A three-compartment model for micropollutants sorption in sludge: methodological approach and insights.

PubMed

Barret, Maialen; Patureau, Dominique; Latrille, Eric; Carrère, Hélène

2010-01-01

In sludge resulting from wastewater treatment, organic micropollutants sorb to particles and to dissolved/colloidal matter (DCM). Both interactions may influence their physical and biological fate throughout the wastewater treatment processes. To our knowledge, sludge has never been considered as a three-compartment matrix, in which micropollutants coexist in three states: freely dissolved, sorbed-to-particles and sorbed-to-DCM. A methodology is proposed to concomitantly determine equilibrium constants of sorption to particles (K(part)) and to DCM (K(DCM)). Polycyclic Aromatic Hydrocarbons (PAHs) were chosen as model compounds for the experiments. The logarithm of estimated equilibrium constants ranged from 3.1 to 4.3 and their usual correlation to PAH hydrophobicity was verified. Moreover, PAH affinities for particles and for DCM could be compared. Affinity for particles was found to be stronger, probably due to their physical and chemical characteristics. This work provided a useful tool to assess the freely dissolved, sorbed-to-particles and sorbed-to-DCM concentrations of contaminants, which are necessary to accurately predict their fate. Besides, guidelines to investigate the link between sorption and the fundamental concept of bioavailability were proposed. (c) 2009 Elsevier Ltd. All rights reserved.

Determination of the partition coefficient between dissolved organic carbon and seawater using differential equilibrium kinetics.

PubMed

Kim, Du Yung; Kwon, Jung-Hwan

2018-05-04

Because the freely dissolved fraction of highly hydrophobic organic chemicals is bioavailable, knowing the partition coefficient between dissolved organic carbon and water (K DOCw ) is crucial to estimate the freely dissolved fraction from the total concentration. A kinetic method was developed to obtain K DOCw that required a shorter experimental time than equilibrium methods. The equilibrium partition coefficients of four polychlorinated biphenyls (PCBs) (2,4,4'-trichlorobiphenyl (PCB 28), 2,2',3,5'-tetrachlorobiphenyl (PCB 44), 2,2',4,5,5'-pentachlorobiphenyl (PCB 101), and 2,2',4,4',5,5'-hexachlorobiphenyl (PCB 153)) between dissolved organic carbon and seawater (K DOCsw ) were determined using seawater samples from the Korean coast. The log K DOCsw values of PCB 28 were measured by equilibrating PCB 28, the least hydrophobic congener, with seawater samples, and the values ranged from 6.60 to 7.20. For the more hydrophobic PCBs (PCB 44, PCB 101, and PCB 153), kinetic experiments were conducted to determine the sorption rate constants (k 2 ) and their log K DOCsw values were obtained by comparing their k 2 with that of PCB 28. The calculated log K DOCsw values were 6.57-7.35 for PCB 44, 6.23-7.44 for PCB 101, and 6.35-7.73 for PCB 153. The validity of the proposed method was further confirmed using three less hydrophobic polycyclic aromatic hydrocarbons. This kinetic method shortened the experimental time to obtain the K DOCsw values of the more hydrophobic PCBs, which did not reach phase equilibrium. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microbially driven export of labile organic carbon from the Greenland ice sheet

NASA Astrophysics Data System (ADS)

Musilova, Michaela; Tranter, Martyn; Wadham, Jemma; Telling, Jon; Tedstone, Andrew; Anesio, Alexandre M.

2017-04-01

Glaciers and ice sheets are significant sources of dissolved organic carbon and nutrients to downstream subglacial and marine ecosystems. Climatically driven increases in glacial runoff are expected to intensify the impact of exported nutrients on local and regional downstream environments. However, the origin and bioreactivity of dissolved organic carbon from glacier surfaces are not fully understood. Here, we present simultaneous measurements of gross primary production, community respiration, dissolved organic carbon composition and export from different surface habitats of the Greenland ice sheet, throughout the ablation season. We found that microbial production was significantly correlated with the concentration of labile dissolved organic species in glacier surface meltwater. Further, we determined that freely available organic compounds made up 62% of the dissolved organic carbon exported from the glacier surface through streams. We therefore conclude that microbial communities are the primary driver for labile dissolved organic carbon production and recycling on glacier surfaces, and that glacier dissolved organic carbon export is dependent on active microbial processes during the melt season.

Discharge, water quality, and native fish abundance in the Virgin River, Utah, Nevada, and Arizona, in support of Pah Tempe Springs discharge remediation efforts

USGS Publications Warehouse

Miller, Matthew P.; Lambert, Patrick M.; Hardy, Thomas B.

2014-01-01

Pah Tempe Springs discharge hot, saline, low dissolved-oxygen water to the Virgin River in southwestern Utah, which is transported downstream to Lake Mead and the Colorado River. The dissolved salts in the Virgin River negatively influence the suitability of this water for downstream agricultural, municipal, and industrial use. Therefore, various remediation scenarios to remove the salt load discharged from Pah Tempe Springs to the Virgin River are being considered. One concern about this load removal is the potential to impact the ecology of the Virgin River. Specifically, information is needed regarding possible impacts of Pah Tempe Springs remediation scenarios on the abundance, distribution, and survival of native fish in the Virgin River. Future efforts that aim to quantitatively assess how various remediation scenarios to reduce the load of dissolved salts from Pah Tempe Springs into the Virgin River may influence the abundance, distribution, and survival of native fish will require data on discharge, water quality, and native fish abundance. This report contains organized accessible discharge, water quality, and native fish abundance data sets from the Virgin River, documents the compilation of these data, and discusses approaches for quantifying relations between abiotic physical and chemical conditions, and fish abundance.

Determination of silicone rubber and low-density polyethylene diffusion and polymer/water partition coefficients for emerging contaminants.

PubMed

Pintado-Herrera, Marina G; Lara-Martín, Pablo A; González-Mazo, Eduardo; Allan, Ian J

2016-09-01

There is a growing interest in assessing the concentration and distribution of new nonregulated organic compounds (emerging contaminants) in the environment. The measurement of freely dissolved concentrations using conventional approaches is challenging because of the low concentrations that may be encountered and their temporally variable emissions. Absorption-based passive sampling enables the estimation of freely dissolved concentrations of hydrophobic contaminants of emerging concern in water. In the present study, calibration was undertaken for 2 polymers, low-density polyethylene (LDPE) and silicone rubber for 11 fragrances, 5 endocrine-disrupting compounds, 7 ultraviolet (UV) filters, and 8 organophosphate flame retardant compounds. Batch experiments were performed to estimate contaminant diffusion coefficients in the polymers (Dp ), which in general decreased with increasing molecular weight. The values for fragrances, endocrine-disrupting compounds, and UV filters were in ranges similar to those previously reported for polycyclic aromatic hydrocarbons, but were 1 order of magnitude lower for organophosphate flame retardant compounds. Silicone rubber had higher Dp values than LDPE and was therefore selected for further experiments to calculate polymer/water partition coefficients (KPW ). The authors observed a positive correlation between log KPW and log octanol/water partition coefficient values. Field testing of silicone rubber passive samplers was undertaken though exposure in the River Alna (Norway) for an exposure time of 21 d to estimate freely dissolved concentration. Some fragrances and UV filters were predominant over other emerging and regulated contaminants, at levels up to 1600 ng L(-1) for galaxolide and 448 ng L(-1) for octocrylene. Environ Toxicol Chem 2016;35:2162-2172. © 2016 SETAC. © 2016 SETAC.

Measuring nonpolar organic contaminant partitioning in three Norwegian sediments using polyethylene passive samplers.

PubMed

Allan, Ian J; Ruus, Anders; Schaanning, Morten T; Macrae, Kenneth J; Næs, Kristoffer

2012-04-15

Freely dissolved pore water concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), penta- and hexachlorobenzene (PeCB and HCB), octachlorostyrene (OCS), p,p'-DDE and p,p'-DDD were measured in bottom sediments from three sites in Norway. Sediments were from Aker Brygge, site of a former shipyard in the inner part of Oslofjord, Frierfjord in the Grenlandsfjord area, impacted during the 50 year-long activity of a magnesium smelter plant, and from Kristiansand harbour, site with high industrial activity. Low density polyethylene (LDPE) membrane samplers were exposed to these sediments in laboratory incubation under constant and low-level agitation for periods of 1, 2, 6, 13, 23 and 50 days. Freely dissolved pore water concentrations were estimated from contaminant masses accumulated and sampling rates obtained from the measurement of kinetics of dissipation of performance reference compounds (PRCs). Marked differences in freely dissolved PAH concentrations and resulting organic carbon-normalised sediment-pore water partition coefficients, logK(TOC), between these three sediments could be observed despite the generally similar total sediment concentrations. In contrast with the PAH data, partitioning of PCBs and other organochlorine compounds (OCs) was relatively similar in all three sediments. For sediments from Frierfjord and Kristiansand, logK(TOC) values were lower for PCBs/OCs than for PAHs, indicating higher availability. Similar partitioning of PAHs and PCBs/OCs was found for sediments from Aker Brygge. No simple logK(oc)-logK(ow) relationships could model these data successfully. These results support the notion that the assessment of the risk posed by these compounds present in sediments in most cases requires actual measurement of contaminant availability. Copyright © 2012 Elsevier B.V. All rights reserved.

How does predation affect the bioaccumulation of hydrophobic organic compounds in aquatic organisms?

PubMed

Xia, Xinghui; Li, Husheng; Yang, Zhifeng; Zhang, Xiaotian; Wang, Haotian

2015-04-21

It is well-known that the body burden of hydrophobic organic compounds (HOCs) increases with the trophic level of aquatic organisms. However, the mechanism of HOC biomagnification is not fully understood. To fill this gap, this study investigated the effect of predation on the bioaccumulation of polycyclic aromatic hydrocarbons (PAHs), one type of HOC, in low-to-high aquatic trophic levels under constant freely dissolved PAH concentrations (1, 5, or 10 μg L(-1)) maintained by passive dosing systems. The tested PAHs included phenanthrene, anthracene, fluoranthene, and pyrene. The test organisms included zebrafish, which prey on Daphnia magna, and cichlids, which prey on zebrafish. The results revealed that for both zebrafish and cichlids, predation elevated the uptake and elimination rates of PAHs. The increase of uptake rate constant ranged from 20.8% to 39.4% in zebrafish with the amount of predation of 5 daphnids per fish per day, and the PAH uptake rate constant increased with the amount of predation. However, predation did not change the final bioaccumulation equilibrium; the equilibrium concentrations of PAHs in fish only depended on the freely dissolved concentration in water. Furthermore, the lipid-normalized water-based bioaccumulation factor of each PAH was constant for fish at different trophic levels. These findings infer that the final bioaccumulation equilibrium of PAHs is related to a partition between water and lipids in aquatic organisms, and predation between trophic levels does not change bioaccumulation equilibrium but bioaccumulation kinetics at stable freely dissolved PAH concentrations. This study suggests that if HOCs have not reached bioaccumulation equilibrium, biomagnification occurs due to enhanced uptake rates caused by predation in addition to higher lipid contents in higher trophic organisms. Otherwise, it is only due to the higher lipid contents in higher trophic organisms.

Using SPMDs for monitoring hydrophobic organic compounds in urban river water in Korea compared with using conventional water grab samples

USGS Publications Warehouse

Kim, Un-Jung; Kim, Hee Young; Alvarez, David A.; Lee, In-Seok; Oh, Jeong-Eun

2014-01-01

We aimed to verify the effectiveness of semi-permeablemembrane devices (SPMDs) formonitoring hydrophobic organic compounds, such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), that are not easy to detect using conventional grab samples (because of their low concentrations), in water.We used SPMDs and grab samples to monitor PCBs and PBDEs upstream and downstream of a sewage treatment plant (STP) in the Suyeong River in Busan, Korea. Concentrations in three different phases (freely dissolved, apparently dissolved, and particulate) were measured, to investigate the aquatic fate of PCBs and PBDEs. The freely dissolved (SPMD) concentrations were 2–3 times higher than the apparently dissolved and particulate phase (grab sample) concentrations. No meaningful relationships were found between the total PCB and PBDE concentrations of the grab sample and SPMD sample because of the different partitioning behaviors and detection frequencies of the individual chemicals. However, the summed concentrations of specific PCB and PBDE congeners (that were abundant in all samples) in the grab and SPMD samples correlated well (r2 = 0.7451 for PCBs 28 + 52 + 153, r2 = 0.9987 for PBDEs 28 + 47 + 99). The PBDE concentrations measured using SPMDs decreased with increasing distance from the STP, but no apparent dilution effect was found in the grab samples. Our results show that SPMDs could be used to support grab sampling for specific chemicals, or to trace chemical sources (such as STPs) to the aquatic environment.

Passive Sampling Methods for Contaminated Sediments: Practical Guidance for Selection, Calibration, and Implementation

EPA Science Inventory

This article provides practical guidance on the use of passive sampling methods(PSMs) that target the freely dissolved concentration (Cfree) for improved exposure assessment of hydrophobic organic chemicals in sediments. Primary considerations for selecting a PSM for a specific a...

Effect of pyrolysis temperatures on freely dissolved polycyclic aromatic hydrocarbon (PAH) concentrations in sewage sludge-derived biochars.

PubMed

Zielińska, Anna; Oleszczuk, Patryk

2016-06-01

The aim of this study was to evaluate the effect of sewage sludge pyrolysis on freely dissolved (Cfree) polycyclic aromatic hydrocarbon (PAH) contents in biochars. Four sewage sludges with varying properties and PAH contents were pyrolysed at temperatures of 500 °C, 600 °C or 700 °C. Cfree PAH contents were determined using polyoxymethylene (POM). The contents of Cfree PAHs in the sludges ranged from 262 to 294 ng L(-1). Sewage sludge-derived biochars have from 2.3- to 3.4-times lower Cfree PAH contents comparing to corresponding sewage sludges. The Cfree PAH contents in the biochars ranged between 81 ng L(-1) and 126 ng L(-1). As regards agricultural use of biochar, the lower contents of Cfree PAHs in the biochars compared to the sewage sludges makes biochar a safer material than sewage sludge in terms of PAH contents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Performance of passive sampling with low-density polyethylene membranes for the estimation of freely dissolved DDx concentrations in lake environments.

PubMed

Borrelli, Raffaella; Tcaciuc, A Patricia; Verginelli, Iason; Baciocchi, Renato; Guzzella, Licia; Cesti, Pietro; Zaninetta, Luciano; Gschwend, Philip M

2018-06-01

Laboratory and field studies were used to evaluate the performance of low-density polyethylene (PE) passive samplers for assessing the freely dissolved concentrations of DDT and its degradates (DDD and DDE, together referred to as DDx) in an Italian lake environment. We tested commercially available 25 μm thick PE sheets as well as specially synthesized, 10 μm thick PE films which equilibrated with their surroundings more quickly. We measured PE-water partitioning coefficients (K pew ) of the 10 μm thick PE films, finding good correspondence with previously reported values for thicker PE. Use of the 10 μm PE for ex situ sampling of a lake sediment containing DDx in laboratory tumbling experiments showed repeatability of ±15% (= standard deviation/mean). Next, we deployed replicate 10 μm and 25 μm PE samplers (N = 4 for 10 d and for 30 d) in the water and sediment of a lake located in northern Italy; the results showed dissolved DDx concentrations in the picogram/L range in porewater and the bottom water. Values deduced from 10 μm thick PE films compared well (95% of all comparison pairs matched within a factor of 5) with those obtained using PE films of 25 μm thickness when dissolved DDx concentrations were estimated using performance reference compound (PRC) corrections, whether left at the bed-water interface for 10 or 30 days. These results demonstrated the potential of this sampling method to provide estimation of the truly dissolved DDx concentrations, and thereby the mobile and bio-available fractions in both surface waters and sediment beds. Copyright © 2018 Elsevier Ltd. All rights reserved.

DEVELOPMENT AND APPLICATION OF EQUILIBRIUM PARTITIONING SEDIMENT GUIDELINES IN THE ASSESSMENT OF SEDIMENT PAH CONTAMINATION

EPA Science Inventory

The U.S. Environmental Protection Agency used insights and methods from its water quality criteria program to develop ESGs. The discovery that freely-dissolved contaminants were the toxic form led to equilibrium partitioning being chosen to model the distribution of contaminants...

Cross Validation of Two Partitioning-Based Sampling Approaches in Mesocosms Containing PCB Contaminated Field Sediment, Biota, and Activated Carbon Amendment

EPA Science Inventory

The Gold Standard for determining freely dissolved concentrations (Cfree) of hydrophobic organic compounds in sediment interstitial water would be in situ deployment combined with equilibrium sampling, which is generally difficult to achieve. In the present study, ex situ equilib...

VALIDATION OF AMBIENT WATER QUALITY CRITERIA (AWQC) BIOACCUMULATION METHODOLOGY USING FIELD DATA FROM GREEN BAY AND THE HUDSON RIVER

EPA Science Inventory

In 1998, EPA published its draft revision to the methodology for deriving ambient water quality criteria to protect human health. Four methods were proposed to determine lipid-normalized bioaccumulation factors based on freely-dissolved water concentrations (BAFs) for nonpolar or...

Remote Cameras Reveal Experimental Artifact in a Study of Seed Predation in a Semi-Arid Shrubland.

PubMed

Brown, Alissa J; Deutschman, Douglas H; Braswell, Jessica; McLaughlin, Dana

2016-01-01

Granivorous animals may prefer to predate or cache seed of certain plant species over others. Multiple studies have documented preference for larger, non-native seed by granivores. To accomplish this, researchers have traditionally used indirect inference by relating patterns of seed removal to the species composition of the granivorous animal community. To measure seed removal, researchers present seed to granivorous animals in the field using equipment intended to exclude certain animal taxa while permitting access to others. This approach allows researchers to differentiate patterns of seed removal among various taxa (e.g., birds, small mammals, and insects); however, it is unclear whether the animals of interest are freely using the exclusion devices, which may be a hindrance to discovering the seed dishes. We used video observation to perform a study of seed predation using a custom-built, infrared digital camera and recording system. We presented native and non-native seed mixtures in partitioned Petri dishes both within and outside of exclusion cages. The exclusion cages were intended to allow entrance by rodent taxa while preventing entrance by rabbits and birds. We documented all seed removal visits by granivorous animals, which we identified to the genus level. Genera exhibited varying seed removal patterns based on seed type (native vs. non-native) and dish type (open vs. enclosed). We documented avoidance of the enclosed dishes by all but one rodent taxa, even though these dishes were intended to be used freely by rodents. This suggests that preference for non-native seed occurs differentially among granivorous animals in this system; however, interpretation of these nuanced results would be difficult without the benefit of video observation. When feasible, video observation should accompany studies using in situ equipment to ensure incorrect assumptions do not lead to inappropriate interpretation of results.

Nanofiber Enabled, Multi - Target Passive Sampling Device for Determination of the Freely Dissolved Sediment Pore Water Concentrations of Organic Contaminants

DTIC Science & Technology

2016-06-01

foil. Nanofiber diameters were adjusted between ~100-200 nm by controlling the electrospinning solution (e.g., viscosity , dielectric constant...acetate)/ Clay Nanocomposite Fibers. J Polym Sci Pol Phys 2009, 47, (24), 2501-2508. 36. Piperno, S.; Lozzi, L.; Rastelli, R.; Passacantando, M.; Santucci

Overview of the U.S. EPA/SERDP/ESTCP: Laboratory, Field, and Analytical Procedures for Using Passive Sampling in the Evaluation of Contaminated Sediments: User’s Manual

EPA Science Inventory

Passive sampling can be used for applications at contaminated sediment sites including performing assessments of contaminant bioavailability (i.e., freely dissolved concentration (Cfree)), conducting remedial investigations and feasibility studies, and assessing the potential for...

Equilibrium Partitioning Sediment Benchmarks (ESBs) for the Protection of Benthic Organisms: Procedures for the Determination of the Freely Dissolved Interstitial Water Concentrations of Nonionic Organics

EPA Science Inventory

This document describes procedures to determine the concentrations of nonionic organic chemicals in sediment interstitial waters. In previous ESB documents, the general equilibrium partitioning (EqP) approach was chosen for the derivation of sediment benchmarks because it account...

Overview of the U.S. EPA/SERDP/ESTCP: Laboratory, Field, and Analytical Procedures for Using Passive Sampling in the Evaluation of Contaminated Sediments: User’s Manual.

EPA Science Inventory

Passive sampling is used for applications at contaminated sediment sites including performing assessments of contaminant bioavailability (i.e., freely dissolved concentration (Cfree)), conducting remedial investigations and feasibility studies, and assessing the potential for con...

Spatial and temporal variation of freely dissolved PAHs in an urban river undergoing Superfund remediation

PubMed Central

Sower, GJ; Anderson, K.A.

2014-01-01

Urban rivers with a history of industrial use can exhibit spatial and temporal variations in contaminant concentrations that may significantly affect risk evaluations and even the assessment of remediation efforts. Concentrations of 15 biologically available priority pollutant polycyclic aromatic hydrocarbons (PAHs) were measured over five years along 18.5 miles of the lower Willamette River using passive sampling devices and HPLC. The study area includes the Portland Harbor Superfund megasite with several PAH sources including remediation operations for coal tar at RM 6.3 west and an additional Superfund site, McCormick and Baxter, at RM 7 east consisting largely of creosote contamination. Study results show that organoclay capping at the McCormick and Baxter Superfund Site reduced PAHs from a pre-cap average of 440 ± 422 ng/L to 8 ± 3 ng/L post-capping. Results also reveal that dredging of submerged coal tar nearly tripled nearby freely dissolved PAH concentrations. For apportioning sources, fluoranthene/ pyrene and phenanthrene/anthracene diagnostic ratios from passive sampling devices were established for creosote and coal tar contamination and compared to published sediment values. PMID:19174872

Spatial and temporal variation of freely dissolved polycyclic aromatic hydrocarbons in an urban river undergoing Superfund remediation.

PubMed

Sower, Gregory James; Anderson, Kim A

2008-12-15

Urban rivers with a history of industrial use can exhibit spatial and temporal variations in contaminant concentrations that may significantly affect risk evaluations and even the assessment of remediation efforts. Concentrations of 15 biologically available priority pollutant polycyclic aromatic hydrocarbons (PAHs) were measured over five years along 18.5 miles of the lower Willamette River using passive sampling devices and HPLC. The study area includes the Portland Harbor Superfund megasite with several PAH sources including remediation operations for coal tar at RM 6.3 west and an additional Superfund site, McCormick and Baxter, at RM 7 east consisting largely of creosote contamination. Study results show that organoclay capping at the McCormick and Baxter Superfund Site reduced PAHs from a precap average of 440 +/- 422 ng/L to 8 +/- 3 ng/L postcapping. Results also reveal that dredging of submerged coal tar nearly tripled nearby freely dissolved PAH concentrations. For apportioning sources, fluoranthene/pyrene and phenanthrene/anthracene diagnostic ratios from passive sampling devices were established for creosote and coal tar contamination and compared to published sediment values.

Activated carbon amendment for in-situ remediation

NASA Astrophysics Data System (ADS)

Elmquist, M.; Brändli, R.; Henriksen, T.; Hartnik, T.; Cornelissen, G.

2009-04-01

For the first time in Europe, a novel and innovative remediation technique is used in a field pilot study. This technique is amendment of the soil with two types of activated carbon (AC). Here, one pulverized AC (PAC, 50% < 15µm and 3% >150 µm) and one granular AC (GAC, 1.7-0.43 mm) is tested. The idea of this technique is that the added AC binds organic contaminants so strongly that they cannot be taken up in living organisms or transported to other environmental compartments. Laboratory studies with 2% (wt %) AC amendment to an urban soil reduced the freely dissolved pore water concentrations of PAH by 17% to 99% (Brändli et al. 2008). Several parameters such as dissolved organic carbon (DOC), K, NO2, NO3, NH4, PO4 and PAH, are being measured in this field study. Plant growth and earthworm bioaccumulation tests were also carried out during the summer months. DOC showed a 70% reduction between untreated soil and soil with PAC about one year after the amendment. In the soil mixed with GAC, a 55% reduction could be measured. For K, a 40% lowering value was observed for the soil with GAC compared to no affect for the soil with PAC. NH4 was reduced by 50% for both GAC and PAC amended soils compared to the untreated soil, whereas NO2 and NO3 increased with 2-4 times for the soil with GAC and no effect were seen for the soil with PAC. The freely dissolved PAH concentrations were reduced by 49-78% for the soil with GAC and 82-96% for the soil with PAC. The plant experiment showed best growth rate in the soil with GAC, followed by the untreated soil and least growth was measured on the PAC treated soil. The low growth rate seen in the soil with PAC may come from the fact that DOC and some other nutrients are also being sorbed to the PAC surface together with the organic pollutants and are thereby taken away from the biological cycle. Amendment of soil with AC remediates the soil from organic contaminants when these pollutants are sorbed to the AC surface. This is an easy technique that can be performed to a relatively low cost. However, the AC particles may also sorb other constituents of the effluent water such as DOC and nutrients which in turn may lead to reduced plant growth rate. Therefore, the long-term effects of this amendment technique have to be studied more closely. Reference Rahel C. Brändli, Thomas Hartnik, Thomas Henriksen, Gerard Cornelissen, (2008) Sorption of native polyaromatic hydrocarbons (PAH) to black carbon and amended activated carbon in soil, Chemosphere doi:10.1016/j.chemosphere.2008.08.034

Native oxy-PAHs, N-PACs, and PAHs in historically contaminated soils from Sweden, Belgium, and France: their soil-porewater partitioning behavior, bioaccumulation in Enchytraeus crypticus, and bioavailability.

PubMed

Arp, Hans Peter H; Lundstedt, Staffan; Josefsson, Sarah; Cornelissen, Gerard; Enell, Anja; Allard, Ann-Sofie; Kleja, Dan Berggren

2014-10-07

Soil quality standards are based on partitioning and toxicity data for laboratory-spiked reference soils, instead of real world, historically contaminated soils, which would be more representative. Here 21 diverse historically contaminated soils from Sweden, Belgium, and France were obtained, and the soil-porewater partitioning along with the bioaccumulation in exposed worms (Enchytraeus crypticus) of native polycyclic aromatic compounds (PACs) were quantified. The native PACs investigated were polycyclic aromatic hydrocarbons (PAHs) and, for the first time to be included in such a study, oxygenated-PAHs (oxy-PAHs) and nitrogen containing heterocyclic PACs (N-PACs). The passive sampler polyoxymethylene (POM) was used to measure the equilibrium freely dissolved porewater concentration, Cpw, of all PACs. The obtained organic carbon normalized partitioning coefficients, KTOC, show that sorption of these native PACs is much stronger than observed in laboratory-spiked soils (typically by factors 10 to 100), which has been reported previously for PAHs but here for the first time for oxy-PAHs and N-PACs. A recently developed KTOC model for historically contaminated sediments predicted the 597 unique, native KTOC values in this study within a factor 30 for 100% of the data and a factor 3 for 58% of the data, without calibration. This model assumes that TOC in pyrogenic-impacted areas sorbs similarly to coal tar, rather than octanol as typically assumed. Black carbon (BC) inclusive partitioning models exhibited substantially poorer performance. Regarding bioaccumulation, Cpw combined with liposome-water partition coefficients corresponded better with measured worm lipid concentrations, Clipid (within a factor 10 for 85% of all PACs and soils), than Cpw combined with octanol-water partition coefficients (within a factor 10 for 76% of all PACs and soils). E. crypticus mortality and reproducibility were also quantified. No enhanced mortality was observed in the 21 historically contaminated soils despite expectations from PAH spiked reference soils. Worm reproducibility weakly correlated to Clipid of PACs, though the contributing influence of metal concentrations and soil texture could not be taken into account. The good agreement of POM-derived Cpw with independent soil and lipid partitioning models further supports that soil risk assessments would improve by accounting for bioavailability. Strategies for including bioavailability in soil risk assessment are presented.

Developing sediment remediation goals at superfund sites based on pore water for the protection of benthic organisms from direct toxicity to non-ionic organic contaminants (presentation)

EPA Science Inventory

Passive sampling is becoming a frequently used measurement technique at Superfund sites with contaminated sediments. Passive sampling measures the concentrations of freely dissolved chemicals (Cfrees) in the sediment pore water. Cfree has been found to be a very practical means f...

40 CFR Appendix F to Part 132 - Great Lakes Water Quality Initiative Implementation Procedures

Code of Federal Regulations, 2010 CFR

2010-07-01

... use of this methodology may be found in the Great Lakes Water Quality Initiative Technical Support... (CONTINUED) WATER PROGRAMS WATER QUALITY GUIDANCE FOR THE GREAT LAKES SYSTEM Pt. 132, App. F Appendix F to... that is freely dissolved in the ambient water is different than that used to derive the system-wide...

40 CFR Appendix F to Part 132 - Great Lakes Water Quality Initiative Implementation Procedures

Code of Federal Regulations, 2011 CFR

2011-07-01

... use of this methodology may be found in the Great Lakes Water Quality Initiative Technical Support... (CONTINUED) WATER PROGRAMS WATER QUALITY GUIDANCE FOR THE GREAT LAKES SYSTEM Pt. 132, App. F Appendix F to... that is freely dissolved in the ambient water is different than that used to derive the system-wide...

Passive Sampling Provides Evidence for Neward Bay as a Source of Polychlorinated Dibenzo-p-Dioxins and Furans to the New York/New Jersey, USA, Atmosphere

EPA Science Inventory

Freely dissolved and gas phase polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) were measured in the water column and atmosphere at five locations within Newark Bay (New Jersey, USA) from May 2008 to August 2009 with polyethylene (PE) passive ...

Invasive species compendium: Salvinia molesta D.S. Mitchell

USDA-ARS?s Scientific Manuscript database

Salvinia molesta D.S. Mitchell is an invasive aquatic fern native to a small area of south-eastern Brazil. It has spread throughout the world, forming thick mats of vegetation that decrease dissolved oxygen and pH while outcompeting native vegetation. It has been introduced and established into many...

Speciation and Trends of Organic Nitrogen in Southeastern U.S. Fine Particulate Matter (PM2.5)

EPA Science Inventory

Dissolved free amino acids (FAA; amino acids present in a dissolvable state) and combined AA (CAA; amino acids present in peptides, proteins, or humic complexes) in fine aerosols (PM) are investigated at a semi-urban site in the southeastern US. Detection of native (chemically un...

Evaluation of Total Dissolved Solids and Specific Conductance Water Quality Targets with Paired Single-Species and Mesocosm Community Exposures

EPA Science Inventory

Isolated single-species exposures were conducted in parallel with 42 d mesocosm dosing studies that measured in-situ and whole community responses to different recipes of excess total dissolved solids (TDS). The studies were conducted with cultured species and native taxa from mo...

Remote Cameras Reveal Experimental Artifact in a Study of Seed Predation in a Semi-Arid Shrubland

PubMed Central

Deutschman, Douglas H.; Braswell, Jessica; McLaughlin, Dana

2016-01-01

Granivorous animals may prefer to predate or cache seed of certain plant species over others. Multiple studies have documented preference for larger, non-native seed by granivores. To accomplish this, researchers have traditionally used indirect inference by relating patterns of seed removal to the species composition of the granivorous animal community. To measure seed removal, researchers present seed to granivorous animals in the field using equipment intended to exclude certain animal taxa while permitting access to others. This approach allows researchers to differentiate patterns of seed removal among various taxa (e.g., birds, small mammals, and insects); however, it is unclear whether the animals of interest are freely using the exclusion devices, which may be a hindrance to discovering the seed dishes. We used video observation to perform a study of seed predation using a custom-built, infrared digital camera and recording system. We presented native and non-native seed mixtures in partitioned Petri dishes both within and outside of exclusion cages. The exclusion cages were intended to allow entrance by rodent taxa while preventing entrance by rabbits and birds. We documented all seed removal visits by granivorous animals, which we identified to the genus level. Genera exhibited varying seed removal patterns based on seed type (native vs. non-native) and dish type (open vs. enclosed). We documented avoidance of the enclosed dishes by all but one rodent taxa, even though these dishes were intended to be used freely by rodents. This suggests that preference for non-native seed occurs differentially among granivorous animals in this system; however, interpretation of these nuanced results would be difficult without the benefit of video observation. When feasible, video observation should accompany studies using in situ equipment to ensure incorrect assumptions do not lead to inappropriate interpretation of results. PMID:27764200

Spatial and temporal variation of freely dissolved polycyclic aromatic hydrocarbons in an urban river undergoing Superfund remediation

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

Aregory James Sower; Kim A. Anderson

2008-12-15

Urban rivers with a history of industrial use can exhibit spatial and temporal variations in contaminant concentrations that may significantly affect risk evaluations and even the assessment of remediation efforts. Concentrations of 15 biologically available priority pollutant polycyclic aromatic hydrocarbons (PAHs) were measured over five years along 18.5 miles of the lower Willamette River using passive sampling devices and HPLC. The study area includes the Portland Harbor Superfund megasite with several PAH sources including remediation operations for coal tar at RM 6.3 west and an additional Superfund site, McCormick and Baxter, at RM 7 east consisting largely of creosote contamination.more » Study results show that organoclay capping at the McCormick and Baxter Superfund Site reduced PAHs from a precap average of 440 {+-} 422 ng/L to 8 {+-} 3 ng/L postcapping. Results also reveal that dredging of submerged coal tar nearly tripled nearby freely dissolved PAH concentrations. For apportioning sources, fluoranthene/pyrene and phenanthrene/anthracene diagnostic ratios from passive sampling devices were established for creosote and coal tar contamination and compared to published sediment values. 29 refs., 3 figs., 3 tabs.« less

Dimethylformamide interferes with Coomassie dye staining of proteins on blue native gel electrophoresis.

PubMed

Raghupathy, V; Oommen, Anna; Ramachandran, Anup

2014-06-15

Blue native gel electrophoresis (BN-PAGE) is used extensively for characterization of mitochondrial respiratory complexes and uses the binding of Coomassie brilliant blue G-250 to visualize proteins. Oxidative modification of sulfhydryl groups of such proteins can be evaluated by labeling with iodoacetamide conjugated to biotin (BIAM) and detected with streptavidin peroxidase on Western blots following BN-PAGE. However, dissolving BIAM in dimethylformamide, a recommended solvent, reduces Coomassie blue G staining to proteins during BN-PAGE. This interference is prevented by dissolving BIAM in dimethyl sulfoxide. Precautions in the use of the dye for protein staining subsequent to BIAM labeling are discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Comparative Emulsifying Properties of Octenyl Succinic Anhydride (OSA)-Modified Starch: Granular Form vs Dissolved State

PubMed Central

Marefati, Ali; Gutiérrez, Gemma; Wahlgren, Marie; Rayner, Marilyn

2016-01-01

The emulsifying ability of OSA-modified and native starch in the granular form, in the dissolved state and a combination of both was compared. This study aims to understand mixed systems of particles and dissolved starch with respect to what species dominates at droplet interfaces and how stability is affected by addition of one of the species to already formed emulsions. It was possible to create emulsions with OSA-modified starch isolated from Quinoa as sole emulsifier. Similar droplet sizes were obtained with emulsions prepared at 7% (w/w) oil content using OSA-modified starch in the granular form or molecularly dissolved but large differences were observed regarding stability. Pickering emulsions kept their droplet size constant after one month while emulsions formulated with OSA-modified starch dissolved exhibited coalescence. All emulsions stabilized combining OSA-modified starch in granular form and in solution showed larger mean droplet sizes with no significant differences with respect to the order of addition. These emulsions were unstable due to coalescence regarding presence of free oil. Similar results were obtained when emulsions were prepared by combining OSA-modified granules with native starch in solution. The degree of surface coverage of starch granules was much lower in presence of starch in solution which indicates that OSA-starch is more surface active in the dissolved state than in granular form, although it led to unstable systems compared to starch granule stabilized Pickering emulsions, which demonstrated to be extremely stable. PMID:27479315

Utilizing Sediment Tracer Studies to Evaluate Transport Pathways at the Mouth of the Columbia River, USA

DTIC Science & Technology

2011-05-01

native sediment and placed in dissolving starch bags weighing ~ 20 kg each. Each bag of tracer:sediment mix was placed within a 50-75 m radius of the DZ...with the XY coordinate recorded for each bag release point via DGPS. The starch bags dissolved within 4 minutes of making contact with water

Evaluation of Titanium Dioxide as a Binding Phase for the Passive Sampling of Glyphosate and Aminomethyl Phosphonic Acid in an Aquatic Environment.

PubMed

Fauvelle, Vincent; Nhu-Trang, Tran-Thi; Feret, Thibaut; Madarassou, Karine; Randon, Jérôme; Mazzella, Nicolas

2015-06-16

Glyphosate is the most widely used herbicide on a world scale for the last 40 years, for both urban and agricultural uses. Here we describe the first passive sampling method for estimating the concentration of glyphosate and AMPA (aminomethyl phosphonic acid, one of its major degradation products) in surface water. The sampling method is based on a newly developed configuration of the diffusive gradient in thin-film (DGT) technique, which includes a TiO2 binding phase, already in use for a wide range of anions. Glyphosate and AMPA were retained well on a TiO2 binding phase, and elution in a 1 mL of 1 M NaOH led to recoveries greater than 65%. We found no influence of pH or flow velocity on the diffusion coefficients through 0.8 mm polyacrylamide gels, although they did increase with temperature. TiO2 binding gels were able to accumulate up to 1167 ng of P for both glyphosate and AMPA, and linear accumulation was expected over several weeks, depending on environmental conditions. DGT sampling rates were close to 10 mL day(-1) in ultrapure water, while they were less than 1 mL day(-1) in the presence of naturally occurring ions (e.g., copper, iron, calcium, magnesium). These last results highlighted (i) the ability of DGT to measure only the freely dissolved fraction of glyphosate and AMPA in water and (ii) the needs to determine which fraction (total, particulate, dissolved, freely dissolved) is indeed bioactive.

Agricultural land-use change in a Mexican oligotrophic desert depletes ecosystem stability.

PubMed

Hernández-Becerra, Natali; Tapia-Torres, Yunuen; Beltrán-Paz, Ofelia; Blaz, Jazmín; Souza, Valeria; García-Oliva, Felipe

2016-01-01

Global demand for food has led to increased land-use change, particularly in dry land ecosystems, which has caused several environmental problems due to the soil degradation. In the Cuatro Cienegas Basin (CCB), alfalfa production irrigated by flooding impacts strongly on the soil. In order to analyze the effect of such agricultural land-use change on soil nutrient dynamics and soil bacterial community composition, this work examined an agricultural gradient within the CCB which was comprised of a native desert grassland, a plot currently cultivated with alfalfa and a former agricultural field that had been abandoned for over 30 years. For each site, we analyzed C, N and P dynamic fractions, the activity of the enzyme phosphatase and the bacterial composition obtained using 16S rRNA clone libraries. The results showed that the cultivated site presented a greater availability of water and dissolved organic carbon, these conditions promoted mineralization processes mediated by heterotrophic microorganisms, while the abandoned land was limited by water and dissolved organic nitrogen. The low amount of dissolved organic matter promoted nitrification, which is mediated by autotrophic microorganisms. The microbial N immobilization process and specific phosphatase activity were both favored in the native grassland. As expected, differences in bacterial taxonomical composition were observed among sites. The abandoned site exhibited similar compositions than native grassland, while the cultivated site differed. The results suggest that the transformation of native grassland into agricultural land induces drastic changes in soil nutrient dynamics as well as in the bacterial community. However, with the absence of agricultural practices, some of the soil characteristics analyzed slowly recovers their natural state.

Metrosiderous polymorpha Guad. Ohia lehua.

Treesearch

Ken Adee; C. Eugene Conrad

1990-01-01

Ohia lehua (Metrosideros polymorpha) is the most abundant and widespread tree in Hawaii. This slow growing native hardwood seeds freely and often starts as an epiphyte in fern forests. It is the first tree to appear on new lava flows where it offers watershed protection. The wood is of fine even texture and takes a good polish. It is used for...

Surface microlayer enrichment of polycyclic aromatic hydrocarbons in lower Chesapeake Bay

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

Liu, K.; Dickhut, R.M.

1995-12-31

Surface microlayer samples were collected with a rotating cylinder sampler in the York River and Elizabeth River tributaries of lower Chesapeake Bay every other month from May 1994 to June, 1995. Spatial and temporal variabilities were also investigated over an annual cycle as well as shorter periods (i.e. days). All the samples were analyzed for 17 polycyclic aromatic hydrocarbons, total suspended particulate matter (TSP), particular organic carbon (POC), total nitrogen(TN) and dissolved organic carbon (DOC), and selected samples for chlorophyll. TSP in the surface microlayer was 10 to 100 times higher than that in the related bulk water. Particle associatedmore » PAH concentrations were 20--50 times those in bulk surface water, whereas PAH concentrations in freely dissolved phase of the surface microlayer were 5--60 times higher than dissolved concentrations in the bulk water. Particulate PAH concentrations increase with TSP in the surface microlayer and dissolved PAH concentrations increase with DOC. Overall, surface microlayer characteristics were found to be significantly affected by hydrological and meteorological parameters.« less

D2N: Distance to the native.

PubMed

Mishra, Avinash; Rana, Prashant Singh; Mittal, Aditya; Jayaram, B

2014-10-01

Root-mean-square-deviation (RMSD), of computationally-derived protein structures from experimentally determined structures, is a critical index to assessing protein-structure-prediction-algorithms (PSPAs). The development of PSPAs to obtain 0Å RMSD from native structures is considered central to computational biology. However, till date it has been quite challenging to measure how far a predicted protein structure is from its native - in the absence of a known experimental/native structure. In this work, we report the development of a metric "D2N" (distance to the native) - that predicts the "RMSD" of any structure without actually knowing the native structure. By combining physico-chemical properties and known universalities in spatial organization of soluble proteins to develop D2N, we demonstrate the ability to predict the distance of a proposed structure to within ±1.5Ǻ error with a remarkable average accuracy of 93.6% for structures below 5Ǻ from the native. We believe that this work opens up a completely new avenue towards assigning reliable structures to whole proteomes even in the absence of experimentally determined native structures. The D2N tool is freely available at http://www.scfbio-iitd.res.in/software/d2n.jsp. Copyright © 2014 Elsevier B.V. All rights reserved.

Agricultural land-use change in a Mexican oligotrophic desert depletes ecosystem stability

PubMed Central

Hernández-Becerra, Natali; Tapia-Torres, Yunuen; Beltrán-Paz, Ofelia; Blaz, Jazmín; Souza, Valeria

2016-01-01

Background Global demand for food has led to increased land-use change, particularly in dry land ecosystems, which has caused several environmental problems due to the soil degradation. In the Cuatro Cienegas Basin (CCB), alfalfa production irrigated by flooding impacts strongly on the soil. Methods In order to analyze the effect of such agricultural land-use change on soil nutrient dynamics and soil bacterial community composition, this work examined an agricultural gradient within the CCB which was comprised of a native desert grassland, a plot currently cultivated with alfalfa and a former agricultural field that had been abandoned for over 30 years. For each site, we analyzed C, N and P dynamic fractions, the activity of the enzyme phosphatase and the bacterial composition obtained using 16S rRNA clone libraries. Results The results showed that the cultivated site presented a greater availability of water and dissolved organic carbon, these conditions promoted mineralization processes mediated by heterotrophic microorganisms, while the abandoned land was limited by water and dissolved organic nitrogen. The low amount of dissolved organic matter promoted nitrification, which is mediated by autotrophic microorganisms. The microbial N immobilization process and specific phosphatase activity were both favored in the native grassland. As expected, differences in bacterial taxonomical composition were observed among sites. The abandoned site exhibited similar compositions than native grassland, while the cultivated site differed. Discussion The results suggest that the transformation of native grassland into agricultural land induces drastic changes in soil nutrient dynamics as well as in the bacterial community. However, with the absence of agricultural practices, some of the soil characteristics analyzed slowly recovers their natural state. PMID:27602304

Response of PAH-degrading genes to PAH bioavailability in the overlying water, suspended sediment, and deposited sediment of the Yangtze River.

PubMed

Xia, Xinghui; Xia, Na; Lai, Yunjia; Dong, Jianwei; Zhao, Pujun; Zhu, Baotong; Li, Zhihuang; Ye, Wan; Yuan, Yue; Huang, Junxiong

2015-06-01

The degrading genes of hydrophobic organic compounds (HOCs) serve as indicators of in situ HOC degradation potential, and the existing forms and bioavailability of HOCs might influence the distribution of HOC-degrading genes in natural waters. However, little research has been conducted to study the relationship between them. In the present study, nahAc and nidA genes, which act as biomarkers for naphthalene- and pyrene-degrading bacteria, were selected as model genotypes to investigate the response of polycyclic aromatic hydrocarbon (PAH)-degrading genes to PAH bioavailability in the overlying water, suspended sediment (SPS), and deposited sediment of the Yangtze River. The freely dissolved concentration, typically used to reflect HOC bioavailability, and total dissolved, as well as sorbed concentrations of PAHs were determined. Phylogenetic analysis showed that all the PAH-ring hydroxylating dioxygenase gene sequences of Gram-negative bacteria (PAH-RHD[GN]) were closely related to nahAc, nagAc, nidA, and uncultured PAH-RHD genes. The PAH-RHD[GN] gene diversity as well as nahAc and nidA gene copy numbers decreased in the following order: deposited sediment>SPS>overlying water. The nahAc and nidA gene abundance was not significantly correlated with environmental parameters but was significantly correlated with the bioavailable existing forms of naphthalene and pyrene in the three phases. The nahAc gene copy numbers in the overlying water and deposited sediment were positively correlated with freely dissolved naphthalene concentrations in the overlying and pore water phases, respectively, and so were nidA gene copy numbers. This study suggests that the distribution and abundance of HOC-degrading bacterial population depend on the HOC bioavailability in aquatic environments. Copyright © 2015 Elsevier Ltd. All rights reserved.

The effect of humic acids on biodegradation of polycyclic aromatic hydrocarbons depends on the exposure regime.

PubMed

Tejeda-Agredano, Maria-Carmen; Mayer, Philipp; Ortega-Calvo, Jose-Julio

2014-01-01

Binding of polycyclic aromatic hydrocarbons (PAHs) to dissolved organic matter (DOM) can reduce the freely dissolved concentration, increase apparent solubility or enhance diffusive mass transfer. To study the effects of DOM on biodegradation, we used phenanthrene and pyrene as model PAHs, soil humic acids as model DOM and a soil Mycobacterium strain as a representative degrader organism. Humic acids enhanced the biodegradation of pyrene when present as solid crystals but not when initially dissolved or provided by partitioning from a polymer. Synchronous fluorescence spectrophotometry, scintillation counting and a microscale diffusion technique were applied in order to determine the kinetics of dissolution and diffusive mass transfer of pyrene. We suggest that humic acids can enhance or inhibit biodegradation as a result of the balance of two opposite effects, namely, solubilization of the chemicals on the one hand and inhibition of cell adhesion to the pollutant source on the other. Copyright © 2013 Elsevier Ltd. All rights reserved.

A Study of the Diffusion, Electrochemical Mobility and Removal of Dissolved Copper in a Saturated Porous Medium.

DTIC Science & Technology

1980-11-01

aqueous solutions : use of activity coefficients in transition-state models: Geochimica et Cosmochimica Acta, v...native state at 25°C at any activity level below 10+46.0 in an aqueous solution . Because such an activity level is impossible, sodium cannot be reduced...stoichiometric coefficients . It is necessary to calculqte the activity coefficients of dissolved copper in the test solutions in order to render an

Reconnaissance of water quality at four swine farms in Jackson County, Florida, 1993

USGS Publications Warehouse

Collins, J.J.

1996-01-01

The quality of ground water on four typical swine farms in Jackson County, Florida, was studied by analyzing water samples from wastewater lagoons, monitoring wells, and supply wells. Water samples were collected quarterly for 1 year and analyzed for the following dissolved species: nitrate, nitrite, ammonium nitrogen, phosphorus, potassium, sulfate, chloride, calcium, magnesium, fluoride, total ammonium plus organic nitrogen, total phosphorus, alkalinity, carbonate, and bicarbonate. Additionally, the following field constituents were determined in the water samples: temperature, specific conductance, pH, dissolved oxygen, and fecal streptococcus and fecal coliform bacteria. Chemical changes in swine waste as it leaches and migrates through the saturated zone were examined by comparing median values and ranges of water- quality data from farm wastewater in lagoons, shallow pond, shallow monitoring wells, and deeper farm supply wells. The effects of hydrogeologic settings and swine farmland uses on shallow ground-water quality were examined by comparing the shallow ground-water-quality data set with the results of the chemical analyses of water from the Upper Floridan aquifer, and to land uses adjacent to the monitoring wells. Substantial differences occur between the quality of diluted swine waste in the wastewater lagoons, and that of the water quality found in the shallow pond, and the ground water frm all but two of the monitoring wells of the four swine farms. The liquid from the wastewater lagoons and ground water from two wells adjacent to and down the regional gradient from a lagoon on one site, have relatively high values for the following properties and constituents: specific conductance, dissolved ammonia nitrogen, dissolved potassium, and dissolved chloride. Ground water from all other monitoring wells and farm supply wells and the surface water pond, have relatively much lower values for the same properties and constituents. To determine the relation between land uses and ground-water quality on the four swine farms, ground-water-quality data were divided according to the following land uses: confined operations in which swine are kept in houses and not allowed to roam freely, and unconfined operations in which swine are allowed to roam freely in determined areas. Confined operations had lagoons to receive the diluted swine wastes washed from the houses.

Increasing Regulatory Acceptance of Passive Samplers

DTIC Science & Technology

2010-12-01

microextraction ( SPME ) • Accumulate freely-dissolved organic contaminants from surrounding water into a solid phase • Contaminant concentrations of the...based on SPME (pg/L) D i s s o l v e d C o n c e n t r a t i o n b a s e d o n M u s s e l s ( p g / L ) 4,4’-DDE 4,4’-DDD 4,4’-DDT 1:1 line

Deriving sediment Interstitial Water Remediation Goals ...

EPA Pesticide Factsheets

Background/Objectives. Passive sampling is becoming a frequently used measurement technique at Superfund sites with contaminated sediments. Passive sampling measures the concentrations of freely dissolved chemicals (Cfrees) in the sediment interstitial water. The freely dissolved chemical is a good surrogate for and a very practical means for estimating the concentrations of bioavailable chemical in the sediments. Building from this approach, a methodology is proposed to derive sediment Interstitial Water Remediation Goals (IWRGs) for the protection of benthic organisms from direct toxicity using Cfrees measured with passive sampling.Approach/Activities. In the early 2000s, EPA developed and released Equilibrium Partitioning Sediment Benchmarks (ESBs) for a series of chemicals. ESBs are intended to be chemical concentrations below which unacceptable toxicity to benthic organisms does not occur. The ESBs (expressed with the units of ug/g OC) were derived using the equations:ESB= K_OC×FCV where K_OC=0.00028+0.983K_OWThe KOC is the organic carbon normalized sediment-water chemical partition coefficient, FCV is the Final Chronic Value from EPA’s ambient water quality criteria for the protection of aquatic life, and KOW is the n-octanol/water partition coefficient for the chemical. At a specific site, the remedial goal (CS:ESB µg/kg-dw) in sediment are then derived using the site-specific fraction of organic carbon in the sediment (fOC:SS) at the site:C_

Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling*

PubMed Central

Larance, Mark; Kirkwood, Kathryn J.; Tinti, Michele; Brenes Murillo, Alejandro; Ferguson, Michael A. J.; Lamond, Angus I.

2016-01-01

We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754). PMID:27114452

Freely Drifting Swallow Float Array: August 1990 NATIVE 1 Experiment (First Deployment)

DTIC Science & Technology

1991-02-01

jump around record 1520, indicating that the apparent increase in float 2’s hydrophone sensitivity occurred only at the lower infra - sonic ...and d) the infrasonic acoustic data. The infrasonic data include the RMS levels of the pressure and the three components of parti- cle velocity for all...active intensity spectra. A description of the Swallow float infrasonic data acquisition system, along with calibration curves, is given in Appendix 1

The use of geographic information for fire management planning in Yosemite National Park

USGS Publications Warehouse

Van Wagtendonk, Jan W.; van Wagtendonk, Kent A.; Meyer, Joseph B.; Paintner, Kara J.

2002-01-01

Fire has played a critical role in the ecosystems of Yosemite National park for millennia. Before the advent of Euro-Americans, lightning fires and fires set by Native Americans burned freely across the landscape. These fires burned periodically, with the interval between fires dependent on the availability of ignition sources, adequate fuels, and weather conducive to burning. As a result, different vegetation types burned at different intervals.

Bisphenol A in Solid Waste Materials, Leachate Water, and Air Particles from Norwegian Waste-Handling Facilities: Presence and Partitioning Behavior.

PubMed

Morin, Nicolas; Arp, Hans Peter H; Hale, Sarah E

2015-07-07

The plastic additive bisphenol A (BPA) is commonly found in landfill leachate at levels exceeding acute toxicity benchmarks. To gain insight into the mechanisms controlling BPA emissions from waste and waste-handling facilities, a comprehensive field and laboratory campaign was conducted to quantify BPA in solid waste materials (glass, combustibles, vehicle fluff, waste electric and electronic equipment (WEEE), plastics, fly ash, bottom ash, and digestate), leachate water, and atmospheric dust from Norwegian sorting, incineration, and landfill facilities. Solid waste concentrations varied from below 0.002 mg/kg (fly ash) to 188 ± 125 mg/kg (plastics). A novel passive sampling method was developed to, for the first time, establish a set of waste-water partition coefficients, KD,waste, for BPA, and to quantify differences between total and freely dissolved concentrations in waste-facility leachate. Log-normalized KD,waste (L/kg) values were similar for all solid waste materials (from 2.4 to 3.1), excluding glass and metals, indicating BPA is readily leachable. Leachate concentrations were similar for landfills and WEEE/vehicle sorting facilities (from 0.7 to 200 μg/L) and dominated by the freely dissolved fraction, not bound to (plastic) colloids (agreeing with measured KD,waste values). Dust concentrations ranged from 2.3 to 50.7 mg/kgdust. Incineration appears to be an effective way to reduce BPA concentrations in solid waste, dust, and leachate.

Partitioning of fluoranthene between free and bound forms in stormwater runoff and other urban discharges using passive dosing.

PubMed

Birch, Heidi; Mayer, Philipp; Lützhøft, Hans-Christian Holten; Mikkelsen, Peter Steen

2012-11-15

Partitioning of fluoranthene in stormwater runoff and other urban discharges was measured by a new analytical method based on passive dosing. Samples were collected at the inlet (n = 11) and outlet (n = 8) from a stormwater retention pond in Albertslund (Denmark), and for comparison samples were also obtained at a municipal wastewater treatment plant, a power plant, a contaminated site and a waste deposit in Copenhagen (n = 1 at each site). The freely dissolved concentration of (14)C-fluoranthene in the samples was controlled by equilibrium partitioning from a pre-loaded polymer and the total sample concentration measured. The measurements yielded free fractions of fluoranthene in stormwater in the range 0.04-0.15 in the inlet during the first part of the runoff events increasing to 0.3-0.5 at the end of the events and in the outlet from the retention pond. The enhanced capacity of the different stormwater samples for carrying fluoranthene was 2-23 relative to pure water and decreasing during rain events. The enhanced capacity of stormwater showed a different relationship with suspended solid concentrations than the other types of urban discharges. Partitioning of fluoranthene to dissolved organic carbon was lower than partitioning to particulate organic carbon. Partitioning of fluoranthene to particulate organic matter in the 19 stormwater samples yielded a log K(POM) of 5.18. The presented results can be used in stormwater quality modeling and assessment of efficiency of stormwater treatment systems. This work also shows the potential of the passive dosing method to obtain conversion factors between total concentrations, which are needed for comparison with water quality criteria, and freely dissolved concentrations, which are more related to toxicity and obtained by the use of most passive samplers. Copyright © 2012 Elsevier Ltd. All rights reserved.

Effects of anthropogenic surfactants on the conversion of marine dissolved organic carbon and microgels.

PubMed

Shiu, Ruei-Feng; Lee, Chon-Lin

2017-04-15

The possible impact of three types of anthropogenic surfactants on the ability of marine dissolved organic carbon (DOC) to form self-assembled microgels was evaluated. The behavior of existing native microgels was also examined in the presence of surfactants. These results reveal that the release of surfactants even at low concentrations into the aquatic environment could effectively hinder the self-assembly of DOC polymers. The extent of the size reduction had the following order: anionic, cationic, and non-ionic. Furthermore, charged surfactants can disrupt existing native microgels, converting large assemblies into smaller particles. One possible mechanisms is that surfactants are able to enhance the stability of DOC polymers and disrupt aggregates due to their surface charges and protein-denaturing activities. These findings suggest that the ecological system is altered by anthropogenic surfactants, and provide useful information for ecological assessments of different types of surfactants and raise warnings about surfactant applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Native species behaviour mitigates the impact of habitat-forming invasive seaweed.

PubMed

Wright, Jeffrey T; Byers, James E; Koukoumaftsis, Loni P; Ralph, Peter J; Gribben, Paul E

2010-06-01

Habitat-forming invasive species cause large, novel changes to the abiotic environment. These changes may elicit important behavioural responses in native fauna, yet little is known about mechanisms driving this behaviour and how such trait-mediated responses influence the fitness of native species. Low dissolved oxygen is a key abiotic change created by the habitat-forming invasive seaweed, Caulerpa taxifolia, which influences an important behavioural response (burrowing depth) in the native infaunal bivalve Anadara trapezia. In Caulerpa-colonised areas, Anadara often emerged completely from the sediment, and we experimentally demonstrate that water column hypoxia beneath the Caulerpa canopy is the mechanism instigating this "pop-up" behaviour. Importantly, pop-up in Caulerpa allowed similar survivorship to that in unvegetated sediment; however, when we prevented Anadara from popping-up, they suffered >50% mortality in just 1 month. Our findings not only highlight the substantial environmental alteration by Caulerpa, but also an important role for the behaviour of native species in mitigating the effects of habitat-forming invasive species.

Using polyacrylate-coated SPME fibers to quantify sorption of polar and ionic organic contaminants to dissolved organic carbon.

PubMed

Haftka, Joris J-H; Scherpenisse, Peter; Jonker, Michiel T O; Hermens, Joop L M

2013-05-07

A passive sampling method using polyacrylate-coated solid-phase microextraction (SPME) fibers was applied to determine sorption of polar and ionic organic contaminants to dissolved organic carbon (DOC). The tested contaminants included pharmaceuticals, industrial chemicals, hormones, and pesticides and represented neutral, anionic, and cationic structures. Prior to the passive sampler application, sorption of the chemicals to the fibers was characterized. This was needed in order to accurately translate concentrations measured in fibers to freely dissolved aqueous concentrations during the sorption tests with DOC. Sorption isotherms of neutral compounds to the fiber were linear, whereas isotherms of basic chemicals covered a nonlinear and a linear range. Sorption of acidic and basic compounds to the fiber was pH-dependent and was dominated by sorption of the neutral sorbate species. Fiber- and DOC-water partition coefficients of neutral compounds were both linearly related to octanol-water partition coefficients (log Kow). The results of this study show that polyacrylate fibers can be used to quantify sorption to DOC of neutral and ionic contaminants, having multiple functional groups and spanning a wide hydrophobicity range (log Kow = 2.5-7.5).

Heavy metal immobilization via microbially induced carbonate precipitation and co-precipitation

NASA Astrophysics Data System (ADS)

Lauchnor, E. G.; Stoick, E.

2017-12-01

Microbially induced CaCO3 precipitation (MICP) has been successfully used in applications such as porous media consolidation and sealing of leakage pathways in the subsurface, and it has the potential to be used for remediation of metal and radionuclide contaminants in surface and groundwater. In this work, MICP is investigated for removal of dissolved heavy metals from contaminated mine discharge water via co-precipitation in CaCO3 or formation of other metal carbonates. The bacterially catalyzed hydrolysis of urea produces inorganic carbon and ammonium and increases pH and the saturation index of carbonate minerals to promote precipitation of CaCO3. Other heavy metal cations can be co-precipitated in CaCO3 as impurities or by replacing Ca2+ in the crystal lattice. We performed laboratory batch experiments of MICP in alkaline mine drainage sampled from an abandoned mine site in Montana and containing a mixture of heavy metals at near neutral pH. Both a model bacterium, Sporosarcina pasteurii, and a ureolytic bacterium isolated from sediments on the mine site were used to promote MICP. Removal of dissolved metals from the aqueous phase was determined via inductively coupled plasma mass spectrometry and resulting precipitates were analyzed via electron microscopy and energy dispersive x-ray spectroscopy (EDX). Both S. pasteurii and the native ureolytic isolate demonstrated ureolysis, increased the pH and promoted precipitation of CaCO3 in batch tests. MICP by the native bacterium reduced concentrations of the heavy metals zinc, copper, cadmium, nickel and manganese in the water. S. pasteurii was also able to promote MICP, but with less removal of dissolved metals. Analysis of precipitates revealed calcium carbonate and phosphate minerals were likely present. The native isolate is undergoing identification via 16S DNA sequencing. Ongoing work will evaluate biofilm formation and MICP by the isolate in continuous flow, gravel-filled laboratory columns. This research demonstrates that MICP can be promoted in natural, contaminated water containing a mixture of potentially toxic heavy metals and native bacteria adapted to the environment may be more successful in driving removal of heavy metals via MICP.

PAH toxicity at aqueous solubility in the fish embryo test with Danio rerio using passive dosing.

PubMed

Seiler, Thomas-Benjamin; Best, Nina; Fernqvist, Margit Møller; Hercht, Hendrik; Smith, Kilian E C; Braunbeck, Thomas; Mayer, Philipp; Hollert, Henner

2014-10-01

As part of the risk assessment process within REACh, prior to manufacturing and distribution of chemical substances their (eco)toxicological impacts have to be investigated. The fish embryo toxicity test (FET) with the zebrafish Danio rerio has gained a high significance as an in vitro alternative to animal testing in (eco)toxicology. However, for hydrophobic organic chemicals it remains a technical challenge to ensure constant freely dissolved concentration at the maximum exposure level during such biotests. Passive dosing with PDMS silicone was thus applied to control the freely dissolved concentration of ten PAHs at their saturation level in the FET. The experiments gave repeatable results, with the toxicity of the PAHs generally increasing with the maximum chemical activities of the PAHs. HPLC analysis confirmed constant exposure at the saturation level. In additional experiments, fish embryos without direct contact to the silicone surface showed similar mortalities as those exposed with direct contact to the silicone. Silicone oil overlaying the water phase as a novel passive dosing phase had no observable effects on the development of the fish embryos until hatching. This study provides further data to support the close relationship between the chemical activity and the toxicity of hydrophobic organic compounds. Passive dosing from PDMS silicone enabled reliable toxicity testing of (highly) hydrophobic substances at aqueous solubility, providing a practical way to control toxicity exactly at the maximum exposure level. This approach is therefore expected to be useful as a cost-effective initial screening of hydrophobic chemicals for potential adverse effects to freshwater vertebrates. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fate of polychlorinated biphenyls in a contaminated lake ecosystem: combining equilibrium passive sampling of sediment and water with total concentration measurements of biota.

PubMed

Mäenpää, Kimmo; Leppänen, Matti T; Figueiredo, Kaisa; Mayer, Philipp; Gilbert, Dorothea; Jahnke, Annika; Gil-Allué, Carmen; Akkanen, Jarkko; Nybom, Inna; Herve, Sirpa

2015-11-01

Equilibrium sampling devices can be applied to study and monitor the exposure and fate of hydrophobic organic chemicals on a thermodynamic basis. They can be used to determine freely dissolved concentrations and chemical activity ratios and to predict equilibrium partitioning concentrations of hydrophobic organic chemicals in biota lipids. The authors' aim was to assess the equilibrium status of polychlorinated biphenyls (PCBs) in a contaminated lake ecosystem and along its discharge course using equilibrium sampling devices for measurements in sediment and water and by also analyzing biota. The authors used equilibrium sampling devices (silicone rubber and polyethylene [PE]) to determine freely dissolved concentrations and chemical activities of PCBs in the water column and sediment porewater and calculated for both phases the corresponding equilibrium concentrations and chemical activities in model lipids. Overall, the studied ecosystem appeared to be in disequilibrium for the studied phases: sediment, water, and biota. Chemical activities of PCBs were higher in sediment than in water, which implies that the sediment functioned as a partitioning source of PCBs and that net diffusion occurred from the sediment to the water column. Measured lipid-normalized PCB concentrations in biota were generally below equilibrium lipid concentrations relative to the sediment (CLip ⇌Sed ) or water (CLip ⇌W ), indicating that PCB levels in the organisms were below the maximum partitioning levels. The present study shows the application versatility of equilibrium sampling devices in the field and facilitates a thermodynamic understanding of exposure and fate of PCBs in a contaminated lake and its discharge course. © 2015 SETAC.

Microbial and geochemical investigations of dissolved organic carbon and microbial ecology of native waters from the Biscayne and Upper Floridan Aquifers

USGS Publications Warehouse

Lisle, John T.; Harvey, Ron W.; Aiken, George R.; Metge, David W.

2010-01-01

Groundwater resources in the United States are under ever-increasing demands for potable, irrigation, and recreational uses. Additionally, aquifer systems are being used or targeted for use as storage areas for treated surface waters and (or) groundwaters via injection (for example, aquifer storage and recovery). To date, the influence that the nutrients, including carbon, in the injected water have on native microbial communities and the biogeochemistry in the subsurface zones used for storage of the injectate has not been determined. In this report, we describe a series of experiments that establishes a baseline dataset for the quantity and quality of organic and inorganic carbon and nutrients in the Biscayne Aquifer (BA) and Upper Floridan Aquifer (UFA) in south Florida. The most significant differences between the BA (26 meters below surface) and UFA (366 meters below surface) are the average specific conductance (0.552 and 6.12 microsiemens per centimeter, respectively), dissolved oxygen (1.6 and 0 milligrams per liter, respectively), and oxidation-reduction potential (40.3 and -358 millivolts, respectively). The dissolved organic carbon from the BA is characterized by carbon originating from terrestrial sources and microbial activities, while the UFA has a distinctive microbial signature. Acetate and lactate are the dominant carbon constituents in both aquifers. Additionally, components of the dissolved organic carbon from the UFA have a total trihalomethane-formation potential that is approximately threefold greater than the maximum contaminat level of 80 micrograms per liter established by the U.S. Environmental Protection Agency. The average native bacterial abundances in the aquifers are similar with 4.69x10^4 cells per milliliter in the BA and 1.33x10^4 cells per milliliter in the UFA. The average bacteriophage abundances are also similar with 1.15x10^5 virus-like particles in the BA and 1.92x10^5 virus-like particles in the UFA. Interestingly, ciliated protozoa are present in both aquifers. The average abundance of ciliates in the BA (2.97x10^3 ciliates per milliliter) is approximately twentyfold greater than abundances in the UFA (1.39x10^2 ciliates per milliliter). Collectively, these data indicate that microbial processes are the dominant contributor to the cycling of carbon and inorganic carbon in the BA and may be the only carbon cycling process in the UFA, as this aquifer has not had a terrestrial influx of carbon for more than 15,000 years. The rates of carbon, in the form of acetate, utilization by the native microbial communities are significantly different between the two aquifers. Based on data from 14C-acetate-utilization experiments, the microbial communities in the BA turn over the native acetate in 2.5 years, whereas communities in the UFA turn over native acetate in 6.8 years. These data support the hypothesis derived from the microbial-abundance data, in that the carbon for bacterial maintainence and growth is recycled from bacterial biomass released during cell lysis, especially in the UFA. An in situ diffusion chamber was designed to retain bacterial cells within the chamber while allowing native water constituents to move through the chamber. A series of 1-week deployments of chambers filled with fluorescent beads, inactivated native bacteria and laboratory grown and viable bacteria into the UFA, permitted by the State of Florida Environmental Protection Agency, was successfully completed. This was the first time this type of deployment into an aquifer system that is used for potable water supply has been permitted within the United States. This technology will allow, for the first time, in situ studies on the survival of microbial indicators of fecal pollution and true pathogens in groundwater systems.

Alkaline phosphatase activity of water column fractions and seagrass in a tropical carbonate estuary, Florida Bay

NASA Astrophysics Data System (ADS)

Koch, Marguerite S.; Kletou, Demetris C.; Tursi, Rosanna

2009-08-01

Few phosphorus-depleted coastal ecosystems have been examined for their ability to hydrolyze phosphomonoesters. We examined seasonal (August 2006-April 2007) alkaline phosphatase activity in Florida Bay, a phosphorus-limited shallow estuary, using fluorescent substrate at low concentrations (≤2.0 μM). In situ dissolved inorganic and organic phosphorus levels and phosphomonoester concentrations were also determined. Water column alkaline phosphatase activity was partitioned into two particulate size fractions (>1.2 and 0.2-1.2 μm) and freely dissolved enzymes (<0.2 μm). Water column alkaline phosphatase activity was also compared to leaf and epiphyte activity of the dominant tropical seagrass Thalassia testudinum. Our results indicate: (1) potential alkaline phosphatase activity in Florida Bay is high compared to other marine ecosystems, resulting in rapid phosphomonoester turnover times (˜2 h). (2) Water column alkaline phosphatase activity dominates, and is split equally between particulate and dissolved fractions. (3) Alkaline phosphatase activity was highest during cyanobacterial blooms, but not when normalized to chl a. These results suggest that dissolved, heterotrophic and autotrophic alkaline phosphatase activity is stimulated by phytoplankton blooms. (4) The dissolved alkaline phosphatase activity is relatively constant, while the particulate activity is seasonally and spatially dynamic, typically associated with phytoplankton blooms. (5) Phosphomonoester concentrations throughout the bay are low, even though potential hydrolysis rates are high. We propose that bioavailable dissolved organic P is hydrolyzed by dissolved and microbial alkaline phosphatase enzymes in Florida Bay. High alkaline phosphatase activity in the bay is also promoted by long hydraulic residence times. This background activity is primarily driven by carbon and phosphorus limitation of microorganisms, and regeneration of enzymes associated with cell lysis. Pulses of inorganic phosphorus and labile organic phosphorus and nitrogen may stimulate autotrophs, particularly cyanobacteria, which in turn promote biological activity that increase alkaline phosphatase activity of both autotrophs and heterotrophs in the bay.

Chemical analyses of elutriates, native water, and bottom material from the Chetco, Rogue, and Columbia rivers in western Oregon

USGS Publications Warehouse

Fuhrer, Gregory J.

1984-01-01

Chemical analyses of elutriates, bottom sediment, and water samples for selected metals, nutrients and organic compounds including insecticides, herbicides, and acid/neutral extractables have been made to provide data to determine short-term water-quality conditions associated with dredging operations in rivers and estuaries. Between April and August 1982, data were collected from the Chetco and Rogue River estuaries in southwestern Oregon, and from the mouth of the Columbia River in the northwestern Oregon to Cathlamet Bay, 18.2 miles upstream. In an elutriation test, bottom materials from a potential dredge site are mixed with native water - collected from either a dredge or disposal site - and the liquid portion of the mixture is removed, filtered, and chemically analyzed. Presented in this report are chemical and physical analyses of elutriates, native water, and bottom material for selected metals, ammonia, organic carbon, pesticides, particle size, and gas chromatographic/mass spectrometric semi-quantitative organic scans. Elutriate and bottom-material samples were screened specifically for phenolic compounds, particularly the chlorinated phenols; phenol was the only compound identified. Elutriate-test results showed variability for selected trace-metal concentrations of dissolved chemicals as follows: in micrograms per liter, arsenic ranged from < 1 to 15, cadmium from 1 to 210, copper from < 1 to 13, chromium from < 1 to 5, and nickel from 2 to 18. Results of computations to determine the amount of a constituent associated with bottom material and interstitial water and subsequently released (dissolved) into the elutriate-test native-mixing water are presented for selected trace metals. The highest elutriate-test release was 35 percent for manganese; the second highest, 5 percent for cadmium. All other computed releases were less than or equal to 1 percent. (USGS)

Effects of quantity, quality, and contact time of dissolved organic matter on bioconcentration of benzo[a]pyrene in the nematode Caenorhabditis elegans

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

Haitzer, M.; Hoess, S.; Burnison, B.K.

1999-03-01

Quantity and quality of dissolved organic matter (DOM) and the time allowed for DOM to interact with organic contaminants can influence their bioavailability. The authors studied the effect of natural aquatic DOM that had been in contact with benzo[a]pyrene (B[a]P) for 1 to 12 d on the bioconcentration of B[a]P in the nematode Caenorhabditis elegans. Dissolved organic matter quality and quantity was varied by using DOM from three different sources, each in three different concentrations. A model, based on the assumption that only freely dissolved B[a]P is bioavailable, was employed to estimate biologically determined partition coefficients [K{sub p}(biol.)]. Expressing themore » data for each combination of DOM source and contact time in a single K{sub p} (biol.) value allowed a direct comparison of the effects of different DOM qualities and contact times. The results show that the effect of DOM from a specific source was dependent on DOM quantity, but they also observed a distinct effect of DOM quality (represented by different sampling locations) on the bioconcentration of B[a]P. Contact time had no significant influence for the effects of two DOM sources on the bioconcentration of B[a]P. However, the third DOM source was significantly more effective with increased contact time, leading to lower B[a]P bioconcentration in the nematodes.« less

Extraction of an urease-active organo-complex from soil.

NASA Technical Reports Server (NTRS)

Burns, R. G.; El-Sayed, M. H.; Mclaren, A. D.

1972-01-01

Description of an extraction from a Dublin clay loam soil of a colloidal organic matter complex that is urease active and, by X-ray analysis, free of clays. Urease activity in the clay-free precipitates, as in the soil, was not destroyed by the activity of an added proteolytic enzyme, pronase. This is attributed to the circumstance that native soil urease resides in organic colloidal particles with pores large enough for water, urea, ammonia, and carbon dioxide to pass freely, but nevertheless small enough to exclude pronase.

