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.
SEEK ID: https://fairdomhub.org/studies/261
Experimentalists: Tobias Maier
- People (4)
- Programmes (1)
- Projects (1)
- Investigations (1)
- Assays (1)
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Institutions: CRG Centre for Genomic Regulationhttps://orcid.org/0000-0001-7568-4353
Universitat Autónoma de Barcelona : Barcelona, Spain Dra. biotechnolog
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 ...
Projects that do not fall under current programmes.
Projects: Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology, iRhythmics, INBioPharm, EmPowerPutida, Systo models, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, Multiscale modelling of state transitions in the host-microbiome-brain network, Extremophiles metabolsim, NAD COMPARTMENTATION, Agro-ecological modelling, Bergen(Ziegler lab) project AF-NADase, NAMPT affinity, Stress granules, Modelling COVID-19 epidemics, Bio-crop, ORHIZON, Coastal Data, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, hybrid sequencing, HOST-PAR, BioCreative VII, Boolean modeling of Parkinson disease map, Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish, Selective Destruction in Ageing, Viral Metagenomic, Synthetic biology in Synechococcus for bioeconomy applications (SynEco), testproject, SDBV ephemeral data exchanges, Test project, The BeeProject, PHENET, LiceVault, EbN1 Systems Biology, UMRPégase, DeCipher, Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum, middle ear, datamgmt, Institut Pasteur's projects, The nucleus of Prorocentrum cordatum, qpcr
Web page: Not specified
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 ...
- To develop a whole-cell dynamic model framework of the metabolism of M. pneumoniae
- To build upon M. pneumoniae models to develop a genome-scale, constraint-based model of M. hyopneumoniae for vaccine optimization
- 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 ...
Submitter: Niels Zondervan
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
Submitter: Niels Zondervan
Assay type: Transcriptional Profiling
Technology type: Technology Type
Investigation: Modelling of M. pneumoniae metabolism
Organisms: No organisms
SOPs: No SOPs
Snapshots: No snapshots
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
Investigations: Modelling of M. pneumoniae metabolism
Authors: T. Maier, J. Marcos, J. A. Wodke, B. Paetzold, M. Liebeke, R. Gutierrez-Gallego, L. Serrano
Date Published: 20th Apr 2013
Publication Type: Not specified
PubMed ID: 23598864
Citation: Mol Biosyst. 2013 Jul;9(7):1743-55. doi: 10.1039/c3mb70113a. Epub 2013 Apr 19.