bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of genetic loci and candidate genes related to soybean flowering through genome wide association study
Authors: Li Minmin , Liu Ying , Tao Yahan , Xu Chongjing , Li Xin , Zhang Xiaoming , Han Yingpeng , Yang Xue , Sun Jingzhe , Li Wenbin , Li Dongmei , Zhao Xue , Zhao Lin 
Published: December 2019

Abstract
Background
As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. To examine the genetic architecture of soybean growth periods, we performed a genome-wide association study (GWAS) using a panel of 278 soybean accessions and 34,710 single nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) higher than 0.04 detected by the specific-locus amplified fragment sequencing (SLAF-seq) with a 6.14-fold average sequencing depth. GWAS was conducted by a compressed mixed linear model (CMLM) involving in both relative kinship and population structure.

Results
GWAS revealed that 37 significant SNP peaks associated with soybean flowering time or other growth periods related traits including full bloom, beginning pod, full pod, beginning seed, and full seed in two or more environments at -log10(P) > 3.75 or -log10(P) > 4.44 were distributed on 14 chromosomes, including chromosome 1, 2, 3, 5, 6, 9, 11, 12, 13, 14, 15, 17, 18, 19. Fourteen SNPs were novel loci and 23 SNPs were located within known QTLs or 75 kb near the known SNPs. Five candidate genes (Glyma.05G101800, Glyma.11G140100, Glyma.11G142900, Glyma.19G099700, Glyma.19G100900) in a 90 kb genomic region of each side of four significant SNPs (Gm5_27111367, Gm11_10629613, Gm11_10950924, Gm19_34768458) based on the average LD decay were homologs of Arabidopsis flowering time genes of AT5G48385.1, AT3G46510.1, AT5G59780.3, AT1G28050.1, and AT3G26790.1. These genes encoding FRI (FRIGIDA), PUB13 (plant U-box 13), MYB59, CONSTANS, and FUS3 proteins respectively might play important roles in controlling soybean growth periods.

Conclusions
This study identified putative SNP markers associated with soybean growth period traits, which could be used for the marker-assisted selection of soybean growth period traits. Furthermore, the possible candidate genes involved in the control of soybean flowering time were predicted.
Genetic deletion of Sphk2 confers protection against Pseudomonas aeruginosa mediated differential expression of genes related to virulent infection and inflammation in mouse lung
Authors: Ebenezer David L. , Fu Panfeng , Krishnan Yashaswin , Maienschein-Cline Mark , Hu Hong , Jung Segun , Madduri Ravi , Arbieva Zarema , Harijith Anantha , Natarajan Viswanathan 
Published: December 2019

AbstractBackgroundPseudomonas aeruginosa(PA) is an opportunistic Gram-negative bacterium that causes serious life threatening and nosocomial infections including pneumonia.PAhas the ability to alter host genome to facilitate its invasion, thus increasing the virulence of the organism. Sphingosine-1- phosphate (S1P), a bioactive lipid, is known to play a key role in facilitating infection. Sphingosine kinases (SPHK) 1&2 phosphorylate sphingosine to generate S1P in mammalian cells. We reported earlier thatSphk2−/−mice offered significant protection against lung inflammation, compared to wild type (WT) animals. Therefore, we profiled the differential expression of genes between the protected group ofSphk2−/−and the wild type controls to better understand the underlying protective mechanisms related to theSphk2deletion in lung inflammatory injury. Whole transcriptome shotgun sequencing (RNA-Seq) was performed on mouse lung tissue using NextSeq 500 sequencing system.ResultsTwo-way analysis of variance (ANOVA) analysis was performed and differentially expressed genes followingPAinfection were identified using whole transcriptome ofSphk2−/−mice and their WT counterparts. Pathway (PW) enrichment analyses of the RNA seq data identified several signaling pathways that are likely to play a crucial role in pneumonia caused byPAsuch as those involved in: 1. Immune response toPAinfection and NF-κB signal transduction; 2. PKC signal transduction; 3. Impact on epigenetic regulation; 4. Epithelial sodium channel pathway; 5. Mucin expression; and 6. Bacterial infection related pathways.Our genomic data suggests a potential role for SPHK2 inPA-induced pneumonia through elevated expression of inflammatory genes in lung tissue. Further, validation by RT-PCR on 10 differentially expressed genes showed 100% concordance in terms of vectoral changes as well as significant fold change.ConclusionUsingSphk2−/−mice and differential gene expression analysis, we have shown here that S1P/SPHK2 signaling could play a key role in promotingPApneumonia. The identified genes promote inflammation and suppress others that naturally inhibit inflammation and host defense. Thus, targeting SPHK2/S1P signaling inPA-induced lung inflammation could serve as a potential therapy to combatPA-induced pneumonia.
Interactions between Yersinia pestis V-antigen (LcrV) and human Toll-like receptor 2 (TLR2) in a modelled protein complex and potential mechanistic insights
Authors: Wei Tiandi , Gong Jing , Qu Guojing , Wang Mingyu , Xu Hai 
Published: December 2019

