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Next-generation sequencing applications in clinical bacteriology
Publication date: December 2017 Source:Biomolecular Detection and Quantification, Volume 14 Author(s): Yair Motro, Jacob Moran-Gilad With the rapid advances in next generation sequencing (NGS) technologies, clinical and public health microbiology laboratories are increasingly adopting NGS technology in their workflows into their existing diagnostic cycles. In this bacteriology focused review, we review aspects and considerations for applying NGS in the clinical microbiology settings, and highlight the impact of such implementation on the analytical and post-analytical stages of diagnosis (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - October 23, 2017 Category: Molecular Biology Source Type: research

Evaluation of relative quantification of alternatively spliced transcripts using droplet digital PCR
Conclusions Our study recognizes the potential and validity of digital PCR but shows the value of a highly optimized qPCR for the relative quantification of isoforms. Cost efficiency and simplicity turned out to be better for RT-qPCR. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - September 21, 2017 Category: Molecular Biology Source Type: research

Quantification of mitochondrial DNA copy number in suspected cancer patients by a well optimized ddPCR method
Publication date: Available online 31 August 2017 Source:Biomolecular Detection and Quantification Author(s): Ashfaque A. Memon, Bengt Zöller, Anna Hedelius, Xiao Wang, Emelie Stenman, Jan Sundquist, Kristina Sundquist Changes in mitochondrial DNA (mtDNA) content is a useful clinical biomarker for various diseases, however results are controversial as several analytical factors can affect measurement of mtDNA. MtDNA is often quantified by taking ratio between a target mitochondrial gene and a reference nuclear gene (mtDNA/nDNA) using quantitative real time PCR often on two separate experiments. It measures relati...
Source: Biomolecular Detection and Quantification - September 1, 2017 Category: Molecular Biology Source Type: research

*K-means and cluster models for cancer signatures
We present *K-means clustering algorithm and source code by expanding statistical clustering methods applied in https://ssrn.com/abstract=2802753 to quantitative finance. *K-means is statistically deterministic without specifying initial centers, etc. We apply *K-means to extracting cancer signatures from genome data without using nonnegative matrix factorization (NMF). *K-means’ computational cost is a fraction of NMF’s. Using 1389 published samples for 14 cancer types, we find that 3 cancers (liver cancer, lung cancer and renal cell carcinoma) stand out and do not have cluster-like structures. Two clusters have espec...
Source: Biomolecular Detection and Quantification - August 2, 2017 Category: Molecular Biology Source Type: research

The Unyvero P55 ‘sample-in, answer-out’ pneumonia assay: A performance evaluation
Conclusions The Unyvero P55 is a rapid pathogen detection test for lower respiratory specimens, which identifies a larger number of pathogens than routine microbiology. The clinical significance of these additional organisms is yet to be determined. Further studies are required to determine the effect of the test in practise on antimicrobial prescribing and patient outcomes. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - June 29, 2017 Category: Molecular Biology Source Type: research

How to speed up the polymerase chain reaction
Publication date: Available online 20 June 2017 Source:Biomolecular Detection and Quantification Author(s): Stephen A. Bustin Reducing the time taken to run qPCR assays on today’s qPCR cyclers is rather straightforward and requires no specialised reagents or instruments. As the first article in a new series of short technical reports, I demonstrate that it is possible to reduce significantly both denaturation temperatures and cycling times, whilst retaining sensitivity and specificity of the original qPCR conditions. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - June 21, 2017 Category: Molecular Biology Source Type: research

The continuing problem of poor transparency of reporting and use of inappropriate methods for RT-qPCR
Publication date: Available online 23 May 2017 Source:Biomolecular Detection and Quantification Author(s): Stephen Bustin Attendance at this year’s European Calcified Tissue Society’s (ECTS) Congress reveals that the methods used to obtain qPCR results continue to be significantly flawed and that and their reporting remain inadequate. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - May 24, 2017 Category: Molecular Biology Source Type: research

Methods to determine limit of detection and limit of quantification in quantitative real-time PCR (qPCR)
Publication date: Available online 29 April 2017 Source:Biomolecular Detection and Quantification Author(s): Amin Forootan, Robert Sjöback, Jens Björkman, Björn Sjögreen, Lucas Linz, Mikael Kubista Quantitative Real-Time Polymerase Chain Reaction, better known as qPCR, is the most sensitive and specific technique we have for the detection of nucleic acids. Even though it has been around for more than 30 years and is preferred in research applications, it has yet to win broad acceptance in routine practice. This requires a means to unambiguously assess the performance of specific qPCR analyses. Here we present m...
Source: Biomolecular Detection and Quantification - April 29, 2017 Category: Molecular Biology Source Type: research

