Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    ARM-Net: Alzheimer’s Recovery Micro-TNT Network 1.Biological Engineering Application I am developing ARM-Net, a synthetic biology tool designed to overexpress CCT4 specifically in microglia. Unlike the full TRiC/CCT complex, CCT4　can function independently or as homo-oligomers to promote microtubule synthesis. By boosting these chaperonins, I aim to induce the formation of Tunneling Nanotubes (TNTs) between microglia, creating an “Intercellular Care Network” (ICN)

  • Week 10 Advanced Imaging & Measurement Technology

  • Week 2 Pre Questions

    I have answered the following questions to prepare for the lecture on DNA design and synthesis. These answers are based on the slides provided by Professor Jacobson, Dr. LeProust, and Professor Church. Question,1 Natures 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?

  • Week 2: DNA Design and Characterization

    This week, I focused on the design, simulation, and cloning workflow for CCT4, the core component of my project, ICN (Intercellular Care Network).

  1. Part 1: Benchling and In Silico Gel Art Benchling Simulation Having long been interested in Benchling, I used this assignment to dive deep into the tool. Instead of the suggested Lambda DNA, I worked with the CCT4 protein sequence relevant to my project. I simulated restriction digests using the following enzymes:

  • Week 3 pentrons Bio-Art & Lab Automation

    Assignment: Telecaster Guitar Bio-Art This week’s task was to create a Python script for the Opentrons OT-2 robot to draw an artistic design on an agar plate using colored bacteria.

  1. Design Concept: The Telecaster My design is based on the Fender Telecaster, an iconic electric guitar. I used different fluorescent proteins to represent the components:

  • Week 4 Protein Design I— Conceptual Questions

    Week 4: Protein Design I — Conceptual Questions Part A: Conceptual Questions The following nine questions were selected from the set provided by Professor Shuguang Zhang to explore the fundamental principles of protein structure and molecular evolution.

  1. How many molecules of amino acids do you take with a piece of 500 grams of meat? (Assumed: 100 Daltons per amino acid, meat is ~20% protein) If 500g of meat contains approximately 100g of protein, and the average molecular weight of an amino acid is 100 g/mol:

  • Week 5 Protein Design Part II

    Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM Amino acid sequence obtained from UniProt MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ A4V-mutated amino acid sequence MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ index Binder Pseudo Perplexity 0 WRYPVVAVALKE 11.483049924471887 1 WHYPVAALAHKX 9.549261526750376 2 WHYYAAGVRHKX 16.81952501470461 3 WHYGAVAVRLKX 9.353984730828607 Part 2: Evaluate Binders with AlphaFold3 The A4V-mutant human SOD1 sequence and each peptide were submitted as separate chains to AlphaFold3 to model protein–peptide complexes. The predicted ipTM scores varied among the peptides, indicating differences in binding confidence. The peptides generally appeared to bind on the protein surface, with some localizing near the N-terminus where the A4V mutation is located, while others interacted with regions of the β-barrel structure. Most peptides were surface-bound rather than deeply buried

  • Week 6 Genetic Circuits Part I: Assembly Technologies

    Assignment: DNA Assembly & Chromophore Engineering 1. Phusion High-Fidelity PCR Master Mix Analysis Question: What are some components in the Phusion Master Mix and what is their purpose?

  • Week 7 Genetic Circuits Part II: Neuromorphic Circuits

    1.What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Graded and Continuous Responses: Unlike a simple ON/OFF switch, IANNs process signals as a gradient. This allows the cell to tune its response level (e.g., producing exactly 50% output) based on the input concentration, which is essential for maintaining homeostasis.

  • Week 9 Cell-Free Systems

    Homework Part A: General and Lecturer-Specific Questions 1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Cell-free protein synthesis (CFPS) offers significant advantages over traditional in vivo methods by removing the constraints of cell viability.