bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 infects brain choroid plexus and disrupts the blood-CSF-barrier
Authors: Pellegrini Laura , Albecka Anna , Mallery Donna L. , Kellner Max J. , Paul David , Carter Andrew P. , James Leo C. , Lancaster Madeline A. 
Published: August 2020

AbstractCoronavirus disease-19 (COVID-19), caused by the SARS-CoV-2 virus, leads primarily to respiratory symptoms that can be fatal, particularly in at risk individuals. However, neurological symptoms have also been observed in patients, including headache, seizures, stroke, and fatigue. The cause of these complications is not yet known, and whether they are due to a direct infection of neural cells, such as neurons and astrocytes, or through indirect effects on supportive brain cells, is unknown. Here, we use brain organoids to examine SARS-CoV-2 neurotropism. We examine expression of the key viral receptor ACE2 in single-cell RNA sequencing (scRNA-seq) revealing that only a subset of choroid plexus cells but not neurons or neural progenitors express this entry factor. We then challenge organoids with both SARS-CoV-2 spike protein pseudovirus and live virus to demonstrate high viral tropism for choroid plexus epithelial cells but not stromal cells, and little to no infection of neurons or glia. We find that infected cells of the choroid plexus are an apolipoprotein and ACE2 expressing subset of epithelial barrier cells. Finally, we show that infection with live SARS-CoV-2 leads to barrier breakdown of the choroid plexus. These findings suggest that neurological complications may result from effects on the choroid plexus, an important barrier that normally prevents entry of immune cells and cytokines into the cerebrospinal fluid (CSF) and brain.
Perspectives on the design and performance of upper-limb wearable stimulation devices for stroke survivors with hemiplegia and spasticity
Authors: Seim Caitlyn E. , Ritter Brandon , Starner Thad E. , Flavin Kara , Lansberg Maarten G. , Okamura Allison M. 
Published: August 2020

AbstractBackgroundVibrotactile stimulation may improve limb function after stroke; however, current studies are limited by the stationary and clinic-based apparatus used to apply this stimulation. A wearable device could provide vibrotactile stimulation in a mobile form factor, enabling further study of this technique.ObjectiveThe aim of this work is twofold: (1) Design and validate a wearable device for stroke survivors that provides vibrotactile stimulation to the upper limb, and (2) Understand features that influence stroke survivors’ interaction with an upper-limb wearable device.MethodsA vibrotactile glove was designed to apply stimulation to the stroke-affected hand. This device, the vibrotactile stimulation (VTS) Glove, features small electronics, provides hours of stimulation, and has the appearance of a fingerless fitness glove. We performed two studies. In Study 1, sixteen stroke survivors were given the glove and asked to wear it for three hours daily for eight weeks. Usage time, indicating adherence, was calculated by onboard sensors. The device was evaluated using a log of damages and feedback from participants. Self-reported behaviors during glove use were also collected. In Study 2, eight stroke survivors evaluated new device prototypes in a three-round iterative design study. Interviews were used to collect participant feedback as they donned and doffed the prototypes. Task completion time and correctness were measured. Thematic content analysis was used to define actionable design revisions between each round of evaluation and identify key perspectives on design principles.ResultsThe VTS Glove is lightweight, wireless, and durable. Based on Study 1, adherence appears feasible. Each participant recorded over 140 hours wearing the VTS Glove. Participants reported wearing the glove during activities such as church, social events, dining out, and using the computer. However, 69% of participants struggled to extend or insert their fingers to don the device. Our analysis in Study 2 identified six other relevant perspectives from survivors regarding the wearable devices: hand supination is difficult, grip varies without awareness, devices may lead to sweat, separate finger attachments require dexterity, social comfort is perceived as unimportant, and the affected hand is infrequently used. New device designs with revised features (VTS Phalanx, VTS Armband, and VTS Palm) could be donned in an average time of 48 seconds (vs. 5.05 minutes to don the VTS Glove).
Expression partitioning of duplicate genes at single cell resolution inArabidopsisroots
Authors: Coate Jeremy E. , Farmer Andrew D. , Schiefelbein John , Doyle Jeff J. 
Published: August 2020

