Metabolomics measurements

Projects that do not fall under current programmes.

The MycoSynVac project AIMS at using cutting-edge synthetic biology methodologies to engineer Mycoplasma pneumoniae as a universal chassis for vaccination. Designing a universal Mycoplasma chassis that can be deployed as single- or multi-vaccine in a range of animal hosts. Annually, infections caused by Mycoplasma species in poultry, cows, and pigs result in multimillion Euro losses in the USA and Europe. There is no effective vaccination against many Mycoplasmas that infect pets, humans and farm ...

1. To develop a whole-cell dynamic model framework of the metabolism of M. pneumoniae
2. To build upon M. pneumoniae models to develop a genome-scale, constraint-based model of M. hyopneumoniae for vaccine optimization
3. To deploy the metabolic model(s) to: 1) the rational design and optimization of the vaccine chassis; 2) aid the development of a higher-growth rate chassis; 3) assist the development of a nutrient optimized a serum-free growth medium and; 4) assess, at genome scale, the metabolic ...

Metabolomics time series measurements for internal metabolites for 6h, 24h and 48h for multiple experiments. Largely based on MAss spectrometry, bioluminescence kits to measure NAD, NADH at 24h, other time points are infered from relative measurements times the absolute measurements at 24h.

Measurements of external metabolites based on growth curve data. Flux estimates for uptake of external metabolites such as glucose and production rates for external metabolites lactate and acetate

Contains the analysis of the internal metabolite concentrations of the 40 independend samples Pearson correlation was used to generate heatmaps Pearson correlation with p-value cutof of 0.001 was used and as input for a correlation network (grouping using H-clust) Principal component analysis was performed on samples, F-ion and H-ion data combined and seperately Zip files contains the data (FC.txt), PCA and heatmap plots and the script to re-generate these plots

Simple overview of all samples used for training, internal validation by copasi en external validation. Overview of samples metadata, mean metabolite concentration and enzyme concentrations used in the model. Only metabolites present in the model are shown.

Contains time series metabolomics measurements in mM from different experiments. Measurements of these internal metabolites should be combined with Growth curve A measurements forthe external metabolites. Contains mean and standard deviation for a few but not all mutants based on multiple time series experiments carried out over the years. Daniel 3rd experiment data is the most complete and is together with Wodke and Tobias measurements used as training data for the model.

Contains for all samples, mean metabolite concentration and shows enzyme concentration used in model fitting and simmulations. Only metabolite present in the model are shown.

Contains: -Relative metabolite measurements at different time points from all experiments -Absolute metabolite measurements for amino-acid analysis of the proteome and the cytosol -Effect on adding CaCl2, KCl or NaCl to the medium on growth -Effect of spiking of growth medium with additional amino acids

Contains relative mutant (OE, KO) perturbation and time series samples metabolite concentrations and enzyme fold change of targeted enzymes used for model validation. Measured are the relative fold change, Mean and SD of log2 fold change values are based on multiple measurements per sample (minimum of three). Contains input data for Automated Model simulations pipeline to load and update the models metabolite concentrations and enzyme parameters to simulate all sample using a custom python script ...

Master file, aggregates metabolite concentrations inside and outside the cell, protein copy number and flux estimates for metabolites in the core model. Based on all internal metabolite concentrations, external metabolite concentrations from growth curve data, flux of glucose, lactate and acetate based on growth curve data and protein copy number data for enzyme concentrations. Combines absolute and relative measurements and metabolomics measurements from different experiment to get an as complete ...

Contains growth curve data such as Glucose uptake rate, lactate and acetate production at different time points. Growth curve A was used train the model with external glucose concentration as well as external lactate, acetate concentration and estimated glucose acetate and lactate flux

Contains relative metabolite concentrations for 40 samples based on technical triplicates. Medium and SD values were calculated and used for 1000 sampled simmulations (sampling from the measurement distribution per metabolite) per sample. Also contains annotion to link metabolite concentrations and protein fold change measurements for OE and KO mutants to the model as well as external glucose, acetate and lactate concentrations. A SBtab like format was used to easily load the MEAN and SD metabolite ...

Contains the FC metabolite concentration values data and a R script to perform PCA, generate hetamaps and a correlation network.

Metabolomics perturbation sample preparation and description of how the exact details of the perturbations. Perturbations: -Glucose starvation -Amino acid starvation -Fe2+ depletion -Oxidative stress via H2O2 -Glycerol addition to the medium