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 cells together to accomplish new tasks. Why limit ourselves to those tissues that currently exist? We are working to build a standardized set of molecular interactions that can be used to link different cell types, including from different species or kingdoms, into larger structures, taking advantage of the natural self- organizing properties of cells. Our work in year 2 has focused on two directions for building artificial cell collectives: (A) a “tissue origami” approach in which DNA-mediated cell adhesion is used to attach contractile cells to a sheet of extracellular matrix in a pre-defined pattern, and (B) tissue self-organization using synthetic cell-cell interactions including the use of microfluidic approaches to test regenerative capacity of such self-assembled structures.
Project 4 – Living Bioreactor: The Living Bioreactor project builds on the concept of the cell as a chemical factory, and seeks to improve the production of useful chemical products by re- engineering the physical structure of the cell, for example by changing the volume and surface area of organelles that encapsulate key modules of biochemical pathways of interest. During the year2 our work on this project has focused on two main directions: (A) extending our quantitative analysis of the relation between vacuole size and pH in budding yeast as a proof of 6 concept to demonstrate that organelle size variation can change biochemical function, and (B) development of the flagellar axomene as a scaffold for docking fusion proteins at defined stoichiometries and quantities in a stable, easily purified nanoarray, a project we are working on in partnership with Serotiny Inc (see Knowledge Transfer below). Most recently, with the recruitment of Dr. John Dueber (UCB) as a new Center Faculty Affiliate, we have launched an effort towards developing ways to engineer peroxisomes as chemical factories, to complement our existing effort on vacuoles.
Project 5 – Cell State Inference Engine/Cellular Sentinel: The internal structure of cells is highly sensitive to their external environment. We are building automated tools for inferring extracellular conditions from cell images, suitable for deploying in the field to analyze environmental toxins or pollutants, or equally to be deployed in an industrial setting to track conditions in fermentation processes. We have continued to develop deep-learning based computational methods to analyze shape and behavior of ciliates found in ponds and reservoirs, combined with cheap, portable microscopes to be used as a front end. In parallel, we have implemented image analysis pipelines for reconstructing cellular state spaces and inferring cell state based on analysis of organelle morphology and cell movements. Development of yeast as a cellular sentinel has progressed by building strain collections and image analysis tools to quantitatively map the relation between genetic state and organelle morphology, initially using the vacuole as a model system.
Education
Our educational goals are focused on the mission of driving a new field of engineering based on building cells and building with cells. To do this we need to create awareness, in academia and in the public, of the cell as something that can be engineered, and also to train a new generation of engineers comfortable with using the cell as an engineering medium. Our educational programs encompass four target audiences: undergraduate students, graduate students, high school teachers and their students, and the general public.
Undergraduate Our undergraduate educational program encompasses two aspects: developing new courses around center topics, and providing research experiences for undergraduate students in center labs.
Dr. Ray Esquerra (SFSU) has begun developing curriculum for a new undergraduate course, “Principles of Cellular Engineering”, which he will be launching this coming year and which will be co-taught by UCSF IRACDA postdoc Anum Glasgow. Dr. Esquerra, along with Dr. Tom Zimmerman from IBM, are also in the development phase of a new undergraduate course in microscopy and image analysis to be offered at SFSU. New courses in frugal science and science communication, both inspired by center activities, have been developed at Stanford and SFSU, respectively, and will launch this fall.
Our undergraduate research experience component involves both round-the-year undergraduates, particularly at SFSU, as well as undergraduates from around the country who participate in the summer research training programs at center institutions, for which center investigators are serving as mentors. Year-round undergraduates attend the center Quarterly Meetings, and have presented their work in oral presentations at these meetings. Undergraduate participation is 7 particularly emphasized at the Center Annual Retreat, where undergraduates present posters on their work alongside graduate students and postdocs. Overall, seventy five undergraduates have taken part in research experiences in Center labs thus far. Three of these undergraduates were authors on center publications this past year, and undergraduates presented twenty posters at local and national meetings.
Graduate At the graduate level, we are creating new curricula by taking advantage of the “mini course” format at UCSF, in which faculty can organize 2-3 week long intensive courses on subjects of their choice. In year 2, we ran a second iteration of the graduate minicourse on cellular robotics that we had first implemented in year 1, building on lessons learned from student feedback during year 1. This cellular robotics course, in turn, has provided a basis for development of the high school teacher-student Cellular Construction Workshop. We also launched a new minicourse called “computation by cells” which focused on hands-on experiments to explore the computational capacity of cells using Physarum as a model system, a choice that was based on successful use of Physarum in last summer’s High School workshop. Thus, interestingly, we have found that our graduate and high school educational programs have developed hand in hand. We plan to continue this synergistic development of graduate and high school educational curricula, as it provides another path for collaboration within the center by having graduate students from the minicourse take part in the summer course as guest speakers.
One area of emphasis that spans graduate education and knowledge transfer is our internship program, whereby the center leverages our contacts with industrial partners to create new opportunities for internships for our students, both as a way to catalyze the exchange of ideas but also with an education goal of teaching the students about career pathways outside of the traditional academic route. This year four graduate students (two from UCSF and two from SFSU) did internships at IBM, and one student did an internship at The Exploratorium. We are continuing to expand this program to include more students and an increased set of partner companies and institutions.
K-12 An important aspect of these overarching educational goals is that we believe cellular engineering provides a way to inject concepts of engineering into traditional biological curricula at all levels including K-12. A major component of our educational plan has been to develop high school curricula based on an engineering view of cells. Last summer, we developed a two week hands-on “Cellular Construction Workshop” course for high school science teachers and their students, in which LEGO mindstorms robotics was used to build robots to solve problems and challenges inspired by the challenges that living cells face. This course introduced students to the idea of a design-build-test cycle, as well as teaching programming. At the same time, students performed simple experiments in cell behavior, such as food-searching by Physarum, and hence students with pre-existing interest in engineering were exposed to the excitement of cell biology in a context that they could relate to. Our first summer bootcamp was a striking success, enrolling 14 students and 10 teachers from San Francisco Unified School District, Jefferson Union High School District and West Contra Costa Unified School District. Evaluation and tracking during the past year has shown that this course had a strong impact on the teachers who participated, and has changed the approach they are taking in their own classrooms. A second iteration of this course has started with a wider enrollment of teachers and students from not only SFUSD but also San Jose, Fremont, and Santa Rosa. Our emphasis will 8 continue to be on providing experience for teachers in using cellular engineering as a novel way to teach biology and engineering concepts together.
Public Education Launching a new field requires awareness that the field exists, and to this end we are working to popularize the concept of engineering cells. Our two main venues are Maker Faire events and exhibits at The Exploratorium.
Maker Faire is a series of events held around the country that bring together DIY hobbyists and people interested in electronics, crafts, and science. We feel that this is a sector of the general public who are already “primed” to think about the ideas we want to present. We have developed three hands-on demonstrations for Maker Faire, one based on studying cell behavior in response to mechanical stimulation, using an apparatus developed at UCSF, one based on looking at cells with a portable microscope developed by the team at IBM, and one based on LEGO robots that mimic cellular behaviors. This year we presented these demonstrations at the Rogue Valley Mini Maker Faire (Ashland, OR) and Maker Faire Bay Area 2018 (San Mateo, CA).
The other key part of our public outreach effort is the development of new exhibits and demonstrations at the Exploratorium, one of the world’s largest science museums with a long track record of hands-on science education. Center members at the Exploratorium are working to develop new presentations as part of the ongoing “Cells to Self” exhibit collection. In support of this development, the Exploratorium hosted a “CCC Faire” where center members presented demonstrations of their work to Exploratorium development staff as a way to brainstorm potential new exhibits or demonstrations.
Human Resources and Diversity
We believe that developing a new interdisciplinary field will require the maximum possible diversity of viewpoints and backgrounds. We are working to broaden participation and increase diversity primarily at three levels: graduate and postdoc training, mentorship, and strengthening research infrastructure resources for faculty training minority students. At the level of graduate and postdoctoral training, we are pooling our efforts to attract URM undergraduate students to join our graduate programs and, once in those programs, to encourage them to do their studies in center labs. To this end, center members Marshall (UCSF), Riggs (SFSU) and Bayliss (SFSU) attended the 2016 SACNAS meeting in Long Beach to spread the word about our center to URM undergraduates, especially those presenting posters on engineering disciplines who were interested in biology. Several center members presented outreach talks to URM student groups and undergraduate campuses last fall (2017). Center Director Marshall has joined the SFSU MARC advisory panel as well as the diversity panels for the UCSF Tetrad and IPQB graduate programs. In this way, he is now in a position to help shape diversity policies in these programs, with a view to increasing the number of URM students admitted. He has also become a member of the UCSF Basic Science Faculty Diversity Committee, which is working to increase prioritization of diversity goals in the overall faculty hiring culture. We believe that by working actively to increase awareness of our center, and UCSF overall, as an environment that values diversity (and in fact sees diversity as core to its mission), we take at least a first step towards increasing diversity at all levels from student to faculty recruitment.
9 We believe that mentoring is important for broadening participation. Two of our center faculty, Professors Blake Riggs and Carmen Domingo, have participated in NRMN training (National Research Mentoring Network). At our annual retreat in 2017, we held a two-hour interactive training session on mentoring diversity, prepared by Profs. Domingo and Riggs, mediated by Dr. Riggs, following principles of NRMN training. We are developing another interactive training session at our annual retreat scheduled for July 17-18, 2018.
Within our center’s four academic research institutions (UCSF, SFSU, Berkeley, and Stanford), SFSU has the most diverse faculty and students. SFSU has established a strong research track record and focus even though it has not, historically, received the same level of research infrastructure investment as the other research institutions in the center. Thus, a key element of our plan for broadening participation is to strengthen the research infrastructure at SFSU. We have negotiated access to all UCSF resources and core facilities for center members at SFSU. In this way, our center will strengthen the research capabilities at SFSU and in this way support the career success of those center faculty located there, while at the same time providing more access for SFSU students to the latest cutting edge technological resources available. The past year has witnessed an explosive growth in the number of publications from SFSU center labs, as well as in the number of diverse SFSU center students presenting work at national meetings. We believe these results confirm the effectiveness of our strategy.
We have found that diversity is lowest at the postdoctoral level, and we have spent the past year developing one approach to this problem. The UCSF IRACDA program is a postdoctoral training program that recruits and supports a diverse body of postdoctoral fellows who perform research at UCSF and teaching at SFSU. Our center has partnered with IRACDA to increase the number of host mentors at UCSF and to create a postdoctoral recruitment pipeline for applicants who apply to IRACDA but cannot be accommodated by the limited number of slots they have.
Knowledge Transfer
One key element of our knowledge transfer plan is disseminating information about the concept of cellular engineering to a wide audience. We began by setting up a temporary center website that has served two roles. First, it presents our face to the world and provides information about center members and activities. Second, through a secure sub-directory structure, the website is used to disseminate and collect internal information for the center members, to support annual reporting and coordination of activities. The site, available at http://ccc.ucsf.edu, is built on the Drupal platform to facilitate maintenance and cooperative editing of content. Our longer term goal is to produce a world-leading website for dissemination of scientific ideas from our center in a way that is accessible to the general public, while also providing user pathways that will allow scientific and industrial experts to delve deeper into the work of our center. We have contracted with Anotherwise Company, a web and graphic design firm based in San Francisco, to develop this site. Anotherwise has performed an extensive review of intended audiences, user flows, and desired outcomes, and has used this information to develop a comprehensive web design which is now being implemented with content. Additionally, we have contracted with Janet Iwasa (OneMicron Inc.) to develop custom computer animations for the site that will illustrate key concepts and ideas of the center as well as necessary scientific background in a visually accessible manner. The other side of our web dissemination strategy is harnessing social media. We have created a Twitter feed (@C3STC) which we are using to provide rapid updates on center activities. 10
The second key element of our knowledge transfer plan is industrial collaboration and partnership with existing companies. During this past year, we formalized a partnership with Serotiny, a San Francisco based startup that specializes in computational solutions for synthetic biology, the providing a key element of the CellCAD project. Serotiny maintains a database of molecular “parts” along with formal descriptions of interactions between these parts and algorithms to design multi-part constructs in a combinatorial manner. Our partnership gives us access to Serotiny’s computational tools, thus supporting our own CellCAD and Machine Shop projects, and low cost access to Serotiny’s gene synthesis contracting service, which has already supported development of molecular tools for the Living Bioreactor project. At the same time, the partnership also gives Serotiny access to our growing collection of molecular components and markers, helping them to grow their database while helping us to disseminate our results into the industrial sector.
We are also in the planning stages of a partnership with Zymergen, Inc., a genomics-based company located in the Bay Area with a focus on strain improvement technologies for industrial biotechnology. Based on these discussions, we have launched an initial experimental collaboration between the CCC and Zymergen, based on applying CCC concepts of cell structure and its link to cell function to collections of strains being engineered at Zymergen. This collaboration is providing a foot in the door to the world of industrial cell technology for the Center, will provide a novel way to evaluate cellular phenotypes for Zymergen, and creates the opportunity for center students to learn techniques of industrial microbiology that will inform our future work. So far two students from the Center have been trained in Aspergillus genetics by Zymergen experts as part of the collaboration. This past year we held a field trip for CCC graduate students from UCSF and SFSU to visit the Zymergen facility.
The third element of our knowledge transfer strategy is developing new IP and companies. So far we have filed 6 invention disclosures. We have held meetings with local industry and startup experts, as well as members of our External Advisory Committee with experience in founding startups, to determine how best to use our resources to catalyze the launching of new companies. Based on these discussions over the past year, we have settled on a strategy of using our limited funds to seed research into new ideas developed in center labs for possible industrial solutions that could eventually either serve as the basis for new startups or be licensed to exiting companies. We are currently putting in place a mechanism for soliciting and evaluating ideas for seed level support.
11 Management and Center Integration
It is challenging to put into place a management and leadership structure capable of supporting progress in all goal areas, and at the same time to integrate the six participating institutions into a cohesive unit working together on projects that no individual group could do separately. Managing collaborative programs and coordinating people requires developing relationships and assessing changing needs.
Changes to increase size of management team Our Center Manager, Debra Singer, in consultation with our Evaluator, Michelle Phillips, assessed needs cross-institutionally from Jan-April 2018. To address acceleration of programs and dynamically changing needs among partner organizations, we have readjusted our budget to increase administrative core staffing and bring in expertise in events coordination and executive assistance. Short bios for our administrative team with expertise in program management, financial planning and management, events and communications are included in the Management Section.
External Advisory Committee We have continued to consult and correspond with our nine-member External Advisory Committee for our center, consisting of experts in cell biology, engineering, education, and knowledge transfer, to provide external feedback on our activities. We have appointed Dr. Radhika Nagpal (Harvard University) as Chair of the EAC. We have developed a written EAC Charter, which has been distributed to all EAC members.
Our next formal EAC meeting will be held July 18, 2018, on the second day of our Annual Retreat. EAC minutes and reports can be furnished post submission of this annual report.
Coordination / Communications We continue to use two primary approaches to maintain coordination among the participating institutions of the center: center-wide quarterly meetings and electronic communications. This year we have also increased face-to-face meetings among sub-groups on various projects and are communicating via regular phone conferences with faculty. Project leads have initiated meetings at UCSF, Stanford, SFSU, the Exploratorium and IBM. After observing substantial overlap in membership and interests between the Living Bioreactor and Cell State Inference Engine projects, these two groups have merged their sub-group meetings together.
In 2018 so far we have held two center-wide meetings, both involving students, postdocs, faculty and staff from all six institutions of the center. Both meetings were widely and enthusiastically attended (~80-90 people). The meeting in January emphasized ethics and our keynote speaker was Professor Robert McGinn, of Stanford, one of our bioethics advisors. The focus of the April quarterly meeting held at UCSF was on research – all talks were given by students and postdocs in the Center including center undergraduates.
Our 2-day Annual Retreat in July will be held again at a conference center run by SFSU in Tiburon, CA. The first day will focus on research presentations by students and faculty. On the second day, center students are self-organizing a two hour session to share techniques and methods, an idea for catalyzing collaborations that was initiated by one of our center postdocs at Stanford. Afternoon sessions will focus on Responsible Innovation and on Mentoring Diversity. 12
Students requested funding to organize their own social event series, the first of which was held in April 2018; Zev Garner, co-PI, provided some discretionary funds and Debra Singer and Frank Bayliss helped initiate this event, with center student Will Chadwick (SFSU) taking the lead in organization. Further discretionary funds are available for another activity initiated by students in early summer, and Wendell Lim, co-PI, has supplementary support to cover a series of student/postdoc run CCC meetings in the next period.
For electronic coordination, we are continuing to develop a customized version of the IBM Lab Book software, a social media platform designed for sharing data and computations, linked to data servers hosted at UCSF but with equal access to all center participants. The software has been installed on UCSF servers and work now is focusing on negotiating data access policies with UCSF IT to determine how much access can be shared by this platform. In parallel we have begun exploring Center access to Redcap, UCSF’s standardized data and sample sharing platform. In parallel to these large-scale institutional level resources, we have also launched a center Slack channel that allows direct communications among center faculty, staff, postdocs, and students.
Response to Review and Evaluation We have made a number of changes this year in our center operations, influenced by internal assessment among our team, by perceptive suggestions from our External Advisors, from the Site Visit review panel who visited in November 2017, and from NSF program officials. In addition to those changes already noted above, the following changes were implemented.
One point that was repeatedly raised was the need for objective evaluation of overall programs in the NSF STCs. After reviewing the first reports of our contracted Evaluator, Michelle Phillips of Phillips and Associates, regarding Educational programs, we increased the scope of work for evaluation to encompass overall Center programs as well as the Education and Outreach activities. We have brought her in to attend all center-wide meetings (quarterly meeting, Annual Retreat, annual Site Visit, Evaluators meetings following the STC Directors meeting, and to consult and advise us throughout the year.
Another priority for year 2 has been focusing our plans for Knowledge Transfer and how to administer funds designated for Startups and Seed Funds. These were questions that we had left deliberately open when the center launched with the idea that as center activities crystallized, we would be in a better position to formulate policies for how best to foster development of real world impacts from the knowledge we generate. Based on a series of meetings and consultation with our external advisors with expertise in knowledge transfer, we have formulated plans for supporting seed collaborations/ partnerships with researchers and existing companies whose work precisely fills experimental goals in several of our research projects. In particular, our discussions led by our Entrepreneurship Coordinator, Charlie Craik with our advisors with entrepreneurship experience, Dan Widmaier (Bolt Threads) and Kinkead Reiling, have guided our concrete plans in the next year, described in Knowledge Transfer section. These discussions have led us to begin a partnership with a local startup company, Serotiny.
13 Reviewers at last year’s Site Visit suggested that the scope of the Center’s Ethics training be enlarged to comprise Responsible Innovation, as described by Owen et al., 2013, “Developing a Framework for Responsible Innovation” and elaborated in EU Horizon 2020 framework for responsible research and innovation. We are conducting research regarding responsible conduct of science, innovation and engineering technology, taking into account environmental, societal rights and risks, and unforeseen and unanticipated harms or impacts. We have reached out to experts in the US, including David Guston, PI and Director of the NSF funded Center for Nanotechnology in Society at ASU and founding editor-in-chief of the Journal of Responsible Innovation, and plan a series of talks at Center-wide events in the next year. We consulted our Ethics Panel with expertise in bioethics and the links between technology and society re: RI plans also and are planning a joint meeting with our EAC and Ethics panel this summer.
Brian von Herzon, a member of our EAC and founder of the Climate Foundation, will spend several days with us in July and be our keynote speaker on Responsible Innovation at our retreat.
14 II. RESEARCH
1a. Research goals and objectives Our research mission is to launch a new approach to understanding and designing cells through collaborative interdisciplinary approaches. Our vision for engineering cells revolves around developing tools and approaches to facilitate a design-build-test cycle characteristic of engineering, rather than the hypothesize-test-refine cycle that characterizes scientific research. To make this happen, we will require rational and predictive models to drive design, which makes the design engineering as opposed to tinkering, using software approaches to turn predictive models into design tools, and hitching these design tools to powerful high-throughput strain construction and validation methods based on image analysis. A key aspect of our engineering focus is our vision that real-world applications will drive all research activities. Hence, all of our research projects (see section II.2) are either related to enabling the design-build-test cycle, or else relate to engineering cells with specific application goals in mind. We have designed our research projects specifically to be interdisciplinary, requiring participation by multiple research faculty and groups, as a way to ensure that collaboration is “baked in” to the design of our projects from the very beginning.
1b. Research performance and management indicators During this past year, our primary management indicator has been to launch collaborative projects that are increasingly aligned with the primary research thrust areas, which we term “projects”.
1c. Research problems As with any large collaborative research group, the main challenge is aligning the effort of the individual researchers to focus on large-scale goals of the center. Direct engagement of center students and postdocs has helped to catalyze grassroots level collaborations and better understanding of center goals, with the result that research activities are showing a clearly improved alignment with center goals compared to the previous year.
2a. Research thrust areas 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. For all five projects or thrust areas, we are currently exploring a range of possible approaches, with the goal of consolidating work around areas that are most promising as the work progresses.
Our five projects/thrust areas are:
(1) Cellular Machine Shop (tools/instrumentation/infrastructure for measuring/building cell structures) (2) CellCad (modeling tools for designing cell structures) (3) Cell Legos (engineering multicellular structures) (4) Living Bioreactor (engineering organelles, cells or multicellular structures for making useful products) (5) Cell State Inference Engine / Cellular Sentinel (relating cell microenvironment and internal state to measurable cell structures)
15 2b. Research Progress The remainder of section II will describe our progress in each of the five main projects, organized in terms of sub-projects that are aligned with our Strategic Plan.
Project 1: Cellular Machine Shop (tools/instrumentation/infrastructure for measuring/building cell structures)
The Center for Cellular Construction aims to build a new engineering discipline around constructing living structures. The tools for this engineering discipline are not mature, and this project aims to build and integrate the toolbox necessary for the engineering of cell structure. In order to control cell structure, we need tools for manipulating cell structures in living cells. Therefore, Center researchers have been developing tools including mechanical perturbations (microneedles), optogenetic tools, nanoscale tools, and genetic constructs capable of altering aspects of cell structure in quantitative ways. Similarly, we will require genetic tools for measuring cell structures including fluorescent reporters that cleanly mark specific organelles or subcellular structures. Whether working with labeled or unlabeled cells, new instrumentation for measuring cell structure is needed. Such instrumentation typically involves different forms of microscopy, but additionally requires interfacing microscopy with methods of systematically delivering different manipulations (mechanical, chemical, genetic, etc.). We anticipate that we will generate large amounts of imaging data, and a major challenge is extracting quantitative information from these data. Therefore, we have heavily invested in algorithms for measuring cell structure. Similarly, the large amounts of imaging data and the resulting analysis require new infrastructure/methods for storing, sharing, and comparing data. Finally, once have a clear idea what the overall structure of our data will look like, and how to apply generalizable analytical methods across disparate data types, we will need new infrastructure/methods for automating, standardizing, and prototyping data acquisition, analysis, and storage. This project reports describes our recent efforts in these areas.
Subprojects
1a: New tools for manipulating cell structure 1b: Instrumentation for measuring cell structure 1c: Algorithms for measuring cell structure 1d: Infrastructure/methods for storing, sharing, comparing data 1e: Infrastructure/methods for automating, standardizing or prototyping
Subproject 1a: New tools for manipulating cell structure
(1) Optogenetic control of cell polarity and motility. We developed tools to direct cell polarity and movement with light via optogenetic activation of PI3K signaling in neutrophils. This enables us to control the direction of cell movement and could be relevant for organizing the location and interaction of cells. (2) Lab Personnel : Brian Graziano, Jason Town, Orion Weiner (3) accomplishments : Published this work in JCB. (4) Obstacles: Existing work has been based on manual control of light patterns for optogenetic experiments. Next goal is automated control of light based on automated imaging feedback. Jason has been making good progress on this front. 16 (5) Plans : Continue to develop infrastructure for automated analysis of cell shape and signaling for use in computer-controlled optogenetic experiments for significantly higher throughput and more sophisticated experiments. (6) Center collaborators: exploring a project with the Gartner lab related to Ras/SOS signaling. (7) External Collaborators: n/a (8) Publications: Graziano B., JCB, 2017.
(1) Optogenetic control or protein shuttling in and out of the nucleus. Many signaling pathways are activated when cytosolic factors move into the nucleus, and evidence some genes respond to the frequency with which these nuclear shuttling events occur. However, this idea has not been directly tested. We developed a new modular strategy for shuttling proteins in and out of the nucleus (Figure II.1.1). Our method combines LANS (Light-activated nuclear shuttling) AND LOVTRAP (light activated trapping of proteins and the mitochondria) to produce LANSTrap. To develop LANSTrap, we first developed optimized versions of LANS and LOVTRAP. We then combined these technologies to create a modular tool for driving protein translocation using light (See figure below). Thus far, LANSTrap has been characterized with three different transcription factors that could not be driven into the nucleus with previous optogenetic tools. We will soon be testing additional proteins, such as kinases, with LANSTrap. (2) Lab Personnel: Susan Chen, Lindsey Osimiri, Hana El Samad (3) Accomplishments: combined LANS and LOVTRAP into a single more functional system and validated the system in yeast. (4) Obstacles: Finding a combination of optogenetic tools which provide sufficient signal to background. (5) Plans: Export the technology to mammalian cells and to prepare a manuscript. (6) Center collaborators: none (7) External collaborators: none (8) Papers: in preparation
Figure II.1.1. LANSTrap, an optogenetic method to control protein shuttling in and out of the nucleus.
(1) Optogenetic control of T cell signaling. We developed an approach to control T cell activation using a light-activated ligand for a chimeric antigen receptor. We used this approach to demonstrate that T cells use the lifetime of ligand binding rather than the occupancy of the receptor to trigger
17 downstream responses. This is the first direct evidence of kinetic proofreading in T cell signaling in which the lifetime of ligand binding is the only variable being manipulated. (2) Lab Personnel: Doug Tischer, Derek Britain, Justin McLaurin, Orion Weiner (3) accomplishments: submitted paper (4) obstacles: It was a huge challenge setting this up (first optogenetic system didn’t work—had to switch to a new one), but the new system is working quite robustly now. (5) plans: This is a new use of optogenetics for us on several levels. First, we manipulate the timing (rather than the occupancy) of ligand binding to receptor. This will enable us to more broadly probe the role of single molecule binding/unbinding kinetics in controlling cell signaling, which is thought the be relevant in a wide range of signaling cascades. Second, we use an extracellular handle on a cell surface receptor for this variant of opto. Should be relevant to any receptor that requires its ligand presented on a surface—such as cell-to-cell or cell-to-surface adhesion, notch-delta, and others. (6) center collaborators: None yet, but it would be simple to adapt this to cell-cell interaction assays as would be relevant to the cellular legos project. If we can find the right joint person, I’d be very interested in moving in this direction. (7) external collaborators: Jay Groves (8) papers: Tischer and Weiner, under review.
(1) Glass microneedles for mechanically manipulating cell structure: We developed an approach to mechanically characterize cellular structures in live dividing cells. Our approach is based on glass microneedles that we micromanipulate to deform cellular structures, and we then measure how they respond in space and time. In particular, we have been focusing on the mammalian spindle and kinetochore. For the first time, we have been able to micromanipulate them and pull on them in vivo to directly probe their structural and biochemical response to force. This is a powerful system since there are many candidate proteins underlying these structures’ mechanical integrity and mechanotransduction, and molecular tools are available to perturb them. (2) Lab Personnel: Pooja Suresh, Alexandra Long, Sophie Dumont. (3) Accomplishments: Two posters were presented on this work at the Biophysical Society meeting in Feb 2018. (4) Obstacles: The main challenge has been that our needles are currently not force-calibrated. (5) Plans: We are now working to 1) characterize the spindle’s and kinetochore’s response to force in WT cells, 2)repeat these experiments in different molecular backgrounds to test specific hypotheses, and 3) calibrate microneedles to make absolute force measurements. (6) Center Collaborators: Manu Prakash’s lab is helping us to build simple spindle physical models. (7) External Collaborators: None. (8) Papers: None as yet.
Subproject 1b: New Algorithms for measuring cell structure
(1) Improving resolution using the InCell 6000 high-content imaging system: Since the InCell 6000 Imager was developed primarily for high-throughput scanning, it relies on lower resolution air objectives with lower numerical apertures that permit multi-well plate scanning ability. However, the lower resolution was particularly limiting for those imaging applications that require high-resolution interpretation of subcellular structures. To address this issue, we determined the point spread function for all three objectives in order to apply deconvolution algorithms to improve resolution. We also developed a maximum entropy based deconvolution that performs equally or even exceeds image restoration achieved by entropy-regularized deconvolution methods without requiring data-dependent 18 user-adjustable parameters. By applying our deconvolution algorithm, we now get equivalent resolution of organelle structures obtained using a high NA lens thus making the In Cell suitable for subcellular morphological studies (Figure II.1.2). (2) Lab Personnel: Daniel Elnatan, Jennifer Fung (3) Accomplishments: Manuscript in progress and will upload algorithm for public use (4) Obstacles: In Cell microscope was not aligned to handle the 60X lens. We recognized this problem when we were attempting to obtain point spread functions. We asked GE to realign the scope so the objective no longer hits the slide. (5) Plans: Daniel will be working on a depth dependent deconvolution algorithm. (6) Center Collaborators: Zev Gartner, Mark Chan (7) External Collaborators: none (8) Papers: in preparation
Figure II.1.2. Yeast vacuole visualized with improved deconvolution algorithm from data acquired on the InCell 6000 high throughput imaging platform.
(1) Algorithms for Yeast Cell Segmentation. Segment yeast cells imaged from a 96 well plate with the InCell microscope. Many cells are clumped together, making segmentation difficult. The method creates a grid with a resolution of the expected yeast cell over the entire image. Grid elements (called cams) that straddle the boundary of cell and background migrate to center the white pixels in the cam. (2) Personnel: Tom Zimmerman, Sujoy Biswas (3) Accomplishments: The present approach segments 1700 cells in a 2k x 2k image in one second running on an i7-6600U [email protected] GHz laptop (Lenovo X1) with 16GB memory (Figure II.1.3). (4) Challenges: We need a ground truth to quantify the performance of the algorithm. (5) Plans: Create a set of ground truth images of yeast cell centers and measure the performance of the algorithm. Improve the migration algorithm. (6) Center Collaborators: Mark Chan, Jennifer Fung (7) External Collaborators: none (8) Papers: none yet
Figure II.1.3. Automated segmentation of yeast cells.
(1) Rapid and quantitative crowd-sourced image analysis: We developed Quanti.us, a crowd-sourced image analysis tool that uses micropayments
19 through the Amazon Mechanical Turk interface to rapidly generate large numbers of high quality human annotations of a variety of imaging data types. We provide quantitative validation of the methods, analysis of best-practices, and a variety of pre- and post-processing tools to help the Turkers annotate data and the Quanti.us user to aggregate data and remove outliers. We show that groups of 3 or more Turkers can generate annotations equivalent in quality to that of an expert, and also show integration with machine learning pipelines. (2) Lab Personnel: Alex Hughes, Zev Gartner (3) Accomplishments: Completed project, paper accepted for publication at Nature Methods, and launched website. (4) Obstacles: The major obstacle we are facing is how to maintain quantius as a publically accessible research tool. We have been speaking to CZI, Janelia Farms, and IBM about hosting and maintaining the service. WE have also begun discussion with venture capitalists about possible turning Quanti.us into a for-profit enterprise if we can’t find non-profit support. (5) Plans: Continue to develop user pool by advertising the service and continuing trying to find an organization to host, maintain, and improve the service. (6) Center Collaborators: Simone Bianco, Sujoy Biswas (IBM) (7) External Collaborators: Arjun Raj, Lauren Beck (UPenn) (8) Papers: Hughes et al. Nature Methods (accepted) Quantius: Generic, high-fidelity human annotation of scientific images at 105 - clicks-per-hour Alex J. Hughes, Joseph D. Mornin , Sujoy K. Biswas , David P. Bauer , Simone Bianco , Zev J. Gartner
(1) Algorithms/tools for measuring cellular flows: We have developed Flow-Trace; an open source quantitative tool that enables visualization and characterization of flows generated by single cells. We present a simple, intuitive algorithm for visualizing time-varying flow fields that can reveal complex flow structures with minimal user intervention. We apply this technique to a variety of biological systems, including the swimming currents of invertebrates and the collective motion of swarms of insects. We compare our results with more experimentally difficult and mathematically sophisticated techniques for identifying patterns in fluid flows, and suggest that our tool represents an essential 'middle ground' allowing experimentalists to easily determine whether a system exhibits interesting flow patterns and coherent structures without resorting to more computationally intensive techniques. In addition to being informative, the visualizations generated by our tool are often striking and elegant, illustrating coherent structures directly from videos without the need for computational overlays (Figure II.1.4). Our tool is available as fully documented open-source code for MATLAB, Python or ImageJ at www.flowtrace.org. (2) Personnel: William Gilpin, Vivek Prakash, Manu Prakash (3) Accomplishments: Completed project, paper published in Journal of Experimental Biology (2017) (4) Challenges: We are now scaling up the library of flow patterns generated by single cells as signatures of various behavioral states of living cells. We would need to build a community based approach of mapping a large number of single cells (starting with ciliates) in this repository. (5) Plans: Using flows motile cells produce as a behavioral repertoire is powerful indicator of various metabolic states of a cell. We intend to expand the use of this tool such that anyone with an access to a microscope (such as Foldscope) can collect and deposit data in a common repository. We are currently building this repository website. (6) Center Collaborators: Sophie Dumont (7) External Collaborators: Chris Lowe, Stanford (8) Papers: William Gilpin et al. , Journal of Experimental Biology, 2017.
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Figure II.1.4. FlowTrace algorithm applied to Stentor, a single celled organism being used as a
freshwater cellular sentinel in Project 5 (see below).
(1) Quantitative analysis of the human pancreatic islet architecture. The pancreatic islet is a small tissue tasked with sensing systemic glucose levels and responding with the secretion of several hormones. The structure of this organ in the in vivo context is poorly defined, which makes engineering the structure challenging. We are attempting to image the structure of the major cell types and boundaries in this structure (endothelial cells, pericytes, nerves, beta cells, alpha cells, vascular basement membrane, peri-islet basement membrane) with the idea that this information will help us to build the structure from the bottom up. (2) Personnel: Olivia Creasey, Zev Gartner (3) Accomplishments: We have successfully stained and imaged all the relevant cell types in thick 3D tissues. We have initiated a collaboration with Jennifer Fung’s lab to aid in optimizing imaging, as well as with Loic Royer (CZ Biohub) to use machine learning algorithm to increase our z-resolution. Interesting observations include: abundant pericytes bridging a highly complex internal vasculature; complex vascular basement membrane around vasculature that includes endothelial and pericyte-based components; the observation that all alpha cells make at least one contact with the vascular or peri-islet basement membrane. (4) Challenges: Quantitative imaging is a real challenge. We've optimized our objectives, immersion medium, and mounting medium, as well measured the point spread function of our microscope. This seems to be helping. Identifying the right fixation and staining conditions took over a year but it now complete. (5) Plans: We are transitioning our efforts towards quantitative analysis (as opposed to imaging). We are using Imaris for most of this work. (6) Center Collaborators: Jennifer Fung, Daniel Elnatan (7) External Collaborators: Julie Sneddon (UCSF), Loic Royer (CZ Biohub), (8) Papers: not yet
(1) General algorithms for detecting, segmenting, and tracking cellular structures. The team at IBM is developing a suite of computational tools designed to broadly facilitate projects throughout the center. 21 (2) Personnel: Sujoy Biswas, Vito Pastore, Tom Zimmerman, Simone Bianco (3) Accomplishments: Detection: Our detection algorithm includes two approaches, one involving a deep learning based, end-to-end, structured learning approach (Hughes et. al, see reference below), and another involves learning in frequency domain (with the aid of filters) that is particularly suited for generalizing tasks when the labeled data is not abundant. We have shown the efficacy of the former in locating fluorescently labeled epithelial nuclei in the context of “noisy” annotations, namely, when the annotation are non-reliable, e.g. if they come from non-biological-experts, like Amazon Mechanical Turkers. We have shown the generalization capability of the proposed methodology in such cases. The second kind of detector development is still ongoing, and it aims at real time detection of swimming microorganisms, like Stentor, while identifying their pose/orientation, using a lensless Raspberry-Pi microscope. Since the detector is capable of generalizing from low amount of data, it can be trained and deployed on low end devices, like the Rasp-Pi chip. This is generally not possible with more complicated methods (e.g., deep learning). We have also designed an AI algorithm which is capable of detecting and tracking swimming organisms in real time (see project 5 for details). Segmentation: We have evaluated the segmentation performance of existing deep learning-based (DeepCell, Van Valen et al., 2016) algorithms on publicly available standard dataset. Deep learning requires abundant detailed annotations to succeed. To reduce the annotation burden, we have implemented an active learning framework where the annotator can engage the machine to complete the annotation task with partial supervision (see reference below). We have also started working on images from the InCell 6000 microscope. We are using semi-supervised segmentation algorithms, like discrete optimization techniques for graph partitioning, to obtain fast and reliable segmentation of high throughput high content images. IBM intern and UCSF grad student Jacob Kimmel has developed a novel deep learning architecture for time lapse low contrast image data. The architecture, named CellSegNet, affords a 300x decrease in processing time. Tracking: We are developing specific tracking algorithms to use in partnership with the lensless microscope we invented, with the aim of building a state of the art environmental monitor. Some of the advances made address known problems common to trackers in critical situations (e.g., reliable, long term traffic of crowd/pedestrians/traffic). The algorithms are designed to handle realistic difficult scenarios, like overlap of organisms in heavy clutter, occlusions, and sudden temporary disappearance of objects. As a test scenario, we are using our methodology to track stentors, which change shape and behavior frequently during their movement. We then plan to extend our methodology to track other organisms. Since a part of the tracking involves a robust detection step – to consider various changes in shape and appearance – we are using the filter-based detection methodology mentioned earlier for this purpose. Such filter based detector not only ensures real time performance but also allows online-learning to adapt to the changing shape and appearance. (4) Challenges: none so far (5) Plans: By the end of the year, we plan to provide other members of the center with the algorithms to test on their data (e.g. Sindy Tang’s, Jennifer Fung’s, Mark Chan’s and Wallace Marshall’s labs). (6) Center Collaborators: Alex Hughes, Zev Gartner (Gartner’s lab), Mark Chan, Will Chadwick (Chan’s lab), Jacob Kimmel (Marshall’s lab). (7) External collaborators: Arjun Raj, Lauren Beck (UPenn) (8) papers: A paper has been published with the Gartner group (see below). Another paper is under review. Two additional papers are in draft form. The tracking algorithms have been completed but not yet published. Quantius: Generic, high-fidelity human annotation of scientific images at 105 - clicks-per-hour Alex J. Hughes, Joseph D. Mornin , Sujoy K. Biswas , David P. Bauer , Simone Bianco , Zev J. Gartner, Nature Methods, upcoming. Reducing the annotation burden for cell segmentation, Aritra Chowdhury, Sujoy Biswas, Simone Bianco MICCAI, under review.
