bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-environmental population phenotyping suggests the higher risk of wheatRht-B1bandRht-D1bcultivars in global warming scenarios
Authors: Liu Zihui , Hu Zunkai , Zhu Zhiwei , Cao Junmei , Zhang Jialiang , Ma Xiangyu , Zhang Xinzhong , Wang Xiaoming , Ji Wanquan , Xu Shengbao 
Published: July 2022

ABSTRACTAfter six decades practice, the semi-dwarf allelesRht-B1bandRht-D1b(also calledRht-1andRht-2) had been applied into around 70% current wheat cultivars, laid the foundation for the worldwide wheat production supply, then the agronomic traits controlled by the two alleles still keep unclear except dwarfing wheat. Here 13 agronomic traits were investigated in 400 wheat accessions with seven environments, uncovered the genetic effects ofRht-B1bandRht-D1bon wheat structure and yield traits in different genetic backgrounds and environments, and the distinct genetic effects betweenRht-B1bandRht-D1b, suggesting that the introduction of green revolution alleles profoundly shaped the agronomy traits of modern wheat cultivars. The late-sowing assays and regression analysis based on the phenotypic and their meteorological data showed the accessions containingRht-B1bandRht-D1bare more sensitive to the temperature increase, and theRht-D1bmay lost additional 8% yield compared the cultivars without the green revolution alleles if the average temperature increases 1 °C. These results suggest the application of green revolution are facing more challenges to maintain the futural wheat production supply in global warming scenarios.
ATF5 is a regulator of exercise-induced mitochondrial quality control in skeletal muscle
Authors: Slavin Mikhaela B. , Kumari Rita , Hood David A. 
Published: July 2022

AbstractObjectivesThe Mitochondrial Unfolded Protein Response (UPRmt) is a compartment-specific mitochondrial quality control (MQC) mechanism that uses the transcription factor ATF5 to induce the expression of protective enzymes to restore mitochondrial function. Acute exercise is a stressor that has the potential to temporarily disrupt organellar protein homeostasis, however, the roles of ATF5 and the UPRmt in maintaining basal mitochondrial content, function and exercise-induced MQC mechanisms in skeletal muscle are not known.MethodsATF5 KO and WT mice were examined at rest or after a bout of acute endurance exercise. We measured protein content in whole muscle, nuclear, cytosolic and mitochondrial fractions, in addition to mRNA transcript levels in whole muscle. Using isolated mitochondria, we quantified rates of oxygen consumption and ROS emission to observe the effects of the absence of ATF5 on organelle function.ResultsATF5 KO mice exhibited a larger and less functional muscle mitochondrial pool, most likely a culmination of enhanced biogenesis via increased PGC-1α expression, and attenuated mitophagy. The absence of ATF5 resulted in a reduction in antioxidant proteins and increases in mitochondrial ROS emission, cytosolic cytochrome c, and the expression of mitochondrial chaperones. KO muscle also displayed enhanced exercise-induced stress kinase signaling, but a blunted mitophagic and UPRmt gene expression response, complemented by significant increases in the basal mRNA abundance and nuclear localization of ATF4. Instead of promoting its nuclear translocation, acute exercise caused the enrichment of ATF5 in mitochondrial fractions. We also identified PGC-1α as an additional regulator of the basal expression of UPRmt genes.ConclusionThe transcription factor ATF5 retains a critical role in the maintenance of mitochondrial homeostasis and the appropriate response of muscle to acute exercise for the optimization of mitochondrial quality control.Graphical abstractA modified version of the schematic shown in Fig. 8 will be supplied at a later time.
Engineered Adhesion Molecules Drive Synapse Organization
Authors: Hale W. Dylan , Südhof T. C. , Huganir R. L. 
Published: July 2022

