June 2016

Research articles

    1. Ecology

    Benefits of jasmonate-dependent defenses against vertebrate herbivores in nature

    Ricardo AR Machado et al.
    Uncovering an link between plant defense signaling and vertebrate feeding behavior suggests that large browsers may exert strong selection pressure on jasmonate-dependent secondary metabolites.
    1. Cell Biology

    In vivo super-resolution RESOLFT microscopy of Drosophila melanogaster

    Sebastian Schnorrenberg et al.
    Building on previous work (Grotjohann et al., 2012), low-light super-resolution microscopy has been performed on living transgenic Drosophila larvae and tissues.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    PROP1 triggers epithelial-mesenchymal transition-like process in pituitary stem cells

    María Inés Pérez Millán et al.
    The transcription factor PROP1 controls a genetic network that drives pituitary stem cells to undergo an epithelial-to-mesenchymal-like transition and differentiate.
    1. Genes and Chromosomes
    2. Neuroscience

    Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

    Jennie R Sims et al.
    The OSM-9 TRPV channel is differentially regulated due to developmental programming via modulation by TGF-β signaling, endogenous RNAi and chromatin remodeling pathways.
    1. Immunology

    AXL receptor tyrosine kinase is required for T cell priming and antiviral immunity

    Edward T Schmid et al.
    AXL enables the priming of the antiviral adaptive immune response by limiting the production of type I interferons in dendritic cells.
    1. Biochemistry

    Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides

    Noam Prywes et al.
    Nonenzymatic polymerization can copy templates containing all four RNA monomers, a prerequisite for the transition to the RNA world.
    1. Biochemistry
    2. Cell Biology

    Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62

    Rowena DeJesus et al.
    FACS-based pooled CRISPR screening is a powerful forward genetic tool to interrogate cellular pathways and targets that modulate protein fate.
    1. Neuroscience

    Distinct lateral inhibitory circuits drive parallel processing of sensory information in the mammalian olfactory bulb

    Matthew A Geramita et al.
    Distinct lateral inhibitory circuits affect spiking in olfactory bulb mitral and tufted cells differently, which ultimately allows each cell type to best discriminate between similar odors in separate concentration ranges.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

    Ignacio Mena et al.
    Genome sequence data from 58 Mexican swine influenza A viruses resolves the spatial origin of the virus that originated the influenza pandemic of 2009.
    1. Cancer biology
    2. Cell Biology

    EphrinB2 drives perivascular invasion and proliferation of glioblastoma stem-like cells

    Benjamin Krusche et al.
    EphrinB2 promotes glioblastoma stem-like cell malignancy through the interplay of cell-autonomous and non-cell-autonomous mechanisms and its targeting suppresses tumourigenesis in preclinical models of human glioblastoma.
    1. Developmental Biology and Stem Cells

    Co-expression of Foxa.a, Foxd and Fgf9/16/20 defines a transient mesendoderm regulatory state in ascidian embryos

    Clare Hudson et al.
    Ascidian mesendoderm is a transient regulatory state upstream of mesoderm and endoderm gene regulatory networks and required for the initiation of both.
    1. Biophysics and Structural Biology
    2. Cell Biology

    Atypical calcium regulation of the PKD2-L1 polycystin ion channel

    Paul G DeCaen et al.
    Outward calcium ion currents desensitize the human PKD2-L1 ion channel via a mechanism that is independent of cytosolic motifs.
    1. Computational and Systems Biology
    2. Neuroscience

    Decoupling kinematics and mechanics reveals coding properties of trigeminal ganglion neurons in the rat vibrissal system

    Nicholas E Bush et al.
    Primary sensory neurons of the rat whisker system encode contact with objects in terms of the forces exerted on whiskers, rather than the induced whisker movements.
    1. Neuroscience

    v-SNARE transmembrane domains function as catalysts for vesicle fusion

    Madhurima Dhara et al.
    Structural flexibility of the synaptobrevin-2 transmembrane domain promotes membrane fusion.
    1. Neuroscience

