September 2015

Research articles

    1. Biochemistry
    2. Computational and Systems Biology

    Protein biogenesis machinery is a driver of replicative aging in yeast

    Georges E Janssens et al.
    A comprehensive mapping of the proteome and transcriptome during the complete replicative lifespan of budding yeast predicted an increased abundance of the protein biogenesis machinery is most causal for aging.
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    1. Cell Biology
    2. Immunology

    Distinct mechanisms define murine B cell lineage immunoglobulin heavy chain (IgH) repertoires

    Yang Yang et al.
    The B-1a cell heavy chain antibody repertoire differs dramatically from the follicular and marginal zone B cell repertoire and is defined by distinct mechanisms driven by self antigens rather than antigens derived from the microbiota.
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    1. Neuroscience

    Food odors trigger Drosophila males to deposit a pheromone that guides aggregation and female oviposition decisions

    Chun-Chieh Lin et al.
    The activation of Drosophila Or7a receptors guides aggregation and egg-laying behaviors towards both green leaf volatiles and a male-specific food-odor-induced pheromone.
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    1. Biophysics and Structural Biology

    Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

    Daniel A Keedy et al.
    The conformations of the enzyme cyclophilin A that are essential for its catalytic activity are temperature dependent and exhibit diverse responses, which is consistent with a complex energy landscape.
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    1. Neuroscience

    AMPA receptor mediated synaptic excitation drives state-dependent bursting in Purkinje neurons of zebrafish larvae

    Mohini Sengupta, Vatsala Thirumalai
    In vivo recordings in unanesthetized zebrafish larvae show that Purkinje neurons have two stable membrane potential states and that climbing fiber inputs can toggle them to up states during motor episodes.
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    1. Developmental Biology and Stem Cells
    2. Neuroscience

    Extrinsic and intrinsic signals converge on the Runx1/CBFβ transcription factor for nonpeptidergic nociceptor maturation

    Siyi Huang et al.
    The extrinsic cue NGF and the intrinsic signal Islet1 converge at the level of the Runx1/CBFβ transcription factor complex formation to promote differentiation of a major nociceptor subtype.
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    1. Biochemistry
    2. Biophysics and Structural Biology

    Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics

    Kevin C Hadley et al.
    STOMP is a technique that can determine the proteomic composition of any feature that is identifiable by laser scanning microscopy and is at least one cubic micron in size.
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    1. Neuroscience

    Corticostriatal dynamics encode the refinement of specific behavioral variability during skill learning

    Fernando J Santos et al.
    Recordings from the mouse brain as animals learn a lever pressing task reveal how the motor system optimizes skill learning by reducing variability in those aspects of task performance that are essential for achieving a goal.
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    1. Neuroscience

    Cortical network architecture for context processing in primate brain

    Zenas C Chao et al.
    Large-scale electrocorticography and big data analysis of brain-wide neuronal interactions reveal the architecture of network information flow for context processing in primate brain.
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    1. Cell Biology

    FAM150A and FAM150B are activating ligands for anaplastic lymphoma kinase

    Jikui Guan et al.
    The secreted molecules FAM150A and FAM150B bind to the ALK RTK extracellular domain, potently activating the receptor activation and driving downstream signaling events.
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    1. Immunology
    2. Microbiology and Infectious Disease

    Enteric pathogens deploy cell cycle inhibiting factors to block the bactericidal activity of Perforin-2

    Ryan M McCormack et al.
    Yersinia pseudotuberculosis and enteropathogenic Escherichia coli promote pathogenicity by deamidating the ubiquitin-like protein NEDD8 to block ubiquitin-dependent trafficking of Perforin-2, which is an effector of innate immunity.
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    1. Biochemistry
    2. Cell Biology

    Oligomerization of p62 allows for selection of ubiquitinated cargo and isolation membrane during selective autophagy

