bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maintenance of adaptive dynamics and no detectable load in a range-edge out-crossing plant population
Authors: Takou Margarita , Hämälä Tuomas , Koch Evan M. , Steige Kim A. , Dittberner Hannes , Yant Levi , Genete Mathieu , Sunyaev Shamil , Castric Vincent , Vekemans Xavier , Savo-lainen Outi , de Meaux Juliette 
Published: July 2019

AbstractDuring range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here, we contrast populations of the European sub-speciesArabidopsis lyratassppetraea, which expanded its Northern range after the last glaciation. We document a sharp decline in effective population size in the range-edge population and observe that non-synonymous variants segregate at higher frequencies. We detect a 4.9% excess of derived non-synonymous variants per individual in the range-edge population, suggesting an increase of the genomic burden of deleterious mutations. Inference of the fitness effects of mutations and modeling of allele frequencies under the explicit demographic history of each population predicts a depletion of rare deleterious variants in the range-edge population, but an enrichment for fixed ones, consistent with the bottleneck effect. However, the demographic history of the range-edge population predicts a small net decrease in per-individual fitness. Consistent with this prediction, the range-edge population is not impaired in its growth and survival measured in a common garden experiment. We further observe that the allelic diversity at the self-incompatibility locus, which ensures strict outcrossing and evolves under negative frequency-dependent selection, has remained unchanged. Genomic footprints indicative of selective sweeps are broader in the Northern population but not less frequent. We conclude that the outcrossing speciesA. lyratassppetraeashows a strong resilience to the effect of range expansion.
Template plasmid integration in germline genome-edited cattle
Authors: Norris Alexis L. , Lee Stella S. , Greenlees Kevin J. , Tadesse Daniel A. , Miller Mayumi F. , Lombardi Heather 
Published: July 2019

AbstractWe analyzed publicly available whole genome sequencing data from cattle which were germline genome-edited to introduce polledness. Our analysis discovered the unintended heterozygous integration of the plasmid and a second copy of the repair template sequence, at the target site. Our finding underscores the importance of employing screening methods suited to reliably detect the unintended integration of plasmids and multiple template copies.
Transpeptidase PBP2 governs initial localization and activity of major cell-wall synthesis machinery inEscherichia coli
Authors: Wollrab Eva , Özbaykal Gizem , Vigouroux Antoine , Cordier Baptiste , Simon Francois , Chaze Thibault , Matondo Mariette , van Teeffelen Sven 
Published: July 2019

AbstractBacterial shape is physically determined by the peptidoglycan cell wall. The cell-wall-synthesis machinery responsible for rod shape inEscherichia coliis the processive ‘Rod complex’. Previously, cytoplasmic MreB filaments were thought to govern formation and localization of Rod complexes based on local cell-envelope curvature. However, using single-particle tracking of the transpeptidase PBP2, we found strong evidence that PBP2 initiates new Rod complexes by binding to a substrate different from MreB or any known Rod-complex component. This substrate is likely the cell wall. Consistently, we found only weak correlations between MreB and envelope curvature in the cylindrical part of cells. Residual correlations do not require any curvature-based Rod-complex initiation but can be attributed to persistent rotational motion. Therefore, local cell-wall architecture likely provides the cue for PBP2 binding and subsequent Rod-complex initiation. We also found that PBP2 has a limiting role for Rod-complex activity, thus supporting its central role.
Pathogenic and uncertain genetic variants have clinical cardiac correlates in diverse biobank participants
Authors: Pottinger Tess D. , Puckelwartz Megan J. , Pesce Lorenzo L. , Robinson Avery , Kearns Samuel , Pacheco Jennifer A. , Rasmussen-Torvik Laura J. , Smith Maureen E. , Chisholm Rex , McNally Elizabeth M. 
Published: July 2019

