bluuebunny/crossref_metadata_2025_split huggingface dataset:
HierCC: A multi-level clustering scheme for population assignments based on core genome MLST
Authors: Zhou Zhemin , Charlesworth Jane , Achtman Mark 
Published: November 2020

AbstractMotivationRoutine infectious disease surveillance is increasingly based on large-scale whole genome sequencing databases. Real-time surveillance would benefit from immediate assignments of each genome assembly to hierarchical population structures. Here we present HierCC, a scalable clustering scheme based on core genome multi-locus typing that allows incremental, static, multi-level cluster assignments of genomes. We also present HCCeval, which identifies optimal thresholds for assigning genomes to cohesive HierCC clusters. HierCC was implemented in EnteroBase in 2018, and has since genotyped >400,000 genomes fromSalmonella, Escherichia, YersiniaandClostridioides.AvailabilityImplementation:http://enterobase.warwick.ac.uk/and Source codes:https://github.com/zheminzhou/HierCCContactzhemin.zhou@warwick.ac.ukSupplementary informationSupplementary data are available atBioinformaticsonline.
Chemical composition and insecticidal activity of Aeollanthus pubescens Benth leaf essential oil on the malaria vector Anopheles gambiae (Diptera: Culicidae)
Authors: Bohounton Roméo Barnabé , Djogbénou Luc Salako , Djihinto Oswald Yédjinnavênan , Dedome Oronce Sedjro-Ludolphe , Sovegnon Pierre Marie , Barea Bruno , Adomou Aristide , Villeneuve Pierre , Tchobo Fidèle Paul 
Published: November 2020

AbstractThe use of synthetic insecticides is responsible for many cases of resistance in insects. Therefore, the use of natural molecules of ecological interest with insecticidal properties turns out to be an alternative approach to the use of synthetic insecticides. This study aims at investigating the larvicidal, adulticidal activity and the composition of the essential oil of Aeollanthus pubescens Benth on the major malaria vector Anopheles gambiae.The leaves of Aeollanthus pubescens were collected in the South of the Republic of Benin. Three reference strains of Anopheles gambiae s.s. such as Kisumu, Kiskdr and Acerkis were used. The chemical composition of the essential oil was analysed by gas chromatography coupled to mass spectrometry. Larvae were exposed to the essential oil extract for 24 h. Adult mosquitoes were exposed to the fragment nets coated with the essential oil for 3 min. Larval mortality and adult survivorship were monitored.Fourteen components were identified representing 98.31% of the total of oil. The major components were carvacrol (51.06 %), thymyle acetate (14.01 %) and γ-terpinene (10.60 %). The essential oil has remarkable larvicidal properties with LC50 of 29.26, 22.65, and 28.37 ppm respectively on Kisumu, Acerkis and Kiskdr strains. With the fragment net treated at 165 µg/cm2, the KDT50 of both Acerkis (1.71 s, p < 0.001) and Kiskdr (2.67 s, p < 0.001) individuals were significantly lower than that of Kisumu (3.77 s). The lifespan of the three mosquito strains decreased respectively to one day for Kisumu (p < 0.001), two days for Acerkis (p < 0.001) and three days for Kiskdr (p < 0.001) compared to their control.Our findings show that the Aeollanthus pubescens essential oil is an efficient larvicide and adulticide against malaria vector Anopheles gambiae. This bioinsecticidal activity is a promising discovery for the control of the resistant malaria-transmitting vectors.
Selective BCL-XL Antagonists Eliminate Infected Cells from a Primary Cell Model of HIV Latency but not from Ex Vivo Reservoirs
Authors: Ren Yanqin , Huang Szu Han , Macedo Amanda B. , Ward Adam R. , Alberto Winiffer D. Conce , Klevorn Thais , Leyre Louise , Chan Dora , Truong Ronald , Rohwetter Thomas , Zumbo Paul , Dündar Friederike , Betel Doron , Kovacs Colin , Benko Erika , Bosque Alberto , Jones R. Brad 
Published: November 2020

