Team:UC Davis/Notebook

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Notebook

• February 9, 2020

  First Official Team Meeting!

  The team meets to discuss safety training in fundamental lab safety, BSL1, BSL 2, hazardous waste management, medical waste, and safe use of biological safety cabinets. The team also discusses fundraising (provided by the Genome Center and BioInnovation Group at UC Davis), and begins project research!

• April 22, 2020

  Labs Closures and Literature Searches

  Brainstorming continues toward an in-lab project. The team and faculty remain unsure whether labs will reopen in time. The literature base expands into the team’s mendeley-database.

• May 21, 2020

  Spore_Core is Born

  After indulging in many prospective project ideas, the team decides to focus its efforts on a bioinformatics project. Dr. Ian Korf joins the team as an advisor and python coach.

• June 24, 2020

  JGI Meeting

  After much research in the literature about fungal biosynthetic gene cluster (BGC) regulation, Spore_Core meets with JGI. JGI generously allows Spore_core access to 664 genomes of filamentous fungi. Spore_Core seeks to inspect the promoter regions controlling BGCs for binding site with which to build new parts.

• July 6, 2020

  Motif-Finding

  MEME is established as our motif-finding software of choice. The team begins downloading and practicing. Meanwhile, a team github is created, the promoters from JGI’s genomes are stored in Dr. Korf’s remote machine, and research continues.

• August 4, 2020

  The Data Gap

  After much searching, through literature and online databases (like TRANSFAC), the team realizes how little available data there is for filamentous fungi. The search for actual binding sites proves scarce. However a preliminary Mbed.py starts being constructed to test MEME’s efficiency. Research into the experimental design also begins.

• September 3, 2020

  Computational and Experimental Progress

  Significant progress is made in the design of experimental protocols for Spore_Core’s binding site validation. A comparison between MEME and another motif-finding software, Weeder2.0, is tested. MEME continues as the front-runner. The team’s main software, MEMEop.py, is being built to further test MEME’s parameters on filamentous fungi. The software is made reliable and reproducible based on the team’s interview with a UC Davis bioethics professor.

• September 15, 2020

  Collaborations and Going Social!

  As progress continues to build on the computational and experimental fronts, Spore_Core introduces itself to the world with a Youtube channel and instagram page! Also the first of many collaborations happens with team IISER Berhampur.

• September 30, 2020

  September to Remember

  A landmark for team Spore_Core, September closes out with the completion of MEMEop.py and Mbed.py (along w/ markov versions of both tools), and shifts the focus from development to usability. The promotional video is completed. Lastly, the team presents to Saddleback College in Orange County, CA.

• October 6, 2020

  Back in Class

  With UC Davis’ fall quarter back in session, Spore_Core begins the major push towards finishing the wiki, polishing the software tools to increase usability, coming up with a comprehensive, reproducible lab protocol, and dotting all ‘i’s’ for the software track. Also, the team presents to six classes at Nevada Union High School, and searches for orthologous clusters to ensure accuracy of motif-finding results on real data.

• October 11, 2020

  Last Minute Breakthroughs

  As culturing and transformation protocols near completion, binding sites in gliotoxin and aflatoxin clusters are found as proof of concept! Also, a technique for scoring orthologous clusters is developed, and phylogenetic analyses begin.

• October 23, 2020

  First Round of Experimental Data

  To accomplish our short term goals for this project, we manually selected 12 unknown BGCs from our Aspergillus dataset and completed our motif-finding workflow to find a proposed putative binding site for each cluster.

• November 22, 2020

  Spore_Core Wins Gold!

  Spore_Core won a gold medal in the software track at the iGEM virtual giant jamboree! Thank you to our collaborators, instructors, sponsors, and iGEM!