June 2015

Cover articles

Research articles

    1. Biophysics and Structural Biology
    2. Cell Biology

    Daple is a novel non-receptor GEF required for trimeric G protein activation in Wnt signaling

    Nicolas Aznar et al
    Daple is a guanine nucleotide-exchange factor (GEF) for trimeric G proteins that enables Wnt/Frizzled receptors to transactivate G proteins during non-canonical Wnt signaling.
    Research Article
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    1. Ecology
    2. Epidemiology and Global Health

    The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus

    Moritz UG Kraemer et al
    The limits to the global distribution of the mosquitoes that transmit dengue and chikungunya have been predicted using a species distribution modelling approach.
    Research Article
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    1. Biochemistry
    2. Genes and Chromosomes

    H2A histone-fold and DNA elements in nucleosome activate SWR1-mediated H2A.Z replacement in budding yeast

    Anand Ranjan et al
    Specific elements of the canonical nucleosome are recognized by the multi-component SWR1 chromatin remodeler for ATP-dependent replacement of H2A-H2B dimers with H2A.Z-H2B.
    Short Report
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    1. Developmental Biology and Stem Cells

    A mex3 homolog is required for differentiation during planarian stem cell lineage development

    Shu Jun Zhu et al
    The planarian mex3-1 gene is required for non-stem cell fates and suppresses a stem cell fate in differentiating cells.
    Research Article
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    1. Neuroscience

    Hippocampal place cells construct reward related sequences through unexplored space

    H Freyja Ólafsdóttir et al
    In anticipation of a reward, hippocampal place cells simulate desired journeys through areas that have been seen, but not explored.
    Short Report
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    1. Biochemistry

    Flux analysis of cholesterol biosynthesis in vivo reveals multiple tissue and cell-type specific pathways

    Matthew A Mitsche et al
    Cells use two interdigitated biosynthetic pathways that can be regulated independently to produce diverse bioactive sterols.
    Research Article
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    1. Computational and Systems Biology
    2. Human Biology and Medicine

    Dynamics of preventive vs post-diagnostic cancer control using low-impact measures

    Andrei R Akhmetzhanov, Michael E Hochberg
    A model based on empirical parameter estimates predicts that arresting cancer cell growth by less than 1% per day will produce optimal outcomes in preventing life-threatening cancers, and that such preventive measures are generally more successful than post-diagnostic interventions.
    Research Article
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    1. Developmental Biology and Stem Cells
    2. Genes and Chromosomes

    ATF4 licenses C/EBPβ activity in human mesenchymal stem cells primed for adipogenesis

    Daniel M Cohen et al
    The transcription factor C/EBPβ binds to different DNA sequences depending on whether it binds to ATF4, which enables C/EBPβ to conduct diverse transcriptional programs during adipocyte differentiation by exploiting an expanded motif repertoire.
    Research Article
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    1. Cell Biology
    2. Computational and Systems Biology

    Interplay of cell dynamics and epithelial tension during morphogenesis of the Drosophila pupal wing

    Raphaël Etournay et al
    Autonomous patterns of cell contraction in the context of localized apical extracellular matrix constraints specify tissue stresses that reshape the wing epithelium.
    Research Article
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    1. Human Biology and Medicine
    2. Neuroscience

    Neural population dynamics in human motor cortex during movements in people with ALS

    Chethan Pandarinath et al
    Neural ensemble activity in the human motor cortex contains dynamical structure that is independent of movement parameters and is not well-explained by current models.
    Short Report
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    1. Computational and Systems Biology
    2. Neuroscience

    Age-dependent electroencephalogram (EEG) patterns during sevoflurane general anesthesia in infants

    Laura Cornelissen et al
    Alpha EEG oscillations emerge at 4 months of age during sevoflurane general anesthesia, and unlike in adults, have a widespread spatial distribution that likely reflects differences in brain development.
    Research Article
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    1. Biophysics and Structural Biology

    Thermal fluctuations of immature SOD1 lead to separate folding and misfolding pathways

