乙型脑炎病毒寡核苷酸基因芯片研究

目的:制备检测乙型脑炎病毒寡核苷酸(oligo)基因芯片。方法:应用生物信息学软件设计60-meroligo探针用于制备基因芯片,乙型脑炎病毒(JEV)基因片段经限制性显示技术扩增标记,用于芯片杂交,清洗和干燥后对芯片进行扫描和数据分析。结果:大部分oligo探针都能特异性与相应样品杂交,呈现阳性荧光信号,而阴性对照和空白对照则基本不能检测到荧光信号。结论:实验中建立的oligo基因芯片检测病原体方法可行,具有应用于临床诊断的前景。     

RNAi干扰对K562细胞表达谱的影响

目的 联合运用RNAi技术和cDNA表达谱芯片研究干扰c-mye对K562细胞表达谱的影响。方法 经过RT-PCR和流武细胞仪检测。筛选出干扰效果最好的siRNAs,经Lipofectamine^TM 2000脂质体法转染K562细胞,提取总RNA,逆转录为cDNA,荧光标记后与K562表达谱芯片杂交。结果 经扫描、分析杂交结果,有455个基因表达下调,有12个基因表达上调。结论 基因芯片和RNAi是分析基因功能的有力工具,也是发现新的肿瘤治疗靶标的有效方法。     

青蒿素作用前后K562细胞基因表达谱的改变

目的:利用基因表达谱芯片研究青蒿素对体外培养的人红白血病K562细胞基因表达谱的影响.方法:青蒿素处理K562细胞24 h后,分别提取处理组和对照组细胞的总RNA,将两组RNA纯化为mRNA,逆转录成cDNA,用Cy3和Cv5两种不同的荧光染料进行线性扩增标记,与人全基因组基因表达谱芯片杂交,采用生物信息学方法分析青蒿素处理前后K562细胞基因表达谱的改变.结果:总共发现差异基因238个,其中上调基因136个,下调基因102个,并对其进行生物学功能分类.结论:应用全基因组表达谱芯片并结合Panther生物学软件分析差异表达基因,青蒿素作用K562细胞主要是通过细胞毒作用诱导细胞凋亡,而抑制细胞生长作用并不明显.     

ST1571诱导慢性髓系白血病K562细胞凋亡信号通路的研究

本研究应用基因芯片探讨酪氨酸激酶抑制剂（STI571）对K562细胞生长、增殖的影响，研究STI571诱导细胞凋亡过程中基因表达的变化及STI571诱导K562细胞凋亡的机制。用RD—PCR技术制备基因芯片探针，然后制成飚62细胞表达谱芯片；用相差显微镜观察K562细胞在STI571处理前后的形态变化；用MIT法检测K562细胞的凋亡，用制备的K562细胞表达谱芯片分析基因表达水平。结果表明，在体外培养条件下用1．0μmol／L的STI571处理K562细胞达到一定时间（24小时）后，K562细胞生长明显变缓，出现凋亡细胞的特征。用自制的l（562细胞基因表达谱芯片检测显示，STI571诱导K562细胞凋亡前后的基因表达有差异。杂交检测后发现，经STI571诱导后基因表达下调的基因有9个，表达上调的基因有4个。这些表达变化的基因主要包括细胞周期相关基因、细胞代谢通路相关基因、信号转导和转录调节相关基因及抗凋亡基因。结论：STI571能有效抑制K562细胞生长，诱导K562细胞凋亡；筛选获得的靶基因在K562细胞恶性转化过程中发挥了重要作用，这为药物靶基因的筛选提供了理论基础。     

基因芯片在妇科肿瘤中的应用

基因芯片的出现仅 5年左右 ,但它的开发和应用研究却进展神速。基因芯片又称ＤＮＡ微阵列 ,或ＤＮＡ芯片 ,是指固着在固相载体上的高密度ＤＮＡ微点阵。其原理是探针与靶基因的互补杂交。具体说就是用硅片、玻璃、尼龙膜表面做固相载体 ,有规律地合成数万个代表不同基因的寡核苷酸探针 ,然后将待测样品中的ＤＮＡ、ＲＮＡ、或ｃＤＮＡ用同位素或荧光物标记后 ,与固相载体上的探针进行杂交 ,通过放射自显影或荧光共聚焦显微镜扫描 ,利用计算机对每一个探针上的杂交信号作检测、分析 ,从而显示待测样品大量基因表达图谱。目前基因芯片已被应用…     