    Loss of Frataxin induces iron toxicity, sphingolipid synthesis, and Pdk1/Mef2 activation, leading to neurodegeneration

    Kuchuan Chen et al.
    In Drosophila, the loss of Frataxin causes iron accumulation in the nervous system, which in turn enhances sphingolipid synthesis and activation of PDK1 and Mef2, which leads to neurodegeneration.
    1. Biophysics and Structural Biology

    Reconstitution of selective HIV-1 RNA packaging in vitro by membrane-bound Gag assemblies

    Lars-Anders Carlson et al.
    In vitro reconstitution shows how HIV-1 Gag assemblies on membranes can package the RNA genome in the presence of a vast excess of competing cellular RNAs, and that selectivity and immature lattice assembly are deeply intertwined with one another.
    1. Biochemistry

    Mia40 is a trans-site receptor that drives protein import into the mitochondrial intermembrane space by hydrophobic substrate binding

    Valentina Peleh et al.
    The import of proteins into the intermembrane space of mitochondria is driven by binding to the trans-site receptor Mia40 and not by the oxidation of cysteine residues.
    1. Cell Biology

    Clathrin modulates vesicle scission, but not invagination shape, in yeast endocytosis

    Wanda Kukulski et al.
    Building on previous work (Picco et al., 2015), we use a hybrid imaging approach to address the role of clathrin during endocytosis: we find that it has no role in shaping or elongating membrane invaginations, but it does contribute to the regularity of vesicle scission.
    1. Biochemistry
    2. Cell Biology

    The Lamin B receptor is essential for cholesterol synthesis and perturbed by disease-causing mutations

    Pei-Ling Tsai et al.
    Lamin B receptor may provide a long-sought model system enabling unprecedented studies of protein quality control in the nuclear envelope of mammalian cells.
    1. Immunology
    2. Neuroscience

    Internalization and presentation of myelin antigens by the brain endothelium guides antigen-specific T cell migration

    Melissa A Lopes Pinheiro et al.
    Antigen-specific control of CD4+ T cell trans-migration by brain endothelial cells via presentation of CNS-derived antigens in MHC-II molecules.
    1. Cell Biology
    2. Genes and Chromosomes

    Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory

    Agustina D'Urso et al.
    Epigenetic transcriptional memory employs a novel regulatory strategy to create a heritable poised state by remodeling and repurposing complexes involved in active transcription.
    1. Genes and Chromosomes

    Regulation of alternative polyadenylation by Nkx2-5 and Xrn2 during mouse heart development

    Keisuke Nimura et al.
    A tissue-specific transcription factor is involved in the regulation of alternative polyadenylation in conjunction with a transcription termination factor.
    1. Neuroscience
    2. Biophysics and Structural Biology

    Direct mechanical stimulation of tip links in hair cells through DNA tethers

    Aakash Basu et al.
    The ability of hair cells to produce an electrical signal in response to a mechanical stimulus stems from tension in the elastic tip links within the bundles.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    The E3 ligase Ubr3 regulates Usher syndrome and MYH9 disorder proteins in the auditory organs of Drosophila and mammals

    Tongchao Li et al.
    A novel mechanism links two myosins associated with deafness in auditory organs.
    1. Neuroscience

    Target-specific membrane potential dynamics of neocortical projection neurons during goal-directed behavior

    Takayuki Yamashita, Carl CH Petersen
    A learning-induced, motor-related, projection-specific signal from S1 to S2 accompanies reward-based-learning of a goal-directed sensorimotor transformation of whisker sensation into licking motor output.
    1. Genomics and Evolutionary Biology

    Admixture into and within sub-Saharan Africa

    George BJ Busby et al.
    Gene flow analysis reveals that the genomes of most sub-Saharan populations are the result of recent historical admixture events.
    1. Biochemistry
    2. Biophysics and Structural Biology