    Bettina Wurzer et al.
    Oligomerization of p62/SQSTM1 generates high avidity binding regions that enable it to spatially select for concentrated ubiquitin and ATG8-family proteins.
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    1. Biochemistry
    2. Biophysics and Structural Biology

    Regulation of multispanning membrane protein topology via post-translational annealing

    Reid C Van Lehn et al.
    Coarse-grained modeling reveals a new mechanism for multispanning membrane protein topogenesis, in which misintegrated configurations of the proteins undergo post-translational annealing to reach final, fully integrated multispanning topologies.
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    1. Genes and Chromosomes

    Genomic DNA transposition induced by human PGBD5

    Anton G Henssen et al.
    The human PGBD5 gene encodes an active DNA transposase.
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    1. Biochemistry
    2. Cell Biology

    A mitotic kinase scaffold depleted in testicular seminomas impacts spindle orientation in germ line stem cells

    Heidi Hehnly et al.
    A protein kinase complex that is important for cell division is lost in testicular seminoma, which is a common cancer in men.
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    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Cortical microtubule nucleation can organise the cytoskeleton of Drosophila oocytes to define the anteroposterior axis

    Philipp Khuc Trong et al.
    A three-dimensional description of the cytoskeletal arrangement, cytoplasmic flows, and cargo transport in stage 9 Drosophila oocytes accurately reproduces mRNA localizations in wild-type and mutant oocytes.
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    1. Neuroscience

    A genetic link between discriminative fear coding by the lateral amygdala, dopamine, and fear generalization

    Graham L Jones et al.
    Discrimination of predictive and non-predictive fear stimuli requires plasticity in the lateral amygdala that is regulated by midbrain dopamine neurons.
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    1. Biophysics and Structural Biology

    Molecular architecture of the yeast Mediator complex

    Philip J Robinson et al.
    Integrative modeling of results from chemical cross-linking, electron microscopy, and homology modeling yield a three-dimensional model of the entire Mediator complex in yeast.
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    1. Computational and Systems Biology
    2. Neuroscience

    Competing basal ganglia pathways determine the difference between stopping and deciding not to go

    Kyle Dunovan et al.
    A model based on the architecture of basal ganglia and validated with behavior and neuroimaging distinguishes mechanisms of action cancellation from no-go decisions.
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    1. Neuroscience

    Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus

    Diek W Wheeler et al.
    Hippocampome.org is an online resource that provides free human- and machine-readable access to the comprehensive property-based classification of hippocampal neurons from 14,000 pieces of published experimental evidence.
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    1. Biophysics and Structural Biology
    2. Microbiology and Infectious Disease

    Differential interaction forces govern bacterial sorting in early biofilms

    Enno R Oldewurtel et al.
    Differential physical interactions between bacteria in mixed microcolonies trigger cell sorting.
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    1. Developmental Biology and Stem Cells
    2. Genomics and Evolutionary Biology

    Deployment of a retinal determination gene network drives directed cell migration in the sea urchin embryo

    Megan L Martik, David R McClay
    The gene regulatory network controlling directed cell migration in a sea urchin is strikingly similar to a sub-circuit for eye development in Drosophila, suggesting that ancient systems-level controls may be adapted for diverse functions in different animals.
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    1. Neuroscience

    Reward modulates the effect of visual cortical microstimulation on perceptual decisions

    Nela Cicmil et al.
    Evidence of an interaction between expected reward size and visual cortical microstimulation indicates that expected reward can affect sensory representations.
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    1. Immunology
    2. Microbiology and Infectious Disease

    Perforin-2 is essential for intracellular defense of parenchymal cells and phagocytes against pathogenic bacteria

    Ryan M McCormack et al.
    Perforin-2 deficiency is lethal upon infection with pathogenic bacteria despite the presence of other bactericidal effectors.
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    1. Developmental Biology and Stem Cells

