Integrated Human Practices (IHP) impacted every aspect of our project’s development by (1) confirming that fieldability positively impacts individuals, (2) affirming that selection of an optimal chassis is an issue in the field of synthetic biology, (3) changing the direction of our project, and (4) shaping our project’s design. Because IHP is crucial to any research project, our team interviewed 11 different individuals to hear their thoughts on our project idea and design. We talked to a wide range of individuals spanning many different professions and areas of expertise. During these interviews, we recorded feedback on our project idea, design, and development, which was then implemented into our project.
Results of Our IHP
IHP TakeHome: Importance of Fieldability→ Impact on Project: Inspired our Team to Center our Project around Fieldability
Our team’s goal was to develop a project that positively impacted the world. From our literature review, our team expected that addressing a barrier to fieldability would fulfill this goal. However, before we decided on a project, we wanted to confirm that fieldable constructs really would help others. We met with several people from different occupations and research areas to hear their opinions on implementing fieldable synthetic biology. During these meetings, many of our IHP interviewees mentioned several problems that they were facing, either in their professional or personal lives, that fieldable synthetic biology could potentially solve. During the Virginia Soil Health Coalition Quarterly Meeting, the speakers mentioned the importance of cheap, on-site soil testing methods. Dr. Salerno mentioned potential uses of fieldable synthetic biology to cure coral disease, clean-up oil spills, or even treat wildlife. Dr. Adams explained that fieldable synthetic biology could increase drought tolerance in plants and restore habitats. Our IHP showed us that implementing fieldable systems would help a wide range of people and solve a large number of problems. After confirming the importance of fieldability, our team felt motivated to focus our project on tackling a roadblock to fieldablility.
Please see the image below for additional uses of fieldable synthetic biology mentioned by our IHP interviewees.
IHP TakeHome: Selection of an Optimal Chassis is a Roadblock to Fieldability and Our Software Would Help to Address this Problem → Impact on Project: Influenced our Team to Address Chassis Selection through our project
After conducting a literature review, it appeared that selecting an optimal chassis is a barrier to fieldable synthetic biology. However, our team wanted to confirm with individuals in the field that selection of an effective chassis really is a barrier to them and their work. We met with Dr. Adams, Mr. Marken, and Ms. Ezzamouri, who are all experts in synthetic biology. Dr. Adams explained that there are currently two main ways to decide on a chassis: conducting a literature review or performing 16S sequencing. Performing a literature review is time consuming, and often, the test environments used in papers do not match the environmental conditions of the deployment site. While 16S experiments help determine which species are native to a deployment site, often, researchers have not yet developed the genetic tools to engineer these native organisms. Therefore, to use them, one must first develop the genetic infrastructure to engineer this bacterial species. In addition to Dr. Adams, Mr. Marken and Ms. Ezzamouri shared similar sentiments about chassis selection and remarked that effective chassis selection is also an issue for them. After discussing chassis selection with these experts, we explained our software. They all stated that this software would be incredibly useful to them in their work. Two of these experts, Dr. Adams and Mr. Marken, work in the field of soil synthetic biology. The other, Ms. Ezzamouri, researches human microbiome applications of synthetic biology. Hearing from these experts in widely different areas demonstrates that our software will help advance many different subsections of fieldable synthetic biology. Through these interviews, our team confirmed that selection of an optimal chassis is a barrier to fieldablility and that our software will help researchers to address these problems.
IHP TakeHome: Computational Advances are Critical to Synthetic Biology → Impact on Project: Switching from a wetlab-based project to a largely computational project
Originally, our project planned to tackle several barriers to fieldability using wetlab approaches. However, after our meeting with Mr. Marken, our project direction changed entirely. During our interview, we explained our old project idea to Mr. Marken. As we elaborated, he became very interested in the software component of our project. He detailed the importance of computation to synthetic biology and the value of our software program. A crucial part of IHP is listening to feedback and integrating it into your project. After this interview, it was clear that our software component would provide a great benefit to synthetic biology. As a result, our team decided to switch to a largely computational project, something that our team has never done before. We also spoke with Dr. Adams who further highlighted the importance of computational tools and data accessibility to synthetic biology. After these interviews, it was clear that our software would provide a large benefit. Therefore, in response to IHP feedback, we switched the focus of our project to become largely computational.
