Studies
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PGK-GAPDH reactions were studied in vitro at 30 and 70 using yeast or Sso enzymes
SED-ML: https://jjj.bio.vu.nl/models/experiments/kouril2017_fig4b/simulate https://jjj.bio.vu.nl/models/experiments/kouril2017_fig4c/simulate
Submitter: Theresa Kouril
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: PGK - GAPDH models, PGK-GAPDH 30, PGK-GAPDH 70
PGK reaction at 30 C. Yeast PGK was incubated at 30 C, in the presence or absence of the ATP recycling system, and the conversion of 3 PG to BPG was followed. SED-ML simulations Fig. 1A: https://jjj.bio.vu.nl/models/experiments/kouril2017_fig1a/simulate
Submitter: Jacky Snoep
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: PGK 30C data, PGK 30C model
PGK reaction at 70C. Sulfolobus solfataricus PGK was incubated at 70C in presence and absence of an ATP recycling system. Changes in metabolite concentrations was followed via 31P NMR or enzymatic analyses.
SED-ML: https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3b/simulate https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3c/simulate https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3d/simulate
Submitter: Theresa Kouril
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: PGK 70 data, PGK 70C model
BPG produced with yeast PGK was incubated at 70 C,upon which BPG rapidly dephosphorylates to 3PG. SED-ML: https://jjj.bio.vu.nl/models/experiments/kouril2017_fig2b/simulate
Submitter: Jacky Snoep
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: BPG degradation, BPG stability analysis
Submitter: Jay Moore
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Assays: Metabolic pathway curation
Genotype: Wildtype (M145E) Medium: Phosphate-limited (F134)
Submitter: Jay Moore
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Assays: Online/offline measurements, metabolomics, proteomics, transcriptomics
Submitter: Jan-Willem Veening
Investigation: Chromosome segregation and cell division in Str...
Here you will find guidelines for creating MIAPE compliant proteomics data files as well as examples and links to online tools and resources
Submitter: Katy Wolstencroft
Investigation: Creating data sheet template for 'omics data
Assays: Proteomics Template (gel electrophoresis), Proteomics Templates (Mass spectrometry)
Here you will find guidelines for creating MAGE-TAB compliant transcriptomics data files as well as examples and links to online tools and resources.
Determination of essential amino acids for Streptococcus pyogenes M49
Lactic acid bacteria generally use homolactic fermentation for generation of ATP. Here we studied the role of Arginine and Glutamine metabolism on the general physiology of the lactic acid bacteria Streptococcus pyogenes. A deletion mutant of glnA (glutamine synthetase) has been constructed in the S. pyogenes M49 591 background. The glnA mutant strain shows decreased growth in low glutamine and excess glutamate conditions and no growth at all in low glutamine and low glutamate conditions. An arcA ...
Submitter: Antje Sieg
Investigation: Amino acid metabolism of four LAB species: Stre...
Assays: Characterization of flux distribution of S. pyogenes M9 wild type and th...
The reconstruction of the metabolic networks is done by sequence comparison with already annotated genomes of L. lactis, L. plantarum, B. subtilis and E. coli
Here you will find all pre-liminary data
Pyruvate kinase (PYK, EC 2.7.1.40) is a key step in glycolysis converting phosphoenolpyruvate into pyruvate. The activity of PYK is activator-dependent, with the allosteric activation mostly being due to fructose-1,6-bisphosphate (FBP).
Submitter: Stefan Henrich
Investigation: The Attic
Assays: literature values for allosteric regulation of pyruvate kinase
Pyruvate formate-lyase (PFL) is an important enzyme in the metabolic pathway of lactic acid bacteria (LAB) and is held responsible for the regulation of the shift between homolactic acid to mixed acid fermentation. PFL catalysis the reversible reaction of acetyl-CoA and formate into pyruvate and CoA. A glycyl radical, who is regenerated within the reaction, is involved; therefore, PFL works only under strictly anaerobic conditions. For its activation, the C-terminal domain has to bind to the ...
Submitter: Stefan Henrich
Investigation: The Attic
Assays: Pyruvate formate-lyase (PFL): literature review, structure analysis and ...
