Investigations
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Collection of experiments created by Sawa, M. on the original BioDare and automatically transferred to FAIRDOM Hub.
Collection of models submitted to PLaSMo by Daniel Seaton and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 20..., Modelling circadian regulation of flowering time and hypocotyl elongatio...
Assays: Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 20..., Modelling circadian regulation of flowering time and hypocotyl elongatio...
Due to its high chemical stability, the biodegradation of benzene is the most challenging amongst hydrocarbons. While oxygen-dependent oxygenases are employed by aerobic bacteria to overcome the energy barrier, the mechanism of anaerobic benzene biodegradation is still enigmatic. The sulfate-reducing, clonal enrichment culture BzS1 is capable of benzene degradation under anoxic conditions. In addition, the alkylbenzene toluene may be used as sole source of carbon and energy. In this project, the ...
Submitter: Lars Wöhlbrand
Studies: Shotgun and geLC MS/MS analysis of the solble and membrane protein-enric...
Assays: Membrane protein-enriched fraction of clonal enrichment culture BzS1 dur..., Membrane protein-enriched fraction of clonal enrichment culture BzS1 dur..., Soluble protein fraction of clonal enrichment culture BzS1 during growth..., Soluble protein fraction of clonal enrichment culture BzS1 during growth...
Submitter: Charles Demurjian
Studies: Human cartilage model of the precocious osteoarthritis-inducing COL2A1 p...
Assays: All Metadata, Cell Imaging - Data Linked, Gene Expression Analysis - Data Linked, LC - MS/MS (Proteomics) - Data Linked, Library Creation - Metadata, Proteomics Analysis - Data Linked, RNA Extraction - Metadata, Short Read Sequencing - Data Linked, iPSC Culture and Chondronoid Formation - Metadata
Collection of models submitted to PLaSMo by Rob Smith and automatically transferred to FAIRDOM Hub.
Collection of experiments created by Somers DE on the original BioDare and automatically transferred to FAIRDOM Hub.
Collection of experiments created by Song, Y.H. on the original BioDare and automatically transferred to FAIRDOM Hub.
Drug detoxification dynamics explain the postantibiotic effect
Steady state metabolic fluxes and metabolite concentrations of yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1
Submitter: Maksim Zakhartsev
Studies: Steady state concentrations of metabolites in yeast Saccharomyces cerevi..., Steady state fluxes in yeast Saccharomyces cerevisiae in anaerobic chemo...
Assays: Steady state concentrations of extracellular metabolites in yeast Saccha..., Steady state concentrations of intracellular metabolites in yeast Saccha..., Steady state extracellular fluxes in anaerobic yeast Saccharomyces cerev...
Changing the oxygen availability leads to an adaptation of Escherichia coli at different biological levels. After pertubation of oxygen in chemostat experiments the microorganism(s) will come back to another steady state. This investigation deals with these stationary responses of Escherichia coli within the aerobiosis scale. The change for different biological variables, in different areas of the organism like the electron transport chain, the TCA cycle or globally is investigated by wildtype ...
Submitter: Michael Ederer
Studies: Basic regulatory principles of Escherichia coli’s electron transport cha..., Determination of the impact of specific enzyme reactions and regulatory ..., Quantitative analysis of catabolic carbon and electron fluxes in E. coli..., The Escherichia coli steady state response to oxygen: from molecular int...
Assays: Analysis of by-product formation rates in MG1655, Analysis of gene expression rates at different aerobiosis levels via RT-PCR, ArcA phosphorylation at different aerobiosis levels (steady states), Characterization of E. coli MG1655 and ∆sdhC and ∆frdA isogenic mutant s..., Determination of intracellular metabolite concentrations, Determination of intracellular redox state by means of NAD/NADH ratio, Determination of intracellular redox state by means of ubiquinones (oxd/..., FNR activity at different aerobiosis levels (steady state), Kinetic modelling of Escherichia coli's electron transport chain, Kinetic modelling of Escherichia coli's electron transport chain coupled..., Literature Data from Alexeeva et al., J. Bacteriol., 2000, 2002, 2003, Measurement of cytochrome numbers, Physiological measurements from Sheffield chemostat, Steady State Oxygen Response of E. coli WT and two Electron Transport Ch..., Transcriptional profiling of steady states at different aerobiosis levels
The raw data generated in the scope of the SysMetEx project for RNAseq, proteomics, and imaging analysis. The data was generated on single and mixed species cultures of A. Caldus, L.ferriphilum, and/or S.thermosulfidooxidans. Raw RNA data is combined in an ENA umbrella study summarising all short read data generated in the project. Raw proteomics data is provided for distinct conditions at the pride repository. Imaging data is provided for distinct conditions at a zenodo repository.
Submitter: Malte Herold
Studies: Biofilms on chalcopyrite grains, Continuous cultures, Planktonic cells, Supplemental Files
Assays: Links to code repositories, Microscopy imaging, Proteomics rawdata, Proteomics rawdata, Proteomics rawdata, RNAseq rawdata, RNAseq rawdata, RNAseq rawdata, Supplemental Files
Transcriptional and physiological responses of anaerobic steady state cultures to pulses of electron acceptors, specifically nitrate, trimethylamine-N-oxide (TMAO)
Members of the genus Aromatoleum are cosmopolitan in diverse habitats and utilize a broad range of recalcitrant organic molecules coupled to denitrification or O2-respiration. To gain a holistic understanding of the model organism A. aromaticum EbN1T, we here studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate and acetate utilized under nitrate-reducing vs. oxic conditions. Multi-OMICS (transcriptome, proteome and metabolome) ...
Submitter: Meina Neumann-Schaal
Studies: Experimental multi-OMICS, Genome re-annotation, Metabolic Modelling
Assays: CoA LC/MS Data, Cultivation for multi-OMICS, EbN1 Genome re-annotation, Metabolic modeling of EbN1, Proteomic data, Scenario files for Metano metabolic modeling, Transcriptomic data, non-volatile metabolites GC/MS
Clostridia are very ancient bacteria which evolved before the earth had an oxygen atmosphere. To them the air we breathe is a poison. To survive they produce a spore resting stage, resistant to physical and chemical agents.
Some species cause devastating diseases, such as the superbug Clostridium difficile. On the other hand, most are totally harmless, and make a wide range of chemicals useful to man. The best example is Clostridium acetobutylicum which makes butanol. Butanol is an alcohol, which ...
Submitter: Holger Janssen
Studies: Investigation of different pH values for metabolic shift
Assays: test
