A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene

The diversity of methanogenic Archaea from the gut of 6 humans was investigated by targeting mcrA, a molecular metabolic marker of methanogenesis. Three operational taxonomic units (OTUs) were recovered from about 400 clones analyzed, two of which were attributed to the expected Methanobacteriales Methanobrevibacter smithii (4 volunteers) and Methanosphaera stadtmanae (1 volunteer). The third OTU (1 volunteer) corresponded to a distant phylotype that does not cluster with any of the five methanogenic orders. This result, also supported by 16S archaeal sequences retrieved from the same volunteer, strongly suggests there may be a sixth order and hence potential underestimation of the role of methanogens in gut physiology.     

Detection of baboon cytomegalovirus (BaCMV) by PCR using primers directed against the glycoprotein B gene

We have cloned and sequenced the glycoprotein B genes from five strains of BaCMV, isolated from three subspecies of cynocephalus baboons (olive, yellow and chacma). Primers were designed using conserved DNA regions of the gB gene to allow DNA amplification from all strains of BaCMV. These regions differ sufficiently from human CMV that HCMV strains are not amplified, thus allowing differentiation of BaCMV from HCMV. These diagnostic primers were used to test crude nucleic acid extracts from 27 strains of BaCMV and detected 26 of them. Overall, the sensitivity and specificity of this assay are 96.7 and 100%, respectively. BaCMV strains isolated from yellow and olive baboons were very similar and could be discriminated from strains isolated from chacma baboons using a second set of PCR primers. Phylogenetic analysis of the gB genes supported the inferred close relationship of strains isolated from olive and yellow baboons.     

PCR-RFLP结合克隆测序监测乙肝病毒拉米夫定耐药突变株的产生

目的 建立PCR结合酶切的方法监测慢性乙型肝炎患者体内拉米夫定耐药突变株的产生,并与PCR产物克隆后测序相结合。了解此方法的可靠性和可行性,同时用此方法筛查50例应用拉米夫定治疗的慢性乙型肝炎患者中耐药株的发生情况。方法 拉米夫定治疗的慢性乙型肝炎患者50例,治疗时间9个月-24个月,设计错配PCR结合限制性片段长度多态性方法,快速检测患者体内乙型肝炎病毒（HBV）酪氨酸-蛋氨酸-天门冬氨酸-天门冬氨酸（Tyrosine-Methionine-Aspartic acid-Aspartic acid,YMDD)变异株的发生情况,对筛检耐药株阳性的标本应用PCR产物克隆后测序加以证实。结果 在50例服用拉米夫定患者中发现9斧正患者在用药超过9个月时出现拉米夫定耐药突变株（YMDD变异株）,其中YIDD变异5例,YVDD变异4例,后者有3例合并有1526M突变。结论 本方法在检测YMDD变异方面具人快速简便的特点,经克隆后测序证实,具有较好的可靠性。     

Detection of Listeria monocytogenes in food using a combined enrichment/real-time PCR method targeting the prfA gene

A combined enrichment/real-time PCR method for the detection of Listeria monocytogenes is presented. The method is based on a conventional PCR assay targeting the prfA gene, which has been validated and suggested as an international standard PCR method for identifying L. monocytogenes in food. This real-time PCR assay includes an internal amplification control. Inclusivity and exclusivity were 100% each when testing 100 L. monocytogenes isolates, 30 Listeria spp. isolates other than L. monocytogenes, and 29 non-Listeria isolates. The theoretical detection limit was one copy of the target gene per PCR reaction and the practical detection limit was about 5 copies per PCR. Using the combined enrichment/real-time PCR method, 7.5 CFU/25 ml of artificially contaminated raw milk, and 9, 1, and 1 CFU/15 g of artificially contaminated salmon, paté, and green-veined cheese, respectively, were detected. When analyzing 76 naturally contaminated food samples of various types and comparing the results with the ISO 11290-1 standard method, the relative accuracy was 96%, the relative specificity 100%, and the relative sensitivity, 76.9%.     

