Valorization and Utilization of Waste Conference: AIChE Annual MeetingYear: 2018Proceeding: 2018 AIChE Annual MeetingGroup: Sustainable Engineering ForumSession: Poster Session: Sustainability and Sustainable Biorefineries Time: Wednesday, October 31, 2018 - 3:30pm-5:00pm The ultimate goal of my research is to leverage synthetic biology to transform how we understand cellular transitions and engineer cellular therapies. I. Summary. Synthetic biology aims to harness the power of biological systems to perform tasks such as tumor surveillance, pathogen identification, and metabolite homeostasis. Native biological circuits (e.g. connected networks of genes) query data within the cell to coordinate cellular behaviors in space and time. Within mammalian systems, there exists an enormous opportunity to use synthetic circuitry to dynamically access information in the cell. As a chemical engineer working in molecular systems biology, my research focuses on integrating synthetic circuitry to interrogate and drive cellular behaviors. As a postdoc, I identified topological stress across the genome as a primary barrier to cellular reprogramming. This finding opens completely new questions for how the structure of the human genome stabilizes cellular identity and buffers cells against transitions to pathological states. Additionally, my findings explain why particular circuit designs fail and suggest principles for improving the performance of circuits integrated into the genome. I will establish a leading research program focused on designing and constructing integrated synthetic circuits to probe and actuate changes in DNA topology that drive changes in cell fate. II. Research Accomplishments. Spanning a range of model organisms from yeast to human cells, I have engineered systems for dynamic behaviors across multiple scales from the molecular design of noncoding RNA devices to optimization of large transcriptional networks. Graduate: Working with Dr. Christina Smolke at the California Institute of Technology, I constructed synthetic gene circuits and developed a class of genetic control systems called molecular network diverters. By interfacing these molecular network diverters with the native MAPK signaling pathway, I could temporally and spatially control cellular decision-making events (Galloway, K.E. et al. Science. 2013,). Beyond controlling cell fate, my work highlighted that integrated negative regulators can buffer a system against noise amplification mediated through positive-feedback loops by providing a resistance to amplification (Galloway, K.E. and Franco, E. Computational Methods in Synthetic Biology, 2015). By constructing synthetic circuitry, I will continue to illuminate paradigms in biological control and apply those principles to enhance cellular engineering. Postdoc: As a postdoc at USC in Dr. Justin Ichidas laboratory, my work has focused on elucidating and overcoming the reprogramming roadblocks to the robust generation of mature cell types. Accurately modeling neurological disorders with in vitro cellular models relies on reliable methods to generate the distinct neural subpopulations affected by the disease. When I began my project, the conversion process was extremely inefficient, requiring large-scale efforts to generate only a few hundred cells. Moreover, the central mechanistic rules for direct lineage conversion were undefined. Today, as a direct result of my work to improve the reprogramming process, I can robustly generate thousands of cells with signatures of enhanced maturity (Babos, K.N.*, Galloway, K.E.*, et al. Balancing hyperproliferation, transcription to drive cellular reprogramming. In Preparation.,). In addition to improving the reprogramming process, my work uncovers a previously unrecognized explanation for why only rare cells undergo transcription factor-mediated reprogramming successfully. I found that cellular reprogramming is limited to a small population of cells equipped to process the dual, competing demands of hyperproliferation and hypertranscription. High rates of transcription and replication accelerate the rate of DNA tangling (e.g. supercoiling). Only cells equipped with high expression of topoisomerases, enzymes that relax DNA supercoils, are capable of mediating the massive genomic and transcriptional realignment to convert from one state to another. My findings suggest that topological stress profoundly impacts the function of gene networks (e.g. native or synthetic circuits). By more precisely defining the impact of topological stress on gene circuits, I will elucidate principles for buffering (or alternatively, harnessing) topological stress to enhance the performance and capabilities of genome-integrated synthetic circuits. III. Research Interests: Prokaryotic systems and single-celled eukaryotic organisms have dominated the field of synthetic biology and revealed important paradigms in cellular biology including the role of feedback, noise, and cooperativity. While translation of synthetic biology to mammalian systems has been slower, with the advent of improved genetic tools for mammalian cells (e.g. gene therapy approaches including CRISPR technologies, AAVs), synthetic circuits are positioned to massively reshape how we study and treat diseases. Elucidating the principles of mammalian circuit design offers the opportunity to engineer cellular behaviors and to identify and target diseased states. Further, understanding the how cell types differentially process classes of circuits will improve our ability to predict the response of native transcriptional networks and design systems that are optimally wired for their function and context. Focus 1. Elucidating the systems-level principles of cell fate transitions. >Mapping transcriptional states: Characterizing the influence of hyperproliferation on the transcriptional trajectories between cell states. >Proliferation as a motif: Defining the molecular impact of proliferation on cellular transitions >Measuring transition speed: Characterizing the dynamics of proliferation-mediated transitions between cell states. Focus 2. Integrated gene circuit design >Elucidating principles of three-dimensional circuit design. >T.A.N.G.L.E.S. (Topologically-Affected Network of Genes Linking Expression to State) as probes. > Identifying robust designs for genome-integrated circuits: Mining the mammalian genome for structural designs. >Funding Continuous independent funding as postdoctoral fellow with acquisition of additional mini-grants NIH Ruth L. Kirschstein NRSA Postdoctoral Fellowship (Fall 2015 Fall 2018) California Institute of Regenerative Medicine Postdoctoral Fellowship (Fall 2013 Fall 2015) Doerr USC Stem Cell Challenge Award $10,000 project (2017) Fluidigm USC Single Cell Project Grant $9,000 in reagents and materials (June 2016) >Publications Galloway, K.E.