November 2018

Research articles

    1. Developmental Biology
    2. Evolutionary Biology

    A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates

    Abbey C Thompson et al.
    Regulatory sequences downstream of a key limb identity gene are required for normal sizes of leg bones, and are changed in wild species with dramatic alterations in pelvic structures.
    1. Cancer Biology

    Rejection of immunogenic tumor clones is limited by clonal fraction

    Ron S Gejman et al.
    A new, high-throughput in vivo MHC-I peptide minigene library platform shows that the naive immune system cannot eliminate cells presenting immunogenic antigens found at low frequencies within a growing tumor.
    1. Neuroscience

    Rat behavior and dopamine release are modulated by conspecific distress

    Nina T Lichtenberg et al.
    Rat behavior and dopamine release are preferentially modulated by subjective rather than objective evaluation of outcomes in a social setting.
    1. Chromosomes and Gene Expression

    Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome

    Srivarsha Rajshekar et al.
    Derepression of transcripts from hypomethylated pericentromeric repeats triggers an innate immune response in an animal model of Immunodeficency, Centromere and Facial anomalies (ICF) syndrome.
    1. Biochemistry and Chemical Biology

    Translation attenuation by minocycline enhances longevity and proteostasis in old post-stress-responsive organisms

    Gregory M Solis et al.
    Directly targeting the ribosome to attenuate translation partly mimics the integrated stress response, increasing lifespan and preserving protein folding capacity even in older individuals with dysfunctional stress response signaling.
    1. Biochemistry and Chemical Biology

    Selective agonist of TRPML2 reveals direct role in chemokine release from innate immune cells

    Eva Plesch et al.
    Direct and selective activation of TRPML2 promotes macrophage migration through release of CCL2.
    1. Developmental Biology
    2. Physics of Living Systems

    Theoretical tool bridging cell polarities with development of robust morphologies

    Silas Boye Nissen et al.
    Biological shapes and morphological transitions can emerge from combining directed interactions between cells with apical-basal and planar cell polarity.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Molecular basis for activation of lecithin:cholesterol acyltransferase by a compound that increases HDL cholesterol

    Kelly A Manthei et al.
    Structure of lecithin:cholesterol acyltransferase with a covalent acyl-intermediate mimic and a small molecule activator reveals an active conformation and that the enzyme can be activated via its membrane binding domain.
    1. Neuroscience

    Augmented reality powers a cognitive assistant for the blind

    Yang Liu et al.
    A non-invasive cognitive assistant for blind people endows objects in the environment with voices, allowing users to explore the scene, localize objects, and navigate through a building with minimal training.
    1. Cell Biology

    Splicing factors Sf3A2 and Prp31 have direct roles in mitotic chromosome segregation

    Claudia Pellacani et al.
    Extensive cytological and biochemical analyses show that the conserved Sf3A2 and Prp31 splicing factors bind microtubules and the Ndc80 complex, playing direct mitotic functions in both Drosophila and human mitosis.
    1. Neuroscience

    Endocytosis at the Drosophila blood–brain barrier as a function for sleep

    Gregory Artiushin et al.
    Endocytosis through the Drosophila blood–brain barrier influences and depends upon sleep.
    1. Developmental Biology

    ppargc1a controls nephron segmentation during zebrafish embryonic kidney ontogeny

    Joseph M Chambers et al.
    The transcriptional coactivator ppargc1a regulates the renal progenitor patterning to delineate boundary formation of differentiated segment populations during nephrogenesis.
    1. Neuroscience

    Variance adaptation in navigational decision making

    Ruben Gepner et al.
    Fruit fly larvae adapt their decision-making process to the variability of the environment, illuminating the structure of adaptation in the underlying neural substrates.
    1. Cancer Biology
    2. Genetics and Genomics

    Targets and genomic constraints of ectopic Dnmt3b expression

    Yingying Zhang et al.
    Ectopic expression of Dnmt3b leads to wide-spread CpG island hypermethylation that is largely defined by chromatin state and has some distinct features when compared to the cancer methylome.
    1. Neuroscience

