October 2014

Research articles

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

   General principles for the formation and proliferation of a wall-free (L-form) state in bacteria

   Romain Mercier, Yoshikazu Kawai, Jeff Errington

   A wide range of bacterial species can switch into a cell wall-free state that does not require the FtsZ-based division machinery to proliferate.
2. 1. Neuroscience

   Amygdala neural activity reflects spatial attention towards stimuli promising reward or threatening punishment

   Christopher J Peck, C Daniel Salzman

   Primate amygdala neurons provide a coordinated representation of space and motivational significance whereby amygdala responses to visual stimuli predicting either rewards or aversive stimuli could influence spatial attention in a similar manner.
3. 1. Structural Biology and Molecular Biophysics
   2. Cell Biology

   Real-time observation of signal recognition particle binding to actively translating ribosomes

   Thomas R Noriega, Jin Chen ... Joseph D Puglisi

   The signal recognition particle only stably engages translating ribosome nascent-chain complexes exposing a functional signal sequence.
4. 1. Neuroscience

   Identification of motor neurons and a mechanosensitive sensory neuron in the defecation circuitry of Drosophila larvae

   Wei Zhang, Zhiqiang Yan ... Yuh Nung Jan

   The neural circuit underlying defecation behavior in Drosophila larvae has been identified and characterized.
5. 1. Stem Cells and Regenerative Medicine

   Transient nuclear Prospero induces neural progenitor quiescence

   Sen-Lin Lai, Chris Q Doe

   A low-level pulse of the nuclear Prospero protein is necessary and sufficient to cause neural progenitor cells to enter a quiescent state.
6. 1. Biochemistry and Chemical Biology

   Measurement of average decoding rates of the 61 sense codons in vivo

   Justin Gardin, Rukhsana Yeasmin ... Bruce Futcher

   The translation rates of each yeast codon have been measured in both the A and P sites of the ribosome.
7. 1. Cell Biology

   The role of IMP dehydrogenase 2 in Inauhzin-induced ribosomal stress

   Qi Zhang, Xiang Zhou ... Hua Lu

   The small molecule Inauhzin possesses a dual targeting ability, and activates p53 by targeting two enzymes—SIRT1 and IMP dehydrogenase 2 (IMPDH2)—which are highly expressed in human cancers.
8. 1. Immunology and Inflammation

   CD28 expression is required after T cell priming for helper T cell responses and protective immunity to infection

   Michelle A Linterman, Alice E Denton ... Kenneth GC Smith

   The co-stimulatory molecule CD28 is required after T cell priming for helper T cell polarization in response to an infection.
9. 1. Chromosomes and Gene Expression
   2. Immunology and Inflammation

   Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment

   Brenda Y Han, Shuang Wu ... Jason G Cyster

   A novel zinc finger transcription factor regulates expression of multiple genes in late stage thymocytes and recent thymic emigrants to promote formation of the naïve T cell compartment.
10. 1. Cell Biology

    Adiponectin is essential for lipid homeostasis and survival under insulin deficiency and promotes β-cell regeneration

    Risheng Ye, William L Holland ... Philipp E Scherer

    Under insulinopenic conditions, the hormone adiponectin is essential for lipid uptake specifically in subcutaneous white adipose tissue, and is sufficient to ameliorate islet lipotoxicity.
11. 1. Plant Biology

    The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1

    Yangrong Cao, Yan Liang ... Gary Stacey

    The chitin-triggered immune response is mediated by a LYK5 and CERK1 receptor complex in Arabidopsis.
12. 1. Cell Biology
    2. Neuroscience

    GluN2B-containing NMDA receptors regulate depression-like behavior and are critical for the rapid antidepressant actions of ketamine

    Oliver H Miller, Lingling Yang ... Benjamin J Hall

    The rapid antidepressant actions of low dose ketamine occur through the direct relief of suppression of protein synthesis via antagonism of a subset of NMDA receptors containing the GluN2B subunit.
13. 1. Neuroscience

