Genomic value prediction for quantitative traits under the epistatic model

Abstract Background Most quantitative traits are controlled by multiple quantitative trait loci (QTL). The contribution of each locus may be negligible but the collective contribution of all loci is usually significant. Genome selection that uses markers of the entire genome to predict the genomic values of individual plants or animals can be more efficient than selection on phenotypic values and pedigree information alone for genetic improvement. When a quantitative trait is contributed by epistatic effects, using all markers (main effects) and marker pairs (epistatic effects) to predict the genomic values of plants can achieve the maximum efficiency for genetic improvement. Results In this study, we created 126 recombinant inbred lines of soybean and genotyped 80 makers across the genome. We applied the genome selection technique to predict the genomic value of somatic embryo number (a quantitative trait) for each line. Cross validation analysis showed that the squared correlation coefficient between the observed and predicted embryo numbers was 0.33 when only main (additive) effects were used for prediction. When the interaction (epistatic) effects were also included in the model, the squared correlation coefficient reached 0.78. Conclusions This study provided an excellent example for the application of genome selection to plant breeding

Comparative studies of the anti-thrombotic effects of saffron and HongHua based on network pharmacology

Purpose: To investigate the comparative anti-thrombotic effects of saffron and Honghua, and also to explore possible mechanisms in thrombosis based on network pharmacology. Methods: A network pharmacology model was used for bioactive components, targets and pathways for saffron and HongHua via Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), PharmMapper, Genecard, Uniprot and KEGG databases. In animal experiments, 72 rats were randomly divided into 9 groups: normal control group (NC), model control group (MC), crocetin groups (80, 40, 20 mg/kg), hydroxysafflor yellow A(HSYA) groups (80, 40, 20 mg/kg), and aspirin group (40 mg/kg). Using in vitro thrombosis models and an acute blood stasis model in vivo, the anti-thrombotic effects of these treatments on clotting time, hemorheology parameters, Thromboxane B2 (TXB2), plasmin activator inhibitor (PAI), protein C (PC), protein S (PS), and thrombinantithrombin complex (TAT) were determined and comparisons made for saffron and HongHua. Results: Five potential compounds, 16 anti-thrombotic targets and 27 pathways were predicted for saffron, while 22 compounds, 37 disease targets and 35 pathways were found for HongHua (p < 0.05). Pharmacological experiments revealed that crocetin and HSYA had significant effects on thrombus length, thrombus wet/dry mass, whole blood viscosity (WBV), erythrocyte aggregation index (EAI), clotting time and D-dimer for the high and middle groups. Unlike HSYA, crocetin also had significant and dose-dependent effects on PAI, prothrombin fragment 1+2 (F1+2) and PS and had highly significant effects on TXB2 and TAT. Conclusion: This research provides a systematic, comprehensive and comparative analysis of component, target and anti-thrombotic pathways of saffron and HongHua based on network pharmacology, and also shows that saffron has more significant anti-thrombotic effect than HongHua. Keywords: Saffron; HongHua; Network pharmacology; Anti-thrombosis; Network mode

Application of Hierarchical Facility Location-Routing Problem with Optimization of an Underground Logistic System: A Case Study in China

Facility location problem (FLP) and vehicle routing problem (VRP) are two of the most challenging issues in logistics. This paper presents an exploration of the multinode facility location-routing problem with realistic conditions. The disposal centers, transfer stations, connected collection sites, and unconnected collection sites are built into a new hierarchical model which is solved by Generate Algorithm (GA). Model costs include node construction cost, pipeline construction cost, transport cost, and transfer cost. This paper considers that the transportation is a bidirectional flow not a single flow; each pairs node in the area needs transportation; the dynamic routing selection method is used to determine the routes of unconnected collection sites. FLP and VRP can be both solved in this model. To illustrate the applicability of the model, a case study is presented and the results are discussed. The model in this paper can reduce the cost of the traditional underground logistics system by 6%~8% in experiments

Study on the Process and Mechanism of Slope Failure Induced by Mining under Open Pit Slope: A Case Study from Yanqianshan Iron Mine, China

Mining under an open pit slope results in the collapse and slide of the slope. In this paper, a combination of methods including Google Earth and field investigations is applied to investigate the process of eastern slope failure induced by underground mining in the Yanqianshan Iron Mine over five years. According to the observed ground deformation features, the geomorphic zone of the eastern slope can be divided into four regions (caved rock zone, cracking zone, toppling zone, and sliding zone). Break angles and fracture initiation angles at different times are counted separately. Based on the above work, the process of initiation and development of slope failure is studied. The analysis results show that the process of slope failure could be chronologically divided into three stages. First, a collapse pit, caused by the falling of the overlying strata above the goaf, appeared on the eastern slope. Then, the rock mass around the collapse pit slid into the pit to form a small landslide. Finally, because of mining disturbances and rock creep, a large landslide occurred on the northeastern phyllite slope. The control mechanisms of each failure stage are discussed separately. Finally, the RFPA3D code is employed to simulate the slope failure process under the influence of underground mining. The results are consistent with the field observations, which provided information on deformation failure and the mechanics of the slope that could not be directly observed in the field and deepened the mechanism analysis

