bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transcription and export complex THO/TREX contributes to transcription termination in plants
Authors: Khan Ghazanfar Abbas , Deforges Jules , Reis Rodrigo S. , Hsieh Yi-Fang , Montpetit Jonatan , Antosz Wojciech , Santuari Luca , Hardtke Christian S , Grasser Klaus , Poirier Yves 
Published: March 2020

AbstractTranscription termination has important regulatory functions, impacting mRNA stability, localization and translation potential. Failure to appropriately terminate transcription can also lead to read-through transcription and the synthesis of antisense RNAs which can have profound impact on gene expression. The Transcription-Export (THO/TREX) protein complex plays an important role in coupling transcription with splicing and export of mRNA. However, little is known about the role of the THO/TREX complex in the control of transcription termination. In this work, we show that two proteins of the THO/TREX complex, namely TREX COMPONENT 1 (TEX1 or THO3) and HYPER RECOMBINATION1 (HPR1 or THO1) contribute to the correct transcription termination at several loci inArabidopsis thaliana. We first demonstrate this by showing defective termination intex1andhpr1mutants at the nopaline synthase (NOS) terminator present in a T-DNA inserted between exon 1 and 3 of thePHO1locus in thepho1-7mutant. Read-through transcription beyond the NOS terminator and splicing-out of the T-DNA resulted in the generation of a near full-lengthPHO1mRNA (minus exon 2) in thetex1 pho1-7andhpr1 pho1-7double mutants, with enhanced production of a truncated PHO1 protein that retained phosphate export activity. Consequently, the strong reduction of shoot growth associated with the severe phosphate deficiency of thepho1-7mutant was alleviated in thetex1 pho1-7andhpr1 pho1-7double mutants. Additionally, we show that RNA termination defects intex1andhpr1mutants leads to 3’UTR extensions in several plant genes. These results demonstrate that THO/TREX complex contributes to the regulation of transcription termination.Author summaryProduction of messenger RNAs (mRNAs) involves numerous steps including initiation of transcription, elongation, splicing, termination, as well as export out of the nucleus. All these steps are highly coordinated and failure in any steps has a profound impact on the level and identity of mRNAs produced. The THO/TREX protein complex is associated with nascent RNAs and contributes to several mRNA biogenesis steps, including splicing and export. However, the contribution of the THO/TREX complex to mRNA termination was poorly defined. We have identified a role for two components of the THO/TREX complex, namely the proteins TEX1 and HPR1, in the control of transcription termination in the plantArabidopsis thaliana. We show that thetex1andhpr1mutants have defects in terminating mRNA at the nopaline synthase (NOS) terminator found in T-DNA insertion mutants leading to the transcriptional read-through pass the NOS terminator. We also show thattex1andhpr1mutants have defects in mRNA termination at several endogenous genes, leading to the production of 3’UTR extensions. Together, these results highlight a role for the THO/TREX complex in mRNA termination.
Isolation and characterization of SARS-CoV-2 from the first US COVID-19 patient
Authors: Harcourt Jennifer , Tamin Azaibi , Lu Xiaoyan , Kamili Shifaq , Sakthivel Senthil Kumar. , Murray Janna , Queen Krista , Tao Ying , Paden Clinton R. , Zhang Jing , Li Yan , Uehara Anna , Wang Haibin , Goldsmith Cynthia , Bullock Hannah A. , Wang Lijuan , Whitaker Brett , Lynch Brian , Gautam Rashi , Schindewolf Craig , Lokugamage Kumari G. , Scharton Dionna , Plante Jessica A. , Mirchandani Divya , Widen Steven G. , Narayanan Krishna , Makino Shinji , Ksiazek Thomas G. , Plante Kenneth S. , Weaver Scott C. , Lindstrom Stephen , Tong Suxiang , Menachery Vineet D. , Thornburg Natalie J. 
Published: March 2020

