April 2016

Research articles

    1. Neuroscience

    The Ionotropic Receptors IR21a and IR25a mediate cool sensing in Drosophila

    Lina Ni et al.
    Two members of a widely studied family of chemoreceptors, the "orphan" chemoreceptor IR21a and its putative co-receptor IR25a, act together to mediate cool sensation in fruit fly larvae.
    1. Computational and Systems Biology
    2. Neuroscience

    Neural correlations enable invariant coding and perception of natural stimuli in weakly electric fish

    Michael G Metzen et al.
    Neural circuits in weakly electric fish perform a set of computations to allow natural communication signals to be perceived independently of their context.
    1. Biochemistry
    2. Human Biology and Medicine

    The functional O-mannose glycan on α-dystroglycan contains a phospho-ribitol primed for matriglycan addition

    Jeremy L Praissman et al.
    Disruption of the LG domain-binding phospho-ribitol-containing O-mannose structures on α-dystroglycan results in congenital muscular dystrophy.
    1. Biochemistry
    2. Genes and Chromosomes

    Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

    R Stefan Isaac et al.
    The inhibitory influence of nucleosomes on CRISPR-Cas9 is mitigated by nucleosomal DNA breathing and chromatin remodeling.
    1. Neuroscience

    The role of piriform associative connections in odor categorization

    Xiaojun Bao et al.
    Pharmacological fMRI reveals that associative connections contribute to odor categorization by supporting discrimination and generalization at different stages of the human olfactory system.
    1. Biochemistry

    The ribosomal protein Asc1/RACK1 is required for efficient translation of short mRNAs

    Mary K Thompson et al.
    Asc1/RACK1 promotes the translation of mRNAs associated with the translational closed loop complex, which have short open reading frames and encode proteins required for core metabolic processes.
    1. Neuroscience

    Body side-specific control of motor activity during turning in a walking animal

    Matthias Gruhn et al.
    Turning in an insect is the combined result of body-side-specific modifications in processing of local sensory feedback, and modification of local central pattern generator activity.
    1. Cancer biology

    Synergy between loss of NF1 and overexpression of MYCN in neuroblastoma is mediated by the GAP-related domain

    Shuning He et al.
    A zebrafish model of neuroblastoma reveals that the tumor suppressor NF1 uses different mechanisms to suppress malignant transformation and to down-modulate normal neural crest cell growth during embryogenesis.
    1. Neuroscience

    Analysis of protein phosphorylation in nerve terminal reveals extensive changes in active zone proteins upon exocytosis

    Mahdokht Kohansal-Nodehi et al.
    Global phosphoproteomic analysis in nerve terminal during exocytosis reveals 252 uniquely regulated phosphosites, highlighting complex regulation of active zone proteins at multiple sites and the role of specific kinases/phosphatases.
    1. Neuroscience

    Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons

    Mark S Cembrowski et al.
    Gene expression was analyzed in hippocampal principal cells, enabling cellular phenotyping and revealing novel organizational principles; complementing this, a publicly available website is released to provide outside analysis and visualization of hippocampal RNA-seq data in an accessible fashion.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Regulation of cell protrusions by small GTPases during fusion of the neural folds

    Ana Rolo et al.
    The completion of neural tube closure requires small GTPase-regulated membrane protrusions from non-neural ectoderm cells at the tips of the neural folds.
    1. Biochemistry
    2. Genes and Chromosomes

    The target of the DEAH-box NTP triphosphatase Prp43 in Saccharomyces cerevisiae spliceosomes is the U2 snRNP-intron interaction

    Jean-Baptiste Fourmann et al.
    Prp43 binds to the pre-mRNA and contacts predominantly U2 proteins in the budding yeast spliceosome.
    1. Cell Biology

    ESCRT-III drives the final stages of CUPS maturation for unconventional protein secretion

    Amy J Curwin et al.
    The release of Acb1 protein from yeast cells requires the ESCRT-III complex to stabilize the compartment for unconventional protein secretion (CUPS).
    1. Cell Biology
    2. Human Biology and Medicine

    Sex steroids regulate skin pigmentation through nonclassical membrane-bound receptors

    Christopher A Natale et al.
    Two receptors have been identified that can be targeted in melanocytes with selective small molecule agonists to modulate human skin color.
    1. Computational and Systems Biology
    2. Genomics and Evolutionary Biology

    Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

    David Mavor et al.
    Chemical perturbation-dependent deep mutational scanning data collected by a lab-based interdisciplinary graduate class resolves a paradox between the high evolution conservation and the high mutational tolerance of the protein ubiquitin.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    The global antigenic diversity of swine influenza A viruses

