检测小鼠肝炎病毒的SNaPshot分型技术及其应用

建立一种能对MHV_1、MHV_3、JHM、A_(59) 4种常见小鼠肝炎病毒(Murine Hepatitis Virus,MHV)进行分型检测的SNaPshot新方法。根据MHV 4种常见毒株基因序列比对结果,设计内外两对PCR通用引物和4个单碱基延伸引物,提取MHV 4种常见毒株RNA,逆转录后进行PCR扩增,纯化扩增产物,用SNaPshot方法进行单碱基延伸,将产物进行毛细管凝胶电泳,根据电泳结果分析毒株基因型。优化SNaPshot分析条件,进行灵敏度、特异性分析。用ELISA法和SNaPshot方法检测41例小鼠(Mus musculus)血清样本,将阳性样本进行克隆测序检测。当T1~T4引物修饰的poly T的数量分别为0、3、10和15,其浓度比为4︰6︰5︰10,引物大小分别为16 bp、19 bp、26 bp和31 bp时,SNa Phot分型检测MHV c DNA的最低浓度为1.25 mg/L,特异性为100%,与ELISA和T-克隆测序比较,其准确性为100%(41/41),阳性样本均为JHM毒株。实验结果说明,所建立的SNaPshot检测方法能对MHV_1、MHV_3、JHM、A_(59)进行分型检测,并且具有灵敏、特异、准确的优点。     

Correlation Between Pneumocystis jirovecii Mitochondrial Genotypes and High and Low Fungal Loads Assessed by Single Nucleotide Primer Extension Assay and Quantitative Real‐Time PCR

We designed a single nucleotide primer extension (SNaPshot) assay for Pneumocystis jirovecii genotyping, targeting mt85 SNP of the mitochondrial large subunit ribosomal RNA locus, to improve minority allele detection. We then analyzed 133 consecutive bronchoalveolar lavage (BAL) fluids tested positive for P. jirovecii DNA by quantitative real‐time PCR, obtained from two hospitals in different locations (Hospital 1 [n = 95] and Hospital 2 [n = 38]). We detected three different alleles, either singly (mt85C: 39.1%; mt85T: 24.1%; mt85A: 9.8%) or together (27%), and an association between P. jirovecii mt85 genotype and the patient's place of hospitalization (p = 0.011). The lowest fungal loads (median = 0.82 × 10³ copies/μl; range: 15–11 × 10³) were associated with mt85A and the highest (median = 1.4 × 10⁶ copies/μl; range: 17 × 10³–1.3 × 10⁷) with mt85CTA (p = 0.010). The ratios of the various alleles differed between the 36 mixed‐genotype samples. In tests of serial BALs (median: 20 d; range 4–525) from six patients with mixed genotypes, allele ratio changes were observed five times and genotype replacement once. Therefore, allele ratio changes seem more frequent than genotype replacement when using a SNaPshot assay more sensitive for detecting minority alleles than Sanger sequencing. Moreover, because microscopy detects only high fungal loads, the selection of microscopy‐positive samples may miss genotypes associated with low loads.     

A new method for analysis of mitochondrial DNA point mutations and assess levels of heteroplasmy

Determination of mitochondrial DNA (mtDNA) heteroplasmy for the diagnosis of patients with mitochondrial disorders is a difficult task due to the coexistence of wild-type and mutant genomes. We have developed a new method for genotyping and quantification of heteroplasmic point mutations in mtDNA based on the SNaPshot technology. We compared the data of this method with the widely used "last hot-cycle" PCR-RFLP method by studying 15 patients carrying mtDNA mutations. We showed that SNaPshot is an accurate, reproducible, and sensitive technique for the determination of heteroplasmic mtDNA mutations in different tissues from patients, and it is a promising system to be used in prenatal and postnatal diagnosis of mtDNA-associated disorders.     

Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis

The major goal of this project was the establishment of a tool for rapid mapping of new mutations and genotyping in Arabidopsis consisting of at least 100 evenly spaced framework markers. We assembled a single nucleotide polymorphism (SNP)-based marker set consisting of 112 polymorphic sites with average spacing of 1.15 Mbp derived from an SNP database that we recently developed. This information was used to set up efficient SNP detection reactions based on multiplexed primer extension assays. The 112 Columbia (Col-0)/C24 framework markers were used to assemble 18 multiplexed SNaPshot assays with which up to eight separate loci can be genotyped in a single-tube/single-capillary format. In addition, for 110 framework markers matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) assays have been established for high throughput analyses. We demonstrated the usefulness and the robustness of both procedures of this tool by genotyping 48 BC3F1 individuals created between the accessions Col-0 and C24. Subsets of 10-62 of the established markers discriminate between various combinations of the accessions Col-0, C24, Landsberg erecta (Ler), Cape Verdi Islands (Cvi) and Niederzenz (Nd). Using a subset of 17 evenly distributed and established SNP markers that are also polymorphic between Ler and Col-0, we were able to rapidly map a mutant gene (tbr1) to an interval of 2.3 Mbp in an Ler (tbr1) x Col-0 cross.     

Simultaneous genotyping of multiplex single nucleotide polymorphisms of the K-ras gene with a home-made kit

Accurate and fast genotyping of single nucleotide polymorphisms (SNPs) is important in the human genome project. Here an automated fluorescent method that can rapidly and accurately genotype multiplex known SNPs was developed by using a homemade kit, which has lower cost but higher resolution than commercial kit. With this method, oncogene K-ras was investigated, four known SNPs of K-ras gene exon 1 in 31 coloerctal cancer patients were detected. Results indicate that mutations were present in 8(26%) of 31 patients, and most mutations were localized in codon 12. The presence of these mutations is thought to be a critical step and plays an important role in human colorectal carcinogenesisas.     

Rapid identification of Lactobacillus plantarum group using the SNaPshot minisequencing assay

This study used SNaPshot minisequencing for species identification within the Lactobacillus plantarum group. A SNaPshot minisequencing assay using dnaK as a target gene was developed, and five SNP primers were designed by analysing the conserved regions of the dnaK sequences. The specificity of the minisequencing assay was evaluated using 35 strains of L. plantarum group species. The results showed that the SNaPshot minisequencing assay was able to unambiguously and simultaneously discriminate strains belonging to the species L. plantarum subsp. plantarum, L. plantarum subsp. argentoratensis, Lactobacillus paraplantarum, Lactobacillus pentosus and Lactobacillus fabifermentans. In conclusion, a rapid, accurate and cost-effective assay was successfully developed for species identification of the members of the L. plantarum group.     

Preface

The aim of the study was to introduce a convenient method for identification of differences among individual animals in genes supposed to influence meat performance in pigs. The set of seven candidate genes (IGF2, FOS, MC4R, DGAT1, MYF4, MYF, and MC3R) was used. To determine the genotypes, multiplex polymerase chain reaction (PCR) and minisequencing using SNaPshot system (Applied Biosystems; Forster City, CA, USA) were applied. The efficiency of this gene panel for routine testing in pigs was verified in the Black Pied P?e?tice pig breed by the statistical general linear model. The results showed that both the method and the gene panel are convenient for meat quality testing and offer reproducible results.     

Multiplexed,linkage group-specific SNP marker sets for rapid genetic mapping and fingerprinting of sugar beet (<Emphasis Type="Italic">Beta vulgaris</Emphasis> L.)

A set of single nucleotide polymorphism (SNP) markers has been developed for each of the nine linkage groups of sugar beet. Each set can monitor the polymorphic state at five to six linked marker loci. In each set, the loci selected for marker development are first amplified in a multiplexed reaction. These amplification products are the basis for sequence-specific elongation of primers adjacent to SNP positions. The extension step revealing SNP loci is based on fluorescently labelled nucleotides. In each set, primers developed to reveal SNP alleles differ in length to allow clear peak resolution in capillary electrophoresis. The nine linkage group (LG) –specific sets provide information on the polymorphism at a total of 52 SNP marker loci. Using the SNP-based tool, groups of concerned loci have been anchored to three different linkage maps of sugar beet. In a second experiment, sugar beet breeding lines have been fingerprinted. The use of the nine sets of LG-specific markers in sugar beet genetics and breeding is discussed. The information necessary to specify the 52 marker loci, as well as their map location, and all details concerning SNP assays, including allele type and nature of mutation, are reported.