Being a part of iGEM has given our team the unique opportunity to choose a project that strongly impacts our local community. Although oak wilt is not presently found in Canada, we were fortunate to pursue many different avenues in our project, and held discussions with experts in Michigan, who are currently affected by oak wilt, and experts right here in Ontario, who are actively trying to prevent the spread of oak wilt. Although separated by a border, both sides are unified together in their efforts to pursue research studies on oak wilt as well as joint surveillance efforts. Our team was inspired by the great collaborative efforts of the researchers before us, which helped set the narrative and theme of iGEM Toronto’s Human Practice’s Team: Synergy
syn•er•gy noun: “the interaction or cooperation of two or more organization, substances, or other agents to produce a combined effect greater than the sum of their separate effects”
In our team, we have put in great effort for each relationship, whether it is with stakeholders, educators, or students, to be mutually beneficial and rewarding. As discussed in the following sections, our discussions allowed us to undergo multiple iterative processes with our on-site detection device, allowing us to create and design a tool that would most benefit our stakeholders. Furthermore, our conversations led us to many different individuals, all whom agree that spreading awareness of oak wilt to a wider audience is essential in preventing its spread into Ontario. As we saw our project continue to develop, what originated as a hardware product began to also evolve into an awareness project, where we educated the local community about oak wilt and promoted the STEM field to students of different ages. We are forever grateful for everyone we were able to collaborate with, and am thankful for the incredible positive feedback from our project.
Who is he?
Dr. Marcus Dillon is an Assistant Professor at the University of Toronto, Mississauga Campus. He is both an evolutionary geneticist and microbiologist, and researchs important questions including what determines the fate of host-pathogen interactions? And how do novel infectious diseases emerge?
Dr. Dillon also specializes in infectious plant diseases, and we were interested in his input regarding our plans of creating an on-site detection device to identify a plant pathogen, as well as any other microbiology knowledge including primer design.
The questions we asked:
Major Takeaways:
When creating primers, it is important to consider the balance between selectivity and specificity, and the more general we make our primers, the more error-prone they might become in detection. Furthermore, it is always better to work with DNA than RNA because it is more stable, and it is possible to fluorescently detect the oak wilt DNA.
Dr. Dillon pointed out a lot of added complexity to our project, which created some challenges to our experimental framework. His advice to simplify the steps as much as possible, and to also consider the user experience for our intended audience, helped us refine our wet lab experimental plan.
Who is he?
Dr. Nathan Tanner is a senior scientist at New England Biolabs, where he leads a nucleic acid replication research term that is dedicated to developing reagents and technologies for isothermal amplification.
Recently, Dr. Tanner published an academic paper that utilized an isothermal amplification technique called LAMP (loop-mediated isothermal amplification) with colormetric results to detect the SARS-CoV-2 nucleic acid. We were inspired by his paper and were interested in potentially conducting a similar technique for our project.
The questions we asked:
Major Takeaways:
There are a range of different options for the end detection result, but having a colormetric result is the easiest because you can visually see the result, and is also the most accessible option. New England Biolabs also has a primer design tool that we can use to create our primers, and we will be able to identify a good set of primers based on reaction time.
Dr. Tanner demonstrated a simple way to use LAMP for detection, and used products and reagents that are readily available for us to purchase (from NEB). Furthermore, his consultation demonstrated that LAMP is a reliable technique that we can use on site, and also confirmed the simplicity of using a pH colormetric technique to visualize results.
Who is he?
Dr. Keith Pardee is an Associate Professor at the University of Toronto, Faculty of Pharmacy. He is an innovative researcher in synthetic biology, and works in developing programmable materials with the transcription and translation properties of the cell, along with cell-free systems that are freeze-dried onto a paper disc, for molecular diagnostic tools.
Dr. Pardee’s research has a strong emphasis on designing low-cost diagnostic tools for use in health and education. We believed his cell-free system freeze-dried onto a paper disc would be a great application we could use to bring our detection device on-site.
The questions we asked:
Major Takeaways:
Dr. Pardee was highly knowledgeable in many different isothermal amplification methods, and was able to answer our questions regarding experimental workflow as well as how to potentially freeze-dry our system onto a paper disc.
As our main advisor to our project, we were able to meet with Dr. Pardee monthly to discuss the progress of our experiments, which gave us valuable insight. He provided guidance in how we can freeze-dry our reagents to deploy our experiment in an accessible manner, as well as offered several suggestions regarding how we can quantify our colormetric results.
Who is he?
Tim Payne is the Manager of Forestry at St. Clair Region Conservation Authority. Tim partners with Ministry Natural Resources and Forestry for a eight-week monitoring program from May to June annually. His responsibilities involve in surveying oak trees by capturing beetles to monitor oak wilt spread.
St. Clair Region Conservation Authority locates near the US and Canada’s border across Michigan State. As oak wilt has already been identified and spread in Michigan State, the early detection tool from iGEM Toronto can help to limit the spread. Tim is interested in the device and can assist with the user testing of the device. Tim also provides his expertise and knowledge on oak wilt symptoms and how oak wilt is spread through beetles as well root grasping methods.
