PDF - In This Issue

Summer reading: science in fiction - p471

doi:10.1038/nmeth0709-471

Though somewhat rare, there are a few good fiction books to be found with refreshingly realistic biologists as central characters in laboratory settings.

Abstract - | Full Text - Summer reading: science in fiction | PDF (71 KB) - Summer reading: science in fiction

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions - pp473 - 474

Seunghak Lee, Fereydoun Hormozdiari, Can Alkan & Michael Brudno

doi:10.1038/nmeth.f.256

Full Text - MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions | PDF (308 KB) - MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions | Supplementary information

Limitations and possibilities of small RNA digital gene expression profiling - pp474 - 476

Sam E V Linsen, Elzo de Wit, Georges Janssens, Sheila Heater, Laura Chapman, Rachael K Parkin, Brian Fritz, Stacia K Wyman, Ewart de Bruijn, Emile E Voest, Scott Kuersten, Muneesh Tewari & Edwin Cuppen

doi:10.1038/nmeth0709-474

Full Text - Limitations and possibilities of small RNA digital gene expression profiling | PDF (612 KB) - Limitations and possibilities of small RNA digital gene expression profiling | Supplementary information

RNAiCut: automated detection of significant genes from functional genomic screens - pp476 - 477

Irene M Kaplow, Rohit Singh, Adam Friedman, Chris Bakal, Norbert Perrimon & Bonnie Berger

doi:10.1038/nmeth0709-476

Full Text - RNAiCut: automated detection of significant genes from functional genomic screens | PDF (445 KB) - RNAiCut: automated detection of significant genes from functional genomic screens | Supplementary information

Enabling IMAC purification of low abundance recombinant proteins from E. coli lysates - pp477 - 478

Audur Magnusdottir, Ida Johansson, Lars-Göran Dahlgren, Pär Nordlund & Helena Berglund

doi:10.1038/nmeth0709-477

Full Text - Enabling IMAC purification of low abundance recombinant proteins from E. coli lysates | PDF (579 KB) - Enabling IMAC purification of low abundance recombinant proteins from E. coli lysates | Supplementary information

A question of culture - p481

Natalie de Souza

doi:10.1038/nmeth0709-481

Two groups report culture conditions for long-term in vitro growth of intestinal tissue from the mouse.

Abstract - | Full Text - A question of culture | PDF (182 KB) - A question of culture

Fluorescent proteins: into the infrared - pp482 - 483

Allison Doerr

doi:10.1038/nmeth0709-482a

An engineered infrared fluorescent protein is the first member of a new class of genetically encodable probes, with special advantages over visible-wavelength fluorescent proteins for in vivo imaging.

Abstract - | Full Text - Fluorescent proteins: into the infrared | PDF (137 KB) - Fluorescent proteins: into the infrared

Going with the skewed flow - pp482 - 483

Wayne Peng

doi:10.1038/nmeth0709-482b

Computational and experimental biologists teamed up to develop a new software tool to analyze the rich data generated by new and powerful flow cytometers.

Abstract - | Full Text - Going with the skewed flow | PDF (137 KB) - Going with the skewed flow

News in brief - p483

doi:10.1038/nmeth0709-483

Full Text - News in brief | PDF (89 KB) - News in brief

Grafting as a potent molecular tool - p484

Nicole Rusk

doi:10.1038/nmeth0709-484

Grafting two transgenic plants triggers lateral gene transfer at the graft site but does not elicit long-distance transport of DNA into the scion or root of the graft.

Abstract - | Full Text - Grafting as a potent molecular tool | PDF (93 KB) - Grafting as a potent molecular tool

Fluorescent false neurotransmitters - p486

Daniel Evanko

doi:10.1038/nmeth0709-486

A fluorescent probe designed to incorporate a fluorophore into the structure of a neurotransmitter finds activity-dependent heterogeneity in dopamine release at individual synapses.

Abstract - | Full Text - Fluorescent false neurotransmitters | PDF (89 KB) - Fluorescent false neurotransmitters

Will planets reveal the light of their life? - p487

Michael Eisenstein

doi:10.1038/nmeth0709-487

Optical signatures from organic chemicals may help scientists detect traces of life on other planets.

Abstract - | Full Text - Will planets reveal the light of their life? | PDF (86 KB) - Will planets reveal the light of their life?

Finding multiple needles in one immune haystack - pp489 - 490

Katherine Kedzierska, John Stambas & Peter C Doherty

doi:10.1038/nmeth0709-489

An approach using multiple fluorochrome combinations allows the simultaneous detection of many T-cell populations within a single blood sample.

Abstract - | Full Text - Finding multiple needles in one immune haystack | PDF (288 KB) - Finding multiple needles in one immune haystack

See also: Article by Hadrup et al. | Brief Communication by Newell et al.

Downhill protein folding under pressure - pp490 - 491

Victor Muñoz

doi:10.1038/nmeth0709-490

Sub-microsecond, downhill-reaction protein folding can be investigated by a method to generate large and fast pressure drops. The approach is complementary to nanosecond temperature-jump methods and could provide new insights into the biophysics of protein folding.

