bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic regions associated with chocolate spot (Botrytis fabaeSard.) resistance in faba bean (Vicia fabaL.)
Authors: Gela Tadesse S. , Bruce Margaret , Chang Wei , Stoddard Frederick L. , Schulman Alan H. , Vandenberg Albert , Khazaei Hamid 
Published: November 2021

AbstractChocolate spot (CS), caused byBotrytis fabaeSard., is an important threat to global faba bean production. Growing resistant faba bean cultivars is, therefore, paramount to preventing yield loss. To date, there have been no reported quantitative trait loci (QTLs) associated with CS resistance in faba bean. The objective of this study was to identify genomic regions associated with CS resistance using a recombinant inbred line (RIL) population derived from resistant accession ILB 938. A total of 165 RILs from the cross Mélodie/2 × ILB 938/2 were genotyped and evaluated for CS reactions under replicated controlled climate conditions. QTL analysis identified five loci contributing to CS resistance on faba bean chromosomes 1 and 6, accounting for 5.0–23.4% of the total phenotypic variance. The sequences of SNP markers linked to resistance QTLs on chromosome 1 that have the largest effects encode multiple classes of putative disease and/or defense-related genes. The results of this study not only provide insight into disease-resistance QTLs, but also can be used as potential targets for marker-assisted breeding in faba bean genetic improvement for CS resistance.Key messageQTL mapping identified key genomic regions associated with chocolate spot resistance on faba bean chromosomes 1 and 6, which may serve as novel genetic tools to develop disease-resistant faba bean cultivars.
Inhibition of the TLR4 signalling pathway with TAK-242 reduces RSV infection and cytokine release in primary airway epithelial cells
Authors: Broadbent Lindsay , Roberts Grace C. , Coey Jonathon D. , Barabas Judit , Shields Michael D. , Power Ultan F. ,   the Breathing Together Consortium
Published: November 2021

AbstractRespiratory syncytial virus (RSV) infection is the leading cause of hospitalisation in children worldwide, but there is still no vaccine or anti-viral treatment available. RSV has been implicated in the development of respiratory diseases such as asthma. Toll like receptor 4 (TLR4) has been well characterised in the immune responses to RSV. However, the role of TLR4 in RSV infection remains unclear. To study RSV in the lung epithelium, where RSV preferentially infects ciliated cells, we used a well-differentiated primary airway epithelial cell (WD-PAEC) model: a pseudostratified epithelium that produces mucus and beating cilia. We demonstrate in this physiologically relevant model that TLR4 is a pro-viral factor. Inhibition of TLR4 using TAK-242 significantly reduces RSV titres in WD-PAECs in a dose-dependent manner but has no effect on RSV growth kinetics in a range of immortalised respiratory-derived cell lines. Specific inhibition of a range of downstream effectors of TLR4 signalling in the WD-PAEC model identified p38 MAPK as a pro-viral factor, whereas inhibition of MEK1/2 significantly increased RSV titres. Our data demonstrate a role for TLR4 in RSV infection and highlight the importance of biologically relevant models to study virus-host interactions.Author summaryRespiratory Syncytial Virus (RSV) can cause severe respiratory infection in young children and is responsible for approximately 200,000 deaths worldwide every year. Despite decades of research since the identification of this virus in the 1950s there is still no vaccine or treatment available. Advances in research have led to the development of cell cultures that are very similar to the cells that line human airways. These cultures provide an opportunity to study how viruses interacts with airway cells in a representative model and may provide insights that traditional research models have not yet been able to answer. Using this experimental model we show that a drug, TAK-242 which targets a pathogen recognition receptor on the surface of cells, reduces growth of RSV and dampens the immune response to infection in these airway cells. Our data demonstrate potential targets for RSV treatments and also highlight the importance of using relevant experimental models.
Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacaoL.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential
Authors: Bekele Frances L. , Bidaisee Gillian G. , Allegre Mathilde , Argout Xavier , Fouet Olivier , Boccara Michel , Saravanakumar Duraisamy , Bekele Isaac , Lanaud Claire 
Published: November 2021

