September 2008 Volume 5 Number 9, pp 749 - 850
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EDITORIALS
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Method of the Year 2008: cast your vote! p749
You can now nominate candidates and vote online to help select
the Method of the Year 2008.
doi:10.1038/nmeth0908-749a
http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RL0E3
Target practice pp749 - 750
A constant influx of new methods keeps research on microRNA biology
fast-paced and can provide divergent vantage points.
doi:10.1038/nmeth0908-749b
http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RM0E4
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RESEARCH HIGHLIGHTS
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microRNAs-subtler than you think p753
Two research groups apply quantitative proteomics to study the
effects of micro-RNAs on cellular proteins.
Natalie de Souza
doi:10.1038/nmeth0908-753
http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RN0E5
We the curators pp754 - 755
Two groups describe wiki platforms for community-based curation of
gene annotations or biological pathways.
Allison Doerr
doi:10.1038/nmeth0908-754a
http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RO0E6
Recombination: it takes four pp754 - 755
Researchers use tetrad analysis and high-density oligonucleotide
tiling arrays to generate a high-resolution map of meiotic
recombination events in budding yeast.
Michelle Pflumm
doi:10.1038/nmeth0908-754b
http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RP0E7
News in brief p755
doi:10.1038/nmeth0908-755
http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RQ0E8
New sensors from old p756
A serendipitous discovery reveals that an existing fluorescent
protein is actually a specific sensor for superoxide.
Daniel Evanko
doi:10.1038/nmeth0908-756
http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RR0EA
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NEWS AND VIEWS
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Sex to the rescue pp759 - 760
Applying a classical solution to a cutting-edge problem, two groups
used bacterial conjugation to construct Escherichia coli double
mutants on a genome-wide scale. This will allow comprehensive
genetic interaction screens in bacteria for the first time.
Thomas J Silhavy and Zemer Gitai
doi:10.1038/nmeth0908-759
http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RS0EB
Genetically encoded Ca2+ sensors come of age pp761 - 762
A decade after the introduction of genetically encoded Ca2+ indicator
proteins (GECIs), a new generation of improved GECIs demonstrates
their usefulness for the functional analysis of the mammalian brain
in vivo.
Nathalie L Rochefort and Arthur Konnerth
doi:10.1038/nmeth0908-761
http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RT0EC
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REVIEW
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Quantum dots versus organic dyes as fluorescent labels pp763 - 775
Ute Resch-Genger et al.
doi:10.1038/nmeth.1248
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RU0ED
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RV0EE
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BRIEF COMMUNICATION
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Efficient microRNA capture and bar-coding via enzymatic
oligonucleotide adenylation pp777 - 779
A simplified strategy to enzymatically preadenylate bar-coded
oligonucleotides to be used for capturing microRNAs in biological
samples is described. This efficient method should greatly facilitate
multiplex analysis and profiling of microRNAs.
Francois Vigneault, A Michael Sismour and George M Church
doi:10.1038/nmeth.1244
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RW0EF
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RX0EG
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ARTICLES
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High-throughput, quantitative analyses of genetic interactions in
E. coli pp781 - 787
An array-based high-throughput approach, genetic interaction analysis
technology for Escherichia coli (GIANT-coli), now allows
comprehensive genetic interaction screens in bacteria. The method
uses bacterial conjugation and robotic technology to generate double
mutants on a genome-wide scale. In this issue another paper presents
eSGA, a very similar approach.
Athanasios Typas et al.
doi:10.1038/nmeth.1240
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RY0EH
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4RZ0EI
eSGA: E. coli synthetic genetic array analysis pp789 - 795
An array-based high-throughput approach termed Escherichia coli
synthetic genetic array, or eSGA, now allows comprehensive genetic
interaction screens in bacteria . The method makes use of bacterial
conjugation and robotic technology to generate double mutants on a
genome-wide scale. In this issue, another paper presents GIANT-coli,
a very similar approach.
