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Gene Quantification Newsletter
August  2016

is sponsored by


Streamlined and automated NGS workflow 

  Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in gene expression profiling using qPCR and related methods, which are compiled and summarised on www.Gene-Quantification.info
The focus of this qPCR NEWS issue is:


Streaming portal

Join the updated
eConferences streaming webportal
www.eConferences.de -- Amplify your knowledge in  qPCR, dPCR and NGS!
This streaming portal is dedicated to scientists from the community of qPCR, digital PCR, Next Generation Sequencing (NGS), MicroGenomics (MG) and Molecular Diagnostics (MDx). You’ll find here all the records of 280 presentations held at qPCR & NGS and MG Events in the past years – qPCR 2010 in Vienna  to qPCR & NGS 2015 in Freising-Weihenstephan.
We provide the presentations via movie streaming technology in high quality – high resolution and perfect sound quality in high speed – on any internet browser or mobile device.


microRNA transfer

Cross-kingdom microRNA transfer
from a paracrine & endocrine communication to cross-kingdom communication

Introduction & Overview
In multicellular organisms, the cell-to-cell communication is of particular importance for any physiological process, and the proper organization of the entire organism. Numerous studies over the past years suggest a horizontal transfer of cellular secreted microRNAs between cells, tissues and organs. Hence extracellular RNAs (primarily small non-coding RNAs) represent a novel form of inter-cellular communication by transferring genetic information from a donor cell to a recipient cell. This points to an important new role for small RNAs in inter-cellular communication on the paracrine- and endocrine-level.

Para- and endocrine communication
Small RNAs (primary microRNAs, piRNAs and other small RNA families) can be exported out of the donor cells and transported as free circulating DNA or RNA or by various carriers, e.g. membrane-derived vesicles (exosomes, microvesicles, ectosomes, apoptotic bodies, and more), microRNA-binding protein complexes (RBP), or high density lipoproteins (HDL). Secreted microRNAs can be uptaken and delivered into recipient cells where they function as endogenous microRNAs, simultaneously regulating multiple target genes or signaling pathways.

Cross-kingdom communication
In prokaryotes, this molecular signaling is typically referred to as quorum sensing, whereas in eukaryotic cells, the molecular communication occurs through hormones and cytokines. Recently various publications report that microRNAs can also be transmitted from one species to another, inducing signal interference in distant species, even in a cross-kingdom manner. This new mode of cross-species communication might mediate symbiotic and pathogenic relationships between various organisms.
This can be of enormous importance in the inter-species communication of microorganisms and their hosts or by diet-derived small RNAs. Higher organisms are constantly under attack from pathogens, resulting in severe consequences on global human or veterinary health. Recently also the uptake of plant microRNA is discussed.
Hence small RNA mediated RNA interference (RNAi) is a conserved regulatory mechanism that is involved in almost all eukaryotic cellular processes, including host immunity and pathogen virulence. Recent evidence supports the significant contribution of small RNAs and RNAi to the communication between hosts and some eukaryotic pathogens or symbiotic microorganisms. Mobile silencing signals - most likely small RNAs - are capable of translocating from the host to its interacting organism, and vice versa.


microRNA transfer
selected papers

Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells.
Valadi H, Ekström K, Bossios A, Sjöstrand M, Lee JJ, Lötvall JO.
Nat Cell Biol. 2007 (6): 654-659

Exosomes -- vesicular carriers for intercellular communication.
Simons M and Raposo G.
Curr Opin Cell Biol. 2009 Aug;21(4): 575-581

REVIEW -- New roles for microRNAs in cross-species communication.
Liang H, Zen K, Zhang J, Zhang CY, Chen X.
RNA Biol. 2013 Mar;10(3): 367-370

Unraveling the Mystery of Cancer by Secretory microRNA -- Horizontal microRNA Transfer between Living Cells.
Kosaka N and Ochiya T
Front Genet. 2012 2: 97