    Decision and navigation in mouse parietal cortex

    Michael Krumin et al.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    ASH1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin

    Vincent T Bicocca et al.
    While SET-2 methylates histone H3K36 during transcription, ASH1 methylates this residue in repressed regions, is important for silencing, and can both positively and negatively influence methylation of histone H3K27.
    1. Neuroscience

    A time-stamp mechanism may provide temporal information necessary for egocentric to allocentric spatial transformations

    Avner Wallach et al.
    A novel neural mechanism for precise, unbiased estimation of time intervals in the thalamus of electric fish is likely used for computing distance between object encounters.
    1. Neuroscience

    Sensorimotor pathway controlling stopping behavior during chemotaxis in the Drosophila melanogaster larva

    Ibrahim Tastekin et al.
    The reconstruction of a sensorimotor pathway from the olfactory-sensory neurons down to the pre-motor system reveals a descending neuron that plays a critical role in the organization of larval chemotaxis.
    1. Structural Biology and Molecular Biophysics

    The CryoEM structure of the Saccharomyces cerevisiae ribosome maturation factor Rea1

    Piotr Sosnowski et al.
    The high-resolution structure of Rea1, an essential ribosome maturation factor in Saccharomyces cerevisiae, explains how the ATPase domain is regulated and reveals the linker domain, the mechanical element carrying out ribosome remodeling.
    1. Biochemistry and Chemical Biology

    Random-sequence genetic oligomer pools display an innate potential for ligation and recombination

    Hannes Mutschler et al.
    Random sequence RNA pools display an innate capacity for ligation and recombination, enabling them to “bootstrap” themselves towards higher compositional, informational and structural complexity.
    1. Microbiology and Infectious Disease

    Rotavirus VP3 targets MAVS for degradation to inhibit type III interferon expression in intestinal epithelial cells

    Siyuan Ding et al.
    Rotavirus infection induces phosphorylation and proteasomal degradation of MAVS to suppress host antiviral interferon signaling.
    1. Neuroscience

    Macro-connectomics and microstructure predict dynamic plasticity patterns in the non-human primate brain

    Sean Froudist-Walsh et al.
    Brain recovery after injury can be predicted based on its activity and structure, which may allow us to understand why some brain injuries lead to permanent loss of cognitive function, while others do not.
    1. Neuroscience

    Expanded genetic screening in Caenorhabditis elegans identifies new regulators and an inhibitory role for NAD+ in axon regeneration

    Kyung Won Kim et al.
    A function-based genetic screen using the Caenorhabditis elegans axotomy model identifies new regulators and an inhibitory role for NAD+ in axon regeneration, expanding the understanding of axon injury responses and regeneration.
    1. Computational and Systems Biology
    2. Developmental Biology

    A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment

    Kenneth KH Ng et al.
    The timing and outcome of mammalian cell lineage decisions can be controlled by slow, stochastic events on individual regulatory gene loci.
    1. Ecology

    The lost world of Cuatro Ciénegas Basin, a relictual bacterial niche in a desert oasis

    Valeria Souza et al.
    At Cuatro Ciénegas, the ancestral niche conditions of the ancient shores of Laurentia persisted along with its microbial communities that have been coevolving for a very long time.
    1. Neuroscience

    Bright multicolor labeling of neuronal circuits with fluorescent proteins and chemical tags

    Richi Sakaguchi et al.
    A bright and stochastic multicolor labeling method, Tetbow, facilitates millimeters-scale reconstructions of neuronal circuits at a large scale using tissue clearing.
    1. Structural Biology and Molecular Biophysics

    CryoEM structures of open dimers of gyrase A in complex with DNA illuminate mechanism of strand passage