*, Babos, K.*, and Ichida, J.I. Balancing hyperproliferation, transcription to drive cellular reprogramming. (In preparation). *These authors contributed equally to this work. Galloway, K.E., Babos, K., and Ichida, J.I. Enhancing in vitro disease models of ALS through precise motor neuron subtype engineering. (In preparation). Galloway, K.E*., Yu, H. *., Segil, N. I., and Ichida, J.I. Building a motor neuron enhancer map using ATM-ChIPseq. (In preparation). *These authors contributed equally to this work. Ichida,J.I. Staats, K., Davis-Dusenbery, B.N., Clement, K., Galloway, K.E., Babos, K.N. Son, E.Y., Kiskinis, E., Nicholas Atwater, N. , Gu ,H, Gnirke, A., Alexander Meissner, Kevin Eggan. Comparative genomic analysis of embryonic, lineage-converted, and stem cell-derived motor neurons. Development. (In resubmission). Galloway, K.E. and Ichida, J.I. Modeling neurodegenerative diseases and neurodevelopmental disorders with reprogrammed cells. Stem Cells, Tissue Engineering and Regenerative Medicine. D.A. Warburton, Ed. (World Scientific, New Jersey, 2015). Franco, E., and Galloway, K.E. Feedback loops in biological networks. Computational Methods in Synthetic Biology. M. A. Marchisio, Ed. (Springer New York, 2015), vol. 1244, pp. 193-214. Galloway K.E., Franco, E., and Smolke, C.D. Dynamically reshaping signaling networks to program cell fate via genetic controllers. Science. 2013. 341:1235005. Chen, Y.Y*, Galloway, K.E.*, and Smolke, C.D. Synthetic biology: advancing biological frontiers by building synthetic systems. Genome Biology. 2012. 13:240. * These authors contributed equally to this work. Kostal, J., Mulchandani, A., Gropp, K.E., and Chen, W. A. Temperature Responsive Biopolymer for Mercury Remediation. Environmental Science & Technology. 2003. 37, 4457-4462. Teaching Interests: My comprehensive Chemical Engineering education from UC Berkeley and the California Institute of Technology has equipped me to teach classes in the core Chemical Engineering curriculum (kinetics, transport, and thermodynamics) at both undergraduate and graduate levels. Im also very familiar with control theory and molecular and cellular biology. The problem-solving skills I acquired as a chemical engineer have set me up for success in elucidating the systems principles of biological systems. Thus, I am enthusiastic to teach chemical engineering principles to the next generation of students. Over my four years as a postdoc, I have directly mentored 15 students (5 grad, 8 undergrad, 2 high school) which has motivated me to develop strategies for training my students 1) to be effective in lab and 2) to develop their research and presentation skills. Teaching experience: In addition to serving as a teaching assistant for two classes at Caltech, I taught the freshman chemistry lab at Harvey Mudd College (HMC) in spring 2013. HMC is highly regarded for its focus on teaching and is currently ranked as the #2 engineering school without a doctorate program. Since all HMC students are obligated to take the freshman chemistry course, many students who were uncomfortable in a laboratory setting approached the class with dread. In order to capture my students interest, I began each class by engaging them with a bigger picture view of the purpose of the lab (e.g. why do we care about error propagation, synthesis yields, carbonate chemistry, etc.) as well as a general overview of what to expect. One student noted in the teaching reviews, I thought the way Prof. Galloway started each lab with a little PowerPoint overview (where she went over the prelab if it was confusing, and just generally went over the process (was good)). Helping my students understand the bigger picture of the material made the labs more meaningful and empowering. With this level of engagement, I could challenge the students to think deeper when troubleshooting their experiments and analyzing their results. Whenever a student asks a question, I try to refrain from giving direct answers, instead offering another question that leads them toward answering their initial question. Letting the students discover the answers for themselves helps them to build a better understanding and confidence in their deductive skills. Long-term, I want students to recognize that asking good questions is fundamental to science, whether in theory or in practice. One student reflected that I was always available to answer questions about lab procedure and write-up, and provides ample help without any hand-holding. Overall, my students were engaged and left with a positive view of chemistry. I received excellent evaluations with scores of either 6 or 7 (out of 7) in all categories as well as this gratifying comment: Prof Galloway is extremely supportive of her students and she clearly wants us all to succeed, not only in lab, but in our careers as scientists. Philosophy: While at Caltech, I completed the Caltech Project in Effective Teaching (CPET) certificate program, which introduces teaching pedagogy and practices through six seminars. From CPET, I learned that effective communication is the key to being an excellent teacher. I have become an extremely effective communicator as evidenced by the awards I have won for scientific communication, including the Everhart Lecture Award and First Place at the Annual USC Postdoctoral Symposium. In teaching, I have used techniques introduced to me through CPET training including the Socratic Method, inductive teaching, and story-telling. My goal is to help my students engage with concepts and approach a deeper understanding of scientific principles. In particular, I find that requiring students to draw out systems improves mechanistic understanding, develops intuition for the way processes work, and reduces experimental errors.