AbstractA genome-wide association study was undertaken to unravel marker-trait associations (MTAs) between SNP markers and yield-related traits. It involved a subset of 421 cacao accessions from the large and diverse collection conservedex situat the International Cocoa Genebank Trinidad. An average linkage disequilibrium (r2) of 0.10 at 5.2 Mb was found across several chromosomes. Seventeen significant (P≤ 8.17 × 10-5(–log10 (p) = 4.088)) MTAs of interest, which accounted for 5 to 17% of the explained phenotypic variation, were identified using a Mixed Linear Model in TASSEL version 5.2.50. The most significant MTAs identified were related to seed number and seed length on chromosome 7 and seed number on chromosome 1. Other significant MTAs involved seed length to width ratio on chromosomes 3 and 5 and seed length on chromosomes 4 and 9. It was noteworthy that several yield-related traits,viz., seed length, seed length to width ratio and seed number were associated with markers on different chromosomes, indicating their polygenic nature. Approximately 40 candidate genes that encode embryo and seed development, protein synthesis, carbohydrate transport and lipid biosynthesis and transport were identified in this study. A significant association of fruit surface anthocyanin intensity co-localised with MYB-related protein 308 on chromosome 4. Testing of a genomic selection approach revealed good predictive value (GEBV) for economic traits such as seed number (GEBV = 0.611), seed length (0.6199), seed width (0.5435), seed length to width ratio (0.5503), seed/cotyledon mass (0.6014) and ovule number (0.6325). The findings of this study could facilitate genomic selection and marker-assisted breeding of cacao thereby expediting improvement in the yield potential of cacao planting material.
NGSpop: A desktop software that supports population studies by identifying sequence variations from next-generation sequencing data
Authors: Lee Dong-Jun , Kwon Taesoo , Lee Hye-Jin , Oh Yun-Ho , Kim Jin-Hyun , Lee Tae-Ho 
Published: November 2021

AbstractNext-generation sequencing (NGS) is widely used in all areas of genetic research, such as for genetic disease diagnosis and breeding, and it can produce massive amounts of data. The identification of sequence variants is an important step when processing large NGS datasets; however, currently, the process is complicated, repetitive, and requires concentration, which can be taxing on the researcher. Therefore, to support researchers who are not familiar with bioinformatics in identifying sequence variations regularly from large datasets, we have developed a fully automated desktop software, NGSpop. NGSpop includes functionalities for all the variant calling and visualization procedures used when processing NGS data, such as quality control, mapping, filtering details, and variant calling. In the variant calling step, the user can select the GATK or DeepVariant algorithm for variant calling. These algorithms can be executed using pre-set pipelines and options or customized with the user-specified options. NGSpop is implemented using JavaFX (version 1.8) and can thus be run on Unix like operating systems such as Ubuntu Linux (version 16.04, 18.0.4). Although there are several pipelines and visualization tools available for NGS data analysis, most integrated environments do not support batch processes; thus, variant detection cannot be automated for population-level studies. The NGSpop software, developed in this study, has an easy-to-use interface and helps in rapid analysis of multiple NGS data from population studies.
Biomechanical characteristics of scapula and glenohumeral movements during pitching motion in injury-prone college baseball pitchers
Authors: Miyashita Koji , Koshida Sentaro , Koyama Taro , Ota Kenicihro , Tani Yusuke , Okamune Ryoji 
Published: November 2021

AbstractCoordination of glenohumeral and scapular movements plays an important role in the injury prevention of baseball pitchers. However, there is no objective data establishing the direct relationship between pitching injuries and associated glenohumeral and scapular movements. Therefore, the objectives of the present study were to demonstrate biomechanical differences in scapular and glenohumeral movements during pitching between injury-prone pitchers and healthy college baseball pitchers. Thirty collegiate baseball pitchers were classified into two groups according to their injury status: injury-prone group (N=15, 20.7±1.4 years, 180.1±6.5 cm, 78.9±5.4 kg) and control group (N=15, 20.9±1.1 years, 177.1±6.6 cm, 72.3±6.7 kg). We obtained the pitching motion data using the three-dimensional motion analysis technique with four high-speed cameras. The horizontal abduction angles of the glenohumeral joint during cocking and acceleration phases were significantly greater in injury-prone pitchers [19.0° (95% CI: 14.4–23.6) at foot contact, −4.0° (95% CI: −7.7 to −0.2) at maximum external rotation (MER), and −0.3° (95% CI: −4.8 to −4.2) at ball release] than in healthy controls [11.7 °(95%CI:7.1 to 16.3) at foot contact, −10.0°(95%CI: −13.7 to −6.3) at MER, and −6.9°(95%CI: −11.4 to −2.4)](p<0.01). In addition, the external rotation angle (ER) of the scapula at MER was significantly greater in the injury-prone group [−0.1° (95% CI: −5.0 to 4.8)] than in the control group [−12.3° (95% CI: −17.2 to −7.4)] (p<0.01), but there was no difference in the scapular ER during foot contact between the two groups. These results suggests that injury-prone pitchers have less internal rotation of the scapula and more horizontal abduction of the glenohumeral joint during cocking and acceleration phases. Therefore, sports medicine practitioners may need to pay more attention to coordination of scapular and glenohumeral movements during the cocking and acceleration phases of pitching for prevention of shoulder injuries.
Adaptive coding of stimulus information in human frontoparietal cortex during visual classification
Authors: Wisniewski David , González-García Carlos , Formica Silvia , Woolgar Alexandra , Brass Marcel 
Published: November 2021