Passive sampling methods for contaminated sediments: Risk assessment and management

PubMed Central

Greenberg, Marc S; Chapman, Peter M; Allan, Ian J; Anderson, Kim A; Apitz, Sabine E; Beegan, Chris; Bridges, Todd S; Brown, Steve S; Cargill, John G; McCulloch, Megan C; Menzie, Charles A; Shine, James P; Parkerton, Thomas F

2014-01-01

This paper details how activity-based passive sampling methods (PSMs), which provide information on bioavailability in terms of freely dissolved contaminant concentrations (Cfree), can be used to better inform risk management decision making at multiple points in the process of assessing and managing contaminated sediment sites. PSMs can increase certainty in site investigation and management, because Cfree is a better predictor of bioavailability than total bulk sediment concentration (Ctotal) for 4 key endpoints included in conceptual site models (benthic organism toxicity, bioaccumulation, sediment flux, and water column exposures). The use of passive sampling devices (PSDs) presents challenges with respect to representative sampling for estimating average concentrations and other metrics relevant for exposure and risk assessment. These challenges can be addressed by designing studies that account for sources of variation associated with PSMs and considering appropriate spatial scales to meet study objectives. Possible applications of PSMs include: quantifying spatial and temporal trends in bioavailable contaminants, identifying and evaluating contaminant source contributions, calibrating site-specific models, and, improving weight-of-evidence based decision frameworks. PSM data can be used to assist in delineating sediment management zones based on likelihood of exposure effects, monitor remedy effectiveness, and, evaluate risk reduction after sediment treatment, disposal, or beneficial reuse after management actions. Examples are provided illustrating why PSMs and freely dissolved contaminant concentrations (Cfree) should be incorporated into contaminated sediment investigations and study designs to better focus on and understand contaminant bioavailability, more accurately estimate exposure to sediment-associated contaminants, and better inform risk management decisions. Research and communication needs for encouraging broader use are discussed. Integr Environ Assess Manag 2014;10:224–236. © 2014 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of SETAC. PMID:24343931

Role of fluoranthene and pyrene associated with suspended particles in their bioaccumulation by zebrafish (Danio rerio).

PubMed

Zhai, Yawei; Xia, Xinghui; Xiong, Xinyue; Xia, Lingzi; Guo, Xuejun; Gan, Jay

2018-08-15

Hydrophobic organic compounds (HOCs) tend to be associated with suspended particles in surface aquatic systems, however, the bioavailability of HOCs on suspended particles to fish is not well understood. In this study, a passive dosing device was used to control the freely dissolved concentrations (C free ) of polycyclic aromatic hydrocarbons (PAHs) including fluoranthene and pyrene, and the influence of particle-associated PAHs on their bioaccumulation by zebrafish was investigated. The results showed that, when the C free of PAHs were kept constant, the presence of suspended particles did not significantly affect the steady state of PAH bioaccumulation in zebrafish tissues excluding head and digestive tracts, suggesting that the bioaccumulation steady state was controlled by the freely dissolved concentrations of PAHs. However, suspended particles promoted the uptake and elimination rate constants of PAHs in zebrafish body excluding head and digestive tracts. The uptake rate constants with 0.5 g/L suspended particles were approximately twice of those without suspended particles, and the body burden in zebrafish increased by 16.4% - 109.3% for pyrene and 21.8% - 490.4% for fluoranthene during the first 8-d exposure. This was due to the reasons that suspended particles could be ingested, and part of PAHs associated with them could be desorbed in digestive tract and absorbed by the zebfrafish, leading to the enhancement of uptake rates of PAHs in zebfrafish. The findings obtained from this study indicate that PAHs on suspended particles are partly bioavailable to zebrafish and particle ingestion is an important route in PAH bioaccumulation. Therefore, it is important to consider the bioavailability of HOCs on suspended particles to improve ecological risk assessment. Copyright © 2018 Elsevier Inc. All rights reserved.

Gaseous and Freely-Dissolved PCBs in the Lower Great Lakes Based on Passive Sampling: Spatial Trends and Air-Water Exchange.

PubMed

Liu, Ying; Wang, Siyao; McDonough, Carrie A; Khairy, Mohammed; Muir, Derek C G; Helm, Paul A; Lohmann, Rainer

2016-05-17

Polyethylene passive sampling was performed to quantify gaseous and freely dissolved polychlorinated biphenyls (PCBs) in the air and water of Lakes Erie and Ontario during 2011-2012. In view of differing physical characteristics and the impacts of historical contamination by PCBs within these lakes, spatial variation of PCB concentrations and air-water exchange across these lakes may be expected. Both lakes displayed statistically similar aqueous and atmospheric PCB concentrations. Total aqueous concentrations of 29 PCBs ranged from 1.5 pg L(-1) in the open lake of Lake Erie (site E02) in 2011 spring to 105 pg L(-1) in Niagara (site On05) in 2012 summer, while total atmospheric concentrations were 7.7-634 pg m(-3) across both lakes. A west-to-east gradient was observed for aqueous PCBs in Lake Erie. River discharge and localized influences (e.g., sediment resuspension and regional alongshore transport) likely dominated spatial trends of aqueous PCBs in both lakes. Air-water exchange fluxes of Σ7PCBs ranged from -2.4 (±1.9) ng m(-2) day(-1) (deposition) in Sheffield (site E03) to 9.0 (±3.1) ng m(-2) day(-1) (volatilization) in Niagara (site On05). Net volatilization of PCBs was the primary trend across most sites and periods. Almost half of variation in air-water exchange fluxes was attributed to the difference in aqueous concentrations of PCBs. Uncertainty analysis in fugacity ratios and mass fluxes in air-water exchange of PCBs indicated that PCBs have reached or approached equilibrium only at the eastern Lake Erie and along the Canadian shore of Lake Ontario sites, where air-water exchange fluxes dominated atmospheric concentrations.

Concentration/time-dependent dissipation, partitioning and plant accumulation of hazardous current-used pesticides and 2-hydroxyatrazine in sand and soil.

PubMed

Neuwirthová, Natália; Bílková, Zuzana; Vašíčková, Jana; Hofman, Jakub; Bielská, Lucie

2018-07-01

The dissipation, partitioning dynamics and biouptake was measured for selected hazardous current-used pesticides (conazole fungicides: epoxiconazole, flusilazole, tebuconazole; prochloraz, chlorpyrifos, pendimethalin) and for a transformation product (2-hydroxyatrazine) in agricultural soil and quartz sand as representatives of a real and a worst-case scenario. Dissipation, uptake to Lactuca sativa and the freely dissolved concentration along with the organic carbon-normalized sorption coefficients (K oc ) were determined on days 12, 40, and 90 following the application of compounds at three fortification levels (0.1-1.0-10 mg/kg). Conazole fungicides showed similar dissipation patterns and were more persistent in soil than prochloraz, chlorpyrifos and pendimethalin. 2-Hydroxyatrazine showed a concentration-depended decrease in persistency in soil. Lettuce roots were shown to accumulate higher amounts than shoots where the extent of root uptake was driven by compound partitioning. This was evidenced by the ability of freely dissolved concentration (C free ) to reliably (r 2  = 0.94) predict root uptake. Concentration in leaves did not exceed the maximum residue levels (MRLs) for lettuce, which was likely given by the low root-to-shoot translocation factors (TFs) of the tested compounds varying between 0.007 and 0.14. K oc values were in the range of literature values. Sorption to soil was higher than to sand for all compounds, yet following the K oc dynamics compounds did not appear to be sequestered in soil with increasing residence time. From these results, it follows that the tested compounds may persist in soil but since they did not accumulate in lettuce above MRLs, contamination of the food web is unlikely. Copyright © 2018 Elsevier Ltd. All rights reserved.

Passive sampling methods for contaminated sediments: State of the science for organic contaminants

PubMed Central

Lydy, Michael J; Landrum, Peter F; Oen, Amy MP; Allinson, Mayumi; Smedes, Foppe; Harwood, Amanda D; Li, Huizhen; Maruya, Keith A; Liu, Jingfu

2014-01-01

This manuscript surveys the literature on passive sampler methods (PSMs) used in contaminated sediments to assess the chemical activity of organic contaminants. The chemical activity in turn dictates the reactivity and bioavailability of contaminants in sediment. Approaches to measure specific binding of compounds to sediment components, for example, amorphous carbon or specific types of reduced carbon, and the associated partition coefficients are difficult to determine, particularly for native sediment. Thus, the development of PSMs that represent the chemical activity of complex compound–sediment interactions, expressed as the freely dissolved contaminant concentration in porewater (Cfree), offer a better proxy for endpoints of concern, such as reactivity, bioaccumulation, and toxicity. Passive sampling methods have estimated Cfree using both kinetic and equilibrium operating modes and used various polymers as the sorbing phase, for example, polydimethylsiloxane, polyethylene, and polyoxymethylene in various configurations, such as sheets, coated fibers, or vials containing thin films. These PSMs have been applied in laboratory exposures and field deployments covering a variety of spatial and temporal scales. A wide range of calibration conditions exist in the literature to estimate Cfree, but consensus values have not been established. The most critical criteria are the partition coefficient between water and the polymer phase and the equilibrium status of the sampler. In addition, the PSM must not appreciably deplete Cfree in the porewater. Some of the future challenges include establishing a standard approach for PSM measurements, correcting for nonequilibrium conditions, establishing guidance for selection and implementation of PSMs, and translating and applying data collected by PSMs. Integr Environ Assess Manag 2014;10:167–178. © 2014 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of SETAC. PMID:24307344

Environmental setting of benchmark streams in agricultural areas of eastern Wisconsin

USGS Publications Warehouse

Rheaume, S.J.; Stewart, J.S.; Lenz, B.N.

1996-01-01

Differences in land use/land cover, and riparian vegetation and instream habitat characteristics are presented. Summaries of field measurements of water temperature, pH, specific conductance and concentrations of dissolved oxygen, total organic plus ammonia nitrogen, dissolved ammonium, nitrate plus nitrte as nitrogen, total phosphorus, dissolved orthophosphate, and atrazine are listed. Concentrations of dissolved oxygen for the sampled streams ranged from 6 A to 14.3 and met the standards set by the Wisconsin Department of Natural Resources (WDNR) for supporting fish and aquatic life. Specific conductance ranged from 98 to 753 u,Scm with values highest in RHU's 1 and 3, where streams are underlain by carbonate bedrock. Median pH did not vary greatly among the four RHU's and ranged from 6.7 to 8.8 also meeting the WDNR standards. Concentrations of total organic plus ammonia nitrogen, dissolved ammonium, total phosphorus, and dissolved orthophosphate show little variation between streams and are generally low, compared to concentrations measured in agriculturally-affected streams in the same RHU's during the same sampling period. Concentrations of the most commonly used pesticide in the study unit, atrazine, were low in all streams, and most concentrations were below trn 0.1 u,g/L detection limit. Riparian vegetation for the benchmark streams were characterized by lowland species of the native plant communities described by John T. Curtis in the "Vegetation of Wisconsin." Based on the environmental setting and water-quality information collected to date, these streams appear to show minimal adverse effects from human activity.

Shifts in vegetation affect organic carbon quality in a coastal marsh along the Hudson River Estuary

NASA Astrophysics Data System (ADS)

Zhang, A. H.; Corbett, J. E.; Tfaily, M. M.; Martin, I.; Ho, L.; Sun, E.; Sevilla, L.; Vincent, S.; Newton, R.; Peteet, D. M.

2015-12-01

To better understand carbon storage in coastal salt marshes, samples were collected from Piermont Marsh, NY (40 ̊00' N, 73 ̊55'W) located within the Hudson River Estuary. Porewater from three different vegetation sites was analyzed to compare the quality of the dissolved organic carbon. Sites contained either native or invasive vegetation with variations in live plant root depth. Porewater was taken from 0-3m in 50cm intervals, and sites were dominated either by invasive Phragmites australis, native Eleocharis , or native mixed vegetation (Spartina patens, Scirpus, and Typha angustifolia). Sites dominated by invasive Phragmites australis were found to have lower dissolved organic carbon (DOC) concentrations, lower cDOM absorption values, and more labile organic carbon compounds. The molecular composition of the DOC was determined with Fourier Transform Ion Cyclotron Mass Spectrometry (FT-ICR-MS). Labile DOC components were defined as proteins, carbohydrates, and amino sugars while recalcitrant DOC components were defined as lipids, unsaturated hydrocarbons, lignins, tannins, and condensed hydrocarbons. For the Phragmites, Eleocharis, and mixed vegetation sites, average DOC concentrations with depth were found to be 1.71 ± 1.06, 4.64 ± 1.73, and 4.62 ± 3.5 (mM), respectively and cDOM absorption values with depth were found to be 13.22 ± 4.81, 49.42 ± 10.8, and 35.74 ± 17.49 (m-1). Additionally, DOC concentrations increased with depth in the mixed vegetation and Eleocharis sites, but remained relatively constant in the Phragmites site. The percent of labile compounds in the surface samples were found to be 19.02, 14.64, and 14.07% for the Phragmites, Eleocharis, and mixed vegetation sites, respectively. These findings suggest that sites dominated by Phragmites may have more reactive DOC substrates than sites dominated by native vegetation. These results indicate that the carbon storage in marshes invaded by Phragmites would be expected to decrease over time.

The challenges and opportunities in medical education for digital 'natives' and 'immigrants' in Scotland and abroad.

PubMed

de Wet, Carl; Yelland, Michael

2015-11-01

Although the digital revolution only started towards the end of the twentieth century, it has already dramatically shifted our world away from traditional industries and ushered in a new age of information. Virtually every aspect of our modern lives has either been transformed or challenged, including medical education. This article describes three of the important factors that are causing seismic changes in medical education in Scotland and abroad. The first is the new generation of 'digital natives' that are arriving in medical schools. In response, faculty members have had to become 'digital immigrants' and adapt their pedagogies. Second, the rise of social media has allowed the creation of virtual learning environments and communities that augment but also compete with traditional brick-and-mortar institutions. Finally, an ever-increasing range of e-learning resources promise freely accessible and up-to-date evidence, but their sheer volume and lack of standardisation will require careful curation. © The Author(s) 2015.

Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration.

PubMed

Ward, Collin P; Nalven, Sarah G; Crump, Byron C; Kling, George W; Cory, Rose M

2017-10-03

In sunlit waters, photochemical alteration of dissolved organic carbon (DOC) impacts the microbial respiration of DOC to CO 2 . This coupled photochemical and biological degradation of DOC is especially critical for carbon budgets in the Arctic, where thawing permafrost soils increase opportunities for DOC oxidation to CO 2 in surface waters, thereby reinforcing global warming. Here we show how and why sunlight exposure impacts microbial respiration of DOC draining permafrost soils. Sunlight significantly increases or decreases microbial respiration of DOC depending on whether photo-alteration produces or removes molecules that native microbial communities used prior to light exposure. Using high-resolution chemical and microbial approaches, we show that rates of DOC processing by microbes are likely governed by a combination of the abundance and lability of DOC exported from land to water and produced by photochemical processes, and the capacity and timescale that microbial communities have to adapt to metabolize photo-altered DOC.The role of dissolved organic carbon (DOC) photo-alteration in the microbial respiration of DOC to CO 2 is unclear. Here, the authors show that the impact of this mechanism depends on whether photo-alteration of DOC produces or removes molecules used by native microbial communities prior to light exposure.

The concentration and changes in freely dissolved polycyclic aromatic hydrocarbons in biochar-amended soil.

PubMed

Oleszczuk, Patryk; Kuśmierz, Marcin; Godlewska, Paulina; Kraska, Piotr; Pałys, Edward

2016-07-01

The presence of polycyclic aromatic hydrocarbons (PAHs) in biochars hinders their environmental use. The aim of this study was to determine the freely dissolved (Cfree) PAH content in soil amended with biochar in a long-term (851 days) field experiment. Biochar was added to the soil at a rate of 30 and 45 t/ha. The addition of biochar to the soil resulted in a decrease in Σ13 Cfree PAHs by 25 and 22%, in the soil with the addition of biochar at the rate of 30 and 45 t/ha, respectively. As far as individual PAHs are concerned, in most cases a reduction in Cfree was also observed (from 3.6 to 66%, depending on the biochar rate). During the first 105 days of the experiment, the content of Σ13 Cfree in the biochar-amended soil significantly decreased by 26% (30 t/ha) and 36% (45 t/ha). After this period of time until the end of the experiment, no significant changes in Cfree were observed, regardless of the biochar rate. However, the behavior of individual PAH groups differed depending on the number of rings and experimental treatment. Ultimately, after 851 days of the experiment the content of Σ13 Cfree PAHs was lower by 29% (30 t/ha) and 35% (45 t/ha) compared to the beginning of the study as well as lower by 40% (30 t/ha) and 42% (45 t/ha) than in the control soil. The log KTOC coefficients calculated for the biochar-amended soils were higher immediately after adding biochar and subsequently they gradually decreased, indicating the reduced strength of the interaction between biochar and the studied PAHs. The obtained results show that the addition of biochar to soil does not create a risk in terms of the content of Cfree PAHs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Controlling Styrene Maleic Acid Lipid Particles through RAFT.

PubMed

Smith, Anton A A; Autzen, Henriette E; Laursen, Tomas; Wu, Vincent; Yen, Max; Hall, Aaron; Hansen, Scott D; Cheng, Yifan; Xu, Ting

2017-11-13

The ability of styrene maleic acid copolymers to dissolve lipid membranes into nanosized lipid particles is a facile method of obtaining membrane proteins in solubilized lipid discs while conserving part of their native lipid environment. While the currently used copolymers can readily extract membrane proteins in native nanodiscs, their highly disperse composition is likely to influence the dispersity of the discs as well as the extraction efficiency. In this study, reversible addition-fragmentation chain transfer was used to control the polymer architecture and dispersity of molecular weights with a high-precision. Based on Monte Carlo simulations of the polymerizations, the monomer composition was predicted and allowed a structure-function analysis of the polymer architecture, in relation to their ability to assemble into lipid nanoparticles. We show that a higher degree of control of the polymer architecture generates more homogeneous samples. We hypothesize that low dispersity copolymers, with control of polymer architecture are an ideal framework for the rational design of polymers for customized isolation and characterization of integral membrane proteins in native lipid bilayer systems.

Testing of various membranes for use in a novel sediment porewater isolation chamber for infaunal invertebrate exposure to PCBs.

PubMed

Coleman, Jessica G; Lotufo, Guilherme R; Kennedy, Alan J; Poda, Aimee R; Rushing, Todd S; Ruiz, Carlos E; Bridges, Todd S

2014-07-01

In benthic sediment bioassays, determining the relative contribution to exposure by contaminants in overlying water, porewater, and sediment particles is technically challenging. The purpose of the present study was to assess the potential for membranes to be utilized as a mechanism to allow freely dissolved hydrophobic organic contaminants into a pathway isolation exposure chamber (PIC) while excluding all sediment particles and dissolved organic carbon (DOC). This investigation was conducted in support of a larger effort to assess contaminant exposure pathways to benthos. While multiple passive samplers exist for estimating concentrations of contaminants in porewater such as those using solid-phase micro extraction (SPME) and polyoxymethylene (POM), techniques to effectively isolate whole organism exposure to porewater within a sediment system are not available. We tested the use of four membranes of different pore sizes (0.1-1.2μm) including nylon, polycarbonate, polyethylsulfone, and polytetrafluoroethylene with a hydrophilic coating. Exposures included both diffusion of radiolabeled and non-labeled contaminants across membranes from aqueous, sediment slurry, and whole sediment sources to assess and evaluate the best candidate membrane. Data generated from the present study was utilized to select the most suitable membrane for use in the larger bioavailability project which sought to assess the relevance of functional ecology in bioavailability of contaminated sediments at remediation sites. The polytetrafluoroethylene membrane was selected for use in the PIC, although exclusion of dissolved organic carbon was not achieved. Published by Elsevier Ltd.

Cannabinoids reduce cAMP levels in the striatum of freely moving rats: an in vivo microdialysis study.

PubMed

Wade, Mark R; Tzavara, Eleni T; Nomikos, George G

2004-04-16

The cannabinoid receptor subtype 1 (CB1R) is a member of the G(i)-protein-coupled receptor family and cannabinoid signaling is largely dependent on the suppression of adenylyl cyclase-catalyzed cAMP production. In cell lines transfected with the CB1R or in native tissue preparations, treatment with cannabinoid agonists reduces both basal and forskolin-stimulated cAMP synthesis. We measured extracellular cAMP concentrations in the striatum of freely moving rats utilizing microdialysis to determine if changes in cAMP concentrations in response to CB1R agonists can be monitored in vivo. Striatal infusion of the CB1R agonist WIN55,212-2 (100 microM or 1 mM), dose-dependently decreased basal and forskolin-stimulated extracellular cAMP. These effects were reversed by co-infusion of the CB1R antagonist SR141716A (30 microM), which alone had no effect up to the highest concentration tested (300 microM). These data indicate that changes in extracellular cAMP concentrations in response to CB1R stimulation can be monitored in vivo allowing the study of cannabinoid signaling in the whole animal.

LakeMetabolizer: An R package for estimating lake metabolism from free-water oxygen using diverse statistical models

USGS Publications Warehouse

Winslow, Luke; Zwart, Jacob A.; Batt, Ryan D.; Dugan, Hilary; Woolway, R. Iestyn; Corman, Jessica; Hanson, Paul C.; Read, Jordan S.

2016-01-01

Metabolism is a fundamental process in ecosystems that crosses multiple scales of organization from individual organisms to whole ecosystems. To improve sharing and reuse of published metabolism models, we developed LakeMetabolizer, an R package for estimating lake metabolism from in situ time series of dissolved oxygen, water temperature, and, optionally, additional environmental variables. LakeMetabolizer implements 5 different metabolism models with diverse statistical underpinnings: bookkeeping, ordinary least squares, maximum likelihood, Kalman filter, and Bayesian. Each of these 5 metabolism models can be combined with 1 of 7 models for computing the coefficient of gas exchange across the air–water interface (k). LakeMetabolizer also features a variety of supporting functions that compute conversions and implement calculations commonly applied to raw data prior to estimating metabolism (e.g., oxygen saturation and optical conversion models). These tools have been organized into an R package that contains example data, example use-cases, and function documentation. The release package version is available on the Comprehensive R Archive Network (CRAN), and the full open-source GPL-licensed code is freely available for examination and extension online. With this unified, open-source, and freely available package, we hope to improve access and facilitate the application of metabolism in studies and management of lentic ecosystems.

Reasons for the Invasive Success of a Guppy (Poecilia reticulata) Population in Trinidad

PubMed Central

Sievers, Caya; Willing, Eva-Maria; Hoffmann, Margarete; Dreyer, Christine; Ramnarine, Indar; Magurran, Anne

2012-01-01

The introduction of non-native species into new habitats poses a major threat to native populations. Of particular interest, though often overlooked, are introductions of populations that are not fully reproductively isolated from native individuals and can hybridize with them. To address this important topic we used different approaches in a multi-pronged study, combining the effects of mate choice, shoaling behaviour and genetics. Here we present evidence that behavioural traits such as shoaling and mate choice can promote population mixing if individuals do not distinguish between native and foreign conspecifics. We examined this in the context of two guppy (Poecilia reticulata) populations that have been subject to an introduction and subsequent population mixing event in Trinidad. The introduction of Guanapo River guppies into the Turure River more than 50 years ago led to a marked reduction of the original genotype. In our experiments, female guppies did not distinguish between shoaling partners when given the choice between native and foreign individuals. Introduced fish are therefore likely to benefit from the protection of a shoal and will improve their survival chances as a result. The additional finding that male guppies do not discriminate between females on the basis of origin will further increase the process of population mixing, especially if males encounter mixed shoals. In a mesocosm experiment, in which the native and foreign populations were allowed to mate freely, we found, as expected on the basis of these behavioural interactions, that the distribution of offspring genotypes could be predicted from the proportions of the two types of founding fish. This result suggests that stochastic and environmental processes have reinforced the biological ones to bring about the genetic dominance of the invading population in the Turure River. Re-sampling the Turure for genetic analysis using SNP markers confirmed the population mixing process and showed that it is an on-going process in this river and has led to the nearly complete disappearance of the original genotype. PMID:22693621

Monitoring And Modeling Environmental Water Quality To Support Environmental Water Purchase Decision-making

NASA Astrophysics Data System (ADS)

Null, S. E.; Elmore, L.; Mouzon, N. R.; Wood, J. R.

2016-12-01

More than 25 million cubic meters (20,000 acre feet) of water has been purchased from willing agricultural sellers for environmental flows in Nevada's Walker River to improve riverine habitat and connectivity with downstream Walker Lake. Reduced instream flows limit native fish populations, like Lahontan cutthroat trout, through warm daily stream temperatures and low dissolved oxygen concentrations. Environmental water purchases maintain instream flows, although effects on water quality are more varied. We use multi-year water quality monitoring and physically-based hydrodynamic and water quality modeling to estimate streamflow, water temperature, and dissolved oxygen concentrations with alternative environmental water purchases. We simulate water temperature and dissolved oxygen changes from increased streamflow to prioritize the time periods and locations that environmental water purchases most enhance trout habitat as a function of water quality. Monitoring results indicate stream temperature and dissolved oxygen limitations generally exist in the 115 kilometers upstream of Walker Lake (about 37% of the study area) from approximately May through September, and this reach acts as a water quality barrier for fish passage. Model results indicate that low streamflows generally coincide with critically warm stream temperatures, water quality refugia exist on a tributary of the Walker River, and environmental water purchases may improve stream temperature and dissolved oxygen conditions for some reaches and seasons, especially in dry years and prolonged droughts. This research supports environmental water purchase decision-making and allows water purchase decisions to be prioritized with other river restoration alternatives.

Resonance spectra of a paramagnetic probe dissolved in a viscous medium

NASA Technical Reports Server (NTRS)

Kaplan, J. I.; Gelerinter, E.; Fryburg, G. C.

1972-01-01

A model is presented for calculating the paramagnetic resonance (EPR) spectrum of vanadyl acetylacetonate (VAAC) dissolved in either a liquid crystal or isotropic solvent. It employs density matrix formulation in the rotating reference frame. The molecules occupy several discrete angles with respect to the magnetic field and can relax to neighboring positions in a characteristic time tau(theta). The form of tau(theta) is found from a diffusion approach, and the magnitude of tau(theta) is a measure of how freely the VAAC probe tumbles in the solvent. Spectra are predicted for values of tau between 10 to the minus 11th power sec and 10 to the minus 7th power sec. The EPR spectrum, in the isotropic case, is obtained be summing the contributions from the allowed angles weighted by the polar volume element, sin theta. When applying the model to the nematic liquid crystal case it is also necessary to multiply by the Saupe distribution function. For this case tau(theta) is obtained from the diffusion approach in which two diffusion constants are employed to reflect the difference in the parallel and perpendicular components of the viscosity.

Magnetic actuation of hair cells

NASA Astrophysics Data System (ADS)

Rowland, David; Roongthumskul, Yuttana; Lee, Jae-Hyun; Cheon, Jinwoo; Bozovic, Dolores

2011-11-01

The bullfrog sacculus contains mechanically sensitive hair cells whose stereociliary bundles oscillate spontaneously when decoupled from the overlying membrane. Steady-state offsets on the resting position of a hair bundle can suppress or modulate this native motility. To probe the dynamics of spontaneous oscillation in the proximity of the critical point, we describe here a method for mechanical actuation that avoids loading the bundles or contributing to the viscous drag. Magnetite beads were attached to the tips of the stereocilia, and a magnetic probe was used to impose deflections. This technique allowed us to observe the transition from multi-mode to single-mode state in freely oscillating bundles, as well as the crossover from the oscillatory to the quiescent state.

The effect of vegetation and soil texture on the nature of organics in runoff from a catchment supplying water for domestic consumption.

PubMed

Awad, John; van Leeuwen, John; Abate, Dawit; Pichler, Markus; Bestland, Erick; Chittleborough, David J; Fleming, Nigel; Cohen, Jonathan; Liffner, Joel; Drikas, Mary

2015-10-01

The influence of vegetation and soil texture on the concentration and character of dissolved organic matter (DOM) present in runoff from the surface and sub-surface of zero order catchments of the Myponga Reservoir-catchment (South Australia) was investigated to determine the impacts of catchment characteristics and land management practices on the quality of waters used for domestic supply. Catchments selected have distinct vegetative cover (grass, native vegetation or pine) and contrasting texture of the surface soil horizon (sand or clay loam/clay). Water samples were collected from three slope positions (upper, middle, and lower) at soil depths of ~30 cm and ~60 cm in addition to overland flows. Filtered (0.45 μm) water samples were analyzed for dissolved organic carbon (DOC) and UV-visible absorbance and by F-EEM and HPSEC with UV and fluorescence detection to characterize the DOM. Surface and sub-surface runoff from catchments with clay soils and native vegetation or grass had lower DOC concentrations and lower relative abundances of aromatic, humic-like and high molecular weight organics than runoff from sandy soils with these vegetative types. Sub-surface flows from two catchments with Pinus radiata had similar DOC concentrations and DOM character, regardless of marked variation in surface soil texture. Runoff from catchments under native vegetation and grass on clay soils resulted in lower DOC concentrations and hence would be expected to have lower coagulant demand in conventional treatment for potable water supply than runoff from corresponding sandy soil catchments. However, organics in runoff from clay catchments would be more difficult to remove by coagulation. Surface waters from the native vegetation and grass catchments were generally found to have higher relative abundance of organic compounds amenable to removal by coagulation compared with sub-surface waters. Biophysical and land management practices combine to have a marked influence on the quality of source water used for domestic supply. Copyright © 2015 Elsevier B.V. All rights reserved.

An annual pattern of native embolism in upper branches of four tall conifer species.

PubMed

McCulloh, Katherine A; Johnson, Daniel M; Meinzer, Frederick C; Lachenbruch, Barbara

2011-06-01

The Pacific Northwest of North America experiences relatively mild winters and dry summers. For the tall coniferous trees that grow in this region, we predicted that loss in the hydraulic conductivity of uppermost branches would be avoided because of difficulty reversing accumulated emboli in xylem that is always under negative pressure. To test this hypothesis, we measured native percent loss in hydraulic conductivity (PLC; the decrease of in situ hydraulic conductivity relative to the maximum) monthly throughout 2009 in branches at the tops (∼50 m) of four species in an old growth forest in southern Washington. Contrary to our prediction, freeze-thaw cycles resulted in considerable native PLC. Branches showed hydraulic recovery in the spring and after a moderate increase in native embolism that was observed after an unusually hot period in August. The September recovery occurred despite decreases in the leaf and stem water potentials compared to August values. Recoveries in branches of these trees could not have occurred by raising the water potential enough to dissolve bubbles simply by transporting water from roots and must have occurred either through water absorption through needles and/or refilling under negative pressure. Excluding the August value, native embolism values correlated strongly with air temperature of the preceding 10 d. For three species, we found that branches with lower wood density had higher specific conductivity, but not greater native PLC than branches with higher wood density, which calls into question whether there is any hydraulic benefit to higher wood density in small branches in those species.

Sulfur geochemistry of hydrothermal waters in Yellowstone National Park: I. The origin of thiosulfate in hot spring waters

USGS Publications Warehouse

Xu, Y.; Schoonen, M.A.A.; Nordstrom, D. Kirk; Cunningham, K.M.; Ball, J.W.

1998-01-01

Thiosulfate (S2O2-3), polythionate (SxO2-6), dissolved sulfide (H2S), and sulfate (SO2-4) concentrations in thirty-nine alkaline and acidic springs in Yellowstone National Park (YNP) were determined. The analyses were conducted on site, using ion chromatography for thiosulfate, polythionate, and sulfate, and using colorimetry for dissolved sulfide. Thiosulfate was detected at concentrations typically less than 2 ??mol/L in neutral and alkaline chloride springs with low sulfate concentrations (C1-/SO2-4 > 25). The thiosulfate concentration levels are about one to two orders of magnitude lower than the concentration of dissolved sulfide in these springs. In most acid sulfate and acid sulfate-chloride springs (Cl-/SO2-4 < 10), thiosulfate concentrations were also typically lower than 2 ??mol/L. However, in some chloride springs enriched with sulfate (Cl-/SO2-4 between 10 to 25), thiosulfate was found at concentrations ranging from 9 to 95 ??mol/L, higher than the concentrations of dissolved sulfide in these waters. Polythionate was detected only in Cinder Pool, Norris Geyser basin, at concentrations up to 8 ??mol/L, with an average S-chain-length from 4.1 to 4.9 sulfur atoms. The results indicate that no thiosulfate occurs in the deeper parts of the hydrothermal system. Thiosulfate may form, however, from (1) hydrolysis of native sulfur by hydrothermal solutions in the shallower parts (<50 m) of the system, (2) oxidation of dissolved sulfide upon mixing of a deep hydrothermal water with aerated shallow groundwater, and (3) the oxidation of dissolved sulfide by dissolved oxygen upon discharge of the hot spring. Upon discharge of a sulfide-containing hydrothermal water, oxidation proceeds rapidly as atmospheric oxygen enters the water. The transfer of oxygen is particularly effective if the hydrothermal discharge is turbulent and has a large surface area.

Modified denatured lysozyme effectively solubilizes fullerene c60 nanoparticles in water

NASA Astrophysics Data System (ADS)

Siepi, Marialuisa; Politi, Jane; Dardano, Principia; Amoresano, Angela; De Stefano, Luca; Monti, Daria Maria; Notomista, Eugenio

2017-08-01

Fullerenes, allotropic forms of carbon, have very interesting pharmacological effects and engineering applications. However, a very low solubility both in organic solvents and water hinders their use. Fullerene C60, the most studied among fullerenes, can be dissolved in water only in the form of nanoparticles of variable dimensions and limited stability. Here the effect on the production of C60 nanoparticles by a native and denatured hen egg white lysozyme, a highly basic protein, has been systematically studied. In order to obtain a denatured, yet soluble, lysozyme derivative, the four disulfides of the native protein were reduced and exposed cysteines were alkylated by 3-bromopropylamine, thus introducing eight additional positive charges. The C60 solubilizing properties of the modified denatured lysozyme proved to be superior to those of the native protein, allowing the preparation of biocompatible highly homogeneous and stable C60 nanoparticles using lower amounts of protein, as demonstrated by dynamic light scattering, transmission electron microscopy and atomic force microscopy studies. This lysozyme derivative could represent an effective tool for the solubilization of other carbon allotropes.

Conformational States of the Rapana thomasiana Hemocyanin and Its Substructures Studied by Dynamic Light Scattering and Time-Resolved Fluorescence Spectroscopy

PubMed Central

Georgieva, Dessislava; Schwark, Daniel; Nikolov, Peter; Idakieva, Krassimira; Parvanova, Katja; Dierks, Karsten; Genov, Nicolay; Betzel, Christian

2005-01-01

Hemocyanins are dioxygen-transporting proteins freely dissolved in the hemolymph of mollusks and arthropods. Dynamic light scattering and time-resolved fluorescence measurements show that the oxygenated and apo-forms of the Rapana thomasiana hemocyanin, its structural subunits RtH1 and RtH2, and those of the functional unit RtH2e, exist in different conformations. The oxygenated respiratory proteins are less compact and more asymmetric than the respective apo-forms. Different conformational states were also observed for the R. thomasiana hemocyanin in the absence and presence of an allosteric regulator. The results are in agreement with a molecular mechanism for cooperative dioxygen binding in molluscan hemocyanins including transfer of conformational changes from one functional unit to another. PMID:15533921

A biomimetic approach to the detection and identification of estrogen receptor agonists in surface waters using semipermeable membrane devices (SPMDs) and bioassay-directed chemical analysis.

PubMed

Rastall, Andrew C; Getting, Dominic; Goddard, Jon; Roberts, David R; Erdinger, Lothar

2006-07-01

Some anthropogenic pollutants posses the capacity to disrupt endogenous control of developmental and reproductive processes in aquatic biota by activating estrogen receptors. Many anthropogenic estrogen receptor agonists (ERAs) are hydrophobic and will therefore readily partition into the abiotic organic carbon phases present in natural waters. This partitioning process effectively reduces the proportion of ERAs readily available for bioconcentration by aquatic biota. Results from some studies have suggested that for many aquatic species, bioconcentration of the freely-dissolved fraction may be the principal route of uptake for hydrophobic pollutants with logarithm n-octanol/water partition coefficient (log Kow) values less than approximately 6.0, which includes the majority of known anthropogenic ERAs. The detection and identification of freely-dissolved readily bioconcentratable ERAs is therefore an important aspect of exposure and risk assessment. However, most studies use conventional techniques to sample total ERA concentrations and in doing so frequently fail to account for bioconcentration of the freely-dissolved fraction. The aim of the current study was to couple the biomimetic sampling properties of semipermeable membrane devices (SPMDs) to a bioassay-directed chemical analysis (BDCA) scheme for the detection and identification of readily bioconcentratable ERAs in surface waters. SPMDs were constructed and deployed at a number of sites in Germany and the UK. Following the dialytic recovery of target compounds and size exclusion chromatographic cleanup, SPMD samples were fractionated using a reverse-phase HPLC method calibrated to provide an estimation of target analyte log Kow. A portion of each HPLC fraction was then subjected to the yeast estrogen screen (YES) to determine estrogenic potential. Results were plotted in the form of 'estrograms' which displayed profiles of estrogenic potential as a function of HPLC retention time (i.e. hydrophobicity) for each of the samples. Where significant activity was elicited in the YES, the remaining portion of the respective active fraction was subjected to GC-MS analysis in an attempt to identify the ERAs present. Estrograms from each of the field samples showed that readily bioconcentratable ERAs were present at each of the sampling sites. Estimated log Kow values for the various active fractions ranged from 1.92 to 8.63. For some samples, estrogenic potential was associated with a relatively narrow range of log Kow values whilst in others estrogenic potential was more widely distributed across the respective estrograms. ERAs identified in active fractions included some benzophenones, various nonylphenol isomers, benzyl butyl phthalate, dehydroabietic acid, sitosterol, 3-(4-methylbenzylidine)camphor (4-MBC) and 6-acetyl-1,1,2,4,4,7-hexamethyltetralin (AHTN). Other tentatively identified compounds which may have contributed to the observed YES activity included various polycyclic aromatic hydrocarbons (PAHs) and their alkylated derivatives, methylated benzylphenols, various alkyl-phenols and dialkylphenols. However, potential ERAs present in some active fractions remain unidentified. Our results show that SPMD-YES-based BDCA can be used to detect and identify readily bioconcentratable ERAs in surface waters. As such, this biomimetic approach can be employed as an alternative to conventional methodologies to provide investigators with a more environmentally relevant insight into the distribution and identity of ERAs in surface waters. The use of alternative bioassays also has the potential to expand SPMD-based BDCA to include a wide range of toxicological endpoints. Improvements to the analytical methodology used to identify ERAs or other target compounds in active fractions in the current study could greatly enhance the applicability of the methodology to risk assessment and monitoring programmes.

Activated carbon amendment to sequester PAHs in contaminated soil: a lysimeter field trial.

PubMed

Hale, Sarah E; Elmquist, Marie; Brändli, Rahel; Hartnik, Thomas; Jakob, Lena; Henriksen, Thomas; Werner, David; Cornelissen, Gerard

2012-04-01

Activated carbon (AC) amendment is an innovative method for the in situ remediation of contaminated soils. A field-scale AC amendment of either 2% powder or granular AC (PAC and GAC) to a PAH contaminated soil was carried out in Norway. The PAH concentration in drainage water from the field plot was measured with a direct solvent extraction and by deploying polyoxymethylene (POM) passive samplers. In addition, POM samplers were dug directly in the AC amended and unamended soil in order to monitor the reduction in free aqueous PAH concentrations in the soil pore water. The total PAH concentration in the drainage water, measured by direct solvent extraction of the water, was reduced by 14% for the PAC amendment and by 59% for GAC, 12 months after amendment. Measurements carried out with POM showed a reduction of 93% for PAC and 56% for GAC. The free aqueous PAH concentration in soil pore water was reduced 93% and 76%, 17 and 28 months after PAC amendment, compared to 84% and 69% for GAC. PAC, in contrast to GAC, was more effective for reducing freely dissolved concentrations than total dissolved ones. This could tentatively be explained by leaching of microscopic AC particles from PAC. Secondary chemical effects of the AC amendment were monitored by considering concentration changes in dissolved organic carbon (DOC) and nutrients. DOC was bound by AC, while the concentrations of nutrients (NO(3), NO(2), NH(4), PO(4), P-total, K, Ca and Mg) were variable and likely affected by external environmental factors. Copyright © 2012 Elsevier Ltd. All rights reserved.

Water quality in southern Florida; Florida, 1996-98

USGS Publications Warehouse

McPherson, Benjamin F.; Miller, Ronald L.; Haag, Kim H.; Bradner, Anne

2000-01-01

Major influences and findings for water quality and biology in southern Florida, including the Everglades, are described and illustrated. Samples were collected to determine total phosphorus, dissolved organic carbon, pesticides, mercury, nitrate, volatile organic carbon compounds, and radon-222. Water-management, agricultural, and land-use practices are discussed. Sixty-three species of fish in 26 families were collected; 43 native species, 10 exotic or nonnative species, and 10 species of marine fish that periodically inhabit canals and rivers were identified.

A general microchip surface modification approach using a spin-coated polymer resist film doped with hydroxypropyl cellulose.

PubMed

Sun, Xiuhua; Yang, Weichun; Geng, Yanli; Woolley, Adam T

2009-04-07

We have developed a simple and effective method for surface modification of polymer microchips by entrapping hydroxypropyl cellulose (HPC) in a spin-coated thin film on the surface. Poly(methyl methacrylate-8.5-methacrylic acid), a widely available commercial resist formulation, was utilized as a matrix for dissolving HPC and providing adherence to native polymer surfaces. Various amounts of HPC (0.1-2.0%) dissolved in the copolymer and spun on polymer surfaces were evaluated. The modified surfaces were characterized by contact angle measurement, X-ray photoelectron spectroscopy and atomic force microscopy. The developed method was applied on both poly(methyl methacrylate) and cyclic olefin copolymer microchips. A fluorescently labeled myoglobin digest, binary protein mixture, and human serum sample were all separated in these surface-modified polymer microdevices. Our work exhibits an easy and reliable way to achieve favorable biomolecular separation performance in polymer microchips.

A general microchip surface modification approach using a spin-coated polymer resist film doped with hydroxypropyl cellulose

PubMed Central

Sun, Xiuhua; Yang, Weichun; Geng, Yanli; Woolley, Adam T.

2009-01-01

We have developed a simple and effective method for surface modification of polymer microchips by entrapping hydroxypropyl cellulose (HPC) in a spin-coated thin film on the surface. Poly(methyl methacrylate-8.5-methacrylic acid), a widely available commercial resist formulation, was utilized as a matrix for dissolving HPC and providing adherence to native polymer surfaces. Various amounts of HPC (0.1–2.0%) dissolved in the copolymer and spun on polymer surfaces were evaluated. The modified surfaces were characterized by contact angle measurement, X-ray photoelectron spectroscopy and atomic force microscopy. The developed method was applied on both poly(methyl methacrylate) and cyclic olefin copolymer microchips. A fluorescently labeled myoglobin digest, binary protein mixture, and human serum sample were all separated in these surface-modified polymer microdevices. Our work exhibits an easy and reliable way to achieve favorable biomolecular separation performance in polymer microchips. PMID:19294306

Production of cellulose II from native cellulose by near- and supercritical water solubilization.

PubMed

Sasaki, Mitsuru; Adschiri, Tadafumi; Arai, Kunio

2003-08-27

We explored conditions for dissolving microcrystalline cellulose in high-temperature and high-pressure water without catalyst and in order to produce cellulose II in a rapid and selective manner. For understanding reactions of microcrystalline cellulose in subcritical and supercritical water, its solubilization treatment was conducted using a continuous-flow-type microreactor. It was found that cellulose could dissolve in near- and supercritical water at short treatment times of 0.02-0.4 s, resulting in the formation of cellulose II in relatively high yield after the treatment. Next, characteristics of the cellulose II obtained were investigated. As a result, it was confirmed that the relative crystallinity index and the degree of polymerization of the cellulose II were high values ranging from 80 to 60% and from 50 to 30%, respectively. From these findings, it was suggested that this method had high potential as an alternative technique for the conventional cellulose II production method.

Different effects of plant-derived dissolved organic matter (DOM) and urea on the priming of soil organic carbon.

PubMed

Qiu, Qingyan; Wu, Lanfang; Ouyang, Zhu; Li, Binbin; Xu, Yanyan

2016-03-01

Soil organic carbon (SOC) mineralization is important for the regulation of the global climate and soil fertility. Decomposition of SOC may be significantly affected by the supply of plant-derived labile carbon (C). To investigate the impact of plant-derived dissolved organic matter (DOM) and urea (N) additions on the decomposition of native SOC as well as to elucidate the underlying mechanisms of priming effects (PEs), a batch of incubation experiments was conducted for 250 days by application of (13)C-labeled plant-derived DOM and urea to soils. The direction of PE induced by the addition of DOM was different from the addition of N, i.e. it switched from negative to positive in DOM-amended soils, whereas in the N-treated soil it switched from positive to negative. Adding DOM alone was favorable for soil C sequestration (59 ± 5 mg C per kg soil), whereas adding N alone or together with DOM accelerated the decomposition of native SOC, causing net C losses (-62 ± 4 and -34 ± 31 mg C per kg soil, respectively). These findings indicate that N addition and its interaction with DOM are not favorable for soil C sequestration. Adding DOM alone increased the level of dissolved organic carbon (DOC), but it did not increase the level of soil mineral N. Changes in the ratio of microbial biomass carbon (MBC) to microbial biomass nitrogen (MBN) and microbial metabolic quotient (qCO2) after the addition of DOM and N suggest that a possible shift in the microbial community composition may occur in the present study. Adding DOM with or without N increased the activities of β-glucosidase and urease. Changes in the direction and magnitude of PE were closely related to changes in soil C and N availability. Soil C and N availability might influence the PE through affecting the microbial biomass and extracellular enzyme activity as well as causing a possible shift in the microbial community composition.

JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases.

PubMed

Feng, Guangjie; Burton, Nick; Hill, Bill; Davidson, Duncan; Kerwin, Janet; Scott, Mark; Lindsay, Susan; Baldock, Richard

2005-03-09

Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language. We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture. We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily.

Contact Eczema Caused by True Teak (Tectona Grandis)

PubMed Central

Krogh, H. K.

1962-01-01

An epidemiological study of occupational contact eczema in a furniture factory is presented. The localization, distribution, and clinical features of the skin lesions were characteristic of contact eczema caused by a sensitizing or irritating dust. True teak—Tectona grandis—was the cause of the skin condition. That teak is a fairly potent sensitizer and also contains primary irritants is fully confirmed by the present study. About half the employees who were heavily exposed to teak dust suffered from eczema and/or severe itching. Only 8% of those with slight exposure to teak dust experienced skin symptoms. Patch tests with native teak dust moistened with water were applied on 10 “controls” and 112 workers who were exposed to teak in various working procedures. Moistened teak dust produced toxic reactions in 20·5%, while native teak dust did not have primary irritant effects and was, therefore, considered to be the substance of choice for patch testing; 18·7% of the workers showed an allergic skin reaction to native teak dust. The diagnosis of allergic contact eczema was made in 12·5%, and 6·2% were considered to have latent allergy. Primary irritant (contact) eczema was considered to be present in four individuals who had experienced acute, transitory, eczematous eruptions during the hot part of the summer when they perspired freely. In these cases the patch test to native teak dust was negative. Desensitization or “hardening” was observed in four workers. In most cases the skin lesions were not severe enough to cause sickness absence. The cause of the relatively high percentage of sensitization to teak among the workers in the factory is discussed. The importance of suitable prophylactic measures is stressed. PMID:14459786

Air-Water Exchange of Legacy and Emerging Organic Pollutants across the Great Lakes

NASA Astrophysics Data System (ADS)

Lohmann, R.; Ruge, Z.; Khairy, M.; Muir, D.; Helm, P.

2014-12-01

Organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) are transported to great water bodies via long-range atmospheric transport and released from the surface water as air concentrations continue to diminish. As the largest fresh water bodies in North America, the Great Lakes have both the potential to accumulate and serve as a secondary source of persistent bioaccumulative toxins. OCP and PCB concentrations were sampled at 30+ sites across Lake Superior, Ontario and Erie in the summer of 2011. Polyethylene passive samplers (PEs) were simultaneously deployed in surface water and near surface atmosphere to determine air-water gaseous exchange of OCPs and PCBs. In Lake Superior, surface water and atmospheric concentrations were dominated by α-HCH (average 250 pg/L and 4.2 pg/m3, respectively), followed by HCB (average 17 pg/L and 89 pg/m3, respectively). Air-water exchange varied greatly between sites and individual OCPs, however α-endosulfan was consistently deposited into the surface water (average 19 pg/m2/day). PCBs in the air and water were characterized by penta- and hexachlorobiphenyls with distribution along the coast correlated with proximity to developed areas. Air-water exchange gradients generally yielded net volatilization of PCBs out of Lake Superior. Gaseous concentrations of hexachlorobenzene, dieldrin and chlordanes were significantly higher (p < 0.05) at Lake Erie than Lake Ontario. A multiple linear regression that incorporated meteorological, landuse and population data was used to explain variability in the atmospheric concentrations. Results indicated that landuse (urban and/or cropland) greatly explained the variability in the data. Freely dissolved concentrations of OCPs (

Availability of polycyclic aromatic hydrocarbons to earthworms (Eisenia andrei, Oligochaeta) in field-polluted soils and soil-sediment mixtures.

PubMed

Jager, Tjalling; Baerselman, Rob; Dijkman, Ellen; de Groot, Arthur C; Hogendoorn, Elbert A; de Jong, Ad; Kruitbosch, Jantien A W; Peijnenburg, Willie J G M

2003-04-01

The bioavailability of polycyclic aromatic hydrocarbons (PAHs) for earthworms (Eisenia andrei) was experimentally determined in seven field-polluted soils and 15 soil-sediment mixtures. The pore-water concentration of most PAHs was higher than predicted. However, most of the compound was associated with dissolved organic carbon (DOC) and not directly available for uptake by earthworms. The apparent sorption could be reasonably predicted on the basis of interactions with DOC; however, the biota-soil accumulation factors (BSAFs) for earthworms were up to two orders of magnitude lower than predicted by equilibrium partitioning. The large variability between sites was not fully explained by differences in sorption. Experimental results indicate that the pool of freely dissolved PAHs in the pore water became partially depleted because of uptake by the earthworms and that bioaccumulation is thus also influenced by the kinetics of PAH desorption and mass transport. A pilot study with Lumbricus rubellus showed that steady-state body residues were well correlated to E. andrei. Current results show that depositing dredge spoil on land may lead to increased bioavailability of the lower-molecular-weight PAHs. However, risk assessment can conservatively rely on equilibrium partitioning, but accurate prediction requires quantification of the kinetics of bioavailability.

Differential effects of dissolved organic carbon upon re-entrainment and surface properties of groundwater bacteria and bacteria-sized microspheres during transport through a contaminated, sandy aquifer

USGS Publications Warehouse

Harvey, R.W.; Metge, D.W.; Mohanram, A.; Gao, X.; Chorover, J.

2011-01-01

Injection-and-recovery studies involving a contaminated, sandy aquifer (Cape Cod, Massachusetts) were conducted to assess the relative susceptibility for in situ re-entrainment of attached groundwater bacteria (Pseudomonas stuzeri ML2, and uncultured, native bacteria) and carboxylate-modified microspheres (0.2 and 1.0 μm diameters). Different patterns of re-entrainment were evident for the two colloids in response to subsequent injections of groundwater (hydrodynamic perturbation), deionized water (ionic strength alteration), 77 μM linear alkylbenzene sulfonates (LAS, anionic surfactant), and 76 μM Tween 80 (polyoxyethylene sorbitan monooleate, a very hydrophobic nonionic surfactant). An injection of deionized water was more effective in causing detachment of micrsopheres than were either of the surfactants, consistent with the more electrostatic nature of microsphere’s attachment, their extreme hydrophilicity (hydrophilicity index, HI, of 0.99), and negative charge (zeta potentials, ζ, of −44 to −49 mv). In contrast, Tween 80 was considerably more effective in re-entraining the more-hydrophobic native bacteria. Both the hydrophilicities and zeta potentials of the native bacteria were highly sensitive to and linearly correlated with levels of groundwater dissolved organic carbon (DOC), which varied modestly from 0.6 to 1.3 mg L−1. The most hydrophilic (0.52 HI) and negatively charged (ζ −38.1 mv) indigenous bacteria were associated with the lowest DOC. FTIR spectra indicated the latter community had the highest average density of surface carboxyl groups. In contrast, differences in groundwater (DOC) had no measurable effect on hydrophilicity of the bacteria-sized microspheres and only a minor effect on their ζ. These findings suggest that microspheres may not be very good surrogates for bacteria in field-scale transport studies and that adaptive (biological) changes in bacterial surface characteristics may need to be considered where there is longer-term exposure to contaminant DOC.

Mn-oxidizing Bacteria in Oak Ridge, TN and the Potential for Mercury Remediation

NASA Astrophysics Data System (ADS)

Wright, K. L.; McNeal, K. S.; Han, F. X.

2012-12-01

East Fork Poplar Creek (EFPC) in Oak Ridge, TN was highly contaminated with elemental mercury in the 1950 and 1960. The area is still experiencing the effects of mercury contamination, and researchers are searching for ways to remediate the EFPC. One possible mechanism for bioremediation is the use of biogenic Mn oxides to remove heavy metals from water systems. Six native Pseudomonas bacteria species were isolated from the EFPC in order to examine biogenic Mn oxides production and bioremediation of Oak Ridge slurries. To investigate the biochemical interactions of Pseudomonas and the native microbial communities with Hg, Mn, Fe, S, six different slurry treatment groups were compared using inductively coupled plasma-atomic emission spectrometry (ICP-AES) and cold vapor atomic absorption spectrometry (CVAAS). Oak Ridge slurries were autoclaved to inhibit microbial growth (group 1), autoclaved and amended with HgS (group 2), autoclaved and amended with Pseudomonas isolates and additional HgS (group 3), untreated slurry (group 4), normal slurry amended with HgS (group 5), and normal slurry amended with Pseudomonas isolates and additional HgS (group 6). The comparison of the autoclaved groups with the counterpart untreated and normal Oak Ridge slurries highlighted important microbial interactions. Also, the Pseudomonas isolates were grown separately in a MnSO4 media, and the individual bacteria were monitored for Mn-oxidization using ICP-AES and transmission electron microscopy (TEM). In the slurry sediments, the Pseudomonas isolates did produce Mn oxides which bound to mercury, and mercury bound to organic matter significantly decreased. However, after a significant decrease of dissolved mercury in the water, dissolved mercury was cycled back into the water system on day 10 of the study. Additionally, two individual native Oak Ridge Pseudomonas isolates demonstrated Mn-oxidization. Biogenic Mn oxides have the potential to decrease mercury cycling, however there is need for more in depth and long-term studies to confirm their sustained use as Hg bioremediators.

Towards a universal microbial inoculum for dissolved organic carbon degradation experiments

NASA Astrophysics Data System (ADS)

Pastor, Ada; Catalán, Núria; Gutiérrez, Carmen; Nagar, Nupur; Casas-Ruiz, Joan P.; Obrador, Biel; von Schiller, Daniel; Sabater, Sergi; Petrovic, Mira; Borrego, Carles M.; Marcé, Rafael

2017-04-01

Dissolved organic carbon (DOC) is the largest biologically available pool of organic carbon in aquatic ecosystems and its degradation along the land-to-ocean continuum has implications for carbon cycling from local to global scales. DOC biodegradability is usually assessed by incubating filtered water inoculated with native microbial assemblages in the laboratory. However, the use of a native inoculum from several freshwaters, without having a microbial-tailored design, hampers our ability to tease apart the relative contribution of the factors driving DOC degradation from the effects of local microbial communities. The use of a standard microbial inoculum would allow researchers to disentangle the drivers of DOC degradation from the metabolic capabilities of microbial communities operating in situ. With this purpose, we designed a bacterial inoculum to be used in experiments of DOC degradation in freshwater habitats. The inoculum is composed of six bacterial strains that easily grow under laboratory conditions, possess a versatile metabolism and are able to grow under both aerobic and anaerobic conditions. The mixed inoculum showed higher DOC degradation rates than those from their isolated bacterial components and the consumption of organic substrates was consistently replicated. Moreover, DOC degradation rates obtained using the designed inoculum were responsive across a wide range of natural water types differing in DOC concentration and composition. Overall, our results show the potential of the designed inoculum as a tool to discriminate between the effects of environmental drivers and intrinsic properties of DOC on degradation dynamics.

Biological properties of the Chilean native moss Sphagnum magellanicum.

PubMed

Montenegro, Gloria; Portaluppi, Mariana C; Salas, Francisco A; Díaz, María F

2009-01-01

An ethanol extract prepared from the gametophyte Chilean native moss Sphagnum magellanicum was dried out, weighed and dissolved in distilled water. This extract was then assayed for its antibacterial activity against the G(-) bacteria Azotobacter vinelandii, Erwinia carotovora subsp. carotovora, Enterobacter aerogenes, Escherichia coli, Pseudomonas aeruginosa, Salmonella typhi, Vibrio cholerae, and the G(+) bacteria Staphylococcus aureus subsp. aureus, and Streptococcus type beta. The growth of the cultures of E. carotovora subsp. carotovora, and V. cholerae was inhibited at a concentration of 581 microg/ml of extract, while the cultures of E. coli, S. typhi and Streptococcus type beta were inhibited at a concentration of 1.16 microg/mL of extract. The concentration of phenolic compounds was 4.294 mg/mL; the presence of vanillic, chlorogenic, syringic, caffeic, gallic, 3-4 hydrozybenzoic, p-coumaric and salicylic acids was identified using RP- High Pressure Liquid Chromatography.

A bioenergetics modeling evaluation of top-down control of ruffe in the St. Louis River, western Lake Superior

USGS Publications Warehouse

Mayo, Kathleen R.; Selgeby, James H.; McDonald, Michael E.

1998-01-01

Ruffe (Gymnocephalus cernuus), were accidentally introduced into the St. Louis River estuary, western Lake Superior, in the mid 1980s and it was feared that they might affect native fish through predation on eggs and competition for forage and habitat. In an effort to control the abundance of ruffe and limit dispersal, a top-down control strategy using predators was implemented in 1989. We used bioenergetics modeling to examine the efficacy of top-down control in the St. Louis River from 1991 to 1994. Five predators--northern pike (Esox lucius), walleye (Stizostedion vitreum vitreum), smallmouth bass (Micropterus dolomieui), brown bullhead (Ictalurus nebulosus), and yellow perch (Perca flavescens)--were modeled to determine their consumption of ruffe and four other native prey species-spottail shiner (Notropis hudsonius), emerald shiner (Notropis atherinoides), yellow perch (Perca flavescens), and black crappie (Pomoxis nigromaculatus). Although predators ate as much as 47% of the ruffe biomass in 1 year, they were not able to halt the increase in ruffe abundance. The St. Louis River is an open system that allows predators to move freely out of the system, and the biomass of managed predators did not increase. A selectivity index showed all five predators selected the native prey and avoided ruffe. The St. Louis River has several predator and prey species creating many complex predator-prey interactions; and top-down control of ruffe by the predators examined in this study did not occur.

Synthesis and spectroscopic properties of silica-dye-semiconductor nanocrystal hybrid particles.

PubMed

Ren, Ting; Erker, Wolfgang; Basché, Thomas; Schärtl, Wolfgang

2010-12-07

We prepared silica-dye-nanocrystal hybrid particles and studied the energy transfer from semiconductor nanocrystals (= donor) to organic dye molecules (= acceptor). Multishell CdSe/CdS/ZnS semiconductor nanocrystals were adsorbed onto monodisperse Stöber silica particles with an outer silica shell of thickness 2-23 nm containing organic dye molecules (Texas Red). The thickness of this dye layer has a strong effect on the energy transfer efficiency, which is explained by the increase in the number of dye molecules homogeneously distributed within the silica shell, in combination with an enhanced surface adsorption of nanocrystals with increasing dye amount. Our conclusions were underlined by comparison of the experimental results with numerically calculated FRET efficiencies and by control experiments confirming attractive interaction between the nanocrystals and Texas Red freely dissolved in solution.

Laboratory Investigations of Enhanced Sulfate Reduction as a Groundwater Arsenic Remediation Strategy

PubMed Central

KEIMOWITZ, A. R.; MAILLOUX, B. J.; COLE, P.; STUTE, M.; SIMPSON, H. J.; CHILLRUD, S. N.

2011-01-01

Landfills have the potential to mobilize arsenic via induction of reducing conditions in groundwater and subsequent desorption from or dissolution of arsenic-bearing iron phases. Laboratory incubation experiments were conducted with materials from a landfill where such processes are occurring. These experiments explored the potential for induced sulfate reduction to immobilize dissolved arsenic in situ. The native microbial community at this site reduced sulfate in the presence of added acetate. Acetate respiration and sulfate reduction were observed concurrent with dissolved iron concentrations initially increasing from 0.6 μM (0.03 mg L−1) to a maximum of 111 μM (6.1 mg L−1) and subsequently decreasing to 0.74 μM (0.04 mg L−1). Dissolved arsenic concentrations initially covaried with iron but subsequently increased again as sulfide accumulated, consistent with the formation of soluble thioarsenite complexes. Dissolved arsenic concentrations subsequently decreased again from a maximum of 2 μM (148 μg L−1) to 0.3 μM (22 μg L−1), consistent with formation of sulfide mineral phases or increased arsenic sorption at higher pH values. Disequilibrium processes may also explain this second arsenic peak. The maximum iron and arsenic concentrations observed in the lab represent conditions most equivalent to the in situ conditions. These findings indicate that enhanced sulfate reduction merits further study as a potential in situ groundwater arsenic remediation strategy at landfills and other sites with elevated arsenic in reducing groundwater. PMID:17969686

Picking up the pieces: conserving remnant natural areas in the post-industrial landscape of the Calumet Region

USGS Publications Warehouse

Labus, Paul; Whitman, Richard L.; Nevers, Meredith Becker

1999-01-01

The Calumet Region was shaped by geologic forces, succession, and interacting biomes converging on a unique natural landscape. Over the past 4500 years, a strand plain has formed to the north of a geologic area called Toleston Beach. Sequential and differential primary succession of dune and swale communities in this region allowed species from different biomes to interact freely. In the mid-nineteenth century, commerce and settlement drastically changed the area, and natural areas were fragmented, manipulated, and degraded by cultural intrusions and industrialization. Despite the near obliteration of dune and swale habitat, small fragments of natural land escaped destruction. These native fragments maintained some semblance of the landscape that once covered the region. Currently, these native fragments are threatened by the lingering intrusion of historic contamination and the continuing presence of industry and commerce. Restoration and conservation of these remnants will need to be a process of integrating biological diversity goals into the landscape of the industrialized region through planning and design. We outline here the natural history of the region, the philosophical rationale for conservation, and possible approaches for integrating and maintaining these valuable remnant resources and processes.

Reduced genetic variation and the success of an invasive species.

PubMed

Tsutsui, N D; Suarez, A V; Holway, D A; Case, T J

2000-05-23

Despite the severe ecological and economic damage caused by introduced species, factors that allow invaders to become successful often remain elusive. Of invasive taxa, ants are among the most widespread and harmful. Highly invasive ants are often unicolonial, forming supercolonies in which workers and queens mix freely among physically separate nests. By reducing costs associated with territoriality, unicolonial species can attain high worker densities, allowing them to achieve interspecific dominance. Here we examine the behavior and population genetics of the invasive Argentine ant (Linepithema humile) in its native and introduced ranges, and we provide a mechanism to explain its success as an invader. Using microsatellite markers, we show that a population bottleneck has reduced the genetic diversity of introduced populations. This loss is associated with reduced intraspecific aggression among spatially separate nests, and leads to the formation of interspecifically dominant supercolonies. In contrast, native populations are more genetically variable and exhibit pronounced intraspecific aggression. Although reductions in genetic diversity are generally considered detrimental, these findings provide an example of how a genetic bottleneck can lead to widespread ecological success. In addition, these results provide insights into the origin and evolution of unicoloniality, which is often considered a challenge to kin selection theory.

Hydrogel-laden paper scaffold system for origami-based tissue engineering

PubMed Central

Kim, Su-Hwan; Lee, Hak Rae; Yu, Seung Jung; Han, Min-Eui; Lee, Doh Young; Kim, Soo Yeon; Ahn, Hee-Jin; Han, Mi-Jung; Lee, Tae-Ik; Kim, Taek-Soo; Kwon, Seong Keun; Im, Sung Gap; Hwang, Nathaniel S.

2015-01-01

In this study, we present a method for assembling biofunctionalized paper into a multiform structured scaffold system for reliable tissue regeneration using an origami-based approach. The surface of a paper was conformally modified with a poly(styrene-co-maleic anhydride) layer via initiated chemical vapor deposition followed by the immobilization of poly-l-lysine (PLL) and deposition of Ca2+. This procedure ensures the formation of alginate hydrogel on the paper due to Ca2+ diffusion. Furthermore, strong adhesion of the alginate hydrogel on the paper onto the paper substrate was achieved due to an electrostatic interaction between the alginate and PLL. The developed scaffold system was versatile and allowed area-selective cell seeding. Also, the hydrogel-laden paper could be folded freely into 3D tissue-like structures using a simple origami-based method. The cylindrically constructed paper scaffold system with chondrocytes was applied into a three-ring defect trachea in rabbits. The transplanted engineered tissues replaced the native trachea without stenosis after 4 wks. As for the custom-built scaffold system, the hydrogel-laden paper system will provide a robust and facile method for the formation of tissues mimicking native tissue constructs. PMID:26621717

Hydrogel-laden paper scaffold system for origami-based tissue engineering.

PubMed

Kim, Su-Hwan; Lee, Hak Rae; Yu, Seung Jung; Han, Min-Eui; Lee, Doh Young; Kim, Soo Yeon; Ahn, Hee-Jin; Han, Mi-Jung; Lee, Tae-Ik; Kim, Taek-Soo; Kwon, Seong Keun; Im, Sung Gap; Hwang, Nathaniel S

2015-12-15

In this study, we present a method for assembling biofunctionalized paper into a multiform structured scaffold system for reliable tissue regeneration using an origami-based approach. The surface of a paper was conformally modified with a poly(styrene-co-maleic anhydride) layer via initiated chemical vapor deposition followed by the immobilization of poly-l-lysine (PLL) and deposition of Ca(2+). This procedure ensures the formation of alginate hydrogel on the paper due to Ca(2+) diffusion. Furthermore, strong adhesion of the alginate hydrogel on the paper onto the paper substrate was achieved due to an electrostatic interaction between the alginate and PLL. The developed scaffold system was versatile and allowed area-selective cell seeding. Also, the hydrogel-laden paper could be folded freely into 3D tissue-like structures using a simple origami-based method. The cylindrically constructed paper scaffold system with chondrocytes was applied into a three-ring defect trachea in rabbits. The transplanted engineered tissues replaced the native trachea without stenosis after 4 wks. As for the custom-built scaffold system, the hydrogel-laden paper system will provide a robust and facile method for the formation of tissues mimicking native tissue constructs.

Environmental Impact Statement for the Modernization and Enhancement of Ranges, Airspace, and Training Areas in the Joint Pacific Alaska Range Complex in Alaska. Volume 1 - Executive Summary, Chapters 1 through 10

DTIC Science & Technology

2013-06-01

to short-term behavioral responses and no effects that would be measurable at a population level have been documented. Fish in their native...the sustainable multipurpose use of natural resources (hunting, fishing , trapping, and non- consumptive uses) on military lands, subject to safety...support fish populations year-round, as they freeze in winter or when iced over and lack sufficient dissolved oxygen for fish to survive (USARAK 2004-1

Passivation of high temperature superconductors

NASA Technical Reports Server (NTRS)

Vasquez, Richard P. (Inventor)

1991-01-01

The surface of high temperature superconductors such as YBa2Cu3O(7-x) are passivated by reacting the native Y, Ba and Cu metal ions with an anion such as sulfate or oxalate to form a surface film that is impervious to water and has a solubility in water of no more than 10(exp -3) M. The passivating treatment is preferably conducted by immersing the surface in dilute aqueous acid solution since more soluble species dissolve into the solution. The treatment does not degrade the superconducting properties of the bulk material.

Jwalk and MNXL Web Server: Model Validation using Restraints from Crosslinking Mass Spectrometry.

PubMed

Bullock, J M A; Thalassinos, K; Topf, M

2018-05-07

Crosslinking Mass Spectrometry generates restraints that can be used to model proteins and protein complexes. Previously, we have developed two methods, to help users achieve better modelling performance from their crosslinking restraints: Jwalk, to estimate solvent accessible distances between crosslinked residues and MNXL, to assess the quality of the models based on these distances. Here we present the Jwalk and MNXL webservers, which streamline the process of validating monomeric protein models using restraints from crosslinks. We demonstrate this by using the MNXL server to filter models made of varying quality, selecting the most native-like. The webserver and source code are freely available from jwalk.ismb.lon.ac.uk and mnxl.ismb.lon.ac.uk. m.topf@cryst.bbk.ac.uk, j.bullock@cryst.bbk.ac.uk.

Wildlife mortality investigation and disease research: contributions of the USGS National Wildlife Health Center to endangered species management and recovery

USGS Publications Warehouse

Brand, Christopher J.

2013-01-01

The U.S. Geological Survey—National Wildlife Health Center (NWHC) provides diagnostic services, technical assistance, applied research, and training to federal, state, territorial, and local government agencies and Native American tribes on wildlife diseases and wildlife health issues throughout the United States and its territories, commonwealth, and freely associated states. Since 1975, >16,000 carcasses and specimens from vertebrate species listed under the Endangered Species Act have been submitted to NWHC for determination of causes of morbidity or mortality or assessment of health/disease status. Results from diagnostic investigations, analyses of the diagnostic database, technical assistance and consultation, field investigation of epizootics, and wildlife disease research by NWHC wildlife disease specialists have contributed importantly to the management and recovery of listed species.

Wildlife mortality investigation and disease research: contributions of the USGS National Wildlife Health Center to endangered species management and recovery.

PubMed

Brand, Christopher J

2013-12-01

The U.S. Geological Survey-National Wildlife Health Center (NWHC) provides diagnostic services, technical assistance, applied research, and training to federal, state, territorial, and local government agencies and Native American tribes on wildlife diseases and wildlife health issues throughout the United States and its territories, commonwealth, and freely associated states. Since 1975, >16,000 carcasses and specimens from vertebrate species listed under the Endangered Species Act have been submitted to NWHC for determination of causes of morbidity or mortality or assessment of health/disease status. Results from diagnostic investigations, analyses of the diagnostic database, technical assistance and consultation, field investigation of epizootics, and wildlife disease research by NWHC wildlife disease specialists have contributed importantly to the management and recovery of listed species.

[Risks associated with unrestricted consumption of alkaline-reduced water].

PubMed

Henry, Marc; Chambron, Jacques

2014-01-01

Consumption of alkaline reduced water produced by domestic electrolysis devices was approved in Japan in 1965 by the Minister of Health, Work and Wellbeing, for the treatment of gastrointestinal disorders. Today, these devices are also freely available in France. The commercial information provided with the devices recommends the consumption of 1 to 1.5 liters per day, not only for gastrointestinal disorders but also for numerous other illnesses such as diabetes, cancer and inflammation. Academic research on this subject has been undergoing in Japan since 1990, and has established that the active ingredient is dissolved dihydrogen, which eliminates the free radical HO· in vivo. It has also been shown that electrode degradation during use of the devices releases highly reactive platinum nanoparticles, the toxicity of which is unknown. The authors of this report recommend alerting the French health authorities to the uncontrolled availability of these devices that generate drug substances and should therefore be subject to regulatory requirements.

Expanding understanding of optical variability in Lake Superior with a 4-year dataset

NASA Astrophysics Data System (ADS)

Mouw, Colleen B.; Ciochetto, Audrey B.; Grunert, Brice; Yu, Angela

2017-07-01

Lake Superior is one of the largest freshwater lakes on our planet, but few optical observations have been made to allow for the development and validation of visible spectral satellite remote sensing products. The dataset described here focuses on coincidently observing inherent and apparent optical properties along with biogeochemical parameters. Specifically, we observe remote sensing reflectance, absorption, scattering, backscattering, attenuation, chlorophyll concentration, and suspended particulate matter over the ice-free months of 2013-2016. The dataset substantially increases the optical knowledge of the lake. In addition to visible spectral satellite algorithm development, the dataset is valuable for characterizing the variable light field, particle, phytoplankton, and colored dissolved organic matter distributions, and helpful in food web and carbon cycle investigations. The compiled data can be freely accessed at https://seabass.gsfc.nasa.gov/archive/URI/Mouw/LakeSuperior/.

Structural Characterization of Apomyoglobin Self-Associated Species in Aqueous Buffer and Urea Solution

PubMed Central

Chow, Charles; Kurt, Neşe; Murphy, Regina M.; Cavagnero, Silvia

2006-01-01

The biophysical characterization of nonfunctional protein aggregates at physiologically relevant temperatures is much needed to gain deeper insights into the kinetic and thermodynamic relationships between protein folding and misfolding. Dynamic and static laser light scattering have been employed for the detection and detailed characterization of apomyoglobin (apoMb) soluble aggregates populated at room temperature upon dissolving the purified protein in buffer at pH 6.0, both in the presence and absence of high concentrations of urea. Unlike the β-sheet self-associated aggregates previously reported for this protein at high temperatures, the soluble aggregates detected here have either α-helical or random coil secondary structure, depending on solvent and solution conditions. Hydrodynamic diameters range from 80 to 130 nm, with semiflexible chain-like morphology. The combined use of low pH and high urea concentration leads to structural unfolding and complete elimination of the large aggregates. Even upon starting from this virtually monomeric unfolded state, however, protein refolding leads to the formation of severely self-associated species with native-like secondary structure. Under these conditions, kinetic apoMb refolding proceeds via two parallel routes: one leading to native monomer, and the other leading to a misfolded and heavily self-associated state bearing native-like secondary structure. PMID:16214860

A combined radio- and stable-isotopic study of a California coastal aquifer system

USGS Publications Warehouse

Swarzenski, Peter W.; Baskaran, Mark; Rosenbauer, Robert J.; Edwards, Brian D.; Land, Michael

2013-01-01

Stable and radioactive tracers were utilized in concert to characterize geochemical processes in a complex coastal groundwater system and to provide constraints on the kinetics of rock/water interactions. Groundwater samples from wells within the Dominguez Gap region of Los Angeles County, California were analyzed for a suite of major cations (Na+, K+, Mg2+, Ca2+) and anions (Cl−, SO42−), silica, alkalinity, select trace elements (Ba, B, Sr), dissolved oxygen, stable isotopes of hydrogen (δD), oxygen (δ18O), dissolved inorganic carbon (δ13CDIC), and radioactive isotopes (3H, 222Rn and 223,224,226,228Ra). In the study area, groundwater may consist of a complex mixture of native groundwater, intruded seawater, non-native injected water, and oil-field brine water. In some wells, Cl− concentrations attained seawater-like values and in conjunction with isotopically heavier δ18O values, these tracers provide information on the extent of seawater intrusion and/or mixing with oil-field brines. Groundwater 3H above 1 tritium unit (TU) was observed only in a few select wells close to the Dominguez Gap area and most other well groundwater was aged pre-1952. Based on an initial 14C value for the study site of 90 percent modern carbon (pmc), groundwater age estimates likely extend beyond 20 kyr before present and confirm deep circulation of some native groundwater through multiple aquifers. Enriched values of groundwater δ13CDIC in the absence of SO42− imply enhanced anaerobic microbial methanogenesis. While secular equilibrium was observed for 234U/238U (activity ratios ~1) in host matrices, strong isotopic fractionation in these groundwater samples can be used to obtain information of adsorption/desorption kinetics. Calculated Ra residence times are short, and the associated desorption rate constant is about three orders of magnitude slower than that of the adsorption rate constant. Combined stable- and radio-isotopic results provide unique insights into aquifer characteristics, such as geochemical cycling, rock/water interactions, and subsurface transport and mixing.

