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In this study, we developed a real-time quantitative polymerase chain reaction (qPCR) assay based on a dual-labeled hydrolysis probe to simultaneously detect both duck circovirus (DuCV) 1 and DuCV-2. The reproducibility, sensitivity and specificity of the primer set and probe were evaluated using other duck pathogens. The detection limit was 20 copies per µL. The intra-assay coefficients of variation (CVs) were ≤ 0.73% and the inter-assay CVs were ≤ 1.89%. No cross-reaction occurred with other duck pathogens. In addition, the qPCR assay was successfully applied to the simultaneous detection of DuCV-1 and DuCV-2 in clinical field samples. Therefore, this assay will be useful for laboratory diagnosis and epidemiological field studies of DuCV., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Trichuriasis is a serious threat to the economic development of animal husbandry. This research aimed to establish a droplet digital PCR (ddPCR) method to detect Trichuris spp. for the early diagnosis and prevention of trichuriasis in sheep. The real-time quantitative PCR (qPCR) and ddPCR methods were used for the detection of nematodes by targeted amplification of the ITS gene. Each means was evaluated to optimize the limit of detection and reproducibility. For a recombinant plasmid, the qPCR results showed that the detection limit was 31.7 copies per reaction. In contrast to qPCR, ddPCR was able to detect concentrations below 3.17 copies per reaction. Both assays exhibited good reproducibility. However, the ddPCR method was more stable for low-copy-number detection. This new assay was specific for Trichuris spp. and did not cross-react with other relevant gastrointestinal nematodes. A total of 98 clinical samples were tested with both assays. The results showed that the positive rate of ddPCR (80.6%) was higher than that of qPCR (72.4%). This method could be used as an efficient molecular biology tool to test for Trichuris spp. and could be a new valuable tool for the clinical diagnosis and prevention of trichuriasis., (© American Society of Parasitologists 2020.)

The cytogenetic study of wide hybrids of wheat has both practical and fundamental values. Partial wheat-wheatgrass hybrids (WWGHs) are interesting as a breeding bridge to confer valuable genes to wheat genome, as well as a model object that contains related genomes of Triticeae . The development of cytogenetic markers is a process that requires long and laborious fluorescence in situ hybridization (FISH) testing of various probes before a suitable probe is found. In this study, we aimed to find an approach that allows to facilitate this process. Based on the data sequencing of Thinopyrum ponticum, we selected six tandem repeat (TR) clusters using RepeatExplorer2 pipeline and designed primers for each of them. We estimated the found TRs' abundance in the genomes of Triticum aestivum , Thinopyrum ponticum , Thinopyrum intermedium and four different WWGH accessions using real-time qPCR, and localized them on the chromosomes of the studied WWGHs using fluorescence in situ hybridization. As a result, we obtained three tandem repeat cytogenetic markers that specifically labeled wheatgrass chromosomes in the presence of bread wheat chromosomes. Moreover, we designed and tested primers for these repeats, and demonstrated that they can be used as qPCR markers for quick and cheap monitoring of the presence of certain chromosomes of wheatgrass in breeding programs.

Introduction: Acute lymphoblastic leukemia (ALL) is the first neoplasm where the assessment of early response to therapy by minimal residual disease (MRD) monitoring has proven to be a fundamental tool for guiding therapeutic choices. In recent years, thanks to real-time quantitative PCR (qPCR), MRD monitoring has further achieved higher levels of sensitivity and standardization. However, some outstanding issues still remain to be addressed and emerging technologies hold the promise of improving MRD detection in ALL patients. Areas covered: Through a comprehensive review of the literature, we analyze the state-of-the-art of molecular MRD assessment in ALL to better understand how, in the upcoming years, some of its limitations could be tackled by emerging molecular technologies. Furthermore, we highlight the future role of molecular MRD monitoring in the context of personalized protocols, taking into account the growing genetic complexity in ALL. Expert commentary: Although new molecular technologies are promising tools for MRD assessment, qPCR still remains the gold standard for evaluating MRD in ALL. High-throughput sequencing and droplet digital PCR allow to identify new prognostic factors and/or MRD targets at diagnosis and to perform earlier MRD evaluations, thereby optimizing patient stratification and earlier MRD-based clinical intervention to improve ALL patient outcomes.

Background: Remarkable progress has been made in the quality assurance of Hepatitis B virus (HBV) DNA nucleic amplification techniques (NAT) during the past decade. And this report presents a 10-year external quality assessment (EQA) program performed by National Center for Clinical Laboratories in China since 2003., Method: EQA panels were produced using freeze-dried HBV plasma or negative controls and then calibrated against the first International Standard for HBV DNA., Results: By 2012, total 35,570 qualitative EQA reports and 56,826 quantitative reports have been collected. The overall correct recognition rate in qualitative test increased from 95.15% in 2003 to 97.99% in 2012. The proportion of participants with acceptable quantitative results also rose to 87.99% in 2012 compared with that of 27.53% in 2003. Besides, we observed a satisfactory reproducibility of <5% in all parallel samples. However, some laboratories still had difficulties in exact quantification of some low viral loads, which near to the limits of the dynamic range of the assays., Conclusion: Taking together, current EQA program showed an encouraging improvement of HBV DNA NAT in China. Distributing more challenging samples and increasing the subtypes are still needed in the future., (© 2013 Elsevier B.V. All rights reserved.)

The global prevalence of inflammatory bowel disease (IBD) is on the rise, prompting significant attention from researchers worldwide. IBD entails chronic inflammatory disorders of the intestinal tract, characterized by alternating flares and remissions. Through high-throughput sequencing, numerous studies have unveiled a potential microbial signature for IBD patients showing intestinal enrichment of oralassociated bacteria. Simultaneously, the oral microbiome can be perturbed by intestinal inflammation. Our prior investigation, based on 16S rRNA amplicon sequencing, underscored elevated abundance of Veillonella spp. and Prevotella spp. in the salivary microbiomes of IBD patients. Noteworthy, Prevotella salivae emerged as a distinct species significantly associated with IBD. P. salivae is an under-recognized pathogen that was found to play a role in both oral and systemic diseases. In this study, we delve deeper into the salivary microbiomes of both IBD patients and healthy controls. Employing diverse cultivation techniques and realtime quantitative polymerase chain reactions (RT-qPCR), we gauged the prevalence and abundance of Veillonella spp., Prevotella spp., and P. salivae. Our isolation efforts yielded 407 and 168 strains of Veillonella spp., as well as 173 and 90 strains of Prevotella spp., from the saliva samples of IBD patients and healthy controls, respectively. Veillonella-vancomycin agar emerged as the discerning choice for optimal Veillonella spp. cultivation, while Schaedler kanamycin-vancomycin agar proved to be the most suitable medium for cultivating Prevotella spp. strains. Comparing our RT-qPCR findings to the previous 16S rRNA amplicon sequencing data, the results corroborated the higher abundance of Veillonella spp., Prevotella spp., and P. salivae in the saliva of IBD patients compared to healthy controls. However, it's worth noting that in contrast to RT-qPCR, the 16S rRNA amplicon sequencing data revealed greater absolute abundance of all three bacterial groups in both IBD patients and controls. [ABSTRACT FROM AUTHOR]

