scholarly journals Accurate, Fast and Cost-Effective Diagnostic Test for Monosomy 1p36 Using Real-Time Quantitative PCR

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Pricila da Silva Cunha ◽  
Heloisa B. Pena ◽  
Carla Sustek D’Angelo ◽  
Celia P. Koiffmann ◽  
Jill A. Rosenfeld ◽  
...  
Keyword(s):  
Real Time ◽  
Diagnostic Test ◽  
Quantitative Pcr ◽  
Target Genes ◽  
Cost Effective ◽  
Qpcr Assay ◽  
Deletion Syndrome ◽  
Comparative Genomic ◽  
Real Time Quantitative Pcr ◽  
Subtelomeric Deletion

Monosomy 1p36 is considered the most common subtelomeric deletion syndrome in humans and it accounts for 0.5–0.7% of all the cases of idiopathic intellectual disability. The molecular diagnosis is often made by microarray-based comparative genomic hybridization (aCGH), which has the drawback of being a high-cost technique. However, patients with classic monosomy 1p36 share some typical clinical characteristics that, together with its common prevalence, justify the development of a less expensive, targeted diagnostic method. In this study, we developed a simple, rapid, and inexpensive real-time quantitative PCR (qPCR) assay for targeted diagnosis of monosomy 1p36, easily accessible for low-budget laboratories in developing countries. For this, we have chosen two target genes which are deleted in the majority of patients with monosomy 1p36:PRKCZandSKI. In total, 39 patients previously diagnosed with monosomy 1p36 by aCGH, fluorescentin situhybridization (FISH), and/or multiplex ligation-dependent probe amplification (MLPA) all tested positive on our qPCR assay. By simultaneously using these two genes we have been able to detect 1p36 deletions with 100% sensitivity and 100% specificity. We conclude that qPCR ofPRKCZandSKIis a fast and accurate diagnostic test for monosomy 1p36, costing less than 10 US dollars in reagent costs.

scholarly journals Applying Real-Time Quantitative PCR to Fusarium Crown Rot of Wheat

Plant Disease ◽  
2007 ◽  
Vol 91 (8) ◽  
pp. 1021-1028 ◽  
Author(s):  
A. C. Hogg ◽  
R. H. Johnston ◽  
A. T. Dyer
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Field Experiments ◽  
Qpcr Assay ◽  
Crown Rot ◽  
Yield Reduction ◽  
Fusarium Crown Rot ◽  
Persistent Problem ◽  
Real Time Quantitative Pcr ◽  
Severity Scores

Fusarium crown rot (FCR) of wheat is a persistent problem that causes significant losses worldwide. In Montana, FCR is caused primarily by Fusarium culmorum and F. pseudograminearum. Recently, a real-time quantitative PCR (QPCR) assay was developed for FCR using primers and probes specific for a segment of the trichodiene synthase (tri5) gene. The purpose of this study was to determine the utility of QPCR for accessing FCR severity on wheat in field experiments. In 2004 and 2005, plots of spring and durum wheat were inoculated with varying levels of F. pseudograminearum oat inoculum and grown under rain-fed conditions. Two weeks prior to harvest, plants were collected from the plots and assessed for FCR severity and analyzed by QPCR for Fusarium DNA quantities. Disease severity scores (DSS) and Fusarium DNA quantities were positively correlated with each other for all three cultivars in 2004 but for only the durum cultivar in 2005 (P < 0.05). In 2004, grain yields for both spring wheat cultivars were negatively correlated with Fusarium DNA quantities (P > 0.05). When DSS and Fusarium DNA quantities negatively correlated with yield, both measurements were comparable in predicting yield reduction (R = –0.64 and –0.77, respectively). Results indicate that this QPCR assay is effective in measuring FCR severity in wheat.

scholarly journals Transferring a Quantitative Molecular Diagnostic Test to Multiple Real-Time Quantitative PCR Platforms

2018 ◽  
Vol 20 (4) ◽  
pp. 398-414 ◽  
Author(s):  
Claudia Gürtler ◽  
Mark Laible ◽  
Wolfgang Schwabe ◽  
Heike Steinhäuser ◽  
Xingmin Li ◽  
...  
Keyword(s):  
Real Time ◽  
Diagnostic Test ◽  
Quantitative Pcr ◽  
Molecular Diagnostic ◽  
Real Time Quantitative Pcr ◽  
Molecular Diagnostic Test

Rapid detection of subtelomeric deletion/duplication by novel real-time quantitative PCR using SYBR-green dye

2004 ◽  
Vol 23 (4) ◽  
pp. 368-378 ◽  
Author(s):  
Detlef Boehm ◽  
Sabine Herold ◽  
Alma Kuechler ◽  
Thomas Liehr ◽  
Franco Laccone
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Rapid Detection ◽  
Sybr Green ◽  
Real Time Quantitative Pcr ◽  
Subtelomeric Deletion

Profiling the lncRNA-miRNA-mRNA Interaction Network in the Submandibular Gland of Diabetic Mice

2021 ◽  
Author(s):  
Xijin Shi ◽  
Huimin Liu ◽  
Li Li ◽  
Yan Zhang ◽  
Xin Cong ◽  
...  
Keyword(s):  
Real Time ◽  
Submandibular Gland ◽  
Quantitative Pcr ◽  
Target Genes ◽  
Interaction Network ◽  
Differentially Expressed ◽  
Bioinformatics Analyses ◽  
Real Time Quantitative Pcr ◽  
Network Analyses ◽  
Cerna Network

