Hunting for a Cure

July 26, 2007

Yesterday, the summer research students all went to the Boston Museum of Science, which was awesome.  I’ve never been there before, and had a blast playing with the optical illusions and seeing the dinosaur exhibit.  We also watched an IMAX movie about Jane Goodall and the chimpanzees.  Today I am running IR spectra of alanine in its amide form in D2O and DMSO.  I am taking it at two temperatures: 25 and 55 degrees Celsius, to see if there is a difference in its vibrations.  Tomorrow I will run temperature dependent spectra on my aggregates.  The student vs. faculty softball game is this afternoon too, which will probably be a really good game.

Today is the second to last day of research, and even though I’m really happy to be going home for awhile, it is kind of bittersweet.  Everyone is packing up and moving their things out of Alumni Hall, excited for a vacation to begin, but sad that their experience here has ended.  We will all be back in the fall to continue our research, but for me it means that senior year is finally happening.  This summer has definitely been fun; I spent approximately a month wrestling the SUMO group off of my protein, to finally find aggregates when I least expected them.  I was then able to generate more of these aggregates, and run IR scans to determine their hydrogen bonding patterns.  I finished the summer by taking IR spectra of glutamine and alanine in various solvents, because their peaks will allow us to better identify what causes the aggregate peaks.  Overall, it has been a fantastic summer, and I am eager to continue in the fall.

July 24, 2007

This past weekend was so much fun.  My lab group and I went into Boston to go whale watching.  It was a gorgeous day, and we climbed onto the boat and went 20 miles off of the coast to see about 7 humpback whales in their natural environment.  You would hear the whales before you saw them, and one surfaced right next to where we were standing on the boat and startled us.  We saw them flick their tails up as they dove deep into the water, and they were always in pairs.  We also got a glimpse of a finback whale, but because those are really rare to see, we focused on the humpbacks.  After whale watching, we walked around Boston, heading to Newbury Street to eat dinner.  I have only been to Boston a few times, so it was fun to walk through the streets and parks. 

This week is the last week of research, so we are doing all we can to wrap up the experiments we began this summer.  For the first couple of days, I am concentrating down protein so I can run more SUMO cleavage reactions when school begins.  I have also been working on my poster, which I will present in a summer research symposium when school begins.  Thursday and Friday I will be taking measurements on the IR of the amide form of glutamine and alanine in D2O and DMSO.  I will also run temperature dependant scans of my aggregates. 

Wednesday, I will not be in lab because we are all going to the science museum in Boston for the day.  Most of the students doing science research will be going.  I’ve never been, so I’m looking forward to it. 

July 20, 2007

Yesterday I ran IR scans of glutamine in a solvent comprised of 25% D2O and 75% DMSO.  So far, the data shows a broad peak at about 1630 cm-1.  Basically I was looking to see how the hydrogen bonding would change with more DMSO.  Today or early next week I will fit the data to see how many peaks show up.  Professor Petty also ordered me the amide versions of glutamine and alanine, so I can see what those hydrogen bonding patterns are.  The SUMO protease also arrived yesterday, so today I will set up at least two more SUMO cleavage reactions.  I want to get as many aggregates as possible before the summer ends, so I can run a lot of experiments on them in the fall.  My electrophoresis gel worked for the most part, however I did not find any bands in the SUMO elution columns.  I think that my SUMO protein concentration is just too low to be picked up on the gel.  I am going to have to work on concentrating it down to even smaller volumes than 70 uL. 

Also yesterday was the Chemistry vs. Physics softball game, a challenge that was issued at the beginning of the summer by the physics department.  Needless to say, Chemistry won, even though it was a really good game and physics definitely held their own.  Next week is the faculty vs. students softball game as well.

July 17, 2007

Today I finally managed to fit my D2O data that I took last week on the IR. Professor Petty and I went over all of my data, finding alanine peaks around 1612 wavenumbers, and glutamine peaks around 1619 and 1635 wavenumbers. We were able to tentatively assign the 1619 cm-1 bands to the carbonyl group in the glutamine amino acid, and the other band to the side chain. I am also going to run more scans using 25% D2O and 75% DMSO or Acetonitrile. Tomorrow, I will run a gel on the SUMO cleavage reaction that Kelly concentrated down for me. There is only a week and a half left of summer research, and we are all working really hard to get things done. Amy is working on finishing all of her kinetic experiments, and Kelly will be running some fluorescent measurements using Thioflavin-T, which binds to ordered aggregates. We are hoping to see a difference in the type of aggregates formed by the 32 glutamines and 43 glutamines. In addition, Kelly will run some temperature dependent scans on her aggregates, while I continue with the individual amino acids.

