….or has that boat already sailed?

I’ve read many a blog posting or magazine article declaring that scientists are behind the curve, and we biologists have been slow to pick up the new online tools that are available. I’ve repeatedly asked for examples of other professions that are ahead of the curve that we can use as models (are there social networks of bakers sharing recipes and discussing ovens?), but haven’t seen much offered in response. I tend to think that it’s not a question of scientists being slow, it’s that the tools being offered aren’t very appealing. Note how quickly scientists moved from paper journals to online versions, which only took as long as it did because of the slow progress on the part of journal publishers getting their articles up on the web. The advantages of online journals were obvious, and in comparison, the advantages of joining “Myspace for scientists” are less evident.

Are social networks (”Meet collaborators! Discuss papers!”) ever going to see heavy use from the biology community? Or are we starting to see that they’ve run their course in general, and scientists were prescient in not wasting their time?
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The new edition of Essentials of Glycobiology, ” the largest, most authoritative volume available on the structure, synthesis, and biology of glycans (sugar chains), molecules that coat cell surfaces and proteins and play important roles in many normal and disease processes” came out yesterday. What’s particularly interesting about this edition is that it is simultaneously being released online in a freely accessible version, which will hopefully allow the textbook to reach a wider audience.

The theory often espoused is that online release of books leads to higher sales of the print edition, and for us, this is a good test case. Quoting from the press release, John Inglis, Executive Director and Publisher of CSHL Press notes that,

“We will be tracking its usage and how readers of the site respond to the availability of a print version, for both research and teaching purposes.”

“This is an innovative development in the distribution of an established textbook that we hope will benefit readers, authors and editors, and the publisher,” says Ajit Varki, M.D., the book’s executive editor and a leader of the Consortium of Glycobiology Editors, which initiated the project. Varki is Professor at the University of California, San Diego. The Consortium also includes Professors Richard Cummings, Emory University; Jeffrey Esko, UC San Diego; Hudson Freeze, Burnham Institute for Medical Research; Pamela Stanley, Albert Einstein College of Medicine, New York; Carolyn Bertozzi, UC Berkeley; Gerald Hart, Johns Hopkins University School of Medicine; and Marilynn Etzler, UC Davis.

The online edition of Essentials of Glycobiology can be found here, and the print version can be ordered here.

Laudatory comments on this edition from Nobel Prize winners are below.
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Biofilms are the natural state of an estimated 99% of prokaryotes in the environment and are defined as an aggregation of microorganisms in a self-created matrix on a surface. Examples are plaque on teeth, or the slime on rocks at the bottom of a river. Because these biofilms can’t be effectively cultured in the laboratory, new techniques are being developed to isolate material from the environment, allowing for a better understanding of the microbes responsible for many diseases and infections. The field of metagenomics, “the culture-independent analysis of a mixture of microbial genomes (termed the metagenome) using an approach based either on expression or on sequencing” is rapidly growing. October’s issue of CSH Protocols presents two useful methods for the study of biofilms from the laboratory of Michael J. Franklin, of Montana State University’s Center for Biofilm Engineering.

Isolation of RNA and DNA from Biofilm Samples Obtained by Laser Capture Microdissection Microscopy describes techniques for embedding biofilms in cryoembedding resin, producing thin sections and isolating discrete sections through laser capture microdissection microscopy. RNA or DNA is then extracted from these discrete populations of cells.

qRT-PCR of Microbial Biofilms takes the RNA isolated in the first method and allows analysis of the number of RNA transcripts of specific genes from bacteria growing in biofilms through quantitative reverse transcriptase real time PCR.

This year’s Nobel Prize in Chemistry has been awarded to Osamu Shimomura, Martin Chalfie and Roger Tsien for the discovery and development of Green Fluorescent Protein as a research tool. GFP has revolutionized many aspects of biological research, allowing for real-time imaging of living specimens, rather than the difficult task of trying to piece together a process from a series of dead, fixed and stained specimens. Quoting from DNA Science:

“In the early 1960’s, Osamu Shimomura and Frank Johnson at Princeton University collected specimens of jellyfish in studies to understand their “bioluminescence.” One of the compounds they discovered was named green fluorescent protein (GFP) because it glowed bright green under UV light. Many years later, in 1992, Douglas Prasher at the Woods Hole Oceanographic Institute cloned a cDNA for GFP. In 1994, Prasher and Martin Chalfie at Columbia University were the first to realize the potential for use of GFP as a reporter molecule.”

Tsien comes into the story later, and has been instrumental in understanding how GFP works, and in extending the color palate beyond green into a wide variety of wavelengths, allowing for multi-spectral analysis of many labeled objects at the same time.

CSH Protocols has many articles detailing the use of GFP (with more continually on the way). You can see a list of available protocols here.

The October issue of CSH Protocols presents a new focus on Emerging Model Organisms.

Much of twentieth century biological research has focused on a limited number of model organisms, such as Arabidopsis, C. elegans, mouse, Drosophila, and E. coli. These classical model species, chosen because they are amenable to laboratory research and suitable for studying a range of biological problems, have served to elucidate many biological processes that can be generalized across a wider array of organisms. It is only a slight exaggeration to say that the basic workings of the cell were elucidated mostly from experiments on a few single-celled organisms — primarily E.coli and yeast. Our understanding of animal development was largely based on the genetics of fruit fly and worm and on the manipulation of a handful of amphibians and mouse; most of what we learned about the molecular and developmental biology of plants came from examining Arabidopsis and just a few other species. But biology wasn’t always done this way.
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