Hepatitis C virus in human B lymphocytes transformed by Epstein-Barr virus in vitro by in situ reverse transcriptase-polymerase chain reaction

AIM: To study persistence and replication of hepatitis C virus (HCV) in patients' peripheral blood mononuclear cells (PBMC) cultured in vitro. METHODS: Epstein Barr virus (EBV) was used to transform the hepatitis C virus from a HCV positive patient to permanent lymphoblastoid cell lines (LCL). Positive and negative HCV RNA strands of the cultured cells and growth media were detected by reverse transcriptase-polymerase chain reaction (RT-PCR) each month. Core and NS5 proteins of HCV were further tested using immunohistochemical SP method and in situ RT-PCR. RESULTS: HCV RNA positive strands were consistently detected the cultured cells for one year. The negative-strand RNA in LCL cells and the positive-strand RNA in supernatants were observed intermittently. Immunohistochemical results medicated expression of HCV NS3 and C proteins in LCL cytoplasm mostly. The positive signal of PCR product was dark blue and mainly localized to the LCL cytoplasm. The RT-PCR signal was eliminated by overnight RNase digestion but not DNase digestion. CONCLUSION: HCV may exist and remain functional in a cultured cell line for a long period.

Primary application of a real-time quantitative polymerase chain reaction for the detection of human breast cancer related novel gene-Metadherin expression

Objective:The aim of this study was to detect the expression level of Metadherin (MTDH) in peripheral blood of the breast cancer patients by real-time fluorescence quantitative polymerase chain reaction (PCR),and to explore the relationship between expression of Metadherin gene in the patients peripheral blood and the clinic-pathological features in breast cancer. Methods:Real-time fluorescence quantitative polymerase chain reaction was employed to determine the expression level of Metadherin gene in 80 peripheral blood samples of breast cancer patients and healthy donors. Results:The expression of Metadherin gene in breast cancer patients peripheral blood were positive,in which 34 breast cancer patients were highly expressed,accounting for 55.7%,while the expression of Metadherin gene in normal females peripheral blood were negative,there was statistical significance (Ratio = 2.02±0.81,P < 0.05); Ratio of the Metadherin expression in breast cancer patients peripheral blood and the glyceraldehyde-3-phosphate dehydrogenase expression was 1.15 ± 0.36. REST software analysis showed that the expression of Metadherin gene was significantly up-regulated in breast cancer. Conclusion:The SYBR Green I quantitative real-time polymerase chain reaction method can successfully detect the expression level of Metadherin gene. Expression level of Metadherin gene in breast cancer patients peripheral blood is closely related to survival,and it maybe involved in the development of breast cancer and used as an indicator of prognosis.

Identifying the stability of housekeeping genes to be used for the quantitative real-time PCR normalization in retinal tissue of streptozotocin-induced diabetic rats

AIM:To investigate the stability of the seven housekeeping genes:beta-actin(ActB),glyceraldehyde-3-phosphate dehydrogenase(GAPDH),18s ribosomal unit 5(18s),cyclophilin A(CycA),hypoxanthine-guanine phosphoribosyl transferase(HPRT),ribosomal protein large P0(36B4)and terminal uridylyl transferase 1(U6)in the diabetic retinal tissue of rat model.METHODS:The expression of these seven genes in rat retinal tissues was determined using real-time quantitative reverse transcription polymerase chain reaction(RT-qPCR)in two groups;normal control rats and streptozotocininduced diabetic rats.The stability analysis of gene expression was investigated using geNorm,NormFinder,BestKeeper,and comparative delta-Ct(ΔCt)algorithms.RESULTS:The 36B4 gene was stably expressed in the retinal tissues of normal control animals;however,it was less stable in diabetic retinas.The 18s gene was expressed consistently in both normal control and diabetic rats’retinal tissue.That this gene was the best reference for data normalisation in RT-qPCR studies that used the retinal tissue of streptozotocin-induced diabetic rats.Furthermore,there was no ideal gene stably expressed for use in all experimental settings.CONCLUSION:Identifying relevant genes is a need for achieving RT-qPCR validity and reliability and must be appropriately achieved based on a specific experimental setting.

