Homework
Weekly homework submissions:
Week 01 HW: Principles and Practices
Documentation Class Assignment — DUE BY START OF FEB 10 LECTURE 1. First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. I have a deep interest in Japanese fireworks culture and have incorporated fireworks into my artistic practice. In Japan, fireworks have long carried meanings of memorialization and life, making transience and cyclic time a shared embodied experience. At the same time, contemporary conditions—environmental footprint and responsible deployment—ask us to rethink what fireworks can mean today.
Week 02 HW: DNA Read, Write, & Edit
‘Week 2 — DNA Read, Write, & Edit’ Documentation Make sure to document every step of the in-silico and lab experiments. Make sketches, screenshots, notes, drawings… anything that helps you - and others - understand the experiment. Your documentation should help you - and others - to understand the topic. Don’t be afraid to add things that don’t work. Show your failures - and how you overcame them. Your Documentation should be a description of the amazing journey you are on!
Assignment: Python Script for Opentrons Artwork — DUE BY YOUR LAB TIME! Your task this week is to Create a Python file to run on an Opentrons liquid handling robot. 0. Review this week’s recitation and this week’s lab for details on the Opentrons and programming it. 1. Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. 2. Using the coordinates from the GUI, follow the instructions in the HTGAA26 Opentrons Colab to write your own Python script which draws your design using the Opentrons. ・You may use AI assistance for this coding — Google Gemini is integrated into Colab (see the stylized star bottom center); it will do a good job writing functional Python, while you probably need to take charge of the art concept. ・If you’re a proficient programmer and you’d rather code something mathematical or algorithmic instead of using your GUI coordinates, you may do that instead. 3. If the Python component is proving too problematic even with AI and human assistance, download the full Python script from the GUI website and submit that: 4. If you use AI to help complete this homework or lab, document how you used AI and which models made contributions. 5. Sign up for a robot time slot if you are at MIT/Harvard/Wellesley or at a Node offering Opentrons automation. The Python script you created will be run on the robot to produce your work of art! ・At MIT/Harvard? Lab times are on Thursday Feb.19 between 10AM and 6PM. ・At other Nodes? Please coordinate with your Node. 6. Submit your Python file via this form. Colab Link HTGAA26 Opentrons Colab _ShimadaSayaka
Week 04 HW: Protein Design Part I
‘Week 4 HW: Protein Design Part I’ Documentation Homework: Protein Design I — DUE BY START OF MAR 3 LECTURE Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip): 1. How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) 2. Why do humans eat beef but do not become a cow, eat fish but do not become fish? 3. Why are there only 20 natural amino acids? 4. Can you make other non-natural amino acids? Design some new amino acids. 5. Where did amino acids come from before enzymes that make them, and before life started? 6. If you make an α-helix using D-amino acids, what handedness (right or left) would you expect? 7. Can you discover additional helices in proteins? 8. Why are most molecular helices right-handed? 9. Why do β-sheets tend to aggregate? ・What is the driving force for β-sheet aggregation? 10. Why do many amyloid diseases form β-sheets? ・Can you use amyloid β-sheets as materials? 11. Design a β-sheet motif that forms a well-ordered structure. ☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆☆
Week 05 HW: Protein Design Part II
‘Week 5 — Protein Design Part II’ Documentation Homework: Protein Design II Part A: SOD1 Binder Peptide Design (From Pranam) 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.
Week 06 HW -Genetic Circuits Part I: Assembly Technologies
‘Week 6 — Genetic Circuits Part I: Assembly Technologies’ Documentation Homework: Genetic Circuits Part I: Assembly Technologies Assignment: DNA Assembly Answer these questions about the protocol in this week’s lab:
Week 07 HW -Genetic Circuits Part II: Neuromorphic Circuits
‘Week 7 — Genetic Circuits Part II: Neuromorphic Circuits’ Documentation Homework: Genetic Circuits Part II: Neuromorphic Circuits Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) Answer these questions about the protocol in this week’s lab:
‘week-09-hw-cell-free-systems’ Documentation Homework: Cell Free Systems Homework Part A: General and Lecturer-Specific Questions General homework questions
- Explain the main advantages of cell-free protein synthesis over traditional in vivo methods, specifically in terms of flexibility and control over experimental variables. Name at least two cases where cell-free expression is more beneficial than cell production. 従来の in vivo（生細胞内）法と比べて、cell-free protein synthesis（無細胞タンパク質合成）の主な利点を説明しなさい。 特に、柔軟性と実験条件の制御という観点から述べなさい。 また、細胞内での生産より無細胞発現のほうが有利な例を少なくとも2つ挙げなさい。 Cell-free protein synthesis https://en.wikipedia.org/wiki/Cell-free_protein_synthesis#:~:text=CFPS has many advantages over,required for such a reaction.