Reproducibility of biomedical research – The importance of editorial vigilance
Publication date: Available online 21 February 2017 Source:Biomolecular Detection and Quantification Author(s): Stephen A. Bustin, Jim F. Huggett Many journal editors are a failing to implement their own authors’ instructions, resulting in the publication of many articles that do not meet basic standards of transparency, employ unsuitable data analysis methods and report overly optimistic conclusions. This problem is particularly acute where quantitative measurements are made and results in the publication of papers that lack scientific rigor and contributes to the concerns with regard to the reproducibility of biome...
Source: Biomolecular Detection and Quantification - February 20, 2017 Category: Molecular Biology Source Type: research

Molecular techniques for the personalised management of patients with chronic myeloid leukaemia
Publication date: Available online 14 February 2017 Source:Biomolecular Detection and Quantification Author(s): Mary Alikian, Robert Peter Gale, Jane F Apperley, Letizia Foroni Chronic myeloid leukemia (CML) is the paradigm for targeted cancer therapy. RT-qPCR is the gold standard for monitoring response to tyrosine kinase-inhibitor (TKI) therapy based on the reduction of blood or bone marrow BCR-ABL1. Some patients with CML and very low or undetectable levels of BCR-ABL1 transcripts can stop TKI-therapy without CML recurrence. However, about 60 percent of patients discontinuing TKI-therapy have rapid leukaemia recur...
Source: Biomolecular Detection and Quantification - February 14, 2017 Category: Molecular Biology Source Type: research

Digital PCR, a technique for the future
Publication date: December 2016 Source:Biomolecular Detection and Quantification, Volume 10 Author(s): -->Valerie Taly, Jim Huggett (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - January 28, 2017 Category: Molecular Biology Source Type: research

Measuring E. coli and bacteriophage DNA in cell sonicates to evaluate the CAL1 reaction as a synthetic biology standard for qPCR
Publication date: Available online 29 December 2016 Source:Biomolecular Detection and Quantification Author(s): Alexander Templar, Desmond M. Schofield, Darren N. Nesbeth We measured the impact of the presence of total Escherichia coli (E. coli) cellular material on the performance of the Linear Regression of Efficiency (LRE) method of absolute quantitative PCR (LRE qPCR), which features the putatively universal CAL1 calibration reaction, which we propose as a synthetic biology standard. We firstly used a qPCR reaction in which a sequence present in the lone genomic BirA locus is amplified. Amplification efficiency fo...
Source: Biomolecular Detection and Quantification - December 29, 2016 Category: Molecular Biology Source Type: research

Inhibition of fat cell differentiation in 3T3-L1 pre-adipocytes by all-trans retinoic acid: Integrative analysis of transcriptomic and phenotypic data
In conclusion, the experimental workflow and the integrative microRNA–mRNA data analysis shown in this study represent a possibility for illustrating interactions in highly orchestrated biological processes. Further the applied global microRNA–mRNA interaction network may also be used for the pre-selection of potential new biomarkers with regard to obesity or for the identification of new pharmaceutical targets. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - November 21, 2016 Category: Molecular Biology Source Type: research

Three-color crystal digital PCR
Publication date: Available online 3 November 2016 Source:Biomolecular Detection and Quantification Author(s): J. Madic, A. Zocevic, V. Senlis, E. Fradet, B. Andre, S. Muller, R. Dangla, M.E. Droniou Digital PCR is an exciting new field for molecular analysis, allowing unprecedented precision in the quantification of nucleic acids, as well as the fine discrimination of rare molecular events in complex samples. We here present a novel technology for digital PCR, Crystal Digital PCR™, which relies on the use of a single chip to partition samples into 2D droplet arrays, which are then subjected to thermal cycling ...
Source: Biomolecular Detection and Quantification - November 3, 2016 Category: Molecular Biology Source Type: research

Digital PCR dynamic range is approaching that of real-time quantitative PCR
Publication date: Available online 2 November 2016 Source:Biomolecular Detection and Quantification Author(s): Gerwyn M. Jones, Eloise Busby, Jeremy A. Garson, Paul R. Grant, Eleni Nastouli, Alison S. Devonshire, Alexandra S. Whale Digital PCR (dPCR) has been reported to be more precise and sensitive than real-time quantitative PCR (qPCR) in a variety of models and applications. However, in the majority of commercially available dPCR platforms, the dynamic range is dependent on the number of partitions analysed and so is typically limited to four orders of magnitude; reduced compared with the typical seven orders ...
Source: Biomolecular Detection and Quantification - November 2, 2016 Category: Molecular Biology Source Type: research