Week 1 HW: Final Project Ideas

(1) What you would like to biomanufacture and why?

I would like to develop a genetically modified microbial chassis from an extremophilic bacterium native to the Salar de Uyuni in Bolivia. The goal is to make this bacterium easier to grow, study, and genetically modify in a laboratory, while keeping the biological characteristics that make it adapted to extreme environments. In this way, the bacterium could become a useful platform for future biotechnology research, similar in concept to how E. coli is widely used in laboratories. I am interested in this because studying extremophiles directly in the Salar de Uyuni can be expensive and difficult, and field research gives us limited control over experimental conditions. A more accessible laboratory strain would allow researchers to study these microorganisms in a controlled and reproducible way, and to investigate their physiology, stress responses, and other possible biotechnological properties. The main output would therefore not be one specific product, but a research platform that can support future discoveries. By developing a more accessible extremophilic chassis, we could create new opportunities to study microorganisms from the Salar de Uyuni and explore biotechnology applications that we may not know yet.

(2) What living system would you use?

I would use an extremophilic bacterium from the Salar de Uyuni as the living-system chassis. The starting system would be a wild-type strain isolated from the environment. It would be grown in a controlled laboratory medium designed to support its growth, and we would introduce genetic modifications that could improve its growth, genetic accessibility, or other laboratory characteristics. At a high level, the process would involve growing the bacterium, applying the genetic modifications, and selecting cells with the desired characteristics. The cells would then be tested under controlled laboratory conditions to measure their growth and stability. The main output would be a genetically modified and more laboratory-accessible extremophilic strain, which could then be used as a microbial chassis for future biotechnology research. These steps assume that the selected extremophile can be genetically modified and that its important biological properties can be maintained after the modifications.

(3) How would you use automation?

I would use a desktop liquid-handling robot such as Opentrons together with the extremophilic bacterial chassis. The robot could automate tasks such as preparing culture media, transferring bacterial cultures, and setting up many experiments with different conditions. This would allow us to test several variables in parallel and reduce manual work.

The automation could also be used to compare different genetically modified strains and identify which ones show better growth or stability under laboratory conditions. Data from these experiments could then be collected and analyzed to find the most useful strain for future research. This would make the process more reproducible, scalable, and efficient than doing each experiment manually.

(4) How much would you need to make, and how long would it take?

(a) How much?

Since my target is a laboratory microbial chassis rather than a chemical product, I would define the meaningful scale as a small library of laboratory-adapted strains and experimental conditions. As a first target, I would aim to develop and compare about 100 experimental variants/conditions. If each condition requires approximately 1 mL of culture for initial testing, this would represent about:

100 conditions × 1 mL = 100 mL of total culture

The 100 mL is not the important part of the project; it is a practical scale for screening many conditions while keeping the project manageable. The important output would be the identification of a smaller number of stable strains that can later be studied at larger scale. This approach is inspired by organisms such as Haloferax volcanii, which became useful as a model extremophile because researchers developed reliable cultivation and genetic tools around it.

(b) How long?

I would estimate approximately 2–3 months for an initial prototype, followed by additional time for validation. The first stage would involve establishing reproducible growth conditions, preparing the experimental variants, and comparing their growth and stability. An automated liquid handler such as an Opentrons OT-2 could perform many of the repetitive liquid-transfer and culture-setup tasks in parallel. The OT-2 has 11 deck positions and can use single- or 8-channel pipetting, which makes it suitable for small-scale experimental screening.

This estimate is only a back-of-the-envelope calculation generated from an AI-assisted analysis of published research and available automation specifications, not a validated experimental protocol. The real timeline could be considerably longer because the main uncertainty is not the amount of liquid that can be handled by the robot, but how difficult it is to develop a genetically tractable and stable laboratory strain from the selected extremophile. The experience of H. volcanii shows that establishing a useful extremophile model requires the development of cultivation methods, genetic tools, selectable markers, and other laboratory resources over time.

For a future larger-scale version, I would use automated culture systems or parallel bioreactors rather than a desktop liquid handler. The Opentrons would mainly be a prototyping and screening tool, while larger automated culture infrastructure would be more appropriate once a promising chassis had been identified.

(5) What don’t you know yet?

The first main unknown is whether the selected extremophilic bacterium can be genetically modified efficiently. Some extremophiles may be difficult to transform or may not work well with common genetic tools. We would need to determine which method works and whether the modified bacteria remain stable.

The second unknown is whether we can improve its laboratory growth without losing important characteristics of the original extremophile. We would need to test different culture conditions and compare the modified strain with the original strain to measure growth, stability, and other relevant properties.

The third unknown is whether this bacterium can become a reliable microbial chassis for future research. We do not yet know which genetic modifications would be most useful or what applications the organism could support. This would require experiments to identify its useful biological properties and develop basic tools for working with it.

AI assistance statement: I used AI(ChatGPT) to help me organize my ideas, improve the academic terminology in english, and structure the project. (the question 4 was drafted with AI)