β spectrin-dependent and domain specific mechanisms for Na < sup > + < /sup > channel clustering
Previously, we showed that a hierarchy of spectrin cytoskeletal proteins maintains nodal Na+ channels (Liu et al., 2020). Here, using mice lacking β1, β4, or β1/β4 spectrins, we show this hierarchy does not function at axon initial segments (AIS). Although β1 spectrin, together with AnkyrinR (AnkR), compensates for loss of nodal β4 spectrin, it cannot compensate at AIS. We show AnkR lacks the domain necessary for AIS localization. Wherea s loss of β4 spectrin causes motor impairment and disrupts AIS, loss of β1 spectrin has no discernable effect on central nervous system structure or...
Source: eLife - May 19, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Acetylcholine acts on songbird premotor circuitry to invigorate vocal output
Acetylcholine is well-understood to enhance cortical sensory responses and perceptual sensitivity in aroused or attentive states. Yet little is known about cholinergic influences on motor cortical regions. Here we use the quantifiable nature of birdsong to investigate how acetylcholine modulates the cortical (pallial) premotor nucleus HVC and shapes vocal output. We found that dialyzing the cholinergic agonist carbachol into HVC increased the pitch, amplitude, tempo and stereotypy of song, similar to the natural invigoration of song that occurs when males direct their songs to females. These carbachol-induced effects were ...
Source: eLife - May 19, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Apolipoprotein L-1 renal risk variants form active channels at the plasma membrane driving cytotoxicity
Recently evolved alleles of Apolipoprotein L-1 (APOL1) provide increased protection against African trypanosome parasites while also significantly increasing the risk of developing kidney disease in humans. APOL1 protects against trypanosome infections by forming ion channels within the parasite, causing lysis. While the correlation to kidney disease is robust, there is little consensus concerning the underlying disease mechanism. We show in human cells that the APOL1 renal risk variants have a population of active channels at the plasma membrane, which results in an influx of both Na+ and Ca2+. We propose a model wherein ...
Source: eLife - May 19, 2020 Category: Biomedical Science Tags: Cell Biology Human Biology and Medicine Source Type: research

Predictable properties of fitness landscapes induced by adaptational tradeoffs
Fitness effects of mutations depend on environmental parameters. For example, mutations that increase fitness of bacteria at high antibiotic concentration often decrease fitness in the absence of antibiotic, exemplifying a tradeoff between adaptation to environmental extremes. We develop a mathematical model for fitness landscapes generated by such tradeoffs, based on experiments that determine the antibiotic dose-response curves ofEscherichia coli strains, and previous observations on antibiotic resistance mutations. Our model generates a succession of landscapes with predictable propertie...
Source: eLife - May 19, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Evolutionary Biology Source Type: research

Combining magnetoencephalography with magnetic resonance imaging enhances learning of surrogate-biomarkers
Electrophysiological methods, i.e., M/EEG provide unique views into brain health. Yet, when building predictive models from brain data, it is often unclear how electrophysiology should be combined with other neuroimaging methods. Information can be redundant, useful common representations of multimodal data may not be obvious and multimodal data collection can be medically contraindicated, which reduces applicability. Here, we propose a multimodal model to robustly combine MEG, MRI and fMRI for prediction. We focus on age prediction as a surrogate biomarker in 674 subjects from the Cam-CAN datas...
Source: eLife - May 19, 2020 Category: Biomedical Science Tags: Human Biology and Medicine Neuroscience Source Type: research

Alterations in the amplitude and burst rate of beta oscillations impair reward-dependent motor learning in anxiety
Anxiety results in sub-optimal motor learning, but the precise mechanisms through which this effect occurs remain unknown. Using a motor sequence learning paradigm with separate phases for initial exploration and reward-based learning, we show that anxiety states in humans impair learning by attenuating the update of reward estimates. Further, when such estimates are perceived as unstable over time (volatility), anxiety constrains adaptive behavioral changes. Neurally, anxiety during initial exploration increased the amplitude and the rate of long bursts of sensorimotor and prefrontal beta oscillations (13 –30 Hz). T...
Source: eLife - May 19, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Rarity is a more reliable indicator of land-use impacts on soil invertebrate communities than other diversity metrics
The effects of land use on soil invertebrates – an important ecosystem component – are poorly understood. We investigated land-use impacts on a comprehensive range of soil invertebrates across New Zealand, measured using DNA metabarcoding and six biodiversity metrics. Rarity and phylogenetic rarity – direct measures of the number of speci es or the portion of a phylogeny unique to a site – showed stronger, more consistent responses across taxa to land use than widely used metrics of species richness, effective species numbers, and phylogenetic diversity. Overall, phylogenetic rarity explained the hi...
Source: eLife - May 19, 2020 Category: Biomedical Science Tags: Ecology Source Type: research

CytoCensus, mapping cell identity and division in tissues and organs using machine learning
A major challenge in cell and developmental biology is the automated identification and quantitation of cells in complex multilayered tissues. We developed CytoCensus: an easily deployed implementation of supervised machine learning that extends convenient 2D ‘point-and-click’ user training to 3D detection of cells in challenging datasets with ill-defined cell boundaries. In tests on such datasets, CytoCensus outperforms other freely available image analysis software in accuracy and speed of cell detection. We used CytoCensus to count stem cells and their progeny, and to quantify individual cell divisions from ...
Source: eLife - May 19, 2020 Category: Biomedical Science Tags: Cell Biology Developmental Biology Source Type: research

Retrieval practice facilitates memory updating by enhancing and differentiating medial prefrontal cortex representations
Updating old memories with new, more current information is critical for human survival, yet the neural mechanisms for memory updating in general and the effect of retrieval practice in particular are poorly understood. Using a three-day A-B/A-C memory updating paradigm, we found that compared to restudy, retrieval practice could strengthen new A-C memories and reduce old A-B memory intrusion, but did not suppress A-B memories. Neural activation pattern analysis revealed that compared to restudy, retrieval practice led to stronger target representation in the medial prefrontal cortex (MPFC) during the final test. Criticall...
Source: eLife - May 18, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast
In this study, we report how 10x Genomics' droplet-based single-cell RNA sequencing technology can be modified to allow analysis of yeast cells. The protocol, which is based on in-droplet spheroplasting of the cells, yields an order-of-magnitude higher throughput in comparison to existing methods. After extensive validation of the method, we demonstrate its use by studying the dynamics of the response of isogenic yeast populations to a shift in carbon source, revealing the heterogeneity and underlying molecular processes during this shift. The method we describe opens new avenues for studies focusing on yeast cells, as wel...
Source: eLife - May 18, 2020 Category: Biomedical Science Tags: Chromosomes and Gene Expression Microbiology and Infectious Disease Source Type: research

Pupil diameter encodes the idiosyncratic, cognitive complexity of belief updating
Pupils tend to dilate in response to surprising events, but it is not known whether these responses are primarily stimulus driven or instead reflect a more nuanced relationship between pupil-linked arousal systems and cognitive expectations. Using an auditory adaptive decision-making task, we show that evoked pupil diameter is more parsimoniously described as signaling violations of learned, top-down expectations than changes in low-level stimulus properties. We further show that both baseline and evoked pupil diameter is modulated by the degree to which individual subjects use these violations to update their subsequent e...
Source: eLife - May 18, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

ER-luminal [Ca < sup > 2+ < /sup > ] regulation of InsP < sub > 3 < /sub > receptor gating mediated by an ER-luminal peripheral Ca < sup > 2+ < /sup > -binding protein
Modulating cytoplasmic Ca2+ concentration ([Ca2+]i) by endoplasmic reticulum (ER)-localized inositol 1,4,5-trisphosphate receptor (InsP3R) Ca2+-release channels is a universal signaling pathway that regulates numerous cell-physiological processes. Whereas much is known regarding regulation of InsP3R activity by cytoplasmic ligands and processes, its regulation by ER-luminal Ca2+ concentration ([Ca2+]ER) is poorly understood and controversial. We discovered that the InsP3R is regulated by a peripheral membrane-associated ER-luminal protein that strongly inhibits the channel in the presence of high, physiological [Ca2+]ER. T...
Source: eLife - May 18, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Noradrenergic projections from the locus coeruleus to the amygdala constrain fear memory reconsolidation
Memory reconsolidation is a fundamental plasticity process in the brain that allows established memories to be changed or erased. However, certain boundary conditions limit the parameters under which memories can be made plastic. Strong memories do not destabilize, for instance, although why they are resilient is mostly unknown. Here, we investigated the hypothesis that specific modulatory signals shape memory formation into a state that is reconsolidation-resistant. We find that the activation of the noradrenaline-locus coeruleus system (NOR-LC) during strong fear memory encoding increases molecular mechanisms of stabilit...
Source: eLife - May 18, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Transverse sinus injections drive robust whole-brain expression of transgenes
Convenient, efficient and fast whole-brain delivery of transgenes presents a persistent experimental challenge in neuroscience. Recent advances demonstrate whole-brain gene delivery by retro-orbital injection of virus, but slow and sparse expression and the large injection volumes required make this approach cumbersome, especially for developmental studies. We developed a novel method for efficient gene delivery across the central nervous system in neonatal mice and rats starting as early as P1 and persisting into adulthood. The method employs transverse sinus injections of 2-4 μL of AAV9 at P0. Here, we describe how to...
Source: eLife - May 18, 2020 Category: Biomedical Science Tags: Developmental Biology Neuroscience Source Type: research

Long-term implicit memory for sequential auditory patterns in humans
Memory, on multiple timescales, is critical to our ability to discover the structure of our surroundings, and efficiently interact with the environment. We combined behavioural manipulation and modelling to investigate the dynamics of memory formation for rarely reoccurring acoustic patterns. In a series of experiments, participants detected the emergence of regularly repeating patterns within rapid tone-pip sequences. Unbeknownst to them, a few patterns reoccurred every ~3 minutes. All sequences consisted of the same 20 frequencies and were distinguishable only by the order of tone-pips. Despite this, reoccurring patterns...
Source: eLife - May 18, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

A helminth-derived suppressor of ST2 blocks allergic responses
The IL-33-ST2 pathway is an important initiator of type 2 immune responses. We previously characterised the HpARI protein secreted by the model intestinal nematodeHeligmosomoides polygyrus, which binds and blocks IL-33. Here, we identifyH. polygyrus Binds Alarmin Receptor and Inhibits (HpBARI) and HpBARI_Hom2, both of which consist of complement control protein (CCP) domains, similarly to the immunomodulatory HpARI and Hp-TGM proteins. HpBARI binds murine ST2, inhibiting cell surface detection of ST2, preventing IL-33-ST2 interactions, and inhibiting IL-33 responses in vitro and in an in vivo mouse model of asthma. InH. po...
Source: eLife - May 18, 2020 Category: Biomedical Science Tags: Immunology and Inflammation Microbiology and Infectious Disease Source Type: research

Complexity of frequency receptive fields predicts tonotopic variability across species
Primary cortical areas contain maps of sensory features, including sound frequency in primary auditory cortex (A1). Two-photon calcium imaging in mice has confirmed the presence of these global tonotopic maps, while uncovering an unexpected local variability in the stimulus preferences of individual neurons in A1 and other primary regions. Here we show that local heterogeneity of frequency preferences is not unique to rodents. Using two-photon calcium imaging in layers 2/3, we found that local variance in frequency preferences is equivalent in ferrets and mice. Neurons with multipeaked frequency tuning are less spatially o...
Source: eLife - May 18, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Stochastic bond dynamics facilitates alignment of malaria parasite at erythrocyte membrane upon invasion
Malaria parasites invade healthy red blood cells (RBCs) during the blood stage of the disease. Even though parasites initially adhere to RBCs with a random orientation, they need to align their apex toward the membrane in order to start the invasion process. Using hydrodynamic simulations of a RBC and parasite, where both interact through discrete stochastic bonds, we show that parasite alignment is governed by the combination of RBC membrane deformability and dynamics of adhesion bonds. The stochastic nature of bond-based interactions facilitates a diffusive-like re-orientation of the parasite at the RBC membrane, while R...
Source: eLife - May 18, 2020 Category: Biomedical Science Tags: Physics of Living Systems Source Type: research

