Team:Stanford/Human Practices

Integrated Human Practices:
Interviews and Experimentation

The human practices portion of an iGEM project is perhaps the most important work that a team can do, because it informs all other aspects of the project. The end goal of a project is to create a product: a proof-of-concept for a technology that can effectively solve a problem. In order to create an optimal product and user experience, it is important to develop the technology with all parts in mind: how are we going to develop the product, who are we developing the product for, how can we design the product to best suit their needs, and through what avenue can we work to get the final product to them? Through our human practices interviews and lengthy conversations among the team as we invented our system, we worked to answer those questions and integrated various important considerations into our final design, product, and entrepreneurial plan.

On this page you will find:

1. Summaries of Interviews:
‍ Including descriptions of interviewees, their contributions and insight during our conversations, and our next steps based on the feedback we received.

2. Documentation of Experiments:
Conducted in response to interview feedback, with the aim of testing and verifying the viability of design ideas that were suggested to us.
‍

3. Key Takeaways:
Synthesizing the information we received from people and from our experiments into a solid plan of action moving forward into the entrepreneurial phase.

On our Ethics page, you will find:

4. Ethical Analysis: Another portion of our Human Practices initiative was considering ethics as we thought about entrepreneurship. What are the ethical implications of making our technology open-source? How could we implement our technology in the most ethical manner? What business model would be the most ethical moving forward, and how can we ensure that we allow the most people possible to benefit from our technology? The conclusions we came to guided the actions we took in planning steps forward; for example, it informed how we advertised ourselves as we searched for extending funding from investors. Find the full analysis on our Ethics page, linked below.

Interviews: Gaining Perspective and Feedback

Our Human Practices Focus: Working Towards Implementation As A Viral Test In A Centralized Setting

Creating a live cell that works as a growable diagnostic test for any nucleic acid sequence is a project with a wide variety of applications and implications. In order to narrow the scope of our Human Practices project to allow for in-depth investigation, we decided to focus our interviews on gathering insight on implementation within a first-world clinical, centralized setting. Our team has secured funding to continue to develop our system beyond the iGEM competition, through a program in Stanford's School of Medicine called Stanford Medicine Catalyst, where we have connections to potentially help us deliver the technology to market and to be used by Stanford for widespread COVID-19 testing. Therefore, we felt that focusing on this particular use of SEED was the most relevant.

Methodology

To obtain different perspectives for our interview study, we reached out to a variety of people who are currently doing work related to the COVID-19 pandemic so that we could learn from their experience and expertise.

After verifying that we did not need IRB approval to conduct our interviews, in holding with iGEM’s ethical guidelines, we designed a written consent form (form linked here) to inform our interviewees about what the interviews would look like beforehand.

Once we had obtained the signed consent form from the interviewee, we could go ahead with the interview. Due to social distancing guidelines and our remote working environments, all of the interviews were conducted over Zoom with each interview taking about 20 to 40 minutes.

Though we would brainstorm questions for each interviewee beforehand, the interviews were fairly informal and included follow up questions as well. If notes were not taken during the interview itself, the interview was recorded for the purpose of taking notes at a later date. These notes were then condensed into the interview summaries that you can see below.

Part 1: Informing Interface Design

Dr. Benjamin Pinsky | Associate Professor of Pathology and of Medicine, Stanford School of Medicine

Dr. Pinsky is a Clinical Pathology Specialist and Medical Director of the Clinical Virology Lab for Stanford Health Care and Stanford Children’s Health. His research is focused on the development of novel infectious disease diagnostics. Earlier this year, his lab developed a novel diagnostic for COVID-19 which has been widely used to help address the testing needs of Stanford Hospital as well as Lucile Packard Children’s Hospital. 

Topics of Discussion: Dr. Pinsky felt that the development of new testing modalities would be helpful as we continue to deal with widespread infectious disease because supply chain issues have been one of the main things limiting the production of diagnostic tests. He believes that the development of new tests that do not rely on the same materials or reagents as current tests could help people to be less impacted by supply chain limitations. He also reiterated the potential for at-home testing to help people track their own infection status, but expressed several possible concerns. Some of the potential concerns he has for at-home testing are the drop of testing effectiveness when tests are administered at home, the potential lack of comfort for users administering a test themselves, and the necessity for at-home testing to be inexpensive enough to be very accessible for the general public. 