The two lactic acid bacteria L. lactis and S. pyogenes were studied with respect to the concentration of intracellular metabolites involved in glycolysis in time upon a glucose pulse. Models that describe this behavior are also constructed
Submitter: Martijn Bekker
Investigation: Investigation of glycolysis and pyruvate branch...
Assays: Global sensitivity analysis, Glucose pulsed L. lactis, Glucose pulsed S. pyogenes, Kinetics of L-lactate dehydrogenase from L. lactis, Model of L. lactis glycolysis, Regulation of the activity of lactate dehydrogenases from four lactic ac...
Lactic acid bacteria generally use homolactic fermentation for generation of ATP. Here we studied the role of the lactate dehydrogenase enzyme on the general physiology of the three lactic acid bacteria Lactococcus lactis, Enterococcus faecalis and Streptococcus pyogenes. Surprisingly deletion of the ldh genes hardly affected the growth rate in chemically defined medium, however growth rate was affected in rich medium. Furthermore, deletion of ldh affected the ability for utilization of various ...
Since over 40 enzymes will be investigated for their mRNA abundance, processing, and degradation kinetics, the less tedious and more accurate Next Generation Sequencing of the entire mRNA repertoire of the cell is employed. To optimise the proportion of useful sequence, while including RNA fragments that are products of of degradation, rRNA is depleted using the eukaryotic Ribominus kit (Ambion). Two biological replicates are treated with Sinefungin and Actinomycin D to inhibit RNA processing and ...
Submitter: Abeer Fadda
Investigation: Gene expression in Trypanosoma brucei
Assays: Modelling the gene expression cascade with length-dependent processes, mRNA decay assay, pre-mRNA processing rate
For cells to accurately read out the genomic content, high fidelity during transcription is required. This is mainly established by the accuracy of the active centre of RNA polymerase (RNAP). Based on in vitro experiments with Escherichia coli RNAP it was also suggested that proofreading of transcription via RNA hydrolysis by RNAP may contribute to overall fidelity and processivity. RNAP’s intrinsic cleavage activity is stimulated by the highly conserved Gre factors suggesting that Gre factors ...
Submitter: Jan-Willem Veening
Investigation: Wetlab approach to transcription fidelity
Assays: RNA-Seq
The enzyme Trypanothione Synthetase (TryS) is a complex enzyme that catalyses the two step reaction that forms trypanothione from 2 molecules of GSH and 1 molecule of Spd and the use of ATP
Submitter: Jurgen Haanstra
Investigation: Kinetic understanding of the T. brucei trypanot...
A set of isogenic mutant strains was constructed which lack NADH Dehydrogenase I as well as two terminal oxidases, resulting in strains with linear respiratory chain. The different strains hence differ in the terminal oxidase and express either cytochrome bo, cytochrome bdI or cytochrome bdII. The different strains were cultivated in glucose-limited chemostats with defined low levels of oxygen supply. Biomass and by-product formation, gene expression and the phosphorylation state of the important ...
Submitter: Katja Bettenbrock
Investigation: Analysis of Escherichia coli with linear electr...
Assays: Determination of by-product formation and glucose uptake of mutants with..., Deternination of ArcA phosphroylation level in mutants with linear ETC a..., Gene expression analysis of mutants with linear electron transport chain...
Carbon loss due to instability of gluconeogenic pathway intermediates (BPG, GAP, DHAP) at high temperature in S. solfataricus
Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus
Submitter: Jacky Snoep
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Assays: FBPAase, FBPAase Modelling, GAPDH, GAPDH Modelling, Modelling Metabolite Degradation at High Temperature, PGK, PGK Modelling, Reconstituted Gluconeogenesis System, TPI, TPI Modelling, Temperature Degradation of Gluconeogenic Intermediates
Submitter: Katy Wolstencroft
Investigation: Yeast Glycolytic Oscillations
Assays: Modelling sustained glycolytic oscillations in individual isolated yeast...
Mutant strains in which one or more of the potential glucose uptake systems was deleted have been analyzed in aerobic and anaerobic batch cultures, as well as aerobic chemostat cultures.
Submitter: Sonja Steinsiek
Investigation: Analysis of the glucose transport in Escherichi...
Assays: Aerobic and anaerobic characterization of MG1655 and mutant strains with..., Aerobic and anaerobic characterization of MG1655 and mutant strains with..., Characterization of MG1655 and mutant strains under conditions of glucos..., TFinfer2
Submitter: Matthew Rolfe
Investigation: Dynamical studies for different oxygen availabi...
