November 2015

Research articles

    1. Neuroscience

    Nanoconnectomic upper bound on the variability of synaptic plasticity

    Thomas M Bartol Jr et al.
    Spine heads on the same dendrite receiving input from the same axon are the same size.
    1. Cell Biology

    Interplay between kinesin-1 and cortical dynein during axonal outgrowth and microtubule organization in Drosophila neurons

    Urko del Castillo et al.
    Cortical dynein organizes unipolar microtubule arrays in Drosophila axons by expelling minus-end-out microtubules.
    1. Cell Biology

    Axial contraction and short-range compaction of chromatin synergistically promote mitotic chromosome condensation

    Tom Kruitwagen et al.
    Condensation and segregation of chromosomes during mitosis is caused by a combination of short-range interactions between nucleosomes and the long-range contraction of chromosome arms mediated by condensin.
    1. Developmental Biology and Stem Cells

    The CUL4-DDB1 ubiquitin ligase complex controls adult and embryonic stem cell differentiation and homeostasis

    Jie Gao et al.
    DDB1, a component of the ubiquitin proteasome system, plays a role in both hematopoietic and embryonic stem cell self-renewal and differentiation.
    1. Cell Biology

    Greatwall promotes cell transformation by hyperactivating AKT in human malignancies

    Jorge Vera et al.
    Greatwall is a new oncogene that induces AKT hyperphosphorylation by promoting the degradation of the phosphatase PHLPP.
    1. Neuroscience

    Maturation of metabolic connectivity of the adolescent rat brain

    Hongyoon Choi et al.
    Rat brains mature to increase metabolic connectivity between network components and establish energy efficiency in the midline structures from childhood to early adulthood.
    1. Neuroscience

    Sequential selection of economic good and action in medial frontal cortex of macaques during value-based decisions

    Xiaomo Chen, Veit Stuphorn
    Whenever monkeys are required to choose between multiple options, neural responses indicate that they first select the desired outcome and then use this information to guide their actions.
    1. Cell Biology
    2. Human Biology and Medicine

    Intracellular sphingosine releases calcium from lysosomes

    Doris Höglinger et al.
    Sphingosine acts as a lipid messenger molecule in intracellular signaling networks that are relevant to lysosomal function and Niemann-Pick disease.
    1. Cell Biology
    2. Neuroscience

    Stable G protein-effector complexes in striatal neurons: mechanism of assembly and role in neurotransmitter signaling

    Keqiang Xie et al.
    A G protein in striatal neurons forms preassembled complexes with its downstream enzyme, adenylyl cyclase, which has implications for the pathophysiology of movement disorders.
    1. Neuroscience

    Using an achiasmic human visual system to quantify the relationship between the fMRI BOLD signal and neural response

    Pinglei Bao et al.
    The lower-level retinotopic visual cortex of humans born without the optic chiasm comprises two independent neuronal populations and forms a versatile model for quantifying the relationship between the fMRI BOLD signal and neural response.
    1. Biophysics and Structural Biology
    2. Microbiology and Infectious Disease

    Distinct functional determinants of influenza hemagglutinin-mediated membrane fusion

    Tijana Ivanovic, Stephen C Harrison
    The mechanism of membrane-fusion catalysis in influenza viral infection of target cells is robust against the presence of a large fraction of non-productive viral fusion proteins.
    1. Computational and Systems Biology
    2. Genomics and Evolutionary Biology

    The evolution of adhesiveness as a social adaptation

    Thomas Garcia et al.
    Mathematical modeling supports a scenario where cell-cell adhesion gradually evolves through natural selection, leading to the emergence of cohesive aggregates in microbial populations.
    1. Neuroscience

    Successful retrieval of competing spatial environments in humans involves hippocampal pattern separation mechanisms

    Colin T Kyle et al.
    Functional magnetic resonance imaging and multivariate pattern analysis reveal remapping-like behavior during successful retrieval of competing environments, while unsuccessful retrieval is accompanied by reinstatement of interfering representations.
    1. Biophysics and Structural Biology
    2. Cell Biology

