Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy

[1]  I-Min A. Chen,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[2]  H. Lindorfer,et al.  New data on temperature optimum and temperature changes in energy crop digesters. , 2008, Bioresource technology.

[3]  D. Panescu,et al.  Emerging Technologies , 2008, IEEE Engineering in Medicine and Biology Magazine.

[4]  B. Rittmann Opportunities for renewable bioenergy using microorganisms. , 2008, Biotechnology and bioengineering.

[5]  Regina A. O'Neil,et al.  Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes. , 2008, Microbiology.

[6]  Rick L. Stevens,et al.  Functional metagenomic profiling of nine biomes , 2008, Nature.

[7]  Kathleen E. Duncan,et al.  Bioenergy Production via Microbial Conversion of Residual Oil to Natural Gas , 2008, Applied and Environmental Microbiology.

[8]  R. Mahadevan,et al.  Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis. , 2008, Omics : a journal of integrative biology.

[9]  T. Donohue,et al.  Development of a solar‐powered microbial fuel cell , 2008, Journal of applied microbiology.

[10]  P. Parameswaran,et al.  Evaluation of energy-conversion efficiencies in microbial fuel cells (MFCs) utilizing fermentable and non-fermentable substrates. , 2008, Water research.

[11]  B. Bergman,et al.  Proteomic analysis of the cyanobacterium of the Azolla symbiosis: identity, adaptation, and NifH modification. , 2008, Journal of experimental botany.

[12]  Nikos Kyrpides,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[13]  D. Colquhoun Public health applications of quantitative protein biomarkers , 2008 .

[14]  W. Vermaas,et al.  Small Cab-like Proteins Retard Degradation of Photosystem II-associated Chlorophyll in Synechocystis sp. PCC 6803 , 2007, Journal of Biological Chemistry.

[15]  Bruce E. Rittmann,et al.  Genetic Diversity of Hydrogen-Producing Bacteria in an Acidophilic Ethanol-H2-Coproducing System, Analyzed Using the [Fe]-Hydrogenase Gene , 2007, Applied and Environmental Microbiology.

[16]  C. Saint,et al.  The isolation and microbial community analysis of hydrogen producing bacteria from activated sludge , 2007, Journal of applied microbiology.

[17]  Y. Watanabe,et al.  Significance of Chloroflexi in performance of submerged membrane bioreactors (MBR) treating municipal wastewater. , 2007, Environmental science & technology.

[18]  Samuel Kaplan,et al.  Postgenomic adventures with Rhodobacter sphaeroides. , 2007, Annual review of microbiology.

[19]  D. Lee,et al.  Process stability and microbial community structure in anaerobic hydrogen-producing microflora from food waste containing kimchi. , 2007, Journal of biotechnology.

[20]  Sokhee P. Jung,et al.  Comparison of anode bacterial communities and performance in microbial fuel cells with different electron donors , 2007, Applied Microbiology and Biotechnology.

[21]  Bruce E Logan,et al.  Electricity generation and microbial community analysis of alcohol powered microbial fuel cells. , 2007, Bioresource technology.

[22]  A. Salamov,et al.  Use of simulated data sets to evaluate the fidelity of metagenomic processing methods , 2007, Nature Methods.

[23]  Y. Chisti Biodiesel from microalgae. , 2007, Biotechnology advances.

[24]  Jo‐Shu Chang,et al.  Quantitative analysis of a high-rate hydrogen-producing microbial community in anaerobic agitated granular sludge bed bioreactors using glucose as substrate , 2007, Applied Microbiology and Biotechnology.

[25]  S. Okabe,et al.  Phylogenetic and functional diversity of propionate-oxidizing bacteria in an anaerobic digester sludge , 2007, Applied Microbiology and Biotechnology.

[26]  Stephen J. Callister,et al.  Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes. , 2006, Journal of microbiological methods.

[27]  B. Logan,et al.  Electricity-producing bacterial communities in microbial fuel cells. , 2006, Trends in microbiology.

