bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA
Authors: Bartas Martin , Volná Adriana , Beaudoin Christopher A. , Poulsen Ebbe Toftgaard , Červeň Jiří , Brázda Václav , Špunda Vladimír , Blundell Tom L. , Pečinka Petr 
Published: November 2020

AbstractSARS-CoV-2 is a novel positive-sense single-stranded RNA virus from the Coronaviridae family (genus Betacoronavirus), which has been established as causing the COVID-19 pandemic. The genome of SARS-CoV-2 is one of the largest among known RNA viruses, comprising of at least 26 known protein-coding loci. Studies thus far have outlined the coding capacity of the positive-sense strand of the SARS-CoV-2 genome, which can be used directly for protein translation. However, it has been recently shown that transcribed negative-sense viral RNA intermediates that arise during viral genome replication from positive-sense viruses can also code for proteins. No studies have yet explored the potential for negative-sense SARS-CoV-2 RNA intermediates to contain protein coding-loci. Thus, using sequence and structure-based bioinformatics methodologies, we have investigated the presence and validity of putative negative-sense ORFs (nsORFs) in the SARS-CoV-2 genome. Nine nsORFs were discovered to contain strong eukaryotic translation initiation signals and high codon adaptability scores, and several of the nsORFs were predicted to interact with RNA-binding proteins. Evolutionary conservation analyses indicated that some of the nsORFs are deeply conserved among related coronaviruses. Three-dimensional protein modelling revealed the presence of higher order folding among all putative SARS-CoV-2 nsORFs, and subsequent structural mimicry analyses suggest similarity of the nsORFs to DNA/RNA-binding proteins and proteins involved in immune signaling pathways. Altogether, these results suggest the potential existence of still undescribed SARS-CoV-2 proteins, which may play an important role in the viral lifecycle and COVID-19 pathogenesis.Contactpetr.pecinka@osu.cz; tlb20@cam.ac.uk
Latent class regression improves the predictive acuity and clinical utility of survival prognostication amongst chronic heart failure patients
Authors: Mbotwa John L , de Kamps Marc , Baxter Paul D , Ellison George TH , Gilthorpe Mark S 
Published: November 2020

AbstractThe present study aimed to compare the predictive acuity of latent class regression (LCR) modelling with: standard generalised linear modelling (GLM); and GLMs that include the membership of subgroups/classes (identified through prior latent class analysis; LCA) as alternative or additional candidate predictors. Using real world demographic and clinical data from 1,802 heart failure patients enrolled in the UK-HEART2 cohort, the study found that univariable GLMs using LCA-generated subgroup/class membership as the sole candidate predictor of survival were inferior to standard multivariable GLMs using the same four covariates as those used in the LCA. The inclusion of the LCA subgroup/class membership together with these four covariates as candidate predictors in a multivariable GLM showed no improvement in predictive acuity. In contrast, LCR modelling resulted in a 10-14% improvement in predictive acuity and provided a range of alternative models from which it would be possible to balance predictive acuity against entropy to select models that were optimally suited to improve the efficient allocation of clinical resources to address the differential risk of the outcome (in this instance, survival). These findings provide proof-of-principle that LCR modelling can improve the predictive acuity of GLMs and enhance the clinical utility of their predictions. These improvements warrant further attention and exploration, including the use of alternative techniques (including machine learning algorithms) that are also capable of generating latent class structure while determining outcome predictions, particularly for use with large and routinely collected clinical datasets, and with binary, count and continuous variables.
Genome-wide association mapping identifies Yellow Rust resistance locus in Ethiopian Durum Wheat germplasm
Authors: Alemu Sisay Kidane , Huluka Ayele Badebo , Geletu Kassahun Tesfaye , Uauy Cristobal 
Published: November 2020

