牡丹反转录转座子RT基因的分离与序列分析

以牡丹基因组为模板,利用简并引物进行PCR扩增,得到了编码Ty1-copia类反转录转座子反转录酶(RT基因)的序列,测序后所得序列长度为240 bp,包含2个开放读码框,共编码63个氨基酸。经NCBI中BLAST比对结果显示,洛阳红牡丹RT基因与枸杞、甜菜等RT基因的同源性均在70%以上。经MEGA和DNAstar软件分析表明,该片段在进化上与梅、杨、茶和苹果等落叶木本植物的同源性序列存在更高的同源性和更近的亲缘关系,与枸杞、鹰嘴豆、番茄、草莓等草本植物的同源性序列亲缘性较远。

RT-SHIV rt基因单拷贝PCR扩增方法的建立及初步应用

目的建立RT-SHIV病毒全长rt基因单拷贝PCR扩增方法,用于HIV-1 rt基因体内遗传与变异研究。方法 Oligo软件设计RT-SHIV rt基因特异性扩增引物,梯度稀释方法进行特异性和灵敏度筛选,进而优化退火温度和PCR反应最佳循环数等条件,建立rt基因PCR扩增方法;在此基础上将模板进行有限稀释,摸索rt基因单拷贝PCR扩增条件;使用该方法扩增感染猴体内RT-SHIV病毒rt基因,BioEdit软件进行基因序列分析。结果筛选得到一组巢式PCR引物,成功建立了RT-SHIV rt基因PCR扩增方法;当模板浓度为100 copies/μL时,扩增产物为单拷贝序列;测序结果显示RT-SHIV感染猴d266和d294血浆样本分别存在1处和6处氨基酸突变。结论本研究建立的全长rt基因单拷贝PCR扩增方法特异性好、灵敏度高、重复性强,可以应用于各类RT-SHIV病毒的全长rt基因分析。

菊花Ty1-copia类反转录转座子RT基因的分离与序列分析

以菊花品种‘秋水长流’DNA为试材,利用简并引物对菊花品种‘秋水长流’的DNA进行PCR扩增,对条带进行回收、克隆、测序,并通过生物信息学方法对获得的序列进行了碱基序列分析、同源性分析及聚类分析,以期为进一步探索反转录转座子在菊花遗传多样性形成中的作用奠定基础。结果表明:得到了一条230bp左右的目的条带。28条来自菊花的Ty1-copia反转录转座子反转录酶序列长度变化范围为207～232bp,GC与AT比例为1.06～1.63,同源性范围为25.3%～99.1%。其核苷酸序列经过系统聚类分析后可分为4个家族。所有氨基酸序列出现2～13个不同程度的终止密码子突变。并且将核苷酸序列与NCBI中已登录的不同物种Ty1-copia类反转录转座子反转录酶的核苷酸序列进行聚类分析。在菊花中得到4个家族的Ty1-copia类反转录转座子反转录酶序列在长度、碱基变化上的表现是不完全一致的,且序列同源性上存在多态性。系统进化树分析的结果表明,获得序列与其它植物中的Ty1-copia类反转录转座子反转录酶序列具有较高的同源性。菊花中的Ty1-copia类反转录转座子反转录酶序列间具有较高的异质性。

先天性厚甲症一家系的KRT基因突变分析

目的检测一先天性厚甲症(PC)家系的致病基因KRT6a、KRT6b、KRT16、KRT17,以期找到其可能的致病突变。方法常规收集该家系成员外周静脉血,同时采集同地区100名健康自愿者外周血作为正常对照。分别提取DNA,运用聚合酶链反应(PCR)扩增基因KRT6a、KRT6b、KRT16、KRT17的全部外显子及其侧翼内含子序列,产物纯化后直接行DNA测序,比对分析其基因突变位点和类型。结果 PC患者KRT6a基因第1号外显子存在错义突变c.521T>C(p.Phe174Ser),而正常家系成员和正常对照组均无此突变,KRT6b、KRT16和KRT17基因也未发现致病突变。结论该PC家系的患者存在一个错义突变——KRT6a基因第1号外显子c.521T>C(p.Phe174Ser)。该突变是导致PC发病的分子基础。

