相关论文: Population genetics of translational robustness

The aim of this paper is two-fold. First, we propose a new computational method to investigate the particularities of evolution. Second, we apply this method to a model of gene regulatory networks (GRNs) and explore the evolution of…

Adaptation is a central topic in theoretical biology, of practical importance for analyzing drug resistance mutations. Several authors have used arguments based on extreme value theory in their work on adaptation. There are complications…

The standard genetic code is known to be robust to translation errors and point mutations. We studied how small modifications of the standard code affect its robustness. The robustness was assessed in terms of a proper stability function,…

We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…

Under constant selection, each trait has a fixed fitness, and small mutation rates allow populations to efficiently exploit the optimal trait. Therefore it is reasonable to expect mutation rates will evolve downwards. However, we find this…

The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light of noise? To answer this question, we build a mathematical model to explore the trade-off…

We suggest to simulate evolution of complex organisms constrained by the sole requirement of robustness in their expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence…

Background. Organisms use a variety of mechanisms to protect themselves against perturbations. For example, repair mechanisms fix damage, feedback loops keep homeostatic systems at their setpoints, and biochemical filters distinguish signal…

Expression level is known to be a strong determinant of a protein's rate of evolution. But the converse can also be true: evolutionary dynamics can affect expression levels of proteins. Having implications in both directions fosters the…

In environments that vary frequently and unpredictably, bet-hedgers can overtake the population. Diversifying bet-hedgers have a diverse set of offspring so that, no matter the conditions they find themselves in, at least some offspring…

We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…

It is tempting to believe that we now own the genome. The ability to read and re-write it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles heel exposed by all of the genomic data that has…

The dynamics of adaptation is difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from number fluctuations, called genetic drift, arising in the small number of particularly fit…

Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress caused by…

Gene expression levels are important molecular quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies in recent years have revealed substantial adaptive evolution at the genomic…

Heterozygote disadvantage is potentially a potent driver of population genetic divergence. Also referred to as underdominance, this phenomena describes a situation where a genetic heterozygote has a lower overall fitness than either…

We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…

Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…

The accurate prediction of biological features from genomic data is paramount for precision medicine and sustainable agriculture. For decades, neural network models have been widely popular in fields like computer vision, astrophysics and…

Recent experiments have shown that stochastic effects exerted at the level of translation contribute a substantial portion of the variation in abundance of proteins expressed at moderate to high levels. This study analyzes translational…