Related papers: Synteny in Bacterial Genomes: Inference, Organizat…
A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus…
For a given permutation or set partition there is a natural way to assign a genus. Counting all permutations or partitions of a fixed genus according to cycle lengths or block sizes, respectively, is the main content of this article. After…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
Bacterial colonies are a well-known example of living active matter, exhibiting collective behaviors such as nematic alignment and collective motion that play an important role in the spread of microbial infections. While the underlying…
We present a generic mechanism by which reproducing microorganisms, with a diffusivity that depends on the local population density, can form stable patterns. It is known that a decrease of swimming speed with density can promote separation…
The prospect of new biological and industrial applications that require communication in micro-scale, encourages research on the design of bio-compatible communication networks using networking primitives already available in nature. One of…
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in…
The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of…
The rate at which individual bacterial cells grow depends on the concentrations of cellular components such as ribosomes and proteins. These concentrations continuously fluctuate over time and are inherited from mother to daughter cells,…
Bacteria can spontaneously develop collective motions by aligning their motions in dense systems. Here, we show that bacteria can also respond collectively to an alternating electrical field and form dynamic clusters oscillating at the same…
The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Mechanical interactions among cells in a growing microbial colony can significantly influence the colony's spatial genetic structure and, thus, evolutionary outcomes such as the fates of rare mutations. Here, we computationally investigate…
Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
Colonies of bacteria grown on thin agar plate exhibit fractal patterns as a result of adaptation to their environments. The bacterial colony pattern formation is regulated crucially by chemotaxis, the movement of cells along a chemical…
In many natural synchronization phenomena, communication between individual elements occurs not directly, but rather through the environment. One of these instances is bacterial quorum sensing, where bacteria release signaling molecules in…
Organelle patterning and its heritability remain central mysteries in cell biology, highlighting the fundamental tension between genetic inheritance and self-assembly. Here, we explore the nonequilibrium assembly and emdedded size control…
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly…
We discuss two different ways of chromosomes' and genomes' evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination…