博奥生物芯片公司和美国昂飞公司开展战略合作

2005年4月26日,北京博奥生物芯片有限责任公司和美国加利福尼亚州的昂飞(Affymetrix)公司在人民大会堂召开新闻发布会,宣布两家公司建立战略合作关系。两家公司签署的启动性协议包括共同开发先进的、技术专有的,并可兼容基因芯片系统平台的个人化基因芯片扫描仪以及建立基因芯片服务项目。通过该项目,博奥将在其微阵列服务项目中提供美国昂飞公司的全线基因芯片产品和服务。两公司着力为全球市场共同开发针对科学研究和分子诊断领域的众多互补性产品,这些产品可能包括其它的仪器设备、试剂和服务。两家公司也会以博奥公司强大的工程化和生…     

基因芯片技术与微生物学

基因芯片技术作为生物芯片技术一个发展最完备的分支,近十年来,已经成为国内外研究的一个热点,基因芯片可以分为cDNA芯片和寡核苷酸芯片,cDNA芯片有多种制备方法,在基因表达相关研究方面具有重大价值;寡核苷酸芯片以美国Affymetrix公司的GeneChip为代表,主要应用于杂交测序,单核苷酸多态性分析和突变检测。本文分别对这两种芯片的制备,样品处理,杂交和信号检测分析技术作一综述。对近年来基因芯片技术在微生物学领域的应用进行了介绍。     

基因芯片筛选新疆维吾尔妇女宫颈癌差异表达基因

新疆南部维吾尔族聚居区是宫颈癌高发区. 本文旨在利用基因芯片技术筛选与维吾尔族妇女宫颈癌发生相关的基因. 首先,分别提取5例新疆维吾尔妇女宫颈癌和5例子宫肌瘤组织(对照)的mRNA,逆转录成cDNA,并用Cy3-dUTP标记子宫肌瘤组织的cDNA,用Cy5 dUTP标记宫颈癌组织的cDNA,制成芯片杂交探针.为筛选出宫颈癌组织中差异表达的基因,上述标记探针分别与含有20 000条人类基因的Affymetrix基因芯片进行杂交,杂交信号用GeneChip Scanner 3000扫描仪扫描,并用芯片图像分析软件(SAM software)分析扫描结果.筛选出的差异表达基因经GO(Gene Ontology)分析和KEGG（Kyoto Encyclopedia of Genes and Genomes）信号通路分析,确定其在宫颈癌中的作用.基因芯片筛选结果显示,在宫颈癌组织中发现2 758个差异表达基因,其中1 326个上调基因,1 432个下调基因.GO分析和KEGG信号通路分析表明,表达差异在两倍以上的基因涉及168个信号通路,包括细胞粘附分子、细胞周期以及MAPK和mTOR信号通路等.上述结果表明,基因芯片技术筛选出大量与宫颈癌发生相关的基因,其中表达差异显著的基因涉及细胞粘附分子、细胞周期和mTOR等信号通路.     

基因芯片在地下水污染研究中的应用北大核心

为了较系统地了解基因芯片在地下水污染研究中的应用进展,调研了基因芯片技术及其在地下水污染研究中应用的有关文献,简述了基因芯片原理、分类及实施流程,总结了系统发育寡核苷酸芯片和功能基因芯片在地下水污染研究中的最新应用进展,探讨了基因芯片检测性能、数据分析和应用等方面存在的问题和措施,在基因芯片性能改进和应用方面提出了进一步研究的方向。     

基因芯片在地下水污染研究中的应用

为了较系统地了解基因芯片在地下水污染研究中的应用进展,调研了基因芯片技术及其在地下水污染研究中应用的有关文献,简述了基因芯片原理、分类及实施流程,总结了系统发育寡核苷酸芯片和功能基因芯片在地下水污染研究中的最新应用进展,探讨了基因芯片检测性能、数据分析和应用等方面存在的问题和措施,在基因芯片性能改进和应用方面提出了进一步研究的方向。     

制备炭疽芽胞杆菌检测基因芯片的初步研究

建立制备炭疽芽胞杆菌检测基因芯片的技术,并探讨研制检测炭疽芽胞杆菌基因芯片的方法。酶切炭疽芽胞杆菌的毒素质粒和荚膜质粒,通过建立质粒DNA文库的方法获取探针,并打印在经过氨基化修饰的玻片上,制成用于炭疽芽胞杆菌检测的基因芯片。收集了290个阳性克隆探针,制备了检测炭疽芽胞杆菌的基因芯片。提取炭疽芽胞杆菌质粒DNA与基因芯片杂交,经ScanArray Lite芯片阅读仪扫描得到初步的杂交荧光图像。通过分析探针的杂交信号初步筛选出273个基因片段作为芯片下一步研究的探针。     