Biotransformation model of neutral and weakly polar organic compounds in fish incorporating internal partitioning.

PubMed

Kuo, Dave T F; Di Toro, Dominic M

2013-08-01

A model for whole-body in vivo biotransformation of neutral and weakly polar organic chemicals in fish is presented. It considers internal chemical partitioning and uses Abraham solvation parameters as reactivity descriptors. It assumes that only chemicals freely dissolved in the body fluid may bind with enzymes and subsequently undergo biotransformation reactions. Consequently, the whole-body biotransformation rate of a chemical is retarded by the extent of its distribution in different biological compartments. Using a randomly generated training set (n = 64), the biotransformation model is found to be: log (HLφfish ) = 2.2 (±0.3)B - 2.1 (±0.2)V - 0.6 (±0.3) (root mean square error of prediction [RMSE] = 0.71), where HL is the whole-body biotransformation half-life in days, φfish is the freely dissolved fraction in body fluid, and B and V are the chemical's H-bond acceptance capacity and molecular volume. Abraham-type linear free energy equations were also developed for lipid-water (Klipidw ) and protein-water (Kprotw ) partition coefficients needed for the computation of φfish from independent determinations. These were found to be 1) log Klipidw  = 0.77E - 1.10S - 0.47A - 3.52B + 3.37V + 0.84 (in Lwat /kglipid ; n = 248, RMSE = 0.57) and 2) log Kprotw  = 0.74E - 0.37S - 0.13A - 1.37B + 1.06V - 0.88 (in Lwat /kgprot ; n = 69, RMSE = 0.38), where E, S, and A quantify dispersive/polarization, dipolar, and H-bond-donating interactions, respectively. The biotransformation model performs well in the validation of HL (n = 424, RMSE = 0.71). The predicted rate constants do not exceed the transport limit due to circulatory flow. Furthermore, the model adequately captures variation in biotransformation rate between chemicals with varying log octanol-water partitioning coefficient, B, and V and exhibits high degree of independence from the choice of training chemicals. The present study suggests a new framework for modeling chemical reactivity in biological systems. Copyright © 2013 SETAC.

DOCKSCORE: a webserver for ranking protein-protein docked poses.

PubMed

Malhotra, Sony; Mathew, Oommen K; Sowdhamini, Ramanathan

2015-04-24

Proteins interact with a variety of other molecules such as nucleic acids, small molecules and other proteins inside the cell. Structure-determination of protein-protein complexes is challenging due to several reasons such as the large molecular weights of these macromolecular complexes, their dynamic nature, difficulty in purification and sample preparation. Computational docking permits an early understanding of the feasibility and mode of protein-protein interactions. However, docking algorithms propose a number of solutions and it is a challenging task to select the native or near native pose(s) from this pool. DockScore is an objective scoring scheme that can be used to rank protein-protein docked poses. It considers several interface parameters, namely, surface area, evolutionary conservation, hydrophobicity, short contacts and spatial clustering at the interface for scoring. We have implemented DockScore in form of a webserver for its use by the scientific community. DockScore webserver can be employed, subsequent to docking, to perform scoring of the docked solutions, starting from multiple poses as inputs. The results, on scores and ranks for all the poses, can be downloaded as a csv file and graphical view of the interface of best ranking poses is possible. The webserver for DockScore is made freely available for the scientific community at: http://caps.ncbs.res.in/dockscore/ .

The three-dimensional structure of the native ternary complex of bovine pancreatic procarboxypeptidase A with proproteinase E and chymotrypsinogen C.

PubMed Central

Gomis-Rüth, F X; Gómez, M; Bode, W; Huber, R; Avilés, F X

1995-01-01

The metalloexozymogen procarboxypeptidase A is mainly secreted in ruminants as a ternary complex with zymogens of two serine endoproteinases, chymotrypsinogen C and proproteinase E. The bovine complex has been crystallized, and its molecular structure analysed and refined at 2.6 A resolution to an R factor of 0.198. In this heterotrimer, the activation segment of procarboxypeptidase A essentially clamps the other two subunits, which shield the activation sites of the former from tryptic attack. In contrast, the propeptides of both serine proproteinases are freely accessible to trypsin. This arrangement explains the sequential and delayed activation of the constituent zymogens. Procarboxypeptidase A is virtually identical to the homologous monomeric porcine form. Chymotrypsinogen C displays structural features characteristic for chymotrypsins as well as elastases, except for its activation domain; similar to bovine chymotrypsinogen A, its binding site is not properly formed, while its surface located activation segment is disordered. The proproteinase E structure is fully ordered and strikingly similar to active porcine elastase; its specificity pocket is occluded, while the activation segment is fixed to the molecular surface. This first structure of a native zymogen from the proteinase E/elastase family does not fundamentally differ from the serine proproteinases known so far. Images PMID:7556081

Factors affecting compliance with preventive treatment for tuberculosis at Mistassini Lake, Quebec, Canada.

PubMed

Rideout, M; Menzies, R

1994-02-01

Non-compliance is the most important cause of failure of anti-tuberculous therapy throughout the world. In 1990 and 1991, an outbreak of tuberculosis occurred on the Mistassini Cree territory in Northern Quebec, Canada, and a number of cases of active tuberculosis occurred among known tuberculin-positive contacts who were non-compliant with preventive therapy. To better understand the factors affecting compliance with preventive treatment, a review of patients prescribed preventive treatment over the past 10 y was conducted. A freely-translated, interviewer-administered questionnaire was used to measure personal/lifestyle factors and knowledge/attitudes about tuberculosis. Clinic dossiers were reviewed to assess compliance. One hundred and two (102) subjects prescribed preventive treatment between 1981 and 1991 were interviewed, of whom 33.7% were judged to have been compliant. The most significant factor associated with compliance with preventive therapy was year of therapy. Between 1981 and 1985, 78% completed treatment, compared to less than 20% since 1986 (p < .0001). The major factor identified as associated with this sudden change was a shift in responsibility for tuberculosis treatment follow-up from native community health workers to non-native nurses in 1985/86. We conclude that tuberculosis control programs must be tailored to take into account the importance of cultural factors in promoting compliance with therapy.

Does language guide event perception? Evidence from eye movements

PubMed Central

Papafragou, Anna; Hulbert, Justin; Trueswell, John

2008-01-01

Languages differ in how they encode motion. When describing bounded motion, English speakers typically use verbs that convey information about manner (e.g., slide, skip, walk) rather than path (e.g., approach, ascend), whereas Greek speakers do the opposite. We investigated whether this strong cross-language difference influences how people allocate attention during motion perception. We compared eye movements from Greek and English speakers as they viewed motion events while (a) preparing verbal descriptions, or (b) memorizing the events. During the verbal description task, speakers’ eyes rapidly focused on the event components typically encoded in their native language, generating significant cross-language differences even during the first second of motion onset. However, when freely inspecting ongoing events, as in the memorization task, people allocated attention similarly regardless of the language they speak. Differences between language groups arose only after the motion stopped, such that participants spontaneously studied those aspects of the scene that their language does not routinely encode in verbs. These findings offer a novel perspective on the relation between language and perceptual/cognitive processes. They indicate that attention allocation during event perception is not affected by the perceiver’s native language; effects of language arise only when linguistic forms are recruited to achieve the task, such as when committing facts to memory. PMID:18395705

iAnn: an event sharing platform for the life sciences.

PubMed

Jimenez, Rafael C; Albar, Juan P; Bhak, Jong; Blatter, Marie-Claude; Blicher, Thomas; Brazas, Michelle D; Brooksbank, Cath; Budd, Aidan; De Las Rivas, Javier; Dreyer, Jacqueline; van Driel, Marc A; Dunn, Michael J; Fernandes, Pedro L; van Gelder, Celia W G; Hermjakob, Henning; Ioannidis, Vassilios; Judge, David P; Kahlem, Pascal; Korpelainen, Eija; Kraus, Hans-Joachim; Loveland, Jane; Mayer, Christine; McDowall, Jennifer; Moran, Federico; Mulder, Nicola; Nyronen, Tommi; Rother, Kristian; Salazar, Gustavo A; Schneider, Reinhard; Via, Allegra; Villaveces, Jose M; Yu, Ping; Schneider, Maria V; Attwood, Teresa K; Corpas, Manuel

2013-08-01

We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available. http://iann.pro/iannviewer manuel.corpas@tgac.ac.uk.

Quality of groundwater at and near an aquifer storage and recovery site, Bexar, Atascosa, and Wilson Counties, Texas, June 2004-August 2008

USGS Publications Warehouse

Otero, Cassi L.; Petri, Brian L.

2010-01-01

The U.S. Geological Survey, in cooperation with the San Antonio Water System, did a study during 2004-08 to characterize the quality of native groundwater from the Edwards aquifer and pre- and post-injection water from the Carrizo aquifer at and near an aquifer storage and recovery (ASR) site in Bexar, Atascosa, and Wilson Counties, Texas. Groundwater samples were collected and analyzed for selected physical properties and constituents to characterize the quality of native groundwater from the Edwards aquifer and pre- and post-injection water from the Carrizo aquifer at and near the ASR site. Geochemical and isotope data indicated no substantial changes in major-ion, trace-element, and isotope chemistry occurred as the water from the Edwards aquifer was transferred through a 38-mile pipeline to the aquifer storage and recovery site. The samples collected from the four ASR recovery wells were similar in major-ion and stable isotope chemistry compared to the samples collected from the Edwards aquifer source wells and the ASR injection well. The similarity could indicate that as Edwards aquifer water was injected, it displaced native Carrizo aquifer water, or, alternatively, if mixing of Edwards and Carrizo aquifer waters was occurring, the major-ion and stable isotope signatures for the Carrizo aquifer water might have been obscured by the signatures of the injected Edwards aquifer water. Differences in the dissolved iron and dissolved manganese concentrations indicate that either minor amounts of mixing occurred between the waters from the two aquifers, or as Edwards aquifer water displaced Carrizo aquifer water it dissolved the iron and manganese directly from the Carrizo Sand. Concentrations of radium-226 in the samples collected at the ASR recovery wells were smaller than the concentrations in samples collected from the Edwards aquifer source wells and from the ASR injection well. The smaller radium-226 concentrations in the samples collected from the ASR recovery wells likely indicate some degree of mixing of the two waters occurred rather than continued decay of radium-226 in the injected water. Geochemical and isotope data measured in samples collected in May 2005 from two Carrizo aquifer monitoring wells and in July 2008 from the three ASR production-only wells in the northern section of the ASR site indicate that injected Edwards aquifer water had not migrated to these five sites. Geochemical and isotope data measured in samples collected from Carrizo aquifer wells in 2004, 2005, and 2008 were graphically analyzed to determine if changes in chemistry could be detected. Major-ion, trace element, and isotope chemistry varied spatially in the samples collected from the Carrizo aquifer. With the exception of a few samples, major-ion concentrations measured in samples collected in Carrizo aquifer wells in 2004, 2005, and 2008 were similar. A slightly larger sulfate con-centration and a slightly smaller bicarbonate concentration were measured in samples collected in 2005 and 2008 from well NC1 compared to samples collected at well NC1 in 2004. Larger sodium concentrations and smaller calcium, magnesium, bicarbonate, and sulfate concentrations were measured in samples collected in 2008 from well WC1 than in samples collected at this well in 2004 and 2005. Larger calcium and magnesium concentrations and a smaller sodium concentration were measured in the samples collected in 2008 at well EC2 compared to samples collected at this well in 2004 and 2005. While in some cases the computed percent differences (compared to concentrations from June 2004) in dissolved iron and dissolved manganese concentrations in 11 wells sampled in the Carrizo aquifer in 2005 and 2008 were quite large, no trends that might have been caused by migration of injected Edwards aquifer water were observed. Because of the natural variation in geochemical data in the Carrizo aquifer and the small data set collected for this study, differences in major-ion and

Application of ultrafiltration and stable isotopic amendments to field studies of mercury partitioning to filterable carbon in lake water and overland runoff.

PubMed

Babiarz, Christopher L; Hurley, James P; Krabbenhoft, David P; Gilmour, Cynthia; Branfireun, Brian A

2003-03-20

Results from pilot studies on colloidal phase transport of newly deposited mercury in lake water and overland runoff demonstrate that the combination of ultrafiltration, and stable isotope amendment techniques is a viable tool for the study of mercury partitioning to filterable carbon. Ultrafiltration mass balance calculations were generally excellent, averaging 97.3, 96.1 and 99.8% for dissolved organic carbon (DOC), total mercury (Hg(T)), and methylmercury (MeHg), respectively. Sub nanogram per liter quantities of isotope were measurable, and the observed phase distribution from replicate ultrafiltration separations on lake water agreed within 20%. We believe the data presented here are the first published colloidal phase mercury data on lake water and overland runoff from uncontaminated sites. Initial results from pilot-scale lake amendment experiments indicate that the choice of matrix used to dissolve the isotope did not affect the initial phase distribution of the added mercury in the lake. In addition there was anecdotal evidence that native MeHg was either recently produced in the system, or at a minimum, that this 'old' MeHg partitions to the same subset of DOC that binds the amended mercury. Initial results from pilot-scale overland runoff experiments indicate that less than 20% of newly deposited mercury was transported in the filterable fraction (<0.7 microm). There is some indication of colloidal phase enrichment of mercury in runoff compared to the phase distribution of organic carbon, but the mechanism of this enrichment is unclear. The phase distribution of newly deposited mercury can differ from that of organic carbon and native mercury, suggesting that the quality of the carbon (available ligands), not the quantity of carbon, regulates partitioning. Further characterization of DOC is needed to clarify the underlying mechanisms.

Interactions between magnetite and humic substances: redox reactions and dissolution processes.

PubMed

Sundman, Anneli; Byrne, James M; Bauer, Iris; Menguy, Nicolas; Kappler, Andreas

2017-10-19

Humic substances (HS) are redox-active compounds that are ubiquitous in the environment and can serve as electron shuttles during microbial Fe(III) reduction thus reducing a variety of Fe(III) minerals. However, not much is known about redox reactions between HS and the mixed-valent mineral magnetite (Fe 3 O 4 ) that can potentially lead to changes in Fe(II)/Fe(III) stoichiometry and even dissolve the magnetite. To address this knowledge gap, we incubated non-reduced (native) and reduced HS with four types of magnetite that varied in particle size and solid-phase Fe(II)/Fe(III) stoichiometry. We followed dissolved and solid-phase Fe(II) and Fe(III) concentrations over time to quantify redox reactions between HS and magnetite. Magnetite redox reactions and dissolution processes with HS varied depending on the initial magnetite and HS properties. The interaction between biogenic magnetite and reduced HS resulted in dissolution of the solid magnetite mineral, as well as an overall reduction of the magnetite. In contrast, a slight oxidation and no dissolution was observed when native and reduced HS interacted with 500 nm magnetite. This variability in the solubility and electron accepting and donating capacity of the different types of magnetite is likely an effect of differences in their reduction potential that is correlated to the magnetite Fe(II)/Fe(III) stoichiometry, particle size, and crystallinity. Our study suggests that redox-active HS play an important role for Fe redox speciation within minerals such as magnetite and thereby influence the reactivity of these Fe minerals and their role in biogeochemical Fe cycling. Furthermore, such processes are also likely to have an effect on the fate of other elements bound to the surface of Fe minerals.

Role of dissolved organic carbon upon re-entrainment and surface properties of aquifer bacteria and bacteria-sized microspheres during subsurface transport (Invited)

NASA Astrophysics Data System (ADS)

Harvey, R. W.; Metge, D. W.; Mohanram, A.; Gao, X.; Chorover, J.

2010-12-01

Susceptibilities for in-situ re-entrainment of attached 0.2 and 1.0 μm (diameter) microspheres and groundwater bacteria (Pseudomonas stuzeri and uncultured, native bacteria) were assessed during transport studies involving an organically contaminated, sandy aquifer in Cape Cod, MA. Aquifer sediments between pairs of injection and sampling wells were initially loaded with fluorescently labeled, carboxylated microspheres and bacteria that had been stained with the DNA-specific fluorochrome 4',6-diamidino-2-phenylindole. In response to subsequent hydrodynamic perturbations and injections of deionized water (ionic strength reduction), anionic surfactants (77 μM linear alkylbenzene sulfonates, LAS) and non-ionic surfactant (76 μM polyoxyethylene sorbitan monooleate, Tween 80), differing patterns of re-entrainment were evident for the two colloids. Injections of anionic surfactant and deionized water were the most efficient in causing detachment of the highly hydrophilic and negatively charged microspheres, but largely ineffective in causing re-entrainment of bacteria. In contrast, the nonionic surfactant was highly effective in re-entraining bacteria, but not microspheres. The hydrophobicities and zeta potentials of the indigenous bacteria were highly sensitive to modest concentration changes (0.6 to 1.3 mg L-1) in groundwater dissolved organic carbon (DOC), whereas the microspheres were largely unaffected. The most hydrophilic and negatively charged bacterial community was isolated from groundwater having the lowest DOC. FTIR spectra indicated that the community from the lowest DOC groundwater also had the highest average density of surface carboxyl groups. This indicates that DOC may have a biological effect on native bacteria resulting in changes to surface structures or changes in the makeup of the bacterial community.

Sorption-induced effects of humic substances on mass transfer of organic pollutants through aqueous diffusion boundary layers: the example of water/air exchange.

PubMed

Ramus, Ksenia; Kopinke, Frank-Dieter; Georgi, Anett

2012-02-21

This study examines the effect of dissolved humic substances (DHS) on the rate of water-gas exchange of organic compounds under conditions where diffusion through the aqueous boundary layer is rate-determining. A synthetic surfactant was applied for comparison. Mass-transfer coefficients were determined from the rate of depletion of the model compounds by means of an apparatus containing a stirred aqueous solution with continuous purging of the headspace above the solution. In addition, experiments with continuous passive dosing of analytes into the water phase were conducted to simulate a system where thermodynamic activity of the chemical in the aqueous phase is identical in the presence and absence of DHS. The experimental results show that DHS and surfactants can affect water-gas exchange rates by the superposition of two mechanisms: (1) hydrodynamic effects due to surface film formation ("surface smoothing"), and (2) sorption-induced effects. Whether sorption accelerates or retards mass transfer depends on its effect on the thermodynamic activity of the pollutant in the aqueous phase. Mass transfer will be retarded if the activity (or freely dissolved concentration) of the pollutant is decreased due to sorption. If it remains unchanged (e.g., due to fast equilibration with a sediment acting as a large source phase), then DHS and surfactant micelles can act as an additional shuttle for the pollutants, enhancing the flux through the boundary layer.

Probabilistic approaches to accounting for data variability in the practical application of bioavailability in predicting aquatic risks from metals.

PubMed

Ciffroy, Philippe; Charlatchka, Rayna; Ferreira, Daniel; Marang, Laura

2013-07-01

The biotic ligand model (BLM) theoretically enables the derivation of environmental quality standards that are based on true bioavailable fractions of metals. Several physicochemical variables (especially pH, major cations, dissolved organic carbon, and dissolved metal concentrations) must, however, be assigned to run the BLM, but they are highly variable in time and space in natural systems. This article describes probabilistic approaches for integrating such variability during the derivation of risk indexes. To describe each variable using a probability density function (PDF), several methods were combined to 1) treat censored data (i.e., data below the limit of detection), 2) incorporate the uncertainty of the solid-to-liquid partitioning of metals, and 3) detect outliers. From a probabilistic perspective, 2 alternative approaches that are based on log-normal and Γ distributions were tested to estimate the probability of the predicted environmental concentration (PEC) exceeding the predicted non-effect concentration (PNEC), i.e., p(PEC/PNEC>1). The probabilistic approach was tested on 4 real-case studies based on Cu-related data collected from stations on the Loire and Moselle rivers. The approach described in this article is based on BLM tools that are freely available for end-users (i.e., the Bio-Met software) and on accessible statistical data treatments. This approach could be used by stakeholders who are involved in risk assessments of metals for improving site-specific studies. Copyright © 2013 SETAC.

Predicting bioavailability and accumulation of organochlorine pesticides by Japanese medaka in the presence of humic acid and natural organic matter using passive sampling membranes.

PubMed

Ke, Runhui; Luo, Jianping; Sun, Liwei; Wang, Zijian; Spear, Philip A

2007-10-01

Adsorption to dissolved organic matter (DOM) may significantly decrease the freely dissolved concentration of many hydrophobic organic compounds and, hence, result in reduced bioavailability to aquatic organisms. Here, the suitability of using triolein-embedded cellulose acetate membrane (TECAM) as a biomimetic surrogate to assess the bioavailability of organochlorine pesticides (OCPs) in water in the presence of DOM was explored. The accumulation of OCPs was measured in TECAM and pelagic Japanese medaka (Oryzias latipes) in the laboratory after 12 h exposure to water containing different levels of Aldrich humic acid. Further, OCP uptake by TECAM and medaka in real aqueous environments was evaluated after 30 d exposures in two sites. Laboratory results showed that OCP uptake by medaka consistently decreased with increasing levels of humic acid in the range of 0-15 mg C/L in sample solutions. This tendency was closely mimicked by OCP accumulation in TECAM under the same conditions. Field results showed that TECAM accumulated similar OCP patterns as medaka (r2 = 0.92 for site 1 and r2 = 0.94 for site 2), although comparison of the in-field eight OCP concentrations in TECAM to those in medaka yielded approximately a factor of 3 (on a wet weight basis). These results suggest that the TECAM method can be used as a simple and useful tool to predict the bioavailability and bioaccumulation potential of poorly biotransformed organic compounds in pelagic fish in aqueous environment.

Bioconcentration of perfluoroalkyl substances by Chironomus plumosus larvae in water with different types of dissolved organic matters.

PubMed

Wen, Wu; Xia, Xinghui; Chen, Xi; Wang, Haotian; Zhu, Baotong; Li, Husheng; Li, Yang

2016-06-01

The effects of four types of dissolved organic matters (DOM) on the bioconcentration of perfluoroalkyl substances (PFASs) in Chironomus plumosus larvae have been studied. The PFASs included perfluorooctane sulfonate (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), perfluoroundecanoic acid (PFUnA), and perfluorododecanoic acid (PFDoA). The DOM included humic acid (HA), fulvic acid (FA), tannic acid (TA), and a protein, peptone (PEP), and their concentrations ranged from 0 to 50 mg L(-1). The results showed that, upon bioconcentration equilibrium, the body burdens of longer perfluoroalkyl chain PFASs (PFOS, PFDA, PFUnA and PFDoA) decreased with PEP and HA concentrations while increased with FA and TA concentrations. When FA and TA concentrations increased from 0 to 50 mg L(-1), body burdens of these PFASs increased by 7.5%-148.8% and 5.7%-37.1%, respectively. However, the DOM had no significant impact on the body burdens of shorter perfluoroalkyl chain PFASs (PFOA and PFNA). All of the four types of DOM lowered not only the uptake rate constants (ku) of PFASs due to the decrease of freely dissolved PFAS concentrations, but also the elimination rate constants (ke) due to the inhibition effect of DOM on the PFAS elimination from the larvae. The reduction in the two constants varied with both DOM and PFAS types. In the presence of PEP and HA with larger molecular weights, the ku values decreased more than ke, leading to the decreased body burdens of longer perfluoroalkyl chain PFASs. As for FA and TA with smaller molecular weights, the ke values decreased more than ku, resulting in increased body burdens of longer perfluoroalkyl chain PFASs. This study suggests that the effects of DOM on PFAS bioconcentration depend not only on the concentration but also on the molecule weight of DOM, which should be considered in the bioavailability assessment of PFASs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Equilibrium geochemical modeling of a seasonal thermal energy storage aquifer field test

NASA Technical Reports Server (NTRS)

Stottlemyre, J. S.

1980-01-01

A geochemical mathematical modeling study designed to investigate the well plugging problems encountered at the Auburn University experimental field tests is summarized. The results, primarily of qualitative interest, include: (1) loss of injectivity was probably due to a combination of native particulate plugging and clay swelling and dispersion; (2) fluid-fluid incompatibilities, hydrothermal reactions, and oxidation reactions were of insignificant magnitude or too slow to have contributed markedly to the plugging; and (3) the potential for and contributions from temperature-induced dissolved gas solubility reductions, capillary boundary layer viscosity increases, and microstructural deformation cannot be deconvolved from the available data.

Equilibrium distribution of dissolved sulphur species in water at 25°C and 1 atm total pressure

USGS Publications Warehouse

Garrels, R.M.; Naeser, C.R.

1958-01-01

The Eh-pH diagrams for the equilibrium concentrations in aqueous solution at 25°C of native sulphur and all the various sulphur-containing ions and acids from which the ions are produced have been constructed for systems having a total sulphur concentration of 0.1 molar. The composite of these diagrams indicates that elemental sulphur, H2S, HS− HSO4− and SO4 are the species that predominate in the environments that might be found in nature. This indication is in agreement with the composition of all sulphur-containing minerals.

COPRED: prediction of fold, GO molecular function and functional residues at the domain level.

PubMed

López, Daniel; Pazos, Florencio

2013-07-15

Only recently the first resources devoted to the functional annotation of proteins at the domain level started to appear. The next step is to develop specific methodologies for predicting function at the domain level based on these resources, and to implement them in web servers to be used by the community. In this work, we present COPRED, a web server for the concomitant prediction of fold, molecular function and functional sites at the domain level, based on a methodology for domain molecular function prediction and a resource of domain functional annotations previously developed and benchmarked. COPRED can be freely accessed at http://csbg.cnb.csic.es/copred. The interface works in all standard web browsers. WebGL (natively supported by most browsers) is required for the in-line preview and manipulation of protein 3D structures. The website includes a detailed help section and usage examples. pazos@cnb.csic.es.

Site-directed antibody immobilization using a protein A-gold binding domain fusion protein for enhanced SPR immunosensing.

PubMed

de Juan-Franco, Elena; Caruz, Antonio; Pedrajas, J R; Lechuga, Laura M

2013-04-07

We have implemented a novel strategy for the oriented immobilization of antibodies onto a gold surface based on the use of a fusion protein, the protein A-gold binding domain (PAG). PAG consists of a gold binding peptide (GBP) coupled to the immunoglobulin-binding domains of staphylococcal protein A. This fusion protein provides an easy and fast oriented immobilization of antibodies preserving its native structure, while leaving the antigen binding sites (Fab) freely exposed. Using this immobilization strategy, we have demonstrated the performance of the immunosensing of the human Growth Hormone by SPR. A limit of detection of 90 ng mL(-1) was obtained with an inter-chip variability lower than 7%. The comparison of this method with other strategies for the direct immobilization of antibodies over gold surfaces has showed the enhanced sensitivity provided by the PAG approach.

The role of hemoglobin oxygen affinity in oxygen transport at high altitude.

PubMed

Winslow, Robert M

2007-09-30

Hemoglobin is involved in the regulation of O(2) transport in two ways: a long-term adjustment in red cell mass is mediated by erythropoietin (EPO), a response to renal oxgyenation. Short-term, rapid-response adjustments are mediated by ventilation, cardiac output, hemoglobin oxygen affinity (P50), barriers to O(2) diffusion, and the control of local microvascular tissue perfusion. The distribution of O(2) between dissolved (PO2) and hemoglobin-bound (saturation) is the familiar oxygen equilibrium curve, whose position is noted as P50. Human hemoglobin is not genetically adapted for function at high altitude. However, more specialized species native to high altitudes (guinea pig and bar-headed goose, for example) seem to have a lower P50 than their sea level counterparts, an adaptation that presumably promotes O(2) uptake from a hypoxic environment. Humans, native to very high altitude either in the Andes or Himalayan mountains, also can increase O(2) affinity, not because of a fundamental difference in hemoglobin structure or function, but because of extreme hyperventilation and alkalosis.

ICPMS analysis of proteins separated by Native-PAGE: Evaluation of metaloprotein profiles in human synovial fluid with acute and chronic arthritis.

PubMed

Moyano, Mario F; Mariño-Repizo, Leonardo; Tamashiro, Héctor; Villegas, Liliana; Acosta, Mariano; Gil, Raúl A

2016-07-01

The role of trace elements bound to proteins in the etiology and pathogenesis of rheumatoid arthritis (RA) remains unclear. In this sense, the identification and detection of metalloproteins has a strong and growing interest. Metalloprotein studies are currently carried out by polyacrylamide gel electrophoresis (PAGE) associated to inductively coupled plasma mass spectrometry (ICPMS), and despite that complete information can be obtained for metals such as Fe, Cu and Zn, difficulties due to poor sensitivity for other trace elements such as Sn, As, etc, are currently faced. In the present work, a simple and fast method for the determination of trace metals bound to synovial fluid (SF) proteins was optimized. Proteins from SF (long and short-term RA) were separated in ten fractions by native PAGE, then dissolved in nitric acid and peroxide hydrogen, and analyzed by ICPMS. Fifteen metals were determined in each separated protein fraction (band). Adequate calibration of proteins molecular weight allowed stablishing which protein type were bound to different metals. Copyright © 2016 Elsevier GmbH. All rights reserved.

Hydraulic transport across hydrophilic and hydrophobic nanopores: Flow experiments with water and n-hexane.

PubMed

Gruener, Simon; Wallacher, Dirk; Greulich, Stefanie; Busch, Mark; Huber, Patrick

2016-01-01

We experimentally explore pressure-driven flow of water and n-hexane across nanoporous silica (Vycor glass monoliths with 7- or 10-nm pore diameters, respectively) as a function of temperature and surface functionalization (native and silanized glass surfaces). Hydraulic flow rates are measured by applying hydrostatic pressures via inert gases (argon and helium, pressurized up to 70 bar) on the upstream side in a capacitor-based membrane permeability setup. For the native, hydrophilic silica walls, the measured hydraulic permeabilities can be quantitatively accounted for by bulk fluidity provided we assume a sticking boundary layer, i.e., a negative velocity slip length of molecular dimensions. The thickness of this boundary layer is discussed with regard to previous capillarity-driven flow experiments (spontaneous imbibition) and with regard to velocity slippage at the pore walls resulting from dissolved gas. Water flow across the silanized, hydrophobic nanopores is blocked up to a hydrostatic pressure of at least 70 bar. The absence of a sticking boundary layer quantitatively accounts for an enhanced n-hexane permeability in the hydrophobic compared to the hydrophilic nanopores.

Understanding the rates of nonpolar organic chemical accumulation into passive samplers deployed in the environment: Guidance for passive sampler deployments.

PubMed

Apell, Jennifer N; Tcaciuc, A Patricia; Gschwend, Philip M

2016-07-01

Polymeric passive samplers have become a common method for estimating freely dissolved concentrations in environmental media. However, this approach has not yet been adopted by investigators conducting remedial investigations of contaminated environmental sites. Successful adoption of this sampling methodology relies on an understanding of how passive samplers accumulate chemical mass as well as developing guidance for the design and deployment of passive samplers. Herein, we outline the development of a simple mathematical relationship of the environmental, polymer, and chemical properties that control the uptake rate. This relationship, called a timescale, is then used to illustrate how each property controls the rate of equilibration in samplers deployed in the water or in the sediment. Guidance is also given on how to use the timescales to select an appropriate polymer, deployment time, and suite of performance reference compounds. Integr Environ Assess Manag 2016;12:486-492. © 2015 SETAC. © 2015 SETAC.

Comparing black carbon types in sequestering polybrominated diphenyl ethers (PBDEs) in sediments

PubMed Central

Jia, Fang; Gan, Jay

2014-01-01

Polybrominated diphenyl ethers (PBDEs) are widely found in sediments, especially congeners from the penta-BDE formula. Due to their strong affinity for black carbon (BC), bioavailability of PBDEs may be decreased in BC-amended sediments. In this study, we used a matrix-SPME method to measure the freely dissolved concentration (Cfree) of PBDEs as a parameter of their potential bioavailability and evaluated the differences among biochar, charcoal, and activated carbon. Activated carbon displayed a substantially greater sequestration capacity than biochar or charcoal. At 1% amendment rate in sediment with low organic carbon (OC) content (0.12%), Cfree of six PBDEs was reduced by 47.5–78.0%, 47.3–77.5%, and 94.1–98.3% with biochar, charcoal, and activated carbon, respectively, while the sequestration was more limited in sediment with high OC content (0.87%). Therefore, it is important to consider the type and properties of the BC and the sediment in BC-based remediation or mitigation. PMID:24047549

Monitoring the freely dissolved concentrations of polycyclic aromatic hydrocarbons (PAH) and alkylphenols (AP) around a Norwegian oil platform by holistic passive sampling.

PubMed

Harman, Christopher; Thomas, Kevin V; Tollefsen, Knut Erik; Meier, Sonnich; Bøyum, Olav; Grung, Merete

2009-11-01

In order to assess the environmental impact of aquatic discharges from the offshore oil industry, polar organic chemical integrative samplers (POCIS) and semipermeable membrane devices (SPMDs) were deployed around an oil platform and at reference locations in the North Sea. Exposure to polycyclic aromatic hydrocarbons (PAH) and alkylated phenols (AP) was determined from passive sampler accumulations using an empirical uptake model, the dissipation of performance reference compounds and adjusted laboratory derived sampling rates. Exposure was relatively similar within 1-2 km of the discharge point, with levels dominated by short chained C1-C3 AP isomers (19-51 ngL(-1)) and alkylated naphthalenes, phenanthrenes and dibenzothiophenes (NPD, 29-45 ngL(-1)). Exposure stations showed significant differences to reference sites for NPD, but not always for more hydrophobic PAH. These concentrations are several orders of magnitude lower than those reported to give both acute and sub-lethal effects, although their long term consequences are unknown.

Modelling the fate of micropollutants in the marine environment using passive sampling.

PubMed

Claessens, Michiel; De Laender, Frederik; Monteyne, Els; Roose, Patrick; Janssen, Colin R

2015-07-15

Polydimethylsiloxane sheets were used to determine freely dissolved concentrations (C(diss)) of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) in the Belgian coastal zone. Equilibrium models were used to predict the whole water concentrations (C(ww)) of these compounds as well as their concentrations in sediment, suspended particulate matter (SPM) and biota. In general, contaminant concentrations were predicted well for whole water and biota. C(ww) was increasingly underpredicted as K(oc) increased, possibly because of the presence of black carbon. Concentrations in biota were overestimated by the equilibrium approach when logK(ow) exceeded 6.5, suggesting an increasing role of transformation processes. Concentrations of PAHs and PCBs in sediment and SPM were consistently underpredicted although a good correlation between measured and predicted values was observed. This was potentially due to the use of experimental K(oc) values which have been found to underestimate partitioning of hydrophobic substances to sediment in field studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biodegradation and mineralization of isotopically labeled TNT and RDX in anaerobic marine sediments.

PubMed

Ariyarathna, Thivanka; Vlahos, Penny; Smith, Richard W; Fallis, Stephen; Groshens, Thomas; Tobias, Craig

2017-05-01

The lack of knowledge on the fate of explosive compounds 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), particularly in marine ecosystems, constrains the application of bioremediation techniques in explosive-contaminated coastal sites. The authors present a comparative study on anaerobic biodegradation and mineralization of 15 N-nitro group isotopically labeled TNT and RDX in organic carbon-rich, fine-grained marine sediment with native microbial assemblages. Separate sediment slurry experiments were carried out for TNT and RDX at 23°C for 16 d. Dissolved and sediment-sorbed fractions of parent and transformation products, isotopic compositions of sediment, and mineralization products of the dissolved inorganic N pool ( 15 NH 4 + , 15 NO 3 - , 15 NO 2 - , and 15 N 2 ) were measured. The rate of TNT removal from the aqueous phase was faster (0.75 h -1 ) than that of RDX (0.37 h -1 ), and 15 N accumulation in sediment was higher in the TNT (13%) than the RDX (2%) microcosms. Mono-amino-dinitrotoluenes were identified as intermediate biodegradation products of TNT. Two percent of the total spiked TNT-N is mineralized to dissolved inorganic N through 2 different pathways: denitration as well as deamination and formation of NH 4 + , facilitated by iron and sulfate reducing bacteria in the sediments. The majority of the spiked TNT-N (85%) is in unidentified pools by day 16. Hexahydro-1,3,5-trinitro-1,3,5-triazine (10%) biodegrades to nitroso derivatives, whereas 13% of RDX-N in nitro groups is mineralized to dissolved inorganic N anaerobically by the end of the experiment. The primary identified mineralization end product of RDX (40%) is NH 4 + , generated through either deamination or mono-denitration, followed by ring breakdown. A reasonable production of N 2 gas (13%) was seen in the RDX system but not in the TNT system. Sixty-eight percent of the total spiked RDX-N is in an unidentified pool by day 16 and may include unquantified mineralization products dissolved in water. Environ Toxicol Chem 2017;36:1170-1180. © 2016 SETAC. © 2016 SETAC.

Coupling and Elastic Loading Affect the Active Response by the Inner Ear Hair Cell Bundles

PubMed Central

Strimbu, Clark Elliott; Fredrickson-Hemsing, Lea; Bozovic, Dolores

2012-01-01

Active hair bundle motility has been proposed to underlie the amplification mechanism in the auditory endorgans of non-mammals and in the vestibular systems of all vertebrates, and to constitute a crucial component of cochlear amplification in mammals. We used semi-intact in vitro preparations of the bullfrog sacculus to study the effects of elastic mechanical loading on both natively coupled and freely oscillating hair bundles. For the latter, we attached glass fibers of different stiffness to the stereocilia and observed the induced changes in the spontaneous bundle movement. When driven with sinusoidal deflections, hair bundles displayed phase-locked response indicative of an Arnold Tongue, with the frequency selectivity highest at low amplitudes and decreasing under stronger stimulation. A striking broadening of the mode-locked response was seen with increasing stiffness of the load, until approximate impedance matching, where the phase-locked response remained flat over the physiological range of frequencies. When the otolithic membrane was left intact atop the preparation, the natural loading of the bundles likewise decreased their frequency selectivity with respect to that observed in freely oscillating bundles. To probe for signatures of the active process under natural loading and coupling conditions, we applied transient mechanical stimuli to the otolithic membrane. Following the pulses, the underlying bundles displayed active movement in the opposite direction, analogous to the twitches observed in individual cells. Tracking features in the otolithic membrane indicated that it moved in phase with the bundles. Hence, synchronous active motility evoked in the system of coupled hair bundles by external input is sufficient to displace large overlying structures. PMID:22479461

Water resources of the White Earth Indian Reservation, northwestern Minnesota

USGS Publications Warehouse

Ruhl, J.F.

1989-01-01

Surface water also is a calcium magnesium bicarbonate type. Lake waters are hard and alkaline and are mesotrophic to eutrophic in productivity. Quality of the lake and stream water is suitable for native forms of freshwater biota, although the concentration of total recoverable mercury exceeds the 0.012 micrograms per liter maximum contaminant level; that level, established by USEPA for the organic form of dissolved mercury, is intended to protect against chronic effects on freshwater life. Available information, however, indicates that the amount of mercury in edible tissue from fish in alkaline lakes of northwestern Minnesota is within safe limits. The concentrations of phosphorus and nitrate in the streams are below levels that indicate pollution problems.

Application of ultrafiltration and stable isotopic amendments to field studies of mercury partitioning to filterable carbon in lake water and overland runoff

USGS Publications Warehouse

Babiarz, Christopher L.; Hurley, J.P.; Krabbenhoft, D.P.; Gilmour, C.; Branfireun, B.A.

2003-01-01

Results from pilot studies on colloidal phase transport of newly deposited mercury in lake water and overland runoff demonstrate that the combination of ultrafiltration, and stable isotope amendment techniques is a viable tool for the study of mercury partitioning to filterable carbon. Ultrafiltration mass balance calculations were generally excellent, averaging 97.3, 96.1 and 99.8% for dissolved organic carbon (DOC), total mercury (HgT), and methylmercury (MeHg), respectively. Sub nanogram per liter quantities of isotope were measurable, and the observed phase distribution from replicate ultrafiltration separations on lake water agreed within 20%. We believe the data presented here are the first published colloidal phase mercury data on lake water and overland runoff from uncontaminated sites. Initial results from pilot-scale lake amendment experiments indicate that the choice of matrix used to dissolve the isotope did not affect the initial phase distribution of the added mercury in the lake. In addition there was anecdotal evidence that native MeHg was either recently produced in the system, or at a minimum, that this 'old' MeHg partitions to the same subset of DOC that binds the amended mercury. Initial results from pilot-scale overland runoff experiments indicate that less than 20% of newly deposited mercury was transported in the filterable fraction (<0.7 ??m). There is some indication of colloidal phase enrichment of mercury in runoff compared to the phase distribution of organic carbon, but the mechanism of this enrichment is unclear. The phase distribution of newly deposited mercury can differ from that of organic carbon and native mercury, suggesting that the quality of the carbon (available ligands), not the quantity of carbon, regulates partitioning. Further characterization of DOC is needed to clarify the underlying mechanisms. ?? 2002 Elsevier Science B.V. All rights reserved.

Movement of reservoir-stocked riverine fish between tailwaters and rivers

USGS Publications Warehouse

Spoelstra, J.A.; Stein, R.A.; Royle, J. Andrew; Marschall, E.A.

2008-01-01

The movement of fish from onstream impoundments into connected streams and rivers has traditionally been overlooked in fish stocking decisions but is critical to the ultimate impact of stocking riverine species into reservoirs. Hybrid saugeyes (female walleye Sander vitreus x male sauger S. canadensis) stocked into Deer Creek Reservoir, Ohio, readily move from the reservoir to the tailwater below. Downstream movement of these saugeyes from the tailwater may have consequences for native prey species and parental stocks downstream. We used fixed-station radiotelemetry to quantify the temporal movement patterns of 203 reservoir-stocked saugeyes from the tailwater of the reservoir, the stream flowing from the tailwater, and the river into which the stream flowed. From October 1998 through July 2000, most (75%) saugeyes never left the tailwater, and those that left returned 75% of the time. Overall, saugeyes spent 90% of their time in the tailwater, 7-8% of their time downstream in small streams, and 2-3% of their time farther downstream in the Scioto River (45 km downstream). No radio-tagged saugeyes moved to the Ohio River (155 km downstream). The probability of downstream movement generally increased with increasing flow and when dissolved oxygen dropped to lethal levels in summer. The probability of movement was highest in winter and spring, when it was probably related to spawning, and low in summer (except when dissolved oxygen was low) and fall. The patterns of movement seemed to reflect the relative suitability of tailwater over stream habitat. The predominant use of and return to tailwater habitat after downstream movement limited overall stream and river residence time. Although the daily movement probability for an individual was low, when we apply these rates to all of the stocked saugeyes in the Ohio River drainage, we cannot safely conclude that only small numbers move from reservoir tailwaters to downstream river systems. We recommend that managers refrain from stocking systems for which there are concerns about native species in connected drainages.

Implications of altered rainfall and exotic plants on soil microbial communities and carbon biomass

NASA Astrophysics Data System (ADS)

Castro, S.; Lipson, D.; Cleland, E. E.

2016-12-01

Climate and exotic plant disturbances are among the most significant threats to Mediterranean-type ecosystems, compromising their renowned biodiversity and role in the global carbon cycle. Predicted shifts in rainfall patterns have become a particular concern, especially when interactions with other stressors and effects on biogeochemical processes remain poorly understood. To understand the impacts of altered rainfall on belowground dynamics as well as the role of inter- and intra-annual variation and plant community composition, we monitored soil microbial communities under native and exotic plant dominated plots with rainfall manipulation treatments in a semi-arid Mediterranean-type ecosystem. We measured microbial biomass, respiration rates, and community structure across treatments and vegetation types. Soil moisture and dissolved organic carbon were also measured to characterize abiotic soil properties. The soil moisture gradient established by the rainfall treatments had a positive correlation with microbial biomass carbon under native- and exotic-dominated plots but had no effect on respiration rates. A significant reduction in microbial biomass under exotic plants was found in 2013 but not in 2014 and 2015. Substrate-induced respiration values were higher in the exotic-dominated plots during the spring seasons, resulting in a significant interaction between plant community type and season. Bacterial communities showed little variation except in the Proteobacteria phyla, which was lower in exotic plants-dominated plots. Dissolved organic carbon was significantly reduced in exotic-dominated plots by approximately 26% based on average values of all plots throughout. Our results illustrate that rainfall quantity and exotic plants can cause changes in microbial biomass, community composition and respiration rates jeopardizing soil carbon storage. They also reinforce the importance of temporal variability and the need for repeated sampling to correctly interpret environmental changes in semi-arid ecosystems. We conclude that to improve predictions of the implications of global stressors on biogeochemical cycles in semi-arid ecosystems, there is a need to incorporate microbial data with the understanding that it is highly dependent on temporal dynamics and plant community.

Proposal of Network-Based Multilingual Space Dictionary Database System

NASA Astrophysics Data System (ADS)

Yoshimitsu, T.; Hashimoto, T.; Ninomiya, K.

2002-01-01

The International Academy of Astronautics (IAA) is now constructing a multilingual dictionary database system of space-friendly terms. The database consists of a lexicon and dictionaries of multiple languages. The lexicon is a table which relates corresponding terminology in different languages. Each language has a dictionary which contains terms and their definitions. The database assumes the use on the internet. Updating and searching the terms and definitions are conducted via the network. Maintaining the database is conducted by the international cooperation. A new word arises day by day, thus to easily input new words and their definitions to the database is required for the longstanding success of the system. The main key of the database is an English term which is approved at the table held once or twice with the working group members. Each language has at lease one working group member who is responsible of assigning the corresponding term and the definition of the term of his/her native language. Inputting and updating terms and their definitions can be conducted via the internet from the office of each member which may be located at his/her native country. The system is constructed by freely distributed database server program working on the Linux operating system, which will be installed at the head office of IAA. Once it is installed, it will be open to all IAA members who can search the terms via the internet. Currently the authors are constructing the prototype system which is described in this paper.

Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer

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

Raymond, Amy; Lovell, Scott; Lorimer, Don

2009-12-01

With the goal of improving yield and success rates of heterologous protein production for structural studies we have developed the database and algorithm software package Gene Composer. This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript. In this report, we compare heterologous protein expression levels from native sequences to that of codon engineered synthetic gene constructs designed by Gene Composer. A test set of proteins including a human kinase (P38{alpha}), viral polymerase (HCV NS5B), and bacterial structural protein (FtsZ) were expressed in both E. colimore » and a cell-free wheat germ translation system. We also compare the protein expression levels in E. coli for a set of 11 different proteins with greatly varied G:C content and codon bias. The results consistently demonstrate that protein yields from codon engineered Gene Composer designs are as good as or better than those achieved from the synonymous native genes. Moreover, structure guided N- and C-terminal deletion constructs designed with the aid of Gene Composer can lead to greater success in gene to structure work as exemplified by the X-ray crystallographic structure determination of FtsZ from Bacillus subtilis. These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research.« less

Invasive fishes generate biogeochemical hotspots in a nutrient-limited system.

PubMed

Capps, Krista A; Flecker, Alexander S

2013-01-01

Fishes can play important functional roles in the nutrient dynamics of freshwater systems. Aggregating fishes have the potential to generate areas of increased biogeochemical activity, or hotspots, in streams and rivers. Many of the studies documenting the functional role of fishes in nutrient dynamics have focused on native fish species; however, introduced fishes may restructure nutrient storage and cycling freshwater systems as they can attain high population densities in novel environments. The purpose of this study was to examine the impact of a non-native catfish (Loricariidae: Pterygoplichthys) on nitrogen and phosphorus remineralization and estimate whether large aggregations of these fish generate measurable biogeochemical hotspots within nutrient-limited ecosystems. Loricariids formed large aggregations during daylight hours and dispersed throughout the stream during evening hours to graze benthic habitats. Excretion rates of phosphorus were twice as great during nighttime hours when fishes were actively feeding; however, there was no diel pattern in nitrogen excretion rates. Our results indicate that spatially heterogeneous aggregations of loricariids can significantly elevate dissolved nutrient concentrations via excretion relative to ambient nitrogen and phosphorus concentrations during daylight hours, creating biogeochemical hotspots and potentially altering nutrient dynamics in invaded systems.

Invasive Fishes Generate Biogeochemical Hotspots in a Nutrient-Limited System

PubMed Central

Capps, Krista A.; Flecker, Alexander S.

2013-01-01

Fishes can play important functional roles in the nutrient dynamics of freshwater systems. Aggregating fishes have the potential to generate areas of increased biogeochemical activity, or hotspots, in streams and rivers. Many of the studies documenting the functional role of fishes in nutrient dynamics have focused on native fish species; however, introduced fishes may restructure nutrient storage and cycling freshwater systems as they can attain high population densities in novel environments. The purpose of this study was to examine the impact of a non-native catfish (Loricariidae: Pterygoplichthys) on nitrogen and phosphorus remineralization and estimate whether large aggregations of these fish generate measurable biogeochemical hotspots within nutrient-limited ecosystems. Loricariids formed large aggregations during daylight hours and dispersed throughout the stream during evening hours to graze benthic habitats. Excretion rates of phosphorus were twice as great during nighttime hours when fishes were actively feeding; however, there was no diel pattern in nitrogen excretion rates. Our results indicate that spatially heterogeneous aggregations of loricariids can significantly elevate dissolved nutrient concentrations via excretion relative to ambient nitrogen and phosphorus concentrations during daylight hours, creating biogeochemical hotspots and potentially altering nutrient dynamics in invaded systems. PMID:23342083

Exploring how organic matter controls structural transformations in natural aquatic nanocolloidal dispersions.

PubMed

King, Stephen M; Jarvie, Helen P

2012-07-03

The response of the dispersion nanostructure of surface river bed sediment to the controlled removal and readdition of natural organic matter (NOM), in the absence and presence of background electrolyte, was examined using the technique of small-angle neutron scattering (SANS). Partial NOM removal induced aggregation of the mineral particles, but more extensive NOM removal restored colloidal stability. When peat humic acid (PHA) was added to a NOM-deficient sediment concentration-related structural transformations were observed: at 255 mg/L PHA aggregation of the nanocolloid was actually enhanced, but at 380 mg/L PHA disaggregation and colloidal stability were promoted. The addition of 2 mM CaCl(2) induced mild aggregation in the native sediment but not in sediments with added PHA, suggesting that the native NOM and the PHA respond differently to changes in ionic strength. A first attempt at using SANS to directly characterize the thickness and coverage of an adsorbed PHA layer in a natural nanocolloid is also presented. The results are discussed in the context of a hierarchical aquatic colloidal nanostructure, and the implications for contemporary studies of the role of dissolved organic carbon (DOC) in sustaining the transport of colloidal iron in upland catchments.

In situ microscopy of the self-assembly of branched nanocrystals in solution

DOE PAGES

Sutter, Eli; Tkachenko, Alexei V.; Sutter, Peter; ...

2016-04-04

Here, solution-phase self-assembly of nanocrystals into mesoscale structures is a promising strategy for constructing functional materials from nanoscale components. Liquid environments are key to self-assembly since they allow suspended nanocrystals to diffuse and interact freely, but they also complicate experiments. Real-time observations with single-particle resolution could have transformative impact on our understanding of nanocrystal self-assembly. Here we use real-time in situ imaging by liquid-cell electron microscopy to elucidate the nucleation and growth mechanism and properties of linear chains of octapod-shaped nanocrystals in their native solution environment. Statistical mechanics modelling based on these observations and using the measured chain-length distribution clarifiesmore » the relative importance of dipolar and entropic forces in the assembly process and gives direct access to the interparticle interaction. Our results suggest that monomer-resolved in situ imaging combined with modelling can provide unprecedented quantitative insight into the microscopic processes and interactions that govern nanocrystal self-assembly in solution.« less

In situ microscopy of the self-assembly of branched nanocrystals in solution

NASA Astrophysics Data System (ADS)

Sutter, Eli; Sutter, Peter; Tkachenko, Alexei V.; Krahne, Roman; de Graaf, Joost; Arciniegas, Milena; Manna, Liberato

2016-04-01

Solution-phase self-assembly of nanocrystals into mesoscale structures is a promising strategy for constructing functional materials from nanoscale components. Liquid environments are key to self-assembly since they allow suspended nanocrystals to diffuse and interact freely, but they also complicate experiments. Real-time observations with single-particle resolution could have transformative impact on our understanding of nanocrystal self-assembly. Here we use real-time in situ imaging by liquid-cell electron microscopy to elucidate the nucleation and growth mechanism and properties of linear chains of octapod-shaped nanocrystals in their native solution environment. Statistical mechanics modelling based on these observations and using the measured chain-length distribution clarifies the relative importance of dipolar and entropic forces in the assembly process and gives direct access to the interparticle interaction. Our results suggest that monomer-resolved in situ imaging combined with modelling can provide unprecedented quantitative insight into the microscopic processes and interactions that govern nanocrystal self-assembly in solution.

BioC implementations in Go, Perl, Python and Ruby

PubMed Central

Liu, Wanli; Islamaj Doğan, Rezarta; Kwon, Dongseop; Marques, Hernani; Rinaldi, Fabio; Wilbur, W. John; Comeau, Donald C.

2014-01-01

As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/ PMID:24961236

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics.

PubMed

Parra, R Gonzalo; Schafer, Nicholas P; Radusky, Leandro G; Tsai, Min-Yeh; Guzovsky, A Brenda; Wolynes, Peter G; Ferreiro, Diego U

2016-07-08

The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins' biological behavior. It compares the energy distributions of the native state with respect to structural decoys. The network of minimally frustrated interactions encompasses the folding core of the molecule. Sites of high local frustration often correlate with functional regions such as binding sites and regions involved in allosteric transitions. We present here an upgraded version of a webserver that measures local frustration. The new implementation that allows the inclusion of electrostatic energy terms, important to the interactions with nucleic acids, is significantly faster than the previous version enabling the analysis of large macromolecular complexes within a user-friendly interface. The webserver is freely available at URL: http://frustratometer.qb.fcen.uba.ar. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Prediction of Protein Configurational Entropy (Popcoen).

PubMed

Goethe, Martin; Gleixner, Jan; Fita, Ignacio; Rubi, J Miguel

2018-03-13

A knowledge-based method for configurational entropy prediction of proteins is presented; this methodology is extremely fast, compared to previous approaches, because it does not involve any type of configurational sampling. Instead, the configurational entropy of a query fold is estimated by evaluating an artificial neural network, which was trained on molecular-dynamics simulations of ∼1000 proteins. The predicted entropy can be incorporated into a large class of protein software based on cost-function minimization/evaluation, in which configurational entropy is currently neglected for performance reasons. Software of this type is used for all major protein tasks such as structure predictions, proteins design, NMR and X-ray refinement, docking, and mutation effect predictions. Integrating the predicted entropy can yield a significant accuracy increase as we show exemplarily for native-state identification with the prominent protein software FoldX. The method has been termed Popcoen for Prediction of Protein Configurational Entropy. An implementation is freely available at http://fmc.ub.edu/popcoen/ .

MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure.

PubMed

Kim, Jihoon; Levy, Eric; Ferbrache, Alex; Stepanowsky, Petra; Farcas, Claudiu; Wang, Shuang; Brunner, Stefan; Bath, Tyler; Wu, Yuan; Ohno-Machado, Lucila

2014-10-01

MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours->600% end-to-end performance improvement over state of the art. MAGI's salient features are (i) transfer of large input files in native FASTA with Qualities (FASTQ) format through drag-and-drop operations, (ii) rapid prediction of microRNA target genes leveraging parallel computing with GPU devices, (iii) all-in-one analytics with novel feature extraction, statistical test for differential expression and diagnostic plot generation for quality control and (iv) interactive visualization and exploration of results in web reports that are readily available for publication. MAGI relies on the Node.js JavaScript framework, along with NVIDIA CUDA C, PHP: Hypertext Preprocessor (PHP), Perl and R. It is freely available at http://magi.ucsd.edu. © The Author 2014. Published by Oxford University Press.

LOOS: an extensible platform for the structural analysis of simulations.

PubMed

Romo, Tod D; Grossfield, Alan

2009-01-01

We have developed LOOS (Lightweight Object-Oriented Structure-analysis library) as an object-oriented library designed to facilitate the rapid development of tools for the structural analysis of simulations. LOOS supports the native file formats of most common simulation packages including AMBER, CHARMM, CNS, Gromacs, NAMD, Tinker, and X-PLOR. Encapsulation and polymorphism are used to simultaneously provide a stable interface to the programmer and make LOOS easily extensible. A rich atom selection language based on the C expression syntax is included as part of the library. LOOS enables students and casual programmer-scientists to rapidly write their own analytical tools in a compact and expressive manner resembling scripting. LOOS is written in C++ and makes extensive use of the Standard Template Library and Boost, and is freely available under the GNU General Public License (version 3) LOOS has been tested on Linux and MacOS X, but is written to be portable and should work on most Unix-based platforms.

Using PeptideAtlas, SRMAtlas and PASSEL – Comprehensive Resources for discovery and targeted proteomics

PubMed Central

Kusebauch, Ulrike; Deutsch, Eric W.; Campbell, David S.; Sun, Zhi; Farrah, Terry; Moritz, Robert L.

2014-01-01

PeptideAtlas, SRMAtlas and PASSEL are web-accessible resources to support discovery and targeted proteomics research. PeptideAtlas is a multi-species compendium of shotgun proteomic data provided by the scientific community, SRMAtlas is a resource of high-quality, complete proteome SRM assays generated in a consistent manner for the targeted identification and quantification of proteins, and PASSEL is a repository that compiles and represents selected reaction monitoring data, all in an easy to use interface. The databases are generated from native mass spectrometry data files that are analyzed in a standardized manner including statistical validation of the results. Each resource offers search functionalities and can be queried by user defined constraints; the query results are provided in tables or are graphically displayed. PeptideAtlas, SRMAtlas and PASSEL are publicly available freely via the website http://www.peptideatlas.org. In this protocol, we describe the use of these resources, we highlight how to submit, search, collate and download data. PMID:24939129

Long-term impact of land management in soil biological processes can be assessed by fingerprint of dissolved organic carbon and peroxidase activity in topsoil and subsoil

NASA Astrophysics Data System (ADS)

Hernandez-Soriano, Maria C.; Maclean, Jamie L.; Dalal, Ram C.; Menzies, Neal W.; Kopittke, Peter M.

2015-04-01

The dissolved organic carbon (DOC) is a highly dynamic pool, directly related to biological functions and to the stabilization of organic carbon (OC) through interaction with the mineral phase. Therefore, the characterization of the main components of DOC can be linked to the metabolic status of soil and the turnover of OC and provides a sensitive approach to evaluate the impact of land use on OC turnover in soils. Accordingly, the objective of this study was to derive relationships between DOC characteristics and biochemical activity in soils under contrasting land management. The soil solution was isolated from topsoil and subsoil for three soils (Vertisol, Ferralsol, Acrisol, World Reference Base 2014) collected from undisturbed areas and from a location(s) immediately adjacent which has a long history of agricultural, pasture or afforestation use (>20 years) by centrifugation at 4000 rpm (20 min, 25 °C. The fingerprint of DOC was obtained to identify OC functionalities by spectrofluorometric analyses and Excitation-Emission matrices (EEM) were obtained for all samples. The excitation wavelengths were increased from 250 to 400 nm in 5-nm steps for each excitation wavelength, and emission was detected from 250 to 500 nm in 0.5-nm steps and. Humification index (HIX), freshness index (FrI), fluorescence index (FI) and redox index (RI) were derived from the EEMs. Extracellular laccase activity was examined by monitoring the oxidation of 2,2'-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) at 420 nm. The EEMs revealed a depletion of the humic-like component (250Acrisol>Ferralsol and was always higher for the topsoils compared to the corresponding subsoils. Overall, results indicate that land management has a strong impact on soil biological activity. Importantly, such impact is directly linked to changes in the composition of soil OC, particularly the transformation of OC inputs into oxidized products that can contribute to OC build up in soil. For the first time, we have utilized DOC fingerprinting and extracellular laccase activity as complementary techniques to examine changes in OC speciation in soil solutions. This approach provides a suitable link between variations in biological functions and OC dynamics.

Red shiner invasion and hybridization with blacktail shiner in the upper Coosa River, USA

USGS Publications Warehouse

Walters, D.M.; Blum, M.J.; Rashleigh, Brenda; Freeman, B.J.; Porter, B.A.; Burkhead, N.M.

2008-01-01

Human disturbance increases the invasibility of lotic ecosystems and the likelihood of hybridization between invasive and native species. We investigated whether disturbance contributed to the invasion of red shiner (Cyprinella lutrensis) and their hybridization with native blacktail shiner (C. venusta stigmatura) in the Upper Coosa River System (UCRS). Historical records indicated that red shiners and hybrids rapidly dispersed in the UCRS via large, mainstem rivers since the mid to late 1990s. We measured the occurrence and abundance of parental species and hybrids near tributary-mainstem confluences and characterized populations at these incipient contact zones by examining variation across morphological traits and molecular markers. Red shiners represented only 1.2% of total catch in tributaries yet introgression was widespread with hybrids accounting for 34% of total catch. Occurrence of red shiners and hybrids was highly correlated with occurrence of blacktail shiners, indicating that streams with native populations are preferentially colonized early in the invasion and that hybridization is a key process in the establishment of red shiners and their genome in new habitats. Tributary invasion was driven by post-F1 hybrids with proportionately greater genomic contributions from blacktail shiner. Occurrence of red shiners and hybrids and the relative abundance of hybrids significantly increased with measures of human disturbance including turbidity, catchment agricultural land use, and low dissolved oxygen concentration. Red shiners are a significant threat to Southeast Cyprinella diversity, given that 41% of these species hybridize with red shiner, that five southeastern drainages are invaded, and that these drainages are increasingly disturbed by urbanization. ?? 2007 Springer Science+Business Media B.V.

Application of passive sampling for measuring dissolved concentrations of organic contaminants in the water column at three marine superfund sites.

PubMed

Burgess, Robert M; Lohmann, Rainer; Schubauer-Berigan, Joseph P; Reitsma, Pamela; Perron, Monique M; Lefkovitz, Lisa; Cantwell, Mark G

2015-08-01

Currently, there is an effort under way to encourage remedial project managers at contaminated sites to use passive sampling to collect freely dissolved concentrations (Cfree ) of hydrophobic organic contaminants to improve site assessments. The objective of the present study was to evaluate the use of passive sampling for measuring water column Cfree for several hydrophobic organic contaminants at 3 US Environmental Protection Agency Superfund sites. Sites investigated included New Bedford Harbor (New Bedford, MA, USA), Palos Verdes Shelf (Los Angeles, CA, USA), and Naval Station Newport (Newport, RI, USA); and the passive samplers evaluated were polyethylene, polydimethylsiloxane-coated solid-phase microextraction fibers, semipermeable membrane devices, and polyoxymethylene. In general, the different passive samplers demonstrated good agreement, with Cfree values varying by a factor of 2 to 3. Further, at New Bedford Harbor, where conventional water sample concentrations were also measured (i.e., grab samples), passive sampler-based Cfree values agreed within a factor of 2. These findings suggest that all of the samplers were experiencing and measuring similar Cfree during their respective deployments. Also, at New Bedford Harbor, a strong log-linear, correlative, and predictive relationship was found between polyethylene passive sampler accumulation and lipid-normalized blue mussel bioaccumulation of polychlorinated biphenyls (r(2)  = 0.92, p < 0.05). The present study demonstrates the utility of passive sampling for generating scientifically accurate water column Cfree values, which is critical for making informed environmental management decisions at contaminated sediment sites. Published 2015 SETAC. This article is a US Government work and is in the public domain in the USA.

Nano-sized zeolites as modulators of thiacloprid toxicity on Chironomus riparius

PubMed Central

Wicht, Anna-Jorina; Guluzada, Leyla; Crone, Barbara; Karst, Uwe; Lee, Hwa Jun; Triebskorn, Rita; Haderlein, Stefan B.; Huhn, Carolin; Köhler, Heinz-R.

2017-01-01

This study investigated whether zeolites of different size (Y30 (nano-sized) and H-Beta(OH)-III (forming large aggregates/agglomerates composed of 50 nm small primary particles)) exerted acute toxicity on larvae of the non-biting midge, Chironomus riparius, and whether such zeolites are able to modulate the toxicity of a common insecticide, thiacloprid, by means of adsorption of a dissolved toxicant. We conducted acute toxicity tests with fourth instar larvae of C. riparius. In these tests, larvae were exposed to zeolites or thiacloprid solely, or to mixtures of both compounds. The mixtures comprised 1.0 µg/L thiacloprid in addition to low (5.2 mg/L), medium (18.2 mg/L), and high (391.7 mg/L) zeolite concentrations, resulting in different adsorption rates of thiacloprid. As biological endpoints, changes in mortality rates and in behavior were monitored every 24 h over a total investigation period of 96 h. Furthermore, we conducted chemical analyses of thiacloprid in the medium and the larvae and located the zeolite particles within the larvae by LA-ICP-MS imaging techniques. Our results demonstrate that both types of zeolites did not exert acute toxicity when applied as single-substances, but led to reduced acute toxicity of thiacloprid when applied together with thiacloprid. These results are in line with the sorption properties of zeolites indicating reduced bioavailability of thiacloprid, although our data indicate that thiacloprid can desorb from zeolites to some extent. While freely dissolved (i.e., non-sorbed) fraction of thiacloprid was a good parameter to roughly estimate toxic effects, it did not correlate with measured internal thiacloprid concentrations. Moreover, it was shown that both zeolite types were ingested by the larvae, but no indication for cellular uptake of them was found. PMID:28729952

Volatile Element Fluxes at Copahue Volcano, Argentina

NASA Astrophysics Data System (ADS)

Varekamp, J. C.

2002-05-01

Copahue volcano has a crater lake and acid hot springs that discharge into the Rio Agrio river system. These fluids are very concentrated (up to 6 % sulfate), rich in rock-forming elements (up to 2000 ppm Mg) and small spheres of native sulfur float in the crater lake. The stable isotope composition of the waters (delta 18O =-2.1 to + 3.6 per mille; delta D = -49 to -26 per mille) indicates that the hot spring waters are at their most concentrated about 70% volcanic brine and 30 % glacial meltwater. The crater lake waters have similar mixing proportions but added isotope effects from intense evaporation. Further dilution of the waters in the Rio Agrio gives values closer to local meteoric waters (delta 18O = -11 per mille; delta D = -77 per mille), whereas evaporation in closed ponds led to very heavy water (up to delta 18O = +12 per mille). The delta 34S value of dissolved sulfate is +14.2 per mille, whereas the native sulfur has values of -8.2 to -10.5 per mille. The heavy sulfate probably formed when SO2 disproportionated into bisulfate and native sulfur at about 300 C. We measured the sulfate fluxes in the Rio Agrio, which ranged from 20-40 kilotons S/year. The whole system was releasing sulfur at an equivalent rate of about 250-650 tons SO2/day. From the river flux sulfur values and the stochiometry of the disproportionation reaction we calculated the rate of liquid sulfur storage inside the volcano (6000 m3/year). During the eruptions of 1995/2000, large amounts of that stored liquid sulfur were ejected as pyroclastic sulfur. The calculated rate of rock dissolution (from rock- forming element fluxes in the Rio Agrio) suggests that the void space generated by rock dissolution is largely filled by native sulfur and silica. The S/Cl ratio in the hydrothermal fluids is about 2, whereas glass inclusions have S/Cl = 0.2, indicating the strong preferential degassing of sulfur.

Use of seasonal freshwater wetlands by fishes in a temperate river floodplain

USGS Publications Warehouse

Henning, Julie A.; Gresswell, Robert E.; Fleming, Ian A.

2007-01-01

This study examined the use of freshwater wetland restoration and enhancement projects (i.e. non-estuarine wetlands subject to seasonal drying) by fish populations. To quantify fish use of freshwater emergent wetlands and assess the effect of wetland enhancement (i.e. addition of water control structures), two enhanced and two unenhanced emergent wetlands were compared, as well as two oxbow habitats within the Chehalis River floodplain. Eighteen fish species were captured using fyke nets and emigrant traps from January to the beginning of June, with the most abundant being three-spined stickleback Gasterosteus aculeatus and Olympic mudminnow Novumbra hubbsi. Coho salmon Oncorhynchus kisutch was the dominant salmonid at all sites. Enhanced wetlands, with their extended hydroperiods, had significantly higher abundances of yearling coho salmon than unenhanced wetlands. Both enhanced and unenhanced emergent wetlands yielded higher abundances of non-game native fishes than oxbow habitats. Oxbow habitats, however, were dominated by coho salmon. Fish survival in the wetland habitats was dependent on emigration to the river before dissolved oxygen concentrations decreased and wetlands became isolated and stranding occurred. This study suggests that wetland enhancement projects with an outlet to the river channel appear to provide fishes with important temporary habitats if they have the opportunity to leave the wetland as dissolved oxygen levels deteriorate.

Freshwater mussel population status and habitat quality in the Clinch River, Virginia and Tennessee, USA: a featured collection

USGS Publications Warehouse

Zipper, Carl E.; Beaty, Braven; Johnson, Gregory C.; Jones, Jess W.; Krstolic, Jennifer Lynn; Ostby, Brett J.K.; Wolfe, William J.; Donovan, Patricia

2014-01-01

The Clinch River of southwestern Virginia and northeastern Tennessee is arguably the most important river for freshwater mussel conservation in the United States. This featured collection presents investigations of mussel population status and habitat quality in the Clinch River. Analyses of historic water- and sediment-quality data suggest that water column ammonia and water column and sediment metals, including Cu and Zn, may have contributed historically to declining densities and extirpations of mussels in the river's Virginia sections. These studies also reveal increasing temporal trends for dissolved solids concentrations throughout much of the river's extent. Current mussel abundance patterns do not correspond spatially with physical habitat quality, but they do correspond with specific conductance, dissolved major ions, and water column metals, suggesting these and/or associated constituents as factors contributing to mussel declines. Mussels are sensitive to metals. Native mussels and hatchery-raised mussels held in cages in situ accumulated metals in their body tissues in river sections where mussels are declining. Organic compound and bed-sediment contaminant analyses did not reveal spatial correspondences with mussel status metrics, although potentially toxic levels were found. Collectively, these studies identify major ions and metals as water- and sediment-quality concerns for mussel conservation in the Clinch River.

Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solution.

PubMed Central

Torres, J; Padrós, E

1995-01-01

Fourier transform infrared and UV fourth-derivative spectroscopies were used to study the secondary structure of bacteriorhodopsin and its chymotryptic and one of the sodium borohydride fragments dissolved in chloroform-methanol (1:1, v/v), 0.1 M LiClO4. The C1 fragment (helices C, D, E, F, and G) showed an alpha-helical content of about 53%, whereas C2 (helices A and B) had about 60%, and B2 (helices F and G) about 65% alpha-helix. The infrared main band indicated differences in alpha-helical properties between these fragments. These techniques were also used to obtain information on the interactions among helices. According to the results obtained from the hydrogen/deuterium exchange kinetics, about 40% of the amide protons of C2 are particularly protected against exchange, whereas for the C1 fragment this process is unexpectedly fast. UV fourth-derivative spectra of these samples were used to obtain information about the environment of Trp side chains. The results showed that the Trp residues of C2 are more shielded from the solvent than those of C1 or B2. The results of this work indicate that the specific interactions existing between the transmembrane segments induce different types of helical conformations in native bacteriorhodopsin. PMID:7612847

Potential Aquifer Vulnerability in Regions Down-Gradient from ...

EPA Pesticide Factsheets

Sandstone-hosted roll-front uranium ore deposits originate when U(VI) dissolved in groundwater is reduced and precipitated as insoluble U(IV) minerals. Groundwater redox geochemistry, aqueous complexation, and solute migration are instrumental in leaching uranium from source rocks and transporting it in low concentrations to a chemical redox interface where it is deposited in an ore zone typically containing the uranium minerals uraninite, pitchblende, and/or coffinite; various iron sulfides; native selenium; clays; and calcite. In situ recovery (ISR) of these uranium ores is a process of contacting the uranium mineral deposit with leaching (lixiviant) fluids via injection of the lixiviant into wells drilled into the subsurface aquifer that hosts uranium ore, while other extraction wells pump the dissolved uranium after dissolution of the uranium minerals. Environmental concerns during and after ISR include water quality impacts from: 1) potential excursions of leaching solutions away from the injection zone into down-dip, underlying, or overlying aquifers; 2) potential migration of uranium and its decay products (e.g., Ra, Rn, Pb); and, 3) potential migration of redox-sensitive trace metals (e.g., Fe, Mn, Mo, Se, V), metalloids (e.g., As), and anions (e.g., sulfate). This review describes the geochemical processes that control roll-front uranium transport and fate in groundwater systems, identifies potential aquifer vulnerabilities to ISR operations, identifies

Perlwapin, an Abalone Nacre Protein with Three Four-Disulfide Core (Whey Acidic Protein) Domains, Inhibits the Growth of Calcium Carbonate Crystals

PubMed Central

Treccani, Laura; Mann, Karlheinz; Heinemann, Fabian; Fritz, Monika

2006-01-01

We have isolated a new protein from the nacreous layer of the shell of the sea snail Haliotis laevigata (abalone). Amino acid sequence analysis showed the protein to consist of 134 amino acids and to contain three sequence repeats of ∼40 amino acids which were very similar to the well-known whey acidic protein domains of other proteins. The new protein was therefore named perlwapin. In addition to the major sequence, we identified several minor variants. Atomic force microscopy was used to explore the interaction of perlwapin with calcite crystals. Monomolecular layers of calcite crystals dissolve very slowly in deionized water and recrystallize in supersaturated calcium carbonate solution. When perlwapin was dissolved in the supersaturated calcium carbonate solution, growth of the crystal was inhibited immediately. Perlwapin molecules bound tightly to distinct step edges, preventing the crystal layers from growing. Using lower concentrations of perlwapin in a saturated calcium carbonate solution, we could distinguish native, active perlwapin molecules from denaturated ones. These observations showed that perlwapin can act as a growth inhibitor for calcium carbonate crystals in saturated calcium carbonate solution. The function of perlwapin in nacre growth may be to inhibit the growth of certain crystallographic planes in the mineral phase of the polymer/mineral composite nacre. PMID:16861275

Heat storage in the Hettangian aquifer in Berlin - results from a column experiment

NASA Astrophysics Data System (ADS)

Milkus, Chri(Sch)augott

2015-04-01

Aquifer Thermal Energy Storage (ATES) is a sustainable alternative for storage and seasonal availability of thermal energy. However, its impact on the subsurface flow regime is not well known. In Berlin (Germany), the Jurassic (Hettangian) sandstone aquifer with highly mineralized groundwater (TDS 27 g/L) is currently used for heat storage. The aim of this study was to examine the hydrogeochemical changes that are caused by the induced temperature shift and its effects on the hydraulic permeability of the aquifer. Column experiments were conducted, in which stainless steel columns were filled with sediment from the aquifer and flushed with native groundwater for several weeks. The initial temperature of the experiment was 20°C, comparable to the in-situ conditions within the aquifer. After reaching equilibrium between sediment and water, the temperature was increased to simulate heating of the aquifer. During the experiment, physical and chemical parameters (pH, ORP, dissolved oxygen and dissolved carbon dioxide) were measured at the outflow of the column and the effluent water was sampled. Using a Scanning Electron Microscope, the deposition of precipitated minerals and biofilm on sediment grains was analyzed. Changes in hydraulic properties of the sediment were studied by the use of tracer tests with Uranin.