SEQUENCE ANALYSIS OF THE NS5 REGION OF GBVC/HGV AND DETECTION OF THE VIRUS BY REVERSE TRANSCRIPTASE PCR

GBV C/HGV is a newly identified virus associated with human hepatitis In this study, the nucleotide sequences of the partial NS5 gene of GBV C/HGV derived from sera of 8 Chinese patients were determined The nucleotide homology among the 8 isolates were 92% on average On the basis of sequence analysis, two sets of oligonucleotide primers derived from highly conserved region of GBV C/HGV NS5 gene were designed to establish both sensitive and specific nested PCR for detection of GBV C/HGV RNA 253 Chinese patients were examined for the virus RNA GBV C/HGV RNA positive rates in patients infected with HBV, HCV and patients with chronic non B,non C hepatitis were 18 4%, 19 8% and 8 9% respectively This result suggested that HBV,HCV and GBV C/HGV shared the same transmission risk factors 8 patients with GBV C/HGV and HCV coinfection were retrospectively observed for the response to interferon Coinfection with GBV/HGV did not negatively influence the responsiveness of HCV, and GBV C/HGV was sensitive to interferon to a certain degree

Micro-droplet Digital Polymerase Chain Reaction and Real-Time Quantitative Polymerase Chain Reaction Technologies Provide Highly Sensitive and Accurate Detection of Zika Virus

The establishment of highly sensitive diagnostic methods is critical in the early diagnosis and control of Zika virus(ZIKV)and in preventing serious neurological complications of ZIKV infection. In this study, we established micro-droplet digital polymerase chain reaction(ddPCR) and real-time quantitative PCR(RT-qPCR) protocols for the detection of ZIKV based on the amplification of the NS5 gene. For the ZIKV standard plasmid, the RT-qPCR results showed that the cycle threshold(Ct) value was linear from 10~1 to 10~8 copy/l L, with a standard curve R^2 of 0.999 and amplification efficiency of 92.203%;however, a concentration as low as 1 copy/l L could not be detected. In comparison with RT-qPCR, the dd PCR method resulted in a linear range of 10~1–10~4 copy/l L and was able to detect concentrations as low as 1 copy/l L. Thus, for detecting ZIKV from clinical samples, RT-qPCR is a better choice for high-concentration samples(above 10~1 copy/l L),while ddPCR has excellent accuracy and sensitivity for low-concentration samples. These results indicate that the ddPCR method should be of considerable use in the early diagnosis, laboratory study, and monitoring of ZIKV.

Comparison of Abbott and Da-an real-time PCR for quantitating serum HBV DNA

AIM: To compare the performance of the Da-an real-time hepatitis B virus (HBV) DNA assay and Abbott RealTime HBV assay.

Detection of SYT-SSX fusion transcripts in paraffin-embedded tissues of synovial sarcoma by reverse transcription-polymerase chain reaction

OBJECTIVE: To assess the feasibility of detecting SYT-SSX fusion transcripts in paraffin-embedded tissues of synovial sarcoma by reverse transcription-polymerase chain reaction (RT-PCR). METHODS: RT-PCR was used to amplify the SYT-SSX fusion transcripts using archival formalin-fixed paraffin-embedded tumor specimens from a series of 37 synovial sarcoma cases. To investigate the specificity of the SYT-SSX fusion transcripts, a variety of non-synovial sarcoma tumors were included in the study as negative controls. The detected messages derived from fusion genes were confirmed by subsequent sequence analysis. RESULTS: SYT-SSX fusion transcripts were detected in 33 of 37 (89.2%) synovial sarcomas. None of the 34 cases of non-synovial sarcoma tumors showed amplified products of SYT-SSX fusion transcripts, although PBGD mRNA was detected in all specimens. Among 33 SYT-SSX-positive synovial sarcomas, 22 tumors had an SYT-SSX 1 fusion transcript, whereas 6 tumors had an SYT-SSX2 fusion transcript. Fusion types can not be distinguished in the remaining 5 cases. There was a significant relationship between SYT-SSX fusion type and histologic subtype. All 10 biphasic synovial sarcomas had the SYT-SSX1 fusion, whereas all tumors with SYT-SSX2 were of monophasic morphology (P

Establishment of a new quantitative detection approach to adefovir-resistant HBV and its clinical application

