July 2008 Volume 5 Number 7, pp 577 - 658
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EDITORIAL
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Byte-ing off more than you can chew p577
With access to high-throughput technologies, researchers struggle
to store their raw data. Many just give up.
doi:10.1038/nmeth0708-577
http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYR0E6
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RESEARCH HIGHLIGHTS
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Fish fingers on the menu p579
Zebrafish researchers rejoice! Reverse genetics is now on the menu,
thanks to zinc-finger nucleases.
Veronique Kiermer
doi:10.1038/nmeth0708-579
http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYS0E7
Living droplets pp580 - 581
Tiny droplets of water in oil can serve as miniature culture vessels
for living single cells and multicellular organisms.
Daniel Evanko
doi:10.1038/nmeth0708-580a
http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYT0E8
Chemical biology: New electrophilic probes slide in pp580 - 581
Recently discovered electrophilic probes open the door to
activity-based protein profiling (ABPP) studies of a broader
range of proteins.
Michelle Pflumm
doi:10.1038/nmeth0708-580b
http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYU0EA
News in brief p581
doi:10.1038/nmeth0708-581
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Live-cell map quest p582
A high-resolution interactome map that describes how proteins
interact in living yeast cells is an invaluable reference for the
research community.
Irene Kaganman
doi:10.1038/nmeth0708-582
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NEWS AND VIEWS
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The beginning of the end for microarrays? pp585 - 587
Two complementary approaches, both using next-generation sequencing,
have successfully tackled the scale and the complexity of mammalian
transcriptomes, at once revealing unprecedented detail and allowing
better quantification.
Jay Shendure
doi:10.1038/nmeth0708-585
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Hunting hidden transcripts pp587 - 589
Strategies for the comprehensive identification of transcript
isoforms produced from specific genomic loci make use of and expand
existing tools and resources.
Piero Carninci
doi:10.1038/nmeth0708-587
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Microfluidics: streamlining discovery in worm biology pp589 - 590
Advances in the application of microfluidics technology to
biological assays using the model organism Caenorhabditis
elegans help to automate otherwise time-consuming experiments.
S Elizabeth Hulme, Sergey S Shevkoplyas and Aravinthan Samuel
doi:10.1038/nmeth0708-589
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PERSPECTIVE
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Whispering-gallery-mode biosensing: label-free detection down to
single molecules pp591 - 596
Frank Vollmer and Stephen Arnold
doi:10.1038/nmeth.1221
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYa0EM
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYb0EN
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BRIEF COMMUNICATIONS
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Isoform discovery by targeted cloning, 'deep-well' pooling and
parallel sequencing pp597 - 600
The complete set of coding sequences, including all splice isoforms,
is not known for any metazoan organism. Combination of a normalized
pooling scheme and a new assembly algorithm with 454 sequencing
yields a methodological pipeline for isoform discovery. The validated
pipeline may now be applied genome-wide.
Kourosh Salehi-Ashtiani et al.
doi:10.1038/nmeth.1224
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYc0EO
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYd0EP
Transgenesis via permanent integration of genes in repopulating
spermatogonial cells in vivo pp601 - 603
Conventional techniques for generating transgenic mice are quite
costly, require substantial resources and necessitate killing the
mouse. In contrast, in vivo electroporation of repopulating
spermatogonial cells in the mouse testis can produce male mice for
siring multiple distinctive transgenic founders for over a year.
Suveera Dhup and Subeer S Majumdar
doi:10.1038/nmeth.1225
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYe0EQ
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYf0ER
Lifeact: a versatile marker to visualize F-actin pp605 - 607
Current approaches for live imaging of cellular actin dynamics have
several drawbacks. Now the use of Lifeact, a 17-aa actin-binding
peptide from yeast that is not present in higher eukaryotes, allows
imaging of actin dynamics in live mammalian cells without disruption
of function and without competition with endogenous binding proteins.
Julia Riedl et al.
doi:10.1038/nmeth.1220
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYg0ES
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYh0ET
In vitro whole-organ imaging: 4D quantification of growing mouse
limb buds pp609 - 612
A combination of improved in vitro embryo culture and optical
projection tomography allows development of the mouse limb bud to be
monitored over time. Developmental changes seen in vitro are
benchmarked against in vivo development, and tissue movements
are quantitatively described.
Marit J Boot et al.
doi:10.1038/nmeth.1219
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYi0EU
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYj0EV
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ARTICLES
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Stem cell transcriptome profiling via massive-scale mRNA
sequencing pp613 - 619
Application of next-generation sequencing using the ABI SOLiD
technology to mammalian transcriptome analysis enabled a survey
of the content, the complexity and the developmental dynamics of
the embryonic stem cell transcriptome in the mouse. Also in this
issue, Mortazavi et al. report Illumina technology-based RNA-Seq
analysis of the mouse transcriptome in three different tissues.
Nicole Cloonan et al.
doi:10.1038/nmeth.1223
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYl0EX
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYm0EY
Mapping and quantifying mammalian transcriptomes by
RNA-Seq pp621 - 628
The mouse transcriptome in three tissue types has been analyzed
using Illumina next-generation sequencing technology. This
quantitative RNA-Seq methodology has been used for expression
analysis and splice isoform discovery and to confirm or extend
reference gene models. Also in this issue, another paper reports
application of the ABI SOLiD technology to sequence the transcriptome
in mouse embryonic stem cells.
Ali Mortazavi et al.
doi:10.1038/nmeth.1226
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYn0EZ
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYo0Ea
Efficient targeted transcript discovery via array-based normalization
of RACE libraries pp629 - 635
Sarah Djebali et al.
doi:10.1038/nmeth.1216
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYp0Eb
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYq0Ec
Automated on-chip rapid microscopy, phenotyping and sorting of
C. elegans pp637 - 643
A major bottleneck for genetic approaches in model organisms is the
application of state-of-the-art technologies to phenotyping.
Now, using a microfluidic chip, high-resolution imaging of
fluorescent reporters and accurate sorting is demonstrated
in an automated manner in Caenorhabditis elegans.
Kwanghun Chung, Matthew M Crane and Hang Lu
doi:10.1038/nmeth.1227
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYr0Ed
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYs0Ee
Functional immobilization of signaling proteins enables control
of stem cell fate pp645 - 650
Cells in vivo are exposed not only to soluble factors but also to
immobilized ligands. Controlled immobilization of functional growth
factors yields dose-dependent responses in mouse embryonic stem
cells in vitro and allows the effects of immobilized versus soluble
ligands to be studied.
Kristin Alberti et al.
doi:10.1038/nmeth.1222
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYt0Ef
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYu0Eg
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TECHNOLOGY FEATURE
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Imaging and detection: focusing on software pp651 - 658
In designing microscopy software to take advantage of better hardware,
developers are facing challenges of accessibility, functionality
and usability.
Kelly Rae Chi
doi:10.1038/nmeth0708-651
http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYv0Eh
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APPLICATION NOTE
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Rapid, fail-early identification of toxic compounds in secondary screening
Janice D Broadbridge, Anna Swan and Nicol D Watson
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYw0Ei
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eltq0Xztnp0Hi80ByYx0Ej
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