Archive for January, 2009

sCRACM: ChR2 circuit mapping

Saturday, January 31st, 2009

As has become a hallmark of the Svoboda lab, this new paper in Nature (advance online publication) combines several cutting edge technologies (rAAV-delivered ChR2, most prominently, and 2-photon 1-photon laser stimulation) to do some interesting synaptic physiology.

The subcellular organization of neocortical excitatory connections : Article : Nature.

They used ChR2 (with TTX and 4-AP to block action potentials) to find where on the dendritic tree particular inputs synapsed onto L3 and L5 cells and to measure the strength of those inputs. ChR2 depolarizes the input axon locally (60um spot diameter) at points of (potential) axodendritic contact. If you’ve heard the term “potential synapse” before, then think of this technique as a way of checking potential synapses and seeing if there really is an actual synapse there.

The technique allowed them to map on a L3 barrel cortex pyramidal cell where different thalamic inputs (VPm, POm) and cortical inputs (M1, barrel L2/3, barrel L4):

screenshot001

sCRACM stands for subcellular ChR2-assisted circuit mapping.

LEGO Turing machine

Friday, January 30th, 2009

http://blog.makezine.com/archive/2009/01/the_lego_turing_machine.html

PNAS roundup: Superresolution in 3D and fetal testosterone of traders

Saturday, January 24th, 2009

PNAS has some interesting articles that I came across today:

  1. 3D PALM (open access): Using 2-photon and photoactivatable proteins, the authors image beyond the usual sub-wavelength TIRF limits. They image over multiple microns with 50nm resolution.
  2. Neuroeconomics:  Low digit ratio (2d:4d) predicts financial success in traders. Okay, measure the length of your index and ring fingers. (Not sure if this analysis applies for the ladies; the authors only used men in the study.) Calculate the ratio (2d/4d); longer ring fingers signify greater fetal androgen exposure. The mean value is about 0.96. As the authors say,

    Digit ratios have been found to predict performance in competitive sports, such as soccer, rugby, basketball, and skiing, so 2D:4D may also predict the risk preferences and physical speed required for high-frequency trading.

    A strong correlation (r~0.5) was found between low digit ratios and profits in short-term trading. So, they take on more risk and make more money. What I want to know is how well the low 2d:4d ratio traders did over the last 6 months!

Social neuroscience fMRI: Specious correlations?

Saturday, January 17th, 2009

Nature is reporting on potential flaw in multiple imaging (fMRI) studies of social neuroscience. Ed Vul (a graduate student in my dept) and colleagues have a paper in press that says that many of the high correlations between brain regions and social behavior are implausible, given the inherent variability/noise in fMRI. Furthermore, based on a survey of methods from individual investigators, they created a list of papers that commit, in their view, a statistical mistake (non-independence). Naturally, the authors named in the paper aren’t happy and, according to the Nature article, several rebuttals are in the works. At the very least, to my non-expert eyes, this seems like an important discussion to have about data analysis and methodology.

Not so Blue Brain?

Saturday, January 17th, 2009

This came across my inbox today:

http://blogs.spectrum.ieee.org/tech_talk/2009/01/ibm_pulls_out_of_blue_brain_co.html

Does anyone know anything more about this?

Bistable current photoswitches in neurons

Monday, January 12th, 2009

Bi-stable neural state switches : Article : Nature Neuroscience

Another channelrhodopsin breakthrough from Deisseroth’s lab. This time light is not required to keep the channel open. Light merely triggers opening and closing behavior. Blue-shifted light opens channels and red-shifted light closes them. This looks like another potentially powerful neurotechnology for interrogating circuits and systems.

Relevant fig:

photoswitching channelrhodopsin traces

Personal genomics: Some details for the curious

Sunday, January 11th, 2009

There’s an article in this weekend’s NYT magazine from Steve Pinker on what he’s learned from the first stages of genetic screening (recall he’s part of George Church’s Personal Genome Project, which is attempting to sequence many genomes and make them publicly available along with phenotypic data).

The most interesting tidbits in the story relate to data from SNP array analysis retailer 23andme. Given that the SNP analysis reported that Steve has a large chance of being bald, I have to agree with him that personal genomics has a way to go.