    Nicola S Lewis et al.
    Swine populations worldwide are sporadically infected by influenza viruses from humans and birds leading to geographically heterogeneous swine influenza virus populations that pose epizootic and pandemic threats.
    1. Biochemistry
    2. Cell Biology

    Community effects in regulation of translation

    Paul M Macdonald et al.
    Regulatory elements in an mRNA that act in cis to influence translation can also exert their effects in trans, in a process dependent on assembly of the mRNAs into particles.
    1. Biochemistry
    2. Cell Biology

    The E3 ubiquitin ligase ZNRF2 is a substrate of mTORC1 and regulates its activation by amino acids

    Gerta Hoxhaj et al.
    The ZNRF2 enzyme helps the mTOR protein complex to sense amino acid levels and regulate mammalian cell growth.
    1. Cell Biology

    Synthetic protein interactions reveal a functional map of the cell

    Lisa K Berry et al.
    Forcing protein associations across the proteome reveals the cell's tolerance for diverse protein interactions and reveals the interactions that affect growth.
    1. Developmental Biology and Stem Cells

    Extracellular interactions and ligand degradation shape the nodal morphogen gradient

    Yin Wang et al.
    Diffusivity, extracellular interactions of Nodal ligands with the receptors and inhibitors, and selective ligand destruction collectively shape the Nodal morphogen gradient.
    1. Neuroscience

    The modulation of savouring by prediction error and its effects on choice

    Kiyohito Iigaya et al.
    The anticipation of rewards turns out to have its own hedonic value, on top of that of the reward itself; a wide range of behavioral and neurophysiological data suggest that this anticipation is boosted by prediction errors.
    1. Biochemistry

    Dual functions of a small regulatory subunit in the mitochondrial calcium uniporter complex

    Ming-Feng Tsai et al.
    Studies of EMRE, one of the four essential protein subunits in the mitochondrial calcium uniporter complex that regulates calcium ion levels in mitochondria, reveal new details about the physical interactions between the subunits.
    1. Biochemistry
    2. Biophysics and Structural Biology

    The structure of the core NuRD repression complex provides insights into its interaction with chromatin

    Christopher J Millard et al.
    An extensive interface between the proteins RBBP4 and MTA1 defines the three-dimensional architecture of the core NuRD complex and determines the recruitment of the complex to chromatin.
    1. Neuroscience

    Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior

    Mar Gacias et al.
    Gut microbiota can influence mPFC transcriptional profiles and myelin content, overriding the impact of genetic background in the development of social avoidance behavior.
    1. Cell Biology

    Selective sorting and destruction of mitochondrial membrane proteins in aged yeast

    Adam L Hughes et al.
    A new mitochondrial protein degradation pathway selectively sorts and destroys a subset of the mitochondrial membrane proteome to protect mitochondria in times of stress.
    1. Ecology
    2. Neuroscience

    Airflow and optic flow mediate antennal positioning in flying honeybees

    Taruni Roy Khurana, Sanjay P Sane
    Honeybees determine their flight speed by combining feedback from optic flow and airflow.
    1. Neuroscience

    Neuronal representation of saccadic error in macaque posterior parietal cortex (PPC)

    Yang Zhou et al.
    Neurons in the macaque posterior parietal cortex behave like an error detector that computes the saccadic error by comparing the intended and the actual saccade end-position signals.
    1. Human Biology and Medicine

    Blockade of glucagon signaling prevents or reverses diabetes onset only if residual β-cells persist

    Nicolas Damond et al.
    Contrary to previous reports, a complete absence of glucagon signaling is not sufficient to prevent diabetes after near-total β-cell loss.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Mapping global environmental suitability for Zika virus

    Jane P Messina et al.
    A global map of environmental suitability for Zika virus and the estimated population living at potential risk can help refine public health guidelines, travel advisories and intervention strategies at a crucial time in the global emergence of this arbovirus.
    1. Developmental Biology and Stem Cells
    2. Genomics and Evolutionary Biology

    Evolution of the head-trunk interface in tetrapod vertebrates

    Elizabeth M Sefton et al.
    Both gill musculature and the evolutionarily conserved cucullaris muscle are derived from unsegmented mesoderm adjacent to the first 3 somites, extending the posterior limit of cranial mesoderm.
    1. Biochemistry
    2. Cell Biology

    The glyoxylate shunt is essential for desiccation tolerance in C. elegans and budding yeast