Assays: Transcriptional profiling of E. coli during anaerobic to aerobic and aer...
Submitter: Sebastian Henkel
Investigation: Steady state studies for different oxygen avail...
Assays: No Assays
Submitter: Michael Ederer
Investigation: Steady state studies for different oxygen avail...
Assays: ArcA phosphorylation at different aerobiosis levels (steady states), 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), 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 aim of the study is to assess the global function of RNase Y in RNA processing and degradation in Bacillus subtilis. To this end we constructed a strain allowing controlled depletion of RNase Y and used microarrays to analyze the transcriptome in response to the expression level of RNase Y.
Submitter: Praveen kumar Sappa
Investigation: Identification of targets of the essential RNas...
Assays: Transcritome data_Identification of targets of the essential RNase Y of ...
Conversion from KEGG Reactome Information to SBTOOLBOX2 format.
Submitter: Sebastian Curth
Investigation: Modular Model Building
Assays: Example for model derivation from KEGG, Integration of data into the model
Flux will be measured using the metabolomics platforms based on absolute quantification method (isotope ratio based MS technique) by LC-MS, using heavy-isotope labelled precursors of the metabolites of interest. For example, 15N labelled cysteine, glycine and glutamate will be used to determine rates of synthesis of glutathione. 15N-labelled methionine to measure S-adenosyl methionine (and its decarboxylated form, as well as methionine cycle intermediates). 15N labelled arginine is used as precursor ...
In addition to the highly targeted quantification of metabolites already known to play major roles in oxidative stress, to provide data directly compatible with current models, we will also take an untargeted metabolomics approach. This will enable us to identify other areas of the metabolome influenced by, or influencing, oxidative stress and will allow us to compare changes in each of the stress-inducing stimuli. We have recently pioneered untargeted metabolite profiling of T. brucei using ...
We have already demonstrated that the key metabolites of polyamine biosynthesis (arginine, ornithine, putrescine and spermidine) can be identified using HILIC chromatography coupled to the Orbitrap mass spectrometer, as can glycine, glutamate and cysteine used in glutathione biosynthesis, glutathionyl spermidine and trypanothione itself. Furthermore the key metabolites of the methionine cycle (methionine, S-adenosyl methionine, decarboxylated S-adenosyl methionine, methylthioadenosine) can all ...
Submitter: Dong-Hyun Kim
Investigation: Metabolite profiling, quantification and flux q...
Assays: Intracellular metabolite concentrations in T. brucei under pH stress
Submitter: Daniel Hönicke
Investigation: Altering the expression pattern in Clostridium ...
Assays: Transcriptional analyses of a thioredoxin (trxB, encoded by CAC1548) kno...
Annotation retrieval
Creation of the KEGG based Reactome
Submitter: Sebastian Curth
Investigation: Modular Model Building
Assays: Graph Analysis, KEGG Data Mining
Parasites will be harvested at different growth phases and the total amount of the proteins will be followed by western blot. The absolut concentration will be obtained by comparison with a know amount of the recombinant untagged protein. The thiol redox state of the proteins will be followed by modification of the free cys with methoxy-ethyl-maleinimide poly(ethylenglycol) (Meo-PEG-mal).
Submitter: Alejandro Leroux
Investigation: Kinetic understanding of the T. brucei trypanot...
Assays: No Assays
The enzymes involved in the trypanothione metabolism will be studied in a uniform assay medium that mimics the intracellular milieu of the parasite.
Key enzymes of critical points in the pathways will be targeted for disruption by the generation of RNAi cell lines and lines which drive tetracycline-regulatable ectopic over expression of either wild type enzyme or, if appropriate, dominant-negative or mis-targeted mutants of these. In all cases perturbed lines will be analysed with respect to the mRNA, protein or enzymatic activities of other components of the subsystem, this being directed iteratively by the predictions from systems modelling. ...
Submitter: Sebastian Curth
Investigation: General Method Development
Assays: Theoretical calculation of quenching time and quenching temperature
We developed a new metabolomics protocol, which involved a comparison of different harvesting techniques, quenching solutions and extraction methods.
