Functional interrogation of < i > HOXA9 < /i > regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen
AberrantHOXA9 expression is a hallmark of most aggressive acute leukemias, notably those with KMT2A (MLL) gene rearrangements.HOXA9 overexpression not only predicts poor diagnosis and outcome but also plays a critical role in leukemia transformation and maintenance. However, our current understanding ofHOXA9 regulation in leukemia is limited, hindering development of therapeutic strategies. Here, we generated theHOXA9-mCherry knock-in reporter cell lines to dissectHOXA9 regulation. By utilizing the reporter and CRISPR/Cas9 screens, we identified transcription factors controllingHOXA9 expression, including a novel regulator...
Source: eLife - October 1, 2020 Category: Biomedical Science Tags: Cancer Biology Source Type: research

Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic
Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics, but are still widely overlooked. We identify and characterizeORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence ofORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members ofSevere acute respiratory syndrome-related coronavirus), between human...
Source: eLife - October 1, 2020 Category: Biomedical Science Tags: Evolutionary Biology Microbiology and Infectious Disease Source Type: research

Establishment and maintenance of motor neuron identity via temporal modularity in terminal selector function
Terminal selectors are transcription factors (TFs) that establish during development and maintain throughout life post-mitotic neuronal identity. We previously showed that UNC-3/Ebf, the terminal selector ofC. elegans cholinergic motor neurons (MNs), acts indirectly to prevent alternative neuronal identities (Feng et al., 2020). Here, we globally identify the direct targets of UNC-3. Unexpectedly, we find that the suite of UNC-3 targets in MNs is modified across different life stages, revealing ‘temporal modularity’ in terminal selector function. In all larval and adult stages examined, UNC-3 is required for co...
Source: eLife - October 1, 2020 Category: Biomedical Science Tags: Developmental Biology Neuroscience Source Type: research

The role of cochlear place coding in the perception of frequency modulation
Natural sounds convey information via frequency and amplitude modulations (FM and AM). Humans are acutely sensitive to the slow rates of FM that are crucial for speech and music. This sensitivity has long been thought to rely on precise stimulus-driven auditory-nerve spike timing (time code), whereas a coarser code, based on variations in the cochlear place of stimulation (place code), represents faster FM rates. We tested this theory in listeners with normal and impaired hearing, spanning a wide range of place-coding fidelity. Contrary to predictions, sensitivity to both slow and fast FM correlated with place-coding fidel...
Source: eLife - September 30, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Antinociceptive modulation by the adhesion GPCR CIRL promotes mechanosensory signal discrimination
Adhesion-type GPCRs (aGPCRs) participate in a vast range of physiological processes. Their frequent association with mechanosensitive functions suggests that processing of mechanical stimuli may be a common feature of this receptor family. Previously, we reported that theDrosophila aGPCR CIRL sensitizes sensory responses to gentle touch and sound by amplifying signal transduction in low-threshold mechanoreceptors (Scholz et al., 2017). Here, we show thatCirl is also expressed in high-threshold mechanical nociceptors where it adjusts nocifensive behaviour under physiological and pathological conditions. Optogeneticin vivoex...
Source: eLife - September 30, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Expansion of the circadian transcriptome in < i > Brassica rapa < /i > and genome-wide diversification of paralog expression patterns
An important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Here, we describe the circadian transcriptome in the polyploid cropBrassica rapa. Strikingly, almost three quarters of expressed genes exhibited circadian rhythmicity. Genetic redundancy resulting from whole genome duplication is thought to facilitate evolutionary change through sub- and neo-functionalization among paralogous gene pairs. We observed genome-wide expansion of circadian expression phase among retained paralogous pairs. Using gene regulatory network models, we compared transcription factor targets betwee...
Source: eLife - September 30, 2020 Category: Biomedical Science Tags: Genetics and Genomics Source Type: research

New insights on the modeling of the molecular mechanisms underlying neural maps alignment in the midbrain
We previously identified and modeled a principle of visual map alignment in the midbrain involving the mapping of the retinal projections and concurrent transposition of retinal guidance cues into the superior colliculus providing positional information for the organization of cortical V1 projections onto the retinal map (Savier et al., 2017). This principle relies on mechanisms involving Epha/Efna signaling, correlated neuronal activity and axon competition. Here, using the 3-step map alignment computational model, we predict and validate in vivo the visual mapping defects in a well-characterized mouse model. Our results ...
Source: eLife - September 30, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Neuroscience Source Type: research

