Author Archives: Jordan Reaves

This summer has taught me at least one thing: eight weeks is not much time at all. I never understood the “slow” pace of research. The idea of working on a project for years was strange to me; I never could wrap my head around why so much time was needed. Now, reflecting on what has been the quickest summer I remember, I understand that my research experience was a very short one, and I want more.

Overall, this summer in the lab has been a great experience and has altered my desired career and academic paths. I came into Duke as someone who was very unsure about how to channel my love of science. I considered many paths, including that of a pure PhD scientist or physician scientist, but eventually decided that my place was in patient care with limited involvement in research. I didn’t like the idea of being in an office or not having contact with other people (things that I thought were hallmarks of a career in research).

This summer showed me that I truly love the process of research and scientific inquiry. I love asking questions, understanding and applying techniques and knowledge, and being able to do those things in service of my other passion, patient care, is truly a wonderful thing. When I ruled out a career in research, I really didn’t have enough of an idea of what it was actually like. I just knew it was not as much of a concrete path as a career as an MD can be. I didn’t know how collaborative, social, and fun the lab environment could be.

I’ve now reconsidered what I want. I know that I want to do research in some major capacity. I’m not yet sure if that would be as a PI or an associate of someone else’s lab or in industry, but I do think that I would be more fulfilled by a career in research and patient care than in either alone. Going along with that goal, I am once again very strongly leaning towards pursuing a Medical Scientist Training Program. This summer has shown me how much I love the lab and convinced me that I could be happy despite being in school for all of my 20s. I truly cannot wait to spend more time in lab and get to properly follow a project, maybe even one of mine own, from beginning to end.

I’m choosing to reflect on Dr. West’s talk. Initially, I didn’t like her talk; it made me uneasy. I had previously been considered MSTP programs, decided they were not for me, and set my sights on an MD and a career focused on patient care. In about an hour, I went from 95% sure that’s what I wanted to approximately 10%.

Several things stood out to me in Dr. West’s talk, and I was able to see myself in her stories. I very much resonated when she mentioned having such broad interests and wanting to do everything. I always resented the “favorite subject” question as a kid since I found everything so fascinating. I considered a history double major before I discovered that it would necessitate a bit too much overloading. I also related to something she brought up from her clinical rotations in med school. It was something to the effect of “a bunch of people would happily treat this patient, but very few would be so intrigued to spend 20 years in the lab to figure out what’s going on and how to cure the next patient.” I suppose I would be at home doing either, but after listening to Dr. West I might prefer to do both. I’ve since read a lot more about MSTP programs, and one student I came across had something interesting to say. As a practicing physician, you spend a lot of time with the “known”. Of course, every patient is unique, but generally you know what is going on and how to treat it. Research is the opposite in that you are inherently chasing after and living in the unknown.

One thing I have discovered, is that in my career, I never want to stop learning and going after new knowledge. Obviously, a physician is always learning, but it somehow seems different than the agency to explore nearly any question that one has as a scientist.

Dr. West  did not sell me completely on MD/PhD, but I am very strongly considering it. As Austin put it, she got to me. I am now planning for a career in research in addition to being a clinician. I’m not yet sure exactly what I want that to look like or how to get there, but as I said earlier, being in the unknown is fun.

Mentors: Elizabeth Brooks DVM, Kate Ilich MD

PI: Dwight Koeberl MD PhD

The trifunctional protein is a mitochondrial protein that plays an important role in fatty acid oxidation. Deficiency of this protein is inherited in an autosomal recessive manner and causes cardiomyopathy, fat buildup, decreased muscle strength, and decreased lifespan. It is our lab’s hypothesis that gene therapy using an Adeno-Associated Virus (AAV) vector with a transgene will lead to increased expression of this protein in a HADHB knockout mouse model compared to untreated affected mice.