    YAP controls retinal stem cell DNA replication timing and genomic stability

    Pauline Cabochette et al.
    The Hippo pathway downstream effector YAP regulates S-phase progression to protect neural stem cells of the retina from experiencing genomic instability.
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    1. Biophysics and Structural Biology
    2. Computational and Systems Biology

    Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes

    Juliane Liepe et al.
    Experimental and computational analyses reveal how proteasomal hydrolysis is regulated and show that peptide transport is the rate-limiting step and the main differentiating factor between human standard- and immuno-proteasomes.
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    1. Neuroscience

    Circuit mechanisms encoding odors and driving aging-associated behavioral declines in Caenorhabditis elegans

    Sarah G Leinwand et al.
    Neurotransmission pathways from primary to secondary neurons encode odor and underlie age-related sensory behavioral declines.
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    1. Cell Biology
    2. Human Biology and Medicine

    A novel GSK3-regulated APC:Axin interaction regulates Wnt signaling by driving a catalytic cycle of efficient βcatenin destruction

    Mira I Pronobis et al.
    A new dynamic mechanistic model explains how the destruction complex negatively regulates Wnt signaling in development and oncogenesis.
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    1. Biochemistry
    2. Developmental Biology and Stem Cells

    A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation

    Li Li et al.
    Proteasome-mediated degradation of the TATA-box binding protein (TBP) during terminal differentiation is regulated by the E3 ligase Huwe1 and the deubiquitinase USP10.
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    1. Ecology

    Parental effects alter the adaptive value of an adult behavioural trait

    Rebecca M Kilner et al.
    The adaptive value of social behaviour exhibited in adult life varies with conditions experienced in early life, and poorer conditions may promote conflict over cooperation.
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    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance

    Caroline Colijn, Ted Cohen
    Both within and between hosts, the key factor guiding whether increasing treatment strength will increase or decrease antibiotic resistance is whether inter-strain competition is effective, not whether it is present.
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    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Matrix metalloproteinase 14 is required for fibrous tissue expansion

    Susan H Taylor et al.
    The membrane type I-matrix metalloproteinase is essential for the release of collagen fibrils from plasma membrane fibripositors, which is required for the transition from embryonic to postnatal tendon development.
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    1. Neuroscience

    Central neural circuitry mediating courtship song perception in male Drosophila

    Chuan Zhou et al.
    Anatomical, behavioral and physiological evidence suggests that the aPN1-vPN1-pC1 pathway serves as a labeled line for the processing and transformation of courtship song in male Drosophila.
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    1. Developmental Biology and Stem Cells
    2. Human Biology and Medicine

    TALPID3 controls centrosome and cell polarity and the human ortholog KIAA0586 is mutated in Joubert syndrome (JBTS23)

    Louise A Stephen et al.
    Mutations in KIAA0586 (TALPID3) cause a severe ciliopathy called Joubert syndrome that affects organ, cell and centrosome polarity.
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    1. Biochemistry
    2. Biophysics and Structural Biology

    Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function

    Jason C Bell et al.
    Individual SSB-ssDNA complexes undergo reversible condensation and de-condensation that is modulated by RecOR during recombination.
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    1. Neuroscience

    Modulation of GABA and resting state functional connectivity by transcranial direct current stimulation

    Velicia Bachtiar et al.
    Building on previous work (Stagg et al., 2014), it is shown that transcranial direct current stimulation modulates local GABA concentration and functional connectivity in the human motor cortex.
    Research Advance
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    1. Cell Biology
    2. Human Biology and Medicine

    SPOP mutation leads to genomic instability in prostate cancer

    Gunther Boysen et al.
    SPOP mutations underlie a novel, genomically unstable subclass of prostate cancer by altering DNA repair.
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    1. Neuroscience

    Norepinephrine is required to promote wakefulness and for hypocretin-induced arousal in zebrafish

    Chanpreet Singh et al.
    Experiments in genetically modified zebrafish that are unable to produce norepinephrine show that this neurotransmitter promotes wakefulness by mediating the effects of the neuropeptide hypocretin.
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    1. Neuroscience