Abstract
Background
Yersinia pestis, the etiological pathogen of plague, is capable of repressing the immune response of white blood cells to evade phagocytosis. The V-antigen (LcrV) was found to be involved in this process by binding to human Toll-like Receptor 2 (TLR2). The detailed mechanism behind this LcrV and TLR2 mediated immune response repression, however, is yet to be fully elucidated due to the lack of structural information.

Results
In this work, with protein structure modelling, we were able to construct a structure model of the heterotetramer of Y. pestis LcrV and human TLR2. Molecular dynamics simulation suggests the stability of this structure in aquatic environment. The LcrV model has a dumbbell-like structure with two globule domains (G1 at N-terminus and G2 away from membrane) connected with a coiled-coil linker (CCL) domain. The two horseshoe-shape TLR2 subunits form a V-shape structure, are not in direct contact with each other, and are held together by the LcrV homodimer. In this structure model, both the G1 and CCL domains are involved in the formation of LcrV homodimer, while all three domains are involved in LcrV-TLR2 binding. A mechanistic model was proposed based on this heterotetrameric structure model: The LcrV homodimer separates the TLR2 subunits to inhibit the dimerization of TLR2 and subsequent signal transfer for immune response; while LcrV could also inhibit the formation of heterodimers of TLR2 with other TLRs, and leads to immune response repression.

Conclusions
A heterotetrameric structure of Y. pestis LcrV and human TLR2 was modelled in this work. Analysis of this modelled structure showed its stability in aquatic environments and the role of LcrV domains and residues in protein-protein interaction. A mechanistic model for the role of LcrV in Y. pestis pathogenesis is raised based on this heterotetrameric structure model. This work provides a hypothesis of LcrV function, with which further experimental validation may elucidate the role of LcrV in human immune response repression.
Haplotype block analysis of an Argentinean hexaploid wheat collection and GWAS for yield components and adaptation
Authors: Luján Basile Silvana Marisol , Ramírez Ignacio Abel , Crescente Juan Manuel , Conde Maria Belén , Demichelis Melina , Abbate Pablo , Rogers William John , Pontaroli Ana Clara , Helguera Marcelo , Vanzetti Leonardo Sebastián 
Published: December 2019

Abstract
Background
Increasing wheat (Triticum aestivum L.) production is required to feed a growing human population. In order to accomplish this task a deeper understanding of the genetic structure of cultivated wheats and the detection of genomic regions significantly associated with the regulation of important agronomic traits are necessary steps. To better understand the genetic basis and relationships of adaptation and yield related traits, we used a collection of 102 Argentinean hexaploid wheat cultivars genotyped with the 35k SNPs array, grown from two to six years in three different locations. Based on SNPs data and gene-related molecular markers, we performed a haplotype block characterization of the germplasm and a genome-wide association study (GWAS).

