Team:MiamiU OH/Attributions

iGEM 2021 | Miami University

Attributions

Our Approach

The team began brainstorming and recruiting in April, with the first full team meeting taking place on May 4th. Work on the project began immediately after, with a clear focus on photosynthesis improvement by targeting the Calvin-Benson-Bassham (CBB) cycle. Initially, the majority of project work focused on metabolic research and computational modeling to determine the most feasible redesign for RuBP regeneration. Labwork began July 28 and continued throughout fall.

Thanks to the contributions of our team members and members of the Wang lab, we were able to thoroughly explore in silico modeling of alternative RuBP regeneration pathways and begin significant lab work. Due to the difficulties of achieving complete genetic modification of all genome copies in cyanobacteria, this work is ongoing up to and through the wiki freeze deadline.

All work was internally accomplished by the team, excluding lab work preparations completed by Shrameeta Shinde.

Team Attributions

  • Administrative

    Hope Townsend recruited and assembled the team, tracked competition requirements, delegated and assigned projects, designing a timeline and framework of communication for remote and in-person parties.

    Avery Imes assisted in team recruitment.

    Daria Perminova significantly contributed to the completion of the safety form.

    Annie Nguyen completed our parts registration.

  • Computational Modeling

    Tra Yen Nhu Phan edited all models used in our project. These models were based off of Jared Broddrick’s model for Synechococcus elongatus PCC 7942 (1). Nhu utilized Jupyter Notebook to create Escher maps to visualize the models.

    Hope Townsend edited and created the scripts to run flux analysis and growth analysis. She also analyzed and interpreted all data with some guidance from Dr. Xin Wang and Zhenxiong "Shaun" Jiang.

    Assistance should also be noted from Jared Broddrick, the original author of the model and scripts from which our scripts were based (1) from Susan Golden’s lab at UC-San Diego.

  • Project Design

    Dr. Xin Wang oversaw all project design, guiding student member ideas and verifying products before allowing team progression to the wet lab.

    Avery Imes and Hope Townsend designed the transaldolase alternative pathway with the guidance of Dr. Wang.

    Daria Perminova inspired the initial glycolaldehyde pathway which was then edited by Dr. Wang.

    Avery designed the primers for fragment extension and plasmid assembly used in web lab experiments.

    Annie Nguyen, Daria, and Avery organized metabolite and enzymatic information for the computer modeling team to begin their work.

  • Wet Lab

    Daria Perminova, Avery Imes, Max Brenner, and Hope Townsend all contributed to laboratory work.

    Hope, Avery and Daria contributed to the initial work creating the genetically altered cyanobacterial strains.

    Hope and Avery oversaw the initial Gibson Assembly, amplification of plasmids in Esherichia coli and isolation of the vectors.

    Daria and Avery then finished the transformation into cyanobacteria lines, using segregation and antibiotic selection techniques to push the multi-copy genome toward complete transformation.

    Daria handled the sequencing analysis and verification of transformant cell lines.

    Daria led all lab efforts once the semester began with Max providing significant assistance as needed to finalize segregation and begin growth experiments. This included more transformations, colony maintenance, and growth experiments.

    All work was completed within Dr. Xin Wang’s lab under his direction and supervision. These efforts were greatly assisted by the graduate students of the Wang Lab, Shrameeta Shinde and Zhenxiong “Shaun” Jiang. Shrameeta, although not a member of our team, taught our team members relevant skills such as making media or purifying plasmids from gels, as well as providing some of the background work such as making the initial antibiotic plates used for transformant selection. Shaun supervised much of the lab work and served as our team instructor.

  • Wiki

    As the primary deliverable, the wiki was consequently a joint effort between the entire Miami University iGEM team.

    Kyle Lierer served as the lead developer and designer of the wiki. He was responsible for the following: designing the wiki’s overall appearance from the ground up; developing a continuous integration and continuous deployment pipeline to simplify wiki updates; developing tools to convert Word documents and Markdown files to individual wiki pages; developing tools to automatically add references and definition tooltips to the wiki; built a system to keep track of references and ensure consistency across all pages; designed and edited all of the wiki specific graphics including the logo; edited all pages to ensure they are finalized and consistent in tone and format; helped coordinate wiki deliverable due dates and goals; was the final reviewer for all wiki pages.

    Cameron Headlee was a late addition to the team, volunteering to help Kyle on the development side of the wiki. He contributed by using the tools Kyle built to convert Word documents into individual pages, as well as adding photos and references to those pages.

