Human Practices

Overview

In order to think about the general field of synthetic biology and our project specifically outside of our lab environment, we thought about how our project could be useful to researchers and other iGEM teams, particularly those interested in evolutionary stability and biosynthesis. We thought about how our project could be useful to researchers and other iGEM teams, specifically those interested in evolutionary stability and biosynthesis. Monitoring metabolic cellular capacity and evolutionary stability provides crucial data that can lead to more successful synthetic biology projects. Furthermore, knowing whether or not a part is “burdensome” to its host helps researchers have a more educated hypothesis about the stability of their construct, instead of losing days, weeks, or perhaps even months of their time troubleshooting a part only to discover that it was never reliable in the first place. Companies that spend less time and money on their R&D could lower the price of their product, which is especially useful for those specializing in therapeutics and biosynthesis. This could help make their products more accessible to consumers.

While our project has a broad impact outside of iGEM, our project is especially useful to other iGEM teams and iGEM HQ. Our team transformed and monitored the burden of 330 parts from iGEM distribution kits. We show that our subset of measured plasmids is representative of the entire kit because we used frequently used parts as well as parts of different types. The data for these parts can be useful to other iGEM teams to know which parts are burdensome or toxic to its host. Our project also serves as a quality control for iGEM. Knowing whether or not a part will decrease growth rate or have an impact on cellular capacity helps teams narrow down which parts they will use, allowing teams to spend less time troubleshooting parts that will not work. By being able to identify and avoid burdensome and unstable parts before starting research, they can make sure that their devices will remain functional and not have to waste resources unnecessarily.

This is particularly important for teams with limited resources that are disproportionately affected by evolutionary failure. Teams with lots of resources have the time and money, as well as mentorship and access to facilities, to help them identify and replace broken parts. However, for a team with less resources readily available, part breakage could be a major obstacle to successful completion of their iGEM project. For example, a team with more resources may have convenient access to DNA sequencers, allowing them to quickly confirm part breakage, while a team without easy access to sequencers may spend time trying to figure out why a part is not working.

Furthermore, we also sought opportunities to engage with our campus's synthetic biology center and the public in Austin. These events allowed us to collect new perspectives as well as allowed us to develop our project and its relations to the world in a more comprehensive manner. Engaging with these communities, whether it be learning from someone in the field or educating someone who doesn't have a background in synthetic biology, helped us think about how our project and synthetic biology have broad impacts for a wide variety of people.

Dr. Brian Renda from Gingko Bioworks

Our team believes that it is important to explore evolutionary stability of genetic constructs for a variety of reasons. First, detecting which parts are unstable allows us to find ways to increase evolutionary stability and cellular capacity. This is valuable for labs wanting to maintain high gene expression or function for a long period of time. Furthermore, this allows us to help scientists avoid wasting their time and resources with potentially unstable genetic constructs, allowing them to do more cost-effective research.

In order to facilitate our understanding of the benefits of our assay, as well as learn how to best represent and explain our data, we spoke to Brian Renda from Ginkgo Bioworks, a synthetic biology expert within the industry. Our discussion focused on how to best explore measuring metabolic burden, why it might be useful and problems that he faces with evolutionary stability. Our feedback from Brian helped us think of the importance of evolutionary stability. It was insightful to receive feedback about the importance of metabolic burden as well as how to talk about and represent our data.

“Often times in industry you seek to maximize production of a specific biosynthetic pathway to make your product of interest … Sometimes this can lead to needing to use a majority of the cell's protein synthesis capacity to maximize production. I've seen instances where a single protein in a pathway makes up >50% of a cell's total protein… Also just understanding how much burden a given construct has in a specific backbone is going to only give partially useful data - often times we actually care about how these constructs function in highly engineered strain backgrounds ... Usually the biggest issues we see for genetic stability in industry are around the production of toxic compounds or intermediates and not as much effect of just over-expressing constructs.” -Brian Renda

Our discussion with Brian about our project and metabolic burden was useful in knowing which individuals in industries would think our assay is applicable to their research and would use it. This would help our team with integrating feedback into our project. Talking about our ideas and progress with Brian gave us the opportunity to receive very crucial feedback on how to communicate the idea of metabolic burden in the context of our project and display our data.

2019 Synthetic Biology Day and Undergraduate Research Symposium at the University of Texas at Austin

Diya and Noor at SynBio day.

Alex and Jordan at SynBio day.

Angela and Ginny at SynBio day.

Our team had the opportunity to attend the annual SynBio Day at our University. We also presented at the Undergraduate Research Symposium on our campus. We learned from many experts in the field from our university as well as an opportunity to give a poster presentation. We received some feedback from Dr. Andrew Ellington, a professor of molecular biosciences. This feedback was an opportunity to hear other opinions and make adjustments to our project. Being able to present a poster and give a talk allowed us to see the diversity of the field of Synthetic Biology as well as receive feedback and critique about our poster, presentation skills and our project ideas. We were also able to share with students and faculty about what iGEM is and how it is important for undergraduates to have more independent undergraduate research opportunities.

The Thinkery: Building with Biology

One of the ways in which some of our iGEM team members engaged with the public was through participating in Thinkery’s Building with Biology event. The Thinkery is an Austin located, STEM-centered organization striving to enrich various educational opportunities to both children and their families via the implementation of hands-on learning experiences. Furthermore, Thinkery’s mission is to “create innovative learning experiences that equip and inspire the next generation of creative problem solvers,” which aligns well with iGEM’s core facets of education (through hands-on experiences as well as collaboration) and community (wherein the foundations for working together and mentoring are stressed between both organizations). Our team’s involvement with Thinkery’s Building with Biology event allowed us to pursue a deeper interaction with the general public outside of an academic atmosphere.