AbstractDurum wheat is an important cereal grown in Ethiopia, a country which is also its center for genetic diversity. Yellow (stripe) rust caused by Puccinia striiformis fsp tritici is one of the most devastating diseases threatening Ethiopian wheat production. To identify sources of genetic resistance to combat this pathogen, we conducted a genome wide association study of yellow rust resistance on 300 durum wheat accessions comprising 261 landraces and 39 cultivars. The accessions were evaluated for their field resistance in an alpha lattice design (10 × 30) in two replications at Meraro, Kulumsa and Chefe-Donsa in the 2015 and 2016 main growing seasons. Disease Scoring was carried out using a modified Cobb scale and then converted to Coefficient of Infection (CI). Analysis of the 35K Axiom Array genotyping data resulted in a total of 8,797 polymorphic SNPs of which 7,093 were used in subsequent analyses. Population structure analysis suggested two groups in which the cultivars clearly stood out separately from the landraces. We identified twelve SNPs significantly associated with yellow rust resistance across four chromosomes (1A, 1B, 2B, and 7B). Six of the SNPs (AX-95171339, AX-94436448, AX-95238778, AX-95096041, AX-94730403 & AX-94427201), were consistently identified on chromosome 1B at the three field locations and combined across the six environments. The phenotypic variation (R2) explained by all six SNPs on chromosome 1B ranged from 63.7 – 65.4%. Locus-based analysis of phenotypic values between resistant and susceptible allele resulted in a significant difference at (p < 0.001). Further investigation across the genomic interval encompassing the identified loci indicated the presence of disease resistance protein (NBS-LRR class) family and RPM1 in the vicinity of the loci. This study provides SNPs for tracking the QTL associated with yellow rust resistance in durum wheat improvement programs.
PP2A-Cdc55 phosphatase coordinates actomyosin ring contraction and septum formation during cytokinesis
Authors: Moyano-Rodríguez Yolanda , Vaquero David , Vilalta-Castany Odena , Foltman Magdalena , Sanchez-Diaz Alberto , Queralt Ethel 
Published: November 2020

SummaryEukaryotic cells divide and separate all their components after chromosome segregation by a process called cytokinesis to complete cell division. Cytokinesis is highly regulated by recruitment of the components to the division site and through post-translational modifications such as phosphorylations. The budding yeast mitotic kinases Cdc28-Clb2, Cdc5, and Dbf2-Mob1 phosphorylate several cytokinetic proteins contributing to the regulation of cytokinesis. The PP2A-Cdc55 phosphatase regulates mitosis counteracting Cdk1- and Cdc5-dependent phosphorylation. This prompted us to propose that PP2A-Cdc55 could also be counteracting the mitotic kinases during cytokinesis. Here, we demonstrate that primary septum formation and actomyosin ring contraction are impaired in the absence of PP2A-Cdc55. In addition, by in vivo and in vitro assays, we show that PP2A-Cdc55 dephosphorylates the chitin synthase II (Chs2 in budding yeast) a component of the Ingression Progression Complexes (IPCs) involved in cytokinesis. Interestingly, the non-phosphorylable version of Chs2 rescues the asymmetric AMR contraction observed in cdc55Δ mutant cells. Therefore, timely dephosphorylation of the Chs2 by PP2A-Cdc55 is crucial for proper actomyosin ring contraction. These findings reveal a new mechanism of cytokinesis regulation by the PP2A-Cdc55 phosphatase and extend our knowledge in the involvement of multiple phosphatases during cytokinesis.
Differential host response to a herpesvirus: Marek’s disease virus peptides on chicken MHC class II molecules are derived from only a few genes and illustrate a new mode of peptide binding
Authors: Halabi Samer , Ghosh Michael , Stevanović Stefan , Rammensee Hans-Georg , Bertzbach Luca D. , Kaufer Benedikt B. , Moncrieffe Martin C. , Kaspers Bernd , Härtle Sonja , Kaufman Jim 
Published: November 2020

AbstractViral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viral diseases. An iconic example is Marek’s disease, caused by an oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules present antigenic peptides to T lymphocytes, and it has been hard to understand how such MHC molecules could be involved in susceptibility to Marek’s disease, given the potential number of peptides from over 100 genes. We used a new in vitro infection system and immunopeptidomics to determine peptide motifs for the two class II molecules expressed by the MHC haplotype B2, which is known to confer resistance to Marek’s disease. Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken class II molecules arise from only four viral genes, nearly all having the peptide motif for BL2, the dominantly-expressed class II molecule in chickens. We expressed BL2 linked to several MDV peptides, and determined one X-ray crystal structure, showing how a single small amino acid in the binding site causes a crinkle in the peptide, leading to core binding peptide of ten amino acids, compared to the nine amino acids in all other reported class II molecules. The limited number of potential T cell epitopes from such a complex virus can explain the differential MHC-determined resistance to MDV, but raises questions of mechanism and opportunities for vaccine targets in this important food species, as well as providing a basis for understanding class II molecules in other species including humans.
Valid statistical approaches for clustered data: A Monte Carlo simulation study
Authors: McLaurin Kristen A. , Fairchild Amanda J. , Shi Dexin , Booze Rosemarie M. , Mactutus Charles F. 
Published: November 2020

AbstractThe translation of preclinical studies to human applications is associated with a high failure rate, which may be exacerbated by limited training in experimental design and statistical analysis. Nested experimental designs, which occur when data have a multilevel structure (e.g., in vitro: cells within a culture dish; in vivo: rats within a litter), often violate the independent observation assumption underlying many traditional statistical techniques. Although previous studies have empirically evaluated the analytic challenges associated with multilevel data, existing work has not focused on key parameters and design components typically observed in preclinical research. To address this knowledge gap, a Monte Carlo simulation study was conducted to systematically assess the effects of inappropriately modeling multilevel data via a fixed effects ANOVA in studies with sparse observations, no between group comparison within a single cluster, and interactive effects. Simulation results revealed a dramatic increase in the probability of type 1 error and relative bias of the standard error as the number of level-1 (e.g., cells; rats) units per cell increased in the fixed effects ANOVA; these effects were largely attenuated when the nesting was appropriately accounted for via a random effects ANOVA. Thus, failure to account for a nested experimental design may lead to reproducibility challenges and inaccurate conclusions. Appropriately accounting for multilevel data, however, may enhance statistical reliability, thereby leading to improvements in translatability. Valid analytic strategies are provided for a variety of design scenarios.
DNA polymerase theta suppresses mitotic crossing over
Authors: Carvajal-Garcia Juan , Crown K. Nicole , Ramsden Dale A. , Sekelsky Jeff 
Published: November 2020

AbstractPolymerase theta-mediated end joining (TMEJ) is a chromosome break repair pathway that is able to rescue the lethality associated with the loss of proteins involved in early steps in homologous recombination (e.g., BRCA1/2). This is due to the ability of polymerase theta (Pol θ) to use resected, 3’ single stranded DNA tails to repair chromosome breaks. These resected DNA tails are also the starting substrate for homologous recombination. However, it remains unknown if TMEJ can compensate for the loss of proteins involved in more downstream steps during homologous recombination. Here we expand the number of homologous recombination proteins synthetic lethal with Pol θ to the Holliday junction resolvases SLX4 and GEN1. SLX4 and GEN1 are required for viability in the absence of Pol θ inDrosophila melanogaster,and lack of all three proteins results in very high levels of apoptosis. We observe that flies deficient in Pol θ and SLX4 are extremely sensitive to DNA damaging agents, and mammalian cells require either Pol θ or SLX4 to survive. Our results suggest that TMEJ and Holliday junction formation/resolution share a common DNA substrate, likely a homologous recombination intermediate, that when left unrepaired leads to cell death. One major consequence of Holliday junction resolution by SLX4 and GEN1 is cancer-causing loss of heterozygosity due to mitotic crossing over. We measured mitotic crossovers in flies after a Cas9-induced chromosome break, and observed that this mutagenic form of repair is increased in the absence of Pol θ. This demonstrates that TMEJ can function upstream of the Holiday junction resolvases to protect cells from loss of heterozygosity. Our work argues that Pol θ can thus compensate for the loss of the Holliday junction resolvases by utilizing homologous recombination intermediates, suppressing mitotic crossing over and preserving the genomic stability of cells.Author summaryChromosome breaks are a common threat to the stability of DNA. Mutations in genes involved in the early steps of homologous recombination (BRCA1andBRCA2), a mostly error-free chromosome break repair pathway, lead to hereditary breast cancer. Cells lacking BRCA1 and BRCA2 rely on DNA polymerase theta, a key protein for a more error-prone pathway, for survival. Using fruit flies and mammalian cells, we have shown that mutations in genes involved in later steps of homologous recombination (SLX4andGEN1) also make cells reliant on polymerase theta. Moreover, we have shown that polymerase theta acts upstream of a type of homologous recombination that is error-prone and depends on SLX4 and GEN1. This form of homologous recombination, termed Holliday junction resolution, creates mitotic crossovers, which can lead to loss of heterozygosity and cancer. Our results expand the cellular contexts that make cells depend on polymerase theta for survival, and the substrates that this protein can use to repair chromosome breaks.
Elevated expression of complement C4 in the mouse prefrontal cortex causes schizophrenia-associated phenotypes
Authors: Druart Mélanie , Nosten-Bertrand Marika , Poll Stefanie , Crux Sophie , Nebeling Felix , Delhaye Célia , Dubois Yaëlle , Leboyer Marion , Tamouza Ryad , Fuhrmann Martin , Le Magueresse Corentin 
Published: November 2020

