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Collective Dynamics and Collaborative Killing: Synergistic Elimination of Bacteria by Immune Cells and Viruses

Abstract

Bacteriophage ('phage') - viruses that exclusively infect and lyse bacteria - are highly abundant in the environment. Phage infections of bacteria can release matter, nutrients, and toxins, mediate the transfer of genes, and transform ecosystem function. In practice, phage are increasingly used as a form of biological control, to eliminate or prevent the proliferation of targeted bacteria - usually pathogens - from colonizing surfaces and organisms. The PI recently proposed a model of "immunophage synergy" to explain how phage and innate immune effector cells can, together, eliminate target bacteria in animal hosts, even when neither can do so alone. This model has been tested and validated in animal hosts. This project will integrate novel experimental methods with theory to transform our physical and systems-level understanding of how viruses and innate immune cells jointly modulate the dynamics of bacterial microcolonies and biofilms. It is also highly interdisciplinary, combining the fields of quantitative viral ecology, nonlinear dynamics, cellular biophysics, and soft matter physics. Thus it provides strong interdisciplinary training for students. As a first step, the project will extend a novel theory for synergistic elimination of bacteria by phage and neutrophils (a key component of the mammalian innate immune system). The theory combines principles of quantitative viral ecology, nonlinear dynamics, and mathematical immunology. This project will translate these principles into an explicitly spatial and individual-based context. This new framework will enable analysis of the basis for emergent, collective dynamics given tripartite interactions between phage, bacteria, and neutrophils. Second, this project will enable new in vitro experiments to probe the mechanistic basis for synergistic elimination of bacteria. Integrated research will assess the importance of nonlinear feedback, cellular biophysics, and soft-matter physics in governing tripartite dynamics via the visualization and quantification of interactions. Third, via an iterative and integrative approach, the project will combine new theoretical methods and in vitro techniques to evaluate principled mechanisms for combined use of phage and neutrophils to eliminate entire biofilms at different stages of development. This project will further the interdisciplinary study of the physics of viral and microbial systems, combining the fields of quantitative viral ecology, nonlinear dynamics, cellular biophysics, and soft matter physics. Two physics PhD students will be trained in an interdisciplinary context, i.e., including theory, large-scale computational modeling, and experimental studies of living systems. Research advances will be translated into reproducible software methods for use by the community, disseminated as protocols on protocols.io, with additional training materials and results presented as part of a collaborative workshop to be held in Year 3. The translation of discoveries to the public will be furthered by annual presentation of general interest talks to local communities, including elementary school, middle school and high school students, leveraging established contacts of the PIs. Discoveries of new principles underlying synergistic elimination of bacteria by phage and neutrophils also have the potential to influence the ongoing study of phage therapy for clinical use to treat multi-drug resistant bacterial infections in animals and humans. In immunophage synergy - the catalyzing discovery for this project - nonlinear feedback mechanisms are essential to understand system-level fates. The goal of this project is to develop an integrated approach to understand the physics of complex interactions amongst phage, bacteria, and innate immune effector cells. This project will combine theory of nonlinear dynamics, computational simulations of living systems, and in vitro experiments to: (i) Extend immunophage synergy to an explicitly spatial framework, including the analysis of emergent, collective dynamics. (ii) Establish and characterize physical interactions amongst phage, bacteria, and innate effector cells during bacteria microcolony and biofilm formation. (iii) Test principled combinations of phage and neutrophils to eliminate growing biofilms given environmental and strain heterogeneity. Together, these aims will deepen efforts to understand physical principles and feedback mechanisms by which phage transform bacterial populations given interactions with eukaryotic host organisms. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

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Funding Source

Project Period

2018-2023