Next Steps: Developing Simple Protocols for At-Home Use
This interview inspired our team to try to make our design cheaper and easier to use. Part of this process was investigating ways to make the testing procedure simpler, and developing a concept for a kit that includes all the necessary reagents to enable easy at-home testing. The conversation inspired us to design and implement experiments in lab to try simulating using our system in an at-home environment (which you can read more about below).

Dr. Lisa Goldman Rosas | Associate Professor of Epidemiology, Population Health, and Medicine

Dr. Goldman Rosas is passionate about integrating patients, community organizers, and other important stakeholders into the research process which has been a focal point of her work as the Faculty Director of both the School of Medicine Office of Community Engagement and the Stanford Cancer Institute Community Outreach and Engagement Program. As a part of this work, she helps researchers, community organizers, and patients develop long-lasting, sustainable partnerships that support new and ongoing research. 

Topics of Discussion: Dr. Goldman Rosas gave the team important insight into how to build meaningful and helpful partnerships with the communities we intend to work with. She gave important insight into resources we could take advantage of at Stanford in order to build sustainable partnerships. She also gave insight into how we could develop tools to help people better interface with the test itself. Some of these things included offering the testing procedure in a variety of languages, partnering with trusted community-based organizations when rolling out the test, and ensuring users have accurate and informative information about the test (i.e. its effectiveness, how it works, risks, etc.).

Next Steps: Developing A User Interface Accessible To All People
Dr. Goldman Rosas confirmed the importance of our goal to make testing more accessible for all people. She also gave us important advice and access to resources on how we could build community partnerships that we intend to take advantage of as we continue to work on the project. Finally, she inspired us to look further into ways we could increase the accessibility of our design. 

Prof. Drew Endy | Associate Professor of Bioengineering, Stanford University

 Professor Drew Endy is a leading mind in the field of synthetic biology. A founder of the iGEM competition, he also helped to found the bioengineering majors at both MIT and Stanford, where he now resides as a faculty member and mentor for Stanford’s iGEM team.

Topics of Discussion: Professor Endy helped us understand some of the big picture goals of our diagnostic tool. He pointed out the necessity of a cheap and scalable COVID test in that testing is an important tool for getting rid of the operational consequences of viruses, and knowing your infectious disease status is a responsibility for everyone to keep themselves and those around them safe. He also spoke about how the user experience of COVID testing needs improvement, and that ideally, a test would be non-invasive and always listening - like a smoke detector for your health status. Finally, he pointed us to surveillance testing in sewage water as an innovative way to conduct surveillance testing at an institution, especially with large numbers of students living close together and spurring outbreaks. 

Next Steps: Investigating Alternative Sample Collection Methods
Professor Endy’s guidance helped inform the long term vision of SEED. With the discomfort of the swabs now in mind, we hope to work towards a more desirable method of sample collection, such as a spit test. We were also inspired to make the test as easy to use and access as possible to nudge individual behavior towards getting tested as frequently as possible. We considered the widened scope of applications for our diagnostic, as it doesn’t necessarily need to test samples collected directly from patients to provide useful tracing information.

Dr. Milana Trounce | Clinical Professor in Emergency Medicine, Stanford University

In addition to serving as a Professor of Emergency Medicine at Stanford Medical School, Dr. Trounce also directs the BioSecurity program at Stanford, which focuses on protecting society from pandemics and other threats posed by infectious organisms. 

Topics of Discussion: Dr. Trounce raised some important concerns about SEED, including the ability of non-experts to use the test at home, the mutation of the test itself (since bacteria tend to randomly mutate over generations), and the FDA regulations that our group would face. She was also excited about the implementation of our self-replicating test in the third world, especially in areas that have less resources. 

Next Steps: Ensuring Interchangeability and Accuracy
Dr. Trounce pushed us to consider how we plan to maintain the accuracy or our test over time, which we could potentially validate with a set of future experiments. She also reaffirmed the value of our technology platform in creating a diagnostic that could be used for detecting more than one sequence of DNA. 

Part 2: Informing Implementation

Dr. Ori Tzveili | Medical Director and COVID Operation Chief, Contra Costa County

Dr. Tzveili is a family practitioner who is currently serving as the medical director and COVID operations chief for the county of Contra Costa in Northern California. His responsibilities include managing the county’s testing, contact tracing, lab branches, and policy decisions. With limited county resources, he also guides policies that help triage test distribution.

