Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
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. Biosensors for Animal Health I aim to develop molecular diagnostic biosensors for veterinary medice. Specifically, I am interested in creating biofluorescent biosensor kits capable of detecting animal pathogens in rural and remote areas. This application is particularly relevant in countries such as Peru, where many communities lacated far from urban centers depend on livestock for their livelihood but face limited access to laboratory diagnostic services. This often leads to delayed diagnoses and significant economic losses due to infectius diseases.
Week 2 HW: DNA Read, Write, & Edit
Part 0: Basics of Gel Electrophoresis I reviewed the recorded class recitation. Part 1: Benchling & In-silico Gel Art See the Gel Art: Restriction Digests and Gel Electrophoresis protocol for details. Overview: Make a free account at benchling.com Import the Lambda DNA. Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI HindIII BamHI KpnI EcoRV SacI SalI Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. You might find Ronan’s website a helpful tool for quickly iterating on designs!
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. Post-Lab Questions — DUE BY START OF FEB 24 LECTURE To create the design, I employed several tests: Part 1. I initially performed some tests by modifying the color in the first example provided in Google Colab.
Week 4 HW:Protein design PART I
Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip) Why do humans eat beef but do not become a cow, eat fish but do not become fish? Humans do not transform into fish or cws because dietary components are not assimilated as intact complex structures. When we ingest food, it is processed through a mechanism called digestion, which involves the enzymatic breakdown of macromolecules into their most basic units. These molecules are then used as raw materials to synthesize biomolecules acording to the instructions encoded in human DNA.
Week 5 HW: Protein design part II
Homework — DUE BY START OF MAR 10 LECTURE 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.
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Homework — DUE BY START OF MAR 17 LECTURE Assignment: DNA Assembly Answer these questions about the protocol in this week’s lab: 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The Phusion High-Fidelity master mix contains:
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Homework — DUE BY Mar 31 2PM ET Assignment Part 1: Intracellular Artificial Neural Networks (IANNs)
- What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Tradicional genetic rely on Boolean logic (AND, OR, NOT), producing discrete outputs. In contrast, IAANS are inspired by the perceptron by the perceptron model, where inputs correspond to : Activation is the gene expression threshold, Inputs are molecular concentrations,Weights is regulatory strength. Some advanges are: the continuous signal precessing, wich allows graded rather than binary responses, scalability through multilayer architectures, improved classification of complex cellular states, as multiple biological signals can be integrated and weighted simultaneously.
General homework questions 1. 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. 2. Describe the main components of a cell-free expression system and explain the role of each component. 3. Why is energy provision regeneration critical in cell-free systems? Describe a method you could use to ensure continuous ATP supply in your cell-free experiment. 4. Compare prokaryotic versus eukaryotic cell-free expression systems. Choose a protein to produce in each system and explain why. 5. How would you design a cell-free experiment to optimize the expression of a membrane protein? Discuss the challenges and how you would address them in your setup. 6. Imagine you observe a low yield of your target protein in a cell-free system. Describe three possible reasons for this and suggest a troubleshooting strategy for each. Homework question from Kate Adamala Design an example of a useful synthetic minimal cell as follows:
Week 1 HW: imaging and measurement
Homework — DUE BY START OF Apr 14 LECTURE Homework is partly based on data that will be generated in the Waters Immerse Lab in Cambridge, MA. Students will characterize green fluorescent protein (eGFP, a recombinant protein standard) structure (primary, secondary/tertiary) in the lab using liquid chromatography and mass spectrometry, as well as Keyhole Limpet Hemocyanin (KLH) oligomeric states using charge detection mass spectrometry (CDMS). Data generated in the lab needed to do the homework is included both within this document and in the Appendix of the laboratory protocol.
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Contribute at least one pixel to this global artwork experiment before the editing ends on Sunday 4/19 at 11:59 PM EST. A personalized URL was sent to the email address associated with your Discourse account, and you can discuss the artwork on the Discourse. If you did not have a chance to contribute, it’s okay, just make sure you become a TA this fall! 😉