Sequencing of hepatitis C virus cDNA with polymerase chain reaction directed sequencing *

AIM To explore a rapid and easy sequencing method for hepatitis C virus (HCV) genome, and establish a new sequencing method in China. METHODS Polymerase Chain Reaction (PCR) was combined with DNA sequencing technique. PCR products were purified by agarose gel electrophoresis, polyacrylamide gel electrophoresis (PAGE), Polyethylene glycol (PEG) respectively. Then in the presence of a 5′ labeling PCR primer, purified PCR products were directly sequenced. By this method, HCV NS5b cDNA from two HCV infected individuals (HC 42 and HC 49) were sequenced.

Detection of rare mutation of β-thalassemia by direct sequence analysis of the PCR products

A technique of direct sequence analysis of β-globin gene with the products of amplifi-cation by polymerase chain reaction (PCR) was reported and a case of β-thalassemia with therare mutation in Chinese,‘codon 14/15 (+G)’ was detected by this method.After the se-quence of the mutation site was determined,an analysis of the restriction map of the gene anddot blot hybridization with radioactive allele specific oligonucleotide probe was designed to con-firm the result of DNA sequencing.

Sequence Analysis and Quantitative Detection of Norwalk-like Viruses in Cultured Oysters of China

We isolated 4 Norwalk-like viruses （NLVs） contaminated oysters from 33 Chinese oysters collected from local commercial sources of Shandong Province. After amplification of the RNA-dependent RNA polymerase （RdRp） region of NLVs genomes with RT-PCR, the open reading frame 1 （ORF 1） of the RdRp was sequenced and subjected to multiple-sequence alignment. The results showed that NLVs in the four isolates belong to genogroup Ⅱ. The sequence comparison showed that the similarity between four Chinese oyster isolates were higher than 99.0%, which indicated that NLVs prevalent in close areas have high homogeneity in genome sequences. In addition, the most conserved sequences between diverse NLVs were used to design primers and TaqMan probes, then the real-time quantitative PCR assay was performed. According to the standard curve of GII NLVs, the original amounts （copies） of NLVs in positive patient＇s fecal isolate, positive Japanese oyster isolate, and the Chinese oyster isolate were 8.9× 10^8, 1.25× 10^8 and 4.7× 10^1 respectively. The detecting limit of NLVs was 1 × 10^1 copies. This study will be helpful for routine diagnosis of NLVs pathogens in foods and thus for avoiding food poisoning in the future.

Relationship between autoimmune hepatitis and HLA-DR4 and DRβ allelic sequences in the third hypervariable region in Chinese

AIM To analyze the association of HLA-DRBl with autoimmune hepatitis (AIH) in patients from China.``METHODS In .32 patients and 45 healthy controls,polymerase chain reaction amplification with sequencespecific primers (PCR-SSP) was performed to examine the association of certain alleles or polymorphic sequences of HLA-DRB1 with AIH.``RESULTS HLA-DRB1 typing by PCFLSSP showed that DR4had a significantly increased frequency among patients with AIH versus healthy control (46.9% versus 20.8%;relative risk 3.35, P=0.014). In subtypes of DR4, there was a trend of increase in the gene frequency of DRB10405 in patients with AIH versus healthy controls (21.9%vs 6.3%, P=0.04, but Pc 0.08). In addition, asignificant increase was found in the alleles frequency encoding QRRAA from the third hyperpolymorphic region of DR4 in the patients with AIH (86.7% of DR4 positive patients vs 40.0% in DR4 positive controls, P 0.016, Pc =0.028. RR 9.75).``CONCLUSION AIH in Chinese is associated with HLADR4. There is a relationship between QRRAA sequence within the third hyperpolymorphic region of the DRB allele and AIH in Chinese.