Capripox viruses (CaPVs), including sheep pox virus (SPV), goat pox virus (GPV), and lumpy skin disease virus (LSDV), are the cause of sheep pox (SPP), goat pox (GTP), and lumpy skin disease (LSD) in cattle. These diseases are of great economic significance to farmers, as they are endemic on farms and are a major constraint to international trade in livestock and their products. Capripoxvirus (CaPV) infections produce similar symptoms in sheep and goats, and the three viruses cannot be distinguished serologically. In this study, we developed a real-time quantitative polymerase chain reaction (qPCR) method for identifying CaPV in goats, sheep, and cattle. Clinical samples were tested and verified. The developed assay was highly specific for target viruses, including GPVSPV and LSDV, which had no cross-reaction with other viruses causing similar clinical symptoms. An artificially synthesized positive control plasmid using the CaPV 32 gene inserted into the vector pMD19-T was used as a template, and the correlation coefficient of the linear regression curve (R2) was 0.9916, the estimated amplification efficiency (E) was 96.06%, and the sensitivity (limit of detection, LOD) was 3.80 copies per reaction. Using the clinical samples as a template, the limit of detection (LOD) was 4.91 × 10−5 ng per reaction (1.60 × 10−5–2.13 × 10−3 ng, 95% confidence interval (CI)), which means that this method was one of the most sensitive detection assays for CaPVs. A total of 85 clinical samples from CaPV-infected animals (goats, sheep, and cattle) and 50 clinical samples from healthy animals were used to test and compare the diagnostic results using the Synergy Brands (SYBR) Green-based PCR method recommended by the World Organization of Animal Health (WOAH). Both diagnostic sensitivity (DSe) (95.8–100%, 95% CI) and diagnostic specificity (DSp) (92.9–100%, 95% CI) results of the real-time quantitative PCR (qPCR) and SYBR Green PCR were 100%, and the kappa value (κ) was 1.0 (1-1, 95% CI). In summary, the assay established based on TaqMan probes was advantageous in high specificity, sensitivity, and general applicability and could be a competitive candidate tool for the diagnosis of CaPV in clinically suspected animals. [ABSTRACT FROM AUTHOR]

Ichthyophthiriasis, caused by the parasitic ciliate Ichthyophthirius multifiliis (Ich), is considered one of the most harmful diseases affecting freshwater fish globally. It can cause mass mortalities of fish in intensive farming systems. In such systems, it is thus necessary to detect and quantify the number of Ich in the water so that control measures can be implemented before Ichthyophthiriasis breaks out. In recent years, molecular diagnostic methods have become increasingly important in aquaculture. Real‐time quantitative polymerase chain reaction (qPCR) and droplet digital polymerase chain reaction (ddPCR) have become robust assays for detecting pathogens. In this study, a set of specific primers and a TaqMan‐minor groove binder probe targeting the small‐subunit rDNA (SSU rDNA) of Ich were developed. They were used in qPCR and ddPCR assays to compare the performance of these two different methods in quantitatively detecting Ich. After optimizing the reaction conditions, both qPCR and ddPCR assays were found to have high linearity and quantitative correlations for standard plasmid DNA. When used for the detection of Ich eDNA in water samples, the qPCR assay had a wider detection range, making it a suitable method to screen for the prevalence of Ichthyophthiriasis. However, the ddPCR approach had higher sensitivity, which would help provide advance notice of the disease in complex water environmental samples. [ABSTRACT FROM AUTHOR]

Objective: To determine the function of the chemokine (C-X-C motif) ligand 1 (CXCL1) gene in ovarian cancer cells and to investigate the relationship between CXCL1 gene mRNA expression and ovarian tumor clinical pathology. Methods: Using bioinformatics methods to identify common differentially expressed genes associated with ovarian cancer in the GEO database. Growth curves of A2780 cells with or without CXCL1 expression were plotted by MTT assay. Cell cycles were measured by flow cytometry. Cell colony formation was enumerated in Transwell chambers. Migration and invasion in vitro were investigated using Cell Counting Kit-8 (CCK8), wound healing and Transwell, respectively. The relationship between CXCL1 gene mRNA expression and ovarian tumor clinical pathology was analyzed. Results: CXCL1 was found to be one of the co-upregulated differentially expressed genes in the GEO database. The migration of A2780 cells expressing CXCL1 was significantly higher than that of A2780 cells without CXCL1 expression. CXCL1 mRNA expression in ovarian malignancy was significantly higher than those in benign lesions and the normal control (p <.01). In advanced ovarian cancer (Stages III-IV), CXCL1 mRNA expression was also significantly higher than that in patients with early-stage ovarian cancer (Stages I-II) (p =.005). Kaplan-Meier survival curve showed no correlation between CXCL1 mRNA expression and ovarian cancer prognosis. A Cox proportional hazard model also showed that CXCL1 expression was not an independent prognostic factor for ovarian cancer patients. Conclusions: CXCL1 gene could promotes ovarian cancer A2780 cell proliferation and invasion in vitro, and contributed theoretical knowledge for the target selection in molecular targeted therapy. CXCL1 mRNA over-expression may be correlated with the occurrence and development of ovarian malignancy. Level of plasma CXCL1 might serve as a biomarker for prognosis in ovarian carcinoma patients. [ABSTRACT FROM AUTHOR]

In polymerase chain reaction (PCR)-based nucleic acid quantification, the DNA template type, primer/probe sequence, and instrument platform such as real-time quantitative PCR (qPCR) and digital PCR (dPCR) affect the accuracy and reliability of quantitative results. In this study, a plasmid DNA (pDNA) pBI121-screening, genetically modified (GM) rice SDrice genomic DNA (gDNA), and GM rapeseed SDrape gDNA, all carrying the same 11 screening elements, were used to prepare samples of different levels of gDNA and pDNA in a non-GM gDNA background. The comparison of the dPCR assays targeting the 11 screening elements revealed that the primer/probe set is a key factor that affects the accuracy of dPCR quantification. The optimal PCR method for the 11 screening elements was screened out from among the validated qPCR methods. The accuracy of the qPCR quantification of the low-level pDNA and gDNA test samples was low when pDNA was used as a calibrator, whereas that of the dPCR quantification was high and not affected by variations in template type and detection target. The validated dPCR assays targeting one or two elements can be randomly selected to characterize multiple-target pDNA reference materials (RMs). Low-level pDNA RMs with certified values can be used as quality controls for dPCR assays to avoid significant bias in gDNA quantification. [ABSTRACT FROM AUTHOR]

Congenital cytomegalovirus infection (cCMV) is a common cause of congenital infections, leading to neurodevelopmental sequelae. Real‐time quantitative polymerase chain reaction (qPCR) has been widely used for the diagnosis and assessment of cCMV; however, the correlation between CMV DNA load and the severity of cCMV symptoms has been inconclusive. Droplet digital PCR (ddPCR) offers an improvement over the current qPCR methods through the absolute quantification of viral loads. We compared ddPCR and qPCR results for the quantification of CMV DNA in blood and urine specimens from 39 neonates with cCMV (21 symptomatic and 18 asymptomatic). There was no significant difference in blood CMV DNA loads measured by ddPCR and qPCR, with or without any clinical findings. However, developmental delays at 36 months were significantly more frequently observed in patients with high CMV DNA loads (≥2950 copies/ml), as measured by ddPCR at diagnosis, than in those with lower CMV DNA loads. The association of urine CMV DNA load with symptoms and developmental delay was not observed. CMV DNA loads in the blood might be used as a predictor of developmental outcomes in cCMV patients, and absolute quantitation of viral loads by ddPCR assay could contribute to the standardization of CMV load measurement. [ABSTRACT FROM AUTHOR]

Strawberry (Fragaria x ananassa Duch.) is a favorite fruit of high economic value due to its good taste and high nutrition ingredients. Strawberry is a fruit grown around the world that has distinct genetic structures and indicates diverse levels of precision to different environmental circumstances. Plants respond differently to diverse physiological processes, organizing of biological events, control of hormones, different individuals of the same species, and internal and external factors in developmental stages. Quantitative real-time polymerase chain reaction (RT-qPCR) has become a very useful tool for the determination of plant genetic and physiological changes in gene expression. To obtain more securable gene expression outcomes, RT-qPCR data should be standardized with a control gene that shows homogeneous expression at diverse stages of growth in plants, in different organs, or under various environmental circumstances. We evaluated the gene expression of 8 reference genes, including StRefHISTH4, StRefGAPDH, StRefDBP, StRefActin1, UBQ, aTUB, 18SrRNA, and EF1a in different sets of 2 cultivars, four different organs, various fruit growing stages, and development period samples treated with salt. The genes expressions are greatly dissimilar in various organ samples examined. The expressions of StRefHISH4 and StRefActin 1 were very steady in all the different organs, fruits at various growth stages, and samples treated with salt analyzed. Furthermore, StRefHISH4 and StRefActin 1 showed the steadiest expression in plants cultivated under different development states. The expression of these reference (housekeeping) genes can be utilized for the standardization of real-time PCR outcomes for gene expression examination in many types of samples in strawberries. [ABSTRACT FROM AUTHOR]