Abstract Background: Hyposalivation is one of the common symptoms of diabetes. Although long non-coding RNAs (lncRNAs) have recently been reported to play important roles in the pathogenesis of diabetes, the role of lncRNAs in diabetes-induced hyposalivation remains unknown. Methods: The present study aimed to explore the function of lncRNA-microRNA-mRNA regulatory network in the submandibular gland (SMGs) under the context of diabetes. LncRNA expression profile of the SMGs was analyzed using microarray technology. Differentially expressed lncRNAs were confirmed using real-time quantitative PCR. Bioinformatics analyses were performed, and Coding-non-coding gene co-expression (CNC) and competing endogenous RNA (ceRNA) networks were constructed to explore the potential mechanisms of diabetes-induced hyposalivation. Results: A total of 1,273 differentially expressed lncRNAs (536 up-regulated and 737 downregulated) were identified in the SMGs tissues of db/db mice. CNC and ceRNA network analyses were performed based on five differentially expressed lncRNAs validated by real-time quantitative PCR. Gene Ontology analysis of target genes of CNC network revealed that “calcium ion binding” was a highly enriched molecular function. Kyoto Encyclopedia of Genes and Genomes pathway analysis of target genes of ceRNA network revealed that the “mammalian target of rapamycin signaling pathway” was significantly enriched. Conclusions: On the whole, the findings of the present study may provide insight into the possible mechanism of diabetes-induced hyposalivation.

scholarly journals Conservation of the Nrf2-Mediated Gene Regulation of Proteasome Subunits and Glucose Metabolism in Zebrafish

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Vu Thanh Nguyen ◽  
Yuji Fuse ◽  
Junya Tamaoki ◽  
Shin-ichi Akiyama ◽  
Masafumi Muratani ◽  
...  
Keyword(s):  
Glucose Metabolism ◽  
Real Time ◽  
Quantitative Pcr ◽  
Target Genes ◽  
Defense Mechanism ◽  
Dependent Manner ◽  
Diethyl Maleate ◽  
Real Time Quantitative Pcr ◽  
Evolutionarily Conserved ◽  
Proteasome Subunits

The Keap1-Nrf2 system is an evolutionarily conserved defense mechanism against oxidative and xenobiotic stress. Besides the exogenous stress response, Nrf2 has been found to regulate numerous cellular functions, including protein turnover and glucose metabolism; however, the evolutionary origins of these functions remain unknown. In the present study, we searched for novel target genes associated with the zebrafish Nrf2 to answer this question. A microarray analysis of zebrafish embryos that overexpressed Nrf2 revealed that 115 candidate genes were targets of Nrf2, including genes encoding proteasome subunits and enzymes involved in glucose metabolism. A real-time quantitative PCR suggested that the expression of 3 proteasome subunits (psma3, psma5, and psmb7) and 2 enzymes involved in glucose metabolism (pgd and fbp1a) were regulated by zebrafish Nrf2. We thus next examined the upregulation of these genes by an Nrf2 activator, diethyl maleate, using Nrf2 mutant zebrafish larvae. The results of real-time quantitative PCR and whole-mount in situ hybridization showed that all of these 5 genes were upregulated by diethyl maleate treatment in an Nrf2-dependent manner, especially in the liver. These findings implied that the Nrf2-mediated regulation of the proteasome subunits and glucose metabolism is evolutionarily conserved among vertebrates.

scholarly journals Development of Conventional and Real-Time Quantitative PCR Assays for Diagnosis and Monitoring of Scabies

2015 ◽  
Vol 53 (7) ◽  
pp. 2095-2102 ◽  
Author(s):  
Samson S. Y. Wong ◽  
Rosana W. S. Poon ◽  
Sandy Chau ◽  
Sally C. Y. Wong ◽  
Kelvin K. W. To ◽  
...  
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Copy Number ◽  
Mitochondrial Gene ◽  
Qpcr Assay ◽  
Dna Copy Number ◽  
Predictive Values ◽  
Content Type ◽  
Lesional Skin ◽  
Real Time Quantitative Pcr

Scabies remains the most prevalent, endemic, and neglected ectoparasitic infestation globally and can cause institutional outbreaks. The sensitivity of routine microscopy for demonstration ofSarcoptes scabieimites or eggs in skin scrapings is only about 50%. Except for three studies using conventional or two-tube nested PCR on a small number of cases, no systematic study has been performed to improve the laboratory diagnosis of this important infection. We developed a conventional and a real-time quantitative PCR (qPCR) assay based on the mitochondrial cytochromecoxidase subunit 1 (cox1) gene ofS. scabiei. Thecox1gene is relatively well conserved, with its sequence having no high levels of similarity to the sequences of other human skin mites, pathogenic zoonotic mites, or common house dust mite species. This mitochondrial gene is also present in large quantities in arthropod cells, potentially improving the sensitivity of a PCR-based assay. In our study, both assays were specific and were more sensitive than microscopy in diagnosing scabies, with positive and negative predictive values of 100%. TheS. scabieiDNA copy number in the microscopy-positive specimens was significantly higher than that in the microscopy-negative specimens (medianS. scabieiDNA copy number, 3.604 versus 2.457 log10copies per reaction;P= 0.0213). In the patient with crusted scabies, the qPCR assay performed on lesional skin swabs instead of scrapings revealed that the parasite DNA load took about 2 weeks to become negative after treatment. The utility of using lesional skin swabs as an alternative sample for diagnosis of scabies by PCR should be further evaluated.

Sign in / Sign up

Export Citation Format

Share Document