We tested our hypothesis by examining the disease phenotype and looking directly at protein expression. We looked at wire hang tests, fasted glucose tests, fasted glucose tolerance tests, survivability, and body weight to assess the physical condition of the mouse.

Our preliminarily data does not show dramatic phenotype correction; however, we await more data to see if statistically significant differences are seen. We plan to do a Western Blot to look for presence of TFP, and we await electrophysiology data concerning cardiac function which will be available at the conclusion of the study. We are optimistic about those results.

I want to reflect on Yaneli’s chalk talk. I’m interested in precision and regenerative medicine, and thus I found her talk really interesting. Her research focuses on muscle regeneration, particularly on the role of the TREM2 gene in regulating macrophage polarization.

I liked how she made use of visuals especially when explain methods like inducing ischemia. The connection between macrophages and muscle regenerations is something I’m unfamiliar with, though it seems to have a lot of potential for exploration and therapeutics. The polarization of macrophages was something that wasn’t touched on much, but it seems intriguing upon further Googling. One paper I saw actually mentioned that these cells derive their energy from fatty acid oxidation, which my project is studying. It was really cool to find a link between these seemingly different projects. Though it is a good reminder of how connected the body is. This could something that my lab looks at when thinking about the efficacy of our treatment down the line. I also found a paper exploring TREM2’s potential connections to Alzheimer’s disease.

I’m looking forward to seeing what results Yaneli gets from this study and seeing the potential clinical application of those results. This research could have such wide-ranging effects; tissue regeneration happens all the time from severe burns to minor cuts needed a Band-Aid. This particularly makes me think of my mom, who is a Type 1 Diabetic. If she gets injured, she has trouble healing quickly because of her Diabetes. If this was a therapeutic it could be used to help patients like her heal more quickly shortening time in pain and time for infection to enter the body through a wound. There could also potentially be applications for heart attacks or trauma patients. I’m really excited to see the results of Yaneli’s project and the growth of this research at large.

There isn’t really a “typical day” in my lab. There is a reasonably large variance in what I do day to day. Despite that, I can give the broad categories that the things I do fit under.

The first of these is traditional wet lab stuff. I’ll run PCRs, digest them, and gel them to genotype mice. I sometimes have to transfer samples into different storage mediums. Some of the work that I might be moving in to doing as we have samples that warrant analysis includes assays to measure fat content and western blots to look at protein levels. I also spend some time researching and learning new techniques.

Another large chunk of my time is devoted to running experiments and caring for the animals our lab uses to test our therapies. This includes feeding the dogs we use to test some therapies and injecting dextrose into some of our mice. This also includes tests to look at the efficacy of our therapies. I do a lot of glucose tolerance tests and glucose curves where we look at the animal’s blood glucose over time. I fast the animal, give a dextrose injection in the case of a tolerance test, and check the animal’s blood sugar at various time points. I also perform wire hangs to look at the strength of the mice since their condition effects their muscles. I also help to collect tissue when the animals reach their endpoint, which is really interesting since I get to see anatomy firsthand.

The final “block” of my time is spent doing more desk-oriented tasks. Some of this is inputting the data I collect and then using software to analyze and graph that data. The rest of this time is spent researching. This includes reading papers related to my project to see what others are doing and what parts of their studies could be relevant to our research.

Some days I’ll spend mostly at the bench pipetting and doing proper wet lab stuff. Some days I’ll be in the mouse room for a number of hours, or at my desk for a significant amount of time. Other times, it’s a mix of the three. I do like the variety that my lab has; it helps to break up time and keep me doing something fresh and interesting.

I really enjoyed getting to chat with Dr. Koeberl about his journey, mine, and science in general. It was nice to “break the ice”, get to know a bit more about him, and get some advice moving forward.

We started off by discussing his journey to where he is today. He began in his home state of Minnesota at Carleton college. He then went on to pursue an MD/PhD degree program at Mayo Clinic School of Medicine. He initially planned to pursue only an MD degree; however, opted for the dual degree after interviewers mentioned it. He completed his program in six years writing his thesis on hemophilia.

