双色荧光杂交芯片在近交系小鼠遗传监测中的应用

应用一种新的高通量SNP检测方法-双色荧光杂交芯片技术进行近交系小鼠遗传监测。应用双色荧光杂交芯片技术对4个品系近交系小鼠的多个基因组DNA样本进行SNP分型,整合6个SNP位点的芯片杂交信息,对样本所属品系进行判断。研究结果表明SNP检测方法-双色荧光杂交芯片技术能够对选定的6个SNP位点进行高准确率分型;双色荧光杂交芯片技术是一种高通量SNP检测的良好工具,适合于对少量近交系品系来源的大样本量小鼠进行遗传污染监测和品系鉴定,并具有扩大应用的潜力。     

双色荧光杂交芯片在近交系小鼠遗传监测中的应用

应用一种新的高通量SNP检测方法-双色荧光杂交芯片技术进行近交系小鼠遗传监测。应用双色荧光杂交芯片技术对4个品系近交系小鼠的多个基因组DNA 样本进行SNP分型,整合6个SNP位点的芯片杂交信息,对样本所属品系进行判断。研究结果表明SNP检测方法-双色荧光杂交芯片技术能够对选定的6个SNP位点进行高准确率分型;双色荧光杂交芯片技术是一种高通量SNP检测的良好工具,适合于对少量近交系品系来源的大样本量小鼠进行遗传污染监测和品系鉴定,并具有扩大应用的潜力。     

基因导流杂交法于低密度基因芯片平台上检测乙肝病毒

运用基因导流杂交法在低密度基因芯片平台上检测乙肝病毒DNA（HBV DNA）。设计特异性引物,对HBV基因组DNA中的编码HBV多聚酶蛋白的一段序列进行PCR扩增;根据被扩增片段,设计保守的特异性探针,并将该探针固定在杂交膜上,制备低密度基因芯片：使用导流杂交法将上述扩增产物和低密度基因芯片进行杂交,根据显色反应判断被检测样本有无HBV DNA。基因导流杂交法在低密度基因芯片平台上可以方便、快速、准确地检测乙肝病毒。     

致病性副溶血性弧菌菌落杂交检测体系的优化

对常见食源性致病菌副溶血性弧菌的杂交条件进行了优化。基于副溶血性弧菌的tdh,trh,toxR基因选用了3种探针序列,从菌落杂交样品的预处理方法、杂交时间和显色检测等方面对基于副溶血性弧菌毒力基因的原位杂交实验进行了条件优化。结果表明,采用80℃热固定2 h,37℃预杂交10 min后杂交8 h以及封闭1 h的改良方法可获得高特异性、低背景且着色清晰的实验结果。优化的菌落杂交技术检测副溶血性弧菌与传统检测方法相比,具有高效、准确、可区分致病性菌株的优点,为水产品中副溶血性弧菌致病菌株和非致病菌株的同步检测和筛选提供参考。     

用RAPD标记检测鹅掌楸属种间杂交的花粉污染

根据鹅掌楸属 (LiriodendronL .)的生物学特点 ,实践上常采用不套袋杂交授粉技术 ,理论分析和间接检测结果证明这种杂交授粉方式的花粉污染率低于 1% ,但到目前为止仍缺乏直接的检测证据。本试验首次采用RAPD标记对鹅掌楸属种间不套袋杂交授粉的花粉污染率进行了检测 ,结果证明 93个受检不套袋杂交授粉子代均来自目的父本 ,而非花粉污染所致。通过对所用 4个父本标记谱带在试验群体中出现频率的测定和分析 ,证明这种检测结果的可靠性大于 99% ,从而认为对鹅掌楸属进行不套袋杂交授粉是可行的。并就这一方法在植物学研究领域的应用潜力进行了讨论     

