The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

PubMed Central

Hope Wilkinson, Katheryn; Strait, Jacqueline M.; Hozalski, Raymond M.; Sadowksy, Michael J.; Hamilton, Matthew J.

2015-01-01

The bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (a Variovorax sp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was a Nitrospira sp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; <0.07%) and no ammonia-oxidizing Archaea were detected in the profiles. Quantitative PCR of amoA genes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possess amoA genes similar to those of previously described AOB. PMID:26209671

Transformation of molecular weight distributions of dissolved organic carbon and UV-absorbing compounds at full-scale wastewater-treatment plants.

PubMed

Esparza-Soto, Mario; Fox, Peter; Westerhoff, Paul

2006-03-01

The molecular-weight distribution (MWD) of wastewater dissolved-organic carbon (DOC) was determined in samples from seven full-scale wastewater-treatment plants (WWTPs) that use different biological treatments (air activated sludge [air-AS], pure-oxygen AS [O2-AS], and trickling filters). The research objective was to determine how different biological treatments influenced the MWD of wastewater DOC. Primary sedimentation effluent DOC from most of the WWTPs exhibited a skewed distribution toward the low-molecular-weight fraction (MWF) (40 to 50%, < 0.5 K Daltons [KDa]). The Air-AS effluent DOC exhibited a centrally clustered distribution, with the majority of DOC in the intermediate MWF (0.5 to 3 KDa). The O2-AS effluent DOC exhibited a skewed distribution toward the high MWF (> 3 KDa). The removal of DOC by air- and O2-AS bacteria followed trends predicted by a macromolecule degradation model. Trickling-filter effluent DOC exhibited a skewed distribution toward the high MWF (50% DOC, > 3 KDa).

Effect of biological and chemical oxidation on the removal of estrogenic compounds (NP and BPA) from wastewater: an integrated assessment procedure.

PubMed

Bertanza, Giorgio; Pedrazzani, Roberta; Dal Grande, Mario; Papa, Matteo; Zambarda, Valerio; Montani, Claudia; Steimberg, Nathalie; Mazzoleni, Giovanna; Di Lorenzo, Diego

2011-04-01

A major source of the wide presence of EDCs (Endocrine Disrupting Compounds) in water bodies is represented by direct/indirect discharge of sewage. Recent scientific literature reports data about their trace concentration in water, sediments and aquatic organisms, as well as removal efficiencies of different wastewater treatment schemes. Despite the availability of a huge amount of data, some doubts still persist due to the difficulty in evaluating synergistic effects of trace pollutants in complex matrices. In this paper, an integrated assessment procedure was used, based on chemical and biological analyses, in order to compare the performance of two full scale biological wastewater treatment plants (either equipped with conventional settling tanks or with an ultrafiltration membrane unit) and tertiary ozonation (pilot scale). Nonylphenol and bisphenol A were chosen as model EDCs, together with the parent compounds mono- and di-ethoxylated nonylphenol (quantified by means of GC-MS). Water estrogenic activity was evaluated by applying the human breast cancer MCF-7 based reporter gene assay. Process parameters (e.g., sludge age, temperature) and conventional pollutants (e.g., COD, suspended solids) were also measured during monitoring campaigns. Conventional activated sludge achieved satisfactory removal of both analytes and estrogenicity. A further reduction of biological activity was exerted by MBR (Membrane Biological Reactor) as well as ozonation; the latter contributed also to decrease EDC concentrations. Copyright © 2011 Elsevier Ltd. All rights reserved.

Removal of toxic metals during biological treatment of landfill leachates.

PubMed

Robinson, T

2017-05-01

Progressive implementation of the European Water Framework Directive has resulted in substantial changes in limits for discharges of heavy metals both to watercourses, and to sewer. The objective of this paper is to provide original, real, full-scale data obtained for removal of metals during aerobic biological leachate treatment, and also to report on studies carried out to look at further trace metal removal. Polishing technologies examined and investigated include; the incorporation of ultrafiltration (UF) membranes into biological treatment systems, the use of ion exchange, and of activated carbon polishing processes. Ultrafiltration was able to provide a 60 percent reduction in COD values in treated leachates, compared with COD values found in settled/clarified effluents. Removal rates for COD varied from 30.5 to 79.8 percent. Additionally, ultrafiltration of treated leachates significantly reduced both chromium and nickel concentrations of effluents by 61.6% and 34.3% respectively (median values). Despite mean reductions of chromium (9.7%) and nickel (13.7%) noted during the ion exchange trials, these results would not justify use of this technology for metals removal at full-scale. Further preliminary studies used pulverized activated carbon (PAC) polishing of UF effluents to demonstrate that significant (up to 80 per cent) removal of COD, TOC and heavy metals could readily be achieved by doses of up to 10g/l of suitable activated carbons. Additional evidence is provided that many trace metals are present not in ionic form, but as organic complexes; this is likely to make their removal to low levels more difficult and expensive. Copyright © 2016 Elsevier Ltd. All rights reserved.

Occurrence and removal of pharmaceuticals, hormones, personal care products, and endocrine disrupters in a full-scale water reclamation plant.

PubMed

Tran, Ngoc Han; Gin, Karina Yew-Hoong

2017-12-01

This study provided the first comprehensive data on the occurrence and removal of twenty-five target emerging contaminants (ECs) in a full-scale water reclamation plant (WRP) in the Southeast Asian region. Nineteen out of the twenty-five ECs were ubiquitously detected in raw influent samples. Concentrations of the detected ECs in raw influent samples ranged substantially from 44.3 to 124,966ng/L, depending upon the compound and sampling date. The elimination of ECs in full-scale conventional activated sludge (CAS) and membrane bioreactor (MBR) systems at a local WRP was evaluated and compared. Several ECs, such as acetaminophen, atenolol, fenoprofen, indomethacin, ibuprofen, and oxybenzone, exhibited excellent removal efficiencies (>90%) in biological wastewater treatment processes, while some of the investigated compounds (carbamazepine, crotamiton, diclofenac, and iopamidol) appeared to be persistent in the both CAS and MBR systems. Field-based monitoring results showed that MBR outperformed CAS in the elimination of most target ECs. The relationship between molecular characteristics of ECs (i.e. physicochemical properties and structural features) and their removal efficiencies during biological wastewater treatment was also elucidated. Excellent removal efficiencies (>90%) were often noted for ECs with the sole presence of electron donating groups (i.e. phenolic [OH], amine [NH 2 ], methoxy [OCH 3 ], phenoxy [OC 6 H 5 ], or alkyl groups). Conversely, ECs with the absence of electron donating groups or the predominance of strong electron withdrawing groups (e.g. halogenated, carbonyl, carboxyl, and sulfonamide) tended to show poor removal efficiencies (<30%) in biological wastewater treatment processes. Copyright © 2017 Elsevier B.V. All rights reserved.

Oxygen Transfer in Moving Bed Biofilm Reactor and Integrated Fixed Film Activated Sludge Processes.

PubMed

2017-11-17

A demonstrated approach to design the, so-called, medium-bubble air diffusion network for oxygen transfer into the aerobic zone(s) of moving bed biofilm reactor (MBBR) and integrated fixed-film activated sludge (IFAS) processes is described in this paper. Operational full-scale biological water resource recovery systems treating municipal sewerage demonstrate that medium-bubble air diffusion networks designed using the method presented here provide reliable service. Further improvement is possible, however, as knowledge gaps prevent more rational process designs. Filling such knowledge gaps can potentially result in higher performing and more economical systems. Small-scale system testing demonstrates significant enhancement of oxygen transfer capacity due to the presence of media, but quantification of such effects in full-scale systems is lacking, and is needed. Establishment of the relationship between diffuser submergence, aeration rate, and biofilm carrier fill fraction will enhance MBBR and IFAS aerobic process design, cost, and performance. Limited testing of full-scale systems is available to allow computation of alpha valuess. As with clean water testing of full-scale systems, further full-scale testing under actual operating conditions is required to more fully quantify MBBR and IFAS system oxygen transfer performance under a wide range of operating conditions. Control of MBBR and IFAS aerobic zone oxygen transfer systems can be optimized by recognizing that varying residual dissolved oxygen (DO) concentrations are needed, depending on operating conditions. For example, the DO concentration in the aerobic zone of nitrifying IFAS processes can be lowered during warm weather conditions when greater suspended growth nitrification can occur, resulting in the need for reduced nitrification by the biofilm compartment. Further application of oxygen transfer control approaches used in activated sludge systems to MBBR and IFAS systems, such as ammonia-based oxygen transfer system control, has been demonstrated to further improve MBBR and IFAS system energy-efficiency.

Probabilistic parameter estimation of activated sludge processes using Markov Chain Monte Carlo.

PubMed

Sharifi, Soroosh; Murthy, Sudhir; Takács, Imre; Massoudieh, Arash

2014-03-01

One of the most important challenges in making activated sludge models (ASMs) applicable to design problems is identifying the values of its many stoichiometric and kinetic parameters. When wastewater characteristics data from full-scale biological treatment systems are used for parameter estimation, several sources of uncertainty, including uncertainty in measured data, external forcing (e.g. influent characteristics), and model structural errors influence the value of the estimated parameters. This paper presents a Bayesian hierarchical modeling framework for the probabilistic estimation of activated sludge process parameters. The method provides the joint probability density functions (JPDFs) of stoichiometric and kinetic parameters by updating prior information regarding the parameters obtained from expert knowledge and literature. The method also provides the posterior correlations between the parameters, as well as a measure of sensitivity of the different constituents with respect to the parameters. This information can be used to design experiments to provide higher information content regarding certain parameters. The method is illustrated using the ASM1 model to describe synthetically generated data from a hypothetical biological treatment system. The results indicate that data from full-scale systems can narrow down the ranges of some parameters substantially whereas the amount of information they provide regarding other parameters is small, due to either large correlations between some of the parameters or a lack of sensitivity with respect to the parameters. Copyright © 2013 Elsevier Ltd. All rights reserved.

More than a decade of experience of landfill leachate treatment with a full-scale anammox plant combining activated sludge and activated carbon biofilm.

PubMed

Azari, Mohammad; Walter, Uwe; Rekers, Volker; Gu, Ji-Dong; Denecke, Martin

2017-05-01

The performance of biological treatment for high ammonium removal from landfill leachate has been demonstrated. The plant was upgraded combining the activated sludge process followed by activated carbon reactor. Based on a long-term analysis of data collected from 2006 to 2015, the average total nitrogen removal efficiency of 94% was achieved for wastewaters with a C: N ratio varying from 1 to 5 kg-COD kg-TN -1 . But without the presence of activated carbon reactor, the average of biological removal efficiency for total nitrogen was only 82% ± 6% for the activated sludge stage. It means that up to 20% of the nitrogen in the influent can only be eliminated by microorganisms attached to granular activated carbon. After upgrades of the plant, the energy efficiency showed a reduction in the specific energy demand from 1.6 to less than 0.2 kWh m -3 . Methanol consumption and sludge production was reduced by 91% and 96%, respectively. Fluorescent in situ Hybridization was used for microbial diversity analysis on floccular sludge and granular biofilm samples. Anaerobic ammonium oxidation (anammox) bacteria and nitrifiers were detected and Candidatus Scalindua was found in two forms of flocs and biofilms. Due to stochastic risk assessment based on the long-term data analysis given in this research, the treatment criteria were achieved and the combination of granular activated carbon biofilm process and activated sludge can be a novel and sought approach to better enrich anammox biomass for full-scale treatment applications to reduce operating costs and promote nutrient removal stability and efficiency. Copyright © 2017 Elsevier Ltd. All rights reserved.

Removal of Antibiotics in Biological Wastewater Treatment Systems-A Critical Assessment Using the Activated Sludge Modeling Framework for Xenobiotics (ASM-X).

PubMed

Polesel, Fabio; Andersen, Henrik R; Trapp, Stefan; Plósz, Benedek Gy

2016-10-04

Many scientific studies present removal efficiencies for pharmaceuticals in laboratory-, pilot-, and full-scale wastewater treatment plants, based on observations that may be impacted by theoretical and methodological approaches used. In this Critical Review, we evaluated factors influencing observed removal efficiencies of three antibiotics (sulfamethoxazole, ciprofloxacin, tetracycline) in pilot- and full-scale biological treatment systems. Factors assessed include (i) retransformation to parent pharmaceuticals from e.g., conjugated metabolites and analogues, (ii) solid retention time (SRT), (iii) fractions sorbed onto solids, and (iv) dynamics in influent and effluent loading. A recently developed methodology was used, relying on the comparison of removal efficiency predictions (obtained with the Activated Sludge Model for Xenobiotics (ASM-X)) with representative measured data from literature. By applying this methodology, we demonstrated that (a) the elimination of sulfamethoxazole may be significantly underestimated when not considering retransformation from conjugated metabolites, depending on the type (urban or hospital) and size of upstream catchments; (b) operation at extended SRT may enhance antibiotic removal, as shown for sulfamethoxazole; (c) not accounting for fractions sorbed in influent and effluent solids may cause slight underestimation of ciprofloxacin removal efficiency. Using tetracycline as example substance, we ultimately evaluated implications of effluent dynamics and retransformation on environmental exposure and risk prediction.

The effect of primary sedimentation on full-scale WWTP nutrient removal performance.

PubMed

Puig, S; van Loosdrecht, M C M; Flameling, A G; Colprim, J; Meijer, S C F

2010-06-01

Traditionally, the performance of full-scale wastewater treatment plants (WWTPs) is measured based on influent and/or effluent and waste sludge flows and concentrations. Full-scale WWTP data typically have a high variance which often contains (large) measurement errors. A good process engineering evaluation of the WWTP performance is therefore difficult. This also makes it usually difficult to evaluate effect of process changes in a plant or compare plants to each other. In this paper we used a case study of a full-scale nutrient removing WWTP. The plant normally uses presettled wastewater, as a means to increase the nutrient removal the plant was operated for a period by-passing raw wastewater (27% of the influent flow). The effect of raw wastewater addition has been evaluated by different approaches: (i) influent characteristics, (ii) design retrofit, (iii) effluent quality, (iv) removal efficiencies, (v) activated sludge characteristics, (vi) microbial activity tests and FISH analysis and, (vii) performance assessment based on mass balance evaluation. This paper demonstrates that mass balance evaluation approach helps the WWTP engineers to distinguish and quantify between different strategies, where others could not. In the studied case, by-passing raw wastewater (27% of the influent flow) directly to the biological reactor did not improve the effluent quality and the nutrient removal efficiency of the WWTP. The increase of the influent C/N and C/P ratios was associated to particulate compounds with low COD/VSS ratio and a high non-biodegradable COD fraction. Copyright 2010 Elsevier Ltd. All rights reserved.

Identification of glucose-fermenting bacteria in a full-scale enhanced biological phosphorus removal plant by stable isotope probing.

PubMed

Nielsen, Jeppe Lund; Nguyen, Hien; Meyer, Rikke Louise; Nielsen, Per Halkjær

2012-07-01

Microbiology in wastewater treatment has mainly been focused on problem-causing filamentous bacteria or bacteria directly involved in nitrogen and phosphorus removal, and to a lesser degree on flanking groups, such as hydrolysing and fermenting bacteria. However, these groups constitute important suppliers of readily degradable substrates for the overall processes in the plant. This study aimed to identify glucose-fermenting bacteria in a full-scale enhanced biological phosphorus removal (EBPR) wastewater treatment plant (WWTP), and to determine their abundance in similar WWTPs. Glucose-fermenting micro-organisms were identified by an in situ approach using RNA-based stable isotope probing. Activated sludge was incubated anaerobically with (13)C(6)-labelled glucose, and (13)C-enriched rRNA was subsequently reverse-transcribed and used to construct a 16S rRNA gene clone library. Phylogenetic analysis of the library revealed the presence of two major phylogenetic groups of gram-positive bacteria affiliating with the genera Tetrasphaera, Propionicimonas (Actinobacteria), and Lactococcus and Streptococcus (Firmicutes). Specific oligonucleotide probes were designed for fluorescence in situ hybridization (FISH) to specifically target the glucose-fermenting bacteria identified in this study. The combination of FISH with microautoradiography confirmed that Tetrasphaera, Propionicimonas and Streptococcus were the dominant glucose fermenters. The probe-defined fermenters were quantified in 10 full-scale EBPR plants and averaged 39 % of the total biovolume. Tetrasphaera and Propionicimonas were the most abundant glucose fermenters (average 33 and 4 %, respectively), while Streptococcus and Lactococcus were present only in some WWTPs (average 1 and 0.4 %, respectively). Thus the population of actively metabolizing glucose fermenters seems to occupy a relatively large component of the total biovolume.

Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant.

PubMed

Oh, Seungdae; Hammes, Frederik; Liu, Wen-Tso

2018-01-01

Microorganisms inhabiting filtration media of a drinking water treatment plant can be beneficial, because they metabolize biodegradable organic matter from source waters and those formed during disinfection processes, leading to the production of biologically stable drinking water. However, which microbial consortia colonize filters and what metabolic capacity they possess remain to be investigated. To gain insights into these issues, we performed metagenome sequencing and analysis of microbial communities in three different filters of a full-scale drinking water treatment plant (DWTP). Filter communities were sampled from a rapid sand filter (RSF), granular activated carbon filter (GAC), and slow sand filter (SSF), and from the Schmutzdecke (SCM, a biologically active scum layer accumulated on top of SSF), respectively. Analysis of community phylogenetic structure revealed that the filter bacterial communities significantly differed from those in the source water and final effluent communities, respectively. Network analysis identified a filter-specific colonization pattern of bacterial groups. Bradyrhizobiaceae were abundant in GAC, whereas Nitrospira were enriched in the sand-associated filters (RSF, SCM, and SSF). The GAC community was enriched with functions associated with aromatics degradation, many of which were encoded by Rhizobiales (∼30% of the total GAC community). Predicting minimum generation time (MGT) of prokaryotic communities suggested that the GAC community potentially select fast-growers (<15 h of MGT) among the four filter communities, consistent with the highest dissolved organic matter removal rate by GAC. Our findings provide new insights into the community phylogenetic structure, colonization pattern, and metabolic capacity that potentially contributes to organic matter removal achieved in the biofiltration stages of the full-scale DWTP. Copyright © 2017 Elsevier Ltd. All rights reserved.

An investigation into studying of the activated sludge foaming potential by using physicochemical parameters.

PubMed

Hladikova, K; Ruzickova, I; Klucova, P; Wanner, J

2002-01-01

This paper examines how the physicochemical characteristics of the solids are related to foam formation and describes how the foaming potential of full-scale plants can be assessed. The relations among activated sludge and biological foam hydrophobicity, scum index, aeration tank cover and filamentous population are evaluated. Individual parameter comparison reveals the scumming intensity can be estimated only on the assumption that foams is already established. None of the above mentioned characteristics can be reliably used to predict the foaming episodes at wastewater treatment plants.

Changes in hormone and stress-inducing activities of municipal wastewater in a conventional activated sludge wastewater treatment plant.

PubMed

Wojnarowicz, Pola; Yang, Wenbo; Zhou, Hongde; Parker, Wayne J; Helbing, Caren C

2014-12-01

Conventional municipal wastewater treatment plants do not efficiently remove contaminants of emerging concern, and so are primary sources for contaminant release into the aquatic environment. Although these contaminants are present in effluents at ng-μg/L concentrations (i.e. microcontaminants), many compounds can act as endocrine disrupting compounds or stress-inducing agents at these levels. Chemical fate analyses indicate that additional levels of wastewater treatment reduce but do not always completely remove all microcontaminants. The removal of microcontaminants from wastewater does not necessarily correspond to a reduction in biological activity, as contaminant metabolites or byproducts may still be biologically active. To evaluate the efficacy of conventional municipal wastewater treatment plants to remove biological activity, we examined the performance of a full scale conventional activated sludge municipal wastewater treatment plant located in Guelph, Ontario, Canada. We assessed reductions in levels of conventional wastewater parameters and thyroid hormone disrupting and stress-inducing activities in wastewater at three phases along the treatment train using a C-fin assay. Wastewater treatment was effective at reducing total suspended solids, chemical and biochemical oxygen demand, and stress-inducing bioactivity. However, only minimal reduction was observed in thyroid hormone disrupting activities. The present study underscores the importance of examining multiple chemical and biological endpoints in evaluating and monitoring the effectiveness of wastewater treatment for removal of microcontaminants. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparison between lab- and full-scale applications of in situ aeration of an old landfill and assessment of long-term emission development after completion

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

Hrad, Marlies; Gamperling, Oliver; Huber-Humer, Marion, E-mail: marion.huber-humer@boku.ac.at

Highlights: ► Current data on in situ aeration effects from the first Austrian full-scale case study. ► Data on lasting waste stabilisation after aeration completion. ► Information on the transferability of results from lab- to full-scale aeration. - Abstract: Sustainable landfilling has become a fundamental objective in many modern waste management concepts. In this context, the in situ aeration of landfills has been recognised for its potential to convert conventional anaerobic landfills into biological stabilised state, whereby both current and potential (long-term) emissions of the landfilled waste are mitigated. In recent years, different in situ aeration concepts have been successfullymore » applied in Europe, North America and Asia, all pursuing different objectives and strategies. In Austria, the first full-scale application of in situ landfill aeration by means of low pressure air injection and simultaneous off-gas collection and treatment was implemented on an old, small municipal solid waste (MSW) landfill (2.6 ha) in autumn 2007. Complementary laboratory investigations were conducted with waste samples taken from the landfill site in order to provide more information on the transferability of the results from lab- to full-scale aeration measures. In addition, long-term emission development of the stabilised waste after aeration completion was assessed in an ongoing laboratory experiment. Although the initial waste material was described as mostly stable in terms of the biological parameters gas generation potential over 21 days (GP{sub 21}) and respiration activity over 4 days (RA{sub 4}), the lab-scale experiments indicated that aeration, which led to a significant improvement of leachate quality, was accompanied by further measurable changes in the solid waste material under optimised conditions. Even 75 weeks after aeration completion the leachate, as well as gaseous emissions from the stabilised waste material, remained low and stayed below the authorised Austrian discharge limits. However, the application of in situ aeration at the investigated landfill is a factor 10 behind the lab-based predictions after 3 years of operation, mainly due to technical limitations in the full-scale operation (e.g. high air flow resistivity due to high water content of waste and temporarily high water levels within the landfill; limited efficiency of the aeration wells). In addition, material preparation (e.g. sieving, sorting and homogenisation) prior to the emplacement in Landfill Simulation Reactors (LSRs) must be considered when transferring results from lab- to full-scale application.« less

Comparison of batch sorption tests, pilot studies, and modeling for estimating GAC bed life.

PubMed

Scharf, Roger G; Johnston, Robert W; Semmens, Michael J; Hozalski, Raymond M

2010-02-01

Saint Paul Regional Water Services (SPRWS) in Saint Paul, MN experiences annual taste and odor episodes during the warm summer months. These episodes are attributed primarily to geosmin that is produced by cyanobacteria growing in the chain of lakes used to convey and store the source water pumped from the Mississippi River. Batch experiments, pilot-scale experiments, and model simulations were performed to determine the geosmin removal performance and bed life of a granular activated carbon (GAC) filter-sorber. Using batch adsorption isotherm parameters, the estimated bed life for the GAC filter-sorber ranged from 920 to 1241 days when challenged with a constant concentration of 100 ng/L of geosmin. The estimated bed life obtained using the AdDesignS model and the actual pilot-plant loading history was 594 days. Based on the pilot-scale GAC column data, the actual bed life (>714 days) was much longer than the simulated values because bed life was extended by biological degradation of geosmin. The continuous feeding of high concentrations of geosmin (100-400 ng/L) in the pilot-scale experiments enriched for a robust geosmin-degrading culture that was sustained when the geosmin feed was turned off for 40 days. It is unclear, however, whether a geosmin-degrading culture can be established in a full-scale filter that experiences taste and odor episodes for only 1 or 2 months per year. The results of this research indicate that care must be exercised in the design and interpretation of pilot-scale experiments and model simulations for predicting taste and odor removal in full-scale GAC filter-sorbers. Adsorption and the potential for biological degradation must be considered to estimate GAC bed life for the conditions of intermittent geosmin loading typically experienced by full-scale systems. (c) 2009 Elsevier Ltd. All rights reserved.

Single molecule experimentation in biological physics: exploring the living component of soft condensed matter one molecule at a time.

PubMed

Harriman, O L J; Leake, M C

2011-12-21

The soft matter of biological systems consists of mesoscopic length scale building blocks, composed of a variety of different types of biological molecules. Most single biological molecules are so small that 1 billion would fit on the full-stop at the end of this sentence, but collectively they carry out the vital activities in living cells whose length scale is at least three orders of magnitude greater. Typically, the number of molecules involved in any given cellular process at any one time is relatively small, and so real physiological events may often be dominated by stochastics and fluctuation behaviour at levels comparable to thermal noise, and are generally heterogeneous in nature. This challenging combination of heterogeneity and stochasticity is best investigated experimentally at the level of single molecules, as opposed to more conventional bulk ensemble-average techniques. In recent years, the use of such molecular experimental approaches has become significantly more widespread in research laboratories around the world. In this review we discuss recent experimental approaches in biological physics which can be applied to investigate the living component of soft condensed matter to a precision of a single molecule. © 2011 IOP Publishing Ltd Printed in the UK & the USA

Microautoradiographic study of Rhodocyclus-related polyphosphate-accumulating bacteria in full-scale enhanced biological phosphorus removal plants.

PubMed

Kong, Yunhong; Nielsen, Jeppe Lund; Nielsen, Per Halkjaer

2004-09-01

The ecophysiology of uncultured Rhodocyclus-related polyphosphate-accumulating organisms (PAO) present in three full-scale enhanced biological phosphorus removal (EBPR) activated sludge plants was studied by using microautoradiography combined with fluorescence in situ hybridization. The investigations showed that these organisms were present in all plants examined and constituted 5 to 10, 10 to 15, and 17 to 22% of the community biomass. The behavior of these bacteria generally was consistent with the biochemical models proposed for PAO, based on studies of lab-scale investigations of enriched and often unknown PAO cultures. Rhodocyclus-related PAO were able to accumulate short-chain substrates, including acetate, propionate, and pyruvate, under anaerobic conditions, but they could not assimilate many other low-molecular-weight compounds, such as ethanol and butyrate. They were able to assimilate two substrates (e.g., acetate and propionate) simultaneously. Leucine and thymidine could not be assimilated as sole substrates and could only be assimilated as cosubstrates with acetate, perhaps serving as N sources. Glucose could not be assimilated by the Rhodocyclus-related PAO, but it was easily fermented in the sludge to products that were subsequently consumed. Glycolysis, and not the tricarboxylic acid cycle, was the source that provided the reducing power needed by the Rhodocyclus-related PAO to form the intracellular polyhydroxyalkanoate storage compounds during anaerobic substrate assimilation. The Rhodocyclus-related PAO were able to take up orthophosphate and accumulate polyphosphate when oxygen, nitrate, or nitrite was present as an electron acceptor. Furthermore, in the presence of acetate growth was sustained by using oxygen, as well as nitrate or nitrite, as an electron acceptor. This strongly indicates that Rhodocyclus-related PAO were able to denitrify and thus played a role in the denitrification occurring in full-scale EBPR plants.

Review of feedstock pretreatment strategies for improved anaerobic digestion: From lab-scale research to full-scale application.

PubMed

Carrere, Hélène; Antonopoulou, Georgia; Affes, Rim; Passos, Fabiana; Battimelli, Audrey; Lyberatos, Gerasimos; Ferrer, Ivet

2016-01-01

When properly designed, pretreatments may enhance the methane potential and/or anaerobic digestion rate, improving digester performance. This paper aims at providing some guidelines on the most appropriate pretreatments for the main feedstocks of biogas plants. Waste activated sludge was firstly investigated and implemented at full-scale, its thermal pretreatment with steam explosion being most recommended as it increases the methane potential and digestion rate, ensures sludge sanitation and the heat needed is produced on-site. Regarding fatty residues, saponification is preferred for enhancing their solubilisation and bioavailability. In the case of animal by-products, this pretreatment can be optimised to ensure sterilisation, solubilisation and to reduce inhibition linked to long chain fatty acids. With regards to lignocellulosic biomass, the first goal should be delignification, followed by hemicellulose and cellulose hydrolysis, alkali or biological (fungi) pretreatments being most promising. As far as microalgae are concerned, thermal pretreatment seems the most promising technique so far. Copyright © 2015 Elsevier Ltd. All rights reserved.

Operation of an aquatic worm reactor suitable for sludge reduction at large scale.

PubMed

Hendrickx, Tim L G; Elissen, Hellen H J; Temmink, Hardy; Buisman, Cees J N

2011-10-15

Treatment of domestic waste water results in the production of waste sludge, which requires costly further processing. A biological method to reduce the amount of waste sludge and its volume is treatment in an aquatic worm reactor. The potential of such a worm reactor with the oligochaete Lumbriculus variegatus has been shown at small scale. For scaling up purposes, a new configuration of the reactor was designed, in which the worms were positioned horizontally in the carrier material. This was tested in a continuous experiment of 8 weeks where it treated all the waste sludge from a lab-scale activated sludge process. The results showed a higher worm growth rate compared to previous experiments with the old configuration, whilst nutrient release was similar. The new configuration has a low footprint and allows for easy aeration and faeces collection, thereby making it suitable for full scale application. Copyright © 2011 Elsevier Ltd. All rights reserved.

Comparison between lab- and full-scale applications of in situ aeration of an old landfill and assessment of long-term emission development after completion.

PubMed

Hrad, Marlies; Gamperling, Oliver; Huber-Humer, Marion

2013-10-01

Sustainable landfilling has become a fundamental objective in many modern waste management concepts. In this context, the in situ aeration of landfills has been recognised for its potential to convert conventional anaerobic landfills into biological stabilised state, whereby both current and potential (long-term) emissions of the landfilled waste are mitigated. In recent years, different in situ aeration concepts have been successfully applied in Europe, North America and Asia, all pursuing different objectives and strategies. In Austria, the first full-scale application of in situ landfill aeration by means of low pressure air injection and simultaneous off-gas collection and treatment was implemented on an old, small municipal solid waste (MSW) landfill (2.6ha) in autumn 2007. Complementary laboratory investigations were conducted with waste samples taken from the landfill site in order to provide more information on the transferability of the results from lab- to full-scale aeration measures. In addition, long-term emission development of the stabilised waste after aeration completion was assessed in an ongoing laboratory experiment. Although the initial waste material was described as mostly stable in terms of the biological parameters gas generation potential over 21days (GP21) and respiration activity over 4days (RA4), the lab-scale experiments indicated that aeration, which led to a significant improvement of leachate quality, was accompanied by further measurable changes in the solid waste material under optimised conditions. Even 75weeks after aeration completion the leachate, as well as gaseous emissions from the stabilised waste material, remained low and stayed below the authorised Austrian discharge limits. However, the application of in situ aeration at the investigated landfill is a factor 10 behind the lab-based predictions after 3years of operation, mainly due to technical limitations in the full-scale operation (e.g. high air flow resistivity due to high water content of waste and temporarily high water levels within the landfill; limited efficiency of the aeration wells). In addition, material preparation (e.g. sieving, sorting and homogenisation) prior to the emplacement in Landfill Simulation Reactors (LSRs) must be considered when transferring results from lab- to full-scale application. Copyright © 2013 Elsevier Ltd. All rights reserved.

Quantitative response of nitrifying and denitrifying communities to environmental variables in a full-scale membrane bioreactor.

PubMed

Gómez-Silván, C; Vílchez-Vargas, R; Arévalo, J; Gómez, M A; González-López, J; Pieper, D H; Rodelas, B

2014-10-01

The abundance and transcription levels of specific gene markers of total bacteria, ammonia-oxidizing Betaproteobacteria, nitrite-oxidizing bacteria (Nitrospira-like) and denitrifiers (N2O-reducers) were analyzed using quantitative PCR (qPCR) and reverse-transcription qPCR during 9 months in a full-scale membrane bioreactor treating urban wastewater. A stable community of N-removal key players was developed; however, the abundance of active populations experienced sharper shifts, demonstrating their fast adaptation to changing conditions. Despite constituting a small percentage of the total bacterial community, the larger abundances of active populations of nitrifiers explained the high N-removal accomplished by the MBR. Multivariate analyses revealed that temperature, accumulation of volatile suspended solids in the sludge, BOD5, NH4(+) concentration and C/N ratio of the wastewater contributed significantly (23-38%) to explain changes in the abundance of nitrifiers and denitrifiers. However, each targeted group showed different responses to shifts in these parameters, evidencing the complexity of the balance among them for successful biological N-removal. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

NASA Astrophysics Data System (ADS)

Mei, Ran; Narihiro, Takashi; Nobu, Masaru K.; Kuroda, Kyohei; Liu, Wen-Tso

2016-09-01

Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solids, which assumes no biomass growth associated with digestion. To determine whether this assumption is valid and further evaluate digestion efficiency, this study sampled 35 digester sludge from different reactors at multiple time points together with the feed biomass in a full-scale water reclamation plant at Chicago, Illinois. The microbial communities were characterized using Illumina sequencing technology based on 16S rRNA and 16S rRNA gene (rDNA). 74 core microbial populations were identified and represented 58.7% of the entire digester community. Among them, active populations were first identified using the ratio of 16S rRNA and 16S rDNA (rRNA/rDNA) for individual populations, but this approach failed to generate consistent results. Subsequently, a recently proposed mass balance model was applied to calculate the specific growth rate (μ), and this approach successfully identified active microbial populations in digester (positive μ) that could play important roles than those with negative μ. It was further estimated that 82% of microbial populations in the feed sludge were digested in comparison with less than 50% calculated using current equations.

Upgrading and extended testing of the MSC integrated water and waste management hardware

NASA Technical Reports Server (NTRS)

Bambenek, R. A.; Nuccio, P. P.; Hurley, T. L.; Jasionowski, W. J.

1972-01-01

The results are presented of upgrading and testing an integrated water and waste management system, which uses the compression distillation, reverse osmosis, adsorption filtration and ion-exchange processes to recover potable water from urine, flush water and used wash water. Also included is the development of techniques for extending the useful biological life of biological filters, activated carbon filters and ion-exchange resins to at least 30 days, and presterilizing ion-exchange resins so that sterile water can be recovered from waste water. A wide variety of reverse osmosos materials, surfactants and germicides were experimentally evaluated to determine the best combination for a wash water subsystem. Full-scale module tests with real wash water demonstrated that surface fouling is a major problem.

Zero-valent iron/biotic treatment system for perchlorate-contaminated water: lab-scale performance, modeling, and full-scale implications

EPA Science Inventory

The computer program AQUASIM was used to model biological treatment of perchlorate-contaminated water using zero-valent iron corrosion as the hydrogen gas source. The laboratory-scale column was seeded with an autohydrogenotrophic microbial consortium previously shown to degrade ...

Biological treatment of TMAH (tetra-methyl ammonium hydroxide) in a full-scale TFT-LCD wastewater treatment plant.

PubMed

Hu, Tai-Ho; Whang, Liang-Ming; Liu, Pao-Wen Grace; Hung, Yu-Ching; Chen, Hung-Wei; Lin, Li-Bin; Chen, Chia-Fu; Chen, Sheng-Kun; Hsu, Shu Fu; Shen, Wason; Fu, Ryan; Hsu, Romel

2012-06-01

This study evaluated biological treatment of TMAH in a full-scale methanogenic up-flow anaerobic sludge blanket (UASB) followed by an aerobic bioreactor. In general, the UASB was able to perform a satisfactory TMAH degradation efficiency, but the effluent COD of the aerobic bioreactor seemed to increase with an increased TMAH in the influent wastewater. The batch test results confirmed that the UASB sludge under methanogenic conditions would be favored over the aerobic ones for TMAH treatment due to its superb ability of handling high strength of TMAH-containing wastewaters. Based on batch experiments, inhibitory chemicals present in TFT-LCD wastewater like surfactants and sulfate should be avoided to secure a stable methanogenic TMAH degradation. Finally, molecular monitoring of Methanomethylovorans hollandica and Methanosarcina mazei in the full-scale plant, the dominant methanogens in the UASB responsible for TMAH degradation, may be beneficial for a stable TMAH treatment performance. Copyright © 2012 Elsevier Ltd. All rights reserved.

APPLICATION, PERFORMANCE, AND COSTS OF BIOTREATMENT TECHNOLOGIES FOR CONTAMINATED SOILS

EPA Science Inventory

A critical review of biological treatment processes for remediation of contaminated soils is presented. The focus of the review is on documented cost and performance of biological treatment technologies demonstrated at full- or
field-scale. Some of the data were generated b...

Strategies for the reduction of Legionella in biological treatment systems.

PubMed

Nogueira, R; Utecht, K-U; Exner, M; Verstraete, W; Rosenwinkel, K-H

A community-wide outbreak of Legionnaire's disease occurred in Warstein, Germany, in August 2013. The epidemic strain, Legionella pneumophila Serogruppe 1, was isolated from an industrial wastewater stream entering the municipal wastewater treatment plant (WWTP) in Wartein, the WWTP itself, the river Wäster and air/water samples from an industrial cooling system 3 km downstream of the WWTP. The present study investigated the effect of physical-chemical disinfection methods on the reduction of the concentration of Legionella in the biological treatment and in the treated effluent entering the river Wäster. Additionally, to gain insight into the factors that promote the growth of Legionella in biological systems, growth experiments were made with different substrates and temperatures. The dosage rates of silver micro-particles, hydrogen peroxide, chlorine dioxide and ozone and pH stress to the activated sludge were not able to decrease the number of culturable Legionella spp. in the effluent. Nevertheless, the UV treatment of secondary treated effluent reduced Legionella spp. on average by 1.6-3.4 log units. Laboratory-scale experiments and full-scale measurements suggested that the aerobic treatment of warm wastewater (30-35 °C) rich in organic nitrogen (protein) is a possible source of Legionella infection.

Directed formation of micro- and nanoscale patterns of functional light-harvesting LH2 complexes.

PubMed

Reynolds, Nicholas P; Janusz, Stefan; Escalante-Marun, Maryana; Timney, John; Ducker, Robert E; Olsen, John D; Otto, Cees; Subramaniam, Vinod; Leggett, Graham J; Hunter, C Neil

2007-11-28

The precision placement of the desired protein components on a suitable substrate is an essential prelude to any hybrid "biochip" device, but a second and equally important condition must also be met: the retention of full biological activity. Here we demonstrate the selective binding of an optically active membrane protein, the light-harvesting LH2 complex from Rhodobacter sphaeroides, to patterned self-assembled monolayers at the micron scale and the fabrication of nanometer-scale patterns of these molecules using near-field photolithographic methods. In contrast to plasma proteins, which are reversibly adsorbed on many surfaces, the LH2 complex is readily patterned simply by spatial control of surface polarity. Near-field photolithography has yielded rows of light-harvesting complexes only 98 nm wide. Retention of the native optical properties of patterned LH2 molecules was demonstrated using in situ fluorescence emission spectroscopy.

Governing factors affecting the impacts of silver nanoparticles on wastewater treatment.

PubMed

Zhang, Chiqian; Hu, Zhiqiang; Li, Ping; Gajaraj, Shashikanth

2016-12-01

Silver nanoparticles (nanosilver or AgNPs) enter municipal wastewater from various sources, raising concerns about their potential adverse effects on wastewater treatment processes. We argue that the biological effects of silver nanoparticles at environmentally realistic concentrations (μgL -1 or lower) on the performance of a full-scale municipal water resource recovery facility (WRRF) are minimal. Reactor configuration is a critical factor that reduces or even mutes the toxicity of silver nanoparticles towards wastewater microbes in a full-scale WRRF. Municipal sewage collection networks transform silver nanoparticles into silver(I)-complexes/precipitates with low ecotoxicity, and preliminary/primary treatment processes in front of biological treatment utilities partially remove silver nanoparticles to sludge. Microbial functional redundancy and microbial adaptability to silver nanoparticles also greatly alleviate the adverse effects of silver nanoparticles on the performance of a full-scale WRRF. Silver nanoparticles in a lab-scale bioreactor without a sewage collection system and/or a preliminary/primary treatment process, in contrast to being in a full scale system, may deteriorate the reactor performance at relatively high concentrations (e.g., mgL -1 levels or higher). However, in many cases, silver nanoparticles have minimal impacts on lab-scale bioreactors, such as sequencing batch bioreactors (SBRs), especially when at relatively low concentrations (e.g., less than 1mgL -1 ). The susceptibility of wastewater microbes to silver nanoparticles is species-specific. In general, silver nanoparticles have higher toxicity towards nitrifying bacteria than heterotrophic bacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

Successful startup of a full-scale acrylonitrile wastewater biological treatment plant (ACN-WWTP) by eliminating the inhibitory effects of toxic compounds on nitrification.

PubMed

Han, Yuanyuan; Jin, Xibiao; Wang, Feng; Liu, Yongdi; Chen, Xiurong

2014-01-01

During the startup of a full-scale anoxic/aerobic (A/O) biological treatment plant for acrylonitrile wastewater, the removal efficiencies of NH(3)-N and total Kjeldahl nitrogen (TKN) were 1.29 and 0.83% on day 30, respectively. The nitrification process was almost totally inhibited, which was mainly caused by the inhibitory effects of toxic compounds. To eliminate the inhibition, cultivating the bacteria that degrade toxic compounds with patience was applied into the second startup of the biological treatment plant. After 75 days of startup, the inhibitory effects of the toxic compounds on nitrification were eliminated. The treatment plant has been operated stably for more than 3 years. During the last 100 days, the influent concentrations of chemical oxygen demand (COD), NH(3)-N, TKN and total cyanide (TCN) were 831-2,164, 188-516, 306-542 and 1.17-9.57 mg L(-1) respectively, and the effluent concentrations were 257 ± 30.9, 3.30 ± 1.10, 31.6 ± 4.49 and 0.40 ± 0.10 mg L(-1) (n = 100), respectively. Four strains of cyanide-degrading bacteria which were able to grow with cyanide as the sole carbon and nitrogen source were isolated from the full-scale biological treatment plant. They were short and rod-shaped under scanning electron microscopy (SEM) and were identified as Brevundimonas sp., Rhizobium sp., Dietzia natronolimnaea and Microbacterium sp., respectively.

Onset of meso-scale turbulence in active nematics

NASA Astrophysics Data System (ADS)

Doostmohammadi, Amin; Shendruk, Tyler N.; Thijssen, Kristian; Yeomans, Julia M.

2017-05-01

Meso-scale turbulence is an innate phenomenon, distinct from inertial turbulence, that spontaneously occurs at low Reynolds number in fluidized biological systems. This spatiotemporal disordered flow radically changes nutrient and molecular transport in living fluids and can strongly affect the collective behaviour in prominent biological processes, including biofilm formation, morphogenesis and cancer invasion. Despite its crucial role in such physiological processes, understanding meso-scale turbulence and any relation to classical inertial turbulence remains obscure. Here we show how the motion of active matter along a micro-channel transitions to meso-scale turbulence through the evolution of locally disordered patches (active puffs) from an ordered vortex-lattice flow state. We demonstrate that the stationary critical exponents of this transition to meso-scale turbulence in a channel coincide with the directed percolation universality class. This finding bridges our understanding of the onset of low-Reynolds-number meso-scale turbulence and traditional scale-invariant turbulence in confinement.

Process optimization by decoupled control of key microbial populations: distribution of activity and abundance of polyphosphate-accumulating organisms and nitrifying populations in a full-scale IFAS-EBPR plant.

PubMed

Onnis-Hayden, Annalisa; Majed, Nehreen; Schramm, Andreas; Gu, April Z

2011-07-01

This study investigated the abundance and distribution of key functional microbial populations and their activities in a full-scale integrated fixed film activated sludge-enhanced biological phosphorus removal (IFAS-EBPR) process. Polyphosphate accumulating organisms (PAOs) including Accumulibacter and EBPR activities were predominately associated with the mixed liquor (>90%) whereas nitrifying populations and nitrification activity resided mostly (>70%) on the carrier media. Ammonia oxidizer bacteria (AOB) were members of the Nitrosomonas europaea/eutropha/halophila and the Nitrosomonas oligotropha lineages, while nitrite oxidizer bacteria (NOB) belonged to the Nitrospira genus. Addition of the carrier media in the hybrid activated sludge system increased the nitrification capacity and stability; this effect was much greater in the first IFAS stage than in the second one where the residual ammonia concentration becomes limiting. Our results show that IFAS-EBPR systems enable decoupling of solid residence time (SRT) control for nitrifiers and PAOs that require or prefer conflicting SRT values (e.g. >15 days required for nitrifiers and <5 days preferred for PAOs). Allowing the slow-growing nitrifiers to attach to the carrier media and the faster-growing phosphorus (P)-removing organisms (and other heterotrophs, e.g. denitrifiers) to be in the suspended mixed liquor (ML), the EBPR-IFAS system facilitates separate SRT controls and overall optimization for both N and P removal processes. Copyright © 2011 Elsevier Ltd. All rights reserved.

Bacterial diversity and active biomass in full-scale granular activated carbon filters operated at low water temperatures.

PubMed

Kaarela, Outi E; Härkki, Heli A; Palmroth, Marja R T; Tuhkanen, Tuula A

2015-01-01

Granular activated carbon (GAC) filtration enhances the removal of natural organic matter and micropollutants in drinking water treatment. Microbial communities in GAC filters contribute to the removal of the biodegradable part of organic matter, and thus help to control microbial regrowth in the distribution system. Our objectives were to investigate bacterial community dynamics, identify the major bacterial groups, and determine the concentration of active bacterial biomass in full-scale GAC filters treating cold (3.7-9.5°C), physicochemically pretreated, and ozonated lake water. Three sampling rounds were conducted to study six GAC filters of different operation times and flow modes in winter, spring, and summer. Total organic carbon results indicated that both the first-step and second-step filters contributed to the removal of organic matter. Length heterogeneity analysis of amplified 16S rRNA genes illustrated that bacterial communities were diverse and considerably stable over time. α-Proteobacteria, β-Proteobacteria, and Nitrospira dominated in all of the GAC filters, although the relative proportion of dominant phylogenetic groups in individual filters differed. The active bacterial biomass accumulation, measured as adenosine triphosphate, was limited due to low temperature, low flux of nutrients, and frequent backwashing. The concentration of active bacterial biomass was not affected by the moderate seasonal temperature variation. In summary, the results provided an insight into the biological component of GAC filtration in cold water temperatures and the operational parameters affecting it.

Metabolic systems biology: a brief primer.

PubMed

Edwards, Lindsay M

2017-05-01

In the early to mid-20th century, reductionism as a concept in biology was challenged by key thinkers, including Ludwig von Bertalanffy. He proposed that living organisms were specific examples of complex systems and, as such, they should display characteristics including hierarchical organisation and emergent behaviour. Yet the true study of complete biological systems (for example, metabolism) was not possible until technological advances that occurred 60 years later. Technology now exists that permits the measurement of complete levels of the biological hierarchy, for example the genome and transcriptome. The complexity and scale of these data require computational models for their interpretation. The combination of these - systems thinking, high-dimensional data and computation - defines systems biology, typically accompanied by some notion of iterative model refinement. Only sequencing-based technologies, however, offer full coverage. Other 'omics' platforms trade coverage for sensitivity, although the densely connected nature of biological networks suggests that full coverage may not be necessary. Systems biology models are often characterised as either 'bottom-up' (mechanistic) or 'top-down' (statistical). This distinction can mislead, as all models rely on data and all are, to some degree, 'middle-out'. Systems biology has matured as a discipline, and its methods are commonplace in many laboratories. However, many challenges remain, especially those related to large-scale data integration. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

The use of an active learning approach in a SCALE-UP learning space improves academic performance in undergraduate General Biology.

PubMed

Hacisalihoglu, Gokhan; Stephens, Desmond; Johnson, Lewis; Edington, Maurice

2018-01-01

Active learning is a pedagogical approach that involves students engaging in collaborative learning, which enables them to take more responsibility for their learning and improve their critical thinking skills. While prior research examined student performance at majority universities, this study focuses on specifically Historically Black Colleges and Universities (HBCUs) for the first time. Here we present work that focuses on the impact of active learning interventions at Florida A&M University, where we measured the impact of active learning strategies coupled with a SCALE-UP (Student Centered Active Learning Environment with Upside-down Pedagogies) learning environment on student success in General Biology. In biology sections where active learning techniques were employed, students watched online videos and completed specific activities before class covering information previously presented in a traditional lecture format. In-class activities were then carefully planned to reinforce critical concepts and enhance critical thinking skills through active learning techniques such as the one-minute paper, think-pair-share, and the utilization of clickers. Students in the active learning and control groups covered the same topics, took the same summative examinations and completed identical homework sets. In addition, the same instructor taught all of the sections included in this study. Testing demonstrated that these interventions increased learning gains by as much as 16%, and students reported an increase in their positive perceptions of active learning and biology. Overall, our results suggest that active learning approaches coupled with the SCALE-UP environment may provide an added opportunity for student success when compared with the standard modes of instruction in General Biology.

Performance Comparison of the Digital Neuromorphic Hardware SpiNNaker and the Neural Network Simulation Software NEST for a Full-Scale Cortical Microcircuit Model

PubMed Central

van Albada, Sacha J.; Rowley, Andrew G.; Senk, Johanna; Hopkins, Michael; Schmidt, Maximilian; Stokes, Alan B.; Lester, David R.; Diesmann, Markus; Furber, Steve B.

2018-01-01

The digital neuromorphic hardware SpiNNaker has been developed with the aim of enabling large-scale neural network simulations in real time and with low power consumption. Real-time performance is achieved with 1 ms integration time steps, and thus applies to neural networks for which faster time scales of the dynamics can be neglected. By slowing down the simulation, shorter integration time steps and hence faster time scales, which are often biologically relevant, can be incorporated. We here describe the first full-scale simulations of a cortical microcircuit with biological time scales on SpiNNaker. Since about half the synapses onto the neurons arise within the microcircuit, larger cortical circuits have only moderately more synapses per neuron. Therefore, the full-scale microcircuit paves the way for simulating cortical circuits of arbitrary size. With approximately 80, 000 neurons and 0.3 billion synapses, this model is the largest simulated on SpiNNaker to date. The scale-up is enabled by recent developments in the SpiNNaker software stack that allow simulations to be spread across multiple boards. Comparison with simulations using the NEST software on a high-performance cluster shows that both simulators can reach a similar accuracy, despite the fixed-point arithmetic of SpiNNaker, demonstrating the usability of SpiNNaker for computational neuroscience applications with biological time scales and large network size. The runtime and power consumption are also assessed for both simulators on the example of the cortical microcircuit model. To obtain an accuracy similar to that of NEST with 0.1 ms time steps, SpiNNaker requires a slowdown factor of around 20 compared to real time. The runtime for NEST saturates around 3 times real time using hybrid parallelization with MPI and multi-threading. However, achieving this runtime comes at the cost of increased power and energy consumption. The lowest total energy consumption for NEST is reached at around 144 parallel threads and 4.6 times slowdown. At this setting, NEST and SpiNNaker have a comparable energy consumption per synaptic event. Our results widen the application domain of SpiNNaker and help guide its development, showing that further optimizations such as synapse-centric network representation are necessary to enable real-time simulation of large biological neural networks. PMID:29875620

Biological mechanisms supporting adaptation to ocean acidification in coastal ecosystems

NASA Astrophysics Data System (ADS)

Hendriks, Iris E.; Duarte, Carlos M.; Olsen, Ylva S.; Steckbauer, Alexandra; Ramajo, Laura; Moore, Tommy S.; Trotter, Julie A.; McCulloch, Malcolm

2015-01-01

The direct influence of anthropogenic CO2 might play a limited role in pH regulation in coastal ecosystems as pH regulation in these areas can be complex. They experience large variability across a broad range of spatial and temporal scales, with complex external and internal drivers. Organisms influence pH at a patch scale, where community metabolic effects and hydrodynamic processes interact to produce broad ranges in pH, (˜0.3-0.5 pH units) over daily cycles and spatial scales (mm to m) particularly in shallow vegetated habitats and coral reefs where both respiration and photosynthetic activity are intense. Biological interactions at the ecosystem scale, linked to patchiness in habitat landscapes and seasonal changes in metabolic processes and temperature lead to changes of about 0.3-0.5 pH units throughout a year. Furthermore, on the scale of individual organisms, small-scale processes including changes at the Diffusive Boundary Layer (DBL), interactions with symbionts, and changes to the specific calcification environment, induce additional changes in excess of 0.5 pH units. In these highly variable pH environments calcifying organisms have developed the capacity to alter the pH of their calcifying environment, or specifically within critical tissues where calcification occurs, thus achieving a homeostasis. This capacity to control the conditions for calcification at the organism scale may therefore buffer the full impacts of ocean acidification on an organism scale, although this might be at a cost to the individual. Furthermore, in some areas, calcifiers may potentially benefit from changes to ambient seawater pH, where photosynthetic organisms drawdown CO2.

A comparison of aerobic granular sludge with conventional and compact biological treatment technologies.

PubMed

Bengtsson, Simon; de Blois, Mark; Wilén, Britt-Marie; Gustavsson, David

2018-03-20

The aerobic granular sludge (AGS) technology is growing towards becoming a mature option for new municipal wastewater treatment plants and capacity extensions. A process based on AGS was compared to conventional activated sludge processes (with and without enhanced biological phosphorus removal), an integrated fixed-film activated sludge (IFAS) process and a membrane bioreactor (MBR) by estimating the land area demand (footprint), electricity demand and chemicals' consumption. The process alternatives compared included pre-settling, sludge digestion and necessary post-treatment to achieve effluent concentrations of 8 mg/L nitrogen and 0.2 mg/L phosphorus at 7°C. The alternative based on AGS was estimated to have a 40-50% smaller footprint and 23% less electricity requirement than conventional activated sludge. In relation to the other compact treatment options IFAS and MBR, the AGS process had an estimated electricity usage that was 35-70% lower. This suggests a favourable potential for processes based on AGS although more available experience of AGS operation and performance at full scale is desired.

Investigations into Improving Dewaterability at a Bio-P/Anaerobic Digestion Plant.

PubMed

Alm, Rebecca; Sealock, Adam W; Nollet, Yabing; Sprouse, George

2016-11-01

  Metropolitan Council Environmental Services has observed poorer than expected dewatering performance at its Empire Plant. This plant has both anaerobic digestion and enhanced biological phosphorus removal in its treatment train. A research program using pilot-scale anaerobic digesters investigated potential solutions to the plant's poor dewaterability. The dewaterability goal was to increase the cake solids from 12% total solids (TS) to 16% TS or higher. This research investigated 20 different reactor conditions including chemical, feed sludge, and digested sludge treatments. At the pilot scale, unaerated storage of waste activated sludge prior to thickening and addition of ferric chloride to digestion was found to achieve dewatered cake solids of nearly 17% TS with the added benefit of reducing polymer demand. Issues including the amount of chemical required and the resulting volatile solids destruction influence the viability of the process change, so a full-scale pilot and financial analysis is recommended before making permanent process changes.

Bioterrorism and Biocrimes: The Illicit Use of Biological Agents Since 1900

DTIC Science & Technology

2001-02-01

to white supremacist groups, including the Aryan Nation and the Christian Identity movement, he 5 involve allegations of covert state activities ...toxin to poison livestock in what is now Kenya. The full extent of these activities is not known. Polish Resistance: Multiple reports suggest that...thorough reporting of Aum’s biological warfare activities . See page 47 for additional details. Table 1: Confirmed cases of illicit biological agent activity

Does the Room Matter? Active Learning in Traditional and Enhanced Lecture Spaces.

PubMed

Stoltzfus, Jon R; Libarkin, Julie

2016-01-01

SCALE-UP-type classrooms, originating with the Student-Centered Active Learning Environment with Upside-down Pedagogies project, are designed to facilitate active learning by maximizing opportunities for interactions between students and embedding technology in the classroom. Positive impacts when active learning replaces lecture are well documented, both in traditional lecture halls and SCALE-UP-type classrooms. However, few studies have carefully analyzed student outcomes when comparable active learning-based instruction takes place in a traditional lecture hall and a SCALE-UP-type classroom. Using a quasi-experimental design, we compared student perceptions and performance between sections of a nonmajors biology course, one taught in a traditional lecture hall and one taught in a SCALE-UP-type classroom. Instruction in both sections followed a flipped model that relied heavily on cooperative learning and was as identical as possible given the infrastructure differences between classrooms. Results showed that students in both sections thought that SCALE-UP infrastructure would enhance performance. However, measures of actual student performance showed no difference between the two sections. We conclude that, while SCALE-UP-type classrooms may facilitate implementation of active learning, it is the active learning and not the SCALE-UP infrastructure that enhances student performance. As a consequence, we suggest that institutions can modify existing classrooms to enhance student engagement without incorporating expensive technology. © 2016 J. R. Stoltzfus and J. Libarkin. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

EDCs, estrogenicity and genotoxicity reduction in a mixed (domestic + textile) secondary effluent by means of ozonation: a full-scale experience.

PubMed

Bertanza, G; Papa, M; Pedrazzani, R; Repice, C; Mazzoleni, G; Steimberg, N; Feretti, D; Ceretti, E; Zerbini, I

2013-08-01

WWTP (wastewater treatment plant) effluents are considered to be a major source for the release in the aquatic environment of EDCs (Endocrine-Disrupting Compounds), a group of anthropogenic substances able to alter the normal function of the endocrine system. The application of conventional processes (e.g. activated sludge with biological nitrogen removal) does not provide complete elimination of all these micropollutants and, consequently, an advanced treatment should be implemented. This experimental work was conducted on the tertiary ozonation stage of a 140,000 p.e. activated sludge WWTP, treating a mixed domestic and textile wastewater: an integrated monitoring, including both chemical (nonylphenol, together with the parent compounds mono- and di-ethoxylated, and bisphenol A were chosen as model EDCs) and biological (estrogenic and genotoxic activities) analyses, was carried out. Removal efficiencies of measured EDCs varied from 20% to 70%, depending on flow conditions (ozone dosage being 0.5 gO3/gTOC). Biological tests, furthermore, displayed that the oxidation stage did not significantly reduce (only by 20%) the estrogenicity of the effluent and revealed the presence and/or formation of genotoxic compounds. These results highlight the importance of the application of an integrated (biological+chemical) analytical procedure for a global evaluation of treatment suitability; poor performances recorded in this study have been attributed to the presence of a significant industrial component in the influent wastewater. Copyright © 2013 Elsevier B.V. All rights reserved.

Fall for Science.

ERIC Educational Resources Information Center

Learning, 1992

1992-01-01

Presents a collection of inexpensive autumn science activities for elementary students. A full moon activity encourages observational and critical thinking skills. A pumpkin activity teaches physics. A spider activity teaches biology and alleviates unnecessary fears. A student page has children create a bookmark that shows faces in the full moon.…

Minimizing N2O emissions and carbon footprint on a full-scale activated sludge sequencing batch reactor.

PubMed

Rodriguez-Caballero, A; Aymerich, I; Marques, Ricardo; Poch, M; Pijuan, M

2015-03-15

A continuous, on-line quantification of the nitrous oxide (N2O) emissions from a full-scale sequencing batch reactor (SBR) placed in a municipal wastewater treatment plant (WWTP) was performed in this study. In general, N2O emissions from the biological wastewater treatment system were 97.1 ± 6.9 g N2O-N/Kg [Formula: see text] consumed or 6.8% of the influent [Formula: see text] load. In the WWTP of this study, N2O emissions accounted for over 60% of the total carbon footprint of the facility, on average. Different cycle configurations were implemented in the SBR aiming at reaching acceptable effluent values. Each cycle configuration consisted of sequences of aerated and non-aerated phases of different time length being controlled by the ammonium set-point fixed. Cycles with long aerated phases showed the largest N2O emissions, with the consequent increase in carbon footprint. Cycle configurations with intermittent aeration (aerated phases up to 20-30 min followed by short anoxic phases) were proven to effectively reduce N2O emissions, without compromising nitrification performance or increasing electricity consumption. This is the first study in which a successful operational strategy for N2O mitigation is identified at full-scale. Copyright © 2014 Elsevier Ltd. All rights reserved.

Expression and fast preparation of biologically active recombinant human coagulation factor VII in CHO-K1 cells.

PubMed

Xiao, W; Li, C Q; Xiao, X P; Lin, F Z

2013-12-16

Human coagulation factor VII (FVII) plays an important role in the blood coagulation process and exists in micro amounts in human plasma; therefore, any attempt at the large-scale production of FVII in significant quantities is challenging. The purpose of this study was to express and obtain biologically active recombinant FVII (rFVII) from Chinese hamster ovary K1 (CHO-K1) cells. The full-length FVII cDNA was isolated from a HepG2 cell line and then subcloned in pcDNA3.1 to construct an expression vector, pcDNA-FVII. CHO-K1 cells were transfected with 1 µg pcDNA-FVII. The cell line that stably expressed secretory FVII was screened using 900 µg/mL G418. The FVII copy number in CHO-K1 cells was detected by quantitative polymerase chain reaction (qPCR). The rFVII was purified in ligand affinity chromatography medium. The purified protein was detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis. The biological activity of the purified FVII protein was determined by a prothrombin time assay. Three cell lines that permanently expressed rFVII were screened. The qPCR results demonstrated that each CHO-K1 cell harbored two FVII DNA copies. The SDS-PAGE and Western blot analysis showed that the purified protein was about 50 kDa. The purity of the target protein was 95%. The prothrombin time assay indicated that the FVII-specific activity of rFVII was 2573 ± 75 IU/mg. This method enabled the fast preparation of high-purity rFVII from CHO-K1 cells, and the purified protein had good biological activity.

Identity and ecophysiology of uncultured actinobacterial polyphosphate-accumulating organisms in full-scale enhanced biological phosphorus removal plants.

PubMed

Kong, Yunhong; Nielsen, Jeppe Lund; Nielsen, Per Halkjaer

2005-07-01

Microautoradiography combined with fluorescence in situ hybridization (MAR-FISH) was used to screen for potential polyphosphate-accumulating organisms (PAO) in a full-scale enhanced biological phosphorus removal (EBPR) plant. The results showed that, in addition to uncultured Rhodocyclus-related PAO, two morphotypes hybridizing with gene probes for the gram-positive Actinobacteria were also actively involved in uptake of orthophosphate (Pi). Clone library analysis and further investigations by MAR-FISH using two new oligonucleotide probes revealed that both morphotypes, cocci in clusters of tetrads and short rods in clumps, were relatively closely related to the genus Tetrasphaera within the family Intrasporangiaceae of the Actinobacteria (93 to 98% similarity in their 16S rRNA genes). FISH analysis of the community biomass in the treatment plant investigated showed that the short rods (targeted by probe Actino-658) were the most abundant (12% of all Bacteria hybridizing with general bacterial probes), while the cocci in tetrads (targeted by probe Actino-221) made up 7%. Both morphotypes took up P(i) aerobically only if, in a previous anaerobic phase, they had taken up organic matter from wastewater or a mixture of amino acids. They could not take up short-chain fatty acids (e.g., acetate), glucose, or ethanol under anaerobic or aerobic conditions. The storage compound produced during the anaerobic period was not polyhydroxyalkanoates, as for Rhodocyclus-related PAO, and its identity is still unknown. Growth and uptake of Pi took place in the presence of oxygen and nitrate but not nitrite, indicating a lack of denitrifying ability. A survey of the occurrence of these actinobacterial PAO in 10 full-scale EBPR plants revealed that both morphotypes were widely present, and in several plants more abundant than the Rhodocyclus-related PAO, thus playing a very important role in the EBPR process.

Sequential chemical-biological processes for the treatment of industrial wastewaters: review of recent progresses and critical assessment.

PubMed

Guieysse, Benoit; Norvill, Zane N

2014-02-28

When direct wastewater biological treatment is unfeasible, a cost- and resource-efficient alternative to direct chemical treatment consists of combining biological treatment with a chemical pre-treatment aiming to convert the hazardous pollutants into more biodegradable compounds. Whereas the principles and advantages of sequential treatment have been demonstrated for a broad range of pollutants and process configurations, recent progresses (2011-present) in the field provide the basis for refining assessment of feasibility, costs, and environmental impacts. This paper thus reviews recent real wastewater demonstrations at pilot and full scale as well as new process configurations. It also discusses new insights on the potential impacts of microbial community dynamics on process feasibility, design and operation. Finally, it sheds light on a critical issue that has not yet been properly addressed in the field: integration requires complex and tailored optimization and, of paramount importance to full-scale application, is sensitive to uncertainty and variability in the inputs used for process design and operation. Future research is therefore critically needed to improve process control and better assess the real potential of sequential chemical-biological processes for industrial wastewater treatment. Copyright © 2013 Elsevier B.V. All rights reserved.

Enhanced treatment of secondary municipal wastewater effluent: comparing (biological) filtration and ozonation in view of micropollutant removal, unselective effluent toxicity, and the potential for real-time control.

PubMed

Chys, Michael; Demeestere, Kristof; Ingabire, Ange Sabine; Dries, Jan; Van Langenhove, Herman; Van Hulle, Stijn W H

2017-07-01

Ozonation and three (biological) filtration techniques (trickling filtration (TF), slow sand filtration (SSF) and biological activated carbon (BAC) filtration) have been evaluated in different combinations as tertiary treatment for municipal wastewater effluent. The removal of 18 multi-class pharmaceuticals, as model trace organic contaminants (TrOCs), has been studied. (Biological) activated carbon filtration could reduce the amount of TrOCs significantly (>99%) but is cost-intensive for full-scale applications. Filtration techniques mainly depending on biodegradation mechanisms (TF and SSF) are found to be inefficient for TrOCs removal as a stand alone technique. Ozonation resulted in 90% removal of the total amount of quantified TrOCs, but a post-ozonation step is needed to cope with an increased unselective toxicity. SSF following ozonation showed to be the only technique able to reduce the unselective toxicity to the same level as before ozonation. In view of process control, innovative correlation models developed for the monitoring and control of TrOC removal during ozonation, are verified for their applicability during ozonation in combination with TF, SSF or BAC. Particularly for the poorly ozone reactive TrOCs, statistically significant models were obtained that correlate TrOC removal and reduction in UVA 254 as an online measured surrogate parameter.

Quantitative Tracking of Combinatorially Engineered Populations with Multiplexed Binary Assemblies.

PubMed

Zeitoun, Ramsey I; Pines, Gur; Grau, Willliam C; Gill, Ryan T

2017-04-21

Advances in synthetic biology and genomics have enabled full-scale genome engineering efforts on laboratory time scales. However, the absence of sufficient approaches for mapping engineered genomes at system-wide scales onto performance has limited the adoption of more sophisticated algorithms for engineering complex biological systems. Here we report on the development and application of a robust approach to quantitatively map combinatorially engineered populations at scales up to several dozen target sites. This approach works by assembling genome engineered sites with cell-specific barcodes into a format compatible with high-throughput sequencing technologies. This approach, called barcoded-TRACE (bTRACE) was applied to assess E. coli populations engineered by recursive multiplex recombineering across both 6-target sites and 31-target sites. The 31-target library was then tracked throughout growth selections in the presence and absence of isopentenol (a potential next-generation biofuel). We also use the resolution of bTRACE to compare the influence of technical and biological noise on genome engineering efforts.

Impact of compost process conditions on organic micro pollutant degradation during full scale composting.

PubMed

Sadef, Yumna; Poulsen, Tjalfe Gorm; Bester, Kai

2015-06-01

Knowledge about the effects of oxygen concentration, nutrient availability and moisture content on removal of organic micro-pollutants during aerobic composting is at present very limited. Impact of oxygen concentration, readily available nitrogen content (NH4(+), NO3(-)), and moisture content on biological transformation of 15 key organic micro-pollutants during composting, was therefore investigated using bench-scale degradation experiments based on non-sterile compost samples, collected at full-scale composting facilities. In addition, the adequacy of bench-scale composting experiments for representing full-scale composting conditions, was investigated using micro-pollutant concentration measurements from both bench- and full-scale composting experiments. Results showed that lack of oxygen generally prevented transformation of organic micro-pollutants. Increasing readily available nitrogen content from about 50 mg N per 100 g compost to about 140 mg N per 100 g compost actually reduced micro-pollutant transformation, while changes in compost moisture content from 50% to 20% by weight, only had minor influence on micro-pollutant transformation. First-order micro-pollutant degradation rates for 13 organic micro-pollutants were calculated using data from both full- and bench-scale experiments. First-order degradation coefficients for both types of experiments were similar and ranged from 0.02 to 0.03 d(-1) on average, indicating that if a proper sampling strategy is employed, bench-scale experiments can be used to represent full-scale composting conditions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Pattern Formation on Networks: from Localised Activity to Turing Patterns

PubMed Central

McCullen, Nick; Wagenknecht, Thomas

2016-01-01

Networks of interactions between competing species are used to model many complex systems, such as in genetics, evolutionary biology or sociology and knowledge of the patterns of activity they can exhibit is important for understanding their behaviour. The emergence of patterns on complex networks with reaction-diffusion dynamics is studied here, where node dynamics interact via diffusion via the network edges. Through the application of a generalisation of dynamical systems analysis this work reveals a fundamental connection between small-scale modes of activity on networks and localised pattern formation seen throughout science, such as solitons, breathers and localised buckling. The connection between solutions with a single and small numbers of activated nodes and the fully developed system-scale patterns are investigated computationally using numerical continuation methods. These techniques are also used to help reveal a much larger portion of of the full number of solutions that exist in the system at different parameter values. The importance of network structure is also highlighted, with a key role being played by nodes with a certain so-called optimal degree, on which the interaction between the reaction kinetics and the network structure organise the behaviour of the system. PMID:27273339

Bacterial communities in full-scale wastewater treatment systems.

PubMed

Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena

2016-04-01

Bacterial metabolism determines the effectiveness of biological treatment of wastewater. Therefore, it is important to define the relations between the species structure and the performance of full-scale installations. Although there is much laboratory data on microbial consortia, our understanding of dependencies between the microbial structure and operational parameters of full-scale wastewater treatment plants (WWTP) is limited. This mini-review presents the types of microbial consortia in WWTP. Information is given on extracellular polymeric substances production as factor that is key for formation of spatial structures of microorganisms. Additionally, we discuss data on microbial groups including nitrifiers, denitrifiers, Anammox bacteria, and phosphate- and glycogen-accumulating bacteria in full-scale aerobic systems that was obtained with the use of molecular techniques, including high-throughput sequencing, to shed light on dependencies between the microbial ecology of biomass and the overall efficiency and functional stability of wastewater treatment systems. Sludge bulking in WWTPs is addressed, as well as the microbial composition of consortia involved in antibiotic and micropollutant removal.

Sensor Web in Antarctica: Developing an Intelligent, Autonomous Platform for Locating Biological Flourishes in Cryogenic Environments

NASA Technical Reports Server (NTRS)

Delin, K. A.; Harvey, R. P.; Chabot, N. A.; Jackson, S. P.; Adams, Mike; Johnson, D. W.; Britton, J. T.

2003-01-01

The most rigorous tests of the ability to detect extant life will occur where biotic activity is limited by severe environmental conditions. Cryogenic environments are among the most severe-the energy and nutrients needed for biological activity are in short supply while the climate itself is actively destructive to biological mechanisms. In such settings biological activity is often limited to brief flourishes, occurring only when and where conditions are at their most favorable. The closer that typical regional conditions approach conditions that are actively hostile , the more widely distributed biological blooms will be in both time and space. On a spatial dimension of a few meters or a time dimension of a few days, biological activity becomes much more difficult to detect. One way to overcome this difficulty is to establish a Sensor Web that can monitor microclimates over appropriate scales of time and distance, allowing a continuous virtual presence for instant recognition of favorable conditions. A more sophisticated Sensor Web, incorporating metabolic sensors, can effectively meet the challenge to be in "the right place in the right time". This is particularly of value in planetary surface missions, where limited mobility and mission timelines require extremely efficient sample and data acquisition. Sensor Webs can be an effective way to fill the gap between broad scale orbital data collection and fine-scale surface lander science. We are in the process of developing an intelligent, distributed and autonomous Sensor Web that will allow us to monitor microclimate under severe cryogenic conditions, approaching those extant on the surface of Mars. Ultimately this Sensor Web will include the ability to detect and/or establish limits on extant microbiological activity through incorporation of novel metabolic gas sensors. Here we report the results of our first deployment of a Sensor Web prototype in a previously unexplored high altitude East Antarctic Plateau "micro-oasis" at the MacAlpine Hills, Law Glacier, Antarctica.

