EASME Projects

Enhancing Photosynthesis

The objectives of this project are to leverage the latest computational tools, assembled in novel pipelines, to investigate how the enzymatic pathways of photosynthetic organisms might be enhanced to improve algal bioenergy and crop yields under changing environmental contexts. Improving photosynthesis is obviously a tough task, and the reaction might currently be at a Pareto optimal solution from within the limited set of extant proteins it must work with. A Pareto optimal solution is one where gaining ground in one aspect causes lost ground in another aspect. Pareto solutions are optimal solutions in multi-objective problems, like photosynthesis, which must maximize both speed and specificity; sometimes gains in speed reduce specificity, et cetera.

Thermostable Proteins

Heat denatures and unfolds proteins. Thermostable proteins are adapted to maintain structure and function at high temperatures. Taq polymerase, a thermostable variant of DNA polymerase I, discovered in 1976 Chien et al., is the prototypical example. In a world with changing climates, EASME holds the potential to help agriculture adapt quickly, by learning the differences between regular proteins and their thermostable variants, then solving any environmental problems through speedy evolutionary rescue. By applying EASME we could produce a set of thermostable variants for any protein.

Virus Mutation Prediction

With a database of extant DNA sequences, it is possible to predict which new variants of a viral protein might arise in the future, developing new phylogenetic trees with the origin point in the present. We plan to use this approach to simulate the evolution of tomato spotted wilt virus.