AbstractBackgroundGenome sequencing coupled with electronic heath record data can uncover medically important genetic variation. Interpretation of rare genetic variation and its role in mediating cardiovascular phenotypes is confounded by variants of uncertain significance.Methods and ResultsWe analyzed the whole genome sequence of 900 racially and ethnically diverse biobank participants selected from a single US center. Participants were equally divided among European, African, Hispanic, and mixed race/ethnicities. We evaluated the American College of Medical Genetics and Genomics medically actionable list of 59 genes focusing on the cardiac genes. Variation was interpreted using the most recent reports in ClinVar, a database of medically relevant human variation. We identified 19 individuals with pathogenic/likely pathogenic variants in cardiac actionable genes (2%) and found evidence for clinical correlates in the electronic health record. African ancestry participants had more variants of uncertain significance in the medically actionable genes including the 30 cardiac actionable genes, even when normalized to total variant count per person. Longitudinal measures of left ventricle size, corrected for body surface area, from approximately 400 biobank participants (1,723 patient years) correlated with genetic findings. The presence of one or more uncertain variants in the actionable cardiac genes and a cardiomyopathy diagnosis correlated with increased left ventricular internal diameter in diastole and in systole. In particular, MYBPC3 was identified as a gene with excess variants of uncertain significance.ConclusionsThese data indicate a subset of uncertain variants may confer risk and should not be considered benign.
Efficient RNP-directed human gene targeting reveals SPDEF is required for IL-13-induced mucostasis
Authors: Koh Kyung Duk , Siddiqui Sana , Cheng Dan , Bonser Luke R. , Sun Dingyuan I. , Zlock Lorna T. , Finkbeiner Walter E. , Woodruff Prescott G. , Erle David J. 
Published: July 2019

AbstractPrimary human bronchial epithelial cell (HBEC) cultures are a useful model for studies of lung health and major airway diseases. However, mechanistic studies have been limited by our ability to selectively disrupt specific genes in these cells. Here we optimize methods for gene targeting in HBECs by direct delivery of single guide RNA (sgRNA) and recombinant Cas9 (rCas9) complexes by electroporation, without a requirement for plasmids, viruses, or antibiotic selection. Variations in the method of delivery, sgRNA and rCas9 concentrations, and sgRNA sequences all had effects on targeting efficiency, allowing for predictable control of the extent of gene targeting and for near complete disruption of gene expression. To demonstrate the value of this system, we targeted SPDEF, which encodes a transcription factor previously shown to be essential for the differentiation of MUC5AC-producing goblet cells in mouse models of asthma. Targeting SPDEF led to proportional decreases in MUC5AC expression in HBECs stimulated with IL-13, a central mediator of allergic asthma. Near-complete targeting of SPDEF abolished IL-13-induced MUC5AC expression and goblet cell differentiation. In addition, targeting of SPDEF prevented IL-13-induced impairment of mucociliary clearance, which is likely to be an important contributor to airway obstruction, morbidity, and mortality in asthma. We conclude that direct delivery of sgRNA and rCas9 complexes allows for predictable and efficient gene targeting and enables mechanistic studies of disease-relevant pathways in primary HBECs.
Sleep regulates the glial engulfment receptor Draper to promote Wallerian degeneration
Authors: Stahl Bethany A. , Jaggard James B. , Keene Alex C. 
Published: July 2019

SummarySleep, a universal behavior, is critical for diverse aspects of brain function. Chronic sleep disturbance is associated with numerous health consequences, including neurodegenerative disease and cognitive decline. Neurite damage due to apoptosis, trauma, or genetic factors is a common feature of aging, and clearance of damaged neurons is essential for maintenance of brain function. In the central nervous system, damaged neurites are cleared by Wallerian degeneration, in which activated microglia and macrophages engulf damaged neurons. The fruit fly Drosophila melanogaster provides a powerful model for investigating the relationship between sleep and Wallerian degeneration. Several lines of evidence suggest that glia influence sleep duration, sleep-mediated neuronal homeostasis, and clearance of toxic substances during sleep, raising the possibility that glial engulfment of damaged axons is regulated by sleep. To explore this possibility, we axotomized olfactory receptor neurons and measured the effects of sleep loss or gain on the clearance of damaged neurites. Mechanical sleep deprivation impaired the clearance of damaged neurites, whereas the sleep-promoting drug gaboxadol accelerated clearance. In sleep-deprived animals, multiple markers of glial activation were delayed, including activation of the JAK/STAT pathway, upregulation of the cell corpse engulfment receptor Draper, and innervation of the antennal lobe by glial membranes. These markers were all enhanced when sleep was induced in gaboxadol-treated flies. Taken together, these findings reveal a critical role for sleep in regulation glial activation and engulfment following axotomy, providing a platform for further investigations of the molecular mechanisms underlying sleep-dependent modulation of glial function and neurite clearance.HighlightsSleep deprivation impairs Wallerian degeneration in fruit flies.Pharmacological induction of sleep accelerates Wallerian degeneration.Sleep promotes innervation surrounding damaged neurites by phagocytic glia.Sleep increases levels of the glial activation markers Draper and Stat92E.
Deep sampling of HawaiianCaenorhabditis elegansreveals high genetic diversity and admixture with global populations
Authors: Crombie Timothy A. , Zdraljevic Stefan , Cook Daniel E. , Tanny Robyn E. , Brady Shannon C. , Wang Ye , Evans Kathryn S. , Hahnel Steffen , Lee Daehan , Rodriguez Briana C. , Zhang Gaotian , van der Zwaag Joost , Kiontke Karin C. , Andersen Erik C. 
Published: July 2019