Topics of Discussion: Dr. Tzveili felt that there was potential for an at-home test in that many individuals would make the morally sound decision to disclose a positive test result to their contacts, and when paired with cheap and easy to obtain tests, this would allow for much faster and more effective decentralized contact tracing. He emphasized the importance of having the tests be rapid, so that results are meaningful, and easy to scale, given his experience struggling to obtain access to tests for his county.

Next Steps: Understanding the Implementation Pipeline
This interview affirmed our intended goal of designing a cheap and accessible test that can be used at home. We also learned more about the potential barriers we face with cost and use of a centralized lab facility. That insight helped us inform our Proposed Implementation by giving us insight into the pipeline that we will potentially use to implement this test in the real world.

Christina Agapakis | Creative Director at Gingko Bioworks

Christina Agapakis is currently working at Ginkgo, a synthetic biology company that is currently developing COVID-19 tests, to design a business strategy, product, and service that utilizes a public health perspective to increase the number of people receiving tests. Her work includes clearly communicating the testing process, and designing the testing process to be accessible for everyday use so that Ginkgo’s pandemic response can best serve their community.

Topics of Discussion:  Christina’s experience with developing the user experience for a COVID testing strategy that utilizes synthetic biology was directly applicable to our vision for the implementation of SEED. She spoke to the importance of building a strong brand, building trust, and communicating the potential impact of a tool that uses synthetic biology. She showed us how when she was naming Ginkgo’s testing program -  now dubbed Concentric -  most people using the test are more interested in how the test is able to benefit them and their community instead of how it actually works, putting public health messaging at the center of her communication strategy. Christina also spoke to Ginkgo’s efforts to make Concentric accessible by forming strong relationships with public health researchers at academic institutions to communicate best testing practices, working to lower the price point of their tests, and working with local non-profits to reach people who need testing and advocate increased testing access.

Next Steps: Planning How To Market Our Diagnostic
This interview led us to think critically about the best to communicate the impact of our diagnostic from a public health perspective. Especially as our group moves towards forming a company ourselves, Christina’s analysis of Ginkgo’s positioning in supporting academic research, working with nonprofits, and interfacing with community members was valuable in advising our goals for SEED’s implementation.

Russel Furr | Associate Vice Provost for Environmental Health and Safety at Stanford

Prior to the COVID-19 pandemic, Associate Vice Provost Furr oversaw Stanford’s health and safety programs. He has since taken the lead in coordinating the university’s response activity for the pandemic while managing health and safety issues for all of those on campus.

Topics of Discussion:  Associate Vice Provost Furr spoke to the logistics of implementing current COVID tests and other safety measures on Stanford’s campus. We learned that most tests currently being used at Stanford require sample processing at external labs, containing costs, and ensuring turnaround time. He also spoke to the importance of changing the physical environment, modifying individual behavior, and redesigning processes in addition to testing to keep the rate of transmission at a manageable level. Finally, we talked about the importance of having tests be fast and easy to use and not limiting our testing scope to Stanford but to consider including organizations with limited resources.

Next Steps: Considering Implementation Within Our Stanford Community
In further understanding the testing logistics at our university, Associate Vice Provost Furr helped us to imagine how our test would ideally fit into and improve the current COVID-19 testing infrastructure on campus. We also gained an appreciation for the behavioral and social measures that limit the virus spread in addition to testing measures.

Will Shan and Adonis Rubio| Co-Directors of the Associated Students of Stanford University's COVID Response

Will and Adonis work in tandem with Stanford University and Vaden Health Center to provide input and insight for COVID safety measures on campus, as well as give indispensable feedback to the administration on their COVID response and its effect on students. 

Topics of Discussion:  Will and Adonis gave a full picture of how Stanford is dealing with testing, which provides great insight as to how SEED can be helpful. According to them, while the weekly testing guideline for students on campus does not cause a shortage in testing, it can impact wait-times and general convenience concerns. Also, Stanford does need to nudge a few people to get tested more regularly, which is often difficult because the only incentive in place is the campus compact, which is not formally enforced. Students do have access to a regularly updated COVID dashboard with general information, but there is some difficulty in understanding this data, and in notifying people that they have come into contact with someone SARS-CoV-2 positive. Will and Adonis opine that the ease of testing is most prioritized by students, along with turnaround time, and convenience, and that students share a common desire with administrators for more accurate results. Will and Adonis think that self-administered testing would be really helpful as well as something that wouldn’t require a nasal swab, since although most students tolerate it, they certainly do not prefer it. 

