Thursday, April 23, 2015

My thoughts on Module 2: That was fast

And I don't just mean that since the deadlines are approaching faster than the speed of sound you can't hear them.  This module seemed fast, I just got my class ring, so I feel like college is going fast, but biological engineering is moving fast.  I decided to focus my paper on genome editing and some crazy things have happened.  It started based on a hunch I got after going through my spam email from biology vendors (I went to a vendor fair during my urop and they got a hold of my email).  Now first, I have to give you some perspective on what fast is.  Physics has been around for a while.  Atoms were theorized by Greek philosophers around 500 BCE and proven some time after 1800.  That is what human history was like before modern science, things took a long time.  Now a common way to blow people minds is to state the fact that the first moon landing was 66 years after the first powered flight by the Wright brothers.  That's barely longer than it takes to retire from when your born, there were people who remembered both events.

Now lets talk about Cas9.  Cas9 happened fast.  I'll give you a time line.  In 2005, sequencing revealed that bacteria had viral DNA in their genome and it was theorized this was some kind of DNA based immunity.  In 2007, it was proved by manipulating these loci that there was in fact an immune effect.  In 2001 the guide RNA/Cas9 system was discovered and in 2012 site specific dna cutting was demonstrated.  Not long after, people started trying to use homologous recombination to edit genomes.  Things start to pick up right here.  In march 2013 zebra fish (multicellular and everything) had some genes modified and added with Cas9 (  That same year in December, Adult mice had a genetic disease treated by genome modification using Cas9(  Earlier this year, in April, Nature published an article detailing the ethical debate caused by a team in china editing the genome of non-viable human embryos (  As it turns out, our study in NHEJ capacity as a function of DNA break topology is highly relevant.  The email advertisement I got was advertising some premade genome editing package that used Cas9 directed nickases.  These cut a single strand, so you can use two different guides to have twice the specificity (based on something like  Conveniently, this also means that you can move the recognition site around a little but to get any topology you want (I think, if they kit they were selling didn't it wouldn't be hard to design one that does).  As it also turns out, since NHEJ competes with homologous recombination, down regulating NHEJ is desired (  I am pretty sure we should brush up this study and publish because if you have arbitrary choice over cut topology, using ends with low NHEJ is a free way to improve your genome editing efficiency.
I found that the following gif sums up what its like to do biological engineering, I hope it serves you well.

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