AbstractHIV persists, despite antiviral immune responses and effective antiretroviral therapy, in viral reservoirs that seed rebound viremia if therapy is interrupted. Previously, we showed that the BCL-2 protein contributes to HIV persistence by conferring a survival advantage to reservoir-harboring cells. Here, we demonstrate that many of the BCL-2 family members are overexpressed in HIV-infected CD4+ T-cells, indicating increased tension between pro-apoptotic and pro-survival family members – as well as raising the possibility that the inhibition of pro-survival members may disproportionately affect the survival of HIV-infected cells. Based on these results, we chose to further study BCL2L1 (encoding the protein BCL-XL), due to its consistent overexpression and the availability of selective antagonists. Infection of primary CD4+ T-cells with either a clinical isolate, a CCR5-tropic strain, or a CXCR4-tropic strain of HIV resulted in increased BCL-XL protein expression; and treatment with two selective BCL-XL antagonists, A-1155463 and A-1551852, led to disproportionate cell death compared to uninfected CD4+ T-cells. In a primary cell model of latency, both BCL-XL antagonists drove significant reductions in total HIV DNA and in infectious cell frequencies both alone and in combination with the latency reversing agent bryostatin-1, with little off-target cytotoxicity. However, these antagonists, with or without bryostatin-1, or in combination with the highly potent latency reversing agent combination PMA + ionomycin, failed to reduce total HIV DNA and infectious reservoirs in ex vivo CD4+ T-cells from ART-suppressed donors. Our results add to growing evidence that bonafide reservoir-harboring cells are resistant to multiple “kick and kill” modalities - relative to latency models - and uncover BCL-XL antagonists as a facile approach to probing mechanistic underpinnings. We also interpret our results as encouraging of further exploration of BCL-XL antagonists for cure, where combination approaches may unlock the ability to eliminate ex vivo reservoirs.
Efficient GNE myopathy disease modeling with mutation specific phenotypes in human pluripotent stem cells by base editors
Authors: Park Ju-Chan , Kim Jumee , Jang Hyun-Ki , Lee Seung-Yeon , Kim Keun-Tae , Park Seokwoo , Lee Hyun Sik , Choi Hee-Jung , Park Soon-Jung , Moon Sung-Hwan , Bae Sangsu , Cha Hyuk-Jin 
Published: November 2020

SummaryDespite the great potential of disease modeling with the isogenic pairs of human pluripotent stem cells (hPSCs), the extremely low efficiency of precise gene editing in hPSCs remains a technical hurdle for this approach. Herein, we took advantage of currently available base editors (BEs) to epitomize the isogenic disease model from hPSCs. Using this method, we established 14 hPSCs that harbor point mutations on the GNE gene, including four different mutations found in GNE myopathy patients. Due to lesser activation of p53 by BEs than Cas9, a higher editing efficiency with BEs was achieved. Four different mutations in the epimerase or kinase domains of GNE revealed mutation-specific hyposialylation, which was closely correlated to pathological clinical phenotypes. These mutation-specific hyposialylation patterns were evident in GNE protein structure modeling. Furthermore, treatment with a drug candidate currently under clinical trials showed a mutation-specific drug response in GNE myopathy disease models. These data suggest that isogenic disease models from hPSCs using BEs could serve as a useful tool for mimicking the pathophysiology of GNE myopathy and for predicting drug responses.
Comprehensive benchmarking of metagenomic classification tools for long-read sequencing data
Authors: Marić Josip , Križanović Krešimir , Riondet Sylvain , Nagarajan Niranjan , Šikić Mile 
Published: November 2020