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Aims: The absence of objectionable micro‐organisms in cosmetics and the efficiency of preservatives are still mainly assessed by time‐consuming cultivation‐based methods. We explored the applicability of real‐time quantitative polymerase chain reaction (qPCR) and reported on the behaviour of different bacteria in artificially contaminated creams. Methods and results: Real‐time qPCR on DNA from Burkholderia cepacia, Pluribacter gergoviae, Pseudomonas aeruginosa and Sphingomonas paucimobilis identified specific primer pairs that amplify accurately and efficiently two strains/isolates of each species. Using DNeasy mericon Food Kit, we detected bacterial growth in an inoculated cosmetic cream and persistency of DNA from heat‐inactivated bacteria. We were also able to monitor the growth inhibitory effect of caprylyl glycol and EDTA, also showing how different bacterial species interact depending on the presence/absence of these ingredients. Finally, creams supplemented with the protective cosmetic ingredients revealed the various behaviour of five strains/isolates from P. aeruginosa. Conclusions: Successfully extracting bacterial DNA from artificially contaminated cosmetic creams, we could perform real‐time qPCR to identify and follow the growth of various strains of 4 bacteria species under different conditions. Significance and impact of the study: Real‐time qPCR appears as a promising method to detect bacterial contamination in cosmetic creams and/or to monitor growth inhibition by ingredients. [ABSTRACT FROM AUTHOR]

The implementation of genetically modified organism (GMO) labeling policies requires accurate quantitative methods to measure the GMO content in test samples. A Kemingdao/phospholipase D (KMD/PLD) duplex ddPCR method was established with rice genomic DNA (gDNA) of homozygous KMD as template by optimizing the annealing temperature and cycle number. Duplex ddPCR showed a linear response over the dynamic range from 68 to 175,000 copies, covering four orders of magnitude. The limit of detection (LOD) and limit of quantification (LOQ) for duplex ddPCR were determined to be 9 copies and 34 copies of the rice haploid genome, respectively. A very high dilution factor would result in unacceptable bias and coefficients of variation for determining copy number of the gDNA solution, and more than 1000 copies of the DNA template in one reaction is preferred to obtain accurate quantitative results by duplex PCR. Five blinded DNA samples with copy number ratio of 10%, 5%, 1%, 0.1%, and 0.05%, and three blinded real-life matrix samples with mass fraction of 5%, 1%, and 0.5% were quantified by duplex ddPCR, simplex ddPCR, and qPCR. These three methods all gave comparable GMO content and copy numbers within the required precision, but the duplex ddPCR showed the narrowest uncertainty interval and provided the highest precision in comparison to simplex ddPCR and qPCR. The ddPCR is a more appealing and reliable technology for the accurate quantification of GMO content than simplex ddPCR and qPCR considering the uncertainty and precision of quantitative results, the time consumption of generating droplets, and the cost of ddPCR reagents. [ABSTRACT FROM AUTHOR]

In this study, a method was established for discriminating the true Cervus antlers from its counterfeits using TaqMan real-time quantitative PCR. The method combines the use of true Cervus antlers-specific primers, that amplify a 226 bp fragment from true Cervus antlers DNA, and mammalian-specific primers amplifying a 146 bp fragment from mammalian species DNA, which are used as endogenous control. A TaqMan probe that hybridizes in the 'Cervus antler' and also in the 'mammalian' DNA fragments is used to monitor the amplification of the target gene. The Cervus antler mitochondrial DNA was used as target gene to design the primers and TaqMan probes. The data revealed that the TaqMan real-time PCR-based assay can be used for identification of the true Cervus antlers from counterfeits in a single step. The limit of detection (LOD) was lower than 1 pg of DNA per reaction. [ABSTRACT FROM AUTHOR]

Objective: To study the influence of human papillomavirus (HPV) virions present in different sperm fractions of male partners of women undergoing IUI on fertility outcome.Design: Prospective noninterventional multicenter study.Setting: Inpatient hospital fertility centers.Patient(s): Seven hundred thirty-two infertile couples undergoing 1,753 IUI cycles with capacitated sperm.Intervention(s): None.Main Outcome Measure(s): Biochemical and clinical pregnancy rate in IUI cycles with HPV-positive or HPV-negative semen.Result(s): Five hundred seventy-three infertile couples undergoing 1,362 IUI cycles were enrolled. Work-up of the 1,362 sperm samples that were used for IUI generated 3,444 separate sperm fractions. Each of the sperm fractions was tested with quantitative polymerase chain reaction for 18 different HPV types (6, 11, 16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 67, and 68). HPV prevalence in sperm was 12.5%/IUI cycle. When infectious HPV virions were detected in sperm, a significant decrease in clinical pregnancies was observed when compared with HPV-negative cycles (2.9% vs. 11.1 %/cycle). Above a ratio of 0.66 HPV virions/spermatozoon no pregnancies occurred (sensitivity 100%, specificity 32.5%).Conclusion(s): Women inseminated with HPV-positive sperm had 4 times fewer clinical pregnancies compared with women who had HPV-negative partners. Detection of HPV virions in sperm is associated with a negative IUI outcome and should be part of routine examination and counseling of infertile couples.European Clinical Trials Database Number: 2017-004791-56. [ABSTRACT FROM AUTHOR]

Huperzine A (HupA) is a powerful and selective inhibitor of acetylcholinesterase. It has attracted widespread attention endangering the ultimate plant sources of Lycopodiaceae family. In this study, we used Huperzia serrata , extensively used in Traditional Chinese medicine (TCM), a slow growing vascular plant as the model plant of the Lycopodiaceae family to develop and validate the reference genes. We aim to use gene expression platform to understand the gene expression of different tissues and developmental stages of this medicinal herb. Eight candidate reference genes were selected based on RNA-seq data and evaluated with qRT-PCR. The expression of L/ODC and cytochrome P450s genes known for their involvement in lycopodium alkaloid biosynthesis, were also studied to validate the selected reference genes. The most stable genes were TBP, GAPDH , and their combination (TBP + GAPDH). We report for the first time the reference gene of H. serrata's different tissues which would provide important insights into understanding their biological functions comparing other Lycopodiaceae plants and facilitate a good biopharming approach. [ABSTRACT FROM AUTHOR]

Abstract: Background and Aims: Malolactic fermentation (MLF), accomplished by lactic acid bacteria (LAB), is indispensable for the production of some red wines. As the key additive for wines, sulfur dioxide (SO2) frequently affects LAB growth and MLF development. We aimed to investigate suitable reference genes in Lactobacillus plantarum R23, an excellent LAB with good tolerance to SO2, for a real‐time quantitative PCR analysis of SO2 tolerance. Methods and Results: The expression of eight candidate reference genes under SO2 stress conditions for L. plantarum R23 was analysed, and geNorm and BestKeeper software packages were employed to assess the reference genes. The expression of mleR1 and mleP1 under SO2 stress conditions was used to confirm the results. The geNorm analysis indicated that the stability ranking of reference genes was rpoB > rpoC > recA > ldh > cfal > mtlR > asd2 > gpp. Both software packages suggested that four genes should be selected for accurate normalisation, and the validated experiment further confirmed the suitability of the reference genes revealed in this study. Conclusions: The genes rpoB, rpoC, recA and ldh were the most stably expressed reference genes and thus represent the reference gene combination that should be used to obtain the most accurate results for different SO2 stress conditions in L. plantarum R23. Significance of the Study: This is the first detailed study to evaluate selected reference genes in L. plantarum R23 under SO2 stress conditions, which should allow the quantification of bacterial gene expression levels under SO2 stress conditions and also provide a foundation for the more accurate use of real‐time quantitative PCR in L. plantarum. [ABSTRACT FROM AUTHOR]