Next Steps: Developing Effective Educational Resources for Implementation
Will and Adonis motivated us to consider the educational and instructional component of our test. They recommended including some sort of pamphlet that outlines how SEED would work, and why it is beneficial especially if it became widely available. They also prompted us to consider how to keep our project meaningful by ensuring that people have the desire to test themselves regularly with it.

Experiments: Testing Simpler Protocols

Creating Simple Protocols for At-Home Use

In the laboratory as we worked with our system this summer, we had to rely on having an incubator shaker to grow up liquid cultures and induce natural competence. For potential at-home users, they would not have access to this kind of equipment. In order to gain more insight into how our test could be implemented in an at-home setting, we tried simulating at-home conditions in the lab, not using any lab equipment to induce competence in our cells or to transform them. We attempted to answer the following research questions:

1. Can our cells become competent without shaking?

First, we tried to induce competence in the cells without shaking, but keeping all else the same, continuing to incubate them at 37 degrees. We did this experiment by growing up multiple cultures of cells, adding mannitol (to strain 1276) and xylose (to strain 976) to induce competence, and then leaving half in the initial conditions of a 37 degree Celcius incubator shaker, and leaving the other half in a 37 degree Celcius incubator, without shaking.

Results: It is possible to induce competence in our strains of B. subtilis without the use of a shaker.

2. Can our cells become competent with faster incubation times?

Once we had confirmed that it was possible to induce competence in our cells without the use of shaking, we moved on to testing out more variables. We had established that our cells became competent after 3 hours of incubation with the inducible compound. Our next step was to try incubating the cells for shorter amounts of time, to establish what the minimum incubation time was. We found that we could induce competence and get transformation after 1 hour of incubation at 37 degrees.

Results: It is possible to induce competence in 1-3 hours of incubation at 37 degrees.

3. Can our cells become competent at different temperatures?

After we had established that competence could be induced without shaking, and with only an hour of incubation, the next step was to test the temperatures at which competence could be induced. We incubated cultures at room temperature and 37 degrees. Only the cultures incubated at 37 degrees were transformed. Further testing is needed at a wider range of temperatures to establish a minimum and maximum incubation temperature.

Results: More tests are needed to figure out how to induce competence between room temperature and 37 degrees Celsius.

4. Can B. subtilis become competent without the addition of xylose or mannitol?

To test how competent the cells are without the addition of the inducing compound, we incubated the cells for 3 hours at 37 degrees without adding xylose to strain 1A976 or mannitol to strain 1A1276. Neither of these cultures resulted in transformation, indicating that the inducing compounds are needed to get DNA uptake at reliable rates.

Resuts: Xylose or mannitol are needed to reliably induce competence for our strains of B. subtilis.

5. If yes to any of the above, how does timing of the test change?

We have established that competence can be induced without shaking, at 37 degrees Celsius, with only an hour of incubation. With further testing, competence could be induced at lower temperatures as well. This means we could develop a test that could be performed in an at home setting in just a couple hours, using items common to many households.

Creating Sporulation Protocols for Easy Shipping

For the implementation step of our project, we want to be able to ship our diagnostic cells around the world cheaply and easily. Part of the reason why we chose B. subtilis is because of its ability to sporulate into an inactive state, where it can be sent in foil packets through the mail and stay viable for months, with no refrigeration or nutrients necessary. Part of understanding the implementation pipeline we would use comes from testing how we can get our cells from the petri dishes in our lab, into a mail delivery system. We were able to verify that the following protocol works for that purpose:

SPORULATING AND REVIVING B. SUBTILIS

Sporulation Materials

• 3+ day old culture of Bacillus subtilis
• Heating block
• Liquid media

Sporulation:

Total time: 20 minutes (after cultures grow)

• Allow Bacillus subtilis cultures to grow for 3-5 days (or until they reach their decline phase of growth) at 37 degrees Celsius°C and 200 rpm
• Prepare serial dilutions of the culture (10-2 - 10-6 fold) with liquid media
• Incubate at 80°C for 15 minutes
• Store spores at room temperature in tubes or aluminum foil

Reviving Materials

• Plates
• Nutrient broth
• Sporulated Bacillus subtilis

Reviving Spores:

Total time: 12+ hours

• Add spores to selective media
• Add several drops of nutrient broth to cover spores
• Grow for a minimum of 12 hours at 37°C

