we collected and analyzed surface-water samples for water-quality indicators, including fecal indicator bacteria Escherichia coli, nutrients (nitrogen, phosphorus, carbon), suspended sediment concentration, pharmaceuticals, and hormones. Samples were collected upstream and downstream from different types of visitor use at weekly to biweekly intervals and during summer storms. We conducted a park-wide synoptic sampling campaign during summer 2014, and sampled upstream and downstream from meadows to evaluate the mitigating effect of meadows on water quality. At pack stock stream crossings, Escherichia coli concentrations were greater downstream from crossings than upstream (median downstream increase in Escherichia coli of three colony forming units 100 mL−1), with the greatest increases occurring during storms (median downstream increase in Escherichia coli of 32 CFU 100 mL−1). At backpacker use sites, hormones, and pharmaceuticals (e.g., insect repellent) were detected at downstream sites, and Escherichia coli concentrations were greater at downstream sites (median downstream increase in Escherichia coli of 1 CFU 100 mL−1). Differences in water quality downstream vs. upstream from meadows grazed by pack stock were not detectable for most water-quality indicators, however, Escherichia coli concentrations decreased downstream, suggesting entrapment and die-off of fecal indicator bacteria in meadows. Our results indicate that under current-use levels pack stock trail use and backpacker use are associated with detectable, but relatively minor, effects on water quality, which are most pronounced during storms.

Effects of Backpacker Use, Pack Stock Trail Use, and Pack Stock Grazing on Water-Quality Indicators, Including Nutrients, E. coli, Hormones, and Pharmaceuticals, in Yosemite National Park, USA

NASA Astrophysics Data System (ADS)

Forrester, Harrison; Clow, David; Roche, James; Heyvaert, Alan; Battaglin, William

2017-09-01

We investigated how visitor-use affects water quality in wilderness in Yosemite National Park. During the summers of 2012-2014, we collected and analyzed surface-water samples for water-quality indicators, including fecal indicator bacteria Escherichia coli, nutrients (nitrogen, phosphorus, carbon), suspended sediment concentration, pharmaceuticals, and hormones. Samples were collected upstream and downstream from different types of visitor use at weekly to biweekly intervals and during summer storms. We conducted a park-wide synoptic sampling campaign during summer 2014, and sampled upstream and downstream from meadows to evaluate the mitigating effect of meadows on water quality. At pack stock stream crossings, Escherichia coli concentrations were greater downstream from crossings than upstream (median downstream increase in Escherichia coli of three colony forming units 100 mL-1), with the greatest increases occurring during storms (median downstream increase in Escherichia coli of 32 CFU 100 mL-1). At backpacker use sites, hormones, and pharmaceuticals (e.g., insect repellent) were detected at downstream sites, and Escherichia coli concentrations were greater at downstream sites (median downstream increase in Escherichia coli of 1 CFU 100 mL-1). Differences in water quality downstream vs. upstream from meadows grazed by pack stock were not detectable for most water-quality indicators, however, Escherichia coli concentrations decreased downstream, suggesting entrapment and die-off of fecal indicator bacteria in meadows. Our results indicate that under current-use levels pack stock trail use and backpacker use are associated with detectable, but relatively minor, effects on water quality, which are most pronounced during storms.

Use of low density polyethylene membranes for assessment of genotoxicity of PAHs in the Seine River.

PubMed

Vincent-Hubert, Françoise; Uher, Emmanuelle; Di Giorgio, Carole; Michel, Cécile; De Meo, Michel; Gourlay-France, Catherine

2017-03-01

The genotoxicity of river water dissolved contaminants is usually estimated after grab sampling of river water. Water contamination can now be obtained with passive samplers that allow a time-integrated sampling of contaminants. Since it was verified that low density polyethylene membranes (LDPE) accumulate labile hydrophobic compounds, their use was proposed as a passive sampler. This study was designed to test the applicability of passive sampling for combined chemical and genotoxicity measurements. The LDPE extracts were tested with the umu test (TA1535/pSK1002 ± S9) and the Ames assay (TA98, TA100 and YG1041 ± S9). We describe here this new protocol and its application in two field studies on four sites of the Seine River. Field LDPE extracts were negative with the YG1041 and TA100 and weakly positive with the TA98 + S9 and Umu test. Concentrations of labile mutagenic PAHs were higher upstream of Paris than downstream of Paris. Improvement of the method is needed to determine the genotoxicity of low concentrations of labile dissolved organic contaminants.

Occurrence of immunosuppressive drugs and their metabolites in the sewage-impacted Vistula and Utrata Rivers and in tap water from the Warsaw region (Poland).

PubMed

Giebułtowicz, Joanna; Nałęcz-Jawecki, Grzegorz

2016-04-01

Immunosuppresive therapy following organ transplant frequently includes treatment with tacrolimus and mycophenolic acid derivatives. These pharmaceuticals may enter the environment through wastewater treatment plant (WWTP) effluents and may have a potentially harmful effect on aquatic biota. Tacrolimus, mycophenolic acid and their metabolites were measured at specific points of a large Polish river (Vistula), a smaller river (Utrata) and in tap water samples from the Warsaw region. Analysis was performed using liquid chromatography tandem mass spectrometry, after solid phase extraction for water samples, or QuEChERS extraction for sediments. Residues of tacrolimus were below quantitation limits in both water and sediment samples. However, in water samples mycophenolic acid concentrations were measured at up to 180 ng L(-1) downstream of WWTP outfalls. No immunosuppressive drugs were detected in tap water. Concentrations of mycophenolic acid exceeded the predicted no effect concentration (PNEC) value in some Polish surface water, and risk calculations predicted at least twice higher concentrations in some other countries of the European Union. To the best of the authors' knowledge, this is the first report of these immunosuppressive drug concentrations in the environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Downstream promoter interactions of TFIID TAFs facilitate transcription reinitiation

PubMed Central

Joo, Yoo Jin; Ficarro, Scott B.; Soares, Luis M.; Chun, Yujin; Marto, Jarrod A.; Buratowski, Stephen

2017-01-01

TFIID binds promoter DNA to recruit RNA polymerase II and other basal factors for transcription. Although the TATA-binding protein (TBP) subunit of TFIID is necessary and sufficient for in vitro transcription, the TBP-associated factor (TAF) subunits recognize downstream promoter elements, act as coactivators, and interact with nucleosomes. In yeast nuclear extracts, transcription induces stable TAF binding to downstream promoter DNA, promoting subsequent activator-independent transcription reinitiation. In vivo, promoter responses to TAF mutations correlate with the level of downstream, rather than overall, Taf1 cross-linking. We propose a new model in which TAFs function as reinitiation factors, accounting for the differential responses of promoters to various transcription factor mutations. PMID:29203645

Production of proteases from organic wastes by solid-state fermentation: downstream and zero waste strategies.

PubMed

Marín, Maria; Artola, Adriana; Sánchez, Antoni

2018-04-01

Production of enzymes through solid-state fermentation (SSF) of agro-industrial wastes reports high productivity with low investment. The extraction of the final product from the solid waste and solid disposal represent the main cost of the process. In this work, the complete downstream processes of SSF of two industrial residues for the production of proteases, soy fibre (SF) and a mixture of hair and sludge (HS), were studied in terms of activity recovery, using different extraction parameters (extracting solvent, ratio solid: solvent and extraction mode). Activity after lyophilisation was tested. Solid waste valorisation after extraction was studied using respiration techniques and biogas production tests, as part of a zero waste strategy. Results showed a maximum extraction yield of 91% for SF and 121% for HS, both in agitated mode and distilled water as extraction agent. An average activity recovery of 95 ± 6 and 94 ± 6% for SF and HS, respectively, was obtained after lyophilisation and redissolution. To reduce the cost of extraction, a ratio 1:3 w : v solid-solvent in static mode is advised for SF, and 1:2 w : v extraction ratio in agitated mode for HS, both with distilled water as extracting agent. Both composting and anaerobic digestion are suitable techniques for valorisation of the waste material.

Optimisation of DNA extraction from the crustacean Daphnia

PubMed Central

Athanasio, Camila Gonçalves; Chipman, James K.; Viant, Mark R.

2016-01-01

Daphnia are key model organisms for mechanistic studies of phenotypic plasticity, adaptation and microevolution, which have led to an increasing demand for genomics resources. A key step in any genomics analysis, such as high-throughput sequencing, is the availability of sufficient and high quality DNA. Although commercial kits exist to extract genomic DNA from several species, preparation of high quality DNA from Daphnia spp. and other chitinous species can be challenging. Here, we optimise methods for tissue homogenisation, DNA extraction and quantification customised for different downstream analyses (e.g., LC-MS/MS, Hiseq, mate pair sequencing or Nanopore). We demonstrate that if Daphnia magna are homogenised as whole animals (including the carapace), absorbance-based DNA quantification methods significantly over-estimate the amount of DNA, resulting in using insufficient starting material for experiments, such as preparation of sequencing libraries. This is attributed to the high refractive index of chitin in Daphnia’s carapace at 260 nm. Therefore, unless the carapace is removed by overnight proteinase digestion, the extracted DNA should be quantified with fluorescence-based methods. However, overnight proteinase digestion will result in partial fragmentation of DNA therefore the prepared DNA is not suitable for downstream methods that require high molecular weight DNA, such as PacBio, mate pair sequencing and Nanopore. In conclusion, we found that the MasterPure DNA purification kit, coupled with grinding of frozen tissue, is the best method for extraction of high molecular weight DNA as long as the extracted DNA is quantified with fluorescence-based methods. This method generated high yield and high molecular weight DNA (3.10 ± 0.63 ng/µg dry mass, fragments >60 kb), free of organic contaminants (phenol, chloroform) and is suitable for large number of downstream analyses. PMID:27190714

Cell disruption and lipid extraction for microalgal biorefineries: A review.

PubMed

Lee, Soo Youn; Cho, Jun Muk; Chang, Yong Keun; Oh, You-Kwan

2017-11-01

The microalgae-based biorefinement process has attracted much attention from academic and industrial researchers attracted to its biofuel, food and nutraceutical applications. In this paper, recent developments in cell-disruption and lipid-extraction methods, focusing on four biotechnologically important microalgal species (namely, Chlamydomonas, Haematococcus, Chlorella, and Nannochloropsis spp.), are reviewed. The structural diversity and rigidity of microalgal cell walls complicate the development of efficient downstream processing methods for cell-disruption and subsequent recovery of intracellular lipid and pigment components. Various mechanical, chemical and biological cell-disruption methods are discussed in detail and compared based on microalgal species and status (wet/dried), scale, energy consumption, efficiency, solvent extraction, and synergistic combinations. The challenges and prospects of the downstream processes for the future development of eco-friendly and economical microalgal biorefineries also are outlined herein. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of DNA methylation in FFPE tissues using the MethyLight technology.

PubMed

Dallol, Ashraf; Al-Ali, Waleed; Al-Shaibani, Amina; Al-Mulla, Fahd

2011-01-01

Novel biomarkers are sought after by mining DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissues. Such tissues offer the great advantage of often having complete clinical data (including survival), as well as the tissues are amenable for laser microdissection targeting specific tissue areas. Downstream analysis of such DNA includes mutational screens and methylation profiling. Screening for mutations by sequencing requires a significant amount of DNA for PCR and cycle sequencing. This is self-inhibitory if the gene screened has a large number of exons. Profiling DNA methylation using the MethyLight technology circumvents this problem and allows for the mining of several biomarkers from DNA extracted from a single microscope slide of the tissue of interest. We describe in this chapter a detailed protocol for MethyLight and its use in the determination of CpG Island Methylator Phenotype status in FFPE colorectal cancer samples.

Microfluidic immunocapture of circulating pancreatic cells using parallel EpCAM and MUC1 capture: characterization, optimization and downstream analysis.

PubMed

Thege, Fredrik I; Lannin, Timothy B; Saha, Trisha N; Tsai, Shannon; Kochman, Michael L; Hollingsworth, Michael A; Rhim, Andrew D; Kirby, Brian J

2014-05-21

We have developed and optimized a microfluidic device platform for the capture and analysis of circulating pancreatic cells (CPCs) and pancreatic circulating tumor cells (CTCs). Our platform uses parallel anti-EpCAM and cancer-specific mucin 1 (MUC1) immunocapture in a silicon microdevice. Using a combination of anti-EpCAM and anti-MUC1 capture in a single device, we are able to achieve efficient capture while extending immunocapture beyond single marker recognition. We also have detected a known oncogenic KRAS mutation in cells spiked in whole blood using immunocapture, RNA extraction, RT-PCR and Sanger sequencing. To allow for downstream single-cell genetic analysis, intact nuclei were released from captured cells by using targeted membrane lysis. We have developed a staining protocol for clinical samples, including standard CTC markers; DAPI, cytokeratin (CK) and CD45, and a novel marker of carcinogenesis in CPCs, mucin 4 (MUC4). We have also demonstrated a semi-automated approach to image analysis and CPC identification, suitable for clinical hypothesis generation. Initial results from immunocapture of a clinical pancreatic cancer patient sample show that parallel capture may capture more of the heterogeneity of the CPC population. With this platform, we aim to develop a diagnostic biomarker for early pancreatic carcinogenesis and patient risk stratification.

Correlating field and laboratory rates of particle abrasion, Rio Medio, Sangre de Cristo Mountains, New Mexico

NASA Astrophysics Data System (ADS)

Polito, P. J.; Sklar, L. S.

2006-12-01

River bed sediments commonly fine downstream due to a combination of particle abrasion, selective transport of finer grains, and fining of the local sediment supply from hillslopes and tributaries. Particle abrasion rates can be directly measured in the laboratory using tumbling barrels and annular flumes, however, scaling experimental particle abrasion rates to the field has proven difficult due to the confounding effects of selective transport and local supply variations. Here we attempt to correlate laboratory and field rates of particle abrasion in a field setting where these confounding effects can be controlled. The Rio Medio, which flows westward from the crest of the Sangre de Cristo Mountains in north central New Mexico, is one of several streams studied by John P. Miller in the early 1960's. Several kilometers downstream of its headwaters, the river crosses the Picuris-Pecos fault. Upstream of the fault the river receives quartzite, sandstone and shale clasts from the Ortega Formation, while downstream sediments are supplied by the Embudo Granite. Because the upstream lithologies are not resupplied downstream of the fault, any observed fining of these clasts should be due only to abrasion and selective transport. We hypothesize that we can account for the effects of selective transport by comparing relative fining rates for the different upstream lithologies from both the field and a laboratory tumbler. By correlating laboratory abrasion rates with rock strength, we can predict the relative fining rates due solely to abrasion expected in the field; differences between the predicted and observed fining rates could then be attributed to selective transport. We used point counts to measure bed surface sediment grain size distributions at 15 locations along a 25 kilometer reach of the Rio Medio, beginning just downstream of the fault and ending upstream of a developed area with disturbed channel conditions. We recorded intermediate particle diameter as well as lithologic composition for 100 clasts at each location. To better characterize the size distribution of poorly represented lithologies we also measured every grain we could find of these minority lithologies within a one square meter area on adjacent bar top surfaces. At each sampling site we also measured channel gradient, and bank-full width and depth. We collected gravel samples for laboratory tumbling experiments and larger bedrock blocks from which we extracted cores for the Brazilian tensile splitting strength test. Preliminary results show very rapid fining of the weak sedimentary rocks downstream of the fault, much less rapid fining of the quartzite and a net downstream coarsening of the granitic sediments, which dominate the bed in the downstream end of the study reach. This enigmatic downstream coarsening may be a legacy of Pliestocene glaciation, which is evident in the landscape upstream of the fault. Outburst floods or debris flows from upstream moraines may have delivered large quantities of coarse sediments to downstream reaches, which are now relatively immobile. Despite these complications, the Rio Medio site may yet provide sufficient information to test our proposed method for scaling laboratory particle abrasion rates to the field.

Natural Origin Lycopene and Its "Green" Downstream Processing.

PubMed

Papaioannou, Emmanouil H; Liakopoulou-Kyriakides, Maria; Karabelas, Anastasios J

2016-01-01

Lycopene is an abundant natural carotenoid pigment with several biological functions (well-known for its antioxidant properties) which is under intensive investigation in recent years. Lycopene chemistry, its natural distribution, bioavailability, biological significance, and toxicological effects are briefly outlined in the first part of this review. The second, major part, deals with various modern downstream processing techniques, which are assessed in order to identify promising approaches for the recovery of lycopene and of similar lipophilic compounds. Natural lycopene is synthesized in plants and by microorganisms, with main representatives of these two categories (for industrial production) tomato and its by-products and the fungus Blakeslea trispora, respectively. Currently, there is a great deal of effort to develop efficient downstream processing for large scale production of natural-origin lycopene, with trends strongly indicating the necessity for "green" and mild extraction conditions. In this review, emphasis is placed on final product safety and ecofriendly processing, which are expected to totally dominate in the field of natural-origin lycopene extraction and purification.

Rapid Measurement of Emissions From Military Aircraft Turbine Engines by Downstream Extractive Sampling of Aircraft on the Ground: Results for C-130 and F-15 Aircraft (POSTPRINT)

DTIC Science & Technology

2009-02-01

four Allison T56 -A-15 turboprop engines which can generate in excess of 4500 horsepower at maximum power. This engine type uses a single entry, 14-stage...JP-8 JP-8 þ 100 Aircraft C-130H F-15 Engine Allison T56 P & W F100-PE-100 Composition (Vol %) Aromatics 16.3 12.4 Alkenes 1.6 2.5 Alkanes 82.1 85.1...respectively. Results are shown for the lowest and highest throttle settings for each of the engine types. The intra-engine variability of two T56

Optimized manual and automated recovery of amplifiable DNA from tissues preserved in buffered formalin and alcohol-based fixative.

PubMed

Duval, Kristin; Aubin, Rémy A; Elliott, James; Gorn-Hondermann, Ivan; Birnboim, H Chaim; Jonker, Derek; Fourney, Ron M; Frégeau, Chantal J

2010-02-01

Archival tissue preserved in fixative constitutes an invaluable resource for histological examination, molecular diagnostic procedures and for DNA typing analysis in forensic investigations. However, available material is often limited in size and quantity. Moreover, recovery of DNA is often severely compromised by the presence of covalent DNA-protein cross-links generated by formalin, the most prevalent fixative. We describe the evaluation of buffer formulations, sample lysis regimens and DNA recovery strategies and define optimized manual and automated procedures for the extraction of high quality DNA suitable for molecular diagnostics and genotyping. Using a 3-step enzymatic digestion protocol carried out in the absence of dithiothreitol, we demonstrate that DNA can be efficiently released from cells or tissues preserved in buffered formalin or the alcohol-based fixative GenoFix. This preparatory procedure can then be integrated to traditional phenol/chloroform extraction, a modified manual DNA IQ or automated DNA IQ/Te-Shake-based extraction in order to recover DNA for downstream applications. Quantitative recovery of high quality DNA was best achieved from specimens archived in GenoFix and extracted using magnetic bead capture.

Comparison of Different Buffers for Protein Extraction from Formalin-Fixed and Paraffin-Embedded Tissue Specimens

PubMed Central

Shen, Kaini; Sun, Jian; Cao, Xinxin; Zhou, Daobin; Li, Jian

2015-01-01

We determined the best extraction buffer for proteomic investigation using formalin-fixation and paraffin-embedded (FFPE) specimens. A Zwittergent 3–16 based buffer, sodium dodecyl sulfate (SDS)-containing buffer with/without polyethylene glycol 20000 (PEG20000), urea-containing buffer, and FFPE-FASP protein preparation kit were compared for protein extraction from different types of rat FFPE tissues, including the heart, brain, liver, lung, and kidney. All of the samples were divided into two groups of laser microdissected (LMD) and non-LMD specimens. For both kinds of specimens, Zwittergent was the most efficient buffer for identifying peptides and proteins, was broadly applicable to different tissues without impairing the enzymatic digestion, and was well compatible with mass spectrometry analysis. As a high molecular weight carrier substance, PEG20000 improved the identification of peptides and proteins; however, such an advantage is limited to tissues containing submicrograms to micrograms of protein. Considering its low lytic strength, urea-containing buffer would not be the first alternative for protein recovery. In conclusion, Zwittergent 3–16 is an effective buffer for extracting proteins from FFPE specimens for downstream proteomics analysis. PMID:26580073

Specific phenolic compounds and sensory properties of a new dealcoholized red wine with pomegranate (Punica granatum L.) extract.

PubMed

Tárrega, Maria Amparo; Varela, Paula; Fromentin, Emilie; Feuillère, Nicolas; Issaly, Nicolas; Roller, Marc; Sanz-Buenhombre, Marisa; Villanueva, Sonia; Moro, Carlos; Guadarrama, Alberto; Fiszman, Susana

2014-09-01

The pomegranate (Punica granatum L.) fruit has a long history of human consumption and possesses notable antioxidant and cardiovascular properties. This work evaluated the feasibility to provide a new functional beverage based on a dealcoholized red wine matrix supplemented by a pomegranate extract. The potential bioactive compounds in the pomegranate extract, punicalagin A and B and ellagic acid, were analyzed during the downstream process in order to evaluate the functional dose in the final beverage. The addition of pomegranate extract to the dealcoholized red wine resulted in a product with more intense yeast odor, acidity, yeast flavor, and astringency and with a less intense berry flavor. Consumer acceptance of the product was also investigated and the results revealed the existence of a niche of consumers willing to consume dealcoholized wine enriched with pomegranate extract. After tasting, 50% and 40% of those consumers initially interested by this product concept declared to be interested to purchase the control sample and the functional beverage, respectively. The daily consumption of two servings of 250 mL of this new pomegranate-enriched dealcoholized wine provides 82 mg of total ellagitannins, corresponding to the sum of punicalagin A and B and ellagic acid. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Molecular Fingerprinting of Cyanobacteria from River Biofilms as a Water Quality Monitoring Tool

PubMed Central

Loza, Virginia; Perona, Elvira

2013-01-01

Benthic cyanobacterial communities from Guadarrama River (Spain) biofilms were examined using temperature gradient gel electrophoresis (TGGE), comparing the results with microscopic analyses of field-fixed samples and the genetic characterization of cultured isolates from the river. Changes in the structure and composition of cyanobacterial communities and their possible association with eutrophication in the river downstream were studied by examining complex TGGE patterns, band extraction, and subsequent sequencing of 16S rRNA gene fragments. Band profiles differed among sampling sites depending on differences in water quality. The results showed that TGGE band richness decreased in a downstream direction, and there was a clear clustering of phylotypes on the basis of their origins from different locations according to their ecological requirements. Multivariate analyses (cluster analysis and canonical correspondence analysis) corroborated these differences. Results were consistent with those obtained from microscopic observations of field-fixed samples. According to the phylogenetic analysis, morphotypes observed in natural samples were the most common phylotypes in the TGGE sequences. These phylotypes were closely related to Chamaesiphon, Aphanocapsa, Pleurocapsa, Cyanobium, Pseudanabaena, Phormidium, and Leptolyngbya. Differences in the populations in response to environmental variables, principally nutrient concentrations (dissolved inorganic nitrogen and soluble reactive phosphorus), were found. Some phylotypes were associated with low nutrient concentrations and high levels of dissolved oxygen, while other phylotypes were associated with eutrophic-hypertrophic conditions. These results support the view that once a community has been characterized and its genetic fingerprint obtained, this technique could be used for the purpose of monitoring rivers. PMID:23263954

Improved methods of DNA extraction from human spermatozoa that mitigate experimentally-induced oxidative DNA damage.

PubMed

Xavier, Miguel J; Nixon, Brett; Roman, Shaun D; Aitken, Robert John

2018-01-01

Current approaches for DNA extraction and fragmentation from mammalian spermatozoa provide several challenges for the investigation of the oxidative stress burden carried in the genome of male gametes. Indeed, the potential introduction of oxidative DNA damage induced by reactive oxygen species, reducing agents (dithiothreitol or beta-mercaptoethanol), and DNA shearing techniques used in the preparation of samples for chromatin immunoprecipitation and next-generation sequencing serve to cofound the reliability and accuracy of the results obtained. Here we report optimised methodology that minimises, or completely eliminates, exposure to DNA damaging compounds during extraction and fragmentation procedures. Specifically, we show that Micrococcal nuclease (MNase) digestion prior to cellular lysis generates a greater DNA yield with minimal collateral oxidation while randomly fragmenting the entire paternal genome. This modified methodology represents a significant improvement over traditional fragmentation achieved via sonication in the preparation of genomic DNA from human spermatozoa for downstream applications, such as next-generation sequencing. We also present a redesigned bioinformatic pipeline framework adjusted to correctly analyse this form of data and detect statistically relevant targets of oxidation.

Quantitation of heat-shock proteins in clinical samples using mass spectrometry.

PubMed

Kaur, Punit; Asea, Alexzander

2011-01-01

Mass spectrometry (MS) is a powerful analytical tool for proteomics research and drug and biomarker discovery. MS enables identification and quantification of known and unknown compounds by revealing their structural and chemical properties. Proper sample preparation for MS-based analysis is a critical step in the proteomics workflow because the quality and reproducibility of sample extraction and preparation for downstream analysis significantly impact the separation and identification capabilities of mass spectrometers. The highly expressed proteins represent potential biomarkers that could aid in diagnosis, therapy, or drug development. Because the proteome is so complex, there is no one standard method for preparing protein samples for MS analysis. Protocols differ depending on the type of sample, source, experiment, and method of analysis. Molecular chaperones play significant roles in almost all biological functions due to their capacity for detecting intracellular denatured/unfolded proteins, initiating refolding or denaturation of such malfolded protein sequences and more recently for their role in the extracellular milieu as chaperokines. In this chapter, we describe the latest techniques for quantitating the expression of molecular chaperones in human clinical samples.

Present state and perspective of downstream processing of biologically produced 1,3-propanediol and 2,3-butanediol.

PubMed

Xiu, Zhi-Long; Zeng, An-Ping

2008-04-01

1,3-Propanediol and 2,3-butanediol are two promising chemicals which have a wide range of applications and can be biologically produced. The separation of these diols from fermentation broth makes more than 50% of the total costs in their microbial production. This review summarizes the present state of methods studied for the recovery and purification of biologically produced diols, with particular emphasis on 1,3-propoanediol. Previous studies on the separation of 1,3-propanediol primarily include evaporation, distillation, membrane filtration, pervaporation, ion exchange chromatography, liquid-liquid extraction, and reactive extraction. Main methods for the recovery of 2,3-butanediol include steam stripping, pervaporation, and solvent extraction. No single method has proved to be simple and efficient, and improvements are especially needed with regard to yield, purity, and energy consumption. Perspectives for an improved downstream processing of biologically produced diols, especially 1,3-propanediol are discussed based on our own experience and recent work. It is argued that separation technologies such as aqueous two-phase extraction with short chain alcohols, pervaporation, reverse osmosis, and in situ extractive or pervaporative fermentations deserve more attention in the future.

A Sequential Chemical Extraction and Spectroscopic Assessment of the Potential Bioavailability of Mercury Released From the Inoperative New Idria Mercury Mine, San Benito Co., CA

NASA Astrophysics Data System (ADS)

Jew, A. D.; Luong, P. N.; Rytuba, J. J.; Brown, G. E.

2012-12-01

The inoperative New Idria mercury mine in San Benito Co., CA, is a potential point source of Hg to the Central Valley of California. To determine the phases and the potential bioavailability of Hg present in stream bed deposits downstream of the mine, sequential chemical extractions (SCEs) targeting Hg-bearing phases and synchrotron-based spectroscopic and imaging techniques were used on sediment samples taken from the acid mine drainage (AMD) system, Hg sorbed in the laboratory to ferrihydrite (synthetic 2-line and natural), and Hg associated with diatom-rich samples. In all field samples examined, both the wet and dry seasons, removal of > 97% of the Hg required 1M KOH or harsher chemical treatments. X-ray absorption spectroscopy (XAS) showed that HgS was the dominant inorganic Hg phase present, with no detectable Hg associated with the ferrihydrite. Uptake and subsequent SCE analysis of Hg to both synthetic and natural ferrihydrite showed that 1M MgCl2 removed ≥ 90% of the total Hg, suggesting that Hg does not sorb strongly to ferrihydrite. This finding is surprising, because in most settings ferrihydrite is considered to be a strong adsorbent of heavy metals. Due to the lack of Hg sorption to ferrihydrite in field samples, another pool for the non-HgS/HgSe fraction in sediments is needed. SEM analysis of the downstream samples showed that regardless of pH, freshwater diatoms were present. To determine if diatoms were the sink for dissolved Hg in this system, SCE analysis on commercially available and diatom-rich field samples from the New Idria site and Harley Gulch (Lake County, CA) were completed. The vast majority of Hg in diatom-rich samples was removed by 1M KOH, which corresponds to the non-HgS/HgSe fraction of the New Idria field samples. Analysis for carbon and nitrogen in the diatom-rich samples showed no detectable nitrogen, indicating little to no organic material was left in the samples. We therefore infer that Hg in the diatoms is contained in the silica tests. The possibility of Hg being incorporated in the silica tests of diatoms is surprising, but one of the few known Hg-silicates (Edgarbailyite) was first discovered in the New Idria forming under ambient conditions, thus, a Hg-silicate species is possible. The stability of Hg contained in diatoms is important because it represents a new sink for dissolved Hg in an impacted system that was previously unknown. Freshwater diatoms present in the New Idria drainage system were found to contain significant quantities (30-60%) of Hg in the non-HgS SCE fractions, similar to the New Idria sediments, and are thought to be the major association of Hg in this system. SCE analyses of Hg(II) sorbed to synthetic 2-line and natural ferrihydrite in the laboratory showed that Hg(II) does not bind strongly to either material. The adsorption/incorporation of Hg(II) with the silica tests of diatoms is an important discovery and has major implications for passive remediation strategies for Hg in natural systems. Because the vast majority of Hg contained in sediments downstream of the New Idria site require 1M KOH or harsher chemical treatment for removal, the Hg released from New Idria can be considered to be environmentally stable.

Contrast-enhanced 3D micro-CT of plant tissues using different impregnation techniques.

PubMed

Wang, Zi; Verboven, Pieter; Nicolai, Bart

2017-01-01

X-ray micro-CT has increasingly been used for 3D imaging of plant structures. At the micrometer resolution however, limitations in X-ray contrast often lead to datasets with poor qualitative and quantitative measures, especially within dense cell clusters of plant tissue specimens. The current study developed protocols for delivering a cesium based contrast enhancing solution to varying plant tissue specimens for the purpose of improving 3D tissue structure characterization within plant specimens, accompanied by new image processing workflows to extract the additional data generated by the contrast enhanced scans. Following passive delivery of a 10% cesium iodide contrast solution, significant increases of 85.4 and 38.0% in analyzable cell volumes were observed in pear fruit hypanthium and tomato fruit outer mesocarp samples. A significant increase of 139.6% in the number of analyzable cells was observed in the pear fruit samples along the added ability to locate and isolate better brachysclereids and vasculature in the sample volume. Furthermore, contrast enhancement resulted in significant improvement in the definition of collenchyma and parenchyma in the petiolule of tomato leaflets, from which both qualitative and quantitative data can be extracted with respect to cell measures. However, contrast enhancement was not achieved in leaf vasculature and mesophyll tissue due to fundamental limitations. Active contrast delivery to apple fruit hypanthium samples did yield a small but insignificant increase in analyzable volume and cells, but data on vasculature can now be extracted better in correspondence to the pear hypanthium samples. Contrast delivery thus improved visualization and analysis the most in dense tissue types. The cesium based contrast enhancing protocols and workflows can be utilized to obtain detailed 3D data on the internal microstructure of plant samples, and can be adapted to additional samples of interest with minimal effort. The resulting datasets can therefore be utilized for more accurate downstream studies that requires 3D data.

A comparative study of stream water and stream sediment as geochemical exploration media in the Rio Tanama porphyry copper district, Puerto Rico

USGS Publications Warehouse

Learned, R.E.; Chao, T.T.; Sanzolone, R.F.

1985-01-01

To test the relative effectiveness of stream water and sediment as geochemical exploration media in the Rio Tanama porphyry copper district of Puerto Rico, we collected and subsequently analyzed samples of water and sediment from 29 sites in the rivers and tributaries of the district. Copper, Mo, Pb, Zn, SO42-, and pH were determined in the waters; Cu, Mo, Pb, and Zn were determined in the sediments. In addition, copper in five partial extractions from the sediments was determined. Geochemical contrast (anomaly-to-background quotient) was the principal criterion by which the effectiveness of the two media and the five extractions were judged. Among the distribution patterns of metals in stream water, that of copper most clearly delineates the known porphyry copper deposits and yields the longest discernable dispersion train. The distribution patterns of Mo, Pb, and Zn in water show little relationship to the known mineralization. The distribution of SO42- in water delineates the copper deposits and also the more extensive pyrite alteration in the district; its recognizable downstream dispersion train is substantially longer than those of the metals, either in water or sediment. Low pH values in small tributaries delineate areas of known sulfide mineralization. The distribution patterns of copper in sediments clearly delineate the known deposits, and the dispersion trains are longer than those of copper in water. The partial determinations of copper related to secondary iron and manganese oxides yield the strongest geochemical contrasts and longest recognizable dispersion trains. Significantly high concentrations of molybdenum in sediments were found at only three sites, all within one-half km downstream of the known copper deposits. The distribution patterns of lead and zinc in sediments are clearly related to the known primary lead-zinc haloes around the copper deposits. The recognizable downstream dispersion trains of lead and zinc are shorter than those of copper. ?? 1985.

Diatom Milking: A Review and New Approaches

PubMed Central

Vinayak, Vandana; Manoylov, Kalina M.; Gateau, Hélène; Blanckaert, Vincent; Hérault, Josiane; Pencréac’h, Gaëlle; Marchand, Justine; Gordon, Richard; Schoefs, Benoît

2015-01-01

The rise of human populations and the growth of cities contribute to the depletion of natural resources, increase their cost, and create potential climatic changes. To overcome difficulties in supplying populations and reducing the resource cost, a search for alternative pharmaceutical, nanotechnology, and energy sources has begun. Among the alternative sources, microalgae are the most promising because they use carbon dioxide (CO2) to produce biomass and/or valuable compounds. Once produced, the biomass is ordinarily harvested and processed (downstream program). Drying, grinding, and extraction steps are destructive to the microalgal biomass that then needs to be renewed. The extraction and purification processes generate organic wastes and require substantial energy inputs. Altogether, it is urgent to develop alternative downstream processes. Among the possibilities, milking invokes the concept that the extraction should not kill the algal cells. Therefore, it does not require growing the algae anew. In this review, we discuss research on milking of diatoms. The main themes are (a) development of alternative methods to extract and harvest high added value compounds; (b) design of photobioreactors; (c) biodiversity and (d) stress physiology, illustrated with original results dealing with oleaginous diatoms. PMID:25939034

Downstream Processing of Synechocystis for Biofuel Production

NASA Astrophysics Data System (ADS)

Sheng, Jie

Lipids and free fatty acids (FFA) from cyanobacterium Synechocystis can be used for biofuel (e.g. biodiesel or renewable diesel) production. In order to utilize and scale up this technique, downstream processes including culturing and harvest, cell disruption, and extraction were studied. Several solvents/solvent systems were screened for lipid extraction from Synechocystis. Chloroform + methanol-based Folch and Bligh & Dyer methods were proved to be "gold standard" for small-scale analysis due to their highest lipid recoveries that were confirmed by their penetration of the cell membranes, higher polarity, and stronger interaction with hydrogen bonds. Less toxic solvents, such as methanol and MTBE, or direct transesterification of biomass (without preextraction step) gave only slightly lower lipid-extraction yields and can be considered for large-scale application. Sustained exposure to high and low temperature extremes severely lowered the biomass and lipid productivity. Temperature stress also triggered changes of lipid quality such as the degree of unsaturation; thus, it affected the productivities and quality of Synechocystis-derived biofuel. Pulsed electric field (PEF) was evaluated for cell disruption prior to lipid extraction. A treatment intensity > 35 kWh/m3 caused significant damage to the plasma membrane, cell wall, and thylakoid membrane, and it even led to complete disruption of some cells into fragments. Treatment by PEF enhanced the potential for the low-toxicity solvent isopropanol to access lipid molecules during subsequent solvent extraction, leading to lower usage of isopropanol for the same extraction efficiency. Other cell-disruption methods also were tested. Distinct disruption effects to the cell envelope, plasma membrane, and thylakoid membranes were observed that were related to extraction efficiency. Microwave and ultrasound had significant enhancement of lipid extraction. Autoclaving, ultrasound, and French press caused significant release of lipid into the medium, which may increase solvent usage and make medium recycling difficult. Production of excreted FFA by mutant Synechocystis has the potential of reducing the complexity of downstream processing. Major problems, such as FFA precipitation and biodegradation by scavengers, account for FFA loss in operation. Even a low concentration of FFA scavengers could consume FFA at a high rate that outpaced FFA production rate. Potential strategies to overcome FFA loss include high pH, adsorptive resin, and sterilization techniques.

Water quality, organic chemistry of sediment, and biological conditions of streams near an abandoned wood-preserving plant site at Jackson, Tennessee

USGS Publications Warehouse

Bradfield, A.D.; Flexner, N.M.; Webster, D.A.

1993-01-01

An investigation of water quality, organic sediment chemistry, and biological conditions of streams near an abandoned wood-preserving plant site at Jackson, Tennessee, was conducted during December 1990. The study was designed to assess the extent of possible contamination of water and biota in the streams from creosote-related discharge originating at this Superfund site. Central Creek, adjacent to the plant, had degraded water quality and biological conditions. Water samples from the most downstream station on Central Creek contained 30 micrograms per liter of pentachlorophenol, which exceeds the State's criterion maximum concentrations of 9 micrograms per liter for fish and aquatic life. Bottom-sediment samples from stations on Central Creek contained concentrations of acenaphthene, napthalene, and phenanthrene ranging from 1,400 to 2,500 micrograms per kilogram. Chronic or acute toxicity resulted during laboratory experiments using test organisms exposed to creosote-related contaminants. Sediment elutriate samples from Central Creek caused slightly to highly toxic effects on Ceriodaphnia dubia. Pimephales promelas, and Photobacterium phosphoreum. Fish-tissue samples from this station contained concentrations of naphthalene. dibenzofuran, fluorene, and phenanthrene ranging from 1.5 to 3.9 micrograms per kilogram Blue-green algae at this station represented about 79 percent of the organisms counted, whereas diatoms accounted for only 11 percent. Benthic invertebrate and fish samples from Central Creek had low diversity and density. Sediment samples from a station on the South Fork Forked Deer River downstream from its confluence with Central Creek contained concentrations of acenaphthene, anthracene, chrysene, fluoranthene, fluorene, pyrere, and phenanthrene ranging from 2,800 to 69,000 micrograms per kilogram. Sediment elutriate samples using water as elutriate from this station contained concentrations of extractable organic compounds ranging from an estimated 43 to 420 micrograms per liter. Sediment elutriate samples were toxic to Ceriodaphnia dubta, Pimephales promelas, Photobacterium phosphoreum, and Salenastrum capricornulum.

Paper-Based MicroRNA Expression Profiling from Plasma and Circulating Tumor Cells.

PubMed

Leong, Sai Mun; Tan, Karen Mei-Ling; Chua, Hui Wen; Huang, Mo-Chao; Cheong, Wai Chye; Li, Mo-Huang; Tucker, Steven; Koay, Evelyn Siew-Chuan

2017-03-01

Molecular characterization of circulating tumor cells (CTCs) holds great promise for monitoring metastatic progression and characterizing metastatic disease. However, leukocyte and red blood cell contamination of routinely isolated CTCs makes CTC-specific molecular characterization extremely challenging. Here we report the use of a paper-based medium for efficient extraction of microRNAs (miRNAs) from limited amounts of biological samples such as rare CTCs harvested from cancer patient blood. Specifically, we devised a workflow involving the use of Flinders Technology Associates (FTA) ® Elute Card with a digital PCR-inspired "partitioning" method to extract and purify miRNAs from plasma and CTCs. We demonstrated the sensitivity of this method to detect miRNA expression from as few as 3 cancer cells spiked into human blood. Using this method, background miRNA expression was excluded from contaminating blood cells, and CTC-specific miRNA expression profiles were derived from breast and colorectal cancer patients. Plasma separated out during purification of CTCs could likewise be processed using the same paper-based method for miRNA detection, thereby maximizing the amount of patient-specific information that can be derived from a single blood draw. Overall, this paper-based extraction method enables an efficient, cost-effective workflow for maximized recovery of small RNAs from limited biological samples for downstream molecular analyses. © 2016 American Association for Clinical Chemistry.

Sequence-specific sepsis-related DNA capture and fluorescent labeling in monoliths prepared by single-step photopolymerization in microfluidic devices.

PubMed

Knob, Radim; Hanson, Robert L; Tateoka, Olivia B; Wood, Ryan L; Guerrero-Arguero, Israel; Robison, Richard A; Pitt, William G; Woolley, Adam T

2018-05-21

Fast determination of antibiotic resistance is crucial in selecting appropriate treatment for sepsis patients, but current methods based on culture are time consuming. We are developing a microfluidic platform with a monolithic column modified with oligonucleotides designed for sequence-specific capture of target DNA related to the Klebsiella pneumoniae carbapenemase (KPC) gene. We developed a novel single-step monolith fabrication method with an acrydite-modified capture oligonucleotide in the polymerization mixture, enabling fast monolith preparation in a microfluidic channel using UV photopolymerization. These prepared columns had a threefold higher capacity compared to monoliths prepared in a multistep process involving Schiff-base DNA attachment. Conditions for denaturing, capture and fluorescence labeling using hybridization probes were optimized with synthetic 90-mer oligonucleotides. These procedures were applied for extraction of a PCR amplicon from the KPC antibiotic resistance gene in bacterial lysate obtained from a blood sample spiked with E. coli. The results showed similar eluted peak areas for KPC amplicon extracted from either hybridization buffer or bacterial lysate. Selective extraction of the KPC DNA was verified by real time PCR on eluted fractions. These results show great promise for application in an integrated microfluidic diagnostic system that combines upstream blood sample preparation and downstream single-molecule counting detection. Copyright © 2018 Elsevier B.V. All rights reserved.

Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples.

PubMed

Kresse, Stine H; Namløs, Heidi M; Lorenz, Susanne; Berner, Jeanne-Marie; Myklebost, Ola; Bjerkehagen, Bodil; Meza-Zepeda, Leonardo A

2018-01-01

Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated. DNA and RNA were isolated from five sarcoma archival FFPE blocks, using eight extraction protocols from seven kits from three different commercial vendors. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. For RNA extraction, all protocols gave comparable yields and amplifiable RNA. However, for fusion gene detection using the Archer FusionPlex Sarcoma Assay, the truXTRAC FFPE RNA kit from Covaris and Agencourt FormaPure kit from Beckman Coulter showed the highest percentage of unique read-pairs, providing higher complexity of HTS data and more frequent detection of recurrent fusion genes. truXTRAC simultaneous DNA and RNA extraction gave similar outputs as individual protocols. These findings show that although successful HTS libraries could be generated in most cases, the different protocols gave variable quantity and quality for FFPE nucleic acid extraction. Selecting the optimal procedure is highly valuable and may generate results in borderline quality specimens.

Occurrence and concentrations of selected trace elements and halogenated organic compounds in stream sediments and potential sources of polychlorinated biphenyls, Leon Creek, San Antonio, Texas, 2012–14

USGS Publications Warehouse

Wilson, Jennifer T.

2016-06-23

Sediment samples collected from Leon Creek by the USGS during 2007–9 and 2012–14 at a total of eight sites following identical field and laboratory methods were evaluated to determine if potential PCB sources could be identified. Total PCB concentrations in the sediment samples collected upstream from the Joint Base site were low or nondetections; while concentrations in the samples collected on and downstream from the Joint Base site were greater. Congeners 180 and 138 constituted the greatest proportion of the PCB mixture in samples collected upstream from, on, and downstream from the Joint Base site. Upstream from the Joint Base site, congeners 180 and 138 constituted 50 percent and 35 percent respectively of the PCBs congeners found in the samples. On and downstream from the Joint Base site, congeners 180 and 138 constituted 80 percent and 13 percent respectively of the PCBs congeners found in the samples. Chi-square (C2) tests also indicate that samples collected from the Loop 410 site were statistically different from samples collected from the Joint Base site and sites downstream. The PCB congener pattern in the Leon Creek samples is most like the congener mixture in Aroclor 1260, which is chemically similar to the PCBs detected in the fish samples that resulted in the 2003 fish consumption advisory.

The effect of a non-denaturing detergent and a guanidinium-based inactivation agent on the viability of Ebola virus in mock clinical serum samples.

PubMed

Burton, J E; Easterbrook, L; Pitman, J; Anderson, D; Roddy, S; Bailey, D; Vipond, R; Bruce, C B; Roberts, A D

2017-12-01

The 2014 Ebola outbreak in West Africa required the rapid testing of clinical material for the presence of potentially high titre Ebola virus (EBOV). Safe, fast and effective methods for the inactivation of such clinical samples are required so that rapid diagnostic tests including downstream analysis by RT-qPCR or nucleotide sequencing can be carried out. One of the most commonly used guanidinium - based denaturing agents, AVL (Qiagen) has been shown to fully inactivate EBOV once ethanol is added, however this is not compatible with the use of automated nucleic acid extraction systems. Additional inactivation agents need to be identified that can be used in automated systems. A candidate inactivation agent is Triton X-100, a non-denaturing detergent that is frequently used in clinical nucleic acid extraction procedures and has previously been used for inactivation of EBOV. In this study the effect of 0.1% and 1.0% Triton X-100 (final concentration 0.08% and 0.8% respectively) alone and in combination with AVL on the viability of EBOV (10 6 TCID 50 /ml) spiked into commercially available pooled negative human serum was tested. The presence of viable EBOV in the treated samples was assessed by carrying out three serial passages of the samples in Vero E6 cells (37°C, 5% CO 2 , 1 week for each passage). At the end of each passage the cells were observed for evidence of cytopathic effect and samples were taken for rRT-PCR analysis for the presence of EBOV RNA. Before cell culture cytotoxic components of AVL and Triton X-100 were removed from the samples using size exclusion spin column technology or a hydrophobic adsorbent resin. The results of this study showed that EBOV spiked into human serum was not fully inactivated when treated with either 0.1% (v/v) Triton X-100 for 10 mins or 1.0% (v/v) Triton X-100 for 20 mins (final concentrations 0.08% and 0.8% Triton X-100 respectively). AVL alone also did not consistently provide complete inactivation. Samples treated with both AVL and 0.1% Triton X-100 for 10 or 20 mins were shown to be completely inactivated. This treatment is compatible with downstream analysis by RT-qPCR and next generation sequencing. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Ion beam accelerator system

NASA Technical Reports Server (NTRS)

Aston, Graeme (Inventor)

1984-01-01

A system is described that combines geometrical and electrostatic focusing to provide high ion extraction efficiency and good focusing of an accelerated ion beam. The apparatus includes a pair of curved extraction grids (16, 18) with multiple pairs of aligned holes positioned to direct a group of beamlets (20) along converging paths. The extraction grids are closely spaced and maintained at a moderate potential to efficiently extract beamlets of ions and allow them to combine into a single beam (14). An accelerator electrode device (22) downstream from the extraction grids, is at a much lower potential than the grids to accelerate the combined beam.

The time course of erythrocyte membrane fatty acid concentrations during and after treatment of non-human primates with increasing doses of an omega-3 rich phospholipid preparation derived from krill-oil.

PubMed

Hals, Petter-Arnt; Wang, Xiaoli; Piscitelli, Fabiana; Di Marzo, Vincenzo; Xiao, Yong-Fu

2017-01-21

A commonly used measure to reflect the intake of the long-chain omega-3 fatty acids EPA and DHA is the omega-3 index, defined as the sum of EPA + DHA as % of total fatty acids in erythrocyte membrane. When the omega-3 index changes it follows that the relative fractions of other fatty acids in the membrane are also changed. In the present study, increasing doses of a preparation of omega-3 rich phospholipids extracted from krill oil were administered orally to non-human primates for 12 weeks and the time course of EPA, DHA and 22 other fatty acids in erythrocytes was determined bi-weekly during treatment and for 8 weeks after cessation of treatment. Plasma concentrations of six endocannabinoid-type mediators being downstream metabolites of some fatty acids analyzed in erythrocytes were also determined. Six diabetic, dyslipidemic non-human primates were included, three in a vehicle control group and three being treated with the omega-3 rich phospholipid preparation. The vehicle control and test items were given daily by gavage and the test item doses were 50, 150 and 450 mg phospholipids/kg/day. Each dose level was given for four weeks. Blood was sampled at baseline and thereafter bi-weekly. Fatty acids were determined in erythrocytes by methylation followed by gas-chromatography. Endocannabinoids and endocannabinoid-like mediators were analyzed in plasma by liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry. The treatment resulted in a dose-related increase in the fraction of EPA and DHA in erythrocyte membranes and a dose-related decrease of other poly-unsaturated fatty acids, in particular omega-6 polyunsaturated fatty acids. Erythrocyte concentrations of saturated fatty acids remained unchanged throughout the experiment. Plasma concentrations of endocannabinoids and endocannabinoid-like mediators changed accordingly as those being downstream arachidonic acid decreased, downstream of the saturated palmitic and oleic acids remained unchanged while a downstream EPA metabolite increased. Increasing the omega-3 index by administering an omega-3 rich phospholipid extracted from krill oil did not alter the ratio of unsaturated vs. saturated fatty acids in the erythrocyte membranes but only the relative concentrations of unsaturated fatty acids, in particular unsaturated omega-6 fatty acids. Concentrations of saturated fatty acids remained unchanged.

Effects of Packstock Use and Backpackers on Water Quality in Yosemite National Park, California

NASA Astrophysics Data System (ADS)

Forrester, H.; Clow, D. W.; Roche, J. W.; Heyvaert, A.

2016-12-01

Visitor use, primarily backpacker camping, packstock (horse and mule) trail use, and packstock grazing, in designated Wilderness, increases the potential for negative effects on water quality. To determine the effects of visitor use on water quality in Wilderness in Yosemite National Park, we collected and analyzed surface-water samples for water quality indicators, consisting of fecal indicator bacteria (Escherichia coli), nutrients (nitrogen, phosphorus), suspended sediment concentration (SSC), and hormones (e.g. estrogen compounds) during the summers of 2012-2014. We collected samples upstream and downstream from different types of visitor use at routine intervals (weekly or biweekly) and during storms. Additionally, we sampled upstream and downstream from meadows, and targeted different types of visitor use during a park-wide synoptic sampling campaign (n=63). At packstock stream crossings, statistically significant (P≤0.05) increases in Escherichia coli (E. coli) and SSC occurred downstream from crossings compared to upstream conditions during routine sampling (median difference: 3 CFU 100ml-1, and >0.3 mg l-1, respectively) and during storms (median difference: 32 CFU 100ml-1, and 2.9 mg l-1). At backpacker campsites, during routine sampling, significant increases occurred downstream from backpacker camping for E. coli (median difference: 1 CFU 100ml-1), and estrogen hormones were detected. At packstock grazing areas, which are located in meadows, no significant increases were detected for any of the measured water quality indicators downstream from grazing. Most synoptic sample concentrations were near or below detection limits. Our results indicate that under current use levels: 1) packstock trail use and backpacker camping are associated with detectable effects on water quality, which are most pronounced during storms; 2) increases in water quality indicators were not detected downstream from meadows where packstock were grazed; and 3) environmental processes in meadows provide a valuable ecosystem service by reducing human related sources of microbial contamination.

Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments.

PubMed

Li, Dong; Sharp, Jonathan O; Drewes, Jörg E

2016-01-01

To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction-modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants.

Changes in Rice Pesticide Use and Surface Water Concentrations in the Sacramento River Watershed, California

USGS Publications Warehouse

Orlando, James L.; Kuivila, Kathryn

2004-01-01

Pesticides applied to rice fields in California are transported into the Sacramento River watershed by the release of rice field water. Despite monitoring and mitigation programs, concentrations of two rice pesticides, molinate and thiobencarb, continue to exceed the surface-water concentration performance goals established by the Central Valley Regional Water Quality Control Board. There have been major changes in pesticide use over the past decade, and the total amount of pesticides applied remains high. Molinate use has declined by nearly half, while thiobencarb use has more than doubled; carbofuran has been eliminated and partially replaced by the pyrethroid pesticide lambda-cyhalothrin. A study was conducted in 2002 and 2003 by the U.S. Geological Survey to determine if the changes in pesticide use on rice resulted in corresponding changes in pesticide concentrations in surface waters. During the rice growing season (May-July), water samples, collected weekly at three sites in 2002 and two sites in 2003, were analyzed for pesticides using both solid-phase and liquid-liquid extraction in combination with gas chromatography/mass spectrometry. Analytes included lambda-cyhalothrin, molinate, thiobencarb, and two degradation products of molinate: 2-keto-molinate and 4-keto-molinate. Molinate, thiobencarb, and 4-keto-molinate were detected in all samples, 2-keto-molinate was detected in less than half of the samples, and lambda-cyhalothrin was not detected in any samples. At two of the sites sampled in 2002 (Colusa Basin Drain 1 and Sacramento Slough), concentrations of molinate were similar, but thiobencarb concentrations differed by a factor of five. Although concentrations cannot be estimated directly from application amounts in different watersheds, the ratio of molinate to thiobencarb concentrations can be compared with the ratio of molinate to thiobencarb use in the basins. The higher concentration ratio in the Sacramento Slough Basin, compared with the ratio in the basin area feeding the Colusa Basin Drain 1, is consistent with the higher use ratio, suggesting that differences in application amounts can explain the observed concentration differences. The samples from the downstream site (Tower) sampled in 2002 had the lowest concentrations of pesticides. Performance goals were exceeded for either molinate or thiobencarb in six samples from the upstream sites, but not in any samples from the downstream Tower site. In 2003, concentrations at upstream sites were much lower than the previous year with only one sample containing thiobencarb at a concentration above the performance goal. Lower concentrations could be partially due to delays in rice planting and pesticide application owing to spring rainstorms. Historical data is available on peak concentrations of molinate and thiobencarb measured at Colusa Basin Drain 5 (one of our sites in 2003) since 1981. Implementing holding times for pesticide-treated rice field water in the early 1980s succeeded in decreasing concentrations in surface waters. Detailed pesticide use data is available since 1991 and changing use patterns for molinate and thiobencarb can explain some, but not all, of the trends in peak pesticide concentrations. A stronger relationship is seen between the lengths of time that performance goals were exceeded and the amount of a pesticide applied within a basin. Different extraction and analytical techniques were used to improve the recovery and lower the method detection limit for lambda-cyhalothrin. Recoveries of lambda-cyhalothrin from solid-phase extraction cartridges typically vary, so subsamples were processed by liquid-liquid extraction. The advantage of using a larger sample volume (3 L instead of 1 L) to lower detection limits was offset by poor recovery during the cleanup step using an activated carbon column. Results suggest that as the concentrations of dissolved organic carbon in the sample increase, the recovery g

Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method

PubMed Central

Elekwachi, Chijioke O.; Wang, Zuo; Wu, Xiaofeng; Rabee, Alaa; Forster, Robert J.

2017-01-01

Advances in high throughput, next generation sequencing technologies have allowed an in-depth examination of biological environments and phenomena, and are particularly useful for culture-independent microbial community studies. Recently the use of RNA for metatranscriptomic studies has been used to elucidate the role of active microbes in the environment. Extraction of RNA of appropriate quality is critical in these experiments and TRIzol reagent is often used for maintaining stability of RNA molecules during extraction. However, for studies using rumen content there is no consensus on (1) the amount of rumen digesta to use or (2) the amount of TRIzol reagent to be used in RNA extraction procedures. This study evaluated the effect of using various quantities of ground rumen digesta and of TRIzol reagent on the yield and quality of extracted RNA. It also investigated the possibility of using lower masses of solid-phase rumen digesta and lower amounts of TRIzol reagent than is used currently, for extraction of RNA for metatranscriptomic studies. We found that high quality RNA could be isolated from 2 g of ground rumen digesta sample, whilst using 0.6 g of ground matter for RNA extraction and using 3 mL (a 5:1 TRIzol : extraction mass ratio) of TRIzol reagent. This represents a significant savings in the cost of RNA isolation. These lower masses and volumes were then applied in the RNA-Seq analysis of solid-phase rumen samples obtained from 6 Angus X Hereford beef heifers which had been fed a high forage diet (comprised of barley straw in a forage-to-concentrate ratio of 70:30) for 102 days. A bioinformatics analysis pipeline was developed in-house that generated relative abundance values of archaea, protozoa, fungi and bacteria in the rumen and also allowed the extraction of individual rRNA variable regions that could be analyzed in downstream molecular ecology programs. The average relative abundances of rRNA transcripts of archaea, bacteria, protozoa and fungi in our samples were 1.4 ± 0.06, 44.16 ± 1.55, 35.38 ± 1.64, and 16.37 ± 0.65% respectively. This represents the first study to define the relative active contributions of these populations to the rumen ecosystem and is especially important in defining the role of the anaerobic fungi and protozoa. PMID:28983291

Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method.

PubMed

Elekwachi, Chijioke O; Wang, Zuo; Wu, Xiaofeng; Rabee, Alaa; Forster, Robert J

2017-01-01

Advances in high throughput, next generation sequencing technologies have allowed an in-depth examination of biological environments and phenomena, and are particularly useful for culture-independent microbial community studies. Recently the use of RNA for metatranscriptomic studies has been used to elucidate the role of active microbes in the environment. Extraction of RNA of appropriate quality is critical in these experiments and TRIzol reagent is often used for maintaining stability of RNA molecules during extraction. However, for studies using rumen content there is no consensus on (1) the amount of rumen digesta to use or (2) the amount of TRIzol reagent to be used in RNA extraction procedures. This study evaluated the effect of using various quantities of ground rumen digesta and of TRIzol reagent on the yield and quality of extracted RNA. It also investigated the possibility of using lower masses of solid-phase rumen digesta and lower amounts of TRIzol reagent than is used currently, for extraction of RNA for metatranscriptomic studies. We found that high quality RNA could be isolated from 2 g of ground rumen digesta sample, whilst using 0.6 g of ground matter for RNA extraction and using 3 mL (a 5:1 TRIzol : extraction mass ratio) of TRIzol reagent. This represents a significant savings in the cost of RNA isolation. These lower masses and volumes were then applied in the RNA-Seq analysis of solid-phase rumen samples obtained from 6 Angus X Hereford beef heifers which had been fed a high forage diet (comprised of barley straw in a forage-to-concentrate ratio of 70:30) for 102 days. A bioinformatics analysis pipeline was developed in-house that generated relative abundance values of archaea, protozoa, fungi and bacteria in the rumen and also allowed the extraction of individual rRNA variable regions that could be analyzed in downstream molecular ecology programs. The average relative abundances of rRNA transcripts of archaea, bacteria, protozoa and fungi in our samples were 1.4 ± 0.06, 44.16 ± 1.55, 35.38 ± 1.64, and 16.37 ± 0.65% respectively. This represents the first study to define the relative active contributions of these populations to the rumen ecosystem and is especially important in defining the role of the anaerobic fungi and protozoa.

A Comprehensive Program for Measurement of Military Aircraft Emissions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Mengdawn

2009-11-01

Emissions of gases and particulate matter by military aircraft were characterized inplume by 'extractive' and 'optical remote-sensing (ORS)' technologies. Non-volatile particle size distribution, number and mass concentrations were measured with good precision and reproducibly. Time-integrated particulate filter samples were collected and analyzed for smoke number, elemental composition, carbon contents, and sulfate. Observed at EEP the geometric mean diameter (as measured by the mobility diameter) generally increased as the engine power setting increased, which is consistent with downstream observations. The modal diameters at the downstream locations are larger than that at EEP at the same engine power level. The results indicatemore » that engine particles were processed by condensation, for example, leading to particle growth in-plume. Elemental analysis indicated little metals were present in the exhaust, while most of the exhaust materials in the particulate phase were carbon and sulfate (in the JP-8 fuel). CO, CO{sub 2}, NO, NO{sub 2}, SO{sub 2}, HCHO, ethylene, acetylene, propylene, and alkanes were measured. The last five species were most noticeable under engine idle condition. The levels of hydrocarbons emitted at high engine power level were generally below the detection limits. ORS techniques yielded real-time gaseous measurement, but the same techniques could not be extended directly to ultrafine particles found in all engine exhausts. The results validated sampling methodology and measurement techniques used for non-volatile particulate aircraft emissions, which also highlighted the needs for further research on sampling and measurement for volatile particulate matter and semi-volatile species in the engine exhaust especially at the low engine power setting.« less

On-line casein micelle disruption for downstream purification of recombinant human myelin basic protein produced in the milk of transgenic cows.

PubMed

Al-Ghobashy, Medhat A; Williams, Martin A K; Brophy, Brigid; Laible, Götz; Harding, David R K

2009-06-01

Downstream purification of a model recombinant protein (human myelin basic protein) from milk of transgenic cows is described. The recombinant protein was expressed as a His tagged fusion protein in the milk of transgenic cows and was found associated with the casein micellar phase. While difficulties in obtaining good recoveries were found when employing conventional micelle disruption procedures, direct capture using the cation exchanger SP Sepharose Big Beads was found successful in the extraction of the recombinant protein. Early breakthrough suggested a slow release of the recombinant protein from the micelles and dictated micelle disruption in order to obtain good yields. A new approach for deconstruction of the calcium core of the casein micelles, employing the interaction between the micellar calcium and the active sites of the cation exchanger resin was developed. Milk samples were loaded to the column in aliquots with a column washing step after each aliquot. This sequential loading approach successfully liberated the recombinant protein from the micelles and was found superior to the conventional sample loading approach. It increased the recovery by more than 25%, reduced fouling due to milk components and improved the column hydrodynamic properties as compared to the conventional sample loading approach. Hardware and software modifications to the chromatography system were necessary in order to keep the whole process automated. A second purification step using a Ni2+ affinity column was used to isolate the recombinant protein at purity more than 90% and a recovery percentage of 78%.

Flame Spread Along Free Edges of Thermally Thin Samples in Microgravity

NASA Technical Reports Server (NTRS)

Mell, W. E.; Olson, S. L.; Kashiwagi, T.

2000-01-01

The effects of imposed flow velocity on flame spread along open edges of a thermally thin cellulosic sample in microgravity are studied experimentally and theoretically. In this study, the sample is ignited locally at the middle of the 4 cm wide sample and subsequent flame spread reaches both open edges of the sample. The following flame behaviors are observed in the experiments and predicted by the numerical calculation; in order of increased imposed flow velocity: (1) ignition but subsequent flame spread is not attained, (2) flame spreads upstream (opposed mode) without any downstream flame, and (3) the upstream flame and two separate downstream flames traveling along the two open edges (concurrent mode). Generally, the upstream and downstream edge flame spread rates are faster than the central flame spread rate for an imposed flow velocity of up to 5 cm/s. This is due to greater oxygen supply from the outer free stream to the edge flames than the central flames, For the upstream edge flame, the greater oxygen supply results in a flame spread rate that is nearly independent of, or decreases gradually, with the imposed flow velocity. The spread rate of the downstream edge, however, increases significantly with the imposed flow velocity.

The best practice for preparation of samples from FTA®cards for diagnosis of blood borne infections using African trypanosomes as a model system.

PubMed

Ahmed, Heba A; MacLeod, Ewan T; Hide, Geoff; Welburn, Susan C; Picozzi, Kim

2011-05-07

Diagnosis of blood borne infectious diseases relies primarily on the detection of the causative agent in the blood sample. Molecular techniques offer sensitive and specific tools for this although considerable difficulties exist when using these approaches in the field environment. In large scale epidemiological studies, FTA®cards are becoming increasingly popular for the rapid collection and archiving of a large number of samples. However, there are some difficulties in the downstream processing of these cards which is essential for the accurate diagnosis of infection. Here we describe recommendations for the best practice approach for sample processing from FTA®cards for the molecular diagnosis of trypanosomiasis using PCR. A comparison of five techniques was made. Detection from directly applied whole blood was less sensitive (35.6%) than whole blood which was subsequently eluted from the cards using Chelex®100 (56.4%). Better apparent sensitivity was achieved when blood was lysed prior to application on the FTA cards (73.3%) although this was not significant. This did not improve with subsequent elution using Chelex®100 (73.3%) and was not significantly different from direct DNA extraction from blood in the field (68.3%). Based on these results, the degree of effort required for each of these techniques and the difficulty of DNA extraction under field conditions, we recommend that blood is transferred onto FTA cards whole followed by elution in Chelex®100 as the best approach.

Numerical analyses of evolution of unsteady flow structures in the wake of flapping starling wing model

NASA Astrophysics Data System (ADS)

Krishnan, Krishnamoorthy; Naqavi, Iftekhar Z.; Gurka, Roi

2017-11-01

Understanding the physics of flapping wings at moderate Reynolds number flows takes on greater importance in the context of avian aerodynamics as well as in the design of miniature-aerial-vehicles. Analyzing the characteristics of wake vortices generated downstream of flapping wings can help to explain the unsteady contribution to the aerodynamics loads. In this study, numerical simulations of flow over a bio-inspired pseudo-2D flapping wing model was conducted to characterize the evolution of unsteady flow structures in the downstream wake of flapping wing. The wing model was based on a European starling's wing and wingbeat kinematics were incorporated to simulate a free-forward flight. The starling's wingbeat kinematics were extracted from experiments conducted in a wind tunnel where freely flying starling was measured using high-speed PIV as well as high-speed imaging yielding a series of kinematic images sampled at 500 Hz. The average chord of the wing section was 6 cm and simulations were carried out at a Reynolds number of 54,000, reduced frequency of 0.17, and Strouhal number of 0.16. Large eddy simulation was performed using a second order, finite difference code ParLES. Characteristics of wake vortex structures during the different phases of the wing strokes were examined. The role of wingbeat kinematics in the configuration of downstream vortex patterns is discussed. Evaluated wake topology and lift-drag characteristics are compared with the starling's wind tunnel results.

Submarine Alkalic Lavas Around the Hawaiian Hotspot; Plume and Non-Plume Signatures Determined by Noble Gases

NASA Astrophysics Data System (ADS)

Hanyu, T.; Clague, D. A.; Kaneoka, I.; Dunai, T. J.; Davies, G. R.

2004-12-01

Noble gas isotopic ratios were determined for submarine alkalic volcanic rocks distributed around the Hawaiian islands to constrain the origin of such alkalic volcanism. Samples were collected by dredging or using submersibles from the Kauai Channel between Oahu and Kauai, north of Molokai, northwest of Niihau, Southwest Oahu, South Arch and North Arch volcanic fields. Sites located downstream from the center of the hotspot have 3He/4He ratios close to MORB at about 8 Ra, demonstrating that the magmas erupted at these sites had minimum contribution of volatiles from a mantle plume. In contrast, the South Arch, located upstream of the hotspot on the Hawaiian Arch, has 3He/4He ratios between 17 and 21 Ra, indicating a strong plume influence. Differences in noble gas isotopic characteristics between alkalic volcanism downstream and upstream of the hotspot imply that upstream volcanism contains incipient melts from an upwelling mantle plume, having primitive 3He/4He. In combination with lithophile element isotopic data, we conclude that the most likely source of the upstream magmatism is depleted asthenospheric mantle that has been metasomatised by incipient melt from a mantle plume. After major melt extraction from the mantle plume during production of magmas for the shield stage, the plume material is highly depleted in noble gases and moderately depleted in lithophile elements. Partial melting of the depleted mantle impregnated by melts derived from this volatile depleted plume source may explain the isotopic characteristics of the downstream alkalic magmatism.

RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets.

PubMed

Lazzarato, F; Franceschinis, G; Botta, M; Cordero, F; Calogero, R A

2004-11-01

RRE allows the extraction of non-coding regions surrounding a coding sequence [i.e. gene upstream region, 5'-untranslated region (5'-UTR), introns, 3'-UTR, downstream region] from annotated genomic datasets available at NCBI. RRE parser and web-based interface are accessible at http://www.bioinformatica.unito.it/bioinformatics/rre/rre.html

Depletion of abundant plant RuBisCO protein using the protamine sulfate precipitation method.

PubMed

Kim, Yu Ji; Lee, Hye Min; Wang, Yiming; Wu, Jingni; Kim, Sang Gon; Kang, Kyu Young; Park, Ki Hun; Kim, Yong Chul; Choi, In Soo; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kim, Sun Tae

2013-07-01

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant plant leaf protein, hampering deep analysis of the leaf proteome. Here, we describe a novel protamine sulfate precipitation (PSP) method for the depletion of RuBisCO. For this purpose, soybean leaf total proteins were extracted using Tris-Mg/NP-40 extraction buffer. Obtained clear supernatant was subjected to the PSP method, followed by 13% SDS-PAGE analysis of total, PS-supernatant and -precipitation derived protein samples. In a dose-dependent experiment, 0.1% w/v PS was found to be sufficient for precipitating RuBisCO large and small subunits (LSU and SSU). Western blot analysis confirmed no detection of RuBisCO LSU in the PS-supernatant proteins. Application of this method to Arabidopsis, rice, and maize leaf proteins revealed results similar to soybean. Furthermore, 2DE analyses of PS-treated soybean leaf displayed enriched protein profile for the protein sample derived from the PS-supernatant than total proteins. Some enriched 2D spots were subjected to MALDI-TOF-TOF analysis and were successfully assigned for their protein identity. Hence, the PSP method is: (i) simple, fast, economical, and reproducible for RuBisCO precipitation from the plant leaf sample; (ii) applicable to both dicot and monocot plants; and (iii) suitable for downstream proteomics analysis. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A rapid and efficient SDS-based RNA isolation protocol from different tissues of coffee.

PubMed

Huded, Arun Kumar C; Jingade, Pavankumar; Mishra, Manoj Kumar

2018-03-01

Isolation of high-quality RNA from coffee is challenging because of high level of polysaccharides, polyphenols and other secondary metabolites. In the present study, a rapid and efficient RNA extraction protocol from different tissues of coffee was optimized. Sufficiently high quality and quantity (225.6-454.8 µg/g) of RNA was obtained by using the optimized protocol. The presence of two distinct bands of 28S rRNA and 18S rRNA in agarose gel proved the intactness of the RNA samples. The average spectrophotometric values of the isolated RNA ranged from 1.96 to 2.02 ( A 260/280 ) and 1.95 to 2.14 ( A 260/230 ), indicating the high quality of RNA devoid of polyphenols, polysaccharides and protein contamination. In the optimized protocol, addition of PVPP to the extraction buffer and a brief incubation of samples at 65 °C and subsequent purification with potassium acetate resulted in good-quality RNA isolation. The suitability of RNA for downstream processing was confirmed by PCR amplification with cytochrome c oxidase gene-specific primers. The amplification of a single 392 bp fragment using cDNA and 1.5 kb fragment using genomic DNA samples confirmed the absence of DNA contamination. The present protocol is rapid and yielded good quality and quantity of RNA suitable for functional genomics studies.

A Stochastic Model For Extracting Sediment Delivery Timescales From Sediment Budgets

NASA Astrophysics Data System (ADS)

Pizzuto, J. E.; Benthem, A.; Karwan, D. L.; Keeler, J. J.; Skalak, K.

2015-12-01

Watershed managers need to quantify sediment storage and delivery timescales to understand the time required for best management practices to improve downstream water quality. To address this need, we route sediment downstream using a random walk through a series of valley compartments spaced at 1 km intervals. The probability of storage within each compartment, q, is specified from a sediment budget and is defined as the ratio of the volume deposited to the annual sediment flux. Within each compartment, the probability of sediment moving directly downstream without being stored is p=1-q. If sediment is stored within a compartment, its "resting time" is specified by a stochastic exponential waiting time distribution with a mean of 10 years. After a particle's waiting time is over, it moves downstream to the next compartment by fluvial transport. Over a distance of "n" compartments, a sediment particle may be stored from 0 to n times with the probability of each outcome (store or not store) specified by the binomial distribution. We assign q = 0.02, a stream velocity of 0.5 m/s, an event "intermittency "of 0.01, and assume a balanced sediment budget. Travel time probability density functions have a steep peak at the shortest times, representing rapid transport in the channel of the fraction of sediment that moves downstream without being stored. However, the probability of moving downstream "n" km without storage is pn (0.90 for 5 km, 0.36 for 50 km, 0.006 for 250 km), so travel times are increasingly dominated by storage with increasing distance. Median travel times for 5, 50, and 250 km are 0.03, 4.4, and 46.5 years. After a distance of approximately 2/q or 100 km (2/0.02/km), the median travel time is determined by storage timescales, and active fluvial transport is irrelevant. Our model extracts travel time statistics from sediment budgets, and can be cast as a differential equation and solved numerically for more complex systems.

Peat soil properties and erodibility: what factors affect erosion and suspended sediment yields in peat extraction areas?

NASA Astrophysics Data System (ADS)

Tuukkanen, Tapio; Marttila, Hannu; Kløve, Bjørn

2014-05-01

Peatland drainage and peat extraction operations change soil properties and expose bare peat to erosion forces, resulting in increased suspended sediment (SS) loads to downstream water bodies. SS yields from peat extraction areas are known to vary significantly between sites, but the contribution of peat properties and catchment characteristics to this variation is not well understood. In this study, we investigated peat erosion at 20 Finnish peat extraction sites by conducting in situ and laboratory measurements on peat erodibility and associated peat properties (degree of humification, peat type, bulk density, loss on ignition, porosity, moisture content, and shear strength), and by comparing the results with monitored long-term SS concentrations and loads at each catchment outlet. Here, we used a cohesive strength meter (CSM) to measure direct erosion thresholds for undisturbed soil cores collected from each study site. The results suggested that the degree of peat decomposition clearly affects peat erodibility and explains much of the variation in SS concentration between the study sites. According to CSM tests, critical shear stresses for particle entrainment were lowest (on average) in well-decomposed peat samples, while undecomposed, dry and fiber rich peat generally resisted erosion very well. Furthermore, the results indicated that two separate critical shear stresses often exist in moderately decomposed peat. In these cases, the well-decomposed parts of peat samples eroded first at relatively low shear stresses and remaining peat fibers prevented further erosion until a much higher shear stress was reached. In addition to peat soil properties, the study showed that the erosion of mineral subsoil may play a key role in runoff water SS concentration at peat extraction areas with drainage ditches extending into the mineral soil. The interactions between peat properties and peat erodibility found in this study as well as critical shear stress values obtained can be used for several purposes in e.g. water conservation and sediment management planning for peat extraction areas and other bare peat-covered catchments.

Chemical characterization of sediments and pore water from the upper Clark Fork River and Milltown Reservoir, Montana

USGS Publications Warehouse

Brumbaugh, W. G.; Ingersoll, C.G.; Kemble, N.E.; May, T.W.; Zajicek, J.L.

1994-01-01

The upper Clark Fork River basin in western Montana is widely contaminated by metals from past mining, milling, and smelting activities As part of a comprehensive ecological risk assessment for the upper Clark Fork River, we measured physical and chemical characteristics of surficial sediment samples that were collected from depositional zones for subsequent toxicity evaluations Sampling stations included five locations along the upper 200 km of the river, six locations in or near Milltown Reservoir (about 205 km from the river origin), and two tributary reference sites Concentrations of As, Cd, Cu, Mn, Pb, and Zn decreased from the upper stations to the downstream stations in the Clark Fork River but then increased in all Milltown Reservoir stations to levels similar to uppermost river stations Large percentages (50 to 90%) of the total Cd, Cu, Pb, and Zn were extractable by dilute (3 n) HCl for all samples Copper and zinc accounted for greater than 95% of extractable metals on a molar basis Acid-volatile sulfide (AVS) concentrations were typically moderate (0 6 to 23 μmol/g) in grab sediment samples and appeared to regulate dissolved (filterable) concentrations of Cd, Cu, and Zn in sediment pore waters Acid volatile sulfide is important in controlling metal solubility in the depositional areas of the Clark Fork River and should be monitored in any future studies Spatial variability within a sampling station was high for Cu, Zn, and AVS, therefore, the potential for toxicity to sediment dwelling organisms may be highly localized.

Post-Flight Assessment of Avcoat Thermal Protection System for the Exploration Flight Test-1

NASA Technical Reports Server (NTRS)

Bose, Deepak; Santos, Jose; Rodriguez, Erika; Mahzari, Milad; Remark, Brian; Muppidi, Suman

2016-01-01

On December 5, 2014 NASA conducted the first flight test of its next generation human-class Orion spacecraft. The flight was called the Exploration Flight Test -1 (EFT-1) which lasted for 4 hours and culminated into a re-entry trajectory at 9 km/s. This flight test of the 5-meter Orion Crew Module demonstrated various sub-systems including the Avcoat ablative thermal protection system (TPS) on the heat shield. The Avcoat TPS had been developed from the Apollo-era recipe with a few key modifications. The engineering for thermal sizing was supported by modeling, analysis, and ground tests in arc jet facilities. This paper will describe a postlfight analysis plan and present results from post-recovery inspections, data analysis from embedded sensors, TPS sample extraction and characterization in the laboratory. After the recovery of the vehicle, a full photographic survey and surface scans of the TPS were performed. The recovered vehicle showed physical evidence of flow disturbances, varying degrees of surface roughness, and excessive recession downstream of compression pads. The TPS recession was measured at more than 200 locations of interest on the Avcoat surface. The heat shield was then processed for sample extraction prior to TPS removal using the 7-Axis Milling machine at Marshall Space Flight Center. Around 182 rectangular TPS samples were extracted for subsequent analysis and investigation. The final paper will also present results of sample analysis. The planned investigation includes sidewall imaging, followed by image analysis to characterize TPS response by quantifying different layers in the char and pyrolysis zones. A full postmortem of the instrumentation and sensor ports will also be performed to confirm no adverse effects due to the sensors themselves. A subset of the samples will undergo structural testing and perform detailed characterization of any cracks and integrity of gore seams. Finally, the material will be characterized with layer-by-layer density measurements and SEM investigations to evaluate material morphology at microstructural level including identification of elements and compounds.

Ion beam accelerator system

NASA Technical Reports Server (NTRS)

Aston, G. (Inventor)

1981-01-01

A system is described that combines geometrical and electrostatic focusing to provide high ion extraction efficiency and good focusing of an accelerated ion beam. The apparatus includes a pair of curved extraction grids with multiple pairs of aligned holes positioned to direct a group of beamlets along converging paths. The extraction grids are closely spaced and maintained at a moderate potential to efficiently extract beamlets of ions and allow them to combine into a single beam. An accelerator electrode device downstream from the extraction grids is at a much lower potential than the grids to accelerate the combined beam. The application of the system to ion implantation is mentioned.

High DNA stability in white blood cells and buffy coat lysates stored at ambient temperature under anoxic and anhydrous atmosphere

PubMed Central

Luis, Aurélie; Colotte, Marthe; Tuffet, Sophie; Bonnet, Jacques

2017-01-01

Conventional storage of blood-derived fractions relies on cold. However, lately, ambient temperature preservation has been evaluated by several independent institutions that see economic and logistic advantages in getting rid of the cold chain. Here we validated a novel procedure for ambient temperature preservation of DNA in white blood cell and buffy coat lysates based on the confinement of the desiccated biospecimens under anoxic and anhydrous atmosphere in original hermetic minicapsules. For this validation we stored encapsulated samples either at ambient temperature or at several elevated temperatures to accelerate aging. We found that DNA extracted from stored samples was of good quality with a yield of extraction as expected. Degradation rates were estimated from the average fragment size of denatured DNA run on agarose gels and from qPCR reactions. At ambient temperature, these rates were too low to be measured but the degradation rate dependence on temperature followed Arrhenius’ law, making it possible to extrapolate degradation rates at 25°C. According to these values, the DNA stored in the encapsulated blood products would remain larger than 20 kb after one century at ambient temperature. At last, qPCR experiments demonstrated the compatibility of extracted DNA with routine DNA downstream analyses. Altogether, these results showed that this novel storage method provides an adequate environment for ambient temperature long term storage of high molecular weight DNA in dehydrated lysates of white blood cells and buffy coats. PMID:29190767

High DNA stability in white blood cells and buffy coat lysates stored at ambient temperature under anoxic and anhydrous atmosphere.

PubMed

Fabre, Anne-Lise; Luis, Aurélie; Colotte, Marthe; Tuffet, Sophie; Bonnet, Jacques

2017-01-01

Conventional storage of blood-derived fractions relies on cold. However, lately, ambient temperature preservation has been evaluated by several independent institutions that see economic and logistic advantages in getting rid of the cold chain. Here we validated a novel procedure for ambient temperature preservation of DNA in white blood cell and buffy coat lysates based on the confinement of the desiccated biospecimens under anoxic and anhydrous atmosphere in original hermetic minicapsules. For this validation we stored encapsulated samples either at ambient temperature or at several elevated temperatures to accelerate aging. We found that DNA extracted from stored samples was of good quality with a yield of extraction as expected. Degradation rates were estimated from the average fragment size of denatured DNA run on agarose gels and from qPCR reactions. At ambient temperature, these rates were too low to be measured but the degradation rate dependence on temperature followed Arrhenius' law, making it possible to extrapolate degradation rates at 25°C. According to these values, the DNA stored in the encapsulated blood products would remain larger than 20 kb after one century at ambient temperature. At last, qPCR experiments demonstrated the compatibility of extracted DNA with routine DNA downstream analyses. Altogether, these results showed that this novel storage method provides an adequate environment for ambient temperature long term storage of high molecular weight DNA in dehydrated lysates of white blood cells and buffy coats.

Downstream process options for the ABE fermentation.

PubMed

Friedl, Anton

2016-05-01

Butanol is a very interesting substance both for the chemical industry and as a biofuel. The classical distillation process for the removal of butanol is far too energy demanding, at a factor of 220% of the energy content of butanol. Alternative separation processes studied are hybrid processes of gas-stripping, liquid-liquid extraction and pervaporation with distillation and a novel adsorption/drying/desorption hybrid process. Compared with the energy content of butanol, the resulting energy demand for butanol separation and concentration of optimized hybrid processes is 11%-22% for pervaporation/distillation and 11%-17% for liquid-liquid extraction/distillation. For a novel adsorption/drying/desorption process, the energy demand is 9.4%. But all downstream process options need further proof of industrial applicability. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effects of surface and groundwater interactions on phosphorus transport within streambank sediments.