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。     

反向线性探针杂交在检测实验动物沙门菌中的研究

目的建立简便、快速、准确、灵敏、特异的沙门菌检测方法。方法根据沙门菌argT基因序列设计通用引物和3'、5'均加有polyC的特异性探针。上游引物5'标记生物素,将探针线性固定在硝酸纤维素膜上,使沙门菌PCR扩增产物与探针进行杂交,通过优化杂交条件,建立反向线性探针杂交检测方法。利用该方法对重庆地区74只实验动物进行检测,同时与传统分离培养方法比较。结果反向线性探针杂交方法灵敏度高,对沙门菌PCR扩增产物在3ng/μL以上可有效检测。从细菌分离培养及DNA提取到PCR扩增及反向杂交结束仅需27h。该检测方法特异性高,对6种非沙门菌的检测中,其特异性为100%。应用传统分离培养方法和反向线性探针杂交方法分别检测42只KM小鼠和32只SD大鼠,两种方法检测结果一致性为100%。结论反向线性探针杂交检测方法,具有快速、可靠、敏感和特异的特点,可用于沙门菌感染时的检测,适合应用于实验动物沙门菌的监测。     

用RAPD标记检测鹅掌揪属种间杂交的花粉污染

根据鹅掌揪属（Liriodendron L.）的生物学特点,实践上常采用不套袋杂交授粉技术,理论分析和间接检测结果证明这种杂交授粉方式的花粉污染率低于1%,但目前为止仍缺乏直接的检测证据。本试验首次采用了RAPD标记对鹅掌揪属种间不套袋杂交授粉的花粉污染率进行了检测,结果证明了93个受检不套袋杂交授粉子代均来自目的你枰,而非花粉污染所致。通过对所用4个父本标记谱带在试验群体中的出现频率的测定和分析,证明这种检测的结果的可靠性大于99%,从而认为对鹅掌揪属进行不套袋杂交授粉是可行的。并就这一方法在植物学研究领域的应用潜力进行了讨论。     

亲和素-生物素间接偶联的压电DNA传感器研究

采用3 3′-二巯基硫代丙酸的金电极自组装技术,用乙基3-（3-二甲氨基）碳二亚胺盐酸盐（EDC）和N-羟基磺基琥珀酰亚胺（NHS）偶联剂将亲和素固定于金电极上,联于生物素标记的探针,制备成压电DNA传感器的检测电极,和杂交液中的待检葡萄球菌肠毒素B的ssDNA进行杂交,通过频率信号检测DNA杂交的量,达到检测的目的.采用不同长度的基因片段进行了研究,制作的传感器一致性、特异性都较好;杂交后的电极,电极再生后,传感器可以重复使用.     

两种PCR方法对检测A组轮状病毒膜芯片杂交结果的影响

A组轮状病毒(rotavirus,RV)是导致拿世界婴幼儿腹泻的最主要病原,危害巨大。拟用RT-巢式PCR技术对A组RV的保守序列进行高度扩增,通过固本室内制的膜芯片杂交,实现对该病毒的检测。分别采用对称PCR和不对称PCR扩增,均可得到扩增的目的片段．对称式扩增产物杂交结果不理想。而不对称式扩增得到了大量待检单链产物,同膜芯片杂交获得了理想的杂交结果。显著地提高了对A组RV杂交检测的灵敏度。表明不对称式PCR扩增是一种制备用于芯片杂交大量单链产物的理想方法,尤其是针对富含AT的核酸检测区域。     

Detection of sub-picogram quantities of specific DNA sequences on blot hybridization with biotinylated probes.

A sensitive method for detecting biotinylated DNA probes on dot and Southern blots is described which is based on the principle outlined by Leary et al (1). This system has two main components: detection of biotinylated DNA by a two-step procedure with streptavidin and poly(alkaline phosphatase); and blocking background with Tween 20. 32fg and 80fg of lambda phage DNA was detected on dot and Southern blot hybridizations respectively. 150fg of beta-globin was detected on Southern blots of genomic DNA. This method is fast, reproducible and can detect single copy genes in 0.25 micrograms genomic DNA on Southern blots.     