PCR Based Detection and Phylogenetic Analysis of Fowl Adenovirus Strains Isolated from 2019 Epidemic from Punjab and Sindh, Pakistan

Hydro-Pericardium Hepatitis (HPH) is an emerging infectious disease of commercial poultry, caused by different serotypes of Fowl Adeno Virus. The vertical transmission of the virus into the progeny may results in devastating damage, causing huge economic losses to its farmers. In present study, molecular typing is performed on basis of partially conserved hexon gene sequences, using a unique set of primers having common reverse oligo for simultaneous detection of FAdV1, FAdV-4 and FAdV-11. A total of 14 fowl adeno virus strains were isolated from 100 suspected adeno virus liver samples, collected from different districts in Pakistan, between 2018 and 2019. FASTA’s sequence alignment and phylogenetic analysis revealed that out of the 14, one isolate which belonged to group A showed 27% similarity with FAdV-1, while three isolates showed 99%, 95% & 45% similarity to FAdV-4 (Group C). Whereas, ten isolates showed more than 99% similarity to FAdV-11 (Group D). The serotypes FAdV1, FAdV-4 and FAdV-11 are prevailing in the breeder and broilers. These results hold great importance in rapid, reliable and simultaneous detection of the three FAdV serotypes. Therefore, fowl adeno virus vaccine production for commercial poultry shall be according to the prevalent field serotypes.

Cloning, sequencing and analyzing of the heavy chain V region genes of human polyreactive antibodies

The heavy chain variable region genes of 5 human polyreactive mAbs generated in our laboratory have been cloned and sequenced using polymerase chain reaction (PCR) technique. We found that 2 and 3 mAbs utilized genes of the VHIV and VHIII families, respectively. The former 2 VH segments were in germline configuration. A common VH segment, with the best similarity of 90.1 % to the published VHIII germline genes, was utilized by 2 different rearranged genes encoding the V regions of other 3 mAbs. This strongly suggests that the common VH segment is a unmutated copy of an unidentified germline VHIII gene. All these polyreactive mAbs displayed a large NDN region (VH-D-JH junction). The entire H chain V regions of these polyreactive mAbs are unusually basic. The analysis of the charge properties of these mAbs as well as those of other poly- and mono- reactive mAbs from literatures prompts us to propose that the charged amino acids with a particular distribution along the H chain V region,especially the binding sites (CDRs), may be an important structural feature involved in antibody polyreactivity.

Confirmation of Pearl Millet-Napiergrass Hybrids Using EST-Derived Simple Sequence Repeat (SSR) Markers

Prospects for deploying perennial grasses that are currently considered leading candidates for dedicated energy crops over large acreages are debatable because of several limitations, including vegetative propagation or small seed size, low biomass production during the first growing season, and incomplete assessments of crop invasiveness risk. Pearl Millet-Napiergrass hybrids (“PMN”;Pennisetum glaucum [L.] R. Br. × P. purpureum Schumach.), in contrast, are large-seeded, sterile feedstocks capable of high biomass production during establishment year. Novel methods are warranted for confirmation of PMN hybrids, as traditional morphological observations can be inconclusive and chromosome number determination using cytological methods is laborious and time consuming. Six putative PMN lines were produced in this study, and 10 progeny from each line were evaluated using morphological traits, seed fertility, flow cytometry, and expressed sequence tag-simple sequence repeat (EST-SSR) markers. All putative hybrid lines were sterile and failed to produce seed. The PMN hybrids could not be distinguished from either parent using flow cytometry due to highly similar nuclear genome DNA contents. A number of paternal napiergrass-specific EST-SSRs were identified for each PMN line, and four paternal-specific EST-SSRs conserved across all napiergrass accessions were selected to screen the putative PMN hybrids. These EST-SSRs confirmed that all F1 individuals analyzed were PMN hybrids. The use of paternal-specific markers therefore provides a valuable tool in the development of both “Seeded-yet-Sterile” biofuel PMN feedstocks and additional PMN cultivar-and parental species-specific markers.

Sequence determination of exp-1 Gene of Plasmodium Falciparum Isolate FCC1 /HN

目的 测定恶性疟原虫FCCl／HN株exp-1基因序列。方法 根据exp-1基因已知序列设计合成1对引物，用PCR技术从FCCl／HN株基因组DNA中扩增exp-1基因；将exp-1基因克隆入pMD-18T载体，转化大肠杆菌JMl09感受态细胞，铺x—gal LB平板；挑取阳性菌落，用酶切，PCR扩增进行鉴定。以正确的重组质粒为模板，用双脱氧链末端终止法测定exp-1基因序列。结果 从恶性疟原虫FCCl／HN株基因组DNA中获取exp-1基因，成功克隆入pMD-18T载体；测序表明FCCl／HN株exp-1基因全长937bp，编码162个氨基酸。结论 克隆了恶性疟原虫FCCl／HN株exp-1基因，并测定了其核苷酸序列，为进-步研究其功能奠定基础。

