A protocol for differential display of mRNA expression using either fluorescent or radioactive labeling - pp457 - 470

Peng Liang, Jonathan D Meade & Arthur B Pardee

Published online: 15 March 2007 | doi:10.1038/nprot.2007.46

Abstract - | Full Text - A protocol for differential display of mRNA expression using either fluorescent or radioactive labeling | PDF (486 KB) - A protocol for differential display of mRNA expression using either fluorescent or radioactive labeling

Heterotopic vascularized murine cardiac transplantation to study graft arteriopathy - pp471 - 480

Tomomi Hasegawa, Scott H Visovatti, Matthew C Hyman, Takanori Hayasaki & David J Pinsky

Published online: 15 March 2007 | doi:10.1038/nprot.2007.48

Abstract - | Full Text - Heterotopic vascularized murine cardiac transplantation to study graft arteriopathy | PDF (537 KB) - Heterotopic vascularized murine cardiac transplantation to study graft arteriopathy

A protocol for isolation and culture of human umbilical vein endothelial cells - pp481 - 485

Bruno Baudin, Arnaud Bruneel, Nelly Bosselut & Michel Vaubourdolle

Published online: 15 March 2007 | doi:10.1038/nprot.2007.54

Abstract - | Full Text - A protocol for isolation and culture of human umbilical vein endothelial cells | PDF (197 KB) - A protocol for isolation and culture of human umbilical vein endothelial cells

A simple, robust and semi-automated parasite egg isolation protocol - pp486 - 489

Ted HM Mes, Maarten Eysker & Harm W Ploeger

Published online: 15 March 2007 | doi:10.1038/nprot.2007.56

Abstract - | Full Text - A simple, robust and semi-automated parasite egg isolation protocol | PDF (161 KB) - A simple, robust and semi-automated parasite egg isolation protocol

In vitro screening for molecules that affect virus capsid assembly (and other protein association reactions) - pp490 - 498

Adam Zlotnick, Angela Lee, Christina R Bourne, Jennifer M Johnson, Paul L Domanico & Stephen J Stray

Published online: 15 March 2007 | doi:10.1038/nprot.2007.60

Abstract - | Full Text - In vitro screening for molecules that affect virus capsid assembly (and other protein association reactions) | PDF (281 KB) - In vitro screening for molecules that affect virus capsid assembly (and other protein association reactions)

Acquisition and voxelwise analysis of multi-subject diffusion data with Tract-Based Spatial Statistics - pp499 - 503

Stephen M Smith, Heidi Johansen-Berg, Mark Jenkinson, Daniel Rueckert, Thomas E Nichols, Karla L Miller, Matthew D Robson, Derek K Jones, Johannes C Klein, Andreas J Bartsch & Timothy E J Behrens

Published online: 15 March 2007 | doi:10.1038/nprot.2007.45

Abstract - | Full Text - Acquisition and voxelwise analysis of multi-subject diffusion data with Tract-Based Spatial Statistics | PDF (325 KB) - Acquisition and voxelwise analysis of multi-subject diffusion data with Tract-Based Spatial Statistics

The chemoinvasion assay: a method to assess tumor and endothelial cell invasion and its modulation - pp504 - 511

Adriana Albini & Roberto Benelli

Published online: 15 March 2007 | doi:10.1038/nprot.2006.466

Abstract - | Full Text - The chemoinvasion assay: a method to assess tumor and endothelial cell invasion and its modulation | PDF (323 KB) - The chemoinvasion assay: a method to assess tumor and endothelial cell invasion and its modulation

Immuno-spin trapping analyses of DNA radicals - pp512 - 522

Dario C Ramirez, Sandra E Gomez-Mejiba & Ronald P Mason

Published online: 15 March 2007 | doi:10.1038/nprot.2007.5

Abstract - | Full Text - Immuno-spin trapping analyses of DNA radicals | PDF (291 KB) - Immuno-spin trapping analyses of DNA radicals

Design and construction of targeted AAVP vectors for mammalian cell transduction - pp523 - 531

Amin Hajitou, Roberto Rangel, Martin Trepel, Suren Soghomonyan, Juri G Gelovani, Mian M Alauddin, Renata Pasqualini & Wadih Arap

Published online: 15 March 2007 | doi:10.1038/nprot.2007.51

Abstract - | Full Text - Design and construction of targeted AAVP vectors for mammalian cell transduction | PDF (318 KB) - Design and construction of targeted AAVP vectors for mammalian cell transduction

Labeling, detection and identification of newly synthesized proteomes with bioorthogonal non-canonical amino-acid tagging - pp532 - 540

