MIQE qPCR
& dPCR How to apply the MIQE
guidelines - a visual, interactive and
practical qPCR & dPCR guide
5th Edition (20th
February 2022)
Editors: Afif M. Abdel Nour &
Michael W. Pfaffl
ISBN 9783000488061
Please let us know, if you want to
participate with an own chapter in the next
6th edition of the MIQE qPCR &
dPCR iBook, contact us via
iBook@bioMCC.com
New
book chapters in 5th eds:
Chapter 14 Development of a high-throughput
data analysis method for evaluating
quantitative real-time PCR (qPCR)
assays
by Gregory C. Patton, Ph.D., Andrew N.
Gray, Ph.D., Nathan A. Tanner, Ph.D.,
Janine G. Borgaro, Ph.D., Yan Xu, Ph.D.,
Julie F. Menin, M.S. & Nicole M.
Nichols, Ph.D., New England Biolabs,
Inc.
Quantitative real-time PCR (qPCR), first
demonstrated by Higuchi and colleagues
(Higuchi et al., 1992), is an essential
molecular biology technique for
detecting and quantifying nucleic acids
and a mainstay of molecular diagnostics
workflows. Workflow simplicity and
advances in instrumentation now permit
sizeable quantities of data to be
generated rapidly, with 96, 384, or even
1536 reactions in a single qPCR
experiment. These experiments require
thoughtful design and analysis to
capture all relevant information, such
that accurate and appropriate
conclusions can be drawn.
We sought to develop a suite of general
use qPCR reagents that maintained
performance across various targets and
workflow parameters to simplify
downstream assay design complexity. This
development project involved repeated
data collection on a series of test
panels, each containing multiple
targets. Target were chosen to represent
parameters that have been shown to
impact assay performance, including
variations in primers (e.g., length, GC
content, location) and targets (e.g.,
length, GC content, transcript
abundance). Consistent with MIQE
guidelines, standard curves were used to
evaluate test panel assay performance,
but after reviewing efficiency,
reproducibility and non-template
controls from numerous experiments, it
became clear that a more scalable
approach to data analysis and
visualization was required to better
understand how changes in reagent
composition impacted performance. To
compare various amplicon panels over
multiple qPCR runs, instruments,
reagents and conditions, a
high-throughput data analysis method
termed “dots in boxes” was developed.
The output of this analysis captures key
assay characteristics, including those
highlighted in MIQE guidelines, as a
single data point for each qPCR target.
This method of analysis permits multiple
targets and conditions to be compared in
a single graph, allowing concise
visualization and rapid evaluation of
overall experimental success.
Chapter 20 Digital Microfluidic PCR in
QIAcuity Nanoplates
Kevin Matthaei, Christina Goebel,
Michael Bussmann, Gerald Schock, Afif
Abdel Nour, Andreas Missel; QIAGEN GmbH
QIAcuity systems are designed to
determine absolute amounts of target DNA
in a sample using a digital PCR (dPCR)
approach.
Digital PCR uses the procedure of
end-point PCR but splits the PCR
reaction into many single partitions in
which the template is randomly
distributed across all available
partitions. After PCR, the target
molecule is detected by measuring the
fluorescence – of either
sequence-specific DNA probes or
intercalating dyes – in all positive
partitions. As the template is
distributed randomly, Poisson statistics
can be used to calculate the amount of
target DNA per positive partition. The
total amount of target DNA in all
partitions of a well is then calculated
by multiplying the amount of target DNA
per partition with the number of
positive partitions. Measurement of
target concentration is determined based
on the volume in all analysable
partitions, i.e., partitions filled with
reaction mix, as identified by a
fluorescent dye present in the reaction
mix itself. Absolute quantification by
dPCR eliminates the need for standard
curves to determine amounts of target
DNA in a given sample.
Aside from absolute quantification, the
QIAcuity Software Suite provides
analysis modules for mutation detection,
genome editing analysis, copy number
variation (CNV), and gene expression
analysis.
MIQE & qPCR iBook How to apply the MIQE
guidelines - a visual, interactive and
practical qPCR guide
4th Edition (8th
June 2020)
Editors: Afif M. Abdel Nour &
Michael W. Pfaffl
ISBN 9783000488061
Please let us know, if you want to
participate with an own application or
chapter in the MIQE & qPCR iBook,
contact us via iBook@bioMCC.com
_______________________
Editorial for 4th edition June 2020
The success story of the qPCR and dPCR
MIQE guidelines is continuing!
Editorial for 4th edition published in
June 2020
by Afif M. Abdel Nour & Michael W.
Pfaffl
Yes the story is continuing! More
and more researchers, biological
journals, academic and commercial
institutions worldwide, are supporting
the MIQE guidelines. The very high
recitation record of Scopus and Google
Scholar documents this. As for June
2020, we count multiple thousand
citations for the qPCR MIQE guideline (7.350 by Scopus and
9.800 by Google Scholar) as well
as for the digital MIQE guideline (370 by Scopus and 460
by Google Scholar). Hence, the
qPCR and dPCR MIQE guidelines are a
worldwide standardisation success story,
which are driven forward by scientific
validity and credibility in the PCR
community.
The present 4th edition of the MIQE
& qPCR iBook will push the ‘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. Since the 2nd
edition in July 2016, we provided an
additional MIQE & qPCR eBook
version, which is readable on any eBook
reader device (ePub file). This leaded
to more than 4.800 extra downloads of
the MIQE & qPCR iBook and eBook from
over 40 countries worldwide.
Our goal for the 4th edition is to
update the existing content by new hot
topics, and to create an overall fancy
interactive tool, by interfacing
scientific publications with educating
pictures, videos and scientific talks.
