应用cDNA微阵列芯片技术筛选猪蛔虫性别差异表达基因的研究

采用cDNA微阵列芯片技术，从所构建的猪蛔虫雌、雄成虫cDNA消减文库分别挑取1044和1119个克隆，PCR扩增其插入片段，经纯化后点样于预先处理好的基片上（双点杂交），制备成cDNA微阵列芯片。将分别标记荧光素Cy3-dUTP和Cy5-dUTP的雌虫和雄虫cDNA探针，与制备好的cDNA芯片杂交（平行进行反标杂交试验）。根据每个点杂交后的Ratio值，筛选出双点杂交和正反标中都同时具有表达差异的基因克隆共1559个。将表达差异最明显的前831个克隆进行测序，获得720个有效序列，经生物信息学分析发现，雄虫特异表达的主要精于蛋白和雌虫特异表达的卵巢信息蛋白的基因序列多数与新杆属线虫存在同源性，有31个可能是新的ESTs。性别差异表达基因及其相关生物信息的获得为下一步研究基因功能奠定了基础。     

Construction and application of a bovine immune-endocrine cDNA microarray

A variety of commercial DNA arrays specific for humans and rodents are widely available; however, microarrays containing well-characterized genes to study pathway-specific gene expression are not as accessible for domestic animals, such as cattle, sheep and pigs. Therefore, a small-scale application-targeted bovine immune-endocrine cDNA array was developed to evaluate genetic pathways involved in the immune-endocrine axis of cattle during periods of altered homeostasis provoked by physiological or environmental stressors, such as infection, vaccination or disease. For this purpose, 167 cDNA sequences corresponding to immune, endocrine and inflammatory response genes were collected and categorized. Positive controls included 5 housekeeping genes (glyceraldehydes-3-phosphate dehydrogenase, hypoxanthine phosphoribosyltransferase, ribosomal protein L19, beta-actin, beta2-microglobulin) and bovine genomic DNA. Negative controls were a bacterial gene (Rhodococcus equi 17-kDa virulence-associated protein) and a partial sequence of the plasmid pACYC177. In addition, RNA extracted from un-stimulated, as well as superantigen (Staphylococcus aureus enterotoxin-A, S. aureus Cowan Pansorbin Cells) and mitogen-stimulated (LPS, ConA) bovine blood leukocytes was mixed, reverse transcribed and PCR amplified using gene-specific primers. The endocrine-associated genes were amplified from cDNA derived from un-stimulated bovine hypothalamus, pituitary, adrenal and thyroid gland tissues. The array was constructed in 4 repeating grids of 180 duplicated spots by coupling the PCR amplified 213-630 bp gene fragments onto poly-l-lysine coated glass slides. The bovine immune-endocrine arrays were standardized and preliminary gene expression profiles generated using Cy3 and Cy5 labelled cDNA from un-stimulated and ConA (5 microg/ml) stimulated PBMC of 4 healthy Holstein cows (2-4 replicate arrays/cow) in a time course study. Mononuclear cell-derived cytokine and chemokine (IL-2, IL-1alpha, TNFalpha, IFN-gamma, TGFbeta-1, MCP-1, MCP-2 and MIP-3alpha) mRNA exhibited a repeatable and consistently low expression in un-stimulated cells and at least a two-fold increased expression following 6 and 24 h ConA stimulation as compared to 0 h un-stimulated controls. In contrast, expression of antigen presenting molecules, MHC-DR, MHC-DQ and MHC-DY, were consistently at least two-fold lower following 6 and 24 h ConA stimulation. The only endocrine gene with differential expression following ConA stimulation was prolactin. Additionally, due to the high level of genetic homology between ovine, swine and bovine genes, RNA similarly acquired from sheep and pigs was evaluated and similar gene expression patterns were noted. These data demonstrate that this application-targeted array containing a set of well characterized genes can be used to determine the relative gene expression corresponding to immune-endocrine responses of cattle and related species, sheep and pigs.     

Detection and genotyping of porcine circovirus in naturally infected pigs by oligo-microarray

A rapid and reliable method for the identification of porcine circovirus (PCV) genotypes based on oligonucleotide microarray hybridization has been developed. The genotype-specific oligonucleotides (22-30 mer) immobilized on the surface of glass slides were selected to bind to the multiple target sites within the replication gene that are conserved among individual PCV genotypes. Cy5-labeled DNA targets were amplified in a PCR with primers common to both genotypes. The identification of PCV genotype was based on hybridization with several individual genotype-specific oligonucleotides. This approach combines the high sensitivity of PCR with the selectivity of DNA-DNA hybridization. The utility and feasibility of oligonucleotide microarray hybridization was evaluated by testing standard and 87 clinical isolates. Analysis of the specimens showed that this microarray-based method is capable of unambiguous identification of both genotypes and fivefold more sensitive than gel electrophoresis. Our results indicated that the oligonucleotide array is useful for the identification and discrimination of PCV from clinical isolates and specimens in a clinical laboratory.     

