Bench Marks

Back to Basics

David Crotty — Tue, 13 May 2008 12:22:07 +0000

While it always gives an editor a warm feeling to publish the newest groundbreaking protocol from the bleeding-edge of science, it often takes a good amount of time for these types of methods to trickle into mainstream use. Many labs don’t have access to the specialized equipment or reagents called for, and sometimes it takes a lot of thought to realize how a completely new assay can be applied to one’s own research. Keeping that in mind, it’s not surprising to see that on CSH Protocols, our methods that see the highest use from our readers are usually the most basic ones, the absolute classics common across all labs. As an example, Ethanol Precipitation of DNA is consistently on our list of most read articles every month.

Because readers are seeking out these basic methods, we’re putting special emphasis on getting more into our collection, and May’s issue has some good additions. Dany Adams contributes instructions for Making Solutions from Dry Chemicals and Hydrated Compounds, as well as Making and Diluting Stock Solutions. You can’t get any more basic than that. These articles come from Dany’s tremendously useful book, Lab Math and are great examples of why it’s a book you should hand to every new student as they enter the lab (along with At The Bench, our other primer for survival in the laboratory).

May also brings a nice set of histology protocols, again covering the basics, including Fixation and Permeabilization, Paraffin Embedding, Decalcifying, Preparing Slides and Coverslips and Sectioning. A protocol for Hematoxylin and Eosin Staining, one of the most common histological stains used is also available.

Expect more of these basic methods in future issues but don’t worry, we’re scouting along the bleeding edge as well.

Do blog commenters reflect the general readership?

David Crotty — Fri, 09 May 2008 18:25:19 +0000

I’m giving a talk as part of a forum on blogging for science publishers later this month and have been digging through the usage numbers for this blog. I was surprised at what I found. From my subjective point of view, I would have assumed that the various posts I’ve done on publishing and Web 2.0 were by far the most read on the site, as those are the ones that have spurred nearly all the discussion here and nearly all the incoming links. The numbers tell a different story. While yes, a few Web 2.0 posts have gotten a lot of attention (they rank 2 and 4 in page hits over the history of this blog), the rest of the top 10 are all science and protocol related (one exception–a post on the 25th anniversary of Molecular Cloning). The most read post on this blog is one about Keller explants (are there really that many Xenopus development labs out there?), number 3 is about BLAST and number 5 is about DNA/RNA Delivery. This was both surprising and gratifying–the main reason we created this blog was to help expose our protocol articles and to help researchers find the material they need to get their experiments done. People are using the blog as a discovery tool. Presumably the entries in this blog turn up in Google searches and are leading readers to CSH Protocols.

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Chromosomes are featured in the May issue

David Crotty — Thu, 01 May 2008 15:01:04 +0000

The May issue of CSH Protocols is now live, and in it you’ll find featured articles on classic techniques for the analysis of chromosomes. With the leaps and bounds being made in epigenetics these days, knowing your way around chromatin becomes even more valuable. This month’s freely accessible articles give you methods for chromosome analysis in Drosophila and in Mouse.

Mapping Protein Distributions on Polytene Chromosomes by Immunostaining takes advantage of the formidable size and structure of the large polytene chromosomes found in Drosophila salivary glands. These easily dissected chromosomes allow mapping of chromosomal protein distributions at very high resolution. May’s issue also contains a protocol for the Dissection of Larval Salivary Glands and Polytene Chromosome Preparation.

The second featured method for May, Karyotyping Mouse Cells, is drawn from the widely used laboratory manual Manipulating the Mouse Embryo. A karyotype is a visual presentation of a cell’s chromosomes, and can be used as a test for quickly identifying chromosomal abnormalities.

Phylogenetic methods

David Crotty — Mon, 28 Apr 2008 15:40:03 +0000

Before April’s issue moves to the archives and we welcome in May, I wanted to highlight one of our featured articles for the month, David Mount’s piece on Choosing a Method for Phylogenetic Prediction (freely available as one of our monthly featured articles). The April issue provides three phylogenetic methods protocols, for the Maximum Parsimony Method, for Distance Methods and for the Maximum Likelihood Approach. The featured article gives a nice overview of the three techniques, and why you would choose one over the other.

