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Gene Quantification Newsletter
January 2015

is sponsored by

     
     

Streamlined and automated NGS workflow


 
  Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in quantitative real-time PCR (qPCR and RT-qPCR), which are compiled and summarised on the www.Gene-Quantification.info
The focus of this newsletter issue is:
   


 

Streaming portal

Join the new eConferences streaming webportal -- www.eConferences.de -- Amplify your knowledge!
This portal is dedicated to scientists from the community of qPCR, digital-PCR, NGS and Molecular Diagnostics. You’ll find here all the records from around 200 presentations held at qPCR & NGS Events in the past years. 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, including Android or iOS.

 
EXOSOMES

Exosomes in Molecular Diagnostics & Biomarker Discovery
Exosomes.Gene-Quantification.info

Exosomes are cell-derived vesicles that are present in many tissues and (perhaps) in all biological fluids, including blood, milk, urine, sweat and cell culture supernatant. The reported size of exosomes is between 30 and 100 nm in diameter. There are a lot of release mechanisms proposed. Exosomes are either released from the cell when cytoplasmic multivesicular bodies fuse with the plasma membrane or they are released directly from the plasma membrane. You will find interesting papers about the exosome biogenesis and the exosome release below!
It is becoming increasingly clear that exosomes have specialized functions and play a key role in inter-cellular communication, e.g. in the immune system, in cancer progression, in coagulation, in intercellular signaling, and in cellular waste management. Consequently, there is a growing interest in molecular diagnostic and in clinical application of exosomes. Exosomes can potentially be used for prognosis, therapy, and biomarkers for health or disease, especially in cancer progression and metastasis.
A lot of research is done in exosome purification and isolation, their size and content characterization, by quantifying surface- and intra-luminal proteins, membrane fatty acids, and the high concentrated regulative small RNA.

 
Exosome literature

REVIEW -- Exosomes: current knowledge of their composition, biological functions, and diagnostic and therapeutic potentials.
Vlassov AV, Magdaleno S, Setterquist R, Conrad R.
Biochim Biophys Acta. 2012 1820(7): 940-948

Extracellular vesicles -- exosomes, microvesicles, and friends.
Raposo G and Stoorvogel W
J Cell Biol. 2013 200(4): 373-383

Classification, functions, and clinical relevance of extracellular vesicles.
van der Pol E, Böing AN, Harrison P, Sturk A, Nieuwland R.
Pharmacol Rev. 2012 64(3): 676-705

ExoCarta 2012: database of exosomal proteins, RNA and lipids.
Mathivanan S, Fahner CJ, Reid GE, Simpson RJ.
Nucleic Acids Res. 2012 40 (Database issue): D1241-1244

EVpedia: an integrated database of high-throughput data for systemic analyses of extracellular vesicles.
Kim DK, Kang B, Kim OY, Choi DS, Lee J, Kim SR, Go G, Yoon YJ, Kim JH, Jang SC, Park KS, Choi EJ, Kim KP, Desiderio DM, Kim YK, Lötvall J, Hwang D, Gho YS.
J Extracell Vesicles. 2013: 2 -- eCollection 2013

Biogenesis, secretion, and intercellular interactions of exosomes and other extracellular vesicles.
Colombo M, Raposo G, Théry C.
Annu Rev Cell Dev Biol. 2014;30: 255-289

The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling.
Van Deun J, Mestdagh P, Sormunen R, Cocquyt V, Vermaelen K, Vandesompele J, Bracke M, De Wever O, Hendrix A.
J Extracell Vesicles. 2014 Sep 18;3 -- eCollection 2014.