AbstractRecent efforts to understand the natural niche of the keystone model organismCaenorhabditis eleganshave suggested that this species is cosmopolitan and associated with rotting vegetation and fruits. However, most of the strains isolated from nature have low genetic diversity likely because recent chromosome-scale selective sweeps contain alleles that increase fitness in human-associated habitats. Strains from the Hawaii Islands are highly divergent from non-Hawaiian strains. This result suggests that Hawaiian strains might contain ancestral genetic diversity that was purged from most non-Hawaiian strains by the selective sweeps. To characterize the genetic diversity and niche of HawaiianC. elegans, we sampled across the Hawaiian Islands and isolated 100 newC. elegansstrains. We found thatC. elegansstrains are not associated with any one substrate but are found in cooler climates at high elevations. These Hawaiian strains are highly diverged compared to the rest of the global population. Admixture analysis identified 11 global populations, four of which are from Hawaii. Surprisingly, one of the Hawaiian populations shares recent ancestry with non-Hawaiian populations, including portions of globally swept haplotypes. This discovery provides the first evidence of gene flow between Hawaiian and non-Hawaiian populations. Most importantly, the high levels of diversity observed in Hawaiian strains might represent the complex patterns of ancestral genetic diversity in theC. elegansspecies before human influence.
Tunable hetero-assembly of a plant pseudoenzyme-enzyme complex
Authors: Novikova Irina V. , Zhou Mowei , Du Chen , Parra Marcelina , Kim Doo Nam , VanAernum Zachary L. , Shaw Jared B. , Hellmann Hanjo , Wysocki Vicki H. , Evans James E. 
Published: July 2019

AbstractPseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically non-active. Yet many factors defining why one protein is active while its homolog is inactive remain uncertain. For pseudoenzyme-enzyme pairs, the similarity of both subunits can often hinder conventional characterization approaches. In plants, a pseudoenzyme PDX1.2 positively regulates vitamin B6 production by association with its active catalytic homologs such as PDX1.3 through an unknown mechanism. Here we used an integrative experimental approach to learn that such pseudoenzyme-enzyme pair associations result in hetero-complexes of variable stoichiometry, which are unexpectedly tunable. We also present the atomic structure of the PDX1.2 pseudoenzyme as well as the population averaged PDX1.2-PDX1.3 pseudoenzyme-enzyme pair. Finally, we dissected hetero-dodecamers of each stoichiometry to understand the arrangement of monomers in the hetero-complexes and identified symmetry- imposed preferences in PDX1.2-PDX1.3 interactions. Our results provide a new model of pseudoenzyme-enzyme interactions and their native heterogeneity.
A chimeric Japanese encephalitis vaccine protects against lethal yellow fever virus infection without inducing neutralizing antibodies
Authors: Mishra Niraj , Boudewijns Robbert , Schmid Michael A. , Marques Rafael Elias , Sharma Sapna , Neyts Johan , Dallmeier Kai 
Published: July 2019