Microbial control of mineral–groundwater equilibria:Macroscale to microscale

USGS Publications Warehouse

Bennett, Philip C.; Hiebert, Franz K.; Roger, Jennifer Roberts

2000-01-01

macroscaleprocesses that perturb general groundwater chemistry and therefore mineral–water equilibria; and microscale interactions, where attached organisms locally perturb mineral–water equilibria, potentially releasing limiting trace nutrients from the dissolving mineral.In the contaminated unconfined glacio-fluvial aquifer near Bemidji, Minnesota, USA, carbonate chemistry is influenced primarily at the macroscale. Under oxic conditions, respiration by native aerobic heterotrophs produces excess carbon dioxide that promotes calcite and dolomite dissolution. Aerobic microorganisms do not colonize dolomite surfaces and few occur on calcite. Within the anoxic groundwater, calcite overgrowths form on uncolonized calcite cleavage surfaces, possibly due to the consumption of acidity by dissimilatory iron-reducing bacteria. As molecular oxygen concentration increases downgradient of the oil pool, aerobes again dominate and residual hydrocarbons and ferrous iron are oxidized, resulting in macroscale carbonate-mineral dissolution and iron precipitation.

Occurrence and distribution of trace elements in snow, streams, and streambed sediments, Cape Krusenstern National Monument, Alaska, 2002-2003

USGS Publications Warehouse

Brabets, Timothy P.

2004-01-01

Cape Krusenstern National Monument is located in Northwest Alaska. In 1985, an exchange of lands and interests in lands between the Northwest Alaska Native Association and the United States resulted in a 100-year transportation system easement for 19,747 acres in the monument. A road was then constructed along the easement from the Red Dog Mine, a large zinc concentrate producer and located northeast of the monument, through the monument to the coast and a port facility. Each year approximately 1.3 million tonnes of zinc and lead concentrate are transported from the Red Dog Mine via this access road. Concern about the possible deposition of cadmium, lead, zinc and other trace elements in the monument was the basis of a cooperative project with the National Park Service. Concentrations of dissolved cadmium, dissolved lead, and dissolved zinc from 28 snow samples from a 28 mile by 16 mile grid were below drinking water standards. In the particulate phase, approximately 25 percent of the samples analyzed for these trace elements were higher than the typical range found in Alaska soils. Boxplots of concentrations of these trace elements, both in the dissolved and particulate phase, indicate higher concentrations north of the access road, most likely due to the prevailing southeast wind. The waters of four streams sampled in Cape Krusenstern National Monument are classified as calcium bicarbonate. Trace-element concentrations from these streams were below drinking water standards. Median concentrations of 39 trace elements from streambed sediments collected from 29 sites are similar to the median concentrations of trace elements from the U.S. Geological Survey?s National Water-Quality Assessment database. Statistical differences were noted between trace-element concentrations of cadmium, lead, and zinc at sites along the access road and sites north and south of the access road; concentrations along the access road being higher than north or south of the road. When normalized to 1 percent organic carbon, the concentrations of these trace elements are not expected to be toxic to aquatic life when compared to criteria established by the Canadian government and other recent research.

Shifts in methanogen community structure and function across a coastal marsh transect: effects of exotic Spartina alterniflora invasion

PubMed Central

Yuan, Junji; Ding, Weixin; Liu, Deyan; Kang, Hojeong; Xiang, Jian; Lin, Yongxin

2016-01-01

Invasion of Spartina alterniflora in coastal areas of China increased methane (CH4) emissions. To elucidate the underlying mechanisms, we measured CH4 production potential, methanogen community structure and biogeochemical factors along a coastal wetland transect comprised of five habitat regions: open water, bare tidal flat, invasive S. alterniflora marsh and native Suaeda salsa and Phragmites australis marshes. CH4 production potential in S. alterniflora marsh was 10 times higher than that in other regions, and it was significantly correlated with soil organic carbon, dissolved organic carbon and trimethylamine concentrations, but was not correlated with acetate or formate concentrations. Although the diversity of methanogens was lowest in S. alterniflora marsh, invasion increased methanogen abundance by 3.48-fold, compared with native S. salsa and P. australis marshes due to increase of facultative Methanosarcinaceae rather than acetotrophic and hydrogenotrophic methanogens. Ordination analyses suggested that trimethylamine was the primary factor regulating shift in methanogen community structure. Addition of trimethylamine increased CH4 production rates by 1255-fold but only by 5.61- and 11.4-fold for acetate and H2/CO2, respectively. S. alterniflora invasion elevated concentration of non-competitive trimethylamine, and shifted methanogen community from acetotrophic to facultative methanogens, which together facilitated increased CH4 production potential. PMID:26728134

Nature and chlorine reactivity of organic constituents from reclaimed water in groundwater, Los Angeles County, California

USGS Publications Warehouse

Leenheer, J.A.; Rostad, C.E.; Barber, L.B.; Schroeder, R.A.; Anders, R.; Davisson, M.L.

2001-01-01

The nature and chlorine reactivity of organic constituents in reclaimed water (tertiary-treated municipal wastewater) before, during, and after recharge into groundwater at the Montebello Forebay in Los Angeles County, CA, was the focus of this study. Dissolved organic matter (DOM) in reclaimed water from this site is primarily a mixture of aromatic sulfonates from anionic surfactant degradation, N-acetyl amino sugars and proteins from bacterial activity, and natural fulvic acid, whereas DOM from native groundwaters in the aquifer to which reclaimed water was recharged consists of natural fulvic acids. The hydrophilic neutral N-acetyl amino sugars that constitute 40% of the DOM in reclaimed water are removed during the first 3 m of vertical infiltration in the recharge basin. Groundwater age dating with 3H and 3He isotopes, and determinations of organic and inorganic C isotopes, enabled clear differentiation of recent recharged water from older native groundwater. Phenol structures in natural fulvic acids in DOM isolated from groundwater produced significant trihalomethanes (THM) and total organic halogen (TOX) yields upon chlorination, and these structures also were responsible for the enhanced SUVA and specific fluorescence characteristics relative to DOM in reclaimed water. Aromatic sulfonates and fulvic acids in reclaimed water DOM produced minimal THM and TOX yields.

PHYSICOCHEMICAL PROPERTIES OF THE PROTEOLYTIC ENZYME FROM THE LATEX OF THE MILKWEED, ASCLEPIAS SPECIOSA TORR. SOME COMPARISONS WITH OTHER PROTEASES

PubMed Central

Winnick, Theodore; Davis, Alva R.; Greenberg, David M.

1940-01-01

1. A study has been made of the properties of a hitherto unreported proteolytic enzyme from the latex of the milkweed, Asclepias speciosa. The new protease has been named asclepain by the authors. 2. The results of chemical, diffusion, and denaturation tests indicate that asclepain is a protein. 3. Like papain, asclepain dots milk and digests most proteins, particularly if they are dissolved in concentrated urea solution. Unlike papain, asclepain did not clot blood. 4. The activation and inhibition phenomena of asclepain resemble those of papain, and seem best explained on the assumption that free sulfhydryl in the enzyme is necessary for proteolytic activity. The sulfhydryl of asclepain appears more labile than that of papain. 5. The measurement of pH-activity curves of asclepain on casein, ovalbumin, hemoglobin, edestin, and ovovitellin showed no definite digestion maxima for most of the undenatured proteins, while in urea solution there were well defined maxima near pH 7.0. Native hemoglobin and ovovitellin were especially undigestible, while native casein was rapidly attacked. 6. Temperature-activity curves were determined for asclepain on hemoglobin, casein, and milk solutions. The optimum temperature was shown to increase with decreasing time of digestion. PMID:19873154

Long-term synchronized electrophysiological and behavioral wireless monitoring of freely moving animals

PubMed Central

Grand, Laszlo; Ftomov, Sergiu; Timofeev, Igor

2012-01-01

Parallel electrophysiological recording and behavioral monitoring of freely moving animals is essential for a better understanding of the neural mechanisms underlying behavior. In this paper we describe a novel wireless recording technique, which is capable of synchronously recording in vivo multichannel electrophysiological (LFP, MUA, EOG, EMG) and activity data (accelerometer, video) from freely moving cats. The method is based on the integration of commercially available components into a simple monitoring system and is complete with accelerometers and the needed signal processing tools. LFP activities of freely moving group-housed cats were recorded from multiple intracortical areas and from the hippocampus. EMG, EOG, accelerometer and video were simultaneously acquired with LFP activities 24-h a day for 3 months. These recordings confirm the possibility of using our wireless method for 24-h long-term monitoring of neurophysiological and behavioral data of freely moving experimental animals such as cats, ferrets, rabbits and other large animals. PMID:23099345

Freely Tunable Broadband Polarization Rotator for Terahertz Waves

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

Fan, Ren-Hao; Zhou, Yu; Ren, Xiao-Ping

2014-12-28

A freely tunable polarization rotator for broadband terahertz waves is demonstrated using a three-rotating-layer metallic grating structure, which can conveniently rotate the polarization of a linearly polarized terahertz wave to any desired direction with nearly perfect conversion efficiency. This low-cost, high-efficiency, and freely tunable device has potential applications as material analysis, wireless communication, and THz imaging.

Response of fishes to floodplain connectivity during and following a 500-year flood event in the unimpounded upper Mississippi River

USGS Publications Warehouse

Barko, V.A.; Herzog, D.P.; O'Connell, M. T.

2006-01-01

We examined data collected on fish assemblage structure among three differing floodplain types (broad, moderate, and narrow) during the 1993 flood in the unimpounded reach of the upper Mississippi River. This 500 year flood event provided a unique opportunity to investigate fish-floodplain function because the main river channel is otherwise typically disjunct from approximately 82% of its floodplain by an extensive levee system. Fishes were sampled during three separate periods, and 42 species of adult and young-of-the-year (YOY) fishes were captured. Analysis of similarity (ANOSIM) revealed a significant and distinguishable difference between both adult and YOY assemblage structure among the three floodplain types. Analysis of variance revealed that Secchi transparency, turbidity, water velocity, and dissolved oxygen were significantly different among the floodplain types. However, only depth of gear deployment and Secchi transparency were significantly correlated with adult assemblage structure. None of these variables were significantly correlated with YOY assemblage structure. The numerically abundant families (adult and YOY catches combined) on the floodplain included Centrarchidae, Ictularidae, and Cyprinidae. Both native and non-native fishes were captured on the floodplain, and several of the numerically abundant species that were captured on the floodplain peaked in catch-per-unit-effort 1-3 years after the 1993 flood event. This suggests that some species may have used flooded terrestrial habitat for spawning, feeding, or both. The findings from our study provide much needed insight into fish-floodplain function in a temperate, channelized river system and suggest that lateral connectivity of the main river channel to less degraded reaches of its floodplain should become a management priority not only to maintain faunal biodiversity but also potentially reduce the impacts of non-native species in large river systems.

Fabrication of gold dot, ring, and corpuscle arrays from block copolymer templates via a simple modification of surface energy

NASA Astrophysics Data System (ADS)

Cho, Heesook; Choi, Sinho; Kim, Jin Young; Park, Soojin

2011-12-01

We demonstrate a simple method for tuning the morphologies of as-spun micellar thin films by modifying the surface energy of silicon substrates. When a polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP) copolymer dissolved in o-xylene was spin-coated onto a PS-modified surface, a dimple-type structure consisting of a thick PS shell and P2VP core was obtained. Subsequently, when the films were immersed in metal precursor solutions at certain periods of time and followed by plasma treatment, metal individual dots in a ring-shaped structure, metal nanoring, and metal corpuscle arrays were fabricated, depending on the loading amount of metal precursors. In contrast, when PS-b-P2VP films cast onto silicon substrates with a native oxide were used as templates, only metal dotted arrays were obtained. The combination of micellar thin film and surface energy modification offers an effective way to fabricate various nanostructured metal or metal oxide films.We demonstrate a simple method for tuning the morphologies of as-spun micellar thin films by modifying the surface energy of silicon substrates. When a polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP) copolymer dissolved in o-xylene was spin-coated onto a PS-modified surface, a dimple-type structure consisting of a thick PS shell and P2VP core was obtained. Subsequently, when the films were immersed in metal precursor solutions at certain periods of time and followed by plasma treatment, metal individual dots in a ring-shaped structure, metal nanoring, and metal corpuscle arrays were fabricated, depending on the loading amount of metal precursors. In contrast, when PS-b-P2VP films cast onto silicon substrates with a native oxide were used as templates, only metal dotted arrays were obtained. The combination of micellar thin film and surface energy modification offers an effective way to fabricate various nanostructured metal or metal oxide films. Electronic supplementary information (ESI) available: AFM images of Au nanorings prepared from a mixed solvent and characterization of PS-b-P2VP micellar films. See DOI: 10.1039/c1nr11075f

BioC implementations in Go, Perl, Python and Ruby.

PubMed

Liu, Wanli; Islamaj Doğan, Rezarta; Kwon, Dongseop; Marques, Hernani; Rinaldi, Fabio; Wilbur, W John; Comeau, Donald C

2014-01-01

As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/ Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Epidemiology of brucellosis among cattle in Korea from 2001 to 2011

PubMed Central

Moon, Oun-Kyong; Lee, Soo-Han; Lee, Won-Chang; Her, Moon; Jeong, Wooseog; Jung, Suk-Chan; Kim, Do-Soon

2014-01-01

In the present study, the outbreak patterns of bovine brucellosis in Korea from 2000 to 2011 were analyzed to understand the epidemiological evolution of this disease in the country. A total of 85,521 brucella reactor animals were identified during 14,215 outbreaks over the 12-year study period. The number of bovine brucellosis cases increased after 2003 and peaked in 2006 before decreasing thereafter. The majority of the bovine brucellosis cases were Korean native cattle, Han Woo. The numbers of human brucellosis cases and cattle outbreaks increased and decreased in the same pattern. The correlation coefficient for human and bovine cases per year was 0.96 (95% confidence interval = 0.86~0.99; p < 10-3). The epidemiological characteristics of bovine brucellosis appeared to be affected by the intensity of eradication programs that mainly involved a test-and-slaughter policy. Findings from the present study were based on freely available statistics from web pages maintained by government agencies. This unlimited access to information demonstrates the usefulness of government statistics for continually monitoring the health of animal populations. PMID:25234321

The pPSU Plasmids for Generating DNA Molecular Weight Markers.

PubMed

Henrici, Ryan C; Pecen, Turner J; Johnston, James L; Tan, Song

2017-05-26

Visualizing nucleic acids by gel electrophoresis is one of the most common techniques in molecular biology, and reference molecular weight markers or ladders are commonly used for size estimation. We have created the pPSU1 & pPSU2 pair of molecular weight marker plasmids which produce both 100 bp and 1 kb DNA ladders when digested with two common restriction enzymes. The 100 bp ladder fragments have been optimized to migrate appropriately on both agarose and native polyacrylamide, unlike many currently available DNA ladders. Sufficient plasmid DNA can be isolated from 100 ml E. coli cultures for the two plasmids to produce 100 bp or 1 kb ladders for 1000 gels. As such, the pPSU1 and pPSU2 plasmids provide reference fragments from 50 to 10000 bp at a fraction of the cost of commercial DNA ladders. The pPSU1 and pPSU2 plasmids are available without licensing restrictions to nonprofit academic users, affording freely available high-quality, low-cost molecular weight standards for molecular biology applications.

Coherent Behavior and the Bound State of Water and K+ Imply Another Model of Bioenergetics: Negative Entropy Instead of High-energy Bonds

PubMed Central

Jaeken, Laurent; Vasilievich Matveev, Vladimir

2012-01-01

Observations of coherent cellular behavior cannot be integrated into widely accepted membrane (pump) theory (MT) and its steady state energetics because of the thermal noise of assumed ordinary cell water and freely soluble cytoplasmic K+. However, Ling disproved MT and proposed an alternative based on coherence, showing that rest (R) and action (A) are two different phases of protoplasm with different energy levels. The R-state is a coherent metastable low-entropy state as water and K+ are bound to unfolded proteins. The A-state is the higher-entropy state because water and K+ are free. The R-to-A phase transition is regarded as a mechanism to release energy for biological work, replacing the classical concept of high-energy bonds. Subsequent inactivation during the endergonic A-to-R phase transition needs an input of metabolic energy to restore the low entropy R-state. Matveev’s native aggregation hypothesis allows to integrate the energetic details of globular proteins into this view. PMID:23264833

Heterogeneous Biomedical Database Integration Using a Hybrid Strategy: A p53 Cantcer Research Database

PubMed Central

Bichutskiy, Vadim Y.; Colman, Richard; Brachmann, Rainer K.; Lathrop, Richard H.

2006-01-01

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.) PMID:19458771

Filling the gap: adding super-resolution to array tomography for correlated ultrastructural and molecular identification of electrical synapses at the C. elegans connectome.

PubMed

Markert, Sebastian Matthias; Britz, Sebastian; Proppert, Sven; Lang, Marietta; Witvliet, Daniel; Mulcahy, Ben; Sauer, Markus; Zhen, Mei; Bessereau, Jean-Louis; Stigloher, Christian

2016-10-01

Correlating molecular labeling at the ultrastructural level with high confidence remains challenging. Array tomography (AT) allows for a combination of fluorescence and electron microscopy (EM) to visualize subcellular protein localization on serial EM sections. Here, we describe an application for AT that combines near-native tissue preservation via high-pressure freezing and freeze substitution with super-resolution light microscopy and high-resolution scanning electron microscopy (SEM) analysis on the same section. We established protocols that combine SEM with structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM). We devised a method for easy, precise, and unbiased correlation of EM images and super-resolution imaging data using endogenous cellular landmarks and freely available image processing software. We demonstrate that these methods allow us to identify and label gap junctions in Caenorhabditis elegans with precision and confidence, and imaging of even smaller structures is feasible. With the emergence of connectomics, these methods will allow us to fill in the gap-acquiring the correlated ultrastructural and molecular identity of electrical synapses.

Quantitative Analysis of Uranium Accumulation on Sediments during Field-scale Biostimulation under Variable Bicarbonate Concentrations at the Rifle IFRC Site

NASA Astrophysics Data System (ADS)

Fox, P. M.; Davis, J. A.; Bargar, J.; Williams, K. H.; Singer, D. M.; Long, P.

2011-12-01

Bioremediation of uranium in subsurface environments is an approach that has been used at numerous field sites throughout the U.S in an attempt to lower dissolved U(VI) concentrations in groundwater. At the Rifle IFRC research site in Colorado, biostimulation of the native microbial population through acetate amendment for various periods of time has been tested in order to immobilize uranium through reduction U(VI) to U(IV). While this approach has successfully decreased U(VI) concentrations in the dissolved phase, often to levels below the EPA's maximum contaminant level of 0.13 μM, little work has examined the solid-phase accumulation of U during field-scale biostimulation. The lack of information on solid-phase U accumulation is due in large part to the difficulty of obtaining comparable pre- and post-biostimulation field sediment samples. In addition, the relatively low (<10 ppm) U concentrations present in most sediments preclude the use of spectroscopic techniques such as XAS for examining solid-phase U speciation. However, a recently developed technique of performing column experiments in situ has allowed us to overcome both of these problems, obtaining sediment samples which were exposed to the same biogeochemical conditions as subsurface sediments during the course of biostimulation. During the 2010 Rifle IFRC field experiment (dubbed "Super 8"), a number of in situ columns were deployed in various wells representing regions of the aquifer affected by acetate amendment (ambient bicarbonate) and concomitant acetate and bicarbonate amendment (elevated bicarbonate). Elevated levels of bicarbonate have been shown to cause desorption of U(VI) from the solid phase at the Rifle site under non-stimulated conditions, resulting in higher dissolved U(VI) concentrations in the aquifer. The Super 8 field experiment was designed in part to test the effect of elevated bicarbonate concentrations on U sequestration during biostimulation. Results from this experiment provide a comparison of temporal aqueous and solid-phase U concentrations under ambient and elevated bicarbonate conditions during field-scale biostimulation. Additionally, a subset of in situ columns amended with 20 μM U(VI) were analyzed by XANES in order to determine the relative importance of U(VI) and U(IV) in the solid phase. While the elevated bicarbonate concentrations did not impede reduction and sequestration of U, differences in the behavior of dissolved U(VI) after acetate amendment was stopped demonstrate the importance of U adsorption-desorption reactions in controlling dissolved U concentrations post-biostimulation.

Implantable fiber-optic interface for parallel multisite long-term optical dynamic brain interrogation in freely moving mice

PubMed Central

Doronina-Amitonova, L. V.; Fedotov, I. V.; Ivashkina, O. I.; Zots, M. A.; Fedotov, A. B.; Anokhin, K. V.; Zheltikov, A. M.

2013-01-01

Seeing the big picture of functional responses within large neural networks in a freely functioning brain is crucial for understanding the cellular mechanisms behind the higher nervous activity, including the most complex brain functions, such as cognition and memory. As a breakthrough toward meeting this challenge, implantable fiber-optic interfaces integrating advanced optogenetic technologies and cutting-edge fiber-optic solutions have been demonstrated, enabling a long-term optogenetic manipulation of neural circuits in freely moving mice. Here, we show that a specifically designed implantable fiber-optic interface provides a powerful tool for parallel long-term optical interrogation of distinctly separate, functionally different sites in the brain of freely moving mice. This interface allows the same groups of neurons lying deeply in the brain of a freely behaving mouse to be reproducibly accessed and optically interrogated over many weeks, providing a long-term dynamic detection of genome activity in response to a broad variety of pharmacological and physiological stimuli. PMID:24253232

Implantable fiber-optic interface for parallel multisite long-term optical dynamic brain interrogation in freely moving mice

NASA Astrophysics Data System (ADS)

Doronina-Amitonova, L. V.; Fedotov, I. V.; Ivashkina, O. I.; Zots, M. A.; Fedotov, A. B.; Anokhin, K. V.; Zheltikov, A. M.

2013-11-01

Seeing the big picture of functional responses within large neural networks in a freely functioning brain is crucial for understanding the cellular mechanisms behind the higher nervous activity, including the most complex brain functions, such as cognition and memory. As a breakthrough toward meeting this challenge, implantable fiber-optic interfaces integrating advanced optogenetic technologies and cutting-edge fiber-optic solutions have been demonstrated, enabling a long-term optogenetic manipulation of neural circuits in freely moving mice. Here, we show that a specifically designed implantable fiber-optic interface provides a powerful tool for parallel long-term optical interrogation of distinctly separate, functionally different sites in the brain of freely moving mice. This interface allows the same groups of neurons lying deeply in the brain of a freely behaving mouse to be reproducibly accessed and optically interrogated over many weeks, providing a long-term dynamic detection of genome activity in response to a broad variety of pharmacological and physiological stimuli.

A glycoprotein from mammary gland secreted during involution promotes apoptosis: Structural and biological studies.

PubMed

Chaudhary, Anshul; Kumar, Vinod; Singh, Prashant K; Sharma, Pradeep; Bairagya, Hridoy R; Kaur, Punit; Sharma, Sujata; Chauhan, Shyam S; Singh, Tej P

2018-04-15

Secretory signalling glycoprotein (SPX-40) from mammary gland is highly expressed during involution. This protein is involved in a programmed cell death during tissue remodelling which occurs at the end of lactation. SPX-40 was isolated and purified from buffalo (SPB-40) from the samples obtained during involution. One solution of SPB-40 was made by dissolving it in buffer containing 25 mM Tris-HCl and 50 mM NaCl at pH 8.0. Another solution was made by adding 25% ethanol to the above solution. The biological effects of SPB-40 dissolved in above two solutions were evaluated on MCF-7 breast cancer cell lines. Free SPB-40 indicated significant pro-apoptotic effects while ethanol exposed SPB-40 showed considerably reduced effects on the apoptosis. SPB-40 was crystallized in the native state. The crystals of SPB-40 were soaked in four separate solutions containing 25% acetone, 25% ethanol, 25% butanol and 25% MPD. Four separate data sets were collected and their structures were determined at high resolutions. In all the four structures, the molecules of acetone, ethanol, butanol and MPD respectively were observed in the hydrophobic binding pocket of SPB-40. As a result of which, the conformation of Trp78 was altered thus blocking the binding site in SPB-40 leading to the loss of activity. Copyright © 2018. Published by Elsevier Inc.

The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities

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

Zhang, Zilian; Chen, Yi; Wang, Rui

Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that bacterial EPS rich in uronic acid is resistant to mineralization by microbes and thus has a long residence time in global oceans. To confirm this hypothesis, bacterial EPS rich in galacturonic acid was isolated from Alteromonas sp. JL2810. The EPS was used to amend natural seawater to investigate the bioavailability of this EPS by native populations, in the presence and absence of ammonium and phosphate amendment. The data indicated that the bacterial EPS could not bemore » completely consumed during the cultivation period and that the bioavailability of EPS was not only determined by its intrinsic properties, but was also determined by other factors such as the availability of inorganic nutrients. During the experiment, the humic-like component of fluorescent dissolved organic matter (FDOM) was freshly produced. Bacterial community structure analysis indicated that the class Flavobacteria of the phylum Bacteroidetes was the major contributor for the utilization of EPS. This report is the first to indicate that Flavobacteria are a major contributor to bacterial EPS degradation. Finally, the fraction of EPS that could not be completely utilized and the FDOM (e.g., humic acid-like substances) produced de novo may be refractory and may contribute to the carbon storage in the oceans.« less

Relation of desert pupfish abundance to selected environmental variables in natural and manmade habitats in the Salton Sea basin

USGS Publications Warehouse

Martin, B.A.; Saiki, M.K.

2005-01-01

We assessed the relation between abundance of desert pupfish, Cyprinodon macularius, and selected biological and physicochemical variables in natural and manmade habitats within the Salton Sea Basin. Field sampling in a natural tributary, Salt Creek, and three agricultural drains captured eight species including pupfish (1.1% of the total catch), the only native species encountered. According to Bray-Curtis resemblance functions, fish species assemblages differed mostly between Salt Creek and the drains (i.e., the three drains had relatively similar species assemblages). Pupfish numbers and environmental variables varied among sites and sample periods. Canonical correlation showed that pupfish abundance was positively correlated with abundance of western mosquitofish, Gambusia affinis, and negatively correlated with abundance of porthole livebearers, Poeciliopsis gracilis, tilapias (Sarotherodon mossambica and Tilapia zillii), longjaw mudsuckers, Gillichthys mirabilis, and mollies (Poecilia latipinnaandPoecilia mexicana). In addition, pupfish abundance was positively correlated with cover, pH, and salinity, and negatively correlated with sediment factor (a measure of sediment grain size) and dissolved oxygen. Pupfish abundance was generally highest in habitats where water quality extremes (especially high pH and salinity, and low dissolved oxygen) seemingly limited the occurrence of nonnative fishes. This study also documented evidence of predation by mudsuckers on pupfish. These findings support the contention of many resource managers that pupfish populations are adversely influenced by ecological interactions with nonnative fishes. ?? Springer 2005.

The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities

DOE PAGES

Zhang, Zilian; Chen, Yi; Wang, Rui; ...

2015-11-16

Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that bacterial EPS rich in uronic acid is resistant to mineralization by microbes and thus has a long residence time in global oceans. To confirm this hypothesis, bacterial EPS rich in galacturonic acid was isolated from Alteromonas sp. JL2810. The EPS was used to amend natural seawater to investigate the bioavailability of this EPS by native populations, in the presence and absence of ammonium and phosphate amendment. The data indicated that the bacterial EPS could not bemore » completely consumed during the cultivation period and that the bioavailability of EPS was not only determined by its intrinsic properties, but was also determined by other factors such as the availability of inorganic nutrients. During the experiment, the humic-like component of fluorescent dissolved organic matter (FDOM) was freshly produced. Bacterial community structure analysis indicated that the class Flavobacteria of the phylum Bacteroidetes was the major contributor for the utilization of EPS. This report is the first to indicate that Flavobacteria are a major contributor to bacterial EPS degradation. Finally, the fraction of EPS that could not be completely utilized and the FDOM (e.g., humic acid-like substances) produced de novo may be refractory and may contribute to the carbon storage in the oceans.« less

Dissolved organic carbon from the upper Rio Negro protects zebrafish (Danio rerio) against ionoregulatory disturbances caused by low pH exposure

PubMed Central

Duarte, Rafael M.; Smith, D. Scott; Val, Adalberto L.; Wood, Chris M.

2016-01-01

The so-called “blackwaters” of the Amazonian Rio Negro are rich in highly coloured dissolved organic carbon (DOC), but ion-poor and very acidic, conditions that would cause fatal ionoregulatory failure in most fish. However these blackwaters support 8% of the world’s ichthyofauna. We tested the hypothesis that native DOC provides protection against ionoregulatory dysfunction in this extreme environment. DOCs were isolated by reverse-osmosis from two Rio Negro sites. Physico-chemical characterization clearly indicated a terrigenous origin, with a high proportion of hydroxyl and phenolic sites, high chemical reactivity to protons, and unusual proteinaceous fluorescence. When tested using zebrafish (a model organism), Rio Negro DOC provided almost perfect protection against ionoregulatory disturbances associated with acute exposure to pH 4.0 in ion-poor water. DOC reduced diffusive losses of Na+ and Cl−, and promoted a remarkable stimulation of Na+ uptake that otherwise would have been completely inhibited. Additionally, prior acclimation to DOC at neutral pH reduced rates of branchial Na+ turnover, and provided similar protection against acid-induced ionoregulatory disturbances, even if the DOC was no longer present. These results reinforce the important roles that DOC molecules can play in the regulation of gill functions in freshwater fish, particularly in ion-poor, acidic blackwaters. PMID:26853589

Geology and ground-water resources of the Lake Dakota Plain area, South Dakota

USGS Publications Warehouse

Hopkins, William B.; Petri, Lester R.

1963-01-01

Unconsolidated deposits of Quaternary age mantle the Cretaceous rocks. Although they consist mostly of material that is too fine grained to yield water freely to wells, the Quaternary deposits contain bodies of moderately to highly permeable material that yield water copiously. Such bodies may be located only by exploratory drilling or, possibly, geophysical methods. The water differs widely in amount of mineralization and in chemical composition; the specific conductance of water from 322 wells ranged from 246 to 13,300 micromhos per centimeter. In most of the report area the water is of unsuitable quality for irrigation and domestic use. The principal source of recharge to the Quaternary deposits is infiltrating precipitation. Evapotranspiration accounts for nearly all the water discharged; the amount of water discharging into stream channels and withdrawn from wells is almost negligible by comparison. Irrigation of the area would increase the rate of recharge to the Quaternary deposits and would cause the water table to rise. Probably it would also cause an increase in the concentration of dissolved minerals in much of the ground water. Artificial drainage would be necessary to prevent waterlogging of cropland.

Tracking human footprints in Antarctica through passive sampling of polycyclic aromatic hydrocarbons in inland lakes.

PubMed

Yao, Yao; Meng, Xiang-Zhou; Wu, Chen-Chou; Bao, Lian-Jun; Wang, Feng; Wu, Feng-Chang; Zeng, Eddy Y

2016-06-01

Freely dissolved polycyclic aromatic hydrocarbons (PAHs) were monitored in seven inland lakes of Antarctica by a polyethylene (PE)-based passive sampling technique, with the objective of tracking human footprints. The measured concentrations of PAHs were in the range of 14-360 ng L(-1) with the highest values concentrated around the Russian Progress II Station, indicating the significance of human activities to the loading of PAHs in Antarctica. The concentrations of PAHs in the inland lakes were in the upper part of the PAHs levels in aquatic environments from remote and background regions across the globe. The composition profiles of PAHs indicated that PAHs in the inland lakes were derived mainly from local oil spills, which was corroborated by a large number of fuel spillage reports from ship and plane crash incidents in Antarctica during recent years. Clearly, local human activities, rather than long-range transport, are the dominant sources of PAH contamination to the inland lakes. Finally, the present study demonstrates the efficacy of PE-based passive samplers for investigating PAHs in the aquatic environment of Antarctica under complex field conditions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Overview of the US EPA/SERDP/ESTCP: Laboratory, Field ...

EPA Pesticide Factsheets

Passive sampling can be used for applications at contaminated sediment sites including performing assessments of contaminant bioavailability (i.e., freely dissolved concentration (Cfree)), conducting remedial investigations and feasibility studies, and assessing the potential for contaminant bioaccumulation. Previous research articles and documents have discussed many aspects of passive sampling however no definitive guidance on the laboratory, field and analytical procedures for using passive sampling at contaminated sediment sites has been provided. The document discussed in this presentation provides passive sampler users with the guidance necessary to apply the technology to evaluate contaminated sediments. Contaminants discussed include polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), and the metals, cadmium, copper, nickel, lead and zinc. The document is divided into sections including discussions of different types of samplers used commonly in the United States, the selection and use of performance reference compounds (PRCs), the extraction and instrumental analysis of passive samplers, data analysis and quality assurance/quality control, and a list of passive sampling related references. The document is not intended to serve as a series of standard operating procedures (SOPs) but rather seeks to provide users with the information needed to develop their own SOPs. The document also includes the names of selected passive sam

Passive Sampling in Regulatory Chemical Monitoring of Nonpolar Organic Compounds in the Aquatic Environment.

PubMed

Booij, Kees; Robinson, Craig D; Burgess, Robert M; Mayer, Philipp; Roberts, Cindy A; Ahrens, Lutz; Allan, Ian J; Brant, Jan; Jones, Lisa; Kraus, Uta R; Larsen, Martin M; Lepom, Peter; Petersen, Jördis; Pröfrock, Daniel; Roose, Patrick; Schäfer, Sabine; Smedes, Foppe; Tixier, Céline; Vorkamp, Katrin; Whitehouse, Paul

2016-01-05

We reviewed compliance monitoring requirements in the European Union, the United States, and the Oslo-Paris Convention for the protection of the marine environment of the North-East Atlantic, and evaluated if these are met by passive sampling methods for nonpolar compounds. The strengths and shortcomings of passive sampling are assessed for water, sediments, and biota. Passive water sampling is a suitable technique for measuring concentrations of freely dissolved compounds. This method yields results that are incompatible with the EU's quality standard definition in terms of total concentrations in water, but this definition has little scientific basis. Insufficient quality control is a present weakness of passive sampling in water. Laboratory performance studies and the development of standardized methods are needed to improve data quality and to encourage the use of passive sampling by commercial laboratories and monitoring agencies. Successful prediction of bioaccumulation based on passive sampling is well documented for organisms at the lower trophic levels, but requires more research for higher levels. Despite the existence of several knowledge gaps, passive sampling presently is the best available technology for chemical monitoring of nonpolar organic compounds. Key issues to be addressed by scientists and environmental managers are outlined.

The Synthesis and X-ray Structural Characterization of mer and fac isomers of the Technetium(I) Nitrosyl Complex [TcCl(2)(NO)(PNPpr)].

PubMed

Nicholson, T L; Mahmood, A; Refosco, F; Tisato, F; Müller, P; Jones, A G

2009-08-01

The nitrosyl complex H[TcNOCl(4)] reacts with the tridentate ligand bis[(2-diphenylphosphino)propyl]amine (PNPpr) to yield a mixture of the mer or fac isomers of [TcCl(2)(NO)(PNPpr)]. In acetonitrile, where the ligand is freely soluble, reaction occurs at room temperature to yield mostly the mer isomer with the linear nitrosyl ligand cis to the amine ligand; and the phosphine ligands arranged in a mutually trans orientation. The reaction in methanol requires reflux to dissolve the lipophilic ligand and generates the fac isomer of [TcCl2(NO)(PNPpr)] as the major product, with the tridentate ligand in a facial arrangement, leaving the chlorides and nitrosyl ligand in the remaining facial sites. The steric bulk of the tridentate ligand's diphenylphophino- moieties results in a significant distortion from octahedral geometry, with the P-Tc-P bond angle expanded to 99.48(4)°. The infrared spectra display absorptions from these nitrosyl ligands in the 1700 and 1800 cm(-1) regions for the fac and mer isomers respectively. The ESI(+) mass spectra each display the parent ion at 647 m/z.

Passive sampling methods for contaminated sediments: Practical guidance for selection, calibration, and implementation

PubMed Central

Ghosh, Upal; Driscoll, Susan Kane; Burgess, Robert M; Jonker, Michiel To; Reible, Danny; Gobas, Frank; Choi, Yongju; Apitz, Sabine E; Maruya, Keith A; Gala, William R; Mortimer, Munro; Beegan, Chris

2014-01-01

This article provides practical guidance on the use of passive sampling methods (PSMs) that target the freely dissolved concentration (Cfree) for improved exposure assessment of hydrophobic organic chemicals in sediments. Primary considerations for selecting a PSM for a specific application include clear delineation of measurement goals for Cfree, whether laboratory-based “ex situ” and/or field-based “in situ” application is desired, and ultimately which PSM is best-suited to fulfill the measurement objectives. Guidelines for proper calibration and validation of PSMs, including use of provisional values for polymer–water partition coefficients, determination of equilibrium status, and confirmation of nondepletive measurement conditions are defined. A hypothetical example is described to illustrate how the measurement of Cfree afforded by PSMs reduces uncertainty in assessing narcotic toxicity for sediments contaminated with polycyclic aromatic hydrocarbons. The article concludes with a discussion of future research that will improve the quality and robustness of Cfree measurements using PSMs, providing a sound scientific basis to support risk assessment and contaminated sediment management decisions. Integr Environ Assess Manag 2014;10:210–223. © 2014 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of SETAC. PMID:24288273

Axial and radial nanostructures in electrospun polymer fibers

NASA Astrophysics Data System (ADS)

Greenfeld, Israel; Camposeo, Andrea; Tantussi, Francesco; Pagliara, Stefano; Fuso, Francesco; Allegrini, Maria; Pisignano, Dario; Zussman, Eyal

2013-03-01

The high tensional stresses during electrospinning of semidilute polymer solutions affect the dynamic conformation of the polymer network within the liquid jet, leaving a distinctive trace in the molecular structure after solidification. We investigated such effects in electrospun nanofibers made of conjugated polymers. Modeling the polymer network evolution during electrospinning showed that as the network stretches axially, it contracts towards the jet core. The model represents the semi-flexible conjugated polymer chains as flexible freely-jointed chains, whose joints are bonding defects. Using the conjugated polymer MEH-PPV dissolved in a mixture of THF and DMF solvents, and taking advantage of its unique photophysical characteristics, we investigated optically the variations in the density and orientation of the polymer macromolecules in electrospun nanofibers. In agreement with our model, we found higher density and axial orientation at the fiber core, while lower density and radial orientation closer to the fiber surface. The non-uniformity of the resulting molecular structure can be tuned and exploited in diverse optical and structural applications. We acknowledge: V. Fasano, G. Potente, S. Girardo and E. Caldi for assistance in measurements; United States-Israel BSF, RBNI Institute, and the Israel Science Foundation for financial support.

OptoZIF Drive: a 3D printed implant and assembly tool package for neural recording and optical stimulation in freely moving mice

NASA Astrophysics Data System (ADS)

Freedman, David S.; Schroeder, Joseph B.; Telian, Gregory I.; Zhang, Zhengyang; Sunil, Smrithi; Ritt, Jason T.

2016-12-01

Objective. Behavioral neuroscience studies in freely moving rodents require small, light-weight implants to facilitate neural recording and stimulation. Our goal was to develop an integrated package of 3D printed parts and assembly aids for labs to rapidly fabricate, with minimal training, an implant that combines individually positionable microelectrodes, an optical fiber, zero insertion force (ZIF-clip) headstage connection, and secondary recording electrodes, e.g. for electromyography (EMG). Approach. Starting from previous implant designs that position recording electrodes using a control screw, we developed an implant where the main drive body, protective shell, and non-metal components of the microdrives are 3D printed in parallel. We compared alternative shapes and orientations of circuit boards for electrode connection to the headstage, in terms of their size, weight, and ease of wire insertion. We iteratively refined assembly methods, and integrated additional assembly aids into the 3D printed casing. Main results. We demonstrate the effectiveness of the OptoZIF Drive by performing real time optogenetic feedback in behaving mice. A novel feature of the OptoZIF Drive is its vertical circuit board, which facilities direct ZIF-clip connection. This feature requires angled insertion of an optical fiber that still can exit the drive from the center of a ring of recording electrodes. We designed an innovative 2-part protective shell that can be installed during the implant surgery to facilitate making additional connections to the circuit board. We use this feature to show that facial EMG in mice can be used as a control signal to lock stimulation to the animal’s motion, with stable EMG signal over several months. To decrease assembly time, reduce assembly errors, and improve repeatability, we fabricate assembly aids including a drive holder, a drill guide, an implant fixture for microelectode ‘pinning’, and a gold plating fixture. Significance. The expanding capability of optogenetic tools motivates continuing development of small optoelectric devices for stimulation and recording in freely moving mice. The OptoZIF Drive is the first to natively support ZIF-clip connection to recording hardware, which further supports a decrease in implant cross-section. The integrated 3D printed package of drive components and assembly tools facilities implant construction. The easy interfacing and installation of auxiliary electrodes makes the OptoZIF Drive especially attractive for real time feedback stimulation experiments.

Development and evaluation of geochemical methods for the sourcing of archaeological maize

USGS Publications Warehouse

Benson, L.V.; Taylor, Howard E.; Peterson, K.A.; Shattuck, B.D.; Ramotnik, C.A.; Stein, J.R.

2008-01-01

Strontium (Sr)-isotope values on bone from deer mice pairs from 12 field sites in the Chaco Canyon area, New Mexico, were compared with isotope values of synthetic soil waters from the same fields. The data indicate that mice obtain Sr from near-surface sources and that soil samples collected at depths ranging from 25 to 95 cm contain Sr that is more accessible to the deep roots of maize; thus, synthetic soil solutions provide better data for the sourcing of archaeological maize. However, the Sr-isotope composition of mice may be more valuable in sourcing archaeological remains of animals such as rabbit, turkey, and deer. In a separate study, five Native American maize (Zea mays L. ssp. mays) accessions grown out at New Mexico State University Agricultural Science Center, Farmington, New Mexico were used to determine if soil-water metal pairs partition systematically into cobs and kernels. The sampled maize included landraces from three Native American groups (Acoma, Hopi, Zuni) that still occupy the Four Corners area. Two cobs each were picked from 10 plants of each landrace. Partitioning of the Ba/Mn, Ba/Sr, Ca/Sr, and K/Rb metal pairs from the soil water to the cob appears to behave in a systematic fashion. In addition, 51 rare earth element (REE) pairs also appear to systematically partition from the soil water into cobs; however, the ratios of the REE dissolved in the soil waters are relatively invariant; therefore, the distribution coefficients that describe the partitioning of REE from the soil water to the cob may not apply to archeological cobs grown under chemically heterogeneous conditions. Partitioning of Ba/Rb, Ba/Sr, Mg/P, and Mn/P metal pairs from the soil water to kernels also behaves in a systematic fashion. Given that modern Native American landraces were grown under optimal environmental conditions that may not have been duplicated by prehistoric Native Americans, the distribution coefficients obtained in this study should be used with caution. ?? 2007 Elsevier Ltd. All rights reserved.

Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.

PubMed

Castaño-Díez, Daniel; Kudryashev, Mikhail; Arheit, Marcel; Stahlberg, Henning

2012-05-01

Dynamo is a new software package for subtomogram averaging of cryo Electron Tomography (cryo-ET) data with three main goals: first, Dynamo allows user-transparent adaptation to a variety of high-performance computing platforms such as GPUs or CPU clusters. Second, Dynamo implements user-friendliness through GUI interfaces and scripting resources. Third, Dynamo offers user-flexibility through a plugin API. Besides the alignment and averaging procedures, Dynamo includes native tools for visualization and analysis of results and data, as well as support for third party visualization software, such as Chimera UCSF or EMAN2. As a demonstration of these functionalities, we studied bacterial flagellar motors and showed automatically detected classes with absent and present C-rings. Subtomogram averaging is a common task in current cryo-ET pipelines, which requires extensive computational resources and follows a well-established workflow. However, due to the data diversity, many existing packages offer slight variations of the same algorithm to improve results. One of the main purposes behind Dynamo is to provide explicit tools to allow the user the insertion of custom designed procedures - or plugins - to replace or complement the native algorithms in the different steps of the processing pipeline for subtomogram averaging without the burden of handling parallelization. Custom scripts that implement new approaches devised by the user are integrated into the Dynamo data management system, so that they can be controlled by the GUI or the scripting capacities. Dynamo executables do not require licenses for third party commercial software. Sources, executables and documentation are freely distributed on http://www.dynamo-em.org. Copyright © 2012 Elsevier Inc. All rights reserved.

ISCE: A Modular, Reusable Library for Scalable SAR/InSAR Processing

NASA Astrophysics Data System (ADS)

Agram, P. S.; Lavalle, M.; Gurrola, E. M.; Sacco, G. F.; Rosen, P. A.

2016-12-01

Traditional community SAR/InSAR processing software tools have primarily focused on differential interferometry and Solid Earth applications. The InSAR Scientific Computing Environment (ISCE) was specifically designed to support the Earth Sciences user community as well as large scale operational processing tasks, thanks to its two-layered (Python+C/Fortran) architecture and modular framework. ISCE is freely distributed as a source tarball, allowing advanced users to modify and extend it for their research purposes and developing exploratory applications, while providing a relatively simple user interface for novice users to perform routine data analysis efficiently. Modular design of the ISCE library also enables easier development of applications to address the needs of Ecosystems, Cryosphere and Disaster Response communities in addition to the traditional Solid Earth applications. In this talk, we would like to emphasize the broader purview of the ISCE library and some of its unique features that sets it apart from other freely available community software like GMTSAR and DORIS, including: Support for multiple geometry regimes - Native Doppler (ALOS-1) as well Zero Doppler (ESA missions) systems. Support for data acquired by airborne platforms - e.g, JPL's UAVSAR and AirMOSS, DLR's F-SAR. Radiometric Terrain Correction - Auxiliary output layers from the geometry modules include projection angles, incidence angles, shadow-layover masks. Dense pixel offsets - Parallelized amplitude cross correlation for cryosphere / ionospheric correction applications. Rubber sheeting - Pixel-by-pixel offsets fields for resampling slave imagery for geometric co-registration/ ionospheric corrections. Preliminary Tandem-X processing support - Bistatic geometry modules. Extensibility to support other non-Solid Earth missions - Modules can be directly adopted for use with other SAR missions, e.g., SWOT. Preliminary support for multi-dimensional data products- multi-polarization, multi-frequency, multi-temporal, multi-baseline stacks via the PLANT and GIAnT toolboxes. Rapid prototyping - Geometry manipulation functionality at the python level allows users to prototype and test processing modules at the interpreter level before optimal implementation in C/C++/Fortran.

[Drug consumption and risks of polypharmacotherapy in elderly population].

PubMed

Kubesová, H; Holík, J; Weber, P; Polcarová, V; Matejovský, J; Mazalová, K; Slapák, J

2006-01-01

One of our previous studies was aimed at the consumption of prescribed drugs by the elderly population. The average per day number of drugs was 4.6 (maximum 13). Existence of freely obtainable drugs with massive advertisements brings a question, how many of those drugs it is necessary to add in order to estimate probability of interaction and undesirable drug effects. In order to achieve valid information, students of the sixth year of General medicine program during their practical course at general practitioners were asked to interview randomly selected senior patients. They asked on the number, type, and price of freely obtainable drugs which they use. Data were evaluated from interviews accomplished during academic years 2001/2002 and 2004/2005. Our cohort included 252 men and 148 women with average age of 78.7 years. Average number of freely obtainable drugs was 2.26 at the beginning and 2.32 at the end of study. Only 34% of questioned did not buy any of those drugs at all or only exceptionally, 66% reported buying once a month or weekly. 44% of seniors buy analgetics, 58% buy vitamins, 37% food supplements, 36% non steroid antirheumatics, 46% cold prevention drugs, 30% anti-constipation drugs. Contrary to our expectation, positive correlation between the sums given for the personal participation on the drug costs and that given for freely obtainable drugs was found. It is not possible to expect, that polymorbidic patient with several prescribed drugs would buy less of freely obtainable drugs even due to the financial requirements. Freely obtainable drugs, many of them composites, can represent significant source of interactions and undesirable drug effects. They can also significantly modulate compliance of the senior. The high percentage of seniors buying freely obtainable drugs requires aimed questions on the pharmacological history.

In Vivo Microdialysis and Electroencephalographic Activity in Freely Moving Guinea Pigs Exposed to Organophosphorus Nerve Agents Sarin and VX: Analysis of Acetylcholine and Glutamate

DTIC Science & Technology

2011-01-01

3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE In vivo microdialysis and electroencephalographic activity in freely moving guinea pigs 5a...microdialysis and electroencephalographic activity in freely moving guinea pigs exposed to organophosphorus nerve agents sarin and VX: analysis of...brain seizure activity . This robust double multi- variate design provides greater fidelity when comparing data while also reducing the required number

Seiberg-Witten geometries for Coulomb branch chiral rings which are not freely generated

DOE PAGES

Argyres, Philip C.; Lü, Yongchao; Martone, Mario

2017-06-27

Coulomb branch chiral rings of N = 2 SCFTs are conjectured to be freely generated. While no counter-example is known, no direct evidence for the conjecture is known either. We initiate a systematic study of SCFTs with Coulomb branch chiral rings satisfying non-trivial relations, restricting our analysis to rank 1. The main result of our study is that (rank-1) SCFTs with non-freely generated CB chiral rings when deformed by relevant deformations, always flow to theories with non-freely generated CB rings. This implies that if they exist, they must thus form a distinct subset under RG flows. We also nd manymore » interesting characteristic properties that these putative theories satisfy which may be helpful in proving or disproving their existence using other methods.« less

A new model for the biodegradation kinetics of oil droplets: application to the Deepwater Horizon oil spill in the Gulf of Mexico

PubMed Central

2013-01-01

Oil biodegradation by native bacteria is one of the most important natural processes that can attenuate the environmental impacts of marine oil spills. Existing models for oil biodegradation kinetics are mostly for dissolved oil. This work developed a new mathematical model for the biodegradation of oil droplets and applied the model to estimate the time scale for oil biodegradation under conditions relevant to the Deepwater Horizon oil spill in the Gulf of Mexico. In the model, oil is composed of droplets of various sizes following the gamma function distribution. Each oil droplet shrinks during the microbe-mediated degradation at the oil-water interface. Using our developed model, we find that the degradation of oil droplets typically goes through two stages. The first stage is characterized by microbial activity unlimited by oil-water interface with higher biodegradation rates than that of the dissolved oil. The second stage is governed by the availability of the oil-water interface, which results in much slower rates than that of soluble oil. As a result, compared to that of the dissolved oil, the degradation of oil droplets typically starts faster and then quickly slows down, ultimately reaching a smaller percentage of degraded oil in longer time. The availability of the water-oil interface plays a key role in determining the rates and extent of degradation. We find that several parameters control biodegradation rates, including size distribution of oil droplets, initial microbial concentrations, initial oil concentration and composition. Under conditions relevant to the Deepwater Horizon spill, we find that the size distribution of oil droplets (mean and coefficient of variance) is the most important parameter because it determines the availability of the oil-water interface. Smaller oil droplets with larger variance leads to faster and larger extent of degradation. The developed model will be useful for evaluating transport and fate of spilled oil, different remediation strategies, and risk assessment. PMID:24138161

Stable Isotopic Composition of Dissolved Organic Nitrogen Fueling Brown Tide in a Semi-Arid Texas Estuary

NASA Astrophysics Data System (ADS)

Campbell, J.; Felix, J. D. D.; Wetz, M.; Cira, E.

2017-12-01

Harmful algal blooms (HABs) have the potential to adversely affect the water quality of estuaries and, consequently, their ability to support healthy and diverse ecosystems. Since the early 1990s, Baffin Bay, a semi-arid south Texas estuary, has progressively experienced harmful algal blooms. The primary species of HAB native to the Baffin Bay region, Aureoumbra lagunensis, is unable to utilize nitrate as a nutrient source, but instead relies on forms of reduced nitrogen (such as dissolved organic nitrogen (DON) and ammonium (NH4+)) for survival. DON levels in Baffin Bay (77 ± 10 µM) exceed the DON concentrations of not only typical Texas estuaries, but estuaries worldwide. Additionally, DON accounts for 90% of the total dissolved nitrogen (TDN) in Baffin Bay, followed by NH4+ at 8%, and NO3-+NO2- contributing 2%. Due to the dependence of A. lagunensis on the reduced forms of nitrogen as an energy source and the elevated concentrations of DON throughout the bay, it is important to identify the origin of this nitrogen as well as how it's being processed as it cycles through the ecosystem. The presented work investigates the stable isotopic composition of reactive nitrogen (Nr) (δ15N-DON, δ15N-NH4+, and δ15N-NO3-) in Baffin Bay samples collected monthly at nine stations over the period of one year. The work provides preliminary evidence of Nr sources and mechanisms driving favorable conditions for HAB proliferation. This information can be useful and applicable to estuarine ecosystems in various settings, advancing scientific progress towards mitigating blooms. Additionally, since the elevated concentrations of DON make Baffin Bay uniquely suited to investigate its sources and processing, this project will aid in characterizing the role of this largely unstudied form of Nr, which could provide insight and change perceptions about the role of DON in nitrogen dynamics.

Investigation of runoff generation in small catchments with dissolved veterinary and human pharmaceuticals

NASA Astrophysics Data System (ADS)

Krein, Andreas; Pailler, Jean-Yannick; Guignard, Cédric; Pfister, Laurent; Hoffmann, Lucien

2010-05-01

This investigation focuses on the analysis of four classes of veterinary and human pharmaceuticals in surface water in Luxembourg. The selected pharmaceuticals include four sulfonamides, two tetracyclines, two analgesics, and three hormones. Solid-phase extraction with liquid chromatography-tandem mass spectrometry resulted in detection limits ranging from 0.3 to 2.0 ng/L, allowing the determination of pharmaceuticals in storm waters. The analysis of pharmaceuticals by liquid chromatography-tandem mass spectrometry is a useful tool to trace their behaviour in the aquatic environment. Application of this method to river concentration and flood events revealed high concentrations of ibuprofen, with highest levels during flood events, while concentrations of estrogens and sulfonamides were comparatively low. So far, the yeast estrogen screen has been applied for some of the samples. The measured steroid values were converted to estrogenic activity by taking into account the relative potency of each chemical compared to the reference, estradiol. This method considers the relative affinity of the steroids for the hormone receptor. The measured estrogenic activity in the surface water is regularly at levels larger than 5 ng/L estradiol equivalents which might be of concern to reproductive success of native fish populations. The concentration and transport of xenobiotics in surface waters depend on hydraulic conditions including rainfall pattern and sewage overflow, on the properties of the substances, including sorption, degradation, and metabolism. The analysis of flood events using the rainfall pattern, the hydrograph, and dissolved pharmaceutical chemographs provides an insight into the temporal structure of flood events. The corresponding anthropogenic sources show a high temporal and spatial variability that is caused by different rainfall patterns and distributions, and the different characteristics (e.g. retention capacities) of the combined sewer systems. We can show that the combined sewer overflows deliver an important part of the dissolved pharmaceuticals into the river network.

Freely oriented portable superconducting magnet

DOEpatents

Schmierer, Eric N [Los Alamos, NM; Prenger, F Coyne [Los Alamos, NM; Hill, Dallas D [Los Alamos, NM

2010-01-12

A freely oriented portable superconducting magnet is disclosed. Coolant is supplied to the superconducting magnet from a repository separate from the magnet, enabling portability of the magnet. A plurality of support assemblies structurally anchor and thermally isolate the magnet within a thermal shield. A plurality of support assemblies structurally anchor and thermally isolate the thermal shield within a vacuum vessel. The support assemblies restrain movement of the magnet resulting from energizing and cooldown, as well as from changes in orientation, enabling the magnet to be freely orientable.

The effect of hydrogen peroxide on uranium oxide films on 316L stainless steel

NASA Astrophysics Data System (ADS)

Wilbraham, Richard J.; Boxall, Colin; Goddard, David T.; Taylor, Robin J.; Woodbury, Simon E.

2015-09-01

For the first time the effect of hydrogen peroxide on the dissolution of electrodeposited uranium oxide films on 316L stainless steel planchets (acting as simulant uranium-contaminated metal surfaces) has been studied. Analysis of the H2O2-mediated film dissolution processes via open circuit potentiometry, alpha counting and SEM/EDX imaging has shown that in near-neutral solutions of pH 6.1 and at [H2O2] ⩽ 100 μmol dm-3 the electrodeposited uranium oxide layer is freely dissolving, the associated rate of film dissolution being significantly increased over leaching of similar films in pH 6.1 peroxide-free water. At H2O2 concentrations between 1 mmol dm-3 and 0.1 mol dm-3, formation of an insoluble studtite product layer occurs at the surface of the uranium oxide film. In analogy to corrosion processes on common metal substrates such as steel, the studtite layer effectively passivates the underlying uranium oxide layer against subsequent dissolution. Finally, at [H2O2] > 0.1 mol dm-3 the uranium oxide film, again in analogy to common corrosion processes, behaves as if in a transpassive state and begins to dissolve. This transition from passive to transpassive behaviour in the effect of peroxide concentration on UO2 films has not hitherto been observed or explored, either in terms of corrosion processes or otherwise. Through consideration of thermodynamic solubility product and complex formation constant data, we attribute the transition to the formation of soluble uranyl-peroxide complexes under mildly alkaline, high [H2O2] conditions - a conclusion that has implications for the design of both acid minimal, metal ion oxidant-free decontamination strategies with low secondary waste arisings, and single step processes for spent nuclear fuel dissolution such as the Carbonate-based Oxidative Leaching (COL) process.

Linking carbon and hydrologic fluxes in the critical zone: Observations from high-frequency monitoring of a weathered bedrock vadose zone

NASA Astrophysics Data System (ADS)

Tune, A. K.; Druhan, J. L.; Wang, J.; Cargill, S.; Murphy, C.; Rempe, D. M.

2017-12-01

A principle challenge in quantifying feedbacks between continental weathering and atmospheric CO2 is to improve understanding of how biogeochemical processes in the critical zone influence the distribution and mobility of organic and inorganic carbon. In particular, in landscapes characterized by thin soils and heterogeneous weathered and fractured bedrock, little data exist to inform and constrain predictive models for carbon dynamics. Here, we present the results of an intensive water and gas sampling campaign across an 18 m thick, variably saturated argillite weathering profile in the Eel River CZO. We monitor water content in situ and regularly collect samples of freely-draining water, tightly-held water, and gas through wet and dry seasons using a novel Vadose-zone Monitoring System (VMS) consisting of sensors and samplers distributed across a 20 m long inclined borehole. This novel approach facilitates the interception of gas and water during transport across the entire variably saturated weathering profile. The data demonstrate that seasonal changes in saturation control the vertical distribution and mobility of carbon in the fractured critical zone. Concentrations of gaseous CO2, O2, and dissolved organic and inorganic carbon fluctuate significantly and repeatably with seasonal additions of water infiltrating the weathered bedrock. A persistent vertical structure in the concentrations of dissolved phases and gas concentrations broadly corresponds to depths associated with unsaturated, seasonally saturated, and chronically saturated zones. Associated variations in the vertical structure of mineralogy and elemental composition, including solid phase organic carbon content, are observed in core obtained during drilling. Together, our observations indicate significant respiration of organic carbon at depths greater than the base of the soil, and thus motivate further investigation of the role of heterogeneous weathered, bedrock environments, which are needed to improve quantitative models for feedbacks between terrestrial and atmospheric CO2.

Controls on soil solution nitrogen along an altitudinal gradient in the Scottish uplands.

PubMed

Jackson-Blake, L; Helliwell, R C; Britton, A J; Gibbs, S; Coull, M C; Dawson, L

2012-08-01

Nitrogen (N) deposition continues to threaten upland ecosystems, contributing to acidification, eutrophication and biodiversity loss. We present results from a monitoring study aimed at investigating the fate of this deposited N within a pristine catchment in the Cairngorm Mountains (Scotland). Six sites were established along an elevation gradient (486-908 m) spanning the key habitats of temperate maritime uplands. Bulk deposition chemistry, soil carbon content, soil solution chemistry, soil temperature and soil moisture content were monitored over a 5 year period. Results were used to assess spatial variability in soil solution N and to investigate the factors and processes driving this variability. Highest soil solution inorganic N concentrations were found in the alpine soils at the top of the hillslope. Soil carbon stock, soil solution dissolved organic carbon (DOC) and factors representing site hydrology were the best predictors of NO(3)(-) concentration, with highest concentrations at low productivity sites with low DOC and freely-draining soils. These factors act as proxies for changing net biological uptake and soil/water contact time, and therefore support the hypothesis that spatial variations in soil solution NO(3)(-) are controlled by habitat N retention capacity. Soil percent carbon was a better predictor of soil solution inorganic N concentration than mass of soil carbon. NH(4)(+) was less affected by soil hydrology than NO(3)(-) and showed the effects of net mineralization inputs, particularly at Racomitrium heath and peaty sites. Soil solution dissolved organic N concentration was strongly related to both DOC and temperature, with a stronger temperature effect at more productive sites. Due to the spatial heterogeneity in N leaching potential, a fine-scale approach to assessing surface water vulnerability to N leaching is recommended over the broad scale, critical loads approach currently in use, particularly for sensitive areas. Copyright © 2012 Elsevier B.V. All rights reserved.

Validation of a hospital-laboratory workstation for immunohematologic methods.

PubMed

Schoenfeld, Helge; Pretzel, Karin J; von Heymann, Christian; Neuner, Bruno; Kalus, Ulrich; Kiesewetter, Holger; Pruss, Axel

2010-01-01

The FREELYS Nano system (Diagast) is a manual workstation for ABO/D grouping, Rh phenotyping, K typing, and antibody screening (ABS) for immunoglobulin G (IgG) antibodies only and works with the erythrocyte-magnetized technology (EMT). The principle of EMT is based on magnetization of red blood cells and avoids centrifugation and washing steps. A total of 304 samples were tested with our routine blood bank methods, 100 samples for ABO/D grouping, 196 samples (100 at first evaluation, 96 at second evaluation) for Rh phenotyping and K typing (PK7200, Olympus), and 108 samples for ABS (DiaMed). All samples were tested in parallel with the FREELYS Nano. We found a 100% concordance between the observed (FREELYS Nano) and the expected (Olympus PK7200) results for ABO/D grouping in all 100 samples. For Rh phenotyping and K tests, in 24 of 100 samples false-positive reactions were observed in the first evaluation by the FREELYS Nano. After changing the test kit batch for Rh phenotyping by the manufacturer, a complete concordance in Rh phenotyping and K tests was observed in a second evaluation. For ABS, the FREELYS Nano showed in 4 of 108 samples (3.7%) false-negative reactions for IgG antibodies (two anti-K, one anti-E, one anti-C(w)), and one (0.9%) false-positive reaction. The FREELYS Nano is reliably suited to ABO/D grouping, Rh phenotyping, and K testing. The rate of false-negative reactions for IgG antibodies should be reduced.

Engineering Escherichia coli K12 MG1655 to use starch

PubMed Central

2014-01-01

Background To attain a sustainable bioeconomy, fuel, or valuable product, production must use biomass as substrate. Starch is one of the most abundant biomass resources and is present as waste or as a food and agroindustry by-product. Unfortunately, Escherichia coli, one of the most widely used microorganisms in biotechnological processes, cannot use starch as a carbon source. Results We engineered an E. coli strain capable of using starch as a substrate. The genetic design employed the native capability of the bacterium to use maltodextrins as a carbon source plus expression and secretion of its endogenous α-amylase, AmyA, in an adapted background. Biomass production improved using 35% dissolved oxygen and pH 7.2 in a controlled bioreactor. Conclusion The engineered E. coli strain can use starch from the milieu and open the possibility of optimize the process to use agroindustrial wastes to produce biofuels and other valuable chemicals. PMID:24886307

Freely Accessible Chemical Database Resources of Compounds for in Silico Drug Discovery.

PubMed

Yang, JingFang; Wang, Di; Jia, Chenyang; Wang, Mengyao; Hao, GeFei; Yang, GuangFu

2018-05-07

In silico drug discovery has been proved to be a solidly established key component in early drug discovery. However, this task is hampered by the limitation of quantity and quality of compound databases for screening. In order to overcome these obstacles, freely accessible database resources of compounds have bloomed in recent years. Nevertheless, how to choose appropriate tools to treat these freely accessible databases are crucial. To the best of our knowledge, this is the first systematic review on this issue. The existed advantages and drawbacks of chemical databases were analyzed and summarized based on the collected six categories of freely accessible chemical databases from literature in this review. Suggestions on how and in which conditions the usage of these databases could be reasonable were provided. Tools and procedures for building 3D structure chemical libraries were also introduced. In this review, we described the freely accessible chemical database resources for in silico drug discovery. In particular, the chemical information for building chemical database appears as attractive resources for drug design to alleviate experimental pressure. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Determination of total and available fractions of PAHs by SPME in oily wastewaters: overcoming interference from NAPL and NOM.

PubMed

Gomes, Rui B; Nogueira, Regina; Oliveira, José M; Peixoto, João; Brito, António G

2009-09-01

Polycyclic aromatic hydrocarbons (PAHs) are often found in oily wastewaters. Their presence is usually the result of human activities and has a negative effect on the environment. One important step in addressing this problem is to evaluate the effectiveness of PAH removal by biological processes since these are the most cost-effective treatments known today. Many techniques are presently available for PAH determination in wastewaters. Solid phase microextracion (SPME) is known to be one of the most effective techniques for this purpose. When analyzing complex matrices with substances such as natural organic matter (NOM) and non-aqueous phase liquids (NAPL), it is important to differentiate the free dissolved PAH from matrix-bonded PAH. PAHs associated with the bonded fraction are less susceptible to biological treatment. The present study concerns the development of a simple and suitable methodology for the determination of the freely dissolved and the total fraction of PAHs present in oily wastewaters. The methodology was then applied to an oily wastewater from a fuel station retention basin. Headspace SPME was used for analyzing PAH since the presence of a complex or dirty matrix in direct contact with the fiber may damage it. Four model PAHs-anthracene, fluorene, phenanthrene, and pyrene-were analyzed by GC-MS. Negligible depletion SPME technique was used to determine the free fraction. Total PAH was determined by enhancing the mass transfer from the bonded phase to the freely dissolved phase by temperature optimization and the use of the method of standard additions. The PAH absorption kinetics were determined in order to define the optimal sampling conditions for this method. The fitting of the experimental data to a mathematical model was accomplished using Berkeley Madonna software. Humic acid and silicon oil were used as model NOM and NAPL, respectively, to study the effect of these compounds on the decrease of SPME response. Then, the method was evaluated with wastewater from a fuel station spill retention basin. The SPME kinetic parameters-k (1) (uptake rate), k (2) (desorption rate), and K (SPME) (partition coefficient)-were determined from experimental data modeling. The determination of the free fraction required 15-min sampling to ensure that PAH depletion from sample was below 1%. For total PAH, a 30-min extraction at 100 degrees C ensured the maximum signal response in the GC-MS. For the determination of free and total PAHs, extractions were performed before reaching the SPME equilibrium. The wastewater used in this study had no free fraction of the analyzed PAHs. However, the four studied PAHs were found when the method for total PAH was used. The addition of NOM and NAPL dramatically decreased the efficiency of the SPME. This decrease was the result of a greater partition of the PAHs to the NAPL and NOM phases. This fact was also observed in the analysis of the fuel station spill retention basin, where no free PAH was measured. However, using the method of standard addition for the determination of total PAH, it was possible to quantify all four PAHs. The method developed in the present study was found to be adequate to differentiate between free and total PAH present in oily wastewater. It was determined that the presence of NOM and NAPL had a negative effect on SPME efficiency. The presence of binding substances had a great influence on SPME kinetics. Therefore, it is of extreme importance to determine their degree of interference when analyzing oily wastewaters or results can otherwise be erroneous. Other factors influencing the total PAH determinations should be considered in further studies.

Ecology of Vibrio parahaemolyticus and Vibrio vulnificus in the Coastal and Estuarine Waters of Louisiana, Maryland, Mississippi, and Washington (United States)

PubMed Central

Bowers, John C.; Griffitt, Kimberly J.; Molina, Vanessa; Clostio, Rachel W.; Pei, Shaofeng; Laws, Edward; Paranjpye, Rohinee N.; Strom, Mark S.; Chen, Arlene; Hasan, Nur A.; Huq, Anwar; Noriea, Nicholas F.; Grimes, D. Jay; Colwell, Rita R.

2012-01-01

Vibrio parahaemolyticus and Vibrio vulnificus, which are native to estuaries globally, are agents of seafood-borne or wound infections, both potentially fatal. Like all vibrios autochthonous to coastal regions, their abundance varies with changes in environmental parameters. Sea surface temperature (SST), sea surface height (SSH), and chlorophyll have been shown to be predictors of zooplankton and thus factors linked to vibrio populations. The contribution of salinity, conductivity, turbidity, and dissolved organic carbon to the incidence and distribution of Vibrio spp. has also been reported. Here, a multicoastal, 21-month study was conducted to determine relationships between environmental parameters and V. parahaemolyticus and V. vulnificus populations in water, oysters, and sediment in three coastal areas of the United States. Because ecologically unique sites were included in the study, it was possible to analyze individual parameters over wide ranges. Molecular methods were used to detect genes for thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) as indicators of V. parahaemolyticus and the hemolysin gene vvhA for V. vulnificus. SST and suspended particulate matter were found to be strong predictors of total and potentially pathogenic V. parahaemolyticus and V. vulnificus. Other predictors included chlorophyll a, salinity, and dissolved organic carbon. For the ecologically unique sites included in the study, SST was confirmed as an effective predictor of annual variation in vibrio abundance, with other parameters explaining a portion of the variation not attributable to SST. PMID:22865080

System dynamics modeling of nitrogen removal in a stormwater infiltration basin with biosorption-activated media.

PubMed

Xuan, Zhemin; Chang, Ni-Bin; Wanielista, Martin P; Williams, Evan Shane

2013-07-01

Stormwater infiltration basins, one of the typical stormwater best management practices, are commonly constructed for surface water pollution control, flood mitigation, and groundwater restoration in rural or residential areas. These basins have soils with better infiltration capacity than the native soil; however, the ever-increasing contribution of nutrients to groundwater from stormwater due to urban expansion makes existing infiltration basins unable to meet groundwater quality criteria related to environmental sustainability and public health. This issue requires retrofitting current infiltration basins for flood control as well as nutrient control before the stormwater enters the groundwater. An existing stormwater infiltration basin in north-central Florida was selected, retrofitted, and monitored to identify subsurface physiochemical and biological processes during 2007-2010 to investigate nutrient control processes. This implementation in the nexus of contaminant hydrology and ecological engineering adopted amended soil layers packed with biosorption activated media (BAM; tire crumb, silt, clay, and sand) to perform nutrient removal in a partitioned forebay using a berm. This study presents an infiltration basin-nitrogen removal (IBNR) model, a system dynamics model that simulates nitrogen cycling in this BAM-based stormwater infiltration basin with respect to changing hydrologic conditions and varying dissolved nitrogen concentrations. Modeling outputs of IBNR indicate that denitrification is the biogeochemical indicator in the BAM layer that accounted for a loss of about one third of the total dissolved nitrogen mass input. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Volatile Emissions from Hot Spring Basin, Yellowstone National Park, USA

NASA Astrophysics Data System (ADS)

Werner, C.; Hurwitz, S.; Bergfeld, D.; Evans, W. C.; Lowenstern, J. B.; Jaworowski, C.; Heasler, H.

2007-12-01

The flux and composition of magmatic volatiles were characterized for Hot Spring Basin (HSB), Yellowstone National Park, in August 2006. Diffuse fluxes of CO2 (228 sites) from thermal soil were elevated, with a population distribution similar to that of other acid-sulfate areas in Yellowstone. Thus the estimated diffuse emission rate at HSB is proportionately larger than other areas due to its large area, and could be as high as 1000 td-1 CO2. The diffuse flux of H2S was only above detection limits at 20 of the 31 sites measured. The estimated diffuse H2S emission rate was ~ 4 td-1. Good correlation exists between the log of CO2 flux and shallow soil temperatures, indicating linked steam and gas upflow in the subsurface. The correlation between CO2 and H2S fluxes is weak, and the CO2 / H2S diffuse flux ratio was higher than in fumarolic ratios of CO2 to H2S. This suggests that various reactions, e.g., native sulfur deposition, act to remove H2S from the original gas stream in the diffuse low- temperature environment. Dissolved sulfate flux through Shallow Creek, which drains part of HSB, was ~ 4 td-1. Comparing dissolved sulfate flux to estimates of primary emission of H2S based on fumarolic gas geochemistry gives first order estimates of the sulfur consumed in surficial or subsurface mineral deposition. Total C and S outputs from HSB are comparable to other active volcanic systems.

Partitioning microbial respiration between jet fuel and native organic matter in an organic-rich long time-contaminated aquifer.

PubMed

Bugna, G C; Chanton, J P; Stauffer, T B; MacIntyre, W G; Libelo, E L

2005-07-01

The relative importance of jet fuel biodegradation relative to the respiration of natural organic matter in a contaminated organic-rich aquifer underlying a fire training area at Tyndall Air Force Base, Florida, USA was determined with isotopic measurements. Thirteen wells were sampled and analyzed for BTX (benzene, toluene, xylene), dissolved inorganic carbon (DIC) and CH4 concentrations, and delta13C and 14C of DIC. Results range from non-detectable to 3790 ppb, 1.4-24 mM, 0.2-776 microM, +5.8 per thousand to -22 per thousand, and from 52 to 99 pmc, respectively. Residual fuel was confined to two center wells underlying the fire training area. DIC and CH4 concentrations were elevated down-gradient of the contamination, but also at sites that were not in the apparent flow path of the contaminated groundwater. DIC exhibited greatest delta13C enrichment at highest DIC and CH4 concentrations indicating that CH4 production was an important respiration mode. Radiocarbon-depleted DIC was observed at sites with high hydrocarbon concentrations and down-gradient of the site. The results indicate that while natural attenuation was not rapidly reducing the quantity of free product overlying the aquifer at the site of contamination, it was at least constraining its flow away from the spill site. Apparently under the conditions of this study, BTX was degraded as rapidly as it was dissolved.