A simple and rapid technique for identification of large numbers of individual mosquitoes using DNA hybridization

A general method for obtaining species-specific repetitive DNA sequences is described. The method is based on the detection of recombinant DNA clones containing repetitive sequences using labeled total genomic DNA. These repetitive DNA sequences can be used to identify individual mosquito adults, pupae, and larvae squashed on filter membranes (squash blots). This technique was used to distinguish individuals of the four sibling species of the Anopheles quadrimaculatus complex. Repetitive DNA sequences and squash blots can be of use for rapid identification of other insect species in field collections.     

Comparison of colony and stool blots for detection of enteropathogens by DNA probes.

DNA probes that identify genes coding for heat-labile type I (LT-I) and heat-stable type 1 (ST-I) enterotoxins, enteropathogenic Escherichia coli adherence factor (EAF), and Shigella-like invasiveness (INV) are used to evaluate the sensitivity and specificity of stool blots in comparison with the sensitivity and specificity of colony blots in detecting enteropathogens. The sensitivities of the probes in stool blots are 91.7% for the LT-I probe, 76.9% for the ST-I probes, 78.9% for the EAF probe, and 45.5% for the INV probe. The specificity of all probes is higher than 95%. In general, the stool blot method identifies as many if not more LT-I-, ST-I-, and EAF-producing E. coli infections than the colony blots.     

Enhanced chemiluminescent method for the detection of DNA dot-hybridization assays

A simple enhanced chemiluminescent procedure for the quantitation of DNA hybridization to dot blots is described. The method utilizes DNA probes labeled with biotin, which are detected using a biotinylated streptavidin-horseradish peroxidase complex. The peroxidase enzyme then takes part in an enhanced chemiluminescent reaction with luminol, peroxide, and an enhancer. The method can be used to give quantitative results using a photomultiplier tube or qualitative results by recording the light emission on instant photographic film.     

Covalent genomic DNA modification patterns revealed by denaturing gradient gel blots

Several approaches are used to survey genomic DNA methylation patterns, including Southern blot, PCR, and microarray strategies. All of these methods are based on the use of methylation-sensitive isoschizomer restriction enzyme pairs and/or sodium bisulfite treatment of genomic DNA. They have many limitations, including PCR bias, lack of comprehensive assessment of methylated sites, labor-intensive protocols, and/or the need for expensive equipment. Since the presence of 5-methylcytosine alters the melting properties of DNA molecules, denaturing gradient gel blots (DGG blots), a gene scanning technique which detects differences in DNA fragments based on differential melting behavior, were used to examine genomic modification patterns in normal tissues. Variations in melting behavior, observed as restriction fragment melting polymorphisms (RFMPs), were detected in various tissues from single individuals in all human and mouse genes tested, suggesting the presence of widespread differential cell type-specific DNA modification. Additional DGG blot experiments comparing genomic DNA to unmethylated cloned DNA suggested that the melting variants were most likely caused by DNA methylation differences. The results suggest that the use of DGG blots can provide a comprehensive and rapid method for comparing complex in vivo DNA modification patterns in normal adult somatic cells.     

Detection of DNA sequence polymorphisms in human genomic DNA by using denaturing gradient gel blots.

Denaturing gradient gel electrophoresis can detect sequence differences outside restriction-enzyme recognition sites. DNA sequence polymorphisms can be detected as restriction-fragment melting polymorphisms (RFMPs) in genomic DNA by using blots made from denaturing gradient gels. In contrast to the use of Southern blots to find sequence differences, denaturing gradient gel blots can detect differences almost anywhere, not just at 4-6-bp restriction-enzyme recognition sites. Human genomic DNA was digested with one of several randomly selected 4-bp recognition-site restriction enzymes, electrophoresed in denaturing gradient gels, and transferred to nylon membranes. The blots were hybridized with radioactive probes prepared from the factor VIII, type II collagen, insulin receptor, beta 2-adrenergic receptor, and 21-hydroxylase genes; in unrelated individuals, several RFMPs were found in fragments from every locus tested. No restriction map or sequence information was used to detect RFMPs. RFMPs can be used as genetic markers, because their alleles segregate in a Mendelian manner. Unlike most other methods for detecting DNA sequence polymorphisms, a genomic DNA blot made from one gel can be hybridized consecutively with many (30 or more) different probes.     

