Identification of Cassava MicroRNAs under Abiotic Stress

Edwardsiella ictaluri (E. ictaluri) is one of the main bacterial pathogens in catfish which has caused serious economic loss to yellow catfish (Pelteobagrus fulvidraco) in China. In our previous work, we demonstrated that CypA was up-regulated at the early stage of E. ictaluri infection in yellow catfish and displayed strong chemotactic activity for leukocytes in vitro. However, the effect of CypA on E. ictaluri is unknown in vivo. Therefore, two homozygous transgenic zebrafish lines expressing yellow catfish CypA (TG-CypA-1 and TG-CypA-2) were generated. After challenged with E. ictaluri at a dose of 1.0 x 10(4) CFU per adult fish, both two transgenic lines exhibited a higher resistance to bacterial infection than the wildtype zebrafish. Herein, CypA gene in E. ictalurichallenged yellow catfish was screened for presence of polymorphisms by sequencing and six single nucleotide polymorphisms (SNPs) were identified. SNP association analysis revealed that 528T/C SNP in the first intron was significantly different in disease-susceptible and-resistant groups, which was confirmed in two independent populations of yellow catfish. Moreover, the relative expression of CypA in the resistant group (CC genotype in 528T/C SNP) was significantly higher than that in the susceptible group (TT genotype in 528T/C SNP) in different immune organs of yellow catfish including spleen, head kidney, body kidney and liver. Our results reveal the potential function of CypA in host defense to bacterial infection and suggest the SNP marker in CypA gene associated with the resistance to E. ictaluri may facilitate the selective breeding of disease-resistant yellow catfish in the future

A decision analysis model for KEGG pathway analysis

The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis by grouping thousands of genes into just several hundred pathways, but also can increase the explanatory power for the experiment by identifying active pathways in different conditions. However, current approaches are designed to analyze a biological system assuming that each pathway is independent of the other pathways. A decision analysis model is developed in this article that accounts for dependence among pathways in time-course experiments and multiple treatments experiments. This model introduces a decision coefficient—a designed index, to identify the most relevant pathways in a given experiment by taking into account not only the direct determination factor of each Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway itself, but also the indirect determination factors from its related pathways. Meanwhile, the direct and indirect determination factors of each pathway are employed to demonstrate the regulation mechanisms among KEGG pathways, and the sign of decision coefficient can be used to preliminarily estimate the impact direction of each KEGG pathway. The simulation study of decision analysis demonstrated the application of decision analysis model for KEGG pathway analysis. A microarray dataset from bovine mammary tissue over entire lactation cycle was used to further illustrate our strategy. The results showed that the decision analysis model can provide the promising and more biologically meaningful results. Therefore, the decision analysis model is an initial attempt of optimizing pathway analysis methodology.https://doi.org/10.1186/s12859-016-1285-

Guardian spirit of be (Shaman) and Culture tradition : For ongdin - taban - tnger ritual

This file provide the detailed impact direction data of selected KEGG pathway categories, subcategories and the secondary pathways from− 15 to 300 vs.− 30d in bovine mammary tissue during lactation in Table S2 (a) and (b), respectively. The numbers colored in red color are the filled data by the average of all the other impact values in this pathway, which is the missing data originally. (DOCX 35 kb

Murine Gamma-herpesvirus Immortalization of Fetal Liver-Derived B Cells Requires both the Viral Cyclin D Homolog and Latency-Associated Nuclear Antigen

Human gammaherpesviruses are associated with the development of lymphoproliferative diseases and B cell lymphomas, particularly in immunosuppressed hosts. Understanding the molecular mechanisms by which human gammaherpesviruses cause disease is hampered by the lack of convenient small animal models to study them. However, infection of laboratory strains of mice with the rodent virus murine gammaherpesvirus 68 (MHV68) has been useful in gaining insights into how gammaherpesviruses contribute to the genesis and progression of lymphoproliferative lesions. In this report we make the novel observation that MHV68 infection of murine day 15 fetal liver cells results in their immortalization and differentiation into B plasmablasts that can be propagated indefinitely in vitro, and can establish metastasizing lymphomas in mice lacking normal immune competence. The phenotype of the MHV68 immortalized B cell lines is similar to that observed in lymphomas caused by KSHV and resembles the favored phenotype observed during MHV68 infection in vivo. All established cell lines maintained the MHV68 genome, with limited viral gene expression and little or no detectable virus production - although virus reactivation could be induced upon crosslinking surface Ig. Notably, transcription of the genes encoding the MHV68 viral cyclin D homolog (v-cyclin) and the homolog of the KSHV latency-associated nuclear antigen (LANA), both of which are conserved among characterized γ2-herpesviruses, could consistently be detected in the established B cell lines. Furthermore, we show that the v-cyclin and LANA homologs are required for MHV68 immortalization of murine B cells. In contrast the M2 gene, which is unique to MHV68 and plays a role in latency and virus reactivation in vivo, was dispensable for B cell immortalization. This new model of gammaherpesvirus-driven B cell immortalization and differentiation in a small animal model establishes an experimental system for detailed investigation of the role of gammaherpesvirus gene products and host responses in the genesis and progression of gammaherpesvirus-associated lymphomas, and presents a convenient system to evaluate therapeutic modalities