Potential aquifer vulnerability in regions down-gradient from uranium in situ recovery (ISR) sites.

PubMed

Saunders, James A; Pivetz, Bruce E; Voorhies, Nathan; Wilkin, Richard T

2016-12-01

Sandstone-hosted roll-front uranium ore deposits originate when U(VI) dissolved in groundwater is reduced and precipitated as insoluble U(IV) minerals. Groundwater redox geochemistry, aqueous complexation, and solute migration are important in leaching uranium from source rocks and transporting it in low concentrations to a chemical redox interface where it is deposited in an ore zone typically containing the uranium minerals uraninite, pitchblende, and/or coffinite; various iron sulfides; native selenium; clays; and calcite. In situ recovery (ISR) of uranium ores is a process of contacting the uranium mineral deposit with leaching and oxidizing (lixiviant) fluids via injection of the lixiviant into wells drilled into the subsurface aquifer that hosts uranium ore, while other extraction wells pump the dissolved uranium after dissolution of the uranium minerals. Environmental concerns during and after ISR include water quality degradation from: 1) potential excursions of leaching solutions away from the injection zone into down-gradient, underlying, or overlying aquifers; 2) potential migration of uranium and its decay products (e.g., Ra, Rn, Pb); and, 3) potential mobilization and migration of redox-sensitive trace metals (e.g., Fe, Mn, Mo, Se, V), metalloids (e.g., As), and anions (e.g., sulfate). This review describes the geochemical processes that control roll-front uranium transport and fate in groundwater systems, identifies potential aquifer vulnerabilities to ISR operations, identifies data gaps in mitigating these vulnerabilities, and discusses the hydrogeological characterization involved in developing a monitoring program. Published by Elsevier Ltd.

Caspase inhibition supports proper gene expression in ex vivo mouse limb cultures.

PubMed

De Valck, D; Luyten, F P

2001-10-01

We standardized conditions for ex vivo mouse limb culture to study cartilage maturation and joint formation. We compared 12.5 d.p.c. mouse forelimbs that were cultured either mounted or freely rotating for up to 72 h. Limb outgrowth progressed ex vivo at a variable rate as compared to its development in vivo, spanning approximately 48 h. Although cartilage maturation and joint formation developed grossly normal, aberrant expression of skeletal marker genes was seen. Interestingly, no regression of the interdigital webs took place in mounted cultures, in contrast to limited webbing under freely rotating conditions. Caspase inhibition, by addition of zVAD-fmk to the culture medium of freely rotating limbs, supported proper gene expression associated with skeletal development, and prevented interdigital web regression. Taken together, a freely rotating ex vivo culture for mouse limb outgrowth that is combined with caspase inhibition provides a good model to study cartilage maturation and joint formation.

Extracellular wire tetrode recording in brain of freely walking insects.

PubMed

Guo, Peiyuan; Pollack, Alan J; Varga, Adrienn G; Martin, Joshua P; Ritzmann, Roy E

2014-04-01

Increasing interest in the role of brain activity in insect motor control requires that we be able to monitor neural activity while insects perform natural behavior. We previously developed a technique for implanting tetrode wires into the central complex of cockroach brains that allowed us to record activity from multiple neurons simultaneously while a tethered cockroach turned or altered walking speed. While a major advance, tethered preparations provide access to limited behaviors and often lack feedback processes that occur in freely moving animals. We now present a modified version of that technique that allows us to record from the central complex of freely moving cockroaches as they walk in an arena and deal with barriers by turning, climbing or tunneling. Coupled with high speed video and cluster cutting, we can now relate brain activity to various parameters of the movement of freely behaving insects.

Stable Cu and Zn isotope ratios as tracers of sources and transport of Cu and Zn in contaminated soil

NASA Astrophysics Data System (ADS)

Bigalke, Moritz; Weyer, Stefan; Kobza, Jozef; Wilcke, Wolfgang

2010-12-01

Copper and Zn metals are produced in large quantities for different applications. During Cu production, large amounts of Cu and Zn can be released to the environment. Therefore, the surroundings of Cu smelters are frequently metal-polluted. We determined Cu and Zn concentrations and Cu and Zn stable isotope ratios (δ 65Cu, δ 66Zn) in three soils at distances of 1.1, 3.8, and 5.3 km from a Slovak Cu smelter and in smelter wastes (slag, sludge, ash) to trace sources and transport of Cu and Zn in soils. Stable isotope ratios were measured by multicollector inductively coupled plasma mass spectrometry (MC-ICP-MS) in total digests. Soils were heavily contaminated with concentrations up to 8087 μg g -1 Cu and 2084 μg g -1 Zn in the organic horizons. The δ 65Cu values varied little (-0.12‰ to 0.36‰) in soils and most wastes and therefore no source identification was possible. In soils, Cu became isotopically lighter with increasing depth down to 0.4 m, likely because of equilibrium reactions between dissolved and adsorbed Cu species during transport of smelter-derived Cu through the soil. The δ 66Zn IRMM values were isotopically lighter in ash (-0.41‰) and organic horizons (-0.85‰ to -0.47‰) than in bedrock (-0.28‰) and slag (0.18‰) likely mainly because of kinetic fractionation during evaporation and thus allowed for separation of smelter-Zn from native Zn in soil. In particular in the organic horizons large variations in δ 66Zn values occur, probably caused by biogeochemical fractionation in the soil-plant system. In the mineral horizons, Zn isotopes showed only minor shifts to heavier δ 66Zn values with depth mainly because of the mixing of smelter-derived Zn and native Zn in the soils. In contrast to Cu, Zn isotope fractionation between dissolved and adsorbed species was probably only a minor driver in producing the observed variations in δ 66Zn values. Our results demonstrate that metal stable isotope ratios may serve as tracer of sources, vertical dislocation, and biogeochemical behavior in contaminated soil.

MilQuant: a free, generic software tool for isobaric tagging-based quantitation.

PubMed

Zou, Xiao; Zhao, Minzhi; Shen, Hongyan; Zhao, Xuyang; Tong, Yuanpeng; Wang, Qingsong; Wei, Shicheng; Ji, Jianguo

2012-09-18

Isobaric tagging techniques such as iTRAQ and TMT are widely used in quantitative proteomics and especially useful for samples that demand in vitro labeling. Due to diversity in choices of MS acquisition approaches, identification algorithms, and relative abundance deduction strategies, researchers are faced with a plethora of possibilities when it comes to data analysis. However, the lack of generic and flexible software tool often makes it cumbersome for researchers to perform the analysis entirely as desired. In this paper, we present MilQuant, mzXML-based isobaric labeling quantitator, a pipeline of freely available programs that supports native acquisition files produced by all mass spectrometer types and collection approaches currently used in isobaric tagging based MS data collection. Moreover, aside from effective normalization and abundance ratio deduction algorithms, MilQuant exports various intermediate results along each step of the pipeline, making it easy for researchers to customize the analysis. The functionality of MilQuant was demonstrated by four distinct datasets from different laboratories. The compatibility and extendibility of MilQuant makes it a generic and flexible tool that can serve as a full solution to data analysis of isobaric tagging-based quantitation. Copyright © 2012 Elsevier B.V. All rights reserved.

The efficacy of self-paced study in multitrial learning.

PubMed

de Jonge, Mario; Tabbers, Huib K; Pecher, Diane; Jang, Yoonhee; Zeelenberg, René

2015-05-01

In 2 experiments we investigated the efficacy of self-paced study in multitrial learning. In Experiment 1, native speakers of English studied lists of Dutch-English word pairs under 1 of 4 imposed fixed presentation rate conditions (24 × 1 s, 12 × 2 s, 6 × 4 s, or 3 × 8 s) and a self-paced study condition. Total study time per list was equated for all conditions. We found that self-paced study resulted in better recall performance than did most of the fixed presentation rates, with the exception of the 12 × 2 s condition, which did not differ from the self-paced condition. Additional correlational analyses suggested that the allocation of more study time to difficult pairs than to easy pairs might be a beneficial strategy for self-paced learning. Experiment 2 was designed to test this hypothesis. In 1 condition, participants studied word pairs in a self-paced fashion without any restrictions. In the other condition, participants studied word pairs in a self-paced fashion but total study time per item was equated. The results showed that allowing self-paced learners to freely allocate study time over items resulted in better recall performance. (c) 2015 APA, all rights reserved).

Automated large-scale file preparation, docking, and scoring: evaluation of ITScore and STScore using the 2012 Community Structure-Activity Resource benchmark.

PubMed

Grinter, Sam Z; Yan, Chengfei; Huang, Sheng-You; Jiang, Lin; Zou, Xiaoqin

2013-08-26

In this study, we use the recently released 2012 Community Structure-Activity Resource (CSAR) data set to evaluate two knowledge-based scoring functions, ITScore and STScore, and a simple force-field-based potential (VDWScore). The CSAR data set contains 757 compounds, most with known affinities, and 57 crystal structures. With the help of the script files for docking preparation, we use the full CSAR data set to evaluate the performances of the scoring functions on binding affinity prediction and active/inactive compound discrimination. The CSAR subset that includes crystal structures is used as well, to evaluate the performances of the scoring functions on binding mode and affinity predictions. Within this structure subset, we investigate the importance of accurate ligand and protein conformational sampling and find that the binding affinity predictions are less sensitive to non-native ligand and protein conformations than the binding mode predictions. We also find the full CSAR data set to be more challenging in making binding mode predictions than the subset with structures. The script files used for preparing the CSAR data set for docking, including scripts for canonicalization of the ligand atoms, are offered freely to the academic community.

Balancing exploration and exploitation in population-based sampling improves fragment-based de novo protein structure prediction.

PubMed

Simoncini, David; Schiex, Thomas; Zhang, Kam Y J

2017-05-01

Conformational search space exploration remains a major bottleneck for protein structure prediction methods. Population-based meta-heuristics typically enable the possibility to control the search dynamics and to tune the balance between local energy minimization and search space exploration. EdaFold is a fragment-based approach that can guide search by periodically updating the probability distribution over the fragment libraries used during model assembly. We implement the EdaFold algorithm as a Rosetta protocol and provide two different probability update policies: a cluster-based variation (EdaRose c ) and an energy-based one (EdaRose en ). We analyze the search dynamics of our new Rosetta protocols and show that EdaRose c is able to provide predictions with lower C αRMSD to the native structure than EdaRose en and Rosetta AbInitio Relax protocol. Our software is freely available as a C++ patch for the Rosetta suite and can be downloaded from http://www.riken.jp/zhangiru/software/. Our protocols can easily be extended in order to create alternative probability update policies and generate new search dynamics. Proteins 2017; 85:852-858. © 2016 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Environmental implications of plastic debris in marine settings—entanglement, ingestion, smothering, hangers-on, hitch-hiking and alien invasions

PubMed Central

Gregory, Murray R.

2009-01-01

Over the past five or six decades, contamination and pollution of the world’s enclosed seas, coastal waters and the wider open oceans by plastics and other synthetic, non-biodegradable materials (generally known as ‘marine debris’) has been an ever-increasing phenomenon. The sources of these polluting materials are both land- and marine-based, their origins may be local or distant, and the environmental consequences are many and varied. The more widely recognized problems are typically associated with entanglement, ingestion, suffocation and general debilitation, and are often related to stranding events and public perception. Among the less frequently recognized and recorded problems are global hazards to shipping, fisheries and other maritime activities. Today, there are rapidly developing research interests in the biota attracted to freely floating (i.e. pelagic) marine debris, commonly known as ‘hangers-on and hitch-hikers’ as well as material sinking to the sea floor despite being buoyant. Dispersal of aggressive alien and invasive species by these mechanisms leads one to reflect on the possibilities that ensuing invasions could endanger sensitive, or at-risk coastal environments (both marine and terrestrial) far from their native habitats. PMID:19528053

Environmental implications of plastic debris in marine settings--entanglement, ingestion, smothering, hangers-on, hitch-hiking and alien invasions.

PubMed

Gregory, Murray R

2009-07-27

Over the past five or six decades, contamination and pollution of the world's enclosed seas, coastal waters and the wider open oceans by plastics and other synthetic, non-biodegradable materials (generally known as 'marine debris') has been an ever-increasing phenomenon. The sources of these polluting materials are both land- and marine-based, their origins may be local or distant, and the environmental consequences are many and varied. The more widely recognized problems are typically associated with entanglement, ingestion, suffocation and general debilitation, and are often related to stranding events and public perception. Among the less frequently recognized and recorded problems are global hazards to shipping, fisheries and other maritime activities. Today, there are rapidly developing research interests in the biota attracted to freely floating (i.e. pelagic) marine debris, commonly known as 'hangers-on and hitch-hikers' as well as material sinking to the sea floor despite being buoyant. Dispersal of aggressive alien and invasive species by these mechanisms leads one to reflect on the possibilities that ensuing invasions could endanger sensitive, or at-risk coastal environments (both marine and terrestrial) far from their native habitats.

Diverse, high-quality test set for the validation of protein-ligand docking performance.

PubMed

Hartshorn, Michael J; Verdonk, Marcel L; Chessari, Gianni; Brewerton, Suzanne C; Mooij, Wijnand T M; Mortenson, Paul N; Murray, Christopher W

2007-02-22

A procedure for analyzing and classifying publicly available crystal structures has been developed. It has been used to identify high-resolution protein-ligand complexes that can be assessed by reconstructing the electron density for the ligand using the deposited structure factors. The complexes have been clustered according to the protein sequences, and clusters have been discarded if they do not represent proteins thought to be of direct interest to the pharmaceutical or agrochemical industry. Rules have been used to exclude complexes containing non-drug-like ligands. One complex from each cluster has been selected where a structure of sufficient quality was available. The final Astex diverse set contains 85 diverse, relevant protein-ligand complexes, which have been prepared in a format suitable for docking and are to be made freely available to the entire research community (http://www.ccdc.cam.ac.uk). The performance of the docking program GOLD against the new set is assessed using a variety of protocols. Relatively unbiased protocols give success rates of approximately 80% for redocking into native structures, but it is possible to get success rates of over 90% with some protocols.

Comparative sensitivity of aquatic invertebrate and vertebrate species to wastewater from an operational coal mine in central Queensland, Australia.

PubMed

Lanctôt, C; Wilson, S P; Fabbro, L; Leusch, F D L; Melvin, S D

2016-07-01

Coal excavation and refinement processes generate substantial volumes of contaminated effluent that may be detrimental to aquatic ecosystems. As such, understanding the impacts of coal mine water releases on aquatic animals and ecosystems is essential for effectively managing and protecting neighboring environments. Such information will ultimately be applied towards developing ongoing monitoring strategies that are protective of native wildlife. Despite intensive mining operations in Australia, few studies have documented toxicity associated with coal mine wastewater (CMW) on native species. To address existing knowledge gaps, we investigated acute toxicity (48-96h) using eight native invertebrate species and sub-chronic effects (2 week) using three vertebrate species following exposure to wastewater from two dams (CMW1 and CMW2) located at an open-cut coal mine licensed to discharge into the Fitzroy catchment (Queensland, Australia). Wastewater from these sites is characterized by elevated conductivity, pH, sulfates as well as relatively high total and dissolved metal(loid)s (including As, Al, B, Cu, Mn, Ni, Se and Zn). Acute exposures revealed cladocerans (Daphnia carinata) and planarians (Dugesia sp.) to be the most sensitive species, exhibiting significant mortality after 48 and 96h exposure to CMW2, respectively. Neither wastewater was found to elicit acute toxicity in vertebrates, but a range of sub-lethal morphological effects were observed following the sub-chronic exposures. The overall response pattern was characterized by decreased condition factor and hepatosomatic index in the fish Hypseleotris compressa and Pseudomugil signifier, and in Limnodynastes peronii tadpoles. Tadpoles were generally more sensitive compared to the two fish species. Differences in responses were observed amongst CMW1 and CMW2, which likely relates to differences in physico-chemical properties between sites. Our results have identified several candidate vertebrate and invertebrate species that show promise for ongoing monitoring of water quality and toxicity risk in Central Queensland, Australia. Copyright © 2016 Elsevier Inc. All rights reserved.

Composition of riparian litter input regulates organic matter decomposition: Implications for headwater stream functioning in a managed forest landscape.

PubMed

Lidman, Johan; Jonsson, Micael; Burrows, Ryan M; Bundschuh, Mirco; Sponseller, Ryan A

2017-02-01

Although the importance of stream condition for leaf litter decomposition has been extensively studied, little is known about how processing rates change in response to altered riparian vegetation community composition. We investigated patterns of plant litter input and decomposition across 20 boreal headwater streams that varied in proportions of riparian deciduous and coniferous trees. We measured a suite of in-stream physical and chemical characteristics, as well as the amount and type of litter inputs from riparian vegetation, and related these to decomposition rates of native (alder, birch, and spruce) and introduced (lodgepole pine) litter species incubated in coarse- and fine-mesh bags. Total litter inputs ranged more than fivefold among sites and increased with the proportion of deciduous vegetation in the riparian zone. In line with differences in initial litter quality, mean decomposition rate was highest for alder, followed by birch, spruce, and lodgepole pine (12, 55, and 68% lower rates, respectively). Further, these rates were greater in coarse-mesh bags that allow colonization by macroinvertebrates. Variance in decomposition rate among sites for different species was best explained by different sets of environmental conditions, but litter-input composition (i.e., quality) was overall highly important. On average, native litter decomposed faster in sites with higher-quality litter input and (with the exception of spruce) higher concentrations of dissolved nutrients and open canopies. By contrast, lodgepole pine decomposed more rapidly in sites receiving lower-quality litter inputs. Birch litter decomposition rate in coarse-mesh bags was best predicted by the same environmental variables as in fine-mesh bags, with additional positive influences of macroinvertebrate species richness. Hence, to facilitate energy turnover in boreal headwaters, forest management with focus on conifer production should aim at increasing the presence of native deciduous trees along streams, as they promote conditions that favor higher decomposition rates of terrestrial plant litter.

The effect of water-containing electrolyte on lithium-sulfur batteries

NASA Astrophysics Data System (ADS)

Wu, Heng-Liang; Haasch, Richard T.; Perdue, Brian R.; Apblett, Christopher A.; Gewirth, Andrew A.

2017-11-01

Dissolved polysulfides, formed during Li-S battery operation, freely migrate and react with both the Li anode and the sulfur cathode. These soluble polysulfides shuttle between the anode and cathode - the so-called shuttle effect - resulting in an infinite recharge process and poor Columbic efficiency. In this study, water present as an additive in the Li-S battery electrolyte is found to reduce the shuttle effect in Li-S batteries. Batteries where water content was below 50 ppm exhibited a substantial shuttle effect and low charge capacity. Alternatively, addition of 250 ppm water led to stable charge/discharge behavior with high Coulombic efficiency. XPS results show that H2O addition results in the formation of solid electrolyte interphase (SEI) film with more LiOH on Li anode which protects the Li anode from the polysulfides. Batteries cycled without water result in a SEI film with more Li2CO3 likely formed by direct contact between the Li metal and the solvent. Intermediate quantities of H2O in the electrolyte result in high cycle efficiency for the first few cycles which then rapidly decays. This suggests that H2O is consumed during battery cycling, likely by interaction with freshly exposed Li metal formed during Li deposition.

Laboratory, Field, and Analytical Procedures for Using ...

EPA Pesticide Factsheets

Regardless of the remedial technology invoked to address contaminated sediments in the environment, there is a critical need to have tools for assessing the effectiveness of the remedy. In the past, these tools have included chemical and biomonitoring of the water column and sediments, toxicity testing and bioaccumulation studies performed on site sediments, and application of partitioning, transport and fate modeling. All of these tools served as lines of evidence for making informed environmental management decisions at contaminated sediment sites. In the last ten years, a new tool for assessing remedial effectiveness has gained a great deal of attention. Passive sampling offers a tool capable of measuring the freely dissolved concentration (Cfree) of legacy contaminants in water and sediments. In addition to assessing the effectiveness of the remedy, passive sampling can be applied for a variety of other contaminated sediments site purposes involved with performing the preliminary assessment and site inspection, conducting the remedial investigation and feasibility study, preparing the remedial design, and assessing the potential for contaminant bioaccumulation. While there is a distinct need for using passive sampling at contaminated sediments sites and several previous documents and research articles have discussed various aspects of passive sampling, there has not been definitive guidance on the laboratory, field and analytical procedures for using pas

Effect of long term intake of aspartame on antioxidant defense status in liver.

PubMed

Abhilash, M; Paul, M V Sauganth; Varghese, Mathews V; Nair, R Harikumaran

2011-06-01

The present study evaluates the effect of long term intake of aspartame, the artificial sweetener, on liver antioxidant system and hepatocellular injury in animal model. Eighteen adult male Wistar rats, weighing 150-175 g, were randomly divided into three groups as follows: first group was given aspartame dissolved in water in a dose of 500 mg/kg b.wt.; the second group was given a dose of 1000 mg/kg b.wt.; and controls were given water freely. Rats that had received aspartame (1000 mg/kg b.wt.) in the drinking water for 180 days showed a significant increase in activities of alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and γ-glutamyl transferase (GGT). The concentration of reduced glutathione (GSH) and the activity of glutathione peroxidase (GPx), and glutathione reductase (GR) were significantly reduced in the liver of rats that had received aspartame (1000 mg/kg b.wt.). Glutathione was significantly decreased in both the experimental groups. Histopathological examination revealed leukocyte infiltration in aspartame-treated rats (1000 mg/kg b.wt.). It can be concluded from these observations that long term consumption of aspartame leads to hepatocellular injury and alterations in liver antioxidant status mainly through glutathione dependent system. Copyright © 2011 Elsevier Ltd. All rights reserved.

Experimental Solubility Approach to Determine PDMS-Water Partition Constants and PDMS Activity Coefficients.

PubMed

Grant, Sharon; Schacht, Veronika J; Escher, Beate I; Hawker, Darryl W; Gaus, Caroline

2016-03-15

Freely dissolved aqueous concentration and chemical activity are important determinants of contaminant transport, fate, and toxic potential. Both parameters are commonly quantified using Solid Phase Micro-Extraction (SPME) based on a sorptive polymer such as polydimethylsiloxane (PDMS). This method requires the PDMS-water partition constants, KPDMSw, or activity coefficient to be known. For superhydrophobic contaminants (log KOW >6), application of existing methods to measure these parameters is challenging, and independent measures to validate KPDMSw values would be beneficial. We developed a simple, rapid method to directly measure PDMS solubilities of solid contaminants, SPDMS(S), which together with literature thermodynamic properties was then used to estimate KPDMSw and activity coefficients in PDMS. PDMS solubility for the test compounds (log KOW 7.2-8.3) ranged over 3 orders of magnitude (4.1-5700 μM), and was dependent on compound class. For polychlorinated biphenyls (PCBs) and polychlorinated dibenzo-p-dioxins (PCDDs), solubility-derived KPDMSw increased linearly with hydrophobicity, consistent with trends previously reported for less chlorinated congeners. In contrast, subcooled liquid PDMS solubilities, SPDMS(L), were approximately constant within a compound class. SPDMS(S) and KPDMSw can therefore be predicted for a compound class with reasonable robustness based solely on the class-specific SPDMS(L) and a particular congener's entropy of fusion, melting point, and aqueous solubility.

Indoor air condensate as a novel matrix for monitoring inhalable organic contaminants.

PubMed

Roll, Isaac B; Halden, Rolf U; Pycke, Benny F G

2015-05-15

With the population of developed nations spending nearly 90% of their time indoors, indoor air quality (IAQ) is a critical indicator of human health risks from inhalation of airborne contaminants. We present a novel approach for qualitative monitoring of IAQ through the collection and analysis of indoor air condensate discharged from heat exchangers of heating, ventilation, and air conditioning (HVAC) systems. Condensate samples were collected from six suburban homes and one business in Maricopa County, Arizona, concentrated via solid-phase extraction, analyzed for 10 endocrine disrupting chemicals (EDCs) by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and screened for additional organic compounds by gas chromatography-mass spectrometry (GC-MS). All 10 EDCs were detected in at least one of the sampled buildings. More than 100 additional compounds were detected by GC-MS, of which 40 were tentatively identified using spectral database searches. Twelve compounds listed as designated chemicals for biomonitoring by the California Environmental Contaminant Biomonitoring Program were detected. Microfiltration of condensate samples prior to extraction had no discernable effect on contaminant concentration, suggesting that contaminants were freely dissolved or associated with inhalable, submicron particles. This study is the first to document the utility of HVAC condensate for the qualitative assessment of indoor air for pollutants. Copyright © 2015 Elsevier B.V. All rights reserved.

Investigation of polymorphic transitions of piracetam induced during wet granulation.

PubMed

Potter, Catherine B; Kollamaram, Gayathri; Zeglinski, Jacek; Whitaker, Darren A; Croker, Denise M; Walker, Gavin M

2017-10-01

Piracetam was investigated as a model API which is known to exhibit a number of different polymorphic forms. It is freely soluble in water so the possibility exists for polymorphic transformations to occur during wet granulation. Analysis of the polymorphic form present during lab-scale wet granulation, using water as a granulation liquid, was studied with powder X-ray diffraction and Raman spectroscopy as off-line and inline analysis tools respectively. Different excipients with a range of hydrophilicities, aqueous solubilities and molecular weights were investigated to examine their influence on these solution-mediated polymorphic transitions and experimental results were rationalised using molecular modelling. Our results indicated that as an increasing amount of water was added to the as-received piracetam FIII, a greater amount of the API dissolved which recrystallised upon drying to the metastable FII(6.403) via a monohydrate intermediary. Molecular level analysis revealed that the observed preferential transformation of monohydrate to FII is linked with a greater structural similarity between the monohydrate and FII polymorph in comparison to FIII. The application of Raman spectroscopy as a process analytical technology (PAT) tool to monitor the granulation process for the production of the monohydrate intermediate as a precursor to the undesirable metastable form was demonstrated. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of mediator-type biosensor to wirelessly monitor whole cholesterol concentration in fish.

PubMed

Takase, Mai; Murata, Masataka; Hibi, Kyoko; Huifeng, Ren; Endo, Hideaki

2014-04-01

We developed a wireless monitoring system to monitor fish condition by tracking the change in whole cholesterol concentration. The whole cholesterol concentration of fish is a source of steroid hormones or indicator of immunity level, which makes its detection important for tracking physiological condition of fish. Wireless monitoring system comprises of mediator-type biosensor and wireless transmission device. Biosensor is implantable to fish body, and transmission device is so light, in that fish is allowed to swim freely during monitoring. Cholesterol esterase and oxidase were fixated on to the detection site of biosensor and used to detect the whole cholesterol concentration. However, cholesterol oxidase incorporates oxidation-reduction reaction of oxygen for detection, which concentration fluctuates easily due to change in environmental condition. Meanwhile, mediator-type biosensor enables monitoring of whole cholesterol concentration by using mediator to substitute that oxidation-reduction reaction of oxygen. Characteristic of fabricated mediator-type biosensor was tested. The sensor output current of mediator-type biosensor remained stable compared to output current of non-mediator-type biosensor under fluctuating oxygen concentration of 0-8 ppm, which implied that this sensor is less affected by change in dissolved oxygen concentration. That biosensor was then implanted into fish for wireless monitoring. As a result, approximately 48 h of real-time monitoring was successful.

SUPPRESSION OF HUMORAL IMMUNE RESPONSES BY 2,3,7,8-TETRACHLORODIBENZO-p-DIOXIN INTERCALATED IN SMECTITE CLAY

PubMed Central

Boyd, Stephen A.; Johnston, Cliff T.; Pinnavaia, Thomas J.; Kaminski, Norbert E.; Teppen, Brian J.; Li, Hui; Khan, Bushra; Crawford, Robert B.; Kovalova, Natalia; Kim, Seong-Su; Shao, Hua; Gu, Cheng; Kaplan, Barbara L.F.

2018-01-01

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a highly toxic environmental contaminant found in soils and sediments. Because of its exceptionally low water solubility, this compound exists predominantly in the sorbed state in natural environments. Clay minerals, especially expandable smectite clays, are one of the major component geosorbents in soils and sediments that can function as an effective adsorbent for environmental dioxins, including TCDD. In this study, TCDD was intercalated in the smectite clay saponite by an incipient wetness method. The primary goal of this study was to intercalate TCDD in natural K-saponite clay and evaluate its immunotoxic effects in vivo. The relative bioavailability of TCDD was evaluated by comparing the metabolic activity of TCDD administered in the adsorbed state as an intercalate in saponite and freely dissolved in corn oil. This comparison revealed nearly identical TCDD-induced suppression of humoral immunity, a well-established and sensitive sequela, in a mammalian (mouse) model. This result suggests that TCDD adsorbed by clays is likely to be available for biouptake and biodistribution in mammals, consistent with previous observations of TCDD in livestock exposed to dioxin-contaminated ball clays that were used as feed additives. Adsorption of TCDD by clay minerals does not appear to mitigate risk associated with TCDD exposure substantially. PMID:21994089

Emotions in freely varying and mono-pitched vowels, acoustic and EGG analyses.

PubMed

Waaramaa, Teija; Palo, Pertti; Kankare, Elina

2015-12-01

Vocal emotions are expressed either by speech or singing. The difference is that in singing the pitch is predetermined while in speech it may vary freely. It was of interest to study whether there were voice quality differences between freely varying and mono-pitched vowels expressed by professional actors. Given their profession, actors have to be able to express emotions both by speech and singing. Electroglottogram and acoustic analyses of emotional utterances embedded in expressions of freely varying vowels [a:], [i:], [u:] (96 samples) and mono-pitched protracted vowels (96 samples) were studied. Contact quotient (CQEGG) was calculated using 35%, 55%, and 80% threshold levels. Three different threshold levels were used in order to evaluate their effects on emotions. Genders were studied separately. The results suggested significant gender differences for CQEGG 80% threshold level. SPL, CQEGG, and F4 were used to convey emotions, but to a lesser degree, when F0 was predetermined. Moreover, females showed fewer significant variations than males. Both genders used more hypofunctional phonation type in mono-pitched utterances than in the expressions with freely varying pitch. The present material warrants further study of the interplay between CQEGG threshold levels and formant frequencies, and listening tests to investigate the perceptual value of the mono-pitched vowels in the communication of emotions.

Social exclusion intensifies anxiety-like behavior in adolescent rats.

PubMed

Lee, Hyunchan; Noh, Jihyun

2015-05-01

Social connection reduces the physiological reactivity to stressors, while social exclusion causes emotional distress. Stressful experiences in rats result in the facilitation of aversive memory and induction of anxiety. To determine the effect of social interaction, such as social connection, social exclusion and equality or inequality, on emotional change in adolescent distressed rats, the emotional alteration induced by restraint stress in individual rats following exposure to various social interaction circumstances was examined. Rats were assigned to one of the following groups: all freely moving rats, all rats restrained, rats restrained in the presence of freely moving rats and freely moving rats with a restrained rat. No significant difference in fear-memory and sucrose consumption between all groups was found. Change in body weight significantly increased in freely moving rats with a restrained rat, suggesting that those rats seems to share the stressful experience of the restrained rat. Interestingly, examination of the anxiety-like behavior revealed only rats restrained in the presence of freely moving rats to have a significant increase, suggesting that emotional distress intensifies in positions of social exclusion. These results demonstrate that unequally excluded social interaction circumstances could cause the amplification of distressed status and anxiety-related emotional alteration. Copyright © 2015 Elsevier B.V. All rights reserved.

Cavity Resonator Wireless Power Transfer System for Freely Moving Animal Experiments.

PubMed

Mei, Henry; Thackston, Kyle A; Bercich, Rebecca A; Jefferys, John G R; Irazoqui, Pedro P

2017-04-01

The goal of this paper is to create a large wireless powering arena for powering small devices implanted in freely behaving rodents. We design a cavity resonator based wireless power transfer (WPT) system and utilize our previously developed optimal impedance matching methodology to achieve effective WPT performance for operating sophisticated implantable devices, made with miniature receive coils (<8 mm in diameter), within a large volume (dimensions: 60.96 cm × 60.96 cm × 30 cm). We provide unique cavity design and construction methods which maintains electromagnetic performance of the cavity while promoting its utility as a large animal husbandry environment. In addition, we develop a biaxial receive resonator system to address device orientation insensitivity within the cavity environment. Functionality is demonstrated with chronic experiments involving rats implanted with our custom designed bioelectric recording device. We demonstrate an average powering fidelity of 93.53% over nine recording sessions across nine weeks, indicating nearly continuous device operation for a freely behaving rat within the large cavity resonator space. We have developed and demonstrated a cavity resonator based WPT system for long term experiments involving freely behaving small animals. This cavity resonator based WPT system offers an effective and simple method for wirelessly powering miniaturized devices implanted in freely moving small animals within the largest space.

Environmental features and macrofauna of Kahana Estuary, Oahu, Hawaii

USGS Publications Warehouse

Maciolek, J.A.; Timbol, A.S.

1981-01-01

Lack of ecological information on Hawaiian estuaries prompted an intensive 2-year study of a small (5.7 ha) stream-mouth estuary on windward Oahu. Water quality and macrofauna were sampled weekly at seven stations. The water mass was strongly stratified vertically except during freshets. Average values for water column temperature and bottom salinity were 23.2°C and 12‰ at the head to 28.3°C and 28‰ at the mouth. Dissolved oxygen saturation in the water column varied from about 50% at night to 140% in the afternoon. Usually, bottom waters were 3–6°C warmer than surface waters and sometimes showed severe oxygen depletion.Macrofauna, collected primarily by seining, consisted mainly of decapod crustaceans (four species of crabs, seven species of shrimps) and fishes (24 species). Other typical estuarine taxons (mollusks, barnacles, polychaetes) were scarce or absent. Diversity increased seaward from 14 species near the estuary head to 29 species near the mouth. Three species of crustaceans and six of fishes were captured at all stations. Most abundant were the native prawn, Macrobrachium grandimanus, and mullet, Mugil cephalus. Perennially resident adults occurred among crustaceans and gobioid fishes; most other fishes were present as juveniles and sporadic adults. Comparisons with other data suggest that more than 50 species of native fishes may occur in Hawaiian estuaries, and that estuarine macrofaunal diversity on oceanic islands is much lower than on continents at similar latitudes.

Atomic force microscopy studies of native photosynthetic membranes.

PubMed

Sturgis, James N; Tucker, Jaimey D; Olsen, John D; Hunter, C Neil; Niederman, Robert A

2009-05-05

In addition to providing the earliest surface images of a native photosynthetic membrane at submolecular resolution, examination of the intracytoplasmic membrane (ICM) of purple bacteria by atomic force microscopy (AFM) has revealed a wide diversity of species-dependent arrangements of closely packed light-harvesting (LH) antennae, capable of fulfilling the basic requirements for efficient collection, transmission, and trapping of radiant energy. A highly organized architecture was observed with fused preparations of the pseudocrystalline ICM of Blastochloris viridis, consiting of hexagonally packed monomeric reaction center light-harvesting 1 (RC-LH1) core complexes. Among strains which also form a peripheral LH2 antenna, images of ICM patches from Rhodobacter sphaeroides exhibited well-ordered, interconnected networks of dimeric RC-LH1 core complexes intercalated by rows of LH2, coexisting with LH2-only domains. Other peripheral antenna-containing species, notably Rhodospirillum photometricum and Rhodopseudomonas palustris, showed a less regular organization, with mixed regions of LH2 and RC-LH1 cores, intermingled with large, paracrystalline domains. The ATP synthase and cytochrome bc(1) complex were not observed in any of these topographs and are thought to be localized in the adjacent cytoplasmic membrane or in inaccessible ICM regions separated from the flat regions imaged by AFM. The AFM images have served as a basis for atomic-resolution modeling of the ICM vesicle surface, as well as forces driving segregation of photosynthetic complexes into distinct domains. Docking of atomic-resolution molecular structures into AFM topographs of Rsp. photometricum membranes generated precise in situ structural models of the core complex surrounded by LH2 rings and a region of tightly packed LH2 complexes. A similar approach has generated a model of the highly curved LH2-only membranes of Rba. sphaeroides which predicts that sufficient space exists between LH2 complexes for quinones to diffuse freely. Measurement of the intercomplex distances between adjacent LH2 rings of Phaeospirillum molischianum has permitted the first calculation of the separation of bacteriochlorophyll a molecules in the native ICM. A recent AFM analysis of the organization of green plant photosystem II (PSII) in grana thylakoids revealed the protruding oxygen-evolving complex, crowded together in parallel alignment at three distinct levels of stacked membranes over the lumenal surface. The results also confirmed that PSII-LHCII supercomplexes are displaced relative to one another in opposing grana membranes.

Shallow magmatic degassing into the hydrothermal system of Copahue, Argentina

NASA Astrophysics Data System (ADS)

Varekamp, J.; Ouimette, A.; Kreulen, R.; Delpino, D.; Bermudez, A.

2001-05-01

Copahue volcano has a crater lake and acid hot springs that discharge into the Rio Agrio river system. These fluids are very concentrated (up to 6 percent sulfate), rich in rock-forming elements (up to 2000 ppm Mg) and small spheres of native sulfur float in the crater lake. The stable isotope composition of the waters (delta 18O =-2.1 to + 3.6 per mille; delta D = -49 to -26 per mille) indicates that the hot spring waters are at their most concentrated about 70 percent volcanic brine and 30 percent glacial meltwater. The crater lake waters have similar mixing proportions but added isotope effects from intense evaporation. Further dilution of the waters in the Rio Agrio gives values closer to local meteoric waters (delta 18O = -11 per mille; delta D = -77 per mille), whereas evaporation in closed ponds led to very heavy water (up to delta 18O = +12 per mille). The delta 34S value of dissolved sulfate is +14.2 per mille, whereas the native sulfur has values of -8.2 to -10.5 per mille. The heavy sulfate probably formed when SO2 disproportionated into bisulfate and native sulfur. We measured the sulfate fluxes in the Rio Agrio, and from these flux values and the stoichiometry of the disproportionation reaction we calculated the rate of liquid sulfur storage inside the volcano (6000 m3/year). During the eruptions of 1995/2000, large amounts of that stored liquid sulfur were ejected as pyroclastic sulfur. The calculated rate of rock dissolution (from rock- forming element fluxes in the Rio Agrio) suggests that the void space generated by rock dissolution is largely filled by native sulfur. The isotopic signature of the magmatic sulfur can be reconstituted at about +7 per mille, which is a source signature with superposed effects of shallow degassing. Lead isotope and 129Iodine data from the fluids indicate that subducted components may have played a role in the Copahue magma formation. Primary glass inclusions in plagioclase and olivine have 1110-1670 ppm Cl, 90-400 ppm S and low water contents (0.4 - 1.5 percent). Matrix glasses have similar volatile concentrations as many plagioclase-hosted glass inclusions. The S/Cl ratio in the hydrothermal fluids is about 2, whereas the glass inclusions have S/Cl = 0.2, indicating the strong preferential degassing of sulfur.

Hadfield watches a water bubble float freely in the Node 1

NASA Image and Video Library

2013-01-21

ISS034-E-031694 (21 Jan. 2013) --- Canadian Space Agency astronaut Chris Hadfield, Expedition 34 flight engineer, watches a water bubble float freely between him and the camera, showing his image refracted, in the Unity node of the International Space Station.

Hadfield watches a water bubble float freely in the Node 1

NASA Image and Video Library

2013-01-21

ISS034-E-031695 (21 Jan. 2013) --- Canadian Space Agency astronaut Chris Hadfield, Expedition 34 flight engineer, watches a water bubble float freely between him and the camera, showing his image refracted, in the Unity node of the International Space Station.

View of a stone age adze cutting tool floating freely in the flight deck.

NASA Technical Reports Server (NTRS)

1992-01-01

View of a stone age adze cutting tool floating freely in the forward flight deck and framed by the forward and side windows. On the Earth below, the big island of Hawaii can be seen through the window.

Downflow limestone beds for treatment of net-acidic, oxic, iron-laden drainage from a flooded Anthracite Mine, Pennsylvania, USA: 1. Field evaluation

USGS Publications Warehouse

Cravotta, C.A.; Ward, S.J.

2008-01-01

Passive-treatment systems that route acidic mine drainage (AMD) through crushed limestone and/or organic-rich substrates have been used to remove the acidity and metals from various AMD sources, with a wide range of effects. This study evaluates treatment of net-acidic, oxic, iron-laden AMD with limestone alone, and with organic-rich compost layered with the limestone. In the fall of 2003, a treatment system consisting of two parallel, 500-m2 downflow cells followed by a 400-m2 aerobic settling pond and wetland was installed to neutralize the AMD from the Bell Mine, a large source of AMD and baseflow to the Schuylkill River in the Southern Anthracite Coalfield, in east-central Pennsylvania. Each downflow cell consisted of a lower substrate layer of 1,090 metric tons (t) of dolomitic limestone (60 wt% CaCO3) and an upper layer of 300 t of calcitic limestone (95 wt% CaCO3); one of the downflow cells also included a 0.3 m thick layer of mushroom compost over the limestone. AMD with pH of 3.5-4.3, dissolved oxygen of 6.6-9.9 mg/L, iron of 1.9-5.4 mg/L, and aluminum of 0.8-1.9 mg/L flooded each cell to a depth 0.65 m above the treatment substrates, percolated through the substrates to underlying, perforated outflow pipes, and then flowed through the aerobic pond and wetland before discharging to the Schuylkill River. Data on the flow rates and chemistry of the effluent for the treatment system indicated substantial neutralization by the calcitic limestone but only marginal effects from the dolomitic limestone or compost. Because of its higher transmissivity, the treatment cell containing only limestone neutralized greater quantities of acidity than the cell containing compost and limestone. On average, the treatment system removed 62% of the influent acidity, 47% of the dissolved iron, 34% of the dissolved aluminum, and 8% of the dissolved manganese. Prior to treatment of the Bell Discharge, the Schuylkill River immediately below its confluence with the discharge had pH as low as 4.1 and supported few, if any, fish. However, within the first year of treatment, the pH was maintained at values of 5.0 or greater and native brook trout were documented immediately below the treatment system, though not above. ?? 2008 Springer-Verlag.

Permafrost Degradation and Stream Metabolism in the Arctic: The effect of thaw slump sedimentation on biological productivity and water quality in the Selawik River, Northwest Alaska

NASA Astrophysics Data System (ADS)

Calhoun, J. P.; Crosby, B. T.

2011-12-01

The Selawik River in northwest Alaska, drains ~12,500 km^2 of tree line spruce forest, upland tundra and lowland wetlands. Along the river corridor, high concentrations of fine sediment from a large, young, active retrogressive thaw slump alter the physical and ecological form and function of the stream. This disturbance impacts the entire downstream river corridor, affecting the viability of fish habitat and quality drinking water that subsistence-based native communities depend on. In anticipated warming scenarios, it can be expected that there will be an increase in both the frequency and magnitude of these permafrost degradation features, increasing the extent to which local villages and ecosystems are affected. Our study aims to improve our physical understanding of this system in order to provide biologists, land managers and city officials improved predictive capabilities. Whole stream metabolism (WSM) combines nutrient cycling and organic matter processing to provide an integrated measure of stream health. We utilized a suite of water quality data including temperature, dissolved oxygen, turbidity, pH, pressure, and conductance to calculate WSM values at two experimental reaches up and downstream of the slump over the past three summers. The immediate effects are large magnitude diurnal increases in turbidity, suppressed dissolved oxygen values, and strong attenuation of photosynthetically active radiation (PAR) with depth. We found from 2010 data that, on average, the waters downstream from the slump were 23 times more turbid, had roughly half the dissolved oxygen, and had 4.7 and 2.7 times lower gross primary production (GPP) and ecosystem respiration (ER) respectively. In the summer of 2011, we collected measurements of terrestrial PAR, subsurface PAR, dissolved oxygen and turbidity at multiple river depths at 5 experimental locations. Though turbidity varied roughly by two orders of magnitude and terrestrial PAR increased 850 times between solar midnight and noon, the turbidity suppressed the PAR reaching the bed to almost remove any diurnal signal. The ecological impacts of geomorphic features associated with thawing permafrost is of concern to local populations who rely on their local ecosystems for subsistence, and researchers and land managers interested in the potential impacts of these features under future climate scenarios. Future changes in air temperature and length of the warm season in the Arctic stand to present favorable conditions for generation of more thaw-driven mass wasting processes and subsequent changes to the landscape and its ecosystems.

Effect of carbon and nitrogen addition on nitrous oxide and carbon dioxide fluxes from thawing forest soils

NASA Astrophysics Data System (ADS)

Haohao, Wu; Xingkai, Xu; Cuntao, Duan; TuanSheng, Li; Weiguo, Cheng

2017-07-01

Packed soil-core incubation experiments were done to study the effects of carbon (glucose, 6.4 g C m-2) and nitrogen (NH4Cl and KNO3, 4.5 g N m-2) addition on nitrous oxide (N2O) and carbon dioxide (CO2) fluxes during thawing of frozen soils under two forest stands (broadleaf and Korean pine mixed forest and white birch forest) with two moisture levels (55 and 80% water-filled pore space). With increasing soil moisture, the magnitude and longevity of the flush N2O flux from forest soils was enhanced during the early period of thawing, which was accompanied by great NO3--N consumption. Without N addition, the glucose-induced cumulative CO2 fluxes ranged from 9.61 to 13.49 g CO2-C m-2, which was larger than the dose of carbon added as glucose. The single addition of glucose increased microbial biomass carbon but slightly affected soil dissolved organic carbon pool. Thus, the extra carbon released upon addition of glucose can result from the decomposition of soil native organic carbon. The glucose-induced N2O and CO2 fluxes were both significantly correlated to the glucose-induced total N and dissolved organic carbon pools and influenced singly and interactively by soil moisture and KNO3 addition. The interactive effects of glucose and nitrogen inputs on N2O and CO2 fluxes from forest soils after frost depended on N sources, soil moisture, and vegetation types.

Arsenic mineral dissolution and possible mobilization in mineral-microbe-groundwater environment.

PubMed

Islam, A B M R; Maity, Jyoti Prakash; Bundschuh, Jochen; Chen, Chien-Yen; Bhowmik, Bejon Kumar; Tazaki, Kazue

2013-11-15

Arsenic (As) is widely distributed in the nature as ores or minerals. It has been attracted much attention for the global public health issue, especially for groundwater As contamination. The aim of this study was to elucidate the characteristics of microbes in groundwater where As-minerals were dissolved. An ex situ experiment was conducted with 7 standard As-minerals in bacteria-free groundwater and stored in experimental vessels for 1 year without supplementary nutrients. The pH (6.7-8.4) and EhS.H.E. (24-548 mV) changed between initial (0 day) and final stages (365 days) of experiment. The dissolution of As was detected higher from arsenolite (4240 ± 8.69 mg/L) and native arsenic (4538 ± 9.02 mg/L), whereas moderately dissolved from orpiment (653 ± 3.56 mg/L) and realgar (319 ± 2.56 mg/L) in compare to arsenopyrite (85 ± 1.25mg/L) and tennantite (3 ± 0.06 mg/L). Optical microscopic, scanning electron microscopic observations and flurometric enumeration revealed the abundance of As-resistant bacillus, coccus and filamentous types of microorganisms on the surface of most of As-mineral. 4'-6-Diamidino-2-phenylindole (DAPI)-stained epifluorescence micrograph confirmed the presence of DNA and carboxyfluorescein diacetate (CFDA) staining method revealed the enzymatically active bacteria on the surface of As-minerals such as in realgar (As4S4). Therefore, the microbes enable to survive and mobilize the As in groundwater by dissolution/bioweathering of As-minerals. Copyright © 2012. Published by Elsevier B.V.

Invertebrate and fish assemblage relations to dissolved Oxygen minima in lowland streams of southwestern Louisiana

USGS Publications Warehouse

Justus, B.G.; Mize, Scott V.; Kroes, Daniel; Wallace, James E.

2012-01-01

Dissolved oxygen (DO) concentrations in lowland streams are naturally lower than those in upland streams; however, in some regions where monitoring data are lacking, DO criteria originally established for upland streams have been applied to lowland streams. This study investigated the DO concentrations at which fish and invertebrate assemblages at 35 sites located on lowland streams in southwestern Louisiana began to demonstrate biological thresholds.Average threshold values for taxa richness, diversity and abundance metrics were 2.6 and 2.3 mg/L for the invertebrate and fish assemblages, respectively. These thresholds are approximately twice the DO concentration that some native fish species are capable of tolerating and are comparable with DO criteria that have been recently applied to some coastal streams in Louisiana and Texas. DO minima >2.5 mg/L were favoured for all but extremely tolerant taxa. Extremely tolerant taxa had respiratory adaptations that gave them a competitive advantage, and their success when DO minima were <2 mg/L could be related more to reductions in competition or predation than to DO concentration directly.DO generally had an inverse relation to the amount of agriculture in the buffer area; however, DO concentrations at sites with both low and high amounts of agriculture (including three least-disturbed sites) declined to <2.5 mg/L. Thus, although DO fell below a concentration that was identified as an approximate biological threshold, sources of this condition were sometimes natural (allochthonous material) and had little relation to anthropogenic activity.

Public Library Use of Free E-Resources

ERIC Educational Resources Information Center

Hill, Heather; Bossaller, Jenny

2013-01-01

This article describes a multi-method research project examining the use of various freely available online collections and projects, such as Project Gutenberg, the Internet Archive, and Creative Commons-licensed ebooks, by public libraries. This research begins with the questions: what are libraries doing with freely available materials? Are…

14 CFR 272.8 - Obligation to continue service.

Code of Federal Regulations, 2010 CFR

2010-01-01

... PROCEEDINGS) ECONOMIC REGULATIONS ESSENTIAL AIR SERVICE TO THE FREELY ASSOCIATED STATES § 272.8 Obligation to... eligible Freely Associated State place below the level of essential air service to such place, whether or not the Department has previously determined the level of essential air service to such place, the...

Leveraging freely available remote sensing and ancillary datasets for semi-automated identification of potential wetland areas using a Geographic Information System (GIS).

DOT National Transportation Integrated Search

2016-06-01

The purpose of this study was to develop a wetland identification tool that makes use of freely available geospatial : datasets to identify potential wetland locations at a spatial scale relevant for transportation corridor assessments. The tool was ...

14 CFR 272.8 - Obligation to continue service.

Code of Federal Regulations, 2011 CFR

2011-01-01

... PROCEEDINGS) ECONOMIC REGULATIONS ESSENTIAL AIR SERVICE TO THE FREELY ASSOCIATED STATES § 272.8 Obligation to... eligible Freely Associated State place below the level of essential air service to such place, whether or not the Department has previously determined the level of essential air service to such place, the...

Changes in water extractable organic matter during incubation of forest floor material in the presence of quartz, goethite and gibbsite surfaces

NASA Astrophysics Data System (ADS)

Heckman, Katherine; Vazquez-Ortega, Angelica; Gao, Xiaodong; Chorover, Jon; Rasmussen, Craig

2011-08-01

The release of dissolved organic matter (DOM) from forest floor material constitutes a significant flux of C to the mineral soil in temperate forest ecosystems, with estimates on the order of 120-500 kg C ha -1 year -1. Interaction of DOM with minerals and metals results in sorptive fractionation and stabilization of OM within the soil profile. Iron and aluminum oxides, in particular, have a significant effect on the quantity and quality of DOM transported through forest soils due to their high surface area and the toxic effects of dissolved aluminum on microbial communities. We directly examined these interactions by incubating forest floor material, including native microbiota, for 154 days in the presence of (1) goethite (α-FeOOH), (2) gibbsite (γ-Al(OH) 3), and (3) quartz (α-SiO 2) sand (as a control). Changes in molecular and thermal properties of water extractable organic matter (WEOM, as a proxy for DOM) were evaluated. WEOM was harvested on days 5, 10, 20, 30, 60, 90, and 154, and examined by thermogravimetry/differential thermal analysis (TG/DTA) and diffuse reflectance Fourier transform infrared (DRIFT) spectroscopy. Results indicated significant differences in WEOM quality among treatments, though the way in which oxide surfaces influenced WEOM properties did not seem to change significantly with increasing incubation time. Dissolved organic C concentrations were significantly lower in WEOM from the oxide treatments in comparison to the control treatment. Incubation with goethite produced WEOM with mid-to-high-range thermal lability that was depleted in both protein and fatty acids relative to the control. The average enthalpy of WEOM from the goethite treatment was significantly higher than either the gibbsite or control treatment, suggesting that interaction with goethite surfaces increases the energy content of WEOM. Incubation with gibbsite produced WEOM rich in thermally recalcitrant and carboxyl-rich compounds in comparison to the control treatment. These data indicate that interaction of WEOM with oxide surfaces significantly influences the composition of WEOM and that oxides play an important role in determining the biogeochemistry of forest soil DOM.

Implementation of Fisheries Enhancement Opportunities on the Coeur d'Alene Reservation; Coeur d'Alene Tribe Fish, Water, and Wildlife Program, Progress Report 1996-1998.

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

Vitale, Angelo; Bailey, Dee; Peters, Ron

2003-06-01

As part of an ongoing project to restore fisheries resources in tributaries located on the Coeur d'Alene Indian Reservation, this report details the activities of the Coeur d'Alene Tribe's Fisheries Program for FY 1997 and 1998. This report (1) analyses the effect introduced species and water quality have on the abundance of native trout in Coeur d'Alene Lake and selected target tributaries; (2) details results from an ongoing mark-recapture study on predatory game fish; (3) characterizes spawning habitats in target tributaries and evaluates the effects of fine sediment on substrate composition and estimated emergence success; and (4) provides population estimatesmore » for westslope cutthroat trout in target tributaries. Low dissolved oxygen values in the hypolimnion of Coeur d'Alene Lake continue to be a cause for concern with regard to available fisheries habitat. Four sample sites in 1997 and eight sample sites in 1998 had measured levels of dissolved oxygen below what is considered optimum (6.0 mg/L) for cutthroat trout. As well, two sample points located north of the Coeur d'Alene River showed hypolimnetic dissolved oxygen deficits. This could lead to a more serious problem associated with the high concentration of heavy metals bound up in the sediment north of the Coeur d'Alene River. Most likely these oxygen deficits are a result of allochthonous input of organic matter and subsequent decomposition. Sediment loading from tributaries continues to be a problem in the lake. The build up of sediments at the mouths of all incoming tributaries results in the modification of existing wetlands and provides ideal habitat for predators of cutthroat trout, such as northern pike and largemouth bass. Furthermore, increased sediment deposition provides additional substrate for colonization by aquatic macrophytes, which serve as forage and habitat for other non-native species. There was no significant difference in the relative abundance of fishes in Coeur d'Alene Lake from 1997 to 1998. Four out of the six most commonly sampled species are non-native. Northern pikeminnow and largescale suckers are the only native species among the six most commonly sampled. Northern pikeminnow comprise 8-9% of the electroshocking catch and 18-20% of the gillnet catch. Largescale suckers comprise 24-28% of the electroshocking catch and 9-21% of the gillnet catch. Cutthroat trout and mountain whitefish, on the other hand, comprise less than 1% of the catch when using electroshocking methods and about 1.4% of the gillnet catch. Since 1994, the Coeur d'Alene Tribe Fish, Water and Wildlife Program has conducted an extensive mark-recapture study (Peters et al. 1999). To date, 636 fish have been tagged and 23 fish have been recaptured. We are finding that northern pike have a tendency to migrate from the original sampling site, while largemouth bass appear very territorial, rarely moving from the site where they were tagged. Both species are most commonly associated with shallow, near-shore habitats, where the potential for encountering seasonal migrations of cutthroat trout is maximized. Low-order tributaries provide the most important spawning habitat for cutthroat trout on the Reservation. The mapped distribution of potentially suitable spawning gravel was patchy and did not vary considerably within reaches or between watersheds. Furthermore, the quantity of spawning gravel was low, averaging just 4.1% of measured stream area. The lack of a strong association between spawning gravel abundance and several reach characteristics (gradient, proportion of gravel and pea gravel) corroborates the findings of other authors who suggest that local hydrologic features influence spawning gravel availability. Although the distribution of spawning substrate was patchy within the target watersheds, there is probably adequate habitat to support resident and adfluvial spawners because of currently depressed numbers. Spawning gravels in target tributaries of the Reservation contained proportions of fine sediments comparable to those in egg pockets of salmonid redds in the Rocky Mountain region. At 23 of 29 sample sites, low levels of fine sediment led to high predictions of overall embryo survival (mean = 28.4%). The estimates of fry production potential at sample sites ranged widely (0.0 to 31.2 fry/100 square meters) due, primarily, to the quantity of suitable gravels present. Only in the mainstem of Lake Creek were the proportions of both small and coarse fines considered above the levels for these particle sizes (10% and 30%, respectively) shown to adversely affect salmonid emergence success. Of the 6 sites where high levels of small or coarse fines were recorded, only the sites located in the mainstem of Lake Creek showed supporting evidence for low recruitment.« less

External optical imaging of freely moving mice with green fluorescent protein-expressing metastatic tumors

NASA Astrophysics Data System (ADS)

Yang, Meng; Baranov, Eugene; Shimada, Hiroshi; Moossa, A. R.; Hoffman, Robert M.

2000-04-01

We report here a new approach to genetically engineering tumors to become fluorescence such that they can be imaged externally in freely-moving animals. We describe here external high-resolution real-time fluorescent optical imaging of metastatic tumors in live mice. Stable high-level green flourescent protein (GFP)-expressing human and rodent cell lines enable tumors and metastasis is formed from them to be externally imaged from freely-moving mice. Real-time tumor and metastatic growth were quantitated from whole-body real-time imaging in GFP-expressing melanoma and colon carcinoma models. This GFP optical imaging system is highly appropriate for high throughput in vivo drug screening.

Internal combustion engine having a reactor for afterburning of unburned exhaust gas constituents

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

Maurhoff, G.; Steinwart, J.

1974-08-07

An internal combustion engine is described which has an engine housing and a reactor for afterburning of unburned constituents in the exhaust gas. The reactor has a shell with a periphery and contains a heat-insulated, reactor chamber which is freely movable beyond the point of connection to the shell. The reactor has an inlet nozzle extending freely through the shell and connected to an outlet passage of the engine and has an outlet for escape of the exhaust gases from the reactor chamber. The inlet nozzle protrudes freely into the outlet passage, and the shell has a portion around themore » inlet nozzle in contact with the engine housing.« less

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

PubMed Central

2012-01-01

Background The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Results The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net. PMID:22889332

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.

PubMed

Hanwell, Marcus D; Curtis, Donald E; Lonie, David C; Vandermeersch, Tim; Zurek, Eva; Hutchison, Geoffrey R

2012-08-13

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics.

PubMed

Vaas, Lea A I; Sikorski, Johannes; Michael, Victoria; Göker, Markus; Klenk, Hans-Peter

2012-01-01

The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed '-omics' techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves. The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats. We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data.

Visualization and Curve-Parameter Estimation Strategies for Efficient Exploration of Phenotype Microarray Kinetics

PubMed Central

Vaas, Lea A. I.; Sikorski, Johannes; Michael, Victoria; Göker, Markus; Klenk, Hans-Peter

2012-01-01

Background The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed ‘-omics’ techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves. Methodology The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats. Conclusions We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data. PMID:22536335

Environmental setting and its relations to water quality in the Kanawha River basin

USGS Publications Warehouse

Messinger, Terence; Hughes, C.A.

2000-01-01

The Kanawha River and its major tributary, the New River, drain 12,233 mi2 in West Virginia, Virginia, and North Carolina. Altitude ranges from about 550 ft to more than 4,700 ft. The Kanawha River Basin is mountainous, and includes parts of three physiographic provinces, the Blue Ridge (17 percent), Valley and Ridge (23 percent), and Appalachian Plateaus (60 percent). In the Appalachian Plateaus Province, little of the land is flat, and most of the flat land is in the flood plains and terraces of streams; this has caused most development in this part of the basin to be near streams. The Blue Ridge Province is composed of crystalline rocks, and the Valley and Ridge and Appalachian Plateaus Provinces contain both carbonate and clastic rocks. Annual precipitation ranges from about 36 in. to more than 60 in., and is orographically affected, both locally and regionally. Average annual air temperature ranges from about 43?F to about 55?F, and varies with altitude but not physiographic province. Precipitation is greatest in the summer and least in the winter, and has the least seasonal variation in the Blue Ridge Province. In 1990, the population of the basin was about 870,000, of whom about 25 percent lived in the Charleston, W. Va. metropolitan area. About 75 million tons of coal were mined in the Kanawha River Basin in 1998. This figure represents about 45 percent of the coal mined in West Virginia, and about seven percent of the coal mined in the United States. Dominant forest types in the basin are Northern Hardwood, Oak-Pine, and Mixed Mesophytic. Agricultural land use is more common in the Valley and Ridge and Blue Ridge Provinces than in the Appalachian Plateaus Province. Cattle are the principal agricultural products of the basin. Streams in the Blue Ridge Province and Allegheny Highlands have the most runoff in the basin, and streams in the Valley and Ridge Province and the southwestern Appalachian Plateaus have the least runoff. Streamflow is greatest in the spring and least in the autumn. About 61 percent of the basin's population use surface water from public supply for their domestic needs; about 30 percent use self-supplied ground water, and about nine percent use ground water from public supply. In 1995, total withdrawal of water in the basin was about 1,130 Mgal/d. Total consumptive use was about 118 Mgal/d. Surface water in the Blue Ridge Province is usually dilute (less than 100 mg/L dissolved solids) and well aerated. Dissolved- solids concentrations in streams of the Valley and Ridge Province at low flow are typically greater (150-180 mg/L) than those in the Blue Ridge Province. The Appalachian Plateaus Province contains streams with the most dilute (less than 30 mg/L dissolved solids) and least dilute (more than 500 mg/L dissolved solids) water in the basin. Coal mining has degraded more miles of streams in the basin than any other land use. Streams that receive coal-mine drainage may be affected by sedimentation, and typically contain high concentrations of sulfate, iron, and manganese. Other major water-quality issues include inadequate domestic sewage treatment, present and historic disposal of industrial wastes, and logging, which results in the addition of sediment, nutrients, and other constituents to the water. One hundred eighteen fish species are reported from the Kanawha River system downstream from Kanawha Falls. Of these, 15 are listed as possible, probable, or known introductions. None of these fish species is endemic to the Kanawha River Basin. The New River system has only 46 native fishes, the lowest ratio of native fishes to drainage area of any river system in the eastern United States, and the second-highest proportion of endemic fish species (eight of 46) of any river system in the eastern United States.

Video-Sharing Websites: Tools for Developing Pattern Languages in Children

ERIC Educational Resources Information Center

An, Heejung; Seplocha, Holly

2010-01-01

Children and their families and teachers use video-sharing websites for new types of learning and information sharing. With the expansion of the World Wide Web, the ability to freely exchange pattern-based information has grown exponentially. As noted by Alexander, "pattern language development" is a process in which communities freely share…

Energy and information near black hole horizons

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

Freivogel, Ben, E-mail: benfreivogel@gmail.com

2014-07-01

The central challenge in trying to resolve the firewall paradox is to identify excitations in the near-horizon zone of a black hole that can carry information without injuring a freely falling observer. By analyzing the problem from the point of view of a freely falling observer, I arrive at a simple proposal for the degrees of freedom that carry information out of the black hole. An infalling observer experiences the information-carrying modes as ingoing, negative energy excitations of the quantum fields. In these states, freely falling observers who fall in from infinity do not encounter a firewall, but freely fallingmore » observers who begin their free fall from a location close to the horizon are ''frozen'' by a flux of negative energy. When the black hole is ''mined,'' the number of information-carrying modes increases, increasing the negative energy flux in the infalling frame without violating the equivalence principle. Finally, I point out a loophole in recent arguments that an infalling observer must detect a violation of unitarity, effective field theory, or free infall.« less

Pure Insulin Nanoparticle Agglomerates for Pulmonary Delivery

PubMed Central

Bailey, Mark M.; Gorman, Eric M.; Munson, Eric J.; Berkland, Cory J.

2009-01-01

Diabetes is a set of diseases characterized by defects in insulin utilization, either through autoimmune destruction of insulin-producing cells (Type I) or insulin resistance (Type II). Treatment options can include regular injections of insulin, which can be painful and inconvenient, often leading to low patient compliance. To overcome this problem, novel formulations of insulin are being investigated, such as inhaled aerosols. Sufficient deposition of powder in the peripheral lung to maximize systemic absorption requires precise control over particle size and density, with particles between 1 and 5 μm in aerodynamic diameter being within the respirable range. Insulin nanoparticles were produced by titrating insulin dissolved at low pH up to the pI of the native protein, and were then further processed into microparticles using solvent displacement. Particle size, crystallinity, dissolution properties, structural stability, and bulk powder density were characterized. We have demonstrated that pure drug insulin microparticles can be produced from nanosuspensions with minimal processing steps without excipients, and with suitable properties for deposition in the peripheral lung. PMID:18959432

Phenomenological Transition of an Aluminum Surface in an Ionic Liquid and Its Beneficial Implementation in Batteries.

PubMed

Shvartsev, B; Gelman, D; Amram, D; Ein-Eli, Y

2015-12-29

Aluminum (Al) electrochemical dissolution in organic nonaqueous media and room temperature ionic liquids (RTILs) is partially hampered by the presence of a native oxide. In this work, Al activation in EMIm(HF)2.3F RTIL is reported. It was confirmed that as a result of the interaction of Al with the RTIL, a new film is formed instead of the pristine oxide layer. Aluminum surface modifications result in a transformation from a passive state to the active behavior of the metal. This was confirmed via the employment of electrochemical methods and characterization by XPS, AFM, and TEM. It was shown that the pristine oxide surface film dissolves in EMIm(HF)2.3F, allowing an Al-O-F layer to be formed instead. This newly built up layer dramatically restricts Al corrosion while enabling high rates of Al anodic dissolution. These beneficial features allow the implementation of Al as an anode in advanced portable power sources, such as aluminum-air batteries.

The Effect of Alkaline Concentration on Coconut Husk Crystallinity and the Yield of Sugars Released

NASA Astrophysics Data System (ADS)

Sangian, H. F.; Widjaja, A.

2018-02-01

This work was to analyze the effect of alkaline concentration on coconut coir husk crystallinity and sugar liberated enzymatically. The data showed that the employing of alkaline on lignocellulose transformed the crystallinity. The XRD peaks increased highly which indicated that cellulose was more opened and exposed. After pretreatment, the chemical compositions (cellulose, hemicellulose, and lignin) were changed significantly. The employing 1% alkaline, the cellulosic content inclined if compared to that of non-pretreatment. When the alkaline concentration was added to 4%, the cellulose was decreased slightly which indicated that a part of cellulose and hemicellulose was dissolved into solution. It was found the alkaline pretreatment influenced by the biochemical reaction of treated substrates in producing the reducing sugars. The amounts of sugar liberated enzymatically of coconut husk treated by 1% and 4% alkaline increased to 0.26, and 0.24 g sugar/g (cellulose+hemicellulose), respectively, compared to that of native solid recorded at 0.18 g sugar/g (cellulose+hemicellulose).

Modification of flow and compressibility of corn starch using quasi-emulsion solvent diffusion method.

PubMed

Akhgari, Abbas; Sadeghi, Hasti; Dabbagh, Mohammad Ali

2014-08-01

The aim of this study was to improve flowability and compressibility characteristics of starch to use as a suitable excipient in direct compression tabletting. Quasi-emulsion solvent diffusion was used as a crystal modification method. Corn starch was dissolved in hydrochloric acid at 80°C and then ethanol as a non-solvent was added with lowering temperature until the formation of a precipitate of modified starch. Flow parameters, particle size and thermal behavior of the treated powders were compared with the native starch. Finally, the 1:1 mixture of naproxen and each excipient was tabletted, and hardness and friability of different tablets were evaluated. Larger and well shaped agglomerates were formed which showed different thermal behavior. Treated starch exhibited suitable flow properties and tablets made by the treated powder had relatively high hardness. It was found that recrystallization of corn starch by quasi emulsion solvent diffusion method could improve its flowability and compressibility characteristics.

A review of sediment and nutrient concentration data from Australia for use in catchment water quality models.

PubMed

Bartley, Rebecca; Speirs, William J; Ellis, Tim W; Waters, David K

2012-01-01

Land use (and land management) change is seen as the primary factor responsible for changes in sediment and nutrient delivery to water bodies. Understanding how sediment and nutrient (or constituent) concentrations vary with land use is critical to understanding the current and future impact of land use change on aquatic ecosystems. Access to appropriate land-use based water quality data is also important for calculating reliable load estimates using water quality models. This study collated published and unpublished runoff, constituent concentration and load data for Australian catchments. Water quality data for total suspended sediments (TSS), total nitrogen (TN) and total phosphorus (TP) were collated from runoff events with a focus on catchment areas that have a single or majority of the contributing area under one land use. Where possible, information on the dissolved forms of nutrients were also collated. For each data point, information was included on the site location, land use type and condition, contributing catchment area, runoff, laboratory analyses, the number of samples collected over the hydrograph and the mean constituent concentration calculation method. A total of ∼750 entries were recorded from 514 different geographical sites covering 13 different land uses. We found that the nutrient concentrations collected using "grab" sampling (without a well defined hydrograph) were lower than for sites with gauged auto-samplers although this data set was small and no statistical analysis could be undertaken. There was no statistically significant difference (p<0.05) between data collected at plot and catchment scales for the same land use. This is most likely due to differences in land condition over-shadowing the effects of spatial scale. There was, however, a significant difference in the concentration value for constituent samples collected from sites where >90% of the catchment was represented by a single land use, compared to sites with <90% of the upstream area represented by a single land use. This highlights the need for more single land use water quality data, preferably over a range of spatial scales. Overall, the land uses with the highest median TSS concentrations were mining (∼50,000mg/l), horticulture (∼3000mg/l), dryland cropping (∼2000mg/l), cotton (∼600mg/l) and grazing on native pastures (∼300mg/l). The highest median TN concentrations are from horticulture (∼32,000μg/l), cotton (∼6500μg/l), bananas (∼2700μg/l), grazing on modified pastures (∼2200μg/l) and sugar (∼1700μg/l). For TP it is forestry (∼5800μg/l), horticulture (∼1500μg/l), bananas (∼1400μg/l), dryland cropping (∼900mg/l) and grazing on modified pastures (∼400μg/l). For the dissolved nutrient fractions, the sugarcane land use had the highest concentrations of dissolved inorganic nitrogen (DIN), dissolved organic nitrogen (DON) and dissolved organic phosphorus (DOP). Urban land use had the highest concentrations of dissolved inorganic phosphorus (DIP). This study provides modellers and catchment managers with an increased understanding of the processes involved in estimating constituent concentrations, the data available for use in modelling projects, and the conditions under which they should be applied. Areas requiring more data are also discussed. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Open-access publishing for pharmacy-focused journals.

PubMed

Clauson, Kevin A; Veronin, Michael A; Khanfar, Nile M; Lou, Jennie Q

2008-08-15

Pharmacy-focused journals that are available in open-access (OA), freely accessible, hybrid, or traditional formats were identified. Relevant journals were accessed from PubMed, International Pharmaceutical Abstracts, EMBASE, and the Pharmacology and Pharmacy category of Thomson Scientific Journal Citation Reports. Criteria were established to select journals that satisfied the definition of pharmacy focused. Journals were assessed based on accessibility, copyright transfer requirements, and restrictions. If tracked, the journal's impact factor (IF) was identified according to classification, and medians were calculated for each journal category. A total of 317 pharmacy-focused journals were identified. The majority of pharmacy-focused journals identified were traditional/non-OA (n = 240). A smaller number of journals were freely accessible/ non-OA (n = 37), freely accessible/non-OA with content restrictions (n = 20), or freely available/non-OA with date restrictions (n = 18). The fewest number of journals were completely OA (n = 2). The median IF for the 185 journals whose IF was tracked was 2.029. The median IF for freely accessible and hybrid journals (n = 42) was 2.550, whereas the median IF for traditional journals (n = 143) was 1.900. A very small number of pharmacy-focused journals adhere to the OA paradigm of access. However, journals that adopt some elements of the OA model, chiefly free accessibility, may be more likely to be cited than traditional journals. Pharmacy practitioners, educators, and researchers could benefit from the advantages that OA offers but should understand its financial disadvantages.

CADDIS Volume 2. Sources, Stressors and Responses: Dissolved Oxygen

EPA Pesticide Factsheets

Introduction to the dissolved oxygen module, when to list dissolved oxygen as a candidate cause, ways to measure dissolved oxygen, simple and detailed conceptual model diagrams for dissolved oxygen, references for the dissolved oxygen module.

CADDIS Volume 2. Sources, Stressors and Responses: Dissolved Oxygen - Simple Conceptual Diagram

EPA Pesticide Factsheets

Introduction to the dissolved oxygen module, when to list dissolved oxygen as a candidate cause, ways to measure dissolved oxygen, simple and detailed conceptual model diagrams for dissolved oxygen, references for the dissolved oxygen module.

CADDIS Volume 2. Sources, Stressors and Responses: Dissolved Oxygen - Detailed Conceptual Diagram

EPA Pesticide Factsheets

Introduction to the dissolved oxygen module, when to list dissolved oxygen as a candidate cause, ways to measure dissolved oxygen, simple and detailed conceptual model diagrams for dissolved oxygen, references for the dissolved oxygen module.

Boiling-induced formation of colloidal gold in black smoker hydrothermal fluids

USGS Publications Warehouse

Gartman, Amy; Hannington, Mark; Jamieson, John W.; Peterkin, Ben; Garbe-Schönberg, Dieter; Findlay, Alyssa J; Fuchs, Sebastian; Kwasnitschka, Tom

2017-01-01

Gold colloids occur in black smoker fluids from the Niua South hydrothermal vent field, Lau Basin (South Pacific Ocean), confirming the long-standing hypothesis that gold may undergo colloidal transport in hydrothermal fluids. Six black smoker vents, varying in temperature from 250 °C to 325 °C, were sampled; the 325 °C vent was boiling at the time of sampling and the 250 °C fluids were diffusely venting. Native gold particles ranging from <50 nm to 2 µm were identified in 4 of the fluid samples and were also observed to precipitate on the sampler during collection from the boiling vent. Total gold concentrations (dissolved and particulate) in the fluid samples range from 1.6 to 5.4 nM in the high-temperature, focused flow vents. Although the gold concentrations in the focused flow fluids are relatively high, they are lower than potential solubilities prior to boiling and indicate that precipitation was boiling induced, with sulfide lost upon boiling to exsolution and metal sulfide formation. Gold concentrations reach 26.7 nM in the 250 °C diffuse flow sample, and abundant native gold particles were also found in the fluids and associated sulfide chimney and are interpreted to be a product of colloid accumulation and growth following initial precipitation upon boiling. These results indicate that colloid-driven precipitation as a result of boiling, the persistence of colloids after boiling, and the accumulation of colloids in diffuse flow fluids are important mechanisms for the enrichment of gold in seafloor hydrothermal systems.