    Katarzyna M Soczek et al.
    CryoEM structures of open gyrase A dimers and DNA in two states representing steps either prior to or after passage through the DNA-gate, show where a putative T-segment is found.
    1. Ecology
    2. Evolutionary Biology

    Reconstructing the functions of endosymbiotic Mollicutes in fungus-growing ants

    Panagiotis Sapountzis et al.
    Domestication of endosymbiotic Mollicutes may have resolved nitrogen-recycling challenges for attine ants and enabled the evolutionary derived leaf-cutting ants to fully exploit their herbivorous niches.
    1. Microbiology and Infectious Disease

    Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature

    Fotini Kokou et al.
    Microbiome and transcriptomic profiling of genetically selected tropical fish with high and low tolerance to cold exposure revealed host control over microbiome composition and response to temperature changes.
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    Genome-wide Estrogen Receptor-α activation is sustained, not cyclical

    Andrew N Holding et al.
    Activation of the Estrogen Receptor by estra-2-diol results in sustained binding and the previously described cyclical response kinetics are likely an artefact of observing a highly variable process without replicates.
    1. Cell Biology
    2. Neuroscience

    Proteolytically released Lasso/teneurin-2 induces axonal attraction by interacting with latrophilin-1 on axonal growth cones

    Nickolai V Vysokov et al.
    Lasso and latrophilin-1 interact across the synapse, while shed Lasso binds latrophilin-1 on distant growth cones and attracts them, providing a universal mechanism for short- and long-range axonal guidance.
    1. Neuroscience

    Sucrose intensity coding and decision-making in rat gustatory cortices

    Esmeralda Fonseca et al.
    The neural representation of perceived sucrose intensity was contained in the firing rate and spike-timing of a 'small' population of neurons distributed across the Insula and Orbitofrontal taste cortices.
    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Lipidation-independent vacuolar functions of Atg8 rely on its noncanonical interaction with a vacuole membrane protein

    Xiao-Man Liu et al.
    The core autophagy protein Atg8 plays non-autophagy roles through binding to an integral membrane protein Hfl1, which harbors an unusual Atg8-interacting motif.
    1. Developmental Biology

    The Toll pathway inhibits tissue growth and regulates cell fitness in an infection-dependent manner

    Federico Germani et al.
    Toll pathway inactivation enhances tissue growth and cell fitness when the environment in which animals develop is not deprived of pathogens.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Mycobacterium tuberculosis induces decelerated bioenergetic metabolism in human macrophages

    Bridgette M Cumming et al.
    Quantifiable bioenergetic parameters, determined from extracellular flux analyses, are distinct between macrophages infected with Mycobacteriumtuberculosis or vaccine strain M. bovis BCG, enabling assessment of future vaccine and drug efficacy.
    1. Cell Biology
    2. Developmental Biology

    Angiopoietin-4-dependent venous maturation and fluid drainage in the peripheral retina

    Harri Elamaa et al.
    Identification of importance of Angiopoietin-4 (Angpt4) as a first growth factor that initiates venous specification in the peripheral retina, and Angpt4-dependent mechanism for fluid clearance in the mouse retina.
    1. Biochemistry and Chemical Biology
    2. Cancer Biology

    Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma

    Gerard L Brien et al.
    BRD9 provides the first actionable therapeutic target in synovial sarcoma tumours that is both biochemically and functionally linked to the SS18-SSX fusion protein which drives disease development.
    1. Microbiology and Infectious Disease

    High-resolution mapping of fluoroquinolones in TB rabbit lesions reveals specific distribution in immune cell types

    Landry Blanc et al.
    Penetration of the fluoroquinolones in tuberculosis lesions is heterogeneous even in fully cellular areas, is driven by macrophage content and decreases as the distance from lesion outer rim increases.
    1. Stem Cells and Regenerative Medicine

    Long-term live imaging of the Drosophila adult midgut reveals real-time dynamics of division, differentiation and loss

