Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Governance means different things to different people, but what truly matters to me is building systems that share power rather than seize it. I imagine resilient structures that adapt, nurture well-being in many forms, and thrive on transparency and shared commitment. First, describe a biological engineering application or tool you want to develop and why Plants can be reciprocal and help each other. For example, ectomycorrhizal (ECM) fungi, which form sheaths around roots, help restore soil and make plants more resilient, especially in the face of climate change. I want to create a system inspired by the ectomycorrhizal (ECM) fungi living model of resilience. By mimicking their metabolism and distribution, we could recover and manage resources more wisely, whether in organizations, food systems, or conservation efforts. Imagine a biological pump that naturally generates, transports, and processes information, strengthening our collective resilience.
Week 2 DNA Read, Write, & Edit
Here is the reference of the assignment: https://2026a.htgaa.org/2026a/course-pages/weeks/week-02/lab/index.html Basic Understanding DNA Gel, restriction enzymes, Benchling intro, Twist intro (▶️Recording | 💻Slides) easy content in Spanish: ¿Cómo hacer EDICIÓN GENÉTICA con CRISPR? https://www.youtube.com/watch?v=UaxrYWCyLdY&t=1s As a committed listener in distance, I can only make the benching : First step: https://www.benchling.com/, make an account. Second Step: choose a DNA sequence: https://www.neb.com/en-gb/tools-and-resources/interactive-tools/dna-sequences-and-maps-tool Begin by importing your DNA sequence and use the Digests tool to test the effects of different restriction enzyme(s). Export your final design as a png and compare with your lab results on your Notion page. See the images below for where to find the Digests tool, selecting the “NEB 2-log” ladder in the Virtual Digest tab, and how to have multiple Digests appear in the same Virtual Digest.
basic Concepts Your task this week is to Create a Python file to run on an Opentrons liquid handling robot. Review this week’s recitation and this week’s lab for details on the Opentrons and programming it. 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 using the Opentrons. I took the Elephant as a starting point for my art in OpenTrons. This was an experience we complemented by understanding th step by step how to set up the Opentrons machine
Basics Questions Amino Acids, Protein Structure, and β-Sheets 1. How many molecules of amino acids do you take with a piece of 500 grams of meat? It depends on the type and cut of meat, but a reasonable estimate is about 20–26 g of protein per 100 g of beef. Therefore, 500 g of meat would provide approximately 100–130 g of protein.
Still not really sure what I am doing :-)! Basics Design short peptides that bind mutant SOD1. “Design short peptides that bind mutant SOD1” means creating small, synthetic chains of amino acids (peptides) specifically engineered to attach to a deformed version of the Superoxide Dismutase 1 (SOD1) protein. This is a therapeutic strategy aimed at treating SOD1-related Amyotrophic Lateral Sclerosis (ALS). Mutant SOD1: A faulty version of the SOD1 enzyme produced due to genetic mutations. Unlike healthy SOD1, mutant SOD1 misfolds, becomes unstable, and aggregates (clumps together), leading to toxicity in motor neurons.
week 6 genetic circuits part I'
basic Concepts This week we learn core molecular biology tools and techniques for processing and assembling DNA, including PCR and Gibson Assembly.
- Components of Phusion High-Fidelity PCR Master Mix Phusion Master Mix contains several key components: Phusion Hot Start II DNA Polymerase — A high-fidelity polymerase with a proofreading (3’→5’ exonuclease) domain that corrects misincorporated bases, resulting in ~50× lower error rates than Taq. It also has a processivity-enhancing domain that speeds up elongation. dNTPs (dATP, dCTP, dGTP, dTTP) — The nucleotide building blocks incorporated during strand synthesis. MgCl₂ — Magnesium ions are an essential cofactor for DNA polymerase activity and also stabilize the dNTP substrates. Optimized reaction buffer — Maintains proper pH and ionic conditions for polymerase activity and primer/template annealing. Stabilizers/additives — Help maintain enzyme stability and can improve yield on difficult templates (e.g., GC-rich regions). 2. Factors Determining Primer Annealing Temperature Primer GC content — G·C pairs form 3 hydrogen bonds vs. 2 for A·T, so higher GC content raises the melting temperature (Tm). A rough formula is Tm = 4(G+C) + 2(A+T). Primer length — Longer primers have higher Tm values because more base-pair interactions must be disrupted. Salt/ion concentration — Higher Mg²⁺ or monovalent salt concentrations stabilize the DNA duplex and raise Tm. Primer secondary structure — Hairpins or self-dimers can reduce effective annealing efficiency. Template secondary structure — Highly structured templates may require higher annealing temperatures or additives like DMSO. Mismatches — Deliberate mismatches (e.g., for mutagenesis) lower Tm and require adjusted annealing temperatures. Annealing temperature rule of thumb — Typically set 5°C below the lower Tm of the two primers used. 3. PCR vs. Restriction Enzyme Digests Feature PCR Restriction Enzyme Digest Input template Any DNA (plasmid, genomic, cDNA) Usually plasmid or purified DNA Output Amplified, defined fragment Fragment(s) cut at specific recognition sites End type Blunt (Phusion) or 3’ A-overhang (Taq) Blunt or sticky (cohesive) ends depending on enzyme Precision Defined by primer design; any sequence Defined by restriction site locations in DNA Flexibility Very high — you design the fragment Limited to where restriction sites naturally exist Time ~1–3 hours ~1–2 hours Error risk Polymerase errors possible (mitigated by HiFi) No sequence errors; only wrong cut possible Requires sequence knowledge? Yes, for primer design Yes, to identify restriction sites When to prefer PCR You need to amplify a fragment from a complex mixture (e.g., genomic DNA). You want to add sequences (overhangs, restriction sites, Gibson overlaps) to the ends of a fragment. No convenient restriction sites flank your gene of interest. You are introducing a point mutation or modifying a sequence. When to prefer restriction enzyme digest You are sub-cloning between two vectors that already have compatible restriction sites. You need sticky ends for directional cloning. You want to cut a vector backbone without amplifying it (avoids PCR errors in the vector). Speed and simplicity are priorities when restriction sites are already present. 4. Ensuring Compatibility with Gibson Assembly Gibson Assembly requires fragments with overlapping homologous sequences (~15–30 bp) at their ends. To ensure compatibility:
week 7 genetic circuits part II
What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? IANNs have several advantages over traditional Boolean genetic circuits. First, they can process continuous and graded inputs rather than only treating signals as ON or OFF. This is important because many biological signals, such as metabolite concentrations, transcription factor levels, or signaling gradients, are not binary. Second, IANNs can perform weighted integration of multiple inputs. Instead of responding only when a rigid logical condition is met, they can combine signals with different strengths, similar to how neurons sum inputs.