AIM:To establish the more feasible and sensitive assessment approach to the detection of adefovir (ADV) resistance-associated hepatitis B virus (HBV) quasispecies.METHODS: Based on the characteristics of rtA181V/T and rtN236T mutations, a new approach based on real-time fluorescent quantitative polymerase chain reaction (RT-PCR) was established for the detection of ADV-resistant HBV quasispecies, total HBV DNA, rtA181 and rtN236 mutations in blood samples from 32 chronic hepatitis B (CHB) patients with unsatisfactory curative effect on ADV and compared with routine HBV DNA sequencing.RESULTS: Both the sensitivity and specificity of this new detection approach to ADV-resistant HBV quasispecies were 100%, which were much higher than those of direct HBV DNA sequencing. The approach was able to detect 0.1% of mutated strains in a total plasmid population. Among the 32 clinical patients, single rtA181 and rtN236T mutation and double rtA181T and rtN236T mutations were detected in 20 and 8, respectively, while ADV-resistant mutations in 6 (including, rtA181V/T mutation alone in 5 patients) and no associated mutations in 26.CONCLUSION: This new approach is more feasible and efficient to detect ADV-resistant mutants of HBV and ADV-resistant mutations before and during ADV treatment with a specificity of 100% and a sensitivity of 100%.

Quantitative Analysis of ATP Sulfurylase and Selenocysteine Methyltransferase Gene Expression in Different Organs of Tea Plant (<i>Camellia sinensis</i>)

Tea plant (Camellia sinensis) has unique biological features for the study of cellular and molecular mechanisms, an evergreen broad-leaved woody plant which can accumulate selenium in soil abundant of Selenium. Expression of the genes related to Selenium (Se) metabolism is an adaptation to the soil environment for a long period. The purpose of the present study was to explore if there exist differences of expression about these genes in tea plant between growing in Selenium-abundant and normal soil. A quantitative real-time reverse transcription polymerase chain reaction (Q-RT-PCR) assay was done for quantification of ATP sulfurylase (APS) and selenocysteine methyltransferase (SMT) mRNA normalized to Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene in tea plant. Young leaves, mature leaves and tender roots from tea plants growing in soil abundant of Selenium were respectively obtained from Shitai County, Anhui Province, and also the relevant materials of the selenium un-enriched tea plant planted at agricultural garden of Ahui Agriculture University were taken as control for real-time PCR analysis. The results showed that APS1, APS2 and SMT expression levels for either young or mature leaves in selenium-enriched tea plant were lower than that in ordinary (selenium un-enriched) tea plant. In contrast, the APS1, APS2 and SMT expression level of roots in selenium-enriched tea plant were all higher than that in ordinary tea plant. APS1 gene expression level of roots in selenium-enriched tea plant was about 1.6 times higher than that in the ordinary tea plant, APS2 gene expression level was about 4.8-fold higher than that in the ordinary tea plant, SMT gene expression level was about 3.3 times higher than that in the ordinary tea plant. Among various tissues of selenium-enriched tea plant, APS1 gene relative expression level of young leaves was similar to or slightly higher than mature leaves, and the one of roots was the lowest among them;APS2 gene relative expression level of young leaves was similar to or slightly higher than the roots, and the one of mature leaves was the lowest among them;SMT gene relative expression level of young leaves was similar to or slightly higher than mature leaves, and the one of roots was the highest among them. Our results suggest that there existed correlation between selenium and expression levels of these genes.

Quantitative analysis of a panel of gene expression in prostate cancer——with emphasis on NPY expression analysis

