Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    1. A biological engineering application or tool I want to develop and why: I want to develop an engineered consortium of microorganisms for pilot-scale biomanufacturing on Mars. The microbes will be engineered for self-sufficent surival subject to the multitude of constraints of the red planet. This insitu resource utilization (ISRU) will be a key step towards the goal of the eventual colonization of Mars, by reducing the import from Earth. The current methods of ISRU, although in their rudimentary stages, rely on high energy chemical conversion process. My application aims at providing an alternative to this, and pave way for sustainable biomanufacturing away from the Earth.

  • Week 2 HW: DNA Read, Write, and Edit

    Part 1: Benchling & In-silico Gel Art 1.1 Restriction Digestion Simulation in Benchling: 1.2 DNA Gel Art Using Automation Art: Part 2: Laboratory Work on Gel Electrophoresis Skipped due to lack of access to lab.

  • Week 3 HW: Lab Automation

    1. Opentrons Art: Code: https://colab.research.google.com/drive/1EMIMzVtB1k32tNOAKxGJH9ZDrxwvAGkC JSON file: Download Opentrons art JSON Acknowledgements: This format of coding (uploading a JSON file that contains the coordinates) was inspired from https://www.youtube.com/watch?v=K5nR0eYHLEk&t=4s. Huge thanks to Alireza Hekmati. Coding, in its entirity, was handled by Gemini version 3.0 that was in-built in Collab. Output:
  1. Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. The paper: Slowpoke:An Automated Golden Gate Cloning Workflow for Opentrons OT‑2 and Flex
  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) Assume that the mass of other components like fat, collagen etc. are negligible compared to proteins in meat. Average wight of 1 molecule of amino acid = 100 Dalton = 1.7 * $10^{-24}$ g Weight of piece of meat = 5 * $10^{2}$ g Therefore, number of amino acid molecules = (5 * $10^{2}$) / 1.7 * $10^{-24}$ = 2.94 * $10^{26}$

  • Week 05 HW: Protein Design Part 2

    Part 1: Generate Binders with PepMLM Retrieve sequence and introduce mutation: (Pasted the sequence from UniPort, deleted M at 1st position, changed A to V at 4th position.) ATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Structure of the native sequence- predicted vs actual: Generate 4 peptides using PepMLM Colab: index Binder Pseudo Perplexity 1 WRSPAVAVAHWE 7.76721411356481 2 WRVGWVGVELKE 24.2058244561383 3 WRSPAAXIEHKX 11.243453670563373 4 WRVYAAXIEWGK 20.449723821548965 Known binder: FLYRWLPSRRGG Perplexity score: 22.5252 A note about perplexity score: A key evaluation metric for language models that measures how well a probability model predicts a sample. Lower the score, higher the confidence of the model that the output satisfies the criteria.

  • Week-06-hw-genetic-circuits-part-i

    DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion DNA Polymerase: Pyrococcus-like enzyme that contains a fused processivity-enhancing domain. It provides more than 50 gold higher fidelity than Taq polymerase. dNTPs: contains dATP, dCTP, dGTP, and dTTP that are required for extension reaction of the PCR. Buffers: MgCl2 as a cofactor for polymerase, KCl and TAPS-HCl ([tris(hydroxymethyl)methylamino]propanesulfonic acid) to maintain ionic strength and pH respectively, and beta-meracaptoethanol to maintain enzyme stability. Some other components that are provided seperately: DMSO (Dimethyl sulfoxide) to improve denaturation and primer binding, and nuclease free water as a solvent and matrix to avoid denaturation of the DNA. What are some factors that determine primer annealing temperature during PCR?

  • Week-07-HW-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? They can interpret a range of inputs as opposed to the 0, 1 inputs of traditional genetic circuits. This allows them to aggregate multiple signals and apply the activation fucntion to filter biological noise. Traditional circuits often require a cascade of genetic logic gates, which lead to metabolic burden and competition for substrates. By utilizing weighted interactions, IANNs can accomplish the same task using fewer biolocial components. Nonlinear descision making is a struggle for tradional genetic circuits. They struggle to take into accout the relative ratios and thresholds of a multitude of proteins simultaneously, limiting themselves to simple linear logics. However, using ReLU and sigmoid -like activation behaviours, IANNs can perform complex tasks. Eg: A cell may be engineered to apoptosize only when a commplex profile of cancer markers are met, as oppossed to the presence of some of those markers that may not be cancerous. Describe a useful application for an IANN; include a detailed description of input/output behavior, as well as any limitations an IANN might face to achieve your goal. A useful applicaiton of IANN would be rapid plant cell response when it is infected by a pathogen.

  • week-09-hw-cell-free-systems

    Part A: General & 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. Rapid Iteration and Throughput Direct Use of Linear DNA Templates Traditional methods require time-consuming cloning of DNA into circular plasmids before they can be inserted into a host cell. In CFPS, you can use raw PCR products directly as the instruction manual, allowing you to move from a genetic design to a functional protein in just a few hours.

  • week-10-hw-Imaging-and-Measurement

    Homework: Final Project 1. Identify at least one aspect of your project that you will measure. Answer: The expression level of the L lactate dehydrogenase Gene The concentration of lactic acid 2. Describe all the elements you would like to measure. Answer: Lorem ipsum dolor sit amet.

  1. What technologies will you use (e.g., gel electrophoresis, DNA sequencing, mass spectrometry)? Answer: Lorem ipsum dolor sit amet.