Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter
Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex fromAnoxybacillus flavithermussolved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton a...
Source: eLife - July 31, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Gap junctions deliver malonyl-CoA from soma to germline to support embryogenesis in Caenorhabditis elegans
Gap junctions are ubiquitous in metazoans and play critical roles in important biological processes, including electrical conduction and development. Yet, only a few defined molecules passing through gap junction channels have been linked to specific functions. We isolated gap junction channel mutants that reduce coupling between the soma and germ cells in theC. elegans gonad. We provide evidence that malonyl-CoA, the rate-limiting substrate for fatty acid synthesis (FAS), is produced in the soma and delivered through gap junctions to the germline; there it is used in fatty acid synthesis to critically support embryonic de...
Source: eLife - July 31, 2020 Category: Biomedical Science Tags: Developmental Biology Genetics and Genomics Source Type: research

Molecular principles of assembly, activation, and inhibition in epithelial sodium channel
The molecular bases of heteromeric assembly and link between Na+ self-inhibition and protease-sensitivity in epithelial sodium channels (ENaCs) are not fully understood. Previously, we demonstrated that ENaC subunits – α, β, and γ – assemble in a counterclockwise configuration when viewed from outside the cell with the protease-sensitive GRIP domains in the periphery (Noreng et al., 2018). Here we describe the structure of ENaC resolved by cryo-electron microscopy at 3 Å. We find that a combination of pr ecise domain arrangement and complementary hydrogen bonding network defines the subun...
Source: eLife - July 30, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

An atlas of cell types in the mammalian epididymis and vas deferens
Following testicular spermatogenesis, mammalian sperm continue to mature in a long epithelial tube known as the epididymis, which plays key roles in remodeling sperm protein, lipid, and RNA composition. To understand the roles for the epididymis in reproductive biology, we generated a single cell atlas of the murine epididymis and vas deferens. We recovered key epithelial cell types including principal cells, clear cells, and basal cells, along with associated support cells that include fibroblasts, smooth muscle, macrophages and other immune cells. Moreover, our data illuminate extensive regional specialization of princip...
Source: eLife - July 30, 2020 Category: Biomedical Science Tags: Developmental Biology Genetics and Genomics Source Type: research

Revealing the structure of information flows discriminates similar animal social behaviors
Behavioral correlations stretching over time are an essential but often neglected aspect of interactions among animals. These correlations pose a challenge to current behavioral-analysis methods that lack effective means to analyze complex series of interactions. Here we show that non-invasive information-theoretic tools can be used to reveal communication protocols that guide complex social interactions by measuring simultaneous flows of different types of information between subjects. We demonstrate this approach by showing that the tandem-running behavior of the antTemnothorax rugatulus and that of the termitesCoptoterm...
Source: eLife - July 30, 2020 Category: Biomedical Science Tags: Ecology Physics of Living Systems Source Type: research

Keratinocytes contribute to normal cold and heat sensation
The molecular bases of heteromeric assembly and link between Na+ self-inhibition and protease-sensitivity in epithelial sodium channels (ENaCs) are not fully understood. Previously, we demonstrated that ENaC subunits – α, β, and γ – assemble in a counterclockwise configuration when viewed from outside the cell with the protease-sensitive GRIP domains in the periphery (Noreng et al., 2018). Here we describe the structure of ENaC resolved by cryo-electron microscopy at 3 Å. We find that a combination of pr ecise domain arrangement and complementary hydrogen bonding network defines the subun...
Source: eLife - July 30, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Convergent changes in muscle metabolism depend on duration of high-altitude ancestry across Andean waterfowl
We examined seven high-altitude waterfowl that have inhabited the Andes (3812-4806m elevation) over varying evolutionary time scales, to elucidate changes in biochemical pathways of energy metabolism in flight muscle relative to low-altitude sister-taxa. Convergent changes across high-altitude taxa included increased hydroxyacyl-coA dehydrogenase and succinate dehydrogenase activities, decreased lactate dehydrogenase, pyruvate kinase, creatine kinase, and cytochrome c oxidase activities, and increased myoglobin content. ATP synthase activity increased in only the longest established high-altitude taxa, whereas hexokinase a...
Source: eLife - July 30, 2020 Category: Biomedical Science Tags: Evolutionary Biology Source Type: research