AbstractBackgroundLong reads have gained popularity in the analysis of metagenomics data. Therefore, we comprehensively assessed metagenomics classification tools on the species taxonomic level. We analysed kmer-based tools, mapping-based tools and two general-purpose long reads mappers. We evaluated more than 20 pipelines which use either nucleotide or protein databases and selected 13 for an extensive benchmark. We prepared seven synthetic datasets to test various scenarios, including the presence of a host, unknown species and related species. Moreover, we used available sequencing data from three well-defined mock communities, including a dataset with abundance varying from 0.0001% to 20% and six real gut microbiomes.ResultsGeneral-purpose mappers Minimap2 and Ram achieved similar or better accuracy on most testing metrics than best-performing classification tools. They were up to ten times slower than the fastest kmer-based tools requiring up to four times less RAM. All tested tools were prone to report organisms not present in datasets, except CLARK-S, and they underperformed in the case of the high presence of the host’s genetic material. Tools which use a protein database performed worse than those based on a nucleotide database. Longer read lengths made classification easier, but due to the difference in read length distributions among species, the usage of only the longest reads reduced the accuracy.The comparison of real gut microbiome datasets shows a similar abundance profiles for the same type of tools but discordance in the number of reported organisms and abundances between types. Most assessments showed the influence of database completeness on the reports.ConclusionThe findings indicate that kmer-based tools are well-suited for rapid analysis of long reads data. However, when heightened accuracy is essential, off-the-shelf mappers demonstrate slightly superior performance, albeit at a considerably slower pace. Nevertheless, a combination of diverse categories of tools and databases will likely be necessary to analyse complex samples. Discrepancies observed among tools when applied to real gut datasets, as well as a reduced performance in cases where unknown species or a significant proportion of the host genome is present in the sample, highlight the need for continuous improvement of existing tools. Additionally, regular updates and curation of databases are important to ensure their effectiveness.
A developmentally programmed splicing failure attenuates the DNA damage response during mammalian zygotic genome activation
Authors: Wyatt Christopher D. R. , Pernaute Barbara , Gohr André , Miret-Cuesta Marta , Goyeneche Lucia , Rovira Quirze , Bogdanovic Ozren , Bonnal Sophie , Irimia Manuel 
Published: November 2020

ABSTRACTThe transition from maternal to embryonic transcriptional control is a crucial step in embryogenesis. However, how alternative splicing is regulated during this process and how it contributes to early development is unknown. Using transcriptomic data from pre-implantation stages of human, mouse and cow, we show that the stage of zygotic genome activation (ZGA) exhibits the highest levels of exon skipping diversity reported for any cell or tissue type. Interestingly, much of this exon skipping is temporary, leads to disruptive non-canonical isoforms, and occurs in genes enriched for DNA damage response in the three species. We identified two core spliceosomal components, Snrpb and Snrpd2, as regulators of these patterns. These genes have low maternal expression at the time of ZGA and increase sharply thereafter. Consistently, microinjection of Snrpb/d2 mRNA into mouse zygotes reduces the levels of temporary exon skipping at ZGA, and leads to an increase in etoposide-induced DNA damage response. Altogether, our results suggest that mammalian embryos undergo an evolutionarily conserved and developmentally programmed specific splicing failure at the time of genome activation that attenuates cellular responses to DNA damage at these early stages.
Differential impact of GABAA receptors and gephyrin post-translational modifications on layer 2/3 pyramidal neuron responsiveness in vivo
Authors: Tsai Yuan-Chen , Hleihil Mohammad , Otomo Kanako , Abegg Andrin , Cavaccini Anna , Panzanelli Patrizia , Cramer Teresa , Ferrari Kim David , Barrett Matthew J.P. , Bosshard Giovanna , Karayannis Theofanis , Weber Bruno , Stobart Jillian L. , Tyagarajan Shiva K. 
Published: November 2020

AbstractA diverse set of GABAA receptors (GABAARs) enable synaptic plasticity adaptations at inhibitory postsynaptic sites in collaboration with the scaffolding protein gephyrin. Early studies helped to identify distinctions between GABAAR subtypes allocated within specific functional circuits, but their contribution to the changing dynamics of a microcircuit remains unclear. Here, using the whisker-barrel system in mouse, we assessed the contribution of specific synaptic GABAAR subtypes and gephyrin scaffolding changes to sensory processing in vivo. We monitored spontaneous and evoked Ca2+ transients in layer 2/3 pyramidal cells with the genetically encoded Ca2+ sensor RCaMP1.07. Using Gabra1 or Gabra2 global and conditional knockout mice, we uncovered that α1- and α2-GABAARs determine the sparseness of L2/3 pyramidal neuron encoding. In a cell-type dependent manner, α1-GABAARs and α2-GABAARs affected neuronal excitability and the reliability of neuronal responses after whisker stimulation. We also discerned that gephyrin with its diverse post-translational modifications (PTMs) shows preference for specific GABAAR subtype to facilitate microcircuit activity. Our results underscore the relevance of the diversity of GABAARs within a cortical microcircuit.Key pointsWhile GABAergic inhibition from interneuron subtypes regulates cortical microcircuit activity the molecular determinants have remain unclear.We demonstrate that specific-GABAA receptor subtypes contribute differentially to layer 2/3 neuronal activities in mouse barrel cortex.Importantly, we link the GABAAR contributions to the scaffolding properties of its important postsynaptic density protein gephyrin. We show that different PTMs on gephyrin determines neuronal excitability via GABAAR recruitment and modulation of inhibition within layer 2/3 neurons.Specifically, α1 and α2 subunits containing GABAA receptors, along with their scaffolding protein gephyrin determine the distribution of high, medium and low activity pyramidal neurons during sensory encoding, whereby controlling the total activity of cortical microcircuit.
The C99 domain of the amyloid precursor protein is a disordered membrane phase-preferring protein
Authors: Capone Ricardo , Tiwari Ajit , Hadziselimovic Arina , Peskova Yelena , Hutchison James M. , Sanders Charles R. , Kenworthy Anne K. 
Published: November 2020