    The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helix

    David Barneda et al.
    An interaction between the brown fat protein CIDEA and the phospholipid phosphatidic acid is vital for the expansion of intracellular lipid droplets for energy storage.
    1. Cell Biology

    Actin filaments target the oligomeric maturation of the dynamin GTPase Drp1 to mitochondrial fission sites

    Wei-ke Ji et al.
    A key cellular process is controlled by altering a balance, rather than through an off/on mechanism.
    1. Cell Biology
    2. Computational and Systems Biology

    EGF-dependent re-routing of vesicular recycling switches spontaneous phosphorylation suppression to EGFR signaling

    Martin Baumdick et al.
    Plasticity arising from autocatalytic receptor activation coexists with robustness in ligand responsiveness only by differential endosomal sorting of spontaneous and ligand-activated EGFR as distinct molecular states.
    1. Cell Biology

    De novo centriole formation in human cells is error-prone and does not require SAS-6 self-assembly

    Won-Jing Wang et al.
    Canonical centriole duplication is much less prone to errors than de novo synthesis of centrioles, but neither depends on self-oligomerization of the centriole protein SAS-6.
    1. Neuroscience

    Optimal level activity of matrix metalloproteinases is critical for adult visual plasticity in the healthy and stroke-affected brain

    Justyna Pielecka-Fortuna et al.
    Matrix metalloproteinases play a crucial role in adult visual plasticity in the brains of healthy and stroke-affected mice and their activity has to be within a narrow window for experience-induced plasticity to occur.
    1. Cell Biology
    2. Immunology

    ATP hydrolysis by the viral RNA sensor RIG-I prevents unintentional recognition of self-RNA

    Charlotte Lässig et al.
    Mutations within the ATPase domain of RIG-I in patients with Singleton-Merten Syndrome prevent ATP-hydrolysis dependent dissociation of RIG-I from double-stranded RNA and lead to unintentional constitutive signaling through increased binding of endogenous RNA.
    1. Computational and Systems Biology
    2. Plant Biology

    Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

    Anne Plessis et al.
    Simple mathematical models can relate gene expression to climatic variables in field grown rice.
    1. Biophysics and Structural Biology
    2. Neuroscience

    Single-molecule fluorimetry and gating currents inspire an improved optical voltage indicator

    Jeremy S Treger et al.
    ArcLight, a popular optogenetic reporter of voltage, is studied at both single-molecule and macroscopic levels, which leads to new mechanistic understanding and to the rational design of a faster reporter.
    1. Biochemistry
    2. Cell Biology

    Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the integrated stress response

    Xing-Huang Gao et al.
    ATF4, the master regulator of transcription during the Integrated Stress Response (ISR), causes global changes in cysteine sulfhydration of proteins and this event causes cellular metabolic reprogramming.
    1. Neuroscience

    Guanylate cyclase 1 relies on rhodopsin for intracellular stability and ciliary trafficking

    Jillian N Pearring et al.
    Rather than relying on intrinsic intracellular targeting information, the key phototransduction enzyme guanylate cyclase 1 is delivered to the photosensory cilium with the visual pigment rhodopsin.
    1. Developmental Biology and Stem Cells

    ETS family transcriptional regulators drive chromatin dynamics and malignancy in squamous cell carcinomas

    Hanseul Yang et al.
    Transcription factors of the ETS family govern a cohort of key cancer-associated regulators of malignancy in squamous cell carcinomas.
    1. Developmental Biology and Stem Cells

    Endothelial Ca2+ oscillations reflect VEGFR signaling-regulated angiogenic capacity in vivo

    Yasuhiro Yokota et al.
    Visualization and quantitative analyses of calcium ion oscillations in the endothelial cells of zebrafish embryos reveal how vascular endothelial growth factor (VEGF) and Dll4/Notch signaling regulate sprouting angiogenesis.
    1. Biochemistry
    2. Cell Biology

    The ATPases of cohesin interface with regulators to modulate cohesin-mediated DNA tethering

