Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- First, describe a biological engineering application or tool you want to develop and why. Paratransgenic symbiont to block dengue transmission in Aedes aegypti Mosquito-borne dengue is a global threat, yet current control measures have a vector elimination focus increasingly undermined by insecticide resistance. Vaccines have shown limited efficacy, and with no broadly effective antivirals, dengue prevention still relies heavily on mosquito and larvae control (Hu et al., 2025). Considering this, researchers are leveraging synthetic biology to develop paratransgenic strategies that render A. aegypti mosquitoes refractory to infection by delivering anti-pathogen molecules inside the mosquito, thereby blocking virus replication and transmission (Gao et al., 2025). The biological engineering tool proposed is a synthetic paratransgenic bacterial symbiont designed to live in the gut of A. aegypti mosquitoes and actively block dengue virus transmission. The purpose is to use a naturally mosquito-associated bacterium (such as Asaia spp.) genetically engineered to sense mosquito feeding conditions and secrete antiviral effector molecules directly into the midgut lumen. The gut of A. aegypti offers a strategic intervention point. Dengue virus first encounters the midgut epithelium after a blood meal, and if viral entry is blocked at this stage, systemic infection of the mosquito can be prevented by secretion of viral entry inhibitors, such as peptides. It is an ecologically targeted solution, because it doesn’t intend to eradicate the mosquito populations from their ecosystems, as every part of the trophic network needs to stay in balance.
Week 10 — Advanced Imaging & Measurement Technology
Final Project For this project, several elements will be measured across the experimental, computational, and synthetic biology stages in order to evaluate the performance of the proposed platform. Because the project is structured as a pipeline, the measurable outputs include nucleic acid quality, sequence-derived features, predicted protein properties, and candidate prioritization metrics.
- Metagenomic DNA quality and quantity
Week 11 — Bioproduction & Cloud Labs
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork what you contributed to the community bioart project I tried to transform a hexagon into a bacteriophage by adding some details in the exterior area. I think they were restored to the original picture before deadline what you liked about the project I was reminded of another collaborative project that was funny what about this collaborative art experiment could be made better for next year. Maybe a bigger canvas Part B: Cell-Free Protein Synthesis | Cell-Free Reagents 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 components role is in the cell-free reaction. BL21 (DE3) Star Lysate (includes T7 RNA Polymerase):
Week 2 HW: DNA Read, Write and Edit
Part 1: Benchling & In-silico Gel Art Preliminary notebook sketches illustrating the conceptual design process for the intended latent figure.
Week 2 LP: DNA Read, Write and Edit
In preparation for Week 2’s lecture on “DNA Read, Write, and Edit" answer the following questions in each faculty member’s section Homework Questions from Professor Jacobson
Opentron Art Post-Lab Questions Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. Summary This study introduces Pyhamilton, an open-source Python framework that enables flexible programming of liquid-handling robots for high-throughput biological experimentation. Unlike traditional robotic automation, which merely replicates hand-pipetting protocols, Pyhamilton allows for dynamic decision-making, asynchronous execution, and real-time feedback integration.
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: 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) Why do humans eat beef but do not become a cow, eat fish but do not become fish? Why are there only 20 natural amino acids? Can you make other non-natural amino acids? Design some new amino acids. Where did amino acids come from before enzymes that make them, and before life started? If you make an a-helix using D-amino acids, what handedness (right or left) would you expect? Can you discover additional helices in proteins? Why are most molecular helices right-handed? Why do β-sheets tend to aggregate? What is the driving force for β-sheet aggregation? ANSWERS Question 1 As known, amino acids are the building blocks of proteins. However, meat is not composed entirely of protein; its composition varies depending on the animal and the specific cut. If we consider beef, which contains approximately 23% protein by weight, then in a 500 g portion there would be about 115 g of protein. It is stated that an average amino acid has a molecular weight of approximately 100 Daltons, and since 1 Dalton corresponds to 1 g/mol, this means an average amino acid has a molar mass of roughly 100 g/mol. For an estimate, we divide the total grams of protein by this average molar mass:
Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design Peptide Perplexity ipTM score N terminus B-barrel Dimer interface WRYPAAAAALKX 4.30808 0.3 Close No Surface bound WRYGATVAAHKX 5.811953 0.48 Far No Partially buried WLSGAAALALKX 5.716131 0.45 Close No Surface bound WLYPAAALALKX 8.30171 0.36 Far No Partially buried FLYRWLPSRRGG 0.38 Far No Surface bound The predicted protein–peptide complexes produced relatively low ipTM scores overall, indicating weak confidence in the modeled interactions. The PepMLM-generated peptides showed ipTM values ranging from 0.30 to 0.48. The highest score was observed for the peptide WRYGATVAAHKX (ipTM = 0.48), followed by WLSGAAALALKX (ipTM = 0.45), both of which exceeded the ipTM score of the known SOD1-binding peptide FLYRWLPSRRGG (ipTM = 0.38). Despite these slightly higher scores, none of the predicted peptides appeared to strongly interact with the β-barrel region of SOD1, and most were either surface-bound or only partially buried on the protein surface. Overall, while some PepMLM-generated peptides showed marginally higher ipTM scores than the known binder, the predicted interactions remain weak and uncertain.
