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Comparative GC-MS based metabolomics of S. solfataricus growing on either L-fucose or D-glucose. CoA derivatives were analysed via HPLC-MS
Creators: Jacqueline Wolf, Dietmar Schomburg
Submitter: Jacqueline Wolf
Comparative proteomics of S. solfatricus grown on either L-fucose or D-glucose.
Creators: Jacqueline Wolf, Trong Khoa Pham, Phil Wright
Submitter: Jacqueline Wolf
Publications and patents from the last 6 years
Creator: Vitor Martins dos Santos
Submitter: Vitor Martins dos Santos
List of publications from 2006 till 2016. Note: I retired from the University of Amsterdam in 2010
Creator: Roel Van Driel
Submitter: Roel Van Driel
3rd ERASysAPP – EXCHANGE Day: Networking and Info Day for research projects of the first and second ERASysAPP calls
Creators: Olga Krebs, Katalin Zsuzsanna Nagy, Heide Marie Hess
Submitter: Olga Krebs
Creators: Ron Henkel, Dagmar Waltemath
Submitter: Ron Henkel
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
just cell counts, the area of the grains is separate.
Creator: Antoine Buetti-Dinh
Submitter: Antoine Buetti-Dinh
after shankra, saving the images that could not be analysed earlier. here they are simply treated by imagej change in brightness/contrast. the same can also be done with imagemagic.
Creator: Antoine Buetti-Dinh
Submitter: Antoine Buetti-Dinh
Creator: Antoine Buetti-Dinh
Submitter: Antoine Buetti-Dinh
Strain MK423 was grown under the same conditions as used when growing cells for microscopy analysis; cells of OD600 = 0.4 were diluted 100-fold in C+Y medium with 0.1 mM ZnCl2 and incubated for 2.5 hours until OD600 = 0.15. Cells were then harvested by centrifugation for 5 min at 6500 x g at 4°C. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega) as described previously (Slager et al. 2014 Cell). Fragmentation was performed using Covaris instrument, and libraries ...
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
Strain MK422 was grown under the same conditions as used when growing cells for microscopy analysis; cells of OD600 = 0.4 were diluted 100-fold in C+Y medium with 0.1 mM ZnCl2 and incubated for 2.5 hours until OD600 = 0.15. Cells were then harvested by centrifugation for 5 min at 6500 x g at 4°C. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega) as described previously (Slager et al. 2014 Cell). Fragmentation was performed using Covaris instrument, and libraries ...
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
Strain MK350 was grown under the same conditions as used when growing cells for microscopy analysis; cells of OD600 = 0.4 were diluted 100-fold in C+Y medium with 0.1 mM ZnCl2 and incubated for 2.5 hours until OD600 = 0.15. Cells were then harvested by centrifugation for 5 min at 6500 x g at 4°C. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega) as described previously (Slager et al. 2014 Cell). Fragmentation was performed using Covaris instrument, and libraries ...
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
Supplementary File S2: Kinetic entries for human galactose metabolism. SBML for query: http://sabiork.h-its.org/sabioRestWebServices/searchKineticLaws/sbml?q=Pathway:%22galactose%20metabolism%22%20AND%20Organism:%22homo%20sapiens%22
Creator: Matthias König
Submitter: Matthias König
Kinetic entry 14792 SBML for query http://sabiork.h-its.org/sabioRestWebServices/kineticLaws/14792
Creator: Matthias König
Submitter: Matthias König
L. lactis was grown in rich THY medium, strongly concentrated and glucose-pulsed in a MES buffer. Intracellular metabolite concentration is followed in time.
Creator: Martijn Bekker
Submitter: Martijn Bekker
The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.1 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for ...
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in the model under light growth conditions. In this solution, (i) the photorespiration was set to 0; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set of 0.1 of flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is under-produced in plastid and therefore is additionally imported to cytoplasm. Flux through FQR represents cyclic electron flow through ...
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.5 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is over-produced in plastid and a surplus is exported to cytoplasm. Flux through FQR ...
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; (ii) and ATP transport between plastid and cytoplasm has been set to 0. The last constraint allows finding the ratio between fluxes through FQR (ferredoxin-plastoquinone reductase) and FRN (ferredoxin-NADP oxidoreductase) under which the ATP balance in plastid becomes self-sufficient ...
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; (ii) and cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set to 0. Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for carbon fixation, therefore plastid imports ATP from cytoplasm.
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The solution of Flux Balance Analysis (FBA) represent metabolic flux distribution in the model under dark growth conditions (i.e. constraints)
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Flux Balance Analysis (FBA) constraints for light conditions
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Flux Balance Analysis (FBA) constraints for dark conditions
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The database in ASCII format includes information on compounds and metabolites (trivial name, elemental composition, charge, external database referece, etc) used in the model
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The database in ASCII format includes information on gene (gene models in ATG format, gene definition, catalyzed reactions in the model, external database refeneces, locus information, etc) used in the model
Creators: Maksim Zakhartsev, Irina Medvedeva
Submitter: Maksim Zakhartsev
The database in ASCII format includes information on transformers [reactions, transport steps, polymerizations] (model's identifier, trivial name, EC number, stoichiometric equation, external database referece, activators, belonging to a pathway, etc) used in the model
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The stoichiometric matrix of the multi-compartment metabolic model of growing Arabidopsis thaliana
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev