qPCR Methodology Research Articles

Multiple factors influence telomere length and DNA damage in individuals environmentally exposed to a coal-burning power plant

Coal is a mixture of several chemicals, many of which have mutagenic and carcinogenic effects and are a key contributor to the global burden of mortality and disease. Previous studies suggest that coal is related to telomeric shortening in individuals occupationally exposed, however little is known about the effects of mining and burning coal on the telomeres of individuals living nearby. Therefore, the primary objective of this investigation was to assess the impact of proximity to coal power plants and coal mines on the genomic instability of individuals environmentally exposed, while also exploring potential associations with individual characteristics, oxidative stress, inflammatory responses, and the presence of inorganic elements. This study involved 80 men participants from three cities around a thermoelectric power plant and one city unexposed to coal and byproducts. DNA was extracted from peripheral blood samples obtained from each participant, and the telomeres length (TL) was assessed using quantitative real-time polymerase chain reaction (qPCR) methodology. No significant difference was observed between exposed individuals (6227 ± 2884 bp) when compared to the unexposed group (5638 ± 2452 bp). Nevertheless, TL decrease was associated with age and risk for cardiovascular disease; and longer TL was found to be linked with increased concentrations of silicon and phosphorus in blood samples. No correlations were observed between TL with comet assay (visual score), micronucleus test, oxidative stress, and inflammatory results. Additional research is required to ascertain the potential correlation between these changes and the onset of diseases and premature mortality.

O-278 The vaginal and endometrial microbiome: do they tell the same story?

Abstract Study question Is the composition of the endometrial microbiome comparable to that of the vagina and can vaginal sampling provide sufficient information to characterize the uterine microbiome? Summary answer The compositions of the endometrial and vaginal microbiome are largely comparable and therefore, in most cases, vaginal sampling is sufficient to characterize the uterine microbiome. What is known already A dysbiotic endometrial microbiome (i.e., a shift from a predominance of beneficial bacteria to less favourable species) has been reported in association with adverse pregnancy outcomes in assisted reproductive treatment (ART). If dysbiosis is detected, antibiotics or probiotics can be administered to restore an optimal microbiome. However, characterization of the endometrial microbiome is challenging, involving invasive sampling, and technical difficulties due to the low microbial mass in the endometrium. In contrast, vaginal sampling is considered minimally invasive and microbial analysis is technically less complex. It is important to clarify whether the microbiomes of the endometrium and the vagina are comparable. Study design, size, duration A prospective multi-centre study including 60 ART patients was conducted from June 2022 to August 2023. During the luteal phase (on average day-19), paired vaginal swabs and endometrial biopsies were collected sequentially and stored in a preservation medium for further analysis. Patients and physicians were also asked to complete a questionnaire to identify any lifestyle or medical factors that may have differentially affected the microbial composition of the vagina and endometrium. Participants/materials, setting, methods A carefully validated qPCR methodology was used to accurately assess the presence and relative abundance of the four major lactobacillus species associated with eubiosis (crispatus, gasseri, iners, and jensenii) and the 15 most common bacterial species implicated in dysbiosis. Additionally, the relative abundance of microbial and human DNA was examined. Of note, endometrial analysis required additional tissue lysis. Furthermore, due to the low microbial DNA content in endometrial samples, preamplification was necessary prior to qPCR. Main results and the role of chance The proportion of microbial versus human DNA was approximately 90 times higher in vaginal samples compared to endometrial samples (p < 0.0001). However, the microbial compositions of both the endometrium and the vagina showed remarkable similarities. Lactobacillus species were predominant at both sites, accounting for an average of 86% and 89% of the bacterial population in the vagina and endometrium, respectively (p = 0.6). Of the dysbiotic species, Gardnerella vaginalis was the most common, accounting for 8% (vagina) and 7% (endometrium) of the total bacterial population (p = 1). There was no difference in the average number of distinct microbial species between the two niches (1.8 vs. 2.1; p = 0.3). Direct comparison of paired samples highlighted the high similarity of microbial compositions between both sites and showed strong correlations of species abundances in individual patients (L.crispatus: r = 0.9, L.iners: r = 0.9, L.gasseri: r = 1, L.jensenii: r = 0.9, G.vaginalis: r = 0.7; p < 0.0001/all species). However, the microbial composition differed in four patients (6.6%), with three having a dysbiotic vaginal profile (≥50% dysbiotic species) but a eubiotic endometrial profile (≥50% lactobacillus species) and one showing the reverse pattern. The medical conditions of two patients, including chronic endometritis and use of antibiotics and probiotics in the preceding cycle, may account for the observed differences. Limitations, reasons for caution The species analysed were carefully selected to ensure a comprehensive analysis. Nevertheless, the potential presence of unevaluated species could impact the results. While the included patients displayed diversity in their reproductive histories, it is important to acknowledge that the observed results may still be influenced by underlying causes of infertility. Wider implications of the findings The close similarity between the microbiomes at the two sites investigated suggests that minimally invasive vaginal sampling may be sufficient to characterise the endometrial microbiome. The ease of vaginal sampling and processing is expected to improve patient recruitment in microbiome research and facilitate easier application of clinical microbiome tests. Trial registration number not applicable

P-701 Impact of vaginal microbiome on vaginal absorption of exogenous progesterone: a pilot study

Abstract Study question Does vaginal microbiome have an impact on vaginal absorption of exogenous progesterone (P intake) in artificial cycles? Summary answer Results suggest that the presence of lactobacillus in the vagina may positively impact the uptake of P. What is known already Low serum P levels on ET day decrease significantly live birth rates. About 20% of patients receiving micronized vaginal P show inadequate levels. It is of interest to find out which intrinsic factors might influence on the capacity of absorption (P intake) of vaginal P, and if they could be treated to prevent this situation. Vaginal microbiome hast been suggested as a possible factor, although this has not been addressed yet. The aim of this study was to explore if there is a correlation between vaginal microbiome and pH, and P intake. Study design, size, duration A prospective single-centre cohort pilot study including 92 ART patients was conducted from February 2022 to January 2023 in IVI-RMA Valencia. Embryo transfer was conducted in the context of a hormonal replacement therapy cycle with use of vaginal P (400mg/12h) for luteal phase support. “Progesterone intake” capacity was evaluated according to the vaginal microbiome status (lactobacillus dominant (LDM, >90%) or non-lactobacillus dominant (NLDM) and pH levels determinations (considered normal when moderately acidic ( < =4.8). Participants/materials, setting, methods Samples were taken twice: A) proliferative phase (day of initiation of exogenous P) and B) mid-luteal phase (day of ET, P + 5). Serum E2 and P levels as well as vaginal microbiome and pH were analysed. A validated qPCR methodology was used to accurately assess the presence and relative abundance of the four major lactobacillus species associated with eubiosis (crispatus, gasseri, iners, and jensenii) and the most common bacterial species implicated in dysbiosis. Main results and the role of chance Distribution of LDM and NLDM profiles were comparable between Samples A and B. No significant difference between any of the potential confounding factors (age, BMI,baseline P) between the lactobacillus CST groups (CST-I,-II,-III,-V & lactobacillus) and the dysbiotic CST group (CST-IV) in Samples A and B were observed. Serum P levels on the ET day were significantly higher in LDM profiles both in Sample A (15.2 vs. 12.9ng/mL in NLDM;p=0.009) and B (15.0 vs. 12.8ng/mL;p=0.014). A positive significant correlation was found between serum P levels and Lactobacillus abundance in Samples A (r = 0.28; p = 0.008) and B (r = 0.30; p = 0.004). The relative abundance of Gardnerella vaginalis in Sample A was negatively related to serum P levels on the ET day (r=-0.24;p=0.02). Vaginal pH was significantly lower in LDM profiles both in Sample A (4.9 vs. 5.6 in NLDM; p = 0.002) and B (4.7 vs. 5.1;p<0.001). pH levels were negatively correlated with Lactobacillus abundance in Samples A (r=-0.34;p=0.0012) and B (r=-0.41;p<0.001). Additionally, serum P levels were negatively correlated with pH levels in Sample A (r=-0.14;p=0.191) and B (r=-0.27; p = 0.010). Indeed, when patients are grouped based on a cut-off of P = 8.8ng/mL, patients with a pH ≤ 4.8 have significantly higher P levels than patients with a pH > 4.8. Limitations, reasons for caution This is a pilot study, thus further trials with larger sample sizes should be performed in order to confirm these results. Additionally, vaginal microbiome alone does not explain the total variability in serum P levels measured in artificial cycles when using MVP. Wider implications of the findings We might have found one of the causes of the high heterogeneity on vaginal absorption of MVP in artificial cycles. This finding may help us with patient management when programming an ET in this type of cycles, improving personalised patient care and progressing on luteal phase support individualisation. Trial registration number 2110-VLC-095-EL

B-257 Rapid Implementation of Monkeypox Detection in a Brazilian Diagnostic Laboratory

