Current Research Projects

Yeast-algae co-culture

Co-evolution in a microbial community

Microbes more often than not live in diverse and tightly knit communities where they exchange nutrients and toxins. How do these interactions affect the evolution of each species? Together with the Hom lab at U. Mississippi, we developed an experimental system to address this question. We grow yeast S. cerevisiae and alga C. reinhardtii together and watch how they adapt to each other’s presence.

Team: Sandeep Venkataram, Jesse Yu (STARS student), Eric Hom (Ole Miss) SK

ancient protein evolution

Gene-genome co-evolution

Microbes constantly exchange genetic material with each other. Suppose a gene from one species enters the genome of another species. Unless this alien gene is a very close ortholog, it probably won’t work very well. The alien gene and the host genome will have to adapt to each other. How? Together with the Kacar lab at U. Arizona, we are watching this fascinating gene-genome co-evolution in bacterium E.coli and are trying to understand it.

Team: Sandeep Venkataram, Shohreh Hajizadeh, Ross Monasky, Betül Kaçar (U of Arizona), SK

Metabolic module

Metabolic theory of epistasis

Many mutations affect cellular metabolism and its regulation, which are fairly well understood in model microorganisms. Based on this understanding, can we predict how mutations will interact with each other at the level of metabolic fluxes and, most importantly, fitness? We are developing a metabolic theory to understand epistasis between mutations that perturb metabolic networks. A major question is whether the fundamental laws of thermodynamics constrain the types of interactions that mutations can have.

Team: SK

Yeast gene drive

Evolutionary impact of gene drives

Gene drives are an amazing new molecular technology that in principle allows us to genetically manipulate entire wild populations. For example, we soon might be able to use gene drives to eradicate malaria by making mosquitos immune to P. falciparum. But would gene drives work as we expect if we actually release them into wild populations? Together with the Meyer lab here at UCSD, we constructed model gene-drive systems in yeast. We are now watching them spread in confined laboratory yeast populations and looking for their long-term evolutionary effects.

Team: Krypton Carolino, Justin Meyer, SK

TnSeq trajectories

Evolvability and robustness

"Evolvability" is a jargon term that describes the ability of a population to adapt to a new environment. "Robustness" is the population's ability to survive and maintain fitness in the face of mutational perturbations. Do all genotypes have the same evolvability and the same robustness in all environments? Probably not. We are trying to understand how robustness and evolvability depend on genotype and the environment. We do this by tracking hundreds or even thousands of mutant lineages in yeast populations and measuring their effects on fitness.

Team: Alena Martsul, Huanyu Kuo, Shohreh Hajizadeh, Milo Johnson (Harvard), Michael Desai (Harvard), SK