Daniela C Dieterich, Jennifer J Lee, A James Link, Johannes Graumann, David A Tirrell & Erin M Schuman

Published online: 15 March 2007 | doi:10.1038/nprot.2007.52

Abstract - | Full Text - Labeling, detection and identification of newly synthesized proteomes with bioorthogonal non-canonical amino-acid tagging | PDF (276 KB) - Labeling, detection and identification of newly synthesized proteomes with bioorthogonal non-canonical amino-acid tagging

Chemically induced mouse models of intestinal inflammation - pp541 - 546

Stefan Wirtz, Clemens Neufert, Benno Weigmann & Markus F Neurath

Published online: 15 March 2007 | doi:10.1038/nprot.2007.41

Abstract - | Full Text - Chemically induced mouse models of intestinal inflammation | PDF (236 KB) - Chemically induced mouse models of intestinal inflammation

Freeze-fracture electron microscopy - pp547 - 576

Nicholas J Severs

Published online: 22 March 2007 | doi:10.1038/nprot.2007.55

Abstract - | Full Text - Freeze-fracture electron microscopy | PDF (2,471 KB) - Freeze-fracture electron microscopy

Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes - pp577 - 587

Heike Fiegler, Richard Redon & Nigel P Carter

Published online: 22 March 2007 | doi:10.1038/nprot.2007.53

Abstract - | Full Text - Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes | PDF (529 KB) - Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes

Data analysis of assorted serum peptidome profiles - pp588 - 602

Josep Villanueva, John Philip, Lin DeNoyer & Paul Tempst

Published online: 29 March 2007 | doi:10.1038/nprot.2007.57

Abstract - | Full Text - Data analysis of assorted serum peptidome profiles | PDF (1,135 KB) - Data analysis of assorted serum peptidome profiles | Supplementary information

Sequencing complete mitochondrial and plastid genomes - pp603 - 614

Gertraud Burger, Dennis V Lavrov, Lise Forget & B Franz Lang

Published online: 22 March 2007 | doi:10.1038/nprot.2007.59

Abstract - | Full Text - Sequencing complete mitochondrial and plastid genomes | PDF (260 KB) - Sequencing complete mitochondrial and plastid genomes

See also: Protocol by Lang & Burger

Synthesis and oligonucleotide incorporation of fluorescent cytosine analogue tC: a promising nucleic acid probe - pp615 - 623

Peter Sandin, Per Lincoln, Tom Brown & L Marcus Wilhelmsson

Published online: 22 March 2007 | doi:10.1038/nprot.2007.80

Abstract - | Full Text - Synthesis and oligonucleotide incorporation of fluorescent cytosine analogue tC: a promising nucleic acid probe | PDF (194 KB) - Synthesis and oligonucleotide incorporation of fluorescent cytosine analogue tC: a promising nucleic acid probe

Parallel synthesis of peptide libraries using microwave irradiation - pp624 - 631

Justin K Murray & Samuel H Gellman

Published online: 22 March 2007 | doi:10.1038/nprot.2007.23

Abstract - | Full Text - Parallel synthesis of peptide libraries using microwave irradiation | PDF (1,112 KB) - Parallel synthesis of peptide libraries using microwave irradiation

The use of the Ugi four-component condensation - pp632 - 639

Stefano Marcaccini & Tomás Torroba

Published online: 22 March 2007 | doi:10.1038/nprot.2007.71

Abstract - | Full Text - The use of the Ugi four-component condensation | PDF (251 KB) - The use of the Ugi four-component condensation | Supplementary information

Selenium modification of nucleic acids: preparation of phosphoroselenoate derivatives for crystallographic phasing of nucleic acid structures - pp640 - 646

Pradeep S Pallan & Martin Egli

Published online: 22 March 2007 | doi:10.1038/nprot.2007.74

Abstract - | Full Text - Selenium modification of nucleic acids: preparation of phosphoroselenoate derivatives for crystallographic phasing of nucleic acid structures | PDF (277 KB) - Selenium modification of nucleic acids: preparation of phosphoroselenoate derivatives for crystallographic phasing of nucleic acid structures

See also: Protocol by Pallan & Egli

Selenium modification of nucleic acids: preparation of oligonucleotides with incorporated 2'-SeMe-uridine for crystallographic phasing of nucleic acid structures - pp647 - 651

Pradeep S Pallan & Martin Egli

Published online: 22 March 2007 | doi:10.1038/nprot.2007.75

Abstract - | Full Text - Selenium modification of nucleic acids: preparation of oligonucleotides with incorporated 2'-SeMe-uridine for crystallographic phasing of nucleic acid structures | PDF (190 KB) - Selenium modification of nucleic acids: preparation of oligonucleotides with incorporated 2'-SeMe-uridine for crystallographic phasing of nucleic acid structures

See also: Protocol by Pallan & Egli

Purification of mitochondrial and plastid DNA - pp652 - 660

B Franz Lang & Gertraud Burger

Published online: 22 March 2007 | doi:10.1038/nprot.2007.58

Abstract - | Full Text - Purification of mitochondrial and plastid DNA | PDF (211 KB) - Purification of mitochondrial and plastid DNA

See also: Protocol by Burger et al.

