Hello, my name is Siqi Wu. I am a rising senior at the John D. O’Bryant School. I am currently 17 years old and soon to be 18 years old in September.

If there’s anything I love, it’s Malaysian food. I discovered how delicious Malaysian food is after visiting a Malaysian cuisine a couple of weeks ago. It was a rainy day and I was heading to the graduation for the class of 2014 with three of my friends. After arriving at the building where the graduation ceremony would be held, one of my friend and I were not allowed in because we had on backpacks. We ran around with no luck trying to find a place to put our bags. We saw our Precalculus teacher and our world lit up. However, he laughed at us and once again, we were struggling. It was not until we saw the director of the science department that we managed to get our bags off of us. We went on in to watch the graduation ceremony and the rest is history. Afterwards, we went to a Malaysian cuisine to celebrate. That’s the story of how I discovered the existence of Malaysian food. I ordered a plate of noodles I’ve never heard of before. And when the order came, I slowly lifted the fork to my mouth and placed the noodles inside my mouth. I chewed and 3 seconds later, I died. The dish was just so delicious. That’s the story of how I discovered the rich taste of Malaysian food and fell in love with it. Disclaimer: I didn’t judge from just one dish, I also tried my friend’s dishes.

I also have a huge crush on Science. When people ask me why I like science specifically Chemistry, I am not sure how to answer. When I think of Science, I think of innovation and answers to questions we’ve always wished to know. I guess I’ve always loved Science because it is similar to a place where you can release your thoughts and ideas. There is no wrong in science, your ideas are something to play with until it gets bigger and bigger into something life changing. Look at all the famous Scientists, they started small and changed the world.
This summer, I will be working in the Wagner Lab at Harvard Medical School with Dr. Andras. My project will be on the structural characterization of the Ska1 protein and its interaction with the Ska2 and Ska3 proteins. These proteins are very important in cell division, and in order to get a better understanding of cell division, a better understanding of these proteins and their roles in cell division are needed.

When discussing the subject of cancer, cell division plays an important role. Cancer is caused by mutated DNA in the cells. When those affected cells divide, the cancer spreads. We need to better understand this process (cell division) to figure out ways to stop or slow down the splitting of the cells.
For my project, I am currently working with Dr. Andras in analyzing the hSka1 protein.
We are trying to figure out what buffer conditions the proteinwill be most comfortable in above 40 Celsius. The hSka1 tends to denature above 37 Celsius. The protein likes high amounts of salt.

Weekly Assignment: 7/18/14
For many centuries, cancer has been a major problem in society causing the death of both young and old. The disease is caused by an uncontrolled division of abnormal cells in the body. The Ska1 protein is a very important part of cell division. In order to learn more about cell division such as how to stop or increase it, the structure of the protein and how it interacts with other proteins must be known. We can then modify the protein and it's interaction in order to manipulate cell division. We use assignments to figure out where the parts of the proteins are, and then we figure out the spacing among these parts using nosey to construct a picture of the protein.

