Investigations

62 Investigations visible to you, out of a total of 119
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Studies: ITF_Study_11, ITF_Study_12

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

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...

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
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Studies: ScoCyc metabolic pathway curation, Timeseries 1

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

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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

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

Tool and work flow development for computational biology.

Studies: No Studies

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

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

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

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

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

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

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...

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...

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...

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

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

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

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

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

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

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