携带与未携带松材线虫的松墨天牛转录组差异表达基因分析

【目的】本研究旨在建立携带与未携带松材线虫Bursaphelenchus xylophilus的松墨天牛Monochamus alternatus成虫各组织的转录组数据库,揭示松墨天牛对松材线虫响应的转录组整体表达特征。【方法】以携带和未携带松材线虫的松墨天牛成虫的表皮、气管和脂肪体为材料,采用Illumina HiSeq^TM 2000测序平台开展转录组测序,利用Trinity软件对RNA-Seq数据进行从头组装,利用NCBI数据库进行基因注释。通过DEG-Seq分析携带和未携带松材线虫的松墨天牛成虫中的差异表达基因,对上调表达基因进行GO和KEGG代谢途径富集分析,并通过实时荧光定量PCR技术对部分差异表达的基因包括ENV, CDK1, HSP70-C, HSP70, HSP75, DUO, PABPN1和IGFP基因的表达水平进行验证。【结果】测序过滤后共获得55 059条单基因簇(unigene),平均长度为1 536 bp。将unigene与数据库中的序列进行BLASTX比对,成功注释24 354条unigenes,其中4 022条unigene在GO数据库中获得注释,6 098条unigene在KEGG数据库中获得注释。经过GO与KEGG富集分析显示,松墨天牛成虫携带松材线虫后,差异表达基因主要为与其气管中压力调节、组织与DNA修复、激素响应方面相关的基因。实时荧光定量PCR分析结果显示CDK1, HSP70, HSP75, DUO, PABPN1和IGFP基因的表达量在携带松材线虫的松墨天牛气管中相比未携带松材线虫的松墨天牛气管中的显著上调。【结论】本研究初步阐明松墨天牛携带松材线虫后转录组的整体表达模式,为进一步研究松墨天牛的基因功能及对松材线虫的胁迫响应过程奠定了基础。     

利用转录组测序筛选低切应力作用下人脐静脉内皮细胞的差异表达基因

目的:通过转录组测序分析获得不同切应力作用下人脐静脉内皮细胞的基因的表达谱,为进一步探索切应力影响内皮细胞形态和功能的机制提供依据。方法:以人脐静脉内皮细胞为材料,通过Streamer系统建立6通道可调控切应力的流体动力学细胞模型,以层流切应力(15 dynes/cm~2)为对照,以低切应力(0.1 dynes/cm~2)为实验组,分别加载细胞18 h。提取总RNA逆转录合成cDNA,建立文库,以二代测序平台Illumina HiSeq中进行扩增和测序。结果:序列比对结果显示,有19986个基因比对上,新转录本分析显示各组新转录本数约占总转录本数的50%。基因表达差异分析显示,较对照组,低切应力组表达上调基因983个,表达下调基因701个。GO分析显示,有18499个基因得到了归类注释,绝大多数基因富集到生物学过程。KEGG分析显示,富集Top20的信号通路与细胞周期、DNA复制和细胞分裂、细胞应激和凋亡等生物学过程相关。结论:低切应力作用不仅仅激活内皮细胞中细胞的增殖相关基因,同时也涉及到DNA损伤修复和凋亡相关基因。     

基于简化基因组的花生InDel标记开发和功能解析

InDel在基因组中的分布密度仅次于SNP,可作为动植物群体遗传分析、分子辅助育种等研究领域的有效分子标记。花生是世界范围内重要的油料作物之一。目前,花生栽培种全基因组已经公布,为准确挖掘花生基因组信息提供了重要参考。本研究通过169份花生核心种质的GBS(Genotyping-by-sequencing)测序和比对,共获得大小分布在1～14 bp范围内的10401个InDels。染色体Arahy.16上分布的InDels最多,达741个;而在染色体Arahy.08上分布的最少,有263个。参考基因组注释信息,仅有1167个InDels分布在功能基因相关区域。经GO注释,InDel分子功能主要包括催化活性(catalytic activity)和结合(binding);生物过程主要涉及代谢过程(metabolic process)、单组织过程(single-organism process)和细胞过程(cellular process)。经KEGG通路分析发现,InDels所在的基因区域的功能主要与代谢相关。本研究开发出全基因组水平的InDel标记,并做了相应功能分类和注释,为进一步分子验证和利用提供丰富的基因资源。     

