Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    title: ‘Smart Packaging: Biosensors to Reduce Food Waste’ #h6 Heading ‘Describe a biological engineering application or tool you want to develop and why’ I would be looking to develop bio-responsive materials by including engineered biosensors into food packaging. Using engineered E. coli or B. subtilis with a color-changing sensor that detect spoilage, microbial growth, or pH changes, the packaging will provide a clear visual indicator to help consumers gauge food freshness. Using plant-based polymers like PLA or PHA will ensure the packaging is biodegradable. For example, this could be applied to plastic wraps on meat, prepared foods, etc. This tool would make it easier for companies and consumers to make informed choices about food freshness, safety, and nutrition, supporting sustainability and reducing waste #h6 Heading ‘Governance and policy goals ensuring its contribution to an ethical future’ A key governance goal would be to ensure consumer safety by regulating biosensor accuracy, preventing false positives/negatives that could lead to consumer harm or food waste. Sub-goal would be informed of environmental imapct of the entire life cycle of the packaging, ethical sourcing of the biodegradable polymers (e.g., PLA, PHA), and labeling transparency for companies and consumers. #h6 Heading ‘Potential governance actions by considering: Purpose, Design, Assumptions, Risks of Failure and Success’ Does the option: Option 1 Option 2 Option 3 Enhance Biosecurity • By preventing incidents x • By helping respond x Foster Lab Safety • By preventing incident x • By helping respond x Protect the environment • By preventing incidents x • By helping respond x Other considerations • Minimizing costs and burdens to stakeholders x • Feasibility? x • Not impede research x • Promote constructive applications x

  • Week 2 Lecture Prep: DNA, Read, Write, and Edit

    h1 Heading ‘Assignment W2 Lecture Prep’ h4 Heading ‘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? It depends on the species and cell type, but DNA polymerases exhibit an error rate of approximately 10⁻⁵ to 10⁻⁶ errors per nucleotide during DNA replication. With the help of other proofreading enzymes they can reduce it to ~10⁻⁸ to 10⁻¹⁰ errors per nucleotide, increasing its accuracy, additional repair mechanisms pathways exist to correct these errors and maintain genomic integrity. The human genome contains roughly 3 billion base pairs (3x10⁹), so even with an error rate of 10⁻⁸, there could be several errors during each DNA replication event.

Subsections of Homework

Week 1 HW: Principles and Practices

title: ‘Smart Packaging: Biosensors to Reduce Food Waste’ cover image cover image

#h6 Heading ‘Describe a biological engineering application or tool you want to develop and why’

  1. I would be looking to develop bio-responsive materials by including engineered biosensors into food packaging. Using engineered E. coli or B. subtilis with a color-changing sensor that detect spoilage, microbial growth, or pH changes, the packaging will provide a clear visual indicator to help consumers gauge food freshness. Using plant-based polymers like PLA or PHA will ensure the packaging is biodegradable. For example, this could be applied to plastic wraps on meat, prepared foods, etc. This tool would make it easier for companies and consumers to make informed choices about food freshness, safety, and nutrition, supporting sustainability and reducing waste

#h6 Heading ‘Governance and policy goals ensuring its contribution to an ethical future’

  1. A key governance goal would be to ensure consumer safety by regulating biosensor accuracy, preventing false positives/negatives that could lead to consumer harm or food waste. Sub-goal would be informed of environmental imapct of the entire life cycle of the packaging, ethical sourcing of the biodegradable polymers (e.g., PLA, PHA), and labeling transparency for companies and consumers.

#h6 Heading ‘Potential governance actions by considering: Purpose, Design, Assumptions, Risks of Failure and Success’

Does the option:Option 1Option 2Option 3
Enhance Biosecurity
• By preventing incidentsx
• By helping respondx
Foster Lab Safety
• By preventing incidentx
• By helping respondx
Protect the environment
• By preventing incidentsx
• By helping respondx
Other considerations
• Minimizing costs and burdens to stakeholdersx
• Feasibility?x
• Not impede researchx
• Promote constructive applicationsx

Week 2 Lecture Prep: DNA, Read, Write, and Edit

h1 Heading ‘Assignment W2 Lecture Prep’

h4 Heading ‘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? It depends on the species and cell type, but DNA polymerases exhibit an error rate of approximately 10⁻⁵ to 10⁻⁶ errors per nucleotide during DNA replication. With the help of other proofreading enzymes they can reduce it to ~10⁻⁸ to 10⁻¹⁰ errors per nucleotide, increasing its accuracy, additional repair mechanisms pathways exist to correct these errors and maintain genomic integrity. The human genome contains roughly 3 billion base pairs (3x10⁹), so even with an error rate of 10⁻⁸, there could be several errors during each DNA replication event.

  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 can code for the same amino acid, where there are 64 possible codons, but only 20 standard amino acids. There is also codon redundancy since multiple codons will code for the same amino acid. Many of these sequences do not work well because of codon bias, limited availability of certain tRNAs, effects on mRNA structure and stability, unintended regulatory signals, or problems with translation efficiency and accuracy.

h4 Heading ‘Homework Questions from from Dr. LeProust’

  1. What’s the most commonly used method for oligo synthesis currently? The most commonly used method is solid-phase phosphoramidite chemical synthesis.
  2. Why is it difficult to make oligos longer than 200nt via direct synthesis? Each step of chemical synthesis is slightly imperfect. As the oligo gets longer, small inefficiencies accumulate, leading to more truncated or incorrect sequences and a lower fraction of full-length product.
  3. Why can’t you make a 2000bp gene via direct oligo synthesis? Direct synthesis of very long DNA suffers from too many errors and very low yield. Long genes are made by synthesizing shorter oligos (100-200bp) and then assembling them into the full-length gene using enzymatic methods, which helps correct errors and increases overall accuracy.

h4 Heading ‘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 Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, and Arginine. As lysine is an essential amino acid, its availability likely shaped species/animals dietary habits and metabolism, due to reliance on external sourses, becoming a critical in evolutionary adaptation.