FAIRsharing.5q1k; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

eQuilibrator
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Other names: eQuilibrator

Thermodynamics calculator for biochemical reactions. eQuilibrator is a simple web interface designed to enable easy thermodynamic analysis of biochemical systems. eQuilibrator enables free-text search for biochemical compounds and reactions and provides thermodynamic estimates for both in a variety of conditions.

Webpage:

http://equilibrator.weizmann.ac.il

Publications:

Publications
More detailed information about this field from each metasource.

Energy conservation in chemotrophic anaerobic bacteria
PMID: 860983
metasource: Fairsharing.org
version: FAIRsharing.org: eQuilibrator - the biochemical thermodynamics calculator; eQuilibrator - the biochemical thermodynamics calculator; DOI: https://doi.org/10.25504/FAIRsharing.5q1k; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

Group contribution method for thermodynamic analysis of complex metabolic networks
PMID: 18645197
metasource: Fairsharing.org
version: FAIRsharing.org: eQuilibrator - the biochemical thermodynamics calculator; eQuilibrator - the biochemical thermodynamics calculator; DOI: https://doi.org/10.25504/FAIRsharing.5q1k; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
PMID: 22645166
metasource: Fairsharing.org
version: FAIRsharing.org: eQuilibrator - the biochemical thermodynamics calculator; eQuilibrator - the biochemical thermodynamics calculator; DOI: https://doi.org/10.25504/FAIRsharing.5q1k; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

Biochemical thermodynamics: applications of Mathematica
PMID: 16878778
metasource: Fairsharing.org
version: FAIRsharing.org: eQuilibrator - the biochemical thermodynamics calculator; eQuilibrator - the biochemical thermodynamics calculator; DOI: https://doi.org/10.25504/FAIRsharing.5q1k; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

http://dx.doi.org/10.1093/nar/GKR874
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Energy conservation in chemotrophic anaerobic bacteria PubMed citations: 853.