大蹄蝠全基因组微卫星分布特征分析

脊椎动物基因组含有丰富的微卫星信息。本研究对翼手目动物中的大蹄蝠全基因组及其基因的微卫星分布特征进行分析,并对含有微卫星编码序列的基因进行注释分析。结果表明,大蹄蝠全基因组大小为2.24 Gb,共含有497 883个微卫星,其中,数量和比例最多的是单碱基和二碱基重复类型,分别有173 953个(34.94%)和222 591个(44.71%),相对丰度分别为77.78 loci/Mb和99.52 loci/Mb。微卫星数量从单碱基重复到六碱基重复单元最多的类型分别为(A)n、(AC)n、(TAT)n、(TTTA)n、(AACAA)n和(TATCTA)n,比例分别为95.14%、55.25%、38.41%、22.17%、48.68%和20.30%。不同基因区和基因间区的数量及丰度不同,其中基因间区的微卫星数量及其丰度最大,分别为322 666个和2 541.57 loci/Mb,编码区的微卫星数量及其丰度最小,分别为1 461个和461.98 loci/Mb。基因间区和全基因组的微卫星的分布特征相似。编码区最多的微卫星类型为三碱基重复单元,外显子最多的微卫星类型为单碱基、二碱基和三碱基重...     

Association of angiotensin-converting enzyme (ACE) gene insertion–deletion polymorphism with spondylarthropathies

Summary Low back pain (LBP) is a common medical problem. Interaction between genetic and environmental factors predisposes individuals to LBP even at an early age. Inflammatory back pain or spondylarthropathies include ankylosing spondylitis (AS), psoriatic arthritis (PSA), reactive arthritis enteropathic and undifferentiated arthropathies. Angiotensin-converting enzyme (ACE) plays an important role in circulatory homeostasis, physiology of vasculature and inflammation. The insertion–deletion (I/D) polymorphism of the ACE gene has been shown to determine the plasma and tissue levels of ACE especially in the synovial fluid. The aim of this study was to investigate an association between ACE gene I/D polymorphism and inflammatory back pain (spondylarthropathies) secondary to ankylosing spondylitis (AS), psoriatic arthritis, inflammatory bowel disease and undifferentiated spondylarthropathies. The prevalence of ACE gene I/D polymorphism genotypes was determined in 63 patients with inflammatory back pain by polymerase chain reaction (PCR) and compared with that in 111 healthy controls. Of the 63 patients studied, 45 (71.4%) were with AS, 13 (20.6%) were with PSA, 4 (6.3%) were with reactive arthropathy and 1 (1.6%) manifested undifferentiated arthropathy. There were 43 males and 20 females. Mean age of patients was 39.0 ± 11.36 years, age at onset of spondylarthropathy was 27.7 ± 7.49 years and disease duration was 10.3 ± 7.74 months. The controls were selected to match with the patients group in terms of gender ratio, age and ethnicity. The ACE gene polymorphism showed an overall significant difference between patients and controls (p = 0.050). When the ID and II genotype frequency was combined and compared with that for DD genotype amongst patient and control groups, a considerably higher incidence was detected for ID and II genotypes than the DD genotype in spondylarthropathy patients compared to that in the controls (p = 0.036). This study showed a significant association of the I-allele of ACE gene I/D polymorphism with spondylarthropathy in Kuwaiti Arabs.     