Efficacy and safety of low-dose IL-2 in the treatment of systemic lupus erythematosus: A randomised, double-blind, placebo-controlled trial

Objectives Open-labelled clinical trials suggested that low-dose IL-2 might be effective in treatment of systemic lupus erythematosus (SLE). A double-blind and placebocontrolled trial is required to formally evaluate the safety and efficacy of low-dose IL-2 therapy. Methods A randomised, double-blind and placebocontrolled clinical trial was designed to treat 60 patients with active SLE. These patients received either IL-2 (n=30) or placebo (n=30) with standard treatment for 12 weeks, and were followed up for additional 12 weeks. IL-2 at a dose of 1 million IU or placebo was administered subcutaneously every other day for 2 weeks and followed by a 2-week break as one treatment cycle. The primary endpoint was the SLE Responder Index-4 (SRI-4) at week 12. The secondary endpoints were other clinical responses, safety and dynamics of immune cell subsets. Results At week 12, the SRI-4 response rates were 55.17% and 30.00% for IL-2 and placebo, respectively (p=0.052). At week 24, the SRI-4 response rate of IL-2 group was 65.52%, compared with 36.67% of the placebo group (p=0.027). The primary endpoint was not met at week 12. Low-dose IL-2 treatment resulted in 53.85% (7/13) complete remission in patients with lupus nephritis, compared with 16.67% (2/12) in the placebo group (p=0.036). No serious infection was observed in the IL-2 group, but two in placebo group. Besides expansion of regulatory T cells, low-dose IL-2 may also sustain cellular immunity with enhanced natural killer cells. Conclusions Low-dose IL-2 might be effective and tolerated in treatment of SThe work was supported by the National Natural Science Foundation of China (31530020,31570880,81471601,81601417 and 81701598), Peking-Tsinghua Center for Life Sciences to ZG LI, Beijing Sci-Tech Committee Z171100000417007,Clinical Medicine Plus X-Young Scholars Project of Peking University (PKU2019LCXQ013) supported by the Fundamental Research Funds for the Central Universities, Beijing Nova Program Z171100001117025, National Key Research and Development Program of China (2017YFC0909003 to DY), BellberryViertel Senior Medical Research Fellowship to DY and Beijing SL PHARM

Research on Fault Tree Reconstruction Based on Contingency

The fault tree analysis (FTA) method is an important analysis method for safety system engineering. Traditional accident analysis theory agrees that basic events lead to top events, but it does not fully consider that the accident process is accidental, and the calculation results exaggerate the probability of accident occurrence. This paper selects typical collision accidents, analyzes the shortcomings of the existing fault tree, indicates that there is a contingency in the accident process, constructs a probability fault tree based on the traditional fault tree, and puts forward concepts of “probability AND gate” and “probability OR gate”. In addition, based on the traditional quantitative analysis method of fault trees, calculations of the occurrence probability, probability importance coefficient, and critical importance coefficient of top events are modified, and the modified quantitative calculation is applied to accident cases

Incorporating Patent Analysis in Axiomatic Design for New Product Development

Axiomatic design theory is widely used in new product development by providing design solutions through mapping between functional requirements and design parameters. However, the theory does not provide a method to help designer obtain and select design parameters. To this end, this paper introduces patent analysis to overcome the deficiency. Firstly, functional requirements are transformed into patent search terms, and design parameters are obtained from patents. Secondly, morphological matrix is used to represent the relationships between target function and multiple design parameters. Thirdly, design parameters with higher patent frequency are chose and combined into a new scheme. Finally, the scheme is evaluated by the independent axiom of Axiomatic Design theory. The methodology is demonstrated and validated with a case study of spa shower