NATURE METHODS
January 2010 Volume 7 Number 1, pp 1 - 85
Visit Nature Methods online to browse the journal.
Now available at http://links.ealert.nature.com/ctt?kn=165&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Please note that you need to be a subscriber to enjoy full text
access to Nature Methods online. To purchase a subscription,
please visit:
http://links.ealert.nature.com/ctt?kn=86&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Alternatively, to recommend a subscription to your library, please visit
http://links.ealert.nature.com/ctt?kn=52&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
=========================== ADVERTISEMENT ===========================
Are you a formulation scientist or material science engineer? We're looking for a formulation that binds biocides to surfaces that are exposed to an aqueous environment. Take your past experience and apply it here to win $20,000.
Challenge 8993161 - Biocide Formulation
http://links.ealert.nature.com/ctt?kn=208&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
=========================== ADVERTISEMENT ===========================
An Emergence & Convergence mini-symposium
Epigenetic Dynamics in the Immune System
San Antonio, TX, USA - February 19, 2010
This mini-symposium aims to foster interdisciplinary discussion, and to advance our understanding of the ways in which epigenetic factors exert broad influence over the immune system.
Application deadline: January 4, 2010
To apply today and for more information visit:
http://links.ealert.nature.com/ctt?kn=60&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
=====================================================================
----------------------
SPECIAL FEATURE
----------------------
Method of the Year 2009
Nature Methods' Method of the Year 2009 goes to induced pluripotency
for its potential for biological discovery. This series of
articles-and the related video-showcase how induced pluripotency
is coming into its own in 2009 as a tool for discovery in both basic
and disease biology and explore the incredible impact this area
promises to have in biological research. The Methods to Watch
feature provides a glimpse of future Methods of the Year and the
Reader's Choice shows methods nominated by readers and editors,
and the votes that they received.
http://links.ealert.nature.com/ctt?kn=169&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
----------------------
EDITORIAL
----------------------
Special feature: Method of the Year
Method of the Year 2009 p1
doi:10.1038/nmeth.f.294
The ability to return mature body cells to a pluripotent state has
wide-ranging potential as a tool for discovery in both disease and
basic biology.
http://links.ealert.nature.com/ctt?kn=111&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
----------------------
THIS MONTH
----------------------
The author file p3
doi:10.1038/nmeth0110-03
Supercharged SRM: synthetic peptides bring high-throughput
assays to targeted proteomics.
http://links.ealert.nature.com/ctt?kn=113&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
----------------------
CORRESPONDENCE
----------------------
A red-shifted Renilla luciferase for transient reporter-gene
expression pp5 - 6
Andreas Markus Loening, Anca Dragulescu-Andrasi and Sanjiv
Sam Gambhir
doi:10.1038/nmeth0110-05
http://links.ealert.nature.com/ctt?kn=110&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Restricted ethnic diversity in human embryonic stem cell
lines pp6 - 7
Louise C Laurent et al.
doi:10.1038/nmeth0110-06
http://links.ealert.nature.com/ctt?kn=66&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
----------------------
RESEARCH HIGHLIGHTS
----------------------
The mobile microscope p9
Daniel Evanko
doi:10.1038/nmeth0110-09
A miniature head-mounted two-photon microscope small enough
for a rat to carry allows researchers to visualize neuronal signaling
while the animal freely interacts with its environment.
http://links.ealert.nature.com/ctt?kn=68&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Bring on the promoters pp10 - 11
Nicole Rusk
doi:10.1038/nmeth0110-10a
High-throughput saturation mutagenesis determines the contribution
of each base in a core promoter to overall promoter strength.
http://links.ealert.nature.com/ctt?kn=71&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
The importance of being negative pp10 - 11
Allison Doerr
doi:10.1038/nmeth0110-10b
The Negatome is a database of non-interacting protein pairs that can
be used for training protein-protein interaction prediction
algorithms.
http://links.ealert.nature.com/ctt?kn=73&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
News in brief p11
doi:10.1038/nmeth0110-11
http://links.ealert.nature.com/ctt?kn=75&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Caught in action p12
Michael Eisenstein
doi:10.1038/nmeth0110-12
Screening reveals a chemical activator that triggers apoptosis by
locking inactive but dynamic proenzymes into a more active state,
suggesting a promising strategy for targeting proteases.