ABSTRACTGene duplication is a key evolutionary phenomenon, prevalent in all organisms but particularly so in plants, where whole genome duplication (WGD; polyploidy) is a major force in genome evolution. Much effort has been expended in attempting to understand the evolution of duplicate genes, addressing such questions as why some paralogue pairs rapidly return to single copy status whereas, in other pairs, paralogues are retained and may (or may not) diverge in expression pattern or function. The effect of a gene—its site of expression and thus the initial locus of its function—occurs at the level of a cell comprising a single cell type at a given state of the cell’s development. Thus, it is critical to understand the expression of duplicated gene pairs at a cellular level of resolution. UsingArabidopsis thalianaroot single cell transcriptomic data we identify 36 cell clusters, each representing a cell type at a particular developmental state, and analyze expression patterns of over 11,000 duplicate gene pairs produced by three cycles of polyploidy as well as by various types of single gene duplication mechanisms. We categorize paralogue pairs by their patterns of expression, identifying pairs showing strongly biased paralogue/homoeologue expression in different cell clusters. Notably, the precision of cell-level expression data permits the identification of pairs showing alternate bias, with each paralogue comprising 90% or greater of the pair’s expression in different cell clusters, consistent with subfunctionalization at the cell type or cell state level, and, in some cases, at the level of individual cells. We identify a set of over 7,000 genes whose expression in all 36 cell clusters suggests that the single copy ancestor of each was also expressed in all root cells. With this cell-level expression information we hypothesize that there have been major shifts in expression for the majority of duplicated genes, to different degrees depending, as expected, on gene function and duplication type, but also on the particular cell type and state.
A mating-induced reproductive gene promotesAnophelestolerance toPlasmodium falciparuminfection
Authors: Marcenac Perrine , Shaw W. Robert , Kakani Evdoxia G. , Mitchell Sara N. , South Adam , Werling Kristine , Marrogi Eryney , Abernathy Daniel G. , Yerbanga Rakiswendé Serge , Dabiré Roch K. , Diabaté Abdoulaye , Lefèvre Thierry , Catteruccia Flaminia 
Published: August 2020

AbstractAnophelesmosquitoes have transmittedPlasmodiumparasites for millions of years, yet it remains unclear whether they suffer fitness costs to infection. Here we report that the fecundity of virgin and mated females of two important vectors—Anopheles gambiaeandAnopheles stephensi—is not affected by infection withPlasmodium falciparum, demonstrating that these human malaria parasites do not inflict reproductive costs to their natural mosquito hosts. Additionally, parasite development is not impacted by mating status. However, in field studies using differentP. falciparumisolates inAnopheles coluzzii, we find thatMating-Induced Stimulator of Oogenesis(MISO), a female reproductive gene strongly induced after mating by the sexual transfer of the steroid hormone 20-hydroxyecdysone (20E), protects females from incurring fecundity costs to infection.MISO-silenced females produce fewer eggs as they become increasingly infected withP. falciparum, while parasite development is not impacted by this gene silencing. Interestingly, previous work had shown that sexual transfer of 20E has specifically evolved inCelliaspecies of theAnophelesgenus, driving the co-adaptation of MISO. Our data therefore suggest that evolution of male-female sexual interactions may have promotedAnophelestolerance toP. falciparuminfection in theCelliasubgenus, which comprises the most important malaria vectors.Author summaryPlasmodium falciparum, the deadliest form of human malaria, is transmitted when femaleAnophelesmosquitoes bite people and take a blood meal in order to develop eggs. To date, it is still poorly understood whetherAnophelesmosquitoes that get infected withP. falciparumsuffer fitness costs. Here, we find that the number of eggs produced byAnopheles gambiaeandAnopheles stephensifemales is not affected byP. falciparuminfection, and that the mating status of the mosquitoes does not impact the parasite. However, in field experiments infecting a related species,Anopheles coluzzii, withP. falciparumusing blood from donors in Burkina Faso, we find that interfering with the expression of a gene normally triggered by the sexual transfer of the steroid hormone 20-hydroxyecdysone induces increasing costs to egg development as females become more infected withP. falciparum, with no impacts on the parasite. The results of our study suggest that pathways triggered by mating may helpAnophelesprevent reproductive costs associated withP. falciparuminfection, providing new insights into evolutionary strategies adopted by anophelines in the face of a longstanding association withPlasmodiumparasites.
Isolation of high yield and quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts
Authors: Stegmayr John , Alsafadi Hani N. , Langwiński Wojciech , Niroomand Anna , Lindstedt Sandra , Leigh Nicholas D. , Wagner Darcy E. 
Published: August 2020

