Sunday, July 6, 2014

DIY Biology

It's been quite awhile since my last post and my interests have taken a radical shift into the world of biology. I am currently attending Quest University and a whole new universe of labs and all their related shit that has opened up to me. I haven't lost interests in DIY electronics and have been working on combining the two skills. So here's a brief overview of what I've been working on:

Bio-Indicator Plasmid based on Green Flourescent Protein

An annotated view of my new plasmid using a program
called SnapGene
First to demystify a "plasmid": a plasmid is a circular piece of DNA that encodes a series of genes. This plasmid can be shoved inside of a bacterial cell, usually E. coli and made to induce those genes. Imagine a DIY electronics analogy: Imagine that the bacterial host cell is a microcontroller and the plasmid as the code that you upload into the microcontroller, or in the case of cells, you transform the host cell with the plasmid. So essentially I set out to create a brand new plasmid based off of a previous bioluminescent plasmid called pGFP. My new plasmid has an added tail to the bioluminescent protein that makes it attracted to 2+ metal ions. This tail is called a 6his tag, because it adds a tail of six histidine amino acids. My goal in this project is to be able to detect metal ions that are harmful to the environment, specifically copper and nickel ions.  I have successfully created my new plasmid using PCR, restriction enzymes, and a couple other lab techniques. My next goal is to isolate the GFP protein with the 6his tail and see if I can quantify the concentration of metal ions in water.
Glowing colonies of E. coli transformed with my new plasmid, you can see the
green fluorescence on a UV lightbox 

PCR: DIY Thermal Cycler
PCR is a lab technique that allows you to amplify a specific piece of DNA from a small amount of template DNA. PCR has huge potential in diverse areas of biology: it can be used to screen for specific genes in humans, it can be used to mutate and create new plasmids and much more. PCR uses a piece of lab equipment called a thermal cycler to carry out a PCR reaction. A thermal cycler simply cycles a small tube through a series of temperature cycles that allow an enzyme called DNA Polymerase to make copies of DNA. An alumni from Quest built a proof of concept thermal cycler from simple electronic components. He successfully performed PCR, but the speed of his thermal cycler was really slow. A commercial PCR machine might take an hour and a half for a reaction, that same reaction in his DIY thermal cycler would take 5 hours. I have taken over his project and aim to build a DIY thermal cycler that has comparable speed to a commercial machine but at 1/10 of the price.