24 papers · ranked by Valyu relevance
Owen Z. Woody, Andrew C. Doxey, Brendan J. McConkey
Classical studies of the evolution of gene function have predominantly focused on mutations within protein coding regions. With the advent of microarrays, however, it has become possible to evaluate the transcriptional activity of a gene as an additional characteristic of function. Recent studies have revealed an…
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…
Soumitra Pal, Brian Oliver, Teresa M. Przytycka
While DNA sequence evolution has been well studied, the expression of genes is also subject to evolution. Yet the evolution of gene expression is currently not well understood. In recent years, new tissue/organ specific gene expression datasets spanning several organisms across the tree of life, have become available…
Jenny Chen, Ross Swofford, Jeremy Johnson, Beryl B. Cummings + 5 more
Characterizing the evolutionary history of a gene’s expression profile is a critical component for understanding the relationship between genotype, expression, and phenotype. However, it is not well-established how best to distinguish the different evolutionary forces acting on gene expression. Here, we use RNA-seq…
Alisha K Holloway, Mara K. N Lawniczak, Jason G Mezey, David J Begun + 2 more
Detailed studies of individual genes have shown that gene expression divergence often results from adaptive evolution of regulatory sequence. Genome-wide analyses, however, have yet to unite patterns of gene expression with polymorphism and divergence to infer population genetic mechanisms underlying expression…
Elisa Buchberger, Micael Reis, Ting-Hsuan Lu, Nico Posnien
Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide…
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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…
Armita Nourmohammad, Joachim Rambeau, Torsten Held, Johannes Berg + 1 more
'Michael Lässig'] 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 level. However, the evolutionary modes of gene expression…
Carlo G. Artieri, Hunter B. Fraser
Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged far behind. Here we have applied ribosome profiling—which measures both global…
Marc Robinson‐Rechavi
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which allows comparisons which are both large scale and evolutionarily relevant. The…
Eva L. Koch, Frédéric Guillaume
Gene expression is known to be highly responsive to the environment and important for adjustment of metabolism but there is also growing evidence that differences in gene regulation contribute to species divergence and differences among locally adapted populations. However, most studies so far investigated populations…
Clare C. Rittschof, Kimberly A. Hughes
Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances…
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…
J. Davila-Velderrain, E. R. Alvarez-Buylla
Understanding the mapping of genotypes into phenotypes is a central challenge of current biological research. Such mapping, conceptually represents a developmental mechanism through which phenotypic variation can be generated. Given the nongenetic character of developmental dynamics, phenotypic variation to a great…
Hong-Yan Shih, Harry Mickalide, David T. Fraebel, Nigel Goldenfeld + 1 more
'Seppe Kuehn'] Abstract. 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 populations from microbes to higher animals. Phenotypic…
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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…
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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…
Ken Nishikawa, Akira R. Kinjo
The Weismann barrier, or the impossibility of inheritance of acquired traits, comprises a foundation of modern biology, and it has been a major obstacle in establishing the connection between evolution and ontogenesis. We propose the cooperative model based on the assumption that evolution is achieved by a cooperation…
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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…
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…
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…
Susanna C. Manrubia, José A. Cuesta, Jacobo Aguirre, Sebastian E. Ahnert + 14 more
'Sebastian E. Ahnert' 'Lee Altenberg' 'Alejandro V. Cano' 'Pablo Catalán' 'Ramón Dı́az-Uriarte' 'Santiago F. Elena' 'Juan Antonio García-Martín' 'Paulien Hogeweg' 'Bhavin S. Khatri' 'Joachim Krug' 'Ard A. Louis' 'Nora S. Martin' 'Joshua L. Payne' 'Matthew J. Tarnowski' 'Marcel Weiß'] Understanding how genotypes map…
Anja Knorrscheidt, Pascal Püllmann, Eugen Schell, Dominik Homann + 2 more
Directed evolution requires the screening of enzyme libraries in biological matrices. Available assays are mostly substrate or enzyme specific. Chromatographic techniques like LC and GC overcome this limitation, but require long analysis times. The herein developed multiple injections in a single experimental run…