Day 3 PROGRESS!!!

Today was a really good day and I'm excited to tell about it. Flashback to yesterday, right as Tom and I were about to start my first experiment, Doctor Willey realized that they had to do something very important for this article they are about to publish. We stopped and Tom did his thing. Flashforward to today, for the whole morning, Tom and I set up proper dilatations of DNA so that we could titrate properly (essentially we are just trying to find how many of the unknown molecules we have based upon a set ratio of fluorescence). Then, Tom walked through the experiment, doing all of the pipetting (which is a pain) and explaining why he was doing each step and telling little helpful tidbits of lab procedure. He then had me do the exact same thing back to him. Luckily, I pick up on things quickly, but just the pipetting caused my muscles to shake and nearly spasm. It looked so much easier when he did it! But, he did say that I did a very good job (even better for my first time... EVER). We put the samples we had made up into the PCR machine. We then went to lunch. Yes, I know. Very anticlimactic.

We then came back (I did faster than he because he got stuck at Fricker's) and ran the amplified samples through a fancy and expensive (worth over $30000,  I didn't even think about touching it) machine that performed electrophoresis to see how long the strands are. Just to give a frame of reference, our DNA in each cell has billions and billions of base pairs. The genes we were interested in have roughly 500. Then, based upon different dilutions, we could set up proportions to see roughly the amount of molecules from this test. We are testing to see if two different extraction methods have RNA (therefore cDNA) that are in the same proportion. 

....You should be confused. I sure was, and if you have any questions, please ask!

Below are pictures of where I worked:

PCR machine:

My little comfy station: 

Quotes from Emporer of all Maladies

Tom gave me a really good book about cancer called "Emporer of all Maladies" by Siddhartha Mukherjee, and it has some interesting descriptions of cancer for people who don't know too much about cancer:

"Cell division allows us as organisms to grow, to adapt, to recover, to repair- to live. And distorted and unleashed, it allows cancer cells to grow, to flourish, to adapt, to recover, and to repair- to live at the cost of our living. Cancer cells grow faster, adapt better. They are more perfect versions of ourselves." (6)

"Cancer is an expansionist disease; it invades through tissues, sets up colonies in hostile landscape, seeking "sanctuary" in one organ and then immigrating to another. It lives desperately, inventively, fiercely, territorially, cannily, and defensively-at time, as if teaching us how to survive. To confront cancer is to encounter a parallel species, one perhaps more adapted to survival than even we are.

This image- of cancer as our desperate, malevolent, contemporary doppelgänger- is so haunting because it is at least partly true. A cancer cell is an astonishing perversion of the normal cell. Cancer is a phenomenally successful invader and colonizer in part because itnexploitsnthe very features that make us successful as a species or as an organism." (36)

Wow. It's amazing we even stand a chance.

Project WOOT!

So, I talked to Tom and Dr. Willey and they came up with the experiment I'm going to partake in. They think they have developed a biomarker for detecting lung cancer based upon 14 genes found in RNA. However, there currently two types of RNA extraction for this test: Trizol reagents and Quigen columns. One is more practical for use in most laboratories, but they don't know if they both will read the same gene expression. They want to see if the RNA is the same quality and amount even if the same pieces with extracted from the two different methods.

Revised SMART goals

1. I will listen more than I normally do so I can truly learn from what Doctor  Willey and Tom say.

I will ask questions that will lead me to what I want to know and try to learn more about this subject. I will actively listen to their responses and measure myself based upon how well I can articulate what I learned.

2. When working by myself, I will stay focused on the task at hand, making sure to follow the proper procedure of the lab/activity.

I will remained focused even when working alone. I will pay attention to procedures so that my data is solid. Tom will help me determine if I'm getting good data.

3. When working in the lab, I will be efficient and cautious so that I do not waste or break the expensive materials

I will make sure not to break things so that I'm not wasting the labs resources. I will be able to tell based upon my our lab experiences.

Career?

So Tom and I talked today about what I want to do in life. This was a hard question because... Well... I'm 16 with 80% of my life still ahead of me. He told me about this process at UTMC where I could apply now and automatically get into UT Med School. I would get a lot of scholarships (most likely) and graduate with a medical degree while having a fraction of the debt most graduates would have. One problem:

Going on this path means I won't be making too much money OR have a choice to leave until I am 32ish.... That's a pretty huge commitment. I know I like research and science, but that's an extremely large decision. He also told me that doctors are going to stop making as much money, which could obviously affect my decision.

His biggest advice was to not worry about how much money I make (but make enough to get by) and go for a job I enjoy.

Decisions, decisions :/

Day 1 Morning

So, today is my first day with Doctor Willey at UTMC! It's super cool here and super nerdy here I love it!

We started with basically going over what PCR is. If you don't know what PCR is, it is basically just replicating certain strains of DNA many, many, MANY times so that you can study the DNA sequence more. Click here for more info. I have a pretty good understand of what it is and will hopefully do it again soon.

Thomas (Tom) Blomquist was the primary person I talked to. We talked about a lot of things. Crash course on what cancer is: one cell that has certain mutations that cause it to not cease replicating. I asked why we haven't gotten a cure. Sadly, he stated that since there are so many different types of mutations (at varying locations and degrees), we have an extremely hard time developing a cure. However, it is easier to determine which sequence change causes cancer for younger people. With older people, there have been a countless number of very slight mutations from cell replication. With younger people, they haven't had as much cell replication (therefore mutations), so the sequence is easier to discern.

I've done a lot of reading and this afternoon I'm planning on designing an experiment for Winterim... So YAY! More info to come


Also, here's my school for the next few weeks:

Thad

SMART goals

1. To actively engage in the lab activity that I am assigned so that I am beneficial to whomever I'm working with.
2. To further my understanding about genome sequencing and how it applies to lung cancer and to everyday life.
3. To behave courteously to all the personnel that I have interactions with at UTMC.
4. To effectively accomplish any of the tasks that I am given and report exactly what happened in the lab.