Regulation of mammalian gene expression by exogenous microRNAs.
Liang H, Huang L, Cao J, Zen K, Chen X, Zhang CY.
Wiley Interdiscip Rev RNA. 2012 Sep-Oct;3(5): 733-742

Conversations between kingdoms -- small RNAs.
Weiberg A, Bellinger M, Jin H
Curr Opin Biotechnol. 2015 Apr;32:2207-215

Diet-Derived MicroRNAs: Separating the Dream from Reality.
Katherine Cottrill & Stephen Y. Chan
microRNA Diagn. Ther. 2014 (1): 46-57

Role of plant MicroRNA in cross-species regulatory networks of humans.
Zhang H, Li Y, Liu Y, Liu H, Wang H, Jin W, Zhang Y, Zhang C, Xu D
BMC Syst Biol. 2016 Aug 8;10(1): 60

Nonfunctional ingestion of plant miRNAs in silkworm revealed by digital droplet PCR and transcriptome analysis.
Jia L, Zhang D, Xiang Z, He N
Sci Rep. 2015 Jul 21;5: 12290

... and much more Cross-Kingdom-Transfer.Gene-Quantification.info

2nd edition

How to apply the MIQE guidelines - a visual, interactive and practical qPCR guide

2nd edition published 26th July 2016
Editors:  Afif M. Abdel Nour & Michael W. Pfaffl
ISBN 9783000488061
Free download via iTunes  https://itunes.apple.com/book/miqe-qpcr/id993276375?mt=11

MIQE & qPCR Preface:   The qPCR and dPCR MIQE guidelines – A success story!
(Editorial for 2nd edition published 26. July 2016)

The MIQE guidelines and the resulting scientific validity will be supported by more and more researchers, biological journals, academic and commercial institutions. Today in July 2016 we count more than 4650 citations for the MIQE guideline applied in qPCR and around 160 citations for the digital PCR (dPCR) MIQE guideline (measured by Google Scholar). Hence the qPCR and dPCR MIQE guidelines are a worldwide full success story which will be driven forward by the scientific community, e.g. MIQE.Gene-Quantification.info

The present second edition of the MIQE & qPCR iBook should help to spread this MIQE idea even further in any laboratory worldwide and beyond in the scientists’ workflow and minds. It should clearly show how to apply the guidelines and serve as a handy, visual, interactive and practical guide. For now in the first year after publication of the first edition we could count more than 1200 downloads of the MIQE & qPCR iBook from more than 30 countries. Our goal for the second edition is to update the existing content by new chapters, and to improve this fancy interactive tool, interfacing scientific publications with educating pictures, videos and scientific talks. We implemented multiple new chapters, describing the significance of the reverse transcription reaction, why qPCR assay validation is so important for high sensitivity and good reproducibility, and one reviewing chapter about the necessity of performing quality control at all levels in the qPCR workflow. In summary we are proud to present a selection of international highly recognized authors from the academic field as well from industrial research presenting their latest applications. Described qPCR / dPCR methods and applications are linked to the MIQE context and show it on the basis of educational questionnaires or interactive ‘how to do’ instruction sheets. The at-hand MIQE & qPCR iBook should deliver the MIQE guidelines directly to the researcher and help to solve the daily problems in the molecular biology laboratory using quantitative PCR, digital PCR, single-cell qPCR, microRNA applications or any comparable techniques using PCR.

We hope you like our explanatory, interactive and educational iBook concept, showing the advantages of the MIQE guidelines in an easy and understandable way, and to guarantee the successful qPCR or dPCR application at the lab bench.