Abstract: Environmental DNA (eDNA) analysis is a rapid, cost‐effective, non‐invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species‐specific survey tool for rare or invasive species across a broad range of ecosystems. Recently, eDNA and “metabarcoding” have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding is as sensitive as targeted approaches for rare species detection remains to be evaluated. The great crested newt Triturus cristatus is a flagship pond species of international conservation concern and the first UK species to be routinely monitored using eDNA. We evaluate whether eDNA metabarcoding has comparable sensitivity to targeted real‐time quantitative PCR (qPCR) for T. cristatus detection. Extracted eDNA samples (N = 532) were screened for T. cristatus by qPCR and analysed for all vertebrate species using high‐throughput sequencing technology. With qPCR and a detection threshold of 1 of 12 positive qPCR replicates, newts were detected in 50% of ponds. Detection decreased to 32% when the threshold was increased to 4 of 12 positive qPCR replicates. With metabarcoding, newts were detected in 34% of ponds without a detection threshold, and in 28% of ponds when a threshold (0.028%) was applied. Therefore, qPCR provided greater detection than metabarcoding but metabarcoding detection with no threshold was equivalent to qPCR with a stringent detection threshold. The proportion of T. cristatus sequences in each sample was positively associated with the number of positive qPCR replicates (qPCR score) suggesting eDNA metabarcoding may be indicative of eDNA concentration. eDNA metabarcoding holds enormous potential for holistic biodiversity assessment and routine freshwater monitoring. We advocate this community approach to freshwater monitoring to guide management and conservation, whereby entire communities can be initially surveyed to best inform use of funding and time for species‐specific surveys. [ABSTRACT FROM AUTHOR]

Endometrial clear‐cell carcinoma (ECC) is relatively rare. The expression of diagnostic markers in this disease is similar to that of clear‐cell carcinoma, but the molecular carcinogenic events and therapeutic targets are mostly unknown. MET gene amplification has been reported in various cancers, including ovarian clear‐cell carcinomas; however, the MET gene status has not previously been examined in ECC. We performed real‐time quantitative PCR (QPCR) and fluorescence in situ hybridization (FISH) to analyze the MET gene statuses of 12 ECC cases. We found MET amplifications in two cases (2/12; 16.7%) by both methods. Of the 12 cases, 9 were pure clear‐cell carcinomas, and 3 were mixed types that included mixes with endometrioid carcinomas in 2 cases, and the remaining case was a heterologous‐type carcinosarcoma that primarily consisted of a clear‐cell carcinoma component and a scarce chondrosarcoma component. Both of the MET amplification cases were mixed; one contained endometrioid features, and the other chondrosarcoma features. This is the first report to analyze the statuses of the MET gene in ECCs, and the two mixed cases exhibited amplifications that are shared with ovarian clear‐cell carcinomas. Further studies with larger numbers of cases are necessary to reveal the relationship between ECC and MET amplification. [ABSTRACT FROM AUTHOR]

In organic potato production in Europe, only copper-based fungicides allow to directly control Phytophthora infestans (the causal agent of late blight). Due to environmental concerns caused by the repeated and excessive use of Cu before the nineties, the EU legislation has promoted alternatives approaches such as the use of biocontrol agents (e.g. arbuscular mycorrhizal fungi – AMF). Here, two field trials were conducted over two climatic-contrasting growing seasons. Trial 1 was characterized by a dry and hot cultural season with low pressure of P. infestans , while trial 2 was conducted under high humidity and relatively low temperatures with high pressure of the pathogen. In both trials, sprouted potato tubers were inoculated with AMF in the greenhouse before transplanting to the field. A Real-Time quantitative PCR assay was designed to target the inoculant strain Rhizophagus irregularis MUCL 41833 as well as the native Rhizophagus irregularis strains. In both trials, the inoculated AMF was detected in the roots at harvest, demonstrating the capacity of the inoculated strain to incorporate the microbiome of the potato plants. In the first trial, disease severity in AMF pre-colonized potato plants was markedly decreased and the onset of late blight symptoms was delayed by 10 days. In contrast, in the second trial no differences were noticed between AMF pre-colonized and control plants. In both trials, no mycorrhizal effect was noticed on tuber yield. As a conclusion, disease severity of P. infestans , measured by symptoms development on leaves, was decreased in AMF pre-colonized plants under conditions of low pressure of late blight and over a short period of time, while under conditions more adequate to the pathogen, no reduction in symptoms was noticed. [ABSTRACT FROM AUTHOR]

Fatty acid binding proteins (FABPs) belonging to the lipocalin protein family, have an affinity for fatty acids (FAs) and participate in both the transport of FAs and lipid metabolism. In this study, a 909-bp full-length pt-FABP cDNA containing a 411-bp open reading frame (ORF) was obtained from the swimming crab Portunus trituberculatus. Quantitative real-time PCR revealed that during larval development, pt-FABP expression increased gradually from the zoea to the megalopa, and decreased in the juvenile crab. pt-FABP mRNA was detected at the highest level in the testis, followed by the muscles, with the lowest level in the hepatopancreas. The composition of fatty acids in three different tissues from crabs of different sex was detected by gas chromatography-mass spectrometry (GC-MS). The results indicated that the FA profile was in accordance with the expression of pt-FABP, which suggested that pt-FABP participates in the unsaturated fatty acid transportation and storage system of P. trituberculatus. [ABSTRACT FROM AUTHOR]

BACKGROUND: MicroRNA-195 acts as a tumor suppressor in a variety of cancers. However, its clinical significance in pediatric acute myeloid leukemia (AML) remains largely undefined. OBJECTIVE: To investigate the diagnostic and prognostic relevance of miR-195 in this malignancy. METHODS: Expression levels of miR-195 in peripheral blood and bone marrow samples of patients with pediatric AML and normal controls were detected by real-time quantitative PCR. Then, receiver-operating characteristic (ROC) curve analysis, Kaplan-Meier method, and Cox regression analysis were performed to evaluate the diagnostic and prognostic relevance of serum miR-195 in pediatric AML. RESULTS: Compared to normal controls, the expression levels of miR-195 in both bone marrow and patients' sera were significantly decreased (both P < 0.001). In addition, serum miR-195 had an optimal diagnostic cut-off point (2.09) for pediatric AML with sensitivity of 68.87% and specificity of 96.23%. The area under the ROC curve (AUC) based on serum miR-195 was 0.910. Moreover, patients with low serum miR-195 level more often had French-American-British classification subtype M7 (P = 0.02), unfavorable karyotypes (P = 0.01), and shorter relapse-free and overall survivals (both P = 0.001) than those with high serum miR-195 level. Furthermore, the multivariate analysis identified serum miR-195 level as an independent prognostic factor for both relapse-free and overall survivals. CONCLUSION: The findings of this study suggest that the aberrant expression of miR-195 may play crucial roles in the development and progression of pediatric AML patients. Serum miR-195 may serve as a promising marker for monitoring the occurrence of this disease and predicting the clinical outcome of patients. [ABSTRACT FROM AUTHOR]

The genus Chaetoceros is among the most species-rich marine planktonic diatoms. Most Chaetoceros are considered important primary producers in various marine environments, but because of their small size, we know little about their ecology and distribution. Therefore, from 2008 to 2012, we examined the occurrence of C. tenuissimus Meunier, one of the smallest members in the genus, and its infectious viruses in western Japanese coastal waters. Using real-time quantitative PCR, we found that C. tenuissimus was widely detected throughout our study sites, with a maximum concentration of 2.4 × 10 cells/l in May 2012. Sediment analysis revealed that C. tenuissimus resting-stage cells were present at potentially high levels, despite its infectious viruses being detected in the same region. The present study suggests that C. tenuissimus remains highly productive even when surrounded by its infectious viruses. This tolerance to viral infection, along with the diatom's fast growth rate, suggests that C. tenuissimus might play an important role in maintaining the growth of important filter feeders. [ABSTRACT FROM AUTHOR]