853 articles citing: Energy conservation in chemotrophic anaerobic bacteria

Integrated Kinetic Modelling and Microbial Profiling Provide Insights Into Biological Sulfate-Reducing Reactor Design and Operation. PMID:35845424
Effect of Select Tannin Sources on Pathogen Control and Microbial Nitrogen Metabolism in Composted Poultry Litter Intended for Use as a Ruminant Crude Protein Feedstuff. PMID:35799835
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. PMID:35710409
Investigating Abiotic and Biotic Mechanisms of Pyrite Reduction. PMID:35615515
Engineering Acetogenic Bacteria for Efficient One-Carbon Utilization. PMID:35615514
Genetic Evidence Reveals the Indispensable Role of the rseC Gene for Autotrophy and the Importance of a Functional Electron Balance for Nitrate Reduction in Clostridium ljungdahlii. PMID:35615511
Hydrogenotrophs-Based Biological Biogas Upgrading Technologies. PMID:35557857
Unraveling Anaerobic Metabolisms in a Hypersaline Sediment. PMID:35369499
Deciphering functional redundancy and energetics of malate oxidation in mycobacteria. PMID:35337802
Pre-incubation conditions determine the fermentation pattern and microbial community structure in fermenters at mild hydrostatic pressure. PMID:35312065
Comparative Genomics on Cultivated and Uncultivated Freshwater and Marine "Candidatus Manganitrophaceae" Species Implies Their Worldwide Reach in Manganese Chemolithoautotrophy. PMID:35285693
Homo-Acetogens: Their Metabolism and Competitive Relationship with Hydrogenotrophic Methanogens. PMID:35208852
Structural evolution of the ancient enzyme, dissimilatory sulfite reductase. PMID:35122336
Enoyl-Coenzyme A Respiration via Formate Cycling in Syntrophic Bacteria. PMID:35100874
Deconstructing Methanosarcina acetivorans into an acetogenic archaeon. PMID:34992140
Minimal Pathway for the Regeneration of Redox Cofactors. PMID:34984417
Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA). PMID:34966373
Proteomic Analysis of a Syntrophic Coculture of Syntrophobacter fumaroxidans MPOBT and Geobacter sulfurreducens PCAT. PMID:34950111
The monofunctional CO dehydrogenase CooS is essential for growth of Thermoanaerobacter kivui on carbon monoxide. PMID:34919167
Dynamics of the ruminal microbial ecosystem, and inhibition of methanogenesis and propiogenesis in response to nitrate feeding to Holstein calves. PMID:34754962
Evolutionary Aspects of the Oxido-Reductive Network of Methylglyoxal. PMID:34718825
Shedding Light on Microbial "Dark Matter": Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake. PMID:34707591
Antimicrobial Activities of Chitosan Derivatives. PMID:34683932
Sex Steroid Hormones as a Balancing Factor in Oral Host Microbiome Interactions. PMID:34660339
Electron carriers involved in autotrophic and heterotrophic acetogenesis in the thermophilic bacterium Thermoanaerobacter kivui. PMID:34647163
A Heterodimeric Reduced-Ferredoxin-Dependent Methylenetetrahydrofolate Reductase from Syngas-Fermenting Clostridium ljungdahlii. PMID:34643446
Energy Conservation in Fermentations of Anaerobic Bacteria. PMID:34589068
Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments. PMID:34584214
Effects of combined tannic acid/fluoride on sulfur transformations and methanogenic pathways in swine manure. PMID:34555107
Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria. PMID:34480656
Nitrate Reduction Stimulates and Is Stimulated by Phenazine-1-Carboxylic Acid Oxidation by Citrobacter portucalensis MBL. PMID:34465028
Improvement of CO2 and Acetate Coupling into Lactic Acid by Genetic Manipulation of the Hyperthermophilic Bacterium Thermotoga neapolitana. PMID:34442767
Microbiome Structure and Function in Woodchip Bioreactors for Nitrate Removal in Agricultural Drainage Water. PMID:34421841
Is reduced ferredoxin the physiological electron donor for MetVF-type methylenetetrahydrofolate reductases in acetogenesis? A hypothesis. PMID:34255221
DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data. PMID:34241589
nZVI Impacts Substrate Conversion and Microbiome Composition in Chain Elongation From D- and L-Lactate Substrates. PMID:34211964
Enrichment of Autotrophic Denitrifiers From Anaerobic Sludge Using Sulfurous Electron Donors. PMID:34163455
Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds. PMID:34145392
Propionate Production from Carbon Monoxide by Synthetic Cocultures of Acetobacterium wieringae and Propionigenic Bacteria. PMID:33990298
The rumen microbiome: balancing food security and environmental impacts. PMID:33981031
A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria. PMID:33931420
Functional genome-centric view of the CO-driven anaerobic microbiome. PMID:33911204
Illumina Sequencing and Metabolomics Analysis Reveal Thiamine Modulation of Ruminal Microbiota and Metabolome Characteristics in Goats Fed a High-Concentrate Diet. PMID:33897666
Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. PMID:33851978
The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors. PMID:33672143
The pyruvate:ferredoxin oxidoreductase of the thermophilic acetogen, Thermoanaerobacter kivui. PMID:33660937
Anaerobic microbial methanol conversion in marine sediments. PMID:33587796
Methanogens: pushing the boundaries of biology. PMID:33525834
Energy Conservation in the Acetogenic Bacterium Clostridium aceticum. PMID:33513854
Novel Extracellular Electron Transfer Channels in a Gram-Positive Thermophilic Bacterium. PMID:33505370
Physiological, genomic, and sulfur isotopic characterization of methanol metabolism by Desulfovibrio carbinolicus. PMID:33444327
Metabolic energy conservation for fermentative product formation. PMID:33438829
Overcoming Energetic Barriers in Acetogenic C1 Conversion. PMID:33425882
Effect of Cultivation Parameters on Fermentation and Hydrogen Production in the Phylum Thermotogae. PMID:33396970
Long-Chain Fatty Acids Degradation by Desulfomonile Species and Proposal of "Candidatus Desulfomonile Palmitatoxidans". PMID:33391191
Comprehensive Bioenergetic Evaluation of Microbial Pathway Variants in Syntrophic Propionate Oxidation. PMID:33293404
Comparative proteomics of Geobacter sulfurreducens PCAT in response to acetate, formate and/or hydrogen as electron donor. PMID:33185968
The Iron-Sulfur Flavoprotein DsrL as NAD(P)H:Acceptor Oxidoreductase in Oxidative and Reductive Dissimilatory Sulfur Metabolism. PMID:33178160
Sulfate Alters the Competition Among Microbiome Members of Sediments Chronically Exposed to Asphalt. PMID:33133031
A bioenergetic model to predict habitability, biomass and biosignatures in astrobiology and extreme conditions. PMID:33081642
An Experimentally Evaluated Thermodynamic Approach to Estimate Growth of Photoheterotrophic Purple Non-sulfur Bacteria. PMID:33013778
Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics. PMID:33001550
Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models. PMID:32994290
Diverse Energy-Conserving Pathways in Clostridium difficile: Growth in the Absence of Amino Acid Stickland Acceptors and the Role of the Wood-Ljungdahl Pathway. PMID:32967909
Defining Genomic and Predicted Metabolic Features of the Acetobacterium Genus. PMID:32934112
Effect of Sub-Stoichiometric Fe(III) Amounts on LCFA Degradation by Methanogenic Communities. PMID:32906848
CO2 reduction driven by a pH gradient. PMID:32900930
Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF. PMID:32843629
Biohydrogen production beyond the Thauer limit by precision design of artificial microbial consortia. PMID:32796915
Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia. PMID:32793172
13C Electron Nuclear Double Resonance Spectroscopy Shows Acetyl-CoA Synthase Binds Two Substrate CO in Multiple Binding Modes and Reveals the Importance of a CO-Binding "Alcove". PMID:32786751
Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. PMID:32709258
Effect of Biofuels on Biodegradation of Benzene and Toluene at Gasoline Spill Sites. PMID:32699493
Bacterial chemolithoautotrophy via manganese oxidation. PMID:32669693
Older Than Genes: The Acetyl CoA Pathway and Origins. PMID:32655499
Ethanol and lactic acid production from sugar and starch wastes by anaerobic acidification. PMID:32624943
Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste. PMID:32620171
Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae. PMID:32605988
Competition for Hydrogen Prevents Coexistence of Human Gastrointestinal Hydrogenotrophs in Continuous Culture. PMID:32547517
Carbon recycling efficiency and phosphate turnover by marine nitrifying archaea. PMID:32426487
Ethanol Metabolism Dynamics in Clostridium ljungdahlii Grown on Carbon Monoxide. PMID:32414802
Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions. PMID:32351469
The effect of anode potential on current production from complex substrates in bioelectrochemical systems: a case study with glucose. PMID:32248443
Systems Analysis of NADH Dehydrogenase Mutants Reveals Flexibility and Limits of Pseudomonas taiwanensis VLB120's Metabolism. PMID:32245760
Modeling ethanol production through gas fermentation: a biothermodynamics and mass transfer-based hybrid model for microbial growth in a large-scale bubble column bioreactor. PMID:32231709
It does not always take two to tango: "Syntrophy" via hydrogen cycling in one bacterial cell. PMID:32203116
Autocatalytic chemical networks at the origin of metabolism. PMID:32156207
Co-cultivation of Thermoanaerobacter strains with a methanogenic partner enhances glycerol conversion. PMID:32154666
Phylogenomic analysis of novel Diaforarchaea is consistent with sulfite but not sulfate reduction in volcanic environments on early Earth. PMID:32066874
Physiological limits to life in anoxic subseafloor sediment. PMID:32065239
Extracellular Electron Uptake by Acetogenic Bacteria: Does H2 Consumption Favor the H2 Evolution Reaction on a Cathode or Metallic Iron? PMID:31998274
From an extremophilic community to an electroautotrophic production strain: identifying a novel Knallgas bacterium as cathodic biofilm biocatalyst. PMID:31996786
Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. PMID:31996394
Mathematical modelling supports the existence of a threshold hydrogen concentration and media-dependent yields in the growth of a reductive acetogen. PMID:31982985
Bacterial culture through selective and non-selective conditions: the evolution of culture media in clinical microbiology. PMID:31956419
How does electron transfer occur in microbial fuel cells? PMID:31955250
Identification of a Redox Active Thioquinoxalinol Sulfate Compound Produced by an Anaerobic Methane-Oxidizing Microbial Consortium. PMID:31909345
New AMP-forming acid:CoA ligases from Streptomyces lividans, some of which are posttranslationally regulated by reversible lysine acetylation. PMID:31677300
Structural comparisons of phosphoenolpyruvate carboxykinases reveal the evolutionary trajectories of these phosphodiester energy conversion enzymes. PMID:31662435
Energy-converting hydrogenases: the link between H2 metabolism and energy conservation. PMID:31630229
Effect of Quorum Sensing on the Ability of Desulfovibrio vulgaris To Form Biofilms and To Biocorrode Carbon Steel in Saline Conditions. PMID:31628147
Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a Novel Fumarate-Fermenting Microorganism From a Deep Fractured Carbonate Aquifer of the US Great Basin. PMID:31611860
Amino Acid and Sugar Catabolism in the Marine Bacterium Phaeobacter inhibens DSM 17395 from an Energetic Viewpoint. PMID:31604772
Energy Conservation and Hydrogenase Function in Methanogenic Archaea, in Particular the Genus Methanosarcina. PMID:31533962
Pseudomonas spp. are key players in agricultural biogas substrate degradation. PMID:31492882
Subseafloor life and its biogeochemical impacts. PMID:31388058
A Mathematical Model for the Hydrogenotrophic Metabolism of Sulphate-Reducing Bacteria. PMID:31379794
N2O formation by nitrite-induced (chemo)denitrification in coastal marine sediment. PMID:31366952
Mechanism of Sulfate Activation Catalyzed by ATP Sulfurylase - Magnesium Inhibits the Activity. PMID:31312415
Metabolites of the Anaerobic Degradation of n-Hexane by Denitrifying Betaproteobacterium Strain HxN1. PMID:31294892
Characterization of thiosulfate reductase from Pyrobaculum aerophilum heterologously produced in Pyrococcus furiosus. PMID:31278423
A Real-Time Multiplexed Microbial Growth Intervalometer for Capturing High-Resolution Growth Curves. PMID:31231321
Protein Acetylation in Bacteria. PMID:31091420
Electrical energy storage with engineered biological systems. PMID:31073327
Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer. PMID:31064258
Interrogating metabolism as an electron flow system. PMID:31008413
Methyl (Alkyl)-Coenzyme M Reductases: Nickel F-430-Containing Enzymes Involved in Anaerobic Methane Formation and in Anaerobic Oxidation of Methane or of Short Chain Alkanes. PMID:30951290
Microbial substrate preference dictated by energy demand, not supply. PMID:30944580
Energy metabolism in anaerobic eukaryotes and Earth's late oxygenation. PMID:30935869
Distribution, Evolution, Catalytic Mechanism, and Physiological Functions of the Flavin-Based Electron-Bifurcating NADH-Dependent Reduced Ferredoxin: NADP+ Oxidoreductase. PMID:30881354
Physiological adaptations to serpentinization in the Samail Ophiolite, Oman. PMID:30872803
Methane-Linked Mechanisms of Electron Uptake from Cathodes by Methanosarcina barkeri. PMID:30862748
Effect of Lactate on the Microbial Community and Process Performance of an EBPR System. PMID:30833933
Formation of phenylacetic acid and phenylpropionic acid under different overload conditions during mesophilic and thermophilic anaerobic digestion. PMID:30787959
Subsurface Microbial Hydrogen Cycling: Natural Occurrence and Implications for Industry. PMID:30769950
Characterization of an Aldehyde Oxidoreductase From the Mesophilic Bacterium Aromatoleum aromaticum EbN1, a Member of a New Subfamily of Tungsten-Containing Enzymes. PMID:30766522
A review of the mechanisms of mineral-based metabolism in early Earth analog rock-hosted hydrothermal ecosystems. PMID:30689069
Butanol Synthesis Routes for Biofuel Production: Trends and Perspectives. PMID:30678076
Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes. PMID:30658976
Reductive metabolism of the important atmospheric gas isoprene by homoacetogens. PMID:30643199
Respiratory Selenite Reductase from Bacillus selenitireducens Strain MLS10. PMID:30642986
Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments. PMID:30619130
Complex Multimeric [FeFe] Hydrogenases: Biochemistry, Physiology and New Opportunities for the Hydrogen Economy. PMID:30564206
Hydrogen cross-feeders of the human gastrointestinal tract. PMID:30563420
Inhibition Studies with 2-Bromoethanesulfonate Reveal a Novel Syntrophic Relationship in Anaerobic Oleate Degradation. PMID:30366998
The Shape Effect on Polymer Nanoparticle Transport in a Blood Vessel. PMID:30271591
Sensitizing bacterial cells to antibiotics by shape recovery triggered biofilm dispersion. PMID:30267885
Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. PMID:30245936
Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment. PMID:30206424
Kinetic modelling and synergistic impact evaluation for the anaerobic co-digestion of distillers' grains and food waste by ethanol pre-fermentation. PMID:30155637
O2 versus N2O respiration in a continuous microbial enrichment. PMID:30054702
Lipoate-binding proteins and specific lipoate-protein ligases in microbial sulfur oxidation reveal an atpyical role for an old cofactor. PMID:30004385
A non-linear model of hydrogen production by Caldicellulosiruptor saccharolyticus for diauxic-like consumption of lignocellulosic sugar mixtures. PMID:29977336
Galacturonate Metabolism in Anaerobic Chemostat Enrichment Cultures: Combined Fermentation and Acetogenesis by the Dominant sp. nov. "Candidatus Galacturonibacter soehngenii". PMID:29959255
Uncoupling Fermentative Synthesis of Molecular Hydrogen from Biomass Formation in Thermotoga maritima. PMID:29959252
Genome Sequence of Acetomicrobium hydrogeniformans OS1. PMID:29954899
Comparison of Acetate-butyrate and Acetate-ethanol Metabolic Pathway in Biohydrogen Production. PMID:29928635
The hunt for the most-wanted chemolithoautotrophic spookmicrobes. PMID:29873717
Metabolic reconstruction and experimental verification of glucose utilization in Desulfurococcus amylolyticus DSM 16532. PMID:29797222
The Membrane-Bound C Subunit of Reductive Dehalogenases: Topology Analysis and Reconstitution of the FMN-Binding Domain of PceC. PMID:29740408
Insight into Energy Conservation via Alternative Carbon Monoxide Metabolism in Carboxydothermus pertinax Revealed by Comparative Genome Analysis. PMID:29728389
Efficient whole cell biocatalyst for formate-based hydrogen production. PMID:29619089
Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD+ (Rnf) as Electron Acceptors: A Historical Review. PMID:29593673
Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways. PMID:29540717
Different Metabolomic Responses to Carbon Starvation between Light and Dark Conditions in the Purple Photosynthetic Bacterium, Rhodopseudomonas palustris. PMID:29540639
Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus. PMID:29524843
Acetyl Phosphate as a Primordial Energy Currency at the Origin of Life. PMID:29502283
Tools for studying growth patterns and chemical dynamics of aggregated Pseudomonas aeruginosa exposed to different electron acceptors in an alginate bead model. PMID:29479470
Mediative mechanism of bicarbonate on anaerobic propionate degradation revealed by microbial community and thermodynamics. PMID:29460248
Functional Characterization of Three Specific Acyl-Coenzyme A Synthetases Involved in Anaerobic Cholesterol Degradation in Sterolibacterium denitrificans Chol1S. PMID:29374035
A Flexible System for Cultivation of Methanococcus and Other Formate-Utilizing Methanogens. PMID:29348732
P2X4 Receptor in Silico and Electrophysiological Approaches Reveal Insights of Ivermectin and Zinc Allosteric Modulation. PMID:29326590
Protein engineering of oxidoreductases utilizing nicotinamide-based coenzymes, with applications in synthetic biology. PMID:29318201
Using Thermodynamics to Predict the Outcomes of Nitrate-Based Oil Reservoir Souring Control Interventions. PMID:29312252
Efficient Hydrogen-Dependent Carbon Dioxide Reduction by Escherichia coli. PMID:29290558
In Streptomyces lividans, acetyl-CoA synthetase activity is controlled by O-serine and Nɛ -lysine acetylation. PMID:29266439
Enhancing methane production from food waste fermentate using biochar: the added value of electrochemical testing in pre-selecting the most effective type of biochar. PMID:29255486
Molecular hydrogen: a preventive and therapeutic medical gas for various diseases. PMID:29254278
The Consequences of Being in an Infectious Biofilm: Microenvironmental Conditions Governing Antibiotic Tolerance. PMID:29231866
Long-term adaptation of Escherichia coli to methanogenic co-culture enhanced succinate production from crude glycerol. PMID:29230577
Targeted redox and energy cofactor metabolomics in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum. PMID:29213318
Investigation of different nitrogen reduction routes and their key microbial players in wood chip-driven denitrification beds. PMID:29208961
