相关论文: Selection, Mutations and Codon Usage in Bacterial …
The dynamics of growth of bacterial populations has been extensively studied for planktonic cells in well-agitated liquid culture, in which all cells have equal access to nutrients. In the real world, bacteria are more likely to live in…
One of the most challenging problems in microbiology is to understand how a small fraction of microbes that resists killing by antibiotics can emerge in a population of genetically identical cells, the phenomenon known as persistence or…
In a letter published in Molecular Biology Evolution [10], Chen and Zhang argue that the variation of the mutation rate along the Escherichia coli genome that we recently reported [3] cannot be evolutionarily optimised. To support this…
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…
Bacterial populations in natural conditions are expected to experience stochastic environmental fluctuations, and in addition, environments are affected by bacterial activities since they consume substrates and excrete various chemicals. We…
The theory of evolution by natural selection cannot be used to evaluate the truth value of the following proposition: Through evolution, there exists at least one species that can adapt to any one given environment. To address this issue,…
In the crystal basis model of the genetic code, it is deduced that the sum of usage probabilities of the codons with C and A in the third position for the quartets and/or sextets is independent of the biological species for vertebrates. A…
Motivation: Gene blocks are genes co-located on the chromosome. In many cases, genes blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain,…
We show how concepts from statistical physics, such as order parameter, thermodynamic limit, and quantum phase transition, translate into biological concepts in mutation-selection models for sequence evolution and can be used there. The…
Natural selection and random drift are competing phenomena for explaining the evolution of populations. Combining a highly fit mutant with a population structure that improves the odds that the mutant spreads through the whole population…
The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
The genetic code underlying protein synthesis is a canonical example of a degenerate biological system. Degeneracies in physical and biological systems can be lifted by external perturbations thus allowing degenerate systems to exhibit a…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…
Bioconvection, a phenomenon arising from the collective motion of motile microorganisms, plays a crucial role in shaping microbial distributions, fluid dynamics, and bloom formation in aquatic environments. While extensive research has…
We describe the evolution of $E.coli$ populations through a Bak-Sneppen type model which incorporates random mutations. We show that, for a value of the mutation level which coincides with the one estimated from experiments, this model…
Since penicillin was discovered about 90 years ago, we have become used to using drugs to eradicate unwanted pathogenic cells. However, using drugs to kill bacteria, viruses or cancer cells has the serious side effect of selecting for…
Recently, Lenski et al [Elena,Lenski,Travisano] have carried out several experiments on bacterial evolution. Their findings support the theory of punctuated equilibrium in biological evolution. They have further quantified the relative…
Evolution of a universe with homogeneous extra dimensions is studied with the benefit of a well-chosen parameter space that provides a systematic, useful, and convenient way for analysis. In this model we find a natural evolution pattern…
We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…