May’s issue of Cold Spring Harbor Protocols saw the publication of the final two species from Volume I of our “Emerging Model Organisms” series. These articles have been collected and made available as a laboratory manual. June’s issue brings us the first species from Volume II, the Honeybee (Apis mellifera).

Because of their obviously important role in pollination, a great deal of recent research has gone into investigating diseases which affect honeybees, such as Colony Collapse Disorder. Bees also exhibit remarkable social behavior, complex learning and memory and language skills, making them an excellent system for neuroscience research into these topics. The haplo-diploid sex determination system of bees is also of great interest. The sequenced genome of honeybees has allowed for comparisons with other species, with some surprising results. The genes underlying circadian rhythms in bees are much more like those in mouse than those found in Drosophila. The same goes for DNA methylation in gene regulation, where bees, like mammals but unlike Drosophila, methylate DNA on CpG residues.

Protocols are provided for Fixation and Storage of Honeybee Tissues, Whole-Mount In Situ Hybridization of Honeybee Tissues, In Situ Hybridization of Sectioned Honeybee Tissues, Immunohistochemistry on Honeybee Embryos, and RNA Interference (RNAi) in Honeybee Embryos.

Each month’s issue of Cold Spring Harbor Protocols will feature new (and newly revisited) model organisms, and the next set will be collected in Volume II of the manual series, out some time early next year.

In a speech given to the White House Radio & TV Correspondents dinner, with President Obama in attendance, the always-entertaining John Hodgman addresses the latest chapter in the great conflict of our age, jocks versus nerds. With the previous eight years under the thumb of a “jock” administration, we scientists should take particular pleasure in having the “first modern nerd President” in office. Very funny stuff.

Mutational analysis has long been a valuable tool for deciphering gene function. However, systematic repeated targeting of a single locus is difficult and is not a routine approach in multicellular organisms. Yikang Rong and colleagues at the National Cancer Institute have developed the Site-specific Integrase mediated Repeated Targeting (SIRT) method to facilitate targeted mutagenesis in Drosophila melanogaster. SIRT targets a landing site for the phage phiC31 integrase and allows the generation of several genetic variants at a locus of interest without having to perform multiple experiments. SIRT requires the construction of a series of plasmid vectors with varying arrangements of DNA elements. By taking advantage of bacterial recombineering approaches, SIRT bypasses the shortcomings of traditional cloning techniques that rely on the availability of convenient restriction enzyme cut sites. SIRT Combines Homologous Recombination, Site-Specific Integration, and Bacterial Recombineering for Targeted Mutagenesis in Drosophila, is one of June’s featured articles in Cold Spring Harbor Protocols. Like all of our featured articles, the protocol is freely available to subscribers and non-subscribers alike.

RNA-binding proteins play important roles in all aspects of RNA metabolism, particularly in the regulation of mRNAs and subsequent control of gene expression. RNA Immunoprecipitation (RIP), much like Chromatin Immunoprecipitation (ChIP), is a method for analyzing the interactions between proteins and nucleic acids. In the June issue of Cold Spring Harbor Protocols, Jesper Svejstrup and colleagues from the London Research Institute provide RNA Immunoprecipitation to Determine RNA-Protein Associations In Vivo, a detailed set of instructions for RIP analysis. Proteins and RNAs are cross-linked by formaldehyde treatment and immunoprecipitated. RNAs are then recovered and characterized by RT-PCR. The method is particularly useful for kinetic analysis of interactions at different timepoints and under different environmental conditions.

Time to catch up on some interesting links:

The End Of Free
Last week’s posting at the Scholarly Kitchen, discussing the idea of using free content as a marketing tool, and how some uses are reaching the end of their usefulness. I have a new blog entry there that will be out on Monday discussing Microsoft’s Bing and Google’s Wave.

Teen Practices
Very interesting set of observations of how teenagers use technology. Twitter and e-mail are boring things that old people use. Once again proving the idea that different tools are appropriate at different stages of one’s life and social development. This study backs it up with more numbers.

Landmark study: DRM truly does make pirates out of us all
A few weeks back, I wrote about the Kindle’s DRM:

By providing a product that suffers the limitations of lock-in and prevents users from doing the things they’re used to doing with books, Amazon is encouraging potentially honest customers to become copyright infringers.

This study offers further evidence for such behavior, and argues against DRM.

If Research Papers Had A Comments Section
A cautionary tale, in cartoon form.

Another Blogger Leaves the Seed Blogs
Some dissension in the ranks over at ScienceBlogs. Like we’re seeing at the Nature Networks, these clubhouses are hitting some rough waters.

For Wired, a Revival Lacks Ads
Interesting article on Wired Magazine’s struggles. It notes that Chris Anderson of “Long Tail” fame seems to make around $35-50,000 per lecture he gives to businesses. Ironic in that the concepts he champions seem to be failing at the actual business he runs.

And it wouldn’t be right to end one of these without some Web 2.0 cynicism/snark. So I’ll offer up Conan O’Brien’s painfully accurate Twitter Tracker, and this lovely Social Media Venn Diagram t-shirt.

High-throughput whole-genome analysis is becoming a standard laboratory approach for investigating cellular processes. Next-generation sequencing is replacing microarrays as the technique of choice for genome-scale analysis, because it offers advantages in both sensitivity and scale. The June issue of Cold Spring Harbor Protocols features Native Chromatin Preparation and Illumina/Solexa Library Construction from Keji Zhao and colleagues at the National Heart, Lung and Blood Institute. The article describes sample preparation for sequencing of chromatin-immunoprecipitated DNA (ChIP-Seq) to analyze histone modification patterns using native chromatin and the Solexa/Illumina Genome Analyzer. Step-by-step instructions are given for purification of human CD4+ T cells from lymphocytes and chromatin fragmentation using micrococcal nuclease (MNase) digestion, followed by chromatin immunoprecipitation (ChIP) and construction of a library for sequencing.