A physiological perspective on the origin and evolution of photosynthesis. PMID:29177446
The Minimum Biological Energy Quantum. PMID:29123504
Imaging of Cellular Oxidoreductase Activity Suggests Mixotrophic Metabolisms in Thiomargarita spp. PMID:29114021
Electron carriers in microbial sulfate reduction inferred from experimental and environmental sulfur isotope fractionations. PMID:29087380
The origin of heredity in protocells. PMID:29061892
Synthesis of Heterologous Mevalonic Acid Pathway Enzymes in Clostridium ljungdahlii for the Conversion of Fructose and of Syngas to Mevalonate and Isoprene. PMID:29054870
Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria. PMID:28928722
Metagenomic Characterization of Candidatus Smithella cisternae Strain M82_1, a Syntrophic Alkane-Degrading Bacteria, Enriched from the Shengli Oil Field. PMID:28781346
Structural Basis for the Mechanism of ATP-Dependent Acetone Carboxylation. PMID:28775283
Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids. PMID:28762640
Physiological Evidence for Isopotential Tunneling in the Electron Transport Chain of Methane-Producing Archaea. PMID:28710268
The deep, hot biosphere: Twenty-five years of retrospection. PMID:28674200
Case Study: Microbial Ecology and Forensics of Chinese Drywall-Elemental Sulfur Disproportionation as Primary Generator of Hydrogen Sulfide. PMID:28639032
The Physiology of Phagocytosis in the Context of Mitochondrial Origin. PMID:28615286
Influence of Phosphorus and Cell Geometry on the Fractionation of Sulfur Isotopes by Several Species of Desulfovibrio during Microbial Sulfate Reduction. PMID:28611734
Effect of Flooding and the nosZ Gene in Bradyrhizobia on Bradyrhizobial Community Structure in the Soil. PMID:28592720
Electrochemical Potential Influences Phenazine Production, Electron Transfer and Consequently Electric Current Generation by Pseudomonas aeruginosa. PMID:28572797
Effects of electron acceptors on sulphate reduction activity in activated sludge processes. PMID:28547567
Co-existence of Methanogenesis and Sulfate Reduction with Common Substrates in Sulfate-Rich Estuarine Sediments. PMID:28529500
Expanding the substrates for a bacterial hydrogenlyase reaction. PMID:28488566
Comparative metabolomic studies of Alkanivorax xenomutans showing differential power output in a three chambered microbial fuel cell. PMID:28466301
Hydrogen production and microbial kinetics of Clostridium termitidis in mono-culture and co-culture with Clostridium beijerinckii on cellulose. PMID:28429329
On the Edge of Research and Technological Application: A Critical Review of Electromethanogenesis. PMID:28425974
Radiative Energy Budgets of Phototrophic Surface-Associated Microbial Communities and their Photosynthetic Efficiency Under Diffuse and Collimated Light. PMID:28400749
Energy Metabolism during Anaerobic Methane Oxidation in ANME Archaea. PMID:28321009
Physiology, phylogeny, early evolution, and GAPDH. PMID:28265765
Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman. PMID:28223966
Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms. PMID:28206708
A Ferredoxin- and F420H2-Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea. PMID:28174314
Metabolic engineering of Clostridium autoethanogenum for selective alcohol production. PMID:28111249
Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats. PMID:28106880
Competition between Methanogens and Acetogens in Biocathodes: A Comparison between Potentiostatic and Galvanostatic Control. PMID:28106846
Redox potential as a master variable controlling pathways of metal reduction by Geobacter sulfurreducens. PMID:28045456
Fermentation of glycerol by Anaerobium acetethylicum and its potential use in biofuel production. PMID:28004884
Effect of Nickel Levels on Hydrogen Partial Pressure and Methane Production in Methanogens. PMID:27992585
An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers. PMID:27872277
Piezo-tolerant natural gas-producing microbes under accumulating pCO2. PMID:27826355
Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester. PMID:27815274
Microbial copper resistance: importance in biohydrometallurgy. PMID:27790868
Influence of haem environment on the catalytic properties of the tetrathionate reductase TsdA from Campylobacter jejuni. PMID:27789780
Ratiometric fluorescent pH-sensitive polymers for high-throughput monitoring of extracellular pH. PMID:27721974
The Two Sets of DMSO Respiratory Systems of Shewanella piezotolerans WP3 Are Involved in Deep Sea Environmental Adaptation. PMID:27656177
Shifting the balance of fermentation products between hydrogen and volatile fatty acids: microbial community structure and function. PMID:27633926
Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia. PMID:27625634
"Hot" acetogenesis. PMID:27623994
Process Optimization on Micro-Aeration Supply for High Production Yield of 2,3-Butanediol from Maltodextrin by Metabolically-Engineered Klebsiella oxytoca. PMID:27603922
A Novel F420-dependent Thioredoxin Reductase Gated by Low Potential FAD: A TOOL FOR REDOX REGULATION IN AN ANAEROBE. PMID:27590343
Biomethanation of Syngas Using Anaerobic Sludge: Shift in the Catabolic Routes with the CO Partial Pressure Increase. PMID:27536280
Electron acceptor redox potential globally regulates transcriptomic profiling in Shewanella decolorationis S12. PMID:27503002
Comparative Genomics of Syntrophic Branched-Chain Fatty Acid Degrading Bacteria. PMID:27431485
Analysis of propionate-degrading consortia from agricultural biogas plants. PMID:27364538
A stable genetic polymorphism underpinning microbial syntrophy. PMID:27258948
Isolation and Characterization of Electrochemically Active Subsurface Delftia and Azonexus Species. PMID:27242768
Gas Fermentation-A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks. PMID:27242719
Energetics and Application of Heterotrophy in Acetogenic Bacteria. PMID:27208103
One step beyond a ribosome: The ancient anaerobic core. PMID:27150504
Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol. PMID:27140643
Exploring the directionality of Escherichia coli formate hydrogenlyase: a membrane-bound enzyme capable of fixing carbon dioxide to organic acid. PMID:27139710
Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions. PMID:27122598
Classic Spotlight: Electron Bifurcation, a Unifying Concept for Energy Conservation in Anaerobes. PMID:27080054
Microbial diversity arising from thermodynamic constraints. PMID:27035705
Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. PMID:27015005
Effects of carbon-to-sulfur (C/S) ratio and nitrate (N) dosage on Denitrifying Sulfur cycle-associated Enhanced Biological Phosphorus Removal (DS-EBPR). PMID:26983801
Expanding the Diet for DIET: Electron Donors Supporting Direct Interspecies Electron Transfer (DIET) in Defined Co-Cultures. PMID:26973614
Insights on Alterations to the Rumen Ecosystem by Nitrate and Nitrocompounds. PMID:26973609
Nitrate and Inhibition of Ruminal Methanogenesis: Microbial Ecology, Obstacles, and Opportunities for Lowering Methane Emissions from Ruminant Livestock. PMID:26904008
Graphene oxide-dependent growth and self-aggregation into a hydrogel complex of exoelectrogenic bacteria. PMID:26899353
Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes. PMID:26833419
Peat: home to novel syntrophic species that feed acetate- and hydrogen-scavenging methanogens. PMID:26771931
A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea. PMID:26733968
Metagenome-Based Metabolic Reconstruction Reveals the Ecophysiological Function of Epsilonproteobacteria in a Hydrocarbon-Contaminated Sulfidic Aquifer. PMID:26696999
Control of Microbial Sulfide Production with Biocides and Nitrate in Oil Reservoir Simulating Bioreactors. PMID:26696994
Bioenergetic constraints for conversion of syngas to biofuels in acetogenic bacteria. PMID:26692897
Evaluating the potential impact of proton carriers on syntrophic propionate oxidation. PMID:26670292
Cytoplasmic CopZ-Like Protein and Periplasmic Rusticyanin and AcoP Proteins as Possible Copper Resistance Determinants in Acidithiobacillus ferrooxidans ATCC 23270. PMID:26637599
Limits to Dihydrogen Incorporation into Electron Sinks Alternative to Methanogenesis in Ruminal Fermentation. PMID:26635743
The EutQ and EutP proteins are novel acetate kinases involved in ethanolamine catabolism: physiological implications for the function of the ethanolamine metabolosome in Salmonella enterica. PMID:26448059
Formate, acetate, and propionate as substrates for sulfate reduction in sub-arctic sediments of Southwest Greenland. PMID:26379631
NADPH-generating systems in bacteria and archaea. PMID:26284036
Untargeted metabolomics studies employing NMR and LC-MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis. PMID:26273237
Genome Wide Re-Annotation of Caldicellulosiruptor saccharolyticus with New Insights into Genes Involved in Biomass Degradation and Hydrogen Production. PMID:26196387
Distribution of iron- and sulfate-reducing bacteria across a coastal acid sulfate soil (CASS) environment: implications for passive bioremediation by tidal inundation. PMID:26191042
Energy Conservation Associated with Ethanol Formation from H2 and CO2 in Clostridium autoethanogenum Involving Electron Bifurcation. PMID:26148714
Cable Bacteria in Freshwater Sediments. PMID:26116678
Amino Acid and Peptide Utilization Profiles of the Fluoroacetate-Degrading Bacterium Synergistetes Strain MFA1 Under Varying Conditions. PMID:26111963
Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana. PMID:26053393
Assessment of the stoichiometry and efficiency of CO2 fixation coupled to reduced sulfur oxidation. PMID:26052315
Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PMID:26035711
Gut Microbiome and Obesity: A Plausible Explanation for Obesity. PMID:26029487
Metabolic energy-based modelling explains product yielding in anaerobic mixed culture fermentations. PMID:25992959
2,3-Butanediol Metabolism in the Acetogen Acetobacterium woodii. PMID:25934628
Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming. PMID:25918393
Enrichment of DNRA bacteria in a continuous culture. PMID:25909972
Shifts in metabolic hydrogen sinks in the methanogenesis-inhibited ruminal fermentation: a meta-analysis. PMID:25699029
Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum: structural and functional insights into thiosulfate oxidation. PMID:25673691
A dynamic periplasmic electron transfer network enables respiratory flexibility beyond a thermodynamic regulatory regime. PMID:25635641
Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. PMID:25615435
Degradation of acetaldehyde and its precursors by Pelobacter carbinolicus and P. acetylenicus. PMID:25536080
A genome-guided analysis of energy conservation in the thermophilic, cytochrome-free acetogenic bacterium Thermoanaerobacter kivui. PMID:25523312
Identification of S-nitroso-CoA reductases that regulate protein S-nitrosylation. PMID:25512491
Genomic, proteomic, and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans. PMID:25512312
Multiple sulfur isotope signatures of sulfite and thiosulfate reduction by the model dissimilatory sulfate-reducer, Desulfovibrio alaskensis str. G20. PMID:25505449
New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”. PMID:25501486
Molybdenum and tungsten-dependent formate dehydrogenases. PMID:25476858
Adaptation of anaerobic cultures of Escherichia coli K-12 in response to environmental trimethylamine-N-oxide. PMID:25471524
Improved conversion efficiencies for n-fatty acid reduction to primary alcohols by the solventogenic acetogen "Clostridium ragsdalei". PMID:25410829
Minimization of extracellular space as a driving force in prokaryote association and the origin of eukaryotes. PMID:25406691
Reduced catabolic protein expression in Clostridium butyricum DSM 10702 correlate with reduced 1,3-propanediol synthesis at high glycerol loading. PMID:25401066
The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium. PMID:25400628
Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria. PMID:25383604
Biohydrogen Production by the Thermophilic Bacterium Caldicellulosiruptor saccharolyticus: Current Status and Perspectives. PMID:25371332
Single gene insertion drives bioalcohol production by a thermophilic archaeon. PMID:25368184
Intracellular metabolite levels shape sulfur isotope fractionation during microbial sulfate respiration. PMID:25362045
Cell-free metabolic engineering: biomanufacturing beyond the cell. PMID:25319678
Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils. PMID:25303715
Shifting the metallocentric molybdoenzyme paradigm: the importance of pyranopterin coordination. PMID:25267303
Anaerobic activation of p-cymene in denitrifying betaproteobacteria: methyl group hydroxylation versus addition to fumarate. PMID:25261521
The Gibbs free energy of formation of halogenated benzenes, benzoates and phenols and their potential role as electron acceptors in anaerobic environments. PMID:25231938
Metabolism leaves its mark on the powerhouse: recent progress in post-translational modifications of lysine in mitochondria. PMID:25228883
Microbial redox processes in deep subsurface environments and the potential application of (per)chlorate in oil reservoirs. PMID:25225493
Bacterial formate hydrogenlyase complex. PMID:25157147
Hydrogen formation and its regulation in Ruminococcus albus: involvement of an electron-bifurcating [FeFe]-hydrogenase, of a non-electron-bifurcating [FeFe]-hydrogenase, and of a putative hydrogen-sensing [FeFe]-hydrogenase. PMID:25157086
Characterization of the frhAGB-encoding hydrogenase from a non-methanogenic hyperthermophilic archaeon. PMID:25142159
Collateral damage: microbiota-derived metabolites and immune function in the antibiotic era. PMID:25121745
Essentiality of succinate dehydrogenase in Mycobacterium smegmatis and its role in the generation of the membrane potential under hypoxia. PMID:25118234
Centimeter-long electron transport in marine sediments via conductive minerals. PMID:25050525
Identification of genes specifically required for the anaerobic metabolism of benzene in Geobacter metallireducens. PMID:24904558
The impact of intestinal inflammation on the nutritional environment of the gut microbiota. PMID:24803011
Metabolic compensation of fitness costs associated with overexpression of the multidrug efflux pump MexEF-OprN in Pseudomonas aeruginosa. PMID:24777101
Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus. PMID:24763368
Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens. PMID:24762737
Towards a computational model of a methane producing archaeum. PMID:24729742
Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. PMID:24710389
The drive to life on wet and icy worlds. PMID:24697642
Biogenic hydrogen conversion of de-oiled jatropha waste via anaerobic sequencing batch reactor operation: process performance, microbial insights, and CO2 reduction efficiency. PMID:24672398
Habitable worlds with no signs of life. PMID:24664917
Metabolic efficiency of Geobacter sulfurreducens growing on anodes with different redox potentials. PMID:24554342
Structure, function, and mechanism of the nickel metalloenzymes, CO dehydrogenase, and acetyl-CoA synthase. PMID:24521136
Radiative energy budget reveals high photosynthetic efficiency in symbiont-bearing corals. PMID:24478282
Temperature regulation of anaerobic degradation of organic matter. PMID:24415380
Anaerobic bioprocessing of organic wastes. PMID:24415229
Metabolism of hyperthermophiles. PMID:24414410
Microbial population and functional dynamics associated with surface potential and carbon metabolism. PMID:24351938
New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20. PMID:24242254
Methanogenic fermentation of benzoate in an enrichment culture. PMID:24232164
Product inhibition in sludge digestion. PMID:24232163
Physiological ecology of acetylene reduction (nitrogen fixation) in a Delaware salt marsh. PMID:24226967
Isolation and partial characterization of aClostridium species transforming para-hydroxybenzoate and 3,4-dihydroxybenzoate and producing phenols as the final transformation products. PMID:24193968
Nitrate and periplasmic nitrate reductases. PMID:24141308
Genome-enabled studies of anaerobic, nitrate-dependent iron oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans. PMID:24065960
The contribution of genes required for anaerobic respiration to the virulence of Salmonella enterica serovar Gallinarum for chickens. PMID:24031452
Thermophilic biohydrogen production: how far are we? PMID:23948723
Nitrate ammonification by Nautilia profundicola AmH: experimental evidence consistent with a free hydroxylamine intermediate. PMID:23847604
MrpA functions in energy conversion during acetate-dependent growth of Methanosarcina acetivorans. PMID:23836862
Syntrophic propionate oxidation via butyrate: a novel window of opportunity under methanogenic conditions. PMID:23787899
Early bioenergetic evolution. PMID:23754820
Metabolic engineering of Caldicellulosiruptor bescii yields increased hydrogen production from lignocellulosic biomass. PMID:23731756
4-Hydroxyphenylacetate decarboxylase activating enzyme catalyses a classical S-adenosylmethionine reductive cleavage reaction. PMID:23716017
Relevance and diversity of Nitrospira populations in biofilters of brackish RAS. PMID:23705006
Salmonella uses energy taxis to benefit from intestinal inflammation. PMID:23637594
Ammonia oxidation pathways and nitrifier denitrification are significant sources of N2O and NO under low oxygen availability. PMID:23576736
Phenothiazine derivative-accelerated microbial extracellular electron transfer in bioelectrochemical system. PMID:23563590
Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients. PMID:23514780
An electron-bifurcating caffeyl-CoA reductase. PMID:23479729
The dynamics of gut-associated microbial communities during inflammation. PMID:23478337
A proteomic view at the biochemistry of syntrophic butyrate oxidation in Syntrophomonas wolfei. PMID:23468890
Isolation, characterization and evaluation of hyper 2-propanol producing bacteria from Singapore environment. PMID:23361972
A reversible electron-bifurcating ferredoxin- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Moorella thermoacetica. PMID:23316038
Genome-guided analysis of physiological and morphological traits of the fermentative acetate oxidizer Thermacetogenium phaeum. PMID:23259483
Linking genome content to biofuel production yields: a meta-analysis of major catabolic pathways among select H2 and ethanol-producing bacteria. PMID:23249097
Antitubercular pharmacodynamics of phenothiazines. PMID:23228936
Pyruvate catabolism and hydrogen synthesis pathway genes of Clostridium thermocellum ATCC 27405. PMID:23100718
Distribution of CO(2) fixation and acetate mineralization pathways in microorganisms from extremophilic anaerobic biotopes. PMID:23065059
A Single-cell genome for Thiovulum sp. PMID:23023751
Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression. PMID:22994686
Simultaneous ANAMMOX and denitrification (SAD) process in batch tests. PMID:22961442
A comprehensive and quantitative review of dark fermentative biohydrogen production. PMID:22925149
Phosphoketolase pathway for xylose catabolism in Clostridium acetobutylicum revealed by 13C metabolic flux analysis. PMID:22865845