Web 2.0, a digitized echo chamber

David Crotty — Mon, 21 Apr 2008 18:39:04 +0000

John Sack, director of Stanford’s Highwire Press recently speculated that we may be reaching a tipping point in the hype cycle of Web 2.0, where we’re actually starting to see some practical consideration and thoughtful critical analysis of these technologies, rather than the usual constant stream of evangelism and cheerleading. If so, it’s certainly welcome, and a few recent articles back up his viewpoint:

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Forward genetics in the mouse

David Crotty — Tue, 15 Apr 2008 21:04:03 +0000

This month’s issue of CSH Protocols features an article by Andrew Salinger and Monica Justice, detailing a technique for Mouse Mutagenesis Using N-Ethyl-N-Nitrosourea (ENU) (article is freely available as one of our featured protocols). Back in the ancient days of my graduate school work, the idea of doing large scale forward genetics in mouse was unthinkable. Who had the space, let alone the funding and personnel to keep and track all of those cages? It was always one of those reasons we grumbled about the Drosophila labs, and the incredibly cool tools they had at their disposal. Over the years, the techniques were refined, and now, according to Justice, screens like this are an “established as part of a mouse geneticist’s toolkit,” and can be effective even in labs with very limited amounts of mouse space. So it’s nice to see this incredibly productive method readily available for use in mouse. Now if we can just do something about that pesky internal development that’s so limiting to imaging experiments…..

Jacob Nielsen on Web 2.0

David Crotty — Fri, 11 Apr 2008 15:40:52 +0000

Continuing along in the quest to evaluate Web 2.0 tools for biologists, I came across two recent articles, one by web usability guru Jacob Nielsen and one featuring an interview with him. Some valuable points found within:

He offers some cautionary advice on the actual patterns of user involvement on websites that follow the Web 2.0 dictum of having the users create the content:

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Retroviral Vectors

David Crotty — Mon, 07 Apr 2008 19:41:05 +0000

April’s issue of CSH Protocols features a set of articles on the production and use of retroviral vectors for gene transfer from Kenneth Cornetta, Karen Pollok and Dusty Miller. Retroviral Vectors for Gene Transfer provides an overview of the subject, drawing on the more than twenty years of experience researchers have with the use of these vectors. The advantages of retroviral vectors are detailed (efficiency, integration and ease of production) along with the disadvantages (inactivation, a requirement for cell division and possible oncogenic activation). The authors discuss important aspects of vector design and choice of packaging cell lines.

Four protocols are provided, two for production of viral vectors, and two for their use in transducing cells. Detailed methods are offered for Retroviral Vector Production by Transient Transfection, and for the Generation of Stable Vector-Producing Cells. Once vectors are generated, they can easily be used to Transduce Cell Lines which are actively proliferating. However, using retroviral vectors with primitive progenitor or stem cells, which are not continuously dividing, is much less efficient. In Transduction of Primary Hematopoietic Cells by Retroviral Vectors, the authors describe two interventions to improve efficiency of transfer, the use of cytokines and other growth factors to stimulate cell cycling, and the use of matrix proteins to mediate colocalization of target cells and vector.

Web 2.0: In defense of editors

David Crotty — Mon, 07 Apr 2008 15:14:29 +0000

Ran into a few very interesting (and very different) articles last week, which I wanted to comment on (more posts to follow).

First up is a blog posting on Sciencebase that quotes chemist (and blogger) Joerg Kurt Wegner, with a proposal that the solution for information overload is to do away with editorial oversight and instead rely on social software. Now, obviously, I’m heavily biased here, and I admit that up front. I’m an editor, it’s what I do for a living, and if I didn’t think I made valuable contributions, I would do something else. That said, there are several problems with Wegner’s proposal.
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Web 2.0 for Biologists–Are any of the current tools worth using?

David Crotty — Fri, 04 Apr 2008 01:57:17 +0000

This is a presentation I gave last weekend at the Southwest Regional Society for Developmental Biology Meeting. It’s an updated version of an earlier talk posted here. It’s kind of a 180 degrees turn from the previous talk, in that the first one was delivered to publishers, and this one was delivered to scientists. Here I’ve tried to include the thoughtful comments and helpful suggestions that readers made on the first talk, and have also tried to point out currently useful tools and interesting future directions. I don’t come at this subject from the point of view of a programmer, that’s not my background. I’m approaching it as 1) a publisher, who wants to build these tools into our journals and online products to make them more useful, and 2) as a former research scientist, with a thought toward what tools would have made my life easier when I was at the bench. The same caveat applies as last time–I work for a biology publisher, and am a former biologist. My comments and analysis of the culture here refer to that culture specifically (and I’ll try to avoid using the generic word “scientist” where it’s inappropriate). Different cultures have different needs. Certain fields of science collect types of data that more obviously fit in with Web 2.0 approaches. These approaches may not apply directly to the world of wet-bench biology, but they do serve as valuable pointers and directions worth watching. I want to be clear that I’m not writing Web 2.0 off as useless. What I’m interested in doing is separating the wheat from the chaff. Much of what is currently being done under this umbrella is useless and doomed. But there are some gems already available and despite many likely failures, aspects of those failures are worth recognizing and incorporating into future efforts.

If you read the first talk, sorry for the redundancies, and sorry for re-using some of the same jokes. I’ll work on new ones for the next presentation.

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