The editors implemented the following
new chapters:
“ddPCR –
droplet digital PCR”
authored by Afif Abdel Nour
"Reproducible
and Sensitive Assays using 3-
and 6-colour Crystal Digital
PCR™ for Detecting Point
Mutations in Human Breast
Cancer"authored
by scientists from Stilla
Technologie
"The influence
of plastic consumables on qPCR"
authored by application specialists
by Eppendorf
In summary, we are proud
to present a selection of international
highly recognized authors from the
academic field and from industrial
research, presenting their latest
research applications. The described
qPCR and dPCR methods and applications
are tightly linked to the MIQE context,
and show it clearly based on educational
questionnaires or interactive ‘how to
do’ instruction sheets. The at-hand MIQE
& qPCR iBook & eBook 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.
The editors hope you like our
explanatory, interactive and educational
iBook, eBook and ePub concept, showing
the advantages of the MIQE guidelines in
an easy and understandable way. The
proper application and recommendation
mentioned in that publication should
guarantee the successful qPCR or dPCR
application in the lab, and will help
authors, reviewers, editors, and
researchers to evaluate the quality of
the presented publication.
The editors Afif M. Abdel Nour & Michael
W. Pfaffl
MIQE &
qPCR iBook How to apply the MIQE
guidelines - a visual, interactive and
practical qPCR guide
3rd Edition (12th
July 2019)
Editors: Afif M. Abdel Nour &
Michael W. Pfaffl
ISBN 9783000488061 Free
download via iTunes or Apple Books
-- https://books.apple.com/de/book/MIQE-qPCR/id993276375 An ePub version will
follow asap, early in 2020 :-) 2nd
Editions is still available
published October 2017 --
Download
ePub Version for any eBook
reader Please let us know, if
you want to participate with an own
application or chapter in the MIQE &
qPCR iBook, contact us via
iBook@bioMCC.com
MIQE & qPCR 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
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
PCR 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
New Chapters in
2nd edition:
Editorial
Reverse Transcription
qPCR Assay validation
Quality control in
qPCR
MIQE & qPCR iBook
How to apply the MIQE guidelines - a
visual, interactive and practical qPCR
guide
1st
edition
published 11th May 2015
Editors: Afif M. Abdel Nour &
Michael W. Pfaffl
ISBN 9783000488061
Throughout
the
past 30 years Polymerase Chain Reaction
(PCR) has proven to be the most powerful
technique in a scientist toolbox. Only
few techniques had a comparable success
story like PCR. This iBook will guide
you in better practicing in your
laboratory thanks to the MIQE guideline.
MIQE &
qPCR iBook – a digital publication:
How making the MIQE guidelines
easier to follow.
Afif M. Abdel Nour &
Michael W. Pfaffl
Presentation at qPCR & NGS 2015
Symposium -- http://www.eConferences.de/MIQE-qPCR-iBook/
Chapters in 1st
edition:
Preface
Introduction
& The history of MIQE
Quantification
strategies
RNA quality
control
qPCR
oligonucleotides / Primer
design software
qPCR
instrumentation
Selection of
reference
genes
Data analysis
& statistics
MIQE compliant
qPCR workflow control
MIQE guidelines
and microRNA
Digital PCR
Applications and Assays
MIQE compliance
using qPCR arrays
MIQE
translations & online
applications
Credits &
Imprint
Afif Abdel Nour
& Michael W. Pfaffl
Stephen Bustin
et al.
MW Pfaffl
Eva Schmidt et
al.
James Flynn et
al.
Nick Newton et
al.
Philip
Zimmermann et al.
Mikael Kubista,
Amin Forootan et al.
M Hren, K
Zupancic, T Berto et al.
Ditte Andreasen,
et al.
Yann Jouvenot
& Viresh Patel
Greg Shipley
Afif Abdel Nour
Afif Abdel Nour
& Michael W. Pfaffl
Please
let us know, if you want to
participate with an own
application or chapter in the
MIQE & qPCR iBook. Contact
us via iBook@bioMCC.com
an iTunes eBook
series
Definitive qPCR edited
by Stephen Bustin
About the qPCR Expert
Series
This constitutes a series of books that
are up-to-date and easily affordable for
students and filled with honest opinions
about qPCR initially, but expanding to
deal with other molecular techniques.
Each technique is placed into its
historical context and the books explain
why certain procedures are carried out
the way they are, and identify the
critical issues that determine the
success or failure of an experimental
procedure. Electronic media are ideal
for this purpose, as update can be
issued within minutes of a new
instrument, protocol, enzyme or method
becoming available. From the reader’s
point of view, the fact that this update
is going to be free means that he/she
will always have the latest information
at his/her finger tips with the added
security that the information has been
vetted and verified prior to being
included in the e-book.
Conventional publishing has two big
disadvantages:
the time from completing the
writing of a book to it being
published can be a long one. In an
area as fast-moving as molecular
biology, this means that concepts,
protocols and instruments may be
well past their sell-by date by the
time a book appears.
academic publications are
very expensive and certainly beyond
the financial reach of many students
and post-doctoral researchers,
particularly in developing
countries. Whatever the reason for
the high prices, they mean that the
individuals most in need of advice
find it difficult to obtain.
Furthermore, many peer-reviewed
journals focussing on techniques are
not freely accessible, posing
further problems for advice seekers.
The Expert Series breaks down each
technique into its constituent parts and
provides exhaustive information about
that sub section. So if someone is
interested in qPCR in general, without
feeling the need to explore this
technology in depth, they can buy the
Basic Principles, which will give them
all the information they require but not
get bogged down in detail about which
analysis method is the best the use
under what circumstances. Conversely,
someone already au fait with the topic
might be more interested in Assay
Optimisation and obtain all the relevant
information from that volume.
Each book will be issued in two formats:
iBooks that can be purchased through
Apple's iTunes store in around 50
countries as well as in a PDF format,
which can be bought in any country
around the world using a secure site and
credit card payment.
