March 2015

Research articles

    1. Plant Biology

    Flowering time and seed dormancy control use external coincidence to generate life history strategy

    Vicki Springthorpe, Steven Penfield
    Models of plant behaviour show that flowering early in a warming world is an adaptive strategy to insulate progeny seed behaviour from the affects of climate change.
    1. Cell Biology
    2. Neuroscience

    CaRuby-Nano: a novel high affinity calcium probe for dual color imaging

    Mayeul Collot et al.
    CaRuby-Nano is a novel red-emitting and highly sensitive functionalizable calcium indicator with a wide range of applications in neuroscience and cell biology.
    1. Cell Biology
    2. Neuroscience

    A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila

    Sonal Nagarkar-Jaiswal et al.
    A large collection of functional EGFP tagged proteins derived from MiMIC insertions allows examination of protein expression in unfixed tissues and efficient tissue specific reversible knock down of proteins.
    1. Ecology
    2. Genomics and Evolutionary Biology

    Brood care in a 100-million-year-old scale insect

    Bo Wang et al.
    The discovery of the earliest direct evidence of brood care in insects demonstrates a remarkably conserved egg-brooding reproductive strategy within scale insects in stasis for nearly 100 million years.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Spectrin regulates Hippo signaling by modulating cortical actomyosin activity

    Hua Deng et al.
    A contractile structural protein of the membrane-associated cytoskeleton is a Hippo signaling component that works through the regulation of non-muscle myosin activity in Drosophila.
    1. Biochemistry
    2. Cell Biology

    The Rab6-regulated KIF1C kinesin motor domain contributes to Golgi organization

    Peter L Lee et al.
    Rab6A binds directly to both the C-terminus and the N-terminal motor domain of the kinesin KIF1C to regulate vesicle motility and Golgi organization.
    1. Genes and Chromosomes

    The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism

    Timothy J Parnell et al.
    A combination of genetics, expression, genomic localization, and genomic nucleosome profiling demonstrates antagonism between two chromatin remodelers that reveal different mechanisms at different promoter architectures.
    1. Biochemistry
    2. Cell Biology

    Oxyntomodulin regulates resetting of the liver circadian clock by food

    Dominic Landgraf et al.
    The gut-released peptide oxyntomodulin mediates the alignment of liver clock gene and metabolic transcript rhythms with the timing of food intake by postprandial induction of hepatic Per gene expression.
    1. Cell Biology

    G-protein-coupled receptors regulate autophagy by ZBTB16-mediated ubiquitination and proteasomal degradation of Atg14L

    Tao Zhang et al.
    Under normal nutritional conditions, G-protein coupled receptors can control autophagy by regulating the degradation of key autophagic regulator Atg14L through ZBTB16-mediated ubiquitination and proteasome degradation.
    1. Developmental Biology and Stem Cells

    Hematopoietic stem and progenitor cells regulate the regeneration of their niche by secreting Angiopoietin-1

    Bo O Zhou et al.
    Normal hematopoietic stem and progenitor cells slow the regeneration of their niche after injury to minimize leakage from the niche vasculature.
    1. Neuroscience

    The self-organization of grid cells in 3D

    Federico Stella, Alessandro Treves
    A computational model for the formation of neural networks of grid cells in virtual bats suggests that the highly ordered networks presumed to support spatial navigation in two dimensions cannot be routinely established in three-dimensional space.
    1. Genomics and Evolutionary Biology
    2. Plant Biology

    Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid

    Jia Wang et al.
    The expression of small RNAs (or sRNAs) is regulated not only by mRNA expression, but also by their own regulatory elements and by sRNA biogenesis genes.
    1. Genes and Chromosomes
    2. Genomics and Evolutionary Biology

    Juxtaposition of heterozygous and homozygous regions causes reciprocal crossover remodelling via interference during Arabidopsis meiosis

    Piotr A Ziolkowski et al.
    Heterozygosity changes the balance between interfering and non-interfering crossovers during Arabidopsis meiosis.
    1. Developmental Biology and Stem Cells

    Post-transcriptional regulation of satellite cell quiescence by TTP-mediated mRNA decay

    Melissa A Hausburg et al.
    The protein Tristetraprolin promotes the decay of MyoD mRNA to maintain satellite cell quiescence.
    1. Biophysics and Structural Biology

