web cellHTS2: A web-application for the analysis of high-throughput screening data

<p>Abstract</p> <p>Background</p> <p>The analysis of high-throughput screening data sets is an expanding field in bioinformatics. High-throughput screens by RNAi generate large primary data sets which need to be analyzed and annotated to identify relevant phenotypic hits. Large-scale RNAi screens are frequently used to identify novel factors that influence a broad range of cellular processes, including signaling pathway activity, cell proliferation, and host cell infection. Here, we present a web-based application utility for the end-to-end analysis of large cell-based screening experiments by cellHTS2.</p> <p>Results</p> <p>The software guides the user through the configuration steps that are required for the analysis of single or multi-channel experiments. The web-application provides options for various standardization and normalization methods, annotation of data sets and a comprehensive HTML report of the screening data analysis, including a ranked hit list. Sessions can be saved and restored for later re-analysis. The web frontend for the cellHTS2 R/Bioconductor package interacts with it through an R-server implementation that enables highly parallel analysis of screening data sets. web cellHTS2 further provides a file import and configuration module for common file formats.</p> <p>Conclusions</p> <p>The implemented web-application facilitates the analysis of high-throughput data sets and provides a user-friendly interface. web cellHTS2 is accessible online at <url>http://web-cellHTS2.dkfz.de</url>. A standalone version as a virtual appliance and source code for platforms supporting Java 1.5.0 can be downloaded from the web cellHTS2 page. web cellHTS2 is freely distributed under GPL.</p

Sulfate-reducing bacterial community response to carbon source amendments in contaminated aquifer microcosms

Microbial sulfate reduction is an important metabolic activity in many reduced habitats. However, little is known about the sulfate-reducing communities inhabiting petroleum hydrocarbon (PHC)-contaminated freshwater aquifer sediments. The purpose of this study was to identify the groups of sulfate-reducing bacteria (SRB) selectively stimulated when sediment from a PHC-contaminated freshwater aquifer was incubated in sulfate-reducing aquifer microcosms that were amended with specific carbon sources (acetate, butyrate, propionate, lactate, and citrate). After 2 months of incubation, the SRB community was characterized using phospholipid fatty acid (PLFA) analysis combined with multivariate statistics as well as fluorescence in situ hybridization (FISH). Molybdate was used to specifically inhibit SRB in separate microcosms to investigate the contribution of non-SRB to carbon source degradation. Results indicated that sulfate reduction in the original sediment was an important process but was limited by the availability of sulfate. Substantially lower amounts of acetate and butyrate were degraded in molybdate treatments as compared to treatments without molybdate, suggesting that SRB were the major bacterial group responsible for carbon source turnover in microcosms. All of the added carbon sources induced changes in the SRB community structure. Members of the genus Desulfobulbus were present but not active in the original sediment but an increase of the fatty acids 15:1ω6c and 17:1ω6c and FISH results showed an enrichment of these bacteria in microcosms amended with propionate or lactate. The appearance of cy17:0 revealed that bacteria affiliated with the Desulfobacteriaceae were responsible for acetate degradation. Desulfovibrio and Desulfotomaculum spp. were not important populations within the SRB community in microcosms because they did not proliferate on carbon sources usually favored by these organisms. Metabolic, PLFA, and FISH results provided information on the SRB community in a PHC-contaminated freshwater environment, which exhibited stimulation patterns similar to other (e.g. marine) environment

Field-scale 13C-labeling of phospholipid fatty acids (PLFA) and dissolved inorganic carbon: tracing acetate assimilation and mineralization in a petroleum hydrocarbon-contaminated aquifer

