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Publisher's Note
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - October 4, 2019 Category: Molecular Biology Source Type: research

Identification of eyeworm (Oxyspirura petrowi) and caecal worm (Aulonocephalus pennula) infection levels in Northern bobwhite quail (Colinus virginianus) of the Rolling Plains, TX using a mobile research laboratory: Implications for regional surveillance
In this study, cloacal swabs are collected from bobwhite in three locations throughout the Rolling Plains and scaled based on amount of feces present on the swab. This data is compared to qPCR standards as a limit of quantification for both eyeworm and caecal worm to define parasitic infection levels. Binary logistic regressions confirm that the probability of detection increases for both eyeworm (Odds Ratio: 2.3738; 95% Confidence Interval: [1.7804, 3.1649]) and caecal worm (Odds Ratio: 2.8516; 95% Confidence Interval: [2.2235, 3.6570]) as swab score increases. Infection levels for eyeworm and caecal worm are based on the...
Source: Biomolecular Detection and Quantification - September 5, 2019 Category: Molecular Biology Source Type: research

Corrigendum to “Considerations and quality controls when analyzing cell-free tumor DNA” [Biomol. Detect. Quantif. 17 (2019) 100078]
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Gustav Johansson, Daniel Andersson, Stefan Filges, Junrui Li, Andreas Muth, Tony E. Godfrey, Anders Ståhlberg (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - June 19, 2019 Category: Molecular Biology Source Type: research

qPCR data analysis: Better results through iconoclasm
We describe improved methods for estimating these and other Cq markers and their standard errors, from a nonlinear algorithm that fits growth profiles to a 4-parameter log-logistic function plus a baseline function. Further, by examining six multidilution, multireplicate qPCR data sets, we find that nonlinear expressions are often preferred statistically for the dependence of Cq on log(N0). This means that the amplification efficiency E depends on N0, in violation of another tenet of qPCR analysis. Neglect of calibration nonlinearity leads to biased estimates of the unknown. By logic, E estimates from calibration fitting p...
Source: Biomolecular Detection and Quantification - June 6, 2019 Category: Molecular Biology Source Type: research

Comparing small urinary extracellular vesicle purification methods with a view to RNA sequencing—Enabling robust and non-invasive biomarker research
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Veronika Mussack, Georg Wittmann, Michael W. PfafflAbstractSmall extracellular vesicles (EVs) are 50–200 nm sized mediators in intercellular communication that reflect both physiological and pathophysiological changes of their parental cells. Thus, EVs hold great potential for biomarker detection. However, reliable purification methods for the downstream screening of the microRNA (miRNA) cargo carried within urinary EVs by small RNA sequencing have yet to be established. To address this knowledge gap, RNA extracted from h...
Source: Biomolecular Detection and Quantification - June 5, 2019 Category: Molecular Biology Source Type: research

Establishing essential quality criteria for the validation of circular RNAs as biomarkers
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Christina Pfafenrot, Christian PreußerAbstractNon-coding RNAs were established in the last decade as a new valuable biomarker class for human diseases. Specifically, circular RNAs (circRNAs) were only recently discovered as a new large group of non-coding RNAs that, due to their circular configuration, are metabolically more stable compared to their linear counterparts and therefore highly suitable for biomarker use. Based on high-throughput sequencing, the catalogs of endogenous circRNAs with disease relevance and correlati...
Source: Biomolecular Detection and Quantification - May 4, 2019 Category: Molecular Biology Source Type: research

Corrigendum to “Development of event-specific qPCR detection methods for genetically modified alfalfa events J101, J163 and KK179” [Biomol. Detect. Quantif. 17 (March) (2019) 100076]
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Patrick Guertler, Lutz Grohmann, Heike Naumann, Melanie Pavlovic, Ulrich Busch (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - May 2, 2019 Category: Molecular Biology Source Type: research

