neurodudes

Today one of our readers brought a new blog to my attention.

LabRigger is a how-to blog with a fresh look (kudos for the design and typography) that already has many interesting and relevant posts up for scientists who like to build. (You know who you are…) Furthermore, it seems especially geared toward neuroscientists and physiology folks. I’ve already added this one to my browser’s bookmarks.

Here are some of my favorites from quickly perusing the site: Printable bolt size charts, Tips on intrinsic optical imaging, Comparison of high NA, low mag objectives, and my favorite, Catalogs as textbooks. (I still remember a neuroscience faculty member here at MIT who told me that he brings science catalogs along on his vacations as “leisure reading” to stay up-to-date on new tools and to generate ideas for experiments.) In fact, I wanted to read just about every post on this blog and I think you will too! And if you’re the author of this blog, please introduce yourself in the comments, too.

Yusuf Tufail, Alexei Matyushov, Nathan Baldwin, Monica L. Tauchmann, Joseph Georges, Anna Yoshihiro, Stephen I. Helms Tillery, William J. Tyler. Transcranial Pulsed Ultrasound Stimulates Intact Brain Circuits. Neuron, Volume 66, Issue 5, 681-694, 10 June 2010.

In motor cortex, ultrasound-stimulated neuronal activity was sufficient to evoke motor behaviors. Deeper in subcortical circuits, we used targeted transcranial ultrasound to stimulate neuronal activity and synchronous oscillations in the intact hippocampus. We found that ultrasound triggers TTX-sensitive neuronal activity in the absence of a rise in brain temperature (<0.01°C). Here, we also report that transcranial pulsed ultrasound for intact brain circuit stimulation has a lateral spatial resolution of approximately 2 mm and does not require exogenous factors or surgical invasion.

Two neat tools concerned with the “connectome” (i.e. the pattern of connections in the nervous system):

Semantic wiki:
http://www.connectome.ch/wiki/Main_Page

Desktop viewer:
http://connectomeviewer.org/viewer “Multi-Modal Multi-Level Network and Neuroimaging Visualization and Analysis” (screencasts)

Expression data is now available for over 60K gene probes over the entire human brain. Click here to access this monster data set!

More info after the jump.

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Craig Venter has made a bacterium from an entirely synthesized genome (link is nice summary in WSJ). Here’s the paper in Science. Now, that that’s taken care of… who will be the first to design a “synthetic biological neural circuit”?

Mosaic (genetics) – Wikipedia, the free encyclopedia.

This has been done for quite awhile but I thought I’d post about it because I think it’s a neat idea — genetically manipulate experimental subjects so that only some cells have the mutation, while others are wild-type.

Want to run your research computations on Amazon’s cloud computing service?

http://aws.amazon.com/education/

No word as to when the next grant applicatiion deadline is, but it looks like an ongoing program.

Thanks to Brad Aimone, who got about $3000 worth of compute time for his research project, for alerting us to this.

When we learn new information we use only a tiny fraction of the neurons in our brain for that particular memory trace. In order to allow the molecular study of those specific neurons we combined elements of the tet system with a promoter that is activated by high level neural activity (the cfos promoter) to generate mice in which a genetic tag can be introduced into neurons that are active at a given point in time. The tag can be maintained for a prolonged period, creating a precise record of the neural activity pattern at a specific point in time. Using fear conditioning we found that the same neurons activated during learning were reactivated when the animal recalled the fearful event. We also found that these neurons were no longer activated following memory extinction, consistent with the idea that extinction modifies a component of the original memory trace.

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http://mloss.org/software/

In addition to an index of over 200 open source machine learning software projects, the “about” section notes that there is an open source tools track of the journal JMLR, and that there are MLOSS workshops sometimes at NIPS and ICML.

You can help with protein folding research!

http://fold.it/

According to the website, currently they are collecting data from the game to see if humans can actually contribute anything beyond what the computers can already do.