Abstract Background Monkeypox is a double-stranded DNA virus (approximately 197 kbp) belonging to the genus Orthopoxivirus. It is responsible for sporadic outbreaks in countries in Africa. Recently, in May 2022 a patient with a recent travel history to Nigeria tested positive for monkeypox in the UK. After that, people with symptoms (usually epithelial pustular lesions) were diagnosed with the virus in several countries, such as Portugal and the United States. In Brazil, the first case was confirmed in June 2022, the patient had traveled to Spain and Portugal. It was in this context that the Technical Operational Nucleus of our laboratory, Sabin Diagnosis and Health, located in Brasilia, capital of Brazil, validated and implemented a test to detect the genetic material of Monkeypox. Thus, in this work we present the implementation of this test. Method For the detection of Monkeypox viral DNA we chose to implement a real-time PCR (qPCR) methodology. The validated samples were swabs and wound scabs. The nucleic acid extraction chosen was using the Virus Pathogen kit from (QIAGEN), ‘midi’ protocol in the qiasymphony equipment (QIAGEN). Later we validated the extraction with the Maxwell RSC Viral Total Nucleic Acid Purification Kit extraction kit (Promega). For qPCR, we selected monkeypox-specific primers and probes, which were not able to recognize other Orthopoxiviruses (such as human pox) to ensure specificity. We used RNASEP-specific primers as an endogenous extraction control. As a positive control (PC) we used a synthetic double-stranded DNA fragment with the target sequence flanked by 10 bp. The limit of detection of the test was performed using serial dilutions of the positive control. Furthermore, given the initial absence of a positive sample for validation, we designed four pairs of primers that amplified four different regions of the viral genome for sequencing by the Sanger technique. The first positive samples were confirmed by sequencing these four regions. Results The protocol was designed in the first week after the confirmation of the first case in Brazil. The first tests with the PC showed the effectiveness of the primers. After adjusting the reaction conditions to assess the specificity of the test, we tested the protocol with samples known to be positive for other viral pathogens and obtained negative results for all of them, confirming the high specificity. After that we experimentally determined the limit of detection (25 copies per reaction). On July 8, 2022, one month after the first confirmed case in Brazil in the state of São Paulo, we released the Monkeypox detection test with the methodology described above. Since then, we have performed 193 tests, of which 59 (31%) were positive, most of them (56–95%) in men. The first 10 positive results were confirmed by genetic sequencing (Sanger). Discussion The implementation of the Monkeypox detection test by our laboratory allowed a quick response for Brazilian patients who needed the test after the virus entered the country.

Development and Application of nanoPCR Method for Detection of Feline Panleukopenia Virus.

Feline panleukopenia (FP) is a severe viral illness caused by the feline panleukopenia virus (FPV), putting sectors like companion cat breeding and endangered feline conservation at risk. The virus has a high morbidity and fatality rate and is found all over the world. We created a novel FPV assay using nanoPCR technology and assessed the method's specificity and sensitivity. The approach amplified a 345 bp nucleic acid fragment with a minimum detection limit of 7.97 × 102 copies/μL, which is about 100 times greater than traditional PCR. We collected anal swabs from 83 cats suspected of FPV infection for practical application, and the FPV-positive rate determined by the nanoPCR approach was 77.1%. In conclusion, the approach is more sensitive than conventional PCR and more convenient and cost-effective than qPCR methodology and may be utilized for the clinical detection of FPV.

Short communication: profiling the expression of Let-7d-5p microRNA in circulating blood of pregnant and nonpregnant cows.

The objective of this work was to determine if specific circulating microRNA (miRNA) differed due to pregnancy status in heifers. Blood samples were collected from heifers 21 d after receiving an in vitro-produced embryo. Pregnancy status was diagnosed 21 d after embryo transfer, equivalent to day 28 of gestation, with rectal ultrasonography. Blood samples from 10 pregnant and 10 nonpregnant heifers were then evaluated for miRNA expression. There were five different miRNAs quantified using delta-delta Ct and qPCR methodology. These miRNAs had previously been associated with early pregnancy in cattle. The miRNA Let-7d-5p was decreased in nonpregnant as compared to pregnant females (P < 0.05). There were no changes in 16-5p, 16-1-3p, 16-2-3p, and 26a-5p associated with pregnancy (P > 0.05). Results demonstrate an opportunity to identify and study the differential expression of miRNAs from the blood of pregnant cows. The Let-7d-5p miRNA is a potential early pregnancy marker and is critical to better understand the early relationships of the cellular and molecular interactions of the cow and embryo.

