Project Team: James T. Van Leuven, Emma Altman

The microbial communities colonizing animal guts are highly influential to host health and development. Animal hosts are impacted by the species of microbes present and temporal changes in their abundances, but the forces governing these dynamics are poorly understood. Bacteriophages modulate bacterial community composition through predation. They also facilitate horizontal gene transfer, stimulate the immune systems of animals, and can be used to fight antibiotic-resistant bacterial infections. The inclusion of bacteriophages in microbial ecosystem models and testing of these models is critical to understand how these viruses contribute to microbial community dynamics and evolution, and ultimately, to host health.

The goal of the proposed research is to test the molecular, ecological, and evolutionary roles of bacteriophages in host-associated microbial communities using honey bees and their associated gut bacteria. We will modify and apply models of microbial community dynamics to time-series data collected on bee microbiota and then test these models by perturbing bee microbiomes. This project will benefit from collaborative research across institutions and will boost interdepartmental research at University of Idaho.

Project Team: Jagdish Patel, Deborah Stenkamp, Dharmesh Patel, Jonathan Barnes

Note: This pilot grant evolved out of the research produced by the working group, Evolution of Tandemly-Replicated Opsin Genes: Molecular Models that Predict Spectral Shifts.

Vision is one of the most sophisticated biochemical system in humans and serves as a primary environmental input. In other organisms, it is the dominant sensory modality for foraging, predator avoidance, and social behaviors including mate selection. Understanding this complex system requires input from a variety of scientific fields. Human visual perception is initiated when light strikes rod and cone photoreceptors within the retina of the eye. Visual pigments (VPs) with distinct peak spectral sensitivities (λ_max) expressed in separate rod and cone photoreceptor populations transmit differential input to retinal neurons. The cone VPs (SWS1, SWS2, Rh2, LWS) are responsible for color perception, whereas the rod VPs (Rh1) are responsible for the perception of objects under dim light condition. A VP consists of a chromophore and associated opsin protein, and its sensitivity to individual colors, i.e., λ_max of VP is determined by chromophore type (11-cis retinal or 11-cis 3,4-dehydroretinal) and the opsin amino acid sequence. Minor differences in opsin sequence can result in large changes in λ_max and/or result in anomalous visual function. 

Direct and accurate prediction of λ_max from opsin sequence was not possible until recently when we developed a molecular modeling approach for a small number of teleost Rh2 cone opsins (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005974) and Rh1 rod opsins (https://science.sciencemag.org/content/364/6440/588)  Our approach overcomes several limitations of previous methods and provides a glimpse into underlying mechanisms for a small set of rod and cone opsin variants. In spite of this step forward, there is a significant gap in our understanding of genome to phenome relationships in opsins. Filling this gap has the potential to fundamentally explain λ_max, basic “rules” through which opsins evolve novel functions, the molecular basis of missense variations that can lead to vision deficiency and provide a platform for engineering the opsin with desirable characteristics. Currently, our group is interested in expanding our molecular modeling-based approach to other class of opsins and investigating underlying mechanism of missense variations affecting opsin function.

Project Team: Matthew Bernards, Nathan Schiele, Dharmeshkumar Patel, Stephanie Haag

In the US, over 130,000 surgical procedures each year require a bone graft material, but almost 30% of grafts fail. Recent studies have implicated albumin as important during bone repair and it has been adapted for improving scaffold integration with bone tissue. This is important because albumin is abundant and cost-effective. In contrast, however, are studies that demonstrate albumin blocking cell adhesion to biomaterials. These contradictions indicate that albumin is bioactive only when in specific conformations. The over-arching goal of this research effort is to deliver bioactive albumin via a tissue engineering platform for enhanced bone repair and regeneration. The development of this platform will address the clinical need for a bone graft with reduced failure rates. To achieve this goal, the bioactive conformation of albumin responsible for bone repair must be identified before it can be incorporated into a scaffold, and this is the objective of the proposed investigation. Our central hypothesis is that albumin has a bioactive conformation that promotes bone repair, that is imparted to albumin upon calcium binding.

First, we will use molecular modeling to determine the conformational landscape of calcium-free and calcium-bound albumin. The conformational preferences of albumin for various calcium-bound conditions will be determined using molecular modeling. Determining conformational preferences of a protein is a challenging problem in molecular modeling so we will tackle it using molecular dynamics or Monte Carlo simulations of coarse-grained protein models. These approaches allow for large-scale conformational changes within the timescale of the simulations. If our hypothesis is correct then changing the binding pattern for calcium will make specific conformation(s) more stable – and these conformations will promote cell adhesion. In parallel, we will identify conformation changes in albumin induced by calcium with Fourier transform infrared spectroscopy (FTIR). The conformational states of albumin adsorbed to tissue culture polystyrene in both a cell adhesive and nonadhesive conformation will be probed using FTIR. After identifying the critical calcium concentration that induces a cell adhesive conformation to albumin, we will use FTIR to quantify differences in the secondary structure of the adsorbed species. These will be directly compared to molecular modeling results obtained in Aim 1, to better delineate conformational changes that facilitate cell adhesion. If our hypothesis is correct then there should be significant changes in the secondary structure upon exposure to calcium.

By pairing molecular modeling with empirical evidence of the secondary structure of albumin it will be possible to delineate the bioactive region of albumin more clearly. This represents a significant step towards the therapeutic application of albumin or subdomains of albumin for bone tissue repair from an implanted scaffold.