PubMed

Thompson, Carol A; McFarland, Anne M S

2010-01-01

Understanding internal stream P transfers is important in controlling eutrophication. To determine the direction of groundwater and surface water interactions and evaluate P retention within streambank sediments, groundwater well pairs, about 5-m deep, were installed at three locations along a second-order, eutrophic stream in north-central Texas. Well cores were analyzed for P, and groundwater levels were monitored for about 2 yr. Water levels in wells furthest upstream always indicated a losing stream, while wells further downstream showed a gaining stream except during flow reversals with storm events and periods with reservoir backwater. Total-P from well cores ranged from 54 to 254 mg kg(-1) and was typically high near surface, decreased downward until redoximorphic features were encountered and then increased notably with depth to near or above surface concentrations. Very little extractable P occurred in sediments from the two upstream well sets; however, the set furthest downstream showed extractable P throughout with a high of 21 mg kg(-1) near the bottom. Repeated wetting-drying at sites A and B as noted by redoximorphic features may have shifted P into more stable sediment-bound forms. The decrease in extractable P at sites A and B compared to site C may be explained by conditions at C that were wetter and potentially anaerobic. Because the overall stream reach was more often losing than gaining, there appears to be a mass flow of P into streambank sediments. Streambank erosion may then transport this P downstream if not controlled.

Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans

PubMed Central

Slatkin, Montgomery

2016-01-01

When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters—including drift times and admixture rates—for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called ‘Demographic Inference with Contamination and Error’ (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%. PMID:27049965

Loosely bound oxytetracycline in riverine sediments from two tributaries of the Chesapeake Bay

USGS Publications Warehouse

Simon, N.S.

2005-01-01

The fate of antibiotics that bind to riverine sediment is not well understood. A solution used in geochemical extraction schemes to determine loosely bound species in sediments, 1 M MgCl2 (pH 8), was chosen to determine loosely bound, and potentially bioavailable, tetracycline antibiotics (TCs), including oxytetracycline (5-OH tetracycline) (OTC) in sediment samples from two rivers on the eastern shore of the Chesapeake Bay. Bottom sediments were collected at sites upstream from, at, and downstream from municipal sewage-treatment plants (STPs) situated on two natural waterways, Yellow Bank Stream, MD, and the Pocomoke River, MD. Concentrations of easily desorbed OTC ranged from 0.6 to approximately 1.2 ??g g-1 dry wt sediment in Yellow Bank Stream and from 0.7 to approximately 3.3 ??g g-1 dry wt sediment in the Pocomoke River. Concentrations of easily desorbable OTC were generally smaller in sediment upstream than in sediment downstream from the STP in the Pocomoke River. STPs and poultry manure are both potential sources of OTC to these streams. OTC that is loosely bound to sediment is subject to desorption. Other researchers have found desorbed TCs to be biologically active compounds.

Electrical Motor Current Signal Analysis using a Modulation Signal Bispectrum for the Fault Diagnosis of a Gearbox Downstream

NASA Astrophysics Data System (ADS)

Haram, M.; Wang, T.; Gu, F.; Ball, A. D.

2012-05-01

Motor current signal analysis has been an effective way for many years of monitoring electrical machines themselves. However, little work has been carried out in using this technique for monitoring their downstream equipment because of difficulties in extracting small fault components in the measured current signals. This paper investigates the characteristics of electrical current signals for monitoring the faults from a downstream gearbox using a modulation signal bispectrum (MSB), including phase effects in extracting small modulating components in a noisy measurement. An analytical study is firstly performed to understand amplitude, frequency and phase characteristics of current signals due to faults. It then explores the performance of MSB analysis in detecting weak modulating components in current signals. Experimental study based on a 10kw two stage gearbox, driven by a three phase induction motor, shows that MSB peaks at different rotational frequencies can be based to quantify the severity of gear tooth breakage and the degrees of shaft misalignment. In addition, the type and location of a fault can be recognized based on the frequency at which the change of MSB peak is the highest among different frequencies.

Imaging of Combustion Species in a Radially-Staged Gas Turbine Combustor

NASA Technical Reports Server (NTRS)

Locke, Randy J.; Hicks, Yolanda R.; Anderson, Robert C.; Ockunzzi, Kelly A.; Schock, Harold J.

1996-01-01

Plannar laser-induced fluorescence (PLIF) is used to characterize the complex flowfield of a unique fuel-lean, radially-staged high pressure gas turbine combustor. PLIF images of OH are presented for two fuel injector configurations. PLIF images of NO, the first acquired at these conditions, are presented and compared with gas sample extraction probe measurements. Flow field imaging of nascent C2 chemiluminescence is also investigated. An examination is made of the interaction between adjoining lean premixed prevaporized (LPP) injectors. Fluorescence interferences at conditions approaching 2000 K and 15 atm are observed and attributed to polycyclic aromatic hydrocarbon (PAH) emissions. All images are acquired at a position immediately downstream of the fuel injectors with combustor burning JP-5 fuel.

Imaging of Combustion Species in a Radially-Staged Gas Turbine Combustor

NASA Technical Reports Server (NTRS)

Locke, Randy J.; Hicks, Yolanda R.; Anderson, Robert C.; Ockunzzi, Kelly A.; Schock, Harold J.

1996-01-01

Planar laser-induced fluorescence (PLIF) is used to characterize the complex flowfield of a unique fuel-lean, radially-staged, high pressure gas turbine combustor. PLIF images of OH are presented for two fuel injector configurations. PLIF images of NO, the first acquired at these conditions, are presented and compared with gas sample extraction probe measurements. Flow field imaging of nascent C2 chemiluminescence is also investigated. An examination is made of the interaction between adjoining lean premixed prevaporized (LPP) injectors. Fluorescence interferences at conditions approaching 2000 K and 15 atm are observed and attributed to polycyclic aromatic hydrocarbon (PAH) emissions. All images are acquired at a position immediately downstream of the fuel injectors with the combustor burning JP-5 fuel.

Isotope tracing of Hg pollution from artisanal small scale gold mining in an aquatic ecosystem of Amapá, Brazil

NASA Astrophysics Data System (ADS)

Adler Miserendino, R.; Silbergeld, E. K.; Guimarães, J. D.; Ghosh, S.; Bergquist, B. A.

2010-12-01

Artisinal small scale gold mining (ASGM) is a central economic activity throughout the developing world. It is both a poverty driven and poverty alleviating process; however, ASGM leads to extensive pollution of waterways through the use of Hg to extract gold from deposits. There have been many studies conducted in the Amazon showing elevated levels of Hg in fish and sediment downstream of ASGM sites; however, the debate continues about the contribution of Hg from ASGM versus other potential sources of Hg. In this study, we investigate whether Hg stable isotope analysis can be used to trace mercury pollution from an ASGM site through an aquatic ecosystem in Amapá, Brazil. We measured the Hg isotopic composition of sediment cores from two lakes, only one of which was heavily impacted by the use of elemental Hg in ASGM, as well as from grab samples at the AGSM site and upstream and downstream from the AGSM site along the river which connects the polluted lake to the ASGM site. Hg from all samples were trapped via combustion using the Leeman Labs Hydra-C mercury analyzer and analyzed for both mass-independent and mass-dependent signatures using cold vapor multi-collector inductively coupled plasma mass spectrometry (CV-MC-ICP-MS). Detectable variations in the Hg isotopic signatures were apparent across our field sites, suggesting stable isotopic analysis has great potential to trace contamination pathways in waterways. Preliminary data demonstrate Hg from the ASGM site has unique isotopic signatures that are seen downstream. However, the impacted lake sediments do not have the mining signature despite having three times more Hg than the non-impacted lake. Based on this data, it may be possible to trace Hg from ASGM and assess whether it is impacting local ecosystems and food webs. Hair and soil samples will also be discussed. This demonstration is essential for the broader application of these tools for understanding and applying Hg isotopic analysis in other contexts. This information may also be useful to help reduce Hg exposure of highly vulnerable populations exposed to Hg from ASGM through these aquatic networks in Amapá, Brazil.

Occurrence of organic wastewater compounds in effluent-dominated streams in Northeastern Kansas

USGS Publications Warehouse

Lee, C.J.; Rasmussen, T.J.

2006-01-01

Fifty-nine stream-water samples and 14 municipal wastewater treatment facility (WWTF) discharge samples in Johnson County, northeastern Kansas, were analyzed for 55 compounds collectively described as organic wastewater compounds (OWCs). Stream-water samples were collected upstream, in, and downstream from WWTF discharges in urban and rural areas during base-flow conditions. The effect of secondary treatment processes on OWC occurrence was evaluated by collecting eight samples from WWTF discharges using activated sludge and six from WWTFs samples using trickling filter treatment processes. Samples collected directly from WWTF discharges contained the largest concentrations of most OWCs in this study. Samples from trickling filter discharges had significantly larger concentrations of many OWCs (p-value < 0.05) compared to samples collected from activated sludge discharges. OWC concentrations decreased significantly in samples from WWTF discharges compared to stream-water samples collected from sites greater than 2000??m downstream. Upstream from WWTF discharges, base-flow samples collected in streams draining predominantly urban watersheds had significantly larger concentrations of cumulative OWCs (p-value = 0.03), caffeine (p-value = 0.01), and tris(2-butoxyethyl) phosphate (p-value < 0.01) than those collected downstream from more rural watersheds.

Bioaerosol DNA Extraction Technique from Air Filters Collected from Marine and Freshwater Locations

NASA Astrophysics Data System (ADS)

Beckwith, M.; Crandall, S. G.; Barnes, A.; Paytan, A.

2015-12-01

Bioaerosols are composed of microorganisms suspended in air. Among these organisms include bacteria, fungi, virus, and protists. Microbes introduced into the atmosphere can drift, primarily by wind, into natural environments different from their point of origin. Although bioaerosols can impact atmospheric dynamics as well as the ecology and biogeochemistry of terrestrial systems, very little is known about the composition of bioaerosols collected from marine and freshwater environments. The first step to determine composition of airborne microbes is to successfully extract environmental DNA from air filters. We asked 1) can DNA be extracted from quartz (SiO2) air filters? and 2) how can we optimize the DNA yield for downstream metagenomic sequencing? Aerosol filters were collected and archived on a weekly basis from aquatic sites (USA, Bermuda, Israel) over the course of 10 years. We successfully extracted DNA from a subsample of ~ 20 filters. We modified a DNA extraction protocol (Qiagen) by adding a beadbeating step to mechanically shear cell walls in order to optimize our DNA product. We quantified our DNA yield using a spectrophotometer (Nanodrop 1000). Results indicate that DNA can indeed be extracted from quartz filters. The additional beadbeating step helped increase our yield - up to twice as much DNA product was obtained compared to when this step was omitted. Moreover, bioaerosol DNA content does vary across time. For instance, the DNA extracted from filters from Lake Tahoe, USA collected near the end of June decreased from 9.9 ng/μL in 2007 to 3.8 ng/μL in 2008. Further next-generation sequencing analysis of our extracted DNA will be performed to determine the composition of these microbes. We will also model the meteorological and chemical factors that are good predictors for microbial composition for our samples over time and space.

Presence of Emerging Per- and Polyfluoroalkyl Substances (PFASs) in River and Drinking Water near a Fluorochemical Production Plant in the Netherlands.

PubMed

Gebbink, Wouter A; van Asseldonk, Laura; van Leeuwen, Stefan P J

2017-10-03

The present study investigated the presence of legacy and emerging per- and polyfluoroalkyl substances (PFASs) in river water collected in 2016 up- and downstream from a fluorochemical production plant, as well as in river water from control sites, in The Netherlands. Additionally, drinking water samples were collected from municipalities in the vicinity from the production plant, as well as in other regions in The Netherlands. The PFOA replacement chemical GenX was detected at all downstream river sampling sites with the highest concentration (812 ng/L) at the first sampling location downstream from the production plant, which was 13 times higher than concentrations of sum perfluoroalkylcarboxylic acids and perfluoroalkanesulfonates (∑PFCA+∑PFSA). Using high resolution mass spectrometry, 11 polyfluoroalkyl acids belonging to the C 2n H 2n F 2n O 2 , C 2n H 2n+2 F 2n SO 4 or C 2n+1 H 2n F 2n+4 SO 4 homologue series were detected, but only in downstream water samples. These emerging PFASs followed a similar distribution as GenX among the downstream sampling sites, suggesting the production plant as the source. Polyfluoroalkyl sulfonates (C 2n H 2 F 4n SO 3 ) were detected in all collected river water samples, and therefore appear to be ubiquitous contaminants in Dutch rivers. GenX was also detected in drinking water collected from 3 out of 4 municipalities in the vicinity of the production plant, with highest concentration at 11 ng/L. Drinking water containing the highest level of GenX also contained two C 2n H 2n F 2n O 2 homologues.

Presence of Emerging Per- and Polyfluoroalkyl Substances (PFASs) in River and Drinking Water near a Fluorochemical Production Plant in the Netherlands

PubMed Central

2017-01-01

The present study investigated the presence of legacy and emerging per- and polyfluoroalkyl substances (PFASs) in river water collected in 2016 up- and downstream from a fluorochemical production plant, as well as in river water from control sites, in The Netherlands. Additionally, drinking water samples were collected from municipalities in the vicinity from the production plant, as well as in other regions in The Netherlands. The PFOA replacement chemical GenX was detected at all downstream river sampling sites with the highest concentration (812 ng/L) at the first sampling location downstream from the production plant, which was 13 times higher than concentrations of sum perfluoroalkylcarboxylic acids and perfluoroalkanesulfonates (∑PFCA+∑PFSA). Using high resolution mass spectrometry, 11 polyfluoroalkyl acids belonging to the C2nH2nF2nO2, C2nH2n+2F2nSO4 or C2n+1H2nF2n+4SO4 homologue series were detected, but only in downstream water samples. These emerging PFASs followed a similar distribution as GenX among the downstream sampling sites, suggesting the production plant as the source. Polyfluoroalkyl sulfonates (C2nH2F4nSO3) were detected in all collected river water samples, and therefore appear to be ubiquitous contaminants in Dutch rivers. GenX was also detected in drinking water collected from 3 out of 4 municipalities in the vicinity of the production plant, with highest concentration at 11 ng/L. Drinking water containing the highest level of GenX also contained two C2nH2nF2nO2 homologues. PMID:28853567

Environmental signatures and effects of an oil and gas wastewater spill in the Williston Basin, North Dakota.

PubMed

Cozzarelli, I M; Skalak, K J; Kent, D B; Engle, M A; Benthem, A; Mumford, A C; Haase, K; Farag, A; Harper, D; Nagel, S C; Iwanowicz, L R; Orem, W H; Akob, D M; Jaeschke, J B; Galloway, J; Kohler, M; Stoliker, D L; Jolly, G D

2017-02-01

Wastewaters from oil and gas development pose largely unknown risks to environmental resources. In January 2015, 11.4ML (million liters) of wastewater (300g/L TDS) from oil production in the Williston Basin was reported to have leaked from a pipeline, spilling into Blacktail Creek, North Dakota. Geochemical and biological samples were collected in February and June 2015 to identify geochemical signatures of spilled wastewaters as well as biological responses along a 44-km river reach. February water samples had elevated chloride (1030mg/L) and bromide (7.8mg/L) downstream from the spill, compared to upstream levels (11mg/L and <0.4mg/L, respectively). Lithium (0.25mg/L), boron (1.75mg/L) and strontium (7.1mg/L) were present downstream at 5-10 times upstream concentrations. Light hydrocarbon measurements indicated a persistent thermogenic source of methane in the stream. Semi-volatile hydrocarbons indicative of oil were not detected in filtered samples but low levels, including tetramethylbenzenes and di-methylnaphthalenes, were detected in unfiltered water samples downstream from the spill. Labile sediment-bound barium and strontium concentrations (June 2015) were higher downstream from the Spill Site. Radium activities in sediment downstream from the Spill Site were up to 15 times the upstream activities and, combined with Sr isotope ratios, suggest contributions from the pipeline fluid and support the conclusion that elevated concentrations in Blacktail Creek water are from the leaking pipeline. Results from June 2015 demonstrate the persistence of wastewater effects in Blacktail Creek several months after remediation efforts started. Aquatic health effects were observed in June 2015; fish bioassays showed only 2.5% survival at 7.1km downstream from the spill compared to 89% at the upstream reference site. Additional potential biological impacts were indicated by estrogenic inhibition in downstream waters. Our findings demonstrate that environmental signatures from wastewater spills are persistent and create the potential for long-term environmental health effects. Published by Elsevier B.V.

Human pharmaceuticals in Portuguese rivers: The impact of water scarcity in the environmental risk.

PubMed

Pereira, André M P T; Silva, Liliana J G; Laranjeiro, Célia S M; Meisel, Leonor M; Lino, Celeste M; Pena, Angelina

2017-12-31

Pharmaceuticals occurrence and environmental risk assessment were assessed in Portuguese surface waters, evaluating the impact of wastewater treatment plants (WWTPs) and river flow rates. Twenty three pharmaceuticals from 6 therapeutic groups, including metabolites and 1 transformation product, were analysed in 72 samples collected from 20 different sites, upstream and downstream the selected WWTPs, in two different seasons. Analysis was performed by solid phase extraction followed by liquid chromatography coupled to tandem mass spectroscopy. Pharmaceuticals were detected in 27.8% of the samples. Selective serotonin reuptake inhibitors (SSRIs), anti-inflammatories and antibiotics presented the highest detection frequencies (27.8, 23.6 and 23.6%, respectively) and average concentrations (37.9, 36.1 and 33.5ngL -1 , respectively). When assessing the impact of WWTPs, an increase of 21.4% in the average concentrations was observed in the samples located downstream these facilities, when compared with the upstream samples. Increased detection frequencies and concentrations were observed at lower flow rates, both when comparing summer and winter campaigns and by evaluating the different rivers. Risk quotients (RQs) higher than one were found for two pharmaceuticals, concerning two trophic levels. However, since Iberian rivers are highly influenced by water scarcity, in drought periods, the flow rates in these rivers can decrease at least ten times from the lowest value observed in the sampling campaigns. In these conditions, RQs higher than 1 would be observed for 5 pharmaceuticals, additionally, all the detected pharmaceuticals (11) would present RQs higher than 0.1. These results emphasize that the river flow rate represents an important parameter influencing pharmaceuticals concentrations, highlighting the ecotoxicological pressure, especially due to water scarcity in drought periods. This should be a priority issue in the environmental policies for minimizing its impact in the aquatic environment. Copyright © 2017 Elsevier B.V. All rights reserved.

Mortality of zebra mussel, Dreissena polymorpha, veligers during downstream transport

USGS Publications Warehouse

Horvath, T.G.; Lamberti, G.A.

1999-01-01

1. Streams flowing from lakes which contain zebra mussels, Dreissena polymorpha, provide apparently suitable habitats for mussel colonization and downstream range expansion, yet most such streams contain few adult mussels. We postulated that mussel veligers experience high mortality during dispersal via downstream transport. They tested this hypothesis in Christiana Creek, a lake-outlet stream in south-western Michigan, U.S.A., in which adult mussel density declined exponentially with distance downstream. 2. A staining technique using neutral red was developed and tested to distinguish quickly live and dead veligers. Live and dead veligers were distinguishable after an exposure of fresh samples to 13.3 mg L-1 of neutral red for 3 h. 3. Neutral red was used to determine the proportion of live veligers in samples taken longitudinally along Christiana Creek. The proportion of live veligers (mean ?? SE) declined from 90 ?? 3% at the lake outlet to 40 ?? 8% 18 km downstream. 4. Veligers appear to be highly susceptible to damage by physical forces (e.g. shear), and therefore, mortality in turbulent streams could be an important mechanism limiting zebra mussel dispersal to downstream reaches. Predictions of zebra mussel spread and population growth should consider lake-stream linkages and high mortality in running waters.

Occurrence of emerging contaminants in water and bed material in the Missouri River, North Dakota, 2007

USGS Publications Warehouse

Damschen, William C.; Lundgren, Robert F.

2009-01-01

The U.S. Geological Survey (USGS), in cooperation with the Standing Rock Sioux Tribe, conducted a reconnaissance study to determine the occurrence of emerging contaminants in water and bed sediment within the Missouri River upstream and downstream from the cities of Bismarck and Mandan, North Dakota, and upstream from the city of Fort Yates, North Dakota, during September-October 2007. At each site, water samples were collected twice and bed-sediment samples were collected once. Samples were analyzed for more than 200 emerging contaminants grouped into four compound classes - wastewater compounds, human-health pharmaceutical compounds, hormones, and antibiotics. Only sulfamethoxazole, an antibiotic, was present at a concentration higher than minimum detection limits. It was detected in a water sample collected downstream from the cities of Bismarck and Mandan, and in bed-sediment samples collected at the two sites downstream from the cities of Bismarck and Mandan and upstream from Fort Yates. Sulfamethoxazole is an antibiotic commonly used for treating bacterial infections in humans and animals.

Chemical and physiological metal bioaccessibility assessment in surface bottom sediments from the Deba River urban catchment: Harmonization of PBET, TCLP and BCR sequential extraction methods.

PubMed

Unda-Calvo, Jessica; Martínez-Santos, Miren; Ruiz-Romera, Estilita

2017-04-01

In the present study, the physiologically based extraction test PBET (gastric and intestinal phases) and two chemical based extraction methods, the toxicity characteristic leaching procedure (TCLP) and the sequential extraction procedure BCR 701 (Community Bureau of Reference of the European Commission) have been used to estimate and evaluate the bioaccessibility of metals (Fe, Mn, Zn, Cu, Ni, Cr and Pb) in sediments from the Deba River urban catchment. The statistical analysis of data and comparison among physiological and chemical methods have highlighted the relevance of simulate the gastrointestinal tract environment since metal bioaccessibility seems to depend on water and sediment properties such as pH, redox potential and organic matter content, and, primordially, on the form in which metals are present in the sediment. Indeed, metals distributed among all fractions (Mn, Ni, Zn) were the most bioaccessible, followed by those predominantly bound to oxidizable fraction (Cu, Cr and Pb), especially near major urban areas. Finally, a toxicological risk assessment was also performed by determining the hazard quotient (HQ), which demonstrated that, although sediments from mid- and downstream sampling points presented the highest metal bioaccessibilities, were not enough to have adverse effects on human health, Cr being the most potentially toxic element. Copyright © 2017 Elsevier Inc. All rights reserved.

Bioprocess considerations for expanded-bed chromatography of crude canola extract: sample preparation and adsorbent reuse.

PubMed

Bai, Yun; Glatz, Charles E

2003-03-30

Compared to the conventional microbial and mammalian systems, transgenic plants produce proteins in a different matrix. This provides opportunities and challenges for downstream processing. In the context of the plant host Brassica napus (canola), this work addresses the bioprocessing challenges of solid fractionation, resin fouling by native plant components (e.g., oil, phenolics, etc.), hydrodynamic stability, and resin reuse for expanded bed adsorption for product capture. Plant tissue processing and subsequent protein extraction typically result in an extract with a high content of solids containing a wide particle-size distribution. Without removal of larger particles, the column inlet distributor plugged. The larger particles (> 50 microm) were easily removed through centrifugal settling comparable to that attainable with a scroll decanter. The remaining solids did not affect the column performance. Less than 4% of the lipids and phenolics in the fed extract bound to STREAMLINE trade mark DEAE resin, and this small proportion could be satisfactorily removed using recommended clean-in-place (CIP) procedures. Hydrodynamic expansion and adsorption kinetics of the STREAMLINE trade mark DEAE resin were maintained throughout 10 cycles of reuse, as was the structural integrity of the resin beads. No significant accumulation of N-rich (e.g., proteins) and C/O-rich components (e.g., oil and phenolics) occurred over the same period. Copyright 2003 Wiley Periodicals Inc. Biotechnol Bioeng 81: 775-782, 2003.

Risk assessment of imidacloprid use in forest settings on the aquatic macroinvertebrate community.

PubMed

Benton, Elizabeth P; Grant, Jerome F; Nichols, Rebecca J; Webster, R Jesse; Schwartz, John S; Bailey, Joseph K

2017-11-01

The isolated effects of a single insecticide can be difficult to assess in natural settings because of the presence of numerous pollutants in many watersheds. Imidacloprid use for suppressing hemlock woolly adelgid, Adelges tsugae (Annand) (Hemiptera: Adelgidae), in forests offers a rare opportunity to assess potential impacts on aquatic macroinvertebrates in relatively pristine landscapes. Aquatic macroinvertebrate communities were assessed in 9 streams in Great Smoky Mountains National Park (southern Appalachian Mountains, USA). The streams flow through hemlock conservation areas where imidacloprid soil drench treatments were applied for hemlock woolly adelgid suppression. Sites were located upstream and downstream of the imidacloprid treatments. Baseline species presence data (pre-imidacloprid treatment) were available from previous sample collections at downstream sites. Downstream and upstream sites did not vary in numerous community measures. Although comparisons of paired upstream and downstream sites showed differences in diversity in 7 streams, higher diversity was found more often in downstream sites. Macroinvertebrate functional feeding groups and life habits were similar between downstream and upstream sites. Downstream and baseline stream samples were similar. While some functional feeding group and life habit species richness categories varied, variations did not indicate poorer quality downstream communities. Imidacloprid treatments applied according to US Environmental Protection Agency federal restrictions did not result in negative effects to aquatic macroinvertebrate communities, which indicates that risks of imidacloprid use in forest settings are low. Environ Toxicol Chem 2017;36:3108-3119. © 2017 SETAC. © 2017 SETAC.

The best practice for preparation of samples from FTA®cards for diagnosis of blood borne infections using African trypanosomes as a model system

PubMed Central

2011-01-01

Background Diagnosis of blood borne infectious diseases relies primarily on the detection of the causative agent in the blood sample. Molecular techniques offer sensitive and specific tools for this although considerable difficulties exist when using these approaches in the field environment. In large scale epidemiological studies, FTA®cards are becoming increasingly popular for the rapid collection and archiving of a large number of samples. However, there are some difficulties in the downstream processing of these cards which is essential for the accurate diagnosis of infection. Here we describe recommendations for the best practice approach for sample processing from FTA®cards for the molecular diagnosis of trypanosomiasis using PCR. Results A comparison of five techniques was made. Detection from directly applied whole blood was less sensitive (35.6%) than whole blood which was subsequently eluted from the cards using Chelex®100 (56.4%). Better apparent sensitivity was achieved when blood was lysed prior to application on the FTA cards (73.3%) although this was not significant. This did not improve with subsequent elution using Chelex®100 (73.3%) and was not significantly different from direct DNA extraction from blood in the field (68.3%). Conclusions Based on these results, the degree of effort required for each of these techniques and the difficulty of DNA extraction under field conditions, we recommend that blood is transferred onto FTA cards whole followed by elution in Chelex®100 as the best approach. PMID:21548975

Using semi-permeable membrane devices and stable nitrogen isotopes to detect anthropogenic influences on the Truckee River, USA

USGS Publications Warehouse

Saito, L.; Rosen, Michael R.; Chandra, S.; Fritsen, C.H.; Arufe, J.A.; Redd, C.

2008-01-01

Stable nitrogen isotopes (??15N) and semipermeable membrane devices (SPMDs) were used together to provide evidence of potential anthropogenic connections to aquatic organisms in the Truckee River, which flows through the Reno/Sparks metropolitan area in Nevada. Crayfish, snail, and periphyton ??15N values, and SPMD toxicity data collected during high and low flow periods at seven primary sites on the river were used with water quality and flow data for the assessment. All biota showed an increase of ??15N on both dates at sites downstream of inflows of a water-quality impaired tributary and urban drain relative to upstream. In addition, most of the lowest ??15N values on each date occurred at the most downstream site on the river. SPMDs sample lipophilic organic contaminants and can be used to assess organic contaminant toxicity to aquatic organisms because they use a membrane that mimics organic contaminant uptake by fish. In this study, results from a fluoroscan test [pyrene index (PI)] of SPMD extracts that responds to higher molecular weight polycyclic aromatic hydrocarbons (PAHs) showed patterns similar to stable isotope data, although observed peaks in PI values occurred in the urban area upstream of where peak ??15N values occurred. The CYP1A biomarker test, which responds to PAHs, certain polychlorinated biphenyls (PCBs), and organochlorines, showed peak toxic equivalents (TEQ) values farther downstream of the urban area. Thus, it is likely that PAHs were contributing to toxicity in the urban area, whereas other nonurban sources of organic carbon may have been present farther downstream. The combined use of stable isotope measurements and SPMDs provided a means of simultaneously examining whether aquatic biota are incorporating constituents from potential food sources (via stable isotopes) or exposure through water (via SPMDs). ?? Mary Ann Liebert, Inc. 2008.

Purification of cardiac myocytes from human heart biopsies for gene expression analysis.

PubMed

Kosloski, L M; Bales, I K; Allen, K B; Walker, B L; Borkon, A M; Stuart, R S; Pak, A F; Wacker, M J

2009-09-01

The collection of gene expression data from human heart biopsies is important for understanding the cellular mechanisms of arrhythmias and diseases such as cardiac hypertrophy and heart failure. Many clinical and basic research laboratories conduct gene expression analysis using RNA from whole cardiac biopsies. This allows for the analysis of global changes in gene expression in areas of the heart, while eliminating the need for more complex and technically difficult single-cell isolation procedures (such as flow cytometry, laser capture microdissection, etc.) that require expensive equipment and specialized training. The abundance of fibroblasts and other cell types in whole biopsies, however, can complicate gene expression analysis and the interpretation of results. Therefore, we have designed a technique to quickly and easily purify cardiac myocytes from whole cardiac biopsies for RNA extraction. Human heart tissue samples were collected, and our purification method was compared with the standard nonpurification method. Cell imaging using acridine orange staining of the purified sample demonstrated that >98% of total RNA was contained within identifiable cardiac myocytes. Real-time RT-PCR was performed comparing nonpurified and purified samples for the expression of troponin T (myocyte marker), vimentin (fibroblast marker), and alpha-smooth muscle actin (smooth muscle marker). Troponin T expression was significantly increased, and vimentin and alpha-smooth muscle actin were significantly decreased in the purified sample (n = 8; P < 0.05). Extracted RNA was analyzed during each step of the purification, and no significant degradation occurred. These results demonstrate that this isolation method yields a more purified cardiac myocyte RNA sample suitable for downstream applications, such as real-time RT-PCR, and allows for more accurate gene expression changes in cardiac myocytes from heart biopsies.

Quality of water in Luxapallia Creek at Columbus, Mississippi

USGS Publications Warehouse

Kalkhoff, Stephen J.

1982-01-01

The results of a water quality study of a short reach of Luxapallila Creek at Columbus, Mississippi, during September 9-12, 1979, indicate that the water is colored (60 units) and has a low dissolved solids content (44 mg/L). The dissolved oxygen concentration, temperature, and pH of the water in Luxapallila Creek changed a slightly downstream through the study reach. The mean specific conductance almost doubled and the five-day biochemical oxygen demand load increased over four times through the study reach. The fecal coliform to fecal streptococcus ration of 3 to 5 samples collected at the downstream site was greater than 4.0, strongly suggesting the presence of human waste. The concentrations of iron and manganese at the downstream site exceeded the U.S. Environmental Protection Agency 's criteria for domestic water supplies. High concentrations of iron, manganese, and lead also were present in a bottom material sample at the downstream site. (USGS)

Evaluating process origins of sand-dominated fluvial stratigraphy

NASA Astrophysics Data System (ADS)

Chamberlin, E.; Hajek, E. A.

2015-12-01

Sand-dominated fluvial stratigraphy is often interpreted as indicating times of relatively slow subsidence because of the assumption that fine sediment (silt and clay) is reworked or bypassed during periods of low accommodation. However, sand-dominated successions may instead represent proximal, coarse-grained reaches of paleo-river basins and/or fluvial systems with a sandy sediment supply. Differentiating between these cases is critical for accurately interpreting mass-extraction profiles, basin-subsidence rates, and paleo-river avulsion and migration behavior from ancient fluvial deposits. We explore the degree to which sand-rich accumulations reflect supply-driven progradation or accommodation-limited reworking, by re-evaluating the Castlegate Sandstone (Utah, USA) and the upper Williams Fork Formation (Colorado, USA) - two Upper Cretaceous sandy fluvial deposits previously interpreted as having formed during periods of relatively low accommodation. Both units comprise amalgamated channel and bar deposits with minor intra-channel and overbank mudstones. To constrain relative reworking, we quantify the preservation of bar deposits in each unit using detailed facies and channel-deposit mapping, and compare bar-deposit preservation to expected preservation statistics generated with object-based models spanning a range of boundary conditions. To estimate the grain-size distribution of paleo-sediment input, we leverage results of experimental work that shows both bed-material deposits and accumulations on the downstream side of bars ("interbar fines") sample suspended and wash loads of active flows. We measure grain-size distributions of bar deposits and interbar fines to reconstruct the relative sandiness of paleo-sediment supplies for both systems. By using these novel approaches to test whether sand-rich fluvial deposits reflect river systems with accommodation-limited reworking and/or particularly sand-rich sediment loads, we can gain insight into large-scale downstream-fining and mass-extraction trends in basins with limited exposure.

Geochemical characteristics of Au in the water systemfrom abandoned gold mines area

NASA Astrophysics Data System (ADS)

Cho, Kanghee; Kim, Bongju; Kim, Byungjoo; Park, Cheonyoung; Choi, Nagchoul

2013-04-01

The AMD (acid mine drainage) poses a threat not only to the aquatic life in mountain streams and rivers, but can also contaminate groundwater and downstream water bodies. Besides pyrite, sulfides of copper, zinc, cadmium, lead and arsenic in the drainage tunnels and tailings piles also undergo similar geochemical reactions, releasing toxic metals and more H+ into the mine drainage. The fate of gold in the AMD system is reduced and precipitated with iron oxides by oxidation-reduction reaction between ferrous/ferric iron and Au3+/Au0. The objective of this study was to investigate the influence of the transport characteristic on the distance through distribution of heavy metals and gold on the interrelation between acid mine drainage and sediments in the abandoned Gwang-yang gold mine, Korea. We conducted to confirm the chemical (chemical analysis and sequential extraction) and mineralogical property (XRD, SEM-EDS and polarization microscope) from AMD, sediments and tailing samples. The result of chemical analysis showed that Fe contents in the AMD and sediments from the upstream to the downstream ranged of 10.99 to 18.60 mg/L and 478.74 to 542.98 mg/kg, respectively. Also the contents of Au and As in the sediment were respectively ranged from 14.06 to 22.85 g/t and 0.245 to 0.612 mg/kg. In XRD analysis of the sediments, x-ray diffracted d-value belong to quartz, geothite was observed. The results of SEM-EDS analysis revealed that iron hydroxide were observed in the sediment and tailing. The result of sequential extraction for Au from the sediment showed that Au predominated in 26 to 27% of Organic matter fraction(STEP 4), and 24 to 25% of Residual fraction(STEP 5).

High Throughput Multispectral Image Processing with Applications in Food Science.

PubMed

Tsakanikas, Panagiotis; Pavlidis, Dimitris; Nychas, George-John

2015-01-01

Recently, machine vision is gaining attention in food science as well as in food industry concerning food quality assessment and monitoring. Into the framework of implementation of Process Analytical Technology (PAT) in the food industry, image processing can be used not only in estimation and even prediction of food quality but also in detection of adulteration. Towards these applications on food science, we present here a novel methodology for automated image analysis of several kinds of food products e.g. meat, vanilla crème and table olives, so as to increase objectivity, data reproducibility, low cost information extraction and faster quality assessment, without human intervention. Image processing's outcome will be propagated to the downstream analysis. The developed multispectral image processing method is based on unsupervised machine learning approach (Gaussian Mixture Models) and a novel unsupervised scheme of spectral band selection for segmentation process optimization. Through the evaluation we prove its efficiency and robustness against the currently available semi-manual software, showing that the developed method is a high throughput approach appropriate for massive data extraction from food samples.

MicroRNAs are suitable for assessment as biomarkers from formalin-fixed paraffin-embedded tissue, and miR-24 represents an appropriate reference microRNA for diffuse large B-cell lymphoma studies.

PubMed

Culpin, Rachel Emily; Sieniawski, Michal; Proctor, Stephen John; Menon, Geetha; Mainou-Fowler, Tryfonia

2013-03-01

Tissue biopsy specimens in the form of formalin-fixed paraffin-embedded tissue (FFPET) represent a valuable resource for biomarker identification and validation. However, to date, they remain an underused asset due to uncertainty regarding RNA extraction and the reliability of downstream techniques, including quantitative RT-PCR. Recently, much interest has emerged in the study of microRNAs; small single-stranded RNAs with a role in transcriptional regulation, that are thought to be well preserved in FFPET. In this study, we show that microRNA expression is comparable between FFPET and matched fresh-frozen samples (miR-17-5p: p=0.01, miR-92: p=0.003), and demonstrate that no significant deterioration in expression occurs over prolonged FFPET storage (p=0.06). Furthermore, microRNA expression is equivalent dependant on RNA extraction method (p<0.001) or DNAse treatment of total RNA (p<0.001). Finally, we validate miR-24 as a suitable reference microRNA for diffuse large B-cell lymphoma (DLBCL) FFPET studies.

Determination of Microalgal Lipid Content and Fatty Acid for Biofuel Production

PubMed Central

Chen, Zhipeng; Wang, Lingfeng

2018-01-01

Biofuels produced from microalgal biomass have received growing worldwide recognition as promising alternatives to conventional petroleum-derived fuels. Among the processes involved, the downstream refinement process for the extraction of lipids from biomass greatly influences the sustainability and efficiency of the entire biofuel system. This review summarizes and compares the current techniques for the extraction and measurement of microalgal lipids, including the gravimetric methods using organic solvents, CO2-based solvents, ionic liquids and switchable solvents, Nile red lipid visualization method, sulfo-phospho-vanillin method, and the thin-layer chromatography method. Each method has its own competitive advantages and disadvantages. For example, the organic solvents-based gravimetric method is mostly used and frequently employed as a reference standard to validate other methods, but it requires large amounts of samples and is time-consuming and expensive to recover solvents also with low selectivity towards desired products. The pretreatment approaches which aimed to disrupt cells and support subsequent lipid extraction through bead beating, microwave, ultrasonication, chemical methods, and enzymatic disruption are also introduced. Moreover, the principles and procedures for the production and quantification of fatty acids are finally described in detail, involving the preparation of fatty acid methyl esters and their quantification and composition analysis by gas chromatography.

Fate of linear alkylbenzene sulfonate in the Mississippi River

USGS Publications Warehouse

Tabor, C.F.; Barber, L.B.

1996-01-01

The 2 800-km reach of the Mississippi River between Minneapolis, MN, and New Orleans, LA, was examined for the occurrence and fate of linear alkylbenzene sulfonate (LAS), a common anionic surfactant found in municipal sewage effluents. River water and bottom sediment were sampled in the summer and fall of 1991 and in the spring of 1992. LAS was analyzed using solid- phase extraction/derivatization/gas chromatography/mass spectrometry. LAS was present on all bottom sediments at concentrations ranging from 0.01 to 20 mg/kg and was identified in 21% of the water samples at concentrations ranging from 0.1 to 28.2 ??g/L. The results indicate that LAS is a ubiquitous contaminant on Mississippi River bottom sediments and that dissolved LAS is present mainly downstream from the sewage outfalls of major cities. The removal of the higher LAS homologs and external isomers indicates that sorption and biodegradation are the principal processes affecting dissolved LAS. Sorbed LAS appears to degrade slowly.

Organic wastewater compounds in water and sediment in and near restored wetlands, Great Marsh, Indiana Dunes National Lakeshore, 2009–11

USGS Publications Warehouse

Egler, Amanda L.; Risch, Martin R.; Alvarez, David A.; Bradley, Paul M.

2013-01-01

A cooperative investigation between the U.S. Geological Survey and the National Park Service was completed from 2009 through 2011 to understand the occurrence, distribution, and environmental processes affecting concentrations of organic wastewater compounds in water and sediment in and near Great Marsh at the Indiana Dunes National Lakeshore in Beverly Shores, Indiana. Sampling sites were selected to represent hydrologic inputs to the restored wetlands from adjacent upstream residential and less developed areas and to represent discharge points of cascading cells within the restored wetland. A multiphase approach was used for the investigation. Discrete water samples and time-integrated passive samples were analyzed for 69 organic wastewater compounds. Continuous water-level information and periodic streamflow measurements characterized flow conditions at discharge points from restored wetland cells. Wetland sediments were collected and analyzed for sorptive losses of organic wastewater compounds and to evaluate of the potential for wetland sediments to biotransform organic wastewater compounds. A total of 52 organic wastewater compounds were detected in discrete water samples at 1 or more sites. Detections of organic wastewater compounds were widespread, but concentrations were generally low and 95 percent were less than 2.1 micrograms per liter. Six compounds were detected at concentrations greater than 2.1 micrograms per liter—four fecal sterols (beta-sitosterol, cholesterol, beta-stigmastanol, and 2-beta coprostanol), one plasticizer (bis-2-ethylhex ylphthalate), and a non-ionic detergent (4-nonylphenol diethoxylate). Two 1-month deployments of time-integrative passive samplers, called polar organic chemical integrative samplers, detected organic wastewater compounds at lower concentrations than were possible with discrete water samples. Isopropyl benzene (solvent), caffeine (plant alkaloid, stimulant), and hexahydrohexamethyl cyclopentabenzopyran (fragrance) were detected in more than half of the extracts from passive samplers, but they were not detected in any discrete water sample. The Yeast Estrogen Screen assay identified measurable estrogenicity in one passive sampler extract from the most downstream wetland site in both the April and November–December 2011 deployments and in passive sampler extracts from one residential and one upstream site in the November–December 2011 deployment only. Surface-water levels in the restored wetland cells were monitored continuously using submersible pressure transducers in hand-driven well points screened in the surface water. Surface-water levels in the wetland cells responded quickly to precipitation and substantially receded within 2 days following the largest rainfall events. Seasonal patterns in water levels generally showed higher and more variable surface-water levels in the wetland cells during spring and early summer. Water levels in the wetland cells fell below the elevation of the control structures and ceased to flow over the spillways during extended dry periods (primarily late summer and early fall). Daily loads of seven organic wastewater compounds, as indicators of septic system effluent, were estimated for samples collected at wetland outlet spillways when flow measurements could be made. Median daily loads of the indicator organic wastewater compounds increased in downstream order, and the largest median loads were measured at the most downstream site. Median daily loads were higher for samples collected in spring and summer than those collected in fall, as the higher seasonal water levels increased streamflow at the wetland outlet spillways. Wetland sediment samples were analyzed for 84 organic wastewater compounds, polycyclic aromatic hydrocarbons, and semivolatile organic compounds to investigate the fate of contaminants in Great Marsh. The top five detected compounds by total mass in wetland sediment samples were beta-sitosterol, beta-stigmastanol, cholesterol, bis(2-ethylhexyl) phthalate, and phenol. Polycyclic aromatic hydrocarbons also were frequently detected in wetland sediment samples. Source apportionment of polycyclic aromatic hydrocarbon detections indicated atmospheric sources of pyrogenic compounds, rather than residential sources. Comparisons of polycyclic aromatic hydrocarbon concentrations in wetland sediment samples to sediment quality target guidelines indicated the potential for harmful effects on sediment-dwelling organisms at several sites. Biodegradation of select endocrine-disrupting compounds (17α-ethinylestradiol, 4-nonylphenol, triclocarban, and bisphenol A) in shallow wetland sediments was evaluated in laboratory experiments by using carbon-14 radiolabeled model contaminants. Substantial biodegradation of certain organic wastewater compounds were demonstrated, primarily in oxic (oxygen containing) environments. One of four modeled compounds, bisphenol A, was biodegraded in anoxic (oxygen free) environments. Only sediments collected nearest residential areas exhibited degradation of the synthetic birth control pharmaceutical, 17α-ethinylestradiol, possibly owing to adaptation and acclimation of the indigenous microbial community to septic discharge and the resultant selection of a microbial capability for biodegradation of 17α-ethinylestradiol.

A new sampler design for measuring sedimentation in streams

USGS Publications Warehouse

Hedrick, Lara B.; Welsh, S.A.; Hedrick, J.D.

2005-01-01

Sedimentation alters aquatic habitats and negatively affects fish and invertebrate communities but is difficult to quantify. To monitor bed load sedimentation, we designed a sampler with a 10.16-cm polyvinyl chloride coupling and removable sediment trap. We conducted a trial study of our samplers in riffle and pool habitats upstream and downstream of highway construction on a first-order Appalachian stream. Sediment samples were collected over three 6-week intervals, dried, and separated into five size-classes by means of nested sieves (U.S. standard sieve numbers 4, 8, 14, and 20). Downstream sediment accumulated in size-classes 1 and 2, and the total amount accumulated was significantly greater during all three sampling periods. Size-classes 3 and 4 had significantly greater amounts of sediment for the first two sampling periods at the downstream site. Differences between upstream and downstream sites narrowed during the 5-month sampling period. This probably reflects changes in site conditions, including the addition of more effective sediment control measures after the first 6-week period of the study. The sediment sampler design allowed for long-term placement of traps without continual disturbance of the streambed and was successful at providing repeat measures of sediment at paired sites. ?? Copyright by the American Fisheries Society 2005.

A novel method to augment extraction of mangiferin by application of microwave on three phase partitioning.

PubMed

Kulkarni, Vrushali M; Rathod, Virendra K

2015-06-01

This work reports a novel approach where three phase partitioning (TPP) was combined with microwave for extraction of mangiferin from leaves of Mangifera indica . Soxhlet extraction was used as reference method, which yielded 57 mg/g in 5 h. Under optimal conditions such as microwave irradiation time 5 min, ammonium sulphate concentration 40% w/v, power 272 W, solute to solvent ratio 1:20, slurry to t -butanol ratio 1:1, soaking time 5 min and duty cycle 50%, the mangiferin yield obtained was 54 mg/g by microwave assisted three phase partitioning extraction (MTPP). Thus extraction method developed resulted into higher extraction yield in a shorter span, thereby making it an interesting alternative prior to down-stream processing.

Energy Extraction from a Hypothetical MHK Array in a Section of the Mississippi River

NASA Astrophysics Data System (ADS)

Barco, J.; James, S. C.; Roberts, J. D.; Jones, C. A.; Jepsen, R. A.

2010-12-01

The world is facing many challenges meeting the energy demands for the future. Growing populations and developing economies as well as increasing energy expenditures highlight the need for a spectrum of energy sources. Concerns about pollution and climate change have led to increased interest in all forms of renewable energy to stabilize or decrease consumption of fossil fuels. One promising renewable is marine and hydrokinetic (MHK) energy, which has the potential to make important contributions to energy portfolios of the future. However, a primary question remains: How much energy can be extracted from MHK devices in rivers and oceans without significant environmental effects? This study focuses on the potential energy extraction from different hypothetical MHK array configurations in a section of the Mississippi River located near to Scotlandville Bend, Louisiana. Bathymetry data, obtained from Free Flow Power Corporation (FFP) via the US Army Corps bathymetry survey library, were interpolated onto a DELFT3D curvilinear, orthogonal grid of the system using ArcGIS 9.3.1. Boundary conditions are constrained by the upstream and downstream river flow rates and gage heights obtained from USGS website. Acoustic Doppler Current Profiler (ADCP) measurements obtained from FFP are used for pre-array model validation. Energy extraction is simulated using momentum sinks recently coded into SNL-EFDC, which is an augmented version of US EPA’s Environmental Fluid Dynamics Code (EFDC). SNL-EFDC model includes a new module which considers energy removal by MHK devices and commensurate changes to the turbulent kinetic energy and turbulent kinetic energy dissipation rate. As expected, average velocities decrease downstream of each MHK device due to energy extraction and blunt-body form drag from the MHK support structures. Changes in the flow field can alter sediment transport dynamics around and downstream of an MHK array; various hypothetical scenarios are examined. This study highlights concepts that should be considered when planning, designing, and optimizing MHK devices arrays in riverine resources. Future efforts will focus on validating and verifying these sorts of models as data become available.

Does biofilm contribute to diel cycling of Zn in High Ore Creek, Montana?

USGS Publications Warehouse

Morris, J.M.; Nimick, D.A.; Farag, A.M.; Meyer, J.S.

2005-01-01

Concentrations of metals cycle daily in the water column of some mining-impacted streams in the Rocky Mountains of the western USA. We hypothesized that biofilm in High Ore Creek, Montana, USA, sorbs and releases Zn on a diel cycle, and this uptake-and-release cycle controls the total and dissolved (0.45-??m filtered) Zn concentrations. We collected water samples from three sites (upstream, middle and downstream at 0, 350 and 650 m, respectively) along a 650-m reach of High Ore Creek during a 47-h period in August 2002 and from the upstream and downstream sites during a 24-h period in August 2003; we also collected biofilm samples at these sites. In 2002 and 2003, total and dissolved Zn concentrations did not exhibit a diel cycle at the upstream sampling site, which was ???30 m downstream from a settling pond through which the creek flows. However, total and dissolved Zn concentrations exhibited a diel cycle at the middle and downstream sampling sites, with the highest Zn concentrations occurring at dawn and the lowest Zn concentrations occurring during late afternoon (>2-fold range of concentrations at the downstream site). Based on (1) concentrations of Zn in biofilm at the three sites and (2) results of streamside experiments that demonstrated Zn uptake and release by nai??ve biofilm during the light and dark hours of a photocycle, respectively, we conclude that Zn uptake in photosynthetic biofilms could contribute a large percentage to the cycling of Zn concentrations in the water column in High Ore Creek. ?? Springer 2005.

Environmental signatures and effects of an oil and gas wastewater spill in the Williston Basin, North Dakota

USGS Publications Warehouse

Cozzarelli, Isabelle M.; Skalak, Katherine; Kent, D.B.; Engle, Mark A.; Benthem, Adam J.; Mumford, Adam; Haase, Karl B.; Farag, Aïda M.; Harper, David; Nagel, S. C.; Iwanowicz, Luke R.; Orem, William H.; Akob, Denise M.; Jaeschke, Jeanne B.; Galloway, Joel M.; Kohler, Matthias; Stoliker, Deborah L.; Jolly, Glenn D.

2017-01-01

Wastewaters from oil and gas development pose largely unknown risks to environmental resources. In January 2015, 11.4 M L (million liters) of wastewater (300 g/L TDS) from oil production in the Williston Basin was reported to have leaked from a pipeline, spilling into Blacktail Creek, North Dakota. Geochemical and biological samples were collected in February and June 2015 to identify geochemical signatures of spilled wastewaters as well as biological responses along a 44-km river reach. February water samples had elevated chloride (1030 mg/L) and bromide (7.8 mg/L) downstream from the spill, compared to upstream levels (11 mg/L and < 0.4 mg/L, respectively). Lithium (0.25 mg/L), boron (1.75 mg/L) and strontium (7.1 mg/L) were present downstream at 5–10 times upstream concentrations. Light hydrocarbon measurements indicated a persistent thermogenic source of methane in the stream. Semi-volatile hydrocarbons indicative of oil were not detected in filtered samples but low levels, including tetramethylbenzenes and di-methylnaphthalenes, were detected in unfiltered water samples downstream from the spill. Labile sediment-bound barium and strontium concentrations (June 2015) were higher downstream from the Spill Site. Radium activities in sediment downstream from the Spill Site were up to 15 times the upstream activities and, combined with Sr isotope ratios, suggest contributions from the pipeline fluid and support the conclusion that elevated concentrations in Blacktail Creek water are from the leaking pipeline. Results from June 2015 demonstrate the persistence of wastewater effects in Blacktail Creek several months after remediation efforts started. Aquatic health effects were observed in June 2015; fish bioassays showed only 2.5% survival at 7.1 km downstream from the spill compared to 89% at the upstream reference site. Additional potential biological impacts were indicated by estrogenic inhibition in downstream waters. Our findings demonstrate that environmental signatures from wastewater spills are persistent and create the potential for long-term environmental health effects.

Recovery of benthic-invertebrate communities in the White River near Indianapolis, Indiana, USA, following implementation of advanced treatment of municipal wastewater

USGS Publications Warehouse

Crawford, Charles G.; Wangsness, David J.

1992-01-01

The City of Indianapolis, Indiana, USA, completed construction of advanced-wastewater-treatment systems to enlarge and upgrade existing secondary-treatment processes at the City’s two municipal wastewater-treatment plants in 1983. These plants discharge their effluent to the White River. A study was begun in 1981 to evaluate the effects of municipal wastewater on the quality of the White River near Indianapolis. As part of this study, benthic-invertebrate samples were collected from one riffle upstream and two riffles downstream from the treatment plants annually from 1981 through 1987 (2 times before and 5 times after the plant improvements became operational). Samples were collected during periods of late-summer or early-fall low streamflow with a Surber sampler. Upstream from the wastewater-treatment plants, mayflies and caddisflies were the predominant organisms in the benthic-invertebrate community (from 32 to 93 percent of all organisms; median value is 67 percent) with other insects and mollusks also present. Before implementation of advanced wastewater-treatment, the benthic-invertebrate community downstream from the wastewater treatment plants was predominantly chironomids and oligochaetes (more than 98 percent of all organisms)-organisms that generally are tolerant of organic wastes. Few intolerant species, such as mayflies or caddisflies were found. Following implementation of advanced wastewater treatment, mayflies and caddisflies became numerically dominant in samples collected downstream from the plants. By 1986, these organisms accounted for more than 90 percent of all organisms found at the two downstream sites. The diversity of benthic invertebrates found in these samples resembled that at the upstream site. The improvement in the quality of municipal wastewater effluent resulted in significant improvements in the water quality of the White River downstream from Indianapolis. These changes in river quality, in turn, have resulted in a shift from mostly pollution-tolerant to mostly pollution-intolerant organisms in the benthic-invertebrate community of the White River downstream from Indianapolis. The recovery was not immediate, however, with one of the downstream sites requiring 3 years before pollution-intolerant organisms became numerically dominant.

Vortex generating flow passage design for increased film cooling effectiveness

NASA Astrophysics Data System (ADS)

Papell, S. S.

1985-07-01

It is an object of the invention to provide a film cooling apparatus of increased effectiveness and efficiency. In accordance with the invention, a cooling fluid is injected into a hot flowing gas through a passageway in a wall which contains and is subject to the hot gas. The passageway is slanted in a downstream direction at an acute angle to the wall. A cusp shape is provided in the passageway to generate vortices in the injected cooling fluid thereby reducing the energy extracted from the hot gas for that purpose. The cusp shape increases both film cooling effectiveness and wall area coverage. The cusp may be at either the downstream or upstream side of the passageway, the former substantially eliminating flow separation of the cooling fluid from the wall immediately downstream of the passageway.

Vortex generating flow passage design for increased film cooling effectiveness

NASA Technical Reports Server (NTRS)

Papell, S. S. (Inventor)

1985-01-01

It is an object of the invention to provide a film cooling apparatus of increased effectiveness and efficiency. In accordance with the invention, a cooling fluid is injected into a hot flowing gas through a passageway in a wall which contains and is subject to the hot gas. The passageway is slanted in a downstream direction at an acute angle to the wall. A cusp shape is provided in the passageway to generate vortices in the injected cooling fluid thereby reducing the energy extracted from the hot gas for that purpose. The cusp shape increases both film cooling effectiveness and wall area coverage. The cusp may be at either the downstream or upstream side of the passageway, the former substantially eliminating flow separation of the cooling fluid from the wall immediately downstream of the passageway.

Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage.

PubMed

Sun, Weimin; Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Chen, Haiyan; Xiao, Qingxiang

2016-10-01

A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities, suggesting that the microbial communities are shaped by three major environmental parameters (i.e., Fe, pH, and TOC). These findings were beneficial to a better understanding of natural attenuation of AMD.

Microfluidic-Based Bacteria Isolation from Whole Blood for Diagnostics of Blood Stream Infection.

PubMed

Zelenin, Sergey; Ramachandraiah, Harisha; Faridi, Asim; Russom, Aman

2017-01-01

Bacterial blood stream infection (BSI) potentially leads to life-threatening clinical conditions and medical emergencies such as severe sepsis, septic shock, and multi organ failure syndrome. Blood culturing is currently the gold standard for the identification of microorganisms and, although it has been automated over the decade, the process still requires 24-72 h to complete. This long turnaround time, especially for the identification of antimicrobial resistance, is driving the development of rapid molecular diagnostic methods. Rapid detection of microbial pathogens in blood related to bloodstream infections will allow the clinician to decide on or adjust the antimicrobial therapy potentially reducing the morbidity, mortality, and economic burden associated with BSI. For molecular-based methods, there is a lot to gain from an improved and straightforward method for isolation of bacteria from whole blood for downstream processing.We describe a microfluidic-based sample-preparation approach that rapidly and selectively lyses all blood cells while it extracts intact bacteria for downstream analysis. Whole blood is exposed to a mild detergent, which lyses most blood cells, and then to osmotic shock using deionized water, which eliminates the remaining white blood cells. The recovered bacteria are 100 % viable, which opens up possibilities for performing drug susceptibility tests and for nucleic-acid-based molecular identification.

Occurrence of betablockers in effluents of wastewater treatment plants from the Lyon area (France) and risk assessment for the downstream rivers.

PubMed

Miège, Cécile; Favier, Maxime; Brosse, Corinne; Canler, Jean-Pierre; Coquery, Marina

2006-11-15

Five betablockers (oxprenolol, metoprolol, propranolol, bisoprolol, betaxolol) were analysed in effluents collected over a 3-month period from wastewater treatment plants (WTP) from the Lyon area in France. The analytical protocol consisted of solid phase extraction of the dissolved aqueous phase on HLB cartridges and analysis by gas chromatography coupled with mass detection (GC-MS) after derivatization. Concentrations of metoprolol, propranolol and bisoprolol varied from 45 to 2838ng/L whereas oxprenolol and betaxolol were never detected in these effluent samples. A high variability of betablockers concentrations and fluxes was observed between WTP effluents and within each WTP over the time period studied. Considering a flux per person for a dry weather period, Fontaine plant was pointed out as the less efficient WTP, which might be explained by its type of treatment (biological aerated filters). But we need additional analysis of effluent and influent waters to confirm this hypothesis. A tentative approach of local environmental risk assessment of propranolol based on the calculation of PEC/PNEC (predicted environmental concentration/predicted non effect concentration) ratio approach lead us to conclude on a negligible risk for the downstream rivers (Rhône river at Ternay and Saône river at Couzon Mt d'Or).

A pro-apoptotic 15-kDa protein from Bacopa monnieri activates caspase-3 and downregulates Bcl-2 gene expression in mouse mammary carcinoma cells.

PubMed

Kalyani, Manjula Ishwara; Lingaraju, Sheela Mysore; Salimath, Bharathi P

2013-01-01

In diseases such as cancer, induction of apoptosis has been a new target for mechanism-based drug discovery. The central component of the process of apoptosis is a proteolytic system involving a family of proteases called caspases. Apoptosis involves characteristic morphological and biochemical events ultimately leading to cell demise. Apoptotic induction is evidently central to the mechanism of action of plant-derived anticancer drugs. Extract of the medicinal plant, Bacopa monnieri, inhibits tumor cell proliferation and accumulation of malignant ascites fluid. The crude sample when subjected to Soxhlet extraction yielded different solvent extracts of which the aqueous extract showed biological activity of apoptosis in Ehrlich ascites tumor cell lines (EAT). Bacopa monnieri water extract (BMWE) treatment of EAT cells produced apoptotic morphological characteristics and in-vivo DNA fragmentation, which is due to the activity of an endogenous endonuclease. The endonuclease responsible for DNA fragmentation acts downstream of caspase-3 activity and is also referred to as caspase-activated DNase (CAD). The CAD constitutively expressed in the cell cytoplasm is translocated into the nucleus upon BMWE treatment, as verified by Western blotting, leading to DNA fragmentation and to programmed cell death. The expression of the pro-apoptotic gene Bax was increased and the expression of the anti-apoptotic gene Bcl-2 was decreased by BMWE treatment. Considering the above results, BMWE was able induce apoptosis in EAT cells via Bax-related caspase-3 activation. This may provide experimental data for the further clinical use of BMWE in cancer.

Nitrification and Microbial Activity in Response to Wastewater Effluent in the Sacramento/San Joaquin River Delta

NASA Astrophysics Data System (ADS)

Challenor, T.; Damashek, J.; Tolar, B. B.; Francis, C.; Casciotti, K. L.

2016-12-01

Nitrification, the oxidation of ammonium (NH4+) to nitrate (NO3-) by a coterie of ammonia-oxidizing bacteria (AOB) and archaea (AOA), is a crucial step in removing nitrogen from marine ecosystems. The Sacramento/San Joaquin River delta receives ammonium-laden effluent from the Sacramento Regional Wastewater Treatment Plant (SRWTP) and nitrate from agriculture runoff. The system provides freshwater to irrigate the Central Valley and drinking water for many millions of people. In recent years, however, this environment has experienced ecological turmoil - the Pelagic Organism Decline (POD) refers to a die-out of fish and other species over the course of three decades. One explanation implicated excessive ammonium input, claiming it limited primary productivity and hurt pelagic fish down the line. A new hypothesis, however, posits that the ecosystem may soon face the opposite problem: over-productivity and hypoxia due to increased light availability and reduced turbidity. Studying the rate of nitrification and the makeup of the microbial community will further elucidate how nutrient loading has impacted this ecosystem. Nitrification rates were calculated from water samples collected in the Sacramento River starting at the SRWTP and moving downstream. Samples were spiked with 15N-labeled ammonium and incubated for 24 hours in triplicate. Four time-points were extracted and the "denitrifier" method was used to measure the isotopic ratio of N over time. DNA and RNA were extracted from filtered water at each site and PCR and qPCR assays were used targeting the amoA gene, which encodes the α-subunit of ammonia monooxygenase, responsible for oxidizing ammonium to nitrite (NO2-). Consistent with previous nitrification data, rates were highest in the lower river downstream of the SRWTP, where nitrate concentrations were correspondingly elevated. AOB predominated in the ammonia oxidizing community, and some clades were unique to this ecosystem. Nitrifying microbes provide an ecological service in reducing ammonium availability, a goal of wastewater regulation. Monitoring the activity of the Sacramento River's nitrifying community will be important for analyzing how this ecosystem responds to future changes that will impact populations of fish and people living in California.

Oxidations of organic matter present in the phosphoric acid 54% by the ozone: characterization of groups carbonyls upstream and downstream of the ozonation

NASA Astrophysics Data System (ADS)

Linda, D.; Louati, A.; Chtara, C.; Kabadou, A.

2012-02-01

This study was focused on the oxidation of organic matter in phosphoric acid 54% by ozone. In order to understand the mechanisms involved in this process, the identification of this matter upstream and downstream of the ozonation was necessary. For the identification, after an extraction by a mixture (dichloro-methanol), the organic phase was divided into two parts: the residue and the extract:-The residue was studied by infrared spectroscopy Fourier Transform (IR-TF). It contains Kérogène which is a mixture of saturated hydrocarbons with high molecular weights. The absorption bands of the FT-IR showed that the residue contains also quantities of amino that correspond to the remains of dinoflagellate cysts, which are abundant in sediments.-The extract has been the subject of a detailed study by, chromatography on silica column, IR-TF spectroscopy and CG-SM. The passage of this extract on a silica column yielded two fractions (saturated fraction and polar fraction). Both of these fractions were analyzed by CG-SM. The yield of the reduction of the organic matter content in the phosphoric acid 54% could not exceed 29%. Therefore, we can conclude that the reduction in the rate of organic matter remains limited by the fact that some compounds are inert towards ozone.

Biogeochemical and hydrological controls in mobilizing Se in a saline wetland environment

NASA Astrophysics Data System (ADS)

Datta, S.; Hettiarachchi, G. M.; Crawford, M.; Karna, R.; Allmendinger, N. E.; Khatiwada, R.

2010-12-01

Selenium (Se) contamination in watersheds remains a challenge to water and land and wildlife managers throughout the west and mid west of US. In that sense, understanding the fundamentals of Se mobilization, fixation and bioconcentration is the current research endeavor. The challenge for Se research is developing watershed-geochemical models that are well founded in Se geochemical/biologcial principles that can be applied in a wide range of situations to inform decisions. Pariette Wetlands, a 9000 acre Bureau of Land Management controlled wetland system composed of 20 ponds located at the confluence of Pariette Draw and the Green River is the present location of this study. The agricultural and irrigation practices and the water-rock interactions leading to salinization can be associated with changes in Se chemistry in the rivers. Since its inception Pariette Wetlands has been home to a rich and diverse wetland ecosystem located in the arid Uintah Basin of Northeastern Utah. Detailed sampling of surficial sediments (0-1 m) from stream banks, channel beds and for water sampling have been undergone in 2 separate field trips throughout the entire reach of the wetland. To establish Pariette Draw’s contribution of Se to the Green river, water and sediments were also sampled from the Green River up and downstream of its confluence with Pariette Draw. In situ measurements of water parameters within the wetland suggest a clear trend of increased pH from upstream, 8, to downstream, 9.2 and combined with TDS suggest a pH controlled saline environment system. The headwaters near Flood Control Dam have an added input of Se from a possible irrigation source upstream in Pleasant Valley area while Se drastically decreases downstream towards the Red Head Pond. Se fractionation in sediments is being analyzed via a sequential extraction procedure to locate the labile fractions of mostly inorganic bound Se. Solid state speciation of Se via μ-XRF aided μ-XANES is being combined with HPLC-MS measured speciation of Se in the water samples. The μ-XRF mapping of Se indicated that Se was highly localized in these surficial sediment samples and therefore, spatially resolved µ-XANES was essential for Se speciation. The µ-XANES speciation of these surficial sediments showed that Se speciation to significantly vary among the 2 sets of seasonal samples (saturated year long versus saturated only seasonally) hence suggesting that continuous drying and wetting cycles or continuous saturation in this environment did have significant impact on sequestration and bioavailability of Se. This work focuses on using this watershed as 'field laboratories' to expand on predicting selenium concentrations from general/fundamental understanding of first-order principles

Preconcentration of DNA using magnetic ionic liquids that are compatible with real-time PCR for rapid nucleic acid quantification.

PubMed

Emaus, Miranda N; Clark, Kevin D; Hinners, Paige; Anderson, Jared L

2018-04-28

Nucleic acid extraction and purification represents a major bottleneck in DNA analysis. Traditional methods for DNA purification often require reagents that may inhibit quantitative polymerase chain reaction (qPCR) if not sufficiently removed from the sample. Approaches that employ magnetic beads may exhibit lower extraction efficiencies due to sedimentation and aggregation. In this study, four hydrophobic magnetic ionic liquids (MILs) were investigated as DNA extraction solvents with the goal of improving DNA enrichment factors and compatibility with downstream bioanalytical techniques. By designing custom qPCR buffers, we directly incorporated DNA-enriched MILs including trihexyl(tetradecyl)phosphonium tris(hexafluoroacetylaceto)nickelate(II) ([P 6,6,6,14 + ][Ni(hfacac) 3 - ]), [P 6,6,6,14 + ] tris(hexafluoroacetylaceto)colbaltate(II) ([Co(hfacac) 3 - ]), [P 6,6,6,14 + ] tris(hexafluoroacetylaceto)manganate(II) ([Mn(hfacac) 3 - ]), or [P 6,6,6,14 + ] tetrakis(hexafluoroacetylaceto)dysprosate(III) ([Dy(hfacac) 4 - ]) into reaction systems, thereby circumventing the need for time-consuming DNA recovery steps. Incorporating MILs into the reaction buffer did not significantly impact the amplification efficiency of the reaction (91.1%). High enrichment factors were achieved using the [P 6,6,6,14 + ][Ni(hfacac) 3 - ] MIL for the extraction of single-stranded and double-stranded DNA with extraction times as short as 2 min. When compared to a commercial magnetic bead-based platform, the [P 6,6,6,14 + ][Ni(hfacac) 3 - ] MIL was capable of producing higher enrichment factors for single-stranded DNA and similar enrichment factors for double-stranded DNA. The MIL-based method was applied for the extraction and direct qPCR amplification of mutation prone-KRAS oncogene fragment in plasma samples. Graphical abstract Magnetic ionic liquid solvents are shown to preconcentrate sufficient KRAS DNA template from an aqueous solution in as short as 2 min without using chaotropic salts or toxic organic solvents. By using custom-designed qPCR buffers, DNA can be directly amplified and quantified from four MILs examined in this study.

The monitoring of organic waste pollution in the sibelis river

NASA Astrophysics Data System (ADS)

Huda, Thorikul; Jannah, Wirdatul

2017-03-01

Has conducted monitoring of organic waste pollution in the River Sibelis of Tegal City of Central Java. Organic wastes that pollute River Sibelis can degrade the quality of well water along the river. Monitoring carried out in the upstream and downstream by chemical oxygen demand (COD) and biochemical oxygen demand (BOD) parameters. COD test methods by titration and the results are used to determine the test sample comparison with the volume of diluent required for analysts BOD. COD test results on the upstream and downstream Sibelis River respectively 58.13 mg/L and 73.97 mg / L so that the ratio of the test sample with diluent volume for BOD analysis is 20: 280 (Sawyer, 1978). BOD test principle is based on the reduction of dissolved oxygen zero day (DO0) and five days (DO5). The result of observation BOD samples at upstream and downstream Sibelis Rivers are 10.7212 mg / L and 5.3792 mg / L respectively. Quality control of BOD testing conducted with measurement accuracy and precision and obtained result are 85.36% and 0.27% respectively. The result of uncertainty measurement for BOD testing at upstream and downstream are ±0.4469 mg/L and ±0.22188 mg/L.

Development of a multimetric index for fish assemblages in a cold tailwater in Tennessee

USGS Publications Warehouse

Ivasauskas, Tomas J.; Bettoli, Phillip William

2014-01-01

Tailwaters downstream of hypolimnetic-release hydropeaking dams exhibit a unique combination of stressors that affects the structure and function of resident fish assemblages. We developed a statistically and biologically defensible multimetric index of fish assemblages for the Caney Fork River below Center Hill Dam, Tennessee. Fish assemblages were sampled at five sites using boat-mounted and backpack electrofishing gear from fall 2009 through summer 2011. A multivariate statistical approach was used to select metrics that best reflected the downstream gradients in abiotic variables. Five metrics derived from boat electrofishing samples and four metrics derived from backpack electrofishing samples were selected for incorporation into the index based on their high correlation with environmental data. The nine metrics demonstrated predictable patterns of increase or decrease with increasing distance downstream of the dam. The multimetric index generally exhibited a pattern of increasing scores with increasing distance from the dam, indicating a downstream recovery gradient in fish assemblage composition. The index can be used to monitor anticipated changes in the fish communities of the Caney Fork River when repairs to Center Hill Dam are completed later this decade, resulting in altered dam operations.

Post-Fragmentation Whole Genome Amplification-Based Method

NASA Technical Reports Server (NTRS)

Benardini, James; LaDuc, Myron T.; Langmore, John

2011-01-01

This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (<400 bp) constitute a library of DNA fragments with defined 3 and 5 termini. Specific primers to these termini are then used to isothermally amplify this library into potentially unlimited quantities that can be used immediately for multiple downstream applications including gel eletrophoresis, quantitative polymerase chain reaction (QPCR), comparative genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at practically every step, particularly nucleic acid extraction. In engineering a molecular means of amplifying nucleic acids directly from single cells in their native state within the sample matrix, this innovation has circumvented entirely the need for DNA extraction regimes in the sample processing scheme.

Quantification of a potent mutagenic 4-amino-3,3'-dichloro-5,4'-dinitrobiphenyl (ADDB) and the related chemicals in water from the Waka River in Wakayama, Japan.

PubMed

Mizuno, Tomoko; Takamura-Enya, Takeji; Watanabe, Tetsushi; Hasei, Tomohiro; Wakabayashi, Keiji; Ohe, Takeshi

2007-06-15

4-Amino-3,3'-dichloro-5,4'-dinitrobiphenyl (ADDB) is a novel chemical exerting strong mutagenicity, especially in the absence of metabolic activation. In addition to mutagenicity, ADDB may also disrupt the endocrine system in vitro. ADDB may be discharged from chemical plants near the Waka River and could be unintentionally formed via post-emission modification of drainage water containing 3,3'-dichlorobenzidine (DCB), which is a precursor in the manufacture of polymers and dye intermediates in chemical plants. The main purpose of this study was to make a comprehensive survey of the behaviour and levels of ADDB and suspected starting material or intermediates of ADDB, i.e., DCB, 3,3'-dichloro-4,4'-dinitrobiphenyl (DDB), and 4-amino-3,3'-dichloro-4'-nitrobipheny (ADNB) in Waka River water samples. We also postulated the formation pathway of ADDB. Water samples were collected at five sampling sites from the Waka River four times between March 2003 and December 2004. Samples were passed through Supelpak2 columns, and adsorbed materials were then extracted with methanol. Extracts were used for quantification of ADDB and the related chemicals by HPLC on reverse-phase columns; mutagenicity was evaluated in the Salmonella assay using the O-acetyltransferase-overexpressing strain YG1024. High levels of ADDB, DCB, DDB, and ADNB (12.0, 20,400, 134.8, and 149.4ng/L-equivalent) were detected in the samples collected at the site where wastewater was discharged from chemical plants into the river. These water samples also showed stronger mutagenicity in YG1024 both with and without S9 mix than the other water samples collected from upstream and downstream sites. The results suggest that ADDB is unintentionally formed from DCB via ADNB in the process of wastewater treatment of drainage water containing DCB from chemical plants.

Long-term purification efficiency of a wetland constructed to treat runoff from peat extraction.

PubMed

Karjalainen, Satu M; Heikkinen, Kaisa; Ihme, Raimo; Kløve, Bjørn

2016-01-01

Peat extraction increases the phosphorus, nitrogen, organic matter, suspended solids, and iron concentrations in runoff, resulting in negative effects on downstream water bodies. Wetlands are commonly used as natural cost-effective solutions to mitigate these negative effects. This study analyzed changes in the quality of runoff water from peat extraction areas and the long-term efficiency of constructed wetlands. The results indicate that the quality of runoff water changed after the initial drainage and during peat extraction. Nitrogen leached at high concentrations in the early stages of peat extraction following drainage, whereas the leaching of iron and phosphorus increased after peat extraction from deeper layers. Comparison of water quality and impurities retained immediately after treatment wetland construction and 14 years later showed that the treatment wetland remained functional, with good retention capacity, over a long period.

Biodegradation of 17β-Estradiol, Estrone and Testosterone in Stream Sediments

NASA Astrophysics Data System (ADS)

Bradley, P. M.; Chapelle, F. H.; Barber, L. B.; McMahon, P. B.; Gray, J. L.; Kolpin, D. W.

2009-12-01

The potentials for in situ biodegradation of 17β-estradiol (E2), estrone (E1), and testosterone (T) were investigated in three, hydrologically-distinct, WWTP-impacted streams in the United States. Relative differences in the mineralization of [4-14C] substrates were assessed in oxic microcosms containing sediment or water-only from locations upstream and downstream of the WWTP outfall in each system. Upstream samples provided insight into the biodegradative potential of sediment microbial communities that were not under the immediate impact of WWTP effluent. Upstream sediment from all three systems demonstrated significant mineralization of the “A” ring of E2, E1 and T, with the potential of T biodegradation consistently greater than of E2 and no systematic difference in the potentials of E2 and E1. Downstream samples provided insight into the impacts of effluent on reproductive hormone biodegradation. Significant “A” ring mineralization was also observed in downstream sediment, with the potentials for E1 and T mineralization being substantially depressed relative to upstream samples. In marked contrast, the potentials for E2 mineralization immediately downstream of the WWTP outfalls were more than double that of upstream samples. E2 mineralization was also observed in water, albeit at insufficient rate to prevent substantial downstream transport in the water column. The results of this study indicate that, in combination with sediment sorption processes which effectively scavenge hydrophobic contaminants from the water column and immobilize them in the vicinity of the WWTP outfall, aerobic biodegradation of reproductive hormones can be an environmentally important mechanism for non-conservative (destructive) attenuation of hormonal endocrine disruptors in effluent-impacted streams.

Quantitative Infrared Image Analysis Of Thermally-Thin Cellulose Surface Temperatures During Upstream and Downstream Microgravity Flame Spread from A Central Ignition Line

NASA Technical Reports Server (NTRS)

Olson, Sandra L.; Lee, J. R.; Fujita, O.; Kikuchi, M.; Kashiwagi, T.

2012-01-01

Surface view calibrated infrared images of ignition and flame spread over a thin cellulose fuel were obtained at 30 Hz during microgravity flame spread tests in the 10 second Japan Microgravity Center (JAMIC). The tests also used a color video of the surface view and color images of the edge view using 35 millimeter 1600 Kodak Ektapress film at 2 Hz. The cellulose fuel samples (50% long fibers from lumi pine and 50% short fibers from birch) were made with an area density of 60 grams per square meters. The samples were mounted in the center of a 12 centimeter wide by 16 centimeter tall flow duct that uses a downstream fan to draw the air through the flow duct. Samples were ignited after the experiment package was released using a straight hot wire across the center of the 7.5 centimeter wide by 14 centimeter long samples. One case, at 1 atmosphere 35%O2 in N2, at a forced flow of 10 centimeters per second, is presented here. In this case, as the test progresses, the single flame begins to separate into simultaneous upstream and downstream flames. Surface temperature profiles are evaluated as a function of time, and temperature gradients for upstream and downstream flame spread are measured. Flame spread rates from IR image data are compared to visible image spread rate data. IR blackbody temperatures are compared to surface thermocouple readings to evaluate the effective emissivity of the pyrolyzing surface. Preheat lengths are evaluated both upstream and downstream of the central ignition point. A surface energy balance estimates the net heat flux from the flame to the fuel surface along the length of the fuel.

Impact of untreated wastewater on a major European river evaluated with a combination of in vitro bioassays and chemical analysis.

PubMed

König, Maria; Escher, Beate I; Neale, Peta A; Krauss, Martin; Hilscherová, Klára; Novák, Jiří; Teodorović, Ivana; Schulze, Tobias; Seidensticker, Sven; Kamal Hashmi, Muhammad Arslan; Ahlheim, Jörg; Brack, Werner

2017-01-01

Complex mixtures of micropollutants, including pesticides, pharmaceuticals and industrial chemicals emitted by wastewater effluents to European rivers may compromise the quality of these water resources and may pose a risk to ecosystem health and abstraction of drinking water. In the present study, an integrated analytical and bioanalytical approach was applied to investigate the impact of untreated wastewater effluents from the city of Novi Sad, Serbia, into the River Danube. The study was based on three on-site large volume solid phase extracted water samples collected upstream and downstream of the untreated wastewater discharge. Chemical screening with liquid chromatography high resolution mass spectrometry (LC-HRMS) was applied together with a battery of in vitro cell-based bioassays covering important steps of the cellular toxicity pathway to evaluate effects on the activation of metabolism (arylhydrocarbon receptor AhR, peroxisome proliferator activated receptor gamma PPARγ), specific modes of action (estrogen receptor ERα, androgen receptor AR) and adaptive stress responses (oxidative stress, inflammation). Increased effects, significantly changed contamination patterns and higher chemical concentrations were observed downstream of the wastewater discharge. A mass balance approach showed that enhanced endocrine disruption was in good agreement with concentrations of detected hormones, while only a smaller fraction of the effects on xenobiotic metabolism (<1%) and adaptive stress responses (0-12%) could be explained by the detected chemicals. The chemical and effects patterns observed upstream of the discharge point were fairly re-established at about 7 km downstream, demonstrating the enormous dilution capacity of this large river. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification of alkyl dimethylbenzylammonium surfactants in water samples by solid-phase extraction followed by ion trap LC/MS and LC/MS/MS

USGS Publications Warehouse

Ferrer, I.; Furlong, E.T.

2001-01-01

A novel methodology was developed for the determination of alkyl (C12, C14, and C16) dimethylbenzylammonium chloride (benzalkonium chloride or BAC, Chemical Abstract Service number: 8001-54-5) in water samples. This method is based on solid-phase extraction (SPE) using polymeric cartridges, followed by high-performance liquid chromatography/ion trap mass spectrometry (LC/MS) and tandem mass spectrometry(MS/MS) detection, equipped with an electrospray interface in positive ion mode. Chromatographic separation was achieved for three BAC homologues by using a C18 column and a gradient of acetonitrile/10 millimolar aqueous ammonium formate. Total method recoveries were higher than 71% in different water matrices. The main ions observed by LC/MS were at mass-to-charge ratios (m/z) of 304, 332, and 360, which correspond to the molecular ions of the C12, C14, and C16 alkyl BAC, respectively. The unequivocal structural identification of these compounds in water samples was performed by LC/MS/MS after isolation and subsequent fragmentation of each molecular ion. The main fragmentation observed for the three different homologues corresponded to the loss of the toluyl group in the chemical structure, which leads to the fragment ions at m/z 212, 240, and 268 and a tropylium ion, characteristic of all homologues, at m/z 91. Detection limits for the methodology developed in this work were in the low nanogram-per-liter range. Concentration levels of BAC - ranging from 1.2 to 36.6 micrograms per liter - were found in surface-water samples collected downstream from different wastewater-treatment discharges, thus indicating its input and persistence through the wastewater-treatment process.

Integration process of fermentation and liquid biphasic flotation for lipase separation from Burkholderia cepacia.

PubMed

Sankaran, Revathy; Show, Pau Loke; Lee, Sze Ying; Yap, Yee Jiun; Ling, Tau Chuan

2018-02-01

Liquid Biphasic Flotation (LBF) is an advanced recovery method that has been effectively applied for biomolecules extraction. The objective of this investigation is to incorporate the fermentation and extraction process of lipase from Burkholderia cepacia using flotation system. Initial study was conducted to compare the performance of bacteria growth and lipase production using flotation and shaker system. From the results obtained, bacteria shows quicker growth and high lipase yield via flotation system. Integration process for lipase separation was investigated and the result showed high efficiency reaching 92.29% and yield of 95.73%. Upscaling of the flotation system exhibited consistent result with the lab-scale which are 89.53% efficiency and 93.82% yield. The combination of upstream and downstream processes in a single system enables the acceleration of product formation, improves the product yield and facilitates downstream processing. This integration system demonstrated its potential for biomolecules fermentation and separation that possibly open new opportunities for industrial production. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of water-quality characteristics and sampling design for streams in North Dakota, 1970–2008

USGS Publications Warehouse

Galloway, Joel M.; Vecchia, Aldo V.; Vining, Kevin C.; Densmore, Brenda K.; Lundgren, Robert F.

