miRNA在绝经后骨质疏松症肾阴虚证中的表达谱特征及生物信息学分析

目的探讨绝经后骨质疏松症(postmenopausal osteoporosis,PMOP)肾阴虚证miRNA的表达谱特征,及对差异表达的miRNA进行生物信息学分析。方法随机选择绝经后骨质疏松症受试者,中医辨证,分为3组:PMOP肾阴虚组3例,PMOP肾阳虚组3例,健康绝经后妇女3例作为对照组。采用人miRNA芯片检测外周血单个核细胞miRNA的表达水平。肾阴虚证组分别与其他两组比较,筛选共同的差异表达基因,实时荧光定量PCR验证芯片结果,并对差异表达的miRNA进行pathway分析及靶基因预测。结果肾阴虚证组与对照组、肾阳虚证组两组比较,筛选出20条共同差异表达miRNA;实时定量PCR验证hsa-miR-411-5p、hsa-miR-143-3p、hsa-miR-95-3p表达的结果与芯片结果相符;pathway分析结果显示,这些差异miRNA主要参与代谢通路、癌症通路、Rap1信号通路、粘着斑信号通路、PI3K-Akt、MAPK信号通路、钙离子信号通路、内质网蛋白加工、c GMP-PKG信号通路、Ras信号通路、Wnt信号通路的调控;结合多个数据库对差异表达的miRNA进行靶基因预测,最终筛选出9个靶基因(RC3H1、SOX11、FUT4、GABRA4、NUFIP2、ONECUT2、PHF20、PURB、ZNF148)。结论建立了PMOP肾阴虚证的miRNA基因表达谱,且这20个差异表达的miRNA可能通过调控PI3K-Akt、MAPK、Wnt等与骨代谢相关信号通路参与PMOP肾阴虚证的发生发展过程。     

Clinical verification of a novel urinary microRNA panal: 133b, -342 and -30 as biomarkers for diabetic nephropathy identified by bioinformatics analysis

BackgroundBecause microvascular disease is one of the major drivers of diabetic complications, early detection of diabetic nephropathy (DN) by assessing the expression of exosomal microRNAs (miRNAs) in DN patients and healthy controls, may be of clinical value. The aim of this study wasto identify a novel miRNA panel of DN by combining bioinformatics analysis of miRNA databases and clinical verification to evaluate the significance of this panel as urine biomarkers for type 2 diabetic nephropathy (T2DN).Patients and MethodsPublic miRNA databases e.g miro-Ontology and miRWalk were analyzed and a novel panel of 3 microRNAs was retrieved. Meanwhile, combinatorial target prediction algorithms were applied. Multiple case-matched normal were examined by quantative RT-PCR for differential expression in urine exosomes from 210 participants, and the three identified miRNAs were validated as DN biomarkers.ResultsWe found urinary exosomalmiR-133b, miR-342, and miR-30a were expressed at significantly elevated levels in T2DN patients (P < 0.001) compared to normal. Furthermore, high-level expression of the 3 miRNAs was associated withHbA1c,systolic-diastolic blood pressure, LDL, serum creatinine, urinary albumin creatinine ratio and estimated glomerular filtration rate(eGFR). Moreover, 39.3%, 19.6% and 17.9% of patients with normo-albuminuria had positive (miR-133b, miR-342 and miR-30a, respectively); indicating the possibility of molecular changes in these patients before onset of albuminuria.ConclusionWe have identified novel urinary exosomal miRNA biomarkers of DN which were altered not only in micro and macroalbuminuric groups but also in some normoalbuminuria cases prior to albuminuria.     

Proteomics by mass spectrometry-Go big or go home?

Mass spectrometry is an important technology for mapping composition and flux in whole proteomes. Over the last 5 years in particular, impressive gains in the depth of proteome coverage have been realized, particularly for model organisms. This review will provide an update on advancements in the key analytical techniques, methods and informatics directed towards whole proteome analysis by mass spectrometry. Practical issues involving sample requirements, analysis time and depth of coverage will be addressed, to gauge how useful data-driven approaches are for solving biological problems. Targeted mass spectrometric methods, based on selected reaction monitoring, are presented as a powerful alternative to data-driven methods. They offer robust, transferable protocols for hypothesis-directed monitoring of limited yet biologically significant tracts of any proteome.     