    Obligate coupling of CFTR pore opening to tight nucleotide-binding domain dimerization

    Csaba Mihályi et al.
    Coupling of CFTR pore opening to nucleotide binding domain dimerization does not depend on ATP binding, but is an inherent property of the channel protein and likely other ABC transporters.
    1. Neuroscience

    Detection of transient synchrony across oscillating receptors by the central electrosensory system of mormyrid fish

    Alejandro Vélez, Bruce A Carlson
    Building on previous work (Baker et al., 2015), further evidence is reported for a novel mechanism for sensory coding based on the detection of oscillatory synchrony among peripheral receptors.
    1. Neuroscience

    A Bayesian model of context-sensitive value attribution

    Francesco Rigoli et al.
    The dependence of incentive value attribution on the anticipation of rewards within a given context is explained via a normative Bayesian account of how rewards map to incentive values.
    1. Neuroscience

    Restoration of Mecp2 expression in GABAergic neurons is sufficient to rescue multiple disease features in a mouse model of Rett syndrome

    Kerstin Ure et al.
    Genetically restoring Mecp2 expression only in GABAergic neurons in a mouse model of Rett syndrome improves inhibitory signaling, extends lifespan and rescues most but not all behavioral deficits.
    1. Developmental Biology and Stem Cells

    Sox9 and Sox8 protect the adult testis from male-to-female genetic reprogramming and complete degeneration

    Francisco J Barrionuevo et al.
    The vertebrate testis-determining gene, Sox9, also controls adult testis maintenance in mammals, acting redundantly with its paralog Sox8.
    1. Neuroscience

    Manipulations of MeCP2 in glutamatergic neurons highlight their contributions to Rett and other neurological disorders

    Xiangling Meng et al.
    Excitatory signaling impairment contributes to neurological deficits shared by Rett syndrome and a number of postnatal neuropsychiatric disorders.
    1. Biochemistry
    2. Genes and Chromosomes

    Polymerase θ is a robust terminal transferase that oscillates between three different mechanisms during end-joining

    Tatiana Kent et al.
    Polymerase θ is among the most proficient terminal transferases known and switches between three different mechanisms of terminal transferase activity.
    1. Ecology
    2. Computational and Systems Biology

    Community-level cohesion without cooperation

    Mikhail Tikhonov
    A model of purely competitive ecological dynamics is shown to be equivalent to adaptive evolution of a single individual, suggesting a new way to formalize the "superorganism" metaphor.
    1. Computational and Systems Biology
    2. Human Biology and Medicine

    Mitochondrial dysfunction remodels one-carbon metabolism in human cells

    Xiaoyan Robert Bao et al.
    Mitochondrial respiratory chain dysfunction inhibits mitochondrial one-carbon metabolism, impairing cellular nucleotide biosynthesis.
    1. Neuroscience

    Sensory experience modifies feature map relationships in visual cortex

    Shaun L Cloherty et al.
    A new form of brain plasticity extends the known limits for how much early sensory input can alter the brain.
    1. Cell Biology

    Kinase-dead ATM protein is highly oncogenic and can be preferentially targeted by Topo-isomerase I inhibitors

    Kenta Yamamoto et al.
    Orphan ATM kinase-domain missense mutations are unexpectedly common and form a potent oncogenic event and a biomarker for Topo-isomerase I inhibitor based therapy.
    1. Biochemistry
    2. Microbiology and Infectious Disease

    A cytoplasmic peptidoglycan amidase homologue controls mycobacterial cell wall synthesis

    Cara C Boutte et al.
    Cell wall biosynthesis in mycobacteria is regulated by an unusual post-translational regulatory system that contributes to antibiotic tolerance during stress.
    1. Genes and Chromosomes

    Enhancer regions show high histone H3.3 turnover that changes during differentiation

    Aimee M Deaton et al.
    Nucleosomes at enhancers are unusually dynamic and change histone turnover rates during differentiation.
    1. Immunology

