Week 1 HW: Principles and Practices

Assignment 1

Background

Malaria is a dangerous disease that affects hundred of millions of people worldwide. Each year, there are almost 300 million cases, with 600,000 deaths, 95% of which are disproportionately in Africa.

The only known cure for malaria for the longest time was quinine, a drug that was used to treat the disease in the 19th century. In the 1970s, Tu Youyou discovered artemisinin, a compound that is more effective in eradicating malaria than quinine. A few years later, she was able to synthesize it on a much larger scale using a modified yeast cell.

I personally caught malaria in 2007 and my father caught dengue in Vietnam in 2005. They are very common diseases that are largely eradicated nowadays thanks to health policies and an improvement in quality of life.

Malaria, however, is adaptive. In 2008, reports came out from Southeast Asian countries that the parasite was evolving to be resistant to artemisinin. More reports came out in 2009, 2011, and 2012.

There are also reports in Vietnam in 2024 that the Rapid Detection Test (RDT) may no longer be effective as the parasite evolved to not express the 2 main proteins that the RDT is built to detect. Meaning, malaria is slowly becoming underdiagnosed and proper diagnoses will require more expensive methods that are not available in many countries.

The rise in resistance is a pain point for the world as many countries’ eradication efforts are now hampered by what is simply selective pressure. This threat must be addressed before the new strains reach the most vulnerable populations, specfically Africa.

Project Goals

There are 5 main species of parasites from the Plasmodium genus that causes malaria in humans, most prevalent being P. falciparum on the African continent and P. vivax outside of Sub-Saharan Africa. We will be focusing on P. falciparum.

For my project, I want to use biological circuitry to create a cure that is also adaptive to the disease. By analyzing the evolutionary mechanism of the parasite, we can synthesize products that can target our treatments to work around its defensive mechanisms.

Also, to adapt to the ever-changing nature of the parasite, I would like to create a circuitry that can adapt to whatever ingredients we feed to cheaply and quickly synthesize new, targeted drugs.

Having a simple-to-replicate medication that can be modified to target different strains of malaria or to target different weaknesses of P. Falciparum will drastically improve life expectancies and help curb malaria deaths worldwide.

Policy Goals

For this biological circuitry idea to work, we will need some ground rules. The design, use, and proliferation of a modified cell containing synthetic circuitry could prove dangerous in many ways. It could either affect the creator, distributor, consumer, or the environment.

Thus, strict emphasis must be placed on safety and containment.

On top of that, the whole point is to make malarial treatments more readily available. Thus accessibility in all its definitions should be considered. Below are some I have come up with:

• Biosafety

  • Make sure the modified cells will not have pathogenic/virulent factors that might cause new disease
  • Ensure containment of bacteria in safe environment
  • Ensure generated product and byproducts are not harmful to patients

• Accessibility

  • Ensure affordability
  • Preservability & Procurement

Actions and Actors

Researchers

Action 1 – Ensure modified cells are not pathogenic/virulent

Creating modified cells comes with a risk of misuse or miscreating a dangerous pathogen. It is important the modified cell does not post any risk at all to the creator, distributor, and user of its products.

1. Purpose: To not design a biohazard for the community
2. Design: Test of pathogenicity before starting the bioreactor
3. Assumptions: The test are enough to ensure no pathogenicity, this is maintained stable in the bioreactor
4. Risks of Failure & “Success”:
   • Failure: there is pathogenicity, people can be sick, directly or indirectly.
   • Success: No pathogens.

Action 2 – Ensure generated product and byproducts are not harmful to the patient

1. Purpose: Elaborate innocuous products that can be used as medicine
2. Design: Previous test in different biological models such as murine models and appropriate clinical trials
3. Assumptions: The effects of the byproducts will not variate between people
4. Risks of Failure & “Success”:
   • Failure: Unexpected outcomes in different patients, potentially dangerous.

Industrial plant designer

Action 3 – Ensure containment of modifed cells in safe environment

1. Purpose: Prevent cell leakage and contact with the environment
2. Design: Appropriate infrastructure for biorreactors and checkpoints to ensure appropriate fluid levels
3. Assumptions: Good practices from the operators in the industrial plant
4. Risks of Failure & “Success”:
   • Failure: leakage that affects the surrounding environment.
   • Success: Very elaborate plant design that is not affordable

Local government and regulating bodies

Action 4 – Government subsidies and support

Derivatives of artemisinins are generally stable in room temperature, but will quickly deteriorate under high humidity and the extreme heat of Africa, South and Southeast Asia. Furthermore, the cost of each dose could range from cents to hundreds of dollars. Government subsidies can help keep prices low (like in Southeast Asia) and proper storage and transport can protect medication stock.

1. Purpose: Make medicine affordable and widely available to vulnerable communities
2. Design: Price controls through public subsidies and partnerships
3. Assumptions: The government will have the budget to invest in health
4. Risks of Failure & “Success”:
   • Failure: Medicine still not affordable to low income families.
   • Success: High subsidies might lead to fake products.

Scoring

After realizing too late that I’ve used the scale backwards, the scoreboard actually has 3 as the most important and 1 as the least important.

In other words, higher scores => more importance for this specific score board.