Detection of low copy number inversions in mouse genomic DNA with unidirectional PCR primers

The recessive brachypodism (bp) mutation, located in the growth/differentiation factor 5 (GDF5) gene, causes highly specific skeletal changes in the limbs of brachypod mice. Although Southern blot analysis does not distinguish sequence disruptions in the GDF5 sequence of brachypod mice, sequencing and mapping GDF5 mRNA reveals the bp mechanism to be an inversion preceded by a small deletion. We report here a simple and sensitive method of bp detection from mouse genomic DNA. Previous bp detection used degenerative PCR sequencing. However, without automation, sequencing is a laborious effort for GDF5 inversion detection. The method developed utilizes two unidirectional primers in PCR (UP-PCR), which allow for quick and sensitive analysis of gel electrophoresed PCR products. UP-PCR of the GDF5 gene in wildtype mouse genomic DNA cannot amplify a fragment due to the unidirectional primers. However, UP-PCR of the GDF5 gene in bp mouse genomic DNA does amplify a fragment from the GDF5 gene. Amplification occurs because of the inverted fragment in bp GDF5. This fragment changes the direction of the second forward primer 180° to the position of a reverse primer. UP-PCR detection of the bp inverted fragment is highly sensitive. Amplified fragments were obtained from the bp genomic DNA in the presence of wildtype genomic DNA in ratios up to 1:10⁶, respectively. The sensitivity and simplicity of this method allow for quick, inexpensive, and reliable detection of the bp inversion. Environ. Mol. Mutagen. 30:260–263, 1997 © 1997 Wiley-Liss, Inc.     

应用顺序特异性引物聚合酶链反应检测华南人群HLA-B座位第4外显子变异

目的：为探明中国华南人群中因HLA-B座位发生基因突变而引起表达变异存在的可能性。方法：用顺序特异性引物聚合酶链反应（PCR-SSP）对75例经血清血分型为纯合型样本再次分型，对有差异的结果使用PCR-SSP方法检测第四外显子突变情况。结果：75例血清学指定为纯合型标本经DNA分型证实有12例为杂合型。12例结果有差异的样本经PCR-SSP法表达变异的筛查发现有1例存在第四外显子额外胞嘧啶插入，经DNA分型发现的第二基因为沉默基因。结论：应用PCR-SSP方法可检测HLA-B等位基因突变，该突变导致HLA-B基因表达无效，进行HLA基因表达变异的检测可提高HLA分型的准确性，更加有效的指导临床进行器官和骨髓的选配。     

Development of a real-time PCR targeting the yidC gene for the detection of Mycoplasma hominis and comparison with quantitative culture

Mycoplasma hominis is an opportunistic human mycoplasma species that can be either commensal or pathogenic. Its detection by culture is considered to comprise the reference technique. Previously reported PCR techniques target the 16S rRNA or the gap gene, although sequence variations among clinical isolates may lead to variations in clinical sensitivity. The present study aimed to develop a specific TaqMan quantitative real-time PCR assay, targeting a gene conserved in all M. hominis isolates, and to compare it with quantitative culture. With the knowledge of the M. hominis PG21 genome sequence, the yidC gene, encoding a membrane protein translocase, was chosen as target. Its intraspecies heterogeneity was checked at the nucleotide level using 31 reference or clinical strains. The limit of detection, the analytical specificity and the reproducibility of the assay were assessed. Moreover, PCR and culture results were compared using 153 urogenital specimens. The limit of detection was seven copies/μL. The analytical specificity was 100%, with good inter- and intra-assay reproducibility. Among the 153 urogenital specimens, the yidC PCR and culture allowed detection of 55 and 45 M. hominis-positive samples, respectively. Comparison of the bacterial load among the 45 specimens found to be M. hominis-positive by both techniques revealed a statistically significant association between the quantitative results obtained. In conclusion, we developed a specific, sensitive and reproducible real-time PCR to detect all M. hominis clinical isolates. This PCR was shown to have higher sensitivity than culture, although both methods were correlated for quantification of M. hominis loads in urogenital specimens.     

Detection of Shigella by a PCR assay targeting the ipaH gene suggests increased prevalence of shigellosis in Nha Trang, Vietnam

Shigella spp. are exquisitely fastidious gram-negative organisms which frequently escape detection by traditional culture methods. To get a more complete understanding of the disease burden caused by Shigella in Nha Trang, Vietnam, real-time PCR was used to detect Shigella DNA. Randomly selected rectal swab specimens from 60 Shigella culture-positive patients and 500 Shigella culture-negative patients detected by population-based surveillance of patients seeking care for diarrhea were processed by real-time PCR. The target of the primer pair is the invasion plasmid antigen H gene sequence (ipaH), carried by all four Shigella species and enteroinvasive Escherichia coli. Shigella spp. could be isolated from the rectal swabs of 547 of 19,206 (3%) patients with diarrhea. IpaH was detected in 55 of 60 (93%) Shigella culture-positive specimens, whereas it was detected in 87 of 245 (36%) culture-negative patients free of dysentery (P < 0.001). The number of PCR cycles required to detect a PCR product was highest for culture-negative, nonbloody diarrheal specimens (mean number of cycles to detection, 36.6) and was lowest for children with culture-positive, bloody diarrheal specimens (mean number of cycles, 25.3) (P < 0.001). The data from real-time PCR amplification indicate that the culture-proven prevalence of Shigella among patients with diarrhea may underestimate the prevalence of Shigella infections. The clinical presentation of shigellosis may be directly related to the bacterial load.     