Sperm-specific COX6B2 enhances oxidative phosphorylation, proliferation, and survival in human lung adenocarcinoma
We describe human COX6B2, a component of cytochrome c oxidase (complex IV).COX6B2 is expressed in human lung adenocarcinoma (LUAD) and expression correlates with reduced survival time. COX6B2, but not its somatic isoform COX6B1, enhances activity of complex IV, increasing oxidative phosphorylation (OXPHOS) and NAD+ generation. Consequently, COX6B2-expressing cancer cells display a proliferative advantage, particularly in low oxygen. Conversely, depletion of COX6B2 attenuates OXPHOS and collapses mitochondrial membrane potential leading to cell death or senescence. COX6B2 is both necessary and sufficient for growth of human...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Cancer Biology Source Type: research

Pregnancy success in mice requires appropriate cannabinoid receptor signaling for primary decidua formation
With implantation mouse stromal cells begin to transform into epithelial-like cells surrounding the implantation chamber forming an avascular zone called the primary decidual zone (PDZ). In mouse, the PDZ forms a transient, size-dependent permeable barrier to protect the embryo from maternal circulating harmful agents. The process of decidualization is critical for early pregnancy maintenance in mice and humans. Mice deficient in cannabinoid receptors, CB1 and CB2, show compromised PDZ with dysregulated angiogenic factors, resulting in the retention of blood vessels and macrophages. This phenotype is replicated inCnr1-/-, ...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Developmental Biology Source Type: research

Feed-forward recruitment of electrical synapses enhances synchronous spiking in the mouse cerebellar cortex
In the cerebellar cortex, molecular layer interneurons use chemical and electrical synapses to form subnetworks that fine-tune the spiking output of the cerebellum. Although electrical synapses can entrain activity within neuronal assemblies, their role in feed-forward circuits is less well explored. By combining whole-cell patch-clamp and 2-photon laser scanning microscopy of basket cells (BCs), we found that classical excitatory postsynaptic currents (EPSCs) are followed by GABAA receptor-independent outward currents, reflecting the hyperpolarization component of spikelets (a synapse-evoked action potential passively pro...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Lef1 expression in fibroblasts maintains developmental potential in adult skin to regenerate wounds
Scars are a serious health concern for burn victims and individuals with skin conditions associated with wound healing. Here, we identify regenerative factors in neonatal murine skin that transforms adult skin to regenerate instead of only repairing wounds with a scar, without perturbing development and homeostasis. Using scRNA-seq to probe unsorted cells from regenerating, scarring, homeostatic, and developing skin, we identified neonatal papillary fibroblasts that form a transient regenerative cell type that promotes healthy skin regeneration in young skin. These fibroblasts are defined by the expression of a canonical W...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Stem Cells and Regenerative Medicine Source Type: research

A physicochemical perspective of aging from single-cell analysis of pH, macromolecular and organellar crowding in yeast
Cellular aging is a multifactorial process that is characterized by a decline in homeostatic capacity, best described at the molecular level. Physicochemical properties such as pH and macromolecular crowding are essential to all molecular processes in cells and require maintenance. Whether a drift in physicochemical properties contributes to the overall decline of homeostasis in aging is not known. Here we show that the cytosol of yeast cells acidifies modestly in early aging and sharply after senescence. Using a macromolecular crowding sensor optimized for long-term FRET measurements, we show that crowding is rather stabl...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Structural Biology and Molecular Biophysics Source Type: research

Genome expansion in early eukaryotes drove the transition from lateral gene transfer to meiotic sex
Prokaryotes acquire genes from the environment via lateral gene transfer (LGT). Recombination of environmental DNA can prevent the accumulation of deleterious mutations, but LGT was abandoned by the first eukaryotes in favour of sexual reproduction. Here we develop a theoretical model of a haploid population undergoing LGT which includes two new parameters, genome size and recombination length, neglected by previous theoretical models. The greater complexity of eukaryotes is linked with larger genomes and we demonstrate that the benefit of LGT declines rapidly with genome size. The degeneration of larger genomes can only b...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Evolutionary Biology Source Type: research

Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir
The latent reservoir is a major barrier to HIV cure. As latently infected cells cannot be phenotyped directly, the features of the in vivo reservoir have remained elusive. Here, we describe a method that leverages high-dimensional phenotyping using CyTOF to trace latently infected cells reactivated ex vivo to their original pre-activation states. Our results suggest that, contrary to common assumptions, the reservoir is not randomly distributed among cell subsets, and is remarkably conserved between individuals. However, reservoir composition differs between tissues and blood, as do cells successfully reactivated by differ...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Microbiology and Infectious Disease Source Type: research

Histone deacetylase knockouts modify transcription, CAG instability and nuclear pathology in Huntington disease mice
Somatic expansion of the Huntington's disease (HD) CAG repeat drives the rate of a pathogenic process ultimately resulting in neuronal cell death. Although mechanisms of toxicity are poorly delineated, transcriptional dysregulation is a likely contributor. To identify modifiers that act at the level of CAG expansion and/or downstream pathogenic processes, we tested the impact of genetic knockout, inHttQ111 mice, ofHdac2 orHdac3 in medium-spiny striatal neurons that exhibit extensive CAG expansion and exquisite disease vulnerability. Both knockouts moderately attenuated CAG expansion, withHdac2 knockout decreasing nuclear h...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Genetics and Genomics Neuroscience Source Type: research

Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway
New therapeutic targets for oral squamous cell carcinoma (OSCC) are urgently needed. We conducted genome-wide CRISPR-Cas9 screens in 21 OSCC cell lines, primarily derived from Asians, to identify genetic vulnerabilities that can be explored as therapeutic targets. We identify known and novel fitness genes and demonstrate that many previously identified OSCC-related cancer genes are non-essential and could have limited therapeutic value, while other fitness genes warrant further investigation for their potential as therapeutic targets. We validate a distinctive dependency on YAP1 and WWTR1 of the Hippo pathway, where the lo...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Cancer Biology Genetics and Genomics Source Type: research

Endothelial TGF- β signaling instructs smooth muscle cell development in the cardiac outflow tract
The development of the cardiac outflow tract (OFT), which connects the heart to the great arteries, relies on a complex crosstalk between endothelial (ECs) and smooth muscle (SMCs) cells. Defects in OFT development can lead to severe malformations, including aortic aneurysms, which are frequently associated with impaired TGF- β signaling. To better understand the role of TGF-β signaling in OFT formation, we generated zebrafish lacking the TGF-β receptor Alk5 and found a strikingly specific dilation of the OFT:alk5-/- OFTs exhibit increased EC numbers as well as extracellular matrix (ECM) and SMC disorganizat...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Developmental Biology Source Type: research

Purkinje cell neurotransmission patterns cerebellar basket cells into zonal modules defined by distinct pinceau sizes
Ram ón y Cajal proclaimed the neuron doctrine based on circuit features he exemplified using cerebellar basket cell projections. Basket cells form dense inhibitory plexuses that wrap Purkinje cell somata and terminate as pinceaux at the initial segment of axons. Here, we demonstrate that HCN1, Kv1.1, P SD95 and GAD67 unexpectedly mark patterns of basket cell pinceaux that map onto Purkinje cell functional zones. Using cell-specific genetic tracing with anAscl1CreERT2 mouse conditional allele, we reveal that basket cell zones comprise different sizes of pinceaux. We tested whether Purkinje cells instruct the assembly...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

A circuit mechanism for decision-making biases and NMDA receptor hypofunction
Decision-making biases can be features of normal behaviour, or deficits underlying neuropsychiatric symptoms. We used behavioural psychophysics, spiking-circuit modelling and pharmacological manipulations to explore decision-making biases during evidence integration. Monkeys showed a pro-variance bias (PVB): a preference to choose options with more variable evidence. The PVB was also present in a spiking circuit model, revealing a potential neural mechanism for this behaviour. To model possible effects of NMDA receptor (NMDA-R) antagonism on this behaviour, we simulated the effects of NMDA-R hypofunction onto either excita...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

