Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
SCOBY DNA Steganography A biological engineering application or tool that I want to develop is a system for biomaterials for artist books that contains the book contents in its DNA. Above is an example of a a previous project of mine, where I was making masks out of SCOBYs, Symbiotic Cultures Of Bacteria and Yeast. A next level project might be to use SCOBY to create pages of artist books, where the the content of the pages (illustrations, text, relief sculptures, etc.) is also written into the DNA of the yeasts and/or bacteria that makes up the SCOBY. The reasons I am interested in this, and believe others will be interested as well, is primarily twofold: 1) I am interested in this as an unusual form of artwork that “grows on you” on multiple levels (such as genetic level, personal level, cultural(!) level, etc.) and 2) I am interested in this as a form of storytelling and story distrubution that can replicate itself, where the DNA creates new copies as the yeast reproduces, then thise new copies are used to create new copies of books.
Week 2 HW: DNA Read, Write, & Edit
Part 1: Benchling & In-silico Gel Art Above is maybe my favorite Gel Electrophoresis design I created. I was trying to make monster faces, so hopefully this looks sort of like a skull with horns! I made this with the “DNA Gel Art Interface” website created by Ronan at https://rcdonovan.com/gel-art
Part 1: Generate an artistic design NOTE: Some of my newer and hopefully maybe better images are toward the end! I generated the above artistic design – a self portrait – using the GUI at opentrons-art.rcdonovan.com – NOTE: BUGSS Lab has colors: orange, green, yellow, purple, red, blue A below is me working on simulating that, redrawing and recoloring little bit in the Google Colab notebok with the six colors at BUGSS Lab. Thanks to Amanda and everyone for helping hack up that code.
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions 1. How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) Meat is about 20% protein, so that is 100 g of protein. There are 6.022e+23 Daltons per gram, so for 100 grams that is 6.022e+25 Daltons. Then if there are 100 Daltons in an average amino acid, we’re back to 6.022e+23 molecules of amino acids.
Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM https://www.uniprot.org/uniprotkb/P00441/entry#sequences “Generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence.” I did this step several times. Here are two examples of my generating four peptides:
Week 6 HW: Genetic Circuits Part I
Assignment: DNA Assembly 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? From New England Biolabs “Phusion High-Fidelity PCR Master Mix with HF Buffer is a 2X master mix consisting of Phusion DNA Polymerase, deoxynucleotides and reaction buffer that has been optimized and includes MgCl2. All that is required is the addition of template, primers and water.”