Dr. Koeberl then went on to UCSF to complete a residency in pediatrics. He followed this up with several fellowships in Medical Genetics at the University of Washington. After working as a pediatrician for a period of time, he began applying to faculty positions. He opted to take a position at Duke for several reasons. First of all, Duke was a place where many new types of treatments for metabolic conditions were being explore. Duke was also a great place to explore the use cases of then lesser known AAV vectors. These things which aligned with Dr. Koeberl’s research interests prompted him to start his career at Duke.

One thing that Dr. Koeberl likes about being a PI is the agency he has to study his own interests. The flexible nature of the work is also appealing. The biggest challenge that a PI faces is funding. It is something that requires continuous work and could necessitate some difficult decisions should money be tight.

His days can be varied but consist of about 4 broad things. The biggest of these is probably writing. This includes writing papers and grants, which also require lots of reading up on literature. Meetings with colleagues, funders, and others also take up a good bit of time. Some of Dr. Koeberl’s time is also spent in clinic where he sees patients with inherited metabolic conditions and as the medical director for the biochemical genetics lab.

Dr. Koeberl identified several things as being critical for one’s success in science. The first of these is having good people you can rely on. This was part of what helped him be successful in starting and continuing his research career. Dependable and capable people make science work. Another critical component of success in science is good communication. Being able to concisely and effectively communicate in oral and written modes is necessary to do well in science. The recommendations he had for developing those skills involved reading. This includes reading scientific literature about your field and books about scientific writing and grant writing (He acknowledges that they may be dry, but maintains that they are helpful).

On a lighter note, I also asked Dr. Koeberl what his favorite project was. It is a current project that we have going surrounding gene editing using CRISPR/Cas9 to treat a glycogen storage disorder. He is excited by the possibilities this technology has to offer and to see it go to clinical trial.

My project this summer is studying the effects of gene therapy for a mitochondrial trifunctional protein (TFP) deficiency. This autosomal recessive mutation effects the function of an octamer protein complex that is responsible for fatty acid oxidation as seen in the figure. Even though our mutation only effects one subunit, it alters the folding of the complex rending the entire complex inactive. This process not only breaks down fatty acids, but it also supplies the acetyl-CoA needed for the citric acid cycle which is produced by the step labeled 3 by the beta subunit. It effects the liver and heart heavily since both rely heavily on fatty acid oxidation as a source of energy. Since this process is unable to occur, those organs are not able to function optimally and have fat build up in their cells (the medical word for this is steatosis). Muscles, which sometimes depend on fatty acid oxidation, are also affected. This condition shortens one’s lifespan significantly, with cardiomyopathy being the typical cause of death.

Our lab’s goal is to correct this using gene therapy to replace the missing enzyme. We are currently trying to do this using an Adeno-associated viral vector (AAV). For anyone not familiar, this can be thought of as a trojan horse. We enclose the DNA coding for the protein missing within the virus and use the virus “machinery” to get inside the cell. The goal here is that the cells can now make the protein, hopefully curing or improving the condition. Some problems that can arise include the cells not taking up the virus, immune response, and the DNA being lost as the cells replicate.

We are testing this AAV therapy in a mouse model with a TFP deficiency. We administer the treatment in affected and control mice. We plan to perform a variety of tests to see if it is effective. This includes glucose tests, strength tests, tests to look at the amount of fat in the liver, Western blots to measure protein levels, and looking at the stained tissue under the microscope to name a few. My role this summer is to help with these tests and look at the data they produce. So far, I have done background reading on the condition, genotyped new litters using PCR and gel electrophoresis, ran some of these tests on our mice to assess the effectiveness of our therapy, and analyzed some of our results using graph software. In the next weeks I will learn how to run more of the tests we need to evaluate the treatment and perform some of them. I’m very excited to follow this project and see where it goes throughout this summer and beyond.