A possible link between olfaction and miscarriage
Unexplained repeated pregnancy loss is associated with an altered perception of male odors and differences in brain regions that process smells. (Source: eLife)
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Unexplained repeated pregnancy loss is associated with altered perceptual and brain responses to men ’s body-odor
Mammalian olfaction and reproduction are tightly linked, a link less explored in humans. Here, we asked whether human unexplained repeated pregnancy loss (uRPL) is associated with altered olfaction, and particularly altered olfactory responses to body-odor. We found that whereas most women with uRPL could identify the body-odor of their spouse, most control women could not. Moreover, women with uRPL rated the perceptual attributes of men's body-odor differently from controls. These pronounced differences were accompanied by an only modest albeit significant advantage in ordinary, non-body-odor-related olfaction in uRPL. Ne...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Modelling the emergence of whisker barrels
Brain development relies on an interplay between genetic specification and self-organization. Striking examples of this relationship can be found in the somatosensory brainstem, thalamus, and cortex of rats and mice, where the arrangement of the facial whiskers is preserved in the arrangement of cell aggregates to form precise somatotopic maps. We show in simulation how realistic whisker maps can self-organize, by assuming that information is exchanged between adjacent cells only, under the guidance of gene expression gradients. The resulting model provides a simple account of how patterns of gene expression can constrain ...
Source: eLife - September 29, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Developmental Biology Source Type: research

Phosphatidylcholines from < i > Pieris brassicae < /i > eggs activate an immune response in Arabidopsis
Recognition of conserved microbial molecules activates immune responses in plants, a process termed pattern-triggered immunity (PTI). Similarly, insect eggs trigger defenses that impede egg development or attract predators, but information on the nature of egg-associated elicitors is scarce. We performed an unbiased bioactivity-guided fractionation of eggs of the butterflyPieris brassicae. Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry of active fractions led to the identification of phosphatidylcholines (PCs). PCs are released from insect eggs, and they induce salicylic acid and H2O2 accumulation, def...
Source: eLife - September 28, 2020 Category: Biomedical Science Tags: Plant Biology Source Type: research

The dynamic interplay between ATP/ADP levels and autophagy sustain neuronal migration in vivo
Cell migration is a dynamic process that entails extensive protein synthesis and recycling, structural remodeling, and considerable bioenergetic demand. Autophagy is one of the pathways that maintain cellular homeostasis. Time-lapse imaging of autophagosomes and ATP/ADP levels in migrating cells in the rostral migratory stream of mice revealed that decreases in ATP levels force cells into the stationary phase and induce autophagy. Pharmacological or genetic impairments of autophagy in neuroblasts using either bafilomycin, inducible conditional mice, or CRISPR/Cas9 gene editing decreased cell migration due to the longer dur...
Source: eLife - September 28, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Defining the function of OmpA in the Rcs stress response
OmpA, a protein commonly found in the outer membrane of Gram-negative bacteria, has served as a paradigm for the study of b-barrel proteins for several decades. InEscherichia coli, OmpA was previously reported to form complexes with RcsF, a surface-exposed lipoprotein that triggers the Rcs stress response when damage occurs in the outer membrane and the peptidoglycan. How OmpA interacts with RcsF and whether this interaction allows RcsF to reach the surface has remained unclear. Here, we integratedin vivo andin vitro approaches to establish that RcsF interacts with the C-terminal, periplasmic domain of OmpA, not with the N...
Source: eLife - September 28, 2020 Category: Biomedical Science Tags: Microbiology and Infectious Disease Source Type: research

Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B
APOBEC3B (A3B)-catalyzed DNA cytosine deamination contributes to the overall mutational landscape in breast cancer. Molecular mechanisms responsible forA3B upregulation in cancer are poorly understood. Here, we show that a single E2F cis-element mediates repression in normal cells and that expression is activated by its mutational disruption in a reporter construct or the endogenousA3B gene. The same E2F site is required forA3B induction by polyomavirus T antigen indicating a shared molecular mechanism. Proteomic and biochemical experiments demonstrate binding of wildtype but not mutant E2F promoters by repressive PRC1.6/E...
Source: eLife - September 28, 2020 Category: Biomedical Science Tags: Cancer Biology Chromosomes and Gene Expression Source Type: research

