Education

Figure 1: Values important to the ASU iGEM team's efforts to build the synbio community.

Arizona State University (ASU) is one of the largest universities in the United States, serving 80,000 students in person and 100,000 online. Despite its size, ASU previously offered limited opportunities for students to learn and explore synthetic biology methods outside of dedicated research labs. Recognizing this deficit, in 2020, two biomedical engineering students founded the student organization DIYbio to bring together students from diverse disciplines and backgrounds who were interested in expanding their knowledge and skills within the field of synthetic biology. To familiarize new students with synthetic biology, they hosted seminars, social events, professional development workshops, and of course, participated in the iGEM competition.


However, at the time, the scope of DIYbio and the ASU iGEM team was limited by funding and a small membership base. After three years of dedicated efforts, we have been able to successfully provide ASU students, as well as elementary, middle, and high school students, with opportunities to engage in meaningful activities that develop practical skills in synthetic biology. Over this past iGEM cycle, we have:


Open Lab

Open lab offers an interactive and collaborative experience for students to engage in hands-on experiments and explore the practical applications of synthetic biology concepts.


Workshops are designed for peer instruction instead of a lecture style, one-way transfer of information. Open Lab is organized as an interactive, collaborative experience where both instructors and attendees learn from one another through activities that promote active participation, problem-solving, and sharing of experiences. Open Lab sessions include students from a wide variety of majors, encompassing both undergraduate and graduate students. This diversity fosters a unique learning environment, allowing participants to share distinct perspectives while working together on the same project.


The projects are meant to span the entire academic year and are designed to provide a unique introduction to essential, basic lab techniques in a way that regular classwork cannot. Each semester, the project focuses on easy-to-digest goals for beginners, supported by step-by-step instructions. Ultimately, Open Lab aims to create a community where students learn to think critically, build confidence in themselves and their ambitions, and discover the joy of science.


2023-2024 Open Lab

Open Lab originated from the efforts of Gabriella Cerna, one of the co-captains of the 2022 iGEM team, and launched in Fall 2023 as a series of three workshops. These workshops guided students through each step of a Golden Gate reaction, bacterial transformation, and miniprep to create E. coli that constitutively expressed the fluorescent protein mScarlet.




The next iteration of Open Lab began in Spring 2024 as a workshop series that spanned the entire semester, giving students more time to become invested in the project and learn even more synthetic biology techniques. Over the course of this Open Lab series, a group of undergraduate students with no prior wet lab experience were able to successfully grow the bioluminescent bacteria Aliivibrio fischeri, extract five Lux genes from its genome using PCR, clone all five genes into a bacterial expression plasmid, and create their own bioluminescent E. coli. For the first time at ASU, students took on the role of instructor, teaching their peers about synthetic biology. They guided each other through the process, from introducing the project goal and designing primers on Benchling to transforming the final product and assaying their synthetic bioluminescence. Students designed and executed every step of the process.


2024-2025 Open Lab

This year, the ASU iGEM team has designed a project to engineer E.coli to produce various carotenoid pigments by manipulating a gene cluster responsible for zeaxanthin diglucoside production.


For the fall semester, we began with the plasmid pAC-EHER, which was developed by Dr. Francis X Cunningham Jr's lab. We ordered this plasmid from Addgene to introduce students to the collaborative power of plasmid repositories and equip them with practical skills in sourcing essential tools for synthetic biology. The pAC-EHER plasmid contains a seven gene carotenoid pathway gene cluster from Erwinia herbicola (now known as Pantoea agglomerans) Eho10. When expressed in E. coli, this cluster facilitates the production of zeaxanthin diglucoside. By systematically removing genes one by one, we aim to create plasmids that produce a spectrum of pigments, including zeaxanthin, beta-carotene, and lycopene.




In the spring semester, we will introduce the concept of inducible promoters by utilizing pBad to express two genes, ZEP and CCS, under arabinose induction. When this plasmid is transformed into E. coli that already contains a plasmid for zeaxanthin production, it will enable the E. coli to synthesize capsanthin and capsorubin.



