Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
First, describe a biological engineering application or tool you want to develop and why Pattern-Based Rapid Diagnostic Platform for Dengue Virus: A rapid diagnostic platform for dengue virus (DENV) that integrates innate immune recognition, molecular recognition, and biosensor engineering to address key limitations of existing diagnostic methods. The proposed system combines mannose-binding lectin for the recognition of viral glycoproteins, dengue-specific aptamers targeting conserved regions of viral proteins, and signal transduction through a portable biosensor to enable rapid readout. This approach is motivated by the fact that current dengue diagnostics are often expensive and exhibit reduced sensitivity and reliability in dengue-endemic regions, particularly in countries like mine (Colombia), where prior flavivirus exposure compromises serological test performance and access to reliable diagnostics is limited by public healthcare infrastructure (Terenteva et al., 2025).
Week 10: Advanced Imaging & Measurement Technology
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. Expression of the Reporter Gene LacZ Please describe all of the elements you would like to measure, and furthermore describe how you will perform these measurements β-galactosidase hydrolyzes chromogenic substrates, producing a colored product that can be visually detected or quantified spectrophotometrically. LacZ will be measured using a colorimetric assay with ONPG, enabling both spectrophotometric quantification and visual detection
Week 11 — Bioproduction & Cloud Labs
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Make a note on your HTGAA webpages including: What you contributed to the community bioart project I made part of the 2026 on the upper left plate What you liked about the project, and what about this collaborative art experiment could be made better for next year.
Week 2 HW: DNA Read, Write and Edit
Part 1: Benchling & In-silico Gel Art Part 3: DNA Design Challenge Protein: mannose-binding protein C precursor Reverse Translate: Aminoacids mslfpslpll llsmvaasys etvtcedaqk tcpaviacss pgingfpgkd grdgtkgekg epgqglrglq gppgklgppg npgpsgspgp kgqkgdpgks pdgdsslaas erkalqtema rikkwltfsl gkqvgnkffl tngeimtfek vkalcvkfqa svatprnaae ngaiqnlike eaflgitdek tegqfvdltg nrltytnwne gepnnagsde dcvlllkngq wndvpcstsh lavcefpi Nucleotid sequence atgagcctgtttccgagcctgccgctgctgctgctgagcatggtggcggcgagctatagc gaaaccgtgacctgcgaagatgcgcagaaaacctgcccggcggtgattgcgtgcagcagc ccgggcattaacggctttccgggcaaagatggccgcgatggcaccaaaggcgaaaaaggc gaaccgggccagggcctgcgcggcctgcagggcccgccgggcaaactgggcccgccgggc aacccgggcccgagcggcagcccgggcccgaaaggccagaaaggcgatccgggcaaaagc ccggatggcgatagcagcctggcggcgagcgaacgcaaagcgctgcagaccgaaatggcg cgcattaaaaaatggctgacctttagcctgggcaaacaggtgggcaacaaattttttctg accaacggcgaaattatgacctttgaaaaagtgaaagcgctgtgcgtgaaatttcaggcg agcgtggcgaccccgcgcaacgcggcggaaaacggcgcgattcagaacctgattaaagaa gaagcgtttctgggcattaccgatgaaaaaaccgaaggccagtttgtggatctgaccggc aaccgcctgacctataccaactggaacgaaggcgaaccgaacaacgcgggcagcgatgaa gattgcgtgctgctgctgaaaaacggccagtggaacgatgtgccgtgcagcaccagccat ctggcggtgtgcgaatttccgatt Codon optimization: ATG AGC CTT TTT CCG AGC CTT CCT CTG CTT TTA CTG TCG ATG GTG GCC GCC AGC TAC AGT GAA ACT GTG ACC TGT GAG GAC GCC CAA AAA ACG TGT CCT GCA GTT ATC GCG TGC AGC TCC CCG GGT ATC AAT GGC TTC CCC GGC AAG GAC GGG CGT GAT GGG ACT AAA GGC GAG AAA GGT GAA CCG GGA CAG GGC TTA CGT GGT TTA CAG GGC CCG CCG GGT AAA TTG GGG CCG CCA GGC AAT CCG GGT CCG