bluuebunny/crossref_metadata_2025_split huggingface dataset:
A burst of transposon expression accompanies the activation of Y chromosome fertility genes during Drosophila spermatogenesis
Authors: Lawlor Matthew A. , Cao Weihuan , Ellison Christopher E. 
Published: May 2021

AbstractTransposable elements (TEs) must replicate in germline cells to pass novel insertions to offspring. In Drosophila melanogaster ovaries, TEs can exploit specific developmental windows of opportunity to evade host silencing and increase their copy numbers. However, TE activity and host silencing in the distinct cell types of the Drosophila melanogaster testis are not well understood. We reanalyzed publicly available single-cell RNA-seq datasets to quantify TE expression in the distinct cell types of the Drosophila testis. We developed a novel method for identification of TE and host gene expression programs and find that a distinct population of early spermatocytes expresses a large number of TEs at much higher levels than other germline and somatic components of the testes. This burst of TE expression coincides with the activation of Y chromosome fertility factors and spermatocyte-specific transcriptional regulators, as well as downregulation of many components of the piRNA pathway. The TEs expressed by this cell population are enriched on the Y chromosome and depleted on the X chromosome relative to other active TEs. These data suggest that some TEs may achieve high insertional activity in males by exploiting a window of opportunity for mobilization created by the activation of spermatocyte-specific and Y-chromosome-specific transcriptional programs.
Binding of SARS-CoV-2 fusion peptide to host membranes
Authors: Schaefer Stefan L. , Jung Hendrik , Hummer Gerhard 
Published: May 2021

AbstractDuring infection the SARS-CoV-2 virus fuses its viral envelope with cellular membranes of its human host. Initial contact with the host cell and membrane fusion are both mediated by the viral spike (S) protein. Proteolytic cleavage of S at the S2′ site exposes its 40 amino acid long fusion peptide (FP). Binding of the FP to the host membrane anchors the S2 domain of S in both the viral and the host membrane. The reorganization of S2 then pulls the two membranes together. Here we use molecular dynamics (MD) simulations to study the two core functions of the SARS-CoV-2 FP: to attach quickly to cellular membranes and to form an anchor strong enough to withstand the mechanical force during membrane fusion. In eight 10 μs-long MD simulations of FP in proximity to endosomal and plasma membranes, we find that FP binds spontaneously to the membranes and that binding proceeds predominantly by insertion of two short amphipathic helices into the membrane interface. Connected via a flexible linker, the two helices can bind the membrane independently, yet binding of one promotes the binding of the other by tethering it close to the target membrane. By simulating mechanical pulling forces acting on the C-terminus of the FP we then show that the bound FP can bear forces up to 250 pN before detaching from the membrane. This detachment force is more than ten-fold higher than an estimate of the force required to pull host and viral membranes together for fusion. We identify a fully conserved disulfide bridge in the FP as a major factor for the high mechanical stability of the FP membrane anchor. We conclude, first, that the sequential binding of two short amphipathic helices allows the SARS-CoV-2 FP to insert quickly into the target membrane, before the virion is swept away after shedding the S1 domain connecting it to the host cell receptor. Second, we conclude that the double attachment and the conserved disulfide bridge establish the strong anchoring required for subsequent membrane fusion. Multiple distinct membrane-anchoring elements ensure high avidity and high mechanical strength of FP-membrane binding.
Convergent use of phosphatidic acid for Hepatitis C virus and SARS-CoV-2 replication organelle formation
Authors: Tabata Keisuke , Prasad Vibhu , Paul David , Lee Ji-Young , Pham Minh-Tu , Twu Woan-Ing , Neufeldt Christopher J. , Cortese Mirko , Cerikan Berati , Si Tran Cong , Lüchtenborg Christian , V’kovski Philip , Hörmann Katrin , Müller André C. , Zitzmann Carolin , Haselmann Uta , Beneke Jürgen , Kaderali Lars , Erfle Holger , Thiel Volker , Lohmann Volker , Superti-Furga Giulio , Brügger Britta , Bartenschlager Ralf 
Published: May 2021

