897 results found
    1. Microbiology and Infectious Disease

    Codon usage bias controls mRNA and protein abundance in trypanosomatids

    Laura Jeacock, Joana Faria, David Horn
    Global relative mRNA and protein abundance in trypanosomatids can be effectively estimated at transcriptomic and proteomic scales based on protein-coding sequences alone.
    1. Microbiology and Infectious Disease

    RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies

    Fiona Tulloch, Nicky J Atkinson ... Peter Simmonds
    Attenuating candidate live virus vaccines by incorporating unfavoured codon pairs to reduce translation efficiency is actually mediated though changes in frequencies of CpG and UpA dinucleotides, which make viruses more visible to the innate immune system.
    1. Developmental Biology

    Distinct responses to rare codons in select Drosophila tissues

    Scott R Allen, Rebeccah K Stewart ... Donald T Fox
    A tissue-wide fluoresence-based screen reveals that not all tissues in an organism (Drosophila) reinforce a hierarchy of codon usage to the same extent, a finding which impacts tissue-specific protein expression and function.
    1. Genetics and Genomics

    Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

    Zhipeng Zhou, Yunkun Dang ... Yi Liu
    Genetic and bioinformatic analyses uncover an unexpected role for codon usage biases in regulating gene expression at the transcriptional level by suppressing premature transcription termination.
    1. Evolutionary Biology
    2. Genetics and Genomics

    The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder

    Catherine A Weibel, Andrew L Wheeler ... Joanna Masel
    Proteins evolve more intrinsic structural disorder under more effective selection, with selection assessed via a novel metric of codon adaptation.
    1. Cell Biology

    MAF1, a repressor of RNA polymerase III-dependent transcription, regulates bone mass

    Ellen Phillips, Naseer Ahmad ... Deborah L Johnson
    Identification of a novel role for the transcriptional repressor, MAF1, and RNA polymerase III-dependent transcription, in osteoblast differentiation, mineralization, and bone biology.
    1. Ecology

    Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment

    Jordan G Okie, Amisha T Poret-Peterson ... James J Elser
    Trait-based metagenomic analysis of an ecosystem fertilization experiment shows that genomic traits that affect the costs and rates of biochemical information-processing mediate community assembly.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    CpG and UpA dinucleotides in both coding and non-coding regions of echovirus 7 inhibit replication initiation post-entry

    Jelke Jan Fros, Isabelle Dietrich ... Peter Simmonds
    RNA virus replication is attenuated by an intrinsic restriction mechanism after introducing CpG/UpA dinucleotides into both non-translated and coding regions of viral genomes, which may be exploited in the design of attenuated virus vaccines.
    1. Biochemistry and Chemical Biology

    Measurement of average decoding rates of the 61 sense codons in vivo

    Justin Gardin, Rukhsana Yeasmin ... Bruce Futcher
    The translation rates of each yeast codon have been measured in both the A and P sites of the ribosome.
    1. Computational and Systems Biology
    2. Evolutionary Biology

    Point of View: Biological causal links on physiological and evolutionary time scales

    Amit Karmon, Yitzhak Pilpel
    Increasing awareness that many causal links in biology might be bi-directional could overcome biases and improve scientific reasoning.

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