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(1) Plankton detection, classification and tracking for environmental modeling with deep learning. Plankton are extremely sensitive to environmental perturbation and can be used as biosensor to assess the health of a water ecosystem. This is an important goal for project 5, but will require instrumentation deployable in remote environments, and powerful analytics to extract information for samples acquired at remote sites. The lensless microscope developed by the IBM group allows to acquire stereo videos of swimming plankton, and derive the 3D location of each plankton. Modification of morphology and behavior is expected following an external stimulus. We have developed an Artificial Intelligence system capable of recognizing plankton species, and detect and classify deviations from standard shapes and behaviors within the species. We have implemented two different approaches based on Convolutional Neural Network (CNN). The first approach uses raw images from videos, and performs with validation accuracy higher than 0.95. It is, however, not computationally efficient for a real-time application, since it requires a lot of computational resources and time for both training and testing. The second approach consists of two fully connected layers, which are trained on 25 pre-selected morphological features from images as input. This method does not use images for training. We tested the developed network on 5 classes, computing the Receiver Operating Characteristics (ROC) Curve. The correspondent extracted average Area Under Curve is equal to 0.91, proving very good classification performances (AUC = 0.5 corresponds to random guess, AUC = 1 corresponds to perfect classification). We have also implemented a plankton classifier using a nearest neighbor approach (KNN). Using 12 features and 900 examples of each class, we achieved an accuracy of 97% in the classification of 5 plankton species. (2) Personnel: Vito Paolo Pastore, Sujoy Biswas, Simone Bianco, Tom Zimmerman (3) Accomplishments: This system was designed in the last year. (4) Challenges: The most critical part of the classification project has been to decide and select the features to analyze, as well as to build a high-quality dataset for training. Our deep learning algorithm has shown to be capable to overcome the problem of morphological similarity between different species. (5) Plans: We aim at both developing and deploying the algorithm together with the microscope on a real life environmental sensing problem. We are planning to adopt an unsupervised approach in order to generalize our result and make the system more robust to the presence of organisms not in the database. An unsupervised approach should be the base of a continuous water quality monitoring system, being able to identify new species, besides deviation in behavior and morphology of the known ones. We plan to add a behavioral component to the network, to improve the performance of the classification in case of morphologically similar species. We imagine the final system to be composed of high efficiency, low complexity algorithms to run a series of raspberry-Pi based lensless microscopes, creating an IoE (Internet of the Environment), or using a Neural chip, like the Intel Movidius Stick, to a device specifically programmed to implement neural networks). (6) Internal collaborators: N/A (7) External collaborators: N/A (8) Papers: N/A
23 (1) Microscopic Tomography. The invention produces a three-dimensional point cloud of a microscopic subject from a series of images collected from a monocular microscope fitted with a single digital camera. The invention is based on the Radon Transform and rotates the subject between a light source (visible light) and detector (microscopic camera). The power of this approach is that many free-living single celled organisms naturally rotate when they swim, allowing us to perform tomographic reconstructions without the need to physically rotate the sample. (2) Personnel: Tom Zimmerman, Simone Bianco (3) Accomplishments: Proof-of-Concept demonstration. By fluorescent labeling the DNA of in living Stentor coeruleus cells, we are able to create a 3D point cloud of the Stentor's macronucleus from a video (2D image sequence) of Stentor swimming in a constrained microfluidic chamber (Figure II.1.5). Patent search conducted. (4) Challenges: No obstacles (5) Plans: File patent. Optimize automatic detection of first and last image in sequence of images. Speed up the algorithm. Create a microfluidic vortex to create a 3D image of plankton that does not naturally rotate like a Stentor does (e.g. dead preserved specimens). (6) Center Collaborators: Wallace Marshall, Rebecca McGillivary (UCSF) (7) External Collaborators: N/A (8) Papers: No, a patent must be filed first.
Figure II.1.5. Three dimensional reconstruction of Stentor macronucleus from natural rotation in living cells via microscopic tomography algorithm
(1) Analytical tools for quantifying and defining chromosome segregation in different cell types: To construct cells of different sizes and shapes, cells must modulate the forces that move chromosomes. We are applying computational tools to analyze experimental data from 3 distinct cell types in C. elegans – large mitotic cells, large meiotic oocytes, and small meiotic sperm cells. Each uses a different combination of forces to achieve chromosome segregation. We are making mathematical and computation models of chromosome segregation to explain the distinct balance of forces generated in each cell type. We are also modeling the ways chromosomes move relative to one another to biorient between meiotic divisions. (2) Lab Personnel: James Gerh, Nick Munoz, Diana Chu (3) Accomplishments: James Gerh gave a talk at the Cytoskeleton Club at UCSF in June 2018. (4) Obstacles: Our challenges include finding students who have expertise in both physics, computer science, and biology to work on this project. I’m actively recruiting students from the Physics department at SFSU currently. (5) Plans: We are continuing to develop the model of chromosome segregation force-balance generation and aim to publish that this year. We are also working on methods to analyze chromosome 24 movements to define stages of biorientation that will be used for publication. We expect to publish a manuscript in collaboration with another lab in Germany on sperm chromosome segregation this year. (6) Center Collaborators: Simone Bianco, Barbara Jones, Elsa Rousseau, Tom Zimmerman (IBM) (7) External Collaborators: Moumita Das (RIT) (8) Papers: Two micropublications (a new format that encouraged rapid publication of research findings): Munoz, NR; Black, CJ; Young, ET; Chu, DS. (2017): New alleles of C. elegans gene cls-2 (R107.6), called xc3, xc4, and xc5. Micropublication: biology. Dataset. https://doi.org/10.17912/W2RQ2X; Munoz, NR; Byrd, DT; Chu, D (2018): New allele of C. elegans gene spch-3 (T27A3.4), called xc2. Micropublication: biology. Dataset.https://doi.org/10.17912/W2995W
(1) Algorithms for Measuring Filopodia: We have been collaborating with Simone Bianco and Sujoy Biswas to develop an algorithm that will allow us to quantitate the number, length, and distribution of filopodia. Images have been provided to the IBM team and are currently being annotated. (2) Lab Personnel: Lisa Galli, Fred Santana, Edward Elizarraras, Laura Burrus (3) Accomplishments: None yet. (4) Obstacles: None yet. (5) Plans: Continue to work with IBM team to develop computational methods of quantitating filopodia. (6) Center Collaborators: Simone Bianco, Sujoy Biswas (IBM) (7) External Collaborators: none (8) Papers: Direct visualization of the Wntless-induced redistribution of WNT1 in developing chick embryos. Galli LM, Santana F, Apollon C, Szabo LA, Ngo K, Burrus LW. Dev Biol. 2018 Apr 30. pii: S0012-1606(18)30086-1. doi: 10.1016/j.ydbio.2018.04.025. [Epub ahead of print] PMID: 29715461
Subproject 1c: Instrumentation for measuring cell structure (also applicable to Project 5 Cell State Inference Engine/Cellular Sentinel)
(1) Drop Microscope. An instrument was designed and built to automatically load and mix multiple liquid samples containing plankton, water, nutrient and chemicals using a rotating disk as a slide and one or more digital optical microscopes (Figure 11.1.6). The instrument was created to test the response of cells to chemicals, to use them as chemical sensors. (2) Personnel: Tom Zimmerman (3) Accomplishments: built the instrument and tested it on cells and chemical treatments. (4) Challenges: The liquid dispensing method was not precise enough and could not deliver a liquid < 50 uL due to the drop forming mechanism. (5) Plans: Replace the liquid dispensing method with a custom designed and built syringe pump. Enable the syringe tip to tip into the liquid drop on the disk to allow an arbitrary amount of liquid (e.g. < 50 uL) to be deposited into the drop. Use instrument to establish baseline of Stentor behavior and deviation of behavior in response to Figure II.1.6. Drop microscope. Fluid droplet administering chemicals. depositor shown on left, imaging microscope on right. Rotating platform allows multiple droplets to (6) Center Collaborators: Jacob Kimmel (UCSF, be repeatedly imaged. IBM intern) 25 (7) External Collaborators: none (8) Papers: none yet
(1) 3D Microscope Using Front Surface Mirror. This invention converts a conventional mono optical microscope into a stereo microscope by replacing the glass slide with a front surface mirror, illuminated from above. The invention relies on the principle that when an object is viewed above a front surface mirror and off axis (not directly below the microscope lens), two images are observed; the directly viewed image of the top of the specimen and a reflected image of the bottom of the specimen. The instrument was invented while working on the Drop Microscope, and provides a way to monitor the swimming of plankton in 3D using a conventional 2D (mono) microscope. (2) Personnel: Tom Zimmerman (IBM) (3) Accomplishments: Proof-of-Concept demonstration. Patent search conducted. (4) Challenges: No obstacles (5) Plans: Review prior art and if invention distinguished over prior art, file a patent. Incorporate into the Drop Microscope. Write software to convert the image into 3D trajectory. (6) Center Collaborators: none (7) External Collaborators: none (8) Papers: none yet
Subproject 1d: Infrastructure/methods for storing, sharing, comparing data
(1) Scalable tools for evaluating large scale video microscopy data: We have developed a scalable, web-based application to annotate large scale video data for evaluation purpose. The annotations share a common format, so storing and sharing of the annotation among the collaborators is very efficient. We are developing a method to make this platform available to multiple users working on the same dataset, to make the system distributive in nature. (2) Personnel: Sujoy Biswas, Simone Bianco (3) Accomplishments: We have successfully deployed the system locally. (4) Challenges: No obstacles (5) Plans: We plan to deploy the system and make it available to center members for shared annotation. (6) Center Collaborators: Amanda Paulson (Gartner lab, IBM intern) (7) External Collaborators: none (8) Papers: none yet
26 Subproject 1e: Infrastructure/methods for automating, standardizing or prototyping
(1) Synthetic cell assembly by acoustic jetting: We are developing a new instrument based on focused acoustics that is capable of creating dynamic cell-like compartments, offering an experimental platform for answering a broad range of fundamental biological questions about cell organization and cell-cell assembly. By incorporating transmembrane proteins into the bilayers and encapsulating complex mixtures of proteins, DNA, and other biomolecules inside the vesicle, the instrument will enable the study the mechanisms of cell-cell junction formation. (2) Personnel: Max Armstrong, Dan Fletcher (3) Accomplishments: We developed a proof-of-concept acoustic jetting system and demonstrated that it is capable of forming giant unilamellar vesicles with control of internal contents and membrane composition. We focused on chamber and transducer design, as well as modeling to better understand the acoustic streaming force that is responsible for vesicle formation. (4) Obstacles: One challenge with our prototype design was the destabilization of membrane bilayers during device calibration, which limited the success of acoustic jetting. We have addressed this issue by separating the transducer from the chamber to isolate the membrane. (5) Plans: To probe the limits of the acoustic jetting technique to form small vesicles with extract, our work in the next year involves building high frequency devices to lower the diffraction limit. For example, we plan on incorporating thin polycrystalline ceramic piezos in the device or by changing to a polymeric or single crystal piezo. Current and new devices will also be actuated under varying operating conditions (pulse time, acceleration, viscosity, position relative to bilayer). (6) Center Collaborators: None (7) external collaboration: None (8) Papers: Paper in preparation
27 Project 2: CellCad (modeling tools for designing cell structures)
This project aims to create tools that will allow us to implement a computational “design” platform for engineering cellular and multicellular structures across length scales. The center vision of developing cells as an engineering medium requires methodologies for predictively specifying organelles with a user-defined molecular-scale architecture, cells with a user-defined organelle scale architecture, and tissues from a user defined cellular scale architecture. Given the complexity and dynamic nature of the living cell, we expect this goal to be challenging and to require computational methods that can predict which changes at one scale of this structural hierarchy (e.g. the molecular scale) one should make to achieve a desired organizational state at another scale of the structural hierarchy (e.g. the cellular scale). From the inception of the center we have envisioned two overall strategies, one based on coarse grained models of size and morphology, and the other based on empirical data analysis using large collections of image data combined with machine learning tools to identify regions of parameter space that have a high likelihood of producing an organelle/cell/tissue of a desired organization. CAD tools will be developed at multiple scales, to design structures of organelles, cells, and artificial tissues.
Subprojects
2a: Assemble coarse-grained models for predicting the size and morphology of living structures 2b: Mine empirical data to identify perturbations/conditions that drive specific morphologies 2c: Build user interfaces for Cell Engineering
Subproject 2a: Assemble coarse-grained models for predicting the size and morphology of living structures
(1) Coarse grained flux analysis framework for integrating models of multiple organelles: Another aspect of CellCAD that requires investigation is to what extent can we alter or tune organelle size or shape parameters without adversely affecting the viability of the cell. Another way to put this is whether or not cells are so robust that we can change anything we want, or is it necessary to take care to avoid dangerous regimes in parameter space. For example, if we arbitrarily change the rate constants governing organelle dynamics, can we inadvertently cause the cell to lose one organelle entirely, or alternatively might some other organelle expand so much that it bursts the cell. (2) Lab Personnel: Nat Hendel, Greyson Lewis, Wallace Marshall (3) Accomplishments: As a first proof of concept, we have explored a rudimentary mathematical model for organelle dynamics in which each organelle is described by a pair of state variables defining its surface area and volume. Exchange of material between organelles occurs via vesicle budding, with a given organelle forming spherical vesicles of constant radius at a rate proportional to the surface area of the organelle. These organelles then move to the target organelle and fuse to it. Using these simple assumptions yields a set of differential equations that can be solved for a steady state solution. Interestingly, even with this very simple model, it is easy to find combinations of parameters that yield the complete loss of an organelle over time. This result already shows the need for predictive tools to choose parameters carefully when re-engineering organelle dynamics. (4) Obstacles: The current model is highly abstract and ignores the possible existence of feedback controls as well as the possibility of organelle volume changing by water flowing across the membrane. (5) Plans: Current work is aiming at making the model more realistic, while also adding analytical tools to better understand the behavior of the model from the viewpoint of multivariate control theory.
28 In particular we hope to implement a barrier certificate framework to delineate safe from dangerous regions of parameter space. (6) Center Collaborators: none right now but will start working with Hana El-Samad as we get to the stage of implementing more advanced methods from control system theory such as stochastic barrier certificates. (7) External Collaborators - none (8) Publication – none so far
(1) Models for hydrodynamic cellular communication: We have recently discovered a new mode of “hydrodynamic” communication amongst single cells – in the species Spirostomum. Being one of the largest single cell ciliate – Spirostomum generates ultra-fast contractions that generate hydraulic waves in the medium which produce flows that can be characterized at medium Reynolds number flows with inertial components – still being a single cell. Using experimental and mathematical models, we further show that Spirostomum can not only generate ultra fast contractions leading to hydrodynamic packets of information propagating from the cell, but also read these packets and subsequently contract – leading to a contraction “soliton” that propagates in a population. Using mathematical models, we show that an extended shape of a cell enables this sensitive measurement. We further built a high- throughput single cell shearing apparatus using a hele-shaw geometry that can be used for a large number of organisms to collect quantitative data. (2) Personnel: Arnold Mathijessen, Manu Prakash (3) Accomplishments: First paper under preparation, to be submitted. (4) Challenges: We will further develop the role of mechanosensitive ion channels in the sensitivity in readout of hydrodynamic strain. (5) Plans: Once the baseline algorithm for predator-prey interactions and search space are established – we will build on this work to find molecular mechanisms underlying these algorithms. Live cytoskeletal labels and genetic perturbations are being developed enabling us to understand the mechanism behind search algorithms single cells apply to find its prey. (6) Center Collaborators: None (7) External Collaborators: None (8) Papers: None
(1) Build models of anaphase chromosome segregation in different cell types: Chromosome segregation is accomplished by all eukaryotic organisms largely with highly conserved fundamental components - chromosomes, microtubules, and motors - that generate forces that push, pull, and stabilize chromosome movement. However, different organisms and cell types balance the forces generated by these players in various ways to achieve cells of distinct size, shape, and function. Thus, it is often difficult to apply knowledge gained from one system about these molecular players to another. Our study focuses on three cell division events in the same organism, C. elegans: mitosis, oocyte meiosis, and sperm meiosis. Our goal is to construct a simple modular model of chromosome segregation in C. elegans that can be applied not only to other cell types in C. elegans, but also different cell types in other organisms. C. elegans is ideal to construct this model because of the wealth of experimental in vivo imaging and genetic mutant analysis available that help to define the physical properties of molecular components and forces that drive chromosome segregation. Using these data, we derive mathematical models that recapitulate chromosome movement in computer simulations. We are applying these models to then chromosome movement to define the balance of pulling, pushing, and stabilizing forces that separate chromosomes in different contexts - mitosis, oocyte meiosis, and sperm meiosis.
29 (2) Lab Personnel: (SFSU): James Gerh, Nick Munoz, Diana Chu; (IBM): Barbara Jones, Elsa Rousseau, Simone Bianco (3) Accomplishments: We have the computer simulations working that recapitulate the chromosome movement as well as that of all the other organelles in the spindle for mitosis. We implemented a model in which the connections between organelles in the spindle is via very stiff springs, which, together with the motors (which we have also implemented), govern the dynamics (Figure II.2.1). We have compared our results to experimental results from the Chu lab, and the match is very good with realistic parameters (see figure). James Gerh will give a talk at the Cytoskeleton Club at UCSF in June 2018. (4) Obstacles: Our challenges include finding students who have expertise in both physics, computer science, and biology to work on this project. Diana Chu is actively recruiting students from the Physics department at SFSU. From a modeling perspective, working with coupled springs can be challenging, in that they can develop highly nonlinear behavior, including sudden dashes of the organelles into the cell wall and into each other. We have to have realistic values for the springs and motors, based on physical and biological principles, and yet we also have to tune the dynamics as well. At this point we believe we have a well-behaved, realistic model. (5) Plans: We are continuing to develop the model of chromosome segregation force-balance generation and aim to publish that this year. We are also working on methods to analyze chromosome movements to define stages of bi-orientation that will be used for publication. We expect to publish a manuscript in collaboration with another lab in Germany on sperm chromosome segregation this year. (6) Center Collaborators: : (SFSU): James Gerh, Nick Munoz, Diana Chu; (IBM): Barbara Jones, Elsa Rousseau, Simone Bianco (7) External Collaborators: Moumita Das (RIT) (8) Papers: Two micropublications (a new format that encouraged rapid publication of research findings): Munoz, NR; Black, CJ; Young, ET; Chu, DS. (2017): New alleles of C. elegans gene cls-2 (R107.6), called xc3, xc4, and xc5. Micropublication: biology. Dataset. https://doi.org/10.17912/W2RQ2X; Munoz, NR; Byrd, DT; Chu, D (2018): New allele of C. elegans gene spch-3 (T27A3.4), called xc2. Micropublication: biology. Dataset.https://doi.org/10.17912/W2995W
Figure II.2.1. Diagram of the spring-motor model for chromosome segregation at initial and later time point. The model simulates the evolution in time of the positions of different objects involved in chromosome segregation (chromosomes, kinetochore, centrosome, astral motor), and linked by microtubules represented by springs. 30
(1) Coarse grained model of viral evolution dynamics. We implemented a numerical study of dynamics in a model for a virus entering a cell, encountering immune response by the cell, and then, with some probability, reproducing and mutating, and then going on to infect the next cell. Some years ago we found this model shows a phase transition in steady state, between two regimes of cell infection. (2) Lab Personnel: Barbara Jones, Simone Bianco (3) Accomplishments: Now with dynamics implemented, we have many results. In our numerical model, we can model a human-scale number of cells: 18,000 or more. We find that evidence of the phase transition as a function of temperature and cell immune strength shows up in all stages of the dynamics. At the critical temperature and immune strength, we see metastable states and other evidence for “glassy dynamics” such as quake events of rapid convergence after long time. Many cell- virus behaviors fall into two strategies. For example, whether the cell infection rate tracks the viral load or is anti-correlated varies according to where on the phase diagram the system is; viral growth rate shows a division of strategies, as does how the system reaches steady state, whether through an increase or a decrease of energy. We are writing a paper. (4) Challenges: The numerical implementation took much development, especially as unexpectedly some metastable states took 100,000 iterations to reach steady state. (5) Plans: We have at least two papers planned. After the first one which will be written soon, we have plans to study the dynamics of the phase transition by introducing realistic noise into the system. (6) Center Collaborators: This work is done in extensive collaborations with Greyson Lewis and Wallace Marshall at UCSF. (7) External Collaborators: No external collaboration (8) Papers: Paper in draft form at this point.
(1) Use models of autonomously folding tissues to design tissue having novel architectures: Many tissues fold due to a mismatch of strain between two tightly conjoined tissue layers. Strains arise due to differences in cell proliferation and/or contractility between layers. In the mouse gut, existing evidence suggest that contractility in a population of cells immediately below the epithelium is tightly coupled to tissue folding, and we reasoned that this phenomenon was amenable to reconstitution in vitro, modeling, and engineering. Therefore, we parameterized a finite element model of tissue folding using quantitative measurements relating tissue strain and tissue geometry (Figure II.2.2). Our measurements demonstrated that contractile cell density along each axis of a tissue is linearly related to the degree of curvature along each axis of a tissue. We were therefore able to model the trajectory of tissue folding, and use it to prototype a variety of unusual tissue folds (Figure II.2.3). (2) Lab Personnel: Hikaru Miyazaki, Jesse Zheng, Max Coyle, Alex Hughes, Zev Gartner (3) Accomplishments: We published a manuscript based on this work in January. (4) Obstacles: Our biggest challenge for this project was understanding the physical processes acting at the level of single cells that allowed for the robust folding of tissues. We found that cells had to (1) generate large strains in gels (as opposed to large forces) and (2) strain the gel at a rate significantly faster than they moved through Figure II.2.2. CAD system for tissue origami using finite the gel. element modeling and empirically determined mechanical parameters.
31 (5) Plans: We have taken this work in vivo, in an effort to demonstrate that the lessons learned in our engineering efforts shed light on how tissue develop normally. The hope is that we can gain a better understanding the molecular underpinning of the processes we described, so as to further our engineering efforts. (6) Center Collaborators: Matt Laurie (7) External Collaborators: Zuzuna Vavrusova, Daniel Chu, Ophir Klein and Rich Schneider (8) Papers: Hughes et al, Dev Cell (2018)
Figure II.2.3. Novel tissue organization designed using OrigamiCAD (right) and validated experimentally (left).
(1) Computational enumeration of tissue branching patterns: Most natural organs have an underlying branching morphology, and controlled branching of self-organized cell collectives is one of the ultimate goals of the Cellular Lego project. We are thus developing computational tools to understand branching morphogenesis, in particular to predict (and therefore design) how final 3D patterning results from local branching directions. These algorithms will form the basis of a CAD system to facilitate design of branching artificial tissues. (2) Lab Personnel: Wallace Marshall (3) Accomplishments: We have developed a formalism known as Branching Tissue Specification Language (BTSL) which can be used to specify any branching pattern. Using this scheme, we have implemented an enumeration program that can generate all possible branching patterns in the specific case of orthogonal bifurcation (Figure II.2.4). We have used this software to compare the actual branching pattern seen in the kidney with the complete set of possible branching patterns, and found that a large number of alternative branching patterns could give a similar 3D distribution of branch- endpoints to that seen in actual kidneys. (4) Obstacles: The big surprise came when a postdoc in collaborator Keith Mostov’s lab found that after the initial orthogonal branching in early development, kidney branches undergo a large angle change, and when we applied this angle change to the computationally generated branching patterns, it completely changed the predictions of the model, and gave the result, reported above, that a wide range of branching patterns give similar final distributions of endpoints. This is an interesting example of how a simple mechanism (decrease of angle between branches) can give rise to a vast expansion of the range of parameter space that results in a successful design.
32 (5) Plans: We are now working in two directions, one to expand the enumeration framework to include other types of branching patterns, such as that seen in the lung, and the second, .to convert the prediction tool into a design tool, with the expectation that eventually it will be possible to specify branching orientation at the cellular level, and we hope to have a design program fully operation by that time. (6) Center Collaborators: Wendell Lim (7) External collaborators: Wei Yu, Keith Mostov (UCSF) (8) Publications: A manuscript is currently in preparation.
Figure II.2.4. Enumerating branching patterns in silico. Figure shows output from branch rendering software that converts a binary number into a sequence of parallel/orthogonal choices in branching directions, with the direction chosen relative to the grandparent branch. Every binary number determines a unique branching pattern, allowing all possible branching patterns to be enumerated simply by stepping through all numbers with a certain total number of bits. Results are then evaluated in terms of various figures of merit such as avoidance of steric clash and distribution of branch termini in 3D.
Subproject 2b: Mine empirical data to identify perturbations/conditions that drive specific morphologies
(1) Building a linear vector space representation of organelle-level cell state: Our main source of empirical data will be systematic genetic and chemical screens using high content imaging. Because organelles interact both biochemically and physically, we expect that even highly specific modifications of one organelle’s biosynthetic pathway will indirectly affect other organelles, creating a challenging problem for multivariate control of cell organization. The simplest framework to think about non-independently controllable organelles is a vector space representation in which the basis vectors represent either single organelle parameters or groups of organelle parameters that co-vary. Such a framework would ultimately provide a strategy to predict, using vector addition, the combined effects of multiple perturbations. (2) Lab Personnel: Amy Chang, Greyson Lewis, Jacob Kimmel, Wallace Marshall
33 (3) Accomplishments: In order to build an organelle-scale cellular state space, we analyzed over 900 genetically identical mouse embryonic fibroblasts using over 200 cell morphological features, describing cell shape, cytoskeletal organization, nuclear geometry, and mitochondrial geometry (Figure II.2.5). Principal components analysis was then used to determine combinations of geometric parameters that co-vary among the population of cells. These principal components define a continuous state space such that the location in space represent a particular organization of a cell. When we inspected the feature loading of the individual principal components, we find that none of them is constructed solely from features describing one part of the cell. Our key finding is that every principal component contains substantial contributions from at least two of the major feature classes (cell shape, cytoskeletal organization, nuclear geometry, and mitochondrial geometry), suggesting that individual organelles do not vary independently of each other. (4) Obstacles: The cell type used, MEFs , is not necessarily directly useful in real world applications for which we envision wanting to use CellCAD as a design tool. (5) Plan: We are working to extend this analysis of feature co-variation to more application-relevant cells (yeast) , which also has the benefit of being able to achieve a wider set of defined perturbations, and use a better set of shape descriptors for the mitochondrion such as persistent homology barcodes. (6) Center Collaborators: none (7) External Collaborators: none (8) Publications: Chang AY, Marshall WF. 2018. Dynamics of living cells in a cytomorphological state space. Submitted
Figure II.2.5. Vector space framework for organelle-scale representation and
prediction of cell state. Principal components analysis of organelle geometry in a clonally identical population of wild-type mouse embryonic fibroblasts, based on 205 cell geometrical features describing cell shape, cytoskeletal organization, nuclear geometry, and mitochondrial geometry extracted from 2D fluorescence images (top panel). The loadings of these first three principal components (bottom panel) all show mixtures of more than one cellular feature, indicating that different organelles show coupled variation.
34 (1) Testing co-inheritance of organelles during asymmetric cell division: One specific mechanistic source of coupling between organelles is physical interactions during inheritance when cells divide. This would cause a given cell to inherit co-varying quantities of more than one organelle, preventing their quantities from being independently controlled. We are quantifying organelle co-inheritance taking advantage of the fact that endoplasmic reticulum is asymmetrically distributed at specific stages in the Drosophila embryo. (2) Personnel: Alia Edington, Blake Riggs (3) Accomplishments. During this past year we have begun investigating the localization of early and recycling endosomes, and mitochondria with respect to the ER during cell division at gastrulation in the early Drosophila embryo. We have generated transgenic Drosophila embryos expressing YFP- Rab5 (early endosome), YFP-Rab11 (recycling endosome), and MitoTracker-red (mitochondria), and are now in a position to investigate and quantify co-inheritance. (4) Obstacles: Constructing a Drosophila line with multiple markers is time consuming, but we have now completed the stage of line construction and are ready to proceed to the proposed measurements. (5) Plans: We will image the multi-reporter transgenic embryos using real-time confocal microscopy during mitosis with respect to markers labeling the ER. Images will be quantitatively measured for colocalization throughout the cell cycle. Understanding interconnections between organelles will allow for more accurate measurements for creations of computer platforms involving cell organization. (6) Center Collaborators: Wallace Marshall (UCSF) (7) External Collaborators: none (8) Publications: none so far
(1) Testing independent addressability of organelle geometry: A number of compounds are known that directly act on individual organelles through known targets. When we apply such compounds, is it really true that only one organelle is affected? We have imaged MEF cells treated with a series of such compounds, and asked whether treatment with compounds targeting one organelle show any effect on any other organelles. (2) Lab personnel: Amy Chang, Ulises Diaz, Wallace Marshall (3) Accomplishments: Our initial experiments have focused on mdivi-1, a small molecule inhibitor of mitochondrial fission that targets mitochondrial dynamic (Cassidy-Stone et al., 2008; Lackner and Nunnari, 2010). We applied this compound to wild-type MEF cells and analyzed the same 205 cell morphology features discussed in our intrinsic co-variation sub-project above. We find (Figure II.2.6) that even though the compound is specific for mitochondrial dynamics, substantial alterations occur in other cellular features such as the nucleus and cytoskeleton. This result directly confirms our hypothesis that cell design faces an independent control problem, and that one cannot simply combine two perturbations identified in studies of individual organelles (either in chemical screens or genetic screens) and hope that their combined effect will be what one naively expects. We conclude that individual organelles are not independently addressable, and that instead we must be approaching the problem of cell design with the expectation that any perturbation will alter combinations of organelles. This result strongly points to the need for predictive software tools (CellCAD) to determine how different perturbations should be combined to yield a desired and predictable outcome. (4) Obstacles: our main limitations so far have been the reliance on small molecule inhibitors, which always raise the specter of off-target chemical effects, and the use of an industrially non-relevant cell type. (5) Plans: We are therefore expanding the analysis to include budding yeast where we can combine genetic mutations instead of chemical perturbations. This has the advantage that a given genetic perturbation only affects a given gene, thus eliminating the potential alternative interpretations due to off target drug effects. 35 (6) Center collaCborators: Jennifer Fung, Mark Chan (7) External Collaborators: none (8) Publications: none so far.
Figure II.2.6. Testing individual addressability of organelles. Organelle specific small molecule mDIVI-1 affects other cell features besides its specific chemical target. Plot shows the ratio of average feature values (Y axis) plotted for a series of image features describing cell shape and cytoskeletal organization, nuclear geometry, and mitochondrial geometry. The key result is that even though mitochondria are the only chemical target, all cellular geometry features are affected.
(1) Testing for additivity of molecular perturbations: Even if individual organelles cannot be independently perturbed, a linear state space framework still provides a simple strategy to design perturbations based on empirical data: if we want to get to a particular point in cell morphological state space, we could combine two perturbations such that the vector sum of their two effects adds up to the desired change in cell morphology. This would represent a simple form of CellCAD based on empirical data. Is this simple strategy sufficient, or will we need to develop more advanced methodologies? As a proof of concept we asked how to molecular perturbations combine within the framework of a linear state space. (2) Lab Personnel: Vito Paolo Pastore, Simone Bianco (3) Accomplishments: We applied two significant genetic perturbations to MEF cells: expression of KRAS and overexpression of Myc. Both genes are known to drive multiple changes in cell behavior. We obtained cells expressing Myc alone, Ras alone, and Myc+Ras in combination. Using image data collected in the Marshall group and analyzed using feature extraction tools developed by the Marshall and Chan groups, and analyzed using dimensionality reduction tools by the Bianco group, we have obtained clear evidence that the combined effect of Myc and Ras is NOT simply the sum of the individual effects of the two perturbations (Figure II.2.7). This indicates a substantial problem for independent control. The Bianco group has built on these results to develop a neural network based computational strategy that allows prediction of the combined effect from the two individual effects. (4) Obstacles: our main limitations has been the fact that Myc and Ras are global perturbations that affect many aspects of cell biology. 36 (5) Plans: As with the other elements of the linear state space control sub-goal, we are shifting to use budding yeast as the model system, since this gives us access to a much wider range of highly specific genetic perturbations. This analysis of non-additivity will serve as the basis for ongoing software development to explore nonlinear approaches to linking perturbations with states. (6) Center collaborators: Mark Chan, Wallace Marshall (7) External collaborators: Davide Ruggero (UCSF) (8) Publications: none so far.
Figure II.2.7. Non-additivity of molecular perturbations in cell morphology space. Top panel: Histograms of the distribution of mitochondrial numbers per cell. Double expression of Ras and Myc has a decreased average number and tighter distribution than either single perturbation alone. Bottom panel: state space based on cell perimeter, mitochondrial area, and mitochondrion number, again showing that cells expressing Ras and Myc do not show a state that is a simple sum of the individual state displacements.
37 Subproject 2c: Build user interfaces for Cellular Engineering
(1) Software for collective and real-world computer aided design: We are collaborating with a research team led by Bret Victor, who is pioneering a new computing platform, Realtalk, that allows code or data to be associated with any object in the room. A network of webcams, projectors, and servers in the ceiling operate seamlessly to track objects, execute object code, and display text, graphics, audio, or video. We are upgrading the Douglas Lab at UCSF with Realtalk and begin to re- envision wet-lab research augmented by this system. With Realtalk, any container, tool, or instrument will be able to display information about itself, anywhere in the laboratory or office space. In the future, a researcher might place two tubes next to each other to see a simulation of what would happen if the contents were mixed. Tubes placed near instruments will display how the sample would be analyzed or transformed. Realtalk-augmented protocols will provide rich step-by-step feedback across multiple length scales. We expect the system will lower barriers to communication, collaboration, and training to greatly accelerate discovery in biological research. (2) Lab Personnel: Tural Aksel, Shawn Douglas (3) Accomplishments: We have installed an instance of Realtalk in our office (GH S472C), and have begun working with Dynamicland to import existing Python code into the system. (4) Obstacles: The major obstacles to the project are simply lack of bandwidth while we finish and publish other ongoing projects in the lab. Later in fall 2018 and spring 2019, we expect to make substantially faster progress with more dedicated effort. (5) Plans: We would like to set up Realtalk in a wet lab environment, ideally the 2nd-floor teaching lab in Genentech Hall, and begin to host hackathons and training sessions with the system. (6) Center Collaborators: Wallace Marshall (+ Athena Lin, Nat Hendel, Rebecca McGillivary) (7) External Collaborators: Bret Victor and his team at Dynamicland, Oakland CA (8) Papers: None yet.
(1) CAD tools for designing and building multidomain proteins: We have partnered with Serotiny, a company founded from members of Center labs (Gartner lab), that aims to use big-data approaches to facilitate the design and synthesis of multidomain proteins. (2) Personnel: Justin Farlow (Serotiny) (3) Accomplishments: We announced to center members that we will be working with Serotiny, and center members (El-Samad, Gartner, Fung, Marshall and others) have placed or will soon place orders with Serotiny for libraries of DNA constructs for testing. (4) Obstacles: working out partnership/IP agreements with UCSF has been challenging. (5) Plans: We have offered center labs $20,000 from our core funds towards purchases of DNA constructs. We hope to catalyze the design-build-test cycle with these funds within the center. (6) Center collaborators: all center members (7) External collaborators: none (8) Papers: none so far
(1) CAD tool for designing experimental protocols: As part of our goal to develop a Computer Aided Design approach for cell biology, we have been analyzing the workflow of a typical cell biologist to identify common tasks that could be automated, and one that came to early attention is the preparation of experimental protocols. A challenge for all researchers, but particular in a large collaborative center, is how to share operational knowledge of experimental protocols. This challenge has contributed to the reproducibility crisis and is clearly an impediment to the progress of research. The
38 solution we have developed is a new software tool called Protocol Planner, which allows experimental protocols to be depicted in a simple graphic format. (Figure II.2.8) (2) Lab Personnel: Tural Aksel, Pablo Damasceno, Shawn Douglas (3) Accomplishments: we have completed initial development of the Protocol Planner software tool and have begun testing it in a series of collaborations. (4) Obstacles: none. (5) Plans: During the next year, we plan to launch a beta version of the Protocol Planner, and continue developing our CAD development platform. (6) Center collaborators: none (7) External collaborators: none (8) Publications: none so far
Figure II.2.8. Protocol Planner. Example graphical protocol representing agarose gel electrophoresis procedure, implemented using Protocol Planner software.
39 Project 3: Cellular Lego (engineering multicellular structures)
A major goal of the Center is to provide strategies for linking living structure across scales. A key scale for engineering is the cell-to-tissue scale. Thus, this project aims to enable the engineering of multicellular structures from simpler cellular building blocks. All living systems build themselves through programs of self-organization. This process begins efficiently from a variety but limited set of initial conditions, then uses cell-cell communication and physical process to guide the temporal evolution of the system to a narrow set of endpoints. To engineer this process, we aim to develop means of controlling the physical constraints of tissue growth, for example, by using cell patterning or printing techniques to establish initial conditions. We also aim to control tissue shape by self- organization – both natural and designed. We also hope to elucidate and then design control over cell number and size during tissue self-organization. Finally, to enable entirely synthetic methods of regulating complex and multistep program of self-organization, we are engineering cell-cell communication modules. Together, these subprojects set the stage for the engineering of multicellular living structures.
Subprojects:
3a: methods for controlling physical constraints of tissue growth 3b: controlling tissue shape by self organization 3c: controlling cell number and size in tissues by self-organization 3d: engineering cell-cell communication
Subproject 3a/3b: controlling physical constraints and controlling tissue shape by self-organization (1) Probing the impact of oncogene expression on the self-organization of the human mammary epithelium. We previously demonstrated that the mammary epithelium has a hard-wired and robust program of self-organization. We found that very few molecular or physical perturbations are capable of breaking this program. However, modeling studies suggested that one of the cell types in the tissue (luminal epithelial cells) was uniquely susceptible to perturbation that increased it cell-ECM adhesion. Because a breakdown in tissue structure/self-organization is necessary for cancer progression, we have hypothesized that a subset of breast cancer oncogenes must act by driving an increase in luminal epithelia cell-ECM adhesion. (2) Personnel: Jennifer Hu, Vasudha Srivastava, James Garbe, Zev Gartner (3) Accomplishments: We have screened GFP (control), Kras, CyclinD1, Akt, p53(-), p16(-), and PI3K for their ability to disrupt tissue architecture, alter gene expression, and change the physical properties of the luminal epithelial cells. Although all molecular perturbations change gene expression and cell physical properties, only PI3K (and preliminarily p16(-)) alter the physical properties of the luminal epithelial cells in a manner that alters tissue architecture. (4) Challenges: The pipeline for generating pure populations of primary human luminal epithelial cells with the desired genetic perturbations is time consuming and challenging. However, we have a solid set of methods in place and we are now moving through our experiments quickly. (5) Plans: We are expanding the set of genes that we are analyzing in our assays and generating large numbers of transcriptional profiles for these cells (single cell and bulk) to understand how these molecular perturbations reprogram the molecular and physical properties of the cells. (6) Internal collaborators: none (7) external collaborators: Mark LaBarge (City of Hope), Andrei Goga (UCSF), Sue Celnicker (LBNL) 40 (8) papers: none yet
(1) Synthetic developmental programs: We have developed synthetic developmental programs that can be used to generate self-organizing multicellular tissues. We link synthetic cell-cell communication, via synNotch receptors, to the regulated expression of adhesion (cadherin) molecules, that drive cell association or segregation. Using circuits of this type, we can flexibly program a diverse set of multicellular structures that mimic key properties of developing tissues: autonomous formation of complex multi compartment structures, increases in cell types (differentiation), formation of asymmetric structure, and the ability to self-repair when damaged (Figure II.3.1). This work shows how minimal networks that link cell communication and morphology can drive self-organization and lays the groundwork for programmed assembly of customized tissues. (2) Personnel: Satoshi Toda, Leonardo Morsut, Wendell Lim (3) Accomplishments: Paper under review (4) Obstacles: n/a (5) Plans: n/a (6) Center collaborators Sindy Tang and Lucas Blauch (Stanford) (7) External Collaborators: Leonardo Morsut (8) papers: Satoshi Toda, Lucas R. Blauch, Sindy K.Y. Tang, Leonardo Morsut, Wendell A. Lim, “Synthetic morphologies: Programming self-organizing multi-cellular structures using engineered cell- cell signaling cascades”, Science (in press).
