TaqMan Probe-based Quantitative PCR Research Articles

Is Artemia susceptible to the microsporidium Ecytonucleospora hepatopenaei (EHP) infection?

Following the three-stage approach of the WOAH (World Organisation for Animal Health) standard on the confirmation of susceptible species to a specific pathogen, Artemia franciscana juveniles were challenged with immersion exposure (IM) in a homogenate suspension of Penaeus vannamei hepatopancreas infected with Ecytonucleospora hepatopenaei (EHP) and per os administration (PO) with chlorella soaked in EHP-infected hepatopancreatic homogenate suspension. Using TaqMan probe-based quantitative PCR, we detected that loads of EHP in A. franciscana juveniles from both the IM and PO groups were about 101 copies/ng-DNA on the 3rd day post-exposure (3 dpe). However, no more EHP was detectable in the challenged A. franciscana juveniles on 7 dpe. Nested PCR targeting the EHP spore wall protein gene did not produce a target band in A. franciscana juveniles on either 3 dpe or 7 dpe. The confirmative evidence of the absence of sustained infection with EHP in the exposed Artemia was substantiated using in situ DIG-labeling-loop-mediated DNA amplification (ISDL) on A. franciscana juvenile sections, which revealed a few weak grey-blue positive signals appeared on 3 dpe but disappeared on 7 dpe. The results indicated that exposure to EHP resulted in the invasion of Artemia in intestinal epithelial cells, but the infection was unable to persist, confirming Artemia is not susceptible to EHP. Therefore, the research countered the assertion of Artemia as a potential EHP reservoir.

Development and application of TaqMan probe-based quantitative PCR assays for the detection of tilapia parvovirus.

Tilapia parvovirus (TiPV) is a novel parvovirus associated with high mortality in Nile tilapia and red hybrid tilapia, leading to severe economic losses for tilapia aquaculture. It is critical to develop a sensitive and accurate assay to detect TiPV in fish tissues. In this study, new TaqMan probe-based quantitative PCR (qPCR) assays targeting the non-structural (NS) and viral protein (VP) genes of TiPV were developed. The standard curves of the assays were 95.64%-98.96% over a wide linear range of 109 -101 copies of the corresponding standard DNA per reaction. The intra- and inter-assay coefficients of variation were in the ranges 0.54%-2.50% and 0.13%-1.17%, respectively, which suggests good repeatability and reproducibility. The detection limit of the TaqMan TiPV assays was 10 copies/µl. The application of the TaqMan qPCR assays to field samples revealed that they had comparable sensitivity to a previously developed SYBR Green qPCR, but more sensitive than the conventional PCR. No cross-reactivity of the TaqMan TiPV assays was found with the samples infected with other viruses and bacteria. Overall, the assays offered high sensitivity and specificity in the detection of low concentrations of TiPV DNA in infected tilapia samples. These new TaqMan qPCR assays could provide a valuable diagnostic tool for the reliable and specific detection of TiPV in experimental and field samples.

Quantification of Enterocytozoon hepatopenaei (EHP) in Penaeid Shrimps from Southeast Asia and Latin America Using TaqMan Probe-Based Quantitative PCR.

We developed a qPCR assay based on the β-tubulin gene sequence for the shrimp microsporidian parasite Enterocytozoon hepatopenaei (EHP). This assay reacted with the hepatopancreas (HP) of EHP-infected shrimps, and the highest copy numbers were found in HP and feces samples from Southeast Asian countries (106–108 copies mg−1), while HP samples from Latin America, Artemia, and EHP-contaminated water showed lower amounts (101–103 copies mg−1 or mL−1 of water). No false positive was found with the normal shrimp genome, live feeds, or other parasitic diseases. This tool will facilitate the management of EHP infection in shrimp farms.

Diagnostic qPCR Assay to Detect Fusarium brasiliense, a Causal Agent of Soybean Sudden Death Syndrome and Root Rot of Dry Bean.