Effect of advanced oxidation on N-nitrosodimethylamine (NDMA) formation and microbial ecology during pilot-scale biological activated carbon filtration.

PubMed

Li, Dong; Stanford, Ben; Dickenson, Eric; Khunjar, Wendell O; Homme, Carissa L; Rosenfeldt, Erik J; Sharp, Jonathan O

2017-04-15

Water treatment combining advanced oxidative processes with subsequent exposure to biological activated carbon (BAC) holds promise for the attenuation of recalcitrant pollutants. Here we contrast oxidation and subsequent biofiltration of treated wastewater effluent employing either ozone or UV/H 2 O 2 followed by BAC during pilot-scale implementation. Both treatment trains largely met target water quality goals by facilitating the removal of a suite of trace organics and bulk water parameters. N-nitrosodimethylamine (NDMA) formation was observed in ozone fed BAC columns during biofiltration and to a lesser extent in UV/H 2 O 2 fed columns and was most pronounced at 20 min of empty bed contact time (EBCT) when compared to shorter EBCTs evaluated. While microbial populations were highly similar in the upper reaches, deeper samples revealed a divergence within and between BAC filtration systems where EBCT was identified to be a significant environmental predictor for shifts in microbial populations. The abundance of Nitrospira in the top samples of both columns provides an explanation for the oxidation of nitrite and corresponding increases in nitrate concentrations during BAC transit and support interplay between nitrogen cycling with nitrosamine formation. The results of this study demonstrate that pretreatments using ozone versus UV/H 2 O 2 impart modest differences to the overall BAC microbial population structural and functional attributes, and further highlight the need to evaluate NDMA formation prior to full-scale implementation of BAC in potable reuse applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biological iron oxidation by Gallionella spp. in drinking water production under fully aerated conditions.

PubMed

de Vet, W W J M; Dinkla, I J T; Rietveld, L C; van Loosdrecht, M C M

2011-11-01

Iron oxidation under neutral conditions (pH 6.5-8) may be a homo- or heterogeneous chemically- or a biologically-mediated process. The chemical oxidation is supposed to outpace the biological process under slightly alkaline conditions (pH 7-8). The iron oxidation kinetics and growth of Gallionella spp. - obligatory chemolithotrophic iron oxidizers - were assessed in natural, organic carbon-containing water, in continuous lab-scale reactors and full-scale groundwater trickling filters in the Netherlands. From Gallionella cell numbers determined by qPCR, balances were made for all systems. The homogeneous chemical iron oxidation occurred in accordance with the literature, but was retarded by a low water temperature (13 °C). The contribution of the heterogeneous chemical oxidation was, despite the presence of freshly formed iron oxyhydroxides, much lower than in previous studies in ultrapure water. This could be caused by the adsorption of natural organic matter (NOM) on the iron oxide surfaces. In the oxygen-saturated natural water with a pH ranging from 6.5 to 7.7, Gallionella spp. grew uninhibited and biological iron oxidation was an important, and probably the dominant, process. Gallionella growth was not even inhibited in a full-scale filter after plate aeration. From this we conclude that Gallionella spp. can grow under neutral pH and fully aerated conditions when the chemical iron oxidation is retarded by low water temperature and inhibition of the autocatalytic iron oxidation. Copyright © 2011 Elsevier Ltd. All rights reserved.

Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors

PubMed Central

Connelly, Stephanie; Shin, Seung G.; Dillon, Robert J.; Ijaz, Umer Z.; Quince, Christopher; Sloan, William T.; Collins, Gavin

2017-01-01

Studies investigating the feasibility of new, or improved, biotechnologies, such as wastewater treatment digesters, inevitably start with laboratory-scale trials. However, it is rarely determined whether laboratory-scale results reflect full-scale performance or microbial ecology. The Expanded Granular Sludge Bed (EGSB) bioreactor, which is a high-rate anaerobic digester configuration, was used as a model to address that knowledge gap in this study. Two laboratory-scale idealizations of the EGSB—a one-dimensional and a three- dimensional scale-down of a full-scale design—were built and operated in triplicate under near-identical conditions to a full-scale EGSB. The laboratory-scale bioreactors were seeded using biomass obtained from the full-scale bioreactor, and, spent water from the distillation of whisky from maize was applied as substrate at both scales. Over 70 days, bioreactor performance, microbial ecology, and microbial community physiology were monitored at various depths in the sludge-beds using 16S rRNA gene sequencing (V4 region), specific methanogenic activity (SMA) assays, and a range of physical and chemical monitoring methods. SMA assays indicated dominance of the hydrogenotrophic pathway at full-scale whilst a more balanced activity profile developed during the laboratory-scale trials. At each scale, Methanobacterium was the dominant methanogenic genus present. Bioreactor performance overall was better at laboratory-scale than full-scale. We observed that bioreactor design at laboratory-scale significantly influenced spatial distribution of microbial community physiology and taxonomy in the bioreactor sludge-bed, with 1-D bioreactor types promoting stratification of each. In the 1-D laboratory bioreactors, increased abundance of Firmicutes was associated with both granule position in the sludge bed and increased activity against acetate and ethanol as substrates. We further observed that stratification in the sludge-bed in 1-D laboratory-scale bioreactors was associated with increased richness in the underlying microbial community at species (OTU) level and improved overall performance. PMID:28507535

The Implementation of Research-based Learning on Biology Seminar Course in Biology Education Study Program of FKIP UMRAH

NASA Astrophysics Data System (ADS)

Amelia, T.

2018-04-01

Biology Seminar is a course in Biology Education Study Program of Faculty of Teacher Training and Education University of Maritim Raja Ali Haji (FKIP UMRAH) that requires students to have the ability to apply scientific attitudes, perform scientific writing and undertake scientific publications on a small scale. One of the learning strategies that can drive the achievement of learning outcomes in this course is Research-Based Learning. Research-Based Learning principles are considered in accordance with learning outcomes in Biology Seminar courses and generally in accordance with the purpose of higher education. On this basis, this article which is derived from a qualitative research aims at describing Research-based Learning on Biology Seminar course. Based on a case study research, it was known that Research-Based Learning on Biology Seminar courses is applied through: designing learning activities around contemporary research issues; teaching research methods, techniques and skills explicitly within program; drawing on personal research in designing and teaching courses; building small-scale research activities into undergraduate assignment; and infusing teaching with the values of researchers.

Bridging scales through multiscale modeling: a case study on protein kinase A.

PubMed

Boras, Britton W; Hirakis, Sophia P; Votapka, Lane W; Malmstrom, Robert D; Amaro, Rommie E; McCulloch, Andrew D

2015-01-01

The goal of multiscale modeling in biology is to use structurally based physico-chemical models to integrate across temporal and spatial scales of biology and thereby improve mechanistic understanding of, for example, how a single mutation can alter organism-scale phenotypes. This approach may also inform therapeutic strategies or identify candidate drug targets that might otherwise have been overlooked. However, in many cases, it remains unclear how best to synthesize information obtained from various scales and analysis approaches, such as atomistic molecular models, Markov state models (MSM), subcellular network models, and whole cell models. In this paper, we use protein kinase A (PKA) activation as a case study to explore how computational methods that model different physical scales can complement each other and integrate into an improved multiscale representation of the biological mechanisms. Using measured crystal structures, we show how molecular dynamics (MD) simulations coupled with atomic-scale MSMs can provide conformations for Brownian dynamics (BD) simulations to feed transitional states and kinetic parameters into protein-scale MSMs. We discuss how milestoning can give reaction probabilities and forward-rate constants of cAMP association events by seamlessly integrating MD and BD simulation scales. These rate constants coupled with MSMs provide a robust representation of the free energy landscape, enabling access to kinetic, and thermodynamic parameters unavailable from current experimental data. These approaches have helped to illuminate the cooperative nature of PKA activation in response to distinct cAMP binding events. Collectively, this approach exemplifies a general strategy for multiscale model development that is applicable to a wide range of biological problems.

Improving anaerobic and aerobic degradation by ultrasonic disintegration of biomass.

PubMed

Neis, Uwe; Nickel, Klaus; Lundén, Anna

2008-11-01

Biological cell lysis is known to be the rate-limiting step of anaerobic biosolids degradation. Due to the slow pace by which this reaction occurs, it is necessary to equip treatment plants with large digesters or alternatively incorporate technological aids. High-power ultrasound used to disintegrate bacterial cells has been utilized as a pre-treatment process prior to anaerobic digestion. Through this application, as seen on pilot- and full-scales, it is possible to attain up to 30% more biogas, an increase in VS-destruction of up to 30% and a reduced sludge mass for disposal. Utilizing ultrasound technology in aerobic applications is a new and innovative approach. Improved denitrification through a more readily available internal carbon source, and less excess sludge mass can be traced to the positive effects that sonication of sludge has on the overall biological wastewater treatment process. Reference full-scale installations suggest that the technology is both technically feasible and economically sound.

Comparison of natural estrogen removal efficiency in the conventional activated sludge process and the oxidation ditch process.

PubMed

Hashimoto, T; Onda, K; Nakamura, Y; Tada, K; Miya, A; Murakami, T

2007-05-01

The presence of natural estrogens, 17beta-estradiol (E2), estrone (E1) and estriol (E3), as well as estrogenic activity in wastewater influents and secondary effluents were investigated in 20 full-scale wastewater treatment plants in Japan. In all of the influent samples, natural estrogens were detected at concentrations above the minimum limits of detection (0.5ng/L). The concentrations of natural estrogens detected in the effluent of oxidation ditch plants were generally lower than previously reported values. On the other hand, in the conventional activated sludge plants, increments of E1 during biological treatment were frequently observed although E2 and E3 were removed effectively in the process. The removal rates of natural estrogens or estrogenic activity show no observed statistical relationship with the solids retention time (SRT) and the hydraulic retention time (HRT). However, the plants with high SRT or HRT generally showed high and stable removal of both natural estrogens and estrogenic activity.

National Wind Technology Center sitewide, Golden, CO: Environmental assessment

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

NONE

1996-11-01

The National Renewable Energy Laboratory (NREL), the nation`s primary solar and renewable energy research laboratory, proposes to expand its wind technology research and development program activities at its National Wind Technology Center (NWTC) near Golden, Colorado. NWTC is an existing wind energy research facility operated by NREL for the US Department of Energy (DOE). Proposed activities include the construction and reuse of buildings and facilities, installation of up to 20 wind turbine test sites, improvements in infrastructure, and subsequent research activities, technology testing, and site operations. In addition to wind turbine test activities, NWTC may be used to support othermore » NREL program activities and small-scale demonstration projects. This document assesses potential consequences to resources within the physical, biological, and human environment, including potential impacts to: air quality, geology and soils, water resources, biological resources, cultural and historic resources, socioeconomic resources, land use, visual resources, noise environment, hazardous materials and waste management, and health and safety conditions. Comment letters were received from several agencies in response to the scoping and predecisional draft reviews. The comments have been incorporated as appropriate into the document with full text of the letters contained in the Appendices. Additionally, information from the Rocky Flats Environmental Technology Site on going sitewide assessment of potential environmental impacts has been reviewed and discussed by representatives of both parties and incorporated into the document as appropriate.« less

Optimization aspects of the biological nitrogen removal process in a full-scale twin sequencing batch reactor (SBR) system in series treating landfill leachate.

PubMed

Remmas, Nikolaos; Ntougias, Spyridon; Chatzopoulou, Marianna; Melidis, Paraschos

2018-03-29

Despite the fact that biological nitrogen removal (BNR) process has been studied in detail in laboratory- and pilot-scale sequencing batch reactor (SBR) systems treating landfill leachate, a limited number of research works have been performed in full-scale SBR plants regarding nitrification and denitrification. In the current study, a full-scale twin SBR system in series of 700 m 3 (350 m 3 each) treating medium-age landfill leachate was evaluated in terms of its carbon and nitrogen removal efficiency in the absence and presence of external carbon source, i.e., glycerol from biodiesel production. Both biodegradable organic carbon and ammonia were highly oxidized [biochemical oxygen demand (BOD 5 ) and total Kjehldahl nitrogen (TKN) removal efficiencies above 90%], whereas chemical oxygen demand (COD) removal efficiency was slightly above 40%, which is within the range reported in the literature for pilot-scale SBRs. As the consequence of the high recalcitrant organic fraction of the landfill leachate, dissimilatory nitrate reduction was restricted in the absence of crude glycerol, although denitrification was improved by electron donor addition, resulting in TN removal efficiencies above 70%. Experimental data revealed that the second SBR negligibly contributed to BNR process, since carbon and ammonia oxidation completion was achieved in the first SBR. On the other hand, the low VSS/SS ratio, due to the lack of primary sedimentation, highly improved sludge settleability, resulting in sludge volume indices (SVI) below 30 mL g -1 .

Multi-scale Observation of Biological Interactions of Nanocarriers: from Nano to Macro

PubMed Central

Jin, Su-Eon; Bae, Jin Woo; Hong, Seungpyo

2010-01-01

Microscopic observations have played a key role in recent advancements in nanotechnology-based biomedical sciences. In particular, multi-scale observation is necessary to fully understand the nano-bio interfaces where a large amount of unprecedented phenomena have been reported. This review describes how to address the physicochemical and biological interactions of nanocarriers within the biological environments using microscopic tools. The imaging techniques are categorized based on the size scale of detection. For observation of the nano-scale biological interactions of nanocarriers, we discuss atomic force microscopy (AFM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). For the micro to macro-scale (in vitro and in vivo) observation, we focus on confocal laser scanning microscopy (CLSM) as well as in vivo imaging systems such as magnetic resonance imaging (MRI), superconducting quantum interference devices (SQUIDs), and IVIS®. Additionally, recently developed combined techniques such as AFM-CLSM, correlative Light and Electron Microscopy (CLEM), and SEM-spectroscopy are also discussed. In this review, we describe how each technique helps elucidate certain physicochemical and biological activities of nanocarriers such as dendrimers, polymers, liposomes, and polymeric/inorganic nanoparticles, thus providing a toolbox for bioengineers, pharmaceutical scientists, biologists, and research clinicians. PMID:20232368

Biography for Todd Shollenberger | NREL

Science.gov Websites

Shollenberger Photo of Todd Shollenberger Todd Shollenberger Research Technician III-Biological biocatalyst fermentation. He has worked on professional research and development projects such as the fermentation production process development, pilot plant to full production scale-up, and quantitative

Volumetric full-range magnetomotive optical coherence tomography

PubMed Central

Ahmad, Adeel; Kim, Jongsik; Shemonski, Nathan D.; Marjanovic, Marina; Boppart, Stephen A.

2014-01-01

Abstract. Magnetomotive optical coherence tomography (MM-OCT) can be utilized to spatially localize the presence of magnetic particles within tissues or organs. These magnetic particle-containing regions are detected by using the capability of OCT to measure small-scale displacements induced by the activation of an external electromagnet coil typically driven by a harmonic excitation signal. The constraints imposed by the scanning schemes employed and tissue viscoelastic properties limit the speed at which conventional MM-OCT data can be acquired. Realizing that electromagnet coils can be designed to exert MM force on relatively large tissue volumes (comparable or larger than typical OCT imaging fields of view), we show that an order-of-magnitude improvement in three-dimensional (3-D) MM-OCT imaging speed can be achieved by rapid acquisition of a volumetric scan during the activation of the coil. Furthermore, we show volumetric (3-D) MM-OCT imaging over a large imaging depth range by combining this volumetric scan scheme with full-range OCT. Results with tissue equivalent phantoms and a biological tissue are shown to demonstrate this technique. PMID:25472770

Can the invasive earthworm, Amynthas agrestis, be controlled with prescribed fire?

Treesearch

Hiroshi Ikeda; Mac A. Callaham Jr.; Joseph J. O' Brien; Benjamin S. Hornsby; Evelyn S. Wenk

2015-01-01

Biological invasions are one of the most significant global-scale problems caused by human activities. Earthworms function as ecosystem engineers in soil ecosystems because their feeding and burrowing activities fundamentally change the physical and biological characteristics of the soils they inhabit. As a result of this “engineering,” earthworm invasions can have...

From 'omics to otoliths: responses of an estuarine fish to endocrine disrupting compounds across biological scales.

PubMed

Brander, Susanne M; Connon, Richard E; He, Guochun; Hobbs, James A; Smalling, Kelly L; Teh, Swee J; White, J Wilson; Werner, Inge; Denison, Michael S; Cherr, Gary N

2013-01-01

Endocrine disrupting chemicals (EDCs) cause physiological abnormalities and population decline in fishes. However, few studies have linked environmental EDC exposures with responses at multiple tiers of the biological hierarchy, including population-level effects. To this end, we undertook a four-tiered investigation in the impacted San Francisco Bay estuary with the Mississippi silverside (Menidia audens), a small pelagic fish. This approach demonstrated links between different EDC sources and fish responses at different levels of biological organization. First we determined that water from a study site primarily impacted by ranch run-off had only estrogenic activity in vitro, while water sampled from a site receiving a combination of urban, limited ranch run-off, and treated wastewater effluent had both estrogenic and androgenic activity. Secondly, at the molecular level we found that fish had higher mRNA levels for estrogen-responsive genes at the site where only estrogenic activity was detected but relatively lower expression levels where both estrogenic and androgenic EDCs were detected. Thirdly, at the organism level, males at the site exposed to both estrogens and androgens had significantly lower mean gonadal somatic indices, significantly higher incidence of severe testicular necrosis and altered somatic growth relative to the site where only estrogens were detected. Finally, at the population level, the sex ratio was significantly skewed towards males at the site with measured androgenic and estrogenic activity. Our results suggest that mixtures of androgenic and estrogenic EDCs have antagonistic and potentially additive effects depending on the biological scale being assessed, and that mixtures containing androgens and estrogens may produce unexpected effects. In summary, evaluating EDC response at multiple tiers is necessary to determine the source of disruption (lowest scale, i.e. cell line) and what the ecological impact will be (largest scale, i.e. sex ratio).

A truncated Wnt7a retains full biological activity in skeletal muscle

NASA Astrophysics Data System (ADS)

von Maltzahn, Julia; Zinoviev, Radoslav; Chang, Natasha C.; Bentzinger, C. Florian; Rudnicki, Michael A.

2013-11-01

Wnt signaling has essential roles during embryonic development and tissue homoeostasis. Wnt proteins are post-translationally modified and the attachment of a palmitate moiety at two conserved residues is believed to be a prerequisite for the secretion and function of Wnt proteins. Here we demonstrate that a mammalian Wnt protein can be fully functional without palmitoylation. We generate a truncated Wnt7a variant, consisting of the C-terminal 137 amino acids lacking the conserved palmitoylation sites and show that it retains full biological activity in skeletal muscle. This includes binding to and signaling through its receptor Fzd7 to stimulate symmetric expansion of satellite stem cells by activating the planar-cell polarity pathway and inducing myofibre hypertrophy by signaling through the AKT/mTOR pathway. Furthermore, this truncated Wnt7a shows enhanced secretion and dispersion compared with the full-length protein. Together, these findings open important new avenues for the development of Wnt7a as a treatment for muscle-wasting diseases and have broad implications for the therapeutic use of Wnts as biologics.

Thermal Destruction Of CB Contaminants Bound On Building ...

EPA Pesticide Factsheets

Symposium Paper An experimental and theoretical program has been initiated by the U.S. EPA to investigate issues of chemical/biological agent destruction in incineration systems when the agent in question is bound on common porous building interior materials. This program includes 3-dimensional computational fluid dynamics modeling with matrix-bound agent destruction kinetics, bench-scale experiments to determine agent destruction kinetics while bound on various matrices, and pilot-scale experiments to scale-up the bench-scale experiments to a more practical scale. Finally, model predictions are made to predict agent destruction and combustion conditions in two full-scale incineration systems that are typical of modern combustor design.

Overall effect of carbon production and nutrient release in sludge holding tank on mainstream biological nutrient removal efficiency.

PubMed

Jabari, Pouria; Yuan, Qiuyan; Oleszkiewicz, Jan A

2017-09-11

The potential of hydrolysis/fermentation of activated sludge in sludge holding tank (SHT) to produce additional carbon for the biological nutrient removal (BNR) process was investigated. The study was conducted in anaerobic batch tests using the BNR sludge (from a full-scale Westside process) and the mixture of BNR sludge with conventional non-BNR activated sludge (to have higher biodegradable particulate chemical oxygen demand (bpCOD) in sludge). The BioWin 4.1 was used to simulate the anaerobic batch test of the BNR sludge. Also, the overall effect of FCOD production and nutrient release on BNR efficiency of the Westside process was estimated. The experimental results showed that the phosphorous uptake of sludge increased during hydrolysis/ fermentation condition up to the point when poly-P was completely utilized; afterwards, it decreased significantly. The BioWin simulation could not predict the loss of aerobic phosphorous uptake after poly-P was depleted. The results showed that in the case of activated sludge with relatively higher bpCOD (originating from plants with short sludge retention time or without primary sedimentation), beneficial effect of SHT on BNR performance is feasible. In order to increase the potential of SHT to enhance BNR efficiency, a relatively low retention time and high sludge load is recommended.

Process Design Manual for Nitrogen Control.

ERIC Educational Resources Information Center

Parker, Denny S.; And Others

This manual presents theoretical and process design criteria for the implementation of nitrogen control technology in municipal wastewater treatment facilities. Design concepts are emphasized through examination of data from full-scale and pilot installations. Design data are included on biological nitrification and denitrification, breakpoint…

National water-quality assessment program : the Albemarle- Pamlico drainage

USGS Publications Warehouse

Lloyd, O.B.; Barnes, C.R.; Woodside, M.D.

1991-01-01

In 1991, the U.S. Geological Survey (USGS) began to implement a full-scale National Water-Quality Assessment (NAWQA) program. Long-term goals of the NAWQA program are to describe the status and trends in the quality of a large, representative part of the Nation's surface- and ground-water resources and to provide a sound, scientific understanding of the primary natural and human factors affecting the quality of these resources. In meeting these goals, the program will produce a wealth of water quality information that will be useful to policy makers and managers at the national, State, and local levels. Study-unit investigations constitute a major component of the NAWQA program, forming the principal building blocks on which national-level assessment activities are based. The 60 study-unit investigations that make up the program are hydrologic systems that include parts of most major river basins and aquifer systems. These study units cover areas of 1,200 to more than 65,000 square miles and incorporate about 60 to 70 percent of the Nation's water use and population served by public water supply. In 1991, the Albemarle-Pamlico drainage was among the first 20 NAWQA study units selected for study under the full-scale implementation plan. The Albemarle-Pamlico drainage study will examine the physical, chemical, and biological aspects of water quality issues in a coordinated investigation of surface water and ground water in the Albemarle-Pamlico drainage basin. The quantity and quality of discharge from the Albemarle-Pamlico drainage basin contribute to some water quality problems in the biologically sensitive waters of Albemarle and Pamlico Sounds. A retrospective analysis of existing water quality data will precede a 3-year period of intensive data-collection and analysis activities. The data resulting from this study and the improved understanding of important processes and issues in the upstream part of the study unit will enhance understanding of the quality of water in Albemarle-Pamlico Sounds, the second largest estuarine system in the United States.

The New Bedford Harbor Superfund Site Long Term ...

EPA Pesticide Factsheets

Background. New Bedford Harbor (NBH), located in southeastern Massachusetts, was designated as a marine Superfund site in 1983 due to sediment contamination by polychlorinated biphenyls (PCBs). Based on risks to human health and the environment, the first two phases of the site cleanup involved dredging PCB-contaminated sediments from the harbor. Therefore, a long-term monitoring program (LTM) was developed to measure spatial and temporal chemical and biological changes in sediment, water, and biota to assess the effects and effectiveness of the remedial activities. Approach. A systematic, probabilistic sampling design was used to select approximately 70 sediment sampling stations. Sediment was collected at each station and chemical (e.g., PCBs, metals), physical (e.g., grain size), and biological (e.g., benthic community) measurements were conducted on all samples. There have been six sample collections to date: 1993-baseline, 1995-post hot spot removal, 1999-prior to full scale dredging, and then at 5 year intervals: 2004, 2009, and 2014. Mussel (Mytilus edulis) bioaccumulation has also been measured twice yearly. Results. There is a decreasing spatial gradient in sediment PCB concentrations from the northern boundary (upper harbor) to the southern boundary (outer harbor) of the site. Along this same transect, there is an increase in biological condition (e.g., benthic community diversity). Temporally, the contaminant and biological gradients have been

Enhancing biological control of basal stem rot disease (Ganoderma boninense) in oil palm plantations.

PubMed

Susanto, A; Sudharto, P S; Purba, R Y

2005-01-01

Basal Stem Rot (BSR) disease caused by Ganoderma boninense is the most destructive disease in oil palm, especially in Indonesia and Malaysia. The available control measures for BSR disease such as cultural practices and mechanical and chemical treatment have not proved satisfactory due to the fact that Ganoderma has various resting stages such as melanised mycelium, basidiospores and pseudosclerotia. Alternative control measures to overcome the Ganoderma problem are focused on the use of biological control agents and planting resistant material. Present studies conducted at Indonesian Oil Palm Research Institute (IOPRI) are focused on enhancing the use of biological control agents for Ganoderma. These activities include screening biological agents from the oil palm rhizosphere in order to evaluate their effectiveness as biological agents in glasshouse and field trials, testing their antagonistic activities in large scale experiments and eradicating potential disease inoculum with biological agents. Several promising biological agents have been isolated, mainly Trichoderma harzianum, T. viride, Gliocladium viride, Pseudomonas fluorescens, and Bacillus sp. A glasshouse and field trial for Ganoderma control indicated that treatment with T. harzianum and G. viride was superior to Bacillus sp. A large scale trial showed that the disease incidence was lower in a field treated with biological agents than in untreated fields. In a short term programme, research activities at IOPRI are currently focusing on selecting fungi that can completely degrade plant material in order to eradicate inoculum. Digging holes around the palm bole and adding empty fruit bunches have been investigated as ways to stimulate biological agents.

Nonequilibrium phase transition in a self-activated biological network.

PubMed

Berry, Hugues

2003-03-01

We present a lattice model for a two-dimensional network of self-activated biological structures with a diffusive activating agent. The model retains basic and simple properties shared by biological systems at various observation scales, so that the structures can consist of individuals, tissues, cells, or enzymes. Upon activation, a structure emits a new mobile activator and remains in a transient refractory state before it can be activated again. Varying the activation probability, the system undergoes a nonequilibrium second-order phase transition from an active state, where activators are present, to an absorbing, activator-free state, where each structure remains in the deactivated state. We study the phase transition using Monte Carlo simulations and evaluate the critical exponents. As they do not seem to correspond to known values, the results suggest the possibility of a separate universality class.

Production of a full-length infectious GFP-tagged cDNA clone of Beet mild yellowing virus for the study of plant-polerovirus interactions.

PubMed

Stevens, Mark; Viganó, Felicita

2007-04-01

The full-length cDNA of Beet mild yellowing virus (Broom's Barn isolate) was sequenced and cloned into the vector pLitmus 29 (pBMYV-BBfl). The sequence of BMYV-BBfl (5721 bases) shared 96% and 98% nucleotide identity with the other complete sequences of BMYV (BMYV-2ITB, France and BMYV-IPP, Germany respectively). Full-length capped RNA transcripts of pBMYV-BBfl were synthesised and found to be biologically active in Arabidopsis thaliana protoplasts following electroporation or PEG inoculation when the protoplasts were subsequently analysed using serological and molecular methods. The BMYV sequence was modified by inserting DNA that encoded the jellyfish green fluorescent protein (GFP) into the P5 gene close to its 3' end. A. thaliana protoplasts electroporated with these RNA transcripts were biologically active and up to 2% of transfected protoplasts showed GFP-specific fluorescence. The exploitation of these cDNA clones for the study of the biology of beet poleroviruses is discussed.

Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology

PubMed Central

de Graaf, Albert A.; Freidig, Andreas P.; De Roos, Baukje; Jamshidi, Neema; Heinemann, Matthias; Rullmann, Johan A.C.; Hall, Kevin D.; Adiels, Martin; van Ommen, Ben

2009-01-01

The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the consideration and interpretation of experimental data at widely differing scales of space and time. In this review, we discuss a selection of available modeling approaches and applications relevant for nutrition. We then put these models into perspective by categorizing them according to their space and time domain. Through this categorization process, we identified a dearth of models that consider processes occurring between the microscopic and macroscopic scale. We propose a “middle-out” strategy to develop the required full-scale, multilevel computational models. Exhaustive and accurate phenotyping, the use of the virtual patient concept, and the development of biomarkers from “-omics” signatures are identified as key elements of a successful systems biology modeling approach in nutrition research—one that integrates physiological mechanisms and data at multiple space and time scales. PMID:19956660

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology.

PubMed

Price, S A; Schmitz, L

2016-04-05

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. © 2016 The Author(s).

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology

PubMed Central

Schmitz, L.

2016-01-01

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. PMID:26977068

Operational and biological analyses of branched water-adjustment and combined treatment of wastewater from a chemical industrial park.

PubMed

Xu, Ming; Cao, Jiashun; Li, Chao; Tu, Yong; Wu, Haisuo; Liu, Weijing

2018-01-01

The combined biological processes of branched water-adjustment, chemical precipitation, hydrolysis acidification, secondary sedimentation, Anoxic/Oxic and activated carbon treatment were used for chemical industrial wastewater treatment in the Taihu Lake Basin. Full-scale treatment resulted in effluent chemical oxygen demand, total nitrogen, NH 3 -N and total phosphorus of 35.1, 5.20, 3.10 and 0.15 mg/L, respectively, with a total removal efficiency of 91.1%, 67.1%, 70.5% and 89.3%, respectively. In this process, short-circuited organic carbon from brewery wastewater was beneficial for denitrification and second-sulfate reduction. The concentration of effluent fluoride was 6.22 mg/L, which also met the primary standard. Gas Chromatography-Mass Spectrometry analysis revealed that many types of refractory compounds were present in the inflow. Microbial community analysis performed in the summer by PCR-denaturing gradient gel electrophoresis and MiSeq demonstrated that certain special functional bacteria, such as denitrificans, phosphorus-accumulating bacteria, sulfate- and perhafnate-reducing bacteria, aromatic compound-degrading bacteria and organic fluoride-degrading bacteria, present in the bio-tanks were responsible for the acceptable specific biological pollutant reduction achieved.

Advanced biological activated carbon filter for removing pharmaceutically active compounds from treated wastewater.

PubMed

Sbardella, Luca; Comas, Joaquim; Fenu, Alessio; Rodriguez-Roda, Ignasi; Weemaes, Marjoleine

2018-04-28

Through their release of effluents, conventional wastewater treatment plants (WWTPs) represent a major pollution point sources for pharmaceutically active compounds (PhACs) in water bodies. The combination of a biological activated carbon (BAC) filter coupled with an ultrafiltration (UF) unit was evaluated as an advanced treatment for PhACs removal at pilot scale. The BAC-UF pilot plant was monitored for one year. The biological activity of the biofilm that developed on the granular activated carbon (GAC) particles and the contribution of this biofilm to the overall removal of PhACs were evaluated. Two different phases were observed during the long-term monitoring of PhACs removal. During the first 9200 bed volumes (BV; i.e., before GAC saturation), 89, 78, 83 and 79% of beta-blockers, psychiatric drugs, antibiotics and a mix of other therapeutic groups were removed, respectively. The second phase was characterized by deterioration of the overall performances during the period between 9200 and 13,800 BV. To quantify the respective contribution of adsorption and biodegradation, a lab-scale setup was operated for four months and highlighted the essential role played by GAC in biofiltration units. Physical adsorption was indeed the main removal mechanism. Nevertheless, a significant contribution due to biological activity was detected for some PhACs. The biofilm contributed to the removal of 22, 25, 30, 32 and 35% of ciprofloxacin, bezafibrate, ofloxacin, azithromycin and sulfamethoxazole, respectively. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Roadmap on semiconductor-cell biointerfaces

NASA Astrophysics Data System (ADS)

Tian, Bozhi; Xu, Shuai; Rogers, John A.; Cestellos-Blanco, Stefano; Yang, Peidong; Carvalho-de-Souza, João L.; Bezanilla, Francisco; Liu, Jia; Bao, Zhenan; Hjort, Martin; Cao, Yuhong; Melosh, Nicholas; Lanzani, Guglielmo; Benfenati, Fabio; Galli, Giulia; Gygi, Francois; Kautz, Rylan; Gorodetsky, Alon A.; Kim, Samuel S.; Lu, Timothy K.; Anikeeva, Polina; Cifra, Michal; Krivosudský, Ondrej; Havelka, Daniel; Jiang, Yuanwen

2018-05-01

This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world.

Integration between chemical oxidation and membrane thermophilic biological process.

PubMed

Bertanza, G; Collivignarelli, M C; Crotti, B M; Pedrazzani, R

2010-01-01

Full scale applications of activated sludge thermophilic aerobic process for treatment of liquid wastes are rare. This experimental work was carried out at a facility, where a thermophilic reactor (1,000 m(3) volume) is operated. In order to improve the global performance of the plant, it was decided to upgrade it, by means of two membrane filtration units (ultrafiltration -UF-, in place of the final sedimentation, and nanofiltration -NF-). Subsequently, the integration with chemical oxidation (O(3) and H(2)O(2)/UV processes) was taken into consideration. Studied solutions dealt with oxidation of both the NF effluents (permeate and concentrate). Based on experimental results and economic evaluation, an algorithm was proposed for defining limits of convenience of this process.

Filamentous Bacterium Eikelboom Type 0092 in Activated Sludge Plants in Australia Is a Member of the Phylum Chloroflexi▿

PubMed Central

Speirs, Lachlan; Nittami, Tadashi; McIlroy, Simon; Schroeder, Sarah; Seviour, Robert J.

2009-01-01

Molecular data show that the filamentous bacterium Eikelboom type 0092, frequently seen in Australian activated sludge plants, is a member of the phylum Chloroflexi. Fluorescence in situ hybridization (FISH) probes designed against cloned 16S rRNA sequences from a full-scale enhanced biological phosphate removal-activated sludge plant community, where this was a dominant filament morphotype, suggest that it can exist as two variants, differing in their trichome diameter. When applied to samples from several treatment plants in eastern Australia, each FISH probe targeted only the type 0092 filament morphotype against which it was designed. The patterns of FISH signals generated with both were consistent with the ribosomes not being evenly distributed but arranged as intracellular aggregates. The FISH survey data showed that these two variants appeared together in most but not all of the plants examined. None stained positively for intracellular presence of either poly-β-hydroxyalkanoates or polyphosphate. PMID:19218415

Effect of selected dimethylaminochalcones on some mitochondrial activities.

PubMed

Vašková, Janka; Reisch, Renáta; Vaško, Ladislav; Poškrobová, Martina; Kron, Ivan; Guzy, Juraj; Perjési, Pál

2013-05-01

Chalcones and their synthetic cyclic analogues have been shown to possess a full scale of biological activities in a variety of experimental systems. They were assessed to be mostly effective in defense against free radicals in the organism, but several compounds exhibited cytotoxic pro-oxidant activities. The respiratory response and antioxidant status in mitochondria were investigated upon addition of 4'-dimethylaminochalcone (1a) and its cyclic analogues, (E)-2-(4'-((CH3)2 N)-benzylidene)-1-indanone (1b), -1-tetralone (1c), and -1-benzosuberone (1d). Selected structures were able to change the respiratory response of mitochondria and showed an ability to modify mitochondrial metabolic and redox efficiency, though they did not indicate redox reactivity towards glutathione in adduct-free incubations. The results of the study indicate that -chalcone and -tetralone derivatives cause suppression of reactive oxygen species affecting mitochondrial respiration by mild uncoupling. In addition, (E)-2-(4'-((CH3)2 N)-indanone (1b), and to a greater extent, -benzosuberone (1d), showed pro-oxidant effects, which partially explain their cytotoxicity.

Time scale of diffusion in molecular and cellular biology

NASA Astrophysics Data System (ADS)

Holcman, D.; Schuss, Z.

2014-05-01

Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function.

Comprehensive Evaluation of Biological Growth Control by Chlorine-Based Biocides in Power Plant Cooling Systems Using Tertiary Effluent

PubMed Central

Chien, Shih-Hsiang; Dzombak, David A.; Vidic, Radisav D.

2013-01-01

Abstract Recent studies have shown that treated municipal wastewater can be a reliable cooling water alternative to fresh water. However, elevated nutrient concentration and microbial population in wastewater lead to aggressive biological proliferation in the cooling system. Three chlorine-based biocides were evaluated for the control of biological growth in cooling systems using tertiary treated wastewater as makeup, based on their biocidal efficiency and cost-effectiveness. Optimal chemical regimens for achieving successful biological growth control were elucidated based on batch-, bench-, and pilot-scale experiments. Biocide usage and biological activity in planktonic and sessile phases were carefully monitored to understand biological growth potential and biocidal efficiency of the three disinfectants in this particular environment. Water parameters, such as temperature, cycles of concentration, and ammonia concentration in recirculating water, critically affected the biocide performance in recirculating cooling systems. Bench-scale recirculating tests were shown to adequately predict the biocide residual required for a pilot-scale cooling system. Optimal residuals needed for proper biological growth control were 1, 2–3, and 0.5–1 mg/L as Cl2 for NaOCl, preformed NH2Cl, and ClO2, respectively. Pilot-scale tests also revealed that Legionella pneumophila was absent from these cooling systems when using the disinfectants evaluated in this study. Cost analysis showed that NaOCl is the most cost-effective for controlling biological growth in power plant recirculating cooling systems using tertiary-treated wastewater as makeup. PMID:23781129

Comprehensive Evaluation of Biological Growth Control by Chlorine-Based Biocides in Power Plant Cooling Systems Using Tertiary Effluent.

PubMed

Chien, Shih-Hsiang; Dzombak, David A; Vidic, Radisav D

2013-06-01

Recent studies have shown that treated municipal wastewater can be a reliable cooling water alternative to fresh water. However, elevated nutrient concentration and microbial population in wastewater lead to aggressive biological proliferation in the cooling system. Three chlorine-based biocides were evaluated for the control of biological growth in cooling systems using tertiary treated wastewater as makeup, based on their biocidal efficiency and cost-effectiveness. Optimal chemical regimens for achieving successful biological growth control were elucidated based on batch-, bench-, and pilot-scale experiments. Biocide usage and biological activity in planktonic and sessile phases were carefully monitored to understand biological growth potential and biocidal efficiency of the three disinfectants in this particular environment. Water parameters, such as temperature, cycles of concentration, and ammonia concentration in recirculating water, critically affected the biocide performance in recirculating cooling systems. Bench-scale recirculating tests were shown to adequately predict the biocide residual required for a pilot-scale cooling system. Optimal residuals needed for proper biological growth control were 1, 2-3, and 0.5-1 mg/L as Cl 2 for NaOCl, preformed NH 2 Cl, and ClO 2 , respectively. Pilot-scale tests also revealed that Legionella pneumophila was absent from these cooling systems when using the disinfectants evaluated in this study. Cost analysis showed that NaOCl is the most cost-effective for controlling biological growth in power plant recirculating cooling systems using tertiary-treated wastewater as makeup.

Diagnosing oceanic nutrient deficiency

PubMed Central

2016-01-01

The supply of a range of nutrient elements to surface waters is an important driver of oceanic production and the subsequent linked cycling of the nutrients and carbon. Relative deficiencies of different nutrients with respect to biological requirements, within both surface and internal water masses, can be both a key indicator and driver of the potential for these nutrients to become limiting for the production of new organic material in the upper ocean. The availability of high-quality, full-depth and global-scale datasets on the concentrations of a wide range of both macro- and micro-nutrients produced through the international GEOTRACES programme provides the potential for estimation of multi-element deficiencies at unprecedented scales. Resultant coherent large-scale patterns in diagnosed deficiency can be linked to the interacting physical–chemical–biological processes which drive upper ocean nutrient biogeochemistry. Calculations of ranked deficiencies across multiple elements further highlight important remaining uncertainties in the stoichiometric plasticity of nutrient ratios within oceanic microbial systems and caveats with regards to linkages to upper ocean nutrient limitation. This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’. PMID:29035255

Diagnosing oceanic nutrient deficiency

NASA Astrophysics Data System (ADS)

Moore, C. Mark

2016-11-01

The supply of a range of nutrient elements to surface waters is an important driver of oceanic production and the subsequent linked cycling of the nutrients and carbon. Relative deficiencies of different nutrients with respect to biological requirements, within both surface and internal water masses, can be both a key indicator and driver of the potential for these nutrients to become limiting for the production of new organic material in the upper ocean. The availability of high-quality, full-depth and global-scale datasets on the concentrations of a wide range of both macro- and micro-nutrients produced through the international GEOTRACES programme provides the potential for estimation of multi-element deficiencies at unprecedented scales. Resultant coherent large-scale patterns in diagnosed deficiency can be linked to the interacting physical-chemical-biological processes which drive upper ocean nutrient biogeochemistry. Calculations of ranked deficiencies across multiple elements further highlight important remaining uncertainties in the stoichiometric plasticity of nutrient ratios within oceanic microbial systems and caveats with regards to linkages to upper ocean nutrient limitation. This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'.

Utilization of Neurophysiological Protocols to Characterize Soldier Response to Irritant Gases. Phase 1.

DTIC Science & Technology

1990-02-15

electrical activity mapping procedures. It is necessary to employ approximately 20 electrodes to conduct full- scale brain mapping procedures, using a...animal groups, likewise, showed no observable differences in the animal’s exploratory behavior, nuzzle response, lid-corneal and ear reflexes, pain ...SPECIFICATIONS FOR THE ENVIRONICS SERIES 100 GAS STANDARDS GENERATOR Accuracy of Flow 0.15 % of Full Scale Linearity 0.15 % of Full Scale Repeatability 0.10

Biological instability in a chlorinated drinking water distribution network.

PubMed

Nescerecka, Alina; Rubulis, Janis; Vital, Marius; Juhna, Talis; Hammes, Frederik

2014-01-01

The purpose of a drinking water distribution system is to deliver drinking water to the consumer, preferably with the same quality as when it left the treatment plant. In this context, the maintenance of good microbiological quality is often referred to as biological stability, and the addition of sufficient chlorine residuals is regarded as one way to achieve this. The full-scale drinking water distribution system of Riga (Latvia) was investigated with respect to biological stability in chlorinated drinking water. Flow cytometric (FCM) intact cell concentrations, intracellular adenosine tri-phosphate (ATP), heterotrophic plate counts and residual chlorine measurements were performed to evaluate the drinking water quality and stability at 49 sampling points throughout the distribution network. Cell viability methods were compared and the importance of extracellular ATP measurements was examined as well. FCM intact cell concentrations varied from 5×10(3) cells mL(-1) to 4.66×10(5) cells mL(-1) in the network. While this parameter did not exceed 2.1×10(4) cells mL(-1) in the effluent from any water treatment plant, 50% of all the network samples contained more than 1.06×10(5) cells mL(-1). This indisputably demonstrates biological instability in this particular drinking water distribution system, which was ascribed to a loss of disinfectant residuals and concomitant bacterial growth. The study highlights the potential of using cultivation-independent methods for the assessment of chlorinated water samples. In addition, it underlines the complexity of full-scale drinking water distribution systems, and the resulting challenges to establish the causes of biological instability.

Biological Instability in a Chlorinated Drinking Water Distribution Network

PubMed Central

Nescerecka, Alina; Rubulis, Janis; Vital, Marius; Juhna, Talis; Hammes, Frederik

2014-01-01

The purpose of a drinking water distribution system is to deliver drinking water to the consumer, preferably with the same quality as when it left the treatment plant. In this context, the maintenance of good microbiological quality is often referred to as biological stability, and the addition of sufficient chlorine residuals is regarded as one way to achieve this. The full-scale drinking water distribution system of Riga (Latvia) was investigated with respect to biological stability in chlorinated drinking water. Flow cytometric (FCM) intact cell concentrations, intracellular adenosine tri-phosphate (ATP), heterotrophic plate counts and residual chlorine measurements were performed to evaluate the drinking water quality and stability at 49 sampling points throughout the distribution network. Cell viability methods were compared and the importance of extracellular ATP measurements was examined as well. FCM intact cell concentrations varied from 5×103 cells mL−1 to 4.66×105 cells mL−1 in the network. While this parameter did not exceed 2.1×104 cells mL−1 in the effluent from any water treatment plant, 50% of all the network samples contained more than 1.06×105 cells mL−1. This indisputably demonstrates biological instability in this particular drinking water distribution system, which was ascribed to a loss of disinfectant residuals and concomitant bacterial growth. The study highlights the potential of using cultivation-independent methods for the assessment of chlorinated water samples. In addition, it underlines the complexity of full-scale drinking water distribution systems, and the resulting challenges to establish the causes of biological instability. PMID:24796923

The Two Ts: Teaching and Technology

ERIC Educational Resources Information Center

Flannery, Maura C.

2004-01-01

A professor of Biology shares his experience at the BioQUEST workshop, which he attended. He talks about the BioQUEST Curriculum Consortium, which is a large-scale college biology project, focusing on active learning strategies, and the use of technology in teaching. The approaches presented at the workshop are described.

Sensitivity of the Halstead and Wechsler Test Batteries to brain damage: Evidence from Reitan's original validation sample.

PubMed

Loring, David W; Larrabee, Glenn J

2006-06-01

The Halstead-Reitan Battery has been instrumental in the development of neuropsychological practice in the United States. Although Reitan administered both the Wechsler-Bellevue Intelligence Scale and Halstead's test battery when evaluating Halstead's theory of biologic intelligence, the relative sensitivity of each test battery to brain damage continues to be an area of controversy. Because Reitan did not perform direct parametric analysis to contrast group performances, we reanalyze Reitan's original validation data from both Halstead (Reitan, 1955) and Wechsler batteries (Reitan, 1959a) and calculate effect sizes and probability levels using traditional parametric approaches. Eight of the 10 tests comprising Halstead's original Impairment Index, as well as the Impairment Index itself, statistically differentiated patients with unequivocal brain damage from controls. In addition, 13 of 14 Wechsler measures including Full-Scale IQ also differed statistically between groups (Brain Damage Full-Scale IQ = 96.2; Control Group Full Scale IQ = 112.6). We suggest that differences in the statistical properties of each battery (e.g., raw scores vs. standardized scores) likely contribute to classification characteristics including test sensitivity and specificity.

The Full-Scale Implementation of an Innovative Biological Ammonia Treatment Process

EPA Science Inventory

Across the United States, high levels of ammonia in drinking water sources can be found, including small communities like Palo, Iowa (approximate population of 1,026). Although ammonia in water does not pose a direct health concern, ammonia nitrification can cause a number of iss...

Evaluation of two pilot scale membrane bioreactors for the elimination of selected surfactants from municipal wastewaters

NASA Astrophysics Data System (ADS)

González, Susana; Petrovic, Mira; Barceló, Damiá

2008-07-01

SummaryThe removal of selected surfactants, linear alkylbenzene sulfonates (LAS), coconut diethanol amides (CDEA) and alkylphenol ethoxylates and their degradation products were investigated using a two membrane bioreactor (MBR) with hollow fiber and plate and frame membranes. The two pilot plants MBR run in parallel to a full-scale conventional activated sludge (CAS) treatment. A total of eight influent samples with the corresponding effluent samples were analysed by solid phase extraction-liquid chromatography-tandem mass spectrometry (SPE-LC-MS-MS). The results indicate that both MBR have a better effluent quality in terms of chemical and biological oxygen demand (COD and BOD), NH4+ , concentration and total suspended solids (TSS). MBR showed a better similar performance in the overall elimination of the total nonylphenolic compounds, achieving a 75% of elimination or a 65% (the same elimination reached by CAS). LAS and CDEA showed similar elimination in the three systems investigated and no significant differences were observed.

Fate of pharmaceuticals in full-scale source separated sanitation system.

PubMed

Butkovskyi, A; Hernandez Leal, L; Rijnaarts, H H M; Zeeman, G

2015-11-15

Removal of 14 pharmaceuticals and 3 of their transformation products was studied in a full-scale source separated sanitation system with separate collection and treatment of black water and grey water. Black water is treated in an up-flow anaerobic sludge blanket (UASB) reactor followed by oxygen-limited autotrophic nitrification-denitrification in a rotating biological contactor and struvite precipitation. Grey water is treated in an aerobic activated sludge process. Concentration of 10 pharmaceuticals and 2 transformation products in black water ranged between low μg/l to low mg/l. Additionally, 5 pharmaceuticals were also present in grey water in low μg/l range. Pharmaceutical influent loads were distributed over two streams, i.e. diclofenac was present for 70% in grey water, while the other compounds were predominantly associated to black water. Removal in the UASB reactor fed with black water exceeded 70% for 9 pharmaceuticals out of the 12 detected, with only two pharmaceuticals removed by sorption to sludge. Ibuprofen and the transformation product of naproxen, desmethylnaproxen, were removed in the rotating biological contactor. In contrast, only paracetamol removal exceeded 90% in the grey water treatment system while removal of other 7 pharmaceuticals was below 40% or even negative. The efficiency of pharmaceutical removal in the source separated sanitation system was compared with removal in the conventional sewage treatment plants. Furthermore, effluent concentrations of black water and grey water treatment systems were compared with predicted no-effect concentrations to assess toxicity of the effluent. Concentrations of diclofenac, ibuprofen and oxazepam in both effluents were higher than predicted no-effect concentrations, indicating the necessity of post-treatment. Ciprofloxacin, metoprolol and propranolol were found in UASB sludge in μg/g range, while pharmaceutical concentrations in struvite did not exceed the detection limits. Copyright © 2015 Elsevier Ltd. All rights reserved.

Upgrading of a small overloaded activated sludge plant using a MBBR system.

PubMed

Andreottola, G; Foladori, P; Gatti, G; Nardelli, P; Pettena, M; Ragazzi, M

2003-01-01

The aim of this research was the application of a biofilm system for the upgrading of a full-scale overloaded activated sludge MWWTP using the MBBR (Moving Bed Biofilm Reactor) technology. The choice of this fixed biomass system appeared appropriate because it offers several advantages including good potential in nitrification process, easiness of management and above all, the possibility to use the existing tank with very few modifications. MBBR system counts only few full-scale plants in Italy at the moment, thus a pilot-scale experimentation was preliminarily carried out. The acquired parameters were used for the fullscale MWWTP upgrading. The upgrading of the activated sludge reactor in the MBBR system has given (1) a relevant increase in the flowrate treated up to 60%; (2) a good efficiency in organic carbon removal and nitrification, equal to 88% and 90% respectively, with HRTs of 5.5-7 h; (3) the overcoming of the hydraulic overload of the secondary settler, applying a lamellar settler. It was observed a good correlation between the results obtained at pilot-scale and those observed in the full-scale plant.

Hibiscus latent Fort Pierce virus in Brazil and synthesis of its biologically active full-length cDNA clone.

PubMed

Gao, Ruimin; Niu, Shengniao; Dai, Weifang; Kitajima, Elliot; Wong, Sek-Man

2016-10-01

A Brazilian isolate of Hibiscus latent Fort Pierce virus (HLFPV-BR) was firstly found in a hibiscus plant in Limeira, SP, Brazil. RACE PCR was carried out to obtain the full-length sequences of HLFPV-BR which is 6453 nucleotides and has more than 99.15 % of complete genomic RNA nucleotide sequence identity with that of HLFPV Japanese isolate. The genomic structure of HLFPV-BR is similar to other tobamoviruses. It includes a 5' untranslated region (UTR), followed by open reading frames encoding for a 128-kDa protein and a 188-kDa readthrough protein, a 38-kDa movement protein, 18-kDa coat protein, and a 3' UTR. Interestingly, the unique feature of poly(A) tract is also found within its 3'-UTR. Furthermore, from the total RNA extracted from the local lesions of HLFPV-BR-infected Chenopodium quinoa leaves, a biologically active, full-length cDNA clone encompassing the genome of HLFPV-BR was amplified and placed adjacent to a T7 RNA polymerase promoter. The capped in vitro transcripts from the cloned cDNA were infectious when mechanically inoculated into C. quinoa and Nicotiana benthamiana plants. This is the first report of the presence of an isolate of HLFPV in Brazil and the successful synthesis of a biologically active HLFPV-BR full-length cDNA clone.

Molecular systems biology of ErbB1 signaling: bridging the gap through multiscale modeling and high-performance computing.

PubMed

Shih, Andrew J; Purvis, Jeremy; Radhakrishnan, Ravi

2008-12-01

The complexity in intracellular signaling mechanisms relevant for the conquest of many diseases resides at different levels of organization with scales ranging from the subatomic realm relevant to catalytic functions of enzymes to the mesoscopic realm relevant to the cooperative association of molecular assemblies and membrane processes. Consequently, the challenge of representing and quantifying functional or dysfunctional modules within the networks remains due to the current limitations in our understanding of mesoscopic biology, i.e., how the components assemble into functional molecular ensembles. A multiscale approach is necessary to treat a hierarchy of interactions ranging from molecular (nm, ns) to signaling (microm, ms) length and time scales, which necessitates the development and application of specialized modeling tools. Complementary to multiscale experimentation (encompassing structural biology, mechanistic enzymology, cell biology, and single molecule studies) multiscale modeling offers a powerful and quantitative alternative for the study of functional intracellular signaling modules. Here, we describe the application of a multiscale approach to signaling mediated by the ErbB1 receptor which constitutes a network hub for the cell's proliferative, migratory, and survival programs. Through our multiscale model, we mechanistically describe how point-mutations in the ErbB1 receptor can profoundly alter signaling characteristics leading to the onset of oncogenic transformations. Specifically, we describe how the point mutations induce cascading fragility mechanisms at the molecular scale as well as at the scale of the signaling network to preferentially activate the survival factor Akt. We provide a quantitative explanation for how the hallmark of preferential Akt activation in cell-lines harboring the constitutively active mutant ErbB1 receptors causes these cell-lines to be addicted to ErbB1-mediated generation of survival signals. Consequently, inhibition of ErbB1 activity leads to a remarkable therapeutic response in the addicted cell lines.

The Biological and Toxicological Activity of Gases and Vapors

PubMed Central

Sánchez-Moreno, Ricardo; Gil-Lostes, Javier; Acree, William E.; Cometto-Muñiz, J. Enrique; Cain, William S.

2010-01-01

A large amount of data on the biological and toxicological activity of gases and vapors has been collected from the literature. Processes include sensory irritation thresholds, the Alarie mouse test, inhalation anesthesia, etc. It is shown that a single equation using only five descriptors (properties of the gases and vapors) plus a set of indicator variables for the given processes can correlate 643 biological and non-lethal toxicological activities of ‘non-reactive’ compounds with a standard deviation of 0.36 log unit. The equation is scaled to sensory irritation thresholds obtained by the procedure of Cometto-Muñiz, and Cain, and provides a general equation for the prediction of sensory irritation thresholds in man. It is suggested that differences in biological/toxicological activity arise primarily from transport from the gas phase to a receptor phase or area, except for odor detection thresholds where interaction with a receptor(s) is important. PMID:19913608

Comparative performance of different scale-down simulators of substrate gradients in Penicillium chrysogenum cultures: the need of a biological systems response analysis.

PubMed

Wang, Guan; Zhao, Junfei; Haringa, Cees; Tang, Wenjun; Xia, Jianye; Chu, Ju; Zhuang, Yingping; Zhang, Siliang; Deshmukh, Amit T; van Gulik, Walter; Heijnen, Joseph J; Noorman, Henk J

2018-05-01

In a 54 m 3 large-scale penicillin fermentor, the cells experience substrate gradient cycles at the timescales of global mixing time about 20-40 s. Here, we used an intermittent feeding regime (IFR) and a two-compartment reactor (TCR) to mimic these substrate gradients at laboratory-scale continuous cultures. The IFR was applied to simulate substrate dynamics experienced by the cells at full scale at timescales of tens of seconds to minutes (30 s, 3 min and 6 min), while the TCR was designed to simulate substrate gradients at an applied mean residence time (τc) of 6 min. A biological systems analysis of the response of an industrial high-yielding P. chrysogenum strain has been performed in these continuous cultures. Compared to an undisturbed continuous feeding regime in a single reactor, the penicillin productivity (q PenG ) was reduced in all scale-down simulators. The dynamic metabolomics data indicated that in the IFRs, the cells accumulated high levels of the central metabolites during the feast phase to actively cope with external substrate deprivation during the famine phase. In contrast, in the TCR system, the storage pool (e.g. mannitol and arabitol) constituted a large contribution of carbon supply in the non-feed compartment. Further, transcript analysis revealed that all scale-down simulators gave different expression levels of the glucose/hexose transporter genes and the penicillin gene clusters. The results showed that q PenG did not correlate well with exposure to the substrate regimes (excess, limitation and starvation), but there was a clear inverse relation between q PenG and the intracellular glucose level. © 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis.

PubMed

Van Landeghem, Sofie; De Bodt, Stefanie; Drebert, Zuzanna J; Inzé, Dirk; Van de Peer, Yves

2013-03-01

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies.

Upgrading of an activated sludge wastewater treatment plant by adding a moving bed biofilm reactor as pre-treatment and ozonation followed by biofiltration for enhanced COD reduction: design and operation experience.

PubMed

Kaindl, Nikolaus

2010-01-01

A paper mill producing 500,000 ton of graphic paper annually has an on-site wastewater treatment plant that treats 7,240,000 m³ of wastewater per year, mechanically first, then biologically and at last by ozonation. Increased paper production capacity led to higher COD load in the mill effluent while production of higher proportions of brighter products gave worse biodegradability. Therefore the biological capacity of the WWTP needed to be increased and extra measures were necessary to enhance the efficiency of COD reduction. The full scale implementation of one MBBR with a volume of 1,230 m³ was accomplished in 2000 followed by another MBBR of 2,475 m³ in 2002. An ozonation step with a capacity of 75 kg O₃/h was added in 2004 to meet higher COD reduction demands during the production of brighter products and thus keeping the given outflow limits. Adding a moving bed biofilm reactor prior to the existing activated sludge step gives: (i) cost advantages when increasing biological capacity as higher COD volume loads of MBBRs allow smaller reactors than usual for activated sludge plants; (ii) a relief of strain from the activated sludge step by biological degradation in the MBBR; (iii) equalizing of peaks in the COD load and toxic effects before affecting the activated sludge step; (iv) a stable volume sludge index below 100 ml/g in combination with an optimization of the activated sludge step allows good sludge separation--an important condition for further treatment with ozone. Ozonation and subsequent bio-filtration pre-treated waste water provide: (i) reduction of hard COD unobtainable by conventional treatment; (ii) controllable COD reduction in a very wide range and therefore elimination of COD-peaks; (iii) reduction of treatment costs by combination of ozonation and subsequent bio-filtration; (iv) decrease of the color in the ozonated wastewater. The MBBR step proved very simple to operate as part of the biological treatment. Excellent control of the COD-removal rate in the ozone step allowed for economical usage and therefore acceptable operation costs in relation to the paper production.

Emergent mechanics of biological structures

PubMed Central

Dumont, Sophie; Prakash, Manu

2014-01-01

Mechanical force organizes life at all scales, from molecules to cells and tissues. Although we have made remarkable progress unraveling the mechanics of life's individual building blocks, our understanding of how they give rise to the mechanics of larger-scale biological structures is still poor. Unlike the engineered macroscopic structures that we commonly build, biological structures are dynamic and self-organize: they sculpt themselves and change their own architecture, and they have structural building blocks that generate force and constantly come on and off. A description of such structures defies current traditional mechanical frameworks. It requires approaches that account for active force-generating parts and for the formation of spatial and temporal patterns utilizing a diverse array of building blocks. In this Perspective, we term this framework “emergent mechanics.” Through examples at molecular, cellular, and tissue scales, we highlight challenges and opportunities in quantitatively understanding the emergent mechanics of biological structures and the need for new conceptual frameworks and experimental tools on the way ahead. PMID:25368421

A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

PubMed Central

Eissing, Thomas; Kuepfer, Lars; Becker, Corina; Block, Michael; Coboeken, Katrin; Gaub, Thomas; Goerlitz, Linus; Jaeger, Juergen; Loosen, Roland; Ludewig, Bernd; Meyer, Michaela; Niederalt, Christoph; Sevestre, Michael; Siegmund, Hans-Ulrich; Solodenko, Juri; Thelen, Kirstin; Telle, Ulrich; Weiss, Wolfgang; Wendl, Thomas; Willmann, Stefan; Lippert, Joerg

2011-01-01

Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multiscale by nature, project work, and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug–drug, or drug–metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach. PMID:21483730

Biological sludge solubilisation for reduction of excess sludge production in wastewater treatment process.

PubMed

Yamaguchi, T; Yao, Y; Kihara, Y

2006-01-01

A novel sludge disintegration system (JFE-SD system) was developed for the reduction of excess sludge production in wastewater treatment plants. Chemical and biological treatments were applied to disintegrate excess sludge. At the first step, to enhance biological disintegration, the sludge was pretreated with alkali. At the second step, the sludge was disintegrated by biological treatment. Many kinds of sludge degrading microorganisms integrated the sludge. The efficiency of the new sludge disintegration system was confirmed in a full-scale experiment. The JFE-SD system reduced excess sludge production by approximately 50% during the experimental period. The quality of effluent was kept at quite a good level. Economic analysis revealed that this system could significantly decrease the excess sludge treatment cost.

Chemical synthesis of biologically active tat trans-activating protein of human immunodeficiency virus type 1.

PubMed Central

Chun, R; Glabe, C G; Fan, H

1990-01-01

Full-length (86-residue) polypeptide corresponding to the human immunodeficiency virus type 1 tat trans-activating protein was chemically synthesized on a semiautomated apparatus, using an Fmoc amino acid continuous-flow strategy. The bulk material was relatively homogeneous, as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and isoelectric focusing, and it showed trans-activating activity when scrape loaded into cells containing a human immunodeficiency virus long terminal repeat-chloramphenicol acetyl-transferase reporter plasmid. Reverse-phase high-pressure liquid chromatography yielded a rather broad elution profile, and assays across the column for biological activity indicated a sharper peak. Thus, high-pressure liquid chromatography provided for enrichment of biological activity. Fast atom bombardment-mass spectrometry of tryptic digests of synthetic tat identified several of the predicted tryptic peptides, consistent with accurate chemical synthesis. Images PMID:2186178

Final Report - Montana State University - Microbial Activity and Precipitation at Solution-Solution Mixing Zones in Porous Media

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

Gerlach, Robin

Background. The use of biological and chemical processes that degrade or immobilize contaminants in subsurface environments is a cornerstone of remediation technology. The enhancement of biological and chemical processes in situ, involves the transport, displacement, distribution and mixing of one or more reactive agents. Biological and chemical reactions all require diffusive transport of solutes to reaction sites at the molecular scale and accordingly, the success of processes at the meter-scale and larger is dictated by the success of phenomena that occur at the micron-scale. However, current understanding of scaling effects on the mixing and delivery of nutrients in biogeochemically dynamicmore » porous media systems is limited, despite the limitations this imposes on the efficiency and effectiveness of the remediation challenges at hand. Objectives. We therefore proposed to experimentally characterize and computationally describe the growth, evolution, and distribution of microbial activity and mineral formation as well as changes in transport processes in porous media that receive two or more reactive amendments. The model system chosen for this project was based on a method for immobilizing 90Sr, which involves stimulating microbial urea hydrolysis with ensuing mineral precipitation (CaCO3), and co-precipitation of Sr. Studies at different laboratory scales were used to visualize and quantitatively describe the spatial relationships between amendment transport and consumption that stimulate the production of biomass and mineral phases that subsequently modify the permeability and heterogeneity of porous media. Biomass growth, activity, and mass deposition in mixing zones was investigated using two-dimensional micro-model flow cells as well as flow cells that could be analyzed using synchrotron-based x-ray tomography. Larger-scale flow-cell experiments were conducted where the spatial distribution of media properties, flow, segregation of biological activity and impact on ancillary constituents (i.e., Sr) was determined. Model simulations accompanied the experimental efforts. Benefits and Outcomes of the Project. The research contributed towards defining the key physical, chemical, and biological processes influencing the form and mobility of DOE priority contaminants (e.g., 60Co, 90Sr, U) in the subsurface. The work conducted and reported herein, will in the future (i) contribute to controlling the juxtaposition of microbial activity, contaminants and amendments, (ii) promote new strategies for delivering amendments, and (iii) allow new approaches for modifying permeability and flow in porous media. We feel that the work has already translated directly to improving the efficiency of amendment based remediation strategies. Products. The results of the project have been published in a number of peer reviewed journal articles. The abstracts and citations to those articles, given in section 2.0 below, make up the bulk of this final report.« less

A Critical Assessment of the Microorganisms Proposed to be Important to Enhanced Biological Phosphorus Removal in Full-Scale Wastewater Treatment Systems.

PubMed

Stokholm-Bjerregaard, Mikkel; McIlroy, Simon J; Nierychlo, Marta; Karst, Søren M; Albertsen, Mads; Nielsen, Per H

2017-01-01

Understanding the microbiology of phosphorus (P) removal is considered essential to knowledge-based optimization of enhanced biological P removal (EBPR) systems. Biological P removal is achieved in these systems by promoting the growth of organisms collectively known as the polyphosphate accumulating organisms (PAOs). Also considered important to EBPR are the glycogen accumulating organisms (GAOs), which are theorized to compete with the PAOs for resources at the expense of P removal efficiency. Numerous studies have sought to identify the PAOs and their GAOs competitors, with several candidates proposed for each over the last few decades. The current study collectively assessed the abundance and diversity of all proposed PAOs and GAOs in 18 Danish full-scale wastewater treatment plants with well-working biological nutrient removal over a period of 9 years using 16S rRNA gene amplicon sequencing. The microbial community structure in all plants was relatively stable over time. Evidence for the role of the proposed PAOs and GAOs in EBPR varies and is critically assessed, in light of their calculated amplicon abundances, to indicate which of these are important in full-scale systems. Bacteria from the genus Tetrasphaera were the most abundant of the PAOs. The " Candidatus Accumulibacter" PAOs were in much lower abundance and appear to be biased by the amplicon-based method applied. The genera Dechloromonas, Microlunatus , and Tessaracoccus were identified as abundant putative PAO that require further research attention. Interestingly, the actinobacterial Micropruina and sbr-gs28 phylotypes were among the most abundant of the putative GAOs. Members of the genera Defluviicoccus, Propionivibrio , the family Competibacteraceae, and the spb280 group were also relatively abundant in some plants. Despite observed high abundances of GAOs (periodically exceeding 20% of the amplicon reads), P removal performance was maintained, indicating that these organisms were not outcompeting the PAOs in these EBPR systems. Phylogenetic diversity within each of the PAOs and GAOs genera was observed, which is consistent with reported metabolic diversity for these. Whether or not key traits can be assigned to sub-genus level clades requires further investigation.

Effects of reduced return activated sludge flows and volume on anaerobic zone performance for a septic wastewater biological phosphorus removal system.

PubMed

Magro, Daniel; Elias, Steven L; Randall, Andrew Amis

2005-01-01

Enhanced biological phosphorous removal (EBPR) performance was found to be adequate with reduced return-activated sludge (RAS) flows (50% of available RAS) to the anaerobic tank and smaller-than-typical anaerobic zone volume (1.08 hours hydraulic retention time [HRT]). Three identical parallel biological nutrient removal pilot plants were fed with strong, highly fermented (160 mg/L volatile fatty acids [VFAs]), domestic and industrial wastewater from a full-scale wastewater treatment facility. The pilot plants were operated at 100, 50, 40, and 25% RAS (percent of available RAS) flows to the anaerobic tank, with the remaining RAS to the anoxic tank. In addition, varying anaerobic HRT (1.08 and 1.5 hours) and increased hydraulic loading (35% increase) were examined. The study was divided into four phases, and the effect of these process variations on EBPR were studied by having one different variable between two identical systems. The most significant conclusion was that returning part of the RAS to the anaerobic zone did not decrease EBPR performance; instead, it changed the location of phosphorous release and uptake. Bringing less RAS to the anaerobic and more to the anoxic tank decreased anaerobic phosphorus release and increased anoxic phosphorus release (or decreased anoxic phosphorus uptake). Equally important is that, with VFA-rich influent wastewater, excessive anaerobic volume was shown to hurt overall phosphorus removal, even when it resulted in increased anaerobic phosphorus release.

Biophysical response of dryland soils to rainfall: implications for wind erosion

NASA Astrophysics Data System (ADS)

Bullard, J. E.; Strong, C. L.; Aubault, H.

2016-12-01

Dryland soils can be highly susceptible to wind erosion due to low vegetation cover. The formation of physical and biological soil crusts between vascular plants can exert some control on the soil surface erodibility. The development of these crusts is highly dependent on rainfall which causes sediment compaction and aggregate breakdown, and triggers photosynthetic activity and an increase soil organic matter within biological soil crusts. Using controlled field experiments, this study tests how biological soil crusts in different dryland geomorphic settings respond to various rainfall amounts (0, 5 or 10 mm) and how this in turn affects the resistance of soils to wind erosion. Results show that 10 mm of rainfall triggers more intense photosynthetic activity (high fluorescence) and a greater increase in extracellular polysaccharide content in biological crusts than 5 mm of rainfall but that the duration of photosynthetic activity is comparable for both quantities of rain. These biological responses have little impact on surface resistance, but results show that soils are more susceptible to wind erosion after rainfall events than in their initial dry state. This unexpected result could be explained by the detachment of surface sediments by raindrop impact and overland flow. The study highlights the complexity of soil erodibility at small scale which is driven by rain, wind and crust, and a necessity to understand how the spatial heterogeneity of crust and their ecophysiology alters small scale processes.

Effect of ozone on biopolymers in biofiltration and ultrafiltration processes.

PubMed

Siembida-Lösch, Barbara; Anderson, William B; Wang, Yulang Michael; Bonsteel, Jane; Huck, Peter M

2015-03-01

The focus of this full-scale study was to determine the effect of ozone on biopolymer concentrations in biofiltration and ultrafiltration (UF) processes treating surface water from Lake Ontario. Ozonation was out of service for maintenance for 9 months, hence, it was possible to investigate ozone's action on biologically active carbon contactors (BACCs) and UF, in terms of biopolymer removal. Given the importance of biopolymers for fouling, this fraction was quantified using a chromatographic technique. Ozone pre-treatment was observed to positively impact the active biomass in biofilters. However, since an increase of the active biomass did not result in higher biopolymer removal, active biomass concentration cannot be a surrogate for biofiltration performance. It was evident that increasing empty bed contact time (EBCT) from 4 to 19 min only had a positive effect on biopolymer removal through BACCs when ozone was out of service. However, as a mass balance experiment showed, ozone-free operation resulted in higher deposition of biopolymers on a UF membrane and slight deterioration in its performance. Copyright © 2014 Elsevier Ltd. All rights reserved.

Performance and completion assessment of an in-situ aerated municipal solid waste landfill - Final scientific documentation of an Austrian case study.

PubMed

Hrad, Marlies; Huber-Humer, Marion

2017-05-01

By converting anaerobic landfills into a biologically stabilized state through accelerating aerobic organic matter degradation, the effort and duration necessary for post-closure procedures can be shortened. In Austria, the first full-scale application of in-situ landfill aeration by means of low pressure air injection with simultaneous off-gas collection and treatment was implemented on an old MSW-landfill and operated between 2007 and 2013. Besides complementary laboratory investigations, which included waste sampling from the landfill site prior to aeration start, a comprehensive field monitoring program was conducted to assess the influence of the aeration measure on the emission behavior of the landfilled waste during the aeration period as well as after aeration completion. Although the initial waste material was described as rather stable, the lab-scale aeration tests indicated a significant improvement of the leachate quality and even the biological solid waste stability. However, the aeration success was less pronounced for the application at the landfill site, mainly due to technical limitations in the full-scale operation. In this paper main performance data of the field investigation are compared to four other scientifically documented case studies along with stability indicators for solid waste and leachate characteristics in order to evaluate the success of aeration as well as the progress of a landfill towards completion and end of post-closure care. A number of quantitative benchmarks and relevant context information for the performance assessment of the five hitherto conducted international aeration projects are proposed aiming to support the systematization and harmonization of available results from diverse field studies and full-scale applications in future. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biological Oxidation of As (III) in a Full-Scale Iron Removal Plant

EPA Science Inventory

The effectiveness of arsenic removal from water is largely dependent on the oxidation state of the arsenic. As (III) is much more difficult to remove relative to the oxidized As (V) form. Arsenic in ground waters across the Midwest is typically in the form of As (III), and ther...