2012-01-01

In response to the need to examine the large amount of historic water-quality data comprehensively across North Dakota and evaluate the efficiency of the State-wide sampling programs, a study was done by the U.S. Geological Survey in cooperation with the North Dakota State Water Commission and the North Dakota Department of Health to describe the water-quality data collected for the various programs and determine an efficient State-wide sampling design for monitoring future water-quality conditions. Although data collected for the North Dakota State Water Commission High-Low Sampling Program, the North Dakota Department of Health Ambient Water-Quality Network, and other projects and programs provide valuable information on the quality of water in streams in North Dakota, the objectives vary among the programs, some of the programs overlap spatially and temporally, and the various sampling designs may not be the most efficient or relevant to the objectives of the individual programs as they have changed through time. One objective of a State-wide sampling program was to evaluate ways to describe the spatial variability of water-quality conditions across the State in the most efficient manner. Weighted least-squares regression analysis was used to relate the average absolute difference between paired downstream and upstream concentrations, expressed as a percent of the average downstream concentration, to the average absolute difference in daily flow between the downstream and upstream pairs, expressed as a percent of the average downstream flow. The analysis showed that a reasonable spatial network would consist of including the most downstream sites in large basins first, followed by the next upstream site(s) that roughly bisect the downstream flows at the first sites, followed by the next upstream site(s) that roughly bisect flows for the second sites. Sampling sites to be included in a potential State-wide network were prioritized into 3 design levels: level 1 (highest priority), level 2 (second priority), and level 3 (third priority). Given the spatial distribution and priority designation (levels 1–3) of sites in the potential spatial network, the next consideration was to determine the appropriate temporal sampling frequency to use for monitoring future water-quality conditions. The time-series model used to detect concentration trends for this report also was used to evaluate sampling designs to monitor future water-quality trends. Sampling designs were evaluated with regard to their sensitivity to detect seasonal trends that occurred during three 4-month seasons—March through June, July through October, and November through February. For the 34 level-1 sites, samples would be collected for major ions, trace metals, nutrients, bacteria, and sediment eight times per year, with samples in January, April (2 samples),May, June, July, August, and October. For the 21 level-2 sites, samples would be collected for major ions, trace metals, and nutrients six times per year (January, April, May, June, August, and October), and for the 26 level-3 sites, samples would be collected for these constituents four times per year (April, June, August, and October).

Aerosols and Particulates Workshop Sampling Procedures and Venues Working Group Summary

NASA Technical Reports Server (NTRS)

Pachlhofer, Peter; Howard, Robert

1999-01-01

The Sampling Procedures and Venues Workgroup discussed the potential venues available and issues associated with obtaining measurements. Some of the issues included Incoming Air Quality, Sampling Locations, Probes and Sample Systems. The following is a summary of the discussion of the issues and venues. The influence of inlet air to the measurement of exhaust species, especially trace chemical species, must be considered. Analysis procedures for current engine exhaust emissions regulatory measurements require adjustments for air inlet humidity. As a matter of course in scientific investigations, it is recommended that "background" measurements for any species, particulate or chemical, be performed during inlet air flow before initiation of combustion, if possible, and during the engine test period as feasible and practical. For current regulatory measurements, this would be equivalent to setting the "zero" level for conventional gas analyzers. As a minimum, it is recommended that measurements of the humidity and particulates in the incoming air be taken at the start and end of each test run. Additional measurement points taken during the run are desirable if they can be practically obtained. It was felt that the presence of trace gases in the incoming air is not a significant problem. However, investigators should consider the ambient levels and influences of local air pollution for species of interest. Desired measurement locations depend upon the investigation requirements. A complete investigation of phenomenology of particulate formation and growth requires measurements at a number of locations both within the engine and in the exhaust field downstream of the nozzle exit plane. Desirable locations for both extractive and in situ measurements include: (1) Combustion Zone (Multiple axial locations); (2) Combustor Exit (Multiple radial locations for annular combustors); (3) Turbine Stage (Inlet and exit of the stage); (4) Exit Nozzle (Multiple axial locations downstream of the nozzle). Actual locations with potential for extractive or non-intrusive measurements depend upon the test article and test configuration. Committee members expressed the importance of making investigators aware of various ports that could allow access to various stages of the existing engines. Port locations are engine si)ecific and might allow extractive sampling or innovative hybrid optical-probe access. The turbine stage region was one the most desirable locations for obtaining samples and might be accessed through boroscope ports available in some engine designs. Discussions of probes and sampling systems quickly identified issues dependent on particular measurement quantities. With general consensus, the group recommends SAE procedures for measurements and data analyses of currently regulated exhaust species (CO2, CO, THC, NO(x),) using conventional gas sampling techniques. Special procedures following sound scientific practices must be developed as required for species and/or measurement conditions not covered by SAE standards. Several issues arose concerning short lived radicals and highly reactive species. For conventional sampling, there are concerns of perturbing the sample during extraction, line losses, line-wall reactions, and chemical reactions during the sample transport to the analyzers. Sample lines coated with quartz.or other materials should be investigated for minimization of such effects. The group advocates the development of innovative probe techniques and non-intrusive optical techniques for measurement of short lived radicals and highly reactive species that cannot be sampled accurately otherwise. Two innovative probe concepts were discussed. One concept uses specially designed probes to transfer optical beams to and from a region of flow inaccessible by traditional ports or windows. The probe can perturb the flow field but must have a negligible impact on the region to be optically sampled. Such probes are referred to as hybrid probes and are under development at AEDC for measurement in the high pressure, high temperature of a combustor under development for power generation. The other concept consists of coupling an instrument directly to the probe. The probe would isolate a representative sample stream, freeze chemical reactions and direct the sample into the analyzer portion of the probe. Thus, the measurement would be performed in situ without sample line losses due either to reactions or binding at the wall surfaces. This concept was used to develop a fast, in situ, time-of-flight mass spectrometer measurement system for temporal quantification of NO in the IMPULSE facility at AEDC. Additional work is required in this area to determine the best probe and sampling technique for each species measurement requirement identified by the Trace Chemistry Working Group. A partial list of Venues was used as a baseline for discussion. Additional venues were added to the list and the list was broken out into the following categories: (1)Engines (a) Sea Level Test Stands (b) Altitude Chambers; (2) Annular Combustor Test Stands, (3) Sector Flametube Test Stands, (4) Fundamentals Rigs/Experiments.

Milk Bottom-Up Proteomics: Method Optimization

PubMed Central

Vincent, Delphine; Ezernieks, Vilnis; Elkins, Aaron; Nguyen, Nga; Moate, Peter J.; Cocks, Benjamin G.; Rochfort, Simone

2016-01-01

Milk is a complex fluid whose proteome displays a diverse set of proteins of high abundance such as caseins and medium to low abundance whey proteins such as ß-lactoglobulin, lactoferrin, immunoglobulins, glycoproteins, peptide hormones, and enzymes. A sample preparation method that enables high reproducibility and throughput is key in reliably identifying proteins present or proteins responding to conditions such as a diet, health or genetics. Using skim milk samples from Jersey and Holstein-Friesian cows, we compared three extraction procedures which have not previously been applied to samples of cows' milk. Method A (urea) involved a simple dilution of the milk in a urea-based buffer, method B (TCA/acetone) involved a trichloroacetic acid (TCA)/acetone precipitation, and method C (methanol/chloroform) involved a tri-phasic partition method in chloroform/methanol solution. Protein assays, SDS-PAGE profiling, and trypsin digestion followed by nanoHPLC-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS/MS) analyses were performed to assess their efficiency. Replicates were used at each analytical step (extraction, digestion, injection) to assess reproducibility. Mass spectrometry (MS) data are available via ProteomeXchange with identifier PXD002529. Overall 186 unique accessions, major and minor proteins, were identified with a combination of methods. Method C (methanol/chloroform) yielded the best resolved SDS-patterns and highest protein recovery rates, method A (urea) yielded the greatest number of accessions, and, of the three procedures, method B (TCA/acetone) was the least compatible of all with a wide range of downstream analytical procedures. Our results also highlighted breed differences between the proteins in milk of Jersey and Holstein-Friesian cows. PMID:26793233

Study of pharmaceuticals in surface and wastewater from Cuernavaca, Morelos, Mexico: Occurrence and environmental risk assessment.

PubMed

Rivera-Jaimes, José Abraham; Postigo, Cristina; Melgoza-Alemán, Rosa María; Aceña, Jaume; Barceló, Damia; López de Alda, Miren

2018-02-01

The present work describes the first known study to date on the occurrence of pharmaceuticals in surface water and wastewater of Cuernavaca, the capital of the state of Morelos (México). Selected pharmaceuticals (a total of 35) were extracted from the collected water samples with a generic solid phase extraction (SPE) protocol and determined in the sample extracts by means of high-performance liquid chromatography coupled to electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS). A screening level risk assessment combining the measured environmental concentrations (MECs) with dose-response data based on predicted no-effect concentrations (PNECs) was also applied to estimate Hazard Quotients (HQs) for the pharmaceuticals detected in the investigated area. A total of twelve pharmaceuticals were found in the water samples analyzed, with detection frequencies above 78% and in most cases of 100%. Overall, the most abundant pharmaceuticals in surface water were the analgesic and anti-inflammatory drugs naproxen (732-4880ng/L), acetaminophen (354-4460ng/L), and diclofenac (258-1398ng/L), and the lipid regulator bezafibrate (286-2100ng/L). On the contrary, other compounds like the β-blocker atenolol and the psychiatric drug carbamazepine were found at only a few ng or tens of ng per liter in the Apatlaco River. Despite the fact that some of the most abundant compounds showed good removal (>97%) during wastewater treatment, concentrations downstream the WWTP were only slightly lower than upstream. This indicates the existence of additional inputs of untreated wastewater into the river. Based on the obtained HQ-values, the concentrations of ibuprofen, sulfamethoxazole, diclofenac and naproxen present in the river could pose a high toxicity risk for the aquatic ecosystem. These findings highlight these pharmaceuticals as relevant organic contaminants in the area of study and the need to further monitor them in order to adopt appropriate measures to safeguard the ecosystem, and eventually human health. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of an oil spill on leafpack-inhabiting macroinvertebrates in the Chariton river, Missouri

USGS Publications Warehouse

Poulton, B.C.; Callahan, E.V.; Hurtubise, R.D.; Mueller, B.G.

1998-01-01

Artificial leaf packs were used to determine the effects of an oil spill on stream macroinvertebrate communities in the Chariton River, Missouri. Plastic mesh leaf retainers with approximately 10 g of leaves from five tree species were deployed at five sites (two upstream of the spill and three downstream) immediately after the spill and one year later. Four macroinvertebrate species dominating the community at upstream sites were virtually eliminated below the spill, including the stonefly Isoperla bilineata, the caddisfly Potamyia flava, the midge Thienemanniella xena, and blackfly larvae (Simulium sp.). Density of collector and shredder functional groups, and number of shredder taxa differed between upstream sites and the two furthest downstream sites during the 1990 sample period (Kruskal-Wallis w/Bonferroni paired comparisons, experiment wise error rate = 0.05). With one exception, no differences between sites were detected in the 1991-1992 sample period, indicating that the benthic community had at least partially recovered from the oil spill after one year. The odds of obtaining a sample with a small abundance of shredders (abundance < median) in 1990 was significantly greater downstream of the spill than upstream, and the odds of obtaining a sample with a small abundance of shredders at downstream sites was greater in 1990 than in 1991-1992. A similar pattern was observed in abundance and taxa richness of the collector functional group. No significant differences between the two sampling periods were detected at upstream sites. Observed effects appeared to be associated with oil sorption and substrate coating, creating conditions unsuitable for successful colonization.

Trace-metal concentrations in sediment and water and health of aquatic macroinvertebrate communities of streams near Park City, Summit County, Utah

USGS Publications Warehouse

Giddings, Elis M.P.; Hornberger, Michelle I.; Hadley, Heidi K.

2001-01-01

The spatial distribution of metals in streambed sediment and surface water of Silver Creek, McLeod Creek, Kimball Creek, Spring Creek, and part of the Weber River, near Park City, Utah, was examined. From the mid-1800s through the 1970s, this region was extensively mined for silver and lead ores. Although some remediation has occurred, residual deposits of tailing wastes remain in place along large sections of Silver Creek. These tailings are the most likely source of metals to this system. Bed sediment samples were collected in 1998, 1999, and 2000 and analyzed using two extraction techniques: a total extraction that completely dissolves all forms of metals in minerals and trace elements associated with the sediment; and a weak-acid extraction that extracts the metals and trace elements that are only weakly adsorbed onto the sediment surface. This latter method is used to determine the more biologically relevant fraction of metal complexed onto the sediment. Water samples were collected in March and August 2000 and were analyzed for total and dissolved trace metals.Concentrations of silver, cadmium, copper, lead, mercury, and zinc in the streambed sediment of Silver Creek greatly exceeded background concentrations. These metals also exceeded established aquatic life criteria at most sites. In the Weber River, downstream of the confluence with Silver Creek, concentrations of cadmium, lead, zinc, and total mercury in streambed sediment also exceeded aquatic life guidelines, however, concentrations of metals in streambed sediment of McLeod and Kimball Creeks were lower than Silver Creek. Water-column concentrations of zinc, total mercury, and methylmercury in Silver Creek were high relative to unimpacted sites, and exceeded water quality criteria for the protection of aquatic organisms. Qualitative measurements of the macroinvertebrate community in Silver Creek were compared to the spatial distribution of metals in streambed sediment. The data indicate that impairment related to metal concentration exists in Silver Creek.

Design of a portable gas chromatography with a conducting polymer nanocomposite detector device and a method to analyze a gas mixture.

PubMed

Pirsa, Sajad

2017-04-01

A portable chromatography device and a method were developed to analyze a gas mixture. The device comprises a chromatographic column for separating components of a sample of the gas mixture. It has an air pump coupled to the inlet of a chromatographic column for pumping air and an injector coupled to the inlet of chromatographic column for feeding the sample using the air as a carrier gas. A detector is arranged downstream from and coupled to the outlet of the chromatographic column. The detector is a nanostructure semiconductive microfiber. The device further comprises an evaluation unit arranged and configured to evaluate each detected component to determine the concentration. The designed portable system was used for simultaneous detection of amines. The possibility of applying dispersive liquid-liquid microextraction for the determination of analytes in trace levels is demonstrated. The reproducibility of this method is acceptable, and good standard deviations were obtained. The relative standard deviation value is less than 6% for all analytes. Finally, the method was successfully applied to the extraction and determination of analytes in water samples. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Body morphology differs in wild juvenile Chinook salmon Oncorhynchus tshawytscha in the Willamette River, Oregon, USA

USGS Publications Warehouse

Billman, E.J.; Whitman, L.D.; Schroeder, R.K.; Sharpe, C.S.; Noakes, David L. G.; Schreck, Carl B.

2014-01-01

Body morphology of juvenile Chinook salmon Oncorhynchus tshawytscha in the upper Willamette River, Oregon, U.S.A., was analysed to determine if variation in body shape is correlated with migratory life-history tactics followed by juveniles. Body shape was compared between migrating juveniles that expressed different life-history tactics, i.e. autumn migrants and yearling smolts, and among parr sampled at three sites along a longitudinal river gradient. In the upper Willamette River, the expression of life-history tactics is associated with where juveniles rear in the basin with fish rearing in downstream locations generally completing ocean ward migrations earlier in life than fish rearing in upstream locations. The morphological differences that were apparent between autumn migrants and yearling smolts were similar to differences between parr rearing in downstream and upstream reaches, indicating that body morphology is correlated with life-history tactics. Autumn migrants and parr from downstream sampling sites had deeper bodies, shorter heads and deeper caudal peduncles compared with yearling smolts and parr from the upstream sampling site. This study did not distinguish between genetic and environmental effects on morphology; however, the results suggest that downstream movement of juveniles soon after emergence is associated with differentiation in morphology and with the expression of life-history variation.

Sluiceway Operations for Adult Steelhead Downstream Passage at The Dalles Dam, Columbia River, USA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khan, Fenton; Royer, Ida M.; Johnson, Gary E.

2013-10-01

This study evaluated adult steelhead (Oncorhynchus mykiss; fallbacks and kelts) downstream passage at The Dalles Dam in the Columbia River, USA, during the late fall, winter, and early spring months between 2008 and 2011. The purpose of the study was to determine the efficacy of operating the dam’s ice-and-trash sluiceway during non-spill months to provide a relatively safe, non-turbine, surface outlet for overwintering steelhead fallbacks and downstream migrating steelhead kelts. We applied the fixed-location hydroacoustic technique to estimate fish passage rates at the sluiceway and turbines of the dam. The spillway was closed during our sampling periods, which generally occurredmore » in late fall, winter, and early spring. The sluiceway was highly used by adult steelhead (91–99% of total fish sampled passing the dam) during all sampling periods. Turbine passage was low when the sluiceway was not operated. This implies that lack of a sluiceway route did not result in increased turbine passage. However, when the sluiceway was open, adult steelhead used it to pass through the dam. The sluiceway may be operated during late fall, winter, and early spring to provide an optimal, non-turbine route for adult steelhead (fallbacks and kelts) downstream passage at The Dalles Dam.« less

[Detection of Physiological Activity of Pharmaceuticals in Wastewater and River Water].

PubMed

Ihara, Masaru; Zhang, Han; Hanamoto, Seiya; Tanaka, Hiroaki

2018-01-01

　Pharmaceuticals are widely found in aquatic environments worldwide. Concern about their potential risks to aquatic species has been raised because they are designed to be biologically active. To address this concern, we must know whether biological activity of pharmaceuticals can be detected in waters. Nearly half of all marketed pharmaceuticals act by binding to the G protein-coupled receptor (GPCR). In this study, we measured the physiological activity of GPCR-acting pharmaceuticals in effluent from a wastewater treatment plant (WWTP) and upstream and downstream of its outfall in Japan during 2 years. We used the in vitro transforming growth factor-α (TGFα) shedding assay, which accurately and sensitively detects GPCR activation, to investigate the antagonistic activities of water extracts against receptors for dopamine (D2) and histamine (H1). Activities detected in waters were quantified as antagonist equivalent quantities (EQs). In WWTP effluent extracts, antagonistic activity was detected at several hundred ng/L of sulpiride-EQ (D2) and several μg/L of diphenhydramine (DIP)-EQ (H1). In downstream river water extracts, antagonistic activity against H1 was around several hundred ng/L of DIP-EQ, higher than that upstream owing to the WWTP effluent. This review discusses the research needed to resolve the concern about potential risks of pharmaceuticals in waters to aquatic species.

Environmental impact of coal mining and coal seam gas production on surface water quality in the Sydney basin, Australia.

PubMed

Ali, A; Strezov, V; Davies, P; Wright, I

2017-08-01

The extraction of coal and coal seam gas (CSG) will generate produced water that, if not adequately treated, will pollute surface and groundwater systems. In Australia, the discharge of produced water from coal mining and related activities is regulated by the state environment agency through a pollution licence. This licence sets the discharge limits for a range of analytes to protect the environment into which the produced water is discharged. This study reports on the impact of produced water from coal mine activities located within or discharging into high conservation environments, such as National Parks, in the outer region of Sydney, Australia. The water samples upstream and downstream from the discharge points from six mines were taken, and 110 parameters were tested. The results were assessed against a water quality index (WQI) which accounts for pH, turbidity, dissolved oxygen, biochemical oxygen demand, total dissolved solids, total phosphorus, nitrate nitrogen and E .coli. The water quality assessment based on the trace metal contents against various national maximum admissible concentration (MAC) and their corresponding environmental impacts was also included in the study which also established a base value of water quality for further study. The study revealed that impacted water downstream of the mine discharge points contained higher metal content than the upstream reference locations. In many cases, the downstream water was above the Australia and New Zealand Environment Conservation Council and international water quality guidelines for freshwater stream. The major outliers to the guidelines were aluminium (Al), iron (Fe), manganese (Mn), nickel (Ni) and zinc (Zn). The WQI of surface water at and downstream of the discharge point was lower when compared to upstream or reference conditions in the majority of cases. Toxicology indices of metals present in industrial discharges were used as an additional tool to assess water quality, and the newly proposed environmental water quality index (EWQI) lead to better trend in the impact of coal and coal seam gas mining activities on surface water quality when compared to the upstream reference water samples. Metal content limits were based on the impact points assigned by the Agency for Toxic Substances and Disease Registry, USA. For environmental and health impact assessment, the approach used in this study can be applied as a model to provide a basis to assess the anthropogenic contribution from the industrial and mining activities on the environment.

Evaluation of wastewater contaminant transport in surface waters using verified Lagrangian sampling

USGS Publications Warehouse

Antweiler, Ronald C.; Writer, Jeffrey H.; Murphy, Sheila F.

2014-01-01

Contaminants released from wastewater treatment plants can persist in surface waters for substantial distances. Much research has gone into evaluating the fate and transport of these contaminants, but this work has often assumed constant flow from wastewater treatment plants. However, effluent discharge commonly varies widely over a 24-hour period, and this variation controls contaminant loading and can profoundly influence interpretations of environmental data. We show that methodologies relying on the normalization of downstream data to conservative elements can give spurious results, and should not be used unless it can be verified that the same parcel of water was sampled. Lagrangian sampling, which in theory samples the same water parcel as it moves downstream (the Lagrangian parcel), links hydrologic and chemical transformation processes so that the in-stream fate of wastewater contaminants can be quantitatively evaluated. However, precise Lagrangian sampling is difficult, and small deviations – such as missing the Lagrangian parcel by less than 1 h – can cause large differences in measured concentrations of all dissolved compounds at downstream sites, leading to erroneous conclusions regarding in-stream processes controlling the fate and transport of wastewater contaminants. Therefore, we have developed a method termed “verified Lagrangian” sampling, which can be used to determine if the Lagrangian parcel was actually sampled, and if it was not, a means for correcting the data to reflect the concentrations which would have been obtained had the Lagrangian parcel been sampled. To apply the method, it is necessary to have concentration data for a number of conservative constituents from the upstream, effluent, and downstream sites, along with upstream and effluent concentrations that are constant over the short-term (typically 2–4 h). These corrections can subsequently be applied to all data, including non-conservative constituents. Finally, we show how data from other studies can be corrected.

Evaluation of wastewater contaminant transport in surface waters using verified Lagrangian sampling.

PubMed

Antweiler, Ronald C; Writer, Jeffrey H; Murphy, Sheila F

2014-02-01

Contaminants released from wastewater treatment plants can persist in surface waters for substantial distances. Much research has gone into evaluating the fate and transport of these contaminants, but this work has often assumed constant flow from wastewater treatment plants. However, effluent discharge commonly varies widely over a 24-hour period, and this variation controls contaminant loading and can profoundly influence interpretations of environmental data. We show that methodologies relying on the normalization of downstream data to conservative elements can give spurious results, and should not be used unless it can be verified that the same parcel of water was sampled. Lagrangian sampling, which in theory samples the same water parcel as it moves downstream (the Lagrangian parcel), links hydrologic and chemical transformation processes so that the in-stream fate of wastewater contaminants can be quantitatively evaluated. However, precise Lagrangian sampling is difficult, and small deviations - such as missing the Lagrangian parcel by less than 1h - can cause large differences in measured concentrations of all dissolved compounds at downstream sites, leading to erroneous conclusions regarding in-stream processes controlling the fate and transport of wastewater contaminants. Therefore, we have developed a method termed "verified Lagrangian" sampling, which can be used to determine if the Lagrangian parcel was actually sampled, and if it was not, a means for correcting the data to reflect the concentrations which would have been obtained had the Lagrangian parcel been sampled. To apply the method, it is necessary to have concentration data for a number of conservative constituents from the upstream, effluent, and downstream sites, along with upstream and effluent concentrations that are constant over the short-term (typically 2-4h). These corrections can subsequently be applied to all data, including non-conservative constituents. Finally, we show how data from other studies can be corrected. © 2013.

Solutions for Northern Kosovo: Lessons Learned in Mostar, Eastern Slavonia, and Brcko

DTIC Science & Technology

2006-08-01

with up to 20,000 jobs dependent on a large complex that included extraction, flotation , smelting, and downstream processing processes. The mines...with Serbia, no one option will serve as the silver bullet for all interested parties. Partition. Kosovo is legally still part of Serbia, although

Fate of antimony and arsenic in contaminated waters at the abandoned Su Suergiu mine (Sardinia, Italy)

USGS Publications Warehouse

Cidu, Rosa; Dore, Elisabetta; Biddau, Riccardo; Nordstrom, D. Kirk

2018-01-01

We investigated the fate of Sb and As downstream of the abandoned Su Suergiu mine (Sardinia, Italy) and surrounding areas. The mined area is a priority in the Sardinian remediation plan for contaminated sites due to the high concentrations of Sb and As in the mining-related wastes, which may impact the Flumendosa River that supplies water for agriculture and domestic uses. Hydrogeochemical surveys conducted from 2005 to 2015 produced time-series data and downstream profiles of water chemistry at 46 sites. Water was sampled at: springs and streams unaffected by mining; adits and streams in the mine area; drainage from the slag heaps; stream water downstream of the slag drainages; and the Flumendosa River downstream from the confluence of the contaminated waters. At specific sites, water sampling was repeated under different flow conditions, resulting in a total of 99 samples. The water samples were neutral to slightly alkaline. Elevated Sb (up to 30 mg L−1) and As (up to 16 mg L−1) concentrations were observed in water flowing from the slag materials from where the Sb ore was processed. These slag materials were the main Sb and As source at Su Suergiu. A strong base, Na-carbonate, from the foundry wastes, had a major influence on mobilizing Sb and As. Downstream contamination can be explained by considering that: (1) the predominant aqueous species, Sb(OH)6 − and HAsO4 −2, are not favored in sorption processes at the observed pH conditions; (2) precipitation of Sb- and As-bearing solid phases was not observed, which is consistent with modeling results indicating undersaturation; and (3) the main decrease in dissolved Sb and As concentrations was by dilution. Dissolved As concentrations in the Flumendosa River did not generally exceed the EU limit of 10 µg L−1, whereas dissolved Sb in the river downstream of the contamination source always exceeded the EU limit of 5 µg L−1. Recent actions aimed at retaining runoff from the slag heaps are apparently not sufficiently mitigating contamination in the Flumendosa River.

Extracting archaeal populations from iron oxidizing systems

NASA Astrophysics Data System (ADS)

Whitmore, L. M.; Hutchison, J.; Chrisler, W.; Jay, Z.; Moran, J.; Inskeep, W.; Kreuzer, H.

2013-12-01

Unique environments in Yellowstone National Park offer exceptional conditions for studying microorganisms in extreme and constrained systems. However, samples from some extreme systems often contain inorganic components that pose complications during microbial and molecular analysis. Several archaeal species are found in acidic, geothermal ferric-oxyhydroxide mats; these species have been shown to adhere to mineral surfaces in flocculated colonies. For optimal microbial analysis, (microscopy, flow cytometry, genomic extractions, proteomic analysis, stable isotope analysis, and others), improved techniques are needed to better facilitate cell detachment and separation from mineral surfaces. As a requirement, these techniques must preserve cell structure while simultaneously minimizing organic carryover to downstream analysis. Several methods have been developed for removing sediments from mixed prokaryotic populations, including ultra-centrifugation, nycodenz gradient, sucrose cushions, and cell straining. In this study we conduct a comparative analysis of mechanisms used to detach archaeal cell populations from the mineral interface. Specifically, we evaluated mechanical and chemical approaches for cell separation and homogenization. Methods were compared using confocal microscopy, flow cytometry analyses, and real-time PCR detection. The methodology and approaches identified will be used to optimize biomass collection from environmental specimens or isolates grown with solid phases.

Atrazine degradation in a small stream in Iowa

USGS Publications Warehouse

Kolpin, D.W.; Kalkhoff, S.J.

1993-01-01

A study was conducted during 1990 through an 11.2-km reach of Roberts Creek in northeastern Iowa to determine the fate of atrazine in a surface water environment Water samples were collected at ~1-month intervals from April through November during stable low to medium flow conditions and analyzed for atrazine and two of its initial biotic degradation products, desethylatrazine and deisopropylatrazine. Samples were collected on the basis of a Lagrangian model of streamflow in order to sample the same parcel of water as it moved downstream. Atrazine concentrations substantially decreased (roughly 25-60%) between water entering and exiting the study reach during four of the seven sampling periods. During these same four sampling periods, the concentrations of the two biotic atrazine degradation products were constant or decreasing downstream, suggesting an abiotic degradation process.

Field and laboratory data describing physical and chemical characteristics of metal-contaminated flood-plain deposits downstream from Lead, west-central South Dakota

USGS Publications Warehouse

Marron, D.C.

1988-01-01

Samples from metal-contaminated flood-plain sediments at 9 sites downstream from Lead, in west-central South Dakota, were collected during the summers of 1985-87 to characterize aspects of the sedimentology, chemistry, and geometry of a deposit that resulted from the discharge of a large volume of mining wastes into a river system. Field and laboratory data include stratigraphic descriptions, chemical contents and grain-size distributions of samples, and surveyed flood-plain positions of samples. This report describes sampling-site locations, and methods of sample collection and preservation, and subsequent laboratory analysis. Field and laboratory data are presented in 4 figures and 11 tables in the ' Supplemental Data ' section at the back of the report. (USGS)

A Reconnaissance of selected organic compounds in streams in tribal lands in Central Oklahoma, January-February 2009

USGS Publications Warehouse

Becker, Carol J.

2010-01-01

The U.S. Geological Survey worked in cooperation with the U.S. Environmental Protection Agency and the Kickapoo Tribe of Oklahoma on two separate reconnaissance projects carried out concurrently. Both projects entailed the use of passive samplers as a sampling methodology to investigate the detection of selected organic compounds at stream sites in jurisdictional areas of several tribes in central Oklahoma during January-February 2009. The focus of the project with the U.S. Environmental Protection Agency was the detection of pesticides and pesticide metabolites using Semipermeable Membrane Devices at five stream sites in jurisdictional areas of several tribes. The project with the Kickapoo Tribe of Oklahoma focused on the detection of pesticides, pesticide metabolites, polycyclic aromatic hydrocarbons, polychlorinated biphenyl compounds, and synthetic organic compounds using Semipermeable Membrane Devices and Polar Organic Chemical Integrative Samplers at two stream sites adjacent to the Kickapoo tribal lands. The seven stream sites were located in central Oklahoma on the Cimarron River, Little River, North Canadian River, Deep Fork, and Washita River. Extracts from SPMDs submerged at five stream sites, in cooperation with the U.S. Environmental Protection Agency, were analyzed for 46 pesticides and 6 pesticide metabolites. Dacthal, a pre-emergent herbicide, was detected at all five sites. Pendimethalin, also a pre-emergent, was detected at one site. The insecticides chlorpyrifos and dieldrin were detected at three sites and p,p'-DDE, a metabolite of the insecticide DDT, also was detected at three sites. SPMDs and POCIS were submerged at the upstream edge and downstream edge of the Kickapoo tribal boundaries. Both sites are downstream from the Oklahoma City metropolitan area and multiple municipal wastewater treatment plants. Extracts from the passive samplers were analyzed for 62 pesticides, 10 pesticide metabolites, 3 polychlorinated biphenyl compounds, 35 polycyclic aromatic hydrocarbons, and 49 synthetic organic compounds. Ten pesticides and four pesticide metabolites were detected at the upstream site and seven pesticides and four pesticide metabolites were detected at the downstream site. Pesticides detected at both sites were atrazine, chlorpyrifos, dacthal, dieldrin, metolachlor, pendimethalin, and trans-nonachlor. Additionally at the upstream site, heptachlor, pentachlorophenol, and prometon were detected. The pesticide metabolites p,p'-DDE, cis-chlordane, and trans-chlordane also were detected at both sites. Polychlorinated biphenyl compounds aroclor-1016/1242, aroclor-1254, and aroclor-1260 were detected at both sites. The upstream site had 16 polycyclic aromatic hydrocarbon detections and the downstream site had 8 detections. Because of chromatographic interference during analysis, a positive identification of 17 polycyclic aromatic hydrocarbons could not be made. Consequently, there may have been a greater number of these compounds detected at both sites. A total of 36 synthetic organic compounds were detected at the two sites adjacent to the Kickapoo tribal lands. The upstream site had 21 synthetic organic compound detections: three detergent metabolites, two fecal indicators, three flame retardants, seven industrial compounds, five compounds related to personal care products, and beta-sitosterol, a plant sterol. Fifteen synthetic organic compounds were detected at the downstream site and included: one fecal indicator, three flame retardants, six industrial compounds, and five compounds related to personal care products.

Effects of Hardened Low-Water Crossings on Periphyton and Water Quality in Selected Streams at the Fort Polk Military Reservation, Louisiana, 1998-99 and 2003-04

USGS Publications Warehouse

Bryan, Barbara W.; Bryan, C. Frederick; Lovelace, John K.; Tollett, Roland W.

2007-01-01

In 2003, the U.S. Geological Survey (USGS), at the request of the U.S. Army Joint Readiness Training Center and Fort Polk, began a follow-up study to determine whether installation and modification of hardened low-water crossings had short-term (less than 1 year) or long-term (greater than 1 year) effects on periphyton or water quality in five streams at the Fort Polk Military Reservation, Louisiana. Periphyton data were statistically analyzed for possible differences between samples collected at upstream and downstream sites and before and after low-water crossings were modified on three streams, Big Brushy Creek, Tributary to East Fork of Sixmile Creek, and Tributary to Birds Creek, during 2003?04. Periphyton data also were analyzed for possible differences between samples collected at upstream and downstream sites on two streams, Tributary to Big Brushy Creek and Little Brushy Creek, during 1998?99 and 2003. Variations in periphyton communities could not be conclusively attributed to the modifications. Most of the significant changes in percent frequency of occurrence and average cell density of the 10 most frequently occurring periphyton taxa were increases at downstream sites after the hardened low-water crossing installations or modifications. However, these changes in the periphyton community are not necessarily deleterious to the community structure. Water-quality data collected from upstream and downstream sites on the five streams during 2003?04 were analyzed for possible differences caused by the hardened crossings. Generally, average water-quality values and concentrations were similar at upstream and downstream sites. When average water-quality values or concentrations changed significantly, they almost always changed significantly at both the upstream and downstream sites. It is probable that observed variations in water quality at both upstream and downstream sites are related to differences in rainfall and streamflow during the sample collection periods rather than an effect of the hardened low-water crossing installations or modifications, but additional study is needed.

Preliminary evaluation of an in vivo fluorometer to quantify algal periphyton biomass and community composition

USGS Publications Warehouse

Harris, Theodore D.; Graham, Jennifer L.

2015-01-01

The bbe-Moldaenke BenthoTorch (BT) is an in vivo fluorometer designed to quantify algal biomass and community composition in benthic environments. The BT quantifies total algal biomass via chlorophyll a (Chl-a) concentration and may differentiate among cyanobacteria, green algae, and diatoms based on pigment fluorescence. To evaluate how BT measurements of periphytic algal biomass (as Chl-a) compared with an ethanol extraction laboratory analysis, we collected BT- and laboratory-measured Chl-a data from 6 stream sites in the Indian Creek basin, Johnson County, Kansas, during August and September 2012. BT-measured Chl-a concentrations were positively related to laboratory-measured concentrations (R2 = 0.47); sites with abundant filamentous algae had weaker relations (R2 = 0.27). Additionally, on a single sample date, we used the BT to determine periphyton biomass and community composition upstream and downstream from 2 wastewater treatment facilities (WWTF) that discharge into Indian Creek. We found that algal biomass increased immediately downstream from the WWTF discharge then slowly decreased as distance from the WWTF increased. Changes in periphyton community structure also occurred; however, there were discrepancies between BT- and laboratory-measured community composition data. Most notably, cyanobacteria were present at all sites based on BT measurements but were present at only one site based on laboratory-analyzed samples. Overall, we found that the BT compared reasonably well with laboratory methods for relative patterns in Chl-a but not as well with absolute Chl-aconcentrations. Future studies need to test the BT over a wider range of Chl-aconcentrations, in colored waters, and across various periphyton assemblages.

Identification of compounds bound to suspended solids causing sub-lethal toxic effects in Daphnia magna. A field study on re-suspended particles during river floods in Ebro River.

PubMed

Rivetti, Claudia; Gómez-Canela, Cristian; Lacorte, Silvia; Díez, Sergi; Lázaro, Wilkinson L; Barata, Carlos

2015-04-01

Identifying chemicals causing adverse effects in organisms present in water remains a challenge in environmental risk assessment. This study aimed to assess and identify toxic compounds bound to suspended solids re-suspended during a prolonged period of flushing flows in the lower part of Ebro River (NE, Spain). This area is contaminated with high amounts of organochlorine and mercury sediment wastes. Chemical characterization of suspended material was performed by solid phase extraction using a battery of non-polar and polar solvents and analyzed by GC-MS/MS and LC-MS/MS. Mercury content was also determined for all sites. Post-exposure feeding rates of Daphnia magna were used to assess toxic effects of whole and filtered water samples and of re-constituted laboratory water with re-suspended solid fractions. Organochlorine and mercury residues in the water samples increased from upstream to downstream locations. Conversely, toxic effects were greater at the upstream site than downstream of the superfund Flix reservoir. A further analysis of the suspended solid fraction identified a toxic component eluted within the 80:20 methanol:water fraction. Characterization of that toxic component fraction by LC-MS/MS identified the phytotoxin anatoxin-a, whose residue levels were correlated with observed feeding inhibition responses. Further feeding inhibition assays conducted in the lab using anatoxin-a produced from Planktothrix agardhii, a filamentous cyanobacteria, confirmed field results. This study provides evidence that in real field situation measured contaminant residues do not always agree with toxic effects. Copyright © 2015 Elsevier B.V. All rights reserved.

Experimental Review of DNA-Based Methods for Wine Traceability and Development of a Single-Nucleotide Polymorphism (SNP) Genotyping Assay for Quantitative Varietal Authentication.

PubMed

Catalano, Valentina; Moreno-Sanz, Paula; Lorenzi, Silvia; Grando, Maria Stella

2016-09-21

The genetic varietal authentication of wine was investigated according to DNA isolation procedures reported for enological matrices and also by testing 11 commercial extraction kits and various protocol modifications. Samples were collected at different stages of the winemaking process of renowned Italian wines Brunello di Montalcino, Lambruschi Modenesi, and Trento DOC. Results demonstrated not only that grape DNA loss is produced by the fermentation process but also that clarification and stabilization operations contribute to the reduction of double-stranded DNA content on wine. Despite the presence of inhibitors, downstream PCR genotyping yielded reliable nuclear and chloroplast SSR markers for must samples, whereas no amplification or inconsistent results were obtained at later stages of the vinification. In addition, a TaqMan genotyping assay based on cultivar-specific single-nucleotide polymorphisms (SNPs) was designed, which allowed assessment of grapevine DNA mixtures. Once the wine matrix limitations are overcome, this sensitive tool may be implemented for the relative quantification of cultivars used for blend wines or frauds.

Hydrologic and water-quality data from Mountain Island Lake, North Carolina, 1994-97

USGS Publications Warehouse

Sarver, K.M.; Steiner, B.C.

1998-01-01

Continuous-record water-level gages were established at three sites on Mountain Island Lake and one site downstream from Mountain Island Dam. The water level of Mountain Island Lake is controlled by Duke Power Company releases at Cowans Ford Dam (upstream) and Mountain Island Dam (downstream). Water levels on Mountain Island Lake measured just downstream from Cowans Ford Dam fluctuated 11.15 feet during the study. Water levels just upstream from the Mountain Island Lake forebay fluctuated 6.72 feet during the study. About 3 miles downstream from Mountain Island Dam, water levels fluctuated 5.31 feet. Sampling locations included 14 sites in Mountain Island Lake, plus one downstream river site. At three sites, automated instruments recorded water temperature, dissolved-oxygen concentration, and specific conductance at 15-minute intervals throughout the study. Water temperatures recorded continuously during the study ranged from 4.2 to 35.2 degrees Celsius, and dissolved-oxygen concentrations ranged from 2.1 to 11.8 milligrams per liter. Dissolved-oxygen concentrations generally were inversely related to water temperature, with lowest dissolved-oxygen concentrations typically recorded in the summer. Specific conductance values recorded continuously during the study ranged from 33 to 89 microsiemens per centimeter; however, mean monthly values were fairly consistent throughout the study at all sites (50 to 61 microsiemens per centimeter). In addition, vertical profiles of water temperature, dissolved-oxygen concentration, specific conductance, and pH were measured at all sampling locations during 24 site visits. Water-quality constituent concentrations were determined for seven reservoir sites and the downstream river site during 17 sampling trips. Water-quality samples were routinely analyzed for biochemical oxygen demand, fecal coliform bacteria, hardness, alkalinity, total and volatile suspended solids, nutrients, total organic carbon, chlorophyll, iron, calcium, and magnesium; the samples were analyzed less frequently for trace metals, volatile organic compounds, semivolatile organic compounds, and pesticides. Maximum dissolved nitrite plus nitrate concentrations determined during the study were 0.348 milligram per liter in the mainstem sites and 2.77 milligrams per liter in the coves. Maximum total phosphorus concentrations were 0.143 milligram per liter in the mainstem sites and 0.600 milligram per liter in the coves. Fecal coliform and chlorophyll a concentrations were less than or equal to 160 colonies per 100 milliliters and 13 micrograms per liter, respectively, in all samples. Trace metals detected in at least one sample included arsenic, chromium, copper, lead, nickel, zinc, and antimony. Concentrations of all trace metals (except zinc) were 5.0 micrograms per liter or less; the maximum zinc concentration was 80 micrograms per liter. One set of bottom material samples was collected from Gar Creek and McDowell Creek for chemical analysis and analyzed for nutrients, trace metals, organochlorine pesticides, and semivolatile organic compounds. The only organochlorine pesticide identified in either sample was p,p'-DDE at an estimated concentration of 0.8 microgram per kilogram. Twenty semivolatile organic compounds, mainly polyaromatic hydrocarbons and plasticizers, were identified.

Characterization of water quality and biological communities, Fish Creek, Teton County, Wyoming, 2007-08

USGS Publications Warehouse

Eddy-Miller, Cheryl A.; Peterson, David A.; Wheeler, Jerrod D.; Leemon, Daniel J.

2010-01-01

Fish Creek, a tributary to the Snake River, is about 25 river kilometers long and is located in Teton County in western Wyoming near the town of Wilson. Public concern about nuisance growths of aquatic plants in Fish Creek have been increasing in recent years. To address this concern, the U.S. Geological Survey conducted a study in cooperation with the Teton Conservation District to characterize the water quality and biological communities in Fish Creek. Water-quality samples were collected for analyses of physical properties and water chemistry (nutrients, nitrate isotopes, and wastewater chemicals) between March 2007 and October 2008 from seven surface-water sites and three groundwater wells. During this same period, aquatic plant and macroinvertebrate samples were collected and habitat characteristics were measured at the surface-water sites. The main objectives of this study were to (1) evaluate nutrient concentrations (that influence biological indicators of eutrophication) and potential sources of nutrients by using stable isotope analysis and other indicator chemicals (such as caffeine and disinfectants) that could provide evidence of anthropogenic sources, such as wastewater or septic tank contamination in Fish Creek and adjacent groundwater, and (2) characterize the algal, macrophyte, and macroinvertebrate communities and habitat of Fish Creek. Nitrate was the dominant species of dissolved nitrogen present in all samples and was the only bioavailable species detected at concentrations greater than the laboratory reporting level in all surface-water samples. Average concentrations of dissolved nitrate in surface water were largest in samples collected from the two sites with seasonal flow near Teton Village and decreased downstream; the smallest concentration was at downstream site A-Wck. Concentrations of dissolved nitrate in groundwater were consistently greater than concentrations in corresponding surface-water sites during the same sampling event. Orthophosphate was the primary dissolved species of phosphorus present in all surface-water and groundwater samples. The average concentration of dissolved orthophosphate in surface water was largest in samples collected from near Teton Village; samples from all other sites had similar average concentrations. Concentrations of dissolved orthophosphate in groundwater also were typically greater than concentrations in corresponding surface-water sites during the same sampling event. The aquatic plant communities in Fish Creek typically were composed of a mixture of macrophytes, macroalgae, microalgae, and moss. The composition of the aquatic plant community in Fish Creek appeared to shift in the downstream direction in 2007. On average, the proportion of macrophytes ranged from about 1 percent at site A-R1U, the most upstream site, to 54 percent of the plant community at site A-R6D, the farthest downstream site sampled during 2007. The downstream increase in macrophytes was accompanied by a downstream decrease in microalgae. The average proportion of microalgae ranged from 80 percent at site A-R1U to 24 percent at site A-R6D. The proportion of the macroalgae Cladophora in the aquatic plant community was relatively high at sites A-Wck and A-R3D in both 2007 and 2008.

Biomonitoring of lead, zinc, and cadmium in streams draining lead-mining and non-mining areas, Southeast Missouri, USA

USGS Publications Warehouse

Besser, John M.; Brumbaugh, William G.; May, Thomas W.; Schmitt, Christopher J.

2007-01-01

We evaluated exposure of aquatic biota to lead (Pb), zinc (Zn), and cadmium (Cd) in streams draining a Pb-mining district in southeast Missouri. Samples of plant biomass (detritus, periphyton, and filamentous algae), invertebrates (snails, crayfish, and riffle benthos), and two taxa of fish were collected from seven sites closest to mining areas (mining sites), four sites further downstream from mining (downstream sites), and eight reference sites in fall 2001. Samples of plant biomass from mining sites had highest metal concentrations, with means 10- to 60-times greater than those for reference sites. Mean metal concentrations in over 90% of samples of plant biomass from mining sites were significantly greater than those from reference sites. Mean concentrations of Pb, Zn, and Cd in most invertebrate samples from mining sites, and mean Pb concentrations in most fish samples from mining sites, were also significantly greater than those from reference sites. Concentrations of all three metals were lower in samples from downstream sites, but several samples of plant biomass from downstream sites had metal concentrations significantly greater than those from reference sites. Analysis of supplemental samples collected in the fall of 2002, a year of above-average stream discharge, had lower Pb concentrations and higher Cd concentrations than samples collected in 2001, near the end of a multi-year drought. Concentrations of Pb measured in fish and invertebrates collected from mining sites during 2001 and 2002 were similar to those measured at nearby sites in the 1970s, during the early years of mining in the Viburnum Trend. Results of this study demonstrate that long-term Pb mining activity in southeast Missouri has resulted in significantly elevated concentrations of Pb, Cd, and Zn in biota of receiving streams, compared to biota of similar streams without direct influence of mining. Our results also demonstrate that metal exposure in the study area differed significantly among sample types, habitats, and years, and that these factors should be carefully considered in the design of biomonitoring studies.

Biomonitoring of lead, zinc, and cadmium in streams draining lead-mining and non-mining areas, Southeast Missouri, USA

USGS Publications Warehouse

Besser, J.M.; Brumbaugh, W.G.; May, T.W.; Schmitt, C.J.

2007-01-01

We evaluated exposure of aquatic biota to lead (Pb), zinc (Zn), and cadmium (Cd) in streams draining a Pb-mining district in southeast Missouri. Samples of plant biomass (detritus, periphyton, and filamentous algae), invertebrates (snails, crayfish, and riffle benthos), and two taxa of fish were collected from seven sites closest to mining areas (mining sites), four sites further downstream from mining (downstream sites), and eight reference sites in fall 2001. Samples of plant biomass from mining sites had highest metal concentrations, with means 10- to 60-times greater than those for reference sites. Mean metal concentrations in over 90% of samples of plant biomass from mining sites were significantly greater than those from reference sites. Mean concentrations of Pb, Zn, and Cd in most invertebrate samples from mining sites, and mean Pb concentrations in most fish samples from mining sites, were also significantly greater than those from reference sites. Concentrations of all three metals were lower in samples from downstream sites, but several samples of plant biomass from downstream sites had metal concentrations significantly greater than those from reference sites. Analysis of supplemental samples collected in the fall of 2002, a year of above-average stream discharge, had lower Pb concentrations and higher Cd concentrations than samples collected in 2001, near the end of a multi-year drought. Concentrations of Pb measured in fish and invertebrates collected from mining sites during 2001 and 2002 were similar to those measured at nearby sites in the 1970s, during the early years of mining in the Viburnum Trend. Results of this study demonstrate that long-term Pb mining activity in southeast Missouri has resulted in significantly elevated concentrations of Pb, Cd, and Zn in biota of receiving streams, compared to biota of similar streams without direct influence of mining. Our results also demonstrate that metal exposure in the study area differed significantly among sample types, habitats, and years, and that these factors should be carefully considered in the design of biomonitoring studies. ?? Springer Science+Business Media B.V. 2006.

Method of and apparatus for testing the integrity of filters

DOEpatents

Herman, R.L.

1985-05-07

A method of and apparatus are disclosed for testing the integrity of individual filters or filter stages of a multistage filtering system including a diffuser permanently mounted upstream and/or downstream of the filter stage to be tested for generating pressure differentials to create sufficient turbulence for uniformly dispersing trace agent particles within the airstream upstream and downstream of such filter stage. Samples of the particle concentration are taken upstream and downstream of the filter stage for comparison to determine the extent of particle leakage past the filter stage. 5 figs.

Method of and apparatus for testing the integrity of filters

DOEpatents

Herman, Raymond L [Richland, WA

1985-01-01

A method of and apparatus for testing the integrity of individual filters or filter stages of a multistage filtering system including a diffuser permanently mounted upstream and/or downstream of the filter stage to be tested for generating pressure differentials to create sufficient turbulence for uniformly dispersing trace agent particles within the airstream upstream and downstream of such filter stage. Samples of the particle concentration are taken upstream and downstream of the filter stage for comparison to determine the extent of particle leakage past the filter stage.

Methods of and apparatus for testing the integrity of filters

DOEpatents

Herman, R.L.

1984-01-01

A method of and apparatus for testing the integrity of individual filters or filter stages of a multistage filtering system including a diffuser permanently mounted upstream and/or downstream of the filter stage to be tested for generating pressure differentials to create sufficient turbulence for uniformly dispersing trace agent particles within the airstram upstream and downstream of such filter stage. Samples of the particel concentration are taken upstream and downstream of the filter stage for comparison to determine the extent of particle leakage past the filter stage.

Optimization of the extraction and purification of the compatible solute ectoine from Halomonas elongate in the laboratory experiment of a commercial production project.

PubMed

Chen, Ruifeng; Zhu, Lijun; Lv, Lihuo; Yao, Su; Li, Bin; Qian, Junqing

2017-06-01

Optimization of compatible solutes (ectoine) extraction and purification from Halomonas elongata cell fermentation had been investigated in the laboratory tests of a large scale commercial production project. After culturing H. elongata cells in developed medium at 28 °C for 23-30 h, we obtained an average yield and biomass of ectoine for 15.9 g/L and 92.9 (OD 600 ), respectively. Cell lysis was performed with acid treatment at moderate high temperature (60-70 °C). The downstream processing operations were designed to be as follows: filtration, desalination, cation exchange, extraction of crude product and three times of refining. Among which the cation exchange and extraction of crude product acquired a high average recovery rate of 95 and 96%; whereas a great loss rate of 19 and 15% was observed during the filtration and desalination, respectively. Combined with the recovering of ectoine from the mother liquor of the three times refining, the average of overall yield (referring to the amount of ectoine synthesized in cells) and purity of final product obtained were 43% and over 98%, respectively. However, key factors that affected the production efficiency were not yields but the time used in the extraction of crude product, involving the crystallization step from water, which spended 24-72 h according to the production scale. Although regarding to the productivity and simplicity on laboratory scale, the method described here can not compete with other investigations, in this study we acquired higher purity of ectoine and provided downstream processes that are capable of operating on industrial scale.

An Improved Total RNA Extraction Method for White Jelly Mushroom Tremella fuciformis Rich in Polysaccharides

PubMed Central

Zhu, Hanyu; Sun, Xueyan; Liu, Dongmei; Zheng, Liesheng; Chen, Liguo

2017-01-01

An improved method for extracting high quality and quantity RNA from a jelly mushroom and a dimorphic fungus—Tremella fuciformis which is especially rich in polysaccharides, is described. RNA was extracted from T. fuciformis mycelium M1332 and its parental monokaryotic yeast-like cells Y13 and Y32. The A260/280 and A260/230 ratios were both approximately 2, and the RNA integrity number was larger than 8.9. The yields of RNA were between 108 and 213 µg/g fresh wt. Downstream molecular applications including reverse transcriptional PCR and quantitative real-time PCR were also performed. This protocol is reliable and may be widely applicable for total RNA extraction from other jelly mushrooms or filamentous fungi rich in polysaccharides. PMID:29371814

Discrete monotron oscillator having one-half wavelength coaxial resonator with one-quarter wavelength gap spacing

DOEpatents

Carlsten, B.E.; Haynes, W.B.

1998-02-03

A discrete monotron oscillator for use in a high power microwave device is formed with a microwave oscillator having a half-wavelength resonant coaxial microwave cavity operating in fundamental TEM mode for microwave oscillation with an inner conductor defining a drift tube for propagating an electron beam and an outer conductor coaxial with the inner conductor. The inner conductor defines a modulating gap and an extraction gap downstream of the modulating gap. The modulating gap and the extraction gap connect the coaxial microwave cavity with the drift tube so that energy for the microwave oscillation is extracted from the electron beam at the extraction gap and modulates the electron beam at the modulating gap. For high power operation, an annular electron beam is used. 8 figs.

Discrete monotron oscillator having one-half wavelength coaxial resonator with one-quarter wavelength gap spacing

DOEpatents

Carlsten, Bruce E.; Haynes, William B.

1998-01-01

A discrete monotron oscillator for use in a high power microwave device is formed with a microwave oscillator having a half-wavelength resonant coaxial microwave cavity operating in fundamental TEM mode for microwave oscillation with an inner conductor defining a drift tube for propagating an electron beam and an outer conductor coaxial with the inner conductor. The inner conductor defines a modulating gap and an extraction gap downstream of the modulating gap. The modulating gap and the extraction gap connect the coaxial microwave cavity with the drift tube so that energy for the microwave oscillation is extracted from the electron beam at the extraction gap and modulates the electron beam at the modulating gap. For high power operation, an annular electron beam is used.

RNA sample preparation applied to gene expression profiling for the horse biological passport.

PubMed

Bailly-Chouriberry, Ludovic; Baudoin, Florent; Cormant, Florence; Glavieux, Yohan; Loup, Benoit; Garcia, Patrice; Popot, Marie-Agnès; Bonnaire, Yves

2017-09-01

The improvement of doping control is an ongoing race. Techniques to fight doping are usually based on the direct detection of drugs or their metabolites by analytical methods such as chromatography hyphenated to mass spectrometry after ad hoc sample preparation. Nowadays, omic methods constitute an attractive development and advances have been achieved particularly by application of molecular biology tools for detection of anabolic androgenic steroids (AAS), erythropoiesis-stimulating agent (ESA), or to control human growth hormone misuses. These interesting results across different animal species have suggested that modification of gene expression offers promising new methods of improving the window of detection of banned substances by targeting their effects on blood cell gene expression. In this context, the present study describes the possibility of using a modified version of the dedicated Human IVD (in vitro Diagnostics) PAXgene® Blood RNA Kit for horse gene expression analysis in blood collected on PAXgene® tubes applied to the horse biological passport. The commercial kit was only approved for human blood samples and has required an optimization of specific technical requirements for equine blood samples. Improvements and recommendations were achieved for sample collection, storage and RNA extraction procedure. Following these developments, RNA yield and quality were demonstrated to be suitable for downstream gene expression analysis by qPCR techniques. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Longitudinal changes in microbial planktonic communities of a French river in relation to pesticide and nutrient inputs.

PubMed

Pesce, Stéphane; Fajon, Céline; Bardot, Corinne; Bonnemoy, Frédérique; Portelli, Christophe; Bohatier, Jacques

2008-02-18

To determine the effects of anthropic activities on river planktonic microbial populations, monthly water samples were collected for 11 months from two sampling sites characterized by differing nutrient and pesticide levels. The difference in trophic level between the two stations was particularly pronounced from May to November. Total pesticide concentrations were notably higher at the downstream station from April to October with a clear predominance of herbicide residues, especially the glyphosate metabolite aminomethylphosphonic acid (AMPA). From spring, algal biomass and density were favored by the high orthophosphate concentrations recorded at the downstream location. However, isolated drops in algal biomass were recorded at this sampling station, suggesting an adverse effect of herbicides on algal communities. No major difference was observed in bacterial heterotrophic production, density, or activity (CTC reduction) between the two sampling stations. No major variation was detected using the fluorescent in situ hybridization (FISH) method, but shifts in bacterial community composition were recorded by PCR-TTGE analysis at the downstream station following high nutrient and pesticide inputs. However, outside the main anthropic pollution period, the water's chemical properties and planktonic microbial communities were very similar at the two sampling sites, suggesting a high recovery potential for this lotic system.

The Impact of Impoundment on Mercury Bioaccumulation in Fish Downstream from a Newly Constructed Reservoir, Wujiang River, Southwest China.

PubMed

Li, Sixin; Zhou, Lianfeng; Chang, Jianbo; Yang, Zhi; Hu, Juxiang; Hongjun, Wang

2017-11-01

Mercury concentrations in fish were investigated downstream from a newly impounded subtropical reservoir in August 2008. After 6-7 months of reservoir impoundment, mean mercury concentration in fish from downstream is significantly increased by 1.9 times. Not only carnivorous fish but also benthic fish had significantly higher total mercury concentrations than others. No significant correlation was found between total mercury concentrations and body length or weight of 13 fish species. Compared with the pre-impoundment, total mercury in fish from downstream is significantly increased by reservoir impoundment, but the increased rate is lower than those in subarctic and temperate areas. Fish samples surpassed the Chinese hygienic standard for tolerances of mercury in foods increased by 4.3%. More attention should be given to fish mercury levels from downstream sites to prevent possible adverse effects on the health of local people.

Novel angiogenesis inhibitory activity in cinnamon extract blocks VEGFR2 kinase and downstream signaling

USDA-ARS?s Scientific Manuscript database

VEGF is one of the most critical factors that induce angiogenesis, and has thus become an attractive target for anti-angiogenesis treatment. However, most of the current anti-VEGF agents that often cause side effects cannot be recommended for long term use. Identification of natural VEGF inhibitors...

Investigation of ion beam space charge compensation with a 4-grid analyzer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ullmann, C., E-mail: c.ullmann@gsi.de; Adonin, A.; Berezov, R.

2016-02-15

Experiments to investigate the space charge compensation of pulsed high-current heavy ion beams are performed at the GSI ion source text benches with a 4-grid analyzer provided by CEA/Saclay. The technical design of the 4-grid analyzer is revised to verify its functionality for measurements at pulsed high-current heavy ion beams. The experimental investigation of space charge compensation processes is needed to increase the performance and quality of current and future accelerator facilities. Measurements are performed directly downstream a triode extraction system mounted to a multi-cusp ion source at a high-current test bench as well as downstream the post-acceleration system ofmore » the high-current test injector (HOSTI) with ion energies up to 120 keV/u for helium and argon. At HOSTI, a cold or hot reflex discharge ion source is used to change the conditions for the measurements. The measurements were performed with helium, argon, and xenon and are presented. Results from measurements with single aperture extraction systems are shown.« less

A highly stable minimally processed plant-derived recombinant acetylcholinesterase for nerve agent detection in adverse conditions

PubMed Central

Rosenberg, Yvonne J.; Walker, Jeremy; Jiang, Xiaoming; Donahue, Scott; Robosky, Jason; Sack, Markus; Lees, Jonathan; Urban, Lori

2015-01-01

Although recent innovations in transient plant systems have enabled gram quantities of proteins in 1–2 weeks, very few have been translated into applications due to technical challenges and high downstream processing costs. Here we report high-level production, using a Nicotiana benthamiana/p19 system, of an engineered recombinant human acetylcholinesterase (rAChE) that is highly stable in a minimally processed leaf extract. Lyophylized clarified extracts withstand prolonged storage at 70 °C and, upon reconstitution, can be used in several devices to detect organophosphate (OP) nerve agents and pesticides on surfaces ranging from 0 °C to 50 °C. The recent use of sarin in Syria highlights the urgent need for nerve agent detection and countermeasures necessary for preparedness and emergency responses. Bypassing cumbersome and expensive downstream processes has enabled us to fully exploit the speed, low cost and scalability of transient production systems resulting in the first successful implementation of plant-produced rAChE into a commercial biotechnology product. PMID:26268538

A highly stable minimally processed plant-derived recombinant acetylcholinesterase for nerve agent detection in adverse conditions.

PubMed

Rosenberg, Yvonne J; Walker, Jeremy; Jiang, Xiaoming; Donahue, Scott; Robosky, Jason; Sack, Markus; Lees, Jonathan; Urban, Lori

2015-08-13

Although recent innovations in transient plant systems have enabled gram quantities of proteins in 1-2 weeks, very few have been translated into applications due to technical challenges and high downstream processing costs. Here we report high-level production, using a Nicotiana benthamiana/p19 system, of an engineered recombinant human acetylcholinesterase (rAChE) that is highly stable in a minimally processed leaf extract. Lyophylized clarified extracts withstand prolonged storage at 70 °C and, upon reconstitution, can be used in several devices to detect organophosphate (OP) nerve agents and pesticides on surfaces ranging from 0 °C to 50 °C. The recent use of sarin in Syria highlights the urgent need for nerve agent detection and countermeasures necessary for preparedness and emergency responses. Bypassing cumbersome and expensive downstream processes has enabled us to fully exploit the speed, low cost and scalability of transient production systems resulting in the first successful implementation of plant-produced rAChE into a commercial biotechnology product.

Fermentative utilization of coffee mucilage using Bacillus coagulans and investigation of down-stream processing of fermentation broth for optically pure l(+)-lactic acid production.

PubMed

Neu, Anna-Katrin; Pleissner, Daniel; Mehlmann, Kerstin; Schneider, Roland; Puerta-Quintero, Gloria Inés; Venus, Joachim

2016-07-01

In this study, mucilage, a residue from coffee production, was investigated as substrate in fermentative l(+)-lactic acid production. Mucilage was provided as liquid suspension consisting glucose, galactose, fructose, xylose and sucrose as free sugars (up to 60gL(-1)), and used directly as medium in Bacillus coagulans batch fermentations carried out at 2 and 50L scales. Using mucilage and 5gL(-1) yeast extract as additional nitrogen source, more than 40gL(-1) lactic acid was obtained. Productivity and yield were 4-5gL(-1)h(-1) and 0.70-0.77g lactic acid per g of free sugars, respectively, irrespective the scale. Similar yield was found when no yeast extract was supplied, the productivity, however, was 1.5gL(-1)h(-1). Down-stream processing of culture broth, including filtration, electrodialysis, ion exchange chromatography and distillation, resulted in a pure lactic acid formulation containing 930gL(-1)l(+)-lactic acid. Optical purity was 99.8%. Copyright © 2016 Elsevier Ltd. All rights reserved.

Using Lagrangian sampling to study water quality during downstream transport in the San Luis Drain, California, USA

USGS Publications Warehouse

Volkmar, E.C.; Dahlgren, R.A.; Stringfellow, W.T.; Henson, S.S.; Borglin, S.E.; Kendall, C.; Van Nieuwenhuyse, E. E.

2011-01-01

To investigate the mechanism for diel (24h) changes commonly observed at fixed sampling locations and how these diel changes relate to downstream transport in hypereutrophic surface waters, we studied a parcel of agricultural drainage water as it traveled for 84h in a concrete-lined channel having no additional water inputs or outputs. Algal fluorescence, dissolved oxygen, temperature, pH, conductivity, and turbidity were measured every 30min. Grab samples were collected every 2h for water quality analyses, including nutrients, suspended sediment, and chlorophyll/pheophytin. Strong diel patterns were observed for dissolved oxygen, pH, and temperature within the parcel of water. In contrast, algal pigments and nitrate did not exhibit diel patterns within the parcel of water, but did exhibit strong diel patterns for samples collected at a fixed sampling location. The diel patterns observed at fixed sampling locations for these constituents can be attributed to algal growth during the day and downstream transport (washout) of algae at night. Algal pigments showed a rapid daytime increase during the first 48h followed by a general decrease for the remainder of the study, possibly due to sedimentation and photobleaching. Algal growth (primarily diatoms) was apparent each day during the study, as measured by increasing dissolved oxygen concentrations, despite low phosphate concentrations (<0.01mgL-1). ?? 2011 Elsevier B.V.

Prevalence of sulfonamide-resistant bacteria, resistance genes and integron-associated horizontal gene transfer in natural water bodies and soils adjacent to a swine feedlot in northern Taiwan.

PubMed

Hsu, Jih-Tay; Chen, Chia-Yang; Young, Chu-Wen; Chao, Wei-Liang; Li, Mao-Hao; Liu, Yung-Hsin; Lin, Chu-Ming; Ying, Chingwen

2014-07-30

Antibiotics are commonly used in swine feed to treat and prevent disease, as well as to promote growth. Antibiotics released into the environment via wastewater could accelerate the emergence of antibiotic-resistant bacteria and resistance genes in the surrounding environment. In this study, we quantified the occurrence of sulfonamides, sulfonamide-resistant microorganisms and resistance genes in the wastewater from a swine farm in northern Taiwan and its surrounding natural water bodies and soils. Sulfonamide levels were similar in the receiving downstream and upstream river water. However, the prevalence of sulfonamide-resistant bacteria and resistance genes, as analyzed by cultivation-dependent and -independent molecular approaches, was significantly greater in the downstream compared to the upstream river water samples. Barcoded-pyrosequencing revealed a highly diverse bacterial community structure in each sample. However, the sequence identity of the sulfonamide resistance gene sul1 in the wastewater and downstream environment samples was nearly identical (99-100%). The sul1 gene, which is genetically linked to class 1 integrons, was dominant in the downstream water bodies and soils. In conclusion, the increased prevalence of sulfonamide resistance genes in the wastewater from a swine farm, independent of the persistent presence of sulfonamides, could be a potential source of resistant gene pools in the surrounding environment. Copyright © 2014 Elsevier B.V. All rights reserved.

Occurrence and partitioning of antibiotic compounds found in the water column and bottom sediments from a stream receiving two wastewater treatment plant effluents in northern New Jersey, 2008.

PubMed

Gibs, Jacob; Heckathorn, Heather A; Meyer, Michael T; Klapinski, Frank R; Alebus, Marzooq; Lippincott, Robert L

2013-08-01

An urban watershed in northern New Jersey was studied to determine the presence of four classes of antibiotic compounds (macrolides, fluoroquinolones, sulfonamides, and tetracyclines) and six degradates in the water column and bottom sediments upstream and downstream from the discharges of two wastewater treatment plants (WWTPs) and a drinking-water intake (DWI). Many antibiotic compounds in the four classes not removed by conventional WWTPs enter receiving waters and partition to stream sediments. Samples were collected at nine sampling locations on 2 days in September 2008. Two of the nine sampling locations were background sites upstream from two WWTP discharges on Hohokus Brook. Another background site was located upstream from a DWI on the Saddle River above the confluence with Hohokus Brook. Because there is a weir downstream of the confluence of Hohokus Brook and Saddle River, the DWI receives water from Hohokus Brook at low stream flows. Eight antibiotic compounds (azithromycin (maximum concentration 0.24 μg/L), ciprofloxacin (0.08 μg/L), enrofloxacin (0.015 μg/L), erythromycin (0.024 μg/L), ofloxacin (0.92 μg/L), sulfamethazine (0.018 μg/L), sulfamethoxazole (0.25 μg/L), and trimethoprim (0.14 μg/L)) and a degradate (erythromycin-H2O (0.84 μg/L)) were detected in the water samples from the sites downstream from the WWTP discharges. The concentrations of six of the eight detected compounds and the detected degradate compound decreased with increasing distance downstream from the WWTP discharges. Azithromycin, ciprofloxacin, ofloxacin, and trimethoprim were detected in stream-bottom sediments. The concentrations of three of the four compounds detected in sediments were highest at a sampling site located downstream from the WWTP discharges. Trimethoprim was detected in the sediments from a background site. Pseudo-partition coefficients normalized for streambed sediment organic carbon concentration were calculated for azithromycin, ciprofloxacin, and ofloxacin. Generally, there was good agreement between the decreasing order of the pseudo-partition coefficients in this study and the order reported in the literature. Published by Elsevier B.V.

Mercury and Methylmercury Related to Historical Mercury Mining in Three Major Tributaries to Lake Berryessa, Upper Putah Creek Watershed, California

NASA Astrophysics Data System (ADS)

Sparks, G. C.; Alpers, C. N.; Horner, T. C.; Cornwell, K.; Izzo, V.

2016-12-01

The relative contributions of total mercury (THg) and methylmercury (MeHg) from upstream historical mercury (Hg) mining districts were examined in the three largest tributaries to Lake Berryessa, a reservoir with water quality impaired by Hg. A fish consumption advisory has been issued for the reservoir; also, in a study of piscivorous birds at 25 California reservoirs, blood samples from Lake Berryessa grebes had the highest THg concentration state-wide. The third and fourth largest historical Hg-producing mining districts in California are within the study area. These mining districts are located within the Pope Creek, Upper Putah Creek, and Knoxville-Eticuera Creeks watersheds. Downstream of the reservoir, Lower Putah Creek drains into the Yolo Bypass, a major source of THg and MeHg to the Sacramento-San Joaquin Delta. Study objectives included: (1) determining if tributaries downstream of historical Hg mining districts and draining to the reservoir are continuing sources of THg and MeHg; (2) characterizing variability of water and streambed sediment parameters in upstream and downstream reaches of each creek; and (3) estimating loads of suspended sediment, THg, and MeHg entering the reservoir from each tributary. Water samples were collected from October 2012 to September 2014 during non-storm and storm events along each tributary and analyzed for general water quality field parameters; unfiltered THg and MeHg; total suspended solids; and total particulate matter. Discharge measurements were made at the time of sample collection; flow and concentration data were combined to compute daily loads. To determine spatial variability, 135 streambed sediment samples were analyzed for THg, organic content (loss on ignition), and grain-size distribution. All three tributaries contribute THg and MeHg to the reservoir. Some consistent spatial trends in THg (water) concentrations were observed over multiple sampling events; THg (water) decreased from upstream to downstream in all three tributaries. Tributary reaches with elevated THg in streambed sediment ("Hg hot spots") are near or downstream from historical Hg mines and Hg-enriched ore deposits. Future Hg load and cycling studies are needed to identify practical remediation approaches for decreasing THg and MeHg loads to Lake Berryessa.

Occurence of antibiotic compounds found in the water column and bottom sediments from a stream receiving two waste water treatment plant effluents in northern New Jersey, 2008

USGS Publications Warehouse

Gibs, Jacob; Heckathorn, Heather A.; Meyer, Michael T.; Klapinski, Frank R.; Alebus, Marzooq; Lippincott, Robert

2013-01-01

An urban watershed in northern New Jersey was studied to determine the presence of four classes of antibiotic compounds (macrolides, fluoroquinolones, sulfonamides, and tetracyclines) and six degradates in the water column and bottom sediments upstream and downstream from the discharges of two wastewater treatment plants (WWTPs) and a drinking-water intake (DWI). Many antibiotic compounds in the four classes not removed by conventional WWTPs enter receiving waters and partition to stream sediments. Samples were collected at nine sampling locations on 2 days in September 2008. Two of the nine sampling locations were background sites upstream from two WWTP discharges on Hohokus Brook. Another background site was located upstream from a DWI on the Saddle River above the confluence with Hohokus Brook. Because there is a weir downstream of the confluence of Hohokus Brook and Saddle River, the DWI receives water from Hohokus Brook at low stream flows. Eight antibiotic compounds (azithromycin (maximum concentration 0.24 μg/L), ciprofloxacin (0.08 μg/L), enrofloxacin (0.015 μg/L), erythromycin (0.024 μg/L), ofloxacin (0.92 μg/L), sulfamethazine (0.018 μg/L), sulfamethoxazole (0.25 μg/L), and trimethoprim (0.14 μg/L)) and a degradate (erythromycin-H2O (0.84 μg/L)) were detected in the water samples from the sites downstream from the WWTP discharges. The concentrations of six of the eight detected compounds and the detected degradate compound decreased with increasing distance downstream from the WWTP discharges. Azithromycin, ciprofloxacin, ofloxacin, and trimethoprim were detected in stream-bottom sediments. The concentrations of three of the four compounds detected in sediments were highest at a sampling site located downstream from the WWTP discharges. Trimethoprim was detected in the sediments from a background site. Pseudo-partition coefficients normalized for streambed sediment organic carbon concentration were calculated for azithromycin, ciprofloxacin, and ofloxacin. Generally, there was good agreement between the decreasing order of the pseudo-partition coefficients in this study and the order reported in the literature.

An integrated approach with the zebrafish model for biomonitoring of municipal wastewater effluent and receiving waters.

PubMed

Li, Caixia; Chen, Qiyu; Zhang, Xiaoyan; Snyder, Shane A; Gong, Zhiyuan; Lam, Siew Hong

2017-12-11

Comprehensive monitoring of water pollution is challenging. With the increasing amount and types of anthropogenic compounds being released into water, there are rising concerns of undetected toxicity. This is especially true for municipal wastewater effluents that are discharged to surface waters. This study was designed to integrate zebrafish toxicogenomics, targeted gene expression, and morphological analyses, for toxicity evaluation of effluent discharged from two previously characterized wastewater treatment plants (WWTPs) in Pima County, Arizona, and their receiving surface water. Zebrafish embryos were exposed to organic extracts from the WWTP1 effluent that were reconstituted to represent 1× and 0.5× of the original concentration. Microarray analyses identified deregulated gene probes that mapped to 1666, 779, and 631 unique human homologs in the 1×, 0.5×, and the intersection of both groups, respectively. These were associated with 18 cellular and molecular functions ranging from cell cycle to metabolism and are involved in the development and function of 10 organ systems including nervous, cardiovascular, haematological, reproductive, and hepatic systems. Superpathway of cholesterol biosynthesis, retinoic acid receptor activation, glucocorticoid receptor and prolactin signaling were among the top 11 perturbed canonical pathways. Real-time quantitative PCR validated the expression changes of 12 selected genes. These genes were then tested on zebrafish embryos exposed to the reconstituted extract of water sampled downstream of WWTP1 and another nearby WWTP2. The expression of several targeted genes were significantly affected by the WWTP effluents and some of the downstream receiving waters. Morphological analyses using four transgenic zebrafish lines revealed potential toxicity associated with nervous, hepatic, endothelial-vascular and myeloid systems. This study demonstrated how information can be obtained using adverse outcome pathway framework to derive biological effect-based monitoring tools. This integrated approach using zebrafish can supplement analytical chemistry to provide more comprehensive monitoring of discharged effluents and their receiving waters. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development and characterization of a pre-treatment procedure to eliminate human monoclonal antibody therapeutic drug and matrix interference in cell-based functional neutralizing antibody assays.

PubMed

Xu, Weifeng; Jiang, Hao; Titsch, Craig; Haulenbeek, Jonathan R; Pillutla, Renuka C; Aubry, Anne-Françoise; DeSilva, Binodh S; Arnold, Mark E; Zeng, Jianing; Dodge, Robert W

2015-01-01

Biological therapeutics can induce an undesirable immune response resulting in the formation of anti-drug antibodies (ADA), including neutralizing antibodies (NAbs). Functional (usually cell-based) NAb assays are preferred to determine NAb presence in patient serum, but are often subject to interferences from numerous serum factors, such as growth factors and disease-related cytokines. Many functional cell-based NAb assays are essentially drug concentration assays that imply the presence of NAbs by the detection of small changes in functional drug concentration. Any drug contained in the test sample will increase the total amount of drug in the assay, thus reducing the sensitivity of NAb detection. Biotin-drug Extraction with Acid Dissociation (BEAD) has been successfully applied to extract ADA, thereby removing drug and other interfering factors from human serum samples. However, to date there has been no report to estimate the residual drug level after BEAD treatment when the drug itself is a human monoclonal antibody; mainly due to the limitation of traditional ligand-binding assays. Here we describe a universal BEAD optimization procedure for human monoclonal antibody (mAb) drugs by using a LC-MS/MS method to simultaneously measure drug (a mutant human IgG4), NAb positive control (a mouse IgG), and endogenous human IgGs as an indicator of nonspecific carry-over in the BEAD eluate. This is the first report demonstrating that residual human mAb drug level in clinical sample can be measured after BEAD pre-treatment, which is critical for further BEAD procedure optimization and downstream immunogenicity testing. Copyright © 2014 Elsevier B.V. All rights reserved.

Hydroxylysyl pyridinoline cross-link concentration affects the textural properties of fresh and smoked Atlantic salmon (Salmo salar L.) flesh.

PubMed

Li, Xuejun; Bickerdike, Ralph; Lindsay, Emma; Campbell, Patrick; Nickell, David; Dingwall, Alastair; Johnston, Ian A

2005-08-24

A simple HPLC method is presented to quantify the low concentration of hydroxylysyl pyridinoline (PYD) cross-links in Atlantic salmon (Salmo salar L.) muscle. The method involved the extraction of tissue with NaOH prior to hydrolysis, which greatly reduced the amount of protein to be hydrolyzed and made downstream operations easier and more reproducible. The concentration of PYD was 426 pmol g(-)(1) dry mass muscle in post-rigor muscle stored at 0 degrees C and sampled 3 d after death. Hydroxproline (HYP) concentration was determined following NaOH extraction as a measure of collagen content. In post-rigor samples, the alkaline-insoluble HYP fraction comprised 18.3% of the total HYP. Scanning electron microscopy revealed shrinkage of muscle fibers and a retraction of the connective tissue matrix in smoked salmon. PYD concentration was relatively resistant to processing to the smoked product, decreasing by around 11.7%, as compared to a 22.2% decrease in HYP. There was a positive correlation between PYD concentration and the firmness of post-rigor muscle samples as measured by an instrumental texture analyzer, explaining 25% of the total variation. A weaker but still significant correlation was found between PYD concentration and firmness in the smoked product. There was no relationship between fillet firmness and total collagen concentration, although the correlation with HYP in the alkaline-insoluble fraction was significant at the 6% level (P = 0.057). Our results indicate that only 1-3% of collagen molecules are linked by nonreducible mature cross-links in harvest size farmed Atlantic salmon and that PYD concentration is an important raw material characteristic for flesh quality.

40 CFR 90.327 - Sampling system requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... each component (pump, sample line section, filters, and so forth) in the heated portion of the sampling... largest thermal mass and the oven temperature need be measured. (b) If water is removed by condensation, monitor the sample gas temperature or sample dew point either within the water trap or downstream. It may...

40 CFR 90.327 - Sampling system requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... each component (pump, sample line section, filters, and so forth) in the heated portion of the sampling... largest thermal mass and the oven temperature need be measured. (b) If water is removed by condensation, monitor the sample gas temperature or sample dew point either within the water trap or downstream. It may...

40 CFR 90.327 - Sampling system requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... each component (pump, sample line section, filters, and so forth) in the heated portion of the sampling... largest thermal mass and the oven temperature need be measured. (b) If water is removed by condensation, monitor the sample gas temperature or sample dew point either within the water trap or downstream. It may...

Analysis of dissolved gas and fluid chemistry in mountainous region of Goaping river watershed in southern Taiwan

NASA Astrophysics Data System (ADS)

Tang, Kai-Wen; Chen, Cheng-Hong; Liu, Tsung-Kwei

2016-04-01

Annual rainfall in Taiwan is up to 2500 mm, about 2.5 times the average value of the world. However due to high topographic relief of the Central Mountain Range in Taiwan, groundwater storage is critical for water supply. Mountain region of the Goaping river watershed in southern Taiwan is one of the potential areas to develop groundwater recharge model. Therefore the target of this study is to understand sources of groundwater and surface water using dissolved gas and fluid chemistry. Four groundwater and 6 surface water samples were collected from watershed, 5 groundwater and 13 surface water samples were collected from downstream. All samples were analyzed for stable isotopes (hydrogen and oxygen), dissolved gases (including nitrogen, oxygen, argon, methane and carbon dioxide), noble gases (helium and radon) and major ions. Hydrogen and oxygen isotopic ratios of surface water and groundwater samples aligned along meteoric water line. For surface water, dissolved gases are abundant in N2 (>80%) and O2 (>10%); helium isotopic ratio is approximately equal to 1 RA (RA is 3He/4He ratio of air); radon-222 concentration is below the detection limit (<200 Bq/m3); and concentrations of major anions and cations are low (Na+ <20 ppm, Ca2+ < 60 ppm, Cl- <2 ppm). All these features indicate that surface waters are predominately recharged by precipitation. For groundwater, helium isotopic ratios (0.9˜0.23 RA) are lower and radon-222 concentrations (300˜6000 Bq/m3) are much higher than the surface water. Some samples have high amounts of dissolved gases, such as CH4 (>20%) or CO2 (>10%), most likely contributed by biogenic or geogenic sources. On the other hand, few samples that have temperature 5° higher than the average of other samples, show significantly high Na+ (>1000 ppm), Ca2+ (>150 ppm) and Cl- (>80 ppm) concentrations. An interaction between such groundwater and local hot springs is inferred. Watershed and downstream samples differ in dissolved gas species and fluid chemistry for groundwater and surface water. The higher hydrogen and oxygen isotopic ratios for surface water from downstream are most probably caused by evaporation. Low radon-222 concentrations of some groundwater from downstream may represent sources from different aquifers. Therefore, we conclude that surface water from downstream are recharged directly from its watershed, but groundwater are influenced by the local geological environment. Keywords: groundwater, dissolved gas, noble gas, radon in water, 3He/4He

Persistence and stability of fish community structure in a southwest New York stream

USGS Publications Warehouse

Hansen, Michael J.; Ramm, Carl W.

1994-01-01

We used multivariate and nonparametric statistics to examine persistence and stability of fish species in the upper 43 km of French Creek, New York. Species occurred in upstream and downstream groups in 1937 that persisted in 1979. However, the downstream group expanded its range in the drainage from 1937 to 1979 at the expense of the upstream group. A dam prevented further upstream expansion of the downstream group. Ranks of species abundances were stable, as tests of group similarity were significant. The abundances and distributions of benthic species were stable across seven sampling dates in 1980 despite several floods and repeated removals by sampling that could have altered community structure. We conclude that the fish community in French Creek persisted and was stable over the 42-yr interval, 1937-1979, and that abundances of benthic species were stable in summer 1980.