    Layer 2/3 pyramidal cells in the medial prefrontal cortex moderate stress induced depressive behaviors

    Prerana Shrestha et al.
    The well-established link between stress and depression could be due to the activity of a population of cells in prefrontal cortex that express a gene mutated in the rare disorder Wolfram syndrome.
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    1. Cell Biology

    GnT1IP-L specifically inhibits MGAT1 in the Golgi via its luminal domain

    Hung-Hsiang Huang et al.
    GnT1IP-L is a membrane bound glycoprotein that interacts with MGAT1 in the Golgi, but not in the endoplasmic reticulum, to regulate complex N-glycan synthesis.
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    1. Cell Biology
    2. Genes and Chromosomes

    Structured illumination with particle averaging reveals novel roles for yeast centrosome components during duplication

    Shannon Burns et al.
    Visualization of yeast spindle pole proteins using a new microscopy method shows that assembly into the nuclear membrane occurs at the same time as duplication.
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    1. Biochemistry
    2. Immunology

    Establishing the role of ATP for the function of the RIG-I innate immune sensor

    David C Rawling et al.
    The immune sensor RIG-I uses ATP-mediated compaction as a signaling trigger and a proofreading mechanism.
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    1. Biophysics and Structural Biology
    2. Computational and Systems Biology

    Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis

    Etai Jacob et al.
    Correlated mutation analysis using a combination of amino acid and codon sequence alignments improves predictions of amino acid residue contacts in proteins.
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    1. Genomics and Evolutionary Biology
    2. Microbiology and Infectious Disease

    Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels

    Lizbeth Sayavedra et al.
    Beneficial symbiotic bacteria encode an exceptional number of toxin-related genes that are all expressed by the symbionts in the host, supporting their key role in host-microbe interactions.
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    1. Genes and Chromosomes
    2. Microbiology and Infectious Disease

    The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo

    Seth R Goldman et al.
    The sigma subunit of bacterial RNA polymerase, classically known as an initiation factor, can also operate as an elongation factor with effects that vary with growth phase.
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    1. Biophysics and Structural Biology
    2. Cell Biology

    The molecular mechanism of nuclear transport revealed by atomic-scale measurements

    Loren E Hough et al.
    NMR spectroscopy has been used to explain a central unresolved issue of nuclear transport, namely how it can be both fast and specific.
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    1. Cell Biology
    2. Developmental Biology and Stem Cells

    NOCA-1 functions with γ-tubulin and in parallel to Patronin to assemble non-centrosomal microtubule arrays in C. elegans

    Shaohe Wang et al.
    The C. elegans ninein homolog NOCA-1 is important for the assembly of non-centrosomal microtubule arrays required for embryo production, nuclear positioning and larval development.
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    1. Developmental Biology and Stem Cells
    2. Neuroscience

    Phosphodiesterase 4D acts downstream of Neuropilin to control Hedgehog signal transduction and the growth of medulloblastoma

    Xuecai Ge et al.
    Neuropilin integrates with Hedgehog signal transduction by a newly identified transducer to control cerebellar neurogenesis and medulloblastoma.
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    1. Epidemiology and Global Health

    The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans

    Katia Koelle, David A Rasmussen
    Deleterious mutations slow down flu's antigenic evolution, make it more punctuated in nature, and reduce the virus's genetic diversity.
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    1. Developmental Biology and Stem Cells
    2. Genes and Chromosomes

    The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development

    Thomas W Bebee et al.
    Large-scale developmental defects in mice occur with the ablation of the epithelial-specific splicing factors Esrp1 and Esrp2.
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    1. Biochemistry
    2. Neuroscience