内皮素—1基因内含子4Taq I片段多态性的研究

根据EDN1第4内含子设计相应引物,建立检测EDN1第4内含子TaqI多态性PCR＋RFLP技术。利用该技术,扩增到具有特异性的PCR产物,长为358bp。经限制性核酸内切酶TaqI酶酶切检测中国汉族人群该片段多态性状况。实验显示中国汉人群中存在该位点的多态性。基因T1的频率为0．664;T2基因型频率为0．336;T1T1基因型频率为0．418;T1T2基因型频率为0．492;T2T2基因型频率为0．090。该位点可作为遗传标记探讨中国人群中与EDN1相关遗传病的关系。     

Detection and identification of Bartonella species pathogenic for humans by PCR amplification targeting the riboflavin synthase gene (ribC)

Several Bartonella species have now been implicated as human pathogens. The recovery of these fastidious organisms in the clinical microbiology laboratory remains difficult, and current methods are still relatively insensitive. Thus, the bartonellae are good candidates for detection by PCR. We have developed a PCR assay which uses a single primer pair targeting the riboflavin synthase gene (ribC) and detected six Bartonella species that have been implicated in human disease, B. henselae, B. quintana, B. bacilliformis, B. clarridgeiae, B. elizabethae, and B. vinsonii subsp. berkhoffii. Species identification is achieved simply by restriction enzyme digestion of the amplicon. This PCR assay appears to be specific for the Bartonella genus because it failed to amplify DNA from several other bacterial species.     

Molecular analyses of microbial diversity associated with the Lonar soda lake in India: an impact crater in a basalt area

The prokaryotic diversity associated with an Indian soda lake (Lonar Crater Lake) located in a basaltic soil area was investigated using a culture-independent approach. Community DNA was extracted directly from four sediment samples obtained by coring to depths of 10-20 cm. Small subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific to the domains Bacteria and Archaea. The PCR products were cloned and sequenced. For the bacterial rDNA clone library, 500 clones were randomly selected for further analysis. After restriction fragment length polymorphism (RFLP) analysis and subsequent sequencing, a total of 44 unique phylotypes were obtained. These phylotypes spanned a wide range within the domain Bacteria, occupying eight major lineages/phyla. 34% of the clones were classified as firmicutes. The other clones were grouped into proteobacteria (29.5%), actinobacteria (6.8%), deinococcus-thermus (4.5%), cytophages-flavobacterium-bacteroidetes (13.3%), planctomycetes (6.8%), cyanobacteria (4.5%) and spirochetes (2.27%). In the case of the archaeal 16S rDNA library, analysis of 250 randomly selected clones revealed the presence of 13 distinct phylotypes; 5 phylotypes were associated with Crenarchaeota and 8 with Euryarchaeota. Most of the euryarchaeota sequences were related to methanogens. Findings from this molecular study of a site investigated for the first time have revealed the presence of a highly diverse bacterial population and a comparatively less diverse archaeal population. The majority ( approximately 80%) of the cloned sequences show little affiliation with known taxa (<97% sequence similarity) and may represent novel taxa/sequences and organisms specifically adapted to this basaltic soda lake environment. Diversity analyses demonstrate greater diversity and evenness of bacterial species compared to a skewed representation of species for Archaea.     

人蛋氨酸合成酶还原酶A66G基因突变频率的检测

目的 建立一种简便、准确、实用的人蛋氨酸合成酶还原酶(MSR)A66G基因突变频率的检测方法,并了解汉族人MSR基因的分布特点。方法 应用聚合酶链反应(PCR)特异性扩增蛋氨酸合成酶还原酶(MSR)A66G基因序列,扩增产物用限制性内切酶NdeI酶切,聚丙烯酰胺凝胶电泳后,观察酶切位点的限制性片段长度多态性(RFLP)图谱。结果 运用PCR-RFLP法检测了150名汉族人蛋氨酸合成酶还原酶(MSR)A66G基因点突变,其中野生型纯合子频率为25.33％,杂合子频率为52.00％,突变型纯合子频率为22.67％。突变等位基因频率为0.4867。结论 该方法简便、快速、准确,适合于一般实验室检测及大规模的人群调查,汉族人MSR基因的分布与其他地区人群的分布无明显差异。     

