Week 01: Principles and Practices
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Week 1 HW: Principles and Practices
1. Application Goal
I want to use CRISPR Cas-9 to knockout the LFY (LEAFY) gene in Arabidopsis thaliana. This serves as a biological engineering tool to provide students with a clear visual confirmation of a successful gene edit—the plant will fail to produce flowers.
2. Governance and Policy Goals
The primary goal is to ensure this tool contributes to an “ethical” future by serving as a standardized educational platform. It allows students to learn gene editing techniques within a framework that provides immediate visual feedback and built-in biosafety (non-reproductive plants).
3. Proposed Governance Actions
Action 1: Standardized Educational CRISPR-LFY Kit
- Purpose: Provide a safe, vetted “kit” for schools to reduce unsafe improvisation.
- Design: * Physical: Use non-integrating systems or low-fertility lines.
- Protocol: SOPs for containment and autoclaving disposal.
- Governance: Mandatory Material Transfer Agreements (MTAs).
- Assumptions: Institutions have BSL-1 facilities; teachers follow SOPs.
- Risks: Failure of containment due to small seed size; success leads to off-target effects if handled poorly.
Action 2: Mandatory Ethics & Risk Training
- Purpose: Ensure students understand the “why” and “should,” not just the “how.”
- Design: A required module covering gene editing ethics and case studies.
- Assumptions: Instructors have the support to teach ethics; students engage meaningfully.
- Risks: Ethics treated as a “checkbox”; success might make students overly cautious.
Action 3: Institutional Oversight & Registration
- Purpose: Ensure all gene editing activities are visible to faculty and Biosafety Officers.
- Design: Registry of constructs used, genes targeted, and disposal methods.
- Assumptions: Biosafety Officers have specific expertise in plant gene editing.
- Risks: Excessive bureaucracy could stifle innovation.
4. Scoring & Prioritization
| Policy Goal | Option 1 (Kit) | Option 2 (Ethics) | Option 3 (Oversight) |
|---|---|---|---|
| Enhance Biosecurity | 1 | 2 | 3 |
| Foster Lab Safety | 2 | 3 | 1 |
| Protect Environment | 1 | 3 | 2 |
| Minimize Cost/Burden | 3 | 1 | 2 |
| Not Impede Research | 1 | 3 | 2 |
Prioritization: I prioritize a combination of Option 1 and Option 3. The kit (Option 1) provides the physical safety mechanism (the LFY knockout ensures no reproduction), while the Biosafety Officer (Option 3) ensures oversight.
Week 2 Lecture Prep
Questions from Professor Jacobson
- DNA Polymerase Error Rate: Approximately 1 in 10 million base pairs.
- Comparison to Genome: The human genome is ~3 billion base pairs. This discrepancy is managed by advanced proofreading and error correction mechanisms.
- Coding Diversity: An average protein (400 amino acids) can be encoded by roughly $10^{194}$ different DNA sequences.
- Constraint Realities: Most of these codes fail due to constraints in transcription, mRNA stability, translation efficiency, and protein folding.
Questions from Dr. LeProust
- Oligo Synthesis: The most common method is Phosphoramidite Chemistry.
- 200nt Limit: Difficult because error rates are cumulative; the yield of pure, correct sequence drops too low.
- 2000bp via Direct Synthesis: Not viable because the probability of a perfect sequence over that length is statistically near zero with current error rates.
Questions from George Church
- The 10 Essential Amino Acids: Arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.
- Lysine Contingency: This concept is flawed because all animals already require lysine from their diet; they do not produce it themselves.
- Aspirin-like Stability: To make protein medicines stable, I would circularize the protein (joining the ends) to prevent degradation by heat, similar to the 2014 Heidelberg iGEM project.
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