Epitranscriptomic technologies and analyses

RNA can interact with RNA-binding proteins(RBPs), mRNA, or other non-coding RNAs(ncRNAs) to form complex regulatory networks. High-throughput CLIP-seq, degradome-seq, and RNA-RNA interactome sequencing methods represent powerful approaches to identify biologically relevant ncRNA-target and protein-ncRNA interactions. However, assigning ncRNAs to their regulatory target genes or interacting RNA-binding proteins(RBPs) remains technically challenging. Chemical modifications to mRNA also play important roles in regulating gene expression. Investigation of the functional roles of these modifications relies highly on the detection methods used. RNA structure is also critical at nearly every step of the RNA life cycle. In this review, we summarize recent advances and limitations in CLIP technologies and discuss the computational challenges of and bioinformatics tools used for decoding the functions and regulatory networks of ncRNAs. We also summarize methods used to detect RNA modifications and to probe RNA structure.     

Oxidative stress induced by beta-amyloid peptide(1-42) is involved in the altered composition of cellular membrane lipids and the decreased expression of nicotinic receptors in human SH-SY5Y neuroblastoma cells

The neurotoxic effects and influence of beta-amyloid peptide (Aβ)_1–42 on membrane lipids and nicotinic acetylcholine receptors (nAChRs) in human SH-SY5Y neuroblastoma cells were investigated in parallel. Exposure of the cultured cells to varying concentrations of Aβ_1–42 evoked a significantly decrease in cellular reduction of MTT (3-(4,5-dimethylthiazol-2-yl)-2,5,diphenyl tetrazolium bromide), together with enhanced lipid peroxidation and protein oxidation. Significant reductions in the total contents of phospholipid and unbiquinone-10, as well as in the levels of the 3 and 7 subunit proteins of nAChRs were detected in cells exposed to Aβ_1–42. In contrast, such treatment had no effect on the total cellular content of cholesterol. Among these alterations, increased lipid peroxidation and decreased levels of cellular phospholipids were most sensitive to Aβ_1–42, occurring at lower concentrations. In addition, when SH-SY5Y cells were pretreated with the antioxidant Vitamin E, prior to the addition of Aβ_1–42, these alterations in neurotoxicity, oxidative stress, composition of membrane lipids and expression of nAChRs were partially prevented. These findings suggest that stimulation of lipid peroxidation by Aβ may be involved in eliciting the alterations in membrane lipid composition and the reduced expression of nAChRs associated with the pathogenesis of AD.     

Molecular dynamics simulation of chitinase I from Thermomyces lanuginosus SSBP to ensure optimal activity

Abstract

The fungal chitinase I obtained from Thermomyces lanuginosus SSBP, a thermophilic deuteromycete, has an optimum growth temperature and pH of 323.15 K and 6.5, respectively. This enzyme plays an important task in the defence mechanism of organisms against chitin-containing parasites by hydrolysing β-1, 4-linkages in chitin. It acts as both anti-fungal and biofouling agents, with some being thermostable and suitable for the industrial applications. Three-dimensional model of chitinase I enzyme was predicted and analysed using various bioinformatics tools. The structure of chitinase I exhibited a well-defined TIM barrel topology with an eight-stranded α/β domain. Structural analysis and folding studies at temperatures ranging from 300 to 375 K using 10 ns molecular dynamics simulations clearly showed the stability of the protein was evenly distributed even at higher temperatures, in accordance with the experimental results. We also carried out a number of 20 ns constant pH molecular dynamics simulations of chitinase I at a pH range 2–6 in a solvent. This work was aimed at establishing the optimum activity and stability profiles of chitinase I. We observed a strong conformational pH dependence of chitinase I and the enzyme retained their characteristic TIM barrel topology at low pH.     

O-糖基化位点预测及糖基化酶催化特点

O-糖链维持所连接蛋白质部分的空间构象。O-糖基化作为生物体内重要的生物过程,其起始步骤具有复杂的高度选择性,迄今为止还未发现固定的模式。人们通过比较已知O-糖基化部位周围的氨基酸序列,推测出O-糖基化位点的一些规律及其酶的催化特性。     

Inhibiting gene expression of alpha3 nicotinic receptor in SH-SY5Y cells with the effects on APP metabolism and antioxidation in Alzheimer's disease

In order to examine the effects of alpha3 nicotinic acetylcholine receptor (nAChR) in connection with the pathogenesis of Alzheimer's disease (AD), neuroblastoma (SH-SY5Y) cells were transfected with small interference RNAs (siRNAs) that target specifically towards alpha3 nAChR. The expressions of alpha3 nAChR mRNA and protein were measured by real-time PCR and Western blotting, respectively. The levels of the alpha-form of secreted amyloid precursor protein (alphaAPPs) and total-APP were determined by Western blotting. SH-SY5Y cells transfected with siRNA were then treated with 1muM beta-amyloid peptide (Abeta)(1-42), following which the levels of lipid peroxidation, the activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px), and the reduction rate of MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] were characterized by utilizing spectrophotometric procedures. As compared to controls, SH-SY5Y cells transfected with siRNA expressed the decreases in the levels of alpha3 nAChR mRNA and protein by 98% and 66% lower levels, respectively; exhibited reduced level of the alphaAPPs; and demonstrated enhanced lipid peroxidation, decreased rate of MTT reduction, and declined activities of SOD and GSH-Px. Inhibited gene expression of the alpha3 nAChR enhanced the toxicity exerted by Abeta. These results indicate that alpha3 nAChR may improve cleavage of APP by alpha-secretase, enhance antioxidation and inhibit the toxicity of Abeta, suggesting that the receptor might play an important role in AD.     

