qPCR NEWS - MAy 2006 - Quantitative real-time RT-PCR and microRNA

qPCR NEWSLETTER - May 2006


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:

- microRNA and quantitative real-time RT-PCR
- recent qPCR review
- BabelFish translation service

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Platform - The reference in qPCR!

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A lot of qPCR companies and independent institutions participate in our
qPCR information platform. On the company sub-pages new real-time
cyclers, consumables, new released kits and detection chemistries, as
well as innovative amplification technologies are presented. Links from
the sub-pages will lead you to the related product pages at the
respective homepage. You are welcome to join our Academic & Industrial
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For further info please contact
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Definition

In genetics, a miRNA (micro-RNA) is a form of single-stranded RNA which
is typically 20-25 nucleotides long, and is thought to regulate the
expression of other genes. miRNAs are RNA genes which are transcribed
from DNA, but are not translated into protein. The DNA sequence that
codes for an miRNA gene is longer than the miRNA. This DNA sequence
includes the miRNA sequence and an approximate reverse complement. When
this DNA sequence is transcribed into a single-stranded RNA molecule,
the miRNA sequence and its reverse-complement base pair to form a
double stranded RNA hairpin loop; this forms a primary miRNA structure
(pri-miRNA). In animals, the nuclear enzyme Drosha cleaves the base of
the hairpin to form pre-miRNA. The pre-miRNA molecule is then actively
transported out of the nucleus into the cytoplasm by Exportin 5, a
carrier protein. The Dicer enzyme cuts 20-25 nucleotides from the base
of the hairpin to release the mature miRNA. In plants, which lack
Drosha homologues, pri- and pre-miRNA processing by Dicer probably
takes place in the nucleus, and mature miRNA duplexes are exported to
the cytosol by Exportin 5.

The function of miRNAs appears to be in gene regulation. For that
purpose, a miRNA is complementary to a part of one or more messenger
RNAs (mRNAs). Animal miRNAs are usually complementary to a site in the
3' UTR whereas plant miRNAs are usually complementary to coding regions
of mRNAs. The annealing of the miRNA to the mRNA then inhibits protein
translation, but sometimes facilitates cleavage of the mRNA. This is
thought to be the primary mode of action of plant miRNAs. In such
cases, the formation of the double-stranded RNA through the binding of
the miRNA triggers the degradation of the mRNA transcript through a
process similar to RNA interference (RNAi), though in other cases it is
believed that the miRNA complex blocks the protein translation
machinery or otherwise prevents protein translation without causing the
mRNA to be degraded. miRNAs may also target methylation of genomic
sites which correspond to targeted mRNAs. miRNAs function in
association with a complement of proteins collectively termed the
miRNP.

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microRNA

non-coding RNAs / DataBase
micro RNA talks
Quantitative real-time RT-PCR applications for miRNA quantification
Human MicroRNA targets
miRU: Plant microRNA Potential Target Finder
Cancer genomics: Small RNAs with big impacts
miRBase - the home of microRNA data

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Quantitative real-time RT-PCR applications for miRNA quantification:

- Facile means for quantifying microRNA expression by real-time PCR.
- Human MicroRNA targets
- siRNAs can function as miRNAs.
- Prediction and validation of microRNAs and their targets.
- A single-molecule method for the quantitation of microRNA gene
expression.
- A high-throughput method to monitor the expression of microRNA
precursors.
- MicroRNA maturation: stepwise processing and subcellular
localization.
- MicroRNA genes are transcribed by RNA polymerase II.
- miRU: an automated plant miRNA target prediction server.
- Real-time quantification of microRNAs by stem-loop RT-PCR.
- Profiling microRNA expression using sensitive cDNA probes and filter
arrays.
- miRNPs: a novel class of ribonucleoproteins containing numerous
microRNAs.
- MicroRNA expression profiling of single whole embryonic stem cells.
- Simple, quantitative primer-extension PCR assay for direct monitoring
of microRNAs and short-interfering RNAs.
- siRNA and miRNA: an insight into RISCs.
- RNA silencing in plants / DNA events: An RNA microcosm

[Only registered users see links. ]

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NEW qPCR REVIEWs

The real-time polymerase chain reaction.
Kubista M, Andrade JM, Bengtsson M, Forootan A, Jonak J, Lind K,
Sindelka R,
Sjoback R, Sjogreen B, Strombom L, Stahlberg A, Zoric N.; Mol Aspects
Med. 2006 (2-3): 95-125.

