A few interesting bits and pieces:

The Rockefeller University Press has responded to Thomson/ISI’s commentary on the JCB’s recent article exposing Impact Factors. Key point:
“In essence, Thomson Scientific is saying that they cannot repeat the experiment, which would be grounds for rejection of a manuscript submitted to any scientific journal.”

Science Progress: a spectacular new website and blog from the Center for American Progress covering scientific developments and governmental science policy issues. Definitely worth adding to your RSS reader.

Jaron Lanier has written an article for Discover Magazine declaring that while “Open Wisdom-of-Crowds” approaches are valuable, they’re not producing much that’s original or groundbreaking. “The open-source software community is simply too turbulent to focus its tests and maintain its criteria over an extended duration, and that is a prerequisite to evolving highly original things.”

Ian Rogers of Yahoo! Music has posted his presentation to the music industry, highlighting the shifting physics of the information world. “The Phyics of Media have changed from a world of limited distribution channels and therefore abundant attention to a world of unlimited distribution and attention scarcity.”

Tandem repeats are short stretches of DNA that are repeated head-to-tail. These are increasingly used as markers in forensic and genotyping research. But not all tandem repeats are created equal, as they display varying rates of stability. A repeat must exhibit enough instability to generate enough heterozygosity in a population to be of use in discriminating between individuals in a population. Too much instability though makes it difficult to look over large evolutionary distances, as it becomes difficult to see relatedness between samples. To determine which repeats are useful as markers, Kevin Verstrepen’s lab at Harvard has created the SERV (”Sequence-Based Estimation of Repeats Variability”) applet, which enables finding repeats in DNA sequences and estimating their variability. First introduced in this Genome Access paper, Sequence-based estimation of minisatellite and microsatellite repeat variability, Verstrepen and colleagues have now written a guide to using the SERV Applet, available in this month’s issue of CSH Protocols.

Legendre, M., Pochet, N., Pak, T., Verstrepen, K.J. (2007). Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Research, 17(12), 1787-1796. DOI: 10.1101/gr.6554007
Legendre, M., Verstrepen, K.J. (2008). Using the SERV Applet to Detect Tandem Repeats in DNA Sequences and to Predict Their Variability. Cold Spring Harbor Protocols, 2008(2), pdb.ip50-pdb.ip50. DOI: 10.1101/pdb.ip50

Scientists and Engineers for America (SEA) is a nonprofit, nonpartisan, educational organization dedicated to, “educating the public about science policy issues, educating members of the scientific community about the political process and ways in which they can effectively participate in elections, influencing elected officials, and ultimately holding politicians accountable through the dissemination of accurate and timely information about the positions they take on science issues.” They’ve just launched a great new tool for tracking your representatives’ record on scientific issues, called the Science, Health And Related Policies (SHARP) Network. SHARP is a wiki based resource, allowing you to edit and update any information on a given politician. It covers important issues such as stem cell funding, global warming, energy policies and funding for education among others.

This is a tremendously useful website. I’ve read a few articles that attempt to detail the current presidential candidates’ science positions but have found them incomplete and often contradictory. Here we’ve got one resource that puts it all together in an easily read, easily searched manner. If you’re a working scientist, or just have an interest in science policy, I urge you to check it out and participate. With the deplorable state of science funding in this country, we need to hold our leaders responsible for investing in our future, not to mention making sound decisions based on real science, rather than pandering to public opinion or the whims of corporate donors.

The January Issue of CSH Protocols features several articles detailing the use of nanoparticles for gene delivery. Drug delivery methods using nanoparticles have revolutionized the field. The traditional methods for drug delivery, via oral and intravenous routes, are inefficient, non-specific and expensive. Nanoparticles allow for much greater control over delivery, targeting to specific tissues, higher stability (which allows lower doses to be used) and they can be manufactured cheaply in large quantities. Nanoparticles made from natural polymers are preferred over synthetic ones because of their greater biocompatibility and biodegradibility.

These advances in therapeutic drug delivery techniques also bring benefits to researchers at the laboratory bench. Just as nanoparticles can be used for drug delivery, they can also be used for DNA delivery. Once inside the cell, the key to efficient transfection is getting the DNA through the nuclear membrane. Mansoor Amiji’s group at Northeastern University contribute a series of articles on the use of gelatin nanoparticles for gene delivery, including a general overview, preparation and loading of gelatin nanoparticles, studying intracellular trafficking using TEM and gold-encapsulated nanoparticles, and analysis of transfection using fluorescence microscopy and FACS. In the same issue, you’ll find a protocol for preparation and transfection using biodegradable nanoparticles made from biocompatible polymers such as poly(D,L-lactide-co-glycolide) (PLGA) or polylactide (PLA) from Vinod Labhasetwar’s group at the University of Nebraska.

You can also find several related articles in previous issues of CSH Protocols, including Lipoplex and LPD Nanoparticles for In Vivo Gene Delivery, Bioresponsive Targeted Charge Neutral Lipid Vesicles for Systemic Gene Delivery and An Overview of Condensing and Noncondensing Polymeric Systems for Gene Delivery.

January’s issue of CSH Protocols is now available online, and it contains a set of protocols from Cathy Krull’s lab at the University of Michigan. The articles provide methods for electroporating your gene of interest into somites, neural crest cells and motor neurons. The accessibility of the chick embryo has long made it a standard model organism for developmental biology, and methods like these greatly enhance our abilities to tag and track cells, as well as to genetically manipulate the embryo. They’re even valuable for labs not working with avian systems, particularly mouse labs, because they offer the opportunity to get a quick and easy look at expression and potential effects of experimental constructs. Unlike making a transgenic mouse, an expensive and time-consuming process, working with chick eggs is inexpensive, and relatively rapid. Testing your mouse constructs in the chick embryo is a great way to fine tune the constructs themselves to ensure proper expression. It can also give insight into potential effects of construct expression, which can save valuable time once your transgenic mice are available, as you may already know where to start analyzing.