Mutagenesis

Today will be an educational blog post. This past week I started the beginning of my own experiment. Now, the big picture of the experiment is to learn more about the binding site of anti-depressant drugs. Not a lot is known about HOW these drugs work on a molecular level. We know they bind to the transporter in the cell membrane (see earlier post), and plug the gate, so that neurotransmitters cannot get back into the cell. We are not quite sure where the drug actually binds though. These experiments will test different areas on the transporter protein to see if they are involved in the binding. Before we go any further, let's work our way down to the molecular level.

• The neuron cell is enclosed by a cell wall
• The cell wall has transporters embedded in it. (rainbow colored thing in picture)
• The transporter is a large coiled protein.
• Protein is made of a long string of amino acids. (The numbers in the darker image are used to identify specific amino acids. So the 320th amino acid on the protein chain is F for phenylalanine. There are 20 different amino acids)
• Amino acids are coded from the DNA sequence.

Now let's work back up:

• If we change letters in the DNA, a different amino acid will be coded.
• If we have a different amino acid, the shape, and or chemical properties will change in that section of the protein.
• That change in shape and chemical properties may or may not effect the ability for the transporter to do it's job.
• If the mutation causes more neurotransmitters to get through the transporter, than we know that the mutation effected the binding area of the inhibitory drug, and is there for an important section of the protein. 

By making many different mutations, we can begin to see what area the drug is actually binding to, and what areas it could be forced to bind to. Mutagenesis basically means that a mutation is created at a defined site in the DNA molecule. I have found 15 locations on the transporter that I would like mutate. I figured out which amino acids are in those locations. I decided what amino acid I wanted to change it to. I then found the triplet on the DNA that codes for that specific amino acid. For example, on the DNA strand TGT would code for a cystine amino acid. If I want to mutate that into tyrosine, I would change it to TAT. 

It's as simple as that. After hours of preparation and research to figure out what to mutate, where to mutate, and what to mutate it to, we just delete a triplet and add a new one. Bam. 

Nerd Herd

So my section of the dorm is full of nerds. We are all interns for either neuroscience or chemical engineering. I feel right at home :) I can be myself. I can tell science jokes and everyone understands! I can actually talk to them about the research I am doing in my lab and they actually understand the terms I use. No offense to my family, but it is really hard to explain what I am doing when you aren't fluent in biology talk. 

But other than the fact that they can relate to me, it's just nice to have friends here. I was a little hesitant coming here, because it was like starting freshman year all over again. It was easy to make friends with the Neuroscience interns, because we all lived together, we all eat at the same times, and we have scheduled events that we all attend together for the program. It was also pretty easy to make friends with the chemistry people too, mostly because we live with them, and because we share that nerd bond. (if any of you guys read this, take this post as a compliment). 


So other than hanging out in the dorms together, eating meals, and talking about science, we do other fun stuff together. Last weekend we all went to a movie, and then bowling (but bowling was closing soon, so we left). On Wednesday we all went to this documentary showing about grizzly bears. On Fridays we have what is called "networking" in our schedule, where we all meet and talk about what we are doing in lab. We basically get paid to talk to our friends for an hour and eat food. Last night after dinner someone decided that it would be fun to all play basketball. Now, imagine a group of 8 science nerds who all suck at basketball. It was hilarious. Probably the best game of basketball I have ever played. It ended in blood. After that we had a movie night in the lounge. Someone brought their big screen tv out, and we moved all the couches, and we connected to netflix. It's been fun getting to know these people. We have known each other less than 2 weeks, and we are already acting like we have been friends for life. It should be a fun summer.

What do people DO in North Dakota?

