bluuebunny/crossref_metadata_2025_split huggingface dataset:
The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues
Authors: Muyas Francesc , Zapata Luis , Guigó Roderic , Ossowski Stephan 
Published: July 2019

AbstractBackgroundMosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of embryonic mosaic mutations (EMMs) have only been studied in few tissues and their contribution to genetic disorders is unknown. Therefore, we investigated how frequent mosaic mutations occur during embryogenesis across all germ layers and tissues.ResultsUsing RNA sequencing data from the Genotype-Tissue Expression (GTEx) cohort comprising 49 normal tissues and 570 individuals, we found that new-borns on average harbour 0.5 - 1 EMMs in the exome affecting multiple organs (1.3230 × 10−8 per nucleotide per individual), a similar frequency as reported for germline de novo mutations. Our multi-tissue, multi-individual study design allowed us to distinguish mosaic mutations acquired during different stages of embryogenesis and adult life, as well as to provide insights into the rate and spectrum of mosaic mutations. We observed that EMMs are dominated by a mutational signature associated with spontaneous deamination of methylated cytosines and the number of cell divisions. After birth, cells continue to accumulate somatic mutations, which can lead to the development of cancer. Investigation of the mutational spectrum of the gastrointestinal tract revealed a mutational pattern associated with the food-borne carcinogen aflatoxin, a signature that has so far only been reported in liver cancer.ConclusionIn summary, our multi-tissue, multi-individual study reveals a surprisingly high number of embryonic mosaic mutations in coding regions, implying novel hypotheses and diagnostic procedures for investigating genetic causes of disease and cancer predisposition.
Area compressibility moduli of the monolayer leaflets of asymmetric bilayers from simulations
Authors: Nagle J. F. 
Published: July 2019

AbstractExtraction from simulations of the area compressibility moduli of the monolayers in a bilayer is considered theoretically. A statistical mechanical derivation shows that the bilayer modulus is the sum of the two monolayer moduli, as is often supposed, but contrary to a recent study. Seemingly plausible assumptions regarding fluctuations are tested rigorously. Prospects for future research are discussed.SignificanceIt is important to describe the properties of both leaflets of generally asymmetric Biomembranes. One such property is the area compressibility modulus. This MS rigorously establishes the fundamental theory that corrects a recent BJ paper. The theory is straightforward but substantial enough that it was not readily apparent why the previous theory was incorrect. This is why this MS should be considered a new paper and not just a comment. Another reason is that this MS points to an alternative method, used only once previously, for extracting the leaflet area compressibility modulus from simulations.
Megakaryocyte TGFβ1 Partitions Hematopoiesis into Immature Progenitor/Stem Cells and Maturing Precursors
Authors: Di Giandomenico Silvana , Kermani Pouneh , Molle Nicole , Yabut Maria Mia , Zeinah Ghaith Abu , Stephens Thomas , Messali Nassima , Rafii Shahin , Scandura Joseph M. 
Published: July 2019

SummaryErythropoiesis is a multiweek program coupling massive proliferation with progressive cellular differentiation ultimately enabling a limited number of hematopoietic stem cells (HSCs) to yield millions of erythrocytes per second1. Erythropoietin (Epo) is essential for red blood cell (RBC) production but this cytokine acts well after irreversible commitment of hematopoietic progenitor cells (HPCs) to an erythroid fate. It is not known if terminal erythropoiesis is tethered to the pool of available immature hematopoietic stem and progenitor cells (HSPCs). We now report that megakaryocyte-derived TGFβ1 compartmentalizes hematopoiesis by coupling HPC numbers to production of mature erythrocytes. Genetic deletion of TGFβ1 specifically in megakaryocytes (TGFβ1ΔMk/ΔMk) increased functional HSPCs including committed erythroid progenitors, yet total bone marrow and spleen cellularity and peripheral blood cell counts were entirely normal. Instead, excess erythroid precursors underwent apoptosis, predominantly those erythroblasts expressing the Epo receptor (Epor) but not Kit. Despite there being no deficiency of plasma Epo inTGFβ1ΔMk/ΔMkmice, exogenous Epo rescued survival of excess erythroid precursors and triggered exuberant erythropoiesis. In contrast, exogenous TGFβ1 caused anemia and failed to rescue erythroid apoptosis despite its ability to restore downstream TGFβ-mediated Smad2/3 phosphorylation in HSPCs. Thus, megakaryocytic TGFβ1 regulates the size of the pool of immature HSPCs and in so doing, improves the efficiency of erythropoiesis by governing the feed of lineage-committed erythroid progenitors whose fate is decided by extramedullary renal Epo-producing cells sensing the need for new RBCs. Independent manipulation of distinct immature Epo-unresponsive HSPCs within the hematopoietic compartments offers a new strategy to overcome chronic anemias or possibly other cytopenias.
BR-bodies provide selectively permeable condensates that stimulate mRNA decay and prevent release of decay intermediates
Authors: Al-Husini Nadra , Tomares Dylan T. , Pfaffenberger Zechariah , Muthunayake Nisansala S. , Samad Mohammad A. , Zuo Tiancheng , Bitar Obaidah , Aretakis James R. , Bharmal Mohammed-Husain M. , Gega Alisa , Biteen Julie S. , Childers W. Seth , Schrader Jared M. 
Published: July 2019