MeCP2 in cholinergic interneurons of nucleus accumbens regulates fear learning
Methyl-CpG-binding protein 2 (MeCP2) encoded by theMECP2 gene is a transcriptional regulator whose mutations cause Rett syndrome (RTT).Mecp2-deficient mice show fear regulation impairment; however, the cellular and molecular mechanisms underlying this abnormal behavior are largely uncharacterized. Here, we showed thatMecp2 gene deficiency in cholinergic interneurons of the nucleus accumbens (NAc) dramatically impaired fear learning. We further found that spontaneous activity of cholinergic interneurons inMecp2-deficient mice decreased, mediated by enhanced inhibitory transmission via α2-containing GABAA receptors. Wi...
Source: eLife - May 18, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Automated task training and longitudinal monitoring of mouse mesoscale cortical circuits using home cages
We report improved automated open-source methodology for head-fixed mesoscale cortical imaging and/or behavioral training of home cage mice using Raspberry Pi-based hardware. Staged partial and probabilistic restraint allows mice to adjust to self-initiated headfixation over 3 weeks' time with ~50% participation rate. We support a cue-based behavioral licking task monitored by a capacitive touch-sensor water spout. While automatically head-fixed, we acquire spontaneous, movement-triggered, or licking task-evoked GCaMP6 cortical signals. An analysis pipeline marked both behavioral events, as well as analyzed brain fluoresce...
Source: eLife - May 15, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Inter-domain dynamics drive cholesterol transport by NPC1 and NPC1L1 proteins
Transport of LDL-derived cholesterol from lysosomes into the cytoplasm requires NPC1 protein; NPC1L1 mediates uptake of dietary cholesterol. We introduced single disulfide bonds into NPC1 and NPC1L1 to explore the importance of inter-domain dynamics in cholesterol transport. Using a sensitive method to monitor lysosomal cholesterol efflux, we found that NPC1 ’s N-terminal domain need not release from the rest of the protein for efficient cholesterol export. Either introducing single disulfide bonds to constrain lumenal/extracellular domains or shortening a cytoplasmic loop abolishes transport activity by both NPC1 an...
Source: eLife - May 15, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Cell Biology Source Type: research

Connectomic analysis reveals an interneuron with an integral role in the retinal circuit for night vision
Night vision in mammals depends fundamentally on rod photoreceptors and the well-studied rod bipolar (RB) cell pathway. The central neuron in this pathway, the AII amacrine cell (AC), exhibits a spatially tuned receptive field, composed of an excitatory center and an inhibitory surround, that propagates to ganglion cells, the retina ’s projection neurons. The circuitry underlying the surround of the AII, however, remains unresolved. Here, we combined structural, functional and optogenetic analyses of the mouse retina to discover that surround inhibition of the AII depends primarily on a single interneuron type, the N...
Source: eLife - May 15, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Efficient targeted integration directed by short homology in zebrafish and mammalian cells
Efficient precision genome engineering requires high frequency and specificity of integration at the genomic target site. Here, we describe a set of resources to streamline reporter gene knock-ins in zebrafish and demonstrate the broader utility of the method in mammalian cells. Our approach uses short homology of 24 –48 bp to drive targeted integration of DNA reporter cassettes by homology-mediated end joining (HMEJ) at high frequency at a double strand break in the targeted gene. Our vector series, pGTag (plasmids for Gene Tagging), contains reporters flanked by a universal CRISPR sgRNA sequence which enable s in v...
Source: eLife - May 15, 2020 Category: Biomedical Science Tags: Developmental Biology Genetics and Genomics Source Type: research

Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by proteome-wide PhIP-Seq
The identification of autoantigens remains a critical challenge for understanding and treating autoimmune diseases. Autoimmune polyendocrine syndrome type 1 (APS1), a rare monogenic form of autoimmunity, presents as widespread autoimmunity with T and B cell responses to multiple organs. Importantly, autoantibody discovery in APS1 can illuminate fundamental disease pathogenesis, and many of the antigens found in APS1 extend to more common autoimmune diseases. Here, we performed proteome-wide programmable phage-display (PhIP-Seq) on sera from a cohort of people with APS1 and discovered multiple common antibody targets. These...
Source: eLife - May 15, 2020 Category: Biomedical Science Tags: Human Biology and Medicine Immunology and Inflammation Source Type: research

Stimulation strength controls the rate of initiation but not the molecular organization of TCR-induced signalling
Millions of na ïve T cells with different TCRs may interact with a peptide-MHC ligand, but very few will activate. Remarkably, this fine control is orchestrated using a limited set of intracellular machinery. It remains unclear whether changes in stimulation strength alter the programme of signalling events leadi ng to T cell activation. Using mass cytometry to simultaneously measure multiple signalling pathways during activation of murine CD8+ T cells, we found a programme of distal signalling events that is shared, regardless of the strength of TCR stimulation. Moreover, the relationship between transcription of ear...
Source: eLife - May 15, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Immunology and Inflammation Source Type: research