Stimulation of methane generation from nonproductive coal by addition of nutrients or a microbial consortium

USGS Publications Warehouse

Jones, Elizabeth J.P.; Voytek, Mary A.; Corum, Margo D.; Orem, William H.

2010-01-01

Biogenic formation of methane from coal is of great interest as an underexploited source of clean energy. The goal of some coal bed producers is to extend coal bed methane productivity and to utilize hydrocarbon wastes such as coal slurry to generate new methane. However, the process and factors controlling the process, and thus ways to stimulate it, are poorly understood. Subbituminous coal from a nonproductive well in south Texas was stimulated to produce methane in microcosms when the native population was supplemented with nutrients (biostimulation) or when nutrients and a consortium of bacteria and methanogens enriched from wetland sediment were added (bioaugmentation). The native population enriched by nutrient addition included Pseudomonas spp., Veillonellaceae, and Methanosarcina barkeri. The bioaugmented microcosm generated methane more rapidly and to a higher concentration than the biostimulated microcosm. Dissolved organics, including long-chain fatty acids, single-ring aromatics, and long-chain alkanes accumulated in the first 39 days of the bioaugmented microcosm and were then degraded, accompanied by generation of methane. The bioaugmented microcosm was dominated by Geobacter sp., and most of the methane generation was associated with growth of Methanosaeta concilii. The ability of the bioaugmentation culture to produce methane from coal intermediates was confirmed in incubations of culture with representative organic compounds. This study indicates that methane production could be stimulated at the nonproductive field site and that low microbial biomass may be limiting in situ methane generation. In addition, the microcosm study suggests that the pathway for generating methane from coal involves complex microbial partnerships.

OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.

PubMed

Zhou, Guangyan; Xia, Jianguo

2018-06-07

Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majority of them focus on protein-protein interaction (PPI) or metabolic networks, and visualizations often suffer from 'hairball' effects when networks become large. To help address these limitations, we developed OmicsNet - a novel web-based tool that allows users to easily create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space. Users can upload one or multiple lists of molecules of interest (genes/proteins, microRNAs, transcription factors or metabolites) to create and merge different types of biological networks. The 3D network visualization system was implemented using the powerful Web Graphics Library (WebGL) technology that works natively in most major browsers. OmicsNet supports force-directed layout, multi-layered perspective layout, as well as spherical layout to help visualize and navigate complex networks. A rich set of functions have been implemented to allow users to perform coloring, shading, topology analysis, and enrichment analysis. OmicsNet is freely available at http://www.omicsnet.ca.

Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm

PubMed Central

Nugent, Timothy; Jones, David T.

2010-01-01

Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has been directed toward developing a method to pack the helices together. Here, we present a novel approach to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of transmembrane proteins. Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM) classifier to predict per residue lipid exposure with 69% accuracy. This information is combined with additional features to train a second SVM to predict residue contacts which are then used to determine helix-helix interaction with up to 65% accuracy under stringent cross-validation on a non-redundant test set. Our method is also able to discriminate native from decoy helical packing arrangements with up to 70% accuracy. Finally, we employ a force-directed algorithm to construct the optimal helical packing arrangement which demonstrates success for proteins containing up to 13 transmembrane helices. This software is freely available as source code from http://bioinf.cs.ucl.ac.uk/memsat/mempack/. PMID:20333233

GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking

NASA Astrophysics Data System (ADS)

Baek, Minkyung; Shin, Woong-Hee; Chung, Hwan Won; Seok, Chaok

2017-07-01

Protein-ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein-ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein-ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.

Matching native electrical stimulation by graded chemical stimulation in isolated mouse adrenal chromaffin cells.

PubMed

Fulop, Tiberiu; Smith, Corey

2007-11-30

Adrenal chromaffin cells release multiple transmitters in response to sympathetic stimulation. Modest cell firing, matching sympathetic tone, releases small freely soluble catecholamines. Elevated electrical firing rates matching input under sympathetic stress results in release of catecholamines as well as semi-soluble vaso- and neuro-active peptides packaged within the dense core of the secretory granule. This activity-dependent differential transmitter release has been shown to rely on a mechanistic shift in the mode of exocytosis through the regulated dilation of the secretory fusion pore between granule and cell surface membranes. However, biochemical description of the mechanism regulating fusion pore dilation remains elusive. In the experimental setting, electrical stimulation designed to mimic sympathetic input, is achieved through single-cell voltage-clamp. While precise, this approach is incompatible with biochemical and proteomic analysis, both of which require large sample sizes. We address this limitation in the current study. We describe a bulk chemical stimulation paradigm calibrated to match defined electrical activity. We utilize calcium and single-cell amperometric measurements to match extracellular potassium concentrations to physiological electrical stimulation under sympathetic tone as well as acute stress conditions. This approach provides larger samples of uniformly stimulated cells for determining molecular players in activity-dependent differential transmitter release from adrenal chromaffin cells.

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

PubMed

Olechnovič, Kliment; Venclovas, Ceslovas

2014-07-01

The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Wilderness and the paradox of individual freedom

Treesearch

Randy J. Tanner

2007-01-01

Wilderness, whether designated as such or not, is often portrayed as the embodiment of freedom. The type of freedom to be enjoyed, though, is not clear. Freedom in wilderness may be constructed negatively—individuals freely experience wilderness without societal constraints; or, freedom may be constructed positively— individuals freely experience the fundamental...

"Just Google It"--The Scope of Freely Available Information Sources for Doctoral Thesis Writing

ERIC Educational Resources Information Center

Grigas, Vincas; Juzeniene, Simona; Velickaite, Jone

2017-01-01

Introduction: Recent developments in the field of scientific information resource provision lead us to the key research question, namely,what is the coverage of freely available information sources when writing doctoral theses, and whether the academic library can assume the leading role as a direct intermediator for information users. Method:…

Five Years of Helping Chemists to Create an Online Presence Using Freely Available Resources (ACS Fall meeting 1 of 12)

EPA Science Inventory

For over twenty-five years Antony Williams has been delivering presentations to chemists about how to utilize freely available websites to help create an online presence. Over the years he has presented on LinkedIn for a professional CV, ResearchGate for sharing papers and resear...

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

Argyres, Philip C.; Lü, Yongchao; Martone, Mario

Coulomb branch chiral rings of N = 2 SCFTs are conjectured to be freely generated. While no counter-example is known, no direct evidence for the conjecture is known either. We initiate a systematic study of SCFTs with Coulomb branch chiral rings satisfying non-trivial relations, restricting our analysis to rank 1. The main result of our study is that (rank-1) SCFTs with non-freely generated CB chiral rings when deformed by relevant deformations, always flow to theories with non-freely generated CB rings. This implies that if they exist, they must thus form a distinct subset under RG flows. We also nd manymore » interesting characteristic properties that these putative theories satisfy which may be helpful in proving or disproving their existence using other methods.« less

Zinc oxide nanoparticles affect carbon and nitrogen mineralization of Phoenix dactylifera leaf litter in a sandy soil.

PubMed

Rashid, Muhammad Imtiaz; Shahzad, Tanvir; Shahid, Muhammad; Ismail, Iqbal M I; Shah, Ghulam Mustafa; Almeelbi, Talal

2017-02-15

We investigated the impact of zinc oxide nanoparticles (ZnO NPs; 1000mgkg -1 soil) on soil microbes and their associated soil functions such as date palm (Phoenix dactylifera) leaf litter (5gkg -1 soil) carbon and nitrogen mineralization in mesocosms containing sandy soil. Nanoparticles application in litter-amended soil significantly decreased the cultivable heterotrophic bacterial and fungal colony forming units (cfu) compared to only litter-amended soil. The decrease in cfu could be related to lower microbial biomass carbon in nanoparticles-litter amended soil. Likewise, ZnO NPs also reduced CO 2 emission by 10% in aforementioned treatment but this was higher than control (soil only). Labile Zn was only detected in the microbial biomass of nanoparticles-litter applied soil indicating that microorganisms consumed this element from freely available nutrients in the soil. In this treatment, dissolved organic carbon and mineral nitrogen were 25 and 34% lower respectively compared to litter-amended soil. Such toxic effects of nanoparticles on litter decomposition resulted in 130 and 122% lower carbon and nitrogen mineralization efficiency respectively. Hence, our results entail that ZnO NPs are toxic to soil microbes and affect their function i.e., carbon and nitrogen mineralization of applied litter thus confirming their toxicity to microbial associated soil functions. Copyright © 2016 Elsevier B.V. All rights reserved.

In Vivo Biotransformation Rates of Organic Chemicals in Fish: Relationship with Bioconcentration and Biomagnification Factors.

PubMed

Lo, Justin C; Letinski, Daniel J; Parkerton, Thomas F; Campbell, Dave A; Gobas, Frank A P C

2016-12-20

In vivo dietary bioaccumulation experiments for 85 hydrophobic organic substances were conducted to derive the in vivo gastrointestinal biotransformation rates, somatic biotransformation rates, bioconcentration factors (BCF), and biomagnification factors (BMF) for improving methods for bioaccumulation assessment and to develop an in vivo biotransformation rate database for QSAR development and in vitro to in vivo biotransformation rate extrapolation. The capacity of chemicals to be biotransformed in fish was found to be highly dependent on the route of exposure. Somatic biotransformation was the dominant pathway for most chemicals absorbed via the respiratory route. Intestinal biotransformation was the dominant metabolic pathway for most chemicals absorbed via the diet. For substances not biotransformed or transformed exclusively in the body of the fish, the BCF and BMF appeared to be closely correlated. For substances subject to intestinal biotransformation, the same correlation did not apply. We conclude that intestinal biotransformation and bioavailability in water can modulate the relationship between the BCF and BMF. This study also supports a fairly simple rule of thumb that may be useful in the interpretation of dietary bioaccumulation tests; i.e., chemicals with a BMF L of <1 tend to exhibit BCFs based on either the freely dissolved (BCF WW,fd ) or the total concentration (BCF WW,t ) of the chemical in the water that is less than 5000.

The organic pollutant status of rivers in Bosnia and Herzegovina as determined by a combination of active and passive sampling methods.

PubMed

Harman, Christopher; Grung, Merete; Djedjibegovic, Jasmina; Marjanovic, Aleksandra; Fjeld, Eirik; Braaten, Hans Fredrik Veiteberg; Sober, Miroslav; Larssen, Thorjørn; Ranneklev, Sissel Brit

2018-04-15

There is an overall lack of data concerning the pollution status of Bosnia Herzegovina, which is confounded by fragmented national environmental management. The present study aimed to provide some initial data for concentrations of priority substances in two major Bosnian Rivers, using two types of passive sampler (PS) as well as by using high volume water sampling (HVWS). Overall, concentrations of most persistent organic pollutants (POPs), including polychlorinated biphenyls (PCBs) and legacy pesticides, were shown to be low. However, around the town of Doboj on the Bosna River, concentrations of polycyclic aromatic hydrocarbons (PAH) breached European standards for several compounds and reached 67 ng L -1 for freely dissolved concentrations and 250 ng L -1 for total concentrations. In general, contamination was lower in the Neretva River compared to the Bosna, although for brominated diphenyl ethers (PBDEs), results suggested an active source of PBDEs at one location based on the ratio of congeners 47 and 99. Direct comparisons between the different sampling techniques used are not straightforward, but similar patterns of PAH contamination were shown by HVWS and PS in the Bosna River. There are both scientific and practical considerations when choosing which type of sampling technique to apply, and this should be decided based on the goals of each individual study.

Cross Validation of Two Partitioning-Based Sampling Approaches in Mesocosms Containing PCB Contaminated Field Sediment, Biota, and Activated Carbon Amendment.

PubMed

Schmidt, Stine N; Wang, Alice P; Gidley, Philip T; Wooley, Allyson H; Lotufo, Guilherme R; Burgess, Robert M; Ghosh, Upal; Fernandez, Loretta A; Mayer, Philipp

2017-09-05

The Gold Standard for determining freely dissolved concentrations (C free ) of hydrophobic organic compounds in sediment interstitial water would be in situ deployment combined with equilibrium sampling, which is generally difficult to achieve. In the present study, ex situ equilibrium sampling with multiple thicknesses of silicone and in situ pre-equilibrium sampling with low density polyethylene (LDPE) loaded with performance reference compounds were applied independently to measure polychlorinated biphenyls (PCBs) in mesocosms with (1) New Bedford Harbor sediment (MA, U.S.A.), (2) sediment and biota, and (3) activated carbon amended sediment and biota. The aim was to cross validate the two different sampling approaches. Around 100 PCB congeners were quantified in the two sampling polymers, and the results confirmed the good precision of both methods and were in overall good agreement with recently published LDPE to silicone partition ratios. Further, the methods yielded C free in good agreement for all three experiments. The average ratio between C free determined by the two methods was factor 1.4 ± 0.3 (range: 0.6-2.0), and the results thus cross-validated the two sampling approaches. For future investigations, specific aims and requirements in terms of application, data treatment, and data quality requirements should dictate the selection of the most appropriate partitioning-based sampling approach.

Role of black carbon in the sorption of polychlorinated dibenzo-p-dioxins and dibenzofurans at the Diamond Alkali superfund site, Newark Bay, New Jersey.

PubMed

Lambert, Matthew K; Friedman, Carey; Luey, Pamela; Lohmann, Rainer

2011-05-15

The sorption of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) to organic carbon (OC) and black carbon (BC) was measured in two sediment cores taken near the Diamond Alkali superfund site (DA) in the Passaic River and Newark Bay, New Jersey (U.S.A.). An OC partitioning model and a BC-inclusive, Freundlich distribution model were used to interpret measurements of freely dissolved PCDD/Fs using passive samplers in sediment incubations, together with measured sedimentary concentrations of OC, BC, and PCDD/Fs. Samples were also analyzed for polycyclic aromatic hydrocarbons (PAHs) as controls on the two distribution models. The OC partitioning model underpredicted the distribution of PAHs and PCDD/Fs by 10-100-fold. The Freundlich model predicted the distribution of PAHs at the DA to within a factor of 2-3 of observations. Black carbon-water partition coefficients (K(iBC)) for PCDD/Fs, derived from literature results of both field and laboratory studies differed up to 1000-fold from values derived from this study. Contrary to expectations, PCDDs displayed stronger sorption than either PCDFs or PAHs relative to their subcooled liquid aqueous solubilities. Even though the presence of BC in the sediments reduced the overall bioavailability of PCDD/Fs by >90%, the sediments at 2 m depth continue to display the highest pore water activities of PCDD/Fs.

Wirelessly powered and remotely controlled valve-array for highly multiplexed analytical assay automation on a centrifugal microfluidic platform.

PubMed

Torres Delgado, Saraí M; Kinahan, David J; Nirupa Julius, Lourdes Albina; Mallette, Adam; Ardila, David Sáenz; Mishra, Rohit; Miyazaki, Celina M; Korvink, Jan G; Ducrée, Jens; Mager, Dario

2018-06-30

In this paper we present a wirelessly powered array of 128 centrifugo-pneumatic valves that can be thermally actuated on demand during spinning. The valves can either be triggered by a predefined protocol, wireless signal transmission via Bluetooth, or in response to a sensor monitoring a parameter like the temperature, or homogeneity of the dispersion. Upon activation of a resistive heater, a low-melting membrane (Parafilm™) is removed to vent an entrapped gas pocket, thus letting the incoming liquid wet an intermediate dissolvable film and thereby open the valve. The proposed system allows up to 12 heaters to be activated in parallel, with a response time below 3 s, potentially resulting in 128 actuated valves in under 30 s. We demonstrate, with three examples of common and standard procedures, how the proposed technology could become a powerful tool for implementing diagnostic assays on Lab-on-a-Disc. First, we implement wireless actuation of 64 valves during rotation in a freely programmable sequence, or upon user input in real time. Then, we show a closed-loop centrifugal flow control sequence for which the state of mixing of reagents, evaluated from stroboscopically recorded images, triggers the opening of the valves. In our last experiment, valving and closed-loop control are used to facilitate centrifugal processing of whole blood. Copyright © 2018 Elsevier B.V. All rights reserved.

Assessment of bioavailable fraction of POPS in surface water bodies in Johannesburg City, South Africa, using passive samplers: an initial assessment.

PubMed

Amdany, Robert; Chimuka, Luke; Cukrowska, Ewa; Kukučka, Petr; Kohoutek, Jiří; Tölgyessy, Peter; Vrana, Branislav

2014-09-01

In this study, the semipermeable membrane device (SPMD) passive samplers were used to determine freely dissolved concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) in selected water bodies situated in and around Johannesburg City, South Africa. The devices were deployed for 14 days at each sampling site in spring and summer of 2011. Time weighted average (TWA) concentrations of the water-borne contaminants were calculated from the amounts of analytes accumulated in the passive samplers. In the area of interest, concentrations of analytes in water ranged from 33.5 to 126.8 ng l(-1) for PAHs, from 20.9 to 120.9 pg l(-1) for PCBs and from 0.2 to 36.9 ng l(-1) for OCPs. Chlorinated pesticides were mainly composed of hexachlorocyclohexanes (HCHs) (0.15-36.9 ng l(-1)) and dichlorodiphenyltrichloromethane (DDT) with its metabolites (0.03-0.55 ng l(-1)). By applying diagnostic ratios of certain PAHs, identification of possible sources of the contaminants in the various sampling sites was performed. These ratios were generally inclined towards pyrogenic sources of pollution by PAHs in all study sites except in the Centurion River (CR), Centurion Lake (CL) and Airport River (AUP) that indicated petrogenic origins. This study highlights further need to map up the temporal and spatial variations of these POPs using passive samplers.

Suppression of humoral immune responses by 2,3,7,8-tetrachlorodibenzo-p-dioxin intercalated in smectite clay.

PubMed

Boyd, Stephen A; Johnston, Cliff T; Pinnavaia, Thomas J; Kaminski, Norbert E; Teppen, Brian J; Li, Hui; Khan, Bushra; Crawford, Robert B; Kovalova, Natalia; Kim, Seong-Su; Shao, Hua; Gu, Cheng; Kaplan, Barbara L F

2011-12-01

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a highly toxic environmental contaminant found in soils and sediments. Because of its exceptionally low water solubility, this compound exists predominantly in the sorbed state in natural environments. Clay minerals, especially expandable smectite clays, are one of the major component geosorbents in soils and sediments that can function as an effective adsorbent for environmental dioxins, including TCDD. In this study, TCDD was intercalated in the smectite clay saponite by an incipient wetness method. The primary goal of this study was to intercalate TCDD in natural K-saponite clay and evaluate its immunotoxic effects in vivo. The relative bioavailability of TCDD was evaluated by comparing the metabolic activity of TCDD administered in the adsorbed state as an intercalate in saponite and freely dissolved in corn oil. This comparison revealed nearly identical TCDD-induced suppression of humoral immunity, a well-established and sensitive sequela, in a mammalian (mouse) model. This result suggests that TCDD adsorbed by clays is likely to be available for biouptake and biodistribution in mammals, consistent with previous observations of TCDD in livestock exposed to dioxin-contaminated ball clays that were used as feed additives. Adsorption of TCDD by clay minerals does not appear to mitigate risk associated with TCDD exposure substantially. Copyright © 2011 SETAC.

Variations in the bioavailability of polycyclic aromatic hydrocarbons in industrial and agricultural soils after bioremediation.

PubMed

Guo, Meixia; Gong, Zongqiang; Allinson, Graeme; Tai, Peidong; Miao, Renhui; Li, Xiaojun; Jia, Chunyun; Zhuang, Jie

2016-02-01

The aim of this study was to demonstrate the variations in bioavailability remaining in industrial and agricultural soils contaminated by polycyclic aromatic hydrocarbons (PAHs) after bioremediation. After inoculation of Mycobacterium sp. and Mucor sp., PAH biodegradation was tested on a manufactured gas plant (MGP) soil and an agricultural soil. PAH bioavailability was assessed before and after biodegradation using solid-phase extraction (Tenax-TA extraction) and solid-phase micro-extraction (SPME) to represent bioaccessibility and chemical activity of PAHs, respectively. Only 3- and 4-ring PAHs were noticeably biodegradable in the MGP soil. PAH biodegradation in the agricultural soil was different from that in the MGP soil. The rapidly desorbing fractions (F(rap)) extracted by Tenax-TA and the freely dissolved concentrations of 3- and 4-ring PAHs determined by SPME from the MGP soil decreased after 30 days biodegradation; those values of the 5- and 6-ring PAHs changed to a lesser degree. For the agricultural soil, the F(rap) values of the 3- and 4-ring PAHs also decreased after the biodegradation experiment. The Tenax-TA extraction and the SPME have the potential to assess variations in the bioavailability of PAHs and the degree of biodegradation in contaminated MGP soils. In addition, Tenax-TA extraction is more sensitive than SPME when used in the agricultural soil. Copyright © 2015 Elsevier Ltd. All rights reserved.

Polymer chain collapse induced by many-body dipole correlations.

PubMed

Budkov, Yu A; Kalikin, N N; Kolesnikov, A L

2017-04-01

We present a simple analytical theory of a flexible polymer chain dissolved in a good solvent, carrying permanent freely oriented dipoles on the monomers. We take into account the dipole correlations within the random phase approximation (RPA), as well as a dielectric heterogeneity in the internal polymer volume relative to the bulk solution. We demonstrate that the dipole correlations of monomers can be taken into account as pairwise ones only when the polymer chain is in a coil conformation. In this case the dipole correlations manifest themselves through the Keesom interactions of the permanent dipoles. On the other hand, the dielectric heterogeneity effect (dielectric mismatch effect) leads to the effective interaction between the monomers of the polymeric coil. Both of these effects can be taken into account by renormalizing the second virial coefficient of the monomer-monomer volume interactions. We establish that in the case when the solvent dielectric permittivity exceeds the dielectric permittivity of the polymeric material, the dielectric mismatch effect competes with the dipole attractive interactions, leading to polymer coil expansion. In the opposite case, both the dielectric mismatch effect and the dipole attractive interaction lead to the polymer coil collapse. We analyse the coil-globule transition caused by the dipole correlations of monomers within the many-body theory. We demonstrate that accounting for the dipole correlations higher than the pairwise ones smooths this pure electrostatics driven coil-globule transition of the polymer chain.

Effect of steam activated biochar application to industrially contaminated soils on bioavailability of polycyclic aromatic hydrocarbons and ecotoxicity of soils.

PubMed

Kołtowski, Michał; Hilber, Isabel; Bucheli, Thomas D; Oleszczuk, Patryk

2016-10-01

The aim of this study was to determine the effect of steam activation of biochars on the immobilization of freely dissolved (Cfree) and bioaccessible fraction (Cbioacc) of PAHs in soils. Additionally, the toxicity to various organisms like Vibrio fischeri, Lepidium sativum and Folsomia candida was measured before and after the amendment of biochars to soils. Three biochars produced from willow, coconut and wheat straw were steam activated and added to three different soils with varying content and origin of PAHs (coke vs. bitumen). The soils with the addition of the biochars (activated and non-activated) were incubated for a period of 60days. Steam activation of the biochars resulted in more pronounced reduction of both Cfree and Cbioacc. The range of the increase in effectiveness was from 10 to 84% for Cfree and from 50 to 99% for Cbioacc. In contrast, the effect of activation on the toxicity of the soils studied varied greatly and was specific to a particular test and soil type. Essentially, biochar activation did not result in a change of phytotoxicity, but it increased or decreased (depending on the parameter, type of biochar, contaminant source, and soil and soil type) the toxic effect to F. candida, and decreased the toxicity of leachates to V. fischeri. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of Hydrologic and Water-Quality Characteristics of Two Native Tallgrass Prairie Streams with Agricultural Streams in Missouri and Kansas

USGS Publications Warehouse

Heimann, David C.

2009-01-01

This report presents the results of a study by the U.S. Geological Survey, in cooperation with the Missouri Department of Natural Resources, to analyze and compare hydrologic and water-quality characteristics of tallgrass prairie and agricultural basins located within the historical distribution of tallgrass prairie in Missouri and Kansas. Streamflow and water-quality data from two remnant, tallgrass prairie basins (East Drywood Creek at Prairie State Park, Missouri, and Kings Creek near Manhattan, Kansas) were compared to similar data from agricultural basins in Missouri and Kansas. Prairie streams, especially Kings Creek in eastern Kansas, received a higher percentage of base flow and a lower percentage of direct runoff than similar-sized agricultural streams in the region. A larger contribution of direct runoff from the agricultural streams made them much flashier than prairie streams. During 22 years of record, the Kings Creek base-flow component averaged 66 percent of total flow, but base flow was only 16 to 26 percent of flows at agricultural sites of various record periods. The large base-flow component likely is the result of greater infiltration of precipitation in prairie soils and the resulting greater contribution of groundwater to streamflow. The 1- and 3-day annual maximum flows were significantly greater at three agricultural sites than at Kings Creek. The effects of flashier agricultural streams on native aquatic biota are unknown, but may be an important factor in the sustainability of some native aquatic species. There were no significant differences in the distribution of dissolved-oxygen concentrations at prairie and agricultural sites, and some samples from most sites fell below the 5 milligrams per liter Missouri and Kansas standard for the protection of aquatic life. More than 10 percent of samples from the East Drywood Creek prairie stream were less than this standard. These data indicate low dissolved-oxygen concentrations during summer low-flow periods may be a natural phenomenon for small prairie streams in the Osage Plains. Nutrient concentrations including total nitrogen, ammonia, nitrate, and total phosphorus were significantly less in base-flow and runoff samples from prairie streams than from agricultural streams. The total nitrogen concentration at all sites other than one of two prairie sampling sites were, on occasion, above the U.S. Environmental Protection Agency recommended criterion for total nitrogen for the prevention of nutrient enrichment, and typically were above this recommended criterion in runoff samples at all sites. Nitrate and total phosphorus concentrations in samples from the prairie streams generally were below the U.S. Environmental Protection Agency recommended nutrient criteria in base-flow and runoff samples, whereas samples from agricultural sites generally were below the criteria in base-flow samples and generally above in runoff samples. The lower concentrations of nutrient species in prairie streams is likely because prairies are not fertilized like agricultural basins and prairie basins are able to retain nutrients better than agricultural basins. This retention is enhanced by increased infiltration of precipitation into the prairie soils, decreased surface runoff, and likely less erosion than in agricultural basins. Streamflow in the small native prairie streams had more days of zero flow and lower streamflow yields than similar-sized agricultural streams. The prairie streams were at zero flow about 50 percent of the time, and the agricultural streams were at zero flow 25 to 35 percent of the time. Characteristics of the prairie basins that could account for the greater periods of zero flow and lower yields when compared to agricultural streams include greater infiltration, greater interception and evapotranspiration, shallower soils, and possible greater seepage losses in the prairie basins. Another difference between the prairie and agricultural strea

Formation of silk fibroin nanoparticles in water-miscible organic solvent and their characterization

NASA Astrophysics Data System (ADS)

Zhang, Yu-Qing; Shen, Wei-De; Xiang, Ru-Li; Zhuge, Lan-Jian; Gao, Wei-Jian; Wang, Wen-Bao

2007-10-01

When Silk fibre derived from Bombyx mori, a native biopolymer, was dissolved in highly concentrated neutral salts such as CaCl2, the regenerated liquid silk, a gradually degraded peptide mixture of silk fibroin, could be obtained. The silk fibroin nanoparticles were prepared rapidly from the liquid silk by using water-miscible protonic and polar aprotonic organic solvents. The nanoparticles are insoluble but well dispersed and stable in aqueous solution and are globular particles with a range of 35-125 nm in diameter by means of TEM, SEM, AFM and laser sizer. Over one half of the ɛ-amino groups exist around the protein nanoparticles by using a trinitrobenzenesulfonic acid (TNBS) method. Raman spectra shows the tyrosine residues on the surface of the globules are more exposed than those on native silk fibers. The crystalline polymorph and conformation transition of the silk nanoparticles from random-coil and α-helix form (Silk I) into anti-parallel β-sheet form (Silk II) are investigated in detail by using infrared, fluorescence and Raman spectroscopy, DSC, 13C CP-MAS NMR and electron diffraction. X-ray diffraction of the silk nanoparticles shows that the nanoparticles crystallinity is about four fifths of the native fiber. Our results indicate that the degraded peptide chains of the regenerated silk is gathered homogeneously or heterogeneously to form a looser globular structure in aqueous solution. When introduced into excessive organic solvent, the looser globules of the liquid silk are rapidly dispersed and simultaneously dehydrated internally and externally, resulting in the further chain-chain contact, arrangement of those hydrophobic domains inside the globules and final formation of crystalline silk nanoparticles with β-sheet configuration. The morphology and size of the nanoparticles are relative to the kinds, properties and even molecular structures of organic solvents, and more significantly to the looser globular substructure of the degraded silk fibroin in aqueous solution. It is possible that the silk protein nanoparticles are potentially useful in biomaterials such as cosmetics, anti-UV skincare products, industrial materials and surface improving materials, especially in enzyme/drug delivery system as vehicle.

Application of UV-visible absorption spectroscopy combined with two-dimensional correlation for insight into DOM fractions from native halophyte soils in a larger estuarine delta.

PubMed

Wei, Huaibin; Yu, Huibin; Pan, Hongwei; Gao, Hongjie

2018-05-01

UV-visible absorption spectroscopy combined with principal component analysis (PCA) and two-dimensional correlation (2D correlation) is used to trace components of dissolved organic matter (DOM) extracted from soils in a larger estuarine delta and to investigate spatial variations of DOM fractions. Soil samples of different depths were collected from native halophyte soils along a saline gradient, i.e., Suaeda salsa Comm. (SSC), Chenopodium album Comm. (CAC), Phragmites australis Comm. (PAC), and Artemisia selengensis Comm. (ASC). Molecular weights of DOM within the SSC soil profile were the lowest, followed by the CAC, PAC, and ASC soil profiles. Humification degree of DOM within the ASC soil profile was the highest, followed by the PAC, SSC, and CAC soil profiles. DOM within the soil profiles mainly contained phenolic, carboxylic, microbial products, and aromatic and alkyl groups through the PCA, which presented the significant differentiation among the four native halophyte soil profiles. The 2D UV correlation spectra of DOM within the SSC soil profile indicated that the variations of the phenolic groups were the largest, followed by the carboxylic groups, microbial products, and humified organic materials according to the band changing order of 285 → 365 → 425 → 520 nm. The 2D UV correlation spectra of DOM within the CAC soil profiles determined that the decreasing order of the variations was phenolic groups > carboxylic groups > microbial products according the band changing order of 285 → 365 → 425 nm. The 2D UV correlation spectra of DOM within the PAC soil profile proved that the variations of the phenolic groups were larger than those of the carboxylic groups according to the band changing order of 285 → 365 nm. The 2D UV correlation spectra of DOM within the ASC soil profile demonstrated that the variations of the phenolic groups were larger than those of the other DOM fractions according to the broad cross-peak at 285/365-700 nm.

A Set of Free Cross-Platform Authoring Programs for Flexible Web-Based CALL Exercises

ERIC Educational Resources Information Center

O'Brien, Myles

2012-01-01

The Mango Suite is a set of three freely downloadable cross-platform authoring programs for flexible network-based CALL exercises. They are Adobe Air applications, so they can be used on Windows, Macintosh, or Linux computers, provided the freely-available Adobe Air has been installed on the computer. The exercises which the programs generate are…

The Importance of Reading Naturally: Evidence from Combined Recordings of Eye Movements and Electric Brain Potentials

ERIC Educational Resources Information Center

Metzner, Paul; von der Malsburg, Titus; Vasishth, Shravan; Rösler, Frank

2017-01-01

How important is the ability to freely control eye movements for reading comprehension? And how does the parser make use of this freedom? We investigated these questions using coregistration of eye movements and event-related brain potentials (ERPs) while participants read either freely or in a computer-controlled word-by-word format (also known…

A Freely-Available Authoring System for Browser-Based CALL with Speech Recognition

ERIC Educational Resources Information Center

O'Brien, Myles

2017-01-01

A system for authoring browser-based CALL material incorporating Google speech recognition has been developed and made freely available for download. The system provides a teacher with a simple way to set up CALL material, including an optional image, sound or video, which will elicit spoken (and/or typed) answers from the user and check them…

40 CFR 430.40 - Applicability; description of the dissolving sulfite subcategory.

Code of Federal Regulations, 2011 CFR

2011-07-01

... dissolving sulfite subcategory. 430.40 Section 430.40 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Dissolving Sulfite Subcategory § 430.40 Applicability; description of the dissolving sulfite... at dissolving sulfite mills. ...

40 CFR 430.40 - Applicability; description of the dissolving sulfite subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... dissolving sulfite subcategory. 430.40 Section 430.40 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Dissolving Sulfite Subcategory § 430.40 Applicability; description of the dissolving sulfite... at dissolving sulfite mills. ...

Template-free preparation of crystalline Ge nanowire film electrodes via an electrochemical liquid-liquid-solid process in water at ambient pressure and temperature for energy storage.

PubMed

Gu, Junsi; Collins, Sean M; Carim, Azhar I; Hao, Xiaoguang; Bartlett, Bart M; Maldonado, Stephen

2012-09-12

The direct electrodeposition of crystalline germanium (Ge) nanowire film electrodes from an aqueous solution of dissolved GeO(2) using discrete 'flux' nanoparticles capable of dissolving Ge(s) has been demonstrated. Electrodeposition of Ge at inert electrode substrates decorated with small (<100 nm), discrete indium (In) nanoparticles resulted in crystalline Ge nanowire films with definable nanowire diameters and densities without the need for a physical or chemical template. The Ge nanowires exhibited strong polycrystalline character as-deposited, with approximate crystallite dimensions of 20 nm and a mixed orientation of the crystallites along the length of the nanowire. Energy dispersive spectroscopic elemental mapping of individual Ge nanowires showed that the In nanoparticles remained at the base of each nanowire, indicating good electrical communication between the Ge nanowire and the underlying conductive support. As-deposited Ge nanowire films prepared on Cu supports were used without further processing as Li(+) battery anodes. Cycling studies performed at 1 C (1624 mA g(-1)) indicated the native Ge nanowire films supported stable discharge capacities at the level of 973 mA h g(-1), higher than analogous Ge nanowire film electrodes prepared through an energy-intensive vapor-liquid-solid nanowire growth process. The cumulative data show that ec-LLS is a viable method for directly preparing a functional, high-activity nanomaterials-based device component. The work presented here is a step toward the realization of simple processes that make fully functional energy conversion/storage technologies based on crystalline inorganic semiconductors entirely through benchtop, aqueous chemistry and electrochemistry without time- or energy-intensive process steps.

Biomanufacturing process analytical technology (PAT) application for downstream processing: Using dissolved oxygen as an indicator of product quality for a protein refolding reaction.

PubMed

Pizarro, Shelly A; Dinges, Rachel; Adams, Rachel; Sanchez, Ailen; Winter, Charles

2009-10-01

Process analytical technology (PAT) is an initiative from the US FDA combining analytical and statistical tools to improve manufacturing operations and ensure regulatory compliance. This work describes the use of a continuous monitoring system for a protein refolding reaction to provide consistency in product quality and process performance across batches. A small-scale bioreactor (3 L) is used to understand the impact of aeration for refolding recombinant human vascular endothelial growth factor (rhVEGF) in a reducing environment. A reverse-phase HPLC assay is used to assess product quality. The goal in understanding the oxygen needs of the reaction and its impact to quality, is to make a product that is efficiently refolded to its native and active form with minimum oxidative degradation from batch to batch. Because this refolding process is heavily dependent on oxygen, the % dissolved oxygen (DO) profile is explored as a PAT tool to regulate process performance at commercial manufacturing scale. A dynamic gassing out approach using constant mass transfer (k(L)a) is used for scale-up of the aeration parameters to manufacturing scale tanks (2,000 L, 15,000 L). The resulting DO profiles of the refolding reaction show similar trends across scales and these are analyzed using rpHPLC. The desired product quality attributes are then achieved through alternating air and nitrogen sparging triggered by changes in the monitored DO profile. This approach mitigates the impact of differences in equipment or feedstock components between runs, and is directly inline with the key goal of PAT to "actively manage process variability using a knowledge-based approach." (c) 2009 Wiley Periodicals, Inc.

The role of irrigation runoff and winter rainfall on dissolved organic carbon loads in an agricultural watershed

USGS Publications Warehouse

Oh, Neung-Hwan; Pellerin, Brian A.; Bachand, Philip A.M.; Hernes, Peter J.; Bachand, Sandra M.; Ohara, Noriaki; Kavvas, M. Levent; Bergamaschi, Brian A.; Horwath, William R.

2013-01-01

We investigated the role of land use/land cover and agriculture practices on stream dissolved organic carbon (DOC) dynamics in the Willow Slough watershed (WSW) from 2006 to 2008. The 415 km2watershed in the northern Central Valley, California is covered by 31% of native vegetation and the remaining 69% of agricultural fields (primarily alfalfa, tomatoes, and rice). Stream discharge and weekly DOC concentrations were measured at eight nested subwatersheds to estimate the DOC loads and yields (loads/area) using the USGS developed stream load estimation model, LOADEST. Stream DOC concentrations peaked at 18.9 mg L−1 during summer irrigation in the subwatershed with the highest percentage of agricultural land use, demonstrating the strong influence of agricultural activities on summer DOC dynamics. These high concentrations contributed to DOC yields increasing up to 1.29 g m−2 during the 6 month period of intensive agricultural activity. The high DOC yields from the most agricultural subwatershed during the summer irrigation period was similar throughout the study, suggesting that summer DOC loads from irrigation runoff would not change significantly in the absence of major changes in crops or irrigation practices. In contrast, annual DOC yields varied from 0.89 to 1.68 g m−2 yr−1 for the most agricultural watershed due to differences in winter precipitation. This suggests that variability in the annual DOC yields will be largely determined by the winter precipitation, which can vary significantly from year to year. Changes in precipitation patterns and intensities as well as agricultural practices have potential to considerably alter the DOC dynamics.

Assessment of Pollutant Removal Efficiency and Drainage Capacity in Stormwater Biofilters

NASA Astrophysics Data System (ADS)

Carroll, S. J.; Mills, H.; Reagan, A.; Triassi, M.; Bauer, S.; Matiasek, S. J.; Libby, R.; Meddings, C.

2016-12-01

Urban stormwater runoff contributes to flooding and impacts water quality with increased sediment and pollutant loads. Biofilters are vegetated filtration systems designed to mitigate stormwater by enhancing infiltration, sedimentation, contaminant sorption and uptake. Despite the rapid implementation of biofilters as stormwater management solutions, their performance is mainly evaluated in terms of flood reduction while their pollutant removal efficiency is rarely assessed. We investigated the effect of biofilter composition on drainage capacity and individual pollutant removal in test columns. Triplicate columns consisted of layers of pebbles, fine sand, filtration mix (test variable), mulch, lava rock and Santa Barbara sedges. The filtration mix was one of five combinations of coarse sand and local loam soil ranging from 100% sand to 100% soil. Consistent with differences in pore size distribution, hydraulic conductivity values were lowest in 100% soil biofilters (3.0 ± 0.6 mm/h) and highest in the 100% sand biofilters (22.7 ± 4.2 mm/h). A synthetic mixture of nutrients, metals, and salts in proportions representative of stormwater composition was applied to the test columns. Biofilters removed over 98% of dissolved copper, nickel, and zinc, and at least 67% of dissolved lead, even when applying synthetic runoff with metal concentrations three orders of magnitude larger than in actual stormwater. In addition, biofilters oxygenated, neutralized, and decreased the turbidity of stormwater. Ammonium was quantitatively removed from synthetic runoff (97-100%), while nitrate and phosphate were poorly retained (48-64%) or even leached from sand biofilters. This study demonstrated that, while decreasing drainage capacity, adding even a small proportion of native soil to the filtration media significantly increases pollutant removal of biofilters. With proper consideration of the filtration mixture, biofiltration systems can effectively remediate urban stormwater.

Comparison of homeopathic globules prepared from high and ultra-high dilutions of various starting materials by ultraviolet light spectroscopy.

PubMed

Klein, Sabine D; Wolf, Ursula

2016-02-01

Homeopathic globules are commonly used in clinical practice, while research focuses on liquid potencies. Sequential dilution and succussion in their production process has been proposed to change the physico-chemical properties of the solvent(s). It has been reported that aqueous potencies of various starting materials showed significant differences in ultraviolet light transmission compared to controls and between different dilution levels. The aim of the present study was to repeat and expand these experiments to homeopathic globules. Globules were specially produced for this study by Spagyros AG (Gümligen, Switzerland) from 6 starting materials (Aconitum napellus, Atropa belladonna, phosphorus, sulfur, Apis mellifica, quartz) and for 6 dilution levels (6x, 12x, 30c, 200c, 200CF (centesimal discontinuous fluxion), 10,000CF). Native globules and globules impregnated with solvents were used as controls. Globules were dissolved in ultrapure water, and absorbance in the ultraviolet range was measured. The average absorbance from 200 to 340nm was calculated and corrected for differences between measurement days and instrumental drift. Statistically significant differences were found for A. napellus, sulfur, and A. mellifica when normalized average absorbance of the various dilution levels from the same starting material (including control and solvent control globules) was compared. Additionally, absorbance within dilution levels was compared among the various starting materials. Statistically significant differences were found among 30c, 200c and 200CF dilutions. This study has expanded previous findings from aqueous potencies to globules and may indicate that characteristics of aqueous high dilutions may be preserved and detectable in dissolved globules. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Crude oil in a shallow sand and gravel aquifer-II. Organic geochemistry

USGS Publications Warehouse

Eganhouse, R.P.; Baedecker, M.J.; Cozzarelli, I.M.; Aiken, G.R.; Thorn, K.A.; Dorsey, T.F.

1993-01-01

Crude oil spilled from a pipeline break in a remote area of north-central Minnesota has contaminated a shallow glacial outwash aquifer. Part of the oil was sprayed over a large area to the west of the pipeline and part of it accumulated in an oil body that floats at the water table to the east of the point of discharge. Total dissolved organic carbon (TDOC) concentrations in shallow groundwater collected in the oil spray area reach 16 mg/l. This is nearly an order of magnitude higher than the TDOC concentrations of native groundwater (???2-3 mg/l). The additional TDOC derives from the partial degradation of petroleum residues deposited at the land surface and transported to the aquifer by vertical recharge. In the vicinity of the oil body, TDOC concentrations in groundwater are 48 mg/l, 58% of the TDOC being composed of non-volatile organic C. The majority of the volatile DOC (63%) is a mixture of low-molecular-weight saturated, aromatic and alicyclic hydrocarbons derived from the oil. Downgradient from the oil body along the direction of groundwater flow, concentrations of all measured constituents of the TDOC pool decrease. Concentrations begin to decline most rapidly, however, in the zone where dissolved O2 concentrations begin to increase, ???50 m downgradient from the leading edge of the oil. Within the anoxic zone near the oil body, removal rates of isometric monoaromatic hydrocarbons vary widely. This indicates that the removal processes are mediated mainly by microbiological activity. Molecular and spectroscopic characterization of the TDOC and its spatial and temporal variation provide evidence of the importance of biogeochemical processes in attenuating petroleum contaminants in this perturbed subsurface environment. ?? 1993.

Effectiveness of vegetation buffers surrounding playa wetlands at contaminant and sediment amelioration

USGS Publications Warehouse

Haukos, David A.; Johnson, Lacrecia A.; Smith, Loren M.; McMurry, Scott T.

2016-01-01

Playa wetlands, the dominant hydrological feature of the semi-arid U.S. High Plains providing critical ecosystem services, are being lost and degraded due to anthropogenic alterations of the short-grass prairie landscape. The primary process contributing to the loss of playas is filling of the wetland through accumulation of soil eroded and transported by precipitation from surrounding cultivated watersheds. We evaluated effectiveness of vegetative buffers surrounding playas in removing metals, nutrients, and dissolved/suspended sediments from precipitation runoff. Storm water runoff was collected at 10-m intervals in three buffer types (native grass, fallow cropland, and Conservation Reserve Program). Buffer type differed in plant composition, but not in maximum percent removal of contaminants. Within the initial 60 m from a cultivated field, vegetation buffers of all types removed >50% of all measured contaminants, including 83% of total suspended solids (TSS) and 58% of total dissolved solids (TDS). Buffers removed an average of 70% of P and 78% of N to reduce nutrients entering the playa. Mean maximum percent removal for metals ranged from 56% of Na to 87% of Cr. Maximum removal was typically at 50 m of buffer width. Measures of TSS were correlated with all measures of metals and nutrients except for N, which was correlated with TDS. Any buffer type with >80% vegetation cover and 30–60 m in width would maximize contaminant removal from precipitation runoff while ensuring that playas would continue to function hydrologically to provide ecosystem services. Watershed management to minimize erosion and creations of vegetation buffers could be economical and effective conservation tools for playa wetlands.

Long-term performance monitoring for a permeable reactive barrier at the U.S. Coast Guard Support Center, Elizabeth City, North Carolina.

PubMed

Puls, R W; Blowes, D W; Gillham, R W

1999-08-12

A continuous hanging iron wall was installed in June, 1996, at the U. S. Coast Guard (USCG) Support Center near Elizabeth City, NC, United States, to treat overlapping plumes of chromate and chlorinated solvent compounds. The wall was emplaced using a continuous trenching machine whereby native soil and aquifer sediment was removed and the iron simultaneously emplaced in one continuous excavation and fill operation. To date, there have been seven rounds (November 1996, March 1997, June 1997, September 1997, December 1997, March 1998, and June 1998) of performance monitoring of the wall. At this time, this is the only full-scale continuous 'hanging' wall installed as a permeable reactive barrier to remediate both chlorinated solvent compounds and chromate in groundwater. Performance monitoring entails the following: sampling of 10-5 cm PVC compliance wells and 15 multi-level samplers for the following constituents: TCE, cis-dichloroethylene (c-DCE), vinyl chloride, ethane, ethene, acetylene, methane, major anions, metals, Cr(VI), Fe(II), total sulfides, dissolved H(2), Eh, pH, dissolved oxygen, specific conductance, alkalinity, and turbidity. Electrical conductivity profiles have been conducted using a Geoprobe to verify emplacement of the continuous wall as designed and to locate upgradient and downgradient wall interfaces for coring purposes. Coring has been conducted in November, 1996, in June and September, 1997, and March, 1998, to evaluate the rate of corrosion on the iron surfaces, precipitate buildup (particularly at the upgradient interface), and permeability changes due to wall emplacement. In addition to several continuous vertical cores, angled cores through the 0.6-m thick wall have been collected to capture upgradient and downgradient wall interfaces along approximate horizontal flow paths for mineralogic analyses.

(L)-Valine production with minimization of by-products' synthesis in Corynebacterium glutamicum and Brevibacterium flavum.

PubMed

Hou, Xiaohu; Chen, Xinde; Zhang, Yue; Qian, He; Zhang, Weiguo

2012-12-01

Corynebacterium glutamicum ATCC13032 and Brevibacterium flavum JV16 were engineered for L-valine production by over-expressing ilvEBN ( r ) C genes at 31 °C in 72 h fermentation. Different strategies were carried out to reduce the by-products' accumulation in L-valine fermentation and also to increase the availability of precursor for L-valine biosynthesis. The native promoter of ilvA of C. glutamicum was replaced with a weak promoter MPilvA (P-ilvAM1CG) to reduce the biosynthetic rate of L-isoleucine. Effect of different relative dissolved oxygen on L-valine production and by-products' formation was recorded, indicating that 15 % saturation may be the most appropriate relative dissolved oxygen for L-valine fermentation with almost no L-lactic acid and L-glutamate formed. To minimize L-alanine accumulation, alaT and/or avtA was inactivated in C. glutamicum and B. flavum, respectively. Compared to high concentration of L-alanine accumulated by alaT inactivated strains harboring ilvEBN ( r ) C genes, L-alanine concentration was reduced to 0.18 g/L by C. glutamicum ATCC13032MPilvA△avtA pDXW-8-ilvEBN ( r ) C, and 0.22 g/L by B. flavum JV16avtA::Cm pDXW-8-ilvEBN ( r ) C. Meanwhile, L-valine production and conversion efficiency were enhanced to 31.15 g/L and 0.173 g/g by C. glutamicum ATCC13032MPilvA△avtA pDXW-8-ilvEBN ( r ) C, 38.82 g/L and 0.252 g/g by B. flavum JV16avtA::Cm pDXW-8-ilvEBN ( r ) C. This study provides combined strategies to improve L-valine yield by minimization of by-products' production.

[Agricultural land use impacts on aquatic macroinvertebrates in small streams from La Vieja river (Valle del Cauca, Colombia].

PubMed

Giraldo, Lina Paola; Chará, Julián; Zúñiga, Maria del Carmen; Chará-Serna, Ana Marcela; Pedraza, Gloria

2014-04-01

The expansion of the agricultural frontier in Colombia has exerted significant pressure on its aquatic ecosystems during the last few decades. In order to determine the impacts of different agricultural land uses on the biotic and abiotic characteristics of first and second order streams of La Vieja river watershed, we evaluated 21 streams located between 1,060 and 1,534 m asl in the municipalities of Alcalá, Ulloa, and Cartago (Valle del Cauca, Colombia). Seven streams were protected by native vegetation buffers, eight had influence of coffee and plantain crops, and six were influenced by cattle ranching. Habitat conditions, channel dimensions, water quality, and aquatic macroinvertebrates were studied in each stream. Streams draining cattle ranching areas had significantly higher dissolved solids, higher phosphorus, higher alkalinity, higher conductivity, and lower dissolved oxygen than those covered by cropland and forests. Coarse substrates and diversity of flow regimes were significantly higher in cropland and protected streams when compared to streams affected by cattle ranching, whereas the percent of silt and slow currents was significantly higher in the latter. A total of 26,777 macroinvertebrates belonging to 17 orders, 72 families and 95 genera were collected. The most abundant groups were Diptera 62.8%, (Chironomidae 49.6%, Ceratopogonidae 6.7%), Mollusca 18.8% (Hydrobiidae 7.2%, Sphaeriidae 9.6%) and Trichoptera 5.7% (Hydropsychidae 3.7%). The Ephemeroptera, Trichoptera, and Plecoptera orders, known for their low tolerance to habitat perturbation, had high abundance in cropland and forested streams, whereas Diptera and Mollusca were more abundant in those impacted by cattle ranching. Results indicate that streams draining forests and croplands have better physical and biological conditions than those draining pastures, and highlight the need to implement protective measures to restore the latter.

40 CFR 430.40 - Applicability; description of the dissolving sulfite subcategory.

Code of Federal Regulations, 2014 CFR

2014-07-01

... dissolving sulfite subcategory. 430.40 Section 430.40 Protection of Environment ENVIRONMENTAL PROTECTION... SOURCE CATEGORY Dissolving Sulfite Subcategory § 430.40 Applicability; description of the dissolving... production of pulp at dissolving sulfite mills. ...

40 CFR 430.40 - Applicability; description of the dissolving sulfite subcategory.

Code of Federal Regulations, 2012 CFR

2012-07-01

... dissolving sulfite subcategory. 430.40 Section 430.40 Protection of Environment ENVIRONMENTAL PROTECTION... SOURCE CATEGORY Dissolving Sulfite Subcategory § 430.40 Applicability; description of the dissolving... production of pulp at dissolving sulfite mills. ...

40 CFR 430.40 - Applicability; description of the dissolving sulfite subcategory.

Code of Federal Regulations, 2013 CFR

2013-07-01

... dissolving sulfite subcategory. 430.40 Section 430.40 Protection of Environment ENVIRONMENTAL PROTECTION... SOURCE CATEGORY Dissolving Sulfite Subcategory § 430.40 Applicability; description of the dissolving... production of pulp at dissolving sulfite mills. ...

Low cadence interval training at moderate intensity does not improve cycling performance in highly trained veteran cyclists

PubMed Central

Kristoffersen, Morten; Gundersen, Hilde; Leirdal, Stig; Iversen, Vegard V.

2014-01-01

Purpose: The aim of the present study was to investigate effects of low cadence training at moderate intensity on aerobic capacity, cycling performance, gross efficiency, freely chosen cadence, and leg strength in veteran cyclists. Method: Twenty-two well trained veteran cyclists [age: 47 ± 6 years, maximal oxygen consumption (VO2max): 57.9 ± 3.7 ml · kg−1 · min−1] were randomized into two groups, a low cadence training group and a freely chose cadence training group. Respiratory variables, power output, cadence and leg strength were tested before and after a 12 weeks training intervention period. The low cadence training group performed 12 weeks of moderate [73–82% of maximal heart rate (HRmax)] interval training (5 × 6 min) with a cadence of 40 revolutions per min (rpm) two times a week, in addition to their usual training. The freely chosen cadence group added 90 min of training at freely chosen cadence at moderate intensity. Results: No significant effects of the low cadence training on aerobic capacity, cycling performance, power output, cadence, gross efficiency, or leg strength was found. The freely chosen cadence group significantly improved both VO2max (58.9 ± 2.4 vs. 62.2 ± 3.2 ml · kg−1 · min−1), VO2 consumption at lactate threshold (49.4 ± 3.8 vs. 51.8 ± 3.5 ml · kg−1 · min−1) and during the 30 min performance test (52.8 ± 3.0 vs. 54.7 ± 3.5 ml · kg−1 · min−1), and power output at lactate threshold (284 ± 47 vs. 294 ± 48 W) and during the 30 min performance test (284 ± 42 vs. 297 ± 50 W). Moreover, a significant difference was seen when comparing the change in freely chosen cadence from pre- to post between the groups during the 30 min performance test (2.4 ± 5.0 vs. −2.7 ± 6.2). Conclusion: Twelve weeks of low cadence (40 rpm) interval training at moderate intensity (73–82% of HRmax) twice a week does not improve aerobic capacity, cycling performance or leg strength in highly trained veteran cyclists. However, adding training at same intensity (% of HRmax) and duration (90 min weekly) at freely chosen cadence seems beneficial for performance and physiological adaptations. PMID:24550843

Ground-water quality of coastal aquifer systems in the West Coast Basin, Los Angeles County, California, 1999-2002

USGS Publications Warehouse

Land, Michael; Reichard, Eric G.; Crawford, Steven M.; Everett, Rhett; Newhouse, Mark W.; Williams, Colin F.

2004-01-01

The extensive use of ground water throughout the Central and West Coast Basins of Los Angeles County during the first half of the 20th century resulted in declining water levels, widespread seawater intrusion, and deterioration of water quality along most reaches of the coast. In order to control seawater intrusion in the West Coast Basin, freshwater is injected into a series of wells at two seawater barrier projects. In order to better understand the processes of seawater intrusion and the efficiency of current barrier operation, data were collected from multiple-well monitoring sites installed by the U.S. Geological Survey, from local observation wells, and from production wells. The occurrence and areal extent of native, saline, and recently injected ground water near the coast were defined through the collection and analysis of inorganic and isotopic water-quality data and geophysical logs. Most water in the West Coast Basin with a dissolved-solids concentration less than 500 milligrams per liter generally has a sodium-bicarbonate to sodium/calcium-bicarbonate character. Water with a dissolved-solids concentration greater than 1,000 milligrams per liter also contains variable amounts of calcium and sodium, but chloride is predominant. Most of these high-dissolved-solids wells are perforated in the Upper aquifer systems; several have dissolved-chloride values near that of seawater. Elevated chloride concentrations were measured at many wells in both the Upper and Lower aquifer systems inland from the barrier projects. Although water levels have increased in many wells over the last 30 years, some of the wells do not show a corresponding decrease in dissolved chloride. A detailed assessment of saline ground water was provided by examining the ratios of chloride to bromide, iodide, and boron. Seawater-freshwater mixing lines were constructed using all three ratios. These ion ratios also identify water affected by mixing with injected imported water and oil-field brine water. Isotopic data -oxygen-18, deuterium, strontium-87, boron-11, tritium, and carbon-14-also were collected. The stable isotopes oxygen-18 and deuterium were used to distinguish between isotopically heavier water that originated in the Los Angeles Forebay, isotopically lighter water that originated in the Montebello Forebay, local recharge, and water containing a mixture of seawater and imported water. Tritium data were used to identify recent water (less than 50 years old) present in the Upper and Lower aquifer systems inland from the seawater barrier projects, and present locally near the Dominguez Gap. Carbon-14 data indicate that water with uncorrected ages ranging from about 4,000 years to more than 20,000 years before present occurs in the Lower aquifer systems and in the Pico unit. Borehole electromagnetic conductivity logs, combined with gamma-ray logs, were used to identify potential saline zones throughout the entire well depth; this provides an indicator of intrusion in zones that are not being monitored by a piezometer. Temperature logging was used to track the thermal effects of the cooler water used for injection. Specific-conductance logs provided a screening-level indicator of poor-quality water in monitoring wells.

Changes in Extracellular Striatal Acetylcholine and Brain Seizure Activity Following Acute Exposure to Nerve Against in Freely Moving Guinea Pigs

DTIC Science & Technology

2010-01-01

Literature 3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE Changes in extracellular striatal acetylcholine and brain seizure activity following...Acetylcholine, acetylcholinesterase, choline, guinea pig, in vivo microdialysis, nerve agents, organophosphorus compounds, sarin, seizure activity ...RESEARCH ARTICLE Changes in extracellular striatal acetylcholine and brain seizure activity following acute exposure to nerve agents in freely

12 CFR 563b.505 - May my directors, officers, and their associates freely trade shares?

Code of Federal Regulations, 2011 CFR

2011-01-01

... 12 Banks and Banking 5 2011-01-01 2011-01-01 false May my directors, officers, and their associates freely trade shares? 563b.505 Section 563b.505 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY CONVERSIONS FROM MUTUAL TO STOCK FORM Standard Conversions Post-Conversion § 563b.505 May my directors, officers, and their...

12 CFR 563b.505 - May my directors, officers, and their associates freely trade shares?

Code of Federal Regulations, 2012 CFR

2012-01-01

... 12 Banks and Banking 6 2012-01-01 2012-01-01 false May my directors, officers, and their associates freely trade shares? 563b.505 Section 563b.505 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY CONVERSIONS FROM MUTUAL TO STOCK FORM Standard Conversions Post-Conversion § 563b.505 May my directors, officers, and their...

"Freely Ye Have Received, Freely Give" (Matthew 10: 8)--How Giving Away Religious Digital Books Influences the Print Sales of Those Books

ERIC Educational Resources Information Center

Hilton, John, III.

2010-01-01

Lack of access prevents many from benefiting from educational resources. Digital technologies now enable educational resources, such as books, to be openly available to those with access to the Internet. This study examined the financial viability of a religious publisher's putting free digital versions of eight of its books on the Internet. The…

Basalt Weathering, Nutrient Uptake, And Carbon Release By An Exotic And A Native Arizona Grass Species Under Different Temperature Conditions

NASA Astrophysics Data System (ADS)

Gallas, G.; Dontsova, K.; Chorover, J.; Hunt, E.; Ravi, S.

2010-12-01

During this past summer, the National Science Foundation funded a 10-week Research Experience for Undergraduates (REU) program “Environmental and Earth Systems Research at Biosphere 2”. This program provides undergraduates with an opportunity to conduct guided research in environmental and Earth systems science and has resulted in this work. Biosphere 2 allows for the exploration of complex questions in Earth sciences because of its large scale and the precise control allowed over many experimental elements. The goal of this study was to observe plant-mediated weathering of granular basalt under two temperature conditions. Two grass species were studied, one native to Arizona: Tanglehead, Heteropogan contortus, and one exotic to Arizona: Buffelgrass, Pennisetum ciliar. The grasses were grown in pots located in the Desert and the Savannah Biomes in the Biosphere 2 to take advantage of a 4° C temperature difference. Understanding differences in how native and invasive grasses weather soil and take up nutrients may explain the mechanism behind current invasion of Sonoran Desert by exotic species and help predict response of native and invasive vegetation to expected increase in temperatures. Each biome also contained three replicate “control” pots without vegetation, and mixtures of the two grass species to observe possible competition between the species. Three factors were compared in this study: 1. Temperature: the same species of grass under two different temperature conditions 2. Species: Native Arizonan species vs. a species exotic to Arizona 3. Temporal: How the grasses use resources differently as they grow Leachate samples were collected and analyzed for pH, electrical conductivity, total organic carbon, total nitrogen, inorganic carbon by high temperature combustion coupled with infrared gas analysis; F-, Cl-, Br-, NO3-, NO2-, SO42-, and PO43- by ion chromatography; and cations and metals by ICP-MS. The data trends indicate that plants enhanced basalt weathering. All of the leachate samples showed higher pH than the input water, and the pH was elevated in treatments that contained grass. This indicated that in the presence of vegetation there was more proton absorption. The trends in total nitrogen concentrations indicate a dependence on temperature; the same can be said of anion concentrations. Anion leaching is lower at higher temperatures possibly due to greater plant uptake. Both organic and inorganic carbon concentrations were found to be higher in grass treatments than in control treatments. Because both dissolved CO2 and soluble organic exudates encourage mineral dissolution, this could be causative of the weathering enhancements observed. Denudation of nutrient elements differed between plant species and between temperatures, possibly relating to plant uptake and secondary mineral formation. This study gives unique insight into plant-mineral interactions as a function of plant species and temperature that is essential for understanding Earth systems under changing climate.

A freely-moving monkey treadmill model.

PubMed

Foster, Justin D; Nuyujukian, Paul; Freifeld, Oren; Gao, Hua; Walker, Ross; I Ryu, Stephen; H Meng, Teresa; Murmann, Boris; J Black, Michael; Shenoy, Krishna V

2014-08-01

Motor neuroscience and brain-machine interface (BMI) design is based on examining how the brain controls voluntary movement, typically by recording neural activity and behavior from animal models. Recording technologies used with these animal models have traditionally limited the range of behaviors that can be studied, and thus the generality of science and engineering research. We aim to design a freely-moving animal model using neural and behavioral recording technologies that do not constrain movement. We have established a freely-moving rhesus monkey model employing technology that transmits neural activity from an intracortical array using a head-mounted device and records behavior through computer vision using markerless motion capture. We demonstrate the flexibility and utility of this new monkey model, including the first recordings from motor cortex while rhesus monkeys walk quadrupedally on a treadmill. Using this monkey model, we show that multi-unit threshold-crossing neural activity encodes the phase of walking and that the average firing rate of the threshold crossings covaries with the speed of individual steps. On a population level, we find that neural state-space trajectories of walking at different speeds have similar rotational dynamics in some dimensions that evolve at the step rate of walking, yet robustly separate by speed in other state-space dimensions. Freely-moving animal models may allow neuroscientists to examine a wider range of behaviors and can provide a flexible experimental paradigm for examining the neural mechanisms that underlie movement generation across behaviors and environments. For BMIs, freely-moving animal models have the potential to aid prosthetic design by examining how neural encoding changes with posture, environment and other real-world context changes. Understanding this new realm of behavior in more naturalistic settings is essential for overall progress of basic motor neuroscience and for the successful translation of BMIs to people with paralysis.

40 CFR 430.10 - Applicability; description of the dissolving kraft subcategory.

Code of Federal Regulations, 2012 CFR

2012-07-01

... dissolving kraft subcategory. 430.10 Section 430.10 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... CATEGORY Dissolving Kraft Subcategory § 430.10 Applicability; description of the dissolving kraft subcategory. The provisions of this subpart apply to discharges resulting from the production of dissolving...

40 CFR 430.10 - Applicability; description of the dissolving kraft subcategory.

Code of Federal Regulations, 2014 CFR

2014-07-01

... dissolving kraft subcategory. 430.10 Section 430.10 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... CATEGORY Dissolving Kraft Subcategory § 430.10 Applicability; description of the dissolving kraft subcategory. The provisions of this subpart apply to discharges resulting from the production of dissolving...

40 CFR 430.10 - Applicability; description of the dissolving kraft subcategory.

Code of Federal Regulations, 2013 CFR

2013-07-01

... dissolving kraft subcategory. 430.10 Section 430.10 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... CATEGORY Dissolving Kraft Subcategory § 430.10 Applicability; description of the dissolving kraft subcategory. The provisions of this subpart apply to discharges resulting from the production of dissolving...

Dissolved trace elements in a nitrogen-polluted river near to the Liaodong Bay in Northeast China.

PubMed

Bu, Hongmei; Song, Xianfang; Guo, Fen

2017-01-15

Dissolved trace element concentrations (Ba, Fe, Mn, Si, Sr, and Zn) were investigated in the Haicheng River near to the Liaodong Bay in Northeast China during 2010. Dissolved Ba, Fe, Mn, and Sr showed significant spatial variation, whereas dissolved Fe, Mn, and Zn displayed seasonal variations. Conditions such as water temperature, pH, and dissolved oxygen were found to have an important impact on redox reactions involving dissolved Ba, Fe, and Zn. Dissolved Fe and Mn concentrations were regulated by adsorption or desorption of Fe/Mn oxyhydroxides and the effects of organic carbon complexation on dissolved Ba and Sr were found to be significant. The sources of dissolved trace elements were found to be mainly from domestic sewage, industrial waste, agricultural surface runoff, and natural origin, with estimated seasonal and annual river fluxes established as important inputs of dissolved trace elements from the Haicheng River into the Liaodong Bay or Bohai Sea. Copyright © 2016 Elsevier Ltd. All rights reserved.

Between soap bubbles and vesicles: The dynamics of freely floating smectic bubbles

NASA Astrophysics Data System (ADS)

Stannarius, Ralf; May, Kathrin; Harth, Kirsten; Trittel, Torsten

2013-03-01

The dynamics of droplets and bubbles, particularly on microscopic scales, are of considerable importance in biological, environmental, and technical contexts. We introduce freely floating bubbles of smectic liquid crystals and report their unique dynamic properties. Smectic bubbles can be used as simple models for dynamic studies of fluid membranes. In equilibrium, they form minimal surfaces like soap films. However, shape transformations of closed smectic membranes that change the surface area involve the formation and motion of molecular layer dislocations. These processes are slow compared to the capillary wave dynamics, therefore the effective surface tension is zero like in vesicles. Freely floating smectic bubbles are prepared from collapsing catenoid films and their dynamics is studied with optical high-speed imaging. Experiments are performed under normal gravity and in microgravity during parabolic flights. Supported by DLR within grant OASIS-Co.

Compound Wing Vertical Takeoff and Landing Small Unmanned Aircraft System

NASA Technical Reports Server (NTRS)

Logan, Michael J. (Inventor); Motter, Mark A. (Inventor); Deloach, Richard (Inventor); Vranas, Thomas L. (Inventor); Prendergast, Joseph M. (Inventor); Lipp, Brittney N. (Inventor)

2017-01-01

Systems, methods, and devices are provided that enable robust operations of a small unmanned aircraft system (sUAS) using a compound wing. The various embodiments may provide a sUAS with vertical takeoff and landing capability, long endurance, and the capability to operate in adverse environmental conditions. In the various embodiments a sUAS may include a fuselage and a compound wing comprising a fixed portion coupled to the fuselage, a wing lifting portion outboard of the fixed portion comprising a rigid cross member and a controllable articulating portion configured to rotate controllable through a range of motion from a horizontal position to a vertical position, and a freely rotating wing portion outboard of the wing lifting portion and configured to rotate freely based on wind forces incident on the freely rotating wing portion.

Comparison of two freely available software packages for mass spectrometry imaging data analysis using brains from morphine addicted rats.

PubMed

Bodzon-Kulakowska, Anna; Marszalek-Grabska, Marta; Antolak, Anna; Drabik, Anna; Kotlinska, Jolanta H; Suder, Piotr

Data analysis from mass spectrometry imaging (MSI) imaging experiments is a very complex task. Most of the software packages devoted to this purpose are designed by the mass spectrometer manufacturers and, thus, are not freely available. Laboratories developing their own MS-imaging sources usually do not have access to the commercial software, and they must rely on the freely available programs. The most recognized ones are BioMap, developed by Novartis under Interactive Data Language (IDL), and Datacube, developed by the Dutch Foundation for Fundamental Research of Matter (FOM-Amolf). These two systems were used here for the analysis of images received from rat brain tissues subjected to morphine influence and their capabilities were compared in terms of ease of use and the quality of obtained results.

40 CFR 430.10 - Applicability; description of the dissolving kraft subcategory.

Code of Federal Regulations, 2011 CFR

2011-07-01

... dissolving kraft subcategory. 430.10 Section 430.10 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Dissolving Kraft Subcategory § 430.10 Applicability; description of the dissolving kraft subcategory. The provisions of this subpart apply to discharges resulting from the production of dissolving pulp at kraft...

40 CFR 430.10 - Applicability; description of the dissolving kraft subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... dissolving kraft subcategory. 430.10 Section 430.10 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Dissolving Kraft Subcategory § 430.10 Applicability; description of the dissolving kraft subcategory. The provisions of this subpart apply to discharges resulting from the production of dissolving pulp at kraft...

Academic Achievement and Classification of Students from the Freely Associated States in Guam Schools. REL 2017-260

ERIC Educational Resources Information Center

Stewart, Joshua; Stringer, Katie; Arens, Sheila A.; Cicchinelli, Louis F.; San Nicolas, Heidi; Flores, Nieves

2017-01-01

Guam is home to the largest population of migrants from the Freely Associated States (FAS): the Federated States of Micronesia, the Republic of the Marshall Islands, and the Republic of Palau. FAS students made up 22 percent of total student enrollment in Guam public schools in 2012. FAS students face a number of challenges when they enter Guam…

Soil disturbance as a driver of increased stream salinity in a semiarid watershed undergoing energy development

USGS Publications Warehouse

Bern, Carleton R.; Clark, Melanie L.; Schmidt, Travis S.; Holloway, JoAnn M.; Mcdougal, Robert

2015-01-01

Salinization is a global threat to the quality of streams and rivers, but it can have many causes. Oil and gas development were investigated as one of several potential causes of changes in the salinity of Muddy Creek, which drains 2470 km2 of mostly public land in Wyoming, U.S.A. Stream discharge and salinity vary with seasonal snowmelt and define a primary salinity-discharge relationship. Salinity, measured by specific conductance, increased substantially in 2009 and was 53-71% higher at low discharge and 33-34% higher at high discharge for the years 2009-2012 compared to 2005-2008. Short-term processes (e.g., flushing of efflorescent salts) cause within-year deviations from the primary relation but do not obscure the overall increase in salinity. Dissolved elements associated with increased salinity include calcium, magnesium, and sulfate, a composition that points to native soil salts derived from marine shales as a likely source. Potential causes of the salinity increase were evaluated for consistency by using measured patterns in stream chemistry, slope of the salinity-discharge relationship, and inter-annual timing of the salinity increase. Potential causes that were inconsistent with one or more of those criteria included effects from precipitation, evapotranspiration, reservoirs, grazing, irrigation return flow, groundwater discharge, discharge of energy co-produced waters, and stream habitat restoration. In contrast, surface disturbance of naturally salt-rich soil by oil and gas development activities, such as pipeline, road, and well pad construction, is a reasonable candidate for explaining the salinity increase. As development continues to expand in semiarid lands worldwide, the potential for soil disturbance to increase stream salinity should be considered, particularly where soils host substantial quantities of native salts.

Review of the inorganic geochemistry of peats and peatland waters

NASA Astrophysics Data System (ADS)

Shotyk, William

1988-06-01

The major floristic and geochemical differences between bogs, fens, and swamps are summarized, and the most common peat types described. This is followed by a critical, historical review of the literature. The methods used to measure the pH of peatland (mire) waters are examined, and the pH range of various peatland types is reported. In addition, horizontal and vertical pH variations are illustrated, and factors affecting the pH of these waters reviewed. The cause of the low pH of surface waters of Sphagnum bogs (approximately pH 4) is critically investigated, and the relative importance of dissolved CO 2 and other inorganic acids, and organic acids to the low pH is assessed. Cation exchange on the surfaces of Sphagnum mosses is found to be a relatively unimportant acidification mechanism, but important to the chemical ecology of the plants. The redox chemistry of mire waters is described in terms of the geochemistry of such redox indicators as O 2, CO 2, CH 4, CO, H 2, H 2S, SO 42-, native Cu, and siderite (FeCO 3). Published studies of Eh in peatlands are cited, and the problems of Eh measurement and interpretation are explored. The chemical composition of mire waters (major and trace metals, and nonmetallic species) is examined, and factors affecting their composition reported. The abundance and distribution of mineral matter in peats is described, and the occurrence and formation of minerals of Fe (pyrite and other sulphides, siderite, vivianite), Cu (chalcopyrite, native Cu, covellite) and Zn (smithsonite and wurtzite) investigated. The abundance and distribution of major elements (Si, Al, Na, K, Mg, Ca) and trace metals (Ni, V, Cr, Fe, Mn, Cu, U, Zn, Pb) is described, and factors affecting their solubility examined.

Environmental conditions affecting the efficiency and efficacy of piscicides for use in nonnative fish eradication

USGS Publications Warehouse

Brown, Peter James

2010-01-01

Conservation of native fish is a pressing issue for fisheries managers. Conservation efforts often require eliminating threats posed by nonnative fish by eradicating them with piscicides. The piscicides rotenone and antimycin are used for eradication but their application is often inefficient or ineffective. My goal was to increase the efficiency and efficacy of nonnative fish eradication using piscicides. I identified environmental conditions affecting piscicide application, researched methods to overcome these problems, and provided tools that piscicide applicators can use to make piscicide application more efficient and effective. Rotenone and antimycin were exposed to varying levels of sunlight, turbulence, and dissolved organic matter (DOM) to determine the effect these environmental conditions have on piscicides. Bioassay fish were used to determine the toxicity of the piscicides. Sunlight and turbulence affected rotenone and antimycin but DOM did not. Increasing the concentration of chemical can increase the resistance to the effects of these environmental conditions; however, the effects of these conditions are considerable in natural settings. Observations of bioassay fish in stream applications of rotenone were used to develop a statistical model to predict the persistence of the piscicide. The model can be used to predict rotenone persistence in small montane streams and to estimate where rotenone concentrations need to be fortified. I measured the mixing rate of a chemical plume in different channel morphologies and at center or edge applications. Center application had a significantly shorter mixing distance than edge application, but mixing distance was not different among meandering, straight, and riffle/pool morphologies. Application of my findings will increase the efficiency and efficacy of native fish conservation using piscicides.

Diversified cropping systems support greater microbial cycling and retention of carbon and nitrogen

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

King, Alison E.; Hofmockel, Kirsten S.

