Investigations
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Research in Systems Biology involves integrating data and knowledge about the dynamic processes in biological systems in order to understand and model them. By connecting fields such as genomics, proteomics, bioinformatics, mathematics, cell biology, genetics, mathematics, engineering and computer sciences, Systems Biology enables discovery of yet unknown principles underlying the functioning of living cells. At the same time, testable and predictive models of complex cellular pathways and ...
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.
Submitter: Dawie van Niekerk
Studies: Model analysis, Model construction, Model validation
Assays: ALD, ATPASE, Culturing and synchronisation of P. falciparum, ENO, G3PDH, GAPDH, GLC incubation, GLCtr, GLYtr, HK, Inhibition of glucose transport, Inhibition of lactate flux, LACtr, LDH, PFK, PGI, PGK, PGM, PK, PYRtr, Steady state, Supply-demand analysis, TPI, Trophozoite Isolation and Lysate Preparation
Submitter: Ron Henkel
Tool and work flow development for computational biology.
Design principles of nuclear receptor signaling: how complex networking improves signal transduction
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.
Submitter: Araz Zeyniyev
Studies: Arginine and Glutamine metabolism in S. pyogenes, Determination of essential amino acids for Streptococcus pyogenes
Assays: Characterization of flux distribution of S. pyogenes M9 wild type and th..., Construction of in vivo-like buffer for 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
Submitter: Martijn Bekker
Studies: Pre-liminary data from Martijn Bekker, Pyruvate formate-lyase (PFL), allosteric regulation of pyruvate kinase
Assays: Characterization of enzymes involved in butanediol formation, Kinetic behavior of intracellular metabolites of E. faecalis upon a gluc..., Kinetic behavior of intracellular metabolites of L. lactis upon a glucos..., Pyruvate formate-lyase (PFL): literature review, structure analysis and ..., literature values for 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 ...
Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range
Atlantic salmon is a main source of essential ω-3 long-chain polyunsaturated fatty acids (LC-PUFA) in many Western diets, especially eicosapentaenoic acid (20:5n-3, EPA) and docosahexaenoic acid (22:6n-3, DHA). However, farmed salmon meat now contains less healthy ω-3 fatty acids (FA) than before, due to the shift from marine to vegetable lipid feed sources. An important future aquaculture challenge is therefore to maintain a healthy and high EPA/DHA content when farmed salmon is fed a vegetable ...
Submitter: Jon Olav Vik
Studies: GSF1: Salmon feed-switch experiment vegetable and fish oil 2015-2016
Assays: Fatty acid contents in feed using Gas chromatography/FAME analysis, Fatty acid contents in tissues using Gas chromatography/FAME analysis, Feed switch 2015-09 Solbergstranda, pilot proteomics, Feed switch 2015-09, 2016-01 Solbergstranda, gross phenotypes, Feed switch 2015-09, 2016-01 Solbergstranda, gut microbiota composition,..., Lipidomics, Metabolomics, Overview of RNAseq datasets in GenoSysFat, RNA sequencing Feed switch- Liver and Gut
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 ...
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.
Submitter: Alejandro Leroux
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...
Assays: Creating kinetic model of Trypanothione Synthetase, Trypanothione synthetase ATP consumption steady state data, Trypanothione synthetase Gsp and T(SH)2 production measured by HPLC
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.
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.
Submitter: Katja Bettenbrock
Studies: Analysis of Escherichia coli strains with linear respiratory chain
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...
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.
Submitter: Jacky Snoep
Studies: Carbon Loss at High Temperature, Model Gluconeogenesis
Assays: Experimental Validation Gluconeogenesis in S. solfataricus, FBPAase, FBPAase Modelling, GAPDH, GAPDH Modelling, Model Validation Gluconeogenesis in S. solfataricus, Modelling Metabolite Degradation at High Temperature, PGK, PGK Modelling, Reconstituted Gluconeogenesis System, TPI, TPI Modelling, Temperature Degradation of Gluconeogenic Intermediates
Investigating oscillations at the level of yeast populations and individual cells
Submitter: Katy Wolstencroft
Studies: Detailed kinetics of yeast glycolytic oscillation, Sustained glycolytic oscillations in individual isolated yeast cells
Assays: Detailed kinetic model of yeast glycolytic oscillation, Metabolite concentrations in yeast glycolytic oscillations, Modelling sustained glycolytic oscillations in individual isolated yeast...
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 ...
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.
Submitter: Sonja Steinsiek
Studies: Characterization of mutant strains with defects in sugar transport systems
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
Transcriptional and physiological responses of anaerobic steady state cultures to pulses of electron acceptors, specifically nitrate, trimethylamine-N-oxide (TMAO)
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.
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
Submitter: Dong-Hyun Kim
Studies: Metabolic flux measurement, Targeted metabolite analysis, Untargeted metabolite analysis
Assays: Generation of uniformly 13C-labelled E. coli extract, Intracellular metabolite concentrations in T. brucei exposed to oxidativ..., Intracellular metabolite concentrations in T. brucei under pH stress, LC-MS based absolute quantification of extracellular metabolites, LC-MS based absolute quantification of intracellular metabolites, Metabolite profiling on T. brucei exposed to oxidative stress
Automated model building using Taverna workflows from KEGG-Database
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 ...