AbstractAccumulating evidence supports immune involvement in the pathogenesis of schizophrenia, a severe psychiatric disorder. In particular, high expression variants of C4, a gene of the innate immune complement system, were shown to confer susceptibility to schizophrenia. However, how elevated C4 expression may impact brain circuits remains largely unknown. We used in utero electroporation to overexpress C4 in the mouse prefrontal cortex (PFC). We found reduced glutamatergic input to pyramidal cells of juvenile and adult, but not of newborn C4-overexpressing (C4-OE) mice, together with decreased spine density, which mirrors spine loss observed in the schizophrenic cortex. Using time-lapse two-photon imaging in vivo, we observed that these deficits were associated with decreased dendritic spine gain and elimination in juvenile C4-OE mice, which may reflect poor formation and/or stabilization of immature spines. In juvenile and adult C4-OE mice we found evidence for NMDA receptor hypofunction, another schizophrenia-associated phenotype, and synaptic accumulation of calcium-permeable AMPA receptors. Alterations in cortical GABAergic networks have been repeatedly associated with schizophrenia. We found that functional GABAergic transmission was reduced in C4-OE mice, in line with diminished GABA release probability from parvalbumin interneurons, lower GAD67 expression and decreased intrinsic excitability in parvalbumin interneurons. These cellular abnormalities were associated with working memory impairment. Our results substantiate the causal relationship between an immunogenetic risk factor and several distinct cortical endophenotypes of schizophrenia, and shed light on the underlying cellular mechanisms.
Human induced pluripotent stem cell-derived vessels as dynamic atherosclerosis model on a chip
Authors: Mallone A. , Gericke C. , Hosseini V. , Chahbi K. , Haenseler W. , Emmert M. Y. , von Eckardstein A. , Walther J. H. , Vogel V. , Weber B , Hoerstrup S. P. 
Published: November 2020

AbstractAtherosclerosis is an arterial disease characterized by intravascular plaques. Disease hallmarks are vessel stenosis and hyperplasia, eventually escalating into plaque rupture and acute clinical presentations. Innate immune cells and local variations in hemodynamics are core players in the pathology, but their mutual relationship has never been investigated before due to the lack of modeling systems with adequate degree of complexity. Here, we combined computational fluid dynamics and tissue-engineering to achieve, for the first time in vitro, full atherosclerotic plaque development. Our model incorporates induced pluripotent stem cell-derived populations into small-caliber arteries that are cultured in atheroprone conditions. Using machine-learning-aided immunophenotyping, molecular and nanoprobe-based tensile analyses, we found that immune cells, extracellular matrix components and tensional state were comparable between in vitro and ex vivo human lesions. Our results provide further insights into the relation between hemodynamics and inflammation, introducing a versatile, scalable modeling tool to study atherosclerosis onset and progression.
Scavenger receptor A1 participates in the phagocytosis ofLeptospira interrogansand leads to subsequent high inflammatory responses and bacterial dissemination in leptospirosis
Authors: Wang Yanchun , Fan Xia , Du Lin , Liu Boyu , Xiao Haihan , Zhang Yan , Wu Yunqiang , Liu Fuli , Chang Yung-Fu , Guo Xiaokui , He Ping 
Published: November 2020

