Metabolomics perturbation sample preparation and description of how the exact details of the perturbations.
-Amino acid starvation
-Oxidative stress via H2O2
-Glycerol addition to the medium
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Created: 3rd May 2017 at 09:41
Last updated: 14th Jan 2019 at 16:00
Last used: 4th Jul 2020 at 00:09
Institutions: CRG Centre for Genomic Regulationhttps://orcid.org/0000-0001-7568-4353
Universitat Autónoma de Barcelona : Barcelona, Spain
Institutions: CRG Centre for Genomic Regulationhttps://orcid.org/0000-0002-5276-1392
Luis Serrano did his PhD at the CBM (Madrid, Spain) on Cell Biology. Then he spent 4 years in the laboratory of Prof. A.R. Fehrs (MRC, UK) working in protein folding. In 1993, he became Group Leader at the EMBL (Heidelberg, Germany) working in Protein Folding and design. Ten years later, he was appointed head of the Structural & Computational Biology programme at the EMBL and he started to work on Systems Biology. By the end of 2006 he moved back to Spain to lead a programme working on Systems
Institutions: Wageningen University & Researchhttps://orcid.org/0000-0001-7049-5334
I am a researcher (PhD student) working at Wageningen University & Research as bioinformatician and modeller. I am working as part of the MycoSynVac (http://www.mycosynvac.eu/) project on dynamic modelling of central carbon metabolism in M. pneumoniae, to be extended to full dynamic modelling of metabolism to be implemented in a whole cell model.
I am also looking into possibilities to improve standards in model generation using semantic technologies, improving automatic generation, annotation
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
Studies: Core Model predictions, Core Model training, Core model predicting combined mutations and perturbations, Genome-scale, constraint-based metabolic modeling of M. hyopneumonia, Metabolomics measurements, Proteomics analysis, Transcriptomics of M. pneumoniae at different times of growth
Assays: 40 samples data analysis - metabolite correlation, 40 samples, OE mutants of glycolysis and pyruvate metabolism enzymes com..., All samples data, Comparison of Kcat values from the model and values from literature, Construction and training of the core model, Construction of a Genome Scale Metabolitic model of M. hyopneumoniae, Dynamic model simmulation pipeline, Metabolic control analysis (local and global), Metabolomics external metabolites measurements, Metabolomics internal metabolites, time series measurements, Proteomics assay, Transcriptomics assay of M. pneumoniae at diferent times of growth, Validation by simulating independent mutant and perturbation samples
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
Person responsible: Niels Zondervan
Snapshots: No snapshots
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.
Submitter: Niels Zondervan
Assay type: Experimental Assay Type
Technology type: Mass Spectrometry
Snapshots: No snapshots
Investigation: Modelling of M. pneumoniae metabolism
Study: Metabolomics measurements
Organisms: No organisms
Data files: 40 samples internal metabolite concentrations F..., All_samples_mean_meatbolite_concentration&enzym..., Internal metabolite concentraitons for mutants,..., Internal metabolite concentrations time series, Master file, metabolite concentration, protein ..., Metabolites all experiments, relative measurements