Biomolecular Detection and Quantification This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Digital polymerase chain reaction for characterisation of DNA reference materials
Publication date: Available online 3 May 2016 Source:Biomolecular Detection and Quantification Author(s): Somanath Bhat, Kerry R. Emslie Accurate, reliable and reproducible quantification of nucleic acids (DNA/RNA) is important for many diagnostic applications and in routine laboratory testing, for example, for pathogen detection and detection of genetically modified organisms in food. To ensure reliable nucleic acid measurement, reference materials (RM) that are accurately characterised for quantity of target nucleic acid sequences (in copy number or copy number concentration) with a known measurement uncertainty ...
Source: Biomolecular Detection and Quantification - May 3, 2016 Category: Molecular Biology Source Type: research

Heparinase treatment of heparin-contaminated plasma from coronary artery bypass grafting patients enables reliable quantification of microRNAs
Conclusions The heparinase treatment procedure enables utilization of RT-qPCR for reliable microRNA quantification in heparinized plasma. Graphical abstract (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - April 8, 2016 Category: Molecular Biology Source Type: research

Development of NIST standard reference material 2373: Genomic DNA standards for HER2 measurements
Publication date: June 2016 Source:Biomolecular Detection and Quantification, Volume 8 Author(s): Hua-Jun He, Jamie L. Almeida, Steve P. Lund, Carolyn R. Steffen, Steve Choquette, Kenneth D. Cole NIST standard reference material (SRM) 2373 was developed to improve the measurements of the HER2 gene amplification in DNA samples. SRM 2373 consists of genomic DNA extracted from five breast cancer cell lines with different amounts of amplification of the HER2 gene. The five components are derived from the human cell lines SK-BR-3, MDA-MB-231, MDA-MB-361, MDA-MB-453, and BT-474. The certified values are the ratio...
Source: Biomolecular Detection and Quantification - March 9, 2016 Category: Molecular Biology Source Type: research

Evaluation of microbial qPCR workflows using engineered Saccharomyces cerevisiae
Conclusions The NE095 strain was successfully detected by all participants, with the high concentration indicating a potential target concentration for a reference material. Significance and impact of the study The engineered yeast has potential to support measurement assurance for the analytical process of qPCR, encompassing the method, equipment, and operator, to increase confidence in results and better inform decision-making in areas of applied microbiology. This material can also support process assessment for other DNA-based detection technologies. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - February 22, 2016 Category: Molecular Biology Source Type: research

qPCR based mRNA quality score show intact mRNA after heat stabilization
Publication date: March 2016 Source:Biomolecular Detection and Quantification, Volume 7 Author(s): Oskar Karlsson, Lova Segerström, Robert Sjöback, Ingrid Nylander, Mats Borén Analysis of multiple analytes from biological samples can be challenging as different analytes require different preservation measures. Heat induced enzymatic inactivation is an efficient way to preserve proteins and their modifications in biological samples but RNA quality, as measured by RIN value, has been a concern in such samples. Here, we investigate the effect of heat stabilization compared with standard snap freezing on RNA q...
Source: Biomolecular Detection and Quantification - February 12, 2016 Category: Molecular Biology Source Type: research

Improving the reliability of peer-reviewed publications: We are all in it together
Publication date: Available online 28 December 2015 Source:Biomolecular Detection and Quantification Author(s): Stephen A. Bustin, Tania Nolan The current, and welcome, focus on standardization of techniques and transparency of reporting in the biomedical, peer-reviewed literature is commendable. However, that focus has been intermittent as well as lacklustre and so failed to tackle the alarming lack of reliability and reproducibly of biomedical research. Authors have access to numerous recommendations, ranging from simple standards dealing with technical issues to those regulating clinical trials, suggesting that ...
Source: Biomolecular Detection and Quantification - January 11, 2016 Category: Molecular Biology Source Type: research

Optimization of digital droplet polymerase chain reaction for quantification of genetically modified organisms
Publication date: March 2016 Source:Biomolecular Detection and Quantification, Volume 7 Author(s): Lars Gerdes, Azuka Iwobi, Ulrich Busch, Sven Pecoraro Digital PCR in droplets (ddPCR) is an emerging method for more and more applications in DNA (and RNA) analysis. Special requirements when establishing ddPCR for analysis of genetically modified organisms (GMO) in a laboratory include the choice between validated official qPCR methods and the optimization of these assays for a ddPCR format. Differentiation between droplets with positive reaction and negative droplets, that is setting of an appropriate threshold,...
Source: Biomolecular Detection and Quantification - January 11, 2016 Category: Molecular Biology Source Type: research

Real-time PCR probe optimization using design of experiments approach
In this study, we present the use of statistical design of experiments (DOE) approach as a general guideline for probe optimization and more specifically focus on design optimization of label-free hydrolysis probes that are designated as mediator probes (MPs), which are used in reverse transcription MP PCR (RT-MP PCR). The effect of three input factors on assay performance was investigated: distance between primer and mediator probe cleavage site; dimer stability of MP and target sequence (influenza B virus); and dimer stability of the mediator and universal reporter (UR). The results indicated that the latter dimer stabil...
Source: Biomolecular Detection and Quantification - January 11, 2016 Category: Molecular Biology Source Type: research

