Micropatterning methods are rapidly becoming standard approaches for investigating cellular behaviors such as growth and migration. Adhesive Micropatterns for Cells: A Microcontact Printing Protocol from Matthieu Piel and colleagues at the Institut Curie offers a simple, fast, and efficient method for generating micropatterns for cellular studies. Employing an elastomeric stamp to print proteins on the substrate of choice, this technique does not require much of the expensive equipment and technical expertise needed for most micropatterning methods, making it easier to implement in biology laboratories. The authors have provided a movie that illustrates the technique step-by-step as part of the protocol. The article is a featured protocol for July, and like all our featured articles, it is freely available to subscribers and non-subscribers alike.

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.

May’s issue of Cold Spring Harbor Protocols marks the end of Volume I of our collection of material on Emerging Model Organisms. The final two featured organisms are the bichirs and the African butterfly.

The lineage leading to the teleost fishes, like the zebrafish, has undergone a whole-genome duplication, and there are many differences in the molecular and cellular mechanisms of embryogenesis between teleosts and other actinopterygians (ray-finned fishes) and sarcopterygians (fleshy, or lobe-finned fishes). Polypterus (bichir) is a taxonomic order of fish that diverged from all other actinopterygians ~400 million years ago during the Devonian period, soon after the divarication of an ancestral bony fish into Actinopterygii and Sarcopterygii. Polypterus share several characteristics of cartilaginous fishes and basal bony fishes. Bichirs exhibit holoblastic cleavage, like that seen in amphibians, and different from the meroblastic cleavage of teleosts. As such, it makes for an excellent system to study ancestral states and the divergence of embryonic processes in teleosts and amphibians. The Genus Polypterus (Bichirs): A Fish Group Diverged at the Stem of Ray-Finned Fishes (Actinopterygii) presents an overview of bichirs, and protocols for microinjection and whole-mount in situ hybridization are also available.

The African Butterfly Bicyclus anynana is a valuable model organism for a variety of reasons. A range of phenotypes are readily examined, such as wing color patterns (including eyespots), seasonal forms, male androconia (secondary sexual traits), and a range of life-history traits (relevant to aging research). Many of the phenotypes are directly related to the drastically different environments found during the dry and wet seasons in East Africa, offering an opportunity to study adaptation to environmental conditions. The genus Bicyclus and closely related genera are highly speciose, giving a great variety of closely related species for diversity studies. B. anynana is small and can be reared in large numbers. The African Butterfly Bicyclus anynana: A Model for Evolutionary Genetics and Evolutionary Developmental Biology provides an overview of the species as a model system. Protocols are available for culture and propagation, surgical manipulations, grafts, fixation and dissection, wing dissection, in situ hybridization, immunohistochemistry (embryos), immunohistochemistry (wings), analysis of pheromones, fat content and weight, respirometry, hemolymph extraction, and injection of chemicals.

As noted, this completes the first set of Emerging Model Organisms, and the collected articles are available in a laboratory manual. The second volume begins next month, and the list of species is available here.

The Comet-FISH technique combines the Comet Assay (single-cell gel electrophoresis) with Fluorescent In Situ Hybridization (FISH) to create a tool for the detection of overall and region-specific DNA damage and repair in individual cells. Comet allows separation of fragmented from non-fragmented DNA and quantification of DNA damage and repair. FISH tags specific DNA sequences of interest. Used together, you can identify whether your gene of interest falls within the damaged or undamaged region of DNA within a particular cell. Comet-FISH has been used to detect site-specific breaks in DNA regions that are relevant for development of various diseases, and to study the distribution of DNA damage and repair in the complete genome. Detection via Comet-FISH has also provided insights into mechanisms of cancer development and chemoprevention.

In the May issue of Cold Spring Harbor Protocols, Michael Glei and colleagues from Friedrich-Schiller-University Jena provide Comet Fluorescence In Situ Hybridization (Comet-FISH): Detection of DNA Damage, a set of detailed instructions for performing the Comet-FISH assay.

More interesting articles from the last week or so……

The Comment Is King
A look at comments left on articles in The Washington Post and Slate, which does not bode well for those of us interested in creating commenting systems for science articles.

Will Wolfram make bioinformatics obsolete?
Interesting piece on the potential for Wolfram Alpha to be used as a much easier interface for bioinformatics questions.

Clay Shirky Debunks the WSJ’s “Bloggers For Hire” Feature
The increasingly ubiquitous Clay Shirky does a detailed analysis of Mark Penn’s Wall Street Journal article claiming that there are hordes of people who make their living blogging. Shirky’s pretty much shreds the poorly researched nonsense to pieces.

Too much free
Seth Godin notes that giving away your book or e-book (or whatever) for free is losing its novelty value as a marketing technique.

Wikipedia hoax points to limits of journalists’ research
Two good points made here. 1) Wikipedia is completely untrustworthy, and 2) newspapers continue to hasten their own doom by lowering the quality of journalism they perform.

Kindle wrap-up
New Kindle was announced this week, bigger, even more absurdly expensive, still black and white (which makes it a non-starter for textbooks). Hard to understand why students who are pretty much required to have laptops these days would want an extra big bulky device to lug around as well.
The Kindle Lets Amazon Make a Lot From the Few
Speculation on the Kindle’s business model. Steve Jobs was right, not enough people read to make lots of money selling a device, but Amazon thinks that small group of people will buy lots and lots of e-books, which is where the profit lies.
Publishers Nurture Rivals to Kindle
Meanwhile, publishers are unhappy with Amazon, looking to avoid turning control of their industry over to one company and repeating the mistake the music industry made in ceding control to Apple.

Google book settlement has librarians worried
Librarians weigh in on the increasingly problematic Google Book Settlement.

The Extreme Google Brain
Google’s lead designer left the company recently, and caused a stir with his revelations of how anti-design the company seems to be. This analysis looks at the extreme personality types that thrive in places like Google, and I couldn’t resist this vicious and hilarious description:

My impression of “Googlers,” which I concede is based on little direct knowledge and is prejudicial on its face, is one of undersocialized, uncultured, pampered, arrogant faux-savants who have cultivated an arrested adolescence that the Google working environment further nurtures. Their computer-programming skills, the sole skills valued by the company, camouflage the flaws of their neuroanatomy. Their brains are beautifully suited to the genteel eugenics program that is the Google hiring process but are broken for real-world use.