AbstractIn multicellular organisms, cell-adhesion molecules connect cells into tissues and mediate intercellular signaling between these cells. In vertebrate brains, synaptic cell-adhesion molecules (SAMs) guide the formation, specification, and plasticity of synapses. Some SAMs, when overexpressed in cultured neurons or in heterologous cells co-cultured with neurons, drive formation of synaptic specializations onto the overexpressing cells. However, genetic deletion of the same SAMs from neurons often has no effect on synapse numbers, but frequently severely impairs synaptic transmission, suggesting that most SAMs control the function and plasticity of synapses (i.e., organize synapses) instead of driving their initial establishment (i.e., make synapses). Since few SAMs were identified that mediate initial synapse formation, it is difficult to develop methods that enable experimental control of synaptic connections by targeted expression of these SAMs. To overcome this difficulty, we engineered novel SAMs from bacterial proteins with no eukaryotic homologues that drive synapse formation. We named these engineered adhesion proteins ‘Barnoligin’ and ‘Starexin’ because they were assembled from parts of Barnase and Neuroligin-1 or of Barstar and Neurexins, respectively. Barnoligin and Starexin robustly induce the formation of synaptic specializations in a specific and directional manner in cultured neurons. Synapse formation by Barnoligin and Starexin requires both their extracellular Barnase- and Bastar-derived interaction domains and their Neuroligin- and Neurexin-derived intracellular signaling domains. Our findings support a model of synapse formation whereby trans-synaptic interactions by SAMs drive synapse organization via adhesive interactions that activate signaling cascades.
Spatial host-microbiome sequencing
Authors: Lötstedt Britta , Stražar Martin , Xavier Ramnik , Regev Aviv , Vickovic Sanja 
Published: July 2022

ABSTRACTMucosal and barrier tissues such as the gut, lung or skin, are composed of a complex network of cells and microbes forming a tight niche that prevents pathogen colonization and supports host-microbiome symbiosis. Characterizing these networks at high molecular and cellular resolution is crucial for our understanding of homeostasis and disease. Spatial transcriptomics has emerged as a key technology to positionally profile RNAs at high resolution in tissues. Here, we present spatial host-microbiome sequencing, an all-sequencing based approach that captures tissue histology, polyadenylated RNAs and bacterial 16S sequences directly from tissues on spatially barcoded glass surfaces. We apply our approach to the mouse gut as a model system, use a novel deep learning approach for data mapping and detect spatial niches impacted by microbial biogeography. Spatial host-microbiome sequencing should enhance study of native host-microbe interactions in health and disease.
Varidnaviruses in the human gut: a major expansion of the order Vinavirales
Authors: Yutin Natalya , Rayko Mike , Antipov Dmitry , Mutz Pascal , Wolf Yuri I , Krupovic Mart , Koonin Eugene V 
Published: July 2022

AbstractBackgroundBacteriophages play key roles in the dynamics of the human microbiome. By far the most abundant components of the human gut virome are tailed bacteriophages of the realm Duplodnaviria, in particular, crAss-like phages. However, apart from duplodnaviruses, the gut virome has not been dissected in detail.ResultsHere we report a comprehensive census of a minor component of the gut virome, the tailless bacteriophages of the realm Varidnaviria. Tailless phages are primarily represented in the gut by prophages of the families Corticoviridae and Autolykiviridae that jointly comprise the order Vinavirales and are mostly integrated as prophages in genomes of Alphaproteobacteria and Verrucomicrobia. Phylogenetic analysis of the major capsid proteins (MCP) and packaging ATPases suggests that at least three new families within Vinavirales should be established to accommodate the diversity of prophages from the human gut virome. Previously, only the MCP and ATPase genes were reported to be conserved in all members of Vinavirales. Here we identify a core set of 12 proteins that are shared by most of these viruses including previously undetected lysis enzymes. We further demonstrate that replication system components are frequently replaced in the genomes of Vinavirales, suggestive of selective pressure for escape from yet unknown host defenses or avoidance of incompatibility with coinfecting related viruses.ConclusionsThe results of this analysis show that, in a sharp contrast to marine viromes, varidnaviruses are a minor component of the human gut virome. Moreover, they are primarily represented by proviruses, suggesting that there are few if any active varidnavirus infections in the gut at any given time. These findings complement the existing knowledge of the human gut virome by exploring a group of viruses that was virtually overlooked in previous work.
Impaired Function in Diabetic Patient iPSCs-derived Blood Vessel Organoids Stem from a Subpopulation of Vascular Cells
Authors: Naderi-Meshkin Hojjat , Eleftheriadou Magdalini , Carney Garrett , Cornelius Victoria A , Nelson Clare-Ann , Kelaini Sophia , Yacoub Andrew , Donaghy Clare , Dunne Philip D , Amirkhah Raheleh , Zampetaki Anna , Zeng Lingfang , Stitt Alan W , Grieve David J , Margariti Andriana 
Published: July 2022

AbstractThe presence of both endothelial cells (ECs) and mural cells are central to the proper function of blood vessels in health and pathological changes in diseases including diabetes. Although iPSCs-derived vascular organoids (VOs) provide an appealing in vitro disease model and platform for drug screening, whether these organoids recapitulate human disease remains debatable. Here, we show human diabetic (DB)-VOs represent impaired vascular function including enhanced ROS activity, with higher mitochondrial content and activity, increased pro-inflammatory cytokines, and less regenerative potential in vivo. Using single-cell RNA sequencing, we identify all specialized types of vascular cells (artery, capillary, vein, lymphatic and tip cells, as well as pericytes and vSMCs) within vascular organoids, while demonstrating the dichotomy landscape of ECs and mural cells. Furthermore, we reveal basal heterogeneity within vascular organoids and demonstrate differences between diabetic and non-diabetic VOs. Of note, a subpopulation of ECs significantly enrich for ROS and oxidative phosphorylation hallmarks in DB-VOs, may represent early signs of aberrant angiogenesis in diabetes. This study helps to identify key biomarkers for diabetic disease progression and find signalling molecules amenable to drug intervention.
RMeDPower for Biology: guiding design, experimental structure and analyses of repeated measures data for biological studies
Authors: Shin Min-Gyoung , Kaye Julia A. , Amirani Naufa , Lam Stephanie , Thomas Reuben , Finkbeiner Steven 
Published: July 2022

AbstractReproducibility is science has plagued efforts to understand biology at both basic and biomedical and preclinical research levels. Poor experimental design and execution can result in datasets that are improperly powered to produce rigorous and reproducible results. In order to help biologists better model their data, here we present a statistical package called RMeDPower in R, which is a complete package of statistical tools that allow a scientist to understand the effect size and variance contribution of a set of variables one has within a dataset to a given response. RMeDPower can estimate the effect size of variables within an experiment based on an initial pilot dataset. In this way, RMeDPower can inform the user how to predict the scope, dimension and size of biological data needed for a particular experimental design. RMeDPower employs a generalized linear mixed model (LMM) -based power analysis, specifically targeting cell culture-based biological experimental designs. This package simulates experiments based on user-provided experimental design related variables, such as experiments, plates, and cell lines as random effects variables. This package not only allows us to use pilot data to estimate variance components for power simulation, it also accepts a set of variance components, which is an estimation of variance of the random effects linked to experimental variables and transformed into Intra-class Correlation Coefficients (ICC), as input which is precalculated from different data sets. The latter case is suitable when pilot data has an insufficient number of replications of experimental variables to directly estimate associated variance components. RMeDPower is a powerful package that any scientist or cell biologist can use to determine if a dataset is adequately powered for each experiment and then model accordingly.
Evolution and molecular basis of a novel allosteric property of crocodilian hemoglobin
Authors: Natarajan Chandrasekhar , Signore Anthony V. , Bautista Naim M. , Hoffmann Federico G. , Tame Jeremy R. H. , Fago Angela , Storz Jay F. 
Published: July 2022