进境谷物中转基因油菜籽RT73的定性定量检测

[目的]转基因作物可能会以杂质的形式混入到谷物中,所以要加强对谷物中杂质的转基因成分检测。[方法]利用常规定性PCR方法和实时荧光PCR方法对来源于进境谷物中的32份转基因油菜籽样品进行了转基因油菜RT73的检测。[结果]通过常规定性PCR检测,检出28份转基因油菜籽含RT73;使用ABI7700定量PCR仪进行实时荧光定量PCR检测,检出31份转基因油菜含RT73,其含量分别为0.03%￣97.7%。[结论]其进出口谷物杂质中混有转基因成分,口岸检验检疫机构要加强其检测。

RT-PCR构建人甲胎蛋白全长基因真核表达载体

目的 采用反转录PCR(RT-PCR)构建人甲胎蛋白 (Alpha-Fetoprotein, AFP)全长基因真核表达载体,为下一步应用以AFP蛋白为靶点的基因治疗作准备。方法 体外培养人肝癌细胞HepG2,Trizol裂解细胞,提取总mRNA。设计含有特定酶切位点BglⅡ,SalⅠ和真核启动元件Kozak序列的RT-PCT正反向引物,采用RT-PCR法克隆AFP全长cDNA,使用BglⅡ +SalⅠ双酶切载体pEGFP-C3载体和AFPcDNA,将AFPcDNA连接载体pEGFP-C3,构建新的真核表达载体,命名为pEGFP-AFP。结果 通过测序证明pEGFP-AFP真核表达载体含有AFP全长基因。结论:本研究成功构建人甲胎蛋白基因真核表达载体pEGFP-AFP,为进一步的分子试验和基因治疗打下了基础。

不同品系大鼠RTI基因抗原表达数量的研究

目的研究不同品系大鼠RT1A、RT1B和RT1D基因表达的抗原总数量,以及在CD4+T细胞和CD8+T细胞上表达的数量,为免疫学研究提供数据支持。方法采集四种品系BN、Lewis、F344、SHR大鼠的静脉血,制备淋巴细胞,与有荧光标记的单克隆抗体反应,应用流式细胞术检测抗原数量。结果发现RT1A、RT1B和RT1D基因表达的抗原在不同品系大鼠体内表达的数量不同,其中F344大鼠表达的RT1A抗原最多,BN大鼠表达的RT1B抗原和RT1D抗原均为最多。RT1A、RT1B和RT1D基因表达的抗原在CD4+T细胞和CD8+T细胞上表达的数量也不同,Lewis大鼠在CD4+T细胞上表达的RT1A抗原最多,BN大鼠在CD4+T细胞上表达的RT1B和RT1D抗原最多。F344大鼠在CD8+T细胞上表达的RT1A抗原最多;F344大鼠在CD8+T细胞上表达的RT1B和RT1D抗原最多。同一品系大鼠之间雌雄动物RT1A、RT1B和RT1D基因表达的抗原也不同。结论不同品系大鼠RT1A、RT1B和RT1D基因的抗原总表达数量之间差异有显著性,在CD4+T细胞上和CD8+T细胞上表达的数量差异也有显著性。

人FHIT基因实时荧光定量RT-PCR检测方法的建立

目的:建立检测人脆性组氨酸三联体(fragile histidine triad,FHIT)基因的荧光定量RT-PCR方法。方法:根据GenBank中人FHIT基因序列,在保守区设计合成一对特异引物,将PCR扩增得到的FHIT基因克隆至PMD18-T载体上,构建的重组质粒标准品倍比稀释后运用SYBR Green I染料法绘制标准曲线,并进行融解曲线分析。结果:FHIT基因的标准品稀释度在1×107～1×103copies/μl范围内具有良好的线性关系,Ct值线性范围为14.28～28.36,相关系数为0.998,融解曲线分析表明,产物为特异的单峰,Tm为92.3±0.1℃。结论:建立了人FHIT基因实时荧光定量RT-PCR方法,为在mRNA水平对人FHIT的定量分析奠定了基础。

RT-SHIV感染中国恒河猴及体内传代

目的了解RT-SHIV感染中国恒河猴的感染特点,研究RT-SHIV在中国恒河猴中传代特点;建立RT-SHIV中国恒河猴动物模型,为评价HIV-1药物有效性提供动物平台。方法选择4只健康恒河猴,其中两只动物经上肢静脉感染RT-SHIV病毒,感染急性期采取外周血分离CD8-PBMC,扩增病毒,将新制备的病毒静脉感染另外两只中国恒河猴,通过监测血浆病毒载量,CD4+/CD8+比值,CD4+T淋巴细胞和B淋巴细胞的绝对数,了解实验猴的感染状态,同时分析病毒RT基因变异情况。结果 4只动物均获得系统性感染,且传代动物急性期表现更为强烈,RT基因在感染和传代的过程中共观察到3个氨基酸的改变。结论本研究为RT-SHIV中国恒河猴模型的建立提供了基础信息。