http://links.ealert.nature.com/ctt?kn=77&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
A family tree in a tumor p14
Monya Baker
doi:10.1038/nmeth0110-14
A new technique finds genomic subpopulations to indicate cancer
progression.
http://links.ealert.nature.com/ctt?kn=58&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
----------------------
NEWS FEATURE
----------------------
Special feature: Method of the Year
iPS cells: potent stuff pp17 - 19
Monya Baker
doi:10.1038/nmeth.f.281
Now that the generation of induced pluripotent stem cells is becoming
routine, researchers can get on to the more exciting prospect of
using the cells to make discoveries in disease and basic biology.
Monya Baker reports.
http://links.ealert.nature.com/ctt?kn=61&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
----------------------
PRIMER
----------------------
Special feature: Method of the Year
Primer: induced pluripotency pp20 - 21
Natalie de Souza
doi:10.1038/nmeth.f.293
A brief overview of methods for reprogramming to induced pluripotency
and of the properties of induced pluripotent stem cells.
http://links.ealert.nature.com/ctt?kn=62&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
----------------------
COMMENTARIES
----------------------
Special feature: Method of the Year
The mysteries of induced pluripotency: where will they
lead? pp22 - 24
Andras Nagy and Kristina Nagy
doi:10.1038/nmeth.f.292
The discovery that it is possible to render somatic cells pluripotent
by the exogenous expression of a set of transcription factors
provides an experimental model for studying the molecular nature
of cellular identity.
http://links.ealert.nature.com/ctt?kn=63&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Special feature: Method of the Year
Induced pluripotent stem cell technology for the study of human
disease pp25 - 27
Gabsang Lee and Lorenz Studer
doi:10.1038/nmeth.f.283
iPS cell technology makes patient- and disease-specific human
cells widely available. While technical challenges still remain,
the use of these tools will greatly expand our understanding
of human disease.
http://links.ealert.nature.com/ctt?kn=83&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Special feature: Method of the Year
Stem cell research policy and iPS cells pp28 - 33
Timothy Caulfield et al.
doi:10.1038/nmeth.f.282
The field of induced pluripotent stem cells (iPSCs) will be subject
to a wide range of laws and research ethics policies, many of
which exist as a result of the controversies associated with research
on human embryonic stem cells. Understanding this potentially
complex regulatory environment will help iPSC research move
forward and will inform future policy.
http://links.ealert.nature.com/ctt?kn=81&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
----------------------
METHODS TO WATCH
----------------------
Special feature: Method of the Year
Targeted proteomics p34
Allison Doerr
doi:10.1038/nmeth.f.284
Technology for sensitively and reproducibly detecting targeted
proteins by mass spectrometry picks up speed.
http://links.ealert.nature.com/ctt?kn=82&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Special feature: Method of the Year
Optical imaging of the native brain p34
Daniel Evanko
doi:10.1038/nmeth.f.285
Methodological developments are opening the functioning brain to
cellular-level investigation using light.
http://links.ealert.nature.com/ctt?kn=87&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Special feature: Method of the Year
Mapping genomes in 3D p35
Nicole Rusk
doi:10.1038/nmeth.f.286
Refinements in methods to uncover the higher-order structure of
the genome will allow functional insight into genomic architecture
at high resolution.
http://links.ealert.nature.com/ctt?kn=88&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Special feature: Method of the Year
Single-cell methods p35
Natalie de Souza
doi:10.1038/nmeth.f.287
The ability to study single cells will permit a better understanding
of cellular heterogeneity.
http://links.ealert.nature.com/ctt?kn=84&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Special feature: Method of the Year
Label-free microscopy p36
Daniel Evanko
doi:10.1038/nmeth.f.288
New methods to coax signals from unlabeled biological molecules
may finally fulfill the promise of practical label-free microscopy
with molecular specificity.