Week 6 — Genetic Circuits Part I: Assembly Technologies
What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion High-Fidelity DNA Polymerase A proofreading polymerase with 3′→5′ exonuclease activity, which ensures very low error rates during DNA synthesis. Phusion HF or GC Buffer Provides optimal ionic conditions (Mg²⁺, salts, pH). HF buffer: for standard templates GC buffer: improves amplification of GC-rich or difficult templates dNTPs (400 µM each) Building blocks (dATP, dTTP, dCTP, dGTP) required for DNA strand synthesis. Mg²⁺ (within the buffer) Essential cofactor for polymerase activity and influences enzyme fidelity and efficiency. What are some factors that determine primer annealing temperature during PCR? The annealing temperature in PCR is determined by several factors: Primer melting temperature (Tm) Calculated based on primer sequence (GC content, length). Annealing temperature is typically ~3–5°C below Tm Primer length Longer primers = higher Tm GC content Higher GC = stronger binding = higher annealing temperature Primer sequence composition Secondary structures (hairpins, dimers) affect binding Salt concentration Higher salt stabilizes primer-template binding Polymerase type Some enzymes (like Phusion) require higher annealing temperatures due to their buffer system There are two methods from this class that create linear fragments of DNA: PCR, and restriction enzyme digests. Compare and contrast these two methods, both in terms of protocol as well as when one may be preferable to use over the other. PCR Restriction Enzyme Digests Starting materials Template DNA and primers DNA with restriction sites Key reagents Polymerase, primers and dNTPs Restriction enzyme and buffer Mechanism DNA amplification DNA cutting Temperature profile Multiple cycles Single temperature Control of fragment Defined by primer Defined by enzyme sites Output Many copies of a single fragment Multiple fragments Critical design step Primer design Enzyme selection Time 1 to 3 hours Roughly 1 hour Flexibility High Limited by sequence PCR is generally preferable when you need to generate a specific DNA fragment with precise boundaries or added sequences, such as overlaps for Gibson Assembly, because it allows high flexibility through primer design and can amplify even very small amounts of DNA. In contrast, restriction enzyme digestion is preferable when the DNA already contains suitable restriction sites, making it a simpler and faster method for cutting plasmids or generating fragments without the need for amplification. Therefore, PCR is favored for custom design and low DNA availability, while restriction digestion is best for routine cloning tasks where appropriate sites are already present.
Week 7 — Genetic Circuits Part II: Neuromorphic Circuits
What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? IANNs provide graded and analog computation rather than a strict ON/OFF logic. Enabling cells to integrate multiple inputs with tunable weights and produce continuous outputs that reflect the signal strength, not just presence/absence. IANNs can implement thresholding, nonlinear decision boundaries, and noise tolerance, making them more robust in heterogeneous biological environments. They also allow combinatorial regulation, which is difficult to achieve with simple Boolean gates without increasing the circuit complexity.
Homework Part A: General and Lecturer-Specific Questions 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 offers greater flexibility and control compared to in vivo systems because it allows precise manipulation of reaction conditions such as component concentrations, temperature, and reaction time. Additionally, it eliminates cellular interference, such as metabolic regulation, toxicity effects, and competing pathways, enabling more efficient and tunable protein production. One case where cell-free expression is advantageous is in the production of toxic proteins, such as toxins or antimicrobial peptides, which would otherwise damage or kill the host cell. Another case is the synthesis of proteins requiring non-natural amino acids or specialized conditions, which are difficult to achieve in living cells due to their tightly regulated environment.