Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- Describe a biological engineering application or tool you want to develop and why: I want to develop a diagnostics chip for neuropsychiatric disorders (microarray or microfluidics based). 2. Describe one or more governance/policy goals related to ensuring that this application or tool contributes to an “ethical” future Policy goals would prevent misuse of diagnostics for measurement of features like “intelligence” or personality traits. Policies would need to limit interpretable results to areas of high variability in specific diseases and include diverse populations. 3. Three Governance Actions One: Federal oversight of use of genetic data. Prevention of use of data for non-psychiatric disease related traits. Two: Standardized, valid production of chips. Quality control. Three: Ensuring equal genetic information from diverse ancestries for diagnostics.
Week 2 — DNA Read, Write, & Edit
3.1. Choose your protein. In recitation, we discussed that you will pick a protein for your homework that you find interesting. Which protein have you chosen and why? Using one of the tools described in recitation (NCBI, UniProt, google), obtain the protein sequence for the protein you chose. Chosen Protein: Chromodomain Helicase DNA-binding Protein 8 (CHD8). Why: CHD8 is a “master regulator” of gene expression. It functions as an ATP-dependent chromatin remodeler, meaning it physically moves nucleosomes to open up DNA for transcription. I find it interesting because mutations in CHD8 specifically impact the expression of hundreds of other genes linked to brain development, providing a clear molecular bridge between genetic architecture and neurobiology.
One of the great parts about having an automated robot is being able to precisely mix, deposit, and run reactions without much intervention, and design and deploy experiments remotely. For this week, we’d like for you to do the following: Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode, Python scripts, 3D printed holders, a plan for how to use Ginkgo Nebula, and more. You may reference this week’s recitation slide deck for lab automation details. While your description/project idea doesn’t need to be set in stone, we would like to see core details of what you would automate. This is due at the start of lecture and does not need to be tested on the Opentrons yet.