Abstract: Aim: The aims of this study were to compare leukocyte relative telomere length (RTL) in knee osteoarthritis (OA) patients and healthy controls and to investigate associations between plasma angiogenic cytokine concentrations and leukocyte RTL. Method: Eighty knee OA patients and 60 age‐matched controls were enrolled. Leukocyte RTL was assessed using real‐time quantitative polymerase chain reaction (qPCR). Angiogenic cytokines were measured by a multiplex immunoassay. Results: Leukocyte RTL in knee OA patients was significantly lower than that in healthy controls (1.1 ± 0.4 vs. 1.3 ± 0.6, P = 0.039). Plasma angiopoietin‐2, follistatin, granulocyte‐colony stimulating factor (G‐CSF), hepatocyte growth factor (HGF), interleukin‐8 (IL‐8), platelet endothelial cell adhesion molecule‐1 (PECAM‐1), and vascular endothelial growth factor (VEGF) levels in knee OA patients were higher than those in controls (P < 0.01). Correlation analysis revealed significant negative correlations between leukocyte RTL and plasma levels of HGF (r = −0.377, P = 0.017), VEGF (r = −0.405, P = 0.009) and G‐CSF (r = −0.347, P = 0.026). In contrast, plasma angiopoietin‐2, follistatin, IL‐8, leptin, platelet‐derived growth factor‐BB and PECAM‐1 were not correlated with leukocyte RTL. Conclusion: Telomere length was shortened in knee OA patients compared to healthy controls. Plasma HGF, VEGF and G‐CSF were negatively correlated with leukocyte RTL, suggesting involvement of telomere shortening and these cytokines in knee OA. [ABSTRACT FROM AUTHOR]

Pyropia haitanensis has prominent stress-resistance characteristics and is endemic to China. Studies into the stress responses in these algae could provide valuable information on the stress-response mechanisms in the intertidal Rhodophyta. Here, the effects of salinity and light intensity on the quantum yield of photosystem II in Py. haitanensis were investigated using pulse-amplitude-modulation fluorometry. Total RNA and genomic DNA of the samples under different stress conditions were isolated. By normalizing to the genomic DNA quantity, the RNA content in each sample was evaluated. The cDNA was synthesized and the expression levels of seven potential internal control genes were evaluated using qRT-PCR method. Then, we used geNorm, a common statistical algorithm, to analyze the qRT-PCR data of seven reference genes. Potential genes that may constantly be expressed under different conditions were selected, and these genes showed stable expression levels in samples under a salinity treatment, while tubulin, glyceraldehyde-3-phosphate dehydrogenase and actin showed stability in samples stressed by strong light. Based on the results of the pulse amplitude-modulation fluorometry, an absolute quantification was performed to obtain gene copy numbers in certain stress-treated samples. The stably expressed genes as determined by the absolute quantification in certain samples conformed to the results of the geNorm screening. Based on the results of the software analysis and absolute quantification, we proposed that elongation factor 3 and 18S ribosomal RNA could be used as internal control genes when the Py. haitanensis blades were subjected to salinity stress, and that α-tubulin and 18S ribosomal RNA could be used as the internal control genes when the stress was from strong light. In general, our findings provide a convenient reference for the selection of internal control genes when designing experiments related to stress responses in Py. haitanensis. [ABSTRACT FROM AUTHOR]

Objective Histamine is an important chemical mediator in the development of allergic rhinitis and plays a key role in eliciting the nasal symptoms of the disorder. Histamine may also affect smell as a neurotransmitter. However, whether histamine receptors are present in the mammalian olfactory epithelium has not yet been examined. The aim of this study was to investigate the expression and distribution of histamine H 1 , H 2 , and H 3 receptors in rat olfactory epithelium. Methods Real-time quantitative PCR and immunohistochemical staining were performed to examine the mRNA level and protein expression and localization of histamine receptors (H 1 , H 2 , and H 3 ) in rat olfactory epithelium. Results We demonstrated that mRNAs encoding histamine H 1 , H 2 , and H 3 receptors were detected in rat olfactory epithelium. Immunohistochemistry also showed strong positive staining for these receptors. Co-localization of histamine H 1 , H 2 , and H 3 receptors with olfactory mature protein revealed that these three histamine receptors were mainly localized in olfactory receptor neurons. Conclusions These findings indicate that histamine H 1 , H 2 , and H 3 receptors are present in rat olfactory epithelium and may play a physiological role in olfactory transmission. [ABSTRACT FROM AUTHOR]

The “sex-hormone” estrogen-17β promotes several cognitive functions and is a master regulator of brain bioenergetics via the estrogen receptors α and β ( ERα and ERβ ). In this work, by using Real-Time PCR analysis, we evaluated the effect of aging and high fat diet (HFD) on ERα and ERβ expression in rat hippocampus and cortex. In young rats, ERβ is abundant in cortex and ERα in hippocampus. During the aging, in the cortex, we observe a general decrease in ERα and ERβ expression; in hippocampus ERα increases and ERβ decreases. ER expression patterns in rat brain are also affected by the administration of an HFD. In cortex, after 4 weeks of HFD, ERβ transcripts are down-regulated, whereas ERα levels remain unchanged; after 12 weeks, both ERα and ERβ expression is up-regulated. In the hippocampus, the level of ERβ transcripts does not change following HDF, whereas ERα expression is affected by HDF, in a time-dependent manner: it increases after the 4-week treatment and decreases after 12 weeks. Possible involvements of these receptors in the control of cortex and hippocampus functions during aging and in the modulation of energetic metabolism and feeding behaviour are discussed. [ABSTRACT FROM AUTHOR]

Background: The study was aimed to quantitatively detect mRNA levels of the catalytic subunit of telomerase (hTERT) in both peripheral blood and circulating tumor cells (CTCs) of patients with nasopharyngeal carcinoma (NPC) and explore its significance in early diagnosis and treatment of NPC.Methods: hTERT mRNA levels in peripheral blood and CTCs of 33 NPC patients before and after treatment with intensity-modulated radiation therapy (IMRT) or/and chemotherapy and 24 healthy controls were measured using real-time quantitative PCR (qPCR) and their correlations to clinic pathological factors of NPC were analyzed.Results: Peripheral hTERT mRNA content was 10.75 ± 4.29 in NPC patients and 0.95 ± 0.37 in control subjects (P < 0.05), and had a significant correlation with patients' clinical stage, T stage, and N stage (P < 0.05). Treatment of NPC patients at stages I and II with simple IMRT significantly reduced hTERT mRNA level from 5.60 ± 2.33 to 3.43 ± 1.42 (P < 0.05) and treatment of patients at advanced stage (III and IV) with induction chemotherapy followed by IMRT significantly reduced hTERT mRNA levels from 12.68 ± 3.08 to 10.68 ± 2.48 to 3.13 ± 1.69 (P < 0.05), respectively. In addition, the study also showed that hTERT mRNA content in CTCs of NPC patients was 10.65 ± 4.28, evidently higher than that of 1.09 ± 0.40 in control subjects (P < 0.05) and hTERT mRNA level in CTCs of NPC patients was obviously correlated to patients' clinical stage, T stage and N stage (P < 0.05). After treatment, hTERT mRNA level in CTCs of NPC patients lowered from 10.65 ± 4.28 to 5.59 ± 2.32 (P < 0.05). The correlation analysis found that hTERT mRNA level in peripheral blood and CTCs of NPC patients were highly correlated with a correlation coefficient of 0.981.Conclusions: hTERT mRNA levels in peripheral blood and CTCs of NPC patients were significantly enhanced compared to that in healthy controls and highly correlated. Changes in hTERT mRNA level was closely correlated to patients' clinical stage and T stage. Radiochemotherapy could effectively reduce hTERT mRNA level in peripheral blood and CTCs. Thus, it is possible using the joint detection of hTERT mRNA level in peripheral blood and CTCs as a new biomarker for early diagnosis, treatment efficacy and prognosis of NPC. [ABSTRACT FROM AUTHOR]

