475794 Increasing the Scale and Rate of Metabolic Engineering through Systems Synthetic Biology

Sunday, November 13, 2016
Continental 4 & 5 (Hilton San Francisco Union Square)
Nathan Crook, Pathology, Washington University in Saint Louis, Saint Louis, MO

Research Interests:

Biological systems are fantastic platforms for solving myriad world issues, as they contain a universe of highly specific catalysts, self-replicate, undergo evolution to improve function, and integrate information about their surroundings to adjust their behavior. As we strive for ever-increasing yields of green fuels and chemicals, and as we attempt to move our designs from the laboratory to the real world (e.g. the microbiome), critical gaps are arising between the theoretical behavior of engineered organisms and the ways in which they behave in reality. To fill these gaps, my graduate and postdoctoral work have benchmarked an approach to metabolic engineering which fuses emerging systems-level understanding of processes occurring at the whole-cell/community level with high-throughput, iterative design. In this poster, I will highlight several of my recent efforts which demonstrate the promise of a systems synthetic biology approach to more quickly merge engineering goals with biological reality.

My graduate research focused on expediting the development cycle of engineered yeast, which is a workhorse organism for the production of diverse chemicals, yet can be time-consuming and unpredictable to engineer. In particular, tuning the rate of enzyme synthesis, improving enzyme catalytic properties, and streamlining the genetic background of the yeast host are each critical to optimizing a bioprocess, yet poor quantitative models and slow genetic tools often made these design cycles “shots in the dark”. To improve enzyme synthesis, I quantified the rate-limiting potential of RNA secondary structure and nucleosome occupancy and in response developed computational techniques which exploit these phenomena to enable metabolic engineers to achieve desired enzyme levels in a single design cycle. In addition, because the design rules governing biocatalyst properties and host performance remain undiscovered, I further developed in vivo continuous evolution and RNA interference, respectively, for high-throughput optimization of these qualities in yeast, enabling such design rules to be inferred as the optimization proceeds. In each case, my innovative approaches expedited the design cycle by several orders of magnitude over the current state-of-the-art and provide a toolset for my future lab to use when exploring alternate behaviors, use locations, and genetic backgrounds of engineered microorganisms.

As one of my goals while an independent researcher, I aim to broaden the scope of metabolic engineering to include the microbial communities that live in the human gut, as this complex ecosystem plays critical roles in the extraction of nutrients, production of vitamins, and the progression of disease, yet whose engineering is currently regarded as a “grand challenge” in human health. The critical and growing importance of the gut microbiome was recently highlighted by the announcement of the National Microbiome Initiative this year. As this organ is, in its simplest sense, a packed bed reactor, chemical engineers are ideally poised to make significant contributions in this area. In my postdoctoral work, I am laying the foundation for engineering this system through the discovery of factors enabling specified residence time and gene expression levels in engineered probiotics using high-throughput experimental and computational approaches. Looking ahead, the techniques and design principles I have developed will enable my future lab to engineer “smart” probiotics which monitor the gut environment for signatures of disease and subsequently synthesize and deliver therapeutics in close proximity to affected areas. Additionally, integration with approaches developed during my graduate work will enable the construction of highly robust therapeutic strains which adjust their genetic content for improved function in response to changing environmental conditions. Third, these engineered strains will enable the elucidation and control of the three-dimensional structure of gut microbiota, enabling further insight and control over disease progression through modeling the currently unknown spatial reaction networks in the gut. It is clear through these examples that developing solutions for this and related microbial communities, as well as advancing microbial production of fuels and chemicals to the commercial scale, requires the use of high-throughput methods to both develop improved strains and also improve quantitative understanding of increasingly complex engineerable biological systems. My lab will be uniquely positioned at the forefront of the development and implementation of this systems synthetic biology approach to address pressing challenges in health, energy, and the environment.

Teaching Interests:

When I was a freshman in high school, a substitute teacher for geometry once asked the class if a student could introduce the material. To my astonishment, the class unanimously agreed that I should do it. It was an unforgettable experience to explain the surface areas and volumes of pyramids to my classmates at the same time I myself was learning the material – and I was pleasantly surprised to find that I enjoyed it. It was satisfying to see the eyes of my fellow students light up as difficult concepts came within their reach, and were then able to use that concept to solve problems. I reasoned that if it was this much fun to teach material “cold”, it would be even more rewarding to teach things I know a lot about - and I was right! During graduate school, I gained an enjoyment for the puzzle of designing effective homework and quiz problems. I especially enjoyed leading office hours where I was able to interact face-to-face with my students and match their individual learning style. I am eager to broaden my impact as a professor by improving the engagement of diverse groups of students with chemical engineering and thereby provide a foundation upon which a variety of careers can be built.