This is a question that I have asked a variety of people. It is also a question that people from back home have asked me. Being surrounded by fields, I would assume people have to get creative. Grand Fork, ND, home to the University of North Dakota is 75 miles north of Fargo, and is located right on the eastern boarder, next to Minnesota. It's a small college town, but it has a lot to offer (more so than Waynesburg that is). Whenever I get a chance to talk to locals, I asked them what they do for fun. Here are some of the responses I have gotten:

• Sleep
• Watch movies
• Catfish noodling
• Drink
• Frisbee golf
• Go to Fargo
• Go to Canada
• Go to Minnesota

Since this list was a little boring, we decided to look into local events. These are the options we were given for this weekend:

• School bus races
• Art festival
• Stargazing
• Movie theater
• Bowling
• Laser tag
• Annual rhubarb festival

Of all these suggestions, we chose to attend the Art Festival. They had hundreds of booths set up with a wide variety of art from local artists. There was ceramics, paintings, photography, basket weaving, wood works, jewelry, clothing, and all sorts of food and even some live music. It was the perfect day for an outdoor festival. After a cold week with the temperatures not reaching above 60, it finally was sunny and 70! I have been freezing all week long, so this was wonderful. It was 35 degrees when I walked to work Wednesday morning! I am so glad I brought two blankets that I didn't think I would need. Let's just say we haven't had to turn on the air conditioning at all yet. I really hope it will not be like this all summer. Boy am I glad that I am here in the summer instead of winter. They said it gets down to negative 40 degrees here!!! I can't even imagine. 

Hopefully we won't run out of things to do here. I am thankful I have a car, and I am able to get off campus whenever I need to. So far I have used it to go to Walmart (for and ICEE), Target, the movie theater, and church. I pretty much walk if I am going some place on campus. The school of medicine, where I work, is about a 15 minute walk from my dorm. I have walked every day because I didn't get my parking pass until the end of the week. I will probably start driving though, so I can sleep in, and so that I don't waste 30 minutes of my lunch break walking to the dinning center and back. 

Stay tuned for more exciting adventures.

First Week Down

9 more to go. This week has been mixed emotions for me. The first day in Grand Forks ND was Sunday. I got in around 4:30, and it was sunny and warm at about 80 degrees. As I drove through the college town, I was just eager to NOT drive any further. I found the parking lot in front of my dorm-to-be, and just sat there for a minute taking it all in. I was praising God that I had gotten here with no car trouble, no traffic jams, and no bad weather. It was seriously a problem free road trip. I walked into my building, with NO clue what I was supposed to do. The door was locked, but I saw a phone number on the door. I called the number, and an RA came and let me in. I signed a couple papers, they gave me my keys, and sent me on my way. They didn't even show me where my room was. I wandered around and eventually found 316B and got into my room. I began to wonder how on earth I was going to move all my stuff from the parking lot to the third floor all by myself (I brought a lot of stuff, and some of the boxes were pretty heavy). Well after my first trip, the RA showed me a cart I could use to roll my stuff in. That was much easier, and after about 4 or 5 trips, all my stuff was in my room. My roommate wasn't getting in until 8 or so, so I had some time to unpack and settle in.  A little while later I met my suite-mates, who share a connected bathroom with us. 


Monday was the first big day. All the research students met in the morning for a meeting. There are 9 of us in the program that I am in (REU neuroscience). There are 3 other research programs running at the same time though, so we all met together. Most of the other programs are for students from the University of North Dakota, but our program is mostly people from out of state. We sat through a welcome meeting, several lectures, a few training seminars, and things of that nature. I had to pass a test about the proper treatment of lab animals. At the end of the day I got to meet my professor, Keith Henry, who I will be working with in the lab. He has his only lab where he studies neuroscience physiology. Working in the lab for him are 2 grad students, 2 medical school students, and 2 lab technicians. I am the only undergrad, so I'm the baby of the lab. The first day I was only there for an hour, but Dr. Henry just lectured me about all the research they are doing. It was a lot to take in, and it felt a little over my head. I have only learned the very basics of the nervous system and the functioning of neurons, so he had to basically start from square one and explain everything before he could get to the point of what their research is actually testing. After a week of asking questions and slowly getting the big picture, I am more confident in what they are actually doing, and I feel like I really understand it! For the sake of this blog though, I think I will try to put it into terms you will all understand. And maybe through some big words in just for fun. 

