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
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Created: 8th May 2017 at 09:23
Last updated: 20th Nov 2019 at 00:04
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, MRC-UNICORN, Test project for Sciender, qPCR, Artificial organelles_Pathogen digestion, Supplementary Information 2 associated with the manuscript entitled " Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", FAIR Functional Enrichment, PTPN11 mutagenesis, Supplementary Information 2 associated with the manuscript entitled "Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", iPlacenta- Placenta on a chip, Near Surface Wave-Coherent Measurements of Temperature and Humidity, A Meta-Analysis of Functional Recovery of Aphasia after Stroke by Acupuncture Combined with Language Rehabilitation Training, Phytoplankton phenology in the Bay of Biscay: using remote sensing to assess and raise awareness of climate change impacts on the sea, Master-BIDS, Endometriosis, Vitis Data Crop, MESI-STRAT Review, Establishing an innovative and transnational feed production approach for reduced climate impact of the aquaculture sector and future food supply, ARAX: a web-based computational reasoning system for translational biomedicine, Adaptation of Salmonella enterica, I AM FRONTIER, ., PhD Nicotinic Acetylcholine Receptors, SFB1361 playground, Amaizing, Conspicuous chloroplast with LHC‒PSI/II‒megacomplex and diverse PBPs in the marine dinoflagellate Prorocentrum cordatum, icpm-kth, Catabolic network of the gut bacteria P. vulgatus, SDBV/HITS, sample project, TestingSeek, Genomic Medicine, Remodeling of cIV, Virtual Human Platform for Safety Assessment, PROMISEANG, URGI, Matsutake, UNDESIRABLE EFFECTS OF POST COVID-19 VACCINATION: A DESCRIPTIVE STUDY, WINTER 2022, Semantic Table Interpretation in Chemistry, MS identification of L infantum proteins related to their drug resistance patterns for new drug targets identification and ecotoxicological evaluations of their environmental and interspecies impact, the Supplementary materials for paper, ToxiGen - Reproductive toxicity and transgenerational effects of petroleum mixtures in fish, PhotoBoost, Measurement of Fisheries Provisioning Services and its Pressure to Support Sustainability of Fisheries in The Jatigede Reservoir, Indonesia, FIsh data on 2022 in the Jatigede Reservoir
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
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
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
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
Snapshots: No snapshots
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.
Date Published: 4th Apr 2013
Publication Type: Not specified
PubMed ID: 23549481
Citation: Mol Syst Biol. 2013;9:653. doi: 10.1038/msb.2013.6.