    Neural mechanisms of economic commitment in the human medial prefrontal cortex

    Konstantinos Tsetsos, Valentin Wyart ... Christopher Summerfield

    A striking dissociation exists in the medial prefrontal cortex, with different brain regions responding to value when commitments are deferred to the future and when prospects are judged to be undesirable.
14. 1. Microbiology and Infectious Disease

    Favipiravir elicits antiviral mutagenesis during virus replication in vivo

    Armando Arias, Lucy Thorne, Ian Goodfellow

    Favipiravir, a novel nucleoside analogue, can clear a persistent norovirus infection in vivo through lethal mutagenesis.
15. 1. Neuroscience

    Non-linear developmental trajectory of electrical phenotype in rat substantia nigra pars compacta dopaminergic neurons

    Martial A Dufour, Adele Woodhouse ... Jean-Marc Goaillard

    The development of the electrical phenotype of neurons can be precisely quantified and dissected using a combination of multi-variate statistical analyses and a systematic electrophysiological characterization of electrical properties.
16. 1. Neuroscience

    Neurotrophin-3 regulates ribbon synapse density in the cochlea and induces synapse regeneration after acoustic trauma

    Guoqiang Wan, Maria E Gómez-Casati ... Gabriel Corfas

    Overexpression of the growth factor neurotrophin-3 helps to repair noise-induced damage in the mouse inner ear by promoting the regeneration of damaged synapses.
17. 1. Physics of Living Systems
    2. Cell Biology

    Phase transitions of multivalent proteins can promote clustering of membrane receptors

    Sudeep Banjade, Michael K Rosen

    A new and general mechanism describes the organization of membrane proteins and their cytoplasmic ligands into micrometer-scale clusters, based on polymerization and concomitant phase separation of multivalent proteins.
18. 1. Immunology and Inflammation

    Female resistance to pneumonia identifies lung macrophage nitric oxide synthase-3 as a therapeutic target

    Zhiping Yang, Yuh-Chin T Huang ... Lester Kobzik

    Activation of lung macrophage nitric oxide synthase-3 improves both bacterial clearance and outcome in primary and secondary pneumonia models.
19. 1. Developmental Biology

    A host beetle pheromone regulates development and behavior in the nematode Pristionchus pacificus

    Jessica K Cinkornpumin, Dona R Wisidagama ... Ray L Hong

    A lipid-binding protein mediates both attraction and hypersensitivity to a beetle sex pheromone in a specific type of nematode-insect relationship known as necromeny.
20. 1. Cell Biology

    Oscillatory phase separation in giant lipid vesicles induced by transmembrane osmotic differentials

    Kamila Oglęcka, Padmini Rangamani ... Atul N Parikh

    Spontaneous osmoregulation in giant phospholipid vesicles, which is characterized by oscillations in vesicle size and membrane tension, couples to the compositional degrees of freedom at the membrane surface to produce oscillations in domain texture and induce isothermal phase change.
21. 1. Neuroscience

    Semaphorin 5A inhibits synaptogenesis in early postnatal- and adult-born hippocampal dentate granule cells

    Yuntao Duan, Shih-Hsiu Wang ... Roman J Giger

    Mice that lack the autism susceptibility gene Semaphorin 5A show excess excitatory synapse formation in dentate granule neurons and also altered social behavior, adding to evidence that a surplus of synapses contributes to the behavioral changes observed in autism spectrum disorders.
22. 1. Cell Biology

    Counteracting suppression of CFTR and voltage-gated K⁺ channels by a bacterial pathogenic factor with the natural product tannic acid

    Yajamana Ramu, Yanping Xu ... Zhe Lu

    Tannic acid acts as an ‘antidote’ against the negative effects of a bacterial enzyme, which can both aggravate cystic fibrosis and enable the anthrax bacteria to evade the immune responses elicited by a typical live vaccine.
23. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli

    Dipali G Sashital, Candacia A Greeman ... James R Williamson

    Comprehensive structural and compositional characterization of the in vivo 30S ribosomal assembly landscape reveals parallel pathways for 3′-domain formation and a previously unknown role for the assembly factor RimP.
24. 1. Developmental Biology
    2. Genetics and Genomics

    Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition

    Xiao-Yong Li, Melissa M Harrison ... Michael B Eisen

    Drosophila melanogaster embryos undergo a dramatic genomic transformation in the hour preceding gastrulation, as thousands of promoters and regulatory regions become biochemically distinct before they become active.
25. 1. Developmental Biology
    2. Neuroscience

    Mitochondrial fusion but not fission regulates larval growth and synaptic development through steroid hormone production

    Hector Sandoval, Chi-Kuang Yao ... Hugo J Bellen

    The dual role of Drosophila Mitofusin in steroid hormone production and cholesterol ester storage, which is evolutionary conserved by the combined expression of the two mammalian Mitofusins, ensures proper synaptic development.
26. 1. Neuroscience

    Early intrinsic hyperexcitability does not contribute to motoneuron degeneration in amyotrophic lateral sclerosis

    Félix Leroy, Boris Lamotte d'Incamps ... Daniel Zytnicki

    Contrary to a long-standing hypothesis, the neuronal death that leads to muscle wastage in amyotrophic lateral sclerosis does not result from overactivity of those neurons during development.
27. 1. Stem Cells and Regenerative Medicine
    2. Immunology and Inflammation

    The basic leucine zipper transcription factor NFIL3 directs the development of a common innate lymphoid cell precursor

    Xiaofei Yu, Yuhao Wang ... Lora V Hooper

    The transcription factor NFIL3 is essential for the development of a committed bone marrow precursor that gives rise to all known innate lymphoid cell lineages in mice.
28. 1. Neuroscience

    Synaptic organization of the Drosophila antennal lobe and its regulation by the Teneurins

    Timothy J Mosca, Liqun Luo

    A comprehensive synapse-level analysis of a fly central-brain region has led to the identification of molecules that are necessary for mediating the normal density of connections.
29. 1. Structural Biology and Molecular Biophysics
    2. Microbiology and Infectious Disease

    A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family

    Qing Yao, Qiuhe Lu ... Feng Shao

    Protein heptosyltransferases modify a group of bacterial autotransporters for virulence function and employ a novel structural mechanism for the processive hyperglycosylation of the autotransporter.
30. 1. Biochemistry and Chemical Biology
    2. Evolutionary Biology

    Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity

    Conor J Howard, Victor Hanson-Smith ... Liam J Holt

    Reconstructing ancestral enzymes has revealed that a switch in kinase substrate preference evolved via an expanded specificity intermediate that is tolerated in vivo, thus providing a path for kinase diversification.
31. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    A clathrin coat assembly role for the muniscin protein central linker revealed by TALEN-mediated gene editing

    Perunthottathu K Umasankar, Li Ma ... Linton M Traub

    The muniscin protein FCHO1 interacts with, and activates, the adapter protein-2 complex (AP-2) to promote the assembly of clathrin-coated vesicles.
32. 1. Plant Biology

    Dynamic F-actin movement is essential for fertilization in Arabidopsis thaliana

    Tomokazu Kawashima, Daisuke Maruyama ... Frédéric Berger

    The movement of F-actin filaments, which is regulated by actin-myosin interactions together with a female gamete-specific Rho-GTPase, enables migration of the Arabidopsis sperm cell nucleus towards the female nucleus; which might account for the loss of centrosomes in flowering plants.
33. 1. Cell Biology

    The membrane-associated proteins FCHo and SGIP are allosteric activators of the AP2 clathrin adaptor complex

    Gunther Hollopeter, Jeffrey J Lange ... Erik M Jorgensen

    Endocytosis is triggered by membrane-associated proteins that transform the clathrin adaptor into an active complex.
34. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Structure of catalase determined by MicroED

