August 2008 Volume 5 Number 8, pp 659 - 748
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EDITORIAL
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Going for algorithm gold p659
The use of organized competition to evaluate algorithm performance
would be very beneficial for small communities, not just large ones.
doi:10.1038/nmeth0808-659
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lN0Ec
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RESEARCH HIGHLIGHTS
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Induced pluripotency: is there a silver bullet? p661
Ongoing efforts show promise in replacing reprogramming factors with
small molecules for making induced pluripotent stem cells.
Natalie de Souza
doi:10.1038/nmeth0808-661
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lO0Ed
A time stamp for proteins pp662 - 663
A new protein tag simplifies labeling and visualization of newly
synthesized target proteins in tissue and whole animals.
Daniel Evanko
doi:10.1038/nmeth0808-662a
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lP0Ee
Talk among histones pp662 - 663
Using chemically assembled ubiquitylated histone H2B, researchers
demonstrate that direct cross-talk results in methylation of a lysine
on another histone.
Irene Kaganman
doi:10.1038/nmeth0808-662b
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lQ0Ef
News in brief p663
doi:10.1038/nmeth0808-663
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lR0Eg
Surviving the gas phase p664
Researchers demonstrate a method for observing intact membrane
protein complexes by mass spectrometry.
Allison Doerr
doi:10.1038/nmeth0808-664
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lS0Eh
Unraveling the nucleosome p666
Next-generation sequencing-based studies locate nucleosomes
at high resolution throughout several genomes.
Michelle Pflumm
doi:10.1038/nmeth0808-666
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lT0Ei
Multiplexing MRI p668
By engineering magnetic microstructures, researchers demonstrate
the potential for multiplexed MRI.
Allison Doerr
doi:10.1038/nmeth0808-668
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lU0Ej
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NEWS AND VIEWS
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Single-particle tracking: connecting the dots pp671 - 672
Algorithms for analyzing single-particle tracking images to obtain
the paths of individual particles are challenged by high-density data.
Improvements in algorithms help to overcome these limitations.
Michael J Saxton
doi:10.1038/nmeth0808-671
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lV0Ek
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PERSPECTIVE
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Engineering GPCR signaling pathways with RASSLs pp673 - 678
Bruce R Conklin et al.
doi:10.1038/nmeth.1232
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lW0El
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lX0Em
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BRIEF COMMUNICATIONS
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Alta-Cyclic: a self-optimizing base caller for next-generation
sequencing pp679 - 682
A new base caller for the Illumina Genome Analyzer uses machine
learning to compensate for noise factors and improves accuracy
for up to 78-base-pair sequencing reads.
Yaniv Erlich et al.
doi:10.1038/nmeth.1230
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lY0En
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lZ0Eo
Improving membrane voltage measurements using FRET with new
fluorescent proteins pp683 - 685
Designing fluorescent protein-based sensors that display large
changes in fluorescence resonance energy transfer (FRET) is
challenging. Redesign of a FRET-based voltage sensor using new
fluorescent proteins increased the sensor response to changes
in membrane voltage and measurements at warmer temperatures
displayed faster kinetics comparable to action potentials.
Hidekazu Tsutsui, Satoshi Karasawa, Yasushi Okamura and Atsushi
Miyawaki
doi:10.1038/nmeth.1235
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1la0Ev
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lb0Ew
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ARTICLES
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Dynamic multiple-target tracing to probe spatiotemporal cartography
of cell membranes pp687 - 694
Single-particle tracking methods allow detailed analysis of protein
movement in cells, but existing tracking algorithms have substantial
limitations, particularly at high particle densities. A new software
tool overcomes some of these limitations and can be used to track
high-density particles in cell membranes. Also in this issue,
Jaqaman et al. describe an alternative software tool for high-density
single-particle tracking.
Arnauld Serge, Nicolas Bertaux, Herve Rigneault and Didier Marguet
doi:10.1038/nmeth.1233
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1le0Ez
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lf0E1
Robust single-particle tracking in live-cell time-lapse
sequences pp695 - 702
Single-particle tracking methods allow detailed analysis of protein
movement in cells, but existing tracking algorithms have substantial
limitations, particularly at high particle densities. A new software
tool overcomes some of these limitations and is used to track CD36
receptors and assay the lifetime of clathrin-coated pits. Also in
this issue, Serge et al. describe an alternative software tool for
high-density single-particle tracking.
