Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Important: I use ChatGPT and Gemini to help me organize my ideas, translate some concepts and reunite everything!!
Week 2 HW: DNA Read, Write and Edit
ā> This image shows DNA fragments separated by agarose gel electrophoresis and stained with a fluorescent dye, performed during my Genetic Engineering course. Part 1: Benchling and In-silico Gel Art According to the instructions, this is the Gel I designed for p53 human protein (tried my best to make it look like a butterfly iām sorry!!) Part 3: DNA Design Challenge
Week 1 HW: Principles and Practices
Week 3: Lab Automation Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. Olsen J.V. et al. Fully Automated Workflow for Integrated Sample Digestion and Evotip Loading Enabling High-Throughput Clinical Proteomics (2024) Mol Cell Proteomics 23(7), 100790. DOI 10.1016/j.mcpro.2024.100790 This article describes a fully automated workflow for preparing clinical proteomics samples, from protein digestion to loading peptides into Evotips (disposable, tip-based C18 reversed-phase trap columns), ready for LC-MS/MS analysis. They use the Opentrons OT-2 liquid-handling robot, which controls all preparation steps without manual intervention after the initial loading of reagents. The process combines protein capture through aggregation on magnetic beads with enzymatic digestion and, without centrifugation steps, directly transfers the peptides to Evotips using positive pressure, all programmed through downloadable scripts from the Evosep website. Using this method, up to 192 samples can be processed in parallel in approximately 6 h, which equals to 100 samples/day and eliminates human variability. In tests with HeLa lysates, the workflow identified ~8.000 protein groups and ~130.000 peptides using an 11.5-min gradient on the Orbitrap Astral, demonstrating high sensitivity and reproducibility. It was also applied to 192 plasma samples from patients with metastatic melanoma, revealing clinically relevant protein changes.