    Bovine F1Fo ATP synthase monomers bend the lipid bilayer in 2D membrane crystals

    Chimari Jiko et al.
    The transmembrane shape of the F1Fo ATP synthase monomer provides the molecular basis of high curvature at the ridges of mammalian mitochondrial cristae.
    1. Cell Biology
    2. Genomics and Evolutionary Biology

    Neurofibromin controls macropinocytosis and phagocytosis in Dictyostelium

    Gareth Bloomfield et al.
    Inactivation of the Dictyostelium orthologue of the tumour suppressor Neurofibromin (NF1) enables amoebae to ingest dissolved nutrients using macropinocytosis more rapidly, and to prey on larger organisms using phagocytosis.
    1. Cell Biology
    2. Human Biology and Medicine

    Lpcat3-dependent production of arachidonoyl phospholipids is a key determinant of triglyceride secretion

    Xin Rong et al.
    The enzyme Lpcat3 plays a unique role in the incorporation of arachidonic acid into membranes, which is required for the production of lipoproteins.
    1. Genomics and Evolutionary Biology

    RNA chaperones buffer deleterious mutations in E. coli

    Marina Rudan et al.
    The overexpression of RNA chaperones, including several DEAD box RNA helicases, enhances the fitness of mutationally compromised E. coli strains.
    1. Developmental Biology and Stem Cells
    2. Plant Biology

    Three ancient hormonal cues co-ordinate shoot branching in a moss

    Yoan Coudert et al.
    The mosses and angiosperms have independently evolved mechanisms that use the same hormones-auxin, cytokinin and strigolactone-to regulate lateral shoot branching.
    1. Genes and Chromosomes

    Recombination occurs within minutes of replication blockage by RTS1 producing restarted forks that are prone to collapse

    Michael O Nguyen et al.
    Homologous recombination is the default response to replication impedance by the RTS1 barrier, leading to restarted replication forks that suffer frequent collapse, triggering further rounds of recombination downstream of the barrier.
    1. Genes and Chromosomes
    2. Genomics and Evolutionary Biology

    Non-crossover gene conversions show strong GC bias and unexpected clustering in humans

    Amy L Williams et al.
    In humans, non-crossover gene conversion events transmit GC alleles in 68% of cases and exhibit a complex pattern of multiple disconnected tracts clustered within 20–30 kilobase intervals.
    1. Genomics and Evolutionary Biology

    Experimental evolution reveals hidden diversity in evolutionary pathways

    Peter A Lind et al.
    Genetic architecture governs the evolvability of adaptive paths providing a framework for evolutionary forecasting.
    1. Biochemistry
    2. Genes and Chromosomes

    Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells

    Patrick Laurette et al.
    The PBAF chromatin-remodelling complex is essential for the proliferation of melanocytes and melanoma cells and is recruited to critical regulatory elements by physical and functional interactions with MITF, a transcription factor and master regulator of melanoma.
    1. Developmental Biology and Stem Cells

    In vitro generation of human pluripotent stem cell derived lung organoids

    Briana R Dye et al.
    Directed differentiation of stem cells can generate ventral-anterior foregut spheroids that can expand into three-dimensional lung organoids with striking structural, cellular and molecular similarities to the human fetal lung.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    FBN-1, a fibrillin-related protein, is required for resistance of the epidermis to mechanical deformation during C. elegans embryogenesis

    Melissa Kelley et al.
    A fibrillin-related protein, FBN-1, is a key component of the apical extracellular matrix and prevents epidermal cell deformation by biomechanical forces during morphogenesis of the C. elegans embryo.
    1. Cell Biology
    2. Developmental Biology and Stem Cells

    The polarity protein Baz forms a platform for the centrosome orientation during asymmetric stem cell division in the Drosophila male germline

    Mayu Inaba et al.
    The stem cell orientation checkpoint senses the correct orientation of centrosomes via their interactions with a protein called Bazooka.
    1. Ecology
    2. Neuroscience

    Range-dependent flexibility in the acoustic field of view of echolocating porpoises (Phocoena phocoena)

    Danuta M Wisniewska et al.
    Harbor porpoises dynamically control biosonar field of view as they track and capture prey, focusing the beam through deformations to the melon.
    1. Cell Biology
    2. Human Biology and Medicine

