Cold Spring Harbor Protocols features methods for analyzing genomes and plant cells|
COLD SPRING HARBOR, N.Y. (Monday, June 2, 2008) – With the sequencing of the human genome came the startling revelation that the number of copies of a genes and other DNA sequences can vary widely between individuals. This Copy Number Variation (or CNV), contributes to our species’ genetic diversity but it has also been linked to genetic diseases. This month’s issue of Cold Spring Harbor Protocols ( www.cshprotocols.org/TOCs/toc6_08.dtl ) features a new method for detecting copy number variation.
Copy Number Variation Detection Via High-Density SNP Genotyping describes the use of PennCNV, a new computational tool for CNV detection in data from genomic arrays. Developed in the laboratory of Maja Bucan ( http://www.neurogenome.org ) at the University of Pennsylvania, the software is freely available for download ( http://www.neurogenome.org/cnv/penncnv/ ). Analysis with PennCNV will provide a more comprehensive understanding of genome variation and will aid in studies seeking the causes of genetic diseases. The protocol is freely accessible on the website for Cold Spring Harbor Protocols ( http://www.cshprotocols.org/cgi/content/full/2008/7/pdb.top46 )
The second featured method for June, Isolation and Whole-Cell Patch Clamping of Arabidopsis Guard Cell Protoplasts, provides a method for analyzing ion differences across membranes, a vital step in understanding cellular responses to internal and external stimuli. This is particularly difficult to study in plant cells because they are surrounded by cell walls that make traditional techniques impossible. Pennsylvania State University’s Sarah Assmann ( http://www.bio.psu.edu/People/Faculty/Assmann/Lab/ ), provides a protocol that describes the isolation of plant cells without cell walls and the patch clamp method of measuring electrical differences inside and outside of these cells. This method is freely accessible on the website for Cold Spring Harbor Protocols ( http://www.cshprotocols.org/cgi/content/full/2008/7/pdb.prot5014 ).
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Cold Spring Harbor Protocols ( www.cshprotocols.org ) is a monthly peer-reviewed journal of methods used in a wide range of biology laboratories. It is structured to be highly interactive, with each protocol cross-linked to related methods, descriptive information panels, and illustrative material to maximize the total information available to investigators. Each protocol is clearly presented and designed for easy use at the bench—complete with reagents, equipment, and recipe lists. Life science researchers can access the entire collection via institutional site licenses, and can add their suggestions and comments to further refine the techniques.
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