AbstractBiomolecular condensates play a key role in organizing RNAs and proteins into membraneless organelles. Bacterial RNP-bodies (BR-bodies) are a biomolecular condensate containing the RNA degradosome mRNA decay machinery, but the biochemical function of such organization remains poorly defined. Here we define the RNA substrates of BR-bodies through enrichment of the bodies followed by RNA-seq. We find that long, poorly translated mRNAs, small RNAs, and antisense RNAs are the main substrates, while rRNA, tRNA, and other conserved ncRNAs are excluded from these bodies. BR-bodies stimulate the mRNA decay rate of enriched mRNAs, helping to reshape the cellular mRNA pool. We also observe that BR-body formation promotes complete mRNA decay, avoiding the build-up of toxic endo-cleaved mRNA decay intermediates. The combined selective permeability of BR-bodies for both, enzymes and substrates together with the stimulation of the sub-steps of mRNA decay provide an effective organization strategy for bacterial mRNA decay.
Aquatic biodiversity enhances multiple nutritional benefits to humans
Authors: Bernhardt Joey R. , O’Connor Mary I. 
Published: July 2019

AbstractHumanity depends on biodiversity for health, well-being and a stable environment. As biodiversity change accelerates, we are still discovering the full range of consequences for human health and well-being. Here, we test the hypothesis -- derived from biodiversity - ecosystem functioning theory -- that species richness and ecological functional diversity allow seafood diets to fulfill multiple nutritional requirements, a condition necessary for human health. We analyzed a newly synthesized dataset of 7245 observations of nutrient and contaminant concentrations in 801 aquatic animal taxa, and found that species with different ecological traits have distinct and complementary micronutrient profiles, but little difference in protein content. The same complementarity mechanisms that generate positive biodiversity effects on ecosystem functioning in terrestrial ecosystems also operate in seafood assemblages, allowing more diverse diets to yield increased nutritional benefits independent of total biomass consumed. Notably, nutritional metrics that capture multiple micronutrients essential for human well-being depend more strongly on biodiversity than common ecological measures of function such as productivity, typically reported for grasslands and forests. Further, we found that increasing species richness did not increase the amount of protein in seafood diets, and also increased concentrations of toxic metal contaminants in the diet. Seafood-derived micronutrients are important for human health and are a pillar of global food and nutrition security. By drawing upon biodiversity-ecosystem functioning theory, we demonstrate that ecological concepts of biodiversity can deepen our understanding of nature’s benefits to people and unite sustainability goals for biodiversity and human well-being.Significance statementFood security is not simply about maintaining yields, it is also about the need for a stable supply of nutritionally diverse foods. Obtaining nutritious food is a major challenge facing humanity and diverse aquatic ecosystems can help meet this goal. To test how aquatic biodiversity affects human health, we assembled a new dataset of nutrients, contaminants and ecological traits of 801 aquatic species. We used ecological models to quantify the role of species richness and ecological functional diversity and found that these biodiversity dimensions enhanced seafood micronutrient provisioning by the same mechanisms that link biodiversity to productivity in grasslands, forests and other systems. Our results underscore the need to minimize aquatic biodiversity loss to sustain and improve human well-being.
Greb1is required for axial elongation and segmentation in vertebrate embryos
Authors: Prajapati Ravindra Singh , Mitter Richard , Vezzaro Annalisa , Ish-Horowicz David 
Published: July 2019