Q-PCR Methodology for Monitoring the Thermophilic Hydrogen Producers Enriched from Elephant Dung

This study aims to create a quantitative polymerase chain reaction (q-PCR) methodology for monitoring the hydrogen-producing mixed cultures enriched from elephant dung using alpha-cellulose as a carbon source through five generations of repetitive sub-culture. The enriched thermophilic mixed cultures from the fifth cultivation cycle gave the highest hydrogen yield of 170.3 mL H2/g cellulose and were used to generate hydrogen from sawdust. Clostridium sp. and Thermoanaerobacterium sp. were the dominant bacteria in thermophilic mixed cultures with high hydrogen yield, according to polymerase chain reaction-denatured gradient gel electrophoresis (PCR-DGGE). q-PCR primers Chis150F and ClostIR, TherF and TherR, and BacdF and BacdR were developed to amplify the 16S rRNA genes of Clostridium sp., Thermoanaerobacterium sp., and Bacillus sp., respectively, for the quantification of hydrogen-producing bacteria in biohydrogen fermentation. Similar q-PCR analysis of Clostridium sp., Thermoanaerobacterium sp., and Bacillus sp. 16S rRNA gene amplification during hydrogen production from cellulose and sawdust revealed increasing gene copy number with time. The molecular approaches developed in this study can be used to monitor microbial communities in hydrogen fermentation processes efficiently.

Role of adipose tissue-derived cytokines in the progression of inflammatory breast cancer in patients with obesity

BackgroundInflammatory breast cancer (IBC) represents a deadly aggressive phenotype of breast cancer (BC) with a unique clinicopathological presentation and low survival rate. In fact, obesity represents an important risk factor for BC. Although several studies have identified different cellular-derived and molecular factors involved in IBC progression, the role of adipocytes remains unclear. Cancer-associated adipose tissue (CAAT) expresses a variety of adipokines, which contribute to tumorigenesis and the regulation of cancer stem cell (CSC). This research investigated the potential effect of the secretome of CAAT explants from patients with BC on the progression and metastasis of the disease.MethodsThis study established an ex-vivo culture of CAAT excised from IBC (n = 13) vs. non-IBC (n = 31) patients with obesity and profiled their secretome using a cytokine antibody array. Furthermore, the quantitative PCR (qPCR) methodology was used to validate the levels of predominant cytokines at the transcript level after culture in a medium conditioned by CAAT. Moreover, the impact of the CAAT secretome on the expression of epithelial-mesenchymal transition (EMT) and cells with stem cell (CSC) markers was studied in the non-IBC MDA-MB-231 and the IBC SUM-149 cell lines. The statistical differences between variables were evaluated using the chi-squared test and unpaired a Student’s t-test.ResultsThe results of cytokine array profiling revealed an overall significantly higher level of a panel of 28 cytokines secreted by the CAAT ex-vivo culture from IBC patients with obesity compared to those with non-IBC. Of note, interleukin-6 (IL-6), interleukin-8 (IL-8), and monocyte chemo-attractant protein 1 (MCP-1) were the major adipokines secreted by the CAAT IBC patients with obesity. Moreover, the qPCR results indicated a significant upregulation of the IL-6, IL-8, and MCP-1 mRNAs in CAAT ex-vivo culture of patients with IBC vs. those with non-IBC. Intriguingly, a qPCR data analysis showed that the CAAT secretome secretions from patients with non-IBC downregulated the mRNA levels of the CD24 CSC marker and of the epithelial marker E-cadherin in the non-IBC cell line. By contrast, E-cadherin was upregulated in the SUM-149 cell.ConclusionsThis study identified the overexpression of IL-6, IL-8, and MCP-1 as prognostic markers of CAAT from patients with IBC but not from those with non-IBC ; moreover, their upregulation might be associated with IBC aggressiveness via the regulation of CSC and EMT markers. This study proposed that targeting IL-6, IL-8, and MCP-1 may represent a therapeutic option that should be considered in the treatment of patients with IBC.

