Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Describe a biological engineering application or tool you want to develop and why. One application that might be worth exploring would be in the realm of data storage for an imagined, hypothetical semi-exposed media. For this context special proteins could be designed in applications that bind to sequences that code for hidden malware or faulty sequences and or act for preserving media. I imagine that both this media design and this protein use would be niche but nonetheless fun to design for. Modalities could be as a gentle spray or as a settled solution that could be extracted.
Week 2 HW: DNA Read, Write, and Edit
Part 0: Basics of Gel Electrophoresis [This was a pure watch session. Thus there’s nothing to add here.] Part 1: Benchling & In-silico Gel Art Restriction Enzymes Simulated on Lambda_NEB: EcoRI, HindIII, BamHI, KpnI, EcoRV, SacI, and SalI Simple Art produced by way of Paul Vanouse’s Latent Figure Protocol artworks through the use of RC Donovan’s Gel Art Iteration Tool (https://rcdonovan.com/gel-art): “4 corners”, using EcoRI and SalI in Lanes 1 and 10.
Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. DeRoo, J.B., Jones, A.A., Slaughter, C.K., Ahr, T.W., Stroup, S.M., Thompson, G.B. and Snow, C.D., 2025. Automation of protein crystallization scaleup via Opentrons-2 liquid handling. SLAS technology, 32, p.100268. https://doi.org/10.1016/j.slast.2025.100268 This work describes an approach by which an Opentrons-2 liquid handling robot was used for automating sitting drop protein crystallization trials. This ability also improve comparability of products produced, improving studies that depend on their proper manufacture. An important detail is how the Opentrons-2 can prove a cost-effective option for laboratory operations. For example, at the time of writing, the Opentrons-2 can be purchased for around 13.5K USD vs that of a Gryphon machine at around 65K USD.
Week 4 HW: Protein Design Part I
Part A: Conceptual Questions We were allowed answer 9 out of 11 of the following 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) I expect answers to vary since meat composition vary. Water composition of meat is estimated to be about 65-80% meat. Some estimates have proteins make up around 1/5 to less than 1/3 of overall muscle tissue.
Week 5 HW: Protein Design Part II
This week’s homework was divided into 3 parts. Part A involved SOD1 Binder Peptide Design. That was broken into 3 parts: Part 1: Part 1: Generate Binders with PepMLM A) Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. Done B) Using the PepMLM Colab linked from the HuggingFace PepMLM-650M model card: Done C) Generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
Part 1: DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Some of the components include the Phusion DNA Polymerease (key to PCR), dNTPs (these are used to synthesize new DNA), and buffering materials to stabilize the environmental conditions during the raction. What are some factors that determine primer annealing temperature during PCR? Some of these include buffer conditions, primer melting temperature, primer length, and GC content.
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
Part 1: What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? IANNs are great for analog computation, while also being scalable in deployment and useful for approximating functions. 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. Disease diagnostics. Inputs would be expressions levels of biomarkers and signals deemed harmful. Outputs could be in the form of a gene with a strong signal or that is therapetic in nature. Strong limitations could come from unintended interactions with the output, as well as cross-talk generated. Noise within the biological system could affected outputs as well.
Week 9 HW: Week 9 — Cell-Free Systems
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. To Be Added Describe the main components of a cell-free expression system and explain the role of each component. To Be Added Why is energy provision regeneration critical in cell-free systems? Describe a method you could use to ensure continuous ATP supply in your cell-free experiment.
Week 10 HW: Week 10 — Advanced Imaging & Measurement Technology
Homework: Final Project (Measurement Draft) The main aspect of my project that I will measure is the functional activity of a mutated InaZ construct, specifically whether it increases ice nucleation efficiency relative to a control InaZ construct. I will perform this measurement using a controlled freezing assay in which replicate samples are cooled gradually and monitored for the onset of ice formation. The primary data collected will be the temperature at which freezing begins in each sample. Ice formation will be detected through optical observation of crystal formation and through temperature sensors that record the freezing point. In addition, I would verify the identity of the mutated construct using PCR, gel electrophoresis, and DNA sequencing. PCR and gel electrophoresis would be used to confirm the presence and approximate size of the inserted DNA, while DNA sequencing would confirm that the engineered inaZ mutation is correct. Together, these measurements allow me to confirm both that the construct was built properly and that it produces the intended increase in ice nucleation activity.
Week 11 HW: Bioproduction & Cloud Labs
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! 😉