    Cihan Erkut et al.
    Roundworms and yeast can survive extreme desiccation only by switching their metabolism into a gluconeogenic mode and producing very high amounts of trehalose via the glyoxylate shunt.
    1. Cell Biology

    α8β1 integrin regulates nutrient absorption through an Mfge8-PTEN dependent mechanism

    Amin Khalifeh-Soltani et al.
    The milk protein Mfge8 promotes fat uptake and slows gastrointestinal motility to optimize nutrient absorption.
    1. Ecology
    2. Genomics and Evolutionary Biology

    Heart fossilization is possible and informs the evolution of cardiac outflow tract in vertebrates

    Lara Maldanis et al.
    The discovery of a fossil heart in Rhacolepis buccalis demonstrates that it is possible to scrutinize the fossil record for important clues on cardiac structure and evolution.
    1. Genes and Chromosomes
    2. Neuroscience

    Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation

    Ryuta Ishimura et al.
    Activation of the integrated stress response by stalled translation elongation complexes attenuates neurodegeneration, and demonstrates a protective link between a decrease in the rate of translation initiation and defects in translation elongation.
    1. Neuroscience

    Acute inhibition of neurosteroid estrogen synthesis suppresses status epilepticus in an animal model

    Satoru M Sato, Catherine S Woolley
    Seizures stimulate estrogen synthesis in the brain and acutely inhibiting brain estrogen synthesis suppresses seizures, in both sexes, without additional interventions.
    1. Genomics and Evolutionary Biology
    2. Microbiology and Infectious Disease

    Evolutionary diversification of the trypanosome haptoglobin-haemoglobin receptor from an ancestral haemoglobin receptor

    Harriet Lane-Serff et al.
    The ligand specificity and expression profile of the haptoglobin-haemoglobin receptor has diversified throughout the evolution of trypanosomes.
    1. Developmental Biology and Stem Cells
    2. Neuroscience

    Retrograde fibroblast growth factor 22 (FGF22) signaling regulates insulin-like growth factor 2 (IGF2) expression for activity-dependent synapse stabilization in the mammalian brain

    Akiko Terauchi et al.
    Feedback signaling between the synapse and nucleus via FGF22 and IGF2 directs the activity-dependent stabilization of presynaptic terminals in the mouse hippocampus.
    1. Biophysics and Structural Biology
    2. Neuroscience

    Synaptotagmin-1 C2B domain interacts simultaneously with SNAREs and membranes to promote membrane fusion

    Shen Wang et al.
    When the Ca2+-binding loops of the C2B domain insert into a membrane, interactions with a phospholipid and the SNARE complex allow synaptotagmin-1 to bend the membrane.
    1. Neuroscience

    Direct neural pathways convey distinct visual information to Drosophila mushroom bodies

    Katrin Vogt et al.
    Building on previous work (Vogt et al. 2014), separate visual pathways have been identified to convey information for brightness and color to the learning-related area of the Drosophila brain.
    1. Genomics and Evolutionary Biology
    2. Neuroscience

    Neural clocks and Neuropeptide F/Y regulate circadian gene expression in a peripheral metabolic tissue

    Renske Erion et al.
    Neuropeptide F/Y from neurons drives rhythmic expression of detoxification-related genes in a peripheral metabolic tissue in flies and mice.
    1. Cancer biology
    2. Developmental Biology and Stem Cells

    A long non-coding RNA targets microRNA miR-34a to regulate colon cancer stem cell asymmetric division

    Lihua Wang et al.
    A novel long non-coding RNA targets microRNA miR-34a for epigenetic silencing and initiates asymmetric division of colon cancer stem cells.
    1. Computational and Systems Biology

    Distributed task-specific processing of somatosensory feedback for voluntary motor control

    Mohsen Omrani et al.
    Somatosensory feedback is transmitted to many sensory and motor cortical regions within 25 milliseconds and ongoing behavioural tasks alter the spatiotemporal pattern of this perturbation-related activity, supporting rapid motor responses to attain behavioural goals.
    1. Neuroscience

    Sex differences in cerebellar synaptic transmission and sex-specific responses to autism-linked Gabrb3 mutations in mice

    Audrey A Mercer et al.
    Male and female mice differ in basal cerebellar physiology, including the magnitude of synaptic excitation by metabotropic glutamate receptors, kinetics of synaptic inhibition, intrinsic properties, and responses to autism-linked mutations.
    1. Developmental Biology and Stem Cells

    The Apelin receptor enhances Nodal/TGFβ signaling to ensure proper cardiac development