Evaluation of a direct phage DNA detection-based Taqman qPCR methodology for quantification of phage and its application in rapid ultrasensitive identification of Acinetobacter baumannii

BackgroundRapid phage enumeration/quantitation and viable bacteria determination is critical for phage application and treatment of infectious patients caused by the pathogenic bacteria.MethodsIn the current study, a direct phage DNA detection-based Taqman qPCR methodology for quantification of phage P53 and rapid ultrasensitive identification of Acinetobacter baumannii (A. baumannii) was evaluated.ResultsThe assay was capable of quantifying P53 phage DNA without DNA extraction and the detection limit of the assay was 550 PFU/mL. The agreement bias between the quantitative results of three different phage concentrations in this assay and double agar overlay plaque assay were under 3.38%. Through the built detection system, down to 1 log CFU/mL of viable A. baumannii can be detected within 4 h in A. baumannii spiked swab and bronchoalveolar lavage fluid samples. Compared with the Taqman qPCR that targets the conserved sequence of A. baumannii, the sensitivity of the assay built in this study could increase four orders of magnitude.ConclusionsThe methodology offers a valid alternative for enumeration of freshly prepared phage solution and diagnosis of bacterial infection caused by A. baumannii or other bacterial infection in complicated samples through switching to phages against other bacteria. Furthermore, the assay could offer drug adjustment strategy timely owing to the detection of bacteria vitality.

Impaired transcriptional compensation for oxidative damage in a porcine model of ischaemic cardiomyopathy

Abstract Background The prognosis of heart failure remains poor. Energetic imbalances related to mitochondrial dysfunction, impaired oxidative phosphorylation and oxidative damage have been implicated in the pathogenesis or worsening of heart failure (1,2). Improved understanding of the metabolic alterations in heart failure may provide new biomarkers or therapeutic targets. Purpose We explored mutation rate, mitochondrial copy number and regional mitochondrial gene transcription in a porcine model of ischaemic cardiomyopathy. Specifically, we investigated the Dloop region – a promotor for mitochondrial DNA- in which mutations have been implicated in many cancers. We hypothesised that there may be differences in mutation rate and oxidative damage within the mitochondrial genome. Methods 15 female Yorkshire pigs were studied. 7 animals underwent percutaneous balloon catheter myocardial infarction followed by termination at 4 weeks. A group of 8 healthy animals served as controls. Reverse transcription quantitative PCR (RT-qPCR) assays were performed to determine the gene expression levels of mitochondrial DNA codified genes (ND1, ND2, ND4, ATP6 and ND6). Quantitative PCR (qPCR) methodology was modified to obtain the relative mitochondrial copy number, mutation rate, and oxidative damage according to established methods (3–5). Results Significant mitochondrial transcriptional activity of the genes studied was seen in both groups (see Table 1 and 2). When examining the ND2-ND6 region (excluding the Dloop) in control animals, we note an inverse correlation with increased oxidative damage corresponding to a significantly lower mutation rate (p=0.017). There was no correlation between the mutation rate and oxidative damage in the ND6-ND2- including Dloop- region. However, when examining the Dloop specifically, there was a marked inverse correlation between oxidative damage and mutation rate (p=0.007). This suggests that in controls, there is regional variation in the susceptibility to damage within the mitochondrial genome which may trigger repair mechanisms. Indeed, the relative mitochondrial copy number was inversely associated to the mutation rate (p=0.08) in controls. In contrast, in the chronic animals, we noted no correlation with the level of oxidative damage in the ND2-ND6, D-loop, or ND6–2 regions compared to mutation rate (p=0.52, p=0.53 and p=0.17 respectively). This indicates that there is a loss in the ability to instigate repair mechanisms in the setting of ischaemic cardiomyopathy. Conclusions This study demonstrates that in control animals, there appears to be regional variation in the ability to mitigate against mutations in response to oxidative damage within the mitochondrial genome. In contrast, this protection and/or the effectiveness of repair mechanisms appear to be impaired in the setting of ischaemic cardiomyopathy. This may be a driver, and in turn a therapeutic target, for adverse remodelling in this setting. Funding Acknowledgement Type of funding sources: Other. Main funding source(s): This research work was supported by grants awarded to Professor Ascione: the British Heart Foundation (BHF) (BHF IG/14/2/30991, BHF RM/13/2/30158), and the Medical Research Council (MRC) (MRC MR/L012723/1).

A Reliable and Standardizable Differential PCR and qPCR Methodology Assesses HER2 Gene Amplification in Gastric Cancer.