By being involved with the community in Austin, our team was able to interact with people from all sorts of skill and knowledge levels. From adults whom had already heard of synthetic biology to some degree to children whom had very little idea about synthetic biology, our team was able to get engaged and teach others about not only iGEM , but synthetic biology as a whole and how it could affect them in a way that reaches outside of the laboratory level. The extent at how this topic was discussed varied from individual to individual. With children, our team mostly worked on teaching them about synthetic biology in a simple and fun way for them to understand and potentially gain an interest in. For adults, our team mostly answered their questions about synthetic biology and talked to them about iGEM, and how it provided educational opportunities in STEM studies and fields of research. Our team emphasized the way in which working on iGEM helps provide an experience in working within a laboratory setting as well as expanding one’s own knowledge.

UT Natural Science Week: Painting With Bacteria

We interacted with students and staff about our project at the Painting With Bacteria event at UT’s Natural Science week. In this event, people had the opportunity to ”paint” with E. coli bacteria transformed with different colored chromoproteins. We introduced the idea of metabolic burden by showing people some colorless colonies that had appeared on chromoprotein plates that had been streaked out previously. We explained how some of the cells had stopped producing the chromoprotein because it was too much of a burden on the cell and a mutation in the chromoprotein construct resulted in a fitness advantage. We also talked about why it is important in the synthetic biology industry that we understand and quantify the metabolic burden of particular constructs, and exemplified this by talking about biosensors and indicators.

We also spoke with Dr. David Vanden Bout, the Senior Associate Dean and professor in the College of Natural Sciences at UT about the applications of cellular capacity outside of the lab. We asked him about what he knew about metabolic burden, and he responded by talking about how in processes where cells are producing a useful substance, it is important that the cells can continuously manufacture the substance over time.

Furthermore, we also met a UT graduate student whose research on plant cells utilized the concept of metabolic burden. We talked about how it is important to understand the burden on a microbiological level and emphasized the value of communicating research to the public. Overall, the event was interesting and informative, and we were able to meet people from different backgrounds and explain to them concepts behind our research such as metabolic burden and evolutionary stability, while gaining understanding of their perspectives on those ideas and how they affected their research. From these interactions, we now have a better appreciation of the practical applications that stem from our project.

UT grad student Maddie with Michelle and Emily.

Michelle showing chromoprotein plates.

Emily explaining metabolic burden.

Feedback from iGEM Collaborators

In order to understand the impact of our research on the synthetic biology community, we had conversations with the iGEM teams that we collaborated with and discussed how metabolic burden affected their projects.

Texas Tech University

Us: "Were you aware of the concept of burden before we spoke with you and what was the extent of your knowledge?"
TTU: "I was aware of the concept of burden before I knew what y'all's iGEM project was. We read papers various papers that discussed microbial production, scale up, etc., and in these papers, the concept of burden was introduced to me. I understood the basic definition of burden and the implications of burden."

Us: "How did your understanding change after we talked with you about burden?"
TTU: "I gained an understanding of how exactly burden can be measured. While I understood what burden was, I wasn't entirely sure of various methods individuals may employ in order to actually measure burden."

Us: "Do you think burden is a relevant concern within your own iGEM project (maybe you have an example of this?)?"
TTU: "Burden is highly relevant to our iGEM project. We are using microbes to produce various compounds. If the parts we are using are taking away from the cell's resources and ability to conduct basic metabolic functions, it would affect us greatly."

Us: "Do you think “burden” is an important issue for synthetic biologists and why?"
TTU: "Burden is an important issue for synthetic biologists because it can affect the cellular capacity of the microorganisms they are working with. It can affect which constructs they can work with and what constructs will be more efficient for them versus others."

Us: "Does understanding burden make a positive change?"
TTU: "I think understanding burden can make a positive change because it can make work that synthetic biologists conduct more calculated. Rather than creating constructs without thinking about the implications the constructs can have on the cell, burden allows for synthetic biologists to be more aware."

Impact on Future iGEM Teams

In order to more effectively standardize our measurements and help the iGEM community, an application of our project would be to perform a burden measurement for every part the iGEM registry. This would be done by transforming all functioning parts of the iGEM registry into our host strain and running them through our assay. This could even be something carried out by iGEM HQ labs. In order to test reproducibility, it could be helpful for multiple iGEM teams to do this while also working on their own projects or even having a whole collaborative iGEM project.

The data collected by this “iGEM wide” burden monitor project would be very useful to iGEM teams and synthetic biologists. Specifically, those who are interested in expressing a construct that carries out a function for biosynthesis or a biosensor. Because researchers often want higher gene expression, it is very useful to know how much burden a construct imposes on the host cell.

Teams being able to compare burden values will benefit further research in multiple ways. Teams will be able to more thoroughly study evolutionary stability by knowing how long it takes their part to break. Moreover, by being able to standardly characterize parts as imposing a high burden or not, teams will be more selective when choosing parts to work with. as a result, teams will be able to avoid wasting resources replacing parts. This will especially benefit teams with less resources who cannot afford to work with unreliable, burdensome parts. We hope our project will create a more inclusive iGEM competition by leveling out the playing field for all teams and encourage teams with less resources to participate. This standardized burden measurement will also possibly encourage teams to think about and test burden in organisms outside of E. coli and further research how to alleviate burden from the host cell of a genetic construct.

Team:Austin UTexas/Human Practices