AbstractDouble membrane vesicles (DMVs) are used as replication organelles by phylogenetically and biologically distant pathogenic RNA viruses such as hepatitis C virus (HCV) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Viral DMVs are morphologically analogous to DMVs formed during autophagy, and although the proteins required for DMV formation are extensively studied, the lipids driving their biogenesis are largely unknown. Here we show that production of the lipid phosphatidic acid (PA) by acylglycerolphosphate acyltransferase (AGPAT) 1 and 2 in the ER is important for DMV biogenesis in viral replication and autophagy. Using DMVs in HCV-replicating cells as model, we found that AGPATs are recruited to and critically contribute to HCV replication and DMV formation. AGPAT1/2 double knockout also impaired SARS-CoV-2 replication and the formation of autophagosome-like structures. By using correlative light and electron microscopy, we observed the relocalization of AGPAT proteins to HCV and SARS-CoV-2 induced DMVs. In addition, an intracellular PA sensor accumulated at viral DMV formation sites, consistent with elevated levels of PA in fractions of purified DMVs analyzed by lipidomics. Apart from AGPATs, PA is generated by alternative pathways via phosphotidylcholine (PC) and diacylglycerol (DAG). Pharmacological inhibition of these synthesis pathways also impaired HCV and SARS-CoV-2 replication as well as formation of autophagosome-like DMVs. These data identify PA as an important lipid used for replication organelle formation by HCV and SARS-CoV-2, two phylogenetically disparate viruses causing very different diseases, i.e. chronic liver disease and COVID-19, respectively. In addition, our data argue that host-targeting therapy aiming at PA synthesis pathways might be suitable to attenuate replication of these viruses.One Sentence SummaryPhosphatidic acid is important for the formation of double membrane vesicles, serving as replication organelles of hepatitis C virus and SARS-CoV-2, and offering a possible host-targeting strategy to treat SARS-CoV-2 infection.
A dual sequence and culture-based survey of maize rhizosphere protists reveals dominant, plant-enriched, and culturable community members
Authors: Taerum Stephen J. , Micciulla Jamie , Corso Gabrielle , Steven Blaire , Gage Daniel J. , Triplett Lindsay R. 
Published: May 2021

AbstractProtists play important roles in shaping the microbial community of the rhizosphere. However, there is still a limited understanding of how plants shape the protist community, and how well protist isolate collections might represent rhizosphere protist composition and function in downstream studies. We sought to determine whether maize roots select for a distinct protist community in the field, and whether the common or dominant members of that community are readily culturable using standard protist isolation methods. We sequenced 18S and 16S rRNA genes from the rhizospheres of maize grown in two sites, and isolated 103 protists into culture from the same roots. While field site had the greatest effect, rhizospheres in both sites had distinct protist composition from the bulk soils, and certain taxa were enriched in both sites. Enriched taxa were correlated to bacterial abundance patterns. The isolated protists represented six supergroups, and the majority corresponded to taxa found in the sequencing survey. Twenty-six isolates matched eight of the 89 core rhizosphere taxa. This study demonstrates that maize roots select for a distinct protist community, but also illustrate the potential challenges in understanding the function of the dominant protist groups in the rhizosphere.Originality-Significance StatementThis is the first study comparing cultivation-dependent and independent methods for studying the protist community of plant roots, and the first untargeted analysis of the maize rhizosphere’s effect on protist communities. We show that maize in different sites select for distinct communities and overlapping enriched taxa, but that isolating the most important plant-associated protists may be a challenge for researchers.
CRISPR screens for lipid regulators reveal a role for ER-bound SNX13 in lysosomal cholesterol export
Authors: Lu Albert , Hsieh Frank , Enrich Carlos , Pfeffer Suzanne R. 
Published: May 2021