Figure II.3.1. Self-organization of multi-layer cell assemblies using SynNotch system. Top panel shows how cell adhesion and communication allows self-assembly of a multi layer system in which cells can enter three different states depending on position in the aggregate. Bottom panel shows the ability of these multi-layer structures to regenerate their normal organization following mechanical wounding, thus recapitulating an essential aspect of living tissues.
(1) A role for mitotic spindle rotation for cell placement during development. During development, generation of cellular diversity and establishment of tissues giving rise to the adult body plan is accomplished through an asymmetric partitioning of cell fate determinants during cell division. This unequal inheritance of determinants has been shown to be important for cell fate selection, however the underlying mechanism surrounding these asymmetric divisions are poorly understood. Specifically, 41 there is little known about the initial steps involving how cells divide and are positioned during development to form into complex structures and tissues. In order to investigate the early steps in cell fate selection, we focus on the start of gastrulation in the early Drosophila melanogaster embryo. After fertilization, the Drosophila embryo goes through 13 rounds of syncytial development (without a conventional cell division) and at the 14th interphase, the embryo forms ~6000 cells simultaneously and begins gastrulation. It is the corresponding 14th mitosis at gastrulation that the embryo begins formation of the adult body plan, with dramatic cellular rotations and rearrangements leading to the formation of complex cellular structures. Preliminary data from the Riggs lab describes a novel planar mitotic spindle rotation at mitosis 14 prior to cell fate selection and tissue formation. Our working hypothesis is that these spindle rotation events are necessary for proper establishment of the division plane and cellular placement for cell fate selection and establishment of cellular architecture. (2) Personnel: Cecilia Brown, Jessica Bolivar-McPeek, Blake Riggs (3) Accomplishments: Creation of an photo-convertible Endoplasmic Reticulum (ER) Drosophila line for labeling a cell to track its location and lineage (4) Obstacles: Photo-conversion of the ER proved not to be a reliable marker for tracking cell fate, as the photo-conversion does not last due to membrane fluidity. In addition, our Zeiss 710 confocal microscope, which has the laser capacity for photo-conversion, does not have the speed in the Z-plane to follow cell division due to the dramatic movements during gastrulation in the early embryo. (5) Plans: We have since been provided with a photo-convertible histone Drosophila line for cell fate tracking purposes (Michael Wente, University of Rochester). We will use this line to photo-convert the nucleus of cells that display rotation events and follow the lineage of cell movement after establishment of the division plane during the 14th mitosis. We will accomplish this by use of the Zeiss 880 point scanning confocal microscope (with Airyscan), housed at the Gladstone Institute. This will allow for a baseline measurement of cell positioning after rotation during mitosis, in which we can investigate cell to cell signaling pathways, including Notch / Delta, for involvement in early cell positioning events. (6) Center Collaborators: We have started initial collaboration with Simone Bianco, IBM for this project. Simone will assist us in creating algorithms towards tracking cell movement and changes in cell shape and division. Cecilia Brown will be participating in a summer internship at IBM with Simone Bianco for quantitative analysis of our real-time microscope data. (7) External Collaborators: None (8) Papers: del Castillo et al. (2018) Mol Bio Cell (submitted). Eritano, A. S. et al. (2017) Mol Bio Cell . vol 28 pp. 1530 – 1538
Subproject 3c: Controlling cell number and size in tissues
(1) Population dynamics in top-heavy differentiation hierarchies. The steady state distribution of cell types in a tissue depends on the topology of intrinsic lineage hierarchies, parameters like self-renewal and differentiation rates, as well as the initial conditions of the culture. We have been investigating a specific lineage hierarchy which we call a “top-heavy” lineage topology – where the least differentiated cell is the most rapidly proliferating and there is a one-way differentiation hierarchy. We believe this type of lineage hierarchy may be a good model of cell dynamics found in many human tumors. (2) Personnel: Amanda Paulson, Zev Gartner (3) Accomplishments: We have characterized an in vitro system exhibiting a top-heavy lineage hierarchy, and who that it is bistable under a very limited set of initial conditions, and that perturbations that affect parameters such as differentiation and survival rates affect the steady state distributions of cell types. 42 (4) Challenges: quantitative measurements of system parameters has been challenging, forcing us to infer ranges of these values from experiments. (5) Plans: we plan to test several hypotheses of our model of the next several months in advance of submitting a publication on the topic. (6) Internal Collaborations: none (7) External Collaborations: none (8) Papers: none
Subproject 3d: Cell-cell communication engineering
1) Probing cell communication through signaling filopodia: We have been studying the role of filopodia in Wnt signaling and the induction of new filopodia by Wnt signaling. We are currently trying to develop a system that will allow us to demonstrate the functionality of these filopodia in Wnt signaling. We are using oligos to specifically modulate the distance between Wnt producing and receiving cells on slides for live imaging. Wnt producing cells will be visualized with WNT1- GFP. Wnt responding cells will be labeled with a membrane marker and a Wnt reporter that can be used in live cells. We are currently designing different reporters that may be useful in this system. We are further working to determine whether the induction of new filopodia is most closely associated with the Wnt production machinery or Wnt reception machinery. We have also been working on developing a genome wide siRNA screen to identify gene s that regulate filopodia formation and length. To date, we have shown that we can indeed visualize filopodia in live cells using the InCell 6000. 2) Personnel: Lisa Galli, Laura Burrus, Fred Santana 3) Accomplishments: We have learned how to plate cells in a grid and have shown that WNT1 and WLS induce new filopodia in chick embryos (and likely in cultured cells). 4) Challenges: Manufacturing the slides for plating cells in a grid is difficult and exceedingly labor intensive. We don’t have the optimal cells for this project yet. 5) Plans: While Lisa has learned how to plate cells in a grid, we no w need to optimize the cells that we are using for this project. It is likely that we will need to make stably transfected cells rather than using transiently transfected cells. This will also be required for the genome wide screen. 6) Center Collaborators: Zev Gartner (UCSF), Andrew Bremer (UCSF and Berkeley) 7) External collaborators: none. 8) Papers: none yet
(1) Reconstitution of tight junction assembly in vitro: Tight junctions are critical structures in epithelial cells that control the flux of ions, solutes, and macromolecules into and out of epithelial tissues. To understand and engineer their “molecular fence” function, we are working to reconstitute parts of tight junction assembly in vitro. We are inserting purified claudins into giant unilamellar vesicles using our jetting technique and studying interactions between them. (2) Personnel: Brian Belardi, Tiama Hamkins-Indik, Dan Fletcher (3) Accomplishments: This year, we focused on the question of whether claudins alone are able to form adhesive interfaces and partition lipids and proteins. Using jetted GUVs containing claudin-4, we found that dense claudin-claudin interfaces form spontaneously between membranes and are sufficient to drive partitioning of extracellular membrane proteins but not of lipids. (4) Obstacles: Incorporation of claudins, which are four-pass transmembrane proteins, was challenging, but we now have a protocol in place to accomplish this.
43 (5) Plans: In the next year, we plan to incorporate additional tight junction components into the lumen of the GUV, including actin and ZO-1, to explore their effects on claudin organization and protein partitioning. We also plan to carry out live cell experiments to investigate how changes in tight junction organization affect transport. (6) Center Collaborators: Wendell Lim. (7) External collaborators: None. (8) Papers: in preparation
(1) Establish rules for emergent collective dynamics of cellular components: Cells collectively can achieve function that individual cells cannot. This inspires us to establish fundamental rules for collective ensembles. Our goal is to establish theoretical and experimental systems for collective dynamics in multi-cellular systems. We have chosen Planarian system (flatworms) as a model organism to study the role of emergent dynamics in ciliary ensembles. We developed live imaging techniques to measure microscopic dynamics of Planarian ventral cilia while the animal is freely behaving in a chamber. By developing RNAi based ciliary perturbations (mucus type, ciliary defects, epithelial defects) we are developing a phase space of emergent collective dynamics and deciphering molecular players that enable these collective modes. This work will further provide rules for collective flocking in engineered systems. (2) Personnel: Guillermina Ramirez-San Juan, Matthew Bull, Wallace Marshall, Manu Prakash (3) Accomplishments: We have recently demonstrated that live imaging of individual cilia in behaving animals is possible; for the first time in Planarian system. We have also demonstrated that RNAi constructs for disrupting various aspects of cilia development and growth give rise to distinct behavior phenotypes. (4) Challenges: One obstacle that exists is the capacity to measure ciliary fields in the entire animals. Since the animals are large (millimeter scale), that is currently not possible and we have to reconstruct the overall dynamics from patches of ciliary patterns. (5) Plans: We intend to submit the first paper quantifying ciliary patterns in wild type and perturbed phenotypes to build a phase space of emergence of coordinated activity in ciliary arrays. (6) Center Collaborators: Dr. Ramirez-San Juan is a joint postdoc who spends equal time in the Prakash and Marshall labs. (7) External Collaborators: None. (8) Papers: None.
(1) Cell-cell signaling through cAMP/Erk/Ca2+. This project has two goals: (i) Disentangling the mechanisms ERK/PKA/Ca2+ signal propagation between cells and (ii) Investigating collective epithelial transcriptional responses to spatially non-uniform cAMP perturbations. (2) Personnel: Michael Chevalier, Joao Fonseca, Hana El Samad (3) accomplishments: We have made significant progress towards both goals of this project using experimental and computational approaches. Specifically, we have focused on the coupling of cAMP from emitter cells, which contain optogenetically controlled adenylyl cyclase (bPAC), to receiver cells (no bPAC). We are interested in how this coupling affects the resulting ERK and PKA signals in each of these cell types and as a function of emitter cluster size. Experimentally, we have applied various chemical perturbations to inhibit different aspects of the system, including gap-junction inhibition, PKA inhibition, and PDE inhibition. In conjunction with the experiments, we have developed a multicellular computational model guided by the results from these experiments. This has allowed us to test different intracellular regulations and cell-cell coupling regulations for different configurations of emitter and receiver cells, and different combinations of genetic and chemical perturbations. In the last nine months we have focused on how cell-cell coupling of cAMP through gap-junctions sculpts 44 the shape of ERK and PKA signals. Specifically, Figure II.3.2a-b shows typical ERK signals in emitter and receiver cells for small clusters of emitter cells. It was also clear that the ensuing dynamic ERK inhibition profiles are different between emitter cells and adjacent receiver cells, with ERK inhibition exhibiting a pronounced overshoot at about 10 minutes after bPAC induction only in the emitter cells (Figure II.3.2a). These results are reproducible in single cells, and preserved by averaging over multiple cells (Figure II.3.2b). Through further interrogations (chemical perturbations to inhibit different aspects of the system, including gap-junction inhibition, PKA inhibition, and PKA inhibition) we aimed to untangle the intracellular and cell-cell coupling regulation of the ERK and PKA signals. The development of a computational model that is predictive of new experiments is a key component of this objective moving forward. (5) Plans: While we have focused the past 9 months on understanding the regulation of the Erk and PKA signals, we will repeat the chemical perturbation experiments for the calcium signals as well to get a fuller picture of the coupled pathway dynamics. We have dual reporter strains for Erk and Ca2+ for this. We are excited to further explore and elucidate the role of cAMP and potential other mechanisms in the dynamics of gap-junctions and the resulting cell-cell coupling of cAMP. We will update the computational model to test mechanisms and predictions relating to gap-junction regulation and potential mechanistic models which are cAMP independent. We plan to publish results from this project within the next six months. We will also focus on developing the strains necessary to measure transcriptional responses for emitter clusters and locally adjacent receiver cells. (6) Center Collaborators: none (7) External collaborators: none (8) Papers: none yet
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Figure II.3.2. Erk signals from small clusters of emitter and bPAC cells exhibit overshoot. (a) bPAC activation (left of dashed line) results in inactivation of ERK (high ERK-KTR nuclear/cytosplasmic ratio) in emitter cells that express bPAC (cell 1, for example, barcoded with a fluorescent reporter to distinguish from non-bPAC cells) and in neighboring receiver cells (non-bPAC cells 2-4). (b) Left image depicts single cluster (white label – emitter cells; yellow label: adjacent receiver cells). Center Plots: average inactivation of ERK (high ERK-KTR nuclear/cytosplasmic ratio) of emitters, their adjacent receivers, and the bPAC input. (c) Basic illustration of the multi-cellular model where each cell has an intracellular circuit and couple to other cells through gap junctions.
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Project 4: Living Bioreactor (engineering organelles, cells or multicellular structures for making useful products)
We envision a variety of applications for engineered living structures, but are particularly excited about the notion of using organelles, cells, and groups of cells as “living bioreactors,” analogous to chemical factories, to more efficiently organize the multiple chemical reactions that would go into building a specialty or commodity chemical product. We aim to harness our ability to specify the organization of intracellular and multi-cellular structures (projects 1, 2, and 3) to implement an entirely new approach to metabolic engineering for production of biofuel and other high value compounds. We have implemented a number of subprojects towards realizing these goals. We begin with engineering of organelle internal environments using hypothesis testing. We are applying this strategy to a number of organelles, but most notably the vacuole and peroxisome. Along similar lines, we are also applying engineering of organelle structure/size/shape. Progress in this area has included overall cell size, cytoskeletal organelles, and vacuoles. We then plan to leverage progress in these areas to engineer organelles to make a specific molecule/product. We are beginning to explore this subprojects, for examples, by targeting proteins and enzymes to the peroxisome. Ultimately, we will aim to link the goals of this project with the tools developed in projects 1, 2, and 3 to enable more predictive and high- throughput methods for engineering chemical production in engineered organelles.
Subprojects:
4a: engineering organelle internal environment 4b: engineering organelle structure/size/shape/number 4c: engineering organelles to make a specific molecule/product
Subproject 4a: Engineering organelle internal environment
1) Develop multiplexed single cell analysis devices compatible with incubation and chemical testing. We are building a device designed to immobilize yeast to provide access to introduced chemical moiety as well as having ability to read out cellular charges. In related projects we aim to design, implement, iterate microfluidic devices to: (i) test and measure methyl halide production using fluorescent reporter bacteria and validate with GC/MS measurements, (ii) design a work flow for these devices compatible with high throughput screening. (2) Personnel: Luke Blauch, Jian Wei Khor, Sindy Tang (3) Accomplishments: have prototyped a microfluidic yeast trap chamber that can trap >50 yeast cells obtained from Mark Chan’s lab (Figure II.4.1). This chamber can also allow a pH gradient to be applied across the width of the chamber by using laminar flow. (4) Challenges: No. (5) Plans: Continue to test the chamber for long-term incubation and high-resolution imaging of yeast cells for >24 hours. We will also test Cell-Tak as a substrate for the microfluidic chamber to simplify the design and increase the density of yeast cells trapped. (6) Center Collaborators: Mark Chan (SFSU), Jennifer Fung (UCSF), Wendell Lim (UCSF), Wallace Marshall (UCSF), Simone Bianco (IBM), Thomas Zimmerman (IBM) (7) External collaboration: No (8) Papers: none yet.
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Figure II.4.1. Microfluidic device for trapping yeast cells during live imaging.
(1) Tuning vacuole size and internal environment in budding and fission yeast. We study the mechanisms by which vacuole size in budding & fission yeast is regulated, as well as the functional impacts of this regulation. Specific projects include: (i) Can vacuole size be used to tune organelle and cytoplasmic pH? (ii) Does vacuole size impact its ability to perform degradative and other chemistries? (iii) What is the impact of cell cycle on vacuole size? (iv) How does vacuole size depend on cell shape and division? (v) How is vacuole transferred asymmetrically between mother and bud? (2) Personnel: Mark Chan, Jean Luke Campos, Roberto Carlos Segura, Jasmine Sims, Will Chadwick, Angeline Chemel (3) Accomplishments: We have established a way to measure pH within individual vacuoles and cells using BCECF as a pH indicator and FM4-64 as a vacuole membrane indicator (Figure II.4.2). Preliminary evidence indicates that for a particular genetic background, vacuoles that vary in size do not vary in pH. We have found that the vacuole undergoes characteristic size changes with respect to the cell cycle, indicating that cell-cycle perturbations may be a way to affect vacuole size in a predictable way. We have begun a series of parallel experiments in S. pombe, exploring first how vacuoles scale in volume, surface area, and number with respect to cell length using a new image analysis procedure developed in collaboration with IBM (Figure II.4.3). Analysis of individual cells undergoing budding has shown that vacuole inheritance occurs throughout the cell cycle, but may occur in discrete transfer events. (4) Challenges: Image analysis continues to present challenges in throughput, especially with one step which requires manual input. This is especially true for Project D, as S. pombe cells typically contain 20+ vacuoles which can be near the resolution limit of light. (5) Plans: (i) With respect to pH, preliminary evidence shows that mutants in vacuole size show altered pH from wild-type; and within wild-type, vacuoles of different size do not show a strong correlation with pH. To address this discrepancy, we continue to collect data on both wild-type and vacuole size mutants. In particular, we will test whether this observation holds if other proteins involved in pH homeostasis (ex. proton pumps & exchangers) are genetically deleted. In this way we hope to gain control over the chemical environment within the vacuole. (6) Center Collaborators: Sujoy Biswas and Simone Bianco (IBM Almaden), Sindy Tang (Stanford), Daniel Elnatan and Jennifer Fung (UCSF) (7) External collaborators: Fred Chang (UCSF) (8) Papers: N/A 48
Figure II.4.2. Measuring pH inside the vacuole in living yeast using BCECF (green) to indicate pH and FM4-64 (red) to outline the vacuole surface.
Figure II.4.3. Automated reconstruction
of vacuole surface in S. pombe cells.
Subproject 4b: engineering organelle structure/size/shape/number
(1) Self-organizing of actin-based morphology. Cell protrusions are a key organelle necessary for sensing and moving around the microenvironment. Different actin nucleators build very different shaped protrusions, but we don’t know how local protein interactions produce large scale control of these cell shapes. (2) Personnel: Anne Pipathsouk, Rachel Brunetti, Brian Graziano, Jason Town, Orion Weiner (3) Accomplishments: We discovered a nanoscale template for cell shape that could explain how an essential actin regulator (the WAVE complex) builds sheetlike protrusions through generating and sensing membrane curvature. We also developed tools to control nanoscale cell shape through nanopatterned surfaces and image cell shape at a variety of scales (super-resolution light microscopy, light-sheet microscopy, high-pressure freezing followed by tomography). WASP may use a different set of rules to control membrane invaginations. (4) Challenges: It’s been slow going getting the nanopatterns we need for this work and making new ones that are better suited to our questions, but we found a new collaborator that should be able to help us move this forward. (5) Plans: Develop nanopatterned surfaces to directly test role of shape in behavior, use knockouts to test some possible shape sensors. (6) Center Collaborators: Sophie Dumont’s lab is helping with the cell squisher that we use in conjunction with nanopatterned surfaces. (7) External Collaborators: David Drubin, Gaudenz Danuser, Bianxiao Cui (8) Papers: We hope to finish up the first paper on this project in the coming year.
(1) Regulation of cell volume for polarity/motility. Neutrophils increase their volume in response to chemoattractant stimulation, and artificially increasing/decreasing volume also increases/decreases directed cell movement suggesting a direct relationship between cell shape and cell behaviors. We are adapting a range of assays to accurately measure cell volume and have made some surprising findings of the pathways that regulate cell volume. (2) Personnel: Tamas Nagy, Brian Graziano, Suvrajit Saha, Orion Weiner
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Project 5: Cell State Inference Engine / Cellular Sentinel (relating cell microenvironment and internal state to measurable cell structures)
The first 4 projects of the Center aim to develop a set of tools and predictive algorithms for going from transcriptional programs, to living structures, to function. In the natural environment, the transcriptional programs that determine cell structure derive from what cells sense in their microenvironment. Thus, a quantitative understanding of how cell structure relates to transcriptional programs will also teach us about how cell structure relates to microenvironment. Solving this “inverse problem” will allow us to use cell structure as a direct readout of what cells are experiencing in any given environment. Thus, the scientific vision of this project is to create a software platform for converting images of cells into estimates of cell environment and signaling state. Towards this vision, we are working on several subprojects. First, we are working to relate microenvironment to cell/tissue structures by asking whether measurable cell structures (and the underlying transcriptional programs that regulate them) change when cells are placed in different microenvironments. Second, we are working to build devices to monitor cell structure remotely. More specifically, we will need imaging platforms that can be deployed remotely to assess how cells in the field or clinic are changing shape. Third, we integrate information from this aim with the tools and algorithms developed in projects 1-4 to build computational models that relate cell structure to specific microenvironments or cell states. Together, these subprojects will lay the foundation for using cellular structure as a direct readout of their internal and external molecular state.
Subprojects:
5a: relate micro-environment to cell/tissue structure 5b: build devices to monitor cell structure remotely 5c: build computational models that relate cell structure to specific microenvironments or cell states
Subproject 5a: relate microenvironment to cell/tissue structure
(1) Evaluating the suitability of yeast as a biosensor. Towards this goal we are in the process of characterizing morphological changes of several potentially environmental sensitive organelles. One direction we are taking is to explore the range of organelle dyes and fluorescent tags to best characterize an organelle’s morphology. We have made Cy5-tagged polyethyleneimine (PEI) to delineate the cell boundary and to simultaneously immobilize the cell to the imaging surface. We are using VPH1-GFP to detect vacuole morphology and pVT100-dsRED to detect mitochondria. Morphological changes in the vacuole was chosen as our initial test case, since vacuole morphology is relatively simple compared to other types of morphological changes. We are 50% done with transforming the yeast deletion collection with the VPH1-GFP which would give us the ability to sample the range of vacuole morphological space. In addition, together with IBM, we are developing image segmentation and deep learning recognition algorithms to classify the spectrum of vacuolar structure. (2) Personnel: Daniel Elnatan, Ashwini Oke, Harry Bevir, Tanya Gromova, Jennifer Fung (3) Accomplishments: We have increased the number of VPH1-GFP transformants and developed a Cy5-tagged PEI stain that allows us to quickly develop a training set for IBM’s deep learning algorithms. (4) Challenges: In Cell 60X was not aligned properly even after maintenance and crashed into the coverslip, which was a major reason why we could not get even reasonable quality images with the 60X objective. This has now been fixed and image quality is vastly improved, especially when combined with the new deconvolution strategy discussed above under Project 1. 52
(5) Plans: We plan to finish the transformation of the VPH1-GFP strain into the yeast deletion collection. This will allow us to determine whether we can easily determine the range of morphological changes in vacuole structure. (6) Internal Collaborators: Mark Chan - SFSU, Simone Bianco, Sujoy Biwas – IBM (7) External Collaborators: No (8) Papers: No papers yet.
(1) Massively high-throughput interrogation of microenvironmental perturbations on cell state at the single cell level. We have developed a cost-effective barcoding strategy that allows single cell analysis of populations of 100s to 1000s of cells across hundreds to thousands of different conditions. We use lipid-conjugated oligonucleotides that passively incorporate into live cell surfaces, and that interface seamlessly with the now ubiquitous droplet-microfluidics based single celled sequencing platforms. (2) Personnel: Chris McGinnis, Lyndsay Murrow, David Patterson, Danny Conrad, Vasudha Srivastava, Zev Gartner (3) Accomplishments: We have demonstrated barcoding of 96 samples in a single experiment using primary tissue, cultured cells, and dissociated organs. We have optimized the oligonucleotides to allow efficient computational deconvolution of samples post-sequencing. We have also collected microscopy images of samples under each environmental condition with the goal that these can be related back to the transcriptional data and specific perturbations. (4) Challenges: Sequencing at this scale is incredibly expensive. However, as the method has been proven, we are able to decrease the costs of our experiments by over an order of magnitude. (5) Plans: We aim to complete this study and submit a publication in July or August. (6) Internal collaborators: n/a (7) External collaborators: Zena Werb, Julianne Winkler, Eric Chow (8) Papers: in preparation
(1) Interrogating 1000’s of Stentor cells structures and outputs. A major challenge for the high throughput analysis of cell structure-microenvironment interactions is to establish assays that allow large numbers of cells to be analyzed under highly standardized conditions. We are developing droplet microfluidic approaches to enable this type of analysis. (2) Personnel: Luke Blauch, Jian Wei Khor, Kevin Zhang, Sindy Tang (3) Accomplishments: We have successfully encapsulated Stentor cells in droplets which allows us to leverage the high throughput nature of droplet microfluidics to screen for Stentor shape/behavior to the microenvironment in the droplet. We have started developing machine learning methods to extract Stentor shape and motion as a readout for the chemical exposure inside the droplet. (4) Challenges: No. (5) Plans: Continue developing the machine learning methods to correlate cell shape/structure/behavior to chemical environment. We will test the toxicity test kit (“ToxCast” from EPA. (6) Center Collaborators Mark Chan (SFSU), Jennifer Fung (UCSF), Wendell Lim (UCSF), Wallace Marshall (UCSF), Simone Bianco (IBM), Thomas Zimmerman (IBM) (7) External collaboration: None. (8) Papers: None yet.
(1) Designing cellular sensors for environmental chemicals. We are using bacterial CooA transcription activation scheme as a chassis for engineering cellular sensors for environmental chemicals. Current goals are: (1) Modularize the molecular signaling mechanism to be sensitive to a range of chemical 53 signals. This goal requires revealing the molecular mechanism of conformational signaling, and designing systematic approaches to control chemical selectivity. 2) Develop modular methods to incorporate bacterial chemical sensing mechanisms into yeast. An effective and portable strategy would enable the ability to add modular selectivity in cellular responses to chemical signals. Currently we are designing organelle targeting and methods to optimally interface transcription regulation between systems. (2) Personnel: Ray Esquerra (3) Accomplishments: We designed and implemented our expression system for reporting in vivo expression of CooA and its chemical dependent activation of gene expression; an IPTG inducible CooA gene and a pCOOF inducible red-fluorescent protein was placed into a pMX plasmid. When IPTG is added to the cells, they express CooA. Exposure to the small signaling molecule, CO, induces a conformational change in CooA allowing it to bind to the pCOOF promotor, and thus express RFP. This assay template will allow us to test the activity of rationally engineered CooA systems that will have designed sensitivity to external chemical signals. Initial beta testing was successful; we can induce RFP expression by CooA with added CO. In addition, during this funding period we also came up with a method for measuring the microviscosity within a cell. (4) Challenges: We discovered that the CooA protein is best expressed in a reducing cellular environment; indicating we need to redesign the protein to express in the relatively oxidative environment of the cell, but we can first simply lower oxygen tension to stabilize CooA expression. We also designed an expression system to purify and characterize CooA with the goal of designing chemical selectivity to gene regulation. (5) Plans: We hope to optimize the expression system in the next funding period or work with other center members to identify or build oxidizing chemical compartments into cells. A goal for this funding period is to develop hybrid strategies (computational and experimental) to systematically incorporate chemical binding sites from the large family of heme proteins into the CooA heme domain to produce a rationally engineered specific chemical sensor. We will submit this work for publication (with two CCC undergraduate co-authors) to the Journal of Physical Chemistry C. (6) Center Collaborators: none (7) External Collaborators: none (8) Papers: none yet.
(1) The effects of microenvironmental nitric oxide induction on myotome formation. We are working to understand how ectoderm generated nitric oxide affects the morphology and differentiation of early muscle (myotomes). (2) Personnel: Wilfred Denetclaw (3) Accomplishments: We show by titin antibody labeling that chicken embryos do not produce myotomes until the embryo makes 12 somites, and that only the most cranial 1-3 positioned somites express myotome (and chicken embryos completes somitogenesis after making 53 somite pairs). We have now also shown that the somite myotome formation rate is linear and intersects with the rate of somitogenesis when it makes the final somite pair. We have performed experiments in which we add or inhibit nitric oxide formation using the Nitric oxide donor (DETA-NONOate) or NOS inhibitor (L- NAME). We added these compounds as pulse treatments to the embryo ectoderm layer, in ovo, for 6 hours and observed altered rates of somite myotome formation, accelerating it forward or delaying it by 2 somites, respectively, over the control rate. Thus, we show ectoderm nitric oxide regulates the first expression of myotome in somites. We followed up on this work by testing the effect of ectoderm nitric oxide on the regulation of myotome differentiation rates by myosin heavy chain expression in somites. Initial experiments show L-NAME treatment strongly halts myosin heavy chain expression in somites, but does not affect the rate of somitogenesis. We have also shown that NO is formed in the 54 ectoderm layer and that nitric oxide signals into the dorsal somite epithelium, and in maturing somites in the dermomyotome layer were muscle precursor cells are located for myotome formation. Because these cells are sensitive to reactive nitrogen and oxygen species, our work suggests the early chicken embryo can be used as a cellular sentinel to test environmental toxic compounds on a whole animal system. (4) Challenges: none (5) Plans: we plan to write up these findings over the summer of 2018 for publication (6) Center Collaborators: Wallace Marshall (7) External Collaborators: none (8) papers: none yet.
(1) Algorithms for inferring cell state from cell motility. The overall idea of the cell state inference engine is to be able to infer the state of a cell, as influenced by its environment, by probing its internal structure. A key requirement is a way to determine what states a cell is in. We have explored two approaches. One method is to use cell motility as a state indicator. By tracking cells as they move across a dish and analyzing their trajectories, we compute a large set of numerical descriptors of trajectory shape, and then perform PCA to reduce the dimensionality of the behavioral state space. This motility-based analysis complements the morphological state-space analysis described above as part of our data-driven approach for CellCAD. (2) Personnel: Jacob Kimmel, Wallace Marshall (3) Accomplishments: We have published our approach for inferring cell state using motility, along with a description of our software (Heteromotility, available on Github), as well as the key result that the space is continuous, that differentiation causes stem cells to occupy progressively smaller regions of state space, and that state transitions violate detailed balance. (Kimmel et al., Plos Comp Bio 2017) (4) Challenges: One challenge in our approach thus far has been the reliance on hand-crafted descriptors of cell motion or geometry. We have begun to move beyond this limitation by using Deep Learning to infer classes of cell trajectories with distinctly different shapes. The resulting software, which we have named Lanternfish, is now freely available on Github and is described in a preprint (Kimmel et al., bioRxiv). (5) Plans: Our main plans are to apply Heteromotility and Lanternfish to other types of motile cells, for example freshwater pond organisms, and to probe the ability of organelle-targeting chemicals to shift cells in state space, as an initial step towards mapping external chemical inputs onto cellular state (6) Center collaborators: none (7) External Collaborators: Andrew Brack (UCSF), Barbara Panning (UCSF) (8) Papers: (a) Kimmel JC, Chang AY, Brack AS, Marshall WF. 2018. Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance. PLoS Computational Biology 2018 14(1): e1005927. (b) Kimmel JC, Brack A, Marshall WF. 2018. Deep convolutional neural networks allow analysis of cell motility during stem cell differentiation and neoplastic transformation. Manuscript submitted. Preprint: bioRxiv. 2017 doi: https://doi.org/10.1101/159202
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(1) Algorithms for measuring cellular behavior in a predator-prey system: We have developed an automated system for long term (several days) high throughput (large field of view), low cost ($100) imaging instrumentation and associated algorithms for three-dimensional recording of behavioral states of single cells engaged in a predator-prey interaction. We choose a predator-prey system that allows us to discretely quantify a successful behavior in a classical description of predator-prey dynamics. By tracking every morphological parameter in a highly dynamic cell, we correlate search strategy for predator-prey interactions in a confined “reduced” ecosystem in a culture. By performing molecular perturbations while measuring morphological dynamics, we quantify how a single cell computes a efficient search algorithm. (2) Personnel: Scott Coyle, Hongquan Li, Manu Prakash (3) Accomplishments: First paper under preparation, to be submitted. (4) Challenges: none (5) Plans: We could further improve on our three-dimensional tracking capabilities. Once the baseline algorithm for predator-prey interactions and search space are established – we will build on this work to find molecular mechanisms underlying these algorithms. Live cytoskeletal labels and genetic perturbations are being developed enabling us to understand the mechanism behind search algorithms single cells apply to find its prey. (6) Center Collaborators: None (7) External Collaborators: None (8) Papers: None
Subproject 5b: build devices to monitor cell structure remotely
(1) Submerged immersive microscope for real time collaborative sample analysis. Proof-of-concept experiments have verified the operating principles of a submerged immersive microscope (Figure II.5.1). The novel microscope is composed of a head mounted display controlling the position of a shadow microscope submerged in a large volume of plankton-laden water. The system is based on a raspberry PI platform, and uses inexpensive consumer electronics. The IBM team has built the submerged immersive microscope prototype and demonstrated its use for plankton tracking at a TED talk. A paper on the using the system to study quantitatively plankton in a large sample is being drafted. (2) Personnel: Tom Zimmerman, Simone Bianco (3) Accomplishments: Project completed. A TED talk has been given on the prototype (https://www.youtube.com/watch?v=VxE_itIllxE). A paper is being written (4) Challenges: none (5) Plans: We plan to extend the system to multiple users in a virtual space. The system can be used for real time collaborative exploration, as well as education purposes. (6) Center Collaborators: N/A Figure II.5.1. Submersed immersive (7) External Collaborators: N/A microscope. (8) Papers: Draft not yet available
56
(1) Digital Lensless Microscope with Operating System. A portable lensless microscope based on a Raspberry Pi Zero microcomputer and an OV5647 image sensor has been designed and constructed (Figure II.5.2). The inexpensive microscope can be used widely in the lab and schools due to its low cost (<$20 bill of materials), digital storage (USB, hard drive) and programmability (Linux operating system with Python built-in). (2) Personnel: Tom Zimmerman (IBM), Vito Paolo Pastore (3) Accomplishments: Eight units have been built and used in a Microscope Hackathon (https://hackccc.org/) and shared with other researchers to enable viewing and capturing of HD video of plankton. A prototype of a stereo version, with supporting Python code, has been built. The microscope was deployed in a first grade science classroom microscopy demo to look at ciliates in pond water. (4) Challenges: No obstacles (5) Plans: Establish relationships to manufacture the microscopes so they can be purchased for education and research. Provide a library of python code for detection, tracking, classification. Improve the usability of the stereo version, for example interface it to a VR platform and head mounted display. Develop image post-processing to improve the image by reducing diffraction effects. (6) Center Collaborators: Daniel Elnatan (UCSF) (7) External Collaborators: Joe DeRisi (UCSF) (8) Papers: N/A
Figure II.5.2. Lenseless microscope for low cost high resolution imaging in the field. Left panel shows the microscope housed in PVC tubing. Right panel shows image of living pond organisms with sufficient resolution to resolve ciliary beating.
57
(1) High-throughput flow-through microscopy: We have recently demonstrated a low cost ($100), high-throughput imaging platform for flow-through microscopy in the field. This instrument and other related microscopes developed in our lab (malariascope, Foldscope) allow us to provide powerful automated and manual microscopy capability in field conditions. This capability will allow for teams developing “reporter cells” to be probed in ecological conditions and data coming from these instruments analyzed in field conditions to provide a live monitoring platform at ecological scale. (2) Personnel: Hongquan Li, Thibaut Pollina, Manu Prakash (3) Accomplishments: We deployed our first flow-through microscope in Antarctica on a sailboat (Yvinec). The data is coming from this sailboat via a satellite link. (4) Challenges: The goal this year is to deploy 30 microscopes around the world. Ensuring low cost of manufacturing will be a major goal moving forward; with a target price of $100 per instrument. Connectivity in deep regions of the ocean is limited; so sailors might need to send data once they arrive at a port. (5) Plans: Next year, we aim to build a network of 30 sailors around the world continuously sending data via satellite links and our high-throughput flow-through microscopes. (6) Center Collaborators: None (7) External Collaborators: This work is in collaboration with “Plankton-Planet” (https://plankton- planet.org) team from France and US and the Tara expedition (https://oceans.taraexpeditions.org). (8) Papers: The first paper on this work is being prepared for submission.
5c: Build computational models that relate cell structure to specific micro- environments or cell states
Our plan is to use the same modeling and/or data-driven frameworks for relating structure to environment that we are already developing for the CellCAD project. Therefore, for updated status of these modeling efforts, please refer to the section on Project 2, above.
58 III. EDUCATION
1a. Overall education goals and objectives The Center has two overarching education goals: 1. to build a coherent pathway from high school to careers in Cellular Engineering that effectively integrates the research developments of the Center into all educational activities; 2. to establish Cellular Engineering as an inclusive field that works at all levels (K-12, undergraduate, graduate/postdoctoral, and faculty) to broaden participation in STEM. Education activities in year two have built upon the foundation established in the first year. Critically, we have continued to strengthen our culture of cross-center inclusiveness and collaboration involving Center members at all levels and from all member institutions. The education efforts and work across the Center as a whole continue our commitment to broadening participation in STEM.
1b. Performance and management indicators period Our performance and management indicators remain unchanged from the previous reporting period.
1c. Problems encountered and plans to address these problems As detailed later in this report, we continue to make good progress on our Education goals. Our two largest education activities – the Cellular Construction Workshop serving high school teachers and students and the Exploratorium’s Cells-to-Self exhibit are both well underway. Across all education activities, we now have a blueprint that will help inform and guide the work in future years. We are continuing to explore and identify the best strategies to communicate across the Center and this remains a challenge. Optimizing communication channels will help with announcing and promoting events, recruiting Center volunteers, and sharing opportunities with all Center members.
2a. Internal educational activities Center-wide educational program in Ethics and Responsible Innovation In year two of this award, we launched our first Center-wide educational activity – a day-long Ethics symposium attended by faculty, postdocs, graduate students, undergraduates, and center staff. This symposium, the focus of the Center’s January quarterly meeting, sought to introduce all Center members to the field of ethics as a mode of inquiry and problem-solving. This was specifically designed to be different than the typical Responsible Conduct of Research course, which all trainees at all of the Center sites receive already. Instead, our ethics educational program is focused on ethics of innovation, and is guided by the concept that “Ethics can be the source of technological development rather than just a constraint and technological progress can create moral progress rather than just moral problems” (Van den Hoven et al., 2012).
Our goals in planning this day long event were to 1) help Center members develop a foundational level understanding of ethics as a robust discipline, with core tenets that can (and should) inform how the Center pursues its research agenda, 2) to begin an ongoing conversation across the Center about the ethical considerations that may affect whether or how we pursue a line of inquiry, the ethical implications of our work, as well as how at this nascent stage of developing a discipline we build ethics into the fabric of the field.