This study was conducted to determine the feasibility of labeling phospholipid-derived fatty acids (PLFA) of an active microbial population with a 13C-labeled organic substrate in the denitrifying zone of a petroleum hydrocarbon-contaminated aquifer during a single-well push-pull test. Anoxic test solution was prepared from 500 l of groundwater with addition of 0.5 mM Br− as a conservative tracer, 0.5 mM NO3−, and 0.25 mM [2-13C]acetate. At 4, 23 and 46 h after injection, 1000 l of test solution/groundwater mixture were sequentially extracted. During injection and extraction phases we measured Br−, NO3− and acetate concentrations, characterized the microbial community structure by PLFA and fluorescent in situ hybridization (FISH) analyses, and determined 13C/12C ratios in dissolved inorganic carbon (DIC) and PLFA. Computed first-order rate coefficients were 0.63±0.08 day−1 for NO3− and 0.70±0.05 day−1 for acetate consumption. Significant 13C incorporation in DIC and PLFA was detected as early as 4 h after injection. At 46 h we measured δ13C values of up to 5614‰ in certain PLFA (especially monounsaturated fatty acids), and up to 59.8‰ in extracted DIC. Profiles of enriched PLFA and FISH analysis suggested the presence of active denitrifiers. Our results demonstrate the applicability of 13C labeling of PLFA and DIC in combination with FISH to link microbial structure and activities at the field scale during a push-pull tes

Nonuse values of climate policy : an empirial study in Xinjiang and Beijing

Climate policy measures can be roughly subdivided into mitigation measures and adaptation measures. Mitigation policy aims at a reduction of greenhouse gas emissions with the overall goal of slowing down climate change and global warming. Since greenhouse gases like CO2, Methane etc. are global pollutants which have the same effect on world climate irrespective of where they are emitted mitigation policy creates benefits for people all over the world. Adaptation policy on the other hand does not seek to influence the world climate but, instead, is meant to reduce the negative consequences of climate change for a specific region. The benefits created by adaptation policy are, therefore, only of local importance while mitigation policy yields global benefits. This difference has, of course, consequences for the welfare economic appraisal of mitigation policy measures as compared to adaptation policy measures. Since the wellbeing of many more people worldwide is affected by mitigation measures than by adaptation measures the former will always appear more attractive in a cost-benefit analysis than the latter, at least from a global perspective. In this paper we want to show that adaption policy measures are often undervalued in cost-benefit analyses because only their so-called use values are considered, while the nonuse values they create are neglected. The use value of a commodity accrues from a direct utilization of that commodity. In an environmental context the use value of e.g. a beautiful landscape is felt by those people who visit this landscape. Beyond this use value the landscape might also have a value for people who never visit it but still enjoy the knowledge that in their country such a beautiful landscape exists and that endangered animals and plants are preserved there. This value that originates from the mere existence of a (market or environmental) good is often called its nonuse value because it is independent of a direct (and empirically observable) utilization of this good. If it can be shown that some adaptation policy measures in the context of climate policy create also nonuse values in addition to the use values this might lead to a new assessment of such measures and it might increase their chances of being approved in the political decision process. It is obvious that the systematic undervaluation of adaptation policy measures resulting from the neglect of the nonuse values they create might have the consequence that they are declined because they do not pass the cost-benefit test, though they create high nonuse values which are not considered in this test. Of course, the existence of nonuse values depends on the cultural background of the people affected by these measures and of the society they live in. Especially in an emerging country like China many people might still underestimate the importance of climate adaptation measures in comparison with economic policy measures triggering the economic growth of the country, especially if the adaptation measures are conducted in faraway regions of the country. In this study we test empirically the hypothesis that also in a growth-oriented economy like China non-materialistic values like the nonuse values of climate policy are perceived and respected by the population. This should especially hold for the better educated people living in big cities like Beijing. Therefore, we conduct a survey in Beijing where we ask people to assess a climate change adaptation project to be implemented in a faraway region, in this case in the Tarim basin in Xinjiang. In this survey we find that also Beijing citizens feel responsible for the environmental conditions in Xinjiang, especially under the impression of climate change. We find that they are even willing to contribute personally to financing a public project for the improvement of the living conditions in this remote (as viewed from Beijing) region. The rest of the paper is organized as follows: the next chapter focuses on the importance of nonuse values in environmental cost-benefit analyses; information concerning the impact of climate change on the Tarim area is provided in chapter three; the survey method and sampling procedure are introduced in chapter four; in chapter five results of the survey in Beijing are presented and analyzed, followed by some concluding remarks

