Studies

127 Studies visible to you, out of a total of 205

Internal metabolites concentrations for time series data (not pulse experiments) and for mutant OE, KO mutants and perturbations

Person responsible: Niels Zondervan

Assays: No Assays

External metabolite concentrations from growth curve data. Growth curve A was used to estimate Lactate, Acetea and Glucose flux for 6h and 24h data

Person responsible: Niels Zondervan

Assays: No Assays

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...

No description specified

Person responsible: Andreas Ankenbauer

Assays: Model split up of grwoth rates, sampling for transcriptome analysing

No description specified

Assays: Metabolic pathway curation

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

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

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.

Assays: Enzyme assays using cell-free extracts of S. solfataricus

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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Assays: Galactose Modelling

Experimental study for hands on session

Assays: How to use templates to structure experimental data

No description specified

Person responsible: Ron Henkel

Assays: BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var

No description specified

Assays: Sally whole genome sequence

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, Templates for RNA-Seq data

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
...

Person responsible: Thomas Harvey

Assays: Lipidomics, Microscopy, RNA sequencing, Viability test

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
...

Person responsible: Thomas Harvey

Assays: Lipidomics, Microscopy, RNA sequencing, Viability test

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
...

Person responsible: Thomas Harvey

Assays: Lipidomics, Microscopy, RNA sequencing, Viability test

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
...

Person responsible: Thomas Harvey

Assays: Lipidomics, Microscopy, RNA sequencing, Viability test

No description specified

Person responsible: Fabian Grammes

Assays: Sally HiSeq, Sally Miseq

(corresponding to Figure 4 of the original publication)

Person responsible: Dagmar Waltemath

Assays: increased affinity of calmodulin for calcium

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,
...

Person responsible: Graceline Tina Kirubakaran

Assays: Tissue panel for gene expression in ZF, Med, RT, Tissue panel for gene expression in ZF,Med,RT- RNA sequencing

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

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...

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 ...

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

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