Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
To make things tidy, I decided to answer most of the questions about the biological engineering application in sections of a separate project idea page. PLEASE NOTE: on the project page accessible through the link I have been unable to show two images: an image of Van Gogh’s Sunflowers painting and a diagram showing how I’ve scored the actions I’ve suggested. It doesn’t appear to load the image, yet the build log indicates it’s a success. I’m not sure what the problem is but it means you won’t see those two pictures.
Week 2 DNA Read, Write and Edit
Assignment 2 I created a Benchling account, loaded up the Lambda DNA, and then tried different combinations of the following restriction enzymes. EcoRI HindIII BamHI KpnI EcoRV SacI SalI I note that the Automation Art tools produces randomly created electrophoresis ladders, but I excluded Ndel, Pvull and Xhol - because they were not in the list we were supposed to use.
Assignment 3 Following on from last week’s assignment, I decided to use Vincent van Gogh’s Sunflowers painting (the one hanging in the National Gallery) for my art subject. I tried to download an image of the painting and upload it to the Opentrons automated art interface. Importing it made some artistic effects I didn’t want - it flooded the background with yellow, left out the blue streaks and didn’t do much to distinguish between orange and yellows. Importing it created something that wasn’t recognisable.
Part A: Conceptual Questions Choosing 9 of 11 questions to answer Q1. 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) I’ve made some assumptions: The meat mass does not include air or water. The meat mass does not include organic materials that are not amino acids A Dalton is a unit of mass used to express atomic and molecular weights. I used this converter to determine how many Daltons are in 500 grams of organic material. 500 g = 3.011086821E+26 daltons. If an amino acid is 100 daltons, then 500 g would contain 3.011086821E+24 molecules.
Part 1: Generate Binders with PepMLM Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. I visited the Uniprot page for (P00441)[https://www.uniprot.org/uniprotkb/P00441/entry#sequences] and the normal sequence is: 012345… MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ A4V represents one mutation where the ‘A’ changes to a ‘V’ at position 4: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ I found additional information about the AV4 mutation on the ALS Association’s page
Week 6 Genetic Circuits Part I: Assembly Technologies
Genetic Circuits Part I: Assembly Technologies 1 What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? A product page for Fisher Scientific indicate: “Phusion High-Fidelity PCR Master Mix is convenient 2X mix containing Phusion DNA Polymerase, nucleotides, and optimized reaction buffer including MgCl2. Two master mix formulations are available: with HF Buffer (F-531S and F-531L) and with GC Buffer (F-532S and F-532L).”1
Week 7 Genetic Circuits Part II: Neuromorphic Circuits
Genetic Circuits Part II: Neuromorphic Circuits Part 1: Intracellular Artificial Neural Networks (IANNs) 1 What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Describe a useful application for an IANN; include a detailed description of input/output behavior, as well as any limitations an IANN might face to achieve your goal.
Week 9 — Cell-Free Systems General homework questions 1. Explain the main advantages of cell-free protein synthesis over traditional in vivo methods, specifically in terms of flexibility and control over experimental variables. Name at least two cases where cell-free expression is more beneficial than cell production. The greatest advantage the cell-free protein synthesis has over in vivo methods is that the viability of the cell does not have to be maintained in order to maintain the viability of the protein synthesis. By allowing proteins to be grown in an open environment, greater control can be exercised over the key factors that produce the protein. Materials can be added to help protein production which may otherwise be toxic to cell populations. Scientists can control ion concentrations, cofactors and energy sources. Enhancing and prohibiting materials can also be added. Growing proteins in a cell-free environment also means protein production does not have to accommodate cloning of cells.
Week 10: Advanced Imaging & Measurement Technology
Homework: Final Project Please identify at least one (ideally many) aspect(s) of your project that you will measure. It could be the mass or sequence of a protein, the presence, absence, or quantity of a biomarker, etc. Please describe all of the elements you would like to measure, and furthermore describe how you will perform these measurements. What are the technologies you will use (e.g., gel electrophoresis, DNA sequencing, mass spectrometry, etc.)? Describe in detail
Week 11: Bioproduction and Cloud Labs
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Contribute at least one pixel to this global artwork experiment before the editing ends on Sunday 4/19 at 11:59 PM EST. A personalized URL was sent to the email address associated with your Discourse account, and you can discuss the artwork on the Discourse. If you did not have a chance to contribute, it’s okay, just make sure you become a TA this fall! 😉 Make a note on your HTGAA webpages including: what you contributed to the community bioart project (e.g., “I made part of the DNA on the bottom right plate”) what you liked about the project, and what about this collaborative art experiment could be made better for next year.
Be sure you’ve seen the updated week 11 homework which is due by the end of the course. Done.
Week 13: AI, SynBio, and Scaling Health Innovation (ARPA-H)
Homework: Work on your Final Project Present it May 12 (MIT/Harvard) or May 13 (Committed Listeners Done!
Homework: Finish your Final Project. Present it May 12 (MIT/Harvard) or May 13 (Committed Listeners) Done!