June 2015

Research articles

1. 1. Structural Biology and Molecular Biophysics
   2. Cell Biology

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

   Nicolas Aznar, Krishna K Midde ... Pradipta Ghosh

   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.
2. 1. Ecology
   2. Epidemiology and Global Health

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

   Moritz UG Kraemer, Marianne E Sinka ... Simon I Hay

   The limits to the global distribution of the mosquitoes that transmit dengue and chikungunya have been predicted using a species distribution modelling approach.
3. 1. Biochemistry and Chemical Biology
   2. Chromosomes and Gene Expression

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

   Anand Ranjan, Feng Wang ... Carl Wu

   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.
4. 1. Neuroscience

   Hippocampal place cells construct reward related sequences through unexplored space

   H Freyja Ólafsdóttir, Caswell Barry ... Hugo J Spiers

   In anticipation of a reward, hippocampal place cells simulate desired journeys through areas that have been seen, but not explored.
5. 1. Stem Cells and Regenerative Medicine

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

   Shu Jun Zhu, Stephanie E Hallows ... Bret J Pearson

   The planarian mex3-1 gene is required for non-stem cell fates and suppresses a stem cell fate in differentiating cells.
6. 1. Biochemistry and Chemical Biology

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

   Matthew A Mitsche, Jeffrey G McDonald ... Jonathan C Cohen

   Cells use two interdigitated biosynthetic pathways that can be regulated independently to produce diverse bioactive sterols.
7. 1. Computational and Systems Biology

   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.
8. 1. Developmental Biology
   2. Chromosomes and Gene Expression

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

   Daniel M Cohen, Kyoung-Jae Won ... David J Steger

   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.
9. 1. Stem Cells and Regenerative Medicine
   2. Genetics and Genomics

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

   Irene Gallego Romero, Bryan J Pavlovic ... Yoav Gilad

   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.
10. 1. Computational and Systems Biology
    2. Neuroscience

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

    Laura Cornelissen, Seong-Eun Kim ... Charles B Berde

    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.
11. 1. Cell Biology
    2. Neuroscience

    A genetic toolkit for tagging intronic MiMIC containing genes

    Sonal Nagarkar-Jaiswal, Steven Z DeLuca ... Hugo J Bellen

    Building on previous work (Nagarkar-Jaiswal et al., 2015), we report an elegant genetic strategy for endogenous tagging of MiMIC containing genes.
12. 1. Medicine
    2. Neuroscience

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

    Chethan Pandarinath, Vikash Gilja ... Krishna V Shenoy

    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.
13. 1. Structural Biology and Molecular Biophysics

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

    Ashok Sekhar, Jessica AO Rumfeldt ... Lewis E Kay

    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.
14. 1. Cell Biology
    2. Physics of Living Systems

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

    Raphaël Etournay, Marko Popović ... Suzanne Eaton

    Autonomous patterns of cell contraction in the context of localized apical extracellular matrix constraints specify tissue stresses that reshape the wing epithelium.
15. 1. Neuroscience

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

    William N Grimes, Logan R Graves ... Fred Rieke

    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.
16. 1. Chromosomes and Gene Expression

    Promoter nucleosome dynamics regulated by signalling through the CTD code

    Philippe Materne, Jayamani Anandhakumar ... Damien Hermand

    Phosphorylation of the C-terminal domain (CTD) of RNA Polymerase II controls nucleosomes dynamics at specific promoters to regulate transcription.
17. 1. Neuroscience

    A Cambrian origin for vertebrate rods

    Sabrina Asteriti, Sten Grillner, Lorenzo Cangiano

    Several key functional features of jawed vertebrate rods are also present in lamprey photoreceptors, indicating that our Cambrian ancestors possessed dim light vision.
18. 1. Microbiology and Infectious Disease

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

    Shengwei Hu, Jun Qiao ... Hongsheng Ouyang

    A transgenic small hairpin RNA can provide a viable tool for enhancing resistance to viral infection in livestock and improve animal well-being.
19. 1. Cell Biology