ABSTRACTThe etiologic agent of the outbreak of pneumonia in Wuhan China was identified as severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) in January, 2020. The first US patient was diagnosed by the State of Washington and the US Centers for Disease Control and Prevention on January 20, 2020. We isolated virus from nasopharyngeal and oropharyngeal specimens, and characterized the viral sequence, replication properties, and cell culture tropism. We found that the virus replicates to high titer in Vero-CCL81 cells and Vero E6 cells in the absence of trypsin. We also deposited the virus into two virus repositories, making it broadly available to the public health and research communities. We hope that open access to this important reagent will expedite development of medical countermeasures.Article SummaryScientists have isolated virus from the first US COVID-19 patient. The isolation and reagents described here will serve as the US reference strain used in research, drug discovery and vaccine testing.
Identification and Optimization of cell active 4-anilino-quin(az)oline Inhibitors for Protein Kinase Novel 3 (PKN3)
Authors: Asquith Christopher R. M. , Temme Louisa , Laitinen Tuomo , Pickett Julie , Kwarcinski Frank E. , Sinha Parvathi , Wells Carrow I. , Tizzard Graham J. , Zutshi Reena , Drewry David H. 
Published: March 2020

AbstractThe development of a small library of 4-anilinoquinolines led to the identification of 7-iodo-N-(3,4,5-trimethoxyphenyl)quinolin-4-amine16as a potent inhibitor of Protein Kinase Novel 3 (PKN3) with an IC50of 1.3 μM in cells. Compound16presents a useful potential tool compound to study the biology of PKN3 including links to pancreatic and prostate cancer, along with T-cell acute lymphoblastic leukemia. These compounds may be useful tools to explore the therapeutic potential of PKN3 inhibition in prevention of a broad range of infectious and systemic diseases.
Optogenetic activation of afferent pathways in brain slices and modulation of responses by volatile anesthetics
Authors: Murphy Caitlin A. , Raz Aeyal , Banks Matthew I. 
Published: March 2020

ABSTRACTAnesthetics influence consciousness in part via their actions on thalamocortical circuits. However, the extent to which volatile anesthetics affect distinct cellular and network components of these circuits remains unclear.Ex vivobrain slices provide a means by which investigators may probe discrete components of complex networks and disentangle potential mechanisms underlying the effects of volatile anesthetics on evoked responses. To isolate potential cell type- and pathway-specific drug effects in brain slices, investigators must be able to independently activate afferent fiber pathways, identify non-overlapping populations of cells, and apply volatile anesthetics to tissue in aqueous solution. In this protocol, we describe methods to measure optogenetically-evoked responses to two independent afferent pathways to neocortex inex vivobrain slices. We record extracellular responses to assay network activity and conduct targeted whole-cell patch clamp recordings in somatostatin- and parvalbumin-positive interneurons. We also describe a means by which to deliver physiologically relevant concentrations of isoflurane via artificial cerebral spinal fluid to modulate cellular and network responses.SUMMARYEx vivobrain slices can be used to study the effects of volatile anesthetics on evoked responses to afferent inputs. We employ optogenetics to independently activate thalamocortical and corticocortical afferents to non-primary neocortex, and we modulate synaptic and network responses with isoflurane.
AHistoplasma capsulatumlipid metabolic map identifies antifungal targets
Authors: Zamith-Miranda Daniel , Heyman Heino M. , Burnet Meagan C. , Couvillion Sneha P. , Zheng Xueyun , Munoz Nathalie , Nelson William C. , Kyle Jennifer E. , Zink Erika M. , Weitz Karl K. , Bloodsworth Kent J. , Clair Geremy , Zucker Jeremy D. , Teuton Jeremy R. , Payne Samuel H. , Kim Young-Mo , Gil Morayma Reyes , Baker Erin S. , Bredeweg Erin L. , Nosanchuk Joshua D. , Nakayasu Ernesto S. 
Published: March 2020