Abstract - | Full Text - Downhill protein folding under pressure | PDF (175 KB) - Downhill protein folding under pressure

See also: Article by Dumont et al.

Agouti C57BL/6N embryonic stem cells for mouse genetic resources - pp493 - 495

Stephen J Pettitt, Qi Liang, Xin Y Rairdan, Jennifer L Moran, Haydn M Prosser, David R Beier, Kent C Lloyd, Allan Bradley & William C Skarnes

doi:10.1038/nmeth.1342

Mouse embryonic stem cell lines from the C57BL/6 strain are reported. The lines are highly germline competent, suitable for high-throughput genetic manipulation and will enable the generation of large knockout mouse resources.

Abstract - | Full Text - Agouti C57BL/6N embryonic stem cells for mouse genetic resources | PDF (362 KB) - Agouti C57BL/6N embryonic stem cells for mouse genetic resources | Supplementary information

Simultaneous detection of many T-cell specificities using combinatorial tetramer staining - pp497 - 499

Evan W Newell, Lawrence O Klein, Wong Yu & Mark M Davis

doi:10.1038/nmeth.1344

Combinations of fluorescently labeled peptide–major histocompatability (pMHC) tetramers are used to simultaneously detect T cells with multiple antigen specificities from human blood samples. Also in this issue, Hadrup et al. present a very similar combinatorial encoding approach.

Abstract - | Full Text - Simultaneous detection of many T-cell specificities using combinatorial tetramer staining | PDF (434 KB) - Simultaneous detection of many T-cell specificities using combinatorial tetramer staining | Supplementary information

See also: News and Views by Kedzierska et al.

Protein interaction platforms: visualization of interacting proteins in yeast - pp500 - 502

Alexa M Schmitz, Monica F Morrison, Akochi O Agunwamba, Max L Nibert & Cammie F Lesser

doi:10.1038/nmeth.1337

The protein interaction platform or PIP assay uses a viral scaffolding protein fused to a bait and a fluorescent reporter protein fused to putative prey as the basis for a simple visual screen for protein-protein interactions in yeast.

Abstract - | Full Text - Protein interaction platforms: visualization of interacting proteins in yeast | PDF (384 KB) - Protein interaction platforms: visualization of interacting proteins in yeast | Supplementary information

Quantitative analysis of gene expression in a single cell by qPCR - pp503 - 506

Kiyomi Taniguchi, Tomoharu Kajiyama & Hideki Kambara

doi:10.1038/nmeth.1338

There have been many attempts to measure gene expression in single cells but counting several different mRNAs in the same cell has been a challenge. A reusable single-cell cDNA library immobilized on beads allows quantitative measurement of multiple mRNAs in a single cell with a large dynamic range and small experimental error.

Abstract - | Full Text - Quantitative analysis of gene expression in a single cell by qPCR | PDF (416 KB) - Quantitative analysis of gene expression in a single cell by qPCR | Supplementary information

Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection - pp507 - 510

Daniel S Herman, G Kees Hovingh, Oleg Iartchouk, Heidi L Rehm, Raju Kucherlapati, J G Seidman & Christine E Seidman

doi:10.1038/nmeth.1343

Concatenated PCR products serve as subgenomic traps in this targeted genome capture technique; subsequent high-throughput sequencing allows the detection of nucleotide and structural variations in the captured genomic regions.

Abstract - | Full Text - Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection | PDF (550 KB) - Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection | Supplementary information

In vivo fluorescence imaging with high-resolution microlenses - pp511 - 512

Robert P J Barretto, Bernhard Messerschmidt & Mark J Schnitzer

doi:10.1038/nmeth.1339

A combination of gradient refractive index lenses with plano-convex lenses produces high-resolution microlenses with image quality similar to a conventional high quality microscope objective. The microlenses are capable of imaging dendritic spines on hippocampal neurons in live mice.

Abstract - | Full Text - In vivo fluorescence imaging with high-resolution microlenses | PDF (306 KB) - In vivo fluorescence imaging with high-resolution microlenses | Supplementary information

'Injecting' yeast - pp513 - 514

Daniel Riveline & Paul Nurse

doi:10.1038/nmeth.1335

Using a topographically patterned substrate for immobilization of single yeast cells and a piezo-impact micromanipulator to transiently disrupt the cell wall, molecules can be physically introduced into yeast.

Abstract - | Full Text - 'Injecting' yeast | PDF (282 KB) - 'Injecting' yeast | Supplementary information

Reaching the protein folding speed limit with large, sub-microsecond pressure jumps - pp515 - 519

Charles Dumont, Tryggvi Emilsson & Martin Gruebele

doi:10.1038/nmeth.1336

Although fast temperature jump methods to study protein folding dynamics have long been applied, pressure has been a neglected thermodynamic parameter. A method to generate rapid and large drops in pressure is complementary to fast temperature jump methods and could be useful for direct comparisons to molecular dynamics simulations.