    Ashish R Deshwar et al.
    The Apelin receptor acts as a rheostat to ensure that the proper levels of Nodal signaling are achieved for proper cell fate specification at the onset of gastrulation, in particular for cardiac progenitor development.
    1. Biophysics and Structural Biology
    2. Genes and Chromosomes

    The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome

    Kathleen L McCann et al.
    A single missense mutation in an RNA recognition motif within a nucleolar protein disrupts ribosome assembly and contributes to human pathology.
    1. Biochemistry
    2. Biophysics and Structural Biology

    The GIRK1 subunit potentiates G protein activation of cardiac GIRK1/4 hetero-tetramers

    Kouki K Touhara et al.
    The GIRK1 subunit contains a defective Na+-binding site but behaves as if it is permanently bound to a sodium ion, and therefore increases the affinity of Gβγ to GIRK1/4 hetero-tetrameric channels in lipid membranes.
    1. Computational and Systems Biology
    2. Developmental Biology and Stem Cells

    Synchronization of endothelial Dll4-Notch dynamics switch blood vessels from branching to expansion

    Benedetta Ubezio et al.
    Increasing levels of the growth factor Vegfa disrupt blood vessel branching morphogenesis and drive diameter increase by synchronizing Notch signalling fluctuations between endothelial cells.
    1. Biochemistry
    2. Biophysics and Structural Biology

    Cooperative regulation by G proteins and Na+ of neuronal GIRK2 K+ channels

    Weiwei Wang et al.
    Determining how GIRK2 activity depends on the concentration of Gβγ subunits in lipid membranes at different Na+ concentrations has allowed the Gβγ concentration generated during GABAB activation in neurons to be estimated.
    1. Biochemistry
    2. Cell Biology

    ESCRT-III activation by parallel action of ESCRT-I/II and ESCRT-0/Bro1 during MVB biogenesis

    Shaogeng Tang et al.
    Building on previous work (Tang et al., 2015), novel ESCRT-III subunit Snf7 auto-activation mutants are used to reveal two parallel ubiquitin-dependent pathways during multivesicular endosome biogenesis.
    1. Developmental Biology and Stem Cells

    Wnt, Ptk7, and FGFRL expression gradients control trunk positional identity in planarian regeneration

    Rachel Lander, Christian P Petersen
    Signaling molecules expressed in overlapping body-wide transcriptional gradients determine central axis positional identity in whole-body regeneration.
    1. Biochemistry
    2. Biophysics and Structural Biology

    Time-resolved multimodal analysis of Src Homology 2 (SH2) domain binding in signaling by receptor tyrosine kinases

    Joshua A Jadwin et al.
    The recruitment of SH2-containing proteins to Epidermal Growth Factor in cells happens more slowly than predicted by in vitro techniques.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Activation of PTHrP-cAMP-CREB1 signaling following p53 loss is essential for osteosarcoma initiation and maintenance

    Mannu K Walia et al.
    The loss of p53 in bone cells activates critical signaling pathways; these are also essential in bone cancer.
    1. Ecology
    2. Neuroscience

    Select forelimb muscles have evolved superfast contractile speed to support acrobatic social displays

    Matthew J Fuxjager et al.
    In situ measurements of muscular twitch speed reveal one of the fastest vertebrate limb muscles on record, which evolved in association with extravagant courtship displays that include rapid limb movements.
    1. Neuroscience

    Demixed principal component analysis of neural population data

    Dmitry Kobak et al.
    A new data analysis tool provides a concise way of visualizing neural data that summarizes all the relevant features of the population response in a single figure.
    1. Computational and Systems Biology
    2. Developmental Biology and Stem Cells

    Noise modulation in retinoic acid signaling sharpens segmental boundaries of gene expression in the embryonic zebrafish hindbrain

    Julian Sosnik et al.
    Direct measurements of retinoic acid using fluorescence lifetime imaging reveal a new role for cellular retinoic acid binding proteins in noise attenuation that is critical to sharpen hindbrain rhombomere boundaries.
    1. Ecology

    Sequential phenotypic constraints on social information use in wild baboons

    Alecia J Carter et al.
    Social information is a process encompassing information acquisition, application and exploitation that is constrained by an individual’s social, behavioural and demographic phenotype.
    1. Neuroscience

    Astrocytes contribute to synapse elimination via type 2 inositol 1,4,5-trisphosphate receptor-dependent release of ATP

    Junhua Yang et al.
    Astrocytes regulate the pruning of excitatory synapses during early life through ATP signaling.
    1. Immunology

    Lys29-linkage of ASK1 by Skp1−Cullin 1−Fbxo21 ubiquitin ligase complex is required for antiviral innate response