Direct translation of climbing fiber burst-mediated sensory coding into post-synaptic Purkinje cell dendritic calcium
Climbing fibers (CFs) generate complex spikes (CS) and Ca2+ transients in cerebellar Purkinje cells (PCs), serving as instructive signals. The so-called 'all-or-none' character of CSs has been questioned since the CF burst was described. Although recent studies have indicated a sensory-driven enhancement of PC Ca2+ signals, how CF responds to sensory events and contributes to PC dendritic Ca2+ and CS remains unexplored. Here, single or simultaneous Ca2+ imaging of CFs and PCs in awake mice revealed the presynaptic CF Ca2+ amplitude encoded the sensory input's strength and directly influenced post-synaptic PC dendritic Ca2+...
Source: eLife - September 28, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Testicular hormones mediate robust sex differences in impulsive choice in rats
Impairments in choosing optimally between immediate and delayed rewards are associated with numerous psychiatric disorders. Such ‘intertemporal’ choice is influenced by genetic and experiential factors; however, the contributions of biological sex are understudied and data to date are largely inconclusive. Rats were used to determine how sex and gonadal hormones influence choices between small, immediate and large, delaye d rewards. Females showed markedly greater preference than males for small, immediate over large, delayed rewards (greater impulsive choice). This difference was neither due to differences in ...
Source: eLife - September 28, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

Experience, circuit dynamics and forebrain recruitment in larval zebrafish prey capture
Experience strongly influences behavior, but little is known about how experience is encoded in the brain, and how changes in neural activity are implemented at a network level to improve performance. Here we investigate how differences in experience impact brain circuitry and behavior in larval zebrafish prey capture. We find that experience of live prey compared to inert food increases capture success by boosting capture initiation. To explore the underlying neural basis, we studied the effects of prior experience of live prey on behavior and brain activity. In response to live prey, animals with and without prior experi...
Source: eLife - September 28, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research

POMK regulates dystroglycan function via LARGE1-mediated elongation of matriglycan
Matriglycan [-GlcA- β1,3-Xyl-α1,3-]n serves as a scaffold in many tissues for extracellular matrix proteins containing laminin-G domains including laminin, agrin, and perlecan. Like-acetylglucosaminyltransferase-1 (LARGE1) synthesizes and extends matriglycan on α-dystroglycan (α-DG)during skeletal muscle differentiation and regeneration; however, the mechanisms which regulate matriglycan elongation are unknown. Here, we show that Protein O-Mannose Kinase (POMK), which phosphorylates mannose of core M3 (GalNac- β1,3-GlcNac-β1,4-Man) preceding matriglycan synthesis, is required for LARGE1-med...
Source: eLife - September 25, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Source Type: research

Molecular basis for substrate specificity of the Phactr1/PP1 phosphatase holoenzyme
PPP-family phosphatases such as PP1 have little intrinsic specificity. Cofactors can target PP1 to substrates or subcellular locations, but it remains unclear how they might confer sequence-specificity on PP1. The cytoskeletal regulator Phactr1 is a neuronally-enriched PP1 cofactor that is controlled by G-actin. Structural analysis showed that Phactr1 binding remodels PP1's hydrophobic groove, creating a new composite surface adjacent to the catalytic site. Using phosphoproteomics, we identified mouse fibroblast and neuronal Phactr1/PP1 substrates, which include cytoskeletal components and regulators. We determined high-re...
Source: eLife - September 25, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Structural Biology and Molecular Biophysics Source Type: research

Symbiont-mediated cytoplasmic incompatibility: what have we learned in 50 years?
Cytoplasmic incompatibility (CI) is the most common symbiont-induced reproductive manipulation. Specifically, symbiont-induced sperm modifications cause catastrophic mitotic defects in the fertilized embryo and ensuing lethality in crosses between symbiotic males and either aposymbiotic females or females harboring a different symbiont strain. However, if the female carries the same symbiont strain, then embryos develop properly, thereby imparting a relative fitness benefit to symbiont-transmitting mothers. Thus, CI drives maternally-transmitted bacteria to high frequencies in arthropods worldwide. In the past two decades,...
Source: eLife - September 25, 2020 Category: Biomedical Science Tags: Evolutionary Biology Genetics and Genomics Source Type: research