基因芯片检测5种动物冠状病毒的初步研究

采用蔗糖密度梯度离心,纯化浓缩犬冠状病毒(CCV)、猫冠状病毒(FCV)、猫传染性腹膜炎病毒(FIPV)、猪传染性胃肠炎病毒(TGEV)、猪呼吸道冠状病毒(PRCV)的细胞培养物,分别设计7,17,11,10和4对引物,构建了49个基因片段的克隆。煮沸裂解法制备质粒DNA,回收PCR扩增产物,点制冠状病毒基因芯片。抽提病毒总RNA,利用Cy3-dCTP随机渗入反转录PCR标记,与芯片进行杂交检测,淘汰交叉的克隆片段。结果表明:克隆CCV1,CCV2,CCV5和CCV7可特异诊断CCV,克隆FCV6,FCV7,FCV8和FCV9可特异诊断FCV,克隆FIPV2,FIPV7,FIPV8和FIPV9可特异诊断FIPV,克隆PRCV1,PRCV2和PRCV3可特异诊断PRCV,克隆TGEV3,TGEV4,TGEV5和TGEV6可特异诊断TGEV。将这些特异克隆扩增片段重新点制基因芯片,与病毒PCR产物杂交,未发现交叉现象。基因芯片检测比传统PCR敏感1000倍,可有效应用于这5种动物冠状病毒的检测与区分。     

Joint analysis of multiple cDNA microarray studies via multivariate mixed models applied to genetic improvement of beef cattle

In functional genomic laboratories, it is common to use the same microarray slide across studies, each investigating a unique biological question, and each analyzed separately due to computational limitations and/or because there is no hybridization of samples from different studies on one slide. However, the question of analyzing data from multiple studies is a major current issue in microarray data analysis because there are gains to be made in the accuracy of estimated effects by exploiting a covariance structure between gene expression data across studies. We propose an approach for combining multiple studies using multivariate mixed models, with the assumption of a nonzero correlation among genes across experiments, while imposing a null residual covariance. We applied this method to jointly analyze three experiments in genetics of cattle with a total of 54 arrays, each with 19,200 spots and 7,638 elements. The resulting seven-variate model contains 752,476 equations and 56 covariances. To identify differentially expressed genes, we applied model-based clustering to a linear combination of the random gene x variety interaction effect. We enhanced the biological interpretation of the results by applying an iterative algorithm to identify the gene ontology classes that significantly changed in each experiment. We found 118 elements with coordinate expression that clustered into distinct biological functions such as adipogenesis and protein turnover. These results contribute to our understanding of the mechanistic processes involved in adipogenesis and nutrient partitioning.     

DNA microarray-based identification and typing of Actinobacillus pleuropneumoniae

A DNA microarray system was prepared and shown to facilitate identification and typing of Actinobacillus pleuropneumoniae. The DNA microarray, composed of 18 DNA polymerase chain reaction (PCR) amplicons printed on glass slides and arranged in 3 subarrays, was developed. These target DNA included 1 or multiple fragments of the outer membrane lipoprotein, apx toxin, capsular polysaccharide, and disulfide bound formation protein E (dsbE)-like genes of A. pleuropneumoniae. These arrayed target DNA retained their expceted hybridization properties. The hybridization signal intensities ranged from the least-intense to the most-intense, 4626 to 9789 arbitrary fluorescence units, respectively. Cy3-probes of A. pleuropneumoniae strains labeled with multiplex PCR were hybridized to the DNA microarray. A total of 51 different A. pleuropneumoniae strains representing serotype 1 to 12 reference strains and clinical isolates were detected and typed by the DNA microarray. Twelve reference serotypes produced 11 distinct target DNA hybridization patterns, and hybridization patterns of serotypes 1 (n = 7), 3 (n = 5), and 7 (n = 6) field isolates were identical to hybridization patterns of reference serotypes 1, 3, and 7, respectively. Non-serotyped isolates 4, 6, and 11 (out of 21) from diseased pigs had identical hybridization patterns to reference serotypes 3, 7, and 1, respectively. The results show that the DNA microarray system described in the present study is a valuable tool for identifying and typing reference strains and isolates of A. pleuropneumoniae, and enables relatively rapid identification of non-serotyped isolates.     