Full-scale production of VFAs from sewage sludge by anaerobic alkaline fermentation to improve biological nutrients removal in domestic wastewater.

PubMed

Liu, He; Han, Peng; Liu, Hongbo; Zhou, Guangjie; Fu, Bo; Zheng, Zhiyong

2018-07-01

A full-scale project of thermal-alkaline pretreatment and alkaline fermentation of sewage sludge was built to produce volatile fatty acids (VFAs) which was then used as external carbon source for improving biological nitrogen and phosphorus removals (BNPR) in wastewater plant. Results showed this project had efficient and stable performances in VFA production, sludge reduce and BNPR. Hydrolysis rate in pretreatment, VFAs yield in fermentation and total VS reduction reached 68.7%, 261.32 mg COD/g VSS and 54.19%, respectively. Moreover, fermentation liquid with VFA presented similar efficiency as acetic acid in enhancing BNPR, obtaining removal efficiencies of nitrogen and phosphorus up to 72.39% and 89.65%, respectively. Finally, the project also presented greater economic advantage than traditional processes, and the net profits for VFAs and biogas productions are 9.12 and 3.71 USD/m 3 sludge, respectively. Long-term operation indicated that anaerobic alkaline fermentation for VFAs production is technically and economically feasible for sludge carbon recovery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microwave Digestion and Furnace Atomic Absorption Method for the Quantification of Nano-scale TiO2 in Aqueous Samples

EPA Science Inventory

Many nanomaterials posses physical, and potentially biological, activity that is unique relative to their macro-scaled or soluble forms. One such property is surface plasmon resonance; a phenomenon that can generate or facilitate photoreactivity. Optimization of these properties ...

Efficient, ultra-high-affinity chromatography in a one-step purification of complex proteins

PubMed Central

Vassylyeva, Marina N.; Klyuyev, Sergiy; Vassylyev, Alexey D.; Wesson, Hunter; Zhang, Zhuo; Renfrow, Matthew B.; Wang, Hengbin; Higgins, N. Patrick; Chow, Louise T.; Vassylyev, Dmitry G.

2017-01-01

Protein purification is an essential primary step in numerous biological studies. It is particularly significant for the rapidly emerging high-throughput fields, such as proteomics, interactomics, and drug discovery. Moreover, purifications for structural and industrial applications should meet the requirement of high yield, high purity, and high activity (HHH). It is, therefore, highly desirable to have an efficient purification system with a potential to meet the HHH benchmark in a single step. Here, we report a chromatographic technology based on the ultra-high-affinity (Kd ∼ 10−14–10−17 M) complex between the Colicin E7 DNase (CE7) and its inhibitor, Immunity protein 7 (Im7). For this application, we mutated CE7 to create a CL7 tag, which retained the full binding affinity to Im7 but was inactivated as a DNase. To achieve high capacity, we developed a protocol for a large-scale production and highly specific immobilization of Im7 to a solid support. We demonstrated its utility with one-step HHH purification of a wide range of traditionally challenging biological molecules, including eukaryotic, membrane, toxic, and multisubunit DNA/RNA-binding proteins. The system is simple, reusable, and also applicable to pulldown and kinetic activity/binding assays. PMID:28607052

Effect of posttranslational modifications on enzyme function and assembly.

PubMed

Ryšlavá, Helena; Doubnerová, Veronika; Kavan, Daniel; Vaněk, Ondřej

2013-10-30

The detailed examination of enzyme molecules by mass spectrometry and other techniques continues to identify hundreds of distinct PTMs. Recently, global analyses of enzymes using methods of contemporary proteomics revealed widespread distribution of PTMs on many key enzymes distributed in all cellular compartments. Critically, patterns of multiple enzymatic and nonenzymatic PTMs within a single enzyme are now functionally evaluated providing a holistic picture of a macromolecule interacting with low molecular mass compounds, some of them being substrates, enzyme regulators, or activated precursors for enzymatic and nonenzymatic PTMs. Multiple PTMs within a single enzyme molecule and their mutual interplays are critical for the regulation of catalytic activity. Full understanding of this regulation will require detailed structural investigation of enzymes, their structural analogs, and their complexes. Further, proteomics is now integrated with molecular genetics, transcriptomics, and other areas leading to systems biology strategies. These allow the functional interrogation of complex enzymatic networks in their natural environment. In the future, one might envisage the use of robust high throughput analytical techniques that will be able to detect multiple PTMs on a global scale of individual proteomes from a number of carefully selected cells and cellular compartments. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine. Copyright © 2013 Elsevier B.V. All rights reserved.

Full activation of RNaseL in animal cells requires binding of 2-5A within ankyrin repeats 6 to 9 of this interferon-inducible enzyme.

PubMed

Díaz-Guerra, M; Rivas, C; Esteban, M

1999-02-01

To define protein domains important for activation of the interferon (IFN)-induced enzyme 2-5A-dependent RNaseL, we have generated vaccinia virus (VV) recombinants able to express in cultured cells truncated forms of this protein and compared their biologic activities with those producing the wild-type enzyme, with and without coexpression of 2-5A synthetase. Our results show that full activation of RNaseL requires binding of 2-5A oligonucleotides within amino acid positions 212-339, corresponding to ankyrin repeats 6 to 9. The protein kinase and ribonuclease domains of RNaseL, amino acids 340-741, are sufficient for a constitutively active enzyme that is unresponsive to excess 2-5A. These results demonstrate in vivo the importance of the ankyrin domains in the biologic function of RNaseL. We suggest that ankyrin repeats act as key modulators of RNaseL activity.

Control of biological growth in recirculating cooling systems using treated secondary effluent as makeup water with monochloramine.

PubMed

Chien, Shih-Hsiang; Chowdhury, Indranil; Hsieh, Ming-Kai; Li, Heng; Dzombak, David A; Vidic, Radisav D

2012-12-01

Secondary-treated municipal wastewater, an abundant and widely distributed impaired water source, is a promising alternative water source for thermoelectric power plant cooling. However, excessive biological growth is a major challenge associated with wastewater reuse in cooling systems as it can interfere with normal system operation as well as enhance corrosion and scaling problems. Furthermore, possible emission of biological aerosols (e.g., Legionella pneumophila) with the cooling tower drift can lead to public health concerns within the zone of aerosol deposition. In this study, the effectiveness of pre-formed and in-situ-formed monochloramine was evaluated for its ability to control biological growth in recirculating cooling systems using secondary-treated municipal wastewater as the only makeup water source. Bench-scale studies were compared with pilot-scale studies for their ability to predict system behavior under realistic process conditions. Effectiveness of the continuous addition of pre-formed monochloramine and monochloramine formed in-situ through the reaction of free chlorine with ammonia in the incoming water was evaluated in terms of biocide residual and its ability to control both planktonic and sessile microbial populations. Results revealed that monochloramine can effectively control biofouling in cooling systems employing secondary-treated municipal wastewater and has advantages relative to use of free chlorine, but that bench-scale studies seriously underestimate biocide dose and residual requirements for proper control of biological growth in full-scale systems. Pre-formed monochloramine offered longer residence time and more reliable performance than in-situ-formed monochloramine due to highly variable ammonia concentration in the recirculating water caused by ammonia stripping in the cooling tower. Pilot-scale tests revealed that much lower dosing rate was required to maintain similar total chlorine residual when pre-formed monochloramine was used as compared to in-situ-formed monochloramine. Adjustment of biocide dose to maintain monochloramine residual above 3mg/L is needed to achieve successful biological growth control in recirculating cooling systems using secondary-treated municipal effluent as the only source of makeup water. Copyright © 2012 Elsevier Ltd. All rights reserved.

Combined quantity management and biological treatment of sludge liquor at Hamburg's wastewater treatment plants--first experience in operation with the Store and Treat process.

PubMed

Laurich, F

2004-01-01

Store and Treat (SAT) is a new concept for the management of ammonium-rich process waste waters at wastewater treatment plants. It combines the advantages of quantity management and separate biological treatment, whereby both operations are carried out in the same tank. Now the first full-scale application of that method was realized in Hamburg. As first experience shows the process can help to increase nitrogen removal and to reduce energy consumption.

Full-scale results for TAM limestone injection

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

Baer, S.

1996-12-31

Information is outlined on the use of thermally active marble (TAM) sorbents in boilers. Data are presented on: the comparison of TAM to limestone; NOVACON process development history; CFB test history; CFB pilot scale test; full-scale CFB trial; August, 1996 CFB demonstration; Foster Wheeler Mount Carmel sorbent feed rate comparison and Ca:S comparison; unburned carbon is ash; and advantages and savings in CFB boilers.

The Fate of Major Royal Jelly Proteins during Proteolytic Digestion in the Human Gastrointestinal Tract.

PubMed

Mureşan, Carmen I; Schierhorn, Angelika; Buttstedt, Anja

2018-04-25

Royal jelly (RJ) is a beehive product with a complex composition, major royal jelly proteins (MRJPs) being the most abundant proteins. Cell culture and animal studies suggest various biological activities for the full-length/native MRJPs. In the field of apitherapy, it is assumed that MRJPs can positively affect human health. However, whenever RJ is administered orally, the availability for assimilation in the gastrointestinal tract is a prerequisite for MRJPs to have any effect on humans. We here show that MRJPs vary in resistance to pepsin digestion with MRJP2 being most stable and still present as full-length protein after 24 h of digestion. In the intestinal phase, using trypsin and chymotrypsin, MRJPs are rapidly digested with MRJP2 again showing longest stability (40 min), suggesting that MRJPs can reach the small intestine as full-length proteins but then have to be resorbed quickly if full-length proteins are to fulfill any biological activity.

Active chiral fluids.

PubMed

Fürthauer, S; Strempel, M; Grill, S W; Jülicher, F

2012-09-01

Active processes in biological systems often exhibit chiral asymmetries. Examples are the chirality of cytoskeletal filaments which interact with motor proteins, the chirality of the beat of cilia and flagella as well as the helical trajectories of many biological microswimmers. Here, we derive constitutive material equations for active fluids which account for the effects of active chiral processes. We identify active contributions to the antisymmetric part of the stress as well as active angular momentum fluxes. We discuss four types of elementary chiral motors and their effects on a surrounding fluid. We show that large-scale chiral flows can result from the collective behavior of such motors even in cases where isolated motors do not create a hydrodynamic far field.

Influence of basin-scale and mesoscale physical processes on biological productivity in the Bay of Bengal during the summer monsoon

NASA Astrophysics Data System (ADS)

Muraleedharan, K. R.; Jasmine, P.; Achuthankutty, C. T.; Revichandran, C.; Dinesh Kumar, P. K.; Anand, P.; Rejomon, G.

2007-03-01

Physical forcing plays a major role in determining biological processes in the ocean across the full spectrum of spatial and temporal scales. Variability of biological production in the Bay of Bengal (BoB) based on basin-scale and mesoscale physical processes is presented using hydrographic data collected during the peak summer monsoon in July-August, 2003. Three different and spatially varying physical processes were identified in the upper 300 m: (I) anticyclonic warm gyre offshore in the southern Bay; (II) a cyclonic eddy in the northern Bay; and (III) an upwelling region adjacent to the southern coast. In the warm gyre (>28.8 °C), the low salinity (33.5) surface waters contained low concentrations of nutrients. These warm surface waters extended below the euphotic zone, which resulted in an oligotrophic environment with low surface chlorophyll a (0.12 mg m -3), low surface primary production (2.55 mg C m -3 day -1) and low zooplankton biovolume (0.14 ml m -3). In the cyclonic eddy, the elevated isopycnals raised the nutricline upto the surface (NO 3-N > 8.2 μM, PO 4-P > 0.8 μM, SiO 4-Si > 3.5 μM). Despite the system being highly eutrophic, response in the biological activity was low. In the upwelling zone, although the nutrient concentrations were lower compared to the cyclonic eddy, the surface phytoplankton biomass and production were high (Chl a - 0.25 mg m -3, PP - 9.23 mg C m -3 day -1), and mesozooplankton biovolume (1.12 ml m -3) was rich. Normally in oligotrophic, open ocean ecosystems, primary production is based on ‘regenerated’ nutrients, but during episodic events like eddies the ‘production’ switches over to ‘new production’. The switching over from ‘regenerated production’ to ‘new production’ in the open ocean (cyclonic eddy) and establishment of a new phytoplankton community will take longer than in the coastal system (upwelling). Despite the functioning of a cyclonic eddy and upwelling being divergent (transporting of nutrients from deeper waters to surface), the utilization of nutrients leading to enhanced biological production and its transfer to upper trophic levels in the upwelling region imply that the energy transfer from primary production to secondary production (mesozooplankton) is more efficient than in the cyclonic eddy of the open ocean. The results suggest that basin-scale and mesoscale processes influence the abundance and spatial heterogeneity of plankton populations across a wide spatial scale in the BoB. The multifaceted effects of these physical processes on primary productivity thus play a prominent role in structuring of zooplankton communities and could consecutively affect the recruitment of pelagic fisheries.

Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks.

PubMed

Ibarbalz, Federico M; Figuerola, Eva L M; Erijman, Leonardo

2013-07-01

Biological degradation of domestic and industrial wastewater by activated sludge depends on a common process of separation of the diverse self-assembled and self-sustained microbial flocs from the treated wastewater. Previous surveys of bacterial communities indicated the presence of a common core of bacterial phyla in municipal activated sludge, an observation consistent with the concept of ecological coherence of high taxonomic ranks. The aim of this work was to test whether this critical feature brings about a common pattern of abundance distribution of high bacterial taxa in industrial and domestic activated sludge, and to relate the bacterial community structure of industrial activated sludge with relevant operational parameters. We have applied 454 pyrosequencing of 16S rRNA genes to evaluate bacterial communities in full-scale biological wastewater treatment plants sampled at different times, including seven systems treating wastewater from different industries and one plant that treats domestic wastewater, and compared our datasets with the data from municipal wastewater treatment plants obtained by three different laboratories. We observed that each industrial activated sludge system exhibited a unique bacterial community composition, which is clearly distinct from the common profile of bacterial phyla or classes observed in municipal plants. The influence of process parameters on the bacterial community structure was evaluated using constrained analysis of principal coordinates (CAP). Part of the differences in the bacterial community structure between industrial wastewater treatment systems were explained by dissolved oxygen and pH. Despite the ecological relevance of floc formation for the assembly of bacterial communities in activated sludge, the wastewater characteristics are likely to be the major determinant that drives bacterial composition at high taxonomic ranks. Copyright © 2013 Elsevier Ltd. All rights reserved.

Live cell refractometry using Hilbert phase microscopy and confocal reflectance microscopy.

PubMed

Lue, Niyom; Choi, Wonshik; Popescu, Gabriel; Yaqoob, Zahid; Badizadegan, Kamran; Dasari, Ramachandra R; Feld, Michael S

2009-11-26

Quantitative chemical analysis has served as a useful tool for understanding cellular metabolisms in biology. Among many physical properties used in chemical analysis, refractive index in particular has provided molecular concentration that is an important indicator for biological activities. In this report, we present a method of extracting full-field refractive index maps of live cells in their native states. We first record full-field optical thickness maps of living cells by Hilbert phase microscopy and then acquire physical thickness maps of the same cells using a custom-built confocal reflectance microscope. Full-field and axially averaged refractive index maps are acquired from the ratio of optical thickness to physical thickness. The accuracy of the axially averaged index measurement is 0.002. This approach can provide novel biological assays of label-free living cells in situ.

Live Cell Refractometry Using Hilbert Phase Microscopy and Confocal Reflectance Microscopy†

PubMed Central

Lue, Niyom; Choi, Wonshik; Popescu, Gabriel; Yaqoob, Zahid; Badizadegan, Kamran; Dasari, Ramachandra R.; Feld, Michael S.

2010-01-01

Quantitative chemical analysis has served as a useful tool for understanding cellular metabolisms in biology. Among many physical properties used in chemical analysis, refractive index in particular has provided molecular concentration that is an important indicator for biological activities. In this report, we present a method of extracting full-field refractive index maps of live cells in their native states. We first record full-field optical thickness maps of living cells by Hilbert phase microscopy and then acquire physical thickness maps of the same cells using a custom-built confocal reflectance microscope. Full-field and axially averaged refractive index maps are acquired from the ratio of optical thickness to physical thickness. The accuracy of the axially averaged index measurement is 0.002. This approach can provide novel biological assays of label-free living cells in situ. PMID:19803506

The quest for a new modelling framework in mathematical biology. Comment on "On the interplay between mathematics and biology: Hallmarks towards a new systems biology" by N. Bellomo et al.

NASA Astrophysics Data System (ADS)

Eftimie, Raluca

2015-03-01

One of the main unsolved problems of modern physics is finding a "theory of everything" - a theory that can explain, with the help of mathematics, all physical aspects of the universe. While the laws of physics could explain some aspects of the biology of living systems (e.g., the phenomenological interpretation of movement of cells and animals), there are other aspects specific to biology that cannot be captured by physics models. For example, it is generally accepted that the evolution of a cell-based system is influenced by the activation state of cells (e.g., only activated and functional immune cells can fight diseases); on the other hand, the evolution of an animal-based system can be influenced by the psychological state (e.g., distress) of animals. Therefore, the last 10-20 years have seen also a quest for a "theory of everything"-approach extended to biology, with researchers trying to propose mathematical modelling frameworks that can explain various biological phenomena ranging from ecology to developmental biology and medicine [1,2,6]. The basic idea behind this approach can be found in a few reviews on ecology and cell biology [6,7,9-11], where researchers suggested that due to the parallel between the micro-scale dynamics and the emerging macro-scale phenomena in both cell biology and in ecology, many mathematical methods used for ecological processes could be adapted to cancer modelling [7,9] or to modelling in immunology [11]. However, this approach generally involved the use of different models to describe different biological aspects (e.g., models for cell and animal movement, models for competition between cells or animals, etc.).

JEM spotlight: Monitoring the treatment efficiency of a full scale ozonation on a sewage treatment plant with a mode-of-action based test battery.

PubMed

Escher, Beate I; Bramaz, Nadine; Ort, Christoph

2009-10-01

Tertiary treatment of wastewater with ozone is a promising technique for removing residual micropollutants that remain after secondary biological treatment. We monitored the performance of a full-scale ozonation reactor on a sewage treatment plant in Switzerland with a screening battery of bioassays. Six toxicity endpoints were selected that covered non-specific toxicity, as well as selected receptor-mediated modes of action and reactive toxicity. Non-specific toxicity was assessed with two bioassays, the bioluminescence inhibition of the marine luminescent bacterium Vibrio Fischeri and the growth inhibition of the green algae Pseudokirchneriella subcapitata. Treatment efficiency was around 90% for the secondary treatment, but only 65% and 76% for the ozonation step in the two non-specific endpoints, respectively. This finding is consistent with this type of oxidation reaction because ozone only modifies the organic molecules but does not mineralize them fully leaving residual toxicity of the transformation products. In contrast, the specific receptor-mediated endpoints of inhibition of photosystem II in algae and estrogenicity were largely reduced by ozonation. While compounds inhibiting photosynthesis proved to be rather recalcitrant toward biological treatment with only 47% removal, an additional 86% removal by ozonation yielded an overall treatment efficiency in the entire treatment chain of 89%. The effect on estrogenicity, quantified with the yeast estrogen screen, was even more significant: A treatment efficiency of 95% in the secondary treatment, 86% during ozonation plus a small effect by biological sand filtration yielded an overall treatment efficiency of 99.5%. Insecticides that inhibit acetylcholinesterase were fairly resistant to degradation, but an overall treatment efficiency of 91% was achieved in two steps: 72% in biological treatment and 60% during ozonation. Finally, no significant genotoxicity was observed with the umuC test after ozonation, while the influent showed a genotoxic response when it was enriched by a factor of 15 to 60. Treatment efficiency increased with the ozone dose and remained virtually unchanged over ozone doses above 500 g ozone per kg dissolved organic carbon. The reduction of toxicity can be rationalized by the chemical oxidation processes likely to occur for each group of chemicals that are typical for a given mode of toxic action. For comparison, tertiary treatment with powdered activated carbon was also evaluated, which poses a viable alternative to ozonation with respect to removal of micropollutants.

Research at NASA's NFAC wind tunnels

NASA Technical Reports Server (NTRS)

Edenborough, H. Kipling

1990-01-01

The National Full-Scale Aerodynamics Complex (NFAC) is a unique combination of wind tunnels that allow the testing of aerodynamic and dynamic models at full or large scale. It can even accommodate actual aircraft with their engines running. Maintaining full-scale Reynolds numbers and testing with surface irregularities, protuberances, and control surface gaps that either closely match the full-scale or indeed are those of the full-scale aircraft help produce test data that accurately predict what can be expected from future flight investigations. This complex has grown from the venerable 40- by 80-ft wind tunnel that has served for over 40 years helping researchers obtain data to better understand the aerodynamics of a wide range of aircraft from helicopters to the space shuttle. A recent modification to the tunnel expanded its maximum speed capabilities, added a new 80- by 120-ft test section and provided extensive acoustic treatment. The modification is certain to make the NFAC an even more useful facility for NASA's ongoing research activities. A brief background is presented on the original facility and the kind of testing that has been accomplished using it through the years. A summary of the modification project and the measured capabilities of the two test sections is followed by a review of recent testing activities and of research projected for the future.

Biological consequences of ENSO: What have we learned recently?

NASA Astrophysics Data System (ADS)

Chavez, F.; Messié, M.

2013-12-01

A comprehensive theory regarding the biological response to El Niño was developed from observations during the 1982-83 event. The theory has withstood the test of time but additional information from remote sensing and growing in situ databases has allowed for a more comprehensive evaluation of the biological consequences of the full ENSO cycle on global scales and in relation to other climatic variability and change. Here we review the major developments over the past few decades that include a greater appreciation for the cool or La Niña phase and the relation of ENSO to other climatic variability including the Pacific Decadal Oscillation and the North Pacific Gyre Oscillation. The use of ENSO as an analog for biological consequences of a warmer world is also discussed.

TVB-EduPack—An Interactive Learning and Scripting Platform for The Virtual Brain

PubMed Central

Matzke, Henrik; Schirner, Michael; Vollbrecht, Daniel; Rothmeier, Simon; Llarena, Adalberto; Rojas, Raúl; Triebkorn, Paul; Domide, Lia; Mersmann, Jochen; Solodkin, Ana; Jirsa, Viktor K.; McIntosh, Anthony Randal; Ritter, Petra

2015-01-01

The Virtual Brain (TVB; thevirtualbrain.org) is a neuroinformatics platform for full brain network simulation based on individual anatomical connectivity data. The framework addresses clinical and neuroscientific questions by simulating multi-scale neural dynamics that range from local population activity to large-scale brain function and related macroscopic signals like electroencephalography and functional magnetic resonance imaging. TVB is equipped with a graphical and a command-line interface to create models that capture the characteristic biological variability to predict the brain activity of individual subjects. To enable researchers from various backgrounds a quick start into TVB and brain network modeling in general, we developed an educational module: TVB-EduPack. EduPack offers two educational functionalities that seamlessly integrate into TVB's graphical user interface (GUI): (i) interactive tutorials introduce GUI elements, guide through the basic mechanics of software usage and develop complex use-case scenarios; animations, videos and textual descriptions transport essential principles of computational neuroscience and brain modeling; (ii) an automatic script generator records model parameters and produces input files for TVB's Python programming interface; thereby, simulation configurations can be exported as scripts that allow flexible customization of the modeling process and self-defined batch- and post-processing applications while benefitting from the full power of the Python language and its toolboxes. This article covers the implementation of TVB-EduPack and its integration into TVB architecture. Like TVB, EduPack is an open source community project that lives from the participation and contribution of its users. TVB-EduPack can be obtained as part of TVB from thevirtualbrain.org. PMID:26635597

Occurrence, distribution, and potential influencing factors of sewage sludge components derived from nine full-scale wastewater treatment plants of Beijing, China.

PubMed

Wang, Xu; Li, Meiyan; Liu, Junxin; Qu, Jiuhui

2016-07-01

Millions of tons of waste activated sludge (WAS) produced from biological wastewater treatment processes cause severe adverse environmental consequences. A better understanding of WAS composition is thus very critical for sustainable sludge management. In this work, the occurrence and distribution of several fundamental sludge constituents were explored in WAS samples from nine full-scale wastewater treatment plants (WWTPs) of Beijing, China. Among all the components investigated, active heterotrophic biomass was dominant in the samples (up to 9478mg/L), followed by endogenous residues (6736mg/L), extracellular polymeric substances (2088mg/L), and intracellular storage products (464mg/L) among others. Moreover, significant differences (p<0.05) were observed in composition profiles of sludge samples among the studied WWTPs. To identify the potential parameters affecting the variable fractions of sludge components, wastewater source as well as design and operational parameters of WWTPs were studied using statistical methods. The findings indicated that the component fraction of sewage sludge depends more on wastewater treatment alternatives than on wastewater characteristics among other parameters. A principal component analysis was conducted, which further indicated that there was a greater proportion of residual inert biomass in the sludge produced by the combined system of the conventional anaerobic/anoxic/oxic process and a membrane bioreactor. Additionally, a much longer solids retention time was also found to influence the sludge composition and induce an increase in both endogenous inert residues and extracellular polymeric substances in the sludge. Copyright © 2016. Published by Elsevier B.V.

The OME Framework for genome-scale systems biology

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

Palsson, Bernhard O.; Ebrahim, Ali; Federowicz, Steve

The life sciences are undergoing continuous and accelerating integration with computational and engineering sciences. The biology that many in the field have been trained on may be hardly recognizable in ten to twenty years. One of the major drivers for this transformation is the blistering pace of advancements in DNA sequencing and synthesis. These advances have resulted in unprecedented amounts of new data, information, and knowledge. Many software tools have been developed to deal with aspects of this transformation and each is sorely needed [1-3]. However, few of these tools have been forced to deal with the full complexity ofmore » genome-scale models along with high throughput genome- scale data. This particular situation represents a unique challenge, as it is simultaneously necessary to deal with the vast breadth of genome-scale models and the dizzying depth of high-throughput datasets. It has been observed time and again that as the pace of data generation continues to accelerate, the pace of analysis significantly lags behind [4]. It is also evident that, given the plethora of databases and software efforts [5-12], it is still a significant challenge to work with genome-scale metabolic models, let alone next-generation whole cell models [13-15]. We work at the forefront of model creation and systems scale data generation [16-18]. The OME Framework was borne out of a practical need to enable genome-scale modeling and data analysis under a unified framework to drive the next generation of genome-scale biological models. Here we present the OME Framework. It exists as a set of Python classes. However, we want to emphasize the importance of the underlying design as an addition to the discussions on specifications of a digital cell. A great deal of work and valuable progress has been made by a number of communities [13, 19-24] towards interchange formats and implementations designed to achieve similar goals. While many software tools exist for handling genome-scale metabolic models or for genome-scale data analysis, no implementations exist that explicitly handle data and models concurrently. The OME Framework structures data in a connected loop with models and the components those models are composed of. This results in the first full, practical implementation of a framework that can enable genome-scale design-build-test. Over the coming years many more software packages will be developed and tools will necessarily change. However, we hope that the underlying designs shared here can help to inform the design of future software.« less

Repurposing High-Throughput Image Assays Enables Biological Activity Prediction for Drug Discovery.

PubMed

Simm, Jaak; Klambauer, Günter; Arany, Adam; Steijaert, Marvin; Wegner, Jörg Kurt; Gustin, Emmanuel; Chupakhin, Vladimir; Chong, Yolanda T; Vialard, Jorge; Buijnsters, Peter; Velter, Ingrid; Vapirev, Alexander; Singh, Shantanu; Carpenter, Anne E; Wuyts, Roel; Hochreiter, Sepp; Moreau, Yves; Ceulemans, Hugo

2018-05-17

In both academia and the pharmaceutical industry, large-scale assays for drug discovery are expensive and often impractical, particularly for the increasingly important physiologically relevant model systems that require primary cells, organoids, whole organisms, or expensive or rare reagents. We hypothesized that data from a single high-throughput imaging assay can be repurposed to predict the biological activity of compounds in other assays, even those targeting alternate pathways or biological processes. Indeed, quantitative information extracted from a three-channel microscopy-based screen for glucocorticoid receptor translocation was able to predict assay-specific biological activity in two ongoing drug discovery projects. In these projects, repurposing increased hit rates by 50- to 250-fold over that of the initial project assays while increasing the chemical structure diversity of the hits. Our results suggest that data from high-content screens are a rich source of information that can be used to predict and replace customized biological assays. Copyright © 2018 Elsevier Ltd. All rights reserved.

Once upon a (slow) time in the land of recurrent neuronal networks….

PubMed

Huang, Chengcheng; Doiron, Brent

2017-10-01

The brain must both react quickly to new inputs as well as store a memory of past activity. This requires biology that operates over a vast range of time scales. Fast time scales are determined by the kinetics of synaptic conductances and ionic channels; however, the mechanics of slow time scales are more complicated. In this opinion article we review two distinct network-based mechanisms that impart slow time scales in recurrently coupled neuronal networks. The first is in strongly coupled networks where the time scale of the internally generated fluctuations diverges at the transition between stable and chaotic firing rate activity. The second is in networks with finitely many members where noise-induced transitions between metastable states appear as a slow time scale in the ongoing network firing activity. We discuss these mechanisms with an emphasis on their similarities and differences. Copyright © 2017 Elsevier Ltd. All rights reserved.

Prioritization of pharmaceuticals for potential environmental hazard through leveraging a large scale mammalian pharmacological dataset

EPA Science Inventory

To proceed in the investigation of potential effects of thousands of active pharmaceutical ingredients (API) which may enter the aquatic environment, a cohesive research strategy, specifically a prioritization is paramount. API are biologically active, with specific physiologica...

A Chemoinformatics Approach to the Discovery of Lead-Like Molecules from Marine and Microbial Sources En Route to Antitumor and Antibiotic Drugs

PubMed Central

Pereira, Florbela; Latino, Diogo A. R. S.; Gaudêncio, Susana P.

2014-01-01

The comprehensive information of small molecules and their biological activities in the PubChem database allows chemoinformatic researchers to access and make use of large-scale biological activity data to improve the precision of drug profiling. A Quantitative Structure–Activity Relationship approach, for classification, was used for the prediction of active/inactive compounds relatively to overall biological activity, antitumor and antibiotic activities using a data set of 1804 compounds from PubChem. Using the best classification models for antibiotic and antitumor activities a data set of marine and microbial natural products from the AntiMarin database were screened—57 and 16 new lead compounds for antibiotic and antitumor drug design were proposed, respectively. All compounds proposed by our approach are classified as non-antibiotic and non-antitumor compounds in the AntiMarin database. Recently several of the lead-like compounds proposed by us were reported as being active in the literature. PMID:24473174

Stochastic cycle selection in active flow networks

NASA Astrophysics Data System (ADS)

Woodhouse, Francis; Forrow, Aden; Fawcett, Joanna; Dunkel, Jorn

2016-11-01

Active biological flow networks pervade nature and span a wide range of scales, from arterial blood vessels and bronchial mucus transport in humans to bacterial flow through porous media or plasmodial shuttle streaming in slime molds. Despite their ubiquity, little is known about the self-organization principles that govern flow statistics in such non-equilibrium networks. By connecting concepts from lattice field theory, graph theory and transition rate theory, we show how topology controls dynamics in a generic model for actively driven flow on a network. Through theoretical and numerical analysis we identify symmetry-based rules to classify and predict the selection statistics of complex flow cycles from the network topology. Our conceptual framework is applicable to a broad class of biological and non-biological far-from-equilibrium networks, including actively controlled information flows, and establishes a new correspondence between active flow networks and generalized ice-type models.

Temporal and spatial variability of soil biological activity at European scale

NASA Astrophysics Data System (ADS)

Mallast, Janine; Rühlmann, Jörg

2015-04-01

The CATCH-C project aims to identify and improve the farm-compatibility of Soil Management Practices including to promote productivity, climate change mitigation and soil quality. The focus of this work concentrates on turnover conditions for soil organic matter (SOM). SOM is fundamental for the maintenance of quality and functions of soils while SOM storage is attributed a great importance in terms of climate change mitigation. The turnover conditions depend on soil biological activity characterized by climate and soil properties. Soil biological activity was investigated using two model concepts: a) Re_clim parameter within the ICBM (Introductory Carbon Balance Model) (Andrén & Kätterer 1997) states a climatic factor summarizing soil water storage and soil temperature and its influence on soil biological activity. b) BAT (biological active time) approach derived from model CANDY (CArbon and Nitrogen Dynamic) (Franko & Oelschlägel 1995) expresses the variation of soil moisture, soil temperature and soil aeration as a time scale and an indicator of biological activity for soil organic matter (SOM) turnover. During an earlier stage both model concepts, Re_clim and BAT, were applied based on a monthly data to assess spatial variability of turnover conditions across Europe. This hampers the investigation of temporal variability (e.g. intra-annual). The improved stage integrates daily data of more than 350 weather stations across Europe presented by Klein Tank et al. (2002). All time series data (temperature, precipitation and potential evapotranspiration and soil texture derived from the European Soil Database (JRC 2006)), are used to calculate soil biological activity in the arable layer. The resulting BAT and Re_clim values were spatio-temporal investigated. While "temporal" refers to a long-term trend analysis, "spatial" includes the investigation of soil biological activity variability per environmental zone (ENZ, Metzger et al. 2005 representing similar conditions for precipitation, temperature and relief) to identify ranges and hence turnover conditions for each ENZ. We will discuss the analyzed results of both concepts to assess SOM turnover conditions across Europe for historical weather data and for Spain focusing on climate scenarios. Both concepts help to separate different turnover activities and to indicate organic matter input in order to maintain the given SOM. The assessment could provide recommendations for adaptations of soil management practices. CATCH-C is funded within the 7th Framework Programme for Research, Technological Development and Demonstration, Theme 2 - Biotechnologies, Agriculture & Food (Grant Agreement N° 289782).

NH4+ ad-/desorption in sequencing batch reactors: simulation, laboratory and full-scale studies.

PubMed

Schwitalla, P; Mennerich, A; Austermann-Haun, U; Müller, A; Dorninger, C; Daims, H; Holm, N C; Rönner-Holm, S G E

2008-01-01

Significant NH4-N balance deficits were found during the measurement campaigns for the data collection for dynamic simulation studies at five full-scale sequencing batch reactor (SBR) waste water treatment plants (WWTPs), as well as during subsequent calibrations at the investigated plants. Subsequent lab scale investigations showed high evidence for dynamic, cycle-specific NH4+ ad-/desorption to the activated flocs as one reason for this balance deficit. This specific dynamic was investigated at five full-scale SBR plants for the search of the general causing mechanisms. The general mechanism found was a NH4+ desorption from the activated flocs at the end of the nitrification phase with subsequent nitrification and a chemical NH4+ adsorption at the flocs in the course of the filling phases. This NH4+ ad-/desorption corresponds to an antiparallel K+ ad/-desorption.One reasonable full-scale application was investigated at three SBR plants, a controlled filling phase at the beginning of the sedimentation phase. The results indicate that this kind of filling event must be specifically hydraulic controlled and optimised in order to prevent too high waste water break through into the clear water phase, which will subsequently be discarded. IWA Publishing 2008.

Engineering Design and Operation Report: Biological Treatment Process for the Removal of Ammonia from a Small Drinking Water System in Iowa: Pilot to Full-Scale

EPA Science Inventory

Many regions in the United States have excessive levels of ammonia in their drinking water sources (e.g., ground and surface waters) as a result of naturally occurring processes, agricultural and urban runoff, concentrated animal feeding operations, municipal wastewater treatment...

Active Flap Control of the SMART Rotor for Vibration Reduction

NASA Technical Reports Server (NTRS)

Hall, Steven R.; Anand, R. Vaidyanathan; Straub, Friedrich K.; Lau, Benton H.

2009-01-01

Active control methodologies were applied to a full-scale active flap rotor obtained during a joint Boeing/ DARPA/NASA/Army test in the Air Force National Full-Scale Aerodynamic Complex 40- by 80-foot anechoic wind tunnel. The active flap rotor is a full-scale MD 900 helicopter main rotor with each of its five blades modified to include an on-blade piezoelectric actuator-driven flap with a span of 18% of radius, 25% of chord, and located at 83% radius. Vibration control demonstrated the potential of active flaps for effective control of vibratory loads, especially normal force loads. Active control of normal force vibratory loads using active flaps and a continuous-time higher harmonic control algorithm was very effective, reducing harmonic (1-5P) normal force vibratory loads by 95% in both cruise and approach conditions. Control of vibratory roll and pitch moments was also demonstrated, although moment control was less effective than normal force control. Finally, active control was used to precisely control blade flap position for correlation with pretest predictions of rotor aeroacoustics. Flap displacements were commanded to follow specific harmonic profiles of 2 deg or more in amplitude, and the flap deflection errors obtained were less than 0.2 deg r.m.s.

The Potential of Text Mining in Data Integration and Network Biology for Plant Research: A Case Study on Arabidopsis[C][W

PubMed Central

Van Landeghem, Sofie; De Bodt, Stefanie; Drebert, Zuzanna J.; Inzé, Dirk; Van de Peer, Yves

2013-01-01

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein–protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies. PMID:23532071

A fast atlas-guided high density diffuse optical tomography system for brain imaging

NASA Astrophysics Data System (ADS)

Dai, Xianjin; Zhang, Tao; Yang, Hao; Jiang, Huabei

2017-02-01

Near infrared spectroscopy (NIRS) is an emerging functional brain imaging tool capable of assessing cerebral concentrations of oxygenated hemoglobin (HbO) and deoxygenated hemoglobin (HbR) during brain activation noninvasively. As an extension of NIRS, diffuse optical tomography (DOT) not only shares the merits of providing continuous readings of cerebral oxygenation, but also has the ability to provide spatial resolution in the millimeter scale. Based on the scattering and absorption properties of nonionizing near-infrared light in biological tissue, DOT has been successfully applied in the imaging of breast tumors, osteoarthritis and cortex activations. Here, we present a state-of-art fast high density DOT system suitable for brain imaging. It can achieve up to a 21 Hz sampling rate for a full set of two-wavelength data for 3-D DOT brain image reconstruction. The system was validated using tissue-mimicking brain-model phantom. Then, experiments on healthy subjects were conducted to demonstrate the capability of the system.

Engineering plant metabolism into microbes: from systems biology to synthetic biology.

PubMed

Xu, Peng; Bhan, Namita; Koffas, Mattheos A G

2013-04-01

Plant metabolism represents an enormous repository of compounds that are of pharmaceutical and biotechnological importance. Engineering plant metabolism into microbes will provide sustainable solutions to produce pharmaceutical and fuel molecules that could one day replace substantial portions of the current fossil-fuel based economy. Metabolic engineering entails targeted manipulation of biosynthetic pathways to maximize yields of desired products. Recent advances in Systems Biology and the emergence of Synthetic Biology have accelerated our ability to design, construct and optimize cell factories for metabolic engineering applications. Progress in predicting and modeling genome-scale metabolic networks, versatile gene assembly platforms and delicate synthetic pathway optimization strategies has provided us exciting opportunities to exploit the full potential of cell metabolism. In this review, we will discuss how systems and synthetic biology tools can be integrated to create tailor-made cell factories for efficient production of natural products and fuel molecules in microorganisms. Copyright © 2012 Elsevier Ltd. All rights reserved.

Mixing characterisation of full-scale membrane bioreactors: CFD modelling with experimental validation.

PubMed

Brannock, M; Wang, Y; Leslie, G

2010-05-01

Membrane Bioreactors (MBRs) have been successfully used in aerobic biological wastewater treatment to solve the perennial problem of effective solids-liquid separation. The optimisation of MBRs requires knowledge of the membrane fouling, biokinetics and mixing. However, research has mainly concentrated on the fouling and biokinetics (Ng and Kim, 2007). Current methods of design for a desired flow regime within MBRs are largely based on assumptions (e.g. complete mixing of tanks) and empirical techniques (e.g. specific mixing energy). However, it is difficult to predict how sludge rheology and vessel design in full-scale installations affects hydrodynamics, hence overall performance. Computational Fluid Dynamics (CFD) provides a method for prediction of how vessel features and mixing energy usage affect the hydrodynamics. In this study, a CFD model was developed which accounts for aeration, sludge rheology and geometry (i.e. bioreactor and membrane module). This MBR CFD model was then applied to two full-scale MBRs and was successfully validated against experimental results. The effect of sludge settling and rheology was found to have a minimal impact on the bulk mixing (i.e. the residence time distribution).

Full-scale evaluation of a multi-component additive for efficient control of activated sludge filamentous bulking.

PubMed

Seka, M A; Van DeWiele, T; Verstraete, W

2002-01-01

A multi-component additive formulated for a more efficient control of activated sludge filamentous bulking was evaluated at a full-scale treatment plant experiencing severe filamentous bulking. It was found that, besides offering an immediate improvement of sludge settling, the multi-component additive was able to eliminate the filamentous bacteria causing the bulking. Hence, contrary to ordinary additives, this novel additive yielded immediate as well as long-term improvements in sludge sedimentation upon a few additions. Preliminary lab-scale toxicity tests showed that the treatment of the sludge by the additive should not impart any toxicity to the resulting effluent.

Leveraging unsupervised training sets for multi-scale compartmentalization in renal pathology

NASA Astrophysics Data System (ADS)

Lutnick, Brendon; Tomaszewski, John E.; Sarder, Pinaki

2017-03-01

Clinical pathology relies on manual compartmentalization and quantification of biological structures, which is time consuming and often error-prone. Application of computer vision segmentation algorithms to histopathological image analysis, in contrast, can offer fast, reproducible, and accurate quantitative analysis to aid pathologists. Algorithms tunable to different biologically relevant structures can allow accurate, precise, and reproducible estimates of disease states. In this direction, we have developed a fast, unsupervised computational method for simultaneously separating all biologically relevant structures from histopathological images in multi-scale. Segmentation is achieved by solving an energy optimization problem. Representing the image as a graph, nodes (pixels) are grouped by minimizing a Potts model Hamiltonian, adopted from theoretical physics, modeling interacting electron spins. Pixel relationships (modeled as edges) are used to update the energy of the partitioned graph. By iteratively improving the clustering, the optimal number of segments is revealed. To reduce computational time, the graph is simplified using a Cantor pairing function to intelligently reduce the number of included nodes. The classified nodes are then used to train a multiclass support vector machine to apply the segmentation over the full image. Accurate segmentations of images with as many as 106 pixels can be completed only in 5 sec, allowing for attainable multi-scale visualization. To establish clinical potential, we employed our method in renal biopsies to quantitatively visualize for the first time scale variant compartments of heterogeneous intra- and extraglomerular structures simultaneously. Implications of the utility of our method extend to fields such as oncology, genomics, and non-biological problems.

THE FUTURE OF TOXICOLOGY-PREDICTIVE TOXICOLOGY ...

EPA Pesticide Factsheets

A chemistry approach to predictive toxicology relies on structure−activity relationship (SAR) modeling to predict biological activity from chemical structure. Such approaches have proven capabilities when applied to well-defined toxicity end points or regions of chemical space. These approaches are less well-suited, however, to the challenges of global toxicity prediction, i.e., to predicting the potential toxicity of structurally diverse chemicals across a wide range of end points of regulatory and pharmaceutical concern. New approaches that have the potential to significantly improve capabilities in predictive toxicology are elaborating the “activity” portion of the SAR paradigm. Recent advances in two areas of endeavor are particularly promising. Toxicity data informatics relies on standardized data schema, developed for particular areas of toxicological study, to facilitate data integration and enable relational exploration and mining of data across both historical and new areas of toxicological investigation. Bioassay profiling refers to large-scale high-throughput screening approaches that use chemicals as probes to broadly characterize biological response space, extending the concept of chemical “properties” to the biological activity domain. The effective capture and representation of legacy and new toxicity data into mineable form and the large-scale generation of new bioassay data in relation to chemical toxicity, both employing chemical stru

Population dynamics in controlled unsteady-state systems: An application to the degradation of glyphosate in a sequencing batch reactor

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

Devarakonda, M.S.

1988-01-01

Control over population dynamics and organism selection in a biological waste treatment system provides an effective means of engineering process efficiency. Examples of applications of organism selection include control of filamentous organisms, biological nutrient removal, industrial waste treatment requiring the removal of specific substrates, and hazardous waste treatment. Inherently, full scale biological waste treatment systems are unsteady state systems due to the variations in the waste streams and mass flow rates of the substrates. Some systems, however, have the capacity to impose controlled selective pressures on the biological population by means of their operation. An example of such a systemmore » is the Sequencing Batch Reactor (SBR) which was the experimental system utilized in this research work. The concepts of organism selection were studied in detail for the biodegradation of a herbicide waste stream, with glyphosate as the target compound. The SBR provided a reactor configuration capable of exerting the necessary selective pressures to select and enrich for a glyphosate degrading population. Based on results for bench scale SBRs, a hypothesis was developed to explain population dynamics in glyphosate degrading systems.« less

Mechanisms of N2O production in biological wastewater treatment under nitrifying and denitrifying conditions.

PubMed

Wunderlin, Pascal; Mohn, Joachim; Joss, Adriano; Emmenegger, Lukas; Siegrist, Hansruedi

2012-03-15

Nitrous oxide (N2O) is an important greenhouse gas and a major sink for stratospheric ozone. In biological wastewater treatment, microbial processes such as autotrophic nitrification and heterotrophic denitrification have been identified as major sources; however, the underlying pathways remain unclear. In this study, the mechanisms of N2O production were investigated in a laboratory batch-scale system with activated sludge for treating municipal wastewater. This relatively complex mixed population system is well representative for full-scale activated sludge treatment under nitrifying and denitrifying conditions. Under aerobic conditions, the addition of nitrite resulted in strongly nitrite-dependent N2O production, mainly by nitrifier denitrification of ammonia-oxidizing bacteria (AOB). Furthermore, N2O is produced via hydroxylamine oxidation, as has been shown by the addition of hydroxylamine. In both sets of experiments, N2O production was highest at the beginning of the experiment, then decreased continuously and ceased when the substrate (nitrite, hydroxylamine) had been completely consumed. In ammonia oxidation experiments, N2O peaked at the beginning of the experiment when the nitrite concentration was lowest. This indicates that N2O production via hydroxylamine oxidation is favored at high ammonia and low nitrite concentrations, and in combination with a high metabolic activity of ammonia-oxidizing bacteria (at 2 to 3 mgO2/l); the contribution of nitrifier denitrification by AOB increased at higher nitrite and lower ammonia concentrations towards the end of the experiment. Under anoxic conditions, nitrate reducing experiments confirmed that N2O emission is low under optimal growth conditions for heterotrophic denitrifiers (e.g. no oxygen input and no limitation of readily biodegradable organic carbon). However, N2O and nitric oxide (NO) production rates increased significantly in the presence of nitrite or low dissolved oxygen concentrations. Copyright © 2011 Elsevier Ltd. All rights reserved.

Bioprocess scale-up/down as integrative enabling technology: from fluid mechanics to systems biology and beyond.

PubMed

Delvigne, Frank; Takors, Ralf; Mudde, Rob; van Gulik, Walter; Noorman, Henk

2017-09-01

Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale-up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory-scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology. For that purpose, a full scale-up/down computational framework is already available. This framework links computational fluid dynamics (CFD), metabolic flux analysis and agent-based modelling (ABM) for a better understanding of the cell lifelines in a heterogeneous environment. Ultimately, this framework can be used for the design of scale-down simulators and/or metabolically engineered cells able to cope with environmental fluctuations typically found in large-scale bioreactors. However, this framework still needs some refinements, such as a better integration of gas-liquid flows in CFD, and taking into account intrinsic biological noise in ABM. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Activity-dependent self-regulation of viscous length scales in biological systems

NASA Astrophysics Data System (ADS)

Nandi, Saroj Kumar

2018-05-01

The cellular cortex, which is a highly viscous thin cytoplasmic layer just below the cell membrane, controls the cell's mechanical properties, which can be characterized by a hydrodynamic length scale ℓ . Cells actively regulate ℓ via the activity of force-generating molecules, such as myosin II. Here we develop a general theory for such systems through a coarse-grained hydrodynamic approach including activity in the static description of the system providing an experimentally accessible parameter and elucidate the detailed mechanism of how a living system can actively self-regulate its hydrodynamic length scale, controlling the rigidity of the system. Remarkably, we find that ℓ , as a function of activity, behaves universally and roughly inversely proportional to the activity of the system. Our theory rationalizes a number of experimental findings on diverse systems, and comparison of our theory with existing experimental data shows good agreement.

IFMIF: overview of the validation activities

NASA Astrophysics Data System (ADS)

Knaster, J.; Arbeiter, F.; Cara, P.; Favuzza, P.; Furukawa, T.; Groeschel, F.; Heidinger, R.; Ibarra, A.; Matsumoto, H.; Mosnier, A.; Serizawa, H.; Sugimoto, M.; Suzuki, H.; Wakai, E.

2013-11-01

The Engineering Validation and Engineering Design Activities (EVEDA) for the International Fusion Materials Irradiation Facility (IFMIF), an international collaboration under the Broader Approach Agreement between Japan Government and EURATOM, aims at allowing a rapid construction phase of IFMIF in due time with an understanding of the cost involved. The three main facilities of IFMIF (1) the Accelerator Facility, (2) the Target Facility and (3) the Test Facility are the subject of validation activities that include the construction of either full scale prototypes or smartly devised scaled down facilities that will allow a straightforward extrapolation to IFMIF needs. By July 2013, the engineering design activities of IFMIF matured with the delivery of an Intermediate IFMIF Engineering Design Report (IIEDR) supported by experimental results. The installation of a Linac of 1.125 MW (125 mA and 9 MeV) of deuterons started in March 2013 in Rokkasho (Japan). The world's largest liquid Li test loop is running in Oarai (Japan) with an ambitious experimental programme for the years ahead. A full scale high flux test module that will house ∼1000 small specimens developed jointly in Europe and Japan for the Fusion programme has been constructed by KIT (Karlsruhe) together with its He gas cooling loop. A full scale medium flux test module to carry out on-line creep measurement has been validated by CRPP (Villigen).

Fundamentals of microfluidic cell culture in controlled microenvironments†

PubMed Central

Young, Edmond W. K.; Beebe, David J.

2010-01-01

Microfluidics has the potential to revolutionize the way we approach cell biology research. The dimensions of microfluidic channels are well suited to the physical scale of biological cells, and the many advantages of microfluidics make it an attractive platform for new techniques in biology. One of the key benefits of microfluidics for basic biology is the ability to control parameters of the cell microenvironment at relevant length and time scales. Considerable progress has been made in the design and use of novel microfluidic devices for culturing cells and for subsequent treatment and analysis. With the recent pace of scientific discovery, it is becoming increasingly important to evaluate existing tools and techniques, and to synthesize fundamental concepts that would further improve the efficiency of biological research at the microscale. This tutorial review integrates fundamental principles from cell biology and local microenvironments with cell culture techniques and concepts in microfluidics. Culturing cells in microscale environments requires knowledge of multiple disciplines including physics, biochemistry, and engineering. We discuss basic concepts related to the physical and biochemical microenvironments of the cell, physicochemical properties of that microenvironment, cell culture techniques, and practical knowledge of microfluidic device design and operation. We also discuss the most recent advances in microfluidic cell culture and their implications on the future of the field. The goal is to guide new and interested researchers to the important areas and challenges facing the scientific community as we strive toward full integration of microfluidics with biology. PMID:20179823

Monitoring the performances of a real scale municipal solid waste composting and a biodrying facility using respiration activity indices.

PubMed

Evangelou, Alexandros; Gerassimidou, Spyridoula; Mavrakis, Nikitas; Komilis, Dimitrios

2016-05-01

Objective of the work was to monitor two full-scale commingled municipal solid waste (MSW) mechanical and biological pretreatment (MBT) facilities in Greece, namely a biodrying and a composting facility. Monitoring data from a 1.5-year sampling period is presented, whilst microbial respiration indices were used to monitor the decomposition process and the stability status of the wastes in both facilities during the process. Results showed that in the composting facility, the organic matter reduced by 35 % after 8 weeks of combined composting/curing. Material exiting the biocells had a moisture content of less than 30 % (wb) indicating a moisture limitation during the active composting process. The static respiration indexes indicated that some stabilization occurred during the process, but the final material could not be characterized as stable compost. In the biodrying facility, the initial and final moisture contents were 50 % and less than 20 % wb, respectively, and the biodrying index was equal to 4.1 indicating effective biodrying. Lower heating values at the inlet and outlet were approximately 5.5 and 10 MJ/wet kg, respectively. The organic matter was reduced by 20 % during the process and specifically from a range of 63-77 % dw (inlet) to a range of 61-70 % dw. A significant respiration activity reduction was observed for some of the biodrying samples. A statistically significant correlation among all three respiration activity indices was recorded, with the two oxygen related activity indices (CRI7 and SRI24) observing the highest correlation.

Elevational characteristics of the archaeal community in full-scale activated sludge wastewater treatment plants at a 3,660-meter elevational scale.

PubMed

Niu, Lihua; Zhang, Xue; Li, Yi; Wang, Peifang; Zhang, Wenlong; Wang, Chao; Wang, Qing

2017-07-01

Due to the important roles of archaea in wastewater treatment processes, archaeal communities have been studied extensively in various anaerobic reactors, but the knowledge of archaeal communities in full-scale activated sludge wastewater treatment plants (WWTPs) remains quite poor. In this study, 454-pyrosequencing was for the first time employed to investigate archaeal communities from 20 full-scale activated sludge WWTPs distributed at a 3,660-meter elevational scale in China. Results showed that archaeal communities from WWTPs were dominated by Methanosarcinales (84.6%). A core archaeal population (94.5%) composed of Methanosaeta, Methanosarcina, Methanogenium and Methanobrevibacter was shared among WWTPs. The elevational pattern of archaeal communities was observed in WWTPs, with an elevational threshold associated with archaeal community richness and structures at approximately 1,500 meters above sea level (masl). A declining trend in community richness with increasing elevation was observed at higher elevations, whereas no trend was presented at lower elevations. Spearman correlation analysis indicated that the archaeal community richness at higher elevations was associated with more environmental variables than that at lower elevations. Redundancy analysis indicated that wastewater variables were the dominant contributors to the variation of community structures at higher elevations, followed by operational variables and elevation.

Molecular Characterization of the Bacterial Communities in the Different Compartments of a Full-Scale Reverse-Osmosis Water Purification Plant ▿

PubMed Central

Bereschenko, L. A.; Heilig, G. H. J.; Nederlof, M. M.; van Loosdrecht, M. C. M.; Stams, A. J. M.; Euverink, G. J. W.

2008-01-01

The origin, structure, and composition of biofilms in various compartments of an industrial full-scale reverse-osmosis (RO) membrane water purification plant were analyzed by molecular biological methods. Samples were taken when the RO installation suffered from a substantial pressure drop and decreased production. The bacterial community of the RO membrane biofilm was clearly different from the bacterial community present at other locations in the RO plant, indicating the development of a specialized bacterial community on the RO membranes. The typical freshwater phylotypes in the RO membrane biofilm (i.e., Proteobacteria, Cytophaga-Flexibacter-Bacteroides group, and Firmicutes) were also present in the water sample fed to the plant, suggesting a feed water origin. However, the relative abundances of the different species in the mature biofilm were different from those in the feed water, indicating that the biofilm was actively formed on the RO membrane sheets and was not the result of a concentration of bacteria present in the feed water. The majority of the microorganisms (59% of the total number of clones) in the biofilm were related to the class Proteobacteria, with a dominance of Sphingomonas spp. (27% of all clones). Members of the genus Sphingomonas seem to be responsible for the biofouling of the membranes in the RO installation. PMID:18621875

Pilot-scale studies on biological treatment of hypersaline wastewater at low temperature.

PubMed

Peng, Y Z; Zhu, G B; Wang, S Y; Yu, D S; Cui, Y W; Meng, X S

2005-01-01

In order to investigate the feasibility of biological treatment of hypersaline wastewater produced from toilet flushing with seawater at low temperature, pilot-scale studies were established with plug-flow activated sludge process at low temperature (5-9 degrees C) based on bench-scale experiments. The critical salinity concentration of 30 g/L, which resulted from the cooperation results of the non-halophilic bacteria and the halophilic bacteria, was drawn in bench-scale experiments. Pilot-scale studies showed that high COD removal efficiency, higher than 80%, was obtained at low temperature when 30 percent seawater was introduced. The salinity improved the settleability of activated sludge, and average sludge value dropped down from 38% to 22.5% after adding seawater. Seawater salinity had a strong negative effect on notronomonas and nitrobacter growth, but much more on the nitrobacter. The nitrification action was mainly accomplished by nitrosomonas. Bench-scale experiments using two SBRs were carried out for further investigation under different conditions of salinities, ammonia loadings and temperatures. Biological nitrogen removal via nitrite pathway from wastewater containing 30 percent seawater was achieved, but the ammonia removal efficiency was strongly related not only to the influent ammonia loading at different salinities but also to temperature. When the ratio of seawater to wastewater was 30 percent, and the ammonia loading was below the critical value of 0.15 kgNH4+-N/(kgMLSS.d), the ammonia removal efficiency via nitrite pathway was above 90%. The critical level of ammonia loading was 0.15, 0.08 and 0.03 kgNH4+-N/(kgMLSS.d) respectively at the different temperature 30 degrees C, 25 degrees C and 20 degrees C when the influent ammonia concentration was 60-80 mg/L and pH was 7.5-8.0.

FLASH Technology: Full-Scale Hospital Waste Water Treatments Adopted in Aceh

NASA Astrophysics Data System (ADS)

Rame; Tridecima, Adeodata; Pranoto, Hadi; Moesliem; Miftahuddin

2018-02-01

A Hospital waste water contains a complex mixture of hazardous chemicals and harmful microbes, which can pose a threat to the environment and public health. Some efforts have been carried out in Nangroe Aceh Darussalam (Aceh), Indonesia with the objective of treating hospital waste water effluents on-site before its discharge. Flash technology uses physical and biological pre-treatment, followed by advanced oxidation process based on catalytic ozonation and followed by GAC and PAC filtration. Flash Full-Scale Hospital waste water Treatments in Aceh from different district have been adopted and investigated. Referring to the removal efficiency of macro-pollutants, the collected data demonstrate good removal efficiency of macro-pollutants using Flash technologies. In general, Flash technologies could be considered a solution to the problem of managing hospital waste water.

Validation of a multi-phase plant-wide model for the description of the aeration process in a WWTP.

PubMed

Lizarralde, I; Fernández-Arévalo, T; Beltrán, S; Ayesa, E; Grau, P

2018-02-01

This paper introduces a new mathematical model built under the PC-PWM methodology to describe the aeration process in a full-scale WWTP. This methodology enables a systematic and rigorous incorporation of chemical and physico-chemical transformations into biochemical process models, particularly for the description of liquid-gas transfer to describe the aeration process. The mathematical model constructed is able to reproduce biological COD and nitrogen removal, liquid-gas transfer and chemical reactions. The capability of the model to describe the liquid-gas mass transfer has been tested by comparing simulated and experimental results in a full-scale WWTP. Finally, an exploration by simulation has been undertaken to show the potential of the mathematical model. Copyright © 2017 Elsevier Ltd. All rights reserved.

Status of the Flooding Fragility Testing Development

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

Pope, C. L.; Savage, B.; Bhandari, B.

2016-06-01

This report provides an update on research addressing nuclear power plant component reliability under flooding conditions. The research includes use of the Component Flooding Evaluation Laboratory (CFEL) where individual components and component subassemblies will be tested to failure under various flooding conditions. The resulting component reliability data can then be incorporated with risk simulation strategies to provide a more thorough representation of overall plant risk. The CFEL development strategy consists of four interleaved phases. Phase 1 addresses design and application of CFEL with water rise and water spray capabilities allowing testing of passive and active components including fully electrified components.more » Phase 2 addresses research into wave generation techniques followed by the design and addition of the wave generation capability to CFEL. Phase 3 addresses methodology development activities including small scale component testing, development of full scale component testing protocol, and simulation techniques including Smoothed Particle Hydrodynamic (SPH) based computer codes. Phase 4 involves full scale component testing including work on full scale component testing in a surrogate CFEL testing apparatus.« less

Activity-based protein profiling: from enzyme chemistry to proteomic chemistry.

PubMed

Cravatt, Benjamin F; Wright, Aaron T; Kozarich, John W

2008-01-01

Genome sequencing projects have provided researchers with a complete inventory of the predicted proteins produced by eukaryotic and prokaryotic organisms. Assignment of functions to these proteins represents one of the principal challenges for the field of proteomics. Activity-based protein profiling (ABPP) has emerged as a powerful chemical proteomic strategy to characterize enzyme function directly in native biological systems on a global scale. Here, we review the basic technology of ABPP, the enzyme classes addressable by this method, and the biological discoveries attributable to its application.

Pattern formation and collective effects in populations of magnetic microswimmers

NASA Astrophysics Data System (ADS)

Vach, Peter J.; Walker, Debora; Fischer, Peer; Fratzl, Peter; Faivre, Damien

2017-03-01

Self-propelled particles are one prototype of synthetic active matter used to understand complex biological processes, such as the coordination of movement in bacterial colonies or schools of fishes. Collective patterns such as clusters were observed for such systems, reproducing features of biological organization. However, one limitation of this model is that the synthetic assemblies are made of identical individuals. Here we introduce an active system based on magnetic particles at colloidal scales. We use identical but also randomly-shaped magnetic micropropellers and show that they exhibit dynamic and reversible pattern formation.

Ecoregional management in southern Costa Rica: Finding a role for adaptive collaborative management

Treesearch

John Schelhas; Louise E. Buck; Charles C. Geisler; Eva Wollenberg

2001-01-01

Recent thinking in conservation biology stresses the importance of conservation at a regional scale that includes both protected areas and the lands that surround and connect them (Schelhas and Greenberg. 1996; Laurance and Bierregaard. 1997; Soulé dnd Terborgh. 1999) . The need to develop governance systems that can incorporate the full diversity of landholders and...

A full-scale biological treatment system application in the treated wastewater of pharmaceutical industrial park.

PubMed

Lei, Ge; Ren, Hongqiang; Ding, Lili; Wang, Feifei; Zhang, Xingsong

2010-08-01

A full-scale combined biological system is used for the treatment of treated wastewater discharged from a pharmaceutical industrial park. This treated water is rich in NH(4)(+)-N (average in 86.4 mg/L), low in COD/NH(4)(+)-N (average in 3.4) and low in BOD(5)/COD ratio (average in 0.24) with pH varying from 7.16 to 7.78. The final effluent of the combined treatment process was stably below 100mg/L COD and 20mg/L NH(4)(+)-N, separately, with organic loading rate of 4954 kg COD/d and 92.5 kg NH(4)(+)-N/d. It is found that the BOD(5)/COD ratio could be raised from 0.24 to 0.35, and the production of total VFAs account for 9.57% of the total COD via the treatment of hydrolysis/acidification. MBBR and oxidation ditch represent 35.4% and 60.7% of NH(4)(+)-N removal, 30.2% and 61.5% of COD removal, separately, of the total treatment process. PCR-DGGE is used for microbial community analysis of MBBR and oxidation ditch. (c) 2010. Published by Elsevier Ltd. All rights reserved.

Sludge reduction in a small wastewater treatment plant by electro-kinetic disintegration.

PubMed

Chiavola, Agostina; Ridolfi, Alessandra; D'Amato, Emilio; Bongirolami, Simona; Cima, Ennio; Sirini, Piero; Gavasci, Renato

2015-01-01

Sludge reduction in a wastewater treatment plant (WWTP) has recently become a key issue for the managing companies, due to the increasing constraints on the disposal alternatives. Therefore, all the solutions proposed with the aim of minimizing sludge production are receiving increasing attention and are tested either at laboratory or full-scale to evaluate their real effectiveness. In the present paper, electro-kinetic disintegration has been applied at full-scale in the recycle loop of the sludge drawn from the secondary settlement tank of a small WWTP for domestic sewage. After the disintegration stage, the treated sludge was returned to the biological reactor. Three different percentages (50, 75 and 100%) of the return sludge flow rate were subjected to disintegration and the effects on the sludge production and the WWTP operation efficiency evaluated. The long-term observations showed that the electro-kinetic disintegration was able to drastically reduce the amount of biological sludge produced by the plant, without affecting its treatment efficiency. The highest reduction was achieved when 100% return sludge flow rate was subjected to the disintegration process. The reduced sludge production gave rise to a considerable net cost saving for the company which manages the plant.

Integrated anaerobic/aerobic biological treatment for intensive swine production.

PubMed

Bortone, Giuseppe

2009-11-01

Manure processing could help farmers to effectively manage nitrogen (N) surplus load. Many pig farms have to treat wastewater. Piggery wastewater treatment is a complex challenge, due to the high COD and N concentrations and low C/N ratio. Anaerobic digestion (AD) could be a convenient pre-treatment, particularly from the energetic view point and farm income, but this causes further reduction of C/N ratio and makes denitrification difficult. N removal can only be obtained integrating anaerobic/aerobic treatment by taking into account the best use of electron donors. Experiences gained in Italy during development of integrated biological treatment approaches for swine manure, from bench to full scale, are reported in this paper. Solid/liquid separation as pre-treatment of raw manure is an efficient strategy to facilitate liquid fraction treatment without significantly lowering C/N ratio. In Italy, two full scale SBRs showed excellent efficiency and reliability. Current renewable energy policy and incentives makes economically attractive the application of AD to the separated solid fraction using high solid anaerobic digester (HSAD) technology. Economic evaluation showed that energy production can reduce costs up to 60%, making sustainable the overall treatment.

Complete solids retention activated sludge process.

PubMed

Amanatidou, E; Samiotis, G; Trikoilidou, E; Pekridis, G; Tsikritzis, L

2016-01-01

In a slaughterhouse's full-scale extended aeration activated sludge wastewater treatment plant (WWTP), operating under complete solids retention time, the evolution of mixed liquor suspended solids (MLSS) and mixed liquor volatile suspended solids (MLVSS) concentration, food to micro-organisms ratio (F/M) and substrate utilization rate (SUR) were studied for over a year. Biomass growth phases in correlation to sludge biological and morphological characteristics were studied. Three distinguished growth phases were observed during the 425 days of monitoring. The imposed operational conditions led the process to extended biomass starvation conditions, minimum F/M, minimum SUR and predator species growth. MLSS and MLVSS reached a stabilization phase (plateau phase) where almost zero sludge accumulation was observed. The concept of degradation of the considered non-biodegradable particulate compounds in influent and in biomass (cell debris) was also studied. Comparison of evolution of observed sludge yields (Yobs) in the WWTP with Yobs predictions by activated sludge models verified the degradation concept for the considered non-biodegradable compounds. Control of the sedimentation process was achieved, by predicting the solids loading rate critical point using state point analysis and stirred/unstirred settling velocity tests and by applying a high return activated sludge rate. The nitrogen gas related sedimentation problems were taken into consideration.

Synthesis, Characterization, and Multimillion-Atom Simulation of Halogen-Based Energetic Materials for Agent Defeat

DTIC Science & Technology

2013-04-01

DTRA-TR-13-23 Synthesis, Characterization, and Multimillion -Atom Simulation of Halogen-Based Energetic Materials for Agent Defeat Approved for...reagents for the destruction of biologically active materials and a simulation of their reactions on a multimillion atom scale with quantum...explosives for destruction of chemical & biological agents. Multimillion -atom molecular dynamics simulations with quantum mechanical accuracy were

An Overview of Active Flow Control Enhanced Vertical Tail Technology Development

NASA Technical Reports Server (NTRS)

Lin, John C.; Andino, Marlyn Y.; Alexander, Michael G.; Whalen, Edward A.; Spoor, Marc A.; Tran, John T.; Wygnanski, Israel J.

2016-01-01

This paper summarizes a joint NASA/Boeing research effort to advance Active Flow Control (AFC) technology to enhance aerodynamic efficiency of a vertical tail. Sweeping jet AFC technology was successfully tested on subscale and full-scale models as well as in flight. The subscale test was performed at Caltech on a 14% scale model. More than 50% side force enhancement was achieved by the sweeping jet actuation when the momentum coefficient was 1.7%. AFC caused significant increases in suction pressure on the actuator side and associated side force enhancement. Subsequently, a full-scale Boeing 757 vertical tail model equipped with sweeping jets was tested at the National Full-Scale Aerodynamics Complex 40- by 80-Foot Wind Tunnel at NASA Ames Research Center. There, flow separation control optimization was performed at near flight conditions. Greater than 20% increase in side force were achieved for the maximum rudder deflection of 30deg at the key sideslip angles (0deg and -7.5deg) with a 31-actuator AFC configuration. Based on these tests, the momentum coefficient is shown to be a necessary, but not sufficient parameter to use for design and scaling of sweeping jet AFC from subscale tests to full-scale applications. Leveraging the knowledge gained from the wind tunnel tests, the AFC-enhanced vertical tail technology was successfully flown on the Boeing 757 ecoDemonstrator in the spring of 2015.

Positive feedback can lead to dynamic nanometer-scale clustering on cell membranes

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

Wehrens, Martijn; Rein ten Wolde, Pieter; Mugler, Andrew, E-mail: amugler@purdue.edu

2014-11-28

Clustering of molecules on biological membranes is a widely observed phenomenon. A key example is the clustering of the oncoprotein Ras, which is known to be important for signal transduction in mammalian cells. Yet, the mechanism by which Ras clusters form and are maintained remains unclear. Recently, it has been discovered that activated Ras promotes further Ras activation. Here we show using particle-based simulation that this positive feedback is sufficient to produce persistent clusters of active Ras molecules at the nanometer scale via a dynamic nucleation mechanism. Furthermore, we find that our cluster statistics are consistent with experimental observations ofmore » the Ras system. Interestingly, we show that our model does not support a Turing regime of macroscopic reaction-diffusion patterning, and therefore that the clustering we observe is a purely stochastic effect, arising from the coupling of positive feedback with the discrete nature of individual molecules. These results underscore the importance of stochastic and dynamic properties of reaction diffusion systems for biological behavior.« less

A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation.

PubMed

Lowder, Levi G; Zhang, Dengwei; Baltes, Nicholas J; Paul, Joseph W; Tang, Xu; Zheng, Xuelian; Voytas, Daniel F; Hsieh, Tzung-Fu; Zhang, Yong; Qi, Yiping

2015-10-01

The relative ease, speed, and biological scope of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated Protein9 (Cas9)-based reagents for genomic manipulations are revolutionizing virtually all areas of molecular biosciences, including functional genomics, genetics, applied biomedical research, and agricultural biotechnology. In plant systems, however, a number of hurdles currently exist that limit this technology from reaching its full potential. For example, significant plant molecular biology expertise and effort is still required to generate functional expression constructs that allow simultaneous editing, and especially transcriptional regulation, of multiple different genomic loci or multiplexing, which is a significant advantage of CRISPR/Cas9 versus other genome-editing systems. To streamline and facilitate rapid and wide-scale use of CRISPR/Cas9-based technologies for plant research, we developed and implemented a comprehensive molecular toolbox for multifaceted CRISPR/Cas9 applications in plants. This toolbox provides researchers with a protocol and reagents to quickly and efficiently assemble functional CRISPR/Cas9 transfer DNA constructs for monocots and dicots using Golden Gate and Gateway cloning methods. It comes with a full suite of capabilities, including multiplexed gene editing and transcriptional activation or repression of plant endogenous genes. We report the functionality and effectiveness of this toolbox in model plants such as tobacco (Nicotiana benthamiana), Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa), demonstrating its utility for basic and applied plant research. © 2015 American Society of Plant Biologists. All Rights Reserved.

Functionally relevant microorganisms to enhanced biological phosphorus removal performance at full-scale wastewater treatment plants in the United States.

