Synthetic Biology Chassis Toolkit for Public Domain Use

[smklusza]

Project Lead: Stephen Klusza (smklusza)

Mentor: TBA

Welcome to OLS-2! This issue will be used to track your project and progress during the program. Please use this checklist over the next few weeks as you start Open Life Science program 🎉.

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Week 1 (31 August - 4 September 2020): Meet your mentor!

• Create an account on GitHub
• Check if you have access to the HackMD notes set up for your meetings with your mentor
• Prepare to meet your mentor(s) by completing a short homework provided in the HackMD notes
• Complete your own copy of the open leadership self-assessment and share it to your mentor
  If you're a group, each teammate should complete this assessment individually. This is here to help you set your own personal goals during the program. No need to share your results, but be ready to share your thoughts with your mentor.
• Make sure you know when and how you'll be meeting with your mentor.

Before Week 2 (7 - 11 September 2020): Cohort Call (Welcome to Open Life Science!)

• Create an issue on the OLS-2 GitHub repository for your OLS work and share the link to your mentor.

• Draft a brief vision statement using your goals

  This lesson from the Open Leadership Training Series (OLTS) might be helpful

• Leave a comment on this issue with your draft vision statement & be ready to share this on the call

• Check the Syllabus for notes and connection info for all the cohort calls.

Before Week 3 (14 - 18 September 2020): Meet your mentor!

• Look up two other projects and comment on their issues with feedback on their vision statement
• Complete this compare and contrast assignment about current and desired community interactions and value exchanges
• Complete your Open Canvas (instructions, canvas)
• Share a link to your Open Canvas in your GitHub issue
• Start your Roadmap
• Comment on your issue with your draft Roadmap
• Suggest a cohort name at the bottom of the shared notes and vote on your favorite with a +1

Before Week 4 (21 - 25 September 2020): Cohort Call (Tooling and roadmapping for Open projects)

• Look up two other projects and comment on their issues with feedback on their open canvas.

Week 5 and later

• Create a GitHub repository for your project
• Add the link to your repository in your issue
• Use your canvas to start writing a README.md file, or landing page, for your project
• Link to your README in a comment on this issue
• Add an open license to your repository as a file called LICENSE.md
• Add a Code of Conduct to your repository as a file called CODE_OF_CONDUCT.md
• Invite new contributors to into your work!

This issue is here to help you keep track of work as you start Open Life Science program. Please refer to the OLS-2 Syllabus for more detailed weekly notes and assignments past week 4.

[smklusza]

VISION STATEMENT *Reworked with Hemingway editor 9/23/2020)

The purpose of this project is to create a gene cloning system that is completely free to use. Many cloning technologies and systems contain restrictions on their use which promotes inequality. The initial step is the identification of compatible parts for this project. The second step is the creation of a community that can bring people together to make this idea a reality. The last step is to distribute this system to interested parties all over the world.

[smklusza]

Here is a link to my OpenCanvas: https://docs.google.com/presentation/d/17SpQxl5MaXJ2BPzH40fbJb6zXx2DSbkc38mdDhIMst0/edit?usp=sharing

[tlaguna]

Hi @smklusza! I love your project idea. At the beginning of my career I did a lot of cloning!! So I am very aware of the issues with commercial vectors.

Nice vision statement and open canvas, by the way.

I was wondering if you have thought about who will produce the kits and where they will be stored. Do you plan to involve companies?

[smklusza]

thanks @tlaguna ! That is a very good question. Right now, there is the FreeGenesProject at Stanford (https://stanford.freegenes.org/) that sends out genes free of charge to anyone interested in obtaining them. The Openbioeconomy website (https://openbioeconomy.org/projects/open-enzyme-collections/) is coordinating with FreeGenesProject to take the public domain technologies featured in the Public Domain Gazette and put them in E, coli expression vectors. So at a minimum, anything developed in this project would hopefully be included in kits available from the FreeGenesProject.

(As an aside, one thing I haven't had a chance to detail in this project yet is that the organism of choice for this project is Bacillus subtilis and other species within this genus. With the exception of the yeast project at FreeGenes, everything is optimized for E. coli expression. I am focusing on Bacillus subtilis since DNA can be stored in endospores without a need for refrigeration, which would definitely increase accessibility to cloning and synbio).

I would like to see these reagents/kits re-distributed through partially-decentralized hubs of open-life scientists and enthusiasts in different parts of the world. For instance, if I sent kits to three individuals in Europe, any further requests coming from Europe would ideally be filled by the initial recipients and the people that receive from them. The idea is to keep postage costs as low as possible, as it would defeat the purpose to charge people to access these kits. It is a long-term goal to come up with a system that can track distribution so that individuals can request reagents from the nearest person.

[WasifaRahman]

Hello @tlaguna ! The project is very exciting and cloning is one of my favorite topic in biology. To make it useful for public domain would be great and people can collaborate into this idea with your excellent concept.
Waiting for the project to meet its destination.

[smklusza]

This is a roadmap in progress and will be finalized as roadmap.md for the final github repository for this project

PROJECT VISION AND STATEMENT

The purpose of this project is to create a gene cloning system that is completely free to use. Many cloning technologies and systems contain restrictions on their use which promotes inequality. The initial step is the identification of compatible parts for this project. The second step is the creation of a community that can bring people together to make this idea a reality. The last step is to distribute this system to interested parties all over the world.

SHORT-TERM MILESTONE: DESIGN THE CHASSIS

1. Pick the bacterial genus and species which will house the public domain synthetic biology chassis

The bacterium of interest is Bacillus subtilis and possibly other Bacillus species as well. B. subtilis is a motile bacteria that is classified as BioSafety level 1 (BSL-1) which is the safest category in terms of human health. B. subtilis is also capable of creating endospores that are resistant to changes in the environment and is a potential way to store bacteria without the need for a freezer. B. subtilis is also quite adept at secreting materials outside of the cell. (SMK 10/2/2020)

2. Design an open vector in which will allow cloning and expression in bacteria of interest.

3. Design a Multiple Cloning Site within the vector compatible with available public domain restriction enzymes.

MEDIUM-TERM MILESTONE: CREATE THE INITIAL CHASSIS

1. Isolate bacteria of interest from environmental samples.

2. Isolate and engineer open cloning vector from bacterial plasmid.

3. Transform bacteria with open vector and validate gene expression from vector.

LONG-TERM MILESTONE: DISTRIBUTION OF CHASSIS AND FURTHER DEVELOPMENT

1. Initial deposition of new chassis with public domain kits available from the FreeGenesProject and other suitable distribution channels.

2. Identify additional public domain technologies to incorporate into further iterations of the chassis.

3. Create a partially-decentralized distribution lists of recipients who can serve as distributors of the chassis in their regional area.

[malvikasharan]

@all-contributors please add @smklusza for idea and content.

[allcontributors]

@malvikasharan

I've put up a pull request to add @smklusza! 🎉

[LauraCarter]

@smklusza the steps in your Roadmap seem very clear and well-thought out! Have you thought about some documentation and outreach steps as well? It looks from your Open Canvas as though you are also trying to reach non-scientists, who might be interested in the project if they understand more about why this work is important and what kind of things can be done with the kits.