基于高通量测序的全基因组关联研究策略

全基因组关联研究（Genome-wide association study, GWAS）是人类复杂疾病研究的重要组成部分之一,在群体水平检测全基因组范围的遗传变异与可观测性状间的遗传关联。传统的GWAS是以芯片（Array）技术获得高密度的遗传变异,尽管硕果累累,但也存在不少问题。如：所谓的“缺失的遗传力”,即利用关联分析检测达到全基因组水平显著的遗传变异位点只能解释小部分遗传力;在某些性状上不同研究的结果一致性较弱;显著关联的遗传变异位点的功能较难解释等。高通量测序技术,也称第二代测序（Next-generation sequencing, NGS）技术,可以快速、准确地产出高通量的变异位点数据,为解决以上问题提供了可行的方案。基于NGS技术的GWAS方法（NGS-GWAS）,可在一定程度上弥补传统GWAS的不足。文章对NGS-GWAS策略和方法进行了系统性调研,提出了目前较为可行的NGS-GWAS的实施策略和方法,并对NGS-GWAS如何应用于个体化医疗（Personalized medicine, PM）进行了展望。     

基于ChIP-Seq进行肿瘤睾丸抗原XAGE-1b基因表达蛋白的DNA结合位点鉴定

XAGE-1b（X antigen family member 1B）属于XAGE亚家族,是一种肿瘤 睾丸抗原（cancer/testis antigen,CTA）,表达于正常人睾丸组织和多种类型的肿瘤细胞中.本实验室前期研究发现,该基因在涎腺腺样囊性癌高转移细胞系中呈高表达.为了进一步研究XAGE-1b下游调控基因,本实验采用ChIP Seq技术筛查XAGE 1b蛋白质可能存在的DNA结合片段. 结果发现,XAGE-1b下游调控基因富集于细胞分裂（cell division,P-Value＝7.95e-04）、细胞周期调控（cell cycle,P-Value＝5.532e-03）、及癌症相关基因（GESA/MSigDB module_11,P-Value＝2.010e-06）中．同时发现,XAGE-1b下游调控多个基因的表达产物（NCBI/interactions 22827,P-Value＝4.678e-06）能与原癌基因c-Myc的启动子抑制蛋白PUF60发生蛋白质相互作用,并通过qPCR进行了验证．这些研究对阐明XAGE-1b在肿瘤细胞的增殖和转移中的作用有重要意义.     

flg22诱导的拟南芥转录组分析及芥子油苷代谢途径的变化

flg22是细菌鞭毛蛋白N端的一段保守性极高的区域,能够诱导植物天然的免疫反应,为全面了解植物在受到细菌性病原菌侵害后的系统响应,利用Illumina Hiseq2000对flg22处理和未处理的拟南芥幼苗进行转录组测序。对两组数据进行差异表达分析,共获得1 200个差异表达基因,包括290个下调基因和910个上调基因。对差异表达基因进行GO富集分析和KEGG pathway富集分析,结果显示,flg22处理后,拟南芥在能量代谢、氨基酸代谢及次生代谢产物的生物合成等方面产生了巨大变化。芥子油苷是一类在植物防御病原菌的天然免疫反应中起重要作用的次生代谢产物,因此对芥子油苷代谢途径的变化进行了深入分析。根据测序结果,Flg22处理后吲哚族芥子油苷合成途径的基因表达水平显著提高,而脂肪族芥子油苷代谢途径几乎没有变化,进一步对吲哚族芥子油苷合成途径的关键酶基因进行Real Time RT-PCR的分析,验证了测序结果的正确性,证明了吲哚族芥子油苷在植物抗病防御反应中的重要作用。这为深入理解病原菌诱导的植物防御性反应及吲哚族芥子油苷的抗病机制提供了大量参考数据。     

