About This Project

The access to educational resources for hands on biotech in the classroom, globally, is heavily constrained by the exotic and/or regulated reagents used in routine bioengineering protocols. The need for antibiotics in molecular cloning is a very large barrier to entry for educators, especially in the Global South. I have prototyped a positive selection system and wish to refine protocols for modern cloning using table sugar in safe laboratory E. coli and beyond.

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What is the context of this research?

For the last 15 years I have been an amateur biologist and equipping my home lab with the tools and reagents necessary to conduct basic research has been an extreme challenge. Learning that this challenge also applies to educators in formal labs, where even undergraduate institutions in developing economies are unable to proceed with research due to lack of access has motivated me to find an alternative that uses universally accessible reagents. After some time digging the literature, I noticed that most workhorse lab E. coli strains lack the sucrose metabolism machinery, while this trait is readily available in wild pathogenic E. coli. By complementing this operon on a plasmid, one can leverage positive selection in minimal media.

What is the significance of this project?

Nothing is more effective at educating and inspiring the next generation of scientists as hands on laboratory activities. Biotechnology impacts every facet of modern life and students learning of this today need the tools to fully comprehend and engage with the methods researchers use to engage with the living world. Universal access to quality education is a moral mandate, and tools that enable and empower educators to add more hands-on experiences to their curricula should be a topic of active research. I want to see more people inspired by the living world, knowing they too have the competence and power to build with biology to tackle the grand challenges our species must overcome. There is no better place to inspire than in a classroom setting, and no better time to start than today.

What are the goals of the project?

The goal of this project is to establish a series of sugar-selected plasmids for the molecular cloning of genes into E. coli using modern techniques like Golden Braid without antibiotics, with the stretch goal of engineering other species to function under the same paradigm. Through gene knockouts and directed evolution, we can develop more robust strains better suited to this way of working. Regardless of the deliverable, we will develop educational materials to guide teachers with minimal resources on how to conduct laboratory investigations using our technology. All the materials and plasmids will be fully open source under MIT and Creative Commons licensure to encourage sharing and remixing of this tech.

Budget

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The initial synthesis of a proof of concept has been paid for out of pocket, and the results are very promising. Exploring alternative sugars for multiple selection markers, making MoClo compatible entry vectors using sugar metabolism, and knocking out sugar metabolism genes in other laboratory workhorse species will require financial support. The bulk of the cost will be DNA synthesis so we can codon optimize for orthogonal. MoClo compatible parts based off of native hexose metabolism machinery. We reserve any residual funding for deep sequencing of any strains we develop so both the plasmids AND the microbial chassis will be fully sequenced and open source. The last bit of budget will be for minipreps and agar stabs to distribute materials to educators.

Endorsed by

This is an extremely important project. Equity and accessibility to molecular cloning materials is an enormous problem, particularly in underdeveloped countries in the global south. The ability to use cheap, stable, readily available selective agents would revolutionize cloning for a wide range of people and organizations. I endorse this project with my strongest recommendation

Project Timeline

We wish to develop this within two calendar years at most, with quarterly reports and open call for beta testing at each milestone.

May 07, 2024

Project Launched

Aug 01, 2024

Initial Proof of Concept  - Sucrose Shuttle Vector

Nov 01, 2024

Transformation Pipeline via Minimal Media

Jan 01, 2025

Fully Antibiotic-Free Plasmid Validation

Apr 01, 2025

Alternative Sugar Mechanism for Counterselection

Meet the Team

Sebastian S. Cocioba
Sebastian S. Cocioba
Independent Researcher

Affiliates

Binomica Labs
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Sebastian S. Cocioba

I'm an amateur biologist working out of my home lab in New York as part of Binomica Labs, an educational and research non-profit where we develop the hardware, software, wetware, and thoughtware necessary to enable anyone to explore the living world. I have almost a decade of experience in embedded hardware systems and have built and/or repaired many of the tools I use in my day to day practice. As my day job, I work as a research contractor in the plant bioengineering sector (Currently employed at Deep Science Ventures) where my hardware skills often overlap to meet bespoke client needs. Everything that I make is expensed out of pocket and entirely open source, where I try my best to document my projects such that anyone can easily reproduce both my designs and results as well was modify said designs to fit their needs. I believe in a world where free and open communication of ideas is possible, and where the resources to act upon these ideas are readily available. My small part in making this world a reality is in the development and documentation of easily understood and easily repairable tools that grow with the user's skills. There are more questions about the living world than there are stars in the observable universe so I highly recommend getting out there and exploring your the splendor of your local environment. There are countless life forms awaiting description!

Lab Notes

Nothing posted yet.

Additional Information

This project is part of a larger body of work called Flowers For Everyone, which is actively being developed in this open lab notebook. Link here: Flowers For Everyone


Project Backers

  • 43Backers
  • 119%Funded
  • $11,992Total Donations
  • $278.88Average Donation
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