    Ashok Sekhar et al
    Solution NMR spectroscopy reveals the energy landscape of immature Cu, Zn-superoxide dismutase and leads to atomic resolution structural models of transiently populated non-native oligomers.
    Research Article
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    1. Developmental Biology and Stem Cells
    2. Genomics and Evolutionary Biology

    A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

    Irene Gallego Romero et al
    A panel of chimpanzee induced pluripotent stem cells (iPSCs) will help realise the potential of iPSCs in primate studies, and in combination with genomic technologies, transform studies of comparative evolution.
    Tools and Resources
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    1. Cell Biology
    2. Neuroscience

    A genetic toolkit for tagging intronic MiMIC containing genes

    Sonal Nagarkar-Jaiswal et al
    Building on previous work (Nagarkar-Jaiswal et al., 2015), we report an elegant genetic strategy for endogenous tagging of MiMIC containing genes.
    Research Advance
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    1. Genes and Chromosomes

    Promoter nucleosome dynamics regulated by signalling through the CTD code

    Philippe Materne et al
    Phosphorylation of the C-terminal domain (CTD) of RNA Polymerase II controls nucleosomes dynamics at specific promoters to regulate transcription.
    Research Article
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    1. Neuroscience

    A Cambrian origin for vertebrate rods

    Sabrina Asteriti et al
    Several key functional features of jawed vertebrate rods are also present in lamprey photoreceptors, indicating that our Cambrian ancestors possessed dim light vision.
    Research Article
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    1. Neuroscience

    A simple retinal mechanism contributes to perceptual interactions between rod- and cone-mediated responses in primates

    William N Grimes et al
    A combination of physiological and perceptual experiments show that the responses of rod photoreceptors inhibit those of cones more than vice versa, and reveal both the site of the retinal interaction and the underlying mechanism.
    Short Report
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    1. Biophysics and Structural Biology
    2. Cell Biology

    Single-fluorophore membrane transport activity sensors with dual-emission read-out

    Cindy Ast et al
    Building on previous work (De Michele et al., 2013), we report the development of dual-emission AmTrac sensors for in vivo analysis of transporter activity.
    Research Advance
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    1. Cell Biology

    The mesh is a network of microtubule connectors that stabilizes individual kinetochore fibers of the mitotic spindle

    Faye M Nixon et al
    Microtubules of mitotic spindle fibers are positioned and held together by a meshwork of multipolar connectors.
    Research Article
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    1. Microbiology and Infectious Disease

    Transgenic shRNA pigs reduce susceptibility to foot and mouth disease virus infection

    Shengwei Hu et al
    A transgenic small hairpin RNA can provide a viable tool for enhancing resistance to viral infection in livestock and improve animal well-being.
    Short Report
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    1. Cell Biology
    2. Immunology

    Plasma membrane overgrowth causes fibrotic collagen accumulation and immune activation in Drosophila adipocytes

    Yiran Zang et al
    Excess membrane can trap outgoing extracellular matrix proteins in secreting cells, leading to pericellular deposits that cause tissue damage.
    Research Article
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    1. Biophysics and Structural Biology

    Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition

    Zhu Liu et al
    Lys63-linked diubiquitin exists as an ensemble of conformational states, each responsible for binding to a target protein through conformational selection.
    Research Article
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    1. Computational and Systems Biology

    Tuning the speed-accuracy trade-off to maximize reward rate in multisensory decision-making

    Jan Drugowitsch et al
    Building on previous work (Drugowitsch et al., 2014), it is shown that decision-makers adjust their speed-accuracy trade-off flexibly from one moment to the next, based on evidence available from multiple sensory modalities, in order to nearly maximize their reward rate.
    Research Advance
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    1. Biochemistry
    2. Genes and Chromosomes

    Compensatory induction of MYC expression by sustained CDK9 inhibition via a BRD4-dependent mechanism

    Huasong Lu et al
    A new potent and selective CDK9 inhibitor induces the expression of the proto-oncogene MYC via a mechanism that depends on the bromodomain protein BRD4.
    Research Article
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    1. Neuroscience

    The neuropeptide tachykinin is essential for pheromone detection in a gustatory neural circuit

