Labs
Lab writeups:
Pipetting Basics 🧪 First time in a wet lab very exciting! I learned about the different pipette ranges: P20 1–20 µL, P200 20–200 µL, P1000 100–1000 µL and when to use each one appropriately. I also practiced proper pipetting technique holding the pipette vertically identifying the first and second stops when pressing the plunger and carefully controlling the release to ensure accurate and precise liquid handling.
Week 2 Lab: DNA Read Write Edit
Lab Overview 🧬 Restriction enzymes ✂️ In Lab 2 I learned how restriction enzymes can be used to cut DNA at very specific sequences, almost like precise molecular scissors. These enzymes recognize short DNA sequences called restriction sites and cleave the DNA at or near those locations, allowing us to deliberately fragment genetic material in a controlled way.
Opentrons 🧫 In Lab 3 I learnt about Opentrons and how lab automation can turn biology into something creative and visual. We used the Opentrons OT-2 pipetting robot to precisely deposit genetically engineered E. coli onto black charcoal agar plates. These bacteria were engineered to express fluorescent proteins in different colors, so when the plates were placed under UV light, the patterns we programmed glowed brightly.
Refer to week 4’s homework section for this weeks lab :)
Refer to week 5’s homework section for this weeks lab :)
Week 6 Lab: PCR & Gibson Assembly
🧬 PCR and Gibson Assembly Workflow In this two-day lab, we used PCR and Gibson Assembly to engineer mutations in the chromophore region of the purple Acropora millepora chromoprotein (amilCP) in order to generate a range of orange, pink, and blue colour variants. Two separate PCR reactions were performed to generate the DNA fragments required for Gibson Assembly. The insert PCR region extended from 24 base pairs upstream of the chromophore to just beyond the transcription terminator of the gene. The forward primer was specifically designed with an intentional mismatch to introduce a site-directed mutation into the mUAV plasmid DNA. After assembly, the mutated plasmids were transformed into chemically competent E. coli cells for expression and analysis of the resulting colour phenotypes.
Week 7: Neuromorphic Circuits and Mycelium
🧠 Neuromorphic Circuits This two-day lab became a major source of inspiration for my final project! Using a library of plasmids from the Ron Weiss Lab and HEK293 cells, we designed and built an intracellular artificial neural network (IANN). Unlike traditional synthetic genetic circuits that are largely limited to digital logic, IANNs can perform analog computation and act as universal function approximators, meaning that with enough intracellular artificial neurons they can generate highly complex and tunable cellular responses.
Week 9 Lab: Protein Purification
This lab introduced the fundamentals of protein extraction and purification workflows commonly used in synthetic biology and bioengineering. It was particularly valuable for my final project, since our system required growing and extracting GFP protein before conjugating it to magnetic microparticles. It was also useful to understand how magnetic separation and purification methods can be integrated into biological systems, as my project similarly uses magnets both to purify ligand-conjugated particles and to actively control their interactions with cells. To isolate our protein of interest, we first grew the cells and then lysed them using a combination of B-PER (Bacterial Protein Extraction Reagent) and sonication, producing a lysate solution containing the total protein content of the cells.
Week 10 Lab: Mass Spectrometry
This week we did a lab at Waters Corp on Liquid Chromatography Mass Spectrometry, one of the core technologies used for modern protein characterization. Their lab was so cool!! Using enhanced Green Fluorescent Protein (eGFP) as the model system, the lab showed how proteins can be analyzed at multiple levels ranging from overall molecular weight and folding state to their exact amino acid sequence. I found it especially interesting because the workflow progressively “breaks down” the protein from an intact structure into smaller peptide fragments, revealing different layers of biological information at each stage. We also briefly explored Charge Detection Mass Spectrometry (CDMS), which can analyze extremely large biological complexes that are too massive for conventional mass spectrometry techniques.