Introductory Courses

My prior experience and interests make me ideally suited to teach mass and energy balances, kinetics, and transport. I utilize several strategies for improving student learning over the “information fire hose” format of the traditional lecture. First, problem-based learning engages students and makes often abstract concepts easier to grasp, as I found when I encouraged students to play with silly putty in preparation for a lab involving non-newtonian fluids. Second, peer-teaching formats such as “Think-Pair-Share” have been shown to be effective at enhancing conceptual understanding over traditional formats. I implement these techniques during lecture or recitation by allowing students solve problems in small groups, and then reconvening to discuss the challenges they encountered. Third, through exit surveys in which students briefly describe what they learned after each lecture, I simultaneously facilitate student reflection (critical to improving future recall) and gauge my teaching effectiveness. Fourth, learning how to study is something that students often get no formal training in, and is especially critical during introductory courses in order successfully transition students from high school to college. I teach metacognition (i.e. learning how to learn) through in-class activities, for example, where students write down the point they are most confused about and then form small groups to address each other’s confusion. Finally, just as feedback is critical to the consistent performance of a chemical process, mid-semester course evaluations enable me to quickly adapt to the changing needs of my students by refining my teaching style, class format, and content. Through these efforts I provide a robust framework for my students to tackle any problems they face in their chosen field.

Advanced Courses

My expertise makes me well-suited for the development of a course on biochemical and metabolic engineering, including advanced enzyme kinetics, flux balance analysis, and the kinetics of cell growth. I can also develop a bioinformatics course for metabolic engineers which could be used either as a standalone class or as a module (e.g. in a computational methods or the metabolic engineering course mentioned above). This course would cover the principles and techniques of high-throughput sequencing analysis, RNA and protein structure prediction, and flux balance analysis. In these courses, I will use current literature to inspire discussion of underlying theories and techniques. Then, proposal writing will allow students to creatively combine what they have learned with the state-of-the-art in the field. Evaluation of these proposals will be facilitated through the formation of in-class review sections, allowing students to practice both project conception and critique. Taken together, I envision that these courses will provide guidance in areas which too often are left to be picked up on-the-fly after graduation.


My primary goals as an advisor are to develop in my mentees 1) a critical understanding of their field, 2) a framework to advance their field, and 3) the ability to effectively communicate their findings and goals with others. To do so, I will organize regular journal clubs to develop critical reading skills, teach new concepts, and serve as launch points for brainstorming sessions. I will provide my mentees with a model for effective lab management, including the keeping of electronic records (via a lab wiki) and centralized inventories. A wiki enables the creation of a core knowledge base, promoting efficient lab work and allowing new members to acclimate quickly. I will also strongly encourage mentorship of undergraduate researchers to increase focus on experimental design and develop teaching skills. In addition to authoring papers and presenting at conferences, teaching assistantships train clear communication and in this setting I will encourage my mentees to develop evaluation material and lead several lectures with my guidance. To combine experimental design and communication, my mentees will also be involved in grantwriting, which has the secondary benefit of providing familiarity with the various funding agencies and facilitating efficient acquisition of funding in the future. Throughout this process, roadblocks will naturally occur both in and out of the lab, and I view them as opportunities for discovering something new, scientifically and personally. I will re-evaluate shared goals with each mentee through yearly self-evaluations, and use individual development plans to achieve them. Through these efforts, I aim to guide mentees towards a career which is well-suited to their interests and expertise.

Commitment to Diversity and Inclusion

My research is framed by the principle that the most effective and novel solutions to problems arise by assembling a diverse collection of microbes and assessing each in an unbiased fashion. I embrace this principle in the classroom and lab by valuing diversity in those I teach, facilitating collaborations between individuals of different backgrounds, cultivating a growth mindset in my mentees, and rewarding alternative points of view during group discussions. I further aim to increase participation of underrepresented groups in my research through the creation of a day-long synthetic biology workshop connecting high school teachers in underprivileged areas to the concepts and techniques of engineering living systems, and providing digital materials for teaching these concepts their students. This workshop will be complemented by a program in which promising high school students which would not otherwise have the opportunity to do research are connected with a member of my lab to undertake a project over the summer. I aim to integrate these programs with existing outreach efforts to repair the leaky STEM pipeline and increase the diversity of perspectives available for solving the challenges of the future.

Extended Abstract: File Not Uploaded