January 2015

Research articles

1. 1. Microbiology and Infectious Disease

   Experimentally guided models reveal replication principles that shape the mutation distribution of RNA viruses

   Michael B Schulte, Jeremy A Draghi ... Raul Andino

   A mathematical model that combines stochasticity and spatial structure describes the dynamics of the viral population during an infection cycle, and fitting the model to RNA and virus abundances over time shows that poliovirus follows a geometric replication mode.
2. 1. Biochemistry and Chemical Biology
   2. Microbiology and Infectious Disease

   Angiomotin functions in HIV-1 assembly and budding

   Gaelle Mercenne, Steven L Alam ... Wesley I Sundquist

   Angiomotin (AMOT) is a cellular host factor that links HIV-1 to the ubiquitin E3 ligase, NEDD4L, and promotes virion assembly and envelopment.
3. 1. Microbiology and Infectious Disease

   Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses

   Ci-Xiu Li, Mang Shi ... Yong-Zhen Zhang

   Extensive genetic diversity and novel genome structures in RNA viruses from arthropods shed important new light on the ancestry and evolutionary history of major classes of vertebrate and plant viruses.
4. 1. Chromosomes and Gene Expression
   2. Evolutionary Biology

   A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA

   Natasha M O'Brown, Brian R Summers ... David M Kingsley

   An identical DNA base pair change has occurred in divergent sticklebacks to alter the expression of a major developmental gene controlling armor plates, thus providing a molecular link between particular enhancer changes, cell signaling, and repeated skeletal evolution in natural populations.
5. 1. Structural Biology and Molecular Biophysics
   2. Cell Biology

   Non-catalytic motor domains enable processive movement and functional diversification of the kinesin-14 Kar3

   Christine Mieck, Maxim I Molodtsov ... Stefan Westermann

   The kinesin-14 motor Kar3 moves along microtubules using a previously undescribed mechanism that critically requires the presence of a non-catalytic head.
6. 1. Neuroscience

   A cortical disinhibitory circuit for enhancing adult plasticity

   Yu Fu, Megumi Kaneko ... Michael P Stryker

   Building on previous work (Kaneko and Stryker, 2014), we report that the specific population of inhibitory neurons that increases the responses of neurons in the visual cortex during locomotion will also, when activated or blocked artificially, dramatically alter adult cortical plasticity, revealing that the aerobic exercise of locomotion is not necessary.
7. 1. Genetics and Genomics

   Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator

   Katharine R Grabek, Cecilia Diniz Behn ... Sandra L Martin

   In the torpid hibernator, when transcription is inhibited, enhanced stability and polyadenylation explain increased abundance of crucial transcripts required for intense non-shivering thermogenesis during arousal.
8. 1. Neuroscience

   Learning the specific quality of taste reinforcement in larval Drosophila

   Michael Schleyer, Daisuke Miura ... Bertram Gerber

   The finding that fly maggots, equipped with only 10,000 neurons, process reinforcement not only by value but also by specific quality reveals a basic operating principle of brains and challenges current models of memory organization.
9. 1. Biochemistry and Chemical Biology

   Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression

   Dmitry E Andreev, Patrick BF O'Connor ... Pavel V Baranov

   Most of the mRNAs whose translation is resistant to the stress-induced repression of protein synthesis contain upstream open reading frames that are efficiently translated under normal conditions.
10. 1. Cell Biology
    2. Cancer Biology

    Defective apical extrusion signaling contributes to aggressive tumor hallmarks

    Yapeng Gu, Jill Shea ... Jody Rosenblatt

    Disrupting extrusion, a process that drives epithelial cell death, leads to increased cell survival, poor barrier function, and enhanced cell invasion and, thereby, promotes tumor initiation and progression.
11. 1. Evolutionary Biology

    Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns

    Alexander S Mikheyev, Timothy A Linksvayer

    Genes associated with age-based division of labor in ants exist in distinct regulatory and evolutionary contexts; genes up-regulated in young nurses are loosely connected and rapidly evolving while genes up-regulated in old foragers are highly connected and conserved.
12. 1. Neuroscience

    Temporal structure in associative retrieval

    Zeb Kurth-Nelson, Gareth Barnes ... Peter Dayan

    Neural representations are fast-evolving trajectories, and distinct components of these trajectories reappear during retrieval with distinct consequences for learning.
13. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    A molecular basis for the differential roles of Bub1 and BubR1 in the spindle assembly checkpoint

    Katharina Overlack, Ivana Primorac ... Andrea Musacchio

    The mechanism behind the recruitment of the spindle assembly checkpoint protein BubR1 to the kinetochore illustrates how gene duplication and sub-functionalization can influence the functional complexity of a protein network.
14. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Phenotypic complementation of genetic immunodeficiency by chronic herpesvirus infection

