October 2009 Volume 6 Number 10, pp 687 - 781
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SPECIAL FEATURE
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Five Year Anniversary Special
Nature Methods celebrates its five year anniversary with commentaries
discussing the impact and progress of methodological developments
in the life sciences. We also include a fun selection of papers and
covers from our pages.
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EDITORIAL
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Special Feature: Five Year Anniversary Special
In celebration of methods p687
doi:10.1038/nmeth1009-687
As evidenced by the cake adorning the cover, Nature Methods is five
years old. To celebrate this anniversary, we look at methodological
development and its role in scientific inquiry.
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CORRESPONDENCE
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Online image analysis software for photoactivation localization
microscopy pp689 - 690
Per Niklas Hedde et al.
doi:10.1038/nmeth1009-689
http://links.ealert.nature.com/ctt?kn=144&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
My5C: web tools for chromosome conformation capture
tudies pp690 - 691
Bryan R Lajoie, Nynke L van Berkum, Amartya Sanyal and Job Dekker
doi:10.1038/nmeth1009-690
http://links.ealert.nature.com/ctt?kn=149&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
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RESEARCH HIGHLIGHTS
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Two photons as exciting as one p693
Natalie de Souza
doi:10.1038/nmeth1009-693
Channelrhodopsin-2 can be efficiently activated by infrared
two-photon excitation light and stimulates action potentials in
cultured neurons.
http://links.ealert.nature.com/ctt?kn=136&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
'Blue' lighting cell signaling research pp694 - 695
Irene Kaganman
doi:10.1038/nmeth1009-694a
By fusing a light-sensitive domain of an oat plant protein to Rac1,
researchers created a genetically encoded protein fusion that can
be reversibly activated with blue light and control cell movement-an
attractive alternative to current caging tools.
http://links.ealert.nature.com/ctt?kn=140&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
A leader anyone can follow pp694 - 695
Michael Eisenstein
doi:10.1038/nmeth1009-694b
The development of leader sequences that stimulate mRNA translation
in a species-independent manner could offer new possibilities for
eukaryotic protein production and proteomic research.
http://links.ealert.nature.com/ctt?kn=13&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
News in brief p695
doi:10.1038/nmeth1009-695
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Illuminating lipids p696
Allison Doerr
doi:10.1038/nmeth1009-696
Visualization of choline-containing phospholipids in cells and
in vivo is made possible by the metabolic incorporation of a
choline analog with an alkyne handle for click chemistry-based
labeling.
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Engineering bacteria in yeast p698
Nicole Rusk
doi:10.1038/nmeth1009-698
Bacterial genomes shuttled into yeast can be easily altered before
transplantation back into bacteria.
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HISTORICAL COMMENTARIES
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Special Feature: Five Year Anniversary Special
Technical matters: method, knowledge and infrastructure in
twentieth-century life science pp701 - 705
Angela N H Creager and Hannah Landecker
doi:10.1038/nmeth1009-701
Conceptual breakthroughs in science tend to garner accolades and
attention. But, as the invention of tissue culture and the
development of isotopic tracers show, innovative methods open up
new fields and enable the solution of longstanding problems.
http://links.ealert.nature.com/ctt?kn=26&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Special Feature: Five Year Anniversary Special
Seeing things: from microcinematography to live cell
imaging pp707 - 709
Hannah Landecker
doi:10.1038/nmeth1009-707
From histology to microcinematography, from cytochemistry to live
cell imaging, the history of visualization technology in the life
sciences may be understood as a series of cycles of action and
reaction between static and dynamic modes of representing life.
http://links.ealert.nature.com/ctt?kn=118&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
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COMMENTARIES
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Special Feature: Five Year Anniversary Special
Is sequencing enlightenment ending the dark age of the
transcriptome? pp711 - 713
Piero Carninci
doi:10.1038/nmeth1009-711
Sequencing-based technologies for RNA discovery are playing
a key role in deciphering the transcriptome and hold the potential
to provide us with a census of RNAs and their functions.
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Special Feature: Five Year Anniversary Special
Engineered fluorescent proteins: innovations and
applications pp713 - 717
Michael W Davidson and Robert E Campbell
doi:10.1038/nmeth1009-713
Despite expansion of the fluorescent protein and optical highlighter
palette into the orange to far-red range of the visible spectrum,
achieving performance equivalent to that of EGFP has continued to
elude protein engineers.
http://links.ealert.nature.com/ctt?kn=113&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Special Feature: Five Year Anniversary Special
Comparative analysis to guide quality improvements in
proteomics pp717 - 719
Matthias Mann
doi:10.1038/nmeth1009-717
The potential of mass spectrometry-based proteomics to advance
biology and biomedicine is nearly unlimited but so is its potential
for generating bad data. Apart from the pursuit of technological
progress in protocols and instruments, stringent comparative
analyses of different approaches are critical for fully developing
the discipline.
http://links.ealert.nature.com/ctt?kn=115&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Special Feature: Five Year Anniversary Special
From information to knowledge: new technologies for defining
gene function pp721 - 723
Sean R Collins, Jonathan S Weissman and Nevan J Krogan
doi:10.1038/nmeth1009-721
A wide range of methodology will be needed to bridge the gap
between genome sequence and mechanistic understanding in biology.
