Multiple functions of flagellar motility and chemotaxis in bacterial physiology
Most swimming bacteria are capable of following gradients of nutrients, signaling molecules
and other environmental factors that affect bacterial physiology. This tactic behavior became …
and other environmental factors that affect bacterial physiology. This tactic behavior became …
[HTML][HTML] Using genome-scale models to predict biological capabilities
Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have
been under development since the first whole-genome sequences appeared in the mid …
been under development since the first whole-genome sequences appeared in the mid …
A universal trade-off between growth and lag in fluctuating environments
The rate of cell growth is crucial for bacterial fitness and drives the allocation of bacterial
resources, affecting, for example, the expression levels of proteins dedicated to metabolism …
resources, affecting, for example, the expression levels of proteins dedicated to metabolism …
[HTML][HTML] Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources
Quantitative views of cellular functions require precise measures of rates of biomolecule
production, especially proteins—the direct effectors of biological processes. Here, we …
production, especially proteins—the direct effectors of biological processes. Here, we …
Constraint-based models predict metabolic and associated cellular functions
The prediction of cellular function from a genotype is a fundamental goal in biology. For
metabolism, constraint-based modelling methods systematize biochemical, genetic and …
metabolism, constraint-based modelling methods systematize biochemical, genetic and …
[HTML][HTML] Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics
WR Harcombe, WJ Riehl, I Dukovski, BR Granger… - Cell reports, 2014 - cell.com
The interspecies exchange of metabolites plays a key role in the spatiotemporal dynamics of
microbial communities. This raises the question of whether ecosystem-level behavior of …
microbial communities. This raises the question of whether ecosystem-level behavior of …
Glycolytic strategy as a tradeoff between energy yield and protein cost
Contrary to the textbook portrayal of glycolysis as a single pathway conserved across all
domains of life, not all sugar-consuming organisms use the canonical Embden–Meyerhoff …
domains of life, not all sugar-consuming organisms use the canonical Embden–Meyerhoff …
Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction
Growth is a fundamental process of life. Growth requirements are well‐characterized
experimentally for many microbes; however, we lack a unified model for cellular growth …
experimentally for many microbes; however, we lack a unified model for cellular growth …
[HTML][HTML] Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
D Machado, M Herrgård - PLoS computational biology, 2014 - journals.plos.org
Constraint-based models of metabolism are a widely used framework for predicting flux
distributions in genome-scale biochemical networks. The number of published methods for …
distributions in genome-scale biochemical networks. The number of published methods for …
[HTML][HTML] Aerobic glycolysis in the human brain is associated with development and neotenous gene expression
Aerobic glycolysis (AG; ie, nonoxidative metabolism of glucose despite the presence of
abundant oxygen) accounts for 10%–12% of glucose used by the adult human brain. AG …
abundant oxygen) accounts for 10%–12% of glucose used by the adult human brain. AG …