Possibilities and limitations of current technologies for quantification of biological extracellular vesicles and synthetic mimics.
Maas SL, de Vrij J, van der Vlist EJ, Geragousian B, van Bloois L, Mastrobattista E, Schiffelers RM, Wauben MH, Broekman ML, Nolte-'t Hoen EN
J Control Release. 2014 200C: 87-96

Extracellular vesicle sizing and enumeration by nanoparticle tracking analysis.
Gardiner C, Ferreira YJ, Dragovic RA, Redman CW, Sargent IL.
J Extracell Vesicles. 2013 -- eCollection 2013

Quantitative and stoichiometric analysis of the microRNA content of exosomes.
Chevillet JR, Kang Q, Ruf IK, Briggs HA, Vojtech LN, Hughes SM, Cheng HH, Arroyo JD, Meredith EK, Gallichotte EN, Pogosova-Agadjanyan EL, Morrissey C, Stirewalt DL, Hladik F, Yu EY, Higano CS, Tewari M
Proc Natl Acad Sci U S A. 2014 111(41): 14888-14893

Therapeutic potential of extracellular vesicles.
Merino AM, Hoogduijn MJ, Borras FE, Franquesa M
Front Immunol. 2014 Dec 19;5: 658

... and much more Exosomes.Gene-Quantification.info

 

Register and submit your abstract NOW
for
qPCR & NGS 2015

Registration.qPCR-NGS-2015.net

 

 

 

 

 

 

 

 

 

Register and submit your abstract NOW
for
qPCR & NGS 2015

Registration.qPCR-NGS-2015.net

Call for Talk and Poster abstracts!
Register now for the symposium in March 2015


qPCR & NGS 2015 Event
"Advanced Molecular Diagnostics for Biomarker Discovery"

7th international qPCR & NGS Event -- Symposium & Industrial Exhibition & Application Workshops
23-27 March 2015
TUM School of Life Sciences
Technical University of Munich, Freising-Weihenstephan, Germany
www.qPCR-NGS-2015.net

The great international interest in the previous qPCR & NGS Events from 2004 till 2013 with a constant audience of more than 500 participants from all over the world motivates repeating the success next year in March 2015. We broaden our focus in genomics applications from quantitative RT-PCR, over digital PCR to the latest Next Generation Sequencing technologies. The date for the 7th International qPCR Symposium & Exhibition & Application Workshops is from the 23rd to the 27th March 2015. Parallel to the scientific symposium an industrial exhibition will take place where around 35-40 international companies will be presenting their newest qPCR, dPCR and NGS services and technologies. The symposium will be followed by various qPCR & NGS Workshops taking place March 26th and 27th powered by TATAA Biocenter, Bio-Rad, Qiagen, Genomatix and other leaders in the field.
Event location is the central lecture hall complex and the foyer at TUM (Technical University of Munich) in Freising Weihenstephan, Germany. The TUM and the Biotech region around Munich are part of the largest Biotech cluster in Europe, located close to the Munich airport (MUC) directly in the heart of Bavaria. Event location on Google maps  http://goo.gl/maps/3p3gx

The focus of the qPCR & NGS 2015 Event is "Advanced Molecular Diagnostics for Biomarker Discovery"

The symposium is based on around 60-70 lectures and 100 posters presented by international recognised experts in their application fields. The emphasis will be on unbiased, didactic and scientific information exchange. One third of the talks will be presented by invited speakers, one third of the speakers will be selected from the submitted abstracts and one third will be given to qPCR and NGS company R&D representatives. Various poster sessions will be held in parallel in a separate poster exhibition hall. All scientific contributions will be published in an abstract book (qPCR & NGS 2015 Proceedings incl. ISBN). All talks will be recorded and made public in autumn 2015 via the www.eConferences.de streaming platform together with around 200 talks from qPCR 2010 onwards.

Leading academic researchers and industrial contributors in the field will participate in the symposium, which will be an arena for fruitful discussions between researchers of different backgrounds. The Symposium Talks, Poster Sessions, Industrial Exhibition and associated qPCR & NGS Application Workshops offer an overview of the present knowledge and future developments in qPCR, next generation sequencing and gene expression measurement technology and its wide applications in research.