Finding the mutations that drive resistance
Mutations that allow tumors to evolve and become resistant to treatment can be readily identified with a new sequencing approach. (Source: eLife)
Source: eLife - May 15, 2020 Category: Biomedical Science Tags: Cancer Biology Genetics and Genomics Source Type: research

Untangling the immune basis of disease susceptibility
Interactions between immune cell receptors and proteins that determine disease susceptibility shed light on how different arms of the immune system are involved in three viral infections and Crohn's disease. (Source: eLife)
Source: eLife - May 14, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Immunology and Inflammation Source Type: research

Reconstitution reveals two paths of force transmission through the kinetochore
Partitioning duplicated chromosomes equally between daughter cells is a microtubule-mediated process essential to eukaryotic life. A multi-protein machine, the kinetochore, drives chromosome segregation by coupling the chromosomes to dynamic microtubule tips, even as the tips grow and shrink through the gain and loss of subunits. The kinetochore must harness, transmit, and sense mitotic forces, as a lack of tension signals incorrect chromosome-microtubule attachment and precipitates error correction mechanisms. But though the field has arrived at a 'parts list' of dozens of kinetochore proteins organized into subcomplexes,...
Source: eLife - May 14, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Cell Biology Source Type: research

Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature
The transcriptional activation and repression during NK cell ontology are poorly understood. Here, using single-cell RNA-sequencing, we reveal a novel role for T-bet in suppressing the immature gene signature during murine NK cell development. Based on transcriptome, we identified five distinct NK cell clusters and define their relative developmental maturity in the bone marrow. Transcriptome-based machine-learning classifiers revealed that half of the mTORC2-deficient NK cells belongs to the least mature NK cluster. Mechanistically, loss of mTORC2 results in an increased expression of signature genes representing immature...
Source: eLife - May 14, 2020 Category: Biomedical Science Tags: Immunology and Inflammation Source Type: research

Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing
Copy number alterations (CNAs) play an important role in molding the genomes of breast cancers and have been shown to be clinically useful for prognostic and therapeutic purposes. However, our knowledge of intra-tumoral genetic heterogeneity of this important class of somatic alterations is limited. Here, using single-cell sequencing, we comprehensively map out the facets of copy number alteration heterogeneity in a cohort of breast cancer tumors. Ou/var/www/html/elife/12-05-2020/backup/r analyses reveal: genetic heterogeneity of non-tumor cells (i.e. stroma) within the tumor mass; the extent to which copy number heterogen...
Source: eLife - May 13, 2020 Category: Biomedical Science Tags: Cancer Biology Genetics and Genomics Source Type: research

A role for fat precursors in the marrow
A group of cells that can become adipocytes controls the formation of blood vessels in the bone marrow, and also regulates the differentiation of resident mesenchymal progenitor cells. (Source: eLife)
Source: eLife - May 13, 2020 Category: Biomedical Science Tags: Cell Biology Source Type: research

A critical re-evaluation of fMRI signatures of motor sequence learning
Despite numerous studies, there is little agreement about what brain changes accompany motor sequence learning, partly because of a general publication bias that favors novel results. We therefore decided to systematically reinvestigate proposed functional magnetic resonance imaging correlates of motor learning in a preregistered longitudinal study with four scanning sessions over 5 weeks of training. Activation decreased more for trained than untrained sequences in premotor and parietal areas, without any evidence of learning-related activation increases. Premotor and parietal regions also exhibited changes in the fine-gr...
Source: eLife - May 13, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Synergistic roles of Synaptotagmin-1 and complexin in calcium-regulated neuronal exocytosis
Calcium (Ca2+)-evoked release of neurotransmitters from synaptic vesicles requires mechanisms both to prevent un-initiated fusion of vesicles (clamping) and to trigger fusion following Ca2+-influx. The principal components involved in these processes are the vesicular fusion machinery (SNARE proteins) and the regulatory proteins, Synaptotagmin-1 and Complexin. Here, we use a reconstituted single-vesicle fusion assay under physiologically-relevant conditions to delineate a novel mechanism by which Synaptotagmin-1 and Complexin act synergistically to establish Ca2+-regulated fusion. We find that under each vesicle, Synaptota...
Source: eLife - May 13, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Spontaneous and evoked neurotransmission are partially segregated at inhibitory synapses
We report picrotoxin, a GABAAR antagonist, blocks neurotransmission in a use-dependent manner at rat hippocampal synapses and therefore can be used to interrogate synaptic properties. Using this tool, we uncovered partial segregation of inhibitory spontaneous and evoked neurotransmission. We found up to 40% of the evoked response is mediated through GABAARs which are only activated by evoked neurotransmission. These data indicate GABAergic spontaneous and evoked neurotransmission processes are partially non-overlapping, suggesting they may serve divergent roles in neuronal signaling. (Source: eLife)
Source: eLife - May 13, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