    Judy Lisette Martin et al.
    A new platform for imaging live Drosophila adults yields vivid movies of the midgut over prolonged time scales, opening the door to the real-time study of organ renewal dynamics in a near-native context.
    1. Cell Biology
    2. Developmental Biology

    Shear-induced damped oscillations in an epithelium depend on actomyosin contraction and E-cadherin cell adhesion

    Ehsan Sadeghipour et al.
    Cell movement toward and away from the midline of an epithelium over tens of hours are caused by spontaneous or externally-applied shear forces to eliminate force imbalances within the tissue.
    1. Neuroscience

    Decoding hierarchical control of sequential behavior in oscillatory EEG activity

    Atsushi Kikumoto, Ulrich Mayr
    Mental codes that track our position within complex, behavioral sequences, have been hard to pin down empirically, but can be identified and traced over time using oscillatory EEG activity.
    1. Chromosomes and Gene Expression

    A whole lifespan mouse multi-tissue DNA methylation clock

    Margarita V Meer et al.
    A robust mouse multi-tissue age predictor is presented that can be used to assess the DNA methylation age of mouse tissues and test the effects of longevity interventions.
    1. Chromosomes and Gene Expression

    Translesion polymerase kappa-dependent DNA synthesis underlies replication fork recovery

    Peter Tonzi et al.
    Translesion polymerase kappa promotes replication fork restart to maintain genome stability during conditions of nucleotide deprivation.
    1. Neuroscience

    Dopamine neurons drive fear extinction learning by signaling the omission of expected aversive outcomes

    Ximena I Salinas-Hernández et al.
    Dopamine signaling is necessary for normal fear extinction learning.
    1. Cell Biology

    Comment on ‘Orthogonal lipid sensors identify transbilayer asymmetry of plasma membrane cholesterol’

    Kevin C Courtney et al.
    We challenge a recent report that most of the cholesterol in the plasma membrane of mammalian cells is in the exofacial leaflet.
    1. Ecology

    Meta-analysis challenges a textbook example of status signalling and demonstrates publication bias

    Alfredo Sánchez-Tójar et al.
    Meta-analysis takes down a textbook example in behavioural and evolutionary ecology, and demonstrates the existence of biases in the current scientific publishing culture.
    1. Neuroscience

    Molecular mechanisms that stabilize short term synaptic plasticity during presynaptic homeostatic plasticity

    Jennifer M Ortega et al.
    Genetic and electrophysiological experiments define how homeostatic signaling stabilizes both the gain and short-term dynamic properties of neurotransmitter release, ensuring that synaptic information transfer remains robust to external perturbation.
    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Structural basis of tubulin recruitment and assembly by microtubule polymerases with tumor overexpressed gene (TOG) domain arrays

    Stanley Nithianantham et al.
    TOG (tumor overexpressed gene) domains organize then polymerize tubulins at microtubule plus ends.
    1. Neuroscience

    Oxytocin-mediated social enrichment promotes longer telomeres and novelty seeking

    Jamshid Faraji et al.
    Social enrichment supports longevity.
    1. Cell Biology
    2. Neuroscience

    Rescue of cognitive function following fractionated brain irradiation in a novel preclinical glioma model

    Xi Feng et al.
    Whole-brain radiotherapy, but not glioma growth in distal region from the hippocampus, results in impaired recognition memory, which can be prevented by CSF-1R inhibitor-mediated microglia depletion.
    1. Cancer Biology

    Targeting MYC dependency in ovarian cancer through inhibition of CDK7 and CDK12/13

    Mei Zeng et al.
    A multi-transcriptional CDKs inhibitor suppresses MYC and induces regression of ovarian tumors, indicating that targeting CDK7, 12, 13 with THZ1 may be an effective approach for treating MYC-dependent malignancies.
    1. Neuroscience

    Cerebellar learning using perturbations

    Guy Bouvier et al.
    A proposal for a complete cellular/network implementation of trial-and-error motor learning in the olivo-cerebellar system.
    1. Neuroscience

    Hedonic processing in humans is mediated by an opioidergic mechanism in a mesocorticolimbic system

    Christian Buchel et al.
    The pleasure of rewards in humans is mediated by an opioidergic mechanism.
    1. Neuroscience

    TrpV1 receptor activation rescues neuronal function and network gamma oscillations from Aβ-induced impairment in mouse hippocampus in vitro

    Hugo Balleza-Tapia et al.
    TrpV1 receptor activation rescues cognition-relevant network dynamics in mouse hippocampus in an acute Alzheimer disease model providing a novel therapeutic target.
    1. Computational and Systems Biology
    2. Neuroscience

    Subunit exchange enhances information retention by CaMKII in dendritic spines

    Dilawar Singh, Upinder Singh Bhalla
    Due to subunit-exchange, CaMKII can store information at diverse time-scales and might play a central role in the memory maintenance.
    1. Ecology

    Global warming reduces leaf-out and flowering synchrony among individuals

    Constantin M Zohner et al.
    Individuals differ in how their leaf-out and flowering are regulated by abiotic stimuli and, under climate warming, this leads to reduced within-population phenological synchrony, impacting mutualistic and antagonistic community interactions.
    1. Structural Biology and Molecular Biophysics

    New tools for automated high-resolution cryo-EM structure determination in RELION-3

    Jasenko Zivanov et al.
    RELION-3 calculates single-particle reconstructions to higher resolution and with less user-interactions than previously available versions.
    1. Computational and Systems Biology
    2. Developmental Biology

    Tuned polymerization of the transcription factor Yan limits off-DNA sequestration to confer context-specific repression

    C Matthew Hope et al.
    Tuned protein–protein interaction affinity optimizes the repressive function of the ETS family transcription factor Yan in order to contribute specificity and robustness to cell fate specification in the developing Drosophila eye.
    1. Cancer Biology
    2. Stem Cells and Regenerative Medicine

    T-ALL leukemia stem cell 'stemness' is epigenetically controlled by the master regulator SPI1

    Haichuan Zhu et al.
    The identification of key determinants of LSC “stemness” and LSC differentiation that is reversible through an epigenetic mechanism may have considerable implications in understanding leukemia and designing effective therapies.
    1. Structural Biology and Molecular Biophysics

    Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core

    Andrew J Borst et al.
    An integrative structural and biophysical workflow indicates engagement of VRC01 germline antibodies can occur with a gp120 426c core construct containing all wild-type N-linked glycosylation sites, including the Asn276 glycan.
    1. Cell Biology
    2. Neuroscience

    The insulin/IGF signaling cascade modulates SUMOylation to regulate aging and proteostasis in Caenorhabditis elegans

    Lorna Moll et al.
    By controlling the SUMOylation of the protein CAR-1, the aging-regulating pathways downstream of the Insulin/IGF signaling cascade and of the germ cells of the nematode Caenorhabditis elegans are integrated.
    1. Neuroscience

    Light-dependent pathways for dopaminergic amacrine cell development and function

    Teona Munteanu et al.
    Rods, not ipRGCs, are the major retinal photoreceptor impacting development of dopaminergic signaling in the retina.
    1. Cell Biology
    2. Neuroscience

    CRELD1 is an evolutionarily-conserved maturational enhancer of ionotropic acetylcholine receptors

    Manuela D'Alessandro et al.
    The protein disulphide isomerase CRELD1 controls the biosynthesis of nicotinic acetylcholine receptors in nematode and mouse muscle.
    1. Cell Biology

    A pathway for Parkinson’s Disease LRRK2 kinase to block primary cilia and Sonic hedgehog signaling in the brain

    Herschel S Dhekne et al.
    Pathogenic LRRK2kinase requires Rab10 and RILPL1 to block primary cilia formation, shortening cilia on cholinergic neurons needed for a hedgehog driven circuit that supports dopaminergic neurons in mouse brain.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    A bacterial immunomodulatory protein with lipocalin-like domains facilitates host–bacteria mutualism in larval zebrafish