Submitter: John Raedts
Investigation: Identification of regulatory metabolites in the...
The Lactate dehydrogenases (LDH) are key metabolic enzymes in lactic acid bacteria (LAB). The LDH ( E.C. 1.1.1.27) catalyzes the reaction of pyruvate and NADH into lactate and NAD+.We have carried out an experimental and computational study of the effects of fructose-1,6-bisphosphate (FBP), phosphate (Pi) and ionic strength (NaCl concentration) on 3 LDHs from 3 LABs studied at pH 6 and pH 7.
Submitter: Silvio Hering
Investigation: Investigation of glycolysis and pyruvate branch...
Assays: Kinetics of L-lactate dehydrogenase from S. pyogenes, E. faecalis, and L...
During the last few years scientists became increasingly aware that average data obtained from microbial population based experiments are not representative of the behavior, status or phenotype of single cells. Due to this new insight the number of single cell studies rises continuously (for recent reviews see (1,2,3)). However, many of the single cell techniques applied do not allow monitoring the development and behavior of one specific single cell in time (e.g. flow cytometry or standard ...
Submitter: Jan-Willem Veening
Investigation: Wetlab approach to transcription fidelity
Assays: Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae usin...
The output of the initial model of redox metabolism will be compared to experimental flux and metabolite data. Deviations between model and experiment will be prioritized together with WP2. We will apply Metabolic Control Analysis (Fell 1992 PMID: 1530563) to diagnose which enzymes control the deviating metabolite concentrations and/or rates. When the agreement between model and experiment is sufficient we will first link it to the existing model of trypanosome glycolysis and repeat the same ...
Submitter: Jurgen Haanstra
Investigation: Dynamic modelling of redox metabolism and gene ...
Assays: No Assays
Our current gene-expression model (Haanstra et al. 2008 PMID: 19008351) will be parameterized for the different genes of interest. The framework of this gene expression model has been used to include mRNA half life data into the model of glycolysis For the enzymes of redox metabolism we will use newly measured rates of transcription, RNA precursor degradation, mRNA degradation, concentrations of mature mRNAs and proteins, enzyme turnover, Vmax values and metabolic fluxes (WP3&5). Regulation ...
Submitter: Jurgen Haanstra
Investigation: Dynamic modelling of redox metabolism and gene ...
Assays: No Assays
We are in the process of construct an ODE model of the trypanothione pathway. As input we will use newly determined and existing kinetic data and measured metabolite concentrations at the boundaries (from WP3&6). Recently the glycolysis model was extended with the pentose phosphate pathway. This pathway will yield the NAPDH that maintains trypanothione in a reduced state. For some complex enzymes (i.e trypanothione synthase) we are intensively discussing the kinetic data obtained on the ...
Submitter: Jurgen Haanstra
Investigation: Dynamic modelling of redox metabolism and gene ...
Assays: No Assays
These templates can be used for a selection of metabolomics data types. There is a MASTER template for general use and adaptation as well as several more specific templates for particular types of experiment (e.g. HPLC), or specific assay types (e.g glucose pulse)
Submitter: Olga Krebs
Investigation: Creating data sheet template for 'omics data
Assays: Metabolomics Master Template, Standard-based Excel template for metabolomics data
Multi experimental approach to define the gene expression remodelling under potassium starvation conditions.
Submitter: Falko Krause
Investigation: K+ Starvation in Saccharomyces cerevisiae
Assays: LacZ Reporters, RT-PCR, Time Course Micro Array Experiment
How does the Volume, internal pH, membrane potential and intracellular cation content change in a time dependent scale during potassium limitation.
Submitter: Falko Krause
Investigation: K+ Starvation in Saccharomyces cerevisiae
Assays: External Potassium Concentration, External pH changes, How does internal potassium change (/decrease) during several hours of p..., How starvation affect protein content in yeast cells, Membrane Potential, Protein Concentration, Time courses of the internal pH changes, Volume determination during starvation at different times.
How do the fluxes of rubidium (potassium) change during potassium starvation.
Submitter: Falko Krause
Investigation: K+ Starvation in Saccharomyces cerevisiae
Assays: Ammonium fluxes, Potassium fluxes, Proton fluxes
What is the proteome of starved cells. Main characteristics?
