Contains the absolute copy number per locus tag during growth between 0.25 and 96hours of growth
Growth in batch, cells attached to the bottom of the flask, non-aerated, non-stirred
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
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.
Person responsible: Niels Zondervan
Snapshots: No snapshots
Contributor: Niels Zondervan
Assay type: Transcriptional Profiling
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Modelling of M. pneumoniae metabolism
Organisms: No organisms
SOPs: No SOPs
Authors: T. Maier, J. Marcos, J. A. Wodke, B. Paetzold, M. Liebeke, R. Gutierrez-Gallego, Luis Serrano
Date Published: 20th Apr 2013
Journal: Mol Biosyst
PubMed ID: 23598864
Citation: Mol Biosyst. 2013 Jul;9(7):1743-55. doi: 10.1039/c3mb70113a. Epub 2013 Apr 19.