Simple SummaryPatients with gastric cancer may present variations in the copy number of the HER2 gene in their primary tumors. The techniques used to detect these variations and HER2 overexpression render false positive and negative results with high frequency, and robust methodologies are required to assess this amplification and confidently select patients who may benefit from HER2-specific monoclonal antibody-based therapies. We addressed this issue by molecular biology techniques using DNA samples from tumor or distal tissue of gastric cancer patients. The HER2 and a control (IFNG) gene were subjected to differential (diffPCR) and quantitative PCR (qPCR). A cut-off point above which patients can be deemed positive was set based on the HER2/IFNG ratio, achieved using DNA from 30 healthy donors. Both, diffPCR and qPCR, identified the presence of somatic HER2 amplifications in 25% of patients in DNA from tumoral tissue, but not distal, paired tissue samples. Immunohistochemistry and immunofluorescence detected HER2 overexpression in tumor, but not distal, tissue of the patients previously identified as HER2+ by diffPCR and qPCR. Thus, the molecular biology-based techniques herein reported can identify patients with HER2 gene amplification and suitable for immune-based therapies.We have applied two PCR techniques, differential PCR (diffPCR) and qPCR for the identification of HER2 gene amplifications in genomic DNA of tumor and distal gastric samples from patients with gastric cancer. The diffPCR technique consists of the simultaneous amplification of the HER2 gene and a housekeeping gene by conventional PCR and the densitometric analysis of the bands obtained. We established a cut-off point based on the mean and standard deviation analyzing the DNA of 30 gastric tissues from patients undergoing non-cancer gastrectomy. diffPCR and qPCR yielded consistent results. HER2-overexpression was detected in 25% of patients and was further confirmed by immunohistochemistry and immunofluorescence. The approaches herein described may serve as complementary and reliable methods to assess HER2 amplification.

Large-scale comparison of E. coli levels determined by culture and a qPCR method (EPA Draft Method C) in Michigan towards the implementation of rapid, multi-site beach testing

Fecal pollution remains a challenge for water quality managers at Great Lakes and inland recreational beaches. The fecal indicator of choice at these beaches is typically Escherichia coli (E. coli), determined by culture-based methods that require over 18 h to obtain results. Researchers at the United States Environmental Protection Agency (EPA) have developed a rapid E. coli qPCR methodology (EPA Draft Method C) that can provide same-day results for improving public health protection with demonstrated sensitivity, specificity, and data acceptance criteria. However, limited information is currently available to compare the occurrence of E. coli determined by cultivation and by EPA Draft Method C (Method C). This study provides a large-scale data collection effort to compare the occurrence of E. coli determined by these alternative methods at more than 100 Michigan recreational beach and other sites using the complete set of quantitative data pairings and selected subsets of the data and sites meeting various eligibility requirements. Simple linear regression analyses of composite (pooled) data indicated a correlation between results of the E. coli monitoring approaches for each of the multi-site datasets as evidenced by Pearson R-squared values ranging from 0.452 to 0.641. Theoretical Method C threshold values, expressed as mean log10 target gene copies per reaction, that corresponded to an established E. coli culture method water quality standard of 300 MPN or CFU /100 mL varied only from 1.817 to 1.908 for the different datasets using this model. Different modeling and derivation approaches that incorporated within and between-site variability in the estimates also gave Method C threshold values in this range but only when relatively well-correlated datasets were used to minimize the error. A hypothetical exercise to evaluate the frequency of water impairments based on theoretical qPCR thresholds corresponding to the E. coli water quality standard for culture methods suggested that the methods may provide the same beach notification outcomes over 90% of the time with Method C results differing from culture method results that indicated acceptable and unacceptable water quality at overall rates of 1.9% and 6.6%, respectively. Results from this study provide useful information about the relationships between E. coli determined by culture and qPCR methods across many diverse freshwater sites and should facilitate efforts to implement qPCR-based E. coli detection for rapid recreational water quality monitoring on a large scale in the State of Michigan.

Use of nucleic acids amplification methods in Marek's disease diagnosis and pathogenesis studies.

Marek's disease (MD) is a lymphoproliferative disease of chickens with strong economic impact on poultry industry. Although successful vaccination has enabled control of the disease, outbreaks occur in commercial flocks, resulting in substantial economic losses. Together with vaccination, accurate and fast diagnosis of MD remain the most important tools for its efficient control. MD diagnosis currently relies mainly on the identification of its causative agent, Marek's disease virus type 1 (MDV-1). Nucleic acid amplification techniques have been successfully applied for identification of MDV DNA in field samples and also for studies of virus-host interactions. In this review we want to summarize recent advances in the development of standard and quantitative PCR techniques and their use in rapid MD diagnosis, including differentiation of pathogenic and vaccine MD viruses. PCR protocols have served as a useful tool for clarification of processes associated with MDV infection in chickens, such as virus spread and release, and effect of vaccine virus on progress of MD. Here, we also describe a novel multi-species qPCR methodology for identification and quantification of MDV DNA, enabling its detection in various bird species that are the most susceptible to MDV infection. Keywords: Marek's disease; MDV; diagnosis; nucleic acid detection; duplex quantitative PCR.