Submitter: Falko Krause
Investigation: K+ Starvation in Saccharomyces cerevisiae
Submitter: Falko Krause
Investigation: K+ Starvation in Saccharomyces cerevisiae
Are there one or several stationary states for physiological parameters dependent on external KCl? For which range of external potassium the cell is able to maintain a constant pH, potassium content, membrane potential and volume?
Submitter: Falko Krause
Investigation: K+ Starvation in Saccharomyces cerevisiae
Assays: Stable membrane potential, Stable pH, Stable potassium concentration, Stable volume
Submitter: Falko Krause
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Assays: No Assays
Submitter: Falko Krause
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Assays: Internal pH, Membrane Potential, Potassium Concentration, Protein Concentration, Volume
Submitter: Falko Krause
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Assays: Insilico Promotor Anaysis
How does the current mediated by Trk1,2 depend on external and internal ion concentrations? How is the membrane potential shifted by the concentrations of various ions, especially ammonium?
Does the general proteome of yeast cells change in a strain lacking Trk1,2 transporter? Under which conditions?
Submitter: Falko Krause
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Assays: 2D Gel Analysis
Studies on the effect of deletion of genes encoding 14-3-3 proteins on the transcriptional response of yeast cells to potassium starvation.
Submitter: Falko Krause
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Assays: No Assays
Studies on genetic interactions between genes encoding 14-3-3 proteins and genes encoding transporters to elucidate which transporter(s) are regulated by 14-3-3 proteins.
Submitter: Falko Krause
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Assays: No Assays
Bioinformatic studies to elucidate the role of 14-3-3 proteins in cation homeostasis.
Submitter: Falko Krause
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Assays: In silico Promotor Anaysis, Interaction Database Analysis
How does the flux of potassium, hydrogen change during potassium uptake? Which ions are involved in maintaining the required charge balance?
Submitter: Falko Krause
Investigation: Potassium uptake in Saccharomyces cerevisiae
Assays: Additional fluxes, Potassium fluxes, Proton fluxes
How does the transport of potassium and hydrogen ions effect the concentrations in the near surrounding of the cell.
Submitter: Falko Krause
Investigation: Potassium uptake in Saccharomyces cerevisiae
Assays: Potassium changes, Proton changes
How does the current mediated by Trk1,2 depend on external and internal ion concentrations? How is the membrane potential shifted by the concentrations of various ions, especially ammonium?
At external potassium concentrations in the range of 10uM to 1mM Trk is major cellular uptake system for potassium. This system responds to the activiy of the proton pump. Transmembrane fluxes of protons and potassium cations are analysed in a signal-response relationship.
This study aims to establish the optimum conditions and assay methods for measuring ATP levels
Submitter: Martin Valachovic
Investigation: Effect of Benzoic Acid on ATP Levels
Assays: Compare ATP extraction methods
To see changes in ATP levels in cells with induced ABC transporters. Cells with Pdr12 pump by 10 mM benzoic acid are used.
Submitter: Martin Valachovic
Investigation: Effect of Benzoic Acid on ATP Levels
ATP levels of cells stressed with higher concentrations of benzoic acid (30 mM and 50 mM).
Submitter: Martin Valachovic
Investigation: Effect of Benzoic Acid on ATP Levels
Assays: ATP measurement under 30mM benzoic acid stress, ATP measurement under 50mM benzoic acid stress
Effect of benzoate treatment (high concentrations) on ATP levels and Pdr12 expression after pretreatment of cells with low concentrations of benzoic acid.
Cell survival was determined under different benzoic acid concentrations
Submitter: Holger Janssen
Investigation: The effect of pH upon the metabolic shift in Cl...
Assays: Comparison of the proteome between pH 5.7 (acidogenesis) and pH 4.5 (sol...
Submitter: Holger Janssen
Investigation: The effect of pH upon the metabolic shift in Cl...
Assays: Study of the end products of the acidogenesis and solventogenesis pathways
Mathematical modelling of the dynamic shift experiments and the effect of pH upon gene regulation.
B. subtilis was grown in minimal media in a chemostat at different growth rates (µ= max, µ=0.1, µ=0.4) and in the presence of 1.2M NaCl (µ=0.1) with or without glycinebetaine. Transcriptome, proteome and metabolome were investigated.
