Homework
Weekly homework submissions:
Week 1: Principles and Practices
Class Assignment Project Idea Chronic wounds and surgical site infections affect millions of patients and cost heathcare systems tens of billions of dollars annually, yet closure devices often remain as passive stitches that do not actively orchestrate local immunity or regeneration [1][2]. Drug-eluting sutures have shown that suture material can safely deliver local therapeutics, but current designs provide only finite, non-adaptive release of single agents such as antibiotics or growth factors [3][4]. Cell-filled sutures packed with mesenchymal stem cells already demonstrate that viable cells can be integrated into suture structures and enhance healing, but these cells are unmodified and lack controllable, multi-functional outputs [5]. Separately, engineered combinatorial cell devices in fiber-like formats can secrete optimized cocktails of growth factors to accelerate wound and bone repair, but they are not load-bearing sutures and do not address infection or scar modulation at the incision line [6].
Week 2: DNA Read, Write, and Edit
Benchling and In-Silico Gel Art Simulate Restriction Enzyme Digest I found this process quite intuitive, as I’ve done similar simulations with the application SnapGene, but it was interesting to notice the small interface differences between the two!
Python script for Opentrons artwork For the art portion of this week’s assignment, I decided to code Yoshi from Super Mario Brothers since the Designer Cells node only had the red and green colors. I used this photo as reference. From there, I started to code for the Opentron automation.
Conceptual Questions (Question 1) A 500g piece of meat would weight about 3.011x1026 Daltons, and since each amino acid is equal to about 100 Daltons, that would mean that by consuming this piece of meat, you are consuming 3.011x1024 amino acids. (Questions 2) When we eat sources of meat, we physically and enzymatically break down the proteins into amino acids, fatty acids, and sugars, which in turn are used to provide energy to our bodies.
SOD1 binder peptide design Generate binders with PepMLM The original SOD1 sequence[1] is as follows: >sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ The A4V mutation changes the alanine to valine at codon 4, which results in
DNA Assembly (Question 1) Within Phusion High-Fidelity Master Mix [1], there is a Phusion DNA Polymerase (which enzymatically synthesizes the DNA in the 5’ to 3’ direction), nucleotides (the building blocks of the synthesized DNA), and an optimized reaction buffer (maintains optimal conditions for the polymerase). (Question 2) Some factors that determine primer annealing temperature are the primer length, the GC content, and the salt concentration.
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General questions Individual final project