Team:Stony Brook/Implementation

Team:Stony_Brook/Implementation -
Proposed Implementation

The threat of gene flow is a major concern when it comes to preserving agrobiodiversity. Currently, indoor farming works to mitigate the risk of gene flow by providing some degree of control over the plants being grown. However, it has no inherent mechanism preventing the escape of transgenes. Our system's implementation in a real world setting could help mitigate the deleterious effects of gene flow by providing more control to farmers.


Synthetic Biology

Synthetic biology is a well established but ever-growing interdisciplinary field of research. The engineering of synthetic circuitry in bacterial, yeast, and animal systems have prompted considerable advances for the understanding and manipulation of genetic and metabolic networks; however, the implementation of these synthetic circuits in the plant field lags behind. Through our plant-based research, we found an underwhelming amount of existing applications in the plant field that utilize light-regulated (optogenetic) switches for the targeted interrogation and control of cellular processes. This is surprising given the plethora of advantages that an optogenetic based approach. An optogenetic approach allows unparalleled spatiotemporal precision and reversible control over cellular signaling, overcoming the many limitations of chemically induced systems. Furthermore, it eliminates the toxic effect posed by a chemically-based approach, although with an optogenetic approach, it depends on the wavelength of light being used.

One of the apparent reasons that optogenetics lags behind in plant research is because of the undesirable system activation, otherwise known as “dark activity.” This causes an optogenetic switch to activate upon exposure to light outside of its excitatory frequency. However, in a study conducted by Ochoa-Fernandez et al., (2020) they were able to overcome the issue by engineering an optogenetic tool, termed plant usable light-switch elements (PULSE), to reversibly control gene expression in plants without having to worry about dark activity caused by ambient light.

Optogenetic Kill-switch to Prevent the Effects of Gene Flow

We hope to minimize the deleterious effects of gene flow by incorporating our optogenetic killswitch in a variety of plants. Given that the core signaling component of the CLV-WUS pathway is relatively conserved in a diversity of plants such as tomato (Solanum lycopersicum), maize (Zea mays), and rice (Oryza sativa), we anticipate our system to function in other major crops as well, especially those grown in farms.

Potential Users


Indoor farming, which includes both vertical farms and greenhouses, allows farmers to grow their products in a controlled environment. With the indoor farming industry projected to reach upwards of 22 billion USD by 2026 (Pulindindi et al., 2018), this growth scenario is growing more common every year.

Conveniently, UV-B light is absent in these environments, allowing us to utilize indoor farms as part of the solution. Our UV-B light-activated killswitch would be implemented in GM crops cultivated in these controlled environments. If these plants do somehow find a way to escape to the natural environment, this killswitch would be able to prevent further growth by exploiting RNAi to silence the WUSCHEL gene, a key player in plant development. Combining the controlled environment of indoor farms with our optogenetic killswitch that prevents crops growing inside from being grown outdoors, the net risk of gene flow is decreased. Indoor farmers would be at greater liberty to modify their crops without worrying about the deleterious ecological effects of gene flow.

Human Practices

We are thankful that we were able to talk to many farmers to gain their perspective of what they thought about LightSwitch. Jennifer Ross (HeartBeet Farms), David Lopez (Babylon Farms), Maxwell Carmack (Square Roots Farms), and Mike Axelrod (Stony Brook University) all helped us gain a better understanding of how farmers would perceieve our system and what their attitudes would be if we were to implement it in their farms. We asked them two questions that related to the integration of our system in indoor farms.

Firstly, we wanted to know that if there was a way to prevent GMOs from spreading transgenic traits to other crops, such as through the implementation of our kill-switch, would it be beneficial for their work. From talking to farmers, we learned that our kill-switch is something they can see being implemented, but it would be difficult to gain support from the general public. We would have to first diminish the negative stigma surrounding the word “genetically modified.” Because of this, we issued educational initiatives, which are outlined in our Education page. Additionally, to promote transparency between the scientific community and the public, we established a wet lab protocol outlining what procedures we would have done in order to integrate our system in N. benthamiana. These protocols are outlined on our Experiments page. We hope that our efforts to make our project as clear and understandable as possible would aid in its future implementation in the natural environment.

Secondly, we asked if they could anticipate any potential drawbacks of using our system in farms. One farmer inquired about how our system would impact the nutritional value of the crops that had our system. Through the help of Dr. Creasey, we learned that there is no evidence that genetically modified food has less nutritional value than their “natural” counterparts. In actuality, genetically modified food usually has increased nutritional value. Once more, we were told that the biggest drawback of our system would be the reluctance of consumers from accepting it solely because genetically modified products are deemed to be “unnatural,” or inherently bad. This reinforced the need for our team to promote transparency between our project and society.

Potential Challenges

Fear of GMOs

As mentioned before, the current negative stigma around the use of GMOs has unfortunately been increasing, as there has been less openness between the scientific community and the general public. We believe that the implementation of our system can only occur if the public is fully aware of the potential harms of gene flow and how it can be contained with the issuance of our kill switch. When people hear “genetically modified,” they automatically correlate that to being the opposite of what is “natural” and thus, deem it bad. However, many products that are commonly enjoyed by consumers such as corn, cotton, soybeans, and even potatoes, are USDA approved, genetically modified crops grown right here in the United States (Digital, 2020)! There is a need for scientists to effectively communicate their work to the general public. We hope that our team, and many others in iGEM, are one of the few that do.

Lack of Results

Our team was one of the few iGEM teams around the world that were unable to conduct any wet lab experiments. Because of this, we were unable to determine the true effectiveness of our system in our model organism. We hope for future research to establish a proof of concept model in N. benthamiana through transient expression of UVR8-COP1 induced transcription of our syn-tasiRNA to demonstrate the efficiency of this optogenetic system.


Digital, G. (2020, January 25). Which genetically engineered crops and animals are approved in the US? Genetic Literacy Project.

Ochoa-Fernandez, R., Abel, N. B., Wieland, F.-G., Schlegel, J., Koch, L.-A., Miller, J. B., Engesser, R., Giuriani, G., Brandl, S. M., Timmer, J., Weber, W., Ott, T., Simon, R., & Zurbriggen, M. D. (2020). Optogenetic control of gene expression in plants in the presence of ambient white light. Nature Methods, 17(7), 717–725.

Pulidindi, K., & Chakraborty, S. (2018). Vertical Farming Market Trends: Growth Potential 2019-2026. Retrieved from