    Shruti Shankar et al
    The cellular and molecular substrates that underlie the programmed behavioral response to a gustatory sex pheromone have been identified.
    Research Article
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    1. Neuroscience

    Synaptic representation of locomotion in single cerebellar granule cells

    Kate Powell et al
    The first patch-clamp recordings from single cerebellar granule cells during locomotion reveal that the entire step sequence can be predicted from both excitatory synaptic input and output spikes from a single neuron.
    Short Report
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    1. Computational and Systems Biology
    2. Genomics and Evolutionary Biology

    Expression noise facilitates the evolution of gene regulation

    Luise Wolf et al
    In-lab evolution of synthetic promoters has revealed a novel general mechanism for de novo evolution of gene regulation, and highlights the crucial role of expression noise in this process.
    Research Article
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    1. Neuroscience

    Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans

    Andrés Vidal-Gadea et al
    With the aid of a pair of sensory neurons, the nematode worm C. elegans is able to detect the Earth's magnetic field and use it to navigate towards food sources.
    Research Article
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    1. Plant Biology

    Prioritizing plant defence over growth through WRKY regulation facilitates infestation by non-target herbivores

    Ran Li et al
    A chewing herbivore induced WRKY transcription factor induces jasmonate-dependent defences and supresses gibbererellin-dependent growth, the latter of which renders rice plants more susceptible to secondary infestation by a piercing-sucking herbivore.
    Research Article
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    1. Cell Biology
    2. Microbiology and Infectious Disease

    Dynamic subcellular localization of a respiratory complex controls bacterial respiration

    François Alberge et al
    The localization of respiratory complexes in the cell membrane emerges as a critical factor for controlling respiration in bacteria.
    Research Article
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    1. Genes and Chromosomes
    2. Genomics and Evolutionary Biology

    A simple method for generating high-resolution maps of genome-wide protein binding

    Peter J Skene, Steven Henikoff
    Building on previous work (Skene et al., 2014), we show that a new ChIP-seq protocol provides superior resolution and ease of use at low sequence depth of coverage for generating genome-wide maps of protein binding.
    Research Advance
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    1. Computational and Systems Biology
    2. Neuroscience

    Dynamical feature extraction at the sensory periphery guides chemotaxis

    Aljoscha Schulze et al
    A computational model for the control of chemotaxis in the Drosophila larva clarifies the link between the peripheral encoding of naturalistic olfactory stimuli and action selection.
    Research Article
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    1. Biophysics and Structural Biology
    2. Plant Biology

    The structure of plant photosystem I super-complex at 2.8 Å resolution

    Yuval Mazor et al
    The crystal structure of higher plant PSI-LHCI complex reveals intricate details responsible for light harvesting.
    Research Article
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    1. Genomics and Evolutionary Biology

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

    Dave W Anderson et al
    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.
    Research Article
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    1. Plant Biology

    Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100

    Shouan Liu et al
    A genome-wide view of the gene regulatory network governed by WRKY33 has identified key targets that negatively regulate ABA biosynthesis to provide immunity against infection by a necrotrophic fungus.
    Research Article
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    1. Neuroscience

    Loss of the liver X receptor LXRα/β in peripheral sensory neurons modifies energy expenditure

    Virginie Mansuy-Aubert et al
    In sensory neurons, the receptors LXRα and LXRβ sense dietary-derived molecules to regulate whole body energy expenditure, and present a possible target for new anti-obesity agents.
    Short Report
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    1. Neuroscience

    Deletion of a kinesin I motor unmasks a mechanism of homeostatic branching control by neurotrophin-3

    Thomas O Auer et al
    Disrupting synapse formation between the retina and the brain in zebrafish larvae-by eliminating the molecular motor Kif5A-triggers a compensatory increase in the branching of retinal axons aimed at restoring synapse number.
    Research Article
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    1. Biochemistry
    2. Cell Biology

    MAF1 represses CDKN1A through a Pol III-dependent mechanism

    Yu-Ling Lee et al
    Pol II-mediated transcription and chromatin looping of CDKN1A are repressed by MAF1 through the regulation of Pol III activity.
    Research Article
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    1. Biochemistry
    2. Genes and Chromosomes