Objective： To investigate molecular alterations associating with prostate carcinoma progression and potentially provide information toward more accurate prognosis/diagnosis. Methods： A set of laser captured microdissected （LCM） specimens from 300 prostate cancer （PCa） patients undergoing radical prostatectomy （RP） were defined. Ten patients representing ＂aggressive＂ PCa, and 10 representing ＂non-aggressive＂ PCa were selected based on prostate-specific antigen （PSA） recurrence, Gleason score, pathological stage and tumor cell differentiation, with matched patient age and race between the two groups. Normal and neoplastic prostate epithelial cells were collected with LCM from frozen tissue slides obtained from the RP specimens. The expressions of a panel of genes, including NPY, PTEN, AR, AMACR, DD3, and GSTP1, were measured by quantitative real-time RT-PCR （TaqMan）, and correlation was analyzed with clinicopathological features. Results： The expressions of AMACR and DD3 were consistently up-regulated in cancer cells compared to benign prostate epithelial cells in all PCa patients, whereas GSTP1 expression was down regulated in each patient. NPY, PTEN and AR exhibited a striking difference in their expression patterns between aggressive and non-aggressive PCas （P=0.0203, 0.0284, and 0.0378, respectively, Wilcoxon rank sum test）. The lower expression of NPY showed association with ＂aggressive＂ PCas based on a larger PCa patient cohort analysis （P=0.0037, univariate generalized linear model （GLM） analysis）. Conclusion： Despite widely noted heterogeneous nature of PCa, gene expression alterations ofAM,4CR, DD3, and GSTP1 in LCM-derived PCa epithelial cells suggest for common underlying mechanisms in the initiation of PCa. Lower NPY expression level is significantly associated with more aggressive clinical behavior of PCa; PTEN and AR may have potential in defining PCa with aggressive clinical behavior. Studies along these lines have potential to define PCa-associated gene expression alterations and likely co-regulation of genes/pathways critical in the biology of PCa onset/progression.

The diagnostic significance of the detection of cytokeratin 19 mRNA by quantitative RT-PCR in benign and malignant pleural effusions

Objective: To evaluate the diagnostic significance of detecting cytokeratin 19 (CK19) mRNA by quantitative reverse transcription polymerase chain reaction (RT-PCR) in benign and malignant pleural effusions. Methods: CK19 mRNA was examined by quantitative RT-PCR and CK19 was detected by Enzyme-linked immunoadsorbent assay (ELISA) in 32 patients with malignant pleural effusions and 35 patients with benign pleural effusions. Results: On the threshold of 200 copies/μl, the positive rate of CK19 mRNA in patients with malignant pleural effusions was 62.5%. The positive rates of CK19 mRNA and CK19 in the malignant pleural effusions were significantly higher than those in the benign group (P<0.01). Furthermore, the positive rate of CK19 mRNA was higher than that of CK19 in the malignant group (P<0.05). Conclusion: Detection of CK19 mRNA can be a promising diagnostic marker in differential diagnosis of benign and malignant pleural effusions.

Reference genes for quantitative RT-PCR data in gastric tissues and cell lines

AIM:To evaluate the suitability of reference genes in gastric tissue samples and cell lines.METHODS:The suitability of genes ACTB,B2M,GAPDH,RPL29,and 18S rRNA was assessed in21 matched pairs of neoplastic and adjacent nonneoplastic gastric tissues from patients with gastric adenocarcinoma,27 normal gastric tissues from patients without cancer,and 4 cell lines using reverse transcription quantitative real-time polymerase chain reaction(RT-qPCR).The ranking of the best single and combination of reference genes was determined by NormFinder,geNorm,BestKeeper,and DataAssist.In addition,GenEx software was used to determine the optimal number of reference genes.To validate the results,the mRNA expression of a target gene,DNMT1,was quantified using the different reference gene combinations suggested by the various software packages for normalization.RESULTS:ACTB was the best reference gene for all gastric tissues,cell lines and all gastric tissues plus cell lines.GAPDH+B2M or ACTB+B2M was the best combination of reference genes for all the gastric tissues.On the other hand,ACTB+B2M was the best combination for all the cell lines tested and was also the best combination for analyses involving all the gastric tissues plus cell lines.According to the GenEx software,2 or 3 genes were the optimal number of references genes for all the gastric tissues.The relative quantification of DNMT1 showed similar patterns when normalized by each combination of reference genes.The level of expression of DNMT1 in neoplastic,adjacent non-neoplastic and normal gastric tissues did not differ when these samples were normalized using GAPDH+B2M(P=0.32),ACTB+B2M(P=0.61),or GAPDH+B2M+ACTB(P=0.44).CONCLUSION:GAPDH+B2M or ACTB+B2M is the best combination of reference gene for all the gastric tissues,and ACTB+B2M is the best combination for the cell lines tested.

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.

