Rhizomet (Environmental Heavy Metal Bio-Extraction Project)
We are Washington iGEM: a team of undergraduates at the University of Washington dedicated to solving problems in medicine and the environment using synthetic biology. Our project goal is to engineer E. coli to extract lead and arsenic from wastewater with target proteins, and construct a biofilm-based filter. We currently own lab space within the UW Biochemistry Department and will conduct our wetlab research at this site. Due to the experimental nature of our project, we estimate the total cost of our project to be $25,000-$30,000 and are thus requesting CSF to provide $17,000 - $22,000 to fund the remainder of our project. In addition to the negative health effects on ecological life, heavy metal pollution affects human health in detrimental ways and is the cause of millions of deaths and disabilities worldwide. With the guidance from professors, mentors, and advisors, the Washington iGEM team is strongly motivated to cure local water used by the University of Washington/Puget Sound area and beyond.
Here is a link to our website which shows all of our prior research projects:
Our team is primarily run by UW undergraduates students who are strongly motivated to induce environmental change. We had a recruitment cycle in Winter 2021, and currently, we consist of 24 undergraduate students who are all divided into subteams: Drylab, Wetlab, Human Practices, Web Development, Fundraising, and Design. Our team consists of members from various majors such as bioengineering, biochemistry, computer science, biology, and business, all of which are essential in executing a successful project, allowing collaboration of students from different backgrounds. The team is also assisted by three advisors who are dedicated past team members as well as UW graduates. In addition, Dr. Frank DiMaio, a UW professor from the Biochemistry Department, provides our team with his expertise in protein modeling, and Dr. Mari Wrinkler from the Civil & Environmental Engineering Department mentors us in kinetic modeling. We are also communicating with Anna Lauko, a graduate student from the Baker Lab, who has expressed interest to be our mentor for our wetlab research. Our team is thus well equipped to handle our project’s goals.
Wetlab: in charge of the hands-on parts of synthetic biology. Focus on executing lab experiments, analyzing data, and sending parameters for drylab modeling.
Drylab: responsible for the creation of complex systems that require extensive computational modeling of proteins and reaction kinetics. Aim to optimally improve the function of existing proteins and design novel proteins to robustly develop the project by utilizing cutting edge software and applying biochemical knowledge.
Human Practices: facilitate discussions with faculty, advisors, professionals, and impacted citizens from the Puget Sound area and beyond to explore topics regarding ethical, social, political, economic, biosafety, and biosecurity factors related to the project’s research. Human Practices seeks to expand upon the technical aspects of the project to fit in a real-world context.
Web Development: maintains the portal between the team and the rest of the world. In charge of creating a project wiki page that illustrates clear visualizations of our project’s experimental data and processes.
Fundraising: manages all the finances and the raising of funds for the project. Responsible for applying to grants, presenting on crowdfunding platforms, and contacting potential sponsors, such as UW departments and companies that have similar goals.
Design: responsible for creating graphics, videos, and animations for our team’s website, presentations, public events, and merchandise.
Even though we already had a recruitment cycle earlier this year, any UW student with a passion for synthetic biology, environmental sustainability, and health are always welcome to join our team. Due to our team’s organizational structure, new members are easily able to make a difference and we pride ourselves on how well we’ve been able to maintain an environment for members to stay actively involved. Over the past year, we’ve noticed an abundance of students at UW who would like to get involved in research, and a large portion of them are interested in synthetic biology as well. Especially amidst the pandemic, only a limited number of them can get into research labs. Thus, our team aims to be inclusive by offering the opportunity for students to gain skills applicable in any lab and allow them to gain more experience in their field of interest. We also plan on including UW students during the implementation of our product. In order for the implementation phase of our project to be successful, we realize that a big part of the UW community will need to support us. We also would like to involve members of the community during the installation or launch of our product.
Education & Outreach:
Outreach - Partnerships:
We are devoted to educating the UW and the local community on pollution. Forming partnerships with other organizations with aligning interests and similar visions is an outreach goal. From a long-term and professional standpoint, our team plans to partner with local companies conducting similar research to host events and spread awareness to the general public about pollution and how synthetic biology is a sustainable solution. Our team is currently in contact with the Washington Department of Ecology, Teck American, and the Everett and Tacoma (Asarco) Smelter Restoration Sites, as well as non-profit groups such as The Northport Project and Environment Washington. As far as educational outreach within the UW community, during the upcoming school year, we hope to partner with other RSOs that are involved in environmental sustainability such as EcoReps, UW SEED, SeaDawgs, SAGE, and UW Net Impact to collaborate on a university-wide event. We are planning this event to be a synthetic biology workshop because we want to provide more opportunities for UW students, especially underclassmen, to gain tangible research experience. Those who participate in this workshop will get to perform a series of mini-experiments that parallel the research conducted by modern synthetic biologists. We have already initiated contact with some of the listed RSOs and we have everything in place on our end to execute this workshop event. Additionally, we plan to raise awareness about the problem through holding a variety of educational outreach events at the UW, catering to both faculty and students. Our annual Fall flagship panel event allows students to ask questions and learn more about our project and synthetic biology as a whole. We will include team members, professors and other experts in the field. Our team is currently in the midst of reaching out to those in the Department of Biochemistry, Oceanography, Bioengineering, and Civil and Environmental Engineering to gauge the interest of potential faculty speakers. Our goal through this event is to pique students’ interest in solving problems that affect the world around them through synthetic biology. This will also give our team the opportunity to publicize our heavy metal extraction project and earn support from UW students. We held a similar event in 2019, which consisted of a diverse panel. UW professors such as Dr. James Carothers and Dr. Jesse Zalatan, as well as local research scientists participated, and we believe a similar event will be worthwhile in our outreach efforts this year. For all our outreach events, we will use our non-CSF funds to support these events, though we expect these costs to be fairly minimal.
Outreach - Education:
Synbio for Everyone, which branched out from Washington iGEM, focuses on spreading knowledge about synthetic biology to younger children, and is currently expanding from the area of synbio to all sciences. They concentrate on improving synthetic biology education accessibility and reducing education equity gaps in STEM through outreach events. In 2019, we collectively published a 200-page curriculum, which has been translated into 20+ languages, and has been implemented in local underserved schools, STEM events, and in three different continents. This contributed to our team winning the Best Education and Public Engagement Award in the 2019 international iGEM Jamboree competition. Synbio for Everyone is now more involved in nonprofit STEM educational projects. However, we work together in our outreach efforts. In collaboration with Synbio for Everyone, we have many future events planned. For example, we want to host an event where we will teach synthetic biology to middle schools in the local Seattle area through a hands-on approach. We want to be involved in inspiring the next generation of scientists which is why we feel this endeavor is worthwhile. We also plan to host a science fair event for elementary school students. We have developed simple, fun, and safe mini-science experiments for kids to rotate through, that will teach them basic science concepts.
Outreach - Communication:
In terms of formally publicizing our research, all our findings and results will be kept track under the official Washington iGEM RSO Page (http://students.washington.edu/uwigem/#/) and the Washington iGEM Wiki Page (https://2021.igem.org/Team:Washington). It will include information about all parts of the project, from project description, design, experiments and results, modeling, and parts, to stakeholders and collaborators involved, available to the public. We also provide updates to the project as it progresses, both on our websites and on social media. Our primary method of communication to the UW community is through social media platforms such as Instagram, Twitter, and Facebook. We will advertise our events and project accolades through these media.
- Environmental Justice
We define long term as longer than 6 months. After 6 months, when we have developed our solution, we plan to participate in the international iGEM Jamboree competition, the UW Undergraduate Research Symposium, and the Environmental Innovation Challenge, where we hope to receive more funding to further our project. If successful, we hope to build this project up into a startup. As a startup, we would employ the Lean Startup methodology, where we will refine our product while constantly getting feedback from stakeholders. This way we wouldn’t waste any resources, and effectively use the funds given to us. Not only do we envision our project to benefit many stakeholders in Washington state, but other locations around the nation and the world. As a startup and due to the theme of our project, we would heavily value corporate social responsibility. Many of the places we have identified that are affected by heavy metal toxins, do not have equitable access to clean water and are overexposed to environmentally unsafe pollutants. Low income communities have higher clean water insecurity, which is why these locations take priority in our long-term implementation timeline. Our project aims to address and advocate for environmental and social sustainability.
Our current biofilm based filter targets arsenic and lead, but we plan on refining its design and potentially develop a more versatile device that can extract other toxic heavy metals. There are not any current plans of commercializing our product, but we plan on forming local government partnerships that would allow us to treat polluted waters. In the long term, we will continue managing this project with our mentors giving us advice and feedback.