IHP TakeHome: Feedback on our Project Design → Impact to our Project: Made Changes to Our Software Program and Wetlab Work Based on Feedback
IHP impacted our project design, including our software development, wetlab work, and inclusivity work. First, our team received feedback on our software design. Our original plan was to develop a purely neural network-based prediction system. During our interview with Mr. Marken, he suggested that a regression model would be helpful to augment our prediction efforts. In response to his thoughts, our team added a regression-based model into our software in addition to our neural network. Now, each software program generates a ranked list of ideal chassis. This way, our toolkit provides researchers with a choice of which predictive method to use.
In addition to a neural network and multivariate regression, our software also incorporates genome scale metabolic models (GEMs) to provide a prediction of bacterial growth rate in a specific environment. During our interview, Ms. Ezzamouri introduced us to several GEM databases that were helpful to our project development. Using GEMs, our team was able to model the impacts of circuit-incorporation on bacterial growth for our partnership with GastonDay-Shangde iGEM. When starting this partnership, our team was having difficulties modeling circuit incorporation. As part of our IHP process, we met with Dr. Kunjapur. Dr. Kunjapur produces a YouTube video series (@Kunjapur Lab Academy) that explains the use of genome scale metabolic models in synthetic biology. These videos were extremely useful to our team during project development. As a result, we reached out to him to ask about the issues that we were having with our GEM models. He suggested that adding sink reactions to the model may help with our modeling issue. After following his advice, our model worked!
In addition to feedback on the modeling portion of our software, we also received advice on the environmental factors considered as part of our prediction. Dr. Franzluebbers and Dr. Adams both suggested that temperature and moisture content were important factors to include as inputs for our software, as both affect bacterial survivability. Additionally, Mr. Marken highlighted that the incorporation of abiotic factors into a model is something that he has not seen in the literature. He highlighted that adding phosphorus, nitrogen, and carbon as inputs would allow researchers to predict bacterial growth in low nutrient environments. At Mr. Marken’s suggestion, our team added all of these parameters into our model.
Second, IHP feedback impacted our 16S wetlab experiments. First, our inspiration for conducting these experiments came from our IHP interview with Dr. Adams. During our meeting, we discussed the lack of publicly available data and how it is preventing advances in mathematical simulations. Our team was able to relate to this problem. We experienced difficulties finding parameters (ex. temperature, carbon-content, moisture-content) associated with much of the 16S data available. After this discussion, our team felt motivated to do something to address this issue. We decided to conduct our own 16S sequencing. We wanted to be sure that we measured all the assorted environmental parameters, allowing others to easily access information that we found hard to find. When performing this 16S, we received advice about our procedure and PCR techniques from Dr. Salerno. With her suggestions, we completed our 16S sequencing and plan to make it publicly available.
IHP feedback impacted our inclusivity work and by extension our educational efforts. When meeting with Dr. Adams, we discussed the importance of including ecologists in discussions about fieldable synthetic biology. As part of our inclusivity work, our team decided to reach out to our Environmental Science Department to try to get our university’s synthetic biology class to count as an elective for their major. Further, IHP also influenced our educational efforts. For our educational materials, our team wanted to help underrepresented groups learn about synthetic biology and computation. Dr. Stephens mentioned the importance of visualization as educational motivation. Her statement inspired our team to develop several visual methods to teach about synthetic biology. We created a board game and a board game expansion pack to help others learn about the field of synthetic biology.
Interview Summaries
Randolph Chambers: 220517
Randolph Chambers is a professor of Biology at William & Mary and at the Virginia Institute of Marine Science. His work includes several topics, such as Diamond Terrapin conservation, stormwater management, and soil composition.
