Investigations

61 Investigations visible to you, out of a total of 123

The aim of this project is to develop a detailed kinetic model of the CcpA-dependent regulatory network, the key regulon of flux regulation in B. subtilis. Thereby involved are more than 300 genes e.g. catabolism, overflow metabolism, the TCA cycle and amino acid anabolism which are regulated via carbon catabolite regulation (CCR)

Studies: Glucose starvation specific responses – Quantification of thermodynamic ...

Protein abundance of AKT and ERK pathway components governs cell-type- specific regulation of proliferation

Studies: Figure 2: Model calibration with time-resolved quantitative immunoblot d...

Basically extending SYSMO-LAB 1st phase into second with addition of fourth species, Lb. plantarum. The main focus is amino acid metabolism. primary metabolisms, like glycolysis is also interest.

Studies: Arginine and Glutamine metabolism in S. pyogenes, Determination of essential amino acids for Streptococcus pyogenes

The Sulfolobus systems biology (‘‘SulfoSYS’’)-project represented the first (hyper-)thermophilic Systems Biology project, funded within the European trans-national research initiative ‘‘Systems Biology of Microorganisms’’. Within the SulfoSYS-project, focus lies on studying the effect of temperature variation on the central carbohydrate metabolism (CCM) of S. solfataricus that is characterized by the branched Entner–Doudoroff (ED)-like pathway for sugar (glucose, galactose) degradation and the
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Studies: Pilot experiment - S. solfataricus grown at 70 and 80 C.

The electron transport chain of E. coli is branched. Different NAD Dehydrogenases and terminal oxidases are known to be expressed at different oxygen availabilities. By deleting multiple genes mutant strains were constructed that posses a linear electron transport chain. These mutants were investigated in continous bioreactor experiments with limiting glucose and varying oxygen supply.

Studies: Analysis of Escherichia coli strains with linear respiratory chain

Cultures grown under standard SUMO conditions were analyzed with respect to heterogeneity in gene expression. To this end GFP reporter strains were constructed and GFP expression at single cell level was monitored by flow cytometry.

Studies: No Studies

In Escherichia coli several systems are known to transport glucose into the cytoplasm. A series of mutant strains were constructed, which lack one or more of these uptake systems. These were analyzed in aerobic and anaerobic batch cultures, as well as glucose limited continuous cultivations.

Studies: Characterization of mutant strains with defects in sugar transport systems

Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range

Studies: Figure 3A: Model calibration with experimental data of JAK2-STAT5 signal...

An investigation in the central carbon metabolism of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.

Studies: Carbon Loss at High Temperature, Model Gluconeogenesis

This investigation contains spreadsheet templates and examples for SEEK users to download and use for structuring experimental data. These templates were developed by the SysMO-DB team and the SysMO PALs

Studies: Creating Templates for Proteomics, Creating Templates for Transcriptomics, Creating template for metabolomics data

No description specified

Studies: No Studies

Aim. Constructing a predictive, dynamic model of the redox metabolism of trypanosomes. Aided by
this model we will quantify the impact of gene-expression and metabolic regulation on redox
metabolism. The model will be constructed in an iterative cycle of experimentation – modelling –
analysis – experimentation, such that it can be extended and refined based on new experimental
insights.

Studies: Iterative cycles of model improvement and extension., Modelling of gene expression and Regulation Analysis., Modelling of redox metabolism.

Changing the oxygen availability leads to an adaptation of Escherichia coli at different biological levels. After pertubation of oxygen in chemostat experiments there are very quick responses. This investigation deals with this dynamical behaviour (transitions) 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 and mutants experiments
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Studies: The Escherichia coli dynamical response to oxygen: from molecular intera...

Investigation of how the ENA1 gene is transcriptionally regulated.

Studies: Modelling of the Signaling network regulating the ENA1-gene transcription

Aim: To provide quantitative data that will allow modeling of gene expression for all enzymes of redox metabolism and the pentose phosphate pathway. Modeling will be used to predict enzyme levels based on the integration of an RNA degradation model with translation and protein degradation rates.