Long non-coding RNAs in regulation of adipogenesis and adipose tissue function
Complex interaction between genetics, epigenetics, environment, and nutrition affect the physiological activities of adipose tissues and their dysfunctions, which lead to several metabolic diseases including obesity or type 2 diabetes. Here, adipogenesis appears to be a process characterized by an intricate network that involves many transcription factors and long noncoding RNAs (lncRNAs) that regulate gene expression. LncRNAs are being investigated to determine their contribution to adipose tissue development and function. LncRNAs possess multiple cellular functions, and they regulate chromatin remodeling, along with tran...
Source: eLife - July 30, 2020 Category: Biomedical Science Tags: Human Biology and Medicine Source Type: research

A unified computational model for cortical post-synaptic plasticity
Signalling pathways leading to post-synaptic plasticity have been examined in many types of experimental studies, but a unified picture on how multiple biochemical pathways collectively shape neocortical plasticity is missing. We built a biochemically detailed model of post-synaptic plasticity describing CaMKII, PKA, and PKC pathways and their contribution to synaptic potentiation or depression. We developed a statistical AMPA-receptor-tetramer model, which permits the estimation of the AMPA-receptor-mediated maximal synaptic conductance based on numbers of GluR1s and GluR2s predicted by the biochemical signalling model. W...
Source: eLife - July 30, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Neuroscience Source Type: research

Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations
Nanodiscs are membrane mimetics that consist of a protein belt surrounding a lipid bilayer, and are broadly used for characterization of membrane proteins. Here, we investigate the structure, dynamics and biophysical properties of two small nanodiscs, MSP1D1 ΔH5 and ΔH4H5. We combine our SAXS and SANS experiments with molecular dynamics simulations and previously obtained NMR and EPR data to derive and validate a conformational ensemble that represents the structure and dynamics of the nanodisc. We find that it displays conformational heterogeneity wi th various elliptical shapes, and with substantial differenc...
Source: eLife - July 30, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Neuropathogenesis of SARS-CoV-2 infection
The COVID-19 pandemic caused by the SARS-CoV-2 has recently emerged as a serious jolt to human life and economy. Initial knowledge established pulmonary complications as the chief symptom, however, the neurological aspect of the disease is also becoming increasingly evident. Emerging reports of encephalopathies and similar ailments with the detection of the virus in the CSF has elicited an urgent need for investigating the possibility of neuroinvasiveness of the virus, which cannot be ruled out given the expression of low levels of ACE2 receptors in the brain. Sensory impairments of the olfactory and gustatory systems have...
Source: eLife - July 30, 2020 Category: Biomedical Science Tags: Epidemiology and Global Health Neuroscience Source Type: research

Apoptotic neurodegeneration in whitefly promotes the spread of TYLCV
The mechanism by which plant viruses manipulate the behavior of insect vectors has largely been described as indirect manipulation through modifications of the host plant. However, little is known about the direct interaction of the plant virus on the nervous system of its insect vector, and the substantial behavioral effect on virus transmission. Using a system consisting of aTomato yellow leaf curl virus (TYLCV) and its insect vector whitefly, we found that TYLCV caused caspase-dependent apoptotic neurodegeneration with severe vacuolar neuropathological lesions in the brain of viruliferous whitefly by inducing a putative...
Source: eLife - July 30, 2020 Category: Biomedical Science Tags: Microbiology and Infectious Disease Source Type: research

Accurate and versatile 3D segmentation of plant tissues at cellular resolution
We present results of PlantSeg applications in diverse developmental contexts. PlantSeg is free and open-source, with both a command line and a user-friendly graphical interface (https://github.com/hci-unihd/plant-seg). (Source: eLife)
Source: eLife - July 29, 2020 Category: Biomedical Science Tags: Plant Biology Source Type: research

