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Gene Quantification Newsletter
April 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), 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.

 
 

Microvesicles and Exosomes in Molecular Diagnostics
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. 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.

 
 
Optimising the mircrovesicle and exosome isolation

Standardization of sample collection, isolation and analysis methods in extracellular vesicle research.
Witwer KW, Buzás EI, Bemis LT, Bora A, Lässer C, Lötvall J, Nolte-'t Hoen EN, Piper MG, Sivaraman S, Skog J, Théry C, Wauben MH, Hochberg F.
J Extracell Vesicles. 2013 May 27;2

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.

Methods of isolating extracellular vesicles impact down-stream analyses of their cargoes.
Douglas D. Taylor & Sahil Shah
Methods (2015)

Comparison of ultracentrifugation, density gradient separation, and immunoaffinity capture methods for isolating human colon cancer cell line LIM1863-derived exosomes.
Tauro BJ, Greening DW, Mathias RA, Ji H, Mathivanan S, Scott AM, Simpson RJ.
Methods. 2012 Feb;56(2): 293-304

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

Single-step isolation of extracellular vesicles by size-exclusion chromatography.
Böing AN, van der Pol E, Grootemaat AE, Coumans FA, Sturk A, Nieuwland R
J Extracell Vesicles. 2014 8;3 -- eCollection 2014.

Current methods for the isolation of extracellular vesicles.
Momen-Heravi F, Balaj L, Alian S, Mantel PY, Halleck AE, Trachtenberg AJ, Soria CE, Oquin S, Bonebreak CM, Saracoglu E, Skog J, Kuo WP.
Biol Chem. 2013 Oct;394(10): 1253-1262

Methods for extracellular vesicles isolation in a hospital setting.
Sáenz-Cuesta M, Arbelaiz A, Oregi A, Irizar H, Osorio-Querejeta I, Muñoz-Culla M, Banales JM, Falcón-Pérez JM, Olascoaga J, Otaegui D.
Front Immunol. 2015 Feb 13;6: 50

... ... more papers here Exosomes.Gene-Quantification.info

 
Exosome Function and Physiology

Microvesicles as mediators of intercellular communication in cancer -- the emerging science of cellular 'debris'.
Lee TH, D'Asti E, Magnus N, Al-Nedawi K, Meehan B, Rak J.
Semin Immunopathol. 2011 Sep;33(5): 455-467

Secreted microRNAs -- a new form of intercellular communication.
Chen X, Liang H, Zhang J, Zen K, Zhang CY.
Trends Cell Biol. 2012 22(3):125-32

Extracellular vesicle-depleted fetal bovine and human sera have reduced capacity to support cell growth.
Eitan E, Zhang S, Witwer KW, Mattson MP
J Extracell Vesicles. 2015 Mar 26;4: 26373 -- eCollection 2015

Extracellular vesicles -- potential roles in regenerative medicine.
De Jong OG, Van Balkom BW, Schiffelers RM, Bouten CV, Verhaar MC
Front Immunol. 2014 Dec 3;5: 608

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

The Trojan exosome hypothesis.
Gould SJ, Booth AM, Hildreth JE.
Proc Natl Acad Sci U S A. 2003 100(19): 10592-10297

... ... more papers here Exosomes.Gene-Quantification.info

 
 

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 3D Gene 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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