The challenge at hand is developing an extraction method to reduce the level of heavy metal pollution in water. Heavy metal toxicity is responsible for many health crises. It interferes with blood, bones, and the nervous system, resulting in anemia, osteoporosis, and cognitive defects. The true extent of damage is difficult to quantify due to the many adverse health effects, but lead poisoning alone accounts for half a million deaths a year and 9.3 million disabilities (WHO). Smelters have historically been strong contributors to heavy metal pollution in the environment, and their cleanup efforts have been extremely expensive.
How This Project Addresses the Sustainability Challenge:
We want to develop a sustainable synthetic biological solution to extract heavy metals from wastewater. Our goal is to engineer E. coli to extract lead and arsenic from wastewater with target proteins, and construct a biofilm-based filter. The use of biotechnology has been increasingly popular and commonly used due to its sustainability and more cost efficient aspects. Engineering bacteria, such as E. coli, with the target proteins and designing them in a way to extract heavy metals avoids releasing more toxic and inorganic compounds back into the environment. Most E. coli are actually harmless and found in the human intestinal tract. They are the most common organism engineered in labs and can be easily manipulated with well documented details and extensive reference literature. We are currently working on extracting arsenic and lead from water because we identified that abnormally high concentrations of these heavy metals are pervasive in the environment and have the potential to cause serious acute and chronic diseases such as pulmonary disease and cardiovascular disease. Compared to current in-use remediation procedures that involve excavating and replacing wastewater and polluted soil, our solution, by addressing this problem at its source, will be much more cost-effective and efficient in preventing heavy metals from impacting the environment, benefitting both the smelters and the people affected. For example, by collaborating with Teck Resources, a smelter upstream of many cities along the Columbia River, to treat heavy metal pollution at its source, our solution has the potential to benefit large populations of people in Eastern Washington.
All experimental research will be conducted in our laboratory in the UW Biochemistry Department. Though we suspect lead and arsenic to be the primary contributors to heavy metal pollution in waters, we don’t know for certain that UW/Lake Washington/Puget Sound is solely affected by these specific metals and to what extent these waters are polluted. Thus, we would need to execute a feasibility study to determine how to best suit the needs of the Pacific Northwest. Once we know what specifically needs to be improved, we can swiftly modify our synthesized proteins to extract harmful agents in local waters. Currently, our human practices team has conducted a preliminary extensive literature review, and have found studies that highlight heavy metal pollution in bodies of water bordering the UW, including Lake Union, Shilshole Bay, and the strait of water that connects them. Additionally, sites like Everett, Tacoma, and Northport have high concentrations of heavy metals that exceed safety limits set by the Washington Department of Ecology. With Lake Washington and Lake Union being in such close proximity to our research base, UW will be a great starting point for preliminary installation in terms of a testing site for our biofilm-based filter. Areas located around smelters such as Everett affected by heavy metal polluted wastewater and contaminated soils that pose significant risks to human and wildlife health can be prioritized following successful results at UW.
From our research, we believe that although the UW campus itself has a lower concentration of heavy metals compared to manufacturing sites, we can still produce significant results by focusing on bodies of water proximal to the UW with industrial and shipping activity, such as Lake Union and other nearby areas, such as the UW’s Union Bay Natural Area. Taking into account UW’s environmental sustainability and conservation goals, reliance on waterways, and how many UW departments conduct health and ecological research in local Seattle waters, we envision our project to have an immediate impact on the UW community. After establishing that our product indeed makes a difference, we can expand to other areas outside of UW, such as Northport, Everett, and Tacoma, that are affected with chronic and acute debilitating diseases.
Out of the total amount we are requesting from CSF to fund our project, we expect nearly 100% of the funds to be allocated to research. As for implementation costs, we plan on using our existing funds to purchase necessary testing equipment. Since the physical implementation of this restoration project is mainly driven through student efforts and volunteers, the labor and high overhead costs can be largely omitted from the implementation costs of our project. The remaining cost of implementation can be partially attributed to monitoring the levels of heavy metal pollution using analytical services provided by the College of Forest Resources to analyze and ensure the efficacy of our product. Each test costs $14, so testing would cost $700 for 50 tests total, with multiple water analyses before and after our product installation. More details in regards to how we will utilize funds can be found in our budget document.
Explain how the impacts will be measured:
Our project’s impacts are currently being measured and published on our team’s website on a monthly basis.