William & Mary is located in the Chesapeake Bay watershed. When deciding on our project topic, our team was interested in benefiting our local community and local watershed. We met with Dr. Chambers to discuss problems that our watershed was facing. He mentioned several issues that he felt were largely impacting the watershed. First, he mentioned phosphorus and nitrogen pollution. These forms of pollution lead to increased algae growth and environmental “dead zones”, limiting the already decreasing habitat for aquatic animals. Next, he mentioned CO2 produced by marine organisms when creating calcium carbonate as an issue impacting climate change. He emphasized the importance of minimizing CO2 release and was interested in using synthetic biology to create calcium carbonate without producing CO2. He also mentioned potentially using calcium carbonate to cement soil together to prevent erosion. We discussed pollution from septic systems as another pollution form directly affecting the Chesapeake Bay Watershed. Dr. Chambers explained that septic tanks release contaminants, such as antibiotics and hormones, directly into the soil. Further, he stated that often septic tank materials are used as fertilizers, even on William & Mary’s campus. These fertilizers have been exposed to ultraviolet light to kill any bacteria, but contaminants, such as antibiotics, are often not removed. This lack of antibiotic removal leads directly to soil pollution. Discussing these problems with Dr. Chambers emphasized the importance of synthetic biology to the field of bioremediation. This discussion helped our team to understand the potential value of synthetic biology systems in natural environments.
Main Impacts to our Project:
- Confirmed that there is a large potential positive impact to be gained from using fieldable synthetic biology systems
Mr. John Marken: 220614
John Marken is a Bioengineering PhD student at the California Institute of Technology (Caltech). He has extensive experience in working in soil synthetic biology and modeling.
We decided to speak with Mr. Marken early on in our project in order to ensure the direction we were heading was feasible and necessary for the field. After our extensive literature, we found that a major issue preventing fieldable implementation of circuits is selection of an optimal chassis. Mr. Marken agreed that the literature was extremely limited in this area.
After sharing our idea of modeling bacterial growth from abiotic factors, he advised that when modeling bacterial growth, biotic factors, such as phage, were extremely, if not more, important than abiotic factors. However, he said that as far as he has seen, no one has modeled bacterial growth in this way, and that a model based on abiotic factors would be valuable to establish the limits of bacterial growth in a given environment. He also advised that we use a regression-based model for bacterial survivability as opposed to our current idea for an artificial neural network-based model. After this interview, we incorporated a linear regression into our software to augment our artificial neural network. When asked about our working concept for a bacterial growth model, Mr. Marken commented that our current strategy would likely be effective, but that we should consider adding factors that model growth in terms of carbon, nitrogen, and phosphorus limitation in a soil environment. Mr. Marken added that there is little modern work in this area, particularly in modeling the expression of circuits in bioengineered bacteria.
During our discussion, Mr. Marken stressed the importance of computational methods to the field of synthetic biology and the potential of our software. This meeting motivated our team to computationally solve a biological problem, something many of our team members had never done before. In response to his feedback, our team decided to change our project from the Foundational Advance Track to the Software Track. Through our meeting with Mr. Marken, our team confirmed that selection of an effective chassis is a barrier to fieldability, determined that our software program is useful to synthetic biologists, and changed our project direction to strengthen our software program.
Main Impacts to our Project:
Virginia Soil Health Coalition Quarterly Meeting: 220616
The Virginia Soil Health Coalition Quarterly Meeting (June 16, 2022) featured speakers from a variety of perspectives, such as farmers and soil scientists, discussing reducing nitrogen fertilizer use in the agricultural industry. It was moderated by Mr. Chris Lawrence, Cropland Agronomist from the United States Department of Agriculture. We decided to attend this meeting since we think it is important to integrate the voices of non-academic stakeholders, who would be heavily impacted by the implementation of fieldable synthetic biology systems, with academics. Throughout the meeting, there was recurring emphasis on the necessity of precise, on-site, cheap methods of soil testing on farms (which is perhaps a problem that synthetic biology could tackle if it had the infrastructure for implementation outside of the laboratory). As we learned in the meeting, currently, guidance on the appropriate amount of nitrogen fertilizer for any given farmer to use is calculated using only their projected yield, with no consideration of current nitrogen content of soil or other related biotic and abiotic factors that can vary dramatically between farms and even within one farm. This is why stakeholders advocated for farmers to gain more awareness of the biological processes happening on their property. They could accomplish this goal through both the implementation of simple, accessible soil testing, as well as through controlled experimentation across the farm, such as by varying fertilizer use in adjacent plots. One of the Virginia farmers, Paul Davis, doubled down on the importance of annually testing different locations on his farm for a variety of soil factors, and advocated for the use of paper strips to do so, claiming he was able to cut his nitrogen fertilizer use in half but increase his yield due to the knowledge and confidence he gained from data collection. A soil ecologist, Dr. Alan Franzluebbers (who we later interviewed), claimed that it is this precision of knowledge that is one of the most lacking components of soil management.
