Bench Marks

One of December’s featured protocols comes from Azad Bonni’s lab at Harvard, and describes the culture of granule neurons from the post-natal rat cerebellum. From the article’s introduction:

“Primary cultures of granule neurons from the post-natal rat cerebellum provide an excellent model system for molecular and cell biological studies of neuronal development and function. The cerebellar cortex, with its highly organized structure and few neuronal subtypes, offers a well-characterized neural circuitry. Many fundamental insights into the processes of neuronal apoptosis, migration, and differentiation in the mammalian central nervous system have come from investigating granule neurons in vitro. Granule neurons are the most abundant type of neurons in the brain. In addition to the sheer volume of granule neurons, the homogeneity of the population and the fact that they can be transfected with ease render them ideal for elucidating the molecular basis of neuronal development.”

Like all of our featured articles, Cultures of Cerebellar Granule Neurons is freely available to subscribers and non-subscribers alike.

Just back in from the ASCB meeting, so much to catch up on. But I thought I’d be remiss if I didn’t highlight the set of emerging model organisms featured in this month’s issue of Cold Spring Harbor Protocols:
The Demosponge Amphimedon queenslandica is the first poriferan to have its genome sequenced, assembled and annotated and it represents one of the most (if not the most) ancient phyla of multicellular animals alive today. Protocols are provided for isolation of embryos, in situ hybridization, cell labeling and tracking, and genotyping.

Dictyostelium discoideum, known as “The Social Ameba” has a long history in scientific research, and is more a “classic” system than an emerging one. A unicellular eukaryote, D. discoideum can form a multicellular structure when nutrient conditions are limiting. The cellular and molecular aspects of their multicellular lifestyle have been studied in detail, and general principles for cell-to-cell communication, intracellular signaling, and cytoskeletal organization during cell motility have been derived from this work and have been found to be conserved across all eukaryotes. Protocols are provided for growth, multicellular development, making stocks, transformation, electroporation, selection of transformants, DNA extraction, and RNA extraction.

The Two-Spotted Cricket Gryllus bimaculatus has been widely used to study insect physiology and neurobiology. Its capacity for regeneration and amenability toward RNAi-based methods makes it an excellent system for the study of development and regeneration.

The Dogfish Scyliorhinus canicula is a relatively small shark that is fairly easy to maintain in the laboratory. It provides a window into the oft-neglected (due to technical difficulties) study of chondrichthyans, which should provide valuable insight due to their evolutionary position. It also allows anaylsis of the elaborate physiological and sensory systems used by sharks.

Cold Spring Harbor Laboratory Press has long been known for the creation of influential laboratory manuals like Molecular Cloning (aka “Maniatis”). CSH Protocols was created in order to move our manual publishing program into the online world. One of the interesting opportunities this creates is the ability to, in a sense, reverse engineer things. Instead of commissioning a manual, publishing it as a book and adding the protocols to the journal’s collection, we’re also interested in creating new print manuals based on the journal’s content.

New printing technologies have made it easier to produce high quality books and magazines. It’s now becoming feasible for us to re-mix and re-combine material from a variety of sources into a small, focused volume on one particular subject. Our first attempt is a collection of articles detailing methods for Immunohistochemistry, chosen because it is in such widespread use in so many fields of biological research. While not a comprehensive treatment of the topic, the collection covers the basic methods and includes specialized protocols for common laboratory organisms (yeast, plants, C. elegans, Drosophila, zebrafish, Xenopus and mouse). Our generous sponsors (Santa Cruz Biotechnology, Sigma-Aldrich, AbD Serotec and R&D Systems) have enabled us to distribute this experiment to you free of charge.

For now, this mini-manual is only available the CSHL Press booth at major meetings, and in Grace Auditorium at Cold Spring Harbor Laboratory meetings. Please come by our booth at the ASCB Meeting (Booth #311) this week and grab a copy for your lab.
(more…)

Well, at least I can assure you that this is one mistake that CSHL Press has never made:
“Science journal mistakenly uses flyer for Macau brothel to illustrate report on China” (link via BoingBoing)

Last month’s issue of CSH Protocols included a set of articles covering the construction of Nucleic Acid Programmable Protein Arrays (NAPPA). December’s issue brings articles detailing the use of these arrays for identifying protein: protein interactions. The articles include a set of general guidelines, and two protocols on the coexpression of a query protein on NAPPA slides and the detection of query proteins on NAPPA slides. These protocols come from Cold Spring Harbor Laboratory’s superb Proteomics course. Course directors Andrew Link and Josh LaBaer have put together a new laboratory manual based on the course that features further information on NAPPA, and is due out this month.

Haven’t done one of these for a while, so time to clear out some bookmarks to interesting stories:

David Byrne gets evolution
As a Talking Heads fan since, well, ever (yes, I am old), I’ve very much enjoyed reading David Byrne’s blog, particularly his recent travelogue posts from his current tour. Reading this post, his musings on bringing back extinct species, I was pleased to see him eloquently explain one of the more misunderstood concepts about evolution:

“We wrongly, I think, persist in believing that evolution is some kind of “progress” — a series of more or less linear improvements in each species — and that animals alive today, including us, are therefore “better” than what came before. Xenophobic thinking, seems to me. Critters that came before, and stayed around way longer than we did, were extremely evolutionarily successful in that they had adapted beautifully to the environment that existed around them. For example, if present-day animals were somehow transported back millions of years, we might find ourselves less suited for survival than our hairy pals. We’d be the ones that would go extinct. Evolution is not absolute.”

Byrne and Brian Eno’s new album, by the way, is definitely in my top 5 for the year.

Open Access and Citations
Another study asking whether open access provides an advantage to getting citations for your articles. This one says no.

New Kindle leaked
Photos of the next-gen Kindle have leaked, looks like they’ve caught up from the 80′s to the late 90′s/early 00′s in their design sense. One wonders what this leak will do to holiday sales, whether there will be something of an “Osborne Effect” (which is always an interesting misnomer). Also, there’s this competing reader.

Business Book Breakdown
I think this commentary should be extended to books about Web 2.0, or the onrushing digital revolution. I keep buying them, reading the first 50 pages or so, then putting them down and never returning. Most would make great magazine articles or blog entries, but stretching a few ideas out over several hundred pages never seems to work.

December’s issue of CSH Protocols is out, and one of our featured articles this month describes the isolation and growth of Bone Marrow-Derived Macrophages. Macrophages are specialized cells that carry out numerous tasks in the immune system such as phagocytosis, antigen presentation, cytokine production and migration. Cultured cells can be used to study these functions, as well as assays for gene expression, gene function and interaction with microbes. This protocol comes from Bo Porse and colleagues at the University of Copenhagen, and like all of our featured articles, can be freely accessed by subscribers and non-subscribers.