Occurrence of pharmaceuticals, hormones, and organic wastewater compounds in Pennsylvania waters, 2006-09

USGS Publications Warehouse

Reif, Andrew G.; Crawford, J. Kent; Loper, Connie A.; Proctor, Arianne; Manning, Rhonda; Titler, Robert

2012-01-01

Concern over the presence of contaminants of emerging concern, such as pharmaceutical compounds, hormones, and organic wastewater compounds (OWCs), in waters of the United States and elsewhere is growing. Laboratory techniques developed within the last decade or new techniques currently under development within the U.S. Geological Survey now allow these compounds to be measured at concentrations in nanograms per liter. These new laboratory techniques were used in a reconnaissance study conducted by the U.S. Geological Survey, in cooperation with the Pennsylvania Department of Environmental Protection, to determine the occurrence of contaminants of emerging concern in streams, streambed sediment, and groundwater of Pennsylvania. Compounds analyzed for in the study are pharmaceuticals (human and veterinary drugs), hormones (natural and synthetic), and OWCs (detergents, fragrances, pesticides, industrial compounds, disinfectants, polycyclic aromatic hydrocarbons, fire retardants and plasticizers). Reconnaissance sampling was conducted from 2006 to 2009 to identify contaminants of emerging concern in (1) groundwater from wells used to supply livestock, (2) streamwater upstream and downstream from animal feeding operations, (3) streamwater upstream from and streamwater and streambed sediment downstream from municipal wastewater effluent discharges, (4) streamwater from sites within 5 miles of drinking-water intakes, and (5) streamwater and streambed sediment where fish health assessments were conducted. Of the 44 pharmaceutical compounds analyzed in groundwater samples collected in 2006 from six wells used to supply livestock, only cotinine (a nicotine metabolite) and the antibiotics tylosin and sulfamethoxazole were detected. The maximum concentration of any contaminant of emerging concern was 24 nanograms per liter (ng/L) for cotinine, and was detected in a groundwater sample from a Lebanon County, Pa., well. Seven pharmaceutical compounds including acetaminophen, caffeine, carbamazepine, and the four antibiotics tylosin, sulfadimethoxine, sulfamethoxazole, and oxytetracycline were detected in streamwater samples collected in 2006 from six paired stream sampling sites located upstream and downstream from animal-feeding operations. The highest reported concentration of these seven compounds was for the antibiotic sulfamethoxazole (157 ng/L), in a sample from the downstream site on Snitz Creek in Lancaster County, Pa. Twenty-one pharmaceutical compounds were detected in streamwater samples collected in 2006 from five paired stream sampling sites located upstream or downstream from a municipal wastewater-effluent-discharge site. The most commonly detected compounds and maximum concentrations were the anticonvulsant carbamazepine, 276 ng/L; the antihistamine diphenhydramine, 135 ng/L; and the antibiotics ofloxacin, 329 ng/L; sulfamethoxazole, 1,340 ng/L; and trimethoprim, 256 ng/L. A total of 51 different contaminants of emerging concern were detected in streamwater samples collected from 2007 through 2009 at 13 stream sampling sites located downstream from a wastewater-effluent-discharge site. The concentrations and numbers of compounds detected were higher in stream sites downstream from a wastewater-effluent-discharge site than in stream sites upstream from a wastewater-effluent-discharge site. This finding indicates that wastewater-effluent discharges are a source of contaminants of emerging concern; these contaminants were present more frequently in the streambed-sediment samples than in streamwater samples. Antibiotic compounds were often present in both the streamwater and streambed-sediment samples, but many OWCs were present exclusively in the streambed-sediment samples. Compounds with endocrine disrupting potential including detergent metabolites, pesticides, and flame retardants, were present in the streamwater and streambed-sediment samples. Killinger Creek, a stream where wastewater-effluent discharges contribute a large percentage of the total flow, stands out as a stream with particularly high numbers of compounds detected and detected at the highest concentrations measured in the reconnaissance sampling. Nineteen contaminants of emerging concern were detected in streamwater samples collected quarterly from 2007 through 2009 at 27 stream sites within 5 miles of a drinking-water intake. The number of contaminants and the concentrations detected at the stream sites within 5 miles of drinking-water intakes were generally very low (concentrations less than 50 ng/L), much lower than those at sites downstream from a wastewater-effluent discharge. The most commonly detected compounds and maximum concentrations were caffeine, 517 ng/L; carbamazepine, 95 ng/L; sulfamethoxazole, 146 ng/L; and estrone, 3.15 ng/L. The concentrations and frequencies of detection of some of the contaminants of emerging concern appear to vary by season, which could be explained by compound use, flow regime, or differences in degradation rates. Concentrations of some contaminants were associated with lower flows as a result of decreased in-stream dilution of wastewater effluents or other contamination sources. Twenty-two contaminants of emerging concern were detected once each in streamwater samples collected in 2007 and 2008 from 16 fish-health stream sites located statewide. The highest concentrations were for the OWCs, including flame retardants tri(2-butoxyethyl)phosphate (604 ng/L) and tri(2-chloroethyl)phosphate (272 ng/L) and the fragrance isoquinoline (330 ng/L). Far fewer numbers of contaminants of emerging concern were detected at the fish-health sites than at the wastewater-effluent-discharge sites. Most of the fish-health sites were not located directly downstream from a wastewater-effluent discharge, but there were multiple wastewater-effluent discharges in the drainage basins upstream from the sampling sites. No distinct pattern of contaminant occurrence could be discerned for the fish-health stream sites

Nutrient Concentrations, Loads, and Yields in the Eucha-Spavinaw Basin, Arkansas and Oklahoma, 2002-2004

USGS Publications Warehouse

Tortorelli, Robert L.

2006-01-01

The City of Tulsa, Oklahoma, uses Lake Eucha and Spavinaw Lake in the Eucha-Spavinaw basin in northwestern Arkansas and northeastern Oklahoma for public water supply. Taste and odor problems in the water attributable to blue-green algae have increased in frequency over time. Changes in the algae community in the lakes may be attributable to increases in nutrient levels in the lakes, and in the waters feeding the lakes. The U.S. Geological Survey, in cooperation with the City of Tulsa, conducted an investigation to summarize nitrogen and phosphorus concentrations and provide estimates of nitrogen and phosphorus loads, yields, and flow-weighted concentrations in the Eucha-Spavinaw basin for a 3-year period from January 2002 through December 2004. This report provides information needed to advance knowledge of the regional hydrologic system and understanding of hydrologic processes, and provides hydrologic data and results useful to multiple parties for interstate compacts. Nitrogen and phosphorus concentrations were significantly greater in runoff samples than in base-flow samples at Spavinaw Creek near Maysville, Arkansas; Spavinaw Creek near Colcord, Oklahoma, and Beaty Creek near Jay, Oklahoma. Runoff concentrations were not significantly greater than in base-flow samples at Spavinaw Creek near Cherokee, Arkansas; and Spavinaw Creek near Sycamore, Oklahoma. Nitrogen concentrations in base-flow samples significantly increased in the downstream direction in Spavinaw Creek from the Maysville to Sycamore stations then significantly decreased from the Sycamore to the Colcord stations. Nitrogen in base-flow samples from Beaty Creek was significantly less than in those from Spavinaw Creek. Phosphorus concentrations in base-flow samples significantly increased from the Maysville to Cherokee stations in Spavinaw Creek, probably due to a point source between those stations, then significantly decreased downstream from the Cherokee to Colcord stations. Phosphorus in base-flow samples from Beaty Creek was significantly less than phosphorus in base-flow samples from Spavinaw Creek downstream from the Maysville station. Nitrogen concentrations in runoff samples were not significantly different among the stations on Spavinaw Creek; however, the concentrations at Beaty Creek were significantly less than at all other stations. Phosphorus concentrations in runoff samples were not significantly different among the three downstream stations on Spavinaw Creek, and not significantly different at the Maysville station on Spavinaw Creek and the Beaty Creek station. Phosphorus and nitrogen concentrations in runoff samples from all stations generally increased with increasing streamflow. Estimated mean annual nitrogen total loads from 2002-2004 were substantially greater at the Spavinaw Creek stations than at Beaty Creek and increased in a downstream direction from Maysville to Colcord in Spavinaw Creek, with the load at the Colcord station about 2 times that of Maysville station. Estimated mean annual nitrogen base-flow loads at the Spavinaw Creek stations were about 5 to 11 times greater than base-flow loads at Beaty Creek. The runoff component of the annual nitrogen total load for Beaty Creek was 85 percent, whereas, at the Spavinaw Creek stations, the range in the runoff component was 60 to 66 percent. Estimated mean annual phosphorus total loads from 2002-2004 were greater at the Spavinaw Creek stations from Cherokee to Colcord than at Beaty Creek and increased in a downstream direction from Maysville to Colcord in Spavinaw Creek, with the load at the Colcord station about 2.5 times that of Maysville station. Estimated mean annual phosphorus base-flow loads at the Spavinaw Creek stations were about 2.5 to 19 times greater than at Beaty Creek. Phosphorus base-flow loads increased about 8 times from Maysville to Cherokee in Spavinaw Creek; the base-flow loads were about the same at the three downstream stations. The runoff component

Contaminants in ospreys from the Pacific Northwest: I. Trends and Patterns in polychlorinated dibenzo-p-dioxins and -dibenzofurans in eggs and plasma

USGS Publications Warehouse

Elliott, J.E.; Machmer, M.M.; Henny, Charles J.; Wilson, L.K.; Norstrom, R.J.

1998-01-01

Osprey (Pandion haliaetus) eggs were collected from 1991 to 1997 at nests (na??=a??121) upstream and downstream of bleached kraft pulp mills and at reference sites in the Fraser and Columbia River drainage systems of British Columbia, Washington, and Oregon. Blood samples were collected from nestling ospreys during the 1992 breeding season on the Thompson River. Samples were analyzed for polychlorinated dibenzo-p-dioxins (PCDDs) and -dibenzofurans (PCDFs). Mean concentrations of 2,3,7,8-TCDD were significantly higher in eggs collected in 1991 at downstream compared to upstream nests near pulp mills at Kamloops and Castlegar, British Columbia. There were no significant temporal trends in 2,3,7,8-TCDD, -TCDF or other measured compounds at a sample of nests monitored between 1991 and 1994 downstream of the Castlegar pulp mill, despite changes in bleaching technology (CIO2 substitution). However, by 1997 concentrations of 2,3,7,8-TCDD and -TCDF were significantly lower than previous years in nests sampled downstream at both Castlegar and Kamloops. An unusual pattern of higher chlorinated PCDDs and PCDFs was found in many of the osprey eggs collected in this study, and considerable individual variation in the pattern existed among eggs from the same site. For example, eggs from four different nests at one study area (Quesnel) on the Fraser River had concentrations of 1,2,3,4,6,7,8-HpCDD ranging from <1 to 1,100 ng/kg and OCDD from <1 to 7,000 ng/kg wet weight. Higher mean concentrations of HpCDD and OCDD were found in eggs from the Thompson River, a tributary of the Fraser, compared to the Columbia River, and concentrations were generally higher at nests upstream of pulp mills. In plasma samples, 1,2,3,4,6,7,8-HpCDD and OCDD were the main compounds detected, with no significant differences measured between samples upstream versus downstream or earlier versus later in the breeding season. Use of chlorophenolic wood preservatives by lumber processors was considered the main source of higher chlorinated PCDD/Fs throughout the systems, based on patterns of trace PCDFs in eggs and significant correlations between egg concentrations of pentachlorophenol and both HpCDD (ra??=a??0.891, pa??

Contaminants in ospreys from the Pacific Northwest: I. Trends and patterns in polychlorinated dibenzo-p-dioxins and -dibenzofurans in eggs and plasma.

PubMed

Elliott, J E; Machmer, M M; Henny, C J; Wilson, L K; Norstrom, R J

1998-11-01

Osprey (Pandion haliaetus) eggs were collected from 1991 to 1997 at nests (n = 121) upstream and downstream of bleached kraft pulp mills and at reference sites in the Fraser and Columbia River drainage systems of British Columbia, Washington, and Oregon. Blood samples were collected from nestling ospreys during the 1992 breeding season on the Thompson River. Samples were analyzed for polychlorinated dibenzo-p-dioxins (PCDDs) and -dibenzofurans (PCDFs). Mean concentrations of 2,3,7,8-TCDD were significantly higher in eggs collected in 1991 at downstream compared to upstream nests near pulp mills at Kamloops and Castlegar, British Columbia. There were no significant temporal trends in 2,3,7,8-TCDD, -TCDF or other measured compounds at a sample of nests monitored between 1991 and 1994 downstream of the Castlegar pulp mill, despite changes in bleaching technology (CIO2 substitution). However, by 1997 concentrations of 2, 3,7,8-TCDD and -TCDF were significantly lower than previous years in nests sampled downstream at both Castlegar and Kamloops. An unusual pattern of higher chlorinated PCDDs and PCDFs was found in many of the osprey eggs collected in this study, and considerable individual variation in the pattern existed among eggs from the same site. For example, eggs from four different nests at one study area (Quesnel) on the Fraser River had concentrations of 1,2,3,4,6,7,8-HpCDD ranging from <1 to 1,100 ng/kg and OCDD from <1 to 7,000 ng/kg wet weight. Higher mean concentrations of HpCDD and OCDD were found in eggs from the Thompson River, a tributary of the Fraser, compared to the Columbia River, and concentrations were generally higher at nests upstream of pulp mills. In plasma samples, 1,2,3,4,6,7,8-HpCDD and OCDD were the main compounds detected, with no significant differences measured between samples upstream versus downstream or earlier versus later in the breeding season. Use of chlorophenolic wood preservatives by lumber processors was considered the main source of higher chlorinated PCDD/Fs throughout the systems, based on patterns of trace PCDFs in eggs and significant correlations between egg concentrations of pentachlorophenol and both HpCDD (r = 0.891, p < 0.01) and OCDD (r = 0.870, p < 0.01).

Gas phase oxidation downstream of a catalytic combustor

NASA Technical Reports Server (NTRS)

Tien, J. S.; Anderson, D. N.

1979-01-01

Effect of the length available for gas-phase reactions downstream of the catalytic reactor on the emission of CO and unburned hydrocarbons was investigated. A premixed, prevaporized propane/air feed to a 12/cm/diameter catalytic/reactor test section was used. The catalytic reactor was made of four 2.5 cm long monolithic catalyst elements. Four water cooled gas sampling probes were located at positions between 0 and 22 cm downstream of the catalytic reactor. Measurements of unburned hydrocarbon, CO, and CO2 were made. Tests were performed with an inlet air temperature of 800 K, a reference velocity of 10 m/s, pressures of 3 and 600,000 Pa, and fuel air equivalence ratios of 0.14 to 0.24. For very lean mixtures, hydrocarbon emissions were high and CO continued to be formed downstream of the catalytic reactor. At the highest equivalence ratios tested, hydrocarbon levels were much lower and CO was oxidized to CO2 in the gas phase downstream. To achieve acceptable emissions, a downstream region several times longer than the catalytic reactor could be required.

Kinetics of Hydrogen Oxidation Downstream of Lean Propane and Hydrogen Flames

NASA Technical Reports Server (NTRS)

Fine, Burton

1961-01-01

The decay of hydrogen was measured downstream of lean, flat, premixed hydrogen and propane-air flames seated on cooled porous burners. Experimental variables included temperature, pressure, initial equivalence ratio and diluent. Sampling of burned gas was done through uncooled quartz orifice probes, and the analysis was based on gas chromatography. An approximate treatment of the data in which diffusion was neglected led to the following rate expression for the zone downstream of hydrogen flames d[H (sub 2)] divided by (d times t) equals 1.7 times 10 (sup 10) [H (sub 2)] (sup 3) divided by (sub 2) [O (sub 2)]e (sup (-8100 divided by RT)) moles per liters per second. On the basis of a rate expression of this form, the specific rate constant for the reaction downstream of hydrogen flames was about three times as great as that determined downstream of propane flames. This result was explained on the basis of the existence of a steady state between hydrogen and carbon monoxide in the burned gas downstream of propane flames.

Polychlorinated Biphenyls (PCBs) in Catfish and Carp Collected from the Rio Grande Upstream and Downstream of Los Alamos National Laboratory: Revision 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilbert J. Gonzales

2008-05-12

Concern has existed for years that the Los Alamos National Laboratory (LANL), a complex of nuclear weapons research and support facilities, has released polychlorinated biphenyls (PCBs) to the environment that may have reached adjacent bodies of water through canyons that connect them. In 1997, LANL's Ecology Group began measuring PCBs in fish in the Rio Grande upstream and downstream of ephemeral streams that cross LANL and later began sampling fish in Abiquiu and Cochiti reservoirs, which are situated on the Rio Chama and Rio Grande upstream and downstream of LANL, respectively. In 2002, we electroshocked channel catfish (Ictalurus punctatus) andmore » common carp (Carpiodes carpio) in the Rio Grande upstream and downstream of LANL and analyzed fillets for PCB congeners. We also sampled soils along the Rio Chama and Rio Grande drainages to discern whether a background atmospheric source of PCBs that could impact surface water adjacent to LANL might exist. Trace concentrations of PCBs measured in soil (mean = 4.7E-05 {micro}g/g-ww) appear to be from background global atmospheric sources, at least in part, because the bimodal distribution of low-chlorinated PCB congeners and mid-chlorinated PCB congeners in the soil samples is interpreted to be typical of volatilized PCB congeners that are found in the atmosphere and dust from global fallout. Upstream catfish (n = 5) contained statistically (P = 0.047) higher concentrations of total PCBs (mean = 2.80E-02 {micro}g/g-ww) than downstream catfish (n = 10) (mean = 1.50E-02 {micro}g/g-ww). Similarly, upstream carp (n = 4) contained higher concentrations of total PCBs (mean = 7.98E-02 {micro}g/g-ww) than downstream carp (n = 4) (3.07E-02 {micro}g/g-ww); however, the difference was not statistically significant (P = 0.42). The dominant PCB homologue in all fish samples was hexachlorobiphenyls. Total PCB concentrations in fish in 2002 are lower than 1997; however, differences in analytical methods and other uncertainties exist. A review of historical quantitative PCB data for fish from the Rio Grande and Abiquiu and Cochiti reservoirs does not indicate a distinct contribution of PCBs from LANL to fish in the Rio Grande or Cochiti. Analysis of homologue patterns for fish does not provide sufficient evidence of a LANL contribution. Nevertheless, concentrations of PCBs in fillets of fish sampled from the Rio Grande are indicative of potential adverse chronic health impact from consumption of these fish on a long-term basis.« less

Prion extraction methods: comparison of bead beating, ultrasonic disruption and repeated freeze-thaw methodologies for the recovery of functional renilla-prion fusion protein from bacteria

USDA-ARS?s Scientific Manuscript database

Molecular DNA technology allows for production of mammalian proteins in bacteria at sufficient quantities for downstream use and analysis. Variation in design and engineering of DNA expression vectors imparts selective alterations resulting in the generation of fusion proteins with intrinsic report...

Sampling and detection of airborne influenza virus towards point-of-care applications.

PubMed

Ladhani, Laila; Pardon, Gaspard; Meeuws, Hanne; van Wesenbeeck, Liesbeth; Schmidt, Kristiane; Stuyver, Lieven; van der Wijngaart, Wouter

2017-01-01

Airborne transmission of the influenza virus contributes significantly to the spread of this infectious pathogen, particularly over large distances when carried by aerosol droplets with long survival times. Efficient sampling of virus-loaded aerosol in combination with a low limit of detection of the collected virus could enable rapid and early detection of airborne influenza virus at the point-of-care setting. Here, we demonstrate a successful sampling and detection of airborne influenza virus using a system specifically developed for such applications. Our system consists of a custom-made electrostatic precipitation (ESP)-based bioaerosol sampler that is coupled with downstream quantitative polymerase chain reaction (qPCR) analysis. Aerosolized viruses are sampled directly into a miniaturized collector with liquid volume of 150 μL, which constitutes a simple and direct interface with subsequent biological assays. This approach reduces sample dilution by at least one order of magnitude when compared to other liquid-based aerosol bio-samplers. Performance of our ESP-based sampler was evaluated using influenza virus-loaded sub-micron aerosols generated from both cultured and clinical samples. Despite the miniaturized collection volume, we demonstrate a collection efficiency of at least 10% and sensitive detection of a minimum of 3721 RNA copies. Furthermore, we show that an improved extraction protocol can allow viral recovery of down to 303 RNA copies and a maximum sampler collection efficiency of 47%. A device with such a performance would reduce sampling times dramatically, from a few hours with current sampling methods down to a couple of minutes with our ESP-based bioaerosol sampler.

40 CFR 91.327 - Sampling system requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., sample line section, filters, and so forth) in the heated portion of the sampling system that has a... mass and the oven temperature need be measured. (b) If water is removed by condensation, monitor the sample gas temperature or sample dew point either within the water trap or downstream. It may not exceed...

40 CFR 91.327 - Sampling system requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., sample line section, filters, and so forth) in the heated portion of the sampling system that has a... mass and the oven temperature need be measured. (b) If water is removed by condensation, monitor the sample gas temperature or sample dew point either within the water trap or downstream. It may not exceed...

40 CFR 91.327 - Sampling system requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., sample line section, filters, and so forth) in the heated portion of the sampling system that has a... mass and the oven temperature need be measured. (b) If water is removed by condensation, monitor the sample gas temperature or sample dew point either within the water trap or downstream. It may not exceed...

Scaling-up and ionic liquid-based extraction of pectinases from Aspergillus flavipes cultures.

PubMed

Wolf-Márquez, Vicente E; Martínez-Trujillo, M Aurora; Aguilar Osorio, Guillermo; Patiño, Faustino; Álvarez, María S; Rodríguez, Ana; Sanromán, M Ángeles; Deive, Francisco J

2017-02-01

The viability of the scaling-up of pectinases production by Aspergillus flavipes at 5L-bioreactor scale has been demonstrated by keeping constant the power input, and a drastic increase in the endo- and exopectinolytic enzyme production was recorded (7- and 40-fold, respectively). The main process variables were modelled by means of logistic and Gompertz equations. In order to overcome the limitations of the conventional downstream strategies, a novel extraction strategy was proposed on the basis of the adequate salting-out potential of two biocompatible cholinium-based ionic liquids (N 1112OH Cl and N 1112OH H 2 PO 4 ) in aqueous solutions of Tergitol, reaching more than 90% of extraction. Copyright © 2016 Elsevier Ltd. All rights reserved.

Time Series Analysis of Heavy Metal Concentrations along the Watershed Gradient in Cameron Highlands: Geospatial Approaches

NASA Astrophysics Data System (ADS)

Haron, S. H.; Ismail, B. S.; Mispan, M. R.; Abd Rahman, N. F.; Khalid, K.; Rasid, M. Z. Abdul; Sidek, L. M.

2016-03-01

Heavy metal, particularly cadmium, lead, and arsenic, constitute a significant potential threat to human health. Some metals are extremely toxic to humans and the toxic heavy metals of greatest concern include cadmium, lead, and arsenic. The objective of the study conducted was to determine the accumulation and distribution status of heavy metal cadmium (Cd) in the sediment of Bertam River from September 2014 to February 2015 in the agricultural areas of Cameron Highlands, Malaysia. The sediment samples were collected randomly in three replicates from ten sampling points in the agricultural areas of Cameron Highlands. The heavy metals in the sediment were extracted using the wet acid method and the sample concentrations are then tested for metal concentrations by the spectrography method using Inductively Coupled Plasma (ICP) spectrography. Inverse distance weighting (IDW) was used to create a map of metal concentrations for a point on the polygon dataset spatial interpolation. There is an increasing trend of Cd from the upstream to downstream stations along Bertam River during the rainy season. The activity range of Cd is 0.07 to 2.83 µg/g during the rainy season, whereas, during the dry season, Cd activity ranged from 0.26-0.83µg/g.

System automatically supplies precise analytical samples of high-pressure gases

NASA Technical Reports Server (NTRS)

Langdon, W. M.

1967-01-01

High-pressure-reducing and flow-stabilization system delivers analytical gas samples from a gas supply. The system employs parallel capillary restrictors for pressure reduction and downstream throttling valves for flow control. It is used in conjunction with a sampling valve and minimizes alterations of the sampled gas.

Water quality in the New River from Calexico to the Salton Sea, Imperial County, California

USGS Publications Warehouse

Setmire, James G.

1984-01-01

The New River enters the United States at Calexico, Calif., after it crosses the international boundary. Water-quality data from routine collection indicated that the New River was degraded by high organic and bacterial content. Intensive sampling for chemical and physical constituents and properties of the river was done May 9-13, 1977, to quantify the chemical composition of the water and to identify water-quality problems. Concentrations of total organic carbon in the New River at Calexico ranged from 80 to 161 milligrams per liter and dissolved organic carbon ranged from 34 to 42 milligrams per liter; the maximum chemical oxygen demand was 510 milligrams per liter. Intensive sampling for chemical and biological characteristics was done in the New River from May 1977 to June 1978 to determine the occurrence of the organic material and its effects on downstream water quality. Dissolved-oxygen concentration was measured along longitudinal profiles of the river from Calexico to the Salton Sea. A dissolved-oxygen sag downstream from the Calexico gage varied seasonally. The sag extended farther downstream and had lower concentrations of dissolved oxygen during the summer months than during the winter months. The sag of zero dissolved-oxygen concentration extended 26 miles in July 1977. In December 1976, the sag extended 20 miles but the minimum dissolved-oxygen concentration was 2.5 milligrams per liter. The greatest diel (24-hour) variation in dissolved-oxygen concentration occurred in the reach from the Calexico gage to Lyons Crossing, 8.8 miles downstream. High concentrations of organic material were detected as far as Highway 80, 19.5 miles downstream from the international boundary. Biological samples analyzed for benthic invertebrates showed that water at the Calexico and Lyons Crossing sites, nearest the international boundary, was of such poor quality that very few bottom-dwelling organisms could survive. Although the water was of poor quality at Keystone Road, 36 miles downstream, it was able to support a benthic community. The April sample had more than 9,150 organisms on a multiplate sampler, 8,770 of which were of one species. Farther downstream at the Westmorland gage, the water quality, as indicated by the number and diversity of organisms, had improved over that at the Keystone site. The Alamo River at its outlet to the Salton Sea--the control site--had the greatest diversity of all the study sites. This diversity, when compared with the diversity at the Westmorland gage, indicated that the effects of the degraded water quality observed at the New River at Calexico are detected as far as 62 miles downstream. Standard bacteria indicator tests indicate that fecal contamination exists in the New River. Counts of fecal coliform bacteria ranged from 180,000 to 2,800,000 colonies per 100 milliliters for the 20-mile reach from Calexico to Highway 80, and fecal streptococcal bacteria ranged from 5,000 to 240,000 colonies per 100 milliliters.

Water Quality and Biological Characteristics of the Middle Fork of the Saline River, Arkansas, 2003-06

USGS Publications Warehouse

Galloway, Joel M.; Petersen, James C.; Shelby, Erica L.; Wise, Jim A.

2008-01-01

The Middle Fork of the Saline River has many qualities that have been recognized by State and Federal agencies. The Middle Fork provides habitat for several rare aquatic species and is part of a larger stream system (the Upper Saline River) that is known for relatively high levels of species richness and relatively high numbers of species of concern. Water-quality samples were collected and streamflow was measured by the U.S. Geological Survey at three sites in the Middle Fork Basin between October 2003 and October 2006. The Arkansas Department of Environmental Quality collected discrete synoptic water-quality samples from eight sites between January 2004 and October 2006. The Arkansas Department of Environmental Quality also sampled fish (September-October 2003) and benthic macroinvertebrate communities (September 2003-December 2005) at five sites. Streamflow varied annually among the three streamflow sites from October 2003 to October 2006. The mean annual streamflow for Brushy Creek near Jessieville (MFS06) was 0.72 cubic meters per second for water years 2004-2006. The Middle Fork below Jessieville (MFS05) had a mean annual streamflow of 1.11 cubic meters per second for water years 2004-2006. The Middle Fork near Owensville (MFS02), the most downstream site, had a mean annual streamflow of 3.01 cubic meters per second. The greatest streamflows at the three sites generally occurred in the winter and spring and the least in the summer. Nutrient dynamics in the Middle Fork are controlled by activities in the basin and processes that occur in the stream. Point sources and nonpoint sources of nutrients occur in the Middle Fork Basin that could affect the water-quality. Nitrogen and phosphorus concentrations generally were greatest in Mill Creek (MFS04E) and in the Middle Fork immediately downstream from the confluence with Mill Creek (MFS04) with decreasing concentrations at sites farther downstream in Middle Fork. The site in Mill Creek is located downstream from a wastewater-treatment plant discharge and concentrations at sites farther downstream probably had lesser concentrations because of dilution effects and from algal uptake. Nutrient concentrations generally were significantly greater during high-flow conditions compared to base-flow conditions. Flow-weighted nutrient concentrations were computed for the three streamflow sites and were compared to 82 relatively undeveloped sites identified across the Nation, to the Alum Fork of the Saline River near Reform, Arkansas, and to the Illinois River south of Siloam Springs, Arkansas, a site influenced by numerous point and nonpoint sources of nutrients. Annual flow-weighted nutrient concentrations for MFS06, MFS05, and MFS02 were greater than relatively undeveloped sites, but were substantially less than the Illinois River south of Siloam Springs. Fecal indicator bacteria concentrations were slightly greater at MFS06 and MFS05 compared to concentrations at MFS02 for October 2003 to October 2006. MFS05 had the greatest E.coli concentrations and MFS06 had the greatest fecal coliform concentrations. Overall, fecal indicator bacteria concentrations were significantly greater for samples collected during high-flow conditions compared to samples collected during low-flow conditions at all three sites. Suspended-sediment concentrations did not vary significantly among MFS06, MFS05, and MFS02 for all the samples collected from October 2003 to October 2006. Suspended-sediment concentrations were significantly greater in samples collected during high-flow conditions compared to samples collected during base-flow conditions. Synoptic samples indicated varied total suspended-solids distributions from upstream to downstream in the Middle Fork between January 2004 and October 2006. Overall, total suspended-solids values were the greatest at site MFS02 and decreased at sites upstream and downstream. Turbidity measured when water-quality samples were

Successful application of FTA Classic Card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes.

PubMed

Owor, Betty E; Shepherd, Dionne N; Taylor, Nigel J; Edema, Richard; Monjane, Adérito L; Thomson, Jennifer A; Martin, Darren P; Varsani, Arvind

2007-03-01

Leaf samples from 155 maize streak virus (MSV)-infected maize plants were collected from 155 farmers' fields in 23 districts in Uganda in May/June 2005 by leaf-pressing infected samples onto FTA Classic Cards. Viral DNA was successfully extracted from cards stored at room temperature for 9 months. The diversity of 127 MSV isolates was analysed by PCR-generated RFLPs. Six representative isolates having different RFLP patterns and causing either severe, moderate or mild disease symptoms, were chosen for amplification from FTA cards by bacteriophage phi29 DNA polymerase using the TempliPhi system. Full-length genomes were inserted into a cloning vector using a unique restriction enzyme site, and sequenced. The 1.3-kb PCR product amplified directly from FTA-eluted DNA and used for RFLP analysis was also cloned and sequenced. Comparison of cloned whole genome sequences with those of the original PCR products indicated that the correct virus genome had been cloned and that no errors were introduced by the phi29 polymerase. This is the first successful large-scale application of FTA card technology to the field, and illustrates the ease with which large numbers of infected samples can be collected and stored for downstream molecular applications such as diversity analysis and cloning of potentially new virus genomes.

Quantification of Protozoa and Viruses from Small Water Volumes

PubMed Central

Bonilla, J. Alfredo; Bonilla, Tonya D.; Abdelzaher, Amir M.; Scott, Troy M.; Lukasik, Jerzy; Solo-Gabriele, Helena M.; Palmer, Carol J.

2015-01-01

Large sample volumes are traditionally required for the analysis of waterborne pathogens. The need for large volumes greatly limits the number of samples that can be processed. The goals of this study were to compare extraction and detection procedures for quantifying protozoan parasites and viruses from small volumes of marine water. The intent was to evaluate a logistically simpler method of sample collection and processing that would facilitate direct pathogen measures as part of routine monitoring programs. Samples were collected simultaneously using a bilayer device with protozoa capture by size (top filter) and viruses capture by charge (bottom filter). Protozoan detection technologies utilized for recovery of Cryptosporidium spp. and Giardia spp. were qPCR and the more traditional immunomagnetic separation—IFA-microscopy, while virus (poliovirus) detection was based upon qPCR versus plaque assay. Filters were eluted using reagents consistent with the downstream detection technologies. Results showed higher mean recoveries using traditional detection methods over qPCR for Cryptosporidium (91% vs. 45%) and poliovirus (67% vs. 55%) whereas for Giardia the qPCR-based methods were characterized by higher mean recoveries (41% vs. 28%). Overall mean recoveries are considered high for all detection technologies. Results suggest that simultaneous filtration may be suitable for isolating different classes of pathogens from small marine water volumes. More research is needed to evaluate the suitability of this method for detecting pathogens at low ambient concentration levels. PMID:26114244

Quantification of Protozoa and Viruses from Small Water Volumes.

PubMed

Bonilla, J Alfredo; Bonilla, Tonya D; Abdelzaher, Amir M; Scott, Troy M; Lukasik, Jerzy; Solo-Gabriele, Helena M; Palmer, Carol J

2015-06-24

Large sample volumes are traditionally required for the analysis of waterborne pathogens. The need for large volumes greatly limits the number of samples that can be processed. The aims of this study were to compare extraction and detection procedures for quantifying protozoan parasites and viruses from small volumes of marine water. The intent was to evaluate a logistically simpler method of sample collection and processing that would facilitate direct pathogen measures as part of routine monitoring programs. Samples were collected simultaneously using a bilayer device with protozoa capture by size (top filter) and viruses capture by charge (bottom filter). Protozoan detection technologies utilized for recovery of Cryptosporidium spp. and Giardia spp. were qPCR and the more traditional immunomagnetic separation-IFA-microscopy, while virus (poliovirus) detection was based upon qPCR versus plaque assay. Filters were eluted using reagents consistent with the downstream detection technologies. Results showed higher mean recoveries using traditional detection methods over qPCR for Cryptosporidium (91% vs. 45%) and poliovirus (67% vs. 55%) whereas for Giardia the qPCR-based methods were characterized by higher mean recoveries (41% vs. 28%). Overall mean recoveries are considered high for all detection technologies. Results suggest that simultaneous filtration may be suitable for isolating different classes of pathogens from small marine water volumes. More research is needed to evaluate the suitability of this method for detecting pathogens at low ambient concentration levels.

A novel virtual hub approach for multisource downstream service integration

NASA Astrophysics Data System (ADS)

Previtali, Mattia; Cuca, Branka; Barazzetti, Luigi

2016-08-01

A large development of downstream services is expected to be stimulated starting from earth observations (EO) datasets acquired by Copernicus satellites. An important challenge connected with the availability of downstream services is the possibility for their integration in order to create innovative applications with added values for users of different categories level. At the moment, the world of geo-information (GI) is extremely heterogeneous in terms of standards and formats used, thus preventing a facilitated access and integration of downstream services. Indeed, different users and data providers have also different requirements in terms of communication protocols and technology advancement. In recent years, many important programs and initiatives have tried to address this issue even on trans-regional and international level (e.g. INSPIRE Directive, GEOSS, Eye on Earth and SEIS). However, a lack of interoperability between systems and services still exists. In order to facilitate the interaction between different downstream services, a new architectural approach (developed within the European project ENERGIC OD) is proposed in this paper. The brokering-oriented architecture introduces a new mediation layer (the Virtual Hub) which works as an intermediary to bridge the gaps linked to interoperability issues. This intermediation layer de-couples the server and the client allowing a facilitated access to multiple downstream services and also Open Data provided by national and local SDIs. In particular, in this paper an application is presented integrating four services on the topic of agriculture: (i) the service given by Space4Agri (providing services based on MODIS and Landsat data); (ii) Gicarus Lab (providing sample services based on Landsat datasets) and (iii) FRESHMON (providing sample services for water quality) and services from a several regional SDIs.

Persistence and potential effects of complex organic contaminant mixtures in wastewater-impacted streams

USGS Publications Warehouse

Barber, Larry B.; Keefe, Steffanie H.; Brown, Greg K.; Furlong, Edward T.; Gray, James L.; Kolpin, Dana W.; Meyer, Michael T.; Sandstrom, Mark W.; Zaugg, Steven D.

2013-01-01

Natural and synthetic organic contaminants in municipal wastewater treatment plant (WWTP) effluents can cause ecosystem impacts, raising concerns about their persistence in receiving streams. In this study, Lagrangian sampling, in which the same approximate parcel of water is tracked as it moves downstream, was conducted at Boulder Creek, Colorado and Fourmile Creek, Iowa to determine in-stream transport and attenuation of organic contaminants discharged from two secondary WWTPs. Similar stream reaches were evaluated, and samples were collected at multiple sites during summer and spring hydrologic conditions. Travel times to the most downstream (7.4 km) site in Boulder Creek were 6.2 h during the summer and 9.3 h during the spring, and to the Fourmile Creek 8.4 km downstream site times were 18 and 8.8 h, respectively. Discharge was measured at each site, and integrated composite samples were collected and analyzed for >200 organic contaminants including metal complexing agents, nonionic surfactant degradates, personal care products, pharmaceuticals, steroidal hormones, and pesticides. The highest concentration (>100 μg L–1) compounds detected in both WWTP effluents were ethylenediaminetetraacetic acid and 4-nonylphenolethoxycarboxylate oligomers, both of which persisted for at least 7 km downstream from the WWTPs. Concentrations of pharmaceuticals were lower (<1 μg L–1), and several compounds, including carbamazepine and sulfamethoxazole, were detected throughout the study reaches. After accounting for in-stream dilution, a complex mixture of contaminants showed little attenuation and was persistent in the receiving streams at concentrations with potential ecosystem implications.

Transport of perfluoroalkyl substances (PFAS) from an arctic glacier to downstream locations: implications for sources.

PubMed

Kwok, Karen Y; Yamazaki, Eriko; Yamashita, Nobuyoshi; Taniyasu, Sachi; Murphy, Margaret B; Horii, Yuichi; Petrick, Gert; Kallerborn, Roland; Kannan, Kurunthachalam; Murano, Kentaro; Lam, Paul K S

2013-03-01

Perfluoroalkyl substances (PFAS) have been globally detected in various environmental matrices, yet their fate and transport to the Arctic is still unclear, especially for the European Arctic. In this study, concentrations of 17 PFAS were quantified in two ice cores (n=26), surface snow (n=9) and surface water samples (n=14) collected along a spatial gradient in Svalbard, Norway. Concentrations of selected ions (Na(+), SO4(2-), etc.) were also determined for tracing the origins and sources of PFAS. Perfluorobutanoate (PFBA), perfluorooctanoate (PFOA) and perfluorononanoate (PFNA) were the dominant compounds found in ice core samples. Taking PFOA, PFNA and perfluorooctane-sulfonate (PFOS) as examples, higher concentrations were detected in the middle layers of the ice cores representing the period of 1997-2000. Lower concentrations of C8-C12 perfluorocarboxylates (PFCAs) were detected in comparison with concentrations measured previously in an ice core from the Canadian Arctic, indicating that contamination levels in the European Arctic are lower. Average PFAS concentrations were found to be lower in surface snow and melted glacier water samples, while increased concentrations were observed in river water downstream near the coastal area. Perfluorohexanesulfonate (PFHxS) was detected in the downstream locations, but not in the glacier, suggesting existence of local sources of this compound. Long-range atmospheric transport of PFAS was the major deposition pathway for the glaciers, while local sources (e.g., skiing activities) were identified in the downstream locations. Copyright © 2012 Elsevier B.V. All rights reserved.

Prediction of autosomal STR typing success in ancient and Second World War bone samples.

PubMed

Zupanič Pajnič, Irena; Zupanc, Tomaž; Balažic, Jože; Geršak, Živa Miriam; Stojković, Oliver; Skadrić, Ivan; Črešnar, Matija

2017-03-01

Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded. Therefore the new commercial qPCR kits able to assess the degree of degradation are potentially able to predict the success of downstream short tandem repeat (STR) typing. The goal of this study was to verify the quantification step using the PowerQuant kit with regard to its suitability as a screening method for autosomal STR typing success on ancient and Second World War (WWII) skeletal remains. We analysed 60 skeletons excavated from five archaeological sites and four WWII mass graves from Slovenia. The bones were cleaned, surface contamination was removed and the bones ground to a powder. Genomic DNA was obtained from 0.5g of bone powder after total demineralization. The DNA was purified using a Biorobot EZ1 device. Following PowerQuant quantification, DNA samples were subjected to autosomal STR amplification using the NGM kit. Up to 2.51ng DNA/g of powder were extracted. No inhibition was detected in any of bones analysed. 82% of the WWII bones gave full profiles while 73% of the ancient bones gave profiles not suitable for interpretation. Four bone extracts yielded no detectable amplification or zero quantification results and no profiles were obtained from any of them. Full or useful partial profiles were produced only from bone extracts where short autosomal (Auto) and long degradation (Deg) PowerQuant targets were detected. It is concluded that STR typing of old bones after quantification with the PowerQuant should be performed only when both Auto and Deg targets are detected simultaneously with no respect to [Auto]/[Deg] ratio. Prediction of STR typing success could be made according to successful amplification of Deg fragment. The PowerQuant kit is capable of identifying bone DNA samples that will not yield useful STR profiles using the NGM kit, and it can be used as a predictor of autosomal STR typing success of bone extracts obtained from ancient and WWII skeletal remains. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Spatial distribution of organic contaminants in three rivers of Southern England bound to suspended particulate material and dissolved in water.

PubMed

Wilkinson, John L; Hooda, Peter S; Swinden, Julian; Barker, James; Barton, Stephen

2017-09-01

The spatial distribution of pharmaceuticals, personal care products (PPCPs) and other emerging contaminants (ECs) such as plasticisers, perflourinated compounds (PFCs) and illicit drug metabolites in water and bound to suspended particulate material (SPM) is not well-understood. Here, we quantify levels of thirteen selected contaminants in water (n=88) and their partition to suspended particulate material (SPM, n=16) in three previously-unstudied rivers of Greater London and Southern England during a key reproduction/spawning period. Analysis was conducted using an in-house validated method for Solid Phase Extraction followed by High-Performance Liquid Chromatography-Tandem Mass-Spectrometry. Analytes were extracted from SPM using an optimised method for ultrasonic-assisted solvent extraction. Detection frequencies of contaminants dissolved in water ranged from 3% (ethinylestradiol) to 100% (bisphenol-A). Overall mean concentrations in the aqueous-phase ranged from 14.7ng/L (benzoylecgonine) to 159ng/L (bisphenol-A). Sewage treatment works (STW) effluent was the predominant source of pharmaceuticals, while plasticisers/perfluorinated compounds may additionally enter rivers via other sources. In SPM, detection frequencies ranged from 44% (PFOA) to 94% (hydroxyacetophenone). Mean quantifiable levels of analytes bound to SPM ranged from 13.5ng/g dry SPM (0.33ng bound/L water) perfluorononanoic acid to 2830ng/g dry SPM (14.3ng bound/L water) perfluorooctanesulfonic acid. Long chain (>C7) amphipathic and acidic PFCs were found to more preferentially bind to SPM than short chain PFCs and other contaminants (Kd=34.1-75.5 vs <5 respectively). Per capita daily contributions of studied contaminants entering rivers ranged from 0.157μg/person/day of benzoylecgonine (cocaine metabolite) to 58.6μg/person/day of bisphenol-A. The large sample size of this work (n=104) enabled ANOVA followed by Tukey HSD post-hoc tests to establish significant trends in PPCP/EC spatial distribution from headwaters through downstream stretches of studied rivers. Novel findings include environmental Kd calculations, the occurrence of contaminants in river headwaters, increases in contaminant metabolite concentrations downstream of STW effluents revealing possible in-river degradation or de-conjugation, the influence of polarity and acidity in the partition of contaminants to particulate-material, among others. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Sequencing Insights into Microbial Communities in the Water and Sediments of Fenghe River, China.

PubMed

Lu, Sidan; Sun, Yujiao; Zhao, Xuan; Wang, Lei; Ding, Aizhong; Zhao, Xiaohui

2016-07-01

The connection between microbial community structure and spatial variation and pollution in river waters has been widely investigated. However, water and sediments together have rarely been explored. In this study, Illumina high-throughput sequencing was performed to analyze microbes in 24 water and sediment samples from natural to anthropogenic sources and from headstream to downstream areas. These data were used to assess variability in microbial community structure and diversity along in the Fenghe River, China. The relationship between bacterial diversity and environmental parameters was statistically analyzed. An average of 1682 operational taxonomic units was obtained. Microbial diversity increased from the headstream to downstream and tended to be greater in sediment compared with water. The water samples near the headstream endured relatively low Shannon and Chao1 indices. These diversity indices and the number of observed species in the water and sediment samples increase downstream. The parameters also differ in the two river tributaries. Community structures shift based on the extent of nitrogen pollution variation in the sediment and water samples. The four most dominant genera in the water community were Escherichia, Acinetobacter, Comamonadaceae, and Pseudomonas. In the sediments, the most dominant genera were Stramenopiles, Flavobacterium, Pseudomonas, and Comamonadaceae. The number of ammonia-oxidizing archaea in the headstream water slightly differed from that in the sediment but varied considerably in the downstream sediments. Statistical analysis showed that community variation is correlated with changes in ammonia nitrogen, total nitrogen, and nitrate nitrogen. This study identified different microbial community structures in river water and sediments. Overall this study emphasized the need to elucidate spatial variations in bacterial diversity in water and sediments associated with physicochemical gradients and to show the effects of such variation on waterborne microbial community structures.

Antidepressant pharmaceuticals in two U.S. effluent-impacted streams: Occurrence and fate in water and sediment and selective uptake in fish neural tissue

USGS Publications Warehouse

Schultz, M.M.; Furlong, E.T.; Kolpin, D.W.; Werner, S.L.; Schoenfuss, H.L.; Barber, L.B.; Blazer, V.S.; Norris, D.O.; Vajda, A.M.

2010-01-01

Antidepressant pharmaceuticals are widely prescribed in the United States; release of municipal wastewater effluent is a primary route introducing them to aquatic environments, where little is known about their distribution and fate. Water, bed sediment, and brain tissue from native white suckers (Catostomus commersoni)were collected upstream and atpoints progressively downstream from outfalls discharging to two effluentimpacted streams, Boulder Creek (Colorado) and Fourmile Creek (Iowa). A liquid chromatography/tandem mass spectrometry method was used to quantify antidepressants, including fluoxetine, norfluoxetine (degradate), sertraline, norsertraline (degradate), paroxetine, Citalopram, fluvoxamine, duloxetine, venlafaxine, and bupropion in all three sample matrices. Antidepressants were not present above the limit of quantitation in water samples upstream from the effluent outfalls but were present at points downstream at ng/L concentrations, even at the farthest downstream sampling site 8.4 km downstream from the outfall. The antidepressants with the highest measured concentrations in both streams were venlafaxine, bupropion, and Citalopram and typically were observed at concentrations of at least an order of magnitude greater than the more commonly investigated antidepressants fluoxetine and sertraline. Concentrations of antidepressants in bed sediment were measured at ng/g levels; venlafaxine and fluoxetine were the predominant chemicals observed. Fluoxetine, sertraline, and their degradates were the principal antidepressants observed in fish brain tissue, typically at low ng/g concentrations. Aqualitatively different antidepressant profile was observed in brain tissue compared to streamwater samples. This study documents that wastewater effluent can be a point source of antidepressants to stream ecosystems and that the qualitative composition of antidepressants in brain tissue from exposed fish differs substantially from the compositions observed in streamwater and sediment, suggesting selective uptake. ?? 2010 American Chemical Society.

Enhanced extraction of butyric acid under high-pressure CO2 conditions to integrate chemical catalysis for value-added chemicals and biofuels.

PubMed

Chun, Jaesung; Choi, Okkyoung; Sang, Byoung-In

2018-01-01

Extractive fermentation with the removal of carboxylic acid requires low pH conditions because acids are better partitioned into the solvent phase at low pH values. However, this requirement conflicts with the optimal near-neutral pH conditions for microbial growth. CO 2 pressurization was used, instead of the addition of chemicals, to decrease pH for the extraction of butyric acid, a fermentation product of Clostridium tyrobutyricum , and butyl butyrate was selected as an extractant. CO 2 pressurization (50 bar) improved the extraction efficiency of butyric acid from a solution at pH 6, yielding a distribution coefficient ( D ) 0.42. In situ removal of butyric acid during fermentation increased the production of butyric acid by up to 4.10 g/L h, an almost twofold increase over control without the use of an extraction process. In situ extraction of butyric acid using temporal CO 2 pressurization may be applied to an integrated downstream catalytic process for upgrading butyric acid to value-added chemicals in an organic solvent.

Transverse beam splitting made operational: Key features of the multiturn extraction at the CERN Proton Synchrotron

NASA Astrophysics Data System (ADS)

Huschauer, A.; Blas, A.; Borburgh, J.; Damjanovic, S.; Gilardoni, S.; Giovannozzi, M.; Hourican, M.; Kahle, K.; Le Godec, G.; Michels, O.; Sterbini, G.; Hernalsteens, C.

2017-06-01

Following a successful commissioning period, the multiturn extraction (MTE) at the CERN Proton Synchrotron (PS) has been applied for the fixed-target physics programme at the Super Proton Synchrotron (SPS) since September 2015. This exceptional extraction technique was proposed to replace the long-serving continuous transfer (CT) extraction, which has the drawback of inducing high activation in the ring. MTE exploits the principles of nonlinear beam dynamics to perform loss-free beam splitting in the horizontal phase space. Over multiple turns, the resulting beamlets are then transferred to the downstream accelerator. The operational deployment of MTE was rendered possible by the full understanding and mitigation of different hardware limitations and by redesigning the extraction trajectories and nonlinear optics, which was required due to the installation of a dummy septum to reduce the activation of the magnetic extraction septum. This paper focuses on these key features including the use of the transverse damper and the septum shadowing, which allowed a transition from the MTE study to a mature operational extraction scheme.

Economic Assessment of Supercritical CO2 Extraction of Waxes as Part of a Maize Stover Biorefinery.

PubMed

Attard, Thomas M; McElroy, Con Robert; Hunt, Andrew J

2015-07-31

To date limited work has focused on assessing the economic viability of scCO2 extraction to obtain waxes as part of a biorefinery. This work estimates the economic costs for wax extraction from maize stover. The cost of manufacture (COM) for maize stover wax extraction was found to be € 88.89 per kg of wax, with the fixed capital investment (FCI) and utility costs (CUT) contributing significantly to the COM. However, this value is based solely on scCO2 extraction of waxes and does not take into account the downstream processing of the biomass following extraction. The cost of extracting wax from maize stover can be reduced by utilizing pelletized leaves and combusting the residual biomass to generate electricity. This would lead to an overall cost of € 10.87 per kg of wax (based on 27% combustion efficiency for electricity generation) and €4.56 per kg of wax (based on 43% combustion efficiency for electricity generation). A sensitivity analysis study showed that utility costs (cost of electricity) had the greatest effect on the COM.

Applications of supercritical fluid extraction (SFE) of palm oil and oil from natural sources.

PubMed

Akanda, Mohammed Jahurul Haque; Sarker, Mohammed Zaidul Islam; Ferdosh, Sahena; Manap, Mohd Yazid Abdul; Ab Rahman, Nik Norulaini Nik; Ab Kadir, Mohd Omar

2012-02-10

Supercritical fluid extraction (SFE), which has received much interest in its use and further development for industrial applications, is a method that offers some advantages over conventional methods, especially for the palm oil industry. SC-CO₂ refers to supercritical fluid extraction (SFE) that uses carbon dioxide (CO₂) as a solvent which is a nontoxic, inexpensive, nonflammable, and nonpolluting supercritical fluid solvent for the extraction of natural products. Almost 100% oil can be extracted and it is regarded as safe, with organic solvent-free extracts having superior organoleptic profiles. The palm oil industry is one of the major industries in Malaysia that provides a major contribution to the national income. Malaysia is the second largest palm oil and palm kernel oil producer in the World. This paper reviews advances in applications of supercritical carbon dioxide (SC-CO₂) extraction of oils from natural sources, in particular palm oil, minor constituents in palm oil, producing fractionated, refined, bleached, and deodorized palm oil, palm kernel oil and purified fatty acid fractions commendable for downstream uses as in toiletries and confectionaries.

Microwave-Assisted Extraction for Microalgae: From Biofuels to Biorefinery

PubMed Central

Pandhal, Jagroop

2018-01-01

The commercial reality of bioactive compounds and oil production from microalgal species is constrained by the high cost of production. Downstream processing, which includes harvesting and extraction, can account for 70–80% of the total cost of production. Consequently, from an economic perspective extraction technologies need to be improved. Microalgal cells are difficult to disrupt due to polymers within their cell wall such as algaenan and sporopollenin. Consequently, solvents and disruption devices are required to obtain products of interest from within the cells. Conventional techniques used for cell disruption and extraction are expensive and are often hindered by low efficiencies. Microwave-assisted extraction offers a possibility for extraction of biochemical components including lipids, pigments, carbohydrates, vitamins and proteins, individually and as part of a biorefinery. Microwave technology has advanced since its use in the 1970s. It can cut down working times and result in higher yields and purity of products. In this review, the ability and challenges in using microwave technology are discussed for the extraction of bioactive products individually and as part of a biorefinery approach. PMID:29462888

Economic Assessment of Supercritical CO2 Extraction of Waxes as Part of a Maize Stover Biorefinery

PubMed Central

Attard, Thomas M.; McElroy, Con Robert; Hunt, Andrew J.

2015-01-01

To date limited work has focused on assessing the economic viability of scCO2 extraction to obtain waxes as part of a biorefinery. This work estimates the economic costs for wax extraction from maize stover. The cost of manufacture (COM) for maize stover wax extraction was found to be €88.89 per kg of wax, with the fixed capital investment (FCI) and utility costs (CUT) contributing significantly to the COM. However, this value is based solely on scCO2 extraction of waxes and does not take into account the downstream processing of the biomass following extraction. The cost of extracting wax from maize stover can be reduced by utilizing pelletized leaves and combusting the residual biomass to generate electricity. This would lead to an overall cost of €10.87 per kg of wax (based on 27% combustion efficiency for electricity generation) and €4.56 per kg of wax (based on 43% combustion efficiency for electricity generation). A sensitivity analysis study showed that utility costs (cost of electricity) had the greatest effect on the COM. PMID:26263976

Constraints upon the Response of Fish and Crayfish to Environmental Flow Releases in a Regulated Headwater Stream Network

PubMed Central

Chester, Edwin T.; Matthews, Ty G.; Howson, Travis J.; Johnston, Kerrylyn; Mackie, Jonathon K.; Strachan, Scott R.; Robson, Belinda J.

2014-01-01

In dry climate zones, headwater streams are often regulated for water extraction causing intermittency in perennial streams and prolonged drying in intermittent streams. Regulation thereby reduces aquatic habitat downstream of weirs that also form barriers to migration by stream fauna. Environmental flow releases may restore streamflow in rivers, but are rarely applied to headwaters. We sampled fish and crayfish in four regulated headwater streams before and after the release of summer-autumn environmental flows, and in four nearby unregulated streams, to determine whether their abundances increased in response to flow releases. Historical data of fish and crayfish occurrence spanning a 30 year period was compared with contemporary data (electrofishing surveys, Victoria Range, Australia; summer 2008 to summer 2010) to assess the longer–term effects of regulation and drought. Although fish were recorded in regulated streams before 1996, they were not recorded in the present study upstream or downstream of weirs despite recent flow releases. Crayfish (Geocharax sp. nov. 1) remained in the regulated streams throughout the study, but did not become more abundant in response to flow releases. In contrast, native fish (Gadopsis marmoratus, Galaxias oliros, Galaxias maculatus) and crayfish remained present in unregulated streams, despite prolonged drought conditions during 2006–2010, and the assemblages of each of these streams remained essentially unchanged over the 30 year period. Flow release volumes may have been too small or have operated for an insufficient time to allow fish to recolonise regulated streams. Barriers to dispersal may also be preventing recolonisation. Indefinite continuation of annual flow releases, that prevent the unnatural cessation of flow caused by weirs, may eventually facilitate upstream movement of fish and crayfish in regulated channels; but other human–made dispersal barriers downstream need to be identified and ameliorated, to allow native fish to fulfil their life cycles in these headwater streams. PMID:24647407

High pH microbial ecosystems in a newly discovered, ephemeral, serpentinizing fluid seep at Yanartaş (Chimera), Turkey

PubMed Central

Meyer-Dombard, D'Arcy R.; Woycheese, Kristin M.; Yargıçoğlu, Erin N.; Cardace, Dawn; Shock, Everett L.; Güleçal-Pektas, Yasemin; Temel, Mustafa

2015-01-01

Gas seeps emanating from Yanartaş (Chimera), Turkey, have been documented for thousands of years. Active serpentinization produces hydrogen and a range of carbon gases that may provide fuel for life. Here we report a newly discovered, ephemeral fluid seep emanating from a small gas vent at Yanartaş. Fluids and biofilms were sampled at the source and points downstream. We describe site conditions, and provide microbiological data in the form of enrichment cultures, Scanning electron microscopy (SEM), carbon and nitrogen isotopic composition of solids, and PCR screens of nitrogen cycle genes. Source fluids are pH 11.95, with a Ca:Mg of ~200, and sediments under the ignited gas seep measure 60°C. Collectively, these data suggest the fluid is the product of active serpentinization at depth. Source sediments are primarily calcite and alteration products (chlorite and montmorillonite). Downstream, biofilms are mixed with montmorillonite. SEM shows biofilms distributed homogeneously with carbonates. Organic carbon accounts for 60% of the total carbon at the source, decreasing downstream to <15% as inorganic carbon precipitates. δ13C ratios of the organic carbon fraction of solids are depleted (−25 to −28‰) relative to the carbonates (−11 to −20‰). We conclude that heterotrophic processes are dominant throughout the surface ecosystem, and carbon fixation may be key down channel. δ15N ratios ~3‰, and absence of nifH in extracted DNA suggest that nitrogen fixation is not occurring in sediments. However, the presence of narG and nirS at most locations and in enrichments indicates genomic potential for nitrate and nitrite reduction. This small seep with shallow run-off is likely ephemeral, but abundant preserved microterracettes in the outflow and the surrounding area suggest it has been present for some time. This site and others like it present an opportunity for investigations of preserved deep biosphere signatures, and subsurface-surface interactions. PMID:25646094

High pH microbial ecosystems in a newly discovered, ephemeral, serpentinizing fluid seep at Yanartaş (Chimera), Turkey.

PubMed

Meyer-Dombard, D'Arcy R; Woycheese, Kristin M; Yargıçoğlu, Erin N; Cardace, Dawn; Shock, Everett L; Güleçal-Pektas, Yasemin; Temel, Mustafa

2014-01-01

Gas seeps emanating from Yanartaş (Chimera), Turkey, have been documented for thousands of years. Active serpentinization produces hydrogen and a range of carbon gases that may provide fuel for life. Here we report a newly discovered, ephemeral fluid seep emanating from a small gas vent at Yanartaş. Fluids and biofilms were sampled at the source and points downstream. We describe site conditions, and provide microbiological data in the form of enrichment cultures, Scanning electron microscopy (SEM), carbon and nitrogen isotopic composition of solids, and PCR screens of nitrogen cycle genes. Source fluids are pH 11.95, with a Ca:Mg of ~200, and sediments under the ignited gas seep measure 60°C. Collectively, these data suggest the fluid is the product of active serpentinization at depth. Source sediments are primarily calcite and alteration products (chlorite and montmorillonite). Downstream, biofilms are mixed with montmorillonite. SEM shows biofilms distributed homogeneously with carbonates. Organic carbon accounts for 60% of the total carbon at the source, decreasing downstream to <15% as inorganic carbon precipitates. δ(13)C ratios of the organic carbon fraction of solids are depleted (-25 to -28‰) relative to the carbonates (-11 to -20‰). We conclude that heterotrophic processes are dominant throughout the surface ecosystem, and carbon fixation may be key down channel. δ(15)N ratios ~3‰, and absence of nifH in extracted DNA suggest that nitrogen fixation is not occurring in sediments. However, the presence of narG and nirS at most locations and in enrichments indicates genomic potential for nitrate and nitrite reduction. This small seep with shallow run-off is likely ephemeral, but abundant preserved microterracettes in the outflow and the surrounding area suggest it has been present for some time. This site and others like it present an opportunity for investigations of preserved deep biosphere signatures, and subsurface-surface interactions.

Pharmaceuticals and other organic chemicals in selected north-central and northwestern Arkansas streams

USGS Publications Warehouse

Haggard, B.E.; Galloway, J.M.; Green, W.R.; Meyer, M.T.

2006-01-01

Recently, our attention has focused on the low level detection of many antibiotics, pharmaceuticals, and other organic chemicals in water resources. The limited studies available suggest that urban or rural streams receiving wastewater effluent are more susceptible to contamination. The purpose of this study was to evaluate the occurrence of antibiotics, pharmaceuticals, and other organic chemicals at 18 sites on seven selected streams in Arkansas, USA, during March, April, and August 2004. Water samples were collected upstream and downstream from the influence of effluent discharges in northwestern Arkansas and at one site on a relatively undeveloped stream in north-central Arkansas. At least one antibiotic, pharmaceutical, or other organic chemical was detected at all sites, except at Spavinaw Creek near Mayesville, Arkansas. The greatest number of detections was observed at Mud Creek downstream from an effluent discharge, including 31 pharmaceuticals and other organic chemicals. The detection of these chemicals occurred in higher frequency at sites downstream from effluent discharges compared to those sites upstream from effluent discharges; total chemical concentration was also greater downstream. Wastewater effluent discharge increased the concentrations of detergent metabolites, fire retardants, fragrances and flavors, and steroids in these streams. Antibiotics and associated degradation products were only found at two streams downstream from effluent discharges. Overall, 42 of the 108 chemicals targeted in this study were found in water samples from at least one site, and the most frequently detected organic chemicals included caffeine, phenol, para-cresol, and acetyl hexamethyl tetrahydro naphthalene (AHTN). ?? ASA, CSSA, SSSA.

Salinization may attack you from behind: upconing and related long-term downstream salinization in the Amsterdam Water Supply Dunes (Invited)

NASA Astrophysics Data System (ADS)

Olsthoorn, T.

2010-12-01

Groundwater from the Amsterdam Water Supply Dunes (GE: 52.35°N 4.55°E) has been used for the drinking water supply of Amsterdam since 1853. During the first half of the 20th century, severe intrusion and upconing occurred, with many of the wells turning brackish or saline. Already in 1903, the hydrologist/director of the Amsterdam Water Supply, Pennink, predicted this, based on his unique sand-box modeling, which he published in 1915 in the form of a large-size hard-bound book in four languages showing detailed black and white photographs of his tests. This book is now on the web: http://www.citg.tudelft.nl/live/pagina.jsp?id=68e12562-a4d2-489a-b82e-deca5dd32c42&lang=en Pennink devoted much of his work on saltwater upconing below wells, which he so feared. He simulated simultaneous flow of fresh and salt water, using milk to represent the saltwater having about the same density. With our current modeling tools, we can simulate his experiments, allowing to better understand his setup and even to verify our code. Pennink took interest in the way these cones form and in the point at which the salt water enters the screen. Surprizing, at least to many, is that this entry point is not necessarily the screen bottom. Measurements of the salinity distribution in salinized wells in the Amsterdam Water Supply Dune area confirmed this thirty years later when salinzation was severely occurring. The curved cone shape under ambient flow conditions provides part of the explanation why a short-term shut down of a well almost immediately diminishes salt concentrations, but salinization downstream of the wells in case with substantial lateral groundwater flow is not affected. Downstream salinization due to extraction was clearly shown in Pennink's experiments. However, the phenomenon seems still largely unknown or ignored. Downstream salinization also affects downstream heads for years after extraction has stopped. The presentation demonstrates and explains these local and more widespread phenomena using field data collected over time and verification by the numerical model. With substantial lateral flow salt water may well enter wells above the bottom of the screen.

Comparing different post-mortem human samples as DNA sources for downstream genotyping and identification.

PubMed

Calacal, Gayvelline C; Apaga, Dame Loveliness T; Salvador, Jazelyn M; Jimenez, Joseph Andrew D; Lagat, Ludivino J; Villacorta, Renato Pio F; Lim, Maria Cecilia F; Fortun, Raquel D R; Datar, Francisco A; De Ungria, Maria Corazon A

2015-11-01

The capability of DNA laboratories to perform genotyping procedures from post-mortem remains, including those that had undergone putrefaction, continues to be a challenge in the Philippines, a country characterized by very humid and warm conditions all year round. These environmental conditions accelerate the decomposition of human remains that were recovered after a disaster and those that were left abandoned after a crime. When considerable tissue decomposition of human remains has taken place, there is no other option but to extract DNA from bone and/or teeth samples. Routinely, femur shafts are obtained from recovered bodies for human identification because the calcium matrix protects the DNA contained in the osteocytes. In the Philippines, there is difficulty in collecting femur samples after natural disasters or even human-made disasters, because these events are usually characterized by a large number of fatalities. Identification of casualties is further delayed by limitation in human and material resources. Hence, it is imperative to test other types of biological samples that are easier to collect, transport, process and store. We analyzed DNA that were obtained from body fluid, bone marrow, muscle tissue, clavicle, femur, metatarsal, patella, rib and vertebral samples from five recently deceased untreated male cadavers and seven male human remains that were embalmed, buried for ∼ 1 month and then exhumed. The bodies had undergone different environmental conditions and were in various stages of putrefaction. A DNA extraction method utilizing a detergent-washing step followed by an organic procedure was used. The utility of bone marrow and vitreous fluid including bone marrow and vitreous fluid that was transferred on FTA(®) cards and subjected to autosomal STR and Y-STR DNA typing were also evaluated. DNA yield was measured and the presence or absence of PCR inhibitors in DNA extracts was assessed using Plexor(®)HY. All samples were amplified using PowerPlex(®)21 and PowerPlexY(®)23 systems and analyzed using the AB3500 Genetic Analyzer and the GeneMapper(®) ID-X v.1.2 software. PCR inhibitors were consistently detected in bone marrow, muscle tissue, rib and vertebra samples. Amplifiable DNA was obtained in a majority of the samples analyzed. DNA recovery from 0.1g biological material was adequate for successful genotyping of most of the non-bone and bone samples. Complete DNA profiles were generated from bone marrow, femur, metatarsal and patella with 0.1 ng DNA template. Using 0.5 ng DNA template resulted in increased allele recovery and improved intra- and inter-locus peak balance. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Characterization of sediment transport upstream and downstream from Lake Emory on the Little Tennessee River near Franklin, North Carolina, 2014–15

USGS Publications Warehouse

Huffman, Brad A.; Hazell, William F.; Oblinger, Carolyn J.

2017-09-06

Federal, State, and local agencies and organizations have expressed concerns regarding the detrimental effects of excessive sediment transport on aquatic resources and endangered species populations in the upper Little Tennessee River and some of its tributaries. In addition, the storage volume of Lake Emory, which is necessary for flood control and power generation, has been depleted by sediment deposition. To help address these concerns, a 2-year study was conducted in the upper Little Tennessee River Basin to characterize the ambient suspended-sediment concentrations and suspended-sediment loads upstream and downstream from Lake Emory in Franklin, North Carolina. The study was conducted by the U.S. Geological Survey in cooperation with Duke Energy. Suspended-sediment samples were collected periodically, and time series of stage and turbidity data were measured from December 2013 to January 2016 upstream and downstream from Lake Emory. The stage data were used to compute time-series streamflow. Suspended-sediment samples, along with time-series streamflow and turbidity data, were used to develop regression models that were used to estimate time-series suspended-sediment concentrations for the 2014 and 2015 calendar years. These concentrations, along with streamflow data, were used to compute suspended-sediment loads. Selected suspended-sediment samples were collected for analysis of particle-size distribution, with emphasis on high-flow events. Bed-load samples were also collected upstream from Lake Emory.The estimated annual suspended-sediment loads (yields) for the upstream site for the 2014 and 2015 calendar years were 27,000 short tons (92 short tons per square mile) and 63,300 short tons (215 short tons per square mile), respectively. The annual suspended-sediment loads (yields) for the downstream site for 2014 and 2015 were 24,200 short tons (75 short tons per square mile) and 94,300 short tons (292 short tons per square mile), respectively. Overall, the suspended-sediment load at the downstream site was about 28,300 short tons greater than the upstream site over the study period.As expected, high-flow events (the top 5 percent of daily mean flows) accounted for the majority of the sediment load; 80 percent at the upstream site and 90 percent at the downstream site. A similar relation between turbidity (the top 5 percent of daily mean turbidity) and high loads was also noted. In general, when instantaneous streamflows at the upstream site exceeded 5,000 cubic feet per second, increased daily loads were computed at the downstream site. During low to moderate flows, estimated suspended-sediment loads were lower at the downstream site when compared to the upstream site, which suggests that sediment deposition may be occurring in the intervening reach during those conditions. During the high-flow events, the estimated suspended-sediment loads were higher at the downstream site; however, it is impossible to say with certainty whether the increase in loading was due to scouring of lake sediment, contributions from the additional source area, model error, or a combination of one or more of these factors. The computed loads for a one-week period (December 24–31, 2015), during which the two largest high-flow events of the study period occurred, were approximately 52 percent of the 2015 annual sediment load (36 percent of 2-year load) at the upstream site and approximately 72 percent of the 2015 annual sediment load (57 percent of 2-year load) at the downstream site. Six bedload samples were collected during three events; two high-flow events and one base-flow event. The contribution of bedload to the total sediment load was determined to be insignificant for sampled flows. In general, streamflows for long-term streamgages in the study area were below normal for the majority of the study period; however, flows during the last 3 months of the study period were above normal, including the extreme events during the last week of the study period.

Effects of nonpoint and selected point contaminant sources on stream-water quality and relation to land use in Johnson County, northeastern Kansas, October 2002 through June 2004

USGS Publications Warehouse

Lee, Casey J.; Mau, D.P.; Rasmussen, T.J.

2005-01-01

Water and sediment samples were collected by the U.S. Geological Survey in 12 watersheds in Johnson County, northeastern Kansas, to determine the effects of nonpoint and selected point contaminant sources on stream-water quality and their relation to varying land use. The streams studied were located in urban areas of the county (Brush, Dykes Branch, Indian, Tomahawk, and Turkey Creeks), developing areas of the county (Blue River and Mill Creek), and in more rural areas of the county (Big Bull, Captain, Cedar, Kill, and Little Bull Creeks). Two base-flow synoptic surveys (73 total samples) were conducted in 11 watersheds, a minimum of three stormflow samples were collected in each of six watersheds, and 15 streambed-sediment sites were sampled in nine watersheds from October 2002 through June 2004. Discharge from seven wastewater treatment facilities (WWTFs) were sampled during base-flow synoptic surveys. Discharge from these facilities comprised greater than 50 percent of streamflow at the farthest downstream sampling site in six of the seven watersheds during base-flow conditions. Nutrients, organic wastewater-indicator compounds, and prescription and nonprescription pharmaceutical compounds generally were found in the largest concentrations during base-flow conditions at sites at, or immediately downstream from, point-source discharges from WWTFs. Downstream from WWTF discharges streamflow conditions were generally stable, whereas nutrient and wastewater-indicator compound concentrations decreased in samples from sites farther downstream. During base-flow conditions, sites upstream from WWTF discharges had significantly larger fecal coliform and Escherichia coli densities than downstream sites. Stormflow samples had the largest suspended-sediment concentrations and indicator bacteria densities. Other than in samples from sites in proximity to WWTF discharges, stormflow samples generally had the largest nutrient concentrations in Johnson County streams. Discharge from WWTFs with trickling-filter secondary treatment processes had the largest concentrations of many potential contaminants during base-flow conditions. Samples from two of three trickling-filter WWTFs exceeded Kansas Department of Health and Environment pH- and temperature-dependent chronic aquatic-life criteria for ammonia when early-life stages of fish are present. Discharge from trickling-filter facilities generally had the most detections and largest concentrations of many organic wastewater-indicator compounds in Johnson County stream-water samples. Caffeine (stimulant), nonylphenol-diethoxylate (detergent surfactant), and tris(2-butoxyethyl) phosphate (floor polish, flame retardant, and plasticizer) were found at concentrations larger than maximum concentrations in comparable studies. Land use and seasonality affected the occurrence and magnitude of many potential water-quality contaminants originating from nonpoint sources. Base-flow samples from urban sites located upstream from WWTF discharges had larger indicator bacteria densities and wastewater-indicator compound concentrations than did base-flow samples from sites in nonurban areas. Dissolved-solids concentrations were the largest in winter stormflow samples from urban sites and likely were due to runoff from road-salt application. One sample from an urban watershed had a chloride concentration of 1,000 milligrams per liter, which exceeded the Kansas Department of Health and Environment's acute aquatic-life use criterion (860 milligrams per liter) likely due to effects from road-salt application. Pesticide concentrations were the largest in spring stormflow samples collected in nonurban watersheds. Although most wastewater-indicator compounds were found at the largest concentrations in samples from WWTF discharges, the compounds 9-10, anthraquinone (bird repellent), caffeine (stimulant), carbazole (component of coal tar, petroleum products), nonylphenol-diethoxylate (detergent surfactant),

Reproductive health of bass in the Potomac, U.S.A., drainage: part 2. Seasonal occurrence of persistent and emerging organic contaminants.

PubMed

Alvarez, David A; Cranor, Walter L; Perkins, Stephanie D; Schroeder, Vickie L; Iwanowicz, Luke R; Clark, Randal C; Guy, Christopher P; Pinkney, Alfred E; Blazer, Vicki S; Mullican, John E

2009-05-01

The seasonal occurrence of organic contaminants, many of which are potential endocrine disruptors, entering the Potomac River, USA, watershed was investigated using a two-pronged approach during the fall of 2005 and spring of 2006. Passive samplers (semipermeable membrane device and polar organic chemical integrative sampler [POCIS]) were deployed in tandem at sites above and below wastewater treatment plant discharges within the watershed. Analysis of the samplers resulted in detection of 84 of 138 targeted chemicals. The agricultural pesticides atrazine and metolachlor had the greatest seasonal changes in water concentrations, with a 3.1- to 91-fold increase in the spring compared with the level in the previous fall. Coinciding with the elevated concentrations of atrazine in the spring were increasing concentrations of the atrazine degradation products desethylatrazine and desisopropylatrazine in the fall following spring and summer application of the parent compound. Other targeted chemicals (organochlorine pesticides, polycyclic aromatic hydrocarbons, and organic wastewater chemicals) did not indicate seasonal changes in occurrence or concentration; however, the overall concentrations and number of chemicals present were greater at the sites downstream of wastewater treatment plant discharges. Several fragrances and flame retardants were identified in these downstream sites, which are characteristic of wastewater effluent and human activities. The bioluminescent yeast estrogen screen in vitro assay of the POCIS extracts indicated the presence of chemicals that were capable of producing an estrogenic response at all sampling sites.

Reproductive health of bass in the potomac, USA, drainage: part 2. Seasonal occurrence of persistent and emerging organic contaminants

USGS Publications Warehouse

Alvarez, D.A.; Cranor, W.L.; Perkins, S.D.; Schroeder, V.L.; Iwanowicz, L.R.; Clark, R.C.; Guy, C.P.; Pinkney, A.E.; Blazer, V.S.; Mullican, J.E.

2009-01-01

The seasonal occurrence of organic contaminants, many of which are potential endocrine disruptors, entering the Potomac River, USA, watershed was investigated using a two-pronged approach during the fall of 2005 and spring of 2006. Passive samplers (semipermeable membrane device and polar organic chemical integrative sampler [POCIS]) were deployed in tandem at sites above and below wastewater treatment plant discharges within the watershed. Analysis of the samplers resulted in detection of 84 of 138 targeted chemicals. The agricultural pesticides atrazine and metolachlor had the greatest seasonal changes in water concentrations, with a 3.1 - to 91 -fold increase in the spring compared with the level in the previous fall. Coinciding with the elevated concentrations of atrazine in the spring were increasing concentrations of the atrazine degradation products desethylatrazine and desisopropylatrazine in the fall following spring and summer application of the parent compound. Other targeted chemicals (organochlorine pesticides, polycyclic aromatic hydrocarbons, and organic wastewater chemicals) did not indicate seasonal changes in occurrence or concentration; however, the overall concentrations and number of chemicals present were greater at the sites downstream of wastewater treatment plant discharges. Several fragrances and flame retardants were identified in these downstream sites, which are characteristic of wastewater effluent and human activities. The bioluminescent yeast estrogen screen in vitro assay of the POCIS extracts indicated the presence of chemicals that were capable of producing an estrogenic response at all sampling sites. ?? 2009 SETA.

Adaptation of Laser Microdissection Technique for the Study of a Spontaneous Metastatic Mammary Carcinoma Mouse Model by NanoString Technologies

PubMed Central

Saylor, Karen L.; Anver, Miriam R.; Salomon, David S.; Golubeva, Yelena G.

2016-01-01

Laser capture microdissection (LCM) of tissue is an established tool in medical research for collection of distinguished cell populations under direct microscopic visualization for molecular analysis. LCM samples have been successfully analyzed in a number of genomic and proteomic downstream molecular applications. However, LCM sample collection and preparation procedure has to be adapted to each downstream analysis platform. In this present manuscript we describe in detail the adaptation of LCM methodology for the collection and preparation of fresh frozen samples for NanoString analysis based on a study of a model of mouse mammary gland carcinoma and its lung metastasis. Our adaptation of LCM sample preparation and workflow to the requirements of the NanoString platform allowed acquiring samples with high RNA quality. The NanoString analysis of such samples provided sensitive detection of genes of interest and their associated molecular pathways. NanoString is a reliable gene expression analysis platform that can be effectively coupled with LCM. PMID:27077656

In-line carbon nanofiber reinforced hollow fiber-mediated liquid phase microextraction using a 3D printed extraction platform as a front end to liquid chromatography for automatic sample preparation and analysis: A proof of concept study.

PubMed

Worawit, Chanatda; Cocovi-Solberg, David J; Varanusupakul, Pakorn; Miró, Manuel

2018-08-01

A novel concept for automation of nanostructured hollow-fiber supported microextraction, combining the principles of liquid-phase microextraction (LPME) and sorbent microextraction synergically, using mesofluidic platforms is proposed herein for the first time, and demonstrated with the determination of acidic drugs (namely, ketoprofen, ibuprofen, diclofenac and naproxen) in urine as a proof-of-concept applicability. Dispersed carbon nanofibers (CNF) are immobilized in the pores of a single-stranded polypropylene hollow fiber (CNF@HF) membrane, which is thereafter accommodated in a stereolithographic 3D-printed extraction chamber without glued components for ease of assembly. The analytical method involves continuous-flow extraction of the acidic drugs from a flowing stream donor (pH 1.7) into an alkaline stagnant acceptor (20 mmol L -1 NaOH) containing 10% MeOH (v/v) across a dihexyl ether impregnated CNF@HF membrane. The flow setup features entire automation of the microextraction process including regeneration of the organic film and on-line injection of the analyte-laden acceptor phase after downstream neutralization into a liquid chromatograph (LC) for reversed-phase core-shell column-based separation. Using a 12-cm long CNF@HF and a sample volume of 6.4 mL, linear dynamic ranges of ketoprofen, naproxen, diclofenac and ibuprofen, taken as models of non-steroidal anti-inflammatory drugs, spanned from ca. 5-15 µg L -1 to 500 µg L -1 with enhancement factors of 43-97 (against a direct injection of 10 µL standards into LC), and limits of detection from 1.6 to 4.3 µg L -1 . Relative recoveries in real urine samples ranged from 97% to 105%, thus demonstrating the reliability of the automatic CNF@HF-LPME method for in-line matrix clean-up and determination of drugs in urine at therapeutically relevant concentrations. Copyright © 2018 Elsevier B.V. All rights reserved.

Clustering gene expression regulators: new approach to disease subtyping.

PubMed

Pyatnitskiy, Mikhail; Mazo, Ilya; Shkrob, Maria; Schwartz, Elena; Kotelnikova, Ekaterina

2014-01-01

One of the main challenges in modern medicine is to stratify different patient groups in terms of underlying disease molecular mechanisms as to develop more personalized approach to therapy. Here we propose novel method for disease subtyping based on analysis of activated expression regulators on a sample-by-sample basis. Our approach relies on Sub-Network Enrichment Analysis algorithm (SNEA) which identifies gene subnetworks with significant concordant changes in expression between two conditions. Subnetwork consists of central regulator and downstream genes connected by relations extracted from global literature-extracted regulation database. Regulators found in each patient separately are clustered together and assigned activity scores which are used for final patients grouping. We show that our approach performs well compared to other related methods and at the same time provides researchers with complementary level of understanding of pathway-level biology behind a disease by identification of significant expression regulators. We have observed the reasonable grouping of neuromuscular disorders (triggered by structural damage vs triggered by unknown mechanisms), that was not revealed using standard expression profile clustering. For another experiment we were able to suggest the clusters of regulators, responsible for colorectal carcinoma vs adenoma discrimination and identify frequently genetically changed regulators that could be of specific importance for the individual characteristics of cancer development. Proposed approach can be regarded as biologically meaningful feature selection, reducing tens of thousands of genes down to dozens of clusters of regulators. Obtained clusters of regulators make possible to generate valuable biological hypotheses about molecular mechanisms related to a clinical outcome for individual patient.