This meeting was not directly related to synthetic biology, and was an unusual example of Integrated Human Practices, as we were simply attendees of an open meeting. However, we gained valuable insight into the needs of farmers, who would likely be the recipient of several fieldable synthetic biology systems as suggested by Dr. Bryn Adams. This testing should not involve putting expensive laboratory equipment into the field, but rather cheap and easy mechanisms that farmers can use readily throughout their farm. The need for these on site assessment methods further emphasizes the importance of developing SynBio systems for use outside of the laboratory. Further, it is necessary to consider the opinions and thoughts of people who would likely be impacted by the use of these systems, which is why our team chose to attend this meeting.
Main Impacts to our Project:
- Confirmed that fieldable synthetic biology systems could be useful for agricultural purposes
Dan Schwartz: 220617
Mr. Dan Schwartz is a soil scientist at the Northern Virginia Soil and Water Conservation District. He specializes in mapping soil types and has participated heavily in public education on soil knowledge. We decided to meet with Mr. Schwartz due to his 19 years of experience in resolving soil issues in Northern Virginia and his expertise in soil structure and soil testing. We hoped to gain his insight on some of the most urgent local soil issues.
Mr. Schwartz stated that climate change and population growth is putting heavy stress on soil. In order to support the planet’s population, it is crucial to increase yields on agricultural soil while also maintaining healthy soil structures. He then described some of the most significant pollutants he has encountered in the field, including forever chemicals persisting in the soil such as PFAS and PCBs. When elaborating on soil issues specific to Virginia, Mr. Schwartz mentioned watershed erosion at the Chesapeake Bay. He suggested that in order to prevent sediment runoff, the best way is simply to have “healthy normal soil”. Sediment runoff can be prevented by having healthy soil containing a sufficient amount of organic matter including plant roots, microbes, fungus, and other contents. He specifically explained the role of glomalin, a sticky glycoprotein secreted by fungi that improves soil stability. Mr. Schwartz also guided us to various soil classification websites.
We ended with a discussion on the Virginian soil health policies, and currently there are very few laws which regulate people taking actions to preserve soil health. That is why soil scientists like Mr. Schwartz and NGOs are advocating for people in Virginia to take care of their soil. Our conversation with Mr. Schwartz gave us great information on the current status of soil in Virginian land and introduced us to some issues that using synthetic biology outside the laboratory could solve.
Main Impacts to our Project:
- Confirmed that there are many issues in soil environments that could be solved by synthetic biology
Jessica Stephens: 220621
Dr. Jessica Stephens is the president of Williamsburg Community Growers (WCG). Williamsburg Community Growers is an organization that runs a community garden and teaching farm in our local Williamsburg area. Given the soil engineering component of our software, our team wanted to get Dr. Stephens’ thoughts on local soil issues and to hear her ideas about our project. Dr. Stephens mentioned three main soil-related issues that she has encountered. First, she explained that much of the soil located on WCG’s grounds is heavily compacted. WCG is located next to several large powerlines. Constructing these powerlines required heavy machinery which compressed the soil, making it more difficult to grow plants in these areas. This problem becomes amplified as the distance to the power lines decreases. Second, she noted an issue with clay soil in her own personal garden. Like the WCG soil, clay soil is heavily compact, making it difficult to utilize for growing purposes. She described several methods that can be used to help aerate compacted soil, such as adding compost or wood chips to the area. However, these methods are time-consuming and require 2 to 3 years to improve the affected area. Third, she mentioned an issue with potential contaminants in her own home garden. As her home garden is located in a domestic area, she does not know if any contaminants are present due to the actions of a previous owner or neighbor.
Talking with Dr. Stephens further emphasized the importance of soil bioengineering. She highlighted the value of developing a way to more rapidly de-compact soil and she suggested that finding a way to measure contaminant levels in soil would be helpful to gardeners to know which contaminants are present in their soil. After meeting with Dr. Stephens and hearing about the potential problems that could be solved using synthetic biology outside of the laboratory, our team was even more motivated to tackle the issue of fieldability.
In addition to operating a community and teaching garden, WCG also dedicates itself to educating the local community about the benefits of locally grown produce and teaches individuals about gardening practices and techniques. We wanted to ask another organization about their education programs and how they engage the local community. Dr. Stephens mentioned that in their education program visual results are a motivator to encourage students. Being able to compare a well-grown plot to an underdeveloped one is an easy way to motivate students to achieve their goals. While our project is not directly related to plant growth, we plan to incorporate many visual aids to illustrate the importance of synthetic biology outside the laboratory.
