Duke University | Howard Hughes Undergraduate Program

Each day begins with a meeting with the other Howard Hughes students from about 8:30 to 9:30, where we listen to seminars with varying degrees of interest.  Then, I take the hike to my lab in the Medical Science Research Building (about a 10-minute walk, give or take).  From there, each day is different.  Today, for example, I am depleting IgA out of milk samples for an experiment later this week.  On Friday I spent all my time making agar plates, a long and tedious process.  Some days I have the pleasure of counting bacterial colonies, which is rather mind-numbing due to the fact that there are literally thousands of colonies on a single plate.  Of course, I consider the day a sucess if I get to use liquid nitrogen to freeze things (bacteria, IgA samples, parafilm, pieces of laboratory equipment, etc).  

Sometimes the monotony is broken by new discoveries I make.  For instance, about two weeks ago I found a drawer at my lab bench containing dozens of micropipets of all shapes and sizes.  I was thrilled, because until that point, I had had to borrow other people's pipets when they weren't looking.  Now I have a large supply of pipets at my dispense.

Another, less cheerful discovery I made last week was in the autoclave room.  My impression of the autoclave up until this point was based on its outside appearance, which resembled the entrance to a nuclear submarine.  The only visible entry point of the autoclave was a large, heavy hatch set in a metal wall.  However, this particular time when I was in the autoclave room, a draft blew open a hidden door in the metal wall (I say it was hidden because I think the door handle snapped off, so it was flush with the wall).  Venturing through this door, I discovered the true face of the autoclave: a small box with a bunch of pipes, covered by decaying insulation and an expired approval certificate from Cherie Berry.  Needless to say, my bubble was thoroughly burst.

 I've already briefly discussed my research project in my Pulitzer Prize-winning blog post, "Me and My Lab," so I'll try to go into a bit more depth here.  In the human gut exist biofilms, which, though once thought to be detrimental, actually exist in perfect harmony with the immune system.  It is a symbiotic relationship, by which us humans obtain vitamin K and protection from disease, and the bacteria obtain a safe place to live.  However, as a fetus, everything is not so hunky-dory.  When you are born, there are no biofilms in your gut, and you don't usually consume large amounts of bacteria.  Instead, you drink your mother's milk, which has a very low concentration of bacteria.  The concentration is so low, in fact, that the IgA molecules that normally help to bind bacteria together completely cover the bacterial surfaces, and since IgA doesn't stick to other IgA, the bacteria don't stick to your gut, and you, in theory, would grow up to be a sickly, runty baby.  However, this is not the case, so Dr. Parker (my lab's PI) has hypothesized that in milk there exists some protein that can bind IgA molecules to each other, and therefore help biofilms form even in low bacterial concentrations.  Thus my project is investigating this protein and trying to determine some of its properties.

So far, I have been trying to aggregate bacteria in test tubes with plain IgA, milk, and BSA (as a control).  Then I have carefully plated the bacteria and observed the colony formation that occurs.  My results have so far confirmed that milk does indeed help bacteria to aggregate, in low concentrations, whereas plain IgA is ineffective at low concentrations.  I will next be investigating whether the unknown protein in milk binds bacteria directly or whether it acts as an intermediary between IgA molecules.

What follows is a transcript (almost verbatim, except for the occasional "um" or whatever) of my interview with Dr. Parker, my mentor in the Howard Hughes Program.