癌症基因组测序方案制定的研究进展

癌症的基因组测序对于癌症的预防、诊断、预后、治疗以及基础生物学研究都有巨大的潜在的应用价值,正是由于其方向广泛,所以基因组测序的方案制定对于实现特定的研究目标,就显得尤为重要。同时,了解了基因组测序方案制定的规则,也有助于评估如今快速增长的发表文献的正确性和重要性。主要论述高通量测序技术在癌症基因组测序中的实际应用,并讨论癌症基因组测序在方案设计和方法学上如何调整,才能更好地实现特定的研究目的。     

miRDOA:集数据存储与在线分析于一体的综合型microRNA数据库

miRNA(microRNA)是一类小的非编码RNA,普遍存在于动物、植物等多个物种中,研究表明在原生生物以及病毒中也有miRNA。miRNA在生物的成长、发育、细胞凋亡、神经紊乱、癌症等多个方面都起到至关重要的作用,miRNA还可作为Biomarker应用于癌症等疾病的诊断和治疗。miRDOA (miRNA Database and Online Analysis)数据库存储了二百多个物种的miRNA相关信息,提供了基本的浏览和搜索功能。用户可以通过物种来浏览miRNA相关数据,也可以通过miRNA、靶基因或者序列进行检索。除此之外,miRDOA还提供了在线分析模块,主要对高通量测序数据进行初步分析,在此基础上,添加了靶基因预测、表达谱数据差异分析,以及在线BLAST功能。miRDOA是一个完全免费的开源的数据库网站,并实时更新。     

Cloning and expression of swine myostatin gene and its application in animal immunization trial

An important performance trait target in swine breeding is the percentage of the lean meat within the total consumable pork. China has numerous indige-nous swine breeds, but the percentage of the lean meat percentage is generally low. Thus, increasing the per-centage of the lean meat would improve the pork qual-ity, which would have great importance in the devel-opment of our livestock industry as well as the opti-mization of the consumers’ dietary. Throughout the years researchers have been …     

Coral reef crisis in deep and shallow reefs: 30 years of constancy and change in reefs of Curacao and Bonaire

Coral reefs are thought to be in worldwide decline but available data are practically limited to reefs shallower than 25 m. Zooxanthellate coral communities in deep reefs (30–40 m) are relatively unstudied. Our question is: what is happening in deep reefs in terms of coral cover and coral mortality? We compare changes in species composition, coral mortality, and coral cover at Caribbean (Curacao and Bonaire) deep (30–40 m) and shallow reefs (10–20 m) using long-term (1973–2002) data from permanent photo quadrats. About 20 zooxanthellate coral species are common in the deep-reef communities, dominated by Agaricia sp., with coral cover up to 60%. In contrast with shallow reefs, there is no decrease in coral cover or number of coral colonies in deep reefs over the last 30 years. In deep reefs, non-agaricid species are decreasing but agaricid domination will be interrupted by natural catastrophic mortality such as deep coral bleaching and storms. Temperature is a vastly fluctuating variable in the deep-reef environment with extremely low temperatures possibly related to deep-reef bleaching. An erratum to this article can be found at     

R-ISSR as a new tool for genomic fingerprinting, mapping, and gene tagging

In the present study we propose and test the concept of R-ISSR, a new tool for genomic fingerprinting, mapping, and gene tagging. The concept is based on the fact that primers for inter-simple sequence repeat (ISSR) and random-amplified polymorphic DNA (RAPD) analysis elicit different genomic information, and the combined use of these 2 kinds of primers in the same polymerase chain reaction (PCR) reactions might reveal new genomic loci that could not be detected with either technique alone. The feasibility of this tool was first electronically simulated with sequence analysis software andArabidopsis chromosome sequence. Next, different combinations of ISSR and RAPD primers were applied in real PCR reactions to detect new genomic loci in 2 maize lines (Q319 and 1145). Sequencing gels were used to separate PCR products and showed good resolving ability in comparison with agarose gels. RAPD primers could be successfully used with ISSR primers for the detection of new genomic loci and applied in a new way for genomic mapping, fingerprinting, and gene tagging.     

中国北方汉族人群肌型肌酸激酶基因（CKMM）A/G多态研究

为研究中国汉族群体CKMM基因NcoI 酶切位点的遗传多态性以及该位点的具体多态形式, 采用PCR-RFLP技术, 对306例无血缘关系的健康中国北方汉人的染色体进行检测,并对3种基因型的扩增产物进行基因测序。用卡方检验对所得等位基因频率、基因型频率与其他种族进行比较。结果NcoI 位点多态性测序结果为：A/G颠换; 等位基因频率是A=86%,G=14%;基因型频率为：A/A=74%, A/G=24% , G/G=2%;经卡方检验符合Hardy－Weinberg遗传平衡定律;认为中国汉族群体CKMM 基因NcoI酶切位点具有遗传多态性。其基因型频率和等位基因频率在男女间没有显著性差异,与欧美人群相比有极显著差异,而与韩国人相比没有显著性差异。