AbstractPrecision-cut lung slices (PCLS) have gained increasing interest as a model to study lung biology and disease, as well as for screening novel therapeutics. In particular, PCLS derived from human tissue can better recapitulate some aspects of lung biology and disease as compared to PCLS derived from animals (e.g.clinical heterogeneity), but access to human tissue is limited. A number of different experimental readouts have been established for use with PCLS, but obtaining high yield and quality RNA for downstream gene expression analysis has remained challenging. This is particularly problematic for utilizing the power of next-generation sequencing techniques, such as RNA-sequencing (RNA-seq), for non-biased and high through-put analysis of PCLS human cohorts. In the current study, we present a novel approach for isolating high quality RNA from a small amount of tissue, including diseased human tissue, such as idiopathic pulmonary fibrosis (IPF). We show that the RNA isolated using this method is of sufficient quality for both RT-qPCR and RNA-seq analysis. Furthermore, the RNA-seq data from human PCLS was comparable to data generated from native tissue and could be used in several established computational pipelines, including deconvolution of bulk RNA-seq data using publicly available single-cell RNA-seq data sets. Deconvolution using Bisque revealed a diversity of cell populations in human PCLS derived from distal lung tissue, including several immune cell populations, which correlated with cell populations known to be present and aberrant in human disease, such as IPF.
Ferrets not infected by SARS-CoV-2 in a high-exposure domestic setting
Authors: Sawatzki Kaitlin , Hill Nichola , Puryear Wendy , Foss Alexa , Stone Jonathon , Runstadler Jonathan 
Published: August 2020

AbstractFerrets (Mustela putorius furo) are mustelids of special relevance to laboratory studies of respiratory viruses and have been shown to be susceptible to SARS-CoV-2 infection and onward transmission. Here, we report the results of a natural experiment where 29 ferrets in one home had prolonged, direct contact and constant environmental exposure to two humans with symptomatic COVID-19. We observed no evidence of SARS-CoV-2 transmission from humans to ferrets based on RT-PCR and ELISA. To better understand this discrepancy in experimental and natural infection in ferrets, we compared SARS-CoV-2 sequences from natural and experimental mustelid infections and identified two surface glycoprotein (Spike) mutations associated with mustelids. While we found evidence that ACE2 provides a weak host barrier, one mutation only seen in ferrets is located in the novel S1/S2 cleavage site and is computationally predicted to decrease furin activity. These data support that host factors interacting with the novel S1/S2 cleavage site may be a barrier in ferret SARS-CoV-2 susceptibility and that domestic ferrets are at low risk of natural infection from currently circulating SARS-CoV-2. This may be overcome in laboratory settings using concentrated viral inoculum, but the effects of ferret host-adaptations require additional investigation.
Restricted differentiative capacity of Wt1-expressing peritoneal mesothelium in postnatal and adult mice
Authors: Wilm Thomas P , Tanton Helen , Mutter Fiona , Foisor Veronica , Middlehurst Ben , Ward Kelly , Benameur Tarek , Hastie Nicholas , Wilm Bettina 
Published: August 2020

AbstractPreviously, genetic lineage tracing based on the mesothelial marker Wt1, appeared to show that peritoneal mesothelial cells have a range of differentiative capacities and are the direct progenitors of vascular smooth muscle in the intestine. However, it was not clear whether this was a temporally limited process or continued throughout postnatal life. Here, using a conditional Wt1-based genetic lineage tracing approach, we demonstrate that the postnatal and adult peritoneum covering intestine, mesentery and body wall only maintained itself and failed to contribute to other visceral tissues. Pulse-chase experiments of up to 6 months revealed that Wt1-expressing cells remained confined to the peritoneum and failed to differentiate into cellular components of blood vessels or other tissues underlying the peritoneum. Ablation of Wt1 in adult mice did not result in changes to the intestinal wall architecture. In the heart, we observed that Wt1-expressing cells maintained the epicardium and contributed to coronary vessels in newborn and adult mice. Our results demonstrate that Wt1-expressing cells in the peritoneum have limited differentiation capacities, and that contribution of Wt1-expressing cells to cardiac vasculature is based on organ-specific mechanisms.
Towards Reproducible Brain-Wide Association Studies
Authors: Marek Scott , Tervo-Clemmens Brenden , Calabro Finnegan J. , Montez David F. , Kay Benjamin P. , Hatoum Alexander S. , Donohue Meghan Rose , Foran William , Miller Ryland L. , Feczko Eric , Miranda-Dominguez Oscar , Graham Alice M. , Earl Eric A. , Perrone Anders J. , Cordova Michaela , Doyle Olivia , Moore Lucille A. , Conan Greg , Uriarte Johnny , Snider Kathy , Tam Angela , Chen Jianzhong , Newbold Dillan J. , Zheng Annie , Seider Nicole A. , Van Andrew N. , Laumann Timothy O. , Thompson Wesley K. , Greene Deanna J. , Petersen Steven E. , Nichols Thomas E. , Yeo B.T. Thomas , Barch Deanna M. , Garavan Hugh , Luna Beatriz , Fair Damien A. , Dosenbach Nico U.F. 
Published: August 2020

