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Article
Open AccessWhole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies
When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Euka...
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Protocol
Metabolic Modeling of Wine Fermentation at Genome Scale
Wine fermentation is an ancient biotechnological process mediated by different microorganisms such as yeast and bacteria. Understanding of the metabolic and physiological phenomena taking place during this pro...
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Article
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community
Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear as system-wide studie...
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Article
Open AccessPublisher Correction: MEMOTE for standardized genome-scale metabolic model testing
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
MEMOTE for standardized genome-scale metabolic model testing
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Article
Open AccessThe common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints
Living cells can express different metabolic pathways that support growth. The criteria that determine which pathways are selected in which environment remain unclear. One recurrent selection is overflow metab...
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Article
Open AccessA systematic assessment of current genome-scale metabolic reconstruction tools
Several genome-scale metabolic reconstruction software platforms have been developed and are being continuously updated. These tools have been widely applied to reconstruct metabolic models for hundreds of mic...
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Article
A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris
Leuconostoc mesenteroides subsp. cremoris is an obligate heterolactic fermentative lactic acid bacterium that is mostly used in industrial dairy fermentations. The phosphoketolase pathway (PKP) is a unique featur...
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Article
Open AccessIn vivo characterisation of fluorescent proteins in budding yeast
Fluorescent proteins (FPs) are widely used in many organisms, but are commonly characterised in vitro. However, the in vitro properties may poorly reflect in vivo performance. Therefore, we characterised 27 FPs i...
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Article
Open AccessAdaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength
A central theme in (micro)biology is understanding the molecular basis of fitness i.e. which strategies are successful under which conditions; how do organisms implement such strategies at the molecular level;...
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Reference Work Entry In depth
Ecophysiology of Acetoclastic Methanogens
Acetate is the most important precursor for methane in the degradation of organic matter. Only two genera of methanogenic archaea, Methanosarcina and Methanothrix (former Methanosaeta), are able to grow with acet...
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Living Reference Work Entry In depth
Ecophysiology of Acetoclastic Methanogens
Acetate is the most important precursor for methane in the degradation of organic matter. Only two genera of methanogenic archaea, Methanosarcina and Methanothrix (former Methanosaeta), are able to grow with acet...
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Article
Open AccessDynamic elementary mode modelling of non-steady state flux data
A novel framework is proposed to analyse metabolic fluxes in non-steady state conditions, based on the new concept of dynamic elementary mode (dynEM): an elementary mode activated partially depending on the ti...
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Article
Open AccessLow affinity uniporter carrier proteins can increase net substrate uptake rate by reducing efflux
Many organisms have several similar transporters with different affinities for the same substrate. Typically, high-affinity transporters are expressed when substrate is scarce and low-affinity ones when it is ...
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Chapter and Conference Paper
An Integrated Model Quantitatively Describing Metabolism, Growth and Cell Cycle in Budding Yeast
Computational models are expected to increase understanding of how complex biological functions arise from the interactions of large numbers of gene products and biologically active low molecular weight molecu...
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Article
Open AccessEvolutionary pressures on microbial metabolic strategies in the chemostat
Protein expression is shaped by evolutionary processes that tune microbial fitness. The limited biosynthetic capacity of a cell constrains protein expression and forces the cell to carefully manage its protein...
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Article
Open AccessStrategies for structuring interdisciplinary education in Systems Biology: an European perspective
Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and...
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Article
Open AccessA novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods
The lactic acid bacterium Lactobacillus rhamnosus GG is the most studied probiotic bacterium with proven health benefits upon oral intake, including the alleviation of diarrhea. The mission of the Yoba for Life f...
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Article
Open AccessLactic Acid Bacteria: embarking on 30 more years of research
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Article
Open AccessGene network requirements for regulation of metabolic gene expression to a desired state
Gene circuits that control metabolism should restore metabolic functions upon environmental changes. Whether gene networks are capable of steering metabolism to optimal states is an open question. Here we pres...