This volume deals with the
practical steps required to
characterise, optimise and validate a
qPCR assay. It deals with all aspects of
laboratory organisation, instruments,
pipettes, plasticware and reagents as
well as
providing protocols for
optimisation of annealing temperatures,
primer concentration and determining
assay efficiency. The 320 pages are
richly illustrated with examples, tips,
explanations and all information is
hyperlinked to provide access to the
huge amount
of information that is
available online, but not always
found in obvious places.
This book will be invaluable to anyone
wanting to design, validate or trouble
shoot qPCR assays. Its easily accessible
language takes the reader through the
complex steps that make up a successful
qPCR assay and will result, it is hoped,
in data that are accurate, robust and
biologically relevant.
This book provides a detailed insight
into the principles of the real-time
quantitative polymerase chain reaction
(qPCR). The narrative places the
protocols, reagents and instruments into
their historical and scientific contexts
and provides a detailed explanation of
the concepts that have made this
technology the enabling molecular
technology par excellence. The different
chapters describe the background to
oligonucleotide synthesis, DNA
polymerases, trace the route from
endpoint to real-time PCR and explain
the basics of fluorescence and
instrumentation. The book then describes
the various chemistries used in qPCR in
individual chapters dealing with
DNA-binding reporters,
primer/fluorochrome combination as well
as structured and unstructured probes.
The final chapter deals with MIQE and
describes the events that led to its
realisation. An appendix lists reagents,
provides a summary of all qPCR
instruments on the market to-day and
lists a wide range of web-based
resources. The book is illustrated
throughout with detailed diagrammes and
is targeted both at aspiring as well as
experienced users of this ubiquitous
technology.
Contents
1. PCR
1.1. Introduction
1.2. Oligonucleotide
synthesis
1.3. Reagents
2. Real-time PCR
2.1. The road to qPCR
2.2. Fluorescence
2.3. Instrumentation
3. Chemistries
3.1. DNA-binding
reporters
3.2.
Primer/fluorophore combinations
3.3. Unstructured
probes
3.4. Allosteric toggle
probes
4. MIQE
4.1. Measles virus and
gut pathology
4.2. The case for MIQE
5. Appendices
This book provides an exhaustive guide
to assay design for quantitative
real-time PCR. The book describes the
basic concepts important for amplicon
selection and primer and probe design.
There are step-by-step examples for
designing probe-based and SYBR Green
assays targeting mRNA and fungal
pathogens using several popular design
programs. These are then exposed to
extensive in silico analysis to identify
the optimum amplicon/primer/probe
combination. There is a detailed
trouble-shooting guide, a listing of
instruments, reagents and additional
information available on the internet,
all with hyperlinks. In addition,
Keynote presentations (iBook format
only) summarise the main concepts of
standard assay design, multiplex assay
design and explaining the rationale
behind MIQE, the guidelines for qPCR
publication transparency.
Contents:
1. Introduction
1.1. Why assay design
is important
1.2. Why design your
own assay?
1.3. Tools for assay
design
2. Amplicons
2.1. Amplicon
selection – mRNA
2.2. Amplicon
selection – pathogen
3. Primers and Probes
3.1. Design – mRNA
3.2. In silico
validation – mRNA
3.3. Design and in
silico validation-pathogen
3.4. Multiplex PCR
4. What can go wrong?
5. Appendices
5.1. Design principles
and comparisons
5.2. Reagents &
Instrumentation
5.3. MIQE
5.4. Web-based
resources
The assessment of nucleic acid purity
and integrity is one of the essential
steps preceding microarray, qPCR and
sequencing experiments. Both quality
parameters have direct effects on the
reliability, accuracy and
biological/clinical relevance of results
obtained using these molecular
techniques.
This book discusses both provides a
detailed overview of the important
evaluation criteria that make up
successful nucleic acid quality control,
with the main focus on RNA. It traces
the historical context of nucleic acid
extraction, describes prokaryotic and
eukaryotic in vivo RNA degradation
mechanisms, summarises information about
the different instruments used to assess
nucleic acid quality and analyses RNA
and DNA purity as well as RNA integrity
in detail. The appendices contain a
general illustration of some of the
molecular methods that rely on high
quality nucleic acids and a set of
figures making the case for MIQE, the
guidelines laid out for qPCR assay
design and publication.
The book is extensively referenced and
hyperlinked to additional sources of
information. It is ideal for anyone
wanting to find all relevant information
about nucleic acid quality assessment in
one convenient place.
Contents
1. The Basics
1.1. Introduction
1.2. Nucleic acid
extraction
1.3. RNA and a little
DNA
2. Instruments
2.1. Nano
Spectrophotometers
2.2. Lab on a chip
2.3. Agilent
Bioanalyser 2100
2.4. BioRad Experion
2.5. Agilent 2200
tapestation et al
3. Quality
3.1. Introduction
3.2. Inhibition
3.3. Integrity
4. Appendices
4.1. Protocols
4.2. In vitro
measurements
4.3. MIQE
4.4. Reagents and
Instrumentation
4.5. Web-based
information
New releases -
Available over the next few months
(~January, May and August 2013)
Our high level PCR books bring
together expert international authors
under the skilled editorship of
leading scientists to produce
state-of-the-art compendiums of
current research. Aimed at the
research scientist, graduate student,
medical reseacher and other
professionals, these books are highly
recommended for all PCR laboratories.