    Pivotal role for skin transendothelial radio-resistant anti-inflammatory macrophages in tissue repair

    Olga Barreiro et al.
    A new type of skin perivascular macrophages with extramedullary origin, access to blood and exclusive anti-inflammatory reparative properties has been characterized.
    1. Cell Biology
    2. Genes and Chromosomes

    Phosphorylation acts positively and negatively to regulate MRTF-A subcellular localisation and activity

    Richard Panayiotou et al.
    G-actin binding controls the susceptibility of MRTF-A to phosphorylation, which works in concert with multiple NES elements to regulate MRTF-A subcellular localisation and activity.
    1. Neuroscience

    p21-activated kinase 1 restricts tonic endocannabinoid signaling in the hippocampus

    Shuting Xia et al.
    PAK1 regulates inhibitory synaptic transmission in mice through a cyclooxygenase-2 dependent restriction in tonic, but not phasic, secretion of endocannabinoids.
    1. Neuroscience

    Gustatory-mediated avoidance of bacterial lipopolysaccharides via TRPA1 activation in Drosophila

    Alessia Soldano et al.
    Fruit flies can taste and avoid food contaminated with a bacterial toxin using the same channel protein that functions in humans as sensor of noxious chemical stimuli.
    1. Neuroscience

    Interactions between respiratory oscillators in adult rats

    Robert TR Huckstepp et al.
    Active expiration in anesthetized rats is driven by the lateral parafacial region, but requires an additional form of excitation from another source.
    1. Biophysics and Structural Biology
    2. Neuroscience

    A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging

    Nicholas James Sofroniew et al.
    An optical microscopy approach with an ultra-large field of view but retained subcellular resolution allows simultaneous imaging of neural activity in widely dispersed brain regions.
    1. Biochemistry
    2. Plant Biology

    A new synthetic biology approach allows transfer of an entire metabolic pathway from a medicinal plant to a biomass crop

    Paulina Fuentes et al.
    A combination of chloroplast transformation with nuclear transformation and large-scale metabolic screening of supertransformed plant lines has enabled an entire biochemical pathway to be transferred from a medicinal plant to a high-biomass crop.
    1. Neuroscience

    Somatic and vicarious pain are represented by dissociable multivariate brain patterns

    Anjali Krishnan et al.
    Understanding others' pain is grounded in cognitive rather than sensory faculties.
    1. Cancer biology
    2. Developmental Biology and Stem Cells

    Neural stem cell-encoded temporal patterning delineates an early window of malignant susceptibility in Drosophila

    Karine Narbonne-Reveau et al.
    Sequentially expressed temporal transcription factors in neural stem cells during early development determine which progeny can undergo malignant transformation upon dedifferentiation.
    1. Neuroscience

    Serial grouping of 2D-image regions with object-based attention in humans

    Danique Jeurissen et al.
    The human visual system groups the individual features of objects together into a coherent whole via a serial, attention-demanding process.
    1. Developmental Biology and Stem Cells
    2. Plant Biology

    Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy

    Natalie M Clark et al.
    The mechanistic basis of molecular movement and interactions within plant root cells can be quantified using scanning fluorescence correlation spectroscopy.
    1. Neuroscience

    Astrocyte morphology is confined by cortical functional boundaries in mammals ranging from mice to human

    Raya Eilam et al.
    The structural morphology of astrocyte processes is constrained by functional boundaries in the mouse, rat and human cortex.
    1. Biochemistry
    2. Biophysics and Structural Biology

    Architecture and RNA binding of the human negative elongation factor

    Seychelle M Vos et al.
    The structural architecture of the 4-subunit, RNA-binding human negative elongation factor NELF is derived by a combination of X-ray crystallography and protein crosslinking.
    1. Cancer biology
    2. Cell Biology

    Nerve growth factor receptor negates the tumor suppressor p53 as a feedback regulator