For this year's Open Lab, students will learn a variety of techniques, including but not limited to, Inverse PCR, Gibson Assembly, restriction digestion, and site-directed mutagenesis. Our final goal is to extract these pigments to use as natural dyes!


To date, we have hosted four Open Lab sessions, with two additional sessions planned for this semester and six more for the next semester. Below, we have provided descriptions of all of our past and upcoming events, along with their associated presentations, worksheets, reflections, and the improvements made from one session to the next.




In preparation for the Open Lab series, we guided approximately 45 students through the process of creating a Benchling account and taught them essential functions like annotations and primer design. Following this introduction, we challenged the students to work together in groups to apply their newly acquired skills to design primers for amplifying GFP from a plasmid.




In our first Open Lab session, we provided an overview of this year's Open Lab project, introduced the concept of plasmids, and had each group perform their own restriction enzyme digest on ZD.3, a modified version of pAC-EHER.



Reflections and improvements


By emphasizing that Open Lab is a low-stakes, enjoyable, and evolving program, we created a space where students felt comfortable sharing concerns, either in person or through a QR code survey. We prioritized showing that we were learning alongside them and committed to improving their understanding.


During this session, some students struggled with the calculations for setting up restriction enzyme digests. While the process seemed straightforward to us, our slide explanations were inadequate for those less familiar with unit conversions. Additionally, the lab's shelving made it hard for students to see the presentation.


To improve, we'll create worksheets for the next Open Lab with relevant equations and space for calculations.



Since many of the students attending Open Lab were eager to get involved in research, we hosted an interactive workshop to guide them through the different types of research opportunities available and offer them advice on how to effectively reach out and apply. We highlighted unique research opportunities both at and outside of ASU and shared our own personal experiences of joining research labs. Students looking to apply brought their resumes and application materials for personalized, targeted feedback.




In this Open Lab session, we began with an active recall activity to review what we had worked on at Open Lab 1, followed by each group performing their own ligation reaction.




Reflections and improvements


When creating the worksheet, we reflected the challenges of Open Lab #1 and on our own challenges learning these techniques and designed questions to help students understand the reactions at a molecular level. For example, we asked them to compare their DNA during the digest and ligation reactions—was it linear or circular? Though we had hinted at these ideas in presentations, we saw the value in having students think through and apply what they learned to reach these often-overlooked conclusions.



In this Open Lab session, students learned how to pick colonies from a plate and prepare liquid cultures. They then split into groups to determine which restriction digest could be used to differentiate the ideal product, Z.1 (the plasmid that produces zeaxanthin), from the cloning backbone, ZD.3 (the plasmid that produces zeaxanthin diglucoside).



Reflections and improvements


Picking colonies: Observing students during this Open Lab revealed that there were gaps in our explanations and highlighted missed details that were hindering their learning. For instance, contamination prevention techniques are already second nature to us, but they are not immediately obvious to beginners. We did not think to mention simple mistakes like leaving plate lids off for too long or poking toothpicks into the agar until we saw the students make them.


We have made a note of these common errors and will highlight them in future Open Labs so that students can become aware of them. We also realized the value of demos because many students learn visually. Seeing techniques in action alongside their explanations would help reduce mistakes and reinforce understanding.


Virtual digest: In the second half of the Open Lab session, we demonstrated a virtual plasmid digest to illustrate the importance of using a differential digest to distinguish between the backbone and a successful clone. However, after the demo, some students struggled to apply their newly acquired knowledge to the practice scenario we provided them with. The reason for this issue was not the biological concept itself but rather the learning curve associated with Benchling. As such, in the future, when introducing concepts with accompanying software, we will provide students with worksheets that allow them to first grasp the new concept before moving on to learning the software involved.



