Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Week 1: Principles & Practices- Class Assignment First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. Lactate Biosensor Tattoo for competition swimmers! I propose developing a semi-permanent, waterproof biosensor tattoo that detects lactate levels in athletes during pool training. The system would rely on engineered biological circuits that respond to lactate and trigger a visible fluorescent or colorimetric signal, functioning as a traffic-light-style, semi-quantitative indicator of physiological stress. The idea is connected to course topics such as genetic circuit design and fluorescent protein signaling. Lactate would act as the biological input, while the output would be a color change generated by chromoproteins or fluorescent reporters, similar to the chromophore and genetic circuit. This tool doesn’t pretend to replace clinical blood tests or provide precise measurements. Instead, it will support athletic training by providing real-time visual feedback, reducing invasive blood sampling, and minimizing medical waste, such as needles and collection tubes. This idea is inspired by my personal experience as a competitive swimmer, where lactate monitoring required repeated finger pricks during intense training sessions. I am particularly interested in exploring how biological sensing circuits and fluorescence-based outputs could be adapted to function under demanding conditions such as exercise, pool conditions, and temperature variation. Biology pipeline of the application (circuit-inspired sensing) Swimmer (physiological lactate production):
Week 2 HW: DNA Read, Write, and Edit
Prelecture Homework: In preparation for Week 2’s lecture on “DNA Read, Write, and Edit," please review these materials: Lecture 2 slides as posted below. The associated papers that are referenced in those slides. In addition, answer these questions in each faculty member’s section: Homework Questions from Professor Jacobson: Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy? The biological machinery of copying DNA (polymerase) has an error rate of approximately 1 mistake per 10⁶ bases during replication when proofreading is active. (slide 8). This error is a variation based on the error rate, from 103 to 108. Compared to the length of the human genome, which is about 3.2 billion base pairs (≈3.2 × 10⁹ bp). This means that even with this high fidelity, thousands of errors could theoretically occur each time a genome is copied. (slide 10).
Week 3: Lab Automation Part 1: Phyton Code & Agar Design Documentation: For the first part of the Lab Automation assignment, I worked with Opentrons Python code using Google Colab. During this process, I used ChatGPT primarily as a debugging and learning aid. It helps me resolve execution errors, install missing packages (via pip), and understand how to structure the notebook so the design can be visualized correctly. Because the shared notebook relies on Opentrons hardware-specific functions (such as load_labware), the code was adapted to allow local visualization without a physical robot. My draft version originally included labware definitions intended for real laboratory execution, but these were temporarily removed to enable Plotly-based visualization. If you are interested in reading my code, please enter the following link: https://colab.research.google.com/drive/18Pb0JAgtB5Sv8v3VHhfop3mpF-nUiMp8?usp=drive_link The agar design was inspired by the ducks from Spirited Away (Studio Ghibli), based on my own drawing, combined with online references. The final pixel-art layout was generated using the Opentrons Art Generator and can be viewed here: https://opentrons-art.rcdonovan.com/?id=5s7w0mpt758a7af
Week 4 HW: Protein Design Part I
Week 4: Protein Design Part I Part A: Conceptual Questions Answering 9 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) What we know: a. Meat ~ 20% of protein
Week 5 HW: Protein Design Part II
Week 5: Protein Design Part II Part A: SOD1 Binder Peptide Design (From Pranam): What I know about SOD1 and its mutation: (Berdyński et al., 2022) Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS) ALS is a heterogeneous, severe neurodegenerative disorder, the hallmark of which is an adult-onset loss of upper and lower motor neurons. It leads to a progressive paresis and atrophy of skeletal muscles, resulting in quadriplegia and fatal respiratory failure. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation. Challenge of this week: Design short peptides that bind mutant SOD1 & then decide which ones are worth advancing toward therapy.
Week 6 HW: Genetic circuits part I
Genetic circuits part I: Assembly Technologies Note Part 1–> At Lab section: week 6 Part 2: Asimov Kernel Based on the exploration of the Bacterial Demos repository, genetic circuits were analyzed and simulated with the use of the Asimov Kernel platform.
week-07-hw-genetic-circuits-part-II
Week 7 Part 1: Intracellular Artificial Neural Networks 1. Advantages of IANNs vs traditional genetic circuits Traditional genetic circuits usually behave like Boolean logic systems (ON/OFF), meaning they respond in discrete states (e.g., gene expressed or not). In contrast, IANNs offer several key advantages:
Week 9: Cell-Free systems! Part A: General and Lecturer-Specific Questions General 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 (CFPS) offers important advantages over traditional in vivo expression because it provides a more open, flexible, and controllable reaction environment. Since there is no living cell to maintain, the researcher can directly adjust variables such as ionic strength, pH, redox conditions, DNA template concentration, cofactors, chaperones, detergents, lipids, or energy substrates without worrying about cell viability. CFPS is also typically faster, allowing protein production in hours rather than requiring cell growth, transformation, and induction steps over longer periods. In addition, it facilitates rapid prototyping of constructs and reaction conditions (Garenne et al., 2021; Jewett et al., 2008).
Week 10: Imaging and measurement
Week 10: Advanced Imaging & Measurement Technology Homework: Waters Part I — Molecular Weight Before calculation, I visited the webpage from Expasy https://web.expasy.org/compute_pi/ and copied the sequence I am working on: eGFP sequence: MVSKGEELFTG VVPILVELDG DVNGHKFSVS GEGEGDATYG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKQ HDFFKSAMPE GYVQERTIFF KDDGNYKTRA EVKFEGDTLV NRIELKGIDF KEDGNILGHK LEYNYNSHNV YIMADKQKNG IKVNFKIRHN IEDGSVQLAD HYQQNTPIGD GPVLLPDNHY LSTQSALSKD PNEKRDHMVL LEFVTAAGIT LGMDELYKLE HHHHHH Where it contains at the end His-purification tag with (HHHHH) and a linker (LE) previously.