Homework
Weekly homework submissions:
Week 1 Homework: Principles and Practices
Exchangeable Fabs As an undergraduate student, I worked on a project that required the use of multiple antibodies to bind specific epitopes and stain them. Nonetheless, antibodies are not cheap; they take a long time to get to Latin American laboratories, and they usually suffer from thawing and unthawing processes, causing them to lose efficacy. On another note, commercial antibodies are not fully characterized; therefore, other protein interactions are not screened beforehand, leading to cross-reactivity, which ultimately leads to less reliable results [1].
Week 2 Homework Section 1: DNA Read, Write, and Edit
Homework Questions from Professor Jacobson 1. Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome? How does biology deal with that discrepancy? The intrinsic error rate of DNA polymerase is approximately 1 error per 10⁶ nucleotides incorporated. Given that the human genome is approximately 3.2 × 10⁹ base pairs, this would imply on the order of ~3,200 errors per genome replication if no corrective mechanisms were present.
Week 2 Homework Section 2: DNA Read, Write and Edit
Part 1: Benchling and in silico gel art Using benchling, and after some time playing around with Ronan’s website for iteration, I decided to created the expression “OH”. Part 3: DNA Design Challenge 3.1. Choose your protein I decided to work with the E Protein of the Zika virus Brazil strain.
Week 3 Homework: Lab Automation
Part 1: Python Script for Opentrons Artwork Using GUI opentrons-art.rcdonovan.com, I created two designs, one using a whole range of colors and the other using just red and green (https://opentrons-art.rcdonovan.com/?id=zk5r154b9r6q995). mplum_points = [(-4.4, 24.2),(-2.2, 24.2),(0, 24.2),(-6.6, 22),(-4.4, 22),(2.2, 22),(-6.6, 19.8),(-4.4, 19.8),(2.2, 19.8),(-6.6, 17.6),(-4.4, 17.6),(-2.2, 17.6),(0, 17.6),(2.2, 17.6),(-6.6, 15.4),(-4.4, 15.4),(-2.2, 15.4),(-6.6, 13.2),(-4.4, 13.2),(-6.6, 11),(-4.4, 11),(-6.6, 8.8),(-4.4, 8.8),(-6.6, 6.6),(-4.4, 6.6),(-2.2, 6.6),(-6.6, 4.4),(-4.4, 4.4),(-2.2, 4.4),(-6.6, 2.2),(-4.4, 2.2),(-2.2, 2.2),(-6.6, 0),(-4.4, 0),(-2.2, 0),(-6.6, -2.2),(-4.4, -2.2),(-2.2, -2.2),(-6.6, -4.4),(-4.4, -4.4),(-2.2, -4.4),(-6.6, -6.6),(-4.4, -6.6),(-2.2, -6.6),(-6.6, -8.8),(-4.4, -8.8),(-2.2, -8.8),(-6.6, -11),(-4.4, -11),(-2.2, -11),(-6.6, -13.2),(-4.4, -13.2),(-2.2, -13.2),(-6.6, -15.4),(-4.4, -15.4),(-2.2, -15.4),(-4.4, -17.6)] mko2_points = [(0, 15.4),(2.2, 15.4),(-2.2, 13.2),(0, 13.2),(2.2, 13.2),(4.4, 13.2),(-2.2, 11),(0, 11),(2.2, 11),(4.4, 11),(-2.2, 8.8),(0, 8.8),(2.2, 8.8),(4.4, 8.8),(0, 6.6),(2.2, 6.6)] ultramarine_points = [(-2.2, 22),(0, 22),(-2.2, 19.8),(0, 19.8)] electra2_points = [(4.4, 2.2),(6.6, 2.2),(8.8, 2.2),(11, 2.2),(13.2, 2.2),(15.4, 2.2),(17.6, 2.2),(8.8, 0),(13.2, 0),(6.6, -2.2),(13.2, -2.2),(15.4, -2.2),(17.6, -2.2),(4.4, -4.4),(13.2, -4.4),(2.2, -6.6),(4.4, -6.6),(6.6, -6.6),(8.8, -6.6),(13.2, -6.6)] megfp_points = [(-4.4, 24.2),(-2.2, 24.2),(0, 24.2),(-6.6, 22),(-4.4, 22),(2.2, 22),(-6.6, 19.8),(-4.4, 19.8),(2.2, 19.8),(-6.6, 17.6),(-4.4, 17.6),(-2.2, 17.6),(0, 17.6),(2.2, 17.6),(-6.6, 15.4),(-4.4, 15.4),(-2.2, 15.4),(-6.6, 13.2),(-4.4, 13.2),(-6.6, 11),(-4.4, 11),(-6.6, 8.8),(-4.4, 8.8),(-6.6, 6.6),(-4.4, 6.6),(-2.2, 6.6),(-6.6, 4.4),(-4.4, 4.4),(-2.2, 4.4),(-6.6, 2.2),(-4.4, 2.2),(-2.2, 2.2),(-6.6, 0),(-4.4, 0),(-2.2, 0),(-6.6, -2.2),(-4.4, -2.2),(-2.2, -2.2),(-6.6, -4.4),(-4.4, -4.4),(-2.2, -4.4),(-6.6, -6.6),(-4.4, -6.6),(-2.2, -6.6),(-6.6, -8.8),(-4.4, -8.8),(-2.2, -8.8),(-6.6, -11),(-4.4, -11),(-2.2, -11),(-6.6, -13.2),(-4.4, -13.2),(-2.2, -13.2),(-6.6, -15.4),(-4.4, -15.4),(-2.2, -15.4),(-4.4, -17.6)] mrfp1_points = [(-2.2, 22),(0, 22),(-2.2, 19.8),(0, 19.8),(0, 15.4),(2.2, 15.4),(-2.2, 13.2),(0, 13.2),(2.2, 13.2),(4.4, 13.2),(-2.2, 11),(0, 11),(2.2, 11),(4.4, 11),(-2.2, 8.8),(0, 8.8),(2.2, 8.8),(4.4, 8.8),(0, 6.6),(2.2, 6.6)] I submitted my design but I still have some inquiries about the python file.