This is just the most basic diagram I could find to show you the important steps of neural functions that I am specifically researching. So you have neurons (nerve cells) that communicate to each other with chemical signals called neurotransmitters. These neurotransmitters are release out of the cell and into the synaptic gap between two neurons. Some of the neurotransmitters attach to receptors on the next cell, and the signal is passed on to that cell, and so on and so forth. The neurotransmitters that are floating around in that synaptic gap are recycled back into the cell that they came from. In order to get back in the cell, they are taken in by a re-uptake transporter in the plasma membrane. This transporter has an active site that the neurotransmitter will chemically bind to, and when calcium and sodium are also present, the transporter will open to the inside of the cell, placing the neurotransmitter back into the cytoplasm to be reused. Ok, so if the transporter is structurally changed, the neurotransmitter may not fit properly, or may need to bind in a different area. If the DNA that codes for the proteins that make up these transporters is mutated, then the structure will change. We are testing different DNA mutations in the lab to see which ones work best, and which ones don't work at all. 

I'm starting this blog for 7 reasons

1. I have nothing better to do tonight
2. I want Angie to have more than one follower, and I have to have a blog to follow someone I think
3. I am 1500 miles away from my friends and family, so this may help them to stay connected with me
4. Andrew Juntunen deleted his facebook and needs to know what's up in my life
5. I do a lot of cool things
6. Both of my sisters have a blog, so I should too
7. I'm not sure if many people will care enough to read my blog, but I know my grandma will, and that's enough for me

So as some of you may know, today is my 3rd day in North Dakota. I just bought my first car 3 weeks ago, and it is here with me. I packed my car full of all my belongings, because I am going straight to college after the summer here. I drove over 1,500 miles to get here (my first official roadtrip). 


The roadtrip consisted of 3 stops: Pittsburgh (Brandon), Danville IL (BOP), and Rochester MN (Random people that my parents went to college with). The trip was fun. I drove in NY, PA, OH, IN, IL, WI, MN, and ND. I tried to take a picture at every state boarder welcome sign, but I missed PA and MN. The coolest one was Wisconsin. All the rest were boring. Impressions of each state: (And if you haven't noticed already, I love lists)

• Ohio-long and boring
• Indiana-the only cool part was seeing Indianapolis
• Illinois-REAL flat. Ridiculously high gas prices 
• Wisconsin-Too many billboards about cheese, cool rock formations though
• Minnesota- Crossing the Mississippi was the coolest looking place I have every seen, and then after that the state got real boring real fast. I did stop by the Mall of America though. Got lost walking around with out a map. And who knew they would have 10 roller coasters!?
• North Dakota- Flat, pretty sunsets, and A LOT of farms, and this is my home for the next 10 weeks

Okay, now we can get to the point of why I am here in this crazy boring state. I applied for this research internship at the University of North Dakota back in February. There are hundreds of REU (Research Experience for Undergraduates) internships at various colleges across the country that are funded by the National Science Foundation. I was overwhelmed by the choices and had no idea how to narrow down the list of places to apply. Don't ask my why I chose this one, because I don't have an answer. I also applied for one in Boston. I had planned to apply for several others, just to up my chances, but I got lazy and figured I wasn't going to get one either way. Applications were due in March, so I figured I would hear back sometime in April. I didn't hear back from either school by the beginning of May, so I had given up hope. Well 3 days before heading home for the summer I received an acceptance letter from ND. I was in utter shock. Of course I jumped at the opportunity, and here I am. 

I have so much more to say, but I am going to save that for another day. Stay tuned for posts about the internship, the research that I am doing, the things I am learning, and the adventures I am having. Thanks for reading.