基因芯片在人白细胞抗原A19组基因快速分型中的应用研究

目的　建立基因芯片快速检测人白细胞抗原A1 9(HLA A1 9)分型方法。方法　利用基因芯片技术 ,根据HLA A位点不同基因亚型的独特序列设计探针 ,制成分型芯片 ;待检测样品经聚合酶链反应 (PCR)标记上荧光之后 ,与芯片进行杂交 ,根据杂交产生的荧光信号值 ,分析确定样品A位点的基因亚型。对 1 2 0份移植供受者的HLA A基因分型 ,并对 1 1份样品作基因测序。结果　仅用 2 5h ,HLA A1 9基因分型芯片可准确分辨出A1 9抗原 9大类 (A2 90 1、A2 9XX、A30 0 1、A30 0 6、A30XX、A31、A32、A34和A74 )。结论　HLA A1 9组基因芯片分型方法 ,分辨率高、特异性强、重复性好、操作简便、结果直观 ,适于临床应用     

伊马替尼耐药K562/G的microRNA表达谱分析及与FOXO3/Bcl-6信号通路关系的研究

目的:探讨CML耐药细胞株K562/G耐药相关的FOXO3/Bcl-6信号通路及相关microRNA(miRNA)机制。方法:采用MTT法检测伊马替尼对K562/G的耐药性;采用Western blot法检测耐药株和敏感株细胞中FOXO3和Bcl-6蛋白的表达情况,实时荧光定量PCR检测FOXO3及Bcl-6 mRNA的表达。运用miRNA芯片技术筛查K562与K562/G细胞之间差异表达的miRNA,进一步筛选FOXO3/Bcl-6信号通路的靶向miRNA。结果:K562/G较K562细胞株的FOXO3及Bcl-6蛋白表达均明显升高(P<0.01);Bcl-6 mRNA的表达水平无明显差异,而K562/G细胞中FOXO3 mRNA表达明显升高(P<0.05)。miRNA芯片结果显示,K562/G与K562细胞之间有109条miRNA存在显著的差异,其中上调miRNA为81个,下调miRNA有28个。经生物信息学反向预测,其中miR-6718-5p、miR-5195-5p、miR-4711-3p、miR-4763-5p、miR-4664-5p和miR-3176与该信号通路相关。结论:伊马替尼耐药与FOXO3/Bcl-6信号通路相关,并且K562/G与K562细胞存在miRNA表达显著差异。     

基因芯片技术在肺系病证研究中的应用

基因芯片(Genechip),又称DNA芯片,DNA微阵列(DNAmicroarray),是上世纪90年代兴起的一项前沿生物技术,是将大量的DNA片段按预先设计的排列方式固化在载体表面如硅片、玻片,并以次为探针,在一定的条件下,与样品中待测的靶基因片段杂交,通过检测杂交后的信号,实现对靶基因的快速检测。基因芯片可以分为很多种类,常见并广泛应用的有cDNA微阵列(cDNAmicroarray)和寡核苷酸阵列芯片(Oligo microarray)2种。[1]基因芯片技术以一种系统、整体的方法进行研究,打破了“一种疾病,一种基因”的陈旧模式,整体宏观地研究生物体基因的表达及功能。…     

基因芯片技术应用和展望

基因芯片 (GeneChip)通常指DNA芯片 ,其基本原理是将指大量寡核苷酸分子固定于支持物上 ,然后与标记的样品进行杂交 ,通过检测杂交信号的强弱进而判断样品中靶分子的数量。基因芯片的概念现已泛化到生物芯片 (biochip)、微阵列 (MICroarray)、DNA芯片 (DNAchip) ,甚至蛋白芯片。基因芯片集成了探针固相原位合成技术、照相平板印刷技术、高分子合成技术、精密控制技术和激光共聚焦显微技术 ,使得合成、固定高密度的数以万计的探针分子以及对杂交信号进行实时、灵敏、准确的检测分析变得切实可行。基因芯片技术在分子生物学研究领域、医…     

K562细胞及其耐药细胞株K562/A02细胞白血病耐药相关microRNA筛选

目的 通过检测慢性粒细胞白血病急变细胞系K562及其阿霉素耐药株K562/A02的微小RNA(microRNA、miR)表达差异,探讨microRNA与白血病化疗耐药的关系.方法 MTT法检测K562/A02及其亲本细胞系K562的耐药性能;流式细胞术检测K562与K562/A02细胞的P-gp表达;运用microRNA芯片技术筛查K562与K562/A02细胞之间差异表达的microRNA,随后用实时荧光定量RT-PCR方法进一步证实.结果 阿霉素耐药株K562/A02相对于其亲本细胞系K562对阿霉素的耐药倍数为180倍;K562细胞P-gp的表达率为0.2%,K562/A02细胞P-gp的表达率为86%;microRNA芯片结果显示K562/A02与K562细胞之间有22种microRNA表达存在显著的差异(P<0.01),表达差异在2倍以上的有9种,其中miR-221、miR-155、miR-451在K562/A02细胞表达上调,而miR-98、miR-181a、let-7f、miR-424、let-7g和miR-563则表达下调.实时荧光定量RT-PCR进一步证实了上述结果,并显示miR-451、miR-155、miR-221、let-7f、miR-424在两种细胞中表达差异显著.结论 K562/A02与K562细胞存在microRNA表达差异,其中miR-451、miR-155和miR-221在K562/A02中表达显著上调,而let-7f、miR-424则显著下调,提示microRNA可能参与白血病耐药形成,差异表达的microRNA可能为逆转白血病耐药提供新的作用靶点.     