    Xiang Zhou et al.
    The nerve growth factor receptor (NGFR) protein regulates p53 via two negative feedback mechanisms, which are hijacked by cancer cells.
    1. Developmental Biology and Stem Cells

    Metabolic reprogramming during neuronal differentiation from aerobic glycolysis to neuronal oxidative phosphorylation

    Xinde Zheng et al.
    The shutoff of aerobic glycolysis in neuronal differentiation is essential for neuronal survival.
    1. Neuroscience

    Place cells on a maze encode routes rather than destinations

    Roddy M Grieves et al.
    Place cells in the rat hippocampus encode positions along well-learned routes as opposed to intended destinations.
    1. Neuroscience

    Anatomical organization of presubicular head-direction circuits

    Patricia Preston-Ferrer et al.
    Presubicular head-direction circuits are cell-type specific, with long-range projections reaching the 'grid-cell area' medial entorhinal cortex.
    1. Microbiology and Infectious Disease

    A lipoprotein/β-barrel complex monitors lipopolysaccharide integrity transducing information across the outer membrane

    Anna Konovalova et al.
    Mutations that block assembly of the interlocked RcsF/β barrel protein complex prevent detection of lipopolysaccharide stress and activation of Rcs signal transduction pathway.
    1. Cell Biology
    2. Computational and Systems Biology

    Global, quantitative and dynamic mapping of protein subcellular localization

    Daniel N Itzhak et al.
    A spatial proteomics method can capture physiological protein subcellular localization changes in response to a stimulus, resolving all major organelles.
    1. Developmental Biology and Stem Cells
    2. Genes and Chromosomes

    Targeted, homology-driven gene insertion in stem cells by ZFN-loaded ‘all-in-one’ lentiviral vectors

    Yujia Cai et al.
    Building on previous work (Cai et al., 2014), HIV-derived lentiviral vectors are harnessed to insert user-defined genes into a safe locus in the genome of human stem cells.
    1. Microbiology and Infectious Disease

    Evidence of human infection by a new mammarenavirus endemic to Southeastern Asia

    Kim R Blasdell et al.
    New mammarenaviruses have been identified from rodents in Cambodia and Thailand, and the Cardamones variant of Wēnzhōu virus has been found in Cambodian patients presenting with fever and respiratory symptoms.
    1. Neuroscience

    Murine Fam65b forms ring-like structures at the base of stereocilia critical for mechanosensory hair cell function

    Bo Zhao et al.
    Super-resolution microscopy reveals a highly organized compartment in the stereocilia of mechanosensory hair cells of the inner ear, which is critical for hair cell function and affected in disease.
    1. Genes and Chromosomes

    Nucleosome disassembly during human non-homologous end joining followed by concerted HIRA- and CAF-1-dependent reassembly

    Xuan Li, Jessica K Tyler
    The human genome is unpackaged to allow DNA breaks to be joined back together, and then repackaged into chromosomes afterwards.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Pentagone internalises glypicans to fine-tune multiple signalling pathways

    Mark Norman et al.
    Glypican proteins, required for morphogen signalling in Drosophila wing development, are endocytosed and degraded by the feedback regulator Pentagone.
    1. Biochemistry
    2. Cell Biology

    Golgi self-correction generates bioequivalent glycans to preserve cellular homeostasis

    Haik Mkhikian et al.
    Structurally dissimilar N-glycans can be functionally equivalent, and are produced via a self-correcting feature of the Golgi.
    1. Neuroscience

    Peripheral optogenetic stimulation induces whisker movement and sensory perception in head-fixed mice

    Sunmee Park et al.
    Light can be used to trigger the contraction of facial muscles and movement of the whiskers in transgenic mice, aiding the study of active sensation.
    1. Neuroscience

    An evolutionarily conserved mechanism for cAMP elicited axonal regeneration involves direct activation of the dual leucine zipper kinase DLK

    Yan Hao et al.
    Axonal damage sensing kinase DLK is a direct target and mediator of the cAMP effector kinase PKA in a unified mechanism for stimulating axonal regeneration.
    1. Cell Biology
    2. Immunology