http://links.ealert.nature.com/ctt?kn=85&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Special feature: Method of the Year
High-throughput phenotyping p36
Natalie de Souza
doi:10.1038/nmeth.f.289
Automated methods to score phenotypes in model organisms continue
to develop and will permit previously inaccessible areas of biology
to be probed.
http://links.ealert.nature.com/ctt?kn=79&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Special feature: Method of the Year
Synthetic life p37
Allison Doerr
doi:10.1038/nmeth.f.290
Will new methods and an emerging understanding of the minimal
requirements for cellular life be sufficient to construct a synthetic
organism?
http://links.ealert.nature.com/ctt?kn=80&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Special feature: Method of the Year
A direct view of the fifth base p37
Nicole Rusk
doi:10.1038/nmeth.f.291
Will some single molecule sequencing strategies be able to deliver
on the promise of direct methyl cytosine sequencing?
http://links.ealert.nature.com/ctt?kn=78&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
----------------------
NEWS AND VIEWS
----------------------
Reduce, reuse, reprogram pp39 - 40
Thomas P Zwaka
doi:10.1038/nmeth0110-39
Mouse lines with inducible reprogramming factors expressed from
a single genomic locus will allow reprogramming studies in multiple
cell types and defined genetic backgrounds.
http://links.ealert.nature.com/ctt?kn=205&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Sorting cardiomyocytes: a simple solution after all? pp40 - 42
Christine Mummery
doi:10.1038/nmeth0110-40
Cardiomyocytes can be sorted to high purity upon staining them with
a dye that labels mitochondria. This permits the preparation of pure
populations of cardiomyocytes differentiated from stem cells.
http://links.ealert.nature.com/ctt?kn=181&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
----------------------
BRIEF COMMUNICATIONS
----------------------
High-throughput generation of selected reaction-monitoring assays
for proteins and proteomes pp43 - 46
Paola Picotti et al.
doi:10.1038/nmeth.1408
Selected reaction monitoring (SRM) is a powerful mass spectrometry
technology to reliably detect selected protein targets, even those at
very low abundance, but requires tedious assay development for
each protein of interest. High-throughput SRM assay development
is now possible by using crude synthetic peptide libraries without
purification to represent each protein target.
Abstract: http://links.ealert.nature.com/ctt?kn=180&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=185&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Chromatin profiling by directly sequencing small quantities of
immunoprecipitated DNA pp47 - 49
Alon Goren et al.
doi:10.1038/nmeth.1404
Single-molecule sequencing of poly(A)-tailed chromatin
immunoprecipitated DNA proves equal in sensitivity and accuracy
to amplification-based sequencing technologies and allows analysis
of samples sizes as small as 50 pg.
Abstract: http://links.ealert.nature.com/ctt?kn=184&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=187&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Floxin, a resource for genetically engineering mouse
ESCs pp50 - 52
Veena Singla et al.
doi:10.1038/nmeth.1406
An efficient system for the reversion and modification of mouse
gene trap alleles is presented. It is applicable to available
collections of gene trap embryonic stem cell lines.
Abstract: http://links.ealert.nature.com/ctt?kn=186&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=189&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
A reprogrammable mouse strain from gene-targeted embryonic stem
cells pp53 - 55
Matthias Stadtfeld, Nimet Maherali, Marti Borkent and Konrad
Hochedlinger
doi:10.1038/nmeth.1409
A mouse strain in which cellular reprogramming factors are expressed
from a defined genomic locus is presented. It will enable studies of
reprogramming in multiple cell types as well as facilitate
comparisons between induced pluripotent stem cells and embryonic
stem cells. Also in this issue, a paper by Carey et al. presents
related tools.
Abstract: http://links.ealert.nature.com/ctt?kn=188&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=176&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Single-gene transgenic mouse strains for reprogramming adult somatic
cells pp56 - 59
Bryce W Carey et al.
doi:10.1038/nmeth.1410
Mouse strains in which three or four cellular reprogramming factors
are expressed from a defined genomic locus are presented. They will
enable studies of reprogramming in multiple cell types as well as
facilitate comparisons between induced pluripotent stem cells and
embryonic stem cells. Also in this issue, a paper from Stadtfeld
et al. presents related tools.
