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.

Our second featured article for the May issue of Cold Spring Harbor Protocols is Systematic Monitoring of Protein Complex Composition and Abundance by Blue-Native PAGE, written by Harvey Millar and colleagues from the University of Western Australia. The article describes multiple experimental approaches using polyacrylamide gel electrophoresis (PAGE). Blue-native PAGE (BN-PAGE) allows a range of protein complexes to be visualized. When combined with sodium dodecyl sulfate PAGE (SDS-PAGE), the procedure can resolve the complexes and their subunits by their molecular weight. In conjunction with differential in-gel electrophoresis (DIGE), BN-PAGE can be used to quantify changes in protein complex abundance or subunit composition between different samples. A detailed methodology is provided for BN-PAGE, SDS-PAGE, and DIGE, and like all of our featured articles, it is freely accessible to subscribers and non-subscribers alike.

The May issue of Cold Spring Harbor Protocols is out and it contains a set of articles detailing the use of adenovirus vectors for gene transfer. Genetically modified adenoviruses serve as one of the most versatile and efficient gene delivery systems in use today. Laboratories throughout the world use adenoviruses for the delivery of DNA to cells for basic science and for gene therapy applications. Unlike most other vectors, adenoviruses can infect post-mitotic cells, which makes them particularly useful as vectors for gene delivery into cells like neurons.

In one of May’s featured articles, Robin Parks and colleagues from the Ottawa Health Research Institute provide Construction and Characterization of Adenovirus Vectors, a set of detailed instructions for the generation, propagation, purification, and characterization of adenovirus vectors. Like all of our featured articles, the protocol is freely accessible to subscribers and non-subscribers alike.

In addition, the May issue also contains a set of methods for Cell and Tissue Targeting from David Curiel and colleagues. Transfecting specific cells in a mixed population can be a difficult process. Adenovirus vectors are well-characterized, so they are excellent candidates for modification for targeting to specific cell types. The protocols here describe the creation of adenovirus vectors that enable targeting at the level of binding and entry in targeted cells through primary and/or secondary receptors (transduction), and protein expression of the transgene in the targeted cells (transcription/translation). The articles are:
Construction of Adenovirus Vectors with RGD-Modified Fiber for Transductional Targeting
Construction of Fusion Proteins for Transductional Targeting
and
Construction of Adenovirus Vectors for Transcriptional Targeting