SPUD: a quantitative PCR assay for the detection of inhibitors in
nucleic acid
preparations.
Nolan T, Hands RE, Ogunkolade W, Bustin SA.; Anal Biochem. 2006 351(2):
308-310

Real-time reverse transcription PCR and the detection of occult disease
in colorectal cancer.
Bustin SA, Mueller R. Mol Aspects Med. 2006 27(2-3): 192-223

Faster quantitative real-time PCR protocols may lose sensitivity and
show increased variability. Hilscher C, Vahrson W, Dittmer DP. Nucleic
Acids Res. 2005 33(21): e182.

Comparison of in vitro and in vivo reference genes for internal
standardization ofreal-time PCR data.
Gilsbach R, Kouta M, Bonisch H, Bruss M. Biotechniques. 2006 40(2):
173-177

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TRANSLATOR - DIRECTORY

An Alta Vista BabelFish translation service of our English written Gene
Quantification homepage is NOW available for all sub-pages.

Translation of the page content can be performed from English to
Chinese, German, Japanese, Korean, French, Italian, Portuguese and
Spanish.

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A lot of links and keywords are listed in our DIRECTORY

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Upcoming Events World-wide academic and commercial qPCR Events are
listed at [Only registered users see links. ]

Symposia, Meetings, Conferences, Workshops, Seminars, Online-Seminars,
qPCR Education Program.....etc.
submit your qPCR event here [Only registered users see links. ]


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TATAA Biocenter Germany qPCR Application workshops:

[Only registered users see links. ]

TATAA Biocenter have found that the worldwide demand for training in
the field of quantitative real-time PCR (qPCR) is huge. To coordinate
this we aim to arrange practical courses, e.g. 3-day Core Module and
1-day or 2-day Biostatistics Module:

The basic qPCR Core Module contains three workshop days:
First workshop day will be directed to people planning or considering
using qPCR in their research and also users not yet fully familiar will
quantitative PCR. Second day targets more advanced users and people
concentrating on different quantification strategies. The third day
focuses on aspects in sample preparation and reverse transcription. The
additional qPCR Biostatistics Module explains statistics applicable to
qPCR and teaches how to use statistics to interpret qPCR gene
expression data, and classify samples based on qPCR expression
profiling.
Courses contain both, theoretical seminars and practical hands-on
training with experienced supervision. Practical training will be
performed on three different real-time PCR cyclers, using multiple
detection chemistries. The Biostatistics Module is further based on
computer-based demonstrations. Please bring your own Laptop !
qPCR courses are held in regularly in Göteborg, Sweden and in
Freising-Weihenstephan, Germany (near Munich, very close to the Munich
Airport - MUC). Depending on the occasion different prices may apply.
Also different course modules are available on the different occasions.
Further customized workshops and specialized trainings will be held as
well across Europe and world-wide. TATAA Biocenter Germany courses are
held in cooperation with the Institute of Physiology, located at the
Technical University of Munich, in Freising-Weihenstephan.

Workshop details => 3-days core module
Download => short qPCR basic course description at the TATAA Biocenter
Germany
Location => world-wide access to TATAA Biocenter Germany in Freising
Weihenstephan
Download Map => local access to TATAA Biocenter Germany (map of
Freising-Weihenstephan)
Lab View => some photos of our lab equipment
Registration => TATAA Biocenter Workshops (Germany and world-wide)

Course Occasions 2006:

16th - 19th May 2006 ( fully booked )
27th - 30th June 2006 ( still availibility )
25th - 29th September 2006 ( still availibility )
23rd - 27th October 2006 ( still availibility )
20th - 24th November 2006 ( still availibility )

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Please send the qPCR NEWS to further scientists and friends who are
interested in qPCR and in our Academic & Industrial Information
Platform for qPCR.

best regards

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages
[Only registered users see links. ]

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