Dr. Phillip Kyriakakis

February 14, 2025

Attendees: Ansh, Khushi, Avery, Paul, Nick, Anandita, Sameer, Zoya, Alisha

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.

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.

Implementation

We looked for stakeholders in our local community

Dr. Sukrit Silas

April 18, 2025

Attendees: Ansh, Zoya, Avery, Khushi, Anandita, Nikhil, Sameer, Meghna, Alyssa, Alisha, Paul, Sara

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.

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.

Implementation

Our team researched if we could conduct the project Dr. Silas suggested. We looked into how to safely work with phages and discussed how we could use AI in our project.

Community Integration and Lab Space

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.

Implementation

We decided to not attempt a phage project in order to remain integrated with our community.

Team Poll

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.

Project Selection

May 2025

With our project decided, we met with our secondary investigator, Chris Hernandez, who is a professor at University of California, San Francisco. At this point the project idea was only defined as designing a “living” material that would grow or build itself (hence “living houses"). We discussed biomineralization, which is Chris’s specialty, and how to ensure our project helps the community. We discussed a variety of problems, including plastics and microplastics returning to the environment after capture. With Chris’s advice, we pivoted our project to address local problems.

Implementation

Our project “living houses” was redefined as “rock the plastics,” where we trap plastics with biomineralization.

UC Berkeley Bioengineering Symposium

May 2025

Attendees: Avery, Alyssa, Zoya

Our team attended a symposium hosted by iGEM at Berkeley, University of California Berkeley’s only hands-on genetic engineering club for undergraduates. Many speakers gave keynote addresses, including Dr. Leah Guthrie, Priyam Baruah, and Vishnu Rajan Tejus. Many iGEM at Berkeley teams presented their projects including CheRMiT: Chemical Reactions Mining via Transformers, de novo Design of Inhibitory Peptide for Protein-Protein Interactions, CRISPR-Based One-Step Plasmid Assembly in Vivo, One-Step Self-Clearing CRISPR-Based Gene Knockout System, Engineering TEM-1 beta-Lactamase with de novo Scaffolds, and Engineering L. Lactis to Express Antifungals that Inhibit Mold Growth. The event also included poster presentations and networking opportunities.

Key Feedback:

• Contact with other synthetic biology teams and researchers.
• Advice on reaching out to sponsors and partnerships.
• Clear language, definitions, and understanding who your audience is a necessity for scientific communication

Implementation

We discussed the importance of accessible language to avoid confusion and increase understanding when explaining scientific ideas to the public and others.

Brenda Goeden

May 2025

Attendees: Avery, Ansh, Baxter

Brenda Goeden is the Sediment Program Manager at San Francisco Bay Conservation and Development Commission, a government commission dedicated to the protection, enhancement and responsible use of the San Francisco Bay. She has over 25 years of experience in sediment work, working with dredging in the San Francisco bay and sand mining. She explained the various issues conservationists face when working with dredging and sand mining, including disrupting local wildlife and using up nonrenewable resources. She suggested that our biomineralized material would be most useful in replacing layers of sand or gravel used in backfilling foundations.

Key Feedback

• Replace backfill gravel or sand layers with calcium carbonate from microplastics.
• Look at SFEI, 5 Gyres (Carolynn Box).
• Piggyback on similar pre-existing projects, especially for permits.

Implementation

Because dredging and backfilling is a major issue in the San Francisco Bay Area, we decided we wanted to address it to protect our community. We decided to use our material to replace non renewable materials used in backfilling. This became the primary application of the material we designed.

Carolynn Box

Awaiting text

Win Cowger

July 9, 2025

Attendees: Ansh, Paul, Khushi

Win Cowger (A.K.A Dr. Trash) is the director of the Moore Plastics Center. He has published multiple research papers cataloguing microplastic types and their patterns of movement in the San Francisco Bay and other areas in California that are polluted by microplastics. He works with multiple nonprofit organizations in order to put innovative microplastics mitigation strategies into practice.

Key Feedback

Dr. Cowger advised that we should focus on capturing only fluorescent spheres for two reasons: because it would be easier to verify results on a fluorescent material and it’s less complicated to test our protocol on only one carefully controlled type of microplastic than on an assortment of plastics of various different compositions. He also said that it would be difficult to ensure that our biomineralization process captures only plastics.

Implementation

We decided to implement our project on filtered water only to remove the issue of non-plastic capture. In addition, we’ll be testing on only one form of common microplastic because of Win’s advice.

Dr. Kelsey Defrates

July 1, 2025 and July 8, 2025

Attendees: Ansh, Alyssa

Dr. Kelsey Defrates is a postdoc 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 Kelsey 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.

Implementation

Our team used the protocols, media, S. pasteurii, media protocols, growing protocols, glycerol stock protocols, BHI broth CMM- broth, and S. pasteurii glycerol stock Dr. Defrates provided.

Dr. Brian Ross

July 2, 2025

Attendees: Alexei, Alisha, Nikhil, Sameer

Dr. 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 postdoc in computational biology at the University of Washington and the University of Colorado. He currently works as a biophysicist, with experience in programmable modeling.

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).

Shanno Bonnano

July 8, 2025

Attendees: Alyssa, Ansh, Khushi, Avery, Alexei, Alisha, Sameer, Rohan, Nikhil, Nick

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 Shanna online, where we asked about potentially creating a fusion protein with urease and csgA. Shanna informed us that her team had experience fusing smaller proteins to csgA, and that larger, multi-subunit proteins like urease might present a challenge. Shanna 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 Shanna)

Implementation

Due to Shanna’s advice, we decided to use a Congo Red assay instead of a Thioflavin T assay for quantification of curli fibers. It was also due to Shanna’s recommendations that we ran a pull down as well as fluorescence based assay for Curli fibers.

Shohreh Vanaei

July 27, 2025

Attendees: Ansh, Khushi

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 Shohreh 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, Shohreh 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, Shohreh 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.

Implementation

We were able to utilize the strain Shoreh provided us to act as a positive control in our biofilm formation assays. Further, to counteract the issue of aggregate formation, we utilized a strategy Shoreh mentioned was used in Joshi lab—taking a grid of measurements in a plate reader.