Phage-mediated acquisition of a type III secreted effector protein boosts growth of salmonella by nitrate respiration. PMID:22691391
An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. PMID:22645166
Contributions of the microbial hydrogen economy to colonic homeostasis. PMID:22585131
Electron bifurcation involved in the energy metabolism of the acetogenic bacterium Moorella thermoacetica growing on glucose or H2 plus CO2. PMID:22582275
Glycerol as a substrate for aerobic succinate production in minimal medium with Corynebacterium glutamicum. PMID:22513227
An ancient pathway combining carbon dioxide fixation with the generation and utilization of a sodium ion gradient for ATP synthesis. PMID:22479398
Spatial patterns of iron- and methane-oxidizing bacterial communities in an irregularly flooded, riparian wetland. PMID:22375139
Physiological and proteomic adaptation of "Aromatoleum aromaticum" EbN1 to low growth rates in benzoate-limited, anoxic chemostats. PMID:22366417
Biohydrogen production from arabinose and glucose using extreme thermophilic anaerobic mixed cultures. PMID:22330180
There Must be an Acetogen Somewhere. PMID:22319520
Diclofenac and 2-anilinophenylacetate degradation by combined activity of biogenic manganese oxides and silver. PMID:22221449
Reassessment of hydrogen tolerance in Caldicellulosiruptor saccharolyticus. PMID:22189215
Anaerobic degradation of 4-methylbenzoate by a newly isolated denitrifying bacterium, strain pMbN1. PMID:22179254
Olivine-respiring bacteria isolated from the rock-ice interface in a lava-tube cave, a Mars analog environment. PMID:22165996
Carbon and sulfur back flux during anaerobic microbial oxidation of methane and coupled sulfate reduction. PMID:22160711
Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. PMID:22139506
Characterization of Phascolarctobacterium succinatutens sp. nov., an asaccharolytic, succinate-utilizing bacterium isolated from human feces. PMID:22081579
Thiosulfate reduction in Salmonella enterica is driven by the proton motive force. PMID:22081391
Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. PMID:22071343
eQuilibrator--the biochemical thermodynamics calculator. PMID:22064852
Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions. PMID:21965410
A kinetic model for quantitative evaluation of the effect of hydrogen and osmolarity on hydrogen production by Caldicellulosiruptor saccharolyticus. PMID:21914204
Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications. PMID:21866228
Alkane degradation under anoxic conditions by a nitrate-reducing bacterium with possible involvement of the electron acceptor in substrate activation. PMID:21837252
In silico evidence for gluconeogenesis from fatty acids in humans. PMID:21814506
The respiratory molybdo-selenoprotein formate dehydrogenases of Escherichia coli have hydrogen: benzyl viologen oxidoreductase activity. PMID:21806784
Genetics and molecular biology of the electron flow for sulfate respiration in desulfovibrio. PMID:21747813
Recent progress toward hydrogen medicine: potential of molecular hydrogen for preventive and therapeutic applications. PMID:21736547
Early evolution without a tree of life. PMID:21714942
Formate formation and formate conversion in biological fuels production. PMID:21687599
Identification and isolation of active N2O reducers in rice paddy soil. PMID:21677691
Competing formate- and carbon dioxide-utilizing prokaryotes in an anoxic methane-emitting fen soil. PMID:21478308
The role of iron in tumour cell proliferation. PMID:21324793
In Salmonella enterica, the sirtuin-dependent protein acylation/deacylation system (SDPADS) maintains energy homeostasis during growth on low concentrations of acetate. PMID:21306440
The thermodynamic landscape of methanogenic PAH degradation. PMID:21255289
Thermodynamics of microbial growth coupled to metabolism of glucose, ethanol, short-chain organic acids, and hydrogen. PMID:21216913
Stable coexistence of two Caldicellulosiruptor species in a de novo constructed hydrogen-producing co-culture. PMID:21192828
Identification of missing genes and enzymes for autotrophic carbon fixation in crenarchaeota. PMID:21169482
Physiological characteristics of the extreme thermophile Caldicellulosiruptor saccharolyticus: an efficient hydrogen cell factory. PMID:21092203
Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes. PMID:21072677
Revisiting the thermodynamic theory of optimal ATP stoichiometries by analysis of various ATP-producing metabolic pathways. PMID:20922363
Bacterial Na+-translocating ferredoxin:NAD+ oxidoreductase. PMID:20921383
Microbial electrosynthesis - revisiting the electrical route for microbial production. PMID:20844557
Characterizing the metabolism of Dehalococcoides with a constraint-based model. PMID:20811585
The genus Thermotoga: recent developments. PMID:20718299
NADP+ reduction with reduced ferredoxin and NADP+ reduction with NADH are coupled via an electron-bifurcating enzyme complex in Clostridium kluyveri. PMID:20675474
Microbial community changes in response to ethanol or methanol amendments for U(VI) reduction. PMID:20601514
Heme biosynthesis is coupled to electron transport chains for energy generation. PMID:20484676
Effect of methanogenic substrates on anaerobic oxidation of methane and sulfate reduction by an anaerobic methanotrophic enrichment. PMID:20445975
Effect of methanogenic substrates on anaerobic oxidation of methane and sulfate reduction by an anaerobic methanotrophic enrichment. PMID:20445975
Dissecting the in vivo metabolic potential of two human gut acetogens. PMID:20444704
Design and analysis of synthetic carbon fixation pathways. PMID:20410460
Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus. PMID:19955419
Syntrophy in anaerobic global carbon cycles. PMID:19897353
Methane and the gastrointestinal tract. PMID:19830557
Involvement of NADH:acceptor oxidoreductase and butyryl coenzyme A dehydrogenase in reversed electron transport during syntrophic butyrate oxidation by Syntrophomonas wolfei. PMID:19648244
Identification of the [FeFe]-hydrogenase responsible for hydrogen generation in Thermoanaerobacterium saccharolyticum and demonstration of increased ethanol yield via hydrogenase knockout. PMID:19648238
Electron transfer in syntrophic communities of anaerobic bacteria and archaea. PMID:19609258
The electron transfer system of syntrophically grown Desulfovibrio vulgaris. PMID:19581361
Cell-free protein synthesis energized by slowly-metabolized maltodextrin. PMID:19558718
Enrichment and isolation of Bacillus beveridgei sp. nov., a facultative anaerobic haloalkaliphile from Mono Lake, California, that respires oxyanions of tellurium, selenium, and arsenic. PMID:19536453
Syntrophic degradation of cadaverine by a defined methanogenic coculture. PMID:19465531
Cultivation of methanogens under low-hydrogen conditions by using the coculture method. PMID:19465530
The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production. PMID:19411328
Thermodynamic analysis of biodegradation pathways. PMID:19288443
Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). PMID:19270133
A novel Dehalobacter species is involved in extensive 4,5,6,7-tetrachlorophthalide dechlorination. PMID:19218402
Metabolism of hydroxylated and fluorinated benzoates by Syntrophus aciditrophicus and detection of a fluorodiene metabolite. PMID:19114508
NinaB combines carotenoid oxygenase and retinoid isomerase activity in a single polypeptide. PMID:19020100
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. PMID:19000309
Purification, crystallization and preliminary X-ray analysis of adenylylsulfate reductase from Desulfovibrio vulgaris Miyazaki F. PMID:18997328
Electricity generation by anaerobic bacteria and anoxic sediments from hypersaline soda lakes. PMID:18836685
Comparison of electrode reduction activities of Geobacter sulfurreducens and an enriched consortium in an air-cathode microbial fuel cell. PMID:18836002
Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation. PMID:18801467
Coordination and binding geometry of methyl-coenzyme M in the red1m state of methyl-coenzyme M reductase. PMID:18712421
Syntrophic growth on formate: a new microbial niche in anoxic environments. PMID:18708519
Purification and characterization of active-site components of the putative p-cresol methylhydroxylase membrane complex from Geobacter metallireducens. PMID:18658262
Group contribution method for thermodynamic analysis of complex metabolic networks. PMID:18645197
The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). PMID:18631365
Genetic analysis of trimethylamine N-oxide reductases in the light organ symbiont Vibrio fischeri ES114. PMID:18606737
Competition and coexistence of sulfate-reducing bacteria, acetogens and methanogens in a lab-scale anaerobic bioreactor as affected by changing substrate to sulfate ratio. PMID:18305937
The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota. PMID:18218977
The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. PMID:18218779
Microbial diversity and genomics in aid of bioenergy. PMID:18193465
Degradation of glyoxylate and glycolate with ATP synthesis by a thermophilic anaerobic bacterium, Moorella sp. strain HUC22-1. PMID:18083850
Energy conservation via electron-transferring flavoprotein in anaerobic bacteria. PMID:18039764
Coupled ferredoxin and crotonyl coenzyme A (CoA) reduction with NADH catalyzed by the butyryl-CoA dehydrogenase/Etf complex from Clostridium kluyveri. PMID:17993531
Two sub-states of the red2 state of methyl-coenzyme M reductase revealed by high-field EPR spectroscopy. PMID:17690920
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. PMID:17593909
Pyocyanin alters redox homeostasis and carbon flux through central metabolic pathways in Pseudomonas aeruginosa PA14. PMID:17526704
Genes, enzymes, and regulation of para-cresol metabolism in Geobacter metallireducens. PMID:17449613
Identification of anaerobic selenate-respiring bacteria from aquatic sediments. PMID:17435005
Formation of tellurium nanocrystals during anaerobic growth of bacteria that use Te oxyanions as respiratory electron acceptors. PMID:17277198
On the origin of biochemistry at an alkaline hydrothermal vent. PMID:17255002
Growth yields in bacterial denitrification and nitrate ammonification. PMID:17209072
Hydrogen metabolism in Shewanella oneidensis MR-1. PMID:17189435
Thermodynamics-based metabolic flux analysis. PMID:17172310
Cyclohexane carboxylate and benzoate formation from crotonate in Syntrophus aciditrophicus. PMID:17158621
Microbial communities involved in anaerobic degradation of unsaturated or saturated long-chain fatty acids. PMID:17158619
Differential regulation of the three methanol methyltransferase isozymes in Methanosarcina acetivorans C2A. PMID:17015666
Characterization of (R)-2-hydroxyisocaproate dehydrogenase and a family III coenzyme A transferase involved in reduction of L-leucine to isocaproate by Clostridium difficile. PMID:16957230
Simulating the contribution of coaggregation to interspecies hydrogen fluxes in syntrophic methanogenic consortia. PMID:16820513
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. PMID:16738551
Methanosarcina spp. drive vinyl chloride dechlorination via interspecies hydrogen transfer. PMID:16598001
Electron transfer-driven ATP synthesis in Methanococcus voltae is not dependent on a proton electrochemical gradient. PMID:16593614
In vitro studies on reductive vinyl chloride dehalogenation by an anaerobic mixed culture. PMID:16535722
Complete reductive dechlorination of 1,2-dichloropropane by anaerobic bacteria. PMID:16535654
Sulfur production by obligately chemolithoautotrophic thiobacillus species. PMID:16535627
Cometabolic transformation and cleavage of nitrodiphenylamines by three newly isolated sulfate-reducing bacterial strains. PMID:16535317
Bacterial Dissimilatory Reduction of Arsenic(V) to Arsenic(III) in Anoxic Sediments. PMID:16535314
The importance of hydrogen in landfill fermentations. PMID:16535310
Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. PMID:16535298
Acetogenic capacities and the anaerobic turnover of carbon in a kansas prairie soil. PMID:16535237
Adaptation of psychrophilic and psychrotrophic sulfate-reducing bacteria to permanently cold marine environments. PMID:16535228
Growth of Strain SES-3 with Arsenate and Other Diverse Electron Acceptors. PMID:16535143
Interspecies Electron Transfer during Propionate and Butyrate Degradation in Mesophilic, Granular Sludge. PMID:16535082
Criteria and methodology for identifying respiratory denitrifiers. PMID:16534960
Pure-culture growth of fermentative bacteria, facilitated by H2 removal: bioenergetics and H2 production. PMID:16461652
Life by a new decarboxylation-dependent energy conservation mechanism with Na as coupling ion. PMID:16453537
Effect of inhibition of acetoclastic methanogenesis on growth of archaeal populations in an anoxic model environment. PMID:16391040
The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. PMID:16385054
Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum. PMID:16352836
Molecular basis of a bacterial consortium: interspecies catabolism of atrazine. PMID:16349478
Isolation, Growth, and Metabolism of an Obligately Anaerobic, Selenate-Respiring Bacterium, Strain SES-3. PMID:16349362
Anaerobic degradation of propionate by a mesophilic acetogenic bacterium in coculture and triculture with different methanogens. PMID:16349350
Novel processes for anaerobic sulfate production from elemental sulfur by sulfate-reducing bacteria. PMID:16349323
Substrate Preference in a Strain of Megasphaera elsdenii, a Ruminal Bacterium, and Its Implications in Propionate Production and Growth Competition. PMID:16349276
Thermophilic sulfate reduction in hydrothermal sediment of lake tanganyika, East Africa. PMID:16349249
Regulation of Product Formation in Bacteroides xylanolyticus X5-1 by Interspecies Electron Transfer. PMID:16349240
Complete oxidation of propionate, valerate, succinate, and other organic compounds by newly isolated types of marine, anaerobic, mesophilic, gram-negative, sulfur-reducing eubacteria. PMID:16348934
H(2)-CO(2)-Dependent Anaerobic O-Demethylation Activity in Subsurface Sediments and by an Isolated Bacterium. PMID:16348928
Growth of syntrophic propionate-oxidizing bacteria with fumarate in the absence of methanogenic bacteria. PMID:16348912
Dissimilatory Fe(III) Reduction by the Marine Microorganism Desulfuromonas acetoxidans. PMID:16348888
Inhibition of Butyrate Oxidation by Formate during Methanogenesis. PMID:16348880
Bacterial disproportionation of elemental sulfur coupled to chemical reduction of iron or manganese. PMID:16348835
Carbon Monoxide, Hydrogen, and Formate Metabolism during Methanogenesis from Acetate by Thermophilic Cultures of Methanosarcina and Methanothrix Strains. PMID:16348788
Reciprocal isomerization of butyrate and isobutyrate by the strictly anaerobic bacterium strain WoG13 and methanogenic isobutyrate degradation by a defined triculture. PMID:16348708
Redox Cycling of Iron Supports Growth and Magnetite Synthesis by Aquaspirillum magnetotacticum. PMID:16348681
Enrichment of Thermophilic Propionate-Oxidizing Bacteria in Syntrophy with Methanobacterium thermoautotrophicum or Methanobacterium thermoformicicum. PMID:16348632
Influence of CO(2)-HCO(3) Levels and pH on Growth, Succinate Production, and Enzyme Activities of Anaerobiospirillum succiniciproducens. PMID:16348570
Fermentation of Inulin by Clostridium thermosuccinogenes sp. nov., a Thermophilic Anaerobic Bacterium Isolated from Various Habitats. PMID:16348411
Anaerobic Oxidation of Toluene, Phenol, and p-Cresol by the Dissimilatory Iron-Reducing Organism, GS-15. PMID:16348226
CO(2) Incorporation and 4-Hydroxy-2-Methylbenzoic Acid Formation during Anaerobic Metabolism of m-Cresol by a Methanogenic Consortium. PMID:16348121
Requirement for a Microbial Consortium To Completely Oxidize Glucose in Fe(III)-Reducing Sediments. PMID:16348080
Selenate reduction to elemental selenium by anaerobic bacteria in sediments and culture: biogeochemical significance of a novel, sulfate-independent respiration. PMID:16348014
Diffusion of the Interspecies Electron Carriers H(2) and Formate in Methanogenic Ecosystems and Its Implications in the Measurement of K(m) for H(2) or Formate Uptake. PMID:16347966
Effects of Organic Acid Anions on the Growth and Metabolism of Syntrophomonas wolfei in Pure Culture and in Defined Consortia. PMID:16347899
Hydrogen and Formate Oxidation Coupled to Dissimilatory Reduction of Iron or Manganese by Alteromonas putrefaciens. PMID:16347876
Influence of alternate electron acceptors on the metabolic fate of hydroxybenzoate isomers in anoxic aquifer slurries. PMID:16347868
Presence of an unusual methanogenic bacterium in coal gasification waste. PMID:16347791
Product inhibition of butyrate metabolism by acetate and hydrogen in a thermophilic coculture. PMID:16347751
Photoexcretion and fate of glycolate in a hot spring cyanobacterial mat. PMID:16347684
Hydrogen partial pressures in a thermophilic acetate-oxidizing methanogenic coculture. PMID:16347656
Bioenergetic conditions of butyrate metabolism by a syntrophic, anaerobic bacterium in coculture with hydrogen-oxidizing methanogenic and sulfidogenic bacteria. PMID:16347645
High Pressure Enhances the Growth Rate of the Thermophilic Archaebacterium Methanococcus thermolithotrophicus without Extending Its Temperature Range. PMID:16347635
Reductive carboxylation of propionate to butyrate in methanogenic ecosystems. PMID:16347557
Control of Interspecies Electron Flow during Anaerobic Digestion: Significance of Formate Transfer versus Hydrogen Transfer during Syntrophic Methanogenesis in Flocs. PMID:16347526
Isolation and Characterization of a Thermophilic Bacterium Which Oxidizes Acetate in Syntrophic Association with a Methanogen and Which Grows Acetogenically on H(2)-CO(2). PMID:16347518
Control of Interspecies Electron Flow during Anaerobic Digestion: Role of Floc Formation in Syntrophic Methanogenesis. PMID:16347517
Calorimetric versus Growth Microbial Analysis of Cellulase Enzymes Acting on Cellulose. PMID:16347508
Methane Production from Formate by Syntrophic Association of Methanobacterium bryantii and Desulfovibrio vulgaris JJ. PMID:16347251
Rapid microbial mineralization of toluene and 1,3-dimethylbenzene in the absence of molecular oxygen. PMID:16347188
Acetate Synthesis from H(2) plus CO(2) by Termite Gut Microbes. PMID:16347157
Effect of nitrate on biogenic sulfide production. PMID:16347078
A new sulfur-reducing, extremely thermophilic eubacterium from a submarine thermal vent. PMID:16347075
Growth of methanogenic bacteria in pure culture with 2-propanol and other alcohols as hydrogen donors. PMID:16347050
Method for detection of microorganisms that produce gaseous nitrogen oxides. PMID:16347040
Sulfate reduction relative to methane production in high-rate anaerobic digestion: microbiological aspects. PMID:16347019
Gas metabolism evidence in support of the juxtaposition of hydrogen-producing and methanogenic bacteria in sewage sludge and lake sediments. PMID:16346879
PA-1, a Versatile Anaerobe Obtained in Pure Culture, Catabolizes Benzenoids and Other Compounds in Syntrophy with Hydrogenotrophs, and P-2 plus Wolinella sp. Degrades Benzenoids. PMID:16346852