    Gamze Çamdere et al.
    A critical second step in DNA tethering by cohesin occurs after its stable binding to DNA, and this second step is modulated by the Smc3 ATPase active site in Saccharomyces cerevisiae.
    1. Biophysics and Structural Biology
    2. Computational and Systems Biology

    CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling

    C Keith Cassidy et al.
    An atomic model of the bacterial chemosensory array obtained through the synthesis of cryo-electron tomography and large-scale molecular-dynamics simulations reveals a new kinase conformation during signaling events.
    1. Computational and Systems Biology
    2. Developmental Biology and Stem Cells

    Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation

    Nicolás Peláez et al.
    The maturation of multi-potent immature cells in the larval eye in Drosophila is regulated by a transcription factor that displays unexpected heterogeneous dynamics during the cells’ transitions towards differentiated states.
    1. Ecology
    2. Neuroscience

    Burst muscle performance predicts the speed, acceleration, and turning performance of Anna’s hummingbirds

    Paolo S Segre et al.
    Maneuverability is thought to be limited by either intrinsic constraints or physiological capacity, and automated tracking of flying hummingbirds reveals that muscle capacity explains much of the variation in their flight trajectories.
    1. Biochemistry
    2. Biophysics and Structural Biology

    Inhibition by small-molecule ligands of formation of amyloid fibrils of an immunoglobulin light chain variable domain

    Boris Brumshtein et al.
    Ligands that bind dimers of light chain variable domains inhibit the formation of amyloid fibrils.
    1. Biophysics and Structural Biology
    2. Cell Biology

    Kinesin Kip2 enhances microtubule growth in vitro through length-dependent feedback on polymerization and catastrophe

    Anneke Hibbel et al.
    The budding yeast kinesin Kip2 is a polymerase that uses its processive motility in a positive feedback loop to promote microtubule growth.
    1. Microbiology and Infectious Disease

    An aspartyl protease defines a novel pathway for export of Toxoplasma proteins into the host cell

    Michael J Coffey et al.
    The Toxoplasma parasite requires an enzyme called ASP5 to cleave proteins for export into host cells.
    1. Neuroscience

    A network of autism linked genes stabilizes two pools of synaptic GABAA receptors

    Xia-Jing Tong et al.
    Mobile and immobile GABAA receptors in the C. elegans neuromuscular synapse are stabilized by two distinct protein scaffolds.
    1. Neuroscience

    Reward signal in a recurrent circuit drives appetitive long-term memory formation

    Toshiharu Ichinose et al.
    A recurrent reward circuit in Drosophila, comprised of specific dopamine neurons and a single class of mushroom body output neurons, transforms a nascent memory trace into a stable long-term memory.
    1. Neuroscience

    Identification of a Munc13-sensitive step in chromaffin cell large dense-core vesicle exocytosis

    Kwun Nok M Man et al.
    Munc13 proteins are key determinants of large dense-core vesicle (LDCV)-dependent catecholamine release in chromaffin cells.
    1. Biochemistry
    2. Human Biology and Medicine

    Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing

    Li Zhang et al.
    Inhibiting PRMT1 enzymatic activity promotes megakaryocyte terminal differentiation via RBM15-mediated RNA metabolism, which is dysregulated in hematological malignancies.
    1. Genes and Chromosomes
    2. Human Biology and Medicine

    Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

    Ana R Grosso et al.
    Transcription beyond annotated gene boundaries expands the diversity of the cancer transcriptome with overexpressed oncogenes and RNA chimeras.
    1. Neuroscience

    The intellectual disability gene Kirrel3 regulates target-specific mossy fiber synapse development in the hippocampus

    E Anne Martin et al.
    Loss of Kirrel3 selectively reduces DG-GABA mossy fiber filopodia and causes CA3 neuron hyper-activity during brain development.
    1. Cell Biology

    Salt-inducible kinases mediate nutrient-sensing to link dietary sugar and tumorigenesis in Drosophila

    Susumu Hirabayashi, Ross L Cagan
    The ability of tumors to respond to nutritional signals is mediated by Salt-inducible kinases, which ensure tumor growth under nutrient-rich conditions including obesity.
    1. Neuroscience

