bluuebunny/crossref_metadata_2025_split huggingface dataset:
A causal approach to understanding management factors, reproductive underperformance and reproductive infections in dairy cattle
Authors: Softic Adis , Asmare Kassahun , Granquist Erik Georg , Godfroid Jacques , Fejzic Nihad , Skjerve Eystein 
Published: March 2019

AbstractThe objective of this study was to investigate causal associations between cattle farms’ management practices and reproductive disorders (abortion, stillbirth, retention of placenta, metritis). Besides, direct causal associations between farms’ management and reproductive infections (Chlamydia abortus, Coxiella burnetii, and Neospora caninum), reproductive disorders and infections were also investigated in this study. As a secondary objective, constraints that affect the production in cattle farms were examined. The study was carried out in the north-western (Una-Sana), western (Canton 10) and central part (Central Bosnia Canton) of Bosnia and Herzegovina. A total of 201 farms were selected for participation. A semi-structured questionnaire-based interview was conducted among farmers/managers from January 1st to August 31st, 2015. The 40 questions were divided into three groups: socio-demographic, management, and information on reproductive performances in cattle. Supplementary questions were asked about the perceived primary constraints of the production.A multivariable mixed-effects logistic regression was used to screen management factors for potential statistical influence. All investigated outcomes were associated with farms’ management. The final multivariable models were merged into a Structural Equation Model (SEM). The causal model was then specified graphically. The SEM model showed that herds that experienced abortions (OR=4.3) and stillbirth (OR=6.7) were associated with N. caninum seropositivity. Also, herds that experienced retention of placenta were strongly associated with the occurrence of metritis (OR=10.1). C. abortus and C. burnetii herd seropositivities were mainly associated with environmental factors and contact with potential intermediate hosts.Our study demonstrated that management practices on dairy farms in Bosnia and Herzegovina contributed to the occurrence of severe reproductive outcomes and reproductive infections. N. caninum seems to be an infectious agent that substantially contributed to the reproductive underperformance. Further we demonstrate the need for using causal models in understanding complex relationships.
Approach for Semi-Automated Measurement of Fiber Diameter in Murine and Canine Skeletal Muscle
Authors: Stevens Courtney R. , Sledziona Michael , Moore Timothy P. , Dong Lynn , Cheetham Jonathan 
Published: March 2019

AbstractCurrently available software tools for automated segmentation and analysis of muscle cross-section images often perform poorly in cases of weak or non-uniform staining conditions. To address these issues, our group has developed the MyoSAT (Myofiber Segmentation and Analysis Tool) image-processing pipeline.MyoSAT combines several unconventional approaches including advanced background leveling, Perona-Malik anisotropic diffusion filtering, and Steger’s line detection algorithm to aid in pre-processing and enhancement of the muscle image. Final segmentation is based upon marker-based watershed segmentation.Validation tests using collagen V labeled murine and canine muscle tissue demonstrate that MyoSAT can determine mean muscle fiber diameter with an average accuracy of ~97%. The software has been tested to work on full muscle cross-sections and works well even under non-optimal staining conditions.The MyoSAT software tool has been implemented as a macro for the freely available ImageJ software platform. This new segmentation tool allows scientists to efficiently analyze large muscle cross-sections for use in research studies and diagnostics.
Sterol-O acyltransferase 1 is inhibited by gga-miR-181a-5p and gga-miR-429-3p through the TGFβ pathway in endodermal epithelial cells of Japanese quail
Authors: Lin Han-Jen , Lin Chiao-Wei , Mersmann Harry J. , Ding Shih-Torng 
Published: March 2019