    Donna A MacDuff, Tiffany A Reese ... Herbert W Virgin

    HOIL-1 deficiency in mice results in a severe immunodeficiency that is effectively complemented by chronic infection with a murine gamma-herpesvirus.
15. 1. Cell Biology

    Controlling fertilization and cAMP signaling in sperm by optogenetics

    Vera Jansen, Luis Alvarez ... Dagmar Wachten

    Optogenetics is a non-invasive way to study cAMP signaling in sperm cells, which is able to control sperm motility and fertilization.
16. 1. Structural Biology and Molecular Biophysics
    2. Evolutionary Biology

    Methylation at the C-2 position of hopanoids increases rigidity in native bacterial membranes

    Chia-Hung Wu, Maja Bialecka-Fornal, Dianne K Newman

    Methylation specifically enhances the ability of hopanoids to rigidify membranes under physiologically relevant conditions, which impacts the current interpretation of the 2-methylhopane fossil record.
17. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Global biogeographic sampling of bacterial secondary metabolism

    Zachary Charlop-Powers, Jeremy G Owen ... Sean F Brady

    Pyro-sequencing of two genes involved in bacterial secondary metabolism provides new insights into the rich reservoir of biologically active small molecules found in environmental bacteria.
18. 1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria

    Matthew V Kotlajich, Daniel R Hron ... Robert Landick

    Bridged H-NS filaments inhibit transcript elongation by bacterial RNA polymerase by enhancing backtracking and increasing Rho-dependent termination at a subset of pause sites that are normally poor Rho substrates.
19. 1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    The contrasting phylodynamics of human influenza B viruses

    Dhanasekaran Vijaykrishna, Edward C Holmes ... Ian G Barr

    The analysis of the genomes of two lineages of influenza B virus (Victoria and Yamagata) reveal that their phylodynamics are fundamentally different, and are determined by a complex relationship between virus transmission, age of infection and receptor binding preference.
20. 1. Cell Biology

    Reliable cell cycle commitment in budding yeast is ensured by signal integration

    Xili Liu, Xin Wang ... Chao Tang

    The decision to commit to cell division-the Start transition-in budding yeast is governed by time integration of G1 cyclin-CDK activity by the transcription factor Whi5.
21. 1. Neuroscience

    The topography of frequency and time representation in primate auditory cortices

    Simon Baumann, Olivier Joly ... Timothy D Griffiths

    fMRI data from macaques suggest that sounds with similar temporal characteristics activate neighbouring regions of auditory cortex, giving rise to a topographic map broadly analogous to that for sound frequencies.
22. 1. Cell Biology
    2. Developmental Biology

    Mitochondrial Ca²⁺ uptake by the voltage-dependent anion channel 2 regulates cardiac rhythmicity

    Hirohito Shimizu, Johann Schredelseker ... Jau-Nian Chen

    Enhancing mitochondrial Ca²⁺ uptake effectively suppresses aberrant Ca²⁺ induced arrhythmogenic events in zebrafish, mouse and human cardiomyocytes, demonstrating a critical role for mitochondria in the regulation of cardiac rhythmicity.
23. 1. Neuroscience

    Delay-dependent contributions of medial temporal lobe regions to episodic memory retrieval

    Maureen Ritchey, Maria E Montchal ... Charan Ranganath

    The anterior and posterior parts of the hippocampus have distinct roles in the retrieval of contextual information in memories of recent experiences.
24. 1. Structural Biology and Molecular Biophysics
    2. Plant Biology

    Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography

    Benjamin D Engel, Miroslava Schaffer ... Wolfgang Baumeister

    The first 3D views of the native algal chloroplast provide new insights into thylakoid biogenesis, photosynthesis, and carbon fixation.
25. 1. Neuroscience

    Knockdown of hypothalamic RFRP3 prevents chronic stress-induced infertility and embryo resorption

    Anna C Geraghty, Sandra E Muroy ... Daniela Kaufer

    A chronic stressor prior to mating has lasting negative consequences on the fertility and fecundity of female rats, which can be prevented by blocking a single hypothalamic reproductive inhibitory hormone.
26. 1. Chromosomes and Gene Expression

    Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

    Anne E Dodson, Jasper Rine

    Single-cell and single-molecule analyses of transient gene expression revealed hitherto unrecognized dynamics in heterochromatin function and defined novel roles for a heterochromatin establishment factor and an understudied sirtuin.
27. 1. Structural Biology and Molecular Biophysics

    Structure of a low-population intermediate state in the release of an enzyme product

    Alfonso De Simone, Francesco A Aprile ... Michele Vendruscolo

    Product release from human lysozyme is mediated by an intermediate state with transient weak interactions between the product and enzyme.
28. 1. Stem Cells and Regenerative Medicine

    Bioengineered human myobundles mimic clinical responses of skeletal muscle to drugs