Sequential chemiluminescent detection of target DNAs without stripping and reprobing.

We present a simple method for sequential chemiluminescent detections of two different DNA loci on a single Southern blot. First, an enzyme-linked DNA probe for a unique sequence is detected with a horse-radish peroxidase (HRP) substrate followed by the detection of another enzyme-linked DNA probe for a different unique sequence with an alkaline phosphatase (AP) substrate that simultaneously inhibits the chemiluminescence generated by HRP. Such sequential detection steps eliminate the need to strip and reprobe blots and can be performed with no intervening steps.     

Genome mapping by arbitrary amplification of yeast artificial chromosomes

Several methods have been described for using the polymerase chain reaction (PCR) to isolate fragments of DNA for genome mapping. We have developed an approach for isolating discrete fragments by amplifying DNA with single oligonucleotides (10-mers) with arbitrarity selected sequences. The method is rapid and technically simple. We isolated fragments from a contig of three yeast artificial chromosomes (YACs) from the human Xq28 chromosomal region. We purified YACs yWXD 37, yWXD348, and yWXD705 from a preparative pulsed field gel. Amplifications of each YAC were performed with single 10-mers as the PCR primers and the products were visualized on agarose gels. These fragments have been successfully used as hybridization probes against Southern blots containing the YACs and against blots containing human genomic DNA and somatic cell hybrids containing Xq28 as their only human constituent. The results have been concordant with the known order of the YACs. We have also successfully combined 10-mers with primers derived from vector arm sequences to isolate YAC ends. We discuss several uses of this method in comparative mapping and in filling in gaps in physical and genetic maps.     

Impartial comparative analysis of measurement of leukocyte telomere length/DNA content by Southern blots and qPCR

Telomere length/DNA content has been measured in epidemiological/clinical settings with the goal of testing a host of hypotheses related to the biology of human aging, but often the conclusions of these studies have been inconsistent. These inconsistencies may stem from various reasons, including the use of different telomere length measurement techniques. Here, we report the first impartial evaluation of measurements of leukocyte telomere length by Southern blot of the terminal restriction fragments and quantitative PCR (qPCR) of telomere DNA content, expressed as the ratio of telomeric product (T)/single copy gene (S) product. Blind measurements on the same samples from 50 donors were performed in two independent laboratories on two different occasions. Both the qPCR and Southern blots displayed highly reproducible results as shown by r values > 0.9 for the correlations between results obtained by either method on two occasions. The inter-assay CV measurement for the qPCR was 6.45%, while that of the Southern blots was 1.74%. The relation between the results generated by Southern blots versus those generated by qPCR deviated from linearity. We discuss the ramifications of these findings with regard to measurements of telomere length/DNA content in epidemiological/clinical circumstances.     

Sensitive chemiluminescent detection of digoxigenin-labeled nucleic acids: a fast and simple protocol and its applications.

A fast and simple protocol for the chemiluminescent detection of digoxigenin-labeled nucleic acids with anti-digoxigenin antibody Fab fragments coupled to alkaline phosphatase and 3-(4-methoxyspiro[1,2-dioxetane-3,2'-tricyclo-[3.3.1.1 (3,7)]decan]-4- yl)phenyl phosphate as substrate is described. The washing and blocking procedure was optimized to yield low background even on positively charged nylon membranes. The sensitivity of the system is equal or better than radioactive methods. Exposure to x-ray or Polaroid film for up to 30 minutes is sufficient for the detection of 70 femtograms of homologous DNA. Human single-copy genes are detected in Southern blots of as low as 0.3 microgram total placental DNA. Blots can be reprobed multiple times very easily. The advantages of the digoxigenin system are high sensitivity, absence of background and ease of reprobing and are illustrated by applications for single-copy gene detection in genomic blots of human DNA, Northern hybridizations to rare mRNA, detection of E. coli genes on blots of genomic digests after pulse field gel electrophoresis, as well as for nonradioactive DNA sequencing blots with digoxigenin-labeled primers.