PDF - In This Issue

What's in a test? - p783

doi:10.1038/nmeth1109-783

Abstract - What's in a test? | Full Text - What's in a test? | PDF (65 KB) - What's in a test?

Spin filter–based sample preparation for shotgun proteomics - p785

Daniel C Liebler & Amy-Joan L Ham

doi:10.1038/nmeth1109-785a

Full Text - Spin filter–based sample preparation for shotgun proteomics | PDF (108 KB) - Spin filter–based sample preparation for shotgun proteomics | Supplementary information

Reply to "Spin filter–based sample preparation for shotgun proteomics" - pp785 - 786

Jacek R Winiewski & Matthias Mann

doi:10.1038/nmeth1109-785b

Full Text - Spin filter–based sample preparation for shotgun proteomics | PDF (195 KB) - Spin filter–based sample preparation for shotgun proteomics | Supplementary information

Improved visualization of protein consensus sequences by iceLogo - pp786 - 787

Niklaas Colaert, Kenny Helsens, Lennart Martens, Joël Vandekerckhove & Kris Gevaert

doi:10.1038/nmeth1109-786

Full Text - Improved visualization of protein consensus sequences by iceLogo | PDF (324 KB) - Improved visualization of protein consensus sequences by iceLogo | Supplementary information

Faster than a speeding blood cell - p789

Michael Eisenstein

doi:10.1038/nmeth1109-789

A new in vivo imaging strategy produces detailed maps of tumor microvasculature and lymphatic vessels without injected labels.

Abstract - Faster than a speeding blood cell | Full Text - Faster than a speeding blood cell | PDF (276 KB) - Faster than a speeding blood cell

A fluid situation - pp790 - 791

Natalie de Souza

doi:10.1038/nmeth1109-790a

By monitoring the size-dependence of particle distribution in the lamellipodium, fluid flow in moving cells can be measured.

Abstract - A fluid situation | Full Text - A fluid situation | PDF (162 KB) - A fluid situation

The true RNA-seq - pp790 - 791

Nicole Rusk

doi:10.1038/nmeth1109-790b

With a modified polymerase and optimized oligonucleotide chemistry, Helicos' single-molecule sequencer takes on RNA.

Abstract - The true RNA-seq | Full Text - The true RNA-seq | PDF (162 KB) - The true RNA-seq

News in brief - p791

doi:10.1038/nmeth1109-791

Full Text - News in brief | PDF (90 KB) - News in brief

Keep your eye on the atom - p792

Allison Doerr

doi:10.1038/nmeth1109-792

Researchers use atomic force microscopy to image the chemical structure of the small molecule pentacene, with atomic resolution.

Abstract - Keep your eye on the atom | Full Text - Keep your eye on the atom | PDF (157 KB) - Keep your eye on the atom

Silence restored - p794

Michael Eisenstein

doi:10.1038/nmeth1109-794

Certain yeast previously assumed to lack RNA interference machinery instead have alternative enzyme variants, which can in turn be transplanted to truly deficient species.

Abstract - Silence restored | Full Text - Silence restored | PDF (87 KB) - Silence restored

You too can play with an edge - pp797 - 798

Michael Costanzo, Anastasia Baryshnikova, Corey Nislow, Brenda Andrews & Charles Boone

doi:10.1038/nmeth1109-797

Abstract - You too can play with an edge | Full Text - You too can play with an edge | PDF (1,484 KB) - You too can play with an edge

See also: Brief Communication by Ear & Michnick | Article by Dreze et al.

Adding a spatial dimension to the proteome - pp798 - 800

Kay Grünewald

doi:10.1038/nmeth1109-798

Abstract - Adding a spatial dimension to the proteome | Full Text - Adding a spatial dimension to the proteome | PDF (391 KB) - Adding a spatial dimension to the proteome

See also: Article by Beck et al.