Real-time PCR assay targeting the actin gene for the detection of Cryptosporidium parvum in calf fecal samples

Cryptosporidium parvum infection is very important with respect to public health, owing to foodborne and waterborne outbreaks and gastrointestinal illness in immunocompetent and immunocompromised persons. In cattle, infection with this species manifests either as a subclinical disease or with diarrheal illness, which occurs more often in the presence of other infectious agents than when alone. The aim of this study was to develop a real-time polymerase chain reaction (PCR) assay for the detection of C. parvum in calf fecal samples and to compare the results of this assay with those of the method routinely used for the diagnosis of Cryptosporidium spp., nested PCR targeting the 18S rRNA gene. Two hundred and nine fecal samples from calves ranging in age from 1 day to 6 months were examined using real-time PCR specific for the actin gene of C. parvum and by a nested PCR targeting the 18S rRNA gene of Cryptosporidium spp. Using real-time PCR detection, 73.2% (153 out of 209) of the samples were positive for C. parvum, while 56.5% (118 out of 209) of the samples were positive for Cryptosporidium spp. when the nested PCR amplification method was used for the detection. The analytical sensitivity of the real-time PCR was approximately one C. parvum oocyst. There was no significant nonspecific DNA amplification of any of the following species and genotype: Cryptosporidium andersoni, Cryptosporidium baileyi, Cryptosporidium bovis, Cryptosporidium canis, Cryptosporidium galli, Cryptosporidium ryanae, Cryptosporidium serpentis, or avian genotype II. Thus, we conclude that real-time PCR targeting the actin gene is a sensitive and specific method for the detection of C. parvum in calf fecal samples.     

Detection of large deletions in the LDL receptor gene with quantitative PCR methods

Background  

Familial Hypercholesterolemia (FH) is a common genetic disease and at the molecular level most often due to mutations in the LDL receptor gene. In genetically heterogeneous populations, major structural rearrangements account for about 5% of patients with LDL receptor gene mutations.     

Detection of telomerase in hepatocellular carcinomas using a PCR ELISA assay: comparison with hTR expression

BACKGROUND: While telomerase is undetectable in most normal somatic tissues, telomerase activation has been detected in many immortal cell lines and various cancers. AIM: To investigate telomerase expression in hepatocellular carcinoma, and to assess the expression of the RNA component of telomerase, hTR. METHODS: 39 hepatocellular carcinomas were studied using a telomerase polymerase chain reaction (PCR) enzyme linked immunosorbent assay, which does not require radioactive PCR amplification and yields a semiquantitative measurement. Expression of hTR was also assessed by a non-radioactive in situ hybridisation procedure. The correlations between these two markers and the clinicopathological data were analysed. RESULTS: Telomerase activity was detected in 23 of 39 hepatocellular carcinoma specimens (59%). Comparison of hepatocellular carcinoma with and without telomerase expression, or with high and low telomerase (10 cases v 13 cases), showed no differences in the principal clinicopathological data. Although median survival was lower in the group with detectable telomerase activity than in that with undetectable activity (510 v 720 days) the difference was not significant (log-rank test, p = 0.08). hTR expression was detected in 11 of 14 cases of hepatocellular carcinoma tested (78%) and in four of 12 samples of adjacent non-cancerous tissue (33%). Five tumours and four non-cancerous tissues were positive for hTR, whereas no telomerase activity was detected in these. CONCLUSIONS: The presence of telomerase activity in hepatocellular carcinomas is confirmed. No correlation was observed between clinicopathological data and telomerase expression in hepatocellular carcinoma, but survival seemed better in the absence of telomerase expression. hTR seems to be more widely expressed than telomerase.     

Detection of yellow fever virus: a comparison of quantitative real-time PCR and plaque assay

Yellow fever virus quantitation is performed routinely by cultivation of virus containing samples using susceptible cells. Counting of the resulting plaques provides a marker for the number of infectious particles present in the sample. This assay usually takes up to 5 days before results are obtained and must be carried out under L2 or L3 laboratory conditions, depending on the yellow fever virus strain used. For clinical diagnosis of yellow fever virus infections the cell culture-based approach takes too long and is of limited practical relevance. Recently, due to its considerable sensitivity, PCR has become a promising method for virus detection. However, whilst PCR can detect virus-specific nucleic acids, it does not allow conclusions to be drawn regarding the infectious potential of the virus detected. Nonetheless, for diagnostic purposes, a rapid, specific and sensitive virus PCR is preferable. Therefore, two independent yellow fever virus-specific real-time PCR assays were established and compared the viral RNA loads to the results of a traditional plaque assay. The estimated ratio of yellow fever virus genomes to infectious particles was between 1000:1 and 5000:1; both approaches displayed a comparable precision of <45%. A significant correlation between genome number as determined by real-time PCR and the corresponding number of plaques in paired samples was found with a Pearson coefficient of correlation of r=0.88 (P<0.0001).     