ABSTRACTDuring vertebrate embryonic development, the formation of axial structures is driven by a population of stem-like cells that reside in a region of the tailbud called the chordoneural hinge (CNH). We have compared the CNH transcriptome with those of surrounding tissues and shown that the CNH and tailbud mesoderm are transcriptionally similar, and distinct from the presomitic mesoderm. Amongst CNH-enriched genes are several that are required for axial elongation, includingWnt3a, Cdx2, Brachyury/TandFgf8, and androgen/estrogen receptor nuclear signalling components such asGreb1. We show that the pattern and duration of tailbudGreb1expression is conserved in mouse, zebrafish, and chicken embryos, and thatGreb1is required for axial elongation and somitogenesis in zebrafish embryos. The axial truncation phenotype ofGreb1morphant embryos is explained by much reduced expression ofNo tail(Ntl/Brachyury) which is required for axial progenitor maintenance. Posterior segmentation defects in the morphants (including misexpression of genes such asmespb, myoDandpapC) appear to result, in part, from lost expression of the segmentation clock gene,her7.
Next-Gen sequencing of novel pandemic swine flu [A(H1N1)pdm09] virus in India revealed novel mutations across the genome
Authors: Dash Paban Kumar , Pattabiraman Chitra , Tandel Kundan , Sharma Shashi , Kumar Jyoti S , Siddappa Shilpa , Gowda Malali , Krishna Sudhir , Parida Man Mohan 
Published: July 2019

AbstractThe Influenza A H1N1 virus of 2009 was the first pandemic flu virus of the 21st century. Identifying the emergence of mutations in rapidly mutating Influenza viruses that allow increased transmission or confer resistance are invaluable to global outbreak response. Here we recovered 5 complete Influenza A genomes from 4 oropharygeal swabs and one cell culture isolate from a severe Indian outbreak of flu in early 2015. Multiple amino acids substitutions including those known to confer resistance to Oseltamivir and increased pathogenecity in mice were found in the Neuraminidase gene. Additional mutations both reported and novel were found throughout the genome compared to the vaccine strain (California/04/2009). All eight segments of the complete genomes were found to be genetically related to the 2009 pandemic strain, A(H1N1)pdm09 and belonging to the emerging genogroup 6B. This group was found to be of south East Asian origin by time scale phylogentic analysis. A phylogeographic analysis revealed 39 significant migration events among globally circulating viruses. This study is the first extensive complete genome and phylogeographic analysis of 2015 Indian A(H1N1) pdm09 viruses. We report several novel mutations in the 2015 Indian strains which need to be evaluated for effect on viral replication, transmission and resistance to therapy. The identification of mutant A(H1N1)pdm09 from India warrants continuous monitoring of viral evolution for implementation of suitable medical countermeasures.
Responses of Neurons in the Rostral Ventrolateral Medulla (RVLM) of Conscious Felines to Anticipated and Passive Movements
Authors: Miller Derek M. , Joshi Asmita , Kambouroglos Emmanuel T. , Engstrom Isaiah C. , Bielanin John P. , Wittman Samuel R. , McCall Andrew A. , Barman Susan M. , Yates Bill J. 
Published: July 2019