PubMed

Gu, April Z; Saunders, A; Neethling, J B; Stensel, H D; Blackall, L L

2008-08-01

The abundance and relevance ofAccumulibacter phosphatis (presumed to be polyphosphate-accumulating organisms [PAOs]), Competibacter phosphatis (presumed to be glycogen-accumulating organisms [GAOs]), and tetrad-forming organisms (TFOs) to phosphorus removal performance at six full-scale enhanced biological phosphorus removal (EBPR) wastewater treatment plants were investigated. Coexistence of various levels of candidate PAOs and GAOs were found at these facilities. Accumulibacter were found to be 5 to 20% of the total bacterial population, and Competibacter were 0 to 20% of the total bacteria population. The TFO abundance varied from nondetectable to dominant. Anaerobic phosphorus (P) release to acetate uptake ratios (P(rel)/HAc(up)) obtained from bench tests were correlated positively with the abundance ratio of Accumulibacter/(Competibacter +TFOs) and negatively with the abundance of (Competibacter +TFOs) for all plants except one, suggesting the relevance of these candidate organisms to EBPR processes. However, effluent phosphorus concentration, amount of phosphorus removed, and process stability in an EBPR system were not directly related to high PAO abundance or mutually exclusive with a high GAO fraction. The plant that had the lowest average effluent phosphorus and highest stability rating had the lowest P(rel)/HAc(up) and the most TFOs. Evaluation of full-scale EBPR performance data indicated that low effluent phosphorus concentration and high process stability are positively correlated with the influent readily biodegradable chemical oxygen demand-to-phosphorus ratio. A system-level carbon-distribution-based conceptual model is proposed for capturing the dynamic competition between PAOs and GAOs and their effect on an EBPR process, and the results from this study seem to support the model hypothesis.

Performance Enhancement of a Full-Scale Vertical Tail Model Equipped with Active Flow Control

NASA Technical Reports Server (NTRS)

Whalen, Edward A.; Lacy, Douglas; Lin, John C.; Andino, Marlyn Y.; Washburn, Anthony E.; Graff, Emilio; Wygnanski, Israel J.

2015-01-01

This paper describes wind tunnel test results from a joint NASA/Boeing research effort to advance active flow control (AFC) technology to enhance aerodynamic efficiency. A full-scale Boeing 757 vertical tail model equipped with sweeping jet actuators was tested at the National Full-Scale Aerodynamics Complex (NFAC) 40- by 80-Foot Wind Tunnel (40x80) at NASA Ames Research Center. The model was tested at a nominal airspeed of 100 knots and across rudder deflections and sideslip angles that covered the vertical tail flight envelope. A successful demonstration of AFC-enhanced vertical tail technology was achieved. A 31- actuator configuration significantly increased side force (by greater than 20%) at a maximum rudder deflection of 30deg. The successful demonstration of this application has cleared the way for a flight demonstration on the Boeing 757 ecoDemonstrator in 2015.

Biological oxygen demand in soils and hydrogel compositions for plant protection of the rhizosphere

NASA Astrophysics Data System (ADS)

Valentinovich Smagin, Andrey

2018-02-01

Potential biological activity of mineral and organogenic samples from light-textured sod-podzolic soils as well as of hydrogel compositions for protecting the root layer from pathogenic microflora and unfavorable edaphic factors were studied in laboratory conditions by oxygen consumption under the optimal hydrothermic conditions with portable gas analyzers. We have conducted ecological standardization of biological activity and organic matter destruction estimated by biological oxygen demand (BOD) in the widespread sandy soils. The primary outcome was the scale of gradations of biological oxygen uptake in soils with a range of quantities of potential biological activity from “very low” (<2 g·m-3·hour-1) to “extremely high” (>140 g·m-3·hour-1), obtained on the basis of statistical processing of data array 1308 measurements. Acrylic polymer hydrogels had BOD = 0.2-2 g·m-3·hour-1, which corresponded to the periods of their half-lives from 0.2±0.1 to 6.8± 4.5 years, or relatively low resistance to biodestruction. In contrast to the pure gels, hydrogel compositions for rhizosphere based on ionic and colloidal silver showed low biological activity (BOD=0.01-0.2 g·m-3· hour-1) and, accordingly, significant resistance to biodegradation with half-lives from 5 to 70 years and above.

Boeing Smart Rotor Full-scale Wind Tunnel Test Data Report

NASA Technical Reports Server (NTRS)

Kottapalli, Sesi; Hagerty, Brandon; Salazar, Denise

2016-01-01

A full-scale helicopter smart material actuated rotor technology (SMART) rotor test was conducted in the USAF National Full-Scale Aerodynamics Complex 40- by 80-Foot Wind Tunnel at NASA Ames. The SMART rotor system is a five-bladed MD 902 bearingless rotor with active trailing-edge flaps. The flaps are actuated using piezoelectric actuators. Rotor performance, structural loads, and acoustic data were obtained over a wide range of rotor shaft angles of attack, thrust, and airspeeds. The primary test objective was to acquire unique validation data for the high-performance computing analyses developed under the Defense Advanced Research Project Agency (DARPA) Helicopter Quieting Program (HQP). Other research objectives included quantifying the ability of the on-blade flaps to achieve vibration reduction, rotor smoothing, and performance improvements. This data set of rotor performance and structural loads can be used for analytical and experimental comparison studies with other full-scale rotor systems and for analytical validation of computer simulation models. The purpose of this final data report is to document a comprehensive, highquality data set that includes only data points where the flap was actively controlled and each of the five flaps behaved in a similar manner.

Discovery of Newer Therapeutic Leads for Prostate Cancer

DTIC Science & Technology

2009-06-01

promising plant extracts and then prepare large-scale quantities of the plant extracts using supercritical fluid extraction techniques and use this...quantities of the plant extracts using supercritical fluid extraction techniques. Large scale plant collections were conducted for 14 of the top 20...material for bioassay-guided fractionation of the biologically active constituents using modern chromatography techniques. The chemical structures of

Assessment of energy-saving strategies and operational costs in full-scale membrane bioreactors.

PubMed

Gabarrón, S; Ferrero, G; Dalmau, M; Comas, J; Rodriguez-Roda, I

2014-02-15

The energy-saving strategies and operational costs of stand-alone, hybrid, and dual stream full-scale membrane bioreactors (MBRs) with capacities ranging from 1100 to 35,000 m(3) day(-1) have been assessed for seven municipal facilities located in Northeast Spain. Although hydraulic load was found to be the main determinant factor for the energy consumption rates, several optimisation strategies have shown to be effective in terms of energy reduction as well as fouling phenomenon minimization or preservation. Specifically, modifications of the biological process (installation of control systems for biological aeration) and of the filtration process (reduction of the flux or mixed liquor suspended solids concentration and installation of control systems for membrane air scouring) were applied in two stand-alone MBRs. After implementing these strategies, the yearly specific energy demand (SED) in flat-sheet (FS) and hollow-fibre (HF) stand-alone MBRs was reduced from 1.12 to 0.71 and from 1.54 to 1.12 kW h(-1) m(-3), respectively, regardless of their similar yearly averaged hydraulic loads. The strategies applied in the hybrid MBR, namely, buffering the influent flow and optimisation of both biological aeration and membrane air-scouring, reduced the SED values by 14%. These results illustrate that it is possible to apply energy-saving strategies to significantly reduce MBR operational costs, highlighting the need to optimise MBR facilities to reconsider them as an energy-competitive option. Copyright © 2014 Elsevier Ltd. All rights reserved.

Achieving low effluent NO3-N and TN concentrations in low influent chemical oxygen demand (COD) to total Kjeldahl nitrogen (TKN) ratio without using external carbon source

NASA Astrophysics Data System (ADS)

Cao, Jiashun; Oleyiblo, Oloche James; Xue, Zhaoxia; Otache, Y. Martins; Feng, Qian

2015-07-01

Two mathematical models were used to optimize the performance of a full-scale biological nutrient removal (BNR) activated treatment plant, a plug-flow bioreactors operated in a 3-stage phoredox process configuration, anaerobic anoxic oxic (A2/O). The ASM2d implemented on the platform of WEST2011 software and the BioWin activated sludge/anaerobic digestion (AS/AD) models were used in this study with the aim of consistently achieving the designed effluent criteria at a low operational cost. Four ASM2d parameters (the reduction factor for denitrification , the maximum growth rate of heterotrophs (µH), the rate constant for stored polyphosphates in PAOs ( q pp), and the hydrolysis rate constant ( k h)) were adjusted. Whereas three BioWin parameters (aerobic decay rate ( b H), heterotrophic dissolved oxygen (DO) half saturation ( K OA), and Y P/acetic) were adjusted. Calibration of the two models was successful; both models have average relative deviations (ARD) less than 10% for all the output variables. Low effluent concentrations of nitrate nitrogen (N-NO3), total nitrogen (TN), and total phosphorus (TP) were achieved in a full-scale BNR treatment plant having low influent chemical oxygen demand (COD) to total Kjeldahl nitrogen (TKN) ratio (COD/TKN). The effluent total nitrogen and nitrate nitrogen concentrations were improved by 50% and energy consumption was reduced by approximately 25%, which was accomplished by converting the two-pass aerobic compartment of the plug-flow bioreactor to anoxic reactors and being operated in an alternating mode. Findings in this work are helpful in improving the operation of wastewater treatment plant while eliminating the cost of external carbon source and reducing energy consumption.

Control of biofouling by xanthine oxidase on seawater reverse osmosis membranes from a desalination plant: enzyme production and screening of bacterial isolates from the full-scale plant.

PubMed

Nagaraj, V; Skillman, L; Li, D; Xie, Z; Ho, G

2017-07-01

Control of biofouling on seawater reverse osmosis (SWRO) membranes is a major challenge as treatments can be expensive, damage the membrane material and often biocides do not remove the polymers in which bacteria are embedded. Biological control has been largely ignored for biofouling control. The objective of this study was to demonstrate the effectiveness of xanthine oxidase enzyme against complex fouling communities and then identify naturally occurring bacterial strains that produce the free radical generating enzyme. Initially, 64 bacterial strains were isolated from different locations of the Perth Seawater Desalination Plant. In our preceding study, 25/64 isolates were selected from the culture collection as models for biofouling studies, based on their prevalence in comparison to the genomic bacterial community. In this study, screening of these model strains was performed using a nitroblue tetrazolium assay in the presence of hypoxanthine as substrate. Enzyme activity was measured by absorbance. Nine of 25 strains tested positive for xanthine oxidase production, of which Exiguobacterium from sand filters and Microbacterium from RO membranes exhibited significant levels of enzyme production. Other genera that produced xanthine oxidase were Marinomonas, Pseudomonas, Bacillus, Pseudoalteromonas and Staphylococcus. Strain variations were observed between members of the genera Microbacterium and Bacillus. Xanthine oxidase, an oxidoreductase enzyme that generates reactive oxygen species, is endogenously produced by many bacterial species. In this study, production of the enzyme by bacterial isolates from a full-scale desalination plant was investigated for potential use as biological control of membrane fouling in seawater desalination. We have previously demonstrated that free radicals generated by a commercially available xanthine oxidase in the presence of a hypoxanthine substrate, effectively dispersed biofilm polysaccharides on industrially fouled membranes. Bacterial xanthine oxidase production in the presence of hypoxanthine may prove to be a cost effective, in situ method for alleviation of fouling. © 2017 The Society for Applied Microbiology.

Assessment of full-scale biological nutrient removal systems upgraded with physico-chemical processes for the removal of emerging pollutants present in wastewaters from Mexico.

PubMed

Estrada-Arriaga, Edson Baltazar; Cortés-Muñoz, Juana Enriqueta; González-Herrera, Arturo; Calderón-Mólgora, César Guillermo; de Lourdes Rivera-Huerta, Ma; Ramírez-Camperos, Esperanza; Montellano-Palacios, Leticia; Gelover-Santiago, Silvia Lucila; Pérez-Castrejón, Sara; Cardoso-Vigueros, Lina; Martín-Domínguez, Alejandra; García-Sánchez, Liliana

2016-11-15

Two full-scale biological nutrient removal systems upgraded with three physico-chemical processes (coagulation, chemical precipitation, and neutral Fenton) were evaluated in order to determine the removal of emerging pollutants (EPs) present in municipal wastewater from Mexico. Between 41 and 55 EPs were detected in the influents of two wastewater treatment plants (WWTPs), including personal care products (PPCPs), antibiotics, analgesics, antiepileptics, antilipidemics, antihypertensives, antiseptics, stimulants, and hormones. Emerging pollutants were detected at concentrations ranging from 0.69ng/L to 94,600ng/L. High concentrations of emerging pollutants were found during dry season. WWTP 1, integrated by oxidation ditches and UV light lamps, showed removal efficiencies of EPs between 20% and 22%. On the other hand, WWTP 2 consisted of anaerobic/anoxic/aerobic tanks coupled with two disinfection processes; chlorine dioxide and UV light lamps, for which the removal of EPs was significant (up to 80%). The concentrations of emerging pollutants in WWTP 1 effluent was found within a range

A SCALE-UP Mock-Up: Comparison of Student Learning Gains in High- and Low-Tech Active-Learning Environments.

PubMed

Soneral, Paula A G; Wyse, Sara A

2017-01-01

Student-centered learning environments with upside-down pedagogies (SCALE-UP) are widely implemented at institutions across the country, and learning gains from these classrooms have been well documented. This study investigates the specific design feature(s) of the SCALE-UP classroom most conducive to teaching and learning. Using pilot survey data from instructors and students to prioritize the most salient SCALE-UP classroom features, we created a low-tech "Mock-up" version of this classroom and tested the impact of these features on student learning, attitudes, and satisfaction using a quasi--experimental setup. The same instructor taught two sections of an introductory biology course in the SCALE-UP and Mock-up rooms. Although students in both sections were equivalent in terms of gender, grade point average, incoming ACT, and drop/fail/withdraw rate, the Mock-up classroom enrolled significantly more freshmen. Controlling for class standing, multiple regression modeling revealed no significant differences in exam, in-class, preclass, and Introduction to Molecular and Cellular Biology Concept Inventory scores between the SCALE-UP and Mock-up classrooms. Thematic analysis of student comments highlighted that collaboration and whiteboards enhanced the learning experience, but technology was not important. Student satisfaction and attitudes were comparable. These results suggest that the benefits of a SCALE-UP experience can be achieved at lower cost without technology features. © 2017 P. A. G. Soneral and S. A. Wyse. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Application of triple collocation in ground-based validation of soil moisture active/passive (SMAP) level 2 data products

USDA-ARS?s Scientific Manuscript database

The validation of the soil moisture retrievals from the recently-launched NASA Soil Moisture Active/Passive (SMAP) satellite is important prior to their full public release. Uncertainty in attempts to characterize footprint-scale surface-layer soil moisture using point-scale ground observations has ...

Modelling and Dosimetry for Alpha-Particle Therapy

PubMed Central

Sgouros, George; Hobbs, Robert F.; Song, Hong

2015-01-01

As a consequence of the high potency and short range of alpha-particles, radiopharmaceutical therapy with alpha-particle emitting radionuclides is a promising treatment approach that is under active pre-clinical and clinical investigation. To understand and predict the biological effects of alpha-particle radiopharmaceuticals, dosimetry is required at the micro or multi-cellular scale level. At such a scale, highly non-uniform irradiation of the target volume may be expected and the utility of a single absorbed dose value to predict biological effects comes into question. It is not currently possible to measure the pharmacokinetic input required for micro scale dosimetry in humans. Accordingly, pre-clinical studies are required to provide the pharmacokinetic data for dosimetry calculations. The translation of animal data to the human requires a pharmacokinetic model that links macro- and micro-scale pharmacokinetics thereby enabling the extrapolation of micro-scale kinetics from macroscopic measurements. These considerations along with a discussion of the appropriate physical quantity and related units for alpha-particle radiopharmaceutical therapy are examined in this review. PMID:22201712

Performance evaluation of a full-scale innovative swine waste-to-energy system.

PubMed

Xu, Jiele; Adair, Charles W; Deshusses, Marc A

2016-09-01

Intensive monitoring was carried out to evaluate the performance of a full-scale innovative swine waste-to-energy system at a commercial swine farm with 8640 heads of swine. Detailed mass balances over each unit of the system showed that the system, which includes a 7600m(3) anaerobic digester, a 65-kW microturbine, and a 4200m(3) aeration basin, was able to remove up to 92% of the chemical oxygen demand (COD), 99% of the biological oxygen demand (BOD), 77% of the total nitrogen (TN), and 82% of the total phosphorous (TP) discharged into the system as fresh pig waste. The overall biogas yield based on the COD input was 64% of the maximum theoretical, a value that indicates that even greater environmental benefits could be obtained with process optimization. Overall, the characterization of the materials fluxes in the system provides a greater understanding of the fate of organics and nutrients in large scale animal waste management systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Micropollutant removal by attached and suspended growth in a hybrid biofilm-activated sludge process.

PubMed

Falås, P; Longrée, P; la Cour Jansen, J; Siegrist, H; Hollender, J; Joss, A

2013-09-01

Removal of organic micropollutants in a hybrid biofilm-activated sludge process was investigated through batch experiments, modeling, and full-scale measurements. Batch experiments with carriers and activated sludge from the same full-scale reactor were performed to assess the micropollutant removal rates of the carrier biofilm under oxic conditions and the sludge under oxic and anoxic conditions. Clear differences in the micropollutant removal kinetics of the attached and suspended growth were demonstrated, often with considerably higher removal rates for the biofilm compared to the sludge. For several micropollutants, the removal rates were also affected by the redox conditions, i.e. oxic and anoxic. Removal rates obtained from the batch experiments were used to model the micropollutant removal in the full-scale process. The results from the model and plant measurements showed that the removal efficiency of the process can be predicted with acceptable accuracy (± 25%) for most of the modeled micropollutants. Furthermore, the model estimations indicate that the attached growth in hybrid biofilm-activated sludge processes can contribute significantly to the removal of individual compounds, such as diclofenac. Copyright © 2013 Elsevier Ltd. All rights reserved.

Multi-point monitoring of nitrous oxide emissions in three full-scale conventional activated sludge tanks in Europe.

PubMed

Bellandi, Giacomo; Porro, Jose; Senesi, Elisa; Caretti, Cecilia; Caffaz, Simone; Weijers, Stefan; Nopens, Ingmar; Gori, Riccardo

2018-02-01

The large global warming potential of nitrous oxide (N 2 O) is currently of general concern for the water industry, especially in view of a new regulatory framework concerning the carbon footprint of water resource recovery facilities (WRRFs). N 2 O can be generated through different biological pathways and from different treatment steps of a WRRF. The use of generic emission factors (EF) for quantifying the emissions of WRRFs is discouraged. This is due to the number of different factors that can affect how much, when and where N 2 O is emitted from WRRFs. The spatial and temporal variability of three WRRFs in Europe using comparable technologies is presented. An economically feasible and user-friendly method for accounting for the contribution of anoxic zones via direct gas emission measurements was proven. The investigation provided new insights into the contribution from the anoxic zones versus the aerobic zones of biological WRRF tanks and proved the unsuitability of the use of a single EF for the three WRRFs. Dedicated campaigns for N 2 O emissions assessment are to be advised. However, similarities in the EF magnitude can be found considering treatment strategy and influent water composition.

Scales and scaling in turbulent ocean sciences; physics-biology coupling

NASA Astrophysics Data System (ADS)

Schmitt, Francois

2015-04-01

Geophysical fields possess huge fluctuations over many spatial and temporal scales. In the ocean, such property at smaller scales is closely linked to marine turbulence. The velocity field is varying from large scales to the Kolmogorov scale (mm) and scalar fields from large scales to the Batchelor scale, which is often much smaller. As a consequence, it is not always simple to determine at which scale a process should be considered. The scale question is hence fundamental in marine sciences, especially when dealing with physics-biology coupling. For example, marine dynamical models have typically a grid size of hundred meters or more, which is more than 105 times larger than the smallest turbulence scales (Kolmogorov scale). Such scale is fine for the dynamics of a whale (around 100 m) but for a fish larvae (1 cm) or a copepod (1 mm) a description at smaller scales is needed, due to the nonlinear nature of turbulence. The same is verified also for biogeochemical fields such as passive and actives tracers (oxygen, fluorescence, nutrients, pH, turbidity, temperature, salinity...) In this framework, we will discuss the scale problem in turbulence modeling in the ocean, and the relation of Kolmogorov's and Batchelor's scales of turbulence in the ocean, with the size of marine animals. We will also consider scaling laws for organism-particle Reynolds numbers (from whales to bacteria), and possible scaling laws for organism's accelerations.

Bioluminescence-Based Method for Measuring Assimilable Organic Carbon in Pretreatment Water for Reverse Osmosis Membrane Desalination ▿

PubMed Central

Weinrich, Lauren A.; Schneider, Orren D.; LeChevallier, Mark W.

2011-01-01

A bioluminescence-based assimilable organic carbon (AOC) test was developed for determining the biological growth potential of seawater within the reverse osmosis desalination pretreatment process. The test uses Vibrio harveyi, a marine organism that exhibits constitutive luminescence and is nutritionally robust. AOC was measured in both a pilot plant and a full-scale desalination plant pretreatment. PMID:21148685

Biological framework for soil aggregation: Implications for ecological functions.

NASA Astrophysics Data System (ADS)

Ghezzehei, Teamrat; Or, Dani

2016-04-01

Soil aggregation is heuristically understood as agglomeration of primary particles bound together by biotic and abiotic cementing agents. The organization of aggregates is believed to be hierarchical in nature; whereby primary particles bond together to form secondary particles and subsequently merge to form larger aggregates. Soil aggregates are not permanent structures, they continuously change in response to internal and external forces and other drivers, including moisture, capillary pressure, temperature, biological activity, and human disturbances. Soil aggregation processes and the resulting functionality span multiple spatial and temporal scales. The intertwined biological and physical nature of soil aggregation, and the time scales involved precluded a universally applicable and quantifiable framework for characterizing the nature and function of soil aggregation. We introduce a biophysical framework of soil aggregation that considers the various modes and factors of the genesis, maturation and degradation of soil aggregates including wetting/drying cycles, soil mechanical processes, biological activity and the nature of primary soil particles. The framework attempts to disentangle mechanical (compaction and soil fragmentation) from in-situ biophysical aggregation and provides a consistent description of aggregate size, hierarchical organization, and life time. It also enables quantitative description of biotic and abiotic functions of soil aggregates including diffusion and storage of mass and energy as well as role of aggregates as hot spots of nutrient accumulation, biodiversity, and biogeochemical cycles.

Identifying the underlying causes of biological instability in a full-scale drinking water supply system.

PubMed

Nescerecka, Alina; Juhna, Talis; Hammes, Frederik

2018-05-15

Changes in bacterial concentration and composition in drinking water during distribution are often attributed to biological (in)stability. Here we assessed temporal biological stability in a full-scale distribution network (DN) supplied with different types of source water: treated and chlorinated surface water and chlorinated groundwater produced at three water treatment plants (WTP). Monitoring was performed weekly during 12 months in two locations in the DN. Flow cytometric total and intact cell concentration (ICC) measurements showed considerable seasonal fluctuations, which were different for two locations. ICC varied between 0.1-3.75 × 10 5  cells mL -1 and 0.69-4.37 × 10 5  cells mL -1 at two locations respectively, with ICC increases attributed to temperature-dependent bacterial growth during distribution. Chlorinated water from the different WTP was further analysed with a modified growth potential method, identifying primary and secondary growth limiting compounds. It was observed that bacterial growth in the surface water sample after chlorination was primarily inhibited by phosphorus limitation and secondly by organic carbon limitation, while carbon was limiting in the chlorinated groundwater samples. However, the ratio of available nutrients changed during distribution, and together with disinfection residual decay, this resulted in higher bacterial growth potential detected in the DN than at the WTP. In this study, bacterial growth was found to be higher (i) at higher water temperatures, (ii) in samples with lower chlorine residuals and (iii) in samples with less nutrient (carbon, phosphorus, nitrogen, iron) limitation, while this was significantly different between the samples of different origin. Thus drinking water microbiological quality and biological stability could change during different seasons, and the extent of these changes depends on water temperature, the water source and treatment. Furthermore, differences in primary growth limiting nutrients in different water sources could contribute to biological instability in the network, where mixing occurs. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Impacts of Migraine among Outpatients with Major Depressive Disorder at a Two-Year Follow-Up

PubMed Central

Hung, Ching-I; Liu, Chia-Yih; Yang, Ching-Hui; Wang, Shuu-Jiun

2015-01-01

Background No study has investigated the impacts of migraine on depression, anxiety, and somatic symptoms and remission at the two-year follow-up point among patients with major depressive disorder (MDD). This study aimed to investigate the above issues. Methods Psychiatric outpatients with MDD recruited at baseline were investigated at a two-year follow-up (N = 106). The Hamilton Depression Rating Scale, Hospital Anxiety and Depression Scale, and Depression and Somatic Symptoms Scale were used. Migraine was diagnosed according to the International Classification of Headache Disorders, 2nd edition. The patients were divided into no migraine, inactive migraine, and active migraine subgroups. Multiple logistic regressions were used to investigate the significant factors related to full remission of depression. Results Among patients without pharmacotherapy at the follow-up, patients with active migraine had significantly greater severities of anxiety and somatic symptoms as compared with patients without migraine; moreover, patients with active migraine had the lowest improvement percentage and full remission rate. There were no significant differences in depression, anxiety, and somatic symptoms between patients with inactive migraine and those without migraine. Active headache at follow-up was a significant factor related to a lower full remission rate. Conclusions Active headache at follow-up was associated with a lower rate of full remission and more residual anxiety and somatic symptoms at follow-up among patients with migraine. Physicians should integrate a treatment plan for depression and migraine for the treatment of patients with MDD. PMID:26000962

The Impacts of Migraine among Outpatients with Major Depressive Disorder at a Two-Year Follow-Up.

PubMed

Hung, Ching-I; Liu, Chia-Yih; Yang, Ching-Hui; Wang, Shuu-Jiun

2015-01-01

No study has investigated the impacts of migraine on depression, anxiety, and somatic symptoms and remission at the two-year follow-up point among patients with major depressive disorder (MDD). This study aimed to investigate the above issues. Psychiatric outpatients with MDD recruited at baseline were investigated at a two-year follow-up (N = 106). The Hamilton Depression Rating Scale, Hospital Anxiety and Depression Scale, and Depression and Somatic Symptoms Scale were used. Migraine was diagnosed according to the International Classification of Headache Disorders, 2nd edition. The patients were divided into no migraine, inactive migraine, and active migraine subgroups. Multiple logistic regressions were used to investigate the significant factors related to full remission of depression. Among patients without pharmacotherapy at the follow-up, patients with active migraine had significantly greater severities of anxiety and somatic symptoms as compared with patients without migraine; moreover, patients with active migraine had the lowest improvement percentage and full remission rate. There were no significant differences in depression, anxiety, and somatic symptoms between patients with inactive migraine and those without migraine. Active headache at follow-up was a significant factor related to a lower full remission rate. Active headache at follow-up was associated with a lower rate of full remission and more residual anxiety and somatic symptoms at follow-up among patients with migraine. Physicians should integrate a treatment plan for depression and migraine for the treatment of patients with MDD.

Plant systems biology: network matters.

PubMed

Lucas, Mikaël; Laplaze, Laurent; Bennett, Malcolm J

2011-04-01

Systems biology is all about networks. A recent trend has been to associate systems biology exclusively with the study of gene regulatory or protein-interaction networks. However, systems biology approaches can be applied at many other scales, from the subatomic to the ecosystem scales. In this review, we describe studies at the sub-cellular, tissue, whole plant and crop scales and highlight how these studies can be related to systems biology. We discuss the properties of system approaches at each scale as well as their current limits, and pinpoint in each case advances unique to the considered scale but representing potential for the other scales. We conclude by examining plant models bridging different scales and considering the future prospects of plant systems biology. © 2011 Blackwell Publishing Ltd.

Does the Room Matter? Active Learning in Traditional and Enhanced Lecture Spaces

PubMed Central

Stoltzfus, Jon R.; Libarkin, Julie

2016-01-01

SCALE-UP–type classrooms, originating with the Student-Centered Active Learning Environment with Upside-down Pedagogies project, are designed to facilitate active learning by maximizing opportunities for interactions between students and embedding technology in the classroom. Positive impacts when active learning replaces lecture are well documented, both in traditional lecture halls and SCALE-UP–type classrooms. However, few studies have carefully analyzed student outcomes when comparable active learning–based instruction takes place in a traditional lecture hall and a SCALE-UP–type classroom. Using a quasi-experimental design, we compared student perceptions and performance between sections of a nonmajors biology course, one taught in a traditional lecture hall and one taught in a SCALE-UP–type classroom. Instruction in both sections followed a flipped model that relied heavily on cooperative learning and was as identical as possible given the infrastructure differences between classrooms. Results showed that students in both sections thought that SCALE-UP infrastructure would enhance performance. However, measures of actual student performance showed no difference between the two sections. We conclude that, while SCALE-UP–type classrooms may facilitate implementation of active learning, it is the active learning and not the SCALE-UP infrastructure that enhances student performance. As a consequence, we suggest that institutions can modify existing classrooms to enhance student engagement without incorporating expensive technology. PMID:27909018

Field Markup Language: biological field representation in XML.

PubMed

Chang, David; Lovell, Nigel H; Dokos, Socrates

2007-01-01

With an ever increasing number of biological models available on the internet, a standardized modeling framework is required to allow information to be accessed or visualized. Based on the Physiome Modeling Framework, the Field Markup Language (FML) is being developed to describe and exchange field information for biological models. In this paper, we describe the basic features of FML, its supporting application framework and its ability to incorporate CellML models to construct tissue-scale biological models. As a typical application example, we present a spatially-heterogeneous cardiac pacemaker model which utilizes both FML and CellML to describe and solve the underlying equations of electrical activation and propagation.

Microbial Community Composition of Polyhydroxyalkanoate-Accumulating Organisms in Full-Scale Wastewater Treatment Plants Operated in Fully Aerobic Mode

PubMed Central

Oshiki, Mamoru; Onuki, Motoharu; Satoh, Hiroyasu; Mino, Takashi

2013-01-01

The removal of biodegradable organic matter is one of the most important objectives in biological wastewater treatments. Polyhydroxyalkanoate (PHA)-accumulating organisms (PHAAOs) significantly contribute to the removal of biodegradable organic matter; however, their microbial community composition is mostly unknown. In the present study, the microbial community composition of PHAAOs was investigated at 8 full-scale wastewater treatment plants (WWTPs), operated in fully aerobic mode, by fluorescence in situ hybridization (FISH) analysis and post-FISH Nile blue A (NBA) staining techniques. Our results demonstrated that 1) PHAAOs were in the range of 11–18% in the total number of cells, and 2) the microbial community composition of PHAAOs was similar at the bacterial domain/phylum/class/order level among the 8 full-scale WWTPs, and dominant PHAAOs were members of the class Alphaproteobacteria and Betaproteobacteria. The microbial community composition of α- and β-proteobacterial PHAAOs was examined by 16S rRNA gene clone library analysis and further by applying a set of newly designed oligonucleotide probes targeting 16S rRNA gene sequences of α- or β-proteobacterial PHAAOs. The results demonstrated that the microbial community composition of PHAAOs differed in the class Alphaproteobacteria and Betaproteobacteria, which possibly resulted in a different PHA accumulation capacity among the WWTPs (8.5–38.2 mg-C g-VSS−1 h−1). The present study extended the knowledge of the microbial diversity of PHAAOs in full-scale WWTPs operated in fully aerobic mode. PMID:23257912

Light limitation plays a central role in regulating DOM reactions in temperate watersheds

NASA Astrophysics Data System (ADS)

Yoon, B.; Hosen, J. D.; Kyzivat, E.; Fair, J. H.; Weber, L.; Aho, K. S.; Stubbins, A.; Lowenthal, R. S.; Raymond, P. A.

2017-12-01

Biological uptake and photochemical oxidation determine how much dissolved organic matter (DOM) can be removed and exported from inland waters. It is thus critical to understand the control on the biological and photochemical oxidation of DOM, and identify potential synergy between these two DOM removal processes. Yet, the variability of biological and photochemical lability, and the prevalence of priming effects between the two removal mechanisms are poorly understood at larger spatiotemporal scale. To address this knowledge gap, we analyzed the lability of 900 samples collected throughout the Connecticut River across two years (n = 510 for biolability, n=394 for photolability). Furthermore, we measured the effect of photochemical priming for biological removal and of biological priming for photochemical removal (n= 151, n=146, respectively). Our results show that photolability is on average 5 times greater than biolability, and that the mass of photolabile DOM can be predicted from UV absorbance at 254 nm. Photochemical DOM removal also led to additional "unlocking" of previously bio-recalcitrant DOM in 80% of the samples, and increased the biological lability by threefold on average. Scaling further, we extrapolate our model to estimate that the DOM fluxes leaving the Connecticut River and the Mississippi River are 49% and 45% photolabile, respectively. The significant photoreactivity observed across the samples and the subsequent increase in biolability demonstrate that sunlight is a more potent agent of DOM removal than the biological reactions. Yet, the photolability of DOM fluxes leaving the Connecticut River and Mississippi River indicates that the full photo-oxidation potential is not achieved due to light limitation.

Small wastewater treatment plants in mountain areas: combination of septic tank and biological filter.

PubMed

Maunoir, S; Philip, H; Rambaud, A

2007-01-01

Research work has been carried out for more than 20 years by Eparco and the University of Montpellier (France) on the application of biological wastewater treatment processes for small communities. This research has led to a new process which is particularly suitable for remote populations, taking into account several specificities such as as the seasonal fluctuations in the population, the accessibility of the site, the absence of a power supply on site, the reduced area of land available and the low maintenance. Thus, the process, which combines a septic tank operating under anaerobic conditions and a biological aerobic filter, is a solution for wastewater treatment in mountain areas. This paper presents the process and three full-scale applications in the region of the Alps.

Contribution of assimilable organic carbon to biological fouling in seawater reverse osmosis membrane treatment.

PubMed

Weinrich, Lauren; LeChevallier, Mark; Haas, Charles N

2016-09-15

Biological fouling occurs on RO membranes when bacteria and nutrients are present in conditions that are conducive to growth and proliferation of the bacteria. Controlling microbial growth on the membranes is typically limited to biocide application (i.e., disinfectants) in seawater RO plants. However, biological growth and subsequent fouling has not been well-managed. Pretreatment has not been focused on nutrient limitation. This project used a biological assay, the assimilable organic carbon (AOC) test to evaluate pretreatment effects on the nutrient supply. The AOC test provided a useful surrogate measurement for the biodegradability or biofouling potential of RO feed water. Biofouling observed in controlled conditions at the bench- and pilot-scale resulted in statistically significant correlations between AOC and the operational effects caused by biofouling. Membrane fouling rates are observed through operational changes over time such as increased differential pressure between the membrane feed and concentrate locations and decreased permeate flux through the membrane. In full scale plants there were strong correlations when AOC was used as a predictor variable for increased differential pressure (0.28-0.55 bar from September-December 2012) and decreased specific flux (1.40 L per hour/(m(2) · bar)). Increased differential pressure was associated with RO membrane biological fouling when the median AOC was 50 μg/L during pilot testing. Conditions were also evaluated at the bench-scale using a flat sheet RO membrane. In a comparison test using 30 and 1000 μg/L AOC, fouling was detected on more portions of the membrane when AOC was higher. Biofilm and bacterial deposits were apparent from scanning electron microscope imaging and biomass measurements using ATP. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biology meets physics: Reductionism and multi-scale modeling of morphogenesis.

PubMed

Green, Sara; Batterman, Robert

2017-02-01

A common reductionist assumption is that macro-scale behaviors can be described "bottom-up" if only sufficient details about lower-scale processes are available. The view that an "ideal" or "fundamental" physics would be sufficient to explain all macro-scale phenomena has been met with criticism from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological processes such as gene regulation and evolution. This paper takes a step back in asking whether bottom-up modeling is feasible even when modeling simple physical systems across scales. By comparing examples of multi-scale modeling in physics and biology, we argue that the "tyranny of scales" problem presents a challenge to reductive explanations in both physics and biology. The problem refers to the scale-dependency of physical and biological behaviors that forces researchers to combine different models relying on different scale-specific mathematical strategies and boundary conditions. Analyzing the ways in which different models are combined in multi-scale modeling also has implications for the relation between physics and biology. Contrary to the assumption that physical science approaches provide reductive explanations in biology, we exemplify how inputs from physics often reveal the importance of macro-scale models and explanations. We illustrate this through an examination of the role of biomechanical modeling in developmental biology. In such contexts, the relation between models at different scales and from different disciplines is neither reductive nor completely autonomous, but interdependent. Copyright © 2016 Elsevier Ltd. All rights reserved.

Functional model of biological neural networks.

PubMed

Lo, James Ting-Ho

2010-12-01

A functional model of biological neural networks, called temporal hierarchical probabilistic associative memory (THPAM), is proposed in this paper. THPAM comprises functional models of dendritic trees for encoding inputs to neurons, a first type of neuron for generating spike trains, a second type of neuron for generating graded signals to modulate neurons of the first type, supervised and unsupervised Hebbian learning mechanisms for easy learning and retrieving, an arrangement of dendritic trees for maximizing generalization, hardwiring for rotation-translation-scaling invariance, and feedback connections with different delay durations for neurons to make full use of present and past informations generated by neurons in the same and higher layers. These functional models and their processing operations have many functions of biological neural networks that have not been achieved by other models in the open literature and provide logically coherent answers to many long-standing neuroscientific questions. However, biological justifications of these functional models and their processing operations are required for THPAM to qualify as a macroscopic model (or low-order approximate) of biological neural networks.

Non-aqueous homogenous biocatalytic conversion of polysaccharides in ionic liquids using chemically modified glucosidase.

PubMed

Brogan, Alex P S; Bui-Le, Liem; Hallett, Jason P

2018-06-25

The increasing requirement to produce platform chemicals and fuels from renewable sources means advances in biocatalysis are rapidly becoming a necessity. Biomass is widely used in nature as a source of energy and as chemical building blocks. However, recalcitrance towards traditional chemical processes and solvents provides a significant barrier to widespread utility. Here, by optimizing enzyme solubility in ionic liquids, we have discovered solvent-induced substrate promiscuity of glucosidase, demonstrating an unprecedented example of homogeneous enzyme bioprocessing of cellulose. Specifically, chemical modification of glucosidase for solubilization in ionic liquids can increase thermal stability to up to 137 °C, allowing for enzymatic activity 30 times greater than is possible in aqueous media. These results establish that through a synergistic combination of chemical biology (enzyme modification) and reaction engineering (solvent choice), the biocatalytic capability of enzymes can be intensified: a key step towards the full-scale deployment of industrial biocatalysis.

Biofiltration: an innovative air pollution control technology for VOC emissions.

PubMed

Leson, G; Winer, A M

1991-08-01

Biofiltration is a relatively recent air pollution control (APC) technology in which off-gases containing biodegradable volatile organic compounds (VOC) or inorganic air toxics are vented through a biologically active material. This technology has been successfully applied in Germany and The Netherlands in many full-scale applications to control odors, VOC and air toxic emissions from a wide range of industrial and public sector sources. Control efficiencies of more than 90 percent have been achieved for many common air pollutants. Due to lower operating costs, biofiltration can provide significant economic advantages over other APC technologies if applied to off-gases that contain readily biodegradable pollutants in low concentrations. Environmental benefits include low energy requirements and the avoidance of cross media transfer of pollutants. This paper reviews the history and current status of biofiltration, outlines its underlying scientific and engineering principles, and discusses the applicability of biofilters for a wide range of specific emission sources.

Multi-scale computational modeling of developmental biology.

PubMed

Setty, Yaki

2012-08-01

Normal development of multicellular organisms is regulated by a highly complex process in which a set of precursor cells proliferate, differentiate and move, forming over time a functioning tissue. To handle their complexity, developmental systems can be studied over distinct scales. The dynamics of each scale is determined by the collective activity of entities at the scale below it. I describe a multi-scale computational approach for modeling developmental systems and detail the methodology through a synthetic example of a developmental system that retains key features of real developmental systems. I discuss the simulation of the system as it emerges from cross-scale and intra-scale interactions and describe how an in silico study can be carried out by modifying these interactions in a way that mimics in vivo experiments. I highlight biological features of the results through a comparison with findings in Caenorhabditis elegans germline development and finally discuss about the applications of the approach in real developmental systems and propose future extensions. The source code of the model of the synthetic developmental system can be found in www.wisdom.weizmann.ac.il/~yaki/MultiScaleModel. yaki.setty@gmail.com Supplementary data are available at Bioinformatics online.

Agonist Met antibodies define the signalling threshold required for a full mitogenic and invasive program of Kaposi's Sarcoma cells.

PubMed

Bardelli, Claudio; Sala, Marilena; Cavallazzi, Umberto; Prat, Maria

2005-09-09

We previously showed that the Kaposi Sarcoma line KS-IMM express a functional Met tyrosine kinase receptor, which, upon HGF stimulation, activates motogenic, proliferative, and invasive responses. In this study, we investigated the signalling pathways activated by HGF, as well as by Met monoclonal antibodies (Mabs), acting as full or partial agonists. The full agonist Mab mimics HGF in all biological and biochemical aspects. It elicits the whole spectrum of responses, while the partial agonist Mab induces only wound healing. These differences correlated with a more prolonged and sustained tyrosine phosphorylation of the receptor and MAPK evoked by HGF and by the full agonist Mab, relative to the partial agonist Mab. Since Gab1, JNK and PI 3-kinase are activated with same intensity and kinetics by HGF and by the two agonist antibodies, it is concluded that level and duration of MAPK activation by Met receptor are crucial for the induction of a full HGF-dependent mitogenic and invasive program in KS cells.

Sequencing biological acidification of waste-activated sludge aiming to optimize phosphorus dissolution and recovery.

PubMed

Guilayn, Felipe; Braak, Etienne; Piveteau, Simon; Daumer, Marie-Line

2017-06-01

Phosphorus (P) recovery in wastewater treatment plants (WWTP) as pure crystals such as struvite (MgNH 4 PO 4 .6H 2 O), potassium struvite (KMgPO 4 .6H 2 O) and calcium phosphates (e.g. Ca 3 (PO 4 ) 2 ) is an already feasible technique that permits the production of green and marketable fertilizers and the reduction of operational costs. Commercial crystallizers can recovery more than 90% of soluble P. However, most of the P in WWTP sludge is unavailable for the processes (not dissolved). P solubilization and separation are thus the limiting steps in P-crystallization. With an innovative two-step sequencing acidification strategy, the current study has aimed to improve biological P solubilization on waste-activated sludge (WAS) from a full-scale plant. In the first step (P-release), low charges of organic waste were used as co-substrates of WAS pre-fermentation, seeking to produce volatile fatty acids to feed the P-release by Polyphosphate-accumulating organisms, while keeping its optimal metabolic pH (6-7). In this phase, milk serum, WWTP grease, urban organic waste and collective restaurant waste were individually applied as co-substrates. In the second step (P-dissolution), pH 4 was aimed at as it allows the dissolution of the most common precipitated species of P. Biological acidification was performed by white sugar addition, as a carbohydrate-rich organic waste model, which was compared to chemical acidification by HCl (12M) addition. With short retention times (48-96 h) and without inoculum application, all experiences succeeded on P solubilization (37-55% of soluble P), principally when carbohydrate-rich co-substrates were applied. Concentrations from 270 to 450 mg [Formula: see text] were achieved. [Formula: see text].

Characterizing and predicting species distributions across environments and scales: Argentine ant occurrences in the eye of the beholder

USGS Publications Warehouse

Menke, S.B.; Holway, D.A.; Fisher, R.N.; Jetz, W.

2009-01-01

Aim: Species distribution models (SDMs) or, more specifically, ecological niche models (ENMs) are a useful and rapidly proliferating tool in ecology and global change biology. ENMs attempt to capture associations between a species and its environment and are often used to draw biological inferences, to predict potential occurrences in unoccupied regions and to forecast future distributions under environmental change. The accuracy of ENMs, however, hinges critically on the quality of occurrence data. ENMs often use haphazardly collected data rather than data collected across the full spectrum of existing environmental conditions. Moreover, it remains unclear how processes affecting ENM predictions operate at different spatial scales. The scale (i.e. grain size) of analysis may be dictated more by the sampling regime than by biologically meaningful processes. The aim of our study is to jointly quantify how issues relating to region and scale affect ENM predictions using an economically important and ecologically damaging invasive species, the Argentine ant (Linepithema humile). Location: California, USA. Methods: We analysed the relationship between sampling sufficiency, regional differences in environmental parameter space and cell size of analysis and resampling environmental layers using two independently collected sets of presence/absence data. Differences in variable importance were determined using model averaging and logistic regression. Model accuracy was measured with area under the curve (AUC) and Cohen's kappa. Results: We first demonstrate that insufficient sampling of environmental parameter space can cause large errors in predicted distributions and biological interpretation. Models performed best when they were parametrized with data that sufficiently sampled environmental parameter space. Second, we show that altering the spatial grain of analysis changes the relative importance of different environmental variables. These changes apparently result from how environmental constraints and the sampling distributions of environmental variables change with spatial grain. Conclusions: These findings have clear relevance for biological inference. Taken together, our results illustrate potentially general limitations for ENMs, especially when such models are used to predict species occurrences in novel environments. We offer basic methodological and conceptual guidelines for appropriate sampling and scale matching. ?? 2009 The Authors Journal compilation ?? 2009 Blackwell Publishing.

Human seizures couple across spatial scales through travelling wave dynamics

NASA Astrophysics Data System (ADS)

Martinet, L.-E.; Fiddyment, G.; Madsen, J. R.; Eskandar, E. N.; Truccolo, W.; Eden, U. T.; Cash, S. S.; Kramer, M. A.

2017-04-01

Epilepsy--the propensity toward recurrent, unprovoked seizures--is a devastating disease affecting 65 million people worldwide. Understanding and treating this disease remains a challenge, as seizures manifest through mechanisms and features that span spatial and temporal scales. Here we address this challenge through the analysis and modelling of human brain voltage activity recorded simultaneously across microscopic and macroscopic spatial scales. We show that during seizure large-scale neural populations spanning centimetres of cortex coordinate with small neural groups spanning cortical columns, and provide evidence that rapidly propagating waves of activity underlie this increased inter-scale coupling. We develop a corresponding computational model to propose specific mechanisms--namely, the effects of an increased extracellular potassium concentration diffusing in space--that support the observed spatiotemporal dynamics. Understanding the multi-scale, spatiotemporal dynamics of human seizures--and connecting these dynamics to specific biological mechanisms--promises new insights to treat this devastating disease.

Live Scale Active Shooter Exercise: Lessons Learned

ERIC Educational Resources Information Center

Ervin, Randy

2008-01-01

On October 23, 2007, the Lake Land College Public Safety Department conducted a full-scale live exercise that simulated an active shooter and barricaded hostage. In this article, the author will emphasize what they learned, and how they intend to benefit from it. He will list the law enforcement issues and general issues they encountered, and then…

Weak synchronization and large-scale collective oscillation in dense bacterial suspensions

NASA Astrophysics Data System (ADS)

Wu, Yilin

Collective oscillatory behavior is ubiquitous in nature and it plays a vital role in many biological processes. Collective oscillations in biological multicellular systems often arise from coupling mediated by diffusive chemicals, by electrochemical mechanisms, or by biomechanical interaction between cells and their physical environment. In these examples, the phase of some oscillatory intracellular degree of freedom is synchronized. Here, in contrast, we discovered a unique 'weak synchronization' mechanism that does not require long-range coupling, nor even inherent oscillation of individual cells: We found that millions of motile cells in dense bacterial suspensions can self-organize into highly robust collective oscillatory motion, while individuals move in an erratic manner. Over large spatial scales we found that the phase of the oscillations is in fact organized into a centimeter scale traveling wave. We present a model of noisy self-propelled particles with strictly local interactions that accounts faithfully for our observations. These findings expand our knowledge of biological self-organization and reveal a new type of long-range order in active matter systems. The mechanism of collective oscillation uncovered here may inspire new strategies to control the self-organization of active matter and swarming robots. This work is supported by funding from CUHK Direct research Grants (4053019, 4053079, 4053130), the Research Grants Council of HKSAR (RGC Ref. No. CUHK 409713), and from the National Natural Science Foundation of China (NSFC 21473152).

The New Bedford Harbor Superfund site long-term monitoring program (1993-2009).

PubMed

Nelson, William G; Bergen, Barbara J

2012-12-01

New Bedford Harbor (NBH), located in southeastern Massachusetts, was designated as a marine Superfund site in 1983 due to sediment contamination by polychlorinated biphenyls (PCBs). Based on risks to human health and the environment, the first two phases of the site cleanup involved dredging PCB-contaminated sediments from the harbor. Therefore, a long-term monitoring program (LTM) was developed to measure spatial and temporal chemical and biological changes in sediment, water, and biota to assess the effects and effectiveness of the remedial activities. A systematic, probabilistic sampling design was used to select sediment sampling stations. This unbiased design allowed the three segments of the harbor to be compared spatially and temporally to quantify changes resulting from dredging the contaminated sediments. Sediment was collected at each station, and chemical (e.g., PCBs and metals), physical (e.g., grain size), and biological (e.g., benthic community) measurements were conducted on all samples. This paper describes the overall NBH-LTM approach and the results from the five rounds of sample collections. There is a decreasing spatial gradient in sediment PCB concentrations from the northern boundary (upper harbor) to the southern boundary (outer harbor) of the site. Along this same transect, there is an increase in biological condition (e.g., benthic community diversity). Temporally, the contaminant and biological gradients have been maintained since the 1993 baseline collection; however, since the onset of full-scale remediation, PCB concentrations have decreased throughout the site, and one of the benthic community indices has shown significant improvement in the lower and outer harbor areas.

Sludge Retention Time as a Suitable Operational Parameter to Remove Both Estrogen and Nutrients in an Anaerobic–Anoxic–Aerobic Activated Sludge System

PubMed Central

Zeng, Qingling; Li, Yongmei; Yang, Shijia

2013-01-01

Abstract Estrogen in wastewater are responsible for a significant part of the endocrine-disrupting effects observed in the aquatic environment. The effect of sludge retention time (SRT) on the removal and fate of 17β-estradiol (E2) and 17α-ethinylestradiol (EE2) in an anaerobic–anoxic–oxic activated sludge system designed for nutrient removal was investigated by laboratory-scale experiments using synthetic wastewater. With a hydraulic retention time of 8 h, when SRT ranged 10–25 days, E2 was almost completely removed from water, and EE2 removal efficiency was 65%–81%. Both estrogens were easily sorbed onto activated sludge. Distribution coefficients (Kd) of estrogens on anaerobic sludge were greater than those on anoxic and aerobic sludges. Mass balance calculation indicated that 99% of influent E2 was degraded by the activated sludge process, and 1% remained in excess sludge; of influent EE2, 62.0%–80.1% was biodegraded; 18.9%–34.7% was released in effluent; and 0.88%–3.31% remained in excess sludge. Optimal SRT was 20 days for both estrogen and nutrient removal. E2 was almost completely degraded, and EE2 was only partly degraded in the activated sludge process. Residual estrogen on excess sludge must be considered in the sludge treatment and disposal processes. The originality of the work is that removal of nutrients and estrogens were linked, and optimal SRT for both estrogen and nutrient removal in an enhanced biological phosphorus removal system was determined. This has an important implication for the design and operation of full-scale wastewater treatment plants. PMID:23633892

Fullerene C60 and graphene photosensibiles for photodynamic virus inactivation

NASA Astrophysics Data System (ADS)

Belousova, I.; Hvorostovsky, A.; Kiselev, V.; Zarubaev, V.; Kiselev, O.; Piotrovsky, L.; Anfimov, P.; Krisko, T.; Muraviova, T.; Rylkov, V.; Starodubzev, A.; Sirotkin, A.; Grishkanich, A.; Kudashev, I.; Kancer, A.; Kustikova, M.; Bykovskaya, E.; Mayurova, A.; Stupnikov, A.; Ruzankina, J.; Afanasyev, M.; Lukyanov, N.; Redka, D.; Paklinov, N.

2018-02-01

A solid-phase photosensitizer based on aggregated C60 fullerene and graphene oxide for photodynamic inactivation of pathogens in biological fluids was studied. The most promising technologies of inactivation include the photodynamic effect, which consists in the inactivation of infectious agents by active oxygen forms (including singlet oxygen), formed when light is activated by the photosensitizer introduced into the plasma. Research shows features of solid-phase systems based on graphene and fullerene C60 oxide, which is a combination of an effective inactivating pathogens (for example, influenza viruses) reactive oxygen species formed upon irradiation of the photosensitizer in aqueous and biological fluids, a high photostability fullerene coatings and the possibility of full recovery photosensitizer from the biological environment after the photodynamic action.

Copper deficiency can limit nitrification in biological rapid sand filters for drinking water production.

PubMed

Wagner, Florian B; Nielsen, Peter Borch; Boe-Hansen, Rasmus; Albrechtsen, Hans-Jørgen

2016-05-15

Incomplete nitrification in biological filters during drinking water treatment is problematic, as it compromises drinking water quality. Nitrification problems can be caused by a lack of nutrients for the nitrifying microorganisms. Since copper is an important element in one of the essential enzymes in nitrification, we investigated the effect of copper dosing on nitrification in different biological rapid sand filters treating groundwater. A lab-scale column assay with filter material from a water works demonstrated that addition of a trace metal mixture, including copper, increased ammonium removal compared to a control without addition. Subsequently, another water works was investigated in full-scale, where copper influent concentrations were below 0.05 μg Cu L(-1) and nitrification was incomplete. Copper dosing of less than 5 μg Cu L(-1) to a full-scale filter stimulated ammonium removal within one day, and doubled the filter's removal from 0.22 to 0.46 g NH4-N m(-3) filter material h(-1) within 20 days. The location of ammonium and nitrite oxidation shifted upwards in the filter, with an almost 14-fold increase in ammonium removal rate in the filter's top 10 cm, within 57 days of dosing. To study the persistence of the stimulation, copper was dosed to another filter at the water works for 42 days. After dosing was stopped, nitrification remained complete for at least 238 days. Filter effluent concentrations of up to 1.3 μg Cu L(-1) confirmed that copper fully penetrated the filters, and determination of copper content on filter media revealed a buildup of copper during dosing. The amount of copper stored on filter material gradually decreased after dosing stopped; however at a slower rate than it accumulated. Continuous detection of copper in the filter effluent confirmed a release of copper to the bulk phase. Overall, copper dosing to poorly performing biological rapid sand filters increased ammonium removal rates significantly, achieving effluent concentrations of below 0.01 mg NH4-N L(-1), and had a long-term effect on nitrification performance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Establishment of a sensor testbed at NIST for plant productivity monitoring

NASA Astrophysics Data System (ADS)

Allen, D. W.; Hutyra, L.; Reinmann, A.; Trlica, A.; Marrs, J.; Jones, T.; Whetstone, J. R.; Logan, B.; Reblin, J.

2017-12-01

Accurate assessments of biogenic carbon fluxes is challenging. Correlating optical signatures to plant activity allows for monitoring large regions. New methods, including solar-induced fluorescence (SIF), promise to provide more timely and accurate estimate of plant activity, but we are still developing a full understanding of the mechanistic leakage between plant assimilation of carbon and SIF. We have initiated a testbed to facilitate the evaluation of sensors and methods for remote monitoring of plant activity at the NIST headquarters. The test bed utilizes a forested area of mature trees in a mixed urban environment. A 1 hectare plot within the 26 hectare forest has been instrumented for ecophysiological measurements with an edge (100 m long) that is persistently monitored with multimodal optical sensors (SIF spectrometers, hyperspectral imagers, thermal infrared imaging, and lidar). This biological testbed has the advantage of direct access to the national scales maintained by NIST of measurements related to both the physical and optical measurements of interest. We offer a description of the test site, the sensors, and preliminary results from the first season of observations for ecological, physiological, and remote sensing based estimates of ecosystem productivity.

Scaling Laws Applied to a Modal Formulation of the Aeroservoelastic Equations

NASA Technical Reports Server (NTRS)

Pototzky, Anthony S.

2002-01-01

A method of scaling is described that easily converts the aeroelastic equations of motion of a full-sized aircraft into ones of a wind-tunnel model. To implement the method, a set of rules is provided for the conversion process involving matrix operations with scale factors. In addition, a technique for analytically incorporating a spring mounting system into the aeroelastic equations is also presented. As an example problem, a finite element model of a full-sized aircraft is introduced from the High Speed Research (HSR) program to exercise the scaling method. With a set of scale factor values, a brief outline is given of a procedure to generate the first-order aeroservoelastic analytical model representing the wind-tunnel model. To verify the scaling process as applied to the example problem, the root-locus patterns from the full-sized vehicle and the wind-tunnel model are compared to see if the root magnitudes scale with the frequency scale factor value. Selected time-history results are given from a numerical simulation of an active-controlled wind-tunnel model to demonstrate the utility of the scaling process.

Proven Alternatives for Aboveground Treatment of Arsenic in Groundwater

DTIC Science & Technology

2002-10-01

Contaminant of Concern by Mediaa Media Number of Sites Groundwater 380 Soil 372 Sediment 154 Surface Water 86 Debris 77 Sludge 45 Solid Waste 30 Leachate ...issue paper does not address three technologies that have been used to treat water containing arsenic: • Biological treatment • Phytoremediation ...arsenic in water, and no aboveground treatments of groundwater conducted at full scale were found. Phytoremediation and electrokinetics are not

Need for multiscale planning for conservation of urban bats.

PubMed

Gallo, Travis; Lehrer, Elizabeth W; Fidino, Mason; Kilgour, R Julia; Wolff, Patrick J; Magle, Seth B

2017-11-10

For over a century there have been continual efforts to incorporate nature into urban planning. These efforts (i.e., urban reconciliation) aim to manage and create habitats that support biodiversity within cities. Given that species select habitat at different spatial scales, understanding the scale at which urban species respond to their environment is critical to the success of urban reconciliation efforts. We assessed species-habitat relationships for common bat species at 50-m, 500-m, and 1 km spatial scales in the Chicago (U.S.A.) metropolitan area and predicted bat activity across the greater Chicago region. Habitat characteristics across all measured scales were important predictors of silver-haired bat (Lasionycteris noctivagans) and eastern red bat (Lasiurus borealis) activity, and big brown bat (Eptesicus fuscus) activity was significantly lower at urban sites relative to rural sites. Open vegetation had a negative effect on silver-haired bat activity at the 50-m scale but a positive effect at the 500-m scale, indicating potential shifts in the relative importance of some habitat characteristics at different scales. These results demonstrate that localized effects may be constrained by broader spatial patterns. Our findings highlight the importance of considering scale in urban reconciliation efforts and our landscape predictions provide information that can help prioritize urban conservation work. © 2017 Society for Conservation Biology.

Seasonal bacterial community succession in four typical wastewater treatment plants: correlations between core microbes and process performance.

PubMed

Zhang, Bo; Yu, Quanwei; Yan, Guoqi; Zhu, Hubo; Xu, Xiang Yang; Zhu, Liang

2018-03-15

To understand the seasonal variation of the activated sludge (AS) bacterial community and identify core microbes in different wastewater processing systems, seasonal AS samples were taken from every biological treatment unit within 4 full-scale wastewater treatment plants. These plants adopted A2/O, A/O and oxidation ditch processes and were active in the treatment of different types and sources of wastewater, some domestic and others industrial. The bacterial community composition was analyzed using high-throughput sequencing technology. The correlations among microbial community structure, dominant microbes and process performance were investigated. Seasonal variation had a stronger impact on the AS bacterial community than any variation within different wastewater treatment system. Facing seasonal variation, the bacterial community within the oxidation ditch process remained more stable those in either the A2/O or A/O processes. The core genera in domestic wastewater treatment systems were Nitrospira, Caldilineaceae, Pseudomonas and Lactococcus. The core genera in the textile dyeing and fine chemical industrial wastewater treatment systems were Nitrospira, Thauera and Thiobacillus.

Amyris, Inc. Integrated Biorefinery Project Summary Final Report - Public Version

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

Gray, David; Sato, Suzanne; Garcia, Fernando

The Amyris pilot-scale Integrated Biorefinery (IBR) leveraged Amyris synthetic biology and process technology experience to upgrade Amyris’s existing Emeryville, California pilot plant and fermentation labs to enable development of US-based production capabilities for renewable diesel fuel and alternative chemical products. These products were derived semi-synthetically from high-impact biomass feedstocks via microbial fermentation to the 15-carbon intermediate farnesene, with subsequent chemical finishing to farnesane. The Amyris IBR team tested and provided methods for production of diesel and alternative chemical products from sweet sorghum, and other high-impact lignocellulosic feedstocks, at pilot scale. This enabled robust techno-economic analysis (TEA), regulatory approvals, and amore » basis for full-scale manufacturing processes and facility design.« less

Bacterial communities and enzymatic activities in the vegetation-activated sludge process (V-ASP) and related advantages by comparison with conventional constructed wetland.

PubMed

Yuan, Jiajia; Dong, Wenyi; Sun, Feiyun; Zhao, Ke; Du, Changhang; Shao, Yunxian

2016-11-01

A new-developed vegetation-activated sludge process (V-ASP) was implemented for decentralized domestic wastewater treatment, and studied in lab-scale and full-scale. The main purpose of this work was the investigation of biomass activities and microbial communities in V-ASP by comparison with conventional constructed wetland (CW), to unveil the causations of its consistently higher pollutants removal efficiencies. Compared with CWs, V-ASP has greater vegetation nitrogen and phosphorus uptake rates, higher biomass and enzymatic activities, and more bacteria community diversity. The microbial community structure was comprehensively analyzed by using high-throughput sequencing. It was observed that Proteobacteria was dominated in both CWs and V-ASPs, while their subdivisions distribution was rather different. V-ASPs contained a higher nitrite-oxidizing bacteria (Nitrospira) abundances that resulted in a consistently better nitrogen removal efficiency. Hence, a long-term experiment of full-scale V-ASP displayed stably excellent capability in resistance of influent loading shocks and seasonal temperature effect. Copyright © 2016 Elsevier Ltd. All rights reserved.

Behavioral characteristics of very-low-birth-weight infants of varying biologic risk at 6, 15, and 24 months of age.

PubMed

Oehler, J M; Thompson, R J; Goldstein, R F; Gustafson, K E; Brazy, J E

1996-01-01

To explore the relationship between developmental outcome and behavior of very-low-birth-weight (VLBW) infants (< or = 1500 g) at high and low biologic risk. Descriptive, ex post facto. Clinic for follow-up of infants at high risk. A convenience sample of 102 VLBW infants, free of major congenital anomalies, who completed 6-, 15-, and 24-month developmental testing and who were part of a larger study of 274 VLBW infants. Bayley Scales of Infant Development. Infants at high biologic risk, versus infants at low biologic risk, were less attentive and active through age 15 months and were less adept in gross and fine motor skills through age 24 months (p < or = 0.05-0.001). Infants with continuous delay were less attentive than infants with no delay or late delay through age 24 months, less active through age 15 months (p < or = 0.001-0.001), and less skilled in motor behaviors through age 24 months (p < or = 0.05-0.001). Infants at high biologic risk and infants with developmental delays are less attentive, less active, and less skilled in motor tasks during the first 15-24 months of life, suggesting an association between biologic risk and behavior and developmental delay and behavior.

Auditory Power-Law Activation Avalanches Exhibit a Fundamental Computational Ground State

NASA Astrophysics Data System (ADS)

Stoop, Ruedi; Gomez, Florian

2016-07-01

The cochlea provides a biological information-processing paradigm that we are only beginning to understand in its full complexity. Our work reveals an interacting network of strongly nonlinear dynamical nodes, on which even a simple sound input triggers subnetworks of activated elements that follow power-law size statistics ("avalanches"). From dynamical systems theory, power-law size distributions relate to a fundamental ground state of biological information processing. Learning destroys these power laws. These results strongly modify the models of mammalian sound processing and provide a novel methodological perspective for understanding how the brain processes information.

Regional synchrony in full-scale activated sludge bioreactors due to deterministic microbial community assembly

PubMed Central

Griffin, James S; Wells, George F

2017-01-01

Seasonal community structure and regionally synchronous population dynamics have been observed in natural microbial ecosystems, but have not been well documented in wastewater treatment bioreactors. Few studies of community dynamics in full-scale activated sludge systems facing similar meteorological conditions have been done to compare the importance of deterministic and neutral community assembly mechanisms. We subjected weekly activated sludge samples from six regional full-scale bioreactors at four wastewater treatment plants obtained over 1 year to Illumina sequencing of 16S ribosomal RNA genes, resulting in a library of over 17 million sequences. All samples derived from reactors treating primarily municipal wastewater. Despite variation in operational characteristics and location, communities displayed temporal synchrony at the individual operational taxonomic unit (OTU), broad phylogenetic affiliation and community-wide scale. Bioreactor communities were dominated by 134 abundant and highly regionally synchronized OTU populations that accounted for over 50% of the total reads. Non-core OTUs displayed abundance-dependent population synchrony. Alpha diversity varied by reactor, but showed a highly reproducible and synchronous seasonal fluctuation. Community similarity was dominated by seasonal changes, but individual reactors maintained minor stable differences after 1 year. Finally, the impacts of mass migration driven by direct biomass transfers between reactors was investigated, but had no significant effect on community similarity or diversity in the sink community. Our results show that population dynamics in activated sludge bioreactors are consistent with niche-driven assembly guided by seasonal temperature fluctuations. PMID:27996980

Biologically active protein fragments containing specific binding regions of serum albumin or related proteins

NASA Technical Reports Server (NTRS)

Carter, Daniel C. (Inventor)

1998-01-01

In accordance with the present invention, biologically active protein fragments can be constructed which contain only those specific portions of the serum albumin family of proteins such as regions known as subdomains IIA and IIIA which are primarily responsible for the binding properties of the serum albumins. The artificial serums that can be prepared from these biologically active protein fragments are advantageous in that they can be produced much more easily than serums containing the whole albumin, yet still retain all or most of the original binding potential of the full albumin proteins. In addition, since the protein fragment serums of the present invention can be made from non-natural sources using conventional recombinant DNA techniques, they are far safer than serums containing natural albumin because they do not carry the potentially harmful viruses and other contaminants that will be found in the natural substances.

Use of food waste-recycling wastewater as an alternative carbon source for denitrification process: A full-scale study.

PubMed

Kim, Eunji; Shin, Seung Gu; Jannat, Md Abu Hanifa; Tongco, Jovale Vincent; Hwang, Seokhwan

2017-12-01

Using organic wastes as an alternative to commercial carbon sources could be beneficial by reducing costs and environmental impacts. In this study, food waste-recycling wastewater (FRW) was evaluated as an alternative carbon source for biological denitrification over a period of seven months in a full-scale sewage wastewater treatment plant. The denitrification performance was stable with a mean nitrate removal efficiency of 97.2%. Propionate was initially the most persistent volatile fatty acid, but was completely utilized after 19days. Eubacteriacea, Saprospiraceae, Rhodocyclaceae and Comamonadaceae were the major bacterial families during FRW treatment and were regarded as responsible for hydrolysis (former two) and nitrate removal (latter two) of FRW. These results demonstrate that FRW can be an effective external carbon source; process stabilization was linked to the acclimation and function of bacterial populations to the change of carbon source. Copyright © 2017 Elsevier Ltd. All rights reserved.

Energy savings by reduced mixing in aeration tanks: results from a full scale investigation and long term implementation at Avedoere wastewater treatment plant.

PubMed

Sharma, A K; Guildal, T; Thomsen, H R; Jacobsen, B N

2011-01-01

The aim of this project was to investigate the potential of reducing number of mixers in the biological treatment process and thereby achieve energy and economical savings and contribute to cleaner environment. The project was carried out at Avedoere wastewater treatment plant and a full scale investigation was conducted to study the effect of reduced mixing on flow velocity, suspended solid sedimentation, concentration gradients of oxygen and SS with depth and treatment efficiency. The only negative effect observed was on flow velocity; however the velocity was above the critical velocity. The plant has been operating with 50% of its designed number of mixers since September 2007 and long term results also confirm that reduced mixing did not have any negative effect on treatment efficiency. The estimated yearly electricity saving is 0.75 GWh/year.

Unexpected Levels of Biological Activity during the Polar Night Offer New Perspectives on a Warming Arctic.

PubMed

Berge, Jørgen; Daase, Malin; Renaud, Paul E; Ambrose, William G; Darnis, Gerald; Last, Kim S; Leu, Eva; Cohen, Jonathan H; Johnsen, Geir; Moline, Mark A; Cottier, Finlo; Varpe, Øystein; Shunatova, Natalia; Bałazy, Piotr; Morata, Nathalie; Massabuau, Jean-Charles; Falk-Petersen, Stig; Kosobokova, Ksenia; Hoppe, Clara J M; Węsławski, Jan Marcin; Kukliński, Piotr; Legeżyńska, Joanna; Nikishina, Daria; Cusa, Marine; Kędra, Monika; Włodarska-Kowalczuk, Maria; Vogedes, Daniel; Camus, Lionel; Tran, Damien; Michaud, Emma; Gabrielsen, Tove M; Granovitch, Andrei; Gonchar, Anya; Krapp, Rupert; Callesen, Trine A

2015-10-05

The current understanding of Arctic ecosystems is deeply rooted in the classical view of a bottom-up controlled system with strong physical forcing and seasonality in primary-production regimes. Consequently, the Arctic polar night is commonly disregarded as a time of year when biological activities are reduced to a minimum due to a reduced food supply. Here, based upon a multidisciplinary ecosystem-scale study from the polar night at 79°N, we present an entirely different view. Instead of an ecosystem that has entered a resting state, we document a system with high activity levels and biological interactions across most trophic levels. In some habitats, biological diversity and presence of juvenile stages were elevated in winter months compared to the more productive and sunlit periods. Ultimately, our results suggest a different perspective regarding ecosystem function that will be of importance for future environmental management and decision making, especially at a time when Arctic regions are experiencing accelerated environmental change [1]. Copyright © 2015 Elsevier Ltd. All rights reserved.

Short-Term Effect of Vermicompost Application on Biological Properties of an Alkaline Soil with High Lime Content from Mediterranean Region of Turkey

PubMed Central

Uz, Ilker; Tavali, Ismail Emrah

2014-01-01

This study was conducted to investigate direct short-term impact of vermicompost on some soil biological properties by monitoring changes after addition of vermicompost as compared to farmyard manure in an alkaline soil with high lime content from semiarid Mediterranean region of Turkey. For this purpose, mixtures of soil and organic fertilizers in different doses were incubated under greenhouse condition. Soil samples collected in regular intervals were analyzed for biological parameters including dehydrogenase, β-glucosidase, urease, alkaline phosphatase activities, and total number of aerobic mesophilic bacteria. Even though soil dehydrogenase activity appeared to be dose-independent based on overall evaluation, organic amendments were found to elevate dehydrogenase activity when sampling periods are evaluated individually. β-glucosidase, urease, alkaline phosphatase activity, and aerobic mesophilic bacterial numbers in vermicompost treatments fluctuated but remained significantly above the control. A slight but statistically significant difference was detected between organic amendments in terms of urease activity. Vermicompost appeared to more significantly increase bacterial number in soil. Clearly, vermicompost has a potential to be used as an alternative to farmyard manure to improve and maintain soil biological activity in alkaline calcareous soils from the Mediterranean region of Turkey. Further studies are needed to assess its full potential for these soils. PMID:25254238

Impact of oxidation on protein therapeutics: Conformational dynamics of intact and oxidized acid-β-glucocerebrosidase at near-physiological pH

PubMed Central

Bobst, Cedric E; Thomas, John J; Salinas, Paul A; Savickas, Philip; Kaltashov, Igor A

2010-01-01

The solution dynamics of an enzyme acid-β-glucocerebrosidase (GCase) probed at a physiologically relevant (lysosomal) pH by hydrogen/deuterium exchange mass spectrometry (HDX-MS) reveals very uneven distribution of backbone amide protection across the polypeptide chain. Highly mobile segments are observed even within the catalytic cavity alongside highly protective segments, highlighting the importance of the balance between conformational stability and flexibility for enzymatic activity. Forced oxidation of GCase that resulted in a 40–60% reduction in in vitro biological activity affects the stability of some key structural elements within the catalytic site. These changes in dynamics occur on a longer time scale that is irrelevant for catalysis, effectively ruling out loss of structure in the catalytic site as a major factor contributing to the reduction of the catalytic activity. Oxidation also leads to noticeable destabilization of conformation in remote protein segments on a much larger scale, which is likely to increase the aggregation propensity of GCase and affect its bioavailability. Therefore, it appears that oxidation exerts its negative impact on the biological activity of GCase indirectly, primarily through accelerated aggregation and impaired trafficking. PMID:20945356

[Structural Study in the Platform for Drug Discovery, Informatics, and Structural Life Science].

