Phillip Kyriakakis, Ph.D. is a Senior Research Scientist in the Bioengineering Department at Stanford University and a member of the Wu Tsai Institute for Neuroscience.

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What We Learned

Our team visited Dr. Kyriakakis’ lab at Stanford. He gave a presentation on his research in optogenetics, explaining how it enables scientists to use light to control neurons and other cells. After the presentation, we split into two groups to tour different areas of his lab, where we also had the chance to briefly meet a member of the Stanford iGEM team. Dr. Kyriakakis highlighted opportunities for collaboration and pointed us toward local resources and mentors who could support our work.

Key Takeaways

• Seek local resources and mentorship: Connect with nearby universities, labs, and experts for advice and potential collaboration.
• Learn from peers: Engaging with teams like Stanford iGEM can provide new perspectives and build community connections.

Dr. Sukrit Silas is a Principal Investigator at the Gladstone Institutes and an expert in phage-bacteria dynamics and bacterial immune systems. His group is particularly interested in phage accessory genes—small proteins that allow phages to evade bacterial defenses.

What We Learned

Our team visited Dr. Silas’ lab at the Gladstone Institutes while exploring a possible phage-based iGEM project. He explained the challenges of phage therapy, particularly how phages tend to be effective only against very specific bacterial strains, and how defenses like receptor shielding can block infection even when receptors appear to match. He also introduced his lab’s ongoing work testing accessory genes by expressing them in E. coli to map their role in infection. His postdoc discussed how AI and computational tools can predict host range, model resistance, and guide cocktail design. Importantly, Dr. Silas suggested a potential iGEM direction: testing phage cocktails—combinations of different phages—to broaden effectiveness against E. coli. Ultimately, this idea was not feasible for us since community labs such as BioCurious prohibit phage use, and we lacked access to phage-dedicated containment facilities.

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Key Takeaways

• Phage-host interactions are highly strain-specific, unlike antibiotics.
• Receptor shielding is a key bacterial defense blocking many infections.
• Dr. Silas’ lab is creating a functional map of accessory genes to understand how phages evade defenses.
• AI modeling can help predict phage-host interactions and optimize cocktails.
• A strong project idea was to test phage cocktails, but this was not possible due to biosafety limits.

From the beginning, our team knew we wanted to integrate community projects and efforts into our project. Due to this, we decided to conduct wetlab work at BioCurious, a community biotech lab. Unfortunately, BioCurious has a policy against working with phages in order to protect other member’s work.

April 2025

Simultaneously as discussing community labs, we polled our members on which project they would like to pursue. At this point we had narrowed down to three ideas: Phage therapy (ruled out), living houses, and grass water loss. Living Houses won with 58.8% of the vote, making it our official project.

Dr. Kelsey Defrates is a postdoctoral scholar at Dr. Hernandez’s lab at UCSF. She focuses on materials characterization, particularly working with materials created using protein polymerization. She also works with S.pastuerii based biomineralization.

We met with Dr. Defrates twice over video call, and discussed further over email. During that time, Kelsey has provided us with the protocols, media, and S. pasteurii needed to do biomineralization, as we are using S. pasteurii as a biomineralization positive control in our project.

Key Feedback

CMM- acts as negative control, add CaCl2 to create CMM+ (the precipitation media). We should use fine-grain beach-like sand if possible, but playground sand will still work. Dr. Defrates also provided protocols, media, S. pasteurii, media protocols, growing protocols, glycerol stock protocols, BHI broth CMM- broth, and S. pasteurii glycerol stock.

Dr. Brian Ross has a bachelor of science in aerospace, aeronautical, and astronautical engineering from the University of Maryland and a PhD from MIT on physics. He’s previously worked as a postdoctoral scholar in computational biology at the University of Washington and the University of Colorado. He currently works as a biophysicist, with experience in programmable modeling.

Advice

We met with Dr. Ross online where he provided us with a lot of background and helpful information guiding our Drylab, mainly making sure our plan for Drylab was on track and would actually be beneficial to the wetlab. Dr. Ross explained that code will not be the main problem; the difficulty is more about implementing the ODE function and finding the proper variables (we would have to get some from literature).

Ms. Shanna Bonnano is a graduate student at Neel Joshi’s Biologically Fabricated Materials Lab, working on curli secretion and responsive biofilm materials. She has previously investigated secretion trade-offs in E. coli and tunable living composites, and her current research focuses on developing engineered probiotics for targeted delivery and treatment of gastrointestinal diseases.

Advice

Through an email, we got insight on curli quantification methods and got feedback on our synthetically designed plasmid pET-csg-sazCA-amp. We later met Ms. Bonnano online, where we asked about potentially creating a fusion protein with urease and csgA. Ms. Bonnano informed us that her team had experience fusing smaller proteins to csgA, and that larger, multi-subunit proteins like urease might present a challenge. Ms. Bonnano was also a great help in sending us E. coli with the plasmid that would express a fusion protein of csgA and a GFP antibody.

Key Feedback

• The Joshi Lab uses a Congo Red assay to quantify curli fiber expression.
• Their plasmids use all the natural RBSs. Ours don’t, not for csgB, but it should be fine (according to Ms. Bonnano).

Ms. Shohreh Vanaei is a PhD student at Dr. Neel Joshi’s Biologically Fabricated Materials lab. At Northeastern University, her current research centers on the development of engineered microbial systems for rapid and accessible detection of chemical & biological compounds.

Advice

We met Ms. Vanaei when visiting Joshi lab in person at Northeastern University. She prepared and provided us with a E.coli Mach1 strain transformed with pBbB8k-csg-NbGFP, a plasmid which the Joshi lab had confirmed expresses Curli fibers and showed us around the lab. She also brought to our attention the concern of protein aggregate formation when using Congo red assays. While in the lab, Ms. Vanaei described how they may use PDMS microfluidic devices, noting that they had to use specialized molds since 3d prints did not have high enough resolution. However, when we mentioned how large our mold was, Ms. Vanaei mentioned that should be okay.

Key Feedback

• Congo red can form aggregates with curli fibers leading to inconsistent spec readings.
• 3d printed inverse molds should be sufficient for us to make PDMS devices of the size we are making.

We met with the University of California, Santa Cruz iGEM team for a joint collaboration. The UCSC team presented their project on their solution to detoxifying contaminated solutions and gave feedback on our team’s work and presentation.

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Key Feedback

The UCSC team was very impressed by all the work our team accomplished. In terms of research, they recommended using RNA sequencing to check if our construct was working correctly. In terms of presentation, they advised us to have a clear goal when presenting to communicate clearly.