Development and applications of a BRAF oligonucleotide microarray

We herein describe the development of a sensitive microarray hybridization method called competitive DNA hybridization (CDH) and its use for analysis of BRAF somatic mutations. These mutations have been identified in many human cancers, and fast, reliable BRAF mutation detection may one day facilitate directed therapy of BRAF-mutated tumors. Our fast, reliable mutation detection by CDH is based on the principle that competition among multiple fluorescent-labeled samples for binding to shared wild-type sequences should reduce nonspecific results and increase the positive signals of unshared mutated sequences. The positive signals can then be discriminated based on the labeling of each sample (ie, with Cy3, Cy5, or Alexa-594). For testing of this method, we developed a BRAF oligonucleotide microarray containing 65 mutation types (more than 95% of the known BRAF mutations) and validated this microarray with 20 colorectal cancer tissues/cancer cell lines with BRAF mutations and 60 BRAF-negative samples. In sum, we were able to screen up to nine cancer samples on a single BRAF microarray (three per CDH on three regions per slide), indicating that this method may dramatically decrease the experimental time, cost, and effort of mutation detection in BRAF and other genes amenable to microarray analysis.     

丙型肝炎病毒1b亚型诊断芯片的制备与实验室研究

目的建立一种简单有效的制备、筛选丙型肝炎病毒(HCV)1b亚型cDNA基因芯片探针的技术。方法应用cDNA文库法制备芯片探针，限制性内切酶Sau3AI消化HCV-1b全长cDNA。所得的酶切片段在72℃补平加单个碱基A，然后与pMD18-T载体连接，AT克隆，用载体引物进行PCR初步鉴定，并测序。将筛选出的片段打印在氨基修饰的玻片上制备成cDNA芯片并进行杂交验证分析。样品标记采用限制性显示PCR(Restriction Display PCR RD—PCR)技术。结果应用cDNA文库法，共得到22大小相对一致(250—750bp)的基因片段，序列分析表明，均属于HCV—1b基因，可以作为诊断芯片探针；芯片杂交结果显示，样品和诊断基因芯片杂交的敏感性和特异性均佳。结论用cDNA文库法收集片段是一种快速、简便制备芯片探针的实用方法；制备的诊断芯片可以用于检测HCV-1b RNA，具有敏感、检测结果较为可靠的优点。     

Detection of multiple human herpes viruses by DNA microarray technology.

BACKGROUND: The detailed characterization of virus DNA is a challenge, and the genotyping that has been achieved to date has only been possible because researchers have sent a great deal of time and effort to do so. Instead of the simultaneous detection of hundreds of viruses on a single high-density DNA-chip at very high costs per chip, we present here an alternative approach using a well-designed and tailored microarray which can establish whether or not a handful of viral genes are present in a clinical sample. METHODS: In this study we applied a new concept of microarray-based, optimized and robust biochemistry for molecular diagnostics of the herpesviruses. For comparison, all samples were genotyped using standard procedures. RESULTS: The biochemical procedure of a knowledge-based, low-density microarray was established based on the molecular diagnostics of human herpes viruses: herpes simplex virus (HSV) HSV-1, HSV-2, varicella zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), and HHV-6. The study attempted to optimize parameters of microarray design, surface chemistry, oligonucleotide probe spotting, sample labeling and DNA hybridization to the developed DNA microarray. The results of 12 900 hybridization reactions on about 150 configured herpes virus microarrays showed that the established microarray-based typing procedure was reproducible, virus-specific and sufficiently sensitive with a lower limit of 100 viral copies per mL sample. CONCLUSIONS: The developed method utilizes low-fluorescence background coverslips, epoxy surface chemistry, standardized oligonucleotide probe spotting, PCR-labeling with Cy3 of isolated DNA, array hybridization, and detecting of specific spot fluorescence by an automatic microarray reader. We expect the configured microarray approach to be the method for high-throughput associated studies on human herpes viruses.     