PubMed

Senda, Toshiya

2016-01-01

The Platform for Drug Discovery, Informatics, and Structural Life Science (PDIS), which has been launched since FY2012, is a national project in the field of structural biology. The PDIS consists of three cores - structural analysis, control, and informatics - and aims to support life science researchers who are not familiar with structural biology. The PDIS project is able to provide full-scale support for structural biology research. The support provided by the PDIS project includes protein purification with various expression systems, large scale protein crystallization, crystal structure determination, small angle scattering (SAXS), NMR, electron microscopy, bioinformatics, etc. In order to utilize these methods of support, PDIS users need to submit an application form to the one-stop service office. Submitted applications will be reviewed by three referees. It is strongly encouraged that PDIS users have sufficient discussion with researchers in the PDIS project before submitting the application. This discussion is very useful in the process of project design, particularly for beginners in structural biology. In addition to this user support, the PDIS project has conducted R&D, which includes the development of synchrotron beamlines. In the PDIS project, PF and SPring-8 have developed beamlines for micro-crystallography, high-throughput data collection, supramolecular assembly, and native single anomalous dispersion (SAD) phasing. The newly developed beamlines have been open to all users, and have accelerated structural biology research. Beamlines for SAXS have also been developed, which has dramatically increased bio-SAXS users.

Fungal Phytotoxins with Potential Herbicidal Activity to Control Chenopodium album.

PubMed

Cimmino, Alessio; Masi, Marco; Evidente, Marco; Evidente, Antonio

2015-06-01

This review deals with the isolation and chemical and biological characterization of phytotoxins produced by Ascochyta caulina and Phoma chenopodiicola proposed as mycoherbicides for the biological control of Chenopodium album, a worldwide spread weed which causes serious problems to some agrarian crops, including sugar beet and maize. Studies on the structure activity relationships and on the modes of actions of toxins isolated are also described, as well as the optimization of analytical methods focused on selection of the best fungal toxin producers. The attempts to scale up production of these phytotoxins aimed to obtain sufficient amounts for their application in greenhouse and field trials are also reported.

Axinellamines as Broad-Spectrum Antibacterial Agents: Scalable Synthesis and Biology

PubMed Central

2015-01-01

Antibiotic-resistant bacteria present an ongoing challenge to both chemists and biologists as they seek novel compounds and modes of action to out-maneuver continually evolving resistance pathways, especially against Gram-negative strains. The dimeric pyrrole–imidazole alkaloids represent a unique marine natural product class with diverse primary biological activity and chemical architecture. This full account traces the strategy used to develop a second-generation route to key spirocycle 9, culminating in a practical synthesis of the axinellamines and enabling their discovery as broad-spectrum antibacterial agents, with promising activity against both Gram-positive and Gram-negative bacteria. While their detailed mode of antibacterial action remains unclear, the axinellamines appear to cause secondary membrane destabilization and impart an aberrant cellular morphology consistent with the inhibition of normal septum formation. This study serves as a rare example of a natural product initially reported to be devoid of biological activity surfacing as an active antibacterial agent with an intriguing mode of action. PMID:25328977

Full-scale monitoring of wind and suspension bridge response

NASA Astrophysics Data System (ADS)

Snæbjörnsson, J. T.; Jakobsen, J. B.; Cheynet, E.; Wang, J.

2017-12-01

Monitoring of real structures is important for many reasons. For structures susceptible to environmental actions, full-scale observations can provide valuable information about the environmental conditions at the site, as well as the characteristics of the excitation acting on the structure. The recorded data, if properly analyzed, can be used to validate and/or update experiments and models used in the design of new structures, such as the load description and modelling of the structural response. Various aspects of full-scale monitoring are discussed in the paper and the full-scale wind engineering laboratory at the Lysefjord suspension bridge introduced. The natural excitation of the bridge comes from wind and traffic. The surrounding terrain is complex and its effect on the wind flow can only be fully studied on site, in full-scale. The monitoring program and associated data analysis are described. These include various studies of the relevant turbulence characteristics, identification of dynamic properties and estimation of wind- and traffic-induced response parameters. The overall monitoring activity also included a novel application of the remote optical sensing in bridge engineering, which is found to have an important potential to complement traditional “single-point” wind observations by sonic anemometers.

Biologically important compounds in synfuels processes

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

Clark, B R; Ho, C; Griest, W H

1980-01-01

Crude products, by-products and wastes from synfuel processes contain a broad spectrum of chemical compounds - many of which are active in biological systems. Discerning which compound classes are most important is necessary in order to establish effective control over release or exposure. Polycyclic aromatic hydrocarbons (PAH), multialkylated PAH, primary aromatic amines and N-heterocyclic PAH are significant contributors to the overall mutagenic activities of a large number of materials examined. Ames test data show that the basic, primary aromatic amine fraction is the most active. PAHs, multialkylated PAHs and N-heterocyclic PAHs are all components of the neutral fraction. In nearlymore » all cases, the neutral fractions contribute the largest portion of the mutagenic activity, while the basic primary aromatic amine fractions have the highest specific activity. Neutral fractions are usually the largest (wt %) whereas the total basic fractions are small by comparison; thus, the overall greater contribution of the neutral fraction to the mutagenic activity of most samples. Biologically active constituents are isolated in preparative scale amounts from complex mixtures utilizing combinations of liquid-liquid extraction and various liquid chromatographic column-eluant combinations. Fractions are characterized using a combination of spectroscopic techniques and gas chromatography/mass spectrometry.« less

Dpp Signaling Activity Requires Pentagone to Scale with Tissue Size in the Growing Drosophila Wing Imaginal Disc

PubMed Central

Pyrowolakis, George; Bergmann, Sven; Affolter, Markus

2011-01-01

The wing of the fruit fly, Drosophila melanogaster, with its simple, two-dimensional structure, is a model organ well suited for a systems biology approach. The wing arises from an epithelial sac referred to as the wing imaginal disc, which undergoes a phase of massive growth and concomitant patterning during larval stages. The Decapentaplegic (Dpp) morphogen plays a central role in wing formation with its ability to co-coordinately regulate patterning and growth. Here, we asked whether the Dpp signaling activity scales, i.e. expands proportionally, with the growing wing imaginal disc. Using new methods for spatial and temporal quantification of Dpp activity and its scaling properties, we found that the Dpp response scales with the size of the growing tissue. Notably, scaling is not perfect at all positions in the field and the scaling of target gene domains is ensured specifically where they define vein positions. We also found that the target gene domains are not defined at constant concentration thresholds of the downstream Dpp activity gradients P-Mad and Brinker. Most interestingly, Pentagone, an important secreted feedback regulator of the pathway, plays a central role in scaling and acts as an expander of the Dpp gradient during disc growth. PMID:22039350

Allometric Scaling of the Active Hematopoietic Stem Cell Pool across Mammals

PubMed Central

Dingli, David; Pacheco, Jorge M.

2006-01-01

Background Many biological processes are characterized by allometric relations of the type Y = Y 0 Mb between an observable Y and body mass M, which pervade at multiple levels of organization. In what regards the hematopoietic stem cell pool, there is experimental evidence that the size of the hematopoietic stem cell pool is conserved in mammals. However, demands for blood cell formation vary across mammals and thus the size of the active stem cell compartment could vary across species. Methodology/Principle Findings Here we investigate the allometric scaling of the hematopoietic system in a large group of mammalian species using reticulocyte counts as a marker of the active stem cell pool. Our model predicts that the total number of active stem cells, in an adult mammal, scales with body mass with the exponent ¾. Conclusion/Significance The scaling predicted here provides an intuitive justification of the Hayflick hypothesis and supports the current view of a small active stem cell pool supported by a large, quiescent reserve. The present scaling shows excellent agreement with the available (indirect) data for smaller mammals. The small size of the active stem cell pool enhances the role of stochastic effects in the overall dynamics of the hematopoietic system. PMID:17183646

Nanoelectronics-biology frontier: From nanoscopic probes for action potential recording in live cells to three-dimensional cyborg tissues.

PubMed

Duan, Xiaojie; Fu, Tian-Ming; Liu, Jia; Lieber, Charles M

2013-08-01

Semiconductor nanowires configured as the active channels of field-effect transistors (FETs) have been used as detectors for high-resolution electrical recording from single live cells, cell networks, tissues and organs. Extracellular measurements with substrate supported silicon nanowire (SiNW) FETs, which have projected active areas orders of magnitude smaller than conventional microfabricated multielectrode arrays (MEAs) and planar FETs, recorded action potential and field potential signals with high signal-to-noise ratio and temporal resolution from cultured neurons, cultured cardiomyocytes, acute brain slices and whole animal hearts. Measurements made with modulation-doped nanoscale active channel SiNW FETs demonstrate that signals recorded from cardiomyocytes are highly localized and have improved time resolution compared to larger planar detectors. In addition, several novel three-dimensional (3D) transistor probes, which were realized using advanced nanowire synthesis methods, have been implemented for intracellular recording. These novel probes include (i) flexible 3D kinked nanowire FETs, (ii) branched intracellular nanotube SiNW FETs, and (iii) active silicon nanotube FETs. Following phospholipid modification of the probes to mimic the cell membrane, the kinked nanowire, branched intracellular nanotube and active silicon nanotube FET probes recorded full-amplitude intracellular action potentials from spontaneously firing cardiomyocytes. Moreover, these probes demonstrated the capability of reversible, stable, and long-term intracellular recording, thus indicating the minimal invasiveness of the new nanoscale structures and suggesting biomimetic internalization via the phospholipid modification. Simultaneous, multi-site intracellular recording from both single cells and cell networks were also readily achieved by interfacing independently addressable nanoprobe devices with cells. Finally, electronic and biological systems have been seamlessly merged in 3D for the first time using macroporous nanoelectronic scaffolds that are analogous to synthetic tissue scaffold and the extracellular matrix in tissue. Free-standing 3D nanoelectronic scaffolds were cultured with neurons, cardiomyocytes and smooth muscle cells to yield electronically-innervated synthetic or 'cyborg' tissues. Measurements demonstrate that innervated tissues exhibit similar cell viability as with conventional tissue scaffolds, and importantly, demonstrate that the real-time response to drugs and pH changes can be mapped in 3D through the tissues. These results open up a new field of research, wherein nanoelectronics are merged with biological systems in 3D thereby providing broad opportunities, ranging from a nanoelectronic/tissue platform for real-time pharmacological screening in 3D to implantable 'cyborg' tissues enabling closed-loop monitoring and treatment of diseases. Furthermore, the capability of high density scale-up of the above extra- and intracellular nanoscopic probes for action potential recording provide important tools for large-scale high spatio-temporal resolution electrical neural activity mapping in both 2D and 3D, which promises to have a profound impact on many research areas, including the mapping of activity within the brain.

Nanoelectronics-biology frontier: From nanoscopic probes for action potential recording in live cells to three-dimensional cyborg tissues

PubMed Central

Duan, Xiaojie; Fu, Tian-Ming; Liu, Jia; Lieber, Charles M.

2013-01-01

Summary Semiconductor nanowires configured as the active channels of field-effect transistors (FETs) have been used as detectors for high-resolution electrical recording from single live cells, cell networks, tissues and organs. Extracellular measurements with substrate supported silicon nanowire (SiNW) FETs, which have projected active areas orders of magnitude smaller than conventional microfabricated multielectrode arrays (MEAs) and planar FETs, recorded action potential and field potential signals with high signal-to-noise ratio and temporal resolution from cultured neurons, cultured cardiomyocytes, acute brain slices and whole animal hearts. Measurements made with modulation-doped nanoscale active channel SiNW FETs demonstrate that signals recorded from cardiomyocytes are highly localized and have improved time resolution compared to larger planar detectors. In addition, several novel three-dimensional (3D) transistor probes, which were realized using advanced nanowire synthesis methods, have been implemented for intracellular recording. These novel probes include (i) flexible 3D kinked nanowire FETs, (ii) branched intracellular nanotube SiNW FETs, and (iii) active silicon nanotube FETs. Following phospholipid modification of the probes to mimic the cell membrane, the kinked nanowire, branched intracellular nanotube and active silicon nanotube FET probes recorded full-amplitude intracellular action potentials from spontaneously firing cardiomyocytes. Moreover, these probes demonstrated the capability of reversible, stable, and long-term intracellular recording, thus indicating the minimal invasiveness of the new nanoscale structures and suggesting biomimetic internalization via the phospholipid modification. Simultaneous, multi-site intracellular recording from both single cells and cell networks were also readily achieved by interfacing independently addressable nanoprobe devices with cells. Finally, electronic and biological systems have been seamlessly merged in 3D for the first time using macroporous nanoelectronic scaffolds that are analogous to synthetic tissue scaffold and the extracellular matrix in tissue. Free-standing 3D nanoelectronic scaffolds were cultured with neurons, cardiomyocytes and smooth muscle cells to yield electronically-innervated synthetic or ‘cyborg’ tissues. Measurements demonstrate that innervated tissues exhibit similar cell viability as with conventional tissue scaffolds, and importantly, demonstrate that the real-time response to drugs and pH changes can be mapped in 3D through the tissues. These results open up a new field of research, wherein nanoelectronics are merged with biological systems in 3D thereby providing broad opportunities, ranging from a nanoelectronic/tissue platform for real-time pharmacological screening in 3D to implantable ‘cyborg’ tissues enabling closed-loop monitoring and treatment of diseases. Furthermore, the capability of high density scale-up of the above extra- and intracellular nanoscopic probes for action potential recording provide important tools for large-scale high spatio-temporal resolution electrical neural activity mapping in both 2D and 3D, which promises to have a profound impact on many research areas, including the mapping of activity within the brain. PMID:24073014

Truss Optimization for a Manned Nuclear Electric Space Vehicle using Genetic Algorithms

NASA Technical Reports Server (NTRS)

Benford, Andrew; Tinker, Michael L.

2004-01-01

The purpose of this paper is to utilize the genetic algorithm (GA) optimization method for structural design of a nuclear propulsion vehicle. Genetic algorithms provide a guided, random search technique that mirrors biological adaptation. To verify the GA capabilities, other traditional optimization methods were used to generate results for comparison to the GA results, first for simple two-dimensional structures, and then for full-scale three-dimensional truss designs.

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

Not Available

The Istanbul Water and Sewerage Administration (ISKI) was formed in 1982, and since that time a phased program of sewage collection and treatment has been implemented. Fifteen waste treatment plants, ranging from full scale biological treatment to pre-treatment, are in the design or planning stage, and over 2,000 km of collection lines have been installed. Concurrent with the program is an increasing emphasis on industrial waste treatment, which results in the production of both non-hazardous and hazardous sludges.

Materials and Process Activities for NASA's Composite Crew Module

NASA Technical Reports Server (NTRS)

Polis, Daniel L.

2012-01-01

In January 2007, the NASA Administrator and Associate Administrator for the Exploration Systems Mission Directorate chartered the NASA Engineering and Safety Center (NESC) to design, build, and test a full-scale Composite Crew Module (CCM). The overall goal of the CCM project was to develop a team from the NASA family with hands-on experience in composite design, manufacturing, and testing in anticipation of future space exploration systems being made of composite materials. The CCM project was planned to run concurrently with the Orion project s baseline metallic design within the Constellation Program so that features could be compared and discussed without inducing risk to the overall Program. The materials and process activities were prioritized based on a rapid prototype approach. This approach focused developmental activities on design details with greater risk and uncertainty, such as out-of-autoclave joining, over some of the more traditional lamina and laminate building block levels. While process development and associated building block testing were performed, several anomalies were still observed at the full-scale level due to interactions between process robustness and manufacturing scale-up. This paper describes the process anomalies that were encountered during the CCM development and the subsequent root cause investigations that led to the final design solutions. These investigations highlight the importance of full-scale developmental work early in the schedule of a complex composite design/build project.

Dewetting and Hydrophobic Interaction in Physical and Biological Systems

PubMed Central

Berne, Bruce J.; Weeks, John D.; Zhou, Ruhong

2013-01-01

Hydrophobicity manifests itself differently on large and small length scales. This review focuses on large length scale hydrophobicity, particularly on dewetting at single hydrophobic surfaces and drying in regions bounded on two or more sides by hydrophobic surfaces. We review applicable theories, simulations and experiments pertaining to large scale hydrophobicity in physical and biomoleclar systems and clarify some of the critical issues pertaining to this subject. Given space constraints, we could not review all of the significant and interesting work in this very active field. PMID:18928403

Sense and sensitivity in bioprocessing-detecting cellular metabolites with biosensors.

PubMed

Dekker, Linda; Polizzi, Karen M

2017-10-01

Biosensors use biological elements to detect or quantify an analyte of interest. In bioprocessing, biosensors are employed to monitor key metabolites. There are two main types: fully biological systems or biological recognition coupled with physical/chemical detection. New developments in chemical biosensors include multiplexed detection using microfluidics. Synthetic biology can be used to engineer new biological biosensors with improved characteristics. Although there have been few biosensors developed for bioprocessing thus far, emerging trends can be applied in the future. A range of new platform technologies will enable rapid engineering of new biosensors based on transcriptional activation, riboswitches, and Förster Resonance Energy Transfer. However, translation to industry remains a challenge and more research into the robustness biosensors at scale is needed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genome-scale biological models for industrial microbial systems.

PubMed

Xu, Nan; Ye, Chao; Liu, Liming

2018-04-01

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

Defining ecologically relevant scales for spatial protection with long-term data on an endangered seabird and local prey availability.

PubMed

Sherley, Richard B; Botha, Philna; Underhill, Les G; Ryan, Peter G; van Zyl, Danie; Cockcroft, Andrew C; Crawford, Robert J M; Dyer, Bruce M; Cook, Timothée R

2017-12-01

Human activities are important drivers of marine ecosystem functioning. However, separating the synergistic effects of fishing and environmental variability on the prey base of nontarget predators is difficult, often because prey availability estimates on appropriate scales are lacking. Understanding how prey abundance at different spatial scales links to population change can help integrate the needs of nontarget predators into fisheries management by defining ecologically relevant areas for spatial protection. We investigated the local population response (number of breeders) of the Bank Cormorant (Phalacrocorax neglectus), a range-restricted endangered seabird, to the availability of its prey, the heavily fished west coast rock lobster (Jasus lalandii). Using Bayesian state-space modeled cormorant counts at 3 colonies, 22 years of fisheries-independent data on local lobster abundance, and generalized additive modeling, we determined the spatial scale pertinent to these relationships in areas with different lobster availability. Cormorant numbers responded positively to lobster availability in the regions with intermediate and high abundance but not where regime shifts and fishing pressure had depleted lobster stocks. The relationships were strongest when lobsters 20-30 km offshore of the colony were considered, a distance greater than the Bank Cormorant's foraging range when breeding, and may have been influenced by prey availability for nonbreeding birds, prey switching, or prey ecology. Our results highlight the importance of considering the scale of ecological relationships in marine spatial planning and suggest that designing spatial protection around focal species can benefit marine predators across their full life cycle. We propose the precautionary implementation of small-scale marine protected areas, followed by robust assessment and adaptive-management, to confirm population-level benefits for the cormorants, their prey, and the wider ecosystem, without negative impacts on local fisheries. © 2017 Society for Conservation Biology.

Removal of pharmaceuticals from wastewater by biological processes, hydrodynamic cavitation and UV treatment.

PubMed

Zupanc, Mojca; Kosjek, Tina; Petkovšek, Martin; Dular, Matevž; Kompare, Boris; Širok, Brane; Blažeka, Željko; Heath, Ester

2013-07-01

To augment the removal of pharmaceuticals different conventional and alternative wastewater treatment processes and their combinations were investigated. We tested the efficiency of (1) two distinct laboratory scale biological processes: suspended activated sludge and attached-growth biomass, (2) a combined hydrodynamic cavitation-hydrogen peroxide process and (3) UV treatment. Five pharmaceuticals were chosen including ibuprofen, naproxen, ketoprofen, carbamazepine and diclofenac, and an active metabolite of the lipid regulating agent clofibric acid. Biological treatment efficiency was evaluated using lab-scale suspended activated sludge and moving bed biofilm flow-through reactors, which were operated under identical conditions in respect to hydraulic retention time, working volume, concentration of added pharmaceuticals and synthetic wastewater composition. The suspended activated sludge process showed poor and inconsistent removal of clofibric acid, carbamazepine and diclofenac, while ibuprofen, naproxen and ketoprofen yielded over 74% removal. Moving bed biofilm reactors were filled with two different types of carriers i.e. Kaldnes K1 and Mutag BioChip™ and resulted in higher removal efficiencies for ibuprofen and diclofenac. Augmentation and consistency in the removal of diclofenac were observed in reactors using Mutag BioChip™ carriers (85%±10%) compared to reactors using Kaldnes carriers and suspended activated sludge (74%±22% and 48%±19%, respectively). To enhance the removal of pharmaceuticals hydrodynamic cavitation with hydrogen peroxide process was evaluated and optimal conditions for removal were established regarding the duration of cavitation, amount of added hydrogen peroxide and initial pressure, all of which influence the efficiency of the process. Optimal parameters resulted in removal efficiencies between 3-70%. Coupling the attached-growth biomass biological treatment, hydrodynamic cavitation/hydrogen peroxide process and UV treatment resulted in removal efficiencies of >90% for clofibric acid and >98% for carbamazepine and diclofenac, while the remaining compounds were reduced to levels below the LOD. For ibuprofen, naproxen, ketoprofen and diclofenac the highest contribution to overall removal was attributed to biological treatment, for clofibric acid UV treatment was the most efficient, while for carbamazepine hydrodynamic cavitation/hydrogen peroxide process and UV treatment were equally efficient. Copyright © 2012 Elsevier B.V. All rights reserved.

Luminopsins integrate opto- and chemogenetics by using physical and biological light sources for opsin activation

PubMed Central

Berglund, Ken; Clissold, Kara; Li, Haofang E.; Wen, Lei; Park, Sung Young; Gleixner, Jan; Klein, Marguerita E.; Lu, Dongye; Barter, Joseph W.; Rossi, Mark A.; Augustine, George J.; Yin, Henry H.; Hochgeschwender, Ute

2016-01-01

Luminopsins are fusion proteins of luciferase and opsin that allow interrogation of neuronal circuits at different temporal and spatial resolutions by choosing either extrinsic physical or intrinsic biological light for its activation. Building on previous development of fusions of wild-type Gaussia luciferase with channelrhodopsin, here we expanded the utility of luminopsins by fusing bright Gaussia luciferase variants with either channelrhodopsin to excite neurons (luminescent opsin, LMO) or a proton pump to inhibit neurons (inhibitory LMO, iLMO). These improved LMOs could reliably activate or silence neurons in vitro and in vivo. Expression of the improved LMO in hippocampal circuits not only enabled mapping of synaptic activation of CA1 neurons with fine spatiotemporal resolution but also could drive rhythmic circuit excitation over a large spatiotemporal scale. Furthermore, virus-mediated expression of either LMO or iLMO in the substantia nigra in vivo produced not only the expected bidirectional control of single unit activity but also opposing effects on circling behavior in response to systemic injection of a luciferase substrate. Thus, although preserving the ability to be activated by external light sources, LMOs expand the use of optogenetics by making the same opsins accessible to noninvasive, chemogenetic control, thereby allowing the same probe to manipulate neuronal activity over a range of spatial and temporal scales. PMID:26733686

Fiber networks amplify active stress

PubMed Central

Ronceray, Pierre; Broedersz, Chase P.

2016-01-01

Large-scale force generation is essential for biological functions such as cell motility, embryonic development, and muscle contraction. In these processes, forces generated at the molecular level by motor proteins are transmitted by disordered fiber networks, resulting in large-scale active stresses. Although these fiber networks are well characterized macroscopically, this stress generation by microscopic active units is not well understood. Here we theoretically study force transmission in these networks. We find that collective fiber buckling in the vicinity of a local active unit results in a rectification of stress towards strongly amplified isotropic contraction. This stress amplification is reinforced by the networks’ disordered nature, but saturates for high densities of active units. Our predictions are quantitatively consistent with experiments on reconstituted tissues and actomyosin networks and shed light on the role of the network microstructure in shaping active stresses in cells and tissue. PMID:26921325

Beyond the vent: New perspectives on hydrothermal plumes and pelagic biology

NASA Astrophysics Data System (ADS)

Phillips, Brennan T.

2017-03-01

Submarine hydrothermal vent fields introduce buoyant plumes of chemically altered seawater to the deep-sea water column. Chemoautotrophic microbes exploit this energy source, facilitating seafloor-based primary production that evidence suggests may transfer to pelagic consumers. While most hydrothermal plumes have relatively small volumes, there are recent examples of large-scale plume events associated with periods of eruptive activity, which have had a pronounced effect on water-column biology. This correlation suggests that hydrothermal plumes may have influenced basin-scale ocean chemistry during periods of increased submarine volcanism during the Phanerozoic eon. This paper synthesizes a growing body of scientific evidence supporting the hypothesis that hydrothermal plumes are the energetic basis of unique deep-sea pelagic food webs. While many important questions remain concerning the biology of hydrothermal plumes, this discussion is not present in ongoing management efforts related to seafloor massive sulfide (SMS) mining. Increased research efforts, focused on high-resolution surveys of midwater biology relative to plume structures, are recommended to establish baseline conditions and monitor the impact of future mining-based disturbances to the pelagic biosphere.

Failure mode prediction for composite structural insulated panels with MgO board facings

NASA Astrophysics Data System (ADS)

Smakosz, Łukasz; Kreja, Ireneusz

2018-01-01

Sandwich panels are readily used in civil engineering due to their high strength to weight ratio and the ease and speed of assembly. The idea of a sandwich section is to combine thin and durable facings with a light-weight core and the choice of materials used allows obtaining the desired behaviour. Panels in consideration consist of MgO (magnesium oxide) board facings and expanded polystyrene core and are characterized by immunity to biological corrosion, a high thermal insulation and a relatively low impact on environment. Customizing the range of panels to meet market needs requires frequent size changes, leading to different failure modes, which are identified in a series of costly full-scale laboratory tests. A nonlinear numerical model was created with a use of a commercial ABAQUS code and a user-defined procedure, which is able to reproduce observed failure mechanisms; its parameters were established on the basis of small-scale tests and numerical experiments. The model was validated by a comparison with the results of the full-scale bending and compression tests. The results obtained were in satisfactory agreement with the test data.

Application of chemical, biological and membrane separation processes in textile industry with recourse to zero effluent discharge--a case study.

PubMed

Nandy, T; Dhodapkar, R S; Pophali, G R; Kaul, S N; Devotta, S

2005-09-01

Environmental concerns associated with textile processing had placed the textile sector in a Southern State of India under serious threat of survival. The textile industries were closed under the orders of the Statutory Board for reason of inadequate compliance to environmental discharge norms of the State for the protection of the drinking water source of the State capital. In compliance with the direction of the Board for zero effluent discharge, advanced treatment process have been implemented for recovery of boiler feed quality water with recourse to effluent recycling/reuse. The paper describes to a case study on the adequacy assessment of the full scale effluent treatment plant comprising chemical, biological and filtration processes in a small scale textile industry. In addition, implementation of measures for discernable improvement in the performance of the existing units through effective operation & maintenance, and application of membrane separation processes leading to zero effluent discharge is also highlighted.

Flow Separation Control on A Full-Scale Vertical Tail Model Using Sweeping Jet Actuators

NASA Technical Reports Server (NTRS)

Andino, Marlyn Y.; Lin, John C.; Washburn, Anthony E.; Whalen, Edward A.; Graff, Emilio C.; Wygnanski, Israel J.

2015-01-01

This paper describes test results of a joint NASA/Boeing research effort to advance Active Flow Control (AFC) technology to enhance aerodynamic efficiency. A full-scale Boeing 757 vertical tail model equipped with sweeping jets AFC was tested at the National Full-Scale Aerodynamics Complex 40- by 80-Foot Wind Tunnel at NASA Ames Research Center. The flow separation control optimization was performed at 100 knots, a maximum rudder deflection of 30deg, and sideslip angles of 0deg and -7.5deg. Greater than 20% increments in side force were achieved at the two sideslip angles with a 31-actuator AFC configuration. Flow physics and flow separation control associated with the AFC are presented in detail. AFC caused significant increases in suction pressure on the actuator side and associated side force enhancement. The momentum coefficient (C sub mu) is shown to be a useful parameter to use for scaling-up sweeping jet AFC from sub-scale tests to full-scale applications. Reducing the number of actuators at a constant total C(sub mu) of approximately 0.5% and tripling the actuator spacing did not significantly affect the flow separation control effectiveness.

Systems metabolic engineering of microorganisms to achieve large-scale production of flavonoid scaffolds.

PubMed

Wu, Junjun; Du, Guocheng; Zhou, Jingwen; Chen, Jian

2014-10-20

Flavonoids possess pharmaceutical potential due to their health-promoting activities. The complex structures of these products make extraction from plants difficult, and chemical synthesis is limited because of the use of many toxic solvents. Microbial production offers an alternate way to produce these compounds on an industrial scale in a more economical and environment-friendly manner. However, at present microbial production has been achieved only on a laboratory scale and improvements and scale-up of these processes remain challenging. Naringenin and pinocembrin, which are flavonoid scaffolds and precursors for most of the flavonoids, are the model molecules that are key to solving the current issues restricting industrial production of these chemicals. The emergence of systems metabolic engineering, which combines systems biology with synthetic biology and evolutionary engineering at the systems level, offers new perspectives on strain and process optimization. In this review, current challenges in large-scale fermentation processes involving flavonoid scaffolds and the strategies and tools of systems metabolic engineering used to overcome these challenges are summarized. This will offer insights into overcoming the limitations and challenges of large-scale microbial production of these important pharmaceutical compounds. Copyright © 2014 Elsevier B.V. All rights reserved.

An ancestral host defence peptide within human β-defensin 3 recapitulates the antibacterial and antiviral activity of the full-length molecule

PubMed Central

Nigro, Ersilia; Colavita, Irene; Sarnataro, Daniela; Scudiero, Olga; Zambrano, Gerardo; Granata, Vincenzo; Daniele, Aurora; Carotenuto, Alfonso; Galdiero, Stefania; Folliero, Veronica; Galdiero, Massimiliano; Urbanowicz, Richard A.; Ball, Jonathan K.; Salvatore, Francesco; Pessi, Antonello

2015-01-01

Host defence peptides (HDPs) are critical components of innate immunity. Despite their diversity, they share common features including a structural signature, designated “γ-core motif”. We reasoned that for each HDPs evolved from an ancestral γ-core, the latter should be the evolutionary starting point of the molecule, i.e. it should represent a structural scaffold for the modular construction of the full-length molecule, and possess biological properties. We explored the γ-core of human β-defensin 3 (HBD3) and found that it: (a) is the folding nucleus of HBD3; (b) folds rapidly and is stable in human serum; (c) displays antibacterial activity; (d) binds to CD98, which mediates HBD3 internalization in eukaryotic cells; (e) exerts antiviral activity against human immunodeficiency virus and herpes simplex virus; and (f) is not toxic to human cells. These results demonstrate that the γ-core within HBD3 is the ancestral core of the full-length molecule and is a viable HDP per se, since it is endowed with the most important biological features of HBD3. Notably, the small, stable scaffold of the HBD3 γ-core can be exploited to design disease-specific antimicrobial agents. PMID:26688341

From single cilia to collective waves in human airway ciliated tissues

NASA Astrophysics Data System (ADS)

Cicuta, Pietro; Chioccioli, Maurizio; Feriani, Luigi; Pellicciotta, Nicola; Kotar, Jurij

I will present experimental results on activity of motile cilia on various scales: from waveforms on individual cilia to the synchronised motion in cilia carpets of airway cells. Model synthetic experiments have given us an understanding of how cilia could couple with each other through forces transmitted by the fluid, and thus coordinate to beat into well organized waves (previous work is reviewed in Annu. Rev. Condens. Matter Phys. 7, 1-26 (2016)). Working with live imaging of airway human cells at the different scales, we can now test whether the biological system satisfies the ``simple'' behavior expected of the fluid flow coupling, or if other factors of mechanical forces transmission need to be accounted for. In general being able to link from the scale of molecular biological activity up to the phenomenology of collective dynamics requires to understand the relevant physical mechanism. This understanding then allows informed diagnostics (and perhaps therapeutic) approaches to a variety of diseases where mucociliary clearance in the airways is compromised. We have started exploring particularly cystic fibrosis, where the rheological properties of the mucus are affected and prevent efficient cilia synchronization. ERC Grant HydroSync.

Bedform development and morphodynamics in mixed cohesive sediment substrates: the importance of winnowing and flocculation

NASA Astrophysics Data System (ADS)

Ye, Leiping; Parsons, Daniel; Manning, Andrew

2016-04-01

There remains a lack of process-based knowledge of sediment dynamics within flows over bedforms generated in complex mixtures of cohesionless sand and biologically-active cohesive muds in natural estuarine flow systems. The work to be presented forms a part of the UK NERC "COHesive BEDforms (COHBED)" project which aims to fill this gap in knowledge. Herein results from a field survey in sub-tidal zone of Dee estuary (NW, England) and a set of large-scale laboratory experiments, conducted using mixtures of non-cohesive sands, cohesive muds and Xanthan gum (as a proxy for the biological stickiness of Extracellular Polymeric Substances (EPS)) will be presented. The results indicate the significance of biological-active cohesive sediments in controlling winnowing rates and flocculation dynamics, which contributes significantly to rates of bedform evolution.

Biological treatment of winery wastewater: an overview.

PubMed

Andreottola, G; Foladori, P; Ziglio, G

2009-01-01

The treatment of winery wastewater can realised using several biological processes based both on aerobic or anaerobic systems using suspended biomass or biofilms. Several systems are currently offered by technology providers and current research envisages the availability of new promising technologies for winery wastewater treatment. The present paper intends to present a brief state of the art of the existing status and advances in biological treatment of winery wastewater in the last decade, considering both lab, pilot and full-scale studies. Advantages, drawbacks, applied organic loads, removal efficiency and emerging aspects of the main biological treatments were considered and compared. Nevertheless in most treatments the COD removal efficiency was around 90-95% (remaining COD is due to the un-biodegradable soluble fraction), the applied organic loads are very different depending on the applied technology, varying for an order of magnitude. Applied organic loads are higher in biofilm systems than in suspended biomass while anaerobic biofilm processes have the smaller footprint but in general a higher level of complexity.

Natural disturbance production functions

Treesearch

Jeffrey P. Prestemon; D. Evan Mercer; John M. Pye

2008-01-01

Natural disturbances in forests are driven by physical and biological processes. Large, landscape scale disturbances derive primarily from weather (droughts, winds, ice storms, and floods), geophysical activities (earthquakes, volcanic eruptions), fires, insects, and diseases. Humans have invented ways to minimize their negative impacts and reduce their rates of...

Influence of sludge properties and hydraulic loading on the performance of secondary settling tanks--full-scale operational results.

PubMed

Vestner, R J; Günthert, F Wolfgang

2004-01-01

Full-scale investigations at a WWTP with a two-stage secondary settling tank process revealed relationships between significant operating parameters and performance in terms of effluent suspended solids concentration. Besides common parameters (e.g. surface overflow rate and sludge volume loading rate) feed SS concentration and flocculation time must be considered. Concentration of the return activated sludge may help to estimate the performance of existing secondary settling tanks.

Testing and Analysis of the First Plastic Melt Waste Compactor Prototype

NASA Technical Reports Server (NTRS)

Pace, Gregory S.; Fisher, John W.

2005-01-01

A half scale Plastic Melt Waste Compactor prototype has been developed at NASA Ames Research Center. The half scale prototype unit will lead to the development of a full scale Plastic Melt Waste Compactor prototype that is representative of flight hardware that would be used on near and far term space missions. This report details the testing being done on the prototype Plastic Melt Waste Compactor by the Solid Waste Management group at NASA Ames Research Center. The tests are designed to determine the prototype's functionality, simplicity of operation, ability to contain and control noxious off-gassing, biological stability of the processed waste, and water recovery potential using a waste composite that is representative of the types of wastes produced on the International Space Station, Space Shuttle, MIR and Skylab missions.

[The advance in synthetic biology: towards a microbe-derived paclitaxel intermediates].

PubMed

Wang, Wei; Yang, Yan; Zheng, Xiao-Dong; Huang, Shu-Qiong; Guo, Lei; Kong, Jian-Qiang; Cheng, Ke-Di

2013-02-01

The synthetic biology matures to promote the heterologous biosynthesis of the well-known drug paclitaxel that is one of the most important and active chemotherapeutic agents for the first-line clinical treatment of cancer. This review focuses on the construction and regulation of the biosynthetic pathway of paclitaxel intermediates in both Escherichia coli and Saccharomyces cerevisiae. In particular, the review also features the early efforts to design and overproduce taxadiene and the bottleneck of scale fermentation for producing the intermediates.

Stochastic cycle selection in active flow networks.

PubMed

Woodhouse, Francis G; Forrow, Aden; Fawcett, Joanna B; Dunkel, Jörn

2016-07-19

Active biological flow networks pervade nature and span a wide range of scales, from arterial blood vessels and bronchial mucus transport in humans to bacterial flow through porous media or plasmodial shuttle streaming in slime molds. Despite their ubiquity, little is known about the self-organization principles that govern flow statistics in such nonequilibrium networks. Here we connect concepts from lattice field theory, graph theory, and transition rate theory to understand how topology controls dynamics in a generic model for actively driven flow on a network. Our combined theoretical and numerical analysis identifies symmetry-based rules that make it possible to classify and predict the selection statistics of complex flow cycles from the network topology. The conceptual framework developed here is applicable to a broad class of biological and nonbiological far-from-equilibrium networks, including actively controlled information flows, and establishes a correspondence between active flow networks and generalized ice-type models.

Stochastic cycle selection in active flow networks

PubMed Central

Woodhouse, Francis G.; Forrow, Aden; Fawcett, Joanna B.; Dunkel, Jörn

2016-01-01

Active biological flow networks pervade nature and span a wide range of scales, from arterial blood vessels and bronchial mucus transport in humans to bacterial flow through porous media or plasmodial shuttle streaming in slime molds. Despite their ubiquity, little is known about the self-organization principles that govern flow statistics in such nonequilibrium networks. Here we connect concepts from lattice field theory, graph theory, and transition rate theory to understand how topology controls dynamics in a generic model for actively driven flow on a network. Our combined theoretical and numerical analysis identifies symmetry-based rules that make it possible to classify and predict the selection statistics of complex flow cycles from the network topology. The conceptual framework developed here is applicable to a broad class of biological and nonbiological far-from-equilibrium networks, including actively controlled information flows, and establishes a correspondence between active flow networks and generalized ice-type models. PMID:27382186

Encyrtid parasitoids of soft scale insects: biology, behavior, and their use in biological control.

PubMed

Kapranas, Apostolos; Tena, Alejandro

2015-01-07

Parasitoids of the hymenopterous family Encyrtidae are one of the most important groups of natural enemies of soft scale insects and have been used extensively in biological control. We summarize existing knowledge of the biology, ecology, and behavior of these parasitoids and how it relates to biological control. Soft scale stage/size and phenology are important determinants of host range and host utilization, which are key aspects in understanding how control by these parasitoids is exerted. Furthermore, the nutritional ecology of encyrtids and their physiological interactions with their hosts affect soft scale insect population dynamics. Lastly, the interactions among encyrtids, heteronomous parasitoids, and ants shape parasitoid species complexes and consequently have a direct impact on the biological control of soft scale insects.

Nitrous Oxide Production at a Fully Covered Wastewater Treatment Plant: Results of a Long-Term Online Monitoring Campaign.

PubMed

Kosonen, Heta; Heinonen, Mari; Mikola, Anna; Haimi, Henri; Mulas, Michela; Corona, Francesco; Vahala, Riku

2016-06-07

The nitrous oxide emissions of the Viikinmäki wastewater treatment plant were measured in a 12 month online monitoring campaign. The measurements, which were conducted with a continuous gas analyzer, covered all of the unit operations of the advanced wastewater-treatment process. The relation between the nitrous oxide emissions and certain process parameters, such as the wastewater temperature, influent biological oxygen demand, and ammonium nitrogen load, was investigated by applying online data obtained from the process-control system at 1 min intervals. Although seasonal variations in the measured nitrous oxide emissions were remarkable, the measurement data indicated no clear relationship between these emissions and seasonal changes in the wastewater temperature. The diurnal variations of the nitrous oxide emissions did, however, strongly correlate with the alternation of the influent biological oxygen demand and ammonium nitrogen load to the aerated zones of the activated sludge process. Overall, the annual nitrous oxide emissions of 168 g/PE/year and the emission factor of 1.9% of the influent nitrogen load are in the high range of values reported in the literature but in very good agreement with the results of other long-term online monitoring campaigns implemented at full-scale wastewater-treatment plants.

Carbon source recovery from excess sludge by mechanical disintegration for biological denitrification.

PubMed

Zubrowska-Sudol, M

2018-04-01

The goal of the study was to evaluate the possibility of carbon source recovery from excess sludge by mechanical disintegration for biological denitrification. The total efficiency of denitrification, unit demand for organic compounds for denitrification, unit volume of disintegrated sludge and unit cost of nitrogen removal as a function of energy density used for excess sludge disintegration (70, 140 and 210 kJ/L) were analyzed. In the study a full-scale disc disintegrator was used (motor power: 30 kWh, motor speed: 2,950 rpm). It was shown that the amounts of organic compounds released from the activated sludge flocs at all tested levels of energy density are high enough to be used to intensify the removal of nitrogen compounds from wastewater. It was also documented that the energy density provided during process of disintegration was an important factor determining the characteristics of organic compounds obtained under the disintegration for their use in order to intensify the process of denitrification. The highest value of total efficiency of denitrification (50.5 ± 3.1 mg N/L) was obtained for carbon source recovery from excess sludge at 70 kJ/L, but the lowest unit cost of nitrogen removal occurred for 140 kJ/L (0.0019 ± 0.0011 EUR/g N).

Cost minimization in a full-scale conventional wastewater treatment plant: associated costs of biological energy consumption versus sludge production.

PubMed

Sid, S; Volant, A; Lesage, G; Heran, M

2017-11-01

Energy consumption and sludge production minimization represent rising challenges for wastewater treatment plants (WWTPs). The goal of this study is to investigate how energy is consumed throughout the whole plant and how operating conditions affect this energy demand. A WWTP based on the activated sludge process was selected as a case study. Simulations were performed using a pre-compiled model implemented in GPS-X simulation software. Model validation was carried out by comparing experimental and modeling data of the dynamic behavior of the mixed liquor suspended solids (MLSS) concentration and nitrogen compounds concentration, energy consumption for aeration, mixing and sludge treatment and annual sludge production over a three year exercise. In this plant, the energy required for bioreactor aeration was calculated at approximately 44% of the total energy demand. A cost optimization strategy was applied by varying the MLSS concentrations (from 1 to 8 gTSS/L) while recording energy consumption, sludge production and effluent quality. An increase of MLSS led to an increase of the oxygen requirement for biomass aeration, but it also reduced total sludge production. Results permit identification of a key MLSS concentration allowing identification of the best compromise between levels of treatment required, biological energy demand and sludge production while minimizing the overall costs.

Small, mobile, persistent: Trifluoroacetate in the water cycle - Overlooked sources, pathways, and consequences for drinking water supply.

PubMed

Scheurer, Marco; Nödler, Karsten; Freeling, Finnian; Janda, Joachim; Happel, Oliver; Riegel, Marcel; Müller, Uwe; Storck, Florian Rüdiger; Fleig, Michael; Lange, Frank Thomas; Brunsch, Andrea; Brauch, Heinz-Jürgen

2017-12-01

Elevated concentrations of trifluoroacetate (TFA) of more than 100 μg/L in a major German river led to the occurrence of more than 20 μg/L TFA in bank filtration based tap waters. Several spatially resolved monitoring programs were conducted and discharges from an industrial company were identified as the point source of TFA contamination. Treatment options for TFA removal were investigated at full-scale waterworks and in laboratory batch tests. Commonly applied techniques like ozonation or granulated activated carbon filtration are inappropriate for TFA removal, whereas TFA was partly removed by ion exchange and completely retained by reverse osmosis. Further investigations identified wastewater treatment plants (WWTPs) as additional TFA dischargers into the aquatic environment. TFA was neither removed by biological wastewater treatment, nor by a retention soil filter used for the treatment of combined sewer overflows. WWTP influents can even bear a TFA formation potential, when appropriate CF 3 -containing precursors are present. Biological degradation and ozonation batch experiments with chemicals of different classes (flurtamone, fluopyram, tembotrione, flufenacet, fluoxetine, sitagliptine and 4:2 fluorotelomer sulfonate) proved that there are yet overlooked sources and pathways of TFA, which need to be addressed in the future. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nanoscale patterning controls inorganic-membrane interface structure

NASA Astrophysics Data System (ADS)

Almquist, Benjamin D.; Verma, Piyush; Cai, Wei; Melosh, Nicholas A.

2011-02-01

The ability to non-destructively integrate inorganic structures into or through biological membranes is essential to realizing full bio-inorganic integration, including arrayed on-chip patch-clamps, drug delivery, and biosensors. Here we explore the role of nanoscale patterning on the strength of biomembrane-inorganic interfaces. AFM measurements show that inorganic probes functionalized with hydrophobic bands with thicknesses complimentary to the hydrophobic lipid bilayer core exhibit strong attachment in the bilayer. As hydrophobic band thickness increases to 2-3 times the bilayer core the interfacial strength decreases, comparable to homogeneously hydrophobic probes. Analytical calculations and molecular dynamics simulations predict a transition between a `fused' interface and a `T-junction' that matches the experimental results, showing lipid disorder and defect formation for thicker bands. These results show that matching biological length scales leads to more intimate bio-inorganic junctions, enabling rational design of non-destructive membrane interfaces.The ability to non-destructively integrate inorganic structures into or through biological membranes is essential to realizing full bio-inorganic integration, including arrayed on-chip patch-clamps, drug delivery, and biosensors. Here we explore the role of nanoscale patterning on the strength of biomembrane-inorganic interfaces. AFM measurements show that inorganic probes functionalized with hydrophobic bands with thicknesses complimentary to the hydrophobic lipid bilayer core exhibit strong attachment in the bilayer. As hydrophobic band thickness increases to 2-3 times the bilayer core the interfacial strength decreases, comparable to homogeneously hydrophobic probes. Analytical calculations and molecular dynamics simulations predict a transition between a `fused' interface and a `T-junction' that matches the experimental results, showing lipid disorder and defect formation for thicker bands. These results show that matching biological length scales leads to more intimate bio-inorganic junctions, enabling rational design of non-destructive membrane interfaces. Electronic supplementary information (ESI) available: Breakthrough rate as a function of force plots for 5 nm, 10 nm and ∞-probes.. See DOI: 10.1039/c0nr00486c

Nanoelectronics Meets Biology: From Novel Nanoscale Devices for Live Cell Recording to 3D Innervated Tissues†

PubMed Central

Duan, Xiaojie; Lieber, Charles M.

2013-01-01

High spatio-temporal resolution interfacing between electrical sensors and biological systems, from single live cells to tissues, is crucial for many areas, including fundamental biophysical studies as well as medical monitoring and intervention. This focused review summarizes recent progresses in the development and application of novel nanoscale devices for intracellular electrical recordings of action potentials, and the effort of merging electronic and biological systems seamlessly in three dimension using macroporous nanoelectronic scaffolds. The uniqueness of these nanoscale devices for minimally invasive, large scale, high spatial resolution, and three dimensional neural activity mapping will be highlighted. PMID:23946279

Scaling trace organic contaminant adsorption capacity by granular activated carbon.

PubMed

Corwin, Christopher J; Summers, R Scott

2010-07-15

The role of particle size on the reduction of granular activated carbon (GAC) adsorption capacity for trace organic contaminants by dissolved organic matter (DOM) is examined and applied to performance scale-up. The adsorption capacity reduction, termed fouling, must be scalable in order to use bench scale tests, such as the rapid small-scale column test (RSSCT) to predict full-scale breakthrough. Equilibrium adsorption capacity tests with GAC preloaded with DOM and RSSCT breakthrough curves at three different GAC particle sizes indicate that GAC adsorption capacity is dependent on GAC particle size when DOM is present. Thus, the RSSCT cannot be expected to match full-scale results regardless of which RSSCT design approach is used (constant or proportional diffusivity), unless a scaling factor is applied to the results. Proportional diffusivity RSSCT breakthrough curves demonstrate that surface concentration of DOM is not a good measure of fouling. It is hypothesized that pore blockage is the mechanism responsible for the dependence on particle size. As GAC particle size increases, the microporous surface area behind a constricted pore also increases. The result is lower adsorption capacity per mass of adsorbent in the larger GAC particles. A scaling methodology for equilibrium and breakthrough data is presented that accounts for the dependence of NOM preloading effects on GAC particle diameter.

The use of fly larvae for organic waste treatment.

PubMed

Čičková, Helena; Newton, G Larry; Lacy, R Curt; Kozánek, Milan

2015-01-01

The idea of using fly larvae for processing of organic waste was proposed almost 100 years ago. Since then, numerous laboratory studies have shown that several fly species are well suited for biodegradation of organic waste, with the house fly (Musca domestica L.) and the black soldier fly (Hermetia illucens L.) being the most extensively studied insects for this purpose. House fly larvae develop well in manure of animals fed a mixed diet, while black soldier fly larvae accept a greater variety of decaying organic matter. Blow fly and flesh fly maggots are better suited for biodegradation of meat processing waste. The larvae of these insects have been successfully used to reduce mass of animal manure, fecal sludge, municipal waste, food scrapes, restaurant and market waste, as well as plant residues left after oil extraction. Higher yields of larvae are produced on nutrient-rich wastes (meat processing waste, food waste) than on manure or plant residues. Larvae may be used as animal feed or for production of secondary products (biodiesel, biologically active substances). Waste residue becomes valuable fertilizer. During biodegradation the temperature of the substrate rises, pH changes from neutral to alkaline, ammonia release increases, and moisture decreases. Microbial load of some pathogens can be substantially reduced. Both larvae and digested residue may require further treatment to eliminate pathogens. Facilities utilizing natural fly populations, as well as pilot and full-scale plants with laboratory-reared fly populations have been shown to be effective and economically feasible. The major obstacles associated with the production of fly larvae from organic waste on an industrial scale seem to be technological aspects of scaling-up the production capacity, insufficient knowledge of fly biology necessary to produce large amounts of eggs, and current legislation. Technological innovations could greatly improve performance of the biodegradation facilities and decrease production costs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Directed Evolution as a Powerful Synthetic Biology Tool

PubMed Central

Cobb, Ryan E.; Sun, Ning; Zhao, Huimin

2012-01-01

At the heart of synthetic biology lies the goal of rationally engineering a complete biological system to achieve a specific objective, such as bioremediation and synthesis of a valuable drug, chemical, or biofuel molecule. However, the inherent complexity of natural biological systems has heretofore precluded generalized application of this approach. Directed evolution, a process which mimics Darwinian selection on a laboratory scale, has allowed significant strides to be made in the field of synthetic biology by allowing rapid identification of desired properties from large libraries of variants. Improvement in biocatalyst activity and stability, engineering of biosynthetic pathways, tuning of functional regulatory systems and logic circuits, and development of desired complex phenotypes in industrial host organisms have all been achieved by way of directed evolution. Here, we review recent contributions of directed evolution to synthetic biology at the protein, pathway, network, and whole cell levels. PMID:22465795

Programming languages for synthetic biology.

PubMed

Umesh, P; Naveen, F; Rao, Chanchala Uma Maheswara; Nair, Achuthsankar S

2010-12-01

In the backdrop of accelerated efforts for creating synthetic organisms, the nature and scope of an ideal programming language for scripting synthetic organism in-silico has been receiving increasing attention. A few programming languages for synthetic biology capable of defining, constructing, networking, editing and delivering genome scale models of cellular processes have been recently attempted. All these represent important points in a spectrum of possibilities. This paper introduces Kera, a state of the art programming language for synthetic biology which is arguably ahead of similar languages or tools such as GEC, Antimony and GenoCAD. Kera is a full-fledged object oriented programming language which is tempered by biopart rule library named Samhita which captures the knowledge regarding the interaction of genome components and catalytic molecules. Prominent feature of the language are demonstrated through a toy example and the road map for the future development of Kera is also presented.

Hygroscopic motions of fossil conifer cones

NASA Astrophysics Data System (ADS)

Poppinga, Simon; Nestle, Nikolaus; Šandor, Andrea; Reible, Bruno; Masselter, Tom; Bruchmann, Bernd; Speck, Thomas

2017-01-01

Conifer cones represent natural, woody compliant structures which move their scales as passive responses to changes in environmental humidity. Here we report on water-driven opening and closing motions in coalified conifer cones from the Eemian Interglacial (approx. 126,000-113,000 years BP) and from the Middle Miocene (approx. 16.5 to 11.5 million years BP). These cones represent by far the oldest documented evidence of plant parts showing full functionality of such passive hydraulically actuated motion. The functional resilience of these structures is far beyond the biological purpose of seed dispersal and protection and is because of a low level of mineralization of the fossils. Our analysis emphasizes the functional-morphological integrity of these biological compliant mechanisms which, in addition to their biological fascination, are potentially also role models for resilient and maintenance-free biomimetic applications (e.g., adaptive and autonomously moving structures including passive hydraulic actuators).

A watershed approach to ecosystem monitoring in Denali National Park and preserve, Alaska

USGS Publications Warehouse

Thorsteinson, L.K.; Taylor, D.L.

1997-01-01

The National Park Service and the National Biological Service initiated research in Denali National Park and Preserve, a 2.4 million-hectare park in southcentral Alaska, to develop ecological monitoring protocols for national parks in the Arctic/Subarctic biogeographic area. We are focusing pilot studies on design questions, on scaling issues and regionalization, ecosystem structure and function, indicator selection and evaluation, and monitoring technologies. Rock Creek, a headwater stream near Denali headquarters, is the ecological scale for initial testing of a watershed ecosystem approach. Our conceptual model embraces principles of the hydrological cycle, hypotheses of global climate change, and biological interactions of organisms occupying intermediate, but poorly studied, positions in Alaskan food webs. The field approach includes hydrological and depositional considerations and a suite of integrated measures linking key aquatic and terrestrial biota, environmental variables, or defined ecological processes, in order to establish ecological conditions and detect, track, and understand mechanisms of environmental change. Our sampling activities include corresponding measures of physical, chemical, and biological attributes in four Rock Creek habitats believed characteristic of the greater system diversity of Denali. This paper gives examples of data sets, program integration and scaling, and research needs.

A pilot-scale study on PVA gel beads based integrated fixed film activated sludge (IFAS) plant for municipal wastewater treatment.

PubMed

Kumar Singh, Nitin; Singh, Jasdeep; Bhatia, Aakansha; Kazmi, A A

2016-01-01

In the present study, a pilot-scale reactor incorporating polyvinyl alcohol gel beads as biomass carrier and operating in biological activated sludge mode (a combination of moving bed biofilm reactor (MBBR) and activated sludge) was investigated for the treatment of actual municipal wastewater. The results, during a monitoring period of 4 months, showed effective removal of chemical oxygen demand (COD), biological oxygen demand (BOD) and NH3-N at optimum conditions with 91%, ∼92% and ∼90% removal efficiencies, respectively. Sludge volume index (SVI) values of activated sludge varied in the range of 25-72 mL/g, indicating appreciable settling characteristics. Furthermore, soluble COD and BOD in the effluent of the pilot plant were reduced to levels well below discharge limits of the Punjab Pollution Control Board, India. A culture dependent method was used to enrich and isolate abundant heterotrophic bacteria in activated sludge. In addition to this, 16S rRNA genes analysis was performed to identify diverse dominant bacterial species in suspended and attached biomass. Results revealed that Escherichia coli, Pseudomonas sp. and Nitrosomonas communis played a significant role in biomass carrier, while Acinetobactor sp. were dominant in activated sludge of the pilot plant. Identification of ciliated protozoa populations rendered six species of ciliates in the plant, among which Vorticella was the most dominant.

Recombinant production of enzymatically active male contraceptive drug target hTSSK2 - Localization of the TSKS domain phosphorylated by TSSK2.

PubMed

Shetty, Jagathpala; Sinville, Rondedrick; Shumilin, Igor A; Minor, Wladek; Zhang, Jianhai; Hawkinson, Jon E; Georg, Gunda I; Flickinger, Charles J; Herr, John C

2016-05-01

The testis-specific serine/threonine kinase 2 (TSSK2) has been proposed as a candidate male contraceptive target. Development of a selective inhibitor for this kinase first necessitates the production of highly purified, soluble human TSSK2 and its substrate, TSKS, with high yields and retention of biological activity for crystallography and compound screening. Strategies to produce full-length, soluble, biologically active hTSSK2 in baculovirus expression systems were tested and refined. Soluble preparations of TSSK2 were purified by immobilized-metal affinity chromatography (IMAC) followed by gel filtration chromatography. The biological activities of rec.hTSSK2 were verified by in vitro kinase and mobility shift assays using bacterially produced hTSKS (isoform 2), casein, glycogen synthase peptide (GS peptide) and various TSKS peptides as target substrates. Purified recombinant hTSSK2 showed robust kinase activity in the in vitro kinase assay by phosphorylating hTSKS isoform 2 and casein. The ATP Km values were similar for highly and partially purified fractions of hTSSK2 (2.2 and 2.7 μM, respectively). The broad spectrum kinase inhibitor staurosporine was a potent inhibitor of rec.hTSSK2 (IC50 = 20 nM). In vitro phosphorylation experiments carried out with TSKS (isoform 1) fragments revealed particularly strong phosphorylation of a recombinant N-terminal region representing aa 1-150 of TSKS, indicating that the N-terminus of human TSKS is phosphorylated by human TSSK2. Production of full-length enzymatically active recombinant TSSK2 kinase represents the achievement of a key benchmark for future discovery of TSSK inhibitors as male contraceptive agents. Copyright © 2016 Elsevier Inc. All rights reserved.

Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems

PubMed Central

Cilfone, Nicholas A.; Kirschner, Denise E.; Linderman, Jennifer J.

2015-01-01

Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing Mycobacterium tuberculosis infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level. PMID:26366228

Techno-economic evaluation of the application of ozone-oxidation in a full-scale aerobic digestion plant.

PubMed

Chiavola, Agostina; D'Amato, Emilio; Gori, Riccardo; Lubello, Claudio; Sirini, Piero

2013-04-01

This paper deals with the application of the ozone-oxidation in a full scale aerobic sludge digester. Ozonation was applied continuously to a fraction of the biological sludge extracted from the digestion unit; the ozonated sludge was then recirculated to the same digester. Three different ozone flow rates were tested (60,500 and 670g O3 h(-1)) and their effects evaluated in terms of variation of the total and soluble fractions of COD, nitrogen and phosphorous, of total and volatile suspended solids concentrations and Sludge Volume Index in the aerobic digestion unit. During the 7-month operation of the ozonation process, it was observed an appreciable improvement of the aerobic digestion efficiency (up to about 20% under the optimal conditions) and of the sludge settleability properties. These results determined an average reduction of about 60% in the biological sludge extracted from the plant and delivered to final disposal. A thorough economic analysis showed that this reduction allowed to achieve a significant cost saving for the plant with respect to the previous years operated without ozonation. Furthermore, it was determined the threshold disposal cost above which implementation of the ozone oxidation in the aerobic digestion units of similar WWTPs becomes economically convenient (about 60€t(-1) of sludge). Copyright © 2013 Elsevier Ltd. All rights reserved.

Selection and Application of Sulfide Oxidizing Microorganisms Able to Withstand Thiols in Gas Biodesulfurization Systems.

PubMed

Roman, Pawel; Klok, Johannes B M; Sousa, João A B; Broman, Elias; Dopson, Mark; Van Zessen, Erik; Bijmans, Martijn F M; Sorokin, Dimitry Y; Janssen, Albert J H

2016-12-06

After the first commercial applications of a new biological process for the removal of hydrogen sulfide (H 2 S) from low pressure biogas, the need arose to broaden the operating window to also enable the removal of organosulfur compounds from high pressure sour gases. In this study we have selected microorganisms from a full-scale biodesulfurization system that are capable of withstanding the presence of thiols. This full-scale unit has been in stable operation for more than 10 years. We investigated the microbial community by using high-throughput sequencing of 16S rRNA gene amplicons which showed that methanethiol gave a competitive advantage to bacteria belonging to the genera Thioalkalibacter (Halothiobacillaceae family) and Alkalilimnicola (Ectothiorhosdospiraceae family). The sulfide-oxidizing potential of the acclimatized population was investigated under elevated thiol loading rates (4.5-9.1 mM d -1 ), consisting of a mix of methanethiol, ethanethiol, and propanethiol. With this biomass, it was possible to achieve a stable bioreactor operation at which 80% of the supplied H 2 S (61 mM d -1 ) was biologically oxidized to elemental sulfur. The remainder was chemically produced thiosulfate. Moreover, we found that a conventionally applied method for controlling the oxygen supply to the bioreactor, that is, by maintaining a redox potential set-point value, appeared to be ineffective in the presence of thiols.

Synthetic biology: An emerging research field in China

PubMed Central

Pei, Lei; Schmidt, Markus; Wei, Wei

2011-01-01

Synthetic biology is considered as an emerging research field that will bring new opportunities to biotechnology. There is an expectation that synthetic biology will not only enhance knowledge in basic science, but will also have great potential for practical applications. Synthetic biology is still in an early developmental stage in China. We provide here a review of current Chinese research activities in synthetic biology and its different subfields, such as research on genetic circuits, minimal genomes, chemical synthetic biology, protocells and DNA synthesis, using literature reviews and personal communications with Chinese researchers. To meet the increasing demand for a sustainable development, research on genetic circuits to harness biomass is the most pursed research within Chinese researchers. The environmental concerns are driven force of research on the genetic circuits for bioremediation. The research on minimal genomes is carried on identifying the smallest number of genomes needed for engineering minimal cell factories and research on chemical synthetic biology is focused on artificial proteins and expanded genetic code. The research on protocells is more in combination with the research on molecular-scale motors. The research on DNA synthesis and its commercialisation are also reviewed. As for the perspective on potential future Chinese R&D activities, it will be discussed based on the research capacity and governmental policy. PMID:21729747

Volume 35, AMT-1 Cruise Report and Preliminary Results

NASA Technical Reports Server (NTRS)

Hooker, Stanford B. (Editor); Firestone, Elaine R. (Editor); Robins, David B.; Bale, Anthony J.; Moore, Gerald F.; Rees, Nigel W.; Gallienne, Christopher P.; Westbrooke, Anthony G.; Maranon, Emilio; Spooner, William H.;

A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.

PubMed

Kang, Tianyu; Ding, Wei; Zhang, Luoyan; Ziemek, Daniel; Zarringhalam, Kourosh

2017-12-19

Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is currently feasible to generate omic-scale biological measurements for all patients in a study, providing an opportunity for machine learning models to identify molecular markers for disease diagnosis and progression. However, the high variability of genetic background in human populations hampers the reproducibility of omic-scale markers. In this paper, we develop a biological network-based regularized artificial neural network model for prediction of phenotype from transcriptomic measurements in clinical trials. To improve model sparsity and the overall reproducibility of the model, we incorporate regularization for simultaneous shrinkage of gene sets based on active upstream regulatory mechanisms into the model. We benchmark our method against various regression, support vector machines and artificial neural network models and demonstrate the ability of our method in predicting the clinical outcomes using clinical trial data on acute rejection in kidney transplantation and response to Infliximab in ulcerative colitis. We show that integration of prior biological knowledge into the classification as developed in this paper, significantly improves the robustness and generalizability of predictions to independent datasets. We provide a Java code of our algorithm along with a parsed version of the STRING DB database. In summary, we present a method for prediction of clinical phenotypes using baseline genome-wide expression data that makes use of prior biological knowledge on gene-regulatory interactions in order to increase robustness and reproducibility of omic-scale markers. The integrated group-wise regularization methods increases the interpretability of biological signatures and gives stable performance estimates across independent test sets.

Evaluation of the Logistic Model for GAC Performance in Water Treatment

EPA Science Inventory

Full-scale field measurement and rapid small-scale column test data from the Greater Cincinnati (Ohio) Water Works (GCWW) were used to calibrate and investigate the application of the logistic model for simulating breakthrough of total organic carbon (TOC) in granular activated c...

Molecular/clinical correlations in females with fragile X

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

Sobesky, W.E.; Riddle, J.; Hagerman, R.J.

1996-08-09

Females who are affected by fragile X syndrome (FXS) can have significant physical, neuropsychological and emotional involvement. This study was designed to explore the relationships between these three domains and to learn how the degree of involvement in each of these phenotypic areas relates to molecular parameters including CGG repeat length and activation ratio (the proportion of normal FMR1 alleles on the active X chromosome). Three groups of females were studied: 35 women who grew up in a fragile X family but do not carry an FMR1 mutation, 92 women with a premutation, and 29 women with a full mutation.more » Correlations between neurocognitive, physical and emotional traits were calculated for each of the three groups. Within the full mutation group significant correlations were seen between schizotypal traits and full scale IQ. The Lie scale was significantly correlated with the physical findings index. The activation ratio correlated significantly with the measure of executive function (r = .50, P = .01). There was a trend toward correlations of activation ratio with the physical index score, outer ear prominence and IQ. CGG repeat number significantly correlated only with the physical index (r = .44, P = .0 1). Thus, activation ratio may be the more pertinent molecular parameter in full mutation women in determining the degree of cognitive and physical phenotypic involvement. 29 refs., 2 tabs.« less

Risk assessment of Giardia from a full scale MBR sewage treatment plant caused by membrane integrity failure.

PubMed

Zhang, Yu; Chen, Zhimin; An, Wei; Xiao, Shumin; Yuan, Hongying; Zhang, Dongqing; Yang, Min

2015-04-01

Membrane bioreactors (MBR) are highly efficient at intercepting particles and microbes and have become an important technology for wastewater reclamation. However, many pathogens can accumulate in activated sludge due to the long residence time usually adopted in MBR, and thus may pose health risks when membrane integrity problems occur. This study presents data from a survey on the occurrence of water-borne Giardia pathogens in reclaimed water from a full-scale wastewater treatment plant with MBR experiencing membrane integrity failure, and assessed the associated risk for green space irrigation. Due to membrane integrity failure, the MBR effluent turbidity varied between 0.23 and 1.90 NTU over a period of eight months. Though this turbidity level still met reclaimed water quality standards (≤5 NTU), Giardia were detected at concentrations of 0.3 to 95 cysts/10 L, with a close correlation between effluent turbidity and Giardia concentration. All β-giardin gene sequences of Giardia in the WWTP influents were genotyped as Assemblages A and B, both of which are known to infect humans. An exponential dose-response model was applied to assess the risk of infection by Giardia. The risk in the MBR effluent with chlorination was 9.83×10(-3), higher than the acceptable annual risk of 1.0×10(-4). This study suggested that membrane integrity is very important for keeping a low pathogen level, and multiple barriers are needed to ensure the biological safety of MBR effluent. Copyright © 2015. Published by Elsevier B.V.

Full-scale treatment of wastewater from a biodiesel fuel production plant with alkali-catalyzed transesterification.

PubMed

De Gisi, Sabino; Galasso, Maurizio; De Feo, Giovanni

2013-01-01

The treatment of wastewater derived from a biodiesel fuel (BDF) production plant with alkali-catalyzed transesterification was studied at full scale. The investigated wastewater treatment plant consisted of the following phases: primary adsorption/coagulation/flocculation/sedimentation processes, biological treatment with the combination of trickling filter and activated sludge systems, secondary flocculation/sedimentation processes, and reverse osmosis (RO) system with spiral membranes. All the processes were developed in a continuous mode, while the RO experiment was performed with batch tests. Two types of BDF wastewater were considered: the first wastewater (WW1) had an average total chemical oxygen demand (COD), pH and feed flow rate of 10,850.8 mg/L, 5.9 and 2946.7 L/h, respectively, while the second wastewater (WW2) had an average total COD, pH and feed flow rate of 43,898.9 mg/L, 3.3 and 2884.6 L/h, respectively. The obtained results from the continuous tests showed a COD removal percentage of more than 90% for the two types of wastewater considered. The removal of biorefractory COD and salts was obtained with a membrane technology in order to reuse the RO permeate in the factory production cycle. The rejections percentage of soluble COD, chlorides and sulphates were 92.8%, 95.0% and 99.5%, respectively. Because the spiral membranes required a high number of washing cycles, the use of plane membranes was preferable. Finally, the RO reject material should be evaporated using the large amount of inexpensive heat present in this type of industry.

Simultaneous denitrification and denitrifying phosphorus removal in a full-scale anoxic-oxic process without internal recycle treating low strength wastewater.

PubMed

Wang, Qibin; Chen, Qiuwen

2016-01-01

Performance of a full-scale anoxic-oxic activated sludge treatment plant (4.0×10(5) m(3)/day for the first-stage project) was followed during a year. The plant performed well for the removal of carbon, nitrogen and phosphorus in the process of treating domestic wastewater within a temperature range of 10.8°C to 30.5°C. Mass balance calculations indicated that COD utilization mainly occurred in the anoxic phase, accounting for 88.2% of total COD removal. Ammonia nitrogen removal occurred 13.71% in the anoxic zones and 78.77% in the aerobic zones. The contribution of anoxic zones to total nitrogen (TN) removal was 57.41%. Results indicated that nitrogen elimination in the oxic tanks was mainly contributed by simultaneous nitrification and denitrification (SND). The reduction of phosphorus mainly took place in the oxic zones, 61.46% of the total removal. Denitrifying phosphorus removal was achieved biologically by 11.29%. Practical experience proved that adaptability to gradually changing temperature of the microbial populations was important to maintain the plant overall stability. Sudden changes in temperature did not cause paralysis of the system just lower removal efficiency, which could be explained by functional redundancy of microorganisms that may compensate the adverse effects of temperature changes to a certain degree. Anoxic-oxic process without internal recycling has great potential to treat low strength wastewater (i.e., TN<35 mg/L) as well as reducing operation costs. Copyright © 2015. Published by Elsevier B.V.

7th Annual Systems Biology Symposium: Systems Biology and Engineering

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

Galitski, Timothy P.

2008-04-01

Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering aremore » now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."« less

Drug delivery across length scales.

PubMed

Delcassian, Derfogail; Patel, Asha K; Cortinas, Abel B; Langer, Robert

2018-02-20

Over the last century, there has been a dramatic change in the nature of therapeutic, biologically active molecules available to treat disease. Therapies have evolved from extracted natural products towards rationally designed biomolecules, including small molecules, engineered proteins and nucleic acids. The use of potent drugs which target specific organs, cells or biochemical pathways, necessitates new tools which can enable controlled delivery and dosing of these therapeutics to their biological targets. Here, we review the miniaturisation of drug delivery systems from the macro to nano-scale, focussing on controlled dosing and controlled targeting as two key parameters in drug delivery device design. We describe how the miniaturisation of these devices enables the move from repeated, systemic dosing, to on-demand, targeted delivery of therapeutic drugs and highlight areas of focus for the future.

Multiscale mechanobiology: computational models for integrating molecules to multicellular systems

PubMed Central

Mak, Michael; Kim, Taeyoon

2015-01-01

Mechanical signals exist throughout the biological landscape. Across all scales, these signals, in the form of force, stiffness, and deformations, are generated and processed, resulting in an active mechanobiological circuit that controls many fundamental aspects of life, from protein unfolding and cytoskeletal remodeling to collective cell motions. The multiple scales and complex feedback involved present a challenge for fully understanding the nature of this circuit, particularly in development and disease in which it has been implicated. Computational models that accurately predict and are based on experimental data enable a means to integrate basic principles and explore fine details of mechanosensing and mechanotransduction in and across all levels of biological systems. Here we review recent advances in these models along with supporting and emerging experimental findings. PMID:26019013

The relevance of nanoscale biological fragments for ice nucleation in clouds

NASA Astrophysics Data System (ADS)

O‧Sullivan, D.; Murray, B. J.; Ross, J. F.; Whale, T. F.; Price, H. C.; Atkinson, J. D.; Umo, N. S.; Webb, M. E.