用聚合酶链反应检测结肠癌人乳头状瘤病毒基因

目的　应用聚合酶链反应,检测人乳头状瘤病毒(Humanpapillomavirus,HPV)基因与结肠癌及癌区周边组织的相关性。方法　将结肠镜检获取的72例活检标本进行病理检测,其中结肠癌46例,非癌26例(结肠癌周边组织标本10例),标本用蜡块包埋与固定液两种方法固定,用聚合酶链反应(PCR)特定DNA片段体外扩增法。结果　结、直肠癌人乳头状瘤毒基因检测阳性率434%,结、直肠癌周边组织阳性率10%,非癌组织阳性率为0%。结论　癌区组织基因(HPVs)检测率较高,与非癌对照组相比,差异有显著性(P<0.05),癌组织中HPVs主要以HPV1633型和HPV18型为主,统计学分析表明结、直肠癌的发生、发展与HPV感染有一定的相关性,尤以HPV16型关系更为密切。     

Multiplex real-time PCR targeting the RNase P RNA gene for detection and identification of Candida species in blood

We have developed a single-tube multiplex real-time PCR method for the detection of the eight most common Candida species causing septicemia: Candida albicans, C. dubliniensis, C. famata, C. glabrata, C. guilliermondii, C. krusei, C. parapsilosis, and C. tropicalis. The method developed targets the RNase P RNA gene RPR1. Sequences of this gene were determined for seven of the Candida species and showed surprisingly large sequence variation. C. glabrata was found to have a gene that was five times longer gene than those of the other species, and the nucleotide sequence similarity between C. krusei and C. albicans was as low as 55%. The multiplex PCR contained three probes that enabled the specific detection of C. albicans, C. glabrata, and C. krusei and a fourth probe that allowed the general detection of the remaining species. The method was able to detect 1 to 10 genome copies when the detection limit was tested repeatedly for the four species C. albicans, C. glabrata, C. krusei, and C. guilliermondii. No significant difference in the detection limit was seen when the multiplex format was compared with single-species PCR, i.e., two primers and one probe. The method detected eight clinically relevant Candida species and did not react with other tested non-Candida species or human DNA. The assay was applied to 20 blood samples from nine patients and showed a sensitivity similar to that of culture.     

Detection of structural gene mutations and promoter polymorphisms in the mannan-binding lectin (MBL) gene by polymerase chain reaction with sequence-specific primers

This study describes a new approach to the determination of all known mannan-binding lectin (MBL) mutations. The distribution of known variants of the MBL gene in a population of healthy unrelated Danes was determined and the genotype was correlated with the plasma MBL concentrations. The following genetic polymorphisms were studied: three point mutations in the promoter region at position -550 (H/L variants), -221 (X/Y variants), -70 (nt C or T), one point mutation in the 5' untranslated (UT) region at position +4 (P/Q variants) and three point mutations located at codons 52, 54 and 57 in exon 1 of the MBL gene, at nucleotide positions 223, 230 and 239, respectively. To perform genotyping, we designed sequence specific primers for a polymerase chain reaction (PCR-SSP). PCR-SSP is a powerful technique for the discrimination of alleles resulting from single base substitutions and is a widely used technique. Another major advantage of the PCR-SSP method is its ability to determine whether sequence motifs are in cis or trans. The frequencies of variants in exon 1 obtained by PCR-SSP were completely comparable to results obtained by previously described PCR methods, restriction fragment length polymorphism (RFLP) and site-directed mutagenesis (SDM). This PCR-SSP method is performed with standard laboratory equipment and has the capacity to detect all genetic variants in 100 samples in 2 days at an estimated total cost of GBP 11 per sample. Analysing the correlation between MBL haplotype and plasma MBL levels, we confirmed that three different structural variants, B, C and D and the promoter haplotypes HY, LY and LX have a dominant effect on the concentration of MBL. The HY haplotype is associated with the highest plasma concentration, the LY haplotype with intermediate levels and the LX haplotype with the lowest levels. The LX haplotype was found to be associated with very low levels of MBL similar to those found in association with the structural B genotype. The gene frequencies of variants in the MBL gene in the Danish population studied correspond to previous reports on Caucasian populations.