Clustering Gene Expression Regulators: New Approach to Disease Subtyping

PubMed Central

Pyatnitskiy, Mikhail; Mazo, Ilya; Shkrob, Maria; Schwartz, Elena; Kotelnikova, Ekaterina

2014-01-01

One of the main challenges in modern medicine is to stratify different patient groups in terms of underlying disease molecular mechanisms as to develop more personalized approach to therapy. Here we propose novel method for disease subtyping based on analysis of activated expression regulators on a sample-by-sample basis. Our approach relies on Sub-Network Enrichment Analysis algorithm (SNEA) which identifies gene subnetworks with significant concordant changes in expression between two conditions. Subnetwork consists of central regulator and downstream genes connected by relations extracted from global literature-extracted regulation database. Regulators found in each patient separately are clustered together and assigned activity scores which are used for final patients grouping. We show that our approach performs well compared to other related methods and at the same time provides researchers with complementary level of understanding of pathway-level biology behind a disease by identification of significant expression regulators. We have observed the reasonable grouping of neuromuscular disorders (triggered by structural damage vs triggered by unknown mechanisms), that was not revealed using standard expression profile clustering. For another experiment we were able to suggest the clusters of regulators, responsible for colorectal carcinoma vs adenoma discrimination and identify frequently genetically changed regulators that could be of specific importance for the individual characteristics of cancer development. Proposed approach can be regarded as biologically meaningful feature selection, reducing tens of thousands of genes down to dozens of clusters of regulators. Obtained clusters of regulators make possible to generate valuable biological hypotheses about molecular mechanisms related to a clinical outcome for individual patient. PMID:24416320

Genotoxic substances in the St. Lawrence system. 1: Industrial genotoxins sorbed to particulate matter in the St. Lawrence, St. Maurice, and Saguenay rivers, Canada

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, P.A.; Rasmussen, J.B.; Blaise, C.

1998-02-01

Previous investigations of organic genotoxins in industrial effluents discharged into the St. Lawrence River system (Quebec, Canada) indicated that a substantial fraction of the genotoxicity is adsorbed to suspended particulate matter. This study used the SOS Chromotest to investigate the presence, potency, and behavior of particle-bound genotoxins in the downstream ecosystem. The results indicate that although extracts of both suspended and sedimented particulate matter are genotoxic, suspended particulate matter samples are more potent in the absence of S9 activation, with the reverse being true for bottom sediments. The results confirmed a positive relationship between the genotoxicity of bottom sediment extractsmore » and sediment organic matter content. A similar relationship between organic matter content and total polycyclic aromatic hydrocarbon (PAH) concentration indicates that putative genotoxins have physicochemical properties similar to the PAH class of contaminants. Conversion of PAH values to benzo[a]pyrene equivalents indicates that measured PAHs only account for a small fraction ({approximately}10%) of the observed SOS Chromotest response. Sites that receive discharges from foundries, aluminum refineries, and petroleum refineries yielded several of the most genotoxic samples. Further analyses revealed that the genotoxicity of suspended and sedimented particulate matter extracts is empirically related to the genotoxicity of industrial discharges. Comparisons of total genotoxicity levels in suspended particulates and bottom sediments suggest that direct-acting substances adsorbed to suspended matter are rapidly degraded and/or converted to more stable progenotoxins upon deposition. Further research is required to test this hypothesis and investigate effects on indigenous biota.« less

40 CFR 89.308 - Sampling system requirements for gaseous emissions.

Code of Federal Regulations, 2010 CFR

2010-07-01

...) For each component (pump, sample line section, filters, and so forth) in the heated portion of the... mass and the oven temperature need be measured. (b) If water is removed by condensation, the sample gas temperature shall be monitored within the water trap or the sample dewpoint shall be monitored downstream. In...

40 CFR 89.308 - Sampling system requirements for gaseous emissions.

Code of Federal Regulations, 2014 CFR

2014-07-01

...) For each component (pump, sample line section, filters, and so forth) in the heated portion of the... mass and the oven temperature need be measured. (b) If water is removed by condensation, the sample gas temperature shall be monitored within the water trap or the sample dewpoint shall be monitored downstream. In...

40 CFR 89.308 - Sampling system requirements for gaseous emissions.

Code of Federal Regulations, 2013 CFR

2013-07-01

...) For each component (pump, sample line section, filters, and so forth) in the heated portion of the... mass and the oven temperature need be measured. (b) If water is removed by condensation, the sample gas temperature shall be monitored within the water trap or the sample dewpoint shall be monitored downstream. In...

40 CFR 89.308 - Sampling system requirements for gaseous emissions.

Code of Federal Regulations, 2011 CFR

2011-07-01

...) For each component (pump, sample line section, filters, and so forth) in the heated portion of the... mass and the oven temperature need be measured. (b) If water is removed by condensation, the sample gas temperature shall be monitored within the water trap or the sample dewpoint shall be monitored downstream. In...

40 CFR 89.308 - Sampling system requirements for gaseous emissions.

Code of Federal Regulations, 2012 CFR

2012-07-01

...) For each component (pump, sample line section, filters, and so forth) in the heated portion of the... mass and the oven temperature need be measured. (b) If water is removed by condensation, the sample gas temperature shall be monitored within the water trap or the sample dewpoint shall be monitored downstream. In...

A novel microalgal lipid extraction method using biodiesel (fatty acid methyl esters) as an extractant.

PubMed

Huang, Wen-Can; Park, Chan Woo; Kim, Jong-Duk

2017-02-01

Although microalgae are considered promising renewable sources of biodiesel, the high cost of the downstream process is a significant obstacle in large-scale biodiesel production. In this study, a novel approach for microalgal biodiesel production was developed by using the biodiesel as an extractant. First, wet microalgae with 70% water content were incubated with a mixture of biodiesel/methanol and penetration of the mixture through the cell membrane and swelling of the lipids contained in microalgae was confirmed. Significant increases of lipid droplets were observed by confocal microscopy. Second, the swelled lipid droplets in microalgae were squeezed out using mechanical stress across the cell membrane and washed with methanol. The lipid extraction efficiency reached 68%. This process does not require drying of microalgae or solvent recovery, which the most energy-intensive step in solvent-based biodiesel production. Copyright © 2016 Elsevier Ltd. All rights reserved.

Extraction of oil from microalgae for biodiesel production: A review.

PubMed

Halim, Ronald; Danquah, Michael K; Webley, Paul A

2012-01-01

The rapid increase of CO(2) concentration in the atmosphere combined with depleted supplies of fossil fuels has led to an increased commercial interest in renewable fuels. Due to their high biomass productivity, rapid lipid accumulation, and ability to survive in saline water, microalgae have been identified as promising feedstocks for industrial-scale production of carbon-neutral biodiesel. This study examines the principles involved in lipid extraction from microalgal cells, a crucial downstream processing step in the production of microalgal biodiesel. We analyze the different technological options currently available for laboratory-scale microalgal lipid extraction, with a primary focus on the prospect of organic solvent and supercritical fluid extraction. The study also provides an assessment of recent breakthroughs in this rapidly developing field and reports on the suitability of microalgal lipid compositions for biodiesel conversion. Copyright © 2012 Elsevier Inc. All rights reserved.

2013 Flood Waters "Flush" Pharmaceuticals and other Contaminants of Emerging Concern into the Water and Sediment of the South Platte River, Colorado

NASA Astrophysics Data System (ADS)

Battaglin, W. A.; Bradley, P. M.; Paschke, S.; Plumlee, G. S.; Kimbrough, R.

2016-12-01

In September 2013, heavy rainfall caused severe flooding in Rocky Mountain National Park (ROMO) and environs extending downstream into the main stem of the South Platte River. In ROMO, flooding damaged infrastructure and local roads. In the tributary canyons, flooding damaged homes, septic systems, and roads. On the plains, flooding damaged several wastewater treatment plants. The occurrence and fate of pharmaceuticals and other contaminants of emerging concern (CECs) in streams during flood conditions is poorly understood. We assessed the occurrence and fate of CECs in this flood by collecting water samples (post-peak flow) from 4 headwaters sites in ROMO, 7 sites on tributaries to the South Platte River, and 6 sites on the main stem of the South Platte; and by collecting flood sediment samples (post-flood depositional) from 14 sites on tributaries and 10 sites on the main stem. Water samples were analysed for 110 pharmaceuticals and 69 wastewater indicators. Sediment samples were analysed for 57 wastewater indicators. Concentrations and numbers of CECs detected in water increased markedly as floodwaters moved downstream and some were not diluted despite the large flow increases in downstream reaches of the affected rivers. For example, in the Cache la Poudre River in ROMO, no pharmaceuticals and 1 wastewater indicator compound (camphor) were detected. At Greeley, the Cache la Poudre was transporting 19 pharmaceuticals [total concentration of 0.69 parts-per-billion (ppb)] and 22 wastewater indicators (total concentration of 2.81 ppb). In the South Platte downstream from Greeley, 24 pharmaceuticals (total concentration of 1.47 ppb) and 24 wastewater indicators (total concentration of 2.35 ppb) were detected. Some CECs such as the combustion products pyrene, fluoranthene, and benzo(a)pyrene were detected only at sub-ppb concentrations in water, but were detected at concentrations in the hundreds of ppb in flood sediment samples.

Impact of Tropopause Structures on Deep Convective Transport Observed during MACPEX

NASA Astrophysics Data System (ADS)

Mullendore, G. L.; Bigelbach, B. C.; Christensen, L. E.; Maddox, E.; Pinkney, K.; Wagner, S.

2016-12-01

Deep convection is the most efficient method of transporting boundary layer mass to the upper troposphere and stratosphere (UTLS). The Mid-latitude Airborne Cirrus Properties Experiment (MACPEX) was conducted during April of 2011 over the central U.S. With a focus on cirrus clouds, the campaign flights often sampled large cirrus anvils downstream from deep convection and included an extensive observational suite of chemical measurements on a high altitude aircraft. As double-tropopause structures are a common feature in the central U.S. during the springtime, the MACPEX campaign provides a good opportunity to gather cases of deep convective transport in the context of both single and double tropopause structures. Sampling of chemical plumes well downstream from convection allows for sampling in relatively quiescent conditions and analysis of irreversible transport. The analysis presented includes multiple methods to assess air mass source and possible convective processing, including back trajectories and ratios of chemical concentrations. Although missions were flown downstream of deep convection, recent processing by convection does not seem likely in all cases that high altitude carbon monoxide plumes were observed. Additionally, the impact of single and double tropopause structures on deep convective transport is shown to be strongly dependent on high stability layers.

Evaluation Of A Powder-Free DNA Extraction Method For Skeletal Remains.

PubMed

Harrel, Michelle; Mayes, Carrie; Gangitano, David; Hughes-Stamm, Sheree

2018-02-07

Bones are often recovered in forensic investigations, including missing persons and mass disasters. While traditional DNA extraction methods rely on grinding bone into powder prior to DNA purification, the TBone Ex buffer (DNA Chip Research Inc.) digests bone chips without powdering. In this study, six bones were extracted using the TBone Ex kit in conjunction with the PrepFiler ® BTA™ DNA extraction kit (Thermo Fisher Scientific) both manually and via an automated platform. Comparable amounts of DNA were recovered from a 50 mg bone chip using the TBone Ex kit and 50 mg of powdered bone with the PrepFiler ® BTA™ kit. However, automated DNA purification decreased DNA yield (p < 0.05). Nevertheless, short tandem repeat (STR) success was comparable across all methods tested. This study demonstrates that digestion of whole bone fragments is an efficient alternative to powdering bones for DNA extraction without compromising downstream STR profile quality. © 2018 American Academy of Forensic Sciences.

Downstream extraction process development for recovery of organic acids from a fermentation broth.

PubMed

Bekatorou, Argyro; Dima, Agapi; Tsafrakidou, Panagiotia; Boura, Konstantina; Lappa, Katerina; Kandylis, Panagiotis; Pissaridi, Katerina; Kanellaki, Maria; Koutinas, Athanasios A

2016-11-01

The present study focused on organic acids (OAs) recovery from an acidogenic fermentation broth, which is the main problem regarding the use of OAs for production of ester-based new generation biofuels or other applications. Specifically, 10 solvents were evaluated for OAs recovery from aqueous media and fermentation broths. The effects of pH, solvent/OAs solution ratios and application of successive extractions were studied. The 1:1 solvent/OAs ratio showed the best recovery rates in most cases. Butyric and isobutyric acids showed the highest recovery rates (80-90%), while lactic, succinic, and acetic acids were poorly recovered (up to 45%). The OAs recovery was significantly improved by successive 10-min extractions. Alcohols presented the best extraction performance. The process using repeated extractions with 3-methyl-1-butanol led to the highest OAs recovery. However, 1-butanol can be considered as the most cost-effective option taking into account its price and availability. Copyright © 2016 Elsevier Ltd. All rights reserved.

Analytical and numerical studies of positive ion beam expansion for surface treatment applications

NASA Astrophysics Data System (ADS)

Lounes-Mahloul, Soumya; Bendib, Abderrezeg; Oudini, Noureddine

2018-01-01

The aim of this work is to study the expansion in vacuum, of a positive ion beam with the use of one dimensional (1D) analytic model and a two dimensional Particle-In-Cell (2D-PIC) simulation. The ion beam is extracted and accelerated from preformed plasma by an extraction system composed of two polarized parallel perforated grids. The results obtained with both approaches reveal the presence of a potential barrier downstream the extraction system which tends to reflect the ion flux. The dependence of the critical distance for which all extracted ions are reflected, is investigated as a function of the extracted ion beam current density. In particular, it is shown that the 1D model recovers the well-known Child-Langmuir law and that the 2D simulation presents a significant discrepancy with respect to the 1D prediction. Indeed, for a given value of current density, the transverse effects lead to a greater critical distance.

Sequences downstream of AAUAAA signals affect pre-mRNA cleavage and polyadenylation in vitro both directly and indirectly.

PubMed Central

Ryner, L C; Takagaki, Y; Manley, J L

1989-01-01

To investigate the role of sequences lying downstream of the conserved AAUAAA hexanucleotide in pre-mRNA cleavage and polyadenylation, deletions or substitutions were constructed in polyadenylation signals from simian virus 40 and adenovirus, and their effects were assayed in both crude and fractionated HeLa cell nuclear extracts. As expected, these sequences influenced the efficiency of both cleavage and polyadenylation as well as the accuracy of the cleavage reaction. Sequences near or upstream of the actual site of poly(A) addition appeared to specify a unique cleavage site, since their deletion resulted, in some cases, in heterogeneous cleavage. Furthermore, the sequences that allowed the simian virus 40 late pre-RNA to be cleaved preferentially by partially purified cleavage activity were also those at the cleavage site itself. Interestingly, sequences downstream of the cleavage site interacted with factors not directly involved in catalyzing cleavage and polyadenylation, since the effects of deletions were substantially diminished when partially purified components were used in assays. In addition, these sequences contained elements that could affect 3'-end formation both positively and negatively. Images PMID:2566911

Adjustable shear stress erosion and transport flume

DOEpatents

Roberts, Jesse D.; Jepsen, Richard A.

2002-01-01

A method and apparatus for measuring the total erosion rate and downstream transport of suspended and bedload sediments using an adjustable shear stress erosion and transport (ASSET) flume with a variable-depth sediment core sample. Water is forced past a variable-depth sediment core sample in a closed channel, eroding sediments, and introducing suspended and bedload sediments into the flow stream. The core sample is continuously pushed into the flow stream, while keeping the surface level with the bottom of the channel. Eroded bedload sediments are transported downstream and then gravitationally separated from the flow stream into one or more quiescent traps. The captured bedload sediments (particles and aggregates) are weighed and compared to the total mass of sediment eroded, and also to the concentration of sediments suspended in the flow stream.

Fit for purpose frozen tissue collections by RNA integrity number-based quality control assurance at the Erasmus MC tissue bank.

PubMed

Kap, Marcel; Oomen, Monique; Arshad, Shazia; de Jong, Bas; Riegman, Peter

2014-04-01

About 5000 frozen tissue samples are collected each year by the Erasmus Medical Center tissue bank. Two percent of these samples are randomly selected annually for RNA isolation and RNA Integrity Number (RIN) measurement. A similar quality assessment was conducted during centralization of a 20-year-old tissue collection from the cancer institute, a 15-year-old liver sample archive (-80°C), and a 13-year-old clinical pathology frozen biopsy archive (Liquid Nitrogen). Samples were divided into either high-quality (RIN ≥6.5) or low-quality overall categories, or into four "fit-for-purpose" quality groups: RIN <5: not reliable for demanding downstream analysis; 5 ≤RIN <6: suitable for RT-qPCR; 6 ≤RIN <8: suitable for gene array analysis; and RIN ≥8: suitable for all downstream techniques. In general, low RIN values were correlated with fatty, fibrous, pancreatic, or necrotic tissue. When the percentage of samples with RIN ≥6.5 is higher than 90%, the tissue bank performance is adequate. The annual 2011 quality control assessment showed that 90.3% (n=93) of all samples had acceptable RIN values; 97.4% (n=39) of the cancer institute collection had RIN values above 6.5; and 88.6% (n=123) of samples from the liver sample archive collection had RIN values higher than 6.5. As the clinical pathology biopsy collection contained only 58.8% (n=24) acceptable samples, the procurement protocols used for these samples needed immediate evaluation. When the distribution of RIN values of the different collections were compared, no significant differences were found, despite differences in average storage time and temperature. According to the principle of "fit-for-purpose" distribution, the vast majority of samples are considered good enough for most downstream techniques. In conclusion, an annual tissue bank quality control procedure provides useful information on tissue sample quality and sheds light on where and if improvements need to be made.

Purifying, Separating, and Concentrating Cells From a Sample Low in Biomass

NASA Technical Reports Server (NTRS)

Benardini, James N.; LaDuc, Myron T.; Diamond, Rochelle

2012-01-01

Frequently there is an inability to process and analyze samples of low biomass due to limiting amounts of relevant biomaterial in the sample. Furthermore, molecular biological protocols geared towards increasing the density of recovered cells and biomolecules of interest, by their very nature, also concentrate unwanted inhibitory humic acids and other particulates that have an adversarial effect on downstream analysis. A novel and robust fluorescence-activated cell-sorting (FACS)-based technology has been developed for purifying (removing cells from sampling matrices), separating (based on size, density, morphology), and concentrating cells (spores, prokaryotic, eukaryotic) from a sample low in biomass. The technology capitalizes on fluorescent cell-sorting technologies to purify and concentrate bacterial cells from a low-biomass, high-volume sample. Over the past decade, cell-sorting detection systems have undergone enhancements and increased sensitivity, making bacterial cell sorting a feasible concept. Although there are many unknown limitations with regard to the applicability of this technology to environmental samples (smaller cells, few cells, mixed populations), dogmatic principles support the theoretical effectiveness of this technique upon thorough testing and proper optimization. Furthermore, the pilot study from which this report is based proved effective and demonstrated this technology capable of sorting and concentrating bacterial endospore and bacterial cells of varying size and morphology. Two commercial off-the-shelf bacterial counting kits were used to optimize a bacterial stain/dye FACS protocol. A LIVE/DEAD BacLight Viability and Counting Kit was used to distinguish between the live and dead cells. A Bacterial Counting Kit comprising SYTO BC (mixture of SYTO dyes) was employed as a broad-spectrum bacterial counting agent. Optimization using epifluorescence microscopy was performed with these two dye/stains. This refined protocol was further validated using varying ratios and mixtures of cells to ensure homogenous staining compared to that of individual cells, and were utilized for flow analyzer and FACS labeling. This technology focuses on the purification and concentration of cells from low-biomass spacecraft assembly facility samples. Currently, purification and concentration of low-biomass samples plague planetary protection downstream analyses. Having a capability to use flow cytometry to concentrate cells out of low-biomass, high-volume spacecraft/ facility sample extracts will be of extreme benefit to the fields of planetary protection and astrobiology. Successful research and development of this novel methodology will significantly increase the knowledge base for designing more effective cleaning protocols, and ultimately lead to a more empirical and true account of the microbial diversity present on spacecraft surfaces. Refined cleaning and an enhanced ability to resolve microbial diversity may decrease the overall cost of spacecraft assembly and/or provide a means to begin to assess challenging planetary protection missions.

Wind tunnel measurements of the dilution of tailpipe emissions downstream of a car, a light-duty truck, and a heavy-duty truck tractor head.

PubMed

Chang, Victor W C; Hildemann, Lynn M; Chang, Cheng-hisn

2009-06-01

The particle and gaseous pollutants in vehicle exhaust emissions undergo rapid dilution with ambient air after exiting the tailpipe. The rate and extent of this dilution can greatly affect both the size evolution of primary exhaust particles and the potential for formation of ultrafine particles. Dilution ratios were measured inside of a wind tunnel in the region immediately downstream of the tailpipe using model vehicles (approximately one-fifth to one-seventh scale models) representing a light-duty truck, a passenger car, and a heavy-duty tractor head (without the trailer). A tracer gas (ethene) was released at a measured flow rate from the tailpipe, and 60 sampling probes placed downstream of the vehicle simultaneously sampled gas tracer concentrations in the near-wake (first few vehicle heights) and far-wake regions (beyond 10 vehicle heights). Tests using different tunnel wind speeds show the range of dilution ratios that can be expected as a function of vehicle type and downstream distance (i.e., time). The vehicle shape quite strongly influences dilution profiles in the near-wake region but is much less important in the far-wake region. The tractor generally produces higher dilution rates than the automobile and light-duty truck under comparable conditions.

Influence of wastewater treatment plant discharges on microplastic concentrations in surface water.

PubMed

Estahbanati, Shirin; Fahrenfeld, N L

2016-11-01

The abundance of microplastic particles in the marine environment is well documented, but less is known about microplastics in the freshwater environment. Wastewater treatment plants (WWTPs) may not effectively remove microplastics allowing for their release to the freshwater environment. To investigate concentration of microplastic in fresh water and the impact of WWTP effluent, samples were collected upstream and downstream of four major municipal WWTPs on the Raritan River, NJ. Microplastics were categorized into three quantitative categories (500-2000 μm, 250-500 μm, 125-250 μm), and one semi-quantitative category (63-125 μm). Then, microplastics were classified as primary (manufactured in small size) or secondary (derived from larger plastics) based on morphology. The concentration of microplastics in the 125-250 and 250-500 μm size categories significantly increased downstream of WWTP. The smaller size classes, often not quantified in microplastic studies, were in high relative abundance across sampling sites. While primary microplastics significantly increased downstream of WWTP, secondary microplastic was the dominant type in the quantitative size categories (66-88%). A moderate correlation between microplastic and distance downstream was observed. These results have implications for understanding the fate and transport of microplastics in the freshwater environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Meltwater export of prokaryotic cells from the Greenland ice sheet.

PubMed

Cameron, Karen A; Stibal, Marek; Hawkings, Jon R; Mikkelsen, Andreas B; Telling, Jon; Kohler, Tyler J; Gözdereliler, Erkin; Zarsky, Jakub D; Wadham, Jemma L; Jacobsen, Carsten S

2017-02-01

Microorganisms are flushed from the Greenland Ice Sheet (GrIS) where they may contribute towards the nutrient cycling and community compositions of downstream ecosystems. We investigate meltwater microbial assemblages as they exit the GrIS from a large outlet glacier, and as they enter a downstream river delta during the record melt year of 2012. Prokaryotic abundance, flux and community composition was studied, and factors affecting community structures were statistically considered. The mean concentration of cells exiting the ice sheet was 8.30 × 10 4 cells mL -1 and we estimate that ∼1.02 × 10 21 cells were transported to the downstream fjord in 2012, equivalent to 30.95 Mg of carbon. Prokaryotic microbial assemblages were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Cell concentrations and community compositions were stable throughout the sample period, and were statistically similar at both sample sites. Based on our observations, we argue that the subglacial environment is the primary source of the river-transported microbiota, and that cell export from the GrIS is dependent on discharge. We hypothesise that the release of subglacial microbiota to downstream ecosystems will increase as freshwater flux from the GrIS rises in a warming world. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

RNA extraction from self-assembling peptide hydrogels to allow qPCR analysis of encapsulated cells.

PubMed

Burgess, Kyle A; Workman, Victoria L; Elsawy, Mohamed A; Miller, Aline F; Oceandy, Delvac; Saiani, Alberto

2018-01-01

Self-assembling peptide hydrogels offer a novel 3-dimensional platform for many applications in cell culture and tissue engineering but are not compatible with current methods of RNA isolation; owing to interactions between RNA and the biomaterial. This study investigates the use of two techniques based on two different basic extraction principles: solution-based extraction and direct solid-state binding of RNA respectively, to extract RNA from cells encapsulated in four β-sheet forming self-assembling peptide hydrogels with varying net positive charge. RNA-peptide fibril interactions, rather than RNA-peptide molecular complexing, were found to interfere with the extraction process resulting in low yields. A column-based approach relying on RNA-specific binding was shown to be more suited to extracting RNA with higher purity from these peptide hydrogels owing to its reliance on strong specific RNA binding interactions which compete directly with RNA-peptide fibril interactions. In order to reduce the amount of fibrils present and improve RNA yields a broad spectrum enzyme solution-pronase-was used to partially digest the hydrogels before RNA extraction. This pre-treatment was shown to significantly increase the yield of RNA extracted, allowing downstream RT-qPCR to be performed.

Nutrient Concentrations, Loads, and Yields in the Eucha-Spavinaw Basin, Arkansas and Oklahoma, 2002-2006

USGS Publications Warehouse

Tortorelli, Robert L.

2008-01-01

The City of Tulsa, Oklahoma, uses Lake Eucha and Spavinaw Lake in the Eucha-Spavinaw basin in northwestern Arkansas and northeastern Oklahoma for public water supply. Taste and odor problems in the water attributable to blue-green algae have increased in frequency. Changes in the algae community in the lakes may be attributable to increases in nutrient levels in the lakes, and in the waters feeding the lakes. The U.S. Geological Survey, in cooperation with the City of Tulsa, investigated and summarized nitrogen and phosphorus concentrations and provided estimates of nitrogen and phosphorus loads, yields, and flow-weighted concentrations in the Eucha-Spavinaw basin for three 3-year periods - 2002-2004, 2003-2005, and 2004-2006, to update a previous report that used data from water-quality samples for a 3-year period from January 2002 through December 2004. This report provides information needed to advance knowledge of the regional hydrologic system and understanding of hydrologic processes, and provides hydrologic data and results useful to multiple agencies for interstate agreements. Nitrogen and phosphorus concentrations were significantly greater in runoff samples than in base-flow samples for all three periods at Spavinaw Creek near Maysville, Arkansas; Spavinaw Creek near Colcord, Oklahoma, and Beaty Creek near Jay, Oklahoma. Runoff concentrations were not significantly greater than base-flow concentrations at Spavinaw Creek near Cherokee, Arkansas; and Spavinaw Creek near Sycamore, Oklahoma except for phosphorus during 2003-2005. Nitrogen concentrations in base-flow samples significantly increased downstream in Spavinaw Creek from the Maysville to Sycamore stations then significantly decreased from the Sycamore to the Colcord stations for all three periods. Nitrogen in base-flow samples from Beaty Creek was significantly less than in samples from Spavinaw Creek. Phosphorus concentrations in base-flow samples significantly increased from the Maysville to Cherokee stations in Spavinaw Creek for all three periods, probably because of a wastewater-treatment plant point source between those stations, and then significantly decreased downstream from the Cherokee to Colcord stations. Phosphorus in base-flow samples from Beaty Creek was significantly less than phosphorus in base-flow samples from Spavinaw Creek downstream from the Maysville station. Nitrogen concentrations in runoff samples were not significantly different among the stations on Spavinaw Creek for most of the three periods, except during 2003-2005 when runoff samples at the Colcord station were less than at the Sycamore station; however, the concentrations at Beaty Creek were significantly less than at all other stations. Phosphorus concentrations in runoff samples were not significantly different among the three downstream stations on Spavinaw Creek and were significantly different at the Maysville station on Spavinaw Creek and the Beaty Creek station, only during 2004-2006. Phosphorus and nitrogen concentrations in runoff samples from all stations generally increased with increasing streamflow. Estimated mean annual nitrogen total loads for the three 3-year periods were substantially greater at the Spavinaw Creek stations than at Beaty Creek and increased downstream from Maysville to Colcord in Spavinaw Creek, with the load at the Colcord station about 2 times that at Maysville station. Estimated mean annual nitrogen base-flow loads at the Spavinaw Creek stations were about 5 to 11 times greater than base-flow loads at Beaty Creek. The runoff component of the annual nitrogen total load for Beaty Creek was 85 to 89 percent; whereas, the range in the runoff component at the Spavinaw Creek stations was 60 to 71 percent. Estimated mean annual phosphorus total loads for the three 3-year periods were greater at the Spavinaw Creek stations from Cherokee to Colcord than at Beaty Creek and increased downstream from Maysville to Colcord in Spavinaw Creek, wit

Specific Interaction between Redox Phospholipid Polymers and Plastoquinone in Photosynthetic Electron Transport Chain.

PubMed

Tanaka, Kenya; Kaneko, Masahiro; Ishikawa, Masahito; Kato, Souichiro; Ito, Hidehiro; Kamachi, Toshiaki; Kamiya, Kazuhide; Nakanishi, Shuji

2017-04-19

Redox phospholipid polymers added in culture media are known to be capable of extracting electrons from living photosynthetic cells across bacterial cell membranes with high cytocompatibility. In the present study, we identify the intracellular redox species that transfers electrons to the polymers. The open-circuit electrochemical potential of an electrolyte containing the redox polymer and extracted thylakoid membranes shift to positive (or negative) under light irradiation, when an electron transport inhibitor specific to plastoquinone is added upstream (or downstream) in the photosynthetic electron transport chain. The same trend is also observed for a medium containing living photosynthetic cells of Synechococcus elongatus PCC7942. These results clearly indicate that the phospholipid redox polymers extract photosynthetic electrons mainly from plastoquinone. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of signal transduction in cell-free extracts and rafts of Xenopus eggs.

PubMed

Tokmakov, Alexander A; Iwasaki, Tetsushi; Sato, Ken-Ichi; Fukami, Yasuo

2010-05-01

Intracellular signaling during egg activation/fertilization has been extensively studied using intact eggs, which can be manipulated by microinjection of different mRNAs, proteins, or chemical drugs. Furthermore, egg extracts, which retain high CSF activity (CSF-arrested extracts), were developed for studying fertilization/activation signal transduction, which have significant advantages as a model system. The addition of calcium to CSF-arrested extracts initiates a plethora of signaling events that take place during egg activation. Hence, the signaling downstream of calcium mobilization has been successfully studied in the egg extracts. Moreover, despite disruption of membrane-associated signaling compartments and ordered compartmentalization during extract preparation, CSF-arrested extracts can be successfully used to study early signaling events, which occur upstream of calcium release during egg activation/fertilization. In combination with the CSF-arrested extracts, activated egg rafts can reproduce some events of egg activation, including PLCgamma activation, IP3 production, transient calcium release, MAPK inactivation, and meiotic exit. This becomes possible due to complementation of the sperm-induced egg activation signaling machinery present in the rafts with the components of signal transduction system localized in the extracts. Herein, we describe protocols for studying molecular mechanisms of egg fertilization/activation using cell-free extracts and membrane rafts prepared from metaphase-arrested Xenopus eggs.

40 CFR 80.69 - Requirements for downstream oxygenate blending.

Code of Federal Regulations, 2013 CFR

2013-07-01

... PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Reformulated Gasoline § 80.69 Requirements for... produced or imported. (7) Conduct a quality assurance sampling and testing program to be carried out at the.... (i) The sampling and testing program shall be conducted as follows: (A) All samples shall be...

40 CFR 80.69 - Requirements for downstream oxygenate blending.

Code of Federal Regulations, 2014 CFR

2014-07-01

... PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Reformulated Gasoline § 80.69 Requirements for... produced or imported. (7) Conduct a quality assurance sampling and testing program to be carried out at the.... (i) The sampling and testing program shall be conducted as follows: (A) All samples shall be...

40 CFR 80.69 - Requirements for downstream oxygenate blending.

Code of Federal Regulations, 2012 CFR

2012-07-01

... PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Reformulated Gasoline § 80.69 Requirements for... produced or imported. (7) Conduct a quality assurance sampling and testing program to be carried out at the.... (i) The sampling and testing program shall be conducted as follows: (A) All samples shall be...

Characterization of organic composition in snow and surface waters in the Athabasca Oil Sands Region, using ultrahigh resolution Fourier transform mass spectrometry.

PubMed

Yi, Y; Birks, S J; Cho, S; Gibson, J J

2015-06-15

This study was conducted to characterize the composition of dissolved organic compounds present in snow and surface waters in the Athabasca Oil Sands Region (AOSR) with the goal of identifying whether atmospherically-derived organic compounds present in snow are a significant contributor to the compounds detected in surface waters (i.e., rivers and lakes). We used electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) to characterize the dissolved organic compound compositions of snow and surface water samples. The organic profiles obtained for the snow samples show compositional differences between samples from near-field sites (<5 km from oil sands activities) and those from more distant locations (i.e., far-field sites). There are also significant compositional differences between samples collected in near-field sites and surface water samples in the AOSR. The composition of dissolved organic compounds at the upstream Athabasca River site (i.e., Athabasca River at Athabasca) is found to be different from samples obtained from downstream sites in the vicinity of oil sands operations (i.e., Athabasca River at Fort McMurray and Athabasca River at Firebag confluence). The upstream Athabasca River sites tended to share some compositional similarities with far-field snow deposition, while the downstream Athabasca River sites are more similar to local lakes and tributaries. This contrast likely indicates the relative role of regional snowmelt contributions to the Athabasca River vs inputs from local catchments in the reach downstream of Fort McMurray. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of urbanization, construction activity, management practices, and impoundments on suspended-sediment transport in Johnson County, northeast Kansas, February 2006 through November 2008

USGS Publications Warehouse

Lee, Casey J.; Ziegler, Andrew C.

2010-01-01

The U.S. Geological Survey, in cooperation with the Johnson County, Kansas, Stormwater Management Program, investigated the effects of urbanization, construction activity, management practices, and impoundments on suspended-sediment transport in Johnson County from February 2006 through November 2008. Streamgages and continuous turbidity sensors were operated at 15 sites within the urbanizing 57-square-mile Mill Creek Basin, and 4 sites downstream from the other largest basins (49 to 66 square miles) in Johnson County. The largest sediment yields in Johnson County were observed downstream from basins with increased construction activity. Sediment yields attributed to the largest (68 acre) active construction site in the study area were 9,300 tons per square mile in 2007 and 12,200 tons per square mile in 2008; 5 to 55 times larger than yields observed at other sampling sites. However, given erodible soils and steep slopes at this site, sediment yields were relatively small compared to the range in historic values from construction sites without erosion and sediment controls in the United States (2,300 to 140,000 tons per square mile). Downstream from this construction site, a sediment forebay and wetland were constructed in series upstream from Shawnee Mission Lake, a 120-acre reservoir within Shawnee Mission Park. Although the original intent of the sediment forebay and constructed wetland were unrelated to upstream construction, they were nonetheless evaluated in 2008 to characterize sediment removal before stream entry into the lake. The sediment forebay was estimated to reduce 33 percent of sediment transported to the lake, whereas the wetland did not appear to decrease downstream sediment transport. Comparisons of time-series data and relations between turbidity and sediment concentration indicate that larger silt-sized particles were deposited within the sediment forebay, whereas smaller silt and clay-sized sediments were transported through the wetland and into the lake. Data collected at sites up and downstream from the constructed wetland indicated that hydraulic retention alone did not substantially reduce sediment loading to Shawnee Mission Lake. Mean-daily turbidity values at sampling sites downstream from basins with increased construction activity were compared to U.S. Environmental Protection Agency turbidity criteria designed to reduce discharge of pollutants from construction sites. The U.S. Environmental Protection Agency numeric turbidity criteria specifies that effluent from construction sites greater than 20 acres not exceed a mean-daily turbidity value of 280 nephelometric turbidity units beginning in 2011; this criteria will apply to sites greater than 10 acres beginning in 2014. Although numeric criteria would not have been applicable to data from sampling sites in Johnson County because they were not directly downstream from construction sites and because individual states still have to determine additional details as to how this criteria will be enforced, comparisons were made to characterize the potential of construction site effluent in Johnson County to exceed U.S. Environmental Protection Agency Criteria, even under extensive erosion and sediment controls. Numeric criteria were exceeded at sampling sites downstream from basins with increased construction activity for multiple days during the study period, potentially indicating the need for additional erosion and sediment controls and (or) treatment to bring discharges from construction sites into compliance with future numeric turbidity criteria. Among sampling sites in the Mill Creek Basin, sediment yields from the urbanizing Clear Creek Basin were approximately 2 to 3 times those from older, more stable urban or rural basins. Sediments eroded from construction sites adjacent to or surrounding streams appear to be more readily transported downstream, whereas sediments eroded from construction sites in headwater areas are more likely to

Water Quality in Surface Water: A Preliminary Assessment of Heavy Metal Contamination of the Mashavera River, Georgia

PubMed Central

Urushadze, Teo

2018-01-01

Water quality contamination by heavy metal pollution has severe effects on public health. In the Mashavera River Basin, an important agricultural area for the national food system in Georgia (e.g., vegetable, dairy and wine production), water contamination has multiple influences on the regional and country-wide health. With new industrial activities in the region, sediment extraction, and discharge of untreated wastewater into the river, its tributaries and irrigation canals, a comprehensive study of water quality was greatly needed. This study examined sediment and water samples from 17 sampling sites in the Mashavera River Basin during the high and low precipitation seasons. The results were characterized utilizing the Geo-accumulation Index (Igeo), Enrichment Factor (EF), Pollution Load index (PLI), Contamination Factor (CF) and Metal Index (MI). According to the CFs, Cu > Cd > Zn > Pb > Fe > Mn > Ni > Cr > Hg is the descending order for the content of all observed heavy metals in sediments collected in both seasons. Fe and As were additionally examined in water samples. Overall, As, Cd and Pb, all highly toxic elements, were found in high concentrations in downstream sample sites. According to these results, comprehensive monitoring with narrow intervals between sampling dates, more sample sites along all waterways, and proximate observation of multiple trace metal elements are highly recommended. Moreover, as the part of the water quality governance system, an immediate and sustainable collective action by all stakeholders to control the pollution level is highly recommended, as this issue is linked to the security of the national food system and poses a local public health risk. PMID:29597320

Irreversible sorption of trace concentrations of perfluorocarboxylic acids to fiber filters used for air sampling

NASA Astrophysics Data System (ADS)

Arp, Hans Peter H.; Goss, Kai-Uwe

Due to the apparent environmental omnipresence of perfluorocarboxylic acids (PFAs), an increasing number of researchers are investigating their ambient particle- and gas-phase concentrations. Typically this is done using a high-volume air sampler equipped with Quartz Fiber Filters (QFFs) or Glass Fiber Filters (GFFs) to sample the particle-bound PFAs and downstream sorbents to sample the gas-phase PFAs. This study reports that at trace, ambient concentrations gas-phase PFAs sorb to QFFs and GFFs irreversibly and hardly pass through these filters to the downstream sorbents. As a consequence, it is not possible to distinguish between particle- and gas-phase concentrations, or to distinguish concentrations on different particle size fractions, unless precautions are taken. Failure to take such precautions could have already caused reported data to be misinterpreted. Here it is also reported that deactivating QFFs and GFFs with a silylating agent renders them suitable for sampling PFAs. Based on the presented study, a series of recommendations for air-sampling PFAs are provided.

Sample processor for the automatic extraction of families of compounds from liquid samples and/or homogenized solid samples suspended in a liquid

NASA Technical Reports Server (NTRS)

Jahnsen, Vilhelm J. (Inventor); Campen, Jr., Charles F. (Inventor)

1980-01-01

A sample processor and method for the automatic extraction of families of compounds, known as extracts, from liquid and/or homogenized solid samples are disclosed. The sample processor includes a tube support structure which supports a plurality of extraction tubes, each containing a sample from which families of compounds are to be extracted. The support structure is moveable automatically with respect to one or more extraction stations, so that as each tube is at each station a solvent system, consisting of a solvent and reagents, is introduced therein. As a result an extract is automatically extracted from the tube. The sample processor includes an arrangement for directing the different extracts from each tube to different containers, or to direct similar extracts from different tubes to the same utilization device.

Determination of the promoter region of mouse ribosomal RNA gene by an in vitro transcription system.

PubMed Central

Yamamoto, O; Takakusa, N; Mishima, Y; Kominami, R; Muramatsu, M

1984-01-01

Sequences required for a faithful and efficient transcription of a cloned mouse ribosomal RNA gene (rDNA) are determined by testing a series of deletion mutants in an in vitro transcription system utilizing two kinds of mouse cellular extract. Deletion of sequences upstream of -40 or downstream of +52 causes only slight reduction in promoter activity as compared with the "wild-type" template. For upstream deletion mutants, the removal of a sequence between -40 and -35 causes a significant decrease in the capacity to direct efficient initiation. This decrease becomes more pronounced when the deletion reaches -32 and the sequence A-T-C-T-T-T, conserved among mouse, rat, and human rDNAs, is lost. Residual template activity is further reduced as more upstream sequence is deleted and finally becomes undetectable when the deletion is extended from -22 down to -17, corresponding to the loss of the conserved sequence T-A-T-T-G. As for downstream deletion mutants, the removal of the sequence downstream of +23 causes some (and further deletions up to +11 cause a more) serious decrease in template activity in vitro. These deletions involve other conserved sequences downstream of the transcription start site. However, the removal of the original transcription start site does not abolish the transcription initiation completely, provided that the whole upstream sequence is intact. Images PMID:6320178

Characterization of Rous sarcoma virus polyadenylation site use in vitro

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maciolek, Nicole L.; McNally, Mark T.

2008-05-10

Polyadenylation of Rous sarcoma virus (RSV) RNA is inefficient, as approximately 15% of RSV RNAs represent read-through transcripts that use a downstream cellular polyadenylation site (poly(A) site). Read-through transcription has implications for the virus and the host since it is associated with oncogene capture and tumor induction. To explore the basis of inefficient RSV RNA 3'-end formation, we characterized RSV polyadenylation in vitro using HeLa cell nuclear extracts and HEK293 whole cell extracts. RSV polyadenylation substrates composed of the natural 3' end of viral RNA and various lengths of upstream sequence showed little or no polyadenylation, indicating that the RSVmore » poly(A) site is suboptimal. Efficiently used poly(A) sites often have identifiable upstream and downstream elements (USEs and DSEs) in close proximity to the conserved AAUAAA signal. The sequences upstream and downstream of the RSV poly(A) site deviate from those found in efficiently used poly(A) sites, which may explain inefficient RSV polyadenylation. To assess the quality of the RSV USEs and DSEs, the well-characterized SV40 late USEs and/or DSEs were substituted for the RSV elements and vice versa, which showed that the USEs and DSEs from RSV are suboptimal but functional. CstF interacted poorly with the RSV polyadenylation substrate, and the inactivity of the RSV poly(A) site was at least in part due to poor CstF binding since tethering CstF to the RSV substrate activated polyadenylation. Our data are consistent with poor polyadenylation factor binding sites in both the USE and DSE as the basis for inefficient use of the RSV poly(A) site and point to the importance of additional elements within RSV RNA in promoting 3' end formation.« less

Mechanical cell disruption of Parachlorella kessleri microalgae: Impact on lipid fraction composition.

PubMed

Clavijo Rivera, E; Montalescot, V; Viau, M; Drouin, D; Bourseau, P; Frappart, M; Monteux, C; Couallier, E

2018-05-01

Samples of nitrogen-starved Parachlorella kessleri containing intact cells (IC), cells ground by bead milling (BM), and cells subjected to high-pressure cell disruption (HPD), together with their supernatants after centrifugation, were compared for granulometry and lipid profiles. The effects of disruption on the lipid profile and organisation were evaluated. The quantity of lipids available for extraction increased with disruption, and up to 81% could be recovered in supernatants after centrifugation, but a marked reorganization occurred. The proportion of amphiphilic free fatty acids and lysophosphatidylcholine increased during disruption due to their release or owing to lipid degradation by enzymes or physical conditions. This effect was more marked in HPD than in BM. Lipids contained in the aqueous phase, after disruption and centrifugation, were enriched in unsaturated fatty acids, BM leading to larger droplets than HPD. The larger liquid lipid droplet would be easier to recover in the following downstream processing. Copyright © 2018 Elsevier Ltd. All rights reserved.

Surveying the repair of ancient DNA from bones via high-throughput sequencing.

PubMed

Mouttham, Nathalie; Klunk, Jennifer; Kuch, Melanie; Fourney, Ron; Poinar, Hendrik

2015-07-01

DNA damage in the form of abasic sites, chemically altered nucleotides, and strand fragmentation is the foremost limitation in obtaining genetic information from many ancient samples. Upon cell death, DNA continues to endure various chemical attacks such as hydrolysis and oxidation, but repair pathways found in vivo no longer operate. By incubating degraded DNA with specific enzyme combinations adopted from these pathways, it is possible to reverse some of the post-mortem nucleic acid damage prior to downstream analyses such as library preparation, targeted enrichment, and high-throughput sequencing. Here, we evaluate the performance of two available repair protocols on previously characterized DNA extracts from four mammoths. Both methods use endonucleases and glycosylases along with a DNA polymerase-ligase combination. PreCR Repair Mix increases the number of molecules converted to sequencing libraries, leading to an increase in endogenous content and a decrease in cytosine-to-thymine transitions due to cytosine deamination. However, the effects of Nelson Repair Mix on repair of DNA damage remain inconclusive.

Mitogen- and Stress-Activated Kinase 1 (MSK1) Regulates Cigarette Smoke-Induced Histone Modifications on NF-κB-dependent Genes

PubMed Central

Sundar, Isaac K.; Chung, Sangwoon; Hwang, Jae-woong; Lapek, John D.; Bulger, Michael; Friedman, Alan E.; Yao, Hongwei; Davie, James R.; Rahman, Irfan

2012-01-01

Cigarette smoke (CS) causes sustained lung inflammation, which is an important event in the pathogenesis of chronic obstructive pulmonary disease (COPD). We have previously reported that IKKα (I kappaB kinase alpha) plays a key role in CS-induced pro-inflammatory gene transcription by chromatin modifications; however, the underlying role of downstream signaling kinase is not known. Mitogen- and stress-activated kinase 1 (MSK1) serves as a specific downstream NF-κB RelA/p65 kinase, mediating transcriptional activation of NF-κB-dependent pro-inflammatory genes. The role of MSK1 in nuclear signaling and chromatin modifications is not known, particularly in response to environmental stimuli. We hypothesized that MSK1 regulates chromatin modifications of pro-inflammatory gene promoters in response to CS. Here, we report that CS extract activates MSK1 in human lung epithelial (H292 and BEAS-2B) cell lines, human primary small airway epithelial cells (SAEC), and in mouse lung, resulting in phosphorylation of nuclear MSK1 (Thr581), phospho-acetylation of RelA/p65 at Ser276 and Lys310 respectively. This event was associated with phospho-acetylation of histone H3 (Ser10/Lys9) and acetylation of histone H4 (Lys12). MSK1 N- and C-terminal kinase-dead mutants, MSK1 siRNA-mediated knock-down in transiently transfected H292 cells, and MSK1 stable knock-down mouse embryonic fibroblasts significantly reduced CS extract-induced MSK1, NF-κB RelA/p65 activation, and posttranslational modifications of histones. CS extract/CS promotes the direct interaction of MSK1 with RelA/p65 and p300 in epithelial cells and in mouse lung. Furthermore, CS-mediated recruitment of MSK1 and its substrates to the promoters of NF-κB-dependent pro-inflammatory genes leads to transcriptional activation, as determined by chromatin immunoprecipitation. Thus, MSK1 is an important downstream kinase involved in CS-induced NF-κB activation and chromatin modifications, which have implications in pathogenesis of COPD. PMID:22312446

Metals transport in the Sacramento River, California, 1996-1997; Volume 1, Methods and data

USGS Publications Warehouse

Alpers, Charles N.; Taylor, Howard E.; Domagalski, Joseph L.

2000-01-01

Metals transport in the Sacramento River, northern California, was evaluated on the basis of samples of water, suspended colloids, streambed sediment, and caddisfly larvae that were collected on one to six occasions at 19 sites in the Sacramento River Basin from July 1996 to June 1997. Four of the sampling periods (July, September, and November 1996; and May-June 1997) took place during relatively low-flow conditions and two sampling periods (December 1996 and January 1997) took place during high-flow and flooding conditions; respectively. Tangential-flow ultrafiltration with 10,000 nominal molecular weight limit, or daltons (0.005 micrometer equivalent), pore-size membranes was used to separate metals in streamwater into ultrafiltrate (operationally defined dissolved fraction) and retentate (colloidal fraction) components, respectively. Conventional filtration with capsule filters (0.45 micrometer pore-size) and membrane filters (0.40 micrometer pore-size) and total-recoverable analysis of unfiltered (whole-body) samples were done for comparison at all sites. Because the total-recoverable analysis involves an incomplete digestion of particulate matter, a more reliable measurement of whole-water concentrations is derived from the sum of the dissolved component that is based on the ultrafiltrate plus the suspended component that is based on a total digestion of colloid concentrates from the ultra-filtration retentate. Metals in caddisfly larvae were determined for whole-body samples and cytosol extracts, which are intercellular solutions that provide a more sensitive indication of the metals that have been bioaccumulated. Trace metals in acidic, metal-rich drainage from abandoned and inactive sulfide mines were observed to enter the Sacramento River system (specifically, into both Shasta Lake and Keswick Reservoir) in predominantly dissolved form, as operationally defined using ultrafiltrates. The predominant source of acid mine drainage to Keswick Reservoir is Spring Creek, which drains the Iron Mountain mine area. Copper concentrations in filtered samples from Spring Creek taken during December 1996, January 1997, and May 1997 ranged from 420 to 560 micrograms per liter. Below Keswick Dam, copper concentrations in conventionally filtered samples ranged from 0.5 micrograms per liter during September 1996 to 9.4 micrograms per liter during January 1997; the latter concentration exceeded the applicable water-quality standard. The proportion of trace metals that was dissolved (versus colloidal) in samples collected at Shasta and Keswick dams decreased in the order cadmium zinc > copper > aluminum iron lead mercury. At four sampling sites on the Sacramento River at various distances downstream of Keswick Dam (Bend Bridge, 71 kilometers; Colusa, 256 kilometers; Verona, 360 kilometers; and Freeport, 412 kilometers) concentrations of these seven metals were predominantly colloidal during both high- and low-flow conditions. Because copper compounds are used extensively as algaecides in rice farming, agricultural drainage at the Colusa Basin Drain was sampled in June 1997 during a period shortly after copper applications to newly planted rice fields. Copper concentrations ranged from 1.3 to 3.0 micrograms per liter in filtered samples and from 12 to 13 micrograms per liter in whole-water samples (total recoverable analysis). These results are consistent with earlier work by the U.S. Geological Survey indicating that copper in rice-field drainage likely represents a detectable, but relatively minor source of copper to the Sacramento River. Lead isotope data from suspended colloids and streambed sediments collected during October and November 1996 indicate that lead from acid mine drainage sources became a relatively minor component of the total lead at the site located 71 kilometers downstream of Keswick Dam and beyond. Cadmium, copper, and zinc concentrations in caddisfly larvae were elevated at several sites downstream of Keswick Dam,

Water quality in the lower Puyallup River valley and adjacent uplands, Pierce County, Washington

USGS Publications Warehouse

Ebbert, J.C.; Bortleson, Gilbert C.; Fuste, L.A.; Prych, E.A.

1987-01-01

The quality of most ground and surface water within and adjacent to the lower Puyallup River valley is suitable for most typical uses; however, some degradation of shallow groundwater quality has occurred. High concentrations of iron and manganese were found in groundwater, sampled at depths of < 40 ft, from wells tapping alluvial aquifers and in a few wells tapping deeper aquifers. Volatile and acid- and base/neutral-extractable organic compounds were not detected in either shallow or deep groundwater samples. The quality of shallow groundwater was generally poorer than that of deep water. Deep ground water (wells set below 100 ft) appears suitable as a supplementary water supply for fish-hatchery needs. Some degradation of water quality, was observed downstream from river mile 1.7 where a municipal wastewater-treatment plant discharges into the river. In the Puyallup River, the highest concentrations of most trace elements were found in bed sediments collected downstream from river mile 1.7. Median concentrations of arsenic, lead, and zinc were higher in bed sediments from small streams compared with those from the Puyallup River, possibly because the small stream drainages, which are almost entirely within developed areas, receive more urban runoff as a percentage of total flow. Total-recoverable trace-element concentrations exceeded water-quality criteria for acute toxicity in the Puyallup River and in some of the small streams. In most cases, high concentrations of total-recoverable trace elements occurred when suspended-sediment concentrations were high. Temperatures in all streams except Wapato Creek and Fife Dutch were within limits (18 C) for Washington State class A water. Minimum dissolved oxygen concentrations were relatively low at 5.6 and 2.0 mg/L, respectively, for Wapato Creek and Fife Dutch. The poorest surface-water quality, which can be characterized as generally unsuitable for fish, was in Fife Dutch, a manmade channel and therefore uncharacteristic of other small streams. (Author 's abstract)

Polonium-210 levels in different environmental samples.

PubMed

Fonollosa, E; Peñalver, A; Aguilar, C; Borrull, F

2015-12-01

Polonium-210 is analysed in different samples which can be affected by the presence of a dicalcium phosphate plant (DCP). Particularly, it was determined in sludge samples from a drinking water treatment plant located downstream of the phosphate plant. From the obtained results, it was not possible to establish a correlation with the industrial activities carried out in the DCP plant since the measured activities were comparable to the reported in the literature for normal soils. This isotope was also monitored in different biota species (as mussels) taken also downstream of the DCP, and the potential risk of their ingestion by calculating the total effective doses was evaluated. As a result, it is important to highlight that the ingestion of these mussels does not constitute a risk for the population since the found doses were lower than the values published by UNSCEAR.

Phase I of the Kissimmee River restoration project, Florida, USA: impacts of construction on water quality.

PubMed

Colangelo, David J; Jones, Bradley L

2005-03-01

Phase I of the Kissimmee River restoration project included backfilling of 12 km of canal and restoring flow through 24 km of continuous river channel. We quantified the effects of construction activities on four water quality parameters (turbidity, total phosphorus flow-weighted concentration, total phosphorus load and dissolved oxygen concentration). Data were collected at stations upstream and downstream of the construction and at four stations within the construction zone to determine if canal backfilling and construction of 2.4 km of new river channel would negatively impact local and downstream water quality. Turbidity levels at the downstream station were elevated for approximately 2 weeks during the one and a half year construction period, but never exceeded the Florida Department of Environmental Protection construction permit criteria. Turbidity levels at stations within the construction zone were high at certain times. Flow-weighted concentration of total phosphorus at the downstream station was slightly higher than the upstream station during construction, but low discharge limited downstream transport of phosphorus. Total phosphorus loads at the upstream and downstream stations were similar and loading to Lake Okeechobee was not significantly affected by construction. Mean water column dissolved oxygen concentrations at all sampling stations were similar during construction.

Sediment-phosphorus dynamics can shift aquatic ecology and cause downstream legacy effects after wildfire in large river systems.

PubMed

Emelko, Monica B; Stone, Micheal; Silins, Uldis; Allin, Don; Collins, Adrian L; Williams, Chris H S; Martens, Amanda M; Bladon, Kevin D

2016-03-01

Global increases in the occurrence of large, severe wildfires in forested watersheds threaten drinking water supplies and aquatic ecology. Wildfire effects on water quality, particularly nutrient levels and forms, can be significant. The longevity and downstream propagation of these effects as well as the geochemical mechanisms regulating them remain largely undocumented at larger river basin scales. Here, phosphorus (P) speciation and sorption behavior of suspended sediment were examined in two river basins impacted by a severe wildfire in southern Alberta, Canada. Fine-grained suspended sediments (<125 μm) were sampled continuously during ice-free conditions over a two-year period (2009-2010), 6 and 7 years after the wildfire. Suspended sediment samples were collected from upstream reference (unburned) river reaches, multiple tributaries within the burned areas, and from reaches downstream of the burned areas, in the Crowsnest and Castle River basins. Total particulate phosphorus (TPP) and particulate phosphorus forms (nonapatite inorganic P, apatite P, organic P), and the equilibrium phosphorus concentration (EPC0 ) of suspended sediment were assessed. Concentrations of TPP and the EPC0 were significantly higher downstream of wildfire-impacted areas compared to reference (unburned) upstream river reaches. Sediments from the burned tributary inputs contained higher levels of bioavailable particulate P (NAIP) - these effects were also observed downstream at larger river basin scales. The release of bioavailable P from postfire, P-enriched fine sediment is a key mechanism causing these effects in gravel-bed rivers at larger basin scales. Wildfire-associated increases in NAIP and the EPC0 persisted 6 and 7 years after wildfire. Accordingly, this work demonstrated that fine sediment in gravel-bed rivers is a significant, long-term source of in-stream bioavailable P that contributes to a legacy of wildfire impacts on downstream water quality, aquatic ecology, and drinking water treatability. © 2015 John Wiley & Sons Ltd.

Factors affecting food chain transfer of mercury in the vicinity of the Nyanza site, Sudbury River, Massachusetts

USGS Publications Warehouse

Haines, T.A.; May, T.W.; Finlayson, R.T.; Mierzykowski, S.E.

2003-01-01

The influence of the Nyanza Chemical Waste Dump Superfund Site on the Sudbury River, Massachusetts, was assessed by analysis of sediment, fish prey organisms, and predator fish from four locations in the river system. Whitehall Reservoir is an impoundment upstream of the site, and Reservoir #2 is an impoundment downstream of the site. Cedar Street is a flowing reach upstream of the site, and Sherman Bridge is a flowing reach downstream of the site. Collections of material for analysis were made three times, in May, July, and October. Sediment was analyzed for acid-volatile sulfide (AVS), simultaneously-extracted (SEM) metals (As, Cd, Cr, Hg, Pb, Sb, Zn), and total recoverable Hg. The dominant predatory fish species collected at all sites, largemouth bass (Micropterus salmoides), was analyzed for the same suite of metals as sediment. Analysis of stomach contents of bass identified small fish (yellow perch Perca flavescens, bluegill Lepomis macrochirus, and pumpkinseed Lepomis gibbosus), crayfish, and dragonfly larvae as the dominant prey organisms. Samples of the prey were collected from the same locations and at the same times as predator fish, and were analyzed for total and methyl mercury. Results of AVS and SEM analyses indicated that sediments were not toxic to aquatic invertebrates at any site. The SEM concentrations of As, Cd, and Cr were significantly higher at Reservoir #2 than at the reference sites, and SEM As and Cd were significantly higher at Sherman Bridge than at Cedar St. Sediment total Hg was elevated only at Reservoir #2. Hg was higher at site-influenced locations in all fish species except brown bullhead (Ameiurus nebulosus). Cd was higher in bluegill, black crappie (Pomoxis nigromaculatus), and brown bullhead, and Cr was higher in largemouth bass fillet samples but not in whole-body samples. There were no seasonal differences in sediment or prey organism metals, but some metals in some fish species did vary over time in an inconsistent manner. Predator fish Hg concentration was significantly linearly related to weighted prey organism methyl Hg concentration. Largemouth bass Hg was significantly lower at Reservoir #2 in our study than in previous investigations in 1989 and 1990. High concentrations of inorganic Hg remain in river sediment as a result of operation of the Nyanza site, and fish Hg concentrations in river reaches downstream of the site are elevated compared to upstream reference sites. However, the differences are relatively small and Hg concentrations in largemouth bass from the site-influenced locations are no higher than those from some other, nearby uncontaminated sites. We hypothesize that this results from burial of contaminated sediment with cleaner material, which reduces bioavailability of contaminants and possibly reduces methylation of mercury.

Protective pathways against colitis mediated by appendicitis and appendectomy

PubMed Central

Cheluvappa, R; Luo, A S; Palmer, C; Grimm, M C

2011-01-01

Appendicitis followed by appendectomy (AA) at a young age protects against inflammatory bowel disease (IBD). Using a novel murine appendicitis model, we showed that AA protected against subsequent experimental colitis. To delineate genes/pathways involved in this protection, AA was performed and samples harvested from the most distal colon. RNA was extracted from four individual colonic samples per group (AA group and double-laparotomy control group) and each sample microarray analysed followed by gene-set enrichment analysis (GSEA). The gene-expression study was validated by quantitative reverse transcription–polymerase chain reaction (RT–PCR) of 14 selected genes across the immunological spectrum. Distal colonic expression of 266 gene-sets was up-regulated significantly in AA group samples (false discovery rates < 1%; P-value < 0·001). Time–course RT–PCR experiments involving the 14 genes displayed down-regulation over 28 days. The IBD-associated genes tnfsf10, SLC22A5, C3, ccr5, irgm, ptger4 and ccl20 were modulated in AA mice 3 days after surgery. Many key immunological and cellular function-associated gene-sets involved in the protective effect of AA in experimental colitis were identified. The down-regulation of 14 selected genes over 28 days after surgery indicates activation, repression or de-repression of these genes leading to downstream AA-conferred anti-colitis protection. Further analysis of these genes, profiles and biological pathways may assist in developing better therapeutic strategies in the management of intractable IBD. PMID:21707591

New procedure for recovering extra- and intracellular DNA from marine sediment samples

NASA Astrophysics Data System (ADS)

Alawi, M.; Kallmeyer, J.

2012-12-01

Extracellular DNA (eDNA) is a ubiquitous biological compound in aquatic sediment and soil. Despite major methodological advances, analysis of DNA from sediment is still technically challenging, not just because of the co-elution of inhibitory substances, but also due to co-elution of extracellular DNA, which potentially leads to an overestimate of the actual diversity. Previous studies suggested that eDNA might play an important role in biogeochemical element cycling, horizontal gene transfer and stabilization of biofilm structures. Several protocols based on the precipitation of eDNA e.g. with CTAB and ethanol have already been published. However, using these methods we did not succeed in quantifying very low amounts of eDNA (e.g. <1μg eDNA/g dry wt) in marine sediment even when using DNA carriers like glycogen. Since the recovery of eDNA by precipitation strongly depends on its concentration, these previously published procedures are not adequate for deep biosphere sediment due to the low eDNA content. We have focused on the question whether eDNA could be a source of nitrogen and phosphorus for microbes in the subseafloor biosphere. Therefore we developed a new method for the (semi)-quantitative extraction of eDNA from sediment. The new extraction procedure is based on sequential washing of the sediment to remove simultaneously eDNA and microbial cells without lysing them. After separation of the cells by centrifugation, the eDNA was extracted from the supernatant and purified by adsorption onto a solid phase, followed by removal of the solids and subsequent elution of the pure eDNA. Intracellular DNA (iDNA) was extracted and purified from the cell pellet using a commercial DNA extraction kit. Additional to a very low detection limit and reproducible quantification, this new method allows separation and purification of both extracellular and intracellular DNA to an extent that inhibitors are removed and downstream applications like PCR can be performed. To evaluate the new extraction method two sediments with rather opposing composition were analyzed. Sediment from the South Pacific Gyre, the most oligotrophic oceanic region on earth and organic-rich Baltic Sea sediment (Northern Germany) were processed. Using this new procedure high purity genomic iDNA and eDNA with a molecular size range between 20 bp and 50k bp can be simultaneously recovered even from very oligotrophic sediment with very low cell abundances. The main fraction of recovered eDNA was suitable for downstream applications like PCR and had a molecular size that indicates minimal shearing. Despite about two decades of research many questions about deep subsurface life remain unanswered. The fact that microbes can be found even in deep oligotrophic marine sediment raises the fundamental questions of the types and availability of substrates and their biogeochemical cycling. This is the first study that provides evidence that eDNA is an important potential substrate for microorganisms in the deep biosphere. Also, our results show a link between cell counts and eDNA content, indicating that the eDNA pool in the investigated sediment consist mainly of microbial DNA. Comparative sequence analysis of extracted iDNA and eDNA will provide deeper insights into the origin and turnover of eDNA and the apparent microbial community composition in the deep biosphere.

Sediment Budgeting in Dam-Affected Rivers: Assessing the Influence of Damming, Tributaries, and Alluvial Valley Sediment Storage on Sediment Regimes

NASA Astrophysics Data System (ADS)

Wilcox, A. C.; Dekker, F. J.; Riebe, C. S.

2014-12-01

Although sediment supply is recognized as a fundamental driver of fluvial processes, measuring how dams affect sediment regimes and incorporating such knowledge into management strategies remains challenging. To determine the influences of damming, tributary supply, and valley morphology and sediment storage on downstream sediment supply in a dryland river, the Bill Williams River (BWR) in western Arizona, we measured basin erosion rates using cosmogenic nuclide analysis of beryllium-10 (10Be) at sites upstream and downstream of a dam along the BWR, as well as from tributaries downstream of the dam. Riverbed sediment mixing calculations were used to test if the dam, which blocks sediment supply from the upper 85% of the basin's drainage area, increases the proportion of tributary sediment to residual upstream sediment in mainstem samples downstream of the dam. Erosion rates in the BWR watershed are more than twice as large in the upper catchment (136 t km-2 yr-1) than in tributaries downstream of Alamo Dam (61 t km-2 yr-1). Tributaries downstream of the dam have little influence on mainstem sediment dynamics. The effect of the dam on reducing sediment supply is limited, however, because of the presence of large alluvial valleys along the mainstem BWR downstream of the dam that store substantial sediment and mitigate supply reductions from the upper watershed. These inferences, from our 10Be derived erosion rates and mixing calculations, are consistent with field observations of downstream changes in bed material size, which suggest that sediment-deficit conditions are restricted to a 10 km reach downstream of the dam, and limited reservoir bathymetry data. Many studies have suggested that tributary sediment inputs downstream of dams play a key role in mitigating dam-induced sediment deficits, but here we show that in a dryland river with ephemeral tributaries, sediment stored in alluvial valleys can also play a key role and in some cases trumps the role of tributaries.

Suspect screening and target quantification of human pharmaceutical residues in the surface water of Wuhan, China, using UHPLC-Q-Orbitrap HRMS.

PubMed

Asghar, Muhammad Ali; Zhu, Qingxin; Sun, Shutang; Peng, Yue'e; Shuai, Qin

2018-04-20

In this study we developed a systematic method for suspect screening and target quantification of the human pharmaceutical residues in water, via solid phase extraction (SPE) followed by liquid chromatography-high resolution mass spectrometry (LC-HRMS). We then proceeded to study the occurrences and distribution of the pharmaceuticals in the surface waters of Wuhan, China, by analyzing water samples from lakes, rivers and municipal sewage. Initially, 33 human pharmaceuticals were identified from East Lake without using purchasing standards. Of these, 29 were later confirmed by using standards, and quantified using the aforementioned SPE pretreatment method and LC-HRMS analysis in full MS scan mode. The 29 compounds included 8 antibiotics, 9 metabolites, and 12 miscellaneous pharmaceuticals. The highest proportions of pharmaceutical residues were detected downstream of the Yangtze River and in the lakes close to the central city. Metformin, cotinine, and trans-3-hydroxy cotinine, were frequently encountered in all the surface water samples. High concentrations (>120 ng/l) of caffeine, metformin, theobromine, and valsartan were detected in the surface water samples; the removal rates of these compounds in the municipal sewage treatment plant were also high. In contrast, although the concentrations of 4-AAA and metoprolol acid in the surface water were high, the removal rates of these residues in the sewage treatment plant were low. Copyright © 2018. Published by Elsevier B.V.

Water quality in the Little Sac River basin near Springfield, Missouri, 1999-2001

USGS Publications Warehouse

Smith, Brenda J.

2002-01-01

The Little Sac River, north of Springfield, Missouri, flows through mainly agricultural and forest land. However, the quality of the river water is a concern because the river flows into Stockton Lake, which is a supplemental drinking water source for Springfield. Large bacterial densities and nutrient concentrations are primary concerns to the water quality of the river.A 29-river mile reach of the Little Sac River is on the 1998 list of waters of Missouri designated under section 303(d) of the Federal Clean Water Act because of fecal coliform densities larger than the Missouri Department of Natural Resources standard (hereinafter referred to as Missouri standard) of 200 colonies per 100 milliliters for whole-body contact recreation. During an investigation of the water quality in the Little Sac River by the U.S. Geological Survey, in cooperation with the Watershed Committee of the Ozarks, fecal coliform bacteria densities exceeded the Missouri standard (the standard applies from April 1 through October 31) in one sample from a site near Walnut Grove. At other sites on the Little Sac River, the Missouri standard was exceeded in two samples and equalled in one sample upstream from the Northwest Wastewater Treatment Plant (NW WTP) and in one sample immediately downstream from the NW WTP.Effluent from the NW WTP flows into the Little Sac River. Annually from April 1 through October 31, the effluent is disinfected to meet the Missouri standard for whole-body contact recreation. Fecal coliform bacteria densities in samples collected during this period generally were less than 100 colonies per 100 milliliters. For the rest of the year when the effluent was not disinfected, the bacteria densities in samples ranged from 50 (sample collected on November 1, 2000) to 10,100 colonies per 100 milliliters (both counts were non-ideal). When the effluent was disinfected and the fecal coliform bacteria density was small, samples from sites upstream and downstream from the NW WTP had a bacteria density larger than the density in the effluent. Other sources of bacteria are likely to be present in the study area in addition to the NW WTP. These potential sources include effluent from domestic septic systems and animal wastes.Nutrient concentrations in the Little Sac River immediately downstream from the NW WTP were affected by effluent from the NW WTP and possibly other sources. At two sites upstream from the NW WTP, median nitrite plus nitrate concentrations were 1.1 and 1.4 milligrams per liter. The median nitrite plus nitrate concentration for the effluent from the NW WTP was 6.4 milligrams per liter, and the median concentration decreased downstream in the Little Sac River to 2.2, 1.2, and 0.56 milligrams per liter.The effects of the effluent from the NW WTP on the water quality of the Little Sac River downstream from the NW WTP were reflected in an increase in discharge (effluent from the NW WTP can be as much as 50 percent of the flow at the site about 1.5 river miles downstream from the NW WTP), an increase in specific conductance values, an increase in several inorganic constituent concentrations, including calcium, magnesium, and sulfate, and a large increase in sodium and chloride concentrations. The effluent from the NW WTP seemed to have no effect on the pH value, temperature, and dissolved oxygen concentrations in the Little Sac River.Results of repetitive element polymerase chain reaction (rep-PCR) pattern analysis indicated that most Escherichia coli (E. coli) bacteria in water samples probably were from nonhuman sources, such as horses and cattle. The rep-PCR pattern analysis indicated that horses were an important source of E. coli downstream from the NW WTP, which was consistent with horses pastured adjacent to the sampling site. Fecal coliform bacteria loads increased upstream from the NW WTP from the most upstream site to the site immediately upstream from the NW WTP. Loads in the effluent from the NW WTP and also tho

Methods of downstream processing for the production of biodiesel from microalgae.

PubMed

Kim, Jungmin; Yoo, Gursong; Lee, Hansol; Lim, Juntaek; Kim, Kyochan; Kim, Chul Woong; Park, Min S; Yang, Ji-Won

2013-11-01

Despite receiving increasing attention during the last few decades, the production of microalgal biofuels is not yet sufficiently cost-effective to compete with that of petroleum-based conventional fuels. Among the steps required for the production of microalgal biofuels, the harvest of the microalgal biomass and the extraction of lipids from microalgae are two of the most expensive. In this review article, we surveyed a substantial amount of previous work in microalgal harvesting and lipid extraction to highlight recent progress in these areas. We also discuss new developments in the biodiesel conversion technology due to the importance of the connectivity of this step with the lipid extraction process. Furthermore, we propose possible future directions for technological or process improvements that will directly affect the final production costs of microalgal biomass-based biofuels. Copyright © 2013 Elsevier Inc. All rights reserved.

Embryotoxic and genotoxic effects of sewage effluents in zebrafish embryo using multiple endpoint testing.

PubMed

Babić, Sanja; Barišić, Josip; Višić, Hrvoje; Sauerborn Klobučar, Roberta; Topić Popović, Natalija; Strunjak-Perović, Ivančica; Čož-Rakovac, Rozelindra; Klobučar, Göran

2017-05-15

Wastewater treatment plant (WWTP) effluents are often complex mixtures of various organic and inorganic substances. Quality control of wastewaters and sludges has been regulated with measuring several physico-chemical parameters and sometimes using biological methods with non-specific responses, while synergistic action mechanisms of contaminants in such complex mixtures is still unknown. Toxic effects of wastewaters within and downstream of the WWTP in City of Virovitica, Croatia, were tested on zebrafish Danio rerio using a set of biomarkers that enabled an insight in wastewaters toxic potential on embryos at the cellular, tissue and the whole organism level during an early ontogenesis (24 and 48 hpf). Exposure of embryos to the wastewater samples from WWTP Virovitica increased mortality and abnormality rate. Heart rate, spontaneous movements and pigmentation formation were also markedly affected. Biochemical markers confirmed the presence of MXR inhibitors in all tested wastewater samples, indicating the increase of pollutant accumulation in the cell/organism. Also, a tendency of DNA damage decrease measured with Comet assay was evident in wastewater samples downstream from WWTP although control levels were not reached in any environmental sample. Histopathological analysis showed that exposure to tested samples resulted in impaired muscle organization, notochord malformation and retardation in eye and brain development at embryos 48 hpf. Furthermore, semi-quantitative histopathology assessment indicated increased percentage of embryo defects in river water sampled several kilometers downstream from the WWTP, confirming toxic potential of WWTP effluents. Extension of the zebrafish embryotoxicity test (ZET) with biochemical and histopathological biomarkers could serve as a guiding principle in biomonitoring of wastewater contamination. Copyright © 2017 Elsevier Ltd. All rights reserved.

Streamflow and water-quality conditions including geologic sources and processes affecting selenium loading in the Toll Gate Creek watershed, Aurora, Arapahoe County, Colorado, 2007

USGS Publications Warehouse

Paschke, Suzanne S.; Runkel, Robert L.; Walton-Day, Katherine; Kimball, Briant A.; Schaffrath, Keelin R.

2013-01-01

Toll Gate Creek is a perennial stream draining a suburban area in Aurora, Colorado, where selenium concentrations have consistently exceeded the State of Colorado aquatic-life standard for selenium of 4.6 micrograms per liter since the early 2000s. In cooperation with the City of Aurora, Colorado, Utilities Department, a synoptic water-quality study was performed along an 18-kilometer reach of Toll Gate Creek extending from downstream from Quincy Reservoir to the confluence with Sand Creek to develop a detailed understanding of streamflow and concentrations and loads of selenium in Toll Gate Creek. Streamflow and surface-water quality were characterized for summer low-flow conditions (July–August 2007) using four spatially overlapping synoptic-sampling subreaches. Mass-balance methods were applied to the synoptic-sampling and tracer-injection results to estimate streamflow and develop spatial profiles of concentration and load for selenium and other chemical constituents in Toll Gate Creek surface water. Concurrent groundwater sampling determined concentrations of selenium and other chemical constituents in groundwater in areas surrounding the Toll Gate Creek study reaches. Multivariate principal-component analysis was used to group samples and to suggest common sources for dissolved selenium and major ions. Hydrogen and oxygen stable-isotope ratios, groundwater-age interpretations, and chemical analysis of water-soluble paste extractions from core samples are presented, and interpretation of the hydrologic and geochemical data support conclusions regarding geologic sources of selenium and the processes affecting selenium loading in the Toll Gate Creek watershed.

Time of travel and dispersion of solutes in a 36.4-mile reach of the North Platte River downstream from Casper, Wyoming

USGS Publications Warehouse

Armentrout, G.W.; Larson, L.R.

1984-01-01

Time-of-travel and dispersion measurements made during a dye study November 7-8, 1978, are presented for a reach of the North Platte River from Casper, Wyo., to a bridge 2 miles downstream from below the Dave Johnston Power Plant. Rhodamine WT dye was injected into the river at Casper, and the resultant dye cloud was traced by sampling as it moved downstream. Samples were taken in three equal-flow sections of the river 's lateral transect at three sites, then analyzed in a fluorometer. The flow in the river was 940 cubic feet per second. The data consist of measured stream mileages and time, distance, and concentration graphs of the dye cloud. The peak concentration traveled through the reach in 24 hours, averaging 1.5 miles per hour; the leading edge took about 22 hours, averaging 1.7 miles per hour; and the trailing edge took 35 hours, averaging 1.0 mile per hour. Data from this study were compared with methods for estimating time of travel for a range of stream discharges.

White sucker (Catostomus commersoni) growth and sexual maturation in pulp mill-contaminated and reference rivers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gagnon, M.M.; Bussieres, D.; Dodson, J.J.

1995-02-01

Induction of hepatic ethoxyresorufin-O-deethylase (EROD) activity and accumulation of chlorophenolic compounds typical of bleached-kraft mill effluent (BKME) in fish sampled downstream of a pulp mill on the St. Maurice River, Quebec, Canada, provided evidence of chemical exposure to BKME. In comparison, fish sampled over the same distances and in similar habitats in a noncontaminated reference river, the Gatineau River, demonstrated low EROD activity and contamination levels. Accelerated growth of white suckers occurred between 2 and 10 years of age in both rivers at downstream stations relative to upstream stations, suggesting the existence of gradients of nutrient enrichment independent of BKMEmore » contamination. The impact of BKME exposure was expressed as reduced investment in reproduction, as revealed by greater length at maturity, reduced gonad size, and more variable fecundity. These effects were not obvious in simple upstream-downstream comparisons, but became evident when fish from the uncontaminated Gatineau River showed increased gonadal development and reduced age and size at maturity in response to enhanced growth rates.« less

Biodegradation of 17β-estradiol, estrone, and testosterone in stream sediments

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.; Barber, L.B.; McMahon, P.B.; Gray, J.L.; Kolpin, D.W.

2009-01-01

The release of endocrine-disrupting chemicals (EDCs) in wastewater treatment plant (WWTP) effluent poses a significant threat to the ecology of surface water receptors, due to impacts on the hormonal control, sexual development, reproductive success and community structure of the indigenous aquatic organisms and associated wildlife. Among the EDCs commonly observed in WWTP effluent, the natural [e.g., 17??-estradiol (E2) and estrone (E1)] and synthetic [e.g., ethynylestradiol (EE2)] estrogens are particular concerns owing to their high endocrine reactivity in both in vitro and in vivo laboratory models. These reproductive hormones have been identified as the primary cause of estrogenic effects in wastewater effluent, with greater than 95% of the estrogen receptor agonist activity in effluent attributed to this contaminant group. The potentials for in situ biodegradation of 17??-estradiol (E2), estrone (E1), and testosterone (T) were investigated in three, hydrologically-distinct, WWTP-impacted streams in the United States. Relative differences in the mineralization of [4-14C] substrates were assessed in oxic microcosms containing sediment or water-only from locations upstream and downstream of the WWTP outfall in each system. Upstream samples provided insight into the biodegradative potential of sediment microbial communities that were not under the immediate impact of WWTP effluent. Upstream sediment from all three systems demonstrated significant mineralization of the "A" ring of E2, E1 and T, with the potential of T biodegradation consistently greater than of E2 and no systematic difference in the potentials of E2 and E1. Downstream samples provided insight into the impacts of effluent on reproductive hormone biodegradation. Significant "A" ring mineralization was also observed in downstream sediment, with the potentials for E1 and T mineralization being substantially depressed relative to upstream samples. In marked contrast, the potentials for E2 mineralization immediately downstream of the WWTP outfalls were more than double that of upstream samples. E2 mineralization was also observed in water, albeit at insufficient rate to prevent substantial downstream transport in the water column. The results of this study indicate that, in combination with sediment sorption processes which effectively scavenge hydrophobic contaminants from the water column and immobilize them in the vicinity of the WWTP outfall, aerobic biodegradation of reproductive hormones can be an environmentally important mechanism for nonconservative (destructive) attenuation of hormonal endocrine disruptors in effluent-impacted streams.

Tritium as tracer of groundwater pollution extension: case study of Andralanitra landfill site, Antananarivo-Madagascar

NASA Astrophysics Data System (ADS)

Ramaroson, Voahirana; Rakotomalala, Christian Ulrich; Rajaobelison, Joel; Fareze, Lahimamy Paul; Razafitsalama, Falintsoa A.; Rasolofonirina, Mamiseheno

2018-05-01

This study aims to understand the extension of groundwater pollution downstream of a landfill, Andralanitra-Antananarivo-Madagascar. Twenty-one samples, composed of dug well waters, spring waters, river, and lake, were measured in stable isotopes ( δ 2H, δ 18O) and tritium. Results showed that only two dug well waters, collected at the immediate vicinity of the landfill, have high tritium activities (22.82 TU and 10.43 TU), probably of artificial origin. Both upstream and further downstream of the landfill, tritium activities represent natural source, with values varying from 0.17 TU to 1.46 TU upstream and from 0.88 TU to 1.88 TU further downstream. Stable isotope data suggest that recharge occurs through infiltration of slightly evaporated rainfall. Using the radioactive decay equation, the calculated tracer ages related to two recent ground water samples collected down gradient of the landfill lay between [8-15] years and [4-7] years, taking into account the uncertainty of tritium measurements. For the calculation, a value of 2.36 TU was taken as A o. The latter was estimated based on similarity between stable isotope compositions of nearby spring and dug well waters as well as tritium activities of the local precipitation. Calculation of the tritium activities from the contaminated water point having 22.82 TU to further downstream using the calculated tracer ages showed values of one order of magnitude higher than the measured values. The absence of hydrological connection from the contaminated water point to further downstream the landfill would explain the lower tritium activities measured. Groundwater pollution seems to be limited to the closest proximity of the landfill.

Assessment of elemental concentrations in streams of the New Lead Belt in southeastern Missouri, 2002-05

USGS Publications Warehouse

Brumbaugh, William G.; May, Thomas W.; Besser, John M.; Allert, Ann L.; Schmitt, Christopher J.

