Zobrazeno 1 - 10
of 17
pro vyhledávání: '"Daan H. de Groot"'
Autor:
Tom J. Clement, Erik B. Baalhuis, Bas Teusink, Frank J. Bruggeman, Robert Planqué, Daan H. de Groot
Publikováno v:
Patterns, Vol 2, Iss 1, Pp 100177- (2021)
Summary: The metabolic capabilities of cells determine their biotechnological potential, fitness in ecosystems, pathogenic threat levels, and function in multicellular organisms. Their comprehensive experimental characterization is generally not feas
Externí odkaz:
https://doaj.org/article/542d7c9dba304aa99302afe355e88bd2
Publikováno v:
Metabolites, Vol 11, Iss 5, p 257 (2021)
Genome-scale stoichiometric modeling methods, in particular Flux Balance Analysis (FBA) and variations thereof, are widely used to investigate cell metabolism and to optimize biotechnological processes. Given (1) a metabolic network, which can be rec
Externí odkaz:
https://doaj.org/article/53423e9c8e064d71b0b86fdb1edbbc25
In many bacteria, translating ribosomes are excluded from the nucleoid, while amino-acid and energy-supplying metabolic enzymes spread evenly throughout the cytoplasm. Here we show with time-lapse fluorescence microscopy that this inhomogeneous organ
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::89ec10006f8e0878a017f449c30fc18d
https://doi.org/10.1101/2023.04.18.537336
https://doi.org/10.1101/2023.04.18.537336
Publikováno v:
Bioinformatics (Oxford, England), 39(3):btad095, 1-2. Oxford University Press
MotivationCharacterizing all steady-state flux distributions in metabolic models remains limited to small models due to the explosion of possibilities. Often it is sufficient to look only at all possible overall conversions a cell can catalyze ignori
Microbes in the wild face highly variable and unpredictable environments, and are naturally selected for their average growth rate across environments. Apart from using sensory-regulatory systems to adapt in a targeted manner to changing environments
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c03fcc6f3e1e2dbe683bdeb9b472fb68
https://doi.org/10.1101/2022.04.12.488059
https://doi.org/10.1101/2022.04.12.488059
Autor:
Anjani S. Bisseswar, Rinke J. van Tatenhove-Pel, Herwig Bachmann, Daan H. de Groot, Bas Teusink
Publikováno v:
van Tatenhove-Pel, R J, de Groot, D H, Bisseswar, A S, Teusink, B & Bachmann, H 2021, ' Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth ', ISME Journal, vol. 15, no. 10, pp. 3050-3061 . https://doi.org/10.1038/s41396-021-00986-y
The ISME Journal: multidisciplinary journal of microbial ecology, 15(10)
The ISME Journal
ISME Journal, 15(10), 3050-3061. Nature Publishing Group
The ISME Journal: multidisciplinary journal of microbial ecology, 15(10)
The ISME Journal
ISME Journal, 15(10), 3050-3061. Nature Publishing Group
As natural selection acts on individual organisms the evolution of costly cooperation between microorganisms is an intriguing phenomenon. Introduction of spatial structure to privatize exchanged molecules can explain the evolution of cooperation. How
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a8002749bcd9beb80aceab74d4fd8d91
https://hdl.handle.net/1871.1/ca6e9a96-7cbe-4227-b490-9c0c8657edef
https://hdl.handle.net/1871.1/ca6e9a96-7cbe-4227-b490-9c0c8657edef
Autor:
Nick Crang, Gerhard Saalbach, Philip S. Poole, R. George Ratcliffe, Antonis Papachristodoulou, Carolin C. M. Schulte, Rachel M. Wheatley, Jason Terpolilli, Daan H. de Groot, Khushboo Borah, Nicholas J. Kruger
Publikováno v:
Science Advances
Catabolism of dicarboxylates at low oxygen drives N2 fixation and promotes ammonia secretion in rhizobium-legume symbioses.
Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which catabolize plant-derived dicarb
Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which catabolize plant-derived dicarb
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d314b44357c01fadc804a0f3b7a5178a
https://doi.org/10.1126/sciadv.abh2433
https://doi.org/10.1126/sciadv.abh2433
Publikováno v:
van Pelt-KleinJan, E, de Groot, D H & Teusink, B 2021, ' Understanding FBA solutions under multiple nutrient limitations ', Metabolites, vol. 11, no. 5, 257, pp. 1-24 . https://doi.org/10.3390/metabo11050257
Metabolites, Vol 11, Iss 257, p 257 (2021)
Metabolites
Metabolites, 11(5):257, 1-24. Multidisciplinary Digital Publishing Institute (MDPI)
Volume 11
Issue 5
Metabolites, Vol 11, Iss 257, p 257 (2021)
Metabolites
Metabolites, 11(5):257, 1-24. Multidisciplinary Digital Publishing Institute (MDPI)
Volume 11
Issue 5
Genome-scale stoichiometric modeling methods, in particular Flux Balance Analysis (FBA) and variations thereof, are widely used to investigate cell metabolism and to optimize biotechnological processes. Given (1) a metabolic network, which can be rec
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ea700b5986d724b268b30be5154a2d37
https://hdl.handle.net/1871.1/9050443c-7fd1-4863-a53d-259f9386e80c
https://hdl.handle.net/1871.1/9050443c-7fd1-4863-a53d-259f9386e80c
Autor:
Philip S. Poole, Carolin C. M. Schulte, Rachel M. Wheatley, Daan H. de Groot, R. George Ratcliffe, Gerhard Saalbach, Antonis Papachristodoulou, Jason Terpolilli, Nick Crang, Nicholas J. Kruger, Khushboo Borah
Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which use plant-derived dicarboxylates as energy and electron sources for reduction of atmospheric N2 into ammonia for secretion to plants. Using heterogeneous genome
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::30b0620ca7d1cf06b09fe906e10f2798
https://doi.org/10.1101/2021.02.16.431433
https://doi.org/10.1101/2021.02.16.431433
Publikováno v:
PLoS Computational Biology, Vol 16, Iss 1, p e1007559 (2020)
PLoS Computational Biology, 16:e1007559. Public Library of Science
de Groot, D H, Hulshof, J, Teusink, B, Bruggeman, F J & Planqué, R 2020, ' Elementary Growth Modes provide a molecular description of cellular self-fabrication ', PLoS Computational Biology, vol. 16, e1007559 . https://doi.org/10.1371/journal.pcbi.1007559
PLoS Computational Biology
PLoS Computational Biology, 16:e1007559. Public Library of Science
de Groot, D H, Hulshof, J, Teusink, B, Bruggeman, F J & Planqué, R 2020, ' Elementary Growth Modes provide a molecular description of cellular self-fabrication ', PLoS Computational Biology, vol. 16, e1007559 . https://doi.org/10.1371/journal.pcbi.1007559
PLoS Computational Biology
In this paper we try to describe all possible molecular states (phenotypes) for a cell that fabricates itself at a constant rate, given its enzyme kinetics and the stoichiometry of all reactions. For this, we must understand the process of cellular g