ODELAM Rapid sequence-independent detection of drug resistance in isolates of < i > Mycobacterium tuberculosis < /i >
We present ODELAM (One-cell Doubling Evaluation of Living Arrays of Mycobacterium), a time-lapse microscopy-based method that observes individual cells growing into microcolonies. ODELAM enables rapid quantitative measures of growth kinetics in as little as 30 hours under a wide variety of environmental conditions. We demonstrate ODELAM's utility by identifying ofloxacin resistance in cultured clinical isolates of Mtb and benchmark its performance with standard minimum inhibitory concentration (MIC) assays. In Mtb isolate, ODELAM identified ofloxacin heteroresistance and identifies the presence of drug resistant colony for...
Source: eLife - May 13, 2020 Category: Biomedical Science Tags: Microbiology and Infectious Disease Source Type: research

Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo
Type 1 metabotropic glutamate receptors (mGluR1s) are key elements in neuronal signaling. While their function is well documented in slices, requirements for their activation in vivo are poorly understood. We examine this question in adult mice in vivo using 2-photon imaging of cerebellar molecular layer interneurons (MLIs) expressing GCaMP. In anesthetized mice, parallel fiber activation evokes beam-like Cai rises in postsynaptic MLIs which depend on co-activation of mGluR1s and ionotropic glutamate receptors (iGluRs). In awake mice, blocking mGluR1 decreases Cai rises associated with locomotion. In vitro studies and free...
Source: eLife - May 13, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Dissecting the phenotypic and functional heterogeneity of mouse inflammatory osteoclasts by the expression of < i > Cx3cr1 < /i >
Bone destruction relies on interactions between bone and immune cells. Bone-resorbing osteoclasts (OCLs) were recently identified as innate immune cells activating T cells toward tolerance or inflammation. Thus, pathological bone destruction not only relies on increased osteoclast differentiation, but also on the presence of inflammatory OCLs (i-OCLs), part of which expressCx3cr1. Here, we investigated the contribution of mouse Cx3cr1+ and Cx3cr1neg i-OCLs to bone loss. We showed that Cx3cr1+ and Cx3cr1neg i-OCLs differ considerably in transcriptional and functional aspects. Cx3cr1neg i-OCLs have a high ability to resorb b...
Source: eLife - May 13, 2020 Category: Biomedical Science Tags: Cell Biology Immunology and Inflammation Source Type: research

Cohesin and condensin extrude DNA loops in a cell-cycle dependent manner
Loop extrusion by structural maintenance of chromosomes complexes (SMCs) has been proposed as a mechanism to organize chromatin in interphase and metaphase. However, the requirements for chromatin organization in these cell cycle phases are different, and it is unknown whether loop extrusion dynamics and the complexes that extrude DNA also differ. Here, we usedXenopus egg extracts to reconstitute and image loop extrusion of single DNA molecules during the cell cycle. We show that loops form in both metaphase and interphase, but with distinct dynamic properties. Condensin extrudes DNA loops non-symmetrically in metaphase, w...
Source: eLife - May 12, 2020 Category: Biomedical Science Tags: Cell Biology Chromosomes and Gene Expression Source Type: research

Ant collective cognition allows for efficient navigation through disordered environments
The cognitive abilities of biological organisms only make sense in the context of their environment. Here, we study longhorn crazy ant collective navigation skills within the context of a semi-natural, randomized environment. Mapping this biological setting into the 'Ant-in-a-Labyrinth' framework which studies physical transport through disordered media allows us to formulate precise links between the statistics of environmental challenges and the ants' collective navigation abilities. We show that, in this environment, the ants use their numbers to collectively extend their sensing range. Although this extension is modera...
Source: eLife - May 12, 2020 Category: Biomedical Science Tags: Ecology Physics of Living Systems Source Type: research

