PDF - In This Issue

Special Feature: Method of the Year

Method of the Year 2008 - p1

doi:10.1038/nmeth.f.244

With its tremendous potential for understanding cellular biology now poised to become a reality, super-resolution fluorescence microscopy is our choice for Method of the Year.

Abstract - | Full Text - Method of the Year 2008 | PDF (53 KB) - Method of the Year 2008

Maturing interactions - p2

doi:10.1038/nmeth0109-2

The maturation of large-scale protein-protein interaction methodologies calls for improved methods to assess performance and data quality.

Abstract - | Full Text - Maturing interactions | PDF (52 KB) - Maturing interactions

Predicting free energy changes using structural ensembles - pp3 - 4

Alexander Benedix, Caroline M Becker, Bert L de Groot, Amedeo Caflisch & Rainer A Böckmann

doi:10.1038/nmeth0109-3

Full Text - Predicting free energy changes using structural ensembles | PDF (431 KB) - Predicting free energy changes using structural ensembles | Supplementary information

Targeted translational profiling - p7

Nicole Rusk

doi:10.1038/nmeth0109-7

Tagging ribosomes in a cell type–specific way allows the isolation of mRNAs that are being translated in these cells.

Abstract - | Full Text - Targeted translational profiling | PDF (421 KB) - Targeted translational profiling

Paving the path to single-molecule structures - pp8 - 9

Allison Doerr

doi:10.1038/nmeth0109-8a

A new generation of brilliant X-ray laser sources will be coming online within the next few years. Researchers now show that using these lasers to determine the structures of single molecules should be possible.

Abstract - | Full Text - Paving the path to single-molecule structures | PDF (143 KB) - Paving the path to single-molecule structures

Global instability - pp8 - 9

Amy Donner

doi:10.1038/nmeth0109-8b

Scientists create a high-throughput platform for proteome-scale assessment of protein stability.

Abstract - | Full Text - Global instability | PDF (143 KB) - Global instability

News in brief - p9

doi:10.1038/nmeth0109-9

Full Text - News in brief | PDF (80 KB) - News in brief

Good news travels fast - p10

Michael Eisenstein

doi:10.1038/nmeth0109-10

A new spin on a popular imaging technique allows researchers to accurately visualize tumors deep within the tissues of live mice.

Abstract - | Full Text - Good news travels fast | PDF (134 KB) - Good news travels fast

They know why the caged bird sings... slower - p12

Allison Doerr

doi:10.1038/nmeth0109-12

A device to cool localized areas of the zebra finch brain allows researchers to investigate how the timing of birdsong is controlled.

Abstract - | Full Text - They know why the caged bird sings... slower | PDF (82 KB) - They know why the caged bird sings... slower

Special Feature: Method of the Year

Super-resolution microscopy: breaking the limits - pp15 - 18

Kelly Rae Chi

doi:10.1038/nmeth.f.234

After a long period of measured development and a recent surge of technical advances driven by physicists, super-resolution fluorescence microscopy emerged in 2008 as a powerful tool for biologists. Kelly Rae Chi reports.

Abstract - | Full Text - Super-resolution microscopy: breaking the limits | PDF (765 KB) - Super-resolution microscopy: breaking the limits

Special Feature: Method of the Year

Primer: fluorescence imaging under the diffraction limit - pp19 - 20

Daniel Evanko

doi:10.1038/nmeth.f.235

A brief description of the theory and methods behind super-resolution fluorescence imaging.

Abstract - | Full Text - Primer: fluorescence imaging under the diffraction limit | PDF (355 KB) - Primer: fluorescence imaging under the diffraction limit

Special Feature: Method of the Year

Putting super-resolution fluorescence microscopy to work - pp21 - 23

Jennifer Lippincott-Schwartz & Suliana Manley

doi:10.1038/nmeth.f.233

Super-resolution microscopy is poised to revolutionize our understanding of the workings of the cell. But the technology still has some limitations, and these must be taken into consideration if widespread application is to yield biological insight.

Abstract - | Full Text - Putting super-resolution fluorescence microscopy to work | PDF (371 KB) - Putting super-resolution fluorescence microscopy to work

Special Feature: Method of the Year

Microscopy and its focal switch - pp24 - 32

Stefan W Hell

doi:10.1038/nmeth.1291

Abstract - | Full Text - Microscopy and its focal switch | PDF (513 KB) - Microscopy and its focal switch

Special Feature: Method of the Year

Induced pluripotency - p33

Natalie de Souza

doi:10.1038/nmeth.f.236

Methods to reprogram somatic cells to pluripotency have improved and will improve further; more biological studies of these cells are forthcoming.