AbstractMagnetic resonance imaging (MRI) continues to drive many important neuroscientific advances. However, progress in uncovering reproducible associations between individual differences in brain structure/function and behavioral phenotypes (e.g., cognition, mental health) may have been undermined by typical neuroimaging sample sizes (median N=25)1,2. Leveraging the Adolescent Brain Cognitive Development (ABCD) Study3(N=11,878), we estimated the effect sizes and reproducibility of these brain-wide associations studies (BWAS) as a function of sample size. The very largest, replicable brain-wide associations for univariate and multivariate methods were r=0.14 and r=0.34, respectively. In smaller samples, typical for brain-wide association studies (BWAS), irreproducible, inflated effect sizes were ubiquitous, no matter the method (univariate, multivariate). Until sample sizes started to approach consortium-levels, BWAS were underpowered and statistical errors assured. Multiple factors contribute to replication failures4–6; here, we show that the pairing of small brain-behavioral phenotype effect sizes with sampling variability is a key element in wide-spread BWAS replication failure. Brain-behavioral phenotype associations stabilize and become more reproducible with sample sizes of N⪆2,000. While investigator-initiated brain-behavior research continues to generate hypotheses and propel innovation, large consortia are needed to usher in a new era of reproducible human brain-wide association studies.
Bacillusendospore appendages form a novel family of disulfide-linked pili
Authors: Pradhan Brajabandhu , Liedtke Janine , Sleutel Mike , Lindbäck Toril , Llarena Ann-Katrin , Brynildsrud Ola , Aspholm Marina , Remaut Han 
Published: August 2020

SummaryBacillus cereus sensu latois a group of Gram-positive endospore-forming bacteria with high ecological diversity. Their endospores are decorated with micrometer-long appendages of unknown identity and function. Here we isolate endospore appendages (Enas) from the food poisoning outbreak strainB. cereusNVH 0075-95 and find proteinaceous fibers of two main morphologies. By using cryo-EM and 3D helical reconstruction we show thatBacillusEnas form a novel class of Gram-positive pili. Enas consist of single domain subunits with jellyroll topology that are laterally stacked by β-sheet augmentation. Enas are longitudinally stabilized by disulfide bonding through N-terminal connector peptides that bridge the helical turns. Together, this results in flexible pili that are highly resistant to heat, drought and chemical damage. Phylogenomic analysis reveals the presence of definedenaclades amongst different eco- and pathotypes. We propose Enas to represent a novel class of pili specifically adapted to the harsh conditions encountered by bacterial spores.
Histidine Protonation Controls Structural Heterogeneity in the Cyanobacteriochrome AnPixJg2
Authors: Rao Aditya G. , Wiebeler Christian , Sen Saumik , Cerutti David S. , Schapiro Igor 
Published: August 2020

AbstractCyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that bind a linear tetrapyrrole as a chromophore. They show photochromicity by having two stable states that can be interconverted by the photoisomerization of the chromophore. Hence, these photochemical properties make them an attractive target for biotechnological applications. However, their application is impeded by structural heterogeneity that reduces the yield of the photoconversion. The heterogeneity can originate either from the chromophore structure or the protein environment. Here, we study the origin of the heterogeneity in AnPixJg2, a representative member of the red/green cyanobacteriochrome family, that has a red absorbing parental state and a green absorbing photoproduct state. Using molecular dynamics simulations and umbrella sampling we have identified the protonation state of a conserved histidine residue as a trigger for structural heterogeneity. When the histidine is in a neutral form, the chromophore structure is homogenous, while in a positively charged form, the chromophore is heterogeneous with two different conformations. We have identified a correlation between the protonation of the histidine and the structural heterogeneity of the chromophore by detailed characterization of the interactions in the protein binding site. Our findings reconcile seemingly contradicting spectroscopic studies that attribute the heterogeneity to different sources. Furthermore, we predict that circular dichroism can be used as a diagnostic tool to distinguish different substates.Significance statementCyanobacteriochromes are photoreceptor proteins that have attracted attention for their immense potential in bioimaging and optogenetics applications. This is due to their desirable properties such as compactness, photochromicity and diverse spectral tuning. Despite these advantages, nature has set a limitation in the form of structural heterogeneity that presents a drawback for its application in biotechnology. We have identified a histidine residue in the vicinity of the chromophore as the origin of the heterogeneity in red/green CBCRs. The protonation state of this conserved histidine alters an extended network of protein-chromophore interactions and induces heterogeneity. Furthermore, theoretical CD spectroscopy has revealed easy identification of heterogeneity. Hence, our study paves the way for rational design and optimization of protein properties.
Selective dephosphorylation by PP2A-B55 directs the meiosis I - meiosis II transition in oocytes
Authors: Swartz S. Zachary , Nguyen Hieu T. , McEwan Brennan C. , Adamo Mark E. , Cheeseman Iain M. , Kettenbach Arminja N. 
Published: August 2020

AbstractMeiosis is a specialized cell cycle that requires sequential changes to the cell division machinery to facilitate changing functions. To define the mechanisms that enable the oocyte-to-embryo transition, we performed time-course proteomics in sea star oocytes from prophase I through the first embryonic cleavage. Although protein levels are broadly stable, dynamic waves of phosphorylation underlie each meiotic stage. We find that the phosphatase PP2A-B55 is reactivated at the Meiosis I/II transition resulting in the preferential dephosphorylation of threonine residues. Selective dephosphorylation is critical for directing the MI / MII transition as altering PP2A-B55 substrate preferences disrupts key cell cycle events after meiosis I. In addition, threonine to serine substitution of a conserved phosphorylation site in the substrate INCENP prevents its relocalization at anaphase I. Thus, through its inherent phospho-threonine preference, PP2A-B55 rewires the cell division apparatus to direct the MI / MII transition.
Sourdoughs fermented by autochthonousLactobacillusstrains improve the quality of gluten-free bread
Authors: Nami Yousef , Gharekhani Mehdi , Aalami Mehran , Hejazi Mohammad Amin 
Published: August 2020

ABSTRACTSourdoughs based on fermentation by lactobacilli have the potential to produce gluten-free maize-based bread with acceptable technological and rheological characteristics, nutritional quality and a more prolonged shelf life. Of the 17 treatments compared (with or without sourdough, and involving single and multiple LAB species), treatments 12C (Lactobacillus brevis, L. sanfranciscensis+L. plantarum) and 8C (L. brevis+L. paralimentarius) showed the lowest rate of complex modulus, while treatments 11C (L. sanfranciscensis+L. brevis+L. paralimentarius) and 2C (L. brevis) led to the greatest reduction in baking loss. The crumb moisture content of all of the formulations decreased with storage. Breads produced with treatment 2C (L. brevis) had the highest crumb moisture content when freshly baked; while loaves produced with treatment 3C (L. paralimentarius) had the highest crumb moisture content after four days of storage. A sensory evaluation indicated that sourdough-based maize breads were superior to both control and chemically acidified breads. The optimal treatments were to use sourdough seeded with treatment 2C (L. brevis), with treatment 4C (L. plantarum), with treatment 8C (L. brevis+L. paralimentarius) or with treatment 11C (L. sanfranciscensis+L. brevis+L. paralimentarius).Significance StatementOf the 17 treatments compared, treatments 12C and 8C showed the lowest rate of complex modulus, while treatments 11C and 2C led to the greatest reduction in baking loss. The optimal treatments were to use sourdough seeded with treatment 2C, with treatment 4C, with treatment 8C or with treatment 11C.