A5070958079- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Fungal and yeast genetics research
- Biofuel production and bioconversion
- Bioinformatics and Genomic Networks
- Probiotics and Fermented Foods
- Protein Structure and Dynamics
- Bacterial Genetics and Biotechnology
- Evolution and Genetic Dynamics
- Fermentation and Sensory Analysis
- Microbial Metabolites in Food Biotechnology
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Peroxisome Proliferator-Activated Receptors
- Photosynthetic Processes and Mechanisms
- Mitochondrial Function and Pathology
- Gut microbiota and health
- thermodynamics and calorimetric analyses
- Metabolism, Diabetes, and Cancer
- Enzyme Catalysis and Immobilization
- Metabolomics and Mass Spectrometry Studies
- Diabetes, Cardiovascular Risks, and Lipoproteins
- Pancreatic function and diabetes
- Photoreceptor and optogenetics research
- Nonlinear Dynamics and Pattern Formation
Vrije Universiteit Amsterdam
2016-2025
TiFN
2008-2023
University of Amsterdam
1996-2020
Molecules for Health (United States)
2019
Amsterdam University of Applied Sciences
2019
GGD Amsterdam
2018
Amsterdam UMC Location Vrije Universiteit Amsterdam
2014-2018
Cancer Genomics Centre
2007-2017
BioDetection Systems (Netherlands)
2017
Google (United States)
2016
This paper examines whether the in vivo behavior of yeast glycolysis can be understood terms vitro kinetic properties constituent enzymes. In nongrowing, anaerobic, compressed Saccharomyces cerevisiae values parameters most glycolytic enzymes were determined. For other appropriate literature collected. By inserting these into a model for glycolysis, fluxes and metabolites calculated. Under same conditions metabolite levels measured. our first model, branch reactions ignored. failed to reach...
Perspective3 November 2009Open Access Shifts in growth strategies reflect tradeoffs cellular economics Douwe Molenaar Corresponding Author Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, The Netherlands Top Institute Food and Nutrition, Wageningen, Kluyver Genomics of Industrial Fermentation, Delft, Consortium Systems Biology, Search more papers by this author Rogier van Berlo Information Communication Theory Group, Faculty Electrical Engineering, Mathematics...
Cells need to adapt dynamic environments. Yeast that fail cope with changes in the abundance of glucose can undergo growth arrest. We show this failure is caused by imbalanced reactions glycolysis, essential pathway energy metabolism most organisms. The imbalance arises largely from fundamental design making state glycolysis a generic risk. unbalanced coexisted vital cells. Spontaneous, nongenetic metabolic variability among individual cells determines which reached and, consequently,...
Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition end-products, but also their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible food fermentations. Their niche depends on own properties as well those the other species. Here, we apply computational approach, which uses only genomic and metagenomic information functional annotation genes, to find that...
Significance More than 70 years ago, Monod described the phenomenon of diauxic growth bacteria, observation that in presence two alternative sugars, cells first use one them and then, after a short lag phase, switch to other. Until now it had been assumed all population engage outgrowth on second sugar major metabolic adaptation enzymatic composition has occurred, which takes time (hence phase growth). Here, we show actually only subpopulation is fit enough partake present an evolutionary...
Maximization of growth rate is an important fitness strategy for bacteria. Bacteria can achieve this by expressing proteins at optimal concentrations, such that resources are not wasted. This exemplified Escherichia coli the increase its ribosomal protein-fraction with rate, which precisely matches increased protein synthesis demand. These findings and others have led to hypothesis E. aims maximize in environments support growth. However, what kind regulatory required a robust, adjustment...
Several genome-scale metabolic reconstruction software platforms have been developed and are being continuously updated. These tools widely applied to reconstruct models for hundreds of microorganisms ranging from important human pathogens species industrial relevance. However, these platforms, as yet, not systematically evaluated with respect quality, best potential uses intrinsic capacity generate high-quality, models. It is therefore unclear users which tool fits the purpose their research.
A central focus in studies of microbial communities is the elucidation relationships between genotype, phenotype, and dynamic community structure. Here, we present a new computational method called flux balance analysis (cFBA) to study metabolic behavior communities. cFBA integrates comprehensive capacities individual microorganisms terms (genome-scale) stoichiometric models metabolism, interactions species abiotic processes. In addition, considers constraints deriving from reaction...
