Duke University | Howard Hughes Undergraduate Program

Yeah, I know the program got over a while ago, guys. But... I just couldn't talk about it for a while. It's an emotional thing, okay? *sniff sniff*

This was an amazing summer. HH gave me the opportunity to really see what the day to day lives of people invovled in research, from undergrads to grad students, postdocs to PIs, are really like. It very happily confirmed my desire to do research in college and beyond. I was lucky to be in an encouraging, fun lab environment that stressed work hard, play hard - a great approach to the often tiring challenge that is research. All of the 6 AM mornings and 7 PM nights were completely worth it. I had the chance to learn a lot and have fun at the same time. If you're a 2010 HH kid and you've been put in the Haase lab, congrats! Shoot me an email and I'll let you know where the nerf guns are ;)

Now on to school - I'm taking a break from frantically doing the packing that I haven't been able to these past two weeks. It is going to be an amazing senior year, filled with college apps, clubs, and ...class... of course. NCSSM is a magical place, and I'm also incredibly lucky to have that opportunity. Life feels like I'm living on cloud nine - don't ask me that when I'm up at midnight writing a paper in a couple of weeks, though.

I'll continue to do research this year, try to work really hard, and figure out where I want to go and what I want to do. Not such a tall order, right?

Yes, we all know that Dr. Steven B. Haase is slightly wary of interviews. As in, he dodges them at any cost. So if you want to learn more about him, you just have to be... subtle about it. As a disclaimer, I would like to say that I did NOT walk into Steve's office with the intention of tricking him into telling me about himself. I actually just wanted to talk to him about how the summer had gone/applying to colleges/plans for senior year. About halfway through the conversation, I decided that life lessons from Steve involved a lot of backstory. How convenient!

STEVE'S STORY (mostly): Originally wanted to be a marine biologist (aka the new Jacques Cousteau. Hey, if you're going to do something, do it big.) Went to the Colorado State for undergrad, with the intention of transferring to the University of Washington. Took a molecular biology class sophomore year and was like... "whoa. this is cool." Went to Stanford for grad school. Worked in the genetics center, also in the med school. Wrote the all-important 1999 Nature paper. Interviewed at a lot of different schools (UT-Austin, Yale, etc.) before coming to Duke in 2003. Started working with yeast. Continued to be cool.

So, the majority of that you could have found out by doing a little research. But, Steve's experiences have also helped him formulate a series of philosophies on life, liberty, and not burning out.

STEVE'S GUIDE TO A GOOD LIFE (paraphrased):
1. Do something deeply instead of spreading yourself too thin.
Quote: "Any advisee who comes in wanting to do a double major, I ask them if they have a good reason. If they don't, and most of them don't, I laugh. And tell them not to." If you try to do everything - overbook yourself with clubs, overload on classes, do a triple major and an MD/PhD and research at the same time, you'll end up learning very little about a lot of things. Truly diving into a subject allows you to learn the skills necessary to doing a job, any job, and those are always translatable. There is literally no way to do everything, and you'll be a lot happier if you actually learn about something in depth.

2. It's okay to change your mind.
Quote: "I could decide that I want to become a physicist. Right now. So, I would take some classes, do some reading, because I already know how to think about science. I know how to ask questions. That's the important skill." Many different paths can lead to the same goal, and you don't have to be afraid of changing what you want or dead set on one thing. As long as you work hard to develop yourself into someone who can think, and learn, you can be successful even if you start completely over in something new. That doesn't mean change your mind all the time - it means be confident in the fact that your skills are useful.

3. Science is not about experiments; it's about questions.
Quote: "Sometimes I feel like undergrads come in the lab and they just flounder... it becomes about learning the experiments and not about asking questions, about understanding the science. Then it's no fun anymore." Never cease to see research, and science in general, as the opportunity to ask questions. There is no excuse to not learn something if you just ask. You can have a pile of data, but if you don't know what it means, it doesn't matter. So keep in mind that science is about asking good questions and looking for the answers.

4. "Don't be a spaz."
Enough said.
 

I've already gotten numerous complaints about long posts, so I'll spare you details of my research project... hey, if you're an informed reader, you've already seen that post :)

The biggest hurdle I've faced so far has involved... ahh... weird cells? In one of the first experiments I ran, I saw cells that were basically having issues with cytokinesis - two cells that were still connected would bud as if they had separated. It became a part of my project to basically do some troubleshooting experiments and figure out why the cells were displaying this weird phenotype.

Did I figure it out? Basically... it was one of the reagents. Did I spend almost two weeks doing it? Basically... and now it's crunch time. If I want to get through all of my intended experiments in the week and a half we have left, I don't have any room to mess up. = the woes of research.

But I've learned a lot, from sterile technique, PCR, and gels, to timecourses, proper care of yeast and how to be a good lab citizen. I have data - it's not beautiful, but I understand what it is and what I'm going to do with it. I've reaffirmed my growing interest in and love for research. Watching all of the other members in my lab, I can see myself doing this as soon as I walk into college, in grad school, and beyond. Research is equal parts frustration, joy, learning, and... just research. = the joys. Yeah.

So, I sort of have a track record of long blog posts. Sorry *grin* This one will also fall in line, just because, depending on what I'm doing, there are two 'typical' days in my lab.

1) A Timecourse Day

7:30 - come into the lab early to count and dilute my cells that I grew up the previous day.