欧猥迭宫绦虫膜联蛋白E1基因的生物信息学分析

目的:从欧猥迭宫绦虫成虫cDNA文库中识别出膜联蛋白E1(Annexin E1)基因,并对其进行生物信息学分析和功能预测。方法:从欧猥迭宫绦虫cDNA文库中获取Annexin E1基因的核酸序列,应用NCBI、ExPASy等多种生物信息学在线分析工具结合Vector NTI Advance10、Geneious Pro等软件包,对所获基因及其编码蛋白的基本理化特征、亚细胞定位、保守功能域、抗原表位、二级结构及拓扑结构等进行预测,建立蛋白质三级空间结构模型及构建其分子进化树。结果:Annexin E1编码354个氨基酸残基,理论分子量为40168.0Da,具有4个完整的保守功能域。位于细胞内,无信号肽及跨膜结构,存在6个潜在抗原表位。二级结构主要以α螺旋为主,结构和功能有关的位点高度保守,具有多个磷酸化位点。在进化的过程中与绦虫类亲缘较近,而与脊椎类亲缘较远。结论:Annexin E1编码蛋白及潜在的抗原表位与宿主同源性低,可能作为研发新型免疫诊断方法的理想分子靶标。     

Preliminary safety assessment of a membrane-bound delta 9 desaturase candidate protein for transgenic oilseed crops

A gene encoding delta 9 desaturase (D9DS), an integral membrane protein, is being considered for incorporation into oilseed crops to reduce saturated fatty acids and thus improve human nutritional value. Typically, a safety assessment for transgenic crops involves purifying heterologously produced transgenic proteins in an active form for use in safety studies. Membrane-bound proteins have been very difficult to isolate in an active form due to their inherent physicochemical properties. Described here are methods used to derive enriched preparations of the active D9DS protein for use in early stage safety studies. Results of these studies, in combination with bioinformatic results and knowledge of the mode of action of the protein, along with a history of safe consumption of related proteins, provides a weight of evidence supporting the safety of the D9DS protein in food and feed.     

生物信息学方法优化依硫磷酸联合方案治疗骨髓增生异常综合征的应用研究

目的 采用生物信息学方法分析依硫磷酸治疗骨髓增生异常综合征(MDS)的机制,据此优化依硫磷酸联合方案治疗MDS.方法 (1)生物信息学方法:利用开放性的人类基因组表达数据库和互联网平台.①分析依硫磷酸调控人类基因组表达谱的变化和MDS人类基因组表达谱的特点;②筛选依硫磷酸可能作用的靶基因,据此预测联合用药的可行性;③采用人类基因组表达谱相似性分析的方法,预测可能具有治疗MDS作用的药物.(2)临床研究:以传统方法治疗无效的MDS患者(WHO分型)为对象,共18例患者(男17例,女1例),其中难治性贫血(RA)7例,难治性贫血伴环型铁粒幼细胞增多(RARS)2例,难治性血细胞减少症伴有多系发育异常(RCMD)9例,中位年龄79岁.采用依硫磷酸联合重组人红细胞生成素(rhEPO)方案治疗,具体用药为:依硫磷酸静滴0.4 g/d,每周5 d,连续4周,rhEPO皮下注射6000IU,每周3次.停药2周后评估疗效.结果 依硫磷酸对人类基因组2.6%的基因具有调控作用,其中主要是凋亡、细胞周期和分化有关的基因,包括促进EPO通路下游功能基因ELKI表达和抑制细胞周期D1表达的作用.依硫磷酸联合EPO方案治疗MDS,红系、粒系和血小板反应率分别为83.3%、66.7%和55.6%.结论 在筛选依硫磷酸调控的靶基因和优化骨髓增生异常综合征治疗方案方面,生物信息学方法具有方便、快捷、经济和有效的优点,可作为一种补充手段用于MDS发病机制和临床治疗的研究.     

