bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 growth, furin-cleavage-site adaptation and neutralization using serum from acutely infected, hospitalized COVID-19 patients
Authors: Klimstra William B. , Tilston-Lunel Natasha L. , Nambulli Sham , Boslett James , McMillen Cynthia M. , Gilliland Theron , Dunn Matthew D. , Sun Chengqun , Wheeler Sarah E , Wells Alan , Hartman Amy L. , McElroy Anita K. , Reed Douglas S. , Rennick Linda J. , Duprex W. Paul 
Published: June 2020

AbstractSARS-CoV-2, the causative agent of COVID-19, emerged at the end of 2019 and by mid-June 2020, the virus has spread to at least 215 countries, caused more than 8,000,000 confirmed infections and over 450,000 deaths, and overwhelmed healthcare systems worldwide. Like SARS-CoV, which emerged in 2002 and caused a similar disease, SARS-CoV-2 is a betacoronavirus. Both viruses use human angiotensin-converting enzyme 2 (hACE2) as a receptor to enter cells. However, the SARS-CoV-2 spike (S) glycoprotein has a novel insertion that generates a putative furin cleavage signal and this has been postulated to expand the host range. Two low passage (P) strains of SARS-CoV-2 (Wash1: P4 and Munich: P1) were cultured twice in Vero-E6 cells and characterized virologically. Sanger and MinION sequencing demonstrated significant deletions in the furin cleavage signal of Wash1: P6 and minor variants in the Munich: P3 strain. Cleavage of the S glycoprotein in SARS-CoV-2-infected Vero-E6 cell lysates was inefficient even when an intact furin cleavage signal was present. Indirect immunofluorescence demonstrated the S glycoprotein reached the cell surface. Since the S protein is a major antigenic target for the development of neutralizing antibodies we investigated the development of neutralizing antibody titers in serial serum samples obtained from COVID-19 human patients. These were comparable regardless of the presence of an intact or deleted furin cleavage signal. These studies illustrate the need to characterize virus stocks meticulously prior to performing either in vitro or in vivo pathogenesis studies.
GenNet framework: interpretable neural networks for phenotype prediction
Authors: van Hilten Arno , Kushner Steven A. , Kayser Manfred , Ikram M. Arfan , Adams Hieab H.H. , Klaver Caroline C.W. , Niessen Wiro J. , Roshchupkin Gennady V. 
Published: June 2020

Deep learning is rarely used in population genomics because of the computational burden and challenges in interpreting neural networks. Here, we propose GenNet, a novel open-source deep learning framework for predicting phenotypes from genetic variants. In this framework, interpretable and memory-efficient neural network architectures are constructed by embedding biological knowledge from public databases, resulting in neural networks that contain only biological plausible connections.We applied the framework to seventeen phenotypes from a case-control study, a population-based study and the UK Biobank. Interpreting the networks revealed well-replicated genes such asHERC2andOCA2for hair and eye color and novel genes such asZNF773andPCNTfor schizophrenia. Additionally, the framework obtained an AUC of 0.74 in the held-out test set and identified ubiquitin mediated proteolysis, endocrine system and viral infectious diseases as most predictive biological pathways for schizophrenia.GenNet is a freely available, end-to-end deep learning framework that allows researchers to develop and use interpretable neural networks to obtain novel insights into the genetic architecture of complex traits and diseases.
Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride
Authors: Pezzotti Giuseppe , Ohgitani Eriko , Shin-Ya Masaharu , Adachi Tetsuya , Marin Elia , Boschetto Francesco , Zhu Wenliang , Mazda Osam 
Published: June 2020

