Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    Application Idea: The development of an engineered bacterial biosensor for real-time hydration detection as a preventive health measure in aging populations. An engineered skin bacterium, applied as a lotion on the wrist or forearm, could detect body hydration levels and generate an electric current detectable by an electronic wearable component. Why develop this application? Water is vital for health, and yet, neglecting hydration is common. The elderly are particularly vulnerable. Dehydration perturbs the gastrointestinal (GI) tract, leading to difficulty passing stool and overall adverse effects on GI health.

  • Week 2 HW: DNA, Read, Write and Edit

    PART 1 Benchling & In-silico Gel Art Make a free account at benchlig.com Import the Lambda DNA Genome sequence of the lambda phage at the NCBI database.

  • Week 3 HW: Lab Automation

    1. Create a Python file Generate an artistic design using the GUI at opentrons-art.rcdonovan.com Using the coordinates from the GUI, follow the instructions in the HTGAA26 Opentrons CoLab to write your own Python script that draws your design. To become familiar with the Python Opentrons API, I adopted a dot array script from the example scripts and reproduced it with changes to create different patterns of assorted dot arrays.

  • Week 4 HW: Protein Design Part I

    Part A. Conceptual Questions Answer any NINE of the following 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) Based on Gemini AI: 100 Dalton = 1.66054e-22 gram

  • Week 5 HW: Protein Design Part II

    Part A: SOD1 Binder Peptide Design Superoxide dismutase 1 (SOD1) is a cytosolic enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. In its native state, it forms a stable homodimer and binds copper and zinc. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Ala to Val at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation.

  • Week 6 HW: Genetic Circuits Part I

    Assignment: DNA Assembly Answer the following questions about the protocol in:

  1. What are some components in the Phusion High-Fidelity PCR Master Mix, and what is their purpose? Below are the components found in the New England Biolab’s Phusion HF PCR Master Mix: •Phusion DNA Polymerase: It performs 5’ → 3’ polymerase activity and 5’ → 3’exonuclease (proofreading) activity with greater fidelity, >50x better in comparison to regular Taq polymerase. Because it is a fusion polymerase with an Sso7d domain, it adds nucleotides more quickly, reducing the required extension time. Due to the exonuclease activity. Phusion polymerase produces blunt ends.

  • Week 7 HW: Genetic Circuits Part II

    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? A Boolean function is based on a binary system where it can only assign two values, such as "true" or "false", or as in numeric values: "0" or "1". This is akin to digital systems. Complexities in the biological systems cannot be adequately represented by binary input/output. Because signals in biological systems, such as concentrations of regulatory proteins, vary in gradation. So, a Boolean genetic circuit would have limitations in interpreting the complexities of a biological system. IANNs are based on analog systems where weights are implemented. Examples of weights include variable concentrations of regulatory proteins, promoter strengths, and RBS efficiencies. These make positive or negative regulatory output. IANNs also integrate dose-response analysis, from inhibitory to non-inhibitory concentrations of a typical sigmoidal curve. IANNs consider biases such as taking into account whether promoters could be leaky. Advantageous parts are the ability to handle a great level of complexity due to the gradation that living systems have. 2. Describe a useful application for an IANN; include a detailed description of input/output behavior, as well as any limitations an IANN might face to achieve your goal.

  • Week 9 HW: Cell-Free-Systems

    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.

  • Week 10 HW: Imaging and Measurement

    Homework: Final Project Please identify at least one (ideally many) aspect(s) of your project that you will measure. It could be the mass or sequence of a protein, the presence, absence, or quantity of a biomarker, etc. My final project focuses on the development of a biosensor based on a capture nanobody and reporter DNA aptamer, enabling the detection of a protein biomarker for the body’s iron status.

  • Week 11 HW: Bioproduction & Cloud Lab

    Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Contribute at least one pixel to this global artwork experiment before the editing ends on Sunday 4/19 at 11:59 PM EST. A personalized URL was sent to the email address associated with your Discourse account, and you can discuss the artwork on the Discourse. If you did not have a chance to contribute, it’s okay, just make sure you become a TA this fall! 😉