2007-01-01

Concerns about possible effects of lead-mining activities on the water quality of federally protected streams located in southeastern Missouri prompted a suite of multidisciplinary studies to be conducted by the U.S. Geological Survey. As part of this investigation, a series of biological studies were initiated in 2001 for streams in the current mining region and the prospecting area. In this report, results are examined for trace elements and other selected chemical measurements in sediment, surface water, and sediment interstitial (pore) water sampled between 2002 and 2005 in association with these biological studies. Compared to reference sites, fine sediments collected downstream from mining areas were enriched in metals by factors as large as 75 for cadmium, 62 for cobalt, 171 for nickel, 95 for lead, and 150 for zinc. Greatest metal concentrations in sediments collected in 2002 were from sites downstream from mines on Strother Creek, Courtois Creek, and the West Fork Black River. Sediments from sites on Bee Fork, Logan Creek, and Sweetwater Creek also were noticeably enriched in lead. Sediments in Clearwater Lake, at least 75 kilometers downstream from mining activity, had metal concentrations that were 1.5 to 2.1 times greater than sediments in an area of the lake with no upstream mining activity. Longitudinal sampling along three streams in 2004 indicated that sediment metal concentrations decreased considerably a few kilometers downstream from mining activities; however, in Strother Creek some metals were still enriched by a factor of five or more as far as 13 kilometers downstream from the Buick tailings impoundment. Compared with 2002 samples, metals concentrations were dramatically lower in sediments collected in 2004 at an upper West Fork Black River site, presumably because beneficiation operations at the West Fork mill ceased in 2000. Concentrations of metals and sulfate in sediment interstitial (pore) waters generally tracked closely with metal concentrations in sediments. Metals, including cobalt, nickel, lead, and zinc, were elevated substantially in laboratory-produced pore waters of fine sediments collected near mining operations in 2002 and 2004. Passive diffusion samplers (peepers) buried 4 to 6 centimeters deep in riffle-run stream sediments during 2003 and 2005 had much lower pore-water metal concentrations than the laboratory-produced pore waters of fine sediments collected in 2002 and 2004, but each sampling method produced similar patterns among sites. The combined mean concentration of lead in peeper samples from selected sites located downstream from mining activities for six streams was about 10-fold greater than the mean of the reference sites. In most instances, metals concentrations in surface water and peeper water were not greatly different, indicating considerable exchange between the surface water and pore water at the depths and locations where peepers were situated. Passive sampling probes used to assess metal lability in pore waters of selected samples during 2004 sediment toxicity tests indicated that most of the filterable lead in the laboratory-prepared pore water was relatively non-labile, presumably because lead was complexed by organic matter, or was present as colloidal species. In contrast, large percentages of cobalt and nickel in pore water appeared to be labile. Passive integrative samplers deployed in surface water for up to 3 weeks at three sites in July 2005 confirmed the presence of elevated concentrations of labile metals downstream from mining operations on Strother Creek and, to a lesser extent, Bee Fork. These samplers also indicated a considerable increase in metal loadings occurred for a few days at the Strother Creek site, which coincided with moderate increases in stream discharges in the area.

THE LIBERATION OF ARSENOSUGARS FROM MATRIX COMPONENTS IN DIFFICULT TO EXTRACT SEAFOOD SAMPLES UTILIZING TMAOH/ACETIC ACID SEQUENTIALLY IN A TWO-STAGE EXTRACTION PROCESS

EPA Science Inventory

Sample extraction is one of the most important steps in arsenic speciation analysis of solid dietary samples. One of the problem areas in this analysis is the partial extraction of arsenicals from seafood samples. The partial extraction allows the toxicity of the extracted arse...

Performance evaluation of the QIAGEN EZ1 DSP Virus Kit with Abbott RealTime HIV-1, HBV and HCV assays.

PubMed

Schneider, George J; Kuper, Kevin G; Abravaya, Klara; Mullen, Carolyn R; Schmidt, Marion; Bunse-Grassmann, Astrid; Sprenger-Haussels, Markus

2009-04-01

Automated sample preparation systems must meet the demands of routine diagnostics laboratories with regard to performance characteristics and compatibility with downstream assays. In this study, the performance of QIAGEN EZ1 DSP Virus Kit on the BioRobot EZ1 DSP was evaluated in combination with the Abbott RealTime HIV-1, HCV, and HBV assays, followed by thermalcycling and detection on the Abbott m2000rt platform. The following performance characteristics were evaluated: linear range and precision, sensitivity, cross-contamination, effects of interfering substances and correlation. Linearity was observed within the tested ranges (for HIV-1: 2.0-6.0 log copies/ml, HCV: 1.3-6.9 log IU/ml, HBV: 1.6-7.6 log copies/ml). Excellent precision was obtained (inter-assay standard deviation for HIV-1: 0.06-0.17 log copies/ml (>2.17 log copies/ml), HCV: 0.05-0.11 log IU/ml (>2.09 log IU/ml), HBV: 0.03-0.07 log copies/ml (>2.55 log copies/ml)), with good sensitivity (95% hit rates for HIV-1: 50 copies/ml, HCV: 12.5 IU/ml, HBV: 10 IU/ml). No cross-contamination was observed, as well as no negative impact of elevated levels of various interfering substances. In addition, HCV and HBV viral load measurements after BioRobot EZ1 DSP extraction correlated well with those obtained after Abbott m2000sp extraction. This evaluation demonstrates that the QIAGEN EZ1 DSP Virus Kit provides an attractive solution for fully automated, low throughput sample preparation for use with the Abbott RealTime HIV-1, HCV, and HBV assays.

Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb

PubMed Central

Kahan, Anat; Ben-Shaul, Yoram

2016-01-01

For many animals, chemosensation is essential for guiding social behavior. However, because multiple factors can modulate levels of individual chemical cues, deriving information about other individuals via natural chemical stimuli involves considerable challenges. How social information is extracted despite these sources of variability is poorly understood. The vomeronasal system provides an excellent opportunity to study this topic due to its role in detecting socially relevant traits. Here, we focus on two such traits: a female mouse’s strain and reproductive state. In particular, we measure stimulus-induced neuronal activity in the accessory olfactory bulb (AOB) in response to various dilutions of urine, vaginal secretions, and saliva, from estrus and non-estrus female mice from two different strains. We first show that all tested secretions provide information about a female’s receptivity and genotype. Next, we investigate how these traits can be decoded from neuronal activity despite multiple sources of variability. We show that individual neurons are limited in their capacity to allow trait classification across multiple sources of variability. However, simple linear classifiers sampling neuronal activity from small neuronal ensembles can provide a substantial improvement over that attained with individual units. Furthermore, we show that some traits are more efficiently detected than others, and that particular secretions may be optimized for conveying information about specific traits. Across all tested stimulus sources, discrimination between strains is more accurate than discrimination of receptivity, and detection of receptivity is more accurate with vaginal secretions than with urine. Our findings highlight the challenges of chemosensory processing of natural stimuli, and suggest that downstream readout stages decode multiple behaviorally relevant traits by sampling information from distinct but overlapping populations of AOB neurons. PMID:26938460

Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb.

PubMed

Kahan, Anat; Ben-Shaul, Yoram

2016-03-01

For many animals, chemosensation is essential for guiding social behavior. However, because multiple factors can modulate levels of individual chemical cues, deriving information about other individuals via natural chemical stimuli involves considerable challenges. How social information is extracted despite these sources of variability is poorly understood. The vomeronasal system provides an excellent opportunity to study this topic due to its role in detecting socially relevant traits. Here, we focus on two such traits: a female mouse's strain and reproductive state. In particular, we measure stimulus-induced neuronal activity in the accessory olfactory bulb (AOB) in response to various dilutions of urine, vaginal secretions, and saliva, from estrus and non-estrus female mice from two different strains. We first show that all tested secretions provide information about a female's receptivity and genotype. Next, we investigate how these traits can be decoded from neuronal activity despite multiple sources of variability. We show that individual neurons are limited in their capacity to allow trait classification across multiple sources of variability. However, simple linear classifiers sampling neuronal activity from small neuronal ensembles can provide a substantial improvement over that attained with individual units. Furthermore, we show that some traits are more efficiently detected than others, and that particular secretions may be optimized for conveying information about specific traits. Across all tested stimulus sources, discrimination between strains is more accurate than discrimination of receptivity, and detection of receptivity is more accurate with vaginal secretions than with urine. Our findings highlight the challenges of chemosensory processing of natural stimuli, and suggest that downstream readout stages decode multiple behaviorally relevant traits by sampling information from distinct but overlapping populations of AOB neurons.

Liquid/Gas Separator Handles Varying Loads

NASA Technical Reports Server (NTRS)

Mann, John

1992-01-01

Liquid/gas separator includes two independent motors, one for pumping mixture and other for drawing off extracted gas. Two materials moved at speeds best suited for them. Liquid expelled radially outward from separator rotor. Entrained gas released, flows axially through rotor, and leaves through fan at downstream end. Unit developed to separate air from urine in spacecraft wastewater-treatment system, also functions in normal gravity. Made largely of titanium to resist corrosion.

Wingtip vortex turbine

NASA Technical Reports Server (NTRS)

Patterson, James C., Jr. (Inventor)

1990-01-01

A means for extracting rotational energy from the vortex created at aircraft wing tips which consists of a turbine with blades located in the crossflow of the vortex and attached downstream of the wingtip. The turbine has blades attached to a core. When the aircraft is in motion, rotation of a core transmits energy to a centrally attached shaft. The rotational energy thus generated may be put to use within the airfoil or aircraft fuselage.

Analysis of RNA Processing Reactions Using Cell Free Systems: 3' End Cleavage of Pre-mRNA Substrates in vitro

PubMed Central

Jablonski, Joseph; Clementz, Mark; Ryan, Kevin; Valente, Susana T.

2014-01-01

The 3’ end of mammalian mRNAs is not formed by abrupt termination of transcription by RNA polymerase II (RNPII). Instead, RNPII synthesizes precursor mRNA beyond the end of mature RNAs, and an active process of endonuclease activity is required at a specific site. Cleavage of the precursor RNA normally occurs 10-30 nt downstream from the consensus polyA site (AAUAAA) after the CA dinucleotides. Proteins from the cleavage complex, a multifactorial protein complex of approximately 800 kDa, accomplish this specific nuclease activity. Specific RNA sequences upstream and downstream of the polyA site control the recruitment of the cleavage complex. Immediately after cleavage, pre-mRNAs are polyadenylated by the polyA polymerase (PAP) to produce mature stable RNA messages. Processing of the 3’ end of an RNA transcript may be studied using cellular nuclear extracts with specific radiolabeled RNA substrates. In sum, a long 32P-labeled uncleaved precursor RNA is incubated with nuclear extracts in vitro, and cleavage is assessed by gel electrophoresis and autoradiography. When proper cleavage occurs, a shorter 5’ cleaved product is detected and quantified. Here, we describe the cleavage assay in detail using, as an example, the 3’ end processing of HIV-1 mRNAs. PMID:24835792

Microscale to Manufacturing Scale-up of Cell-Free Cytokine Production—A New Approach for Shortening Protein Production Development Timelines

PubMed Central

Zawada, James F; Yin, Gang; Steiner, Alexander R; Yang, Junhao; Naresh, Alpana; Roy, Sushmita M; Gold, Daniel S; Heinsohn, Henry G; Murray, Christopher J

2011-01-01

Engineering robust protein production and purification of correctly folded biotherapeutic proteins in cell-based systems is often challenging due to the requirements for maintaining complex cellular networks for cell viability and the need to develop associated downstream processes that reproducibly yield biopharmaceutical products with high product quality. Here, we present an alternative Escherichia coli-based open cell-free synthesis (OCFS) system that is optimized for predictable high-yield protein synthesis and folding at any scale with straightforward downstream purification processes. We describe how the linear scalability of OCFS allows rapid process optimization of parameters affecting extract activation, gene sequence optimization, and redox folding conditions for disulfide bond formation at microliter scales. Efficient and predictable high-level protein production can then be achieved using batch processes in standard bioreactors. We show how a fully bioactive protein produced by OCFS from optimized frozen extract can be purified directly using a streamlined purification process that yields a biologically active cytokine, human granulocyte-macrophage colony-stimulating factor, produced at titers of 700 mg/L in 10 h. These results represent a milestone for in vitro protein synthesis, with potential for the cGMP production of disulfide-bonded biotherapeutic proteins. Biotechnol. Bioeng. 2011; 108:1570–1578. © 2011 Wiley Periodicals, Inc. PMID:21337337

Occurrence of organic wastewater compounds in drinking water, wastewater effluent, and the Big Sioux River in or near Sioux Falls, South Dakota, 2001-2004

USGS Publications Warehouse

Sando, Steven K.; Furlong, Edward T.; Gray, James L.; Meyer, Michael T.

2006-01-01

The U.S. Geological Survey (USGS) in cooperation with the city of Sioux Falls conducted several rounds of sampling to determine the occurrence of organic wastewater compounds (OWCs) in the city of Sioux Falls drinking water and waste-water effluent, and the Big Sioux River in or near Sioux Falls during August 2001 through May 2004. Water samples were collected during both base-flow and storm-runoff conditions. Water samples were collected at 8 sites, which included 4 sites upstream from the wastewater treatment plant (WWTP) discharge, 2 sites downstream from the WWTP discharge, 1 finished drinking-water site, and 1 WWTP effluent (WWE) site. A total of 125 different OWCs were analyzed for in this study using five different analytical methods. Analyses for OWCs were performed at USGS laboratories that are developing and/or refining small-concentration (less than 1 microgram per liter (ug/L)) analytical methods. The OWCs were classified into six compound classes: human pharmaceutical compounds (HPCs); human and veterinary antibiotic compounds (HVACs); major agricultural herbicides (MAHs); household, industrial,and minor agricultural compounds (HIACs); polyaromatic hydrocarbons (PAHs); and sterol compounds (SCs). Some of the compounds in the HPC, MAH, HIAC, and PAH classes are suspected of being endocrine-disrupting compounds (EDCs). Of the 125 different OWCs analyzed for in this study, 81 OWCs had one or more detections in environmental samples reported by the laboratories, and of those 81 OWCs, 63 had acceptable analytical method performance, were detected at concentrations greater than the study reporting levels, and were included in analyses and discussion related to occurrence of OWCs in drinking water, wastewater effluent, and the Big Sioux River. OWCs in all compound classes were detected in water samples from sampling sites in the Sioux Falls area. For the five sampling periods when samples were collected from the Sioux Falls finished drinking water, only one OWC was detected at a concentration greater than the study reporting level (metolachlor; 0.0040 ug/L). During base-flow conditions, Big Sioux River sites upstream from the WWTP discharge had OWC contributions that primarily were from nonpoint animal or crop agriculture sources or had OWC concentrations that were minimal. The influence of the WWTP discharge on OWCs at downstream river sites during base-flow conditions ranged from minimal influence to substantial influence depending on the sampling period. During runoff conditions, OWCs at sites upstream from the WWTP discharge probably were primarily contributed by nonpoint animal and/or crop agriculture sources and possibly by stormwater runoff from nearby roads. OWCs at sites downstream from the WWTP discharge probably were contributed by sources other than the WWTP effluent discharge, such as stormwater runoff from urban and/or agriculture areas and/or resuspension of OWCs adsorbed to sediment deposited in the Big Sioux River. OWC loads generally were substantially smaller for upstream sites than downstream sites during both base-flow and runoff conditions.discharge had OWC contributions that primarily were from nonpoint animal or crop agriculture sources or had OWC concentrations that were minimal. The influence of the WWTP discharge on OWCs at downstream river sites during base-flow conditions ranged from minimal influence to substantial influence depending on the sampling period. During runoff conditions, OWCs at sites upstream from the WWTP discharge probably were primarily contributed by nonpoint animal and/or crop agriculture sources and possibly by stormwater runoff from nearby roads. OWCs at sites downstream from the WWTP discharge probably were contributed by sources other than the WWTP effluent discharge, such as stormwater runoff from urban and/or agriculture areas and/or resuspension of OWCs adsorbed to sediment deposited in the Big Sioux River. OWC loads generally were substantially smaller for

Sediment characteristics in the San Antonio River Basin downstream from San Antonio, Texas, and at a site on the Guadalupe River downstream from the San Antonio River Basin, 1966-2013

USGS Publications Warehouse

Crow, Cassi L.; Banta, J. Ryan; Opsahl, Stephen P.

2014-01-01

San Antonio and surrounding municipalities in Bexar County, Texas, are in a rapidly urbanizing region in the San Antonio River Basin. The U.S. Geological Survey, in cooperation with the San Antonio River Authority and the Texas Water Development Board, compiled historical sediment data collected between 1996 and 2004 and collected suspended-sediment and bedload samples over a range of hydrologic conditions in the San Antonio River Basin downstream from San Antonio, Tex., and at a site on the Guadalupe River downstream from the San Antonio River Basin during 2011–13. In the suspended-sediment samples collected during 2011–13, an average of about 94 percent of the particles was less than 0.0625 millimeter (silt and clay sized particles); the 50 samples for which a complete sediment-size analysis was performed indicated that an average of about 69 percent of the particles was less than 0.002 millimeter. In the bedload samples collected during 2011–13, an average of 51 percent of sediment particles was sand-sized particles in the 0.25–0.5 millimeter-size range. In general, the loads calculated from the samples indicated that bedload typically composed less than 1 percent of the total sediment load. A least-squares log-linear regression was developed between suspended-sediment concentration and instantaneous streamflow and was used to estimate daily mean suspended-sediment loads based on daily mean streamflow. The daily mean suspended-sediment loads computed for each of the sites indicated that during 2011–12, the majority of the suspended-sediment loads originated upstream from the streamflow-gaging station on the San Antonio River near Elmendorf, Tex. A linear regression relation was developed between turbidity and suspended-sediment concentration data collected at the San Antonio River near Elmendorf site because the high-resolution data can facilitate understanding of the complex suspended-sediment dynamics over time and throughout the river basin.

DNA adsorption to and elution from silica surfaces: influence of amino acid buffers.

PubMed

Vandeventer, Peter E; Mejia, Jorge; Nadim, Ali; Johal, Malkiat S; Niemz, Angelika

2013-09-19

Solid phase extraction and purification of DNA from complex samples typically requires chaotropic salts that can inhibit downstream polymerase amplification if carried into the elution buffer. Amino acid buffers may serve as a more compatible alternative for modulating the interaction between DNA and silica surfaces. We characterized DNA binding to silica surfaces, facilitated by representative amino acid buffers, and the subsequent elution of DNA from the silica surfaces. Through bulk depletion experiments, we found that more DNA adsorbs to silica particles out of positively compared to negatively charged amino acid buffers. Additionally, the type of the silica surface greatly influences the amount of DNA adsorbed and the final elution yield. Quartz crystal microbalance experiments with dissipation monitoring (QCM-D) revealed multiphasic DNA adsorption out of stronger adsorbing conditions such as arginine, glycine, and glutamine, with DNA more rigidly bound during the early stages of the adsorption process. The DNA film adsorbed out of glutamate was more flexible and uniform throughout the adsorption process. QCM-D characterization of DNA elution from the silica surface indicates an uptake in water mass during the initial stage of DNA elution for the stronger adsorbing conditions, which suggests that for these conditions the DNA film is partly dehydrated during the prior adsorption process. Overall, several positively charged and polar neutral amino acid buffers show promise as an alternative to methods based on chaotropic salts for solid phase DNA extraction.

Water Sources of Temperate Upland Swamps of Eastern Australia. Implications for Groundwater Management and Climate Change.

NASA Astrophysics Data System (ADS)

Cowley, K.; Fryirs, K.; Chisari, R.; Hose, G. C.

2016-12-01

Temperate upland swamps in Eastern Australia are endangered ecological communities under State and National legislation. They occur in headwaters of low order streams on low relief plateaus, providing base flow to streams that contribute to Sydney's major drinking water supplies that support some 4.5 million people. The swamps are also subject to aquifer interference activities from long wall mining and groundwater extraction, and are threatened by a changing climate. It is therefore critical that we understand their water source, storage capacity and residence times. We collected seasonal water samples from perched swamp aquifers in two highland regions of Eastern Australia for analysis of hydrogen and oxygen isotopes and compared them with rainwater, surface water and deeper groundwater to determine whether the swamps were primarily rainwater or groundwater fed. 222Rn was used as an environmental tracer to calculate residence times and relative groundwater/surface water ratios. We found over 60% of the swamps were sensitive to evaporation which has implications for swamp health in a warmer climate. Over a third of water from the perched swamp aquifer is derived from deeper sandstone aquifers with residence times of between 1.2 and 15 days. This swamp-groundwater connectivity means that mining activities or large-scale groundwater extraction could interfere with a significant component of the swamps' water source, its water storage capacity and downstream contributions to Sydney's drinking water supplies.

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction.

PubMed

Patel, Palak G; Selvarajah, Shamini; Boursalie, Suzanne; How, Nathan E; Ejdelman, Joshua; Guerard, Karl-Philippe; Bartlett, John M; Lapointe, Jacques; Park, Paul C; Okello, John B A; Berman, David M

2016-08-21

Formalin-fixed paraffin embedded tissue (FFPET) represents a valuable, well-annotated substrate for molecular investigations. The utility of FFPET in molecular analysis is complicated both by heterogeneous tissue composition and low yields when extracting nucleic acids. A literature search revealed a paucity of protocols addressing these issues, and none that showed a validated method for simultaneous extraction of RNA and DNA from regions of interest in FFPET. This method addresses both issues. Tissue specificity was achieved by mapping cancer areas of interest on microscope slides and transferring annotations onto FFPET blocks. Tissue cores were harvested from areas of interest using 0.6 mm microarray punches. Nucleic acid extraction was performed using a commercial FFPET extraction system, with modifications to homogenization, deparaffinization, and Proteinase K digestion steps to improve tissue digestion and increase nucleic acid yields. The modified protocol yields sufficient quantity and quality of nucleic acids for use in a number of downstream analyses, including a multi-analyte gene expression platform, as well as reverse transcriptase coupled real time PCR analysis of mRNA expression, and methylation-specific PCR (MSP) analysis of DNA methylation.

Recent developments of downstream processing for microbial lipids and conversion to biodiesel.

PubMed

Yellapu, Sravan Kumar; Bharti; Kaur, Rajwinder; Kumar, Lalit R; Tiwari, Bhagyashree; Zhang, Xiaolei; Tyagi, Rajeshwar D

2018-05-01

With increasing global population and depleting resources, there is an apparent demand for radical unprecedented innovation to satisfy the basal needs of lives. Hence, non-conventional renewable energy resources like biodiesel have been worked out in past few decades. Biofuel (e.g. Biodiesel) serves to be the most sustainable answer to solve "food vs. fuel crisis". In biorefinery process, lipid extraction from oleaginous microbial lipids is an integral part as it facilitates the release of fatty acids. Direct lipid extraction from wet cell-biomass is favorable in comparison to dry-cell biomass because it eliminates the application of expensive dehydration. However, this process is not commercialized yet, instead, it requires intensive research and development in order to establish robust approaches for lipid extraction that can be practically applied on an industrial scale. This review aims for the critical presentation on cell disruption, lipid recovery and purification to support extraction from wet cell-biomass for an efficient transesterification. Copyright © 2018 Elsevier Ltd. All rights reserved.

Optimization of a wet microalgal lipid extraction procedure for improved lipid recovery for biofuel and bioproduct production.

PubMed

Sathish, Ashik; Marlar, Tyler; Sims, Ronald C

2015-10-01

Methods to convert microalgal biomass to bio based fuels and chemicals are limited by several processing and economic hurdles. Research conducted in this study modified/optimized a previously published procedure capable of extracting transesterifiable lipids from wet algal biomass. This optimization resulted in the extraction of 77% of the total transesterifiable lipids, while reducing the amount of materials and temperature required in the procedure. In addition, characterization of side streams generated demonstrated that: (1) the C/N ratio of the residual biomass or lipid extracted (LE) biomass increased to 54.6 versus 10.1 for the original biomass, (2) the aqueous phase generated contains nitrogen, phosphorous, and carbon, and (3) the solid precipitate phase was composed of up to 11.2 wt% nitrogen (70% protein). The ability to isolate algal lipids and the possibility of utilizing generated side streams as products and/or feedstock material for downstream processes helps promote the algal biorefinery concept. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nutrients, suspended sediment, and pesticides in waters of the Red River of the North Basin, Minnesota, North Dakota, and South Dakota, 1970-90

USGS Publications Warehouse

Tornes, L.H.; Brigham, M.E.

1994-01-01

A relatively large fraction of stream samples had detectable quantities of 2,4-D, a- and y-HCH, and atrazine. These samples covered time spans of as much as 15 years and were from sites downstream from large drainage basins; however, concentrations were well below US EPA MCLs. One county-level study showed higher 2,4-D concentrations at upstream sites than at the outlet from a small basin. This indicates that downstream sites may fail to show impaired water-quality and the fate of pesticides used in the basin. Following the 1972 ban on DDT, concentrations of DDT in fish samples from the Red River of the North quickly decreased. Fish concentrations of DDE and DDD decreased more slowly. Low levels of DDE and DDD were detected in fish 14 years after the DDT ban.

Pilot study of natural attenuation of arsenic in well water discharged to the Little River above Lake Thunderbird, Norman, Oklahoma, 2012

USGS Publications Warehouse

Andrews, William J.; Masoner, Jason R.; Rendon, Samuel H.; Smith, Kevin A.; Greer, James R.; Chatterton, Logan A.

2013-01-01

The City of Norman, Oklahoma, wanted to augment its water supplies to meet the needs of an increasing population. Among the city’s potential water sources are city wells that produce water that exceeds the 10 micrograms per liter primary drinking-water standard for arsenic. The City of Norman was interested in investigating low-cost means of using natural attenuation to remove arsenic from well water and augment the water supply of Lake Thunderbird, the primary water source for the city. The U.S. Geological Survey, in cooperation with the City of Norman, conducted a preliminary investigation (pilot study) to determine if discharge of water from those wells into the Little River over a 12-day period would reduce arsenic concentrations through natural-attenuation processes. Water in the Little River flows into Lake Thunderbird, the principal water source for the city, so the discharged well water would improve the water balance of that reservoir. During this pilot study, 150–250 gallons per minute from each of six city wells were discharged to the Little River over a 12-day period. Water-quality samples were collected from the wells during discharge and from the river before, during, and after well discharges. Streambed-sediment samples were collected at nine sites in the river before and after the well-discharge period. Water discharge from the six wells added 0.3 kilogram per day of arsenic to the river at the nearest downstream streamflow-gaging station. Dissolved arsenic concentration in the Little River at the closest downstream sampling site from the wells increased from about 4 micrograms per liter to as much as 24 micrograms per liter. Base flow in the river increased by about 1.7 cubic feet per second at the nearest downstream streamflow-gaging station. Streamflow in the river was two-thirds of that expected from the amount of water discharged from the wells because of seepage to soils and evapotranspiration of well water along drainage ways to the river. Arsenic concentrations at the nearest downstream streamflow-gaging station were less than arsenic concentrations measured in many of the well-water samples during the well-pumping period. Arsenic concentrations, loads, and yields in the Little River generally decreased downstream from the closest streamflow-gaging station to the wells by 50 percent or more, indicating removal of about 0.25 kilogram or 0.53 pound per day of arsenic during base-flow conditions. Measured river-water arsenic concentrations near the confluence of the Little River with Lake Thunderbird were in compliance with the primary drinking-water standard. Arsenic concentrations measured at four downstream stations in the Little River also were less than established criteria set for protection of aquatic biota. After well discharges to the Little River were stopped, arsenic concentrations, loads, and yields in the river gradually decreased over 14 days to concentrations measured prior to the well-water discharges. Cumulative loads of arsenic discharged at the wells and the closest and farthest downstream streamflow-gaging stations indicated removal of about 2.5 kilograms of arsenic as well-water flowed to and down the river. Arsenic concentrations in streambed-sediment samples collected before and after the well-water discharges were not significantly different. Results of this pilot study indicate that using natural-attenuation processes to remove arsenic from water and supplement city water supplies may be a viable, relatively low-cost method for attenuating arsenic in well water and for augmenting the water supply of Lake Thunderbird.

Downstream processing of stevioside and its potential applications.

PubMed

Puri, Munish; Sharma, Deepika; Tiwari, Ashok K

2011-01-01

Stevioside is a natural sweetener extracted from leaves of Stevia rebaudiana Bertoni, which is commercially produced by conventional (chemical/physical) processes. This article gives an overview of the stevioside structure, various analysis technique, new technologies required and the advances achieved in recent years. An enzymatic process is established, by which the maximum efficacy and benefit of the process can be achieved. The efficiency of the enzymatic process is quite comparable to that of other physical and chemical methods. Finally, we believe that in the future, the enzyme-based extraction will ensure more cost-effective availability of stevioside, thus assisting in the development of more food-based applications. Copyright © 2011 Elsevier Inc. All rights reserved.

SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.

PubMed

Blattmann, Peter; Heusel, Moritz; Aebersold, Ruedi

2016-01-01

SWATH-MS is an acquisition and analysis technique of targeted proteomics that enables measuring several thousand proteins with high reproducibility and accuracy across many samples. OpenSWATH is popular open-source software for peptide identification and quantification from SWATH-MS data. For downstream statistical and quantitative analysis there exist different tools such as MSstats, mapDIA and aLFQ. However, the transfer of data from OpenSWATH to the downstream statistical tools is currently technically challenging. Here we introduce the R/Bioconductor package SWATH2stats, which allows convenient processing of the data into a format directly readable by the downstream analysis tools. In addition, SWATH2stats allows annotation, analyzing the variation and the reproducibility of the measurements, FDR estimation, and advanced filtering before submitting the processed data to downstream tools. These functionalities are important to quickly analyze the quality of the SWATH-MS data. Hence, SWATH2stats is a new open-source tool that summarizes several practical functionalities for analyzing, processing, and converting SWATH-MS data and thus facilitates the efficient analysis of large-scale SWATH/DIA datasets.

Multi-component wind measurements of wind turbine wakes performed with three LiDARs

NASA Astrophysics Data System (ADS)

Iungo, G. V.; Wu, Y.-T.; Porté-Agel, F.

2012-04-01

Field measurements of the wake flow produced from the interaction between atmospheric boundary layer and a wind turbine are performed with three wind LiDARs. The tested wind turbine is a 2 MW Enercon E-70 located in Collonges, Switzerland. First, accuracy of mean values and frequency resolution of the wind measurements are surveyed as a function of the number of laser rays emitted for each measurement. Indeed, measurements performed with one single ray allow maximizing sampling frequency, thus characterizing wake turbulence. On the other hand, if the number of emitted rays is increased accuracy of mean wind is increased due to the longer sampling period. Subsequently, two-dimensional measurements with a single LiDAR are carried out over vertical sections of the wind turbine wake and mean wake flow is obtained by averaging 2D measurements consecutively performed. The high spatial resolution of the used LiDAR allows characterizing in details velocity defect present in the central part of the wake and its downstream recovery. Single LiDAR measurements are also performed by staring the laser beam at fixed directions for a sampling period of about ten minutes and maximizing the sampling frequency in order to characterize wake turbulence. From these tests wind fluctuation peaks are detected in the wind turbine wake at blade top-tip height for different downstream locations. The magnitude of these turbulence peaks is generally reduced by moving downstream. This increased turbulence level at blade top-tip height observed for a real wind turbine has been already detected from previous wind tunnel tests and Large Eddy simulations, thus confirming the presence of a source of dangerous fatigue loads for following wind turbines within a wind farm. Furthermore, the proper characterization of wind fluctuations through LiDAR measurements is proved by the detection of the inertial subrange from spectral analysis of these velocity signals. Finally, simultaneous measurements with two LiDARs are performed over the mean vertical symmetry plane of the wind turbine wake, while a third LiDAR measures the incoming wind over a vertical plane parallel to the mean wind direction and lying outside of the wake. One LiDAR is placed in proximity of the wind turbine location and measures pointing downstream, whereas a second LiDAR is located along the mean wind direction at a downstream distance of 6.5 diameters and measures pointing upstream. For these measurements axial and vertical velocity components are retrieved only for measurement points where the two laser beams result to be roughly orthogonal. Statistics of the two velocity components show in the near wake at hub height strong flow fluctuations with magnitudes about 30% of the mean value, and a gradual reduction for downstream distances larger than three rotor diameters.

Downstream movement of recently transformed sea lampreys, Petromyzon marinus, in Carp Lake River, Michigan

USGS Publications Warehouse

Applegate, Vernon C.; Brynildson, Clifford L.

1951-01-01

A total of 7,969 downstream migrants were taken in the 1948–49 season; 16,235 in 1949–50, and 15,103 in 1950–51. Measurements of representative samples from the total catch of sea lamprey migrants of the 1948–49 and 1949–50 seasons revealed a range in length of 95 to 190 millimeters and an average length of 145 millimeters (3.7 to 7.5 inches; mean –5.7 inches).

Use of the semipermeable membrane device as an in situ sampler of waterborne bioavailable PCDD and PCDF residues at sub-parts-per-quadrillion concentrations

USGS Publications Warehouse

Lebo, Jon A.; Gale, Robert W.; Petty, Jimmie D.; Tillitt, Donald E.; Huckins, James N.; Meadows, John C.; Orazio, Carl E.; Echols, Kathy R.; Schroeder, Dennis J.; Inmon, Lloyd E.

1995-01-01

Semipermeable membrane devices (SPMDs) were used to passively sample aqueous polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) in Bayou Meto, AR. The two sites were upstream and downstream from the confluence with a tributary that delivers PCDDs and PCDFs to the Bayou. Following dialysis, cleanup, and fractionation, four replicate 17-9 SPMD samples from each site were analyzed by GUMS, and four were evaluated by H411E bioassay. Traces of only OCDD and HpCDDs were detected in samples from the upstream site. The four samples from below the tributary contained averages of 1550 ± 80 pg of 2,3,7,8-TCDD, 1640 ± 80 pg of 2,3,7,8-TCDF, and lesser quantities of other congeners. The TCDD equivalents obtained by bioassay of replicate SPMD samples agreed well with results obtained by GC/MS. The quantities of 2,3,7,8- TCDD and 2,3,7,8-TCDF sequestered by SPMDs at the downstream site were used to estimate the aqueous concentrations for both compounds as 2 pg/L.

Urban contributions of glyphosate and its degradate AMPA to streams in the United States

USGS Publications Warehouse

Kolpin, D.W.; Thurman, E.M.; Lee, E.A.; Meyer, M.T.; Furlong, E.T.; Glassmeyer, S.T.

2006-01-01

Glyphosate is the most widely used herbicide in the world, being routinely applied to control weeds in both agricultural and urban settings. Microbial degradation of glyphosate produces aminomethyl phosphonic acid (AMPA). The high polarity and water-solubility of glyphosate and AMPA has, until recently, made their analysis in water samples problematic. Thus, compared to other herbicides (e.g. atrazine) there are relatively few studies on the environmental occurrence of glyphosate and AMPA. In 2002, treated effluent samples were collected from 10 wastewater treatment plants (WWTPs) to study the occurrence of glyphosate and AMPA. Stream samples were collected upstream and downstream of the 10 WWTPs. Two reference streams were also sampled. The results document the apparent contribution of WWTP effluent to stream concentrations of glyphosate and AMPA, with roughly a two-fold increase in their frequencies of detection between stream samples collected upstream and those collected downstream of the WWTPs. Thus, urban use of glyphosate contributes to glyphosate and AMPA concentrations in streams in the United States. Overall, AMPA was detected much more frequently (67.5%) compared to glyphosate (17.5%).

Strategies and equipment for sampling suspended sediment and associated toxic chemicals in large rivers - with emphasis on the Mississippi River

USGS Publications Warehouse

Meade, R.H.; Stevens, H.H.

1990-01-01

A Lagrangian strategy for sampling large rivers, which was developed and tested in the Orinoco and Amazon Rivers of South America during the early 1980s, is now being applied to the study of toxic chemicals in the Mississippi River. A series of 15-20 cross-sections of the Mississippi mainstem and its principal tributaries is sampled by boat in downstream sequence, beginning upriver of St. Louis and concluding downriver of New Orleans 3 weeks later. The timing of the downstream sampling sequence approximates the travel time of the river water. Samples at each cross-section are discharge-weighted to provide concentrations of dissolved and suspended constituents that are converted to fluxes. Water-sediment mixtures are collected from 10-40 equally spaced points across the river width by sequential depth integration at a uniform vertical transit rate. Essential equipment includes (i) a hydraulic winch, for sensitive control of vertical transit rates, and (ii) a collapsible-bag sampler, which allows integrated samples to be collected at all depths in the river. A section is usually sampled in 4-8 h, for a total sample recovery of 100-120 l. Sampled concentrations of suspended silt and clay are reproducible within 3%.

Water Quality of the Snake River and Five Eastern Tributaries in the Upper Snake River Basin, Grand Teton National Park, Wyoming, 1998-2002

USGS Publications Warehouse

Clark, Melanie L.; Sadler, Wilfrid J.; O'Ney, Susan E.

2004-01-01

To address water-resource management objectives of the National Park Service in Grand Teton National Park, the U.S. Geological Survey in cooperation with the National Park Service has conducted water-quality sampling in the upper Snake River Basin. Routine sampling of the Snake River was conducted during water years 1998-2002 to monitor the water quality of the Snake River through time. A synoptic study during 2002 was conducted to supplement the routine Snake River sampling and establish baseline water-quality conditions of five of its eastern tributaries?Pilgrim Creek, Pacific Creek, Buffalo Fork, Spread Creek, and Ditch Creek. Samples from the Snake River and the five tributaries were collected at 12 sites and analyzed for field measurements, major ions and dissolved solids, nutrients, selected trace metals, pesticides, and suspended sediment. In addition, the eastern tributaries were sampled for fecal-indicator bacteria by the National Park Service during the synoptic study. Major-ion chemistry of the Snake River varies between an upstream site above Jackson Lake near the northern boundary of Grand Teton National Park and a downstream site near the southern boundary of the Park, in part owing to the inputs from the eastern tributaries. Water type of the Snake River changes from sodium bicarbonate at the upstream site to calcium bicarbonate at the downstream site. The water type of the five eastern tributaries is calcium bicarbonate. Dissolved solids in samples collected from the Snake River were significantly higher at the upstream site (p-value<0.001), where concentrations in 43 samples ranged from 62 to 240 milligrams per liter, compared to the downstream site where concentrations in 33 samples ranged from 77 to 141 milligrams per liter. Major-ion chemistry of Pilgrim Creek, Pacific Creek, Buffalo Fork, Spread Creek, and Ditch Creek generally did not change substantially between the upstream sites near the National Park Service boundary with the National Forest and the downstream sites near the Snake River; however, variations in the major ions and dissolved solids existed between basins. Variations probably result from differences in geology between the tributary basins. Concentrations of dissolved ammonia, nitrite, and nitrate in all samples collected from the Snake River and the five eastern tributaries were less than water-quality criteria for surface waters in Wyoming. Concentrations of total nitrogen and total phosphorus in samples from the Snake River and the tributaries generally were less than median concentrations determined for undeveloped streams in the United States; however, concentrations in some samples did exceed ambient total-nitrogen and total-phosphorus criteria for forested mountain streams in the Middle Rockies ecoregion recommended by the U.S. Environmental Protection Agency to address cultural eutrophication. Sources for the excess nitrogen and phosphorus probably are natural because these basins have little development and cultivation. Concentrations of trace metals and pesticides were low and less than water-quality criteria for surface waters in Wyoming in samples collected from the Snake River and the five eastern tributaries. Atrazine, dieldrin, EPTC, or tebuthiuron were detected in estimated concentrations of 0.003 microgram per liter or less in 5 of 27 samples collected from the Snake River. An estimated concentration of 0.008 microgram per liter of metolachlor was detected in one sample from the Buffalo Fork. The estimated concentrations were less than the reporting levels for the pesticide analytical method. Suspended-sediment concentrations in 43 samples from the upstream site on the Snake River ranged from 1 to 604 milligrams per liter and were similar to suspended-sediment concentrations in 33 samples from the downstream site, which ranged from 1 to 648 milligrams per liter. Suspended-sediment concentrations in 38 samples collected from the tributary streams ranged from 1 t

An analytical framework for extracting hydrological information from time series of small reservoirs in a semi-arid region

NASA Astrophysics Data System (ADS)

Annor, Frank; van de Giesen, Nick; Bogaard, Thom; Eilander, Dirk

2013-04-01

Small water reservoirs for water resources management have as important socio-economic advantage that they bring water close to villages and households. This proximity allows for many water uses in addition to irrigation, such as fisheries, household water, building materials (loam, reeds), tourism and recreation, and cattle watering. These positive aspects are offset by the relatively large evaporative losses in comparison to larger reservoirs, although, it is not exactly known how large these losses are. For decision makers, investors and donors, the decision to construct a small reservoir should be multifactored; and based on economic, socio-cultural and environmental factors. For the latter, getting the water balance and the energy budget of small reservoirs right is key for any environmental impact analyses. For Northern Ghana, the relation between volume of a small reservoir and its' surface area has been established in a robust equation as: Volume = 0.00857Area1.4367 with the surface area explaining more than 95% of the variation in water volume of the reservoirs. This allows the use of remote sensing observations for estimating water volume of small reservoirs in northern Ghana. Hydrological analyses of time series of small reservoir areas comprises estimates of evaporation fluxes and cumulative surface runoff curves. Once the reservoirs are full, spillage will occur and volumes and surface areas remain stable at their maximum extents. This implies that the time series of reservoir surface area contains information concerning the on-set of downstream surface runoff. This on-set does not coincide with the on-set of the rainy season but largely depends on the distribution of rainfall events and storage capacity in the subsurface. The main requirement for this analysis is that the reservoir has negligible seepage losses or water influx from the underlying subsurface. In our research, we carried out a time series analysis of surface area extent for about 45 small reservoirs in the Upper East Region of Ghana. Reservoirs without obvious large seepage losses (field survey) were selected. To verify this, stable water isotopic samples are collected from groundwater upstream and downstream from the reservoir. By looking at possible enrichment of downstream groundwater, a good estimate of seepage can be made in addition to estimates on evaporation. We estimated the evaporative losses and compared those with field measurements using eddy correlation measurements. Lastly, we determined the cumulative surface runoff curves for the small reservoirs .We will present this analytical framework for extracting hydrological information from time series of small reservoirs and show the first results for our study region of northern Ghana.

Anomalies in Trace Metal and Rare-Earth Loads below a Waste-Water Treatment Plant

NASA Astrophysics Data System (ADS)

Antweiler, R.; Writer, J. H.; Murphy, S.

2013-12-01

The changes in chemical loads were examined for 54 inorganic elements and compounds in a 5.4-km reach of Boulder Creek, Colorado downstream of a waste water treatment plant (WWTP) outfall. Elements were partitioned into three categories: those showing a decrease in loading downstream, those showing an increase, and those which were conservative, at least over the length of the study reach. Dissolved loads which declined - generally indicative of in-stream loss via precipitation or sorption - were typically rapid (occurring largely before the first sampling site, 2.3 km downstream); elements showing this behavior were Bi, Cr, Cs, Ga, Ge, Hg, Se and Sn. These results were as expected before the experiment was performed. However, a large group (28 elements, including all the rare-earth elements, REE, except Gd) exhibited dissolved load increases indicating in-stream gains. These gains may be due to particulate matter dissolving or disaggregating, or that desorption is occurring below the WWTP. As with the in-stream loss group, the processes tended to be rapid, typically occurring before the first sampling site. Whole-water samples collected concurrently also had a large group of elements which showed an increase in load downstream of the WWTP. Among these were most of the group which had increases in the dissolved load, including all the REE (except Gd). Because whole-water samples include both dissolved and suspended particulates within them, increases in loads cannot be accounted for by invoking desorption or disaggregation mechanisms; thus, the only source for these increases is from the bed load of the stream. Further, the difference between the whole-water and dissolved loads is a measure of the particulate load, and calculations show that not only did the dissolved and whole-water loads increase, but so did the particulate loads. This implies that at the time of sampling the bed sediment was supplying a significant contribution to the suspended load. In general, it seems untenable as a hypothesis to suppose that the stream bed material can permanently supply the source of the in-stream load increases of a large group of inorganic elements. We propose that the anomalous increase in loads was more a function of the time of sampling (both diurnally and seasonally) and that sampling at different times of day or different seasons during the year would give contradictory results to those seen here. If this is so, inorganic loading studies must include multiple sampling both over the course of a day and during different seasons and flow regimes.

The roles of the binodal curve and the spinodal curve in expansions from the supercritical state with flashing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knuth, Eldon L.; Miller, David R.; Even, Uzi

2014-12-09

Data extracted from time-of-flight (TOF) measurements made on steady-state He free jets at Göttingen already in 1986 and for pulsed Ne free jets investigated recently at Tel Aviv have been added to an earlier plot of terminal condensed-phase mass fraction x{sub 2∞} as a function of the dimensionless scaling parameter Γ. Γ characterizes the source (fluid species, temperature, pressure and throat diameter); values of x{sub 2∞} are extracted from TOF measurements using conservation of energy in the free-jet expansion. For nozzles consisting of an orifice in a thin plate; the extracted data yield 22 data points which are correlated satisfactorilymore » by a single curve. The Ne free jets were expanded from a conical nozzle with a 20° half angle; the three extracted data points stand together but apart from the aforementioned curve, indicating that the presence of the conical wall influences significantly the expansion and hence the condensation. The 22 data points for the expansions via an orifice consist of 15 measurements with expansions from the gas-phase side of the binodal curve which crossed the binodal curve downstream from the sonic point and 7 measurements with expansions of the gas-phase product of the flashing which occurred after an expansion from the liquid-phase side of the binodal curve crossed the binodal curve upstream from the sonic point. The association of these 22 points with a single curve supports the alternating-phase model for flows with flashing upstream from the sonic point proposed earlier. In order to assess the role of the spinodal curve in such expansions, the spinodal curves for He and Ne were computed using general multi-parameter Helmholtz-free-energy equation-of-state formulations. Then, for the several sets of source-chamber conditions used in the free-jet measurements, thermodynamic states at key locations in the free-jet expansions (binodal curve, sonic point and spinodal curve) were evaluated, with the expansion presumed to be metastable from the binodal curve to the spinodal curve. TOF distributions with more than two peaks (interpreted earlier as superimposed alternating-state TOF distributions) indicated flashing of the metastable flow downstream from the binodal curve but upstream from the sonic point. This relatively early flashing is due apparently to destabilizing interactions with the walls of the source. If the expansion crosses the binodal curve downstream from the nozzle, the metastable fluid does not interact with surfaces and flashing might be delayed until the expansion reaches the spinodal curve. It is concluded that, if the expansion crosses the binodal curve before reaching the sonic point, the resulting metastable fluid downstream from the binodal curve interacts with the adjacent surfaces and flashes into liquid and vapor phases which expand alternately through the nozzle; the two associated alternating TOF distributions are superposed by the chopping process so that the result has the appearance of a single distribution with three peaks.« less

AFM fluid delivery/liquid extraction surface sampling/electrostatic spray cantilever probe

DOEpatents

Van Berkel, Gary J.

2015-06-23

An electrospray system comprises a liquid extraction surface sampling probe. The probe comprises a probe body having a liquid inlet and a liquid outlet, and having a liquid extraction tip. A solvent delivery conduit is provided for receiving solvent liquid from the liquid inlet and delivering the solvent liquid to the liquid extraction tip. An open liquid extraction channel extends across an exterior surface of the probe body from the liquid extraction tip to the liquid outlet. An electrospray emitter tip is in liquid communication with the liquid outlet of the liquid extraction surface sampling probe. A system for analyzing samples, a liquid junction surface sampling system, and a method of analyzing samples are also disclosed.

Selenium and Other Elements in Water and Adjacent Rock and Sediment of Toll Gate Creek, Aurora, Arapahoe County, Colorado, December 2003 through March 2004

USGS Publications Warehouse

Herring, J.R.; Walton-Day, Katherine

2007-01-01

Streamwater and solid samples (rock, unconsolidated sediment, stream sediment, and efflorescent material) in the Toll Gate Creek watershed, Colorado, were collected and analyzed for major and trace elements to determine trace-element concentrations and stream loads from December 2003 through March 2004, a period of seasonally low flow. Special emphasis was given to selenium (Se) concentrations because historic Se concentrations exceeded current (2004) stream standards. The goal of the project was to assess the distribution of Se concentration and loads in Toll Gate Creek and to determine the potential for rock and unconsolidated sediment in the basin to be sources of Se to the streamwater. Streamwater samples and discharge measurements were collected during December 2003 and March 2004 along Toll Gate Creek and its two primary tributaries - West Toll Gate Creek and East Toll Gate Creek. During both sampling periods, discharge ranged from 2.5 liters per second to 138 liters per second in the watershed. Discharge was greater in March 2004 than December 2003, but both periods represent low flow in Toll Gate Creek, and results of this study should not be extended to periods of higher flow. Discharge decreased moving downstream in East Toll Gate Creek but increased moving downstream along West Toll Gate Creek and the main stem of Toll Gate Creek, indicating that these two streams gain flow from ground water. Se concentrations in streamwater samples ranged from 7 to 70 micrograms per liter, were elevated in the upstream-most samples, and were greater than the State stream standard of 4.6 micrograms per liter. Se loads ranged from 6 grams per day to 250 grams per day, decreased in a downstream direction along East Toll Gate Creek, and increased in a downstream direction along West Toll Gate Creek and Toll Gate Creek. The largest Se-load increases occurred between two sampling locations on West Toll Gate Creek during both sampling periods and between the two sampling locations on the main stem of Toll Gate Creek during the December 2003 sampling. These load increases may indicate that sources of Se exist between these two locations; however, Se loading along West Toll Gate Creek and Toll Gate Creek primarily was characterized by gradual downstream increases in load. Linear regressions between Se load and discharge for both sampling periods had large, significant values of r2 (r2 > 0.96, p < 0.0001) because increases in Se load (per unit of flow increase) were generally constant. This relation is evidence for a constant addition of water having a relatively constant Se concentration over much of the length of Toll Gate Creek, a result which is consistent with a ground-water source for the Se loads. Rock outcroppings along the stream were highly weathered, and Se concentrations in rock and other solid samples ranged from below detection (1 part per million) to 25 parts per million. One sample of efflorescence (a surface encrustation produced by evaporation) had the greatest selenium concentration of all solid samples, was composed of thenardite (sodium sulfate), gypsum (calcium sulfate) and minor halite (sodium chloride), and released all of its Se during a 30-minute water-leaching procedure. Calculations indicate there was an insufficient amount of this material present throughout the watershed to account for the observed Se load in the stream. However, this material likely indicates zones of ground-water discharge that contain Se. This report did not identify an unequivocal source of Se in Toll Gate Creek. However, multiple lines of evidence indicate that ground-water discharge supplies Se to Toll Gate Creek: (1) the occurrence of elevated Se concentrations in the stream throughout the watershed and in the headwater regions, upstream from industrial sources; (2) the progressive increase in Se loads moving downstream, which indicates a continuous input of Se along the stream rather than input from point sources; (3) the occurr

MALDI-typing of infectious algae of the genus Prototheca using SOM portraits.

PubMed

Wirth, Henry; von Bergen, Martin; Murugaiyan, Jayaseelan; Rösler, Uwe; Stokowy, Tomasz; Binder, Hans

2012-01-01

MALDI-typing has become a frequently used approach for the identification of microorganisms and recently also of invertebrates. Similarity-comparisons are usually based on single-spectral data. We apply self-organizing maps (SOM) to portray the MS-spectral data with individual resolution and to improve the typing of Prototheca algae by using meta-spectra representing prototypes of groups of similar-behaving single spectra. The MALDI-TOF peaklists of more than 300 algae extracts referring to five Prototheca species were transformed into colored mosaic images serving as molecular portraits of the individual samples. The portraits visualize the algae-specific distribution of high- and low-amplitude peaks in two dimensions. Species-specific pattern of MS intensities were readily discernable in terms of unique single spots of high amplitude MS-peaks which collect characteristic fingerprint spectra. The spot patterns allow the visual identification of groups of samples referring to different species, genotypes or isolates. The use of meta-peaks instead of single-peaks reduces the dimension of the data and leads to an increased discriminating power in downstream analysis. We expect that our SOM portray method improves MS-based classifications and feature selection in upcoming applications of MALDI-typing based species identifications especially of closely related species. Copyright © 2011. Published by Elsevier B.V.

The effects of liming an Adirondack lake watershed on downstream water chemistry: Effects of liming on stream chemistry

USGS Publications Warehouse

Burns, Douglas A.

1996-01-01

Calcite treatment of chronically acidic lakes has improved fish habitat, but the effects on downstream water quality have not previously been examined. In this study, the spatial and temporal effects of watershed CaCO3 treatment on the chemistry of a lake outlet stream in the Adirondack Mountains of New York were examined. Before CaCO3 treatment, the stream was chronically acidic. During spring snowmelt before treatment, pH and acid-neutralizing capacity (ANC) in the outlet stream declined, and NO3- and inorganic monomeric aluminum (AlIM) concentrations increased sharply. During that summer, SO42- and NO3- concentrations decreased downstream, and dissolved organic carbon (DOC) concentrations and ANC increased, in association with the seasonal increase in decomposition of organic matter and the attendant SO42--reduction process. A charge-balance ANC calculation closely matched measured downstream changes in ANC in the summer and indicated that SO42- reduction was the major process contributing to summer increases in ANC. Increases in Ca2+ concentration and ANC began immediately after CaCO3 application, and within 3 months, exceeded their pretreatment values by more than 130 ??eq/L. Within 2 months after treatment, downstream decreases in Ca2+ concentration, ANC, and pH, were noted. Stream mass balances between the lake and the sampling site 1.5 km downstream revealed that the transport of all chemical constituents was dominated by conservative mixing with tributaries and ground water; however, non-conservative processes resulted in significant Ca2+ losses during the 13-month period after CaCO3 treatment. Comparison of substrate samples from the buffered outlet stream with those from its untreated tributaries showed that the percentage of cation-exchange sites occupied by Ca2+, as well as non-exchangeable Ca, were higher in the outlet-stream substrate than in tributary-stream substrate. Mass-balance data for Ca2+, H+, AlIM, and DOC revealed net downstream losses of these constituents and indicated that a reasonable set of hypothesized reactions involving AlIM, HCO3-, Ca2+, SO42-, NO3-7, and DOC could have caused the measured changes in stream acid/base chemistry. In the summer, the sharp decrease in ANC continued despite significant downstream decreases in SO42- concentrations. After CaCO3 treatment, reduction of SO42- was only a minor contributor to ANC changes relative to those caused by Ca2+ dilution from acidic tributaries and acidic ground water, and Ca2+ interactions with stream substrate. ?? 1996 Kluwer Academic Publishers.

Methylation of Hg downstream from the Bonanza Hg mine, Oregon

USGS Publications Warehouse

Gray, John E.; Hines, Mark E.; Krabbenhoft, David P.; Thoms, Bryn

2012-01-01

Speciation of Hg and conversion to methyl-Hg were evaluated in stream sediment, stream water, and aquatic snails collected downstream from the Bonanza Hg mine, Oregon. Total production from the Bonanza mine was >1360t of Hg, during mining from the late 1800s to 1960, ranking it as an intermediate sized Hg mine on an international scale. The primary objective of this study was to evaluate the distribution, transport, and methylation of Hg downstream from a Hg mine in a coastal temperate climatic zone. Data shown here for methyl-Hg, a neurotoxin hazardous to humans, are the first reported for sediment and water from this area. Stream sediment collected from Foster Creek flowing downstream from the Bonanza mine contained elevated Hg concentrations that ranged from 590 to 71,000ng/g, all of which (except the most distal sample) exceeded the probable effect concentration (PEC) of 1060ng/g, the Hg concentration above which harmful effects are likely to be observed in sediment-dwelling organisms. Concentrations of methyl-Hg in stream sediment collected from Foster Creek varied from 11 to 62ng/g and were highly elevated compared to regional baseline concentrations (0.11-0.82ng/g) established in this study. Methyl-Hg concentrations in stream sediment collected in this study showed a significant correlation with total organic C (TOC, R2=0.62), generally indicating increased methyl-Hg formation with increasing TOC in sediment. Isotopic-tracer methods indicated that several samples of Foster Creek sediment exhibited high rates of Hg-methylation. Concentrations of Hg in water collected downstream from the mine varied from 17 to 270ng/L and were also elevated compared to baselines, but all were below the 770ng/L Hg standard recommended by the USEPA to protect against chronic effects to aquatic wildlife. Concentrations of methyl-Hg in the water collected from Foster Creek ranged from 0.17 to 1.8ng/L, which were elevated compared to regional baseline sites upstream and downstream from the mine that varied from <0.02 to 0.22ng/L. Aquatic snails collected downstream from the mine were elevated in Hg indicating significant bioavailability and uptake of Hg by these snails. Results for sediment and water indicated significant methyl-Hg formation in the ecosystem downstream from the Bonanza mine, which is enhanced by the temperate climate, high precipitation in the area, and high organic matter.

Water quality effects of herded stream crossings by domestic sheep bands.

PubMed

Clark, Patrick E; Moffet, Corey A; Lewis, Gregory S; Seyfried, Mark S; Hardegree, Stuart P; Pierson, Fredrick B

2012-01-01

Livestock impacts on total suspended solids (TSS) and pathogen (e.g., ) levels in rangeland streams are a serious concern worldwide. Herded stream crossings by domestic sheep () are periodic, necessary managerial events on high-elevation rangelands, but their impacts on stream water quality are largely unknown. We evaluated the effects of herded, one-way crossings by sheep bands (about 2000 individuals) on TSS and concentration and load responses in downstream waters. Crossing trials were conducted during the summers of 2005 and 2006 on two reaches within each of three perennial streams in the Centennial Mountains of eastern Idaho and southwestern Montana. Water samples were collected at 2-min intervals at an upstream background station and at stations 25, 100, 500, and 1500 m downstream just before and during each crossing trial. Crossings produced substantial increases in TSS and concentrations and loads downstream, but these concentration increases were localized and short lived. Maximum TSS concentration was highest 25 m downstream, declined as a function of downstream distance, and at 500 m downstream was similar to background. Post-peak TSS concentrations at all downstream stations decreased to <25 mg L within 24 to 48 min after reaching their maxima. Findings for concentration and load responses were similar to that of TSS but less clear cut. Stream-crossing sheep do affect water quality; therefore, producers and resource managers should continue to evaluate the efficacy of herdsmanship techniques for reducing water quality impact. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Effect of wastewater treatment facility closure on endocrine disrupting chemicals in a Coastal Plain stream

USGS Publications Warehouse

Bradley, Paul M.; Journey, Celeste A.; Clark, Jimmy M.

2016-01-01

Wastewater treatment facility (WWTF) closures are rare environmental remediation events; offering unique insight into contaminant persistence, long-term wastewater impacts, and ecosystem recovery processes. The U.S. Geological Survey assessed the fate of select endocrine disrupting chemicals (EDC) in surface water and streambed sediment one year before and one year after closure of a long-term WWTF located within the Spirit Creek watershed at Fort Gordon, Georgia. Sample sites included a WWTF-effluent control located upstream from the outfall, three downstream effluent-impacted sites located between the outfall and Spirit Lake, and one downstream from the lake's outfall. Prior to closure, the 2.2-km stream segment downstream from the WWTF outfall was characterized by EDC concentrations significantly higher (α = 0.05) than at the control site; indicating substantial downstream transport and limited in-stream attenuation of EDC, including pharmaceuticals, estrogens, alkylphenol ethoxylate (APE) metabolites, and organophosphate flame retardants (OPFR). Wastewater-derived pharmaceutical, APE metabolites, and OPFR compounds were also detected in the outflow of Spirit Lake, indicating the potential for EDC transport to aquatic ecosystems downstream of Fort Gordon under effluent discharge conditions. After the WWTF closure, no significant differences in concentrations or numbers of detected EDC compounds were observed between control and downstream locations. The results indicated EDC pseudo-persistence under preclosure, continuous supply conditions, with rapid attenuation following WWTF closure. Low concentrations of EDC at the control site throughout the study and comparable concentrations in downstream locations after WWTF closure indicated additional, continuing, upstream contaminant sources within the Spirit Creek watershed. 

Improved Butanol-Methanol (BUME) Method by Replacing Acetic Acid for Lipid Extraction of Biological Samples.

PubMed

Cruz, Mutya; Wang, Miao; Frisch-Daiello, Jessica; Han, Xianlin

2016-07-01

Extraction of lipids from biological samples is a critical step in lipidomics, especially for shotgun lipidomics where lipid extracts are directly infused into a mass spectrometer. The butanol-methanol (BUME) extraction method was originally developed to extract lipids from plasma samples with 1 % acetic acid. Considering some lipids are sensitive to acidic environments, we modified this protocol by replacing acetic acid with lithium chloride solution and extended the modified extraction to tissue samples. Although no significant reduction of plasmalogen levels in the acidic BUME extracts of rat heart samples was found, the modified method was established to extract various tissue samples, including rat liver, heart, and plasma. Essentially identical profiles of the majority of lipid classes were obtained from the extracts of the modified BUME and traditional Bligh-Dyer methods. However, it was found that neither the original, nor the modified BUME method was suitable for 4-hydroxyalkenal species measurement in biological samples.

Improved Butanol-Methanol (BUME) Method by Replacing Acetic Acid for Lipid Extraction of Biological Samples

PubMed Central

Cruz, Mutya; Wang, Miao; Frisch-Daiello, Jessica; Han, Xianlin

2016-01-01

Extraction of lipids from biological samples is a critical step in lipidomics, especially for shotgun lipidomics where lipid extracts are directly infused into a mass spectrometer. The butanol-methanol (BUME) extraction method was originally developed to extract lipids from plasma samples with 1% acetic acid. Considering some lipids are sensitive to acidic environments, we modified this protocol by replacing acetic acid with lithium chloride solution and extended the modified extraction to tissue samples. Although no significant reduction of plasmalogen levels in the acidic BUME extracts of rat heart samples was found, the modified method was established to extract various tissue samples, including rat liver, heart, and plasma. Essentially identical profiles of the majority of lipid classes were obtained from the extracts of the modified BUME and traditional Bligh-Dyer methods. However, it was found that neither the original, nor the modified BUME method was suitable for 4-hydroxyalkenal species measurement in biological samples. PMID:27245345

High efficiency ion beam accelerator system

NASA Technical Reports Server (NTRS)

Aston, G.

1981-01-01

An ion accelerator system that successfully combines geometrical and electrostatic focusing principles is presented. This accelerator system uses thin, concave, multiple-hole, closely spaced graphite screen and focusing grids which are coupled to single slot accelerator and decelerator grids to provide high ion extraction efficiency and good focusing. Tests with the system showed a substantial improvement in ion beam current density and collimation as compared with a Pierce electrode configuration. Durability of the thin graphite screen and focusing grids has been proven, and tests are being performed to determine the minimum screen and focusing grid spacing and thickness required to extract the maximum reliable beam current density. Compared with present neutral beam injector accelerator systems, this one has more efficient ion extraction, easier grid alignment, easier fabrication, a less cumbersome design, and the capacity to be constructed in a modular fashion. Conceptual neutral beam injector designs using this modular approach have electrostatic beam deflection plates downstream of each module.

Efficient Removal of Arsenic and Antimony During Blast Furnace Smelting of Lead-Containing Materials

NASA Astrophysics Data System (ADS)

Dosmukhamedov, Nurlan; Kaplan, Valery

2017-02-01

The efficient removal of impurities, As and Sb, from recycled lead-containing materials is a key issue in the selection of the appropriate smelting technology for projects involving metal reuse. Volatilization of impurities such as As and Sb should occur as early as possible in the process, and preferably within the smelting furnace, so that they do not contaminate the industrial environment nor interfere with the operation of downstream equipment. Using of copper-zinc concentrates in the blast furnace process for recycling lead-containing materials achieves: (1) high copper extraction to matte; (2) high lead extraction to lead bullion; and (3) high zinc extraction to slag, while at the same time producing a more efficient volatilization of As and Sb. Based on both laboratory and industrial data and thermodynamic considerations, the advantages of this blast furnace process for the treatment of recycled lead-containing materials are discussed.

Assessment of hydrology, water quality, and trace elements in selected placer-mined creeks in the birch creek watershed near central, Alaska, 2001-05

USGS Publications Warehouse

Kennedy, Ben W.; Langley, Dustin E.

2007-01-01

Executive Summary The U.S. Geological Survey, in cooperation with the Bureau of Land Management, completed an assessment of hydrology, water quality, and trace-element concentrations in streambed sediment of the upper Birch Creek watershed near Central, Alaska. The assessment covered one site on upper Birch Creek and paired sites, upstream and downstream from mined areas, on Frying Pan Creek and Harrison Creek. Stream-discharge and suspended-sediment concentration data collected at other selected mined and unmined sites helped characterize conditions in the upper Birch Creek watershed. The purpose of the project was to provide the Bureau of Land Management with baseline information to evaluate watershed water quality and plan reclamation efforts. Data collection began in September 2001 and ended in September 2005. There were substantial geomorphic disturbances in the stream channel and flood plain along several miles of Harrison Creek. Placer mining has physically altered the natural stream channel morphology and removed streamside vegetation. There has been little or no effort to re-contour waste rock piles. During high-flow events, the abandoned placer-mine areas on Harrison Creek will likely contribute large quantities of sediment downstream unless the mined areas are reclaimed. During 2004 and 2005, no substantial changes in nutrient or major-ion concentrations were detected in water samples collected upstream from mined areas compared with water samples collected downstream from mined areas on Frying Pan Creek and Harrison Creek that could not be attributed to natural variation. This also was true for dissolved oxygen, pH, and specific conductance-a measure of total dissolved solids. Sample sites downstream from mined areas on Harrison Creek and Frying Pan Creek had higher median suspended-sediment concentrations, by a few milligrams per liter, than respective upstream sites. However, it is difficult to attach much importance to the small downstream increase, less than 10 milligrams per liter, in median suspended-sediment concentration for either basin. During low-flow conditions in 2004 and 2005, previously mined areas investigated on Harrison Creek and on Frying Pan Creek did not contribute substantial suspended sediments to sample sites downstream from the mined areas. No substantial mining-related water- or sediment-quality problems were detected at any of the sites investigated in the upper Birch Creek watershed during low-flow conditions. Average annual streamflow and precipitation were near normal in 2002 and 2003. Drought conditions, extreme forest fire impact, and low annual streamflow set apart the 2004 and 2005 summer seasons. Daily mean streamflow for upper Birch Creek varied throughout the period of record-from maximums of about 1,000 cubic feet per second to minimums of about 20 cubic feet per second. Streamflow increased and decreased rapidly in response to rainfall and rapid snowmelt events because the steep slopes, thin soil cover, and permafrost areas in the watershed have little capacity to retain runoff. Median suspended-sediment concentrations for the 115 paired samples from Frying Pan Creek and 101 paired samples from Harrison Creek were less than the 20 milligrams per liter total maximum daily load. The total maximum daily load was set by the U.S. Environmental Protection Agency for the upper Birch Creek basin in 1996. Suspended-sediment paired-sample data were collected using automated samplers in 2004 and 2005, primarily during low-flow conditions. Suspended-sediment concentrations in grab samples from miscellaneous sites ranged from less than 1 milligram per liter during low-flow conditions to 1,386 milligrams per liter during a high-flow event on upper Birch Creek. Streambed-sediment samples were collected at six sites on Harrison Creek, two sites on Frying Pan Creek, and one site on upper Birch Creek. Trace-element concentrations of mercury, lead, and zinc in streambed sedimen

Surface-water-quality assessment of the lower Kansas River basin, Kansas and Nebraska; project data November 1986 through April 1990

USGS Publications Warehouse

Fallon, J.D.; McChesney, J.A.

1993-01-01

Surface-water-quality data were collected from the lower Kansas River Basin in Kansas and Nebraska. The data are presented in 17 tables consisting of physical properties, concentrations of dissolved solids and major ions, dissolved and total nutrients, dissolved and total major metals and trace elements, radioactivity, organic carbon, pesticides and other synthetic-organic compounds, bacteria and chlorophyll-a, in water; particle-size distributions and concentrations of major metals and trace elements in suspended and streambed sediment; and concentrations of synthetic-organic compounds in streambed sediment. The data are grouped within each table by sampling sites, arranged in downstream order. Ninety-one sites were sampled in the study area. These sampling sites are classified in three, non-exclusive categories (fixed, synoptic, and miscellaneous sites) on the basis of sampling frequency and location. Sampling sites are presented on a plate and in 3 tables, cross-referenced by downstream order, alphabetical order, U.S. Geological Survey identification number, sampling-site classification category, and types of analyses performed at each site. The methods used to collect, analyze, and verify the accuracy of the data also are presented. (USGS)

Electrostatic ion thruster optics calculations

NASA Technical Reports Server (NTRS)

Whealton, John H.; Kirkman, David A.; Raridon, R. J.

1992-01-01

Calculations have been performed which encompass both a self-consistent ion source extraction plasma sheath and the primary ion optics including sheath and electrode-induced aberrations. Particular attention is given to the effects of beam space charge, accelerator geometry, and properties of the downstream plasma sheath on the position of the electrostatic potential saddle point near the extractor electrode. The electron blocking potential blocking is described as a function of electrode thickness and secondary plasma processes.

Molecular analysis of HER2 signaling in human breast cancer by functional protein pathway activation mapping

PubMed Central

Wulfkuhle, Julia D.; Berg, Daniela; Wolff, Claudia; Langer, Rupert; Tran, Kai; Illi, Julie; Espina, Virginia; Pierobon, Mariaelena; Deng, Jianghong; DeMichele, Angela; Walch, Axel; Bronger, Holger; Becker, Ingrid; Waldhör, Christine; Höfler, Heinz; Esserman, Laura; Liotta, Lance A.; Becker, Karl-Friedrich; Petricoin, Emanuel F.

2017-01-01

Purpose Targeting of the HER2 protein in human breast cancer represents a major advance in oncology, but relies on measurements of total HER2 protein and not HER2 signaling network activation. We utilized reverse phase protein microarrays (RPMAs) to measure total and phosphorylated HER2 in the context of HER family signaling to understand correlations between phosphorylated and total levels of HER2 and downstream signaling activity. Experimental Design Three independent study sets, comprising a total of 415 individual patient samples from flash frozen core biopsy samples and FFPE surgical and core samples, were analyzed via RPMA. The phosphorylation and total levels of the HER receptor family proteins and downstream signaling molecules were measured in laser capture microdissected (LCM) enriched tumor epithelium from 127 frozen pre-treatment core biopsy samples and whole tissue lysates from 288 FFPE samples and these results were compared to FISH and IHC. Results RPMA measurements of total HER2 were highly concordant (> 90% all sets) with FISH and/or IHC data, as was phosphorylation of HER2 in the FISH/IHC+ population. Phosphorylation analysis of HER family signaling identified HER2 activation in some FISH/IHC- tumors and, identical to that seen with FISH/IHC+ tumors, the HER2 activation was concordant with EGFR and HER3 phosphorylation and downstream signaling endpoint activation. Conclusions Molecular profiling of HER2 signaling of a large cohort of human breast cancer specimens using a quantitative and sensitive functional pathway activation mapping technique reveals IHC-/FISH-/pHER2+ tumors with HER2 pathway activation independent of total HER2 levels and functional signaling through HER3 and EGFR. PMID:23045247

Recovery of biotechnological products using aqueous two phase systems.

PubMed

Phong, Win Nee; Show, Pau Loke; Chow, Yin Hui; Ling, Tau Chuan

2018-04-16

Aqueous two-phase system (ATPS) has been suggested as a promising separation tool in the biotechnological industry. This liquid-liquid extraction technique represents an interesting advance in downstream processing due to several advantages such as simplicity, rapid separation, efficiency, economy, flexibility and biocompatibility. Up to date, a range of biotechnological products have been successfully recovered from different sources with high yield using ATPS-based strategy. In view of the important potential contribution of the ATPS in downstream processing, this review article aims to provide latest information about the application of ATPS in the recovery of various biotechnological products in the past 7 years (2010-2017). Apart from that, the challenges as well as the possible future work and outlook of the ATPS-based recovery method have also been presented in this review article. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Oil cooling system for a gas turbine engine

NASA Technical Reports Server (NTRS)

Coffinberry, G. A.; Kast, H. B. (Inventor)

1977-01-01

A gas turbine engine fuel delivery and control system is provided with means to recirculate all fuel in excess fuel control requirements back to the aircraft fuel tank. This increases the fuel pump heat sink and decreases the pump temperature rise without the addition of valving other than normally employed. A fuel/oil heat exchanger and associated circuitry is provided to maintain the hot engine oil in heat exchange relationship with the cool engine fuel. Where anti-icing of the fuel filter is required, means are provided to maintain the fuel temperature entering the filter at or above a minimum level to prevent freezing thereof. In one embodiment, a divider valve is provided to take all excess fuel from either upstream or downstream of the fuel filter and route it back to the tanks, the ratio of upstream to downstream extraction being a function of fuel pump discharge pressure.

Assessment of suspended-sediment transport, bedload, and dissolved oxygen during a short-term drawdown of Fall Creek Lake, Oregon, winter 2012-13

USGS Publications Warehouse

Schenk, Liam N.; Bragg, Heather M.

2014-01-01

The drawdown of Fall Creek Lake resulted in the net transport of approximately 50,300 tons of sediment from the lake during a 6-day drawdown operation, based on computed daily values of suspended-sediment load downstream of Fall Creek Dam and the two main tributaries to Fall Creek Lake. A suspended-sediment budget calculated for 72 days of the study period indicates that as a result of drawdown operations, there was approximately 16,300 tons of sediment deposition within the reaches of Fall Creek and the Middle Fork Willamette River between Fall Creek Dam and the streamgage on the Middle Fork Willamette River at Jasper, Oregon. Bedload samples collected at the station downstream of Fall Creek Dam during the drawdown were primarily composed of medium to fine sands and accounted for an average of 11 percent of the total instantaneous sediment load (also termed sediment discharge) during sample collection. Monitoring of dissolved oxygen at the station downstream of Fall Creek Dam showed an initial decrease in dissolved oxygen concurrent with the sediment release over the span of 5 hours, though the extent of dissolved oxygen depletion is unknown because of extreme and rapid fouling of the probe by the large amount of sediment in transport. Dissolved oxygen returned to background levels downstream of Fall Creek Dam on December 18, 2012, approximately 1 day after the end of the drawdown operation.

Reconnaissance of toxic substances in the Jordan River, Salt Lake County, Utah

USGS Publications Warehouse

Thompson, Kendall R.

1984-01-01

A reconnaissance of toxic substances in the Jordan River, Salt Lake County, Utah, was made during July, 1980 to October, 1982 as part of a larger study of the river that included studies of sanitary quality, dissolved oxygen, and turbidity. Samples for toxic substances were collected at five sites on the Jordan River, at three major tributaries, and at six storm drains. The toxic substance that most frequently exceeded State standards was total mercury. About 78 percent of the 138 samples for total mercury exceeded the State standard of 0.05 microgram per liter. Other toxic substances that exceeded State standards were: Ammonia-18 percent of the samples analyzed, cadmium--9 percent, copper-9 percent, zinc--6 percent, and lead--2 percent. One sample for cyanide and one for iron also exceeded State standards. The diversity of toxic substances with concentrations large enough to cause them to be problems increased from the upstream sampling site at the Jordan Narrows to the next two downstream sites at 9000 South and 5800 South Streets. Concentrations of trace elements in stream-bottom materials also increased in a downstream direction. Substantial increases first were observed at 5800 South Street, and they were sustained throughout the downstream study area. Iron is transported in the greatest quantity of all the trace elements studied, with a mean load of 110 pounds per day. Notable loads of barium, boron, lead , and zinc also are transported by the river. DDD, DDE, DDT, dieldrin, heptachlor, methoxychlor, PCB, and 2,4-D were detected in bottom materials; and DDE, Silvex, and 2,4-D were detected in water samples. Of 112 organic compounds in the Environmental Protection Agency 's priority pollutant list, only chloroform was detected in the storm drains that empty into the Joran River. Several metals and phenol also were detected in the samples for priority pollutants. (USGS)

The application of alkaline lysis and pressure cycling technology in the differential extraction of DNA from sperm and epithelial cells recovered from cotton swabs.

PubMed

Nori, Deepthi V; McCord, Bruce R

2015-09-01

This study reports the development of a two-step protocol using pressure cycling technology (PCT) and alkaline lysis for differential extraction of DNA from mixtures of sperm and vaginal epithelial cells recovered from cotton swabs. In controlled experiments, in which equal quantities of sperm and female epithelial cells were added to cotton swabs, 5 min of pressure pulsing in the presence of 0.4 M NaOH resulted in 104 ± 6% recovery of female epithelial DNA present on the swab. Following the pressure treatment, exposing the swabs to a second 5-min alkaline treatment at 95 °C without pressure resulted in the selective recovery of 69 ± 6% of the sperm DNA. The recovery of the vaginal epithelia and sperm DNA was optimized by examining the effect of sodium hydroxide concentration, incubation temperature, and time. Following the alkaline lysis steps, the samples were neutralized with 2 M Tris (pH 7.5) and purified with phenol-chloroform-isoamyl alcohol to permit downstream analysis. The total processing time to remove both fractions from the swab was less than 20 min. Short tandem repeat (STR) analysis of these fractions obtained from PCT treatment and alkaline lysis generated clean profiles of female epithelial DNA and male sperm DNA for 1:1 mixtures of female and male cells and predominant male profiles for mixtures up to 5:1 female to male cells. By reducing the time and increasing the recovery of DNA from cotton swabs, this new method presents a novel and potentially useful procedure for forensic differential extractions.

Multi-residue analysis of emerging pollutants in benthic invertebrates by modified micro-quick-easy-cheap-efficient-rugged-safe extraction and nanoliquid chromatography-nanospray-tandem mass spectrometry analysis.

PubMed

Berlioz-Barbier, Alexandra; Buleté, Audrey; Faburé, Juliette; Garric, Jeanne; Cren-Olivé, Cécile; Vulliet, Emmanuelle

2014-11-07

Aquatic ecosystems are continuously contaminated by agricultural and industrial sources. Although the consequences of this pollution are gradually becoming visible, their potential impacts on aquatic ecosystems are poorly known, particularly regarding the risk of bioaccumulation in different trophic levels. To establish a causality relationship between bioaccumulation and disease, experiments on biotic matrices must be performed. In this context, a multi-residue method for the analysis of 35 emerging pollutants in three benthic invertebrates (Potamopyrgus antipodarum, Gammarus fossarum, and Chironomus riparius) has been developed. Because the variation in response of each individual must be taken into account in ecotoxicological studies, the entire analytical chain was miniaturised, thereby reducing the required sample size to a minimum of one individual and scaling the method accordingly. A new extraction strategy based on a modified, optimised and miniaturised "QuEChERS" approach is reported. The procedure involves salting out liquid-liquid extraction of approximately 10-20mg of matrix followed by nano-liquid chromatography-nano electospray ionisation coupled with tandem mass spectrometry. The validated analytical procedure exhibited recoveries between 40 and 98% for all the target compounds and enabled the determination of pollutants on an individual scale in the ng g(-1) concentration. The method was subsequently applied to determine the levels of target analytes in several encaged organisms which were exposed upstream and downstream of an effluent discharge. The results highlighted a bioaccumulation of certain targeted emerging pollutants in three freshwater invertebrates, as well as inter-species differences. 18 out of 35 compounds were detected and eight were quantified. The highest concentrations were measured for ibuprofen in G. fossarum, reaching up to 105 ng g(-1). Copyright © 2014 Elsevier B.V. All rights reserved.

Agricultural land contamination by heavy metals around the former mining site of Bechateur (northern Tunisia)

NASA Astrophysics Data System (ADS)

Daldoul, G.; Soussi, R.; Soussi, F.; Boularbah, A.

2012-04-01

The activity of the former Pb-Zn mine of Jebel Ghozlen (Béchateur. extreme northern Tunisia) generated during the last century large quantities of tailings (extraction, flotation, gravimetry) deposited as three heap between the mine site and the shoreline located 700 m away. Areas surrounding the mine site are agricultural and are crossed by two rivers, one of which crosses the main heap. The minerals that make up these wastes are calcite, dolomite, quartz, gypsum, pyrite, barite, smithsonite, cerussite and galena. The amounts of Zn, Cd and Pb in the wastes vary between 1.3 and 9.3%, 1.1% and 5.7 and 185 and 410 mg kg-1, respectively. Soils in the study area are carbonated and are characterized by a silt-sand texture. The clay fraction is dominated by kaolinite. The chemical analysis of thirty samples collected over an area of 3 km2 shows that the amounts of total organic carbon (TOC) and total sulfur vary from 0.7 % to 2.5 % and 0.08 % to 0.96 %, respectively, while those of Zn, Pb and Cd range from 300 to 22 000 mg kg-1, 85 to 3000 mg kg-1 and 2 to 47 mg kg-1, respectively. The highest concentrations of metals were found in flood plains at 500 m downstream of the mine site. Extraction tests using deionized water and a 0.1 M CaCl2 solution were performed to assess the mobility of Zn, Pb and Cd in contaminated and reference soil samples collected within the study area. The results of extraction with deionized water showed that the leached amounts of Zn and Cd range between 0.2 and 4 mg kg-1 and 0.02 and 0.2 mg kg-1, respectively; while that of Pb is quite near the detection limit. During the extraction with CaCl2 the leached amounts of Zn, Pb and Cd range from 0.3 to 86 mg kg-1, 2 to 6 mg kg-1 and 0.05 to 0.9 mg kg-1, respectively. Thus, the mobility of Cd, Zn and Pb in CaCl2 solution (0.8 %, 0.4 % and 0.3 %, respectively) is higher compared with the extraction with deionized water (0.2%, 0.1% and 0.02 %, respectively). Toxicity tests were conducted on these soils using the MetPlate method. The results show a low bioavailability of contaminants.

Urinary extracellular vesicles for RNA extraction: optimization of a protocol devoid of prokaryote contamination.

PubMed

Tataruch-Weinert, Dorota; Musante, Luca; Kretz, Oliver; Holthofer, Harry

2016-01-01

Urinary extracellular vesicles (UEVs) represent an ideal platform for biomarker discovery. They carry different types of RNA species, and reported profile discrepancies related to the presence/absence of 18s and 28s rRNA remain controversial. Moreover, sufficient urinary RNA yields and respective quality RNA profiles are still to be fully established. UEVs were enriched by hydrostatic filtration dialysis, and RNA content was extracted using 7 different commercially available techniques. RNA quantity was assessed using spectrophotometry and fluorometry, whilst RNA quality was determined by capillary electrophoresis. The presence of prokaryotic transcriptome was stressed when cellular RNA, as a control, was spiked into the UEVs samples before RNA extraction. The presence of bacteria in hydrostatic filtration dialysis above 1,000 kDa molecular weight cut-off and in crude urine was confirmed with growth media plates. The efficiency in removing urinary bacteria was evaluated by differential centrifugation, filtration (0.22 µm filters) and chemical pretreatment (water purification tablet). For volumes of urine >200 ml, the chemical treatment provides ease of handling without affecting vesicle integrity, protein and RNA profiles. This protocol was selected to enrich RNA with 7 methods, and its respective quality and quantity were assessed. The results were given as follows: (a) Fluorometry gave more repeatability and reproducibility than spectrophotometry to assess the RNA yields, (b) UEVs were enriched with small RNA, (c) Ribosomal RNA peaks were not observed for any RNA extraction method used and (d) RNA yield was higher for column-based method designed for urinary exosome, whilst the highest relative microRNA presence was obtained using TRIzol method. Our results show that the presence of bacteria can lead to misidentification in the electrophoresis peaks. Fluorometry is more reliable than spectrophotometry. RNA isolation method must be selected in conjunction with appropriate UEV collection procedure. We also suggested that a minimum 250 ml of urine should be processed to gather enough RNA for robust quantification, qualification and downstream analysis.

