James W
- Research Program Mentor
PhD at Washington University in St. Louis
Expertise
Computational Biology, Genetics, Genomics, Microbiology, Microbiome, Undernutrition, Virology, Protein Evolution, Evolutionary Biology, Biochemistry
Bio
Heading to college I wanted to be a marine biologist, so logically I attended the University of Minnesota, about as far from the ocean as possible. I earned a degree in Fisheries, Wildlife, and Conservation Biology (Fisheries specialization) and a second major in Biology. My undergraduate work explored the relationship between tooth and jaw shape and diet in a family of marine fish called Blennies. I became interested in genomics during my undergraduate course work which led to me working as a research technician studying evolutionary genomics and populations genetics in cavefish for a year after graduation. The aim of this research was to understand the genetics underlying the repeated evolution of cave traits (loss of eyes and pigmentation, altered metabolism etc.) to gain insights into the process of evolution, as well as into molecular mechanisms and genetic pathways that may be relevant to human disease. I am now in the Molecular Genetics and Genomics program at Washington University. Reflecting my broad interests, I did rotations in labs studying experimental evolution in yeast, applying single cell RNA-sequencing to understand development, and the lab I eventually joined studying the role of the gut microbiome in undernutrition. Although I am not currently studying marine biology, the field of gut microbiome research does offer some of the same allure. I think we are just at the tip of the iceberg in terms of understanding the complexities of microbial ecosystems and the mechanisms that regulate them and their interactions with their hosts and find the opportunity for discovery to be exhilarating. The field is inherently interdisciplinary, so I have gained exposure to an array of scientific disciplines, which has been a unique, and sometimes challenging, learning experience. In my free time I enjoy gardening, hiking, theater, live concerts, traveling, spending time with my wife and two rescue Frenchies (Freddy and Lily), and as evidenced by my degree and research prior to graduate school, fishing. I particularly enjoyed fishing on the cold clear lakes of the northern US during my time living up there, and fly fishing for trout on the Ozark streams of Missouri. I find many elements of the research process to be captivating and am excited to share this with others. I also know firsthand how important good mentorship is in creating an environment where your ideas can flourish, while still being polished, making for a fun and productive research experience.Project ideas
Good vs Evil: Are there 'good' and 'bad' actors in the human microbiome?
Many studies of the human microbiome attempt to identify a handful of microbial strains/species that are responsible for a certain phenotype or observed trait. These species are then highlighted as being good guys, important for a healthy microbiome, or bad guys, that are key contributors to a dysbiotic or unhealthy microbiome. However, in a system as complex as most human associated microbiomes, reality is rarely this simple. There are multiple organisms that are claimed to be important in promoting a healthy state in one article and then found to contribute to a disease or unhealthy state in another. A review of the evidence of the good and bad actors of the microbiome, and the context dependence of these findings, would be useful for researchers and a solid introduction to the topic for someone new to the field. Individual projects could be limited in scope to specific diseases or habitats/ecosystems of interest to the student.