Prevalence, risk factors and health consequences of soil-transmitted helminth infection on the Bijagos Islands, Guinea Bissau: A community-wide cross-sectional study.

Soil-transmitted helminths (STH) are endemic and widespread across Sub-Saharan Africa. A community wide soil-transmitted helminth (STH) prevalence survey was performed on the island of Bubaque in Guinea-Bissau using both Kato-katz microscopy and qPCR methodology. Predictors of infection and morbidity indicators were identified using multivariable logistic regression, and diagnostic methods were compared using k statistics. Among 396 participants, prevalence of STH by microscopy was 23.2%, hookworm was the only species identified by this method and the mean infection intensity was 312 eggs per gram. qPCR analysis revealed an overall prevalence of any STH infection of 47.3%, with the majority A. duodenale (32.3%), followed by N. americanus (15.01%) and S. stercoralis (13.2%). A. lumbricoides, and T. trichiura infections were negligible, with a prevalence of 0.25% each. Agreement between diagnostic tests was k = 0.22, interpreted as fair agreement, and infection intensity measured by both methods was only minimally correlated (Rs = -0.03). STH infection overall was more common in females and adults aged 31–40. STH infection was associated with open defaecation, low socio-economic status and further distance to a water-source. The prevalence of anaemia (defined as a binary outcome by the WHO standards for age and sex) was 69.1%, and 44.2% of children were malnourished according to WHO child growth standards. Hookworm infection intensity by faecal egg count showed no statistically significant association with age (Rs 0.06) but S. Stercoralis infection intensity by qPCR cycle threshold was higher in pre-school aged children (Rs = 0.30, p-value 0.03) There was no statistically significant association between STH infection and anaemia (OR 1.0 p = 0.8), stunting (OR 1.9, p-value 0.5) and wasting (OR 2.0, p-value 0.2) in children. This study reveals a persistent reservoir of STH infection across the community, with high rates of anaemia and malnutrition, despite high-coverage of mebendazole mass-drug administration in pre-school children. This reflects the need for a new strategy to soil-transmitted helminth control, to reduce infections and ultimately eliminate transmission.

Assessing BactoMix 5 efficacy for clubroot control in naturally infested soil

The cultivation of cruciferous crops is threatened by extensive yield losses caused by the soil-borne pathogen Plasmodiophora brassicae Woronin, 1877. The objective of the study was to assess the potential of the bacterial product BactoMix 5 for the control of clubroot on a naturally infested soil in growth chamber trials using a P. brassicae-specific qPCR methodology. The results did not show a significant decrease in the P. brassicae in the soil nor a reduction of the disease symptoms on the plants. The native soil microbiota may have exhibited an antagonistic activity against the bacterial species from BactoMix 5 and evoked the poor effect of the product. Therefore, potential biological control agents should be tested with native soil microbiota and the regional production should be advanced to increase the product efficacy in the environment

Quantitative PCR methodology with a volume-based unit for the sophisticated cellular kinetic evaluation of chimeric antigen receptor T cells

Although the cellular kinetics of chimeric antigen receptor T (CAR T) cells are expressed in units of copies/μg gDNA, this notation carries the risk of misrepresentation owing to dramatic changes in blood gDNA levels after lymphocyte-depleting chemotherapy and rapid expansion of CAR T cells. Therefore, we aimed to establish a novel qPCR methodology incorporating a spike-in calibration curve that expresses cellular kinetics in units of copies/μL blood, as is the case for conventional pharmacokinetic studies of small molecules and other biologics. Dog gDNA was used as an external control gene. Our methodology enables more accurate evaluation of in vivo CAR T-cell expansion than the conventional approach; the unit “copies/μL blood” is therefore more appropriate for evaluating cellular kinetics than the unit “copies/μg gDNA.” The results of the present study provide new insights into the relationship between cellular kinetics and treatment efficacy, thereby greatly benefiting patients undergoing CAR T-cell therapy.