2015-01-01

Most studies of the role of biological entities as atmospheric ice-nucleating particles have focused on relatively rare supermicron particles such as bacterial cells, fungal spores and pollen grains. However, it is not clear that there are sufficient numbers of these particles in the atmosphere to strongly influence clouds. Here we show that the ice-nucleating activity of a fungus from the ubiquitous genus Fusarium is related to the presence of nanometre-scale particles which are far more numerous, and therefore potentially far more important for cloud glaciation than whole intact spores or hyphae. In addition, we quantify the ice-nucleating activity of nano-ice nucleating particles (nano-INPs) washed off pollen and also show that nano-INPs are present in a soil sample. Based on these results, we suggest that there is a reservoir of biological nano-INPs present in the environment which may, for example, become aerosolised in association with fertile soil dust particles.

Effect of chemical and biological surfactants on activated sludge of MBR system: microscopic analysis and foam test.

PubMed

Capodici, Marco; Di Bella, Gaetano; Nicosia, Salvatore; Torregrossa, Michele

2015-02-01

A bench-scale MBR unit was operated, under stressing condition, with the aim of stimulating the onset of foaming in the activated sludge. Possible synergies between synthetic surfactants in the wastewater and biological surfactants (Extra-Cellular Polymeric Substances, EPSs) were investigated by changing C/N ratio. The growth of filamentous bacteria was also discussed. The MBR unit provided satisfactory overall carbon removal overall efficiencies: in particular, synthetic surfactants were removed with efficiency higher than 90% and 95% for non-ionic and ionic surfactants, respectively. Lab investigation suggested also the importance to reduce synthetic surfactants presence entering into mixed liquor: otherwise, their presence can significantly worsen the natural foaming caused by biological surfactants (EPSs) produced by bacteria. Finally, a new analytic method based on "ink test" has been proposed as a useful tool to achieve a valuation of EPSs bound fraction. Copyright © 2014 Elsevier Ltd. All rights reserved.

Non-equilibrium assembly of microtubules: from molecules to autonomous chemical robots.

PubMed

Hess, H; Ross, Jennifer L

2017-09-18

Biological systems have evolved to harness non-equilibrium processes from the molecular to the macro scale. It is currently a grand challenge of chemistry, materials science, and engineering to understand and mimic biological systems that have the ability to autonomously sense stimuli, process these inputs, and respond by performing mechanical work. New chemical systems are responding to the challenge and form the basis for future responsive, adaptive, and active materials. In this article, we describe a particular biochemical-biomechanical network based on the microtubule cytoskeletal filament - itself a non-equilibrium chemical system. We trace the non-equilibrium aspects of the system from molecules to networks and describe how the cell uses this system to perform active work in essential processes. Finally, we discuss how microtubule-based engineered systems can serve as testbeds for autonomous chemical robots composed of biological and synthetic components.

The relevance of nanoscale biological fragments for ice nucleation in clouds.

PubMed

O'Sullivan, D; Murray, B J; Ross, J F; Whale, T F; Price, H C; Atkinson, J D; Umo, N S; Webb, M E

2015-01-28

Most studies of the role of biological entities as atmospheric ice-nucleating particles have focused on relatively rare supermicron particles such as bacterial cells, fungal spores and pollen grains. However, it is not clear that there are sufficient numbers of these particles in the atmosphere to strongly influence clouds. Here we show that the ice-nucleating activity of a fungus from the ubiquitous genus Fusarium is related to the presence of nanometre-scale particles which are far more numerous, and therefore potentially far more important for cloud glaciation than whole intact spores or hyphae. In addition, we quantify the ice-nucleating activity of nano-ice nucleating particles (nano-INPs) washed off pollen and also show that nano-INPs are present in a soil sample. Based on these results, we suggest that there is a reservoir of biological nano-INPs present in the environment which may, for example, become aerosolised in association with fertile soil dust particles.

[Progress in synthetic biology of pinocembrin].

PubMed

Guo, Lei; Kong, Jianqiang

2015-04-01

Pinocembrin, belonging to flavanons, was isolated from various plants. Pinocembrin has a variety of pharmacological activities, such as neuroprotective effect, antimicrobial activity, and antioxidant efficacy. Pinocembrin was approved as class I drugs to its phase II clinical trial by CFDA in 2009, mainly used for the treatment of ischemic stroke. As a promising compound, the manufacturing technologies of pinocembrin, including chemical synthesis, extraction from plant and synthetic biology, have attracted many attentions. Compared with the first two technologies, synthetic biology has many advantages, such as environment-friendly and low-cost. Construction of biosynthetic pathway in microorganism offers promising results for large scale pinocembrin production by fermentation after taking lots of effective strategies. This article reviews some of recent strategies in microorganisms to improve the yield, with focus on the selection of appropriate the key enzyme sources, the supply of precursors and cofactors by microorganisms, the choice of substance and the level of the key enzyme expression.

Genetically Engineered Natural Killer Cells as a Means for Adoptive Tumor Immunotherapy.

PubMed

Michen, Susanne; Temme, Achim

2016-01-01

Natural killer (NK) cells are lymphoid cells of the innate immune system; they stand at the first defense line against viruses and transformed cells. NK cells use an array of germline-encoded activating and inhibitory receptors that sense virus-infected cells or malignant cells displaying altered surface expression of activating and inhibitory NK cell ligands. They exert potent cytotoxic responses to cellular targets and thus are candidate effector cells for immunotherapy of cancer. In particular, the genetic engineering of NK cells with chimeric antigen receptors (CARs) against surface-expressed tumor-associated antigens (TAAs) seems promising. In the allogeneic context, gene-modified NK cells compared to T cells may be superior because they are short-lived effector cells and do not cause graft-versus-host disease. Furthermore, their anti-tumoral activity can be augmented by combinatorial use with therapeutic antibodies, chemotherapeutics, and radiation. Today, efforts are being undertaken for large-scale NK-cell expansion and their genetic engineering for adoptive cell transfer. With the recent advances in understanding the complex biological interactions that regulate NK cells, it is expected that the genetic engineering of NK cells and a combinatorial blockade of immune evasion mechanisms are required to exploit the full potential of NK-cell-based immunotherapies.

Chapter 6. Temporal and spatial scales

Treesearch

Robert R. Ziemer

1997-01-01

Human activities have degraded substantial portions of the nation’s ecological resources, including physical and biological aquatic systems. The effects are continuing and cumulative, and few high-quality aquatic ecosystems remain in the United States. Concern about these diminishing resources has resulted in numerous restoration programs. Some are well conceived...

Cosmic ray soil moisture observing systems comos in cap fields at El Reno Oklahoma

USDA-ARS?s Scientific Manuscript database

Soil water content (SWC) partitions rainfall into runoff and infiltration, modulates surface and atmospheric exchanges of water and energy, affects plant growth and crop yields, and impacts chemical and biological activities of soil, among other things. Thus, SWC, especially over large scales, is a...

How-to-Do-It. How Long Is a Long Time?

ERIC Educational Resources Information Center

McComas, William F.

1990-01-01

Presented is an activity designed to help students understand and appreciate the scale and order of the geologic timetable and begin to infer a relationship between biologic, chemical, and geological events. Procedures, background information, student worksheets with answers, and a list of materials are included. (CW)

Simplified Large-Scale Refolding, Purification, and Characterization of Recombinant Human Granulocyte-Colony Stimulating Factor in Escherichia coli

PubMed Central

Kim, Chang Kyu; Lee, Chi Ho; Lee, Seung-Bae; Oh, Jae-Wook

2013-01-01

Granulocyte-colony stimulating factor (G-CSF) is a pleiotropic cytokine that stimulates the development of committed hematopoietic progenitor cells and enhances the functional activity of mature cells. Here, we report a simplified method for fed-batch culture as well as the purification of recombinant human (rh) G-CSF. The new system for rhG-CSF purification was performed using not only temperature shift strategy without isopropyl-l-thio-β-d-galactoside (IPTG) induction but also the purification method by a single step of prep-HPLC after the pH precipitation of the refolded samples. Through these processes, the final cell density and overall yield of homogenous rhG-CSF were obtained 42.8 g as dry cell weights, 1.75 g as purified active proteins, from 1 L culture broth, respectively. The purity of rhG-CSF was finally 99% since the isoforms of rhG-CSF could be separated through the prep-HPLC step. The result of biological activity indicated that purified rhG-CSF has a similar profile to the World Health Organization (WHO) 2nd International Standard for G-CSF. Taken together, our results demonstrate that the simple purification through a single step of prep-HPLC may be valuable for the industrial-scale production of biologically active proteins. PMID:24224041

Active wound dressings based on bacterial nanocellulose as drug delivery system for octenidine.

PubMed

Moritz, Sebastian; Wiegand, Cornelia; Wesarg, Falko; Hessler, Nadine; Müller, Frank A; Kralisch, Dana; Hipler, Uta-Christina; Fischer, Dagmar

2014-08-25

Although bacterial nanocellulose (BNC) may serve as an ideal wound dressing, it exhibits no antibacterial properties by itself. Therefore, in the present study BNC was functionalized with the antiseptic drug octenidine. Drug loading and release, mechanical characteristics, biocompatibility, and antimicrobial efficacy were investigated. Octenidine release was based on diffusion and swelling according to the Ritger-Peppas equation and characterized by a time dependent biphasic release profile, with a rapid release in the first 8h, followed by a slower release rate up to 96 h. The comparison between lab-scale and up-scale BNC identified thickness, water content, and the surface area to volume ratio as parameters which have an impact on the control of the release characteristics. Compression and tensile strength remained unchanged upon incorporation of octenidine in BNC. In biological assays, drug-loaded BNC demonstrated high biocompatibility in human keratinocytes and antimicrobial activity against Staphylococcus aureus. In a long-term storage test, the octenidine loaded in BNC was found to be stable, releasable, and biologically active over a period of 6 months without changes. In conclusion, octenidine loaded BNC presents a ready-to-use wound dressing for the treatment of infected wounds that can be stored over 6 months without losing its antibacterial activity. Copyright © 2014 Elsevier B.V. All rights reserved.

Evaluation of denitrification potential of rotating biological contactors for treatment of municipal wastewater.

PubMed

Hanhan, O; Orhon, D; Krauth, Kh; Günder, B

2005-01-01

In this study the effect of retention time and rotation speed in the denitrification process in two full-scale rotating biological contactors (RBC) which were operated parallel and fed with municipal wastewater is evaluated. Each rotating biological contactor was covered to prevent oxygen input. The discs were 40% submerged. On the axle of one of the rotating biological contactors lamellas were placed (RBC1). During the experiments the nitrate removal performance of the rotating biological contactor with lamellas was observed to be less than the other (RBC2) since the lamellas caused oxygen diffusion through their movement. The highest nitrate removal observed was 2.06 g/m2.d achieved by a contact time of 28.84 minutes and a recycle flow of 1 l/s. The rotation speed during this set had the constant value of 0.8 min(-1). Nitrate removal efficiency on RBC1 was decreasing with increasing rotation speed. On the rotating biological contactor without lamellas no effect on denitrification could be determined within a speed range from 0.67 to 2.1 min-1. If operated in proper conditions denitrification on RBC is a very suitable alternative for nitrogen removal that can easily fulfil the nutrient limitations in coastal areas due to the rotating biological contactors economical benefits and uncomplicated handling.

Foraging mode affects the evolution of egg size in generalist predators embedded in complex food webs.

PubMed

Verdeny-Vilalta, O; Fox, C W; Wise, D H; Moya-Laraño, J

2015-06-01

Ecological networks incorporate myriad biotic interactions that determine the selection pressures experienced by the embedded populations. We argue that within food webs, the negative scaling of abundance with body mass and foraging theory predict that the selective advantages of larger egg size should be smaller for sit-and-wait than active-hunting generalist predators, leading to the evolution of a difference in egg size between them. Because body mass usually scales negatively with predator abundance and constrains predation rate, slightly increasing egg mass should simultaneously allow offspring to feed on more prey and escape from more predators. However, the benefits of larger offspring would be relatively smaller for sit-and-wait predators because (i) due to their lower mobility, encounters with other predators are less common, and (ii) they usually employ a set of alternative hunting strategies that help to subdue relatively larger prey. On the other hand, for active predators, which need to confront prey as they find them, body-size differences may be more important in subduing prey. This difference in benefits should lead to the evolution of larger egg sizes in active-hunting relative to sit-and-wait predators. This prediction was confirmed by a phylogenetically controlled analysis of 268 spider species, supporting the view that the structure of ecological networks may serve to predict relevant selective pressures acting on key life history traits. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Potential for enhancement of aerobic biological removal of recalcitrant organic matter in bleached pulp mill effluents.

PubMed

Mounteer, A H; Souza, L C; Silva, C M

2007-02-01

Increasingly stringent effluent quality limits for bleached kraft pulp mills pose a great challenge to mill wastewater system managers since these limits can require levels of chemical oxygen demand (COD) removal efficiency rarely reported for biological treatment of these types of effluents. The present study was therefore undertaken to better understand the nature of recalcitrant COD in bleached kraft pulp effluents that persists through the biological treatment system. Bleaching effluents from a Brazilian eucalypt bleached kraft pulp mill were collected and treated in a bench-scale sequencing batch reactor. Organic matter in raw and treated effluents was characterized before and after separation into low and high molecular mass fractions. Biological treatment removed 71% of the COD, with 83% removal of the low molecular mass COD but only 36% removal of the high molecular mass COD. Microorganisms capable of degrading the recalcitrant COD were isolated from enrichment cultures of the original activated sludge fed on fractions of the bleaching effluent that presented low biodegradabilities. Use of a microbial consortium composed of ten of these isolates to treat the biologically treated effluent removed a further 12% of the effluent COD, all from the high molecular mass fraction. Results of this research indicate that microorganisms with potential for degrading recalcitrant COD are present in activated sludge, but that these are not metabolically active during normal activated sludge treatment of mill effluents. The use of biological selectors in the treatment system to promote growth of such microorganisms may enhance removal of recalcitrant organic matter.

Oxygen transfer and uptake, nutrient removal, and energy footprint of parallel full-scale IFAS and activated sludge processes.

PubMed

Rosso, Diego; Lothman, Sarah E; Jeung, Matthew K; Pitt, Paul; Gellner, W James; Stone, Alan L; Howard, Don

2011-11-15

Integrated fixed-film activated sludge (IFAS) processes are becoming more popular for both secondary and sidestream treatment in wastewater facilities. These processes are a combination of biofilm reactors and activated sludge processes, achieved by introducing and retaining biofilm carrier media in activated sludge reactors. A full-scale train of three IFAS reactors equipped with AnoxKaldnes media and coarse-bubble aeration was tested using off-gas analysis. This was operated independently in parallel to an existing full-scale activated sludge process. Both processes achieved the same percent removal of COD and ammonia, despite the double oxygen demand on the IFAS reactors. In order to prevent kinetic limitations associated with DO diffusional gradients through the IFAS biofilm, this systems was operated at an elevated dissolved oxygen concentration, in line with the manufacturer's recommendation. Also, to avoid media coalescence on the reactor surface and promote biofilm contact with the substrate, high mixing requirements are specified. Therefore, the air flux in the IFAS reactors was much higher than that of the parallel activated sludge reactors. However, the standardized oxygen transfer efficiency in process water was almost same for both processes. In theory, when the oxygen transfer efficiency is the same, the air used per unit load removed should be the same. However, due to the high DO and mixing requirements, the IFAS reactors were characterized by elevated air flux and air use per unit load treated. This directly reflected in the relative energy footprint for aeration, which in this case was much higher for the IFAS system than activated sludge. Copyright © 2011 Elsevier Ltd. All rights reserved.

Evaluation of Biologically Active Compounds from Calendula officinalis Flowers using Spectrophotometry

PubMed Central

2012-01-01

Background This study aimed to quantify the active biological compounds in C. officinalis flowers. Based on the active principles and biological properties of marigolds flowers reported in the literature, we sought to obtain and characterize the molecular composition of extracts prepared using different solvents. The antioxidant capacities of extracts were assessed by using spectrophotometry to measure both absorbance of the colorimetric free radical scavenger 2,2-diphenyl-1-picrylhydrazyl (DPPH) as well as the total antioxidant potential, using the ferric reducing power (FRAP) assay. Results Spectrophotometric assays in the ultraviolet-visible (UV-VIS) region enabled identification and characterization of the full range of phenolic and flavonoids acids, and high-performance liquid chromatography (HPLC) was used to identify and quantify phenolic compounds (depending on the method of extraction). Methanol ensured more efficient extraction of flavonoids than the other solvents tested. Antioxidant activity in methanolic extracts was correlated with the polyphenol content. Conclusions The UV-VIS spectra of assimilator pigments (e.g. chlorophylls), polyphenols and flavonoids extracted from the C. officinalis flowers consisted in quantitative evaluation of compounds which absorb to wavelengths broader than 360 nm. PMID:22540963

A fresh look at the male-specific region of the human Y chromosome.

PubMed

Jangravi, Zohreh; Alikhani, Mehdi; Arefnezhad, Babak; Sharifi Tabar, Mehdi; Taleahmad, Sara; Karamzadeh, Razieh; Jadaliha, Mahdieh; Mousavi, Seyed Ahmad; Ahmadi Rastegar, Diba; Parsamatin, Pouria; Vakilian, Haghighat; Mirshahvaladi, Shahab; Sabbaghian, Marjan; Mohseni Meybodi, Anahita; Mirzaei, Mehdi; Shahhoseini, Maryam; Ebrahimi, Marzieh; Piryaei, Abbas; Moosavi-Movahedi, Ali Akbar; Haynes, Paul A; Goodchild, Ann K; Nasr-Esfahani, Mohammad Hossein; Jabbari, Esmaiel; Baharvand, Hossein; Sedighi Gilani, Mohammad Ali; Gourabi, Hamid; Salekdeh, Ghasem Hosseini

2013-01-04

The Chromosome-centric Human Proteome Project (C-HPP) aims to systematically map the entire human proteome with the intent to enhance our understanding of human biology at the cellular level. This project attempts simultaneously to establish a sound basis for the development of diagnostic, prognostic, therapeutic, and preventive medical applications. In Iran, current efforts focus on mapping the proteome of the human Y chromosome. The male-specific region of the Y chromosome (MSY) is unique in many aspects and comprises 95% of the chromosome's length. The MSY continually retains its haploid state and is full of repeated sequences. It is responsible for important biological roles such as sex determination and male fertility. Here, we present the most recent update of MSY protein-encoding genes and their association with various traits and diseases including sex determination and reversal, spermatogenesis and male infertility, cancers such as prostate cancers, sex-specific effects on the brain and behavior, and graft-versus-host disease. We also present information available from RNA sequencing, protein-protein interaction, post-translational modification of MSY protein-coding genes and their implications in biological systems. An overview of Human Y chromosome Proteome Project is presented and a systematic approach is suggested to ensure that at least one of each predicted protein-coding gene's major representative proteins will be characterized in the context of its major anatomical sites of expression, its abundance, and its functional relevance in a biological and/or medical context. There are many technical and biological issues that will need to be overcome in order to accomplish the full scale mapping.

Spatio-temporal dynamics of a fish spawning aggregation and its fishery in the Gulf of California

PubMed Central

Erisman, Brad; Aburto-Oropeza, Octavio; Gonzalez-Abraham, Charlotte; Mascareñas-Osorio, Ismael; Moreno-Báez, Marcia; Hastings, Philip A.

2012-01-01

We engaged in cooperative research with fishers and stakeholders to characterize the fine-scale, spatio-temporal characteristics of spawning behavior in an aggregating marine fish (Cynoscion othonopterus: Sciaenidae) and coincident activities of its commercial fishery in the Upper Gulf of California. Approximately 1.5–1.8 million fish are harvested annually from spawning aggregations of C. othonopterus during 21–25 days of fishing and within an area of 1,149 km2 of a biosphere reserve. Spawning and fishing are synchronized on a semi-lunar cycle, with peaks in both occurring 5 to 2 days before the new and full moon, and fishing intensity and catch are highest at the spawning grounds within a no-take reserve. Results of this study demonstrate the benefits of combining GPS data loggers, fisheries data, biological surveys, and cooperative research with fishers to produce spatio-temporally explicit information relevant to the science and management of fish spawning aggregations and the spatial planning of marine reserves. PMID:22359736

Biofiltration: An innovative air pollution control technology for VOC emissions

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

Leson, G.; Winer, A.M.

1991-08-01

Biofiltration is a relatively recent air pollution control (APC) technology in which off-gases containing biodegradable volatile organic compounds (VOC) or inorganic air toxics are vented through a biologically active material. This technology has been successfully applied in Germany and The Netherlands in many full-scale applications to control odors, VOC and air toxic emissions from a wide range of industrial and public sector sources. Control efficiencies of more than 90 percent have been achieved for many common air pollutants. Due to lower operating costs, biofiltration can provide significant economic advantages over other APC technologies if applied to off-gases that contain readilymore » biodegradable pollutants in low concentrations. Environmental benefits include low energy requirements and the avoidance of cross media transfer of pollutants. This paper reviews the history and current status of biofiltration, outlines its underlying scientific and engineering principles, and discusses the applicability of biofilters for a wide range of specific emission sources.« less

Potential New Ligand Systems for Binding Uranyl Ions in Seawater Environments

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

Arnold, John

2014-12-13

Work began this quarter on a new project involving a combined computational and biosynthetic approach to selective recognition of uranyl ion in aqueous solution. This project exploits the results of computational studies to discover new ligand classes. Synthetic studies will follow to generate target systems for uranyl binding and determination of binding constants. The process will be iterative, with results from computation informing synthesis, and vice versa. The theme of the ligand classes to be examined initially will be biologically based. New phosphonate-containing α-amino acid N-carboxyanhydride (NCA) monomers were used recently to prepare well-defined phosphonate-containing poly-peptides and block copolypeptides. Ourmore » first approach is to utilize these phosphate- and phosphonate-containing NCAs for the coordination of uranyl. The work includes the laboratory-scale preparation of a series of NCAs and the full thermodynamic and spectroscopic characterization of the resulting uranyl complexes. We are also evaluating the sequestering activity in different physiological and environmental conditions of these copolymers as well as their biodegradability.« less

Mutant FGF-23 responsible for autosomal dominant hypophosphatemic rickets is resistant to proteolytic cleavage and causes hypophosphatemia in vivo.

PubMed

Shimada, Takashi; Muto, Takanori; Urakawa, Itaru; Yoneya, Takashi; Yamazaki, Yuji; Okawa, Katsuya; Takeuchi, Yasuhiro; Fujita, Toshiro; Fukumoto, Seiji; Yamashita, Takeyoshi

2002-08-01

FGF-23 is involved in the pathogenesis of two similar hypophosphatemic diseases, autosomal dominant hypophosphatemic rickets/osteomalacia (ADHR) and tumor-induced osteomalacia (TIO). We have shown that the overproduction of FGF-23 by tumors causes TIO. In contrast, ADHR derives from missense mutations in FGF-23 gene. However, it has been unclear how those mutations affect phosphate metabolism. Therefore, we produced mutant as well as wild-type FGF-23 proteins and examined their biological activity. Western blot analysis using site-specific antibodies showed that wild-type FGF-23 secreted into conditioned media was partially cleaved between Arg(179) and Ser(180). In addition, further processing of the cleaved N-terminal portion was observed. In constrast, mutant FGF-23 proteins found in ADHR were resistant to the cleavage. In order to clarify which molecule has the biological activity to induce hypophosphatemia, we separated full-length protein, the N-terminal and C-terminal fragments of wild-type FGF-23. When the activity of each fraction was examined in vivo, only the full-length FGF-23 decreased serum phosphate. Mutant FGF-23 protein that was resistant to the cleavage also retained the activity to induce hypophosphatemia. The extent of hypophosphatemia induced by the single administration of either wild-type or the mutant full-length FGF-23 protein was similar. In addition, implantation of CHO cells expressing the mutant FGF-23 protein caused hypophosphatemia and the decrease of bone mineral content. We conclude that ADHR is caused by hypophosphatemic action of mutant full-length FGF-23 proteins that are resistant to the cleavage between Arg(179) and Ser(180).

Regional-Scale Forcing and Feedbacks from Alternative Scenarios of Global-Scale Land Use Change

NASA Astrophysics Data System (ADS)

Jones, A. D.; Chini, L. P.; Collins, W.; Janetos, A. C.; Mao, J.; Shi, X.; Thomson, A. M.; Torn, M. S.

2011-12-01

Future patterns of land use change depend critically on the degree to which terrestrial carbon management strategies, such as biological carbon sequestration and biofuels, are utilized in order to mitigate global climate change. Furthermore, land use change associated with terrestrial carbon management induces biogeophysical changes to surface energy budgets that perturb climate at regional and possibly global scales, activating different feedback processes depending on the nature and location of the land use change. As a first step in a broader effort to create an integrated earth system model, we examine two scenarios of future anthropogenic activity generated by the Global Change Assessment Model (GCAM) within the full-coupled Community Earth System Model (CESM). Each scenario stabilizes radiative forcing from greenhouse gases and aerosols at 4.5 W/m^2. In the first, stabilization is achieved through a universal carbon tax that values terrestrial carbon equally with fossil carbon, leading to modest afforestation globally and low biofuel utilization. In the second scenario, stabilization is achieved with a tax on fossil fuel and industrial carbon alone. In this case, biofuel utilization increases dramatically and crop area expands to claim approximately 50% of forest cover globally. By design, these scenarios exhibit identical climate forcing from atmospheric constituents. Thus, differences among them can be attributed to the biogeophysical effects of land use change. In addition, we utilize offline radiative transfer and offline land model simulations to identify forcing and feedback mechanisms operating in different regions. We find that boreal deforestation has a strong climatic signature due to significant albedo change coupled with a regional-scale water vapor feedback. Tropical deforestation, on the other hand, has more subtle effects on climate. Globally, the two scenarios yield warming trends over the 21st century that differ by 0.5 degrees Celsius. This work demonstrates the importance of land use in shaping future patterns of climate change, both globally and regionally.

On the Scaling of Small, Heat Simulated Jet Noise Measurements to Moderate Size Exhaust Jets

NASA Technical Reports Server (NTRS)

McLaughlin, Dennis K.; Bridges, James; Kuo, Ching-Wen

2010-01-01

Modern military aircraft jet engines are designed with variable geometry nozzles to provide optimum thrust in different operating conditions, depending on the flight envelope. However, the acoustic measurements for such nozzles are scarce, due to the cost involved in making full scale measurements and the lack of details about the exact geometry of these nozzles. Thus the present effort at The Pennsylvania State University and the NASA Glenn Research Center- in partnership with GE Aviation is aiming to study and characterize the acoustic field produced by supersonic jets issuing from converging-diverging military style nozzles. An equally important objective is to validate methodology for using data obtained from small and moderate scale experiments to reliably predict the most important components of full scale engine noise. The experimental results presented show reasonable agreement between small scale and moderate scale jet acoustic data, as well as between heated jets and heat-simulated ones. Unresolved issues however are identified that are currently receiving our attention, in particular the effect of the small bypass ratio airflow. Future activities will identify and test promising noise reduction techniques in an effort to predict how well such concepts will work with full scale engines in flight conditions.

Low-Activity Waste Pretreatment System Additional Engineering-Scale Integrated Test Report

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

Landon, Matt R.; Wilson, Robert A.

Washington River Protections Solutions, LLC’s (WRPS) Low Activity Waste Pretreatment System (LAWPS) Project provides for the early production of immobilized low-activity waste (ILAW) by feeding LAW directly from Tank Farms to the Waste Treatment and Immobilization Plant (WTP) LAW Facility, bypassing the WTP Pretreatment Facility. Prior to the transfer of feed to the WTP LAW Vitrification Facility, tank supernatant waste will be pretreated in the LAWPS to meet the WTP LAW waste acceptance criteria (WAC). Full-scale and engineering-scale testing of critical technology elements, as part of the technology maturation process, are components of the overall LAWPS Project. WRPS awarded themore » engineering-scale integrated testing scope to AECOM via WRPS Subcontract 58349. This report is deliverable MSR-008 of the subcontract.« less

Conferring biological activity to native spider silk: A biofunctionalized protein-based microfiber.

PubMed

Wu, Hsuan-Chen; Quan, David N; Tsao, Chen-Yu; Liu, Yi; Terrell, Jessica L; Luo, Xiaolong; Yang, Jen-Chang; Payne, Gregory F; Bentley, William E

2017-01-01

Spider silk is an extraordinary material with physical properties comparable to the best scaffolding/structural materials, and as a fiber it can be manipulated with ease into a variety of configurations. Our work here demonstrates that natural spider silk fibers can also be used to organize biological components on and in devices through rapid and simple means. Micron scale spider silk fibers (5-10 μm in diameter) were surface modified with a variety of biological entities engineered with pentaglutamine tags via microbial transglutaminase (mTG). Enzymes, enzyme pathways, antibodies, and fluorescent proteins were all assembled onto spider silk fibers using this biomolecular engineering/biofabrication process. Additionally, arrangement of biofunctionalized fiber should in of itself generate a secondary level of biomolecular organization. Toward this end, as proofs of principle, spatially defined arrangement of biofunctionalized spider silk fiber was shown to generate effects specific to silk position in two cases. In one instance, arrangement perpendicular to a flow produced selective head and neck carcinoma cell capture on silk with antibodies complexed to conjugated protein G. In a second scenario, asymmetric bacterial chemotaxis arose from asymmetric conjugation of enzymes to arranged silk. Overall, the biofabrication processes used here were rapid, required no complex chemistries, were biologically benign, and also the resulting engineered silk microfibers were flexible, readily manipulated and functionally active. Deployed here in microfluidic environments, biofunctional spider silk fiber provides a means to convey complex biological functions over a range of scales, further extending its potential as a biomaterial in biotechnological settings. Biotechnol. Bioeng. 2017;114: 83-95. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Culture-Dependent and -Independent Identification of Polyphosphate-Accumulating Dechloromonas spp. Predominating in a Full-Scale Oxidation Ditch Wastewater Treatment Plant.

PubMed

Terashima, Mia; Yama, Ayano; Sato, Megumi; Yumoto, Isao; Kamagata, Yoichi; Kato, Souichiro

2016-12-23

The oxidation ditch process is one of the most economical approaches currently used to simultaneously remove organic carbon, nitrogen, and also phosphorus (P) from wastewater. However, limited information is available on biological P removal in this process. In the present study, microorganisms contributing to P removal in a full-scale oxidation ditch reactor were investigated using culture-dependent and -independent approaches. A microbial community analysis based on 16S rRNA gene sequencing revealed that a phylotype closely related to Dechloromonas spp. in the family Rhodocyclaceae dominated in the oxidation ditch reactor. This dominant Dechloromonas sp. was successfully isolated and subjected to fluorescent staining for polyphosphate, followed by microscopic observations and a spectrofluorometric analysis, which clearly demonstrated that the Dechloromonas isolate exhibited a strong ability to accumulate polyphosphate within its cells. These results indicate the potential key role of Dechloromonas spp. in efficient P removal in the oxidation ditch wastewater treatment process.

Culture-Dependent and -Independent Identification of Polyphosphate-Accumulating Dechloromonas spp. Predominating in a Full-Scale Oxidation Ditch Wastewater Treatment Plant

PubMed Central

Terashima, Mia; Yama, Ayano; Sato, Megumi; Yumoto, Isao; Kamagata, Yoichi; Kato, Souichiro

2016-01-01

The oxidation ditch process is one of the most economical approaches currently used to simultaneously remove organic carbon, nitrogen, and also phosphorus (P) from wastewater. However, limited information is available on biological P removal in this process. In the present study, microorganisms contributing to P removal in a full-scale oxidation ditch reactor were investigated using culture-dependent and -independent approaches. A microbial community analysis based on 16S rRNA gene sequencing revealed that a phylotype closely related to Dechloromonas spp. in the family Rhodocyclaceae dominated in the oxidation ditch reactor. This dominant Dechloromonas sp. was successfully isolated and subjected to fluorescent staining for polyphosphate, followed by microscopic observations and a spectrofluorometric analysis, which clearly demonstrated that the Dechloromonas isolate exhibited a strong ability to accumulate polyphosphate within its cells. These results indicate the potential key role of Dechloromonas spp. in efficient P removal in the oxidation ditch wastewater treatment process. PMID:27867159

Short mechanical biological treatment of municipal solid waste allows landfill impact reduction saving waste energy content.

PubMed

Scaglia, Barbara; Salati, Silvia; Di Gregorio, Alessandra; Carrera, Alberto; Tambone, Fulvia; Adani, Fabrizio

2013-09-01

The aim of this work was to evaluate the effects of full scale MBT process (28 d) in removing inhibition condition for successive biogas (ABP) production in landfill and in reducing total waste impact. For this purpose the organic fraction of MSW was treated in a full-scale MBT plant and successively incubated vs. untreated waste, in simulated landfills for one year. Results showed that untreated landfilled-waste gave a total ABP reduction that was null. On the contrary MBT process reduced ABP of 44%, but successive incubation for one year in landfill gave a total ABP reduction of 86%. This ABP reduction corresponded to a MBT process of 22 weeks length, according to the predictive regression developed for ABP reduction vs. MBT-time. Therefore short MBT allowed reducing landfill impact, preserving energy content (ABP) to be produced successively by bioreactor technology since pre-treatment avoided process inhibition because of partial waste biostabilization. Copyright © 2013 Elsevier Ltd. All rights reserved.

Tertiary ozonation of industrial wastewater for the removal of estrogenic compounds (NP and BPA): a full-scale case study.

PubMed

Bertanza, G; Papa, M; Pedrazzani, R; Repice, C; Dal Grande, M

2013-01-01

Wastewater treatment plant (WWTP) effluents are considered to be a major source for the release in the aquatic environment of endocrine-disrupting compounds (EDCs). Ozone has proved to be a suitable solution for polishing secondary domestic effluents. In this work, the performance of a full-scale ozonation plant was investigated in order to assess the removal efficiency of four target EDCs: nonylphenol, nonylphenol monoethoxylate, nonylphenol diethoxylate and bisphenol A. The studied system was the tertiary treatment stage of a municipal WWTP which receives an important industrial (textile) load. Chemical analyses showed that the considered substances occurred with a significant variability, typical of real wastewaters; based on this, ozonation performance was carefully evaluated and it appeared to be negatively affected by flow-rate increase (during rainy days, with consequent contact time reduction). Moreover, EDCs' measured removal efficiency was lower than what could be predicted based on literature data, because of the relatively high residual content of biorefractory compounds still present after biological treatment.

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

McGrath, M.S.; Nieuwland, J.C.; Lith, C. van

Holzindustie Bruchsal (HIB) was required to treat moderate levels of styrene emissions from their plastic dashboard manufacturing process. After evaluating many types of control technologies, HIB decided to install a Bioton biofiltration system from Monsanto Enviro-Chem Systems Inc. (MEC). After the installation of the Bioton biofilter, HIB and MEC learned that large amounts of butylacetate were also present in the off-gas stream. The presence of butylacetate was found to have inhibitory effects on the removal of styrene. Therefore, MEC performed a series of pilot and laboratory studies to determine if a bacteria strain could be identified that would be capablemore » of removing styrene in the presence of butylacetate. It was found that a specific bacteria strain was capable of achieving high levels of styrene removal without inhibition from butylacetate in laboratory and pilot testing. This strain was inoculated into the full scale system. After acclimation, the full scale inoculation produced a consortium of bacteria that biologically removed the styrene from the dashboard manufacturing process in the presence of butylacetate.« less

Adsorption of N-nitrosodimethylamine precursors by powdered and granular activated carbon.

PubMed

Hanigan, David; Zhang, Jinwei; Herckes, Pierre; Krasner, Stuart W; Chen, Chao; Westerhoff, Paul

2012-11-20

Activated carbon (AC) has been shown to remove precursors of halogenated disinfection byproducts. Granular and powdered activated carbon (GAC, PAC) were investigated for their potential to adsorb N-nitrosodimethylamine (NDMA) precursors from blends of river water and effluent from a wastewater treatment plant (WWTP). At bench scale, waters were exposed to lignite or bituminous AC, either as PAC in bottle point experiments or as GAC in rapid small-scale column tests (RSSCTs). NDMA formation potential (FP) was used as a surrogate for precursor removal. NDMA FP was reduced by 37, 59, and 91% with 3, 8, and 75 mg/L of one PAC, respectively, with a 4-h contact time. In RSSCTs and in full-scale GAC contactors, NDMA FP removal always exceeded that of the bulk dissolved organic carbon (DOC) and UV absorbance at 254 nm. For example, whereas DOC breakthrough exceeded 90% of its influent concentration after 10,000 bed volumes of operation in an RSSCT, NDMA FP was less than 40% of influent concentration after the same bed life of the GAC. At full or pilot scale, high NDMA FP reduction ranging from >60 to >90% was achieved across GAC contactors, dependent upon the GAC bed life and/or use of a preoxidant (chlorine or ozone). In all experiments, NDMA formation was not reduced to zero, which suggests that although some precursors are strongly sorbed, others are not. This is among the first studies to show that AC is capable of adsorbing NDMA precursors, but further research is needed to better understand NDMA precursor chemical properties (e.g., hydrophobicity, molecular size) and evaluate how best to incorporate this finding into full-scale designs and practice.

Environmentally induced amplitude death and firing provocation in large-scale networks of neuronal systems

NASA Astrophysics Data System (ADS)

Pankratova, Evgeniya V.; Kalyakulina, Alena I.

2016-12-01

We study the dynamics of multielement neuronal systems taking into account both the direct interaction between the cells via linear coupling and nondiffusive cell-to-cell communication via common environment. For the cells exhibiting individual bursting behavior, we have revealed the dependence of the network activity on its scale. Particularly, we show that small-scale networks demonstrate the inability to maintain complicated oscillations: for a small number of elements in an ensemble, the phenomenon of amplitude death is observed. The existence of threshold network scales and mechanisms causing firing in artificial and real multielement neural networks, as well as their significance for biological applications, are discussed.

Nanoelectronics meets biology: from new nanoscale devices for live-cell recording to 3D innervated tissues.

PubMed

Duan, Xiaojie; Lieber, Charles M

2013-10-01

High spatiotemporal resolution interfaces between electrical sensors and biological systems, from single live cells to tissues, is crucial for many areas, including fundamental biophysical studies as well as medical monitoring and intervention. Herein, we summarize recent progress in the development and application of novel nanoscale devices for intracellular electrical recording of action potentials and the effort of merging electronic and biological systems seamlessly in three dimensions by using macroporous nanoelectronic scaffolds. The uniqueness of these nanoscale devices for minimally invasive, large-scale, high spatial resolution, and three-dimensional neural activity mapping are highlighted. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

County-scale spatial distribution of soil enzyme activities and enzyme activity indices in agricultural land: implications for soil quality assessment.

PubMed

Tan, Xiangping; Xie, Baoni; Wang, Junxing; He, Wenxiang; Wang, Xudong; Wei, Gehong

2014-01-01

Here the spatial distribution of soil enzymatic properties in agricultural land was evaluated on a county-wide (567 km(2)) scale in Changwu, Shaanxi Province, China. The spatial variations in activities of five hydrolytic enzymes were examined using geostatistical methods. The relationships between soil enzyme activities and other soil properties were evaluated using both an integrated total enzyme activity index (TEI) and the geometric mean of enzyme activities (GME). At the county scale, soil invertase, phosphatase, and catalase activities were moderately spatially correlated, whereas urease and dehydrogenase activities were weakly spatially correlated. Correlation analysis showed that both TEI and GME were better correlated with selected soil physicochemical properties than single enzyme activities. Multivariate regression analysis showed that soil OM content had the strongest positive effect while soil pH had a negative effect on the two enzyme activity indices. In addition, total phosphorous content had a positive effect on TEI and GME in orchard soils, whereas alkali-hydrolyzable nitrogen and available potassium contents, respectively, had negative and positive effects on these two enzyme indices in cropland soils. The results indicate that land use changes strongly affect soil enzyme activities in agricultural land, where TEI provides a sensitive biological indicator for soil quality.

Allelopathy as a potential strategy to improve microalgae cultivation.

PubMed

Bacellar Mendes, Leonardo Brantes; Vermelho, Alane Beatriz

2013-10-21

One of the main obstacles for continuous productivity in microalgae cultivation is the presence of biological contaminants capable of eliminating large numbers of cells in a matter of days or even hours. However, a number of strategies are being used to combat and prevent contamination in microalgae cultivation. These strategies include the use of extreme conditions in the culture media such as high salinity and high pH to create an unfavorable environment for the competitive organisms or predators of the microalgae. Numerous studies have explored the potential of naturally occurring bioactive secondary metabolites, which are natural products from plants and microorganisms, as a source of such compounds. Some of these compounds are herbicides, and marine and freshwater microalgae are a source of these compounds. Microalgae produce a remarkable diversity of biologically active metabolites. Results based on the allelopathic potential of algae have only been described for laboratory-scale production and not for algae cultivation on a pilot scale. The adoption of allelopathy on microalgal strains is an unexplored field and may be a novel solution to improve algae production. Here we present information showing the diversity of allelochemicals from microalgae and the use of an allelopathic approach to control microalgae cultivation on a pilot scale based on R&D activities being carried out in Brazil for biodiesel production.

Allelopathy as a potential strategy to improve microalgae cultivation

PubMed Central

2013-01-01

One of the main obstacles for continuous productivity in microalgae cultivation is the presence of biological contaminants capable of eliminating large numbers of cells in a matter of days or even hours. However, a number of strategies are being used to combat and prevent contamination in microalgae cultivation. These strategies include the use of extreme conditions in the culture media such as high salinity and high pH to create an unfavorable environment for the competitive organisms or predators of the microalgae. Numerous studies have explored the potential of naturally occurring bioactive secondary metabolites, which are natural products from plants and microorganisms, as a source of such compounds. Some of these compounds are herbicides, and marine and freshwater microalgae are a source of these compounds. Microalgae produce a remarkable diversity of biologically active metabolites. Results based on the allelopathic potential of algae have only been described for laboratory-scale production and not for algae cultivation on a pilot scale. The adoption of allelopathy on microalgal strains is an unexplored field and may be a novel solution to improve algae production. Here we present information showing the diversity of allelochemicals from microalgae and the use of an allelopathic approach to control microalgae cultivation on a pilot scale based on R&D activities being carried out in Brazil for biodiesel production. PMID:24499580

Vertical migrations of a deep-sea fish and its prey.

PubMed

Afonso, Pedro; McGinty, Niall; Graça, Gonçalo; Fontes, Jorge; Inácio, Mónica; Totland, Atle; Menezes, Gui

2014-01-01

It has been speculated that some deep-sea fishes can display large vertical migrations and likely doing so to explore the full suite of benthopelagic food resources, especially the pelagic organisms of the deep scattering layer (DSL). This would help explain the success of fishes residing at seamounts and the increased biodiversity found in these features of the open ocean. We combined active plus passive acoustic telemetry of blackspot seabream with in situ environmental and biological (backscattering) data collection at a seamount to verify if its behaviour is dominated by vertical movements as a response to temporal changes in environmental conditions and pelagic prey availability. We found that seabream extensively migrate up and down the water column, that these patterns are cyclic both in short-term (tidal, diel) as well as long-term (seasonal) scales, and that they partially match the availability of potential DSL prey components. Furthermore, the emerging pattern points to a more complex spatial behaviour than previously anticipated, suggesting a seasonal switch in the diel behaviour mode (benthic vs. pelagic) of seabream, which may reflect an adaptation to differences in prey availability. This study is the first to document the fine scale three-dimensional behaviour of a deep-sea fish residing at seamounts.

Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

PubMed Central

Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

2016-01-01

Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

Microbial community compositions in different functional zones of Carrousel oxidation ditch system for domestic wastewater treatment.

PubMed

Xu, Dong; Liu, Sitong; Chen, Qian; Ni, Jinren

2017-12-01

The microbial community diversity in anaerobic-, anoxic- and oxic-biological zones of a conventional Carrousel oxidation ditch system for domestic wastewater treatment was systematically investigated. The monitored results of the activated sludge sampled from six full-scale WWTPs indicated that Proteobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Verrucomicrobia, Acidobacteria and Nitrospirae were dominant phyla, and Nitrospira was the most abundant and ubiquitous genus across the three biological zones. The anaerobic-, anoxic- and oxic-zones shared approximately similar percentages across the 50 most abundant genera, and three genera (i.e. uncultured bacterium PeM15, Methanosaeta and Bellilinea) presented statistically significantly differential abundance in the anoxic-zone. Illumina high-throughput sequences related to ammonium oxidizer organisms and denitrifiers with top50 abundance in all samples were Nitrospira, uncultured Nitrosomonadaceae, Dechloromonas, Thauera, Denitratisoma, Rhodocyclaceae (norank) and Comamonadaceae (norank). Moreover, environmental variables such as water temperature, water volume, influent ammonium nitrogen, influent chemical oxygen demand (COD) and effluent COD exhibited significant correlation to the microbial community according to the Monte Carlo permutation test analysis (p < 0.05). The abundance of Nitrospira, uncultured Nitrosomonadaceae and Denitratisoma presented strong positive correlations with the influent/effluent concentration of COD and ammonium nitrogen, while Dechloromonas, Thauera, Rhodocyclaceae (norank) and Comamonadaceae (norank) showed positive correlations with water volume and temperature. The established relationship between microbial community and environmental variables in different biologically functional zones of the six representative WWTPs at different geographical locations made the present work of potential use for evaluation of practical wastewater treatment processes.

Challenges in the Development of Functional Assays of Membrane Proteins

PubMed Central

Tiefenauer, Louis; Demarche, Sophie

2012-01-01

Lipid bilayers are natural barriers of biological cells and cellular compartments. Membrane proteins integrated in biological membranes enable vital cell functions such as signal transduction and the transport of ions or small molecules. In order to determine the activity of a protein of interest at defined conditions, the membrane protein has to be integrated into artificial lipid bilayers immobilized on a surface. For the fabrication of such biosensors expertise is required in material science, surface and analytical chemistry, molecular biology and biotechnology. Specifically, techniques are needed for structuring surfaces in the micro- and nanometer scale, chemical modification and analysis, lipid bilayer formation, protein expression, purification and solubilization, and most importantly, protein integration into engineered lipid bilayers. Electrochemical and optical methods are suitable to detect membrane activity-related signals. The importance of structural knowledge to understand membrane protein function is obvious. Presently only a few structures of membrane proteins are solved at atomic resolution. Functional assays together with known structures of individual membrane proteins will contribute to a better understanding of vital biological processes occurring at biological membranes. Such assays will be utilized in the discovery of drugs, since membrane proteins are major drug targets.

A critical comparison of systematic calibration protocols for activated sludge models: a SWOT analysis.

PubMed

Sin, Gürkan; Van Hulle, Stijn W H; De Pauw, Dirk J W; van Griensven, Ann; Vanrolleghem, Peter A

2005-07-01

Modelling activated sludge systems has gained an increasing momentum after the introduction of activated sludge models (ASMs) in 1987. Application of dynamic models for full-scale systems requires essentially a calibration of the chosen ASM to the case under study. Numerous full-scale model applications have been performed so far which were mostly based on ad hoc approaches and expert knowledge. Further, each modelling study has followed a different calibration approach: e.g. different influent wastewater characterization methods, different kinetic parameter estimation methods, different selection of parameters to be calibrated, different priorities within the calibration steps, etc. In short, there was no standard approach in performing the calibration study, which makes it difficult, if not impossible, to (1) compare different calibrations of ASMs with each other and (2) perform internal quality checks for each calibration study. To address these concerns, systematic calibration protocols have recently been proposed to bring guidance to the modeling of activated sludge systems and in particular to the calibration of full-scale models. In this contribution four existing calibration approaches (BIOMATH, HSG, STOWA and WERF) will be critically discussed using a SWOT (Strengths, Weaknesses, Opportunities, Threats) analysis. It will also be assessed in what way these approaches can be further developed in view of further improving the quality of ASM calibration. In this respect, the potential of automating some steps of the calibration procedure by use of mathematical algorithms is highlighted.

Summit of the Research Coordination Networks for Undergraduate Biology Education

PubMed Central

Eaton, Carrie Diaz; Allen, Deborah; Anderson, Laurel J.; Bowser, Gillian; Pauley, Mark A.; Williams, Kathy S.; Uno, Gordon E.

2016-01-01

The first summit of projects funded by the National Science Foundation’s Research Coordination Networks for Undergraduate Biology Education (RCN-UBE) program was held January 14–16, 2016, in Washington, DC. Sixty-five scientists and science educators from 38 of the 41 Incubator and Full RCN-UBE awards discussed the value and contributions of RCNs to the national biology education reform effort. The summit illustrated the progress of this innovative UBE track, first awarded in 2009. Participants shared experiences regarding network development and growth, identified best practices and challenges faced in network management, and discussed work accomplished. We report here on key aspects of network evaluation, characteristics of successful networks, and how to sustain and broaden participation in networks. Evidence from successful networks indicates that 5 years (the length of a Full RCN-UBE) may be insufficient time to produce a cohesive and effective network. While online communication promotes the activities of a network and disseminates effective practices, face-to-face meetings are critical for establishing ties between network participants. Creation of these National Science Foundation–funded networks may be particularly useful for consortia of faculty working to address problems or exchange novel solutions discovered while introducing active-learning methods and/or course-based research into their curricula.

High Host Specificity in Encarsia diaspidicola (Hymenoptera: Aphelinidae), a Biological Control Candidate Against the White Peach Scale in Hawaii

USDA-ARS?s Scientific Manuscript database

Pre-introductory host specificity tests were performed with Encarsia diaspidicola, a biological control candidate against the invasive white peach scale, Pseudaulacaspis pentagona. False oleander scale, P. cockerelli, coconut scale, Aspidiotus destructor, cycad scale, Aulacaspis yasumatsui, greenh...

Dynamics of Active Layer Depth across Alaskan Tundra Ecosystems

NASA Astrophysics Data System (ADS)

Ma, C.; Zhang, X.; Song, X.; Xu, X.

2016-12-01

The thickness of the active layer, near-surface layer of Earth material above permafrost undergoing seasonal freezing and thawing, is of considerable importance in high-latitude environments because most physical, chemical, and biological processes in the permafrost region take place within it. The dynamics of active layer thickness (ALT) result from a combination of various factors including heat transfer, soil water content, soil texture, root density, stem density, moss layer thickness, organic layer thickness, etc. However, the magnitude and controls of ALT in the permafrost region remain uncertain. The purpose of this study is to improve our understanding of the dynamics of ALT across Alaskan tundra ecosystems and their controls at multiple scales, ranging from plots to entire Alaska. This study compiled a comprehensive dataset of ALT at site and regional scales across the Alaskan tundra ecosystems, and further analyzed ALT dynamics and their hierarchical controls. We found that air temperature played a predominant role on the seasonality of ALT, regulated by other physical and chemical factors including soil texture, moisture, and root density. The structural equation modeling (SEM) analysis confirmed the predominant role of physical controls (dominated by heat and soil properties), followed by chemical and biological factors. Then a simple empirical model was developed to reconstruct the ALT across the Alaska. The comparisons against field observational data show that the method used in this study is robust; the reconstructed time-series ALT across Alaska provides a valuable dataset source for understanding ALT and validating large-scale ecosystem models.

Hybrid Scheme for Modeling Local Field Potentials from Point-Neuron Networks.

PubMed

Hagen, Espen; Dahmen, David; Stavrinou, Maria L; Lindén, Henrik; Tetzlaff, Tom; van Albada, Sacha J; Grün, Sonja; Diesmann, Markus; Einevoll, Gaute T

2016-12-01

With rapidly advancing multi-electrode recording technology, the local field potential (LFP) has again become a popular measure of neuronal activity in both research and clinical applications. Proper understanding of the LFP requires detailed mathematical modeling incorporating the anatomical and electrophysiological features of neurons near the recording electrode, as well as synaptic inputs from the entire network. Here we propose a hybrid modeling scheme combining efficient point-neuron network models with biophysical principles underlying LFP generation by real neurons. The LFP predictions rely on populations of network-equivalent multicompartment neuron models with layer-specific synaptic connectivity, can be used with an arbitrary number of point-neuron network populations, and allows for a full separation of simulated network dynamics and LFPs. We apply the scheme to a full-scale cortical network model for a ∼1 mm 2 patch of primary visual cortex, predict laminar LFPs for different network states, assess the relative LFP contribution from different laminar populations, and investigate effects of input correlations and neuron density on the LFP. The generic nature of the hybrid scheme and its public implementation in hybridLFPy form the basis for LFP predictions from other and larger point-neuron network models, as well as extensions of the current application with additional biological detail. © The Author 2016. Published by Oxford University Press.

A SCALE-UP Mock-Up: Comparison of Student Learning Gains in High- and Low-Tech Active-Learning Environments

PubMed Central

Soneral, Paula A. G.; Wyse, Sara A.

2017-01-01

Student-centered learning environments with upside-down pedagogies (SCALE-UP) are widely implemented at institutions across the country, and learning gains from these classrooms have been well documented. This study investigates the specific design feature(s) of the SCALE-UP classroom most conducive to teaching and learning. Using pilot survey data from instructors and students to prioritize the most salient SCALE-UP classroom features, we created a low-tech “Mock-up” version of this classroom and tested the impact of these features on student learning, attitudes, and satisfaction using a quasi-­experimental setup. The same instructor taught two sections of an introductory biology course in the SCALE-UP and Mock-up rooms. Although students in both sections were equivalent in terms of gender, grade point average, incoming ACT, and drop/fail/withdraw rate, the Mock-up classroom enrolled significantly more freshmen. Controlling for class standing, multiple regression modeling revealed no significant differences in exam, in-class, preclass, and Introduction to Molecular and Cellular Biology Concept Inventory scores between the SCALE-UP and Mock-up classrooms. Thematic analysis of student comments highlighted that collaboration and whiteboards enhanced the learning experience, but technology was not important. Student satisfaction and attitudes were comparable. These results suggest that the benefits of a SCALE-UP experience can be achieved at lower cost without technology features. PMID:28213582

An Overview of Research Activity at the Launch Systems Testbed

NASA Technical Reports Server (NTRS)

Vu, Bruce; Kandula, Max

2003-01-01

This paper summarizes the acoustic testing and analysis activities at the Launch System Testbed (LST) of Kennedy Space Center (KSC). A major goal is to develop passive methods of mitigation of sound from rocket exhaust jets with ducted systems devoid of traditional water injection. Current testing efforts are concerned with the launch-induced vibroacoustic behavior of scaled exhaust jets. Numerical simulations are also developed to study the sound propagation from supersonic jets in free air and through enclosed ducts. Scaling laws accounting for the effects of important parameters such as jet Mach number, jet velocity, and jet temperature on the far-field noise are investigated in order to deduce full-scale environment from small-scale tests.

Assessing the removal of pharmaceuticals and personal care products in a full-scale activated sludge plant.

PubMed

Salgado, R; Marques, R; Noronha, J P; Carvalho, G; Oehmen, A; Reis, M A M

2012-06-01

This study aimed to investigate the removal mechanisms of pharmaceutical active compounds (PhACs) and musks in a wastewater treatment plant (WWTP). Biological removal and adsorption in the activated sludge tank as well as the effect of UV radiation used for disinfection purposes were considered when performing a mass balance on the WWTP throughout a 2-week sampling campaign. Solid-phase extraction (SPE) was carried out to analyse the PhACs in the influent and effluent samples. Ultrasonic solvent extraction was used before SPE for PhACs analysis in sludge samples. PhAC extracts were analysed by LC-MS. Solid-phase microextraction of liquid and sludge samples was used for the analysis of musks, which were detected by GC-MS. The fluxes of the most abundant compounds (13 PhACs and 5 musks) out of 79 compounds studied were used to perform the mass balance on the WWTP. Results show that incomplete removal of diclofenac, the compound that was found in the highest abundance, was observed via biodegradation and adsorption, and that UV photolysis was the main removal mechanism for this compound. The effect of adsorption to the secondary sludge was often negligible for the PhACs, with the exceptions of diclofenac, etofenamate, hydroxyzine and indapamide. However, the musks showed a high level of adsorption to the sludge. UV radiation had an important role in reducing the concentration of some of the target compounds (e.g. diclofenac, ibuprofen, clorazepate, indapamide, enalapril and atenolol) not removed in the activated sludge tank. The main removal mechanism of PhACs and musks studied in the WWTP was most often biological (45%), followed by adsorption (33%) and by UV radiation (22%). In the majority of the cases, the WWTP achieved >75% removal of the most detected PhACs and musks, with the exception of diclofenac.

Wearable Wide-Range Strain Sensors Based on Ionic Liquids and Monitoring of Human Activities

PubMed Central

Zhang, Shao-Hui; Wang, Feng-Xia; Li, Jia-Jia; Peng, Hong-Dan; Yan, Jing-Hui; Pan, Ge-Bo

2017-01-01

Wearable sensors for detection of human activities have encouraged the development of highly elastic sensors. In particular, to capture subtle and large-scale body motion, stretchable and wide-range strain sensors are highly desired, but still a challenge. Herein, a highly stretchable and transparent stain sensor based on ionic liquids and elastic polymer has been developed. The as-obtained sensor exhibits impressive stretchability with wide-range strain (from 0.1% to 400%), good bending properties and high sensitivity, whose gauge factor can reach 7.9. Importantly, the sensors show excellent biological compatibility and succeed in monitoring the diverse human activities ranging from the complex large-scale multidimensional motions to subtle signals, including wrist, finger and elbow joint bending, finger touch, breath, speech, swallow behavior and pulse wave. PMID:29135928

High-strength wastewater treatment in a pure oxygen thermophilic process: 11-year operation and monitoring of different plant configurations.

PubMed

Collivignarelli, M C; Bertanza, G; Sordi, M; Pedrazzani, R

2015-01-01

This research was carried out on a full-scale pure oxygen thermophilic plant, operated and monitored throughout a period of 11 years. The plant treats 60,000 t y⁻¹ (year 2013) of high-strength industrial wastewaters deriving mainly from pharmaceuticals and detergents production and landfill leachate. Three different plant configurations were consecutively adopted: (1) biological reactor + final clarifier and sludge recirculation (2002-2005); (2) biological reactor + ultrafiltration: membrane biological reactor (MBR) (2006); and (3) MBR + nanofiltration (since 2007). Progressive plant upgrading yielded a performance improvement chemical oxygen demand (COD) removal efficiency was enhanced by 17% and 12% after the first and second plant modification, respectively. Moreover, COD abatement efficiency exhibited a greater stability, notwithstanding high variability of the influent load. In addition, the following relevant outcomes appeared from the plant monitoring (present configuration): up to 96% removal of nitrate and nitrite, due to denitrification; low-specific biomass production (0.092 kgVSS kgCODremoved⁻¹), and biological treatability of residual COD under mesophilic conditions (BOD5/COD ratio = 0.25-0.50), thus showing the complementarity of the two biological processes.

Parent-Adolescent Involvement: The Relative Influence of Parent Gender and Residence

ERIC Educational Resources Information Center

Hawkins, Daniel N.; Amato, Paul R.; King, Valarie

2006-01-01

The 1995 wave of the Add Health study is used to investigate the relative influence of parent gender and residence on patterns of parental involvement with adolescents. Adolescent reports (N=17,330) of shared activities, shared communication, and relationship quality with both biological parents are utilized. A multidimensional scaling analysis…

Oxygenation variability in Mejillones Bay, off northern Chile, during the last two centuries

NASA Astrophysics Data System (ADS)

Díaz-Ochoa, J. A.; Pantoja, S.; de Lange, G. J.; Lange, C. B.; Sánchez, G. E.; Acuña, V. R.; Muñoz, P.; Vargas, G.

2011-01-01

The Peru Chile Current ecosystem is characterized by high biological productivity and important fisheries. Although this system is likely to be severely affected by climate change, its response to current global warming is still uncertain. In this paper, we analyze 10-166 year-old sediments in two cores collected from Mejillones Bay, an anoxic sedimentary setting favorable for the preservation of proxies. Based on a 166-year chronology, we used proxies of bottom-water oxygenation (Mo, V, S, and the (lycopane + n-C35)/n-C31 ratio) and surface water productivity (biogenic opal, counts of diatom valves, biogenic Ba, organic carbon, and chlorins) to reconstruct environmental variations in Mejillones Bay. During the last two centuries, a shift took place in the coastal marine ecosystem of Bahia Mejillones at decadal scales. This shift was characterized by intense ENSO-like activity, large-scale fluctuations in biological export productivity and bottom water oxygenation, and increased eolian activity (inferred from Ti/Al and Zr/Al). This short-term variability was accompanied by a gradual increase of sulfidic conditions that has intensified since the early 1960s.

Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology

PubMed Central

Udy, Dylan B.; Voorhies, Mark; Chan, Patricia P.; Lowe, Todd M.; Dumont, Sophie

2015-01-01

The rat kangaroo (long-nosed potoroo, Potorous tridactylus) is a marsupial native to Australia. Cultured rat kangaroo kidney epithelial cells (PtK) are commonly used to study cell biological processes. These mammalian cells are large, adherent, and flat, and contain large and few chromosomes—and are thus ideal for imaging intra-cellular dynamics such as those of mitosis. Despite this, neither the rat kangaroo genome nor transcriptome have been sequenced, creating a challenge for probing the molecular basis of these cellular dynamics. Here, we present the sequencing, assembly and annotation of the draft rat kangaroo de novo transcriptome. We sequenced 679 million reads that mapped to 347,323 Trinity transcripts and 20,079 Unigenes. We present statistics emerging from transcriptome-wide analyses, and analyses suggesting that the transcriptome covers full-length sequences of most genes, many with multiple isoforms. We also validate our findings with a proof-of-concept gene knockdown experiment. We expect that this high quality transcriptome will make rat kangaroo cells a more tractable system for linking molecular-scale function and cellular-scale dynamics. PMID:26252667

Shock Wave Propagation in Functionally Graded Mineralized Tissue

NASA Astrophysics Data System (ADS)

Nelms, Matthew; Hodo, Wayne; Livi, Ken; Browning, Alyssa; Crawford, Bryan; Rajendran, A. M.

2017-06-01

In this investigation, the effects of shock wave propagation in bone-like biomineralized tissue was investigated. The Alligator gar (Atractosteus spatula) exoskeleton is comprised of many disparate scales that provide a biological analog for potential design of flexible protective material systems. The gar scale is identified as a two-phase, (1) hydroxyapatite mineral and (2) collagen protein, biological composite with two distinct layers where a stiff, ceramic-like ganoine overlays a soft, highly ductile ganoid bone. Previous experimentations has shown significant softening under compressive loading and an asymmetrical stress-strain response for analogous mineralized tissues. The structural features, porosity, and elastic modulus were determined from high-resolution scanning electron microscopy, 3D micro-tomography, and dynamic nanoindentation experiments to develop an idealized computational model for FE simulations. The numerical analysis employed Gurson's yield criterion to determine the influence of porosity and pressure on material strength. Functional gradation of elastic moduli and certain structural features, such as the sawtooth interface, are explicitly modeled to study the plate impact shock profile for a full 3-D analysis using ABAQUS finite element software.

Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology.

PubMed

Udy, Dylan B; Voorhies, Mark; Chan, Patricia P; Lowe, Todd M; Dumont, Sophie

2015-01-01

The rat kangaroo (long-nosed potoroo, Potorous tridactylus) is a marsupial native to Australia. Cultured rat kangaroo kidney epithelial cells (PtK) are commonly used to study cell biological processes. These mammalian cells are large, adherent, and flat, and contain large and few chromosomes-and are thus ideal for imaging intra-cellular dynamics such as those of mitosis. Despite this, neither the rat kangaroo genome nor transcriptome have been sequenced, creating a challenge for probing the molecular basis of these cellular dynamics. Here, we present the sequencing, assembly and annotation of the draft rat kangaroo de novo transcriptome. We sequenced 679 million reads that mapped to 347,323 Trinity transcripts and 20,079 Unigenes. We present statistics emerging from transcriptome-wide analyses, and analyses suggesting that the transcriptome covers full-length sequences of most genes, many with multiple isoforms. We also validate our findings with a proof-of-concept gene knockdown experiment. We expect that this high quality transcriptome will make rat kangaroo cells a more tractable system for linking molecular-scale function and cellular-scale dynamics.

Rain events and their effect on effluent quality studied at a full scale activated sludge treatment plant.

PubMed

Wilén, B M; Lumley, D; Mattsson, A; Mino, T

2006-01-01

The effect of rain events on effluent quality dynamics was studied at a full scale activated sludge wastewater treatment plant which has a process solution incorporating pre-denitrification in activated sludge with post-nitrification in trickling filters. The incoming wastewater flow varies significantly due to a combined sewer system. Changed flow conditions have an impact on the whole treatment process since the recirculation to the trickling filters is set by the hydraulic limitations of the secondary settlers. Apart from causing different hydraulic conditions in the plant, increased flow due to rain or snow-melting, changes the properties of the incoming wastewater which affects process performance and effluent quality, especially the particle removal efficiency. A comprehensive set of on-line and laboratory data were collected and analysed to assess the impact of rain events on the plant performance.

Mapping the patent landscape of synthetic biology for fine chemical production pathways.

PubMed

Carbonell, Pablo; Gök, Abdullah; Shapira, Philip; Faulon, Jean-Loup

2016-09-01

A goal of synthetic biology bio-foundries is to innovate through an iterative design/build/test/learn pipeline. In assessing the value of new chemical production routes, the intellectual property (IP) novelty of the pathway is important. Exploratory studies can be carried using knowledge of the patent/IP landscape for synthetic biology and metabolic engineering. In this paper, we perform an assessment of pathways as potential targets for chemical production across the full catalogue of reachable chemicals in the extended metabolic space of chassis organisms, as computed by the retrosynthesis-based algorithm RetroPath. Our database for reactions processed by sequences in heterologous pathways was screened against the PatSeq database, a comprehensive collection of more than 150M sequences present in patent grants and applications. We also examine related patent families using Derwent Innovations. This large-scale computational study provides useful insights into the IP landscape of synthetic biology for fine and specialty chemicals production. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Broken detailed balance and non-equilibrium dynamics in living systems: a review

NASA Astrophysics Data System (ADS)

Gnesotto, F. S.; Mura, F.; Gladrow, J.; Broedersz, C. P.

2018-06-01

Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as high-fidelity transcription and translation, sensing, adaptation, biochemical patterning, and force generation. While biological systems such as motor enzymes violate detailed balance at the molecular scale, it remains unclear how non-equilibrium dynamics manifests at the mesoscale in systems that are driven through the collective activity of many motors. Indeed, in several cellular systems the presence of non-equilibrium dynamics is not always evident at large scales. For example, in the cytoskeleton or in chromosomes one can observe stationary stochastic processes that appear at first glance thermally driven. This raises the question how non-equilibrium fluctuations can be discerned from thermal noise. We discuss approaches that have recently been developed to address this question, including methods based on measuring the extent to which the system violates the fluctuation-dissipation theorem. We also review applications of this approach to reconstituted cytoskeletal networks, the cytoplasm of living cells, and cell membranes. Furthermore, we discuss a more recent approach to detect actively driven dynamics, which is based on inferring broken detailed balance. This constitutes a non-invasive method that uses time-lapse microscopy data, and can be applied to a broad range of systems in cells and tissue. We discuss the ideas underlying this method and its application to several examples including flagella, primary cilia, and cytoskeletal networks. Finally, we briefly discuss recent developments in stochastic thermodynamics and non-equilibrium statistical mechanics, which offer new perspectives to understand the physics of living systems.

Broken detailed balance and non-equilibrium dynamics in living systems: a review.

PubMed

Gnesotto, F S; Mura, F; Gladrow, J; Broedersz, C P

2018-06-01

Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as high-fidelity transcription and translation, sensing, adaptation, biochemical patterning, and force generation. While biological systems such as motor enzymes violate detailed balance at the molecular scale, it remains unclear how non-equilibrium dynamics manifests at the mesoscale in systems that are driven through the collective activity of many motors. Indeed, in several cellular systems the presence of non-equilibrium dynamics is not always evident at large scales. For example, in the cytoskeleton or in chromosomes one can observe stationary stochastic processes that appear at first glance thermally driven. This raises the question how non-equilibrium fluctuations can be discerned from thermal noise. We discuss approaches that have recently been developed to address this question, including methods based on measuring the extent to which the system violates the fluctuation-dissipation theorem. We also review applications of this approach to reconstituted cytoskeletal networks, the cytoplasm of living cells, and cell membranes. Furthermore, we discuss a more recent approach to detect actively driven dynamics, which is based on inferring broken detailed balance. This constitutes a non-invasive method that uses time-lapse microscopy data, and can be applied to a broad range of systems in cells and tissue. We discuss the ideas underlying this method and its application to several examples including flagella, primary cilia, and cytoskeletal networks. Finally, we briefly discuss recent developments in stochastic thermodynamics and non-equilibrium statistical mechanics, which offer new perspectives to understand the physics of living systems.

Hydrothermal impacts on trace element and isotope ocean biogeochemistry.

PubMed

German, C R; Casciotti, K A; Dutay, J-C; Heimbürger, L E; Jenkins, W J; Measures, C I; Mills, R A; Obata, H; Schlitzer, R; Tagliabue, A; Turner, D R; Whitby, H

2016-11-28

Hydrothermal activity occurs in all ocean basins, releasing high concentrations of key trace elements and isotopes (TEIs) into the oceans. Importantly, the calculated rate of entrainment of the entire ocean volume through turbulently mixing buoyant hydrothermal plumes is so vigorous as to be comparable to that of deep-ocean thermohaline circulation. Consequently, biogeochemical processes active within deep-ocean hydrothermal plumes have long been known to have the potential to impact global-scale biogeochemical cycles. More recently, new results from GEOTRACES have revealed that plumes rich in dissolved Fe, an important micronutrient that is limiting to productivity in some areas, are widespread above mid-ocean ridges and extend out into the deep-ocean interior. While Fe is only one element among the full suite of TEIs of interest to GEOTRACES, these preliminary results are important because they illustrate how inputs from seafloor venting might impact the global biogeochemical budgets of many other TEIs. To determine the global impact of seafloor venting, however, requires two key questions to be addressed: (i) What processes are active close to vent sites that regulate the initial high-temperature hydrothermal fluxes for the full suite of TEIs that are dispersed through non-buoyant hydrothermal plumes? (ii) How do those processes vary, globally, in response to changing geologic settings at the seafloor and/or the geochemistry of the overlying ocean water? In this paper, we review key findings from recent work in this realm, highlight a series of key hypotheses arising from that research and propose a series of new GEOTRACES modelling, section and process studies that could be implemented, nationally and internationally, to address these issues.This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'. © 2015 The Authors.

Hydrothermal impacts on trace element and isotope ocean biogeochemistry

PubMed Central

Dutay, J.-C.; Heimbürger, L. E.; Jenkins, W. J.; Measures, C. I.; Mills, R. A.; Obata, H.; Turner, D. R.; Whitby, H.

