PDF - In This Issue

Method of the Year 2008: cast your vote! - p749

doi:10.1038/nmeth0908-749a

You can now nominate candidates and vote online to help select the Method of the Year 2008.

Abstract - | Full Text - Method of the Year 2008: cast your vote! | PDF (72 KB) - Method of the Year 2008: cast your vote!

Target practice - pp749 - 750

doi:10.1038/nmeth0908-749b

A constant influx of new methods keeps research on microRNA biology fast-paced and can provide divergent vantage points.

Abstract - | Full Text - Target practice | PDF (80 KB) - Target practice

microRNAs—subtler than you think - p753

Natalie de Souza

doi:10.1038/nmeth0908-753

Two research groups apply quantitative proteomics to study the effects of microRNAs on cellular proteins.

Abstract - | Full Text - microRNAs—subtler than you think | PDF (148 KB) - microRNAs—subtler than you think

We the curators - pp754 - 755

Allison Doerr

doi:10.1038/nmeth0908-754a

Two groups describe wiki platforms for community-based curation of gene annotations or biological pathways.

Abstract - | Full Text - We the curators | PDF (218 KB) - We the curators

Recombination: it takes four - pp754 - 755

Michelle Pflumm

doi:10.1038/nmeth0908-754b

Researchers use tetrad analysis and high-density oligonucleotide tiling arrays to generate a high-resolution map of meiotic recombination events in budding yeast.

Abstract - | Full Text - Recombination: it takes four | PDF (218 KB) - Recombination: it takes four

News in brief - p755

doi:10.1038/nmeth0908-755

Full Text - News in brief | PDF (95 KB) - News in brief

New sensors from old - p756

Daniel Evanko

doi:10.1038/nmeth0908-756

A serendipitous discovery reveals that an existing fluorescent protein is actually a specific sensor for superoxide.

Abstract - | Full Text - New sensors from old | PDF (187 KB) - New sensors from old

Sex to the rescue - pp759 - 760

Thomas J Silhavy & Zemer Gitai

doi:10.1038/nmeth0908-759

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.

Abstract - | Full Text - Sex to the rescue | PDF (205 KB) - Sex to the rescue

See also: Article by Typas et al. | Article by Butland et al.

Genetically encoded Ca²⁺ sensors come of age - pp761 - 762

Nathalie L Rochefort & Arthur Konnerth

doi:10.1038/nmeth0908-761

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.

Abstract - | Full Text - Genetically encoded Ca2+ sensors come of age | PDF (220 KB) - Genetically encoded Ca2+ sensors come of age

See also: Article by Wallace et al. | Article by Mank et al.

Quantum dots versus organic dyes as fluorescent labels - pp763 - 775

Ute Resch-Genger, Markus Grabolle, Sara Cavaliere-Jaricot, Roland Nitschke & Thomas Nann

doi:10.1038/nmeth.1248

Abstract - | Full Text - Quantum dots versus organic dyes as fluorescent labels | PDF (610 KB) - Quantum dots versus organic dyes as fluorescent labels | Supplementary information

Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation - pp777 - 779

Francois Vigneault, A Michael Sismour & George M Church

doi:10.1038/nmeth.1244

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.

Abstract - | Full Text - Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation | PDF (177 KB) - Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation | Supplementary information

High-throughput, quantitative analyses of genetic interactions in E. coli - pp781 - 787

Athanasios Typas, Robert J Nichols, Deborah A Siegele, Michael Shales, Sean R Collins, Bentley Lim, Hannes Braberg, Natsuko Yamamoto, Rikiya Takeuchi, Barry L Wanner, Hirotada Mori, Jonathan S Weissman, Nevan J Krogan & Carol A Gross

doi:10.1038/nmeth.1240

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.

Abstract - | Full Text - High-throughput, quantitative analyses of genetic interactions in E. coli | PDF (407 KB) - High-throughput, quantitative analyses of genetic interactions in E. coli | Supplementary information

eSGA: E. coli synthetic genetic array analysis - pp789 - 795

Gareth Butland, Mohan Babu, J Javier Díaz-Mejía, Fedyshyn Bohdana, Sadhna Phanse, Barbara Gold, Wenhong Yang, Joyce Li, Alla G Gagarinova, Oxana Pogoutse, Hirotada Mori, Barry L Wanner, Henry Lo, Jas Wasniewski, Constantine Christopoulos, Mehrab Ali, Pascal Venn, Anahita Safavi-Naini, Natalie Sourour, Simone Caron, Ja-Yeon Choi, Ludovic Laigle, Anaies Nazarians-Armavil, Avnish Deshpande, Sarah Joe, Kirill A Datsenko, Natsuko Yamamoto, Brenda J Andrews, Charles Boone, Huiming Ding, Bilal Sheikh, Gabriel Moreno-Hagelsieb, Jack F Greenblatt & Andrew Emili

doi:10.1038/nmeth.1239

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.