Lichen mimesis in mid-Mesozoic lacewings
Animals mimicking other organisms or using camouflage to deceive predators are vital survival strategies. Modern and fossil insects can simulate diverse objects. Lichens are an ancient symbiosis between a fungus and an alga or a cyanobacterium that sometimes have a plant-like appearance and occasionally are mimicked by modern animals. Nevertheless, lichen models are almost absent in fossil record of mimicry. Here, we provide the earliest fossil evidence of a mimetic relationship between the moth lacewing mimicLichenipolystoechotes gen. nov. and its co-occurring fossil lichen modelDaohugouthallus ciliiferus. We corroborate ...
Source: eLife - July 29, 2020 Category: Biomedical Science Tags: Ecology Evolutionary Biology Source Type: research

The cytokine GDF15 signals through a population of brainstem cholecystokinin neurons to mediate anorectic signalling
The cytokine, GDF15, is produced in pathological states which cause cellular stress, including cancer. When over expressed, it causes dramatic weight reduction, suggesting a role in disease-related anorexia. Here we demonstrate that the GDF15 receptor, GFRAL, is located in a subset of cholecystokinin neurons which span the area postrema and the nucleus of the tractus solitarius of the mouse. GDF15 activates GFRALAP/NTS neurons and supports conditioned taste and place aversions, while the anorexia it causes can be blocked by a monoclonal antibody directed at GFRAL or by disrupting CCK neuronal signalling. The cancer-therape...
Source: eLife - July 29, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

A mechanism for the extension and unfolding of parallel G-quadruplexes by human telomerase at single-molecule resolution
Telomeric G-quadruplexes (G4) were long believed to form a protective structure at telomeres, preventing their extension by the ribonucleoprotein telomerase. Contrary to this belief, we have previously demonstrated that parallel-stranded conformations of telomeric G4 can be extended by human and ciliate telomerase. However, a mechanistic understanding of the interaction of telomerase with structured DNA remained elusive. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) microscopy and bulk-phase enzymology to propose a mechanism for the resolution and extension of parallel G4 by telomerase. Bindi...
Source: eLife - July 29, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Chromosomes and Gene Expression Source Type: research

Cryo-EM structures of human ZnT8 in both outward- and inward-facing conformations
ZnT8 is a Zn2+/H+ antiporter that belongs to SLC30 family and plays an essential role in regulating Zn2+accumulation in the insulin secretory granules of pancreatic β cells. Dysfunction of ZnT8 is associated with both type 1 and 2 diabetes. However, the Zn2+/H+ exchange mechanism of ZnT8 remains unclear due to the lack of high-resolution structures. Here, we report the cryo-EM structures of human ZnT8 (HsZnT8) in both outward- and inward-facing conformations. HsZnT8 forms a dimeric structure with four Zn2+ binding sites within each subunit: a highly conserved primary site in transmembrane domain (TMD) housing the Zn2+...
Source: eLife - July 29, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research

Notch and TLR signaling coordinate monocyte cell fate and inflammation
Conventional Ly6Chi monocytes have developmental plasticity for a spectrum of differentiated phagocytes. Here we show, using conditional deletion strategies in a mouse model of Toll-like receptor (TLR) 7-induced inflammation, that the spectrum of developmental cell fates of Ly6Chi monocytes, and the resultant inflammation, is coordinately regulated by TLR and Notch signaling. Cell-intrinsic Notch2 and TLR7-Myd88 pathways independently and synergistically promote Ly6Clo patrolling monocyte development from Ly6Chi monocytes under inflammatory conditions, while impairment in either signaling axis impairs Ly6Clo monocyte devel...
Source: eLife - July 29, 2020 Category: Biomedical Science Tags: Immunology and Inflammation Source Type: research