Main Impacts to our Project:
- Confirmed that fieldability outside of the laboratory has many different potential applications
- Prompted us to incorporate of visual aids into our education, leading to the development of our Re-Terraforming Earth board game
Alan Franzluebbers: 220624
Dr. Alan Franzluebbers is a research ecologist with the US Department of Agriculture and a USDA Professor of Soil Science at North Carolina State University. His research focuses on characterizing and exploring the complexity of the soil environment, with an emphasis on vertical stratification of organisms. Dr. Franzluebbers recently spoke at the Virginia Soil Health Coalition Quarterly Meeting on June 16, 2022, as noted in our meeting summary. Following this June 16th meeting, we hoped to speak to him directly to learn more about the key issues facing the environment and to hear his opinion on the viability of using bioengineered organisms directly in the soil.
Dr. Franzluebbers noted that, while there is a significant amount of research concerning interactions between soil microorganisms, broad characterization of different microbial communities remains scarce. Such insight affirmed the importance of our survivability software, where researchers can input details about their soil of interest and selection of chassis to verify survivability. With more information detailing the make-up of soil communities, synthetic biologists could better tune their circuits to the context of their experiment, increasing the chances for bacterial survival and circuit functionality. He mentioned that temperature and moisture content specifically have a large impact on soil composition. After Dr. Franzluebbers’ thoughts, we sought to incorporate these factors into our model to improve accuracy.
We asked Dr. Franzluebbers for his opinion on the impact that synthetic biology could have on soil health and remediation. He said that, after considerable vetting, it presents a great opportunity to better the soil environment. However, he also maintained that the biggest obstacle in soil synthetic biology may be counteracting the competition with indigenous bacteria, overcoming the soil microbiome’s natural ability to preserve its general landscape. We plan to help combat this issue with our software. Our software selects the best chassis for a specific area. Through this selection, we are choosing the chassis that is most likely to survive in that area, hopefully giving it the best possible advantage to compete with the local microbiome.
Main Impacts to our Project:
- Confirmed the promise of fieldable synthetic biology to improving the soil environment
- Incorporation of temperature and moisture content into our software as parameters
Joseph Wood: 220726
Bioremediation is how our team originally became interested in fieldability. We even considered bioremediation in the Chesapeake Bay Watershed. As a result, we wanted to talk to an individual at the Chesapeake Bay Foundation to get their opinion and feedback on our project. We decided to talk to Dr. Joseph Wood. Dr. Joseph Wood is a scientist with the Chesapeake Bay Foundation and has a PhD in Integrative Life Sciences.
Dr. Wood highlighted the major pollutants in the bay, which included nutrients like phosphorus and nitrogen, but also micropollutants like PFOS and PCBs. He mentioned that there are few remediation strategies for these pollutants aside from simply isolating the pollutants with cement to prevent further contamination. When discussing these pollutants, he explained that synthetic biology solutions to these contamination issues would be incredibly useful and could have a big impact. Specifically, he discussed potential applications of synthetic biology for denitrification and soil improvement. However, he addressed the importance of on-site applications for bioremediation and noted that while off-site remediation can work it is not the best approach. To us, this statement further highlighted the importance of fieldability in synthetic biology, allowing research to address problems on site and providing further support for our project.
Main Impacts to our Project:
- Confirmed that on-site bioremediation is the most effective form of bioremediation and stated that fieldable synthetic biology could have a large positive impact on bioremediation in the Chesapeake Bay
Bouchra Ezzamouri: 220802
Our software package encompasses chassis selection for human gut microbiome therapeutics. Thus, we reached out to Ms. Bouchra Ezzamouri, a PhD Research Fellow at St John's Institute of Dermatology at King's College London, who has experience in researching the human microbiome, utilizing genome scale metabolic models (GEMS), and an in depth understanding of the applications of synthetic biology systems used in the gut.
After explaining our project, we asked how scientists working with synthetic biology applications in the gut pick a bacterial chassis. As we suspected, Ms. Ezzamouri confirmed that there was no standard way to pick a chassis, and that the decision depends on the intended application and available information.
