Introduction: Radical radiation therapy of head and neck cancers may injure the salivary glands and reduce their function. Single-photon emission computed tomography (SPECT) images maybe used to evaluate function post-therapy. However, accurate quantification is hindered by the partial volume effects (PVEs). The present study involved the introduction of a PVEs quantif...

This study reports on the first quantification of avian influenza virus in the organs of mute swans that died during the epizootic of avian influenza (H5N1) between January and April 2006 in the Czech Republic. The quantitative real-time Reverse Transcriptase PCR (qRT-PCR) assay based on a TaqMan probe was developed for a rapid detection and quantification of avian influenza virus RNA in clinic...

We report on a hybridization assay using DNA microarrays for the quantification of amplification products of the uidA gene of E. coli. Using the stopped-PCR strategy, the amplified target DNA was strongly dependent on the applied gene copies. The quantification was carried out by a flow-through chemiluminescence microarray readout system. The DNA microarrays were based on a poly(ethylene glycol...

The quantification of transcriptomic features is the basis of the analysis of RNA-seq data. We present an integrated alignment workflow and a simple counting-based approach to derive estimates for gene, exon and exon-exon junction expression. In contrast to previous counting-based approaches, EQP takes into account only reads whose alignment pattern agrees with the splicing pattern of the featu...

Real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) is the method of choice for rapid and reproducible measurements of cytokine or growth factor expression in small samples. Fluorescence detection methods for monitoring real-time PCR include fluorogenic probes labelled with reporter and quencher dyes, such as Taqman probes or Molecular Beacons and the dsDNA-binding d...

Molecular methods are being increasingly applied to detect, quantify and study microbial populations in food or during food processes. Among these methods, PCR-based techniques have been the subject of considerable focus and ISO guidelines have been established for the detection of food-borne pathogens. More particularly, real-time quantitative PCR (qPCR) is considered as a method of choice for...

High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the transcriptome of cells. Many transcriptomic studies aim at comparing either abundance levels or the transcriptome composition between given conditions, and as a first step, the sequencing reads must be used as the basis for abundance quantification of transcriptomic features of interest, such as genes or transc...

BACKGROUND Real-time PCR is increasingly being adopted for RNA quantification and genetic analysis. At present the most popular real-time PCR assay is based on the hybridisation of a dual-labelled probe to the PCR product, and the development of a signal by loss of fluorescence quenching as PCR degrades the probe. Though this so-called 'TaqMan' approach has proved easy to optimise in practice, ...

Clonostachys rosea is a potential biocontrol fungus that can produce highly resistant chlamydospores under specific conditions. To investigate the genes related to chlamydospore formation, we identified reliable reference genes for quantification of gene expression in C. rosea 67-1 during sporulation. In this study, nine reference genes, actin (ACT), elongation factor 1 (EF1), glyceraldehyde-3-...

Pneumocystis jiroveci is an important agent of pneumonia in immunocompromised hosts. Usually, this pathogen is detected by Giemsa or direct fluorescence stains of bronchoalveolar lavage (BAL) fluids. Microscopic methods, however, have 2 disadvantages. P. jiroveci is not stable outside the human body, which means that slow sample transport might result in false-negative results. Additionally, ex...