Biological and abiological sulfur reduction at high temperatures. PMID:16346781
Intermediary Metabolism in Clostridium acetobutylicum: Levels of Enzymes Involved in the Formation of Acetate and Butyrate. PMID:16346566
Methanogenesis in a Thermophilic (58 degrees C) Anaerobic Digestor: Methanothrix sp. as an Important Aceticlastic Methanogen. PMID:16346518
Effect of H(2)-CO(2) on Methanogenesis from Acetate or Methanol in Methanosarcina spp. PMID:16346361
Effects of metals on methanogenesis, sulfate reduction, carbon dioxide evolution, and microbial biomass in anoxic salt marsh sediments. PMID:16346294
Pathways of propionate degradation by enriched methanogenic cultures. PMID:16346281
Methanogenesis from methanol and methylamines and acetogenesis from hydrogen and carbon dioxide in the sediments of a eutrophic lake. PMID:16346271
Production and consumption of hydrogen in a eutrophic lake. PMID:16346198
Sulfate reducers can outcompete methanogens at freshwater sulfate concentrations. PMID:16346164
Improved method for determination of respiring individual microorganisms in natural waters. PMID:16346025
Conversion of Cellulose to Methane and Carbon Dioxide by Triculture of Acetivibrio cellulolyticus, Desulfovibrio sp., and Methanosarcina barkeri. PMID:16345841
Volatile Fatty acids and hydrogen as substrates for sulfate-reducing bacteria in anaerobic marine sediment. PMID:16345815
Seasonal rates of methane oxidation in anoxic marine sediments. PMID:16345784
Syntrophomonas wolfei gen. nov. sp. nov., an Anaerobic, Syntrophic, Fatty Acid-Oxidizing Bacterium. PMID:16345745
Anaerobic Degradation of Lactate by Syntrophic Associations of Methanosarcina barkeri and Desulfovibrio Species and Effect of H(2) on Acetate Degradation. PMID:16345708
Propionate-Degrading Bacterium, Syntrophobacter wolinii sp. nov. gen. nov., from Methanogenic Ecosystems. PMID:16345640
Nitrate dissimilation under microaerophilic conditions by a magnetic spirillum. PMID:16345620
Isolation and Characterization of a Thermophilic Strain of Methanosarcina Unable to Use H(2)-CO(2) for Methanogenesis. PMID:16345468
Desulfotomaculum and Methanobacterium spp. dominate a 4- to 5-kilometer-deep fault. PMID:16332873
Effect of temperature on anaerobic ethanol oxidation and methanogenesis in acidic peat from a northern wetland. PMID:16332802
Coaggregation facilitates interspecies hydrogen transfer between Pelotomaculum thermopropionicum and Methanothermobacter thermautotrophicus. PMID:16332758
Proteomic analysis reveals the participation of energy- and stress-related proteins in the response of Pseudomonas putida DOT-T1E to toluene. PMID:16109935
Biological control of hog waste odor through stimulated microbial Fe(III) reduction. PMID:16085869
Loss of the mtr operon in Methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway. PMID:16024727
Characterization of an archaeal malic enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. PMID:15876562
Temperature dependence of methyl-coenzyme M reductase activity and of the formation of the methyl-coenzyme M reductase red2 state induced by coenzyme B. PMID:15846525
Evidence for involvement of an electron shuttle in electricity generation by Geothrix fermentans. PMID:15812057
Anaerobic, nitrate-dependent oxidation of U(IV) oxide minerals by the chemolithoautotrophic bacterium Thiobacillus denitrificans. PMID:15812053
Toxicity of nitrite toward mesophilic and thermophilic sulphate-reducing, methanogenic and syntrophic populations in anaerobic sludge. PMID:15759145
The acetate switch. PMID:15755952
Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow: effect of temperature. PMID:15692859
Molecular characterization of a dechlorinating community resulting from in situ biostimulation in a trichloroethene-contaminated deep, fractured basalt aquifer and comparison to a derivative laboratory culture. PMID:15574933
Anaerobic growth of Methanosarcina acetivorans C2A on carbon monoxide: an unusual way of life for a methanogenic archaeon. PMID:15550538
Dissimilatory oxidation and reduction of elemental sulfur in thermophilic archaea. PMID:15168612
Dissimilatory arsenate reduction with sulfide as electron donor: experiments with mono lake water and Isolation of strain MLMS-1, a chemoautotrophic arsenate respirer. PMID:15128527
The sulphur oxygenase reductase from Acidianus ambivalens is a multimeric protein containing a low-potential mononuclear non-haem iron centre. PMID:15030315
Selenocysteine-containing proteins in anaerobic benzoate metabolism of Desulfococcus multivorans. PMID:15028701
Description of Treponema azotonutricium sp. nov. and Treponema primitia sp. nov., the first spirochetes isolated from termite guts. PMID:15006748
Energy conservation in acetogenic bacteria. PMID:14602585
Toxicity of Al to Desulfovibrio desulfuricans. PMID:12839782
A simple energy-conserving system: proton reduction coupled to proton translocation. PMID:12792025
Influences of pond geochemistry, temperature, and freeze-thaw on terminal anaerobic processes occurring in sediments of six ponds of the McMurdo Ice Shelf, near Bratina Island, Antarctica. PMID:12514045
Isolation and characterization of a sulfur-oxidizing chemolithotroph growing on crude oil under anaerobic conditions. PMID:12513984
Bioenergetic properties of the thermoalkaliphilic Bacillus sp. strain TA2.A1. PMID:12511491
Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions. PMID:12458737
Growth of iron(III)-reducing bacteria on clay minerals as the sole electron acceptor and comparison of growth yields on a variety of oxidized iron forms. PMID:12450850
Carbon monoxide cycling by Desulfovibrio vulgaris Hildenborough. PMID:12374824
Nitrous oxide formation in the Colne estuary in England: the central role of nitrite. PMID:12324378
The Microbial Logic behind the Prevalence of Incomplete Oxidation of Organic Compounds by Acetogenic Bacteria in Methanogenic Environments. PMID:12032612
Propionate formation by Opitutus terrae in pure culture and in mixed culture with a hydrogenotrophic methanogen and implications for carbon fluxes in anoxic rice paddy soil. PMID:11916740
Nitrous oxide formation in the Colne estuary, England: the central role of nitrite. PMID:11872474
Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. PMID:11823233
Benzoate fermentation by the anaerobic bacterium Syntrophus aciditrophicus in the absence of hydrogen-using microorganisms. PMID:11722901
Mechanism of ATP-driven electron transfer catalyzed by the benzene ring-reducing enzyme benzoyl-CoA reductase. PMID:11698658
Reduced coenzyme F420: heterodisulfide oxidoreductase, a proton- translocating redox system in methanogenic bacteria. PMID:11607121
Copper-induced inhibition of growth of Desulfovibrio desulfuricans G20: assessment of its toxicity and correlation with those of zinc and lead. PMID:11571183
Anaerobic mineralization of toluene by enriched sediments with quinones and humus as terminal electron acceptors. PMID:11571145
Oligoglyceric acid synthesis by autocondensation of glyceroyl thioester. PMID:11542077
Prebiotic formation of 'energy-rich' thioesters from glyceraldehyde and N-acetylcysteine. PMID:11541968
Model of early self-replication based on covalent complementarity for a copolymer of glycerate-3-phosphate and glycerol-3-phosphate. PMID:11538679
Origin of fatty acid synthesis: thermodynamics and kinetics of reaction pathways. PMID:11538263
Prebiotic polymerization: oxidative polymerization of 2,3-dimercapto-1-propanol on the surface of iron(III) hydroxide oxide. PMID:11536681
Geochemical constraints on chemolithoautotrophic reactions in hydrothermal systems. PMID:11536667
How long did it take for life to begin and evolve to cyanobacteria? PMID:11536653
Prebiotic sugar synthesis: hexose and hydroxy acid synthesis from glyceraldehyde catalyzed by iron(III) hydroxide oxide. PMID:11536502
The sugar model: catalytic flow reactor dynamics of pyruvaldehyde synthesis from triose catalyzed by poly-l-lysine contained in a dialyzer. PMID:11434102
The sugar model: catalysis by amines and amino acid products. PMID:11296525
Relationship of hydrogen bioavailability to chromate reduction in aquifer sediments. PMID:11282599
Anaerobic initial reaction of n-alkanes in a denitrifying bacterium: evidence for (1-methylpentyl)succinate as initial product and for involvement of an organic radical in n-hexane metabolism. PMID:11160102
Possible ecosystems and the search for life on Europa. PMID:11158549
Diversity of sulfur isotope fractionations by sulfate-reducing prokaryotes. PMID:11157259
Initiation of anaerobic degradation of p-cresol by formation of 4-hydroxybenzylsuccinate in desulfobacterium cetonicum. PMID:11133971
Carbon flux distribution and kinetics of cellulose fermentation in steady-state continuous cultures of Clostridium cellulolyticum on a chemically defined medium. PMID:11114908
Sulfate reduction and possible aerobic metabolism of the sulfate-reducing bacterium Desulfovibrio oxyclinae in a chemostat coculture with Marinobacter sp. Strain MB under exposure to increasing oxygen concentrations. PMID:11055957
Effect of temperature on carbon and electron flow and on the archaeal community in methanogenic rice field soil. PMID:11055925
Tetrahydrofolate and tetrahydromethanopterin compared: functionally distinct carriers in C1 metabolism. PMID:10970772
Thiosulfate disproportionation by Desulfotomaculum thermobenzoicum. PMID:10919837
Energetics of syntrophic propionate oxidation in defined batch and chemostat cocultures. PMID:10877789
Sugars as the optimal biosynthetic carbon substrate of aqueous life throughout the universe. PMID:10836263
Another unusual type of citric acid cycle enzyme in Helicobacter pylori: the malate:quinone oxidoreductase. PMID:10809701
Electricity generation in microbial fuel cells using neutral red as an electronophore. PMID:10742202
Evidence for the presence of an F-type ATP synthase involved in sulfate respiration in Desulfovibrio vulgaris. PMID:10735863
Partitioning effects during terminal carbon and electron flow in sediments of a low-salinity meltwater pond near Bratina Island, McMurdo Ice Shelf, Antarctica. PMID:10584008
Relative importance of trophic group concentrations during anaerobic degradation of volatile fatty acids. PMID:10543816
Simultaneous reduction of nitrate and selenate by cell suspensions of selenium-respiring bacteria. PMID:10508064
Bioenergetics of the Archaea. PMID:10477309
Fraction of electrons consumed in electron acceptor reduction and hydrogen thresholds as indicators of halorespiratory physiology. PMID:10473415
Sulfidogenesis from 2-aminoethanesulfonate (taurine) fermentation by a morphologically unusual sulfate-reducing bacterium, Desulforhopalus singaporensis sp. nov. PMID:10427015
Microbial utilization of electrically reduced neutral red as the sole electron donor for growth and metabolite production. PMID:10388683
Energy conservation by the H2:heterodisulfide oxidoreductase from Methanosarcina mazei Gö1: identification of two proton-translocating segments. PMID:10383977
Utilization of electrically reduced neutral red by Actinobacillus succinogenes: physiological function of neutral red in membrane-driven fumarate reduction and energy conservation. PMID:10198002
Anaerobic degradation of phthalate isomers by methanogenic consortia. PMID:10049876
Isolation from estuarine sediments of a Desulfovibrio strain which can grow on lactate coupled to the reductive dehalogenation of 2,4, 6-tribromophenol. PMID:10049873
An unusual oxygen-sensitive, iron- and zinc-containing alcohol dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus. PMID:9973342
Anaerobic benzene biodegradation linked to nitrate reduction. PMID:9925578
Enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse European sediments. PMID:9835573
Evidence of two oxidative reaction steps initiating anaerobic degradation of resorcinol (1,3-dihydroxybenzene) by the denitrifying bacterium Azoarcus anaerobius. PMID:9658009
Prebiotic amino acid thioester synthesis: thiol-dependent amino acid synthesis from formose substrates (formaldehyde and glycolaldehyde) and ammonia. PMID:9611766
Growth of geobacter sulfurreducens with acetate in syntrophic cooperation with hydrogen-oxidizing anaerobic partners. PMID:9603840
Reduction of 3-chlorobenzoate, 3-bromobenzoate, and benzoate to corresponding alcohols by Desulfomicrobium escambiense, isolated from a 3-chlorobenzoate-dechlorinating coculture. PMID:9471962
Production of succinic acid through overexpression of NAD(+)-dependent malic enzyme in an Escherichia coli mutant. PMID:9212416
Cultivation of Escherichia coli with mixtures of 3-phenylpropionic acid and glucose: steady-state growth kinetics. PMID:9212411
Degradation of bis(2-ethylhexyl) phthalate constituents under methanogenic conditions. PMID:9188196
Energetics of syntrophic cooperation in methanogenic degradation. PMID:9184013
Taurine reduction in anaerobic respiration of Bilophila wadsworthia RZATAU. PMID:9143131
The acetate kinase of Clostridum acetobutylicum strain P262. PMID:9082921
Anaerobic production of alginate by Pseudomonas aeruginosa: alginate restricts diffusion of oxygen. PMID:8955420
Characterization of Desulfitobacterium chlororespirans sp. nov., which grows by coupling the oxidation of lactate to the reductive dechlorination of 3-chloro-4-hydroxybenzoate. PMID:8837437
Sodium-dependent succinate decarboxylation by a new anaerobic bacterium belonging to the genus Peptostreptococcus. PMID:8836437
Granulation in thermophilic upflow anaerobic sludge blanket (UASB) reactors. PMID:8821789
Stimulation of conversion rates and bacterial activity in a silage-fed two-phase biogas process by initiating liquid recirculation. PMID:8821787
Alanine as an end product during fermentation of monosaccharides by Clostridium strain P2. PMID:8821781
Generation of a proton motive force by the anaerobic oxalate-degrading bacterium Oxalobacter formigenes. PMID:8779588
Effect of nitrate on the autotrophic metabolism of the acetogens Clostridium thermoautotrophicum and Clostridium thermoaceticum. PMID:8755890
The relationship between growth enhancement and pet expression in Escherichia coli. PMID:8669901
Characterization of 2-ketoisovalerate ferredoxin oxidoreductase, a new and reversible coenzyme A-dependent enzyme involved in peptide fermentation by hyperthermophilic archaea. PMID:8550513
Sulphate reducing bacteria and hydrogen metabolism in the human large intestine. PMID:8491386
Isolation and characterization of a new spore-forming sulfate-reducing bacterium growing by complete oxidation of catechol. PMID:8481092
Effects of acetate, propionate, and butyrate on the thermophilic anaerobic degradation of propionate by methanogenic sludge and defined cultures. PMID:8476278
Bioenergetics of sulfur reduction in the hyperthermophilic archaeon Pyrococcus furiosus. PMID:8449888
Purine metabolism in Methanococcus vannielii. PMID:8376322
Effects of hydrogen and formate on the degradation of propionate and butyrate in thermophilic granules from an upflow anaerobic sludge blanket reactor. PMID:8368842
Anaerobic oxidation of phenylacetate and 4-hydroxyphenylacetate to benzoyl-coenzyme A and CO2 in denitrifying Pseudomonas sp. Evidence for an alpha-oxidation mechanism. PMID:8352646
Function of methylcobalamin: coenzyme M methyltransferase isoenzyme II in Methanosarcina barkeri. PMID:8352643
Biology, ecology, and biotechnological applications of anaerobic bacteria adapted to environmental stresses in temperature, pH, salinity, or substrates. PMID:8336675
Dehydrogenases involved in the conversion of succinate to 4-hydroxybutanoate by Clostridium kluyveri. PMID:8328804
Dichloromethane as the sole carbon source for an acetogenic mixed culture and isolation of a fermentative, dichloromethane-degrading bacterium. PMID:8285685
Characterization of enzymatic reduction of hexavalent chromium by Escherichia coli ATCC 33456. PMID:8285683
In situ growth and activity and modes of penetration of Escherichia coli in unconsolidated porous materials. PMID:8285677
Nitrate as a preferred electron sink for the acetogen Clostridium thermoaceticum. PMID:8253688
Regulation of the Bacillus subtilis acetate kinase gene by CcpA. PMID:8226682
Study of constancy of hydrogen-consuming flora of human colon. PMID:8131685
Toxic effects of pollutants on the mineralization of acetate in methanogenic river sediment. PMID:8130416
Anaerobic degradation of toluene and o-xylene by a methanogenic consortium. PMID:8117084
Importance of cobalt for individual trophic groups in an anaerobic methanol-degrading consortium. PMID:8117078
Fermentative degradation of triethanolamine by a homoacetogenic bacterium. PMID:8085913
Anaerobic degradation of methylmercaptan and dimethyl sulfide by newly isolated thermophilic sulfate-reducing bacteria. PMID:8074524
Purification of acetaldehyde dehydrogenase and alcohol dehydrogenases from Thermoanaerobacter ethanolicus 39E and characterization of the secondary-alcohol dehydrogenase (2 degrees Adh) as a bifunctional alcohol dehydrogenase--acetyl-CoA reductive thioesterase. PMID:8068002
D-xylose catabolism in Bacteroides xylanolyticus X5-1. PMID:8048843
Fermentation of phenoxyethanol to phenol and acetate by a homoacetogenic bacterium. PMID:7979874
Anaerobic degradation of catechol by Desulfobacterium sp. strain Cat2 proceeds via carboxylation to protocatechuate. PMID:7944370
Effect of inducible thrB expression on amino acid production in Corynebacterium lactofermentum ATCC 21799. PMID:7887627
Regulation of the hemA gene during 5-aminolevulinic acid formation in Pseudomonas aeruginosa. PMID:7883699
Bacterial sodium ion-coupled energetics. PMID:7832594
Catabolic and anabolic enzyme activities and energetics of acetone metabolism of the sulfate-reducing bacterium Desulfococcus biacutus. PMID:7814315
Metabolic pathways and energetics of the acetone-oxidizing, sulfate-reducing bacterium, Desulfobacterium cetonicum. PMID:7778975
Anaerobic biodegradation of methyl esters by Acetobacterium woodii and Eubacterium limosum. PMID:7765371
Microbiological aspects of the removal of chlorinated hydrocarbons from air. PMID:7764923
Electron transport phosphorylation driven by glyoxylate respiration with hydrogen as electron donor in membrane vesicles of a glyoxylate-fermenting bacterium. PMID:7763134
Sequence analysis of the phs operon in Salmonella typhimurium and the contribution of thiosulfate reduction to anaerobic energy metabolism. PMID:7751291
Anaerobic digestion of ice-cream wastewater: a comparison of single and two-phase reactor systems. PMID:7749282
Anaerobic oxidation of ammonium is a biologically mediated process. PMID:7747947
Oxygen regulated gene expression in facultatively anaerobic bacteria. PMID:7747938
Metabolic interactions between anaerobic bacteria in methanogenic environments. PMID:7747937
Metabolism in hyperthermophilic microorganisms. PMID:7747936
Glycine metabolism in anaerobes. PMID:7747933
Metabolism of homocetogens. PMID:7747932
Metabolism of sulfate-reducing prokaryotes. PMID:7747930
Enhanced biodegradation of aromatic pollutants in cocultures of anaerobic and aerobic bacterial consortia. PMID:7741529
Anaerobic digestion and wastewater treatment systems. PMID:7741528
Anaerobic treatment of sulphate-containing waste streams. PMID:7741527
Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. PMID:7710331