10ish - get back to the lab - boy do I want to get back to the lab! recount cells, and, as soon as they get to the right density, add the mating pheromone alpha factor to them to make them "arrest" (stop in the same phase of the cell cycle).

12ish - check the cells to make sure that they have all arrested. If they have, put them into new media, and start my timecourse.

.... 4.5 hours of reading papers, looking at college websites, working on poster stuff, and facebooking, all while running out every 15 minutes to take a sample, later...

4:30ish - clean up everything and sonicate the cells so that any clumps break apart, making for easier counting.

5:00ish - talk to Sara about what's going to happen tomorrow. grow/streak any necessary cells/make notes/organize lab notebook.

5:30ish - go home.

Exciting, yes? Here's the alternative:

2) Counting Day

10ish - count cells. find a sample of about 200 cells for each timepoint and count how many have buds and how many do not.

3ish - create budding curves in excel by plotting percent cells budded against time. enter data into CLOCCS program to get another fit. email results to Sara to add to the lab database.

4ish - talk about what's going to happen tomorrow. set up/grow any cultures.

5:30ish - go home.

Notice all the 'ish' endings... lots of different things happen during the day, changing these times around. The biggest is meetings - we have at least two lab meetings a week, and at other times there will be impromptu discussion sessions. Sometimes Sara and I will meet to go over a concept or idea, or I'll be running a PCR, mutation check timecourse, or other procedure. 

The days are just flying by... but I'm learning a lot. I can't wait until all of my data comes together :)

Let me just say that I am a very, very lucky researcher this summer. My lab was in a perfect position to offer me a project that allows me to learn a LOT, work on my own, and still contribute to their research. In addition, I get to work with three undergrads from VIP, and I get to take advantage of everything they are learning as well. My project is fairly simple to understand, if long.

A basic depiction of the four phases of the cell cycle in eukaryotes.

So this is the cell cycle. Everything has to be very regulated and ordered. That makes sense - if you don't finish replicating your DNA before you start dividing, you get aneuploidy, polyploidy, and messed up chromosomes in general. Therefore, it is very important to understand what regulates the function and correct oscillation of the cell cycle. The established theory is that the majority of periodically transcribed processes - that is, genes and the like that are activated at particular points in the cell cycle, then turned off, then turned on again at the proper time when the cycle restarts - are regulated by complexes between proteins called cyclins and cyclin-dependent kinases, or cyclin-CDK complexes.

The important point to begin with: it is thought that oscillation, or a cell's internal clock, is regulated by cyclin-CDKs. But is it?

Long story short, about ten years ago Dr. Haase performed some experiments using budding yeast that had S-phase and M-phase cyclins deleted from their genomes, cyclins essential for cell cycle progression. The absence of these cyclins prevents the cell from moving past G1 phase. Theoretically, this would cause the cell to arrest at the G1/S border - the cell would be large from its growth phase and budded as if ready to begin DNA replication, but would not have any further cell-cycle activity.

But G1 events cycled as they would in normal wild-type cells, even though S-phase and mitosis did not occur. It was as if parts of the cell involved in periodic events didn't know that a change had occurred in cyclin activity. This indicates the presence of an oscillator that functions independently of cyclin-CDKs. These conclusions were published in the paper "Evidence that a free-running oscillator drives G1 events in the budding yeast cell cycle" (Haase and Reed).

After years of work to understand what this free-running oscillator could be, my lab decided to investigate what would happen to periodic transcription throughout the cell cycle, not just in G1. In experiments with S-phase and mitotic, or M-phase, cyclins deleted, over 70% of the phase specific genes continued to be expressed periodically. These results were published a paper in Nature entitled "Global control of cell-cycle transcription by coupled CDK and network oscillators" (Orlando et al). In short, throughout the cell cycle, oscillation continued even in the absence of cyclin-CDK complexes thought to be essential to cell cycle progression.

So, if it's not cyclin-CDKs, then what does control the oscillation in the cell cycle? The proposed mechanism is a network of transcription factors, that functions either in conjunction with or independently of cyclins to regulate cell cycle transcription.

Cells with different cyclins deleted to prevent certain functions - by counting the buds, we can understand roughly where they are in the cell cycle at any given time.

So, currently, the Haase Lab is trying to describe and characterize this proposed network - what transcription factors are invovled and which ones are the most important. This question is being attacked from two sides - in the lab, we are running experiments with yeast cell lines that have different transcription factors deleted. By letting them grow and taking samples along the way - a "time course" - we can analyze what effect different deletions, and combinations of deletions, have on the period of the cell cycle. Then, the math/stats members of the team use this data to put together a model of the network, and in turn help us determine which tf's are the most important for us to be analyzing.

My job (finally!) is to run experiments with one of these lines, yeast cells with the YHP1 gene deleted. It's not as easy as it sounds - there is a lot of troubleshooting invovled. My cells in particular seem to have trouble with cytokinesis as they progress through the cell cycle - it's difficult to analyze them if you can't tell how many cells you have! But the problem is potentially with one of the reagents I have been using - I will finish another experiment tomorrow that will help us to be more certain. I may also be working with some different methods to sychronize the cells in preparation for time courses. In the end, the work requires a lot of sterile technique, a thorough lab notebook, and my favorite - counting cells.

Hah. Counting cells. If only you guys knew the torture I went through to help my lab help you keep your very important cell cycles in check :)