Evaluation of bias associated with high-multiplex, target-specific pre-amplification
Publication date: Available online 21 December 2015 Source:Biomolecular Detection and Quantification Author(s): Steven T. Okino, Michelle Kong, Haya Sarras, Yan Wang We developed a novel PCR-based pre-amplification (PreAmp) technology that can increase the abundance of over 350 target genes one million-fold. To assess potential bias introduced by PreAmp we utilized ERCC RNA reference standards, a model system that quantifies measurement error in RNA analysis. We assessed three types of bias: amplification bias, dynamic range bias and fold-change bias. We show that our PreAmp workflow introduces only minimal amp...
Source: Biomolecular Detection and Quantification - December 22, 2015 Category: Molecular Biology Source Type: research

Pitfalls in PCR troubleshooting: Expect the unexpected?
Publication date: Available online 10 December 2015 Source:Biomolecular Detection and Quantification Author(s): Livia Schrick, Andreas Nitsche PCR is a well-understood and established laboratory technique often used in molecular diagnostics. Huge experience has been accumulated over the last years regarding the design of PCR assays and their set-up, including in-depth troubleshooting to obtain the optimal PCR assay for each purpose. Here we report a PCR troubleshooting that came up with a surprising result never observed before. With this report we hope to sensitize the reader to this peculiar problem and to save t...
Source: Biomolecular Detection and Quantification - December 11, 2015 Category: Molecular Biology Source Type: research

Incidence and detection of beak and feather disease virus in psittacine birds in the UAE
Publication date: Available online 11 November 2015 Source:Biomolecular Detection and Quantification Author(s): F. Hakimuddin, F. Abidi, O. Jafer, C. Li, U. Wernery, Ch. Hebel, K. Khazanehdari Beak and feather disease is caused by Circovirus, which affects actively growing beak and feather cells of avian species. The disease affects mainly young birds while older birds may overcome the disease with few lasting effects. Due to lack of treatment, the only way to control the disease is through hygiene and early diagnosis. As a diagnostic tool, we have established a Taqman probe based real-time PCR assay to d...
Source: Biomolecular Detection and Quantification - November 11, 2015 Category: Molecular Biology Source Type: research

Guest editor's introduction for BDQ special issue: ‘Advanced Molecular Diagnostics for Biomarker Discovery’
Publication date: September 2015 Source:Biomolecular Detection and Quantification, Volume 5 Author(s): Michael W. Pfaffl (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - October 9, 2015 Category: Molecular Biology Source Type: research

Targeted resequencing and variant validation using pxlence PCR assays
Publication date: Available online 9 October 2015 Source:Biomolecular Detection and Quantification Author(s): Frauke Coppieters, Kimberly Verniers, Kim De Leeneer, Jo Vandesompele, Steve Lefever The advent of next-generation sequencing technologies had a profound impact on molecular diagnostics. PCR is a popular method for target enrichment of disease gene panels. Using our proprietary primer-design pipeline, primerXL, we have created almost one million assays covering over 98% of the human exome. Here we describe the assay specification and both in silico and wet-lab validation of a selected set of 2294 assa...
Source: Biomolecular Detection and Quantification - October 9, 2015 Category: Molecular Biology Source Type: research

Differential amplicons (ΔAmp)—a new molecular method to assess RNA integrity
Publication date: Available online 26 September 2015 Source:Biomolecular Detection and Quantification Author(s): J. Björkman, D. Švec, E. Lott, M. Kubista, R. Sjöback Integrity of the mRNA in clinical samples has major impact on the quality of measured expression levels. This is independent of the measurement technique being next generation sequencing (NGS), Quantitative real-time PCR (qPCR) or microarray profiling. If mRNA is highly degraded or damaged, measured data will be very unreliable and the whole study is likely a waste of time and money. It is therefore common strategy to test the quality of RNA ...
Source: Biomolecular Detection and Quantification - September 26, 2015 Category: Molecular Biology Source Type: research

The potential of circulating extracellular small RNAs (smexRNA) in veterinary diagnostics—Identifying biomarker signatures by multivariate data analysis
Publication date: Available online 19 September 2015 Source:Biomolecular Detection and Quantification Author(s): Spornraft Melanie, Kirchner Benedikt, Michael W. Pfaffl, Riedmaier Irmgard Worldwide growth and performance-enhancing substances are used in cattle husbandry to increase productivity. In certain countries however e.g., in the EU, these practices are forbidden to prevent the consumers from potential health risks of substance residues in food. To maximize economic profit, ‘black sheep‘ among farmers might circumvent the detection methods used in routine controls, which highlights the need for an in...
Source: Biomolecular Detection and Quantification - September 21, 2015 Category: Molecular Biology Source Type: research