January 2008 Volume 5 Number 1, pp 1 - 113
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----------------------
SPECIAL FEATURE
----------------------
Nature Methods' Method of the Year 2007 goes to next-generation
sequencing. This series of articles showcase how these novel
sequencing methods came into their own in 2007 and the incredible
impact they promise to have in a variety of research applications.
The Methods to Watch feature provide a glimpse and a wish list for
future Methods of the Year.
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkAq0EE
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EDITORIAL
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Special Feature: Method of the Year 2007
Method of the Year p1
There are events of the year, persons of the year, images of the
year.... We could not resist: why not a Method of the Year?
doi:10.1038/nmeth1153
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQk0EO
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CORRESPONDENCE
----------------------
Vector-free DNA constructs improve transgene expression in
C. elegans p3
John F Etchberger and Oliver Hobert
doi:10.1038/nmeth0108-3
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQl0EP
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RESEARCH HIGHLIGHTS
----------------------
Inner glow p5
Katherine Stevens
doi:10.1038/nmeth0108-5
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQm0EQ
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQn0ER
Smaller can be better pp6 - 7
Allison Doerr
doi:10.1038/nmeth0108-6a
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQo0ES
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQp0ET
There is a virus going around pp6 - 7
Katherine Stevens
doi:10.1038/nmeth0108-6b
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQq0EU
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQr0EV
News in brief p7
doi:10.1038/nmeth0108-7
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQs0EW
The living brain, unlabeled p8
Natalie de Souza
doi:10.1038/nmeth0108-8
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQt0EX
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQu0EY
----------------------
NEWS FEATURE
----------------------
Special Feature: Method of the Year 2007
The year of sequencing pp11 - 14
In 2007, the next-generation sequencing technologies have come
into their own with an impressive array of successful applications.
Kelly Rae Chi reports.
Kelly Rae Chi
doi:10.1038/nmeth1154
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQv0EZ
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PRIMER
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Special Feature: Method of the Year 2007
Primer: Sequencing-the next generation p15
Different sequencing technologies, at a glance.
Nicole Rusk and Veronique Kiermer
doi:10.1038/nmeth1155
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQw0Ea
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COMMENTARIES
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Special Feature: Method of the Year 2007
Next-generation sequencing transforms today's biology pp16 - 18
A new generation of non-Sanger-based sequencing technologies has
delivered on its promise of sequencing DNA at unprecedented speed,
thereby enabling impressive scientific achievements and novel
biological applications. However, before stepping into the limelight,
next-generation sequencing had to overcome the inertia of a field
that relied on Sanger-sequencing for 30 years.
Stephan C Schuster
doi:10.1038/nmeth1156
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQx0Eb
Special Feature: Method of the Year 2007
Sequence census methods for functional genomics pp19 - 21
Next-generation sequencing technologies are beginning to facilitate
genome sequencing. But in addition, new applications and new assay
concepts have emerged that are vastly increasing our ability
to understand genome function.
Barbara Wold and Richard M Myers
doi:10.1038/nmeth1157
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQy0Ec
----------------------
METHODS TO WATCH
----------------------
Special Feature: Method of the Year 2007
Seeing fluorescence at super-resolution p22
Fluorescence microscopy is being transformed by methods to improve
its resolving power.
Daniel Evanko
doi:10.1038/nmeth1158
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQz0Ed
Special Feature: Method of the Year 2007
Experimental micro-matchmaking p22
Needed: large scale experimental validation of predicted microRNA
targets.
Nicole Rusk
doi:10.1038/nmeth1159
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQ10EQ
Special Feature: Method of the Year 2007
Structural analysis of macromolecular assemblies p23
As proteomic and structural biology methods mature, determining
high-resolution structures of macromolecular assemblies comes
within reach.
Allison Doerr
doi:10.1038/nmeth1160
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQ20ER
Special Feature: Method of the Year 2007
Controlling cells with light p23
New methods using light to control cellular activity promise to
illuminate hidden biology.
Daniel Evanko
doi:10.1038/nmeth1161
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQ30ES
Special Feature: Method of the Year 2007
Top-down mass spectrometry p24
Top-down mass spectrometry offers the ability to sequence intact
proteins-post-translational modifications and all-but is not
yet a high-throughput method.
Allison Doerr
doi:10.1038/nmeth1162
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQ40ET
Special Feature: Method of the Year 2007
Induced pluripotency in human cells p24
Differentiated cells can be reverted to an 'embryonic' state.
But how embryonic are they really?
Natalie de Souza
doi:10.1038/nmeth1163
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQ50EU
Special Feature: Method of the Year 2007
Watching single molecules in cells p25
Examining cell biology at the single-molecule level is
methodologically challenging but offers high rewards.