AGT GGC TCC CCA GGG CCG AAA GGT CAG AAA GGC GAT CCA GGC AAA AGT CCG GAT GGT GAT TCA AGT CTG GCG GCC AGC GAA CGT AAG GCC CTT CAG ACC GAA ATG GCT CGT ATC AAA AAA TGG TTA ACG TTC AGC CTG GGG AAA CAA GTG GGG AAT AAG TTT TTT CTG ACT AAT GGC GAG ATC ATG ACG TTT GAG AAA GTG AAA GCG CTG TGT GTG AAG TTC CAG GCC AGC GTG GCG ACG CCA CGT AAC GCG GCG GAA AAT GGC GCG ATT CAA AAC CTT ATC AAA GAA GAG GCC TTC CTG GGT ATT ACG GAC GAA AAA ACG GAG GGC CAG TTT GTC GAT CTG ACT GGT AAC CGC TTA ACA TAT ACC AAT TGG AAT GAG GGC GAA CCT AAC AAC GCA GGC AGC GAT GAG GAC TGC GTG CTG TTA TTG AAA AAC GGC CAG TGG AAC GAC GTA CCT TGT TCC ACT AGC CAT TTA GCG GTA TGC GAA TTT CCG ATT
Opentrons Artwork opentrons-art.rcdonovan.com/?id=oevp91e27i3m061 Post-Lab Questions Find and describe a published paper that utilizes the Opentrons This article combines an open‑source liquid‑handling robot (Opentrons OT‑One‑S Hood) with four interchangeable modules that perform magnetic‑bead DNA isolation, isothermal recombinase polymerase amplification (RPA) of the ctrA gene, exonuclease digestion to generate single‑stranded DNA, and detection on a paper‑based vertical‑flow microarray (VFM) using anti‑biotin gold nanoparticles for colorimetric read‑out.
Part A. Conceptual 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) Considering that 500 g of meat contains 20% protein, we would have 100 g of protein. After converting the protein mass to moles (assuming an average amino acid mass of 100 Da), this corresponds to approximately 6.022 × 10²³ amino acid molecules.
Week 5 HW: Genetic circuits part 1
Assignment: DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion High-Fidelity DNA polymerase: enzyme responsible for synthesizing new DNA strands while possessing activity, which reduces errors during replication. dNTPs (deoxynucleotide triphosphates): Nucleotide substrates incorporated by DNA polymerase into the elongating DNA strand during synthesis reaction buffer: contain compounds as Tris-HCl that maintains the correct pH and salts like KCl which help stabilize primer binding and enzyme activity
Week 5 HW: Protein design part 2
Part A: SOD1 Binder Peptide Design Part 1: Generate Binders with PepMLM After introducing the A4V mutation. I performed the mutation A5V based on its position in the FASTA sequence. MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Using PepMLM Colab with a K value of 1, I obtained:
Week 7: Genetic Circuits Part II: Neuromorphic Circuits
Assignment Part 1: Intracellular Artificial Neural Networks What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Instead of relying on ON/OFF logic, they process information in a continuous and distributed way, closer to how real cells behave. This allows them to integrate multiple signals with different intensities and avoid the exponential complexity that arises when scaling Boolean circuits. In addition, IANNs are inherently more flexible, since their behavior can be tuned by adjusting interaction strengths rather than completely redesigning the system, enabling more complex and nonlinear decision-making. Overall, they provide a more efficient, scalable, and biologically realistic framework for intracellular computation.
Assignment Part A: General and Lecturer-Specific 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. You can control everything directly. You can adjust pH, temperature, ion concentrations, and cofactors and even add or remove components during the reaction. Also, it’s faster since you don’t need cell growth or maintenance.