Submitter: Sandra Maass
Investigation: Multiomics study of Bacillus subtilis under osm...
Assays: Absolute quantification of proteins by the AQUA-technology, Absolute quantification of proteins using QconCAT technology, Relative quantification of proteins by metabolic labeling, Transcriptome data for chemostat cultivated samples, extracellular metabolites, intracellular metabolites
Here we develop a set of new tools for S. pneumoniae and as a case study we show that S. pneumoniaea SMC is recruited to oriC by ParB and promotes chromosome segregation.
Submitter: Jan-Willem Veening
Investigation: Wetlab approach to transcription fidelity
Assays: ParB-GFP ChIP on chip
Submitter: Nikolay Zenkin
Investigation: Wetlab approach to transcription fidelity
Assays: Kinetics of misincorporation and proofreading by bacterial RNA polymerase
Goals:
- Understanding the regulatory principles of Escherichia coli’s electron transport chain (ETC) for varying oxygen conditions in glucose-limited continuous cultures (especially regulatory loops via the transcription factors FNR and ArcA).
- Explaining the observed phenomena in the measurement data.
- Predicting unmeasured variables especially of the gene expression regulatory loops.
Means:
- Experiments (chemostat experiments within the aerobiosis scale).
- Kinetic modelling (especially ...
Submitter: Gerald Seidel
Investigation: A dynamic model of the CcpA regulation network
Assays: Binding constants for CcpA with HPrSer46P interacting with various cre-e...
Selected strains from the collection of GFP-tagged S. cerevisiae strains are cultivated at different extracellular caion concentrations and the localization of the GFP-tagged protein will be studied by confocal microscopy. The effect of deletion of the BMH1 gene, encoding the major 14-3-3 isoform, will be analyzed.
Submitter: Paul Heusden
Investigation: Role of 14-3-3 proteins in Saccharomyces cerevi...
Assays: No Assays
3 chemostat experiments:
each in 4 biological replicates incl. 1 fed with labelled glucose T = 37°C pH = 7.1 V_R = 300 mL (dasgip parallel bioreactor system) V_G = 9 sL/h (0.5 vvm) M9 Minimal medium + 3,4-dihydroxybenzoate (chelating agent) + 1g/L Glucose n = 1000 rpm
3 conditions:
"reference" without additional sodium chloride as control "stress" supplemented with 1.2M sodium chloride "osmoprotection" supplemented with 1.2M sodium chloride and 1mM glycine betaine (osmoprotectant)
Submitter: Michael Kohlstedt
Investigation: Multiomics study of Bacillus subtilis under osm...
Assays: 13C Metabolic Flux Analysis of Bacillus subtilis 168 in continuous high-...
Provided with genomic data over different pH values we have the opportunity to study the similarity of gene expression profiles and cluster groups of very simlar gene expression profiles. Via PCA we can furthermore study dynamic similarity and compe genes that are possible co-regulators or anti-regulators in the clostridial metabolism.
Submitter: Sebastian Curth
Investigation: The effect of pH upon the metabolic shift in Cl...
Assays: Identification of dynamically similar transcript profiles
The main aim of this experiment is to actively grow B.subtilis in presense of glucose until high optical density in an aerobic fermentor and then, at a definite point of the growth, the glucose supply is shut down which leads to complete glucose exhaustion in the media. Simultaneusly samples for transcriptomics, intra and extracellular metabolomics, intra and extracellular proteomics are harvested through out the experiment.
Submitter: Praveen kumar Sappa
Investigation: The transition from growing to non-growing Baci...
Assays: No Assays
test test
Submitter: Holger Janssen
Investigation: Systems Biology of Clostridium acetobutylicum -...
Assays: test
Experiments using shake flask cultures to measure dynamics associated with sigB response.
Submitter: Ulf Liebal
Investigation: The transition from growing to non-growing Baci...
Assays: No Assays
To model the ENA1 transcriptional regulation a model has to be established. First this will be just a graphical representation, it shall then be extended to a boolean model and shall at one point be converted to a kinetic model.
Mutant strains which carry deletions of important metabolic enzymes, as well as mutant strains with altered regulation, need to adapt by changing fluxes or gene expression to compensate with the absence/differed concentration of these key enzymes. This may give new insights in the regulation of these pathways/enzymes.
