On the front of science demonstrations, I've made a lot of progress as far as pinning down protocols, and now am mainly just waiting for supplies to arrive so I can start testing the techniques and protocols I've conglomerated from resources online and the helpful posts of fellow biohackers on the Diybio google group. I've posted a first tested draft of a human DNA extraction protocol on this blog for the world to start perusing (if the world ever manages to find my blog), and it is workable if not incredibly coarse and still slightly unquantified (ran out of time to test the optimal amount of meat tenderizer protease for the mixture, and will probably need to see results in electrophoresis before I can really determine what ratio and conditions are optimal or even make a difference).
I spent five hours yesterday in the high school lab working on different scales of extraction and trying to coax the DNA I extracted into "spooling" onto a bamboo shoot (as is talked about here, here and just about everywhere else that uses a protocol like the one mine is based off). My conclusion is that either my stirring/enzyme use has somehow not yielded the structural form of DNA that their experiment yields (shearing or DNA structural proteins still coiling the DNA), or that human and animal DNA behaves differently at a macro level. My specialty isn't genetics so I consulted the diybio group, and their answer is "we haven't ever tried 'spooling' DNA". My conclusion is that spooling human DNA most likely isn't possible, and am going to use a centrifuge to pelletize the DNA im trying to extract.
So, yes, I bought my first piece of lab equipment yesterday. A Dremel 300 from a big box store for $49 US, and a Dremelfuge Rotor designed by Cathal Garvey and sold by Shapeways for a total of $58 US with shipping to the USA (not sure where it's coming from). It should arrive by 11/9. It promises to be a good investment, being able to develop (relatively safely; disclaimer: I'm not responsible if you get shot in the leg or eye by an errant centrifuge tube) just over 50,000Gs worth of force. That's as good as a high grade commercial centrifuge I'm told, and I'm excited to see how it works, and will post pictures, text and maybe even a video of it when it comes in.
In the realm of neuroscience I've been splitting my time between continuing to read about research methods in the realm of neuron imaging and current injection (reading what a neuron does, and making it do what I want it to do respectively), and the mathematical models that exist to describe both a single neuron and the computational nature of many neurons acting in concert.
In the realm of neuron imaging I have gone from reading about recording electrodes full circle back to the realm of fluorescence imaging techniques, this time in reference to voltage sensitive dye techniques, which are less complicated than the voltage sensitive proteins I had read about and possible mentioned earlier in the course of this blog.
Also, I'm trying to pin down and wrap my head around the nature of and the specifications of an electrode capable of injecting a current into a single neuron along the lines of those used in the Dynamic Gap technique, which I have been reading about quite enthusiastically. It sounds like the perfect technique for refining and modifying the single neuron model that I think badly needs attention.
And what better segue could I have asked for to talk about computational neuroscience, aka the art and math of figuring out what these neurons we're observing are doing to information? I've been mostly focused on the single neuron models such as Intercept-Fire, the Hodgekin-Huxley model, and the stochastic models derived from the H-H model. In order to look at system level models I'm going to have to have a good grasp on these first. I'm most definitely only doing research at this time, and to be honest am struggling with the math involved, as my last Calculus class was in my senior year of high school, and even then we didn't get very far in the book. So, right now I'm wrestling with the single neuron model, trying to work my way up, fighting on another front with the math involved with any of this. The single greatest resource I've found so far is a computational neuroscience textbook that I randomly found posted on a website in the .ch domain. I haven't had the time to figure out if it's a legally published copy or not, but it has most definitely been a god send for this scientist.
I apologize for the lack of links in the neuroscience part of this post, and will do a link update in the next few days, but I'm too lazy on my last day off to track down all the articles I've been reading. I did at least bother to find the link to the neuroscience textbook I've been reading, as it's sitting in the tab next to this one on my browser. You'll be hearing a lot more from me, and possibly even seeing me, in the coming weeks, as I ramp up my efforts on this science demo, and continue working on my neuroscience pursuits. Now:
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