April 2008 Volume 5 Number 4, pp 275 - 369
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EDITORIAL
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Compare and conquer p275
Experimental comparisons of methods, technology platforms or reagents
are time-consuming and expensive, but hugely beneficial. Enter the
Analysis article format.
doi:10.1038/nmeth0408-275
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CORRESPONDENCE
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Cyclic nucleotide analogs as probes of signaling
pathways pp277 - 278
Heiko Poppe et al.
doi:10.1038/nmeth0408-277
http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSD0Ey
Whole genome-amplified DNA: insights and imputation pp279 - 280
Yik Y Teo et al.
doi:10.1038/nmeth0408-279
http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSE0Ez
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RESEARCH HIGHLIGHTS
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Protein suicide highlights the cell cycle p283
Daniel Evanko
doi:10.1038/nmeth0408-283
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSF0E1
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSG0E2
Mapping the plant methylome pp284 - 285
Nicole Rusk
doi:10.1038/nmeth0408-284a
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSH0E3
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSI0E4
Insulating gene expression pp284 - 285
Katherine Stevens
doi:10.1038/nmeth0408-284b
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSJ0E5
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSK0E6
News in brief p285
doi:10.1038/nmeth0408-285
http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSL0E7
DNA synthesis lights up p286
Allison Doerr
doi:10.1038/nmeth0408-286
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSM0E8
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSN0EA
ChIP-chip put to the test p288
Veronique Kiermer
doi:10.1038/nmeth0408-288
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSO0EB
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSP0EC
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COMMENTARY
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Disaccharide structure code for the easy representation of
constituent oligosaccharides from glycosaminoglycans pp291 - 292
Here we introduce a new shorthand nomenclature for designating the
disaccharide subunit structure of all glycosaminoglycans as a way
to compare compositions and describe linear sequences. Each
disaccharide structural code (DSC) comprises four alphanumeric
characters that reflect the actual substituents and isomeric
characteristics of each component sugar. Larger structures can be
represented easily by forming concatamers. The structural
transparency of this new nomenclature eliminates the need for
ambiguous acronyms or difficult numeric representations.
Roger Lawrence et al.
doi:10.1038/nmeth0408-291
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NEWS AND VIEWS
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Expanding the toolbox for remote control of neuronal
circuits pp293 - 295
Advances in methods that allow targeted remote control of neuronal
activity open new possibilities for investigating and manipulating
the function of neuronal circuits in vivo.
Thomas Knopfel
doi:10.1038/nmeth0408-293
http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSR0EE
SNPing and chipping away at the fly genome pp295 - 296
Although Drosophila melanogaster offers a variety of refined genetic
techniques, it has lagged behind other model organisms in the
high-resolution genotyping arena. A newly developed set of tools
addresses this deficiency and provides a very welcome addition to
the fly geneticists' armory.
Steven Russell
doi:10.1038/nmeth0408-295
http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSS0EF
Levers and fulcrums: progress in cis-regulatory motif models pp297 - 298
A new set of computational methods provide association of
transcription factor binding motifs to gene function.
Ewan Birney
doi:10.1038/nmeth0408-297
http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrST0EG
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BRIEF COMMUNICATIONS
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Genetic control of neuronal activity in mice conditionally expressing
TRPV1 pp299 - 302
Benjamin R Arenkiel et al.
doi:10.1038/nmeth.1190
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSU0EH
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSV0EI
Activation of protein splicing with light in yeast pp303 - 305
Amy B Tyszkiewicz and Tom W Muir
doi:10.1038/nmeth.1189
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSW0EJ
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSX0EK
Genome-wide mapping of allele-specific protein-DNA interactions
in human cells pp307 - 309
Nathaniel D Maynard et al.
doi:10.1038/nmeth.1194
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSY0EL
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSZ0EM
In vivo immunogold labeling confirms large-scale chromatin folding
motifs pp311 - 313
Igor Kireev et al.
doi:10.1038/nmeth.1196
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSa0ET
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSb0EU
Identification of cross-linked peptides from large sequence
databases pp315 - 318
Oliver Rinner et al.
doi:10.1038/nmeth.1192
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSc0EV
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSd0EW
A quantitative analysis software tool for mass spectrometry-based
proteomics pp319 - 322
Sung Kyu Park, John D Venable, Tao Xu and John R Yates, III
doi:10.1038/nmeth.1195
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSe0EX
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSf0EY
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ARTICLES
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High-resolution, high-throughput SNP mapping in Drosophila
melanogaster pp323 - 329
Doris Chen et al.
doi:10.1038/nmeth.1191
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSg0EZ
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSh0Ea
Photochemical control of endogenous ion channels and cellular
excitability pp331 - 338
Doris L Fortin et al.
doi:10.1038/nmeth.1187
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSi0Eb
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSj0Ec
Direct measurement of protein dynamics inside cells using a
rationally designed photoconvertible protein pp339 - 345
Tomoki Matsuda, Atsushi Miyawaki and Takeharu Nagai
doi:10.1038/nmeth.1193
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSk0Ed
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSl0Ee
Systematic identification of mammalian regulatory motifs' target
genes and functions pp347 - 353
Jason B Warner et al.
doi:10.1038/nmeth.1188
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSm0Ef
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSn0Eg
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PROTOCOL
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A sensitive direct human telomerase activity assay pp355 - 360
Scott B Cohen and Roger R Reddel
doi:10.1038/nmeth.f.209
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSo0Eh
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSp0Ei
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TECHNOLOGY FEATURE
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RNAi technologies: a screen whose time has arrived pp361 - 368
Researchers are finally reaping the rewards of large-scale RNA
interference (RNAi) screens in mammalian cells, obtaining insights
into a wide range of biological questions. Nathan Blow takes a look
at the technology advances spearheading this revolution.
Nathan Blow
doi:10.1038/nmeth0408-361
http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSq0Ej
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ADDENDUM
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Addendum: Protein production and purification p369.
Structural Genomics Consortium, Architecture et Fonction des
Macromolecules Biologiques, Berkeley Structural Genomics Center,
China Structural Genomics Consortium, Integrated Center for
Structure and Function Innovation, Israel Structural Proteomics
Center, Joint Center for Structural Genomics, Midwest Center for
Structural Genomics, New York Structural GenomiX Research Center
for Structural Genomics, Northeast Structural Genomics Consortium,
Oxford Protein Production Facility, Protein Sample Production
Facility, Max Delbruck Center for Molecular Medicine, RIKEN
Structural Genomics/Proteomics Initiative & SPINE2-Complexes
doi:10.1038/nmeth0408-369
http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSr0Ek
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APPLICATION NOTES
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Refining epifluorescence imaging and analysis with automated
multiple-band flat-field correction
Douglas Wood, Gilbert Feke, Douglas Vizard and Rao Papineni
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSs0El
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSt0Em
Selecting a cyclic AMP kit for assaying GPCR target activation
Jean-Luc Tardieu
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSu0En
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ejyF0Xztnp0Hi80BrSv0Eo
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