    Increased H+ efflux is sufficient to induce dysplasia and necessary for viability with oncogene expression

    Bree K Grillo-Hill et al.
    Increasing the internal pH of cells can induce dysplasia and enhance oncogene-increased cell growth, while decreasing the internal pH combined with oncogene expression leads to synthetic lethality.
    1. Biochemistry

    The zinc finger proteins ZNF644 and WIZ regulate the G9a/GLP complex for gene repression

    Chunjing Bian et al.
    Repression of gene expression by the histone methyltransferase G9a is guided by two zinc finger proteins that can recognize consensus sequences in DNA.
    1. Cell Biology
    2. Genomics and Evolutionary Biology

    COMP-1 promotes competitive advantage of nematode sperm

    Jody M Hansen et al.
    Nematode sperm respond to competitive environments by modulating cellular pathways involved in migration and storage to ensure their access to oocytes.
    1. Biochemistry

    A secretory kinase complex regulates extracellular protein phosphorylation

    Jixin Cui et al.
    A pseudokinase in the secretory pathway, Fam20A, activates the real Golgi casein kinase, Fam20C, via a unique mechanism that is lost in human diseases.
    1. Neuroscience

    General features of the retinal connectome determine the computation of motion anticipation

    Jamie Johnston, Leon Lagnado
    Feedforward inhibition generates motion anticipation by selectively decreasing sensitivity to a stimulus as it moves across the latter part of a retinal ganglion cell's receptive field.
    1. Immunology
    2. Microbiology and Infectious Disease

    Dengue vascular leakage is augmented by mast cell degranulation mediated by immunoglobulin Fcγ receptors

    Ayesa Syenina et al.
    Building on previous work (St John et al., 2013), we explain why secondary infection by dengue virus is associated with more severe vascular disease than primary infection.
    1. Biophysics and Structural Biology

    Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

    Monarin Uervirojnangkoorn et al.
    Post-refinement methods enable the use of X-ray free electron lasers for biological crystallography of systems in which sample quantity is a limitation.
    1. Genes and Chromosomes
    2. Genomics and Evolutionary Biology

    Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

    Kazuhiro R Nitta et al.
    Drosophila has almost all transcription factor binding specificities available to humans; and human transcription factors with divergent specificities operate in cell types that are not found in fruit flies.
    1. Neuroscience

    Sensitization of neonatal rat lumbar motoneuron by the inflammatory pain mediator bradykinin

    Mouloud Bouhadfane et al.
    The pain mediator bradykinin was found to sensitize spinal motoneurons by a direct postsynaptic action, questioning the role of motoneurons in the assessment of hyperalgesia since the withdrawal motor reflex is commonly used as a surrogate pain model.
    1. Genomics and Evolutionary Biology

    Linking traits based on their shared molecular mechanisms

    Yael Oren et al.
    Systematic analysis of a broad spectrum of behavioral and physiological traits reveals novel relationships among complex traits, and resolves their underlying combination of genetic loci and molecular mechanisms.
    1. Biophysics and Structural Biology
    2. Cell Biology

    Secreted CLCA1 modulates TMEM16A to activate Ca2+-dependent chloride currents in human cells

    Monica Sala-Rabanal et al.
    A functional link between representative family members of the CLCA channel regulator family and TMEM16 channels suggests that these protein families may cooperate in influencing multiple homeostatic and disease physiologies.
    1. Ecology
    2. Genomics and Evolutionary Biology

    Social networks predict gut microbiome composition in wild baboons

    Jenny Tung et al.
    Social interactions can have a direct effect on the composition of the gut microbiome in wild primates.
    1. Biochemistry
    2. Cell Biology

    Actin dynamics tune the integrated stress response by regulating eukaryotic initiation factor 2α dephosphorylation

    Joseph E Chambers et al.
    Monomeric actin forms a crucial component of the eIF2α holophosphatase linking the integrated stress response to actin polymeric status.
    1. Genes and Chromosomes

    Rapid epigenetic adaptation to uncontrolled heterochromatin spreading

    Jiyong Wang et al.
    Redundant pathways prevent heterochromatin spreading and ectopic heterochromatin assembly; and plasticity of heterochromatin assembly allows cells to adapt to heterochromatin stress.
    1. Biochemistry
    2. Biophysics and Structural Biology