Species within clade 2 of the Fusarium solani species complex (FSSC) are significant pathogens of dry bean (Phaseolus vulgaris) and soybean (Glycine max), causing root rot and/or sudden death syndrome (SDS). These species are morphologically difficult to distinguish and often require molecular tools for proper diagnosis to a species level. Here, a TaqMan probe-based quantitative PCR (qPCR) assay was developed to distinguish Fusarium brasiliense from other closely related species within clade 2 of the FSSC. The assay displays high specificity against close relatives and high sensitivity, with a detection limit of 100 fg. This assay was able to detect F. brasiliense from purified mycelia, infected dry bean roots, and soil samples throughout Michigan. When multiplexed with an existing qPCR assay specific to Fusarium virguliforme, accurate quantification of both F. brasiliense and F. virguliforme was obtained, which can facilitate accurate diagnoses and identify coinfections with a single reaction. The assay is compatible with multiple qPCR thermal cycling platforms and will be helpful in providing accurate detection of F. brasiliense. Management of root rot and SDS pathogens in clade 2 of the FSSC is challenging and must be done proactively, because no midseason management strategies currently exist. However, accurate detection can facilitate management decisions for subsequent growing seasons to successfully manage these pathogens.

Detection and analysis of FAM19A4 promoter methylation in cervical exfoliated cells

Objective: To investigate the cinical value of FAM19A4promoter methylation in cervicalexfoliated cells for triage of cervical cancer. Methods: A total of 162 high-risk HPV-infected patients who were pathologically confirmed as different cervical lesions from August 2017 to December 2017 were collected in Guangdong Women and Children Hospital. Taqman probe-based quantitative PCR (qPCR) was used to detect the methylation of FAM19A4 promoterin different grades of cervical lesions, and the value of FAM19A4 methylation in predicting cervical HSIL and the above lesions was calculated by diagnostic test. Results: (1)The positive rates of FAM19A4 methylation in cervical exfoliated cells increased with the severity of cervical lesions, which were 7.69% (4/52) , 34.62% (9/26) , 55.56% (20/36) , 95.83% (46/48) in normal cervix/cervicitis, cervical LSIL, HSIL, and cervical cancer, respectively(P<0.05).(2)There was no significant difference in the detection rates of FAM19A4 methylation between different age groups, pathological types, clinical stage, tumor size and lymph node metastasis status (P>0.05). (3) The specificity and positive predictive value of FAM19A4 methylation in detecting cervical HSIL alone and ≥HSIL lesions were the optimal, with the AUC of 0.69 and 0.84, respectively. When combined with HPV16/18 genotyping, the sensitivity was significantly improved. Conclusions: The detection of FAM19A4 promoter methylation in cervical exfoliated cells has a high clinical value of discriminating ≥HSIL lesions; and the cotest of methylated FAM19A4 and HPV16/18 genotyping can identify ≥HSIL lesions more sensitively.

The clinical significance of FAM19A4 methylation in high-risk HPV-positive cervical samples for the detection of cervical (pre)cancer in Chinese women

BackgroundTo explore the diagnostic value of FAM19A4 methylation in high-risk human papilloma virus (hrHPV)-positive cervical samples from Chinese women for estimating cervical cancer or its precancerous lesions.MethodsCervical samples from 215 women infected with high-risk HPV were collected by smear testing. We purposely chose 61 patients with cervical cancer, 57 with high-grade squamous intraepithelial lesions (HSIL), 31 with low-grade squamous intraepithelial lesions (LSIL), and 66 without cervical intraepithelial neoplasia (CIN) after histological confirmation. Taqman probe-based quantitative PCR (qPCR) was utilized to detect the methylation status of FAM19A4 in the cervical samples and further evaluate the use of this gene in the diagnosis of cervical cancer.Results(1) An increasing level of FAM19A4 methylation was detected with increasing progression of cervical lesions, with methylation rates of 10.61%(7/66), 35.48%(11/31), 56.14%(32/57) and 93.44%(57/61) in no CIN, LSIL, HSIL and cervical carcinoma samples respectively. (2) In all hrHPV-positive samples, the levels of FAM19A4 methylation in HPV16/18 groups were higher than that in 12 other hrHPV groups (P < 0.05), but there was no significant difference between two groups after grouping cervical lesions into cervical cancer, HSIL, LSIL and no CIN groups (P>0.05). (3)There were no significant differences of FAM19A4 methylation in different clinicopathological parameters of cervical cancer. (4) Though the sensitivity of FAM19A4 methylation test was inferior to that of cytology and FAM19A4 combining with HPV16/18 genotyping, but showed the best specificity with 81.44% both for detection HSIL alone and ≥ HSIL, with favorable youden index (YI) and area under curve (AUC).ConclusionFAM19A4 is a specific biomarker of cancerous lesions of the cervix. FAM19A4 methylation analysis may serve as an auxiliary screening method for diagnosis of cervical (pre)cancer. However, in consideration of the limitations of this retrospective study, prospective population-based studies are necessary for further confirmation of the diagnostic value of FAM19A4 methylation for detection of cervical (pre)cancer in Chinese women.