猪瘟病毒基因分型寡核苷酸芯片方法的建立

根据猪瘟病毒（CSFV）E2基因序列,设计41条针对CSFV 3个基因群共10个亚群各亚群寡核苷酸探针。利用欧盟猪瘟诊断手册推荐的CSFV E2基因套式RT-PCR方法,在内套PCR过程中进行Cy3-dCTP掺入荧光标记,制备芯片杂交样品。用标记的PCR产物与寡核苷酸探针阵列杂交,置于GenePix 4100A扫描仪中扫描,利用Ge-nePix Pro 6.0软件分析杂交图像。特异性和灵敏度试验显示,芯片方法与本室发表的CSFV real-time RT-PCR方法的灵敏度相近,芯片探针与猪繁殖与呼吸综合征病毒（PRRSV）、猪2型圆环病毒（PCV2）、猪伪狂犬病毒（PRV）样品无非特异性杂交。以包括1.1、2.1、2.2、2.3亚群的8份CSF阳性样品进行芯片的检测验证,结果表明,通过特异性的杂交图谱或杂交信号分析可准确判定样品所属的基因亚群,寡核苷酸芯片的检测结果与测序的分型结果全部符合。本研究为将寡核苷酸芯片技术用于猪瘟病毒的基因分型和分子流行病学研究奠定了基础。     

禽流感病毒NP基因的真核表达及抗体检测芯片的建立

为建立一种检测A型禽流感病毒(AIV)抗体的蛋白芯片,本研究以AIV总RNA为模板,RT-PCR方法扩增NP基因,与真核表达载体pFastBacHTa连接,并在昆虫细胞中表达.重组蛋白经纯化及western blot鉴定,点样于醛基包被的载玻片上,制备检测AIV抗体的蛋白芯片.确定芯片反应最佳条件为:点样浓度2 mg/mL,固定24 h,1%BSA进行封闭,一抗稀释度1:100,二抗稀释度1:2000.利用蛋白芯片分别对15个亚型流感病毒免疫血清、SPF鸡血清、抗新城疫病毒血清、抗法氏囊病毒血清和现地血清样品进行检测,通过与血凝抑制试验比较,表明建立的蛋白芯片方法具有良好的灵敏性和特异性,为AIV抗体检测及制备检测AIV不同亚型或多种病原抗体的蛋白芯片提供方法.     

DNA微阵列与基因表达研究概况

DNA微阵列技术是 90年代兴起的一种对成百上千甚至上万个基因同时进行检测的新技术 ,它具有高通量和并行化的特点 ,广泛应用于基因表达、预测基因功能、检测基因突变和多态性分析、发现新药物和药物靶器官以及疫苗设计等方面。文章对 DNA微阵列的基本原理、DNA微阵列制备技术、杂交信号检测以及数据分析。 c DNA微阵列与细胞周期相关基因表达、细菌基因表达、病毒基因表达、肿瘤基因表达进行了概述。     

基因芯片技术在猪病毒性疾病诊断中的应用

基因芯片是研究生物大分子功能的新技术,具有高通量、高度平行性、高度自动化的特点。它是通过点样法或原位合成法把大量基因探针或基因片段按特定的排列方式固定在硅片上形成致密有序的DNA分子点阵,按碱基配对的特性与样品DNA杂交,然后通过计算机进行解读和分析,以获取大量信息。在对动物传染病病原体的研究中,基因芯片技术已应用于病原体检测、基因分型、表达谱的分析等。论文就其定义、作用机理、分类、在动物病毒性传染病方面的应用及其存在的问题和发展前景进行了综述。     

泛素化调节因子2真核表达质粒的构建及其在原代肾小管上皮细胞的表达

本试验旨在构建带有增强型绿色荧光蛋白报告基因EGFP及目的基因泛素化调节因子2(Smurf2)的真核表达载体pEGFP-N3-Smurf2,并转染小鼠肾小管上皮细胞检测其表达情况。用RT-PCR法扩增小鼠肾小管上皮细胞Smurf2的CDS区,构建克隆载体pEASY-Zero-Smurf2和真核表达载体pEGFP-N3-Smurf2,酶切并测序鉴定。运用脂质体转染法将pEGFP-N3-Smurf2真核表达载体转染小鼠肾小管上皮细胞,实时荧光定量PCR、免疫印迹检测Smurf2的表达。PCR结果显示扩增出Smurf2基因片段大小约为2247 bp;重组质粒pEGFP-N3-Smurf2的酶切鉴定及测序结果均表明Smurf2基因成功克隆到真核表达载体中;脂质体转染后检测结果显示,转染pEGFP-N3-Smurf2表达载体的肾小管上皮细胞中Smurf2基因mRNA表达量升高且EGFP-Smurf2重组蛋白有表达。本试验成功构建了含有增强型绿色荧光蛋白标记的Smurf2真核表达质粒,转染后能明显提高细胞内Smurf2的表达,为研究Smurf2基因的功能奠定了基础。     