miRNA expression over different time periods (24 and 48 h) using the quantitative RT-PCR and deep sequencing has been evaluated in a model of photochemically induced thrombosis. A combination of two approaches allowed us to determine the miRNA expression patterns caused by ischemia. Nine miRNAs, including let-7f-5p, miR-221-3p, miR-21-5p, miR-30c-5p, miR-30a-3p, miR-223-3p, miR-23a-3p, miR-22-5p, and miR-99a-5p, were differentially expressed in brain tissue and leukocytes of rats 48 h after onset of ischemia. In addition, six miRNAs were differentially expressed in the brain tissue and blood plasma of rats 24 h after exposure, among which miR-145-3p and miR-375-3p were downregulated and miR-19a-3p, miR-92a-3p, miR-188-5p, and miR-532-5p were upregulated. In our opinion, miR-188-5p and miR-532-5p may be considered to be new potential markers of ischemic injury. The level of miRNA expression tended to increase 48 h after the onset of ischemia in brain tissue and leukocytes, which reflects not only the local response in brain tissue due to inflammation, vascular endothelial dysfunction, and disorders of the permeability of the blood-brain barrier, but also the systemic response of the organism to multifactor molecular processes induced by ischemic injury. [ABSTRACT FROM AUTHOR]

Background: miRNAs act in diverse biological processes including development, cell growth, apoptosis, and hematopoiesis, suggesting their role in cancer. Methods: We examined the miRNAs perturbed in CD138+ primary multiple myeloma (MM) cells, using microarray analysis and real-time quantitative PCR (RT-qPCR). Serum miR-4449 expression levels were detected from 71 primary MM patients and 46 healthy controls by RT-qPCR. Results: Our analysis revealed up-regulation of 54 and down-regulation of 28 miRNAs in MM subjects compared to healthy controls. miR-4449 has not been reported in MM. It was found that the relative expression of bone marrow miR-4449 in MM patients (2.14±1.42) was higher than that in healthy controls (0.815±0.165) (U = 8, p = 0.0093). The relative expression of serum miR-4449 in MM patients (2.11±2.10) was significantly higher than that in healthy controls (0.357±0.235) (U = 374, p < 0.0001) and was significantly correlated with β2M, λ light and к light chain concentration (r = 0.480, p = 0.0003; r = 0.560, p < 0.0001; r = 0.560, p < 0.0001), but not correlated with the lactate dehydrogenase (LDH) concentration (r = 0.247, p = 0.0611). The area under the curve (AUC) of the receiver-operating characteristics (ROC) curve of serum miR-4449 was 0.885 (95% CI, 0.826-0.945), which is higher than for other markers. Combining miR- 4449, λ light chain, and β2M together, the sensitivity was highest compared with λ light chain or β2M alone, or combined.Conclusions: The expression levels of serum miR-4449 in MM patients were significantly higher than in healthy controls, suggesting that it may prove to be useful in the auxiliary diagnosis of MM. [ABSTRACT FROM AUTHOR]

Background: Pepino mosaic virus (PepMV) is an emerging plant pathogen that infects tomatoes worldwide. Understanding the factors that influence its evolutionary success is essential for developing new control strategies that may be more robust against the evolution of new viral strains. One of these evolutionary factors is the distribution of mutational fitness effect (DMFE), that is, the fraction of mutations that are lethal, deleterious, neutral, and beneficial on a given viral strain and host species. The goal of this study was to characterize the DMFE of introduced nonsynonymous mutations on a mild isolate of PepMV from the Chilean 2 strain (PepMV-P22). Additionally, we also explored whether the fitness effect of a given mutation depends on the gene where it appears or on epistatic interactions with the genetic background. To address this latter possibility, a subset of mutations were also introduced in a mild isolate of the European strain (PepMV-P11) and the fitness of the resulting clones measured. Results: A collection of 25 PepMV clones each containing a single nucleotide nonsynonymous substitution was created by site-directed mutagenesis and the fitness of each mutant was determined. PepMV-P22 genome showed a high degree of robustness against point mutations, with 80% of mutations being either neutral or even beneficial and only 20% being deleterious or lethal. We found that the effect of mutations strongly depended on the gene in which they were introduced. Mutations with the largest average beneficial effects were those affecting the RdRp gene, in contrast to mutations affecting TGB1 and CP genes, for which the average effects were deleterious. Moreover, significant epistatic interactions were observed between nonsynonymous mutations and the genetic background, meaning that the effect of a given nucleotide substitution on a particular genomic context cannot be predicted by knowing its effect in a different one. Conclusions: Our results indicated that PepMV genome has a surprisingly high robustness against mutations. We also found that fitness consequences of a given mutation differ between the two strains analyzed. This discovery suggests that the strength of selection, and thus the rates of evolution, vary among PepMV strains. [ABSTRACT FROM AUTHOR]

According to the EU and Swiss food legislation, only authorised traits of transgene plants are allowed to be imported and sold to the consumer. In order to control imports of maize products from retailers, efficient and reliable methods for the detection and quantification are a prerequisite. Actually, in the EU, more than 25 gm Maize traits were authorised and are allowed to be sold. To ensure correct labelling and exclude unauthorised gm traits from sale, five multiplex real-time polymerase chain reaction systems were developed and validated. These 20 systems for the most prevalent maize gm traits allow relative multiplex quantification and/or delta-delta Ct method quantification in routine in a reliable, cost- and time-efficient way. [ABSTRACT FROM AUTHOR]

Since 2010, the Loue River (Franche-Comté, East of France) has been suffering from massive fish kills infested bySaprolegnia parasitica. The river supplies inhabitants of the city of Besançon in drinking water, raising the question of a potential risk through both water consumption and use. We developed a real-time quantitative PCR (qPCR) to quantifyS. parasiticain the Loue River as well as in the drinking water. A weak spatial trend is suggested with greater quantities ofS. parasiticaobserved at the sampling station close to the main pumping station. NoS. parasiticaDNA was detected in the tap water connected to pumping stations. The use of qPCR, which combines specificity, practicality, speed and reliability, appears to be an effective tool to monitor the spatial and temporal dynamics of this oomycete and identify the risk period for wild salmonid populations in the field, for fishery management or in aquaculture. [ABSTRACT FROM PUBLISHER]

In this study, a PMAxx-qPCR method for the detection and quantification of viable Bacillus cereus (B. cereus) was established based on the cesA gene that is involved in cereulide synthesis, enterotoxin gene bceT and hemolytic enterotoxin gene hblD combined with modified propidium monoazide (PMAxx). The sensitivity detection limit of the method was as follows: the DNA extracted by the kit reached 140 fg/μL, and the bacterial suspension without enrichment reached 2.24 × 101 CFU/mL; 14 non B. cereus strains of the 17 tested strains all tested as negative, whereas the 2 strains of B. cereus carrying the target virulence gene(s) could be accurately detected. In terms of application, we assembled the constructed PMAxx-qPCR reaction into a detection kit and evaluated its application performance. The results showed that the detection kit has high sensitivity, strong anti-interference capability, and has good application potential. The purpose of this study is to provide a reliable detection method for the prevention and traceability of B. cereus infections. • The PMAxx-qPCR for detection of pathogenic Bacillus cereus was established. • The viable Bacillus cereus and three toxin genes can be detected with the system. • The systems exhibit a high specificity and sensitivity of 2.24 × 101 CFU/mL. • The PMAxx-qPCR kit was developed with a good stability. [ABSTRACT FROM AUTHOR]

