Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Tool Description Biosensor for the detection of stress or diseases in plants useing Escherichia coli chassis. In this system, stress signals or specific markers associated with certain pathogens induce the production of a fluorescent protein like GFP. This biosensor could be used as a tool for the early detection of plant pathologies by exposing the bacteria to the plant extracts or exudates. T
Week 2 HW: DNA Read, Write, & Edit
Part 1: Benchling & In-silico Gel Art I design two gels: Gel A: ‘ART’ Gel B: ‘ATP’ Part 3: DNA Design Challenge 3.1. Choose a protein - TcHMGB For this homework, I chose the protein HMGB from Trypanosoma cruzi (TcHMGB), the parasite that causes Chagas disease. TcHMGB was characterized by the research group in which I carried out my undergraduate thesis. During this work, I constructed a DM28c cell line expressing TcHMGB fused to the biotin ligase TurboID, with the objective of performing a proximity labeling–based interactomics assay.
Python Script for Opentrons Artwork To create the Python file to run on an Opentrons liquid-handling robot, I used the scripts from the file downloaded from http://opentrons-art.rcdonovan.com/ as guide, to write the scripts unthe the ‘#YOUR CODE HERE’ line. I also edited the ‘well_color’ library to add some colors. Google colab cell link: https://colab.research.google.com/drive/1Ke57DkO8O2jpCUDaYyK3krv4kUYFVgn8#scrollTo=pczDLwsq64mk&line=9&uniqifier=1 Simulation visualisation: Post-Lab Questions Descrbe 3 proyects Proyect 1: Engineered Miniproteins to Disrupt and Prevent Bacterial Biofilm Formation THE PROBLEM Biofilms are structured microbial communities embedded in a self-produced extracellular polymeric substance (EPS) matrix composed of polysaccharides, proteins, extracellular DNA and lipids. They form on:
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions 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?
Week 5 HW: Protein Design Part 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. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Alanine → Valine at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation.