Studies

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

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.

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
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Computational modeling of human caffeine clearance by the liver.

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

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

To investigate amino acid degradation pathways in Sulfolobus solfataricus transcriptome, proteome and metabolome analyses were performed on cells grown on caseinhydrolysate as carbon source. Cells grown with glucose served as reference condition. Metabolic modelling was used to compare the efficiency of different degradation routes.

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

First kinetically parameterized mathematical model of the S.solfataricus Entner-Doudoroff (ED) pathway, from Glucose consumption
to Pyruvate production, i.e. the CCM core. This model integrates several sources of biological data,
namely enzyme activities, half-life measurements and metabolomics data.

Experimental study for hands on session

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

Here you will find guidelines for creating MAGE-TAB compliant transcriptomics data files as well as examples and links to online tools and resources.

WP2- In vitro Studies

A novel study with pieces of liver kept alive and “fed” in laboratory dishes, studying for each fish how different feeds affect metabolism and gene activity.

Project description by Tom Harvey
Liver slice methods
Optimization of the liver slice technique is needed before data sets can be generated for use in metabolic models. This will include experiments to determine the optimal harvest time, fatty acid concentration, and inclusion of additives to better mimic the in vivo
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WP2- In vitro Studies

A novel study with pieces of liver kept alive and “fed” in laboratory dishes, studying for each fish how different feeds affect metabolism and gene activity.

Project description by Tom Harvey
Liver slice methods
Optimization of the liver slice technique is needed before data sets can be generated for use in metabolic models. This will include experiments to determine the optimal harvest time, fatty acid concentration, and inclusion of additives to better mimic the in vivo
...

WP2- In vitro Studies

A novel study with pieces of liver kept alive and “fed” in laboratory dishes, studying for each fish how different feeds affect metabolism and gene activity.

Livers from Atlantic Salmon raised on either VO or MA diets (from the saltwater feed switch trial) were sliced and cultured under conditions mimicking VO or MA switch from the feeding trial. VO cultures were supplemented with 11.2µM palmitic acid, and 58.8µM gamma-linoleic acid. MA cultures were supplemented with 24.5µM
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WP2- In vitro Studies

A novel study with pieces of liver kept alive and “fed” in laboratory dishes, studying for each fish how different feeds affect metabolism and gene activity.

Livers from Atlantic Salmon raised on either VO or MA diets (from the freshwater feed switch trial) were sliced and cultured under conditions mimicking VO or MA switch from the feeding trial. VO cultures were supplemented with 11.2µM palmitic acid, 28µM oleic acid, and 30.8µM gamma-linoleic acid. MA cultures were
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(corresponding to Figure 4 of the original publication)

This is a part of Tom´s PhD study.

RNA sequencing is done to quantify the gene expression in various tissues.
Total RNA from several Zebrafish, Medaka, and Rainbow Trout tissues was extracted and sequenced. Illumina TruSeq libraries were prepared in house then sent to the Norwegian Sequencing Center and run on an Illumina HiSeq2500 with 125bp PE reads. This data will be used to study variation in gene expression across tissues and species, providing insights into possible neo-functionalization,
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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.

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
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