    Brent L Nannenga, Dan Shi ... Tamir Gonen

    Building on previous work (Shi et al., 2013), we have used MicroED to determine the structure of catalase at 3.2 Å resolution from a single crystal.
35. 1. Plant Biology

    Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module

    Juliana L Matos, On Sun Lau ... Dominique C Bergmann

    An adult stem-cell lineage terminally differentiates via recruitment of the RETINOBLASTOMA-RELATED protein by a lineage specific transcription factor.
36. 1. Developmental Biology
    2. Genetics and Genomics

    The rosetteless gene controls development in the choanoflagellate S. rosetta

    Tera C Levin, Allison J Greaney ... Nicole King

    The establishment of forward genetics in S. rosetta reveals the first gene known to be required for choanoflagellate multicellular development.
37. 1. Developmental Biology

    Early patterning and specification of cardiac progenitors in gastrulating mesoderm

    W Patrick Devine, Joshua D Wythe ... Benoit G Bruneau

    Multipotent cardiac precursors within a population of mesoderm are rapidly fated to specific anatomic locations in the developing mouse heart.
38. 1. Structural Biology and Molecular Biophysics
    2. Microbiology and Infectious Disease

    Crystal structure of PfRh5, an essential P. falciparum ligand for invasion of human erythrocytes

    Lin Chen, Yibin Xu ... Alan F Cowman

    The crystal structure of a PfRh family protein from a malaria parasite has been solved and shows that PfRh5-which the parasite uses to invade human red blood cells-has a novel protein fold.
39. 1. Cell Biology
    2. Developmental Biology

    Flattop regulates basal body docking and positioning in mono- and multiciliated cells

    Moritz Gegg, Anika Böttcher ... Heiko Lickert

    In cell types that acquire planar cell polarity, the protein Flattop regulates basal body docking and positioning.
40. 1. Developmental Biology
    2. Neuroscience

    The Drosophila Sp8 transcription factor Buttonhead prevents premature differentiation of intermediate neural progenitors

    Yonggang Xie, Xiaosu Li ... Sijun Zhu

    The Drosophila equivalent of the human transcription factor Sp8 acts to ensure that neural progenitor cells undergo an appropriate number of cell divisions, thereby helping to regulate brain development and guard against tumor formation.
41. 1. Stem Cells and Regenerative Medicine

    Trithorax maintains the functional heterogeneity of neural stem cells through the transcription factor Buttonhead

    Hideyuki Komori, Qi Xiao ... Cheng-Yu Lee

    The Drosophila equivalent of the human protein Mixed Lineage Leukemia 1n enables neural stem cells to generate neural progenitors through the fly equivalent of the human transcription factor Sp8, thereby contributing to an increased number and diversity of cell types during brain development.
42. 1. Structural Biology and Molecular Biophysics

    Phosphatidic acid modulation of Kv channel voltage sensor function

    Richard K Hite, Joel A Butterwick, Roderick MacKinnon

    Phosphatidic acid influences the gating of voltage-gated K+ channels through a non-specific surface charge mechanism and through a specific interaction between a voltage sensor arginine and the primary phosphate head group on the cytoplasmic membrane leaflet.
43. 1. Neuroscience

    Regulation of food intake by mechanosensory ion channels in enteric neurons

    William H Olds, Tian Xu

    Manipulating the activity of ‘stretch-sensitive’ ion channels in neurons innervating the digestive system of fruit flies has dramatic effects on food intake, suggesting that these ion channels could be targets for drugs to help tackle obesity.
44. 1. Biochemistry and Chemical Biology

    The glucuronyltransferase B4GAT1 is required for initiation of LARGE-mediated α-dystroglycan functional glycosylation