Urinary extracellular vesicles for RNA extraction: optimization of a protocol devoid of prokaryote contamination

PubMed Central

Tataruch-Weinert, Dorota; Musante, Luca; Kretz, Oliver; Holthofer, Harry

2016-01-01

Background Urinary extracellular vesicles (UEVs) represent an ideal platform for biomarker discovery. They carry different types of RNA species, and reported profile discrepancies related to the presence/absence of 18s and 28s rRNA remain controversial. Moreover, sufficient urinary RNA yields and respective quality RNA profiles are still to be fully established. Methods UEVs were enriched by hydrostatic filtration dialysis, and RNA content was extracted using 7 different commercially available techniques. RNA quantity was assessed using spectrophotometry and fluorometry, whilst RNA quality was determined by capillary electrophoresis. Results The presence of prokaryotic transcriptome was stressed when cellular RNA, as a control, was spiked into the UEVs samples before RNA extraction. The presence of bacteria in hydrostatic filtration dialysis above 1,000 kDa molecular weight cut-off and in crude urine was confirmed with growth media plates. The efficiency in removing urinary bacteria was evaluated by differential centrifugation, filtration (0.22 µm filters) and chemical pretreatment (water purification tablet). For volumes of urine >200 ml, the chemical treatment provides ease of handling without affecting vesicle integrity, protein and RNA profiles. This protocol was selected to enrich RNA with 7 methods, and its respective quality and quantity were assessed. The results were given as follows: (a) Fluorometry gave more repeatability and reproducibility than spectrophotometry to assess the RNA yields, (b) UEVs were enriched with small RNA, (c) Ribosomal RNA peaks were not observed for any RNA extraction method used and (d) RNA yield was higher for column-based method designed for urinary exosome, whilst the highest relative microRNA presence was obtained using TRIzol method. Conclusion Our results show that the presence of bacteria can lead to misidentification in the electrophoresis peaks. Fluorometry is more reliable than spectrophotometry. RNA isolation method must be selected in conjunction with appropriate UEV collection procedure. We also suggested that a minimum 250 ml of urine should be processed to gather enough RNA for robust quantification, qualification and downstream analysis. PMID:27345058

Water exposure assessment of aryl hydrocarbon receptor agonists in Three Gorges Reservoir, China using SPMD-based virtual organisms.

PubMed

Wang, Jingxian; Bernhöft, Silke; Pfister, Gerd; Schramm, Karl-Werner

2014-10-15

SPMD-based virtual organisms (VOs) were deployed at five to eight sites in the Three Gorges Reservoir (TGR), China for five periods in 2008, 2009 and 2011. The water exposure of aryl hydrocarbon receptor (AhR) agonists was assessed by the VOs. The chosen bioassay response for the extracts of the VOs, the induction of 7-ethoxyresorufin-O-deethylase (EROD) was assayed using a rat hepatoma cell line (H4IIE). The results show that the extracts from the VOs could induce AhR activity significantly, whereas the chemically derived 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) equivalent (TEQcal) accounted for <11% of the observed AhR responses (TEQbio). Unidentified AhR-active compounds represented a greater proportion of the TCDD equivalent in VOs from TGR. High TEQbio value in diluted extract and low TEQbio in concentrated extract of the same sample was observed suggesting potential non-additive effects in the mixture. The levels of AhR agonists in VOs from upstream TGR were in general higher than those from downstream reservoir, indicating urbanization effect on AhR agonist pollution. The temporal variation showed that levels of AhR agonists in 2009 and 2011 were higher than those in 2008, and the potential non-additive effects in the area close to the dam were also obviously higher in 2009 and 2011 than in 2008, indicating big changes in the composition of pollutants in the area after water level reached a maximum of 175 m. Although the aqueous concentration of AhR agonists of 0.8-4.8 pg TCDDL(-1) in TGR was not alarming, the tendency of accumulating high concentration of AhR agonists in VO lipid and existence of possible synergism or antagonism in the water may exhibit a potential hazard to local biota being exposed to AhR agonists. Copyright © 2014 Elsevier B.V. All rights reserved.

Application of Integral Pumping Tests to estimate the influence of losing streams on groundwater quality

NASA Astrophysics Data System (ADS)

Leschik, S.; Musolff, A.; Reinstorf, F.; Strauch, G.; Schirmer, M.

2009-05-01

Urban streams receive effluents of wastewater treatment plants and untreated wastewater during combined sewer overflow events. In the case of losing streams substances, which originate from wastewater, can reach the groundwater and deteriorate its quality. The estimation of mass flow rates Mex from losing streams to the groundwater is important to support groundwater management strategies, but is a challenging task. Variable inflow of wastewater with time-dependent concentrations of wastewater constituents causes a variable water composition in urban streams. Heterogeneities in the structure of the streambed and the connected aquifer lead, in combination with this variable water composition, to heterogeneous concentration patterns of wastewater constituents in the vicinity of urban streams. Groundwater investigation methods based on conventional point sampling may yield unreliable results under these conditions. Integral Pumping Tests (IPT) can overcome the problem of heterogeneous concentrations in an aquifer by increasing the sampled volume. Long-time pumping (several days) and simultaneous sampling yields reliable average concentrations Cav and mass flow rates Mcp for virtual control planes perpendicular to the natural flow direction. We applied the IPT method in order to estimate Mex of a stream section in Leipzig (Germany). The investigated stream is strongly influenced by combined sewer overflow events. Four pumping wells were installed up- and downstream of the stream section and operated for a period of five days. The study was focused on four inorganic (potassium, chloride, nitrate and sulfate) and two organic (caffeine and technical-nonylphenol) wastewater constituents with different transport properties. The obtained concentration-time series were used in combination with a numerical flow model to estimate Mcp of the respective wells. The difference of the Mcp's between up- and downstream wells yields Mex of wastewater constituents that increase downstream of the stream. In order to confirm the obtained Mcp's concentrations of additional measurements in the investigated stream were compared with the concentrations in the groundwater up- and downstream of the stream section. The results revealed increased Mcp's downstream of the stream section for chloride, potassium and nitrate, whereas Mcp of sulfate was decreased. Micropollutants caffeine and technical-nonylphenol showed decreased Mcp's downstream of the stream section in 75 % of the cases. Values of Mex could only be given for chloride, potassium, nitrate and caffeine. The comparison of concentrations in the stream with those in the groundwater points to the streambed as a zone where mass accumulation and degradation processes occur. The obtained results imply that the applied method can provide reliable data about the influence of losing streams on groundwater quality.

[Validation of Differential Extraction Kit in forensic sexual assault cases].

PubMed

Wu, Dan; Cao, Yu; Xu, Yan; He, Bai-Fang; Bi, Gang; Zhou, Huai-Gu

2009-12-01

To evaluate the validity of Differential Extraction Kit in isolating spermatozoa and epithelial cell DNA from mixture samples. Selective lysis of spermatid and epithelial cells combined with paramagnetic particle method were applied to extract the DNA from the mock samples under controlled conditions and forensic case samples, and template DNA were analyzed by STR genotype method. This Differential Extraction Kit is efficient to obtain high quality spermatid and epithelial cell DNA from the mixture samples with different proportion of sperm to epithelial cell. The Differential Extraction Kit can be applied in DNA extraction for mixed stain from forensic sexual assault samples.

Effects of selenium supplementation in cattle on aquatic ecosystems in northern California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norman, B.; Nader, G.; Oliver, M.

1992-09-15

The potential impact on aquatic ecosystems of supplementing the diets of beef cattle with selenium (Se) was studied on 4 northern California ranches. All study sites included an area of concentrated use by cattle that had diets supplemented with Se. In each case, a stream flowed through the site and provided a control sampling area upstream and a treated sampling area downstream. Specimens of water, sediment, algae, aquatic plants, aquatic invertebrates, and fish were analyzed fluorometrically for total Se content. Significant differences in Se concentration were not found between specimens from upstream control areas and those from downstream areas subjectedmore » to use by Se-treated cattle. Evidence was not found that Se supplementation in cattle at maximal permitted concentrations caused Se accumulation in associated aquatic ecosystems.« less

Aircraft Particle Emissions eXperiment (APEX)

NASA Technical Reports Server (NTRS)

Wey, C. C.; Anderson, B. E.; Hudgins, C.; Wey, C.; Li-Jones, X.; Winstead, E.; Thornhill, L. K.; Lobo, P.; Hagen, D.; Whitefield, P.

2006-01-01

APEX systematically investigated the gas-phase and particle emissions from a CFM56-2C1 engine on NASA's DC-8 aircraft as functions of engine power, fuel composition, and exhaust plumage. Emissions parameters were measured at 11 engine power, settings, ranging from idle to maximum thrust, in samples collected at 1, 10, and 30 m downstream of the exhaust plane as the aircraft burned three fuels to stress relevant chemistry. Gas-phase emission indices measured at 1 m were in good agreement with the ICAO data and predictions provided by GEAE empirical modeling tools. Soot particles emitted by the engine exhibited a log-normal size distribution peaked between 15 and 40 nm, depending on engine power. Samples collected 30 m downstream of the engine exhaust plane exhibited a prominent nucleation mode.

Water- and Bed-Sediment Quality of Seguchie Creek and Selected Wetlands Tributary to Mille Lacs Lake in Crow Wing County, Minnesota, October 2003 to October 2006

USGS Publications Warehouse

Fallon, James D.; Yaeger, Christine S.

2009-01-01

Mille Lacs Lake and its tributaries, located in east-central Minnesota, are important resources to the public. In addition, many wetlands and lakes that feed Mille Lacs Lake are of high resource quality and vulnerable to degradation. Construction of a new four-lane expansion of U.S. Highway 169 has been planned along the western part of the drainage area of Mille Lacs Lake in Crow Wing County. Concerns exist that the proposed highway could affect the resource quality of surface waters tributary to Mille Lacs Lake. Baseline water- and bed-sediment quality characteristics of surface waters tributary to Mille Lacs Lake were needed prior to the proposed highway construction. The U.S. Geological Survey, in cooperation with the Minnesota Department of Transportation, characterized the water- and bed-sediment quality at selected locations that the proposed route intersects from October 2003 to October 2006. Locations included Seguchie Creek upstream and downstream from the proposed route and three wetlands draining to Mille Lacs Lake. The mean streamflow of Seguchie Creek increased between the two sites: flow at the downstream streamflow-gaging station of 0.22 cubic meter per second was 5.6 percent greater than the mean streamflow at the upstream streamflow-gaging station of 0.21 cubic meter per second. Because of the large amount of storage immediately upstream from both gaging stations, increases in flow were gradual even during intense precipitation. The ranges of most constituent concentrations in water were nearly identical between the two sampling sites on Seguchie Creek. No concentrations exceeded applicable water-quality standards set by the State of Minnesota. Dissolved-oxygen concentrations at the downstream gaging station were less than the daily minimum standard of 4.0 milligrams per liter for 6 of 26 measurements. Constituent loads in Seguchie Creek were greater at the downstream site than the upstream site for all measured, including dissolved chloride (1.7 percent), ammonia plus organic nitrogen (13 percent), total phosphorus (62 percent), and suspended sediment (11 percent) during the study. All constituents had seasonal peaks in spring and fall. The large loads during the fall resulted from unusually large precipitation and streamflow patterns. This caused the two greatest streamflow peaks at both sites to occur during October (2004 and 2005). In Seguchie Creek, bed-sediment concentrations of five metals and trace elements (arsenic, cadmium, chromium, lead, and zinc) exceeded the Interim Sediment Quality Guidelines (ISQG) set by the Canadian Council of Ministers of the Environment. Bed-sediment samples from the upstream site had more exceedances of ISQGs for metals and trace elements than did samples from the downstream site (seven and two exceedances, respectively). Bed-sediment samples from the downstream site had more exceedances of ISQGs (20 exceedances) for semivolatile organic compounds than did samples from the upstream site (8 exceedances), indicating different sources for organic compounds than for metals and trace elements. Concentrations of 11 semivolatile organic compounds exceeded ISQGs: ancenaphthene, acenaphthylene, anthracene, benzo[a]anthracene, benzo[a]pyrene, chrysene, fluoranthene, fluorene, naphthalene, phenanthrene, and pyrene. In bed-sediment samples collected from three wetlands, concentrations of all six metals exceeded ISQGs: arsenic, cadmium, chromium, copper, lead, and zinc. Concentrations of three semivolatile organic compounds exceeded ISQGs: flouranthene, phenanthrene, and pyrene. Results indicate that areas appearing relatively undisturbed and of high resource value can have degraded quality from previous unknown land use.

Comparative Study of the Effect of Sample Pretreatment and Extraction on the Determination of Flavonoids from Lemon (Citrus limon)

PubMed Central

Ledesma-Escobar, Carlos A.; Priego-Capote, Feliciano; Luque de Castro, María D.

2016-01-01

Background Flavonoids have shown to exert multiple beneficial effects on human health, being also appreciated by both food and pharmaceutical industries. Citrus fruits are a key source of flavonoids, thus promoting studies to obtain them. Characteristics of these studies are the discrepancies among sample pretreatments and among extraction methods, and also the scant number of comparative studies developed so far. Objective Evaluate the effect of both the sample pretreatment and the extraction method on the profile of flavonoids isolated from lemon. Results Extracts from fresh, lyophilized and air-dried samples obtained by shaking extraction (SE), ultrasound-assisted extraction (USAE), microwave-assisted extraction (MAE) and superheated liquid extraction (SHLE) were analyzed by LC–QTOF MS/MS, and 32 flavonoids were tentatively identified using MS/MS information. ANOVA applied to the data from fresh and dehydrated samples and from extraction by the different methods revealed that 26 and 32 flavonoids, respectively, were significant (p≤0.01). The pairwise comparison (Tukey HSD; p≤0.01) showed that lyophilized samples are more different from fresh samples than from air-dried samples; also, principal component analysis (PCA) showed a clear discrimination among sample pretreatment strategies and suggested that such differences are mainly created by the abundance of major flavonoids. On the other hand, pairwise comparison of extraction methods revealed that USAE and MAE provided quite similar extracts, being SHLE extracts different from the other two. In this case, PCA showed a clear discrimination among extraction methods, and their position in the scores plot suggests a lower abundance of flavonoids in the extracts from SHLE. In the two PCA the loadings plots revealed a trend to forming groups according to flavonoid aglycones. Conclusions The present study shows clear discrimination caused by both sample pretreatments and extraction methods. Under the studied conditions, liophilization provides extracts with higher amounts of flavonoids, and USAE is the best method for isolation of these compounds, followed by MAE and SE. On the contrary, the SHLE method was the less favorable to extract flavonoids from citrus owing to degradation. PMID:26807979

Are extracted materials truly representative of original samples? Impact of C18 extraction on CDOM optical and chemical properties

NASA Astrophysics Data System (ADS)

Andrew, Andrea; Del Vecchio, Rossana; Zhang, Yi; Subramaniam, Ajit; Blough, Neil

2016-02-01

Some properties of dissolved organic matter (DOM) and chromophoric dissolved organic matter (CDOM) can be easily measured directly on whole waters, while others require sample concentration and removal of natural salts. To increase CDOM content and eliminate salts, solid phase extraction is often employed. Biases following extraction and elution are inevitable, thus raising the question of how truly representative the extracted material is of the original. In this context, we investigated the wavelength dependence of extraction efficiency for C18 cartridges with respect to CDOM optical properties using samples obtained from the Middle Atlantic Bight (MAB) and the Equatorial Atlantic Ocean (EAO). Further, we compared the optical changes of C18 extracts and the corresponding whole water following chemical reduction with sodium borohydride (NaBH4). C18 cartridges preferentially extracted long-wavelength absorbing/emitting material for samples impacted by riverine input. Extraction efficiency overall decreased with offshore distance away from riverine input. Spectral slopes of C18-OM samples were also almost always lower than those of their corresponding CDOM samples supporting the preferential extraction of higher molecular weight absorbing material. The wavelength dependence of the optical properties (absorption, fluorescence emission and quantum yield) of the original water samples and their corresponding extracted material were very similar. C18 extracts and corresponding water samples further exhibited comparable optical changes following NaBH4 reduction, thus suggesting a similarity in nature (structure) of the optically active extracted material, independent of geographical locale. Altogether, these data suggested a strong similarity between C18 extracts and corresponding whole waters, thus indicating that extracts are representative of the CDOM content of original waters.

Are Extracted Materials Truly Representative of Original Samples? Impact of C18 Extraction on CDOM Optical and Chemical Properties

PubMed Central

Andrew, Andrea A.; Del Vecchio, Rossana; Zhang, Yi; Subramaniam, Ajit; Blough, Neil V.

2016-01-01

Some properties of dissolved organic matter (DOM) and chromophoric dissolved organic matter (CDOM) can be easily measured directly on whole waters, while others require sample concentration and removal of natural salts. To increase CDOM content and eliminate salts, solid phase extraction (SPE) is often employed. Biases following extraction and elution are inevitable, thus raising the question of how truly representative the extracted material is of the original. In this context, we investigated the wavelength dependence of extraction efficiency for C18 cartridges with respect to CDOM optical properties using samples obtained from the Middle Atlantic Bight (MAB) and the Equatorial Atlantic Ocean (EAO). Further, we compared the optical changes of C18 extracts and the corresponding whole water following chemical reduction with sodium borohydride (NaBH4). C18 cartridges preferentially extracted long-wavelength absorbing/emitting material for samples impacted by riverine input. Extraction efficiency overall decreased with offshore distance away from riverine input. Spectral slopes of C18-OM samples were also almost always lower than those of their corresponding CDOM samples supporting the preferential extraction of higher molecular weight absorbing material. The wavelength dependence of the optical properties (absorption, fluorescence emission, and quantum yield) of the original water samples and their corresponding extracted material were very similar. C18 extracts and corresponding water samples further exhibited comparable optical changes following NaBH4 reduction, thus suggesting a similarity in nature (structure) of the optically active extracted material, independent of geographical locale. Altogether, these data suggested a strong similarity between C18 extracts and corresponding whole waters, thus indicating that extracts are representative of the CDOM content of original waters. PMID:26904536

Are Extracted Materials Truly Representative of Original Samples? Impact of C18 Extraction on CDOM Optical and Chemical Properties.

PubMed

Andrew, Andrea A; Del Vecchio, Rossana; Zhang, Yi; Subramaniam, Ajit; Blough, Neil V

2016-01-01

Some properties of dissolved organic matter (DOM) and chromophoric dissolved organic matter (CDOM) can be easily measured directly on whole waters, while others require sample concentration and removal of natural salts. To increase CDOM content and eliminate salts, solid phase extraction (SPE) is often employed. Biases following extraction and elution are inevitable, thus raising the question of how truly representative the extracted material is of the original. In this context, we investigated the wavelength dependence of extraction efficiency for C18 cartridges with respect to CDOM optical properties using samples obtained from the Middle Atlantic Bight (MAB) and the Equatorial Atlantic Ocean (EAO). Further, we compared the optical changes of C18 extracts and the corresponding whole water following chemical reduction with sodium borohydride (NaBH4). C18 cartridges preferentially extracted long-wavelength absorbing/emitting material for samples impacted by riverine input. Extraction efficiency overall decreased with offshore distance away from riverine input. Spectral slopes of C18-OM samples were also almost always lower than those of their corresponding CDOM samples supporting the preferential extraction of higher molecular weight absorbing material. The wavelength dependence of the optical properties (absorption, fluorescence emission, and quantum yield) of the original water samples and their corresponding extracted material were very similar. C18 extracts and corresponding water samples further exhibited comparable optical changes following NaBH4 reduction, thus suggesting a similarity in nature (structure) of the optically active extracted material, independent of geographical locale. Altogether, these data suggested a strong similarity between C18 extracts and corresponding whole waters, thus indicating that extracts are representative of the CDOM content of original waters.

Impact of textile dyeing industries effluent on groundwater quality in Karur Amaravathi River basin, Tamil Nadu (India)--a field study.

PubMed

Rajamanickam, R; Nagan, S

2010-10-01

Karur is an industrial town located on the bank of river Amaravathi. There are 487 textile processing units in operation and discharge about 14610 kilo litres per day of treated effluent into the river. The groundwater quality in the downstream is deteriorated due to continuous discharge of effluent. In order to assess the present quality of groundwater, 13 open wells were identified in the river basin around Karur and samples were collected during pre-monsoon, post monsoon and summer, and analyzed for physico-chemical parameters. TDS, total alkalinity, total hardness, calcium, chlorides and sulphates exceeded the desirable limit. Amaravathi River water samples were also colleted at the upstream and downstream of Karur and the result shows the river is polluted. During summer season, there is no flow in the river and the river acts as a drainage for the effluent. Hence, there is severe impact on the groundwater quality in the downstream. The best option to protect the groundwater quality in the river basin is that the textile processing units should adopt zero liquid discharge (ZLD) system and completely recycle the treated effluent.

Speciation of trihalomethane mixtures for the Mississippi, Missouri, and Ohio Rivers

USGS Publications Warehouse

Rathbun, R.E.

1996-01-01

Trihalomethane formation potentials were determined for the chlorination of water samples from the Mississippi, Missouri, and Ohio Rivers. Samples were collected during the summer and fall of 1991 and the spring of 1992 at 12 locations on the Mississippi from New Orleans, LA, to Minneapolis, MN, and on the Missouri and Ohio 1.6 km upstream from their confluences with the Mississippi. Formation potentials were determined as a function of pH and initial free-chlorine concentration. Chloroform concentrations decreased with distance downstream and approximately paralleled the decrease of the dissolved organic-carbon concentration. Bromide concentrations were 3.7-5.7 times higher for the Missouri and 1.4-1.6 times higher for the Ohio than for the Mississippi above their confluences, resulting in an overall increase of the bromide concentration with distance downstream. Variations of the concentrations of the brominated trihalomethanes with distance downstream approximately paralleled the variation of the bromide concentration. Concentrations of all four trihalomethanes increased as the pH increased. Concentrations of chloroform and bromodichloromethane increased slightly and the concentration of bromoform decreased as the initial free-chlorine concentration increased; the chlorodibromomethane concentration had little dependence on the free-chlorine concentration.

Fish embryo tests with Danio rerio as a tool to evaluate surface water and sediment quality in rivers influenced by wastewater treatment plants using different treatment technologies.

PubMed

Thellmann, Paul; Köhler, Heinz-R; Rößler, Annette; Scheurer, Marco; Schwarz, Simon; Vogel, Hans-Joachim; Triebskorn, Rita

2015-11-01

In order to evaluate surface water and the sediment quality of rivers connected to wastewater treatment plants (WWTPs) with different treatment technologies, fish embryo tests (FET) with Danio rerio were conducted using native water and sediment samples collected upstream and downstream of four WWTPs in Southern Germany. Two of these WWTPs are connected to the Schussen River, a tributary of Lake Constance, and use a sand filter with final water purification by flocculation. The two others are located on the rivers Schmiecha and Eyach in the area of the Swabian Alb and were equipped with a powdered activated carbon stage 20 years ago, which was originally aimed at reducing the release of stains from the textile industry. Several endpoints of embryo toxicity including mortality, malformations, reduced hatching rate, and heart rate were investigated at defined time points of embryonic development. Higher embryotoxic potentials were found in water and sediments collected downstream of the WWTPs equipped with sand filtration than in the sample obtained downstream of both WWTPs upgraded with a powdered activated carbon stage.

Protective pathways against colitis mediated by appendicitis and appendectomy.

PubMed

Cheluvappa, R; Luo, A S; Palmer, C; Grimm, M C

2011-09-01

Appendicitis followed by appendectomy (AA) at a young age protects against inflammatory bowel disease (IBD). Using a novel murine appendicitis model, we showed that AA protected against subsequent experimental colitis. To delineate genes/pathways involved in this protection, AA was performed and samples harvested from the most distal colon. RNA was extracted from four individual colonic samples per group (AA group and double-laparotomy control group) and each sample microarray analysed followed by gene-set enrichment analysis (GSEA). The gene-expression study was validated by quantitative reverse transcription-polymerase chain reaction (RT-PCR) of 14 selected genes across the immunological spectrum. Distal colonic expression of 266 gene-sets was up-regulated significantly in AA group samples (false discovery rates < 1%; P-value < 0·001). Time-course RT-PCR experiments involving the 14 genes displayed down-regulation over 28 days. The IBD-associated genes tnfsf10, SLC22A5, C3, ccr5, irgm, ptger4 and ccl20 were modulated in AA mice 3 days after surgery. Many key immunological and cellular function-associated gene-sets involved in the protective effect of AA in experimental colitis were identified. The down-regulation of 14 selected genes over 28 days after surgery indicates activation, repression or de-repression of these genes leading to downstream AA-conferred anti-colitis protection. Further analysis of these genes, profiles and biological pathways may assist in developing better therapeutic strategies in the management of intractable IBD. © 2011 The Authors. Clinical and Experimental Immunology © 2011 British Society for Immunology.

Sources and Transformations of Carbon and Nitrogen in the Potomac River Estuary

NASA Astrophysics Data System (ADS)

Pennino, M. J.; Kaushal, S.; Murthy, S.

2011-12-01

Urbanization has altered the transport of nitrogen (N) and carbon (C) in river ecosystems, making it important to understand how rivers are responding to these increased inputs of C and N. This study examines the capacity of a major tributary of the Chesapeake Bay, the Potomac River, to transform N and C inputs from the world's largest advanced wastewater treatment facility (Washington D.C. Water and Sewer Authority). Surface water and effluent samples were collected monthly for one year, along longitudinal transects of the Potomac River. Water samples were analyzed for the major dissolved and particulate forms of C and N. Nitrate stable isotopes were used to trace the fate of wastewater nitrate, as well as how other nitrate sources vary downriver. Sources of carbon downriver were traced using fluorescence spectroscopy, excitation emission matrices (EEMs), and PARAFAC modeling. Historical influent and effluent data on C and N levels were also compared with regional population growth data, climate change data, and long-term interannual records of C and N levels within downstream stations along the Potomac River. Improvements in treatment technology over the past two decades have shown significant decreases in effluent nitrogen levels, with corresponding decreases overtime of nutrients at downstream sampling stations. Levels of nitrate show increases within the vicinity of the wastewater treatment outfall, but decrease rapidly downstream, potentially indicating nutrient uptake and/or denitrification. Total organic carbon levels show a smaller decrease downstream, resulting in an increase in the C:N ratio downstream. Longitudinal river chemistry data also show that dissolved inorganic nitrogen goes down while total organic nitrogen goes up with distance downriver, indicating biological transformations are taking place along the river. Preliminary data from fluorescence EEMs suggested that more humic-like organic matter is important above the wastewater treatment plant, but more protein-like organic matter is present below the treatment plant. However, this fluorescence signal from wastewater organic matter disappears within 2-4 km downriver, indicating rapid processing of the labile organic matter within the river. Nitrate isotope data for both upriver and downriver samples show a signal from manure or sewage inputs, indicating a potential influence from animal farms upstream in the Potomac. However, only the downriver samples show evidence for denitrification. Additionally, the higher 15N isotope levels of nitrate, which are characteristic of wastewater sources, disappear by 20 km downriver. Majors rivers like the Potomac may have a huge capacity for transforming and processing large carbon and nitrogen inputs within a short distance. Greater knowledge of how land management and climate change impacts these transformations will be important in predicting changes in the amounts, forms, and stoichiometry of nutrient loads to coastal waters.

Estimating the impact of seawater on the production of soil water-extractable organic carbon during coastal erosion.

PubMed

Dou, Fugen; Ping, Chien-Lu; Guo, Laodong; Jorgenson, Torre

2008-01-01

The production of water-extractable organic carbon (WEOC) during arctic coastal erosion and permafrost degradation may contribute significantly to C fluxes under warming conditions, but it remains difficult to quantify. A tundra soil collected near Barrow, AK, was selected to evaluate the effects of soil pretreatments (oven drying vs. freeze drying) as well as extraction solutions (pure water vs. seawater) on WEOC yields. Both oven drying and freeze drying significantly increased WEOC release compared with the original moist soil samples; dried samples released, on average, 18% more WEOC than did original moist samples. Similar results were observed for the production of low-molecular-weight dissolved organic C. However, extractable OC released from different soil horizons exhibited differences in specific UV absorption, suggesting differences in WEOC quality. Furthermore, extractable OC yields were significantly less in samples extracted with seawater compared with those extracted with pure water, likely due to the effects of major ions on extractable OC flocculation. Compared with samples from the active horizons, upper permafrost samples released more WEOC, suggesting that continuously frozen samples were more sensitive than samples that had experienced more drying-wetting cycles in nature. Specific UV absorption of seawater-extracted OC was significantly lower than that of OC extracted using pure water, suggesting more aromatic or humic substances were flocculated during seawater extraction. Our results suggest that overestimation of total terrestrial WEOC input to the Arctic Ocean during coastal erosion could occur if estimations were based on WEOC extracted from dried soil samples using pure water.

A two-dimensional contaminant fate and transport model for the lower Athabasca River

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brownlee, B.G.; Booty, W.G.; MacInnis, G.A.

1995-12-31

The lower Athabasca River flows through the Athabasca Oil Sands deposits in northeastern Alberta. Two oil sands mining/extraction/upgrading plants operate near the river downstream from Fort McMurray. Process water is stored in large tailings ponds. One of the plants (Suncor) has a licensed discharge (mostly cooling water) to the river. This effluent contains low concentrations ({<=} 1 {micro}g/L) of various polycyclic aromatic compounds (PACs). Several tributary streams which cut through oil sands deposits are potential sources of hydrocarbons to the Athabasca. The authors have found that river suspended sediments give positive responses in a number of toxicity tests, using bothmore » direct and indirect (organic-solvent extract) methods. Several environmental impact assessments are required as a result of industry expansion. To provide an assessment tool for PACs, the authors are developing a two-dimensional contaminant fate and transport model for a 120-km portion of the Athabasca River downstream from Fort McMurray. Hydraulic calibration of the model was done using sodium and chloride from a major tributary as tracers. Two groups of compounds are being modelled: (1) PACs from the Suncor effluent, and (2) PACs from natural/background sources. PAC concentrations in the river were typically < 1 ng/L, requiring large volume extractions and highly sensitive analysis. Processes such as sediment-water partitioning and biodegradation are being estimated from field experiments using river water and suspended sediment. Photodegradation is likely unimportant in this turbid river due to low penetration of 280--350 nm light. Initially, volatilization will be modelled using estimated or literature values for Henry`s constants, but may require more refined estimates from laboratory experiments.« less

Evaluation of non-extracted genital swabs for real-time HSV PCR.

PubMed

Miari, Victoria F; Wall, Gavin R; Clark, Duncan A

2015-01-01

Nucleic acid extraction of clinical samples is accepted as a key requirement in molecular diagnostics. At Barts Health NHS Trust, swabs taken from patients with clinical suspicion of HSV infection were routinely extracted on the Qiagen MDx BioRobot prior to testing with a real-time triplex PCR for HSV1, HSV2, and VZV. The aim of this study was to adapt an existing HSV1/HSV2/VZV real-time PCR by replacing VZV with phocine herpesvirus 1 (PhHV) as an internal control (IC) and evaluate whether this adapted assay required the nucleic acid extraction step for predominantly genital swabs. First 313 non-extracted and extracted swabs were tested in parallel with the existing triplex HSV1/HSV2/VZV real-time PCR. The second stage involved testing 176 non-extracted swabs using a triplex real-time PCR for HSV1, HSV2, and PhHV and comparing the results with the samples extracted and tested by the original triplex assay. The results correlated well when the existing assay was used, with only three non-extracted samples that would have been reported as negative compared to the extracted sample result (Cq s 33, 39, 35-two samples HSV1, one sample HSV2). In the evaluation using the adapted assay containing the IC, two of 176 samples were discordant, where a HSV negative non-extracted sample result would have been reported differently to the extracted sample result (Cq s 32, 33-both HSV1). This study demonstrated that it is feasible to test non-extracted swabs for HSV in a real-time PCR that includes an IC. J. Med. Virol. 87: 125-129, 2015. © 2014 Wiley Periodicals, Inc. © 2014 Wiley Periodicals, Inc.

Influence of peak flow changes on the macroinvertebrate drift downstream of a Brazilian hydroelectric dam.

PubMed

Castro, D M P; Hughes, R M; Callisto, M

2013-11-01

Successive daily peak flows from hydropower plants can disrupt aquatic ecosystems and alter the composition and structure of macroinvertebrates downstream. We evaluated the influence of peak flow changes on macroinvertebrate drift downstream of a hydroelectric plant as a basis for determining ecological flows that might reduce the disturbance of aquatic biota. The aim of this study was to assess the influence of flow fluctuations on the seasonal and daily drift patterns of macroinvertebrates. We collected macroinvertebrates during fixed flow rates (323 m3.s-1 in the wet season and 111 m3.s-1 in the dry season) and when peak flows fluctuated (378 to 481 m3.s-1 in the wet season, and 109 to 173 m3.s-1 in the dry season) in 2010. We collected 31,924 organisms belonging to 46 taxa in the four sampling periods. Taxonomic composition and densities of drifting invertebrates differed between fixed and fluctuating flows, in both wet and dry seasons, but family richness varied insignificantly. We conclude that macroinvertebrate assemblages downstream of dams are influenced by daily peak flow fluctuations. When making environmental flow decisions for dams, it would be wise to consider drifting macroinvertebrates because they reflect ecological changes in downstream biological assemblages.

Time resolved flow-field measurements of a turbulent mixing layer over a rectangular cavity

NASA Astrophysics Data System (ADS)

Bian, Shiyao; Driscoll, James F.; Elbing, Brian R.; Ceccio, Steven L.

2011-07-01

High Reynolds number, low Mach number, turbulent shear flow past a rectangular, shallow cavity has been experimentally investigated with the use of dual-camera cinematographic particle image velocimetry (CPIV). The CPIV had a 3 kHz sampling rate, which was sufficient to monitor the time evolution of large-scale vortices as they formed, evolved downstream and impinged on the downstream cavity wall. The time-averaged flow properties (velocity and vorticity fields, streamwise velocity profiles and momentum and vorticity thickness) were in agreement with previous cavity flow studies under similar operating conditions. The time-resolved results show that the separated shear layer quickly rolled-up and formed eddies immediately downstream of the separation point. The vortices convect downstream at approximately half the free-stream speed. Vorticity strength intermittency as the structures approach the downstream edge suggests an increase in the three-dimensionality of the flow. Time-resolved correlations reveal that the in-plane coherence of the vortices decays within 2-3 structure diameters, and quasi-periodic flow features are present with a vortex passage frequency of ~1 kHz. The power spectra of the vertical velocity fluctuations within the shear layer revealed a peak at a non-dimensional frequency corresponding to that predicted using linear, inviscid instability theory.

Carotenoids from microalgae: A review of recent developments.

PubMed

Gong, Mengyue; Bassi, Amarjeet

2016-12-01

Carotenoids have been receiving increasing attention due to their potential health benefits. Microalgae are recognized as a natural source of carotenoids and other beneficial byproducts. However, the production of micro-algal carotenoids is not yet sufficiently cost-effective to compete with traditional chemical synthetic methods and other technologies such as extraction from plant based sources. This review presents the recent biotechnological developments in microalgal carotenoid production. The current technologies involved in their bioprocessing including cultivation, harvesting, extraction, and purification are discussed with a specific focus on downstream processing. The recent advances in chemical and biochemical synthesis of carotenoids are also reviewed for a better understanding of suitable and economically feasible biotechnological strategies. Some possible future directions are also proposed. Copyright © 2016 Elsevier Inc. All rights reserved.

Shifts in microbial community structure and function in surface waters impacted by unconventional oil and gas wastewater revealed by metagenomics

USGS Publications Warehouse

Fahrenfeld, N.L.; Reyes, Hannah Delos; Eramo, Alessia; Akob, Denise M.; Mumford, Adam; Cozzarelli, Isabelle M.

2017-01-01

Unconventional oil and gas (UOG) production produces large quantities of wastewater with complex geochemistry and largely uncharacterized impacts on surface waters. In this study, we assessed shifts in microbial community structure and function in sediments and waters upstream and downstream from a UOG wastewater disposal facility. To do this, quantitative PCR for 16S rRNA and antibiotic resistance genes along with metagenomic sequencing were performed. Elevated conductivity and markers of UOG wastewater characterized sites sampled downstream from the disposal facility compared to background sites. Shifts in overall high level functions and microbial community structure were observed between background sites and downstream sediments. Increases in Deltaproteobacteria and Methanomicrobia and decreases in Thaumarchaeota were observed at downstream sites. Genes related to dormancy and sporulation and methanogenic respiration were 18–86 times higher at downstream, impacted sites. The potential for these sediments to serve as reservoirs of antimicrobial resistance was investigated given frequent reports of the use of biocides to control the growth of nuisance bacteria in UOG operations. A shift in resistance profiles downstream of the UOG facility was observed including increases in acrB and mexB genes encoding for multidrug efflux pumps, but not overall abundance of resistance genes. The observed shifts in microbial community structure and potential function indicate changes in respiration, nutrient cycling, and markers of stress in a stream impacted by UOG waste disposal operations.

Geologic and tributary influences on the chemistry of a headwater stream

Treesearch

Alexander C. Wooten; James Preer; Pamela J. Edwards

1999-01-01

Water samples were collected weekly from June 12 to August 14, 1995, from Big Spring Run (BSR) in West Virginia. BSR originates in Big Spring Cave, where three stream samples were collected. In addition, 18 BSR sites were sampled downstream from the cave, three from its tributaries, and one above and below the stream?s confluence with Elklick Run. Along its length (653...

AN EVALUATION OF SAMPLE DISPERSION MEDIAS USED WITH ACCELERATED SOLVENT EXTRACTION FOR THE EXTRACTION AND RECOVERY OF ARSENICALS FROM LFB AND DORM-2

EPA Science Inventory

An accelerated solvent extraction (ASE) device was evaluated as a semi-automated means for extracting arsenicals from quality control (QC) samples and DORM-2 [standard reference material (SRM)]. Unlike conventional extraction procedures, the ASE requires that the sample be dispe...

Microwave-assisted extraction and mild saponification for determination of organochlorine pesticides in oyster samples.

PubMed

Carro, N; García, I; Ignacio, M-C; Llompart, M; Yebra, M-C; Mouteira, A

2002-10-01

A sample-preparation procedure (extraction and saponification) using microwave energy is proposed for determination of organochlorine pesticides in oyster samples. A Plackett-Burman factorial design has been used to optimize the microwave-assisted extraction and mild saponification on a freeze dried sample spiked with a mixture of aldrin, endrin, dieldrin, heptachlor, heptachorepoxide, isodrin, transnonachlor, p, p'-DDE, and p, p'-DDD. Six variables: solvent volume, extraction time, extraction temperature, amount of acetone (%) in the extractant solvent, amount of sample, and volume of NaOH solution were considered in the optimization process. The results show that the amount of sample is statistically significant for dieldrin, aldrin, p, p'-DDE, heptachlor, and transnonachlor and solvent volume for dieldrin, aldrin, and p, p'-DDE. The volume of NaOH solution is statistically significant for aldrin and p, p'-DDE only. Extraction temperature and extraction time seem to be the main factors determining the efficiency of extraction process for isodrin and p, p'-DDE, respectively. The optimized procedure was compared with conventional Soxhlet extraction.

Transport and Sources of Suspended Sediment in the Mill Creek Watershed, Johnson County, Northeast Kansas, 2006-07

USGS Publications Warehouse

Lee, Casey J.; Rasmussen, Patrick P.; Ziegler, Andrew C.; Fuller, Christopher C.

2009-01-01

The U.S. Geological Survey, in cooperation with the Johnson County Stormwater Management Program, evaluated suspended-sediment transport and sources in the urbanizing, 57.4 mi2 Mill Creek watershed from February 2006 through June 2007. Sediment transport and sources were assessed spatially by continuous monitoring of streamflow and turbidity as well as sampling of suspended sediment at nine sites in the watershed. Within Mill Creek subwatersheds (2.8-16.9 mi2), sediment loads at sites downstream from increased construction activity were substantially larger (per unit area) than those at sites downstream from mature urban areas or less-developed watersheds. Sediment transport downstream from construction sites primarily was limited by transport capacity (streamflow), whereas availability of sediment supplies primarily influenced transport downstream from mature urban areas. Downstream sampling sites typically had smaller sediment loads (per unit area) than headwater sites, likely because of sediment deposition in larger, less sloping stream channels. Among similarly sized storms, those with increased precipitation intensity transported more sediment at eight of the nine monitoring sites. Storms following periods of increased sediment loading transported less sediment at two of the nine monitoring sites. In addition to monitoring performed in the Mill Creek watershed, sediment loads were computed for the four other largest watersheds (48.6-65.7 mi2) in Johnson County (Blue River, Cedar, Indian, and Kill Creeks) during the study period. In contrast with results from smaller watersheds in Mill Creek, sediment load (per unit area) from the most urbanized watershed in Johnson County (Indian Creek) was more than double that of other large watersheds. Potential sources of this sediment include legacy sediment from earlier urban construction, accelerated stream-channel erosion, or erosion from specific construction sites, such as stream-channel disturbance during bridge renovation. The implication of this finding is that sediment yields from larger watersheds may remain elevated after the majority of urban development is complete. Surface soil, channel-bank, suspended-sediment, and streambed-sediment samples were analyzed for grain size, nutrients, trace elements, and radionuclides in the Mill Creek watershed to characterize suspended sediment between surface or channel-bank sources. Although concentrations and activities of cobalt, nitrogen, selenium, total organic carbon, cesium-137, and excess lead-210 had significant differences between surface and channel-bank samples, biases resulting from urban construction, additional sorption of constituents during sediment transport, and inability to accurately represent erosion from rills and gullies precluded accurate characterization of suspended-sediment source.

An Investigation into Heavy Metal Contamination and Mobilization in the Lower Rouge River, Michigan

NASA Astrophysics Data System (ADS)

Shihadeh, M.; Forrester, J.; Napieralski, J. A.

2010-12-01

Similar to many densely populated watersheds in the Great Lakes Basin, the Rouge River in Michigan drains a heavily urbanized watershed, which, over time, has accumulated a substantial amount of contamination due to decades of manufacturing and refining industries. Statistically significant levels of heavy metals have been found in the bed sediment of the Rouge; however, little is known about the mobilization of these contaminated bed sediments. The goal of this study was to ascertain the extent to which these potentially contaminated sediments are mobilized and transported downstream. Suspended sediment samples were collected at four sites along the lower Rouge River using composite depth integrated sediment samples three times per week, resulting in a total of twenty samples from each site. Turbidity was measured simultaneously using a YSI datalogger at all sampling locations. Sediment was also extracted from floodplain soil pits and silted vegetation, as well as river bed sediment cores along stream channel cross-sections. Heavy metal concentrations (As, Cd, Cr, Cu, Fe, Pb, Hg, Ni, Se, Zn) were analyzed using ICP-MS and compared against both background characteristics for Michigan soils and EPA Hazardous Criteria Limits. As expected, a positive correlation exists between turbidity and heavy metal concentrations. Even in the sampling sites furthest upstream, heavy metal concentrations exceeded background soil characteristics, with a few also exceeding hazardous criteria limits. The heavy metal concentrations found in the Lower Rouge affirm the elevated pollution classification of the river, depict the overall influence of industrialization on stream health, and verify that contaminated sediments are being deposited in aquatic and floodplain environments during variable flow or high discharge events. Results from this study emphasize the need to remediate bed sediments in the Rouge and suggest that there may be significant bioaccumulation potential for organisms inhabiting the floodplain corridor.

Online combination of reversed-phase/reversed-phase and porous graphitic carbon liquid chromatography for multicomponent separation of proteomics and glycoproteomics samples.

PubMed

Lam, Maggie P Y; Lau, Edward; Siu, S O; Ng, Dominic C M; Kong, Ricky P W; Chiu, Philip C N; Yeung, William S B; Lo, Clive; Chu, Ivan K

2011-11-01

In this paper, we describe an online combination of reversed-phase/reversed-phase (RP-RP) and porous graphitic carbon (PGC) liquid chromatography (LC) for multicomponent analysis of proteomics and glycoproteomics samples. The online RP-RP portion of this system provides comprehensive 2-D peptide separation based on sequence hydrophobicity at pH 2 and 10. Hydrophilic components (e.g. glycans, glycopeptides) that are not retained by RP are automatically diverted downstream to a PGC column for further trapping and separation. Furthermore, the RP-RP/PGC system can provide simultaneous extension of the hydropathy range and peak capacity for analysis. Using an 11-protein mixture, we found that the system could efficiently separate native peptides and released N-glycans from a single sample. We evaluated the applicability of the system to the analysis of complex biological samples using 25 μg of the lysate of a human choriocarcinoma cell line (BeWo), confidently identifying a total of 1449 proteins from a single experiment and up to 1909 distinct proteins from technical triplicates. The PGC fraction increased the sequence coverage through the inclusion of additional hydrophilic sequences that accounted for up to 6.9% of the total identified peptides from the BeWo lysate, with apparent preference for the detection of hydrophilic motifs and proteins. In addition, RP-RP/PGC is applicable to the analysis of complex glycomics samples, as demonstrated by our analysis of a concanavalin A-extracted glycoproteome from human serum; in total, 134 potentially N-glycosylated serum proteins, 151 possible N-glycosylation sites, and more than 40 possible N-glycan structures recognized by concanavalin A were simultaneously detected. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis of SiO2-Coated Fe3O4 Nanoparticles Using Ultrasound and Its Application in DNA Extraction from Formalin-Fixed, Paraffin-Embedded Human Cancer Tissues

NASA Astrophysics Data System (ADS)

Hieu, Nguyen Minh; Nam, Nguyen Hoang; Huyen, Nguyen Thi; Van Anh, Nguyen Thi; Nghia, Phan Tuan; Khoa, Nguyen Ba; Toan, Nguyen Linh; Luong, Nguyen Hoang

2017-06-01

SiO2-coated Fe3O4 nanoparticles (Fe3O4@SiO2 NPs) were successfully synthesized using ultrasound in order to extract DNA from cancer tissues for application in diagnostics. The core 10.7-nm-diameter Fe3O4 nanoparticles were synthesized by co-precipitation of Fe3+ and Fe2+ as reaction substrates and NH4OH as precipitant, then coated with a thin layer of amorphous silica by a modified Stober method. Further SiO2 coating using alkaline hydrolysis of tetraethyl orthosilicate in ethanol and water mixture was accelerated in the presence of a 37-kHz ultrasound, resulting in the NPs having different sizes of 14.5 nm (version M1), 24.4 nm (version M2), and 34.9 nm (version M3) with saturation magnetization values of 50.2 emu/g, 18.6 emu/g, 10.3 emu/g, respectively. Among the three Fe3O4@SiO2 NPs versions, the M1 NPs allowed extraction of DNAs from 10 mg formalin-fixed and paraffin-embedded (FFPE) tissues of nasopharyngeal carcinoma patients with the highest recovery of about 100-500 ng/ μl and good purity (A260/A280: 1.8-1.9). The extracted DNAs could be used as templates for downstream amplification of 252-bp sequencing specifically for the Braf cancer biomarker gene using polymerase chain reaction (PCR), as well as detection of the pathogenic Epstein-Barr virus (EBV) and the human papilloma-virus (HPV) using real-time PCR. DNA extraction recoveries of both EBV and HPV using Fe3O4@SiO2 NPs M1 were significantly better that those using commercialized Fe3O4@SiO2 microbeads, as indicated by lower threshold cycles of all fluorescent signals including fluorescein amidite (FAM) dye representative for EBV infection, hexachlorofluorescein (HEX) dye representative for β-globin (internal control), and SYBR Green dye representative for HPV infection in tested clinical samples from patients with nasopharyngeal carcinoma (NPC).

Effects of historical lead–zinc mining on riffle-dwelling benthic fish and crayfish in the Big River of southeastern Missouri, USA

USGS Publications Warehouse

Allert, A.L.; DiStefano, R.J.; Fairchild, J.F.; Schmitt, C.J.; McKee, M.J.; Girondo, J.A.; Brumbaugh, W.G.; May, T.W.

2013-01-01

The Big River (BGR) drains much of the Old Lead Belt mining district (OLB) in southeastern Missouri, USA, which was historically among the largest producers of lead–zinc (Pb–Zn) ore in the world. We sampled benthic fish and crayfish in riffle habitats at eight sites in the BGR and conducted 56-day in situ exposures to the woodland crayfish (Orconectes hylas) and golden crayfish (Orconectes luteus) in cages at four sites affected to differing degrees by mining. Densities of fish and crayfish, physical habitat and water quality, and the survival and growth of caged crayfish were examined at sites with no known upstream mining activities (i.e., reference sites) and at sites downstream of mining areas (i.e., mining and downstream sites). Lead, zinc, and cadmium were analyzed in surface and pore water, sediment, detritus, fish, crayfish, and other benthic macro-invertebrates. Metals concentrations in all materials analyzed were greater at mining and downstream sites than at reference sites. Ten species of fish and four species of crayfish were collected. Fish and crayfish densities were significantly greater at reference than mining or downstream sites, and densities were greater at downstream than mining sites. Survival of caged crayfish was significantly lower at mining sites than reference sites; downstream sites were not tested. Chronic toxic-unit scores and sediment probable effects quotients indicated significant risk of toxicity to fish and crayfish, and metals concentrations in crayfish were sufficiently high to represent a risk to wildlife at mining and downstream sites. Collectively, the results provided direct evidence that metals associated with historical mining activities in the OLB continue to affect aquatic life in the BGR.

Sample preparation for the analysis of isoflavones from soybeans and soy foods.

PubMed

Rostagno, M A; Villares, A; Guillamón, E; García-Lafuente, A; Martínez, J A

2009-01-02

This manuscript provides a review of the actual state and the most recent advances as well as current trends and future prospects in sample preparation and analysis for the quantification of isoflavones from soybeans and soy foods. Individual steps of the procedures used in sample preparation, including sample conservation, extraction techniques and methods, and post-extraction treatment procedures are discussed. The most commonly used methods for extraction of isoflavones with both conventional and "modern" techniques are examined in detail. These modern techniques include ultrasound-assisted extraction, pressurized liquid extraction, supercritical fluid extraction and microwave-assisted extraction. Other aspects such as stability during extraction and analysis by high performance liquid chromatography are also covered.

Sand transport in the lower Mississippi River does not yield to dams: Applications for building deltaic land in Louisiana

NASA Astrophysics Data System (ADS)

Nittrouer, J. A.; Viparelli, E.

2013-12-01

The Mississippi Delta is presently undergoing a catastrophic drowning, whereby 5000 km2 of low-lying wetlands have converted to open water. This land loss is primarily the result of: a) relative sea-level rise, occurring due to the combined effect of rapid subsidence associated with subsurface fluids extraction and eustatic rise; b) leveeing and damming of the river and its tributaries, which restricts sediment delivery to and dispersal within the delta; and c) severe excavation of the delta for navigation channels. It has been argued that continued net land loss of the Mississippi Delta is inevitable due to declining measured total (sand and mud) suspended sediment loads over the past 6 decades. However, recent research has documented that the key to delta growth is deposition of sand, which accounts for ~50-70% of modern and ancient (up to 9 m.a.) Mississippi Delta deposits, but comprises only ~20% of the sampled portion of the total load. Here we present new analysis of existing data to show that sand transport has not diminished since dam construction. Furthermore, we produce a numerical model based on the mass balance of bed material loads over the lower 1600 km of the Mississippi River to show that mining of sand from the channel bed continues to replenish downstream sand loads. For example, our model results indicate that it requires approximately 240 years for a reduced sand load to reach the delta apex. Furthermore, our calculations indicate that sand load at the delta apex is reduced by a noticeable amount (17%) only after about 600 years. We also show how channel bed elevations are predicted to change over the lower 1600 km of the river channel due to channel mining. Channel-bed degradation is greatest at the upstream end of the study reach and decreases downstream. After 300 years the wave of significant degradation has just passed ~800 km downstream, or roughly half of our model domain. These results are in contrast to the measurements which concern the reduction of total suspended sediment load, and here we provide a reasonable hypothesis to help explain: sand possesses a much slower time scale of movement through a sand-bed river compared to mud, because sand exchanges with the bed, building dunes and bars that migrate gradually downstream, whereas the mud travels the length of the system in suspension as washload. This produces orders-of-magnitude difference in transport timescales between mud -- which accounts for ~80% of the total suspended sediment load of the Mississippi River -- and sand (bedload and suspended load). Combined with the abundance and availability of sand to be mined within the main channel, the river effectively buffers the reduction of sand load arising due to main-channel dams. Thus the bed of the lower Mississippi River downstream will provide a stable supply of sand to the delta for the foreseeable future.

Identification of organically associated trace elements in wood and coal by inductively coupled plasma mass spectrometry.

PubMed

Richaud, R; Lazaro, M J; Lachas, H; Miller, B B; Herod, A A; Dugwell, D R; Kandiyoti, R

2000-01-01

1-Methyl-2-pyrrolidinone (NMP) was used to extract samples of wood (forest residue) and coal; the extracts were analysed by inductively coupled plasma mass spectrometry (ICP-MS) using two different sample preparation methods, in order to identify trace elements associated with the organic part of the samples. A sample of fly ash was similarly extracted and analysed in order to assess the behaviour of the mineral matter contained within the wood and coal samples. 32% of the biomass was extracted at the higher temperature and 12% at room temperature while only 12% of the coal was extracted at the higher temperature and 3% at room temperature. Less than 2% of the ash dissolved at the higher temperature. Size exclusion chromatograms of the extracts indicated the presence of significant amounts of large molecular mass materials (>1000 mu) in the biomass and coal extracts but not in the ash extract. Trace element analyses were carried out using ICP-MS on the acid digests prepared by 'wet ashing' and microwave extraction. Sixteen elements (As, Ba, Be, Cd, Co, Cr, Cu, Ga, Mn, Mo, Ni, Pb, Sb, Se, V and Zn) were quantified, in the samples before extraction, in the extracts and in the residues. Concentrations of trace elements in the original biomass sample were lower than in the coal sample while the concentrations in the ash sample were the highest. The major trace elements in the NMP extracts were Ba, Cu, Mn and Zn from the forest residue; Ba, Cu, Mn, Pb and Zn from the coal; Cu and Zn from the ash. These elements are believed to be associated with the organic extracts from the forest residue and coal, and also from the ash. Be and Sb were not quantified in the extracts because they were present at too low concentrations; up to 40% of Mn was extracted from the biomass sample at 202 degrees C, while Se was totally extracted from the ash sample. For the forest residue, approximately 7% (at room temperature) and 45% (at 202 degrees C) of the total trace elements studied were in the extract; for the coal, approximately 8% (at room temperature) and 23% (at 202 degrees C) were in the extract. For the ash, only 1.4% of the trace elements were extracted at 202 degrees C, comprising 25% of Cd but less than 1% of Pb. Copyright 2000 John Wiley & Sons, Ltd.

Klamath River Water Quality Data from Link River Dam to Keno Dam, Oregon, 2008

USGS Publications Warehouse

Sullivan, Annett B.; Deas, Michael L.; Asbill, Jessica; Kirshtein, Julie D.; Butler, Kenna D.; Vaughn, Jennifer

2009-01-01

This report documents sampling and analytical methods and presents field data from a second year of an ongoing study on the Klamath River from Link River Dam to Keno Dam in south central Oregon; this dataset will form the basis of a hydrodynamic and water quality model. Water quality was sampled weekly at six mainstem and two tributary sites from early April through early November, 2008. Constituents reported herein include field-measured water-column parameters (water temperature, pH, dissolved oxygen concentration, specific conductance); total nitrogen and phosphorus; particulate carbon and nitrogen; total iron; filtered orthophosphate, nitrite, nitrite plus nitrate, ammonia, organic carbon, and iron; specific UV absorbance at 254 nanometers; chlorophyll a; phytoplankton and zooplankton enumeration and species identification; and bacterial abundance and morphological subgroups. Sampling program results indicated: *Most nutrient and carbon concentrations were lowest in spring, increased starting in mid-June, remained elevated in the summer, and decreased in fall. Dissolved nitrite plus nitrate had a different seasonal cycle and was below detection or at low concentration in summer. *Although total nitrogen and total phosphorus concentrations did not show large differences from upstream to downstream, filtered ammonia and orthophosphate concentrations increased in the downstream direction and particulate carbon and particulate nitrogen generally decreased in the downstream direction. *Large bacterial cells made up most of the bacteria biovolume, though cocci were the most numerous bacteria type. Cocci, with diameters of 0.1 to 0.2 micrometers, were smaller than the filter pore sizes used to separate dissolved from particulate matter. *Phytoplankton biovolumes were dominated by diatoms in spring and by the blue-green alga Aphanizomenon flos-aquae after mid-June. Another blue-green, Anabaena flos-aquae, was noted in samples from late May to late June. Phytoplankton biovolumes generally were highest at the upstream Link River and Railroad Bridge sites and decreased in the downstream direction. *Zooplankton densities were largest in late April. Populations were dominated by rotifers and copepods in early spring, and by rotifers and cladocerans in summer, with cladocerans most common at the most upstream site.

Complementary cereals and legumes for health: Synergistic interaction of sorghum flavones and cowpea flavonols against LPS-induced inflammation in colonic myofibroblasts.

PubMed

Agah, Shima; Kim, Hyemee; Mertens-Talcott, Susanne U; Awika, Joseph M

2017-07-01

Cereals and legumes are traditionally consumed together in many cultures, and may provide complementary health benefits beyond what is known about improved indispensable amino acid intake. Here, we use an in vitro model of inflammatory pathways to investigate whether the different flavonoids in sorghum and cowpea could synergistically reduce inflammation. Interactive effect of combining apigenin and quercetin, as well as extracts (70% acetone, v/v) from a flavone-dominated white sorghum and flavonol-dominated white cowpea, against LPS-induced NF-κB and downstream cytokines (TNF-α, IL-6, IL-8) gene and protein expression was evaluated using the CCD18Co colon myofibroblasts. Combination of apigenin and quercetin, and sorghum and cowpea extracts synergistically downregulated LPS-induced NF-κB gene and protein expression in a dose-dependent manner, with additive effect producing IC 50 values that were 14.6 and 14.0 times, respectively, higher than 1:1 combined treatments. Similar strong synergistic interactions were observed for the downstream cytokines (IC 50 values for additive effect 8.3-21 times higher than combined treatments). Furthermore, the ratios of the different combined treatments significantly affected the magnitude of synergy. Combining the structurally related cereal flavones and legume flavonols elicit strong synergistic anti-inflammatory response in LPS-stimulated nonmalignant colonocytes, likely by targeting interdependent mechanisms. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Flow-Field Measurement of Device-Induced Embedded Streamwise Vortex on a Flat Plate

NASA Technical Reports Server (NTRS)

Yao, Chung-Sheng; Lin, John C.; Allan, Brian G.

2002-01-01

Detailed flow-field measurements were performed downstream of a single vortex generator (VG) using an advanced Stereo Digital Particle Image Velocimetry system. Thc passive flow-control devices examined consisted of a low-profile VG with a device height, h, approximately equal to 20 percent of the boundary-layer thickness, sigma, and a conventional VG with h is approximately sigma. Flow-field data were taken at twelve cross-flow planes downstream of the VG to document and quantify the evolution of embedded streamwise vortex. The effects of device angle of attack on vortex development downstream were compared between the low-profile VG and the conventional VG. Key parameters including vorticity, circulation, trajectory, and half-life radius - describing concentration, strength, path, and size, respectively--of the device-induced streamwise vortex were extracted from the flow-field data. The magnitude of maximum vorticity increases as angle of attack increases for the low-profile VG, but the trend is reversed for the conventional VG, probably due to flow stalling around the larger device at higher angles of attack. Peak vorticity and circulation for the low-profile VG decays exponentially and inversely proportional to the distance downstream from the device. The device-height normalized vortex trajectories for the low-profile VG, especially in the lateral direction, follow the general trends of the conventional VG. The experimental database was used to validate the predictive capability of computational fluid dynamics (CFD). CFD accurately predicts the vortex circulation and path; however, improvements are needed for predicting the vorticity strength and vortex size.

Responses of shortfin eel (Anguilla australis) exposed in situ to pulp and paper effluent.

PubMed

van den Heuvel, Michael R; Landman, Michael J; Tremblay, Louis A

2006-10-01

The responses of shortfin eel (Anguilla australis) to discharges from two pulp and paper mills, municipal wastewater, and a geothermal power plant wastewater were examined. Eels were caged at 3 sites along the Tarawera River, North Island, New Zealand, to explore effects of a 3-wk exposure down a contamination gradient (Ref --> D1 --> D2). Most of the observed effects were seen in eels caged at the furthest downstream site (D2), below all the discharge areas. General hematology in eels was unaffected, as measures did not differ markedly at the two downstream sites compared with the reference site. At D2, eels were significantly lighter per unit length (reduced condition factor), although liver and spleen size (LSI and SSI) were unaffected. Significantly elevated circulating sex steroid concentrations (testosterone and estradiol) were measured in D2 eels and increasing sex steroid levels at both sites downstream of the reference site were observed. Significant ethoxyresorufin O-deethylase (EROD) activity induction was seen in D2 eels and bile chemistry showed significant accumulation of pyrene and retene equivalents. However, significantly greater concentrations of total resin acids were found in the bile of eels from the intermediate site (D1), between the two pulp and paper mills. The higher polycyclic aromatic hydrocarbon (PAH) equivalents found in the bile of D2 eels suggest that resin acid neutrals, particularly retene, are responsible for some of the effects observed in eels at the furthest downstream exposure site. Levels of pulp and paper mill extractives in sediment, including the PAH retene, support this conclusion.

Synoptic patterns leading to hailstorm in Chaharmahal and Bakhtiari province, Iran

NASA Astrophysics Data System (ADS)

Salahi, Bromand; Nohegar, Ahmad; Behrouzi, Mahmoud; Aalijahan, Mehdi

2018-03-01

The purpose of this study was to extract the synoptic patterns of 500 mb geopotential height and the sea level pressure leading to form hail in Chaharmahal and Bakhtiari province, Iran. To this end, at first, we explored hail occurrence in different areas of the province under investigation. Then, using sea level pressure and 500 mb geopotential height data, the patterns of hail occurrence were investigated through hierarchical clustering and Ward's method. The level of 500 mb patterns resulting in hail formation in the area include: (1) settlement of a cut-off low pressure blocking in Turkey and Iran's position in downstream of trough and injection of humidity coming from the Red Sea; (2) settlement of low ridge in northern Europe and Iran lying in downstream of the trough and injection of humidity of the Mediterranean Sea; (3) settlement of a cut-off low pressure in east of Europe and Iran lying in downstream of the trough; and (4) settlement of a deep trough in the Mediterranean Sea, formation of an omega-shaped blocking in Northern Europe and Iran lying in downstream of the trough. At sea level, the following patterns have caused hail formation in Chaharmahal and Bakhtiari province: (1) settlement of low pressure in Iran and Russia accompanying high pressure in Taklimakan Desert and east of Europe; (2) settlement of low pressure in Iran and high pressure in Egypt, northern Europe, and Taklimakan Desert; and (3) settlement of low pressure in Iran, Saudi Arabia and south of Italy and high pressure in Egypt and Siberia.

Diel fluctuations in natural organic matter quality in an oligotrophic cave system

NASA Astrophysics Data System (ADS)

Brown, T.; Engel, A. S.; Pfiffner, S. M.

2016-12-01

Transformations of natural organic matter (NOM) and effects of photochemical degradation on dissolved organic matter (DOM) quality in recharge can be readily studied in cave systems with hydrologic connections between the surface and subsurface. Specifically, diel controls on photodegradation, fresh NOM production, and microbial C cycling were examined from recharge to resurgence of an oligotrophic cave stream in Kentucky. We used NOM isolation and spectroscopic analysis to concentrate and characterize DOM, and lipid profiling to evaluate microbial community structure. A hydrophilic fraction of DOM was isolated from bulk waters in the field using diethylaminoethyl (DEAE) weak anion exchange column chromatography, and isolates were characterized with FTIR spectroscopy to identify differences in macromolecular structure between surface and subsurface (downstream) DOM. Lipids from colloidal NOM (retained on 0.2 µm filter) and stream sediments were extracted using a modified Bligh Dyer method, segregated into classes, and converted to fatty acid methyl esters (FAME) for quantification and identification by GC-MS. During a late summer, low flow, 24-hour sampling event, the quality of surface water DOM recharged at night was 40% richer in aliphatic esters, 30% richer in phenols and alkanes, and elevated in polysaccharides compared with DOM recharged during daylight. IR absorptivity in nocturnal DOM isolates was an order of magnitude lower in the cave stream, with recalcitrant DOM interpreted from bands of aliphatic esters, alkanes, and organo-silicates. Phospholipid fatty acid (PLFA) profiles indicated that the abundance of polyunsaturated PLFA associated with algae, fungi, and higher plants decreased along the flowpath. Cave microbes exhibited elevated trans:cis ratios relative to surface communities, and the ratio increased at night. This suggested that downstream microbial communities existed in a state of reduced activity without inputs of photosynthates at night.

Synergistic Effects of Targeted PI3K Signaling Inhibition and Chemotherapy in Liposarcoma

PubMed Central

Guo, Shang; Lopez-Marquez, Hector; Fan, Kenneth C.; Choy, Edwin; Cote, Gregory; Harmon, David; Nielsen, G. Petur; Yang, Cao; Zhang, Changqing; Mankin, Henry; Hornicek, Francis J.; Borger, Darrell R.; Duan, Zhenfeng

2014-01-01

While liposarcoma is the second most common soft tissue malignant tumor, the molecular pathogenesis in this malignancy is poorly understood. Our goal was therefore to expand the understanding of molecular mechanisms that drive liposarcoma and identify therapeutically-susceptible genetic alterations. We studied a cohort of high-grade liposarcomas and benign lipomas across multiple disease sites, as well as two liposarcoma cell lines, using multiplexed mutational analysis. Nucleic acids extracted from diagnostic patient tissue were simultaneously interrogated for 150 common mutations across 15 essential cancer genes using a clinically-validated platform for cancer genotyping. Western blot analysis was implemented to detect activation of downstream pathways. Liposarcoma cell lines were used to determine the effects of PI3K targeted drug treatment with or without chemotherapy. We identified mutations in the PIK3CA gene in 4 of 18 human liposarcoma patients (22%). No PIK3CA mutations were identified in benign lipomas. Western blot analysis confirmed downstream activation of AKT in both PIK3CA mutant and non-mutant liposarcoma samples. PI-103, a dual PI3K/mTOR inhibitor, effectively inhibited the activation of the PI3K/AKT in liposarcoma cell lines and induced apoptosis. Importantly, combination with PI-103 treatment strongly synergized the growth-inhibitory effects of the chemotherapy drugs doxorubicin and cisplatin in liposarcoma cells. Taken together, these findings suggest that activation of the PI3K/AKT pathway is an important cancer mechanism in liposarcoma. Targeting the PI3K/AKT/pathway with small molecule inhibitors in combination with chemotherapy could be exploited as a novel strategy in the treatment of liposarcoma. PMID:24695632

DNA Methylation and Mutation of Small Colonic Neoplasms in Ulcerative Colitis and Crohn's Colitis: Implications for Surveillance.

PubMed

Johnson, David H; Taylor, William R; Aboelsoud, Mohammed M; Foote, Patrick H; Yab, Tracy C; Cao, Xiaoming; Smyrk, Thomas C; Loftus, Edward V; Mahoney, Douglas W; Ahlquist, David A; Kisiel, John B

2016-07-01

Stool DNA testing in patients with inflammatory bowel disease (IBD) may detect colorectal cancer and advanced precancers with high sensitivity; less is known about the presence of DNA markers in small IBD lesions, their association with metachronous neoplasia, or contribution to stool test positivity. At a single center in 2 blinded phases, we assayed methylated bone morphogenic protein 3, methylated N-Myc downstream-regulated gene 4, and mutant KRAS in DNA extracted from paraffin-embedded benign lesions, and matched control tissues of patients with IBD, who were followed for subsequent colorectal dysplasia. Stool samples from independent cases and controls with lesions <1 cm or advanced neoplasms were assayed for the same markers. Among IBD lesions (29 low-grade dysplasia, 19 serrated epithelial change, and 10 sessile serrated adenoma/polyps), the prevalence of methylation was significantly higher than in mucosae from 44 matched IBD controls (P < 0.0001 for methylated bone morphogenic protein 3 or methylated N-Myc downstream-regulated gene 4). KRAS mutations were more abundant in serrated epithelial change than all other groups (P < 0.001). Subsequent dysplasia was not associated with DNA marker levels. In stools, the sensitivity of methylated bone morphogenic protein 3 as a single marker was 60% for all lesions <1 cm, 63% for low-grade dysplasia ≥1 cm and 81% for high-grade dysplasia/colorectal cancer, all at 91% specificity (P < 0.0001). Selected DNA markers known to be present in advanced IBD neoplasia can also be detected in both tissues and stools from IBD patients with small adenomas and serrated lesions. Mutant KRAS exfoliated from serrated epithelial change lesions might raise false-positive rates. These findings have relevance to potential future applications of stool DNA testing for IBD surveillance.

Methanol Generates Numerous Artifacts during Sample Extraction and Storage of Extracts in Metabolomics Research

PubMed Central

Sauerschnig, Claudia; Doppler, Maria

2017-01-01

Many metabolomics studies use mixtures of (acidified) methanol and water for sample extraction. In the present study, we investigated if the extraction with methanol can result in artifacts. To this end, wheat leaves were extracted with mixtures of native and deuterium-labeled methanol and water, with or without 0.1% formic acid. Subsequently, the extracts were analyzed immediately or after storage at 10 °C, −20 °C or −80 °C with an HPLC-HESI-QExactive HF-Orbitrap instrument. Our results showed that 88 (8%) of the >1100 detected compounds were derived from the reaction with methanol and either formed during sample extraction or short-term storage. Artifacts were found for various substance classes such as flavonoids, carotenoids, tetrapyrrols, fatty acids and other carboxylic acids that are typically investigated in metabolomics studies. 58 of 88 artifacts were common between the two tested extraction variants. Remarkably, 34 of 73 (acidified extraction solvent) and 33 of 73 (non-acidified extraction solvent) artifacts were formed de novo as none of these meth(ox)ylated metabolites were found after extraction of native leaf samples with CD3OH/H2O. Moreover, sample extracts stored at 10 °C for several days, as can typically be the case during longer measurement sequences, led to an increase in both the number and abundance of methylated artifacts. In contrast, frozen sample extracts were relatively stable during a storage period of one week. Our study shows that caution has to be exercised if methanol is used as the extraction solvent as the detected metabolites might be artifacts rather than natural constituents of the biological system. In addition, we recommend storing sample extracts in deep freezers immediately after extraction until measurement. PMID:29271872

DNA extraction for streamlined metagenomics of diverse environmental samples.

PubMed

Marotz, Clarisse; Amir, Amnon; Humphrey, Greg; Gaffney, James; Gogul, Grant; Knight, Rob

2017-06-01

A major bottleneck for metagenomic sequencing is rapid and efficient DNA extraction. Here, we compare the extraction efficiencies of three magnetic bead-based platforms (KingFisher, epMotion, and Tecan) to a standardized column-based extraction platform across a variety of sample types, including feces, oral, skin, soil, and water. Replicate sample plates were extracted and prepared for 16S rRNA gene amplicon sequencing in parallel to assess extraction bias and DNA quality. The data demonstrate that any effect of extraction method on sequencing results was small compared with the variability across samples; however, the KingFisher platform produced the largest number of high-quality reads in the shortest amount of time. Based on these results, we have identified an extraction pipeline that dramatically reduces sample processing time without sacrificing bacterial taxonomic or abundance information.

Seasonal Variations and Resilience of Bacterial Communities in a Sewage Polluted Urban River

PubMed Central

Ouattara, Nouho Koffi; Anzil, Adriana; Verbanck, Michel A.; Brion, Natacha; Servais, Pierre

2014-01-01

The Zenne River in Brussels (Belgium) and effluents of the two wastewater treatment plants (WWTPs) of Brussels were chosen to assess the impact of disturbance on bacterial community composition (BCC) of an urban river. Organic matters, nutrients load and oxygen concentration fluctuated highly along the river and over time because of WWTPs discharge. Tag pyrosequencing of bacterial 16S rRNA genes revealed the significant effect of seasonality on the richness, the bacterial diversity (Shannon index) and BCC. The major grouping: -winter/fall samples versus spring/summer samples- could be associated with fluctuations of in situ bacterial activities (dissolved and particulate organic carbon biodegradation associated with oxygen consumption and N transformation). BCC of the samples collected upstream from the WWTPs discharge were significantly different from BCC of downstream samples and WWTPs effluents, while no significant difference was found between BCC of WWTPs effluents and the downstream samples as revealed by ANOSIM. Analysis per season showed that allochthonous bacteria brought by WWTPs effluents triggered the changes in community composition, eventually followed by rapid post-disturbance return to the original composition as observed in April (resilience), whereas community composition remained altered after the perturbation by WWTPs effluents in the other seasons. PMID:24667680

Visualizing Perturbation Decay in Shocked Granular Materials

NASA Astrophysics Data System (ADS)

Cooper, Marcia; Vogler, Tracy

2017-06-01

A new experiment continuously visualizing shock wave perturbation decay through an increasing thickness of granular material has been tested with a gas gun. The experiment confines powders of either tungsten carbide or cerium oxide into a wedge geometry formed by tilting the downstream observation window, plated with a reflective aluminum film, at a shallow angle from the driver plate. The driver is machined with a sinusoidal wavy pattern for incident shock wave perturbation. After projectile impact, the perturbed shock wave passes through the granular material, first emerging at the wedge toe. Image sequences collected at 5 MHz of reflectivity loss at the plated window-granular material interface capture the spatial variation in wave propagation with increasing sample thickness. Extracting the evolving wavy pattern from the images determines the temporal perturbation amplitude. The data are compared to continuum and mesoscale simulations in normalized terms of perturbation amplitude and wavelength. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Estimation of Time Scales in Unsteady Flows in a Turbomachinery Rig

NASA Technical Reports Server (NTRS)

Lewalle, Jacques; Ashpis, David E.

2004-01-01

Time scales in turbulent and transitional flow provide a link between experimental data and modeling, both in terms of physical content and for quantitative assessment. The problem of interest here is the definition of time scales in an unsteady flow. Using representative samples of data from GEAE low pressure turbine experiment in low speed research turbine facility with wake-induced transition, we document several methods to extract dominant frequencies, and compare the results. We show that conventional methods of time scale evaluation (based on autocorrelation functions and on Fourier spectra) and wavelet-based methods provide similar information when applied to stationary signals. We also show the greater flexibility of the wavelet-based methods when dealing with intermittent or strongly modulated data, as are encountered in transitioning boundary layers and in flows with unsteady forcing associated with wake passing. We define phase-averaged dominant frequencies that characterize the turbulence associated with freestream conditions and with the passing wakes downstream of a rotor. The relevance of these results for modeling is discussed in the paper.

Shale gas development impacts on surface water quality in Pennsylvania.

PubMed

Olmstead, Sheila M; Muehlenbachs, Lucija A; Shih, Jhih-Shyang; Chu, Ziyan; Krupnick, Alan J

2013-03-26

Concern has been raised in the scientific literature about the environmental implications of extracting natural gas from deep shale formations, and published studies suggest that shale gas development may affect local groundwater quality. The potential for surface water quality degradation has been discussed in prior work, although no empirical analysis of this issue has been published. The potential for large-scale surface water quality degradation has affected regulatory approaches to shale gas development in some US states, despite the dearth of evidence. This paper conducts a large-scale examination of the extent to which shale gas development activities affect surface water quality. Focusing on the Marcellus Shale in Pennsylvania, we estimate the effect of shale gas wells and the release of treated shale gas waste by permitted treatment facilities on observed downstream concentrations of chloride (Cl(-)) and total suspended solids (TSS), controlling for other factors. Results suggest that (i) the treatment of shale gas waste by treatment plants in a watershed raises downstream Cl(-) concentrations but not TSS concentrations, and (ii) the presence of shale gas wells in a watershed raises downstream TSS concentrations but not Cl(-) concentrations. These results can inform future voluntary measures taken by shale gas operators and policy approaches taken by regulators to protect surface water quality as the scale of this economically important activity increases.

An experimental investigation of gas fuel injection with X-ray radiography

DOE PAGES

Swantek, Andrew B.; Duke, D. J.; Kastengren, A. L.; ...

2017-04-21

In this paper, an outward-opening compressed natural gas, direct injection fuel injector has been studied with single-shot x-ray radiography. Three dimensional simulations have also been performed to compliment the x-ray data. Argon was used as a surrogate gas for experimental and safety reasons. This technique allows the acquisition of a quantitative mapping of the ensemble-average and standard deviation of the projected density throughout the injection event. Two dimensional, ensemble average and standard deviation data are presented to investigate the quasi-steady-state behavior of the jet. Upstream of the stagnation zone, minimal shot-to-shot variation is observed. Downstream of the stagnation zone, bulkmore » mixing is observed as the jet transitions to a subsonic turbulent jet. From the time averaged data, individual slices at all downstream locations are extracted and an Abel inversion was performed to compute the radial density distribution, which was interpolated to create three dimensional visualizations. The Abel reconstructions reveal that upstream of the stagnation zone, the gas forms an annulus with high argon density and large density gradients. Inside this annulus, a recirculation region with low argon density exists. Downstream, the jet transitions to a fully turbulent jet with Gaussian argon density distributions. This experimental data is intended to serve as a quantitative benchmark for simulations.« less

Downstream processing of biopharmaceutical proteins produced in plants: the pros and cons of flocculants.

PubMed

Buyel, Johannes Felix; Fischer, Rainer

2014-01-01

All biological platforms for the manufacture of biopharmaceutical proteins produce an initially turbid extract that must be clarified to avoid fouling sensitive media such as chromatography resins. Clarification is more challenging if the feed stream contains large amounts of dispersed particles, because these rapidly clog the filter media typically used to remove suspended solids. Charged polymers (flocculants) can increase the apparent size of the dispersed particles by aggregation, facilitating the separation of solids and liquids, and thus reducing process costs. However, many different factors can affect the behavior of flocculants, including the pH and conductivity of the medium, the size and charge distribution of the particulates, and the charge density and molecular mass of the polymer. Importantly, these properties can also affect the recovery of the target protein and the overall safety profile of the process. We therefore used a design of experiments approach to establish reliable predictive models that characterize the impact of flocculants during the downstream processing of biopharmaceutical proteins. We highlight strategies for the selection of flocculants during process optimization. These strategies will contribute to the quality by design aspects of process development and facilitate the development of safe and efficient downstream processes for plant-derived pharmaceutical proteins.

An experimental investigation of gas fuel injection with X-ray radiography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swantek, Andrew B.; Duke, D. J.; Kastengren, A. L.

In this paper, an outward-opening compressed natural gas, direct injection fuel injector has been studied with single-shot x-ray radiography. Three dimensional simulations have also been performed to compliment the x-ray data. Argon was used as a surrogate gas for experimental and safety reasons. This technique allows the acquisition of a quantitative mapping of the ensemble-average and standard deviation of the projected density throughout the injection event. Two dimensional, ensemble average and standard deviation data are presented to investigate the quasi-steady-state behavior of the jet. Upstream of the stagnation zone, minimal shot-to-shot variation is observed. Downstream of the stagnation zone, bulkmore » mixing is observed as the jet transitions to a subsonic turbulent jet. From the time averaged data, individual slices at all downstream locations are extracted and an Abel inversion was performed to compute the radial density distribution, which was interpolated to create three dimensional visualizations. The Abel reconstructions reveal that upstream of the stagnation zone, the gas forms an annulus with high argon density and large density gradients. Inside this annulus, a recirculation region with low argon density exists. Downstream, the jet transitions to a fully turbulent jet with Gaussian argon density distributions. This experimental data is intended to serve as a quantitative benchmark for simulations.« less

Effect-related monitoring: estrogen-like substances in groundwater.

PubMed

Kuch, Bertram; Kern, Frieder; Metzger, Jörg W; von der Trenck, Karl Theo

2010-02-01

Concentration monitoring as a basis for risk assessment is a valid approach only if there is an unambiguous relation between concentration and effect. In many cases, no such unambiguous relation exists, since various substances can exert the same effect with differing potencies. If some or all of these substances contributing to a biological effect are unknown, effect-related monitoring becomes indispensable. Endocrine-disrupting substances in water bodies, including the groundwater, are a prominent example of such a case. The aim of the investigations described here was to detect hormonally active substances in the groundwater downstream of obsolete landfills by using the E-screen assay and to possibly assign the biological effect to individual chemical compounds by means of instrumental analyses carried out in parallel. Grab samples of the groundwater were collected downstream from abandoned landfills and prepared by liquid/liquid extraction. The total estrogenic activity in these samples was determined in vitro by applying the E-screen assay. The human breast cancer cells (MCF-7) used in the E-screen proliferate in response to the presence of estrogenically active compounds. Expressed in concentration units of the reference substance 17beta-estradiol (E2), the test system allows the quantification of estrogenicity with a limit of detection (LOD) in the range of 0.1 ng/L. Aliquots of the samples were screened using gas chromatography/mass spectrometry (GC/MS) in order to quantify known estrogenically active substances and to identify unknown compounds. Estrogen-positive samples were extracted at different pH values, split into acidic, neutral, and basic fractions and analyzed by GC/MS, searching for individual components that display estrogenic activity. Estrogenic activity exceeding the LOD and the provisional benchmark of 0.5 ng E2/L was found at three out of seven abandoned waste disposal sites tested. The low concentrations of known xenoestrogens such as bisphenol-A, nonylphenols, or phthalic acid esters determined by GC/MS, however, were not sufficient to explain the detected activity. Neither natural nor synthetic hormones have caused the activity because these chemical structures are readily degradable and cannot persist in abandoned landfills for decades. The highest activity in the E-screen assay was found in the acidic fractions. Hydroxypolychlorinated biphenyls (PCBs), hydroxylated polycyclic aromatic hydrocarbons (PAHs) and hetero-PAHs, as well as alkylphenols could be identified as further compounds with possible hormonal activity. Estrogenically active substances may occur in the groundwater below obsolete landfills, especially those that contain PCBs or waste from gasworks. These substances are not part of analytical programs routinely applied to contaminated sites and may therefore escape detection and assessment. Analyses using the E-screen assay and GC/MS in parallel have shown that the total estrogenic activity found in groundwater samples is to be ascribed to a multitude of individual compounds, some of which cannot be quantified due to lack of standard substances or assessed due to lack of a standardized procedure for determination of their estrogenic potency. By comparison with provisional guide values for estradiol (0.5 ng/L) and ethynylestradiol (0.3 ng/L), the damaging potential of the total estrogenic activity in groundwater samples can in fact be assessed, but specific remediation measures are impossible unless the hormonal activity can be attributed to individual chemical substances. On the one hand, further analyses of samples taken from possible pollution sources should be conducted in order to characterize the extent of groundwater pollution with xenoestrogens. On the other hand, the most potent individual compounds should be identified according to their estrogenic potency. To this end, bioassay-directed fractionation and structure elucidation should be carried out with concentrated samples.