Anaerobic degradation of malonate via malonyl-CoA by Sporomusa malonica, Klebsiella oxytoca, and Rhodobacter capsulatus. PMID:7710283
Complete oxidation of toluene under strictly anoxic conditions by a new sulfate-reducing bacterium. PMID:7686000
Comparative energetics of glucose and xylose metabolism in ethanologenic recombinant Escherichia coli B. PMID:7668846
Purification, characterization, and metabolic function of tungsten-containing aldehyde ferredoxin oxidoreductase from the hyperthermophilic and proteolytic archaeon Thermococcus strain ES-1. PMID:7642503
Effects of elemental sulfur on the metabolism of the deep-sea hyperthermophilic archaeon Thermococcus strain ES-1: characterization of a sulfur-regulated, non-heme iron alcohol dehydrogenase. PMID:7642502
Pathway of butyrate catabolism by Desulfobacterium cetonicum. PMID:7601855
Purification and characterization of acetylene hydratase of Pelobacter acetylenicus, a tungsten iron-sulfur protein. PMID:7592321
Evidence for anaerobic syntrophic benzoate degradation threshold and isolation of the syntrophic benzoate degrader. PMID:7574591
Primary structure and eubacterial relationships of the pyruvate:ferredoxin oxidoreductase of the amitochondriate eukaryote Trichomonas vaginalis. PMID:7563125
Characteristics of anaerobic oxalate-degrading enrichment cultures from the rumen. PMID:7425629
Isolation and some characteristics of anaerobic oxalate-degrading bacteria from the rumen. PMID:7425628
Utilization of (E)-2-butenoate (crotonate) by Clostridium kluyveri and some other Clostridium species. PMID:7387331
Growth yields and energy generation by Campylobacter sputorum subspecies bubulus during growth in continuous culture with different hydrogen acceptors. PMID:7369827
Origin of hydrogen in methane produced by Methanobacterium thermoautotrophicum. PMID:7364716
Acetyl coenzyme A and coenzyme a contents of growing clostridium kluyveri as determined by isotope assays. PMID:7332407
Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. I. Isolation of new sulfate-reducing bacteria enriched with acetate from saline environments. Description of Desulfobacter postgatei gen. nov., sp. nov. PMID:7283636
Syntrophic association of a butyrate-degrading bacterium and methanosarcina enriched from bovine rumen fluid. PMID:7224635
Energy metabolism in Capnocytophaga ochracea. PMID:7216425
Oxidation of short-chain fatty acids by sulfate-reducing bacteria in freshwater and in marine sediments. PMID:7212933
Degradation patterns and intermediates in the anaerobic digestion of glucose: experiments with 14C-labeled substrates. PMID:7149700
Pyruvate oxidation by the Reiter strain of Treponema phagedenis. PMID:7142105
Fumarate reduction and product formation by the Reiter strain of Treponema phagedenis. PMID:7142104
Evolution of major metabolic innovations in the precambrian. PMID:7133672
Regulation of lactate metabolism in the rumen. PMID:7048723
Carbon monoxide metabolism of the methylotrophic acidogen Butyribacterium methylotrophicum. PMID:7033210
The activities of hydrogenase and enoate reductase in two Clostridium species, their interrelationship and dependence on growth conditions. PMID:7004377
Factors affecting the cellular expression of bacterial luciferase. PMID:6971634
Anaerobic growth of halobacteria. PMID:6933439
Fermentative degradation of polyethylene glycol by a strictly anaerobic, gram-negative, nonsporeforming bacterium, Pelobacter venetianus sp. nov. PMID:6881964
Methane oxidation by Nitrosomonas europaea. PMID:6870854
Purine and glycine metabolism by purinolytic clostridia. PMID:6833177
Characterization of a new type of dissimilatory sulfite reductase present in Thermodesulfobacterium commune. PMID:6826522
Energy coupling to nitrite respiration in the sulfate-reducing bacterium Desulfovibrio gigas. PMID:6822477
Oxidation of hydrogen and reduction of methanol to methane is the sole energy source for a methanogen isolated from human feces. PMID:6822473
Isolation and characterization of new strains of cholesterol-reducing bacteria from baboons. PMID:6798934
Comparison of unitrophic and mixotrophic substrate metabolism by acetate-adapted strain of Methanosarcina barkeri. PMID:6798021
Methane production by the membranous fraction of Methanobacterium thermoautotrophicum. PMID:6778475
Kinetic parameters of lactate dehydrogenases of some rumen bacterial species, the anaerobic ciliate Isotricha prostoma and mixed rumen microorganisms. PMID:6778389
Physiology of dark fermentative growth of Rhodopseudomonas capsulata. PMID:6769916
Denitrification: ecological niches, competition and survival. PMID:6762848
Separation and distribution of thiosulfate-oxidizing enzyme, tetrathionate reductase, and thiosulfate reductase in extracts of marine heterotroph strain 16B. PMID:6630148
Degradation of ethylene glycol and polyethylene glycols by methanogenic consortia. PMID:6614903
Thermodynamic efficiency of microbial growth is low but optimal for maximal growth rate. PMID:6572006
Genetic and physical characterization of lambda transducing phages (lambda frdA) containing the fumarate reductase gene of Escherichia coli K12. PMID:6446651
Pseudomonas aeruginosa mutants affected in anaerobic growth on arginine: evidence for a four-gene cluster encoding the arginine deiminase pathway. PMID:6438064
Rapidly growing rumen methanogenic organism that synthesizes coenzyme M and has a high affinity for formate. PMID:6433795
Nonenzymatic formation of "energy-rich" lactoyl and glyceroyl thioesters from glyceraldehyde and a thiol. PMID:6433034
Formaldehyde oxidation and methanogenesis. PMID:6427185
Arginine degradation in Pseudomonas aeruginosa mutants blocked in two arginine catabolic pathways. PMID:6423933
Single-carbon catabolism in acetogens: analysis of carbon flow in Acetobacterium woodii and Butyribacterium methylotrophicum by fermentation and 13C nuclear magnetic resonance measurement. PMID:6411684
Aerobic denitrification--old wine in new bottles? PMID:6397132
Energy conservation in acidophilic bacteria. PMID:6363899
On the occurrence of enoate reductase and 2-oxo-carboxylate reductase in clostridia and some observations on the amino acid fermentation by Peptostreptococcus anaerobius. PMID:6354130
Energy transduction and solute transport in streptococci. PMID:6312880
Nutritional requirements of Corynebacterium pyogenes. PMID:6288763
Electron transport-linked proton translocation at nitrite reduction in Campylobacter sputorum subspecies bubulus. PMID:6280634
Molecular cloning of the fnr gene of Escherichia coli K12. PMID:6261088
The role of the membrane-bound hydrogenase in the energy-conserving oxidation of molecular hydrogen by Escherichia coli. PMID:6249272
Evolutionary roots of catalysis by nicotinamide and flavins in C-H oxidoreductases and in photosynthesis. PMID:6216447
Two sites of oxygen control in induced synthesis of respiratory nitrate reductase in Escherichia coli. PMID:6174498
Biosynthesis of vitamin K (menaquinone) in bacteria. PMID:6127606
Effects of estradiol and progesterone on Bacteroides melaninogenicus and Bacteroides gingivalis. PMID:6119293
Acetate thiokinase and the assimilation of acetate in methanobacterium thermoautotrophicum. PMID:6111300
A sodium-stimulated membrane-bound fumarate reductase system in Bacteroides amylophilus. PMID:4074073
Metabolic and energetic aspects of the growth of Clostridium butyricum on glucose in chemostat culture. PMID:4062485
A sodium ion gradient as energy source for Peptostreptococcus asaccharolyticus. PMID:4037980
Interaction of acetogens and methanogens in anaerobic freshwater sediments. PMID:4004224
[Metabolic zonation of liver parenchyma. Regulation of the glucostat of the liver]. PMID:3990823
Methanosarcina mutant unable to produce methane or assimilate carbon from acetate. PMID:3840474
Methanogenesis and ATP synthesis in a protoplast system of Methanobacterium thermoautotrophicum. PMID:3782030
Metabolism of polyethylene glycol by two anaerobic bacteria, Desulfovibrio desulfuricans and a Bacteroides sp. PMID:3777930
Carbon monoxide-driven electron transport in Clostridium thermoautotrophicum membranes. PMID:3680181
The triose model: glyceraldehyde as a source of energy and monomers for prebiotic condensation reactions. PMID:3627761
Additional characteristics of one-carbon-compound utilization by Eubacterium limosum and Acetobacterium woodii. PMID:3579266
Physiological adaptations of anaerobic bacteria to low pH: metabolic control of proton motive force in Sarcina ventriculi. PMID:3571164
Acetone-butanol fermentation revisited. PMID:3540574
The functional localization of cytochromes b in the respiratory chain of anaerobically grown Proteus mirabilis. PMID:3524446
Preparation of cell-free extracts and the enzymes involved in fatty acid metabolism in Syntrophomonas wolfei. PMID:3459726
Methanogenic degradation of acetone by an enrichment culture. PMID:3442449
Growth yield increase linked to reductive dechlorination in a defined 3-chlorobenzoate degrading methanogenic coculture. PMID:3442447
Regulation of carbon and electron flow in Propionispira arboris: relationship of catabolic enzyme levels to carbon substrates fermented during propionate formation via the methylmalonyl coenzyme A pathway. PMID:3410821
Energy-dependent transport of nickel by Clostridium pasteurianum. PMID:3335482
Energetics of C1-compound metabolism. PMID:3314701
Tetrathionate reduction and production of hydrogen sulfide from thiosulfate. PMID:3299028
Regulation of carbon flow in Selenomonas ruminantium grown in glucose-limited continuous culture. PMID:3182729
Pathway and sites for energy conservation in the metabolism of glucose by Selenomonas ruminantium. PMID:3141385
Regulation of arginine-ornithine exchange and the arginine deiminase pathway in Streptococcus lactis. PMID:3119567
Carbon monoxide-dependent chemolithotrophic growth of Clostridium thermoautotrophicum. PMID:3116936
The phs gene and hydrogen sulfide production by Salmonella typhimurium. PMID:3108233
Methanogens and the diversity of archaebacteria. PMID:3104748
Yeast PAPS reductase: properties and requirements of the purified enzyme. PMID:3060034
Control of enzyme synthesis in the oxalurate catabolic pathway of Streptococcus faecalis ATCC 11700: evidence for the existence of a third carbamate kinase. PMID:3024601
Phorphorylative electron transport chains lacking a cytochrome bc1 complex. PMID:3015897
Participation of cytochromes in some oxidation-reduction systems in Campylobacter fetus. PMID:2995315
In bacteria which grow on simple reductants, generation of a proton gradient involves extracytoplasmic oxidation of substrate. PMID:2989673
Differential roles for menaquinone and demethylmenaquinone in anaerobic electron transport of E. coli and their fnr-independent expression. PMID:2849923
Structure and function of a menaquinone involved in electron transport in membranes of Clostridium thermoautotrophicum and Clostridium thermoaceticum. PMID:2808299
Glucose metabolism and NADH recycling by Treponema hyodysenteriae, the agent of swine dysentery. PMID:2802610
Electron transport and electrochemical proton gradient in membrane vesicles of Clostridium thermoautotrophicum. PMID:2708323
Reconstitution and properties of a coenzyme F420-mediated formate hydrogenlyase system in Methanobacterium formicicum. PMID:2661536
Characterization of anaerobic sulfite reduction by Salmonella typhimurium and purification of the anaerobically induced sulfite reductase. PMID:2656637
Ammonia assimilation pathways in nitrogen-fixing Clostridium kluyverii and Clostridium butyricum. PMID:2564848
Isolation, characterization, and biological activity of the Methanococcus thermolithotrophicus ferredoxin. PMID:2540148
Cloning, expression, and nucleotide sequence of the Escherichia coli K-12 ackA gene. PMID:2536666
Sodium dependence of acetate formation by the acetogenic bacterium Acetobacterium woodii. PMID:2507527
Coupled enzymatic production of sulfite, thiosulfate, and hydrogen sulfide from sulfur: purification and properties of a sulfur oxygenase reductase from the facultatively anaerobic archaebacterium Desulfurolobus ambivalens. PMID:2493451
Sodium ion transport decarboxylases and other aspects of sodium ion cycling in bacteria. PMID:2444866
Oxidation of benzaldehydes to benzoic acid derivatives by three Desulfovibrio strains. PMID:2389937
Alternative pathways for hydrogen disposal during fermentation in the human colon. PMID:2379871
Characterization of the H2- and CO-dependent chemolithotrophic potentials of the acetogens Clostridium thermoaceticum and Acetogenium kivui. PMID:2376565
Efficiency factors and ATP/ADP ratios in nitrogen-fixing Bacillus polymyxa and Bacillus azotofixans. PMID:2318806
Purification and properties of an acetoacetyl coenzyme A-reacting phosphotransbutyrylase from Clostridium beijerinckii ("Clostridium butylicum") NRRL B593. PMID:2317039
Pyrogallol-to-phloroglucinol conversion and other hydroxyl-transfer reactions catalyzed by cell extracts of Pelobacter acidigallici. PMID:2298693
Evolution of the first metabolic cycles. PMID:2296579
Reductive dehalogenation of carbon tetrachloride by Escherichia coli K-12. PMID:2268147
Anaerobic degradation of acetone by Desulfococcus biacutus spec. nov. PMID:2244787
Clostridium homopropionicum sp. nov., a new strict anaerobe growing with 2-, 3-, or 4-hydroxybutyrate. PMID:2244786
Overproduction of acetate kinase activates the phosphate regulon in the absence of the phoR and phoM functions in Escherichia coli. PMID:2158965
Isolation of Clostridium propionicum strain 19acry3 and further characteristics of the species. PMID:1953298
Electrogenic L-malate transport by Lactobacillus plantarum: a basis for energy derivation from malolactic fermentation. PMID:1917854
Acetate catabolism in the dissimilatory iron-reducing isolate GS-15. PMID:1901574
Bacteriological composition and structure of granular sludge adapted to different substrates. PMID:1892385
Relationship between hydrogen consumption, dehalogenation, and the reduction of sulfur oxyanions by Desulfomonile tiedjei. PMID:1892383
Fermentation of L-tartrate by a newly isolated gram-negative glycolytic bacterium. PMID:1867475
Characterization of metabolic performance of methanogenic granules treating brewery wastewater: role of sulfate-reducing bacteria. PMID:1785921
Reductive dechlorination of high concentrations of tetrachloroethene to ethene by an anaerobic enrichment culture in the absence of methanogenesis. PMID:1768101
Microbial reduction of manganese and iron: new approaches to carbon cycling. PMID:1610166
Carboxylation of phenylphosphate by phenol carboxylase, an enzyme system of anaerobic phenol metabolism. PMID:1592817
Energy conservation in malolactic fermentation by Lactobacillus plantarum and Lactobacillus sake. PMID:1510572
Growth yield increase and ATP formation linked to succinate decarboxylation in Veillonella parvula. PMID:1510569
Fermentative degradation of glutarate via decarboxylation by newly isolated strictly anaerobic bacteria. PMID:1510562
Clostridium neopropionicum sp. nov., a strict anaerobic bacterium fermenting ethanol to propionate through acrylate pathway. PMID:1510558
Enzymes involved in anaerobic degradation of acetone by a denitrifying bacterium. PMID:1368470
Dichloromethane utilized by an anaerobic mixed culture: acetogenesis and methanogenesis. PMID:1368154
Fermentative degradation of dipicolinic acid (pyridine-2,6-dicarboxylic acid) by a defined coculture of strictly anaerobic bacteria. PMID:1368138
Thermodynamic evidence of trophic microniches in methanogenic granular sludge-bed reactors. PMID:1366365
Nisin dissipates the proton motive force of the obligate anaerobe Clostridium sporogenes PA 3679. PMID:1325140
Hydrogen-oxidizing electron transport components in the hyperthermophilic archaebacterium Pyrodictium brockii. PMID:1309514
Oxidoreductases involved in cell carbon synthesis of Methanobacterium thermoautotrophicum. PMID:914779
Growth of desulfovibrio in lactate or ethanol media low in sulfate in association with H2-utilizing methanogenic bacteria. PMID:879775
Acetate assimilation pathway of Methanosarcina barkeri. PMID:762016
Function of fumarate reductase in methanogenic bacteria (Methanobacterium). PMID:727856
Acetate metabolism in Methanosarcina barkeri. PMID:727855
Carbon monoxide oxidation by Clostridium thermoaceticum and Clostridium formicoaceticum. PMID:711675
Effect of medium composition on the growth and asparaginase production of Vibrio succinogenes. PMID:697359
Kinetic parameters and relative turnovers of some important catabolic reactions in digesting sludge. PMID:697354
Growth of a photosynthetic bacterium anaerobically in darkness, supported by "oxidant-dependent" sugar fermentation. PMID:678017
Inhibition of methanogenesis by sulphate reducing bacteria competing for transferred hydrogen. PMID:678014
Studies on an acetate-fermenting strain of Methanosarcina. PMID:677880
Effect of sulfur-containing compounds on anaerobic degradation of cellulose to methane by mixed cultures obtained from sewage sludge. PMID:677869
Isolation and characterization of Desulfovibrio growing on hydrogen plus sulfate as the sole energy source. PMID:623496
Fermentation of fumarate and L-malate by Clostridium formicoaceticum. PMID:618841
Effect of inorganic sulfide on the growth and metabolism of Methanosarcina barkeri strain DM. PMID:572199
Transformation of mercuric chloride and methylmercury by the rumen microflora. PMID:539820
Growth yields and fermentation balance of Bacteroides fragilis cultured in glucose-enriched medium. PMID:438119
Participation of quinone and cytochrome b in tetrathionate reductase respiratory chain of Citrobacter freundii. PMID:435281
Methane synthesis without the addition of adenosine triphosphate by cell membranes isolated from Methanobacterium ruminantium. PMID:435275
Microbial methanogenesis and acetate metabolism in a meromictic lake. PMID:434805
Methanogens: reevaluation of a unique biological group. PMID:390357
Evolutionary aspects of autotrophy. PMID:353476
The biology of methanogenic bacteria. PMID:329834
Growth and methanogenesis by Methanosarcina strain 227 on acetate and methanol. PMID:216307
Fumarate reductase of Clostridium formicoaceticum. A peripheral membrane protein. PMID:214050
Chemiosmotic coupling in Methanobacterium thermoautotrophicum: hydrogen-dependent adenosine 5'-triphosphate synthesis by subcellular particles. PMID:160408
Electron transport phosphorylation coupled to fumarate reduction by H2- and Mg2+-dependent adenosine triphosphatase activity in extracts of the rumen anaerobe Vibrio succinogenes. PMID:149114
Properties and function of the proton-translocating adenosine triphosphatase of Clostridium perfringens. PMID:40963
Solubilization and properties of a particulate hydrogenase from Methanobacterium strain G2R. PMID:37236
Oxidation of carbon monoxide in cell extracts of Pseudomonas carboxydovorans. PMID:33964
ATP hydrolysis and synthesis by the membrane-bound ATP synthetase complex of Methanobacterium thermoautotrophicum. PMID:30747
Growth yields and growth rates of Desulfovibrio vulgaris (Marburg) growing on hydrogen plus sulfate and hydrogen plus thiosulfate as the sole energy sources. PMID:28099
Carbon monoxide oxidation by methanogenic bacteria. PMID:21159
Group contribution method for thermodynamic analysis of complex metabolic networks PubMed citations: 135.