    Tachykinin acts upstream of autocrine Hedgehog signaling during nociceptive sensitization in Drosophila

    Seol Hee Im et al.
    The Drosophila equivalent of Substance P signaling modulates nociceptive sensitization by regulating Hedgehog signaling within nociceptive sensory neurons.
    1. Neuroscience

    Schematic memory components converge within angular gyrus during retrieval

    Isabella C Wagner et al.
    Upon retrieval, the angular gyrus recombines distinct, consolidated schema components into one memory representation.
    1. Developmental Biology and Stem Cells
    2. Genes and Chromosomes

    The human ARF tumor suppressor senses blastema activity and suppresses epimorphic tissue regeneration

    Robert G Hesse et al.
    Evolution of tumor suppressor genes can involve a trade-off because the acquisition of certain anti-cancer characteristics diminishes the ability to regenerate damaged tissue.
    1. Cell Biology

    TANGO1 recruits ERGIC membranes to the endoplasmic reticulum for procollagen export

    António JM Santos et al.
    Building on previous work (Nogueira et al., 2014), we describe a mechanism for the generation of a mega-carrier for the export of bulky procollagen from the endoplasmic reticulum.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Planar cell polarity-mediated induction of neural stem cell expansion during axolotl spinal cord regeneration

    Aida Rodrigo Albors et al.
    During axolotl spinal cord regeneration adult neural stem cells reactivate an embryonic neuroepithelial cell-like gene program that implements planar cell polarity to orient cell divisions, coupling polarized spinal cord growth with stem cell self-renewal.
    1. Neuroscience

    Multivariate analysis of electrophysiological diversity of Xenopus visual neurons during development and plasticity

    Christopher M Ciarleglio et al.
    The diversity of electrophysiological phenotypes of neurons in a functional network increases over development, but can be modulated, and even reduced by sensory experience; allowing them to adapt to a changing and growing brain.
    1. Cell Biology
    2. Neuroscience

    A synaptic F-actin network controls otoferlin-dependent exocytosis in auditory inner hair cells

    Philippe FY Vincent et al.
    A synaptic F-actin network tightly controls the flow of synaptic vesicles during exocytosis at the inner hair cell ribbons.
    1. Biophysics and Structural Biology
    2. Cell Biology

    Claudin-2-dependent paracellular channels are dynamically gated

    Christopher R Weber et al.
    Paracellular, trans-tight junction channels, which communicate between two extracellular compartments without crossing the plasma membrane, are a new class of ion channel with unitary behaviors similar to traditional transmembrane channels.
    1. Neuroscience

    Excitation and inhibition onto central courtship neurons biases Drosophila mate choice

    Benjamin R Kallman et al.
    Pheromones activate excitatory and inhibitory pathways that are integrated to guide mating decisions in Drosophila melanogaster.
    1. Human Biology and Medicine
    2. Immunology

    Bystander hyperactivation of preimmune CD8+ T cells in chronic HCV patients

    Cécile Alanio et al.
    Naïve CD8+ T cells are dysregulated during chronic hepatitis C (HCV) infection, and this is reversible after viral clearance.
    1. Neuroscience

    Sexually divergent expression of active and passive conditioned fear responses in rats

    Tina M Gruene et al.
    Female, but not male rats exhibit an active conditioned fear response, which challenges traditional approaches to measuring fear learning exclusively through freezing, and suggests that females use a more diverse set of threat strategies.
    1. Neuroscience

    Synchronized amplification of local information transmission by peripheral retinal input

    Pablo D Jadzinsky, Stephen A Baccus
    Peripheral retinal input transiently amplifies information transmission from ganglion cells, dynamically allocating the resources of neural activity to times of expected high information content.
    1. Genomics and Evolutionary Biology

    Genetic architecture of natural variation in cuticular hydrocarbon composition in Drosophila melanogaster