AbstractIntroductionViral disease spread by contaminated commonly touched surfaces is a global concern. Silicon nitride, an industrial ceramic that is also used as an implant in spine surgery, has known antibacterial activity. The mechanism of antibacterial action relates to the hydrolytic release of surface disinfectants. It is hypothesized that silicon nitride can also inactivate the coronavirus SARS-CoV-2.MethodsSARS-CoV-2 virions were exposed to 15 wt.% aqueous suspensions of silicon nitride, aluminum nitride, and copper particles. The virus was titrated by the TCD50method using VeroE6/TMPRSS2 cells, while viral RNA was evaluated by real-time RT-PCR. Immunostaining and Raman spectroscopy were used as additional probes to investigate the cellular responses to virions exposed to the respective materials.ResultsAll three tested materials showed >99% viral inactivation at one and ten minutes of exposure. Degradation of viral RNA was also observed with all materials. Immunofluorescence testing showed that silicon nitride-treated virus failed to infect VeroE6/TMPRSS2 cells without damaging them. In contrast, the copper-treated virus suspension severely damaged the cells due to copper ion toxicity. Raman spectroscopy indicated differential biochemical cellular changes due to infection and metal toxicity for two of the three materials tested.ConclusionsSilicon nitride successfully inactivated the SARS-CoV-2 in this study. The mechanism of action was the hydrolysis-mediated surface release of nitrogen-containing disinfectants. Both aluminum nitride and copper were also effective in the inactivation of the virus. However, while the former compound affected the cells, the latter compound had a cytopathic effect. Further studies are needed to validate these findings and investigate whether silicon nitride can be incorporated into personal protective equipment and commonly touched surfaces, as a strategy to discourage viral persistence and disease spread.
Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny
Authors: Pipes Lenore , Wang Hongru , Huelsenbeck John P. , Nielsen Rasmus 
Published: June 2020

AbstractThe rooting of the SARS-CoV-2 phylogeny is important for understanding the origin and early spread of the virus. Previously published phylogenies have used different rootings that do not always provide consistent results. We investigate several different strategies for rooting the SARS-CoV-2 tree and provide measures of statistical uncertainty for all methods. We show that methods based on the molecular clock tend to place the root in the B clade, while methods based on outgroup rooting tend to place the root in the A clade. The results from the two approaches are statistically incompatible, possibly as a consequence of deviations from a molecular clock or excess back-mutations. We also show that none of the methods provide strong statistical support for the placement of the root in any particular edge of the tree. Our results suggest that inferences on the origin and early spread of SARS-CoV-2 based on rooted trees should be interpreted with caution.
Dengue virus strain 2 capsid protein switches the annealing pathway and reduces the intrinsic dynamics of the conserved 5’ untranslated region
Authors: Yong Xin Ee , Raghuvamsi Palur Venkata , Anand Ganesh S. , Wohland Thorsten , Sharma Kamal K. 
Published: June 2020

ABSTRACTThe capsid protein of Dengue Virus strain 2 (DENV2C) is a structural protein with RNA chaperone activity that promotes multiple nucleic acid structural rearrangements, critical for transcription of the single-stranded positive-sense DENV2 genomic RNA. Annealing of the conserved 5’ untranslated region (5’UTR) to either its complementary sequence or to the 3’ untranslated region (3’UTR) occurs during (+)/(−) ds-RNA formation and (+) RNA circularization, respectively, both essential steps during DENV RNA replication. We investigated the effect of DENV2C on the annealing mechanism of two hairpin structures from the 5’UTR region (21-nt upstream AUG region (5’UAR) and 23-nt capsid-coding hairpin (5’cHP)) to their complementary sequences during (+)/(−) ds-RNA formation and (+) RNA circularization. Using fluorescence spectroscopy, DENV2C was found to switch annealing reactions nucleated mainly through kissing-loop intermediates to stem-stem interactions during (+)/(−) ds-RNA formation while it promotes annealing mainly through kissing-loop interactions during the (+) RNA circularization. Using FRET-FCS and trFRET, we determined that DENV2C exerts RNA chaperone activities by modulating intrinsic dynamics and by reducing the kinetically trapped unfavorable conformations of the 5’UTR sequence. Thus, DENV2C is likely to facilitate genome folding into functional conformations required for replication, playing a role in modulating (+)/(−) ds-RNA formation and (+) RNA circularization.
Modulation of root growth by nutrient-defined fine-tuning of polar auxin transport
Authors: Ötvös Krisztina , Marconi Marco , Vega Andrea , O’ Brien Jose , Johnson Alexander , Abualia Rashed , Antonielli Livio , Montesinos Juan Carlos , Zhang Yuzhou , Tan Shutang , Cuesta Candela , Artner Christina , Bouguyon Eleonore , Gojon Alain , Friml Jirí , Gutiérrez Rodrigo A. , Wabnik Krzysztof , Benková Eva 
Published: June 2020

