Extravasation is the process by which circulating tumor cells pass through the walls of blood vessels. August’s issue of CSH Protocols features an article from Duke University’s Xiao-Fan Wang and colleagues describing in vitro assays for measuring this critical step in metastasis. Human umbilical vein endothelial cells (HUVEC) are grown as a monolayer on a membrane to simulate a vessel wall. The transendothelial cell migration (TEM) assay looks at the efficiency of migration through the monolayer, while the vascular permeability assay looks at the effect on permeability of various secreted ECM proteins. As with all featured articles in CSH Protocols, In Vitro Assays for the Extracellular Matrix Protein-Regulated Extravasation Process is freely available to subscribers and nonsubscribers.

I’m happy to say that this week we sent out our first round of royalty payments to authors of original articles in CSH Protocols. Because we’re doing some reprinting of material from our already-published laboratory manuals, we built in a system to pay royalties to the editors of those manuals. We chose at the time to extend those royalties to authors of new material as well. The idea of writing up methods isn’t something that immediately occurs to most laboratories–they’re usually more interested in publishing data, so we’re hoping that these royalty payments will at least serve as something of a motivation for publishing (and continuing to publish) protocols with us. We’re not talking about huge sums of money, but as I recall from my graduate student days, every little bit helps. It also addresses one of the complaints one hears about us greedy science publishers–that we fail to compensate scientists for the work they’ve put into the publication and keep all the cash for ourselves. While CSHL Press is part of a not-for-profit research institute, and any money we make from our publications goes to fund research at Cold Spring Harbor Laboratory, we’re very curious to see what happens from this experiment in revenue-sharing. Does this make a difference to you as an author?

This set of royalties covers the calendar year 2007. A portion of our subscription revenue is set aside and divided among all authors/editors based on the usage of their individual articles during that calendar year. Those who published articles late in the year may not see much in terms of revenue given the relatively small time scale that their articles were available, but hopefully their articles will see a little more use in 2008.

As part of our mission to publish as many “gold standard” laboratory techniques as possible, I’m happy this month to include set of protocols covering the use of bromodeoxyuridine (BrdU) incorporation as a means of measuring DNA replication. The number of cells going through the cell cycle and their rate of progression are important indicators of cell growth. BrdU is a thymidine analog, which gets incorporated into new strands of DNA in a replicating cell in place of thymidine. It can then be detected with anti-BrdU antibodies. August’s issue of CSH Protocols provides three protocols for this method, from Dean Jackson and Peter R. Cook:
Analyzing DNA Replication I: Labeling Animals, Tissues, and Cells with Bromodeoxyuridine (BrdU)
Analyzing DNA Replication II: Fixation and Processing of Tissues and Cells Labeled with Bromodeoxyuridine (BrdU)
Analyzing DNA Replication III: Antibody Labeling of Incorporated Bromodeoxyuridine (BrdU) in Tissues and Cells

So many interesting articles, so little time to blog…
Here’s a quick roundup of some items of interest, before I forget them:

The Many Challenges of the Social Media Industry
Great article that really sums up the issues facing Web 2.0, most are directly applicable to science on the web, particularly the lack of revenue generated, the low barrier to entry causing multiple entrants for every niche, excessive noise, the difficulties in spotting expertise, and the influx of marketers and spammers.

The Importance of Being First
The Scholarly Kitchen looks at the ways scientists are gaming the arXiv system, and submitting their papers at specific times to ensure a higher listing in e-mailed announcements, which results in more citations. This is something very worrying about switching from our current editorially-supervised system of publishing papers to an open system. Sure, the current system isn’t perfect, but things like arXiv and social networks are very open to manipulation. A switch from one to the other may just be a lateral move in terms of bias and favoritism. Note that most of the proponents of Web 2.0 for science are all well-networked and well-versed in how things work, so adoption of these technologies would give the evangelists a distinct advantage over everyone else.

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Artist Jill Scott took part in the “Artists-In-Labs” program which offers annual residencies for artists in laboratories in Switzerland. She’s created a “neuromedia sculpture” based on her experiences in Stephan Neuhauss’ lab (found via the Eastern Blot blog). A section of a documentary film on the program can be found after the jump (follow the “Read The Rest” link below). Neuhauss and colleagues published several of the methods they use for retinal analysis earlier this year in CSH Protocols, and articles on Computer-Based Analysis of the Optokinetic Response in Zebrafish Larvae and Electroretinogram (ERG) Measurements in Larval Zebrafish are available.

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August’s issue of CSH Protocols is now available, and one of the featured protocols this month comes from Inder Verma’s lab, and covers the Design and Cloning of an shRNA into a Lentiviral Vector. Combining the specificity of small interfering RNA (siRNA) silencing with the versatility of lentiviral vectors gives researchers a powerful tool for the investigation of gene function both in vivo and in vitro. There’s also an alternative method available. In the featured method, one undesirable consequence of this procedure is that the siRNA target sequence is also present in the mRNA expressing the marker gene, resulting in somewhat lower expression of the marker. In the alternative method, the position of the silencing cassette is upstream of the marker expression cassette, thus avoiding down-regulation of the marker. But, because the silencing cassette is not in the 3′ LTR, only one copy of the silencing cassette is delivered per viral particle (as opposed to two copies in the featured method).

All of our monthly featured articles are freely available to subscribers and non-subscribers alike.