1. Assume that all of the molecular biology work you'd like to do could be automated, what sort of new biological questions would you ask, or what new types of products would you make?
    1. If biology was automated, I would also assume LLMs would be used to perhaps optimize and develop the processes and experiments. I would begin to ask whether there are any ethical implications around too much replication, or production on a scale that could actually cause ecological imbalances if things ended up leaving the laboratory space.
    2. Would make enzymes that break down non-degradable substances. Make bacteria that can capture elemental carbon and prevent it from entering the atmosphere, can be used in agricultural supplements, etc.
  2. If you could make metric tons of any protein, what would you make and what positive impact could you have?
    1. From point (b) above, it we could create similar to PETase, large amounts of proteins that will break down all the possible non-degradable materials found in landfills, or be able to reduce the methane produced by the organic waste by adding proteins that can consume or process the methane, that would have a huge impact on our waste streams and landfill dumps.

<aside> <img src="/icons/push-pin_green.svg" alt="/icons/push-pin_green.svg" width="40px" /> Key Links: http://docs.google.com/document/d/15-tlrejgbbr4FMpA6rKogTjlv6qXJhFqQm7o_Ppfh-I/edit?tab=t.0#heading=h.jyt74412izch

Key Papers:

  1. Gene expression pattern analysis of a recombinant Escherichia coli strain possessing high growth and lycopene production capability when using fructose as carbon source

  2. Improvement of Biomass Yield and Recombinant Gene Expression in Escherichia coli by Using Fructose as the Primary Carbon Source </aside>

  3. Which genes when transferred into E. coli will induce the production of lycopene and beta-carotene, respectively?

    1. Lycopene: The genes crtE, crtB, and crtI in E. coli induces the production of lycopene.
    2. Beta-Carotene: crtY in addition to the above induces the production of beta-carotene.

  4. Why do the plasmids that are transferred into the E. coli need to contain an antibiotic resistance gene?

    1. Antibiotic resistance genes on plasmids act as a selective marker, so that when E. coli is grown on media that contains the antibiotic, only cells that have successfully taken up the plasmid with the resistance gene will survive. This ensures that the bacteria grown on the media only contains the plasmid of interest.

  5. What outcomes might we expect to see when we vary the media, presence of fructose, and temperature conditions of the overnight cultures?

    1. We may see:

  6. Generally describe what “OD600” measures and how it can be interpreted in this experiment.

    1. It is the optical density measured at 600nm wavelength. This estimates the concentration of cells in a culture, by testing the light scattering caused by the cells. Here, monitoring OD600 determines the growth phase of E. coli, ensuring cells are harvested at optimal density for the maximum pigment production.

  7. What are other experimental setups where we may be able to use acetone to separate cellular matter from a compound we intend to measure?

    1. Acetone can be used to precipitate proteins and break down lipids. It can also be used to extract pigments from plant tissue, precipitate proteins, and separate small molecules from microbial cultures for metabolic analysis.

  8. Why might we want to engineer E. coli to produce lycopene and beta-carotene pigments when Erwinia herbicola naturally produces them?

    1. We would do this due to the rapid and easy growth of E. Coli. It is also very well established and characterized, making it easier for any kind of genetic manipulation to increase production. Further, E. Coli is more easily scaled up, and generally considered a safe option (without biosafety concerns) in most environments.