Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Biological Engineering Application or Tool The proposed application is an AI-guided protein therapeutic discovery and bioproduction platform. The system uses machine learning–based protein design models to generate novel therapeutic protein candidates, such as antimicrobial proteins, enzymes, or biologics optimized for stability and activity. These candidates are then evaluated for manufacturability and functional performance using controlled bioproduction workflows, including microbial expression or cell-free systems. This application reflects an emerging paradigm in biopharmaceutical development, where AI accelerates early-stage discovery while scalable bioproduction determines clinical and commercial feasibility. However, as AI enables rapid de novo protein design, many generated sequences may lack homology to known natural proteins, introducing novel biosecurity and safety risks if not properly governed.
DNA Read, Write, and Synthesis
This week, we were tasked to utilize different tools to be able to virtually read, write, and visualize using samples like lambda DNA from Escherichia coli and the Tumor suppressor gene from humans. Part 1 - Introduction and DNA digest. Gel Electrophoresis Gel - material Electro - Electric Phoresis - to transport It is a method used to transport charged materials using an electric field through a gel (a Semi-liquid substance). Digested fragments of Lambda DNA
Part - 1 What are some components in the Phusion High-Fidelity PCR Master Mix, and what is their purpose? Phusion High-Fidelity PCR Master Mix, commonly produced by Thermo Fisher Scientific, contains a high-fidelity DNA polymerase with proofreading ability, a reaction buffer that maintains optimal conditions, Mg²⁺ ions as a cofactor, dNTPs as building blocks, and stabilizing additives. Together, these components enable accurate and efficient DNA amplification with a low error rate. What are some factors that determine primer annealing temperature during PCR?
A. Conceptual Questions 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) Answer 1 Dalton ≈ 1 g/mol Average amino acid ≈ 100 g/mol If you eat 500 g of (pure) amino acids: number of moles = Gm/ Tm = 500g/100g/mol
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Intracellular artificial neural networks provide more flexible and nuanced behavior than traditional Boolean genetic circuits because they can process inputs in a graded, continuous manner rather than simple on or off states. This allows cells to integrate multiple signals and produce proportional responses, making them better suited for complex decision making and pattern recognition inside biological systems. 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.