ABSTRACTWe report here two genome-wide CRISPR screens carried out to identify genes that when knocked out, alter levels of lysosomal cholesterol or bis(monoacylglycero)phosphate. In addition, these screens were also carried out under conditions of NPC1 inhibition to identify modifiers of NPC1 function in lysosomal cholesterol export. The screens confirm tight co- regulation of cholesterol and bis(monoacylglycero)phosphate levels in cells, and reveal an unexpected role for the ER-localized, SNX13 protein as a negative regulator of lysosomal cholesterol export. In the absence of NPC1 function, SNX13 knockout decreases lysosomal cholesterol, and is accompanied by triacylglycerol-rich lipid droplet accumulation and increased lysosomal bis(monoacylglycero)phosphate. These experiments provide unexpected insight into the regulation of lysosomal lipids and modification of these processes by novel gene products.SUMMARYGenome-wide CRISPR screens carried out with and without NPC1 function identify shared pathways that coordinately control lysosomal cholesterol and bis(monoacylglycero)phosphate. ER-localized SNX13 protein plays an unexpected regulatory role in modifying NPC1 function to regulate cellular cholesterol localization.
Nanopore dwell time analysis permits sequencing and conformational assignment of pseudouridine in SARS-CoV-2
Authors: Fleming Aaron M. , Mathewson Nicole J. , Burrows Cynthia J. 
Published: May 2021

AbstractNanopore devices can directly sequence RNA, and the method has the potential to determine locations of epitranscriptomic modifications that have grown in significance because of their roles in cell regulation and stress response. Pseudouridine (Ψ), the most common modification in RNA, was sequenced with a nanopore system using a protein sensor with a helicase brake in synthetic RNAs with 100% modification at 18 known human pseudouridinylation sites. The new signals were compared to native uridine (U) control strands to characterize base calling and associated errors as well as ion current and dwell time changes. The data point to strong sequence context effects in which Ψ can easily be detected in some contexts while in others Ψ yields signals similar to U that would be false negatives in an unknown sample. We identified that the passage of Ψ through the helicase brake slowed the translocation kinetics compared to U and showed a smaller sequence bias that could permit detection of this modification in RNA. The unique signals from Ψ relative to U are proposed to reflect the syn-anti conformational flexibility of Ψ not found in U, and the difference in π stacking between these bases. This observation permitted analysis of SARS-CoV-2 nanopore sequencing data to identify five conserved Ψ sites on the 3’ end of the viral sub-genomic RNAs, and other less conserved Ψ sites. Using the helicase as a sensor protein in nanopore sequencing experiments enables detection of this modification in a greater number of relevant sequence contexts. The data are discussed concerning their analytical and biological significance.
Receptor binding may directly activate the fusion machinery in coronavirus spike glycoproteins
Authors: Wang Yuzhang , Fallon Lucy , Raguette Lauren , Budhan Stephanie , Belfon Kellon , Stepanenko Darya , Helbock Stephanie , Varghese Sarah , Simmerling Carlos 
Published: May 2021

AbstractSARS-CoV-2, the causative agent of the COVID-19 pandemic, is an enveloped RNA virus. Trimeric spike glycoproteins extend outward from the virion; these class I viral membrane fusion proteins mediate entry of the virus into a host cell and are the dominant antigen for immune response. Cryo-EM studies have generated a large number of structures for the spike either alone, or bound to the cognate receptor ACE2 or antibodies, with the three receptor binding domains (RBDs) seen closed, open, or in various combinations. Binding to ACE2 requires an open RBD, and is believed to trigger the series of dramatic conformational changes in the spike that lead to the shedding of the S1 subunit and transition of the spring-loaded S2 subunit to the experimentally observed post-fusion structure. The steps following ACE2 binding are poorly understood despite extensive characterization of the spike through X-ray, cryo-EM, and computation. Here, we use all-atom simulations, guided by analysis of 81 existing experimental structures, to develop a model for the structural and energetic coupling that connects receptor binding to activation of the membrane fusion machinery.
Accuracies of genomic predictions for disease resistance of striped catfish to Edwardsiella ictaluri using artificial intelligence algorithms
Authors: Vu Nguyen Thanh , Phuc Tran Huu , Oanh Kim Thi Phuong , Van Sang Nguyen , Trang Trinh Thi , Nguyen Nguyen Hong 
Published: May 2021

AbstractAssessments of genomic prediction accuracies using artificial intelligence (AI) algorithms (i.e., machine and deep learning methods) are currently not available or very limited in aquaculture species. The principal aim of this study was to examine the predictive performance of these new methods for disease resistance to Edwardsiella ictaluri in a population of striped catfish Pangasianodon hypophthalmus and to make comparisons with four common methods, i.e., pedigree-based best linear unbiased prediction (PBLUP), genomic-based best linear unbiased prediction (GBLUP), single-step GBLUP (ssGBLUP) and a non-linear Bayesian approach (notably BayesR). Our analyses using machine learning (i.e., ML-KAML) and deep learning (i.e., DL-MLP and DL-CNN) together with the four common methods (PBLUP, GBLUP, ssGBLUP and BayesR) were conducted for two main disease resistance traits (i.e., survival status coded as 0 and 1 and survival time, i.e., days that the animals were still alive after the challenge test) in a pedigree consisting of 560 individual animals (490 offspring and 70 parents) genotyped for 14,154 Single Nucleotide Polymorphism (SNPs). The results using 6470 SNPs after quality control showed that AI methods outperformed PBLUP, GBLUP and ssGBLUP, with the increases in the prediction accuracies for both traits by 9.1 – 15.4%. However, the prediction accuracies obtained from AI methods were comparable to those estimated using BayesR. Imputation of missing genotypes using AlphaFamImpute increased the prediction accuracies by 5.3 – 19.2% in all the methods and data used. On the other hand, there were insignificant decreases (0.3 – 5.6%) in the prediction accuracies for both survival status and survival time when multivariate models were used in comparison to univariate analyses. Interestingly, the genomic prediction accuracies based on only highly significant SNPs (P < 0.00001, 318 - 400 SNPs for survival status and 1362 – 1589 SNPs for survival time) were somewhat lower (0.3 to 15.6%) than those obtained from the whole set of 6,470 SNPs. In most of our analyses, the accuracies of genomic prediction were somewhat higher for survival time than survival status (0/1 data). It is concluded that there are prospects for the application of genomic selection to increase disease resistance to Edwardsiella ictaluri in striped catfish breeding programs.
Single cell transcriptomics and developmental trajectories of murine cranial neural crest cell fate determination and cell cycle progression
Authors: Ji Yu , Zhang Shuwen , Reynolds Kurt , Gu Ran , McMahon Moira , Islam Mohammad , Liu Yue , Imai Taylor , Donham Rebecca , Zhao Huan , Xu Ying , Burkart-Waco Diana , Zhou Chengji J. 
Published: May 2021

AbstractCranial neural crest (NC) cells migrate long distances to populate the future craniofacial regions and give rise to various tissues, including facial cartilage, bones, connective tissues, and cranial nerves. However, the mechanism that drives the fate determination of cranial NC cells remains unclear. Using single-cell RNA sequencing combined genetic fate mapping, we reconstructed developmental trajectories of cranial NC cells, and traced their differentiation in mouse embryos. We identified four major cranial NC cell lineages at different status: pre-epithelial-mesenchymal transition, early migration, NC-derived mesenchymal cells, and neural lineage cells from embryonic days 9.5 to 12.5. During migration, the first cell fate determination separates cranial sensory ganglia, the second generates mesenchymal progenitors, and the third separates other neural lineage cells. We then focused on the early facial prominences that appear to be built by undifferentiated, fast-dividing NC cells that possess similar transcriptomic landscapes, which could be the drive for the facial developmental robustness. The post-migratory cranial NC cells exit the cell cycle around embryonic day 11.5 after facial shaping is completed and initiates further fate determination and differentiation processes. Our results demonstrate the transcriptomic landscapes during dynamic cell fate determination and cell cycle progression of cranial NC lineage cells and also suggest that the transcriptomic regulation of the balance between proliferation and differentiation of the post-migratory cranial NC cells can be a key for building up unique facial structures in vertebrates.
Non-Transgenic Functional Rescue of Neuropeptides
Authors: DiLoreto Elizabeth M. , Reilly Douglas K. , Srinivasan Jagan 
Published: May 2021

AbstractAnimals constantly respond to changes in their environment and internal states via neuromodulation. Neuropeptide genes modulate neural circuits by encoding either multiple copies of the same neuropeptide or different neuropeptides. This architectural complexity makes it difficult to determine the function of discrete and active neuropeptides. Here, we present a novel genetic tool that facilitates functional analysis of individual peptides. We engineeredEscherichia colibacteria to express active peptides and fed loss-of-functionCaenorhabditis elegansto rescue gene activity. Using this approach, we rescued the activity of different neuropeptide genes with varying lengths and functions:trh-1, ins-6, andpdf-1. While some peptides are functionally redundant, others exhibited unique and previously uncharacterized functions. The mechanism of peptide uptake is reminiscent of RNA interference, suggesting convergent mechanisms of gene regulation in organisms. Our rescue-by-feeding paradigm provides a high-throughput screening strategy to elucidate the functional landscape of neuropeptide genes regulating different behavioral and physiological processes.
Repeated origins, gene flow, and allelic interactions of herbicide resistance mutations in a widespread agricultural weed
Authors: Kreiner J.M. , Sandler G. , Stern A.J. , Tranel P.J. , Weigel D , Stinchcombe J.R. , Wright S.I. 
Published: May 2021

AbstractCausal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack an understanding of their evolutionary history: the extent of parallelism in the origins of target-site resistance (TSR), how long these mutations persist, how quickly they spread, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 18 agricultural populations of common waterhemp (Amaranthus tuberculatus), which we show to have undergone a massive expansion over the past century with a contemporary effective population size estimate of 8 × 107. We found variation at seven characterized TSR loci, two of which had multiple amino acid substitutions, and three of which were common. These three common resistance variants show parallelism in their mutational origins, with gene flow having shaped their distribution across the landscape. Allele age estimates supported a strong role of adaptation from de novo mutations, with a median allele age of 30 suggesting that most resistance alleles arose soon after the onset of herbicide use. However, resistant lineages varied in both their age and evidence for selection over two different timescales, implying considerable heterogeneity in the forces that govern their persistence. The evolutionary history of TSR has also been shaped by both intra- and inter-locus allelic interactions. We report a signal of extended haplotype competition between two common TSR alleles, and extreme linkage with genome-wide alleles with known functions in resistance adaptation. Together, this work reveals a remarkable example of spatial parallel evolution in a metapopulation, with important implications for the management of herbicide resistance.
Web-based Psychoacoustics: Hearing Screening, Infrastructure, and Validation
Authors: Mok Brittany A. , Viswanathan Vibha , Borjigin Agudemu , Singh Ravinderjit , Kafi Homeira , Bharadwaj Hari M. 
Published: May 2021

AbstractAnonymous web-based experiments are increasingly and successfully used in many domains of behavioral research. However, online studies of auditory perception, especially of psychoacoustic phenomena pertaining to low-level sensory processing, are challenging because of limited available control of the acoustics, and the unknown hearing status of participants. Here, we outline our approach to mitigate these challenges and validate our procedures by comparing web-based measurements to labbased data on a range of classic psychoacoustic tasks. Individual tasks were created using jsPsych, an open-source javascript front-end library. Dynamic sequences of psychoacoustic tasks were implemented using Django, an open-source library for web applications, and combined with consent pages, questionnaires, and debriefing pages. Subjects were recruited via Prolific, a web-based human-subject marketplace. Guided by a meta-analysis of normative data, we developed and validated a screening procedure to select participants for (putative) normal-hearing status; this procedure combined thresholding of scores in a suprathreshold cocktail-party task with filtering based on survey responses. Headphone use was standardized by supplementing procedures from prior literature with a binaural hearing task. Individuals meeting all criteria were re-invited to complete a range of classic psychoacoustic tasks. Performance trends observed in re-invited participants were in excellent agreement with lab-based data for fundamental frequency discrimination, gap detection, sensitivity to interaural time delay and level difference, comodulation masking release, word identification, and consonant confusions. Our results suggest that web-based psychoacoustics is a viable complement to lab-based research. Source code for our infrastructure is also provided.