Every PCR, microbiology and bioscience
library should have a copy of each of
the following books. http://www.horizonpress.com/pcrbooks
Edited
by:Jim
Huggett and Justin O'Grady Published:2014 Hardback:ISBN
978-1-908230-41-6
£159, $319.Ebook:ISBN
978-1-908230-64-5 £159, $319 The
editors of this book have
commissioned an excellent series of
chapters representing two key
molecular diagnostic areas: cancer
and infectious diseases. The cancer
section deals with the challenges in
identifying genetic, epigenetic and
transcriptomic biomarkers. The
infectious disease section describes
the current clinical applications of
molecular diagnostics for the
detection of viral, bacterial and
fungal pathogens as well as an
example of the use of molecular
diagnostics outside the clinic
environment. A cautionary tale
describing what can go wrong when
molecular methods are applied
incorrectly is also provided and
makes fascinating reading. A
substantial component of the book is
dedicated to the process of
translating a preclinical test to
the bedside and describes the
progress in the near patient
point-of-care molecular diagnostics
market. This is a fundamental
consideration for successful
translation of diagnostics tests
from bench to bedside and is crucial
for molecular diagnostics to have an
impact on patient care. The final
chapter offers a prediction of
future trends in the molecular
diagnostics of infectious diseases.
This volume is essential reading for
anyone involved in the development
or application of molecular
diagnostics and is recommended for
all clinical diagnostics
laboratories.read
more ...
Edited
by:Nick
A. Saunders and Martin A. Lee Published:2013 Hardback:ISBN
978-1-908230-22-5
£159, $319.Ebook:ISBN
978-1-908230-87-4 £159, $319 This
essential manual provides both the
novice and experienced user with an
invaluable reference to a wide-range
of real-time PCR technologies and
applications and provides an
overview of the theory of this
increasingly important technique.
Renowned international authors
present detailed technical insights
into the underlying principles,
methods and practice of real-time
PCR. The initial chapters cover the
important aspects of real-time PCR
including choosing an instrument and
probe system, set-up, nucleic acid
synthesis, sample extraction
controls, and validation and data
analysis. Further chapters provide a
comprehensive overview of important
real-time PCR methodologies such as
quantification, expression analysis
and mutation detection. This is
complemented by the final chapters,
which address the application of
real-time PCR to diagnosis of
infectious diseases, biodefence,
veterinary science, food
authenticity and molecular
haplotyping. This timely and
authoritative volume serves both as
a basic introduction to real-time
PCR and as a source of current
trends and applications for those
already familiar with the
technology. The editors also aim to
stimulate readers of all levels to
develop their own innovative
approaches to real-time PCR. An
essential book for all laboratories
using PCR.read
more ...
Edited
by: David Rodriguez-Lazaro Published:
2013 ISBN:
978-1-908230-15-7 Price:
GB £159 or US $319 Written
by
experts in the field, this book is
an indispensable manual for
scientists in the food industry.
The first section provides an
introduction to real-time PCR,
discusses the use of PCR
diagnostics in food science,
describes the principles and
methods of sample preparation, and
covers the verification and
control of PCR procedures. The
eleven chapters in the second
section cover the use of real-time
PCR to detect various pathogens
including Salmonella, Listeria,
E. coli, Campylobacter,
Yersinia, Staphylococcus,
Clostridium, viruses and
parasites. Also included is a
chapter on the standardisation of
real-time PCR methods in food
microbiology. In the final section
authors cover the use of real-time
PCR for the analysis of
genetically modified organisms,
food allergens and for
identification of animal or plant
species. An invaluable book for
anyone involved in food
microbiology or the detection of
foodborne pathogens and a
recommended volume for all
microbiology laboratories.
read more ...
Edited
by: Martin Filion Published:
2012 ISBN:
978-1-908230-01-0 Price:
GB £159 or US $319 Written
by
experts in the field and aimed
specifically at microbiologists,
this volume describes and explains
the most important aspects of
current qPCR strategies,
instrumentation and software.
Renowned authors cover the
application of qPCR technology in
various areas of applied
microbiology and comment on future
trends. Topics covered include
instrumentation, fluorescent
chemistries, quantification
strategies, data analysis
software, environmental
microbiology, water microbiology,
food microbiology, gene expression
studies, validation of microbial
microarray data and future trends
in qPCR technology. The editor and
authors have produced an
outstanding book that will be
invaluable for all
microbiologists. A recommended
book for all microbiology
laboratories.
read more ...
Edited
by: Suzanne Kennedy and Nick
Oswald Published:
2011 ISBN:
978-1-904455-72-1 Price:
GB £159 or US $319 This book
discusses the strategies for preparing
effective controls and standards for
PCR, when they should be employed and
how to interpret the information they
provide. It highlights the
significance of optimization for
efficiency, precision and sensitivity
of PCR methodology and provides
essential guidance on how to
troubleshoot inefficient reactions.
Experts in PCR describe design and
optimization techniques, discuss the
use of appropriate controls, explain
the significance of standard curves
and explore the principles and
strategies required for effective
troubleshooting. Authors highlight the
importance of sample preparation and
quality, primer design, controlling
inhibitors, avoiding amplicon and
environmental contamination,
optimizing reagent quality and
concentration, and modifying the
thermal cycling protocol for optimal
sensitivity and specificity. In
addition, specific chapters discuss
the history of PCR, the choice of
instrumentation, the applications of
PCR in metagenomics, high resolution
melting analysis, the MIQE guidelines,
and PCR at the microliter scale. The
strategies, tips and advice contained
in this concise volume enable the
scientist to optimize and effectively
troubleshoot a wide range of
techniques including PCR, reverse
transcriptase PCR, real-time PCR and
quantitative PCR. An essential book
for anyone using PCR technology.
read more ...
PCR technology is based
on a simple principle; an enzymatic
reaction that increases the initial
amount of nucleic acids. This method
makes it possible to detect specific
mRNA transcripts in any biological
sample. Performing RT-PCR analysis
does not only comprehend this
experimental PCR step. Following the
whole workflow of a RT-PCR
quantitative analysis, it starts with
the sampling step, followed by nucleic
acid extraction and stabilization,
cDNA synthesis and finally the qPCR
where the mRNA quantification takes
place. Problems arise when
optimization of the experimental work
flow becomes necessary because of high
technical variations. The PCR reaction
itself is a quite stable reaction with
reproducibility between 2-8%.
