Joshua K
- Research Program Mentor
PhD candidate at Michigan State University
Expertise
(1) Using computational and mathematical models to describe biological processes. (2) Plant biology and mycology - particularly the biochemistry and molecular biology of plants and fungi. (3) Biotech for agriculture and energy production.
Bio
I'm interested in building models that describe how plants and microbes function, with the goal of using these models to both better understand these organisms and better engineer them to help create a sustainable future. All of my work in academia and industry has focused on looking for ways to improve production and increase sustainability using biology, albeit from many different angles, all the way from generating genetic data for farmers' plant breeding programs to make better crop varieties to building mathematical models describing the matter and energy limitations of a photosynthesizing plant. I got interested in plant and microbial biology back in high school when I read about Dr. Norman Borlaug, whose research kicked off the Green Revolution and dramatically increased the world's agricultural production. In his later years, Dr. Borlaug shared his vision of how biotechnology could be used not only to help feed people, but to help tackle sustainability issues as well. And aside from its potential impact, I think biotechnology and biological modeling is just very fun! When I'm not doing research, I play video games and spend time with my dog, Makoto, and my two cats, Duchess and Gabriel.Project ideas
Modeling the biosynthesis of valuable biochemical compounds
Tons of valuable chemicals that we use in our everyday life come from, or were originally inspired by, compounds that appear in plants, fungi, and bacteria. This includes most medicines, like the active ingredient in aspirin (salicylic acid), which originally came from the bark of willow trees. And not only are plants and microbes great at making lots of different kinds of chemicals - they can also do it super efficiently as well! Because of this, bioengineers are very interested in putting enzymes, which are proteins that carry out chemical reactions, into easy-to-grow organisms, like the bacterium E. coli, in order to make valuable chemical compounds on an industrial scale. In this project, you will read scientific articles to find chemical compounds - for example, pharmaceutical compounds - that people are interested in synthesizing and harvesting from plants or microbes. Then, you will look at the chemistry involved in making those compounds and see whether the reactions that make them are known and, if so, how feasible it would be to put those reactions into a plant or bacterium. Finally, if it looks feasible, you will modify and then use a model of the plant or microbe's metabolism to predict just how much of that compound you could make under normal growth conditions, allowing you to evaluate how attractive this strategy looks from an industrial standpoint. During this project, you'll learn: (1) how to critically review the literature and identify promising topics to further explore (2) how genes, enzymes, and chemical reactions are related to one another, and how you can find this information (3) what biological/biochemical modeling is, the basics of how to do it, and how to generate and interpret results in a computational biology project The literature review and analysis in this project could be made into a review paper, a short research paper, or a scientific poster. To do the third step of the process, which involves actually working with a computational model, prior experience with Python or another scripting/coding language would be beneficial, but isn't necessarily required.