Virus infection is controlled by hematopoietic and stromal cell sensing of murine cytomegalovirus through STING
Recognition of DNA viruses, such as cytomegaloviruses (CMVs), through pattern-recognition receptor (PRR) pathways involving MyD88 or STING constitute a first-line defense against infections mainly through production of type I interferon (IFN-I). However, the role of these pathways in different tissues is incompletely understood, an issue particularly relevant to the CMVs which have broad tissue tropisms. Herein, we contrasted anti-viral effects of MyD88 versus STING in distinct cell types that are infected with murine CMV (MCMV). Bone marrow chimeras revealed STING-mediated MCMV control in hematological cells, similar to M...
Source: eLife - July 29, 2020 Category: Biomedical Science Tags: Immunology and Inflammation Microbiology and Infectious Disease Source Type: research

A mechanism for < i > hunchback < /i > promoters to readout morphogenetic positional information in less than a minute
Cell fate decisions in the fly embryo are rapid: hunchback genes decide in minutes whether nuclei follow the anterior/posterior developmental blueprint by reading out positional information in the Bicoid morphogen. This developmental system is a prototype of regulatory decision processes that combine speed and accuracy. Traditional arguments based on fixed-time sampling of Bicoid concentration indicate that an accurate readout is impossible within the experimental times. This raises the general issue of how speed-accuracy tradeoffs are achieved. Here, we compare fixed-time to on-the-fly decisions, based on comparing the li...
Source: eLife - July 29, 2020 Category: Biomedical Science Tags: Physics of Living Systems Source Type: research

Growth factor-mediated coupling between lineage size and cell fate choice underlies robustness of mammalian development
Precise control and maintenance of population size is fundamental for organismal development and homeostasis. The three cell types of the mammalian blastocyst are generated in precise proportions over a short time, suggesting a mechanism to ensure a reproducible outcome. We developed a minimal mathematical model demonstrating growth factor signaling is sufficient to guarantee this robustness and which anticipates an embryo's response to perturbations in lineage composition. Addition of lineage-restricted cells bothin vivo andin silico, causes a shift of the fate of progenitors away from the supernumerary cell type, while e...
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Developmental Biology Source Type: research

Obesity causes selective and long-lasting desensitization of AgRP neurons to dietary fat
Body weight is regulated by interoceptive neural circuits that track energy need, but how the activity of these circuits is altered in obesity remains poorly understood. Here we describe thein vivo dynamics of hunger-promoting AgRP neurons during the development of diet-induced obesity in mice. We show that high-fat diet attenuates the response of AgRP neurons to an array of nutritionally-relevant stimuli including food cues, intragastric nutrients, cholecystokinin and ghrelin. These alterations are are specific to dietary fat but not carbohydrate or protein. Subsequent weight loss restores the responsiveness of AgRP neuro...
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

An electrophysiological marker of arousal level in humans
Deep non-rapid eye movement sleep (NREM) and general anesthesia with propofol are prominent states of reduced arousal linked to the occurrence of synchronized oscillations in the electroencephalogram (EEG). Although rapid eye movement (REM) sleep is also associated with diminished arousal levels, it is characterized by a desynchronized, 'wake-like' EEG. This observation implies that reduced arousal states are not necessarily only defined by synchronous oscillatory activity. Using intracranial and surface EEG recordings in four independent data sets, we demonstrate that the 1/f spectral slope of the electrophysiological pow...
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

The identification of dual protective agents against cisplatin-induced oto-and nephrotoxicity using the zebrafish model
This study provides insights into the mechanisms underlying cisplatin-induced oto- and nephrotoxicity and compelling preclinical evidence for the potential utility of dopamine and L-mimosine in the safer administration of cisplatin. (Source: eLife)
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Cancer Biology Human Biology and Medicine Source Type: research

Deciphering the neural signature of human cardiovascular regulation
Cardiovascular regulation is integral to life. Animal studies have identified both neural and endocrine pathways, by which the central nervous system adjusts cardiac output and peripheral vascular resistance to changing physiological demands. The outflow of these pathways is coordinated by various central nervous regions based on afferent information from baroreceptors, chemoreceptors, nociceptors, and circulating hormones, and is modulated by physiologic and behavioural state. In humans, however, knowledge on central cardiovascular regulation below the cortical level is scarce. Here, we show using functional MRI (fMRI) th...
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Human Biology and Medicine Neuroscience Source Type: research