2016-01-01

Hydrothermal activity occurs in all ocean basins, releasing high concentrations of key trace elements and isotopes (TEIs) into the oceans. Importantly, the calculated rate of entrainment of the entire ocean volume through turbulently mixing buoyant hydrothermal plumes is so vigorous as to be comparable to that of deep-ocean thermohaline circulation. Consequently, biogeochemical processes active within deep-ocean hydrothermal plumes have long been known to have the potential to impact global-scale biogeochemical cycles. More recently, new results from GEOTRACES have revealed that plumes rich in dissolved Fe, an important micronutrient that is limiting to productivity in some areas, are widespread above mid-ocean ridges and extend out into the deep-ocean interior. While Fe is only one element among the full suite of TEIs of interest to GEOTRACES, these preliminary results are important because they illustrate how inputs from seafloor venting might impact the global biogeochemical budgets of many other TEIs. To determine the global impact of seafloor venting, however, requires two key questions to be addressed: (i) What processes are active close to vent sites that regulate the initial high-temperature hydrothermal fluxes for the full suite of TEIs that are dispersed through non-buoyant hydrothermal plumes? (ii) How do those processes vary, globally, in response to changing geologic settings at the seafloor and/or the geochemistry of the overlying ocean water? In this paper, we review key findings from recent work in this realm, highlight a series of key hypotheses arising from that research and propose a series of new GEOTRACES modelling, section and process studies that could be implemented, nationally and internationally, to address these issues. This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’. PMID:29035265

Superresolution Imaging using Single-Molecule Localization

PubMed Central

Patterson, George; Davidson, Michael; Manley, Suliana; Lippincott-Schwartz, Jennifer

2013-01-01

Superresolution imaging is a rapidly emerging new field of microscopy that dramatically improves the spatial resolution of light microscopy by over an order of magnitude (∼10–20-nm resolution), allowing biological processes to be described at the molecular scale. Here, we discuss a form of superresolution microscopy based on the controlled activation and sampling of sparse subsets of photoconvertible fluorescent molecules. In this single-molecule based imaging approach, a wide variety of probes have proved valuable, ranging from genetically encodable photoactivatable fluorescent proteins to photoswitchable cyanine dyes. These have been used in diverse applications of superresolution imaging: from three-dimensional, multicolor molecule localization to tracking of nanometric structures and molecules in living cells. Single-molecule-based superresolution imaging thus offers exciting possibilities for obtaining molecular-scale information on biological events occurring at variable timescales. PMID:20055680

Perception of Life as Stressful, not Biological Response to Stress, is Associated with Greater Social Disability in Adults with Autism Spectrum Disorder

PubMed Central

Bishop-Fitzpatrick, Lauren; Minshew, Nancy J.; Mazefsky, Carla A.; Eack, Shaun M.

2016-01-01

This study examined differences between adults with autism spectrum disorder (ASD; N=40) and typical community volunteers (N=25) on measures of stressful life events, perceived stress, and biological stress response (cardiovascular and cortisol reactivity) during a novel social stress task. Additional analyses examined the relationship between stress and social functioning as measured by the Social Adjustment Scale-II and the Waisman Activities of Daily Living scale. Results indicated that adults with ASD experienced significantly more stressful life events and perceived stress, and greater systolic blood pressure reactivity than typical community volunteers. Results also indicated that perceived stress and stressful life events were significantly associated with social disability. Interventions targeting stress management might improve social function in adults with ASD. PMID:27696184

Perception of Life as Stressful, Not Biological Response to Stress, is Associated with Greater Social Disability in Adults with Autism Spectrum Disorder.

PubMed

Bishop-Fitzpatrick, Lauren; Minshew, Nancy J; Mazefsky, Carla A; Eack, Shaun M

2017-01-01

This study examined differences between adults with autism spectrum disorder (ASD; N = 40) and typical community volunteers (N = 25) on measures of stressful life events, perceived stress, and biological stress response (cardiovascular and cortisol reactivity) during a novel social stress task. Additional analyses examined the relationship between stress and social functioning as measured by the Social Adjustment Scale-II and the Waisman Activities of Daily Living scale. Results indicated that adults with ASD experienced significantly more stressful life events and perceived stress, and greater systolic blood pressure reactivity than typical community volunteers. Results also indicated that perceived stress and stressful life events were significantly associated with social disability. Interventions targeting stress management might improve social function in adults with ASD.

Multi-scale biomedical systems: measurement challenges

NASA Astrophysics Data System (ADS)

Summers, R.

2016-11-01

Multi-scale biomedical systems are those that represent interactions in materials, sensors, and systems from a holistic perspective. It is possible to view such multi-scale activity using measurement of spatial scale or time scale, though in this paper only the former is considered. The biomedical application paradigm comprises interactions that range from quantum biological phenomena at scales of 10-12 for one individual to epidemiological studies of disease spread in populations that in a pandemic lead to measurement at a scale of 10+7. It is clear that there are measurement challenges at either end of this spatial scale, but those challenges that relate to the use of new technologies that deal with big data and health service delivery at the point of care are also considered. The measurement challenges lead to the use, in many cases, of model-based measurement and the adoption of virtual engineering. It is these measurement challenges that will be uncovered in this paper.

Association between hemodynamic activity and motor performance in six-month-old full-term and preterm infants: a functional near-infrared spectroscopy study.

PubMed

de Oliveira, Suelen Rosa; de Paula Machado, Ana Carolina Cabral; de Paula, Jonas Jardim; de Moraes, Paulo Henrique Paiva; Nahin, Maria Juliana Silvério; Magalhães, Lívia de Castro; Novi, Sergio L; Mesquita, Rickson C; de Miranda, Débora Marques; Bouzada, Maria Cândida Ferrarez

2018-01-01

This study aimed to assess task-induced activation in motor cortex and its association with motor performance in full-term and preterm born infants at six months old. A cross-sectional study of 73 six-month-old infants was conducted (35 full-term and 38 preterm infants). Motor performance was assessed using the Bayley Scales of Infant Development third edition-Bayley-III. Brain hemodynamic activity during motor task was measured by functional near-infrared spectroscopy (fNIRS). Motor performance was similar in full-term and preterm infants. However, differences in hemodynamic response were identified. Full terms showed a more homogeneous unilateral and contralateral activated area, whereas in preterm-born the activation response was predominantly bilateral. The full-term group also exhibited a shorter latency for the hemodynamic response than the preterm group. Hemodynamic activity in the left sensorimotor region was positively associated with motor performance measured by Bayley-III. The results highlight the adequacy of fNIRS to assess differences in task-induced activation in sensorimotor cortex between groups. The association between motor performance and the hemodynamic activity require further investigation and suggest that fNIRS can become a suitable auxiliary tool to investigate aspects of neural basis on early development of motor abilities.

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

Overend, R.P.; Rivard, C.J.

Gasification is being developed to enable a diverse range of biomass resources to meet modern secondary energy uses, especially in the electrical utility sector. Biological or anaerobic gasification in US landfills has resulted in the installation of almost 500 MW(e) of capacity and represents the largest scale application of gasification technology today. The development of integrated gasification combined cycle generation for coal technologies is being paralleled by bagasse and wood thermal gasification systems in Hawaii and Scandinavia, and will lead to significant deployment in the next decade as the current scale-up activities are commercialized. The advantages of highly reactive biomassmore » over coal in the design of process units are being realized as new thermal gasifiers are being scaled up to produce medium-energy-content gas for conversion to synthetic natural gas and transportation fuels and to hydrogen for use in fuel cells. The advent of high solids anaerobic digestion reactors is leading to commercialization of controlled municipal solid waste biological gasification rather than landfill application. In both thermal and biological gasification, high rate process reactors are a necessary development for economic applications that address waste and residue management and the production and use of new crops for energy. The environmental contribution of biomass in reducing greenhouse gas emission will also be improved.« less

A Study of the Effects of Large Scale Gust Generation in a Small Scale Atmospheric Wind Tunnel: Application to Micro Aerial Vehicles

NASA Astrophysics Data System (ADS)

Roadman, Jason; Mohseni, Kamran

2009-11-01

Modern technology operating in the atmospheric boundary layer could benefit from more accurate wind tunnel testing. While scaled atmospheric boundary layer tunnels have been well developed, tunnels replicating portions of the turbulence of the atmospheric boundary layer at full scale are a comparatively new concept. Testing at full-scale Reynolds numbers with full-scale turbulence in an ``atmospheric wind tunnel'' is sought. Many programs could utilize such a tool including that of Micro Aerial Vehicles (MAVs) and other unmanned aircraft, the wind energy industry, fuel efficient vehicles, and the study of bird and insect fight. The construction of an active ``gust generator'' for a new atmospheric tunnel is reviewed and the turbulence it generates is measured utilizing single and cross hot wires. Results from this grid are compared to atmospheric turbulence and it is shown that various gust strengths can be produced corresponding to days ranging from calm to quite gusty. An initial test is performed in the atmospheric wind tunnel whereby the effects of various turbulence conditions on transition and separation on the upper surface of a MAV wing is investigated using oil flow visualization.

Predicting lymph node output efficiency using systems biology

PubMed Central

Gong, Chang; Mattila, Joshua T.; Miller, Mark; Flynn, JoAnne L.; Linderman, Jennifer J.; Kirschner, D.

2013-01-01

Dendritic cells (DCs) capture pathogens and foreign antigen (Ag) in peripheral tissues and migrate to secondary lymphoid tissues, such as lymph nodes (LNs), where they present processed Ag as MHC-bound peptide (pMHC) to naïve T cells. Interactions between DCs and T cells result, over periods of hours, in activation, clonal expansion and differentiation of antigen-specific T cells, leading to primed cells that can now participate in immune responses. Two-photon microscopy (2PM) has been widely adopted to analyze lymphocyte dynamics and can serve as a powerful in vivo assay for cell trafficking and activation over short length and time scales. Linking biological phenomena between vastly different spatiotemporal scales can be achieved using a systems biology approach. We developed a 3D agent-based cellular model of a LN that allows for the simultaneous in silico simulation of T cell trafficking, activation and production of effector cells under different antigen (Ag) conditions. The model anatomy is based on in situ analysis of LN sections (from primates and mice) and cell dynamics based on quantitative measurements from 2PM imaging of mice. Our simulations make three important predictions. First, T cell encounters by DCs and T cell receptor (TCR) repertoire scanning are more efficient in a 3D model compared with 2D, suggesting that a 3D model is needed to analyze LN function. Second, LNs are able to produce primed CD4+T cells at the same efficiency over broad ranges of cognate frequencies (from 10−5 to 10−2). Third, reducing the time that naïve T cells are required to bind DCs before becoming activated will increase the rate at which effector cells are produced. This 3D model provides a robust platform to study how T cell trafficking and activation dynamics relate to the efficiency of T cell priming and clonal expansion. We envision that this systems biology approach will provide novel insights for guiding vaccine development and understanding immune responses to infection. PMID:23816876

Transcriptomics as a tool for assessing the scalability of mammalian cell perfusion systems.

PubMed

Jayapal, Karthik P; Goudar, Chetan T

2014-01-01

DNA microarray-based transcriptomics have been used to determine the time course of laboratory and manufacturing-scale perfusion bioreactors in an attempt to characterize cell physiological state at these two bioreactor scales. Given the limited availability of genomic data for baby hamster kidney (BHK) cells, a Chinese hamster ovary (CHO)-based microarray was used following a feasibility assessment of cross-species hybridization. A heat shock experiment was performed using both BHK and CHO cells and resulting DNA microarray data were analyzed using a filtering criteria of perfect match (PM)/single base mismatch (MM) > 1.5 and PM-MM > 50 to exclude probes with low specificity or sensitivity for cross-species hybridizations. For BHK cells, 8910 probe sets (39 %) passed the cutoff criteria, whereas 12,961 probe sets (56 %) passed the cutoff criteria for CHO cells. Yet, the data from BHK cells allowed distinct clustering of heat shock and control samples as well as identification of biologically relevant genes as being differentially expressed, indicating the utility of cross-species hybridization. Subsequently, DNA microarray analysis was performed on time course samples from laboratory- and manufacturing-scale perfusion bioreactors that were operated under the same conditions. A majority of the variability (37 %) was associated with the first principal component (PC-1). Although PC-1 changed monotonically with culture duration, the trends were very similar in both the laboratory and manufacturing-scale bioreactors. Therefore, despite time-related changes to the cell physiological state, transcriptomic fingerprints were similar across the two bioreactor scales at any given instance in culture. Multiple genes were identified with time-course expression profiles that were very highly correlated (> 0.9) with bioprocess variables of interest. Although the current incomplete annotation limits the biological interpretation of these observations, their full potential may be realized in due course when richer genomic data become available. By taking a pragmatic approach of transcriptome fingerprinting, we have demonstrated the utility of systems biology to support the comparability of laboratory and manufacturing-scale perfusion systems. Scale-down model qualification is the first step in process characterization and hence is an integral component of robust regulatory filings. Augmenting the current paradigm, which relies primarily on cell culture and product quality information, with gene expression data can help make a substantially stronger case for similarity. With continued advances in systems biology approaches, we expect them to be seamlessly integrated into bioprocess development, which can translate into more robust and high yielding processes that can ultimately reduce cost of care for patients.

Considerations of Scale and Processes in Stream Restoration and Ecological Response

NASA Astrophysics Data System (ADS)

Simon, A.; Shields, D.; Kuhnle, R.; Knight, S.

2005-12-01

Stream restoration as a means of controlling accelerated channel erosion and improving biological function in streams has become pervasive in the United States over the past twenty years. A broad range of practices often involving direct modifications to stream channels and adjacent floodplains, including alterations to morphology and pattern have been used for stream restoration. Because alluvial-channel processes and biological functioning operate as linked, open systems, any restoration project must be placed in the context of existing watershed and channel processes with a quantitative understanding of the rates of transfer of flow energy and materials. This is particularly true of reach-scale projects where local stabilization and habitat improvements may be completely overwhelmed by watershed or channel-system scale instabilities. In this regard, it is unlikely that a reach-scale project will be successful in an unstable alluvial system. This is analogous to constructing bank-stabilization measures in an actively incising channel. A conceptual model of channel response and evolution that marks systematic shifts in channel processes over time and space has been linked to fish-community structure in Mississippi streams. This link reflects changing habitat conditions and sediment-transport regimes over the course of fluvial adjustment. Suspended-sediment concentrations that can increase by orders of magnitude for a given discharge during the incision and mass-wasting phases abrade fish gills and reduce the ability of fish to hunt for food due to reduced water clarity. Similarly, durations of high suspended-sediment concentrations are shown to be inversely related to numbers of benthic macro invertebrates. Streambeds experiencing active incision (Stage III) may be too mobile for benthic macro invertebrate communities to thrive. Channels dominated by mass-wasting processes (Stages IV and V) lose riparian vegetative cover and shading which may result in higher stream temperatures. Aggradation processes typical of Stage V result in loss of interstitial spaces for spawning, de-oxygenation of substrate and may suffocate organisms. Perhaps most importantly, channel widening produces shallower depths at base flow and renders streams less retentive of large wood. Ecological characteristics recover in advanced stages of channel evolution as baseflow channels are narrowed and berms re-vegetate (Stage VI), but full recovery to pre-incision (Stage I) conditions has not been observed for both ecologic and sediment-transport systems. The processes reflected by stages of evolution can operate over entire fluvial networks and over time scales in the order of 100 years. Issues regarding effectiveness or benefit of stream restoration practices, therefore, must address scale. Furthermore, site and approach selection for reach-scale restoration projects should be guided by knowledge of watershed-scale processes. As an example, a grade control structure installed on Hotophia Creek, Mississippi successfully eliminated upstream-progressing incision and resulted in locally improved aquatic populations in the stilling basin. However, the trapping of hydraulically-controlled sediment on the upstream side of the structure resulted in streambed incision, de-stabilization of streambanks and degraded aquatic habitat in downstream reaches not protected by other grade-control structures.

Coke dust enhances coke plant wastewater treatment.

PubMed

Burmistrz, Piotr; Rozwadowski, Andrzej; Burmistrz, Michał; Karcz, Aleksander

2014-12-01

Coke plant wastewater contain many toxic pollutants. Despite physico-chemical and biological treatment this specific type of wastewater has a significant impact on environment and human health. This article presents results of research on industrial adsorptive coke plant wastewater treatment. As a sorbent the coke dust, dozen times less expensive than pulverized activated carbon, was used. Treatment was conducted in three scenarios: adsorptive after full treatment with coke dust at 15 g L(-1), biological treatment enhanced with coke dust at 0.3-0.5 g L(-1) and addition of coke dust at 0.3 g L(-1) prior to the biological treatment. The enhanced biological treatment proved the most effective. It allowed additional removal of 147-178 mg COD kg(-1) of coke dust. Copyright © 2014 Elsevier Ltd. All rights reserved.

Low Activity Waste Pretreatment System Bench-Scale Testing: Supporting Integrated Testing and Facility Safety Analyses - 17171

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

Schonewill, Philip P.; Russell, Renee L.; Daniel, Richard C.

The Low Activity Waste Pretreatment System (LAWPS) is being designed to enable the direct feed of waste to the Hanford Tank Waste Treatment and Immobilization Plant (WTP) Low Activity Waste (LAW) facility to be immobilized. Prior to construction of the LAWPS, pilot-scale integrated testing of the key unit operations (crossflow filtration, ion exchange using spherical resorcinol-formaldehyde (sRF) resin) will be conducted by a team led by Washington River Protection Solutions (WRPS) to increase the technology maturation level of the facility’s critical technology elements. As a part of this effort, Pacific Northwest National Laboratory (PNNL) has conducted a series of bench-scalemore » (or engineering-scale) tests to perform two major objectives: (1) support pilot-scale integrated testing of the LAWPS by supplying information or performance data in advance of operating the pilot-scale facility; and (2) collect data needed to establish or confirm assumptions/approaches planned for implementation in the LAWPS safety basis. The first objective was focused in two technical areas: developing simulants that are representative of expected waste feed and can be produced at larger scales, and using these simulants in a bench-scale crossflow filter to establish expected solid-liquid separation performance. The crossflow filter was also used to observe the efficacy (with respect to filter production rate) of selected operational strategies. The second objective also included two technical areas: measuring the effect of sRF resin on hydrogen generation rate under irradiation, and demonstrating that the planned hydrogen management approach is effective and robust. The hydrogen management strategy involves fluidization of the sRF resin bed in the ion exchange columns and recirculating the liquid, a scenario that is planned for testing at full column height. The full height tests at PNNL also supported full-scale IX column testing conducted as part of the technology maturation plan. The experimental approaches used at PNNL in these four technical areas are summarized and selected key preliminary results are provided.« less

Microbial community structures in foaming and nonfoaming full-scale wastewater treatment plants.

PubMed

de los Reyes, Francis L; Rothauszky, Dagmar; Raskin, Lutgarde

2002-01-01

A survey of full-scale activated-sludge plants in Illinois revealed that filamentous foaming is a widespread problem in the state, and that the causes and consequences of foaming control strategies are not fully understood. To link microbial community structure to foam occurrence, microbial populations in eight foaming and nine nonfoaming full-scale activated-sludge systems were quantified using oligonucleotide hybridization probes targeting the ribosomal RNA (rRNA) of the mycolata; Gordonia spp.; Gordonia amarae; "Candidatus Microthrix parvicella"; the alpha-, beta-, and gamma-subclasses of the Proteobacteria, and members of the Cytophaga-Flavobacteria. Parallel measurements of microbial population abundance using hybridization of extracted RNA and fluorescence in situ hybridization (FISH) showed that the levels of mycolata, particularly Gordonia spp., were higher in most foaming systems compared with nonfoaming systems. Fluorescence in situ hybridization and microscopy suggested the involvement of "Candidatus Microthrix parvicella" and Skermania piniformis in foam formation in other plants. Finally, high numbers of "Candidatus Microthrix parvicella" were detected by FISH in foam and mixed liquor samples of one plant, whereas the corresponding levels of rRNA were low. This finding implies that inactive "Candidatus Microthrix parvicella" cells (i.e., cells with low rRNA levels) can cause foaming.

Comparing cost and process performance of activated sludge (AS) and biological aerated filters (BAF) over ten years of full sale operation.

PubMed

Hansen, R; Thogersen, T; Rogalla, F

2007-01-01

In the early 1990s, the Wastewater Treatment Plant (WWTP) of Frederikshavn, Denmark, was extended to meet new requirements for nutrient removal (8 mg/L TN, 1.5 mg TP/L) as well as to increase its average daily flow to 16,500 m(3)/d (4.5 MGD). As the most economical upgrade of the existing activated sludge (AS) plant, a parallel biological aerated filter (BAF) was selected, and started up in 1995. Running two full scale processes in parallel for over ten years on the same wastewater and treatment objectives enabled a direct comparison in relation to operating performance, costs and experience. Common pretreatment consists of screening, an aerated grit and grease removal and three primary settlers with chemical addition. The effluent is then pumped to the two parallel biological treatment stages, AS with recirculation and an upflow BAF with floating media. The wastewater is a mixture of industrial and domestic wastewater, with a dominant discharge of fish processing effluent which can amount to 50% of the flow. The maximum hydraulic load on the pretreatment section as a whole is 1,530 m(3)/h. Approximately 60% of the sewer system is combined with a total of 32 overflow structures. To avoid the direct discharge of combined sewer overflows into the receiving waters, the total hydraulic wet weather capacity of the plant is increased to 4,330 m(3)/h, or 6 times average flow. During rain, some of the raw sewage can be directed through a stormwater bypass to the BAF, which can be modified in its operation to accommodate various treatment needs: either using simultaneous nitrification/denitrification in all filters with recirculation introducing bottom aeration with full nitrification in some filters for storm treatment and/or post-denitrification in one filter. After treatment, the wastewater is discharged to the Baltic Sea through a 500 m outfall. The BAF backwash sludge, approximately 1,900 m(3) per 24 h in dry weather, is redirected to the AS plant. Primary settler sludge and the combined biosolids from the AS plant are anaerobically digested, with methane gas being used for generation of heat and power. On-line measurements for the parameters NO3, NO2, NH4, temperature as well as dissolved oxygen (DO) are used for control of aeration and external carbon source (methanol). Dosing of flocculants for P-removal is carried out based on laboratory analysis and jar tests. This paper discusses the experience gained from the plant operation during the last ten years, compiling comparative performance and cost data of the two processes, as well as their optimisation.

Bacterial community assembly in activated sludge: mapping beta diversity across environmental variables.

PubMed

Isazadeh, Siavash; Jauffur, Shameem; Frigon, Dominic

2016-12-01

Effect of ecological variables on community assembly of heterotrophic bacteria at eight full-scale and two pilot-scale activated sludge wastewater treatment plants (AS-WWTPs) were explored by pyrosequencing of 16S rRNA gene amplicons. In total, 39 samples covering a range of abiotic factors spread over space and time were analyzed. A core bacterial community of 24 families detected in at least six of the eight AS-WWTPs was defined. In addition to the core families, plant-specific families (observed at <50% AS-WWTPs) were found to be also important in the community structure. Observed beta diversity was partitioned with respect to ecological variables. Specifically, the following variables were considered: influent wastewater characteristics, season (winter vs. summer), process operations (conventional, oxidation ditch, and sequence batch reactor), reactor sizes (pilot-scale vs. full-scale reactors), chemical stresses defined by ozonation of return activated sludge, interannual variation, and geographical locations. Among the assessed variables, influent wastewater characteristics and geographical locations contributed more in explaining the differences between AS-WWTP bacterial communities with a maximum of approximately 26% of the observed variations. Partitioning of beta diversity is necessary to interpret the inherent variability in microbial community assembly and identify the driving forces at play in engineered microbial ecosystem. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Multi-scale, multi-modal analysis uncovers complex relationship at the brain tissue-implant neural interface: new emphasis on the biological interface

NASA Astrophysics Data System (ADS)

Michelson, Nicholas J.; Vazquez, Alberto L.; Eles, James R.; Salatino, Joseph W.; Purcell, Erin K.; Williams, Jordan J.; Cui, X. Tracy; Kozai, Takashi D. Y.

2018-06-01

Objective. Implantable neural electrode devices are important tools for neuroscience research and have an increasing range of clinical applications. However, the intricacies of the biological response after implantation, and their ultimate impact on recording performance, remain challenging to elucidate. Establishing a relationship between the neurobiology and chronic recording performance is confounded by technical challenges related to traditional electrophysiological, material, and histological limitations. This can greatly impact the interpretations of results pertaining to device performance and tissue health surrounding the implant. Approach. In this work, electrophysiological activity and immunohistological analysis are compared after controlling for motion artifacts, quiescent neuronal activity, and material failure of devices in order to better understand the relationship between histology and electrophysiological outcomes. Main results. Even after carefully accounting for these factors, the presence of viable neurons and lack of glial scarring does not convey single unit recording performance. Significance. To better understand the biological factors influencing neural activity, detailed cellular and molecular tissue responses were examined. Decreases in neural activity and blood oxygenation in the tissue surrounding the implant, shift in expression levels of vesicular transporter proteins and ion channels, axon and myelin injury, and interrupted blood flow in nearby capillaries can impact neural activity around implanted neural interfaces. Combined, these tissue changes highlight the need for more comprehensive, basic science research to elucidate the relationship between biology and chronic electrophysiology performance in order to advance neural technologies.

Parallel workflow manager for non-parallel bioinformatic applications to solve large-scale biological problems on a supercomputer.

PubMed

Suplatov, Dmitry; Popova, Nina; Zhumatiy, Sergey; Voevodin, Vladimir; Švedas, Vytas

2016-04-01

Rapid expansion of online resources providing access to genomic, structural, and functional information associated with biological macromolecules opens an opportunity to gain a deeper understanding of the mechanisms of biological processes due to systematic analysis of large datasets. This, however, requires novel strategies to optimally utilize computer processing power. Some methods in bioinformatics and molecular modeling require extensive computational resources. Other algorithms have fast implementations which take at most several hours to analyze a common input on a modern desktop station, however, due to multiple invocations for a large number of subtasks the full task requires a significant computing power. Therefore, an efficient computational solution to large-scale biological problems requires both a wise parallel implementation of resource-hungry methods as well as a smart workflow to manage multiple invocations of relatively fast algorithms. In this work, a new computer software mpiWrapper has been developed to accommodate non-parallel implementations of scientific algorithms within the parallel supercomputing environment. The Message Passing Interface has been implemented to exchange information between nodes. Two specialized threads - one for task management and communication, and another for subtask execution - are invoked on each processing unit to avoid deadlock while using blocking calls to MPI. The mpiWrapper can be used to launch all conventional Linux applications without the need to modify their original source codes and supports resubmission of subtasks on node failure. We show that this approach can be used to process huge amounts of biological data efficiently by running non-parallel programs in parallel mode on a supercomputer. The C++ source code and documentation are available from http://biokinet.belozersky.msu.ru/mpiWrapper .

Simulating biological processes: stochastic physics from whole cells to colonies.

PubMed

Earnest, Tyler M; Cole, John A; Luthey-Schulten, Zaida

2018-05-01

The last few decades have revealed the living cell to be a crowded spatially heterogeneous space teeming with biomolecules whose concentrations and activities are governed by intrinsically random forces. It is from this randomness, however, that a vast array of precisely timed and intricately coordinated biological functions emerge that give rise to the complex forms and behaviors we see in the biosphere around us. This seemingly paradoxical nature of life has drawn the interest of an increasing number of physicists, and recent years have seen stochastic modeling grow into a major subdiscipline within biological physics. Here we review some of the major advances that have shaped our understanding of stochasticity in biology. We begin with some historical context, outlining a string of important experimental results that motivated the development of stochastic modeling. We then embark upon a fairly rigorous treatment of the simulation methods that are currently available for the treatment of stochastic biological models, with an eye toward comparing and contrasting their realms of applicability, and the care that must be taken when parameterizing them. Following that, we describe how stochasticity impacts several key biological functions, including transcription, translation, ribosome biogenesis, chromosome replication, and metabolism, before considering how the functions may be coupled into a comprehensive model of a 'minimal cell'. Finally, we close with our expectation for the future of the field, focusing on how mesoscopic stochastic methods may be augmented with atomic-scale molecular modeling approaches in order to understand life across a range of length and time scales.

Simulating biological processes: stochastic physics from whole cells to colonies

NASA Astrophysics Data System (ADS)

Earnest, Tyler M.; Cole, John A.; Luthey-Schulten, Zaida

2018-05-01

The last few decades have revealed the living cell to be a crowded spatially heterogeneous space teeming with biomolecules whose concentrations and activities are governed by intrinsically random forces. It is from this randomness, however, that a vast array of precisely timed and intricately coordinated biological functions emerge that give rise to the complex forms and behaviors we see in the biosphere around us. This seemingly paradoxical nature of life has drawn the interest of an increasing number of physicists, and recent years have seen stochastic modeling grow into a major subdiscipline within biological physics. Here we review some of the major advances that have shaped our understanding of stochasticity in biology. We begin with some historical context, outlining a string of important experimental results that motivated the development of stochastic modeling. We then embark upon a fairly rigorous treatment of the simulation methods that are currently available for the treatment of stochastic biological models, with an eye toward comparing and contrasting their realms of applicability, and the care that must be taken when parameterizing them. Following that, we describe how stochasticity impacts several key biological functions, including transcription, translation, ribosome biogenesis, chromosome replication, and metabolism, before considering how the functions may be coupled into a comprehensive model of a ‘minimal cell’. Finally, we close with our expectation for the future of the field, focusing on how mesoscopic stochastic methods may be augmented with atomic-scale molecular modeling approaches in order to understand life across a range of length and time scales.

Computational Study of the Genomic and Epigenomic Phenomena

NASA Astrophysics Data System (ADS)

Yang, Wenjing

Biological systems are perhaps the ultimate complex systems, uniquely capable of processing and communicating information, reproducing in their lifetimes, and adapting in evolutionary time scales. My dissertation research focuses on using computational approaches to understand the biocomplexity manifested in the multitude of length scales and time scales. At the molecular and cellular level, central to the complex behavior of a biological system is the regulatory network. My research study focused on epigenetics, which is essential for multicellular organisms to establish cellular identity during development or in response to intracellular and environmental stimuli. My computational study of epigenomics is greatly facilitated by recent advances in high-throughput sequencing technology, which enables high-resolution snapshots of epigenomes and transcriptomes. Using human CD4+ T cell as a model system, the dynamical changes in epigenome and transcriptome pertinent to T cell activation were investigated at the genome scale. Going beyond traditional focus on transcriptional regulation, I provided evidences that post-transcriptional regulation may serve as a major component of the regulatory network. In addition, I explored alternative polyadenylation, another novel aspect of gene regulation, and how it cross-talks with the local chromatin structure. As the renowned theoretical biologist Theodosius Dobzhansky said eloquently, "Nothing in biology makes sense except in the light of evolution''. To better understand this ubiquitous driving force in the biological world, I went beyond molecular events in a single organism, and investigated the dynamical changes of population structure along the evolutionary time scale. To this end, we used HIV virus population dynamics in the host immune system as a model system. The evolution of HIV viral population plays a key role in AIDS immunopathogenesis with its exceptionally high mutation rate. However, the theoretical studies of the effect of recombination have been rather limited. Given the phylogenetic and experimental evidences for the high recombination rate and its important role in HIV evolution and epidemics, I established a mathematical model to study the effect of recombination, and explored the complex behavior of this dynamics system.

3D Printed Bionic Nanodevices.

PubMed

Kong, Yong Lin; Gupta, Maneesh K; Johnson, Blake N; McAlpine, Michael C

2016-06-01

The ability to three-dimensionally interweave biological and functional materials could enable the creation of bionic devices possessing unique and compelling geometries, properties, and functionalities. Indeed, interfacing high performance active devices with biology could impact a variety of fields, including regenerative bioelectronic medicines, smart prosthetics, medical robotics, and human-machine interfaces. Biology, from the molecular scale of DNA and proteins, to the macroscopic scale of tissues and organs, is three-dimensional, often soft and stretchable, and temperature sensitive. This renders most biological platforms incompatible with the fabrication and materials processing methods that have been developed and optimized for functional electronics, which are typically planar, rigid and brittle. A number of strategies have been developed to overcome these dichotomies. One particularly novel approach is the use of extrusion-based multi-material 3D printing, which is an additive manufacturing technology that offers a freeform fabrication strategy. This approach addresses the dichotomies presented above by (1) using 3D printing and imaging for customized, hierarchical, and interwoven device architectures; (2) employing nanotechnology as an enabling route for introducing high performance materials, with the potential for exhibiting properties not found in the bulk; and (3) 3D printing a range of soft and nanoscale materials to enable the integration of a diverse palette of high quality functional nanomaterials with biology. Further, 3D printing is a multi-scale platform, allowing for the incorporation of functional nanoscale inks, the printing of microscale features, and ultimately the creation of macroscale devices. This blending of 3D printing, novel nanomaterial properties, and 'living' platforms may enable next-generation bionic systems. In this review, we highlight this synergistic integration of the unique properties of nanomaterials with the versatility of extrusion-based 3D printing technologies to interweave nanomaterials and fabricate novel bionic devices.

3D Printed Bionic Nanodevices

PubMed Central

Kong, Yong Lin; Gupta, Maneesh K.; Johnson, Blake N.; McAlpine, Michael C.

2016-01-01

Summary The ability to three-dimensionally interweave biological and functional materials could enable the creation of bionic devices possessing unique and compelling geometries, properties, and functionalities. Indeed, interfacing high performance active devices with biology could impact a variety of fields, including regenerative bioelectronic medicines, smart prosthetics, medical robotics, and human-machine interfaces. Biology, from the molecular scale of DNA and proteins, to the macroscopic scale of tissues and organs, is three-dimensional, often soft and stretchable, and temperature sensitive. This renders most biological platforms incompatible with the fabrication and materials processing methods that have been developed and optimized for functional electronics, which are typically planar, rigid and brittle. A number of strategies have been developed to overcome these dichotomies. One particularly novel approach is the use of extrusion-based multi-material 3D printing, which is an additive manufacturing technology that offers a freeform fabrication strategy. This approach addresses the dichotomies presented above by (1) using 3D printing and imaging for customized, hierarchical, and interwoven device architectures; (2) employing nanotechnology as an enabling route for introducing high performance materials, with the potential for exhibiting properties not found in the bulk; and (3) 3D printing a range of soft and nanoscale materials to enable the integration of a diverse palette of high quality functional nanomaterials with biology. Further, 3D printing is a multi-scale platform, allowing for the incorporation of functional nanoscale inks, the printing of microscale features, and ultimately the creation of macroscale devices. This blending of 3D printing, novel nanomaterial properties, and ‘living’ platforms may enable next-generation bionic systems. In this review, we highlight this synergistic integration of the unique properties of nanomaterials with the versatility of extrusion-based 3D printing technologies to interweave nanomaterials and fabricate novel bionic devices. PMID:27617026

Biological features of hepatitis B virus isolates from patients based on full-length genomic analysis.

PubMed

Wen, Yu-Mei; Wang, Yong-Xiang

2009-01-01

The mechanisms for HBV persistence and the pathogenesis of chronic HB have been shown mainly due to defects in host immune responses. However, HBV isolates with different biological features may also contribute to different clinical outcomes and epidemiological implications in viral hepatitis B (HB). This review presents interesting biological features of HBV isolates based on the structural and functional analysis of full-length HBV isolates from various patients. Among isolates from children after failure of HB vaccination, 129L mutant at the 'a' determinant was found with normal binding efficiency to anti-HBs, but with reduced immunogenicity, which could initiate persistent HBV infections. Isolates from fulminant hepatitis (FH) B patients were not all highly replicative, but differences in capacities of anti-HBs induction could be involved in the pathogenesis of FH. The high replicative competency of isolates from hepatocellular carcinoma (HCC) patients could result in enhanced immune-mediated cytopathic effects against HBV viral proteins, and increased transactivating activity by the X protein. The mechanism of a double-spliced variant in enhancing replication of the wild-type virus is presented. The importance of integrating structural and functional analysis to reveal biological features of HBV isolates in viral pathogenesis is discussed.

Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

PubMed Central

Forsberg, Erica M; Huan, Tao; Rinehart, Duane; Benton, H Paul; Warth, Benedikt; Hilmers, Brian; Siuzdak, Gary

2018-01-01

Systems biology is the study of complex living organisms, and as such, analysis on a systems-wide scale involves the collection of information-dense data sets that are representative of an entire phenotype. To uncover dynamic biological mechanisms, bioinformatics tools have become essential to facilitating data interpretation in large-scale analyses. Global metabolomics is one such method for performing systems biology, as metabolites represent the downstream functional products of ongoing biological processes. We have developed XCMS Online, a platform that enables online metabolomics data processing and interpretation. A systems biology workflow recently implemented within XCMS Online enables rapid metabolic pathway mapping using raw metabolomics data for investigating dysregulated metabolic processes. In addition, this platform supports integration of multi-omic (such as genomic and proteomic) data to garner further systems-wide mechanistic insight. Here, we provide an in-depth procedure showing how to effectively navigate and use the systems biology workflow within XCMS Online without a priori knowledge of the platform, including uploading liquid chromatography (LCLC)–mass spectrometry (MS) data from metabolite-extracted biological samples, defining the job parameters to identify features, correcting for retention time deviations, conducting statistical analysis of features between sample classes and performing predictive metabolic pathway analysis. Additional multi-omics data can be uploaded and overlaid with previously identified pathways to enhance systems-wide analysis of the observed dysregulations. We also describe unique visualization tools to assist in elucidation of statistically significant dysregulated metabolic pathways. Parameter input takes 5–10 min, depending on user experience; data processing typically takes 1–3 h, and data analysis takes ~30 min. PMID:29494574

Technical Assessment of the National Full Scale Aerodynamic Complex Fan Blades Repair

NASA Technical Reports Server (NTRS)

Young, Clarence P., Jr.; Dixon, Peter G.; St.Clair, Terry L.; Johns, William E.

1998-01-01

This report describes the principal activities of a technical review team formed to address National Full Scale Aerodynamic Complex (NFAC) blade repair problems. In particular, the problem of lack of good adhesive bonding of the composite overwrap to the Hyduliginum wood blade material was studied extensively. Description of action plans and technical elements of the plans are provided. Results of experiments designed to optimize the bonding process and bonding strengths obtained on a full scale blade using a two-step cure process with adhesive primers are presented. Consensus recommendations developed by the review team in conjunction with the NASA Ames Fan Blade Repair Project Team are provided along with lessons learned on this program. Implementation of recommendations resulted in achieving good adhesive bonds between the composite materials and wooden blades, thereby providing assurance that the repaired fan blades will meet or exceed operational life requirements.

Modeling and Design of a Full-Scale Rotor Blade with Embedded Piezocomposite Actuators

NASA Astrophysics Data System (ADS)

Kovalovs, A.; Barkanov, E.; Ruchevskis, S.; Wesolowski, M.

2017-05-01

An optimization methodology for the design of a full-scale rotor blade with an active twist in order to enhance its ability to reduce vibrations and noise is presented. It is based on a 3D finite-element model, the planning of experiments, and the response surface technique to obtain high piezoelectric actuation forces and displacements with a minimum actuator weight and energy applied. To investigate an active twist of the helicopter rotor blade, a structural static analysis using a 3D finite-element model was carried out. Optimum results were obtained at two possible applications of macrofiber composite actuators. The torsion angle found from the finite-element simulation of helicopter rotor blades was successfully validated by its experimental values, which confirmed the modeling accuracy.

Quantization of Motor Activity into Primitives and Time-Frequency Atoms Using Independent Component Analysis and Matching Pursuit Algorithms

DTIC Science & Technology

2001-10-25

form: (1) A is a scaling factor, t is time and r a coordinate vector describing the limb configuration. We...combination of limb state and EMG. In our early examination of EMG we detected underlying groups of muscles and phases of activity by inspection and...representations of EEG or other biological signals has been thoroughly explored. Such components might be used as a basis for neuroprosthetic control

Recent advances on biological production of difructose dianhydride III.

PubMed

Zhu, Yingying; Yu, Shuhuai; Zhang, Wenli; Zhang, Tao; Guang, Cuie; Mu, Wanmeng

2018-04-01

Difructose dianhydride III (DFA III) is a cyclic difructose containing two reciprocal glycosidic linkages. It is easily generated with a small amount by sucrose caramelization and thus occurs in a wide range of food-stuffs during food processing. DFA III has half sweetness but only 1/15 energy of sucrose, showing potential industrial application as low-calorie sucrose substitute. In addition, it displays many benefits including prebiotic effect, low cariogenicity property, and hypocholesterolemic effect, and improves absorption of minerals, flavonoids, and immunoglobulin G. DFA III is biologically produced from inulin by inulin fructotransferase (IFTase, EC 4.2.2.18). Plenty of DFA III-producing enzymes have been identified. The crystal structure of inulin fructotransferase has been determined, and its molecular modification has been performed to improve the catalytic activity and structural stability. Large-scale production of DFA III has been studied by various IFTases, especially using an ultrafiltration membrane bioreactor. In this article, the recent findings on physiological effects of DFA III are briefly summarized; the research progresses on identification, expression, and molecular modification of IFTase and large-scale biological production of DFA III by IFTase are reviewed in detail.

Modeling of cytometry data in logarithmic space: When is a bimodal distribution not bimodal?

PubMed

Erez, Amir; Vogel, Robert; Mugler, Andrew; Belmonte, Andrew; Altan-Bonnet, Grégoire

2018-02-16

Recent efforts in systems immunology lead researchers to build quantitative models of cell activation and differentiation. One goal is to account for the distributions of proteins from single-cell measurements by flow cytometry or mass cytometry as readout of biological regulation. In that context, large cell-to-cell variability is often observed in biological quantities. We show here that these readouts, viewed in logarithmic scale may result in two easily-distinguishable modes, while the underlying distribution (in linear scale) is unimodal. We introduce a simple mathematical test to highlight this mismatch. We then dissect the flow of influence of cell-to-cell variability proposing a graphical model which motivates higher-dimensional analysis of the data. Finally we show how acquiring additional biological information can be used to reduce uncertainty introduced by cell-to-cell variability, helping to clarify whether the data is uni- or bimodal. This communication has cautionary implications for manual and automatic gating strategies, as well as clustering and modeling of single-cell measurements. © 2018 International Society for Advancement of Cytometry. © 2018 International Society for Advancement of Cytometry.

Safety and Efficacy of Granulocyte/Monocyte Apheresis in Steroid-Dependent Active Ulcerative Colitis with Insufficient Response or Intolerance to Immunosuppressants and/or Biologics [the ART Trial]: 12-week Interim Results

PubMed Central

Akbar, Ayesha; Hart, Ailsa; Subramanian, Sreedhar; Bommelaer, Gilles; Baumgart, Daniel C.; Grimaud, Jean-Charles; Cadiot, Guillaume; Makins, Richard; Hoque, Syed; Bouguen, Guillaume; Bonaz, Bruno

2016-01-01

Background and Aims: Patients with active, steroid-dependent ulcerative colitis with insufficient response or intolerance to immunosuppressants and/or biologic therapies have limited treatment options. Adacolumn, a granulocyte/monocyte adsorptive apheresis device, has shown clinical benefit in these patients. This study aimed to provide additional clinical data regarding the safety and efficacy of Adacolumn in this patient subgroup. Methods: This single-arm, open-label, multicentre trial [ART] was conducted at 18 centres across the UK, France, and Germany. Eligible patients were 18–75 years old with moderate-to-severe, steroid-dependent active ulcerative colitis with insufficient response or intolerance to immunosuppressants and/or biologics. Patients received ≥ 5 weekly apheresis sessions with Adacolumn. The primary endpoint was clinical remission rate [clinical activity index ≤ 4] at Week 12. Results: In all, 86 patients were enrolled. At Week 12, 33/84 [39.3%] of patients in the intention-to-treat population achieved clinical remission, with 47/84 [56.0%] achieving a clinical response [clinical activity index reduction of ≥ 3]. Clinical remission was achieved in 30.0% of patients with previous immunosuppressant and biologic failure; steroid-free clinical remission and response were observed in 22.6% and 35.7% of these patients, respectively. Quality of life [Short Health Scale] significantly improved at Week 12 [p < 0.0001]. The majority of adverse events were of mild/moderate intensity. Conclusions: At Week 12, Adacolumn provided significant clinical benefit in a large cohort of steroid-dependent ulcerative colitis patients with previous failure to immunosuppressant and/or biologic treatment, with a favourable safety profile. These results are consistent with previous studies and support Adacolumn use in this difficult-to-treat patient subgroup. PMID:26818659

Exobiology issues and experiments at a Mars base

NASA Technical Reports Server (NTRS)

Mckay, Christopher P.

1986-01-01

Research in Exobiology, the study of the origin, evolution, and distribution of life in the universe, may be a major component of the science activities at a Mars Base. Exobiology activities would include: continuing the search for life on Mars; searching for evidence for ancient life from a warmer Martian past; research into the chemistry of the biogenic elements and their compounds; and other related activities. Mars provides an opportunity in Exobiology, both for immediate study and for long range and possibly large scale experimentation in planetary biology.

Full-movement neuromuscular electrical stimulation improves plantar flexor spasticity and ankle active dorsiflexion in stroke patients: a randomized controlled study.

PubMed

Wang, Yong-Hui; Meng, Fei; Zhang, Yang; Xu, Mao-Yu; Yue, Shou-Wei

2016-06-01

To investigate whether full-movement neuromuscular electrical stimulation, which can generate full range of movement, reduces spasticity and/or improves motor function more effectively than control, sensory threshold-neuromuscular electrical stimulation, and motor threshold-neuromuscular electrical stimulation in sub-acute stroke patients. A randomized, single-blind, controlled study. Physical therapy room and functional assessment room. A total of 72 adult patients with sub-acute post-stroke hemiplegia and plantar flexor spasticity. Patients received 30-minute sessions of neuromuscular electrical stimulation on the motor points of the extensor hallucis and digitorum longus twice a day, five days per week for four weeks. Composite Spasticity Scale, Ankle Active Dorsiflexion Score, and walking time in the Timed Up and Go Test were assessed at pretreatment, posttreatment, and at two-week follow-up. After four weeks of treatment, when comparing interclass pretreatment and posttreatment, only the full-movement neuromuscular electrical stimulation group had a significant reduction in the Composite Spasticity Scale (mean % reduction = 19.91(4.96)%, F = 3.878, p < 0.05) and improvement in the Ankle Active Dorsiflexion Score (mean scores = 3.29(0.91), F = 3.140, p < 0.05). Furthermore, these improvements were maintained two weeks after the treatment ended. However, there were no significant differences in the walking time after four weeks of treatment among the four groups (F = 1.861, p > 0.05). Full-movement neuromuscular electrical stimulation with a stimulus intensity capable of generating full movement can significantly reduce plantar flexor spasticity and improve ankle active dorsiflexion, but cannot decrease walking time in the Timed Up and Go Test in sub-acute stroke patients. © The Author(s) 2015.

Soil biological activity at European scale - two calculation concepts

NASA Astrophysics Data System (ADS)

Krüger, Janine; Rühlmann, Jörg

2014-05-01

The CATCH-C project aims to identify and improve the farm-compatibility of Soil Management Practices including to promote productivity, climate change mitigation and soil quality. The focus of this work concentrates on turnover conditions for soil organic matter (SOM). SOM is fundamental for the maintenance of quality and functions of soils while SOM storage is attributed a great importance in terms of climate change mitigation. The turnover conditions depend on soil biological activity characterized by climate and soil properties. To assess the turnover conditions two model concepts are applied: (I) Biological active time (BAT) regression approach derived from CANDY model (Franko & Oelschlägel 1995) expresses the variation of air temperature, precipitation and soil texture as a timescale and an indicator of biological activity for soil organic matter (SOM) turnover. (II) Re_clim parameter within the Introductory Carbon Balance Model (Andrén & Kätterer 1997) states the soil temperature and soil water to estimate soil biological activity. The modelling includes two strategies to cover the European scale and conditions. BAT was calculated on a 20x20 km grid basis. The European data sets of precipitation and air temperature (time period 1901-2000, monthly resolution), (Mitchell et al. 2004) were used to derive long-term averages. As we focus on agricultural areas we included CORINE data (2006) to extract arable land. The resulting BATs under co-consideration of the main soil textures (clay, silt, sand and loam) were investigated per environmental zone (ENZs, Metzger et al. 2005) that represents similar conditions for precipitation, temperature and relief to identify BAT ranges and hence turnover conditions for each ENZ. Re_clim was quantified by climatic time series of more than 250 weather stations across Europe presented by Klein Tank et al. (2002). Daily temperature, precipitation and potential evapotranspiration (maximal thermal extent) were used to calculate soil temperature and water storage in the arable layer thereby differentiating soil textures exclusively in main types (clay, silt, sand and loam). Similar to the BAT investigation it was of further interest to investigate how the re_clim parameter range behaves per ENZ. We will discuss the analyzed results of both strategies in a comparative manner to assess SOM turnover conditions across Europe. Both concepts help to separate different turnover activities and to indicate organic matter input in order to maintain the given SOM. The assessment could provide local recommendations for local adaptations of soil management practices. CATCH-C is funded within the 7th Framework Programme for Research, Technological Development and Demonstration, Theme 2 - Biotechnologies, Agriculture & Food (Grant Agreement N° 289782).

Weak synchronization and large-scale collective oscillation in dense bacterial suspensions

NASA Astrophysics Data System (ADS)

Chen, Chong; Liu, Song; Shi, Xia-Qing; Chaté, Hugues; Wu, Yilin

2017-01-01

Collective oscillatory behaviour is ubiquitous in nature, having a vital role in many biological processes from embryogenesis and organ development to pace-making in neuron networks. Elucidating the mechanisms that give rise to synchronization is essential to the understanding of biological self-organization. Collective oscillations in biological multicellular systems often arise from long-range coupling mediated by diffusive chemicals, by electrochemical mechanisms, or by biomechanical interaction between cells and their physical environment. In these examples, the phase of some oscillatory intracellular degree of freedom is synchronized. Here, in contrast, we report the discovery of a weak synchronization mechanism that does not require long-range coupling or inherent oscillation of individual cells. We find that millions of motile cells in dense bacterial suspensions can self-organize into highly robust collective oscillatory motion, while individual cells move in an erratic manner, without obvious periodic motion but with frequent, abrupt and random directional changes. So erratic are individual trajectories that uncovering the collective oscillations of our micrometre-sized cells requires individual velocities to be averaged over tens or hundreds of micrometres. On such large scales, the oscillations appear to be in phase and the mean position of cells typically describes a regular elliptic trajectory. We found that the phase of the oscillations is organized into a centimetre-scale travelling wave. We present a model of noisy self-propelled particles with strictly local interactions that accounts faithfully for our observations, suggesting that self-organized collective oscillatory motion results from spontaneous chiral and rotational symmetry breaking. These findings reveal a previously unseen type of long-range order in active matter systems (those in which energy is spent locally to produce non-random motion). This mechanism of collective oscillation may inspire new strategies to control the self-organization of active matter and swarming robots.

Weak synchronization and large-scale collective oscillation in dense bacterial suspensions.

PubMed

Chen, Chong; Liu, Song; Shi, Xia-Qing; Chaté, Hugues; Wu, Yilin

2017-02-09

Collective oscillatory behaviour is ubiquitous in nature, having a vital role in many biological processes from embryogenesis and organ development to pace-making in neuron networks. Elucidating the mechanisms that give rise to synchronization is essential to the understanding of biological self-organization. Collective oscillations in biological multicellular systems often arise from long-range coupling mediated by diffusive chemicals, by electrochemical mechanisms, or by biomechanical interaction between cells and their physical environment. In these examples, the phase of some oscillatory intracellular degree of freedom is synchronized. Here, in contrast, we report the discovery of a weak synchronization mechanism that does not require long-range coupling or inherent oscillation of individual cells. We find that millions of motile cells in dense bacterial suspensions can self-organize into highly robust collective oscillatory motion, while individual cells move in an erratic manner, without obvious periodic motion but with frequent, abrupt and random directional changes. So erratic are individual trajectories that uncovering the collective oscillations of our micrometre-sized cells requires individual velocities to be averaged over tens or hundreds of micrometres. On such large scales, the oscillations appear to be in phase and the mean position of cells typically describes a regular elliptic trajectory. We found that the phase of the oscillations is organized into a centimetre-scale travelling wave. We present a model of noisy self-propelled particles with strictly local interactions that accounts faithfully for our observations, suggesting that self-organized collective oscillatory motion results from spontaneous chiral and rotational symmetry breaking. These findings reveal a previously unseen type of long-range order in active matter systems (those in which energy is spent locally to produce non-random motion). This mechanism of collective oscillation may inspire new strategies to control the self-organization of active matter and swarming robots.

Chromatin as active matter

NASA Astrophysics Data System (ADS)

Agrawal, Ankit; Ganai, Nirmalendu; Sengupta, Surajit; Menon, Gautam I.

2017-01-01

Active matter models describe a number of biophysical phenomena at the cell and tissue scale. Such models explore the macroscopic consequences of driving specific soft condensed matter systems of biological relevance out of equilibrium through ‘active’ processes. Here, we describe how active matter models can be used to study the large-scale properties of chromosomes contained within the nuclei of human cells in interphase. We show that polymer models for chromosomes that incorporate inhomogeneous activity reproduce many general, yet little understood, features of large-scale nuclear architecture. These include: (i) the spatial separation of gene-rich, low-density euchromatin, predominantly found towards the centre of the nucleus, vis a vis. gene-poor, denser heterochromatin, typically enriched in proximity to the nuclear periphery, (ii) the differential positioning of individual gene-rich and gene-poor chromosomes, (iii) the formation of chromosome territories, as well as (iv), the weak size-dependence of the positions of individual chromosome centres-of-mass relative to the nuclear centre that is seen in some cell types. Such structuring is induced purely by the combination of activity and confinement and is absent in thermal equilibrium. We systematically explore active matter models for chromosomes, discussing how our model can be generalized to study variations in chromosome positioning across different cell types. The approach and model we outline here represent a preliminary attempt towards a quantitative, first-principles description of the large-scale architecture of the cell nucleus.

[Recent advances of synthetic biology for production of functional ingredients in Chinese materia medica].

PubMed

Su, Xin-Yao; Xue, Jian-Ping; Wang, Cai-Xia

2016-11-01

The functional ingredients in Chinese materia medica are the main active substance for traditional Chinese medicine and most of them are secondary metabolites derivatives. Until now,the main method to obtain those functional ingredients is through direct extraction from the Chinese materia medica. However, the income is very low because of the high extraction costs and the decreased medicinal plants. Synthetic biology technology, as a new and microbial approach, can be able to carry out large-scale production of functional ingredients and greatly ease the shortage of traditional Chinese medicine ingredients. This review mainly focused on the recent advances in synthetic biology for the functional ingredients production. Copyright© by the Chinese Pharmaceutical Association.

Toward Active Control of Noise from Hot Supersonic Jets

DTIC Science & Technology

2013-11-15

several laboratory - and full- scale data sets. Two different scaling scenarios are presented for the practising scientist to choose from. The first...As will be detailed below, this simple proof-of-concept experiment yielded good quality data that reveals details about the large-scale 3D structure...the light-field. Co-PI Thurow has recently designed and assembled a plenoptic camera in his laboratory with its key attributes being its compact

Desalination: Status and Federal Issues

DTIC Science & Technology

2009-12-30

on one side and lets purified water through. Reverse osmosis plants have fewer problems with corrosion and usually have lower energy requirements...Texas) and cities are actively researching and investigating the feasibility of large-scale desalination plants for municipal water supplies...desalination research and development, and in construction and operational costs of desalination demonstration projects and full-scale plants

Neural circuit mechanisms of short-term memory

NASA Astrophysics Data System (ADS)

Goldman, Mark

Memory over time scales of seconds to tens of seconds is thought to be maintained by neural activity that is triggered by a memorized stimulus and persists long after the stimulus is turned off. This presents a challenge to current models of memory-storing mechanisms, because the typical time scales associated with cellular and synaptic dynamics are two orders of magnitude smaller than this. While such long time scales can easily be achieved by bistable processes that toggle like a flip-flop between a baseline and elevated-activity state, many neuronal systems have been observed experimentally to be capable of maintaining a continuum of stable states. For example, in neural integrator networks involved in the accumulation of evidence for decision making and in motor control, individual neurons have been recorded whose activity reflects the mathematical integral of their inputs; in the absence of input, these neurons sustain activity at a level proportional to the running total of their inputs. This represents an analog form of memory whose dynamics can be conceptualized through an energy landscape with a continuum of lowest-energy states. Such continuous attractor landscapes are structurally non-robust, in seeming violation of the relative robustness of biological memory systems. In this talk, I will present and compare different biologically motivated circuit motifs for the accumulation and storage of signals in short-term memory. Challenges to generating robust memory maintenance will be highlighted and potential mechanisms for ameliorating the sensitivity of memory networks to perturbations will be discussed. Funding for this work was provided by NIH R01 MH065034, NSF IIS-1208218, Simons Foundation 324260, and a UC Davis Ophthalmology Research to Prevent Blindness Grant.

Hybrid semi-parametric mathematical systems: bridging the gap between systems biology and process engineering.

PubMed

Teixeira, Ana P; Carinhas, Nuno; Dias, João M L; Cruz, Pedro; Alves, Paula M; Carrondo, Manuel J T; Oliveira, Rui

2007-12-01

Systems biology is an integrative science that aims at the global characterization of biological systems. Huge amounts of data regarding gene expression, proteins activity and metabolite concentrations are collected by designing systematic genetic or environmental perturbations. Then the challenge is to integrate such data in a global model in order to provide a global picture of the cell. The analysis of these data is largely dominated by nonparametric modelling tools. In contrast, classical bioprocess engineering has been primarily founded on first principles models, but it has systematically overlooked the details of the embedded biological system. The full complexity of biological systems is currently assumed by systems biology and this knowledge can now be taken by engineers to decide how to optimally design and operate their processes. This paper discusses possible methodologies for the integration of systems biology and bioprocess engineering with emphasis on applications involving animal cell cultures. At the mathematical systems level, the discussion is focused on hybrid semi-parametric systems as a way to bridge systems biology and bioprocess engineering.

[The hyperiricosuria as an indicator of derangement of biologic functions of endoecology and adaptation, biologic reactions of excretion, inflammation and arterial tension].

PubMed

Titov, V N; Oshchepkova, E V; Dmitriev, V A; Gushchina, O V; Shiriaeva, Iu K; Iashin, A Ia

2012-04-01

During millions years in all animals allantoine (oxidized by uricase uric acid) was catabolite of purines and ascorbic acid was an acceptor of active forms of oxygen. The proximal tubules of nephron reabsorbed the trace amounts of uric acid Then during phylogenesis the primates had a mutation of ascorbic acid gen minus. Later on occurred a second spontaneous mutation and uricase gen minus and uric acid became catabolites of purines. In absence of ascorbic acid synthesis ions of urates became a major capturers of active forms of oxygen and all uric acid as before underwent the reabsorption. Later the carriers were formed which began in epithelium of proximal tubules to secrete all uric acid into urine. At every incident of "littering" of intercellular medium with endogenic flogogens (impairment of biologic function of endoecology) under compensatory development of biologic reaction of inflammation the need in inactivation of active forms of oxygen increases. Hence later on in phylogenesis one more stage was formed--post secretory reabsorption of uric acid In the biologic reaction of inflammation epithelium of proximal tubules initiates retentional hyperiricosuria. The general antioxidant activity of human blood plasma in 60% is presented by urates' ions. The excretion of uric acid includes 4 stages: filtration, full reabsorption, secretion and post secretory reabsorption. In phylogenesis these stages formed in sequence. The mild hyperiricosuria is most frequently considered as a non-specific indicator of activation of biologic reaction of inflammation. The productive hyperiricosuria develops more infrequently under surplus of meat food and cytolysis syndrome (intensification of cell loss in vivo). Under concentration of uric acid more than 400 mkmol/l part of urates circulates in intercellular medium in the form of crystals. The microcrystals of uric acid (biologic "litter") initiate the syndrome of systemic inflammatory response as an endogenic flogogen--initiator of inflammation. The uric acid in the form of ion-capturers of active forms of oxygen is involved into in the formation of syndrome of compensatory anti-inflammatory defense. It may be assumed that simultaneously with post-secretory reabsorption of ions of urates in proximal tubules of nephron occurs intensification of philogenetically late post-secretory reabsorption of ions of sodium and activation of of biologic reaction of hydrodynamic and hydraulic pressure in local pool of intravascular medium i.e. arterial tension. The uric acid simultaneously participates in realization of biologic function of endoecology and adaptation, biologic reactions of excretion, inflammation and arterial tension.

Self-Organized Bistability Associated with First-Order Phase Transitions

NASA Astrophysics Data System (ADS)

di Santo, Serena; Burioni, Raffaella; Vezzani, Alessandro; Muñoz, Miguel A.

2016-06-01

Self-organized criticality elucidates the conditions under which physical and biological systems tune themselves to the edge of a second-order phase transition, with scale invariance. Motivated by the empirical observation of bimodal distributions of activity in neuroscience and other fields, we propose and analyze a theory for the self-organization to the point of phase coexistence in systems exhibiting a first-order phase transition. It explains the emergence of regular avalanches with attributes of scale invariance that coexist with huge anomalous ones, with realizations in many fields.

Occurrence and fate of the antidiabetic drug metformin and its metabolite guanylurea in the environment and during drinking water treatment.

PubMed

Scheurer, Marco; Michel, Amandine; Brauch, Heinz-Jürgen; Ruck, Wolfgang; Sacher, Frank

2012-10-01

Metformin, an antidiabetic drug with one of the highest consumption rates of all pharmaceuticals worldwide, is biologically degraded to guanylurea in wastewater treatment plants. Due to high metformin influent concentrations of up to 100 μg/L and its high but incomplete degradation both compounds are released in considerable amounts of up to several tens of μg/L into recipient rivers. This is the first systematic study on their environmental fate and the effectiveness of treatment techniques applied in waterworks to remove metformin and guanylurea from surface water influenced raw waters. The concentrations in surface waters depend strongly on the respective wastewater burden of rivers and creeks and are typically in the range of about 1 μg/L for metformin and several μg/L for guanylurea but can reach elevated average concentrations of more than 3 and 20 μg/L, respectively. Treatment techniques applied in waterworks were investigated by an extended monitoring program in three facilities and accompanied by laboratory-scale batch tests. Flocculation and activated carbon filtration proved to be ineffective for removal of metformin and guanylurea. During ozonation and chlorination experiments with waterworks-relevant ozone and chlorine doses they were partly transformed to yet unknown compounds. The effectiveness of the treatment steps under investigation can be ordered chlorination > ozonation > activated carbon filtration > flocculation. However, most effective for removal of both compounds at the three full-scale waterworks studied proved to be an underground passage (riverbank filtration or artificial groundwater recharge). A biological degradation is most likely as sorption can be neglected. This is based on laboratory batch tests conducted with three different soil materials according to OECD guideline 106. Since such treatment steps were implemented in all three drinking water treatment plants, even traces of metformin and its metabolite guanylurea could not be detected at the end of the treatment trains. Both can only be expected in finished drinking water if surface influenced raw water is used by direct abstraction without underground passage. Copyright © 2012 Elsevier Ltd. All rights reserved.

Methods for increasing the rate of anammox attachment in a sidestream deammonification MBBR.

PubMed

Klaus, Stephanie; McLee, Patrick; Schuler, Andrew J; Bott, Charles

2016-01-01

Deammonification (partial nitritation-anammox) is a proven process for the treatment of high-nitrogen waste streams, but long startup time is a known drawback of this technology. In a deammonification moving bed biofilm reactor (MBBR), startup time could potentially be decreased by increasing the attachment rate of anammox bacteria (AMX) on virgin plastic media. Previous studies have shown that bacterial adhesion rates can be increased by surface modification or by the development of a preliminary biofilm. This is the first study on increasing AMX attachment rates in a deammonification MBBR using these methods. Experimental media consisted of three different wet-chemical surface treatments, and also media transferred from a full-scale mainstream fully nitrifying integrated fixed-film activated sludge (IFAS) reactor. Following startup of a full-scale deammonification reactor, the experimental media were placed in the full-scale reactor and removed for activity rate measurements and biomass testing after 1 and 2 months. The media transferred from the IFAS process exhibited a rapid increase in AMX activity rates (1.1 g/m(2)/day NH(4)(+) removal and 1.4 g/m(2)/day NO(2)(-) removal) as compared to the control (0.2 g/m(2)/day NH(4)(+) removal and 0.1 g/m(2)/day NO(2)(-) removal) after 1 month. Two out of three of the surface modifications resulted in significantly higher AMX activity than the control at 1 and 2 months. No nitrite oxidizing bacteria activity was detected in either the surface modified media or IFAS media batch tests. The results indicate that startup time of a deammonification MBBR could potentially be decreased through surface modification of the plastic media or through the transfer of media from a mature IFAS process.

An effective and simple procedure to isolate abundant quantities of biologically active chemopreventive lunasin-protease inhibitor concentrate (LPIC) from soybean

USDA-ARS?s Scientific Manuscript database

Lunasin is a 5-kDa soybean bioactive peptide with demonstrated anti-cancer and anti-inflammatory properties. The use of lunasin as a chemopreventive agent in large-scale animal studies and human clinical trials is hampered by the paucity of large quantities of lunasin. Recently, purification methods...

Analysis of Eight Oil Spill Dispersants Using Rapid, In Vitro Tests for Endocrine and Other Biological Activity

EPA Science Inventory

The Deepwater Horizon oil spill has led to the use of >1 M gallons of oil spill dispersants, which are mixtures of surfactants and solvents. Because of this large scale use there is a critical need to understand the potential for toxicity of the currently used dispersant and pote...

The forest ecosystem of southeast Alaska: 7. Forest ecology and timber management.

Treesearch

Arland S. Harris; Wilbur A. Farr

1974-01-01

Large-scale use of the timber resource of southeast Alaska began in 1953 after long efforts to establish a timber industry. Development and present status of the industry and present management of the timber resource are summarized, stressing the biological basis for timber management activities in southeast Alaska today. Ecological and silvicultural considerations...

Physical activity and common mental disorders.

PubMed

Harvey, Samuel B; Hotopf, Matthew; Overland, Simon; Mykletun, Arnstein

2010-11-01

Previous studies have suggested that physical activity may have antidepressant and/or anti-anxiety effects. To examine the bidirectional relationship between physical activity and common mental disorders and establish the importance of context, type and intensity of activity undertaken. A clinical examination of 40 401 residents of Norway was undertaken. Participants answered questions relating to the frequency and intensity of both leisure-time and workplace activity. Depression and anxiety were measured using the Hospital Anxiety and Depression Scale (HADS). Biological and social data were also collected. There was an inverse relationship between the amount of leisure-time physical activity and case-level symptoms of depression. This cross-sectional association was only present with leisure-time (as opposed to workplace) activity and was not dependent on the intensity of activities undertaken. Higher levels of social support and social engagement were important in explaining the relationship between leisure activity and depression. Biological changes such as alterations to parasympathetic vagal tone (resting pulse) and changes to metabolic markers had a less important role. Individuals who engage in regular leisure-time activity of any intensity are less likely to have symptoms of depression. The context and social benefits of exercise are important in explaining this relationship.

Introducing memory and association mechanism into a biologically inspired visual model.

PubMed

Qiao, Hong; Li, Yinlin; Tang, Tang; Wang, Peng

2014-09-01

A famous biologically inspired hierarchical model (HMAX model), which was proposed recently and corresponds to V1 to V4 of the ventral pathway in primate visual cortex, has been successfully applied to multiple visual recognition tasks. The model is able to achieve a set of position- and scale-tolerant recognition, which is a central problem in pattern recognition. In this paper, based on some other biological experimental evidence, we introduce the memory and association mechanism into the HMAX model. The main contributions of the work are: 1) mimicking the active memory and association mechanism and adding the top down adjustment to the HMAX model, which is the first try to add the active adjustment to this famous model and 2) from the perspective of information, algorithms based on the new model can reduce the computation storage and have a good recognition performance. The new model is also applied to object recognition processes. The primary experimental results show that our method is efficient with a much lower memory requirement.

The relevance of nanoscale biological fragments for ice nucleation in clouds

PubMed Central

O′Sullivan, D.; Murray, B. J.; Ross, J. F.; Whale, T. F.; Price, H. C.; Atkinson, J. D.; Umo, N. S.; Webb, M. E.

2015-01-01

Most studies of the role of biological entities as atmospheric ice-nucleating particles have focused on relatively rare supermicron particles such as bacterial cells, fungal spores and pollen grains. However, it is not clear that there are sufficient numbers of these particles in the atmosphere to strongly influence clouds. Here we show that the ice-nucleating activity of a fungus from the ubiquitous genus Fusarium is related to the presence of nanometre-scale particles which are far more numerous, and therefore potentially far more important for cloud glaciation than whole intact spores or hyphae. In addition, we quantify the ice-nucleating activity of nano-ice nucleating particles (nano-INPs) washed off pollen and also show that nano-INPs are present in a soil sample. Based on these results, we suggest that there is a reservoir of biological nano-INPs present in the environment which may, for example, become aerosolised in association with fertile soil dust particles. PMID:25626414

Combining SBR systems for chemical and biological treatment: the destruction of the nerve agent VX.

PubMed

Irvine, R L; Haraburda, S S; Galbis-Reig, C

2004-01-01

The US Army is pilot testing the neutralization of VX nerve agent stockpiled at Newport, Indiana using caustic hydrolysis in a Sequencing Batch Reactor (SBR). The resulting hydrolysate was tested at the bench-scale for treatment with activated sludge biodegradation in two distinct studies, one in the SBR and another, in the PACT process. The feed to both biological systems was pretreated to enhance the biodegradability of the hydrolysis products. Both biodegradation studies demonstrated that the hydrolysate could easily meet the Chemical Weapons Convention treaty and US environmental regulations following pretreatment.

77 FR 21985 - Agency Information Collection Activities; Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-12

... activities, and better allocate resources. Data from clinical interviews completed in 2008 were combined with the main interview short scale data to develop a predictive model that was applied to the full main sample to estimate SMI. Follow-up clinical interviews continued to be conducted with NSDUH respondents...

ARSENIC REMOVAL BY FULL SCALE ION EXCHANGE AND ACTIVATED ALUMINA TREATMENT

EPA Science Inventory

This presentation discusses the results of a one year performance evaluation study of two ion exchange plants and two activated alumina plants that were designed and operated for the removal of arsenic from well water. All the plants were shown to be capable of reducing arsenic l...

The relevance of phylogeny to studies of global change.

PubMed

Edwards, Erika J; Still, Christopher J; Donoghue, Michael J

2007-05-01

Phylogenetic thinking has infiltrated many areas of biological research, but has had little impact on studies of global ecology or climate change. Here, we illustrate how phylogenetic information can be relevant to understanding vegetation-atmosphere dynamics at ecosystem or global scales by re-analyzing a data set of carbonic anhydrase (CA) activity in leaves that was used to estimate terrestrial gross primary productivity. The original calculations relied on what appeared to be low CA activity exclusively in C4 grasses, but our analyses indicate that such activity might instead characterize the PACCAD grass lineage, which includes many widespread C3 species. We outline how phylogenetics can guide better taxon sampling of key physiological traits, and discuss how the emerging field of phyloinformatics presents a promising new framework for scaling from organism physiology to global processes.

Large-scale manufacture and characterization of a lentiviral vector produced for clinical ex vivo gene therapy application.

PubMed

Merten, Otto-Wilhelm; Charrier, Sabine; Laroudie, Nicolas; Fauchille, Sylvain; Dugué, Céline; Jenny, Christine; Audit, Muriel; Zanta-Boussif, Maria-Antonietta; Chautard, Hélène; Radrizzani, Marina; Vallanti, Giuliana; Naldini, Luigi; Noguiez-Hellin, Patricia; Galy, Anne

2011-03-01

From the perspective of a pilot clinical gene therapy trial for Wiskott-Aldrich syndrome (WAS), we implemented a process to produce a lentiviral vector under good manufacturing practices (GMP). The process is based on the transient transfection of 293T cells in Cell Factory stacks, scaled up to harvest 50 liters of viral stock per batch, followed by purification of the vesicular stomatitis virus glycoprotein-pseudotyped particles through several membrane-based and chromatographic steps. The process leads to a 200-fold volume concentration and an approximately 3-log reduction in protein and DNA contaminants. An average yield of 13% of infectious particles was obtained in six full-scale preparations. The final product contained low levels of contaminants such as simian virus 40 large T antigen or E1A sequences originating from producer cells. Titers as high as 2 × 10(9) infectious particles per milliliter were obtained, generating up to 6 × 10(11) infectious particles per batch. The purified WAS vector was biologically active, efficiently expressing the genetic insert in WAS protein-deficient B cell lines and transducing CD34(+) cells. The vector introduced 0.3-1 vector copy per cell on average in CD34(+) cells when used at the concentration of 10(8) infectious particles per milliliter, which is comparable to preclinical preparations. There was no evidence of cellular toxicity. These results show the implementation of large-scale GMP production, purification, and control of advanced HIV-1-derived lentiviral technology. Results obtained with the WAS vector provide the initial manufacturing and quality control benchmarking that should be helpful to further development and clinical applications.

