National Science Foundation – Science & Technology Center ANNUAL REPORT Center for Cellular Construction Wallace Marshall, P.I. GENERAL INFORMATION 1a. Date submitted 06/26/18 Reporting period 10/01/17 – 9/30/18* progress reported as of 6/26/18 Name of the Center Center for Cellular Construction Name of the Center Director Wallace Marshall, Ph.D. Lead University University of California, San Francisco Contact information (no changes) Address Biochem. Dept, 600 16th St, GH N372F Phone Number 415 514-4304 Fax Number Email Address of Center Director [email protected] Center URL orhttp://[email protected] Participating Institutions: institutions, role, and name of contact person and other contact information, if changed since last reporting period. No changes in institutions, roles or contact people. Participating institutions San Francisco State University IBM Almaden Research Center Exploratorium Stanford University UC Berkeley 1b. Biographical information for new faculty members by institution. Attach as Appendix A. N/A 1c. Primary person to contact with any questions regarding this report Name of the Individual Debra Singer Center role Center Manager Address UCSF Biochemistry Dept. 600 16th St., Phone Number 415 244-9834 or 415 476-2829 Fax Number Email Address [email protected] National Science Foundation – Science & Technology Center Annual Report 10/1/17 – 9/30/18 Center for Cellular Construction Wallace Marshall, P.I. Table of Contents Pages I. GENERAL INFORMATION 1-2 I.2 Context Statement 4-14 II. RESEARCH 15-58 III. EDUCATION REPORT 59- 79 IV. KNOWLEDGE TRANSFER 80-86 V. EXTERNAL PARTNERSHIPS 87-89 VI. DIVERSITY 90-101 VII. MANAGEMENT 102-111 VIII. CENTER-WIDE OUTPUTS AND ISSUES 112-141 IX. INDIRECT / OTHER IMPACTS 142-143 X. BUDGET 144-163 Appendix Strategic Plan, Annotated with progress 3 NSF Award: DBI-1548297 PI: Wallace Marshall Annual Report for Project Dates: 10/01/17 - 9/30/18 Center for Cellular Construction I.2. Context Statement Overview of Vision and Goals The vision of our center is to develop an engineering discipline that will allow us to design and build cells and tissue with specific three-dimensional structures. These structures will serve as living factories and building blocks for better and more sustainable products, materials, and devices to benefit humankind. Our mission is to launch a new approach to understanding and designing cells. In pursuit of this mission, we will revolutionize industry through novel cell- based approaches to produce chemicals and materials for medical, civil, and consumer applications; we will educate and train a diverse research and manufacturing workforce, and we will engage and inspire the public to embrace the promise of engineering cells to produce the materials and factories of tomorrow. To pursue these goals we have developed plans for integrative research, education, broadening participation, and knowledge transfer, as outlined in our center strategic plan. During this second reporting period, as activities and programs for the Center accelerate, we continue to forge our center into a unified, efficiently integrated group capable of executing our strategic goals. To this end we have supplemented our administrative and management team to bring in needed expertise and staffing, and further built relationships with administrative and management teams from our partner organizations to streamline overall communications and strengthen partnerships. We have focused on encouraging and strengthening collaborations among students, postdocs and researchers across labs and institutions to drive the Center’s main research projects, and have worked out procedures for sharing key resources cross- institutionally, especially giving access to UCSF resources to faculty and students from SFSU, which has accelerated and augmented their research projects for the Center. The activities of our center, to be described below in more detail, have been developed in the form of cross-institutional collaborations. Indeed, we have deliberately designed our projects to be inherently collaborative in nature, thus taking advantage of the diversity of interests and knowledge in the center, allowing us to accomplish tasks that the participating groups could not accomplish individually. During the first two years, we have launched thirty nine new collaborations among the twenty one research and educational faculty at UCSF, SFSU, UC Berkeley, Stanford, IBM, and Exploratorium. This number is up from seventeen collaborations in year 1. All center faculty are involved in one or more collaborative projects. These collaborations have opened a path of communication between students and postdocs at the different participating institutions that we expect to lead to launching of new collaborative projects driven at the grassroots level. The diagram below illustrates the current active collaborations, with each arc indicating an active collaboration in which joint research (black) or educational (red) projects are being carried out by center personnel in both groups joined by the arc. 4 Figure I.1. Collaboration map showing research (black) and education/outreach (red) collaborations currently active in the center. Integrative Research In order to achieve our vision of engineering cells, we have organized our research activities around five Projects, three of which focus on enabling technologies for predictive specification of cell structure and interactions, and two of which focus on applications for cellular engineering. The first three projects (Project 1: Cellular Machine Shop; Project 2: CellCAD; and Project 3: Cellular Lego) are aimed at facilitating a design-build-test cycle for cells and cell collectives, using rational models as design tools. The final two projects (Project 4: Living Bioreactor and Project 5: Cell State Inference Engine) will pursue two broad classes of applications. Project 1 – Cellular Machine Shop: We seek to create an efficient set of approaches and tools for controlling shape and interactions within cells at the organelle scale. The fundamental tools are those of standard cell biology, but in order to achieve the level of reproducibility necessary for an engineering design-build-test cycle, we are re-imagining every step of the build process, from how we barcode strains to how we communicate experimental protocols. Because of the inherent variability of biological systems, we envision high-throughput screening as an integral part of the fabrication cycle, such that a given design will be implemented not with a single construct, but with a constellation of many different construct variants, all of which are then tested by direct imaging of cell structure. For this reason, we have been invested substantial 5 effort towards building robust computational tools for analyzing cellular structure, taking advantage of modern developments in deep learning and image analysis. Examples include new approaches for tracking chromosomes and spindles, locating the surface of organelles, and deconvolving line-scan images from high throughput imaging platforms. All of these individual algorithm development projects have stemmed from collaborations among center labs, especially at SFSU and IBM. Project 2 – CellCAD: Engineering is about building things, but so is tinkering, and part of what sets them apart is that engineering employs predictive models as design tools. To make cell biology into engineering, we seek to harness quantitative models of organelle and cell dynamics to build design software that will help guide decisions about genetic modifications, including gene knockouts and expression of interaction-driving constructs. The output will be a constellation of candidate molecular changes to be implemented using the tools of the Cellular Machine Shop. We envision two approaches: (1) A model-driven strategy in which we use coarse grained theoretical models for organelle dynamics to build design tools by applying control theory concepts to the organelle models, and (2) a data-driven strategy in which we use large datasets as the basis for empirical predictors built with machine learning methods. During year 2 we have focused the data-driven strategy by creating a linear vector-space formalism for describing cell state that allows us to ask fundamental questions about independent controllability and additivity of molecular perturbations. We find that perturbations affecting a given organelle typically affect other organelles as well, creating a significant problem for cellular design that can only be overcome with appropriate computational support, for which neural network-based strategies are now being developed. In parallel, we have found that when simple coarse-grained models for organelle size control are extended to the multiple-organelle case, the potential is high for undesirable outcomes, such as one organelle shrinks down to zero size while another organelle becomes larger than the whole cell. Again, this study argues that cellular design will require computational approaches to avoid such pathological cases. Both studies thus provide a concrete rationale for the need for CellCAD software going forward, something we had hypothesized in our proposal but that we can now demonstrate. Additional CellCAD software development includes completion of a graphical protocol CAD system for communicating experimental procedures in a new way, and Origami CAD tools in support of the Tissue Origami project. Project 3 – Cellular Lego: Plant and animal tissues bring different