ABSTRACTConsiderable evidence demonstrates that the vestibular system contributes to regulating sympathetic nerve activity and blood pressure. Initial studies in decerebrate animals showed that presumed pre-sympathetic neurons in the rostral ventrolateral medulla (RVLM) respond to small-amplitude (<10°) rotations of the body, as in other brain areas that process vestibular signals, despite the fact that such movements do not appreciably affect blood distribution in the body. However, a subsequent experiment in conscious animals showed that few RVLM neurons respond to small-amplitude movements. This study tested the hypothesis that vestibular inputs to RVLM neurons are modulated in conscious animals, such that vestibulosympathetic responses are only elicited when changes in body position are large enough to require changes in sympathetic nerve activity. The activity of approximately a third of RVLM neurons whose firing rate was related to the cardiac cycle, and thus likely received baroreceptor inputs, responded to vestibular inputs elicited by 40° head-up tilts in conscious cats, but not during 10° sinusoidal rotations in the pitch plane that affected the activity of neurons in brain regions providing inputs to the RVLM. These data suggest the existence of brain circuitry that suppresses vestibular influences on the activity of RVLM neurons and the sympathetic nervous system unless these inputs are physiologically warranted. We also determined that RVLM activity is not altered prior to tilts when a light cue is provided signaling the movement. The simplest interpretation of this findings is that feedforward cardiovascular responses are associated with active movement such as occurs during exercise, but not passive movements that require cardiovascular adjustments.
Efficient generation of zebrafish maternal-zygotic mutants through transplantation of ectopically induced and Cas9/gRNA targeted PGCs
Authors: Zhang Fenghua , Li Xianmei , He Mudan , Ye Ding , Xiong Feng , Amin Golpour , Zhu Zuoyan , Sun Yonghua 
Published: July 2019

ABSTRACTThe CRISPR/Cas9 technology has been widely utilized for knocking out genes involved in various biological processes in zebrafish. Despite this technology is efficient for generating different mutations, one of the main drawbacks is low survival rates during embryogenesis when knocking out some embryonic lethal genes. To overcome this problem, we developed a novel strategy using a combination of CRISPR/Cas9 mediated gene knockout with primordial germ cells (PGCs) transplantation to facilitate and speed up the process of zebrafish mutant generation, particularly for embryonic lethal genes. First, we optimized the procedure for gRNA targeted PGCs transplantation (PGCT), by increasing the efficiencies of genome mutation in PGCs and induction of PGCs fates in donor embryos for PGCT. Second, the combined CRISPR/Cas9 with PGCT was utilized for generation of maternal zygotic (MZ) mutants oftcf7l1a(essential gene for head development),pou5f3(essential gene for zygotic genome activation) andchd(essential gene for dorsal development) at F1 generation with high efficiency. Finally, we revealed some novel phenotypes in the maternal zygotic mutant oftcf7l1aandchd, while MZtcf7l1ashowed elevated neural crest development, and MZchdhave stronger ventralization than its zygotic counterparts. Therefore, this study presents an efficient and powerful method for generating MZ mutants of embryonic lethal genes in zebrafish.
HORMA domain proteins and a Pch2-like ATPase regulate bacterial cGAS-like enzymes to mediate bacteriophage immunity
Authors: Ye Qiaozhen , Lau Rebecca K. , Mathews Ian T. , Watrous Jeramie D. , Azimi Camillia S. , Jain Mohit , Corbett Kevin D. 
Published: July 2019

AbstractBacteria are continually challenged by foreign invaders including bacteriophages, and have evolved a variety of defenses against these invaders. Here, we describe the structural and biochemical mechanisms of a bacteriophage immunity pathway found in a broad array of bacteria, including pathogenic E. coli and Pseudomonas aeruginosa. This pathway employs eukaryotic-like HORMA domain proteins that recognize specific peptides, then bind and activate a cGAS/DncV-like nucleotidyltransferase (CD-NTase) to generate a cyclic tri-AMP (cAAA) second messenger; cAAA in turn activates an endonuclease effector, NucC. Signaling is attenuated by a homolog of the AAA+ ATPase Pch2/TRIP13, which binds and likely disassembles the active HORMA-CD-NTase complex. When expressed in non-pathogenic E. coli, this pathway confers immunity against bacteriophage λ infection. Our findings reveal the molecular mechanisms of a bacterial defense pathway integrating a cGAS-like nucleotidyltransferase with HORMA domain proteins for threat sensing through protein detection, and negative regulation by a Pch2-like ATPase.
Structure and mechanism of a cyclic trinucleotide-activated bacterial endonuclease mediating bacteriophage immunity
Authors: Lau Rebecca K. , Ye Qiaozhen , Patel Lucas , Berg Kyle R. , Mathews Ian T. , Watrous Jeramie D. , Whiteley Aaron T. , Lowey Brianna , Mekalanos John J. , Kranzusch Philip J. , Jain Mohit , Corbett Kevin D. 
Published: July 2019