The availability of some sorts of biological samples which require noninvasive collection methods has led to an even greater interest in applying molecular biology on visceral leishmaniasis (VL) diagnosis, since these samples increase the safety and comfort of both patients and health professionals. In this context, this work aimed to evaluate the suitability of the urine as a specimen for Leishmania infantum kinetoplast DNA detection by real-time quantitative PCR (qPCR). Subsequent to the reproducibility analysis, the detection limit of the qPCR assay was set at 5 fg (~ 0.025 parasites) per μL of urine. From the comparative analysis performed with a set of diagnostic criteria (serological and molecular reference tests), concordance value of 96.08% was obtained (VL-suspected and HIV/AIDS patients, n = 51) ( P > 0.05). Kappa coefficient (95% CI) indicated a good agreement between the test and the set of diagnostic criteria ( k = 0.778 ± 0.151). The detection of Leishmania DNA in urine by qPCR was possible in untreated individuals, and in those with or without suggestive renal impairment. Fast depletion of the parasite's DNA in urine after treatment (from one dose of meglumine antimoniate) was suggested by negative qPCR results, thus indicating it as a potential alternative specimen to follow up the efficacy of therapeutic approaches. Even when evaluated in a clinically heterogeneous set of patients, the urine showed good prospect as sample for VL diagnosis by qPCR, also indicating a good negative predictive value for untreated suspected patients. [ABSTRACT FROM AUTHOR]

The H-pyrophosphatase (H -PPase) gene plays an important role in maintaining intracellular proton gradients. Here, we characterized the full-length complementary DNA (cDNA) and DNA of the H -PPase gene ScHP1 in rye ( Secale cereale L. 'Qinling'). We determined the subcellular localization of this gene and predicted the corresponding protein structure. We analysed the evolutionary relationship between ScHP1 and H −PPase genes in other species, and did real-time quantitative polymerase chain reaction to explore the expression patterns of ScHP1 in rye plants subjected to N, P and K deprivation and to cold, high-salt and drought stresses. ScHP1 cDNA included a 2289 bp open reading frame (ORF) encoding 762 amino acid residues with 14 transmembrane domains. The genomic ScHP1 DNA was 4354 bp and contained eight exons and seven introns. ScHP1 was highly homologous with other members of the H -PPase gene family. When the full-length ORF was inserted into the expression vector pA7-YFP, the fluorescent microscopy revealed that ScHP1-YFP fusion protein was located in the plasma membrane. Rye plants that were subjected to N deprivation, cold and high-salt stresses, ScHP1 expression was higher in the leaves than roots. Conversely, plants subjected to P and K deprivation and drought stress, ScHP1 expression was higher in the roots than leaves. Under all the investigated stress conditions, expression of ScHP1 was lower in the stem than in the leaves and roots. Our results imply that ScHP1 functions under abiotic stress response. [ABSTRACT FROM AUTHOR]

Inflammation of the urethra defined by an excess of polymorphonuclear leukocytes in the absence of sexually transmitted Chlamydia trachomatis and Neisseria gonorrhoeae is called non-chlamydial non-gonococcal urethritis (NCNGU). Although Mycoplasma genitalium is now recognised as causing a sexually transmitted infection, the clinical significance of the other Mollicute species is less clear. This study used specific real-time quantitative polymerase chain reaction assays to detect and quantify four Mollicute species, M. genitalium, M. hominis, Ureaplasma urealyticum and U. parvum, in urine specimens from men with and without NCNGU. A total of 165 urine specimens from male patients attending a genitourinary medicine clinic were eligible for the study, with microscopy-confirmed (≥5 polymorphonuclear leukocytes in urethral swab) NCNGU in 75 (45.5%) and non-confirmed NCNGU in 90 (54.5%). Chi-squared statistical analysis indicated a significantly higher prevalence of U. parvum (17.3% vs. 5.6%; p = 0.03) and M. genitalium (12% vs. 0%; p < 0.001) in NCNGU. In a subset analysis, M. genitalium was also significantly (p = 0.03) higher in men who have sex with men (MSM; 13.5%) compared to non-MSM (3.1%). No significant associations were reported for U. urealyticum and M. hominis In conclusion, this study supports a clinically significant role in NGNCU for both U. parvum and M. genitalium. [ABSTRACT FROM AUTHOR]

Droplet digital PCR (ddPCR) after DNA digestion yielded a 28S rDNA copy number of 61 to 86 copies/genome when testing 10 unrelated Aspergillus fumigatus isolates, higher than with quantitative PCR. Unfortunately, ddPCR after DNA digestion did not improve the sensitivity of our PCR assay when testing serum patients with invasive aspergillosis. [ABSTRACT FROM AUTHOR]

Anaerobic fungi (AF) decompose plant material with their rhizoid and multiple cellulolytic enzymes. They disintegrate the complex structure of lignocellulosic substrates, making them more accessible and suitable for further microbial degradation. There is also much interest in their use as biocatalysts for biotechnological applications. Here, three novel polymerase chain reaction (PCR)-based methods for detecting AF and their transcriptional activity in in vitro cultures and environmental samples were developed. Two real-time quantitative PCR (qPCR)-based methods targeting AF were developed: AF-SSU, was designed to quantify the 18S rRNA genes of AF. AF-Endo, measuring transcripts of an endoglucanase gene from the glycoside hydrolase family 5 (GH5), was developed to quantify their transcriptional cellulolytic activity. The third PCR based approach was designed for phylogenetical analysis. It targets the 28S rRNA gene (LSU) of AF revealing their phylogenetic affiliation. The in silico- designed primer/probe combinations were successfully tested for the specific amplification of AF from animal and biogas plant derived samples. In combination, these three methods represent useful tools for the analysis of AF transcriptional cellulolytic activity, their abundance and their phylogenetic placement. [ABSTRACT FROM AUTHOR]

Many products claim to contain wasabi. Due to its high price, original wasabi ( Eutrema wasabi) is often replaced by its cheaper close relative horseradish ( Armoracia rusticana). To analyze such products, we developed a duplex real-time PCR method determining the DNA content of wasabi and horseradish, applying the ΔΔct-method. The developed horseradish-specific system turned out to be highly specific within the plant family Brassicaceae. We validated this duplex real-time PCR system and present results from common commercial products. The system proved to be reliable for uncovering fraudulent practices in the wasabi product group. [ABSTRACT FROM AUTHOR]

Magnaporthe oryzae is a rice blast fungus and plant pathogen that causes a serious rice disease and, therefore, poses a threat to the world's second most important food security crop. Plant transformation technology has become an adaptable system for cultivar improvement and to functionally analyze genes in plants. The objective of this study was to determine the effects (through over-expressing and using the CaMV 35S promoter) of Pikh on MR219 resistance because it is a rice variety that is susceptible to the blast fungus pathotype P7.2. Thus, a full DNA and coding DNA sequence (CDS) of the Pikh gene, 3172 bp, and 1206 bp in length, were obtained through amplifying the gDNA and cDNA template from a PH9-resistant rice variety using a specific primer. Agrobacterium-mediated transformation technology was also used to introduce the Pikh gene into the MR219 callus. Subsequently, transgenic plants were evaluated from the DNA to protein stages using polymerase chain reaction (PCR), semi-quantitative RT-PCR, real-time quantitative PCR and high performance liquid chromatography (HPLC). Transgenic plants were also compared with a control using a real-time quantification technique (to quantify the pathogen population), and transgenic and control plants were challenged with the local most virulent M. oryzae pathotype, P7.2. Based on the results, the Pikh gene encodes a hydrophilic protein with 18 sheets, 4 helixes, and 21 coils. This protein contains 401 amino acids, among which the amino acid sequence from 1 to 376 is a non-cytoplasmic region, that from 377 to 397 is a transmembrane region, and that from 398 to 401 is a cytoplasmic region with no identified disordered regions. The Pikh gene was up-regulated in the transgenic plants compared with the control plants. The quantity of the amino acid leucine in the transgenic rice plants increased significantly from 17.131 in the wild-type to 47.865mg g-1 in transgenic plants. The M. oryzae population was constant at 31, 48, and 72 h after inoculation in transgenic plants, while it was increased in the inoculated control plants. This study successfully clarified that over-expression of the Pikh gene in transgenic plants can improve their blast resistance against the M. oryzae pathotype P7.2. [ABSTRACT FROM AUTHOR]