Foreword - p801

Nicole Rusk

doi:10.1038/nmeth1109-801

Full Text - Foreword | PDF (177 KB) - Foreword

Summary of the Online Focus on next-generation sequencing data analysis - p802 - 803

doi:10.1038/nmeth1109-802

Full Text - Summary of the Online Focus on next-generation sequencing data analysis | PDF (280 KB) - Summary of the Online Focus on next-generation sequencing data analysis

A chemical platform for improved induction of human iPSCs - pp805 - 808

Tongxiang Lin, Rajesh Ambasudhan, Xu Yuan, Wenlin Li, Simon Hilcove, Ramzey Abujarour, Xiangyi Lin, Heung Sik Hahm, Ergeng Hao, Alberto Hayek & Sheng Ding

doi:10.1038/nmeth.1393

A cocktail of three small molecules improves the efficiency of reprogramming human fibroblasts to induced pluripotent stem cells and allows survival of the cells after trypsinization.

Abstract - A chemical platform for improved induction of human iPSCs | Full Text - A chemical platform for improved induction of human iPSCs | PDF (847 KB) - A chemical platform for improved induction of human iPSCs | Supplementary information

Enrichment of glycopeptides for glycan structure and attachment site identification - pp809 - 811

Jonas Nilsson, Ulla Rüetschi, Adnan Halim, Camilla Hesse, Elisabet Carlsohn, Gunnar Brinkmalm & Göran Larson

doi:10.1038/nmeth.1392

Glycan structure, attachment site and the glycoprotein from which it came can be identified with a method to enrich for glycoproteins from complex biological samples, digest them on a bead and release the glycopeptides for mass spectrometry analysis.

Abstract - Enrichment of glycopeptides for glycan structure and attachment site identification | Full Text - Enrichment of glycopeptides for glycan structure and attachment site identification | PDF (349 KB) - Enrichment of glycopeptides for glycan structure and attachment site identification | Supplementary information

A general life-death selection strategy for dissecting protein functions - pp813 - 816

Po Hien Ear & Stephen W Michnick

doi:10.1038/nmeth.1389

Activity of yeast cytosine deaminase can be both positively and negatively selected by adjusting growth conditions. Adapting this life-death selection to a protein complementation assay based on the enzyme allows dissection of protein-protein interactions and protein functions in yeast.

Abstract - A general life-death selection strategy for dissecting protein functions | Full Text - A general life-death selection strategy for dissecting protein functions | PDF (907 KB) - A general life-death selection strategy for dissecting protein functions | Supplementary information

See also: News and Views by Costanzo et al.

Visual proteomics of the human pathogen Leptospira interrogans - pp817 - 823

Martin Beck, Johan A Malmström, Vinzenz Lange, Alexander Schmidt, Eric W Deutsch & Ruedi Aebersold

doi:10.1038/nmeth.1390

Protein complexes can be detected, counted and localized within the bacterium Leptospira interrogans by combining quantitative mass spectrometry–based proteomics analysis with cryo-electron tomography, with the aid of an improved template-matching method.

Abstract - Visual proteomics of the human pathogen : Leptospira interrogans | Full Text - Visual proteomics of the human pathogen Leptospira interrogans | PDF (1,517 KB) - Visual proteomics of the human pathogen Leptospira interrogans | Supplementary information

See also: News and Views by Grünewald

Engineering splicing factors with designed specificities - pp825 - 830

Yang Wang, Cheom-Gil Cheong, Traci M Tanaka Hall & Zefeng Wang

doi:10.1038/nmeth.1379

Engineered splicing factors, consisting of an RNA recognition motif and a functional splicing module, can target a specific mRNA sequence and activate or suppress splicing of endogenous mRNAs.

