Week 5

Hey guys! Hope you're internships are going well. Here's my week!

My internship has been pretty routine. I come and make PCRs and run gels, and that's  basically what I did this week also.

On Monday, I ran a gel testing a primer called upstream 1 (up1 for short) with a row of DNA from a DNA plate. The results were much better than what we had tested before, and the only difference was that, with trial and error, I changed the annealing temperature in the PCR machine from 58 degrees Celsius to 55 degrees. It makes a world of difference! Look for yourself.

Gel with PCR at annealing temperature of 58 degrees Celsius

Gel with PCR at annealing temperature of 55 degrees Celsius (same reagants)

I used exactly the same reagants which were the DNA, up1 primer, GoTaq (which is the Taq polymerase that makes the other strand of DNA by binding nitrogenous bases using the base pair rule after denaturing at 94 degrees Celsius). Seeing how this experiment worked and seeing that the DNA sufficiently amplified in the PCR, I started to do this with other plates of DNA using the same conditions.

On Wednesday, I went into a lab meeting. This week, a guy from the AGI team just talked about what he has been doing lately and some of his results. He mainly dealt with the construction of the BAC library (bacterial artificial chromosome - which is a DNA construct used for transforming and cloning in bacteria, usually E.coli and is often used the sequence genomes) for the Oryza (rice) project. He also mentioned a CHEF gel which I have never heard of and shears (I think that's what they're called), but when I saw pictures of his gels, they looked really cool. Instead of looking like the thin bands above, they was a large chunk in each column. Instead of giving a specific size such as the thin bands above, the results of these shears provide more of a range. But I liked it when he was talking about his methods, and the team was discussing whether these methods were sufficient enough in purifying the DNA when making the BAC library and also what to do next and compare the results.

After the lab meeting, I made a large gel of the PCR that I made on Friday. Here's a picture!

Large gel (GREAT RESULTS!)

For this gel, the PCR used the same up1 primer and same conditions in the PCR machine. The only thing different was that I used a different DNA plate. I was so happy to get such great results!

On Friday, I did another PCR with more DNA plates using the up1 primer and ran some gels. However, I also got to grind some leaves from rice plants, so that we could do DNA extractions the next week. We froze the leaves in liquid nitrogen which was fun. Afterwards, I ground some awns that my mentor collected a while back. 

Well that was my week. Hope you guys are doing well on your internships! See you next time :)