IP < sub > 3 < /sub > mediated global Ca < sup > 2+ < /sup > signals arise through two temporally and spatially distinct modes of Ca < sup > 2+ < /sup > release
The 'building-block' model of inositol trisphosphate (IP3)-mediated Ca2+ liberation posits that cell-wide cytosolic Ca2+ signals arise through coordinated activation of localized Ca2+ puffs generated by stationary clusters of IP3 receptors (IP3Rs). Here, we revise this hypothesis, applying fluctuation analysis to resolve Ca2+ signals otherwise obscured during large Ca2+ elevations. We find the rising phase of global Ca2+ signals is punctuated by a flurry of puffs, which terminate before the peak by a mechanism involving partial ER Ca2+ depletion. The continuing rise in Ca2+, and persistence of global signals even when puff...
Source: eLife - May 12, 2020 Category: Biomedical Science Tags: Cell Biology Structural Biology and Molecular Biophysics Source Type: research

Intelligent classification of platelet aggregates by agonist type
Platelets are anucleate cells in blood whose principal function is to stop bleeding by forming aggregates for hemostatic reactions. In addition to their participation in physiological hemostasis, platelet aggregates are also involved in pathological thrombosis and play an important role in inflammation, atherosclerosis, and cancer metastasis. The aggregation of platelets is elicited by various agonists, but these platelet aggregates have long been considered indistinguishable and impossible to classify. Here we present an intelligent method for classifying them by agonist type. It is based on a convolutional neural network...
Source: eLife - May 12, 2020 Category: Biomedical Science Tags: Cell Biology Human Biology and Medicine Source Type: research

Local emergence in Amazonia of < i > Plasmodium falciparum k13 < /i > C580Y mutants associated with < i > in vitro < /i > artemisinin resistance
We report that mutantpfk13 has emerged independently in Guyana, with genome analysis indicating an evolutionary origin distinct from Southeast Asia.Pfk13 C580Y parasites were observed in 1.6% (14/854) of samples collected in Guyana in 2016 –2017. Introducingpfk13 C580Y or R539T mutations by gene editing into local parasites conferred high levels ofin vitro artemisinin resistance.In vitro growth competition assays revealed a fitness cost associated with thesepfk13 variants, potentially explaining why these resistance alleles have not increased in frequency more quickly in South America. These data place local malaria ...
Source: eLife - May 12, 2020 Category: Biomedical Science Tags: Epidemiology and Global Health Microbiology and Infectious Disease Source Type: research

Bmal1 integrates mitochondrial metabolism and macrophage activation
Metabolic pathways and inflammatory processes are under circadian regulation. While rhythmic immune cell recruitment is known to impact infection outcomes, whether the circadian clock modulates immunometabolism remains unclear. We find the molecular clock Bmal1 is induced by inflammatory stimulants, including Ifn-g/lipopolysaccharide (M1) and tumor-conditioned medium, to maintain mitochondrial metabolism under these metabolically stressed conditions in mouse macrophages. Upon M1 stimulation, myeloid-specificBmal1 knockout (M-BKO) renders macrophages unable to sustain mitochondrial function, enhancing succinate dehydrogenas...
Source: eLife - May 12, 2020 Category: Biomedical Science Tags: Cell Biology Source Type: research

Adult chondrogenesis and spontaneous cartilage repair in the skate, < i > Leucoraja erinacea < /i >
Mammalian articular cartilage is an avascular tissue with poor capacity for spontaneous repair. Here, we show that embryonic development of cartilage in the skate (Leucoraja erinacea) mirrors that of mammals, with developing chondrocytes co-expressing genes encoding the transcription factors Sox5, Sox6 and Sox9. However, in skate, transcriptional features of developing cartilage persist into adulthood, both in peripheral chondrocytes and in cells of the fibrous perichondrium that ensheaths the skeleton. Using pulse-chase label retention experiments and multiplexed in situ hybridization, we identify a population of cyclingS...
Source: eLife - May 12, 2020 Category: Biomedical Science Tags: Developmental Biology Stem Cells and Regenerative Medicine Source Type: research