    Tobias Willer, Kei-ichiro Inamori ... Kevin P Campbell

    Post-phosphoryl modification of α-dystroglycan requires the glucuronyltransferase B4GAT1; this enzyme synthesizes the acceptor glycan that serves as a primer for the glycosyltransferase LARGE to synthesize the laminin-binding glycan.
45. 1. Biochemistry and Chemical Biology

    B4GAT1 is the priming enzyme for the LARGE-dependent functional glycosylation of α-dystroglycan

    Jeremy L Praissman, David H Live ... Lance Wells

    The correct enzymatic activity of a previously misnamed enzyme is defined, placing the enzyme upstream of LARGE in building functional O-mannose structures on α-dystroglycan that are disrupted in multiple forms of congenital muscular dystrophy.
46. 1. Genetics and Genomics

    Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

    Benoit Ballester, Alejandra Medina-Rivera ... Michael D Wilson

    Combinatorial transcription factor binding shared by multiple species enriches for essential biological pathways and coincides with disease-causing regulatory DNA mutations.
47. 1. Ecology
    2. Microbiology and Infectious Disease

    Adaptability of non-genetic diversity in bacterial chemotaxis

    Nicholas W Frankel, William Pontius ... Thierry Emonet

    An experimentally constrained model shows that Escherichia coli faces fitness trade-offs in chemotaxis behaviors, and that adaptation of phenotypic diversity through altered gene regulation permits populations to resolve these trade-offs.
48. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    TORC2-dependent protein kinase Ypk1 phosphorylates ceramide synthase to stimulate synthesis of complex sphingolipids

    Alexander Muir, Subramaniam Ramachandran ... Jeremy Thorner

    TORC2-Ypk1 signaling upregulates flux through the sphingolipid pathway not only by increasing the supply of long-chain base precursors, but also by increasing their use in synthesizing complex sphingolipids.
49. 1. Developmental Biology
    2. Neuroscience

    Delivery of circulating lipoproteins to specific neurons in the Drosophila brain regulates systemic insulin signaling

    Marko Brankatschk, Sebastian Dunst ... Suzanne Eaton

    Yeast specific lipids promote the transport of lipid transfer protein (LTP) across the blood brain barrier to the neurons that regulate systemic insulin signaling.
50. 1. Chromosomes and Gene Expression

    Kinetic competition during the transcription cycle results in stochastic RNA processing

    Antoine Coulon, Matthew L Ferguson ... Daniel R Larson

    Real-time single-molecule visualization of transcription and splicing in living cells reveals that RNA synthesis and processing can occur through multiple pathways on the same gene.
51. 1. Genetics and Genomics
    2. Cancer Biology

    Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer

    Young Seok Ju, Ludmil B Alexandrov ... Peter J Campbell

    Identifying 1,907 mitochondrial somatic mutations from 1,675 tumor tissues provides new insights into the causes and effects of the mitochondrial genome mutations found in human cancers.
52. 1. Cell Biology

    Reconstitution of self-organizing protein gradients as spatial cues in cell-free systems

    Katja Zieske, Petra Schwille

    A minimal cell-like system with defined geometry has been used to investigate the establishment and spatial control of a protein gradient that positions the bacterial cell division machinery.
53. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    A Ras-like domain in the light intermediate chain bridges the dynein motor to a cargo-binding region

    Courtney M Schroeder, Jonathan ML Ostrem ... Ronald D Vale

    The dynein light intermediate chain is a member of the G protein superfamily and links the motor to several intracellular cargo adaptors.
54. 1. Structural Biology and Molecular Biophysics

    Allosteric signalling in the outer membrane translocation domain of PapC usher

    Irene Farabella, Thieng Pham ... Maya Topf

    Input from computational models has enabled the detection of allosteric communication that modulates the gating mechanism of a bacterial outer-membrane protein.
55. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    Identification of human TERT elements necessary for telomerase recruitment to telomeres

    Jens C Schmidt, Andrew B Dalby, Thomas R Cech

    The TEN-domain of human telomerase mediates the direct interaction with TPP1 to drive telomerase recruitment to telomeres.