Designing Primers for H5 and H7 Subtypes of Avian Influenza Virus and Multiplex RT-PCR Amplification

[Objective] The research aimed to design primers that are suitable for detecting H5 and H7 subtypes of avian influenza virus （AIV） ; [Method] DNAStar was used to analyze the homology of the sequences of H5 and H7 subtypes of AIV accessed in GenBank, and design primers（ by Primer Premier 5.0） on high homologous region of these sequences, and then amplified by RT-PCR. [Result] The multiplex RT-PCR amplification, agarose gel electrophoresis and sequencing results showed that the self-designed primers are successful for detecting AIV. [Conclusion] It is feasible to rapidly diagnose AIV through this method.

Molecular Characterization of a Chinese Soybean Mosaic Virus Isolate by RT_PCR, cDNA Sequence Analysis and Direct Expression of PCR Products in Bacteria

Soybean mosaic virus (SMV) causes one of the most severe viral diseases in soybean ( Glycine max L.) and is known to contain many pathogenically and serologically related isolates. In the present study, the authors have obtained cDNAs to all cistrons of a Chinese SMV isolate, SMV_ZK, by RT_PCR. By analysing the nucleotide and amino acid sequence of the HC_PRO, NIb and CP cistrons, it was found that SMV_ZK was highly homologous to the G2 strain of SMV, thus confirming the existence of G2_like isolates in soybean crop in China. The amplified cDNAs were directly cloned into a bacterial expression vector. With the exception of the P3 cistron, expression of the cDNAs of all other cistrons in bacteria gave rise to polypeptides of expected molecular weight. The expressed viral proteins were subsequently purified by gel elution. The preparation of viral_specific cDNAs and gene products will be useful in future functional study of the SMV genome.

Detection of Survivin mRNA in nasopharyngeal carcinoma by real-time fluorescence quantitative RT-PCR

Objective： To establish the method of real time fluorescence quantitative RT-PCR for detecting the expression of Survivin mRNA in nasopharyngeat carcinoma （NPC） tissues. Methods： The total RNA was extracted from NPC cell line CNE-2 and tissues with Trizol and then been transcribed reversely to cDNA, a method of real time fluorescence quantitative RT-PCR for detecting the expression of Survivin mRNA in NPC tissues had been established, in which chronic nasopharyn-gitis patients＇ nasopharynx tissues treated as control group. Results： The expression of Survivin mRNA all could be detected either in CNE-2 cells, NPC tissues or in chronic nasopharyngitis patients＇ nasopharynx tissues, and there was higher the expression level of Survivin mRNA in NPC tissues than which in chronic nasopharyngitis patients＇ nasopharynx tissues, the difference was significant （P 〈 0.01）. The expression of Survivin mRNA could be detected both in stage Ⅰ ＋ Ⅱ and stage Ⅲ ＋ Ⅳ NPC, and there was no significant difference in relative quantifications of gene expression between these two groups （P 〉 0.05）. There was no relationship between Survivin mRNA expression and age and sex of NPC patients （P 〉 0.05）. Conclusion： Real time fluorescence quantitative RT-PCR is a rapid, effective and high sensitive method for detecting the expression of Survivin mRNA in NPC tissues. The overexpression of Survivin mRNA may play some roles in pathogenesis of NPC.

Screening of eye-position related genes with DD-RT-PCR and RDA in the hybrids between Japanese flounder Paralichthys olivaceus and stone flounder Kareius bicoloratus

Flatfish or flounder moves one eye to change body proportion into vertebral asymmetry during metamorphosis, during which some become sinistral while others dextral. However, the mechanism behinds the eye-position has not been well understood. In this research, hybrids between Japanese flounder(♀) and stone flounder (♂) show mixed eye-location in both dextral type and sinistral type, and thus become good samples for studying the eye-migration. mRNAs from pro-metamorphosis sinistral and dextral hybrids larvae were screened with classical differential display RT-PCR (DD-RT-PCR) and representational difference analysis of cDNA (cDNA-RDA); 30 and 47 putative fragments were isolated, respectively. The cDNA fragments of creatine kinase and trypsinogen 2 precursor genes isolated by cDNA-RDA exhibited eye-position expression patterns during metamorphosis. However, none of the fragments was proved to be related to flatfishes’ eye-position specifically. Therefore, further studies and more sensitive gene isolated methods are needed to solve the problems.

