The Deutsche Forschungsgemeinschaft (DFG) is the self-governing organisation for science and research in Germany. It serves all branches of science and the humanities. In organisational terms, the DFG is an association under private law. Its membership consists of German research universities, non-university research institutions, scientific associations and the Academies of Science and the Humanities.
Web page: https://www.dfg.de/en/index.jsp
Funding details:Related items
- People (29)
- Projects (1)
- Institutions (11)
- Investigations (1+3)
- Studies (3+3)
- Assays (4+8)
- Data files (6+9)
- Models (1)
- SOPs (0+5)
- Publications (1)
- Documents (0+4)
Institutions: University of Freiburg
https://orcid.org/0000-0002-5340-3423Expertise: Bioinformatics, Databases, Genetics, Genomics, Systems Biology, Transcriptomics, Microbiology, Microarray analysis
Tools: Bioinformatics, Data analysis, Genetics, Genomics, Microarray analysis, Microbiology, Molecular Biology, Molecular biology techniques (RNA/DNA/Protein), Transcriptomics
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, ZucAt, SysMO-LAB, Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, ErasysApp Funders, EraCoBiotech 2 nd call proposal preparation, Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, Multiscale modelling of state transitions in the host-microbiome-brain network, BESTER, TRALAMINOL, Sustainable co-production, INDIE - Biotechnological production of sustainable indole, Extremophiles metabolsim, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, OLCIR: Optimization of Lung Cancer Therapy with Ionizing Radiation, NAD COMPARTMENTATION, HOTSOLUTE, Stress granules, FAIRDOM Community Workers, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, AquaHealth (ERA-BlueBio), LiSyM Core Infrastructure and Management (LiSyM-PD), Early Metabolic Injury (LiSyM-EMI - Pillar I), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, CC-TOP, BioCreative VII, MESI-STRAT Review, SDBV/HITS, MESI-Review 2024
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), FAIRDOM User meeting, Norwegian University of Science and Technology, University of Rostock, University of Innsbruck
https://orcid.org/0000-0003-3540-0402Expertise: Genetics, Molecular Biology, Bioinformatics, Data Management, Transcriptomics, semantics, Curation, Ontology, Data Modelling
Tools: Cell and tissue culture, Databases, Chip-chip, BioMart, Protege, RightField, SEEK
I am a researcher at the Scientific Databases and Visualization Group at Heidelberg Institute for Theoretical Studies (HITS) , one of the developers of SabioRK - System for the Analysis of Biochemical Pathways - Reaction Kinetics (http://sabiork.h-its.org/) . I am working on design and maintenance of the information systems to store, query and analyse systems biology data; definition and implementation of methods for the integration of data from multiple sources. In **[SySMO-DB ...
Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis. Theyhad and have tremendous influence on the biogeochemical cycles on Earth. Recently,cyanobacteria are increasingly investigated as cell factories for a sustainableeconomy. Despite their global, environmental and rising economic importance, ourknowledge on the regulation of their primary metabolism is fragmented.Cyanobacteria switch between photoautotrophic and heterotrophic modes ofmetabolism during day/night cycles or ...
Programme: DFG founded projects
Public web page: https://gepris.dfg.de/gepris/projekt/397695561
Start date: 1st Sep 2018
Organisms: Synechocystis sp. PCC 6803
Cyanobacterial PFKs were thought to be ATP dependent, but isolation and characterisation of 2 PFK isoenzymes from Synechocystis revealed that they belong to the PFK-A family, use ADP as phosphate donor and form a separate phylogenetic class. Their allosteric regulation via 3-PG and ATP respectively allow for flexible switching between aactive and inactive enzymes dependent on the light and carbon status.
Glucose-6-phosphate dehydrogenase (G6PDH), the enzyme that catalyzes the first step of the oxidative pentose phosphate (OPP) pathway, plays a key role in this process. G6PDH is produced at the onset of nitrogen starvation but remains inactive in dormant cells, only to be rapidly reactivated when nitrogen is restored. In this study, we investigated the mechanisms underlying this enzymatic regulation and found that G6PDH inactivation is primarily due to the accumulation of inhibitory metabolites. ...