纯化探针降低基因芯片杂交结果的背景

研究探针的纯化对基因芯片杂交结果的影响。将乙醇沉淀的探针和用DNA纯化试剂盒纯化的探针分别与基因芯片交,在同等条件下进行杂交后清洗和芯片扫描检测。结果表明,纯化的探针与基因芯片杂交结果的背景低,而未纯化的探针背景强,阳性信号界限比较模糊。运用基因芯片进行基因表达谱研究,要求杂交检测的结果必须低背景。探针的纯化是影响芯片杂交结果的一个重要因素。     

基于异源cDNA基因芯片杂交的鳜鱼肌肉组织基因表达谱初步分析

cDNA基因芯片技术已广泛应用于生物物种间功能基因组和表达谱学研究。然而,鱼类基因芯片开发和应用相对落后。为了筛选与肉质性状相关功能基因,本研究首次试用异源斑马鱼基因cDNA芯片,对两种肉质性状明显差异的鳜鱼和鲢鱼肌肉组织中基因表达进行了比较分析。从两种鱼肌肉组织中提取总RNA,经Biotin荧光标记与拥有15617个cDNA片段的斑马鱼基因芯片（Affymetrix）杂交后,检测出375个表达基因。与鲢鱼比较,鳜鱼肌肉组织锁定的基因中有180个上调表达基因和195个下调表达基因。在鳜鱼肌肉组织180个上调基因中,49个为已知功能基因,131个为未知功能基因。根据基因文库同源功能基因分析,我们将49个已知上调基因按功能大约分为七大类,其中与肌肉结构相关基因包括肌球蛋白重链基因（MYH）、肌纤维间连接基因和细胞骨架结构基因等。同时,我们对与肉质结构性状密切相关的功能基因进行了分析,并结合与鳜鱼优良肉质结构和功能基因表达关系进行了讨论。     

高密度基因芯片探针布局方法

为了提高基因芯片制备质量和检测的准确性,提出两种基因芯片布局方法,一是分子印章凸点优化布局方法,另一种是基于探针杂交解链温度的梯度场布局方法。利用上述两种方法对所设计的高密度基因芯片进行控针布局实验,结果表明,第一种方法能够使制备基因芯片的分子印章上凸点均匀分布,解决误压印问题,从而提高基因芯片的制备质量;而第二种方法能够使基因芯片上的探针按照杂交解链温度有序地组织起来,从而提高基因芯片对碱基错配的辨别力。     

利用基因芯片技术筛选HIV-1F亚型基因限制性显示探针

为筛选限制性显示技术制备的HIV 1F亚型基因探针 ,应用基因芯片打印仪将其有序地打印在玻片上制备基因芯片 .在随机引物延伸的过程中进行HIV样品的荧光标记 ,然后与芯片进行杂交 .杂交后清洗玻片并干燥 ,对芯片进行扫描 ,分析各探针的杂交信号 .从中筛选了 14个基因片段作为芯片下一步研究的探针 .实验证明 ,限制性显示技术是一种制备基因芯片探针的实用方法     

A web-based platform for rice microarray annotation and data analysis

Rice (Oryza sativa) feeds over half of the global population. A web-based integrated platform for rice microarray annotation and data analysis in various biological contexts is presented, which provides a convenient query for comprehensive annotation compared with similar databases. Coupled with existing rice microarray data, it provides online analysis methods from the perspective of bioinformatics. This comprehensive bioinformatics analysis platform is composed of five modules, including data retrieval, microarray annotation, sequence analysis, results visualization and data analysis. The BioChip module facilitates the retrieval of microarray data information via identifiers of “Probe Set ID”, “Locus ID” and “Analysis Name”. The BioAnno module is used to annotate the gene or probe set based on the gene function, the domain information, the KEGG biochemical and regulatory pathways and the potential microRNA which regulates the genes. The BioSeq module lists all of the related sequence information by a microarray probe set. The BioView module provides various visual results for the microarray data. The BioAnaly module is used to analyze the rice microarray’s data set.     