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

    Faye M Nixon, Cristina Gutiérrez-Caballero ... Stephen J Royle

    Microtubules of mitotic spindle fibers are positioned and held together by a meshwork of multipolar connectors.
20. 1. Structural Biology and Molecular Biophysics

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

    Zhu Liu, Zhou Gong ... Chun Tang

    Lys63-linked diubiquitin exists as an ensemble of conformational states, each responsible for binding to a target protein through conformational selection.
21. 1. Cell Biology
    2. Immunology and Inflammation

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

    Yiran Zang, Ming Wan ... José Carlos Pastor-Pareja

    Excess membrane can trap outgoing extracellular matrix proteins in secreting cells, leading to pericellular deposits that cause tissue damage.
22. 1. Structural Biology and Molecular Biophysics
    2. Cell Biology

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

    Cindy Ast, Roberto De Michele ... Wolf B Frommer

    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.
23. 1. Computational and Systems Biology

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

    Jan Drugowitsch, Gregory C DeAngelis ... Alexandre Pouget

    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.
24. 1. Neuroscience

    Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans

    Andrés Vidal-Gadea, Kristi Ward ... Jonathan Pierce-Shimomura

    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.
25. 1. Plant Biology

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

    Ran Li, Jin Zhang ... Yonggen Lou

    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.
26. 1. Neuroscience

    Synaptic representation of locomotion in single cerebellar granule cells

    Kate Powell, Alexandre Mathy ... Michael Häusser

    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.
27. 1. Neuroscience

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

    Shruti Shankar, Jia Yi Chua ... Joanne Y Yew

    The cellular and molecular substrates that underlie the programmed behavioral response to a gustatory sex pheromone have been identified.
28. 1. Computational and Systems Biology
    2. Evolutionary Biology

    Expression noise facilitates the evolution of gene regulation

    Luise Wolf, Olin K Silander, Erik van Nimwegen

    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.
29. 1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

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

    Huasong Lu, Yuhua Xue ... Qiang Zhou

    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.
30. 1. Computational and Systems Biology
    2. Neuroscience

    Dynamical feature extraction at the sensory periphery guides chemotaxis

    Aljoscha Schulze, Alex Gomez-Marin ... Matthieu Louis

    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.
31. 1. Chromosomes and Gene Expression

    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.
32. 1. Cell Biology
    2. Microbiology and Infectious Disease

    Dynamic subcellular localization of a respiratory complex controls bacterial respiration

    François Alberge, Leon Espinosa ... Axel Magalon

    The localization of respiratory complexes in the cell membrane emerges as a critical factor for controlling respiration in bacteria.
33. 1. Neuroscience

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

    Virginie Mansuy-Aubert, Laurent Gautron ... Joel K Elmquist

    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.
34. 1. Neuroscience

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

    Thomas O Auer, Tong Xiao ... Filippo Del Bene

    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.
35. 1. Evolutionary Biology

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

    Dave W Anderson, Alesia N McKeown, Joseph W Thornton

    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.
36. 1. Plant Biology

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

    Shouan Liu, Barbara Kracher ... Imre E Somssich

    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.
37. 1. Structural Biology and Molecular Biophysics
    2. Plant Biology

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

    Yuval Mazor, Anna Borovikova, Nathan Nelson

    The crystal structure of higher plant PSI-LHCI complex reveals intricate details responsible for light harvesting.
38. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    MAF1 represses CDKN1A through a Pol III-dependent mechanism

    Yu-Ling Lee, Yuan-Ching Li ... Ming-Ta Hsu

    Pol II-mediated transcription and chromatin looping of CDKN1A are repressed by MAF1 through the regulation of Pol III activity.
39. 1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

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

    Fabian Blombach, Enrico Salvadori ... Finn Werner

    An archaeal basal transcription factor containing an iron-sulphur cluster sheds light on the evolution of transcription machineries in archaea and eukaryotes.
40. 1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    The genetic architecture of NAFLD among inbred strains of mice

    Simon T Hui, Brian W Parks ... Aldons J Lusis

    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.
41. 1. Cell Biology
    2. Immunology and Inflammation

