NOTEBOOK

Week 1

• April 1, 2023: First day of the iGEM season! Past UW iGEM members introduced the basics of iGEM to the new members this year. Project ideas were also presented to the members, and four main themes were decided: oral vaccines for pacific salmon, degradation of hazardous materials in Washington water bodies, nitrogen fixation, and artificial fish.
• April 5, 2023: Further discussions on the project ideas were made. During this meeting people conducted more literature review and discussed the interest and feasibility of each project idea.
• April 7, 2023: Members of wet lab started online laboratory safety training.

Week 2

• April 14, 2023: All members of wet lab finished their online laboratory safety training.
• April 15, 2023: First vote was cast and the top two choices were subunit vaccine and bioremediation; members who voted for each idea would then do more research and compose a presentation to convince the other side.
• April 16, 2023: The wet lab team decided to defend the subunit vaccine idea, and more literary reviews were conducted.

Week 3

• April 17, 2023: First lab orientation. Dr. Li Sun showed wet lab members the lab that we will be working at for the remainder of the season, as well as some safety information.
• April 18, 2023: Second lab orientation for the rest of the wet lab team.
• April 22, 2023: Second vote is casted and the final choice is bioremediation. The initial project idea is transforming algaes so that they will be able to take up and fix the nitrogen that is present in the water.

Week 4

• April 24, 2023: With a specific project in mind, the wet lab subteam decided to go into the lab and sort through the chemicals we can use. We first did a general clean-up and discarded all things that were expired or no longer in working condition. Then we cleaned the lab benches, racks and other surfaces with alcohol.
• April 25, 2023: Continuing our cleaning, we reorganized the contents of the drawers and cabinets, then applied new labels to those places.

Week 1

• May 1, 2023: More research regarding our project is done, and we started to look for mentors or advisors that can guide us through the project. Through our research we proposed that we could also make use of the metabolites that algae can produce.
• May 3, 2023: With more discussion of our project we realized that doing nitrogen fixation and repurposing metabolites might require too much time that will cause us to not be able to finish either of them. There were also concerns regarding the novelty of modifying algae for nitrogen fixation.
• May 6, 2023: New ideas for our project were presented, we were trying to determine what issue is most prominent to Washington State and what threatens the health of Washington’s water system.

Week 2

• May 13, 2023: After a week long research we eventually decided on PCB degradation as the final goal of our project.

Week 3

• May 15, 2023: Further research shows that cyanobacteria might be a better candidate for genetic transformation than algae, as they are easier to transform.
• May 20, 2023: The entire team agreed that cyanobacteria might be a better option for our project. We decided that our final project will be genetically transforming cyanobacteria so that we will be able to take up and break down PCBs present in Washington’s waste water, after we successfully transformed the cyanobacteria then we will create a biofilm for easy water filtration.

Week 4

• May 22, 2023: Now with a definite project down, we looked for professors that specialize in either PCB degradation, cyanobacteria, or biofilms.
• May 27, 2023: Researched on which types of PCB are more common in Washington State.
• May 28, 2023 to June 5, 2023: The team decided on the type of PCB that we wanted to target: PCB-11, PCB-209, PCB-132.

Week 1

• June 7, 2023 to June 19, 2023: Purchased the necessary materials for our transformation: PCB-11, PCB-209, PCB-132, LB broth, sodium thiosulfate, pET vectors. Some other materials were obtained through grants. Strain of bacteria was decided to be Synechocystis sp. PCC 6803. Did extensive literature review looking for sources of wild type breakdown pathway plasmid due to equipment and cost restrictions from purc

Week 3

• July 21, 2023: Durva, Ethan, and Wenyu went into the lab and prepared plates for future bacteria culturing.

Week 4

• July 24, 2023: Written and revised protocol for natural bacteria transformation.
• July 25, 2023: Maddie, Druva, Ethan, and Anna met with Dr. Matthew Parsek, an expert in biofilms. In the meeting we learned that Dr. Parsek did his PhD work on PCB degradation and got some insights on PCB quantification.
• July 27, 2023: Wenyu and Anna met with Dr. Carrie Harwood, an expert in bacteria transformation. In the meeting she informed us that she does not have a lot of experience with marine bacteria transformation and referred us to Dr. Gabrielle Rocap but we were not able to get in contact with her.

Week 1

• August 1, 2023: More plates with antibiotics (kanamycin) were made in preparation for bacteria.

Week 3

• August 14, 2023: Maddie, Wenyu, and Anna met with Stephen Blaskowski, an expert at marine bacteria, and learned about the hardship of transforming cyanobacteria. In addition to the previous hardship contoured with purchasing cyanobacteria the team decided it might be best to switch to E. coli for transformation, as they are a lot more easier to obtain.
• August 20, 2023: Contacted Ellie Reese, Dr. Beth Traxler, and Brandon Bol, for possible useful chemicals, E. coli transformation tips, and GC-MS machine training respectively.

Week 5

• August 29, 2023: Anna met with Ellie Reese the lab manager for SEFS Genetics Lab to see if they can provide any chemicals that would be helpful for our project, unfortunately none of the chemicals they were needed for our project.

Week 1

• September 1, 2023: Ethan and Anna met with Dr. Beth Traxler, an E. coli expert, and learned about the transformation and culturing process of E. coli.

Week 2

• September 7, 2023 to September 13, 2023: Maddie secured strands of competent E. coli from Yuxin Pan of Dr. Gu’s lab.

Week 3

• September 12, 2023: Sanjana and Anna attend the training session for operating the GC-MS machine.

Week 1

• October 2, 2023: Maddie and Wenyu started the process of transformation of E. coli with the mutated protein that the protein modeling subteam provided us with.