Regulation of BMP4/Dpp retrotranslocation and signaling by deglycosylation
During endoplasmic reticulum-associated degradation (ERAD), the cytoplasmic enzymeN-glycanase 1 (NGLY1) is proposed to removeN-glycans from misfoldedN-glycoproteins after their retrotranslocation from the ER to the cytosol. We previously reported that NGLY1 regulatesDrosophila BMP signaling in a tissue-specific manner (Galeone et al. 2017). Here, we establish theDrosophilaDpp and its mouse ortholog BMP4 as biologically relevant targets of NGLY1 and find, unexpectedly, that NGLY1-mediated deglycosylation of misfolded BMP4 is required for its retrotranslocation. Accumulation of misfolded BMP4 in the ER results in ER stress a...
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Cell Biology Developmental Biology Source Type: research

Ovariectomy uncouples lifespan from metabolic health and reveals a sex-hormone-dependent role of hepatic mTORC2 in aging
Inhibition of mTOR (mechanistic Target Of Rapamycin) signaling by rapamycin promotes healthspan and longevity more strongly in females than males, perhaps because inhibition of hepatic mTORC2 (mTOR Complex 2) specifically reduces the lifespan of males. Here, we demonstrate using gonadectomy that the sex-specific impact of reduced hepatic mTORC2 is not reversed by depletion of sex hormones. Intriguingly, we find that ovariectomy uncouples lifespan from metabolic health, with ovariectomized females having improved survival despite paradoxically having increased adiposity and decreased control of blood glucose levels. Further...
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Genetics and Genomics Human Biology and Medicine Source Type: research

An analog to digital converter controls bistable transfer competence of a widespread integrative and conjugative element
Conjugative transfer of the integrative and conjugative element ICEclc in Pseudomonas requires development of a transfer competence state in stationary phase, which arises only in 3-5% of individual cells. The mechanisms controlling this bistable switch between non-active and transfer competent cells have long remained enigmatic. Using a variety of genetic tools and epistasis experiments in P. putida, we uncovered an 'upstream' cascade of three consecutive transcription factor-nodes, which controls transfer competence initiation. One of the uncovered transcription factors (named BisR) is representative for a new regulator ...
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Genetics and Genomics Microbiology and Infectious Disease Source Type: research

Identifying prostate cancer and its clinical risk in asymptomatic men using machine learning of high dimensional peripheral blood flow cytometric natural killer cell subset phenotyping data
We demonstrate that prostate cancer can be identified by flow cytometric profiling of blood immune cell subsets. Herein, we profiled natural killer (NK) cell subsets in the blood of 72 asymptomatic men with Prostate-Specific Antigen (PSA) levels
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Cancer Biology Computational and Systems Biology Source Type: research

Shared and specific signatures of locomotor ataxia in mutant mice
Several spontaneous mouse mutants with deficits in motor coordination and associated cerebellar neuropathology have been described. Intriguingly, both visible gait alterations and neuroanatomical abnormalities throughout the brain differ across mutants. We previously used the LocoMouse system to quantify specific deficits in locomotor coordination in mildly ataxicPurkinje cell degeneration mice (pcd; Machado et al., 2015). Here, we analyze the locomotor behavior of severely ataxicreeler mutants and compare and contrast it with that ofpcd. Despite clearly visible gait differences, direct comparison of locomotor kinematics a...
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

The effect of climate change on yellow fever disease burden in Africa
Yellow Fever (YF) is an arbovirus endemic in tropical regions of South America and Africa and it is estimated to cause 78,000 deaths a year in Africa alone. Climate change may have substantial effects on the transmission of YF and we present the first analysis of the potential impact on disease burden. We extend an existing model of YF transmission to account for rainfall and a temperature suitability index and project transmission intensity across the African endemic region in the context of four climate change scenarios. We use these transmission projections to assess the change in burden in 2050 and 2070. We find diseas...
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Epidemiology and Global Health Source Type: research

