Wednesday, August 08, 2007

With 'pyro-something' AND 'epigenetics' in the title, you know its gonna be cool

Just found a paper discussing where HIV likes to integrate. Hmm-- Not too particularly interesting, as weve already kinda looked at that.

Whats interesting is the technology these folks used to do something that would have been inconceivable just a few years ago.

Pyrosequencing.

Pyroseqencing takes sequencing to the next level. A process like sequencing the human genome, which took many years and billions of dollars, only takes a few days and a few thousand dollars with pyrosequencing. Yeah. I do NOT want to look through the data that comes out of one of these sequencing assays LOL (though Ive heard the software is good)

So these folks infected some cells with HIV with the hope of characterizing the DNA around integration sites. Then they found ~40,500 different integration sites. *blink* We used to have to find them one at a time. Not 40,500 at a time. Awesome. But again, what could this paper tell us that we didnt already know?

They used various databases and models to figure out HIV integrates:

None of that is experimental (except for the initial sequencing)! Its all technology! 40,500 damn integrations! Awesome!!!

7 comments:

Ezekiel said...
This comment has been removed by the author.
The Factician said...

Yeah, I met a sales rep at the ASM meeting that showed me a 454 sequencing machine. It's simply awesome. Check it out here.

The Factician said...

Doh, I'm an ass. Apparently you've already seen that...

ERV said...

Mysterious undergrad-- Dont feel bad- I dont totally get it either! Like you digest BIG chunks of DNA into little bits, and you attach the tiny bits to magic beads, and one bead goes into a microscopic well, and theres a laser and flashes of light for ATCG and Im fairly certain there is a dragon involved... Thats all I can figure out so far ;)


factician-- hehehe Its exciting! Our core facility might get one! I dont know what I would do with it, but its cool!

Kevin Z said...

You had me at pyro...

By the way, all DNA extractions and sequencing are guided by the noodly appendage of the supreme Flying Spaghetti Monster. This is common knowledge.

rAmen.

ERV said...

Kevin-- I KNEW I was forgetting something :(

Israel Barrantes said...

Integration didn't occur on histone silencing marks either. But... you noticed that the prediction tool they used is only 50% sensitive? Thus probably there are other 40,000 potential integration sites waiting for discovery!