    Lauren M Dembeck et al.
    Genome wide association analyses in a wild-derived Drosophila melanogaster population uncover extensive variation in cuticular hydrocarbon composition, which may present a target for natural selection and adaptive evolution.
    1. Immunology

    A forward genetic screen reveals novel independent regulators of ULBP1, an activating ligand for natural killer cells

    Benjamin G Gowen et al.
    Forward genetic screening has provided insight into the molecular mechanisms and stress pathways that promote tumor cell recognition by natural killer cells.
    1. Human Biology and Medicine

    The chemokine CXCL13 in lung cancers associated with environmental polycyclic aromatic hydrocarbons pollution

    Gui-Zhen Wang et al.
    The chemokine CXCL13 is critical to the development of air pollution- and tobacco smoke-induced lung cancers.
    1. Cell Biology
    2. Neuroscience

    RNA binding protein Caprin-2 is a pivotal regulator of the central osmotic defense response

    Agnieszka Konopacka et al.
    Caprin-2 is up-regulated in the rat hypothalamus by osmotic stress and controls vital homeostatic osmoregulatory mechanisms by altering the length of the poly(A) tail on arginine vasopressin mRNAs.
    1. Biophysics and Structural Biology
    2. Neuroscience

    Knockout of Slo2.2 enhances itch, abolishes KNa current, and increases action potential firing frequency in DRG neurons

    Pedro L Martinez-Espinosa et al.
    Sodium-activated potassium ion currents encoded by the kcnt1 gene delay action potential firing in DRG neurons by activity preceding an action potential.
    1. Developmental Biology and Stem Cells

    Generation of an expandable intermediate mesoderm restricted progenitor cell line from human pluripotent stem cells

    Nathan Kumar et al.
    An expandable cell population derived from human pluripotent stem cells exhibits properties of mesoderm and is restricted to differentiate into derivatives of intermediate mesoderm.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Cell-cycle quiescence maintains Caenorhabditis elegans germline stem cells independent of GLP-1/Notch

    Hannah S Seidel, Judith Kimble
    C. elegans germline stem cells become quiescent under starved conditions, and this quiescence maintains the stem cell state even in the absence of GLP-1/Notch signaling, which is otherwise essential for stem cell maintenance.
    1. Neuroscience

    APP and APLP2 interact with the synaptic release machinery and facilitate transmitter release at hippocampal synapses

    Tomas Fanutza et al.
    A naturally occurring intracellular peptide, derived by processing the Alzheimer's protein APP, reduces synaptic transmission by acting as a dominant negative of APP.
    1. Neuroscience

    Neuromodulation of excitatory synaptogenesis in striatal development

    Yevgenia Kozorovitskiy et al.
    Protein kinase A regulates the rapid, activity-dependent genesis of excitatory synapses during striatal development.
    1. Biochemistry
    2. Biophysics and Structural Biology

    A G-protein activation cascade from Arl13B to Arl3 and implications for ciliary targeting of lipidated proteins

    Katja Gotthardt et al.
    The ciliary G-protein Arl13B – which is often mutated in Joubert syndrome – is the Guanine nucleotide exchange factor for the G-protein Arl3 and exclusively localizes to cilia.
    1. Human Biology and Medicine
    2. Neuroscience

    Propagated infra-slow intrinsic brain activity reorganizes across wake and slow wave sleep

    Anish Mitra et al.
    Human fMRI experiments reveal differences in the propagation of spontaneous brain activity during sleep versus wakefulness.
    1. Developmental Biology and Stem Cells
    2. Genes and Chromosomes

    Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development

    Jan J Zylicz et al.
    Silencing of gene regulatory elements by modifications of DNA-bound proteins promotes the progression of early mouse development.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Protein aggregates are associated with replicative aging without compromising protein quality control

    Juha Saarikangas, Yves Barral
    The aging lineage of budding yeast is differentiated by an early-appearing protein deposit that promotes protein quality control.
    1. Cell Biology

    Crumbs is an essential regulator of cytoskeletal dynamics and cell-cell adhesion during dorsal closure in Drosophila