乳腺癌中PBK/TOPK mRNA表达的临床意义及功能预测

目的通过生物信息学分析PDZ结合激酶/T-淋巴因子激活的杀伤细胞来源的蛋白激酶(PBK/TOPK)在乳腺癌(BRCA)中的表达及临床意义,并预测其潜在的分子通路和生物学功能。方法挖掘Oncomine数据库分析PBK/TOPK信使核糖核酸(mRNA)在不同癌症中的表达情况。下载癌症基因组图谱(TCGA)数据库BRCA和正常乳腺组织的RNA测序数据和临床信息,分析PBK/TOPK mRNA表达与临床特征的相关性。应用Kaplan-Meier Plotter数据库进行生存分析。通过筛选PBK/TOPK相关基因,并进行功能富集分析,预测PBK/TOPK在BRCA中的潜在分子通路和生物学功能。结果PBK/TOPK基因在BRCA组织中的表达显著高于正常乳腺组织(P<0.05),并与雌激素受体(ER)、孕激素受体(PR)、三阴性乳腺癌(TNBC)和绝经状态存在关联性(P<0.05)。生存分析结果显示,PBK/TOPK基因高表达提示BRCA预后不良(P<0.05)。功能富集分析显示PBK/TOPK相似基因主要涉及BRCA细胞分裂、细胞周期调节和微管细胞骨架形成等生物功能,参与BRCA细胞周期等信号通路。结论PBK/TOPK mRNA在BRCA组织中高表达,与BRCA患者预后不良密切相关,可能是BRCA潜在的生物标志物和治疗靶标。     

Web-based method for translating neurodevelopment from laboratory species to humans

Biomedical researchers and medical professionals are regularly required to compare a vast quantity of neurodevelopmental literature obtained from an assortment of mammals whose brains grow at diverse rates, including fast developing experimental rodent species and slower developing humans. In this article, we introduce a database-driven website, which was created to address this problem using statistical-based algorithms to integrate hundreds of empirically derived developing neural events in 10 mammalian species (http://translatingtime.net/). The site, based on a statistical model that has evolved over the past decade, currently incorporates 102 different neurodevelopmental events obtained from 10 species: hamsters, mice, rats, rabbits, spiny mice, guinea pigs, ferrets, cats, rhesus monkeys, and humans. Data are arranged in a Structured Query Language database, which allows comparative brain development measured in postconception days to be converted and accessed in real time, using Hypertext Preprocessor language. Algorithms applied to the database also allow predictions for dates of specific neurodevelopmental events where empirical data are not available, including for the human embryo and fetus. By designing a web-based portal, we seek to make these comparative data readily available to all those who need to efficiently estimate the timing of neurodevelopmental events in the human fetus, laboratory species, or across several different species. In an effort to further refine and expand the applicability of this database, we include a mechanism to submit additional data.     

Poxvirus protein evolution: Family wide assessment of possible horizontal gene transfer events

To investigate the evolutionary origins of proteins encoded by the Poxviridae family of viruses, we examined all poxvirus protein coding genes using a method of characterizing and visualizing the similarity between these proteins and taxonomic subsets of proteins in GenBank. Our analysis divides poxvirus proteins into categories based on their relative degree of similarity to two different taxonomic subsets of proteins such as all eukaryote vs. all virus (except poxvirus) proteins. As an example, this allows us to identify, based on high similarity to only eukaryote proteins, poxvirus proteins that may have been obtained by horizontal transfer from their hosts. Although this method alone does not definitively prove horizontal gene transfer, it allows us to provide an assessment of the possibility of horizontal gene transfer for every poxvirus protein. Potential candidates can then be individually studied in more detail during subsequent investigation.Results of our analysis demonstrate that in general, proteins encoded by members of the subfamily Chordopoxvirinae exhibit greater similarity to eukaryote proteins than to proteins of other virus families. In addition, our results reiterate the important role played by host gene capture in poxvirus evolution; highlight the functions of many genes poxviruses share with their hosts; and illustrate which host-like genes are present uniquely in poxviruses and which are also present in other virus families.     

蛋白质-蛋白质相互作用数据库的研究进展

随着人类蛋白质组学的飞速发展,出现了大量的蛋白质相互作用及其网络数据,因此寻找和预测蛋白质相互作用的生物信息学方法成了研究蛋白质互作必不可少的工具之一,本文主要从生物信息学角度对蛋白质相互作用数据库做一下简单的介绍,包括各数据库的来源、主要功能、应用范围、目前的发展状况及将来的发展方向等方面.