November 2014

Research articles

    1. Neuroscience

    Disruption of thalamic functional connectivity is a neural correlate of dexmedetomidine-induced unconsciousness

    Oluwaseun Akeju et al
    Patterns of communication between the thalamus and the cortex are correlated with anesthesia-induced loss of consciousness and recovery.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biochemistry
    2. Cell Biology

    Phosphatidylinositol 3-kinase and COPII generate LC3 lipidation vesicles from the ER-Golgi intermediate compartment

    Liang Ge et al
    Building on previous work (Ge et al., 2013), it is shown that the ER-Golgi intermediate compartment is a platform for the production of COPII vesicles as precursor membranes for the lipidation of LC3, which is an essential step in autophagosome biogenesis.
    Research Advance
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Developmental Biology and Stem Cells

    CED-3 caspase acts with miRNAs to regulate non-apoptotic gene expression dynamics for robust development in C. elegans

    Benjamin P Weaver et al
    A broadly used gene expression regulatory mechanism inactivates targets by CED-3-caspase-mediated proteolysis and works in parallel to miRNAs for diverse non-apoptotic developmental functions.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Cell Biology

    A bacteriophage tubulin harnesses dynamic instability to center DNA in infected cells

    Marcella L Erb et al
    A bacteriophage tubulin homolog, PhuZ, forms a structure with the biochemical, structural, and functional properties of a simplified, bipolar spindle.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biochemistry
    2. Biophysics and Structural Biology

    Structure and transport mechanism of the sodium/proton antiporter MjNhaP1

    Cristina Paulino et al
    The inward-open and outward-open structures of MjNhaP1 explain the mechanism of electroneutral sodium-proton antiport across the cell membrane.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biochemistry
    2. Biophysics and Structural Biology

    Structure and substrate ion binding in the sodium/proton antiporter PaNhaP

    David Wöhlert et al
    The X-ray structure of the PaNhaP provides a unique view of substrate-ion binding and release in electroneutral sodium/proton antiporters.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Genomics and Evolutionary Biology

    Antibacterial gene transfer across the tree of life

    Jason A Metcalf et al
    Parallel horizontal gene transfer has spread a bacteriolytic gene family to all domains of life, and has bestowed a niche-transcending adaptation in recipients that must deploy antibacterial molecules to survive in a bacterial world.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Developmental Biology and Stem Cells

    Nutritional control of body size through FoxO-Ultraspiracle mediated ecdysone biosynthesis

    Takashi Koyama et al
    In Drosophila melanogaster, nutrition controls body size by acting through the Forkhead Box class O (FoxO)/Ultraspiracle complex to regulate nutrition-sensitive ecdysone biosynthesis, thereby controlling the switch to stop growth.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biophysics and Structural Biology
    2. Human Biology and Medicine

    Connexin26 hemichannels with a mutation that causes KID syndrome in humans lack sensitivity to CO2

    Louise Meigh et al
    Building on previous work (Meigh et al., 2013) we show that A88V, a mutation in connexin26 (Cx26) that causes Keratitis-Ichthyosis-Deafness (KID) syndrome in humans, is linked to a lack of sensitivity to CO2 by Cx26 hemichannels.
    Research Advance
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Plant Biology

    Spontaneous symbiotic reprogramming of plant roots triggered by receptor-like kinases

    Martina Katharina Ried et al
    Ectopic expression of Symbiosis Receptor-like Kinase (SYMRK) in roots of the legume Lotus japonicus resulted in spontaneous activation of nodule organogenesis and mycorrhiza-related gene expression in the absence of microbial symbionts or signalling molecules.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Microbiology and Infectious Disease

    Cell cycle constraints on capsulation and bacteriophage susceptibility

    Silvia Ardissone et al
    A multi-layered and conserved cell cycle mechanism prevents capsulation, long known as a bacterial virulence determinant, in G1-phase and concurrently licenses bacteriophage-mediated genetic exchange prior to entry into S-phase.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Genomics and Evolutionary Biology
    2. Microbiology and Infectious Disease

    Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post–transfer refinement

    Joshua K Michener et al
    Adapting bacteria to use an introduced metabolic pathway recapitulates natural mutations and offers a novel bioremediation strategy.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Neuroscience

    Interpretive monitoring in the caudate nucleus

    Marianna Yanike, Vincent P Ferrera
    The caudate region of the brain signals the context in which sensory evidence is evaluated, helping animals to adapt their behavior to changing conditions.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Cell Biology
    2. Human Biology and Medicine

    Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer

    Keren Yizhak et al
    Genome-scale metabolic modeling of individual cancer cells and healthy human cells identifies specific and selective metabolic vulnerabilities.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biophysics and Structural Biology

    High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force-generation

    Zhiguo Shang et al
    Microtubule attachment fundamentally modifies kinesin's behavior by triggering a ‘clamshell’ opening of the nucleotide cleft, subsequently reversed by ATP binding, that couples to cargo translocation.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Cell Biology
    2. Neuroscience

    Fast retrieval and autonomous regulation of single spontaneously recycling synaptic vesicles