基因芯片检测输血传播病毒方法的实验研究

目的建立基因芯片快速检测经输血传播病毒核酸的方法,进而探讨该方法用于检测临床标本的可行性。方法通过PCR获得TTV病毒ORF1基因的DNA片段,克隆,从重组质粒扩增DNA片段,并点到玻璃载体上,制成芯片。与TTV病毒、甲型肝炎病毒、乙型肝炎病毒及戊型肝炎等病毒的PCR产物进行杂交,以检测探针的特异性。结果该基因芯片探针仅与TTV毒株的PCR产物杂交呈阳性,与对照病毒的PCR产物杂交呈阴性。敏感性试验显示,用该方法检测了27份疑似TTV临床病料,22份阳性;而用PCR法扩增TTV ORF1基因确诊为阳性的只有19份。结论利用基因芯片检测TTV的PCR产物,特异性和敏感性强,可作为TTV临床标本检测方法。     

Multiplexed,targeted gene expression profiling and genetic analysis on electronic microarrays

BACKGROUND: Electronic microarrays comprise independent microelectrode test sites that can be electronically biased positive or negative, or left neutral, to move and concentrate charged molecules such as DNA and RNA to one or more test sites. We developed a protocol for multiplexed gene expression profiling of mRNA targets that uses electronic field-facilitated hybridization on electronic microarrays. METHODS: A multiplexed, T7 RNA polymerase-mediated amplification method was used for expression profiling of target mRNAs from total cellular RNA; targets were detected by hybridization to sequence-specific capture oligonucleotides on electronic microarrays. Activation of individual test sites on the electronic microarray was used to target hybridization to designated subsets of sites and allow comparisons of target concentrations in different samples. We used multiplexed amplification and electronic field-facilitated hybridization to analyze expression of a model set of 10 target genes in the U937 cell line during lipopolysaccharide-mediated differentiation. Performance of multiple genetic analyses (single-nucleotide polymorphism detection, gene expression profiling, and splicing isoform detection) on a single electronic microarray was demonstrated using the ApoE and ApoER2 genes as a model system. RESULTS: Targets were detected after a 2-min hybridization reaction. With noncomplementary capture probes, no signal was detectable. Twofold changes in target concentration were detectable throughout the ( approximately 64-fold) range of concentrations tested. Levels of 10 targets were analyzed side by side across seven time points. By confining electronic activation to subsets of test sites, polymorphism detection, expression profiling, and splicing isoform analysis were performed on a single electronic microarray. CONCLUSIONS: Microelectronic array technology provides specific target detection and quantification with advantages over currently available methodologies for targeted gene expression profiling and combinatorial genomics testing.     

Analysis of microarray data using Z score transformation

High-throughput cDNA microarray technology allows for the simultaneous analysis of gene expression levels for thousands of genes and as such, rapid, relatively simple methods are needed to store, analyze, and cross-compare basic microarray data. The application of a classical method of data normalization, Z score transformation, provides a way of standardizing data across a wide range of experiments and allows the comparison of microarray data independent of the original hybridization intensities. Data normalized by Z score transformation can be used directly in the calculation of significant changes in gene expression between different samples and conditions. We used Z scores to compare several different methods for predicting significant changes in gene expression including fold changes, Z ratios, Z and t statistical tests. We conclude that the Z score transformation normalization method accompanied by either Z ratios or Z tests for significance estimates offers a useful method for the basic analysis of microarray data. The results provided by these methods can be as rigorous and are no more arbitrary than other test methods, and, in addition, they have the advantage that they can be easily adapted to standard spreadsheet programs.     

Molecular identification of Yersinia enterocolitica isolated from pasteurized whole milk using DNA microarray chip hybridization

A DNA microarray chip of four virulence genes and 16S ribosomal DNA gene conserved region among all Gram negative species, including Yersinia, as a positive control was developed and evaluated using 22 Yersinia enterocolitica isolates. Eight different oligonucleotide probes (oligoprobes) with an average size of 22 bp, complementary to the unique sequences of each gene, were designed and immobilized on the surface of chemically modified slides. Multiplex PCR was used to simultaneously amplify DNA target regions of all five genes, and single stranded DNA (ssDNA) samples for microarray analysis were prepared by using a primer extension of amplicons in the presence of one primer of all genes. The presence of genes in Y. enterocolitica was established by hybridization of the fluorescently labeled ssDNA representing different samples of the microarray gene-specific oligoprobes and confirmed by PCR. Results of the study showed specificity of genotyping Y. enterocolitica using multiple microarray-based assays. Final validation of the chip's ability to identify Y. enterocolitica genes from adulterated pasteurized whole milk was confirmed and successful. The limit of chip detection of virulence genes in pasteurized whole milk was found to be 1000 CFU per hybridization.