Genetic, genomic, and functional evolution of genes encoding viral-interacting proteins in great apes

We propose a collaborative and integrative approach to identify and characterize selective signatures indicative of host-pathogen evolutionary conflict in diverse human and great ape populations and species. The Sudmant lab has extensive expertise in genomics and genetics and the Etienne Lab is expert in virus-host interaction and coevolution. Thus, collaboratively our groups are uniquely poised to address the critical scientific questions surrounding the adaptation of great apes to viral infection.

Mapping coastal intertidal ecosystem primary production: coupling remote sensing and atmospheric eddy covariance

Intertidal coastal ecosystems (i.e. mudflats, salt marshes, seagrass beds, etc.) are present all over the world; they are often neglected in the global carbon budget, while these ecosystems are increasingly recognized to be as productive as tropical forests. Despite their potentially high contribution to the overall carbon budget, their actual contribution remains unknown. Moreover, these ecosystems are currently under threat from global changes and human activities.

Investigating the diversity and distribution of fungal viruses in soil

This project will leverage expertise in soil viromics and root-associated arbuscular mycorrhizal fungi to investigate fungal viruses in Mediterranean grasslands. The UC Davis team will visit Lyon to learn field and laboratory methods for identifying, collecting, and analyzing grassland fungi, including protocols for purifying fungal communities from roots and soil. Both teams will apply these approaches to their local grassland soils, which will be sequenced for the recovery of fungal viruses.

Tracer-informed critical zone modelling to connect water ages with hydrological resources and solute exports

The project aims to reveal how water, and the chemical compounds it contains, are stored and released in the mountainous region of the Upper Colorado River. We will use the extensive sets of field observations collected for several years by the Lawrence Berkeley National Laboratory in the East River headwaters, in a novel combination with state-of-the-art numerical simulations of the processes through which water, plants and underground chemistry interact in these landscapes.

Cylindric Partitions

This research project is at the interface between enumerative combinatorics and mathematical physics. It is centered on cylindric partitions, which are combinatorial objects that are connected with different fields: hypergeometric identities, string theory, probability theory and nonequilibrium statistical physics.

Evolution of Gustatory Preferences in Herbivorous Insects

Plant-feeding insects are extraordinarily diverse as a result of their co-diversification with their host plants over 400 million years. One of the major adaptations necessary for herbivorous feeding is the ability to preferentially feed on the appropriate host plants, but how taste evolves in herbivorous insects is not well understood at molecular genetic and neurophysiological levels.

Langlands duality and spectra of quantum integrable systems

The category of finite-dimensional representations of a quantum affine algebra is one of the most studied objects in quantum groups theory with remarkable applications in various branches of Mathematics and Physics. However many important and fundamental questions remain unsolved in this field. The aim of this research project is to make advances in the understanding of the category as well as of its applications to  quantum integrable systems and in the context of the Langlands program.

The Evolution of Specificity in Parallel Pathways of Signaling in Animal Cells

Small GTPases are small protein switches that cycle between "on" states and "off" states and are key stop or go deciders in many important cellular tasks, such as growth or death. There are many distinct versions of these proteins in cells, each with a specific task or pathway. This project will investigate why proteins that interact with a GTPase in one pathway are specifically paired to their distinct GTPase and do not cross talk with GTPases in other pathways. This is a key unanswered question of major biomedical importance.

Mechanism of Homology Search during Genetic Recombination

Despite its importance for genome maintenance, the basic mechanism by which this homologous molecule is identified amidst the genome remains elusive. We tackle this fundamental gap in our understanding of homologous recombination, as well as the poorly characterized role in this process of conserved protein of clinical significance. To this end, we combine in vitro protein biochemistry (Heyer lab) and novel physical assays to monitor intermediates and steps of the repair reaction in cells (Piazza lab).