    Jeremy Leitz, Ege T Kavalali
    Spontaneous fusion of vesicles at synapses is regulated independently of fusion triggered by action potentials, adding to evidence that the two types of fusion have distinct functions.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biochemistry
    2. Genes and Chromosomes

    The long non-coding RNA Dali is an epigenetic regulator of neural differentiation

    Vladislava Chalei et al
    Dali regulates transcription of the Pou3f3 locus locally and binds and regulates active promoters in trans by modulating DNA methylation status.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Developmental Biology and Stem Cells
    2. Human Biology and Medicine

    RUNX1, a transcription factor mutated in breast cancer, controls the fate of ER-positive mammary luminal cells

    Maaike PA van Bragt et al
    Loss of RUNX1, a key regulator of estrogen receptor-positive luminal breast cells, impairs mammary epithelial differentiation and contributes to luminal breast cancer via genetic interactions with a loss of p53 or RB1.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Immunology

    Lymph node stromal cells constrain immunity via MHC class II self-antigen presentation

    Antonio P Baptista et al
    MHC class II-mediated self-antigen presentation by lymph node stromal cells controls regulatory T cell homeostasis, thus safeguarding immune tolerance.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biochemistry
    2. Developmental Biology and Stem Cells

    The dyskerin ribonucleoprotein complex as an OCT4/SOX2 coactivator in embryonic stem cells

    Yick W Fong et al
    A previously unrecognized transcriptional coactivator function of the dyskerin ribonucleoprotein complex and its associated small nucleolar RNA has been uncovered and mediates embryonic stem cell-specific transcription.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Human Biology and Medicine
    2. Microbiology and Infectious Disease

    A genetically attenuated malaria vaccine candidate based on P. falciparum b9/slarp gene-deficient sporozoites

    Ben C L van Schaijk et al
    The preclinical evaluation of a malaria genetically attenuated parasite vaccine candidate suggests that it is both safe and effective.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Computational and Systems Biology
    2. Genes and Chromosomes

    Transcription mediated insulation and interference direct gene cluster expression switches

    Tania Nguyen et al
    The formation of mutually exclusive coding and non-coding transcription units contributes to transcriptional interference and insulation at gene clusters and manages state-switching in response to environmental change.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Neuroscience

    Synaptic plasticity and cognitive function are disrupted in the absence of Lrp4

    Andrea M Gomez et al
    Lrp4 mutant mice display profound deficits in cognitive tasks that assess learning and memory with disruptions in the subcellular organization of synaptic inputs and synaptic plasticity in the hippocampus.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Immunology

    Epigenetic modulation of type-1 diabetes via a dual effect on pancreatic macrophages and β cells

    Wenxian Fu et al
    A short treatment of the NOD mouse model of type-1 diabetes with I-BET151, a small molecule bromodomain blocker, provides long-term protection from disease by inducing macrophages to adapt an anti-inflammatory tenor whilst promoting islet β cell regeneration.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Epidemiology and Global Health

    Modelling the contribution of the hypnozoite reservoir to Plasmodium vivax transmission

    Michael T White et al
    Mathematical models of the build-up and depletion of the hypnozoite reservoir in the liver can inform the design of treatment strategies for preventing Plasmodium vivax relapse infections.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Cell Biology
    2. Human Biology and Medicine

    miR-142 regulates the tumorigenicity of human breast cancer stem cells through the canonical WNT signaling pathway

    Taichi Isobe et al
    Insights into the roles and mechanisms of two of the miRNAs upregulated in human breast cancer stem cells in at least some breast cancers are presented.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Neuroscience

    Intercollicular commissural connections refine the representation of sound frequency and level in the auditory midbrain

    Llwyd David Orton, Adrian Rees
    Deactivation of one side of the auditory midbrain while recording in the other shows that the two sides cooperate in processing frequency and in enhancing the encoding of sound level.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Genes and Chromosomes
    2. Plant Biology

    Transposition-mediated DNA re-replication in maize

    Jianbo Zhang et al
    Transposition reactions that occur during DNA replication and involve the termini of adjacent transposons can induce genome expansion by re-replication of transposon-flanking sequences.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Neuroscience

    MicroRNA-9 controls dendritic development by targeting REST

    Sebastian A Giusti et al
    Conditional transgenic miR-9 sponge mice exhibit developmental defects in dendrite growth due to up-regulation of the transcriptional repressor REST.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Cell Biology

    Role of SAGA in the asymmetric segregation of DNA circles during yeast ageing

    Annina Denoth-Lippuner et al
    The SAGA complex binds non-chromosomal DNA circles and prevents their spreading by attaching them to nuclear pores, thereby leading to the concomitant accumulation of DNA circles and pores in ageing yeast mother cells.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Neuroscience

    Reinstatement of long-term memory following erasure of its behavioral and synaptic expression in Aplysia

    Shanping Chen et al
    Storage of long-term memory in Aplysia does not require stable synapses.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Neuroscience