AbstractNitrogen is an essential macronutrient and its availability in soil plays a critical role in plant growth, development and impacts agricultural productivity. Plants have evolved different strategies to sense and respond to heterogeneous nitrogen distribution. Modulating root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to varying nitrogen sources are poorly understood. Here, using a combination of physiological, livein vivohigh- and super resolution imaging, we describe a novel adaptation strategy of root growth on available nitrogen source. We show that growth,i.e. tissue-specific cell division and elongation rates are fine-tuned by modulating auxin flux within and between tissues. Changes in auxin redistribution are achieved by nitrogen source dependent post-translational modification of PIN2, a major auxin efflux carrier, at an uncharacterized, evolutionary conserved phosphosite. Further, we generate a computer model based on our results which successfully recapitulate our experimental observations and creates new predictions that could broaden our understanding of root growth mechanisms in the dynamic environment.
Genome-wide association study in European patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart
Authors: Lahm Harald , Jia Meiwen , Dreßen Martina , Wirth Felix , Puluca Nazan , Gilsbach Ralf , Keavney Bernard D. , Cleuziou Julie , Beck Nicole , Bondareva Olga , Dzilic Elda , Burri Melchior , König Karl C. , Ziegelmüller Johannes A. , Abou-Ajram Claudia , Neb Irina , Zhang Zhong , Doppler Stefanie A. , Mastantuono Elisa , Lichtner Peter , Eckstein Gertrud , Hörer Jürgen , Ewert Peter , Priest James R. , Hein Lutz , Lange Rüdiger , Meitinger Thomas , Cordell Heather J. , Müller-Myhsok Bertram , Krane Markus 
Published: June 2020

AbstractRationaleGenetic factors undoubtedly contribute to the development of congenital heart disease (CHD), but still remain mostly ill-defined.ObjectiveIdentification of genetic risk factors associated with CHD and functional analysis of SNP-carrying genes.Methods and ResultsGenetic association study of 1,440 Caucasian CHD patients from the German Heart Center Munich collected from March 2009 to June 2016, 2,594 patients of previous studies provided by the Newcastle University and 8,486 controls underwent meta-analysis to detect single nucleotide polymorphisms (SNPs) associated with CHD.Results4,034 Caucasian CHD patients strictly classified according to the Society of Thoracic Surgeons nomenclature and 8,486 controls were included. One SNP on chromosome 5 reached genome-wide significance across all CHD phenotypes (rs185531658,OR:2.16, p=5.28×10−9) and was also indicative for septal defects (OR:2.16, p=6.15×10−8). One region on chromosome 20 pointing to the MACROD2 locus, identified four SNPs (rs150246290,OR:3.78, p=1.27×10−10; rs149890280,OR:3.74, p=1.8×10−10; rs149467721,OR:3.53; p=1.39×10−9, rs77094733,OR:3.53, p=1.73×10−9) in patients with transposition of the great arteries (TGA). A second region was detected on chromosome 8 located at ZBTB10 (rs148563140,OR:3.42, p=3.28×10−8; rs143638934,OR:3.42, p=3.51×10−8) in the same subgroup. Three highly significant risk variants on chromosome 17 (rs76774446,OR:1.60, p=9.95×10−8; rs11874,OR:1.60, p=6.64×10−8; rs17677363,OR:1.60, p=9.81×10−8) within the GOSR2 locus were identified in patients with anomalies of thoracic arteries and veins (ATAV). Genetic variants associated with ATAV are suggested to influence expression of WNT3, and variant rs870142 related to septal defects is proposed to influence expression of MSX1. Cardiac differentiation of human and murine induced pluripotent stem cells and single cell RNAseq analyses of developing murine and human hearts show essential functional roles for MACROD2, GOSR2, WNT3 and MSX1 at all developmental stages.ConclusionsFor the first time genetic risk factors in CHD patients with TGA and ATAV were identified. Several candidate genes play an essential functional role in heart development at the embryonic, newborn and adult stage.
Application of thein vivooxidative stress reporter Hmox1 as mechanistic biomarker of arsenic toxicity
Authors: Inesta-Vaquera Francisco , Navasumrit Panida , Henderson Colin J. , Frangova Tanya G. , Honda Tadashi , Dinkova-Kostova Albena T. , Ruchirawat Mathuros , Wolf C. Roland 
Published: June 2020

