Homework

Weekly homework submissions:

  • 𓃠 Week 1 Homework 𓃠 1. First, describe a biological engineering application or tool you want to develop and why. I want to build a Biological 3D Printer :D It is a quite crazy idea, basically a biological 3D printer takes in a DNA file and prints it and expresses it right away and delivers the target product in vial.
  • 𓃠 Week 2 Homework 𓃠 Part 1: Benchling & In-silico Gel Art Simulate Restriction Enzyme Digestion with the following Enzymes:
  • 𓃠 Week 3 Homework 𓃠 Assignment: Python Script for Opentrons Artwork This is an Ancient Egyptian Pharaoh Figure, this was made using this GUI Also here is the live link to check it out! :D
  • 𓃠 Week 4 Homework 𓃠 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) Proteins make about 20%-30% of the composition of meat, so we can take 25% as the average, this means 500 x 0.25 = 125g protein, to determine molar mass, 1 Dalton is approximately equal to 1 gram per mole (g/mol), so an average amino acid weighs 100 g/mol which when divided by the molar mass of 100 daltons gives 1.25 moles of amino acids, then we can multiply this by Avogadro’s number (6.022x1023), we get 7.5275 x 1023 molecules of amino acids in the 500 grams of meat (this is extremely huge wow XD)
  • 𓃠 Week 5 Homework 𓃠 Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM Here is the Human SOD1 sequence from Uniprot (P00441)
  • 𓃠 Week 6 Homework 𓃠 Assignment: DNA Assembly 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion High-Fidelity PCR Master Mix is basically a pre-optimized solution containing every chemical component needed for DNA amplification except for the DNA template and the primers.
  • 𓃠 Week 7 Homework 𓃠 Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) 1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? IANNs are more suited for biology since they are not constrained with the digital β€œ0 and 1” appraoch, but can follow an Analog appraoch that is more realistic and suited for biology, because biology is not in an On/Off stage but it varies with different values and expression levels and they are more flexible in that they help in designing more Decision Boundaries without having to create new parts from the scratch and as we have seen with the Neuromorphic wizard, it can also tap and work in Advanced areas like β€œDual Region” zones where a cell activates if inputs are strictly below a threshold Or strictly above a threshold, but remains totally inactive in the intermediate zone
  • 𓃠 Week 9 Homework 𓃠 Homework Part A: General and Lecturer-Specific Questions General homework questions 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. Cell-free protein synthesis is basically taking the protein-making machinery out of a living cell and running the process in a test tube. The biggest advantage over traditional in vivo methods (which use living cells) is that you do not have to worry about keeping a cell alive. When you work with living cells, the cell membrane blocks you from easily changing the environment, and the cell’s natural life-cycles get in the way.
  • 𓃠 Week 10 Homework 𓃠 Homework: Final Project Ξ±-Pinene titer: quantity of our target molecule produced per chassis per carbon source. Measured by GC-MS with dodecane overlay extraction from 96-well deep plates. AgPS protein identity and mass: purified AgPS-His6 protein (via Ni-NTA) can be characterized by intact protein LC-MS to confirm correct molecular mass and verify the His6 tag is present. Cell growth (OD₆₀₀): optical density at 600nm across all chassis Γ— carbon source conditions. Measured on the PHERAstar FSX plate reader. Tells us if the strain is healthy while producing. Gene expression (mRNA level): RT-qPCR on the CFX Opus machine using primers targeting AgGPPS2 and AgPS transcripts. Confirms the genes are being transcribed in vivo. π“‹Ή π“‹Ή π“‹Ή π“‹Ή π“‹Ή Homework: Waters Part I β€” Molecular Weight The Theoritical Molecular weight of the eGFP Sequence is 28006.60
  • 𓃠 Week 11 Homework 𓃠 Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork I just want to say, this was soooo fun! :D and i truly love how it changed alot and all the virtual pixel fun wars i’ve had and truces and teamups, it was a really engaging and lovely experience
  • 𓃠 Week 12 Homework 𓃠 No Homework :D Working on Final Project :D π“‹Ή π“‹Ή π“‹Ή π“‹Ή π“‹Ή
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