Discussions for the day were launched by a presentation by Robert McGinn, Stanford University Professor (Teaching) of Management Science and Engineering, and of Science, Technology, and Society (STS), author of The Ethical Engineer, and CCC Advisory Board Member. Dr. McGinn’s presentation was followed by a talk by Center Faculty member Dan Fletcher on the role of the Federal Government in
59 research regulations (and how the relationship between the research community and policy makers influences regulation). After lunch, Center members had time to synthesize what they had heard and apply their developing understanding of ethics and regulation to a discussion of Mary Shelley’s Frankenstein (in honor of the 200th anniversary of its publication). After thinking about ethics in the context of Frankenstein, Center members were asked to discuss the following questions in small groups:
- What sort of review structures would be appropriate in a discipline where we are creating new life forms? - What are the potential benefits and harms from Center research projects? - How do we balance our ethical responsibilities with scientific creativity and passion for moving science forward? - How should we consider communicating about our research, before problems arise, both to gain other perspectives on the risks v. benefits, as well as to help communities impacted by our work understand how they might benefit, what any risks might be, and how we are taking responsibility for those risks? How do we communicate when something goes wrong? - Like Frankenstein, as scientists we are continually pushing the boundaries of knowledge and what is possible and occasionally are blinded by our pursuits. Should you do something just because you can (or to prove you can)? Does Frankenstein illustrate how we as a community can/should set limits in our experimental paths? Discussion groups were composed of a mix of faculty, undergraduates, graduate students, postdoctoral fellows and Center affiliates and were also deliberately cross-institutional to strengthen connections and build relationships among individuals across the Center. Discussions in the groups were robust as participants drew on what they had learned in the morning session, their own research experiences, the context of Frankenstein (and Dr. Frankenstein’s lack of considerations of the potential consequences of his project), and their excitement about the Center’s potential to engineer cells to create innovative solutions to important problems. We are continuing this center-wide educational thread at the next annual retreat, where EAC member Brian von Herzen will present a talk on engineering solutions to global challenges, and how engineering interacts with policy making. We have also begun to leverage existing educational resources in Responsible Innovation that have been developed in Europe. In particular, center leadership members have begun taking an online course in Responsible Research and Innovation developed at the Technical University in Delft. We will incorporate components of this material in future center-wide educational activities.
Summer and Year-round Center Research Experiences for High School Students and Undergraduates One way the Center is expanding awareness of Cellular Engineering and the potential for interesting careers in this field is by hosting both undergraduates and high school students in labs for summer research experiences. Students are recruited for these research experiences by leveraging existing summer programs at participating institutions. During the past two years, five undergraduates at UCSF (through the SRTP and URI programs) and thirty undergraduates at SFSU (through the NIH MARC, NIH RISE, NIH Bridge, NIH BUILD and NSF REU programs at SFSU) took part in summer research experiences. In addition to the summer students, 40 undergraduates took part in year-round research experiences in Center labs, including 36 at SFSU, 3 at UC Berkeley, and 1 at UCSF. All Center undergraduates, whether year-round or summer students, are viewed as full members of the center, and are invited to take part in all Center quarterly meetings, including the educational activities associated with those events, and also the center-wide annual retreat, which is deliberately timed to allow summer students to take part. Undergraduates present their work as talks and posters at these events. By taking part in these quarterly meetings and retreat, the students get to know each other as a cohort, and also become familiar with the research, ideas, and culture of the center and its participating institutions.
60 Coursework Overview Center faculty at UCSF, San Francisco State University (SFSU), and Stanford University have significantly increased their Internal Education Activities as they developed and taught innovative courses that introduce students (undergraduates and graduate students) to the field of Cellular Engineering and its “Big Ideas” while also teaching them the habits of mind and skills needed for a successful career in Cellular Engineering. These courses will be described in more detail, broken out by their intended audience (undergraduates and graduate students), below.
Undergraduate Coursework During the past year, center faculty member Raymond Esquerra has developed curricula for two brand- new undergraduate courses at SF State that integrate innovations developed at the Center and provide undergraduates opportunities to not only learn about Cellular Engineering, but also to gain foundational skills that are directly applicable to careers in this emerging field. Dr. Esquerra’s Biophysics Laboratory course will serve 15 undergraduates each year. In this course, students learn techniques for microscopy and image analysis using on microscopes designed by CCC members at IBM and Stanford. This laboratory course will be offered for the first time in Spring 2019, then annually thereafter.
Dr. Esquerra is also developing a course entitled “Principles of Cellular Engineering” which will focus on mathematical and computational modeling of cellular systems – cross-disciplinary skills that will be critical for success in Cellular Engineering. Notably, this course is being developed in collaboration with a UCSF IRACDA postdoctoral fellow, thereby providing opportunities for a trainee from a background underrepresented in science to gain mentored experience developing and teaching a undergraduate course that integrates cutting edge research developments and techniques. This course, BIOL 674 will launch spring 2019 and will serve 30 students per year.
Dr. Manu Prakash is developing a course to be taught to Stanford Undergraduate and Graduate Students, entitled Frugal Science. This course will be taught in the Fall of 2018 and will introduce students to many of the tools that Dr. Prakash is developing for the CCC. In a project-based setting, students will explore how tools from engineering and physics can be used to solve problems in the life sciences, with a particular focus on low-cost solutions that reduce barriers to entry. The course will have a particular focus on innovations in microscopy at the cellular scale, for use in field conditions. Dr. Diana Chu’s course Exploring and Practicing Science Communication at SF State provides participants (advanced undergraduates as well as Masters students) opportunities to gain critical skills in how to communicate their science to diverse audiences. The goal of the pilot session of the course is to delve into what others have learned about science communication, experiment with tools that communicate our work and goals, and develop skills to engage a broad range of people to how our science is relevant and important. The course will serve 40 students per year and is cross-listed so that students from across the College of Science and Engineering can take it thereby fostering cross- disciplinary communication and collaboration. The course (BIOL719) was proposed and approved by the Biology Dept in 2017 and will be offered for the first time in Fall 2018. Predicted outcomes for the course include that Center Students have the opportunity for training in outreach and communication that will help them communicate the science linked to the CCC to a broad range of audiences. The Cell and Molecular Imaging Center at San Francisco State University provided a total of 146 hours of training on microscopes to eleven Center undergraduates and graduate students. This training is a prerequisite for students to be able to use the microscopes independently in their Center-supported research. Microscopes include: a Nikon C1 Confocal, Nikon Eclipse 80i, Zeiss LSM 710 Confocal, and a Zeiss Cell Observer SD Confocal.
61 Graduate Student Coursework In the past year, Center Faculty at UCSF have greatly expanded their minicourse offerings to provide further opportunities for Center graduate students to gain the knowledge and skills needed to pursue research questions and solve problems in Cellular Engineering.
In late April 2018, Dr. Jennifer Fung and Center PI Wallace Marshall offered their Cellular Robotics course for the second time, serving 12 students. This course focuses on the idea that cells are complex biological machines, capable of making decisions and performing behaviors both individually and in groups. Much of physiology and development hinges on cells executing the correct behaviors at the appropriate times, in response to sensory inputs from their environment. In this respect, cells resemble man-made robots. By viewing cells as robots, controlled by computational circuitry made of genes and signaling molecules, it is possible to apply concepts from engineering and computer science to understand cellular behavior. In order to exploit such concepts, it is important to have a firm foundation in how robots are actually built and programmed. In this minicourse, students explore robotics and computer science as paradigms for cellular behavior, in a hands-on project based setting. Students read key literature on cell behavior in which ideas from computer science and electrical engineering are invoked. Then, they are given challenges - physical tasks for a robot to solve inspired by some of the things that living cells do. The students work in small groups to solve these challenges by building robots using the LEGO Mindstorms system a robotics platform largely intended for children but which is in fact built on a powerful LabView software system and which allows concepts such as path planning and feedback to be rapidly prototyped. After solving a challenge, students discuss and compare their designs, with a particular view to asking whether the robot solved the challenge in a way that resembles how a cell would solve the same problem.
In addition to providing concrete experiences for students to begin to think about how cells translate environmental inputs to outputs (behavior changes), this course introduces students to concepts in computer science and provides an introductory programming experience. This is particularly critical to Cellular Engineering as robotics, machine learning, and computer programming are key tools in the design of high throughput experiments in biology. This course trains students to incorporate robotics into their research and to utilize programming as a tool for scientific analysis. The course also seeks to provide concrete examples of how other researchers in biology are utilizing robotics in their work. This year, Jordan Pollack of Brandeis University, an expert on robotics and artificial intelligence, provided students with a guest lecture on evolutionary robotics. It is important to note that there is close collaboration cross- center between this course (and it’s developers) and the Center-affiliated staff at the UCSF Science & Education Partnership who leverage what is taught in the course to inform the design of their Cellular Construction Workshop for high school students and teachers. Center PI, Wallace Marshall co-organized and taught a second minicourse with a new Center faculty affiliate, Sy Redding in early April 2018. This course, entitled Computation By Cells, explores the idea of the cell as a computer. It is based on the idea of the cell as a machine that can be programmed and re- engineered, which is the key intellectual idea behind the Center. In it’s pilot year, the course served 12 students and met daily over three weeks. The course structure combined guided literature reading with hands-on experiments focusing on the ability of the single-celled ameoba Physarum to solve mazes and other computationally challenging problems. Center PI Wendell Lim collaborated with Center faculty member Hana El Samad to develop another new minicourse offered in the Spring of 2018. The course, Modularity in Biological Regulation, Evolution, and Engineering: Domains, Circuits and Engineered Therapeutic Cells, had students explore key questions that will drive progress in Cellular Engineering including: What are the definitions of modularity? What are examples of modularity in biology? At what scales do we find modularity in biology? Is biology really modular, and if so, why? Students investigated the evolution and engineering of modular proteins and modular circuits in biology and how to harness modularity to engineer useful cells. The project culminated in teams brainstorming cellular design/engineering solutions. The course is designed for 20-25 students annually, and was oversubscribed in this first inaugural year. 62 2b. Participation of Center Students in Professional Development Activities Center students participate in a wide range of professional development activities. These are presented in more detail, below. Each of these activities are consistent with our overarching Center Education goal of building a coherent pathway to careers in Cellular Engineering. Professional development activities help students build their professional networks and develop their communication skills, provide training in key techniques to help the individual move a Center project forward, develop trainee’s knowledge base so that they could more effectively pursue research in Cellular Engineering, helps trainees understand the knowledge transfer/intellectual property process, and help trainees explore careers in industry or informal science education. (Note the information presented below includes only professional development activities for undergraduate and graduate students, not postdoctoral fellows, as specified in the instructions.) Graduate Students: - Presenting their research in both research talk and poster format at a wide range of external conferences including those organized by the: Genetics Society of America, Berkeley Statistical Mechanics Meeting, the American Physical Society, Biophysical Society Meeting, American Society of Cell Biology, Foundations of Nanoscience Meeting, Society for Developmental Biology, and the American Physical Society’s Division of Fluid Dynamics Annual Meeting, Personalized Medicine 10.0, SACNAS, California State University Summer Symposium, ABRCMS, CSUPERB, ASBMB, CSU Student Research Competition, Bay Area Worm Meeting, 21st International C. elegans Meeting, and microTAS; - Opportunities to present their research at events at Center-wide quarterly meetings and at the Center’s annual NSF Site Visit and at events at their home institution such as the SFSU 19th Annual Student Project Showcase - Attending supplemental courses at institutions outside of the Center, such as the Woods Hole Physiology course, to further their knowledge and skills; - Participation in courses on mentoring offered by the UCSF Office of Career and Professional Development; - Participation in the UCSF MIND Career Development program; - Taking advantage of internship opportunities through a range of institutions, including: IBM, the Exploratorium, Caribou Biosciences, and Biotech Connection Bay Area; - Participating in entrepreneurship classes offered at UCSF such as the Business Strategy for Scientists course; Startup 101 - Serving in student government as the Vice President for Finance in the UCSF Graduate and Professional Student Association; - Serving on a wide variety of UCSF committees, including as Chair of the UCSF Student Service Fee Advisory Committee, UC Systemwide Council on Student Fees, UCSF Registered Campus Organization Funding Review Committee, UCSF Library Student Advisory Committee, and the UCSF CCE Partnership Grants Committee; - Participation by Master’s students in a weekly pre-doctoral preparation Colloquium to provide support for PhD program applications; - Active participation in professional societies such as SACNAS and BE-STEM; - Working in a collaborators laboratory (CalTech) for 3-months to finish a paper and learn more advanced machine learning and computer science methodologies; - Serving as a Teaching Assistant in courses taught by Center Faculty; - Participation in a Cell Modeling Hack-a-thon 63 Center graduate students were recognized with awards for their presentations, including a 1st Place Graduate Award at the CSU Student Research Competition, 1st Place Graduate Award at Personalized Medicine 10.0, and a 3rd Place Graduate Award at the 19th Annual Student Project Showcase at SFSU.
Among the activities listed above, a unique feature of our center as an STC is our overall focus on knowledge transfer with industry, which has given us an unusual opportunity for creating new internship programs for our graduate students. As a result of this work, we have been able to create opportunities for our students that would not exist for students outside of the CCC. The internships consist of 3-6 month intensive work experiences at partner companies working on center-related projects. The internships thus not only provide a unique educational opportunity for the students; they catalyze further collaboration and integration within the center and bring new ideas and approaches back to the host labs.
During the past year, the following students have taken part in internships:
Cecilia Brown, SFSU graduate student, Intern at IBM James Gerh – SFSU graduate student, Intern at IBM Jacob Kimmel – UCSF graduate student, Intern at IBM Amanda Paulson - UCSF graduate student, Intern at IBM Jennifer Hu, UCSF graduate student, Intern at the Exploratorium
Undergraduates: - Presenting their research in both research talk and poster format at a wide range of external conferences including those organized by: SACNAS, Personalized Medicine 10.0 - Opportunities to present their research at events at Center-wide quarterly meetings and at events at their home institution such as the SFSU 19th Annual Student Project Showcase - Highlighting their work and potential demonstrations inspired by their research at the Exploratorium Cell Fair We note that several Center undergraduates were recognized with awards for their presentations including a Poster Award at SACNAS, 1st place Undergraduate Award at Personalized Medicine 10.0.
2c. External Educational Activities Center members are deeply committed to Outreach and demonstrate this commitment through participating both in activities organized through the Center as well as initiating their own activities, greatly extending the reach of the Center. Center organized activities are focused on both of our overarching education goals: building a coherent pathway from high school to careers in Cellular Engineering that effectively integrates the research developments of the Center into all educational activities; and establishing Cellular Engineering as an inclusive field that works at all levels (K-12, undergraduate, graduate/postdoctoral, and faculty) to broaden participation in STEM. To these ends, our external education activities serve K-12 teachers and students introducing them to the big ideas of Cellular Engineering, provide opportunities for the public to engage with Cellular Engineering (and critically Center Members) to understand both the problems that drive our work and our approach to solving these problems. We are attentive to diversity and inclusion in all of our activities – working to ensure that our activities are broadly accessible to all in the Bay Area and that through our external activities students from backgrounds underrepresented in the sciences feel welcomed and can begin to see a place for themselves in STEM careers. This section will highlight two of our “signature” education activities in more detail followed by more brief descriptions of the many other ways our Center is working locally, nationally, and internationally to promote interest in and awareness of Cellular Engineering.
64 Exploratorium – Cells to Self – Phase I One of the Exploratorium's major activities as part of the Center is the development of the Cells to Self exhibition. This exhibition will contain many exhibits developed in collaboration with or inspired by CCC work. In December of 2017 the Exploratorium launched the first phase of exhibits. The full exhibition will open in late 2019. In this project year, we anticipate 25,000 members of the general public will engage with the Cells to Self exhibits.
The overall goal of the exhibition is to foster public understanding of how organisms develop from a single cell to a "self," or full adult organism. While the full exhibition will cover topics outside of the CCC (such as personal genomics), at least eight finished exhibits will reflect fundamental concepts from CCC research. The specific goals for the CCC-related exhibits are to:
• Advance public understanding of cell structure, cellular behavior, how cells relate to organismal structure and function, and how engineering might be applied to these fundamentals. • Engage the public with real tools, specimens, and data to advance understanding of current research practices. • Create experiences that foster scientific practices such as making observations, asking questions, and testing hypotheses.
During this reporting period there are two groups of exhibits to report on, those nearing completion of their development (Phase 1) and those that are under active development (Phase 2). The ouputs, outcomes, and impacts for these two phases is different and described below. Phase 1 exhibits: There were four CCC-related exhibits featured in the 2017 Phase 1 opening, and are now currently on the floor: Cell Zoetrope (cells are dynamic – they move and change shape; created using light sheet microscopy data from a partner laboratory); Kombucha (how cells form structures); Planaria - Regenerating Super Worm (how organisms can heal wounds, inspired by the Marshall lab); HeLa - Are Your Cells You? (how humans are made of cells, introduction to Bioethics and the ethical issues surrounding using cells without patient consent). Outputs: The four exhibits described above have been on the floor of the Exploratorium as of December, 2017. Outcomes: We have evaluated these four exhibits through formative evaluation, and have found that they increase public understanding of basic concepts in cell biology, provided the public new insights into the connections between cells and things they know (kombucha, themselves). Visitors had less understanding of the connection between current research or data and the exhibits and making this connection more clear is an area of effort. Quotes from visitors, captured by the Evaluators, provide insight into what people are taking away from the exhibits:
[Cell Zoetrope] I just learned that cells have physical locomotion with feet, that's amazing. [Planaria Regeneration] I found it interesting because it may help us understand how they do it [regenerate], so it was something fascinating biologically. [HeLa Cells] Part is the idea of immortality of cells and what that means for us, another part is the lack of giving permission. Doctors wouldn't do that anymore, our understanding on that has evolved. [Kombucha] It's pretty interesting to see a colony of microorganisms that big, you don't see that much in the natural world. Impact: These are still new exhibits in the area under development so long term impact has not been measured. 65 Phase 2 exhibits: The team is actively working on additional exhibits that focus more actively on helping visitors to bridge the idea of a single cell to the fact that individual cells can come together to form larger structures. In addition, we are in the initial research stage, investigating several ideas different ideas including: Turing Patterns, tissue formation, cell communication, and image recognition. By the end of the reporting period we should have several prototypes on the floor being tested. Outputs: 2-4 prototypes tested with a limited number of visitors by 9/30/2018 Outcomes: limited as will be in prototype stage Impacts: None during this reporting period Connection to Center Research: The Cells to Self exhibits are developed through a collaborative process and many Center labs have been a part, including the Marshall lab, the Fletcher lab, the Gartner lab, and many groups at IBM. These groups present to our team as we brainstorm exhibit ideas, they provide data from their research groups that are incorporated into the exhibits in some way, or they provide feedback over the course of the development process. Interns from Center labs are also embedded in our development process.
Cellular Construction Workshop The Cellular Construction Workshop is a unique two week summer workshop that brings high school teachers and students together to learn about Cellular Engineering to reframe how we think and teach about cells. Through the workshop, participants begin to realize that cells are not mere building blocks but rather that they are dynamic entities, constantly sensing and responding to their environments, and capable of complex behaviors – either singly or in self-organized groups. Participants observe cellular behaviors and then develop models of these behaviors by programming robots. The workshop provides a rich environment for participating teachers to experience the vision of three-dimensional learning described in the Next Generation Science Standards, and support to then bring the lesson modules from the workshop to their classrooms. The CCC launched the Cellular Construction Workshop in Summer 2017 to strong demand from teachers and students. We ultimately accepted a total of 24 participants – 10 teachers and 14 students from eight different schools in three Bay Area School Districts (San Francisco Unified, West Contra Costa Unified, and Jefferson Union High School District). While the Workshop itself took place during the last reporting period, we will share here some of the reported outcomes as the evaluation report was not completed in time for the last annual progress report. Recruitment: Program staff were not aware of any other program that brought teachers and students together as co-learners and viewed this structure as an experiment in the first year. At the outset, we were unsure how teachers would feel about this structure and if it would deter them from participating. Our External Evaluator found the opposite was in fact true. Several of the teachers explicitly cited the importance of their students’ participation as influencing their own decision to participate: I have been teaching for five years and never any other opportunity I’ve had where I can do this with my students… the opportunity I have to be in the classroom with them, as a student with them, is so exciting for me. (Teacher) I also hope to discover where my misconceptions are and where the edges of my knowledge are and also for my students, I really look forward to working with them and hearing the questions that they have and what they don’t understand … it would give a good lens into what I should be teaching and how I can focus the curriculum. (Teacher) Outcomes: Participant learning in the course was primarily evaluated through authentic assessments – successful completion of a series of engineering-design challenges coupled with presentations that explained the significance of the cellular behavior that the robot was designed to model. We also sought to evaluate the participant experience in the workshop, their perceptions of what they had learned, and the
66 impact of the workshop on their interest in STEM careers. This evaluation included both likert-scale questions rating their experiences in the workshop as well as open-ended questions. Participants were given a series of statements pertaining to the workshop and asked to rate them using a four-point scale (strongly disagree (1) -> strongly agree (4)). Students’ ratings are in blue, and teachers’ ratings are in red.
• What I learned in this workshop will be valuable for me in the future (S-3.71, T-3.63) • Overall, I enjoyed this workshop (S-3.71, T-3.75) • I have learned a lot about robots (S-3.64, T-3.88) • I have learned a lot about programming (S-3.57, T-3.75) • I felt the Cellular Construction Workshop was well-planned and organized (S-3.50, T-3.50) • I have made meaningful connections with other participants in this program (S-3.43, T-3.50) • I have learned a lot about working in teams (S-3.36, T-3.13) • I have a better, deeper understanding of what a cell does (how it functions, senses, responds, etc.) (S-3.31, T-3.25) • I better understand how cells can be programmed (S-3.29, T-3.38) • I have a better, deeper understanding of what a cell is and how it is structured (S-3.15, T-3.00) • I have learned a lot about how to use laboratory equipment (S-2.85, T-2.86) With regard to specific skills, participants reported the greatest gains in their computer programming skills (S-3.29, T-3.63) and students similarly reported significant gains in working as part of a team (S- 3.29). Teachers, not surprisingly reported only small gains in their skills in working in teams (T-2.75). Both teachers and students reported smaller gains for their skills in traditional “lab work” as this was not highly emphasized in the course (Biotechnology (S-3.07, T-3.14), Microbiology (S-2.93, T-3.00). Students stated: Before the Cellular Construction Workshop, there were many things I didn't know about how cells and programming a cell was. So this has helped me to learn about it. (Student) The programming was the best part because not a lot of high school students get exposed to this and especially at school. So it's really cool that there's early exposure to this. (Student) Students and teachers alike found tremendous benefit in the pairing of students and teachers as learners: I feel like it definitely helped carry classroom discussions to another level, especially for the students. It would seem that the teachers would bring whole new ideas that students have never really thought about or explored, thus invoking them to think critically too. Working in our small groups to complete little projects too was also fun when combining the two together. Everyone had their own ideas and past experiences to bring to the table, and it brought a whole new dynamic to the learning process. (Student) One of my favorite parts of this programs was being able to interact with teachers. Because the program was outside of school and had teachers from different schools, it was easy to see them not as teachers but as regular people who just happen to be older than me. This made it easier to interact with them and made the whole experience a lot more comfortable. (Student) I thought it was really cool, in that, students usually look to teachers as teachers, and not as active learners with you. In school, a relationship to a teacher usually isn't one of a friendship, but usually it is one of respect so you can learn. However, when working with other teachers, I was able to build a friendly connection with them which really takes away some of the previous thoughts about teachers. We can see that the teachers are just like us, willing to learn and to ask questions. (Student) I like the fact that I was able to work with teachers because it boosted my confidence to see a teacher, someone who knows "everything" have the same struggles as me a student. (Student)
67 I liked it because it demonstrated to me how a student thinks through the problems. (Teacher) I think it was really great to have both teachers and students participate together because it gave opportunities [for me] to make facilitator moves to help my group move forward with the task, but more importantly, it gave me opportunities to struggle and to fail in front of my students. I hope I was able to model for them that mistakes are expected in science and how we learn from them is the important take away. (Teacher) I think having students work alongside of teachers is a great idea. I learned so much about technology from the students I worked with. (Teacher) It is important to note that the teachers expressed a desire for break-out groups, away from the students at discrete times during the workshop. This would serve two purposes: 1) it would provide time for them to work collaboratively on plans to translate the workshop to their classrooms, and 2) it would force the students to push through frustration without relying on their teachers to provide solutions. We are incorporating this suggestion into the 2018 workshop. Students reported that the workshop expanded their view of careers in STEM. I have been interested in STEM since I was a little kid, and this workshop helped me explore this specific branch of STEM. Before I attended this workshop, I was unsure about pursuing a career in cellular engineering, but now I would like to know more about what I need to study in college in order to become an engineer. (Student) I was introduced to the STEM field in high school, but I never had a set idea of what it actually was and what careers were in this field. This workshop definitely opened so many options, ideas, and interests within STEM. Prior to this workshop, I had only taken a high school biology class that would be the closest thing to STEM, but now that I was able to explore engineering along with technology too, I definitely am now looking at this field tightly. In this workshop we were able to connect all aspects of STEM together, and I think that was what made this workshop special. (Student) Teachers reported a strong desire to translate what they had learned to their classrooms: I plan to use the robots for a Biology Enriched course where students that have learned basic cell biology during the cell biology unit will have an opportunity to go deeper into cells by modeling robot phototaxis. BE enriched typically serves ~20 students with about 30-35 hours of course work where students will document their research in a formal lab journal with a digital abstract for displaying their findings. (Teacher) Yes. I think that I will use the programming logic for cellular processes... Having students diagram with written 'code' about what is going on for various cellular processes. I will also be collaborating with a colleague at the workshop with her robotics challenge in her engineering classes. (Teacher) Notably, over the course of the school year, four teachers borrowed the robots from the Center for use with their students. Two other teachers, whose school owned robots, also incorporated aspects of the workshop into their teaching in 2017-18. Teachers also expressed that other aspects of the workshop would aid in their transition to NGSS: Some of the resources for teaching science concepts will be helpful in restructuring lessons for teaching NGSS standards and more current scientific methodologies. I expect the "probes" will be useful formative assessment tools. Lots of good analogies, another take away for NGSS transition. (Teacher) Students and teachers alike reported that they would recommend the program to others: The experience is fun and also educational which is the perfect mixture, as it is very hard to balance the two. Another thing is, this program is nothing like school, besides the fact that you are learning. You aren't reading out of a textbook and you aren't writing that many things down. 68 You are actively engaging in thinking and discussions which is the most important part of learning that is emphasized in this program. This is why I feel this program is right for anyone who wants to have a fun learning experience over the summer. (Student) I would definitely recommend the Cellular Construction Workshop to others because of how eye opening this workshop can actually be. It's a great way for students to explore this field, and to be getting first-hand experience of working with what they're learning makes it even better. This is not a testing and memorizing sort of environment, it's an environment where people are taking understanding in what they are being introduced. I love how everyone gets the opportunity to be able to build, create, and investigate their own learning journey through the workshop. (Student) This workshop has been one of the most practical and applicable professional development opportunities I have ever participated in. I am really excited to be developing a design project using the Lego robots for my biology class. Also the fact that this science is new and happening right now in labs across the world is compelling and so necessary to teach our students to give them access to myriad career opportunities. I am so grateful to have been able to participate in this program and I hope I can work more with UCSF in the future, thank you!! (Teacher) Yes! It was a really great experience for me. It was challenging but supportive. It had knowledgeable facilitators who had a growth mindset. It gave participants opportunities to practice group work, which is hard! (Teacher) Finally, in keeping with our overall goals for the Workshop, both teachers and students reported that participation helped them to reframe how they think about cells: The CCW also taught me to think of cell and cell functions in a different way since I would have never really made the analogy of a cell being similar to a robot and the cell functions being like a coded program. (Student) I felt that this workshop has drastically changed my perspectives on cell biology. I used to think that cell biology was difficult and dry to teach because it involves things that are so microscopic, we can’t see and its actions, while immensely important, don’t connect directly to something tangible and important to me in my life. With this program curriculum, I was able to see how I could get students (and myself) to really appreciated the beauty of cellular function and how these tiny microscopic things can perform such complex tasks. Programming a robot to do what a cell does gave me such respect and amazement and awe for how complex a cell really is. (Teacher) Plans for Summer 2018: The 2nd Cellular Construction Workshop will take place in June 2018 and plans for the summer well underway. Acceptance letters to both students and teachers were recently sent out to 24 participants (teachers and students) representing 13 high schools from around the Bay Area. The 2018 Workshop will be informed by our experiences in 2017 and feedback from participants in that first session. Among the changes being incorporated this year are:
- including alumni from the program to serve as TA’s. This will provide an important leadership experience for the student alumni and will help solidify their knowledge. The alumnus teacher will bring his experience integrating the workshop into his teaching and will lead the breakout sessions with current teachers where they work on curriculum plans for integrating workshop modules into their year. - Identifying local “experts” in the model organisms used in the course who can lead the laboratory sessions with those organisms. This will expose students to additional scientist role models while they engage in a concrete experience. As part of these sessions, the guest scientists will discuss their path to science. We have collaborations with scientists working on Physarum and Hydra currently on the calendar. 69 - Extensive revision to the bacterial transformation module to make more concrete the relationship of this “procedure” to Cellular Engineering. As part of the lesson, participants will explore how you can use cellular engineering to develop biosensors.
Maker Faires and Science Festivals Another core component of our External Education Activities is outreach to the public through Maker Faire and Science Festival events. In this reporting period, The Center for Cellular Construction will host activities at two Maker Faire and Science Festival Events, both in the San Francisco Bay Area. Maker Faire and Science Festival presentations are an opportunity to: 1) communicate the "Big Ideas" of the Center and recent research developments with science interested public audiences, 2) provide opportunities for Center trainees to improve their communication skills, and 3) in discussing the work of the Center with the public, hear from lay people about their perceptions of the Center's work, learn any questions or concerns they may have about engineering cells, and even gather ideas for additional problems that Cellular Engineering may be able to contribute solutions to. The Bay Area Maker Faire (May 19-21) is the largest and oldest Maker Faire in the country. Held at the San Mateo County Event Center, more than 125,000 people from around the world attend the event each year. We anticipate interactions with close to 2,000 people over the course of the weekend. In 2018, the CCC booth will feature a Stentor learning rig (Marshall lab), innovative microscopes (IBM), and robots modeling Stentor behavior (SEP). These exhibits each highlight different areas of the Center’s work – helping attendees understand that studying “simple” single celled organisms can provide profound insights into our understanding of cellular biology and complex behaviors, showcasing innovations in microscopy that are both powering research advances and making visualizing cells more accessible, and developing attendees’ understanding of cells as dynamic and programmable units of life that are capable of complex behaviors. At the Maker Faire, Center PI Wallace Marshall will once again present a public lecture on Extreme Cell Biology. This talk will highlight the remarkable things that a living cell can do, including hunt prey, walk, see, and solve puzzles. The audience is drawn from attendees of the Maker Faire, and hence includes individuals who may lack formal science training but are interested in science and technology. We anticipate an audience size of approximately 50. The lecture is built around pictures and videos, and emphasizes open questions and mysteries. The concluding slides of this lecture focus on the idea of the cell as a machine that can be engineered, and introduce the concept of our center. The Bay Area Science Festival culminates each year with a Discovery Day event where AT&T Park (the baseball stadium that is home to the San Francisco Giants) is transformed into a free interactive science extravaganza. With exhibits from more than 125 universities, government agencies, non- profits, K-12 schools, companies, and science museums, the more than 50,000 attendees have ample opportunities to explore different STEM domains and interact with scientific professionals from these various organizations. The CCC will host a booth on the field during the event on November 3, 2018. Like the Maker Faire, this provides an important opportunity to engage the public in the work of the Center. The Discovery Day, is a free event, and evaluation has demonstrated that the demographics of the attendees match those of the Bay Area fairly closely. Thus this event provides us a great opportunity to meet, share, learn from and inspire our nearest neighbors with the work of the Center.
70 We will pilot evaluation strategies for these types of events at the Maker Faire and refine and revise these strategies at the Bay Area Science Festival in November. Our current evaluation plans involve three strategies: 1) capturing participants’ questions, ideas, and concerns about Cellular Engineering on a “graffiti wall,” 2) using a modified Secret Shopper protocol piloted in the NSF AISL EvalFest project to observe participant interactions with CCC members staffing the booth, and 3) interviewing CCC members about their experiences explaining their work in this setting.
“Life in a Drop of Water” – Microscope Hack-a-thon – April 21,2018 While our Hack-a-thon activities were originally envisioned in the grant proposal as a way to engage computer science professionals with the big data challenges inherent in Center projects such as Cell CAD (Project 2) and Cell State Inference Engine (Project 3), we realized that these events could also be used to engage a more general audience and provide opportunities for them to learn and get excited about cells and engineering. Given that Projects 2 and 3 are not yet in a large scale data collection phase, this seemed a good opportunity to host a hack-a-thon that invited participants to explore the diversity of microscopic life and learn how to build simple yet powerful microscopy tools to explore the world around them. The Hack-a-thon was co-organized by Tom Zimmerman (IBM) and Jessica Allen (UCSF SEP) and was held at the Counter Culture Labs – a biohacking space in a diverse neighborhood in central Oakland, CA. Participants for the hack-a-thon were recruited widely and 33 attendees participated in the day-long event. The participants formed a diverse group – we had undergraduates studying engineering from UC Berkeley and Stanford, as well as a group of Cosmetology students from a local community college who were encouraged to attend by their Health and Safety class instructor, attendees were as young as ten and also included retirees. In advance of the event, the Hack-a-thon’s website (hackccc.org) provided information about the microscopes, tools, and resources available at the events and get ideas for possible projects. Goals for the event included introducing individuals with Computer Science backgrounds to some of the biological questions that require CS skills to solve; increasing access to learning about cells by sharing innovative, powerful, low cost microscope solutions developed at the Center that enable members of the public to explore, learn, and discover. This activity sought to connect the technology development of the Center with the creative and intellectual power of the community to envision new applications and solutions that can use these microscope technologies, and creative ways to share the technologies with the general public. Over the course of the day, participants built microscopes, investigated a wide variety of plankton, wrote python code to track organisms, learned how solder, and used Foldscopes to visualize and investigate questions relevant to their own lives. Social media activity around the event further extended its reach, with more than 5,000 impressions on twitter from the SEP account alone.
71 Evaluation data collected from the event is still being analyzed. Responses to items probing the quality of the event and participants’ experiences were uniformly positive. Attendees appreciated the chance to learn about simple microscope solutions that worked, to see their children engaged in (successfully) building their own microscopes from component parts, discovering the variety of plankton, learning from others, and sharing their accomplishments at the final presentations. Participants made constructive suggestions for future workshops including: offering workshops/ breakout groups so attendees could learn skills such as soldering to aid their microscope building and suggestions for additional materials to be made available to increase the range of projects that could be completed.
Cell Fair – Exploratorium The Exploratorium hosted a Cell Fair featuring Center Labs. At the Fair, Center Labs brought demonstrations that highlight the work of the Center to share with Exploratorium staff. The goals of this Fair were to: - Advance the Exploratorium’s staff and other informal science professional’s understanding of cell biology and cellular engineering, as well as exposure to the tools, data, and people who do this research. - Provide opportunities for Center faculty and students to practice giving demonstrations and talks to a non-specialist audience. A secondary goal was to spread knowledge of the Center and its work beyond the Cells to Self project to the many other departments at the Exploratorium (these include the Global Studios Division, that creates exhibits for museums around the world). Note that this activity is also central to the Exploratorium’s creation of new exhibits as it provided the museum staff an opportunity to see well developed demonstrationss from eight Center groups. Outputs: A day-long event with eight booths from different Center groups hosting demonstrations for 200 museum professionals (most with limited science background). The Fair was also highlighted on the Exploratorium’s social media accounts. Outcomes: More CCC reach within and beyond the Exploratorium. Impacts: Increased awareness of CCC within the Exploratorium, new audiences for the Center’s work.
UCSF Day – World Conference of Science Journalists As one of the hosts of the 2017 World Confefence of Science Journalists, UCSF hosted an open house on October 23,2017 to highlight some of the innovative research taking place there. Two Center laboratories presented their research using a interactive booth format (the Lim lab and the Marshall lab) to attending science journalists. The Marshall Lab booth emphasized the rich behaviors that cells engage in, and the potential value of viewing the cell as a robot or computer that could be engineered to solve real world problems. The Lim lab used kilotbots to demonstrate how cells can communicate with and be influenced by neighboring cells while also presenting some of the problems that advances in Cellular Engineering will help solve. In addition, Center faculty Shawn Douglas hosted a tour of 72 his lab during which time visitors could conduct experiments in a virtual reality setting. Global Foldscope Workshops Center Faculty member Manu Prakash (Stanford) and his lab continued their international effort to introduce the general public, teachers, and students, globally to frugal science – inexpensive yet powerful scientific tools – that make the microscopic world visible. These workshops introduce the research and technological innovations of the Center to a worldwide audience. Events included: 1. Jim Cybulski (PrakashLab alumni and PrakashLab visitor) and Manu Prakash ran a series of Foldscope workshops starting with the President of India palace (focus on science education in India). The series of workshops lasted more than 20 days - with roughly 30 workshops across India including Mumbai, Delhi, Goa and many parts of rural India including Madurai and Velour regions in south India. Several thousand school kids and undergraduate students were trained in microscopy (building foldscope and using the instruments to document biodiversity, ecological measurements and cellular scale environmental indicators). Many of these can be found at http://microcosmos.foldscope.com 2. Rebecca Konte (staff in PrakashLab) from Prakash Lab was present at NSTA 2019 (National Science Teachers Association) for three days and trained and ran Foldscope workshops for more than 30 science teachers across the country. 3. Manu Prakash and Clarice Aiello (Postdoc in PrakashLab) taught a Foldscope workshop at San Quentin prison. Roughly 10 prison inmates participated in 3 hour workshop where they learned how to build microscopes and make observations of the microscopic world - including seeing cells for the first time. This is a part of a ongoing project where we are teaching the power of observing the natural world as a means to teach principles of physical sciences. The prisoners have access to the Foldscope at all times (like checking out a book) and have continued the work. Follow up workshops are planned. 4. With ASSET program, Rebecca Konte (Prakash Lab) and Laks Iyer (NIH) will be teaching a Foldscope workshop for science teachers in the Cornell area. We will be using a ciliate (Tetrahymena) as a principle system for teaching multiple aspects of cellular sentinels and also explore sub-cellular imaging that all participating teachers will be able to take to classrooms. Not only the foldscope, but also mutant and wild strains of several tetrahymena species will be provided for the program. The first version of this workshop was offered in 2017. https://tetrahymenaasset.vet.cornell.edu/2017/01/images-from-the- foldscope-workshop/ 5. Informal and formal Foldscope workshops are held around the world by volunteers. It is difficult to track all the workshops run by volunteers - and some of them are documented in social media or our community.
