相关论文: The adaptive acquisition of single DNA segments dr…

We study the evolution of large but finite asexual populations evolving in fitness landscapes in which all mutations are either neutral or strongly deleterious. We demonstrate that despite the absence of higher fitness genotypes, adaptation…

Cells generally change their internal state to adapt to an environmental change, and accordingly evolve in response to the new conditions. This process involves phenotypic changes that occur over several different time scales, ranging from…

Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here…

The E.coli transcription network has an essentially feedforward structure, with, however, abundant feedback at the level of self-regulations. Here, we investigate how these properties emerged during evolution. An assessment of the role of…

Bacteria evolve resistance to antibiotics by a multitude of mechanisms. A central, yet unsolved question is how resistance evolution affects cell growth at different drug levels. Here we develop a fitness model that predicts growth rates of…

Genotype-to-phenotype maps and the related fitness landscapes that include epistatic interactions are difficult to measure because of their high dimensional structure. Here we construct such a map using the recently collected corpora of…

Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…

Genetic interactions can strongly influence the fitness effects of individual mutations, yet the impact of these epistatic interactions on evolutionary dynamics remains poorly understood. Here we investigate the evolutionary role of…

The accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal…

Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…

Metabolic networks are complex systems that comprise hundreds of chemical reactions which synthesize biomass molecules from chemicals in an organism's environment. The metabolic network of any one organism is encoded by a metabolic…

How adaptive evolution to one environmental stress improves or suppresses adaptation to another is an important problem in evolutionary biology. For instance, in microbiology, the evolution of bacteria to be resistant to different…

Gene-knockout experiments on single-cell organisms have established that expression of a substantial fraction of genes is not needed for optimal growth. This problem acquired a new dimension with the recent discovery that environmental and…

Yeast cells grown in culture can spontaneously synchronize their respiration, metabolism, gene expression and cell division. Such metabolic oscillations in synchronized cultures reflect single-cell oscillations, but the relationship between…

Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…

Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…

Aspects of cell metabolism are modeled by ordinary differential equations describing the change of intracellular chemical concentrations. There is a correspondence between this dynamical system and a complex network. As in the classic…

Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such…

The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard…

In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…