Results
The genetic structure of the collection revealed four subpopulations, reflecting the origin of the germplasm used by the main breeding programs in Argentina. The haplotype block characterization showed 1268 blocks of different sizes spread along the genome, including highly conserved regions like the 1BS chromosome arm where the 1BL/1RS wheat/rye translocation is located. Based on GWAS we identified ninety-seven chromosome regions associated with heading date, plant height, thousand grain weight, grain number per spike and fruiting efficiency at harvest (FEh). In particular FEh stands out as a promising trait to raise yield potential in Argentinean wheats; we detected fifteen haplotypes/markers associated with increased FEh values, eleven of which showed significant effects in all three evaluated locations. In the case of adaptation, the Ppd-D1 gene is consolidated as the main determinant of the life cycle of Argentinean wheat cultivars.

Conclusion
This work reveals the genetic structure of the Argentinean hexaploid wheat germplasm using a wide set of molecular markers anchored to the Ref Seq v1.0. Additionally GWAS detects chromosomal regions (haplotypes) associated with important yield and adaptation components that will allow improvement of these traits through marker-assisted selection.
Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis
Authors: Xin Gui-Liang , Liu Jia-Qian , Liu Jia , Ren Xiao-Long , Du Xiao-Min , Liu Wen-Zhe 
Published: December 2019

AbstractBackgroundGametogenesis is a key step in the production of ovules or pollen in higher plants. The sex-determination aspects of gametogenesis have been well characterized in the model plantArabidopsis. However, little is known about this process in androdioecious plants.Tapiscia sinensisOliv. is a functionally androdioecious tree, with both male and hermaphroditic individuals. Hermaphroditic flowers (HFs) are female-fertile flowers that can produce functional pollen and set fruits. However, compared with male flowers (MFs), the pollen viability and number of pollen grains per flower are markedly reduced in HFs. MFs are female-sterile flowers that fail to set fruit and that eventually drop.ResultsCompared with HF, a notable cause of MF female sterility inT. sinensisis when the early gynoecium meristem is disrupted. During the early stage of HF development (stage 6), the ring meristem begins to form as a ridge around the center of the flower. At this stage, the internal fourth-whorl organ is stem-like rather than carpelloid in MF.A total of 52,945 unigenes were identified as transcribed in MF and HF. A number of differentially expressed genes (DEGs) and metabolic pathways were detected as involved in the development of the gynoecium, especially the ovule, carpel and style. At the early gynoecium development stage, DEGs were shown to function in the metabolic pathways regulating ethylene biosynthesis and signal transduction (upstream regulator), auxin, cytokinin transport and signalling, and sex determination (or flower meristem identity).ConclusionsPathways for the female sterility model were initially proposed to shed light on the molecular mechanisms of gynoecium development at early stages inT. sinensis.
Protective mechanisms of melatonin against selenium toxicity in Brassica napus: insights into physiological traits, thiol biosynthesis and antioxidant machinery
Authors: Ulhassan Zaid , Huang Qian , Gill Rafaqat Ali , Ali Skhawat , Mwamba Theodore Mulembo , Ali Basharat , Hina Faiza , Zhou Weijun 
Published: December 2019

Abstract
Background
The ubiquitous signaling molecule melatonin (N-acetyl-5-methoxytryptamine) (MT) plays vital roles in plant development and stress tolerance. Selenium (Se) may be phytotoxic at high concentrations. Interactions between MT and Se (IV) stress in higher plants are poorly understood. The aim of this study was to evaluate the defensive roles of exogenous MT (0 μM, 50 μM, and 100 μM) against Se (IV) (0 μM, 50 μM, 100 μM, and 200 μM) stress based on the physiological and biochemical properties, thiol biosynthesis, and antioxidant system of Brassica napus plants subjected to these treatments.