The questions we asked:
Major Takeaways:
The biggest takeaway from the meeting with Tim was understanding how oak wilt is so close to Canadian forestry and endangering the tree species. Although oak wilt has not been found in Ontario as of today, St. Clair Conservation Authority captured beetles within its property who carried oak wilt’s fungus DNA, which had highly chances of infecting oaks trees and spread the disease throughout Ontario. This stresses the importance of developing the early detection tool for oak wilt.
After the discussion with Tim, the team understood that infection could happen either through root grasping or beetles infection through open wounds. Therefore, improvement was made and confirmed to continue using sapwood as the sample for DNA extraction step. Hardware team further to investigate to develop the most user friendly tool to collect sapwood sample from the oak tree.
Who are they?
Our team met with a retired forester that helped with oak wilt treatment areas in Menominee County and the State of Michigan, their responsibilities included monitoring oak wilt spread and performing the trenching and subsequent oak removal. The forester wished to remain anonymous, and so we will not use their name on our wiki.
The forester is experienced in the area of oak wilt detection and removal methods of infected oak trees. They provided disadvantages with current methods of detection which included cost ($30-40/ test), time (7-10 days for culturing), and delivery the sample for lab detection. They also addressed the only current solution to prevent oak wilt spread is to remove all the trees within 100 ft from the epicenter.
The questions we asked:
Major Takeaways:
The biggest takeaway from the meeting with the forester was to obtain the realistic data in terms of time and cost associated to current oak wilt detection method. In addition, through the conversation with Bill, the team was able to understand the amount of trees that had to be removed once oak wilt was identified and significantly endangered the source of the carbon storage. This stresses the importance of developing the early detection tool for oak wilt as it could be the way to save trees.
After the discussion with the forester, our project was shaped to develop on-site diagnostic tool that produces fast results and is feasible to our stakeholders, which the device will address the three disadvantages of current detection method. After understanding the needs of the stakeholder, hardware team will focus on the development of the diagnostic tool. However, other improvement that can be made is to consider which oak tree to sample from as the forest can cover thousands of trees and open wounds can hard to detect.
Who is she?
Dr. Smith is the Director of Forestry at the University of Toronto John H. Daniels Faculty of Architecture, Landscape, and Design. Her research investigates invasive species, its insect-insect or insect-plant interactions, and potential avenues to mitigate the potential negative affects on our forests.
Dr. Sandy Smith is connected to the University of Toronto, and was a great opportunity for us to speak to a local expert on forest pathogens and forest management. Furthermore, she has an extensive network with both the provincial and federal government, and is connected to various experts and students studying oak wilt on the field.
The questions we asked:
Major Takeaways:
The biggest takeaway from the meeting with Dr. Smith was the realistic application of our device and considering who would most be interested in utilizing our on-field diagnostic system. Through our conversation with Dr. Smith, we understood that our device would be of a greater interest to government monitoring programs, rather than for the individual homeowner.
Some potential things that we needed to consider for our project based on our conversation with Dr. Smith was to make the device as simple-to-use as possible, so that regardless if it’s used in the forest by non-specialists, or on border control for customs, it will be applicable for everyone to use accurately and correctly.
Who is she?
Ms. DiGasparro is the Program Development Coordinator at the Invasive Species Centre.
She wrote an article in The Professional Forester published by the Ontario Professional Forester Association, about the threat of Oak WIlt to Ontario. We would like to interview her, to know more about the current situation of Oak Wilt in Ontario, and what have the Invasive Species Centre been doing to protect Ontario from the invasive species.
The questions we asked:
Major Takeaways:
The biggest takeaway from Mackenzie is knowing the main advantage of our idea is how we can speed up the testing process of Oak Wilt detection in Ontario. Ms. DiGasparro suggests that the rapid detection of our hardware will allow the CFIA to remove threats from our province in an efficient manner, as the number of invasive species threatening our country is increasing from time to time.
While Ms. DiGasparro liked our project a lot, she suggested us to contact personnel from the CFIA, to know about the newest situation of Oak WIlt in Ontario.
Who are they?
Demian Gomez, PhD, is the Regional Forest Health Coordinator at Texas A&M Forest Service. His responsibilities involve inspecting the trees for recognizing symptoms of oak wilt disease and conducting trees removal process. Demian is collaborating with Dr. Loyd on a few oak wilt projects.
Both are experienced with the knowledge of oak wilt disease. As Texas area is threatened by Oak Wilt, we reached out to them to understand their projects with oak wilt, any improvements could be made to our current designs, as well more importantly looking for collaborating stage on testing our device to obtain feedbacks.
The questions we asked:
Major Takeaways:
Demian and Dr. Loyd are working on similar designs and similar stage with iGEM Toronto. However with some variations as well such as they did not use MCM7 region or they proceed with liquid nitrogen to grind the sample and obtain its DNA. They also identified that with droughts and heat, oak trees experienced similar symptoms as oak wilt disease which made oak wilt even harder to detect. At the end of the meeting, they are happy to collaborate with us to move further with the project and assist with testing the devices. Unfortunately, the timeline does not work with iGEM Toronto as Jamboree is in October, and they will not collect samples until the upcoming spring. However, this positive relationship has been established and can continue for further oak wilt projects next year.