Detecting Factor Ⅺ Deficiency in Holstein Cattle Using PCR Analysis

[Objective] This study established a method to detect Factor Ⅺ by polymerase chain reaction analysis.[Method]A pair of primers was designed and synthesized according to sequences of FⅪ gene in Holstein calves,published in Genbank. Polymerase chain reaction was used to analyze FⅪ deficiency of 576 Holstein calves in Henan,and the result was verified by DNA sequencing. [Result] We detect 576 cows,which include two carriers and one F Ⅺ deficiency,and the result was consistent with the DNA sequencing. The frequency of the FⅪ mutant allele was 0.3%,the carrier was 0.3%,the prevalence was 0.2%.[Conclusion]A method detecting FⅪ by polymerase chain reaction analysis was established. This method is not only simple and convenient,but also has a high accuracy and low cost,which is more suitable for large-scale FⅪ investigation.

染色体核型分析、染色体拷贝数变异测序、荧光定量聚合酶链技术在产前诊断联合应用的价值

目的探讨染色体核型分析、染色体拷贝数变异测序(CNV-seq)、荧光定量聚合酶链技术(QF-PCR)在产前诊断中联合应用的价值。方法选取2022年1月至10月在茂名市人民医院产前诊断中心就诊的具有产前诊断指征的417例孕妇进行穿刺,同时做染色体核型分析、CNV-seq及QF-PCR,比较三种检测方法各自及联合检测的异常检出率及其他特殊情况。结果三种技术共检出63例异常,异常检出率为15.11%。染色体核型分析共检出29例异常核型,染色体核型异常检出率为6.95%。有17例数目异常,其中有7例47,XN,+21、4例47,XN,+18、2例47,XXY、1例45,X、3例嵌合;另有12例结构异常。CNV-seq共检出57例异常,染色体异常检出率为13.67%,其中常见非整倍体17例、大片段CNV(≥10 M)有2例、微小CNV(<10 M)有38例。明确致病性CNVs 17例,可能致病性CNVs或临床意义不明CNVs 23例。有5例异常核型CNV-seq检测为正常。QF-PCR技术共检出17例数目异常,异常检出率为4.08%。染色体核型分析、CNV-seq及QF-PCR三种技术的异常检出率比较,差异有统计学意义(P<0.05)。CNV-seq检测的异常检出率高于核型和QF-PCR检测,差异有统计学意义(P<0.017);核型检测和QF-PCR检测的异常检出率比较,差异无统计学意义(P>0.017)。结论染色体核型分析有利于发现更多的染色体结构异常,CNV-seq有利于发现更多的微小缺失或重复,染色体核型分析和CNV-seq及QF-PCR在产前诊断中实现优势互补,为临床咨询提供准确的实验室依据,加强优生指导。

伪狂犬病病毒Fa株gE基因的克隆与序列的比较分析

根据已发表的伪狂犬病病毒(PRV)的基因序列,设计合成一对引物PCL1和PCL2,以PRVFa株的DNA为模板成功地扩增得到预期的长约1 7kb的特异片段,经酶切鉴定,初步确定为gE基因。将扩增产物经KpnⅠ、EcoRⅠ消化形成粘末端克隆到pUC18质粒,得到了明显大于载体的重组质粒PpgE。重组质粒PpgE经酶切鉴定为含有PRV的gE基因,测序PpgE得到完整的gE基因片段,并与4株不同来源的毒株进行了比较分析。5毒株的gE同源性比较分析发现毒株间同源性最低也高达97%,这体现了gE基因的保守性。分析还表明Fa与TNL同源。同时99%的高同源性也显示Fa、Ea、SH可能是同一毒株。gE序列在1040-1410碱基的高同源性区域作为PRV的PCR检测或作为核酸探针是非常重要的。