饮食习惯与肥胖患儿性早熟的相关性分析

目的探讨饮食习惯与肥胖患儿性早熟的相关性分析。方法选取苏州市吴中人民医院2019年3月至2022年3月期间收治的72例性早熟肥胖患儿作为观察组,另选取同期体检的健康肥胖儿童71例作为常规组。采用实时-逆转录荧光定量聚合酶链反应(RT-qPCR)检测两组外周血miR-125b水平,分析患儿饮食习惯。通过比较两组肥胖儿童的外周血miR-125b、饮食习惯,采用Logistic回归分析法分析外周血miR-125b、饮食习惯与肥胖患儿性早熟的关系。结果观察组外周血miR-125b表达水平高于常规组,差异有统计学意义(P<0.05)。观察组饮食没规律、荤多素少、高添加剂食品占比均高于常规组,差异有统计学意义(P<0.05)。观察组女性患儿、不良饮食习惯占比高于常规组,且经多因素分析显示外周血miR-125b表达水平、女性、不良饮食习惯是肥胖患儿性早熟的独立危险因素,差异有统计学意义(P<0.05)。结论肥胖患儿性早熟外周血miR-125b表达水平高于健康肥胖儿童,不良饮食习惯高于健康肥胖儿童,外周血miR-125b表达水平偏高、不良饮食习惯偏低均为肥胖患儿性早熟的影响因素。

帕利亚姆病毒实时荧光定量RT-PCR检测方法的建立与应用

本研究拟建立帕利亚姆病毒(Palyam virus,PALV)血清型特异性实时荧光定量RT-PCR(qRT-PCR)方法用于临床样本或媒介中PALV血清型鉴定。根据我国流行PALV毒株的基因节段2序列,设计扩增引物和TaqMan探针,建立PALV血清型特异型qRT-PCR方法,对方法的特异性、灵敏性与重复性进行评估;以我国分离的28株PALV和90份核酸阳性血液样本评估检测方法的可靠性;利用建立的方法对采集库蠓样本中携带的PALV进行血清型鉴定。结果显示,建立的PALV血清型qRT-PCR检测方法具有良好的特异性与灵敏性,可检出核酸拷贝数下限在22至28 copies·μL^(-1)。对28株PALV的qRT-PCR检测结果与病毒测序鉴定结果一致;对PALV不同感染阶段哨兵动物血液(90份)中的qRT-PCR鉴定结果与分离病毒的血清型鉴定结果一致;建立的方法可准确鉴定库蠓中携带PALV的血清型。本研究建立的PALV血清型qRT-PCR定型方法具有良好的特异强、敏感性与重复性,可用于PALV感染动物与媒介中PALV血清型的鉴定,具有良好的应用价值。

新型冠状病毒Omicron I1566V突变位点MS2噬菌体病毒样颗粒的构建

目的构建新型冠状病毒Omicron I1566V突变位点MS2噬菌体病毒样颗粒。方法选取并合成带有6×His标签的MS2噬菌体的衣壳蛋白(CP)、成熟蛋白(A蛋白)及Omicron I1566V突变基因序列,插入pACYCDuet-1质粒构建重组载体,通过原核系统诱导表达目的蛋白,纯化重组蛋白后利用透射电镜对蛋白质进行物理表征,最后通过反转录聚合酶链反应(RT-PCR)检测病毒样颗粒的热稳定性及耐核酸酶水解能力。结果成功构建包含有6×His标签的CP、A蛋白和Omicron I1566V突变基因序列的重组载体,经限制性内切酶BamHⅠ和KpnⅠ酶切鉴定和测序验证,结果均与预期相符。经诱导并纯化后,通过电镜观察到了大小均匀、直径为23~28 nm的病毒样颗粒,该病毒样颗粒经核酸酶消化后可在37℃条件下稳定储存20 d以上。结论该研究成功利用MS2噬菌体的CP和A蛋白构建了Omicron I1566V突变位点病毒样颗粒,为该突变位点的RT-PCR检测体系提供了可靠的质量保障。

Epidemiological and Subtype Characterization of Influenza Viruses Infection in Children in Shenzhen, China during Three Consecutive Seasons (January 2016-December 2018)

