For accurate quantification of DNA and RNA from environmental samples, yield loss during nucleic acid purification has to be minimized. Quantitative PCR (qPCR) and reverse transcription (RT)-qPCR require a trade-off between maximizing yield and removing inhibitors. We compared DNA and RNA yield and suitability for quantitative SYBR Green PCR and RT-PCR using the UltraClean and PowerSoil extract...

Porcine diarrhea caused by viruses is a major problem of the pig farming industry and can result in substantial losses of revenue. Thus, diagnosing the infectious agents is important to prevent and control diseases in pigs. We developed novel one-step real-time quantitative RT-PCR (qPCR) assays that can detect four porcine diarrheal viruses simultaneously: porcine epidemic diarrhea virus (PEDV)...

Reverse transcription quantitative PCR (RT-qPCR) is already an established tool for mRNA detection and quantification. Since recently, this technique has been successfully employed for gene expression analyses, and also in individual cells (single cell RT-qPCR). Although the advantages of single cell measurements have been proven several times, a study correlating the expression measured on sin...

Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated i...

The effects of free chlorine disinfection of tap water and wastewater effluents on the infectivity, gene integrity and surface antigens of rotaviruses were evaluated by a bench-scale chlorine disinfection experiments. Plaque assays, integrated cell culture-quantitative RT-PCR (ICC-RT-qPCR), RT-qPCR, and enzyme-linked immunosorbent assays (ELISA), respectively, were used to assess the influence ...

Collection of mosquitoes and testing for vector-borne viruses is a key surveillance activity that directly influences the vector control efforts of public health agencies, including determining when and where to apply insecticides. Vector control districts in California routinely monitor for three human pathogenic viruses including West Nile virus (WNV), Western equine encephalitis virus (WEEV)...

Abstract Potato viruses PLRV, PVY, PVM, PVA, PVX and PVS can cause up to 90% loss of potato harvest. Therefore, they are monitored by law in many countries using DAS-ELISA or conventional real-time RT-qPCR. Previously, we developed a multiplex DiRT-PCR (Direct reverse transcript – polymerase chain reaction), which works directly on diluted tuber sap thus saves time chemical processing for RNA e...

The critical need for surveillance of SARS-CoV-2 variants concern has prompted the development methods that can track in wastewater. Here, we develop and present an open-source method based on allele-specific RT-qPCR (AS RT-qPCR) detects quantifies B.1.1.7 variant, targeting spike protein mutations at three independent genomic loci are highly predictive (HV69/70del, Y144del, A570D). Our assays ...