First Paragraph - | Full Text - Induced pluripotency | PDF (420 KB) - Induced pluripotency

Special Feature: Method of the Year

Synthetic life - p33

Nicole Rusk

doi:10.1038/nmeth.f.237

After constructing a synthetic genome, the challenge is to prove its functionality.

First Paragraph - | Full Text - Synthetic life | PDF (420 KB) - Synthetic life

Special Feature: Method of the Year

Imaging through automation - p34

Daniel Evanko

doi:10.1038/nmeth.f.238

Automated imaging has the power to transform microscopy into a more quantitative technique with new capabilities.

First Paragraph - | Full Text - Imaging through automation | PDF (312 KB) - Imaging through automation

Special Feature: Method of the Year

Quantitative mass spectrometry - p34

Allison Doerr

doi:10.1038/nmeth.f.239

Quantitative mass spectrometry–based proteomics is now being applied on a large scale to address interesting biological questions.

First Paragraph - | Full Text - Quantitative mass spectrometry | PDF (312 KB) - Quantitative mass spectrometry

Special Feature: Method of the Year

Membrane protein structures - p35

Allison Doerr

doi:10.1038/nmeth.f.240

New methods addressing the challenges in membrane protein expression, solubilization and crystallization promise to yield many more atomic structures.

First Paragraph - | Full Text - Membrane protein structures | PDF (163 KB) - Membrane protein structures

Special Feature: Method of the Year

Optical imaging in thick samples - p35

Natalie de Souza

doi:10.1038/nmeth.f.241

Optical methods to image deep into thick samples make it increasingly possible to watch biological processes in vivo.

First Paragraph - | Full Text - Optical imaging in thick samples | PDF (163 KB) - Optical imaging in thick samples

Special Feature: Method of the Year

Experimental micro-matchmaking - p36

Nicole Rusk

doi:10.1038/nmeth.f.242

Although microRNA target predictions are continually improving, high-throughput validation of direct interaction is still needed.

First Paragraph - | Full Text - Experimental micro-matchmaking | PDF (182 KB) - Experimental micro-matchmaking

Special Feature: Method of the Year

Controlling cell function with light - p36

Daniel Evanko

doi:10.1038/nmeth.f.243

The use of light for active cellular control rather than just passive observation continues to make headway.

First Paragraph - | Full Text - Controlling cell function with light | PDF (182 KB) - Controlling cell function with light

Inhibiting microRNA function in vivo - pp37 - 38

Pedro P Medina & Frank J Slack

doi:10.1038/nmeth0109-37

A new strategy is presented to functionally knock down microRNAs in a mouse.

Abstract - | Full Text - Inhibiting microRNA function in vivo | PDF (154 KB) - Inhibiting microRNA function in vivo

Literature-curated protein interaction datasets - pp39 - 46

Michael E Cusick, Haiyuan Yu, Alex Smolyar, Kavitha Venkatesan, Anne-Ruxandra Carvunis, Nicolas Simonis, Jean-François Rual, Heather Borick, Pascal Braun, Matija Dreze, Jean Vandenhaute, Mary Galli, Junshi Yazaki, David E Hill, Joseph R Ecker, Frederick P Roth & Marc Vidal

doi:10.1038/nmeth.1284

Abstract - | Full Text - Literature-curated protein interaction datasets | PDF (261 KB) - Literature-curated protein interaction datasets | Supplementary information

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network - pp47 - 54

Nicolas Simonis, Jean-François Rual, Anne-Ruxandra Carvunis, Murat Tasan, Irma Lemmens, Tomoko Hirozane-Kishikawa, Tong Hao, Julie M Sahalie, Kavitha Venkatesan, Fana Gebreab, Sebiha Cevik, Niels Klitgord, Changyu Fan, Pascal Braun, Ning Li, Nono Ayivi-Guedehoussou, Elizabeth Dann, Nicolas Bertin, David Szeto, Amélie Dricot, Muhammed A Yildirim, Chenwei Lin, Anne-Sophie de Smet, Huey-Ling Kao, Christophe Simon, Alex Smolyar, Jin Sook Ahn, Muneesh Tewari, Mike Boxem, Stuart Milstein, Haiyuan Yu, Matija Dreze, Jean Vandenhaute, Kristin C Gunsalus, Michael E Cusick, David E Hill, Jan Tavernier, Frederick P Roth & Marc Vidal

doi:10.1038/nmeth.1279

High-throughput yeast two-hybrid screening is used to generate the largest C. elegans interactome resource available thus far. Using an empirical quality control framework presented in Venkatesan et al., also online, the data set is evaluated for quality and is used to estimate the total size of the worm interactome.

