The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the circumstantial ones, bounding the outcomes of experiments and guiding engineering approaches. Among different modeling schemes, the quantification of intracellular metabolic fluxes (i.e. the rate of each reaction in cellular metabolism) is of particular interest for metabolic engineering because it describes how carbon and energy flow throughout the cell. In addition to flux analysis, new methods for the effective use of the ever more readily available and abundant -omics data (i.e. transcriptomics, proteomics and metabolomics) are urgently needed

MicrobesOnline: A Community Resource for Data-Integrated Comparative Functional Genomics

VIMSS, the Virtual Institute for Microbial Stress and Survival (http://vimss.lbl.gov), funded by the Dept. of Energy's Genomics:GTL Program, is dedicated to using integrated environmental data and functional genomic and comparative sequence data to understand mechanisms by which bacteria survive in uncertain environments while carrying out processes of interest for bioremediation and energy generation. To support this work, VIMSS developed a Web-based database and workbench for comparative functional genomics of bacteria and archaea. For some time, MicrobesOnline (http://www.microbesonline.org) has been providing a multi-species genome browser, operon and regulon predictions, a gene ontology browser, and a Bioinformatics Workbench for in-depth sequence analysis and community annotation of genomes. We recently incorporated data from Mikhail Gelfand's RegTransDB, which is a well-curated database of cis-regulatory sites and their regulators. VIMSS also is now releasing integrated functional genomic data with novel viewing and mining tools for microarray, proteomic, and phenotype microarray data on the website. The available data mostly are from the VIMSS Experiment/Information Data Repository (EIDR), which holds information and data on biomass production experiments and functional genomic data primarily on Desulfovibrio vulgaris and Shewanella oneidensis (and mutants of both organisms) exposed to stress conditions found at DOE field sites. Selecting an organism or gene of interest on MicrobesOnline will bring up links to information about and data viewers for VIMSS experiments conducted on that organism, or involving that gene or gene product. Information and data integration such as this serves, not only to provide insight into the regulation of stress responses of these microorganisms, but also to document VIMSS experiments, provide contextual access to experimental data of interest, and facilitate planning future experiments. We also are incorporating data release

Energy conservation mechanisms for syntrophic growth of desulfovibrio vulgaris and methanococcus maripaludis

In the absence of electron acceptors, many Desulfovibrio species grow on non-fermentable substrates via syntrophic association with hydrogen consuming methanogens. We examined the physiology of D. vulgaris Hildenborough growing syntrophically with Methanococcus maripaludis LL using a combination of transcriptional and deletion mutant analyses. Syntrophic cocultures were established in chemostats on minimal media amended with lactate but lacking electron acceptor. Replicated whole genome transcriptional analyses identified 169 and 254 genes that were significantly up- or down-regulated, respectively, relative to sulfate-limited monocultures grown at the same generation time. The majority of up-regulated genes were associated with energy production/conservation, signal transduction mechanisms, and amino acid transport/metabolism. A number of the down-regulated genes were associated with signal transduction mechanisms, inorganic ion transport/metabolism and amino acid transport and metabolism. In order to elucidate possible roles of several highly up-regulated genes associated with electron transfer and energy conservation, we constructed mutants of Desulfovibrio deleted in a subset of these genes. Cocultures developed with these mutants displayed a range of growth yields, implicating a putative carbon-monoxide induced hydrogenase (Coo, DVU2286-93) and a high-molecular weight cytochrome (Hmc, DVU0531-6) in energy conservation during syntrophic growth. Mutant monocultures grew to the same density on lactate/sulfate as the wildtype. The cooL and hmc mutants grew significantly slower and to approximately 25% yields of wildtype cocultures. Together, these data suggest a role of these genes in energy conservation of D. vulgaris Hildenborough during syntrophic growth

The Behavior Oriented Design of an Unreal Tournament Character

Abstract. This paper presents a case study for using a relatively recently developed methodology, Behavior Oriented Design, to develop an Intelligent Virtual Agent (IVA). Our usability study was conducted in Unreal Tournament using the game Capture The Flag. The final agent displays reasonably competent behavior: she is able to pursue multiple goals simultaneously and produce well-ordered behavior.

Integrated ecogenomics for determining ecosystem function in uranium-contaminated environments

Bioremediation may offer the only feasible strategy for the nearly intractable problem of metal and radionuclide contamination of soil and groundwater. To understand bioremediation in contaminated environments, it is critical to determine the organisms present in these environments, analyze their responses to stress conditions, and elucidate functional position in the environment.Methods: We used multiple molecular techniques on both sediment and groundwater to develop a better understanding of the functional capability and stress level within the microbial community in relationship to over one hundred geochemical parameters. Due to the low pH (3.5-4.5) and high contaminant levels (e.g., uranium) microbial densities and activities were low. We used a phage polymerase amplification system to construct large and small insert DNA libraries, performed metagenome sequencing, constructed clonal libraries of select functional genes (SSU rRNA gene, nirK, nirS, amoA, pmoA, and dsrAB), used a SSU rDNA Phylochip microarray (9,000 taxa), and a functional gene array (23K genes).Results: SSU rDNA analysis revealed the presence of distinct bacterial phyla, including proteobacteria, acidobacteria, and planctomycetes along the contaminant gradient. Metagenome analysis identified many of the same organisms, and diversity was lower in water than sediment. Analysis with functional gene arrays, phylochip, and specific probes for genes and organisms involved in biogeochemical cycling of C, N, and S, metal resistance, stress response, and contaminant degradation suggested that the dominant species could be biostimulated during in situ uranium reduction.Conclusion: These systems biology field studies could be enabling for strategies to attenuate metal and radionuclide contamination

Comparison of multiple ecogenomics methods for determining ecosystem function in uranium-contaminated environments

Background: Bioremediation may offer the only feasible strategy for the nearly intractable problem of metal and radionuclide contamination of soil and groundwater. To understand bioremediation in contaminated environments, it is critical to determine the organisms present in these environments, analyze their responses to stress conditions, and elucidate functional position in the environment. Methods: We used multiple molecular techniques on both sediment and groundwater to develop a better understanding of the functional capability and stress level within the microbial community in relationship to over one hundred geochemical parameters. Due to the low pH (3.5-4.5) and high contaminant levels (e.g., uranium) microbial densities and activities were low. We used a phage polymerase amplification system to construct large and small insert DNA libraries, performed metagenome sequencing, constructed clonal libraries of select functional genes (SSU rRNA gene, nirK, nirS, amoA, pmoA, and dsrAB), used a SSU rDNA Phylochip microarray (9,000 taxa), and a functional gene array (23K genes). A complete comparison for community differences and similarities between the different techniques was assessed using several bioinformatics techniques. Results: SSU rDNA analysis revealed the presence of distinct bacterial phyla, including proteobacteria, acidobacteria, and planctomycetes along the contaminant gradient. Metagenome analysis identified many of the same organisms, and diversity was lower in water than sediment. Analysis with functional gene arrays, phylochip, and specific probes for genes and organisms involved in biogeochemical cycling of C, N, and S, metal resistance, stress response, and contaminant degradation suggested that the dominant species could be biostimulated during in situ uranium reduction. Several other findings of difference and similarities between methods are presented. Conclusion: These systems biology field studies could be enabling for strategies to attenuate nletal and radionuclide contamination