135 articles citing: Group contribution method for thermodynamic analysis of complex metabolic networks

Design, Analysis, and Implementation of a Novel Biochemical Pathway for Ethylene Glycol Production in Clostridium autoethanogenum. PMID:35543716
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. PMID:35322036
Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA). PMID:34966373
eQuilibrator 3.0: a database solution for thermodynamic constant estimation. PMID:34850162
Curating COBRA Models of Microbial Metabolism. PMID:34719001
Thermodynamics of Potential CHO Metabolites in a Reducing Environment. PMID:34685396
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. PMID:34570771
NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism. PMID:34340747
The influence of the crowding assumptions in biofilm simulations. PMID:34292941
Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis. PMID:33879809
Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions. PMID:33869975
Probabilistic Thermodynamic Analysis of Metabolic Networks. PMID:33755125
New thermodynamic activity-based approach allows predicting the feasibility of glycolysis. PMID:33731762
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis. PMID:33602294
PhenoMapping: a protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models. PMID:33532729
Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions. PMID:33493151
A thermodynamic atlas of carbon redox chemical space. PMID:33376214
The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale. PMID:33371386
Seeding Biochemistry on Other Worlds: Enceladus as a Case Study. PMID:33064954
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. PMID:32986834
Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN. PMID:32499584
Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power. PMID:32421310
Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies. PMID:32140178
Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models. PMID:32001719
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. PMID:31937763
Leloir Glycosyltransferases in Applied Biocatalysis: A Multidisciplinary Approach. PMID:31652818
The MetaCyc database of metabolic pathways and enzymes - a 2019 update. PMID:31586394
JRgui: A Python Program of Joback and Reid Method. PMID:31457399
Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties. PMID:31430276
A Mixed Quantum Chemistry/Machine Learning Approach for the Fast and Accurate Prediction of Biochemical Redox Potentials and Its Large-Scale Application to 315 000 Redox Reactions. PMID:31404220
Construction of a synthetic pathway for the production of 1,3-propanediol from glucose. PMID:31399628
Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models. PMID:31083653
Pareto Optimality Explanation of the Glycolytic Alternatives in Nature. PMID:30796263
Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways. PMID:30647083
Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions. PMID:30590445
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis. PMID:30561545
A genome-scale metabolic model of potato late blight suggests a photosynthesis suppression mechanism. PMID:30537923
Quantum chemistry reveals thermodynamic principles of redox biochemistry. PMID:30356318
Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method. PMID:29874618
A review of computational tools for design and reconstruction of metabolic pathways. PMID:29552648
Find_tfSBP: find thermodynamics-feasible and smallest balanced pathways with high yield from large-scale metabolic networks. PMID:29229946
MitoCore: a curated constraint-based model for simulating human central metabolism. PMID:29178872
The MetaCyc database of metabolic pathways and enzymes. PMID:29059334
Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling. PMID:28959251
Thermodynamic Constraints Improve Metabolic Networks. PMID:28793222
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models. PMID:28727725
A design-build-test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models. PMID:28674555
Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks. PMID:28333921
How important is thermodynamics for identifying elementary flux modes? PMID:28222104
Improvement of whole-cell transamination with Saccharomyces cerevisiae using metabolic engineering and cell pre-adaptation. PMID:28049528
Quantification of Microbial Phenotypes. PMID:27941694
Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations. PMID:27927167
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. PMID:27895706
Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus. PMID:27868089
The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization. PMID:27812109
Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis. PMID:27736793
Metabolic flexibility of mitochondrial respiratory chain disorders predicted by computer modelling. PMID:27697518
Systematic identification and analysis of frequent gene fusion events in metabolic pathways. PMID:27342196
Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling. PMID:27178561
Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB). PMID:27065985
The Influence of Crowding Conditions on the Thermodynamic Feasibility of Metabolic Pathways. PMID:26636950
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. PMID:26527732
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. PMID:26454094
MitoMiner v3.1, an update on the mitochondrial proteomics database. PMID:26432830
Lower glycolysis carries a higher flux than any biochemically possible alternative. PMID:26416228
227 Views of RNA: Is RNA Unique in Its Chemical Isomer Space? PMID:26200431
Elementary Flux Mode Analysis Revealed Cyclization Pathway as a Powerful Way for NADPH Regeneration of Central Carbon Metabolism. PMID:26086807
Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks. PMID:26041773
Sampling with poling-based flux balance analysis: optimal versus sub-optimal flux space analysis of Actinobacillus succinogenes. PMID:25887116
Concepts, challenges, and successes in modeling thermodynamics of metabolism. PMID:25505786
Predictive sulfur metabolism - a field in flux. PMID:25477892
Efficient searching and annotation of metabolic networks using chemical similarity. PMID:25417203
Quantum chemical approach to estimating the thermodynamics of metabolic reactions. PMID:25387603
Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures. PMID:25243355
Network thermodynamic curation of human and yeast genome-scale metabolic models. PMID:25028891
Design and construction of a non-natural malate to 1,2,4-butanetriol pathway creates possibility to produce 1,2,4-butanetriol from glucose. PMID:25008973
Counting and correcting thermodynamically infeasible flux cycles in genome-scale metabolic networks. PMID:24958259
Systematic applications of metabolomics in metabolic engineering. PMID:24957776
Stoichiometry based steady-state hepatic flux analysis: computational and experimental aspects. PMID:24957379
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. PMID:24927599
In vitro characterization of an enzymatic redox cascade composed of an alcohol dehydrogenase, an enoate reductases and a Baeyer-Villiger monooxygenase. PMID:24746588
Biocatalytic potential of vanillin aminotransferase from Capsicum chinense. PMID:24712445
Metabolic modelling in the development of cell factories by synthetic biology. PMID:24688669
Glycine betaine as a direct substrate for methanogens (Methanococcoides spp.). PMID:24162571
Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load. PMID:24086517
Biodegradation-inspired bioproduction of methylacetoin and 2-methyl-2,3-butanediol. PMID:23945710
Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PMID:23935467
Refolding of a thermostable glyceraldehyde dehydrogenase for application in synthetic cascade biomanufacturing. PMID:23894676
Consistent estimation of Gibbs energy using component contributions. PMID:23874165
Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models. PMID:23870272
Applying systems biology methods to the study of human physiology in extreme environments. PMID:23849719
Metingear: a development environment for annotating genome-scale metabolic models. PMID:23766418
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. PMID:23632383
Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways. PMID:23580552
Construction and analysis of the model of energy metabolism in E. coli. PMID:23383083
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. PMID:23110173
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. PMID:23109554
Choline and N,N-dimethylethanolamine as direct substrates for methanogens. PMID:23001649
CardioNet: a human metabolic network suited for the study of cardiomyocyte metabolism. PMID:22929619
Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction. PMID:22768925
A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks. PMID:22737065
Flux-balance modeling of plant metabolism. PMID:22645533
An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. PMID:22645166
Ensemble modeling of cancer metabolism. PMID:22623918
Dynamic metabolomics differentiates between carbon and energy starvation in recombinant Saccharomyces cerevisiae fermenting xylose. PMID:22587303
Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico. PMID:22583864
System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes. PMID:22416224
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. PMID:22367118
Computational tools for the synthetic design of biochemical pathways. PMID:22266781
Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity. PMID:22184215
Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. PMID:22139506
eQuilibrator--the biochemical thermodynamics calculator. PMID:22064852
Whole-genome metabolic network reconstruction and constraint-based modeling. PMID:21943909
A retrosynthetic biology approach to metabolic pathway design for therapeutic production. PMID:21819595
In silico evidence for gluconeogenesis from fatty acids in humans. PMID:21814506
A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle. PMID:21714867
Mathematical models of cell factories: moving towards the core of industrial biotechnology. PMID:21375719
A probabilistic approach to identify putative drug targets in biochemical networks. PMID:21123256
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. PMID:21115436
Metabolically engineered Escherichia coli for biotechnological production of four-carbon 1,4-dicarboxylic acids. PMID:21113642
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. PMID:20823849
High-throughput generation, optimization and analysis of genome-scale metabolic models. PMID:20802497
IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities. PMID:20513391
Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling. PMID:20444261
Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design. PMID:20416071
Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism. PMID:20230840
In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene. PMID:20122273
A protocol for generating a high-quality genome-scale metabolic reconstruction. PMID:20057383
Bacterial ammeline metabolism via guanine deaminase. PMID:20023034
Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. PMID:19783351
A genome-scale metabolic model of Arabidopsis and some of its properties. PMID:19755544
Metabolite and reaction inference based on enzyme specificities. PMID:19696044
Computational framework for predictive biodegradation. PMID:19650084
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. PMID:19555510
Thermodynamic analysis of biodegradation pathways. PMID:19288443
An integrated open framework for thermodynamics of reactions that combines accuracy and coverage PubMed citations: 51.