    Archaeal TFEα/β is a hybrid of TFIIE and the RNA polymerase III subcomplex hRPC62/39

    Fabian Blombach et al
    An archaeal basal transcription factor containing an iron-sulphur cluster sheds light on the evolution of transcription machineries in archaea and eukaryotes.
    Research Article
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    1. Genes and Chromosomes
    2. Genomics and Evolutionary Biology

    The genetic architecture of NAFLD among inbred strains of mice

    Simon T Hui et al
    A system genetics approach reveals a unique molecular signature of non-alcoholic fatty liver disease in mice and identifies novel genetic factors affecting hepatic steatosis.
    Research Article
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    1. Cell Biology
    2. Immunology

    Differential cell autonomous responses determine the outcome of coxsackievirus infections in murine pancreatic α and β cells

    Laura Marroqui et al
    Pancreatic α and β cells have different cell autonomous signatures; this explains why α but not β cells can clear infections by potentially diabetogenic viruses.
    Research Article
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    1. Neuroscience

    Inter-individual stereotypy of the Platynereis larval visual connectome

    Nadine Randel et al
    Building on previous work (Randel et al., 2014), a comparison of the visual neuronal circuitry in two Platynereis larvae, made using serial electron microscopic reconstructions, reveals a high level of stereotypy in the synaptic connectivity.
    Research Advance
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    1. Genes and Chromosomes

    Circular RNA biogenesis can proceed through an exon-containing lariat precursor

    Steven P Barrett et al
    Systematic splice site mutagenesis and the identification of splicing intermediates provides evidence that the dominant mechanism for the generation of circular RNA in fission yeast proceeds through an exon-containing lariat precursor.
    Research Article
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    1. Biophysics and Structural Biology
    2. Cell Biology

    Identification of a lipid scrambling domain in ANO6/TMEM16F

    Kuai Yu et al
    The amino acids that are necessary for phospholipid scrambling by ANO6/TMEM16F can, via domain swapping, confer scrambling activity to the chloride ion channel ANO1 that normally does not scramble phospholipids.
    Research Article
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    1. Developmental Biology and Stem Cells

    Stem cells and fluid flow drive cyst formation in an invertebrate excretory organ

    Hanh Thi-Kim Vu et al
    Planarians provide evidence for a common evolutionary origin of vertebrate and invertebrate excretory systems and provide a novel experimental model to study human kidney diseases.
    Research Article
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    1. Neuroscience

    Functional subregions of the human entorhinal cortex

    Anne Maass et al
    By employing high-field fMRI to measure connectivity with the hippocampus and adjacent parahippocampal structures within the medial temporal lobe, it is shown that the entorhinal cortex can be divided into anterior-lateral and posterior-medial subregions.
    Research Article
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    1. Plant Biology

    Glycosylphosphatidylinositol-anchored proteins as chaperones and co-receptors for FERONIA receptor kinase signaling in Arabidopsis

    Chao Li et al
    FERONIA receptor kinase interacts with phosphatidylinositol-anchored proteins LORELEI and LLG1 to ensure its proper functional location in the cell membrane and engages them as co-receptors on the cell surface to mediate a broad spectrum of growth and signaling processes.
    Research Article
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    1. Neuroscience

    Forebrain deletion of the dystonia protein torsinA causes dystonic-like movements and loss of striatal cholinergic neurons

    Samuel S Pappas et al
    Conditional forebrain deletion of Tor1a generates a dystonia model with face, construct, and predictive validity, and demonstrates that striatal cholinergic interneurons are selectively vulnerable to loss of the dystonia protein torsinA.
    Research Article
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    1. Developmental Biology and Stem Cells

    Tip cell-specific requirement for an atypical Gpr124- and Reck-dependent Wnt/β-catenin pathway during brain angiogenesis

    Benoit Vanhollebeke et al
    The membrane proteins Reck and Gpr124 are integral components of a novel Wnt7a/Wnt7b-specific signaling complex, and there is a distinctive requirement for Wnt/β-catenin signaling in tip cells during angiogenesis in the central nervous system.
    Research Article
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    1. Neuroscience