Weekly Assignment: 7/11/14
hSka1 and DL hSka1 Purification:
We retrieved the cells (cells were grown overnight and is currently in a Falcon Tube) and placed it in an ice bucket. 35mL of Lysis buffer (50mm Tris, 350mm NaCl, 10mm Imidazole, at pH 8). The addition of this buffer will make the proteins attack so a Protease inhibitor cocktail tablet must be added. The reducing agent, 2-Mecrapto-Ethanol(10uL) will be added. We took the cells to the cold room and placed it on the shaker for 15 minutes. This is so that everything that was recently added will mix together. In order to ensure that the cells has been thoroughly mixed, we used a pipette to pipette cells up and down to resuspend the pellet. Then we added 3uL of Benzonase (chops up DNA and RNA) last because it is an enzyme, therefore it is not stable and can be destroyed easily. Then we placed the the cells on the shaker in the cold room for another 10 minutes. Then we transferred the cells onto a small glass beaker and placed it into the ice bucker again (cells must be kept cold). We added water onto the ice around the glass beaker to make the whole surface area of the cells cool. We took the cells to the sonifier and immersed the tip of the sonifier into the cells. Time: 5 minutes, amplitude: 30%, On & Off time is .5 seconds. The sonifier ran for a total of 10 minutes. After the sonification was completed, we checked the cells to see if they were properly lysed. Using a pipette, I pipetted 1000uL of the cells and slowly pipetted them back into the falcon tube. If the drops are nice and smooth, then the cells were properly lysed and ready to be centrifuged. We transferred the cells into two centrifuge tubes and balanced them out. Centrifuge set to 40 minutes and 18,000 rpm. While the cells are being centrifuged, we prepared an eppendorf tube labelling it hSka1 DL Lysis and added 20mL of blue dye to it. Then we took a falcon tube and labeled it Nickel NTA, hSka1 DL. Then we took a 1mL pipette and pipetted 5mL of beets into the falcon tube. After letting the beets settle down, we pipetted the extra liquid on top of the beets. Then we filled up the falcon tube to 50mL with water, shook it, and let the beets settle down again. After the beets settled to the bottom of the falcon tube, we decanted the water and poured 25mL of Lysis buffer onto the beets and let it settle again. After the buffer had settled, we discarded the buffer and kept the beets in the falcon tube. The 40 minutes of centrifuged is over by this time and we went to retrieve the cells from the centrifuge. We prepared an eppendorf tube labeled DL hSka1 Supernatant. We pipetted 20uL of supernatant(liquid above the cells, the Ska1 protein and a bunch of other proteins is in the supernatant) from one of the centrifuge tubes into the eppendorf tube and added 20uL of loading dye. Then we added the supernatant onto the beets. This immobilizes the proteins onto the beets. We put the beets with the supernatant in the cold room on the shaker for 90 minutes. Then we used a yellow filter and poured the supernatant in. All the other liquids and proteins ran through the filter except for the ska1 protein because it is on the beets. The beets bonded with the Ska1 proteins. The proteins has histidine tag and all those histidine tags has lone electron pairs. The lone pairs of electrons form interactions with the 2+ ions that the beets has. Then we poured 20mL of Lysis buffer. After the 20mL runs through the filter, we poured in more to wash the beets.

1.The kinetochore-bound Ska1 complex tracks depolymerizing microtubules and binds to curved protofilaments
Chromosome movement driven by microtubule dynamics is essential for proper cell division. Here, we defined conserved biochemical activities of the Ska1 complex, a key player in coupling chromosome movement to microtubule dynamics. The long-axis of the Ska1 MTBD is approximately the same length as the longest axis of the tubulin monomer (~5 nm). Thus, the Ska1 MTBD domain could interact with consecutive tubulin monomers and the binding surfaces, such as the C-terminal charged tail, could be ideally positioned when the protofilaments assume a curved conformation. Alternatively, the Ska1 MTBD could have a binding site on the tubulin monomer that is unaffected by the conformation of the protofilament. In case of the C. elegans homologue, additional interactions may be formed with dolastatin-10 induced protofilament rings. This will help me get a deeper understanding of what is the Ska1, it's roles in cell division and how it interacts with other proteins.
2.Resonance assignments of the microtubule-binding domain of the C. elegans spindle and kinetochore-associated protein 1
The outer kinetochore Ndc80 complex acts synergistically with the Ska (spindle and kinetochore-associated) complex to harness the energy of depolymerizing microtubules and power chromosome movement. The Ska complex is a hexamer consisting of two copies of the proteins Ska1, Ska2 and Ska3, respectively. The C-terminal domain of the spindle and kinetochore-associated protein 1 (Ska1) is the microtubule-binding domain of the Ska complex. We solved the solution structure of the C. elegans microtubule-binding domain (MTBD) of the protein Ska1 using NMR spectroscopy. Here, we report the resonance assignments of the MTBD of C. elegans Ska1. This will help me understanding the proteins that the Ska1 interacts with and how it interacts with those proteins.
This website has many pictures associated with mitosis.

Weekly Assignment: 7/3/14
Hypothesis: The hSka1 protein will be most comfortable in high amounts of salt so it will not denature as quickly as the hSka1 proteins in lower salt concentrations.
1. Prepare well plate.
2. Prepare different buffers.Hepes pH 7, Hepes pH 7.5, Tris pH 7.5, Mops pH 6.8, Bis-Tris pH 6, Bis Tris Propane pH 7, Tris pH 8, Mes pH 6, Phosphate pH 7, Hepes pH 8
3. Pipette 18uL of each buffer into two similar well plate. (we are doing this so that when we read the temperature at when the protein denatures, it will be more accurate)
4. Pipette 2uL of the protein into the different buffers in the well plates.
5. Take the well plate to the machine that reads when the protein will denature.
6. Analyze the graphs of the proteins in different buffers using matlab. The graphs that reveals that the protein doesn't denature until it is above 40 Celsius are the ones we need. However, the salt and glycerol concentration cannot be too high (too high of a salt concentration will affect the machine negatively). The pH must also not be too high because a pH that is too basic will affect the proteins.