Mining functional gene modules linked with rheumatoid arthritis using a SNP-SNP network

The identification of functional gene modules that are derived from integration of information from different types of networks is a powerful strategy for interpreting the etiology of complex diseases such as rheumatoid arthritis (RA). Genetic variants are known to increase the risk of developing RA. Here, a novel method, the construction of a genetic network, was used to mine functional gene modules linked with RA. A polymorphism interaction analy-sis (PIA) algorithm was used to obtain cooperating single nucleotide polymorphisms (SNPs) that contribute to RA disease. The acquired SNP pairs were used to construct a SNP-SNP network. Sub-networks defined by hub SNPs were then extracted and turned into gene modules by mapping SNPs to genes using dbSNP database. We per-formed Gene Ontology (GO) analysis on each gene module, and some GO terms enriched in the gene modules can be used to investigate clustered gene function for better understanding RA pathogenesis. This method was applied to the Genetic Analysis Workshop 15 (GAW 15) RA dataset. The results show that genes involved in func-tional gene modules, such as CD160 (rs744877) and RUNX1 (rs2051179), are especially relevant to RA, which is supported by previous reports. Furthermore, the 43 SNPs involved in the identified gene modules were found to be the best classifiers when used as variables for sample classification.     

血管内介入治疗颈动脉、椎动脉狭窄的临床疗效和安全性

目的:研究血管内介入治疗颈动脉、椎动脉狭窄的临床疗效和安全性。方法:选择2011年3月~2016年3月在我院进行诊治的210例颈动脉和椎动脉狭窄患者狭窄程度在70%~99%之间,颈、椎动脉直径狭窄率超过70%,所有患者均进行了血管内介入治疗,观察患者的临床表现、DSA和血管超声检查结果和围手术期并发症,并进行随访。结果:经颈部血管听诊发现,有163例(77.62%)患者出现血管杂音,合并高血压103例(49.05%)、高脂血症123例(58.57%)、吸烟76例(36.19%)、糖尿病98例(46.67%)、高同型半胱氨酸血症13例(6.19%);DSA检查发现有126例患者为单纯颅外段颈动脉狭窄,51例患者为单纯椎动脉起始部狭窄,22例患者为颅外段颈动脉合并椎动脉狭窄;术后的颈、椎动脉平均狭窄率为(4.15±7.26)%,明显低于术前的(79.25±6.34)%(P0.05);所有患者均未出现严重神经系统并发症和手术期死亡;术后随访8~36个月,均未出现与支架相关的短暂性脑缺血和新发脑梗死。结论:血管内介入治疗颈动脉、椎动脉狭窄安全有效,具有较高的临床应用价值。     

糖尿病肝脏基因表达谱代谢学分析

目的:探讨糖尿病患者肝脏与正常对照肝脏基因表达谱的变化,并进行代谢通路生物信息学分析.方法:应用Affymetrix的Human Genome U133A array芯片检测糖尿病肝脏组织(n=2)和正常对照肝脏组织(n=2)的基因表达谱变化,通过DAVID分析平台对芯片监测到的表达上调的基因进行KEGG通路分析,并用RT-PCR验证部分基因的表达情况.结果:以比值大于2或小于-2为准,共有492条基因明显上调,820条基因明显下调;在差异表达明显的前20位基因中,涉及氧化应激、免疫炎症反应和脂代谢.KEC-G代谢通路分析显示:该差异表达基因谱符合2型糖尿病的发病机制,其差异表达明显基因的代谢通路涉及胰岛素信号通路、脂代谢、补体和凝血系统、糖代谢、粘附功能和细胞因子和受体的相互作用.RT-PCR证实差异表达明显基因SOD2mRNA和CRPmRNA确实表达明显上调.结论:糖尿病肝脏与正常肝脏组织基因表达谱的变化在代谢通路上主要表现为在糖、脂代谢和胰岛素信号通路、补体和凝血系统等的改变,肝脏在糖尿病发病机制中的作用可能与其参与糖脂代谢和胰岛素的作用异常有关.     