BIOMOD Competition The CCC grant has also supported Center faculty Shawn Douglas’ efforts to organize the BIOMOD Competition. The annual competition invites 25 teams of up to 8 undergraduate students to compete. In 2017, 200 students participated in BIOMOD. Students work with a faculty mentor (and optionally a graduate or postdoc mentor) to gain hands-on research experience working on a novel project that they conceive and execute with guidance from their mentors. The competition emphasizes skills relevant to both intellectual merit and broader impacts: students complete a project website detailing their research, and also produce a 3-minute YouTube video explaining their project in plain English, and fun, innovative storytelling is encouraged. Finally, in the fall, Dr. Douglas organizes and hosts the Jamboree – a symposium where all teams gather in person to present their work. Faculty judges score teams according to published criteria, and the top ranking teams win awards. The competition was founded by Dr. Douglas in 2011 while a postdoc at Harvard University, where it occurred for the first five years. In the past 2 years (2016 and 2017) the competition has been relocated to UCSF. As part of the Jamboree, BIOMOD participants were able to visit the UCSF campus, tour the Douglas lab. Center faculty were invited to attend the Jamboree and interact with students. Members of the Douglas lab attended and helped as conference volunteers and judges 73 Additional External Education Activities Center faculty, affiliates, and trainees also engage in a large number of external education activities that they organize and lead on their own initiative. These activities fall into several categories: presentations to technology professionals, presentations to undergraduates (with an emphasis on underreepresented minority students), presentations to K-12 students and teachers. Details about the activities to each of these groups will be presented, in brief, below.
Presentations to Technology Professionals Activity Name: Scifoo Camp presentation on Extreme Cell Biology Led By: Wallace Marshall Location: Sci Foo Camp, Google Headquarters, Mountain View CA Intended technology professionals and futurists Audience: Approx # of 50 Attendees: Narrative: Presented a lecture highlighting the remarkable things that a living cell can do, including hunt prey, walk, see, and solve puzzles. The audience is drawn from attendees of Sci Foo Camp, an invitation-only event that brings together Silicon Valley technology professionals along with writers, artists, and futurists, to discuss new areas of science and technology and their impact on the future of society. Connection to This lecture was meant to convey the idea that a cell is a machine that can be Center engineered, which is the core concept of our center. Research Outreach to Graduate Students from Other Institutions Activity Name: Presentation at ESADE group Led By: Simone Bianco Location: IBM Research – Almaden Intended Graduate students Audience: Approx # of 60 Attendees: Narrative: Present general idea of CCC to 60 graduate students and faculty from ESADE school of business (EU students, Spanish institution). Connection to Education of non-scientific audience to general principles of cellular engineering Center Research Outreach to Undergraduates Activity Name: Outreach Visit to the MARC LSAMP Student Group at CSU San Jose Led By: Wallace Marshall Location: CSU San Jose Intended URM undergraduate biology and engineering students Audience: Approx # of 20 Attendees: Narrative: Presented a lecture on cell behavior and computation, including discussion of graduate opportunities presented by our STC. Connection to Talk was based on the key center concept of the cell as an intelligent machine that could Center be programmed or engineered. Research
74 Activity Name: Promoting Inclusivity in Cell Biology – A Series of Talks at Local Univerisities Led By: Fred Santana & Sam Goodfellow Location(s): Holy Names University, City College of San Francisco, Skyline College Intended Undergraduates Audience: Approx # of 80 Attendees: Narrative: This series of research talks was presented to undergraduates at local institutions serving significant numbers of minority students. They were aimed at building interest in science careers generally and cell biology specificially. Connection to The talks are closely aligned to the Center goal of establishing Cellular Engineering as Center an inclusive discipline. Research
Activity Name: SACNAS outreach Led By: Sam Goodfellow, Fred Santana, and Edward Elizarraras Location: SFSU Intended Undergraduate and Master’s students Audience: Approx # of 150 Attendees: Narrative: Workshops for students at the SFSU SACNAS Chapter: - Writing a Statement of Purpose, - Foldscope Demo, - Application Kickback (to finalize PhD applications), - Student Training Programs Open House, - and Pi Day. Pi Day was a huge success and milestone as it was designed to promote the inclusion of students from diverse backgrounds in our research labs. - Game Night – while a social event, it is designed to help connect undergraduates from backgrounds underrepresented in science with research opportunities in SFSU labs. Connection to These workshops by Center students are closely aligned to the Center goal of Center establishing Cellular Engineering as an inclusive discipline. Research
Outreach to K-12 Teachers and Students Activity Name: Letters to the Future of Science Led By: Fred Santana Location: St Patrick’s Elementary – San Jose, CA Intended Elementary School Students Audience: Approx # of 30 Attendees: Narrative: The purpose is to reach out to underpriviledged youth and expand their minds on how they view science. These sessions also show the diversity in science with the goal of helping students see themselves in science by connecting with someone that may be just like them. Connection to This series is closely aligned to the Center goal of establishing Cellular Engineering as Center an inclusive discipline. Research 75
Activity Name: Science Night Led By: Fred Santana Location: Beresford Elementary School – San Mateo, CA Intended Elementary School Students Audience: Approx # of 150-200 Attendees: Narrative: An evening of science activities for the students to see how fun and exciting science can be. Created 10 different science-based activities that were led by various students from the SACNAS at SFSU chapter. Roughly 150-200 K-12 students and parents attended. The event went so well that the school would like us to recreate the event next year. Connection to This series is closely aligned to the Center goal of establishing Cellular Engineering as Center an inclusive discipline. Research
Activity Name: IBM Girl’s Summer Camp Led By: Tom Zimmerman Location: IBM Research – Almaden Intended Middle school Audience: Approx # of 22 Attendees: Narrative: IBM Girl’s Summer Camp (San Jose, CA). Hands-on workshop for 22 middle school girls building lensless microscopes. 19 June 2017 Connection to This workshop introduces girls both to some of the innovative microscope technologies Center developed by a Center faculty member and encourages them to explore the world Research around them and learn about cells.
Activity Name: IBM Boys Summer Camp Led By: Tom Zimmerman Location: IBM Research – Almaden Intended Middle school Audience: Approx # of 22 Attendees: Narrative: IBM Boys Summer Camp (San Jose, CA). Hands-on workshop for 22 middle school boys building lensless microscopes.
Connection to This workshop introduces boys both to some of the innovative microscope technologies Center developed by a Center faculty member and encourages them to explore the world Research around them and learn about cells.
Activity Name: Lab Demonstrations Led By: Fred Santana Location: SFSU Intended K thru twelve through community college students Audience: 76 Approx # of 50 Attendees: Narrative: At least 5 different laboratory visit events where Fred and various other biology students conduct lab tours and explain our work. Students varied in from elementary school to community college students. Connection to This series is closely aligned to the Center goal of establishing Cellular Engineering as Center an inclusive discipline. Research
2d. Integration of research and education The original proposal for the Center for Cellular Construction envisioned a Center where research and education was tightly interwoven. We continue to be very cognizant of this goal and have added additional depth to this integration in Year 2 of our education activities. Internal Education Activities In Year 2 of the Center award, Center faculty have developed and/or taught courses that integrate Center research and help trainees develop the knowledge skills and habits of mind of Cellular Engineers. These include courses at SF State and Stanford for undergraduate and Master’s students. These courses, described more fully in our response to question 2c above, integrate microscopy technology developed in Center labs and train students in cutting edge visual analysis methods. Students in the courses courses utilize technologies developed by Simone Bianco’s and Tom Zimmerman’s groups at IBM and by Manu Prakash at Stanford. An additional course at SF State in computational modeling prepares students to understand, analyze, and develop mathematical models of cellular processes – these types of models will be critical to advancing Cellular Engineering and are a core component of the work across all of the Center’s project areas. Finally, Diana Chu’s course on Scientific Communication trains Center students to effectively communicate their both their Center-related research specifically and more generally the “big ideas” of the Center to non-expert audiences.
UCSF faculty continued to develop and offer mini-courses as a way to rapidly prototype new course pedagogies and instructional topics that further the training of Center students. The mini-course format provides an intensive learning experience for students – courses meet daily for three weeks – and typically are small with no more than 25 students and often include more than one faculty member. This format encourages all participants (students and faculty alike) to engage deeply in the subject matter, grapple deeply with ideas through discussions, and learn new laboratory techniques or research skills in a supportive environment. A common feature of these minicourses is time devoted to reading and discussion of current papers directly related to the work of the Center. This second year of funding provided an opportunity for Center PI Wallace Marshall and faculty member Jennifer Fung to refine the design of the Cellular Robotics course based on their experiences in the first year. Center PI Wallace Marshall together with new faculty affiliate Sy Redding launched a new course this year – Computation by Cells – that focused on how cells solve complex problems. In addition, Center PI Wendell Lim and faculty member Hana El-Samad launched a third new course that focused on cellular modularity – and understanding how cellular engineers can harness this modularity to solve engineering problems – a core idea of the Center. This course drew heavily on current research from both the Lim and El-Samad labs.
External Education Activities Center research was also thoroughly integrated into our External Education Activities. While many of these activities seek to build awareness of Cellular Engineering at a foundational level – specifically to increase understanding of the cell as dynamic and complex, a self-contained unit that processes information and engages in a wide range of behaviors – strong connections between the research teams and the leads on the education activities ensures that Center research informs our activities. Below are a few examples of how these connections manifest themselves in our external education activities.
77 Center researchers (faculty and trainees) have been actively engaged in the development and review of exhibits for the Exploratorium’s new Cells to Self installation. This manifests itself in several ways. Center faculty present talks at the Exploratorium, to the exhibit team, to share their research and brainstorm exhibit ideas together. Faculty are also invited to the Exploratorium to preview exhibit prototypes and provide feedback as new the exhibit development process progresses. In addition, there Center researchers have the opportunity to provide “real” data and/or specimens that are used in exhibits. In addition, the Exploratorium hosts three Center trainees a year as interns. While at the Exploratorium, the Intern works closely with exhibit developers providing insights into the Center’s research, ideas for exhibits and demonstrations – facilitated experiences hosted on the floor of the museum – that convey the big ideas of the Center to museum attendees. Lastly the Cell Fair brought Center representatives from across the Center to the Exploratorium to share their research, demonstrations they developed to convey that research, and exhibit ideas with staff from across the Exploratorium. The Cellular Construction Workshop also integrated Center research in a variety of ways. In addition to participants learning about Cellular Engineering more generally and program robots to model cellular behaviors, Center faculty and trainees from both UCSF and SF State were regular guests during the workshop, speaking about their research. This guest speakers were tremendously popular with the Workshop participants. In each of these sessions, the speaker would talk both about their research and their path into a career in science – helping the assembled high school students realized that there are a wide variety of trajectories that can result in fulfilling science careers. Speakers included PI’s Wendell Lim and Wallace Marshall, trainees Athena Lin, Greyson Lewis, Nat Handel, Jasmine Sims, Devan Shah, Rodolfo Villa, and Austin Murchison. In addition, participants toured Center PI Zev Gartner’s laboratory and learned about the Center research conducted there. Center research is also integrated into all our other External Education Activities. Center members at Maker Faires and Science Festival events talk about their work with members of the lay public while engaging them in demonstrations and hands-on activities that highlight core ideas of the Center. Visits to schools K-12 through undergraduate focused on increasing diversity in science with partnerships with groups like SACNAS and highlighted both the exciting research of the Center while introducing students to scientists from backgrounds similar to their own so that the next generation of Cellular Engineers could see themselves in this field.
2e. Describe how the Center is doing with respect to the indicators/metrics listed above. Include any data that have been collected on the indicators/metrics. Overall we have made significant progress towards the milestones described in the Center’s Strategic Planning document, with all year one milestones on target for this year. Data excerpted from our external evaluation reports was integrated into our narrative description in section 2c to help convey a more complete picture of each activity.
2f. Plans for internal and external educational activities for the next reporting period with attention to any major changes in direction or level of activity. Our plans remain consistent with those outlined in the Strategic Plan. While we have discussed some of our plans for the coming year above, a few highlights will be described, below. Prototypes of the Cells to Self Phase 2 exhibits will be piloted by the end of the second year of this grant award. This prototyping process will inform the full development of these exhibits that will take place during year three of the award. Phase 2 exhibits will highlight the work of the Center and in particular will focus on ideas of cell assembly into larger structures, and cell-cell communication. In the third year of the project, the Cellular Construction Workshop, will also begin to focus more on the idea of self-assembly. We will begin to develop lesson modules that focus on this core idea of the Center more explicitly and in this process work with Center labs to identify current research developments that can be modeled, either in the robots or through engaging and accessible hands-on activities that build participants understanding of the complexities of this process.
78 We will continue to share our work at Science Festivals and Maker Faires in the Bay Area and beyond. The Rogue Valley Mini Maker Faire, reported on in Year 1 is not continuing, so we will need to find an alternative Faire or Festival that allows us to reach similar groups – rural, lower-income populations. There is also interest in attending an additional Science Festival such as the Philadelphia Science Festival that has done an extraordinary job of reaching students from urban underrepresented minority groups. Center faculty will continue to develop and refine courses to prepare Center trainees for careers in Cellular Engineering while also introducing other students to the exciting research opportunities in the Center. These courses will prepare students to function at the cross-disciplinary interface that is the focus of the Center’s work and will also ensure they have the knowledge and skills to approach research questions and engineering problems across multiple scales – from the molecular to single cells to multi-cellular assemblies (tissues, organisms, and hybrid bioreactors). Lastly, we will encourage all Center members to engage in Outreach about the Center not limited to Center-organized initiatives. The excitement and initiative of our individual members helps us to share the work of the Center much more broadly than our Center-wide initiatives can do alone.
References Van den Hoven J, Lokhorst GH, Van de Poel I. 2012. Engineering and the problem of moral overload. Sci. Eng. Ethics 18, 143-155.
79 IV. KNOWLEDGE TRANSFER
1a. Overall goals/objective - changes
Our goals for knowledge transfer are (A) to catalyze the transfer of center-developed ideas and results into the real world, so as to have a positive impact on the economy and society, and (B) to gain insights into methods, ideas, and approaches that could be useful for achieving our other center goals by drawing on expertise of partner institutions and companies. With regards to the second goal, we strongly believe that by involving potential knowledge transfer partners early in the development of our center, they can help us direct our research activities towards problems that are of actual relevance in industry, and also to help us train our students in a way that will prepare them to employ cellular engineering approaches in an industrial setting.
1b. Performance & management indicators Our Strategic Plan lists several concrete metrics for knowledge transfer progress. During this first year, our primary effort has been to launch the center and start developing the knowledge that will ultimately be transferred, however we have already been able to make progress towards our knowledge transfer goals, in line with our overall strategy of trying to involve industrial partners in center activities not only as recipients of knowledge but also as sources of advice and ideas. performance indicator: File invention disclosures reflecting center-developed knowledge rationale: invention disclosures provide a direct way to track how many center ideas can at least in principle be commercializable, and also provide both a starting point for pursuing IP protection and a potential pathway to attract industrial partners for more extensive knowledge transfer activities. goal: 2-5 disclosures written per year status: We have written 6 invention disclosures during first two years, as detailed in Center Wide Outputs Section. performance indicator: Disseminate information about center activities to potential industrial partners rationale: Before we can establish knowledge transfer relationships with companies, the companies need to be aware of what the Center is doing. By tracking the number of dialogues we establish with potential industrial partners, we can get an idea of our progress towards the early stages of setting up knowledge transfer interactions. goal: Establish dialogues with 3-5 companies per year status: During the past year, Center investigators from IBM and UCSF have presented non confidential work produced and inspired by CCC research to the following external interested parties: - Agilent - Oregon Health and Science University - Evolva (now progressing to CDA) 80 - Dubai Frontier Foundation - The Government of Lombardia, Italy - Nagase (CDA) - Merck - Google - Calico performance indicator: Establish active collaborations with industrial partners. rationale: Once we have established dialogs with partners, the next step is to move to actual partnership. One approach is through licensing, but another is through direct scientific collaboration. The number of industrial collaborations provides an easily quantified metric for our progress in establishing meaningful interactions with the industrial world. goal: To have three active collaborations in place by year 5 status: As an outcome of our efforts to disseminate information to industry (see above) we have, during the past two years, established a total of four active collaborations with industrial partners, as well as an educational collaboration with a startup founded by a center faculty member. We have therefore completed this milestone ahead of schedule. The specific collaborations are as follows:
(1) We have established a non-confidential collaboration with Zymergen, Inc. to help us learn how to analyze cellular organelle structure in industrial strains of Aspergillus. Through a series of meetings and student visits, two CCC researchers have been trained in Aspergillus methods and have begun working on a project using publically accessible strains but guided by ideas from both Zymergen and the CCC.
(2) We have also established a confidential collaboration with Nagase, Inc. to analyze cell and colony structure of an industrial strain of streptomyces.
(3) We have established a collaboration with DynamicLand (Oakland, CA) to implement their Realtalk computing platform within the CCC, and to customize the platform for use in the framework of molecular biology laboratory workflow.
(4) During this past year, we formalized a partnership with Serotiny, a San Francisco based startup that specializes in computational solutions for synthetic biology, thus providing a key element of the CellCAD project. The founder, Dr. Jason Farlow is a former UCSF graduate student who participated in several of the Entrepreneurship courses supported by the NSF STC that include Start-up 101, Start-up in a Box and the QB3 SBIR Grant writing course. He also attended many of the Entrepreneurship Center lectures and in November, 2017 presented to his work to this community on how Serotiny started and its business model. Serotiny maintains a database of molecular “parts” along with formal descriptions of interactions between these parts and algorithms to design multi-part constructs in a combinatorial manner. Seroniny’s partnership with our center gives us access to Serotiny’s computational tools, thus supporting our own CellCAD and Machine Shop projects and low cost access to Serotiny’s gene synthesis contracting service, which has already supported development of molecular tools for the Living Bioreactor project. At the same time, the partnership also gives Serotiny access to our growing collection of molecular components and markers, helping them to grow their database while
81 helping us to disseminate our results into the industrial sector. A statement of work and formal partnership is currently being negotiated and should be completed this summer.
(5) CCC co-director Wendell Lim founded the company Cellular Design Labs that uses the concepts of cellular engineering to create synthetic cells for immunotherapy applications. In December 2017, the company was acquired by Gilead Sciences. This is an exceptional example of how a company focusing on basic principles of cellular engineering can have a rapid impact at the academia-industry interface to benefit both. UCSF mentors including CCC faculty played a key advisory role, as did the QB3 incubator, local UCSF associated venture capitalists (particularly Brook Byers), and Mission Bay Capital a University based seed venture firm. The ecosystem for entrepreneurship that is supported by the CCC was essential. performance indicator: Center trainees entering industrial workforce. rationale: Since our goal is to help grow a new area of engineering, one measure of success is whether our trainees are in fact able to make use of the center-acquired skill base to take scientific leadership positions in industry. goal: 10 center trainees will have entered the industrial workforce at the level of research scientist or above by year 5 status: 4 center students have been hired as interns at IBM, giving them their first experience of working in an industrial setting. 1 center trainee, Jacob Kimmel, (Ph.D. April 2018) has been hired as a Computational Biologist at Calico Labs, South San Francisco, CA. performance indicator: CCC web site is the top ranked Google search result for term “cellular engineering” rationale: One of the goals of the center is to increase awareness of the cell as an engineering medium, and we intend to use our center web site as one mode of spreading awareness. By tracking the search ranking of our center web site we can determine how well our center is being viewed as driving this field. goal: To have our web site be the top search result for this search term status: Currently our web site, which is still in a temporary form, is not highly listed. However, if combined with the terms UCSF, IBM, or Exploratorium, it does appear in the first page of Google search results. We are currently in the process of a major upgrade to a new, professionally designed web site that will incorporate clean graphic design, carefully planned user experience, search engine optimization, and content development including new computer animations developed by Dr. Janet Iwasa (OneMicron Inc), a world leader in computer animation of cell and molecular biology.
1c. Problems. No significant problems have yet been encountered.
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Cellular sentinels for ocean water Led by Wallace Marshall Organizations Involved (add rows as necessary) Name Address 1 SCCWRP (Southern California Coastal Santa Barbara, CA Water Research Project)
Narrative: The Center has established a collaboration with Dr. Nina Bednarsek of SCCWRP to use cell structure for ocean water monitoring. One of the key goals of research project 5 – Cell State Inference Engine, is using the organelle-scale morphology of cells as an indicator of conditions in the external environment. Although our original proposal envisioned using unicellular organisms, such as pond ciliates, as the key sentinel species, our collaboration with Dr. Bednarsek will involve applying the same tools to monitor ocean water conditions (acidity in particular) by analyzing organelle morphology in planktonic marine invertebrate embryos, which are ideal for this purpose because they are transparent, making imaging of organelles feasible. These embryos are of a similar size scale as the giant ciliates currently being used the Cell State Inference Engine, hence we can adapt identical imaging and analysis tools. This collaborative project thus represents an approach for transferring knowledge obtained in research goal 5 – Cell State Inference Engine, into a real world application.
Quantifying organelle structure in industrial strains of Streptomyces Led by Simone Bianco Organizations Involved (add rows as necessary) Name Address 1 Nagase Inc Tokyo, JP
Narrative: The Bianco lab at IBM has established a confidential collaboration with Nagase, Inc. on studying the relationship between the structure of streptomyces cells and colonies. The aim is to use artificial intelligence algorithms developed at IBM to infer growth conditions related to useful industrial products, and understand potential morphological modifications which may be related to increased or decreased production. The collaboration is at the level of a pilot at the moment, with the possibility of establishing a contract.
Use of a lensless microscope for the detection of impurities in lake waters Led by Simone Bianco Organizations Involved (add rows as necessary) Name Address 1 Israel Water Works Association Israel
Narrative: The Bianco lab at IBM has established a potential collaboration with the Israel Water Works Association. The aim of the collaboration is to use plankton morphology as a potential source of information of water quality. This ties directly into our Cellular Sentinel project. The collaboration is at the preliminary level and no confidential collaboration has been exchanged.
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Survey of deep sea plankton Led by Simone Bianco Organizations Involved (add rows as necessary) Name Address 1 Monterey Bay Aquarium Research Institute Moss Landing, CA Narrative: The Bianco lab at IBM has started a collaboration with Thom Maughan at the Monterey Bay Aquarium Research Institute to develop a lensless microscope for both surface and deep sea plankton survey. We are working on an ultra-low power version of the lensless microscope we have invented which may be equipped on a surface glider, as well as a deep water instrument. Using an unsupervised classification method and a newly designed machine learning algorithm, we plan to help MBARI uncover new species of deep water plankton. The collaboration is non-confidential, and no confidential information is expected to be exchanged.
Survey of deep sea plankton Led by Simone Bianco Organizations Involved (add rows as necessary) Name Address 1 Fabian Cousteau Ocean Learning Center Rhode Island Narrative: Similarly to the previous opportunity, the Bianco lab at IBM has started a collaboration with Fabian Cousteau, CEO of the FC Ocean Learning Center to develop a lensless microscope for deep sea plankton survey on the new underwater learning center being built by the organization. The collaboration is non-confidential, and no confidential information is expected to be exchanged.
End-to-end monitoring system for sea water Led by Simone Bianco Organizations Involved (add rows as necessary) Name Address 1 University of Genova, Italy Genova, Italy Narrative: The Bianco lab at IBM has started a collaboration with the groups of Massimo Maresca and Pierpaolo Baglietto at the University of Genova. Drs. Maresca and Baglietto have designed a cloud based system to help the Italian Government to monitor the water quality of the Italian National Parks of Cinque Terre and Portofino. The collaboration aims at augmenting the existing platform with an AI powered monitoring system based on the IBM lensless microscope, to classify plankton and use its shape and behavior as an indicator of water quality. The collaboration is in its initial stage. The collaboration is non-confidential, and no confidential information is expected to be exchanged.
2b. Outcomes/impacts of the activities Our knowledge transfer work has already had a galvanizing effect on center participants. Many students have become excited about opportunities to work with local companies, possibly as interns, and other students have already begun thinking about ways to translate some of the scientific directions in the center into startups or other commercial activities. So far we have really just created the groundwork for future knowledge transfer, but we feel we have gotten off to a strong start based on our metrics listed in part 1. One CCC student, Rebecca McGillivary, is 85 co-author of a disclosure with IBM’s Tom Zimmerman and Simone Bianco, and UCSF’s Wallace Marshall.
2c. Plans for next period We will continue with our existing knowledge transfer approaches and contacts. Our center Strategic Plan currently specifies that we will begin launching companies during the third year of the center, once enough scientific progress has been accomplished that new IP can be created. During the past funding year, we have extensively researched how best to catalyze the transfer of center knowledge and ideas into the startup space, and as a result of this intensive discussion we are formulating a revised plan that will place greater emphasis on seeding early stage of develop within center labs, so as to better leverage the existing infrastructure, and then only moving to the startup stage as needs dictate when ideas have reached a more mature stage of development and reduction to practice. CCC Knowledge Transfer Coordinator Charles Craik, together with center leadership, has held a series of meetings with experts including our two CCC startup advisors on our EAC, Dan Widmaier and Kinkead Reiling, as well as Cathy Tralau-Stewart, the Associate Director of the Catalyst Program and Director of CTSI T1 Translational Research. All of these discussions led to the conclusion that our knowledge transfer budget could have a larger impact if we placed greater emphasis on developing technological innovations within center labs rather than immediately launching startups with the attendant costs and IP issues.
Most recently, Charles Craik met with Barry Selick, the recently hired Vice Chancellor of Innovation and Partnerships at UCSF, to discuss the knowledge transfer aspects of the Center and to explore the possibility of having key experiments for company creation carried out in UC laboratories to ensure efficient use of the funds. He was very supportive of the idea and is researching the possibility and ramifications of this scenario. By the start of the next funding period, we intend to have consolidated these various sources of advice and input into a concrete plan for seeding commercializable research projects in center labs, which we will then implement by recruiting the appropriate advisors and working out the relevant intellectual property policies.
In parallel to the seeding approach, we will continue pitching our work and ideas to external companies, with the aim to transfer the technology produced by the Center, either through licensing or as part of joint development contracts. These routes are expected to produce revenues for the companies and jobs for the biotech workforce, which will help define the professional figure of a “Cellular Engineer”.
86 in Computational Cellular Mechanics in the Department of Biomedical Engineering, University of Melbourne, Australia. Narrative: The center has established a collaboration with Dr. Rajagopal, whose research focuses on computational models to predict biochemical function of organelles based on their 3D structure. This link between organelle structure and output is a key element of two of our key research projects: Project 2 – CellCAD and Project 4 – Living Bioreactor. Thus far the collaboration has involved a face to face meeting with Wallace Marshall and Dr. Rajagopal, followed up by two conference calls.
Activity: Microscopy for a global community Organization/people involved: Manu Prakash (CCC), Foldoscope.com
Narrative: In the first year, using Foldscopes, the Prakash group has introduced microscopy to a community of >50,000 participants spread across 130 countries. Participants have discovered undefined microscopic species, developed environmental and ecological monitoring programs and used these tools to diagnose diseases in remote settings. The work by the community is documented in a creative commons platform at http://microcosmos.foldscope.com
Activity: Deploying high-throughput flow-through microscopy for oceanic plankton monitoring Organization/people involved: Manu Prakash (CCC), Plankton-Planet, Tara Expedition
Narrative: The Prakash group has recently demonstrated a low cost ($100), high-throughput imaging platform for flow-through microscopy in the field. This instrument and other related microscopes developed in our lab (malariascope, Foldscope) allow us to provide powerful automated and manual microscopy capability in field conditions. This capability will allow for teams developing “reporter cells” to be probed in ecological conditions and data coming from these instruments analyzed in field conditions to provide a live monitoring platform at ecological scale. We deployed our first flow-through microscope in Antarctica on a sailboat (Yvinec). The data is coming from this sailboat via a satellite link. The goal this year is to deploy 30 microscopes around the world. Ensuring low cost of manufacturing will be a major goal moving forward; with a target price of $100 per instrument. Connectivity in deep regions of the ocean is limited; so sailors might need to send data once they arrive at a port. This work is in collaboration with “Plankton-Planet” (https://plankton-planet.org) team from France and US and the Tara expedition (https://oceans.taraexpeditions.org).
Activity: Implementing RealTalk within the CCC Organization/people involved: Shawn Douglas (CCC), Bret Victor (DynamicLand)
Narrative: We are collaborating with a research team led by Bret Victor, who is pioneering a new computing platform, Realtalk, that allows code or data to be associated with any object in the room. A network of webcams, projectors, and servers in the ceiling operate seamlessly to track objects, execute object code, and display text, graphics, audio, or video. We are upgrading the Douglas Lab at UCSF with Realtalk and begin to re-envision wet-lab research augmented by 88 this system. With Realtalk, any container, tool, or instrument will be able to display information about itself, anywhere in the laboratory or office space. In the future, a researcher might place two tubes next to each other to see a simulation of what would happen if the contents were mixed. Tubes placed near instruments will display how the sample would be analyzed or transformed. Realtalk-augmented protocols will provide rich step-by-step feedback across multiple length scales. We expect the system will lower barriers to communication, collaboration, and training to greatly accelerate discovery in biological research. We have installed an instance of Realtalk in the Douglas Lab at UCSF, and have begun working with Dynamicland (Oakland, CA) to import existing Python code into the system.
2b. Other outcomes/impacts Visiting Lecturers: As part of the Cellular Robotics minicourse run by center faculty at UCSF during the past two years, we have invited three visiting lecturers who presented lectures to the course students followed by a seminar for the center as a whole. By inviting lecturers whose area of research was relevant to the course and to the center, we feel this is a further way to help integrate the educational and research activities of the center. The lecturers were: visitors were: Year 1: Ingmar Riedel-Kruse, Stanford University Educational relevance: building liquid handling systems with LEGO mindstorms Research relevance: games based on protist behavior, exhibit at Exploratorium
Year 1: Andras Csirok, University of Kansas Medical Center Educational relevance: using LEGO as a scaffold for building circuits Research relevance: self-organization at multiple scales (relevant to Project 3 Cellular Lego)
Year 2: Jordan Pollack, Brandeis University Educational relevance: evolutionary robotics and LEGO based structures Research relevance: computational simulation and evolution as a design strategy (relevant to Project 2: CellCAD)
2c. Progress Because our approach is to set up external partnerships that relate to our strategic goals, our tracking of progress will focus on the overall strategic goals of the center and not specifically on the external partnerships, which are viewed as part of existing goals.
2d. Plans for partnership activities We plan to continue our existing partnerships, while continuing to explore new potential partnerships. We plan to ask the project leads for research and education to identify areas in which external partnerships might prove useful, and in such cases, we will make an effort to identify and reach out to potential individuals or groups.
See Center-Wide Outputs Section for supplemental table re: partnerships.
89 VI. DIVERSITY
1a. Overall goals for increasing diversity at the Center
Our goals for increasing diversity and broadening participation are structured to achieve the following four strategic outcomes:
1. The Center for Cellular Construction is a model for creating a diverse STEM workforce that is emulated by other institutions.
2. Advancement and retention of students, postdocs, and faculty towards STEM careers has been realized at all levels of participation, from K-12 to faculty.
3. Postdoctoral training has become a key element in promoting diversity and broadening participation.
4. Infrastructure and partnerships between SFSU and other CCC institutions increase opportunities for diverse faculty to succeed in their research.
1b. Performance and Management Indicators
As detailed in our Strategic Plan, we have formulated several criteria as indicators of progress in our efforts to broaden participation.
Metric: 90% Percentage of center URM Masters students entering the STEM workforce Progress years 1 & 2: Of the 14 center MS students (86% URM) graduating during the first 2 funding years, 9 are now enrolled in Ph.D. programs, five are employed in Biomedically related positions (Visiting Scholar at UCSF, Research Associate at UCSF, Intern at Genentech, Program Coordinator in SFSU NIH BUILD program and Research Associate at SFSU, see Table 2.c.). Thus, 100% meet the stated goal, showing that we have been exceeding our target for this key metric.
Metric: All center participants have been trained in best practices for mentoring diverse populations and apply this training to all center activities. Progress years 1 & 2: At our 1st annual retreat in August 2017, Carmen Domingo and Blake Riggs developed a 2-hour interactive workshop in which all attendees participated actively (including the entire center leadership team as well as faculty, staff, students, and postdocs). We will repeat and expand the mentoring training based on the National Research Mentoring Network (NRMN) training program for all Center participants including those newly added to the Center in 2018. The workshop is scheduled to take place during the second day of our annual retreat on July 17 & 18, 2018.
Metric: Proportion of URM postdoctoral fellows increases at least 10% over non-center labs Progress year 1: During the first year we hired two new postdocs within the center, one of whom is an URM, thus putting us at 50% URM for new postdoc hires. We intend to use future postdoc hires as a way to broaden participation at the level of postdoctoral training, which we
90 have identified as the career stage at which participation in our center is currently the least diverse. Progress year 2: During the second year, as more labs ramped up their research activities, additional postdocs were hired, and several postdocs already working in center labs began to work on center projects and receive center funding. There are now 14 center postdocs, of whom 3 are URM. This represents 21% URM among our postdocs. For comparison, a recent analysis of diversity among postdoctoral fellows (Meyers et al., 2018 Life Science Education https://doi.org/10.1371/journal.pone.0190606), based on data from the NSF Survey of Doctorate Recipients, estimates that approximately 11% of postdocs who earned Ph.D. degrees in the U.S. are URM. We are thus doing well in comparison to this nation-wide average. Nevertheless, we recognize that postdoctoral diversity is a key area in which we need to improve further, especially given its importance in eventually addressing diversity at the faculty level nationwide. Our focus going forward is to ensure diversity in additional new hires as they occur. Plans for doing so are discussed in section 2d below.
Metric: 50% increase in publications, presentations, and grants by diverse SFSU faculty Progress: As detailed in the Centerwide Outputs section of this report, we have seen an exponential increase in the number of publications and presentations from SFSU faculty and students, with almost all of this increase involving authorship and presentation by URM students. We believe these numbers strongly confirm our concept of making SFSU a bona fide research partner in the center, rather than simply a pipeline for a small number of students to work at other institutions.
Publications: Year 1 One publication from SFSU faculty. Year 2 Eleven publications from SFSU faculty published or submitted. Seven of these were co- authored by URM undergraduate or masters students. The number of publications showed a greater than 10-fold increase over the first two years of funding, greatly exceeding our initial goal of a 50% increase for this metric.
Presentations at National Meetings (oral and poster) Year 1. 8 presentations by SFSU faculty or students at national meetings Year 2. 23 presentations by SFSU faculty or students at national meetings Note that these numbers do not include an additional large number of presentations held at local and state-wide conferences. Even considering just national meetings, the number of presentations has increased by almost 300%; thus, we have greatly exceeded our target goal for this metric.
Grants Submitted Year 1: 0 Year 2: 1 NSF MRI: Acquisition of a Super-Resolution Confocal Microscope to Advance Research and Research Training Opportunities at San Francisco State University PI Blake Riggs (Chu?) Center faculty Laura Burrus, Mark Chan, Diana Chu, Wilfred Denetclaw, Carmen Domingo served as co-PIs on the grant, and support letters were provided by other center faculty including Wallace Marshall.
91 Although no new grants have yet been awarded based on center work, at least we do see an increase between the first two years. As more publications are generated, these will serve to seed new grant applications in future years.
1c. Problems Encountered
At the graduate level, we need to do a better job of recruiting URM PhD students who join graduate programs at participating institutions into Center labs. This will require a concerted effort to increase the visibility of the center among incoming students, which we will accomplish by taking a major role in the graduate recruiting and admissions processes, so that students are aware of the center and its faculty before they even begin their graduate work.
At the postdoctoral level, we face a different problem, namely that any given center faculty member typically only is contacted by a small number of potential postdoc applicants in any given year, and with such small numbers it can easily happen that none of the applicants are URM students. We believe we can solve this problem by pooling our applicants by hosting center-wide postdoc interviews. Our idea is that when a URM candidate applies to do postdoctoral training in any center lab, they are invited out to interview with the whole center, being given a list of center faculty and asked to consider interviewing with any others that might be of interest. Interview costs will be paid by the center. In this way, the total number of URM postdoctoral candidates exposed to each faculty member is greatly increased, increasing the likelihood of identifying a good fit between candidate and mentor.
2a. Center activities contributing to human resource development in science and engineering in the U.S. – postdoctoral, graduate, undergraduate, and pre-college levels
Activity: Partnership with NSF INCLUDES “SF CALL” Narrative: Center faculty at SFSU have been instrumental in setting up the SFSU NSF INCLUDES “SF CALL”, which focuses on developing computer literacy in the San Francisco Unified School District (SFUSD) will attract large numbers of URM students to SFSU. Students entering SFSU from the SFUSD as freshmen will be targeted to the Promoting INclusivity in Computing (PINC) program focused on women and minorities to participate in a 5-course sequence for computing in the life sciences. The overall goal of the proposed activities is to increase the number of women that gain training in the field of computer science. We have designed a series of courses and structured mentoring activities that will lower the barriers that women experience in entering the computing science discipline. Specifically, we have designed a program for biology majors which consists of 15 units of computer science course work that will allow the students to earn a minor with “Emphasis in Computer Science”. The program consists of five courses of 3 units each. The first three courses (CS 306, 307, and 220) will expose students to basic computing topics such as web design, mobile app development, data structures, and algorithms. More importantly, from the very beginning, the core concepts and tools will be applied to biological problems thus, providing the students an opportunity to connect what they are learning in biology with their new skill sets in computer science. To hone their skills, the last two courses will consist of a group project on a biology related research topic (CSc 690 Special Topics). Here, students will be able to apply their new CS skills to a particular Biology topic of 92 their interest. This four-semester program will provide a strong foundation in computer science that will broaden the career paths of its participants. The PINC program was officially designated as a minor in 2018 and the first class of 21 was graduated in May 2018. Two participants in the PINC program were selected as summer interns at IBM in summer 2018. One PINC participant (Nicole Rodrigues) has been working in the Marshall lab at UCSF to expand her computational and cell biological skills prior to applying to Ph.D programs in the fall.
Activity: SACNAS recruiting Narrative: Frank Bayliss attended the national SACNAS conference Salt Lake City on October 18-21, 2017, which focuses on supporting underserved students in STEM and has a long history of preparing students culturally as well as scientifically and brings large number of prospective students together. Dr. Bayliss worked at the UCSF booth to promote the NSF STC CCC opportunities for student training and visited posters to meet students and encourage them to apply to graduate programs related to center interests at UCSF and SFSU.
Activity: ABRCMS recruiting Narrative: Dr. Bayliss also attended and recruited at the national ABRCMS meeting in Phoenix, AZ in November 2-4, 2017 and similarly worked from the UCSF booth to recruit students and inform faculty from a large number of institutions with significant URM enrollments of the opportunity for their students to apply to SFSU or UCSF for advanced STEM training.
Activity: Mentoring center undergraduate and MS students at meetings Narrative: Dr. Riggs, who is a member of the ASCB Minority Affairs Committee, attended the ASCB meeting December 4-6, 2017 to supervise current SFSU CCC students presenting and applying for admission into PhD programs. He also promoted the CCC to several groups and to faculty at other institutions with significant URM enrollments.