AbstractUnderstanding the evolution of novel protein functions requires data on the mechanistic effects of causative mutations and the extent of coupling between the gain of new function and loss of ancestral function. Here, we use ancestral protein resurrection and directed mutagenesis to dissect the molecular basis of a novel mode of allosteric regulation in crocodilian hemoglobin. We discovered that regulation of Hb-O2affinity via allosteric binding of bicarbonate ions (a biochemical adaptation unique to crocodilians) and the concomitant loss of allosteric regulation by ATP-binding are attributable to non-overlapping sets of substitutions. Gain of bicarbonate-sensitivity involved direct effects of few replacements at key sites in combination with indirect effects of numerous replacements at structurally disparate sites. Due to the context-dependence of causative substitutions, the unique allosteric properties of crocodilian hemoglobin cannot be easily transplanted into divergent homologs of other species.Significance StatementThe extraordinary breath-hold diving capacity of crocodilians is partly attributable to a unique mode of allosterically regulating hemoglobin-oxygenation in circulating red blood cells. We investigated the origin and mechanistic basis of this novel biochemical adaptation by performing directed mutagenesis experiments on resurrected ancestral crocodilian hemoglobins. Our results revealed that evolved changes in allosteric regulation involved the direct effect of few amino acid substitutions at key sites in combination with indirect effects of numerous other substitutions at structurally disparate sites. Such indirect interaction effects suggest that the evolution of novel protein functions may often depend on neutral mutations that produce no adaptive benefit when they first arise, but which contribute to a permissive background for subsequent function-altering mutations at other sites.
Multivariable MR can mitigate bias in two-sample MR using covariable-adjusted summary associations
Authors: Gilbody Joe , Borges Maria Carolina , Smith George Davey , Sanderson Eleanor 
Published: July 2022

AbstractGenome-Wide Association studies (GWAS) are hypothesis free studies that survey the whole genome for polymorphisms associated with a trait of interest. To increase power and to estimate the direct effects of these single nucleotide polymorphisms (SNPs) on a trait GWAS are often conditioned on a covariate (such as body mass index (BMI) or smoking status). This adjustment can introduce bias in the estimated effect of the SNP on the trait. Mendelian randomisation (MR) studies use summary statistics from GWAS estimate the causal effect of a risk factor (or exposure) on an outcome. Covariate adjustment in GWAS can bias the effect estimates obtained from MR studies using the GWAS data. Multivariable MR (MVMR) is an extension of MR that includes multiple traits as exposures. Using simulations we show that MVMR can recover unbiased estimates of the direct effect of the exposure of interest by including the covariate used to adjust the GWAS within the analysis. We show that this method provides consistent effect estimates when either the exposure or outcome of interest has been adjusted for a covariate. We apply this method to estimate the effect of systolic blood pressure (SBP) on type-2 diabetes (T2D) and waist circumference on systolic blood pressure both adjusted and unadjusted for BMI.
Perturbation of protein homeostasis brings plastids at the crossroad between repair and dismantling
Authors: Tadini Luca , Jeran Nicolaj , Domingo Guido , Zambelli Federico , Masiero Simona , Calabritto Anna , Costantini Elena , Forlani Sara , Marsoni Milena , Briani Federica , Vannini Candida , Pesaresi Paolo 
Published: July 2022

AbstractThe chloroplast proteome is a dynamic mosaic of plastid- and nuclear-encoded proteins. Plastid protein homeostasis is maintained through the balance between de novo synthesis and proteolysis. Intracellular communication pathways, including the plastid-to-nucleus signalling and the protein homeostasis machinery, made of stromal chaperones and proteases, shape chloroplast proteome based on developmental and physiological needs. However, the maintenance of fully functional chloroplasts is costly and under specific stress conditions the degradation of damaged chloroplasts is essential to the maintenance of a healthy population of photosynthesising organelles while promoting nutrient redistribution to sink tissues. In this work, we have addressed this complex regulatory chloroplast- quality-control pathway by modulating the expression of two nuclear genes encoding plastid ribosomal proteins PRPS1 and PRPL4. By transcriptomics, proteomics and transmission electron microscopy analyses, we show that the increased expression of PRPS1 gene leads to chloroplast degradation and early flowering, as an escape strategy from stress. On the contrary, the overaccumulation of PRPL4 protein is kept under control by increasing the amount of plastid chaperones and components of the unfolded protein response (cpUPR) regulatory mechanism. This study advances our understanding of molecular mechanisms underlying chloroplast retrograde communication and provides new insight into cellular responses to impaired plastid protein homeostasis.
An empirical examination of board-related and firm-specific drivers on risk disclosure by listed firms in Kenya: a mixed-methods approach
Authors: Mbithi Erastus , Moloi Tankiso , Wangombe David 
Published: July 2022

Purpose
This study aims to examine the effect of board-related and firm-specific drivers on quality of risk disclosure (RD) by listed firms in Kenya.

Design/methodology/approach
This study uses explanatory sequential mixed-method. The quantitative approach uses content analysis to measure quality of RD and panel data regression to examine the effect of board-related and firm-specific factors on quality of RD. The results of regression analysis are informed by qualitative analysis through interviews with preparers of the annual report.