AbstractNutrients are utilized and re-constructed by endodermal epithelial cells (EECs) in yolk sac membranes in avian species. Sterol-O acyltransferase 1 (SOAT1) is the key enzyme to convert cholesterol to cholesteryl ester for delivery to growing embryos. During development, absorption of yolk is matched with significant changes of SOAT1 mRNA and enzyme activity. miRNAs regulate angiogenesis and metabolism during mammalian development. However, the involvement of miRNAs in lipid utilization during avian embryogenesis remains ambiguous.Using a miRNA sequencing technique, we found several candidate miRNAs and confirmed expression patterns with real time PCR. They were selected for as candidates targeting the receptor (TGFβ receptor type 1, TGFBR1) that may regulate SOAT1. Similar to SOAT1 mRNA accumulation, the gga-miR-181a-5p expression was gradually elevated during development, but the concentration of gga-miR-429-3p was in the opposite direction. Transfection with gga-miR-181a-5p or gga-miR-429-3p inhibited TGFBR1 and SOAT1 in EECs. The 3’ untranslated region (3’UTR) of TGFBR1 was then confirmed to be one of the targets of gga-miR-181a-5p and gga-miR-429-3p. Taken together, expression of miRNAs during embryonic development regulates SOAT1 expression by inhibiting the 3’UTR of TGFBR1. This is indicative of possible regulation of avian yolk lipid utilization and modification of hatchability by changing miRNA expressions.
An abscisic acid (ABA) homeostasis regulated by its production, catabolism and transport in peanut leaves in response to drought stress
Authors: Long Haitao , Zheng Zhao , Zhang Yajun , Xing Pengzhan , Wan Xiaorong , Zheng Yixiong , Li Ling 
Published: March 2019

AbstractABA is an important messenger that acts as the signaling mediator for regulating the adaptive response of plants to drought stress. Two production pathways,de novobiosynthesis and hydrolysis of glucose-conjugated ABA by β-glucosidase (BG), increase cellular ABA levels in plants. ABA catabolism via hydroxylation by 8’-hydroxylase (CYP707A), or conjugation by uridine diphosphate glucosyltransferase (UGT), decreases cellular ABA levels. The transport of ABA through ATP-binding cassette (ABC)-containing transporter proteins, members of ABC transporter G family (ABCG), across plasma membrane (PM) is another important pathway to regulate cellular ABA levels. In this study, based on our previously constructed transcriptome of peanut leaves in response to drought stress, fourteen candidate genes involved in ABA production (includingAhZEP,AhNCED1andAhNCED3,AhABA2,AhAAO1andAhAAO2,AhABA3,AhBG11andAhBG24), catabolism (includingAhCYP707A3,AhUGT71K1andAhUGT73B4) and transport (includingAhABCG22-1andAhABCG22-2), were identified homologously and phylogenetically, and further analyzed at the transcriptional level by real-time RT-PCR, simultaneously determining ABA levels in peanut leaves in response to drought. The high sequence identity and very similar subcellular localization of the proteins deduced from 14 identified genes involved in ABA production, catabolism and transport with the reported corresponding enzymes in databases suggest their similar roles in regulating cellular ABA levels. In response to drought stress, ABA accumulation levels in peanut leaves agree very well with the up-regulated expressions of ABA-producing genes (AhZEP,AhNCED1,AhAAO2,AhABA3,AhBG11andAhBG24) and PM-localized ABA importer genes (AhABCG22-1andAhABCG22-2), although the expression of ABA catabolic genes (AhCYP707A3andAhUGT71K1) was also up-regulated. It is likely that drought-responsive induction of catabolic genes helps not only to maintain ABA levels within a permissible range, but also to prepare the plant for degradation of ABA after removal of the stress. These results suggest that ABA homeostasis in peanut leaves in response to drought may be coordinated by a master regulatory circuit that involves production, catabolism, and as well as transport.
Revised subunit order of mammalian septin complexes explains their in vitro polymerization properties
Authors: Soroor Forooz , Kim Moshe S. , Palander Oliva , Balachandran Yadu , Collins Richard , Benlekbir Samir , Rubinstein John , Trimble William S. 
Published: March 2019

ABSTRACTSeptins are conserved GTP-binding cytoskeletal proteins that polymerize into filaments by end-to-end joining of heterooligomeric complexes. In human cells, both hexamers and octamers exist, and crystallography studies predicted the order of the hexamers to be SEPT7-SEPT6-SEPT2-SEPT2-SEPT6-SEPT7, while octamers are thought to have the same core, but with SEPT9 at the ends. However, based on this septin organization, octamers and hexamers would not be expected to co-polymerize due to incompatible ends. Here we isolated hexamers and octamers of specific composition from human cells and show that hexamers and octamers polymerize individually and, surprisingly, with each other. Binding of Borg3 results in distinctive clustering of each filament type. Moreover, we show that the organization of hexameric and octameric complexes is inverted compared to its original prediction. This revised septin organization is congruent with the organization and behavior of yeast septins suggesting that their properties are more conserved than was previously thought.
Distinct matrix composition and mechanics in aged and estrogen-deficient mouse skin
Authors: Saville Charis R , Mallikarjun Venkatesh , Holmes David F , Emmerson Elaine , Derby Brian , Swift Joe , Sherratt Michael J , Hardman Matthew J 
Published: March 2019