Platinum(II) complexes bearing bulky Schiff base ligands anchored onto mesoporous SBA-15 supports as efficient catalysts for hydrosilylation

Reported herein is an easy-to-prepare novel heterogeneous catalyst of platinum complexes bearing binary ligands of bidentate naphthalenolimine and cyclo-1,5-octadiene that are anchored onto mesoporous silica SBA-15. The presence of the binary ligands not only stabilized the platinum, but also enabled the platinum atoms to form nanoclusters with diameters of ca 1nm, and led to high platinum loading (8.69wt%). Moreover, the platinum catalyst exhibited high catalytic activity towards hydrosilylation of terminal alkenes and styrene with silanes under mild and solvent-free conditions, with excellent regioselectivity

IL-17 Activates the IL-6/STAT3 Signal Pathway in the Proliferation of Hepatitis B Virus-Related Hepatocellular Carcinoma

Background/Aims: We performed this study to determine the role of IL-17 in the immune microenvironment of hepatitis B virus- (HBV-) related hepatocellular carcinoma (HCC). Methods: HepG2 cells were treated with IL-17, STAT3 inhibitor S31-201 or IL-6 neutralizing monoclonal antibody (IL-6 mAb). Cell proliferation and migration were compared using the Cell Counting kit-8 (CCK-8) and Transwell assays, respectively. Real-time quantitative PCR (RT-qPCR), Western Blot, ELISA, immunofluorescence and histological staining were used for determining the expression levels of IL-17, IL-6, MCP-1, CCL5, VEGF, STAT3 and p-STAT3. HCC xenograft models were constructed in wild type and IL-17 knockout mice to clarify the effects of IL-17 on HCC in vivo. Results: Exogenous IL-17 enhanced the proliferation and migration of HepG2 cells, and it activated the phosphorylation of STAT3. RT-qPCR and ELISA showed that IL-17 promoted the expression of IL-6. The CCK-8 and Transwell assays showed that S31-201 or IL-6 mAb remarkably reversed the promotion effects of proliferation and migration by exogenous IL-17 in HepG2 cells. Additionally, IL-6 could promote the phosphorylation of STAT3, while IL-6 mAb acted as an inhibitor, and exogenous IL-17 could neutralize the inhibitory effects of IL-6 mAb. In vivo, compared to the wild type mice, the tumor volume, weight, density and size were decreased in IL-17 knockout mice. Additionally, the expression levels of p-STAT3, IL-6, MCP-1, CCL5 and VEGF decreased in IL-17 knockout mice. Conclusions: IL-17 can enhance the proliferation of HepG2 cells in vitro and in vivo via activating the IL-6/STAT3 pathway. Therefore, the IL-17/IL-6/STAT3 signaling pathway is a potential therapeutic target for HBV-related HCC

Genome-Wide Identification of Brassicaceae Hormone-Related Transcription Factors and Their Roles in Stress Adaptation and Plant Height Regulation in Allotetraploid Rapeseed

Phytohormone-related transcription factors (TFs) are involved in regulating stress responses and plant growth. However, systematic analysis of these TFs in Brassicaceae is limited, and their functions in stress adaptation and plant height (PH) regulation remain unclear. In this study, 2115 hormone-related TFs were identified in nine Brassicaceae species. Specific domains were found in several Brassicaceae hormone-related TFs, which may be associated with diverse functions. Syntenic analysis indicated that expansion of these genes was mainly caused by segmental duplication, with whole-genome duplication occurring in some species. Differential expression analysis and gene co-expression network analysis identified seven phytohormone-related TFs (BnaWRKY7, 21, 32, 38, 52, BnaGL3-4, and BnaAREB2-5) as possible key genes for cadmium (Cd) toxicity, salinity stress, and potassium (K) and nitrogen (N) deficiencies. Furthermore, BnaWRKY42 and BnaARR21 may play essential roles in plant height. Weighted gene co-expression network analysis (WGCNA) identified 15 phytohormone-related TFs and their potential target genes regulating stress adaptation and plant height. Among the above genes, BnaWRKY56 and BnaWRKY60 responded to four different stresses simultaneously, and BnaWRKY42 was identified in two dwarf rapeseeds. In summary, several candidate genes for stress resistance (BnaWRKY56 and BnaWRKY60) and plant height (BnaWRKY42) were identified. These findings should help elucidate the biological roles of Brassicaceae hormone-related TFs, and the identified candidate genes should provide a genetic resource for the potential development of stress-tolerant and dwarf oilseed plants