    G-actin provides substrate-specificity to eukaryotic initiation factor 2α holophosphatases

    Ruming Chen et al.
    The biochemical basis for coupling cytoskeletal dynamics to regulated protein synthesis has been revealed.
    1. Neuroscience

    Ventromedial prefrontal cortex stimulation enhances memory and hippocampal neurogenesis in the middle-aged rats

    Albert Liu et al.
    High-frequency stimulation of the ventromedial prefrontal cortex, which enhances memory and hippocampal neurogenesis, is a novel target for treatment of dementia-related diseases.
    1. Genomics and Evolutionary Biology
    2. Plant Biology

    Evolution of alternative biosynthetic pathways for vitamin C following plastid acquisition in photosynthetic eukaryotes

    Glen Wheeler et al.
    Genomic evidence suggests that L-gulonolactone oxidase-the terminal enzyme in vitamin C synthesis, which has been repeatedly lost throughout animal evolution-was lost in plants and other photosynthetic eukaryotes following plastid acquisition.
    1. Neuroscience

    The Ret receptor regulates sensory neuron dendrite growth and integrin mediated adhesion

    Peter Soba et al.
    A cell surface receptor called Ret enables neurons to establish and maintain the organized arrays of dendrites that support communication between neurons.
    1. Genomics and Evolutionary Biology

    Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation

    Christopher E Laumer et al.
    A phylogeny of all major groups of flatworms based on hundreds of genes sheds new light the early evolution of this important metazoan phylum, with particular significance for the original of vertebrate parasitism.
    1. Cell Biology
    2. Immunology

    Actin foci facilitate activation of the phospholipase C-γ in primary T lymphocytes via the WASP pathway

    Sudha Kumari et al.
    T cell receptor signaling is regulated by newly polymerized F-actin foci at the immunological synapse.
    1. Cell Biology
    2. Human Biology and Medicine

    No turnover in lens lipids for the entire human lifespan

    Jessica R Hughes et al.
    The carbon in lens membrane lipids correlates to the year of birth of an individual, a phenomenon that is unprecedented in the current body of literature.
    1. Biophysics and Structural Biology

    2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy

    Melody G Campbell et al.
    Water molecules and amino-acid side chain rotamers have been resolved in the cryoEM structure of T20S proteasome at 2.8 angstroms.
    1. Neuroscience

    Decoding a neural circuit controlling global animal state in C. elegans

    Patrick Laurent et al.
    Sensory neurons that monitor ambient oxygen control a cascade of responses across multiple layers of interneurons to switch the global state of the nematode C. elegans, reprogramming behavior and gene expression to enable escape from or adaptation to surface exposure.
    1. Immunology
    2. Microbiology and Infectious Disease

    Cytotoxic activities of CD8+ T cells collaborate with macrophages to protect against blood-stage murine malaria

    Takashi Imai et al.
    The cytotoxicity exerted by CD8+ T cells against parasitized erythroblasts helps to protect against blood-stage malaria by making parasitized cells susceptible to phagocytosis.
    1. Ecology
    2. Microbiology and Infectious Disease

    Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

    Nicholas A Bokulich et al.
    Mapping microbial landscapes in indoor environments can predict how contaminants and spoilage resistance genes propagate within food-production environments, yielding novel insight for controlling spoilage.
    1. Microbiology and Infectious Disease

    Herpes simplex type 2 virus deleted in glycoprotein D protects against vaginal, skin and neural disease

    Christopher Petro et al.
    An attenuated Herpes simplex type 2 virus deleted in glycoprotein D can be used as an effective vaccine to provide robust transferable humoral immunity and complete protection in murine intravaginal and skin infection models.
    1. Biochemistry
    2. Neuroscience

    DNA damage shifts circadian clock time via Hausp-dependent Cry1 stabilization

    Stephanie J Papp et al.
    The circadian clock proteins, cryptochrome 1 (Cry1) and 2 (Cry2), evolved from bacterial light-activated DNA repair enzymes to detect DNA damage and coordinate the gene expression response.
    1. Biophysics and Structural Biology

    Structural dynamics of myosin 5 during processive motion revealed by interferometric scattering microscopy