    David Flores-Benitez, Elisabeth Knust
    The evolutionarily conserved polarity protein Crumbs links the regulation of cytoskeleton dynamics and cell-cell adhesion with epithelial morphogenesis.
    1. Neuroscience

    Membrane properties specialize mammalian inner hair cells for frequency or intensity encoding

    Stuart L Johnson
    Mammalian primary sensory inner hair cells play an active role in auditory information processing, such that they show a preference for either timing or intensity coding.
    1. Cell Biology

    Re-examining the role of Drosophila Sas-4 in centrosome assembly using two-colour-3D-SIM FRAP

    Paul T Conduit et al.
    Building on previous work (Conduit et al., 2014), and contrary to what was previously thought, it is shown that key centrosomal proteins are not recruited to centrosomes as part of large multi-protein assemblies.
    1. Genomics and Evolutionary Biology
    2. Plant Biology

    Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data

    Clemens L Weiß et al.
    A computational method to authenticate low-coverage ancient DNA experiments shows that putative wheat sequences from 8000 years old sediments are most likely not of ancient origin.
    1. Epidemiology and Global Health

    Ebola virus disease in the Democratic Republic of the Congo, 1976-2014

    Alicia Rosello et al.
    Analysing a compilation of individual-level data gathered across the seven Ebola Virus Disease outbreaks in the Democratic Republic of the Congo reveals factors that contribute to the spread of the disease and mortality.
    1. Biophysics and Structural Biology
    2. Developmental Biology and Stem Cells

    ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation

    Nataliya Nady et al.
    The Mtgr1 protein promotes the maintenance of pluripotency and germ cell formation via its interaction with the stem cell regulator Prdm14.
    1. Biochemistry

    A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation

    Marisa D Ruehle et al.
    During initiation factor-independent RNA structure-driven translation initiation, a flexible RNA element drives the movement of a viral IRES through the ribosome's tRNA binding sites and promotes tRNA binding.
    1. Computational and Systems Biology
    2. Neuroscience

    Attention stabilizes the shared gain of V4 populations

    Neil C Rabinowitz et al.
    Populations of neurons in the macaque visual cortex are subject to shared fluctuations in gain; these signals exhibit anatomical and functional structure, and their variability is diminished under attention.
    1. Biochemistry
    2. Cell Biology

    Translocation of interleukin-1β into a vesicle intermediate in autophagy-mediated secretion

    Min Zhang et al.
    Reconstitution of interleukin-1β secretion in non-macrophage cells implicates how this pro-inflammatory cytokine enters into the unconventional pathway of secretion through autophagy.
    1. Genomics and Evolutionary Biology
    2. Neuroscience

    Temporal transcriptomics suggest that twin-peaking genes reset the clock

    William G Pembroke et al.
    RNA sequencing reveals the finer details of circadian variation in the mammalian master pacemaker over 24 hours, which suggests that transcriptional timing influences clock resetting mechanisms.
    1. Cell Biology

    Role of competition between polarity sites in establishing a unique front

    Chi-Fang Wu et al.
    In budding yeast, nascent polarity sites engage in a winner-takes-all contest to determine a single front.
    1. Cell Biology
    2. Neuroscience

    Tissue acidosis induces neuronal necroptosis via ASIC1a channel independent of its ionic conduction

    Yi-Zhi Wang et al.
    An interaction between the ion channel ASIC1a and the protein RIP1 is responsible for neuronal death caused by tissue acidosis.
    1. Developmental Biology and Stem Cells

    A robust transcriptional program in newts undergoing multiple events of lens regeneration throughout their lifespan

    Konstantinos Sousounis et al.
    Organ regeneration ensures undisturbed genetic activity even during ageing and repeated insults.
    1. Biochemistry
    2. Cell Biology

    Phosphorylation and activation of ubiquitin-specific protease-14 by Akt regulates the ubiquitin-proteasome system

    Daichao Xu et al.
    Akt can regulate the ubiquitin-proteasome system by mediating phosphorylation and activation of USP14, which may have implications in the control of global proteostasis by growth factors and in tumorigenesis.