Abstract - | Full Text - Reaching the protein folding speed limit with large, sub-microsecond pressure jumps | PDF (408 KB) - Reaching the protein folding speed limit with large, sub-microsecond pressure jumps | Supplementary information

See also: News and Views by Muñoz

Parallel detection of antigen-specific T-cell responses by multidimensional encoding of MHC multimers - pp520 - 526

Sine Reker Hadrup, Arnold H Bakker, Chengyi J Shu, Rikke S Andersen, Jerre van Veluw, Pleun Hombrink, Emilie Castermans, Per thor Straten, Christian Blank, John B Haanen, Mirjam H Heemskerk & Ton N Schumacher

doi:10.1038/nmeth.1345

Using combinations of fluorescently labeled peptide–major histocompatability complex (pMHC) tetramers, T-cell populations with multiple antigen specificities can be monitored in parallel from small samples of human blood. Also in this issue, Newell et al. present a very similar combinatorial encoding method for this purpose.

Abstract - | Full Text - Parallel detection of antigen-specific T-cell responses by multidimensional encoding of MHC multimers | PDF (793 KB) - Parallel detection of antigen-specific T-cell responses by multidimensional encoding of MHC multimers | Supplementary information

See also: News and Views by Kedzierska et al.

Doxycycline-dependent photoactivated gene expression in eukaryotic systems - pp527 - 531

Sidney B Cambridge, Daniel Geissler, Federico Calegari, Konstantinos Anastassiadis, Mazahir T Hasan, A Francis Stewart, Wieland B Huttner, Volker Hagen & Tobias Bonhoeffer

doi:10.1038/nmeth.1340

Activation of caged doxycycline or cyanodoxycycline by biologically innocuous doses of UV light allows for precise temporal and spatial control of transgene expression in hippocampal slices, mouse embryos and Xenopus laevis tadpoles.

Abstract - | Full Text - Doxycycline-dependent photoactivated gene expression in eukaryotic systems | PDF (586 KB) - Doxycycline-dependent photoactivated gene expression in eukaryotic systems | Supplementary information

Mapping the structure and conformational movements of proteins with transition metal ion FRET - pp532 - 537

Justin W Taraska, Michael C Puljung, Nelson B Olivier, Galen E Flynn & William N Zagotta

doi:10.1038/nmeth.1341

Fluorescence resonance energy transfer (FRET) between a small-molecule fluorophore donor and a transition metal ion acceptor, a method called 'transition metal ion FRET,' works over shorter distances than the classical FRET approach and can thus be used to monitor very small conformational changes in proteins.

Abstract - | Full Text - Mapping the structure and conformational movements of proteins with transition metal ion FRET | PDF (822 KB) - Mapping the structure and conformational movements of proteins with transition metal ion FRET | Supplementary information

Genomics: catch me if you can - pp539 - 544

Nathan Blow

doi:10.1038/nmeth0709-539

Next-generation sequencing has made decoding entire genomes cheaper and faster. But what about those researchers who only want to sequence a small section of a genome or focus on a couple thousand specific exons? A wave of new technologies has recently emerged that should help these scientists target their sequencing efforts to sequences of interest.

Abstract - | Full Text - Genomics: catch me if you can | PDF (494 KB) - Genomics: catch me if you can

Corrigendum: A HUPO test sample study reveals common problems in mass spectrometry–based proteomics - p546

doi:10.1038/nmeth0709-546a

Full Text - Corrigendum: A HUPO test sample study reveals common problems in mass spectrometry–based proteomics | PDF (57 KB) - Corrigendum: A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

Erratum: Transposon-mediated genome manipulation in vertebrates - p546

doi:10.1038/nmeth0709-546b

Full Text - Erratum: Transposon-mediated genome manipulation in vertebrates | PDF (57 KB) - Erratum: Transposon-mediated genome manipulation in vertebrates

Analysis of 5' transcript heterogeneity by high-throughput sequencing of cDNA

Pietro D Spanu & Ken Doyle

Abstract - | Full Text - Analysis of 5' transcript heterogeneity by high-throughput sequencing of cDNA | PDF (401 KB) - Analysis of 5' transcript heterogeneity by high-throughput sequencing of cDNA

CYP2C9 and VKORC1 genotyping reagents from Idaho Technology: rapid turn-around, accurate results

Jason McKinney, Ranae Lems & Cameron Gundry

Abstract - | Full Text - CYP2C9 and VKORC1 genotyping reagents from Idaho Technology: rapid turn-around, accurate results | PDF (316 KB) - CYP2C9 and VKORC1 genotyping reagents from Idaho Technology: rapid turn-around, accurate results

Fluidigm Dynamic Arrays provide a platform for single-cell gene expression analysis

Martin Pieprzyk & Howard High

Abstract - | Full Text - Fluidigm Dynamic Arrays provide a platform for single-cell gene expression analysis | PDF (436 KB) - Fluidigm Dynamic Arrays provide a platform for single-cell gene expression analysis