Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Part I 1. First, describe a biological engineering application or tool you want to develop and why. I am interested in the development of engineered bee gut bacteria or similar that help bees resist viral infections, pesticide stress but especially harmful varroa mites. The presence of varroa mites in bee colonies place an important pressure on bee health since they attack and feed on them in a parasitism relationship. 1 Instead of genetically modifying bees themselves, I aim to modify their symbiotic bacteria to strengthen colony resilience while minimizing ecological risks. Bees are increasingly threatened by habitat loss, unsustainable agricultural practices, climate change and pollution. Their decline jeopardizes food production, increases costs and exacerbates food insecurity, particularly for rural communities. I am convinced that supporting pollinators will get more and more critical for global food systems and biodiversity and this approach could offer a scalable and ecologically sensitive alternative to chemical treatments currently used in agriculture. Even if it needs human intervention into nature to keep our ecosystem in balance, I think supporting these small often unnoticed pollinators could make a real difference.
Week 2 HW: DNA read/write/edit
Part I: Benchling & In-silico Gel Art Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. Part III: DNA Design Challenge 1. Choose your protein. Since my project proposal from last week focuses on honeybee health, I searched for relevant proteins in Apis mellifera. During this process, I identified three candidates that seemed particularly interesting: Defensin-1, Hymenoptaecin and Vitellogenin. Working with Twist Bioscience’s codon optimization tool, I learned that the tool only accepts sequences within a specific length range — proteins that are too short or too long cannot be optimized. After several iterations, vitellogenin was the only protein for which I could successfully perform codon optimization. Vg, a phospholipoglycoprotein synthesized and stored in the honey bee fat body, is an ancient reproduction-associated protein that provides nutrients to eggs in most oviparous animals. Honey bee queens, who produce hundreds of eggs each day, have high levels of Vg gene expression. It is involved in nutrient storage, immune regulation and longevity in honeybees. Its expression is closely linked to colony health and higher vitellogenin levels are associated with improved immune responses and tolerance to Varroa destructor infestation. 1
Part I: Python Script for Opentrons Artwork Your task this week is to Create a Python file to run on an Opentrons liquid handling robot. Firstly, I used Ronan’s Automation Art Interface to translate my logo into a pixelated biological artwork. The software converted the image into a set of coordinate outputs, where each tuple (x, y) represents the precise millimeter offset from the calibrated center of the agar plate. Each of these coordinate pairs defines the placement of a single 1 µL droplet, allowing the robot to reconstruct the digital logo physically on the plate.
Week 4 HW: Protein Design Part I
Part I: 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) $1 Dalton = 1 g/mol$ The protein content of meat is about 20%.1 That means 500g of meat contain 100g protein. $100g/100g/mol=1mol$ $1mol = Avogadro_constant = 6*10^{23}$
Week 5 HW: protein design part ii
Part A: SOD1 Binder Peptide Design Part I: Generate Binders with PepMLM 1. Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ A4V Mutation -> means one needs to change the A at position 4 to an V. This protein sequence only had one at the fifth position so I changed this Alanine.
Week 6 HW: Genetic Circuits Part I
DNA Assembly Answer these questions about the protocol in this week’s lab: What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Typical components include: Phusion DNA Polymerase A high-fidelity enzyme that synthesizes new DNA strands with very low error rates (proofreading activity → fewer mutations). dNTPs (deoxynucleotide triphosphates) Building blocks (A, T, G, C) used to create new DNA strands. Reaction Buffer (HF buffer) Maintains optimal pH and salt conditions for enzyme activity and fidelity. Mg²⁺ ions (magnesium chloride) Essential cofactor for polymerase activity; affects enzyme efficiency and specificity. Stabilizers (sometimes included) Help maintain enzyme stability during thermal cycling. What are some factors that determine primer annealing temperature during PCR?
Week 7 HW: Genetic Circuits Part II
Part I: Intracellular Artificial Neural Networks (IANNs) 1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Continuous Signal Processing Boolean circuits output only 0 or 1 (OFF/ON) states. IANNs operate on continuous, graded gene expression levels. Ability to Model Complex Relationships Boolean logic is limited to simple combinations of AND/OR/NOT gates. IANNs can approximate complex, nonlinear input–output functions. Efficient Integration of Multiple Inputs
Part A: General and Lecturer-Specific Questions General 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.
Week 10 HW: Imaging and Measurement
Part I: Final Project For your 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. Quantification of pigment concentration through color intensity measurements Analysis of pigment degradation (as a proxy for biochemical stability) under environmental conditions Material–pigment interaction effects on color retention 2. Please describe all of the elements you would like to measure, and furthermore describe how you will perform these measurements.
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Somehow I didn’t receive an email, so I couldn’t contribute. Part B: Cell-Free Protein Synthesis | Cell-Free Reagents 1. Referencing the cell-free protein synthesis reaction composition (the middle box outlined in yellow on the image above, also listed below), provide a 1-2 sentence description of what each component’s role is in the cell-free reaction.