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    1. Genetics and Genomics

    Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae

    Tingting Zhao, Irina O Vvedenskaya ... Craig D Kaplan
    Ssl2 processivity determines the window for transcription start site selection during promoter scanning by RNA polymerase II in Saccharomyces cerevisiae.
    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology

    Coevolution-based inference of amino acid interactions underlying protein function

    Victor H Salinas, Rama Ranganathan
    A deep mutational coupling study demonstrates the ability of sequence coevolution methods to reveal the pattern of amino acid interactions underlying protein function.
    1. Biochemistry and Chemical Biology

    Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

    Suwen Zhao, Ayano Sakai ... Matthew P Jacobson
    Genome neighborhood networks provide an efficient large-scale approach to mine metabolic pathway context for entire families of proteins and enzymes.
    1. Evolutionary Biology

    Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites

    Dave W Anderson, Alesia N McKeown, Joseph W Thornton
    Experimental mapping of the joint sequence space of an ancient transcription factor (TF) and its DNA binding sites reveals that epistasis across the molecular interface permitted the evolution of a new and specific TF-DNA complex.
    1. Neuroscience

    Two single-point mutations shift the ligand selectivity of a pheromone receptor between two closely related moth species

    Ke Yang, Ling-Qiao Huang ... Chen-Zhu Wang
    Differing from its ortholog in Helicoverpa armigera, pheromone receptor HassOr14b is tuned to the major sex pheromone component in H. assulta, and two amino acids in the intracellular domain determine their ligand selectivity.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Philosophy of Biology: The meanings of 'function' in biology and the problematic case of de novo gene emergence

    Diane Marie Keeling, Patricia Garza ... Anne-Ruxandra Carvunis
    A lexicon to help scientists and philosophers discuss the meaning of function in molecular biology more clearly is proposed.
    1. Ecology

    Latent functional diversity may accelerate microbial community responses to temperature fluctuations

    Thomas P Smith, Shorok Mombrikotb ... Thomas Bell
    A novel species-sorting experiment finds that phylogenetically and functionally distinct microbial communities emerge under different temperature conditions due to the resuscitation of latent diversity.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA

    Weiwei Yang, Yu-Cheng Lin ... Laurence Ettwiller
    A novel DNA/RNA modifying enzyme catalyzing a previously unknown 5-carbamoyloxymethylcytosine modification has been discovered using a novel framework called Metagenomics Genome-Phenome Association.
    1. Cell Biology

    6-Phosphogluconate dehydrogenase (6PGD), a key checkpoint in reprogramming of regulatory T cells metabolism and function

    Saeed Daneshmandi, Teresa Cassel ... Pankaj Seth
    6-Phosphogluconate dehydrogenase controls regulatory T cells metabolism with shifts to Th1, Th2, and Th17 phenotypes.
    1. Chromosomes and Gene Expression
    2. Evolutionary Biology

    The life cycle of Drosophila orphan genes

    Nicola Palmieri, Carolin Kosiol, Christian Schlötterer
    The short lifetime of orphan genes is a major factor explaining the stability of gene number in Drosophila.