Autosomal sdY Pseudogenes Explain Discordances Between Phenotypic Sex and DNA Marker for Sex Identification in Atlantic Salmon

Despite the key role that sex-determination plays in evolutionary processes, it is still poorly understood in many species. In salmonids, which are among the best studied fishes, the master sex-determining gene sexually dimorphic on the Y-chromosome (sdY) has been identified. However, sdY displays unexplained discordance to the phenotypic sex, with a variable frequency of phenotypic females being reported as genetic males. Multiple sex determining loci in Atlantic salmon have also been reported, possibly as a result of recent transposition events in this species. We hypothesized the existence of an autosomal copy of sdY, causing apparent discordance between phenotypic and genetic sex, that is transmitted in accordance with autosomal inheritance. To test this, we developed a qPCR methodology to detect the total number of sdY copies present in the genome. Based on the observed phenotype/genotype frequencies and linkage analysis among 2,025 offspring from 64 pedigree-controlled families of accurately phenotyped Atlantic salmon, we identified both males and females carrying one or two autosomal copies of sdY in addition to the Y-specific copy present in males. Patterns across families were highly consistent with autosomal inheritance. These autosomal sdY copies appear to have lost the ability to function as a sex determining gene and were only occasionally assigned to the actual sex chromosome in any of the affected families.

ALL-074: Exosomal MicroRNAs as Minimal Residual Disease Biomarker Candidates in Childhood Acute Lymphoblastic Leukemia

Context Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy. Five-year survival rate is nearly 90%. Measurement of minimal residual disease (MRD) at set time points has become a fundamental part of stratified treatment in ALL. Treatment response is assessed using bone marrow samples. Exosomal microRNAs are putative biomarkers in many malignancies. In childhood leukemia, the potential of exosomal microRNAs as biomarker candidates has not established yet. Objectives The aim of this study was to evaluate exosomal microRNAs in peripheral blood and associated with flow cytometry (FC) MRD in childhood ALL. Design and settings Exosomal fractions of 52 platelet-free plasma samples were obtained from 13 newly diagnosed de novo ALL patients and 6 healthy controls by ultracentrifugation. RNA isolation was carried out using miRNeasy Serum/Plasma Kit (Qiagen). Quantitative real-time PCR was carried out using TaqMan advanced qPCR methodology. Results The expression of the tested microRNAs in exosomal fraction as well as in platelet-free fraction correlated in diagnostic samples but not any other sampling times during the induction therapy. Significant decrease was observed in both miRs between the day of diagnosis and day 15 of induction therapy. Expression changes in one of the tested exosomal microRNAs correlated in every given time point with day 15 FC MRD (p Conclusion Based on our results, certain exosomal microRNAs' expression changes seem to be a better biomarker candidate than circulating microRNAs detected in platelet-free plasma of de novo childhood ALL.

A Circulating MicroRNA Panel for Malignant Germ Cell Tumor Diagnosis and Monitoring.

Reverse transcription (RT) based quantitative PCR (qPCR) for quantifying microRNAs (miRNAs) in in the circulation presents specific challenges. Here, we describe an optimized research protocol to assess serum sample quality and quantify levels of a panel of four test miRNAs (miR-371a-3p, miR-372-3p, miR-373-3p, and miR-367-3p) that enables highly sensitive and specific malignant germ cell tumor (GCT) diagnosis and monitoring. This protocol utilizes a multiplex RT step using Taqman miRNA stem-loop primers. A multiplexed preamplification stage is then employed to increase the sensitivity of the final quantification step, which is performed using standard singleplex Taqman qPCR methodology.

Low expression of miR-20b-5p indicates favorable prognosis in laryngeal squamous cell carcinoma, especially in patients with non-infiltrated regional lymph nodes.

Tumor recurrence and distant metastasis are very common in laryngeal squamous cell carcinoma (LSCC). In this study, we examined the potential prognostic value of microRNA-20b-5p (miR-20b-5p), a component of the tumor-related miR-106a/363 cluster. Total RNA was purified from 105 tissue specimens resected from patients having undergone surgical treatment for primary LSCC. After in vitro polyadenylation and reverse transcription, a sensitive real-time quantitative polymerase chain reaction (qPCR) methodology was applied for the relative quantification of miR-20b-5p levels. Then, we proceeded with biostatistical analysis, seeking to assess the prognostic value of miR-20b-5p expression in LSCC. miR-20b-5p positivity constitutes a predictor of inferior DFS and OS in LSCC (P<0.001 and P=0.002, respectively). The significant prognostic value of miR-20b-5p expression status seems to be independent of tumor size, histological grade, and TNM stage, as revealed by the multivariate bootstrap Cox regression analysis. Kaplan-Meier survival analysis showed also that miR-20b-5p expression status can stratify LSCC patients with non-infiltrated regional lymph nodes (N0) into two subgroups with distinct prognosis (P=0.004 and P=0.004, respectively). The miR-20b-5p expression status is a promising molecular tissue biomarker in LSCC, with an independent prognostic value, and thus merits further validation in larger cohorts of patients.