Establishment of an orthotopic transplantation tumor model of hepatocellular carcinoma in mice

AIM:To improve the outcome of orthotopic transplantation in a mouse model,we used an absorbable gelatin sponge(AGS) in nude mice to establish an orthotopic implantation tumor model.METHODS:MHCC-97L hepatocellular carcinoma(HCC)cells stably expressing the luciferase gene were injected into the subcutaneous region of nude mice.One week later,the ectopic tumors were harvested and transplanted into the left liver lobe of nude mice.The AGS was used to establish the nude mouse orthotopic implantation tumor model.The tumor suppressor gene,paired box gene 5(PAX5),which is a tumor suppressor in HCC,was transfected into HCC cells to validate the model.Tumor growth was measured by bioluminescence imaging technology.Semi-quantitative reverse transcription polymerase chain reaction(RT-PCR) and histopathology were used to confirm the tumorigenicity of the implanted tumor from the MHCC-97L cell line.RESULTS:We successfully developed an orthotopic transplantation tumor model in nude mice with the use of an AGS.The success rate of tumor transplantation was improved from 60% in the control group to 100% in the experimental group using AGS.The detection of fluorescent signals showed that tumors grew in all live nude mice.The mice were divided into 3 groups:AGS-,AGS+/PAX5-and AGS+/PAX5 +.Tumor size was significantly smaller in PAX5 transfected nude mice compared to control mice(P < 0.0001).These fluorescent signal results were consistent with observations made during surgery.Pathologic examination further confirmed that the tissues from the ectopic tumor were HCC.Results from RT-PCR proved that the HCC originated from MHCC-97L cells.CONCLUSION:Using an AGS is a convenient and efficient way of establishing an indirect orthotopic liver transplantation tumor model with a high success rate.

Quantification of Simian Immunodeficiency Virus by SYBR Green RT-PCR Technique

Plasma viral RNA load is widely accepted as the most relevant parameter to assess the status and progression of Simian immunodeficiency virus （SIV） infections. To accurately measure RNA levels of the virus, a one-step fluorescent quantitative assay was established based on the SYBR green Real-time reverse transcription-polymerase chain reaction （RT-PCR）. The lower detection limit of the assay was 10 copies per reaction for the virus. This method was successfully applied to quantify SIVmac251 and SIVmac239 viruses produced in CEMx174 cells. Additionally, the performance of the SYBR green RT-PCR was assessed in a SIVmac251 infected rhesus macaque. The result demonstrated that the method could detect as little as 215 copies per milliliter of plasma and the dynamic pattern of viral load was highly consistent with previous results. With regard to convenience, sensitivity and accuracy our assay represents a realistic alternative to both branched-chain DNA （b-DNA） assays or real-time PCR assays based on TaqMan probes.

Selection of reference genes for qRT-PCR analysis of gene expression in sea cucumber Apostichopus japonicus during aestivation

Quantitative real-time reverse transcription-polymerase chain reaction （qRT-PCR） is a technique that is widely used for gene expression analysis, and its accuracy depends on the expression stability of the internal reference genes used as normalization factors. However, many applications of qRT-PCR used housekeeping genes as internal controls without validation. In this study, the expression stability of eight candidate reference genes in three tissues （intestine, respiratory tree, and muscle） of the sea cucumber Apostichopus japonicus was assessed during normal growth and aestivation using the geNorm, NormFinder, delta CT, and RefFinder algorithms. The results indicate that the reference genes exhibited significantly different expression patterns among the three tissues during aestivation. In general, the β-tubulin （TUBB） gene was relatively stable in the intestine and respiratory tree tissues. The optimal reference gene combination for intestine was 40S ribosomal protein S18 （RPSI 8）, TUBB, and NADH dehydrogenase （NADH）; for respiratory tree, it was β-actin （ACTB）, TUBB, and succinate dehydrogenase cytochrome B small subunit （SDHC）; and for muscle it was α-tubulin （TUBA） and NADH dehydrogenase [ubiquinone] 1α subcomplex subunit 13 （NDUFA13）. These combinations of internal control genes should be considered for use in further studies of gene expression in A.japonicus during aestivation.