Findings
The results reveal that quality of RD is low but greater in the post-regulation than in the pre-regulation period. Additionally, the results of regression and interview analysis show that board-related (board independence and board gender diversity) and firm-specific factors (firm size and leverage) positively influence the quality of RD.

Research limitations/implications
This study focused on listed non-financial firms; this may affect the generalisation of the findings among financial firms.

Practical implications
The findings highlight the effectiveness of the Companies Act in improving RD practice in Kenya. However, the low-quality RD suggests that more consideration should be taken to review the current regulations. This study also suggests that board independence, board gender diversity, leverage and firm size are attributes that require regulatory focus to enhance quality of RD.

Social implications
This study contributes to the ongoing discussions about RD to improve worldwide.

Originality/value
This paper adds to the limited studies investigating RD and drivers using mixed methods in developing countries. Specifically, this study develops a novel measure of RD and examines its drivers (board-related and firm-specific) using agency and institutional theories.
Relationship between educational mismatches and job satisfaction: evidence from Korean young employees’ lifelong learning
Authors: Park Kyung Hee , Luo Nan 
Published: July 2022

Purpose
This study aims to demonstrate whether the educational mismatch prevalent in society can be overcome by various types of lifelong learning and whether lifelong learning can contribute to job satisfaction.

Design/methodology/approach
The participants were 2,559 young Korean employees who graduated from general or specialized vocational high school. This study applied structural equation modeling to verify the mediating effects of lifelong learning on the relationship between educational mismatch and job satisfaction. In addition, this study compared whether the conceptual model results were applied to those who graduated from general school and specialized vocational school through multigroup analysis.

Findings
Regarding the horizontal mismatch, the mediating effect of lifelong learning correlated with job satisfaction was significantly measured in all multigroup models, including the conceptual model. Nevertheless, regarding the vertical mismatch, this study confirmed that informal learning influences job satisfaction differently according to the type of high school from which employees graduated. Furthermore, for those who graduated from specialized vocational school, the relationship between vertical mismatch and job satisfaction was significantly indicated. However, there was no influence of informal learning at the workplace.

Originality/value
This study empirically demonstrated the alternative value of lifelong learning in overcoming the preceding educational mismatch. Moreover, the evidence that such lifelong learning effects may vary depending on the vocational education experiences before entering the labor market is valuable.
Heat transfer enhancement compared to entropy generation by imposing magnetic field and hybrid nanoparticles in mixed convection of a Bingham plastic fluid in a ventilated enclosure
Authors: Dutta Subhasree , Bhattacharyya Somnath , Pop Ioan 
Published: July 2022

Purpose
The purpose of this study is to analyze the nonhomogeneous model on the mixed convection of Al2O3–Fe3O4 Bingham plastic hybrid nanofluid in a ventilated enclosure subject to an externally imposed uniform magnetic field. Entropy generation and the pressure drop are determined to analyze the performance of the heat transfer. The significance of Joule heating arising due to the applied magnetic field on the heat transfer of the yield stress fluid is described.

Design/methodology/approach
The ventilation in the enclosure of heated walls is created by an opening on one vertical wall through which cold fluid is injected and another opening on the opposite vertical wall through which fluid can flow out.

Findings
This study finds that the inclusion of Fe3O4 nanoparticles with the Al2O3-viscoplastic nanofluid augments the heat transfer. This rate of enhancement in heat transfer is higher than the rate by which the entropy generation is increased as well as the enhancement in the pressure drop. The yield stress has an adverse effect on the heat transfer; however, it favors thermal mixing. The magnetic field, which is acting opposite to the direction of the inlet jet, manifests heat transfer of the viscoplastic hybrid nanofluid. The horizontal jet of cold fluid produces the optimal heat transfer.

Originality/value
The objective of this study is to analyze the impact of the inclined cold jet of viscoplastic electrically conducting hybrid nanofluid on heat transfer from the enclosure in the presence of a uniform magnetic field. The combined effect of hybrid nanoparticles and a magnetic field to enhance heat transfer of a viscoplastic fluid in a ventilated enclosure has not been addressed before.