AbstractThe neural mechanisms of how frontal and parietal brain regions support flexible adaptation of behavior remain poorly understood. Here, we used functional magnetic resonance imaging (fMRI) and model-based representational similarity analysis (RSA) to investigate frontoparietal representations of stimulus information during visual classification under varying task demands. Based on prior research, we predicted that increasing perceptual task difficulty should lead to more categorical coding of stimulus information, and that exemplar-level stimulus coding would be restricted to posterior, sensory brain regions. Counter to our expectations, however, we found frontoparietal regions encoded exemplar-level stimulus information. Interestingly, the anterior intraparietal sulcus (aIPS) encoded stimuli equally well regardless of perceptual difficulty, and these representations were directly related to choice behavior (proportion of guessing). Overall, these findings reveal unexpected exemplar-level stimulus coding in frontoparietal cortex, and highlight the role of aIPS in supporting adaptive behavior.
Quantification of vascular networks in photoacoustic mesoscopy
Authors: Brown Emma L. , Lefebvre Thierry L. , Sweeney Paul W. , Stolz Bernadette J. , Gröhl Janek , Hacker Lina , Huang Ziqiang , Couturier Dominique-Laurent , Harrington Heather A. , Byrne Helen M. , Bohndiek Sarah E. 
Published: November 2021

ABSTRACTMesoscopic photoacoustic imaging (PAI) enables non-invasive visualisation of tumour vasculature and has the potential to assess prognosis and therapeutic response. Currently, evaluating vasculature using mesoscopic PAI involves visual or semi-quantitative 2D measurements, which fail to capture 3D vessel network complexity, and lack robust ground truths for assessment of segmentation accuracy. Here, we developed anin silico, phantom,in vivo, andex vivo-validated end-to-end framework to quantify 3D vascular networks captured using mesoscopic PAI. We applied our framework to evaluate the capacity of rule-based and machine learning-based segmentation methods, with or without vesselness image filtering, to preserve blood volume and network structure by employing topological data analysis. We first assessed segmentation performance against ground truth data ofin silicosynthetic vasculatures and a photoacoustic string phantom. Our results indicate that learning-based segmentation best preserves vessel diameter and blood volume at depth, while rule-based segmentation with vesselness image filtering accurately preserved network structure in superficial vessels. Next, we applied our framework to breast cancer patient-derived xenografts (PDXs), with correspondingex vivoimmunohistochemistry. We demonstrated that the above segmentation methods can reliably delineate the vasculature of 2 breast PDX models from mesoscopic PA images. Our results underscore the importance of evaluating the choice of segmentation method when applying mesoscopic PAI as a tool to evaluate vascular networksin vivo.
Influenza A virus hemagglutinin prevents extensive membrane damage upon dehydration
Authors: Iriarte-Alonso Maiara A. , Bittner Alexander M. , Chiantia Salvatore 
Published: November 2021

AbstractWhile the molecular mechanisms of virus infectivity are rather well known, the detailed consequences of environmental factors on virus biophysical properties are poorly understood. Seasonal influenza outbreaks are usually connected to the low winter temperature, but also to the low relative air humidity. Indeed, transmission rates increase in cold regions during winter. While low temperature must slow degradation processes, the role of low humidity is not clear. We studied the effect of relative humidity on a model of influenza A H1N1 virus envelope, a supported lipid bilayer containing the surface glycoprotein hemagglutinin (HA), which is present in the viral envelope in very high density. For complete cycles of hydration, dehydration and rehydration, we evaluate the membrane properties in terms of structure and dynamics, which we assess by combining confocal fluorescence microscopy, raster image correlation spectroscopy, line-scan fluorescence correlation spectroscopy and atomic force microscopy. Our findings indicate that the presence of HA prevents macroscopic membrane damage after dehydration. Without HA, fast membrane disruption is followed by irreversible loss of lipid and protein mobility. Although our model is principally limited by the membrane composition, the macroscopic effects of HA under dehydration stress reveal new insights on the stability of the virus at low relative humidity.
Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences
Authors: Gerardos Andonis , Dietler Nicola , Bitbol Anne-Florence 
Published: November 2021

AbstractInferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families. Does successful inference mainly rely on correlations from structural contacts or from phylogeny, or both? Do these two types of signal combine constructively or hinder each other? To address these questions, we generate and analyze synthetic data produced using a minimal model that allows us to control the amounts of structural constraints and phylogeny. We show that correlations from these two sources combine constructively to increase the performance of partner inference by DCA or MI. Furthermore, signal from phylogeny can rescue partner inference when signal from contacts becomes less informative, including in the realistic case where inter-protein contacts are restricted to a small subset of sites. We also demonstrate that DCA-inferred couplings between non-contact pairs of sites improve partner inference in the presence of strong phylogeny, while deteriorating it otherwise. Moreover, restricting to non-contact pairs of sites preserves inference performance in the presence of strong phylogeny. In a natural data set, as well as in realistic synthetic data based on it, we find that non-contact pairs of sites contribute positively to partner inference performance, and that restricting to them preserves performance, evidencing an important role of phylogeny.Author summaryIn protein sequence data, the amino acid usages at different sites of a protein or of two interacting proteins can be correlated because of functional constraints. For instance, the need to maintain physicochemical complementarity among two sites that are in contact in the three-dimensional structure of a protein complex causes such correlations. However, correlations can also arise due to shared evolutionary history, even in the absence of any functional constraint. While these phylogenetic correlations are known to obscure the inference of structural contacts, we show, using controlled synthetic data, that correlations from structure and phylogeny combine constructively to allow the inference of protein partners among paralogs using just sequences. We also show that pairs of amino acids that are not in contact in the structure have a major impact on partner inference in a natural data set and in realistic synthetic ones. These findings explain the success of methods based on pairwise maximum-entropy models or on information theory at predicting protein partners from sequences among paralogs.
Local adaptation mediated niche expansion in correlation with genetic richness
Authors: Kurokawa Masaomi , Nishimura Issei , Ying Bei-Wen 
Published: November 2021

AbstractAs a central issue in evolution and ecology, the quantitative relationship among the genome, adaptation and the niche was investigated. Local adaptation of five Escherichia coli strains carrying either the wild-type genome or reduced genomes was achieved by experimental evolution. A high-throughput fitness assay of the ancestor and evolved populations across an environmental gradient of eight niches resulted in a total of 80 fitness curves generated from 2,220 growth curves. Further analyses showed that the increases in both local adaptiveness and niche broadness were negatively correlated with genetic richness. Local adaptation caused common niche expansion, whereas niche expansion for generality or speciality was decided by genetic richness. The order of the mutations accumulated stepwise was correlated with the magnitude of the fitness increase attributed to mutation accumulation. Pre-adaptation probably participated in coordination among genetic richness, local adaptation and niche expansion.
IReNA: integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles
Authors: Jiang Junyao , Lyu Pin , Li Jinlian , Huang Sunan , Blackshaw Seth , Qian Jiang , Wang Jie 
Published: November 2021

AbstractAlthough single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) have been widely used, few methods can reliably integrate these data to perform regulatory network analysis. Here, we developed IReNA (Integrated Regulatory Network Analysis) for network inference through integrated analysis of scRNA-seq and scATAC-seq data, network modularization, transcription factor enrichment, and construction of simplified intermodular regulatory networks. Using public datasets, we showed that integrated network analysis of scRNA-seq and scATAC-seq data using IReNA outperformed currently available methods in identifying known regulators. IReNA facilitates the systems-level understanding of biological regulatory mechanisms, and is available at https://github.com/jiang-junyao/IReNA.
Genome-wide mapping of histone modification H3K4me3 in bovine oocytes and early embryos
Authors: Dang Yanna , Luo Lei , Shi Yan , Li Shuang , Wang Shaohua , Zhang Kun 
Published: November 2021

AbstractReprogramming of histone modifications is critical to safeguard correct gene expression profile during preimplantation development. Of interest, trimethylation of lysine 4 on histone 3 (H3K4me3) exhibits a unique and dynamic landscape with a potential species-specific feature. Here, we address how it is reprogrammed and its functional significance during oocyte maturation and early embryonic development in cows. Notably, the overall signal of H3K4me3 decreased sharply during embryonic genome activation (EGA). By using low input ChIP-seq technology, we find widespread broad H3K4me3 domains in oocytes and early cleaved embryos. The broad domains are gradually removed after fertilization, which is obviously seen during EGA. Meanwhile, H3K4me3 become enriched at promoter regions. Interestingly, the gene expression level displays a positive correlation with the relative H3K4me3 signal of their promoters when embryos reach 16-cell stage. Importantly, disruption of H3K4me3 demethylases KDM5A-5C increases H3K4me3 level, decreases the embryonic developmental rate and results in dysregulation of over a thousand genes. Meanwhile, KDM5 deficiency causes a re-destribution of H3K4me3 across genome. In particular, the positive correlation between promoter H3K4me3 enrichment and gene expression level disappear. Overall, we describe the genomic reprogramming of H3K4me3 in a greater resolution during bovine preimplantation development and propose that KDM5-mediated re-distribution of H3K4me3 plays an important role in modulating oocyte-to-embryonic transition.