Climate change and intensive land use reduce soil animal biomass via dissimilar pathways
Global change drivers, such as climate change and land use, may profoundly influence body size, density, and biomass of soil organisms. However, it is still unclear how these concurrent drivers interact in affecting ecological communities. Here, we present the results of an experimental field study assessing the interactive effects of climate change and land-use intensification on body size, density, and biomass of soil microarthropods. We found that the projected climate change and intensive land use decreased their total biomass. Strikingly, this reduction was realized via two dissimilar pathways: climate change reduced ...
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Ecology Source Type: research

A sensorimotor model shows why a spectral jamming avoidance response does not help bats deal with jamming
For decades, researchers have speculated how echolocating bats deal with masking by conspecific calls when flying in aggregations. To date, only a few attempts have been made to mathematically quantify the probability of jamming, or its effects. We developed a comprehensive sensorimotor predator-prey simulation, modeling numerous bats foraging in proximity. We used this model to examine the effectiveness of a spectral Jamming Avoidance Response (JAR) as a solution for the masking problem. We found that foraging performance deteriorates when bats forage near conspecifics, however, applying a JAR does not improve insect sens...
Source: eLife - July 28, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Neuroscience Source Type: research

Mouse T cell priming is enhanced by maturation-dependent stiffening of the dendritic cell cortex
T cell activation by dendritic cells (DCs) involves forces exerted by the T cell actin cytoskeleton, which are opposed by the cortical cytoskeleton of the interacting APC. During an immune response, DCs undergo a maturation process that optimizes their ability to efficiently prime na ïve T cells. Using atomic force microscopy, we find that during maturation, DC cortical stiffness increases via a process that involves actin polymerization. Using stimulatory hydrogels and DCs expressing mutant cytoskeletal proteins, we find that increasing stiffness lowers the agonist dose needed for T cell activation. CD4+ T cells exhi...
Source: eLife - July 27, 2020 Category: Biomedical Science Tags: Cell Biology Immunology and Inflammation Source Type: research

Measuring protein stability in the GroEL chaperonin cage reveals massive destabilization
The thermodynamics of protein folding in bulk solution have been thoroughly investigated for decades. By contrast, measurements of protein substrate stability inside the GroEL/ES chaperonin cage have not been reported. Such measurements require stable encapsulation, i.e. no escape of the substrate into bulk solution during experiments, and a way to perturb protein stability without affecting the chaperonin system itself. Here, by establishing such conditions, we show that protein stability in the chaperonin cage is reduced dramatically by more than 5 kcal mol-1 compared to that in bulk solution. Given that steric confineme...
Source: eLife - July 27, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Structural Biology and Molecular Biophysics Source Type: research

Revealing architectural order with quantitative label-free imaging and deep learning
We report quantitative label-free imaging with phase and polarization (QLIPP) for simultaneous measurement of density, anisotropy, and orientation in unlabeled live cells and tissue slices. We combine QLIPP with deep neural networks to predict fluorescence images of diverse cell and tissue structures. QLIPP images reveal anatomical regions and axon tract orientation in prenatal human brain tissue sections that are not visible using brightfield imaging. We report a variant of UNet architecture, multi-channel 2.5D U-Net, for computationally efficient prediction of fluorescence images in three dimensions and over large fields...
Source: eLife - July 27, 2020 Category: Biomedical Science Tags: Neuroscience Physics of Living Systems Source Type: research

International authorship and collaboration across bioRxiv preprints
Preprints are becoming well established in the life sciences, but relatively little is known about the demographics of the researchers who post preprints and those who do not, or about the collaborations between preprint authors. Here, based on an analysis of 67,885 preprints posted on bioRxiv, we find that some countries, notably the United States and the United Kingdom, are overrepresented on bioRxiv relative to their overall scientific output, while other countries (including China, Russia, and Turkey) show lower levels of bioRxiv adoption. We also describe a set of ‘contributor countries’ (including Uganda,...
Source: eLife - July 27, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Source Type: research