Submitter: Sofia Doello
Investigation: 1 hidden item
Snapshots: No snapshots
Abstract The enzyme Glucose-1-phosphate adenylyltransferase (GlgC, EC:2.7.7.27) catalyses the first step in glycogen synthesis by converting glucose-1-phosphate into ADP-Glucose, which is added in turn to a growing glycogen chain by glycogen synthases. Thus far, the in vitro study of GlgC were mainly performed using colorimetric or radiolabel-based phosphate release assays, limiting the option for analysing this reaction. With this work, we present a novel in vitro continuous assay coupling the ...
Snapshots: Snapshot 1, Snapshot 2
PFK-1 and PFK-2 were cloned and expressed in E. coli, purified, and kinetically characterised in terms of substrates and allosteric regulators.
Submitter: Jacky Snoep
Investigation: ADP dependent cyanobacterial PFK-A
Assays: Experimental data for enzyme kinetic characterisation of PFK-1 and PFK-2, Model simulation of PFK-1 and PFK-2 enzyme kinetics
Snapshots: No snapshots
The purified enzymes were kinetically charactyerised in terms of substrate sensitivity and alloestric regulation.
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: ADP dependent cyanobacterial PFK-A
Study: PFK-1 and PFK-2 kinetics
Organisms: No organisms
SOPs: No SOPs
Data files: Kinetic data for PFK-1 and PFK-2
Snapshots: No snapshots
The experimental data for PFK-1 and PFK-2 were analysed and fitted with a MWC equation. The model is described in Mathematica and the plots in the manuscript are generatedin the notebook.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: ADP dependent cyanobacterial PFK-A
Study: PFK-1 and PFK-2 kinetics
Organisms: No organisms
Models: Mathematica notebook for enzyme kinetic data an...
SOPs: No SOPs
Data files: Kinetic data for PFK-1 and PFK-2
Snapshots: No snapshots
Submitter: Kenric Lee
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: No organisms
SOPs: No SOPs
Data files: GlgC Experimental Data, GlgC Figure Data
Snapshots: No snapshots
Submitter: Sofia Doello
Assay type: Enzymatic Assay
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: No organisms
SOPs: No SOPs
Data files: Effect of metabolites on G6PDH activity
Snapshots: No snapshots
Creator: Sofia Doello
Submitter: Sofia Doello
Investigations: 1 hidden item
All data sets reflected by the figures in this work. Requires Graphpad Prism 7 (or later) to access. A trial version can be downloaded from the Graphpad prism website ( https://www.graphpad.com/demos/ )
Creator: Kenric Lee
Submitter: Kenric Lee
Investigations: 1 hidden item
Studies: Deciphering the tight Metabolite-Level Regulati...
Assays: GlgC coupled assay
Selected data sets from the main figures presented in this work.
Creator: Kenric Lee
Submitter: Kenric Lee
Investigations: 1 hidden item
Studies: Deciphering the tight Metabolite-Level Regulati...
Assays: GlgC coupled assay
Experimental data for kinetic characterisaton of PFK-1 and PFK-2.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Analysis of the sequences of PGM1 from several Synechocystis strains revealed a different annotation for Synechocystis sp. PCC 6803, which included a 16-amino acid N-terminal extension that is missing in the other strains. Additionally, the experimentally validated transcriptional start site from Synechocystis sp. PCC 6803 suggests a shorter open reading frame for PGM1, with Met 17 as putative translational start site. To clarify if the N-terminal extension is an annotation error, we prepared ...
Creator: Sofia Doello
Submitter: Sofia Doello
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 1 hidden item
To test the effecf of phosphorylation of Ser 47 on PGM1 activity, this residue was exchanged for Ala and Asp and the activity of the recombinant proteins was measured in vitro.
Creator: Sofia Doello
Submitter: Sofia Doello
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 1 hidden item
Mathematic notebook for enzyme kinetic analysis and model fit, including figure generation for manuscript.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Not specified
Model format: Mathematica
Environment: Mathematica
Organism: Synechocystis sp. PCC 6803
Investigations: ADP dependent cyanobacterial PFK-A
Studies: PFK-1 and PFK-2 kinetics
Abstract (Expand)
Authors: Sofía Doello, Niels Neumann, Philipp Spät, Boris Maček, Karl Forchhammer
Date Published: 15th Apr 2021
Publication Type: Unpublished
DOI: 10.1101/2021.04.15.439997
Citation: biorxiv;2021.04.15.439997v1,[Preprint]