Ecological succession of the microbial communities of an air-conditioning cooling coil in the tropics.

PubMed

Acerbi, E; Chénard, C; Miller, D; Gaultier, N E; Heinle, C E; Chang, V W-C; Uchida, A; Drautz-Moses, D I; Schuster, S C; Lauro, F M

2017-03-01

Air-conditioning systems harbor microorganisms, potentially spreading them to indoor environments. While air and surfaces in air-conditioning systems are periodically sampled as potential sources of indoor microbes, little is known about the dynamics of cooling coil-associated communities and their effect on the downstream airflow. Here, we conducted a 4-week time series sampling to characterize the succession of an air-conditioning duct and cooling coil after cleaning. Using an universal primer pair targeting hypervariable regions of the 16S/18S ribosomal RNA, we observed a community succession for the condensed water, with the most abundant airborne taxon Agaricomycetes fungi dominating the initial phase and Sphingomonas bacteria becoming the most prevalent taxa toward the end of the experiment. Duplicate air samples collected upstream and downstream of the coil suggest that the system does not act as ecological filter or source/sink for specific microbial taxa during the duration of the experiment. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Evaluation of modeled bacteria loads along an impaired stream reach receiving discharge from a municipal separate storm sewer system in Independence, Mo.

USGS Publications Warehouse

Flickinger, Allison; Christensen, Eric D.

2017-01-01

The Little Blue River in Jackson County, Missouri, was listed as impaired in 2012 due to Escherichia coli (E. coli) from urban runoff and storm sewers. A study was initiated to characterize E. coli concentrations and loads to aid in the development of a total maximum daily load implementation plan. Longitudinal sampling along the stream revealed spatial and temporal variability in E. coli loads. Regression models were developed to better represent E. coli variability in the impaired reach using continuous hydrologic and water-quality parameters as predictive parameters. Daily loads calculated from main-stem samples were significantly higher downstream compared to upstream even though there was no significant difference between the upstream and downstream measured concentrations and no significant conclusions could be drawn from model-estimated loads due to model-associated uncertainty. Increasing sample frequency could decrease the bias and increase the accuracy of the modeled results.

Production of N[sup +] ions from a multicusp ion beam apparatus

DOEpatents

Kango Leung; Kunkel, W.B.; Walther, S.R.

1993-03-30

A method of generating a high purity (at least 98%) N[sup +] ion beam using a multicusp ion source having a chamber formed by a cylindrical chamber wall surrounded by a plurality of magnets, a filament centrally disposed in said chamber, a plasma electrode having an extraction orifice at one end of the chamber, a magnetic filter having two parallel magnets spaced from said plasma electrode and dividing the chamber into arc discharge and extraction regions. The method includes ionizing nitrogen gas in the arc discharge region of the chamber, maintaining the chamber wall at a positive voltage relative to the filament and at a magnitude for an optimum percentage of N[sup +] ions in the extracted ion beams, disposing a hot liner within the chamber and near the chamber wall to limit recombination of N[sup +] ions into the N[sub 2][sup +] ions, spacing the magnets of the magnetic filter from each other for optimum percentage of N[sup 3] ions in the extracted ion beams, and maintaining a relatively low pressure downstream of the extraction orifice and of a magnitude (preferably within the range of 3-8[times]10[sup [minus]4] torr) for an optimum percentage of N[sup +] ions in the extracted ion beam.

Continuous production of biodiesel from microalgae by extraction coupling with transesterification under supercritical conditions.

PubMed

Zhou, Dan; Qiao, Baoquan; Li, Gen; Xue, Song; Yin, Jianzhong

2017-08-01

Raw material for biodiesel has been expanded from edible oil to non-edible oil. In this study, biodiesel continuous production for two kinds of microalgae Chrysophyta and Chlorella sp. was conducted. Coupling with the supercritical carbon dioxide extraction, the oil of microalgae was extracted firstly, and then sent to the downstream production of biodiesel. The residue after decompression can be reused as the material for pharmaceuticals and nutraceuticals. Results showed that the particle size of microalgae, temperature, pressure, molar ration of methanol to oil, flow of CO 2 and n-hexane all have effects on the yield of biodiesel. With the optimal operation conditions: 40mesh algae, extraction temperature 60°C, flow of n-hexane 0.4ml/min, reaction temperature: 340°C, pressure: 18-20MPa, CO 2 flow of 0.5L/min, molar ration of methanol to oil 84:1, a yield of 56.31% was obtained for Chrysophyta, and 63.78% for Chlorella sp. due to the higher lipid content. Copyright © 2017. Published by Elsevier Ltd.

Hyperforin production in Hypericum perforatum root cultures.

PubMed

Gaid, Mariam; Haas, Paul; Beuerle, Till; Scholl, Stephan; Beerhues, Ludger

2016-03-20

Extracts of the medicinal plant Hypericum perforatum are used to treat depression and skin irritation. A major API is hyperforin, characterized by sensitivity to light, oxygen and temperature. Total synthesis of hyperforin is challenging and its content in field-grown plants is variable. We have established in vitro cultures of auxin-induced roots, which are capable of producing hyperforin, as indicated by HPLC-DAD and ESI-MS analyses. The extraction yield and the productivity upon use of petroleum ether after solvent screening were ∼5 mg/g DW and ∼50 mg/L culture after six weeks of cultivation. The root cultures also contained secohyperforin and lupulones, which were not yet detected in intact plants. In contrast, they lacked another class of typical H. perforatum constituents, hypericins, as indicated by the analysis of methanolic extracts. Hyperforins and lupulones were stabilized and enriched as dicyclohexylammonium salts. Upon up-scaling of biomass production and downstream processing, H. perforatum root cultures may provide an alternative platform for the preparation of medicinal extracts and the isolation of APIs. Copyright © 2016 Elsevier B.V. All rights reserved.

Inhibition of p38/CREB phosphorylation and COX-2 expression by olive oil polyphenols underlies their anti-proliferative effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Corona, Giulia; Dipartimento di Biologia Sperimentale, Sez. Patologia Sperimentale, Universita degli Studi di Cagliari, 09042 Monserrato; Deiana, Monica

2007-10-26

We investigated the anti-proliferative effects of an olive oil polyphenolic extract on human colon adenocarcinoma cells. Analysis indicated that the extract contained hydroxytyrosol, tyrosol and the various secoiridoid derivatives, including oleuropein. This extract exerted a strong inhibitory effect on cancer cell proliferation, which was linked to the induction of a G2/M phase cell cycle block. Following treatment with the extract (50 {mu}g/ml) the number of cells in the G2/M phase increased to 51.82 {+-} 2.69% relative to control cells (15.1 {+-} 2.5%). This G2/M block was mediated by the ability of olive oil polyphenols (50 {mu}g/ml) to exert rapid inhibitionmore » of p38 (38.7 {+-} 4.7%) and CREB (28.6 {+-} 5.5%) phosphorylation which led to a downstream reduction in COX-2 expression (56.9 {+-} 9.3%). Our data suggest that olive oil polyphenols may exert chemopreventative effects in the large intestine by interacting with signalling pathways responsible for colorectal cancer development.« less

Anthropogenic impacts on the optical characteristics and biodegradability of dissolved and particulate organic matter in the Han River watershed, South Korea

NASA Astrophysics Data System (ADS)

Shirina Begum, Most; Jin, Hyojin; Yoon, Tae Kyung; Park, Ji-Hyung

2016-04-01

To understand how anthropogenic perturbations such as dams and pollution modify the chemical characteristics and biological transformations of riverine organic matter during transit through urbanized watersheds, we compared the optical characteristics and biodegradability of dissolved organic matter (DOM) and particulate organic matter (POM) along different reaches and urban tributary streams of the Han River watershed during short-term incubations. Laboratory incubations were conducted for 5-7 days at 20-25 oC with filtered or unfiltered water samples collected from up-, mid-, and downstream reaches with different levels of anthropogenic perturbations and three urban streams along the downstream reach that receive effluents from waste water treatment facilities in the metropolitan Seoul. Optical parameters such as ultraviolet absorbance at 254 nm, absorption coefficients at 254 nm and 350 nm, fluorescence index, humic-like fluorescence, microbial humic-like fluorescence, and protein-like fluorescence, and spectral slope at 350-400 nm were significantly correlated with increasing concentration of biodegradable dissolved organic carbon (BDOC) in filtered and unfiltered sample along the Han River up-, mid-, down-, and urban streams. The concentrations of BDOC in the urban streams were 6-12 times higher than in the filtered and unfiltered main-stem river samples, with significantly higher values in presence of POM in the unfiltered samples than in the filtered samples. In a separate 5-day incubation experiment with the unfiltered water sample from a downstream location of the Han River and its urban tributary water in isolation or mixed , the rate of concurrent biodegradation of both DOM and POM, as measured by the cumulative rate of CO2 production, was higher in the mixture than the average rate of the separately incubated samples, indicating the priming effect of mixed organic materials on the biodegradation of allochthonous organic materials from the other site. Greater amounts of CO2 were produced in all the samples than could be explained by BDOC alone, indicating the role of POM as a source of CO2. Faster and more intense changes in the consumed or produced components detected in the differential images between the fluorescence excitation emission matrices collected at intervals also suggested activated organic matter processing and CO2 production upon mixing the mainstem and tributary organic matter. Overall results suggest that dams and urban water pollution leave idiosyncratic imprints in the optical characteristics of DOM along waterways of the dammed and urbanized watershed and that inputs of anthropogenic organic materials via urban tributary streams can exert a strong priming effect on the biodegradation of both DOM and POM downstream.

Review of samples of tailings, soils and stream sediment adjacent to and downstream from the Ruth Mine, Inyo County, California

USGS Publications Warehouse

Rytuba, James J.; Kim, Christopher S.; Goldstein, Daniel N.

2011-01-01

The Ruth Mine and mill are located in the western Mojave Desert in Inyo County, California (fig. 1). The mill processed gold-silver (Au-Ag) ores mined from the Ruth Au-Ag deposit, which is adjacent to the mill site. The Ruth Au-Ag deposit is hosted in Mesozoic intrusive rocks and is similar to other Au-Ag deposits in the western Mojave Desert that are associated with Miocene volcanic centers that formed on a basement of Mesozoic granitic rocks (Bateman, 1907; Gardner, 1954; Rytuba, 1996). The volcanic rocks consist of silicic domes and associated flows, pyroclastic rocks, and subvolcanic intrusions (fig. 2) that were emplaced into Mesozoic silicic intrusive rocks (Troxel and Morton, 1962). The Ruth Mine is on Federal land managed by the U.S. Bureau of Land Management (BLM). Tailings from the mine have been eroded and transported downstream into Homewood Canyon and then into Searles Valley (figs. 3, 4, 5, and 6). The BLM provided recreational facilities at the mine site for day-use hikers and restored and maintained the original mine buildings in collaboration with local citizen groups for use by visitors (fig. 7). The BLM requested that the U.S. Geological Survey (USGS), in collaboration with Chapman University, measure arsenic (As) and other geochemical constituents in soils and tailings at the mine site and in stream sediments downstream from the mine in Homewood Canyon and in Searles Valley (fig. 3). The request was made because initial sampling of the site by BLM staff indicated high concentrations of As in tailings and soils adjacent to the Ruth Mine. This report summarizes data obtained from field sampling of mine tailings and soils adjacent to the Ruth Mine and stream sediments downstream from the mine on June 7, 2009. Our results permit a preliminary assessment of the sources of As and associated chemical constituents that could potentially impact humans and biota.

Quantitative Infrared Image Analysis Of Simultaneous Upstream and Downstream Microgravity Flame Spread over Thermally-Thin Cellulose in Low Speed Forced Flow

NASA Technical Reports Server (NTRS)

Olson, S. L.; Lee, J. R.; Fujita, O.; Kikuchi, M.; Kashiwagi, T.

2013-01-01

The effect of low velocity forced flow on microgravity flame spread is examined using quantitative analysis of infrared video imaging. The objective of the quantitative analysis is to provide insight into the mechanisms of flame spread in microgravity where the flame is able to spread from a central location on the fuel surface, rather than from an edge. Surface view calibrated infrared images of ignition and flame spread over a thin cellulose fuel were obtained along with a color video of the surface view and color images of the edge view using 35 mm color film at 2 Hz. The cellulose fuel samples were mounted in the center of a 12 cm wide by 16 cm tall flow duct and were ignited in microgravity using a straight hot wire across the center of the 7.5 cm wide by 14 cm long samples. Four cases, at 1 atm. 35%O2 in N2, at forced flows from 2 cm/s to 20 cm/s are presented here. This flow range captures flame spread from strictly upstream spread at low flows, to predominantly downstream spread at high flow. Surface temperature profiles are evaluated as a function of time, and temperature gradients for upstream and downstream flame spread are measured. Flame spread rates from IR image data are compared to visible image spread rate data. IR blackbody temperatures are compared to surface thermocouple readings to evaluate the effective emissivity of the pyrolyzing surface. Preheat lengths and pyrolysis lengths are evaluated both upstream and downstream of the central ignition point. A surface energy balance estimates the net heat flux from the flame to the fuel surface along the length of the fuel. Surface radiative loss and gas-phase radiation from soot are measured relative to the net heat feedback from the flame. At high surface heat loss relative to heat feedback, the downstream flame spread does not occur.

Sedimentological downstream effects of dam failure and the role of sediment connectivity: a case study from the Bohemian Massif, Austria

NASA Astrophysics Data System (ADS)

Wurster, Maria-Theresia; Weigelhofer, Gabriele; Pichler-Scheder, Christian; Hein, Thomas; Pöppl, Ronald

2017-04-01

Sediment connectivity describes the potential for sediment transport through catchment systems, further defining locality and characteristics of sedimentation in river channels. Dams generally decrease sediment connectivity and act as temporary sediment sinks. When dams are removed these sediments are being reworked and released downstream. During dam restoration works along a small-sized stream in the Bohemian Massif of Austria in December 2015 a dam failure occurred which led to the entrainment of several tons of fine-grained reservoir sediments further entering and depositing in the downstream channel reaches, located in the Thayatal National Park. Aiming to remove these fine sediment deposits the National Park Authority decided to initiate a flushing event in April 2016. The main aim of the present study was to investigate the effects of dam failure-induced fine sediment release and reservoir flushing on downstream bed sediment characteristics by applying geomorphological mapping (incl. volumetric surveys) and sedimentological analyses (freeze-core sampling and granulometry), further discussing the role of in-channel sediment connectivity. The obtained results have shown that immediately after the dam failure event a total of ca. 18 m3 of fine-grained sediments have accumulated as in-channel sediment bars which were primarily formed in zones of low longitudinal connectivity (e.g. in the backwater areas of woody debris jams, or at slip-off bank locations). The flushing event has been shown to have caused remobilization and downstream translocation of these deposits, further reducing their total volume by approx. 60%. The results of the granulometric analyses of the freeze-core samples have revealed fine sediment accumulation and storage in the upper parts of the channel bed, having further increased after the flushing event. Additionally, effects on chemical conditions and invertebrate community have been observed. These observations clearly indicate a significant influence of vertical connectivity conditions on in-channel fine sediment storage.

Novel sample preparation technique with needle-type micro-extraction device for volatile organic compounds in indoor air samples.

PubMed

Ueta, Ikuo; Mizuguchi, Ayako; Fujimura, Koji; Kawakubo, Susumu; Saito, Yoshihiro

2012-10-09

A novel needle-type sample preparation device was developed for the effective preconcentration of volatile organic compounds (VOCs) in indoor air before gas chromatography-mass spectrometry (GC-MS) analysis. To develop a device for extracting a wide range of VOCs typically found in indoor air, several types of particulate sorbents were tested as the extraction medium in the needle-type extraction device. To determine the content of these VOCs, air samples were collected for 30min with the packed sorbent(s) in the extraction needle, and the extracted VOCs were thermally desorbed in a GC injection port by the direct insertion of the needle. A double-bed sorbent consisting of a needle packed with divinylbenzene and activated carbon particles exhibited excellent extraction and desorption performance and adequate extraction capacity for all the investigated VOCs. The results also clearly demonstrated that the proposed sample preparation method is a more rapid, simpler extraction/desorption technique than traditional sample preparation methods. Copyright © 2012 Elsevier B.V. All rights reserved.

Changes to channel sediments resulting from complex human impacts in a gravel-bed river, Polish Carpathians

NASA Astrophysics Data System (ADS)

Zawiejska, Joanna; Wyżga, Bartłomiej; Hajdukiewicz, Hanna; Radecki-Pawlik, Artur; Mikuś, Paweł

2016-04-01

During the second half of the twentieth century, many sections of the Czarny Dunajec River, Polish Carpathians, were considerably modified by channelization as well as gravel-mining and the resultant channel incision (up to 3.5 m). This paper examines changes to the longitudinal pattern of grain size and sorting of bed material in an 18-km-long river reach. Surface bed-material grain size was established on 47 gravel bars and compared with a reference downstream fining trend of bar sediments derived from the sites with average river width and a vertically stable channel. Contrary to expectations, the extraction of cobbles from the channel bed in the upper part of the study reach, conducted in the past decades, has resulted in the marked coarsening of bed material in this river section. The extraction facilitated entrainment of exposed finer grains and has led to rapid bed degradation, whereas the concentration of flood flows in the increasingly deep and narrow channel has increased their competence and enabled a delivery of the coarse particles previously typical of the upstream reach. The middle section of the study reach, channelized to prevent sediment delivery to a downstream reservoir, now transfers the bed material flushed out from the incising upstream section. With considerably increased transport capacity of the river and with sediment delivery from bank erosion eliminated by bank reinforcements, bar sediments in the channelized section are typified by increased size of the finer fraction and better-than-average sorting. In the wide, multi-thread channel in the lower part of the reach, low unit stream power and high channel-form roughness facilitate sediment deposition and are reflected in relatively fine grades of bar gravels. The study showed that selective extraction of larger particles from the channel bed leads to channel incision at and upstream of the mining site. However, unlike bulk gravel mining, selective extraction does not result in sediment deficit downstream as large volumes of finer bed material are flushed out from the incising channel section. Grain-size analyses of bulk gravels and measurements of 100 coarsest particles within the channel sediment ranging in age from 5200 years BP to the present, performed in this deeply incised section, indicated that grain size of channel sediments changed relatively little since mid-Holocene to the 1960s, but has increased rapidly over the last half-century as a result of human interventions and rapidly progressing channel incision. This study was performed within the scope of the Research Project DEC-2013/09/B/ST10/00056 financed by the National Science Centre of Poland.

Synchronous detection of miRNAs, their targets and downstream proteins in transferred FFPE sections: applications in clinical and basic research.

PubMed

Zhao, Jin-yao; Liu, Chun-qing; Zhao, He-nan; Ding, Yan-Fang; Bi, Tie; Wang, Bo; Lin, Xing-chi; Guo, Gordon; Cui, Shi-ying

2012-10-01

After discovering new miRNAs, it is often difficult to determine their targets and effects on downstream protein expression. In situ hybridization (ISH) and immunohistochemistry (IHC) are two commonly used methods for clinical diagnosis and basic research. We used an optimized technique that simultaneously detects miRNAs, their binding targets and corresponding proteins on transferred serial formalin fixed paraffin embedded (FFPE) sections from patients. Combined with bioinformatics, this method was used to validate the reciprocal expression of specific miRNAs and targets that were detected by ISH, as well as the expression of downstream proteins that were detected by IHC. A complete analysis was performed using a limited number of transferred serial FFPE sections that had been stored for 1-4 years at room temperature. Some sections had even been previously stained with H&E. We identified a miRNA that regulates epithelial ovarian cancer, along with its candidate target and related downstream protein. These findings were directly validated using sub-cellular components obtained from the same patient sample. In addition, the expression of Nephrin (a podocyte marker) and Stmn1 (a recently identified marker related to glomerular development) were confirmed in transferred FFPE sections of mouse kidney. This procedure may be adapted for clinical diagnosis and basic research, providing a qualitative and efficient method to dissect the detailed spatial expression patterns of miRNA pathways in FFPE tissue, especially in cases where only a small biopsy sample can be obtained. Copyright © 2012 Elsevier Inc. All rights reserved.

Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China.

PubMed

Jiang, Zhou; Li, Ping; Jiang, Dawei; Dai, Xinyue; Zhang, Rui; Wang, Yanhong; Wang, Yanxin

2016-01-01

Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73-0.86). Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation), Sulfolobus (sulfur and iron oxidation), Metallosphaera and Acidicaldus (iron oxidation). Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41-95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs.

Pao Pereira Extract Suppresses Castration-Resistant Prostate Cancer Cell Growth, Survival, and Invasion Through Inhibition of NFκB Signaling.

PubMed

Chang, Cunjie; Zhao, Wei; Xie, Bingxian; Deng, Yongming; Han, Tao; Cui, Yangyan; Dai, Yundong; Zhang, Zhen; Gao, Jimin; Guo, Hongqian; Yan, Jun

2014-05-01

Pao extract, derived from bark of Amazonian tree Pao Pereira, is commonly used in South American medicine. A recent study showed that Pao extract repressed androgen-dependent LNCaP prostate cancer cell growth. We hypothesize that Pao extract asserts its anticancer effects on metastatic castration-resistant prostate cancer (CRPC) cells. Pao extract suppressed CRPC PC3 cell growth in a dose- and time-dependent manner, through induction of apoptosis and cell cycle arrest. Pao extract treatment induced cell cycle inhibitors, p21 and p27, and repressed PCNA, Cyclin A and Cyclin D1. Furthermore, Pao extract also induced the upregulation of pro-apoptotic Bax, reduction of anti-apoptotic Bcl-2, Bcl-xL, and XIAP expression, which were associated with the cleavage of PARP protein. Moreover, Pao extract treatment blocked PC3 cell migration and invasion. Mechanistically, Pao extract suppressed phosphorylation levels of AKT and NFκB/p65, NFκB DNA binding activity, and luciferase reporter activity. Pao inhibited TNFα-induced relocation of NFκB/p65 to the nucleus, NFκB/p65 transcription activity, and MMP9 activity as shown by zymography. Consistently, NFκB/p65 downstream targets involved in proliferation (Cyclin D1), survival (Bcl-2, Bcl-xL, and XIAP), and metastasis (VEGFa, MMP9, and GROα/CXCL1) were also downregulated by Pao extract. Finally, forced expression of NFκB/p65 reversed the growth inhibitory effect of Pao extract. Overall, Pao extract induced cell growth arrest, apoptosis, partially through inhibiting NFκB activation in prostate cancer cells. These data suggest that Pao extract may be beneficial for protection against CRPC. © The Author(s) 2013.

Microbiological Water Quality in Relation to Water-Contact Recreation, Cuyahoga River, Cuyahoga Valley National Park, Ohio, 2000 and 2002

USGS Publications Warehouse

Bushon, Rebecca N.; Koltun, G.F.

2004-01-01

The microbiological water quality of a 23-mile segment of the Cuyahoga River within the Cuyahoga Valley National Park was examined in this study. This segment of the river receives discharges of contaminated water from stormwater, combined-sewer overflows, and incompletely disinfected wastewater. Frequent exceedances of Ohio microbiological water-quality standards result in a health risk to the public who use the river for water-contact recreation. Water samples were collected during the recreational season of May through October at four sites on the Cuyahoga River in 2000, at three sites on the river in 2002, and from the effluent of the Akron Water Pollution Control Station (WPCS) both years. The samples were collected over a similar range in streamflow in 2000 and 2002. Samples were analyzed for physical and chemical constituents, as well as the following microbiological indicators and pathogenic organisms: Escherichia coli (E. coli), Salmonella, F-specific and somatic coliphage, enterovirus, infectious enterovirus, hepatitis A virus, Clostridium perfringens (C. perfringens), Cryptosporidium, and Giardia. The relations of the microorganisms to each other and to selected water-quality measures were examined. All microorganisms analyzed for, except Cryptosporidium, were detected at least once at each sampling site. Concentrations of E. coli exceeded the Ohio primary-contact recreational standard (298 colonies per 100 milliliters) in approximately 87 percent of the river samples and generally were higher in the river samples than in the effluent samples. C. perfringens concentrations were positively and significantly correlated with E. coli concentrations in the river samples and generally were higher in the effluent samples than in the river samples. Several of the river samples that met the Ohio E. coli secondary-contact recreational standard (576 colonies per 100 milliliters) had detections of enterovirus, infectious enterovirus, hepatitis A virus, and Salmonella, indicating that there are still risks even when the E. coli standard is not exceeded. River samples in which the secondary-contact recreational standard for E. coli was exceeded showed a higher percentage of the co-occurrence of pathogenic organisms than samples that met the standard. This indicates that in this study area, E. coli is a useful indicator of human health risk. Detections of hepatitis A virus tended to be associated with higher median concentrations of somatic coliphage, F-specific coliphage, and infectious enterovirus. In addition, geometric mean C. perfringens concentrations tended to be higher in samples where hepatitis A virus was present than in samples where hepatitis A virus was absent. Hepatitis A virus was not detected in samples collected upstream from the Akron WPCS; all downstream detections had coincident detections in the Akron WPCS effluent, suggesting that Akron WPCS was a principal source of hepatitis A virus at the downstream sites. Geometric mean concentrations of E. coli were calculated on the basis of analytical results from at least five samples collected at each river site during May, July, and September of 2000. In each case, the Ohio geometric-mean primary-contact recreational standard of 126 col/100 mL was exceeded. E. coli concentrations were significantly correlated with streamflow and increased with streamflow at sites upstream and downstream from the Akron WPCS. This indicates that E. coli loads from sources upstream from the Akron WPCS have the potential to appreciably influence the frequency of attainment of recreational water-quality standards at downstream locations.

DNA Adsorption to and Elution from Silica Surfaces: Influence of Amino Acid Buffers

PubMed Central

Vandeventer, Peter E.; Mejia, Jorge; Nadim, Ali; Johal, Malkiat S.; Niemz, Angelika

2014-01-01

Solid phase extraction and purification of DNA from complex samples typically requires chaotropic salts that can inhibit downstream polymerase amplification if carried into the elution buffer. Amino acid buffers may serve as a more compatible alternative for modulating the interaction between DNA and silica surfaces. We characterized DNA binding to silica surfaces, facilitated by representative amino acid buffers, and the subsequent elution of DNA from the silica surfaces. Through bulk depletion experiments, we found that more DNA adsorbs to silica particles out of positively compared to negatively charged amino acid buffers. Additionally, the type of the silica surface greatly influences the amount of DNA adsorbed, and the final elution yield. Quartz crystal microbalance experiments with dissipation monitoring (QCM-D) revealed multiphasic DNA adsorption out of stronger adsorbing conditions such as arginine, glycine, and glutamine, with DNA more rigidly bound during the early stages of the adsorption process. The DNA film adsorbed out of glutamate was more flexible and uniform throughout the adsorption process. QCM-D characterization of DNA elution from the silica surface indicates an uptake in water mass during the initial stage of DNA elution for the stronger adsorbing conditions, which suggests that for these conditions the DNA film is partly dehydrated during the prior adsorption process. Overall, several positively charged and polar neutral amino acid buffers show promise as an alternative to methods based on chaotropic salts for solid phase DNA extraction. PMID:23931415

40 CFR 1065.230 - Raw exhaust flow meter.

Code of Federal Regulations, 2012 CFR

2012-07-01

... sample NMHC downstream of the cooling for compression-ignition engines, 2-stroke spark-ignition engines, and 4-stroke spark-ignition engines below 19 kW. (3) If cooling causes aqueous condensation, do not...

40 CFR 1065.230 - Raw exhaust flow meter.

Code of Federal Regulations, 2013 CFR

2013-07-01

... sample NMHC downstream of the cooling for compression-ignition engines, 2-stroke spark-ignition engines, and 4-stroke spark-ignition engines below 19 kW. (3) If cooling causes aqueous condensation, do not...

Chemical data and lead isotopic compositions of geochemical baseline samples from streambed sediments and smelter slag, lead isotopic compositions in fluvial tailings, and dendrochronology results from the Boulder River watershed, Jefferson County, Montana

USGS Publications Warehouse

Unruh, Daniel M.; Fey, David L.; Church, Stan E.

2000-01-01

IntroductionAs a part of the U.S. Geological Survey Abandoned Mine Lands Initiative, metal-mining related wastes in the Boulder River study area in northern Jefferson County, Montana, have been evaluated for their environmental effects. The study area includes a 24-km segment of the Boulder River in and around Basin, Montana and three principal tributaries to the Boulder River: Basin Creek, Cataract Creek, and High Ore Creek. Mine and prospect waste dumps and mill wastes are located throughout the drainage basins of these tributaries and in the Boulder River. Mine-waste material has been transported into and down streams, where it has mixed with and become incorporated into the streambed sediments. In some localities, mine waste material was placed directly in stream channels and was transported downstream forming fluvial tailings deposits along the stream banks. Water quality and aquatic habitat have been affected by trace-element-contaminated sediment that moves from mine wastes into and down streams during snowmelt and storm runoff events within the Boulder River watershed.Present-day trace element concentrations in the streambed sediments and fluvial tailings have been extensively studied. However, in order to accurately evaluate the impact of mining on the stream environments, it is also necessary to evaluate the pre-mining trace-element concentrations in the streambed sediments. Three types of samples have been collected for estimation of pre-mining concentrations: 1) streambed sediment samples from the Boulder River and its tributaries located upstream from historical mining activity, 2) stream terrace deposits located both upstream and downstream of the major tributaries along the Boulder River, and 3) cores through sediment in overbank deposits, in abandoned stream channels, or beneath fluvial tailings deposits. In this report, we present geochemical data for six stream-terrace samples and twelve sediment-core samples and lead isotopic data for six terrace and thirteen core samples. Sample localities are in table 1 and figures 1 and 2, and site and sample descriptions are in table 2.Geochemical data have been presented for cores through fluvial tailings on High Ore Creek, on upper Basin Creek, and on Jack Creek and Uncle Sam Gulch. Geochemical and lead isotopic data for modern streambed-sediment samples have been presented by Fey and others.Lead isotopic determinations in bed sediments have been shown to be an effective tool for evaluating the contributions from various sources to the metals in bed sediments. However, in order to make these calculations, the lead isotopic compositions of the contaminant sources must also be known. Consequently, we have determined the lead isotopic compositions of five streambed-sediment samples heavily contaminated with fluvial mine waste immediately downstream from large mines in the Boulder River watershed in order to determine the lead isotopic signatures of the contaminants. Summary geochemical data for the contaminants are presented here and geochemical data for the streambed-sediment samples are given by Fey and others.Downstream from the Katie mill site and Jib tailings, fluvial deposits of mill tailings are present on a 10-m by 50-m bar in the Boulder River below the confluence with Basin Creek. The source of these tailings is not known, but fluvial tailings are also present immediately downstream from the Katie mill site, which is immediately upstream from the confluence with Basin Creek. Nine cores of fluvial tailings from this bar were analyzed.Dendrochronology samples were taken at several stream terrace localities to provide age control on the stream terrace deposits. Trees growing on the surfaces of stream terraces provide a minimum age for the terrace deposits, although floods subsequent to the trees' growth could have deposited post-mining overbank deposits around the trees. Historical data were also used to provide estimates of minimum ages of cultural features and to bracket the age of events.

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, David A.

Oak Ridge Associated Universities (ORAU), under the Oak Ridge Institute for Science and Education (ORISE) contract, collected split surface water samples with Nuclear Fuel Services (NFS) representatives on August 21, 2013. Representatives from the U.S. Nuclear Regulatory Commission (NRC) and the Tennessee Department of Environment and Conservation were also in attendance. Samples were collected at four surface water stations, as required in the approved Request for Technical Assistance number 11-018. These stations included Nolichucky River upstream (NRU), Nolichucky River downstream (NRD), Martin Creek upstream (MCU), and Martin Creek downstream (MCD). Both ORAU and NFS performed gross alpha and gross betamore » analyses, and the comparison of results using the duplicate error ratio (DER), also known as the normalized absolute difference, are tabulated. All DER values were less than 3 and results are consistent with low (e.g., background) concentrations.« less

10 CFR 431.76 - Uniform test method for the measurement of energy efficiency of commercial warm air furnaces.

Code of Federal Regulations, 2010 CFR

2010-01-01

... § 431.75) you must locate one or two sampling tubes within six inches downstream from the flue....75). If you use an open end tube, it must project into the flue one-third of the chimney connector diameter. If you use other methods of sampling CO2, you must place the sampling tube so as to obtain an...

Economic Analysis of an Integrated Annatto Seeds-Sugarcane Biorefinery Using Supercritical CO2 Extraction as a First Step

PubMed Central

Albarelli, Juliana Q.; Santos, Diego T.; Cocero, María José; Meireles, M. Angela A.

2016-01-01

Recently, supercritical fluid extraction (SFE) has been indicated to be utilized as part of a biorefinery, rather than as a stand-alone technology, since besides extracting added value compounds selectively it has been shown to have a positive effect on the downstream processing of biomass. To this extent, this work evaluates economically the encouraging experimental results regarding the use of SFE during annatto seeds valorization. Additionally, other features were discussed such as the benefits of enhancing the bioactive compounds concentration through physical processes and of integrating the proposed annatto seeds biorefinery to a hypothetical sugarcane biorefinery, which produces its essential inputs, e.g., CO2, ethanol, heat and electricity. For this, first, different configurations were modeled and simulated using the commercial simulator Aspen Plus® to determine the mass and energy balances. Next, each configuration was economically assessed using MATLAB. SFE proved to be decisive to the economic feasibility of the proposed annatto seeds-sugarcane biorefinery concept. SFE pretreatment associated with sequential fine particles separation process enabled higher bixin-rich extract production using low-pressure solvent extraction method employing ethanol, meanwhile tocotrienols-rich extract is obtained as a first product. Nevertheless, the economic evaluation showed that increasing tocotrienols-rich extract production has a more pronounced positive impact on the economic viability of the concept. PMID:28773616

Extractions of High Quality RNA from the Seeds of Jerusalem Artichoke and Other Plant Species with High Levels of Starch and Lipid.

PubMed

Mornkham, Tanupat; Wangsomnuk, Preeya Puangsomlee; Fu, Yong-Bi; Wangsomnuk, Pinich; Jogloy, Sanun; Patanothai, Aran

2013-04-29

Jerusalem artichoke (Helianthus tuberosus L.) is an important tuber crop. However, Jerusalem artichoke seeds contain high levels of starch and lipid, making the extraction of high-quality RNA extremely difficult and the gene expression analysis challenging. This study was aimed to improve existing methods for extracting total RNA from Jerusalem artichoke dry seeds and to assess the applicability of the improved method in other plant species. Five RNA extraction methods were evaluated on Jerusalem artichoke seeds and two were modified. One modified method with the significant improvement was applied to assay seeds of diverse Jerusalem artichoke accessions, sunflower, rice, maize, peanut and marigold. The effectiveness of the improved method to extract total RNA from seeds was assessed using qPCR analysis of four selected genes. The improved method of Ma and Yang (2011) yielded a maximum RNA solubility and removed most interfering substances. The improved protocol generated 29 to 41 µg RNA/30 mg fresh weight. An A260/A280 ratio of 1.79 to 2.22 showed their RNA purity. Extracted RNA was effective for downstream applications such as first-stranded cDNA synthesis, cDNA cloning and qPCR. The improved method was also effective to extract total RNA from seeds of sunflower, rice, maize and peanut that are rich in polyphenols, lipids and polysaccharides.

Optimization of microwave-assisted extraction of hydrocarbons in marine sediments: comparison with the Soxhlet extraction method.

PubMed

Vázquez Blanco, E; López Mahía, P; Muniategui Lorenzo, S; Prada Rodríguez, D; Fernández Fernández, E

2000-02-01

Microwave energy was applied to extract polycyclic aromatic hydrocarbons (PAHs) and linear aliphatic hydrocarbons (LAHs) from marine sediments. The influence of experimental conditions, such as different extracting solvents and mixtures, microwave power, irradiation time and number of samples extracted per run has been tested using real marine sediment samples; volume of the solvent, sample quantity and matrix effects were also evaluated. The yield of extracted compounds obtained by microwave irradiation was compared with that obtained using the traditional Soxhlet extraction. The best results were achieved with a mixture of acetone and hexane (1:1), and recoveries ranged from 92 to 106%. The extraction time is dependent on the irradiation power and the number of samples extracted per run, so when the irradiation power was set to 500 W, the extraction times varied from 6 min for 1 sample to 18 min for 8 samples. Analytical determinations were carried out by high-performance liquid chromatography (HPLC) with an ultraviolet-visible photodiode-array detector for PAHs and gas chromatography (GC) using a FID detector for LAHs. To test the accuracy of the microwave-assisted extraction (MAE) technique, optimized methodology was applied to the analysis of standard reference material (SRM 1941), obtaining acceptable results.

Understanding the gap between the estrogenicity of an effluent and its real impact into the wild.

PubMed

Nadzialek, Stéphanie; Vanparys, Caroline; Van der Heiden, Edwige; Michaux, Carole; Brose, François; Scippo, Marie-Louise; De Coen, Wim; Kestemont, Patrick

2010-01-15

To study the reliability between in vitro and in vivo data collected downstream 2 sewage treatment plants (STP) as well as from bleached kraft mill industry (BKME), 5 rivers (3 impacted and 2 references) were investigated in the Walloon region (southern of Belgium). For the in vitro part of the work, water samples were collected to measure the estrogenicity of the 'out' effluent compared to reference sample point by MCF-7 assay. Results indicated significant estrogenicity of effluents from STP and BKME and a weak estrogenicity in reference sites. However, estradiol equivalents (EEQ) estimated into rivers were probably too low to impact wild population. Chemical analysis of 13 compounds of interest indicated that extraction procedure used in this study gave low recoveries of estrogen-like xenobiotics, leading to probably under-estimated MCF-7 responses. Surprisingly, a full scan mode has revealed an unexpected compound in the sample of BKME which was: 7-isopropyl-1,1,4a-trimethyl-1,2,3,4a,9,10,10a-octahydrophenanthrene, a product of pulp mill manufacture. In parallel to in vitro, in vivo assessment of estrogenic impact of effluent was followed on the gudgeon (Gobio gobio). Samples were achieved during 2 different periods of the reproductive cycle, resting period (RP) and pre-spawning period (pSP). Unspecific physiological parameters to estrogenic exposure (gonadosomatic index and systematic testis cell counting) displayed no significant differences related to endocrine disruption of the reproductive tract, only differences were correlated with the reproductive state of fish (RP versus pSP). Concerning the potent biomarker of estrogen exposure, vitellogenin (vtg), only basal induction was revealed but not related to estrogenic exposure. Nevertheless, vtg over-expression was found for male fish presenting a feminization of the reproductive tract captured downstream the STP station of Wégnez in the Vesdre River. Intersexuality, another indicator of the estrogenicity impact in fish, was observed in every site. Actually, ovotestis was systematically formed by protoplasmic oocyte observed in low percentage in every group analysed (impacted and references). Moreover, in fish captured in Wégnez, oocyte diameter was significantly higher compared to the other groups. In this study, only moderate to none impact in population of gudgeon was noticed. Moreover, in this case no discrepancy between in vitro and vivo was viewed although both approaches revealed gaps in monitoring effluent incidence into the environment. We should remain careful in the interpretation when only partial approaches are used in order to characterize impact in the aquatic milieu. Copyright 2009 Elsevier B.V. All rights reserved.

SOURCES AND TRANSFORMATIONS OF NITROGEN, CARBON, AND PHOSPHORUS IN THE POTOMAC RIVER ESTUARY

NASA Astrophysics Data System (ADS)

Pennino, M. J.; Kaushal, S.

2009-12-01

Global transport of nitrogen (N), carbon (C), and phosphorus (P) in river ecosystems has been dramatically altered due to urbanization. We examined the capacity of a major tributary of the Chesapeake Bay, the Potomac River, to transform carbon, nitrogen, and phosphorus inputs from the world’s largest advanced wastewater treatment facility (Washington D.C. Water and Sewer Authority). Surface water and effluent samples were collected along longitudinal transects of the Potomac River seasonally and compared to long-term interannual records of carbon, nitrogen, and phosphorus. Water samples from seasonal longitudinal transects were analyzed for dissolved organic and inorganic nitrogen and phosphorus, total organic carbon, and particulate carbon, nitrogen, and phosphorus. The source and quality of organic matter was characterized using fluorescence spectroscopy, excitation emission matrices (EEMs), and PARAFAC modeling. Sources of nitrate were tracked using stable isotopes of nitrogen and oxygen. Along the river network stoichiometric ratios of C, N, and P were determined across sites and related to changes in flow conditions. Land use data and historical water chemistry data were also compared to assess the relative importance of non-point sources from land-use change versus point-sources of carbon, nitrogen, and phosphorus. Preliminary data from EEMs suggested that more humic-like organic matter was important above the wastewater treatment plant, but more protein-like organic matter was present below the treatment plant. Levels of nitrate and ammonia showed increases within the vicinity of the wastewater treatment outfall, but decreased rapidly downstream, potentially indicating nutrient uptake and/or denitrification. Phosphate levels decreased gradually along the river with a small increase near the wastewater treatment plant and a larger increase and decrease further downstream near the high salinity zone. Total organic carbon levels show a small decrease downstream. Ecological stoichiometric ratios along the river indicate increases in C/N ratios downstream, but no corresponding trend with C/P ratios. The N/P ratios increased directly below the treatment plant and then decreased gradually downstream. The C/N/P ratios remained level until the last two sampling stations within 20 miles of the Chesapeake Bay, where there is a large increase. Despite large inputs, there may be large variations in sources and ecological stoichiometry along rivers and estuaries, and knowledge of these transformations will be important in predicting changes in the amounts, forms, and stoichiometry of nutrient loads to coastal waters.

Improvement of High-throughput Genotype Analysis After Implementation of a Dual-curve Sybr Green I-based Quantification and Normalization Procedure

USDA-ARS?s Scientific Manuscript database

The ability to rapidly screen a large number of individuals is the key to any successful plant breeding program. One of the primary bottlenecks in high throughput screening is the preparation of DNA samples, particularly the quantification and normalization of samples for downstream processing. A ...

Preliminary examination of oxidative stress in juvenile spring Chinook salmon (Oncorhynchus tshawytscha) of wild origin sampled from transport barges

USDA-ARS?s Scientific Manuscript database

Migrating juvenile wild Chinook salmon (Oncorhynchus tshawytscha), collected and loaded onto transport barges at Lower Granite Dam on the Snake River, were sampled from barges at John Day Dam, 348 km downstream, at five-day intervals beginning late April and ending late May. An increase in lipid per...

DETERMINATION OF SULFUR DIOXIDE, NITROGEN OXIDES, AND CARBON DIOXIDE IN EMISSIONS FROM ELECTRIC UTILITY PLANTS BY ALKALINE PERMANGANATE SAMPLING AND ION CHROMATOGRAPHY

EPA Science Inventory

A manual 24-h integrated method for determining SO2, NOx, and CO2 in emissions from electric utility plants was developed and field tested downstream from an SO2 control system. Samples were collected in alkaline potassium permanganate solution contained in restricted-orifice imp...

Automated extraction of DNA from biological stains on fabric from crime cases. A comparison of a manual and three automated methods.

PubMed

Stangegaard, Michael; Hjort, Benjamin B; Hansen, Thomas N; Hoflund, Anders; Mogensen, Helle S; Hansen, Anders J; Morling, Niels

2013-05-01

The presence of PCR inhibitors in extracted DNA may interfere with the subsequent quantification and short tandem repeat (STR) reactions used in forensic genetic DNA typing. DNA extraction from fabric for forensic genetic purposes may be challenging due to the occasional presence of PCR inhibitors that may be co-extracted with the DNA. Using 120 forensic trace evidence samples consisting of various types of fabric, we compared three automated DNA extraction methods based on magnetic beads (PrepFiler Express Forensic DNA Extraction Kit on an AutoMate Express, QIAsyphony DNA Investigator kit either with the sample pre-treatment recommended by Qiagen or an in-house optimized sample pre-treatment on a QIAsymphony SP) and one manual method (Chelex) with the aim of reducing the amount of PCR inhibitors in the DNA extracts and increasing the proportion of reportable STR-profiles. A total of 480 samples were processed. The highest DNA recovery was obtained with the PrepFiler Express kit on an AutoMate Express while the lowest DNA recovery was obtained using a QIAsymphony SP with the sample pre-treatment recommended by Qiagen. Extraction using a QIAsymphony SP with the sample pre-treatment recommended by Qiagen resulted in the lowest percentage of PCR inhibition (0%) while extraction using manual Chelex resulted in the highest percentage of PCR inhibition (51%). The largest number of reportable STR-profiles was obtained with DNA from samples extracted with the PrepFiler Express kit (75%) while the lowest number was obtained with DNA from samples extracted using a QIAsymphony SP with the sample pre-treatment recommended by Qiagen (41%). Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Are two systemic fish assemblage sampling programmes on the upper Mississippi River telling us the same thing?

USGS Publications Warehouse

Dukerschein, J.T.; Bartels, A.D.; Ickes, B.S.; Pearson, M.S.

2013-01-01

We applied an Index of Biotic Integrity (IBI) used on Wisconsin/Minnesota waters of the upper Mississippi River (UMR) to compare data from two systemic sampling programmes. Ability to use data from multiple sampling programmes could extend spatial and temporal coverage of river assessment and monitoring efforts. We normalized for effort and tested fish community data collected by the Environmental Monitoring and Assessment Program-Great Rivers Ecosystems (EMAP-GRE) 2004–2006 and the Long Term Resource Monitoring Program (LTRMP) 1993–2006. Each programme used daytime electrofishing along main channel borders but with some methodological and design differences. EMAP-GRE, designed for baseline and, eventually, compliance monitoring, used a probabilistic, continuous design. LTRMP, designed primarily for baseline and trend monitoring, used a stratified random design in five discrete study reaches. Analysis of similarity indicated no significant difference between EMAP-GRE and LTRMP IBI scores (n=238; Global R= 0.052; significance level=0.972). Both datasets distinguished clear differences only between 'Fair' and 'Poor' condition categories, potentially supporting a 'pass–fail' assessment strategy. Thirteen years of LTRMP data demonstrated stable IBI scores through time in four of five reaches sampled. LTRMP and EMAPGRE IBI scores correlated along the UMR's upstream to downstream gradient (df [3, 25]; F=1.61; p=0.22). A decline in IBI scores from upstream to downstream was consistent with UMR fish community studies and a previous, empirically modelled human disturbance gradient. Comparability between EMAP-GRE (best upstream to downstream coverage) and LTRMP data (best coverage over time and across the floodplain) supports a next step of developing and testing a systemic, multi-metric fish index on the UMR that both approaches could inform.

Effect of Sodium Bisulfite Injection on the Microbial Community Composition in a Brackish-Water-Transporting Pipeline▿†

PubMed Central

Park, Hyung Soo; Chatterjee, Indranil; Dong, Xiaoli; Wang, Sheng-Hung; Sensen, Christoph W.; Caffrey, Sean M.; Jack, Thomas R.; Boivin, Joe; Voordouw, Gerrit

2011-01-01

Pipelines transporting brackish subsurface water, used in the production of bitumen by steam-assisted gravity drainage, are subject to frequent corrosion failures despite the addition of the oxygen scavenger sodium bisulfite (SBS). Pyrosequencing of 16S rRNA genes was used to determine the microbial community composition for planktonic samples of transported water and for sessile samples of pipe-associated solids (PAS) scraped from pipeline cutouts representing corrosion failures. These were obtained from upstream (PAS-616P) and downstream (PAS-821TP and PAS-821LP, collected under rapid-flow and stagnant conditions, respectively) of the SBS injection point. Most transported water samples had a large fraction (1.8% to 97% of pyrosequencing reads) of Pseudomonas not found in sessile pipe samples. The sessile population of PAS-616P had methanogens (Methanobacteriaceae) as the main (56%) community component, whereas Deltaproteobacteria of the genera Desulfomicrobium and Desulfocapsa were not detected. In contrast, PAS-821TP and PAS-821LP had lower fractions (41% and 0.6%) of Methanobacteriaceae archaea but increased fractions of sulfate-reducing Desulfomicrobium (18% and 48%) and of bisulfite-disproportionating Desulfocapsa (35% and 22%) bacteria. Hence, SBS injection strongly changed the sessile microbial community populations. X-ray diffraction analysis of pipeline scale indicated that iron carbonate was present both upstream and downstream, whereas iron sulfide and sulfur were found only downstream of the SBS injection point, suggesting a contribution of the bisulfite-disproportionating and sulfate-reducing bacteria in the scale to iron corrosion. Incubation of iron coupons with pipeline waters indicated iron corrosion coupled to the formation of methane. Hence, both methanogenic and sulfidogenic microbial communities contributed to corrosion of pipelines transporting these brackish waters. PMID:21856836

High Efficiency DNA Extraction by Graphite Oxide/Cellulose/Magnetite Composites Under Na+ Free System

NASA Astrophysics Data System (ADS)

Akceoglu, Garbis Atam; Li, Oi Lun; Saito, Nagahiro

2016-04-01

DNA extraction is the key step at various research areas like biotechnology, diagnostic development, paternity determination, and forensic science . Solid support extraction is the most common method for DNA purification. In this method, Na+ ions have often been applied as binding buffers in order to obtain high extraction efficiency and high quality of DNA; however, the presence of Na+ ions might be interfering with the downstream DNA applications. In this study, we proposed graphite oxide (GO)/magnetite composite/cellulose as an innovative material for Na+-free DNA extraction. The total wt.% of GO was fixed at 4.15% in the GO/cellulose/magnetite composite . The concentration of magnetite within the composites were controlled at 0-3.98 wt.%. The extraction yield of DNA increased with increasing weight percentage of magnetite. The highest yield was achieved at 3.98 wt.% magnetite, where the extraction efficiency was reported to be 338.5 ng/µl. The absorbance ratios between 260 nm and 280 nm (A260/A280) of the DNA elution volume was demonstrated as 1.81, indicating the extracted DNA consisted of high purity. The mechanism of adsorption of DNA was provided by (1) π-π interaction between the aromatic ring in GO and nucleobases of DNA molecule, and (2) surface charge interaction between the positive charge magnetite and anions such as phosphates within the DNA molecules. The results proved that the GO/cellulose/magnetite composite provides a Na+-free method for selective DNA extraction with high extraction efficiency of pure DNA.

Reference Proteome Extracts for Mass Spec Instrument Performance Validation and Method Development

PubMed Central

Rosenblatt, Mike; Urh, Marjeta; Saveliev, Sergei

2014-01-01

Biological samples of high complexity are required to test protein mass spec sample preparation procedures and validate mass spec instrument performance. Total cell protein extracts provide the needed sample complexity. However, to be compatible with mass spec applications, such extracts should meet a number of design requirements: compatibility with LC/MS (free of detergents, etc.)high protein integrity (minimal level of protein degradation and non-biological PTMs)compatibility with common sample preparation methods such as proteolysis, PTM enrichment and mass-tag labelingLot-to-lot reproducibility Here we describe total protein extracts from yeast and human cells that meet the above criteria. Two extract formats have been developed: Intact protein extracts with primary use for sample preparation method development and optimizationPre-digested extracts (peptides) with primary use for instrument validation and performance monitoring

Benchmarking quantitative label-free LC-MS data processing workflows using a complex spiked proteomic standard dataset.

PubMed

Ramus, Claire; Hovasse, Agnès; Marcellin, Marlène; Hesse, Anne-Marie; Mouton-Barbosa, Emmanuelle; Bouyssié, David; Vaca, Sebastian; Carapito, Christine; Chaoui, Karima; Bruley, Christophe; Garin, Jérôme; Cianférani, Sarah; Ferro, Myriam; Van Dorssaeler, Alain; Burlet-Schiltz, Odile; Schaeffer, Christine; Couté, Yohann; Gonzalez de Peredo, Anne

2016-01-30

Proteomic workflows based on nanoLC-MS/MS data-dependent-acquisition analysis have progressed tremendously in recent years. High-resolution and fast sequencing instruments have enabled the use of label-free quantitative methods, based either on spectral counting or on MS signal analysis, which appear as an attractive way to analyze differential protein expression in complex biological samples. However, the computational processing of the data for label-free quantification still remains a challenge. Here, we used a proteomic standard composed of an equimolar mixture of 48 human proteins (Sigma UPS1) spiked at different concentrations into a background of yeast cell lysate to benchmark several label-free quantitative workflows, involving different software packages developed in recent years. This experimental design allowed to finely assess their performances in terms of sensitivity and false discovery rate, by measuring the number of true and false-positive (respectively UPS1 or yeast background proteins found as differential). The spiked standard dataset has been deposited to the ProteomeXchange repository with the identifier PXD001819 and can be used to benchmark other label-free workflows, adjust software parameter settings, improve algorithms for extraction of the quantitative metrics from raw MS data, or evaluate downstream statistical methods. Bioinformatic pipelines for label-free quantitative analysis must be objectively evaluated in their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. This can be done through the use of complex spiked samples, for which the "ground truth" of variant proteins is known, allowing a statistical evaluation of the performances of the data processing workflow. We provide here such a controlled standard dataset and used it to evaluate the performances of several label-free bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, for detection of variant proteins with different absolute expression levels and fold change values. The dataset presented here can be useful for tuning software tool parameters, and also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods. Copyright © 2015 Elsevier B.V. All rights reserved.

Estimating Fluctuating Pressures From Distorted Measurements

NASA Technical Reports Server (NTRS)

Whitmore, Stephen A.; Leondes, Cornelius T.

1994-01-01

Two algorithms extract estimates of time-dependent input (upstream) pressures from outputs of pressure sensors located at downstream ends of pneumatic tubes. Effect deconvolutions that account for distoring effects of tube upon pressure signal. Distortion of pressure measurements by pneumatic tubes also discussed in "Distortion of Pressure Signals in Pneumatic Tubes," (ARC-12868). Varying input pressure estimated from measured time-varying output pressure by one of two deconvolution algorithms that take account of measurement noise. Algorithms based on minimum-covariance (Kalman filtering) theory.

Method and apparatus for measuring flow velocity using matched filters

DOEpatents

Raptis, Apostolos C.

1983-01-01

An apparatus and method for measuring the flow velocities of individual phase flow components of a multiphase flow utilizes matched filters. Signals arising from flow noise disturbance are extracted from the flow, at upstream and downstream locations. The signals are processed through pairs of matched filters which are matched to the flow disturbance frequency characteristics of the phase flow component to be measured. The processed signals are then cross-correlated to determine the transit delay time of the phase flow component between sensing positions.

Wildfire effects on source-water quality--Lessons from Fourmile Canyon fire, Colorado, and implications for drinking-water treatment

USGS Publications Warehouse

Writer, Jeffrey H.; Murphy, Sheila F.

2012-01-01

Forested watersheds provide high-quality source water for many communities in the western United States. These watersheds are vulnerable to wildfires, and wildfire size, fire severity, and length of fire season have increased since the middle 1980s (Westerling and others, 2006). Burned watersheds are prone to increased flooding and erosion, which can impair water-supply reservoirs, water quality, and drinking-water treatment processes. Limited information exists on the degree, timing, and duration of the effects of wildfire on water quality, making it difficult for drinking-water providers to evaluate the risk and develop management options. In order to evaluate the effects of wildfire on water quality and downstream ecosystems in the Colorado Front Range, the U.S. Geological Survey initiated a study after the 2010 Fourmile Canyon fire near Boulder, Colorado. Hydrologists frequently sampled Fourmile Creek at monitoring sites upstream and downstream of the burned area to study water-quality changes during hydrologic conditions such as base flow, spring snowmelt, and summer thunderstorms. This fact sheet summarizes principal findings from the first year of research. Stream discharge and nitrate concentrations increased downstream of the burned area during snowmelt runoff, but increases were probably within the treatment capacity of most drinking-water plants, and limited changes were observed in downstream ecosystems. During and after high-intensity thunderstorms, however, turbidity, dissolved organic carbon, nitrate, and some metals increased by 1 to 4 orders of magnitude within and downstream of the burned area. Increases of such magnitude can pose problems for water-supply reservoirs, drinking-water treatment plants, and downstream aquatic ecosystems.

Mobility of arsenic and its compounds in soil and soil solution: the effect of soil pretreatment and extraction methods.

PubMed

Száková, J; Tlustos, P; Goessler, W; Frková, Z; Najmanová, J

2009-12-30

The effect of soil extraction procedures and/or sample pretreatment (drying, freezing of the soil sample) on the extractability of arsenic and its compounds was tested. In the first part, five extraction procedures were compared with following order of extractable arsenic portions: 2M HNO(3)>0.43 M CH(3)COOH>or=0.05 M EDTA>or=Mehlich III (0.2M CH(3)COOH+0.25 M NH(4)NO(3)+0.013 M HNO(3)+0.015 M NH(4)F+0.001 M EDTA) extraction>water). Additionally, two methods of soil solution sampling were compared, centrifugation of saturated soil and the use of suction cups. The results showed that different sample pretreatments including soil solution sampling could lead to different absolute values of mobile arsenic content in soils. However, the interpretation of the data can lead to similar conclusions as apparent from the comparison of the soil solution sampling methods (r=0.79). For determination of arsenic compounds mild extraction procedures (0.05 M (NH(4))(2)SO(4), 0.01 M CaCl(2), and water) and soil solution sampling using suction cups were compared. Regarding the real soil conditions the extraction of fresh samples and/or in situ collection of soil solution are preferred among the sample pretreatments and/or soil extraction procedures. However, chemical stabilization of the solutions should be allowed and included in the analytical procedures for determination of individual arsenic compounds.

40 CFR 1065.230 - Raw exhaust flow meter.

Code of Federal Regulations, 2014 CFR

2014-07-01

... sample NMHC downstream of the cooling for compression-ignition engines, two-stroke spark-ignition engines, or four-stroke spark-ignition engines at or below 19 kW. (3) The cooling must not cause aqueous...

Occurrence of polycyclic aromatic hydrocarbons below coal-tar-sealed parking lots and effects on stream benthic macroinvertebrate communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scoggins, M.; McClintock, N.L.; Gosselink, L.

2007-12-15

Parking-lot pavement sealants recently have been recognized as a major source of polycyclic aromatic hydrocarbons (PAHs) in urban stream sediments in Austin, Texas. Laboratory and field studies have shown that PAHs in sediments can be toxic to aquatic organisms and can degrade aquatic communities. After identifying increases in concentrations of PAHs in sediments below seal-coated parking lots, we investigated whether the increases had significant effects on stream biota in 5 Austin streams. We sampled sediment chemistry and biological communities above and below the point at which stormwater runoff from the parking lots discharged into the streams, thus providing 5 upstreammore » reference sites and 5 downstream treatment sites. Differences between upstream and downstream concentrations of total PAH ranged from 3.9 to 32 mg/kg. Analysis of the species occurrence data from pool and riffle habitats indicated a significant decrease in community health at the downstream sites, including decreases in richness, intolerant taxa, Diptera taxa, and density. In pool sediments, Chironomidae density was negatively correlated with PAH concentrations, whereas Oligochaeta density responded positively to PAH concentrations. In general, pool taxa responded more strongly than riffle taxa to PAHs, but riffle taxa responded more broadly than pool taxa. Increases in PAH sediment-toxicity units between upstream and downstream sites explained decreases in taxon richness and density in pools between upstream and downstream sites.« less

Development of Technologies for Early Detection and Stratification of Breast Cancer

DTIC Science & Technology

2014-10-01

cancer. Similar screening has been done in urine samples with CYR61 and LCN2 (Figure 2a-b). The Moses lab provided breast cancer urine samples and two ...diseased samples, while CYR61 appears to have two different populations whereas diseased urine samples have lower levels of the protein present. More... system for eDAR so that each isolated cell can be deposited into a well of a 96-well plate for high-throughput downstream single-cell digital

Production, formation, and transport of high-brightness atomic hydrogen beam studies for the relativistic heavy ion collider polarized source upgrade.

PubMed

Kolmogorov, A; Atoian, G; Davydenko, V; Ivanov, A; Ritter, J; Stupishin, N; Zelenski, A

2014-02-01

The RHIC polarized H(-) ion source had been successfully upgraded to higher intensity and polarization by using a very high brightness fast atomic beam source developed at BINP, Novosibirsk. In this source the proton beam is extracted by a four-grid multi-aperture ion optical system and neutralized in the H2 gas cell downstream from the grids. The proton beam is extracted from plasma emitter with a low transverse ion temperature of ∼0.2 eV which is formed by plasma jet expansion from the arc plasma generator. The multi-hole grids are spherically shaped to produce "geometrical" beam focusing. Proton beam formation and transport of atomic beam were experimentally studied at test bench.

The potential of cloud point system as a novel two-phase partitioning system for biotransformation.

PubMed

Wang, Zhilong

2007-05-01

Although the extractive biotransformation in two-phase partitioning systems have been studied extensively, such as the water-organic solvent two-phase system, the aqueous two-phase system, the reverse micelle system, and the room temperature ionic liquid, etc., this has not yet resulted in a widespread industrial application. Based on the discussion of the main obstacles, an exploitation of a cloud point system, which has already been applied in a separation field known as a cloud point extraction, as a novel two-phase partitioning system for biotransformation, is reviewed by analysis of some topical examples. At the end of the review, the process control and downstream processing in the application of the novel two-phase partitioning system for biotransformation are also briefly discussed.

Monitoring to assess progress toward meeting the total maximum daily load for phosphorus in the Assabet River, Massachusetts: phosphorus loads, 2008 through 2010

USGS Publications Warehouse

Zimmerman, Marc J.; Savoie, Jennifer G.

2013-01-01

Wastewater discharges to the Assabet River contribute substantial amounts of phosphorus, which support accumulations of nuisance aquatic plants that are most evident in the river’s impounded reaches during the growing season. To restore the Assabet River’s water quality and aesthetics, the U.S. Environmental Protection Agency required the major wastewater-treatment plants in the drainage basin to reduce the amount of phosphorus discharged to the river by 2012. From October 2008 to December 2010, the U.S. Geological Survey, in cooperation with the Massachusetts Department of Environmental Protection and in support of the requirements of the Total Maximum Daily Load for Phosphorus, collected weekly flow-proportional, composite samples for analysis of concentrations of total phosphorus and orthophosphorus upstream and downstream from each of the Assabet River’s two largest impoundments: Hudson and Ben Smith. The purpose of this monitoring effort was to evaluate conditions in the river before enhanced treatment-plant technologies had effected reductions in phosphorus loads, thereby defining baseline conditions for comparison with conditions following the mandated load reductions. The locations of sampling sites with respect to the impoundments enabled examination of the impoundments’ effects on phosphorus sequestration and on the transformation of phosphorus between particulate and dissolved forms. The study evaluated the differences between loads upstream and downstream from the impoundments throughout the sampling period and compared differences during two seasonal periods of relevance to aquatic plants: April 1 through October 31, the growing season, and November 1 through March 31, the nongrowing season, when existing permit limits allowed average monthly wastewater-treatment-plant-effluent concentrations of 0.75 milligram per liter (growing season) or 1.0 milligram per liter (nongrowing season) for total phosphorus. At the four sampling sites during the growing season, median weekly total phosphorus loads ranged from 110 to 190 kilograms (kg) and median weekly orthophosphorus loads ranged from 17 to 41 kg. During the nongrowing season, median weekly total phosphorus loads ranged from 240 to 280 kg and median weekly orthophosphorus loads ranged from 56 to 66 kg. During periods of low and moderate streamflow, estimated loads of total phosphorus upstream from the Hudson impoundment generally exceeded those downstream during the same sampling periods throughout the study; orthophosphorus loads downstream from the impoundment were typically larger than those upstream. When storm runoff substantially increased the streamflow, loads of total phosphorus and orthophosphorus both tended to be larger downstream than upstream. At the Ben Smith impoundment, both total phosphorus and orthophosphorus loads were generally larger downstream than upstream during low and moderate streamflow, but the differences were not as pronounced as they were at the Hudson impoundment. High flows were also associated with substantially larger total phosphorus and orthophosphorus loads downstream than those entering the impoundment from upstream. In comparing periods of growing- and nongrowing-season loads, the same patterns of loads entering and leaving were observed at both impoundments. That is, at the Hudson impoundment, total phosphorus loads entering the impoundment were greater than those leaving it, and orthophosphorus loads leaving the impoundment were greater than those entering it. At the Ben Smith impoundment, both total phosphorus and orthophosphorus loads leaving the impoundment were greater than those entering it. However, the loads were greater during the nongrowing seasons than during the growing seasons, and the net differences between upstream and downstream loads were about the same. The results indicate that some of the particulate fraction of the total phosphorus loads is sequestered in the Hudson impoundment, where particulate phosphorus probably undergoes some physical and biogeochemical transformations to the dissolved form orthophosphorus. The orthophosphorus may be taken up by aquatic plants or transported out of the impoundments. The results for the Ben Smith impoundment are less clear and suggest net export of total phosphorus and orthophosphorus. Differences between results from the two impoundments may be attributable in part to differences in their sizes, morphology, unmonitored tributaries, riparian land use, and processes within the impoundments that have not been quantified for this study.

Preliminary assessment for DNA extraction on microfluidic channel

NASA Astrophysics Data System (ADS)

Gopinath, Subash C. B.; Hashim, Uda; Uda, M. N. A.

2017-03-01

The aim of this research is to extract, purify and yield DNA in mushroom from solid state mushroom sample by using fabricated continuous high-capacity sample delivery microfluidic through integrated solid state extraction based amino-coated silica bead. This device is made to specifically extract DNA in mushroom sample in continuous inflow process with energy and cost consumption. In this project, we present two methods of DNA extraction and purification which are by using centrifuge (complex and conventional method) and by using microfluidic biosensor (new and fast method). DNA extracted can be determined by using ultraviolet-visible spectroscopy (UV-VIS). The peak obtained at wavelength 260nm after measuring the absorbance of sample proves that DNA is successfully extracted from the mushroom.

[Determination of benzo(alpha)pyrene in food with microwave-assisted extraction].

PubMed

Zhou, Na; Luo, He-Dong; Li, Na; Li, Yao-Qun

2014-03-01

Coupling derivative technique and constant-energy synchronous fluorescence scanning technique, a method of determining benzo[alpha] pyrene in foods by second derivative constant-energy synchronous spectrofluorimetry after microwave-assisted treatment of samples was established using domestic microwave oven. The main factors of influencing the efficiency of microwave extraction were discussed, including the extraction solvent types and amounts, the microwave extraction time, microwave radiation power and cooling time. And the comparison with ultrasonic extraction was made. Low-fat food samples, which were just microwave-extracted with mixed-solvents, could be analyzed immediately by the spectrofluorimetric technique. For high-fat food samples, microwave-assisted saponification and extraction were made at the same time, thus simplifying operation steps and reducing sample analysis time. So the whole sample analysis process could be completed within one hour. This method was simple, rapid and inexpensive. In consequence, it was applied to determine benzo(a)pyrene in food with good reproducibility and the recoveries of benzo(alpha) pyrene ranged from 90.0% to 105.0% for the low fat samples and 83.3% to 94.6% for high-fat samples.

In Vitro Formation of Plant RNA-Induced Silencing Complexes Using an Extract of Evacuolated Tobacco Protoplasts.

PubMed

Iki, Taichiro; Ishikawa, Masayuki; Yoshikawa, Manabu

2017-01-01

Small RNA-mediated gene silencing is involved in a variety of biological processes among many eukaryotic organisms. The silencing effector, generally referred to as RNA-induced silencing complex (RISC), comprises an ARGONAUTE (AGO) protein and a small single-stranded guide RNA in its core. RISCs recognize target genes containing sequences complementary to the guide RNA and repress their expression transcriptionally or posttranscriptionally. In vitro systems that recapitulate RISC assembly are useful not only to decipher the molecular mechanisms underlying the assembly process itself but also to dissect the downstream silencing pathways mediated by RISCs. Here, we describe a method for in vitro plant RISC assembly, which relies on an extract of evacuolated protoplasts derived from Nicotiana tabacum BY-2 suspension-cultured cells. In this extract, synthetic duplexes of small RNAs are incorporated into AGO proteins that are synthesized by in vitro translation, and then duplex unwinding and selective strand elimination result in formation of mature RISCs.

Wasabi leaf extracts attenuate adipocyte hypertrophy through PPARγ and AMPK.

PubMed

Oowatari, Yasuo; Ogawa, Tetsuro; Katsube, Takuya; Iinuma, Kiyohisa; Yoshitomi, Hisae; Gao, Ming

2016-08-01

Hypertrophy of adipocytes in obese adipose tissues causes metabolic abnormality by adipocytokine dysregulation, which promotes type 2 diabetes mellitus, hypertension, and dyslipidemia. We investigated the effects of wasabi (Wasabia japonica Matsum) leaf extracts on metabolic abnormalities in SHRSP.Z-Leprfa/IzmDmcr rats (SHRSP/ZF), which are a model of metabolic syndrome. Male SHRSP/ZF rats aged 7 weeks were divided into two groups: control and wasabi leaf extract (WLE) groups, which received water or oral treatment with 4 g/kg/day WLE for 6 weeks. WLE improved the body weight gain and high blood pressure in SHRSP/ZF rats, and the plasma triglyceride levels were significantly lower in the WLE group. Adipocyte hypertrophy was markedly prevented in adipose tissue. The expression of PPARγ and subsequent downstream genes was suppressed in the WLE group adipose tissues. Our data suggest that WLE inhibits adipose hypertrophy by suppressing PPARγ expression in adipose tissue and stimulating the AMPK activity by increased adiponectin.

Cell-wall disruption and lipid/astaxanthin extraction from microalgae: Chlorella and Haematococcus.

PubMed

Kim, Dong-Yeon; Vijayan, Durairaj; Praveenkumar, Ramasamy; Han, Jong-In; Lee, Kyubock; Park, Ji-Yeon; Chang, Won-Seok; Lee, Jin-Suk; Oh, You-Kwan

2016-01-01

Recently, biofuels and nutraceuticals produced from microalgae have emerged as major interests, resulting in intensive research of the microalgal biorefinery process. In this paper, recent developments in cell-wall disruption and extraction methods are reviewed, focusing on lipid and astaxanthin production from the biotechnologically important microalgae Chlorella and Haematococcus, respectively. As a common, critical bottleneck for recovery of intracellular components such as lipid and astaxanthin from these microalgae, the composition and structure of rigid, thick cell-walls were analyzed. Various chemical, physical, physico-chemical, and biological methods applied for cell-wall breakage and lipid/astaxanthin extraction from Chlorella and Haematococcus are discussed in detail and compared based on efficiency, energy consumption, type and dosage of solvent, biomass concentration and status (wet/dried), toxicity, scalability, and synergistic combinations. This report could serve as a useful guide to the implementation of practical downstream processes for recovery of valuable products from microalgae including Chlorella and Haematococcus. Copyright © 2015 Elsevier Ltd. All rights reserved.

Application of micro-solid-phase extraction for the on-site extraction of heterocyclic aromatic amines in seawater.

PubMed

Basheer, Chanbasha

2018-04-01

An efficient on-site extraction technique to determine carcinogenic heterocyclic aromatic amines in seawater has been reported. A micro-solid-phase extraction device placed inside a portable battery-operated pump was used for the on-site extraction of seawater samples. Before on-site applications, parameters that influence the extraction efficiency (extraction time, type of sorbent materials, suitable desorption solvent, desorption time, and sample volume) were investigated and optimized in the laboratory. The developed method was then used for the on-site sampling of heterocyclic aromatic amines determination in seawater samples close to distillation plant. Once the on-site extraction completed, the small extraction device with the analytes was brought back to the laboratory for analysis using high-performance liquid chromatography with fluorescence detection. Based on the optimized conditions, the calibration curves were linear over the concentration range of 0.05-20 μg/L with correlation coefficients up to 0.996. The limits of detection were 0.004-0.026 μg/L, and the reproducibility values were between 1.3 and 7.5%. To evaluate the extraction efficiency, a comparison was made with conventional solid-phase extraction and it was applied to various fortified real seawater samples. The average relative recoveries obtained from the spiked seawater samples varied in the range 79.9-95.2%. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbiological characterization of aquatic microbiomes targeting taxonomical marker genes and antibiotic resistance genes of opportunistic bacteria.

PubMed

Alexander, Johannes; Bollmann, Anna; Seitz, Wolfram; Schwartz, Thomas

2015-04-15

The dissemination of medically relevant antibiotic resistance genes (ARGs) (blaVIM-1, vanA, ampC, ermB, and mecA) and opportunistic bacteria (Enterococcus faecium/faecalis, Pseudomonas aeruginosa, Enterobacteriaceae, Staphylococcus aureus, and CNS) was determined in different anthropogenically influenced aquatic habitats in a selected region of Germany. Over a period of two years, four differently sized wastewater treatment plants (WWTPs) with and without clinical influence, three surface waters, four rain overflow basins, and three groundwater sites were analyzed by quantitative Polymerase Chain Reaction (qPCR). Results were calculated in cell equivalents per 100 ng of total DNA extracted from water samples and per 100 mL sample volume, which seems to underestimate the abundance of antibiotic resistance and opportunistic bacteria. High abundances of opportunistic bacteria and ARG were quantified in clinical wastewaters and influents of the adjacent WWTP. The removal capacities of WWTP were up to 99% for some, but not all investigated bacteria. The abundances of most ARG targets were found to be increased in the bacterial population after conventional wastewater treatment. As a consequence, downstream surface water and also some groundwater compartments displayed high abundances of all four ARGs. It became obvious that the dynamics of the ARG differed from the fate of the opportunistic bacteria. This underlines the necessity of an advanced microbial characterization of anthropogenically influenced environments. Copyright © 2015 Elsevier B.V. All rights reserved.

Semiautomated Device for Batch Extraction of Metabolites from Tissue Samples

PubMed Central

2012-01-01

Metabolomics has become a mainstream analytical strategy for investigating metabolism. The quality of data derived from these studies is proportional to the consistency of the sample preparation. Although considerable research has been devoted to finding optimal extraction protocols, most of the established methods require extensive sample handling. Manual sample preparation can be highly effective in the hands of skilled technicians, but an automated tool for purifying metabolites from complex biological tissues would be of obvious utility to the field. Here, we introduce the semiautomated metabolite batch extraction device (SAMBED), a new tool designed to simplify metabolomics sample preparation. We discuss SAMBED’s design and show that SAMBED-based extractions are of comparable quality to extracts produced through traditional methods (13% mean coefficient of variation from SAMBED versus 16% from manual extractions). Moreover, we show that aqueous SAMBED-based methods can be completed in less than a quarter of the time required for manual extractions. PMID:22292466

Seasonal and spatial variations of glyphosate residues in surface waters of El Crespo stream, Buenos Aires province, Argentina.

NASA Astrophysics Data System (ADS)

Perez, Debora; Okada, Elena; Aparicio, Virginia; Menone, Mirta; Costa, Jose Luis

2017-04-01

El Crespo stream is located inside a small watershed (52,000 Ha) which is only influenced by farming activities without urban or industrial impact. The watershed can be divided in two areas, the southern area (upstream), mainly composed of intensive crops and the northern area (downstream) used only for extensive livestock. In this sense, "El Crespo" stream in an optimal site for monitoring screening of pesticide residues. The objective of this work was to determine the seasonal and spatial variations of glyphosate (GLY), in surface waters of "El Crespo" stream. We hypothesized that in surface waters of "El Crespo" stream the levels of GLY vary depending of the season and rainfall events. The water sampling was carried out from October to June (2014-2015) in two sites: upstream (US) and downstream (DS), before and after rain events. The water samples were collected by triplicate in 1 L polypropylene bottles and stored at -20°C until analysis. GLY was extracted from unfiltered water samples with a buffer solution (100 mM Na2B4O7•10H2O/100 mM K3PO4, pH=9) and derivatized with 9-fluorenylmethylchloroformate (1 mg/mL in acetonitrile). Afterwards samples were analyzed using liquid chromatography coupled to a tandem mass spectrometer (UPLC-MS/MS). The detection limit (LD) was 0.1 μg/L and the quantification limit (QL) was 0.5 μg/L. The rainfall regime was obtained from the database of INTA Balcarce. GLY was detected in 92.3% of the analyzed samples. In the US site, were GLY is regularly applied, the highest GLY concentration was registered in October (2.15 ± 0.16 μg/L); from November to June, the GLY levels decreased from 1.97 ± 0.17 μg/L to

Evaluation of DNA extraction methods for the analysis of microbial community in biological activated carbon.

PubMed

Zheng, Lu; Gao, Naiyun; Deng, Yang

2012-01-01

It is difficult to isolate DNA from biological activated carbon (BAC) samples used in water treatment plants, owing to the scarcity of microorganisms in BAC samples. The aim of this study was to identify DNA extraction methods suitable for a long-term, comprehensive ecological analysis of BAC microbial communities. To identify a procedure that can produce high molecular weight DNA, maximizes detectable diversity and is relatively free from contaminants, the microwave extraction method, the cetyltrimethylammonium bromide (CTAB) extraction method, a commercial DNA extraction kit, and the ultrasonic extraction method were used for the extraction of DNA from BAC samples. Spectrophotometry, agarose gel electrophoresis and polymerase chain reaction (PCR)-restriction fragment length polymorphisms (RFLP) analysis were conducted to compare the yield and quality of DNA obtained using these methods. The results showed that the CTAB method produce the highest yield and genetic diversity of DNA from BAC samples, but DNA purity was slightly less than that obtained with the DNA extraction-kit method. This study provides a theoretical basis for establishing and selecting DNA extraction methods for BAC samples.

Concentrations of selected pharmaceuticals and antibiotics in south-central Pennsylvania waters, March through September 2006

USGS Publications Warehouse

Loper, Connie A.; Crawford, J. Kent; Otto, Kim L.; Manning, Rhonda L.; Meyer, Michael T.; Furlong, Edward T.

2007-01-01

This report presents environmental and quality-control data from analyses of 15 pharmaceutical and 31 antibiotic compounds in water samples from streams and wells in south-central Pennsylvania. The analyses are part of a study by the U.S. Geological Survey (USGS) in cooperation with the Pennsylvania Department of Environmental Protection (PADEP) to define concentrations of selected emerging contaminants in streams and well water in Pennsylvania. Sampling was conducted at 11 stream sites and at 6 wells in 9 counties of south-central Pennsylvania. Five of the streams received municipal wastewater and 6 of the streams received runoff from agricultural areas dominated by animal-feeding operations. For all 11 streams, samples were collected at locations upstream and downstream of the municipal effluents or animal-feeding operations. All six wells were in agricultural settings. A total of 120 environmental samples and 21 quality-control samples were analyzed for the study. Samples were collected at each site in March/April, May, July, and September 2006 to obtain information on changes in concentration that could be related to seasonal use of compounds.For streams, 13 pharmaceuticals and 11 antibiotics were detected at least 1 time. Detections included analytical results that were estimated or above the minimum reporting limits. Seventy-eight percent of all detections were analyzed in samples collected downstream from municipal-wastewater effluents. For streams receiving wastewater effluents, the pharmaceuticals caffeine and para-xanthine (a degradation product of caffeine) had the greatest concentrations, 4.75 μg/L (micrograms per liter) and 0.853 μg/L, respectively. Other pharmaceuticals and their respective maximum concentrations were carbamazepine (0.516 μg/L) and ibuprofen (0.277 μg/L). For streams receiving wastewater effluents, the antibiotic azithromycin had the greatest concentration (1.65 μg/L), followed by sulfamethoxazole (1.34 μg/L), ofloxacin (0.329 μg/L), and trimethoprim (0.256 μg/L).For streams receiving runoff from animal-feeding operations, the only pharmaceuticals detected were acetaminophen, caffeine, cotinine, diphenhydramine, and carbamazepine. The maximum concentration for pharmaceuticals was 0.053 μg/L. Three streams receiving runoff from animal-feeding operations had detections of one or more antibiotic compound--oxytetracycline, sulfadimethoxine, sulfamethoxazole, and tylosin. The maximum concentration for antibiotics was 0.157 μg/L. The average number of compounds (pharmaceuticals and antibiotics) detected in sites downstream from animal-feeding operations was three. The average number of compounds detected downstream from municipal-wastewater effluents was 13.For wells used to supply livestock, four compounds were detected--two pharmaceuticals (cotinine and diphenhydramine) and two antibiotics (tylosin and sulfamethoxazole). There were five detections in all the well samples. The maximum concentration detected in well water was for cotinine, estimated to be 0.024 μg/L.Seasonal occurrence of pharmaceutical and antibiotic compounds in stream water varied by compound and site type. At four stream sites, the same compounds were detected in all four seasonal samples. At other sites, pharmaceutical or antibiotic compounds were detected only one time in seasonal samples. Winter samples collected in streams receiving municipalwastewater effluent had the greatest number of compounds detected (21). Research analytical methods were used to determine concentrations for pharmaceuticals and antibiotics. To assist in evaluating the quality of the analyses, detailed information is presented on laboratory methodology and results from qualitycontrol samples. Quality-control data include results for nine blanks, nine duplicate environmental sample pairs, and three laboratory-spiked environmental samples as well as the recoveries of compounds in laboratory surrogates and laboratory reagent spikes.