Abstract - | Full Text - eSGA: E. coli synthetic genetic array analysis | PDF (528 KB) - eSGA: E. coli synthetic genetic array analysis | Supplementary information

Single-spike detection in vitro and in vivo with a genetic Ca²⁺ sensor - pp797 - 804

Damian J Wallace, Stephan Meyer zum Alten Borgloh, Simone Astori, Ying Yang, Melanie Bausen, Sebastian Kügler, Amy E Palmer, Roger Y Tsien, Rolf Sprengel, Jason N D Kerr, Winfried Denk & Mazahir T Hasan

doi:10.1038/nmeth.1242

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 in this issue, describe the use of a similar sensor for recording neuronal activity in vivo.

Abstract - | Full Text - Single-spike detection in vitro and in vivo with a genetic Ca2+ sensor | PDF (910 KB) - Single-spike detection in vitro and in vivo with a genetic Ca2+ sensor | Supplementary information

A genetically encoded calcium indicator for chronic in vivo two-photon imaging - pp805 - 811

Marco Mank, Alexandre Ferrão Santos, Stephan Direnberger, Thomas D Mrsic-Flogel, Sonja B Hofer, Valentin Stein, Thomas Hendel, Dierk F Reiff, Christiaan Levelt, Alexander Borst, Tobias Bonhoeffer, Mark Hübener & Oliver Griesbeck

doi:10.1038/nmeth.1243

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.

Abstract - | Full Text - A genetically encoded calcium indicator for chronic in vivo two-photon imaging | PDF (516 KB) - A genetically encoded calcium indicator for chronic in vivo two-photon imaging | Supplementary information

mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein–enriched transcripts - pp813 - 819

Molly Hammell, Dang Long, Liang Zhang, Andrew Lee, C Steven Carmack, Min Han, Ye Ding & Victor Ambros

doi:10.1038/nmeth.1247

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.

Abstract - | Full Text - mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein–enriched transcripts | PDF (249 KB) - mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein–enriched transcripts | Supplementary information

Holographic photolysis of caged neurotransmitters - pp821 - 827

Christoph Lutz, Thomas S Otis, Vincent DeSars, Serge Charpak, David A DiGregorio & Valentina Emiliani

doi:10.1038/nmeth.1241

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.

Abstract - | Full Text - Holographic photolysis of caged neurotransmitters | PDF (553 KB) - Holographic photolysis of caged neurotransmitters | Supplementary information

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data - pp829 - 834

Anton Valouev, David S Johnson, Andreas Sundquist, Catherine Medina, Elizabeth Anton, Serafim Batzoglou, Richard M Myers & Arend Sidow

doi:10.1038/nmeth.1246

A chromatin immunoprecipitation and sequencing (ChIP-Seq) data analysis package, QuEST, facilitates transcription factor binding site discovery at about 20-base-pair resolution.

Abstract - | Full Text - Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data | PDF (349 KB) - Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data | Supplementary information

Imaging dynamic cell-cell junctional coupling in vivo using Trojan-LAMP - pp835 - 841

Yan-Ming Guo, Shiuhwei Chen, Premnath Shetty, Genhua Zheng, Rueyling Lin & Wen-hong Li

doi:10.1038/nmeth.1238

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.

Abstract - | Full Text - Imaging dynamic cell-cell junctional coupling in vivo using Trojan-LAMP | PDF (469 KB) - Imaging dynamic cell-cell junctional coupling in vivo using Trojan-LAMP | Supplementary information

Genomics: when the chemistry is good - pp843 - 850

Nathan Blow

doi:10.1038/nmeth0908-843

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.

Full Text - Genomics: when the chemistry is good | PDF (487 KB) - Genomics: when the chemistry is good

Dry-state, room-temperature storage of DNA and RNA

Anjali G Kansagara, Heather E McMahon & Michael E Hogan

Abstract - | Full Text - Dry-state, room-temperature storage of DNA and RNA | PDF (270 KB) - Dry-state, room-temperature storage of DNA and RNA

Transcriptome sequencing with the Genome Sequencer FLX system

Thomas Jarvie & Timothy Harkins

Abstract - | Full Text - Transcriptome sequencing with the Genome Sequencer FLX system | PDF (303 KB) - Transcriptome sequencing with the Genome Sequencer FLX system

Supernatant in, kinetics out

Alexander Kovacs & Liselotte Kaiser

Abstract - | Full Text - Supernatant in, kinetics out | PDF (268 KB) - Supernatant in, kinetics out