May 2009 Volume 6 Number 5, pp 313 - 393
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FREE ARTICLE
Antibiotics and inhibition of fatty acid biosynthesis
http://links.ealert.nature.com/ctt?kn=91&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
The importance of fatty acid biosynthesis to bacterial survival has made the pathway fertile ground for antibiotic targets, and at least three companies are pursuing compounds that block the process. French researchers, however, have challenged the approach with a paper in Nature that describes how Gram-positive bacteria can assimilate host fatty acids to ensure bacterial survival. What was the reaction of companies developing inhibitors of the pathway?
Find out more by reading the first in-depth analysis of the scientific and commercial potential of the work in SciBX: Science-Business eXchange.
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EDITORIAL
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Methods section remake p313
Nature Methods follows in the footsteps of Nature by ushering in an
Online Methods section, fully integrated with the paper, for all
original research articles.
doi:10.1038/nmeth0509-313
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CORRESPONDENCE
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Massively parallel exon capture and library-free resequencing across
16 genomes pp315 - 316
Emily H Turner et al.
doi:10.1038/nmeth.f.248
http://links.ealert.nature.com/ctt?kn=113&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Lifeact cannot visualize some forms of stress-induced twisted
f-actin p317
Lise N Munsie, Nicholas Caron, Carly R Desmond and Ray Truant
doi:10.1038/nmeth0509-317
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RESEARCH HIGHLIGHTS
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Dawn on the mice p319
By directly delivering light deep into the brain, scientists can now
study the basis of neurological therapy and animal behavior.
Wayne Peng
doi:10.1038/nmeth0509-319
http://links.ealert.nature.com/ctt?kn=48&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Capturing the human methylome pp320 - 321
Pairing bisulfite conversion of the human genome with targeted
enrichment and high-throughput sequencing allows a quantitative
assessment of DNA methylation at base-pair resolution.
Nicole Rusk
doi:10.1038/nmeth0509-320a
http://links.ealert.nature.com/ctt?kn=34&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Sequence is not everything pp320 - 321
A new algorithm for identifying evolutionary constraint incorporates
information on local DNA topology, and leads to the finding that this
topology is conserved across species.
Natalie de Souza
doi:10.1038/nmeth0509-320b
http://links.ealert.nature.com/ctt?kn=15&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
News in brief p321
doi:10.1038/nmeth0509-321
http://links.ealert.nature.com/ctt?kn=16&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Supercharging through the cell membrane p322
Researchers show that superpositively charged GFP enters mammalian
cells with ease and can be used as a nucleic acid delivery vehicle.
Allison Doerr
doi:10.1038/nmeth0509-322
http://links.ealert.nature.com/ctt?kn=19&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
A touching discovery p324
Fake fingertips provide insights into how fingerprints help humans
to feel fine details of surface texture.
Michael Eisenstein
doi:10.1038/nmeth0509-324
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Protein production: no cells required p326
DNA hydrogels improve the efficiency of cell-free protein production.
Allison Doerr
doi:10.1038/nmeth0509-326
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NEWS AND VIEWS
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Without a trace? PiggyBac-ing toward pluripotency pp329 - 330
A transposon-based approach has been added to the growing arsenal
of technologies to produce transgene-free and potentially safer
induced pluripotent stem cells.
Matthias Stadtfeld and Konrad Hochedlinger
doi:10.1038/nmeth0509-329
http://links.ealert.nature.com/ctt?kn=143&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
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REVIEW
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Imaging intracellular RNA distribution and dynamics in living
cells pp331 - 338
Sanjay Tyagi
doi:10.1038/nmeth.1321
Abstract: http://links.ealert.nature.com/ctt?kn=92&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=136&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
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BRIEF COMMUNICATIONS
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Super-resolution video microscopy of live cells by structured
illumination pp339 - 342
The use of a spatial light modulator for illuminating the sample in
structured-illumination microscopy (SIM) increases imaging speed
by three orders of magnitude. The resulting 100-nm resolution and
11-Hz frame rate allowed video imaging of tubulin polymerization and
depolymerization as well as kinesin movement on microtubules.
Peter Kner et al.
doi:10.1038/nmeth.1324
Abstract: http://links.ealert.nature.com/ctt?kn=117&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=78&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Enzymatic assembly of DNA molecules up to several hundred
kilobases pp343 - 345
The combination of 5' exonuclease, DNA polymerase and ligase with
overlapping DNA fragments facilitates the in vitro assembly of large
DNA constructs, including an entire bacterial genome.
Daniel G Gibson et al.
doi:10.1038/nmeth.1318
Abstract: http://links.ealert.nature.com/ctt?kn=50&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=110&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Single molecule-sensitive probes for imaging RNA in live
cells pp347 - 349
Upon binding multiple fluorophores and being complexed into
tetramers, these RNA imaging probes show high sensitivity and
can detect single endogenous RNA molecules at low probe
concentration.