AbstractProcessing of the amyloid precursor protein (APP) via the amyloidogenic pathway is associated with the etiology of Alzheimer’s disease. The cleavage of APP by β-secretase to generate the transmembrane 99-residue C-terminal fragment (C99) and subsequent processing of C99 by γ-secretase to yield amyloid-β (Aβ) peptides are essential steps in this pathway. Biochemical evidence suggests amyloidogenic processing of C99 occurs in cholesterol- and sphingolipid-enriched liquid ordered phase membrane raft domains. However, direct evidence that C99 preferentially associates with rafts has remained elusive. Here, we test this idea by quantifying the affinity of C99-GFP for raft domains in cell-derived giant plasma membrane vesicles. We find that C99 is essentially excluded from ordered domains in HeLa cells, SH-SY5Y cells and neurons, instead exhibiting a strong (roughly 90%) affinity for disordered domains. The strong association of C99 with disordered domains occurs independently of its cholesterol binding activity, homodimerization, or the familial Alzheimer disease Arctic mutation. Finally, we confirm previous studies suggesting that C99 is processed in the plasma membrane by α-secretase, in addition to the well-known γ-secretase. These findings suggest that C99 itself lacks an intrinsic affinity for raft domains, implying either that amyloidogenic processing of the protein occurs in disordered regions of the membrane, that processing involves a marginal sub-population of C99 found in rafts, or that as-yet-unidentified protein-protein interactions involving C99 in living cells drive it into rafts to promote its cleavage therein.
Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection
Authors: Kamel Wael , Noerenberg Marko , Cerikan Berati , Chen Honglin , Järvelin Aino I. , Kammoun Mohamed , Lee Jeff , Shuai Ni , Garcia-Moreno Manuel , Andrejeva Anna , Deery Michael J. , Neufeldt Christopher J. , Cortese Mirko , Knight Michael L. , Lilley Kathryn S. , Martinez Javier , Davis Ilan , Bartenschlager Ralf , Mohammed Shabaz , Castello Alfredo 
Published: November 2020

ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19. SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control SARS-CoV-2 infection remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively which cellular and viral RBPs are involved in SARS-CoV-2 infection. We reveal that the cellular RNA-bound proteome is remodelled upon SARS-CoV-2 infection, having widespread effects on RNA metabolic pathways, non-canonical RBPs and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Amongst them, several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.
Different contrast encoding in ON and OFF visual pathways
Authors: Idrees Saad , Münch Thomas A. 
Published: November 2020

AbstractSubjective visual experience builds on sensory encoding of light reflected by different objects in our environment. Most retinal ganglion cells encode changes in light intensity, quantified as contrast, rather than the absolute intensity. Mathematically, contrast is often defined as a relative change in light intensity. Activity in the visual system and perceptual responses are usually explained with such definitions of contrast. Here, for the first time, we explicitly explored how contrast is actually represented in the visual system. Using mouse retina electrophysiology, we show that response strength of OFF retinal ganglion cells does not represent relative, but absolute changes in light intensity. ON RGC response strength is governed by a combination of absolute and relative change in light intensity. This is true for a wide range of ambient light levels, at least from scotopic to high mesopic regimes. Consequently, light decrements and increments are represented asymmetrically in the retina, which may explain the asymmetries in responses to negative and positive contrast observed throughout the visual system. These findings may help to more thoroughly design and interpret vision science studies where responses are driven by contrast of the visual stimuli.
Modeling Research Project Grant Success Rates from NIH Appropriation History: Extension to 2020
Authors: Berg Jeremy M. 
Published: November 2020