Therefore the source of experimental
variances can often be found in the
pre-PCR analytical steps. Usually this
is neglected and optimization is done
for PCR reaction only. In this chapter
– RT-PCR optimization strategies - the
whole workflow of RT-PCR experiment
will be discussed, because the
identification of the source of
variability is only possible following
error accumulation in every single
step. Reliable data can be created
when the technical variance caused by
the experimental steps is kept as low
as possible. In this chapter many
recommendations to decrease the
technical variance can be found.
Edited
by: Keith E. Herold and
Avraham Rasooly Published:
2009 ISBN:
978-1-904455-47-9 Price:
GB £159 or US $319 The
editors of this book have brought
together expert authors from many
countries to produce a
comprehensive volume focusing on
the applications of LOC technology
in the biomedical and life
sciences. The first section
includes chapters on LOC
biomolecule separation. Separation
of biomolecules is an important
element of various clinical
laboratories and is required for
many "down stream" analytical
applications. Various
electrophoresis and liquid
chromatography applications for
proteins and DNA are described as
well as methods for cell
separation, with an emphasis on
blood cell separation, which have
many important clinical
applications. The second part
includes chapters on analysis and
manipulation technologies. Authors
describe protein, genetic (mainly
PCR) and transcriptome analysis
with examples from research and
clinical applications, as well as
cell manipulation and analysis
including cell viability analysis
and microorganism capturing. A
skillful selection of topics of
exceptional importance to current
science ensures that this book
will be of major value to a wide
range of molecular biologists,
clinical scientists,
microbiologists, biochemists and
anyone interested in LOC
technology or developing
applications for LOC devices.
read more ...
Edited
by:Keith
E. Herold and Avraham Rasooly Published:2009
ISBN:978-1-904455-46-2 Price:GB
£159 or US $319 This
invaluable book describes the latest
methods and novel technologies being
developed for the fabrication of LOC
devices and new approaches for fluid
control and manipulation. Expert
authors from around the world
describe and discuss the newest
technologies for the prototyping of
devices, including replication and
direct machining methods of
fabrication. Part I of the book
covers all aspects of fabrication
including laser micromachining,
silicon and glass micromachining,
PMMA and COC microfluidic
substrates, and xurography (LOC
prototyping with a cutting plotter).
Part II focuses on fluid control and
manipulation for LOC systems. As
well as providing examples of the
use of pumps in microfluidics,
topics covered include
electrokinetic pumping
(electroosmois), electrochemical
pumping and electrowetting, and the
fabrication of a microchip for rapid
polymerase chain reaction (PCR).
This comprehensive volume presents
the current technologies in the
field and includes theoretical and
technical information to enable both
the understanding of the technology
and the reproduction of experiments.
The book aims to help the reader to
understand current LOC technologies,
to perform similar experiments, to
design new LOC systems and to
develop new methodologies and
applications. An essential book for
biologists and clinicians using LOC
technology and developing
applications and also for
engineering, chemical and physical
science researchers developing
analytical technologies. The book
will also be useful as a teaching
tool for bioengineering, biomedical
engineering and biology.read more ...
Edited
by:Julie
Logan, Kirstin Edwards and Nick
Saunders Published:2009
ISBN:978-1-904455-39-4 Price:GB
£159 or US $319 This
essential manual presents a
comprehensive guide to the most
up-to-date technologies and
applications as well as providing an
overview of the theory of this
increasingly important technique.
Renowned experts in the field
describe and discuss the latest PCR
platforms, fluorescent chemistries,
validation software, data analysis,
and internal andexternal
controls. This timely and
authoritative volume also discusses
a wide range of RT-PCR applications
including: clinical diagnostics,
biodefense, RNA expression studies,
validation of array data, mutation
detection, food authenticity and
legislation, NASBA, molecular
halotyping, and much more. An
essential book for all laboratories
using PCR.read more ...
Edited by: Ian M.
Mackay Published:
2007 ISBN:
978-1-904455-18-9 Price:
GB £159 or US $319 The
editor and authors have produced
an excellent book that will be
extremely useful for all
microbiologists. A recommended
book for all microbiology
laboratories.
read more ...
Author: Michael
L. Altshuler Published:
2006 ISBN:
978-1-904455-07-3 Price:
GB £30 or US $60 A
unique PCR troubleshooting guide
that is an essential companion
for anyone who uses the
polymerase chain reaction
technique. Aimed at a reader
with some experience in PCR the
book discusses the many and
varied problems encountered with
PCR together with tips, advice
and procedures to obviate rather
than overcome the PCR problems.
Written in the language of the
laboratory with a little humour
and a down-to-earth approach,
the book is easy to read and
understand. If you fail at PCR,
consult this book! The advice in
these pages is invaluable and is
the sort of advice that is not
usually found elsewhere. In the
words of the author, remember
that there are many other things
in life than PCR ... for
example, isothermal DNA
amplification.
read more ...
This book is a comprehensive manual to
allow both the novice researcher and
the expert to set up and carry out
quantitative PCR assays from scratch.
However, this book also sets out to
explain as many features of qPCR as
possible, provide alternative
viewpoints, methods, and aims to
simulate the researchers into
generating, interpreting, and
publishing data that are reproducible,
reliable, and biologically meaningful.
Contents http://www.iul-press.us/Books/BBT05-PCR/content-pcr.html
Real-time
PCR is based on the conventional
principles of PCR and, with the
simple shift of emphasis from the
end-product to the whole course of
the PCR process, has established
itself as the most sensitive and
specific quantitative PCR method.
