Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Governance and Ethical Framework for Astro-Moss and Bio-textiles.
Week 10 HW: ADVANCED IMAGING & MEASUREMENT TECHNOLOGY
- Final Project I will measure whether DNA stored on paper can be recovered and remain readable after storage. In Aim 0.5, the main measured output is the presence or absence of expected PCR bands from recovered DNA fragments. Fragment A is expected to produce a ~94 bp payload PCR product, and Fragment B is expected to produce a ~166 bp product. I measured this using endpoint PCR followed by 2% E-Gel EX agarose gel electrophoresis.
Week 11 HW: BIOPRODUCTION & CLOUD LABS
A. Master Mix Component Analysis E. coli Lysate BL21 (DE3) Star Lysate: Provides the cellular machinery for transcription and translation, including ribosomes and T7 RNA polymerase. The “Star” mutation helps reduce mRNA degradation. Salts / Buffer Potassium Glutamate: Maintains ionic strength and supports ribosome activity. HEPES-KOH pH 7.5: Keeps the reaction at a stable pH. Magnesium Glutamate: Supplies magnesium ions needed for ribosomes and enzymes. Potassium Phosphate: Acts as a buffer and supports ATP regeneration.
Week 2: DNA Read, Write, & Edit
DNA Design Challenge 3.1 Protein Choice I chose pHluorin (superecliptic pHluorin, SEP) because it makes pH changes visible as a clear signal. pH is a broadly meaningful indicator across scales: it can reflect cellular and bodily conditions (e.g., local acidity in compartments or stress-related microenvironments) and also environmental conditions (e.g., water/soil toxicity or chemical shifts). This makes SEP useful not only as a biosensing concept, but also as an interaction metaphor. Even small changes in conditions can switch what becomes visible.
Week 4 HW: PROTEIN DESIGN PART I
Deinococcus radiodurans. Credit USU/Michael Daly Part B: Protein Analysis and Visualization 1. Briefly describe the protein you selected and why you selected it. I selected the protein from RCSB PDB: 4NOE, which is DdrB, a single-stranded DNA-binding protein from Deinococcus radiodurans (this entry is a protein–ssDNA complex). I chose it because D. radiodurans is well known for extreme radiation tolerance, and DdrB is directly connected to DNA damage response/repair, making it a relevant example for studying UV/radiation-associated protein function with an available 3D structure.
Week 6 HW: Genetic Circuits Part I
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Week 7 HW: Genetic Circuits Part II
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