ABSTRACTCommunication of the likelihood that a grant proposal is funded is important for individual researchers and academic institutions. For research project grants (RPGs) funded by the US National Institutes of Health (NIH), this is measured by the success rate, the fraction of grants reviewed in a given fiscal year that are funded. In 2016, I posted a relatively simple computational model that allowed estimation of these success rates from historical data of NIH appropriations and associated data, based largely on the fact that commitments to fund NIH grants are typically made over four fiscal years rather than coming from a single fiscal year’s appropriations. Data for appropriations and success rates for fiscal years 2016-2020 are now available, allowing this model to be tested without no adjustable parameters. Over this period, the NIH appropriation increased by 29.7% to $39.313 billion, yet the RPG success rate increased from 0.183 to 0.201, a relative increase of only 9.8%. This difference is accurately reproduced by the model, indicating that the modest changes in success rate despite large appropriation increases reflect the consequences of the funding grants from multiple fiscal years and the response of the biomedical research community in submitting an increased number of proposals. The model can also be extended to estimate the success rates for individual institutes with reasonable accuracy.
Separation and Characterization of Endogenous Nucleosomes by Native Capillary Zone Electrophoresis – Top-Down Mass Spectrometry (nCZE-TDMS)
Authors: Jooß Kevin , Schachner Luis F. , Watson Rachel , Gillespie Zachary B. , Howard Sarah A. , Cheek Marcus A. , Meiners Matthew J. , Licht Jonathan D. , Keogh Michael-Christopher , Kelleher Neil L. 
Published: November 2020

AbstractWe report a novel platform (native capillary zone electrophoresis – top-down mass spectrometry; nCZE-TDMS) for the separation and characterization of whole nucleosomes, their histone subunits, and PTMs. As the repeating unit of chromatin, mononucleosomes (Nucs) are a ~200 kDa complex of DNA and histone proteins involved in the regulation of key cellular processes central to human health and disease. Unraveling the covalent modification landscape of histones and their defined stoichiometries within Nucs helps to explain epigenetic regulatory mechanisms. In nCZE-TDMS, online Nuc separation is followed by a three-tier tandem MS approach that measures the intact mass of Nucs, ejects and detects the constituent histones, and fragments to sequence the histone. The new platform was optimized with synthetic Nucs to reduce both sample requirements and cost significantly compared to direct infusion. Limits of detection were in the low attomole range, with linearity over ~three orders of magnitude. The nCZE-TDMS platform was applied to endogenous Nucs from two cell lines distinguished by overexpression or knockout of histone methyltransferase NSD2/MMSET, where analysis of constituent histones revealed changes in histone abundances over the course of the CZE separation. We are confident the nCZE-TDMS platform will help advance nucleosome-level research in the fields of chromatin and epigenetics.
An evaluation of multi-excitation-wavelength standing-wave fluorescence microscopy (TartanSW) to improve sampling density in studies of the cell membrane and cytoskeleton
Authors: Schniete Jana K. , Tinning Peter W. , Scrimgeour Ross C. , Robb Gillian , Kölln Lisa S. , Wesencraft Katrina , Paul Nikki R. , Bushell Trevor J. , McConnell Gail 
Published: November 2020

AbstractConventional standing-wave (SW) fluorescence microscopy uses a single wavelength to excite fluorescence from the specimen, which is normally placed in contact with a first surface reflector. The resulting excitation SW creates a pattern of illumination with anti-nodal maxima at multiple evenly-spaced planes perpendicular to the optical axis of the microscope. These maxima are approximately 90 nm thick and spaced 180 nm apart. Where the planes intersect fluorescent structures, emission occurs, but between the planes are non-illuminated regions which are not sampled for fluorescence. We evaluate a multi-excitation-wavelength SW fluorescence microscopy (which we call TartanSW) as a method for increasing the density of sampling by using SWs with different axial periodicities, to resolve more of the overall cell structure. The TartanSW method increased the sampling density from 50% to 98% over seven anti-nodal planes, with no notable change in axial or lateral resolution compared to single-excitation-wavelength SW microscopy. We demonstrate the method with images of the membrane and cytoskeleton of living and fixed cells.