Week 1 HW: Principles and Practices

Describe a biological engineering application or tool you want to develop and why.

Virus Hunting

The usage of virus hunting to discover viruses in animal populations that might become a pandemic and exploit it as a gene therapy tool. first of all the viruses are isolated from hosts of interest, then sequencing their genome, then characterize the virus. Following steps will be:

1. Developing arrays for the virus detection providing a faster and cheaper way.
2. Exploiting the virus replication machinery to deliver compounds / biopharmaceuticals to humans or animals.

Disocvering potential pandemic pathogens early will prevent its outbreak and prepare us well.

Describe one or more governance policy goals related to ensuring this application contributes to an ethical future & prevents harm.

• Biosafety and biosecurity aims to prevent loss, theft and misuse of highconsequence material. This can be done by providing and implementing risk control measures that address the risks associated with conducting high-consequence research and working with high-consequence material, including other biosecurity-relevant material.

• The intrinsic risks of working with biological agents are not only of a biosafety nature, such as exposure or unintentional release, but also of biosecurity, which includes the theft, misuse, or intended release of biological material.

Describe at least three different potential governance actions by considering the purpose, design, assumptions, and risks of failures & “success”

1. Development of a board to organize and authorize the suitable scientist for conducting virus hunting

• Purpose: The aim is to allow only trained professionals to conduct such procedures
• Design: Every country will have a trusted board that will allow and oversee the virus hunting procedures and these boards will be under the supervision of a central board that will get periodic reports
• Assumptions: Incorrect selection of personnel might lead to inproper viral isolation and process organization leading to its outbreak
• Risks of Failures & Success: This action might fall if not properly implemented

2. Development of an agreed upon method of biological materials disposal

• Purpose: The aim is to control and oversee disposal methods to prevent any outbreaks
• Design: Professionals will be further trained
• Assumptions: Ignoring the right protocol for disposal may lead to an outbreak
• Risks of Failures & Success: not providing the right training and control

3. Providing enough funds to conduct the required procedures in the countries of interest

• Purpose: this action aim to fund labs at developing countries of interest
• Design: The organization will provide the fund and supervise its implementation to buy the right equipment and tools
• Assumption: Corruption or not providing the fund will hinder the virus hunting procedures in that country
• Risk of Failures & Success: Not providing enough funds will stop the required procedures

Score each of your governance actions against your rubric of policy goals.

Based on scores, describe which governance option or combination of options, you would prioritize, and why.

Based on the scores:

• I would prioritize the formation of the board because it is the base upon which every other step will follow.
• I would prioritize as well providing enough funds especially for developing countries in which many have the knowledgeable scientists but not enouhg funds for buying the necessary equipment.

References

• Hunting for the next pandemic virus (no date) ASM.org. Available at: https://asm.org/magazine/2022/fall/hunting-for-the-next-pandemic-virus
• Vaidyanathan, G. (2011) ‘Virus hunters: Catching bugs in the field’, Cell, 147(6), pp. 1209–1211. doi:10.1016/j.cell.2011.11.037.
• World Health Organization. Available at: https://iris.who.int/

Assignment (Final Project)

As part of your final project, design one or more strategies to ensure that your project, and what it enables, contributes to growing an ethical biological future.

Justice

• Equitable Access to All Populations
• The platform is intentionally designed toward a low-cost system rather than instrument-dependent workflows, so that the end product is deployable in under resourced clinics in low and middle income regions where AD diagnostic infrastructure is nearly absent. Equitable access partnerships and open licensing models will be established from the outset, not as an afterthought, to prevent the technology from benefiting high-income populations exclusively.

Assignment (Week 2 Lecture Prep)

Homework Questions from Professor Jacobson

1. Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy?

• The error rate of DNA polymerase is 1:10^6, meaning that it makes 1 mistake per 1000,000 bases
• The human genome contains approximately 3.2 billion base pairs. If polymerase copied it at its raw error rate, each replication would produce: 3,200,000,000 ÷ 1000,000 = 3,200 errors per cell division which is not good
• Biology deal with that discrepancy through three-layer error correction system; nucleotide selectivety, proofreading and mismatch repair (MutS repair system)

2. How many different ways are there to code (DNA nucleotide code) for an average human protein? In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest?

• The genetic code uses 3-base codons (triplets) to specify each amino acid. There are 4 DNA bases (A, T, G, C), giving 4³ = 64 possible codons. Therefore, there are more codons (64) than amino acids (20). So most amino acids can be coded by 2–6 different codons, averaging about 3. A typical human protein is ~375 amino acids long. If each position has ~3 coding options: 3³⁷⁵ ≈ 10¹⁷⁹ possible DNA sequences for the same protein. So the number of DNA sequences that could theoretically encode the same protein is astronomically larger than the number of atoms in existence.
• There are a variety of reasons that all of these different codes don’t work to code for the protein of interest;
  • Codon Usage Bias: Different organisms prefer certain synonymous codons over others, because the matching tRNA molecules are more or less abundant
  • mRNA Secondary Structure: The mRNA sequence folds back on itself into hairpins, loops, and stem structures based on its nucleotide sequence.
  • Splicing Signals are Embedded in the Coding Sequence
  • CpG Dinucleotides and Methylation
  • Cryptic Regulatory Elements
  • Translation Speed and Protein Folding

Homework Questions from Dr. LeProust

1. What’s the most commonly used method for oligo synthesis currently?

• Solid-phase Phosphoramidite method by Caruthers

2. Why is it difficult to make oligos longer than 200nt via direct synthesis?

• The fundamental problem is compounding error. Each coupling step is ~99% efficient, meaning ~1% of strands fail at every base addition. Over hundreds of cycles this multiplies catastrophically

3. Why can’t you make a 2000bp gene via direct oligo synthesis?

• Due to compounding error, at 99% coupling efficiency, a 2000-mer would yield: 0.99²⁰⁰⁰ ≈ 0.000002% perfect product Therefore, the solution, will be to assemble a 2000bp gene from many short oligos (~40–60mers) rather than attempting to synthesize it as one continuous chain.

Homework Question from George Church

1. • The 10 essential amino acids are: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, Arginine.
   • The Lysine Contingency (a fictional genetic failsafe from the Jurassic Park franchise) was a genetic alteration performed in the dinosaur genome. The modification knocked out the ability of the dinosaurs to produce the amino acid lysine. This forced the dinosaurs to depend on lysine supplements provided by the park’s veterinary staff. Since all mammals can synthesize Lysine, the lysine contingency is useless, since dinosaurs can simple prey on other animals to have lysine in their diet