    Functional topography of the human entorhinal cortex

    Tobias Navarro Schröder et al
    By employing high-field fMRI and taking advantage of well-known global connectivity fingerprints and sensitivity to spatial and non-spatial information, it is shown that the entorhinal cortex is primarily divided into anterior and posterior subregions.
    Research Article
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    1. Cell Biology
    2. Neuroscience

    The unfolded protein response is required for dendrite morphogenesis

    Xing Wei et al
    The unfolded protein response regulates neuronal dendrite morphogenesis by controlling the folding of a transmembrane leucine-rich repeat (LRR) protein.
    Research Article
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    1. Neuroscience

    Acoustic duetting in Drosophila virilis relies on the integration of auditory and tactile signals

    Kelly M LaRue et al
    Quantitative behavioral assays and modeling show that acoustic duetting in Drosophila during courtship relies on the detection of precisely timed cues via multiple sensory channels.
    Research Article
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    1. Biochemistry
    2. Biophysics and Structural Biology

    Dynamic regulation of transcription factors by nucleosome remodeling

    Ming Li et al
    Single molecule DNA unzipping reveals a novel model for the regulation of transcription factors and nucleosome positioning via nucleosome remodeling in yeast.
    Research Article
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    1. Human Biology and Medicine

    Evidence that synthetic lethality underlies the mutual exclusivity of oncogenic KRAS and EGFR mutations in lung adenocarcinoma

    Arun M Unni et al
    Co-mutation of two powerful oncogenes in certain cell types may have a lethal effect that explains the mutual exclusivity of the mutations.
    Research Article
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    1. Biophysics and Structural Biology
    2. Cell Biology

    Structural evidence for Scc4-dependent localization of cohesin loading

    Stephen M Hinshaw et al
    Cohesin loading at centromeres depends on a conserved surface cluster of amino-acid residues on the cohesin loading protein, Scc4.
    Research Article
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    1. Biophysics and Structural Biology

    Asymmetric conformational maturation of HIV-1 reverse transcriptase

    Xunhai Zheng et al
    HIV-1 reverse transcriptase uses a metamorphic polymerase domain that minimizes its coding requirements but requires a complex maturation process.
    Research Article
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    1. Computational and Systems Biology
    2. Genes and Chromosomes

    Stochastic modelling, Bayesian inference, and new in vivo measurements elucidate the debated mtDNA bottleneck mechanism

    Iain G Johnston et al
    New modelling, statistics, and experiments show that cellular populations of mitochondrial DNA (mtDNA) evolve during development according to solvable stochastic dynamics involving binomial partitioning and random turnover, facilitating a predictive and quantitative theory of the mtDNA bottleneck.
    Research Article
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    1. Neuroscience

    Rapid categorization of natural face images in the infant right hemisphere

    Adélaïde de Heering, Bruno Rossion
    Diverse photographs of human faces against their natural background trigger a specific electrical response in the right hemisphere of the brain in infants aged 4–6 months.
    Research Article
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    1. Biochemistry
    2. Biophysics and Structural Biology

    Consistent global structures of complex RNA states through multidimensional chemical mapping

    Clarence Yu Cheng et al
    A multidimensional chemical mapping strategy enables confident determination of the structures of non-coding RNAs at 1-nm resolution, including previously intractable riboswitch and human regulon states.
    Research Article
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    1. Biophysics and Structural Biology
    2. Microbiology and Infectious Disease

    An internal thioester in a pathogen surface protein mediates covalent host binding

    Miriam Walden et al
    Bacterial-encoded covalent adhesion is a new molecular principle in host-microbe interactions and may play a key role in host colonization by a wide range of Gram-positive bacteria.
    Research Article
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Magazine

    1. Human Biology and Medicine

    Translational Oncology: A signature for success

    Joaquín M Espinosa, Kelly D Sullivan
    1. Neuroscience

    Face Recognition: Babies get it right

    Hillary Hadley , Lisa Scott