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

    Laura Marroqui, Miguel Lopes ... Decio L Eizirik

    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.
42. 1. Neuroscience

    Inter-individual stereotypy of the Platynereis larval visual connectome

    Nadine Randel, Réza Shahidi ... Gáspár Jékely

    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.
43. 1. Stem Cells and Regenerative Medicine

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

    Hanh Thi-Kim Vu, Jochen C Rink ... Alejandro Sánchez Alvarado

    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.
44. 1. Structural Biology and Molecular Biophysics
    2. Cell Biology

    Identification of a lipid scrambling domain in ANO6/TMEM16F

    Kuai Yu, Jarred M Whitlock ... H Criss Hartzell

    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.
45. 1. Chromosomes and Gene Expression

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

    Steven P Barrett, Peter L Wang, Julia Salzman

    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.
46. 1. Neuroscience

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

    Samuel S Pappas, Katherine Darr ... William T Dauer

    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.
47. 1. Developmental Biology

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

    Benoit Vanhollebeke, Oliver A Stone ... Didier YR Stainier

    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.
48. 1. Neuroscience

    Functional subregions of the human entorhinal cortex

    Anne Maass, David Berron ... Emrah Düzel

    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.
49. 1. Neuroscience

    Functional topography of the human entorhinal cortex

    Tobias Navarro Schröder, Koen V Haak ... Christian F Doeller

    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.
50. 1. Cell Biology
    2. Neuroscience

    The unfolded protein response is required for dendrite morphogenesis

    Xing Wei, Audrey S Howell ... Kang Shen

    The unfolded protein response regulates neuronal dendrite morphogenesis by controlling the folding of a transmembrane leucine-rich repeat (LRR) protein.
51. 1. Plant Biology

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

    Chao Li, Fang-Ling Yeh ... Hen-Ming Wu

    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.
52. 1. Neuroscience

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

    Kelly M LaRue, Jan Clemens ... Mala Murthy

    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.
53. 1. Cancer Biology

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

    Arun M Unni, William W Lockwood ... Harold Varmus

    Co-mutation of two powerful oncogenes in certain cell types may have a lethal effect that explains the mutual exclusivity of the mutations.
54. 1. Biochemistry and Chemical Biology

    Dynamic regulation of transcription factors by nucleosome remodeling

    Ming Li, Arjan Hada ... Michelle D Wang

    Single molecule DNA unzipping reveals a novel model for the regulation of transcription factors and nucleosome positioning via nucleosome remodeling in yeast.
55. 1. Structural Biology and Molecular Biophysics

    Asymmetric conformational maturation of HIV-1 reverse transcriptase

    Xunhai Zheng, Lalith Perera ... Robert E London

    HIV-1 reverse transcriptase uses a metamorphic polymerase domain that minimizes its coding requirements but requires a complex maturation process.
56. 1. Structural Biology and Molecular Biophysics
    2. Cell Biology

    Structural evidence for Scc4-dependent localization of cohesin loading

    Stephen M Hinshaw, Vasso Makrantoni ... Stephen C Harrison

    Cohesin loading at centromeres depends on a conserved surface cluster of amino-acid residues on the cohesin loading protein, Scc4.
57. 1. Computational and Systems Biology
    2. Chromosomes and Gene Expression

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

    Iain G Johnston, Joerg P Burgstaller ... Nick S Jones

    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.
58. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Consistent global structures of complex RNA states through multidimensional chemical mapping

    Clarence Yu Cheng, Fang-Chieh Chou ... Rhiju Das

    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.
59. 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.
60. 1. Structural Biology and Molecular Biophysics
    2. Microbiology and Infectious Disease

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

    Miriam Walden, John M Edwards ... Ulrich Schwarz-Linek

    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.
61. 1. Cell Biology
    2. Chromosomes and Gene Expression

    ATM regulation of IL-8 links oxidative stress to cancer cell migration and invasion

    Wei-Ta Chen, Nancy D Ebelt ... Kyle M Miller

    The ATM kinase has an unanticipated role in tumor progression through the regulation of cell migration by oxidative stress.