Week 1 HW: Principles and Practices

Biological Engineering of Oleaginous Yeasts: Precision Lipids in Food

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

I am developing a Precision Lipid Production Platform by using oleaginous yeast and engineering them. My goal is to engineer yeast cells to produce lipids in a desired composition. By metabolically changing the fatty acids profilies, we can design fats with specific properties. This platform will allow to produce designer fats which are both nutrionally and technofunctionally optimized.

2. 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.

We need to ensure that producing fats with this technology should contribute to food production ethically. The primary focus should be Consumer Safety and Ingredient Transparency.

Goal: Public Health (Preventing Harm)

• Sub-goal 1: Novel Ingredient Screening: Engineered yeast should be screened for toxic ingredients or allergens.
• Sub-goal 2: Biological Containment: Prevent engineered oleaginous yeast to be released to the environment.

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

Action 1: The Open Lipid Profile Database

• Purpose: It should be a requirement to any engineered strain have its full lipid profile uploaded open to the public.
• Design: Actors Academic researchers and biotech companies. To recieve a regulatory approval, full lipid profiels should be provided for third party reviews.
• Assumptions: It assumes that full lipid profile are enough to identify harmful situations.
• Risks of Failure and Success: Success Easier safety verification. Failure Exposes companies secrets by making their lipid profiles available to public.

Action 2: Kill-Switches

• Purpose: Yeast strain must be engineered to be dependent for a specific nutrient, therefore could not survive in the nature by itself.
• Design: Actors Regulatory bodies. Regulatory bodies could approve the engineered strain easier if they are equipped with a kill-switch.
• Assumptions: It assumes that the yeast would not undergo evolutionary changes that overcome the nutrient requirement.
• Risks of Failure and Success: Success Developing a safety caution for bio-production with engineered organisms. Failure If there is even one example showing that this safety caution could be overcome by evolution, the entrie system becomes vulnerable.

Action 3: Economical Preparation

• Purpose: There would be a distruption for lipid producers using the traditional ways.
• Design: Farmers who produce lipid crops should be supported to transition into sustainable bioproduction feedstocks.
• Assumptions: It assumes that industrial scale production will be profitable enough to outcompete the traditional production.
• Risks of Failure and Success: Success It prevents monopoly. Failure It will cause an extra financial burden for the upcoming industry before it is developed.

4. Next, score (from 1-3 with, 1 as the best, or n/a) each of your governance actions against your rubric of policy goals.

5. 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.

I would prioritize Action 1 and Action 2.

Transparency is the foundation to gain the public trust in lab-grown food and genetically engineered organisms. Making data open to public (Action 1) removes the mystery of unknown lab-grown food that might cause a fear. Action 2 will provide a defence mechanism for bith human and ecological harm.

This approach harms commercial privacy to supply publicly available data.

It is uncertain that the killswitch is going to be stable after long term use.

6. Conclusion

While you can work with an organism that is recognized safe, the metabolic pathways of it can be rewired to produce molecules that have potentially harmful applications. There is a a danger while democratising the synthetic biology. Making biological tools accessible to everyone and democratising synthetic biology is really important but it requires a training and auditing.

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?

DNA polymerase has an error rate about 10^6. One mistake for every million nucleotides. But they also have proofreading activities. Human genome is approximately 3.2 billion base pairs. It would have 3200 mutations. Biology developed repair system to tackle this amount of mutations such as mismatch repair or nucleotide excision repair.

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?

Multiple codons code for the same amino acid. If we assume there is at least two different codons for the same amino acid and taken a 100 aa sequence, there will be 2^100 ways to code this sequence. But we do not see such a diversity in reality, because organism prefer certain codons over others, some secondary structures might prevent translation, and GC content should not be too high to make DNA unstable.

Homework Questions from Dr. LeProust:

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

The most common method is solid-phase phosphoramidite chemistry.

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

Depurination risk increases with longer synthesis time.

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

Error rates would not allow to correctly synthesize such a long oligonucleotides.

Homework Question from George Church:

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

The 10 essential amino acids are lysine, methionine, tryptophan, threonine, valine, isoleucine, leucine, arginine, histidine, and phenylalanine. Lysine is already essential for all animals and very abundant. Since almost every plant and animal in nature contains lysine, a dinosaur would find some lysine in the nature easily.

Week 1 Lab: Pipetting

Individual Final Project

Group Final Project