Studies

112 Studies visible to you, out of a total of 243

Personalized liver function tests: A Multiscale Computational Model Predicts Individual Human Liver Function From Single-Cell Metabolism

Understanding how liver function arises from the complex interaction of morphology, perfusion, and metabolism from single cells up to the entire organ requires systems-levels computational approaches. We report a multiscale mathematical model of the Human liver comprising the scales from single hepatocytes, over representation of ultra-structure and micro-circulation
...

Assays: Galactose Modelling

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).

Person responsible: Stefan Henrich

Assays: literature values for allosteric regulation of pyruvate kinase

we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO2 under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue completely dependent on sucrose supply from the mesophyll
...

Assays: Flux Balance Analysis of multi-compartment metabolic model of growing Ar...

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
...

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...

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.

Person responsible: Simon Borger

Assays: No Assays

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
...

Assays: Characterization of flux distribution of S. pyogenes M9 wild type and th...

Effect of benzoate treatment (high concentrations) on ATP levels and Pdr12 expression after pretreatment of cells with low concentrations of benzoic acid.

Person responsible: Martin Valachovic

Assays: No Assays

To see changes in ATP levels in cells with induced ABC transporters. Cells with Pdr12 pump by 10 mM benzoic acid are used.

Person responsible: Martin Valachovic

Assays: ATP measurement under 10mM benzoic acid stress

ATP levels of cells stressed with higher concentrations of benzoic acid (30 mM and 50 mM).

Person responsible: Martin Valachovic

Assays: ATP measurement under 30mM benzoic acid stress, ATP measurement under 50mM benzoic acid stress

Conversion from KEGG Reactome Information to SBTOOLBOX2 format.

Person responsible: Sebastian Curth

Assays: Example for model derivation from KEGG, Integration of data into the model

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
...

Assays: Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae usin...

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.

Assays: B. subtilis Transcription Factor Competition - theoretical interpretation, B. subtilis Transcription Factor Competition - theoretical interpretation

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.

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

Goals:
1. 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).
2. Explaining the observed phenomena in the measurement data.
3. Predicting unmeasured variables especially of the gene expression regulatory loops.

Means:
1. Experiments (chemostat experiments within the aerobiosis scale).
2. Kinetic modelling (especially
...

Assays: Kinetic modelling of Escherichia coli's electron transport chain, Kinetic modelling of Escherichia coli's electron transport chain coupled...

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.

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

Bioinformatic studies to elucidate the role of 14-3-3 proteins in cation homeostasis.

Assays: In silico Promotor Anaysis, Interaction Database Analysis

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.

Assays: No Assays

Carbon loss due to instability of gluconeogenic pathway intermediates (BPG, GAP, DHAP) at high temperature in S. solfataricus

Assays: Experimental Validation Gluconeogenesis in S. solfataricus, Model Validation Gluconeogenesis in S. solfataricus

Cell survival was determined under different benzoic acid concentrations

Person responsible: Martin Valachovic

Assays: No Assays

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.

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

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.

Assays: ParB-GFP ChIP on chip

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

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...

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.

Assays: IPTG induction of sigmaB in BSA115, IPTG induction of sigmaB in BSA115, Stressosome activation dynamics

Predictions made using the core model for combinatorial perturbations to the model simulating combined effects from OE, KO mutants, perturbations and time series concentrations.

Person responsible: Niels Zondervan

Assays: Combinatorial mutant, perturbation and time series predictions

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)

Person responsible: Olga Krebs

Assays: Metabolomics Master Template

Here you will find guidelines for creating MIAPE compliant proteomics data files as well as examples and links to online tools and resources

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.

Assays: Affy Transcriptomics Templates, Chip-chip Excel Template, General Transcriptomics Templates, NimbleGen Transcriptomics Templates, RT-PCR Excel Template

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?

Assays: Current voltage relation for different external KCl, Current-voltage relation for different internal potassium

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?

Assays: Current voltage relation for different external KCl, Current-voltage relation for different internal potassium

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
...

Person responsible: Christine Clayton

Assays: Modelling the gene expression cascade with length-dependent processes, mRNA decay assay, pre-mRNA processing rate

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.

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

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).