Background: Children with seasonal influenza infection cause a significant burden of disease each year in the pediatric clinic. Influenza A and B viruses are the major types responsible for illness. A better understanding of the periodicity facilitates the prevention and control of influenza in children. Objective: This study aims to analyze the epidemiological patterns and subtype characterization of influenza viruses among children in Shenzhen, China. Methods: Influenza samples were collected by nasopharyngeal swabs from influenza like illness patients in Shenzhen Children’s Hospital from January 2016 to December 2018. The positive cases and influenza subtypes were determined by gold labeled antigen detection and reverse transcriptase polymerase chain reaction. The influenza periodicity and age, subtype distribution as well as the association between climate parameters and different influenza subtypes were analyzed by SPSS 22.0. Results: The influenza positive rate during 2016-2018 was 21.0%, with a highest positive rate in the year 2018. The positive rate varied by month, season, and year describing a sequence of peaks presenting primarily in all year including spring, summer and winter. The characteristics of influenza peak were different in each year, with a spring peak in 2016 and a summer plus a winter-spring peaks in 2017 and 2018. In addition, influenza B exhibited a winter-spring seasonal pattern while influenza A displayed a more variable seasonality, highlighting influenza B rather than influenza A which had a negative association with climate parameters. Influenza-positive cases were older than influenza-negative cases (P P Conclusion: Influenza activity in children from Shenzhen typically displays both winter-spring and summer peaks. Influenza A epidemic occurred separately or co-circulated with influenza B, with a winter-spring pattern for influenza B and a much more variable seasonality for influenza A. Influenza B had a negative association with climate parameters. In addition, hospitalization with influenza often occurs in younger individuals infected with influenza A.

基于直扩RT-PCR技术的寨卡病毒快速检测方法的建立

目的建立基于直扩实时荧光定量逆转录聚合酶链反应(RT-PCR)技术的寨卡病毒快速检测方法。方法采用特殊功能的DNA聚合酶,以及优选PCR增强剂,以此建立直扩RT-PCR技术的寨卡病毒快速检测5种样本(全血、血清、唾液、咽拭子和尿)的方法。结果5种样本检测限分别为血清103 PFU/mL,尿、咽拭子和唾液102 PFU/mL,全血104 PFU/mL,标准曲线的拟合优度的可决系数均在0.98以上,扩增效率均在90%~110%;寨卡病毒核酸成功扩增,非寨卡病毒核酸均未能扩增;尿、全血和唾液样本的重复性实验中106 PFU/mL和102 PFU/mL两个浓度的6个重复Ct值的变异系数均<5%。该研究建立的直扩RT-PCR技术的寨卡病毒检测方法与常规RT-PCR技术的检测结果一致,8个寨卡病毒样本,均只检测出2个血清样本,其余62个非寨卡病毒样本及12个阴性样本均未得到扩增。结论成功建立基于直扩RT-PCR技术的寨卡病毒快速检测方法,该方法简便快捷且灵敏度高、特异度强。

Design and use of group-specific primers and probes for real-time quantitative PCR

Real-time quantitative polymerase chain reaction(qPCR)has gained popularity as a technique to detect and quantify a specific group of target microorganisms from various environmental samples including soil,water,sediments,and sludge.Although qPCR is a very useful technique for nucleic acid quantification,accurately quantifying the target microbial group strongly depends on the quality of the primer and probe used.Many aspects of conducting qPCR assays have become increasingly routine and automated;however,one of the most important aspects,designing and selecting primer and probe sets,is often a somewhat arcane process.In many cases,failed or non-specific amplification can be attributed to improperly designed primer-probe sets.This paper is intended to provide guidelines and general principles for designing group-specific primers and probes for qPCR assays.We demonstrate the effectiveness of these guidelines by reviewing the use of qPCR to study anaerobic processes and biologic nutrient removal processes.qPCR assays using group-specific primers and probes designed with this method,have been used to successfully quantify 16S ribosomal Ribonucleic Acid(16S rRNA)gene copy numbers from target methanogenic and ammoniaoxidizing bacteria in various laboratory-and full-scale biologic processes.Researchers with a good command of primer and probe design can use qPCR as a valuable tool to study biodiversity and to develop more efficient control strategies for biologic processes.

