Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Biological Engineering Application & Research Proposal Agnostic Biosurveillance in the Age of Generative AI Important HTGAA | APPLICATION 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.
Week 2 — DNA Read, Write, & Edit
Part 1: Benchling & In-silico Gel Art Simulación de restricción enzimática mediante Benchling 1.1 Enzimas utilizadas para la simulación EcoRI HindIII BamHI KpnI EcoRV SacI SalI Part 3: DNA Design Challenge 3.1 Choose Your Protein Protein: Envelope small membrane protein (Gene: E) Organism: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2) Metadata: Length: 75 amino acids Mass: 8,365 Da Amino Acid Sequence: MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRVPDLLV
Important HTGAA | Question Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. Workflow for the testing of SARS-CoV-2 using Opentrons OT-2 robots Villanueva-Cañas et al. (PLOS ONE, 2021) describe the setup of a full SARS-CoV-2 RT-qPCR testing workflow using Opentrons OT-2 robots. This allowed them to automate what would otherwise be manual pipetting. Instead, they automated the critical steps and connected them like a lab “production line”: multiple OT-2 units to prepare plates and reagents, a system to extract RNA, and then a thermocycler to run the PCR.
Week 4 HW: Protein Design Part I
Important HTGAA | Part A: Protein Analysis and Visualization Pick any protein (from any organism) of your interest that has a 3D structure and answer the following questions:. Briefly describe the protein you selected and why you selected it How long is it? What is the most frequent amino acid?.
Week 5 HW: Protein Design Part II
Important HTGAA | Part A: SOD1 Binder Peptide Design (From Dr Pranam Chatterjee) Retrieve the human SOD1 sequence (P00441) from UniProt, introduce the A4V mutation, use the PepMLM Colab to generate four 12–amino acid peptides conditioned on the mutant sequence, include the known binder FLYRWLPSRRGG for comparison, and record the resulting perplexity scores to assess model confidence.