ABSTRACTLipids play a fundamental role in fungal cell biology, being essential cell membrane components and major targets of antifungal drugs. A deeper knowledge of lipid metabolism is key for developing new drugs and a better understanding of fungal pathogenesis. Here we built a comprehensive map of theHistoplasma capsulatumlipid metabolic pathway by incorporating proteomic and lipidomic analyses. We performed genetic complementation and overexpression ofH. capsulatumgenes inSaccharomyces cerevisiaeto validate reactions identified in the map and to determine enzymes responsible for catalyzing orphan reactions. The map led to the identification of both the fatty acid desaturation and the sphingolipid biosynthesis pathways as targets for drug development. We found that the sphingolipid biosynthesis inhibitor myriocin, the fatty acid desaturase inhibitor thiocarlide and the fatty acid analog 10-thiastearic acid inhibitH. capsulatumgrowth in nanomolar to low micromolar concentrations. These compounds also reduced the intracellular infection in an alveolar macrophage cell line. Overall, this lipid metabolic map revealed pathways that can be targeted for drug development.
Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how convergent diets obfuscate traditional morphological taxonomy
Authors: Kolmann M.A. , Hughes L.C. , Hernandez L.P. , Arcila D. , Betancur R. , Sabaj M.H. , López-Fernández H. , Ortí G. 
Published: March 2020

ABSTRACTThe Amazon and neighboring South American river basins harbor the world’s most diverse assemblages of freshwater fishes. One of the most prominent South American fish families are the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of the top riverine predators as well as the primary seed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial. For example, the sister taxon to serrasalmids is contentious, the relationships of major clades within the family are obfuscated by different methodologies, and half of the extant serrasalmid genera are suggested to be non-monophyletic. We used exon capture to explore the evolutionary relationships among 64 (of 99) species across all 16 serrasalmid genera and their nearest outgroups, including multiple individuals per species in order to account for cryptic lineages. To reconstruct the timeline of serrasalmid diversification, we time-calibrated this phylogeny using two different fossil-calibration schemes to account for uncertainty in taxonomy with respect to fossil teeth. Finally, we analyzed diet evolution across the family and comment on associated changes in dentition, highlighting the ecomorphological diversity within serrasalmids. We document widespread non-monophyly within Myleinae, as well as betweenSerrasalmusandPristobrycon, and propose that reliance on traits like teeth to distinguish among genera is confounded by ecological convergence, especially among herbivorous and omnivorous taxa. We clarify the relationships among all serrasalmid genera, propose new subfamily affiliations, and support hemiodontids as the sister taxon to Serrasalmidae.
Intragenic Complementation ofCellulose Synthase-Like D1alleles in Root Hair Development
Authors: Karas Bogumil J. , Ross Loretta , Novero Mara , Amyot Lisa , Inada Sayaka , Nakano Michiharu , Sakai Tatsuya , Sato Sushei , Murray Jeremy Dale , Bonfante Paola , Szczyglowski Krzysztof 
Published: March 2020

AbstractRoot hair cells form the primary interface of plants with the soil environment, playing key roles in nutrient uptake and plant defense. In addition, they are typically the first cells infected by nitrogen-fixing soil bacteria during the root nodule symbiosis. Here we report a role for theCellulose Synthase-Like D1(CSLD1) gene in root hair development inLotus japonicus. CSLD1 belongs to the cellulose synthase protein family that includes cellulose synthases, and cellulose synthase-like proteins, the latter thought to be involved in the biosynthesis of hemicellulose. We describe 11csld1mutant alleles that have either short (Ljcsld1-1) or variable length roots hairs (Ljcsld1-2to11). Examination ofLjcsld1-1and one variable-length root hair mutant,Ljcsld1-6showed increased root hair cell wall thickness, which inLjcsld1-1was more pronounced, suggesting a possible link with the defect in root nodule symbiosis. In addition,Ljcsld1-1heterozygotes had intermediate root hair lengths, between those of wild type and the homozygotes. Intragenic complementation was observed between alleles with mutations in the N-terminal domain and other alleles, suggesting modularity of CSLD1 function and that it may operate as a homodimer or multimer.One sentence summaryThis research describes novel gain- and loss-of-function mutations at theLotus japonicus CELLULOSE SYNTHASE-LIKE D1locus and analyzes their impact on root hair development.
Minimally invasive brain injections for viral-mediated transgenesis: New tools for behavioral genetics in sticklebacks
Authors: James Noelle , Bell Alison 
Published: March 2020

AbstractBehavioral genetics in non-model organisms is currently gated by technological limitations. However, with the growing availability of genome editing and functional genomic tools, complex behavioral traits such as social behavior can now be explored in diverse organisms. Here we present a minimally invasive neurosurgical procedure for a classic behavioral, ecological and evolutionary system: threespine stickleback (Gasterosteus aculeatus). This method of direct brain injection enables viral-mediated transgenesis and pharmaceutical delivery which bypasses the blood-brain barrier. This method is flexible, fast, and amenable to statistically powerful within-subject experimental designs, making it well-suited for use in genetically diverse animals such as those collected from natural populations.Viral-mediated transgenesis in the brain allows for a direct examination of the genetic mechanisms underlying behavior in wild-caught animals from natural populations. Using this method, we were able to detect changes in aggression from the knockdown of either of two different genes, arginine vasopressin (AVP) and monoamine oxidase (MAOA), in outbred animals in less than one month. In addition, we demonstrate that widely available mammalian plasmids work with this method, lowering the barrier of entry to the technique.
Bayesian Structural Time Series for Biomedical Sensor Data: A Flexible Modeling Framework for Evaluating Interventions
Authors: Liu Jason , Spakowicz Daniel J. , Ash Garrett I. , Hoyd Rebecca , Zhang Andrew , Lou Shaoke , Lee Donghoon , Zhang Jing , Presley Carolyn , Greene Ann , Stults-Kolehmainen Matthew , Nally Laura , Baker Julien S. , Fucito Lisa M. , Weinzimer Stuart A. , Papachristos Andrew V , Gerstein Mark 
Published: March 2020

ABSTRACTThe development of mobile-health technology has the potential to revolutionize personalized medicine. Biomedical sensors (e.g. wearables) can assist with determining treatment plans for individuals, provide quantitative information to healthcare providers, and give objective measurements of health, leading to the goal of precise phenotypic correlates for genotypes. Even though treatments and interventions are becoming more specific and datasets more abundant, measuring the causal impact of health interventions requires careful considerations of complex covariate structures as well as knowledge of the temporal and spatial properties of the data. Thus, biomedical sensor data need to make use of specialized statistical models. Here, we show how the Bayesian structural time series framework, widely used in economics, can be applied to these data. We further show how this framework corrects for covariates to provide accurate assessments of interventions. Furthermore, it allows for a time-dependent confidence interval of impact, which is useful for considering individualized assessments of intervention efficacy. We provide a customized biomedical adaptor tool around a specific Google implementation of the Bayesian structural time series framework that uniformly processes, prepares, and registers diverse biomedical data. We apply the resulting software implementation to a structured set of examples in biomedicine to showcase the ability of the framework to evaluate interventions with varying levels of data richness and covariate complexity. In particular, we show how the framework is able to evaluate an exercise intervention’s effect on stabilizing blood glucose in a diabetes dataset. We also provide a future-anticipating illustration from a behavioral dataset showcasing how the framework integrates complex spatial covariates. Overall, we show the robustness of the Bayesian structural time series framework when applied to biomedical sensor data, highlighting its increasing value for current and future datasets.
CO2reduction driven by a pH gradient
Authors: Hudson Reuben , de Graaf Ruvan , Rodin Mari Strandoo , Ohno Aya , Lane Nick , McGlynn Shawn E. , Yamada Yoichi M.A. , Nakamura Ryuhei , Barge Laura M. , Braun Dieter , Sojo Victor 
Published: March 2020

AbstractAll life on Earth is built of organic molecules, so the primordial sources of reduced carbon are a major open question in studies of the origin of life. A variant of the alkaline-vent theory suggests that organics could have been produced by the reduction of CO2via H2oxidation, facilitated by geologically sustained pH gradients. The process would be an abiotic analog—and proposed evolutionary predecessor—of the modern Wood-Ljungdahl acetyl-Co-A pathway of extant archaea and bacteria. The first energetic bottleneck of the pathway involves the endergonic reduction of CO2with H2to formate, which has proven elusive in low-temperature abiotic settings. Here we show the reduction of CO2with H2at moderate pressures (1.5 bar), driven by microfluidic pH gradients across inorganic Fe(Ni)S precipitates. Isotopic labelling with13C confirmed production of formate. Separately, deuterium (2H) labelling indicated that electron transfer to CO2did not occur via direct hydrogenation with H2. Instead, freshly deposited Fe(Ni)S precipitates appear to facilitate electron transfer in an electrochemical-cell mechanism with two distinct half-reactions. Decreasing the pH gradient significantly, or removing either H2or the precipitate, yielded no detectable product. Our work demonstrates the feasibility of spatially separated, yet electrically coupled geochemical reactions as drivers of otherwise endergonic processes. Beyond corroborating the ability of early-Earth alkaline hydrothermal systems to couple carbon reduction to hydrogen oxidation through geologically plausible and biologically relevant mechanisms, these results may also be of significance for industrial and environmental applications, where other redox reactions could be facilitated using similarly mild approaches.
Overlapping neural representations for the position of visible and imagined objects
Authors: Robinson Amanda K. , Grootswagers Tijl , Shatek Sophia M. , Gerboni Jack , Holcombe Alex O. , Carlson Thomas A. 
Published: March 2020

AbstractHumans can covertly track the position of an object, even if the object is temporarily occluded. What are the neural mechanisms underlying our capacity to track moving objects when there is no physical stimulus for the brain to track? One possibility is that the brain “fills-in” information about imagined objects using internally generated representations similar to those generated by feed-forward perceptual mechanisms. Alternatively, the brain might deploy a higher order mechanism, for example using an object tracking model that integrates visual signals and motion dynamics (Kwon et al., 2015). In the present study, we used electroencephalography (EEG) and time-resolved multivariate pattern analyses to investigate the spatial processing of visible and imagined objects. Participants tracked an object that moved in discrete steps around fixation, occupying six consecutive locations. They were asked to imagine that the object continued on the same trajectory after it disappeared and move their attention to the corresponding positions. Time-resolved decoding of EEG data revealed that the location of the visible stimuli could be decoded shortly after image onset, consistent with early retinotopic visual processes. For processing of unseen/imagined positions, the patterns of neural activity resembled stimulus-driven mid-level visual processes, but were detected earlier than perceptual mechanisms, implicating an anticipatory and more variable tracking mechanism. Encoding models revealed that spatial representations were much weaker for imagined than visible stimuli. Monitoring the position of imagined objects thus utilises similar perceptual and attentional processes as monitoring objects that are actually present, but with different temporal dynamics. These results indicate that internally generated representations rely on top-down processes, and their timing is influenced by the predictability of the stimulus. All data and analysis code for this study are available athttps://osf.io/8v47t/.
Development of nascent focal adhesions in spreading cells
Authors: Ibata Neil , Terentjev Eugene M. 
Published: March 2020

AbstractCell spreading provides one of the simplest configurations in which eukaryotic cells develop angular symmetry-breaking assemblies of mechanosensing and mechanotransducive organelles in preparation for cell differentiation and movement. By identifying the edge of the cell-ECM adhesion area as having an important role in mechanosensor complex aggregation, we consider the spatial patterns arising on this edge, within a 1D lattice model of the nearest-neighbour interaction between individual integrin-mediated mechanosensors. We obtain the Ginzburg-Landau free energy for this model and analyse the spectrum of spatial modes as the cell spreads and increases the contact area. We test the plausibility of our model by comparing its predictions for the azimuthal angular frequency of aggregation of mechanosensors into nascent focal adhesions (FAs) to observations of the paxillin distribution in spreading fibroblasts.STATEMENT OF SIGNIFICANCEThe topic of cell adhesion on substrates is very active, with numerous theoretical, experimental and computer simulation studies probing the mechanisms and signalling pathways of cell response to interacting with substrate. Integrin-based adhesion complexes are known to be the individual units of this process, and their dense aggregation into focal adhesions leads to cells developing asymmetry, polarity, and eventually - locomotion. Here we develop a theoretical model that suggests that physical interactions between individual adhesion complexes is the factor that defines the initial breaking of symmetry of the cell spreading on substrate, and predicts the characteristic wavelength of modulation above the critical size of adhesion area.