[28]  Tong Zhang,et al.  Characterization of Fe-hydrogenase genes diversity and hydrogen-producing population in an acidophilic sludge. , 2006, Journal of biotechnology.

[29]  D. Lovley Bug juice: harvesting electricity with microorganisms , 2006, Nature Reviews Microbiology.

[30]  Derek R Lovley,et al.  Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens. , 2006, Environmental microbiology.

[31]  Lee Ji-young,et al.  Bacterial Communities in Microbial Fuel Cells Enriched with High Concentrations of Glucose and Glutamate , 2006 .

[32]  Derek R. Lovley,et al.  Biofilm and Nanowire Production Leads to Increased Current in Geobacter sulfurreducens Fuel Cells , 2006, Applied and Environmental Microbiology.

[33]  Ronald J Moore,et al.  A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry , 2006, Proteomics.

[34]  Alice Dohnalkova,et al.  Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Samuel Kaplan,et al.  Application of the accurate mass and time tag approach to the proteome analysis of sub-cellular fractions obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and photosynthetic cell cultures. , 2006, Journal of proteome research.

[36]  A. Corma,et al.  Synthesis of transportation fuels from biomass: chemistry, catalysts, and engineering. , 2006, Chemical reviews.

[37]  Bruce E Rittmann,et al.  Microbial ecology to manage processes in environmental biotechnology. , 2006, Trends in biotechnology.

[38]  D. Lovley,et al.  DNA Microarray and Proteomic Analyses of the RpoS Regulon in Geobacter sulfurreducens , 2006, Journal of bacteriology.

[39]  B. Palsson,et al.  Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling , 2006, Applied and Environmental Microbiology.

[40]  Hang-Sik Shin,et al.  Effect of substrate concentration on hydrogen production and 16S rDNA-based analysis of the microbial community in a continuous fermenter , 2006 .

[41]  Regina A. O'Neil,et al.  Potential for Quantifying Expression of the Geobacteraceae Citrate Synthase Gene To Assess the Activity of Geobacteraceae in the Subsurface and on Current-Harvesting Electrodes , 2005, Applied and Environmental Microbiology.

[42]  Y. Yu,et al.  Analysis of community structures in anaerobic processes using a quantitative real-time PCR method. , 2005, Water science and technology : a journal of the International Association on Water Pollution Research.

[43]  P. Hallenbeck,et al.  Fundamentals of the fermentative production of hydrogen. , 2005, Water science and technology : a journal of the International Association on Water Pollution Research.

[44]  T. Mehta,et al.  Extracellular electron transfer via microbial nanowires , 2005, Nature.

[45]  Kelly P. Nevin,et al.  DNA Microarray Analysis of Nitrogen Fixation and Fe(III) Reduction in Geobacter sulfurreducens , 2005, Applied and Environmental Microbiology.

[46]  R. Halden,et al.  Identification and Phenotypic Characterization of Sphingomonas wittichii Strain RW1 by Peptide Mass Fingerprinting Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry , 2005, Applied and Environmental Microbiology.

[47]  Jaai Kim,et al.  Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. , 2005, Biotechnology and bioengineering.

[48]  Steven P Gygi,et al.  The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. , 2005, Methods.

[49]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[50]  Pier Giorgio Righetti,et al.  Critical survey of quantitative proteomics in two-dimensional electrophoretic approaches. , 2004, Journal of chromatography. A.

[51]  L. T. Angenent,et al.  Production of bioenergy and biochemicals from industrial and agricultural wastewater. , 2004, Trends in biotechnology.

[52]  W. Verstraete,et al.  Biofuel Cells Select for Microbial Consortia That Self-Mediate Electron Transfer , 2004, Applied and Environmental Microbiology.

[53]  Debabrata Das,et al.  Improvement of fermentative hydrogen production: various approaches , 2004, Applied Microbiology and Biotechnology.

[54]  Kenji Kida,et al.  Effect of Dilution Rate on Metabolic Pathway Shift between Aceticlastic and Nonaceticlastic Methanogenesis in Chemostat Cultivation , 2004, Applied and Environmental Microbiology.