AbstractInorganic arsenic (iAs) is a naturally occurring metalloid present in drinking water and polluted air exposing millions of people globally. Epidemiological studies have linked iAs exposure to the development of numerous diseases including cognitive impairment, cardiovascular failure and cancer. Despite intense research, an effective therapy for chronic arsenicosis has yet to be developed. Laboratory studies have been of great benefit in establishing the pathways involved in iAs toxicity and providing insights into its mechanism of action. However, thein vivoanalysis of arsenic toxicity mechanisms has been difficult by the lack of reliablein vivobiomarkers of the effects of iAs. To resolve this issue we have applied the use of our recently developed stress reporter models to study iAs toxicity. The reporter mice Hmox1 (oxidative stress/inflammation; HOTT) and p21 (DNA damage) were exposed to iAs at acute and chronic, environmentally relevant, doses. We observed induction of the oxidative stress reporters in several cell types and tissues, which was largely dependent on the activation of transcription factor NRF2. We propose that our HOTT reporter model can be used as a surrogate biomarker of iAs-induced oxidative stress, and it constitutes a first-inclass platform to develop treatments in arsenicosis. Indeed, in a proof of concept experiment, the HOTT reporter mice were able to predict the therapeutic utility of the antioxidantN-acetyl cysteine in the prevention of iAs associated toxicity.
Measurement of stretch-evoked brainstem function using fMRI
Authors: Zonnino Andrea , Farrens Andria J , Ress David , Sergi Fabrizio 
Published: June 2020

ABSTRACTKnowledge on the organization of motor function in the reticulospinal tract (RST) is limited by the lack of methods for measuring RST function in humans. Behavioral studies suggest the involvement of the RST in long latency responses (LLRs). LLRs, elicited by precisely controlled perturbations, can therefore act as a viable paradigm to measure motor-related RST activity using functional Magnetic Resonance Imaging (fMRI).Here we present StretchfMRI, a novel technique developed to study RST function associated with LLRs. StretchfMRI combines robotic perturbations with electromyography and fMRI to simultaneously quantify muscular and neural activity during stretch-evoked LLRs without loss of reliability. Using StretchfMRI, we established the muscle-specific organization of LLR activity in the brainstem. The observed organization is partially consistent with animal models, with activity primarily in the ipsilateral medulla for flexors and in the contralateral pons for extensors, but also include other areas, such as the midbrain and bilateral pontomedullary contributions.
QTL mapping for aggressiveness variation inF. graminearumrevealed one causal mutation in FgVe1 velvet protein
Authors: Laurent B. , Moinard M. , Spataro C. , Chéreau S. , Zehraoui E. , Blanc R. , Lasserre P. , Ponts N. , Foulongne-Oriol M. 
Published: June 2020

ABSTRACTFusarium graminearumis one of the most frequent causal agents of theFusariumHead Blight in the world, a cereal disease spread throughout the world, reducing grain production and quality.F. graminearumisolates are genetically and phenotypically highly diverse. Notably, remarkable variations of aggressiveness between isolates have been observed, which could reflect an adaptive potential of this pathogen. In this study, we aimed to characterize the genetic basis of aggressiveness variation observed in an F1 population, for which genome sequences of both parental strains are available. Aggressiveness was assessed by a panel ofin plantaandin vitroproxies during two phenotyping trials including, among others, disease severity and mycotoxin accumulation in wheat spike. One major and single QTL was mapped for all the traits measured, on chromosome I, that explained up to 90% of the variance for disease severity. The confidence interval at the QTL spanned 1.2 Mb and contained 428 genes on the reference genome. Of these, four candidates were selected based on the postulate that a non-synonymous mutation affecting protein function may be responsible for phenotypic differences. Finally, a mutation was identified and functionally validated in the geneFgVe1, coding for a velvet protein known to be involved in pathogenicity and secondary metabolism production in several fungi.
Characterization of the dynamic resting state of a pentameric ligand-gated ion channel by cryo-electron microscopy and simulations
Authors: Rovšnik U , Zhuang Y , Axelsson L , Forsberg BO , Lim V , Carroni M , Blau C , Howard RJ , Lindahl E 
Published: June 2020