For what factors should we normalize urinary extracellular mRNA biomarkers?
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Pradeep Moon Gunasekaran, James Matthew Luther, James Brian ByrdAbstractmRNA is a critical biomolecule involved in the manifestation of the genetic code into functional protein molecules. Its critical role in the central dogma has made it a key target in many studies to determine biomarkers and drug targets for numerous diseases. Currently, there is a growing body of evidence to suggest that RNA molecules around the size of full-length mRNA transcripts can be assayed in the supernatant of human urine and urinary extracellular...
Source: Biomolecular Detection and Quantification - April 24, 2019 Category: Molecular Biology Source Type: research

Guest editor’s editorial: BDQ Special Issue — “Liquid Biopsy & Next Generation Biomarkers”: Published in conjunction with the 9th Gene Quantification Event in Freising Weihenstephan, Germany www.qPCR-dPCR-NGS-2019.net
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Michael W. Pfaffl (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - April 20, 2019 Category: Molecular Biology Source Type: research

Editorial
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Michael W. Pfaffl (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - March 23, 2019 Category: Molecular Biology Source Type: research

The emerging role of cell-free DNA as a molecular marker for cancer management
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Abel Jacobus Bronkhorst, Vida Ungerer, Stefan HoldenriederAbstractAn increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, phys...
Source: Biomolecular Detection and Quantification - March 19, 2019 Category: Molecular Biology Source Type: research

Investigation of direct counting and sizing of DNA fragments in flow applying an improved data analysis and correction method
In this study, we analysed raw detector signals and the sizing performance for target identification and the effect of coincidence detection concerning concentration measurements. We present data of purified artificial DNA samples measured with the home-built setup. Main emphasis was to develop an improved data analysis method to gain insight into and carefully correct for coincident detection of DNA fragments and for estimation of the amount of fragment dimers. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - March 18, 2019 Category: Molecular Biology Source Type: research

The kinetic requirements of extreme qPCR
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Adam L. Millington, Jessica A. Houskeeper, John F. Quackenbush, James M. Trauba, Carl T. WittwerAbstractThe kinetic requirements of quantitative PCR were experimentally dissected into the stages of DNA denaturation, primer annealing, and polymerase extension. The temperature/time conditions for 2 stages were kept optimal, while the other was limited until the amplification efficiency decreased as measured by an increase in quantification cycle (Cq). Extension was studied in a commercial capillary LightCycler®. Using a rapi...
Source: Biomolecular Detection and Quantification - March 15, 2019 Category: Molecular Biology Source Type: research

Next-generation sequencing of HIV-1 single genome amplicons
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Gustavo H. Kijak, Eric Sanders-Buell, Phuc Pham, Elizabeth A. Harbolick, Celina Oropeza, Anne Marie O’Sullivan, Meera Bose, Charmagne G. Beckett, Mark Milazzo, Merlin L. Robb, Sheila A. Peel, Paul T. Scott, Nelson L. Michael, Adam W. Armstrong, Jerome H. Kim, David M. Brett-Major, Sodsai TovanabutraAbstractThe analysis of HIV-1 sequences has helped understand the viral molecular epidemiology, monitor the development of antiretroviral drug resistance, and design candidate vaccines. The introduction of single genome amplifica...
Source: Biomolecular Detection and Quantification - March 13, 2019 Category: Molecular Biology Source Type: research

Challenging the proposed causes of the PCR plateau phase
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Linda Jansson, Johannes HedmanAbstractDespite the wide-spread use of the polymerase chain reaction (PCR) in various life-science applications, the causes of arrested amplicon generation in late cycles have not been confidently identified. This so-called plateau phase has been attributed to depletion or thermal break-down of primers or nucleotides, thermal inactivation of the DNA polymerase, and product accumulation resulting in competition between primer annealing and product re-hybridization as well as blocking of DNA polyme...
Source: Biomolecular Detection and Quantification - March 4, 2019 Category: Molecular Biology Source Type: research