March
Week 1
- First team meeting, brainstormed ideas for the project
Week 2
- Continuation of Week 1
Week 3
- Narrowed down our project ideas into top two contenders
April
Week 1
- Decided our project topic: Plastic Degradation
Week 2
- Planned for our project to be composed of a drylab component and a wetlab component
Week 3
- Brainstormed end goals and tasks for each component of the project
Week 4
- Continuation of Week 3
May
Week 1
- Began literature review for PETase and PET degradation studies
Week 2
- Off week for finals
Week 3
- Wetlab: Developed initial protocols
- Drylab: Evaluated different methods of creating a model for new protein sequences
Week 4
- Continuation of Week 3
June
Week 1
- Wetlab: Reagents prepared for initial testing of plasmids
- Drylab: Evaluated HMMER and RNN models and their efficacy for sequence analysis and generation
Week 2
- Wetlab: Began practice for plasmid transformation and purification
- Drylab: Decided on using an RNN pipeline, researched prior iGEM teams’ computational work with PETase
Week 3
- Wetlab: Received plasmids, continue work with competent cells
- Drylab: Continued research into previous iGEM work, specifically 2019 iGEM Toronto. Analyzed their pipeline and researched use-cases of UniRep + Docker
Week 4
- Wetlab: Performed plasmid purification and Nanodrop analysis, reviewing errors for coming weeks
- Drylab: Compiled initial set of training sequences from literature review. Also performed sequence alignment of Toronto iGEM’s sequences using BLAST
July
Week 1
- Wetlab: Troubleshooting restriction digest, sequenced extracted DNA
- Drylab: Continued sequence gathering for model training, and set up Docker for pipeline testing. Emailed iGEM Toronto for questions and possible
Week 2
- Wetlab: Performed SDS-PAGE and troubleshooting
- Drylab: Continuation of Week 1, UniRep tutorial started
Week 3
- Wetlab: Ran more SDS-PAGEs, began preparation for protein purification
- Drylab: Began pipeline work, continued literature review for enzyme characteristics like thermostability and catalytic activity
Week 4
- Wetlab: Additional troubleshooting for previous protocols, began collaboration with UT Austin’s wetlab group for protein purification troubleshooting
- Drylab: Tested iGEM Toronto 2019’s initial pipeline for any output, continue studying code architecture for incorporation of our training set
- Attended JulyGEM meetup with other iGEM teams to receive feedback on our progress so far
August
Week 1
- Wetlab: Literature review for protocols, especially alternative lysis
- Drylab: Pipeline tested, several technical issues and platform issues with Docker and Colab debugged. Working to create CRUD table for a PETase web database
Week 2
- Wetlab: Worked on protocols for coming weeks (competent cells)
- Drylab: Completed basic pipeline debugs, able to generate sequence output. Began preparation of training set for the pipeline
Week 3
- Wetlab: No updates, continued work from Week 2
- Drylab: Completed further modifications to pipeline and ran model with our training data, output sequences generated flawlessly. Continued work on web PETase database in collaboration with iGEM Toronto
Week 4
- Wetlab: Began plasmid purification and protein purification prep, update protocols
- Drylab: No updates, aside from further pipeline testing and database work
- Interviewed Dr. Ting Lu in Bioengineering
September
Week 1
- Wetlab: Protein and plasmid purification, ordered mutants
- Drylab: Sent three mutant candidates to wetlab for validation. Began package development
Week 2
- Wetlab: Continuation of Week 1, continued contact with UT Austin for troubleshooting
- Drylab: Drafting master document for wiki and compiling all information. Continued collaboration with iGEM Toronto for PETase sequence database. Package development in progress.
Week 3
- Wetlab: Obtained PET band on SDS-PAGE gel, began prep for FPLC
- Drylab: Continued work on master wiki document
Week 4
- Off-week for midterms and other commitments
October
Week 1
- Wetlab: FPLC preparation and training
- Drylab: Drafting for wiki complete, started illustrations and design work. Initial version of package published on test index
Week 2
- Wetlab: Finalized additional protocols for wiki, continued FPLC prep
- Drylab: Package made available on GitHub. Met with iGEM Toronto for mutant analysis and thermostability predictions. Troubleshooted the wiki pipeline and began incorporating content to the main wiki page
Week 3
- Wetlab: Performed FPLC and began work with mutants
- Drylab: Continued incorporation of content into the wiki before deadline
- Wiki freeze on Oct 21
Week 4
- Worked on the final presentation video