Daniel Evanko
doi:10.1038/nmeth1164
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQ60EV
Special Feature: Method of the Year 2007
A meta-network of -omics p25
Needed: a network of databases to comprehensively link current
knowledge in the biosciences.
Nicole Rusk
doi:10.1038/nmeth1165
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQ70EW
----------------------
NEWS AND VIEWS
----------------------
Life from information pp27 - 28
Methods that improve DNA synthesis with reduced error rate and those
that facilitate cloning of large DNA segments will be valuable in
rebuilding genomes and provide a stepping stone on the way to genome
design.
Christopher A Voigt
doi:10.1038/nmeth0108-27
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkQ80EX
----------------------
REVIEW
----------------------
Live-cell imaging of cAMP dynamics pp29 - 36
Debbie Willoughby and Dermot M F Cooper
doi:10.1038/nmeth1135
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRA0Eh
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRB0Ei
----------------------
BRIEF COMMUNICATIONS
----------------------
Gene synthesis by circular assembly amplification pp37 - 39
Duhee Bang and George M Church
doi:10.1038/nmeth1136
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRC0Ej
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRD0Ek
Bottom-up genome assembly using the Bacillus subtilis
genome vector pp41 - 43
Mitsuhiro Itaya, Kyoko Fujita, Azusa Kuroki and Kenji Tsuge
doi:10.1038/nmeth1143
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRE0El
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRF0Em
In vivo imaging of Drosophila melanogaster pupae with mesoscopic
fluorescence tomography pp45 - 47
Claudio Vinegoni et al.
doi:10.1038/nmeth1149
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRG0En
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRH0Eo
Vector and parameters for targeted transgenic RNA interference
in Drosophila melanogaster pp49 - 51
Jian-Quan Ni et al.
doi:10.1038/nmeth1146
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRI0Ep
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRJ0Eq
GraFix: sample preparation for single-particle electron
cryomicroscopy pp53 - 55
Berthold Kastner et al.
doi:10.1038/nmeth1139
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRK0Er
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRL0Es
Integrating spatially resolved three-dimensional MALDI IMS with
in vivo magnetic resonance imaging pp57 - 59
Tuhin K Sinha et al.
doi:10.1038/nmeth1147
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRM0Et
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRN0Eu
----------------------
ARTICLES
----------------------
Targeted patch-clamp recordings and single-cell electroporation
of unlabeled neurons in vivo pp61 - 67
Kazuo Kitamura et al.
doi:10.1038/nmeth1150
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRO0Ev
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRP0Ew
A proteome chip approach reveals new DNA damage recognition
activities in Escherichia coli pp69 - 74
Chien-Sheng Chen et al.
doi:10.1038/nmeth1148
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRQ0Ex
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRR0Ey
Resolution of de novo HIV production and trafficking
in immature dendritic cells pp75 - 85
Stuart G Turville et al.
doi:10.1038/nmeth1137
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRS0Ez
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRT0E1
Tracking transmitter-gated P2X cation channel activation
in vitro and in vivo pp87 - 93
Esther Richler et al.
doi:10.1038/nmeth1144
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRU0E2
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRV0E3
Targeted pre-mRNA modification for gene silencing
and regulation pp95 - 100
Xinliang Zhao and Yi-Tao Yu
doi:10.1038/nmeth1142
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRW0E4
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRX0E5
----------------------
PROTOCOL
----------------------
Imaging mass spectrometry of proteins and peptides:
3D volume reconstruction pp101 - 108
Malin Andersson, M Reid Groseclose, Ariel Y Deutch
and Richard M Caprioli
doi:10.1038/nmeth1145
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRY0E6
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRZ0E7
----------------------
TECHNOLOGY FEATURE
----------------------
Lab automation: tales along the road to automation pp109 - 112
The benefits of laboratory automation do not come without
considerable effort and patience in setting up the systems.
Nathan Blow talks with two groups at different stages on the
road to automation.
Nathan Blow
doi:10.1038/nmeth0108-109
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRa0EF
----------------------
ERRATA
----------------------
Erratum: Rapid control of protein level in the apicomplexan
Toxoplasma gondii p113
Angelika Herm-Gotz et al.
doi:10.1038/nmeth0108-113a
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRb0EG
Erratum: Following the wires p113
Nathan Blow
doi:10.1038/nmeth0108-113b
http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRc0EH
----------------------
APPLICATION NOTE
----------------------
MicroRNA profiling on a rapidly evolving microfluidic array
Sonja Vorwerk and Peter Roberts
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRd0EI
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eiQi0Xztnp0Hi80BkRe0EJ
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