    Zhou Yu et al.
    By joining the Skp1-Cul1-Rbx1 SCF complex, Fbxo21 interacts with ASK1 and mediates Lys29-linkage of ASK1, leading to type I IFN production.
    1. Developmental Biology and Stem Cells

    Two FGFRL-Wnt circuits organize the planarian anteroposterior axis

    M Lucila Scimone et al.
    Single-cell RNA sequencing identifies an adult regional gene expression map in planarian muscle that includes two FGFRL-Wnt circuits controlling head and trunk tissue pattern.
    1. Biophysics and Structural Biology

    A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies

    Raphael Zahn et al.
    A homopolymer-sphere model is shown to accurately reproduce the interactions that underpin selective gating of macromolecular transport into and out of the cell nucleus.
    1. Computational and Systems Biology
    2. Developmental Biology and Stem Cells

    High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals

    Luciano Marcon et al.
    Realistic reaction-diffusion signaling networks that include cell-autonomous factors can robustly form self-organizing spatial patterns for any combination of diffusion coefficients without requiring differential diffusivity.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    CasExpress reveals widespread and diverse patterns of cell survival of caspase-3 activation during development in vivo

    Austin Xun Ding et al.
    Genetic labeling of cells that survive executioner caspase activity in Drosophila reveals distinct patterns in different tissues.
    1. Biophysics and Structural Biology

    Structural basis for DNA 5´-end resection by RecJ

    Kaiying Cheng et al.
    A structural investigation reveals details of the mechanism by which the nuclease RecJ processes DNA ends to repair double strand breaks.
    1. Genes and Chromosomes

    Cotranslational microRNA mediated messenger RNA destabilization

    Trinh To Tat et al.
    MicroRNAs stimulate the decay of targeted mRNAs while they are associated with translating ribosomes.
    1. Biophysics and Structural Biology
    2. Plant Biology

    Mechanistic insight into a peptide hormone signaling complex mediating floral organ abscission

    Julia Santiago et al.
    A plant peptide hormone controls organ shedding by acting as molecular glue that promotes the interaction between two membrane receptor kinases.
    1. Ecology
    2. Microbiology and Infectious Disease

    Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

    Hanno Teeling et al.
    Dynamic successive blooms of clades of planktonic marine bacteria that can be observed during blooms of marine algae follow discernible patterns, part of which might be explained by substrate-induced forcing.
    1. Biochemistry
    2. Biophysics and Structural Biology

    VEGFR-2 conformational switch in response to ligand binding

    Sarvenaz Sarabipour et al.
    A receptor for vascular endothelial growth factor forms dimers in the absence of its ligand, and ligand-binding leads to structural changes that result in increased kinase phosphorylation.
    1. Plant Biology

    A novel role for the root cap in phosphate uptake and homeostasis

    Satomi Kanno et al.
    Real-time 33P imaging combined with specific complementation of inorganic phosphate transport in the root cap reveals this tissue’s contribution to phosphate uptake.
    1. Biophysics and Structural Biology
    2. Cell Biology

    The size of the EB cap determines instantaneous microtubule stability

    Christian Duellberg et al.
    The EB binding region defines the length of the protective cap that stabilizes growing microtubules.
    1. Developmental Biology and Stem Cells
    2. Human Biology and Medicine

    T-box3 is a ciliary protein and regulates stability of the Gli3 transcription factor to control digit number

    Uchenna Emechebe et al.
    The transcription and splicing factor T-box3 is present in primary cilia, regulates multiple aspects of limb development, and interacts with members of the protein complex required for the stability and processing of the Gli3 transcription factor.
    1. Cell Biology
    2. Plant Biology

    Arabidopsis heterotrimeric G proteins regulate immunity by directly coupling to the FLS2 receptor

    Xiangxiu Liang et al.
    Heterotrimeric G proteins are coupled to and regulate plant receptor signaling, which allows optimum immune activation and enhances the production of reactive oxygen species.
    1. Neuroscience

    Structural development and dorsoventral maturation of the medial entorhinal cortex

    Saikat Ray, Michael Brecht
    The medial entorhinal cortex is important for spatial memory formation and matures from dorsal, where smaller spatial-scales are represented, to ventral, where larger spatial-scales are represented.

Magazine

    1. Cell Biology

    mRNA Decay: How cells kill a "killer" messenger

    Cosmin Saveanu, Alain Jacquier
    1. Neuroscience

    Prediction Error: The expanding role of dopamine

    Bradley B Doll, Nathaniel D Daw