Scott Higgins- Week 2/3

Hey everyone, I’m combining Weeks 2 and 3 because I did essentially the same thing for each day: Read. After learning a bit more about my project from Kayla, I came to the realization that the information from the metabolomics papers I had been researching in the spring was not entirely applicable to the work I will be doing this summer. The project that I am working on relates to drug metabolism, with it’s title being “ Compound cocktails for metabolic profiling for drug efficacy and safety assessment.” The central aim is to take advantage of molecules that are structurally similar to common drugs, by substituting them as substrates to common drug metabolism enzymes. After doing so, a comprehensive metabolic profile will be taken, then inferences can be made regarding how a patient reacts to other compounds that are structurally similar to the molecule. In doing this, one can reduce the cost and time needed to test the safety and efficacy of a drug, compared with the traditional method of individually testing each of the molecules. This will be done with what is known as the “Cocktail Approach” to drug phenotyping. This method of drug analysis utilises a known and approved combination of drugs that are specific and have absolutely zero interaction with each other in the body. Each drug is known as a probe, triggering either a positive or negative interaction with an isoenzyme active in carrying out the drug’s goal. These particular enzymes are often times a part of the CYP450 family, which is responsible for converting a drug from it’s ingestible state to actual chemical products (metabolites) that can do work in the body.

All of this information, and much much more, has been recovered through countless articles that I have been reading for the past two weeks. My post-doc sent me a guide to reading scientific literature, which reminded me that not everyone knows how much we have actually done to prepare for this, and that I had read so many pieces of scientific literature already (with a strategy courtesy of Mr. Sham)! Anyway, the process of selecting molecules is quite tedious, as you need to find a natural compound that is mechanically/structurally similar to a drug and uses the same metabolic pathway as the drug. This requires an extensive search through an online database (http://bioinf-applied.charite.de/supernatural_new/index.php?site=pathway&organism=hsa&pathway_type=Metabolism), with thousands of combinations. I literally spent 2 hours one day just trying to find a match between a drug and a natural household compound without luck.

Other than that, the second week brought another lab meeting, in which my post-doc Kayla presented a literary article about genetics, which was really interesting. Then, the Fourth of July weekend came, leading into Week 3. I usually stay home on Mondays, and Tuesday was the Fourth of July. Late at night on the Fourth I was emailed, saying that the lab meeting would be cancelled on the 5th, so I didn’t have to come in. The reasoning for this cancellation was due to a grueling grant that was due July 5th. I have been learning about a side of professional science that I had never really thought about for more than 6 seconds: funding. Learning about how a grant is structured and formatted, with everything within it being extremely important to the lab’s future, has been so interesting and completely new to me. That Thursday, Dr. Peretz came to visit me! Dr. Peretz, Kayla, and myself chatted for about 30 minutes regarding what I was doing and the operation of the lab. Following this, and a brief tour of the lab, Dr. Peretz and I met up with fellow Columbia EXPer Emily for some good old-fashioned BBQ. It was so refreshing to see familiar faces, and just share experiences with Emily, who is literally right across the street from me. What are the odds!

Speaking of chance, just to take a little sidebar: I was in New York Penn Station during my second week, one of the craziest transportation hubs in the city, with thousands and thousands of people passing through every day. On my walk from the NJ Transit area to the ACE subway line, I saw, in the distance, a familiar Falcon’s face: Diana King. We met eyes, gave each other a quick wave, and continued on with our scientific agenda of the day.

Back to the main experience, I have really gotten to enjoy the material I am working with to create the structure for this project. Coming in to this experience, it is noteworthy to say that the project we are working on is still in its conceptual phase. Nothing is set up for me, leading me and my colleagues to craft this project entirely from scratch, asking interesting scientific questions to try and achieve our goal, which is ever-changing. I also started taking an online course to learn the coding language Python, which Kayla recommended I learn. Commuting is always a blast :-). The subway that I usually take, the Uptown-Bound A train, actually DERAILED half an hour before I got there during my second week here. There’s nothing better than public transportation! I was not on the train, but it caused serious delays in my commute to 168th Street. Will keep you guys updated!