Phosphatidylinositol 3-phosphate and Hsp70 protect < i > Plasmodium falciparum < /i > from heat-induced cell death
Phosphatidylinositol 3-phosphate (PI(3)P) levels inPlasmodium falciparum correlate with tolerance to cellular stresses caused by artemisinin and environmental factors. However, PI(3)P function during thePlasmodium stress response was unknown. Here, we used PI3K inhibitors and antimalarial agents to examine the importance of PI(3)P under thermal conditions recapitulating malarial fever. Live cell microscopy using chemical and genetic reporters revealed that PI(3)P stabilizes the digestive vacuole (DV) under heat stress. We demonstrate that heat-induced DV destabilization in PI(3)P-deficientP. falciparum precedes cell death ...
Source: eLife - September 25, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Microbiology and Infectious Disease Source Type: research

Photosynthesis without β-carotene
Carotenoids are essential in oxygenic photosynthesis: they stabilize the pigment-protein complexes, are active in harvesting sunlight and in photoprotection. In plants, they are present as carotenes and their oxygenated derivatives, xanthophylls. While mutant plants lacking xanthophylls are capable of photoautotrophic growth, no plants without carotenes in their photosystems have been reported so far, which has led to the common opinion that carotenes are essential for photosynthesis. Here, we report the first plant that grows photoautotrophically in the absence of carotenes: a tobacco plant containing only the xanthophyll...
Source: eLife - September 25, 2020 Category: Biomedical Science Tags: Plant Biology Source Type: research

POMK regulates dystroglycan function via LARGE-mediated elongation of matriglycan
Matriglycan [-GlcA- β1,3-Xyl-α1,3-]n serves as a scaffold in many tissues for extracellular matrix proteins containing laminin-G domains including laminin, agrin, and perlecan. Like-acetylglucosaminyltransferase-1 (LARGE1) synthesizes and extends matriglycan on α-dystroglycan (α-DG)during skeletal muscle differentiation and regeneration; however, the mechanisms which regulate matriglycan elongation are unknown. Here, we show thatProtein O-Mannose Kinase (POMK), which phosphorylates mannose of core M3 (GalNac- β1,3-GlcNac-β1,4-Man) preceding matriglycan synthesis, is required for LARGE1-medi...
Source: eLife - September 25, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Source Type: research

A multi-layered and dynamic apical extracellular matrix shapes the vulva lumen in < i > Caenorhabditis elegans < /i >
Biological tubes must develop and maintain their proper diameter in order to transport materials efficiently. These tubes are molded and protected in part by apical extracellular matrices (aECMs) that line their lumens. Despite their importance, aECMs are difficult to imagein vivoand therefore poorly understood.TheC. elegans vulva has been a paradigm for understanding many aspects of organogenesis. Here we describe the vulva luminal matrix, which contains chondroitin proteoglycans, Zona Pellucida (ZP) domain proteins, and other glycoproteins and lipid transporters related to those in mammals. Confocal and transmission elec...
Source: eLife - September 25, 2020 Category: Biomedical Science Tags: Developmental Biology Source Type: research

Hedgehog signaling is required for endomesodermal patterning and germ cell development in the sea anemone < i > Nematostella vectensis < /i >
Two distinct mechanisms for primordial germ cell (PGC) specification are observed within Bilatera: early determination by maternal factors or late induction by zygotic cues. Here we investigate the molecular basis for PGC specification inNematostella, a representative pre-bilaterian animal where PGCs arise as paired endomesodermal cell clusters during early development. We first present evidence that the putative PGCs delaminate from the endomesoderm upon feeding, migrate into the gonad primordia, and mature into germ cells. We then show that the PGC clusters arise at the interface betweenhedgehog1 andpatched domains in th...
Source: eLife - September 24, 2020 Category: Biomedical Science Tags: Developmental Biology Evolutionary Biology Source Type: research

MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly
The glucose-sensing Mondo pathway regulates expression of metabolic genes in mammals. Here, we characterized its function in the zebrafish and revealed an unexpected role of this pathway in vertebrate embryonic development. We showed that knockdown ofmondoa impaired the early morphogenetic movement of epiboly in zebrafish embryos and caused microtubule defects. Expression of genes in the terpenoid backbone and sterol biosynthesis pathways upstream of pregnenolone synthesis was coordinately downregulated in these embryos, including the most downregulated genensdhl. Loss of Nsdhl function likewise impaired epiboly, similar t...
Source: eLife - September 24, 2020 Category: Biomedical Science Tags: Developmental Biology Genetics and Genomics Source Type: research

Correction: A nuclear role for the DEAD-box protein Dbp5 in tRNA export
(Source: eLife)
Source: eLife - September 24, 2020 Category: Biomedical Science Tags: Chromosomes and Gene Expression Source Type: research

Molecular mechanism for direct actin force-sensing by α-catenin
The actin cytoskeleton mediates mechanical coupling between cells and their tissue microenvironments. The architecture and composition of actin networks are modulated by force, but it is unclear how interactions between actin filaments (F-actin) and associated proteins are mechanically regulated. Here, we employ both optical trapping and biochemical reconstitution with myosin motor proteins to show single piconewton forces applied solely to F-actin enhance binding by the human version of the essential cell-cell adhesion protein αE-catenin, but not its homolog vinculin. Cryo-electron microscopy structures of both prot...
Source: eLife - September 24, 2020 Category: Biomedical Science Tags: Cell Biology Structural Biology and Molecular Biophysics Source Type: research

Light-Regulated allosteric switch enables temporal and subcellular control of enzyme activity
Engineered allosteric regulation of protein activity provides significant advantages for the development of robust and broadly applicable tools. However, the application of allosteric switches in optogenetics has been scarce and suffers from critical limitations. Here, we report an optogenetic approach that utilizes an engineered Light-Regulated (LightR) allosteric switch module to achieve tight spatiotemporal control of enzymatic activity. Using the tyrosine kinase Src as a model, we demonstrate efficient regulation of the kinase and identify temporally distinct signaling responses ranging from seconds to minutes. LightR-...
Source: eLife - September 23, 2020 Category: Biomedical Science Tags: Biochemistry and Chemical Biology Cell Biology Source Type: research

Stoichiometric interactions explain spindle dynamics and scaling across 100 million years of nematode evolution
The spindle shows remarkable diversity, and changes in an integrated fashion, as cells vary over evolution. Here, we provide a mechanistic explanation for variations in the first mitotic spindle in nematodes. We used a combination of quantitative genetics and biophysics to rule out broad classes of models of the regulation of spindle length and dynamics, and to establish the importance of a balance of cortical pulling forces acting in different directions. These experiments led us to construct a model of cortical pulling forces in which the stoichiometric interactions of microtubules and force generators (each force genera...
Source: eLife - September 23, 2020 Category: Biomedical Science Tags: Cell Biology Physics of Living Systems Source Type: research

Live imaging of hair bundle polarity acquisition demonstrates a critical timeline for transcription factor Emx2
The asymmetric hair bundle on top of hair cells (HCs), comprises a kinocilium and stereocilia staircase, dictates HC's directional sensitivity. The mother centriole (MC) forms the base of the kinocilium, where stereocilia are subsequently built next to it. Previously we showed that transcription factor Emx2 reverses hair bundle orientation and its expression in the mouse vestibular utricle is restricted, resulting in two regions of opposite bundle orientation (Jiang et al, 2017). Here, we investigated establishment of opposite bundle orientation in embryonic utricles by live-imaging GFP-labeled centrioles in HCs. The daugh...
Source: eLife - September 23, 2020 Category: Biomedical Science Tags: Cell Biology Developmental Biology Source Type: research

Ribosome recycling is not critical for translational coupling in < i > E. coli < /i >
We used ribosome profiling to characterize the biological role of ribosome recycling factor (RRF) inE. coli. As expected, RRF depletion leads to enrichment of post-termination 70S complexes in 3'-UTRs. We also observe that elongating ribosomes are unable to complete translation because they are blocked by non-recycled ribosomes at stop codons. Previous studies have suggested a role for recycling in translational coupling within operons; if a ribosome remains bound to an mRNA after termination, it may re-initiate downstream. We found, however, that RRF depletion did not significantly affect coupling efficiency in reporter a...
Source: eLife - September 23, 2020 Category: Biomedical Science Tags: Chromosomes and Gene Expression Source Type: research

Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events
The spread of antimicrobial resistance and vaccine escape in the human pathogenStreptococcus pneumoniae can be largely attributed to competence-induced transformation. Here, we studied this process at the single-cell level. We show that within isogenic populations, all cells become naturally competent and bind exogenous DNA. We find that transformation is highly efficient and that the chromosomal location of the integration site or whether the transformed gene is encoded on the leading or lagging strand has limited influence on recombination efficiency. Indeed, we have observed multiple recombination events in single recip...
Source: eLife - September 23, 2020 Category: Biomedical Science Tags: Microbiology and Infectious Disease Source Type: research

Why scientific societies should involve more early-career researchers
This article looks at the level of influence ECRs have in 20 scientific societies based in the US and UK, and provides guidelines on how societies can successfully include ECRs in leadership roles. (Source: eLife)
Source: eLife - September 23, 2020 Category: Biomedical Science Source Type: research

Bimodal function of chromatin remodeler < i > Hmga1 < /i > in neural crest induction and Wnt-dependent emigration
During gastrulation, neural crest cells are specified at the neural plate border, as characterized byPax7 expression. Using single-cell RNA sequencing coupled with high resolutionin situ hybridization to identify novel transcriptional regulators, we show that chromatin remodelerHmga1 is highly expressed prior to specification and maintained in migrating chick neural crest cells. Temporally-controlled CRISPR-Cas9-mediated knockouts uncovered two distinct functions ofHmga1 in neural crest development. At the neural plate border,Hmga1 regulates Pax7-dependent neural crest lineage specification. At premigratory stages, a secon...
Source: eLife - September 23, 2020 Category: Biomedical Science Tags: Developmental Biology Source Type: research

Alstrom syndrome gene is a stem cell-specific regulator of centriole duplication in the < i > Drosophila < /i > testis
Asymmetrically dividing stem cells often show asymmetric behavior of the mother versus daughter centrosomes, whereby the self-renewing stem cell selectively inherits the mother or daughter centrosome. Although the asymmetric centrosome behavior is widely conserved, its biological significance remains largely unclear. Here we show that Alms1a, aDrosophila homolog of the human ciliopathy gene Alstrom syndrome, is enriched on the mother centrosome inDrosophila male germline stem cells (GSCs). Depletion ofalms1a in GSCs, but not in differentiating germ cells, results in rapid loss of centrosomes due to a failure in daughter ce...
Source: eLife - September 23, 2020 Category: Biomedical Science Tags: Cell Biology Developmental Biology Source Type: research

Spectral clustering of risk score trajectories stratifies sepsis patients by clinical outcome and interventions received
Sepsis is not a monolithic disease, but a loose collection of symptoms with diverse outcomes. Thus, stratification and subtyping of sepsis patients is of great importance. We examine the temporal evolution of patient state using our previously-published method for computing risk of transition from sepsis into septic shock. Risk trajectories diverge into four clusters following early prediction of septic shock, stratifying by outcome: the highest-risk and lowest-risk groups have a 76.5% and 10.4% prevalence of septic shock, and 43% and 18% mortality, respectively. These clusters differ also in treatments received and median...
Source: eLife - September 22, 2020 Category: Biomedical Science Tags: Computational and Systems Biology Source Type: research

Ribosomal profiling during prion disease uncovers progressive translational derangement in glia but not in neurons
Prion diseases are caused by PrPSc, a self-replicating pathologically misfolded protein that exerts toxicity predominantly in the brain. The administration of PrPSc causes a robust, reproducible and specific disease manifestation. Here we have applied a combination of translating ribosome affinity purification and ribosome profiling to identify biologically relevant prion-induced changes during disease progression in a cell-type specific and genome-wide manner. Terminally diseased mice with severe neurological symptoms showed extensive alterations in astrocytes and microglia. Surprisingly, we detected only minor changes in...
Source: eLife - September 22, 2020 Category: Biomedical Science Tags: Neuroscience Source Type: research