ABSTRACTHormone deficiency has been widely linked to accelerated tissue ageing, and increased incidence of chronic degenerative disease. Furthermore, age-associated hormonal dysregulation is thought to be a major contributing factor to the increased fragility of aged skin. The ageing process is driven by an aggregation of damage to cells and extracellular matrix, which can directly influence the mechanical properties of the tissue. Here we report on the correlation between mechanical properties and composition of skin from ovariectomised and aged mice, to assess the extent to which estrogen deprivation drives dermal ageing. We found that age and estrogen abrogation affected skin mechanical properties in contrasting ways: ageing led to increased tensile strength and stiffness while estrogen deprivation had the opposite effect. Mass spectrometry proteomics showed that the quantity of extractable fibrillar collagen-I decreased with ageing, but no change was observed in ovariectomised mice. This observation, in combination with measurements of tensile strength, was interpreted to reflect changes to the extent of extracellular matrix crosslinking, supported by a significant increase in the staining of advanced glycation endpoints in aged skin. Loss of mechanical strength in the skin following ovariectomy was consistent with a loss of elastic fibres. Other changes in extracellular matrix composition broadly correlated between aged and ovariectomised mice, confirming the important role of estrogen-related pathways in ageing. This study offers new insight into the relationship between tissue composition and mechanics, and suggests that the deleterious effects of intrinsic skin ageing are compounded by factors beyond hormonal dysregulation.
The Rab32/BLOC-3 dependent pathway mediates host- defence against different pathogens in human macrophages
Authors: Baldassarre Massimiliano , Solano-Collado Virtu , Balci Arda , Colamarino Rosa A. , Dambuza Ivy M , Reid Delyth M. , Wilson Heather M , Brown Gordon D , Mukhopadhyay Subhankar , Dougan Gordon , Spanò Stefania 
Published: March 2019

ABSTRACTMacrophages provide a first line of defence against microorganisms, and while some mechanisms to kill pathogens such as the oxidative burst are well described, others are still undefined or unknown. Here we report that the Rab32 GTPase and its guanine nucleotide exchange factor BLOC-3 are central components of a trafficking pathway that controls both bacterial and fungal intracellular pathogens. This broad host-defence mechanism is active in both human and murine macrophages and is independent of well known antimicrobial mechanisms such as the NADPH-dependent oxidative burst, production of nitric oxide and antimicrobial peptides. To survive in human macrophages, Salmonella Typhi actively counteracts the Rab32/BLOC-3 pathway through its Salmonella pathogenicity island-1-encoded type III secretion system. These findings demonstrate that the Rab32/BLOC-3 pathway is a novel and universal host-defence pathway and protects mammalian species from a wide range of intracellular pathogens.
NOD2 and TLR2 Signal via TBK1 and PI31 to Direct Cross-presentation and CD8 T Cell Responses
Authors: Corridoni Daniele , Shiraishi Seiji , Chapman Thomas , Steevels Tessa , Muraro Daniele , Thézénas Marie-Laëtitia , Prota Gennaro , Chen Ji-Li , Gileadi Uzi , Ternette Nicola , Cerundolo Vincenzo , Simmons Alison 
Published: March 2019

