yeah YEAH yeahhhhh........

On Monday Dr. Rainey told us that our blogs weren’t inventive enough…he also said that we needed to add more detail. I mean, I thought everyone was inventive in their own way, however, I can admit that not all of us went into enough detail…myself included. So, since this week was somewhat of a “slow” week, I’ll save the inventiveness and details for next week’s blog. By slow I mean that we didn’t do too many things, however, the things that we did were very time consuming. For instance, on Monday we had to melt down our agarose gel and run out our DNA (Larry did this twice..the first time he broke the gel and second time he found that we had NO DNA PRESENT). In addition to that, DP and I found similarities to each our strains using EZTAXON and BLAST. We also learned that scientist use the 16S Rrna because it has enough variation, unlike 5S that doesn’t have enough and 55S that has too much. We also use the 16S because it has variable regions and highly conserved regions. The highly conserved regions are those that are found in a species or phylum. We now have a 16S rRNA for every validly described species. In addition, we also use it because the database actually exists and we have things to compare it to. I also learned that there are 2 primers needed to sequence DNA, a forward and reverse primer. The forward sequences one strand while the reverse sequences the other (hopefully everyone knows that DNA is doubled stranded).

Unfortunately, Rainey-Bug sent out a mass email to the class saying that even though many our results had been contaminated, we were still responsible for them so that they can be included in the paper. So that’s why I’m here in the lab at 1045 am…early huh? I KNOW!!! I guess it doesn’t matter anyway since my dog got me up at 8am. Anywho, on Wednesday we had to re-streak our stock plates. This is to ensure that the cultures remain pure. Keeping them longer than 20 days makes Rainey-Bug weary!! We also set up PCR using all DNA that we had extracted thus far (with the help of the ALMIGHTY…haha!). Lucky for us there was a pre-mix so we didn’t actually have to make it. We actually have the recipe to make the pre-mix, so if you’d like it, just respond to this blog and leave your name and email and I’ll be sure to get that to you as soon as possible.

Rainey: Class, what is the most critical step in PCR?
Class: (in unison) The annealing temperature

The annealing temperature is very important because it determines if a primer will bind to DNA. The higher the G+C content, the lower the annealing temperature. To the determine the annealing temperature you will need to know that G & C equals 4 degrees and every A & T equals 2 degrees. If the temperature is set too low then the primer probably will not bind to everything.

Sorry guys, there are no pictures to share with you, check back next week (this is to our BLOG followers…if we have any!).