Priorities

Using the score board, it can be seen that in order of importance, Action 2 takes the highest precedent. Action 1 can be argued to be more important as a deadly disease spreading everywhere is an issue anywhere. However, due to some oversight, I just now realized that Action 2 technically encompasses parts of Action 1, in the sense that a patient should not be harmed.

I will argue that is the primary goal of the project. The idea of synthesizing an adaptable product is to cure people, thus, harming people is antithetical to that and utmost priority must be placed on such a duty. Subsidies and storage are important to manipulating and keeping drug prices low, but I don’t think it can take priority over the main utility of the project: curing disease.

Once that is done, we can begin worrying about logistics.

Week 2 Lecture Prep

For Professor Jacobson

Question 1

DNA polymerases are highly accurate but not perfect. Their intrinsic error rate is roughly one mistake per million nucleotides added (10^-6). When this number is compared with the size of the human genome-about 3.2 billion base pairs-it becomes clear that thousands of errors would appear if no additional safeguards existed.

To visualize this, copying the human genome with that error rate would be similar to transcribing a multi-billion-letter manuscript and ending up with a few thousand typos spread across the entire text.

Living systems compensate for this mismatch using several layers of quality control. During DNA synthesis itself, polymerases can remove incorrect bases via a 3' -> 5' exonuclease proofreading activity. Errors that escape this first checkpoint are later corrected by post-replication mismatch repair pathways, such as the MutS system, which scans the DNA and fixes mispaired bases.

Question 2

Coding capacity of DNA for a human protein

Because the genetic code is redundant, a single protein sequence can, in theory, be encoded by an enormous number of distinct DNA sequences. A typical human protein is around 345 amino acids long (≈1,036 bp). Since most amino acids are specified by multiple synonymous codons, the number of possible DNA sequences that could encode the same protein quickly becomes astronomical.

If each amino acid had, on average, three possible codons, the total number of theoretical coding sequences would be on the order of 3³⁴⁵ (approximately 10¹⁶⁵).

However, only a small subset of these sequences is biologically or technically viable. Factors that limit usable coding options include:

Extreme GC or AT content, which promotes problematic secondary structures.

Sequence motifs that destabilize mRNA or promote cleavage.

Codon usage preferences, which vary between organisms and affect translation efficiency.

Long repeats or homopolymers, which complicate synthesis and assembly.

Local thermodynamic constraints, such as unfavorable base pairing energies.

For Dr. LeProust

Question 1

The dominant method for making synthetic oligonucleotides today is phosphoramidite chemistry, introduced in the early 1980s by Caruthers. Despite its age, it remains the foundation of nearly all commercial DNA synthesis platforms.

Question 2

As oligos become longer than ~200 nucleotides, the fraction of incomplete or truncated products increases significantly. Although companies like Twist have demonstrated unusually long directly synthesized fragments (up to ~700 nt), these remain exceptions rather than the norm.

Question 3

Synthesizing a 2 kb gene directly is impractical. Instead, long genes are produced by assembling many shorter oligonucleotides, reducing cumulative error rates and increasing overall accuracy.

For Dr. George Church

Question 1

Animals require ten essential amino acids from their diet: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and arginine.

This fact directly undermines the idea of a “lysine contingency.” Since animals are already incapable of synthesizing lysine, removing lysine biosynthesis does not meaningfully restrict survival. Carnivores obtain lysine from prey, while herbivores consume lysine-containing plants, making lysine universally available within natural food webs. Effective biocontainment strategies must therefore rely on dependencies that do not exist in nature, such as non-standard amino acids or extensively recoded genetic systems, as discussed in Church’s work.

Question 2

Several biological coding systems already exist: DNA–DNA pairing through Watson–Crick rules, DNA–amino acid relationships via the genetic code, and amino acid–DNA recognition in systems like TALEs.

For amino acid–amino acid interactions, a plausible and intuitive “code” could be built from fundamental biochemical properties rather than strict sequences:

• Electrostatic complementarity, where basic residues (K, R, H) interact with acidic ones (D, E).
• Hydrophobic matching, in which nonpolar residues (L, I, V, F, W, A) preferentially associate.
• Polar and hydrogen-bond interactions, involving residues such as S, T, N, Q, and Y.

Together, these principles could form a simple but robust framework for AA:AA recognition.

Question 3.

Sketch Response to Smart Red Blood Cells (Smart-RBC) Program

I propose engineering RBCs with genes from freeze-tolerant organisms like wood frogs (Rana sylvatica) and hibernating mammals that survive extreme cold and low oxygen without cellular damage. Wood frogs naturally produce antifreeze proteins and cryoprotectants (like glucose) that prevent ice crystal formation during winter freezing, while hibernating animals express protective chaperones that maintain function during hypoxia. By inserting these genes into RBC precursor cells before enucleation, the resulting Smart-RBCs would retain protective proteins while eliminating genetic transfer risks. This would temporarily enhance warfighters’ cold tolerance and oxygen delivery in Arctic operations, high-altitude missions, or extreme survival scenarios—without the weeks needed for natural acclimation. Since mature RBCs are enucleated and only last ~120 days, the protection is temporary and safe, providing exactly the performance boost needed when it matters most.

References

Fact sheet about malaria. (n.d.). Retrieved February 9, 2026, from https://www.who.int/news-room/fact-sheets/detail/malaria