2017-03-01

Diversifying biologically simple cropping systems often entails altering other management practices, such as tillage regime or nitrogen (N) source. We hypothesized that the interaction of crop rotation, N source, and tillage in diversified cropping systems would promote microbially-mediated soil C and N cycling while attenuating inorganic N pools. We studied a cropping systems trial in its 10th year in Iowa, USA, which tested a 2-yr cropping system of corn (Zea mays L.)/soybean [Glycine max (L.) Merr.] managed with conventional fertilizer N inputs and conservation tillage, a 3-yr cropping system of corn/soybean/small grain + red clover (Trifolium pratense L.), and amore » 4-yr cropping system of corn/soybean/small grain + alfalfa (Medicago sativa L.)/alfalfa. Three year and 4-yr cropping systems were managed with composted manure, reduced N fertilizer inputs, and periodic moldboard ploughing. We assayed soil microbial biomass carbon (MBC) and N (MBN), soil extractable NH4 and NO3, gross proteolytic activity of native soil, and potential activity of six hydrolytic enzymes eight times during the growing season. At the 0-20cm depth, native protease activity in the 4-yr cropping system was greater than in the 2-yr cropping system by a factor of 7.9, whereas dissolved inorganic N pools did not differ between cropping systems (P = 0.292). At the 0-20cm depth, MBC and MBN the 4-yr cropping system exceeded those in the 2-yr cropping system by factors of 1.51 and 1.57. Our findings suggest that diversified crop cropping systems, even when periodically moldboard ploughed, support higher levels of microbial biomass, greater production of bioavailable N from SOM, and a deeper microbially active layer than less diverse cropping systems.« less

Colloid formation in Hanford sediments reacted with simulated tank waste.

PubMed

Mashal, Kholoud; Harsh, James B; Flury, Markus; Felmy, Andrew R; Zhao, Hongting

2004-11-01

Solutions of high pH, ionic strength, and aluminum concentration have leaked into the subsurface from underground waste storage tanks atthe Hanford Reservation in Washington State. Here, we test the hypothesis that these waste solutions alter and dissolve the native minerals present in the sediments and that colloidal (diameter < 2 microm) feldspathoids form. We reacted Hanford sediments with simulated solutions representative of Hanford waste tanks. The solutions consisted of 1.4 or 2.8 mol/kg NaOH, 0.125 or 0.25 mol/kg NaAlO4, and 3.7 mol/kg NaNO3 and were contacted with the sediments for a period of 25 or 40 days at 50 degrees C. The colloidal size fraction was separated from the sediments and characterized in terms of mineralogy, morphology, chemical composition, and electrophoretic mobility. Upon reaction with tank waste solutions, native minerals released Si and other elements into the solution phase. This Si precipitated with the Al present in the waste solutions to form secondary minerals, identified as the feldspathoids cancrinite and sodalite. The solution phase was modeled with the chemical equilibrium model GMIN for solution speciation and saturation indices with respect to sodalite and cancrinite. The amount of colloidal material in the sediments increased upon reaction with waste solutions. At the natural pH found in Hanford sediments (pH 8) the newly formed minerals are negatively charged, similar to the unreacted colloidal material present in the sediments. The formation of colloidal material in Hanford sediments upon reaction with tank waste solutions is an important aspect to consider in the characterization of Hanford tank leaks and may affect the fate of hazardous radionuclides present in the tank waste.

Monitoring and Surveillance of Marine Invasive Species in Californian Waters by DNA Barcoding: Methodological and Analytical Solutions

NASA Astrophysics Data System (ADS)

Campbell, T. L.; Geller, J. B.; Heller, P.; Ruiz, G.; Chang, A.; McCann, L.; Ceballos, L.; Marraffini, M.; Ashton, G.; Larson, K.; Havard, S.; Meagher, K.; Wheelock, M.; Drake, C.; Rhett, G.

2016-02-01

The Ballast Water Management Act, the Marine Invasive Species Act, and the Coastal Ecosystem Protection Act require the California Department of Fish and Wildlife to monitor and evaluate the extent of biological invasions in the state's marine and estuarine waters. This has been performed statewide, using a variety of methodologies. Conventional sample collection and processing is laborious, slow and costly, and may require considerable taxonomic expertise requiring detailed time-consuming microscopic study of multiple specimens. These factors limit the volume of biomass that can be searched for introduced species. New technologies continue to reduce the cost and increase the throughput of genetic analyses, which become efficient alternatives to traditional morphological analysis for identification, monitoring and surveillance of marine invasive species. Using next-generation sequencing of mitochondrial Cytochrome c oxidase subunit I (COI) and nuclear large subunit ribosomal RNA (LSU), we analyzed over 15,000 individual marine invertebrates collected in Californian waters. We have created sequence databases of California native and non-native species to assist in molecular identification and surveillance in North American waters. Metagenetics, the next-generation sequencing of environmental samples with comparison to DNA sequence databases, is a faster and cost-effective alternative to individual sample analysis. We have sequenced from biomass collected from whole settlement plates and plankton in California harbors, and used our introduced species database to create species lists. We can combine these species lists for individual marinas with collected environmental data, such as temperature, salinity, and dissolved oxygen to understand the ecology of marine invasions. Here we discuss high throughput sampling, sequencing, and COASTLINE, our data analysis answer to challenges working with hundreds of millions of sequencing reads from tens of thousands of specimens.

Solubility of gold in oxidized, sulfur-bearing fluids at 500-850 °C and 200-230 MPa: A synthetic fluid inclusion study

NASA Astrophysics Data System (ADS)

Guo, Haihao; Audétat, Andreas; Dolejš, David

2018-02-01

Although Au solubility in magmatic-hydrothermal fluids has been investigated by numerous previous studies, there is a dearth of data on oxidized (log fO2 > FMQ+2.5; FMQ - fayalite-magnetite-quartz buffer), sulfur-bearing fluids such as those that formed porphyry Cu-Au (-Mo) deposits. We performed experiments to constrain the effects of fluid salinity, HCl content, sulfur content, fO2 and temperature on Au solubility in such oxidized, sulfur-bearing fluids. For this purpose, small aliquots of fluids equilibrated with Au metal were trapped at high pressure and temperature in the form of synthetic fluid inclusions in quartz and were subsequently analyzed by LA-ICP-MS. Additionally, Raman spectra were collected from quartz-hosted fluid inclusions at up to 600 °C to help to identify the nature of dissolved gold and sulfur species. Gold solubility was found to be affected most strongly by the HCl content of the fluid, followed by fO2, fluid salinity and temperature. Compared to these factors the sulfur content of the fluid has relatively little influence. At 600 °C and 100 MPa, fluids with geologically realistic HCl contents (∼1.1 wt%) and salinities (7-50 wt% NaClequiv) dissolve ∼1000-3000 ppm Au at oxygen fugacities controlled by the magnetite-hematite buffer. At even more oxidized conditions (three log units above the hematite-magnetite fO2 buffer), HCl-, NaCl- and H2SO4-rich fluids can dissolve up to 5 wt% Au at 800 °C and 200 MPa. The observed Au solubility trends are controlled by HCl0 species in the Na-H-Cl-SO4 fluid and are quantitatively reproduced by existing thermodynamic data for Au-Cl complexes. In all experiments, AuCl0 and AuCl2- species are predicted to occur in comparable although variable concentrations, and account for more than 95% of Au solutes. Natural, high-temperature (>500 °C) brine inclusions from porphyry Cu-Au (-Mo) deposits contain significantly less Au than gold-saturated brines that were synthesized experimentally, implying that the natural brines were Au-undersaturated. Consequently, gold grades in Au-rich porphyries were not controlled by the precipitation of native Au, but rather by factors that caused the precipitation of Au-bearing hydrothermal sulfides such as bornite.

27 CFR 19.455 - Dissolving of denaturants.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Dissolving of denaturants... Denaturation § 19.455 Dissolving of denaturants. Denaturants which are difficult to dissolve in spirits at... may be liquefied or dissolved in a small quantity of spirits or water in advance of their use in the...

40 CFR 430.00 - Applicability.

Code of Federal Regulations, 2012 CFR

2012-07-01

... subcategorization scheme Types of products covered in the subpart A Dissolving Kraft Dissolving pulp at kraft mills... unbleached kraft chemical recovery system (Va). D Dissolving Sulfite Pulp at dissolving sulfite mills for the...

40 CFR 430.00 - Applicability.

Code of Federal Regulations, 2014 CFR

2014-07-01

... subcategorization scheme Types of products covered in the subpart A Dissolving Kraft Dissolving pulp at kraft mills... unbleached kraft chemical recovery system (Va). D Dissolving Sulfite Pulp at dissolving sulfite mills for the...

40 CFR 430.00 - Applicability.

Code of Federal Regulations, 2013 CFR

2013-07-01

... subcategorization scheme Types of products covered in the subpart A Dissolving Kraft Dissolving pulp at kraft mills... unbleached kraft chemical recovery system (Va). D Dissolving Sulfite Pulp at dissolving sulfite mills for the...

Renewable High-Performance Fibers from the Chemical Recycling of Cotton Waste Utilizing an Ionic Liquid.

PubMed

Asaadi, Shirin; Hummel, Michael; Hellsten, Sanna; Härkäsalmi, Tiina; Ma, Yibo; Michud, Anne; Sixta, Herbert

2016-11-23

A new chemical recycling method for waste cotton is presented that allows the production of virgin textile fibers of substantially higher quality than that from the mechanical recycling methods that are used currently. Cotton postconsumer textile wastes were solubilized fully in the cellulose-dissolving ionic liquid 1,5-diazabicyclo[4.3.0]non-5-enium acetate ([DBNH]OAc) to be processed into continuous filaments. As a result of the heterogeneous raw material that had a different molar mass distribution and degree of polymerization, pretreatment to adjust the cellulose degree of polymerization by acid hydrolysis, enzyme hydrolysis, or blending the waste cotton with birch prehydrolyzed kraft pulp was necessary to ensure spinnability. The physical properties of the spun fibers and the effect of the processing parameters on the ultrastructural changes of the fibers were measured. Fibers with a tenacity (tensile strength) of up to 58 cN tex -1 (870 MPa) were prepared, which exceeds that of native cotton and commercial man-made cellulosic fibers. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Performance Evaluation of Integrated Constructed Wetland for Domestic Wastewater Treatment.

PubMed

Sehar, Shama; Naz, Iffat; Khan, Sumera; Naeem, Sana; Perveen, Irum; Ali, Naeem; Ahmed, Safia

2016-03-01

Simple, budget friendly, laboratory-scale integrated constructed wetland (ICW) was designed to assess domestic wastewater treatment performance at a loading rate of 75 mm/d, planted with native plant species: Veronica-angallis aquatica and compared with non-vegetative control system at various residence times of 4, 8, 12, 16, 20, 24, and 28 days. Results revealed that the vegetated ICW demonstrated superior performance over non-vegetated control: 69.12 vs 17.12%, 67.77 vs 16.04%, 68 vs 16.48%, 71.19 vs 6.56%, 71.54 vs 14.80%, and 72.04 vs 11.41% for total dissolved solids, total suspended solids, phosphates (PO4(-)), sulfate (SO4(-)), nitrate (NO3(-)), and nitrite (NO2(-)), respectively, at 20 days residence times. Reduction in bacterial counts (2.79 × 10(4) CFU/mL) and fecal pathogens (345.5 MPN index/100 mL) was observed in V. aquatica at 20 days residence time. Therefore, the present study highlights not only the presence of vegetation but also appropriate residence time in constructed wetlands for better performances.

Putting pharmaceuticals into the wider context of challenges to fish populations in rivers

PubMed Central

Johnson, Andrew C.; Sumpter, John P.

2014-01-01

The natural range of fish species in our rivers is related to flow, elevation, temperature, local habitat and connectivity. For over 2000 years, humans have altered to varying degrees the river habitat. In the past 200 years, we added to the environmental disruption by discharging poorly treated sewage, nutrients and industrial waste into our rivers. For many rivers, the low point arrived during the period of 1950s–1970s, when rapid economic development overrode environmental concerns and dissolved oxygen concentrations dropped to zero. In these more enlightened times, gross river pollution is a thing of the past in the Developed World. However, persistent legacy chemical contaminants can be found in fish long after their discharge ceased. Changes in habitat quality and morphology caused and continue to cause the disappearance of fish species. The range of fish stressors has now increased as temperatures rise, and non-native fish introductions bring new diseases. The threat from pharmaceuticals to fish populations remains hypothetical, and no studies have yet linked change in fish populations to exposure. PMID:25405969

Hypoxia tolerance of two centrarchid sunfishes and an introduced cichlid from karstic Everglades wetlands of southern Florida, U.S.A.

USGS Publications Warehouse

Schofield, P.J.; Loftus, W.F.; Brown, M.E.

2007-01-01

In this study, the hypoxia tolerance of three Everglades fishes, two native centrarchids (Lepomis gulosus and Lepomis marginatus) and a recently introduced cichlid (Hemichromis letourneuxi), were documented. Aquatic surface respiration (ASR) thresholds were lowest for H. letourneuxi, followed by L. gulosus, then L. marginatus. The ASR thresholds for L. marginatus were within ranges reported for small, freshwater tropical fishes, while those for L. gulosus were similar to swamp-adapted fishes. For H. letourneuxi, ASR thresholds were some of the lowest reported. All three species showed excellent tolerance of low dissolved oxygen levels when allowed access to the surface. When denied surface access, L. marginatus lost equilibrium at a higher oxygen tension than the other species. Overall, although all species easily tolerated hypoxia, H. letourneuxi appeared to be best equipped to deal with hypoxia, followed by L. gulosus, then L. marginatus. Hemichromis letourneuxi also exhibited more aggressive behaviours than the centrarchids. These results suggest that hypoxia is not likely to prevent H. letourneuxi from exploiting the seasonally inundated wetlands of south Florida while expanding its range there.

Hydrogen interactions in aluminum-lithium alloys

NASA Technical Reports Server (NTRS)

Smith, S. W.; Scully, J. R.

1991-01-01

A program is described which seeks to develop an understanding of the effects of dissolved and trapped hydrogen on the mechanical properties of selected Al-Li-Cu-X alloys. A proposal is made to distinguish hydrogen (H2) induced EAC from aqueous dissolution controlled EAC, to correlate H2 induced EAC with mobile and trapped concentrations, and to identify significant trap sites and hydride phases (if any) through use of model alloys and phases. A literature review shows three experimental factors which have impeded progress in the area of H2 EAC for this class of alloys. These are as listed: (1) inter-subgranular fracture in Al-Li alloys when tested in the S-T orientation in air or vacuum make it difficult to readily detect H2 induced fracture based on straight forward changes in fractography; (2) the inherently low H2 diffusivity and solubility in Al alloys is further compounded by a native oxide which acts as a H2 permeation barrier; and (3) H2 effects are masked by dissolution assisted processes when mechanical testing is performed in aqueous solutions.

Enzyme-polymer composites with high biocatalytic activity and stability

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

Kim, Jungbae; Kosto, Timothy J.; Manimala, Joseph C.

2004-08-22

We have applied vacuum-spraying and electrospinning to incorporate an enzyme into a polymer matrix, creating a novel and highly active biocatalytic composite. As a unique technical approach, enzymes were co-dissolved in toluene with polymers, and the solvent was then rapidly removed by injecting the mixture into a vacuum chamber or by electrospinning. Subsequent crosslinking of the enzyme with glutaraldehyde resulted in stable entrapped enzyme within the polymeric matrices. For example, an amorphous composite of alpha-chymotrypsin and polyethylene showed no significant loss of enzymatic activity in aqueous buffer for one month. Nanofibers of alpha-chymotrypsin and polystyrene also showed no decrease inmore » activity for more than two weeks. The normalized activity of amorphous composite in organic solvents was 3-13 times higher than that of native alpha-chymotrypsin. The activity of nanofibers was 5-7 times higher than that of amorphous composite in aqueous buffer solution. The composites of alpha-chymotrypsin and polymers demonstrate the feasibility of obtaining a wide variety of active and stable biocatalytic materials with many combinations of enzymes and polymers.« less

VLF Source Localization with a Freely Drifting Sensor Array

DTIC Science & Technology

1992-09-01

Simultaneous Measurement of Infra - sonic Acoustic Particle Velocity and Acoustic Pressure in the Ocean by F-ely Drifting Swallow Floats," IEEEJ. Ocean. Eng., vol...Pacific. Marine Physical Laboratory’s set of nine freely drifting, infrasonic sensors, capable of recording ocean ambient noise in the 1- to 25-Hz range...Terms. 15. Number of Pages, Swallow float, matched-field processing, infrasonic sensor, vlf source localization 153 16. Price Code. 17. Seorlity

Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio)

PubMed Central

Shang, Chunfeng; Yang, Wenbin; Bai, Lu; Du, Jiulin

2017-01-01

The internal brain dynamics that link sensation and action are arguably better studied during natural animal behaviors. Here, we report on a novel volume imaging and 3D tracking technique that monitors whole brain neural activity in freely swimming larval zebrafish (Danio rerio). We demonstrated the capability of our system through functional imaging of neural activity during visually evoked and prey capture behaviors in larval zebrafish. PMID:28930070

"Go Somewhere, Do Something". How Students Responded to the Opportunity to Complete an Unstructured, Five-Day, Wilderness Solo in the Cantabrian Mountains, Northern Spain

ERIC Educational Resources Information Center

Campbell, Liz

2010-01-01

This study explored the response of 28, second year undergraduate students to an innovative approach to a five-day solo. Periods of solitude are more likely to lead to positive outcomes when they are freely chosen than when they are programmed as part of a course. The extent to which a programmed solo can be "freely chosen" by the…

Columnar transmitter based wireless power delivery system for implantable device in freely moving animals.

PubMed

Eom, Kyungsik; Jeong, Joonsoo; Lee, Tae Hyung; Lee, Sung Eun; Jun, Sang Bum; Kim, Sung June

2013-01-01

A wireless power delivery system is developed to deliver electrical power to the neuroprosthetic devices that are implanted into animals freely moving inside the cage. The wireless powering cage is designed for long-term animal experiments without cumbersome wires for power supply or the replacement of batteries. In the present study, we propose a novel wireless power transmission system using resonator-based inductive links to increase power efficiency and to minimize the efficiency variations. A columnar transmitter coil is proposed to provide lateral uniformity of power efficiency. Using this columnar transmitter coil, only 7.2% efficiency fluctuation occurs from the maximum transmission efficiency of 25.9%. A flexible polymer-based planar type receiver coil is fabricated and assembled with a neural stimulator and an electrode. Using the designed columnar transmitter coil, the implantable device successfully operates while it moves freely inside the cage.

Simple Web-based interactive key development software (WEBiKEY) and an example key for Kuruna (Poaceae: Bambusoideae).

PubMed

Attigala, Lakshmi; De Silva, Nuwan I; Clark, Lynn G

2016-04-01

Programs that are user-friendly and freely available for developing Web-based interactive keys are scarce and most of the well-structured applications are relatively expensive. WEBiKEY was developed to enable researchers to easily develop their own Web-based interactive keys with fewer resources. A Web-based multiaccess identification tool (WEBiKEY) was developed that uses freely available Microsoft ASP.NET technologies and an SQL Server database for Windows-based hosting environments. WEBiKEY was tested for its usability with a sample data set, the temperate woody bamboo genus Kuruna (Poaceae). WEBiKEY is freely available to the public and can be used to develop Web-based interactive keys for any group of species. The interactive key we developed for Kuruna using WEBiKEY enables users to visually inspect characteristics of Kuruna and identify an unknown specimen as one of seven possible species in the genus.

Multiple leading edge vortices of unexpected strength in freely flying hawkmoth

PubMed Central

Johansson, L. Christoffer; Engel, Sophia; Kelber, Almut; Heerenbrink, Marco Klein; Hedenström, Anders

2013-01-01

The Leading Edge Vortex (LEV) is a universal mechanism enhancing lift in flying organisms. LEVs, generally illustrated as a single vortex attached to the wing throughout the downstroke, have not been studied quantitatively in freely flying insects. Previous findings are either qualitative or from flappers and tethered insects. We measure the flow above the wing of freely flying hawkmoths and find multiple simultaneous LEVs of varying strength and structure along the wingspan. At the inner wing there is a single, attached LEV, while at mid wing there are multiple LEVs, and towards the wingtip flow separates. At mid wing the LEV circulation is ~40% higher than in the wake, implying that the circulation unrelated to the LEV may reduce lift. The strong and complex LEV suggests relatively high flight power in hawmoths. The variable LEV structure may result in variable force production, influencing flight control in the animals. PMID:24253180

Navier-Stokes hydrodynamics of thermal collapse in a freely cooling granular gas.

PubMed

Kolvin, Itamar; Livne, Eli; Meerson, Baruch

2010-08-01

We show that, in dimension higher than one, heat diffusion and viscosity cannot arrest thermal collapse in a freely evolving dilute granular gas, even in the absence of gravity. Thermal collapse involves a finite-time blowup of the gas density. It was predicted earlier in ideal, Euler hydrodynamics of dilute granular gases in the absence of gravity, and in nonideal, Navier-Stokes granular hydrodynamics in the presence of gravity. We determine, analytically and numerically, the dynamic scaling laws that characterize the gas flow close to collapse. We also investigate bifurcations of a freely evolving dilute granular gas in circular and wedge-shaped containers. Our results imply that, in general, thermal collapse can only be arrested when the gas density becomes comparable with the close-packing density of grains. This provides a natural explanation to the formation of densely packed clusters of particles in a variety of initially dilute granular flows.

Inclusions in freely suspended smectic films

NASA Astrophysics Data System (ADS)

Stannarius, Ralf; Harth, Kirsten

Smectic liquid crystal phases have a unique property: Like soap solutions, they can form stable freely suspended films. Their aspect ratios can be larger than one million to one. Such films can serve as models for two-dimensional (2D) uids, with or without in-plane anisotropy. Solid or liquid inclusions trapped in these films by capillary forces can move in the film plane and interact with other inclusions, with film thickness gradients or the film boundaries, and even with the local orientation field. We describe preparation techniques to incorporate particles or droplets in thin smectic films, and optical observation methods. Several aspects make inclusions in freely suspended films interesting research objects: They provide rich information on capillary forces as well as surface and interfacial tensions, they can serve as platforms for hydrodynamic studies in 2D, and they may help to understand coalescence dynamics at the transition from 2D to 3D...

The meaning of death: some simulations of a model of healthy and unhealthy consumption.

PubMed

Forster, M

2001-07-01

Simulations of a model of healthy and unhealthy consumption are used to investigate the impact of various terminal conditions on life-span, pathways of health-related consumption and health. A model in which life-span and the 'death' stock of health are fixed is compared to versions in which (i) the 'death' stock of health is freely chosen; (ii) life-span is freely chosen; (iii) both the 'death' stock of health and life-span are freely chosen. The choice of terminal conditions has a striking impact on optimal plans. Results are discussed with reference to the existing demand for health literature and illustrate the application of iterative processes to determine optimal life-span, the role played by the marginal value of health capital in determining optimal plans, and the importance of checking the second-order conditions for the optimal choice of life-span.

Freely Chosen Index Finger Tapping Frequency Is Increased in Repeated Bouts of Tapping.

PubMed

Hansen, Ernst Albin; Ebbesen, Brian Duborg; Dalsgaard, Ane; Mora-Jensen, Mark Holten; Rasmussen, Jakob

2015-01-01

Healthy individuals (n = 40) performed index finger tapping at freely chosen frequency during repeated bouts and before and after near-maximal muscle action consisting of 3 intense flexions of the index finger metacarpal phalangeal joint. One experiment showed, unexpectedly, that a bout of tapping increased the tapping frequency in the subsequent bout. Thus, a cumulating increase of 8.2 ± 5.4% (p < .001) occurred across 4 bouts, which were all separated by 10 min rest periods. Follow-up experiments revealed that tapping frequency was still increased in consecutive bouts when rest periods were extended to 20 min. Besides, near-maximal muscle activation, followed by 5 min rest, did not affect the tapping frequency. In conclusion, freely chosen tapping frequency was increased in repeated bouts of tapping, which were separated by 10-20 min rest periods. The observed phenomenon is suggested to be termed repeated bout rate enhancement.

Clustering impact regime with shocks in freely evolving granular gas

NASA Astrophysics Data System (ADS)

Isobe, Masaharu

2017-06-01

A freely cooling granular gas without any external force evolves from the initial homogeneous state to the inhomogeneous clustering state, at which the energy decay deviates from the Haff's law. The asymptotic behavior of energy in the inelastic hard sphere model have been predicted by several theories, which are based on the mode coupling theory or extension of inelastic hard rods gas. In this study, we revisited the clustering regime of freely evolving granular gas via large-scale molecular dynamics simulation with up to 16.7 million inelastic hard disks. We found novel regime regarding on collisions between "clusters" spontaneously appearing after clustering regime, which can only be identified more than a few million particles system. The volumetric dilatation pattern of semicircular shape originated from density shock propagation are well characterized on the appearing of "cluster impact" during the aggregation process of clusters.

A procedure for quantitation of total oxidized uranium for bioremediation studies

USGS Publications Warehouse

Elias, Dwayne A.; Senko, John M.; Krumholz, Lee R.

2003-01-01

A procedure was developed for the quantitation of complexed U(VI) during studies on U(VI) bioremediation. These studies typically involve conversion of soluble or complexed U(VI) (oxidized) to U(IV) (the reduced form which is much less soluble). Since U(VI) freely exchanges between material adsorbed to the solid phase and the dissolved phase, uranium bioremediation experiments require a mass balance of U in both its soluble and adsorbed forms as well as in the reduced sediment bound phase. We set out to optimize a procedure for extraction and quantitation of sediment bound U(VI). Various extractant volumes to sediment ratios were tested and it was found that between 1:1 to 8:1 ratios (v/w) there was a steady increase in U(VI) recovered, but no change with further increases in v/w ratio.Various strengths of NaHCO3, Na-EDTA, and Na-citrate were used to evaluate complexed U(VI) recovery, while the efficiency of a single versus repeated extraction steps was compared with synthesized uranyl-phosphate and uranyl-hydroxide. Total recovery with 1 M NaHCO3 was 95.7% and 97.9% from uranyl-phosphate and uranyl-hydroxide, respectively, compared to 80.7% and 89.9% using 450 mM NaHCO3. Performing the procedure once yielded an efficiency of 81.1% and 92.3% for uranyl-phosphate and uranyl-hydroxide, respectively, as compared to three times. All other extractants yielded 7.9–82.0% in both experiments.

Technical basis for using passive sampling as a biomimetic extraction procedure to assess bioavailability and predict toxicity of petroleum substances.

PubMed

Redman, A D; Butler, J D; Letinski, D J; Di Toro, D M; Leon Paumen, M; Parkerton, T F

2018-05-01

Solid-phase microextraction fibers coated with polydimethylsiloxane (PDMS) provide a convenient passive sampling format to characterize bioavailability of petroleum substances. Hydrocarbons absorb onto PDMS in proportion to both freely dissolved concentrations and partitioning properties of the individual constituents, which parallels the mechanistic basis used to predict aquatic toxicity in the PETROTOX model. When deployed in a non-depletive manner, combining SPME with thermal desorption and quantification using gas chromatography-flame ionization creates a biomimetic extraction (BE) procedure that has the potential to simplify aquatic hazard assessments of petroleum substances since the total moles of all hydrocarbons sorbed to the fiber can be related to toxic thresholds in target lipid of aquatic organisms. The objective of this work is to describe the technical basis for applying BE measurements to predict toxicity of petroleum substances. Critical BE-based PDMS concentrations corresponding to adverse effects were empirically derived from toxicity tests on different petroleum substances with multiple test species. The resulting species sensitivity distribution (SSD) of PDMS effect concentrations was then compared and found consistent with the previously reported target lipid-based SSD. Further, BE data collected on samples of aqueous media dosed with a wide range of petroleum substances were highly correlated to predicted toxic units derived using the PETROTOX model. These findings provide justification for applying BE in environmental hazard and risk evaluations of petroleum substances and related mixtures. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins

PubMed Central

2014-01-01

Background The advent of human genome sequencing project has led to a spurt in the number of protein sequences in the databanks. Success of structure based drug discovery severely hinges on the availability of structures. Despite significant progresses in the area of experimental protein structure determination, the sequence-structure gap is continually widening. Data driven homology based computational methods have proved successful in predicting tertiary structures for sequences sharing medium to high sequence similarities. With dwindling similarities of query sequences, advanced homology/ ab initio hybrid approaches are being explored to solve structure prediction problem. Here we describe Bhageerath-H, a homology/ ab initio hybrid software/server for predicting protein tertiary structures with advancing drug design attempts as one of the goals. Results Bhageerath-H web-server was validated on 75 CASP10 targets which showed TM-scores ≥0.5 in 91% of the cases and Cα RMSDs ≤5Å from the native in 58% of the targets, which is well above the CASP10 water mark. Comparison with some leading servers demonstrated the uniqueness of the hybrid methodology in effectively sampling conformational space, scoring best decoys and refining low resolution models to high and medium resolution. Conclusion Bhageerath-H methodology is web enabled for the scientific community as a freely accessible web server. The methodology is fielded in the on-going CASP11 experiment. PMID:25521245

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.

PubMed

MacLean, Brendan; Tomazela, Daniela M; Shulman, Nicholas; Chambers, Matthew; Finney, Gregory L; Frewen, Barbara; Kern, Randall; Tabb, David L; Liebler, Daniel C; MacCoss, Michael J

2010-04-01

Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.

The YeastGenome app: the Saccharomyces Genome Database at your fingertips.

PubMed

Wong, Edith D; Karra, Kalpana; Hitz, Benjamin C; Hong, Eurie L; Cherry, J Michael

2013-01-01

The Saccharomyces Genome Database (SGD) is a scientific database that provides researchers with high-quality curated data about the genes and gene products of Saccharomyces cerevisiae. To provide instant and easy access to this information on mobile devices, we have developed YeastGenome, a native application for the Apple iPhone and iPad. YeastGenome can be used to quickly find basic information about S. cerevisiae genes and chromosomal features regardless of internet connectivity. With or without network access, you can view basic information and Gene Ontology annotations about a gene of interest by searching gene names and gene descriptions or by browsing the database within the app to find the gene of interest. With internet access, the app provides more detailed information about the gene, including mutant phenotypes, references and protein and genetic interactions, as well as provides hyperlinks to retrieve detailed information by showing SGD pages and views of the genome browser. SGD provides online help describing basic ways to navigate the mobile version of SGD, highlights key features and answers frequently asked questions related to the app. The app is available from iTunes (http://itunes.com/apps/yeastgenome). The YeastGenome app is provided freely as a service to our community, as part of SGD's mission to provide free and open access to all its data and annotations.

ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models.

PubMed

Maghrabi, Ali H A; McGuffin, Liam J

2017-07-03

Methods that reliably estimate the likely similarity between the predicted and native structures of proteins have become essential for driving the acceptance and adoption of three-dimensional protein models by life scientists. ModFOLD6 is the latest version of our leading resource for Estimates of Model Accuracy (EMA), which uses a pioneering hybrid quasi-single model approach. The ModFOLD6 server integrates scores from three pure-single model methods and three quasi-single model methods using a neural network to estimate local quality scores. Additionally, the server provides three options for producing global score estimates, depending on the requirements of the user: (i) ModFOLD6_rank, which is optimized for ranking/selection, (ii) ModFOLD6_cor, which is optimized for correlations of predicted and observed scores and (iii) ModFOLD6 global for balanced performance. The ModFOLD6 methods rank among the top few for EMA, according to independent blind testing by the CASP12 assessors. The ModFOLD6 server is also continuously automatically evaluated as part of the CAMEO project, where significant performance gains have been observed compared to our previous server and other publicly available servers. The ModFOLD6 server is freely available at: http://www.reading.ac.uk/bioinf/ModFOLD/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Effect of Structural Heat Conduction on the Performance of Micro-combustors and Micro-thrusters

DTIC Science & Technology

2005-01-01

numerical models lends credence to the principles underlying the modified Mallard- Le Chatelier theory, the quantitative discrepancy between the analytical...employs reasoning similar to that used by Mallard and Le Chatelier to predict the velocity of a freely propagating flame but extends it to include the...equation (2-1). 19 2.2.1. Adiabatic theory The thermal theory of Mallard and Le Chatelier applies to freely propagating flame that does not

Comparison of Extracellular Striatal Acetylcholine and Brain Seizure Activity Following Acute Exposure to the Nerve Agents Cyclosarin and Tabun in Freely Moving Guinea Pigs

DTIC Science & Technology

2010-01-01

Literature 3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE Comparison of extracellular striatal acetylcholine and brain seizure activity following...lethality; nerve agents; organophosphorus compounds; seizure activity ; tabun 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER...acetylcholine and brain seizure activity following acute exposure to the nerve agents cyclosarin and tabun in freely moving guinea pigs John C

Liquid level sensing device

DOEpatents

Tokarz, Richard D.

1983-01-01

A liquid level sensing device comprising a load cell supporting a column or stack of segments freely resting on one another. The density of each element is substantially identical to that of the surrounding liquid. The elements are freely guided within a surrounding tube. As each element is exposed above the liquid level, its weight will be impressed through the column to the load cell, thereby providing a signal at the load cell directly proportional to the liquid level elevation.

On-line access to geoscience bibliographic citations

USGS Publications Warehouse

Wild, Emily C.

2012-01-01

On-line geoscience bibliographic citations and access points to citations are exponentially increasing as commercial, non-profit, and government agencies worldwide publish materials electronically. On-line bibliographic tools capture cited works, and open access content allows for freely obtained citations and documents. For this newsletter, citations from the numerous journals and books listed in the "Recent Papers" section of the EXPLORE newsletters from 2008-2011 were used to provide freely-accessible web sites to determine the availability of bibliographic information.

Soot Formation in Freely-Propagating Laminar Premixed Flames

NASA Technical Reports Server (NTRS)

Lin, K.-C.; Hassan, M. I.; Faeth, G. M.

1997-01-01

Soot formation within hydrocarbon-fueled flames is an important unresolved problem of combustion science. Thus, the present study is considering soot formation in freely-propagating laminar premixed flames, exploiting the microgravity environment to simplify measurements at the high-pressure conditions of interest for many practical applications. The findings of the investigation are relevant to reducing emissions of soot and continuum radiation from combustion processes, to improving terrestrial and spacecraft fire safety, and to developing methods of computational combustion, among others. Laminar premixed flames are attractive for studying soot formation because they are simple one-dimensional flows that are computationally tractable for detailed numerical simulations. Nevertheless, studying soot-containing burner-stabilized laminar premixed flames is problematical: spatial resolution and residence times are limited at the pressures of interest for practical applications, flame structure is sensitive to minor burner construction details so that experimental reproducibility is not very good, consistent burner behavior over the lengthy test programs needed to measure soot formation properties is hard to achieve, and burners have poor durability. Fortunately, many of these problems are mitigated for soot-containing, freely-propagating laminar premixed flames. The present investigation seeks to extend work in this laboratory for various soot processes in flames by observing soot formation in freely-propagating laminar premixed flames. Measurements are being made at both Normal Gravity (NG) and MicroGravity (MG), using a short-drop free-fall facility to provide MG conditions.

Contemporary Remotely Sensed Data Products Refine Invasive Plants Risk Mapping in Data Poor Regions.

PubMed

Truong, Tuyet T A; Hardy, Giles E St J; Andrew, Margaret E

2017-01-01

Invasive weeds are a serious problem worldwide, threatening biodiversity and damaging economies. Modeling potential distributions of invasive weeds can prioritize locations for monitoring and control efforts, increasing management efficiency. Forecasts of invasion risk at regional to continental scales are enabled by readily available downscaled climate surfaces together with an increasing number of digitized and georeferenced species occurrence records and species distribution modeling techniques. However, predictions at a finer scale and in landscapes with less topographic variation may require predictors that capture biotic processes and local abiotic conditions. Contemporary remote sensing (RS) data can enhance predictions by providing a range of spatial environmental data products at fine scale beyond climatic variables only. In this study, we used the Global Biodiversity Information Facility (GBIF) and empirical maximum entropy (MaxEnt) models to model the potential distributions of 14 invasive plant species across Southeast Asia (SEA), selected from regional and Vietnam's lists of priority weeds. Spatial environmental variables used to map invasion risk included bioclimatic layers and recent representations of global land cover, vegetation productivity (GPP), and soil properties developed from Earth observation data. Results showed that combining climate and RS data reduced predicted areas of suitable habitat compared with models using climate or RS data only, with no loss in model accuracy. However, contributions of RS variables were relatively limited, in part due to uncertainties in the land cover data. We strongly encourage greater adoption of quantitative remotely sensed estimates of ecosystem structure and function for habitat suitability modeling. Through comprehensive maps of overall predicted area and diversity of invasive species, we found that among lifeforms (herb, shrub, and vine), shrub species have higher potential invasion risk in SEA. Native invasive species, which are often overlooked in weed risk assessment, may be as serious a problem as non-native invasive species. Awareness of invasive weeds and their environmental impacts is still nascent in SEA and information is scarce. Freely available global spatial datasets, not least those provided by Earth observation programs, and the results of studies such as this one provide critical information that enables strategic management of environmental threats such as invasive species.

Contemporary Remotely Sensed Data Products Refine Invasive Plants Risk Mapping in Data Poor Regions

PubMed Central

Truong, Tuyet T. A.; Hardy, Giles E. St. J.; Andrew, Margaret E.

2017-01-01

Invasive weeds are a serious problem worldwide, threatening biodiversity and damaging economies. Modeling potential distributions of invasive weeds can prioritize locations for monitoring and control efforts, increasing management efficiency. Forecasts of invasion risk at regional to continental scales are enabled by readily available downscaled climate surfaces together with an increasing number of digitized and georeferenced species occurrence records and species distribution modeling techniques. However, predictions at a finer scale and in landscapes with less topographic variation may require predictors that capture biotic processes and local abiotic conditions. Contemporary remote sensing (RS) data can enhance predictions by providing a range of spatial environmental data products at fine scale beyond climatic variables only. In this study, we used the Global Biodiversity Information Facility (GBIF) and empirical maximum entropy (MaxEnt) models to model the potential distributions of 14 invasive plant species across Southeast Asia (SEA), selected from regional and Vietnam’s lists of priority weeds. Spatial environmental variables used to map invasion risk included bioclimatic layers and recent representations of global land cover, vegetation productivity (GPP), and soil properties developed from Earth observation data. Results showed that combining climate and RS data reduced predicted areas of suitable habitat compared with models using climate or RS data only, with no loss in model accuracy. However, contributions of RS variables were relatively limited, in part due to uncertainties in the land cover data. We strongly encourage greater adoption of quantitative remotely sensed estimates of ecosystem structure and function for habitat suitability modeling. Through comprehensive maps of overall predicted area and diversity of invasive species, we found that among lifeforms (herb, shrub, and vine), shrub species have higher potential invasion risk in SEA. Native invasive species, which are often overlooked in weed risk assessment, may be as serious a problem as non-native invasive species. Awareness of invasive weeds and their environmental impacts is still nascent in SEA and information is scarce. Freely available global spatial datasets, not least those provided by Earth observation programs, and the results of studies such as this one provide critical information that enables strategic management of environmental threats such as invasive species. PMID:28555147

Dissolved-solids loads discharged from irrigated areas near Manila, Utah, May 2007-October 2012, and relation of loads to selected variables

USGS Publications Warehouse

Thiros, Susan A.; Gerner, Steven J.

2015-01-01

Irrigation improvements began to be implemented in 2007 to reduce dissolved-solids loads discharged from the MWSP area. The theoretical annual net dissolved-solids load where the cumulative NRCS calculated dissolved-solids load reduction is added to the net MWSP dissolved-solids load is what would be expected if there was no irrigation improvement in the area associated with the MWSP. The theoretical data points lie very near the baseline representing the pre-MWSP dissolved-solids load to canal streamflow relation. The proximity of the theoretical data points to the baseline shows that the NRCS calculations of reduction in dissolved-solids load are generally supported by the data collected during this study.

Dissolved-solids transport in surface water of the Muddy Creek Basin, Utah

USGS Publications Warehouse

Gerner, Steven J.

2008-01-01

Muddy Creek is located in the southeastern part of central Utah and is a tributary of the Dirty Devil River, which, in turn, is a tributary of the Colorado River. Dissolved solids transported from the Muddy Creek Basin may be stored in the lower Dirty Devil River Basin, but are eventually discharged to the Colorado River and impact downstream water users. This study used selected dissolved-solids measurements made by various local, State, and Federal agencies from the 1970s through 2006, and additional dissolved-solids data that were collected by the U.S. Geological Survey during April 2004 through November 2006, to compute dissolved-solids loads, determine the distribution of dissolved-solids concentrations, and identify trends in dissolved-solids concentration in surface water of the Muddy Creek Basin. The dissolved-solids concentration values measured in water samples collected from Muddy Creek during April 2004 through October 2006 ranged from 385 milligrams per liter (mg/L) to 5,950 mg/L. The highest dissolved-solids concentration values measured in the study area were in water samples collected at sites in South Salt Wash (27,000 mg/L) and Salt Wash (4,940 to 6,780 mg/L). The mean annual dissolved-solids load in Muddy Creek for the periods October 1976 to September 1980 and October 2005 to September 2006 was smallest at a site near the headwaters (9,670 tons per year [tons/yr]) and largest at a site at the mouth (68,700 tons/yr). For this period, the mean annual yield of dissolved solids from the Muddy Creek Basin was 44 tons per square mile. During October 2005 to September 2006, direct runoff transported as much as 45 percent of the annual dissolved-solids load at the mouth of Muddy Creek. A storm that occurred during October 5?7, 2006 resulted in a peak streamflow at the mouth of Muddy Creek of 7,150 cubic feet per second (ft3/s) and the transport of an estimated 35,000 tons of dissolved solids, which is about 51 percent of the average annual dissolved-solids load at the mouth of Muddy Creek. A significant downward trend in dissolved-solids concentrations from 1973 to 2006 was determined for Muddy Creek at a site just downstream of that portion of the basin containing agricultural land. Dissolved-solids concentrations decreased about 2.1 percent per year; however, the rate of change was a decrease of 1.8 percent per year when dissolved-solids concentrations were adjusted for flow.

Mobility of nutrients and trace metals during weathering in the late Archean

NASA Astrophysics Data System (ADS)

Hao, Jihua; Sverjensky, Dimitri A.; Hazen, Robert M.

2017-08-01

The evolution of the geosphere and biosphere depends on the availability of bio-essential nutrients and trace metals. Consequently, the chemical and isotopic variability of trace elements in the sedimentary record have been widely used to infer the existence of early life and fluctuations in the near-surface environment on the early Earth, particularly fluctuations in the redox state of the atmosphere. In this study, we applied late Archean weathering models (Hao et al., 2017), developed to estimate the behavior of major elements and the composition of late Archean world average river water, to explore the behavior of nutrient and trace metals and their potential for riverine transport. We focused on P, Mn, Cr, and Cu during the weathering of olivine basalt. In our standard late Archean weathering model (pCO2,g = 10-1.5 bars, pH2,g = 10-5.0 bars), crustal apatite was totally dissolved by the acidic rainwater during weathering. Our model quantitatively links the pCO2,g of the atmosphere to phosphate levels transported by rivers. The development of late Archean river water (pH = 6.4) resulted in riverine phosphate of at least 1.7 μmolar, much higher than at the present-day. At the end of the early Proterozoic snowball Earth event when pCO2,g could be 0.01-0.10 bars, river water may have transported up to 70 μmolar phosphate, depending on the availability of apatite, thereby stimulating high levels of oxygenic photosynthesis in the marine environment. Crustal levels of Mn in olivine dissolved completely during weathering, except at large extents of weathering where Mn was stored as a component of a secondary carbonate mineral. The corresponding Mn content of river water, about 1.2 μmolar, is higher than in modern river water. Whiffs of 10-5 mole O2 gas or HNO3 kg-1 H2O resulted in the formation of pyrolusite (MnO2) and abundant hematite and simultaneous dramatic decreases in the concentration of Mn(II) in the river water. Chromite dissolution resulted in negligible dissolved Cr in Archean river water. However, amorphous Cr(OH)3 representing easily-weatherable Cr-bearing minerals dissolved totally during the weathering simulations, resulting in concentrations of Cr(III) in the river water of up to 0.14 μmolar, higher than at the present-day. Late Archean weathering of accessory chalcopyrite produced chalcocite and bornite, and extremely low concentrations of Cu (<10-15 molar) because of the low solubilities of the copper sulfides. However, pulses of either O2,g or HNO3 produced native copper, chalcocite, and bornite, much more hematite, and river water containing levels of dissolved Cu comparable to the present-day. Copper mineralogy predicted by weathering models might provide a new correlation with evidence from studies of copper mineral evolution. Overall, our results implied that the redox state of the atmosphere, the pH of surface waters, and the availability of easily-weatherable minerals are all important factors controlling the dissolution of trace elements in river water. Interpretation of the sedimentary signatures of trace elements should consider not only the redox state but also the pH and availability of accessory minerals.

Knowledge and understanding of dissolved solids in the Rio Grande–San Acacia, New Mexico, to Fort Quitman, Texas, and plan for future studies and monitoring

USGS Publications Warehouse

Moyer, Douglas; Anderholm, Scott K.; Hogan, James F.; Phillips, Fred M.; Hibbs, Barry J.; Witcher, James C.; Matherne, Anne Marie; Falk, Sarah E.

2013-01-01

-Focused Hydrogeology Studies at Inflow Sources: Map dissolved-solids concentrations in the Rio Grande and underlying alluvial aquifer; perform hydrogeologic characterization of subsurface areas containing unusually high concentrations of dissolved solids. -Modeling of Dissolved Solids: Develop models to simulate the transport and storage of dissolved solids in both surface-water and groundwater systems.

Predicting the Fate and Effects of Resuspended Metal Contaminated Sediments

DTIC Science & Technology

2015-12-23

force on the sediment. Over the course of the experiment, dissolved and particulate metal concentrations, dissolved oxygen , temperature , turbidity, pH...dissolved oxygen , and temperature . A 16-hour multiple resuspension was also implemented in the SeFEC, intended to replicate intermittent ship traffic...was sampled at the end of hours 4, 8, 12, and 16. Samples were analyzed for: dissolved metals, pH, dissolved oxygen , and temperature (three

Total dissolved gas, barometric pressure, and water temperature data, lower Columbia River, Oregon and Washington, 1996

USGS Publications Warehouse

Tanner, Dwight Q.; Harrison, Howard E.; McKenzie, Stuart W.

1996-01-01

Increased levels of total dissolved gas pressure can cause gas-bubble trauma in fish downstream from dams on the Columbia River. In cooperation with the U.S. Army Corps of Engineers, the U.S. Geological Survey collected data on total dissolved gas pressure, barometric pressure, water temperature, and dissolved oxygen pressure at 11 stations on the lower Columbia River from the John Day forebay (river mile 215.6) to Wauna Mill (river mile 41.9) from March to September 1996. Methods of data collection, review, and processing are described in this report. Summaries of daily minimum, maximum, and mean hourly values are presented for total dissolved gas pressure, barometric pressure, and water temperature. Hourly values for these parameters are presented graphically. Dissolved oxygen data are not presented in this report because the quality-control data show that the data have poor precision and high bias. Suggested changes to monitoring procedures for future studies include (1) improved calibration procedures for total dissolved gas and dissolved oxygen to better define accuracy at elevated levels of supersaturation and (2) equipping dissolved oxygen sensors with stirrers because river velocities at the shoreline monitoring stations probably cannot maintain an adequate flow of water across the membrane surface of the dissolved oxygen sensor.

A freely-moving monkey treadmill model

NASA Astrophysics Data System (ADS)

Foster, Justin D.; Nuyujukian, Paul; Freifeld, Oren; Gao, Hua; Walker, Ross; Ryu, Stephen I.; Meng, Teresa H.; Murmann, Boris; Black, Michael J.; Shenoy, Krishna V.

2014-08-01

Objective. Motor neuroscience and brain-machine interface (BMI) design is based on examining how the brain controls voluntary movement, typically by recording neural activity and behavior from animal models. Recording technologies used with these animal models have traditionally limited the range of behaviors that can be studied, and thus the generality of science and engineering research. We aim to design a freely-moving animal model using neural and behavioral recording technologies that do not constrain movement. Approach. We have established a freely-moving rhesus monkey model employing technology that transmits neural activity from an intracortical array using a head-mounted device and records behavior through computer vision using markerless motion capture. We demonstrate the flexibility and utility of this new monkey model, including the first recordings from motor cortex while rhesus monkeys walk quadrupedally on a treadmill. Main results. Using this monkey model, we show that multi-unit threshold-crossing neural activity encodes the phase of walking and that the average firing rate of the threshold crossings covaries with the speed of individual steps. On a population level, we find that neural state-space trajectories of walking at different speeds have similar rotational dynamics in some dimensions that evolve at the step rate of walking, yet robustly separate by speed in other state-space dimensions. Significance. Freely-moving animal models may allow neuroscientists to examine a wider range of behaviors and can provide a flexible experimental paradigm for examining the neural mechanisms that underlie movement generation across behaviors and environments. For BMIs, freely-moving animal models have the potential to aid prosthetic design by examining how neural encoding changes with posture, environment and other real-world context changes. Understanding this new realm of behavior in more naturalistic settings is essential for overall progress of basic motor neuroscience and for the successful translation of BMIs to people with paralysis.

Improved marathon performance by in-race nutritional strategy intervention.

PubMed

Hansen, Ernst Albin; Emanuelsen, Anders; Gertsen, Robert Mørkegaard; Sørensen S, S R

2014-12-01

It was tested whether a marathon was completed faster by applying a scientifically based rather than a freely chosen nutritional strategy. Furthermore, gastrointestinal symptoms were evaluated. Nonelite runners performed a 10 km time trial 7 weeks before Copenhagen Marathon 2013 for estimation of running ability. Based on the time, runners were divided into two similar groups that eventually should perform the marathon by applying the two nutritional strategies. Matched pairs design was applied. Before the marathon, runners were paired based on their prerace running ability. Runners applying the freely chosen nutritional strategy (n = 14; 33.6 ± 9.6 years; 1.83 ± 0.09 m; 77.4 ± 10.6 kg; 45:40 ± 4:32 min for 10 km) could freely choose their in-race intake. Runners applying the scientifically based nutritional strategy (n = 14; 41.9 ± 7.6 years; 1.79 ± 0.11 m; 74.6 ± 14.5 kg; 45:44 ± 4:37 min) were targeting a combined in-race intake of energy gels and water, where the total intake amounted to approximately 0.750 L water, 60 g maltodextrin and glucose, 0.06 g sodium, and 0.09 g caffeine per hr. Gastrointestinal symptoms were assessed by a self-administered postrace questionnaire. Marathon time was 3:49:26 ± 0:25:05 and 3:38:31 ± 0:24:54 hr for runners applying the freely chosen and the scientifically based strategy, respectively (p = .010, effect size=-0.43). Certain runners experienced diverse serious gastrointestinal symptoms, but overall, symptoms were low and not different between groups (p > .05). In conclusion, nonelite runners completed a marathon on average 10:55 min, corresponding to 4.7%, faster by applying a scientifically based rather than a freely chosen nutritional strategy. Furthermore, average values of gastrointestinal symptoms were low and not different between groups.

Modelling of PCB trophic transfer in the Gulf of Lions; 3D coupled model application

NASA Astrophysics Data System (ADS)

Alekseenko, Elena; Thouvenin, Benedicte; Tronczynsky, Jacek; Carlotti, Francois; Garreau, Pierre; Tixier, Celine; Baklouti, Melika

2017-04-01

This work aims at assessing the role of plankton in the transfer of PCBs to higher trophic levels in the Gulf of Lions (NW Mediterranean Sea) using a 3D modelling approach, which is coupling biogeochemical and hydrodynamical processes and taking into account the physical-chemical properties of PCBs. Transport of various PCB species were simulated during one year: total dissolved, freely dissolved, particulate, biosorbed on plankton, assimilated by zooplankton. PCB budgets and fluxes into the Gulf of Lions between various species were governed by different processes, such as: adsorption/desorption, bacteria and plankton mortality, zooplankton excretion, grazing, mineralization, volatilization and biodegradation. CB153 (2,2',4,4',5,5' hexachlorobiphényle) congener have been considered in the model, since it presents a large amount of PCB among the other congeners in the environment of the Gulf of Lions. At first, the simulated PCBs distributions within particulate matter and plankton were compared with available in-situ measurements (COSTAS and Merlumed field campaigns) performed in the Gulf of Lions. Two size classes of plankton X (60μ m

VLF Source Localization with a Freely Drifting Acoustic Sensor Array

DTIC Science & Technology

1992-09-01

A,’. vol. 89, no. 3, pp. 1134-1158, March 1991. D’Spain, G. L., W. S. Hodgkiss, and G. L. Edmonds, "The Simultaneous Measurement of Infra - sonic ...RESULTS Marine Physical Laboratory’s set of nine freely drifting, infrasonic sensors, capable of record- ing ocean ambient noise in the I- to 25-Hz range...provide thc ship’s thrust, are a well-known contributor to the infrasonic sound field [Ross, 1976; D’Spain et. al., 1991]. The Swallow float deployment

Numerical simulation of h-adaptive immersed boundary method for freely falling disks

NASA Astrophysics Data System (ADS)

Zhang, Pan; Xia, Zhenhua; Cai, Qingdong

2018-05-01

In this work, a freely falling disk with aspect ratio 1/10 is directly simulated by using an adaptive numerical model implemented on a parallel computation framework JASMIN. The adaptive numerical model is a combination of the h-adaptive mesh refinement technique and the implicit immersed boundary method (IBM). Our numerical results agree well with the experimental results in all of the six degrees of freedom of the disk. Furthermore, very similar vortex structures observed in the experiment were also obtained.

Freely Suspended Nematic Films

NASA Astrophysics Data System (ADS)

Iglesias, Wilder; Choi, Jeffrey; Mann, Elizabeth K.; Jakli, Antal

2011-03-01

Using one of the most commonly studied synthetic molecule, 4-Cyano-4'-pentylbiphenyl (5CB), we were able to pull freely suspended membranes of different thicknesses into circular frames of up to 20mm diameter. Films pulled this way were distorted using a speaker, while a laser light was shone onto them for studying the far field reflection and learn about resonant frequency modes and subtract valuable information about the viscoelastic terms that hold the membrane stable. This work was supported by NFS, grant 0907055.

Surface Enhanced Raman Scattering Monitoring of Chain Alignment in Freely Suspended Nanomembranes

NASA Astrophysics Data System (ADS)

Jiang, Chaoyang; Lio, Wilber Y.; Tsukruk, Vladimir V.

2005-09-01

The molecular chain reorganization in freely standing membranes with encapsulated gold nanoparticles was studied with surface enhanced Raman scattering (SERS) in the course of their elastic deformations. The efficient SERS was enabled by optimizing the design of gold nanoparticle forming chainlike aggregates, thus creating an exceptional ability to conduct in situ monitoring. Small deformations resulted in the radial orientation of side phenyl rings of polymer backbones while larger deflections led to the polymer chains bridging adjacent nanoparticles within one-dimensional aggregates.

Method to Estimate the Dissolved Air Content in Hydraulic Fluid

NASA Technical Reports Server (NTRS)

Hauser, Daniel M.

2011-01-01

In order to verify the air content in hydraulic fluid, an instrument was needed to measure the dissolved air content before the fluid was loaded into the system. The instrument also needed to measure the dissolved air content in situ and in real time during the de-aeration process. The current methods used to measure the dissolved air content require the fluid to be drawn from the hydraulic system, and additional offline laboratory processing time is involved. During laboratory processing, there is a potential for contamination to occur, especially when subsaturated fluid is to be analyzed. A new method measures the amount of dissolved air in hydraulic fluid through the use of a dissolved oxygen meter. The device measures the dissolved air content through an in situ, real-time process that requires no additional offline laboratory processing time. The method utilizes an instrument that measures the partial pressure of oxygen in the hydraulic fluid. By using a standardized calculation procedure that relates the oxygen partial pressure to the volume of dissolved air in solution, the dissolved air content is estimated. The technique employs luminescent quenching technology to determine the partial pressure of oxygen in the hydraulic fluid. An estimated Henry s law coefficient for oxygen and nitrogen in hydraulic fluid is calculated using a standard method to estimate the solubility of gases in lubricants. The amount of dissolved oxygen in the hydraulic fluid is estimated using the Henry s solubility coefficient and the measured partial pressure of oxygen in solution. The amount of dissolved nitrogen that is in solution is estimated by assuming that the ratio of dissolved nitrogen to dissolved oxygen is equal to the ratio of the gas solubility of nitrogen to oxygen at atmospheric pressure and temperature. The technique was performed at atmospheric pressure and room temperature. The technique could be theoretically carried out at higher pressures and elevated temperatures.

Analysis of maximum allowable fragment heights during dissolution of high flux isotope reactor fuel in an h-canyon dissolver

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

Daniel, G.; Rudisill, T.

2017-07-17

As part of the Spent Nuclear Fuel (SNF) processing campaign, H-Canyon is planning to begin dissolving High Flux Isotope Reactor (HFIR) fuel in late FY17 or early FY18. Each HFIR fuel core contains inner and outer fuel elements which were fabricated from uranium oxide (U 3O 8) dispersed in a continuous Al phase using traditional powder metallurgy techniques. Fuels fabricated in this manner, like other SNF’s processed in H-Canyon, dissolve by the same general mechanisms with similar gas generation rates and the production of H 2. The HFIR fuel cores will be dissolved using a flowsheet developed by the Savannahmore » River National Laboratory (SRNL) in either the 6.4D or 6.1D dissolver using a unique insert. Multiple cores will be charged to the same dissolver solution maximizing the concentration of dissolved Al. The recovered U will be down-blended into low-enriched U for subsequent use as commercial reactor fuel. During the development of the HFIR fuel dissolution flowsheet, the cycle time for the initial core was estimated at 28 to 40 h. Once the cycle is complete, H-Canyon personnel will open the dissolver and probe the HFIR insert wells to determine the height of any fuel fragments which did not dissolve. Before the next core can be charged to the dissolver, an analysis of the potential for H 2 gas generation must show that the combined surface area of the fuel fragments and the subsequent core will not generate H 2 concentrations in the dissolver offgas which exceeds 60% of the lower flammability limit (LFL) of H 2 at 200 °C. The objective of this study is to identify the maximum fuel fragment height as a function of the Al concentration in the dissolving solution which will provide criteria for charging successive HFIR cores to an H-Canyon dissolver.« less

Application and evaluation of scale dissolver treatments

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

Fielder, G.D.

1994-12-31

In order to provide an improved basis for the design of barium sulfate scale dissolver treatments both laboratory testing and monitoring of field applications were carried out. The deleterious effects of mixing produced water with dissolver prior to contacting scale are shown. Increasing total dissolved solids (TDS) levels can reduce dissolution depending upon temperature. Precomplexation with divalent cations reduces the capacity of the dissolver to solubilize solid scales. Magnesium may adversely affect dissolver performance at elevated temperatures. Several oil and gas wells were closely monitored during initial flowback after treatment. Samples were collected on a frequent basis and analyzed formore » pH, dissolver content, chlorides and various cations. The resulting data were used to construct flowback profiles for evaluation of the treatments. Evidence of scale dissolution is presented. The presence of an incompatible flush brine was discovered in one case and possible reverse order of addition of preflush and dissolver in another. The importance of establishing and following treatment procedures is briefly discussed.« less

Theoretical technique for predicting the cumulative impact of iron and manganese oxidation in streams receiving discharge from coal mines

USGS Publications Warehouse

Bobay, Keith E.

1986-01-01

Two U.S. Geological Survey computer programs are modified and linked to predict the cumulative impact of iron and manganese oxidation in coal-mine discharge water on the dissolved chemical quality of a receiving stream. The coupled programs calculate the changes in dissolved iron, dissolved manganese, and dissolved oxygen concentrations; alkalinity; and, pH of surface water downstream from the point of discharge. First, the one-dimensional, stead-state stream, water quality program uses a dissolved oxygen model to calculate the changes in concentration of elements as a function of the chemical reaction rates and time-of-travel. Second, a program (PHREEQE) combining pH, reduction-oxidation potential, and equilibrium equations uses an aqueous-ion association model to determine the saturation indices and to calculate pH; it then mixes the discharge with a receiving stream. The kinetic processes of the first program dominate the system, whereas the equilibrium thermodynamics of the second define the limits of the reactions. A comprehensive test of the technique was not possible because a complete set of data was unavailable. However, the cumulative impact of representative discharges from several coal mines on stream quality in a small watershed in southwestern Indiana was simulated to illustrate the operation of the technique and to determine its sensitivity to changes in physical, chemical, and kinetic parameters. Mine discharges averaged 2 cu ft/sec, with a pH of 6.0, and concentrations of 7.0 mg/L dissolved iron, 4.0 mg/L dissolved manganese, and 8.08 mg/L dissolved oxygen. The receiving stream discharge was 2 cu ft/sec, with a pH of 7.0, and concentrations of 0.1 mg/L dissolved iron, 0.1 mg/L dissolved manganese, and 8.70 mg/L dissolved oxygen. Results of the simulations indicated the following cumulative impact on the receiving stream from five discharges as compared with the effect from one discharge: 0.30 unit decrease in pH, 1.82 mg/L increase in dissolved iron, 1.50 mg/L increase in dissolved manganese, and 0.24 mg/L decrease in dissolved oxygen concentration.

Controls on suspended sediment, particulate and dissolved organic carbon export from two adjacent catchments with contrasting land-uses, Exmoor UK.

NASA Astrophysics Data System (ADS)

Glendell, M.; Brazier, R. E.

2012-04-01

The fluvial export of total organic carbon (particulate and dissolved) plays an important role in the transportation of organic carbon from terrestrial to aquatic ecosystems, with implications for the understanding of the global carbon cycle and calculations of regional carbon budgets. The terrestrial biosphere contains large amounts of stored carbon in the soil and vegetation, thus a small change in the terrestrial carbon pool may have significant implications for atmospheric CO2 concentrations. Since the onset of agriculture, human activities have accelerated soil erosion rates 10- to 100- fold above all estimated natural background levels, especially in the uplands and at lower latitudes, whilst increasing DOC concentrations over the past decades have been reported in rivers across Western Europe and North America, raising concerns about potential destabilisation of the terrestrial soil carbon pool. The increased input of fine sediment and organic carbon into aquatic environments is also an important factor in stream water quality, being responsible for direct ecological effects as well as transport of a range of contaminants. Many factors, such as topography, hydrological regime and vegetation are known to influence the fluvial export of carbon from catchments. However, most work to date has focused on DOC losses from either forested or peaty catchments, with only limited studies examining the controls and rates of TOC (dissolved and particulate) fluxes from agricultural catchments, particularly during flood events. This research aims to: • Quantify the fluxes of total suspended sediment, total dissolved and total particulate carbon in two adjacent catchments with contrasting land-uses and • Examine the controlling factors of total fluvial carbon fluxes in a semi-natural and agricultural catchment in order to assess the impact of agricultural land-use on fluvial carbon export. The two contrasting study catchments (the Aller and Horner), in south-west England, cover 50km2 and comprise a lower lying agricultural sub-catchment and an upland sub-catchment with extensive native woodland and heather moorland. 24 months of monitoring characterised the water quality status in both catchments, including TSS, POC and DOC in both baseflow and stormflow conditions. Results indicate that the agricultural catchment exports higher TSS and TOC concentrations, instantaneous loads and total loads on a storm-by-storm basis, though these exports are short-lived as the catchment is hydrologically very responsive. The upland/woodland catchment displays more attenuated behaviour, with longer response times and longer duration events. In addition to flux data, geospatial sampling at >200 locations across each catchment characterised the carbon and nitrogen content and bulk density of the soils across four land-use categories. Analysis of these data suggests a strong relationship between TSS and TOC loads during stormflow and the spatial distribution of contributing source areas of soil with high carbon content, erodibility and land-use controls such as soil compaction within the two study catchments.

Water quality and processes affecting dissolved oxygen concentrations in the Blackwater River, Canaan Valley, West Virginia

USGS Publications Warehouse

Waldron, M.C.; Wiley, J.B.

1996-01-01

The water quality and environmental processes affecting dissolved oxygen were determined for the Blackwater River in Canaan Valley, West Virginia. Canaan Valley is oval-shaped (14 miles by 5 miles) and is located in the Allegheny Mountains at an average elevation of 3,200 feet above sea level. Tourism, population, and real estate development have increased in the past two decades. Most streams in Canaan Valley are a dilute calcium magnesium bicarbonate-type water. Streamwater typicaly was soft and low in alkalinity and dissolved solids. Maximum values for specific conductance, hardness, alkalinity, and dissolved solids occurred during low-flow periods when streamflow was at or near baseflow. Dissolved oxygen concentrations are most sensitive to processes affecting the rate of reaeration. The reaeration is affected by solubility (atmospheric pressure, water temperature, humidity, and cloud cover) and processes that determine stream turbulence (stream depth, width, velocity, and roughness). In the headwaters, photosynthetic dissolved oxygen production by benthic algae can result in supersaturated dissolved oxygen concentrations. In beaver pools, dissolved oxygen consumption from sediment oxygen demand and carbonaceous biochemical oxygen demand can result in dissolved oxygen deficits.

Geochemistry, mineralogy, and chemical modeling of the acid crater lake of Kawah Ijen Volcano, Indonesia

NASA Astrophysics Data System (ADS)

Delmelle, Pierre; Bernard, Alain

1994-06-01

The Kawah Ijen volcano—with a record of phreatic eruptions—has its 1000 m wide crater filled with a lake that has existed for at least one century. At present, the lake waters are hot ( T ≈ 37° C), strongly mineralized (TDS = 105 g/L) and extremely acidic ( pH ≈ 0.4). By its volume, the Javanese lake is probably the largest accumulation in the world of such acidic waters. Mineralogy of the suspended solids within the lake waters suggests that concentrations of Si, Ca, Ti, and Ba are controlled by precipitation of silica, gypsum, anatase, and barite. Lake sediment is composed of chemical precipitates with composition similar to the suspended solids. Thermodynamic calculations predict that the lake waters have reached equilibrium with respect to α-cristobalite, barite, gypsum, anglesite, celestite, and amorphous silica, in agreement with the analytical observations. Significant concentrations of ferric iron suggest that the current lake waters are fairly oxidized. Sulfides are absent in the water column but are always present in the native S spherules that form porous aggregates which float on the lake. The presence of native S provides direct evidence of more reduced conditions at the lake floor where H 2S is probably being injected into the lake. With progressive addition of H 2S to the acid waters, native S, pyrite, and enargite are theoretically predicted to be saturated. Reactions between upward streaming H 2S-bearing gases discharged by subaqueous fumaroles, and metals dissolved in the acidic waters could initiate precipitation of these sulfides. A model of direct absorption of hot magmatic gases into cool water accounts for the extreme acidity of the crater lake. Results show that strongly acidic, sulfate-rich solutions are formed under oxidizing conditions at high gas/water ratios. Reactions between the acidic fluids and the Ijen andesite were modeled to account for elevated cation concentrations in lake water. Current concentrations of conservative rockforming elements are produced by dissolution of approximately 60 g of andesite per kg of acid solution. Complete neutralization of the acid lake waters by reaction with the wallrock produces a theoretical alteration assemblage equivalent to that observed in volcano-hosted, acid-sulfate epithermal ore deposits.

Characteristics and source identification of dissolved trace elements in the Jinshui River of the South Qinling Mts., China.

PubMed

Bu, Hongmei; Wang, Weibo; Song, Xianfang; Zhang, Quanfa

2015-09-01

Dissolved trace elements and physiochemical parameters were analyzed to investigate their physicochemical characteristics and identify their sources at 12 sampling sites of the Jinshui River in the South Qinling Mts., China from October 2006 to November 2008. The two-factor ANOVA indicated significant temporal variations of the dissolved Cu, Fe, Sr, Si, and V (p < 0.001 or p < 0.05). With the exception of Sr (p < 0.001), no significant spatial variations were found. Distributions and concentrations of the dissolved trace elements displayed that dissolved Cu, Fe, Sr, Si, V, and Cr were originated from chemical weathering and leaching from the soil and bedrock. Dissolved Cu, Fe, Sr, As, and Si were also from anthropogenic inputs (farming and domestic effluents). Correlation and regression analysis showed that the chemical and physical processes of dissolved Cu was influenced by water temperature and dissolved oxygen (DO) to some degree. Dissolved Fe and Sr were affected by colloid destabilization or sedimentary inputs. Concentrations of dissolved Si were slightly controlled by biological uptake. Principal component analysis confirmed that Fe, Sr, and V resulted from domestic effluents, agricultural runoff, and confluence, whereas As, Cu, and Si were from agricultural activities, and Cr and Zn through natural processes. The research results provide a reference for ecological restoration and protection of the river environment in the Qinling Mts., China.

A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary.

PubMed

Spietz, Rachel L; Williams, Cheryl M; Rocap, Gabrielle; Horner-Devine, M Claire

2015-01-01

Pelagic ecosystems can become depleted of dissolved oxygen as a result of both natural processes and anthropogenic effects. As dissolved oxygen concentration decreases, energy shifts from macrofauna to microorganisms, which persist in these hypoxic zones. Oxygen-limited regions are rapidly expanding globally; however, patterns of microbial communities associated with dissolved oxygen gradients are not yet well understood. To assess the effects of decreasing dissolved oxygen on bacteria, we examined shifts in bacterial community structure over space and time in Hood Canal, Washington, USA-a glacial fjord-like water body that experiences seasonal low dissolved oxygen levels known to be detrimental to fish and other marine organisms. We found a strong negative association between bacterial richness and dissolved oxygen. Bacterial community composition across all samples was also strongly associated with the dissolved oxygen gradient, and significant changes in bacterial community composition occurred at a dissolved oxygen concentration between 5.18 and 7.12 mg O2 L(-1). This threshold value of dissolved oxygen is higher than classic definitions of hypoxia (<2.0 mg O2 L(-1)), suggesting that changes in bacterial communities may precede the detrimental effects on ecologically and economically important macrofauna. Furthermore, bacterial taxa responsible for driving whole community changes across the oxygen gradient are commonly detected in other oxygen-stressed ecosystems, suggesting that the patterns we uncovered in Hood Canal may be relevant in other low oxygen ecosystems.

Incinerator ash dissolution model for the system: Plutonium, nitric acid and hydrofluoric acid

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

Brown, E V

1988-06-01

This research accomplished two goals. The first was to develop a computer program to simulate a cascade dissolver system. This program would be used to predict the bulk rate of dissolution in incinerator ash. The other goal was to verify the model in a single-stage dissolver system using Dy/sub 2/O/sub 3/. PuO/sub 2/ (and all of the species in the incinerator ash) was assumed to exist as spherical particles. A model was used to calculate the bulk rate of plutonium oxide dissolution using fluoride as a catalyst. Once the bulk rate of PuO/sub 2/ dissolution and the dissolution rate ofmore » all soluble species were calculated, mass and energy balances were written. A computer program simulating the cascade dissolver system was then developed. Tests were conducted on a single-stage dissolver. A simulated incinerator ash mixture was made and added to the dissolver. CaF/sub 2/ was added to the mixture as a catalyst. A 9M HNO/sub 3/ solution was pumped into the dissolver system. Samples of the dissolver effluent were analyzed for dissolved and F concentrations. The computer program proved satisfactory in predicting the F concentrations in the dissolver effluent. The experimental sparge air flow rate was predicted to within 5.5%. The experimental percentage of solids dissolved (51.34%) compared favorably to the percentage of incinerator ash dissolved (47%) in previous work. No general conclusions on model verification could be reached. 56 refs., 11 figs., 24 tabs.« less

7 CFR 760.115 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 7 2010-01-01 2010-01-01 false Deceased individuals or dissolved entities. 760.115... Agricultural Disaster Assistance Programs § 760.115 Deceased individuals or dissolved entities. (a) Payments... or is a dissolved entity if a representative, who currently has authority to enter into a contract...

7 CFR 760.115 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 7 2012-01-01 2012-01-01 false Deceased individuals or dissolved entities. 760.115... Agricultural Disaster Assistance Programs § 760.115 Deceased individuals or dissolved entities. (a) Payments... or is a dissolved entity if a representative, who currently has authority to enter into a contract...

7 CFR 760.115 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 7 2013-01-01 2013-01-01 false Deceased individuals or dissolved entities. 760.115... Agricultural Disaster Assistance Programs § 760.115 Deceased individuals or dissolved entities. (a) Payments... or is a dissolved entity if a representative, who currently has authority to enter into a contract...

7 CFR 760.115 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 7 2014-01-01 2014-01-01 false Deceased individuals or dissolved entities. 760.115... Agricultural Disaster Assistance Programs § 760.115 Deceased individuals or dissolved entities. (a) Payments... or is a dissolved entity if a representative, who currently has authority to enter into a contract...

7 CFR 760.115 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 7 2011-01-01 2011-01-01 false Deceased individuals or dissolved entities. 760.115... Agricultural Disaster Assistance Programs § 760.115 Deceased individuals or dissolved entities. (a) Payments... or is a dissolved entity if a representative, who currently has authority to enter into a contract...

Soluble organic nutrient fluxes

Treesearch

Robert G. Qualls; Bruce L. Haines; Wayne Swank

2014-01-01

Our objectives in this study were (i) compare fluxes of the dissolved organic nutrients dissolved organic carbon (DOC), DON, and dissolved organic phosphorus (DOP) in a clearcut area and an adjacent mature reference area. (ii) determine whether concentrations of dissolved organic nutrients or inorganic nutrients were greater in clearcut areas than in reference areas,...

Simple Web-based interactive key development software (WEBiKEY) and an example key for Kuruna (Poaceae: Bambusoideae)1

PubMed Central

Attigala, Lakshmi; De Silva, Nuwan I.; Clark, Lynn G.

2016-01-01

Premise of the study: Programs that are user-friendly and freely available for developing Web-based interactive keys are scarce and most of the well-structured applications are relatively expensive. WEBiKEY was developed to enable researchers to easily develop their own Web-based interactive keys with fewer resources. Methods and Results: A Web-based multiaccess identification tool (WEBiKEY) was developed that uses freely available Microsoft ASP.NET technologies and an SQL Server database for Windows-based hosting environments. WEBiKEY was tested for its usability with a sample data set, the temperate woody bamboo genus Kuruna (Poaceae). Conclusions: WEBiKEY is freely available to the public and can be used to develop Web-based interactive keys for any group of species. The interactive key we developed for Kuruna using WEBiKEY enables users to visually inspect characteristics of Kuruna and identify an unknown specimen as one of seven possible species in the genus. PMID:27144109

Pan-neuronal calcium imaging with cellular resolution in freely swimming zebrafish.

