There’s a great article by Joseph Esposito in the current issue of the Journal of Electronic Publishing, “Open Access 2.0: Access to Scholarly Publications Moves to a New Phase” (found via the always informative Scholarly Kitchen blog). This article is required reading for anyone interested in the future of science publication, as it takes a hard look at the economic models available. Esposito argues that the problem with many of the current open access offerings is that they’re trying to replicate what’s already offered by established journals, rather than playing to the real strengths of open access, and that there’s certainly room in the market for many different types of offerings.

—article continues—
Read the rest of this entry »

In the past we’ve offered notice of new protocols published via RSS feed, and now we’ve added in this feature for all article types. You can now subscribe via RSS feed to Topic Introductions (articles that provide general and background information, theory and applications for methods) and Information Panels (smaller discrete pieces of information relevant to particular methods). You can catch the feeds here.

June’s issue of CSH Protocols brings a set of articles detailing the use of hormone response in the phenotypic analysis of mutants in plants. The protocols, Phenotypic Analysis of Arabidopsis Mutants: Auxin Hormone Response, Ethylene Hormone Response and Brassinosteroid Hormone Response, are part of a larger set of methods for phenotypic analysis of Arabidopsis mutants which have been published over the last few months (with more on the way soon). Previous articles cover growth parameters in phenotypic analysis, including hypocotyl length and root growth. Next month we’ll add a protocol for using flowering time, and future issues will address the response to the abiotic environment, bacterial pathogens, and oomycete pathogens. Histological and imaging techniques for phenotypic analysis are also part of our growing collection, and include sectioning of fixed material, scanning electron microscopy (SEM) and vital stain for cytoplasm. For information about obtaining mutants in Arabidopsis, please see Setting Up Arabidopsis Crosses and Genetic Analysis of Arabidopsis Mutants.

You’re probably familiar with patch clamping, a fairly common method used to measure currents across biological membranes. Patch clamping hits a roadblock though, when you’re dealing with an organism that has a cell wall. Sarah Assmann’s lab at Penn State University provides one of CSH Protocols’ June featured articles detailing methods for doing electrophysiology in plant cells. The first step is the generation of “protoplasts”, plant cells where the cell walls have been digested away enzymatically. From there, patch clamping follows in a relatively straightforward manner, although there are specific modifications necessary for individual species and cell-types. While this protocol deals with Arabidopsis guard cells, a table is given showing resources for information on cells in a variety of other plant species. Like all of our monthly featured articles, Isolation and Whole-Cell Patch Clamping of Arabidopsis Guard Cell Protoplasts is freely available to subscribers and non-subscribers.

With the sequencing of the human genome came the startling revelation that the number of copies of a given gene 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 features a new method for detecting copy number variation. Like all of our monthly featured protocols, it’s freely accessible for subscribers and non-subscribers alike.

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 at the University of Pennsylvania, the software is freely available for download. Analysis with PennCNV will provide a more comprehensive understanding of genome variation and will aid in studies seeking the causes of genetic diseases. More information on PennCNV can be found in this Genome Research article, PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.

The June issue of CSH Protocols is now out, and it occurred to me that many out there are probably not aware that there’s an easy system in place for receiving alerts via e-mail or RSS when new protocols are available. If you’re reading this blog via an RSS reader you can subscribe to the Table of Contents via RSS. When new articles are posted, you’ll see the abstracts in your RSS reader like you would a blog article. You can also sign up for alerts via e-mail. What’s nice about this system is that you can sign up for alerts when there’s a new Table of Contents, as well as alerts for new articles in a particular subject area, by a specific author or containing a specific keyword. You can also sign up for alerts for when an article is cited, corrected, or when a comment is left on a specific article. We won’t use your e-mail address for anything else (full privacy policy here). Hopefully these tools will help you stay connected and let you know when new useful protocols are available. Let us know if there are other features you’d like to see added.