The editors
Afif M. Abdel Nour & Michael W. Pfaffl


8th Gene Quantification Event
in April 2017

qPCR dPCR & NGS 2017

qPCR dPCR & NGS 2017
8th international Gene Quantification Event
Symposium & Industrial Exhibition & Application Workshops

Main topics:   Liquid Biopsy, Integrative Big Data Analysis, Biomarker Signature … and beyond
3 - 7 April 2017, in Freising-Weihenstephan,
School of Life Sciences, Technical University of Munich, Weihenstephan, Germany

Download Event Announcement Announcement.qPCR-dPCR-NGS-2017.net

Scientific Symposium Sessions:

  • Liquid Biopsy & Circulating Nucleic Acids
  • Advanced Molecular Diagnostics
  • Integrative Big Data Analysis
  • Biomarker Signatures
  • Digital PCR
  • Non-coding RNAs -- microRNA, isomiRs, small RNAs, long non-coding RNAs
  • MicroGenomics & Single-Cells Diagnostics
  • Next Generation Sequencing (NGS)
  • Molecular Diagnostics in Life Science
  • MIQE & QM & Standardisation Strategies in Molecular Diagnostics

Register and submit your scientific contribution (talk or poster abstracts) => Registration.qPCR-dPCR-NGS-2017.net


Publish in Biomolecular Detection and Quantification
The new online, open access, peer-reviewed journal in molecular methodology applications

Biomolecular Detection and Quantification (BDQ) is an open access, peer-reviewed international journal dedicated to championing excellence in molecular study design, measurement, data analysis and reporting. Its focus is on the application of qualitative and quantitative molecular methodologies to all areas of clinical and life sciences. Download the recent BDQ papers on Elsevier Science  Direct.

   BDQ is now listed in PubMed Central (PMC) -- all published papers are free for download!

The journal has two main aims:

  • to provide a forum for discussion and recommendation of guidelines designed to improve the accuracy of molecular measurement, its data analysis and the transparency of its subsequent reporting;
  • to publish molecular biology based studies that adhere to best practice guidelines, both current and future.

We look forward to receiving your paper!

Kind regards,

The Editors
Stephen Bustin, Jim Huggett, Justin O'Grady, Michael W. Pfaffl, Carl Wittwer, Ron Cook

View full editorial board


GenEx 6.1

The most powerful tool for complex qPCR data analysis

Compliant with MIQE and CLSI guidelines

GenEx offers advanced methods to analyze real-time qPCR data with simple mouse clicks

Download a FREE GenEx 6.1 trial version => GenEx.Gene-Quantification.info
GenEx is a popular software for qPCR data processing and analysis. Built in a modular fashion GenEx provides a multitude of functionalities for the qPCR community, ranging from basic data editing and management to advanced cutting-edge data analysis. GenEx 6.1 – the software compliant with MIQE and CLSI guidelines

Basic data editing and management
Arguably the most important part of qPCR experiments is to pre-process the raw data into shape for subsequent statistical analyses. The pre-processing steps need to be performed consistently in correct order and with confidence. GenEx Standard’s streamlined and user-friendly interface ensures mistake-free data handling. Intuitive and powerful presentation tools allow professional illustrations of even the most complex experimental designs.

Advanced cutting-edge data analysis
When you need more advanced analyses GenEx Enterprise is the product for you. Powerful enough to demonstrate feasibility it often proves sufficient for most users demands. Current features include parametric and non-parametric statistical tests, Hierarchical Cluster Analysis (HCA), Heatmap, Principal Component Analysis (PCA, and Artificial Neural Networks. New features are continuously added to GenEx with close attention to customers’ needs.

New features
Sample handling and samples individual biology often contribute to confounding experimental variability. By using the new nested ANOVA feature in GenEx version 5 user will be able to evaluate variance contributions from each step in the experimental procedure. With a good knowledge of the variance contributions, an appropriate distribution of experimental replicates can be selected to minimize confounding variance and maximize the power of the experimental design! For experiments with complex features, such as for example multifactorial diseases, analytical relationships and classifications may not readily be available. The support vector machine feature in the new version of GenEx is so easy to use that it will make this advanced supervised classification method easily available to novice users, while providing access to advanced parameters for experts.

Download a free GenEx 6.1 trail version => http://GenEx.gene-quantification.info


Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages



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