Ms. Ezzamouri also offered advice to us about the modeling aspect of our project. She answered questions that our team had about genome scale metabolic models, which we are utilizing in our model to provide more accurate information on growth rate. Ms. Ezzamouri said that limitations of GEMS include not accounting for phage presence and that GEMs are typically untested in the laboratory. GEMS model a whole functioning bacteria with every biochemical reaction and gene expression. Additionally, she was able to explain more context for how Synthetic Biology applications could utilize GEMs, informing us that investigators typically create GEM systems with artificial sinks added to plan circuit deployments, instead of integrating full models of circuits directly into GEMs. She also sent us a source where we could download GEMS for our model and she brought to our attention the MIGRENE toolbox for Microbial and personalized GEM, Reactobiome and community Network modelling.
Finally, we discussed our model and got feedback on its impact. Ms. Ezzamouri was enthusiastic about our goal. She emphasized how useful of a tool our model would be because it provides more information during the chassis selection process. Previously, we discussed that chassis selection is limited by information on bacterial growth in specific environments, but with our model, Ms. Ezzamouri said: “The more you get a comprehensive image of the natural habitat, the more insight you have of what is really happening. A big issue with omics techniques is isolating specific bacteria. A computational toolbox like this would work in native environment without needing to be cultivated in a lab.” In all, Ms. Ezzamouri served as a valuable resource for learning about more GEM sources, chassis selection in the gut microbiome, and understanding the impact of our project.
Main Impacts to our Project:
- Confirmed that selection of an optimal chassis is an issue in human gut synthetic biology
- Asserted that our software would be useful for her work
- Directed us to several GEM databases
Bryn Adams: 220803
Dr. Bryn Adams works as a scientist for the United States’ DEVCOM Army’s Research Laboratory (ARL). Her paper “The Next Generation of Synthetic Biology Chassis: Moving Synthetic Biology from the Laboratory to the Field” served as a very early inspiration for our project.
After we explained our project, Dr. Adams immediately expressed interest in our software package and told us that it would be very useful for her research. She explained that currently, when deciding on a chassis for a particular environment, she must either conduct a comprehensive literature review to guess which bacteria will survive in her environment of choice, or, if the environment of choice is more “niche,” she must actively travel to the site and collect bacterial samples to figure out which species are able to survive in this area. Both of these methods are very time consuming and she stated that having a more time-efficient method would be preferable for her research. To further complicate the chassis selection issue, if none of the bacteria that have been found at that site have been previously used as a chassis, she must “reinvent the wheel” and dedicate significant time to characterizing parts for that species before she is able to use it as a chassis. Therefore, software that could predict survival of already developed chassis in certain environmental conditions would be useful. Learning about the current, laborious steps synthetic biologists take when undergoing chassis selection validated the necessity of our project and the impact it will have on the field. It also highlighted the importance of a predictive model, which will allow researchers to determine if pre-characterized, well-known chassis will survive in their environment of choice without having to “reinvent the wheel”.
Dr. Adams has experience working with engineered bacteria in soil environments. When asked about some of the potential benefits of soil bioengineering, she mentioned nitrogen fixation for fertilizers, the potential for increasing drought tolerance in plants, restoring habitats, and microbial recycling. In a previous experiment, she tested the implementation of a genetic circuit in soil, and she explained to us that replicating environmental conditions was difficult in a laboratory setting. Her comment gave us an idea. When researchers input a chassis species into our model, they will receive a list of environmental parameters in which this species could survive. Researchers can then use this information to guide microcosm creation for soil testing in the laboratory. When asked what parameters she considered essential to predicting bacterial presence, she mentioned that temperature and moisture levels have a great impact on the ability of bacteria to survive. We have incorporated both of these factors into our own software. She highlighted that with the rising threat of climate change, being able to predict the extremes of bacterial survival (extremely hot/cold and extremely wet/dry environments) would be useful to future researchers, especially those focused on agriculture.
Throughout our conversation, she stressed the importance of advances in data science and computation to the field of synthetic biology, believing that in situ simulations are the future of bioengineering. She also acknowledged that this development is hindered because of a lack of publicly available data. She confirmed our team’s frustrations about a lack of data availability, explaining that a lot of databases are inaccessible, and you often have to be a part of certain communities to even become aware of the existence of certain data. After this conversation, our team left motivated to try and contribute some form of data for future researchers. We decided that performing our own 16S experiments would help us to fulfill this goal.
