大鼠心肌缺血预适应相关基因5的克隆与特性分析

目的采用生物信息学分析表达序列标签AW918640以获得其所代表基因的全长序列,并对该基因进行初步的特性分析。方法利用基因银行(GeneBank)数据库,通过BLAST比对等生物信息学方法进行电子克隆,采用逆转录聚合酶链反应和基因测序等技术进行鉴定,采用mapviewer软件进行染色体定位,ExPASy和SMART软件对获得的全长基因进行翻译和蛋白质功能结构分析。结果AW918640(基因银行登录号)为一个在大鼠心肌缺血预适应后3h表达升高的表达序列标签序列,通过电子克隆得到其所代表基因的全长,且为一新基因,经逆转录取合酶链反应和基因测序证实后,将其命名为心肌缺血预适应相关基因5(MIP5),并在基因银行数据库上登录,登录号为AY553870。心肌缺血预适应相关基因5最大开放读码框为909bp,编码302个氨基酸,含有6个kelch重复基序。结论心肌缺血预适应相关基因5为一与大鼠心肌缺血预适应相关的新基因。     

Emerging food allergens: Identification of polyphenol oxidase as an important allergen in eggplant (Solanum melongena L.)

Although many allergens have been detected in eggplant (Solanum melongena L.), their identity have not been elucidated. The aim of this study was to investigate whether polyphenol oxidase (PPO), an important eggplant enzyme, acts as an allergen. The proteins of eggplant peel extract were separated on phenyl-Sepharose (PS), and analyzed by skin prick test (SPT), ELISA and IgE-immunoblotting; the components were analyzed for PPO activity, presence of protein–bound copper, and recognition by rabbit polyclonal anti-sweet potato PPO antiserum. LC–MS/MS and in silico analysis were employed to identify the separated allergens and prediction of IgE epitopes. Eggplant allergens were separated into 5 components (PS1–PS5), of which component PS2 exhibited high specific PPO activity. SPT and ELISA with PPO-rich pool (PS2) were positive in all 6 eggplant-allergic subjects; the 43, 64 and 71 kDa proteins displayed strong IgE-binding ability. The 64 and 71 kDa IgE-binding proteins show PPO activity, presence of copper, and recognition by anti-sweet potato PPO antiserum, clearly identifying them as PPOs; the 43 kDa protein appears to be a degradation product of the 64 or 71 kDa proteins based on enzymic activity and recognition by PPO antiserum. The 64 kDa protein upon further resolution by SDS-PAGE displayed two components (identified as eggplant PPO1 and PPO4 by LC–MS/MS). Based on bioinformatics approaches, PPO4 has been identified as an allergen since it harbors an IgE epitope. This study clearly demonstrates that the 64 and 71 kDa allergens in eggplant peel are PPOs based on enzymic activity and recognition by PPO antiserum; the 64 kDa copper-containing protein is identified as one of the several eggplant allergens (Sola m PPO4). This is the first instance of polyphenol oxidase being identified as a new food allergen.     

睡眠剥夺相关基因的筛选与生物信息学分析

目的 从分子水平揭示睡眠剥夺对小鼠大脑海马体的影响,为睡眠剥夺相关疾病的基础研究和临床治疗提供新思路。 方法 从基因表达综合数据库(GEO)中下载睡眠剥夺相关基因芯片数据集,利用Qlucore Omics Explorer（QOE）3.0 软件、String、Panther 等工具对睡眠剥夺差异基因进行生物信息学分析。 结果 在101个差异表达基因所编码的蛋白中,有45个存在蛋白与蛋白的相互作用关系;其中涉及主要的生物学通路包括促性腺激素 释放激素受体通路、肾上腺素和去肾上腺素生物合成通路、细胞凋亡信号通路、亨廷顿舞蹈病通路和帕金森病通路等;主要涉及的生物学过程包括代谢过程、生物调节过程、发育过程、细胞定位过程、免疫系统过程和细胞凋亡过程等。 结论 通过生物信息学分析睡眠剥夺相关芯片数据,提示睡眠剥夺能够影响大脑海马体的基因表达,对相关基因的分析可为下一步实验提供有价值的线索。     

系统药理学原理、方法及在中医药中的应用

目的:建立科学有效的现代中药研究体系,是中医药现代化进程中亟待解决的关键问题之一,然而目前从系统和整体水平研究中药的理论和方法均不成熟。方法:本文将综述当前系统药理学的最新进展,阐明如何整合药效学、药动学以及基因、蛋白、药物网络分析等技术,形成一个完整的可供中药药理学、药效学预测和验证的技术体系。结果:重点从中药基础理论、复方解析、注射液的研究、老方优化和新药开发方面介绍系统药理学在中医药中的应用。结论:本文提出的系统药理学研究体系为中药的现代研究提供了新方法学,将有助于系统、深刻地从系统水平和分子水平揭示中药和机体的相互作用机制,从而指导中药新药研发。     

Decreased expression of CLCA2 and the correlating with immune infiltrates in patients with cervical squamous cell carcinoma: A bioinformatics analysis