Abstract - | Full Text - Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network | PDF (631 KB) - Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network | Supplementary information

Cost-effective strategies for completing the interactome - pp55 - 61

Ariel S Schwartz, Jingkai Yu, Kyle R Gardenour, Russell L Finley Jr & Trey Ideker

doi:10.1038/nmeth.1283

Different experimental designs for protein interaction mapping are modeled to compare their efficiency in completing an interactome map. Testing of the strategy that minimized the final experimental cost in an ongoing Drosophila melanogaster interactome project found 450 high-confidence interactions using only 47 microtiter plates.

Abstract - | Full Text - Cost-effective strategies for completing the interactome | PDF (538 KB) - Cost-effective strategies for completing the interactome | Supplementary information

Stable knockdown of microRNA in vivo by lentiviral vectors - pp63 - 66

Bernhard Gentner, Giulia Schira, Alice Giustacchini, Mario Amendola, Brian D Brown, Maurilio Ponzoni & Luigi Naldini

doi:10.1038/nmeth.1277

To study microRNA function in vivo, the authors optimize lentiviral-driven expression of microRNA target sequences in mice and show dose-dependent inhibition of microRNA-mediated regulation of reporter constructs as well as of natural microRNA targets. With the inhibition of a miR-223, they can phenocopy the knockout of this microRNA.

Abstract - | Full Text - Stable knockdown of microRNA in vivo by lentiviral vectors | PDF (358 KB) - Stable knockdown of microRNA in vivo by lentiviral vectors | Supplementary information

Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing - pp67 - 69

Chad Nusbaum, Toshiro K Ohsumi, James Gomez, John Aquadro, Thomas C Victor, Robert M Warren, Deborah T Hung, Bruce W Birren, Eric S Lander & David B Jaffe

doi:10.1038/nmeth.1286

This variant ascertainment algorithm, or VAAL, uses short sequence reads of haploid bacterial genomes to first locally assemble the reads and then compare these assemblies to the reference genome. This allows VAAL to detect all types of variants ranging from single-nucleotide polymorphisms to large insertions or deletions.

Abstract - | Full Text - Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing | PDF (124 KB) - Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing | Supplementary information

An in vitro microfluidic approach to generating protein-interaction networks - pp71 - 74

Doron Gerber, Sebastian J Maerkl & Stephen R Quake

doi:10.1038/nmeth.1289

A combination of in vitro protein synthesis and microfluidics is used to measure protein-protein interactions between 43 proteins in Streptococcus pneumoniae. The method does not require expression within cells and is amenable to large-scale experiments.

Abstract - | Full Text - An in vitro microfluidic approach to generating protein-interaction networks | PDF (492 KB) - An in vitro microfluidic approach to generating protein-interaction networks | Supplementary information

Integrated network analysis platform for protein-protein interactions - pp75 - 77

Jianmin Wu, Tea Vallenius, Kristian Ovaska, Jukka Westermarck, Tomi P Mäkelä & Sampsa Hautaniemi

doi:10.1038/nmeth.1282

A web-based protein-protein interaction (PPI) analysis platform called PINA integrates PPI data from six public databases and provides tools to aid in the construction and analysis of PPI networks, including local recuration and annotation of existing records and manual addition of new records.

Abstract - | Full Text - Integrated network analysis platform for protein-protein interactions | PDF (428 KB) - Integrated network analysis platform for protein-protein interactions | Supplementary information

Infrared laser–mediated gene induction in targeted single cells in vivo - pp79 - 81

Yasuhiro Kamei, Motoshi Suzuki, Kenjiro Watanabe, Kazuhiro Fujimori, Takashi Kawasaki, Tomonori Deguchi, Yoshihiro Yoneda, Takeshi Todo, Shin Takagi, Takashi Funatsu & Shunsuke Yuba

doi:10.1038/nmeth.1278

An infrared laser is used to activate gene expression from a heat shock promoter in single cells in Caenorhabditis elegans, and is shown to be more effective and less detrimental to cells than a visible laser used for this purpose.