Conclusion: Key Takeaways

Interviews

Though we interviewed people from a variety of different backgrounds and disciplines, a few key common themes appeared throughout the conversations:

1. The importance of a cheap test.

The current price of tests is a massive barrier to widespread testing in many public settings. We had approached the development of a cheaper test originally with the goal of making it more accessible to underprivileged communities around the world, but many of our interviewees drew our attention to the needs of public schools in the US. Many public schools in the US have faced prolonged closure, forcing many students to face challenges and inequities with online schooling and parents to face new challenges with childcare. With public schools playing an integral role in the lives of many American families despite their often limited budgets, it is easy to understand why many of our interviewees stressed the reopening of schools as a central benefit of a cheaper test. While we will continue to work with the long-term goal of making this technology open source so that anyone can theoretically have access to it, this insight pushed us to focus our short-term plans for implementation on our immediate community where we are well equipped to build community relationships and make a positive impact. We also plan to test the efficacy of SEED after it has been sporulated, since sporulated bacteria are much cheaper to transport than live cells, thereby lowering the cost of our test.

2. The importance of user-friendliness, especially in an at-home setting.

As our interview made clear, the user experience of most COVID tests could be improved, with most people preferring a form of sample collection that does not involve a deep nasopharyngeal swab. Making the sample collection itself more comfortable is a key step towards incentivizing people to get tested more frequently. Ease of use plays an even larger role in developing a test for at home use, where we need to comply with FDA regulations that ensure that the test is not complicated to use accurately and that the results of the test are easy to comprehend. This prompted the team to plan a series of experiments to begin validating the test in an at-home context, including: testing competence at room temperature, practicing bacterial sporulation and subsequent regrowth, and adding sugars and antibiotic resistance markers to the media so that an intermediate liquid culture step is not necessary. These experiments will constitute the first steps in ensuring that the physical design of our test is as accessible as possible.

3. The importance of having an accurate test.

While this was a straightforward goal for our team from the beginning, the interviews brought more nuance to how we plan to go about achieving this goal. Some pointed out that if our test were available to be used everyday and return results in under an hour, our tests would give an individual more data points to understand their health status, thus improving through probability the long-term “accuracy” of our test even without changing how accurate an individual test is. We were also prompted to be more cognizant of how accurate tests are after they have been replicated multiple times, given how bacteria randomly mutate over generations. To test accuracy, we incorporated key experiments including evaluating the level of competence of the bacteria, and how much DNA they need to detect to produce a read-out. Once we are able to successfully transform a B. subtilis strain and culture it, we plan to repeat these experiments on a colony that results from several generations of growth to determine how well the accuracy of SEED is maintained over time.

4. The importance of clear and transparent communication of how the tech works, and how well.

Whether getting tested on campus or with a separate health care provider, many of our interviewees ran into blocks when trying to learn details about the steps that were taken to ultimately deliver them their results, and how accurate those results were. With our long-term goal of making our test open source, we plan to also communicate the results of our experimentation so that everyone can learn the technicalities of SEED and how it’s different aspects function. We also plan to use a public health lens to format this information in a way that is easy for the general public to understand and glean the information that is most relevant to them (how to operate the test, rate of false negatives, etc.). This information will also be made available in multiple languages to reduce a potential language barrier in understanding or choosing to use our test. We hope that these steps to communicate clearly with the public will allow us to build trust in our test, thereby increasing the number of individuals who use it to inform their COVID-19 status.

Experiments

From our experiments, we were able to verify protocols that could be used for implementation in preparing samples to ship across the world. We were also able to refine our ideas for how an at-home test could be implemented. We learned the following:

• Sporulating Bacillus subtilis and shipping through the mail is a simple and feasible option
• Our cells can grow in liquid cultures without the incubator shaker involved in our protocol. They can become competent without a shaker, which means that all of our protocols could be done within an at-home setting, without expensive lab equipment, potentially using an oven or other warm place for growing cells and inducing competence.
• Our cells can also become competent after only an hour of incubation with the inducing compound, only one third of the traditional incubation time. This brings us one step closer to designing a rapid, at home diagnostic.
• Our cells can grow and become competent at 37 degrees for optimal growth temperature. At-home users could potentially use their ovens at home for growing and competence steps. If set to bread-proofing settings, household ovens can act as incubators that are between 26 and 36 degrees. Our team will continue to test incubation temperatures, times, and other variables to make the test even easier to run at home.