Activity: Faculty visits to URM student groups at other academic institutions Narrative: Dr. Bayliss visited Arizona State University on April 16, 2018 to present a formal presentation to faculty and students on successful approaches to recruiting and training URM students in STEM. These activities have strengthened the partnership between ASU and SFSU/UCSF and will likely result in increased application and admission of students from ASU. Additional visits to URM undergraduate student groups were conducted by other center faculty as follows. These presentations included a research talk on CCC-related research, followed by a talk and discussion about graduate programs and the SRTP summer undergraduate program at UCSF Fall 2016 ( 4 total visits Wallace Marshall CSU Fresno, 10/7/16 Jennifer Fung UC Riverside 10/18/16 Zev Gartner UC Davis MARC student group 10/20/16 Charlie Craik CSU Los Angeles 10/21/16
Fall 2017 ( 2 total visits) 93 Wallace Marshall San Jose State University MARC and LSAMP student groups 11/17/17 Hana El-Samad UC Santa Barbara 11/18/17
Acitivity: Dr. Bayliss and Elizabeth Silva from the UCSF Graduate Division attended and met with BS and MS students at a round table at the California State University Program for Education and Research in Biotechnology (CSUPERB) at the Annual Meeting in Santa Clara, CA on January 6, 2018. Students were informed about graduate school opportunities available at SFSU and UCSF and the Center for Cellular Construction was highlighted.
Activity: Frank Bayliss met with the 30 high school students and teachers participating in the Center Cellular Construction Workshop at UCSF on August 4, 2017 to celebrate their successful completion of the workshop. Dr. Bayliss presented information on opportunities available at SFSU and UCSF to study BioEngineering.
Activity: City College of San Francisco Student Intern Biosymposium Narrative: City College of San Francisco (CCSF) has a highly diverse student body and has developed an innovative internship program for placing their students in research labs related to the biotechnology industry, which is capped by an annual symposium with presentations by the students. After a planning meeting with the director of this program, Dr. Karen Leung, center director Wallace Marshall participated in the annual CCSF intern biosymposium as a poster judge, giving him the chance to interact directly with a large number of students in the program, inform them of the Center, and encourage them to apply to graduate programs at participating institutions.
Activity: City College of San Francisco and Skyline College: Narrative: Students (~25) in the NIH Bridge to the Baccalaureate Program met with Dr. Bayliss at SFSU on June 6, 2017 to discuss Biomedical Research Careers and the opportunity to conduct research in laboratories at SFSU and UCSF while enrolled as BS students.
Activity: Implement a procedure for tracking and reporting diversity of participation Narrative: All participants have been identified along with demographic information (Table VIII.5.) and have been recorded in the CCC Tracking database. By linking this information to all individual center activities, we can now track diversity of participation in all activity areas, which will allow for identification of activity areas that might require additional work in this area.
Activity: Partnership with UCSF SRTP, URI, and SFSU to increase diversity of summer undergraduates Narrative: Although UCSF is a medical school, it does have a robust undergraduate summer research program known as SRTP (Science Research Training Partnership) which attracts students from around the country. An additional undergraduate program known as URI (Undergraduate Research Internship) is run through the department of OB/Gyn at UCSF and has 94 a similarly strong track record of URM participation. Center Director Wallace Marshall is one of two members of the SRTP Diversity committee, in which capacity he personally reads all applications from URM students without any prior triages based on arbitrary criteria such as grades. This puts him in a position to identify students whose interests and experience make them a good fit for the summer program, and then to advocate for them in the program admissions process. He has also strongly encouraged center faculty at UCSF to mentor SRTP summer students. During the past two funding years, center faculty at UCSF have hosted 5 students from the SRTP and URI programs, two of whom were URM. In the long term we hope that by continuing in this direction we will increase the number of URM students who apply to graduate programs at UCSF relevant to the Center, putting us in a stronger position to recruit them into center labs once they join the programs. At SFSU, there are 5 pre-existing summer research training programs for URM students each summer, NIH MARC, NIH RISE, NIH Bridge, NIH BUILD and NSF REU that collectively support in excess 60 students (approximately 30 of whom do their research in CCC labs each summer). All participants conduct research 32+ hours/week, participate in the Doctoral Preparation and GRE workshops 4 hours each/week and present an oral and poster summary of their research at the end of the summer (all 5 groups together). All students are made aware of the CCC and opportunities for them to participate. Four SFSU undergraduates who participated in the SFSU summer programs (MARC) have been admitted into UCSF PhD programs in 2017 and 2018.
Activity: Strengthen research infrastructure and partnerships for diverse faculty at SFSU Narrative: The highly diverse faculty of SFSU have, historically, faced challenges caused by reduced infrastructure support compared to the other institutions in the center. Our Center aims to correct this imbalance by opening access to all core facilities and resources at UCSF to all center faculty at SFSU, which we have done by budgeting core funds specifically for this purpose and negotiating access policies. Thanks to center-led negotiations, SFSU center faculty and their students now have full access to the entire range of core facilities that center faculty from UCSF have. At the same time, UCSF students have been granted access to the SFSU microscopy facility, further promoting collaboration between the two campuses. In addition, seven active collaborations have been established between one or more SFSU faculty and one or more faculty at other institutions, including UCSF, Stanford, and IBM Almaden Research Center.
Activity: CCC faculty participation in SFSU undergraduate student research presentations Narrative: To further support the connection between SFSU and the other center institutions, we are initiating an annual tradition of center faculty from outside SFSU taking part in the spring SFSU College of Science and Engineering Student Project Showcase, by serving as poster judges. This year, Wallace Marshall served as a poster judge at the May 2018 showcase, giving him a chance to meet many SFSU undergraduate and masters students and learn about their research, putting him in a stronger position to act as an advocate for these students when they apply to graduate programs at UCSF.
Activity: Expand the successful model developed between SFSU and UCSF for 95 partnerships between R1 institutions and Minority Serving Institutions to other members of the Center for Cellular Constructions. Narrative: Based on a discussion initiated between Frank Bayliss and Dan Fletcher during the CCC annual retreat in summer 2017, Dr. Bayliss was invited to present a seminar to the UC Berkeley Department of Bioengineering on October 23, 2017. The seminar “Enhancing the Recruitment, Training and Diversity of STEM Students” was successful and one of the current SFSU URM MS students has been accepted into the UCB/UCSF joint PhD program in Bioengineering to start fall 2018.
2b. Impact of these activities on enhancing diversity at the Center
The most immediate impact of our center’s diversity activities has been the establishment of a highly diverse graduate student body at the Masters level, many of whom have already graduated and progressed now to Ph.D. training. We have hired two URM MS graduates as Research Associates in the Lim and Marshall labs in 2017 and this summer a new entering SFSU URM MS student will conduct her MS thesis research in the Lim Lab at UCSF. Because of the success at this specific level, we are focusing most of our additional activities at earlier and later career stages, especially at the undergraduate to graduate transition and at the postdoc recruiting level.
2c. Progress with respect to the indicators/metrics listed above
With respect to the indicators listed above, we have met two of our specified goals. We exceeded our goal of having 90% of URM Masters students continue in the STEM workforce, and we have met our goal of having the entire center membership in attendance at the retreat take part in diversity mentorship training. We have also, thus far, met our goal of having at least a 10% greater proportion of URM postdocs compared to non-center labs (under the assumption that non-center labs are following the national average), and we will be paying careful attention to ensure that this trend continues with future postdoc hires. The metric of increased publications and grants by SFSU faculty as a result of center-mediated access to core research facilities has been achieved in the second year *see section 1b above).
Year 1 We made progress on our more general goal of increasing representation during the first year of the center. Of the eight SFSU faculty in the CCC, 50% are from groups under-represented in STEM and 75% are ethnic minorities. Of CCC postdocs, 20% were URM and 60% are ethnic minorities. These numbers included postdocs who were already working in center labs and who subsequently began working on center projects. If we only consider postdocs who were hired after the center became funded, 50% are URM. Of the 25 CCC MS students supported as participants by the CCC in the first year, 68% were URM and 88% ethnic minorities. Of the 38 undergraduates trained in CCC labs in the first year, 60.5% were URM and 73.6% were ethnic minorities. The seven SFSU Research Investigators sponsored 70 students for training in their labs. The totals for all participants (faculty, MS and BS students), 62% are URM and 78.9% are ethnic minorities (Table VIII.5.). With respect to gender diversity, 36.8% of center faculty, 40% of center postdocs, and 36% of center graduate students are female. Considering these numbers, our biggest deficit is clearly in the realm of postdocs, the only category in which our level of 96 URM participation did not meet or exceed national averages in the first year.
Year 2 Of the eight SFSU faculty in the CCC, 50% are from groups under-represented in STEM and 75% are ethnic minorities. 21% of center postdocs (3 out of 14), 35% of graduate students (Ph.D. and M.S., 28 out of 79), and 71% of center undergraduates (27 out of 38) were URM.
Table 2c. CCC MS Graduates to PhD & Continuing MS Students Yrs Name Eth/Race Mentor MS Post Master's 1&2 1 Gaytan, Norma HA Riggs C&MB PhD Baylor U - 2017 2 Jimenez, Monet HA Chu C&MB PhD U Washington - 2017 3 Lowe, Troy SEA Esquerra Biochem PhD UC Los Angeles - 2017 4 Monroy, Marco HA Chu C&MB PhD UT Southwestern - 2017 5 Ollison, Gerid AA Riggs C&MB PhD U So. California - 2017 6 Gutierrez, Joshua HA Esquerra Biochem PhD New York Univ. - 2017 7 Christopher Pineda HA Domingo C&MB PhD U Michigan - 2018 8 Cecelia Brown AA Riggs C&MB PhD Stanford U - 2018 9 Sam Goodfellow W Burrus C&MB PhD U New Mexico - 2018 10 Lopez-Pazmino, P HA Domingo C&MB Research Associate UCSF - 2017 11 Jacques, Torey AA Riggs C&MB Coord. SFSU NIH BUILD - 2017 12 Elizarraras, Edward HA Burrus C&MB Visiting Scholar UCSF - 2018 13 Lopez, Alejandro HA Esquerra C&MB Research Genentech - 2018 14 Chadwick, Will W Chan C&MB Research Associate SFSU - 2018 15 Corpuz, Crizsel PI Chu C&MB Current Second Year MS 16 Shah, Devan A Denetclaw C&MB Current Second Year MS 17 Sims, Jasmine AA M Chan C&MB Current Second Year MS 18 Murchison, Austin AA Esquerra C&MB Current Second Year MS 19 Gehr, James A Chu C&MB Current Second Year MS 20 Bolivar-McPeek, HA Riggs C&MB Current Second Year MS 21 Hopp, Kellen W Domingo C&MB Current Second Year MS 22 Lanns, Destinee AA Burrus C&MB Current Second Year MS 23 Black, Chris W Chu C&MB Current Second Year MS 24 Garcia, Vivian HA W. Lim C&MB Current Second Year MS 25 Meisnner, Brett W Chu C&MB Current Second Year MS 26 Swinson, Wayne AA Chu C&MB Current Second Year MS 27 Law, Ashley W Esquerra Biochem Current Second Year MS 28 Najibia, Sayeeda A Esquerra Biochem Current Second Year MS 29 Santana, Frederick HA Burrus C&MB Current Second Year MS 30 Lopez, Alejandro HA Esquerra C&MB Current Second Year MS 31 Edington, Alia AA Riggs C&MB Current Second Year MS 32 Ortega, Jose HA Riggs C&MB Current Second Year MS CCC New MS Graduate Students 2018 Yr 2 Name Eth/Race Mentor MS 33 Chang, Catherine A Esquerra Biochem Current First Year MS 34 Refuerzo, Russell PI Esquerra Biochem Current First Year MS 35 Kalbaugh, Erin NA Esquerra Biochem Current First Year MS 36 Pereira, Ashley HA Denetclaw C&MB Current First Year MS 37 Mendoza, Omar HA Denetclaw C&MB Current First Year MS 38 Huang, Wesley A Chu C&MB Current First Year MS 39 Villegas-Parra, A HA Chu C&MB Current First Year MS 40 Kseniya, Konova W Chu C&MB Current First Year MS 41 Kinney, Christian W Chu C&MB Current First Year MS 97 42 Esin, Jeremy W Chan C&MB Current First Year MS 43 Buenafe, Marick PI Esquerra C&MB Current First Year MS 44 Coombes, Coohleen PI Domingo C&MB Current First Year MS 45 Rodrigues, Nicole A Riggs C&MB Current First Year MS 46 Sun, Steven SEA Roy C&MB Current First Year MS 47 Chemel, Angeline SEA Chan C&MB Current First Year MS 48 Piaz, Jesus HA Chu C&MB Current First Year MS 49 Martin, Adrian SEA Denetclaw C&MB Current First Year MS 50 Azanedo, Gabriela HA Chan C&MB Current First Year MS Funded by CCC
CCC BS Graduates to PhD Yr 1&2 Name Eth/Race Mentor BS Post Bachelor's 1 Gabriel Fraley AA/NA Burrus C&MB PhD UC Davis - 2017 2 Talia Hart HA Domingo C&MB PhD Harvard U- 2017 3 Dana Kennedy HA Esquerra Biochem PhD UC San Francisco - 2017 4 Ulises Diaz HA Riggs C&MB PhD UC San Francisco - 2017 5 Campit, Scott PI Esquerra Biochem University of Michigan -2017 6 Garcia, Jason HA Domingo C&MB PhD UC San Francisco - 2018 7 Campos, Jean Luke PI Chan C&MB PhD UC San Francisco - 2018
2d. Plans to enhance diversity for the next reporting period
Activity: Facilitating participation of underrepresented students at an earlier stage Narrative: SFSU, in partnership with SEP and the CCC, submitted a proposal to the NIH NIBIB ESTEEMED PAR-17-221 to support a summer bridge before freshmen matriculation focused on math and chemistry preparation as well as workshops on transitioning to college and then a Freshmen and Sophomore Honors program to prepare URM STEM majors for research careers in science. Under this proposal, these students would receive significant personal funding ($1,000/month) for the first 2-years and then enter one of our 3 NIH funded upper-division Honors programs (NIH MARC, NIH RISE and NIH BUILD). The SF ESTEEMED program was envisioned to work closely with the SEP HIP and CCC programs that support 55 high school rising seniors to conduct summer research at UCSF. The proposal stipulates that Professors Bayliss and Marshall would meet with these students each summer to stimulate and encourage them to apply for the 12 SF ESTEEMED summer bridge and freshmen/sophomore year program positions. Drs. Esquerra and Bayliss are the NIH MARC Honors program directors and Drs. Domingo and Bayliss are the NIH RISE Honors program directors, thus ensuring the SF ESTEEMED students entering upper-division would continue to receive comparable financial and academic support in preparation to enter high quality PhD programs and science careers. These training activities were intended to have a direct impact on the CCC because all the SF ESTEEMED participants would conduct summer research in CCC labs after the sophomore year and would continue in the same labs during their junior and senior years. This proposal was not funded, but we are continuing to look for alternative funding sources to implement this program in the future.
Activity: Increasing diversity of center students at undergraduate and graduate levels Narrative: We will work closely with undergraduate and graduate admissions at SFSU and
98 graduate admissions at UCSF to identify and admit strong applicants. SFSU faculty trained in mentoring a diverse population provided a workshop for all CCC faculty, students, post-docs and staff at our annual Retreat in summer 2017 and will do so again at the upcoming 2018 annual retreat. Center director Wallace Marshall is a member of the UCSF Tetrad Graduate Program Diversity Committee as well of the iPQB Graduate Program Diversity Committee. Tetrad is the main molecular biology graduate program, while iPQB (Integrated Program in Quantitative Biology) is the primary program for computational biology, bioinformatics, and biophysics. In this capacity he personally reads all applications from URM students, discusses the applications during the overall admissions committee meetings, and thus has the opportunity to directly influence both the Tetrad and iPQB graduate programs to carefully consider a larger pool of diverse applicants. Center co-directors Gartner and Lim, as well as faculty members Fung, El- Samad, Weiner, and Dumont, are members of the admissions committees for either Tetrad or iPQB where they are thus able to support the same goal of admitting a more diverse student body. Gartner is Co-Chair of the joint UCB/UCSF Bioengineering PhD program. All center faculty will be expected to participate in annual fall retreats for these two programs, where they will meet with the incoming students each year, tell them about the center, and encourage them to perform rotations in center labs. This will enable the center to recruit URM students from among the incoming student body. The link between CCC labs at SFSU and UCSF has already resulted in an increase in URM Ph.D. students at UCSF. So far, 2 SFSU URM BS students entered UCSF PhD programs in 2017, one of whom (Ulises Diaz) has joined a CCC lab (Wallace Marshall). Another 2 SFSU URM BS students were admitted into UCSF PhD programs in 2018 and will start in the fall. In addition, 3 SFSU MS students entered PhD programs at UCSF and one SFSU URM MS student is performing her MS thesis research in a CCC lab at UCSF (Wendell Lim).
Activity: Leverage IRACDA program to increase postdoctoral diversity
Narrative: Plans are in process for the center to engage more fully with the joint UCSF-SFSU IRACDA program http://iracda.ucsf.edu/ucsf-sfsu-mentors to broaden diversity in the postdoctoral community of the center and to further the professional development for those from varying backgrounds.
The UCSF IRACDA program provides financial support and mentoring for postdocs from under- represented groups in science, as well as professional development and training for teaching. IRACDA scholars in turn mentor and teach SFSU undergraduates, masters and graduate students and provide outreach through SFSU’s NIH BUILD, RISE, MARC, Bridges, and SRTP program to underrepresented groups in the community.
Raymond Esquerra, one of our center SFSU faculty members, is Co-Director of the IRACDA program. He is also Director of SFSU’s NIH-funded MARC Program and serves on the Advisory Committees for SFSU’s RISE and Bridges programs, two programs that aim to increase diversity in the pipeline in biomedical sciences. He has created on-line teaching modules for UCSF postdoctoral researchers to develop their teaching skills and has mentored an SFSU-UCSF postdoctoral scholar, Benjamin Sandler, who is currently an Associate Professor at Ashford University. These experiences make him the ideal liaison between the center and the IRACDA program, and put the center in a strong position to leverage the strength of this program in promoting diversity at the postdoctoral level. Center faculty Laura Burrus, Diana
99 Chu, Wilfred Denetclaw, Carmen Domingo and Blake Riggs are all teaching mentors for the IRACDA program at SFSU.
During year 2,we held a series of discussions with Ray Esquerra and Holly Ingraham (UCSF), the IRACDA Program Directors, to steer IRACDA Scholar applicants to consider center faculty laboratories for their postdoctoral work and visit and interview with center faculty.
Progress: This year was the planning period for this activity and we developed an implementable plan of action for the upcoming funding cycle. The UCSF-SFSU IRACDA program is a highly effective program for providing excellent training for academic careers to its fellows, but also, very importantly, plays a major role in diversifying the postdoctoral population at UCSF. The UCSF CCC seeks to interface with the UCSF-SFSU IRACDA program to 1) coordinate recruitment efforts to assure a diverse pool of CCC postdoctoral fellows, 2) work with the IRACDA program to design an “IRACDA-like” program specifically for the needs of CCC fellows, and 3) coordinate efforts on integrating CCC research and focus into new and exciting courses at SFSU.
Recruitment efforts will be focused on direct-marketing methods (SACNAS, ABRCMS, discipline specific meetings, webpage, Facebook, etc.). In addition, more active personalized recruitment will be used: reaching out to the extensive network of SFSU alumni, connections resulting from URM pipeline training success, and the UCSF-SFSU IRACDA program. The UCSF-IRACDA program will send candidate information of candidates not selected for IRACDA to the CCC for possible placement. The IRACDA program and CCC will refer interested candidates to apply to the IRACDA or a CCC lab. The CCC will invite URM postdoc applicants to any center lab to interview with multiple center labs to increase likelihood of being part of the center.
To help assure that the CCC is an environment that nurtures success in all its postdoctoral fellows, all center postdocs, regardless of their own minority status, are trained in broadening participation issues. This training will be part of the annual retreat and part of other UCSF Training Opportunities (SEP).
The figure below shows the design for the CCC postdoctoral “IRACDA-like” training. Unlike the IRACDA this program has two-paths, the academic and industrial. During the next year the CCC postdocs will join the IRACDA fellows in the teaching workshops, with the longer-term goal of implementing a workshop specifically for CCC post-doctoral fellows the following year. The academic component is modeled after the IRACDA directly, whereas the industrial pathway implements some best-practices learned from the IRACDA program.
The CCC-postdoc teaching experience and professional development activities are designed not to impact research productivity following UCSF-SFSU IRACDA program model. Although the CCC-fellows will be involved thru all aspects of the course, they will only teach ~25% of the course under a mentorship of experienced SFSU faculty.
In the Spring of 2019, IRACDA postdoctoral fellow, Anum Glasgow (teaching mentor: Dr. Ray Esquerra) will develop a new course entitled the “Principles of Cellular Engineering.” In addition, Dr. Ray Esquerra and Dr. Tom Zimmerman (IBM) will develop an undergraduate microscopy and imaging course. In the future, we expect CCC fellows to develop teaching skills by evolving and improving on these courses. 100
101 VII. Management
1a. Organizational Strategy During the first two years of this grant the two major areas of emphasis in our management development work has been to put into place a management and leadership structure capable of supporting all center programs and of integrating the six participating institutions into a cohesive unit working together on projects that no individual group could do separately. Regarding the second goal, we have allocated resources among the participants and institutes according to our original plan with each participating group allocated a fixed quantity of funds, with further funds set aside for shared core resources, educational activities, and knowledge transfer activities.
Our organizational strategy involves several layers of management and interaction. The three Directors, Wallace Marshall, Zev Gartner, and Wendell Lim, share overall decision making, with Dr. Marshall acting as overall Director. Dr. Lim plays a special role as leadership mentor for Drs. Marshall and Gartner, drawing on his experience in running other large centers grants. The Directors interact with the Management Team (see below). Each of the five core research projects has an appointed Project Lead responsible for organizing collaborations around each project (Project 1) Cellular Machine Shop – Wendell Lim; Project 2) CellCAD –Hana El-Samad & Simone Bianco; Project 3) Cellular Lego – Zev Gartner; Project 4) Living Bioreactor – Mark Chan and Sindy Tang; Project 5) Cell State Inference Engine/Cellular Sentinel – Jennifer Fung and Simone Bianco). Additional faculty members serve as Research Coordinator (Zev Gartner), Diversity Coordinator (Frank Bayliss), Knowledge Transfer Coordinator (Charles Craik), Education Coordinator (Rebecca Smith), and Data Management Coordinator (Jennifer Fung). Although management is centered at UCSF, each member institution is represented by an Institutional Coordinator (Diana Chu – SFSU; Sindy Tang – Stanford; Dan Fletcher – UC Berkeley; Simone Bianco – IBM; Jennifer Frazier – Exploratorium). For directing decision making center-wide, we have established a faculty Steering Committee, described in detail below.
Our plan for maintaining organization started with our Strategic Plan, in which we assigned one, and in some cases two, center faculty to oversee progress towards each specific milestone. These individuals report on progress to the leadership team, who then review center-wide progress on a quarterly basis. The leadership team works with the Management Team (see below) to implement center operations in accord with the strategic plan. Feedback concerning plans and activities is provided by the external advisory committee (see below) as well as a professional evaluator hired specifically to provide formative evaluations of center activities (see below). In the past year, we have assembled a faculty Steering Committee (see below) to take over some of the administrative burden by handling routine decision-making tasks that had been handled entirely by the Leadership and Management teams up to that point.
1b. Management Team The first step in building a management team, carried out in year 1, was to put in place a professional administrative team dedicated to coordination of center activities. During this time we hired Debra Singer as Center Manager to coordinate administration of center activities. Ms. Singer is one of the most experienced project managers at UCSF, with over two decades of
102 experience in project management, consulting, and coordinating large multi-PI grants. Three examples of her previous project management experience are as follows:
1) Consortium and Financial Manager for Advanced Light Source Beamline 5.01, a $5 million research instrument at the ALS located at Lawrence Berkeley National Laboratory, administered through UCSF. In this capacity, she was responsible for managing finances and fundraising, helping to build contract structure for Beamline access, drafting and implementing access agreements between UCSF and industry, and structuring beamline access to share time/ expenses with private industry and other academic institutions, while keeping enough shifts for UCSF researchers' needs. This experience in balancing the needs of academia and industry is of tremendous value to the management of the CCC.
2) Project manager for NIH P01 Program Project Grant (Structure and Dynamics of nuclear receptors: R. Fletterick PI. 08/15/00 - 7/31/05), a 6-lab collaborative project based at UCSF. Her participation in this project started with grant writing coordination and organizing the pre- award site visit, then continuing post-award with post-award budget distribution and management, reporting, PI meeting organization, and budget reallocations.
3) Project Manager for NIH U01GM094614 (Structures of Protein Complexes that Regulate Transcription in Embryonic Stem Cells , R. Fletterick, PI. 9/30/10 – 6/30/15). For that project, she managed individual lab budgets, spending and personnel allocation on main project, 2 subcontracts and supplemental related projects, which included revising budgets each fund year based on spending and needs of the various projects. She was also responsible for progress reports, organizing participant meetings, and overseeing large expenditures.
During the first year of our Center, Ms. Singer managed budgetary processes, meeting and event planning, website design and development and plays a significant role in center communications, communicating with the federal agency as well as overseeing myriad administrative tasks. She coordinated our successful grant submission as well as both the pre-award and first year Site Visits, as well as the budgetary risk assessment as part of NSF’s pre-award review process. She is thus highly familiar with all aspects of the center plans and operations. During the first year we also appointed a financial analyst, Olivia Viloria, the UCSF Biochemistry Department’s financial manager, to work with Ms. Singer on overall budget, accounting and subcontract administration. Finally, in the first year we also appointed a Center Data Specialist, Dr. Ashwini Oke, to organize data formats and storage prior to collection.
By the end of the first year, it was becoming clear that the level of administrative work required for the center demanded increased staffing, a point emphasized at the site visit in November 2017. Consequently, we have taken several steps to augment our management and administrative structure.
First, we are formalizing Debra Singer’s role as Managing Director and have rebudgeted funds for an Administrative Core to meet accelerating program activities. After careful analysis of the administrative workload, we identified communications within the center, dissemination out of the center, and arrangement of center meetings, as key areas requiring constant, but predictable, activity. We determined that if a second administrative expert could be brought on board to handle these three tasks, it would free up the Center Managing Director to take care of planning, reporting, and overall leadership activities.
103 We thus hired a MarCom (Marketing and Communications) administrator, Ms. Gigi Benson, who has joined our project after many years of experience in the private sector. She brings a high level of expertise in communications and event planning, allowing her to take over the majority of tasks surrounding center meetings and communications, under the supervision of Ms. Singer. Together, Center Managing Director Debra Singer, Center Financial Analyst Olivia Viloria, and Center MarCom Administrator Gigi Benson, form the Core Administrative Team. The Core Administrative Team meets regularly among themselves, while soliciting input from faculty as necessary. The center directors meet with the core administrative team to monitor progress, identify problems arising, and plan future activities.
We are supplementing administrative needs via support from the UCSF Biochemistry Department, Cellular & Molecular Pharmacology, and Pharmaceutical Chemistry, (our Center PI’s departments), who provide supplementary administrative assistance for large events and programs as needed. We are reviewing needs for administration of the SFSU component and plan in the fund 03 year to add funds for partial support of a program assistant at the Student Enrichment Office, directed by Center Diversity Director, Frank Bayliss.
Second, we have expanded the role of our professional evaluator. During year 1, the Center formalized a contract with Phillips & Associates, a professional evaluation firm. Michelle Phillips, has extensive experience working with NSF-funded projects including several large Center grants including the NSF’s National Center for Engineering and Technology Education (NCETE). During year 1, we started evaluation on a small scale, with Ms. Phillips focusing her evaluation on two of the Center for Cellular Construction’s education/outreach activities – the two-week boot camp for high school students and teachers and the public science events (Maker Faires and Science Festival) programs as these were both launching into full-implementation during that funding period.
The scope of the evaluation was expanded in year 2 to include evaluating more broadly the experience of trainees in the various center activities; documenting the integration of the Center’s various institutions and the value add of bringing these institutions together in the Center; and providing formative evaluation to help the Center continuously improve its culture, communication, collaboration, and education programs. Ms. Phillips has attended all center meetings, and has played a direct role in developing internal evaluation instruments in the form of online surveys for center participants, in order to identify challenges and possible ways to improve center operations and activities. She takes part in all PI-only meetings, so that she can pass along her insights to the rest of the faculty. Phillips & Associates provide their results to the Center Managing Director (Debra Singer) for use in building our annual reports.
Third, at the advice of the site visit panel, we have appointed a Faculty Steering Committee, made up of leaders spanning the center institutions and activity areas. The purpose of this committee is not only to democratize the decision making process, but also to assign decision making responsibilities to designated individuals to handle leadership tasks that had previously been handled exclusively by the center Director and Co-Directors.
In setting up this committee, the center directors met to develop a list of decision-making tasks based on experience gained during the first two years of center operations. We also discussed possible special circumstances that, if they were to arise, would benefit from a wider group of decision makers.
104 Based on these discussions we formulated a total of five decision task areas, three concerning routine decision tasks and two concerning special circumstances. Routine: Resources/IP/Data management (data sharing, resources, knowledge transfer) Meetings (quarterly meetings, annual retreat) Education and Dissemination (coherence, participation, deciding new directions)
Special circumstances: Conflict management (harassment, ethical violations, IP or personal conflicts) Participation/ personnel (sunsetting, affiliates, replacements, succession)
After providing this information to the entire center faculty, we then invited key faculty members who had already proven themselves with a high level of involvement to join the Steering Committee. Our Steering Committee consists of the following seven members:
Diana Chu (SFSU) Orion Weiner (UCSF) Shawn Douglas (UCSF) Rebecca Smith (UCSF/SEP) Jennifer Fung (UCSF) Sindy Tang (Stanford) Simone Bianco (IBM) Jennifer Frazier (Exploratorium)
The Steering Committee members were then assigned specific decision task areas of primary responsibility within the “routine” category, as follows: Resources/IP/Data management (Fung, Bianco, Douglas) Meetings (Chu, Tang) Education and Dissemination (Smith, Frazier, Weiner)
Decision tasks in the “special circumstances” category were not assigned to specific individuals; rather, if those circumstances arise the whole Steering Committee will convene as a group to discuss problems and solutions. Two specific “special circumstances,” namely succession of the leadership team and sunsetting of center faculty who are failing to participate, are currently governed by written policies that are provided to the Steering Committee, who will execute the decisions by majority vote. In all cases, the Steering Committee is tasked with formulating decisions and plans of action, and presenting those plans or decisions to the Directors for approval or modification. Committee members are empowered to consult with center members to obtain information, and then, with approval of the Directors, to work with the Core Administrative Team led by the Center Managing Director, Debra Singer, to implement decisions once approved. Finally, the Steering Committee has been tasked with alerting the Directors of any unanticipated problems within the center beyond those that might have been outlined in the list below. The Center Managing Director will work with the Steering Committee to provide administrative assistance and financial analysis as required for these tasks. For tasks involving communications or meeting arrangement, the Center MarCom Administrator will interact with the Steering Committee to plan schedules and logistics. 105
2a. Center-wide communications The cornerstone of our approach for center communications and coordination is face-to-face meetings of center participants, in which ideas can be shared and problems discussed in an open and interactive manner. We believe that especially in the early stages of a large collaborative project, face-to-face in-person meetings can build a sense of trust and cooperation that simply cannot be achieved any other way. This approach is possible for our center because of the tight geographic distribution of participating institutions in the SF Bay Area, all are in easy driving distance of each other.
Starting with the January 2017 Strategic Planning Meeting, we have begun quarterly center-wide meetings open to all center participants, including undergraduate research students. Quarterly meetings rotate among participating institutions, with transportation provided for those who cannot drive themselves. Parking permits are arranged for all attendees, and meals are provided, so that there is no cost to attending. These quarterly meetings have each had a theme that permeated the presentations – this year the winter quarterly meeting, which was timed to coincide with the 200th anniversary of the publication of the novel Frankenstein, had a theme of ethics and responsible innovation, and included a lecture from Dr. McGinn, of our Ethics Panel, as well as breakout discussion sessions focused on biocontainment and balancing risk. The year 2 Spring quarterly meeting was focused on Research and featured research talks from faculty, postdocs, and students, including undergraduate research students. Each quarterly meeting includes a one-hour faculty breakout session that provides an opportunity to discuss concerns, ideas, and future plans among all center faculty members. During year 2, these faculty breakout sessions have mostly focused on reporting requirements and discussion of how various research projects align with the major themes of the center.
The first Annual Retreat, held in year 1, was focused on mentoring diversity, and included a workshop on mentorship and implicit bias run by center faculty member Blake Riggs, in collaboration with center faculty member, Carmen Domingo, based on their NRMN training experiences. The second Annual Retreat, coming up this July, will continue this theme. We held the retreat in 2017 over two days to allow students, postdocs, faculty, staff and advisors opportunities to meet each other and make their own connections. Responses from participants about the retreat have been overwhelmingly positive, and we are thus following essentially the same format for this year’s retreat.
Ninety-five center members took part in our first annual retreat, out of 158 members for the center as a whole. This included participants from all center institutions. If we divide the number of annual meeting participants from each institution by the number of center members at that institution, we can calculate the percent of center members at each institution who took part in the annual retreat. The results are as follows: UCSF 71% SFSU 36% Stanford 90% UC Berkeley 83% IBM 100% Exploratorium 33%
Stanford, Berkeley, and IBM were thus highly represented at this event, given the number of center members at those institutions. These numbers attest to the high level of participation and 106 engagement among center members across center institutions. The relatively low participation fraction for SFSU was because a substantial number of SFSU participants were undergraduates who had either graduated or were unable to take part over the summer.
In order to coordinate research activities, the Living Bioreactor and Cell State Inference Engine/Cellular Sentinel project groups have organized a series of joint group meetings, taking place roughly every two months and rotating locations between UCSF, SFSU, Stanford, and IBM. The Jan 2018 meeting organized by Sindy Tang included Center leads, S Tang (Stanford), M Chan (SFSU), S. Bianco (IBM), J. Fung (UCSF), T. Zimmerman (IBM), and 8 students and postdocs. The March 2018 meeting was hosted at UCSF by J. Fung, and included center leads, J Fung, W Marshall, S Tang, M Chan, and 7 others from IBM, UCSF, and SFSU involved in these projects. The May 10 2018 meeting was hosted by S. Bianco at IBM, with leads S. Tang and M Chan, J Fung + 14 additional center students and postdocs. The group is planning a one-day subgroup retreat this summer to focus intensively on upcoming plans for the Living Bioreactor and Cell State Inference Engine projects during the next year. In addition to our center-wide meetings, our center has partnered with the UCSF Center for Systems and Synthetic Biology at UCSF to host a monthly research in progress talk series, which we have made open to members of all center labs. This Monday morning meeting series gives us a way to build connections beyond the labs in our center, and creates opportunities for center students and postdocs to present their work to a broader community of interested researchers. During the past year, ten members of center labs have presented their work here.
One new element in our communication strategy introduced this year was our first student- organized social evening. This brought together students from multiple campuses to informally discuss their plans and interests, but more importantly to help build a sense of group identity among student members of the center. The success of this event was such that we plan to continue holding these sessions on a quarterly basis.
Another new element established this year was a Center-wide PI meeting, held May 25, to bring all center faculty together to discuss reporting requirements and future plans for the upcoming year. This meeting augments the faculty breakout sessions at our quarterly meetings, and all of these faculty meetings will be tied together with the monthly conference call system that is now being established.
2b. Electronic Communications Systems As a supplement to our face-to-face meetings, we propose to harness technological solutions that allow day-to-day coordination of activities, access to data, and easy access to materials such as planning documents. Each of these tasks has a different technical solution.
For day-to-day coordination of activities, such as announcement of meetings and seminars, answering questions about resource availability, and so on, we employ a Slack channel dedicated to the CCC students, postdocs, and faculty. Slack gives us rapid, mobile interactivity across all center labs and activities.
107 For data sharing, we are implementing an electronic data sharing system so that center participants at all institutions can not only access each other’s data and models, but more fundamentally find out what data and models currently exist. Our system uses IBM Lab Book as intermediary between the data and computer servers that store information, and the multiple lab notebook and project tracking systems currently in use in different center labs (for example, Jupyter Notebook or Slack). In order to provide data access across institutions, we have negotiated access to the UCSF Box data sharing system, which has the technical capacity to interface with IBM Lab Book, for all center participants. This involved a full IT security risk assessment that was performed internally at UCSF and is now completed. Lab Book is now installed on UCSF servers. Full rollout of this system still awaits formal approval from UCSF IT security, whose primary concern is protecting patient records. The work of the center does not involve any patient records, so we are working to overcome this bureaucratic hurdle. At the same time, we have begun to investigate an alternative data sharing platform, Redcap, which is already operational at UCSF and therefore does not involve any additional IT security obstacles.
For access to shared materials, we are using our Center Website, which currently has a password protected sub-site with access restricted to center members. Center documents and center- specific announcements are uploaded to this site.
2c. Problems of communications Communicating with and organizing a dynamic group of people from various institutions– faculty, staff, students, postdocs – is a challenge. We are learning best methods to reach individual center faculty and post and deliver important information in a few places as the volume of email most of our team receives exponentially increases. During the two years since the founding of the center, we have recognized two dominant problem areas in communications, both of which stem from a reliance on communication via email. We have put in place new approaches designed to solve these problems.
The main communication problem has been the fact that faculty are inundated with emails, making it difficult to capture the attention of all faculty members on a routine basis. This has in some cases resulted in faculty members failing to provide information needed for reporting, or failing to understand what is expected of them in terms of aligning their work with center goals. We have learned that many emails that are sent out to all faculty go unread, lost in the general flood of emails that faculty members receive each day. In discussions with several others managing large programs, with the Research Development Director at UCSF, and with our evaluator, we have learned that this problem is endemic in academia. In effect, email as a communication tool has become too successful; indeed, managing the volume and group discussion is challenging in many organizations. We have researched several technical communication interfaces –but the solution is clear – we need a way to capture the complete attention of center faculty, for specific periods of time, on specific topics that need timely responses. To this end, we have taken three steps to better communicate with our group of academically active, productive and highly committed faculty.
First, we have set aside one hour at the end of every quarterly meeting for a faculty-only breakout discussion. This is where the leadership team can discuss plans and center vision, request information for reporting, and answer any questions that faculty may have. This has 108 proven highly effective in helping faculty align their work with center goals, and has proven invaluable in gathering more complete information for reporting purposes. We also believe that these sessions help faculty feel informed about future plans in the center. The Second step we have taken is to start an annual 1-day faculty meeting, linked to the preparation of the annual report, where all faculty gather to discuss previous feedback, take stock of what we have been doing, and look at the big picture of the center. This also provides an opportunity to collect final pieces of information for the report. Moreover, we have found that this event creates a better sense of group cohesion, something that is critical to having a truly collaborative center. The third step has been to set up a monthly conference call, which we are holding the morning on the first Thursday of every month.
