qPCR NEWS - May 2010 - focus on transcriptional noise in single-cells Dear researcher, dear Gene Quantification page reader, Our newsletter informs about the latest news in quantitative real-time PCR (qPCR and qRT-PCR), which are compiled and summarised on the Gene Quantification homepage. The focus of this newsletter issue is: - UPDATE - single-cell qPCR sub-domain with focus on transcriptional noise =3D> http://singlecell.gene-quantification.info - UPDATE - MIQE press & media review =3D> http://MIQE-PRESS.gene-quanti= fication.info - International qPCR 2010 symposia =3D> http://EVENTS.gene-quantification= ..info - qPCR Application Workshops - and more ... ... ... ---------------------------------------------------------------------------= ----- single-cell qPCR Single-cell molecular-biology is a relatively new scientific branch in biology. The first single-cell analysis were involved in the characterization of mitochondrial DNA in 1988. Single- cell DNA analysis, in particular genomic DNA, is important and may be informative in the analysis of genetics of cell clonality, genetic anticipation and single-cell DNA polymorphisms. Nowadays for most scientists the quantitative transcriptomics in a single-cell is much more important, and the analytical method of choice is the quantitative real-time RT-PCR. The relative abundance of single mRNAs and their up- or down-regulation in a single cell, compared to their neighbour cells, is the goal. The need for quantitative single-cell mRNA analysis is evident given the vast cellular heterogeneity of all tissue cells and the inability of conventional RNA methods, like northern blotting, RNAse protection assay or classical block RT-PCR, to distinguish individual cellular contributions to mRNA abundance differences. ---------------------------------------------------------------------------= ----- The focus of the updated papers in on transcriptional noise in single cells: http://singlecell.gene-quantification.info/ - Stochastic gene expression in a single cell - Nature, nurture, or chance: stochastic gene expression and its consequences - Noise in Gene Expression: Origins, Consequences, and Control - Use of high throughput sequencing to observe genome dynamics at a single cell level - Transcriptional noise and cellular heterogeneity in mammalian macrophages - Stochastic gene expression during cell differentiation: order from disorder? - Resolving cell population heterogeneity: real-time PCR for simultaneous multiplexed gene detection in multiple single-cell samples - Circulating tumour cells in clinical practice: Methods of detection and possible characterization - Quantitative transcription factor analysis of undifferentiated single human embryonic stem cells - Single cell analysis of transcriptional activation dynamics - Single-cell gene expression profiling using reverse transcription quantitative real-time PCR - Spatial expression profiles in the Xenopus laevis oocytes measured with qPCR tomography - Quantitative RT-PCR gene expression analysis of laser microdissected tissue samples - Laser capture microdissection and single-cell RT-PCR without RNA purification http://www.gene-quantification.de/singlecell3.html ---------------------------------------------------------------------------= ----- MIQE - media & press review Efforts to standardize qPCR data meets mixed reviews 05/25/2010 Uduak Grace Thomas; BioTechniques One year ago, an international team of researchers proposed guidelines for the publication of real-time PCR experiments. Since then, there has been mixed response from the scientific community. Uduak Thomas investigates the reasons behind the resistance. Read more =3D> http://MIQE-press.gene-quantification.info Routine lab method's accuracy called into question Catherine Shaffer Nature Medicine Vol 16, page 349 (2010) In 2002, four years after first sparking public controversy over whether the measles, mumps and rubella vaccine causes autism, Andrew Wakefield reported a possible molecular mechanism for the connection. He claimed that a form of irritable bowel disease, which he called autistic enterocolitis, was triggered by the measles virus (Molec. Pathol. 55, 84=9690, 2002). That finding, however, was based on a =93defective experimental technique,=94 Stephen Bustin, a molecular biologist at Barts and the London School of Medicine and Dentistry, told a US federal court in 2007. The problem: Wakefield had incorrectly applied the common laboratory protocol known as quantitative real-time polymerase chain reaction (qPCR) to come to his conclusions. Read more =3D> http://MIQE-press.gene-quantification.info Following MIQE Recommendations - EMBL Heidelberg, Germany Monday 5 July - Friday 9 July 2010 Since the early descriptions of the use of quantitative Real Time PCR, the technique has been adopted in almost every aspect of life science research and is increasingly used for clinical analysis. Over time protocols and strategies have been tried and tested, amended and developed such that there are currently several different approaches. Protocol variations are evident at each step of the RT-qPCR process, from sample acquisition to data analysis (e.g. sample QC, experimental design, assay design