Results
Se (IV) stress inhibited B. napus growth and biomass accumulation, reduced pigment content, and lowered net photosynthetic rate (Pn) and PSII photochemical efficiency (Fv/Fm) in a dose-dependent manner. All of the aforementioned responses were effectively alleviated by exogenous MT treatment. Exogenous MT mitigated oxidative damage and lipid peroxidation and protected the plasma membranes from Se toxicity by reducing Se-induced reactive oxygen species (ROS) accumulation. MT also alleviated osmotic stress by restoring foliar water and sugar levels. Relative to standalone Se treatment, the combination of MT and Se upregulated the ROS-detoxifying enzymes SOD, APX, GR, and CAT, increased proline, free amino acids, and the thiol components GSH, GSSG, GSH/GSSG, NPTs, PCs, and cys and upregulated the metabolic enzymes γ-ECS, GST, and PCS. Therefore, MT application attenuates Se-induce oxidative damage in plants. MT promotes the accumulation of chelating agents in the roots, detoxifies Se there, and impedes its further translocation to the leaves.

Conclusions
Exogenous MT improves the physiological traits, antioxidant system, and thiol ligand biosynthesis in B. napus subjected to Se stress primarily by enhancing Se detoxification and sequestration especially at the root level. Our results reveal better understanding of Se-phytotoxicity and Se-stress alleviation by the adequate supply of MT. The mechanisms of MT-induced plant tolerance to Se stress have potential implications in developing novel strategies for safe crop production in Se-rich soils.

Graphical abstract
The plant defensin gene AtPDF2.1 mediates ammonium metabolism by regulating glutamine synthetase activity in Arabidopsis thaliana
Authors: Yao Junyue , Luo Jin-Song , Xiao Yan , Zhang Zhenhua 
Published: December 2019

Abstract
Background
In plants, ammonium metabolism is particularly important for converting absorbed nitrogen into amino acids. However, the molecular mechanism underlying this conversion remains largely unknown.

Results
Using wild type Arabidopsis thaliana (Col-0) and AtPDF2.1 mutants (pdf2.1–1 and pdf2.1–2), we found that the small cysteine-rich peptide AtPDF2.1, a plant defensin, is involved in regulating ammonium metabolism in the shoot. Ammonium significantly induced the expression of AtPDF2.1 in the shoot and root, particularly in root xylem vascular bundles, as demonstrated by histochemical analysis. Subcellular localization analysis revealed that AtPDF2.1 was localized to the cell wall. Ammonium concentration was higher in the shoot of mutants than in the shoot of Col-0, but no differences were found for total nitrogen content, root ammonium concentration, and the expression of the ammonium transporter gene AtAMT2.1. The activity of glutamine synthetase was significantly decreased in mutants, and the glutamine synthetase family genes GLN1.3 and GLN1.5 were significantly downregulated in mutants compared to Col-0. The activity of nitrate reductase showed no difference between mutants and Col-0.

Conclusions
Overall, these data suggest that AtPDF2.1 affects ammonium metabolism by regulating the expression of GLN1.3 and GLN1.5 through a yet unidentified mechanism.
Differences in the photosynthetic and physiological responses of Leymus chinensis to different levels of grazing intensity
Authors: Liu Min , Gong Jirui , Yang Bo , Ding Yong , Zhang Zihe , Wang Biao , Zhu Chenchen , Hou Xiangyang 
Published: December 2019

Abstract
Background
Grazing is an important land use in northern China. In general, different grazing intensities had a different impact on the morphological and physiological traits of plants, and especially their photosynthetic capacity. We investigated the responses of Leymus chinensis to light, medium, and heavy grazing intensities in comparison with a grazing exclusion control.

Results
With light grazing, L. chinensis showed decreased photosynthetic capacity. The low chlorophyll and carotenoid contents constrained light energy transformation and dissipation, and Rubisco activity was also low, restricting the carboxylation efficiency. In addition, the damaged photosynthetic apparatus accumulated reactive oxygen species (ROS). With medium grazing, more energy was used for thermal dissipation, with high carotene content and high non-photochemical quenching, whereas photosynthetic electron transport was lowest. Significantly decreased photosynthesis decreased leaf C contents. Plants decreased the risk caused by ROS through increased energy dissipation. With high grazing intensity, plants changed their strategy to improve survival through photosynthetic compensation. More energy was allocated to photosynthetic electron transport. Though heavy grazing damaged the chloroplast ultrastructure, adjustment of internal mechanisms increased compensatory photosynthesis, and an increased tiller number facilitated regrowth after grazing.