[55]  R. Breaker,et al.  Gene regulation by riboswitches , 2004, Nature Reviews Molecular Cell Biology.

[56]  Bruce E Logan,et al.  Extracting hydrogen and electricity from renewable resources. , 2004, Environmental science & technology.

[57]  In Seop Chang,et al.  Analysis of microbial diversity in oligotrophic microbial fuel cells using 16S rDNA sequences. , 2004, FEMS microbiology letters.

[58]  Regina A. O'Neil,et al.  Microbial Communities Associated with Electrodes Harvesting Electricity from a Variety of Aquatic Sediments , 2004, Microbial Ecology.

[59]  V. O’Flaherty,et al.  Microbial community structure and methanogenic activity during start-up of psychrophilic anaerobic digesters treating synthetic industrial wastewaters. , 2003, FEMS microbiology ecology.

[60]  S. Gygi,et al.  Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[61]  K. Kida,et al.  Effect of dilution rate on structure of a mesophilic acetate-degrading methanogenic community during continuous cultivation. , 2003, Journal of bioscience and bioengineering.

[62]  Arkady B. Khodursky,et al.  Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[63]  Wen-Tso Liu,et al.  Microbial community dynamics during start-up of acidogenic anaerobic reactors. , 2002, Water research.

[64]  D. Lowy,et al.  Harnessing microbially generated power on the seafloor , 2002, Nature Biotechnology.

[65]  B. Rittmann,et al.  A unified theory for extracellular polymeric substances, soluble microbial products, and active and inert biomass. , 2002, Water research.

[66]  Bruce E Rittmann,et al.  Non-steady state modeling of extracellular polymeric substances, soluble microbial products, and active and inert biomass. , 2002, Water research.

[67]  D. R. Bond,et al.  Electrode-Reducing Microorganisms That Harvest Energy from Marine Sediments , 2002, Science.

[68]  H. D. Stensel,et al.  Wastewater Engineering: Treatment and Reuse , 2002 .

[69]  O. Pulz,et al.  Photobioreactors: production systems for phototrophic microorganisms , 2001, Applied Microbiology and Biotechnology.

[70]  R S Wolfe,et al.  A novel pH2 control on the expression of flagella in the hyperthermophilic strictly hydrogenotrophic methanarchaeaon Methanococcus jannaschii. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[71]  P. Mccarty,et al.  Environmental Biotechnology: Principles and Applications , 2000 .

[72]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[73]  Hideki Harada,et al.  Fluorescence In Situ Hybridization Using 16S rRNA-Targeted Oligonucleotides Reveals Localization of Methanogens and Selected Uncultured Bacteria in Mesophilic and Thermophilic Sludge Granules , 1999, Applied and Environmental Microbiology.

[74]  B. Patel,et al.  Screening and selection of microfungi for microbial biomass protein production and water reclamation from starch processing wastewater , 1999 .

[75]  B. Schink Energetics of syntrophic cooperation in methanogenic degradation , 1997, Microbiology and molecular biology reviews : MMBR.

[76]  J. M. Owens,et al.  Renewable methane from anaerobic digestion of biomass , 1997 .

[77]  M. Ünlü,et al.  Difference gel electrophoresis. A single gel method for detecting changes in protein extracts , 1997, Electrophoresis.

[78]  M. Ronaghi,et al.  Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.

[79]  R. Fleischmann,et al.  Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii , 1996, Science.

[80]  N. Miyajima,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome. , 1995, DNA research : an international journal for rapid publication of reports on genes and genomes.

[81]  M. Uhlén,et al.  Solid phase DNA minisequencing by an enzymatic luminometric inorganic pyrophosphate detection assay. , 1993, Analytical biochemistry.

[82]  S. Zinder,et al.  Hydrogen Partial Pressures in a Thermophilic Acetate-Oxidizing Methanogenic Coculture , 1988, Applied and environmental microbiology.

[83]  W. Owen,et al.  Fundamentals of Anaerobic Digestion of Wastewater Sludges , 1986 .

[84]  I. Gorst Survey of energy resources , 1985 .