AbstractLeptospirosis, caused by pathogenicLeptospiraspecies, has emerged as a widespread zoonotic disease worldwide. Macrophages mediate the elimination of pathogens through phagocytosis and cytokine production. Scavenger receptor A1 (SR-A1), one of the critical receptors mediating this process, plays a complicated role in innate immunity. However, the role of SR-A1 in the immune response against pathogenicLeptospirainvasion is unknown. In the present study, we found that SR-A1 is an important nonopsonic phagocytic receptor on murine macrophages forLeptospira. We also found that leptospiral LPS is the ligand of SR-A1. However, intraperitoneal injection of leptospires into WT mice presented with more severe jaundice, subcutaneous hemorrhaging, and higher bacteria burdens in blood and tissues than that of SR-A1-/-mice. Exacerbated cytokine and inflammatory mediator levels were also observed in WT mice and higher recruited macrophages in the liver than those of SR-A1-/-mice. Our findings collectively reveal that although beneficial in the uptake ofLeptospiraby macrophage, SR-A1 might be exploited byLeptospirato promote bacterial dissemination and modulate inflammatory activation, which causes a more severe infection in the host. These results provide our new insights into the innate immune response during early infection byL. interrogans.
Rat perichondrium transplanted to articular cartilage defects forms articular-like, hyaline cartilage
Authors: Dou Zelong , Muder Daniel , Baroncelli Marta , Bendre Ameya , Gkourogianni Alexandra , Ottosson Lars , Vedung Torbjörn , Nilsson Ola 
Published: November 2020

AbstractReconstruction of articular surfaces destroyed by infection or trauma is hampered by the lack of suitable graft tissues. Perichondrium autotransplants have been used for this purpose. However, the role of the transplanted perichondrium in the healing of resurfaced joints have not been investigated. Perichondrial and periosteal tissues were harvested from rats hemizygous for a ubiquitously expressed enhanced green fluorescent protein (EGFP) transgene and transplanted into full-thickness articular cartilage defects at the trochlear groove of distal femur in wild-type littermates. As an additional control, cartilage defects were left without a transplant (no transplant control). Distal femurs were collected 3, 14, 56, 112 days after surgery. Transplanted cells and their progenies were readily detected in the defects of perichondrium and periosteum transplanted animals but not in defects left without a transplant. Perichondrium transplants expressed SOX9 and with time differentiated into a hyaline cartilage that expanded and filled out the defects with Col2a1-positive chondrocytes and a matrix rich in proteoglycans. Interestingly, at later timepoints the cartilaginous perichondrium transplants were actively remodeled into bone at the transplant-bone interface and at post-surgery day 112 EGFP-positive perichondrium cells at the articular surface were positive for Prg4. In addition, both perichondrium and periosteum transplants contributed cells to the subchondral bone and bone marrow, suggesting differentiation into osteoblast/osteocytes as well as bone marrow cells. In summary, we found that perichondrium transplanted to articular cartilage defects develops into an articular-like, hyaline cartilage that integrates with the subchondral bone, and is maintained for an extended time. The findings indicate that perichondrium is a suitable tissue for repair and engineering of articular cartilage.
Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist
Authors: Isaikina Polina , Tsai Ching-Ju , Dietz Nikolaus , Pamula Filip , Grahl Anne , Goldie Kenneth N. , Guixà-González Ramon , Schertler Gebhard F.X. , Hartley Oliver , Stahlberg Henning , Maier Timm , Deupi Xavier , Grzesiek Stephan 
Published: November 2020

AbstractThe human CC chemokine receptor 5 (CCR5) is a G protein-coupled receptor (GPCR) that plays a major role in inflammation and is involved in the pathology of cancer, HIV, and COVID-19. Despite its significance as a drug target, the activation mechanism of CCR5, i.e. how chemokine agonists transduce the activation signal through the receptor, is yet unknown. Here, we report the cryo-EM structure of wild-type CCR5 in an active conformation bound to the chemokine super-agonist [6P4]CCL5 and the heterotrimeric Gi protein. The structure provides the rationale for the sequence-activity relation of agonist and antagonist chemokines. The N-terminus of agonist chemokines pushes onto an aromatic connector that transmits activation to the canonical GPCR microswitch network. This activation mechanism differs significantly from other CC chemokine receptors that bind shorter chemokines in a shallow binding mode and have unique sequence signatures and a specialized activation mechanism.One-sentence summaryThe structure of CCR5 in complex with the chemokine agonist [6P4]CCL5 and the heterotrimeric Gi protein reveals its activation mechanism