Abstract - | Full Text - Infrared laser–mediated gene induction in targeted single cells in vivo | PDF (313 KB) - Infrared laser–mediated gene induction in targeted single cells in vivo | Supplementary information

An empirical framework for binary interactome mapping - pp83 - 90

Kavitha Venkatesan, Jean-François Rual, Alexei Vazquez, Ulrich Stelzl, Irma Lemmens, Tomoko Hirozane-Kishikawa, Tong Hao, Martina Zenkner, Xiaofeng Xin, Kwang-Il Goh, Muhammed A Yildirim, Nicolas Simonis, Kathrin Heinzmann, Fana Gebreab, Julie M Sahalie, Sebiha Cevik, Christophe Simon, Anne-Sophie de Smet, Elizabeth Dann, Alex Smolyar, Arunachalam Vinayagam, Haiyuan Yu, David Szeto, Heather Borick, Amélie Dricot, Niels Klitgord, Ryan R Murray, Chenwei Lin, Maciej Lalowski, Jan Timm, Kirstin Rau, Charles Boone, Pascal Braun, Michael E Cusick, Frederick P Roth, David E Hill, Jan Tavernier, Erich E Wanker, Albert-László Barabási & Marc Vidal

doi:10.1038/nmeth.1280

A framework based on numerous empirical data, including protein-protein interaction reference sets, provides parameters for assessing the quality and coverage of protein-protein interaction datasets and estimation of the size of the human interactome. Braun et al., also in this issue, use the reference sets to help derive confidence scores for individual protein-protein interactions.

Abstract - | Full Text - An empirical framework for binary interactome mapping | PDF (556 KB) - An empirical framework for binary interactome mapping | Supplementary information

An experimentally derived confidence score for binary protein-protein interactions - pp91 - 97

Pascal Braun, Murat Tasan, Matija Dreze, Miriam Barrios-Rodiles, Irma Lemmens, Haiyuan Yu, Julie M Sahalie, Ryan R Murray, Luba Roncari, Anne-Sophie de Smet, Kavitha Venkatesan, Jean-François Rual, Jean Vandenhaute, Michael E Cusick, Tony Pawson, David E Hill, Jan Tavernier, Jeffrey L Wrana, Frederick P Roth & Marc Vidal

doi:10.1038/nmeth.1281

Use of the protein-protein interaction reference sets reported in this issue in Venkatesan et al. to benchmark four complementary protein-protein interaction assays, followed by the training of a logistic regression model, allows the assignment of standardized confidence scores to individual protein-protein interactions.

Abstract - | Full Text - An experimentally derived confidence score for binary protein-protein interactions | PDF (421 KB) - An experimentally derived confidence score for binary protein-protein interactions | Supplementary information

High-resolution mapping of copy-number alterations with massively parallel sequencing - pp99 - 103

Derek Y Chiang, Gad Getz, David B Jaffe, Michael J T O'Kelly, Xiaojun Zhao, Scott L Carter, Carsten Russ, Chad Nusbaum, Matthew Meyerson & Eric S Lander

doi:10.1038/nmeth.1276

Massively parallel sequencing is a precise way to analyze copy-number variations given the right computational tools. An algorithm now facilitates the detection and fine mapping of copy-number gains and losses from millions of short sequence reads.

Abstract - | Full Text - High-resolution mapping of copy-number alterations with massively parallel sequencing | PDF (1,440 KB) - High-resolution mapping of copy-number alterations with massively parallel sequencing | Supplementary information

High-throughput screening: designer screens - pp105 - 108

Nathan Blow

doi:10.1038/nmeth0109-105

Some researchers say an eighty-year-old statistical method can make setting up and analyzing high-throughput screens and large-scale experiments faster and more efficient. So why are more biologists not flocking to use this tool?

Abstract - | Full Text - High-throughput screening: designer screens | PDF (405 KB) - High-throughput screening: designer screens

Erratum: On display on a bug: a systematic approach to characterize antibodies - p109

Thomas Knorpp & Markus F Templin

doi:10.1038/nmeth0109-109a

Full Text - Erratum: On display on a bug: a systematic approach to characterize antibodies | PDF (40 KB) - Erratum: On display on a bug: a systematic approach to characterize antibodies

Erratum: Much room for improvement in deposition rates of expression microarray datasets - p109

Scott A Ochsner, David L Steffen, Christian J Stoeckert Jr & Neil J McKenna

doi:10.1038/nmeth0109-109b

Full Text - Erratum: Much room for improvement in deposition rates of expression microarray datasets | PDF (40 KB) - Erratum: Much room for improvement in deposition rates of expression microarray datasets