(6iu) Cell-Free Bioprocess Engineering for a Renewable Carbon Future

The potential of cell-free synthetic biology and bioprocess engineering to change the world for the better is tremendous. Previous efforts in this field to date have explored a variety of highly impactful directions, including elucidation of the biochemical basis of life, the ability to conduct highly sophisticated cell-free protein synthesis, and demonstration of complex synthetic gene circuits, to name just a few. With the modern set of biotechnological tools available, the opportunities for further exploiting this approach are continually expanding—from developing low- or negative-carbon energy and chemical systems, to accelerating agricultural engineering, to environmental remediation, to defense biosensing applications. Effective implementation of such cell-free synthetic biology tools and conversion platforms would result in significant global impact; the development of these systems is my central passion.

Research Interests:

For decades, the roles of proteins in living systems have been studied in vitro, forming the basis of our understanding of life at the smallest scales. Modern biotechnology, in harnessing this knowledge, offers the potential to improve the world in many ways, from biorenewable chemicals to agriculture to human health and beyond. Significant hurdles have limited the impact of this research enterprise in some fields however – microbes producing solvents rapidly succumb to the cytotoxic environment they create, agricultural modifications remain bound by the rate of plant growth, and the means available to efficiently debottleneck metabolic pathways are lacking. Cell-free methods—the use of cell lysate or purified enzymes to replicate complicated pathways—allow approaches with the potential to revolutionize these fields, due to their ability to operate in a wide range of conditions, serve as a rapid prototyping platform, and enable effective model-driven pathway optimization.

My previous work at Virginia Tech, and subsequently at Cell-Free Bioinnovations, focused on biological hydrogen production using a purified cell-free pathway. In this project, I combined cellulose and hemicellulose hydrolysis, novel phosphorylation steps, the pentose phosphate pathway, and a soluble hydrogenase to demonstrate the enzymatic co-utilization of C6 and C5 biomass sugars. I then improved the productivity of this pathway dramatically through the use of a kinetic model of the system—experimentally observing a 3-fold rate increase, as predicted, based on adjusting of the ratio of the enzymes in the system.

During my time at NREL I have started applying a similar approach to a very different problem – biological lignin conversion. Once fully proven out, I anticipate model-driven pathway optimization will be widely useful for a number of metabolic engineering problems. Furthermore, this approach is highly complementary to alternative, lysate-based rapid prototyping cell-free efforts. While those approaches offer high throughput, empirical methods especially useful during discovery efforts, my approach allows rational optimization, dramatically accelerating the improvement of the rate, titer, and yield of the products of these novel pathways.

Future research objectives include the use of cell-free as a conversion platform, for the utilization of toxic substrates and/or production of value-added chemicals and fuels that can only be microbially produced at uneconomically low titers—again, a limitation that can often be mitigated through the use of purified enzymatic systems. Additional directions of interest include prototyping plant pathways, to accelerate agricultural engineering, and environmental applications, where complex, specific biochemical transformations could be catalyzed without the introduction of self-replicating entities. Due to my status as a veteran, I remain cognizant of defense synthetic biology needs as well, another role in which cell-free approaches have tremendous potential. In several of these directions I anticipate a number of continued collaborations with NREL researchers into the future.

My ultimate ambition is to help lead the translation of cell-free biotechnology into world-changing technologies. Recently, I had the privilege of serving in a role that I believe sets me up well to be such a pioneer in the field – as a Fellow at the Department of Energy’s Advanced Research Projects Agency (ARPA-E). This role provided an incredible opportunity to lead discussions with researchers at the top of their fields around out-of-the-box, high-impact energy technologies of the future, and to carefully consider the optimal role for biology and bioengineering within the field of renewable energy. I also reviewed hundreds of concept papers, interacted extensively with researchers through pre-proposal white papers, and came to understand well the responsibilities of working on the funding decision-making side of science. My efforts at ARPA-E also dramatically bolstered my network – these contacts that have become an integral part of my research ideation, planning, and execution.

Teaching Interests:

The elements of my teaching philosophy include encouraging participation and critical thinking and connecting the object of instruction with subjects about which the students are passionate. This inquiry-based learning style seeks to harness active student engagement in their educational experience. Related to this approach, I am excited to explore concepts such as research-integrated curricula as well. This approach is often used in design courses, but has significant potential in a chemical engineering laboratory or unit operations laboratory context as well. For example, exploring the concepts of reaction engineering, separations, and analytic approaches through the production of biodiesel or biogas from a waste stream, fermentative conversion of glucose into a potential nutraceutical, or pretreatment and hydrolysis of local agricultural residue. Non-standard chemical and biological engineering subjects I am interested in building courses around include metabolic engineering, enzyme engineering, cell-free systems, anaerobic digestion, process scale-up, and entrepreneurship.

I firmly believe that the example of my own passion for the subjects of biological and chemical engineering can be contagious – creatively presenting the material can make the classroom not only instructional, but inspirational. I was fortunate to witness such exemplary educational leadership multiple times at Virginia Tech. In addition to the exploration of novel research topics, these experiences included the integration of experiential learning (such as demonstrating methane release following agitation of the bottom of a pond), incorporation of specific industry-relevant examples (such as the use of polysaccharides as quick-clotting agents in modern bandages), and the use of cutting-edge web applications (for example, to assess the homology of proteins from different organisms). These experiences significantly informed my own career trajectory, research interests, and teaching philosophy, an effect I hope to replicate for my students.

At present, my teaching experience includes one semester as a teaching assistant for Virginia Tech’s Unit Operations Laboratory, presenting four guest lectures in the Unit Operations classroom portion of that course, and, this Fall, co-instructing the Cell Biology & Biochemistry course at the Colorado School of Mines. The most rewarding teaching I conducted while a graduate student, however, was the mentorship of two REU students during the summer before I defended my Ph.D. Both contributed significantly to the success of my project, and both became co-authors on the resultant publication. I look forward eagerly to building upon these experiences further in my next position.

A unique role I see for myself in the teaching sphere is in my example as a professor who is a veteran and by mentoring fellow veterans. Former members of the military are quite common members of the student population, thanks to support such as the GI Bill – but faculty who have been there themselves are exceptionally rare. Student veterans are incredibly valuable – their passion, dedication, attention to detail, and, very often, ability to set the example and lead their peers, is in my opinion an underutilized resource of human capital. I hope to be lucky enough to encourage some of these veterans to build upon these skills and, if so inclined, contribute to the diversity of the research and development enterprise.