Title: Predictive Biophysical Models for the Evolution and Ecology of Phages

By: Dr. Antoni Luque

Associate Professor

Department of Biology, University of Miami

ABSTRACT: Tailed phages are the most abundant viruses on Earth and play a crucial role in ecosystems by infecting nearly half of all bacteria at any given time. However, a significant challenge in investigating tailed phages is that most cannot be cultivated under laboratory conditions. In my research lab, we are circumventing this problem by integrating theoretical biophysics, bioinformatics, and machine learning to predict the physical structure and infection modes of tailed phages, leveraging the rapid increase in environmental DNA sequencing data. In this talk, I will share two recent advancements in the study of phage evolution and ecology. First, we have predicted, from first principles, the existence of small viral entities related to tailed phages and found metagenomic evidence of their environmental distribution. This discovery is significant because the structural proteins forming the capsid that protects the genome of these tiny viruses illuminate the origin of tailed phages and their relationship with encapsulins, small biochemical cellular compartments assembled from similar structural proteins. Second, we have generalized the classic phage lambda infection model system to predict the phage infection mode—lytic or lysogenic—in marine and animal-associated microbiomes. Characterizing this transition is crucial because lytic infections trigger the production of viral particles, while lysogeny allows the virus to remain latent, often providing new cellular functions. I will conclude by discussing bottlenecks and future potential applications of these two research lines.

BIO: Dr. Luque is a biophysicist who studies the molecular structure and dynamics of viruses using biophysical modeling, machine learning, and bioinformatics. He earned his Ph.D. at the University of Barcelona and was a Postdoctoral Fellow at New York University. Dr. Luque joined the University of Miami in 2023 as an Associate Professor in the Department of Biology after eight years as a principal investigator at the Viral Information Institute at San Diego State University. Dr. Luque has established the generalized theory of viral capsids, guiding the discovery of unknown viruses and the development of new vectors for gene therapy.

Light refreshments will be provided.