Week 1 HW: Principles and Practices

First, describe a biological engineering application or tool you want to develop and why:

Chronic diseases require constant medicines for disease management . Usually multiple drugs are necessary to live comfortably and deal with symptoms of chronic disease causing a large financial burden on patients. My goal is to develop bacterial live biotherapeutic products to medicate patients at intervals or according to specific environmental cues. This bacteria will colonize organs where disease occurs and act as sensor and drug dispensing system to secrete therapeutic molecules according to environmental triggers such as inflammation, osmotic pressure or disease biomarkers, ensuring correct administration of the molecule. The engineered bacteria increase the time before next drug admission is required from daily to biweekly or monthly, substantially decreasing financial load on patients.

Next, describe one or more governance/policy goals related to ensuring that this application or tool contributes to an “ethical” future, like ensuring non-malfeasance (preventing harm). Break big goals down into two or more specific sub-goals:

Safety of microorganisms used and ensuring bacteria not becoming harmful in a direct or indirect way is the most important goal. Bacteria based therapy can gain pathogenic function in the body or reproduce uncontrollably to the detriment of the host. New introduction of engineered bacteria might cause evolutionary drive in the host microbiome or drive out established microorganisms causing adverse affect after drug stop administered. Moreover horizontal gene transfer from engineered bacteria to host microorganisms can cause unwanted spread of genetic elements . To prevent unwanted outcomes described above three goals are established.

Goal 1: Bacterial strains used as a therapeutic product must be fully sequenced

Goal 2: Bacteria that used as a therapeutic product must be engineered with genetic kill switch using both using quorum sensing and specific molecule to prevent uncontrollable growth and unwanted situations

Goal 3: Patient’s microbiota using these products must be monitored while using the product

Next, describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”):

Purpose: Currently engineered bacteria as live biotherapeutics in clinical trials. One of main concerns of this product is consistency and possible unpredictable effects of this product long term

Design: To keep patient safety each patient using these products must be periodically monitored by an administered clinician, these administered clinician must have special training knowing how to handle adverse effects. Special training sessions will be designed by policy makers and biotechnology experts working together to allow for correct assessment

Assumptions: Uncertain if current technology is enough to monitor effects of engineered bacteria long term in situ

Risks of Failure & “Success”: Unwanted spread of modified bacteria leading public harm.

Last, drawing upon this scoring, describe which governance option, or combination of options, you would prioritize, and why. Outline any trade-offs you considered as well as assumptions and uncertainties:

For ensuring public health I would combine goal 2 and goal 3 to prevent adverse effects on patients. Thou it is important to have an option to safely dispose engineered bacteria, it is not useful if effects of bacteria can not be assessed and thoroughly correctly

Pre Week 2 Homework Questions

Homework Questions from Professor Jacobson:

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?

DNA polymerase error rate is approximately once in 108 nucleotides. However, the genome of diploid human cells is approximately 6 billions nucleotides long. This would make 60 errors per cell division. However, repair systems are established to reduce error rate of cell division such as proofreading activity of DNA polymerase and mismatch repairs

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? Amino acids coded by three nucleotide long sequence called codons. Sometimes different codons can be responsible for same amino acids but codon bias makes sure only one of the synonymous codon is used for protein synthesis. Preffering some codons more than others.

Homework Questions from Dr. LeProust:

What’s the most commonly used method for oligo synthesis currently? It is phosphoramidite method

Why is it difficult to make oligos longer than 200nt via direct synthesis? Cycles of phosphoramidite method is not %100 efficient so as length of oligos increase it results in truncated incomplete product

Why can’t you make a 2000bp gene via direct oligo synthesis? Due to truncation of oligos increase astronomically as size of oligos increase chance of completely synthesizing 2000 bp is tiny

Homework Question from George Church:

What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?

Essential amino acids amino acids that aren’t synthesized in organism. 10 essential amino acids for animals are arginine; methionine; histidine; phenylalanine; isoleucine; threonine; leucine; tryptophan; lysine; andvaline;. Lysine contingency is knocking out lysine biosynthesis genes making targets dependent on lysine supplements. However, lysine dependent organisms can survive by eating other organism abındent in lysine .