July 2009 Volume 6 Number 7, pp 471 - 546
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EDITORIAL
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Summer reading: science in fiction p471
Though somewhat rare, there are a few good fiction books to be found
with refreshingly realistic biologists as central characters in
laboratory settings.
doi:10.1038/nmeth0709-471
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CORRESPONDENCE
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MoDIL: detecting small indels from clone-end sequencing with mixtures
of distributions pp473 - 474
Seunghak Lee, Fereydoun Hormozdiari, Can Alkan and Michael Brudno
doi:10.1038/nmeth.f.256
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Limitations and possibilities of small RNA digital gene expression
profiling pp474 - 476
Sam E V Linsen et al.
doi:10.1038/nmeth0709-474
http://links.ealert.nature.com/ctt?kn=137&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
RNAiCut: automated detection of significant genes from functional
genomic screens pp476 - 477
Irene M Kaplow et al.
doi:10.1038/nmeth0709-476
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Enabling IMAC purification of low abundance recombinant proteins from
E. coli lysates pp477 - 478
Audur Magnusdottir et al.
doi:10.1038/nmeth0709-477
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RESEARCH HIGHLIGHTS
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A question of culture p481
Two groups report culture conditions for long-term in vitro growth of
intestinal tissue from the mouse.
Natalie de Souza
doi:10.1038/nmeth0709-481
http://links.ealert.nature.com/ctt?kn=57&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Fluorescent proteins: into the infrared pp482 - 483
An engineered infrared fluorescent protein is the first member of a
new class of genetically encodable probes, with special advantages
over visible-wavelength fluorescent proteins for in vivo imaging.
Allison Doerr
doi:10.1038/nmeth0709-482a
http://links.ealert.nature.com/ctt?kn=135&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Going with the skewed flow pp482 - 483
Computational and experimental biologists teamed up to develop a
new software tool to analyze the rich data generated by new
and powerful flow cytometers.
Wayne Peng
doi:10.1038/nmeth0709-482b
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News in brief p483
doi:10.1038/nmeth0709-483
http://links.ealert.nature.com/ctt?kn=116&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Grafting as a potent molecular tool p484
Grafting two transgenic plants triggers lateral gene transfer at the
graft site but does not elicit long-distance transport of DNA into
the scion or root of the graft.
Nicole Rusk
doi:10.1038/nmeth0709-484
http://links.ealert.nature.com/ctt?kn=15&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Fluorescent false neurotransmitters p486
A fluorescent probe designed to incorporate a fluorophore into the
structure of a neurotransmitter finds activity-dependent
heterogeneity in dopamine release at individual synapses.
Daniel Evanko
doi:10.1038/nmeth0709-486
http://links.ealert.nature.com/ctt?kn=113&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Will planets reveal the light of their life? p487
Optical signatures from organic chemicals may help scientists detect
traces of life on other planets.
Michael Eisenstein
doi:10.1038/nmeth0709-487
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NEWS AND VIEWS
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Finding multiple needles in one immune haystack pp489 - 490
An approach using multiple fluorochrome combinations allows the
simultaneous detection of many T-cell populations within a single
blood sample.
Katherine Kedzierska, John Stambas and Peter C Doherty
doi:10.1038/nmeth0709-489
http://links.ealert.nature.com/ctt?kn=94&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Downhill protein folding under pressure pp490 - 491
Sub-microsecond, downhill-reaction protein folding can be
investigated by a method to generate large and fast pressure
drops. The approach is complementary to nanosecond
temperature-jump methods and could provide new insights
into the biophysics of protein folding.
Victor Munoz
doi:10.1038/nmeth0709-490
http://links.ealert.nature.com/ctt?kn=156&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
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BRIEF COMMUNICATIONS
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Agouti C57BL/6N embryonic stem cells for mouse genetic
resources pp493 - 495
Mouse embryonic stem cell lines from the C57BL/6 strain are reported.
The lines are highly germline competent, suitable for high-throughput
genetic manipulation and will enable the generation of large knockout
mouse resources.
Stephen J Pettitt et al.
doi:10.1038/nmeth.1342
Abstract: http://links.ealert.nature.com/ctt?kn=119&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
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Simultaneous detection of many T-cell specificities using
combinatorial tetramer staining pp497 - 499
Combinations of fluorescently labeled peptide-major
histocompatability (pMHC) tetramers are used to simultaneously
detect T cells with multiple antigen specificities from human blood
samples. Also in this issue, Hadrup et al. present a very similar
combinatorial encoding approach.
Evan W Newell, Lawrence O Klein, Wong Yu and Mark M Davis
doi:10.1038/nmeth.1344
Abstract: http://links.ealert.nature.com/ctt?kn=81&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=125&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Protein interaction platforms: visualization of interacting proteins
in yeast pp500 - 502
The protein interaction platform or PIP assay uses a viral
scaffolding protein fused to a bait and a fluorescent reporter
rotein fused to putative prey as the basis for a simple visual
screen for protein-protein interactions in yeast.
Alexa M Schmitz et al.
doi:10.1038/nmeth.1337
Abstract: http://links.ealert.nature.com/ctt?kn=54&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=31&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Quantitative analysis of gene expression in a single cell by
qPCR pp503 - 506
There have been many attempts to measure gene expression in single
cells but counting several different mRNAs in the same cell has been
a challenge. A reusable single-cell cDNA library immobilized on beads
allows quantitative measurement of multiple mRNAs in a single cell
with a large dynamic range and small experimental error.