PubMed

Kim, Dal Hyung; Kim, Jungsoo; Marques, João C; Grama, Abhinav; Hildebrand, David G C; Gu, Wenchao; Li, Jennifer M; Robson, Drew N

2017-11-01

Calcium imaging with cellular resolution typically requires an animal to be tethered under a microscope, which substantially restricts the range of behaviors that can be studied. To expand the behavioral repertoire amenable to imaging, we have developed a tracking microscope that enables whole-brain calcium imaging with cellular resolution in freely swimming larval zebrafish. This microscope uses infrared imaging to track a target animal in a behavior arena. On the basis of the predicted trajectory of the animal, we applied optimal control theory to a motorized stage system to cancel brain motion in three dimensions. We combined this motion-cancellation system with differential illumination focal filtering, a variant of HiLo microscopy, which enabled us to image the brain of a freely swimming larval zebrafish for more than an hour. This work expands the repertoire of natural behaviors that can be studied with cellular-resolution calcium imaging to potentially include spatial navigation, social behavior, feeding and reward.

Mapping brain function in freely moving subjects

PubMed Central

Holschneider, Daniel P.; Maarek, Jean-Michel I.

2014-01-01

Expression of many fundamental mammalian behaviors such as, for example, aggression, mating, foraging or social behaviors, depend on locomotor activity. A central dilemma in the functional neuroimaging of these behaviors has been the fact that conventional neuroimaging techniques generally rely on immobilization of the subject, which extinguishes all but the simplest activity. Ideally, imaging could occur in freely moving subjects, while presenting minimal interference with the subject’s natural behavior. Here we provide an overview of several approaches that have been undertaken in the past to achieve this aim in both tethered and freely moving animals, as well as in nonrestrained human subjects. Applications of specific radiotracers to single photon emission computed tomography and positron emission tomography are discussed in which brain activation is imaged after completion of the behavioral task and capture of the tracer. Potential applications to clinical neuropsychiatry are discussed, as well as challenges inherent to constraint-free functional neuroimaging. Future applications of these methods promise to increase our understanding of the neural circuits underlying mammalian behavior in health and disease. PMID:15465134

Flow Meter Based on Freely Suspended Smectic Liquid Crystal Films

NASA Astrophysics Data System (ADS)

Green, Adam; Qi, Zhiyuan; Park, Cheol; Glaser, Matthew; Maclennan, Joseph; Clark, Noel

We present the realization of a idealized 2D hydrodynamic system coupled to air-flow, and show that freely suspended films (FSF) of smectic liquid crystals can be used as a novel flow-meter. Freely-suspended films of liquid crystals are one of the closest physical realizations of an idealized 2D fluid. The velocity of air-flow above a film suspended above a channel can be inferred by studying the velocity profile of the smectic film. This velocity profile can be measured using digital video microscopy to track the inclusions present in the moving film. The velocity profile is then fitted to the coupled 2D solutions of an embedded fluid in air, and the velocity of the air can then be extracted. This flow meter serves as a demonstration of a robust test-bed for further exploration of 2D hydrodynamics. This work was supported by NASA Grant No. NNX-13AQ81G, NSF MRSEC Grant No. DMR-0820579, and DMR-1420736.

Constraints on arm selection processes when reaching: degrees of freedom and joint amplitudes interact to influence limb selection.

PubMed

Kim, Wondae; Buchanan, John; Gabbard, Carl

2011-01-01

With an interest in identifying the variables that constrain arm choice when reaching, the authors had 11 right-handed participants perform free-choice and assigned-limb reaches at 9 object positions. The right arm was freely selected 100% of the time when reaching to positions at 30° and 40° into right hemispace. However, the left arm was freely selected to reach to positions at -30° and -40° in left hemispace 85% of the time. A comparison between free- and assigned-limb reaching kinematics revealed that free limb selection when reaching to the farthest positions was constrained by joint amplitude requirements and the time devoted to limb deceleration. Differences between free- and assigned-arm reaches were not evident when reaching to the midline and positions of ±10°, even though the right arm was freely selected most often for these positions. Different factors contribute to limb selection as a function of distance into a specific hemispace.

Chronic, Wireless Recordings of Large Scale Brain Activity in Freely Moving Rhesus Monkeys

PubMed Central

Schwarz, David A.; Lebedev, Mikhail A.; Hanson, Timothy L.; Dimitrov, Dragan F.; Lehew, Gary; Meloy, Jim; Rajangam, Sankaranarayani; Subramanian, Vivek; Ifft, Peter J.; Li, Zheng; Ramakrishnan, Arjun; Tate, Andrew; Zhuang, Katie; Nicolelis, Miguel A.L.

2014-01-01

Advances in techniques for recording large-scale brain activity contribute to both the elucidation of neurophysiological principles and the development of brain-machine interfaces (BMIs). Here we describe a neurophysiological paradigm for performing tethered and wireless large-scale recordings based on movable volumetric three-dimensional (3D) multielectrode implants. This approach allowed us to isolate up to 1,800 units per animal and simultaneously record the extracellular activity of close to 500 cortical neurons, distributed across multiple cortical areas, in freely behaving rhesus monkeys. The method is expandable, in principle, to thousands of simultaneously recorded channels. It also allows increased recording longevity (5 consecutive years), and recording of a broad range of behaviors, e.g. social interactions, and BMI paradigms in freely moving primates. We propose that wireless large-scale recordings could have a profound impact on basic primate neurophysiology research, while providing a framework for the development and testing of clinically relevant neuroprostheses. PMID:24776634

ChemoPy: freely available python package for computational biology and chemoinformatics.

PubMed

Cao, Dong-Sheng; Xu, Qing-Song; Hu, Qian-Nan; Liang, Yi-Zeng

2013-04-15

Molecular representation for small molecules has been routinely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes. To facilitate extensive studies of drug molecules, we developed a freely available, open-source python package called chemoinformatics in python (ChemoPy) for calculating the commonly used structural and physicochemical features. It computes 16 drug feature groups composed of 19 descriptors that include 1135 descriptor values. In addition, it provides seven types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pairs fingerprints, topological torsion fingerprints and Morgan/circular fingerprints. By applying a semi-empirical quantum chemistry program MOPAC, ChemoPy can also compute a large number of 3D molecular descriptors conveniently. The python package, ChemoPy, is freely available via http://code.google.com/p/pychem/downloads/list, and it runs on Linux and MS-Windows. Supplementary data are available at Bioinformatics online.

Native plant diversity increases herbivory to non-natives

PubMed Central

Pearse, Ian S.; Hipp, Andrew L.

2014-01-01

There is often an inverse relationship between the diversity of a plant community and the invasibility of that community by non-native plants. Native herbivores that colonize novel plants may contribute to diversity–invasibility relationships by limiting the relative success of non-native plants. Here, we show that, in large collections of non-native oak trees at sites across the USA, non-native oaks introduced to regions with greater oak species richness accumulated greater leaf damage than in regions with low oak richness. Underlying this trend was the ability of herbivores to exploit non-native plants that were close relatives to their native host. In diverse oak communities, non-native trees were on average more closely related to native trees and received greater leaf damage than those in depauperate oak communities. Because insect herbivores colonize non-native plants that are similar to their native hosts, in communities with greater native plant diversity, non-natives experience greater herbivory. PMID:25232143

Raw liquid waste treatment process

NASA Technical Reports Server (NTRS)

Humphrey, Marshall F. (Inventor)

1980-01-01

A raw sewage treatment process is disclosed in which substantially all the non-dissolved matter, which is suspended in the sewage water is first separated from the water, in which at least organic matter is dissolved. The non-dissolved material is pyrolyzed to form an activated carbon and ash material without the addition of any conditioning agents. The activated carbon and ash material is added to the water from which the non-dissolved matter was removed. The activated carbon and ash material absorbs organic matter and heavy metal ions, it is believed, are dissolved in the water and is thereafter supplied in a counter current flow direction and combined with the incoming raw sewage to facilitate the separation of the non-dissolved settleable materials from the sewage water. The used carbon and ash material together with the non-dissolved matter which was separated from the sewage water are pyrolyzed to form the activated carbon and ash material.

Raw Liquid Waste Treatment System and Process

NASA Technical Reports Server (NTRS)

Humphrey, M. F. (Inventor)

1974-01-01

A raw sewage treatment process is disclosed in which substantially all the non-dissolved matter, suspended in the sewage water is first separated from the water, in which at least organic matter remains dissolved. The non-dissolved material is pyrolyzed to form an activated carbon and ash material without the addition of any conditioning agents. The activated carbon and ash material is added to the water from which the non-dissolved matter was removed. The activated carbon and ash material adsorbs the organic matter dissolved in the water and is thereafter supplied in a counter flow direction and combined with the incoming raw sewage to at least facilitate the separation of the non-dissolved settleable materials from the sewage water. Carbon and ash material together with the non-dissolved matter which was separated from the sewage water are pyrolyzed to form the activated carbon and ash material.

Prediction model of dissolved oxygen in ponds based on ELM neural network

NASA Astrophysics Data System (ADS)

Li, Xinfei; Ai, Jiaoyan; Lin, Chunhuan; Guan, Haibin

2018-02-01

Dissolved oxygen in ponds is affected by many factors, and its distribution is unbalanced. In this paper, in order to improve the imbalance of dissolved oxygen distribution more effectively, the dissolved oxygen prediction model of Extreme Learning Machine (ELM) intelligent algorithm is established, based on the method of improving dissolved oxygen distribution by artificial push flow. Select the Lake Jing of Guangxi University as the experimental area. Using the model to predict the dissolved oxygen concentration of different voltage pumps, the results show that the ELM prediction accuracy is higher than the BP algorithm, and its mean square error is MSEELM=0.0394, the correlation coefficient RELM=0.9823. The prediction results of the 24V voltage pump push flow show that the discrete prediction curve can approximate the measured values well. The model can provide the basis for the artificial improvement of the dissolved oxygen distribution decision.

An analysis of un-dissolved powders of instant powdered soup by using ultrasonographic image

NASA Astrophysics Data System (ADS)

Kawaai, Yukinori; Kato, Kunihito; Yamamoto, Kazuhiko; Kasamatsu, Chinatsu

2008-11-01

Nowadays, there are many instant powdered soups around us. When we make instant powdered soup, sometimes we cannot dissolve powders perfectly. Food manufacturers want to improve this problem in order to make better products. Therefore, they have to measure the state and volume of un-dissolved powders. Earlier methods for analyzing removed the un-dissolved powders from the container, the state of the un-dissolved power was changed. Our research using ultrasonographic image can measure the state of un-dissolved powders with no change by taking cross sections of the soup. We then make 3D soup model from these cross sections of soup. Therefore we can observe the inside of soup that we do not have ever seen. We construct accurate 3D model. We can visualize the state and volume of un-dissolved powders with analyzing the 3D soup models.

7 CFR 760.908 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 7 2010-01-01 2010-01-01 false Deceased individuals or dissolved entities. 760.908... § 760.908 Deceased individuals or dissolved entities. (a) Payments may be made for eligible losses suffered by an eligible participant who is now a deceased individual or is a dissolved entity if a...

7 CFR 1413.113 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 10 2011-01-01 2011-01-01 false Deceased individuals or dissolved entities. 1413.113... PROGRAMS Durum Wheat Quality Program § 1413.113 Deceased individuals or dissolved entities. (a) Payment may... individual or is a dissolved entity if a representative who currently has authority to enter into a contract...

7 CFR 760.908 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 7 2013-01-01 2013-01-01 false Deceased individuals or dissolved entities. 760.908... § 760.908 Deceased individuals or dissolved entities. (a) Payments may be made for eligible losses suffered by an eligible participant who is now a deceased individual or is a dissolved entity if a...

7 CFR 1413.113 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 10 2012-01-01 2012-01-01 false Deceased individuals or dissolved entities. 1413.113... PROGRAMS Durum Wheat Quality Program § 1413.113 Deceased individuals or dissolved entities. (a) Payment may... individual or is a dissolved entity if a representative who currently has authority to enter into a contract...

7 CFR 760.908 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 7 2012-01-01 2012-01-01 false Deceased individuals or dissolved entities. 760.908... § 760.908 Deceased individuals or dissolved entities. (a) Payments may be made for eligible losses suffered by an eligible participant who is now a deceased individual or is a dissolved entity if a...

7 CFR 1413.113 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 10 2013-01-01 2013-01-01 false Deceased individuals or dissolved entities. 1413.113... PROGRAMS Durum Wheat Quality Program § 1413.113 Deceased individuals or dissolved entities. (a) Payment may... individual or is a dissolved entity if a representative who currently has authority to enter into a contract...

7 CFR 760.908 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 7 2014-01-01 2014-01-01 false Deceased individuals or dissolved entities. 760.908... § 760.908 Deceased individuals or dissolved entities. (a) Payments may be made for eligible losses suffered by an eligible participant who is now a deceased individual or is a dissolved entity if a...

7 CFR 1413.113 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 10 2014-01-01 2014-01-01 false Deceased individuals or dissolved entities. 1413.113... PROGRAMS Durum Wheat Quality Program § 1413.113 Deceased individuals or dissolved entities. (a) Payment may... individual or is a dissolved entity if a representative who currently has authority to enter into a contract...

7 CFR 760.908 - Deceased individuals or dissolved entities.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 7 2011-01-01 2011-01-01 false Deceased individuals or dissolved entities. 760.908... § 760.908 Deceased individuals or dissolved entities. (a) Payments may be made for eligible losses suffered by an eligible participant who is now a deceased individual or is a dissolved entity if a...

Exoenzyme activities as indicators of dissolved organic matter composition in the hyporheic zone of a floodplain river

Treesearch

Sandra M. Clinton; Rick T. Edwards; Stuart E.G. Findlay

2010-01-01

We measured the hyporheic microbial exoenzyme activities in a floodplain river to determine whether dissolved organic matter (DOM) bioavailability varied with overlying riparian vegetation patch structure or position along flowpaths. Particulate organic matter (POM), dissolved organic carbon (DOC), dissolved oxygen (DO), electrical conductivity and temperature were...

Biochemical Oxygen Demand and Dissolved Oxygen. Training Module 5.105.2.77.

ERIC Educational Resources Information Center

Kirkwood Community Coll., Cedar Rapids, IA.

This document is an instructional module package prepared in objective form for use by an instructor familiar with the azide modification of the Winkler dissolved oxygen test and the electronic dissolved oxygen meter test procedures for determining the dissolved oxygen and the biochemical oxygen demand of a wastewater sample. Included are…

[Flow injection-spectrophotometric determination of total dissolved nitrogen in seawater based on quantificational solenoid valves].

PubMed

Han, Bin; Cao, Lei; Zheng, Li; Zang, Jia-ye; Wang, Xiao-ru

2012-01-01

Using three pipe clamp solenoid valves to replace the traditional six-port valve for sample quota, a set of multi-channel flow injection analyzer was designed in the present paper. The authors optimized optimum instrumental testing condition, and realized determination and analysis of total dissolved nitrogen in seawaters. The construction of apparatus is simple and it has the potential to be used for analysis of total dissolved nitrogen. The sample throughput of total dissolved nitrogen was 27 samples per hour. The linear range of total dissolved nitrogen was 50.0-1 000.0 microgN x L(-3) (r > or = 0.999). The detection limit was 7.6 microgN x L(-3). The recovery of total dissolved nitrogen was 87.3%-107.2%. The relative standard deviation for total dissolved nitrogen was 1.35%-6.32% (n = 6). After the t-test analysis, it does not have the significance difference between this method and national standard method. It is suitable for fast analysis of total dissolved nitrogen in seawater.

A linear solvation energy relationship model of organic chemical partitioning to dissolved organic carbon.

PubMed

Kipka, Undine; Di Toro, Dominic M

2011-09-01

Predicting the association of contaminants with both particulate and dissolved organic matter is critical in determining the fate and bioavailability of chemicals in environmental risk assessment. To date, the association of a contaminant to particulate organic matter is considered in many multimedia transport models, but the effect of dissolved organic matter is typically ignored due to a lack of either reliable models or experimental data. The partition coefficient to dissolved organic carbon (K(DOC)) may be used to estimate the fraction of a contaminant that is associated with dissolved organic matter. Models relating K(DOC) to the octanol-water partition coefficient (K(OW)) have not been successful for many types of dissolved organic carbon in the environment. Instead, linear solvation energy relationships are proposed to model the association of chemicals with dissolved organic matter. However, more chemically diverse K(DOC) data are needed to produce a more robust model. For humic acid dissolved organic carbon, the linear solvation energy relationship predicts log K(DOC) with a root mean square error of 0.43. Copyright © 2011 SETAC.

Dissolver vessel bottom assembly

DOEpatents

Kilian, Douglas C.

1976-01-01

An improved bottom assembly is provided for a nuclear reactor fuel reprocessing dissolver vessel wherein fuel elements are dissolved as the initial step in recovering fissile material from spent fuel rods. A shock-absorbing crash plate with a convex upper surface is disposed at the bottom of the dissolver vessel so as to provide an annular space between the crash plate and the dissolver vessel wall. A sparging ring is disposed within the annular space to enable a fluid discharged from the sparging ring to agitate the solids which deposit on the bottom of the dissolver vessel and accumulate in the annular space. An inlet tangential to the annular space permits a fluid pumped into the annular space through the inlet to flush these solids from the dissolver vessel through tangential outlets oppositely facing the inlet. The sparging ring is protected against damage from the impact of fuel elements being charged to the dissolver vessel by making the crash plate of such a diameter that the width of the annular space between the crash plate and the vessel wall is less than the diameter of the fuel elements.

Non-native Ants Are Smaller than Related Native Ants.

PubMed

McGlynn, Terrence P

1999-12-01

I compare the sizes of non-native and native ants to evaluate how worker size may be related to the ability of a species to invade new habitats. I compare the size of 78 non-native ant species belonging to 26 genera with the size of native congeneric species; native ants are larger than non-native ants in 22 of 26 genera. Ants were sorted by genera into fighting and nonfighting groups, based on observations of interspecific interactions with other ant species. In all of the genera with monomorphic worker castes that fight during competition, the non-native species were smaller than the native species. The genera that engage in combat had a higher frequency of significantly smaller size in non-native ants. I selected Wasmannia auropunctata for further studies, to compare native and non-native populations. Specimens of W. auropunctata from non-native populations were smaller than conspecific counterparts from its native habitat. I consider hypotheses to explain why non-native ants are smaller in size than native ants, including the role of colony size in interspecific fights, changes in life history, the release from intraspecific fighting, and climate. The discovery that fighting non-natives are smaller than their closest native relatives may provide insight into the mechanisms for success of non-native species, as well as the role of worker size and colony size during interspecific competition.

The influence of dissolved oxygen on winter habitat selection by largemouth bass: an integration of field biotelemetry studies and laboratory experiments.

PubMed

Hasler, C T; Suski, C D; Hanson, K C; Cooke, S J; Tufts, B L

2009-01-01

In this study, field biotelemetry and laboratory physiology approaches were coupled to allow understanding of the behavioral and physiological responses of fish to winter hypoxia. The biotelemetry study compared dissolved oxygen levels measured throughout the winter period with continually tracked locations of nine adult largemouth bass obtained from a whole-lake submerged telemetry array. Fish habitat usage was compared with habitat availability to assess whether fish were selecting for specific dissolved oxygen concentrations. The laboratory study examined behavioral and physiological responses to progressive hypoxia in juvenile largemouth bass acclimated to winter temperatures. Results from the dissolved oxygen measurements made during the biotelemetry study showed high variance in under-ice dissolved oxygen levels. Avoidance of water with dissolved oxygen <2.0 mg/L by telemetered fish was demonstrated, but significant use of water with intermediate dissolved oxygen levels was also found. Results from the lab experiments showed marked changes in behavior (i.e., yawning and vertical movement) at <2.0 mg/L of dissolved oxygen but no change in tissue lactate, an indicator of anaerobic metabolism. Combined results of the biotelemetry and laboratory studies demonstrate that a dissolved oxygen content of 2.0 mg/L may be a critical threshold that induces behavioral responses by largemouth bass during the winter. In addition, the use by fish of areas with intermediate levels of dissolved oxygen suggests that there are multiple environmental factors influencing winter behavior.

A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary

PubMed Central

Spietz, Rachel L.; Williams, Cheryl M.; Rocap, Gabrielle; Horner-Devine, M. Claire

2015-01-01

Pelagic ecosystems can become depleted of dissolved oxygen as a result of both natural processes and anthropogenic effects. As dissolved oxygen concentration decreases, energy shifts from macrofauna to microorganisms, which persist in these hypoxic zones. Oxygen-limited regions are rapidly expanding globally; however, patterns of microbial communities associated with dissolved oxygen gradients are not yet well understood. To assess the effects of decreasing dissolved oxygen on bacteria, we examined shifts in bacterial community structure over space and time in Hood Canal, Washington, USA−a glacial fjord-like water body that experiences seasonal low dissolved oxygen levels known to be detrimental to fish and other marine organisms. We found a strong negative association between bacterial richness and dissolved oxygen. Bacterial community composition across all samples was also strongly associated with the dissolved oxygen gradient, and significant changes in bacterial community composition occurred at a dissolved oxygen concentration between 5.18 and 7.12 mg O2 L-1. This threshold value of dissolved oxygen is higher than classic definitions of hypoxia (<2.0 mg O2 L-1), suggesting that changes in bacterial communities may precede the detrimental effects on ecologically and economically important macrofauna. Furthermore, bacterial taxa responsible for driving whole community changes across the oxygen gradient are commonly detected in other oxygen-stressed ecosystems, suggesting that the patterns we uncovered in Hood Canal may be relevant in other low oxygen ecosystems. PMID:26270047

Invasive non-native plants have a greater effect on neighbouring natives than other non-natives.

PubMed

Kuebbing, Sara E; Nuñez, Martin A

2016-09-12

Human activity is creating a global footprint by changing the climate, altering habitats and reshuffling the distribution of species. The movement of species around the globe has led to the naturalization and accumulation of multiple non-native species within ecosystems, which is frequently associated with habitat disturbance and changing environmental conditions. However, interactions among species will also influence community composition, but little is known about the full range of direct and indirect interactions among native and non-native species. Here, we show through a meta-analysis of 1,215 pairwise plant interactions between 274 vascular plant species in 21 major habitat types that interactions between non-native plants are asymmetrical with interactions between non-native and native plants. Non-native plants were always bad neighbours, but the negative effect of non-natives on natives was around two times greater than the effect of non-natives on other non-natives. In contrast, the performance of non-native plants was five times higher in the presence of a neighbouring native plant species than in the presence of a neighbouring non-native plant species. Together, these results demonstrate that invaded plant communities may accumulate additional non-native species even if direct interactions between non-natives species are negative. Put another way, invasions may be more likely to lead to more invasions, requiring more active management of ecosystems by promoting native species restoration to undermine invasive positive feedback and to assist native species recovery in invaded ecosystems.

The Evolution of Deepwater Dissolved Oxygen in the Northern South China Sea During the Past 400 ka

NASA Astrophysics Data System (ADS)

Wang, N.; Huang, B.; Dong, Y.

2016-12-01

Reconstruction of dissolved oxygen in paleo-ocean contributes toward understanding the history of ocean circulation, climate, causes of extinctions, and the evolution of marine organisms. Based on analysis of benthic foraminifera oxygen index (BFOI), the redox-sensitive trace elements (Mo/Al), the percentage of epifaunal benthic foraminifera and infaunal/epifaunal ratio at core MD12-3432, we reconstruct the evolution of deep water dissolved oxygen in northern South China Sea (SCS) during the past 400 ka and discuss the mechanisms of variable dissolved oxygen. Both BFOI and Mo/Al are redox indicators. Similar trends confirm that they reflect the variation of dissolved oxygen in seawater since 400 ka accurately. BFOI and Mo/Al indicate that dissolved oxygen was high in MIS 11-MIS 7 and decreased gradually during MIS 6- MIS 2. The percentage of epifauna decreased and infaunal/epifaunal ratio increased with decreasing dissolved oxygen. By comparison of dissolved oxygen and productivity indexes such as phytoplankton total (PT) and species abundances, we found that when PT fluctuated in the average range of 1000-1500 ng/g, the abundances of Bulimina and Uvigerina which represent high productivity increased. However, when PT reached the range of 2500-3000 ng/g, the abundances of Bulimina and Uvigerina didn't increase, but the abundances of dysoxic species Chilostomella oolina and Globobulimina pacifica increased and the dissolved oxygen reached low value. The reasons may be that the decomposition of excessive organic matter consumed more dissolved oxygen. The low dissolved oxygen suppressed the growth of Bulimina and Uvigerina and accelerated the boom of C. oolina and G. oolina. The dissolved oxygen is not only associated with productivity, but also affected by the thermohaline circulation. Benthic foraminifera F. favus is the representative species in Pacific deep water. Its appearance at 194 ka, 205 ka, 325, the 328 ka in MD12-3432 indicate that the upper border of western Pacific deep water was beyond the sill of Bashi Strait and high dissolved oxygen deep water was brought into Northern SCS. The millennium-scale rapid variability and decline of dissolved oxygen in MIS 4, 3, 2 may be caused by fluctuations and slowdown of thermohaline circulation transported from the northern Atlantic to the northern SCS.

Specific Conductance and Dissolved-Solids Characteristics for the Green River and Muddy Creek, Wyoming, Water Years 1999-2008

USGS Publications Warehouse

Clark, Melanie L.; Davidson, Seth L.

2009-01-01

Southwestern Wyoming is an area of diverse scenery, wildlife, and natural resources that is actively undergoing energy development. The U.S. Department of the Interior's Wyoming Landscape Conservation Initiative is a long-term science-based effort to assess and enhance aquatic and terrestrial habitats at a landscape scale, while facilitating responsible energy development through local collaboration and partnerships. Water-quality monitoring has been conducted by the U.S. Geological Survey on the Green River near Green River, Wyoming, and Muddy Creek near Baggs, Wyoming. This monitoring, which is being conducted in cooperation with State and other Federal agencies and as part of the Wyoming Landscape Conservation Initiative, is in response to concerns about potentially increased dissolved solids in the Colorado River Basin as a result of energy development. Because of the need to provide real-time dissolved-solids concentrations for the Green River and Muddy Creek on the World Wide Web, the U.S. Geological Survey developed regression equations to estimate dissolved-solids concentrations on the basis of continuous specific conductance using relations between measured specific conductance and dissolved-solids concentrations. Specific conductance and dissolved-solids concentrations were less varied and generally lower for the Green River than for Muddy Creek. The median dissolved-solids concentration for the site on the Green River was 318 milligrams per liter, and the median concentration for the site on Muddy Creek was 943 milligrams per liter. Dissolved-solids concentrations ranged from 187 to 594 milligrams per liter in samples collected from the Green River during water years 1999-2008. Dissolved-solids concentrations ranged from 293 to 2,485 milligrams per liter in samples collected from Muddy Creek during water years 2006-08. The differences in dissolved-solids concentrations in samples collected from the Green River compared to samples collected from Muddy Creek reflect the different basin characteristics. Relations between specific conductance and dissolved-solids concentrations were statistically significant for the Green River (p-value less than 0.001) and Muddy Creek (p-value less than 0.001); therefore, specific conductance can be used to estimate dissolved-solids concentrations. Using continuous specific conductance values to estimate dissolved solids in real-time on the World Wide Web increases the amount and improves the timeliness of data available to water managers for assessing dissolved-solids concentrations in the Colorado River Basin.

Dissolved and colloidal copper in the tropical South Pacific

NASA Astrophysics Data System (ADS)

Roshan, Saeed; Wu, Jingfeng

2018-07-01

Copper (Cu) as a bioactive trace metal in the ocean has widely been studied in the context of chemical speciation. However, this trace metal is extremely understudied in the context of physical speciation (i.e., size- or molecular weight-partitioning), which may help in characterizing dissolved Cu species. In this study, we determine total dissolved Cu (<0.2 μm) distribution and its physical speciation along the US GEOTRACES 2013 cruise, a 4300-km east-west transect in the tropical South Pacific. The distribution of dissolved Cu is rather uniform horizontally and exhibits a linear increase with depth from surface to 2500-3000 m, below which it varies less significantly both vertically and horizontally. Dissolved Cu shows a strong correlation with silicate (SiO44-) in the upper 1500 m, which is in agreement with previous studies in other regions. This correlation is weaker but with higher slope at depths below 1500 m, which supports the sedimentary source hypothesis. Although hydrothermal activity at the East Pacific Rise (EPR) does not show a readily evident impact on the dissolved Cu distribution, high-quality data at 2300-2800 m allow for diagnosing a subtle westward decrease in the background-subtracted dissolved Cu component. This component of dissolved Cu poorly correlates with mantle-derived 3He (R2 = 0.41), indicating a possible hydrothermal source for dissolved Cu, in contrast to previous studies. For the first time in a major basin, we also determined the physical speciation of dissolved Cu, which shows that Cu species lighter than 10 kDa (Da = 1 g mol-1) dominate the pool of dissolved Cu (<0.2 μm) below 1000 m with a contribution of 61 ± 6% (fraction of total dissolved). 39 ± 6% of dissolved Cu at depths below 1000 m, thus, occurs in the pool of colloidal matter (10 kDa-0.2 μm). Moreover, using a suite of molecular weight cutoffs indicate that Cu species are distributed between two distinct molecular weight classes: the lighter than 5 kDa and heavier than 300 kDa classes, which form 53 ± 6% and 37 ± 7% of dissolved Cu at 2200-2800 m, respectively. The Cu species with molecular weight between 5 kDa and 300 kDa contribute only to 10 ± 12% of the pool at 2200-2800 m. These results offer new insights into structure, reactivity and bioavailability of oceanic Cu compounds. As an organic-dominating metal, Cu physical speciation may also shed light on size-reactivity spectrum of dissolved organic matter (DOM) in the deep ocean.

Bidirectional clear speech perception benefit for native and high-proficiency non-native talkers and listeners: Intelligibility and accentednessa

PubMed Central

Smiljanić, Rajka; Bradlow, Ann R.

2011-01-01

This study investigated how native language background interacts with speaking style adaptations in determining levels of speech intelligibility. The aim was to explore whether native and high proficiency non-native listeners benefit similarly from native and non-native clear speech adjustments. The sentence-in-noise perception results revealed that fluent non-native listeners gained a large clear speech benefit from native clear speech modifications. Furthermore, proficient non-native talkers in this study implemented conversational-to-clear speaking style modifications in their second language (L2) that resulted in significant intelligibility gain for both native and non-native listeners. The results of the accentedness ratings obtained for native and non-native conversational and clear speech sentences showed that while intelligibility was improved, the presence of foreign accent remained constant in both speaking styles. This suggests that objective intelligibility and subjective accentedness are two independent dimensions of non-native speech. Overall, these results provide strong evidence that greater experience in L2 processing leads to improved intelligibility in both production and perception domains. These results also demonstrated that speaking style adaptations along with less signal distortion can contribute significantly towards successful native and non-native interactions. PMID:22225056

Electrolytic dissolver

DOEpatents

Wheelwright, E.J.; Fox, R.D.

1975-08-26

This patent related to an electrolytic dissolver wherein dissolution occurs by solution contact including a vessel of electrically insulative material, a fixed first electrode, a movable second electrode, means for insulating the electrodes from the material to be dissolved while permitting a free flow of electrolyte therebetween, means for passing a direct current between the electrodes and means for circulating electrolyte through the dissolver. (auth)

Surface-water hydrology and quality, and macroinvertebrate and smallmouth bass populations in four stream basins in southwestern Wisconsin, 1987-90

USGS Publications Warehouse

Graczyk, David J.; Lillie, Richard A.; Schlesser, Roger A.; Mason, John W.; Lyons, John D.; Kerr, Roger A.; Graczyk, David J.

1993-01-01

Low concentrations of dissolved oxygen constituted the most detrimental water-quality problem affecting smallmouth bass populations. Dissolved-oxygen concentrations were occasionally less than 3 milligrams per liter, a dissolved-oxygen concentration that may be detrimental to early-life stages of smallmouth bass in the streams; however, smallmouth bass were apparently able to withstand these low dissolved-oxygen concentrations and seem to have survived in some situations when dissolved-oxygen concentration decreased to1 milligram per liter.

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

PubMed

Cock, Peter J A; Antao, Tiago; Chang, Jeffrey T; Chapman, Brad A; Cox, Cymon J; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J L

2009-06-01

The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Biopython is freely available, with documentation and source code at (www.biopython.org) under the Biopython license.

Increased in vivo release of neuropeptide S in the amygdala of freely moving rats after local depolarisation and emotional stress.

PubMed

Ebner, Karl; Rjabokon, Alesja; Pape, Hans-Christian; Singewald, Nicolas

2011-10-01

Intracerebral microdialysis in conjunction with a highly sensitive radioimmunoassay was used to study the in vivo release of neuropeptide S (NPS) within the amygdala of freely moving rats. NPS was consistently detected in basolateral amygdala dialysates and the release considerably enhanced in response to local depolarisation as well as exposure to forced swim stress. Thus, our data demonstrate for the first time emotional stress-induced release of NPS in the amygdala supporting a functional role of endogenous NPS in stress/anxiety-related phenomena.

Cyclic biogeochemical processes and nitrogen fate beneath a subtropical stormwater infiltration basin

USGS Publications Warehouse

O'Reilly, Andrew M.; Chang, Ni-Bin; Wanielista, Martin P.

2012-01-01

A stormwater infiltration basin in north–central Florida, USA, was monitored from 2007 through 2008 to identify subsurface biogeochemical processes, with emphasis on N cycling, under the highly variable hydrologic conditions common in humid, subtropical climates. Cyclic variations in biogeochemical processes generally coincided with wet and dry hydrologic conditions. Oxidizing conditions in the subsurface persisted for about one month or less at the beginning of wet periods with dissolved O2 and NO3- showing similar temporal patterns. Reducing conditions in the subsurface evolved during prolonged flooding of the basin. At about the same time O2 and NO3- reduction concluded, Mn, Fe and SO42- reduction began, with the onset of methanogenesis one month later. Reducing conditions persisted up to six months, continuing into subsequent dry periods until the next major oxidizing infiltration event. Evidence of denitrification in shallow groundwater at the site is supported by median NO3-–N less than 0.016 mg L-1, excess N2 up to 3 mg L-1 progressively enriched in δ15N during prolonged basin flooding, and isotopically heavy δ15N and δ18O of NO3- (up to 25‰ and 15‰, respectively). Isotopic enrichment of newly infiltrated stormwater suggests denitrification was partially completed within two days. Soil and water chemistry data suggest that a biogeochemically active zone exists in the upper 1.4 m of soil, where organic carbon was the likely electron donor supplied by organic matter in soil solids or dissolved in infiltrating stormwater. The cyclic nature of reducing conditions effectively controlled the N cycle, switching N fate beneath the basin from NO3- leaching to reduction in the shallow saturated zone. Results can inform design of functionalized soil amendments that could replace the native soil in a stormwater infiltration basin and mitigate potential NO3- leaching to groundwater by replicating the biogeochemical conditions under the observed basin.

Content in Native Literature Programs.

ERIC Educational Resources Information Center

Grant, Agnes

Including Native literature in school curricula is an important way of enhancing the Native student's self-concept and providing accurate Native cultural knowledge to Native and non-Native students alike. Nevertheless, Canadian school literature programs generally contain neither contemporary nor traditional Native literature. Some programs…

Electrochemically reduced water exerts superior reactive oxygen species scavenging activity in HT1080 cells than the equivalent level of hydrogen-dissolved water

PubMed Central

Hamasaki, Takeki; Harada, Gakuro; Nakamichi, Noboru; Kabayama, Shigeru; Teruya, Kiichiro; Fugetsu, Bunshi; Gong, Wei; Sakata, Ichiro; Shirahata, Sanetaka

2017-01-01

Electrochemically reduced water (ERW) is produced near a cathode during electrolysis and exhibits an alkaline pH, contains richly dissolved hydrogen, and contains a small amount of platinum nanoparticles. ERW has reactive oxygen species (ROS)-scavenging activity and recent studies demonstrated that hydrogen-dissolved water exhibits ROS-scavenging activity. Thus, the antioxidative capacity of ERW is postulated to be dependent on the presence of hydrogen levels; however, there is no report verifying the role of dissolved hydrogen in ERW. In this report, we clarify whether the responsive factor for antioxidative activity in ERW is dissolved hydrogen. The intracellular ROS scavenging activity of ERW and hydrogen-dissolved water was tested by both fluorescent stain method and immuno spin trapping assay. We confirm that ERW possessed electrolysis intensity-dependent intracellular ROS-scavenging activity, and ERW exerts significantly superior ROS-scavenging activity in HT1080 cells than the equivalent level of hydrogen-dissolved water. ERW retained its ROS-scavenging activity after removal of dissolved hydrogen, but lost its activity when autoclaved. An oxygen radical absorbance capacity assay, the 2,2-diphenyl-1-picrylhydrazyl assay and chemiluminescence assay could not detect radical-scavenging activity in both ERW and hydrogen-dissolved water. These results indicate that ERW contains electrolysis-dependent hydrogen and an additional antioxidative factor predicted to be platinum nanoparticles. PMID:28182635

Dissolved-Solids Load in Henrys Fork Upstream from the Confluence with Antelope Wash, Wyoming, Water Years 1970-2009

USGS Publications Warehouse

Foster, Katharine; Kenney, Terry A.

2010-01-01

Annual dissolved-solids load at the mouth of Henrys Fork was estimated by using data from U.S. Geological Survey streamflow-gaging station 09229500, Henrys Fork near Manila, Utah. The annual dissolved-solids load for water years 1970-2009 ranged from 18,300 tons in 1977 to 123,300 tons in 1983. Annual streamflows for this period ranged from 14,100 acre-feet in 1977 to 197,500 acre-feet in 1983. The 25-percent trimmed mean dissolved-solids load for water years 1970-2009 was 44,300 tons per year at Henrys Fork near Manila, Utah. Previous simulations using a SPAtially Referenced Regression On Watershed attributes (SPARROW) model for dissolved solids specific to water year 1991 conditions in the Upper Colorado River Basin predicted an annual dissolved-solids load of 25,000 tons for the Henrys Fork Basin upstream from Antelope Wash. On the basis of computed dissolved-solids load data from Henrys Fork near Manila, Utah, together with estimated annual dissolved-solids load from Antelope Wash and Peoples Canal, this prediction was adjusted to 37,200 tons. As determined by simulations with the Upper Colorado River Basin SPARROW model, approximately 56 percent (14,000 tons per year) of the dissolved-solids load at Henrys Fork upstream from Antelope Wash is associated with the 21,500 acres of irrigated agricultural lands in the upper Henrys Fork Basin.

Electrochemically reduced water exerts superior reactive oxygen species scavenging activity in HT1080 cells than the equivalent level of hydrogen-dissolved water.

PubMed

Hamasaki, Takeki; Harada, Gakuro; Nakamichi, Noboru; Kabayama, Shigeru; Teruya, Kiichiro; Fugetsu, Bunshi; Gong, Wei; Sakata, Ichiro; Shirahata, Sanetaka

2017-01-01

Electrochemically reduced water (ERW) is produced near a cathode during electrolysis and exhibits an alkaline pH, contains richly dissolved hydrogen, and contains a small amount of platinum nanoparticles. ERW has reactive oxygen species (ROS)-scavenging activity and recent studies demonstrated that hydrogen-dissolved water exhibits ROS-scavenging activity. Thus, the antioxidative capacity of ERW is postulated to be dependent on the presence of hydrogen levels; however, there is no report verifying the role of dissolved hydrogen in ERW. In this report, we clarify whether the responsive factor for antioxidative activity in ERW is dissolved hydrogen. The intracellular ROS scavenging activity of ERW and hydrogen-dissolved water was tested by both fluorescent stain method and immuno spin trapping assay. We confirm that ERW possessed electrolysis intensity-dependent intracellular ROS-scavenging activity, and ERW exerts significantly superior ROS-scavenging activity in HT1080 cells than the equivalent level of hydrogen-dissolved water. ERW retained its ROS-scavenging activity after removal of dissolved hydrogen, but lost its activity when autoclaved. An oxygen radical absorbance capacity assay, the 2,2-diphenyl-1-picrylhydrazyl assay and chemiluminescence assay could not detect radical-scavenging activity in both ERW and hydrogen-dissolved water. These results indicate that ERW contains electrolysis-dependent hydrogen and an additional antioxidative factor predicted to be platinum nanoparticles.

Summary and evaluation of the quality of stormwater in Denver, Colorado, 2006-2010

USGS Publications Warehouse

Stevens, Michael R.; Slaughter, Cecil B.

2012-01-01

Stormwater in the Denver area was sampled by the U.S. Geological Survey, in cooperation with the Urban Drainage and Flood Control District, in a network of 5 monitoring stations - 3 on the South Platte River and 2 on streams tributary to the South Platte River, Sand Creek, and Toll Gate Creek beginning in January 2006 and continuing through December 2010. Stormwater samples were analyzed at the U.S. Geological Survey National Water Quality Laboratory during 2006-2010 for water-quality properties such as pH, specific conductance, hardness, and residue on evaporation at 105 degrees Celsius; for constituents such as major ions (calcium, magnesium), organic carbon and nutrients, including ammonia plus organic nitrogen, ammonia, dissolved nitrite plus nitrate, total phosphorus, and orthophosphate; and for metals, including total recoverable and dissolved phases of copper, lead, manganese, and zinc. Samples collected during selected storms were also analyzed for bacteriological indicators such as Escherichia coli and fecal coliform at the Metro Wastewater Reclamation Laboratory. About 200 stormwater samples collected during storms characterize the quality of storm runoff during 2006-2010. In general, the quality of stormwater (2006-2010) has improved for many water-quality constituents, many of which had lower values and concentrations than those in stormwater collected in 2002-2005. However, the physical basis, processes, and the role of dilution that account for these changes are complex and beyond the scope of this report. The water-quality sampling results indicate few exceptions to standards except for dissolved manganese, dissolved zinc, and Escherichia coli. Stormwater collected at the South Platte River below Union Avenue station had about 10 percent acute or chronic dissolved manganese exceedances in samples; samples collected at the South Platte River at Denver station had less than 5 percent acute or chronic dissolved manganese exceedances. In contrast, samples collected at Toll Gate Creek above 6th Avenue at Aurora station, Sand Creek at mouth near Commerce City station, and the South Platte River at Henderson station, each had about 30 to 50 percent exceedances of both acute and chronic dissolved manganese standards. Of the samples collected at Sand Creek at mouth near Commerce City, 1 sample exceeded the acute standard and 4 samples exceeded the chronic standard for dissolved zinc, but no samples collected from the other sites exceeded either standard for zinc. Almost all samples of stormwater analyzed for Escherichia coli exceeded Colorado numeric standards. A numerical standard for fecal coliform is no longer applicable as of 2004. Results from the 2002-2005 study indicated that the general quality of stormwater had improved during 2002-2005 compared to 1998-2001, having fewer exceedances of Colorado standards, and showing downward trends for many water-quality values and concentrations. These trends coincided with general downward or relatively similar mean streamflows for the 2002-2005 compared to 1998-2001, which indicates that dilution may be a smaller influence on values and concentrations than other factors. For this report, downward trends were indicated for many constituents at each station during 2006-2010 compared to 2002-2005. The trends for mean streamflow for 2006-2010 compared to 2002-2005 are upward at all sites except for the South Platte River at Henderson, indicating that dilution by larger flows could be a factor in the downward concentration trends. At the South Platte River below Union Avenue station, downward trends were indicated for hardness, dissolved ammonia, dissolved orthophosphate, and dissolved copper. Upward trends at South Platte River below Union Avenue were indicated for pH. At the South Platte River at Denver station, downward trends were indicated for total ammonia plus organic nitrogen, dissolved ammonia, dissolved nitrite plus nitrate, dissolved orthophosphate, total phosphorus, dissolved organic carbon, and dissolved lead, manganese, and zinc, and total recoverable zinc. An upward trend in properties and constituents at South Platte River at Denver was indicated for pH. At Toll Gate Creek above 6th Avenue at Aurora, downward trends were indicated for residue on evaporation, total ammonia plus organic nitrogen, dissolved ammonia, dissolved orthophosphate, total phosphorus, and total recoverable copper, lead, manganese, and zinc. Upward trends in properties and constituents at Toll Gate Creek above 6th Avenue at Aurora were indicated for pH, specific conductance, and dissolved nitrite plus nitrate. At Sand Creek at mouth near Commerce City, downward trends were indicated for hardness, dissolved calcium, total ammonia plus organic nitrogen, and dissolved ammonia, orthophosphate, manganese, and zinc. An upward trend in properties and constituents at Sand Creek at mouth near Commerce City was indicated for pH. Downward trends at South Platte River at Henderson were indicated for specific conductance, hardness, dissolved magnesium, residue on evaporation, total ammonia plus organic nitrogen, dissolved ammonia, dissolved nitrite plus nitrate, dissolved orthophosphate, total phosphorus, dissolved lead and manganese, and total recoverable copper, lead, manganese, and zinc.

Do Wildfires Promote Woody Species Invasion in a Fire-Adapted Ecosystem? Post-fire Resprouting of Native and Non-native Woody Plants in Central Argentina.

PubMed

Herrero, M Lucrecia; Torres, Romina C; Renison, Daniel

2016-02-01

We asked whether prescribed fire could be a useful management tool to reduce invasion by non-native plants in an ecosystem where native plants are supposed to be adapted to fires. Specifically, we compare the post-fire resprouting response of native and non-native woody species in Chaco Serrano forest of central Argentina. The measurements were carried out in five burnt areas where we selected ten native and seven non-native species. Our response variables were (1) post-fire survival, (2) types of resprouts, and (3) the growth of the resprouts. Our main results show that one year after the fire, survivals of native and non-native species were 0.84 and 0.89, respectively, with variances in survival seven times smaller in the native species group. Type of resprout was also less variable in native species, while growth of the resprouts was similar in native and non-native groups. We interpret that in most cases, the burning a forest with mixed native and non-native plants through prescribed fires will not differentially stop the invasion by non-native woody species even in ecosystems which are presumed to be relatively resistant to fires such as our study area.

Dissolved solids in basin-fill aquifers and streams in the southwestern United States

USGS Publications Warehouse

Anning, David W.; Bauch, Nancy J.; Gerner, Steven J.; Flynn, Marilyn E.; Hamlin, Scott N.; Moore, Stephanie J.; Schaefer, Donald H.; Anderholm, Scott K.; Spangler, Lawrence E.

2007-01-01

The U.S. Geological Survey National Water-Quality Assessment Program performed a regional study in the Southwestern United States (Southwest) to describe the status and trends of dissolved solids in basin-fill aquifers and streams and to determine the natural and human factors that affect dissolved solids. Basin-fill aquifers, which include the Rio Grande aquifer system, Basin and Range basin-fill aquifers, and California Coastal Basin aquifers, are the most extensively used ground-water supplies in the Southwest. Rivers, such as the Colorado, the Rio Grande, and their tributaries, are also important water supplies, as are several smaller river systems that drain internally within the Southwest, or drain externally to the Pacific Ocean in southern California. The study included four components that characterize (1) the spatial distribution of dissolved-solids concentrations in basin-fill aquifers, and dissolved-solids concentrations, loads, and yields in streams; (2) natural and human factors that affect dissolved-solids concentrations; (3) major sources and areas of accumulation of dissolved solids; and (4) trends in dissolved-solids concentrations over time in basin-fill aquifers and streams, and the relation of trends to natural or human factors.

Insight into dissolved organic matter fractions in Lake Wivenhoe during and after a major flood.

PubMed

Aryal, Rupak; Grinham, Alistair; Beecham, Simon

2016-03-01

Dissolved organic matter is an important component of biogeochemical processes in aquatic environments. Dissolved organic matter may consist of a myriad of different fractions and resultant processing pathways. In early January 2011, heavy rainfall occurred across South East Queensland, Australia causing significant catchment inflow into Lake Wivenhoe, which is the largest water supply reservoir for the city of Brisbane, Australia. The horizontal and vertical distributions of dissolved organic matter fractions in the lake during the flood period were investigated and then compared with stratified conditions with no catchment inflows. The results clearly demonstrate a large variation in dissolved organic matter fractions associated with inflow conditions compared with stratified conditions. During inflows, dissolved organic matter concentrations in the reservoir were fivefold lower than during stratified conditions. Within the dissolved organic matter fractions during inflow, the hydrophobic and humic acid fractions were almost half those recorded during the stratified period whilst low molecular weight neutrals were higher during the flood period compared to during the stratified period. Information on dissolved organic matter and the spatial and vertical variations in its constituents' concentrations across the lake can be very useful for catchment and lake management and for selecting appropriate water treatment processes.

Calibration of a dissolved-solids model for the Yampa River basin between Steamboat Springs and Maybell, northwestern Colorado

USGS Publications Warehouse

Parker, R.S.; Litke, D.W.

1987-01-01

The cumulative effects of changes in dissolved solids from a number of coal mines are needed to evaluate effects on downstream water use. A model for determining cumulative effects of streamflow, dissolved-solids concentration, and dissolved-solids load was calibrated for the Yampa River and its tributaries in northwestern Colorado. The model uses accounting principles. It establishes nodes on the stream system and sums water quantity and quality from node to node in the downstream direction. The model operates on a monthly time step for the study period that includes water years 1976 through 1981. Output is monthly mean streamflow, dissolved-solids concentration, and dissolved-solids load. Streamflow and dissolved-solids data from streamflow-gaging stations and other data-collection sites were used to define input data sets to initiate and to calibrate the model. The model was calibrated at four nodes and generally was within 10 percent of the observed values. The calibrated model can compute changes in dissolved-solids concentration or load resulting from the cumulative effects of new coal mines or the expansion of old coal mines in the Yampa River basin. (USGS)

The distribution and stabilisation of dissolved Fe in deep-sea hydrothermal plumes

NASA Astrophysics Data System (ADS)

Bennett, Sarah A.; Achterberg, Eric P.; Connelly, Douglas P.; Statham, Peter J.; Fones, Gary R.; German, Christopher R.

2008-06-01

We have conducted a study of hydrothermal plumes overlying the Mid-Atlantic Ridge near 5° S to investigate whether there is a significant export flux of dissolved Fe from hydrothermal venting to the oceans. Our study combined measurements of plume-height Fe concentrations from a series of 6 CTD stations together with studies of dissolved Fe speciation in a subset of those samples. At 2.5 km down plume from the nearest known vent site dissolved Fe concentrations were ˜ 20 nM. This is much higher than would be predicted from a combination of plume dilution and dissolved Fe(II) oxidation rates, but consistent with stabilisation due to the presence of organic Fe complexes and Fe colloids. Using Competitive Ligand Exchange-Cathodic Stripping Voltammetry (CLE-CSV), stabilised dissolved Fe complexes were detected within the dissolved Fe fraction on the edges of one non-buoyant hydrothermal plume with observed ligand concentrations high enough to account for stabilisation of ˜ 4% of the total Fe emitted from the 5° S vent sites. If these results were representative of all hydrothermal systems, submarine venting could provide 12-22% of the global deep-ocean dissolved Fe budget.

Trend analysis of selected water-quality constituents in the Verde River Basin, central Arizona

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

Baldys, S.

1990-01-01

Temporal trends of eight water quality constituents at six data collection sites in the Verde River basin in central Arizona were investigated using seasonal Kendall tau and ordinary least-squares regression methods of analysis. The constituents are dissolved solids, dissolved sulfate, dissolved arsenic, total phosphorus, pH, total nitrite plus nitrate-nitrogen, dissolved iron, and fecal coliform bacteria. Increasing trends with time in dissolved-solids concentrations of 7 to 8 mg/L/yr at Verde River near Camp Verde were found at significant level. An increasing trend in dissolved-sulfate concentrations of 3.59 mg/L/yr was also found at Verde River near Camp Verde, although at nonsignificant levels.more » Statistically significant decreasing trends with time in dissolved-solids and dissolved-sulfate concentrations were found at Verde River above Horseshoe Reservoir, which is downstream from Verde River near Camp Verde. Observed trends in the other constituents do not indicate the emergence of water quality problems in the Verde River basin. Analysis of the eight water quality constituents generally indicate nonvarying concentration levels after adjustment for seasonality and streamflow were made.« less

Assessing bioavailability of DDT and metabolites in marine sediments using solid-phase microextraction with performance reference compounds.

PubMed

Bao, Lian-Jun; Jia, Fang; Crago, J; Zeng, Eddy Y; Schlenk, D; Gan, Jay

2013-09-01

Solid-phase microextraction (SPME) has often been used to estimate the freely dissolved concentration (Cfree ) of organic contaminants in sediments. A significant limitation in the application of SPME for Cfree measurement is the requirement for attaining equilibrium partition, which is often difficult for strongly hydrophobic compounds such as DDT. A method was developed using SPME with stable isotope-labeled analogues as performance reference compounds (PRCs) to measure Cfree of DDT and metabolites (DDTs) in marine sediments. Six (13) C-labeled or deuterated PRCs were impregnated into polydimethylsiloxane (PDMS) fiber before use. Desorption of PRCs from PDMS fibers and absorption of DDTs from sediment were isotropic in a range of sediments evaluated ex situ under well-mixed conditions. When applied to a historically contaminated marine sediment from a Superfund site, the PRC-SPME method yielded Cfree values identical to those found by using a conventional equilibrium SPME approach (Eq-SPME), whereas the time for mixing was reduced from 9 d to only 9 h. The PRC-SPME method was further evaluated against bioaccumulation of DDTs by Neanthes arenaceodentata in the contaminated sediment with or without amendment of activated carbon or sand. Strong correlations were consistently found between the derived equilibrium concentrations on the fiber and lipid-normalized tissue residues for DDTs in the worms. Results from the present study clearly demonstrated the feasibility of coupling PRCs with SPME sampling to greatly shorten sampling time, thus affording much improved flexibility in the use of SPME for bioavailability evaluation. Copyright © 2013 SETAC.

Effects of crude oil on water and tracer movement in the unsaturated and saturated zones.

PubMed

Delin, Geoffrey N; Herkelrath, William N

2017-05-01

A tracer test was conducted to aid in the investigation of water movement and solute transport at a crude-oil spill site near Bemidji, Minnesota. Time of travel was measured using breakthrough curves for rhodamine WT and bromide tracers moving from the soil surface through oil-contaminated and oil-free unsaturated zones to the saturated zone. Results indicate that the rates of tracer movement were similar in the oil-free unsaturated and saturated zones compared to the oily zones. These results are somewhat surprising given the oil contamination in the unsaturated and saturated zones. Rhodamine tracer breakthrough in the unsaturated and saturated zones in general was delayed in comparison to bromide tracer breakthrough. Peak tracer concentrations for the lysimeters and wells in the oily zone were much greater than at the corresponding depths in the oil-free zone. Water and tracer movement in the oily zone was complicated by soil hydrophobicity and decreased oil saturations toward the periphery of the oil. Preferential flow resulted in reduced tracer interaction with the soil, adsorption, and dispersion and faster tracer movement in the oily zone than expected. Tracers were freely transported through the oily zone to the water table. Recharge calculations support the idea that the oil does not substantially affect recharge in the oily zone. This is an important result indicating that previous model-based assumptions of decreased recharge beneath the oil were incorrect. Results have important implications for modeling the fate and transport of dissolved contaminants at hydrocarbon spill sites. Published by Elsevier B.V.

Equilibrium sampling through membranes (ESTM) of acidic organic pollutants using hollow fibre modules in continuous steady-state mode.

PubMed

Larsson, Niklas; Utterback, Karl; Toräng, Lars; Risberg, Johan; Gustafsson, Per; Mayer, Philipp; Jönsson, Jan Ke

2009-08-01

Hollow fibre (HF) membrane modules were applied in continuous mode for equilibrium sampling through membranes (ESTM) of polar organic pollutants. Phenolic compounds (chlorophenols, cresols and phenol) served as model substances and ESTM was tuned towards the measurement of freely dissolved concentrations (C(free)). HF membrane modules were constructed using thin-walled membrane, 1-m module length and low packing density in order to optimise the uptake kinetics of the analytes into the acceptor solution. Such custom made devices were tested and compared to commercially available modules. The former modules performed best for continuous ESTM. The custom made modules provided steady-state equilibrium within 20-40 min and enrichment that was in general agreement with calculated distribution ratios between acceptor and sample. In experiments during which sample concentration was changed, acceptor response time to decreased sample concentration was around 30 min for custom built modules. In the presence of commercial humic acids, analytes showed lower steady-state enrichment, which is due to a decrease in C(free). Continuous ESTM may be automated and is suggested for use in online determination of C(free) of pollutants and studies on sorption of pollutants. Future studies should include optimisation of the membrane liquid and factors regarding the residence time of the acceptor solution in the fibre lumen. Qualitative aspects of DOM should also be included, as natural DOM can be fractionated. C(free) could be correlated to DOM properties that have previously been shown to influence sorption, such as aromaticity, carboxylic acid content and molecular size.

Enhanced percutaneous permeability of diclofenac using a new U-type dilutable microemulsion.

PubMed

Shevachman, Marina; Garti, Nissim; Shani, Arnon; Sintov, Amnon C

2008-04-01

Enhanced systemic absorption in vivo and percutaneous penetration in vitro was demonstrated after transdermal administration of diclofenac sodium formulated in U-type microemulsion. Diclofenac sodium was solubilized in a typical four-component system consisting of an oil, polyoxyethylene-10EO-oleyl alcohol (Brij 96V) as the surfactant, and 1-hexanol along water dilution line W46 (40 wt % surfactant and 60 wt % oil phase before water titration). Viscosity and small angle X-ray scattering measurements have evidenced bicontinuous structures within water fractions of 0.25 and 0.5 along the dilution line. Self-diffusion NMR studies showed that drug molecules accumulated in the interfacial film and, to some extent, dissolved in the oil. Relative to a commercial macro-emulsion cream (Voltaren Emulgel), microemulsions containing paraffin oil or isopropyl myristate increased the in vivo transdermal penetration rate of diclofenac by two order of magnitude, whereas the rat plasma levels were increased by one order of magnitude. The in vitro data obtained from excised rat skin were comparable to the in vivo results, but suffered from discrepancies from the ideal in vivo-in vitro correlation, which might be explained by optimal in vitro conditions of perfusion and hydration. It has also been found that when jojoba oil is formulated as the oil phase in the microemulsion, the penetration rate of the drug decreases significantly. Based on the three-dimensional structure of jojoba oil, the wax is presumed to prevent the drug from being freely diffused into the skin while migrating from the interfacial film into the continuous oil phase.

Estimating risk at a Superfund site using passive sampling devices as biological surrogates in human health risk models.

PubMed

Allan, Sarah E; Sower, Gregory J; Anderson, Kim A

2011-10-01

Passive sampling devices (PSDs) sequester the freely dissolved fraction of lipophilic contaminants, mimicking passive chemical uptake and accumulation by biomembranes and lipid tissues. Public Health Assessments that inform the public about health risks from exposure to contaminants through consumption of resident fish are generally based on tissue data, which can be difficult to obtain and requires destructive sampling. The purpose of this study is to apply PSD data in a Public Health Assessment to demonstrate that PSDs can be used as a biological surrogate to evaluate potential human health risks and elucidate spatio-temporal variations in risk. PSDs were used to measure polycyclic aromatic hydrocarbons (PAHs) in the Willamette River; upriver, downriver and within the Portland Harbor Superfund megasite for 3 years during wet and dry seasons. Based on an existing Public Health Assessment for this area, concentrations of PAHs in PSDs were substituted for fish tissue concentrations. PSD measured PAH concentrations captured the magnitude, range and variability of PAH concentrations reported for fish/shellfish from Portland Harbor. Using PSD results in place of fish data revealed an unacceptable risk level for cancer in all seasons but no unacceptable risk for non-cancer endpoints. Estimated cancer risk varied by several orders of magnitude based on season and location. Sites near coal tar contamination demonstrated the highest risk, particularly during the dry season and remediation activities. Incorporating PSD data into Public Health Assessments provides specific spatial and temporal contaminant exposure information that can assist public health professionals in evaluating human health risks. Copyright © 2011 Elsevier Ltd. All rights reserved.

Estimating risk at a Superfund site using passive sampling devices as biological surrogates in human health risk models

PubMed Central

Allan, Sarah E.; Sower, Gregory J.; Anderson, Kim A.

2013-01-01

Passive sampling devices (PSDs) sequester the freely dissolved fraction of lipophilic contaminants, mimicking passive chemical uptake and accumulation by biomembranes and lipid tissues. Public Health Assessments that inform the public about health risks from exposure to contaminants through consumption of resident fish are generally based on tissue data, which can be difficulties to obtain and requires destructive sampling. The purpose of this study is to apply PSD data in a Public Health Assessment to demonstrate that PSDs can be used as a biological surrogate to evaluate potential human health risks and elucidate spatio-temporal variations in risk. PSDs were used to measure polycyclic aromatic hydrocarbons (PAHs) in the Willamette River; upriver, downriver and within the Portland Harbor Superfund megasite for three years during wet and dry seasons. Based on an existing Public Health Assessment for this area, concentrations of PAHs in PSDs were substituted for fish tissue concentrations. PSD measured PAH concentrations captured the magnitude, range and variability of PAH concentrations reported for fish/shellfish from Portland Harbor. Using PSD results in place of fish data revealed an unacceptable risk level for cancer in all seasons but no unacceptable risk for non-cancer endpoints. Estimated cancer risk varied by several orders of magnitude based on season and location. Sites near coal tar contamination demonstrated the highest risk, particularly during the dry season and remediation activities. Incorporating PSD data into Public Health Assessments provides specific spatial and temporal contaminant exposure information that can assist public health professionals in evaluating human health risks. PMID:21741671

Particle-scale measurement of PAH aqueous equilibrium partitioning in impacted sediments.

PubMed

Ghosh, Upal; Hawthorne, Steven B

2010-02-15

This research investigated the particle-scale processes that control aqueous equilibrium partitioning of PAHs in manufactured gas plant (MGP) site sediments. Dominant particle types in impacted sediments (sand, wood, coal/coke, and pitch) were physically separated under a microscope for equilibrium assessments. Solid-phase microextraction (SPME) combined with selected ion monitoring GC/MS and perdeuterated PAH internal standards were used to determine freely dissolved PAH concentrations in small (0.1-1 mL) water samples at concentrations as low as microg/L (for lower molecular weight PAHs) to ng/L (for higher molecular weight PAHs). For every particle class the initial release of PAHs into the aqueous phase was rapid, and an apparent equilibrium was reached in a matter of days. The average ratio of aqueous total PAH concentration for pitch vs coal/coke particles for eight sediment samples was 20. Thus, sediments that had aged in the field for many decades were not at equilibrium and were still going through a slow process of contaminant mass transfer between the different particle types. A possible consequence of this slow aging process is further lowering of the activity of the chemical as mass transfer is achieved to new sorption sites with time. This study also found that the presence of black carbon even at the level of (1)/(3) of sediment organic carbon does not necessarily imply a BC-dominated sorption behavior, rather source pitch particles if present may dominate PAH partitioning. To our knowledge this is the first report of equilibrium partitioning assessment conducted at the sediment particle scale.

Assessing Bioavailability of DDT and Metabolites in Marine Sediments using Solid-Phase Microextraction with Performance Reference Compounds

PubMed Central

Bao, Lian-Jun; Jia, Fang; Crago, J.; Zeng, Eddy Y.; Schlenk, D.; Gan, Jay

2014-01-01

Solid-phase microextraction (SPME) has often been used to estimate the freely dissolved concentration (Cfree) of organic contaminants in sediments. A significant limitation in the application of SPME for Cfree measurement is the requirement for attaining equilibrium partition, which is often difficult for strongly hydrophobic compounds such as DDT. A method was developed using SPME with stable isotope-labeled analogues as performance reference compounds (PRCs) to measure Cfree of DDT and metabolites (DDTs) in marine sediments. Six 13C-labeled or deuterated PRCs were impregnated into polydimethylsiloxane (PDMS) fiber before use. Desorption of PRCs from PDMS fibers and absorption of DDTs from sediment were isotropic in a range of sediments evaluated ex situ under well-mixed conditions. When applied to a historically contaminated marine sediment from a Superfund site, the PRC-SPME method yielded Cfree values identical to those found by using a conventional equilibrium SPME approach (Eq-SPME), wherease the time for mixing was reduced from 9 d to only 9 h. The PRC-SPME method was further evaluated against bioaccumulation of DDTs by Neanthes arenaceodentata in the contaminated sediment with or without amendment of activated carbon or sand. Strong correlations were consistently found between the derived equilibrium concentrations on the fiber and lipid-normalized tissue residues for DDTs in the worms. Results from the present study clearly demonstrated the feasibility of coupling PRCs with SPME sampling to greatly shorten sampling time, thus affording much improved flexibility in the use of SPME for bioavailability evaluation. Environ Toxicol Chem 2013;32:1946–1953. PMID:23661411

Screening for Stockholm Convention persistent organic pollutants in the Bosna River (Bosnia and Herzogovina).

PubMed

Harman, Christopher; Grung, Merete; Djedjibegovic, Jasmina; Marjanovic, Aleksandra; Sober, Miroslav; Sinanovic, Kemo; Fjeld, Eirik; Rognerud, Sigurd; Ranneklev, Sissel Brit; Larssen, Thorjørn

2013-02-01

The Stockholm Convention, which aspires to manage persistent organic pollutants (POPs) at the international level, was recently ratified in Bosnia and Herzegovina (BiH). Despite this fact, there is in general a paucity of data regarding the levels of POPs in the environment in BiH. In the present study, screening for POPs was conducted in one of the country's major rivers, the Bosna. A two-pronged approach was applied using passive samplers to detect the freely dissolved and bioavailable concentrations in the water phase and sediment analysis to provide an integrated measure of historical contamination. At several places along the river, the concentrations of polycyclic aromatic hydrocarbons (PAH) were high and exhibited potential for both chronic and acute effects to biota. River water also showed elevated concentrations of PAH, up to 480 ng L(-1) near the city of Doboj, and diagnostic ratios suggested combustion sources for the contamination present in both types of sample. The levels of the other contaminants measured-polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs) and polybrominated diphenyl ethers--were generally low in the water phase. However, PCBs and some OCPs were present in river sediments at levels which breach the international criteria and thus suggest potential for ecological damage. Additionally, the levels of heptachlor breached these criteria in many of the sites investigated. This study presents the first screening data for some of these Stockholm Convention relevant compounds in BiH and reveals both low concentrations of some chemical groups, but significant point sources and historic contamination for others.

Bioavailability assessments following biochar and activated carbon amendment in DDT-contaminated soil.

PubMed

Denyes, Mackenzie J; Rutter, Allison; Zeeb, Barbara A

2016-02-01

The effects of 2.8% w/w granulated activated carbon (GAC) and two types of biochar (Burt's and BlueLeaf) on DDT bioavailability in soil (39 μg/g) were investigated using invertebrates (Eisenia fetida), plants (Cucurbita pepo spp. pepo) and a polyoxymethylene (POM) passive sampler method. Biochar significantly reduced DDT accumulation in E. fetida (49%) and showed no detrimental effects to invertebrate health. In contrast, addition of GAC caused significant toxic effects (invertebrate avoidance and decreased weight) and did not significantly reduce the accumulation of DDT into invertebrate tissue. None of the carbon amendments reduced plant uptake of DDT. Bioaccumulation of 4,4'DDT and 4,4'-DDE in plants (C. pepo spp. pepo) and invertebrates (E. fetida) was assessed using bioaccumulation factors (BAFs) and compared to predicted bioavailability using the freely-dissolved porewater obtained from a polyoxymethylene (POM) equilibrium biomimetic method. The bioavailable fraction predicted by the POM samplers correlated well with measured invertebrate uptake (<50% variability), but was different from plant root uptake by 134%. A literature review of C. pepo BAFs across DDT soil contamination levels and the inclusion of field data from a 2.5 μg/g DDT-contaminated site found that these plants exhibit a concentration threshold effect at [DDT](soil) > 10 μg/g. The results of these studies illustrate the importance of including plants in bioavailability studies as the use of carbon materials for in situ contaminant sorption moves from predominantly sediment to soil remediation technologies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effects of soil water saturation on sampling equilibrium and kinetics of selected polycyclic aromatic hydrocarbons.

PubMed

Kim, Pil-Gon; Roh, Ji-Yeon; Hong, Yongseok; Kwon, Jung-Hwan

2017-10-01

Passive sampling can be applied for measuring the freely dissolved concentration of hydrophobic organic chemicals (HOCs) in soil pore water. When using passive samplers under field conditions, however, there are factors that might affect passive sampling equilibrium and kinetics, such as soil water saturation. To determine the effects of soil water saturation on passive sampling, the equilibrium and kinetics of passive sampling were evaluated by observing changes in the distribution coefficient between sampler and soil (K sampler/soil ) and the uptake rate constant (k u ) at various soil water saturations. Polydimethylsiloxane (PDMS) passive samplers were deployed into artificial soils spiked with seven selected polycyclic aromatic hydrocarbons (PAHs). In dry soil (0% water saturation), both K sampler/soil and k u values were much lower than those in wet soils likely due to the contribution of adsorption of PAHs onto soil mineral surfaces and the conformational changes in soil organic matter. For high molecular weight PAHs (chrysene, benzo[a]pyrene, and dibenzo[a,h]anthracene), both K sampler/soil and k u values increased with increasing soil water saturation, whereas they decreased with increasing soil water saturation for low molecular weight PAHs (phenanthrene, anthracene, fluoranthene, and pyrene). Changes in the sorption capacity of soil organic matter with soil water content would be the main cause of the changes in passive sampling equilibrium. Henry's law constant could explain the different behaviors in uptake kinetics of the selected PAHs. The results of this study would be helpful when passive samplers are deployed under various soil water saturations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Determination of polydimethylsiloxane–water partition coefficients for ten 1-chloro-4-[2,2,2-trichloro-1-(4-chlorophenyl)ethyl]benzene-related compounds and twelve polychlorinated biphenyls using gas chromatography/mass spectrometry

USGS Publications Warehouse

Eganhouse, Robert P.

2016-01-01

Polymer-water partition coefficients (Kpw) of ten DDT-related compounds were determined in pure water at 25 °C using commercial polydimethylsiloxane-coated optical fiber. Analyte concentrations were measured by thermal desorption-gas chromatography/full scan mass spectrometry (TD–GC/MSFS; fibers) and liquid injection-gas chromatography/selected ion monitoring mass spectrometry (LI–GC/MSSIM; water). Equilibrium was approached from two directions (fiber uptake and depletion) as a means of assessing data concordance. Measured compound-specific log Kpw values ranged from 4.8 to 6.1 with an average difference in log Kpw between the two approaches of 0.05 log units (∼12% of Kpw). Comparison of the experimentally-determined log Kpw values with previously published data confirmed the consistency of the results and the reliability of the method. A second experiment was conducted with the same ten DDT-related compounds and twelve selected PCB (polychlorinated biphenyl) congeners under conditions characteristic of a coastal marine field site (viz., seawater, 11 °C) that is currently under investigation for DDT and PCB contamination. Equilibration at lower temperature and higher ionic strength resulted in an increase in log Kpw for the DDT-related compounds of 0.28–0.49 log units (61–101% of Kpw), depending on the analyte. The increase in Kpw would have the effect of reducing by approximately half the calculated freely dissolved pore-water concentrations (Cfree). This demonstrates the importance of determining partition coefficients under conditions as they exist in the field.

Spatially referenced statistical assessment of dissolved-solids load sources and transport in streams of the Upper Colorado River Basin

USGS Publications Warehouse

Kenney, Terry A.; Gerner, Steven J.; Buto, Susan G.; Spangler, Lawrence E.

2009-01-01

The Upper Colorado River Basin (UCRB) discharges more than 6 million tons of dissolved solids annually, about 40 to 45 percent of which are attributed to agricultural activities. The U.S. Department of the Interior estimates economic damages related to salinity in excess of $330 million annually in the Colorado River Basin. Salinity in the UCRB, as measured by dissolved-solids load and concentration, has been studied extensively during the past century. Over this period, a solid conceptual understanding of the sources and transport mechanisms of dissolved solids in the basin has been developed. This conceptual understanding was incorporated into the U.S. Geological Survey Spatially Referenced Regressions on Watershed Attributes (SPARROW) surface-water quality model to examine statistically the dissolved-solids supply and transport within the UCRB. Geologic and agricultural sources of dissolved solids in the UCRB were defined and represented in the model. On the basis of climatic and hydrologic conditions along with data availability, water year 1991 was selected for examination with SPARROW. Dissolved-solids loads for 218 monitoring sites were used to calibrate a dissolved-solids SPARROW model for the UCRB. The calibrated model generally captures the transport mechanisms that deliver dissolved solids to streams of the UCRB as evidenced by R2 and yield R2 values of 0.98 and 0.71, respectively. Model prediction error is approximated at 51 percent. Model results indicate that of the seven geologic source groups, the high-yield sedimentary Mesozoic rocks have the largest yield of dissolved solids, about 41.9 tons per square mile (tons/mi2). Irrigated sedimentary-clastic Mesozoic lands have an estimated yield of 1,180 tons/mi2, and irrigated sedimentary-clastic Tertiary lands have an estimated yield of 662 tons/mi2. Coefficients estimated for the seven landscape transport characteristics seem to agree well with the conceptual understanding of the role they play in the delivery of dissolved solids to streams in the UCRB. Predictions of dissolved-solids loads were generated for more than 10,000 stream reaches of the stream network defined in the UCRB. From these estimates, the downstream accumulation of dissolved solids, including natural and agricultural components, were examined in selected rivers. Contributions from each of the 11 dissolved-solids sources were also examined at select locations in the Grand, Green, and San Juan Divisions of the UCRB. At the downstream boundary of the UCRB, the Colorado River at Lees Ferry, Arizona, monitoring site, the dissolved-solids contribution of irrigated agricultural lands and natural sources were about 45 and 57 percent, respectively. Finally, model predictions, including the contributions of natural and agricultural sources for selected locations in the UCRB, were compared with results from two previous studies.

76 FR 46832 - Notice of Submission of Proposed Information Collection to OMB; Assessment of Native American...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-03

... Proposed Information Collection to OMB; Assessment of Native American, Alaska Native, and Native Hawaiian Housing Needs AGENCY: Office of the Chief Information Officer, HUD. ACTION: Notice. SUMMARY: The proposed... consistent information describing the needs of the Native American, Alaska Native, and Native Hawaiian...

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

PubMed Central

MacLean, Brendan; Tomazela, Daniela M.; Shulman, Nicholas; Chambers, Matthew; Finney, Gregory L.; Frewen, Barbara; Kern, Randall; Tabb, David L.; Liebler, Daniel C.; MacCoss, Michael J.

2010-01-01

Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Availability: Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project. Contact: brendanx@u.washington.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20147306

Frustration-guided motion planning reveals conformational transitions in proteins

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

Budday, Dominik; Fonseca, Rasmus; Leyendecker, Sigrid

Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here in this paper, we present a new, robotics-inspired motion planning procedure called dCCRRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eightmore » proteins determined in two conformations separated by, on average, 7.5Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. Additionally, we then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions.Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/.« less