贵州布依族、仡佬族、仫佬族、毛南族、壮族Y-SNP的初步研究

为分析贵州布依族、仡佬族、仫佬族、毛南族、壮族父系遗传结构, 探讨其起源及迁徒。通过聚合酶链式反应-限制性内切酶长度多态性(PCR-RFLP)方法检测贵州境内5个民族10个SNP位点构成的Y染色体单倍型, 并以省内苗族为对照分析其父系遗传结构。结果显示5个民族集中于Y-SNP中H8单倍型, 苗族样本集中于Y-SNP中的H8、H11与H12单倍型。说明贵州省布依族、仡佬族、仫佬族、毛南族、壮族5个民族之间有密切联系, 且与国内其他地域有较大的遗传差异, 是一个相对独立的群体。     

贵州三都水族Y染色体上7个STR基因座的遗传多态性分析

采用多重PCR技术, 结合ABI PRISMTM 377 DNA Sequencer四色荧光标记进行基因扫描分型, 对中国贵州三都水族群体进行7个Y-STR基因座的多态性分析, 计算其基因频率、遗传多样性及单倍型多样性, 获取相应的遗传多态信息.结果显示: 在94个无关男性样本中, DYS19、DYS389Ⅰ、DYS389Ⅱ、DYS390、DYS391、DYS392、DYS393等基因座分别检出6, 4, 6, 2, 3, 5, 4种等位基因, 遗传多样性在0.124(DYS389Ⅰ)～0.630(DYS19)之间; 由此组成的单倍型为27种, 单倍型多样性0.868.此7个Y-STR基因座在贵州三都水族群体中具有较好的多态性, 单倍型具有较高的遗传多态.     

贵州瑶族3支系Y-DNA及线粒体DNA序列多态性分析

采用PCR－RFLP技术,通过观察由12个单核苷酸多态位点(SNPs)组成的Y染色体单倍型及由9个多态位点组成的线粒体DNA单倍型在贵州瑶族中的分布,分析贵州瑶族父系及母系遗传结构,探讨其起源及迁徙。结果显示,97份男性样本分别属于H7、H8、H9、H11 4种Y-DNA单倍型,苗瑶语系特异Y-DNA单倍型H7的平均频率为92.4%;通过对线粒体DNA基因分型,得到8种单倍型,可归入B4、B5、D4、D5和N*单倍型类群中,CoⅡ/tRNA^Lys区域间的9bp缺失平均频率为58.2%。结果提示贵州瑶族父系遗传结构单一,具有典型的苗瑶族群特征,又存在与其他族群的融合。母系遗传结构相对复杂,9 bp缺失是贵州瑶族的母系遗传结构特征。      

人多肽N-乙酰氨基半乳糖转移酶2基因反义RNA表达质粒的构建及其功能的初步研究

反义封闭人多肽N-乙酰氨基半乳糖转移酶2 (pp-GalNAc-T2)的基因表达, 对胃癌细胞SGC7901中转化生长因子-β1(TGF-β1)与基质金属蛋白酶2 (MMP2)基因表达及细胞增殖有影响.在对几株肿瘤细胞的pp-GalNAc-T2基因表达水平进行分析后, 以高表达pp-GalNAc-T2的人胃癌细胞株SGC7901的总RNA为模板, 利用RT-PCR方法扩增两段不同长度pp-GalNAc-T2基因片段, 构建反义表达载体转染胃癌细胞SGC7901, 通过Ｇ418筛选, 建立一系列旨在封闭胃癌细胞SGC7901 ppGalNAc-T2基因表达的亚细胞克隆.通过流式细胞术、荧光显微镜、RT-PCR及Western印迹检测反义封闭pp-GalNAc-T2基因RNA表达后胃癌细胞SGC7901增殖以及TGF-β1、MMP2表达水平的变化. 反义封闭pp-GalNAc-T2基因表达后, 胃癌细胞SGC7901 pp-GalNAc-T2的表达水平明显降低, 细胞分裂增殖减慢, 表明反义封闭pp-GalNAc-T2基因表达对胃癌细胞SGC7901的生长增殖有影响.结果还显示, 反义封闭pp-GalNAc-T2基因表达可使TGF-β1、MMP2基因在mRNA与蛋白质表达水平均增加, 提示pp-GalNAc-T2基因表达可能对胃癌细胞SGC7901浸润转移产生影响.以上结果表明, pp-GalNAc-T2基因在肿瘤细胞中广泛表达, 并可能与肿瘤的增殖及浸润转移相关.     

大鼠尾壳核头部一氧化氮合酶阳性神经元区域性分布和脑缺血后变化

用还原型尼克酰胺腺嘌呤二核苷酸黄递酶法，观察了大鼠尾壳核头部背内侧区，背外侧区，腹内侧区和腹外侧区一氧化氮合酶阳性神经元的分布和形态特征。并在夹闭双侧颈总动脉２小时后，观察这些区域一氧化氮合酶阳性神经元的变化。