Real-time PCR is, like any other
modern method in molecular
genetics, expanding, with
potential applications even in
proteomics.
With
a
variety of detection
chemistries, an increasing
number of platforms, multiple
choices for analytical methods
and the jargon emerging along
with these developments,
real-time PCR is facing the risk
of becoming an intimidating
method, especially for
beginners. Real-Time PCR
provides the basics, explains
how they are exploited to run a
real-time PCR assay, how the
assays are run and where these
assays are informative in real
life. It doesn't cover every
aspect of real-time PCR, but
addresses the most practical
aspects of the techniques with
the emphasis on 'how to do it in
the laboratory'. Keeping with
the spirit of the Advanced
Methods Series, most chapters
provide an experimental protocol
as an example of a specific
assay.
The
BIOS
Advanced Methods series is
intended for advanced
undergraduates, graduate
students and established
research scientists. Titles in
this series are designed to
cover current important areas of
research in life sciences, and
include both theoretical
background and detailed
protocols. The aim is to give
researchers sufficient theory,
supported by references, to take
the given protocols and adapt
them to their particular
experimental systems.
Early, rapid and
sensitive veterinary molecular
diagnostics - real time PCR
applications
Erika Pestana, Sandor Belak, Adama
Diallo, John R. Crowther, Gerrit J.
Viljoen
2010, 310 pages, Englisch
Springer Netherland
This book gives a comprehensive
account of the practical aspects of
Real time PCR and its application to
veterinary diagnostic laboratories.
The optimisation of assays to help
diagnose livestock diseases is
stressed and exemplified through
assembling standard operating
procedures from many laboratory
sources. Theoretical aspects of PCR
are dealt with as well as quality
control features necessary to maintain
an assured testing system. The book
will be helpful to all scientists
involved in diagnostic applications of
molecular techniques, but is designed
primarily to offer developing country
scientists a collection of working
methods in a single source. The book
is an adjunct to the Molecular
Diagnostic PCR Handbook published in
2005.
The invention of the polymerase chain
reaction (PCR) won the Nobel Prize in
Chemistry in 1994 and remains one of
the most important scientific
discoveries of the twentieth century.
More than 50,000 researchers in the
United States use PCR replication
technology, and yet a book has not
been published on the subject in more
than ten years. In this book, Dr.
Stephen A. Bustin, a world-renowned
PCR expert, examines in detail the
latest innovations and the overall
impact of PCR on many areas of
molecular research. The book contains
personal reflections, opinions, and
comments by leading authorities on the
many applications of the PCR and how
this technology has revolutionized
their respective areas of interest.
This book conveys the ways in which
PCR has overcome many obstacles in
life science and clinical research and
also charts the PCR's development from
time-consuming, low throughput,
non-quantitative procedure to today's
rapid, high throughput, quantitative
super method.
PCR Technology:
Current Innovations, Third Edition
Editors:
Tania Nolan, Sigma Life Science Custom
Products, Haverhill, UK
Stephen A. Bustin, Anglia Ruskin
University, Cambridge, UK
Published: June 13, 2013 by CRC Press
Content:457 Pages | 161 Illustrations
ISBN 9781439848050
Summary
PCR’s simplicity as a molecular
technique is, in some ways,
responsible for the huge amount of
innovation that surrounds it, as
researchers continually think of new
ways to tweak, adapt, and re-formulate
concepts and applications. PCR
Technology: Current Innovations, Third
Edition is a collection of novel
methods, insights, and points of view
that provides a critical and timely
reference point for anyone wishing to
use this technology.
Features:
Covers all aspects of PCR
and real-time PCR
Uses an accessible writing
style appealing to a broad range
of readers
Examines buffer and
oligonucleotide components
Discusses assay design and
instruments
Presents a plethora of
applications and innovations
Supplies detailed "how to"
information and protocols, along
with tips and tricks from
recognized experts
Topics in this forward-thinking
volume include:
The purification and
handling of PCR templates
The effect of the
manufacture and purification of
the oligonucleotide on PCR
behavior
Optimum buffer composition
Probe options
The design and optimization
of qPCR assays
Issues surrounding the
development and refinement of
instrumentation
Effective controls to
protect against uncertainties due
to reaction variability
Covering all aspects of PCR
and real-time PCR, the book
contains detailed protocols that
make it suitable as both a
reference and an instruction
manual. Each chapter presents
detailed guidelines as well as
helpful hints and tips supplied by
authors who are recognized experts
in their fields. In addition to
descriptions of current technology
and best practices, the book also
provides information about new
developments in the PCR arena.
Quantitative Real-Time PCR: Methods
and Protocols focuses on different
applications of qPCR ranging from
microbiological detections (both viral
and bacterial) to pathological
applications. Several chapters deal
with quality issues which regard the
quality of starting material, the
knowledge of the minimal information
required to both perform an assay and
to set the experimental plan, while
the others focus on translational
medicine applications that are ordered
following an approximate logical order
of their medical application. The last
part of the book gives you an idea of
an emerging digital PCR technique that
is a unique qPCR approach for
measuring nucleic acid, particularly
suited for low level detection and to
develop non-invasive diagnosis.
Written for the Methods in Molecular
Biology series, most chapters include
introductions to their respective
topics, lists of the necessary
materials and reagents, step-by-step,
laboratory protocols and tips on
troubleshooting and avoiding known
pitfalls.
Practical and authoritative,
Quantitative Real-Time PCR: Methods
and Protocols aims to aid researchers
seeking to devise new qPCR-based
approaches related to his or her area
of investigation.