    Joanna Andrecka et al.
    Single molecule imaging reveals how the molecular motor myosin 5 walks in a compass-like spinning motion along its actin track resulting in efficient, robust and unidirectional motion on the nanoscale.
    1. Biophysics and Structural Biology
    2. Cell Biology

    Importin-β modulates the permeability of the nuclear pore complex in a Ran-dependent manner

    Alan R Lowe et al.
    The Ran GTPase plays a role in defining the physical properties of the nuclear pore complex transport channel by remodeling the binding interactions of importin-β with the nucleoporin Nup153 at the nuclear face of the pore.
    1. Neuroscience

    Ventromedial hypothalamic neurons control a defensive emotion state

    Prabhat S Kunwar et al.
    Stimulation of specific neurons within the hypothalamus triggers a fear-like emotion state and behavioral response in mice, challenging the textbook view that the hypothalamus serves simply as a relay for emotion states encoded in the amygdala.
    1. Genes and Chromosomes
    2. Genomics and Evolutionary Biology

    A map of directional genetic interactions in a metazoan cell

    Bernd Fischer et al.
    A systematic analysis of gene–gene dependencies using high-throughput imaging of cells detects causal and temporal relationships between genes.
    1. Cell Biology
    2. Plant Biology

    Auxin regulates SNARE-dependent vacuolar morphology restricting cell size

    Christian Löfke et al.
    Vacuolar morphologenesis correlates with cell size and is required for auxin-dependent inhibition of growth.
    1. Genes and Chromosomes
    2. Neuroscience

    Death following traumatic brain injury in Drosophila is associated with intestinal barrier dysfunction

    Rebeccah J Katzenberger et al.
    Use of a newly developed experimental model in fruit flies reveals that death following traumatic brain injury is largely due to a mechanism by which brain damage triggers disruption of the intestinal barrier, leading to elevated levels of glucose in the circulatory system with deleterious consequences.
    1. Biochemistry
    2. Cell Biology

    The prenyltransferase UBIAD1 is the target of geranylgeraniol in degradation of HMG CoA reductase

    Marc M Schumacher et al.
    The inhibition of sterol-accelerated degradation of HMG CoA reductase by the vitamin K2 synthetic enzyme UBIAD1 may contribute to the accumulation of cholesterol that is associated with Schnyder corneal dystrophy.
    1. Biophysics and Structural Biology
    2. Cell Biology

    Tuning myosin-driven sorting on cellular actin networks

    Rizal F Hariadi et al.
    Competition between the antagonistic motor proteins myosin V and myosin VI finely tunes unidirectional transport of cargo on different actin architectures.
    1. Human Biology and Medicine
    2. Neuroscience

    A striatal-enriched intronic GPCR modulates huntingtin levels and toxicity

    Yuwei Yao et al.
    A cell-surface receptor called Gpr52 is able to lower the levels of the disease-causing protein mutant huntingtin and suppress its toxicity when knocked-down, making this receptor a promising drug target in Huntington's disease.
    1. Epidemiology and Global Health

    Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area

    JA Guerra-Assunção et al.
    A study of tuberculosis cases in the Karonga district of Malawi reveals that the main lineages of M. tuberculosis differ in their transmission patterns and virulence.
    1. Neuroscience

    A social chemosignaling function for human handshaking

    Idan Frumin et al.
    After shaking hands with a stranger, human volunteers often subliminally bring their hand to their nose and sniff it, possibly to collect important olfactory information.
    1. Neuroscience

    Impaired fast-spiking interneuron function in a genetic mouse model of depression

    Jonas-Frederic Sauer et al.
    Truncated Disrupted-in-schizophrenia 1 (Disc 1) ablates signaling of parvalbumin-expressing interneurons in the prefrontal cortex and underlies depression-related behaviour in mice.
    1. Genomics and Evolutionary Biology
    2. Microbiology and Infectious Disease

    Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

    Tali Raveh-Sadka et al.
    Rapid yet comprehensive, genome-resolved analysis of fecal samples from premature infants reveals little overlap in strain composition of gut microbial communities, despite co-hospitalization, and suggests the existence of barriers to strain dispersal.

Magazine

    1. Neuroscience

    Social Chemosignaling: The scent of a handshake

    Gün R Semin, Ana Rita Farias
    1. Genes and Chromosomes

    Epigenetics: Silencing sounds off

    Yu-Fan Chen, Marc R Gartenberg