    Rhonda Krehbiel served as the wiki’s lead editor, focusing on effective communication. Everything on the wiki was extensively proofread and edited for improved grammar, fluidity, and readability for all pages. She was also the author of the Human Practices page.

    Avery Imes served as the wiki’s lead coordinator. She was responsible for making sure that all content for the wiki was finished and appropriately formatted so that Kyle and Rhonda had time to edit and finalize the wiki pages. She was a significant author on several pages and the final reviewer for all pages. She also served as an author or editor for Safety and Security, Proposed Implementation, Human Practices, Project Description, Proof of Concept, Contributions, Plant Synthetic Biology, and Project Design.

    Nicholas Nocevski helped write the front page summary for the modeling page. Hope Townsend wrote the multipage analysis and significantly edited and added to the front page summary.

    Daria Perminova was an author on the Safety and Security, Contributions, Lab Notebook, Engineering Success, and Proof of Concept pages.

    Hope edited the drafts for Proposed Implementation, Project Description, Education/Outreach, Integrative Human Practices, Proof of Concept, and Engineering Success. She also described the pathways in Project Design. She also described the pathways in Project Design.

    Mackenzie Britton was the author of the Education/Outreach page and wrote the short descriptions of each section.

    Max Brenner was the author of the plant synthesis page, helped with formatting the lab notebook, and created the key word-definition dictionary used to generate glossary terms for the wiki.

  • Collaboration & Outreach

    Hope Townsend was the link between our team and the Madrid_UCM iGEM team, guiding them through how to use computational modeling for their pathway analysis.

    Hope wrote the Modeling section of the iGEM Phototroph Handbook in collaboration with the Bielefeld and Marburg teams.

    Daria Perminova presented our project progress at the Wright State Science Symposium.

    Hope initiated the general curriculum and framework of the educational outreach and integrative human practices plans that the rest of the team brought to life. She also created the plasmid cutting activity for the educational video.

    Mackenzie Britton created the Chutes and Ladders activity and helped create the Education video.

    Avery Imes presented and helped create the presentation at The Knoll’s community. She also created the children’s educational video with Mackenzie.

    Rhonda helped create the introductory slides for both presentations and assisted in contacting the community for outreach efforts. She also led the team discussion and reflection on Integrated Human Practices.

    Camaryn Bennett reached out to possible communities for education linkages.

    Hope and Avery wrote the Frontiers article with the guidance of Dr. Wang. Hope wrote the base draft and created the Biorender figures. Avery edited the base draft and wrote the Lasting Applications portion.

  • Promotional Video

    Avery Imes and Kyle Lierer served as the primary contributors to the project’s promotional video. Working together, they crafted our two-minute promotional video featured on the wiki’s homepage.

    Avery is responsible for the voiceover as well as providing key points brought up in the video.

    Kyle served as the lead script writer, video editor, and coordinator.

  • Presentation Video

    All team members excluding Camaryn Bennet, Cameron Headlee, Nicholas Nocevski, and Annie Nguyen helped write the script for the Presentation Video.

    Kyle Lierer and Hope Townsend served as the lead script editors.

    Kyle Lierer served as the lead video editor, coordinator, and graphic designer.

    Avery Imes, Daria Perminova, and Max Brenner served as the presenters.

    Annie Nguyen, Daria Perminova, Hope Townsend, Mackenzie Britton, Tra Yen Nhu Phan and created all used Biorender figures.

Our Resources

Miami University irregularly offers synthetic biology as the subject focus for an advanced Topics in Microbiology course. Due to the variable nature of this course, its materials are not available online. Recently, the course focused on synthetic biology when taught by our team principal investigator, Dr. Xin Wang. Although none of our team members have had the privilege of enrolling in the course during the iGEM competition, this competition did inspire several of us to embrace an interest in synthetic biology and enroll in the course in future semesters.

Our team is extremely thankful for the guidance and generosity of the Wang Microbiology Lab, who not only allowed our team to use their lab space, cyanobacteria strains, and lab materials, but consistently provided their advice, skills, and time. We would also like to acknowledge Dr. Luis Actis, who provided project support and advice.

This work was funded by the National Science Foundation grant number 2042182.

References

1. Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, Lee JJ, Golden SS, Palsson BO. 2016. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. PNAS 113:E8344–E8353. (https://doi.org/10.1073/pnas.1613446113)

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