AbstractNOD2 and TLR2 recognize components of bacterial cell wall peptidoglycan and direct defense against enteric pathogens. CD8+ T cells are important for immunity to such pathogens but how NOD2 and TLR2 induce antigen specific CD8+ T cell responses is unknown. Here, we define how these pattern recognition receptors (PRRs) signal in primary dendritic cells (DCs) to influence MHC class I antigen presentation. We show NOD2 and TLR2 phosphorylate PI31 via TBK1 following activation in DCs. PI31 interacts with TBK1 and Sec16A at endoplasmic reticulum exit sites (ERES), which positively regulates MHC class I peptide loading and immunoproteasome stability. Following NOD2 and TLR2 stimulation, depletion of PI31 or inhibition of TBK1 activity in vivo impairs DC cross-presentation and CD8+ T cell activation. DCs from Crohn’s patients expressing NOD2 polymorphisms show dysregulated cross-presentation and CD8+ T cell responses. Our findings reveal unidentified mechanisms that underlie CD8+ T cell responses to bacteria in health and in Crohn’s.
GCNA preserves genome integrity and fertility across species
Authors: Bhargava Varsha , Goldstein Courtney D. , Russell Logan , Xu Lin , Ahmed Murtaza , Li Wei , Casey Amanda , Servage Kelly , Kollipara Rahul , Picciarelli Zachary , Kittler Ralf , Yatsenko Alexander , Carmell Michelle , Orth Kim , Amatruda James F. , Yanowitz Judith L. , Buszczak Michael 
Published: March 2019

SUMMARYThe propagation of species depends on the ability of germ cells to protect their genome in the face of numerous exogenous and endogenous threats. While these cells employ a number of known repair pathways, specialized mechanisms that ensure high-fidelity replication, chromosome segregation, and repair of germ cell genomes remain incompletely understood. Here, we identify Germ Cell Nuclear Acidic Peptidase (GCNA) as a highly conserved regulator of genome stability in flies, worms, zebrafish, and humans. GCNA contains a long acidic intrinsically disordered region (IDR) and a protease-like SprT domain. In addition to chromosomal instability and replication stress, GCNA mutants accumulate DNA-protein crosslinks (DPCs). GCNA acts in parallel with a second SprT domain protein Spartan. Structural analysis reveals that while the SprT domain is needed to limit meiotic and replicative damage, most of GCNA’s function maps to its IDR. This work shows GCNA protects germ cells from various sources of damage, providing novel insights into conserved mechanisms that promote genome integrity across generations.HighlightsGCNA ensures genomic stability in germ cells and early embryos across speciesGCNA limits replication stress and DNA double stranded breaksGCNA restricts DNA-Protein Crosslinks within germ cells and early embryosThe IDR and SprT domains of GCNA govern distinct aspects of genome integrityGraphic Abstract
Reorientation and propulsion in fast-starting zebrafish larvae: an inverse dynamics analysis
Authors: Voesenek Cees J. , Pieters Remco P. M. , Muijres Florian T. , van Leeuwen Johan L. 
Published: March 2019

AbstractMost fish species use fast starts to escape from predators. Zebrafish larvae perform effective fast starts immediately after hatching. They use a C-start, where the body curls into a C-shape, and then unfolds to accelerate. These escape responses need to fulfil a number of functional demands, under the constraints of the fluid environment and the larva’s body shape. Primarily, the larvae need to generate sufficient escape speed in a wide range of possible directions, in a short-enough time. In this study, we examined how the larvae meet these demands. We filmed fast starts of zebrafish larvae with a unique five-camera setup with high spatiotemporal resolution. From these videos, we reconstructed the three-dimensional swimming motion with an automated method and from these data calculated resultant hydrodynamic forces and, for the first time, 3D torques. We show that zebrafish larvae reorient mostly in the first stage of the start by producing a strong yaw torque, often without using the pectoral fins. This reorientation is expressed as the body angle, a measure that represents the rotation of the complete body, rather than the commonly used head angle. The fish accelerates its centre of mass mostly in stage 2 by generating a considerable force peak while the fish “unfolds”. The escape direction of the fish correlates strongly with the amount of body curvature in stage 1, while the escape speed correlates strongly with the duration of the start. This may allow the fish to independently control the direction and speed of the escape.Summary statementFish larvae can independently adjust the direction and speed of their fast start escape response, a manoeuvre crucial for survival.
Manure substitution of chemical fertilizer affect soil microbial community diversity, structure and function in greenhouse vegetable production systems
Authors: Luan Haoan , Gao Wei , Huang Shaowen , Tang Jiwei , Li Mingyue , Zhang Huaizhi , Chen Xinping 
Published: March 2019