1999～2003年鲍氏不动杆菌耐药变迁与β-内酰胺酶表型及基因型检测

目的了解5年来鲍氏不动杆菌的耐药性变迁、产β内酰胺酶(BLA)及BLA基因型存在状况。方法采用微量稀释法测定在1999年1月～2003年12月间,自临床分离的549株鲍氏不动杆菌对23种抗菌药物的敏感性、三维试验法检测超广谱β内酰胺酶(ESBLs)、AmpC酶、聚合酶链反应(PCR)及序列分析的方法分析BLA基因型。结果5年中总敏感率居前4位的依次是亚胺培南(96.4%)、多黏菌素E(93.0%)、美罗培南(92.9%)和哌拉西林/他唑巴坦(30.1%),其余在0.0～20.9%之间;5年间亚胺培南的抗菌活性最高,且历年不减,敏感率>95.0%;其次是多黏菌素E和美罗培南,敏感率分别>88.0%和84.0%;5年间耐药率上升最快的是阿莫西林/克拉维酸、头孢曲松、头孢噻肟、哌拉西林和哌拉西林/他唑巴坦;ESBLs及AmpC酶单独阳性率分别为30.0%和1.7%,48.3%菌株同时产ESBLs和AmpC两种酶;BLA基因TEM和SHV阳性率分别为100.0%和29.2%,基因型分别为TEM1、SHV12、SHV48和SHV56;OXA、CTXM、PER和VEB基因均阴性。结论近5年间鲍氏不动杆菌对大多数常用广谱抗生素的耐药性在逐年增强,并且多重耐药、产ESBLs及AmpC酶状况相当严重,BLA基因TEM和SHV携带率高;亚胺培南仍是抗多重耐药鲍氏不动杆菌感染最有效的抗生素。

PCR检测草莓镶脉病毒的稳定性研究

利用改进的CTAB法提取了优质的草莓总DNA,可以稳定地进行草莓植株中SVBV的PCR检测。对PCR检测草莓植株中SVBV的反应体系进行了优化,结果表明,Promega公司的Taq酶与TaKaRa公司的PCR反应缓冲液配合使用效果较好,适宜引物浓度为0.5μmol/L,退火温度为53℃。20μLPCR反应液中包含0.001μL总DNA时能扩增出SVBV特异谱带,相当于能够从不足1μg的草莓新鲜叶片中检测出SVBV。基于对SVBV中国分离物外壳蛋白基因的序列分析比较,设计并筛选了检测SVBV的理想引物,提高了利用PCR检测草莓植株中SVBV方法的稳定性。

柑桔黄龙病病原DNA片段的克隆及序列分析

本研究利用聚合酶链式反应技术 (PCR) ,合成了中国柑桔黄龙病病原的一段 DNA片段。将此片段插入到 p UC18的 Eco RI位点 ,并转化进大肠杆菌 (Escherichia coli)的 DH5α菌株中。通过 PCR鉴定 ,限制性内切酶 (Eco RI)酶切分析及核苷酸序列分析 ,均表明克隆成功。序列分析结果显示 ,克隆片段与已知相应序列间同源性达 98.6 %。该研究为制备柑桔黄龙病病原 DNA分子探针奠定了基础。

提高石蜡包埋组织中提取DNA质量的实验研究

目的 :确定从石蜡包埋组织中提取 DNA的最佳条件。方法 :改变石蜡切片厚度、组织脱蜡时间、消化液蛋白酶 K浓度、组织消化时间等参数 ,组合出 96种不同提取 DNA的条件 ,比较各种条件下所提取 DNA的数量和质量。结果 :各种条件均可以提取出一定数量的 DNA,但有些条件所提取的 DNA不适合于做 PCR及 DNA序列测定。结论 :从石蜡包埋组织中提取 DNA的最佳条件为 ,1 0 .0 μm组织切片 ;切片脱蜡 2次 ,脱蜡时间分别为 2 h和 1 2 h;消化液中蛋白酶 K浓度5 0 0 mg· L-1;组织消化 1 2