Demian and Dr. Loyd suggested the ideas of mass sampling which can effectively cover tree samples in a large area. As well, they also mentioned temperature is key to preserve the same, as the temperature is too high the fungus species will die, which made detection harder in Texas. All the suggestions they have made provided iGEM Toronto more considerations to think about. Improvement to be made is to maintain this relationship from human practice team for any future collaborations.
Who is she?
She is a creative technologist at Design Fabrication Zone. She specializes in digital and physical fabrication, as well as creative coding.
The questions we asked:
Major Takeaways:
We improved our dipstick liquid mixing mechanism and connector 3D model. We also brainstormed a heating and cooling algorithm for the heating unit control.
Who are they?
They are Coding technologist at Design Fabrication Zone. They specialize in system control, experience design, and product safety support.
The questions we asked:
Major Takeaways:
They helped with brainstorming heating and cooling mechanism, the electronic components needed for our electronic design, and safety awareness on using our hardware design on-site in a forestry context.
Who is he?
He is an associate professor and New Media program director at RTS School of Media. He specializes in electronic component design and fabrication.
The questions we asked:
Major Takeaways:
We analyzed other existing heating modules and tested electronic components that potentially work for our design.
Who is he?
He is an Assistant Professor teaching at New Media, specializing in creative applications of software, hardware, and networks, interactive experience design, and electronic system design.
The questions we asked:
Major Takeaways:
He helps us design fungal sample collection from a tree, liquid-mixing structure design, calculation of heat loss, portable power supply, and dynamic temperature control.
Who is he?
He is the Assistant Professor of Evolutionary Genomics at the University of Toronto Scarborough
The questions we asked:
Major Takeaways:
He provided us access to his lab (Wang’s lab). He helped us with performing DNA extraction of Zancudomyces culisetae (a fungal specie), PCR, and gel electrophoresis, which proves the effectiveness of the dipstick DNA extraction method for fungal samples.
The generation of our project idea, developing an on-site device for oak wilt detection, led to many different ideas regarding the design and creation of our device. From our initial literature search and research into the threat of oak wilt in Ontario, we were confident that our device would have a great impact on current monitoring efforts in both Michigan and Ontario. These beliefs were further supported by our conversations with our stakeholders, who gave us continual suggestions and support during our design process to ensure the sucess of our project. By incorportating the suggestions of our stakeholders, we were able to combine the efforts of scientists, government experts, members of the general community, and environmental activitists, into our project.
At the beginning of our design period, we were able to speak to many great scientists in the field that gave us advice regarding LAMP and on-site detection techniques to ensure the validity of our design.
After creating a design for the wet lab’s experimental flow, we were able to talk to a variety of experts to recieve feedback for the device’s usability in the field from stakeholers who have experience with identifying and monitoring oak wilt.
We were also able to speak to many experts regarding our hardware design to ensure our device’s usability in-field, including liquid mixing, heating and cooling mechanisms, and electronic circuitry.
The ideas of our stakeholders and industry experts helped shape our project, demonstrating the importance of collaboration and interative feedback. In this next section, we detail how we integrated feedback into our project’s design and proposed implementation
In our project’s on-site device, professors and industry experts gave us design feedback in two main categories: (1) wetlab, and (2) hardware.
For wetlab, it was important for the team to choose an isothermal amplification technique that can be used on-field that is also sensitive and reliable. Additionally, the team aimed to have the results of the test be easy to understand and visualize. During the project, the wetlab team spoke to three experts that provided valuable insight into how we can better our project and achieve our targets. Dr. Dillon is an Assistant Professor in microbiology at the University of Toronto, and our meeting with him helped design our experimental workflow as well as guidance into primer design. Dr. Dillon pointed out a lot of additional complexity in our design, and suggested for us to streamline it as much as possible. Another expert, Dr. Tanner, a senior scientist at New England Biolabs, met with our team to discuss the useage of LAMP and using pH as a technique to visualize our results. Dr. Tanner was able to suggest different products to use in our experiments, and gave us advice on how to troublehoot and verify our results such as through gel electrophoresis. Finally, Dr. Pardee helped our team understand how to utilize freeze-drying in order to improve the shelf-life and portability of our proposed on-site device. This insight was expecially valuable since being able to freeze-dry our reagents allowed us to create a design that is more appealing for our stakeholders to use.
The hardware team spoke to many experts that helped them create a simple to use device that can be used on-field. In order for LAMP to work in field, the device requires many different components that all need to work together. Megan Schoeppich helped the team in multiple different areas, such as for liquid mixing for the LAMP reagents and sample, as well as for the heating and cooling mechanism required to increase the temperature for the LAMP reaction. Dr. Argo also helped with the liquid mixing design of the device, and additionally helped the team design the electronic parts to supply power to the device while on-field. Dr. Daniels also helped the hadware team with the electronic circuit design along with Ofir Rosen, who also provided valuable insight into the heating and cooling mechanism of the design.