Conclusions
Overall, the plants adopted different strategies by adjusting their metabolism and growth in response to their changing environment.
Maternally inherited coronary heart disease is associated with a novel mitochondrial tRNA mutation
Authors: Zhang Zhenxiao , Liu Mingyang , He Jianshuai , Zhang Xiaotian , Chen Yuehua , Li Hui 
Published: December 2019

Abstract
Background
Coronary heart disease (CHD) is the most common cause of mortality globally, yet mitochondrial genetic mutations associated with CHD development remain incompletely understood.

Methods
The subjects from three Chinese families with LHON underwent clinical, genetic, molecular, and biochemical evaluations. Biochemical characterizations included measuring the effects of the15910C > T mutation on tRNAThr levels, enzymatic activity of electron transport chain complexes, membrane permeability, and the mitochondria-mediated generation of both reactive oxygen species (ROS) and adenosine triphosphate (ATP).

Results
We characterize mitochondrial genetic mutations in a three-generation Chinese family exhibiting signs of maternally inherited CHD. Of the 24 different family members in this pedigree we assessed, CHD was detected in 6, with variable severity and age of first appearance. When we sequenced the mitochondrial genomes of these individuals, we found a tRNAThr 15910C > T mutation of the Eastern Asian haplogroup M7b’c. This mutation is predicted to destabilize the strongly conserved (24C-10G) base-pairing, thereby disrupting tRNAThr functionality. When we performed Northern blotting, we detected we observed a 37.5% reduction in tRNAThr levels at baseline in cybrid cell lines bearing the 15910C > T mutation. When we conducted western blot analysis, we detected a ~ 24.96% decrease in mitochondrial translation rates in these same cells.

Conclusions
In the present report, Together these findings suggest a possible link between this 15910C > T tRNAThr mutation and CHD, potentially offering new avenues for future disease intervention.
Self-reported data in environmental health studies: mail vs. web-based surveys
Authors: Cantuaria Manuella Lech , Blanes-Vidal Victoria 
Published: December 2019

AbstractBackgroundInternet has been broadly employed as a facilitator for epidemiological surveys, as a way to provide a more economical and practical alternative to traditional survey modes. A current trend in survey research is to combine Web-based surveys with other survey modes by offering the participant the possibility of choosing his/her preferred response method (i.e. mixed-mode approach). However, studies have also demonstrated that the use of different survey modes may produce different responses to the same questions, posing potential challenges on the use of mixed-mode approaches.MethodsIn this paper, we have implemented a statistical comparison between mixed-mode survey responses collected via mail (i.e. paper) and Web methods obtained from a cross-sectional study in non-urban areas of Denmark. Responses provided by mail and Web participants were compared in terms of: 1) the impact of reminder letters in increasing response rates; 2) differences in socio-demographic characteristics between response groups; 3) changes on the likelihood of reporting health symptoms and negative attitudes towards environmental stressors. Comparisons were mainly performed by two sample t-test, Pearson’s Chi-squared test and multinomial logistic regression models.ResultsAmong 3104 contacted households, 1066 residents decided to participate on the study. Out of those, 971 selected to respond via mail, whereas 275 preferred the Web method. The majority of socio-demographic characteristics between these two groups of respondents were shown to be statistically different. The use of mailed surveys increased the likelihood of reporting health symptoms and negative attitudes towards environmental stressors, even after controlling for demographic characteristics. Furthermore, the use of reminder letters had a higher positive impact in increasing responses of Web surveys when compared to mail surveys.ConclusionsOur main findings suggest that the use of mail and Web surveys may produce different responses to the same questions posed to participants, but, at the same time, may reach different groups of respondents, given that the overall characteristics of both groups considerably differ. Therefore, the tradeoff between using mixed-mode survey as a way to increase response rate and obtaining undesirable measurement changes may be attentively considered in future survey studies.