Assays: No Assays

We developed a new metabolomics protocol, which involved a comparison of different harvesting techniques, quenching solutions and extraction methods.

Assays: Test extraction methods, Test quenching buffers

No description specified

Person responsible: Sebastian Curth

Assays: Theoretical calculation of quenching time and quenching temperature

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?

Person responsible: Falko Krause

Assays: Stable membrane potential, Stable pH, Stable potassium concentration, Stable volume

How does the transport of potassium and hydrogen ions effect the concentrations in the near surrounding of the cell.

Person responsible: Falko Krause

Assays: Potassium changes, Proton changes

Growth-factor deprived mCFU-E cells (5x106 cells per condition) and BaF3-EpoR cells (1x107 cells per condition) were stimulated with different Epo doses and absolute concentrations were determined for pEpoR (B), pAKT (C), ppERK (D). The scale for pS6 (E) was estimated in arbitrary units. GTP-Ras (F) and ppERK were determined upon stimulation with indicated, color-coded Epo doses. pEpoR was analyzed by immunoprecipitation followed by immunoblotting, GTP-Ras was analyzed after pulldown using a
...

Assays: Mathematical models of the Epo-induced AKT, ERK and S6 activation., Source data for Figure 2: Experimental time-resolved quantitative immuno...

Transcriptional response to a sudden increase in extracellular ligand (hormone), for the six network designs of (A). The transcriptional response is taken to equal the ratio ReNrL/Retotal, i.e., the fraction of REs attaching ligand-bound NR. The ligand concentration was increased from 0 to 0.005 nM and maintained constant at the latter level. The observation that design 6 is higher than all other designs at long times is robust for parameter changes up to a factor of 3.

Assays: Model nuclear receptor (NR) signaling

For all experiments, primary CFU-E cells were starved and stimulated with 5 U/ml Epo. At the indicated time points, samples were subjected to quantitative immunoblotting. Experimental data (black circles) with estimated standard errors and trajectories of the best fit (solid lines) are represented. Mass spectrometry data represent replicates of four independent experiments.

Assays: Model for JAK2/STAT5 signaling, Source data for Figure 3A: Experimental quantitative immunoblotting data.

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
...

Assays: 13C Metabolic Flux Analysis of Bacillus subtilis 168 in continuous high-...

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.

Assays: No Assays

No description specified

Assays: Whole genome sequencing (Illumina)

No description specified

Person responsible: Ron Henkel

Assays: BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var

Computational modeling of human caffeine clearance by the liver.

More information available from
https://github.com/matthiaskoenig/caffeine

Assays: No Assays

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.

Assays: Identification of dynamically similar transcript profiles

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.

Assays: Transcritome data_Identification of targets of the essential RNase Y of ...

test test

Assays: test

How do the fluxes of rubidium (potassium) change during potassium starvation.

Person responsible: Falko Krause

Assays: Ammonium fluxes, Potassium fluxes, Proton fluxes

How does the flux of potassium, hydrogen change during potassium uptake? Which ions are involved in maintaining the required charge balance?

Person responsible: Falko Krause

Assays: Additional fluxes, Potassium fluxes, Proton fluxes

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
...

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.

Assays: Trypanothione synthetase ATP consumption steady state data, Trypanothione synthetase Gsp and T(SH)2 production measured by HPLC

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

Assays: Creating kinetic model of Trypanothione Synthetase

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.

Assays: Describing of membrane potential changes in response to proton fluxes., Determination of kinetic properties based on MIFE flux data and measurem..., Modelling of the Trk-current

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.

Assays: Kinetics of L-lactate dehydrogenase from S. pyogenes, E. faecalis, and L...

No description specified

Person responsible: Falko Krause

Assays: HPLC-MS, NMR

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
...

Assays: Generation of uniformly 13C-labelled E. coli extract, LC-MS based absolute quantification of extracellular metabolites, LC-MS based absolute quantification of intracellular metabolites

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

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

Internal metabolites concentrations for time series data (not pulse experiments) and for mutant OE, KO mutants and perturbations
External metabolite concentrations for time series data (not pulse experiments) and for mutant OE, KO mutants and perturbations
Mutant (OE, KO, perturbation) metabolite measurements

Person responsible: Niels Zondervan

Assays: Metabolomics external metabolites measurements

This study includes all the experimental data, SOPs and modelling files for the individual reactions used for the model construction.