 Christian: How did you end up with a career in science?
Dr. Parker: Any career in science is pretty easy to get: you get a degree in science...you apply for a job, you get your doc[torate degree]. Now how I got my specific career is a bit different-it's much more challenging to get a job at a university doing research as a professor. I think it requires being in the right place at the right time, quite a bit, it requires certain skill sets that you develop over time. I started out at a very early age studying science, younger than you, even, I started...really concentrating on science. All of those things add together to really help you, but not guarantee you get a career in science.
Christian: Where did you go to college?
Dr. Parker: I went to college at the University of Arkansas, then went to graduate school at the University of Nebraska...then I came here for a post-doc. I was working for a well-known and very famous professor here. After a while I was running one of the sections of this lab. When he left, he went to the Mayo Clinic, Duke offered me a job here...again, I was in the right place at the right time... I still run a section of a lab, it's not a huge lab, it's a small lab, it's the right size for me- the size that I like.
Christian: What have been your favorite research projects?
Dr. Parker: Hmm! Well, we discovered the function of the human appendix, 'course, that was nice. That was a lot of fun. We're working on some things dealing with protein folding, and we've recently done some work in evolutionary biology. That was fun. The things that we did related to gut immunity and the function of the appendix, that may have been the most fun. That's such an old problem, Leonardo Da Vinci was working on that problem.
Chrisitan: What projects do you plan on working on in the future?
Dr. Parker: You never know. You ask me what I plan to do, which may be totally different from what I end up doing. That being said, what we really are interested in is looking at allergens and autoimmune diseases. I work...examining what's going on in the lungs of people with asthma, which is a type of allergic disease. The plan right now is to look at the immune system of laboratory rodents that are essentially raised under wild life or natural conditions, that have a lot of parasites. That, we believe is the way the immune system is designed to be in harmony with a lot of parasites and other kinds of things you would normally find objectionable. If I had to pick one project that we will be working on in five years, I would say that's it.
Christian: Do any of your previous projects carry over any, or are you starting from scratch?
Dr. Parker: If you Google me, you'll see I'm known for two things, primarily. One is the appendix, the second one is looking at wild rats. I'm one of the few people doing serious research in immunology on wild rats, publishing studies on wild rats. So we're on our way, we didn't start from ground zero. We've got a huge pile of work that's coming out soon, you can't Google that. That'll make a big splash, it's really telling us a lot about our immune system and how it's naturally meant to work.
Christian: Have you ever had any laboratory accidents?
Dr. Parker: Ha ha ha. Oh what a fun question. I remember-I don't know how much I should say on this. Ha ha ha. Yes- that's the answer, yes I've had some laboratory accidents. Nobody was ever seriously injured. Twice in my career as a chemist we had to evacuate part of a building which, you know, that wasn't too good. But nobody's life was in danger. I have seen some very serious accidents dealing with organic solvents...I've never been involved in one where anyone was seriously hurt. It's mostly failure to follow safety guidelines. One time in particular, the most dramatic accident I ever saw, somebody was not wearing their safety goggles. That was a pretty gruesome thing, so yeah, always wear your safety goggles.
Christian: Do you have any advice for the aspiring scientists on the internet who will read this interview?
Dr. Parker: I think if you just like solving problems, if you think that looking at problems is a fun thing to do, and you're willing to spend a tremendous amount of time and effort and energy, just looking at and playing around with whatever problem it may be. It might be how haemoglobin from turtles works, I did that project as an undergraduate. Or how exactly it is that plants sense light, I did that project as a graduate student. It doesn't matter, if you just enjoy looking at problems, you'll do well in science. If you're trying to save the planet, science is not the right way to go, most people get burned out. That's not saying you can't save the planet, but you have to be able to work for years and years just on little problems that most people would think are trivial. And if you stumble on to something, you might save the planet, or find out what the appendix is for, or something like that, but that almost never happens.
Christian: Thanks

Hello, my name is Christian Johnson.  I just started the Howard Hughes Precollege Program in the Biological Sciences on Monday (as did everyone else).  In this blog post I will try to give a description of myself and my research lab.

I live in Chapel Hill, North Carolina, and I attend the North Carolina School of Science and Mathematics in Durham, North Carolina.  I previously attended Chapel Hill High School in (you guessed it!) Chapel Hill.  I run cross country and track, and play Ultimate (Frisbee) as well.  However, I am also very interested in all aspects of science, hence my enrollment in the Howard Hughes program.  I am a member of my school's Science Bowl team, which is a lot of fun.  

My lab is headed by Dr. William Parker, and is located on the 4th floor of the Medical Science Research Building.  Everyone here is very nice and willing to help me with my research tasks.  For my project this summer, I will be investigating how proteins in milk can cause IgA molecules to bind to each other, and thus help create biofilms in the gut.  These biofilms are very important, because they help prevent disease and help to make essential vitamins.  So far this week, I have learned how to make plates of agar, how to plate bacteria without disturbing their colonialization, and how to count bacteria.  I also learned the proper way to use the tissue culture room and the autoclave.

This is my lab bench.

This is the refrigerator.  

This is the storage room.  Note the large container of liquid nitrogen.