AbstractLigand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. Biophysical and pharmacological development in this family relies on high-quality structural data in multiple, subtly distinct functional states. However, structural data remain limited, particularly for the unliganded or resting state. Here we report cryo-electron microscopy structures of theGloeobacter violaceusligand-gated ion channel (GLIC) under resting and activating conditions (neutral and low pH). Parallel models were built either manually or using recently developed density-guided molecular simulations. The moderate resolution of resting-state reconstructions, particularly in the extracellular domain, was improved under activating conditions, enabling the visualization of residues at key subunit interfaces including loops B, C, F, and M2–M3. Combined with molecular dynamics simulations, the cryo-electron microscopy structures at different pH describe a heterogeneous population of closed channels, with activating conditions condensing the closed-channel energy landscape on a pathway towards gating.
Gnotobiotic rainbow trout (Oncorhynchus mykiss) model reveals endogenous bacteria that protect againstFlavobacterium columnareinfection
Authors: Pérez-Pascual David , Vendrell-Fernández Sol , Audrain Bianca , Bernal-Bayard Joaquín , Patiño-Navarrete Rafael , Petit Vincent , Rigaudeau Dimitri , Ghigo Jean-Marc 
Published: June 2020

ABSTRACTThe health and environmental risks associated with antibiotic use in aquaculture have promoted bacterial probiotics as an alternative approach to control fish infections in vulnerable larval and juvenile stages. However, evidence-based identification of probiotics is often hindered by the complexity of bacteria-host interactions and host variability in microbiologically uncontrolled conditions. While these difficulties can be partially resolved using gnotobiotic models harboring no or reduced microbiota, most host-microbe interaction studies are carried out in animal models with little relevance for fish farming. Here we studied host-microbiota-pathogen interactions in a germ-free and gnotobiotic model of rainbow trout (Oncorhynchus mykiss), one of the most widely cultured salmonids. We demonstrated that germ-free larvae raised in sterile conditions displayed no significant difference in growth after 35 days compared to conventionally-raised larvae, but were extremely sensitive to infection byFlavobacterium columnare, a common freshwater fish pathogen causing major economic losses worldwide. Furthermore, re-conventionalization with 11 culturable species from the conventional trout microbiota conferred resistance toF. columnareinfection. Using mono-re-conventionalized germ-free trout, we identified that this protection is determined by a commensalFlavobacteriumstrain displaying antibacterial activity againstF. columnare. Finally, we demonstrated that use of gnotobiotic trout is a suitable approach for the systematic identification of both endogenous and exogenous probiotic bacterial strains that may protect teleostean hosts againstF. columnareand other pathogens. This study establishes a novel and ecologically-relevant gnotobiotic model that will improve the sustainability and health of aquaculture.
Identification of sex differences in tumor-specific T cell infiltration in bladder tumor-bearing mice treated with BCG immunotherapy
Authors: Rousseau Matthieu , O’Brien Conan J O , Antequera Eduardo , Zdimerova Hana , Cansever Dilay , Canton Tracy , Scharff Anna Zychlinsky , Ingersoll Molly A 
Published: June 2020

AbstractBladder cancer is the fourth most common cancer for men. However, women are often diagnosed with later stage disease and have poorer outcomes. Whether immune-based sex differences contribute to this discrepancy is unclear. In addition, models to investigate tumor-specific immunity in bladder cancer, in the context of tumor development or response to therapy, are lacking. To address this specific unmet need, we incorporated a commonly used model antigen, ovalbumin, into two well-established models of bladder cancer; the orthotopic MB49 cell line model and the carcinogenic BBN bladder cancer model. We tested the utility of these models to investigate tumor-specific immunity in the context of immunotherapy in both sexes. We found that BCG vaccination, prior to weekly BCG instillation does not impart an immune-specific benefit to tumor-bearing mice in the context of multiple BCG instillations. Furthermore, tumors developed in the testes in male mice, precluding the use of the MB49 model to directly investigate sex-based immune differences. In the BBN model, we observed that more tumor antigen-specific CD8+T cells infiltrated male bladders compared to female bladders in the context of BCG immunotherapy and that these cells had the highest levels of the exhaustion marker PD-1. We propose our modified BBN model will contribute to our understanding of how tumor-specific immunity arises in bladder cancer. Additionally, the BBN bladder cancer model may help to uncover sex differences in tumor-specific immunity, which would provide valuable information for the development of new treatments or combination therapies for bladder cancer in women and men.