Assays: ALD, ATPASE, Culturing and synchronisation of P. falciparum, ENO, G3PDH, GAPDH, GLCtr, GLYtr, HK, LACtr, LDH, PFK, PGI, PGK, PGM, PK, PYRtr, TPI, Trophozoite Isolation and Lysate Preparation

Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus

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

This study includes the experimental data for model validation and the model predictions of that data set.

Assays: GLC incubation, Steady state

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
...

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
...

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.

Assays: Boolean Network Simulation, Bottom up creation of the network from literature, Yeast Interaction Network Analysis

Mathematical modelling of the dynamic shift experiments and the effect of pH upon gene regulation.

Assays: Steady state study of the effect of gene regulation on yields of end-pro..., Time-dependent simulations

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.

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

No description specified

Assays: Insilico Promotor Anaysis

Does the general proteome of yeast cells change in a strain lacking Trk1,2 transporter? Under which conditions?

Assays: 2D Gel Analysis

What is the proteome of starved cells. Main characteristics?

Person responsible: Falko Krause

Assays: 2D-Gel Electrophoresis, Protein Identification - MS

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
...

Person responsible: Stefan Henrich

Assays: Pyruvate formate-lyase (PFL): literature review, structure analysis and ...

No description specified

Person responsible: Falko Krause

Assays: No Assays

No description specified

Assays: No Assays

Creation of the KEGG based Reactome

Person responsible: Sebastian Curth

Assays: Graph Analysis, KEGG Data Mining

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

Person responsible: Not available

Assays: Genome-Scale Model Enterococcus faecalis V583, Genome-scale model of Streptococcus pyogenes

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.

Assays: No Assays

No description specified

Assays: Metabolic pathway curation

Steady state concentrations of metabolites in yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1

Assays: Steady state concentrations of extracellular metabolites in yeast Saccha..., Steady state concentrations of intracellular metabolites in yeast Saccha...

Steady state fluxes in yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1

Assays: Steady state extracellular fluxes in anaerobic yeast Saccharomyces cerev...

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
...

Assays: BIOLOG substrate utilization assay, Maximal specific growth rates of the three lactic acid bacteria and thei..., Physiological characterization of Lactic acid bacteria grown in C-limite...

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.
...

Assays: Generation of RNAi cell lines in T.brucei brucei 2T1 cell line, Induction of RNA interference in T.brucei brucei 2T1 cell line

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
...

Assays: Intracellular metabolite concentrations in T. brucei under pH stress

This study aims to establish the optimum conditions and assay methods for measuring ATP levels

Person responsible: Martin Valachovic

Assays: Compare ATP extraction methods

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
...

Assays: RNA-Seq

Genotype: Wildtype (M145E)
Medium: Phosphate-limited (F134)

Assays: Online/offline measurements, metabolomics, proteomics, transcriptomics

Multi experimental approach to define the gene expression remodelling under potassium starvation conditions.

Person responsible: Falko Krause

Assays: LacZ Reporters, RT-PCR, Time Course Micro Array Experiment

No description specified

Assays: No Assays

Annotation retrieval

Person responsible: Sebastian Curth

Assays: No Assays

Growth of B.subtilis in shakeflask at 57°C; 16°C, 37°C(Control) and 1,2M NaCl in SMM.

Assays: Tiling array analysis of continuous growth stress conditions in SMM

Studies on the effect of deletion of genes encoding 14-3-3 proteins on the transcriptional response of yeast cells to potassium starvation.

Assays: No Assays

Contains copy number per locus tag at different times of Growth between 0.25h and 96 hours.
M. pneumoniae was grown in Batch, cells attached to the bottom of the flask (single cell layer), non stirred, non aerated.

Person responsible: Niels Zondervan

Assays: No Assays

Experiments using shake flask cultures to measure dynamics associated with sigB response.

Assays: No Assays

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
...

Assays: Intracellular metabolite concentrations in T. brucei exposed to oxidativ..., Metabolite profiling on T. brucei exposed to oxidative stress

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