RNA
quality control is a crucial step in
guaranteeing integer nondegraded RNA
and receiving meaningful results in
gene expression profiling
experiments, using micro-array,
RT-qPCR (Reverse-Transcription
quantitative PCR), or
Next-Generation-Sequencing by
RNA-Seq or small-RNA Seq. Therefore,
assessment of RNA integrity and
purity is very essential prior to
gene expression analysis of sample
RNA to ensure the accuracy of any
downstream applications. RNA samples
should be nondegraded or fragmented
and free of protein, genomic DNA,
nucleases, and enzymatic inhibitors.
Herein we describe the current
state-of-the-art RNA quality
assessment by combining UV/Vis
spectrophotometry and microfl uidic
capillary electrophoresis.
Protein
coding RNAs are
posttranscriptionally regulated by
microRNAs, a class of small
noncoding RNAs. Insights in
messenger RNA (mRNA) and microRNA
(miRNA) regulatory interactions
facilitate the understanding of fi
ne-tuning of gene expression and
might allow better estimation of
protein synthesis. However, in
silico predictions of mRNA–microRNA
interactions do not take into
account the specifi c transcriptomic
status of the biological system and
are biased by false positives. One
possible solution to predict rather
reliable mRNA-miRNA relations in the
specifi c biological context is to
integrate real mRNA and miRNA
transcriptomic data as well as in
silico target predictions. This
chapter addresses the workfl ow and
methods one can apply for expression
profi ling and the integrative
analysis of mRNA and miRNA data, as
well as how to analyze and interpret
results, and how to build up models
of posttranscriptional regulatory
networks.
This
volume explores microRNA function in
a wide array of human disorders,
providing a clinical basis for
precision medicine and personalized
therapies using these molecules. The
twenty-one chapters, all authored by
internationally-renowned experts,
open with an introduction
contextualizing microRNA
manipulation within today’s
initiatives towards precision
medicine. The following chapters
explore the clinical role of
microRNAs in the diagnosis and
treatment of metabolic and
cardiovascular disorders, focusing
on mitochondrial fitness, arterial
hypertension, cardiovascular
remodeling, cerebrovascular disease,
pulmonary hypertension, diabetic
kidney disease, and kidney
transplantation. The subsequent
chapters discuss the importance of
microRNAs in the wound healing
process and in skin disease, in the
pathogenesis of allergy, in human
ovulation, and in infection. The
book concludes with chapters
which outline the emerging role of
microRNAS in doping and detail
microRNA profiling.
MicroRNAs
(miRNAs)
are RNA molecules, conserved by
evolution, that regulate gene
expressions and their recent
discovery is revolutionising both
basic biomedical research and drug
discovery. Expression levels of
MiRNAs have been found to vary
between tissues and with
developmental stages and hence
evaluation of the global expression
of miRNAs potentially provides
opportunities to identify regulatory
points for many different biological
processes. This wide-ranging
reference work, written by leading
experts from both academia and
industry, will be an invaluable
resource for all those wishing to
use miRNA techniques in their own
research, from graduate students,
post-docs and researchers in
academia to those working in R&D
in biotechnology and pharmaceutical
companies who need to understand
this emerging technology. From the
discovery of miRNAs and their
functions to their detection and
role in disease biology, this volume
uniquely integrates the basic
science with industry application
towards drug validation, diagnostic
and therapeutic development.
Forewords by: Sidney Altman, Yale
University, Winner of the Nobel
Prize in Chemistry, 1989 and Victor
R. Ambros, Dartmouth Medical School,
Co-discoverer of MicroRNAs.
MicroRNAs
in Medicine Editor(s):
Charles H. Lawrie Published
Online: 1 Nov 2013, Online
ISBN: 9781118300312
MicroRNAs
in Medicine provides an access point
into the current literature on
microRNA for both scientists and
clinicians, with an up-to-date look
at what is happening in the emerging
field of microRNAs and their
relevance to medicine. Each chapter
is a comprehensive review, with
descriptions of the latest microRNA
research written by international
leaders in their field. Opening with
an introduction to what microRNAs
are and how they function, the book
goes on to explore the role of
microRNAs in normal physiological
functions, infectious diseases,
non-infectious diseases, cancer,
circulating microRNAs as
non-invasive biomarkers, and finally
their potential as novel
therapeutics.
Including
background
information on the field as well as
reviews of the latest research
breakthroughs, MicroRNAs in Medicine
is a one-stop source of information
to satisfy the specialists and
non-specialists alike, appealing to
students, researchers, and
clinicians interested in
understanding the potential of
microRNAs in medicine and research.
Since
their discovery, microRNAs have
revolutionized cell biology and
completely changed the way we view
the regulation of gene expression.
These short regulating RNAs are now
known to be involved in all cellular
and developmental pathways and all
major types of disease so far
investigated. This Nature Reprint
Collection presents some of the
recent advances in moving microRNAs
from basic research into the clinic
both as diagnostic biomarkers and
therapeutic targets.
Read the collection and learn
more about:
microRNA
qPCR profiling to identify
minimally invasive biomarkers in
biofluids
The
prognostic importance of microRNA
in situ hybridization against
miR-21
The
potential of microRNAs as
therapeutic targets in
cardiovascular disease, diabetes
and epilepsy
MicroRNA
and Cancer -- Methods and
Protocols
Humana Press 2011
Edited by Wei Wu; Institute for
Biocomplexity and Informatics,
Department of Biological Science,
University of Calgary, Calgary, AB,
Canada
The
discovery of microRNAs (miRNAs or
miRs) heralded a new and an exciting
era in biology and started a new
chapter in human gene regulation.
