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Nature Protocols is an online resource for protocols, including authoritative, peer-reviewed 'Nature Protocols' and an interactive 'Protocols Network'. The two create a dynamic forum for scientists to upload and comment on protocols.

Above image provided by Asli Silahtaroglu and Eugene Berezikov and is from the protocol 10.1038/nprot.2007.313

Featured Protocols

NUCLEIC ACID BASED MOLECULAR BIOLOGY

Loop-mediated isothermal amplification (LAMP) of gene sequences

By Norihiro Tomita, Yasuyoshi Mori, Hidetoshi Kanda and Tsugunori Notomi.

This protocol describes the loop-mediated isothermal amplification (LAMP) method of gene amplification. It also uses a fluorescent metal indicator system to allow simple visual detection of products.

CELL AND TISSUE CULTURE

3-D organotypic tissue arrays

By Celeste Nelson, Jamie Inman and Mina Bissell.

A simple micromolding method is described that enables the construction of 3-D arrays of organotypic epithelial tissue structures that approximate in vivo histology. Patterned tissue arrays can be produced in 3-4 h, that undergo morphogenesis over the following one to three days.

IMAGING

Colocalization of fluorescent markers in confocal microscope images of plant cells

By Andrew P French, Steven Mills, Ranjan Swarup, Malcolm J Bennett & Tony P Pridmore.

Immunocytochemical techniques for whole-mount in situ protein localization in plants

By Michael Sauer, Tomasz Paciorek, Eva Benková and Jiri Friml.

French et al. describe how to perform quantitative statistical colocalization on two-color confocal images, specifically of plant cells, and include a description of the alignment of the microscope. An excellent related protocol is that from Friml’s group.

BIOCHEMISTRY AND PROTEIN ANALYSIS

Southwestern blotting in investigating transcriptional regulation

By Francis K.Y. Siu, Leo T.O. Lee & Billy K.C. Chow.

Detecting protein-protein interactions by far western blotting

By Yuliang Wu, Qiang Li and Xing-Zhen Chen.

These two protocols describe different blotting methods to investigate protein-protein and protein-DNA interactions. In both techniques, proteins are firstly separated by polyacrylamide gel electrophoresis and blotted onto a membrane. Membranes are then probed to detect target interactions using either oligonucleotide probes (southwestern) or protein probes (far western).

SPECTROSCOPY AND STRUCTURAL ANALYSIS

Ambient Molecular Imaging by Desorption Electrospray Ionization (DESI) Mass Spectrometry

By Wiseman, Ifa, Venter & Cooks.

DESI does not require sample preparation besides production of microtome tissue slices and does not involve ionization matrices. It allows analysis of ordinary objects or pre-processed samples under ambient conditions. For instance, it can identify and record spatial distributions of lipids and drug molecules in tissue sections.