Recent advances in high-throughput genetic screening address
this task.
http://links.ealert.nature.com/ctt?kn=109&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
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FIVE YEARS OF METHODS
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Special Feature: Five Year Anniversary Special
Five years of Methods pp724 - 725
doi:10.1038/nmeth1009-724
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NEWS AND VIEWS
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Staging worms for next-generation analysis pp727 - 728
L Ryan Baugh
doi:10.1038/nmeth1009-727
Automated stage-specific sorting of Caenorhabditis elegans embryos
enables next-generation molecular and biochemical analysis of
development.
http://links.ealert.nature.com/ctt?kn=148&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
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BRIEF COMMUNICATIONS
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Nanoscale 3D cellular imaging by axial scanning transmission
electron tomography pp729 - 731
Martin F Hohmann-Marriott et al.
doi:10.1038/nmeth.1367
Using an axial detector, scanning transmission electron microscopy
allows three-dimensional tomographic reconstruction of
micrometer-thick sections of biological samples, at a resolution
comparable to that obtained on thin sections.
Abstract: http://links.ealert.nature.com/ctt?kn=37&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=139&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Somatic cell nuclear transfer in zebrafish pp733 - 735
Kannika Siripattarapravat et al.
doi:10.1038/nmeth.1369
Technical modifications of existing methods lead to a somatic cell
nuclear transfer method in the zebrafish, which yields adult cloned
fish with healthy offspring that carry donor traits.
Abstract: http://links.ealert.nature.com/ctt?kn=32&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=69&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Genetically encoded FRET sensors to monitor intracellular Zn2+
homeostasis pp737 - 740
Jan L Vinkenborg et al.
doi:10.1038/nmeth.1368
A series of genetically encoded fluorescent sensors for intracellular
Zn2+ with binding affinities spanning the picomolar and nanomolar
ranges show that cytosolic Zn2+ is buffered at ~0.4 nM. Targeting
of the sensors to insulin-containing secretory granules indicates a
free Zn2+ concentration between 1 and 100 muM in these organelles.
Abstract: http://links.ealert.nature.com/ctt?kn=33&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=70&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Proteomics strategy for quantitative protein interaction profiling in
cell extracts pp741 - 744
Kirti Sharma et al.
doi:10.1038/nmeth.1373
Quantitative information is necessary to determine which protein
interactions are the most relevant in a cellular context. A defined
set of affinity purification experiments combined with quantitative
mass spectrometry analysis allows the determination of dissociation
constants for all protein targets interacting with an introduced
ligand.
Abstract: http://links.ealert.nature.com/ctt?kn=59&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=76&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
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Direct PCR from plant tissues
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Finnzymes' Phire Plant Direct PCR Kit allows DNA amplification
directly from plant tissues such as leaves and seeds. No DNA isolation is
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ARTICLES
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Large-scale sorting of C. elegans embryos reveals the dynamics
of small RNA expression pp745 - 751
Marlon Stoeckius et al.
doi:10.1038/nmeth.1370
Fluorescence-activated cell sorting of worm embryos promises to
replace manual sorting of staged embryos and yields large populations
highly enriched in specific developmental stages, allowing
high-throughput genomic analysis.
Abstract: http://links.ealert.nature.com/ctt?kn=57&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=143&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
A Flp-nick system to study repair of a single protein-bound nick
in vivo pp753 - 757
Ida Nielsen et al.
doi:10.1038/nmeth.1372
By targeting a mutant Flp recombinase that forms a covalent
protein-DNA complex to a single FRT site placed anywhere in
the yeast genome, the authors can study repair pathways activated
by a single genomic insult as well as events at the site of damage.
Abstract: http://links.ealert.nature.com/ctt?kn=58&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=91&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
An approach for extensibly profiling the molecular states of cellular
subpopulations pp759 - 765
Lit-Hsin Loo et al.
doi:10.1038/nmeth.1375
Computational compensation for the loss of information from a
cellular marker visualized in one fluorescence channel increases
the number of markers that can be used to study a population of
cells. This should allow a more detailed molecular understanding
of heterogeneity in a cellular population.
Abstract: http://links.ealert.nature.com/ctt?kn=55&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=97&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Tn-seq: high-throughput parallel sequencing for fitness and genetic
interaction studies in microorganisms pp767 - 772
Tim van Opijnen, Kip L Bodi and Andrew Camilli
doi:10.1038/nmeth.1377
High-throughput sequencing of Mariner transposon insertion libraries
is used for quantitative studies of fitness and of genetic
interactions in Streptococcus pneumoniae. The approach should allow
similar studies in several microorganismal species.
Abstract: http://links.ealert.nature.com/ctt?kn=56&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=106&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
=========================== ADVERTISEMENT ===========================
Nature Methods is 5 years old!!!
To celebrate the 5-year anniversary of Nature Methods launch, the October 2009 issue will contain a special feature highlighting critical methods developments and their importance in biological research.
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TECHNOLOGY FEATURE
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Getting inside their minds pp773 - 781
Michael Eisenstein
doi:10.1038/nmeth1009-773
Neuroscientists are taking advantage of powerful new tools for
fluorescence imaging that enable detailed visualization of the
structure and activity of neuronal circuits within the living brain.
http://links.ealert.nature.com/ctt?kn=101&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
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APPLICATION NOTES
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Optimized library preparation method for next-generation sequencing
Fraz Syed, Haiying Grunenwald and Nicholas Caruccio
Abstract: http://links.ealert.nature.com/ctt?kn=53&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=41&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
In vivo real-time optical coherence tomography imaging of Drosophila
for cardiovascular research
Jon Holmes
Abstract: http://links.ealert.nature.com/ctt?kn=54&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=35&m=34085723&r=MTc2NjExMzUwMAS2&b=2&j=NTg2Njg1MzkS1&mt=1&rt=0
=========================== ADVERTISEMENT ===========================
Method of the Year 2009
Help Nature Methods select the breakthrough laboratory method of the year for 2009.
To cast your vote and nominate candidate methods visit:
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