In this Open lab session, we celebrated the successful cloning of Z.1! We shared the differential digest we did in real life and the pros and cons of the various options to reiterate last week's concepts. We discussed the principles of PCR and inverse PCR, highlighting the differences between the two techniques. Students then set up an inverse PCR reaction to cause a mutation in the start codon of crtY.



Reflections and improvements


During the meeting, we realized our slides were too lecture-heavy. While designed to have many visuals, introducing several new topics at once overwhelmed students, and made them hesitant to ask questions. This highlighted the importance of gradually building up topics. Even though we've discussed PCR often, students still struggle with it, so introducing inverse PCR in this Open Lab may have been premature. While it's our goal to cover a variety of techniques throughout the year, we now see the need to ensure comprehension before moving forward.




Open Lab 5: DpnI Digest and Glycerol Stock 10/07/24


In this Open Lab session, we will introduce the use of a DpnI digest to eliminate template DNA by applying it to the PCR reactions from Open Lab 4. Students will also learn how to create a glycerol stock of the Z.1 plasmid.



Open Lab 6: Gel Electrophoresis and Cloning Activity 11/04/24


In this Open Lab session, students will run a differential digest of our clones to determine whether we should proceed with sequencing. They will first practice loading a gel using food dye before loading their group's digest. While the gel is running, students will be given a cloning activity that challenges them to use their problem-solving skills and knowledge gained from previous Open Labs to arrange the steps of the cloning process in the correct order.





Open Lab 7: Inverse PCR Spring 2025


In this Open Lab session, we will reintroduce the project, recap last semester's events, and explain how we will use inverse PCR to remove the gene crtY. Students will complete a recap worksheet and conduct the inverse PCR reaction.





Open Lab 8: Miniprep and Intro to Transformation Controls Spring 2025


In this Open Lab session, students will perform a miniprep of the transformants from the inverse PCR reactions conducted in Open Lab 7. We will also introduce the concept of positive and negative transformation controls.





Open Lab 9: Design Primers for Gibson Assembly Spring 2025


In this Open Lab session, we will introduce Gibson Assembly, the vector pBAD, and the concepts of induction and repression in gene expression. Using Benchling, groups of students will work together to design primers that amplify the genes CCS and ZEP while also incorporating the appropriate Gibson overlaps.





Open Lab 10: gBlock Amplification and Backbone Digest Spring 2025


In this Open Lab session, we will discuss the concept of DNA synthesis and introduce companies like TWIST and IDT. Students will then set up a PCR reaction to amplify the gBlocks for the genes CCS and ZEP using the primers designed in Open Lab 9. If time permits, they will also set up a restriction enzyme digest of the Gibson backbone.





Open Lab 11: Gel Purification Spring 2025


In this Open lab session, students will gel purify the digests and PCR reactions from Open Lab 10. We will also discuss troubleshooting tips and considerations for gel electrophoresis.





Open Lab 12: Gibson Assembly Spring 2025


In the final Open Lab of the year, we will set up the Gibson reaction using the gel-purified amplified inserts and the digested backbone. We will also play an Open Lab Jeopardy game as a fun way to recap and conclude the year!




For more detailed information about planning, protocols, and sequences used, please refer to our 2024-2025 Guide to Open Lab


Achievements and Testimonies

Open Lab was nominated for an Outstanding Educational Program Award and received the Sun Devil Way Award. Most importantly, many DIYbio members who gained their first experience in synthetic biology by participating in the Spring 2024 project have since become student leaders. As the initiative grows, we are committed to continue creating a space for students from all backgrounds to develop foundational skills in synthetic biology and to inspire others.


