Student Research at Duke

The Howard Hughes Research Fellows Program this summer has been fabulous in so many aspects!

Professional musicians love to share their experience when starting to learn their instruments as a beginner, trying to recall their first music lesson as a 4-year old. Years later if I were to become a professional researcher, I definitely won’t hesitate to share my wonderful stories from the Howard Hughes Research Fellows Program in 2007.

The fellows seem to not only enjoy their research experience in the labs but also form bonds with other fellows during various social events throughout the program. For me personally, the most valuable part of the program is being able to experience how it is like to work in a lab full time. Throughout my freshman year at Duke I also worked in the lab during the time in between my classes, approximately 2 hours a day. My previous lab experience is actually quite different from what I did this summer, which involves planning and carrying out experiments with fairly long protocols. Most of the procedures will take days to complete, and despite all the hard work and effort, experiments oftentimes didn’t show promising results. I realized that one of the most important traits for becoming a good scientist is patience, especially in the field of molecular biology, since what’s happening in the 1 ml tube is not always within our control. When reading journals like Nature or Science, I can probably finish and understand a well-written paper in 30 minutes, but oftentimes I fail to realize the author might have spent months, or even years, to obtain the data presented in the paper. Research indeed took a great deal of time, but the satisfactory feeling when getting even a small bit of positive results is enough to move me forward.

During the first half of the program I have discussed numerous important papers related to motor proteins with my PI, Dr. Endow. Understanding the major findings of each paper is not enough; we actually examined the papers to a very detailed level by looking at the methods and the biochemical data displayed. I really appreciate Dr. Endow and my co-worker Mark by sharing their knowledge and insightful opinions in our daily discussion. I felt like I had learned a great deal of new things about motor proteins through these discussions, and I was also able to grasp the effective strategies of reading professional publication in the future.

For people who are planning to apply for summer research programs, I sincerely recommended the Howard Hughes Research Fellows Program at Duke University.

All the way through elementary school, I wished I could become a great musician. I went to an elementary school with an intensive music curriculum, learning to play piano and viola. Just like all my other classmates, I spent most part of my childhood practicing music, hoping one day I could perform on the world-renowned stage as a professional violist. I was only thirteen years old then, and I was passionate about what I was doing. I could stay in the practice room alone for hours, repeating small musical phrases for hundreds of times just to make it closer to perfection. I felt content when I had my viola in hands, and I was able to envision myself performing on the professional stage in front of thousands of audience. That is, I had a goal in mind, and this is extremely important no matter what you do.

After I came to America, I volunteered at a senior living residence which housed approximately 45 seniors diagnosed with Alzheimer’s. At first I was trying to think how I could serve these residents to the best of my ability. I decided to serve them through viola by playing old folksongs that they were familiar with. Most of the residents were not very responsive when I played at first, but after visiting the residents a few more times, I knew that my music had indeed touched them. I could felt their sentiments towards my music as I observed their responses: some laughed, some smiled, and some cried. To the residents, I was only a stranger when I first visited, but we gradually became close friends who shared happy and sad stories with each other. If my presence made them happy, I felt even more joyful myself. This kind of happiness is irreplaceable, and this kind of satisfaction cannot be gained from hard work or materialistic pursuits. By interacting with these senior residents, I realized the secret of gaining real happiness is through helping the others and fulfilling their needs; if the ultimate goal of my life is to make people happy, I’ll become the happiest person in the world. There are tons of ways I can make people happy. As long as I have a sincere heart and as long as I am able to use my talent, I will serve the others well. This is what makes me to consider becoming a physician, who is able to address the physical needs of the others most directly. The pursuit of happiness is my goal, and in order to achieve this I need to first make the others happy and healthy.

As I mentioned in the chalktalk, my primary goal for this summer is to create a mutant Ncd motor protein by mutating one single amino acid residue. As of right now, I have not been able to obtain this mutant motor protein, which constitutes the primary step of my project. At the beginning of June it seemed like everything is going very well. All of my PCR products gave accurate bands and good yields. I was able to obtain correct overlapping fragments with decent concentration. After ligated the overlapped PCR fragment (mutated DNA) into the vector, I conducted transformation. I miniprep my culture samples and the DNA turned out to be incorrect. I have repeated these procedures for numerous times, about 7 times actually, but none of the result turned out as expected. I have tried two different vectors, PMW and BS, and I’ll continue to try in the next couple weeks. After repeating the experiment for so many times, I used up all my mutated DNA. So I have to start over from the very beginning by running PCRs.

image from PDB

image from PDB

A lot of the things that we went over during Responsible Conduct in Research seem like common sense at the first glance, but it is just surprising how often we neglect them in the research environment. One thing Dr. Mclay mentioned in his seminar really caught my attention is that most of the unethical behaviors in research is due to negligence and carelessness instead of intentional cheating. Having worked in a lab myself, I realize how easy it is to make mistake if not paying enough attention to my work, since most of the procedures in the labs are very detail-oriented.

I really enjoyed the movie, And The Band Played On. This movie definitely carries through its messages regarding ethical research conducts from many different perspectives, touching on issues like clinical experiments on human, privacy protection for patients, and the integrity of being a scientist. The protagonist in the movie, Don Francis, set up a good model for us to follow. His passion for research and his eagerness to search for the truth are the key characteristics of a good scientist.

cultures on shaker

three plates with colonies: blue white screening

incubator for ligation

Yesterday I did a ligation, trying to piece the BlueScript vector with the mutated DNA I made from PCR. I then did a transformation in the afternoon, expecting to see the colonies when I come in this morning. This morning when I check the plate, there are colony growth except all of the colonies are still very small, and their pigments are not fully developed either. I’ll have to incubate them for a couple more hours and I will find out if I’ve gotton the correct plasmids. The screening method I used is called Blue-white screening. If I have ligased my mutated DAN into the BlueScript vector, then my colonies should turn out white instead of blue. Here is how it works.

On the media plate we added IPTG and Xgal. Our vector contains the Lac operon that includes gene that encodes beta-galactosidase. The plasmid will express the amino terminus of the beta-galactosidase fragment while the host cell will express the C terminus fragment. Even though both of these fragments would not function on its own, they can function if both fragments are present at the same time by alpha complementation. If foreign DNA is inserted into the vector, N-terminus of the beta-galactosidase would not be produced, thus alpha complementation would not work. Therefore, if a foreign piece of DNA is inserted into the plasmid, no functional copy of the beta-galactosidase would be produced. IPTG is a substance that would induce the expression of Beta-galactosidase by mimicking lactose and binding to the repressor of the Lac operon. Thus, in the presence of IPTG, the repressors are inactivated and so transcription can occur. X gal is a galactoside that contains galactose. Beta-galactosidase would break the Xgal into galactose and a hydroxyindole. And the oxidation of the indole produces blue substance. If no beta-galactosidase is present, then Xgal would not be cleaved, thus the cell colony would be white.

I am looking forward to see if I get any white colonies.