Key Performance Indicators:
- Scientific Progress: Verification of our product (system, proteins, or bacteria) with lab work through the use of spectrometry and other methods will show the accuracy of our filter. Recording the number of hours of total research completed on a daily basis will help ensure we adhere to our project’s timeline. We are at the planning stages of our project, so currently, this serves as the strongest performance measure.
- Prototype Success: Once we develop a viable prototype, recording how many liters of water we clean will be a suitable measurement. We will do so by comparing the concentration and amount of heavy metals detected before and after the treatment. A significant reduction in heavy metals would indicate success, and as of now, our target is 80% removal of heavy metals in contaminated samples.
- Environmental Education: we plan on hosting a variety of events for outreach purposes. This will help expose our project’s goals to the general public, and attendance at these events can be monitored to determine its success.
- Competition Success: We plan on applying for various environmental challenges, and the feedback that we receive from these events will help evaluate the progress of our project. We expect to present at the international iGEM Jamboree competition in Fall 2021, the UW Undergraduate Research Symposium, and the Alaska Airlines Environmental Challenge in the near future. The feedback that we receive from these events will help evaluate the progress of our project and recommendations on how to improve our product design.
- Implementation Sites: Expanding from the lab, we have identified multiple towns and stakeholders affected by wastewater pollution. Having the opportunity to work with the local government and various environmental organizations to use our designed product will highlight the success of our project on a grander scale. From a long term perspective, the number of sites in which our filter is implemented will serve as the next measurement.
This funding request is a: Grant
If this is a loan, what is the estimated payback period?:
|Molecular Biology Reagents||750|
|gDNA Extraction Kits||750|
|PCR: Mastermix, Polymerase, Cleanup Kits/Purification Kits||450|
|Gels: Agarose, SDS||300|
|Western Blot Setup||6000|
|Genewiz - Synthesized DNA||750|
|Western Blot - Primary and Secondary Antibodies||1000|
|Geneious (Software, 1 year, 5 Activations)||2000|
|Applied Math Department||500||N/A|
|Institute of Protein Design (IPD)||2000||N/A|
|Husky Seed Fund||5000||February 2022|
|EarthLab Innovation Grant||5000||January 2022|
|Alaska Airlines Environmental Innovation Challenge Prototype Funding||2500||November 2021|
|Subteam||Task||Timeframe||Estimated Completion Date|
|Drylab||Develop ODEs to Describe Bacterial Remediation||May - Jun 18||Jun 18, 2021|
|Drylab||Model and Stimulate Bacterial Growth and Metal Absorption||Jun 18 - Jul 16||Jul 16, 2021|
|Drylab||Model Existing Protein Binding Sites||May - Jul 16||Jul 16, 2021|
|Drylab||Optimize the Structure of the Heavy Metal Binding Protein||Jul 16 - Aug 13||Aug 13, 2021|
|Drylab||Validate and Optimize Model Parameters||Aug 13 - Sept 30||Sept 30, 2021|
|Drylab||Prepare Models and Findings for the Wiki||Jul 16 - Oct 1||Oct 1, 2021|
|Wetlab||Software (Geneious) Training||May - Jun 30||Jun 30, 2021|
|Wetlab||Finalize Product Design and Protocol||May - Jul 20||Jul 20, 2021|
|Wetlab||Preparation for Lab Work||Jul 20 - Aug 15||Aug 15, 2021|
|Wetlab||Complete Lab Work and Process Results||Aug 15 - Oct 15||Oct 15, 2021|
|Wetlab||Finalize Wiki Entries||Oct 15 - Oct 25||Oct 15, 2021|
|Human Practices||Continue Stakeholder Discussions for Regions Beyond the Puget Sound||Aug 1 - Sept 30||Sept 30, 2021|
|Human Practices||Develop Educational Outreach Materials||Jun 14 - Aug 31||Aug 31, 2021|
|Human Practices||Collaborate with UW Departments: Oceanography, Fisheries, Forestry, UW Wetlands, etc.||May - Jun 30||Jun 30, 2021|
|Human Practices||Implementation of Product||Sept 16 - Nov 30||Nov 30, 2021|
|Human Practices||Implement Educational Outreach to Local and Affected Populations||Aug 1 - Sept 30||Sept 30, 2021|
|Human Practices||Receive and Address Project Feedback from Affected Populations in the Greater Puget Sound Area||Jun 1 - Jul 31||Jul 31, 2021|