PARTIAL DELTETION OF p53 GENE IN α PARTICLE－INDUCED TRANSFORMANT OF SYRIAN HAMSTER EMBRYO CELLS

The mutation of p53 gene was detected in Syrian hamster embryo(SHE) cells neoplastically initiated with a particles.The level of the p53 mRNA in transformant was obviously higher than that in non-irradiated counterpart,as measured by Northern blot analysis of total RNA.A pair of primers were designed based on p53 cDNA sequence to produce the whole length of coding sequence about 1.2 kilobase(Kb) by reverse transcription of mRNA followed by the polymerase chain reaction(RTPCR),but the length of fragment amplified from transformant mRNA was about 0.3Kb,remarkably shorter than that from normal SHE cells.Imrnunohistochemical analysis of p53 protein showed that no heavy staining was found on slice of tumor derived from transformant inoculated in nude mice with hamster specific p53 monocloned antibody HD200.The results implied that p53 gene had been mutated by deletion,which might lead to loss of p53 protein expression but the increased expression of p53 remained in a particle-induced SHE transformant.

Identification of normalization factors for quantitative realtime RT-PCR analysis of gene expression in Pacific abalone Haliotis discus hannai

Quantitative real-time reverse transcription-polymerase chain reaction （qRT-PCR） is widely used in studies of gene expression. In most of these studies, housekeeping genes are used as internal references without validation. To identify appropriate reference genes for qRT-PCR in Pacific abalone Haliotis discus hannai, we examined the transcription stability of six housekeeping genes in abalone tissues in the presence and absence of bacterial infection. For this purpose, abalone were infected with the bacterial pathogen Fibrio anguillarum for 12 h and 48 h. The mRNA levels of the housekeeping genes in five tissues （digestive glands, foot muscle, gill, hemocyte, and mantle） were determined by qRT-PCR. The PCR data was subsequently analyzed with the geNorm and NormFinder algorithms. The results show that in the absence of bacterial infection, elongation factor-l-alpha and beta-actin were the most stably expressed genes in all tissues, and thus are suitable as cross-tissue type normalization factors. However, we did not identify any universal reference genes post infection because the most stable genes varied between tissue types. Furthermore, for most tissues, the optimal reference genes identified by both algorithms at 12 h and 48 h post-infection differed. These results indicate that bacterial infection induced significant changes in the expression of abalone housekeeping genes in a manner that is dependent on tissue type and duration of infection. As a result, different normalization factors must be used for different tissues at different infection points.

猴免疫缺陷病毒(SIVmac239)恒河猴适应株耐9-(2-磷酸甲氧丙基)腺嘌呤(PMPA)突变位点筛查

目的初步明确猴免疫缺陷病毒(SIVmac239)耐9-(2-磷酸甲氧丙基)腺嘌呤(PMPA)突变基因位点,指导SIV/恒河猴模型在药物评价中的应用。方法 SIVmac239恒河猴适应株感染恒河猴,之后进行PMPA治疗,测定不同时间点血浆病毒载量和外周血CD4+T细胞数;使用CEMx174细胞进行药物敏感实验。单拷贝PCR测定病毒rt基因变异情况。结果 PMPA治疗不能有效降低感染猴血浆病毒载量,且对血CD4+T细胞数没有显著影响;细胞水平药物敏感实验证实该病毒株对PMPA不敏感。序列比对发现S205L和M502I可能影响到病毒对PMPA的药物敏感性。结论本研究为SIV/恒河猴模型的合理使用及HIV-1的临床治疗提供了信息。

Cloning of cDNA Encoding COMT from Chinese White Poplar ( Populus tomentosa ), Sequence Analysis and Specific Expression

The cDNA fragment encoding caffeic acid 3_O_methyltransferase (COMT) in Chinese white poplar ( Populus tomentosa Carr.) was isolated and cloned by RT_PCR technique. The size of the cDNA fragment is 1 080 bp, which almost covers the whole cDNA_encoding region. Authors’ cDNA fragment in P. tomentosa shares 98.7% homology with the reported corresponding cDNA in the P. tremuloids at nucleotide level, 99.4% homology at amino acid level, respectively. The analysis of Northern dot hybridization showed that COMT is expressed specifically in the developing secondary xylem of stem during the season of xylem differentiation, which means the linkage between the gene expression for a monolignol biosynthetic enzyme and seasonal regulation of xylem development in woody plant.