Genomic microarrays in the spotlight

Microarray-based comparative genomic hybridization (array-CGH) has emerged as a revolutionary platform, enabling the high-resolution detection of DNA copy number aberrations. In this article we outline the use and limitations of genomic clones, cDNA clones and PCR products as targets for genomic microarray construction. Furthermore, the applications and future aspects of these arrays for DNA copy number analysis in research and diagnostics, epigenetic profiling and gene annotation are discussed. These recent developments of genomic microarrays mark only the beginning of a new generation of high-resolution and high-throughput tools for genetic analysis.     

Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays

Background  

Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions for routine data analysis.     

DNA microarray technology in toxicogenomics of aquatic models: methods and applications

Toxicogenomics represents the merging of toxicology with genomics and bioinformatics to investigate biological functions of genome in response to environmental contaminants. Aquatic species have traditionally been used as models in toxicology to characterize the actions of environmental stresses. Recent completion of the DNA sequencing for several fish species has spurred the development of DNA microarrays allowing investigators access to toxicogenomic approaches. However, since microarray technology is thus far limited to only a few aquatic species and derivation of biological meaning from microarray data is highly dependent on statistical arguments, the full potential of microarray in aquatic species research has yet to be realized. Herein we review some of the issues related to construction, probe design, statistical and bioinformatical data analyses, and current applications of DNA microarrays. As a model a recently developed medaka (Oryzias latipes) oligonucleotide microarray was described to highlight some of the issues related to array technology and its application in aquatic species exposed to hypoxia. Although there are known non-biological variations present in microarray data, it remains unquestionable that array technology will have a great impact on aquatic toxicology. Microarray applications in aquatic toxicogenomics will range from the discovery of diagnostic biomarkers, to establishment of stress-specific signatures and molecular pathways hallmarking the adaptation to new environmental conditions.     

dsDNA芯片的DNA结合蛋白质计算机模拟系统

dsDNA芯片(double-stranded DNA microarray)是用于DNA结合蛋白质表达研究的新技术,应用一种新的dsDNA芯片制作方法,研究了dsDNA探针设计,开发了相应的计算机模拟系统—DBP软件。可实现芯片上dsDNA探针的选取以及DNA结合蛋白质检测的实验过程模拟,功能包括模拟酶切、模拟电泳、模拟杂交等实验环节。DBP系统包括了可以不断完善的DNA结合蛋白质数据库。对研究dsDNA芯片,检测和分析在生物 体中DNA结合蛋白质的表达谱,揭示细胞的分化和凋亡、信号转导、DNA转录调控的分子机制有重要意义。     

Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary

MOTIVATION: High-throughput technologies such as DNA sequencing and microarrays have created the need for automated annotation of large sets of genes, including whole genomes, and automated identification of pathways. Ontologies, such as the popular Gene Ontology (GO), provide a common controlled vocabulary for these types of automated analysis. Yet, while GO offers tremendous value, it also has certain limitations such as the lack of direct association with pathways. RESULTS: We demonstrated the use of the KEGG Orthology (KO), part of the KEGG suite of resources, as an alternative controlled vocabulary for automated annotation and pathway identification. We developed a KO-Based Annotation System (KOBAS) that can automatically annotate a set of sequences with KO terms and identify both the most frequent and the statistically significantly enriched pathways. Results from both whole genome and microarray gene cluster annotations with KOBAS are comparable and complementary to known annotations. KOBAS is a freely available stand-alone Python program that can contribute significantly to genome annotation and microarray analysis.     

Mismatch formation in solution and on DNA microarrays: how modified nucleosides can overcome shortcomings of imperfect hybridization caused by oligonucleotide composition and base pairing

The DNA microarray technology is a well-established and widely used technology although it has several drawbacks. The accurate molecular recognition of the canonical nucleobases of probe and target is the basis for reliable results obtained from microarray hybridization experiments. However, the great flexibility of base pairs within the DNA molecule allows the formation of various secondary structures incorporating Watson-Crick base pairs as well as non-canonical base pair motifs, thus becoming a source of inaccuracy and inconsistence. The first part of this report provides an overview of unusual base pair motifs formed during molecular DNA interaction in solution highlighting selected secondary structures employing non-Watson-Crick base pairs. The same mispairing phenomena obtained in solution are expected to occur for immobilized probe molecules as well as for target oligonucleotides employed in microarray hybridization experiments the effect of base pairing and oligonucleotide composition on hybridization is considered. The incorporation of nucleoside derivatives as close shape mimics of the four canonical nucleosides into the probe and target oligonucleotides is discussed as a chemical tool to resolve unwanted mispairing. The second part focuses non-Watson-Crick base pairing during hybridization performed on microarrays. This is exemplified for the unusual stable dG.dA base pair.