Abstract: http://links.ealert.nature.com/ctt?kn=57&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=59&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
=========================== ADVERTISEMENT ===========================
Qualify today for your free subscription!
Ensure you are abreast of the most significant research by qualifying for your free subscription to Nature Methods.
To subscribe visit:
http://links.ealert.nature.com/ctt?kn=26&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
=====================================================================
----------------------
ARTICLES
----------------------
Nongenetic method for purifying stem cell-derived
cardiomyocytes pp61 - 66
Fumiyuki Hattori et al.
doi:10.1038/nmeth.1403
Staining with a mitochondrial dye permits high-purity isolation of
cardiomyocytes from embryonic and induced pluripotent stem cells
of several species, without genetic modification.
Abstract: http://links.ealert.nature.com/ctt?kn=74&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=76&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Engineering a polarity-sensitive biosensor for time-lapse imaging of
apoptotic processes and degeneration pp67 - 73
Yujin E Kim, Jeannie Chen, Jonah R Chan and Ralf Langen
doi:10.1038/nmeth.1405
A polarity-sensitive annexin-based biosensor called pSIVA becomes
strongly fluorescent only after reversibly binding to the plasma
membrane. pSIVA allows live-cell imaging of the apoptotic process
in degenerating neurons in vitro and in vivo.
Abstract: http://links.ealert.nature.com/ctt?kn=69&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=72&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Integrated analysis of receptor activation and downstream signaling
with EXTassays pp74 - 80
Anna Botvinnik, Sven P Wichert, Tobias M Fischer and Moritz J Rossner
doi:10.1038/nmeth.1407
By combining a protein complementation assay with a transcriptional
reporter assay based on short expressed oligonucleotide tags (EXTs),
the authors monitor tyrosine kinase receptor dimerization in
conjunction with effector recruitment and downstream signaling.
Abstract: http://links.ealert.nature.com/ctt?kn=65&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=67&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
----------------------
TECHNOLOGY FEATURE
----------------------
IPSCs: One cell to rule them all? pp81 - 85
Michael Eisenstein
doi:10.1038/nmeth0110-81
Rapid progress with induced pluripotent stem cells is bringing
scientists closer to understanding their strengths and weaknesses
as embryonic stem cell stand-ins.
http://links.ealert.nature.com/ctt?kn=64&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
=========================== ADVERTISEMENT ===========================
Nature Reprint Collection
Immuno-epigenetics
Epigenetic mechanisms are increasingly appreciated to have an important role in immune cell functional diversity and adaptability, and understanding these mechanisms holds considerable potential for revealing new opportunities to therapeutically modulate the immune response in a range of diseases.
This special collection brings together articles from Nature, Nature Immunology, Nature Reviews Immunology and Nature Reviews Drug Discovery that have contributed to advances and discussions in the field of immune cell epigenetics.
Read the Collection online for FREE:
http://links.ealert.nature.com/ctt?kn=94&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
Produced with Support from:
GlaxoSmithKline
http://links.ealert.nature.com/ctt?kn=157&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
=====================================================================
You have been sent this Table of Contents Alert because you have
opted in to
receive it. You can change or discontinue your e-mail alerts at
any time,
by modifying your preferences on your nature.com account at:
http://links.ealert.nature.com/ctt?kn=43&m=34519504&r=MTc2NjExMzUwMAS2&b=2&j=NjMyNzg0OTMS1&mt=1&rt=0
(You will need to log in to be recognised as a nature.com
registrant).
For further technical assistance, please contact our registration
department:
registration@nature.com
For print subscription enquiries, please contact our subscription
department:
subscriptions@nature.com
For other enquiries, please contact our customer feedback department:
feedback@nature.com
Nature Publishing Group | 75 Varick Street, 9th Floor | New York |
NY 10013-1917 | USA
Nature Publishing Group's worldwide offices:
London - Paris - Munich - New Delhi - Tokyo - Melbourne -
San Diego - San Francisco - Washington - New York - Boston
(c) Copyright 2010 Nature Publishing Group
=====================================================================