    Cell type-specific pharmacology of NMDA receptors using masked MK801

    Yunlei Yang et al.
    The small molecule NMDA-receptor antagonist MK801 has been genetically targeted to specific cell types in brain tissue to examine the role of NMDA receptors in cocaine-induced synaptic plasticity.
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    1. Biochemistry
    2. Biophysics and Structural Biology

    Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets

    Nicole T Schirle et al.
    Argonaute proteins directly contact adenosine nucleotides in some miRNA target sites, leading to enhanced repression of the target mRNA.
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    1. Developmental Biology and Stem Cells
    2. Genomics and Evolutionary Biology

    Characterization of the finch embryo supports evolutionary conservation of the naive stage of development in amniotes

    Siu-Shan Mak et al.
    Finch embryos are laid at an earlier stage than other avian embryos and contain cells with similar properties to pluripotent embryonic stem cells from mice.
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    1. Computational and Systems Biology
    2. Developmental Biology and Stem Cells

    A balance of positive and negative regulators determines the pace of the segmentation clock

    Guy Wiedermann et al.
    Computational modelling together with experimental manipulation indicate that the stability and turnover of activated Notch is inextricably linked to the regulation of the pace of segmentation clock gene expression in the presomitic mesoderm.
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    1. Genomics and Evolutionary Biology

    Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa

    Lee R Berger et al.
    A new hominin species has been unearthed in the Dinaledi Chamber of the Rising Star cave system in the largest assemblage of a single species of hominins yet discovered in Africa.
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    1. Genomics and Evolutionary Biology

    Geological and taphonomic context for the new hominin species Homo naledi from the Dinaledi Chamber, South Africa

    Paul HGM Dirks et al.
    A new hominin species found in a South African cave is part of one of the most unusual hominin fossil assemblages on record.
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    1. Cell Biology

    The GARP complex is required for cellular sphingolipid homeostasis

    Florian Fröhlich et al.
    The retrograde vesicular trafficking GARP complex, which is mutated in a neurodegenerative disease, is important for sphingolipid homeostasis in yeast and mammalian cells.
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    1. Biochemistry
    2. Cell Biology

    Wss1 metalloprotease partners with Cdc48/Doa1 in processing genotoxic SUMO conjugates

    Maxim Y Balakirev et al.
    Wss1 is both a metalloprotease and SUMO ligase found in association with Cdc48 and Doa1 and accumulating in the vacuole upon DNA damage.
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    1. Biochemistry
    2. Biophysics and Structural Biology

    CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex

    Brian Bae et al.
    The crystal structure of Thermus transcription activation complexes containing the transcriptional activator CarD reveals a new mechanism for the activation of transcription.
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    1. Biochemistry
    2. Biophysics and Structural Biology

    Structure of a bacterial RNA polymerase holoenzyme open promoter complex

    Brian Bae et al.
    The crystal structure of bacterial RNA polymerase bound to the transcription bubble reveals key features that support the formation of a double-strand/single-strand DNA junction at the upstream edge of the −10 element where bubble formation initiates.
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    1. Biochemistry
    2. Biophysics and Structural Biology

    Structural determinants of nuclear export signal orientation in binding to exportin CRM1

    Ho Yee Joyce Fung et al.
    Some nuclear export signals (NESs) bind to the transport receptor CRM1 in the opposite orientation to those previously studied.
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    1. Neuroscience

    Activities of visual cortical and hippocampal neurons co-fluctuate in freely moving rats during spatial behavior

    Daniel Christopher Haggerty, Daoyun Ji
    As rats learn to traverse back and forth on a track, visual cortical neurons fire at specific locations and functionally interact with those hippocampal place cells representing the same locations.
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    1. Neuroscience

    A thesaurus for a neural population code

    Elad Ganmor et al.
    The activity patterns of populations of neurons in the retina are organized as semantic clusters (analogous to synonyms), in which component patterns bear little physical resemblance to one another but convey the same meaning.
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    1. Developmental Biology and Stem Cells
    2. Plant Biology

    Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana

    Philip Wolff et al.
    Hybridization barriers in Arabidopsis thaliana can be established by paternally expressed imprinted genes (PEGs) that affect cellularization of the endosperm during seed development.
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    1. Genes and Chromosomes
    2. Plant Biology

    Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense

    Claudia Castillo-González et al.
    A viral protein hijacks the key effector of transcriptional gene silencing, Su(var)3-9, to evade host plant surveillance.
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    1. Neuroscience

    A neural command circuit for grooming movement control

    Stefanie Hampel et al.
    The identification of a neural circuit that drives a specific grooming movement in Drosophila reveals that it may also control movement parameters, such as duration.
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    1. Neuroscience

    Network structure of brain atrophy in de novo Parkinson's disease

    Yashar Zeighami et al.
    The pattern of atrophy in Parkinson's disease is consistent with the disease spreading via intrinsic brain networks.
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    1. Developmental Biology and Stem Cells
    2. Neuroscience

    Axon injury triggers EFA-6 mediated destabilization of axonal microtubules via TACC and doublecortin like kinase

    Lizhen Chen et al.
    Severing axons in C. elegans reveals a mechanism by which the axons sense acute damage and respond by sequential remodeling of their microtubule cytoskeleton.
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    1. Neuroscience

    A principle of economy predicts the functional architecture of grid cells

    Xue-Xin Wei et al.
    Mathematical modeling suggests that grid cells in the rodent brain use fundamental principles of number theory to maximize the efficiency of spatial mapping, enabling animals to accurately encode their location with as few neurons as possible.
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    1. Developmental Biology and Stem Cells
    2. Neuroscience

    Feeding state-dependent regulation of developmental plasticity via CaMKI and neuroendocrine signaling

    Scott J Neal et al.
    CaMKI and neuroendocrine signaling integrate information about food status to regulate a developmental decision in C. elegans.
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    1. Developmental Biology and Stem Cells

    Amotl2a interacts with the Hippo effector Yap1 and the Wnt/β-catenin effector Lef1 to control tissue size in zebrafish

    Sobhika Agarwala et al.
    The cell junction-associated protein Amotl2a controls tissue size in the zebrafish lateral line primordium by limiting the activity of the Hippo effector Yap1 and the Wnt effector Lef1.
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    1. Biophysics and Structural Biology
    2. Genomics and Evolutionary Biology

    Large-scale determination of previously unsolved protein structures using evolutionary information

    Sergey Ovchinnikov et al.
    A new method of protein structure prediction that incorporates residue–residue co-evolution information into the Rosetta structure prediction program was used to develop models for 58 large protein families that had no previous structural information.
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    1. Cell Biology
    2. Genes and Chromosomes

    Sir2 phosphorylation through cAMP-PKA and CK2 signaling inhibits the lifespan extension activity of Sir2 in yeast

    Woo Kyu Kang et al.
    The deacetylase Sir2 fine-tunes transcription of PMA1 and other aging related genes in a cAMP-PKA and CK2 signaling dependent manner.
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    1. Neuroscience

    Keratinocytes can modulate and directly initiate nociceptive responses

    Kyle M Baumbauer et al.
    Optogenetics reveals that keratinocytes can evoke action potential firing in several types of cutaneous sensory afferents, including those that transmit thermal, mechanical and pain stimuli.
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    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Mapping influenza transmission in the ferret model to transmission in humans

    Michael G Buhnerkempe et al.
    Influenza transmission among ferrets correlates strongly with transmission among humans, so the ferret model for influenza transmission is a valid tool for pandemic potential in humans.
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    1. Genomics and Evolutionary Biology
    2. Neuroscience

    Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss

    Fredrick E Henry et al.
    Cell type-specific transcriptomics in energy homeostasis neurons has identified hundreds of genes and multiple signaling pathways that are regulated by weight loss in mice, as well as several previously unexamined genes that can regulate appetite and body weight.
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