Comparison of bacterial quantities in left and right colon biopsies and faeces

AIM:To compare quantities of predominant and pathogenic bacteria in mucosal and faecal samples.METHODS:Twenty patients undergoing diagnostic colonoscopy with endoscopically and histologically normal mucosa were recruited to the study,14 subjects of which also supplied faecal(F) samples between 15 d to 105 d post colonoscopy.Mucosal biopsies were taken from each subject from the midportion of the ascending colon(right side samples,RM) and the sigmoid(left side samples,LM).Predominant intestinal and mucosal bacteria including clostridial 16S rRNA gene clusters Ⅳ and ⅩⅣab,Bacteroidetes,Enterobacteriaceae,Bifidobacterium spp.,Akkermansia muciniphila(A.muciniphila),Veillonella spp.,Collinsella spp.,Faecalibacterium prausnitzii(F.prausnitzii) and putative pathogens such asEscherichia coli(E.coli),Clostridium difficile(C.difficile),Helicobacter pylori(H.pylori) and Staphylococcus aureus(S.aureus) were analysed by quantitative polymerase chain reaction(qPCR).Host DNA was quantified from the mucosal samples with human glyceraldehyde 3-phosphate dehydrogenase gene targeting qPCR.Paired t tests and the Pearson correlation were applied for statistical analysis.RESULTS:The most prominent bacterial groups were clostridial groups Ⅳ and ⅩⅣa+b andBacteroidetes and bacterial species F.prausnitzii in both sample types.H.pylori and S.aureus were not detected and C.difficile was detected in only one mucosal sample and three faecal samples.E.coli was detected in less than half of the mucosal samples at both sites,but was present in all faecal samples.All detected bacteria,except Enterobacteriaceae,were present at higher levels in the faeces than in the mucosa,but the different locations in the colon presented comparable quantities(RM,LM and F followed byP 1 for RMvs F,P 2 for LMvs F andP 3 for RM vs LM:4.17 ± 0.60 log 10 /g,4.16 ± 0.56 log 10 /g,5.88 ± 1.92 log 10 /g,P 1 = 0.011,P 2 = 0.0069,P 3 = 0.9778 forA.muciniphila;6.25 ± 1.3 log 10 /g,6.09 ± 0.81 log 10 /g,8.84 ± 1.38 log 10 /g,P 1 < 0.0001,P 2 = 0.0002,P 3 = 0.6893 forBacteroidetes;5.27 ± 1.68 log 10 /g,5.38 ± 2.06 log 10 /g,8.20 ± 1.14 log 10 /g,P 1 < 0.0001,P 2 ≤ 0.0001,P 3 = 0.7535 forBifidobacterium spp.;6.44 ± 1.15 log 10 /g,6.07 ±1.45 log 10 /g,9.74 ±1.13 log 10 /g,P 1 < 0.0001,P 2 ≤ 0.0001,P 3 = 0.637 forClostridium cluster Ⅳ;6.65 ± 1.23 log 10 /g,6.57 ± 1.52 log 10 /g,9.13 ± 0.96 log 10 /g,P 1 < 0.0001,P 2 ≤ 0.0001,P 3 = 0.9317 forClostridium cluster ⅩⅣa;4.57 ± 1.44 log10/g,4.63 ± 1.34 log10/g,7.05 ± 2.48 log 10 /g,P 1 = 0.012,P 2 = 0.0357,P 3 = 0.7973 for Collinsella spp.;7.66 ± 1.50 log 10 /g,7.60 ± 1.05 log 10 /g,10.02 ± 2.02 log 10 /g,P 1 ≤ 0.0001,P 2 = 0.0013,P 3 = 0.9919 forF.prausnitzsii;6.17 ± 1.3 log 10 /g,5.85 ± 0.93 log 10 /g,7.25 ± 1.01 log 10 /g,P 1 = 0.0243,P 2 = 0.0319,P 3 = 0.6982 for Veillonella spp.;4.68 ± 1.21 log 10 /g,4.71 ± 0.83 log 10 /g,5.70 ± 2.00 log 10 /g,P 1 = 0.1927,P 2 = 0.0605,P 3 = 0.6476 forEnterobacteriaceae).TheBifidobacterium spp.counts correlated significantly between mucosal sites and mucosal and faecal samples(Pearson correlation coefficients 0.62,P = 0.040 and 0.81,P = 0.005 between the right mucosal sample and faeces and the left mucosal sample and faeces,respectively).CONCLUSION:Non-invasive faecal samples do not reflect bacterial counts on the mucosa at the individual level,except for bifidobacteria often analysed in probiotic intervention studies.