ABSTRACTSoil microbial community and enzyme activities together affect various ecosystem functions of soils. Fertilization, as important agricultural management practices, are known to modify soil microbial characteristics; however, inconsistent results have been reported. The aim of this research therefore was to make a comparative study of the effects of different fertilization patterns (No N inputs (No N), 100% chemical fertilizer-N (CN) inputs (4/4CN) and different substitution rates of CN by organic manure-N (MN) (3/4CN+1/4MN, 2/4CN+2/4MN and 1/4CN+3/4MN)) on soil physicochemical properties, enzyme activities and microbial attributes in a GVP of Tianjin, China. Manure substitution of chemical fertilizer, especially at higher substitution rate (2/4CN+2/4MN and 1/4CN+3/4MN), improved soil physicochemical properties (higher soil organic C (SOC) and nutrient contents; lower bulk densities), promoted microbial growth (higher total phospholipid fatty acids and microbial biomass C contents) and activity (higher soil hydrolase activities). Manure addition caused a remarkable increase of the fungi/bacteria ratio and a distinct shift in the fungal (bacterial) community to greater abundance of arbuscular mycorrhizal fungi (G+ bacteria) compared with saprotrophic fungi (G− bacteria). These changes drove shifts toward fungal-dominated soil microbial communities and then optimized microbial community structure. Also, manure application increased soil biodiversity (microbial community and enzyme function), indicated by increased Shannon–Wiener diversity. Redundancy analysis indicated that the most possible mechanism of the impacts of different fertilization patterns on soil microbial characteristics may be the mediation of SOC and nutrient (N) availability (especially SOC) in this GVP of China. In conclusion, manure substitution of chemical fertilizer, especially at higher substitution rate, was more efficient for improving soil quality and biological functions.
Genetic determinants of gut microbiota composition and bile acid profiles in mice
Authors: Kemis Julia H. , Linke Vanessa , Barrett Kelsey L. , Boehm Frederick J. , Traeger Lindsay L. , Keller Mark P. , Rabaglia Mary E. , Schueler Kathryn L. , Stapleton Donald S. , Gatti Daniel M. , Churchill Gary A. , Amador-Noguez Daniel , Russell Jason D. , Yandell Brian S. , Broman Karl W. , Coon Joshua J. , Attie Alan D. , Rey Federico E. 
Published: March 2019

AbstractThe microbial communities that inhabit the distal gut of humans and other mammals exhibit large inter-individual variation. While host genetics is a known factor that influences gut microbiota composition, the mechanisms underlying this variation remain largely unknown. Bile acids (BAs) are hormones that are produced by the host and chemically modified by gut bacteria. BAs serve as environmental cues and nutrients to microbes, but they can also have antibacterial effects. We hypothesized that host genetic variation in BA metabolism and homeostasis influence gut microbiota composition. To address this, we used the Diversity Outbred (DO) stock, a population of genetically distinct mice derived from eight founder strains. We characterized the fecal microbiota composition and plasma and cecal BA profiles from 400 DO mice maintained on a high-fat high-sucrose diet for ∼22 weeks. Using quantitative trait locus (QTL) analysis, we identified several genomic regions associated with variations in both bacterial and BA profiles. Notably, we found overlapping QTL forTuricibacter sp.and plasma cholic acid, which mapped to a locus containing the gene for the ileal bile acid transporter,Slc10a2. Mediation analysis and subsequent follow-up validation experiments suggest that differences inSlc10a2gene expression associated with the different strains influences levels of both traits and revealed novel interactions betweenTuricibacterand BAs. This work illustrates how systems genetics can be utilized to generate testable hypotheses and provide insight into host-microbe interactions.Author summaryInter-individual variation in the composition of the intestinal microbiota can in part be attributed to host genetics. However, the specific genes and genetic variants underlying differences in the microbiota remain largely unknown. To address this, we profiled the fecal microbiota composition of 400 genetically distinct mice, for which genotypic data is available. We identified many loci of the mouse genome associated with changes in abundance of bacterial taxa. One of these loci is also associated with changes in the abundance of plasma bile acids—metabolites generated by the host that influence both microbiota composition and host physiology. Follow up validation experiments provide mechanistic insights linking host genetic differences, with changes in ileum gene expression, bile acid-bacteria interactions and bile acid homeostasis. Together, this work demonstrates how genetic approaches can be used to generate testable hypothesis to yield novel insight into how host genetics shape gut microbiota composition.