Philip J Santangelo et al.
doi:10.1038/nmeth.1316
Abstract: http://links.ealert.nature.com/ctt?kn=122&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=88&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
An ultramarine fluorescent protein with increased photostability
and pH insensitivity pp351 - 353
A fluorescent protein, Sirius, with the most blue-shifted emission
spectrum to date, is reported. Sirius allows extended multicolor
imaging as well as imaging in acidic environments owing to its
pH insensitivity.
Wataru Tomosugi et al.
doi:10.1038/nmeth.1317
Abstract: http://links.ealert.nature.com/ctt?kn=133&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=11&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Photoconversion in orange and red fluorescent proteins pp355 - 358
Several red and orange fluorescent proteins are reported to be
photoconvertible. Specifically, three red fluorescent proteins that
can be switched to green, and two orange fluorescent proteins that
can be switched to far red are reported.
Gert-Jan Kremers et al.
doi:10.1038/nmeth.1319
Abstract: http://links.ealert.nature.com/ctt?kn=29&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=162&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Universal sample preparation method for proteome
analysis pp359 - 362
A method, filter-aided sample preparation (FASP) combines the
advantages of in-gel and in-solution digestion for mass
spectrometry-based proteomics, allowing deeper proteomic coverage
in a shorter analysis time, using small sample amounts.
Jacek R Wisniewski, Alexandre Zougman, Nagarjuna
Nagaraj and Matthias Mann
doi:10.1038/nmeth.1322
Abstract: http://links.ealert.nature.com/ctt?kn=159&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=116&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
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ARTICLES
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Generation of transgene-free induced pluripotent mouse stem cells by
the piggyBac transposon pp363 - 369
piggyBac transposons carrying reprogramming factors are used to
reprogram mouse embryonic fibroblasts, with efficiencies equivalent
to retroviral transduction, and then removed from the induced
pluripotent state cell genome without a trace.
Kosuke Yusa, Roland Rad, Junji Takeda and Allan Bradley
doi:10.1038/nmeth.1323
Abstract: http://links.ealert.nature.com/ctt?kn=76&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=150&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Isolation of human iPS cells using EOS lentiviral vectors to select
for pluripotency pp370 - 376
Lentiviral vectors that express a fluorescent reporter and a selectable
marker in pluripotent cells improve and simplify isolation of induced
pluripotent stem cell lines in mouse and human.
Akitsu Hotta et al.
doi:10.1038/nmeth.1325
Abstract: http://links.ealert.nature.com/ctt?kn=163&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=74&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
mRNA-Seq whole-transcriptome analysis of a single cell pp377 - 382
Previous whole-transcriptome analysis by RNA-Seq required hundreds of
thousands of cells or microgram amounts of RNA. A modification of the
cDNA library preparation method now allows unbiased capture of the
majority of genes expressed in a single blastomere and oocyte. cDNA
sequencing on the SOLiD platform facilitates the quantitative
analysis of the transcriptome complexity in a single cell.
Fuchou Tang et al.
doi:10.1038/nmeth.1315
Abstract: http://links.ealert.nature.com/ctt?kn=87&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=106&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Combined atomic force microscopy and side-view optical imaging for
mechanical studies of cells pp383 - 387
An atomic force microscope with a side-view fluorescent imaging path
facilitates the direct correlation of mechanical force measurements
with observations of changes in cell shape and cytoskeleton
rearrangements resulting from the applied forces or during active
generation of forces by the cell. The combined instrument could help
lead to insights in understanding cell mechanics, contractility and
cell-cell adhesion.
Ovijit Chaudhuri, Sapun H Parekh, Wilbur A Lam and Daniel A Fletcher
doi:10.1038/nmeth.1320
Abstract: http://links.ealert.nature.com/ctt?kn=33&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=145&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
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TECHNOLOGY FEATURE
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Proteins and proteomics: life on the surface pp389 - 393
Surface plasmon resonance sensing has entered the next phase of
development as researchers advance array-based applications using
the technique. Could these new approaches change the way scientists
explore protein interactions?
Nathan Blow
doi:10.1038/nmeth0509-389
http://links.ealert.nature.com/ctt?kn=161&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
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APPLICATION NOTES
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Enhanced red and far-red fluorescent proteins for in vivo imaging
Ilya Kelmanson
Abstract: http://links.ealert.nature.com/ctt?kn=135&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=45&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Accelerating searches of research grants and scientific literature
with novo|seekSM
Ramon Alonso Allende
Abstract: http://links.ealert.nature.com/ctt?kn=126&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=121&m=32812078&r=MTc2NjExMzUwMAS2&b=2&j=NDgzMjcyMTUS1&mt=1&rt=0
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