July 12, 2007

Well, my SUMO cleavage worked!  I was able to get a decent amount of aggregates, so Prof. Petty is working on figuring out what measurements we are going to take on them.  Today, I also took IR scans of the solid amino acids, to compare to the measurements taken with the amino acids in various solvents.  I am currently peak fitting my data, to see how many peaks each amino acid/solvent combination has.  I am finding some of the peaks to be at similar wavenumbers as my aggregate measurements.  When all of my data is analyzed and processed, we will be able to get more information about glutamine’s behavior.  I am taking tomorrow off for a long weekend, but Monday I will be continuing the data analysis, as well as taking an electrophoresis gel on my SUMO cleavage.  I will concentrate down my elution buffers from the purification, to see if I can get the SUMO protein band to show up.  If all goes well, I will have a nice gel that shows the original protein, the cleaved protein, and the SUMO group and SUMO protease in the elution lanes.  That will definitely prove that the cleavage works. 

July 10, 2007

This week is going well; I spent yesterday and today taking IR scans of individual glutamine and alanine amino acids in various solvents to see their bands.  The bands will hopefully give us an idea of the way each amino acid hydrogen bonds to the solvents, and will help me identify the peaks in my aggregate spectra.  Tomorrow, I will be purifying yet another SUMO cleavage reaction, cross your fingers and hope for the best!  I will also continue taking IR spectra of the amino acids.  Today I did not get a chance to take scans of each without a solvent, so I need to do that tomorrow. 

Today I also seriously began the graduate school search.  Right now I am leaning towards environmental engineering, and looking into master’s and doctoral degree programs.  None, so far, require chemistry GRE scores, so I will be able to apply early in the fall, and hopefully that means I will find out early.  Actually filling out the applications and getting all of my material together will be my major project in August, when I go home. 

This past weekend was awesome.  I went into Boston for only the second time in my life with my roommate Kyleen, and we walked Newbury Street.  We took the commuter rail from Worcester to South Station in Boston, and then the T from the Red Line to the Green Line.  By the way, I’m really proud that I now know how to find my way through Boston’s subway system.  We had a great lunch at Stephanie’s on Newbury St., and walked through pretty much every shop on the street.  One thing I really regret is not taking advantage of Boston being so close before, but I definitely will my senior year.

July 5, 2007

Well, I’m back at work after a really great holiday. On Tuesday night, a bunch of us walked up the Hart Lawn and watched the Worcester fireworks. It’s an awesome view; you can see them above the buildings and everything. A lot of the Worcester community also congregated there. On Wednesday, we had a cook-out on Caro Street.

Today I came into work to find that my electrophoresis gel had a few extra bands on it, which leads me to believe that something in my purification was contaminated. I think it was the resin, so today I am running a gel on the crude protein that I just purified. Hopefully I will find that the resin was bad, and not that the extra bands are supposed to be there, because I have really no explanation for them. In the meantime, Kelly and I will continue our purifications with a different resin.

July 3, 2007

This week is a short week because of the Fourth of July, so I’m spending it purifying more protein and continuing on with the SUMO cleavage reaction.  Yesterday, I purified that reaction, and found a precipitate in the bottom of one of the Eppendorf tubes.  Hopefully it is aggregates, but I will not be sure until I take an IR of it.  Today, I ran a gel with Kelly that had both of our protein on it, and then will be able to compare each SUMO cleavage reaction.  Thursday all of the bands on the gel will show up, and we will be able to see how efficient the protease is, and if our protocol is successful.  I am also taking an IR scan of the nickel resin used in the purification column, just in case it gets mixed in with the cleaved protein.  I also put together a PowerPoint presentation of my data up to this point for a group meeting on Friday.  Basically it is full of pictures of gels and fitted IR spectra. 

Tomorrow I have the day off for the Fourth, so some of the research students and other people on campus for the summer are having a cook-out on Caro Street.  Tonight is the fireworks also, so I will be sitting on the Hart lawn to watch them over Worcester.  I hope everyone has a great Independence Day!!

June 27, 2007

Today I worked on analyzing my solid aggregate IR data.  Using the program Igor, I was able to fit each broad peak with smaller ones that correspond to different structures.  For example, my aggregate data after 5 hours had four broader peaks that actually were eight peaks.  My next step is to try to fully deuterate the protein, because one of the peaks is probably due to the Amide II band.  Tomorrow I will research ways to do that, and help Kelly take her first IR measurements of her newly aggregated pQ43 protein, which she got today.  I will also continue to concentrate down my protein and run another SUMO cleavage.  I need as many aggregates as possible so I can successfully run temperature dependent measurements in the liquid IR cell. 

I’m beginning to get really excited for my senior year.  A lot of my friends are living off campus, Kendig, Caro, College and Boyden Streets will be amazing.  All of the juniors who were abroad will be back, and my friends and I are already starting to plan out the entire year. 

June 25, 2007

Last Thursday I took the IR spectra of the solid aggregate protein.  We found three really interesting peaks, one which we are hoping is the peak due to hydrogen bonding.  I am planning on disrupting the hydrogen bonding by using various solvents.  I added dimethyl sulfoxide after my spectra was taken to try to break apart the bonds, but unfortunately there was not enough aggregates on the stage to tell.  Today, I tried taking measurements using the liquid cell, with the aggregates suspended in D2O.  It was really hard to keep air bubbles from inside the cell, so tomorrow I will be using a different method to fill it.  I’m hoping that will go well, and then I will be able to see if there is a difference between the solid aggregates and aggregates suspended in a solvent.