Homework Part A

<aside> <img src="/icons/exclamation-mark_orange.svg" alt="/icons/exclamation-mark_orange.svg" width="40px" /> These homework questions are based on lecture questions! Mandatory for Committed Listeners.

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Patrick Boyle’s Lecture Questions:

  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?

Assuming molecular biology will be fully automated

With complete automation of molecular biology techniques, I would focus on developing precision immune modulation systems. This would allow us to address two critical areas:

First, I would explore enhanced immune activation pathways by developing platforms that can rapidly engage dendritic cells and other antigen-presenting cells with customized molecular signatures. This would enable faster, more targeted immune responses against evolving pathogens and cancers. For example, we could design systems that dynamically adjust cancer neoantigens presented to the immune system based on real-time tumor mutation analysis.

Second, I would investigate targeted immune suppression mechanisms for autoimmune and inflammatory conditions. By precisely identifying and selectively deactivating hyperresponsive immune cell populations without compromising overall immune function, we could create treatments for conditions like rheumatoid arthritis, multiple sclerosis, and inflammatory bowel disease with fewer side effects than current immunosuppressants.

The ultimate product would be a comprehensive immune modulation platform that could rapidly analyze a patient's immunological status and deploy customized molecular interventions—either stimulatory or suppressive—with cell-type and tissue specificity. Such technology would transform our approach to infectious diseases, cancer immunotherapy, autoimmune disorders, and transplantation medicine by providing precise control over immune function at the molecular level.

  1. If you could make metric tons of any protein, what would you make and what positive impact could you have?

If I could produce metric tons of any protein, I would focus on specific recombinant human growth factors, particularly nerve growth factor (NGF), epidermal growth factor (EGF), and vascular endothelial growth factor (VEGF). These would enable transformative applications in regenerative medicine and tissue engineering. In acute wound healing, a combination of EGF and VEGF could dramatically accelerate repair processes by stimulating rapid re-epithelialization and promoting robust vascularization. For severe trauma and burn victims, these proteins could reduce healing time by 50-70%, minimize scarring, and prevent the development of chronic wounds that currently affect millions of patients globally. The availability of these proteins at industrial scale would make advanced wound healing accessible even in resource-limited settings. For neurodegenerative conditions, abundant NGF and brain-derived neurotrophic factor (BDNF) could revolutionize treatment approaches. In spinal cord injuries, these neurotrophic factors could promote axonal regeneration and neuroplasticity, potentially restoring function to paralyzed limbs. For conditions like Alzheimer's and Parkinson's disease, these proteins could slow or potentially reverse neuronal death when delivered through advanced targeted systems. The industrial-scale production of these growth factors would also enable their incorporation into advanced biomaterials and 3D-printed tissue constructs, accelerating the development of lab-grown organs and tissues for transplantation, further addressing the critical organ shortage crisis worldwide.

Homework Part B

<aside> <img src="/icons/exclamation-mark_orange.svg" alt="/icons/exclamation-mark_orange.svg" width="40px" /> These homework questions are based on the Bio Production Lab! Mandatory for both Committed Listeners and MIT/Harvard students.

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<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?

Genes for Lycopene and Beta-Carotene Production in E. coli for lycopene production, the key genes are:

crtE (encoding GGPP synthase) crtB (encoding phytoene synthase) crtI (encoding phytoene desaturase)

For beta-carotene production, the same genes plus:

crtY (encoding lycopene β-cyclase)

These genes are typically sourced from microorganisms like Deinococcus, Erwinia, or Pantoea species.

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

Antibiotic resistance genes in plasmids serve several critical functions:

They provide selective pressure to maintain engineered pathways under cultivation They allow for selection of successfully transformed E. coli cells They help maintain plasmid stability during cell division and propagation They enable researchers to isolate only the bacteria containing the desired genetic constructs

Without antibiotic selection, plasmids could be lost during cell division, reducing overall yield and production stability.

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