Growth rate is a near-universal selective pressure across microbial species. High growth rates require hundreds of metabolic enzymes, each with different nonlinear kinetics, to be precisely tuned within the bounds set by physicochemical constraints. Yet, behaviour many species characterized simple relations between rate, enzyme expression levels and rates. We asked if this simplicity could outcome optimisation evolution. Indeed, when maximized—in static environment under mass-conservation...
Abstract 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 constraints. Eukaryal cells contain metabolically active organelles such mitochondria, competing for cytosolic space resources, the nature of relevant constraints remain determined cells. Here, we present a comprehensive metabolic model yeast cell, based on its full reaction network extended with...
A genome-scale metabolic model of the lactic acid bacterium Lactobacillus plantarum WCFS1 was constructed based on genomic content and experimental data. The complete includes 721 genes, 643 reactions, 531 metabolites. Different stoichiometric modeling techniques were used for interpretation complex fermentation data, as L. is adapted to nutrient-rich environments only grows in media supplemented with vitamins amino acids. (i) Based input output fluxes, maximal ATP production estimated...
Tradeoffs provide a rationale for the outcome of natural selection. A prominent example is negative correlation between growth rate and biomass yield in unicellular organisms. This tradeoff leads to dilemma, where optimization advantageous an individual, whereas would be population. High-rate strategies are observed broad variety organisms such as Escherichia coli , yeast, cancer cells. Growth suspension cultures favors fast-growing organisms, spatial structure importance evolution...
In the presence of cyanide, populations yeast cells can exhibit sustained oscillations in concentration glycolytic metabolites, NADH and ATP. This study attempts to answer long‐standing question whether how individual are synchronized. It shows that mixing two cell oscillate 180° out phase only transiently abolishes macroscopic oscillation. After a few minutes, fluorescence mixed population resumes up original amplitude. At low densities, addition acetaldehyde causes transient oscillations....
ABSTRACT On the basis of annotated genome we reconstructed metabolic pathways lactic acid bacterium Lactobacillus plantarum WCFS1. After automatic reconstruction by Pathologic tool Pathway Tools ( http://bioinformatics.ai.sri.com/ptools/ ), resulting pathway-genome database, LacplantCyc, was manually curated extensively. The current database contains refinements to existing routes and new gram-positive bacterium-specific reactions that were not present in MetaCyc database. These include, for...
The genomes of four Lactobacillus reuteri strains isolated from human breast milk and the gastrointestinal tract have been recently sequenced as part Human Microbiome Project. Preliminary genome comparisons suggested that these belong to two different clades, previously shown differ with respect antimicrobial production, biofilm formation, immunomodulation. To explain possible mechanisms survival in host probiosis, we completed a detailed genomic comparison milk–derived isolates...
Abstract Background The genomic information of a species allows for the genome-scale reconstruction its metabolic capacity. Such gives support to engineering, but also integrative bioinformatics and visualization. Sequence-based automatic reconstructions require extensive manual curation, which can be very time-consuming. Therefore, we present method accelerate time-consuming process network query species. exploits availability well-curated networks uses high-resolution predictions gene...
Next-generation sequencing experiments have shown that microRNAs (miRNAs) are expressed in many different isoforms (isomiRs), whose biological relevance is often unclear. We found mature miR-21, the most widely researched miRNA because of its importance human disease, produced two prevalent isomiR forms differ by 1 nt at their 3' end, and moreover end miR-21 posttranscriptionally adenylated noncanonical poly(A) polymerase PAPD5. PAPD5 knockdown caused an increase expression level, suggesting...
In the study of metabolic networks, optimization techniques are often used to predict flux distributions, and hence, phenotype. Flux balance analysis in particular has been successful predicting phenotypes. However, an inherent limitation a stoichiometric approach such as is that it can only distributions result maximal yields. Hence, previous attempts use FBA fluxes Lactobacillus plantarum failed, this lactic acid bacterium produces lactate, even under glucose-limited chemostat conditions,...
Abstract Fluorescent proteins (FPs) are widely used in many organisms, but commonly characterised vitro . However, the properties may poorly reflect vivo performance. Therefore, we 27 FPs using Saccharomyces cerevisiae as model organism. We linked via a T2A peptide to control FP, producing equimolar expression of 2 from 1 plasmid. Using this strategy, for brightness, photostability, photochromicity and pH-sensitivity, achieving comprehensive characterisation. Many showed different compared...