As usual the qPCR & NGS Event is structured in three parts:

   1. Symposium & Poster Sessions, taking place March 23 - 25   Sessions.qPCR-NGS-2015.net
   2. Industrial Exhibition with around 40 companies, taking place March 23 - 25   Exhibition.qPCR-NGS-2015.net
   3. qPCR & NGS Application Workshops, taking place March 26 - 27    Workshops.qPCR-NGS-2015.net

Follow our promotion trailer on YouTube => www.youtube.com/watch?v=44nJ43gzXJQ
Up to now confirmed speakers => Talks.qPCR-NGS-2015.net
Download the latest event flyer => Event-announcement.qPCR-NGS-2015.net 

Symposium Talk & Poster Sessions:

    * Main topic:   Advanced Molecular Diagnostics
    * Main topic:   Biomarker Discovery
    * Main topic:   Next Generation Sequencing (NGS)
       - NGS overview talks - information technology in the era of NGS
       - Pre NGS - sample prep & setup & library generation
       - NGS - new sequencing technologies (e.g. single molecule and pore sequencing)
       - NGS - data analysis (data management, mapping, alignment algorithms, data de novo assembly)
       - NGS - diagnostic applications
    * MicroGenomics & Single-cells diagnostics
    * Circulating Nucleic Acids
    * Molecular Diagnostics in Agriculture, Veterinary Medicine, Food & Environmental Science
    * MIQE & QM & Standardisation strategies in molecular diagnostics
    * Digital PCR  &  Nano-fluidics
    * Non-coding RNAs -- microRNA, small RNAs, long non-coding RNAs
    * qPCR Data Analysis -- BioStatistics & BioInformatics

Register for the symposium and the workshops => Registration.qPCR-NGS-2015.net
View our previous talks and the event trailer on our streaming server -- www.eConferences.de

 
 

NEW Journal -- "Biomolecular Detection and Quantification" -- Call for submissions

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.

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.

Benefits of publishing open access with Elsevier's Biomolecular Detection and Quantification - www.journals.elsevier.com/biomolecular-detection-and-quantification/

  • Peer-reviewed journal indexed by Scopus and supporting ORCID and Crossref to help maintain your publication record.
  • A renowned and respected editorial team with extensive knowledge of your research field. BDQ was established by a group of scientists based on their experience developing and publishing the Minimum Information for Publication of Quantitative Real-Time (and Digital) PCR Experiments (the MIQE and digital MIQE guidelines).
  • Reaching key audiences with 10 million active users per month using our publishing platform ScienceDirect.
  • Choice of user licenses so authors can decide how best to publish open access.
  • A discount on the publication fee for a limited time.

For more information about publishing Open Access with Elsevier, including funding body arrangements, institutional agreements and more, visit: www.elsevier.com/openaccess

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:
real-time PCR data analysis software
 

GenEx 6 available - The most powerful tool for complex qPCR data analysis
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. Download GenEx User Guide

TATAA Biocenter, Europe´s leading provider of genomic services using quantitative real-time PCR (qPCR), and MultiD Analyses, Europe’s prime software developer for the analysis of multivariate data, release GenEx version 6 for accurate analysis of qPCR data compliant with current Clinical Laboratory Standards Institute (CLSI) guidelines.

The new analyses in GenEx 6 include: Estimating PCR efficiency, testing for outliers, testing linear model, estimating dynamic range, estimating random error, estimating limit of detection, estimating limit of quantification, estimating concentrations of unknowns, evaluation of precision, and verification of precision. For all estimates confidence intervals are calculated.
Additional new features include: Transcript distribution for single cell analysis, Survival Analysis, Receiver Operator Characteristics (ROC), Wizard for ProSeek protein analysis, and reader for 3DGene microRNA analysis.

View our GenEx webpage and download a FREE GenEx 6 trial version => GenEx.Gene-Quantification.info

Join all GenEx talks by Prof. Mikael Kubista held at recent qPCR & NGS Events => www.eConferences.de/multid/

 

Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages

 

   

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