Non-invasive measurement of bioelectric currents with a vibrating probe - pp661 - 669

Brian Reid, Richard Nuccitelli & Min Zhao

Published online: 29 March 2007 | doi:10.1038/nprot.2007.91

Abstract - | Full Text - Non-invasive measurement of bioelectric currents with a vibrating probe | PDF (368 KB) - Non-invasive measurement of bioelectric currents with a vibrating probe

Mixed-culture assays for analyzing neuronal synapse formation - pp670 - 676

Thomas Biederer & Peter Scheiffele

Published online: 29 March 2007 | doi:10.1038/nprot.2007.92

Abstract - | Full Text - Mixed-culture assays for analyzing neuronal synapse formation | PDF (192 KB) - Mixed-culture assays for analyzing neuronal synapse formation

Pulsed-field gel electrophoresis - pp677 - 684

Jill Herschleb, Gene Ananiev & David C Schwartz

Published online: 29 March 2007 | doi:10.1038/nprot.2007.94

Abstract - | Full Text - Pulsed-field gel electrophoresis | PDF (602 KB) - Pulsed-field gel electrophoresis | Supplementary information

MetaNetwork: a computational protocol for the genetic study of metabolic networks - pp685 - 694

Jingyuan Fu, Morris A Swertz, Joost JB Keurentjes & Ritsert C Jansen

Published online: 29 March 2007 | doi:10.1038/nprot.2007.96

Abstract - | Full Text - MetaNetwork: a computational protocol for the genetic study of metabolic networks | PDF (957 KB) - MetaNetwork: a computational protocol for the genetic study of metabolic networks | Supplementary information

Uptake and release protocol for assessing membrane binding and permeation by way of isothermal titration calorimetry - pp695 - 704

Alekos D Tsamaloukas, Sandro Keller & Heiko Heerklotz

Published online: 29 March 2007 | doi:10.1038/nprot.2007.98

Abstract - | Full Text - Uptake and release protocol for assessing membrane binding and permeation by way of isothermal titration calorimetry | PDF (340 KB) - Uptake and release protocol for assessing membrane binding and permeation by way of isothermal titration calorimetry | Supplementary information

A protocol describing pharynx counts and a review of other assays of apoptotic cell death in the nematode worm Caenorhabditis elegans - pp705 - 714

Hillel T Schwartz

Published online: 29 March 2007 | doi:10.1038/nprot.2007.93

Abstract - | Full Text - A protocol describing pharynx counts and a review of other assays of apoptotic cell death in the nematode worm Caenorhabditis elegans | PDF (580 KB) - A protocol describing pharynx counts and a review of other assays of apoptotic cell death in the nematode worm Caenorhabditis elegans

Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry - pp715 - 726

Helena Hernández & Carol V Robinson

Published online: 22 March 2007 | doi:10.1038/nprot.2007.73

Abstract - | Full Text - Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry | PDF (1,483 KB) - Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox - pp727 - 738

Scott A Becker, Adam M Feist, Monica L Mo, Gregory Hannum, Bernhard Ø Palsson & Markus J Herrgard

Published online: 29 March 2007 | doi:10.1038/nprot.2007.99

Abstract - | Full Text - Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox | PDF (359 KB) - Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox | Supplementary information

Global single-cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis - pp739 - 752

Kazuki Kurimoto, Yukihiro Yabuta, Yasuhide Ohinata & Mitinori Saitou

Published online: 29 March 2007 | doi:10.1038/nprot.2007.79

Abstract - | Full Text - Global single-cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis | PDF (382 KB) - Global single-cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis

A real-time method of imaging glucose uptake in single, living mammalian cells - pp753 - 762

Katsuya Yamada, Mikako Saito, Hideaki Matsuoka & Nobuya Inagaki

Published online: 29 March 2007 | doi:10.1038/nprot.2007.76

Abstract - | Full Text - A real-time method of imaging glucose uptake in single, living mammalian cells | PDF (764 KB) - A real-time method of imaging glucose uptake in single, living mammalian cells