(4gg) Characterization and Engineering of Non-Model Fungal and Algal Systems

Biological systems present attractive alternatives for traditional industrial processes in the search for new and more environmentally friendly technologies. While there has been massive progress in the bioengineering of primarily well-studied, model microbial systems, the enormous number of severely understudied—or simply unstudied—microorganisms presents a vast source of novel engineering functionalities and applications. Inspired by the hidden potential in these diverse microbial systems, my graduate and postdoctoral work has focused on the application of both experimental and computational approaches to characterize and engineer technologically promising, yet understudied microorganisms from across the tree of life. In this poster, I will cover my prior experiences in the bioengineering of non-model microbes and layout my future vision for my research.

My graduate research focused on the development and applications of genome-scale metabolic models and associated optimization algorithms to bacterial systems. I was specifically focused on both the model-guided engineering of cyanobacterial biofuel-production strains as well as the development of a computational pipeline to identify novel metabolic pathways and products beyond the chemical space of “natural” metabolism. This work established for me the challenges and rewards of engineering non-model biological systems, wherein “engineering” research necessarily coincides with fundamental biological discoveries. As such, in my postdoctoral work, I focused in on two additional categories of poorly studied microorganisms that are nonetheless united in their significant biotechnological potential: the diatom algae and the anaerobic gut fungi.

Diatoms are unicellular, eukaryotic algae recognized for their extraordinary ability to synthesize intricately nano- and micro-patterned cell walls made almost entirely of hydrated silica. While there is increasing interest in the biosynthetic potential of diatoms for producing bio-silica-based materials, with applications ranging from catalyst support to drug delivery to micro-optics, the bioengineering of diatom-derived materials is in its infancy, in part due to a poor understanding of the mechanisms underpinning siliceous cell wall synthesis. To address this lack of knowledge, I have been investigating the genetic and molecular mechanisms of diatom silicification, with the goal of more precisely controlling and engineering this process. In one example from this work, I have collaborated with the Joint Genome Institute (JGI) under its Algal Genomics initiative to sequence novel diatom genomes and incorporate them into a comparative genomics approach that has enabled me to identify both new members of known silicification-associated protein families as well as potentially novel genes involved in diatom silica formation. Additionally, by employing an untargeted proteomics approach on actively forming silica structures, I am working to directly identify additional proteins underlying the mechanisms of silica deposition and pattern formation. Lastly, in order to experimentally validate and engineer the proteins identified by the aforementioned analyses, I am utilizing and further developing a small but growing set of diatom genetic and synthetic biology tools. My future lab will use the tools and analyses I have established for use in these organisms to further characterize these novel silicification-associated proteins and initiate the engineering of diatom biosilica.

Like the diatoms, the anaerobic gut fungi are a significantly understudied group of microorganisms that are increasingly recognized for their biosynthetic and biodegradative abilities. These fungi, which are obligate anaerobes found predominantly in the digestive tracts of herbivores, possess an expansive array of uncharacterized carbohydrate-active enzymes, indicating a high-degree of potential for applications involving the processing and conversion of lignocellulosic material. Furthermore, as these fungi natively exist in a competitive microbial environment, they are believed to possess diverse secondary metabolites with potential for therapeutic applications. However, our ability to fully understand and access the biotechnological potential of these fungi is severely hampered by an almost complete lack of genetic tools. To overcome these restrictions, I have been working within a multi-lab collaborative effort to establish tools and techniques for the genetic manipulation of these fungi. The ongoing development and application of these tools, which I will continue in my future lab, will significantly expand the scope of studies that can be performed on the anaerobic gut fungi and will usher in the development of engineered fungal strains to address pressing biotechnological applications.

My lab will expand upon the above foundational work in diatoms and anaerobic fungi to further establish these two clades of organisms as biotechnological platforms. The range and combination of experience I have across both computational and experimental bioengineering, including constraint-based metabolic modeling, bioinformatics analyses, metabolic engineering, genome engineering, and synthetic biology approaches, will significantly position us to accelerate the engineering potential of these organisms.

Teaching Interests:

Like many people, when I think about my educational experiences, I think specifically about those teachers who have made a significant impact on me. Either by being passionate about their course subject, by introducing me to exciting new ways of thinking, or by being exceptional at the act of teaching itself, those individuals have shown me what is possible in a truly successful class and have shaped my conception of teaching as an art and a skill; one that I have since strived to learn and practice effectively.

My philosophy on teaching has been shaped both by my experiences as a student and by a number of teaching experiences that I have had to date. In general, it centers around thoughtfully considering several interrelated areas in any given teaching situation: 1) how does learning occur within a classroom environment, 2) what should students’ experiences be as course participants, and 3) what are the methodologies that can be used to effectively teach a given course. To develop my own answers to these questions and to further my own development as a teacher, I have intentionally sought out teaching opportunities, such as giving guest lectures in advanced level engineering courses during my PhD, as well as participating in several courses through the DELTA teaching program at the University of Wisconsin-Madison, one of which explicitly covered “Teaching in Science and Engineering: The College Classroom”.

Regarding specific courses, my background education is in Chemical Engineering and I can teach any lower level course. The areas of my research have particularly suited me to teach undergraduates in the areas of mass and energy balances, transport, and kinetics. Additionally, my modeling background has prepared me to teach computationally focused undergraduate engineering courses. For advanced courses, my expertise makes me well suited to teach and develop courses covering bioprocessing, biochemical and metabolic engineering, and computational modeling of biological systems.

As a critical part of my pedagogy, I am broadly interested in and committed to promoting learning environments that support and include the needs and interests of diverse students in all aspects. The aforementioned teaching course that I participated in highlighted for me a number of ways that learning diversity needs to be supported, including both diversity of individual learning styles as well as the ways that cultural backgrounds interact in the college classroom. Above all, I value and look forward to supporting students in achieving their educational goals.