Integrated nanoscale tools for interrogating living cells

NASA Astrophysics Data System (ADS)

Jorgolli, Marsela

The development of next-generation, nanoscale technologies that interface biological systems will pave the way towards new understanding of such complex systems. Nanowires -- one-dimensional nanoscale structures -- have shown unique potential as an ideal physical interface to biological systems. Herein, we focus on the development of nanowire-based devices that can enable a wide variety of biological studies. First, we built upon standard nanofabrication techniques to optimize nanowire devices, resulting in perfectly ordered arrays of both opaque (Silicon) and transparent (Silicon dioxide) nanowires with user defined structural profile, densities, and overall patterns, as well as high sample consistency and large scale production. The high-precision and well-controlled fabrication method in conjunction with additional technologies laid the foundation for the generation of highly specialized platforms for imaging, electrochemical interrogation, and molecular biology. Next, we utilized nanowires as the fundamental structure in the development of integrated nanoelectronic platforms to directly interrogate the electrical activity of biological systems. Initially, we generated a scalable intracellular electrode platform based on vertical nanowires that allows for parallel electrical interfacing to multiple mammalian neurons. Our prototype device consisted of 16 individually addressable stimulation/recording sites, each containing an array of 9 electrically active silicon nanowires. We showed that these vertical nanowire electrode arrays could intracellularly record and stimulate neuronal activity in dissociated cultures of rat cortical neurons similar to patch clamp electrodes. In addition, we used our intracellular electrode platform to measure multiple individual synaptic connections, which enables the reconstruction of the functional connectivity maps of neuronal circuits. In order to expand and improve the capability of this functional prototype device we designed and fabricated a new hybrid chip that combines a front-side nanowire-based interface for neuronal recording with backside complementary metal oxide semiconductor (CMOS) circuits for on-chip multiplexing, voltage control for stimulation, signal amplification, and signal processing. Individual chips contain 1024 stimulation/recording sites enabling large-scale interfacing of neuronal networks with single cell resolution. Through electrical and electrochemical characterization of the devices, we demonstrated their enhanced functionality at a massively parallel scale. In our initial cell experiments, we achieved intracellular stimulations and recordings of changes in the membrane potential in a variety of cells including: HEK293T, cardiomyocytes, and rat cortical neurons. This demonstrated the device capability for single-cell-resolution recording/stimulation which when extended to a large number of neurons in a massively parallel fashion will enable the functional mapping of a complex neuronal network.

Toward Better Physics Labs for Future Biologists

NASA Astrophysics Data System (ADS)

Giannini, John; Moore, Kim; Losert, Wolfgang

2014-03-01

We have developed a set of laboratories and hands on activities to accompany a new two-semester interdisciplinary physics course that has been successfully developed and tested in two small test classes of students at the University of Maryland, College Park (UMD) in 2012-2013, and is currently being used on a wider scale. We have designed the laboratories to be taken accompanying a reformed course in the student's second year, with calculus, biology, and chemistry as prerequisites. This permits the laboratories to include significant content on physics relevant to cellular scales, from chemical interactions to random motion and charge screening in fluids. One major focus of the laboratories is to introduce the students to research-grade equipment and modern physics analysis tools in contexts relevant to biology, while maintaining the pedagogically valuable open-ended laboratory structure of reformed laboratories. Lab development procedures along with some preliminary student results from these two small test classes are discussed.

In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development.

PubMed

Ozerov, Ivan V; Lezhnina, Ksenia V; Izumchenko, Evgeny; Artemov, Artem V; Medintsev, Sergey; Vanhaelen, Quentin; Aliper, Alexander; Vijg, Jan; Osipov, Andreyan N; Labat, Ivan; West, Michael D; Buzdin, Anton; Cantor, Charles R; Nikolsky, Yuri; Borisov, Nikolay; Irincheeva, Irina; Khokhlovich, Edward; Sidransky, David; Camargo, Miguel Luiz; Zhavoronkov, Alex

2016-11-16

Signalling pathway activation analysis is a powerful approach for extracting biologically relevant features from large-scale transcriptomic and proteomic data. However, modern pathway-based methods often fail to provide stable pathway signatures of a specific phenotype or reliable disease biomarkers. In the present study, we introduce the in silico Pathway Activation Network Decomposition Analysis (iPANDA) as a scalable robust method for biomarker identification using gene expression data. The iPANDA method combines precalculated gene coexpression data with gene importance factors based on the degree of differential gene expression and pathway topology decomposition for obtaining pathway activation scores. Using Microarray Analysis Quality Control (MAQC) data sets and pretreatment data on Taxol-based neoadjuvant breast cancer therapy from multiple sources, we demonstrate that iPANDA provides significant noise reduction in transcriptomic data and identifies highly robust sets of biologically relevant pathway signatures. We successfully apply iPANDA for stratifying breast cancer patients according to their sensitivity to neoadjuvant therapy.

In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development

PubMed Central

Ozerov, Ivan V.; Lezhnina, Ksenia V.; Izumchenko, Evgeny; Artemov, Artem V.; Medintsev, Sergey; Vanhaelen, Quentin; Aliper, Alexander; Vijg, Jan; Osipov, Andreyan N.; Labat, Ivan; West, Michael D.; Buzdin, Anton; Cantor, Charles R.; Nikolsky, Yuri; Borisov, Nikolay; Irincheeva, Irina; Khokhlovich, Edward; Sidransky, David; Camargo, Miguel Luiz; Zhavoronkov, Alex

2016-01-01

Signalling pathway activation analysis is a powerful approach for extracting biologically relevant features from large-scale transcriptomic and proteomic data. However, modern pathway-based methods often fail to provide stable pathway signatures of a specific phenotype or reliable disease biomarkers. In the present study, we introduce the in silico Pathway Activation Network Decomposition Analysis (iPANDA) as a scalable robust method for biomarker identification using gene expression data. The iPANDA method combines precalculated gene coexpression data with gene importance factors based on the degree of differential gene expression and pathway topology decomposition for obtaining pathway activation scores. Using Microarray Analysis Quality Control (MAQC) data sets and pretreatment data on Taxol-based neoadjuvant breast cancer therapy from multiple sources, we demonstrate that iPANDA provides significant noise reduction in transcriptomic data and identifies highly robust sets of biologically relevant pathway signatures. We successfully apply iPANDA for stratifying breast cancer patients according to their sensitivity to neoadjuvant therapy. PMID:27848968

Ultrasonic disintegration of biosolids for improved biodegradation.

PubMed

Nickel, Klaus; Neis, Uwe

2007-04-01

Biological cell lysis is known to be the rate-limiting step of anaerobic biosolids degradation. Shear forces generated by low frequency ultrasound can be used to disintegrate bacterial cells in sewage sludge. Thus, the quantity of dissolved organic substrate is increased. Consequently, the degradation rate and the biodegradability of organic biosolids mass are improved. Fundamental pilot-studies showed a significantly accelerated biosolids degradation with less digested sludge being produced and increased biogas production being attained. A full-scale ultrasound reactor system was developed for continuous operation under real life conditions on sewage treatment plants (STP).

The Dark Matter of Biology.

PubMed

Ross, Jennifer L

2016-09-06

The inside of the cell is full of important, yet invisible species of molecules and proteins that interact weakly but couple together to have huge and important effects in many biological processes. Such "dark matter" inside cells remains mostly hidden, because our tools were developed to investigate strongly interacting species and folded proteins. Example dark-matter species include intrinsically disordered proteins, posttranslational states, ion species, and rare, transient, and weak interactions undetectable by biochemical assays. The dark matter of biology is likely to have multiple, vital roles to regulate signaling, rates of reactions, water structure and viscosity, crowding, and other cellular activities. We need to create new tools to image, detect, and understand these dark-matter species if we are to truly understand fundamental physical principles of biology. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Estimation of hospital efficiency--do different definitions and casemix measures for hospital output affect the results?

PubMed

Vitikainen, Kirsi; Street, Andrew; Linna, Miika

2009-02-01

Hospital efficiency has been the subject of numerous health economics studies, but there is little evidence on how the chosen output and casemix measures affect the efficiency results. The aim of this study is to examine the robustness of efficiency results due to these factors. Comparison is made between activities and episode output measures, and two different output grouping systems (Classic and FullDRG). Non-parametric data envelopment analysis is used as an analysis technique. The data consist of all public acute care hospitals in Finland in 2005 (n=40). Efficiency estimates were not found to be highly sensitive to the choice between episode and activity descriptions of output, but more so to the choice of DRG grouping system. Estimates are most sensitive to scale assumptions, with evidence of decreasing returns to scale in larger hospitals. Episode measures are generally to be preferred to activity measures because these better capture the patient pathway, while FullDRGs are preferred to Classic DRGs particularly because of the better description of outpatient output in the former grouping system. Attention should be paid to reducing the extent of scale inefficiency in Finland.

New analogs of the CART peptide with anorexigenic potency: the importance of individual disulfide bridges.

PubMed

Blechová, Miroslava; Nagelová, Veronika; Záková, Lenka; Demianová, Zuzana; Zelezná, Blanka; Maletínská, Lenka

2013-01-01

The CART (cocaine- and amphetamine-regulated transcript) peptide is an anorexigenic neuropeptide that acts in the hypothalamus. The receptor and the mechanism of action of this peptide are still unknown. In our previous study, we showed that the CART peptide binds specifically to PC12 rat pheochromocytoma cells in both the native and differentiated into neuronal phenotype. Two biologically active forms, CART(55-102) and CART(61-102), with equal biological activity, contain three disulfide bridges. To clarify the importance of each of these disulfide bridges in maintaining the biological activity of CART(61-102), an Ala scan at particular S-S bridges forming cysteines was performed, and analogs with only one or two disulfide bridges were synthesized. In this study, a stabilized CART(61-102) analog with norleucine instead of methionine at position 67 was also prepared and was found to bind to PC12 cells with an anorexigenic potency similar to that of CART(61-102). The binding study revealed that out of all analogs tested, [Ala(68,86)]CART(61-102), which contains two disulfide bridges (positions 74-94 and 88-101), preserved a high affinity to both native PC12 cells and those that had been differentiated into neurons. In food intake and behavioral tests with mice after intracerebroventricular administration, this analog showed strong and long-lasting anorexigenic potency. Therefore, the disulfide bridge between cysteines 68 and 86 in CART(61-102) can be omitted without a loss of biological activity, but the preservation of two other disulfide bridges and the full-length peptide are essential for biological activity. Copyright © 2012 Elsevier Inc. All rights reserved.

Efficient digital implementation of a conductance-based globus pallidus neuron and the dynamics analysis

NASA Astrophysics Data System (ADS)

Yang, Shuangming; Wei, Xile; Deng, Bin; Liu, Chen; Li, Huiyan; Wang, Jiang

2018-03-01

Balance between biological plausibility of dynamical activities and computational efficiency is one of challenging problems in computational neuroscience and neural system engineering. This paper proposes a set of efficient methods for the hardware realization of the conductance-based neuron model with relevant dynamics, targeting reproducing the biological behaviors with low-cost implementation on digital programmable platform, which can be applied in wide range of conductance-based neuron models. Modified GP neuron models for efficient hardware implementation are presented to reproduce reliable pallidal dynamics, which decode the information of basal ganglia and regulate the movement disorder related voluntary activities. Implementation results on a field-programmable gate array (FPGA) demonstrate that the proposed techniques and models can reduce the resource cost significantly and reproduce the biological dynamics accurately. Besides, the biological behaviors with weak network coupling are explored on the proposed platform, and theoretical analysis is also made for the investigation of biological characteristics of the structured pallidal oscillator and network. The implementation techniques provide an essential step towards the large-scale neural network to explore the dynamical mechanisms in real time. Furthermore, the proposed methodology enables the FPGA-based system a powerful platform for the investigation on neurodegenerative diseases and real-time control of bio-inspired neuro-robotics.

Day/night temperature differences (DNTD) trigger changes in nutrient removal and functional bacteria in membrane bioreactors.

PubMed

Zhang, Shaoqing; Sheng, Binbin; Lin, Wenting; Meng, Fangang

2018-09-15

Temperature is a well-known environmental stress that influences both microbial metabolism and community structure in the biological wastewater treatment systems. In this study, responses of biological performance and sludge microbiota to the long-term day/night temperature differences (DNTD) were investigated in membrane bioreactors (MBRs). The results showed that the functional bacteria could sustained their ecological functions at low DNTD (20/30 °C), resulting in relatively stable performance with respect to nutrient removal. However, when the activated sludge was subjected to a high DNTD (17/33 °C), the effluent concentrations of COD, TN and TP were significantly higher in MBR-B than that in MBR-A. In addition, more severe membrane fouling occurred under the perturbation of high DNTD as revealed by the transmembrane pressure (TMP) profile, which was mainly attributed to the accumulation of extracellular polymeric substances (EPS). The results of 16S rRNA gene sequencing showed that DNTD showed negligible effect on the bacterial community structures. Nonetheless, the functional bacteria responded differently to DNTD, which were in accordance with the bioreactor performances. Specifically, Nitrospina (NOB) and Tetrasphaera (PAOs) appeared to be sensitive to both low and high DNTD. In contrast, a low DNTD showed marginal effects on the denitrifiers, while a high DNTD significantly decreased their abundances. More strikingly, filamentous bulking bacteria were found to be well-adapted to DNTD, indicating their tolerance to the daily temperature fluctuation. This study will advance our knowledge regarding the response of microbial ecology of activated sludge to daily temperature variations in full-scale MBRs. Copyright © 2018 Elsevier B.V. All rights reserved.

Green house gas emissions from composting and mechanical biological treatment.

PubMed

Amlinger, Florian; Peyr, Stefan; Cuhls, Carsten

2008-02-01

In order to carry out life-cycle assessments as a basis for far-reaching decisions about environmentally sustainable waste treatment, it is important that the input data be reliable and sound. A comparison of the potential greenhouse gas (GHG) emissions associated with each solid waste treatment option is essential. This paper addresses GHG emissions from controlled composting processes. Some important methodological prerequisites for proper measurement and data interpretation are described, and a common scale and dimension of emission data are proposed so that data from different studies can be compared. A range of emission factors associated with home composting, open windrow composting, encapsulated composting systems with waste air treatment and mechanical biological waste treatment (MBT) are presented from our own investigations as well as from the literature. The composition of source materials along with process management issues such as aeration, mechanical agitation, moisture control and temperature regime are the most important factors controlling methane (CH4), nitrous oxide (N2O) and ammoniac (NH3) emissions. If ammoniac is not stripped during the initial rotting phase or eliminated by acid scrubber systems, biofiltration of waste air provides only limited GHG mitigation, since additional N2O may be synthesized during the oxidation of NH3, and only a small amount of CH4 degradation occurs in the biofilter. It is estimated that composting contributes very little to national GHG inventories generating only 0.01-0.06% of global emissions. This analysis does not include emissions from preceding or post-treatment activities (such as collection, transport, energy consumption during processing and land spreading), so that for a full emissions account, emissions from these activities would need to be added to an analysis.

Resolving the substructure of molecular clouds in the LMC

NASA Astrophysics Data System (ADS)

Wong, Tony; Hughes, Annie; Tokuda, Kazuki; Indebetouw, Remy; Wojciechowski, Evan; Bandurski, Jeffrey; MC3 Collaboration

2018-01-01

We present recent wide-field CO and 13CO mapping of giant molecular clouds in the Large Magellanic Cloud with ALMA. Our sample exhibits diverse star-formation properties, and reveals comparably diverse molecular cloud properties including surface density and velocity dispersion at a given scale. We first present the results of a recent study comparing two GMCs at the extreme ends of the star formation activity spectrum. Our quiescent cloud exhibits 10 times lower surface density and 5 times lower velocity dispersion than the active 30 Doradus cloud, yet in both clouds we find a wide range of line widths at the smallest resolved scales, spanning nearly the full range of line widths seen at all scales. This suggests an important role for feedback on sub-parsec scales, while the energetics on larger scales are dominated by clump-to-clump relative velocities. We then extend our analysis to four additional clouds that exhibit intermediate levels of star formation activity.

Intracellular Fluid Mechanics: Coupling Cytoplasmic Flow with Active Cytoskeletal Gel

NASA Astrophysics Data System (ADS)

Mogilner, Alex; Manhart, Angelika

2018-01-01

The cell is a mechanical machine, and continuum mechanics of the fluid cytoplasm and the viscoelastic deforming cytoskeleton play key roles in cell physiology. We review mathematical models of intracellular fluid mechanics, from cytoplasmic fluid flows, to the flow of a viscous active cytoskeletal gel, to models of two-phase poroviscous flows, to poroelastic models. We discuss application of these models to cell biological phenomena, such as organelle positioning, blebbing, and cell motility. We also discuss challenges of understanding fluid mechanics on the cellular scale.

Interfacing Neural Network Components and Nucleic Acids

PubMed Central

Lissek, Thomas

2017-01-01

Translating neural activity into nucleic acid modifications in a controlled manner harbors unique advantages for basic neurobiology and bioengineering. It would allow for a new generation of biological computers that store output in ultra-compact and long-lived DNA and enable the investigation of animal nervous systems at unprecedented scales. Furthermore, by exploiting the ability of DNA to precisely influence neuronal activity and structure, it could be possible to more effectively create cellular therapy approaches for psychiatric diseases that are currently difficult to treat. PMID:29255707

Advances in the Biology and Chemistry of Sialic Acids

PubMed Central

Chen, Xi; Varki, Ajit

2010-01-01

Sialic acids are a subset of nonulosonic acids, which are nine-carbon alpha-keto aldonic acids. Natural existing sialic acid-containing structures are presented in different sialic acid forms, various sialyl linkages, and on diverse underlying glycans. They play important roles in biological, pathological, and immunological processes. Sialobiology has been a challenging and yet attractive research area. Recent advances in chemical and chemoenzymatic synthesis as well as large-scale E. coli cell-based production have provided a large library of sialoside standards and derivatives in amounts sufficient for structure-activity relationship studies. Sialoglycan microarrays provide an efficient platform for quick identification of preferred ligands for sialic acid-binding proteins. Future research on sialic acid will continue to be at the interface of chemistry and biology. Research efforts will not only lead to a better understanding of the biological and pathological importance of sialic acids and their diversity, but could also lead to the development of therapeutics. PMID:20020717

Organic core-sheath nanowire artificial synapses with femtojoule energy consumption.

PubMed

Xu, Wentao; Min, Sung-Yong; Hwang, Hyunsang; Lee, Tae-Woo

2016-06-01

Emulation of biological synapses is an important step toward construction of large-scale brain-inspired electronics. Despite remarkable progress in emulating synaptic functions, current synaptic devices still consume energy that is orders of magnitude greater than do biological synapses (~10 fJ per synaptic event). Reduction of energy consumption of artificial synapses remains a difficult challenge. We report organic nanowire (ONW) synaptic transistors (STs) that emulate the important working principles of a biological synapse. The ONWs emulate the morphology of nerve fibers. With a core-sheath-structured ONW active channel and a well-confined 300-nm channel length obtained using ONW lithography, ~1.23 fJ per synaptic event for individual ONW was attained, which rivals that of biological synapses. The ONW STs provide a significant step toward realizing low-energy-consuming artificial intelligent electronics and open new approaches to assembling soft neuromorphic systems with nanometer feature size.

Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of heterogeneous Fenton oxidation and biological process.

PubMed

Xu, Peng; Han, Hongjun; Zhuang, Haifeng; Hou, Baolin; Jia, Shengyong; Xu, Chunyan; Wang, Dexin

2015-04-01

Laboratorial scale experiments were conducted in order to investigate a novel system integrating heterogeneous Fenton oxidation (HFO) with anoxic moving bed biofilm reactor (ANMBBR) and biological aerated filter (BAF) process on advanced treatment of biologically pretreated coal gasification wastewater (CGW). The results indicated that HFO with the prepared catalyst (FeOx/SBAC, sewage sludge based activated carbon (SBAC) which loaded Fe oxides) played a key role in eliminating COD and COLOR as well as in improving the biodegradability of raw wastewater. The surface reaction and hydroxyl radicals (OH) oxidation were the mechanisms for FeOx/SBAC catalytic reaction. Compared with ANMBBR-BAF process, the integrated system was more effective in abating COD, BOD5, total phenols (TPs), total nitrogen (TN) and COLOR and could shorten the retention time. Therefore, the integrated system was a promising technology for engineering applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mutagenic activity of disinfection by-products

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

Cognet, L.; Courtois, Y.; Mallevialle, J.

1986-11-01

Data on raw water quality, disinfection treatment practices, and the resulting mutagenic properties of the treated water were compiled from pilot- and full-scale treatment experiments to evaluate that parameter which might produce variability in the results of a mutagenic study. Analysis of the data and comparison of treatment practices indicated that the measured mutagenic activity is strongly related to the characteristics of the organic matter in the raw water, the methodology used to sample and detect mutagens, the scale of the study both in terms of treatment flow and period of study, and the point at which and the conditionsmore » under which oxidants are added during treatment. Conclusions regarding disinfection systems in full-scale water treatment plants include the following: When raw water is pretreated and high concentrations of organics are present in the raw water, both ozonation and chlorination increased mutagenic activity. However, no significant difference in mutagenicity was found between the two oxidants. Both in the case of a nitrified groundwater and a clarified surface water, the mutagenic activity of the water after ozonation was related to its mutagenic activity before ozonation. With ozonation, mutagenic activity decreased after granular activated carbon (GAC) filtration. Thus, when GAC filtration follows ozone disinfection, early addition of oxidants may not be deleterious to the finished water quality. When chlorine or chlorine dioxide is added after GAC filtration, chlorine dioxide was found to produce a less mutagenic water than chlorine. Although these conclusions suggest means of controlling mutagenic activity during treatment, it must be stressed that the measurement of mutagenicity is a presumptive index of contamination level.« less

Soft active matter: a contemporary example of Edwardsian statistical mechanics

NASA Astrophysics Data System (ADS)

Liverpool, Tanniemola

Colonies of swimming bacteria, algae or spermatozoa are examples of active systems composed of interacting units that consume energy and collectively generate motion and mechanical stresses. Due to the anisotropy of their interactions, these active particles can exhibit orientational order at high concentrations and have been called ``living liquid crystals''. Biology at the cellular and multicellular scale provides numerous examples of these active systems. They provide a novel class of experimentally accessible system far from equilibrium. Their rich collective behaviour includes non-equilibrium phase transitions and pattern formation on mesoscopic scales. Interestingly however, some of the theoretical insights gained from field theories applied to equilibrium soft matter systems can be used to explain aspects of their behaviour, but with a number of surprising new twists. I will describe and summarise recent theoretical results characterising the behaviour of such soft active systems highlighting in particular the effects of their internal dynamics on their macroscopic behaviour. With support of the EPSRC Grant No. EP/G026440/1.

Familial influences on the full range of variability in attention and activity levels during adolescence: A longitudinal twin study.

PubMed

Peng, Chun-Zi; Grant, Julia D; Heath, Andrew C; Reiersen, Angela M; Mulligan, Richard C; Anokhin, Andrey P

2016-05-01

To investigate familial influences on the full range of variability in attention and activity across adolescence, we collected maternal ratings of 339 twin pairs at ages 12, 14, and 16, and estimated the transmitted and new familial influences on attention and activity as measured by the Strengths and Weaknesses of Attention-Deficit/Hyperactivity Disorder Symptoms and Normal Behavior Scale. Familial influences were substantial for both traits across adolescence: genetic influences accounted for 54%-73% (attention) and 31%-73% (activity) of the total variance, and shared environmental influences accounted for 0%-22% of the attention variance and 13%-57% of the activity variance. The longitudinal stability of individual differences in attention and activity was largely accounted for by familial influences transmitted from previous ages. Innovations over adolescence were also partially attributable to familial influences. Studying the full range of variability in attention and activity may facilitate our understanding of attention-deficit/hyperactivity disorder's etiology and intervention.

SMART Rotor Development and Wind-Tunnel Test

NASA Technical Reports Server (NTRS)

Lau, Benton H.; Straub, Friedrich; Anand, V. R.; Birchette, Terry

2009-01-01

Boeing and a team from Air Force, NASA, Army, Massachusetts Institute of Technology, University of California at Los Angeles, and University of Maryland have successfully completed a wind-tunnel test of the smart material actuated rotor technology (SMART) rotor in the 40- by 80-foot wind-tunnel of the National Full-Scale Aerodynamic Complex at NASA Ames Research Center, figure 1. The SMART rotor is a full-scale, five-bladed bearingless MD 900 helicopter rotor modified with a piezoelectric-actuated trailing-edge flap on each blade. The development effort included design, fabrication, and component testing of the rotor blades, the trailing-edge flaps, the piezoelectric actuators, the switching power amplifiers, the actuator control system, and the data/power system. Development of the smart rotor culminated in a whirl-tower hover test which demonstrated the functionality, robustness, and required authority of the active flap system. The eleven-week wind tunnel test program evaluated the forward flight characteristics of the active-flap rotor, gathered data to validate state-of-the-art codes for rotor noise analysis, and quantified the effects of open- and closed-loop active-flap control on rotor loads, noise, and performance. The test demonstrated on-blade smart material control of flaps on a full-scale rotor for the first time in a wind tunnel. The effectiveness and the reliability of the flap actuation system were successfully demonstrated in more than 60 hours of wind-tunnel testing. The data acquired and lessons learned will be instrumental in maturing this technology and transitioning it into production. The development effort, test hardware, wind-tunnel test program, and test results will be presented in the full paper.

Office of the Assistant Secretary for Preparedness and Response; HHS Public Health Emergency Medical Countermeasures Enterprise implementation plan for chemical, biological, radiological and nuclear threats. Notice.

PubMed

2007-04-23

The United States faces serious public health threats from the deliberate use of weapons of mass destruction (WMD)--chemical, biological, radiological, or nuclear (CBRN)--by hostile States or terrorists, and from naturally emerging infectious diseases that have a potential to cause illness on a scale that could adversely impact national security. Effective strategies to prevent, mitigate, and treat the consequences of CBRN threats is an integral component of our national security strategy. To that end, the United States must be able to rapidly develop, stockpile, and deploy effective medical countermeasures to protect the American people. The HHS Public Health Emergency Medical Countermeasures Enterprise (PHEMCE) has taken a holistic, end-to-end approach that considers multiple aspects of the medical countermeasures mission including research, development, acquisition, storage, maintenance, deployment, and guidance for utilization. Phase one of this approach established the HHS PHEMCE Strategy for Chemical, Biological, Radiological, and Nuclear Threats (HHS PHEMCE Strategy). The HHS PHEMCE Strategy, published in the Federal Register on March 20, 2007, described a framework of strategic policy goals and objectives for identifying medical countermeasure requirements and establishing priorities for medical countermeasure evaluation, development and acquisition. These strategic policy goals and objectives were used to establish the Four Pillars upon which this HHS Public Health Emergency Medical Countermeasures Enterprise Implementation Plan (HHS PHEMCE Implementation Plan) is based. The HHS PHEMCE Implementation Plan considers the full spectrum of medical countermeasures-related activities, including research, development, acquisition, storage/maintenance, deployment, and utilization. The HHS PHEMCE Implementation Plan is consistent with the President's Biodefense for the 21st Century and is aligned with the National Strategy for Medical Countermeasures against Weapons of Mass Destruction.

Sub-Scale Orion Parachute Test Results from the National Full-Scale Aerodynamics Complex 80- By 120-ft Wind Tunnel

NASA Technical Reports Server (NTRS)

Anderson, Brian P.; Greathouse, James S.; Powell, Jessica M.; Ross, James C.; Schairer, Edward T.; Kushner, Laura; Porter, Barry J.; Goulding, Patrick W., II; Zwicker, Matthew L.; Mollmann, Catherine

2017-01-01

A two-week test campaign was conducted in the National Full-Scale Aerodynamics Complex 80 x 120-ft Wind Tunnel in support of Orion parachute pendulum mitigation activities. The test gathered static aerodynamic data using an instrumented, 3-tether system attached to the parachute vent in combination with an instrumented parachute riser. Dynamic data was also gathered by releasing the tether system and measuring canopy performance using photogrammetry. Several canopy configurations were tested and compared against the current Orion parachute design to understand changes in drag performance and aerodynamic stability. These configurations included canopies with varying levels and locations of geometric porosity as well as sails with increased levels of fullness. In total, 37 runs were completed for a total of 392 data points. Immediately after the end of the testing campaign a down-select decision was made based on preliminary data to support follow-on sub-scale air drop testing. A summary of a more rigorous analysis of the test data is also presented.

Auditory evoked potential could reflect emotional sensitivity and impulsivity

PubMed Central

Kim, Ji Sun; Kim, Sungkean; Jung, Wookyoung; Im, Chang-Hwan; Lee, Seung-Hwan

2016-01-01

Emotional sensitivity and impulsivity could cause interpersonal conflicts and neuropsychiatric problems. Serotonin is correlated with behavioral inhibition and impulsivity. This study evaluated whether the loudness dependence of auditory evoked potential (LDAEP), a potential biological marker of central serotonergic activity, could reflect emotional sensitivity and impulsivity. A total of 157 healthy individuals were recruited, who performed LDAEP and Go/Nogo paradigms during electroencephalogram measurement. Barratt impulsivity scale (BIS), Conners’ Adult ADHD rating scale (CAARS), and affective lability scale (ALS) were evaluated. Comparison between low and high LDAEP groups was conducted for behavioural, psychological, and event-related potential (ERP) measures. The high LDAEP group showed significantly increased BIS, a subscale of the CAARS, ALS, and false alarm rate of Nogo stimuli compared to the low LDAEP group. LDAEP showed significant positive correlations with the depression scale, ALS scores, subscale of the CAARS and Nogo-P3 amplitude. In the source activity of Nogo-P3, the cuneus, lingual gyrus, and precentral gyrus activities were significantly increased in the high LDAEP group. Our study revealed that LDAEP could reflect emotional sensitivity and impulsivity. LDAEP, an auditory evoked potential could be a useful tool to evaluate emotional regulation. PMID:27910865

Ixekizumab improves patient-reported outcomes up to 52 weeks in bDMARD-naïve patients with active psoriatic arthritis (SPIRIT-P1).

PubMed

Gottlieb, Alice B; Strand, Vibeke; Kishimoto, Mitsumasa; Mease, Philip; Thaçi, Diamant; Birt, Julie; Lee, Chin H; Shuler, Catherine L; Lin, Chen-Yen; Gladman, Dafna D

2018-06-25

To report patient-reported outcomes of patients with PsA treated with ixekizumab up to 52 weeks. In SPIRIT-P1, biologic-naïve patients with active PsA were randomized to ixekizumab 80 mg every 4 weeks (IXEQ4W; N = 107) or every 2 weeks (IXEQ2W; N = 103) following a 160 mg starting dose, adalimumab 40 mg every 2 weeks (ADA; N = 101) or placebo (PBO; N = 106) during the initial 24-week double-blind treatment period. At week 24 (week 16 for inadequate responders), ADA (8-week washout before starting ixekizumab) and PBO patients were re-randomized to IXEQ2W or IXEQ4W. Patients receiving ixekizumab at week 24 received the same dose during the extension period (EP) to week 52. Patients completed measures including the Dermatology Life Quality Index (DLQI), Itch Numeric Rating Scale, 36-Item Short Form Health Survey version 2, European Quality of Life 5 Dimensions Visual Analogue Scale and Work Productivity and Activity Impairment Questionnaire-Specific Health Problem. The IXEQ4W, IXEQ2W and ADA groups reported significant improvements in DLQI at week 24; 22% (PBO), 53% (IXEQ4W), 63% (IXEQ2W) and 54% (ADA) of patients reported DLQI scores of 0/1. The IXEQ4W, IXEQ2W and ADA groups reported significant improvements in Itch Numeric Rating Scale, 36-Item Short Form Health Survey version 2 physical component summary and some domain scores, and European Quality of Life 5 Dimensions Visual Analogue Scale at weeks 12 and 24; and in three of four Work Productivity and Activity Impairment Questionnaire-Specific Health Problem domains at week 24. Results are also presented through week 52 for the EP. In biologic-naïve patients with active PsA, ixekizumab significantly improved skin symptoms, health-related quality of life and work productivity. ClinicalTrials.gov, http://clinicaltrials.gov, NCT01695239; EU Clinical Trials Register, https://www.clinicaltrialsregister.eu, EudraCT2011-002326-49.

Cellular Electron Cryotomography: Toward Structural Biology In Situ.

PubMed

Oikonomou, Catherine M; Jensen, Grant J

2017-06-20

Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.

Calibration and simulation of two large wastewater treatment plants operated for nutrient removal.

PubMed

Ferrer, J; Morenilla, J J; Bouzas, A; García-Usach, F

2004-01-01

Control and optimisation of plant processes has become a priority for WWTP managers. The calibration and verification of a mathematical model provides an important tool for the investigation of advanced control strategies that may assist in the design or optimization of WWTPs. This paper describes the calibration of the ASM2d model for two full scale biological nitrogen and phosphorus removal plants in order to characterize the biological process and to upgrade the plants' performance. Results from simulation showed a good correspondence with experimental data demonstrating that the model and the calibrated parameters were able to predict the behaviour of both WWTPs. Once the calibration and simulation process was finished, a study for each WWTP was done with the aim of improving its performance. Modifications focused on reactor configuration and operation strategies were proposed.

Disintegration of excess activated sludge--evaluation and experience of full-scale applications.

PubMed

Zábranská, J; Dohányos, M; Jenícek, P; Kutil, J

2006-01-01

Anaerobic digestion of sewage sludge can be improved by introducing a disintegration of excess activated sludge as a pretreatment process. The disintegration brings a deeper degradation of organic matter and less amount of output sludge for disposal, a higher production of biogas and consequently energy yield, in some cases suppression of digesters foaming and better dewaterability. The full-scale application of disintegration by a lysate-thickening centrifuge was monitored long term in three different WWTPs. The evaluation of contribution of disintegration to biogas production and digested sludge quality was assessed and operational experience is discussed. Increment of specific biogas production was evaluated in the range of 15-26%, organic matter in digested sludge significantly decreased to 48-49%. Results proved that the installation of a disintegrating centrifuge in WWTPs of different sizes and conditions would be useful and beneficial.

Discrimination of Single Base Pair Differences Among Individual DNA Molecules Using a Nanopore

NASA Technical Reports Server (NTRS)

Vercoutere, Wenonah; DeGuzman, Veronica

2003-01-01

The protein toxin alpha-hemolysin form nanometer scale channels across lipid membranes. Our lab uses a single channel in an artificial lipid bilayer in a patch clamp device to capture and examine individual DNA molecules. This nanopore detector used with a support vector machine (SVM) can analyze DNA hairpin molecules on the millisecond time scale. We distinguish duplex stem length, base pair mismatches, loop length, and single base pair differences. The residual current fluxes also reveal structural molecular dynamics elements. DNA end-fraying (terminal base pair dissociation) can be observed as near full blockades, or spikes, in current. This technique can be used to investigate other biological processes dependent on DNA end-fraying, such as the processing of HIV DNA by HIV integrase.

Identifying Catchment-Scale Predictors of Coal Mining Impacts on New Zealand Stream Communities.

PubMed

Clapcott, Joanne E; Goodwin, Eric O; Harding, Jon S

2016-03-01

Coal mining activities can have severe and long-term impacts on freshwater ecosystems. At the individual stream scale, these impacts have been well studied; however, few attempts have been made to determine the predictors of mine impacts at a regional scale. We investigated whether catchment-scale measures of mining impacts could be used to predict biological responses. We collated data from multiple studies and analyzed algae, benthic invertebrate, and fish community data from 186 stream sites, including un-mined streams, and those associated with 620 mines on the West Coast of the South Island, New Zealand. Algal, invertebrate, and fish richness responded to mine impacts and were significantly higher in un-mined compared to mine-impacted streams. Changes in community composition toward more acid- and metal-tolerant species were evident for algae and invertebrates, whereas changes in fish communities were significant and driven by a loss of nonmigratory native species. Consistent catchment-scale predictors of mining activities affecting biota included the time post mining (years), mining density (the number of mines upstream per catchment area), and mining intensity (tons of coal production per catchment area). Mining was associated with a decline in stream biodiversity irrespective of catchment size, and recovery was not evident until at least 30 years after mining activities have ceased. These catchment-scale predictors can provide managers and regulators with practical metrics to focus on management and remediation decisions.

Identifying Catchment-Scale Predictors of Coal Mining Impacts on New Zealand Stream Communities

NASA Astrophysics Data System (ADS)

Clapcott, Joanne E.; Goodwin, Eric O.; Harding, Jon S.

2016-03-01

Coal mining activities can have severe and long-term impacts on freshwater ecosystems. At the individual stream scale, these impacts have been well studied; however, few attempts have been made to determine the predictors of mine impacts at a regional scale. We investigated whether catchment-scale measures of mining impacts could be used to predict biological responses. We collated data from multiple studies and analyzed algae, benthic invertebrate, and fish community data from 186 stream sites, including un-mined streams, and those associated with 620 mines on the West Coast of the South Island, New Zealand. Algal, invertebrate, and fish richness responded to mine impacts and were significantly higher in un-mined compared to mine-impacted streams. Changes in community composition toward more acid- and metal-tolerant species were evident for algae and invertebrates, whereas changes in fish communities were significant and driven by a loss of nonmigratory native species. Consistent catchment-scale predictors of mining activities affecting biota included the time post mining (years), mining density (the number of mines upstream per catchment area), and mining intensity (tons of coal production per catchment area). Mining was associated with a decline in stream biodiversity irrespective of catchment size, and recovery was not evident until at least 30 years after mining activities have ceased. These catchment-scale predictors can provide managers and regulators with practical metrics to focus on management and remediation decisions.

Full scale remediation of an explosives-contaminated site at Yorktown Naval Weapons Station using the SABRE{trademark} process

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

Kaake, R.H.; Bono, J.; Yergovich, T.

Characterization of a former weapons loading and assembly facility identified soil contaminated with the explosives TNT (2,4,6-trinitrotoluene) and RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine). The site contains of a variety of discrete soil types that include clay, sand, and humus. A portion of the site is also periodically submerged due to tidal action. Treatability studies were performed in conjunction with the Army Corps of Engineers Waterways Experiment Station. Studies indicated the SABRE Process could successfully treat the soil to the specified treatment goals. A full scale demonstration of the Simplot Anaerobic Biological Remediation (SABRE{trademark}) Process was carried out at the Yorktown, Virginia Naval Weaponsmore » Station. Over 650 yd{sup 3} of soil was treated to less than 2.5 mg/kg TNT in approximately 30 days. Initial concentrations were estimated to be 450 mg/kg. The soil was screened and placed into an in-ground, double-lined biocell using a soil fluidizing system.« less

Predictors of short-term work-related disability among active duty US Navy personnel: a cohort study in patients with acute and subacute low back pain.

PubMed

Hiebert, Rudi; Campello, Marco A; Weiser, Sherri; Ziemke, Gregg W; Fox, Bryan A; Nordin, Margareta

2012-09-01

Musculoskeletal disorders of the spine in the US military account for the single largest proportion of the absence of sickness causes leading to early termination. We explored if selected psychological and physical factors were associated with poor outcome after episodes of low back pain (LBP). To identify clinical, demographic, and psychological factors predictive of work duty status after a complaint of LBP. A prospective clinical cohort of US Navy personnel treated for LBP. Eligible cases were active duty US Navy or Marine Corps personnel presenting to an emergency clinic or primary care clinic with a complaint of LBP, where the index episode of LBP was no more than 12 weeks duration before enrollment. The subject's work status (full duty, light duty, sick in quarters [SIQ], limited duty, or medically released to full duty) was abstracted from the subject's electronic medical record at approximately 4 weeks and then again 12 weeks after study enrollment. Work status in this study population is assigned by a Navy health-care provider at the time of a clinical visit and based on the health-care provider's determination of medical fitness for duty. This study collapsed work status into two groups, "full duty" (consisting of "full duty" and "medically released to full duty") and "not at full duty" (consisting of "light duty," "SIQ," and "limited duty"). Volunteers completed a baseline questionnaire consisting of recommended well-validated measures, including attitudes and beliefs about LBP and work (Fear-Avoidance Beliefs Questionnaire [FABQ] and the Tampa Scale of Kinesiophobia), distress (the Pain Catastrophizing Scale), clinical depression (The Center for Epidemiologic Studies Depression scale), a numeric pain intensity scale, self-perceived disability (Oswestry Disability Index), and general health status (12-Item Short Form Health Survey). Navy health-care providers conducted a back pain-specific medical evaluation. Associations are expressed as multivariate-adjusted prevalence ratios (PRs) estimated using Poisson regression. Two hundred fifty-three participants were enrolled. Work status outcome was collected for 239 participants. Predictors of "not at full duty" at 4 weeks after enrollment included having back pain for 4 weeks or less before study enrollment (PR, 2.69; 95% CI, 1.21-5.97) and increased FABQ Work subscale score (PR, 1.05; 95% CI, 1.01-1.08). The sole predictor of work status at 12 weeks after enrollment was increased FABQ Physical Activity (FABQ Physical) subscale score (PR=1.14; 95% CI, 1.00-1.30). The findings that fear-avoidance beliefs were predictive of subsequent work status among active duty service personnel in this study population (after adjusting for clinical, demographic, and psychological covariates) suggest the clinical utility of addressing these factors during treatment of back pain episodes in the military. These findings reflect the important role that psychological factors may play in the return to work process in an active duty military population. Copyright © 2012 Elsevier Inc. All rights reserved.

RELEVANT ASPECTS OF MEDIUM-SCALE TIDs RELATED WITH MIDLATITUDES SPREAD- F OBSERVED BY ALL-SKY IMAGING SYSTEM IN THE SOUTHERN HEMISPHERE OVER TWO FULL SOLAR CYCLES

NASA Astrophysics Data System (ADS)

Pimenta, A. A.

2009-12-01

Using ground-based measurements we investigate the occurrence of medium-scale TIDs (MSTIDs) in the OI 630 nm nightglow emission all-sky images in the Brazilian low latitudes region related with midlatitude Spread F, during over two full solar cycles. The OI 630 nm images obtained during these periods show thermospheric dark band structures (MSTIDs) in low latitudes region propagating from southeast to northwest. These dark patches moved with average speed of about 50-200 m/s. Only during low solar activity period (LSA), ascending solar activity period (ASA) and descending solar activity period the DBS occurrences were observed in the OI630 nm nightglow emission all-sky images. However, during high solar activity (HAS) we didn’t observe the DBS in the all-sky images. In addition, ionospheric data over two stations in Brazil, one at the magnetic equator (São Luís) and the other close to the southern crest of the equatorial ionization anomaly (Cachoeira Paulista) were used to study this kind of structures during high and low solar activity periods. It should be pointed out that these thermospheric/ionospheric events are not related to geomagnetic disturbed conditions. In this work, we present and discuss this phenomenon in the Brazilian sector over two full solar cycles under different solar activity conditions. A possible mechanism for generation of these dark band structures is presented.

Assessment of biogas production from MBT waste under different operating conditions.

PubMed

Pantini, Sara; Verginelli, Iason; Lombardi, Francesco; Scheutz, Charlotte; Kjeldsen, Peter

2015-09-01

In this work, the influence of different operating conditions on the biogas production from mechanically-biologically treated (MBT) wastes is investigated. Specifically, different lab-scale anaerobic tests varying the water content (26-43% w/w up to 75% w/w), the temperature (from 20 to 25°C up to 55°C) and the amount of inoculum have been performed on waste samples collected from a full-scale Italian MBT plant. For each test, the gas generation yield and, where applicable, the first-order gas generation rates were determined. Nearly all tests were characterised by a quite long lag-phase. This result was mainly ascribed to the inhibition effects resulting from the high concentrations of volatile fatty acids (VFAs) and ammonia detected in the different stages of the experiments. Furthermore, water content was found as one of the key factor limiting the anaerobic biological process. Indeed, the experimental results showed that when the moisture was lower than 32% w/w, the methanogenic microbial activity was completely inhibited. For the higher water content tested (75% w/w), high values of accumulated gas volume (up to 150Nl/kgTS) and a relatively short time period to deplete the MBT waste gas generation capacity were observed. At these test conditions, the effect of temperature became evident, leading to gas generation rates of 0.007d(-1) at room temperature that increased to 0.03-0.05d(-1) at 37°C and to 0.04-0.11d(-1) at 55°C. Overall, the obtained results highlighted that the operative conditions can drastically affect the gas production from MBT wastes. This suggests that particular caution should be paid when using the results of lab-scale tests for the evaluation of long-term behaviour expected in the field where the boundary conditions change continuously and vary significantly depending on the climate, the landfill operative management strategies in place (e.g. leachate recirculation, waste disposal methods), the hydraulic characteristics of disposed waste, the presence and type of temporary and final cover systems. Copyright © 2015 Elsevier Ltd. All rights reserved.

Full-scale control of Mycolata foam by FEX-120 addition.

PubMed

Kragelund, C; Nilsson, B; Eskilsson, K; Bøgh, A M; Nielsen, P H

2010-01-01

Foaming incidents in activated sludge treatment plants are a worldwide problem and occur on a regular basis in both municipal and industrial activated sludge treatment plants. Foaming is most often caused by excessive growth of filamentous bacteria, especially the gram-positive ones affiliated within the Actinobacteria, e.g. the branched Mycolata or Candidatus Microthrix parvicella. Previous studies have shown that populations of Microthrix can be controlled by addition of certain polyaluminium compounds, but until now no effective chemicals have been identified to control other important foam formers such as the Mycolata. A new chemical (FilamentEx, FEX-120) was tested in full-scale in a Swedish wastewater treatment plant (WWTP) with immense foaming problems. In total, three different dosing events were carried out for more than 1 year. After only 8-17 weeks in each period, all foam had disappeared, and dosing of FEX-120 was stopped. Another 11 full-scale WWTPs in different countries were treated with FEX-120 because of severe Mycolata foaming on process tanks. In nine out of 11 plants, where the causative organisms were Gordonia or Skermania, a significant reduction of foam up to 100% was observed after treatment for approx. 10 weeks. In two WWTPs with unknown Mycolata organisms, no reduction was observed.

Nutritional, biochemical, and pharmaceutical potential of proteins and peptides from jatropha: review.

PubMed

Devappa, Rakshit K; Makkar, Harinder P S; Becker, Klaus

2010-06-09

Increased bioenergy consciousness and high demand for animal products have propelled the search for alternative resources that could meet the dual demands. Jatropha seeds have potential to fit these roles in view of their multipurpose uses, broad climatic adaptability features, and high oil and protein contents. During the past five years many large-scale cultivation projects have been undertaken to produce jatropha seed oil as a feedstock for the biodiesel industry. The present review aims at providing biological significance of jatropha proteins and peptides along with their nutritional and therapeutic applications. The nutritional qualities of the kernel meal and protein concentrates or isolates prepared from seed cake are presented, enabling their efficient use in animal nutrition. In addition, (a) biologically active proteins involved in plant protection, for example, aquaporin and betaine aldehyde dehydrogenase, which have roles in drought resistance, and beta-glucanase, which has antifungal activity, as well as those having pharmaceutical properties, and (b) cyclic peptides with various biological activities such as antiproliferative, immunomodulatory, antifungal, and antimalarial activity are discussed. It is expected that the information collated will open avenues for new applications of proteins present in jatropha plant, thereby contributing to enhance the financial viability and sustainability of a jatropha-based biodiesel industry.

A new settling velocity model to describe secondary sedimentation.

PubMed

Ramin, Elham; Wágner, Dorottya S; Yde, Lars; Binning, Philip J; Rasmussen, Michael R; Mikkelsen, Peter Steen; Plósz, Benedek Gy

2014-12-01

Secondary settling tanks (SSTs) are the most hydraulically sensitive unit operations in biological wastewater treatment plants. The maximum permissible inflow to the plant depends on the efficiency of SSTs in separating and thickening the activated sludge. The flow conditions and solids distribution in SSTs can be predicted using computational fluid dynamics (CFD) tools. Despite extensive studies on the compression settling behaviour of activated sludge and the development of advanced settling velocity models for use in SST simulations, these models are not often used, due to the challenges associated with their calibration. In this study, we developed a new settling velocity model, including hindered, transient and compression settling, and showed that it can be calibrated to data from a simple, novel settling column experimental set-up using the Bayesian optimization method DREAM(ZS). In addition, correlations between the Herschel-Bulkley rheological model parameters and sludge concentration were identified with data from batch rheological experiments. A 2-D axisymmetric CFD model of a circular SST containing the new settling velocity and rheological model was validated with full-scale measurements. Finally, it was shown that the representation of compression settling in the CFD model can significantly influence the prediction of sludge distribution in the SSTs under dry- and wet-weather flow conditions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Gold nanoparticles as nanosources of heat

NASA Astrophysics Data System (ADS)

Baffou, Guillaume

2018-04-01

Under illumination at their plasmonic resonance wavelength, gold nanoparticles can absorb incident light and turn into efficient nanosources of heat remotely controllable by light. This fundamental scheme is at the basis of an active field of research coined thermoplasmonics and encompasses numerous applications in physics, chemistry and biology at the micro and nano scales. Warning, no authors found for 2018Phot........48.

High yield bacterial expression, purification and characterisation of bioactive Human Tousled-like Kinase 1B involved in cancer.

PubMed

Bhoir, Siddhant; Shaik, Althaf; Thiruvenkatam, Vijay; Kirubakaran, Sivapriya

2018-03-19

Human Tousled-like kinases (TLKs) are highly conserved serine/threonine protein kinases responsible for cell proliferation, DNA repair, and genome surveillance. Their possible involvement in cancer via efficient DNA repair mechanisms have made them clinically relevant molecular targets for anticancer therapy. Innovative approaches in chemical biology have played a key role in validating the importance of kinases as molecular targets. However, the detailed understanding of the protein structure and the mechanisms of protein-drug interaction through biochemical and biophysical techniques demands a method for the production of an active protein of exceptional stability and purity on a large scale. We have designed a bacterial expression system to express and purify biologically active, wild-type Human Tousled-like Kinase 1B (hTLK1B) by co-expression with the protein phosphatase from bacteriophage λ. We have obtained remarkably high amounts of the soluble and homogeneously dephosphorylated form of biologically active hTLK1B with our unique, custom-built vector design strategy. The recombinant hTLK1B can be used for the structural studies and may further facilitate the development of new TLK inhibitors for anti-cancer therapy using a structure-based drug design approach.

Seasonal-related effects on ammonium removal in activated carbon filter biologically enhanced by heterotrophic nitrifying bacteria for drinking water treatment.

PubMed

Qin, Wen; Li, Wei-Guang; Gong, Xu-Jin; Huang, Xiao-Fei; Fan, Wen-Biao; Zhang, Duoying; Yao, Peng; Wang, Xiao-Ju; Song, Yang

2017-08-01

To determine the potential effects of seasonal changes on water temperature and water quality upon removal of ammonium and organic carbon pollutants and to characterize the variations in microbial characteristics, a pilot-scale activated carbon filter biologically enhanced with heterotrophic nitrifying bacteria was investigated for 528 days. The results show that 69.2 ± 28.6% of ammonium and 23.1 ± 11.6% of the dissolved organic carbon were removed by the biologically enhanced activated carbon (BEAC) reactor. It is shown that higher biodegradable dissolved organic carbon enhances ammonium removal, even at low temperatures. The C/N ratio consumed by the BEAC reactor reached a steady value (i.e., 3.3) after 2 months of operation. Despite seasonal fluctuations and competition of the indigenous community, the heterotrophic nitrifying bacteria (Acinetobacter sp. HRBLi 16 and Acinetobacter harbinensis strain HITLi 7) remained relatively stable. The amount of carbon source was the most significant environmental parameter and dramatically affected the microbial community compositions in the BEAC reactor. The present study provides new insights into the application of a BEAC reactor for ammonium removal from drinking water, resisting strong seasonal changes.

Living Nanomachines

NASA Astrophysics Data System (ADS)

Carlier, M.-F.; Helfer, E.; Wade, R.; Haraux, F.

The living cell is a kind of factory on the microscopic scale, in which an assembly of modular machines carries out, in a spatially and temporally coordinated way, a whole range of activities internal to the cell, including the synthesis of substances essential to its survival, intracellular traffic, waste disposal, and cell division, but also activities related to intercellular communication and exchanges with the outside world, i.e., the ability of the cell to change shape, to move within a tissue, or to organise its own defence against attack by pathogens, injury, and so on. These nanomachines are made up of macromolecular assemblies with varying degrees of complexity, forged by evolution, within which work is done as a result of changes in interactions between proteins, or between proteins and nucleic acids, or between proteins and membrane components. All these cell components measure a few nanometers across, so the mechanical activity of these nanomachines all happens on the nanometric scale. The directional nature of the work carried out by biological nanomachines is associated with a dissipation of energy. As examples of protein assemblies, one could mention the proteasome, which is responsible for the degradation of proteins, and linear molecular motors such as actomyosin, responsible for muscle contraction, the dynein-microtubule system, responsible for flagellar motility, and the kinesin-microtubule system, responsible for transport of vesicles, which transform chemical energy into motion. Nucleic acid-protein assemblies include the ribosome, responsible for synthesising proteins, polymerases, helicases, elongation factors, and the machinery of DNA replication and repair; the mitotic spindle is an integrated system involving several of these activities which drive chromosome segregation. The machinery coupling membranes and proteins includes systems involved in the energy metabolism, such as the ATP synthase rotary motor, signalling cascades, endocytosis and phagocytosis complexes, and also dynamic membrane-cytoskeleton complexes which generate protrusion forces involved in cell adhesion and migration. The ideas of molecular recognition and controlled interfaces between biological components provide the underlying mechanisms for biological machinery and networks [1]. Many proteins illustrate this principle by their modular organisation into domains. The juxtaposition of catalytic domains of known function and domains of interaction with different partners leads to the emergence of new biological functions. It can also create threshold mechanisms, or biological switches, by triggering the activity of a given domain only when several partners interact with the regulatory domains. Many of these interaction domains are well understood. They exist inside different proteins, in particular, in cell signaling networks, and could potentially be used as building blocks in the construction of new proteins.

Modelling the Wake of the Marquesas Archipelago

NASA Astrophysics Data System (ADS)

Raapoto, H.; Martinez, E. C.; Petrenko, A. A.; Doglioli, A. M.; Maes, C.

2017-12-01

In this study, a high-resolution ( 2.5 km) numerical model was set up to investigate the fine-scale activity within the region of the Marquesas archipelago where a strong biological enhancement occurs. This has never been performed before. The robustness of the model results is assessed by comparison with remote sensing and in situ observations. Our results highlight regions of warm waters leeward of the different islands with high eddy kinetic energy (EKE) on their sides. The analysis of energy conversion terms reveals contributions to EKE variability by wind, baroclinic and barotropic instabilities. The use of a geometry-based eddy detection algorithm reveals eddy generation in the wake of the largest islands, with both an inshore and offshore effect. Maximum eddy activity occurs in austral winter following the seasonality of both wind stress and EKE intensity. Most eddies have a radius between 20 and 30 km and are generally cyclonic rather than anticyclonic. Significant vertical velocities are observed in the proximity of the islands, associated with topography induced flow separation. Eddy trapping inshore waters are advected offshore in the wake of the islands. The overall influence of these fine-scale dynamics could explain the strong biological enhancement of the archipelago.

77 FR 34959 - Agency Information Collection Activities: Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-12

..., direct program activities, and better allocate resources. Data from clinical interviews completed in 2008 were combined with the main interview short scale data to develop a predictive model that was applied to the full main sample to estimate SMI. Follow-up clinical interviews continued to be conducted with...

Ammonia-oxidizing bacteria dominate ammonia oxidation in a full-scale wastewater treatment plant revealed by DNA-based stable isotope probing.

PubMed

Pan, Kai-Ling; Gao, Jing-Feng; Li, Hong-Yu; Fan, Xiao-Yan; Li, Ding-Chang; Jiang, Hao

2018-05-01

A full-scale wastewater treatment plant (WWTP) with three separate treatment processes was selected to investigate the effects of seasonality and treatment process on the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB). And then DNA-based stable isotope probing (DNA-SIP) was applied to explore the active ammonia oxidizers. The results of high-throughput sequencing indicated that treatment processes varied AOB communities rather than AOA communities. AOA slightly outnumbered AOB in most of the samples, whose abundance was significantly correlated with temperature. DNA-SIP results showed that the majority of AOB amoA gene was labeled by 13 C-substrate, while just a small amount of AOA amoA gene was labeled. As revealed by high-throughput sequencing of heavy DNA, Nitrosomonadaceae-like AOB, Nitrosomonas sp. NP1, Nitrosomonas oligotropha and Nitrosomonas marina were the active AOB, and Nitrososphaera viennensis dominated the active AOA. The results indicated that AOB, not AOA, dominated active ammonia oxidation in the test WWTP. Copyright © 2018 Elsevier Ltd. All rights reserved.

Fiber networks amplify active stress

NASA Astrophysics Data System (ADS)

Lenz, Martin; Ronceray, Pierre; Broedersz, Chase

Large-scale force generation is essential for biological functions such as cell motility, embryonic development, and muscle contraction. In these processes, forces generated at the molecular level by motor proteins are transmitted by disordered fiber networks, resulting in large-scale active stresses. While fiber networks are well characterized macroscopically, this stress generation by microscopic active units is not well understood. I will present a comprehensive theoretical study of force transmission in these networks. I will show that the linear, small-force response of the networks is remarkably simple, as the macroscopic active stress depends only on the geometry of the force-exerting unit. In contrast, as non-linear buckling occurs around these units, local active forces are rectified towards isotropic contraction and strongly amplified. This stress amplification is reinforced by the networks' disordered nature, but saturates for high densities of active units. I will show that our predictions are quantitatively consistent with experiments on reconstituted tissues and actomyosin networks, and that they shed light on the role of the network microstructure in shaping active stresses in cells and tissue.

In vitro transcripts of wild-type and fluorescent protein-tagged triticum mosaic virus (family potyviridae) are biologically active in wheat

USDA-ARS?s Scientific Manuscript database

Triticum mosaic virus (TriMV) (genus Poacevirus, family Potyviridae) is a recently described eriophyid mite-transmitted wheat virus. In vitro RNA transcripts generated from full-length cDNA clones of TriMV proved infectious on wheat, and the progeny virus was efficiently transmitted by wheat curl m...

Information on black-footed ferret biology collected within the framework of ferret conservation

USGS Publications Warehouse

Biggins, Dean E.

2012-01-01

Once feared to be extinct, black-footed ferrets (Mustela nigripes) were rediscovered near Meeteetse, Wyoming, in 1981, resulting in renewed conservation and research efforts for this highly endangered species. A need for information directly useful to recovery has motivated much monitoring of ferrets since that time, but field activities have enabled collection of data relevant to broader biological themes. This special feature is placed in a context of similar books and proceedings devoted to ferret biology and conservation. Articles include general observations on ferrets, modeling of potential impacts of ferrets on prairie dogs (Cynomys spp.), discussions on relationships of ferrets to prairie dog habitats at several spatial scales (from individual burrows to patches of burrow systems) and a general treatise on the status of black-footed ferret recovery.

Adding the third dimension on adaptive optics retina imager thanks to full-field optical coherence tomography

NASA Astrophysics Data System (ADS)

Blavier, Marie; Blanco, Leonardo; Glanc, Marie; Pouplard, Florence; Tick, Sarah; Maksimovic, Ivan; Mugnier, Laurent; Chènegros, Guillaume; Rousset, Gérard; Lacombe, François; Pâques, Michel; Le Gargasson, Jean-François; Sahel, José-Alain

2009-02-01

Retinal pathologies, like ARMD or glaucoma, need to be early detected, requiring imaging instruments with resolution at a cellular scale. However, in vivo retinal cells studies and early diagnoses are severely limited by the lack of resolution on eye-fundus images from classical ophthalmologic instruments. We built a 2D retina imager using Adaptive Optics to improve lateral resolution. This imager is currently used in clinical environment. We are currently developing a time domain full-field optical coherence tomograph. The first step was to conceive the images reconstruction algorithms and validation was realized on non-biological samples. Ex vivo retina are currently being imaged. The final step will consist in coupling both setups to acquire high resolution retina cross-sections.

Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data.

PubMed

Miannay, Bertrand; Minvielle, Stéphane; Magrangeas, Florence; Guziolowski, Carito

2018-03-21

The integration of gene expression profiles (GEPs) and large-scale biological networks derived from pathways databases is a subject which is being widely explored. Existing methods are based on network distance measures among significantly measured species. Only a small number of them include the directionality and underlying logic existing in biological networks. In this study we approach the GEP-networks integration problem by considering the network logic, however our approach does not require a prior species selection according to their gene expression level. We start by modeling the biological network representing its underlying logic using Logic Programming. This model points to reachable network discrete states that maximize a notion of harmony between the molecular species active or inactive possible states and the directionality of the pathways reactions according to their activator or inhibitor control role. Only then, we confront these network states with the GEP. From this confrontation independent graph components are derived, each of them related to a fixed and optimal assignment of active or inactive states. These components allow us to decompose a large-scale network into subgraphs and their molecular species state assignments have different degrees of similarity when compared to the same GEP. We apply our method to study the set of possible states derived from a subgraph from the NCI-PID Pathway Interaction Database. This graph links Multiple Myeloma (MM) genes to known receptors for this blood cancer. We discover that the NCI-PID MM graph had 15 independent components, and when confronted to 611 MM GEPs, we find 1 component as being more specific to represent the difference between cancer and healthy profiles.

Challenges and opportunities in synthetic biology for chemical engineers

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

Luo, YZ; Lee, JK; Zhao, HM

Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement. (C) 2012 Elsevier Ltd. All rights reserved.

Challenges and opportunities in synthetic biology for chemical engineers

PubMed Central

Luo, Yunzi; Lee, Jung-Kul; Zhao, Huimin

2012-01-01

Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement. PMID:24222925

Challenges and opportunities in synthetic biology for chemical engineers.

PubMed

Luo, Yunzi; Lee, Jung-Kul; Zhao, Huimin

2013-11-15

Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement.

Model-based evaluation of two BNR processes--UCT and A2N.

PubMed

Hao, X; Van Loosdrecht, M C; Meijer, S C; Qian, Y

2001-08-01

The activity of denitrifying P-accumulating bacteria (DPB) has been verified to exist in most WWTPs with biological nutrient removal (BNR). The modified UCT process has a high content of DPB. A new BNR process with a two-sludge system named A2N was especially developed to exploit denitrifying dephosphatation. With the identical inflow and effluent standards, an existing full-scale UCT-type WWTP and a designed A2N process were evaluated by simulation. The used model is based on the Delft metabolical model for bio-P removal and ASM2d model for COD and N removal. Both processes accommodate denitrifying dephosphatation, but the A2N process has a more stable performance in N removal. Although excess sludge is increased by 6%, the A2N process leads to savings of 35, 85 and 30% in aeration energy, mixed liquor internal recirculation and land occupation respectively, as compared to the UCT process. Low temperature has a negative effect on growth of poly-P bacteria, which becomes to especially appear in the A2N process.

The biodrying concept: an innovative technology creating energy from sewage sludge.

PubMed

Winkler, M-K H; Bennenbroek, M H; Horstink, F H; van Loosdrecht, M C M; van de Pol, G-J

2013-11-01

A full-scale biodrying installation was treating 150 kton (wet weight) of dewatered waste activated sludge per year. The waste was treated at thermophilic conditions (65-75 °C) in a 2-step forced aeration process reducing the total wet sludge weight by 73%. The final product had a high caloric value (7700-10,400 (kJ/kg)), allowing a combustion for energy generation in external facilities. The resulting product met the European microbial and heavy metal quality standards needed for an application as organic fertilizer. The facility used <0.5 MW of electricity and recovered 9.3 MW from biologically produced heat, which was internally used for the heating of office buildings. Produced ammonia, originating from the microbial conversion of organic matter, was recovered from the ventilated air in an acid gas scrubber as an ammonium sulphate solution 40% (w/w) (7.3 kton/year) and was sold as substitute for artificial fertilizers. The sustainability of this process is discussed relative to other sludge handling processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Aerobic Sludge Granulation in a Full-Scale Sequencing Batch Reactor

PubMed Central

Li, Jun; Ding, Li-Bin; Cai, Ang; Huang, Guo-Xian; Horn, Harald

2014-01-01

Aerobic granulation of activated sludge was successfully achieved in a full-scale sequencing batch reactor (SBR) with 50,000 m3 d−1 for treating a town's wastewater. After operation for 337 days, in this full-scale SBR, aerobic granules with an average SVI30 of 47.1 mL g−1, diameter of 0.5 mm, and settling velocity of 42 m h−1 were obtained. Compared to an anaerobic/oxic plug flow (A/O) reactor and an oxidation ditch (OD) being operated in this wastewater treatment plant, the sludge from full-scale SBR has more compact structure and excellent settling ability. Denaturing gradient gel electrophoresis (DGGE) analysis indicated that Flavobacterium sp., uncultured beta proteobacterium, uncultured Aquabacterium sp., and uncultured Leptothrix sp. were just dominant in SBR, whereas uncultured bacteroidetes were only found in A/O and OD. Three kinds of sludge had a high content of protein in extracellular polymeric substances (EPS). X-ray fluorescence (XRF) analysis revealed that metal ions and some inorganics from raw wastewater precipitated in sludge acted as core to enhance granulation. Raw wastewater characteristics had a positive effect on the granule formation, but the SBR mode operating with periodic feast-famine, shorter settling time, and no return sludge pump played a crucial role in aerobic sludge granulation. PMID:24822190

Bridging the physical scales in evolutionary biology: From protein sequence space to fitness of organisms and populations

PubMed Central

Bershtein, Shimon; Serohijos, Adrian W.R.; Shakhnovich, Eugene I.

2016-01-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. PMID:27810574

Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.

PubMed

Bershtein, Shimon; Serohijos, Adrian Wr; Shakhnovich, Eugene I

2017-02-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multiscale polar theory of microtubule and motor-protein assemblies

DOE PAGES

Gao, Tong; Blackwell, Robert; Glaser, Matthew A.; ...

2015-01-27

Microtubules and motor proteins are building blocks of self-organized subcellular biological structures such as the mitotic spindle and the centrosomal microtubule array. These same ingredients can form new “bioactive” liquid-crystalline fluids that are intrinsically out of equilibrium and which display complex flows and defect dynamics. It is not yet well understood how microscopic activity, which involves polarity-dependent interactions between motor proteins and microtubules, yields such larger-scale dynamical structures. In our multiscale theory, Brownian dynamics simulations of polar microtubule ensembles driven by cross-linking motors allow us to study microscopic organization and stresses. Polarity sorting and cross-link relaxation emerge as two polar-specificmore » sources of active destabilizing stress. On larger length scales, our continuum Doi-Onsager theory captures the hydrodynamic flows generated by polarity-dependent active stresses. Finally, the results connect local polar structure to flow structures and defect dynamics.« less

Root Systems Biology: Integrative Modeling across Scales, from Gene Regulatory Networks to the Rhizosphere1

PubMed Central

Hill, Kristine; Porco, Silvana; Lobet, Guillaume; Zappala, Susan; Mooney, Sacha; Draye, Xavier; Bennett, Malcolm J.

2013-01-01

Genetic and genomic approaches in model organisms have advanced our understanding of root biology over the last decade. Recently, however, systems biology and modeling have emerged as important approaches, as our understanding of root regulatory pathways has become more complex and interpreting pathway outputs has become less intuitive. To relate root genotype to phenotype, we must move beyond the examination of interactions at the genetic network scale and employ multiscale modeling approaches to predict emergent properties at the tissue, organ, organism, and rhizosphere scales. Understanding the underlying biological mechanisms and the complex interplay between systems at these different scales requires an integrative approach. Here, we describe examples of such approaches and discuss the merits of developing models to span multiple scales, from network to population levels, and to address dynamic interactions between plants and their environment. PMID:24143806

Effects of clinically relevant MPL mutations in the transmembrane domain revealed at the atomic level through computational modeling.

PubMed

Lee, Tai-Sung; Kantarjian, Hagop; Ma, Wanlong; Yeh, Chen-Hsiung; Giles, Francis; Albitar, Maher

2011-01-01

Mutations in the thrombopoietin receptor (MPL) may activate relevant pathways and lead to chronic myeloproliferative neoplasms (MPNs). The mechanisms of MPL activation remain elusive because of a lack of experimental structures. Modern computational biology techniques were utilized to explore the mechanisms of MPL protein activation due to various mutations. Transmembrane (TM) domain predictions, homology modeling, ab initio protein structure prediction, and molecular dynamics (MD) simulations were used to build structural dynamic models of wild-type and four clinically observed mutants of MPL. The simulation results suggest that S505 and W515 are important in keeping the TM domain in its correct position within the membrane. Mutations at either of these two positions cause movement of the TM domain, altering the conformation of the nearby intracellular domain in unexpected ways, and may cause the unwanted constitutive activation of MPL's kinase partner, JAK2. Our findings represent the first full-scale molecular dynamics simulations of the wild-type and clinically observed mutants of the MPL protein, a critical element of the MPL-JAK2-STAT signaling pathway. In contrast to usual explanations for the activation mechanism that are based on the relative translational movement between rigid domains of MPL, our results suggest that mutations within the TM region could result in conformational changes including tilt and rotation (azimuthal) angles along the membrane axis. Such changes may significantly alter the conformation of the adjacent and intrinsically flexible intracellular domain. Hence, caution should be exercised when interpreting experimental evidence based on rigid models of cytokine receptors or similar systems.

Pandemic pharmaceutical dosing effects on wastewater treatment: no adaptation of activated sludge bacteria to degrade the antiviral drug oseltamivir (Tamiflu®) and loss of nutrient removal performance.

PubMed

Slater, Frances R; Singer, Andrew C; Turner, Susan; Barr, Jeremy J; Bond, Philip L

2011-02-01

The 2009-2010 influenza pandemic saw many people treated with antivirals and antibiotics. High proportions of both classes of drugs are excreted and enter wastewater treatment plants (WWTPs) in biologically active forms. To date, there has been no study into the potential for influenza pandemic-scale pharmaceutical use to disrupt WWTP function. Furthermore, there is currently little indication as to whether WWTP microbial consortia can degrade antiviral neuraminidase inhibitors when exposed to pandemic-scale doses. In this study, we exposed an aerobic granular sludge sequencing batch reactor, operated for enhanced biological phosphorus removal (EBPR), to a simulated influenza-pandemic dosing of antibiotics and antivirals for 8 weeks. We monitored the removal of the active form of Tamiflu(®), oseltamivir carboxylate (OC), bacterial community structure, granule structure and changes in EBPR and nitrification performance. There was little removal of OC by sludge and no evidence that the activated sludge community adapted to degrade OC. There was evidence of changes to the bacterial community structure and disruption to EBPR and nitrification during and after high-OC dosing. This work highlights the potential for the antiviral contamination of receiving waters and indicates the risk of destabilizing WWTP microbial consortia as a result of high concentrations of bioactive pharmaceuticals during an influenza pandemic. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Brazilian infant motor and cognitive development: Longitudinal influence of risk factors.

PubMed

Pereira, Keila Rg; Valentini, Nadia C; Saccani, Raquel

2016-12-01

Infant developmental delays have been associated with several risk factors, such as familial environmental, individual and demographic characteristics. The goal of this study was to longitudinally investigate the effects of maternal knowledge and practices, home environment and biological factors on infant motor and cognitive outcomes. This was a prospective cohort study with a sample of 49 infants from Southern Brazil. The infants were assessed three times over 4 months using the Alberta Infant Motor Scale and the Bayley Scale of Infant Development (Mental Development Scale). Parents completed the Daily Activities Scale of Infants, the Affordances in The Home Environment for Motor Development - Infant Scale, the Knowledge of Infant Development Inventory and a demographic questionnaire. Generalized estimating equation with Bonferroni method as the follow-up test and Spearman correlation and multivariate linear backward regression were used. Cognitive and motor scores were strongly associated longitudinally and increased over time. Associations between the home affordances, parental practices and knowledge, and motor and cognitive development over time were observed. This relationship explained more variability in motor and cognitive scores compared with biological factors. Variability in motor and cognitive development is better explained by environment and parental knowledge and practice. The investigation of factors associated with infant development allows the identification of infants at risk and the implementation of educational programs and parental training to minimize the effects of developmental delay. © 2016 Japan Pediatric Society.