脱发相关差异表达基因的生物信息学分析

利用生物信息学方法分析脱发相关差异表达基因,有望帮助了解脱发发生发展的分子机制。本研究从NCBI的子数据库GEO中选择基因表达谱GSE45512和GSE45513数据集,利用R语言limma工具包,筛选出两个物种斑秃样本与正常样本的共同显著差异表达基因。对这部分基因进行功能注释和蛋白互作网络分析,同时对全部差异表达基因进行基因集富集分析。结果发现,人头皮斑秃样本共筛选出225个差异表达基因;C3H/HeJ小鼠自发斑秃皮肤样本共筛选出337个差异表达基因;两个物种的共同显著差异表达基因有23个。GO功能富集分析和蛋白互作网络分析显示,这部分差异基因显著富集于免疫相关功能,并且彼此间存在蛋白互作关系。基因集富集分析显示两个物种的差异基因都能显著富集到趋化因子信号通路、细胞因子受体相互作用、金葡菌感染及抗原加工与呈递通路;而且人的下调差异基因不仅映射到了人类表型数据库的脱发表型,也映射到皮肤附属物病理相关表型。综上所述,本研究通过生物信息方法分析脱发皮肤组织与正常皮肤组织的差异表达基因,最终筛选出23个在人和小鼠中共同存在的显著差异表达基因;此外,分析发现脱发与免疫过程及皮肤附属物病变密切相关,这些结果为脱发的诊断和治疗提供了新思路。     

Identification and Genetic Analysis of a Novel Allelic Variation of <i>Brittle-1</i> with Endosperm Mutant in Maize

Endosperm mutants are critical to the studies on both starch synthesis and metabolism and genetic improvement of starch quality in maize. In the present study, a novel maize endosperm mutant A0178 of natural variation was used as the experimental material and identified and then characterized. Through phenotypic identification, genetic analysis, main ingredients measurement and embryo rescue, development of genetic mapping population from A0178, the endosperm mutant gene was located. The results showed that the mutant exhibited extremely low germination ability as attributed to the inhibited embryo development, and amounts of sugars were accumulated in the mutant seeds and more sugars content was detected at 23 days after pollination (DAP) in A0178 than B73. Employing genetic linkage analysis, the mutant trait was mapped in the bin 5.04 on chromosome 5. Sequence analysis showed that two sites of base transversion and insertion presented in the protein coding region and non-coding region of the mutant brittle-1 (bt1), the adenylate translocator encoding gene involved in the starch synthesis. The single base insertion in the coding region cause frameshift mutation, early termination and lose of function of Brittle-1 (BT1). All results suggested that bt1 is a novel allelic gene and the causal gene of this endosperm mutant, providing insights on the mechanism of endosperm formation in maize.     

Aliphatic suberin confers salt tolerance to Arabidopsis by limiting Na+ influx,K+ efflux and water backflow

Plant and Soil - Uncontrolled uptake of Na+ is the reason that many species are sensitive to salinity. Suberin is a protective barrier found in the walls of root endodermal cells that appears to be...     

Effects of Bacillus Subtilis-Zinc on Rats with Congenital Zinc Deficiency

Biological Trace Element Research - This study investigated the effects of dietary supplementation of Bacillus subtilis-zinc on growth rates of the body and organs, nutrient utilization, microbial...     

Reference gene selection and validation for mRNA expression analysis by RT-qPCR in murine M1- and M2-polarized macrophage

Molecular Biology Reports - Murine bone marrow-derived macrophages (M0) and M1- and M2-polarized macrophages are being widely used as a laboratory model for polarized macrophages related molecular...     

Screening of optimal reference genes for qRT-PCR and preliminary exploration of cold resistance mechanisms in Prunus mume and Prunus sibirica varieties

Molecular Biology Reports - Prunus sibirica and Prunus mume are closely related plant species that differ in cold tolerance. Hybrids of P. sibirica and true mume, belonging to the apricot mei...     

Novel Role of HAX-1 in Neurons Protection After Spinal Cord Injury Involvement of IRE-1

Neurochemical Research - Spinal cord injury (SCI) is one of the diseases with high probability of causing disability in human beings, and there is no reliable treatment at present. Neuronal...     

C1188D mutation abolishes specific recognition between MLL1-CXXC domain and CpG site by inducing conformational switch of flexible N-terminal

Mixed lineage leukemia protein (MLL1 protein) recognizes the CpG site via its CXXC domain and is frequently associated with leukemia. The specific recognition is abolished by C1188D mutation, which also prevents MLL-related leukemia. In this paper, multiple molecular dynamic (MD) simulations were performed to investigate the mechanism of recognition and influences of C1188D mutation. Started from fully dissociated DNA and MLL1-CXXC domain, remarkably, the center of mass (COM) of MLL1-CXXC domain quickly concentrates on the vicinity of the CpG site in all 53 short MD simulations. Extended simulations of the wild type showed that the native complex formed in 500 ns among 4 of 53 simulations. In contrast, the C1188D mutant COM distributed broadly around the DNA and the native complex was not observed in any of the extended simulations. Simulations on the apo MLL1-CXXC domain further suggest that the wild type protein remained predominantly in an open form that closely resembles its structure in the native complex whereas C1188D mutant formed predominantly compact structures in which the N- terminal bends to D1188. This conformational switch hinders the formation of encounter complex, thus abolishes the recognition. Our study also provides clues to the study mechanism of recognition, by the CXXC domain from proteins like DNA methyltransferase and ten-eleven translocation enzymes.     

Identification of methylation-driven genes related to prognosis in clear-cell renal cell carcinoma

With the participation of the existing treatment methods, the prognosis of advanced clear-cell renal cell carcinoma (ccRCC) is poor. More evidence indicates the presence of methylation in ccRCC cancer cells, but there is a lack of studies on methylation-driven genes in ccRCC. We analyzed the open data of ccRCC in The Cancer Genome Atlas database to obtain ccRCC-related methylation-driven genes, and then carried out pathway enrichment, survival, and joint survival analyses. More important, we deeply explored the correlation between differential methylation sites and the expression of these driving genes. Finally, we screened 29 methylation-driven genes via MethylMix, of which six were significantly associated with the survival of ccRCC patients. This study demonstrated that the effect of hypermethylation or hypomethylation on prognosis is different, and the level of methylation of key methylation sites is associated with gene expression. We identified methylation-driven genes independently predicting prognosis in ccRCC, which offers theoretical support in bioinformatics for the study of methylation in ccRCC and a new perspective for the epigenetic study of ccRCC.