    Lauran Madden, Mark Juhas ... Nenad Bursac

    A novel bioengineered human skeletal muscle model with accurate physiological and pharmacological responses may provide a useful tool for preclinical testing.
29. 1. Cell Biology
    2. Neuroscience

    Neuron-wide RNA transport combines with netrin-mediated local translation to spatially regulate the synaptic proteome

    Sangmok Kim, Kelsey C Martin

    The spatial regulation of gene expression within neurons occurs primarily at the level of local translation rather than by stimulus-induced RNA targeting from nucleus to synapse.
30. 1. Genetics and Genomics
    2. Neuroscience

    The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing

    Shahar Alon, Sandra C Garrett ... Eli Eisenberg

    The first example of an animal where RNA-editing dramatically reshapes the entire proteome demonstrates that editing must be a critical evolutionary and adaptive force.
31. 1. Cell Biology
    2. Neuroscience

    Activity and Ca²⁺ regulate the mobility of TRPV1 channels in the plasma membrane of sensory neurons

    Eric N Senning, Sharona E Gordon

    Channel activity is a novel regulatory mechanism for channel mobility in the plasma membrane.
32. 1. Immunology and Inflammation

    The transforming growth factor beta signaling pathway is critical for the formation of CD4 T follicular helper cells and isotype-switched antibody responses in the lung mucosa

    Heather D Marshall, John P Ray ... Susan M Kaech

    Differentiation of CD4 T cells into CD4 T follicular helper cells during viral infection in mice is promoted by tumor growth factor beta.
33. 1. Genetics and Genomics

    A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy

    Qing Feng, Lauren Snider ... Robert K Bradley

    Expression of the disease gene DUX4 inhibits RNA quality control in skeletal muscle, thereby stabilizing thousands of aberrant RNAs, including its own transcript.
34. 1. Cell Biology

    Potassium dependent rescue of a myopathy with core-like structures in mouse

    M Gartz Hanson, Jonathan J Wilde ... Lee Niswander

    A mouse model of human muscle myopathy is used to provide mechanistic insight, identify possible biomarkers of disease, and suggest possible therapeutic strategies to alleviate muscle weakness.
35. 1. Neuroscience

    A single pair of neurons links sleep to memory consolidation in Drosophila melanogaster

    Paula R Haynes, Bethany L Christmann, Leslie C Griffith

    Dorsal paired medial neurons, which are required for memory consolidation, promote sleep by inhibiting the excitation of mushroom body neurons.
36. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    Nup98 FG domains from diverse species spontaneously phase-separate into particles with nuclear pore-like permselectivity

    Hermann Broder Schmidt, Dirk Görlich

    How nuclear pore complexes establish their permeability barrier has been a long-standing question; now, this process can be reconstituted by a surprisingly simple and rapid self-assembly of Nup98 FG domains into selective FG phases.
37. 1. Neuroscience

    Normalisation of brain connectivity through compensatory behaviour, despite congenital hand absence

    Avital Hahamy, Stamatios N Sotiropoulos ... Tamar R Makin

    Building on previous work (Makin et al., 2013), we show that the brains of individuals born without a hand adaptively change to compensate for their disability.
38. 1. Developmental Biology
    2. Evolutionary Biology

    Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita

    Karl R Wotton, Eva Jiménez-Guri ... Johannes Jaeger

    Quantitative system-level analysis of a pattern-forming gene regulatory network in a non-model organism shows that dynamic changes in gene expression evolve through quantitative system drift.
39. 1. Neuroscience

    Interplay between population firing stability and single neuron dynamics in hippocampal networks

    Edden Slomowitz, Boaz Styr ... Inna Slutsky

    Neuronal networks balance flexibility with stability by allowing the firing rate of individual neurons within a network to vary over time, while ensuring that the average firing rate across the network remains constant.
40. 1. Cell Biology
    2. Developmental Biology

    miR-128 regulates neuronal migration, outgrowth and intrinsic excitability via the intellectual disability gene Phf6

    Eleonora Franzoni, Sam A Booker ... F Gregory Wulczyn

    The regulation of Phf6 by miR-128 is a developmental timing mechanism that influences cortical lamination, neuronal morphology and intrinsic excitability.
41. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    Proteomic analysis of the response to cell cycle arrests in human myeloid leukemia cells

    Tony Ly, Aki Endo, Angus I Lamond

    Building on previous work (Ly et al., 2014), we show that elutriated cells and arrested cells have similar patterns of DNA content and cyclin expression: however, a large fraction of the proteome changes detected in arrested cells are found to reflect arrest-specific responses rather than physiological cell cycle regulation.
42. 1. Structural Biology and Molecular Biophysics

    Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5′ splice site recognition

    Yasushi Kondo, Chris Oubridge ... Kiyoshi Nagai

    The complete architecture of human spliceosomal U1 snRNP and its interaction with the 5′ splice site of pre-mRNA are described in atomic detail.