Kiyomi Taniguchi, Tomoharu Kajiyama and Hideki Kambara
doi:10.1038/nmeth.1338
Abstract: http://links.ealert.nature.com/ctt?kn=112&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=26&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Filter-based hybridization capture of subgenomes enables resequencing
and copy-number detection pp507 - 510
Concatenated PCR products serve as subgenomic traps in this targeted
genome capture technique; subsequent high-throughput sequencing
allows the detection of nucleotide and structural variations in the
captured genomic regions.
Daniel S Herman et al.
doi:10.1038/nmeth.1343
Abstract: http://links.ealert.nature.com/ctt?kn=122&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=42&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
In vivo fluorescence imaging with high-resolution
microlenses pp511 - 512
A combination of gradient refractive index lenses with plano-convex
lenses produces high-resolution microlenses with image quality
similar to a conventional high quality microscope objective. The
microlenses are capable of imaging dendritic spines on hippocampal
neurons in live mice.
Robert P J Barretto, Bernhard Messerschmidt and Mark J Schnitzer
doi:10.1038/nmeth.1339
Abstract: http://links.ealert.nature.com/ctt?kn=91&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=23&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
'Injecting' yeast pp513 - 514
Using a topographically patterned substrate for immobilization of
single yeast cells and a piezo-impact micromanipulator to transiently
disrupt the cell wall, molecules can be physically introduced into
yeast.
Daniel Riveline and Paul Nurse
doi:10.1038/nmeth.1335
Abstract: http://links.ealert.nature.com/ctt?kn=131&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=47&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
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ARTICLES
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Reaching the protein folding speed limit with large, sub-microsecond
pressure jumps pp515 - 519
Although fast temperature jump methods to study protein folding
dynamics have long been applied, pressure has been a neglected
thermodynamic parameter. A method to generate rapid and large
drops in pressure is complementary to fast temperature jump
methods and could be useful for direct comparisons to molecular
dynamics simulations.
Charles Dumont, Tryggvi Emilsson and Martin Gruebele
doi:10.1038/nmeth.1336
Abstract: http://links.ealert.nature.com/ctt?kn=11&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=107&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Parallel detection of antigen-specific T-cell responses by
multidimensional encoding of MHC multimers pp520 - 526
Using combinations of fluorescently labeled peptide-major
histocompatability complex (pMHC) tetramers, T-cell populations
with multiple antigen specificities can be monitored in parallel
from small samples of human blood. Also in this issue, Newell et al.
present a very similar combinatorial encoding method for
this purpose.
Sine Reker Hadrup et al.
doi:10.1038/nmeth.1345
Abstract: http://links.ealert.nature.com/ctt?kn=28&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=145&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Doxycycline-dependent photoactivated gene expression in eukaryotic
systems pp527 - 531
Activation of caged doxycycline or cyanodoxycycline by biologically
innocuous doses of UV light allows for precise temporal and spatial
control of transgene expression in hippocampal slices, mouse embryos
and Xenopus laevis tadpoles.
Sidney B Cambridge et al.
doi:10.1038/nmeth.1340
Abstract: http://links.ealert.nature.com/ctt?kn=157&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=123&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Mapping the structure and conformational movements of proteins with
transition metal ion FRET pp532 - 537
Fluorescence resonance energy transfer (FRET) between a
small-molecule fluorophore donor and a transition metal ion
acceptor, a method called 'transition metal ion FRET,' works
over shorter distances than the classical FRET approach and
can thus be used to monitor very small conformational changes
in proteins.
Justin W Taraska et al.
doi:10.1038/nmeth.1341
Abstract: http://links.ealert.nature.com/ctt?kn=155&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=101&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
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TECHNOLOGY FEATURE
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Genomics: catch me if you can pp539 - 544
Next-generation sequencing has made decoding entire genomes
cheaper and faster. But what about those researchers who only
want to sequence a small section of a genome or focus on a
couple thousand specific exons? A wave of new technologies
has recently emerged that should help these scientists target their
sequencing efforts to sequences of interest.
Nathan Blow
doi:10.1038/nmeth0709-539
http://links.ealert.nature.com/ctt?kn=128&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
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CORRIGENDUM
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Corrigendum: A HUPO test sample study reveals common problems
in mass spectrometry-based proteomics p546
doi:10.1038/nmeth0709-546a
http://links.ealert.nature.com/ctt?kn=77&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
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ERRATUM
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Erratum: Transposon-mediated genome manipulation in vertebrates p546
doi:10.1038/nmeth0709-546b
http://links.ealert.nature.com/ctt?kn=120&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
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APPLICATION NOTES
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Analysis of 5' transcript heterogeneity by high-throughput
sequencing of cDNA
Pietro D Spanu and Ken Doyle
Abstract: http://links.ealert.nature.com/ctt?kn=117&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=17&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
CYP2C9 and VKORC1 genotyping reagents from Idaho Technology: rapid
turn-around, accurate results
Jason McKinney, Ranae Lems and Cameron Gundry
Abstract: http://links.ealert.nature.com/ctt?kn=79&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=152&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Fluidigm Dynamic Arrays provide a platform for single-cell
gene expression analysis
Martin Pieprzyk and Howard High
Abstract: http://links.ealert.nature.com/ctt?kn=148&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=95&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
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