ObjectiveCalcium-activated chloride channel 2 (CLCA2) is closely related to the invasion, metastasis, and prognosis of some common malignant tumors. The present study aimed to evaluate the role of CLCA2 in cervical squamous cell carcinoma (CESC) using bioinformatics analysis.Materials and methodsThe mRNA sequencing data and the corresponding clinical data were obtained from Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database respectively. Then univariate analysis of variance was used to analyze the differential mRNA expression of CLCA2 between normal, cervical Intraepithelial neoplasia (CIN), and CESC tissues and clinicopathological characteristics. The Gene Expression Profiling Interactive Analysis (GEPIA) was used to assess the association between CLCA2 and Disease-Free Survival (DFS), overall survival (OS). The Gene Set Enrichment Analysis (GSEA) was used to explore the associated signaling pathways. The Tumor Immune Estimation Resource (TIMER) was used to predict the potential biological roles of CLCA2 in tumor-immune of CESC.ResultsCLCA2 expression was significantly decreased in CESC tissues compared with normal and CIN tissues (P < 0.05). Meanwhile, obese patients had lower levels of CLCA2 expression than normal-weight CESC patients (P < 0.05). However, there was no significant difference in the expression level of CLCA2 in patients with different T stage, lymph node status, metastasis, and FIGO stage in CC(P > 0.05). The survival analysis indicated that for DFS, CESC with high CLCA2 expression was associated with better prognoses compared with those with low expression levels (P < 0.05). But for the OS, there was no difference. GSEA revealed that 4 pathways exhibited significant differential enrichment in the CLCA2 high-expression phenotype, including the P53 signaling pathway, the ERBB signaling pathway, the NOTCH signaling pathway, and the ubiquitin-mediated proteolysis. The TIMER reveals the expression of CLCA2 showed a significant inverse association with the number of B cells, Macrophage cells, and Dendritic Cell infiltration.ConclusionThe present study indicates that CLCA2 expression may be a potential prognostic marker for patients with CESC.     

人白细胞介素-36α蛋白的二级结构及其B细胞抗原表位的预测

目的预测并分析人白细胞介素-36α蛋白的二级结构及其潜在的B细胞抗原表位。方法以人IL-36α蛋白的氨基酸序列为基础,采用生物信息软件和互联网服务器预测人IL-36α蛋白的二级结构及其亲水性、可及性和柔韧性,根据预测结果综合分析IL-36α蛋白可能的B细胞抗原表位。结果IL-36α蛋白潜在的B细胞抗原表位位于N端8～12、33～38、111～116和143～149氨基酸区段。结论预测了IL-36α蛋白的二级结构和B细胞抗原表位,为进一步研究IL-36α的生物学活性部位及利用合成肽制备抗IL-36α的多克隆抗体提供了理论依据。     

生物信息学专业新生专业认知度调查分析

预设调查问卷对中南大学23名生物信息学专业新生的专业认知度进行调查,从专业录取意愿、重新选择专业意愿、专业了解程度、专业喜欢程度和专业预期等角度进行分析,提出有针对性的对策和建议,包括加强招生宣传开展新生入学教育、职业规划教育、适时进行心理沟通、丰富学习方式、建立合理的课程体系等方面。     

重组人 BMP-2 诱导 C3H10T1/2 间质干细胞定向成骨分化早期基因表达谱分析简

目的 研究间质干细胞早期定向成骨分化基因表达谱,为研究基因对早期成骨定向分化调控机制提供实验基础.方法 分别提取重组人骨形成蛋白2（rhBMP-2）诱导组和对照组C3H10T1/2细胞总RNA,进行扩增标记后,与ArraySTAR小鼠基因芯片杂交,应用生物信息学软件GeneSpring和GATHER对基因芯片数据进行分析.应用STRING在线软件对差异表达基因构建蛋白互作网络并进行网络分析.结果 C3H10T1/2早期成骨分化中,主要富集发育、器官形成等分子功能本体以及细胞因子-细胞因子受体作用信号通路.成骨分化1d和4d均上调表达基因42个,下调表达基因45个.网络分析研究表明：Egfr、Cxcl 12等信号分子参与调控rhBMP-2诱导成骨分化.结论 筛选的差异表达基因和信号分子对早期成骨分化调控具有重要作用,为进一步全面解析早期成骨定向分化提供实验基础.     

泛素结合酶基因生物信息学与功能分析

目的：生物信息学的发展为通过在线软件预测新基因的相关信息提供了众多有重要价值的参考信息。文中利用生物信息学方法预测泛素结合酶2S（ ubiquitin-conjugating enzyme 2S, UBE2S）生物学功能。方法以人肝癌HepG2细胞为材料,从构建的cDNA文库基因组中筛选和克隆了UBE2S基因。利用NCBI的BLAST在线分析工具分别对GenBank的非冗余核酸数据库和非冗余蛋白质数据库序列进行比对分析;采用NCBI ORF finder在线分析工具预测开放阅读框;利用ExPASy在线工具ProtParam统计基因中各种氨基酸含量,并预测理论分子量和等电点;应用ProtScale程序进行蛋白质的疏水性分析;蛋白质亚细胞定位采用在线工具（ nibb．ac．jp／form．html）预测,通过NCBI数据库GenBank分析蛋白质保守结构域;采用Protfun在线工具预测UBE2S的功能分类;采用同源模型服务软件SWISS-MODEL预测UBE2S的三维结构;采用MEGA5．05软件进行系统进化树的构建。结果 UBE2S基因编码241个氨基酸,预测相对分子质量为23770,理论等电点为8．81。跨膜结构域分析表明,UBE2S蛋白不含跨膜位点;亚细胞定位预测,UBE2S蛋白具有生长因子、离心通道、结构蛋白功能的概率为8．904、0．313和0．291。同源性比较分析结果表明,其碱基序列与已经报道的其他12个物种的相似率为90％～97％,且符合种属之间的进化关系。结论 UBE2S蛋白结构和功能的分析不仅丰富了其家族基因信息,还将为后续肝癌发生发展的分子机制实验研究奠定基础。