    Annah S Rolig et al.
    Discovery of a secreted protein from resident gut bacteria that reduced intestinal innate immune responses which would otherwise simultaneously compromise both bacterial and host survival.
    1. Ecology
    2. Microbiology and Infectious Disease

    Immune-mediated hookworm clearance and survival of a marine mammal decrease with warmer ocean temperatures

    Mauricio Seguel et al.
    In years with colder ocean temperatures, fur seal pups receive more maternal care and have a better energy balance, clearing hookworm infection earlier, which increases their chances of survival.
    1. Neuroscience

    Current and future goals are represented in opposite patterns in object-selective cortex

    Anouk Mariette van Loon et al.
    Multivoxel pattern of fMRI data reveals how the brain distinguishes between relevant and irrelevant representations as representations adapt to the order in which they are required in multiple task sequences.
    1. Developmental Biology

    A novel mechanism of gland formation in zebrafish involving transdifferentiation of renal epithelial cells and live cell extrusion

    Richard W Naylor et al.
    A rare example of direct transdifferentiation is discovered in zebrafish in which kidney epithelial cells change into an endocrine gland and undergo live-cell extrusion from the renal tubule.
    1. Neuroscience

    Value-based attentional capture affects multi-alternative decision making

    Sebastian Gluth et al.
    Speeded value-based decisions between two options can be affected by a third, high-value distractor that captures attention and slows down the choice process.
    1. Evolutionary Biology
    2. Neuroscience

    Recalibrating timing behavior via expected covariance between temporal cues

    Benjamin J De Corte et al.
    Rats act as if they expect that the delays associated with temporal cues will covary due to a common causal factor.
    1. Neuroscience

    Altered hippocampal interneuron activity precedes ictal onset

    Mitra L Miri et al.
    GABAergic interneuron populations in the hippocampus exhibit cell-type-specific patterns of disruption in advance of seizure onset.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Plasmodium-specific atypical memory B cells are short-lived activated B cells

    Damián Pérez-Mazliah et al.
    Plasmodium-specific atypical memory B cells generated to naturally (mosquito) transmitted rodent malaria infection are short-lived activated B cells, and do not prevent resolution of infection or generation of long-lived memory.
    1. Neuroscience

    CA2 neuronal activity controls hippocampal low gamma and ripple oscillations

    Georgia M Alexander et al.
    Hippocampal area CA2 controls low gamma and ripple oscillations, brain waves known to be impaired in schizophrenia, implicating this important brain region in cognition.
    1. Neuroscience

    Deletion of KCNQ2/3 potassium channels from PV+ interneurons leads to homeostatic potentiation of excitatory transmission

    Heun Soh et al.
    Loss of potassium channel activity from fast-spiking interneurons increases their excitability leading to unexpectedly increased fast excitatory transmission and seizure susceptibility.
    1. Neuroscience

    A resource for the Drosophila antennal lobe provided by the connectome of glomerulus VA1v

    Jane Anne Horne et al.
    FIB-SEM is used to identify comprehensively and reconstruct 192 neurons and their complete connectome for glomerulus VA1v of the Drosophila antennal lobe, in particular to reconstruct its local interneurons.
    1. Structural Biology and Molecular Biophysics

    Cryo-EM structure of the mechanically activated ion channel OSCA1.2

    Sebastian Jojoa-Cruz et al.
    Structures of OSCA1.2, a member of a newly characterized family of mechanically activated ion channels, provide insights into mechanism of channel gating by membrane tension.
    1. Evolutionary Biology
    2. Structural Biology and Molecular Biophysics

    OSCA/TMEM63 are an evolutionarily conserved family of mechanically activated ion channels

    Swetha E Murthy et al.
    A family of proteins (OSCA/TMEM63) that encode mechanosensitive ion channels has been characterized in plants, flies, and mammals.