Homework

Weekly homework submissions:

  • Week 1 : Principles and Practices

    1. Describe a biological engineering application or tool you want to develop and why. The oximeter, used to detect oxygen saturation, has known disparities accross different skin tones, due to the melanins ability to absorb near infered light (NIR) (Clarice). These disparaiteis result in patients or darker skin tone showing higher oxigen saturation and appearing healthier than they are. This resulted in black and hispanic patients recived delayed treated for COVID 19, due to systematic overestmation of oxygen saturation (Fawzy et al.) Genetic circuits in a synthetic biological application, that engineers DNA, RNA and protiens to programmable; functions such as biosensors that can be programmed to react to enviromental factors. I want to use this biological engineering application to engineer genetic circuits to sense a CO2 or O2 saturations in the epidermis. Using a biosensor that does not depend on NIR will increase the accuracy of oxygen readings and result in more equitable care 2. Describe one or more governance/policy goals related to ensuring that this application or tool contributes to an “ethical” future Loosly refering the TAPIC framework from the World Health Organisation, focusing on transparency, acccountability, participation, intergrity and Capacity. The below are three goals that are built on the TAPIC framework(“TAPIC”). 1. Reduce Physical and Ecological Harm Governance should ensure that engineered organisms using genetic circuits are designed with robust biosafety and biosecurity features such as kill switches that trigger cell death in inappropriate environments, or activation only under specific conditions such as defined temperature or oxygen saturation. In addition, long‑term post‑deployment monitoring of surrounding environments and exposed people, coupled with clear procedures for recalls and adverse event reporting, should be required so that emerging harms can be detected and mitigated early.

  • Week 2: DNA Read/Write/Edit :

    1. Benchling & In-silico Gel Art 3. Protein Design Challenge 3.1 Protein Choice pHRed is a red fluorecent protein used to detect the pH in live cells. CO2 acts as an acid in the blood and forms carbonic acid (Garcia and Ramirez) and reduces the pH, so this can be used to create a biosensor to detect the pH of blood. Using the of pH is a more accurate data point to understand the condition of the blood and is currently done throught an artiel blood gas test (Cleveland Clinic). The protein sequence is blow NSRIATEGRIDTRFRGSIKNVTVSGENHETFDLINIFRDKSSVGIVKNLGEATITEKTSYDYTHTGDYLISATPVPFTFTEFDKLVRFSPXDFEQFESIEIQFRTKEPRGVLLFVGPDNAHTDYVCLEFYDRNLYLAFGIDGKDYRKQMNPKGTFVTTGNFHTIFIKRDRNHKFTAKFENVEVDIGDQSGHQREFGSYTYIGGIDNPSRLPWYVWSREGFVGCINYMRVNEDKYIDPRGKNNQYSGDIAGVDIGKCLNDVRHCTASHCEG

  • Week 3: Homework

  • Week 4: PROTEIN DESIGN PART I

    Part A- Conceptual Questions 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) Beef contains approximately 22g of protein per 100g 22 grams x 5= 110gram of protein in 500g of beef 1 Dalton ≈ 1g/mol 110g of protein / 100g/mol= 1.1mol 1.1x6.02×10²³= 6.6x10²³

  • Week 5: Protien Design 2

    Part A - SOD1 Binder Peptide Design (From Pranam) FLYRWLPSRRGG Binder Pseudo Perplexity 0 WRSGVAAAAWKK 7.129399 Binder Pseudo Perplexity 0 WHYYAYAAALKE 14.080622 Binder Pseudo Perplexity 0 WLYPAYAVALGE 15.854594 Binder Pseudo Perplexity 0 HHYYVAGVAHKK 21.58328 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQWHSGPVXLEWWX MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQWLYPAAAAAHKX MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQWLYPAYAVALGE MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQHHYYVAGVAHKK MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ 3 HHYYVAGVAHKK WLYPAYAVALGE

  • Week 6: GENETIC CIRCUITS PART I

    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 Phusion DNA polymerase, nucleotides, and an optimized reaction buffer including MgCl2 Phusion DNA polymerase is the enzyme that copies the DNA template, with high proofreading fidelity for accurate amplification. dNTPs (nucleotides) is the building blocks the polymerase incorporates into the new DNA strand. Optimized reaction buffer keeps the reaction conditions suitable for efficient polymerase activity, including pH and salt conditions.

  • Week 7: GENETIC CIRCUITS PART II

    What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Traditioanl circuits use operate in binary and, or, not. IANN continuously sense and respond to the inputs instead of just their presence or absence. This makes them better suited for complex bioprocesses that vary in space and time, such as metabolically or environmentally sensitive cell behaviors. It also filters noise and variables which is ideal in fluctuating enviroment like the body.