to BioTechniques free email alert service to receive content updates.
Kevin Ahern, Ph.D.
BioTechniques, Vol. 46, No. 6, May 2009, p. 397
Full Text (PDF)


To achieve the 50,000-fold reduction in size necessary to squeeze eukaryotic DNA into the confines of the nucleus, cells rely on DNA-binding proteins. The product of these interactions is, of course, chromatin. Histones are the major players, but there are a surprising number of other proteins, too. Overseeing the many components of the chromosomal game of life—as well as the proteins of RNA interference—is ChromDB (The Chromatin Database), hosted at the University of Arizona. Employing comparative analysis to enhance understanding of the chromatin plant proteome, ChromDB's collection of useful online tools includes BLAST, a Pfam domain viewer, RNAi vector information, and sequence extractors. There's also an informative, educational segment entitled Chromatin for Beginners.


Reception and Channels

Regulating the movement of materials and, in multicellular organisms, playing important communication roles, membrane proteins are essential cellular conduits between the environment of the cytoplasm and everything outside of the plasma membrane. An impressive collection of these membrane protein types, and their structures and functions, are on view at the International Union of Pharmacology (IUPHAR) site where two databases (G protein–coupled receptors and ion channels) cut a wide swath through the playing field. A very useful page called Latest Pairings provides literature references for the most recently identified ligand-receptor interactions.


Deeply Rooted

Although it may be mixing metaphors to describe PlantGDB as having a lot of horsepower, it's the easiest way to describe in a single word the scope and utility of this National Science Foundation (NSF)–funded site of resources for comparative plant genomics. These roots run deep, with a list of available content that includes sequence data on over 70,000 plants, expressed sequence tag (EST) assemblies for over 150 species, and more tools and genome browsers than you can shake a stem at. Funded by the NSF “to develop plant species-specific EST and genome survey sequence (GSS) databases, to provide web-accessible tools, and inter-species query capabilities, genome browsing and annotation,” PlantGDB is expansive, up-to-date (sequence updates coincide with Genbank), easy to navigate, and growing rapidly.



Research objects too small to be viewed in a light microscope pose special challenges for scientists hoping to bring them to life. Grayscale electron micro-graphic depictions once held sway, but they can be rather blurry and their resolution is limited, so they are increasingly being replaced by images made using a clearer set of “lenses”—3-D renderings from X-ray crystallography data. The beauty of this approach is apparent in the accompanying image from Jean-Yves Sgro's Virusworld web pages, hosted at the University of Wisconsin. Unlike the colorization of classic black and white movies, in which purists argue the “ambience” of the original is lost, virtually no one complains about the accuracy or the altered feel of virus depictions. In fact, the reverse is true, with most viewers responding favorably to the illustrations.

© 2009 Jean-Yves Sgro,


Enzyme-assisted Suicide

When wayward eukaryotic cells receive “death sentences,” the role of the primary executioners is played by a family of enzymes residing inside them, known as caspases. Caspases act by cleaving polypeptide substrates adjacent to aspartate residues with tetrapeptide motifs, and these unique proteases get activated and take their cues from apoptotic signaling cascades. They also play roles in the immune system in the activation of cytokines. Casbase (The Caspases Database) contains data that the curators at the National University of Singapore extract from primary databases and published literature. Information for the substrates acted upon by the enzymes is included also.


Bioblogging for Dollars

Are we poised for a boom in the biotechnology sector? Will the enhanced focus on high technology in the Obama administration usher in a new biotech renaissance? Some think that the retooling of the American economy is pointing to these scenarios, but others aren't so sure. One thing you can depend on, though, is Biojobblog; it has all the insights. Coverage includes tips for job hunters (salary negotiations, professions in demand, ask-the-recruiter, dressing for success, alternative career paths), job cuts, market analysis, and perspectives on fields ranging from social media to interesting web sites. The homepage has up-to-the-minute news and insightful analysis, too. Biojobblog is an easy way to stay on top of the rapidly changing biotechnology landscape.