The second main communication problem has been that students have inadvertently been left out of communications about the center, leading to reduced awareness of center goals and plans, and a lack of center identity among some of the students. This concern was voiced by the students at the year 1 site visit, and is very much understandable. There are at least two reasons for this problem. First, during the first year we mainly relied on email communication to faculty, with the expectation that faculty would pass on information to students in their groups. This did not always happen. Second, while there were extensive planning meetings involving the faculty to help bond them into a cohesive group, students were not involved in these activities. Hence, there has been a strong unmet need for ways to “socialize” students into the center culture and vision. During the past year, we have taken several steps to overcome this problem. First, we have made a point to invite students to present their work at every quarterly meeting, and prior to the meeting, the Center Director meets one-on-one with each student to discuss their talk and how their work fits in with the overall mission and vision of the center. Second, we have set up a Slack channel and google mailing list that can be used to directly communicate with all center members including all students, thus avoiding the previous bottleneck in information distribution when we relied only on emails to faculty. Third, in order to encourage a sense of group identity among the students from different institutions, this year we started a student organized social meeting, with the first event held Friday, April 13th at the SoMa StrEat Food Park, a food truck park near UCSF. The event was organized by Will Chadwick, an SFSU student from the Chan lab, and paid for with non-federal discretionary funds by co-PI, Zev Gartner. Based on the success of this initial event, we are now scheduling this as a quarterly activity. Debra Singer, Frank Bayliss, Zev Gartner and Diana Chu are informal mentors, helping to facilitate student events.
We expect that the steps outlined in this section will go a long way to overcoming the communications challenges we have faced thus far, but we will continue to monitor the effectiveness of these steps and make further adjustments if needed.
3. Names and Affiliations of the Center’s External Advisors The External Advisory Committee for our center was set up in the first year of the center, based on the goal of assembling a group of academic and industrial sector scientific leaders who were chosen because their fields of expertise complement the key areas of interest for the center:
Radhika Nagpal (Dept. of Computer Science, Harvard University) Jennifer Lippincott-Schwartz (HHMI, Janelia Farm Campus) Neda Bagheri (Dept. of Chemical and Biological Engineering, Northwestern University) Wenying Shou (Fred Hutchinson Cancer Research Center) 109 Erin Dolan (Dept. of Biochemistry and Molecular Biology, University of Georgia) Carlos Gutierrez (Dept. Chemistry and Biochemistry, CSU Los Angeles) Brian von Herzen (CEO, Rapid Prototypes; Director, The Climate Foundation) Kinkead Reiling (Co-founder, Amyris) Dan Widmaier (CEO, Bolt Threads)
Dr. Nagpal is designated as the EAC Chair.
Appropriate NDAs have been executed with all advisors, and all have been provided with copies of our Strategic Plan. An EAC Charter has been written and provided to all EAC members. In year 1, six members of the EAC attended our first Annual Center Retreat, after which we held a half-day EAC meeting in a separate room with two additional EAC members connecting via Skype. The center director held face to face meetings with the three EAC members who were not present in person at the retreat (Jennifer Lippincott-Schwartz, Brian von Herzen, and Erin Dolan), in order to obtain more detailed feedback and suggestions. In year 2, four EAC members are scheduled to attend the annual (July 2018) retreat in person, and two will conference call. The center director is scheduling personal meetings with the others.
Because our plans to engineer new types of cells raise bioethical concerns, we have also constituted an Ethics Panel consisting of the following bioethics experts:
Megan Palmer (Center for International Security and Cooperation, Stanford University) Barbara Koenig (Director, UCSF Program in Bioethics) Robert McGinn (Center for Work, Technology & Organization, Stanford University)
Dr. McGinn took part in our January 2018 quarterly meeting, which was focused on ethics, presenting a lecture on ethics in engineering and leading discussions among the students.
Responsible Innovation At the suggestion of our site visit panel, and with the guidance of our Ethics Panel and EAC, we have launched a center initiative to go beyond the norm in ethics training in technology and innovation by incorporating the tenets of Responsible Innovation (RI) in Center for Cellular Construction programs. RI, including innovation as a solution to moral overload, active advocacy for standards taking into account downstream environmental and social impacts, and responding responsibly, has been extensively embraced by the EU and we intend to learn from their direction and to leverage resources being developed for education in RI. We are actively engaging with leaders in this field to communicate and develop ethics training aligned with this framework. Center leadership has begun participating in an online course in RI developed by the Technical University in Delft in order to obtain a baseline knowledge of RI concepts and applications that can guide overall center educational plans in this direction. Brian von Herzen, a member of our EAC (A.B. in Physics, Magna Cum Laude, from Princeton University and his Ph.D. in Computer and Planetary Science from Caltech where he was the recipient of the prestigious Hertz Fellowship) and Executive Director of the Climate Foundation is uniquely positioned to advise us on world developments and help us develop training.
Prof. von Herzen will be with us for our full retreat in July, and will be keynote speaker on Responsible Innovation on July 18th, informing on updates in the field and recent meetings at the United Nations on this topic. 110
We are also in touch with David Guston of ASU, Director of the NSF Center for Nanotechnology and founding editor-in-chief of the Journal of Responsible Innovation, who, while unable to join our EAC himself due to his many other responsibilities, is helping to guide our search for suitable advisors to recruit to our EAC.
4. Changes to the Center’s Strategic Plan
Based on feedback from the Year 1 site visit, from our EAC, from our professional Evaluators at Phillips & Associates, and from our own discussions and reporting, we appear to be on track in terms of executing our original strategic plan, and our goals continue to reflect the overall vision and mission of the center. We have thus focused on efficiency of execution, building effective teams and launching new collaborations, rather than modifying the actual strategic plan. As our activities continue to evolve, and as we include additional evaluation activities in the future, we expect to make changes as necessary.
111 VIII. Center wide Outputs and Issues
1.a. Publications
Peer Reviewed Publications supported by center funds bold indicates center faculty underline indicates center undergraduates
1. Murrow LM, Weber RJ, Gartner ZJ. 2017. Dissecting the stem cell niche with organoid models: an engineering-based approach. Development 144, 998-1007.
2. Tang SKY, Marshall WF. 2017. Self-repairing cells: how single cells heal membrane ruptures and restore lost structures. Science. 2017 356, 1022-1025.
3. Blauch LR, Gai Y, Khor JW, Sood P, Marshall WF, Tang SKY. 2017. Microfluidic guillotine for single-cell wound repair studies. Proc Natl Acad Sci U S A. 114, 7283-88.
4. Eritano AS, Altamirano A, Beyeler S, Gaytan N, Velasquez M, Riggs B. 2017 The endoplasmic reticulum is partitioned asymmetrically during mitosis prior to cell fate selection in proneuronal cells in the early Drosophila embryo. Mol. Biol. Cell. 28, 1530-38.
5. Chang AY, Marshall WF. 2017. Organelles – understanding noise and heterogeneity in cell biology at an intermediate scale. J. Cell Sci. 130, 819-826.
6. Munoz NR, Black CJ, Young ET, Chu, DS. 2017. New alleles of C. elegans gene cls-2 (R107.6), called xc3, xc4, and xc5. Micropublication: biology. Dataset. https://doi.org/10.17912/W2RQ2X
7. Fung, JC 2017. Kinetochores: Importance of Being Fashionably Late. Cell Syst. 4:585-586
8. Allard CAH, Decker F, Weiner OD, Toettcher JE, Graziano BR. 2017. A size-invariant bud-length timer enables robustness in yeast cell size control. bioRxiv https://doi.org/10.1101/211714 (Preprint, not peer reviewed)
9. Hueschen CL, Kenny SJ, Xu K, Dumont S. 2017. NuMA recruits dynein activity to microtubule minus- ends at mitosis. eLife, 6:e29328
10. Zhang ZB, Wang QY, Ke YX, Liu SY, Ju JQ, Lim WA, Tang C, Wei P. 2017. Design of Tunable Oscillatory Dynamics in a Synthetic NF-κB Signaling Circuit. Cell Systems. pii: S2405-4712(17)30437-4.
11. Hughes AJ, Miyazaki H, Coyle MC, Zhang J, Laurie MT, Chu D, Vavrusova Z, Schneider RA, Klein OD, Gartner ZJ. 2018. Engineered tissue folding by mechanical compaction of the mesenchyme. Dev. Cell. 44, 165-178.
12. Kimmel JC, Chang AY, Brack AS, Marshall WF. 2018. Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance. PLoS Computational Biology 2018 14(1): e1005927.
13. Tang Z, Hu Y, Wang Z, Jiang K, Zhan C, Marshall WF, Tang N. 2018. Mechanical forces program the orientation of cell division during airway tube morphogenesis. Dev. Cell 2018 44: 313-325.
14. Liang SI, van Lengerich B, Eichel K, Cha M, Patterson DM, Yoon TY, von Zastrow M, Jura N, Gartner ZJ. 2018 Phosphorylated EGFR Dimers Are Not Sufficient to Activate Ras. Cell Rep. 22, 2593-2600 112
15. Hu JL, Todhunter ME, LaBarge MA, Gartner ZJ. 2018. Opportunities for organoids as new models of aging. J Cell Biol. 217(1):39-50
16. King D, Ma J, Armendariz A, Yu K. 2018. Developing interactive exhibits with Scientists: Three example collaborations from the Life Sciences collection at the Exploratorium. Integr. Comp. Biol. doi: 10.1093/icb/icy010. [Epub ahead of print] note: first author Denise King is part of the biology group at Exploratorium working on CCC-related exhibits
17. Munoz, NR; Byrd, DT; Chu, D 2018. New allele of C. elegans gene spch-3 (T27A3.4), called xc2. Micropublication: biology. Dataset. https://doi.org/10.17912/W2995W
18. Kandogan E, Roth M, and Terrizzano I. 2018. Context Analytics as a Catalyst for Accelerating Science. Communications of the ACM, Vol. 9, No. 4, Article 39. [Last author Ignacio Terrizzano is part of the IBM research group led by Simone Bianco]
19. Galli LM, Santana F, Apollon C, Szabo LA, Ngo K, Burrus LW. 2018. Direct visualization of the Wntless-induced redistribution of WNT1 in developing chick embryos. Dev Biol. 439, 53-64
20. Chu DS 2018. Zinc: A small molecule with a big impact on sperm function. PLoS Biol 16, e2006204.
21. Vergara HM, Ramirez J, Rosing T, Nave C, Blandino R, Saw D, Saraf P, Piexoto G, Coombes C, Adams M, Domingo CR. 2018. miR-206 is required for changes in cell adhesion that drive muscle morphogenesis in Xenopus laevis. Dev. Biol. 438, 94-110.
22. Owens MT, Trujillo G, Seidel SB, Harrison CD, Farrar KM, Benton HP, Blair JR, Boyer KE, Breckler JL, Burrus LW, Byrd DT, Caporale N, Carpenter EJ, Chan YM, Chen JC, Chen L, Chen LH, Chu DS, Cochlan WP, Crook RJ, Crow KD, de la Torre JR, Denetclaw WF, Dowdy LM, Franklin D, Fuse M, Goldman MA, Govindan B, Green M, Harris HE, He ZH, Ingalls SB, Ingmire P, Johnson ARB, Knight JD, LeBuhn G, Light TL, Low C, Lund L, Márquez-Magaña LM, Miller-Sims VC, Moffatt CA, Murdock H, Nusse GL, Parker VT, Pasion SG, Patterson R, Pennings PS, Ramirez JC, Ramirez RM, Riggs B, Rohlfs RV, Romeo JM, Rothman BS, Roy SW, Russo-Tait T, Sehgal RNM, Simonin KA, Spicer GS, Stillman JH, Swei A, Tempe LC, Vredenburg VT, Weinstein SL, Zink AG, Kelley LA, Domingo CR, Tanner KD. 2018. Collectively Improving Our Teaching: Attempting Biology Department-wide Professional Development in Scientific Teaching. CBE Life Sci Educ. 17(1). pii: ar2.
23. Hughes AJ, Mornin JD, Biswas SK, Bauer DP, Bianco S, Gartner ZJ. 2018. Quantius: Generic, high- fidelity human annotation of scientific images at 100,000 - clicks-per-hour Nature Methods in press.
24. Arter M, Hurtado-Nieves V, Oke A, Zhuge T, Wettstein R, Fung JC, Blanco MG and Matos J. 2018. Regulated crossing-over requires inactivation of Yen1/GEN1 resolvase during meiotic prophase I. Developmental Cell, in press.
25. Elting MW, Suresh P, Dumont S. 2018. The spindle: Integrating architecture and mechanics from molecular- to cellular-scales. Trends in Cell Biology in press.
26. Chowdhury A, Biswas S, Bianco S. 2018. Active deep learning reduces the annotation burden in automatic cell segmentation. MICCAI Conference Proceedings, under review.
27. Kimmel JC, Brack A, Marshall WF. 2018. Deep convolutional neural networks allow analysis of cell motility during stem cell differentiation and neoplastic transformation. Submitted. Preprint: bioRxiv. 2017 doi: https://doi.org/10.1101/159202
113 28. Chen E, Esquerra RM, Melendez PA, Chandrasekaran SS, Kliger DS. 2018. Microviscosity in E. coli cells from time-resolved linear dichroism measurements . Submitted
29. Toda S, Blauch LR, Tang SKY, Morsut L, Lim WA. 2018. Synthetic morphologies: Programming self-organizing multicellular structures using engineered cell-cell signaling cascades. Submitted
30. Condon A, Kirchner H, Lariviere D, Marshall WF, Noireaux V, Tlusty T, Fourmentin E. 2018. Will biologists become computer scientists? Submitted
31. Castillo U, Gnazzo MM, Semaya E, Lam Y, Riggs B, Hall DH, Gelfand VI,and Skop AR. 2018. Conserved role for Ataxin-2 in mediating ER dynamics in embryos and neurons. Submitted
32. Chang AY, Marshall WF. 2018. Dynamics of living cells in a cytomorphological state space. Submitted
Books and Book Chapters 1. Marshall WF. 2017. Introduction to quantitative cell biology. Morgan and Claypool Life Sciences, Santa Rosa, CA. 58 pp.
2. Bayliss, F., Peterfreund, A., & Rath, K. (in press). Programmatic mentoring. In J. McClinton, D. S. Mitchell, G. B. Hughes, & M. A. Melton (Eds.) Mentoring at Minority Serving Institutions (MSIs): Theory, Design, Practice, and Impact.
3. Fengjiao Liu, Lucas R. Blauch, and Sindy K. Y. Tang, Quantifying Phenotypes in Single Cells using Droplet Microfluidics, submitted.
4. Eroy-Reveles, A. A., Hsu, E., Rath, K. A., Peterfreund, A. R., & Bayliss, F. (In press). History and Evolution of STEM Supplemental Instruction at San Francisco State University, a Large, Urban, Minority- Serving Institution. To be published in Diversity in Higher Education series by Emerald Publishing.
1.b. Conference Presentations
1. 7/14/17 Wallace Marshall. Simple math: an example from flagellar length control. (Keynote Talk) NSF workshop: Finding your Inner Modeler. Chicago, Il.
2. 7/15/17. Charles Craik. The path to a PhD. AMGEN Scholars Symposium. Los Angeles, CA
3. 7/16/17 Sindy Tang. Mechanics of fluids and solids (discussion leader). Gordon Conference on Soft Condensed Matter Physics. New London, NH.
4. 7/31/17 Sophie Dumont. Cell Division: Mechanical Integrity with Dynamic Parts. Gordon Research Conference on Motile and Contractile Systems, New London, NH
5. 8/2/17 Orion Weiner. A Template for Actin Organization at the Leading Edge. Gordon Research Conference on Motile and Contractile Systems, New London, NH
6. 10/7/17 Jacob Kimmel (Marshall lab). Inferring stem cell states from cell motility behavior reveals a dynamic state system and broken detailed balance. Northern California Computational Biology Society. Santa Cruz, CA
114 7. 10/16/17 Wendell Lim Synthetic Immunology: Hacking Immune Cells. KI/MIT Immune Engineering Symposium, Boston, MA
8. 10/21/17 Sindy Tang A Microfluidic Guillotine For Single-Cell Wound Repair Studies. International Conference on Miniaturized systems for chemistry and life sciences (MicroTAS 2017), Savannah, GA.
9. 11/8/17 Zev Gartner. Cold Spring Harbor Laboratory Meeting on Single Cell Analysis, Cold Spring Harbor, NY
10. 11/13/17 Zev Gartner Building Tissues to Understand How Tissues Build Themselves. EPFL conference on Engineering Multicellular Self-Organization, Lausanne Switzerland
11. 11/14/17 Leonardo Morsut (Lim lab) Programming Cells to Self-Organize in Structured Multicellular Organoids Using Engineered Cell-Cell Signaling Cascades. EPFL conference on Engineering Multicellular Self-Organization, Lausanne Switzerland
12. 11/27/17 Sindy Tang Order and Chaos: collective behavior of crowded drops in microfluidic systems. Materials Research Society Fall Meeting, Boston MA.
13. 12/3/17 Jennifer Frazier. Creating Exhibits with Real Tools and Data to Engage the Public. ASCB Annual Meeting, Philadelphia PA
14. 12/4/17 Wendell Lim Programming and Perturbing Cell Signaling Networks. Northwestern University, Center for Synthetic Biology, Evanston, IL.
15. 12/5/17 Nathan Hendel (Marshall Lab) Diffusion as a ruler: modeling kinesin diffusion as a length sensor for intraflagellar transport. Talk, ASCB Annual Meeting, Philadelphia PA
16. 12/10/17 Rebecca Smith. Cellular Construction: Modeling Cells as Biological Machines. Presentation. California STEAM Symposium (San Francisco, CA).
17. 1/11/18 John Paul Bugay (Domingo Lab) Analyzing the Function of Muscle Specific MicroRNAs in Xenopus laevis. Annual CSU Biotechnology Symposium (CSUPERB) Santa Clara, CA
18. 2/11/18 Wendell Lim Optimizing Synthetic Biology Tools for T Cell Therapies. Keystone Symposia Conference. Emerging Cellular Therapies: T Cells and Beyond, Keystone, CO.
19. 2/17/18 Wallace Marshall How cells measure length. Biophysical Society Annual Meeting, San Francisco, CA
20. 2/17/18 Daniel Fletcher Shaping Actin Network Organization and Composition with Force. Biophysical Society Annual Meeting, San Francisco, CA
21. 2/20/18 Wallace Marshall How Cells Build Geometry: Looking for Finite State Machines in the algorithmic assembly of cellular structures. I2Cell Conference, Eynsham Hall, UK
22. 2/22/18 Jacob Kimmel (Marshall Lab) Inferring cell state from motility behavior reveals a dynamic state system and broken detailed balance. Winter qBio meeting, Maui, Hawaii
23. 2/22/18 Nat Hendel (Marshall Lab) Diffusion as a ruler: Modeling kinesin diffusion as a length sensor for intraflagellar transport. Winter qBio meeting, Maui, Hawaii
115 24. 2/22/18 Joao Fonseca (El-Samad lab) Biphasic response of PKA to cAMP results in changes of epithelial behavior. Winter qBio meeting, Maui, Hawaii
25. 2/22/18 Satoshi Toda (Lim Lab) Synthetic morphologies: Programming self-organizing multi-cellular structures using engineered cell-cell signaling cascades. Winter qBio meeting, Maui, Hawaii
26. 2/23/18 Simone Bianco. Investigating the relationship between cellular structure and function with deep learning. Winter qBio meeting, Maui, Hawaii
27. 2/26/18 Zev Gartner. Building Tissues to Understand How Tissues Build Themselves. Pittcon, Philadephia PA
28. 3/3/18 Peter Freund, A. R., Rath, K. A., & Frank Bayliss, Programmatic Mentoring: Providing Mentoring as a Community, Going Beyond Mentor/Protégé Pairs. Presentation at the 10th Annual Conference on Understanding Interventions that Broaden Participation in Science Careers, Baltimore, MD.
29. 3/5/18 Wallace Marshall How cells measure length: clocks, rulers, and diffusion. American Physical Society March Meeting, Los Angeles, CA
30. 3/8/18 Barbara Jones (Bianco Lab). Thermodynamics and statistical mechanics of viral evolution beyond equilibrium. American Physical Society March Meeting, Los Angeles, CA
31. 3/11/18 Orion Weiner. A template for actin organization at the leading edge Orion Weiner, EMBL Symposium on Tissue Self-organization, Heidelberg, Germany
32. 3/13/18 Zev Gartner Tissue Origami: engineering tissue folding by mechanical compaction of the mesenchyme. EMBL Symposium on Tissue Self-organization, Heidelberg, Germany
33. 3/17/2018 Tom Zimmerman How to build a microscope from scratch, Women in Engineering conference, San Jose State University.
34. 3/21/18 Wendell Lim Biological design principles: learning by building. Mosbacher Kolloquium: Synthetic Biology - from Understanding to Application. Mosbach, Germany
35. 4/17/18 Shawn Douglas Programmable DNA origami design with Cadnano 2.5. Foundations of Nanoscience (FNANO) Conference, Snowbird, UT
36. 4/22/18 Jasmine Sims (Chan lab). Effect of the Cell Cycle on Vacuole Size in S. cerevisiae Yeast. Experimental Biology 2018 San Diego, CA
37. 4/24/18 Simone Bianco. Investigating the relationship between cellular structure and function with deep learning. (Invited plenary) International Symposium for Tissue Phenomics, Cambridge, MA
38. 5/4/18 Devan Shah (Denetclaw lab) Endoderm Nitric Oxide Focally Elevated “Hotspots” at the Heart Fields Signals in Early Cardiogenesis in Chicken Embryos. 32nd Annual CSU System-Wide Research Competition. Sacramento, CA,
39. 5/5/18 Christopher Black (Chu lab). Sex-specific kinetochore and phosphatase features in C. elegans sperm meiosis. Bay Area Worm Meeting, Santa Cruz, CA
40. 5/13/18 Wallace Marshall. Synthetic cells: short, medium, and long term goals. NSF Synthetic and Artificial Cells Workshop. Alexandria, VA.
116 41. 5/24/18 Wendell Lim. Biological Design Principles: Learning by Hacking Cell Behavior. Vanderbilt Cell Dynamics Symposium. Nashville, TN
42. 5/31/18 Tom Zimmerman. (Invited plenary) Innovation and AI microscopy, Startup Village conference, Moscow, Russia.
43. 6/4/18 James Gerh (Chu lab). Modelling chromosome segregation using C. elegans , Bay Area Cytoskeleton Meeting, San Francisco, CA
44. 6/4/18 Dan Fletcher. Off-label uses of the actin cytoskeleton. Bay Area Cytoskeleton Meeting, San Francisco, CA
45. 6/4/18 Christine Hueschen (Dumont lab). Spindle turbulence and mitotic cell motility in the absence of microtubule end-clustering. Bay Area Cytoskeleton Meeting, San Francisco, CA
46. 6/16/18 Zev Gartner Hacking Cell Biology to understand human tissue. World Ophthalmology Conference. Barcelona, Spain
47. 6/20/18 Zev Gartner Programming Tissue Self-Organization. Gordon Research Conference on Biointerface Science, Il Ciocco, Italy
Posters
1. 6/21/17 Criszel Corpuz (Chu lab) HIS-35: a novel histone H2A protein involved in fertility. 21st International C. elegans conference, Los Angeles, CA
2. 6/21/17 James Gerh (Chu lab) GSP-3/4 Phosphatases Play Essential Regulatory Roles in the Journey from Spermatogenesis to Fertilization. 21st International C. elegans conference, Los Angeles, CA
3. 6/21/17 Nicholas Munoz (Chu lab) Understanding sister chromosome movements between sperm meiotic division. 21st International C. elegans conference, Los Angeles, CA
4. 7/13/17 John Paul Bugay (Domingo lab undergraduate) Analyzing the Function of Muscle Specific MicroRNAs in Xenopus laevis; Society for Developmental Biology (SDB) 76th Annual Meeting; Minneapolis, MN
5. 7/13/17 Jason Garcia (Domingo lab undergraduate) Determining target genes regulated by MIR-206/ MIR-1 during skeletal muscle Society for Developmental Biology (SDB) 76th Annual Meeting; Minneapolis, MN
6. 8/6/17 Jennifer Frazier Creating New Genres of Museum Exhibits with Scientific Visualization. Gordon Research Conference on Visualization in Science and Education, Lewiston, Maine.
7. 8/12/17 Jason Garcia (Domingo lab undergraduate) Determining Target Genes Regulated 6y mir-206 and mir-1 during early skeletal muscle development in Xenopus laevis. International Xenopus Meeting, Seattle, WA
8. 10/19/17 Roberto Carlos Segura (Chan lab undergraduate) Comparing Vacuolar pH to Vacuolar Size. SACNAS Scientific Conference 2017, Salt Lake City, Utah 10/19/17 Gerardo Aguilar (Riggs lab undergraduate) Understanding the Gene conflict that leads to retroposed Genes. SACNAS Scientific Conference 2017, Salt Lake City, Utah
9. 10/19/17 Jason Garcia (Domingo lab undergraduate) Determining Target Genes Regulated by Mir- 117 206/Mir-1 during Early Skeletal Muscle Development in Xenopus. SACNAS Scientific Conference 2017, Salt Lake City, Utah
10. 10/21/17 Luke Blauch (Tang lab) An On-Chip Guillotine For High-Throughput Single-Cell Wound Repair Studies International Conference on Miniaturized systems for chemistry and life sciences (MicroTAS 2017), Savannah, GA.
11. 10/23/17 Barbara Jones (Bianco Lab) and Greyson Lewis (Marshall Lab) Thermodynamics and statistical mechanics of viral evolution: non-equilibrium behavior. BaMBA 11: Biology and Mathematics , San Francisco, CA
12. 11/1/17 Natasha Nand (Riggs lab undergraduate) Preforming Deficiency Screens on Jagunal Interactions that Aid in Cell Fate Determination. ABRCMS 2017, Phoenix, AZ . 13. 11/1/17 Nicole Rodrigues (Riggs lab undergraduate) The Actin cytoskeleton and the PNG Kinase Complex Activator GNU in Drosophila Oocytes. ABRCMS 2017, Phoenix, AZ
14. 11/1/17 Steven Sun (Esquerra lab undergraduate) Resolving Heme Reaction Intermediates In Nitric Oxide Synthase with Cryogenic Magnetic Circular Dichroism. ABRCMS 2017, Phoenix, AZ
15. 11/1/2017 Marick Buenafe, (Esquerra lab undergraduate) Characterizing Reaction Intermediates in Neuronal Nitric Oxide Synthase catalysis using Magnetic Circular Dichroism at Cryogenic Temperatures. ABRCMS 2017, Phoenix, AZ
16. 11/1/17 Johnson Yang (Domingo lab undergraduate) Muscle development in the frog, Xenopus tropicalis. ABRCMS 2017, Phoenix, AZ
17. 12/3/17 Blake Riggs The endoplasmic reticulum is partitioned asymmetrically during mitosis before cell fate selection in proneural cells in the early Drosophila embryo. ASCB Annual Meeting, Philadelphia PA
18. 12/3/17 Jacob Kimmel (Marshall Lab) Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance. ASCB Annual Meeting, Philadelphia PA
19. 12/3/17 Greyson Lewis (Marshall Lab) Graph fingerprints of mitochondria and mitochondrial-like networks. ASCB Annual Meeting, Philadelphia PA
20. 12/3/17 Scott Coyle (Prakash Lab) Unravelling calcium programmed hunting biodynamics of the swan-necked predatory ciliate Lacrymaria. ASCB Annual Meeting, Philadelphia PA
21. 12/3/17 Jonathan Kuhn (Dumont Lab) Controlling candidate physical inputs to the spindle assembly checkpoint ASCB Annual Meeting, Philadelphia PA
22. 12/3/17 Samuel Goodfellow (Burrus lab) Wnt signaling in migratory neural crest cells in the chick spinal cord. ASCB Annual Meeting, Philadelphia PA
23. 12/5/17 Jean Luke Campos (Chan Lab undergraduate) Single cell analysis of vacuolar pH using confocal microscopy. ASCB Annual Meeting, Philadelphia PA
24. 12/5/17 Vasudha Srivastava (Gartner Lab) Cellular Construction Workshop – Modeling Cells as Biological Machines. ASCB Annual Meeting, Philadelphia PA
118 25. 12/5/17 Devan Shah (Denetclaw Lab) Endoderm nitric oxide focally elevated “hotspots” at the heart forming regions (HFRs) signals in early cardiogenesis in chicken embryos. ASCB Annual Meeting, Philadelphia PA
26. 12/5/17 Guillermina Ramirez-San Juan (Marshall and Prakash Labs) Biophysical interactions between cilia and mucus underlie directed fluid transport in the ventral epithelium of the planarian Schmidtea mediterranea. ASCB Annual Meeting, Philadelphia PA
27. 12/10/17 Jessica Allen (Smith group, UCSF SEP). Cellular Robots. STEAM Student Showcase. California STEAM Symposium (San Francisco, CA).
28. 1/11/18 Jason Garcia (Domingo lab undergraduate) "Determining Target Genes Regulated 6y mir-206 and mir-1 during early skeletal muscle development in Xenopus laevis" CSU Biotechnology Symposium (CSUPERB); Santa Clara, CA
29. 2/19/18 Christina Hueschen (Dumont lab) NuMa Recruits Dynein Activity to Microtubule Minus-Ends at Mitosis. Biophysical Society Annual Meeting, San Francisco, CA
30. 2/19/18 Jonathan Kuhn (Dumont lab) Controlling Candidate Physical Inputs to the Spindle Assembly Checkpoint. Biophysical Society Annual Meeting, San Francisco, CA
31. 2/19/18 Alexandra Long (Dumont lab) Probing how the Mammalian Kinetochore Holds on to Growing Versus Shrinking Microtubules. Biophysical Society Annual Meeting, San Francisco, CA
32. 2/19/18 Pooja Suresh (Dumont lab) Probing the Physical and Molecular Basis of the Mammalian Mitotic Spindle’s Response to Force. Biophysical Society Annual Meeting, San Francisco, CA
33. 2/19/18 Nat Hendel (Marshall lab) Diffusion as a Ruler: Modeling Kinesin Diffusion as a Length Sensor for Intraflagellar Transport. Biophysical Society Annual Meeting, San Francisco, CA
34. 2/20/18 Greyson Lewis (Marshall lab) Conserved Dynamic Characteristics of Mitochondrial Networks. Biophysical Society Annual Meeting, San Francisco, CA
35. 3/12/18 Guillermina Ramirez-San Juan (Marshall and Prakash lab) Biophysical interactions between cilia and mucus underlie directed fluid transport in the ventral epithelium of the planaria S. mediterranea . EMBO conference on tissue self-organization. Heidelberg, Germany
36. 4/13/18 Sydney Alvarado (Riggs lab undergraduate) A Deficiency Screen for Genetic Interactors of Jagunal in Drosophila. 59th Annual Drosophila Research Conference, Philadelphia, PA
37. 4/13/18 Cecilia Brown (Riggs lab). Tracking Centrosomes to Follow Endoplasmic Reticulum Inheritance in Drosophila Embryos. 59th Annual Drosophila Research Conference, Philadelphia, PA
38. 4/13/18 Jose Ortega (Riggs lab). Proper Endoplasmic Reticulum partitioning is necessary for mitotic progression in Drosophila neuroblast. 59th Annual Drosophila Research Conference, Philadelphia, PA
39. 4/16/18 Parsa Nafisi (Douglas lab). pScaf: A novel plasmid enabling phage- based production of single-stranded DNA scaffolds of custom size and sequence. Foundations of Nanoscience (FNANO) Conference, Snowbird, UT
40. 4/16/18 Suraj Makhija (Douglas lab). Toward Immunomodulatory DNA Origami Nanodevices. Foundations of Nanoscience (FNANO) Conference, Snowbird, UT
119 41. 4/18/18 Tural Aksel (Douglas lab). DNA nanotechnology platform for high- throughput cryo-EM studies of small proteins. Foundations of Nanoscience (FNANO) Conference, Snowbird, UT
42. 4/19/18 Pablo Damasceno (Douglas lab). Toward Programmable DNA Origami Lattices. Foundations of Nanoscience (FNANO) Conference, Snowbird, UT
43. 5/4/18 Jean Luke Campos (Chan lab undergraduate) Single cell analysis of vacuolar pH using confocal microscopy. SFSU COSE Student Project Showcase; SF, CA
44. 5/4/18 Nicole Rodrigues (Riggs and Marshall lab undergraduate) The Search for Mitochondria in Stentor; SFSU COSE Student Project Showcase; San Francisco, CA
45. 5/4/18 Steven Sun (Esquerra lab undergraduate) Resolving Heme Reaction Intermediates In nitric oxide synthase with Cryogenic Magnetic Circular Dichroism. SFSU COSE Student Project Showcase; San Francisco, CA
46. 5/4/18 Ariana Yancey (Riggs lab undergraduate) The Asymmetric Partitioning of ER in Drosophila Embryos; SFSU COSE Student Project Showcase; SF, CA
47. 5/4/18 Alia Edington (Riggs lab) Charactering the segregation of organelles during asymmetric divisions of proneural cells in Drosophila. SFSU COSE Student Project Showcase, San Francisco CA
48. 5/4/18 Criszel Corpuz (Chu lab) Maternal and Paternal histone HIS-35 differentially reprograms embryonic chromatin in C. elegans. SFSU COSE Student Project Showcase, San Francisco CA
49. 5/4/18 Frederick Santana (Burrus lab) Branching out: filopodia as a mechanism for WNT1 transport in the developing spinal cord. SFSU COSE Student Project Showcase, San Francisco CA
50. 5/4/18 Jasmine Sims (Chan lab) Effects of the cell cycle on vacuole size in S. cerevisiae. SFSU COSE Student Project Showcase, San Francisco CA
51. 5/4/18 Jose Ortega (Riggs lab) Proper endoplasmic reticulum partitioning is necessary for mitotic progression in Drosophila neuroblast. SFSU COSE Student Project Showcase, San Francisco CA
52. 5/4/18 Oscar Mendoza (Denetclaw lab) NO means yes in regulation of primary myotome differentiation. SFSU COSE Student Project Showcase, San Francisco CA
53. 5/4/18 William Chadwick (Chan lab) Size and localization of vacuoles in fission yeast. SFSU COSE Student Project Showcase, San Francisco CA
54. 5/4/18 Sita Chandrasekaran (Esquerra lab undergraduate) The Molecular Mechanism of Intermolecular Signal Transduction in Cystathionine Synthase (Cbs); SFSU COSE Student Project Showcase; San Francisco, CA
55. 5/4/2018 Angeline K. Chemel (Chan lab undergraduate) Inheritance and Biogenesis in S. cerevisiae. SFSU COSE Student Project Showcase; San Francisco, CA
56. 6/4/18 Jessica Bolivar-McPeek (Riggs lab) Investigating spindle rotation during mid-blastula transition of Drosophila melanogaster. Bay Area Cytoskeleton Meeting, San Francisco, CA
1.c. Other Dissemination Activities
120 Departmental seminars on topics relevant to the Center 8/4/17 Blake Riggs Baskin School of Engineering, UC Santa Cruz 9/25/17 Wendell Lim Dundee Cell Signaling Lecture, University of Dundee, Scotland
10/27/17 Simone Bianco. What robots can learn from cells. GRASP lab, UPENN.
11/23/17 Wallace Marshall Control systems for regulating size within cells. Dept. Mechanical Engineering, Johns Hopkins University
3/21/18 Wallace Marshall Control systems for regulating size within cells Seminar, Dept. of Electrical and Computer Engineering, Texas A&M
3/26/18 Wallace Marshall Pattern formation and regeneration in single cells. Center for Engineering Mechanobiology (CEMB), Washington University, St. Louis MO
Outreach Activities: 6/9/2017 Tom Zimmerman (IBM) San Jose Girls Camp Electronic Workshop: “How to build a microscope”
7/10/17 TED talk by Manu Prakash on “lifesaving scientific tools made of paper”
8/5/17 “Extreme Cell Biology” general-audience lecture. Presented by Wallace Marshall at SciFoo Camp, Google Headquarters, Mountain View, CA.
7/31/2017 Tom Zimmerman (IBM) San Jose Boys Camp Electronic Workshop: “How to build a microscope”
8/4/17 Tom Zimmerman (IBM) “Smart World Conference”: presented three workshops on “Rapid development and deployment of environmental sensors”
11/4/17 Shawn Douglas (UCSF) organized the BIOMOD competition http://biomod.net/, with student teams are focused on nanoscale engineering and cellular manipulation. The BIOMOD competition, formerly a partnership with Harvard, is run by the BIOMOD Foundation, an independent 501(c)3 non-profit corporation. San Francisco, CA.
10/29/17 World Congress of Science Journalists. The Marshall and Lim groups, and Jessica Allen from Rebecca Smith’s SEP group, presented hands-on exhibits based on CCC research and educational projects for WCSJ attendees. San Francisco, CA
9/23/17 Rogue valley Mini Maker Faire. CCC students and postdocs from UCSF, SFSU, and IBM, presented hands-on exhibits of cell behavior and cell-inspired robotics. Ashland, OR.
12/2/17 TED talk by Simone Bianco and Tom Zimmerman on “The wonderful world of life in a drop water”
3/17/2018 Tom Zimmerman (IBM), Demo of lensless microscope at the “Women in Engineering” conference at SJ State University.
3/21/18 Walker Public Lecture: “Extreme Cell Biology”. Wallace Marshall, presented at Texas A&M, College Station, TX.
4/13/18 Tom Zimmerman (IBM) microscope workshop for 120 students (4 classes @ 30/class), 4th & 5th grade Regnart elementary schools (Cupertino, CA) 121
4/21/18 Tom Zimmerman, Vito Pastore, Sujoy Biswas (IBM), Rebecca Smith, Jessica Allen (SEP) Microscope Hackathon for ~40 participants at Counter Culture Lab (Bio-hacker space in Oakland, CA),
4/22/18 Tom Zimmerman, Vito Pastore, Sujoy Biswas (IBM) Microscope workshop for 80 students (4 classes @ 20/class), 9-12 grade, MIT AI Conference Kid's Day Event, Intercontinental Hotel, SF
5/18/18 Bay Area Maker Faire. Marshall group (UCSF), Bianco group (IBM), and Smith group (UCSF SEP), together with students and postdocs from UCSF, SFSU, Stanford, and IBM labs, presented hands-on exhibits of cell behavior, lenseless microcopy, and cell-inspired robotics. San Mateo Convention Center, San Mateo, CA.
5/19/18 “Extreme Cell Biology” public lecture. Presented by Wallace Marshall at the San Mateo Bay Area Maker Faire. San Mateo, CA.
