27 papers · ranked by Valyu relevance
Alex Dornburg, Rittika Mallik, Zheng Wang, Moisés A. Bernal + 7 more
'Brian Thompson' 'Elspeth A. Bruford' 'Daniel W. Nebert' 'Vasilis Vasiliou' 'Laurel R. Yohe' 'Jeffrey A. Yoder' 'Jeffrey P. Townsend'] Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational…
Pei Lin, Guang-An Lu, Zhongqi Liufu, Yi-Xin Zhao + 3 more
Unlike in genotypic evolution, there are few general rules governing phenotypic evolution with one of them being the small-step evolution. More specifically, natural selection tends to favor mutations of smaller phenotypic effects than of larger ones. This postulate can be viewed as a logical extension of Fisher’s…
Simon Aubé, Lou Nielly-Thibault, Christian R. Landry
How changes in the different steps of protein synthesis – transcription, translation and degradation – contribute to differences of protein abundance among genes is not fully understood. There is however accumulating evidence that transcriptional divergence might have a prominent role. Here, we show that yeast…
Soumitra Pal, Brian Oliver, Teresa M. Przytycka
Gene expression evolution is typically modeled with the stochastic Ornstein-Uhlenbeck (OU) process. It has been suggested that the estimation of within-species variations using replicated data can increase the predictive power of such models, but this hypothesis has not been fully tested. We developed EvoGeneX, a…
Simon Aubé, Lou Nielly-Thibault, Christian R. Landry, Justin C. Fay
How changes in the different steps of protein synthesis-transcription, translation and degradation-contribute to differences of protein abundance among genes is not fully understood. There is however accumulating evidence that transcriptional divergence might have a prominent role. Here, we show that yeast paralogous…
Maëlle Daunesse, Eulalie Liorzou, Elise Parey, Diego Villar + 1 more
Changes in gene expression and regulation are central to mammalian phenotypic evolution. Yet, distinguishing adaptive gene expression shifts from neutral divergence remains challenging. Here, we integrate comparative transcriptomics and regulatory genomics to investigate how natural selection has shaped gene expression…
Arnaud Le Rouzic, Apolline Petit, Arthur Jallet, Justine Vergne + 2 more
Adaptation to new environments often involves multiple genes and can induce substantial changes in biological systems, but the overall consequences of the genetic response to specific environmental pressures remain poorly understood. Here, we investigate the large-scale effects of adaptation to new temperature regimes…
Mallory A. Ballinger, Katya L. Mack, Sylvia M. Durkin, Eric A. Riddell + 1 more
Changes in gene expression are proposed to play a major role in adaptive evolution. While it is known that gene expression is highly sensitive to the environment, very few studies have determined the influence of genetic and environmental effects on adaptive gene regulation in natural populations. Here, we utilize…
Yuheng Huang, Justin B. Lack, Grant T. Hoppel, John E. Pool
The relationships between adaptive evolution, phenotypic plasticity, and canalization remain incompletely understood. Theoretical and empirical studies have made conflicting arguments on whether adaptive evolution may enhance or oppose the plastic response. Gene regulatory traits offer excellent potential to study the…
Pavithra Venkataraman, Christian R Landry
Predicting the fitness effects of mutations is central to understanding molecular evolution and interpreting genome sequence data. Such predictions remain challenging due to the inter-dependent roles of coding and non-coding genetic variation. While coding mutations alter protein structure, stability, activity, and…
Nataša Puzović, Tanvi Madaan, Julien Y. Dutheil
Expression noise, the variability of the amount of gene product among isogenic cells grown in identical conditions, originates from the inherent stochasticity of diffusion and binding of the molecular players involved in transcription and translation. It has been shown that expression noise is an evolvable trait and…
Jianzhi Zhang
Genomics, an interdisciplinary field of biology on the structure, function, and evolution of genomes, has revolutionized many subdisciplines of life sciences, including my field of evolutionary biology, by supplying huge data, bringing high-throughput technologies, and offering a new approach to biology. In this…
Elia Mascolo, Réka Borbély, Santiago Herrera-Álvarez, Călin C. Guet + 2 more
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events…
Kunihiko Kaneko
evolved biological systems Authors: ['Kunihiko Kaneko'] Living systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a hierarchical biological…
Reza Rahmanzadeh
First, mutations leading to genetic novelties in a given species during evolution should be guided by the environment surrounding that species. Second, environment and germline are connected with each other via soma-germline messengers e.g., non-coding RNAs (ncRNAs). Third, based on the information that germline…
Arnaud N’Guessan, Wen Yuan Tong, Hamed Heydari, Alex N Nguyen Ba
Genotype-phenotype mapping (GPM), or the association of trait variation to genetic variation, has been a long-lasting problem in biology. The existing approaches to this problem allowed researchers to partially understand within– and between-species variation as well as the emergence or evolution of phenotypes.…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Authors not listed
RNA droplets assembled from co-transcriptionally folded nanostructures have recently emerged as a promising platform for constructing protocells and minimal synthetic cell models. In these systems, a custom-designed DNA template encodes an RNA nanostar, which is produced by transcription and self-assembles into…
Tetsuhiro Hatakeyama, Ryudo Ohbayashi
The preferred conditions for evolutionary innovation is a fundamental question, but little is known, in part because the question involves rare events. We focused on the potential role of polyploidy in the evolution of novel traits. There are two hypotheses regarding the effects of polyploidy on evolution: Polyploidy…
Tetsuhiro S. Hatakeyama
Phenotypic plasticity and genetic assimilation play key roles in adaptive evolution, yet their underlying mechanism has lacked a unified physical description. A major theoretical difficulty lies in the fundamental difference in timescales, as phenotypic plasticity occurs rapidly within a generation whereas genetic…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Michael Yarus
Evolutionary theorizing resembles building an aircraft while also piloting it; new results change the scaffold for older ideas, requiring revised strategy to remain airborne. A calculated kinetic pathway exists (1) that, under explicit quantitative assumptions, delivers the SGC (Standard Genetic Code). The pathway and…
Authors not listed
We present a chemical framework in which adaptive organization is achieved by tuning a gated quantum resonator (adaptive genomic resonator) {driven quantum oscillator} across a driven, dissipative reaction manifold (fitness landscape) {Hamiltonian potential surface}. In this view, catalytic elements set gain and phase…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
Robert Worden
In 1995 I wrote a paper 'A Speed Limit for Evolution' – whose main result was that evolution must proceed rather slowly, in accordance with the earlier views and intuitions of many authors. The abstract of the paper said: 'An upper bound on the speed of evolution is derived. The bound concerns the amount of genetic…
Bethan S. Jones, Connie M. Ross, Gabriel Foley, Nico Kress + 5 more
Selective, one-step C-H activation of fatty acids from biomass is an attractive concept in sustainable chemistry. Biocatalysis has shown promise for generating high-value hydroxy acids but to date enzyme discovery has relied on laborious screening and produced limited hits, which predominantly oxidise the sub-terminal…
Andrea Iglesias-Ramas, Samuele Pio Lipani, Rosalind J. Allen
Population genetics lies at the heart of evolutionary theory. This topic forms part of many biological science curricula but is rarely taught to physics students. Since physicists are becoming increasingly interested in biological evolution, we aim to provide a brief introduction to population genetics, written for…