Homework
Weekly homework submissions:
Week 1 HW: hw-principles-and-practices
The Prometheus Symbiont 🎅1.“The Prometheus Symbiont” is a conceptual, living medical system designed to symbiotically integrate with the human body. It merges biomimetic photosynthesis, synthetic biology, and flexible electronics, aiming to shift medicine from “passive treatment” to active, sustained life maintenance and enhancement. You can think of it as a sunlight-powered, wearable or implantable “second life-support system.” 🎅The Prometheus Symbiont is not merely a technological concept; it is more akin to a philosophical proposition about the future form of life. It blurs the boundaries between therapy and enhancement, between human and machine. Its ultimate significance may lie in compelling us to re-examine: “what constitutes health, and indeed, what it means to be human.”
Week 2 HW: DNA Read, Write, & Edit
Homework — DUE BY FEB 17 2PM MIT TIME 👨🦰Part 0: Basics of Gel Electrophoresis Keypoint: Gel Electrophoresis: Used for separating, identifying, and purifying fragments of DNA, RNA, or proteins. Gel Preparation: Add agarose powder to the buffer, heat until melted, pour the solution into the gel tray, insert the comb, and allow it to cool and solidify. Sample Loading: Remove the comb, place the gel into the electrophoresis tank, and add buffer until the gel is covered. Mix the DNA sample with loading buffer, then load the mixture into the wells.
ヾ(≧▽≦*)oAssignment: Python Script for Opentrons Artwork — DUE BY YOUR LAB TIME! The Biopunk lab hasn’t contacted me yet. The Opentrons API is a Python framework for writing automated biology lab protocols. 1.Load labware (containers, tip racks, plates); 2.Load instruments (pipettes); 3.Define your liquid handling steps; The basic artistic GUI will involve: Getting coordinates from the GUI tool; Writing a Python script that moves the pipette to those positions; Using the HTGAA26 Colab notebook as your template:https://ddls.aicell.io/course/ddls-2025/module-6/lab/#-what-is-a-code-agent;
Week 4 HW: hw-protein-design-part-i
🐉 Project Objective: Bacteriophage Engineering This document outlines the core learning experience and the collaborative framework designed to drive an optimized bacteriophage project.
- Mastery of Basic Concepts Phage Biology: Understanding the lytic and lysogenic life cycles, and the structural modularity of viral components (Capsid, Tail, Baseplate). Synthetic Biology Framework: Introduction to the “Design-Build-Test-Learn” (DBTL) cycle in viral engineering. Therapeutic Potential: Exploring the role of phages in addressing antimicrobial resistance (AMR) and precision microbiome editing. 2. Amino Acid Structure & Biochemistry Chemical Taxonomy: Categorization of the 20 standard amino acids based on hydrophobicity, charge, and polarity. Side-Chain Interactions: Analyzing how hydrogen bonds, salt bridges, and disulfide bridges dictate protein stability. Conformational Constraints: Understanding the Ramachandran plot and the energetic landscape of protein folding. 3. 3D Protein Visualization & Analysis Software Proficiency: Hands-on training with professional-grade tools such as PyMOL, ChimeraX, or NGL Viewer. Structural Mapping: Visualizing surface electrostatic potentials, hydrophobicity, and potential binding pockets. Superimposition: Learning to align wild-type and mutant structures to assess structural deviations (RMSD). 4. Diversity of ML-based Design Tools Structure Prediction: Leveraging AlphaFold 3 or RoseTTAFold for high-accuracy 3D modeling of viral proteins. Fixed-Backbone Design: Using ProteinMPNN to redesign amino acid sequences for a specific structural scaffold. Generative Scaffolding: Implementing RFdiffusion for de novo design of receptor-binding motifs and functional binders. Sequence Modeling: Utilizing Protein Language Models (e.g., ESM-3) to predict the impact of specific mutations on protein function. 👩🦰 Part A: Fundamental Principles & Frontiers in Protein Engineering This section covers fundamental inquiries into biochemistry, evolutionary biology, and structural protein design.
Week 5 HW: hw-protein-design-part-ii
🐉 Part A: SOD1 Binder Peptide Design (From Pranam) Background：Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. In its native state, it forms a stable homodimer and binds copper and zinc. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Alanine → Valine at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation.
Week 6 HW: hw-genetic-circuits-part-i
Week 6 — Genetic Circuits I: DNA Assembly Technologies Molecular Biology Lab Report: PCR & Assembly Techniques Components of Phusion High-Fidelity PCR Master MixPhusion Master Mix is a convenient 2X concentrated solution containing:Phusion DNA Polymerase: A pyrococcus-like enzyme fused with a processivity-enhancing domain. It provides extremely high fidelity ($50\times$ higher than Taq) and speed.dNTPs: The building blocks ($dATP, dTTP, dCTP, dGTP$) for the new DNA strand.Reaction Buffer: Maintains optimal pH and provides ionic strength.MgCl2: A necessary cofactor for polymerase activity.