    Notch1 regulated autophagy controls survival and suppressor activity of activated murine T-regulatory cells

    Nimi Marcel, Apurva Sarin
    Notch1 activates autophagy to regulate the survival of T-regulatory cells from mice.
    1. Genomics and Evolutionary Biology

    The Arabidopsis thaliana mobilome and its impact at the species level

    Leandro Quadrana et al.
    Population genomics in Arabidopsis thaliana uncovers an extensive repertoire of active transposable element families at the species level and reveals their importance as a source of rare alleles with large effects.
    1. Biophysics and Structural Biology
    2. Neuroscience

    Complexin induces a conformational change at the membrane-proximal C-terminal end of the SNARE complex

    Ucheor B Choi et al.
    Complexin can have two conformations when bound to a ternary SNARE complex, one of which induces a conformational change of the SNARE complex at the C-terminus.
    1. Neuroscience

    CELF RNA binding proteins promote axon regeneration in C. elegans and mammals through alternative splicing of Syntaxins

    Lizhen Chen et al.
    Genetics and genomics approaches reveal a conserved post-transcriptional regulatory mechanism that promotes adult axon regeneration from worm to mammals.
    1. Biochemistry
    2. Biophysics and Structural Biology

    Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5α

    Jonathan M Wagner et al.
    Higher-order assembly enables and links pathogen recognition and downstream steps in the TRIM5-mediated anti-HIV response.
    1. Biochemistry
    2. Biophysics and Structural Biology

    Kinetics of initiating polypeptide elongation in an IRES-dependent system

    Haibo Zhang et al.
    The retarding effect of a ribosome-bound internal ribosome entry site on eukaryotic protein synthesis is largely overcome following translocation of tripeptidyl-tRNA.
    1. Genes and Chromosomes

    Multi-step coordination of telomerase recruitment in fission yeast through two coupled telomere-telomerase interfaces

    Xichan Hu et al.
    A telomerase recruitment mechanism delivers cell cycle information to the telomere-telomerase interface to ensure timely telomerase engagement at the telomere.
    1. Cell Biology

    Exercise promotes the expression of brain derived neurotrophic factor (BDNF) through the action of the ketone body β-hydroxybutyrate

    Sama F Sleiman et al.
    A potential link between metabolic changes resulting from exercise and gene expression in the brain has been revealed.
    1. Plant Biology

    Testing the Münch hypothesis of long distance phloem transport in plants

    Michael Knoblauch et al.
    Measurements of physiological and geometrical parameters of the sieve tube system in Ipomoea nil provide strong support for pressure driven mass flow.
    1. Immunology
    2. Microbiology and Infectious Disease

    Primate TRIM5 proteins form hexagonal nets on HIV-1 capsids

    Yen-Li Li et al.
    To protect mammals against retroviral infections, TRIM5 restriction factors recognize viral capsids by forming complementary hexagonal nets that can adapt to the patterns of capsid protein subunits on the viral capsid surface.
    1. Biophysics and Structural Biology
    2. Cell Biology

    A mitofusin-dependent docking ring complex triggers mitochondrial fusion in vitro

    Tobias Brandt et al.
    A combination of an in vitro mitochondrial fusion assay with electron cryo-tomography (cryo-ET) reveals distinct steps and protein complexes during mitofusin-dependent fusion between adjacent mitochondrial outer membranes.
    1. Cell Biology

    MiniCORVET is a Vps8-containing early endosomal tether in Drosophila

    Péter Lőrincz et al.
    An unconventional endosomal tether in Drosophila melanogaster only has four of the six subunits found in the yeast complex.
    1. Neuroscience

    ELKS controls the pool of readily releasable vesicles at excitatory synapses through its N-terminal coiled-coil domains

    Richard G Held et al.
    The presynaptic active zone protein ELKS provides synapse-specific control of the pool of readily releasable vesicles and release probability.