EbN1 Systems Biology
OverviewProgramme: Independent Projects
SEEK ID: https://fairdomhub.org/projects/287
Public web page: Not specified
Organisms: Aromatoleum aromaticum
FAIRDOM PALs: No PALs for this Project
Project created: 20th Apr 2022
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Projects: EbN1 Systems Biology
Institutions: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Projects: SulfoSys, PSYSMO, SulfoSys - Biotec, EbN1 Systems Biology
Institutions: University of Braunschweig
Projects: EbN1 Systems Biology, Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum, The nucleus of Prorocentrum cordatum, Conspicuous chloroplast with LHC‒PSI/II‒megacomplex and diverse PBPs in the marine dinoflagellate Prorocentrum cordatum, Proteogneomics of Desulfobacteraceae members
Institutions: Carl von Ossietzky University of Oldenburg Institute for Chemistry and Biology of the Marine Environment (ICBM)
https://orcid.org/0000-0001-7253-3373
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, 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, ImmPort - data sharing, MESI-Review 2024, REWIRED: comparative RNA-seq and ATAC-seq in six salmonids and six outgroup telest fishes, REWIRED, Data Repository, APPN Test Project, Enhanced Anticancer Effect of Thymidylate Synthase Dimer Disrupters Promoting Intracellular Accumulation, BIDS, BioRECIPE representation format, UMass Chan BioImage DMS Core_FAIR Metadata Templates, Function, control and engineering of microbial methylotrophy, Pectobacterium pangenome, New Optical Coherence Tomography Biomarkers Identified with Deep Learning for Risk Stratification of Patients with Age-related Macular Degeneration, Virulence-related genes expression in planktonic mixed cultures of Candida albicans and non-albicans Candida species, Screening of Secondary Plant Metabolites on Antihelmintic Activity in Ascaris scum, Munich Cluster for Systems Neurology, Test project May 2024, Biospecimen Collection Protocol, Winter Wheat (Triticum aestivum L.) Grain Yield, Quality, and Net Photosynthesis When Grown Under Semi-Transparent Cadmium Telluride Photovoltaic Modules Near Maturity, Benefit for All FAIR Data, Implementation of Nanopore Sequencing for Detection of Treatment Induced Transcriptomic and Epitranscriptomic Changes in Leukaemic Tumour Models, DPL, Glycogen Metabolism in bacteria, ILS Ceramide Ring Trial, Project Test, DeepCurate, Revisiting mutational resistance to ampicillin and cefotaxime in Haemophilus influenzae, Cancer Systems Biology Consortium (CSBC), Biochemical characterization of the feedforward loop between CDK1 and FOXM1 in epidermal stem cells, Drug Discovery and Biotechnology Standard Operating Procedures, EDITH (Ecosystem Digital Twins in Health) test project, Fluid flow project, Smart Garden Watering System, The role of different fatty acids, AQUACIRCLE, IDIM, Sampling vicinity of industrial settings for pathogens and GMO identification, RNA-seq data for paper, RNA-seq data
Web page: Not specified
Members of the genus Aromatoleum are cosmopolitan in diverse habitats and utilize a broad range of recalcitrant organic molecules coupled to denitrification or O2-respiration. To gain a holistic understanding of the model organism A. aromaticum EbN1T, we here studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate and acetate utilized under nitrate-reducing vs. oxic conditions. Multi-OMICS (transcriptome, proteome and metabolome) ...
Submitter: Meina Neumann-Schaal
Studies: Experimental multi-OMICS, Genome re-annotation, Metabolic Modelling
Assays: CoA LC/MS Data, Cultivation for multi-OMICS, EbN1 Genome re-annotation, Metabolic modeling of EbN1, Proteomic data, Scenario files for Metano metabolic modeling, Transcriptomic data, non-volatile metabolites GC/MS
Submitter: Meina Neumann-Schaal
Investigation: Systems biology investigation of aromatic compo...
Assays: CoA LC/MS Data, Cultivation for multi-OMICS, Proteomic data, Transcriptomic data, non-volatile metabolites GC/MS
Submitter: Meina Neumann-Schaal
Investigation: Systems biology investigation of aromatic compo...
Assays: EbN1 Genome re-annotation
Submitter: Meina Neumann-Schaal
Investigation: Systems biology investigation of aromatic compo...
Assays: Metabolic modeling of EbN1, Scenario files for Metano metabolic modeling
Submitter: Sarah Kirstein
Assay type: Experimental Assay Type
Technology type: Gas Chromatography Mass Spectrometry
Investigation: Systems biology investigation of aromatic compo...
Study: Experimental multi-OMICS
Submitter: Patrick Becker
Assay type: Transcriptomics
Technology type: Rna-seq
Investigation: Systems biology investigation of aromatic compo...
