Homework Part A-Patrick Boyle’s Lecture Questions:
If all molecular biology work could be automated, I would use that capability to explore more ambitious and complex biological questions that are currently limited by time and resources.
For example, I would investigate how thousands of genetic variants simultaneously affect protein function or entire metabolic pathways, using high-throughput gene editing combined with automated phenotyping. This could significantly advance our understanding of multifactorial diseases such as cancer or neurodegenerative disorders.
Automation would also enable the accelerated design of novel biotechnological products, such as personalized vaccines tailored to a patient's genetic profile, enzymes optimized for greener industrial processes, or even synthetic cellular systems capable of making complex biological decisions, such as releasing a drug only in the presence of specific molecular markers.
If I could produce metric tons of any protein, I would choose to manufacture enzymes capable of degrading pharmaceutical residues, such as antibiotics, painkillers, or contraceptives, which often end up in rivers and water bodies due to insufficiently treated wastewater.
The positive impact would be significant for both the environment and public health. Even at very low concentrations, these pharmaceutical contaminants can disrupt hormonal balances in aquatic organisms, impair fish reproduction, and—most concerningly—promote the emergence and spread of antibiotic-resistant bacteria.
Moreover, these residues don’t remain confined to aquatic ecosystems. They can make their way back into the human body through the consumption of contaminated water, fish, or crops irrigated with recycled water. As a result, people are continually exposed to trace amounts of drugs, which silently contributes to the growing problem of antimicrobial resistance—a global health threat recognized by the WHO.
Producing these enzymes at an industrial scale would allow their application in wastewater treatment plants, where they could effectively break down pharmaceuticals before they reach the environment. In doing so, we would be protecting biodiversity, reducing selective pressure on bacteria, and safeguarding human health in a proactive and sustainable way.
Homework Part B
For the laboratory portion of this assignment, you will characterize lycopene production in E.coli with the pAC-LYC plasmid, and beta-carotene production in E.coli with the pAC-BETA plasmid. Note, the pAC-LYC plasmid contains three genes from Erwinia herbicola: CrtE, Crtl, and CrtB. The pAC-BETA plasmid produces beta-carotene through the addition of the Erwinia herbicola CrtY gene.
The plasmids transferred into E. coli must carry a resistance gene, such as chloramphenicol resistance, because when the culture is grown, this antibiotic is added and only the transformed bacteria will be able to survive. This step is very important, as it allows for subsequent procedures such as colony PCR
When applying the experimental design in which the culture medium, the presence of fructose, and the temperature conditions are varied, the results we can expect are directly related to the growth of E. coli, and therefore to the efficiency of lycopene and beta-carotene production. In other words, we can expect greater or lesser E. coli growth, and greater or lesser lycopene and beta-carotene production.
This will allow the selection of the combination of variables that results in the highest E. coli growth and the greatest production of lycopene and beta-carotene.