Featured Protocols
On this page the Editors have selected particular protocols to highlight the diverse scope of the Nature Protocols content.
Functional analysis
Featured here are three methods useful for investigating key regulators of cellular pathways: protein kinases. Kinase activity can be measured using either radiolabeled ATP (Hastie et al.) or a FRET kinase probe based on pleckstrin (Brumbaugh et al.). A method for determining protein kinase sequence specificity is also described (Turk et al.).
Imaging
Monitoring development
Protocol by Hatta et al.Kaede, a green fluorescent protein from the stony coral Trachyphyllia geoffroyi, can be readily photoconverted to red by exposure to UV light. Hatta et al. show how Kaede can be used as a tool to study zebrafish cells during development. Injecting Kaede into fertilized eggs allows the labeling and monitoring of individual cells, whose movements can be monitored as development proceeds. This protocol can be applied to single axonal tracing in differentiating neurons.
Gene expression
Protocol by Choi and Schweizer
The lack of suitable tools has often frustrated microbiologists' attempts to implement key recombinant DNA techniques, such as gene cloning and reporter gene tagging. In an attempt to overcome the limitations associated with existing vectors, Herbert Schweizer and his team have developed a panel of easy-to-use, broad host-range mini-Tn7 transposon-based vectors that integrate at specific sites (attTn7) in the host genome. Here, they describe how to use these vectors in bacterial strains with different types and numbers of attTn7 sites.
Molecular interaction
ChIP-chip
Protocol by Lee et al.
Physical interactions between proteins and DNA govern many aspects of cell function, from gene expression to DNA repair. These interactions can be studied in living cells using chromatin immunoprecipitation (ChIP). Growing interest in mapping protein:DNA interactions on a genome-wide scale has resulted in the combination of ChIP with microarray analysis (ChIP-chip). The protocol presented here was developed in the lab of Richard Young, one of the early pioneers of this technique.
Protocols Network
Neurospheres
Protocol by Pacey et al.
In this protocol, uploaded directly by the authors, methods for neural stem cell culture are described, including dissection and isolation of cells, cryopreservation and preparation for immunocytochemistry.
Bioinformatics
Predicting functional associations
Protocol by Margolin et al.Modern technologies can gather vast quantities of information about gene and protein interactions, but analysing this data can be problematic. In this article, Andrea Califano and colleagues describe the use of ARACNE, an algorithm for predicting functional associations, as a method for carrying out these analyses.