Microbial assimilation of plant-derived carbon in soil traced by isotope analysis

The flow of new and native plant-derived C in the rhizosphere of an agricultural field during one growing season was tracked, the ratios in different soil C pools were quantified, and the residence times (τs) were estimated. For this the natural differences in 13C abundances of: (1) C4 soil (with a history of C4 plant, Miscanthus sinensis, cultivation), (2) C3 soil (history of C3 plant cultivation), and (3) C4/3 soil (C4 soil, planted with a C3 plant, Triticum aestivum) were used. Total amounts and δ13C values of total soil C, non-hydrolysable C, light fraction C, water-soluble C, microbial biomass C, and phospholipid fatty acids (PLFA) were determined. Using the δ13C values of soil C in a mixing and a 1-box model enabled the quantification of relative contributions of C3 plant and C4 plant C to the total amount of the respective C pools in the C4/3 soil and their τs. Compared to early spring (March), the percentage of C3 plant C increased in all pools in June and August, showing the addition of new C to the different soil C fractions. In August the contribution of new C to microbial biomass C and water-soluble C reached 64 and 89%, respectively. The τs of these pools were 115 and 147 days. The δ13C values of the dominant soil PLFA, 18:1ω7c, cy19:0, 18:1ω9c, 16:0, and 10Me16:0, showed wide ranges (−35.1 to −13.0‰) suggesting that the microbial community utilized different pools as C sources during the season. The δ13C values of PLFA, therefore, enabled the analysis of the metabolically active populations. The majority of δ13C values of PLFA from the C4/3 soil were closely related to those of PLFA from the C3 soil when T. aestivum biomass contributions to the soil were high in June and August. Specific populations reacted differently to changes in environmental conditions and supplies of C sources, which reflect the high functional diversity of soil microorganism

Biodegradation in seawater of PAH and alkylphenols from produced water of a North Sea Platform

Operational planned discharges of produced water (PW) to the marine environment from offshore oil production installations, contain low concentrations of dispersed oil compounds, like polycyclic aromatic hydrocarbons (PAH) and alkylated phenols (APs). Biotransformation in natural seawater (SW) of naphthalene/PAH and phenol/AP in field-collected PW from a North Sea platform was investigated in this biodegradation study. The PW was diluted in SW from a Norwegian fjord, and the biodegradation study was performed in slowly rotating carousels at environmental conditions (13⁰C) over a period of 62 days. Naphthalene/PAH and phenol/AP biotransformation was determined by first-order rate kinetics, after normalization against the recalcitrant biomarker 17α(H),21β(H)-Hopane. The results from this study showed total biotransformation half-lives ranging from 10 to 19 days for groups of naphthalenes and PAH, while half-lives for APs (C0- to C9-alkylated) were 10 to 14 days. Biotransformation half-lives of single components ranged from 8 to >100 days for naphthalenes and PAHs (median 16 days), and from 6 to 72 days (median 15 days) for phenols and AP. Four of the tested PAHs (chrysene, benzo(b)fluoranthene, benzo(e)pyrene, benzo(g,h,i,)perylene) and one AP (4-tert-butylphenol) showed biotransformation half-lives >50 days. This is one of a few studies that has investigated the potential for biodegradation of PW in natural SW. Methods and data from this study may be used as a part of Risk Based Approaches (RBA) for assessments of environmental fate of PW released to the marine environment and as part of the persistence related to risk.acceptedVersio

Tracing toluene-assimilating sulfate-reducing bacteria using 13C-incorporation in fatty acids and whole-cell hybridization