Creating Awareness: Videos describing Center activities 5/13/17 Youtube video on Lenseless Microscopy being developed as part of the Cellular Sentinel Project. https://www.youtube.com/watch?time_continue=16&v=Co6AL5jYhG8
04/18/18 Youtube video: Swimming with Plankton https://www.youtube.com/watch?v=ynyjBlVWYWg&t=23s
04/18/18 Youtube video: Swimming with Plankton at 360 degrees https://www.youtube.com/watch?v=e9fPBriiLs8&t=5s
7/10/17 video of TED talk by Manu Prakash https://www.ted.com/talks/manu_prakash_lifesaving_scientific_tools_made_of_paper/transcript)
12/2/17 video of TED talk by Simone Bianco and Tom Zimmerman https://www.ted.com/talks/simone_bianco_and_tom_zimmerman_the_wonderful_world_of_life_in_a_drop_ of_water
CCC-produced Youtube video: CCC Diversity of Disciplines https://www.youtube.com/watch?v=R3A7zKrprrs
CCC-produced Youtube video: Meet Monet Jimenez https://www.youtube.com/watch?v=Vaiadg3pr44
IBM 5 in 5 Science Slam Video: Tom Zimmerman talking about AI-powered lenseless microscopes for Cellular Sentinel project. The project was highlighted by IBM as one of the 5 technologies which may change the world in the next 5 years. https://www.youtube.com/watch?v=Vg92XGT0VhQ
CCC produced video, for 2018 NSF STEM for All Video Showcase “Transforming the Educational Landscape: Center student Criszel Corpuz, with the SEP, made a video about the Center’s Cellular Construction Workshop (the Center’s summer program for high school students and teachers). http://videohall.com/p/1151
122 2. Awards and Honors
2017 Hana El-Samad: Chan Zuckerberg BioHub Investigator 2017 Zev Gartner: Chan Zuckerberg BioHub Investigator 2017 Manu Prakash: Chan Zuckerberg BioHub Investigator 2017 Charles Craik: Fellow of the American Academy of Arts and Sciences 2017 Wallace Marshall: ASCB Fellow, American Society for Cell Biology 2017 Manu Prakash: Rolling Stone Magazine’s 25 People Shaping the Future in Tech
2017 Manu Prakash: Tau Beta Pi Teaching Award, Stanford University 2017 Daniel Fletcher: Bakar Fellowship for STEM entrepreneurship 2017 Manu Prakash: Popular Science/NSF “Vizzies” Experts’ Choice Award 2017 Manu Prakash: WIRED Next List: 20 tech visionaries who are creating the future. 2017 Jacob Kimmel (Marshall lab): NSF Graduate Research Fellowship 2017 Devan Shah (Denetclaw Lab): Graduate student winner, Biological and Agricultural Sciences, CSU Research Competition. 2017 Manu Prakash: INDEX Design Award from the Danish government 2017 Frederick Santana (Burrus lab): Genentech Fellowship 2017 Jacob Kimmel (Marshall lab): PhRMA Foundation Informatics Fellowship 2017 Jacob Kimmel (Marshall lab): UCSF Discovery Fellow 2017 Olivia Creasey (Gartner lab): UCSF Discovery Fellow 2017 Lila Neahring (Dumont lab): Hertz Fellowship 2017 Orion Weiner: Outstanding Faculty Mentor Award, UCSF 2018 Sophie Dumont: Outstanding Faculty Mentor Award, UCSF 2018 Jacob Kimmel (Marshall lab): Best Poster prize, Nvidia Deep Learning in Biomedicine Workshop, San Francisco, CA. 2018 Jennifer Hu (Gartner lab): UCSF Grad Slam Finalist 2018 Katie Cabral (Gartner lab): UCSF Grad Slam Finalist 2018 Criszel Corpuz (Chu lab): 1st Place Graduate Division COSE SFSU Showcase 2018 Simone Bianco: SIAM Visiting Lecturer Program Award 2018 Greyson Lewis (Marshall lab): NSF graduate research fellowship 2018 Wendell Lim: Byers Distinguished Professorship, UCSF 2018 Rebecca Smith: John and Samuel Bard Award in Science and Medicine, Bard College 2018 Blake Riggs: Promoted to a regular member of the Minorities Affairs Committee (MAC) of the American Society for Cell Biology (ASCB) 2018 Wendell Lim: German Society for Biochemistry and Molecular Biology - Feodor Lynen Medal
Career Promotions for CCC Faculty 123
2017 Carmen Domingo: Appointed Interim Dean, SFSU College of Science and Engineering 2017 Laura Burrus: Appointed Chair, SFSU Dept. of Biology 2018 Zev Gartner: Promoted to Full Professor
3. Students who graduated (undergrad, MS and PhD) during this reporting period-
Marshall Lab, UCSF: Jacob Kimmel, Ph.D. April 2018 Placement: Computational Biologist, Calico Labs, South San Francisco, CA Amy Chang, Ph.D. January 2018 Placement: Postdoctoral Researcher, UCSF
See Diversity Section for Table re: undergrad and MS students.
4. Outputs of Knowledge Transfer Activities
Invention disclosures on work related to and funded by the Center for Cellular Construction
5/2/17 P201701636 – Immersive Submerged Stereo Microscope, Thomas G. Zimmerman, IBM Research. Search in progress.
4/25/17 P201701401 – Autonomous Plankton Sampler, Thomas G. Zimmerman, IBM Research. Search in progress.
4/25/17 P201701399 – Generating 3D Models of Microscopic Subject from a Sequence of Images, Thomas G. Zimmerman, Simone Bianco, IBM Research; Rebecca McGillivary, Wallace Marshall, UC San Francisco. Search concluded. To be filed.
7/9/17 P201703701 – Drop Microscope For High Throughput Viewing and Analysis of Specimens, Thomas G. Zimmerman, IBM Research. Search in progress.
7/9/19 P201703703 – 3D Microscope Using Front Surface Mirror, Thomas G. Zimmerman, IBM Research. Search in progress.
7/11/17 SF2017-165 – Live bioreactor for nanofabrication. Wallace Marshall, UC San Francisco, Hongmin Qin, Texas A&M.
Patents
CHIMERIC ANTIGEN RECEPTOR AND METHODS OF USE 15/801,133 11/02/2017 THEREOF. Wendell A Lim, James J Onuffer, Chia Yung Wu
METHODS AND COMPOSITIONS FOR RNA-DIRECTED TARGET DNA MODIFICATION AND FOR RNA-DIRECTED MODULATION OF TRANSCRIPTION. Wendell A Lim, Lei Qi, 15/803,424 11/03/2017 Jennifer A Doudna, Martin Jinek, Emmanuelle Charpentier, Krzysztof Chylinski, James "Jamie" H. Doudna Cate 124
FORCE SENSOR CLEAVAGE DOMAIN CONTAINING CHIMERIC POLYPEPTIDES AND METHODS OF USE 62/587,296 11/16/2017 THEREOF. Wendell A Lim, Kole T Roybal, Joseph Choe, Paul Langridge, Gary Struhl
5. Participant table with demographic information – Table VIII.5
Table is appended at the end of this section.
Total Participants: 197 Total Affiliates: 15
125 6. Summary list of all Center’s research, education, knowledge transfer & other institutional partners
EXTERNAL PARTNERSHIPS
Organization Organization Contact Name Nature of Nature of Partner’s 160 Name Type* and Partner** contribution – In Kind hours Address or Monetary- or Leveraged more Contribution*** ? Y/N) 1 Texas A&M Academic Hongman Qin, Dept of Knowledge N University Institution Biology, TAMU Transfer Dept of Biology 3258 TAMU Biological Sciences Bldg West College Station, TX 77843
2 Arizona State Academic Athena Aktipis Education Exhibition partner with N University Institution Exploratorium Cell structures exhibit design
3 UIUC Academic Alek Aksimentiev Research Collaboration with N Institution Douglas lab, UCSF Software Infrastructure for Sustained Innovation 4 Department International Education Collaboration with N of (Government) Prakash lab - microgrant Biotechnolog program across India y, India for students and educators, to fund foldscopes
5 Southern NGO Nina Bednarsek Knowledge N California 3535 Harbor Blvd., transfer Coastal Suite 110 Water Costa Mesa, CA 92626 Research Project
6 Monterey Non-profit Thom Maughan Research The IBM team will use an N Bay Collaboration to test and MBARI-built vehicle to Aquarium deploy Bianco Lab deploy and test the Research underwater plankton plankton microscope in Institute microscopes on MBARI the Monterey Bay. buoys and Liquid Robotics’ Wave Glider.
7 Nagase, Inc. Industry Ziaoli Liu Knowledge Collaboration established. N Transfer Monetary contribution to be defined.
126 8 Universita’ International Massimo Maresca Research The IBM team will make N di Genova (Academic) use of the existing University resources (buoy, drones, sensor platforms) to monitor plankton. 9 Israel Water International Knowledge Collaboration established. N Works (Government) Transfer Monetary contribution to Association be defined.
1 Fabian NGO Fabian Cousteau Education The IBM plankton N 0 Cousteau microscope will be hosted Ocean on the newly formed Learning underwater station the FC Center OLC is developing for research purposes. The FC OLC will man the microscope underwater. 1 Reed Industry Dr. Eric C. Henry Knowledge Collaboration established. N 1 Mariculture (Research Scientist, transfer Monetary contribution to Process Engineer. Research be defined. Collaboration with the Bianco Lab to apply plankton microscopy instruments and image analysis software to assist in their commercial plankton culturing
*For organization type, please indicate whether the partner organization is a company, national laboratory, Federal government, state/local government, NGO, or other
**For type of partner, please indicate whether the partner organization is a research, education, knowledge transfer, diversity, or other partner. You may list more than one type, if applicable.
*** Note: Information added based on internal report submitted to Dragana Brzakovic, 6/22/18
External Partners:
Exploratorium exhibition partnerships: Athena Aktipis, Arizona State Univ (Cell Structures exhibit to open with the Cells to Self exhibit.)
Prakash lab, in collaboration with the Dept. of Biotechnology, India, launched a microgrant program across India for students and educators, to fund foldscopes. 700 kits shipped Dec. 2017.
Douglas lab initiated a collaboration with Alek Aksimentiev (UIUC) & applied to NSF for an SI2:SSE grant (Software Infrastructure for Sustained Innovation).
127 7. Summary table for NSF Reporting
For internal NSF reporting purposes, provide a Summary Table with the following information:
1 NUMBER OF PARTICIPATING INSTITUTIONS
(all academic institutions that participate in activities at 4 the Center)
this value should match the number of institutions listed in Section I, Item 1 of the report plus other additional academic 2 institutionsNUMBER that OF participateINSTITUTIONAL in Center activitiesPARTNERS as listed in the table above. (total number of non-academic participants, including industry, 2 states, and other federal agencies, at the Center)
this value should match the number of partners listed in the 3 tableTOTAL in Section LEVERAGED VIII, Item SUPPORT 6 (above) FOR THE CURRENT YEAR $275,000
(sum of funding for the Center from all sources other than NSF- STC) [Leveraged funding should include both cash and in- kind support that are related to Center activities, but not funds awarded to individual PIs.]
this value should match the total of funds in Section X, Item 4 of “Total” minus “NSF-STC” for cash and in-kind support
4 NUMBER OF PARTICIPANTS
(total number of people who utilize center facilities; not just 197 persons directly supported by NSF) . Please EXCLUDE affiliates
this value should match the total number of participants listed in Section VIII, Item 5 (above)
128 8. Media Publicity Received
Press Releases
6/29/17 Stanford press release on microfluidic guillotine developed by the Tang lab being used to cut organoids as part of the Cellular Legos project. https://me.stanford.edu/news/microscopic-guillotine-cuts-cells-two
11/13/17 UCSF press release on Bay Area Science Festival, noting robotics demonstration run by Center labs https://www.ucsf.edu/news/2017/11/408971/expanded-discovery-day-event-att-park-caps-2017-bay-area- science-festival
12/28/17 UCSF press release on tissue origami developed as part of the Cellular Legos project https://www.ucsf.edu/news/2017/12/409516/engineers-hack-cell-biology-create-3d-shapes-living-tissue
2/12/18 UCSF press release: Hana El-Samad advises young women to pursue an education in STEM fields to drive ingenuity, imagination and discovery: https://www.instagram.com/p/BfHOf_knEMn/
4/20/18 IBM Press Release on Lensless Microscopy developed as part of the Cellular Sentinel project https://www.research.ibm.com/5-in-5/ai-microscope/
5/31/18 UCSF Press Release on self-organizing cell collectives being developed as part of Cellular Legos project https://www.ucsf.edu/news/2018/05/410596/synthetic-tissues-build- themselves?utm_source=ucsf_tw&utm_medium=tw&utm_campaign=2018_cells_self_assemble&utm_term =
Media Coverage
11/14/17 ASCB announcement of ASCB Fellows including CCC Director Wallace Marshall http://www.ascb.org/ascb-post/member-news/ascb-names-67-society-fellows-2017/
1/25/18 Quanta magazine article about CCC development of tissue origami for the Cellular Legos project https://www.quantamagazine.org/tissue-engineers-hack-lifes-code-for-3-d-folded-shapes-20180125/
1/2/18 3Dprint.com 3D Printing Newsletter article about tissue origami developed for the Cellular Legos project https://3dprint.com/198845/3d-cell-patterning-living-tissue/
3/26/18 CCC research featured in Discovery Magazine article on “Cradles of Innovation” http://discovermagazine.com/galleries/2018/cradles-of-innovation
4/20/18 ABC7 News feature on Lensless microscope being developed at IBM as part of the Cellular Sentinel Project http://abc7news.com/pets-animals/new-microscope-to-help-track-climate-change-pollution-impact-on- plankton/3372272/
4/20/18 INC.COM article about AI-driven lensless microscopes at IBM being developed for the Cellular Sentinel Project https://www.inc.com/greg-satell/5-technologies-ibm-hopes-to-pioneer-in-next-5-years-that-every- business-should-know-about.html 129
03/19/18 Fox Business: IBM creating robots to clean the ocean. IBM’s President of Research Arvind Krishna, talks about the Cellular Sentinel project and IBM’s AI-powered lensless microscopes. https://www.youtube.com/watch?v=fTiqDXuDzkQ
03/22/18 Wired interview with Simone Bianco and Tom Zimmerman “Robot Microscopes Demystify Plankton, the Sea's Most Vital Residents” . https://www.wired.com/story/robot-microscopes-demystify-plankton-the-seas-most-vital-residents/
04/11/18 Oceans Deeply interview with Simone Bianco and Tom Zimmerman. “What’s Next: Swarms of AI- Powered Robotic Microscopes to Study Plankton” https://www.newsdeeply.com/oceans/articles/2018/04/11/whats-next-swarms-of-ai-powered-robotic- microscopes-to-study-plankton
6/12/18 “Startup Science: How the Idea for Synthetic Cells Took Silicon Valley By Storm” Article/ interview with Wendell Lim. https://www.ucsf.edu/news/2018/06/410626/startup-science-how-wendell-lims-idea-synthetic-cells-took- silicon-valley- storm?utm_source=exacttarget&utm_medium=email&utm_campaign=pulsetoday&utm_content=edition72
130 Table VIII.V. All Center Participants
• Category: (a) undergraduate students, (b) graduate students, (c) faculty, (d) visiting faculty, (e) other research scientists, (f) postdoct orates, (g) pre-college student (h) teachers, (i) educators and (j) other participants
• Institutional Affiliation: the primary institution at which an individual is employed or affiliated with (e.g. for a faculty member, this would be their home university).
• Department: if participant is associated with a University, please list the academic department with which they are affiliated, if applicable. • Gender: Female, Male.
• Disability: (select one or more) Hearing Impairment, Visual Impairment, Mobility/ Orthopedic Impairment, Other, None.
• Ethnicity: (choose one) Hispanic or Latino, Not Hispanic or Latino.
• Race: (select one or more) American Indian or Alaskan Native, Asian, Black or African American, Native Hawaiian or Other Paci fic Islander, White.
• Citizenship: (choose one) U.S. Citizen, Permanent Resident, Other non-U.S. Citizen 131 Table III. V. Demographic Information – Center for Cellular Construction Participants
Name Category Institutional Department and Gender Disability Ethnicity Race Visa/ Citizenship Affiliation LAB Status Aksel, Tural F UCSF CMP / DOUGLAS M None Not Hispanic/Latino White Decline to State Aldalali, Nusaibah G SFUSD Biochem/SEP F None Not Hispanic/Latino White Decline to State
Allen, Jessica J UCSF Biochem/SEP F None Not Hispanic/Latino White Decline to State
Alvardo, Sydney A SFSU Biology F None Hispanic/Latino White Decline to State
Amendariz, Angela J Exploratorium F None Hispanic/Latino White Decline to State Apollon, Chantilly D Holy Names U Biology F None Not Hispanic/Latino White Decline to State
Armstrong, Max B UC Berkeley Bioengineering / M None Not Hispanic/Latino White Decline to State FLETCHER Avalos-Perez, Jeremy A UCSF Ob/Gyn/FUNG M None Hispanic/Latino White Decline to State
Azanedo, Gabriela B SFSU Biology F None Latino White Decline to State Bauer, David B UCSF Biochem / MARSHALL M None Not Hispanic/Latino White Decline to State
Bayliss, Frank C SFSU Biology M None Not Hispanic/Latino White Decline to State
Benson, Gigi J UCSF Biochem F Decline to Not Hispanic/Latino White Decline to State State Bevir, Harry E UCSF Ob/Gyn/FUNG M None Not Hispanic/ Latino Caucasian Decline to State Bianco, Simone E IBM ADLab M Decline to Declined to state Declined to Decline to State State state Biswas, Sujoy Kumar F IBM ADLab / BIANCO M Decline to Declined to state Declined to Decline to State State state Black, Christopher B SFSU Biology M None Not Hispanic/Latino White Decline to State
Blauch, Luke B Stanford Mechanical M None Not Hispanic/Latino White Decline to State Engineering/Tang Bolivar, Jessica B SFSU Biology F None Hispanic / Latino White Decline to State 132 Bremer, Andrew B UCSF Pharm Chem/GARTNER M None Not Hispanic/Latino White Decline to State Name Category Institutional Department and Gender Disability Ethnicity Race Visa/ Citizenship Affiliation LAB Status Britain, Derek B UCSF Biochem / WEINER M None Not Hispanic/Latino White Decline to State
Brown, Cecilia B SFSU Biology F None Not Hispanic/Latino Black Decline to State
Brunetti, Rachel B UCSF Biochem / WEINER F None Not Hispanic/Latino White Decline to State
Bugay, John Paul A SFSU Biology M None Not Hispanic/Latino PI Decline to State
Bunafe, Marick A/B SFSU Biology M None Not Hispanic/Latino Pac Islander Decline to State
Burrus, Laura C SFSU Biology M None Not Hispanic/Latino White Decline to State
Cabral, Katelyn B UCSF Pharm Chem/GARTNER F None Not Hispanic/Latino White Decline to State
Cadiz, Brenda F U of PR, Biology F None Hispanic/Latino White Decline to State Humacao Campos, Luke A SFSU Biology M None Not Hispanic/Latino PI Decline to State
Brown, Cecelia B SFSU & IBM Riggs lab _-SFSU F None Not Hispanic/Latino Black Decline to State ADLAB/Bianco (Internship) Chadwick, Will B SFSU Biology M None Not Hispanic/Latino White Decline to State
Chan, Annette I SFSU Biology F None Not Hispanic / Latino Asian Decline to State
Chan, Eunice G FUSD Biochem/SEP F None Decline to State Decline to Decline to State State Chan, Mark C SFSU Biology M None Not Hispanic/Latino Asian Decline to State
Chan, Wei-Pei H FUSD Biochem/SEP M None Not Hispanic/Latino Asian Decline to State
Chandrasekaran, Sita A SFSU Chem&Biochem F None Not Hispanic/Latino Asian Decline to State
Chang, Amy B UCSF Biochem / MARSHALL F None Not Hispanic/Latino Asian Decline to State
133 Chang, Catherine B SFSU Chem&Biochem F None Not Hispanic/Latino Asian Decline to State Name Category Institutional Department and Gender Disability Ethnicity Race Visa/ Citizenship Affiliation LAB Status Chemel, Angeline B SFSU Biology F None Not Hispanic/Latino Asian /White Decline to State
Chevalier, Michael E UCSF Biochem/EL-SAMAD M None Not Hispanic/Latino White Decline to State Chu, Diana C SFSU Biology F None Not Hispanic/Latino Asian Decline to State
Clendenny, Melissa A SFSU Biology F none Hispanic/Latino White Decline to State Cole, Russell E UCSF Pharm Chem/GARTNER M None Not Hispanic/Latino White Decline to State
Coombes, Coohleen A/B SFSU Biology F None Not Hispanic/Latino PI Decline to State
Corpuz, Criszel B SFSU Biology F None Not Hispanic/Latino Pac Ilander Decline to State
Coyle, Scott F Stanford Bioengineering/PRAKAS M None Not Hispanic/Latino White Decline to State H Craik, Charles C UCSF Pharm Chem / CRAIK M None Not Hispanic/Latino White Decline to State
Creasey, Olivia B UCSF Pharm Chem/GARTNER F None Not Hispanic/Latino White Decline to State
Dalton, Jayden A SFSU Biology F None Not Hispanic/Latino Black Decline to State
Damasceno, Pablo F UCSF CMP / DOUGLAS M None Hispanic/Latino White Decline to State Dania Haq A SFSU Biology F None Not Hispanic/Latino White Decline to State
Denetclaw, Wilfred C SFSU Biology M None Not Hispanic/Latino Amer Indian Decline to State Diaz, Ulises B UCSF Biochem/MARSHALL M None Hispanic/Latino White Decline to State Domingo, Carmen C SFSU Biology F None Hispanic/Latino White Decline to State Douglas, Shawn C UCSF Cellular & Molecular M None Hispanic/Latino White Decline to State Pharmacology (CMP) Dumont, Sophie C UCSF Cell & Tissue Bio F None Not Hispanic/Latino White Decline to State
Edington, Alia B SFSU Biology F None Not Hispanic / Latino Black Decline to State
El Natan, Daniel E UCSF Ob/Gyn/FUNG M None Not Hispanic/Latino South East Decline to State Asian 134 El-Samad, Hana C UCSF Biochem/EL-SAMAD F None Not Hispanic/Latino White Decline to State Name Category Institutional Department and Gender Disability Ethnicity Race Visa/ Citizenship Affiliation LAB Status Elizarraras, Edward B SFSU Biology M None Hispanic/Latino White Decline to State Esin, Jeremy B SFSU Biology M None Not Hispanic/Latino White Decline to State
Esquerra, Ray C SFSU Chem&Biochem M None Hispanic/Latino White Decline to State Farhan, Anas G AUSD Biochem/SEP M None Not Hispanic/Latino White Decline to State
Fletcher, Daniel C UC Berkeley Bioengineering M None Not Hispanic/Latino White Decline to State
Frazier, Jennifer E Exploratorium F None Not Hispanic/ Latino White Decline to State
Fung, Jennifer C UCSF Ob/Gyn/FUNG F None Not Hispanic/ Latino Chinese Decline to State
Galli, Lisa E SFSU Biology F none Not Hispanic/Latino White Decline to State
Galvan, Luigi A UC Berkeley Bioengineering / M None Not Hispanic/Latino Philippino Decline to State FLETCHER Gao, Angela G FUSD Biochem/SEP F None Not Hispanic/Latino Asian Decline to State
Garcia Almadena, A UCSF Pharm Chem/GARTNER M none Hispanic/Latino Decline to State Derek Garcia, Jason A SFSU Biology M None Hispanic/Latino White Decline to State Gartner, Zev C UCSF Pharm Chem M None Not Hispanic/Latino White Decline to State
Gaytan, Norma B SFSU Biology F None Hispanic/Latino White Decline to State Gehr, James B SFSU Biology M None Not Hispanic/Latino White Decline to State Genuth, Miriam B UCSF Biochem / WEINER F None Not Hispanic/Latino White Decline to State
George, Kathi J Exploratorium F None Not Hispanic/Latino White Decline to State
Gonzales, Juliet A SFSU Chem&Biochem F None Hispanic/Latino White Decline to State Goodfellow, Sam B SFSU Biology M None Not Hispanic/Latino White Decline to State Gromova, Tanya E UCSF Ob/Gyn/FUNG F None Not Hispanic/ Latino Caucasian Decline to State 135 Guan, Yaxuan G SFUSD Biochem/SEP F None Not Hispanic/Latino Asian Decline to State Name Category Institutional Department and Gender Disability Ethnicity Race Visa/ Citizenship Affiliation LAB Status Hamkins-Indik, Tiama B UC Berkeley Bioengineering / F None Not Hispanic/Latino White Decline to State FLETCHER Hartono, Wiputra A SFSU Chem&Biochem M None Hispanic/Latino Pac Islander Decline to State Hendel, Nat B UCSF Biochem / MARSHALL M None Not Hispanic/Latino White Decline to State
Hernandez, Paulina A SFSU Chem&Biochem F None Hispanic/Latino White Decline to State Hoops, Kellen B SFSU Biology Trans to M None Not Hispanic/Latino White Decline to State Hu, Jennifer B UCSF Pharm Chem/GARTNER F None Not Hispanic/Latino Asian Decline to State
Hughes, Alex F UCSF Pharm Chem/GARTNER M None Not Hispanic/Latino White Decline to State
Jacques, Torey B SFSU Biology M None Not Hispanic/Latino Black Decline to State
James Gerh B IBM ADLAB/Bianco M Declined to Declined to state Declined to Decline to State State State Jessica Sawanna A SFSU Biology F None Not Hispanic/Latino Asian Decline to State
Joao Fonseca E UCSF Biochem/EL-SAMAD M None Not Hispanic/Latino white Decline to State
Jones, Barbara E IBM ADLab /Bianco F Declined to Declined to state Declined to Decline to State State state Kalbaugh, Erin B SFSU Chem&Biochem F None Not Hispanic/Latino AI/AN Decline to State
Khor, Jian Wei B Stanford Mechanical M None Not Hispanic/Latino Asian Decline to State Engineering/Tang Kimmel, Jacob B UCSF/ IBM Biochem/ Marshall & M Decline to Declined to state Declined to Decline to State IBM State state King, Briana G SFUSD Biochem/SEP F None Not Hispanic/Latino Black or African- Decline to State American & Asian
King, Denise J Exploratorium F None Hispanic/Latino White Decline to State
Kinney, Christen B SFSU Biology F None Not Hispanic/Latino White Decline to State
136 Kseniya Konova B SFSU Biology F None Not Hispanic/Latino White Decline to State Name Category Institutional Department and Gender Disability Ethnicity Race Visa/ Citizenship Affiliation LAB Status Kuei, Katy H FUSD Biochem/SEP F None Not Hispanic/Latino Asian Decline to State
Kuhn, Jonathan B UCSF Cell & Tissue Bio / M None Not Hispanic/Latino White Decline to State DUMONT Lak, Rhozhin A SFSU Biology F None Not Hispanic / Latino White Decline to State Lanns, Destinee B SFSU Biology F None Not Hispanic/Latino Black Decline to State
Law, Ashley B SFSU Chem&Biochem F None Not Hispanic/Latino White Decline to State
Lee, Kirby A UCSF Pharm Chem/GARTNER Decilne to State Decline to State Decilne to State Decline to State Levy, Jacqueline H SVUSD Biochem/SEP F None Not Hispanic/Latino White Decline to State
Lewis, Greyson B UCSF Biochem / MARSHALL M None Not Hispanic/Latino White Decline to State
Li, Amy Laishan A UC Berkeley Bioengineering / F None Not Hispanic/Latino Asian Decline to State FLETCHER Li, Selena A UC Berkeley Bioengineering / F None Not Hispanic/Latino Asian Decline to State FLETCHER Lim, Wendell C UCSF Cellular and Molecular M None Not Hispanic/Latino Asian Decline to State Pharmacology Lin, Athena G UCSF Biochem / MARSHALL F None Asian Asian /White Decline to State Liu, Zairan B UCSF Biochem / WEINER F None Not Hispanic/Latino Asian Decline to State
Long, Alexandra B UCSF Cell & Tissue Bio / F None Not Hispanic/Latino White Decline to State DUMONT Lopez, Alejandro B SFSU Biology M None Hispanic/Latino White Decline to State Louie, Justin H NUSD Biochem/SEP M None Not Hispanic/Latino Asian Decline to State
Ma, Huixin G SFUSD Biochem/SEP F None Not Hispanic/Latino Asian Decline to State
Macquarrie, Jaycee G NUSD Biochem/SEP F None Not Hispanic/Latino White Decline to State Makhija, Suraj B UCSF CMP / DOUGLAS M None Not Hispanic/Latino White Decline to State
Marshall, Wallace C UCSF Biochem M None Not Hispanic/Latino White Decline to State 137 Martin, Adrian B SFSU Biology M None Not Hispanic/Latino Asian Decline to State Name Category Institutional Department and Gender Disability Ethnicity Race Visa/ Citizenship Affiliation LAB Status Mathijssen, Arnold F Stanford Bioengineering/PRAK M None Not Hispanic/Latino White Decline to State ASH Mclaurin, Justin B UCSF Biochem / WEINER M None Not Hispanic/Latino African Decline to State American Meisnner, Brett A/B SFSU Biology M None Not Hispanic/Latino White Decline to State
Melendez, Phillip A SFSU Chem&Biochem M None Hispanic/Latino White Decline to State Mendez, Liam G CVUSD Biochem/SEP M None Hispanic/Latino Decline to State Mishreky, Patrick G CVUSD Biochem/SEP M None Not Hispanic/Latino White Decline to State
Miyazaki, Hikaru B UCSF Pharm Chem/GARTNER F None Not Hispanic/Latino Asian Decline to State
Moore, Jeremy A UCSF Biochem/MARSHALL M None Decline to State Decline to Decline to State State Muhammad Bin Siraj A SFSU Biology M None Not Hispanic/Latino Asian Decline to State
Murchison, Austin B SFSU Biology M None Not Hispanic/Latino Black Decline to State
Murrow, Lyndsay F UCSF Pharm Chem/GARTNER F None Not Hispanic/Latino White Decline to State
Nafisi, Parsa B UCSF CMP / DOUGLAS M None Not Hispanic/Latino White Decline to State
Nagy, Tamas B UCSF Biochem / WEINER M None Not Hispanic/Latino White Decline to State
Najibia, Sayeeda B SFSU Chem&Biochem F None Not Hispanic/Latino Asian Decline to State
Nand, Natasha A SFSU Biology F None Not Hispanic / Latino Asian Decline to State
Navarro, Erik B UCSF CMP / DOUGLAS M None Hispanic/Latino White Decline to State Nzerem, Madu A SFSU Biology M None Not Hispanic/Latino Black Decline to State
Oke, Ashwini E UCSF Ob/Gyn/FUNG F None Not Hispanic/Latino Indian Decline to State
Oluoch, Benazir A SFSU Chem&Biochem F None Not Hispanic/Latino Black Decline to State
138 Omar Mendoza B SFSU Biology M None Hispanic/Latino White Decline to State Ortega, Jose B SFSU Biology M None Hispanic / Latino White Decline to State Name Category Institutional Department and Gender Disability Ethnicity Race Visa/ Citizenship Affiliation LAB Status Osimiri, Lindsey B UCSF/UCB Bionegineering F None Not Hispanic/Latino African Decline to State program/El-SAMAd American Paiz, Jesus B SFSU Biology M None Hispanic/Latino White Decline to State Paraiso, Melissa J UCSF Biochem F None Hispanic/Latino White Decline to State Pastore, Vito Paolo F IBM ADLab / BIANCO M Declined to Declined to state Declined to Decline to State State state Patterson, David F UCSF Pharm Chem/GARTNER M None Not Hispanic/Latino White Decline to State Paulson, Amanda B UCSF & IBM Pharm Chem/GARTNER F None Hispanic White Decline to State - Intern, ADLab/BIANCO Peraza, Alma A SFSU Biology F None Hispanic / Latino White Decline to State Pereira, Ashley B SFSU Biology F None Hispanic/Latino White Decline to State Pineda, Christopher E UCSF Biochem/MARSHALL M None Hispanic/Latino White Decline to State
Pipathsouk, Anne B UCSF Biochem / WEINER F None Not Hispanic/Latino White Decline to State
Prakash, Manu C Stanford Bioengineering/PRAKAS M None Not Hispanic/Latino Asian Decline to State H Puri, Natasha E UCSF Biochem / WEINER F None Not Hispanic/Latino Asian Decline to State
Ramirez-San Juan, F UCSF & Biochemistry & F None Hispanic/Latino White Decline to State Guillermina Stanford Biophysics/ MARSHALL& PRAKASH Ramirez, Aura A SFSU Biology F None Hispanic/Latino White Decline to State Ramirez, Julio E SFSU Biology M None Hispanic/Latino White Decline to State Refuerzo, Russell B SFSU Chem&Biochem M None Hispanic/Latino Pac Islander Decline to State Reidy, Ryan H JUSD Biochem/SEP M None Not Hispanic/Latino White Decline to State
Reyes, Efren B UCSF Pharm Chem/GARTNER M None Hispanic/Latino N/A Decline to State Riggs, Blake C SFSU Biology M None Not Hispanic/Latino Black Decline to State
Rocha, Victor A SFSU Chem&Biochem M None Hispanic/Latino White Decline to State UCSF/SFSU Biochem/MARSHALL None Hispanic/Latino White/Asian Decline to State 139 Rodrigues, Nicole A F Ross, Angela G FUSD Biochem/SEP F None Not Hispanic/Latino Asian Decline to State Name Category Institutional Department and Gender Disability Ethnicity Race Visa/ Citizenship Affiliation LAB Status Roth, Kaitlin G WCCUSD Biochem/SEP F None Not Hispanic/Latino Asian Decline to State
Rousseau, Elsa F IBM ADLab / BIANCO F Decline to Declined to state Declined to Decline to State State state Ruiz, Donovon A SFSU Chem&Biochem M None Hispanic/Latino White Decline to State Saha, Suvrajit F UCSF Biochem / WEINER M None Not Hispanic/Latino Asian Decline to State
Sahiner, Tuba A SFSU Biology F None Not Hispanic/Latino White Decline to State Sanchez, Austin A SFSU Chem&Biochem M None Hispanic/Latino White Decline to State Santana, Frederick B SFSU Biology M None Hispanic/Latino White Decline to State Segura, R Carlos A SFSU Biology M None Latino White Decline to State Shabazz, Khayla A SFSU Biology F None Not Hispanic / Latino Black Decline to State
Shah, Devan B SFSU Biology M None Not Hispanic/Latino Asian Decline to State
Sims, Jasmine B SFSU Biology F None Not Hispanic/Latino Black Decline to State
Singer, Debra J UCSF Biochem F None Not Hispanic/Latino White Decline to State
Smith, Rebecca c & i UCSF Biochem/SEP F None Not Hispanic/Latino White Decline to State
Solis, Ricardo A SFSU Biology M None Hispanic / Latino White Decline to State Srivastava, Vasudha F UCSF Biochem/GARTNER/SEP F None Not Hispanic/Latino Asian Decline to State
Sun, Steven A/B SFSU Biology M None Not Hispanic/Latino Asian Decline to State
Suresh, Pooja B UCSF Cell & Tissue Bio / F None Not Hispanic/Latino Asian Decline to State DUMONT Susan Chen B UCSF Biochem/EL-SAMAD F None Not Hispanic/Latino asian Decline to State
Swinson, Wayne B SFSU Biology M None Not Hispanic/Latino Black Decline to State
Tang, Sindy C Stanford Mechanical Engineering F None Not Hispanic/Latino Asian Decline to State
140 Terrizzano, Ignacio E IBM ADLab / BIANCO M Decline to Declined to state Declined to Decline to State State state Name Category Institutional Department and Gender Disability Ethnicity Race Visa/ Citizenship Affiliation LAB Status Tischer, Doug B UCSF Biochem / WEINER M None Not Hispanic/Latino White Decline to State
Toda, Satoshi F UCSF Cellular and Molecular M None Not Hispanic/Latino Asian Decline to State Pharmacology/Lim Town, Jason B UCSF Biochem / WEINER M None Not Hispanic/Latino White Decline to State
Tran, Ngoc-Han B UCSF CMP / DOUGLAS F None Not Hispanic/Latino Asian Decline to State
Trocker, Matthew* J Exploratorium M None Not Hispanic/Latino White Decline to State
Vargas, Kevin A SFSU Computer Sci M None Hispanic/Latino White Decline to State Villegas-Parra, A/B College of Biology F None Hispanic/Latino White Decline to State Amayrani San Mateo Viloria, Olivia J UCSF Biochem F None Not Hispanic/Latino White Decline to State
Weiner, Orion C UCSF Biochem M None Not Hispanic/Latino White Decline to State
Wesley Huang A/B SFSU Biology M None Not Hispanic/Latino Asian Decline to State
Yancy, Ariana A SFSU Biology F None Not Hispanic / Latino Black Decline to State
Yang, Johnson A SFSU Biology M None Not Hispanic/Latino Asian Decline to State
Zhang, Jesse B UCSF Pharm Chem/GARTNER M Non Not Hispanic/Latino Asian Decline to State
Zimmerman, Thomas E IBM ADLab / BIANCO M Decline to Declined to state Declined to Decline to State State state
141 X. INDIRECT / OTHER IMPACTS
1. Center Engagement in international Activities
Activity: Research collaborations with international groups Organization/people involved: • Diana Chu (CCC) with Thomas Mueller-Reichert (Technische Universitaet, Dresden) • Orion Weiner (CCC) with Mathieu Piel (Institute Curie, Paris) • Wallace Marshall (CCC) with Vijay Rajagopal (University of Melbourne Australia) • Wallace Marshall (CCC) with Nan Tang (NIBS, Beijing China) Narrative: We have established, and will continue to seek out, collaborations with outside investigators whose expertise complements ours, and who can help us reach our goals by contributing their unique perspectives and knowledge. Among our external collaborations are the above listed international collaborations, which have the added effect of allowing our center work to impact research abroad.
Activity: CCC research featured in news program on biohacking by NHK television Organization/people involved: NHK television, Producer Takashi Shinno Narrative: NHK, the national public broadcasting station of Japan, is producing a special report program on biohacking, and as part of this program they filmed the CCC exhibit at the Bay Area Maker Faire in May 2018.
Activity: Participation in study of knowledge transfer by Japan Science and Technology Agency. Organization/people involved: Dr. Eimi Tomita, from the Center for Research and Development Strategy of the Japan Science and Technology Agency Narrative: Wallace Marshall met with Dr. Tomita to discuss how our center plans to conduct knowledge transfer activities. Dr. Tomita is tasked with studying knowledge transfer between academia and industry in the US so as to help the JST propose new policies to encourage such interactions in Japan.
Activity: Translating BIOMOD textbook from Japanese to English. Organization/people involved: Co-authors of the BIOMED Textbook include Satoshi Murata, Shin-ichiro M. Nomura, Ken Sugawara (Tohoku University), Shogo Hamada (Cornell University), Kei Fujiwara (Keio University), Hisashi Tadakuma (Kyoto University). Narrative: Shawn Douglas is working with Japanese professors to translate and edit an English- language version of a textbook. Here is a link for a free copy of the book: https://leanpub.com/biomod/c/n1BEoT11tHzJ (BIOMOD Foundation takes all proceeds from sales to recoup the translation costs from the original Japanese version of this book). Shawn is planning for a “cellular engineering” chapter co-authored by CCC members. During the past year, translation of the first six chapters, out of a total of eight, has been completed and made available online.
Activity: Micro-grant program for educational microscopy in India Organization/people involved: Department of Biotechnology, India Narrative: In collaboration with Department of Biotechnology, India – Manu Prakash announced a micro-grant program across India where children and educators can apply for
142 micro-grants and foldscope kits across the country. Over 700 applications from all states in India have been received, and the final kits were shipped in December 2017.
Activity: International foldscope workshops Organization/people involved: Syrian Kids, New Zealand Public Schools Auckland, Hong Kong Makers Community Narrative: Within the past year, the Prakash group has held foldscope workshops outside the U.S., in Refugee camps at Lebanon-Syria border (Syrian kids), New Zealand Public schools, Auckland (50 students), Hong Kong Makers community (50+ students), as well as groups based in the Amazon rainforest in Ecuador, and in Haiti, Guatemala, Mexico and more.
2. Other Outputs
None
143