偏头痛相关酶和KEGG通路分析

搜集与偏头痛相关的编码酶的基因,利用KEGG通路分析目标基因的分布和功能,促进偏头痛遗传学研究和新药靶点研究。以＂gene name＂AND migraine检索PUBMED数据库,从原始文献中搜集并整理偏头痛相关酶基因数据,用DAVID在线分析工具对数据进行处理。搜索得到31个偏头痛酶基因,对7条KEGG代谢通路进行了分析：色氨酸代谢通路、酪氨酸代谢通路、精氨酸和脯氨酸代谢通路、叶酸一碳单位循环代谢通路、药物代谢通路、外源物质细胞色素P450代谢通路、肾素血管紧张素代谢通路。其中药物代谢通路包括9个药物,又以高选择性5-羟色胺重摄取抑制剂西酞普兰的应用前景最大。DDC、DBH、MTHFD1等6个偏头痛相关基因需要完善多态性研究。CYP450和单胺氧化酶在偏头痛的病理和治疗中都占有重要的地位。通过分析疾病相关酶基因的代谢通路,有助于了解疾病的分子病理基础,并为新药设计提供可靠靶点。     

Association between I/D polymorphism in the ACE gene and sarcoidosis in Turkish patients

Sarcoidosis is a chronic inflammatory disease with a complex pathogenesis and unknown etiology characterized by noncaseating granulomas that invade the lungs, eyes, liver and other organs. Insertion (I)/deletion (D) polymorphism in the gene encoding the angiotensin-converting enzyme (ACE) has been studied to examine the genetic predisposition to sarcoidosis in different populations, but the results have been inconsistent and inconclusive. This study aimed to determine the frequencies of the genotypes and alleles of I/D polymorphism in the ACE gene in Turkish patients as a distinct ethnic group and to investigate whether such polymorphism is associated with predisposition to sarcoidosis. Genomic DNA samples obtained from 154 individuals (70 patients with sarcoidosis and 84 healthy controls) were used in the study. The DNA was amplified using polymerase chain reactions using allele-specific primers. The amplified products were analyzed by 2 % agarose gel electrophoresis followed by UV transillumination. The allele frequencies and genotype distribution of the groups were analyzed using the Chi square test. There were no significant differences between the controls and sarcoidosis cases with respect to genotype distribution (χ² = 4.202, p = 0.122) and allele frequencies (χ² = 1.358, p = 0.244). Our results suggest that I/D polymorphism in the ACE gene does not cause a genetic predisposition to sarcoidosis in Turkish patients.     

全麻下颈动脉内膜剥脱术的麻醉体会

目的:评价颈动脉内膜剥脱术(CEA)麻醉疗效,以及经颅多普勒超声(TCD)、微血管多普勒超声(MVD)应用的价值,以及适合颈动脉内膜剥脱术的适合麻醉方法。方法:回顾性分析苏州大学附属一医院脑卒中中心2012年5月至2013年5月所进行的颈动脉内膜剥脱术治疗的19名颅外颈动脉狭窄患者的资料。患者临床症状均伴有不同程度的脑缺血症状。颈动脉狭窄程度2例中度狭窄,17例重度狭窄。所有手术操作均全麻下在显微镜下操作。1例采用补片成形。18例术中采用TCD及MVD监测下完成,1例未采用超声监测。结果:手术成功率为100%,无死亡率。术前脑缺血症状术后患者均有恢复。未发现过度灌注的并发症。麻醉效果达到预期目的。结论:颈动脉内膜剥脱术在多普勒超声MVD及TCD监测下治疗颅外颈动脉狭窄是一种安全、有效的措施;全身麻醉下行CEA手术安全可靠。     

Assessment of gene set analysis methods based on microarray data

Gene set analysis (GSA) incorporates biological information into statistical knowledge to identify gene sets differently expressed between two or more phenotypes. It allows us to gain an insight into the functional working mechanism of cells beyond the detection of differently expressed gene sets. In order to evaluate the competence of GSA approaches, three self-contained GSA approaches with different statistical methods were chosen; Category, Globaltest and Hotelling's T² together with their assayed power to identify the differences expressed via simulation and real microarray data. The Category does not take care of the correlation structure, while the other two deal with correlations.