Polar lipid-derived fatty acids (PLFA) commonly found in sulfate-reducing bacteria were detected in high abundance in the sediment harvested from a monitoring well of a petroleum-hydrocarbon (PHC)-contaminated aquifer. Aquifer microcosms were incubated under sulfate-reducing conditions with [methyl-14C]toluene to determine the 14C-mass balances and with [methyl-13C]toluene to follow the flow of carbon from toluene into biomarker fatty acids. An aliquot was used to establish an aquifer-derived toluene-degrading sulfate-reducing consortium, which grew well in liquid medium. Whole-cell hybridization using 16S rRNA-targeted oligonucleotide probes specific for different phylogenetic levels within the sulfate-reducing bacteria was applied in order to characterize the sulfate-reducing populations in the original sediment, the aquifer microcosms, and the aquifer-derived consortium. In the aquifer microcosms, the 14C quantification revealed that 61.6% of the [methyl-14C]toluene was mineralized and 2.7% was assimilated. Following [methyl-13C]toluene depletion (<1 μM), the highest 13C-enrichment was found in PLFA 16:1ω5c. In addition, biomarker fatty acids characteristic for the genera Desulfobacter and Desulfobacula (cy17:0 and 10Me16:0) were also 13C-enriched, contrary to those of other sulfate-reducing genera, e.g. Desulfovibrio and Synthrophobacter (i17:1ω7c), Desulfobulbus and Desulforhabdus (15:1ω6c and 17:1ω6c). Although hybridization detection rates remained low, indicating low bacterial activities, 43% (aquifer sediment) and 30% (aquifer microcosm) of the total active bacteria belonged to the Desulfobacteriaceae thus supporting the PLFA-based results. Desulfobacter-species (42%), which belong to the Desulfobacteriaceae, dominated the community of the consortium. Our study showed that carbon stable isotope analysis in combination with whole-cell hybridization could link toluene degradation in aquifer microcosms to the metabolic activity of the Desulfobacter-like populations. These populations could play an important role in the clean up of aromatic PHC-contaminated aquifer

GenomeRNAi: a database for cell-based RNAi phenotypes

RNA interference (RNAi) has emerged as a powerful tool to generate loss-of-function phenotypes in a variety of organisms. Combined with the sequence information of almost completely annotated genomes, RNAi technologies have opened new avenues to conduct systematic genetic screens for every annotated gene in the genome. As increasing large datasets of RNAi-induced phenotypes become available, an important challenge remains the systematic integration and annotation of functional information. Genome-wide RNAi screens have been performed both in Caenorhabditis elegans and Drosophila for a variety of phenotypes and several RNAi libraries have become available to assess phenotypes for almost every gene in the genome. These screens were performed using different types of assays from visible phenotypes to focused transcriptional readouts and provide a rich data source for functional annotation across different species. The GenomeRNAi database provides access to published RNAi phenotypes obtained from cell-based screens and maps them to their genomic locus, including possible non-specific regions. The database also gives access to sequence information of RNAi probes used in various screens. It can be searched by phenotype, by gene, by RNAi probe or by sequence and is accessible a

Chinese urbanites and the preservation of rare species in remote parts of the country: the example of eaglewood

Based on a Contingent Valuation study in Shanghai we assess peoples willingness to contribute personally to the alleviation of environmental problems occurring in distant parts of the country. One split of our survey assessed Shanghai residents willingness to pay for the preservation of rainforest in Yunnan, while the other split referred to the willingness to pay for the preservation of a single plant species (i.e. eaglewood) growing in this rainforest. The objectives of this study were twofold. Firstly, we wanted to find out if people living in big Chinese cities like Shanghai take an interest in the environmental problems existing in some remote parts of the country and if they are willing to contribute personally to remedy these problems. Secondly, we wanted to learn more about the motivation behind this kind of empathy, if it exists. We were especially interested in the question if this empathy refers to the specific environmental problems we addressed in our surveys or if it is motivated more by a general feeling of obligation towards environmental issues

GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update

The GenomeRNAi database (http://www.genomernai.org/) contains phenotypes from published cell-based RNA interference (RNAi) screens in Drosophila and Homo sapiens. The database connects observed phenotypes with annotations of targeted genes and information about the RNAi reagent used for the perturbation experiment. The availability of phenotypes from Drosophila and human screens also allows for phenotype searches across species. Besides reporting quantitative data from genome-scale screens, the new release of GenomeRNAi also enables reporting of data from microscopy experiments and curated phenotypes from published screens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality that are available for the Drosophila and the human genome. The new version also facilitates the integration with other genomic data sets and contains expression profiling (RNA-Seq) data for several cell lines commonly used in RNAi experiments