Khuloud Jaqaman et al.
doi:10.1038/nmeth.1237
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lg0E2
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lh0E3
Automated analysis of embryonic gene expression with cellular
resolution in C. elegans pp703 - 709
Automated imaging of the Caenorhabditis elegans embryo now
allows monitoring of the timing and relative expression of individual
reporter genes at single-cell resolution over almost all of embryonic
development. Future systematic analysis could be used to reveal
gene expression patterns of every cell during development.
John Isaac Murray et al.
doi:10.1038/nmeth.1228
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1li0E4
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lj0E5
A comprehensive strategy enabling high-resolution functional analysis
of the yeast genome pp711 - 718
To increase the range and precision of genetic interaction studies in
Saccharomyces cerevisiae, a collection of hypomorphic alleles of
essential yeast genes and a highly sensitive flow cytometry-based
growth competition assay are presented. Also in this issue,
Yan et al. present a similar strain collection, tagged with unique
bar-code identifiers, and use this collection in pooled chemical
genetic screens.
David K Breslow et al.
doi:10.1038/nmeth.1234
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lk0E6
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1Xb0Ec
Yeast Barcoders: a chemogenomic application of a universal
donor-strain collection carrying bar-code identifiers pp719 - 725
A library of universal Saccharomyces cerevisiae Barcoder strains
for efficient tagging is presented. It is used to tag a collection of
hypomorphic alleles of essential yeast genes and applied to
chemical genetic screens. Also in this issue, Breslow et al.
present a similar collection of hypomorphic alleles, coupled
with a sensitive growth assay for improved genetic interaction
studies.
Zhun Yan et al.
doi:10.1038/nmeth.1231
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1ll0E7
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1Xa0Eb
Detection of heteromerization of more than two proteins by sequential
BRET-FRET pp727 - 733
Many proteins, including G protein-coupled receptors (GPCRs),
interact to form oligomers at the cell surface. A combination of
bioluminescence resonance energy transfer (BRET) and
fluorescence resonance energy transfer (FRET) in a technique
called sequential resonance energy transfer (SRET) extends
these methods to study higher-order oligomers of GPCRs or
other proteins.
Paulina Carriba et al.
doi:10.1038/nmeth.1229
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lm0E8
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1ln0EA
Colloid-guided assembly of oriented 3D neuronal
networks pp735 - 740
In vitro studies of neuronal function have mainly been limited to
two-dimensional networks of cultured neurons. Use of transparent
colloids as a moveable support for neuronal growth allows user-guided
construction of optically accessible three-dimensional networks whose
function can be manipulated and measured.
Sophie Pautot, Claire Wyart and Ehud Y Isacoff
doi:10.1038/nmeth.1236
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lo0EB
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lp0EC
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TECHNOLOGY FEATURE
----------------------
Mass spectrometry and proteomics: hitting the mark pp741 - 747
Mass spectrometry instrumentation has made strides in recent years
in terms of dynamic range and sensitivity, putting researchers in a
better position to use the technology to tackle the challenges of
disease biomarker discovery and validation.
Nathan Blow
doi:10.1038/nmeth0808-741
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lq0ED
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CORRIGENDA
----------------------
Corrigendum: Identification of cross-linked peptides from large
sequence databases p748
Oliver Rinner et al.
doi:10.1038/nmeth0808-748a
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lr0EE
Corrigendum: BAC TransgeneOmics: a high-throughput method for
exploration of protein function in mammals p748
Ina Poser et al.
doi:10.1038/nmeth0808-748b
http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1ls0EF
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APPLICATION NOTES
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SuperSpinner D 1000: a disposable bioreactor for efficient lab-scale
cultivation of animal cells
Kathrin Schmale
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lt0EG
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lu0EH
Noninvasive, in vivo quantification of asthma severity using
fluorescence molecular tomography
Houari Korideck and Jeffrey D Peterson
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lv0EI
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emac0Xztnp0Hi80B1lw0EJ
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