51 articles citing: An integrated open framework for thermodynamics of reactions that combines accuracy and coverage

Design, Analysis, and Implementation of a Novel Biochemical Pathway for Ethylene Glycol Production in Clostridium autoethanogenum. PMID:35543716
eQuilibrator 3.0: a database solution for thermodynamic constant estimation. PMID:34850162
Thermodynamics of Potential CHO Metabolites in a Reducing Environment. PMID:34685396
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. PMID:34570771
Evaluation of Heterologous Biosynthetic Pathways for Methanol-Based 5-Aminovalerate Production by Thermophilic Bacillus methanolicus. PMID:34262896
Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis. PMID:33879809
Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions. PMID:33869975
Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity. PMID:33850714
Metabolic energy conservation for fermentative product formation. PMID:33438829
A thermodynamic atlas of carbon redox chemical space. PMID:33376214
The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale. PMID:33371386
Thermodynamic Limits and Optimality of Microbial Growth. PMID:33286054
Seeding Biochemistry on Other Worlds: Enceladus as a Case Study. PMID:33064954
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. PMID:32986834
In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers. PMID:32184362
Leloir Glycosyltransferases in Applied Biocatalysis: A Multidisciplinary Approach. PMID:31652818
Fluxomic Analysis Reveals Central Carbon Metabolism Adaptation for Diazotroph Azotobacter vinelandii Ammonium Excretion. PMID:31520074
A Mixed Quantum Chemistry/Machine Learning Approach for the Fast and Accurate Prediction of Biochemical Redox Potentials and Its Large-Scale Application to 315 000 Redox Reactions. PMID:31404220
Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions. PMID:30590445
Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H. PMID:30446608
Quantum chemistry reveals thermodynamic principles of redox biochemistry. PMID:30356318
OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli. PMID:30248096
Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method. PMID:29874618
In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host. PMID:29276507
Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. PMID:28903046
Properties of Intermediates in the Catalytic Cycle of Oxalate Oxidoreductase and Its Suicide Inactivation by Pyruvate. PMID:28514140
How important is thermodynamics for identifying elementary flux modes? PMID:28222104
Synthetic metabolism: metabolic engineering meets enzyme design. PMID:28152442
Quantification of Microbial Phenotypes. PMID:27941694
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. PMID:27895706
A network property necessary for concentration robustness. PMID:27759015
In Vivo Analysis of NH4+ Transport and Central Nitrogen Metabolism in Saccharomyces cerevisiae during Aerobic Nitrogen-Limited Growth. PMID:27637876
Efficient Reconstruction of Predictive Consensus Metabolic Network Models. PMID:27563720
pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism. PMID:27551079
Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy. PMID:27336167
Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling. PMID:27178561
Design Principles as a Guide for Constraint Based and Dynamic Modeling: Towards an Integrative Workflow. PMID:26501332
Lower glycolysis carries a higher flux than any biochemically possible alternative. PMID:26416228
NADPH-generating systems in bacteria and archaea. PMID:26284036
The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism. PMID:26061898
Quantum chemical approach to estimating the thermodynamics of metabolic reactions. PMID:25387603
Intracellular metabolite levels shape sulfur isotope fractionation during microbial sulfate respiration. PMID:25362045
Metabolic modelling in the development of cell factories by synthetic biology. PMID:24688669
Pathway thermodynamics highlights kinetic obstacles in central metabolism. PMID:24586134
Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load. PMID:24086517
Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PMID:23935467
Consistent estimation of Gibbs energy using component contributions. PMID:23874165
Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models. PMID:23870272
Model-driven elucidation of the inherent capacity of Geobacter sulfurreducens for electricity generation. PMID:23718629
Glycolytic strategy as a tradeoff between energy yield and protein cost. PMID:23630264
A proof for loop-law constraints in stoichiometric metabolic networks. PMID:23146116
Biochemical thermodynamics: applications of Mathematica PubMed citations: 24.

24 articles citing: Biochemical thermodynamics: applications of Mathematica

Determining the quantitative relationship between glycolysis and GAPDH in cancer cells exhibiting the Warburg effect. PMID:33545174
Comprehensive Bioenergetic Evaluation of Microbial Pathway Variants in Syntrophic Propionate Oxidation. PMID:33293404
Perturbation of phosphoglycerate kinase 1 (PGK1) only marginally affects glycolysis in cancer cells. PMID:32217690
Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements. PMID:26951675
Evidence That Does Not Support Pyruvate Kinase M2 (PKM2)-catalyzed Reaction as a Rate-limiting Step in Cancer Cell Glycolysis. PMID:26917721
Lower glycolysis carries a higher flux than any biochemically possible alternative. PMID:26416228
A general framework for thermodynamically consistent parameterization and efficient sampling of enzymatic reactions. PMID:25874556
Network thermodynamic curation of human and yeast genome-scale metabolic models. PMID:25028891
Beyond Warburg effect--dual metabolic nature of cancer cells. PMID:24820099
Pathway thermodynamics highlights kinetic obstacles in central metabolism. PMID:24586134
Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria. PMID:23946717
Consistent estimation of Gibbs energy using component contributions. PMID:23874165
Oxygen response of the wine yeast Saccharomyces cerevisiae EC1118 grown under carbon-sufficient, nitrogen-limited enological conditions. PMID:23001663
Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction. PMID:22768925
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. PMID:21115436
Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism. PMID:20230840
Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. PMID:19783351
Determination of rapid-equilibrium kinetic parameters of ordered and random enzyme-catalyzed reaction A+B=P+Q. PMID:19558174
On the hydrophobicity of nitrogen dioxide: could there be a "lens" effect for NO(2) reaction kinetics? PMID:19540354
Determination of kinetic parameters of enzyme-catalyzed reaction a + B + C --> products with the minimum number of velocity measurements. PMID:19159341
anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. PMID:18416814
Rapid-equilibrium rate equations for the enzymatic catalysis of A+B=P+Q over a range of pH. PMID:18061334
Thermodynamic properties of enzyme-catalyzed reactions involving cytosine, uracil, thymine, and their nucleosides and nucleotides. PMID:17240519
Changes in binding of hydrogen ions in enzyme-catalyzed reactions. PMID:17011697
http://dx.doi.org/10.1093/nar/GKR874

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metabolic and signaling pathways
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