    Variance predicts salience in central sensory processing

    Ann M Hermundstad et al
    Psychophysical measures of human sensitivity to visual patterns reveal that the brain preferentially processes those features of stimuli that are more variable in the natural world.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Neuroscience

    Drep-2 is a novel synaptic protein important for learning and memory

    Till F M Andlauer et al
    Drep-2 is the first representative of the evolutionary conserved CIDE-N protein family found at synapses and is required for associative learning by functionally intersecting with metabotropic signaling.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Neuroscience

    Dendritic Na+ spikes enable cortical input to drive action potential output from hippocampal CA2 pyramidal neurons

    Qian Sun et al
    In the hippocampus, dendritic Na + spikes are required for signals from the entorhinal cortex to drive action potentials in CA2-but not CA1 or CA3-pyramidal neurons.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biophysics and Structural Biology
    2. Microbiology and Infectious Disease

    Ionic selectivity and thermal adaptations within the voltage-gated sodium channel family of alkaliphilic Bacillus

    Paul G DeCaen et al
    Not all members of the bacteria sodium channel family are sodium channels - those found in Bacillus are highly adaptable and can be converted into many selectivity types.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Immunology

    Autophagy is a critical regulator of memory CD8+ T cell formation

    Daniel J Puleston et al
    Autophagy is required for CD8+ T cell memory formation; in aged individuals autophagy levels are diminished, and increasing autophagy enhances their CD8+ T cell responses.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Cell Biology

    A stress assembly that confers cell viability by preserving ERES components during amino-acid starvation

    Margarita Zacharogianni et al
    Amino-acid starvation leads to the formation of a reversible stress assembly, the Sec body, which is a pro-survival reservoir for components of the ER exit sites.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Genomics and Evolutionary Biology

    Predicting evolution from the shape of genealogical trees

    Richard A Neher et al
    A general method for inferring fitness from a sample of nucleotide sequences can predict the progenitor of next year's seasonal influenza.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biochemistry
    2. Biophysics and Structural Biology

    Structural basis of diverse membrane target recognitions by ankyrins

    Chao Wang et al
    The 24 ankyrin repeats of ankyrin proteins form an extended solenoid that provides an extremely conserved groove for binding to numerous targets via combinatorial usage of multiple weak interaction sites.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biophysics and Structural Biology
    2. Neuroscience

    The accessory helix of complexin functions by stabilizing central helix secondary structure

    Daniel T Radoff et al
    A deeply conserved feature of complexin's secondary structure underlies its inhibitory function despite poor primary sequence conservation.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Genes and Chromosomes
    2. Genomics and Evolutionary Biology

    Evolving a 24-hr oscillator in budding yeast

    Gregg A Wildenberg, Andrew W Murray
    New complex traits can evolve through the elimination of genes in multiple unrelated pathways, rather than through the creation of new gene functions.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biochemistry
    2. Biophysics and Structural Biology

    Lis1 regulates dynein by sterically blocking its mechanochemical cycle

    Katerina Toropova et al
    Structural and functional studies reveal how a ubiquitous regulator of dynein keeps the microtubule-based motor in a persistent track-bound state.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Cell Biology

    Integrated control of transporter endocytosis and recycling by the arrestin-related protein Rod1 and the ubiquitin ligase Rsp5

    Michel Becuwe, Sébastien Léon
    A novel regulatory step in the endocytic pathway, which occurs post-internalization, takes place at the trans-Golgi network and involves the arrestin-related protein Rod1 and the ubiquitin ligase Rsp5.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Genomics and Evolutionary Biology
    2. Human Biology and Medicine

    Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state

    Yarden Katz et al
    Genetic mouse models and human cell lines show that Musashi proteins promote an epithelial/luminal state and inhibit epithelial–mesenchymal transition (EMT), and genome-wide maps of translational regulatory targets connect Musashi proteins to an epithelial alternative splicing program and to the regulation of EMT.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Neuroscience

    Functional fission of parvalbumin interneuron classes during fast network events

    Csaba Varga et al
    There is surprising functional splitting of major hippocampal GABA cell classes during high-frequency network oscillations that doubles the repertoire of spatio-temporal patterns of GABA release.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Genes and Chromosomes

    The transcription factor FOXL2 mobilizes estrogen signaling to maintain the identity of ovarian granulosa cells

    Adrien Georges et al
    FOXL2 maintenance of ovarian identity is not solely due to a simple direct repression of Sox9 but to the mobilization of estrogen signalling by FOXL2.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Biochemistry

    Identification of ‘erasers’ for lysine crotonylated histone marks using a chemical proteomics approach

    Xiucong Bao et al
    Sirt3 functions as decrotonylase to regulate histone crotonylation dynamics.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf
    1. Genes and Chromosomes
    2. Human Biology and Medicine

    Dominant drug targets suppress the emergence of antiviral resistance

    Elizabeth J Tanner et al
    When antiviral compounds target oligomeric assemblages, the formation of chimeric oligomers within cells can negate selection for naturally occurring drug-resistant variants.
    Research Article
    Available as full, typeset article htmlAvailable as authors' accepted manuscript pdf