Submitter: Sonja Steinsiek
Investigation: Steady state studies for different oxygen avail...
Assays: Analysis of by-product formation rates in MG1655, Analysis of gene expression rates at different aerobiosis levels via RT-PCR, Characterization of E. coli MG1655 and ∆sdhC and ∆frdA isogenic mutant s..., Determination of intracellular metabolite concentrations
The pilot experiment has been set up in order to develop uniform SOPs for the Sulfosys consortium. It comprises proteomics, transcriptomics, metabolomics as well as enzymatic essays. Cells for all the members of the consortium have been obtained from the same batch fermentations according to fermentation SOP of Sulfosys. The pilot resulted in creating a procedures for all the techniques used in consortium.
Submitter: Pawel Sierocinski
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Assays: Comparison of proteome of S. solfataricus at 70 and 80C, Comparison of transcriptome of S. solfataricus at 70 and 80C, Enzyme activity tests for S. solfataricus, Fermentation of S. solfataricus at 70 and 80C in a batch fermenter, Intracellular metabolomics of S. solfataricus at 70 and 80C
Cells are starved. Potassium and subsequently glucose are added to the medium. Proton and potassium fluxes across the plasma membrane are recorded before and after these events for WT and mutants lacking specific transporter proteins.
In this kind of studies sigmaB stress response is induced by the addition of artificial inducers of sigmaB. For example simgaB is downstream of a Pspac promoter and induced by the addition of IPTG. A ctc::lacZ reporter gene is used to monitor sigmaB activity.
Submitter: Ulf Liebal
Investigation: The transition from growing to non-growing Baci...
Assays: IPTG induction of sigmaB in BSA115, IPTG induction of sigmaB in BSA115, Stressosome activation dynamics
The steady state anaerobic culture (D = 0.1 h-1) was pertrubed by sudden increase of the extracellular glucose up to 1 g/L and both extra- and intracellular transient metabolite concentrations were measured
Submitter: Maksim Zakhartsev
Investigation: Kinetic analysis of metabolic system using tran...
Assays: Biomass weight during glucose pulse, Cellular size and granularity during glucose pulse, Dynamics of extracellular metabolites during glucose pulse, Dynamics of intracellular metabolites during glucose pulse, Dynamics of macromolecules during glucose pulse, MOSES: dynamic model of glucose pulse
The aim of the study is to test the interplay of the effects of different transcriptional regulators on gene expression during different environmental responses in B. subtilis. For a selected set of transcriptional regulators native proteins are fusion-labelled. The intensity of expression of each reporter protein is measured in the absence of several transcriptional regulators that compete for the RNA polymerase.
Steady state fluxes in yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1
Submitter: Maksim Zakhartsev
Investigation: Steady state metabolic fluxes and metabolite co...
Assays: Steady state extracellular fluxes in anaerobic yeast Saccharomyces cerev...
Steady state concentrations of metabolites in yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1
The main aim of this experiment is to actively grow B.subtilis in presense of glucose until high optical density in an aerobic fermentor and then, at a definite point of the growth, the glucose supply is shut down which leads to complete glucose exhaustion in the media. Simultaneusly samples for transcriptomics, intra and extracellular metabolomics, intra and extracellular proteomics are harvested through out the experiment.
Submitter: Praveen kumar Sappa
Investigation: The transition from growing to non-growing Baci...
Assays: 2D-gelbased analysis of intracellular proteins, Absolute quantification of proteins by the AQUA-technology, Fermentation-BM5_SysMo, Gene expression(Transcriptome), Relative quantification of proteins by metabolic labeling, metabolome-LCMS
Growth of B.subtilis in shakeflask at 57°C; 16°C, 37°C(Control) and 1,2M NaCl in SMM.
Submitter: Praveen kumar Sappa
Investigation: Redefining the Complete Transcriptome of Bacill...
Assays: Tiling array analysis of continuous growth stress conditions in SMM
BMM EtOH, 16, 57 SMM NaCl
Submitter: Praveen kumar Sappa
Investigation: Redefining the Complete Transcriptome of Bacill...
Submitter: Praveen kumar Sappa
Investigation: Redefining the Complete Transcriptome of Bacill...
Assays: Tiling Array analysis of glucose strarved B. subtilis cells