An interplay among experimental studies of protein synthesis, evolutionary theory, and comparisons of DNA sequence data has shed light on the roles of natural selection and genetic drift in 'silent' DNA evolution.
Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae
Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate
Suppression of the negative effect of minor arginine codons on gene expression; preferential usage of minor codons within the first 25 codons of the Escherichia coli genes
Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do 'prefer' optimal codons
Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons
Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases
The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications
Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs
Synonymous substitution-rate constants in Escherichia coli and Salmonella typhimurium and their relationship to gene expression and selection pressure
Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes
The effect of background selection against deleterious mutations on weakly selected, linked variants
Variation in synonymous substitution rates among mammalian genes and the correlation between synonymous and nonsynonymous divergences
Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?
Selection costs of amino acid substitutions in ColE1 and ColIa gene clusters harbored by Escherichia coli
Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli
Global mRNA stability is not associated with levels of gene expression in Drosophila melanogaster but shows a negative correlation with codon bias
Codon bias and noncoding GC content correlate negatively with recombination rate on the Drosophila X chromosome
The effect of local nucleotides on synonymous codon usage in the honeybee (Apis mellifera L.) genome
An analytical model of gene evolution with 9 mutation parameters: an application to the amino acids coded by the common circular code
Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift
Evaluation of codon biology in citrus and Poncirus trifoliata based on genomic features and frame corrected expressed sequence tags
Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics
Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome
Nucleotide substitution rate estimation in enterobacteria: approximate and maximum-likelihood methods lead to similar conclusions
A strong effect of AT mutational bias on amino acid usage in Buchnera is mitigated at high-expression genes
Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region
The surprising negative correlation of gene length and optimal codon use--disentangling translational selection from GC-biased gene conversion in yeast
Effect of exonic splicing regulation on synonymous codon usage in alternatively spliced exons of Dscam
Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes
Synonymous codon usage bias is correlative to intron number and shows disequilibrium among exons in plants
Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids
Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences
In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation
A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation
scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes
Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea)
Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families
Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila
Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation
Temperature adaptation of synonymous codon usage in different functional categories of genes: a comparative study between homologous genes of Methanococcus jannaschii and Methanococcus maripaludis
Determining the relationship of gene expression and global mRNA stability in Drosophila melanogaster and Escherichia coli using linear models
Nature of selective constraints on synonymous codon usage of rice differs in GC-poor and GC-rich genes
Reinvestigating the codon and amino acid usage of S. cerevisiae genome: a new insight from protein secondary structure analysis
Associations of the 5-hydroxytryptamine (serotonin) receptor 1B gene (HTR1B) with alcohol, cocaine, and heroin abuse
Identification of circular codes in bacterial genomes and their use in a factorization method for retrieving the reading frames of genes
Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana
An analytical model of gene evolution with six mutation parameters: an application to archaeal circular codes
Determination of mutation trend in proteins by means of translation probability between RNA codes and mutated amino acids
Phylogenetic relationships of the Cobitoidea (Teleostei: Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution
Cancer, Warts, or Asymptomatic Infections: Clinical Presentation Matches Codon Usage Preferences in Human Papillomaviruses
The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses
The action of selection on codon bias in the human genome is related to frequency, complexity, and chronology of amino acids
Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation
Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein
Hydrophobicity and aromaticity are primary factors shaping variation in amino acid usage of chicken proteome
Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly
Synonymous codon usage bias in plant mitochondrial genes is associated with intron number and mirrors species evolution
Accounting for experimental noise reveals that mRNA levels, amplified by post-transcriptional processes, largely determine steady-state protein levels in yeast
Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens
Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity
Measuring the coding potential of genomic sequences through a combination of triplet occurrence patterns and RNY preference
Large-scale nucleotide optimization of simian immunodeficiency virus reduces its capacity to stimulate type I interferon in vitro
Genome-wide patterns of codon bias are shaped by natural selection in the purple sea urchin, Strongylocentrotus purpuratus
Translational selection is operative for synonymous codon usage in Clostridium perfringens and Clostridium acetobutylicum
Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers
Dissimilation of synonymous codon usage bias in virus-host coevolution due to translational selection.
Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals
Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness
Polyploidization is accompanied by synonymous codon usage bias in the chloroplast genomes of both cotton and wheat
The combined influence of codon composition and tRNA copy number regulates translational efficiency by influencing synonymous nucleotide substitution
The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China.
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
Evolution of Pluripotency
Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.
Lipidomics & Rhinovirus Infection
Lipidomics can be used to examine the lipid species involved with pathogenic conditions, such as viral associated inflammation. Discovered the latest research on Lipidomics & Rhinovirus Infection.
Spatio-Temporal Regulation of DNA Repair
DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.
Chronic Fatigue Syndrome
Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.
Torsion dystonia is a movement disorder characterized by loss of control of voluntary movements appearing as sustained muscle contractions and/or abnormal postures. Here is the latest research.
Archaeal RNA Polymerase
Archaeal RNA polymerases are most similar to eukaryotic RNA polymerase II but require the support of only two archaeal general transcription factors, TBP (TATA-box binding protein) and TFB (archaeal homologue of the eukaryotic general transcription factor TFIIB) to initiate basal transcription. Here is the latest research on archaeal RNA polymerases.
Alzheimer's Disease: MS4A
Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.
Central Pontine Myelinolysis
Central Pontine Myelinolysis is a neurologic disorder caused most frequently by rapid correction of hyponatremia and is characterized by demyelination that affects the central portion of the base of the pons. Here is the latest research on this disease.