A single-cell survey of < i > Drosophila < /i > blood
Drosophila blood cells, called hemocytes, are classified into plasmatocytes, crystal cells, and lamellocytes based on the expression of a few marker genes and cell morphologies, which are inadequate to classify the complete hemocyte repertoire. Here, we used single-cell RNA sequencing (scRNA-seq) to map hemocytes across different inflammatory conditions in larvae. We resolved plasmatocytes into different states based on the expression of genes involved in cell cycle, antimicrobial response, and metabolism together with the identification of intermediate states. Further, we discovered rare subsets within crystal cells and l...
Source: eLife - May 12, 2020 Category: Biomedical Science Tags: Developmental Biology Immunology and Inflammation Source Type: research

Heterogeneity of proteome dynamics between connective tissue phases of adult tendon
Maintenance of connective tissue integrity is fundamental to sustain function, requiring protein turnover to repair damaged tissue. However, connective tissue proteome dynamics remain largely undefined, as do differences in turnover rates of individual proteins in the collagen and glycoprotein phases of connective tissue extracellular matrix (ECM). Here, we investigate proteome dynamics in the collagen and glycoprotein phases of connective tissues by exploiting the spatially distinct fascicular (collagen-rich) and interfascicular (glycoprotein-rich) ECM phases of tendon. Using isotope labelling, mass spectrometry and bioin...
Source: eLife - May 12, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Structural Biology and Molecular Biophysics Source Type: research

Tgfb3 collaborates with PP2A and Notch signaling pathways to inhibit retina regeneration
Neuronal degeneration in the zebrafish retina stimulates M üller glia (MG) to proliferate and generate multipotent progenitors for retinal repair. Controlling this proliferation is critical to successful regeneration. Previous studies reported that retinal injury stimulates pSmad3 signaling in injury-responsive MG. Contrary to these findings, we report pSm ad3 expression is restricted to quiescent MG and suppressed in injury-responsive MG. Our data indicates that Tgfb3 is the ligand responsible for regulating pSmad3 expression. Remarkably, although overexpression of either Tgfb1b or Tgfb3 can stimulate pSmad3 expressi...
Source: eLife - May 12, 2020 Category: Biomedical Science Tags: Stem Cells and Regenerative Medicine Source Type: research

A mammalian < i > Wnt5a –Ror2–Vangl2 < /i > axis controls the cytoskeleton and confers cellular properties required for alveologenesis
Alveolar formation increases the surface area for gas-exchange and is key to the physiological function of the lung. Alveolar epithelial cells, myofibroblasts and endothelial cells undergo coordinated morphogenesis to generate epithelial folds (secondary septa) to form alveoli. A mechanistic understanding of alveologenesis remains incomplete. We found that the planar cell polarity (PCP) pathway is required in alveolar epithelial cells and myofibroblasts for alveologenesis in mammals. Our studies uncovered aWnt5a –Ror2–Vangl2 cascade that endows cellular properties and novel mechanisms of alveologenesis. This in...
Source: eLife - May 12, 2020 Category: Biomedical Science Tags: Developmental Biology Source Type: research

Mechanics and kinetics of dynamic instability
During dynamic instability, self-assembling microtubules (MTs) stochastically alternate between phases of growth and shrinkage. This process is driven by the presence of two distinct states of MT subunits, GTP- and GDP-bound tubulin dimers, that have different structural properties. Here, we use a combination of analysis and computer simulations to study the mechanical and kinetic regulation of dynamic instability in three-dimensional (3D) self-assembling MTs. Our model quantifies how the 3D structure and kinetics of the distinct states of tubulin dimers determine the mechanical stability of MTs. We further show that dynam...
Source: eLife - May 11, 2020 Category: Biomedical Science Tags: Physics of Living Systems Source Type: research

Genetic transformation of < i > Spizellomyces punctatus < /i > , a resource for studying chytrid biology and evolutionary cell biology
Chytrids are early-diverging fungi that share features with animals that have been lost in most other fungi. They hold promise as a system to study fungal and animal evolution, but we lack genetic tools for hypothesis testing. Here, we generated transgenic lines of the chytridSpizellomyces punctatus, and used fluorescence microscopy to explore chytrid cell biology and development during its life cycle. We show that the chytrid undergoes multiple rounds of synchronous nuclear division, followed by cellularization, to create and release many daughter ‘zoospores’. The zoospores, akin to animal cells, crawl using a...
Source: eLife - May 11, 2020 Category: Biomedical Science Tags: Evolutionary Biology Source Type: research