H9N2亚型禽流感病毒神经氨酸酶基因的克隆及表达

根据已知H9N2亚型禽流感病毒神经氨酸酶(NA)基因序列设计,合成克隆引物。自H9N2亚型病毒感染的鸡胚尿囊液中提取总RNA,反转录后采用高可信度DNA聚合酶(PyobestTMDNAPolymerase)扩增NA基因,采用Invitrogen定向表达系统(ChampionTMpETdirectionalTOPOexpressionsystem)进行克隆表达,纯化获得N末端携带多聚组氨酸标签的重组NA,分子量约54·7ku。经免疫印迹及ELISA分析重组NA的免疫反应性和免疫动物分析其免疫原性,结果表明:重组NA能与H9N2亚型病毒抗血清发生特异性结合,且其免疫动物后能诱导机体产生特异性抗体,具有良好的抗原性。     

水牛抑制素α亚基基因的克隆与原核表达

采用RT-PCR方法从水牛卵巢总RNA中扩增抑制素α亚基基因,并克隆入pMD18-T载体,进行PCR、双酶切及测序鉴定.序列分析结果表明:水牛抑制素α亚基基因编码序列长为1 083 bp,编码360个氨基酸,与牛、人、猪抑制素α亚基基因CDS成熟蛋白氨基酸的同源性分别为96%、80%、87%,表明抑制素α亚基是一组在进化上高度保守的蛋白质.将水牛抑制素α亚基基因CDS克隆到pET-30a表达载体中,转化宿主菌BL21(DE3)进行原核表达.在1 mmol/L IPTG 中,37 ℃诱导表达4 h后抑制素α亚基基因重组蛋白可成功获得表达.将表达产物进行SDS-PAGE分析,结果表达产物主要以包涵体形式存在,分子质量约为40 ku.     

Construction of a microarray specific to the chicken immune system: profiling gene expression in B cells after lipopolysaccharide stimulation

The objective of this study was to profile gene expression in cells of the chicken immune system. A low-density immune-specific microarray was constructed that contained genes with known functions in the chicken immune system, in addition to chicken-expressed sequence tags (ESTs) homologous with mammalian immune system genes, which were systematically characterized by bioinformatic analyses. Genes and ESTs that met the annotation criteria were amplified and placed on a microarray. The microarray contained 84 immune system gene elements. As a means of calibration, the microarray was then used to examine gene expression in chicken B cells after lipopolysaccharide stimulation. Differential gene expression was observed at 6, 12, and 24 h but not at 48 h after stimulation. The results were validated by semiquantitative polymerase chain reaction. The microarray showed a high degree of reproducibility, as demonstrated by intra- and interassay correlation coefficients of 0.97 and 0.95, respectively. Thus, the low-density microarray developed in this study may be used as a tool for monitoring gene expression in the chicken immune system.     

蜜蜂球囊菌全长cDNA文库的构建与分析

本试验利用TRIzol试剂盒提取蜜蜂球囊菌总RNA,通过Oligotex纯化试剂盒将mRNA反转录成cDNA,再以第一链cDNA为模板合成第二链cDNA,该cDNA产物经分级分离和体外包装,即获得蜜蜂球囊菌cDNA原始文库,其滴度测定为1.6×106PFU/mL,扩增后的滴度是1.5×109PFU/mL;取适量扩增文库稀释并铺平板,蓝白斑筛选独立噬菌斑,用M13±通用引物进行PCR扩增后,文库的重组率达到90%,插入cDNA片段的长度在0.5~2 kb。该文库的构建,有利于筛选目的基因,便于深入研究蜜蜂白垩病的侵染机制,最终有效防制白垩病。     

禽白血病病毒B、E和J亚群基因芯片检测方法的建立

目的基于多重PCR技术,建立禽白血病病毒(ALV)的B、E、J亚群的基因芯片分型和检测方法。方法根据NCBI已收录的ALV三个亚群的参考毒株cDNA序列,在各亚群特异性基因突变区两端选取其保守区域,设计合成三个亚群的通用上游引物1条,以及B、E亚群的通用下游引物和J亚群下游引物各1条,将上述引物用Cy3标记,建立多重PCR体系;参考靶序列内部的三个亚群各自的保守区域,选择亚群之间基因突变位点多的区域,设计合成5条寡核苷酸探针,制作寡核苷酸探针基因检测芯片;以寄主细胞DF-1中提取传代ALV的cDNA,以及合成NCBI收录的各亚群参考毒株的cDNA序列作为检测模板;利用Cy3标记的PCR扩增产物,与基因芯片进行杂交反应,扫描结果。结果芯片准确检测并分型三个亚群的参考毒株,其检测灵敏度能够达到102个基因拷贝,且与禽类常见的四种病毒均无交叉反应。结论本研究结果证明,基因芯片技术是一种ALV的B、E和J亚群进行检测和分型的有效方法,且具有较高的特异性和灵敏度,为今后在临床应用中快速鉴别诊断ALV等免疫抑制病提供可行性。