Beyond institutional achievements, we also have numerous positive testimonials from students who have participated in Open Lab. Many reported that the hands-on experience boosted their confidence and understanding of synthetic biology concepts, while others highlighted the collaborative environment and sense of community as key factors that enhanced their learning experience and fostered lasting connections with their peers. Here's what they have to say:


Sophia Cerna, Attended Open Lab Spring 2024 and instructed Fall 2024


Open Lab was a critical space for me as I was starting to get involved in research. Our weekly meetings were an environment where I felt like I could be silly while, simultaneously, I was being exposed to new techniques and being able to teach and share what I already did know. As students are then built up into the next generation of leaders in this program, they have not only become proficient in synthetic biology techniques, but they also learned the important skill of how to communicate based on your audience. As I look back in retrospect, I see how difficult it would've been to learn the skills I have now if I wasn't taught them in a simpler, interactive form through Open Lab.


Ryan Crane Attended Open Lab Spring 2024 and Fall 2024 2024


Open lab was a really awesome experience. I had never learned about or done anything remotely syn bio related before, so the opportunity to learn something different and hands-on that I was not learning in my classes made me want to keep coming and continue to learn more. I also really enjoyed the fun, no-pressure environment and I appreciated how cool everyone was. I liked how silly the slides were sometimes, it made it clear that we were just a bunch of undergrads learning about awesome stuff together and not something more stressful. Overall, I enjoyed coming and would recommend it.


Nicole Salazar Attended Open Lab Spring 2024 and instructed Fall 2024


I think it was very productive to practice wet lab skills in a low stakes environment with more experienced people supervising and being available for help. I liked how it prepared us well to work by ourselves in the summer during iGEM.


Braeden Sullivan Attended Open Lab Spring 2024 and Fall 2024


My experience in Open Lab provided me with an experience that took me beyond the typical biology classroom experience. I started to learn skills and habits that made me feel more confident in pursuing more advanced avenues in my career.It was a fantastic way to build connections amongst my peers as we could respectively explore our interests over what we were working on. Along with friends, I made lots of higher level connections, I was allowed to talk to upper level classmen who gave me recommendations and advice of opportunities to look into and skill sets to hone in on. I recommend an open lab experience in every sense, its fundamental teaching and outreach is unmatched by anything.



Art and Science Events

At the end of the 2023 iGEM cycle, Gabriella also led activities that utilized art to help students learn basic lab techniques and showcase just how awesome synthetic biology is. She hosted events like agar art, making DIY plasmid bracelets, and a paint-by-numbers pipette workshop. These fun events, organized by DIYbio, aimed to lower the barriers to lab work and have become a valuable contribution to the ASU iGEM team's mission of fostering friendships and a community through synthetic biology.


These events inspired the 2024 iGEM team to further explore the integration of art and science to enhance the educational experience. This idea was solidified after attending the ART X SCIENCE event hosted by the Phoenix Bioscience Core, where our team witnessed how the fusion of art and science can ignite people's curiosity, even about topics that they have never heard of before. We also sought to leverage art as a powerful tool for engagement and learning, prompting us to incorporate it into our planned educational events.




Our first art and science event was a Pipette Paint Workshop, where we introduced the basic concepts of synthetic biology and taught pipetting techniques. We organized this event because we observed that pipetting errors are common among newcomers to researchers, including our own team. The workshop attracted 56 attendees from various majors, with the majority being freshmen. Participants had the option to choose from a selection of templates or come up with their own original designs to create artwork on a plate!





Through a two-part agar art series, we brought "Agar Man", a human-shaped figure crafted from agar plates, to life. During the first hands-on workshop, we discussed the different types of media that can be used to make plates. Students then learned how to pour agar plates, using colored dye as a substitute for antibiotics.




In the second session, we explored various techniques for plating bacteria, including quadrant streaking and bead plating. Students then had the chance to experiment with different bacterial plating techniques, using white paint as a stand-in for actual bacteria on the agar plates made during the first Agar Man event. We plan to showcase the completed Agar Man at various ASU events to promote DIYbio and attract new club members.



Ethical Framework for Researchers

Rather than creating an ethical framework just for our project we developed a general one with case studies for all researchers. To ensure it addresses real concerns, we interviewed ASU graduate students about the broader implications of research, including their own.