Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    Living lab TerraPods, Lebanon The halfpipe of Doom- How to grow good? For the first weeks lecture we had an introduction to the fundamental principles of synthetic biology and the HTGAA program. The focus of the lecture was on the governance and ethics of synthetic biology. David S. Kong discussed the balance between decentralized and centralized synBio development and the importance of thrust (something we are lacking these days). As a global community we have largely agreed to certain rules (e.g. bioweapon treaty 1975) however emerging synBio technologies also allow a much broader audience to participate in the development (e.g. community labs/ biohackers) that might not necessary always align with large governmental policies. He draws the parallel to how the early governance of the internet have allowed for a decentralized scaling that have contributed to an increased “computer literacy”. This might allow us to make better (although not perfect) personal decisions for how to use this new technology. Coming from a background of community focused biolab practice this was an interesting topic and made me think of the importance for a global bio-literacy. It also got me to think about the importance to apply these principals in a simple enough way that it doesn’t stifle participation.

  • Week 2 HW: dna read write and edit

    Part 1: Benchling & In-silico Gel Art My original idea was to make a circle, but after some trial and error I realized it would be a bit too complicated—so I settled on an arch (bridge). 1a) I imported the sequence for lambda DNA. 1b) In Benchling, I ran all 7 restriction enzymes we had available to see which ones gave:

  • Week 03 — Opentrons: Automation Art + Post-Lab Questions

    Part 1 — Automation Art (OT-2 “printing” a design) This week I designed a microscope icon as “automation art” and converted it into a grid of XY dot coordinates that can be dispensed by the Opentrons OT-2 onto an agar plate.

  1. Design → coordinate map I started from the course Automation Art Interface, which makes it easy to draw a dot pattern on a circular “canvas.”
  1. How many amino acid molecules are in 500 g of meat? If 500 g of meat is about 20% protein, that gives about 100 g protein. Since one amino acid is about 100 g/mol, that is about 1 mole, or ~6 × 10^23 molecules.

  • Week 5 HW: Protein design part 2

    Part 1: Generate Binders with PepMLM For this exercise, I used the human SOD1 target protein and introduced the A4V mutation. I then used PepMLM to generate four candidate 12-amino-acid peptide binders against the mutant target sequence. As requested in the assignment, I also included the known binder peptide FLYRWLPSRRGG for comparison. What is a A4V mutation:

  • week-06-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? The Phusion High-Fidelity PCR Master Mix contains at least three key components: Phusion DNA polymerase, deoxynucleotides (dNTPs), and an optimized reaction buffer that includes MgCl₂. The polymerase is the enzyme that synthesizes new DNA strands during PCR, the dNTPs are the nucleotide building blocks incorporated into the new DNA, and the buffer/MgCl₂ provide the chemical environment and cofactor needed for efficient polymerase activity. According to the website of (New England)[https://www.neb.com/en/products/m0531-phusion-high-fidelity-pcr-master-mix-with-hf-buffer?srsltid=AfmBOorWPUiBMtKsQJJH0VLGPzLYHtMYELtt0wf7AQB0YZYF4nrTfFsz] the main benefit of rgw Master mix is high fidelity (50X comparing to Taq) and fast extension times.

  • Week 07 HW: Genetic circuits part ii

    Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions?** Intracellular artificial neural networks (IANNs) have a major advantage over traditional Boolean genetic circuits because they can process graded, continuous signals rather than only treating inputs as ON/OFF states. In biological systems, many relevant signals such as metabolite concentration, RNA abundance, stress level etc are not naturally binary. Neural-network-like circuits are better suited to integrate these analog inputs and make decisions based on their combined strength. Rizik e.g 2022

  • Week 09 HW: cell free systems

    Advantages of cell-free systems Cell-free protein synthesis (CFPS) offers a highly flexible and controllable environment compared to in vivo expression systems. Because there are no living cells, experimental conditions such as pH, ionic strength, redox environment, DNA concentration, cofactors, and additives can be directly tuned without affecting cell viability. This enables rapid optimization and prototyping of genetic constructs. Additionally, CFPS is significantly faster, allowing protein production within hours instead of requiring cell growth, transformation, and induction steps.

  • week-10-hw-imaging and measurment

    ##Final Project ?? Waters Part I — Molecular Weight The predicted molecular weight of the full eGFP construct, including the LE linker and His6-tag, is approximately 28,006.6 Da based on the amino acid sequence. Mature eGFP forms an internal chromophore, which results in a mass loss of approximately 20 Da. Therefore, the expected molecular weight of mature eGFP is approximately 27,986.6 Da.