So fierce, So Fresh, So Fly

Mentorship:

Last Thursday, I went to mentorship.

You see, I've begun taking a MoWeTh Chemistry 121 class at Cal Poly, so now mentorship shall take place on either Tuesday or Thursday.  Upon talking to a certain inter at Oak Crest, though, it has been decided that I shall only come on Thursdays.  You see, from 1:30PM to 6:00PM on TuTh, interesting things happen at the lab, which will more likely than not last at least 4 hours.  With everything going on, tackling this beast two times a week is a bit much, so I shall just tackle it once a week.

By "beast", I mean RNA extraction from tar samples.  The project is fully underway now.  In fact, last Thursday, I helped the intern out in finding primers for genes coding for certain cell functions characterizing a thriving population of microbes.  What in the world am I talking about, you ask?

Let me remind of this tar extraction business and how it works:
1.) Collect tar samples
2.)Extract RNA with fancy, magical protocol
3.)Convert to cDNA and run PCR on genetic material
4.) Analyze.

Recall that PCR stands for polymerase chain reaction and is used to amplify DNA - meaning that the DNA multiplies into many times more than what you began with.  You don't just amplify ALL of the DNA, though - you must choose certain genes to amplify.  In fact, PCR tells us whether a gene we are interested in is there or not.  What we are looking for in the tar extraction project (which I shall now call TEP), is genes coding for functional proteins that indicate whether microbes in the tar are thriving or not - like cell division.

The computer I used to work my magic, and some researchers in the Fish Tank.
That guy to the left has amazing facial hair...

A primer is a a strand of nucleic acid that specifies a certain gene.  When mixed up with the genetic material from a sample and placed through PCR, it acts as a sign saying "Hey, polymerase, amplify this gene right here!".  You can make your own primer Primer-BLAST, or use one made by some other lab.  This requires that you sift through paper upon paper, searching for the best primer - and that is what I did on Thursday.

I found of bunch of primers and ran them through Nucleotide-BLAST to see how general they are.  BLAST tells us how what organisms the primer was found in, and according to which papers.  Ideally, we wanted a primer found in E. coli, since that would mean that it is a general primer found in many organisms.

What we do, then, is run PCR on the cDNA and analyze our results.  Are these organisms still multiplying?  If so, they must be thriving.  Upon establishing that, we can continue to investigate these "bugs" as Dr. Crane puts it.  HOW are they thriving?  What unique proteins do they produce?

Independent Component 2:

I'm kind of behind on that Systems Biology class, but am frantically catching up!  There is so much complexity at the cellular level.  I mean, look at this:

And that's a fairly simple one!

Life is filled with self-sameness across scales.  You see it in snowflakes, economics, and here in biological relationships, whether it be in a network or a food web.

Other:

On Monday, I attend the Admitted Students Day at Pomona College - and finally mailed my acceptance of their offer of admission the next day!  It was a fantastic day - and I made two friends.  What a relief.  The aspect of college I had been the most nervous about was the prospect of having to make new friends...

Anyway, I talked to a plethora of interesting people with lots of information to give.  The geology department representative we're pretty cool and one, the chair of the department, actually, agreed to give me a tour of the facilities at some point before early May.  Hopefully, that shall happen next week, but we shall see.

It's funny: if not for senior project, I would not be in this position.  I would not have known about geomicrobiology or Kenneth Nealson, and perhaps would not have engaged Dr. Gaines enough for him to give me this amazing opportunity.  I wouldn't have felt confident enough to approach the molecular biology table, or even the PPE table.  Senior project - and iPoly in general, actually - has allowed me to find a level of comfort, of courage, of audacity I don't think I would have achieved elsewhere.

For me, it wasn't the candy sales that these last three four have prepared me for but, rather, this Monday.  See you next year, Pomona College.

The mascot of Pomona College - the majestic sagehen.
So fierce, so fresh, so fly.