Study: Experimental multi-OMICS
Submitter: Lars Wöhlbrand
Assay type: Protein Identification
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: Systems biology investigation of aromatic compo...
Study: Experimental multi-OMICS
Submitter: Patrick Becker
Assay type: Genomics
Technology type: Technology Type
Investigation: Systems biology investigation of aromatic compo...
Study: Genome re-annotation
All files for metabolic modeling using the Metano toolbox, including the scenarios and flux balance analyses.
Submitter: Julia Koblitz
Biological problem addressed: Model Analysis Type
Investigation: Systems biology investigation of aromatic compo...
Study: Metabolic Modelling
All flux balance analyses of the stoichiometric model
Submitter: Julia Koblitz
Biological problem addressed: Modelling analysis
Investigation: Systems biology investigation of aromatic compo...
Study: Metabolic Modelling
Harvest optical densites and methods of transcriptom, proteom and metabolom samples for all tested substrat conditions.
Submitter: Meina Neumann-Schaal
Assay type: Experimental Assay Type
Technology type: Cultivation experiment
Investigation: Systems biology investigation of aromatic compo...
Study: Experimental multi-OMICS
Submitter: Meina Neumann-Schaal
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography Mass Spectrometry
Investigation: Systems biology investigation of aromatic compo...
Study: Experimental multi-OMICS
Submitter: Daniel Wünsch
Provider Name: DSMZ-German Collection of Microorganisms and Cell Cultures GmbH
Provider's strain ID: DSM19018, Type strain
Organism: Aromatoleum aromaticum
Genotypes: wild-type
Phenotypes: wild-type
Comment: Not specified
Comparative flux balance analysis file. All values are given in mmol/g/h. Fluxes were optimized to maximize BIOMASS.
Creators: None
Submitter: Julia Koblitz
DownloadCreators: Meina Neumann-Schaal, Dietmar Schomburg, Julia Koblitz
Submitter: Julia Koblitz
Uptake and growth rates, and biomass yields are compared in vivo and in silico.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for aerobic growth on 3-Hydroxybenzoate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for anaerobic growth on 3-Hydroxybenzoate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for aerobic growth on 4HPP.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for anaerobic growth on 4HPP.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for aerobic growth on acetate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for anaerobic growth on acetate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for aerobic growth on Benzoate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for anaerobic growth on benzoate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for aerobic growth on L-phenylalanine.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for anaerobic growth on L-phenylalanine.
Creators: None
Submitter: Julia Koblitz
Creators: None
Submitter: Lars Wöhlbrand
Creators: None
Submitter: Lars Wöhlbrand
Creators: None
Submitter: Patrick Becker
Creators: None
Submitter: Patrick Becker
Creators: None
Submitter: Patrick Becker
Creators: None
Submitter: Patrick Becker
Creators: Katrin Ripken, Sarah Kirstein
Submitter: Sarah Kirstein
Stoichiometric model in SBML format using the acetate-aerobic standard scenario.
Please note that SBML was exported using the sbmlwriter class of Metano. This file was not used for the actual analyses.
Creator: Julia Koblitz
Submitter: Julia Koblitz
Model type: Stoichiometric model
Model format: SBML
Environment: Not specified
This stoichiometric model of Aromatoleum aromaticum EbN1 is a genome-scale model and comprises 655 enzyme-catalyzed reactions and 731 distinct metabolites.
The model is in the plain-text reaction format of Metano that is human-readable and can be opened with every text editor. To run this version of the model, please use the Metano Modeling Toolbox (mmtb.brenda-enzymes.org) and the associated scenario files.
Creators: Julia Koblitz, Dietmar Schomburg, Meina Neumann-Schaal
Submitter: Julia Koblitz
Model type: Stoichiometric model
Model format: Not specified
Environment: Not specified
Creators: Sarah Kirstein, Katrin Ripken
Submitter: Sarah Kirstein
Creator: Lars Wöhlbrand
Submitter: Lars Wöhlbrand
Creators: Sarah Kirstein, Katrin Ripken, Esther Wenzel
Submitter: Sarah Kirstein
Creators: Katrin Ripken, Esther Wenzel, Sarah Kirstein
Submitter: Sarah Kirstein
Creators: Katrin Ripken, Sarah Kirstein
Submitter: Sarah Kirstein
Creators: Katrin Ripken, Esther Wenzel, Sarah Kirstein
Submitter: Sarah Kirstein
Creators: Katrin Ripken, Sarah Kirstein
Submitter: Sarah Kirstein
Creators: Daniel Wünsch, Patrick Becker
Submitter: Daniel Wünsch
Supplementary table containing all reactions, genes, and metabolites involved in the metabolic model iAA835 .
Creator: Julia Koblitz
Submitter: Julia Koblitz