Abstract - Engineering splicing factors with designed specificities | Full Text - Engineering splicing factors with designed specificities | PDF (1,162 KB) - Engineering splicing factors with designed specificities | Supplementary information

High-resolution, long-term characterization of bacterial motility using optical tweezers - pp831 - 835

Taejin L Min, Patrick J Mears, Lon M Chubiz, Christopher V Rao, Ido Golding & Yann R Chemla

doi:10.1038/nmeth.1380

Optically trapping an individual E. coli cell allows the long-term quantification of bacterial swimming phenotype: the stochastic transitions between 'running' and 'tumbling' as well as changes in swimming speed and direction.

Abstract - High-resolution, long-term characterization of bacterial motility using optical tweezers | Full Text - High-resolution, long-term characterization of bacterial motility using optical tweezers | PDF (949 KB) - High-resolution, long-term characterization of bacterial motility using optical tweezers | Supplementary information

High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology - pp837 - 842

Marieke Simonis, Petra Klous, Irene Homminga, Robert-Jan Galjaard, Erik-Jan Rijkers, Frank Grosveld, Jules P P Meijerink & Wouter de Laat

doi:10.1038/nmeth.1391

Chromatin conformation capture on chip, or 4C, a technique developed to investigate the interaction of one chromosomal region with the rest of the chromatin, can also provide high resolution mapping of translocations and inversions in selected chromosomal regions.

Abstract - High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology | Full Text - High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology | PDF (1,010 KB) - High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology | Supplementary information

'Edgetic' perturbation of a C. elegans BCL2 ortholog - pp843 - 849

Matija Dreze, Benoit Charloteaux, Stuart Milstein, Pierre-Olivier Vidalain, Muhammed A Yildirim, Quan Zhong, Nenad Svrzikapa, Viviana Romero, Géraldine Laloux, Robert Brasseur, Jean Vandenhaute, Mike Boxem, Michael E Cusick, David E Hill & Marc Vidal

doi:10.1038/nmeth.1394

A combination of forward and reverse two hybrid screening allows systematic identification of 'edgetic' or edge-specific alleles, which encode proteins that have lost a single physical interaction but for which other interactions remain unperturbed.

Abstract - 'Edgetic' perturbation of a : C. elegans: BCL2 ortholog | Full Text - 'Edgetic' perturbation of a C. elegans BCL2 ortholog | PDF (969 KB) - 'Edgetic' perturbation of a C. elegans BCL2 ortholog | Supplementary information

See also: News and Views by Costanzo et al.

Antibody production branches out - pp851 - 856

Alan Dove

doi:10.1038/nmeth1109-851

Antibodies, the molecular workhorses of protein research, have traditionally been one of the most difficult reagents to procure. Using innovative new technologies, though, a burgeoning antibody production industry is turning these molecules into commodities.

Abstract - Antibody production branches out | Full Text - Antibody production branches out | PDF (549 KB) - Antibody production branches out

Next-generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition

Fraz Syed, Haiying Grunenwald & Nicholas Caruccio

Abstract - Next-generation sequencing library preparation: simultaneous fragmentation and tagging using : in vitro: transposition | Full Text - Next-generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition | PDF (332 KB) - Next-generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition

SENSOLUX^® stand-alone version: noninvasive determination of pH and DO in shake flasks

Kathrin Schmale

Abstract - SENSOLUX: [reg]: stand-alone version: noninvasive determination of pH and DO in shake flasks | Full Text - SENSOLUX® stand-alone version: noninvasive determination of pH and DO in shake flasks | PDF (298 KB) - SENSOLUX® stand-alone version: noninvasive determination of pH and DO in shake flasks

hMSC differentiation marker detection using Thermo Scientific Solaris^™ qPCR Gene Expression Assays

Zaklina Strezoska, Yuriy Fedorov & Melissa L Kelley

Abstract - hMSC differentiation marker detection using Thermo Scientific Solaris: [trade]: qPCR Gene Expression Assays | Full Text - hMSC differentiation marker detection using Thermo Scientific Solaris™ qPCR Gene Expression Assays | PDF (373 KB) - hMSC differentiation marker detection using Thermo Scientific Solaris™ qPCR Gene Expression Assays