Gareth Butland et al.
doi:10.1038/nmeth.1239
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Ra0EP
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rb0EQ
Single-spike detection in vitro and in vivo with a genetic Ca2+
sensor pp797 - 804
Measurement of in vivo neuronal activity with single neuron and
single action potential resolution is important for studying neuronal
function. Delivery of a FRET-based fluorescent Ca2+ indicator protein
using adeno-associated virus results in high expression levels
allowing in vivo detection of single action potentials at low firing
rates. Griesbeck et al., also online, describe the use of a similar
sensor for recording neuronal activity in vivo.
Damian J Wallace et al.
doi:10.1038/nmeth.1242
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rc0ER
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rd0ES
A genetically encoded calcium indicator for chronic in vivo
two-photon imaging pp805 - 811
To study long-term changes in neuronal circuits at single-cell
resolution, a Troponin C-based Ca2+ indicator protein has been
reengineered to increase the signal strength. This allows repeated
measurements, over days and weeks, of orientation selective neurons
in mouse visual cortex. Hasan et al., also in this issue, describe
the use of a similar sensor for recording neuronal activity in vivo.
Marco Mank et al.
doi:10.1038/nmeth.1243
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Re0ET
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rf0EU
mirWIP: microRNA target prediction based on microRNA-containing
ribonucleoprotein-enriched transcripts pp813 - 819
A new prediction algorithm for microRNA targets, mirWIP, is
presented. The algorithm weights target site features based on
their enrichment in an experimentally defined immunoprecipitation
dataset and identifies verified miRNA-mRNA interactions in
Caenorhabditis elegans with improved specificity compared to current
methods.
Molly Hammell et al.
doi:10.1038/nmeth.1247
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rg0EV
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rh0EW
Holographic photolysis of caged neurotransmitters pp821 - 827
Holographic illumination allows the production of complex,
user-defined, two-dimensional illumination patterns. Used to
manipulate light-sensitive molecules in cells, this system permits
their simultaneous excitation at multiple locations of arbitrary
shape and size-facilitating spatial and temporal regulation
of cell function.
Christoph Lutz et al.
doi:10.1038/nmeth.1241
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Ri0EX
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rj0EY
Genome-wide analysis of transcription factor binding sites based on
ChIP-Seq data pp829 - 834
A chromatin immunoprecipitation and sequencing (ChIP-Seq) data
analysis package, QuEST, facilitates transcription factor binding
site discovery at about 20-base-pair resolution.
Anton Valouev et al.
doi:10.1038/nmeth.1246
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rk0EZ
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rl0Ea
Imaging dynamic cell-cell junctional coupling in vivo using
Trojan-LAMP pp835 - 841
Cell-cell coupling via gap junctions has been extensively studied in
vitro and in heterologous systems, but in vivo studies are still few.
A new class of photoactivatable bioconjugates is now used to monitor
gap junctional coupling in living Caenorhabditis elegans.
Yan-Ming Guo et al.
doi:10.1038/nmeth.1238
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rm0Eb
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rn0Ec
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TECHNOLOGY FEATURE
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Genomics: when the chemistry is good pp843 - 850
Could the latest high-throughput technologies propel chemical
genomics screens forward in academic settings? After 18 months
of careful design and planning, scientists at the Broad Institute's
chemical biology platform are about to flip the switches
and find out.
Nathan Blow
doi:10.1038/nmeth0908-843
http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rp0Ee
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APPLICATION NOTES
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Dry-state, room-temperature storage of DNA and RNA
Anjali G Kansagara, Heather E McMahon and Michael E Hogan
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rq0Ef
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rr0Eg
Transcriptome sequencing with the Genome Sequencer FLX system
Thomas Jarvie and Timothy Harkins
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rs0Eh
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rt0Ei
Supernatant in, kinetics out
Alexander Kovacs and Liselotte Kaiser
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Ru0Ej
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enDv0Xztnp0Hi80B4Rv0Ek
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