In this study, the seasonal difference and the observable presence/absence of human adenovirus (HAdV) in the Puzih River basin in Taiwan was investigated. A total of 288 water samples were collected from 24 sites from March 2014 to February 2015. Human AdV analysis of sample was subjected to viral concentration using a GN-6 Metricel® filter, followed by DNA extraction, nested-PCR, and qPCR. Human AdV was detected in 34.3 % (99/288) of the entire river water sample. A higher percentage of HAdV (76.4 %) was obtained during the winter. The HAdV median concentration was relatively high in fall (1.4 × 10 copies/L) and winter (2.8 × 10 copies/L). Significant difference and correlation were found between the seasonal variation of HAdV and water quality parameters, including heterotrophic plate count, total coliform, water temperature, and turbidity. The most frequently identified HAdV (subgenus F) serotype was 41. Human AdV-41 is the main cause of gastroenteritis and should be considered for associated human health risk potential in the Puzih River basin. [ABSTRACT FROM AUTHOR]

Background/aim: Midkine (MK), a heparin-binding growth factor, has an important role in cancer progression. The aim of this study was to determine MK expression in breast tissue and the preoperative and postoperative serum levels of patients with breast cancer. Background/aim: Midkine (MK), a heparin-binding growth factor, has an important role in cancer progression. The aim of this study was to determine MK expression in breast tissue and the preoperative and postoperative serum levels of patients with breast cancer. Results: MK expression was observed in 44 (72.1%) of 61 breast cancer patients. In breast cancer patients the serum MK levels (3.68 ± 2.13 ng/mL (mean ± SD)) were significantly higher than in the control group (1.77 ± 0.38 ng/mL) before tumor removal (P = 0.000). After tumor removal, serum MK levels (2.47 ± 1.00 ng/mL) were significantly (P = 0.000) decreased according to preoperative levels. Increased serum levels of MK were related with tumor stages when clinical parameters were analyzed. Results: MK expression was observed in 44 (72.1%) of 61 breast cancer patients. In breast cancer patients the serum MK levels (3.68 ± 2.13 ng/mL (mean ± SD)) were significantly higher than in the control group (1.77 ± 0.38 ng/mL) before tumor removal (P = 0.000). After tumor removal, serum MK levels (2.47 ± 1.00 ng/mL) were significantly (P = 0.000) decreased according to preoperative levels. Increased serum levels of MK were related with tumor stages when clinical parameters were analyzed. [ABSTRACT FROM AUTHOR]

Two-component systems (TCSs) have been shown to participate in plant responses to drought. In this study, results of real-time quantitative PCR (RT-qPCR) of 26 selected dehydration-responsive TCS-related genes in roots and shoots of two Vietnamese soybean cultivars (DT51 and MTD720) with contrasting drought-tolerant phenotypes suggest a positive correlation between the number of drought-inducible TCS genes and their drought-tolerant ability. In addition, expression analyses of the roots and shoots indicated that DT51 and MTD720 had distinct drought-responsive TCS expression profiles, suggesting that expression of TCS-related genes are genotype and tissue dependent. Furthermore, nine TCS genes ( GmHK07, 16, GmHP08, GmRR04, 16, 32, 34, GmPRR39, and 44) potentially associated with enhanced drought tolerance were identified. Particularly, GmRR34, showing its higher expression levels under both normal and drought conditions in DT51 roots versus MTD720 roots, might be a potential positive regulator of drought tolerance. On the other hand, GmPRR44 was highly recommended as a potential negative regulator of drought tolerance because it exhibited lower expression levels in both tissues of the drought-tolerant DT51 than in those of the drought-sensitive MTD720 under both stressed and unstressed conditions. These two genes deserve in-depth characterization as promising candidates for development of soybean cultivars with improved drought tolerance by using genetic engineering. [ABSTRACT FROM AUTHOR]

We evaluated whether propidium monoazide (PMA) combined with real-time quantitative PCR (qPCR) is suitable for detecting viable Mycobacterium fortuitum after chlorine, ozone, and ultraviolet (UV) disinfection. PMA-qPCR was effective in determining the viability of M . fortuitum compared with qPCR based on the membrane integrity. However, with a mild chlorine concentration, PMA-qPCR as an alternative method was not applicable due to a large gap between loss of culturability and membrane integrity damage. In ozonation, PMA-qPCR was able to differentiate between viable and injured mycobacteria, and the results were similar to those obtained by the culture method. Interestingly, PMA-qPCR was successful in monitoring the viability after UV disinfection due to the long UV exposure needed to effectively inactivate M . fortuitum . The findings of the present study suggested that the characteristics of disinfectants and the M . fortuitum resistance to disinfectants play critical roles in determining the suitability of PMA-qPCR for evaluating the efficacy of disinfection methods. [ABSTRACT FROM AUTHOR]

Objectives To study the role of microRNA-873 (miR-873) in suppressing morphine-induced macrophage apoptosis and morphine dependence, and to identify molecular targets within the miR-873 pathway for the treatment of immune suppression and morphine addiction. Methods As morphine elevates TLR9 expression and induces TLR9-mediated apoptosis, we used TLR9 knockout Balb/C mice to study TLR9-independent effects of miR-873 on morphine-induced macrophage apoptosis. Forty TLR9-knockout mice were randomly and equally assigned to morphine group and control group. Following the administration of morphine, miR-873 mimics or miR negative control was injected into mice in each group. Using freshly isolated macrophages from mice and RAW264.7 murine macrophage cell line, miR-873 level was determined by qRT-PCR and morphine induced apoptosis was measured by TUNEL assays. Western blotting was used to detect and quantify the expression level of A20, a protein that negatively regulates inflammation and TNF-induced apoptosis. Results qRT-PCR analysis revealed a markedly lower expression of miR-873 in freshly isolated peritoneal macrophages, liver tissue and spleen tissue in the morphine group compared with the corresponding tissues in the control group. TUNEL assays showed that the apoptosis rates in the morphine groups treated with miR-873 mimics was markedly lower than their respective control groups. Western blotting results showed that A20 expression level was sharply elevated in the experimental groups treated with miR-873 mimics than the negative and blank control groups. Conclusions Our results show that miR-873 elevates A20 levels and inhibits morphine-induced macrophage apoptosis. [ABSTRACT FROM AUTHOR]

Plasmids pGE1 (2.5 kb), pGE2 (7.2 kb), and pGE3 (5.5 kb) were isolated from Gluconacetobacter europaeus KGMA0119, and sequence analyses revealed they harbored 3, 8, and 4 genes, respectively. Plasmid copy numbers (PCNs) were determined by real-time quantitative PCR at different stages of bacterial growth. When KGMA0119 was cultured in medium containing 0.4% ethanol and 0.5% acetic acid, PCN of pGE1 increased from 7 copies/genome in the logarithmic phase to a maximum of 12 copies/genome at the beginning of the stationary phase, before decreasing to 4 copies/genome in the late stationary phase. PCNs for pGE2 and pGE3 were maintained at 1–3 copies/genome during all phases of growth. Under a higher concentration of ethanol (3.2%) the PCN for pGE1 was slightly lower in all the growth stages, and those of pGE2 and pGE3 were unchanged. In the presence of 1.0% acetic acid, PCNs were higher for pGE1 (10 copies/genome) and pGE3 (6 copies/genome) during the logarithmic phase. Numbers for pGE2 did not change, indicating that pGE1 and pGE3 increase their PCNs in response to acetic acid. Plasmids pBE2 and pBE3 were constructed by ligating linearized pGE2 and pGE3 into pBR322. Both plasmids were replicable in Escherichia coli , Acetobacter pasteurianus and G. europaeus , highlighting their suitability as vectors for acetic acid bacteria. [ABSTRACT FROM AUTHOR]