44株阴沟肠杆菌耐药基因分析

目的了解解放军第98医院临床分离的阴沟肠杆菌耐药基因存在状况。方法采用聚合酶链反应及序列分析的方法分析44株阴沟肠杆菌中15种耐药相关基因。结果44株中,12种基因blaTEM、blaOXA-1群、blaMIR、blaDHA、aac(3)-Ⅱ、aac(6′)-Ⅰ、ant(3″)-Ⅰ、intⅠ1、qacE△1-sul1、dfrA1、dfrA17、qnr的阳性株数分别为24株(54.50%)、3株(6.82%)、35株(79.50%)、5株(11.40%)、11株(25.00%)、31株(70.50%)、15株(34.10%)、38株(86.40%)、36株(81.80%)、1株(2.27%)、20株(45.05%)、3株(6.82%),bla0XA-1群基因PCR产物经序列分析确认为blaOXA-1型广谱β-内酰胺酶基因,其他3种基因blaSHV、blaCTX-M-1群、blaOXA-10群均阴性。结论临床分离的阴沟肠杆菌至少存在12种耐药相关基因;在阴沟肠杆菌中检出blaOXA-1、dfrA1、dfrA17和qnr基因均为国内首次报道。

抗人CD_3单链抗体基因的构建及序列分析

本文在已克隆抗人ＣＤ３抗体ＶＨ和Ｖｋ基因的基础上，设计并合成了ＰＣＲ引物。两个外侧引物分别含有ＥｃｏＲＩ和ＳａｌＩ酶切位点及起始码和终止码序列，４个内侧引物各含部分连接肽基因序列。用加端ＰＣＲ分别在ＶＨ基因３＇端和Ｖｋ基因５＇端延伸部分连接肽基因序列，回收后混合运火；应用重叠延伸拼接法，将ＶＨ和Ｖｋ基因通过Ｌｉｎｋｅｒ序列串联为单链抗体基因；利用ＰＣＲ产物两端预先设计的ＳａｌＩ和ＥｃｏＲＩ酶切位点，将其克隆到ｐＵＣ１９质粒中，筛选到阳性克隆。经双脱氧终止法序列测定：ＶＨ和ＶＫ基因及Ｌｉｎｋｅｒ序列均正确，为用基因工程技术生产单链抗体奠定了基础。

TA克隆及双链DNA测序：介绍一种快速克隆及分析PCR产物的方法

将人酸性纤维母细胞生长因子’（ａＦＧＦ’）ｃＤＮＡ的ＰＣＲ产物以ＴＡ连接方式克隆入ｐＣＲ￣（ＴＭ）ＩＩ质粒，然后采用Ｔ７和Ｓｐ６启动子特异性引物对克隆的片段以双脱氧未端终止法进行双链ＤＮＡ测序。

夏威夷椰子超氧化物歧化酶基因片段的克隆与序列分析

以热带植物夏威夷椰子(Chamaedoreacostricana)基因组DNA为模板,根据SOD基因保守序列设计特异引物进行PCR扩增,得到特异基因片段.回收该基因片段,与pMD182T载体连接,并转化到感受态大肠杆菌ER2566细胞,获得Cu·ZnSOD基因片段的克隆.序列分析表明夏威夷椰子Cu·ZnSOD基因片段含3个外显子和3个内含子,编码64个氨基酸,与玉米、红薯和白杨相应氨基酸序列的同源性分别为82.81%,81.25%,81.25%和79.69%.

合肥市产超广谱β-内酰胺酶菌株TEM型耐药基因分布

目的 了解 1999～ 2 0 0 0年合肥市多所医院临床分离的产超广谱 β 内酰胺酶 (ESBLs)肺炎克雷伯菌和大肠埃希菌中 ,TEM型 β 内酰胺酶基因型分布。方法 酶抑制剂增强的肉汤稀释法筛选出产ESBLs细菌 ,PCR扩增其TEM型 β 内酰胺酶编码基因片段 ,克隆入pGEM Teasy载体 ,双脱氧链终止法测定核苷酸序列并确定TEM基因型。结果 98株产ESBLs菌株中有 79株产TEM型 β 内酰胺酶 ,其中TEM 1型 75株和TEM 10型 4株。结论 合肥市产ESBLs肺炎克雷伯菌和大肠埃希菌中存在 2种TEM型 β 内酰胺酶 ,在国内首次报道一种新的 β 内酰胺酶(TEM 10 )。