Homework
Weekly homework submissions:
Week 1: Principles and Practices
Question 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.
Lab: Opentrons Art
Protein Design Part I (Thras Karydis, Jon Kaufman)
Lab: Protein Design IWeek 10: Imaging and Measurement
Week 10: Imaging and Measurement title: “Week 10 — Advanced Imaging & Measurement Technology” linkTitle: “Week 10 (Apr 7)” weight: 200 description: | Advanced Imaging & Measurement Tech (Evan Daugharthy, Waters Corp.) Lab: Mass Spectrometry This lecture presents a range of advanced technologies to do precision measurement of proteins at atomic scales, characterizing chemical composition, and detecting protein sequence and structure.
Week 11: Building Genomes Homework — DUE BY START OF APR 21 LECTURE (TBD)
Week 12: Bioproduction Homework — DUE BY START OF APR 28 LECTURE (TBD)
Week 13: Bio Design Living Materials
Week 13: Bio Design Living Materials Homework: Work on your Final Project Present it May 12 (MIT/Harvard) or May 13 (Committed Listeners)
Week 14: Biofabrication Homework: Finish your Final Project Present it May 12 (MIT/Harvard) or May 13 (Committed Listeners)
Week 2: DNA Read, Write, and Edit
Week 2: DNA Read, Write, and Edit Part 1: Benchling & In-silico Gel Art 1.1 Import Lambda DNA Simulate Restriction Enzyme Digestion Virtual Gel Part 2: Gel Art I have chosen to create a gel art of a person doing a jumping jack through randomization method.
Week 5: Protein Design Part II
Week 5: Protein Design Part II Homework — DUE BY START OF MAR 10 LECTURE Part A: SOD1 Binder Peptide Design 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 6: Genetic Circuits Part I
Week 6: Genetic Circuits Part I Homework — DUE BY START OF MAR 17 LECTURE Assignment: DNA Assembly Answer these questions about the protocol in this week’s lab:
Week 7: Genetic Circuits Part II
Week 7: Genetic Circuits Part II Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? An artificual neuron is a weighted summation through an activation function that produces outputs, eventually they form networks to become ANN. Intracellular artificial networks still have weighted summation and a non-linear activation function, but we can consider implementing gene circuits as these activation functions. The main difference is that IANNs will have two inputs that can do addition and subtraction. On the one hand, a promoter that through transcription makes a gene, and through translation we create proteins, we can perform addition on this. To subtract, we can treat input x1 as an endoribonuclease CasE that will bind and cleaves the RNA on the sequence and produce output. x1 is negative weight and x2 is positve weight, where the function is max(x2-x1,0). This is also referred to as Sequestration. Sequestration involves using an endorribonucleus to transcribe into mRNA to produce non-linearity (applying single turnover enzyme to remove it out of circulation).
Week 9: Cell-Free Systems Homework — DUE BY START OF Apr 7 LECTURE 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. Cell-free systems help us understand biology ‘from scratch’ to bioengineer from smaller units. There’s wider flexibility for scaffolding biology from the ground-up and controlling the environments in a complete model. Existing living cells as we know it are already incredibly complex and hence less controlled in experimental settings. Synthetic cell engineering allows flexibility in size of the cell, proteins, and even expanding largely on the chemistry of the cell. So the two scenarios could be if you want to control the size of the cell and want uniform control it might be ideal to use cell-free system. The other scenario might be to engineer a specific chemical environment or want chemical diversity in the experiment that is not naturally common/ compatible with cells. Compared to in-vivo expression where you have to create plasmids, cell-free protein expressions are faster and cheaper to construct and can also help you through quick iterations with linear fragments and without plasmids.