AbstractBacteria possess an array of defenses against foreign invaders, including diverse nucleases that target and destroy the genome of an invading bacteriophage or foreign DNA element. A recently-described bacteriophage immunity pathway employs a cGAS/DncV-like nucleotidyltransferase to produce a cyclic tri-AMP second messenger, which activates the DNA endonuclease effector NucC. Here, we show that NucC is related to restriction enzymes but uniquely assembles into a homotrimer in solution. cAAA binding in a conserved allosteric pocket promotes assembly of two NucC trimers into a homohexamer competent for double-strand DNA cleavage. We propose that NucC mediates bacteriophage immunity either through global activation, causing altruistic cell death and abortive infection, or through local activation and targeted phage genome destruction. Finally, we identify NucC homologs in type III CRISPR-Cas systems, where they likely function as accessory nucleases activated by cyclic oligoadenylate second messengers synthesized by these systems’ effector complexes.
Gsα stimulation of mammalian adenylate cyclases regulated by their hexahelical membrane anchors
Authors: Seth Anubha , Finkbeiner Manuel , Grischin Julia , Schultz Joachim E. 
Published: July 2019

AbstractMammalian adenylate cyclases (ACs) are pseudoheterodimers with dissimilar hexahelical membrane-anchors, isoform-specifically conserved for more than half a billion years. We exchanged both membrane anchors of the AC isoform 2 by the isosteric quorum-sensing receptor fromVibrio, CqsS, which has a ligand,Cholera-Autoinducer-1 (CAI-1). In the chimera, AC activity was stimulated by Gsα, CAI-1 had no effect. Surprisingly, CAI-1 inhibited Gsα stimulation. We report that Gsα stimulation of human AC isoforms 2, 3, 5, and 9 expressed in Sf9 cells is inhibited by serum as is AC activity in membranes from rat brain cortex. AC2 activation by forskolin or forskolin/Gsα was similarly inhibited. Obviously, serum contains as yet unidentified factors affecting AC activity. The data establish a linkage in ACs, in which the membrane anchors, as receptors, transduce extracellular signals to the cytosolic catalytic dimer. A mechanistic three state model of AC regulation is presented compatible with all known regulatory inputs into mammalian ACs. The data allow designating the membrane anchors of mammalian ACs as orphan receptors and establish a new level of AC regulation.
Molecular determinants of large cargo transport into the nucleus
Authors: Paci Giulia , Lemke Edward A 
Published: July 2019

AbstractTransport of molecules between the nucleus and the cytoplasm is tightly regulated by the nuclear pore complex (NPC). Even very large cargoes such as many pathogens, mRNAs and pre-ribosomal subunits can pass the NPC intact. Compared to small import complexes, for such large cargoes >15 nm there is very little quantitative understanding of the mechanism for efficient transport, the role of multivalent binding to nuclear transport receptors via nuclear localisation sequences (NLSs) and effects of size differences. Here, we assayed nuclear import kinetics in cells for a total of 30 large cargo models based on four capsid-like particles in the size range of 17-36 nm, with tuneable numbers of up to 240 NLSs. We show that the requirements for transport scale non-linearly with size and obey a minimal cut off of functional import requiring more than 10 NLS in the lowest case. Together, our results reveal the key molecular determinants on large cargo import kinetics in cells.
Centrioles are amplified via rosette formation in cycling progenitors of olfactory sensory neurons
Authors: Ching Kaitlin , Stearns Tim 
Published: July 2019

AbstractOlfaction in most animals is mediated by neurons bearing cilia that are accessible to the environment. Olfactory sensory neurons (OSNs) in chordates usually have multiple cilia, each with a centriole at its base. OSNs differentiate from stem cells in the olfactory epithelium, and how the epithelium generates cells with many centrioles—about 16 in mouse—is not yet understood. We show that centrioles are amplified via centriole rosette formation in both embryonic development and turnover of the olfactory epithelium in adults, and rosette-bearing cells often have free centrioles in addition. Cells with amplified centrioles can go on to divide, with centrioles clustered at each pole. Additionally, we found that immediate neuronal precursors amplify centrioles concomitantly with elevation of mRNA for Plk4 and Stil, key regulators of centriole duplication. Our findings highlight the importance of accounting for centriole amplification in neuron regeneration therapies derived from olfactory epithelia.