ABSTRACTRecent massive outbreaks of yellow fever virus (YFV) in West Africa and Brazil resulted in rapid depletion of global vaccine emergency stockpiles and raised concerns about being not prepared against future YFV epidemics. Here we report that a live-attenuated virus similar to the Japanese encephalitis virus (JEV) vaccine JE-CVax/Imojev®that consists of YFV-17D vaccine from which the structural (prM/E) genes have been replaced with those of the JEV SA14-14-2 vaccine strain confers full protection in mice against lethal YFV challenge. In contrast to the YFV-17D mediated protection against YFV, this protection is not mediated by neutralizing antibodies but correlates with YFV-specific non-neutralizing antibodies and T cell responses against cell-associated YFV NS1 and other YFV non-structural (NS) proteins. Our findings reveal the importance of YFV NS proteins to mediate protection and demonstrate that chimeric flavivirus vaccines, such as Imojev®can confer protection against two flaviviruses. This dual protection has implications for the possible off-label use of JE-CVax in case of emergency and vaccine shortage during YFV outbreaks. In addition, populations in Asia that have been vaccinated with Imojev®may already be protected against YFV should outbreaks ever occur on that continent as feared by WHO.IMPORTANCEEfficient and safe vaccines exist against yellow fever (e.g. YFV-17D) that provide long-lasting protection by rapidly inducing neutralizing antibody responses. However, vaccine supply cannot cope with an increasing demand posed by massive urban outbreaks in recent years. Here we report that JE-CVax/Imojev®, a YFV-17D-based chimeric Japanese encephalitis vaccine also efficiently protects against YFV infection in mice. In case of shortage of the YFV vaccine during yellow fever outbreaks, (off-label) use of JE-CVax/Imojev®may be considered. Moreover, wider use of JE-CVax/Imojev®in Asia may lower the risk of the much-feared YFV spill over to the continent. More in general chimeric vaccines that combine surface antigens and replication machineries of two distinct flaviviruses can be considered dual vaccines, for the latter pathogen without induction of surface-specific antibodies. Following this rationale, novel flavivirus vaccines that do not hold a risk for antibody-dependent enhancement (ADE) of infection [inherent to current dengue vaccines and dengue vaccine candidates] could be designed.
A stochastic model of gene expression with polymerase recruitment and pause release
Authors: Cao Z. , Filatova T. , Oyarzún D. A. , Grima R. 
Published: July 2019

AbstractTranscriptional bursting is a major source of noise in gene expression. The telegraph model of gene expression, whereby transcription switches between “on” and “off” states, is the dominant model for bursting. Recently it was shown that the telegraph model cannot explain a number of experimental observations from perturbation data. Here we study an alternative model that is consistent with the data and which explicitly describes RNA polymerase recruitment and polymerase pause release, two steps necessary for mRNA production. We derive the exact steady-state distribution of mRNA numbers and an approximate steady-state distribution of protein numbers which are given by generalized hypergeometric functions. The theory is used to calculate the relative sensitivity of the coefficient of variation of mRNA fluctuations for thousands of genes in mouse fibroblasts. This indicates that the size of fluctuations is mostly sensitive to the rate of burst initiation and the mRNA degradation rate. Furthermore we show that (i) the time-dependent distribution of mRNA numbers is accurately approximated by a modified telegraph model with a Michaelis-Menten like dependence of the effective transcription rate on RNA polymerase abundance. (ii) the model predicts that if the polymerase recruitment rate is comparable or less than the pause release rate, then upon gene replication the mean number of RNA per cell remains approximately constant. This gene dosage compensation property has been experimentally observed and cannot be explained by the telegraph model with constant rates.Statement of SignificanceThe random nature of gene expression is well established experimentally. Mathematical modelling provides a means of understanding the factors leading to the observed stochasticity. There is evidence that the classical two-state model of stochastic mRNA dynamics (the telegraph model) cannot describe perturbation experiments and a new model that includes polymerase dynamics has been proposed. In this paper, we present the first detailed study of this model, deriving an exact solution for the mRNA distribution in steady-state conditions, an approximate time-dependent solution and showing the model can explain gene dosage compensation. As well, we use the theory together with transcriptomic data, to deduce which parameters when perturbed lead to a maximal change in the size of mRNA fluctuations.
Toxicity and bioaccumulation of Cadmium, Copper and Zinc in a direct comparison at equitoxic concentrations in common carp (Cyprinus carpio) juveniles
Authors: Delahaut Vyshal , Rašković Božidar , Salvado Marta Satorres , Bervoets Lieven , Blust Ronny , De Boeck Gudrun 
Published: July 2019

AbstractThe individual toxicity and bioaccumulation of cadmium (Cd), copper (Cu) and zinc (Zn) towards common carp juveniles was evaluated in a direct comparison in two experimental setups. First, the fish were exposed for 10 days to different metal concentrations. Accumulated metals were quantified and showed a positive dose dependent uptake for cadmium and copper, but not for zinc. Toxicity was in the order Cd>Cu>Zn with 96h LC50values (concentration where 50% of the animals dies within 96h) for Cd at 0.20±0.16 μM, Cu at 0.77±0.03 μM, and Zn at 29.89±9.03 μM respectively, and incipient lethal levels (concentration where 50% of the animals survives indefinitely) at 0.16 μM, 0.77 μM and 28.33 μM respectively. Subsequently, a subacute exposure experiment was conducted, where carp juveniles were exposed to 2 equitoxic concentrations (10% and 50% of LC5096 h) of the three metals. The gill metal content was quantified after 1, 3 and 7 days, and was correlated to electrolyte levels and structural damage of the gill tissue and associated pathological effects. Again a significant dose-dependent increase in gill cadmium and copper, but not in zinc, was observed during the 7-day exposure. Copper clearly affected the sodium levels in the gill tissue, while zinc and cadmium did not significantly alter any of the gill electrolytes. The overall histopathological effects (e.g. hyperemia and hypertrophy) of the metal exposures were mild for most of the alterations, and no metal specific pattern was elucidated for the tested metals except oedema of the primary epithelium which typically occurred in both levels of Zn exposure.
Titrating gene expression with series of systematically compromised CRISPR guide RNAs
Authors: Jost Marco , Santos Daniel A. , Saunders Reuben A. , Horlbeck Max A. , Hawkins John S. , Scaria Sonia M. , Norman Thomas M. , Hussmann Jeffrey A. , Liem Christina R. , Gross Carol A. , Weissman Jonathan S. 
Published: July 2019

AbstractBiological phenotypes arise from the degrees to which genes are expressed, but the lack of tools to precisely control gene expression limits our ability to evaluate the underlying expression-phenotype relationships. Here, we describe a readily implementable approach to titrate expression of human genes using series of systematically compromised sgRNAs and CRISPR interference. We empirically characterize the activities of compromised sgRNAs using large-scale measurements across multiple cell models and derive the rules governing sgRNA activity using deep learning, enabling construction of a compact sgRNA library to titrate expression of ∼2,400 genes involved in central cell biology and a genome-widein silicolibrary. Staging cells along a continuum of gene expression levels combined with rich single-cell RNA-seq readout reveals gene-specific expression-phenotype relationships with expression level-specific responses. Our work provides a general tool to control gene expression, with applications ranging from tuning biochemical pathways to identifying suppressors for diseases of dysregulated gene expression.
FungalRoot: Global online database of plant mycorrhizal associations
Authors: Soudzilovskaia Nadejda A. , Vaessen Stijn , Barcelo Milargos , He Jinhong , Rahimlou Saleh , Abarenkov Kessy , Brundrett Mark C. , Gomes Sofia , Merckx Vincent , Tedersoo Leho 
Published: July 2019

SummaryThe urgent need to better understand profound impacts of mycorrhizas on functioning of terrestrial ecosystems, along with recent debates on resolving plant mycorrhizal associations, indicate that there is a great need for a comprehensive data of plant mycorrhizal associations able to support testing of ecological, biogeographic and phylogenetic hypotheses.Here present a database, FungalRoot, which summarizes publicly available data on plant mycorrhizal type and intensity of root colonization by mycorrhizal fungi, accompanied by rich meta-data. We collected and digitized data on plant mycorrhizal colonization intensity published until April 2019 in 9 globally most important languages. The data were assessed for quality and updated for plant taxonomy.The FungalRoot database contains 36,303 species by site observations for 14,870 plant species, tripling the previously available amount in any compilation. The great majority of ectomycorrhizal and ericod mycorrhizal plants are trees and shrubs, 92% and 85% respectively. The majority of arbuscular mycorrhizal and of non-mycorrhizal plant species are herbaceous (50% and 70%).Besides acting as a compilation of referenced observations, our publicly available database provides a recommendation list of plant mycorrhizal status for ecological and evolutionary analyses to promote research on the links between above- and belowground biodiversity and functioning of terrestrial ecosystems.