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First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes
(2016)Molecular Biology and EvolutionThe temporal change of phenotypes during the adaptive process remains largely unexplored, as do the genetic changes that affect these phenotypic changes. Here we focused on three mutations that rose to high frequency in the early stages of adaptation within 12 Escherichia coli populations subjected to thermal stress (42 °C). All the mutations were in the rpoB gene, which encodes the RNA polymerase beta subunit. For each mutation, we ...Journal Article -
Quantifying Age-dependent Extinction from Species Phylogenies
(2016)Systematic BiologySeveral ecological factors that could play into species extinction are expected to correlate with species age, i.e., time elapsed since the species arose by speciation. To date, however, statistical tools to incorporate species age into likelihood-based phylogenetic inference have been lacking. We present here a computational framework to quantify age-dependent extinction through maximum likelihood parameter estimation based on phylogenetic ...Journal Article -
Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant Pathogen Erwinia Tracheiphila
(2016)Genome Biology and EvolutionModern industrial agriculture depends on high-density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared with ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, ...Journal Article -
Insights and Perspectives on Sensory-Motor Integration and Rehabilitation
(2016)Multisensory ResearchThe present review focuses on the flow and interaction of somatosensory-motor signals in the central and peripheral nervous system. Specifically, where incoming sensory signals from the periphery are processed and interpreted to initiate behaviors, and how ongoing behaviors produce sensory consequences encoded and used to fine-tune subsequent actions. We describe the structure–function relations of this loop, how these relations can be ...Journal Article -
Post-transcriptional control of executioner caspases by RNA-binding proteins
(2016)Genes & DevelopmentCaspases are key components of apoptotic pathways. Regulation of caspases occurs at several levels, including transcription, proteolytic processing, inhibition of enzymatic function, and protein degradation. In contrast, little is known about the extent of post-transcriptional control of caspases. Here, we describe four conserved RNA-binding proteins (RBPs)—PUF-8, MEX-3, GLD-1, and CGH-1—that sequentially repress the CED-3 caspase in ...Journal Article -
LRH-1-dependent programming of mitochondrial glutamine processing drives liver cancer
(2016)Genes & DevelopmentVarious tumors develop addiction to glutamine to support uncontrolled cell proliferation. Here we identify the nuclear receptor liver receptor homolog 1 (LRH-1) as a key regulator in the process of hepatic tumorigenesis through the coordination of a noncanonical glutamine pathway that is reliant on the mitochondrial and cytosolic transaminases glutamate pyruvate transaminase 2 (GPT2) and glutamate oxaloacetate transaminase 1 (GOT1), which ...Journal Article -
Lagrangian analysis of sea-ice dynamics in the Arctic Ocean
(2016)Polar ResearchIn this study, we present Lagrangian diagnostics to quantify changes in the dynamical characteristics of the Arctic sea-ice cover from 2006 to 2014. Examined in particular is the evolution in finite-time Lyapunov exponents (FTLEs), which monitor the rate at which neighbouring particle trajectories diverge, and stretching rates throughout the Arctic. In this analysis, we compute FTLEs for the Arctic ice-drift field using the 62.5 km daily ...Journal Article