and validation, normalisation, biostatistical interpretation, reporting, etc). It is now apparent that these adaptations may result in differences in the final biological conclusion of the study. This workshop is based upon the MIQE guidelines. Each step of the RT- qPCR process will be discussed and protocol variations illustrated practically. The student will be instructed in best practice and acceptable alternative strategies. More events =3D> http://events.gene-quan= tification.info ---------------------------------------------------------------------------= ----- qPCR 2010 in Vienna International qPCR Symposium & Exhibition 7-9th April 2010 http://www.qpcr2010-vienna.net/ Topic: "The ongoing evolution of qPCR" 330 attendee from 37 contries and 39 international companies in the industrial exhibition participate at the event 7 - 9th April 2010 in Vienna. During the symposium the presented talks and slides were recorded in high sound quality and movie resolution and they will be made available as eConfernce qPCR 2010 on our streaming server eConference.qPCR2010-Vienna.net or http://eConference.bioeps.com Up to now you can listen to our eSeminar and eConference promotion trailer =3D> http://trailer.qPCR2010-Vienna.net All symposium participants have FREE access for a limted time to the recorded talks and to the updated online proceedings including all participants contact data. If you are interested to listen to the talks and presented slides you are welcome to register as USER in our ConfTool registration system We will inform upon the eConference is available! The talks by the plenary lecturer, selected invited academic and industrial speakers will be published in METHODS special qPCR Vol 50 issue 4 (April 2010) with the title =93The ongoing evolution of qPCR=94 =3D> TOC and HTML and PDFs Symposium sessions: MIQE and QM strategies in qPCR High throughput quantitative PCR =96 digital PCR HRM =96 High Resolution Melting - Epigenetics CNA - Circulating nucleic acids Single-cell qPCR RNAi - microRNA - siRNA Applications =96 miRNA normalisation qPCR BioStatistics & BioInformatics ---------------------------------------------------------------------------= ----- BioEPS GmbH - qPCR Application Workshops Life Science is still a growing sector and new methods and technologies are continously developed. Therefore permanent training and education becomes so important. With our specific course program we are offering a range of high- quality course modules, in cooperation with different companies to give a general and independent overview of existing qPCR technologies and systems. Our course issues are based on skilled know-how from own research studies and publications. Our aim is to point out a critical way of thinking to increase the quality and outcome of experimental data. All courses are held regularly in Freising-Weihenstephan, Germany, in German and English language. Further customized workshops and specialized trainings will be held as well across Europe and world-wide. Workshops are powered by BioEPS GmbH, located at the campus of the Technical University of Munich, in Freising-Weihenstephan, very close to the Munich Airport (MUC). For more information and registration, please see our web page =3D> http://workshops.gene-quantification.info Course Occasions 2010: 3-day qPCR Basic Module 2-day BioStatistics & Expression Profiling Module 3-day single-cell qPCR 2-day microRNA qPCR 1-day HRM 2-das qPCR-R data analysis NEW ! 1-day Project Management NEW ! 2-day Quality Management NEW ! Course dates 2010: 14 - 15 June 2010 (E) 2-day microRNA & qPCR (Mon.-Tue.) 12 - 14 July 2010 (E) 3-day qPCR Basic Module (Mon. - Wed.) 15 July 2010 (E) 1-day HRM Module (Thu.) 4 - 6 October 2010 (E) 3-day qPCR Basic Module (Mon. - Wed.) 7 October 2010 (E) 1-day HRM Module (Thu.) 11 - 12 October 2010 (E) 2-day qPC-R - data analysis using R packages (Mon.-Tue.) 18 - 20 October 2010 (E) 3-day single-cell & qPCR (Mon. - Wed.) 21 - 22 October 2010 (E) 2-day BioStatistics Module (Thu. - Fri.) 8 - 9 November 2010 (E) 2-day microRNA & qPCR (Mon.-Tue.) 29 November - 1 December 2010 (E) 3-day qPCR Basic Module (Mon. - Wed.) 2 - 3 December 2010 (E) 2-day BioStatistics Module (Thu. - Fri.) (E) Download course brochure 2010 =3D> http://www.gene-quantification.de/bioeps= -course-programm-2010.pdf Register here =3D> http://site.bioeps.com/index.php?option=3Dcom_seminar&It= emid=3D6 ---------------------------------------------------------------------------= ----- Forward Please send the qPCR NEWS to further scientists and friends who are interested in qPCR ! Best regards, Michael W. Pfaffl responsible Editor of the Gene Quantification Pages http://www.gene-quantification.info ---------------------------------------------------------------------------= ----- If this newsletter is not displayed correctly by your email client, please use following link: http://qPCRnews.gene-quantification.info/ The qPCR NEWS and the Gene Quantification Pages are educational sites with the only purpose of facilitating access to qPCR related information on the internet. The qPCR NEWS and the Gene Quantification Pages are edited by Michael W. Pfaffl. 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