Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
🧬 1. First, describe a biological engineering application or tool you want to develop and why. Here are some ideas that I brainstormed: 🩹 Regenerative Medicine Autologous skin grafts to replace necrotic, cancerous, scarred, or miscoloured tissue etc Synthetic skin models for surgeons or tattoo artists to practice on Self regenerating organs (for people with damaged organs, cancer, people who need transplants i.e. bioink) Cure for frostbite → regenerating cell tissue or even whole digits or limbs! Growing teeth in a lab to replace damaged or missing teeth! Regeneration of spinal column 🧪 Cures Targeting misfolded proteins (prions) in the brain Making malarial mosquitos infertile (* ethical considerations) Synthesising biofuel AIDS cure Cancer detection mechanism to cause cellular death/induce apoptosis in abnormal cells Cure for sickle cell Cure for cataracts by growing autologous lenses Cure for blindness or eyesight degeneration Making VADs → (HKU hydrogel transistors, electrical interaction with living cells) Helping diabetics to endogenously produce effective insulin 🛡️ Prophylaxis Predicting/modelling viruses and vaccines (* ethics/dangers must be taken into consideration) 🏭 Biomaterial/Industrial applications Manufacturing leather without the need for mass animal slaughter Bioplastic on industrial scale (mitigation of microplastic crisis) Industrially producing natural inks Bioremediation: Landfills Radioactive sites Sewage systems 🎭 Fun ideas Tabulating or transcribing music on plants (patterns on leaves → gene expression) Bioluminescent lamps for: industrial applications architectural applications (can be used practically in hospitals, clubs as exit signs etc) design/decor! bioluminescent paint hair dye/cosmetics Printing the taste of a meal! for art/deisgn installation involving the coding of Hana programme/Hana AI to detect what is in an image and “print out” certain proteins? that correspond to flavours etc edible Print out QR codes on biomaterial to be scanned and play music for art/design installations or if not QR codes then fun characters or shapes (presets) that can be scanned by Hana programme/Hana AI which then play certain songs? stills from films even? covers of albums? Mushroom testing kit which prints out species name on flesh of mushroom or testing strip once pricked or sample collected (kind of like pregnancy test but not, more like DNA sequencing mushrooms to determine what species that are) Sustainable nail polish Generating music from colony of bacteria for art/design/science installation . . . In the end I decided that I would like to pursue further the idea of printing an image as well as the taste of a food/meal using edible media. I would like to call it “Tastemaker” or “Yum Dot Com.” This project highlights the sensory potential of biological engineering, whilst sitting at the intersection of biology, technology, design, the culinary, and the quotidian human experience.
🧬 3.1 Choose your protein I was thinking of choosing between two proteins Titin (also known as connectin) which is the largest known protein encoded by the TTN gene. In humans it accounts for 0.5kg of body weight! Titin is important in muscle cells, acting as a molecular spring. It is the third most abundant protein in muscles, giving them their elasticity, structural integrity, and stability. Green fluorescent protein or GFP which is found in the crystal jelly or hydromedusa (Aequorea Victoria), as well as various species of coral, sea anemones, and crustaceans. GFP is often used as a reporter gene in cell as well as molecular biology. Scientists have created many organisms which can express GFP which is thusly a proof of concept that a gene can be expressed by a given organism. This protein has been introduced and expressed by many species, maintained in their genome, and even passed on to their offspring; such organisms include bacteria, yeast, fungi, fish, and mammalian cells, including those of humans.
🤖 Part I: Python Script for Opentrons Artwork I wanted to do a yin and yang symbol so I went about designing it on the very helpful website made by Ronan! https://opentrons-art.rcdonovan.com This is my design
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) On average 100g of meat 🥩 contains 26g of protein = 26% protein 100:26 ∴ 500:130g 1 amino acid = 100 daltons ≈ 1.66 × 10⁻²²g
Week 5 HW: Protein Design Part II
Part 1: Generate Binders with PepMLM 🐧 Human SOD1 Sequence from UniProt (154 amino acids): https://www.uniprot.org/uniprotkb/P00441/entry https://www.uniprot.org/uniprotkb/P00441/entry#sequences Click to view Human SOD1 Sequence MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Click to view Human SOD1 Sequence with A4V mutation which causes ALS MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ I had to manually reset the code as I was not able to change the parameters with the sliding scales. I was stuck with generating a single 15 peptide long binder at a time. Thankfully I was able to change this by editing the back end of the form, but also by forcing the code to make 4 binders that were 12 peptides long.
Week 6 HW: Genetic Circuits Part I
Answer these questions about the protocol in this week’s lab 🥼🧪🔬🧫 : 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion-High Fidelity PCR Master Mix contains Phusion DNA Polymerase → High fidelity, thermostable enzyme for fast, robust, and accurate DNA amplification in PCR; it is used particualrly for cloning and sequencing
Week 7 HW: Genetic Circuits Part II
Summary"Cancer wil ultimately be a chronic disease." - Rob Weiss I have to say this was one of my favourite lectures. 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? Boolean functions are binary, representing either on or off. Whereas the logic of IANNS (Interfering RNA-based Analog Neural Networks or Intracellular Artificial Neural Networks?) is more nuanced and geared towards more brain-like information processing. They can detect not merely whether a signal is present or not, but how strong it is. This is important because, in short, biology is messy!
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. Cell-free protein synthesis leverages biology as an engineering tool (Kate). Living cells require a lot of resources such as the correct amounts of
Week 10 HW: Imaging and Measurement
Waters Part I — Molecular Weight 💦 We will analyze an eGFP standard on a Waters Xevo G3 QTof MS system to determine the molecular weight of intact eGFP and observe its charge state distribution in the native and denatured (unfolded) states. The conditions for LC-MS analysis of intact protein cause it to unfold and be detected in its denatured form (due to the solvents and pH used for analysis).