Plan: The amounts of a protein in a cell can be determined by the rates of transcription, mRNA processing, translation, mRNA turnover and protein degradation. In trypanosomes analysis is simpler because
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Studies: Determination and integration of abundance, processing efficiency, and d...

methods developed during COSMIC

Studies: Development of a rapid quenching system

The investigation entails the construction and validation of a detailed mathematical model for glycolysis of the malaria parasite Plasmodium falciparum in the blood stage trophozoite form.

Studies: Model analysis, Model construction, Model validation

No description specified

Studies: Hands-On: Tyson1991 - Cell Cycle 6 var

Despite a long history in using C. acetobutylicum, little is known about the regulation of the metabolic shift, the characteristics of key-regulatory elements as well as bottlenecks of the metabolism. Goal of the collaborative project ´COSMIC-2` (Clostridium acetobutylicum Systems Microbiology 2; part of ‘SysMO’) is to increase the knowledge of this clostridial metabolism and its regulatory patterns. The focus will be on the key regulatory and metabolic events that occur during the shift from the
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Studies: Developement metabolomics protocol

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.

Studies: Identification of targets of the essential RNase Y of Bacillus subtilis

Challenge: Comparative analyses, as demonstrated by comparative genomics and bioinformatics, are extremely powerful for (i) transfer of information from (experimentally) well-studied organisms to the other organisms, and (ii) when coupled to functional and phenotypic information, insight in the relative importance of components to the observed differences and simalities. The central principle of this proposal is that important aspects of the functional differences between organisms derive not
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Studies: Comparative modeling and phosphate dependence flux distributions and glu..., Kinetics of L-lactate dehydrogenase from S. pyogenes, E. faecalis and L...., Reconstructing the metabolic pathways of S. pyogenes and E. faecalis fro..., Study of the physiological characterization of three lactic acid bacteri...

Experimental approaches to evaluate cellular response to Potassium limitation. For this purpose, a series of isogenic strains derived from BY4741 and lacking one (TRK1 or TRK2) or both TRK genes encoding specific potassium uptake systems was constructed using the homologous recombination and Cre-lox system.

Studies: Analysis of proton and potassium fluxes, Experimental approaches to determine the dependence of volume, pH and me..., Ion Flux Changes, Key Cell-Physiological Parameters, Long Term Metabolomic Profile, Proteomic Studies, Pysiological Model, Transcriptional Profile

Investigation of dynamics of the central metabolism (glycolysis, PPP, anaplerotic reactions, purines) of yeast Saccharomyces cerevisiae in anaerobic conditions

Studies: Metabolic perturbation of the steady state culture by glucose pulse

Aim. To provide critical quantitative parameter information and to model redox balance by determining the cellular concentration of all enzymes involved in the trypanothione-dependent hydroperoxide detoxification system of trypanosomes and by performing the kinetic characterization of the involved enzymes under pseudo-physiological conditions.

Studies: Determination of the redox state and the total concentration of the tryp..., Kinetic characterization of trypanothione-dependent enzymes, Kinetic modelling of Trypanothione Synthetase to elucidate the enzyme me...

Design principles of nuclear receptor signaling: how complex networking improves signal transduction

Studies: Figure 2B: Transcriptional response to a sudden increase in extracellul...

Integrated systems biology approach including transcriptome, metabolome, biochemistry, proteome analyses and modelling to elucidate the catabolic pathway for L-fucose in S. solfataricus P2.

Studies: Comparison of S. solfataricus grown on l-fucose and d-glucose

Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped
...

Studies: Analysis of central carbon and energy metabolisms of growing Arabidopsis...

Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.

One of these activities is antibiotic production and is widespread in streptomycetes
...

Studies: ScoCyc metabolic pathway curation, Timeseries 1

The aims of this investigation is to quantify metabolites associated with pathways involved in stress responses for parameterising models of oxidative stress metabolism; the measurement of metabolic fluxes of metabolites of interest with intracellular concentrations

Studies: Metabolic flux measurement, Targeted metabolite analysis, Untargeted metabolite analysis

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Studies: No Studies

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.

Studies: A Multiscale Computational Model of Human Galactose Metabolism, Human Caffeine Metabolism

A further investigation of the variation of FNR number in E.coli Cyo/Cyd mutants is carrying out at different oxygen supply levels. The agent-based FNR and ArcBA model is going to be used for this prediction. The number of Cyo or Cyd and other unrelated agents would be set as ‘0’ at the initial XML file with which the model starts. According to the restrictions of supercomputer ‘Iceberg’ (serviced provided by the University of Sheffield), certain parameters, such as memory per node, would be
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Studies: No Studies

A key insight, emerging from discussions and data between the projects PIs, was the importance of switching rates in bistable systems.
While the existence of multiple steady states in bistable systems can be described by universal models (that do not differ between
different systems), switching rates from one stable state to another depend on the molecular details of the system under consideration.

Studies: No Studies

Automated model building using Taverna workflows from KEGG-Database

Studies: Automated Model Building, Reactome Analysis, Transcriptome Analysis

High salinity chemostat cultivation, multiomics sampling (proteome, transcriptome, metabolome, fluxome) and modelling of carbon core metabolism of Bacillus subtilis 168.

Studies: B. subtilis_SysMo2_Chemostat_growthrate-salt, Fluxome analysis of Bacillus subtilis 168 under osmotic stress

Properties of cells lacking the NHA1 gene.

Studies: Current-voltage relations

Multiply perturbations of trypanosome redox metabolism, closing the feedback loop between experimentation and in silioc modelling, allowing model refinement or, where there are unexpected outcomes, re-evaluation.
Providing a dynamic picture of cell physiology by examining programmed metabolic changes during the developmental life-cycle of these parasites as they adapt to very different external milieus, including distinct levels of oxidative stress and unique adaptations of their redox balance
...

Studies: Targeted disruption and over expression of critical enzymes

Experimental approaches to study the mechanism and ions involved in potassium uptake after long term potassium starvation.

Studies: External concentration changes, Ion Flux Changes of Potassnium Uptake Investigation

Bacillus subtilis was subjected to various stress conditions like high temperature(57°C), low temperature(16°C), high osmalarity(1.2M NaCl). The above mentioned stress conditions are again split into two different types as 'continuous stress condition' and 'sudden shock'. All the conditions were then done in biological triplicates.
Transcriptome for these samples was then analysed with Nimblegen Tiling array.

Studies: Transcriptome analysis of glucose starvation in B. subtilis, Transcriptome of continuously stressed B. subtilis, Transcriptome of shocked B. subtilis cells

Investigation of the role of 14-3-3 proteins in the S. cerevisiae cation homeostasis

Studies: Role of 14-3-3 proteins in the localization of proteins involved in cati...

Steady state metabolic fluxes and metabolite concentrations of yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1

Studies: Steady state concentrations of metabolites in yeast Saccharomyces cerevi..., Steady state fluxes in yeast Saccharomyces cerevisiae in anaerobic chemo...

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
...

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...

Transcriptional and physiological responses of anaerobic steady state cultures to pulses of electron acceptors, specifically nitrate, trimethylamine-N-oxide (TMAO)

Studies: No Studies

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
...

Studies: Investigation of different pH values for metabolic shift

Here SYSMO-LAB put all there pre-liminary data files or models ordered per person and project

Studies: Pre-liminary data from Martijn Bekker, Pyruvate formate-lyase (PFL), allosteric regulation of pyruvate kinase

The objective of this project is an integrated understanding the metabolic, proteomic and genetic network that controls the transition from growth to glucose starvation. This transition is a fundamental ecophysiological response that serves as a scientific model for environmental signal integration and is pivotal for industrial fermentations of Bacillus that occur predominantly under nutrient starvation.

Keywords:
Glucose starvation, Transcriptomics, Proteomics, Metabolomics,Bacillus subtilis,

Studies: B. subtilis Transcription Factor Competition, Batchfermentation exp-starv01_090204, Biphase Batch Fermentation(2009/02/04), Controlled sigmaB induction in shake flask, Transition to starvation in shake flask

Tool and work flow development for computational biology.

Studies: No Studies

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Investigating oscillations at the level of yeast populations and individual cells

Studies: Detailed kinetics of yeast glycolytic oscillation, Sustained glycolytic oscillations in individual isolated yeast cells

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