The miRNAs, a class of small
endogenous noncoding RNAs (~22 nt),
fine tune the gene expression at the
posttranscriptional level through
mainly binding 3′-UTR of mRNAs. They
are involved in stem cell
self-renewal, cellular development,
differentiation, proliferation, and
apoptosis. Small miRNAs have big
impacts in cancer development. Among
the many miRNAs, a subset of miRNAs
were identified as regulators of
neoplastic transformation, tumor
progression, invasion, and
metastasis as well as
tumor-initiating cells (cancer stem
cells). The widespread deregulation
of miRNomes in diverse cancers when
compared to normal tissues have been
unveiled. The oncomirs (oncogenic
miRNAs), TSmiRs (tumor suppressive
miRNAs), and MetastamiRs (miRNAs
associated to cancer metastasis)
comprise an importantpart of the
cancer genome and confer pivotal
diagnostic and prognostic
significance. Moreover, cancer
associated miRNAs are proving
worthwhile for developing effective
cancer biomarkers for individualized
medicine and potential therapeutic
targets. This book provides the
latest and foremost miRNAs knowledge
of cancer research applications from
scientists all over the world. It is
organized in two parts: the first
part begins with a general
introduction of miRNA biogenesis
which is followed by chapters on the
computational prediction of new
microRNAs in cancer, the innovative
technologies for modulating miRNAs
of interests, and an overview of
miRNA-based therapeutic approaches
for cancer treatment. The second
part of the book provides
experimental and computational
procedures in miRNA detection with
diverse techniques, miRNA library construction,
epigenetic
regulation of miNRAs, microRNA::mRNA
regulatory networks predicted
with
computational analysis in cancer
cells or tissues, and the principle
of designing the
miRNA-mimics for miRNA activation.
These chapters have been written for
practical use in
laboratories for graduate students,
postdoctoral fellows, and scientists
in cancer research.
The contributors have shared their
most valuable experiences in the
translation of miRNA
knowledge into cancer research. MicroRNA
is a fast growing field, and
microRNA knowledge is a pivotal
element of cancer biology.
An individual miRNA interferes with
a broad range of mRNAs; conversely,
a single mRNA could
be targeted by a variety of miRNAs.
The complexity of miRNA::mRNA
interaction is
far-reaching and a bit beyond our
understanding to date. This book is
expected to provide the
basic
principles of experimental and
computational methods for microRNA
study in cancer research
and provide a firm grounding for
those who wish to develop further
applications. I am
especially indebted to Prof. Shu
Zheng and Dr. Suzanne D. Conzen for
giving me the
opportunity to gain substantial
experience in cancer research. I
would like to thank Dr.
Gunglin
Li for his kind support. Without
their confidence and continuous
support, many things
would not have been possible. I also
thank Prof. John Walker for his
encouragement. Finally,
I
am grateful to all of the
contributing authors for providing
such high quality
manuscripts.
The
last decade has seen a dramatic
development in the fi eld of micro
RNAs (miRNAs). Starting with a small
set of small noncoding regulatory
RNAs in D. melanogaster and C.
elegans miRNAs are now regarded as
important regulatory components in
many eukaryotic species including
humans. The number of reported
miRNAs exceeds 1,000 and many of
these miRNAs have been implicated in
important biological processes and
human diseases. In this volume of
“Methods in Molecular Biology” we
concentrate on the pathway of
microRNA maturation. After its
synthesis, the primary miRNA
transcript (pri-miRNA) is cleaved by
indonuclease called Drosha to yield
the precursor miRNA (pre-miRNA).
After being transported to the
cytoplasm, the latter is further
cleaved by another nuclease called
Dicer to yield the mature
double-stranded miRNA. This mature
miRNA consists of the active guide
strand which remains bound to the
miRNA effector complex, whereas the
passenger strand is degraded. These
few relatively simple steps
(although the cellular machinery
promoting this pathway is rather
complex) are common to most miRNAs
and thus are highly important to
study. In this book we concentrate
on three important aspects of this
maturation pathway: First of all, we
give an overview over the current
knowledge of the pathway of miRNA
maturation (Chapter 1 ) and how this
pathway relates to human disease
(Chapter 2 ). In the third review,
established and novel approaches to
manipulate miRNA maturation and
activity are described. During the
last 5 years many correlations
between the levels of certain miRNAs
and various human malignancies have
been identifi ed, and in some cases
the causative role of certain miRNAs
in disease formation has been shown.
Specifi c miRNAs can regulate
certain proteins causing or
preventing disease formation. These
miRNA–disease correlations call for
easy for easy and reliable methods
for quantifying specifi c miRNA
species from biological samples, a
topic which is only partially
covered in this book. While miRNAs
today have somehow lost their
“exotic” touch with many standard
methods established in laboratories
around the world, novel methods with
the potential to expand the view on
miRNAs are currently being
developed. Such innovation can arise
from improving existing methods or
by the development of completely new
methods allowing for addressing
questions other than previous ones.
In this book, established methods
(qRT-PCR of miRNA maturation
components,qRT-PCR of miRNAs) are
completed with fl uorescent and
nonfl uorescent methods for
homogenous assays of Dicer-mediated
miRNA maturation or an in vivo assay
for Drosha activity. Since miRNAs
appear to be emerging drug targets,
anti-miRs are already commercially
available. Less common is the use of
biologically stable PNA as anti-miRs
or even miRNA maturation inhibitors,
doubtlessly adding to the arsenal of
current oligonucleotide approaches
to manipulate miRNA activity. Apart
from oligonucleotides affecting
miRNA activity, which are already
under clinical investigation, there
is a huge interest in finding small
molecules with equivalent effects.
Specially adapted luciferase assays
have proven as powerful tools for
identifying candidate small molecule
miRNA effectors. I am convinced that
the collection of methods of this
book is suitable to widen the view
on miRNA as biological mediators and
potential drug targets and thus
stimulate futurer esearch in this
highly dynamic and thrilling topic.
Nucleic
Acids Research Methods
Each of the collections on this page
is a category-specific archive of
Methods published in NAR from
1999 to the present. The numbers in
parentheses show the number of
articles currently in each collection. http://nar.oxfordjournals.org/collections/