Interrogating the recognition landscape of a conserved HIV-specific TCR reveals distinct bacterial peptide cross-reactivity
T cell cross-reactivity ensures that diverse pathogen-derived epitopes encountered during a lifetime are recognized by the available TCR repertoire. A feature of cross-reactivity where previous exposure to one microbe can alter immunity to subsequent, non-related pathogens has been mainly explored for viruses. Yet cross-reactivity to additional microbes is important to consider, especially in HIV infection where gut-intestinal barrier dysfunction could facilitate T cell exposure to commensal/pathogenic microbes. Here we evaluated the cross-reactivity of a ‘public’, HIV-specific, CD8 T cell-derived TCR (AGA1 TCR...
Source: eLife - July 27, 2020 Category: Biomedical Science Tags: Immunology and Inflammation Source Type: research

Par protein localization during the early development of < i > Mnemiopsis leidyi < /i > suggests different modes of epithelial organization in the Metazoa
In bilaterians and cnidarians, epithelial cell-polarity is regulated by the interactions between Par proteins, Wnt/PCP signalling pathway, and cell-cell adhesion. Par proteins are highly conserved across Metazoa, including ctenophores. But strikingly, ctenophore genomes lack components of the Wnt/PCP pathway and cell-cell adhesion complexes raising the question if ctenophore cells are polarized by mechanisms involving Par proteins. Here, by using immunohistochemistry and live-cell imaging of specific mRNAs, we describe for the first time the subcellular localization of selected Par proteins in blastomeres and epithelial ce...
Source: eLife - July 27, 2020 Category: Biomedical Science Tags: Developmental Biology Evolutionary Biology Source Type: research

A quantitative modelling approach to zebrafish pigment pattern formation
Pattern formation is a key aspect of development. Adult zebrafish exhibit a striking striped pattern generated through the self-organisation of three different chromatophores. Numerous investigations have revealed a multitude of individual cell-cell interactions important for this self-organisation, but it has remained unclear whether these known biological rules were sufficient to explain pattern formation. To test this, we present an individual-based mathematical model incorporating all the important cell-types and known interactions. The model qualitatively and quantitatively reproduces wild type and mutant pigment patt...
Source: eLife - July 27, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Developmental Biology Source Type: research

Microglial calcium signaling is attuned to neuronal activity in awake mice
Microglial calcium signaling underlies a number of key physiological processes in situ, but has not been studiedin vivo in awake mice. Using multiple GCaMP6 variants targeted to microglia, we assessed how microglial calcium signaling responds to alterations in neuronal activity across a wide physiological range. We find that only a small subset of microglial somata and processes exhibited spontaneous calcium transients in a chronic window preparation. However, hyperactive shifts in neuronal activity (kainate status epilepticus and CaMKIIa Gq DREADD activation) trigger increased microglial process calcium signaling, often c...
Source: eLife - July 27, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Dissecting transcriptional amplification by MYC
SupraphysiologicalMYC levels are oncogenic. Originally considered a typical transcription factor recruited to E-boxes (CACGTG), another theory posits MYC a global amplifier increasing output at all active promoters. Both models rest on large-scale genome-wide ”-omics’. Because the assumptions, statistical parameter and model choice dictates the ‘-omic’ results, whether MYC is a general or specific transcription factor remains controversial. Therefore, an orthogonal series of experiments interrogated MYC’s effect on the expression of synthetic r eporters. Dose-dependently, MYC increased output ...
Source: eLife - July 27, 2020 Category: Biomedical Science Tags: Cancer Biology Computational and Systems Biology Source Type: research

Intrinsic control of muscle attachment sites matching
Myogenesis is an evolutionarily conserved process. Little known, however, is how the morphology of each muscle is determined, such that movements relying upon contraction of many muscles are both precise and coordinated. EachDrosophila larval muscle is a single multinucleated fiber whose morphology reflects expression of distinctive identity Transcription Factors (iTFs). By deleting transcription cis-regulatory modules of one iTF, Collier, we generated viable muscle identity mutants, allowing live imaging and locomotion assays. We show that both selection of muscle attachment sites and muscle/muscle matching is intrinsic t...
Source: eLife - July 24, 2020 Category: Biomedical Science Tags: Developmental Biology Source Type: research

Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration
Migrating cells need to coordinate distinct leading and trailing edge dynamics but the underlying mechanisms are unclear. Here, we combine experiments and mathematical modeling to elaborate the minimal autonomous biochemical machinery necessary and sufficient for this dynamic coordination and cell movement. RhoA activates Rac1 via DIA and inhibits Rac1 via ROCK, while Rac1 inhibits RhoA through PAK. Our data suggest that in motile, polarized cells, RhoA –ROCK interactions prevail at the rear, whereas RhoA-DIA interactions dominate at the front where Rac1/Rho oscillations drive protrusions and retractions. At the rear...
Source: eLife - July 24, 2020 Category: Biomedical Science Tags: Cell Biology Computational and Systems Biology Source Type: research

Dynamics of gaze control during prey capture in freely moving mice
Many studies of visual processing are conducted in constrained conditions such as head- and gaze-fixation, and therefore less is known about how animals actively acquire visual information in natural contexts. To determine how mice target their gaze during natural behavior, we measured head and bilateral eye movements in mice performing prey capture, an ethological behavior that engages vision. We found that the majority of eye movements are compensatory for head movements, thereby serving to stabilize the visual scene. During movement, however, periods of stabilization are interspersed with non-compensatory saccades that ...
Source: eLife - July 24, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Estrogen exacerbates mammary involution through neutrophil dependent and independent mechanism
There is strong evidence that the pro-inflammatory microenvironment during post-partum mammary involution promotes parity-associated breast cancer. Estrogen exposure during mammary involution drives tumour growth through neutrophils' activity. However, how estrogen and neutrophils influence mammary involution are unknown. Combined analysis of transcriptomic, protein, and immunohistochemical data in BALB/c mice showed that estrogen promotes involution by exacerbating inflammation, cell death and adipocytes repopulation. Remarkably, 88% of estrogen-regulated genes in mammary tissue were mediated through neutrophils, which we...
Source: eLife - July 24, 2020 Category: Biomedical Science Tags: Developmental Biology Immunology and Inflammation Source Type: research

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos
Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa ’s role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread bindin...
Source: eLife - July 23, 2020 Category: Biomedical Science Tags: Developmental Biology Genetics and Genomics Source Type: research

Chronic ethanol consumption compromises neutrophil function in acute pulmonary < i > Aspergillus fumigatus < /i > infection
This study establishes a new paradigm in innate immune response in chronic ethanol consumers. (Source: eLife)
Source: eLife - July 23, 2020 Category: Biomedical Science Tags: Immunology and Inflammation Microbiology and Infectious Disease Source Type: research

Antagonistic control of DDK binding to licensed replication origins by Mcm2 and Rad53
Eukaryotic replication origins are licensed by the loading of the replicative DNA helicase, Mcm2-7, in inactive double hexameric form around DNA. Subsequent origin activation is under control of multiple protein kinases that either promote or inhibit origin activation, which is important for genome maintenance. Using the reconstituted budding yeast DNA replication system, we find that the flexible N-terminal extension (NTE) of Mcm2 promotes the stable recruitment of Dbf4-dependent kinase (DDK) to Mcm2-7 double hexamers, which in turn promotes DDK phosphorylation of Mcm4 and -6 and subsequent origin activation. Conversely, ...
Source: eLife - July 23, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Chromosomes and Gene Expression Source Type: research

Altered expression of a quality control protease in < i > E. coli < /i > reshapes the in vivo mutational landscape of a model enzyme
Protein mutational landscapes are shaped by the cellular environment, but key factors and their quantitative effects are often unknown. Here we show that Lon, a quality control protease naturally absent in commonE. coli expression strains, drastically reshapes the mutational landscape of the metabolic enzyme dihydrofolate reductase (DHFR). Selection under conditions that resolve highly active mutants reveals that 23.3% of all single point mutations in DHFR are advantageous in the absence of Lon, but advantageous mutations are largely suppressed when Lon is reintroduced. Protein stability measurements demonstrate extensive ...
Source: eLife - July 23, 2020 Category: Biomedical Science Tags: Structural Biology and Molecular Biophysics Source Type: research