Finally, we discussed the importance of integrating ecology and synthetic biology together. She agreed with the importance of reaching out to ecologists and including them in synthetic biology conversations. As a result, our team reached out to the Environmental Science Department at our school to encourage them to add a synthetic biology class to their elective list.
Main Impacts to our Project:
- Stated that our software would be useful to her
- Mentioned that there is a need for better chassis selection methods
- Confirmed the potential uses and positive impacts of fieldable soil synthetic biology systems
- Incorporation of temperature and moisture levels as parameters for our software
- Integration of synthetic biology with other disciplines
- Highlighted the importance of computational advances to synthetic biology
- Potential use of our software to help research predict changes in bacterial survivability due to climate change
- Potential use of our software to guide microcosm creation for laboratory experiments
- Inspiration for performing 16S experiments
Jennifer Salerno: 220805
Dr. Salerno is a microbial ecologist studying microorganisms and their impact on organism health and ecosystem function. She has worked on characterizing pathogens in coral and fish disease, researching microbial indicators of health in aquatic systems, and the microspatial scale of soil microorganisms. Due to bacterial communities being integral to her research, Dr. Salerno has extensively utilized 16s rRNA sequencing for microbial analysis.
We reached out to Dr. Salerno for her expertise on 16S experimentation. This year, our project is focused on the analysis of 16S data and we had several questions for Dr. Salerno about potential inaccuracies from using 16S data for our program. She mentioned that there are several different factors that can affect the accuracy of a 16S experiment, including bias from PCRs, sequencing, and extraction kits. She specifically highlighted that more common species are often overrepresented in 16S studies while less common species are often underrepresented, if at all detected, and noted that this is something that our team should consider when analyzing the results of our experiments. In addition to explaining potential inaccuracies, she also offered advice to us on our general PCR procedure for our own 16S experiments.
When we explained our project idea, Dr. Salerno noted that this program could be useful for environmental microbiologists. She mentioned that using microbes outside of the laboratory would be useful for a multitude of tasks, such as oil spill bioremediation and treatments for wildlife and crops. She specifically mentioned an application related to a disease found in corals, stony coral tissue loss disease. She explained that this disease is believed to be caused by bacteria. However, bacteria has yet to be confirmed as the sole cause. She thought that bacteria could be potentially used to cure this disease and knowing which bacteria to choose for deployment would be extremely helpful.
Main Impacts to our Project:
- Feedback on our 16S procedure
- Confirmation that fieldable synthetic biology systems would be helpful to solve problems in marine environments
- Stated that our software would be helpful for environmental microbiologists
Aditya Kunjapur: 220812
We reached out to Dr. Kunjapur due to his expertise in metabolic engineering. Dr. Kunjapur has a series of youtube videos (@ Kunjapur Lab Academy) that discuss the uses of genome scale metabolic models (GEMs) in synthetic biology, which were helpful to the development of our project. When meeting with him, we explained how we were using empirical methods of data gathering to make determinations of relative abundance in various soil samples. Additionally, we presented him with an issue that we were having in our collaboration with GastonDay-Shangde iGEM. For this collaboration, we were trying to model the production of cinnamaldehyde and its effect on the growth rate of the chassis. However, we were encountering an issue in which optimizing for cinnamaldehyde production resulted in no bacterial growth; whereas optimizing for growth resulted in no cinnamaldehyde production.
Dr. Kunjapur confirmed our suspicions about the inadequacies of GEM models to account for accurate production of anything other than biomass accumulation. He also pointed out that cinnamaldehyde is toxic, and in the context of our GastonDay-Shangde collaboration, our models may be inaccurate because the cells will be killed. He suggested that creating sink reactions may be necessary to induce production of cinnamaldehyde in our model. Also, he explained that we could multiply our biomass production and our cinnamaldehyde production results together and optimize for the product as it would force cinnamaldehyde production. Our team implemented his sink reaction solution and we were able to get our model to work, which we could then apply to modeling circuit induction in chassis outside of the laboratory! He stated that he was interested in our project and wanted us to send updates/solutions to certain issues when we finish our project.
Main Impacts to our Project:
- Inclusion of sink reactions into our circuit-incorporation modeling GEM