Immune response of olive flounder (Paralichthys olivaceus) infected with the myxosporean parasite Kudoa septempunctata

This study evaluated the pathophysiological, biochemical, and immunological status of olive flounder (Paralichthys olivaceus) infected with the myxosporean parasite Kudoa septempunctata. Flounder fish collected from Kudoa-infected and uninfected farms were confirmed by microscopic and TaqMan probe-based quantitative PCR screening. Morphological, biochemical, histological, and immune gene expression analyses were performed on uninfected and infected hosts to assess the effect of K. septempunctata. Histological studies confirmed the presence of Kudoa myxospores in the trunk muscles of infected flounder fish. Serum biochemical parameters, including the levels of myeloperoxidase activity, superoxide dismutase activity, alanine aminotransferase, alkaline phosphatase, amylase, bilirubin, total protein, cholesterol, calcium, potassium, sodium, phosphorus, glucose, and galactose, were found to exhibit no significant variations (p > 0.05) between uninfected and infected flounder fish. However, immune-related genes such as Mx, lysozyme, signal transducer and activator of transcription 1, interferon-γ, interferon regulatory factor, and tumour necrosis factor showed significantly elevated expression (p < 0.05) in the trunk muscles of infected flounder fish while no significant differences were noted in uninfected fish trunk muscle and head-kidney of infected and uninfected flounder fish.

1020 Establishment of Taqman Probe-Based Quantitative PCR Assays for Evaluation of Bacterial Markers in Human Fecal Samples

1020 Establishment of Taqman Probe-Based Quantitative PCR Assays for Evaluation of Bacterial Markers in Human Fecal Samples

Quantitative PCR-Based Parasite Burden Estimation of Babesia gibsoni in the Vector Tick, Haemaphysalis longicornis (Acari: Ixodidae), Fed on an Experimentally Infected Dog

Most causative agents of babesiosis, Babesia parasites, are transmitted transovarially in ixodid ticks. In this study, B. gibsoni, the causative agent of canine babesiosis which has transovarial transmission, was detected in tissues of the vector tick, Haemaphysalis longicornis using a modified quantitative PCR assay. Conventional PCR results showed that the newly designed primer set, which amplifies a 143-bp fragment of rhoptry-associated protein-1 (BgRAP-1) gene in B. gibsoni, was 100 times more sensitive than primers targeting P18 gene encoding 18 kDa protein of B. gibsoni, which was recently renamed as thrombospondin related adhesive protein (BgTRAP) gene, in an artificially generated sample solution containing metagenomic DNA (B. gibsoni DNA extracted from infected dog blood mixed with tick DNA). The TaqMan probe-based quantitative PCR (qPCR) for BgRAP-1 could also detect infected RBCs (iRBCs) at levels of 3.5 × 10(5) to 3.5 × 10(1)/μl, a range that is broader than that of a past SYBR Green-based qPCR method for P18/BgTRAP, which had a detection limit of 3.5 × 10(3) iRBCs/μl. Using this qPCR assay, we attempted to quantify the B. gibsoni burden in tick ovaries and embryonated eggs. Levels of infection were normalized to the copy number of tick's genomic DNA fragment of ribosomal DNA internal transcribed spacer region 2 (ITS2) for the standardization. According to this, low levels of parasite burden were quantified in ovaries and eggs. This detection system is sensitive and is recommended as a tool for elucidating the biological interactions between the vector tick H. longicornis and the parasite, B. gibsoni.