Labs
Lab writeups:
Note: This document is a theoretical completion of the lab assignment. I did not perform the experiments in person or virtually. The answers below are based on pre‑lab reading, known formulas, and expected outcomes – provided solely to have the assignment completed. Overview & Objective This lab introduces foundational techniques of pipetting and serial dilutions. By the end, students should be able to use P20, P200, and P1000 pipettes accurately, perform dilutions, and prepare solutions with desired concentrations. The lab includes colour mixing (Part 1) and a serial dilution to obtain 100 µM of a mystery substance (MS) followed by a final reaction mix (Part 2).
Note on completion status: The virtual part (Benchling design, virtual digest, gel art simulation) was completed as an assignment. The wet lab part (restriction digest setup, gel casting, electrophoresis, imaging) is theoretical – not performed in person or virtually. The answers below are based on pre‑lab reading, known protocols, and expected outcomes, provided to have a complete reference. Overview & Objective This 3‑hour lab introduces DNA gel electrophoresis and restriction enzyme‑based DNA manipulation, with an artistic outcome inspired by Paul Vanouse’s Latent Figure Protocol. Skills gained include using Benchling, setting up restriction digests, preparing agarose gels, running electrophoresis, and imaging results. Gel electrophoresis is a fundamental molecular biology tool for verifying DNA fragment sizes.
Completion status: This lab was completed virtually (coding, simulation, and design). The physical wet lab (running the robot with real bacteria and plates) was not performed. The virtual design originally planned more colors, but only two fluorescent bacterial strains (two colors) were available, so the pattern was simplified accordingly. The final simulated result image is shown below. Overview & Objective In this two‑day lab, we program the Opentrons OT‑2 pipetting robot to deposit genetically engineered E. coli (expressing fluorescent proteins) onto black charcoal agar plates, creating glowing bio‑art. The lab combines synthetic biology, automation, and art. Skills gained: writing Opentrons Python protocols, simulating robot moves, and understanding fluorescent proteins (GFP, RFP, etc.).
Lab (Week 4) — Protein Design Part I
This week’s Lab work is effectively part of this week’s Homework; see that assignment and document your work there.
Lab (Week 5) — Protein Design Part II
This week’s Lab work is effectively part of this week’s Homework; see that assignment and document your work there.
Lab (Week 6) — Gibson Assembly
Completion status: This lab was completed virtually (in silico primer design, virtual PCR, Gibson assembly simulation, and sequence analysis). The physical wet lab (PCR thermocycling, DpnI digest, DNA purification, Gibson assembly, transformation of E. coli, and plate incubation) was not performed. All results below are theoretical, based on the published paper (Liljeruhm et al., 2018) and the provided protocol. Overview & Objective In this two‑day lab, we change the chromophore of the purple Acropora millepora chromoprotein (amilCP) to orange, pink, and blue mutants by PCR‑based mutagenesis and Gibson assembly. The amilCP gene is carried on the mUAV plasmid (Addgene). We amplify two fragments – a backbone (origin, chloramphenicol resistance, promoter, RBS) and an insert (chromophore region + terminator) – with overlapping ends. The insert forward primer contains the desired mutation(s). After DpnI digestion (to remove template plasmid), we purify the fragments, assemble them via Gibson, and transform into chemically competent E. coli. Only cells with the correctly assembled plasmid survive on chloramphenicol and express coloured chromoproteins.
Lab (Week 7) — Neuromorphic Circuits
Completion status: This lab was completed virtually (circuit design using the Google Sheet template, in silico simulation of OT‑2 instructions). The wet lab component (OT‑2 building of plasmids, transfection into HEK293 cells, and observation of results) was not performed – neither in person nor virtually. The following report describes the designed artificial neural network circuit and the theoretical steps. Pre‑Lab Overview We familiarize ourselves with two key concepts:
Lab (Week 9) — Cell-Free Systems
Completion status: This lab was completed theoretically (no physical or virtual wet lab performed). All procedures, results, and analyses below are based on the provided protocol and scientific literature. The homework questions are answered in full. Overview & Objective In this lab, we demonstrate the functionality of a Cell-Free Transcription-Translation (TXTL) system using an E. coli extract. We express the reporter protein amilGFP from a T7-IPTG‑inducible plasmid. IPTG acts as an inducer by inhibiting the LacI repressor, allowing T7 RNA polymerase to transcribe the gene. The goal is to quantify amilGFP production at different IPTG concentrations over an 8‑hour incubation at 30°C, using fluorescence measurement (ex 492 nm / em 506 nm) either in a plate reader or via end‑point imaging.
Lab (Week 10) — Mass Spectrometry
Completion status: This lab was completed theoretically (no physical or virtual wet lab performed). All procedures, data, and analyses below are based on the provided protocol, the figures in the Appendix, and standard LC-MS principles. The report follows the logical progression from intact mass determination to native/denatured comparison, peptide mapping, and CDMS analysis of megadalton complexes. Introduction and Background Modern bioengineering relies on precise protein characterization. Liquid chromatography–mass spectrometry (LC-MS) provides three critical pieces of information: molecular weight, amino acid sequence, and protein folding/structure. This lab introduces LC-MS using enhanced Green Fluorescent Protein (eGFP) and Keyhole Limpet Hemocyanin (KLH). The workflow proceeds from intact protein analysis (denaturing and native conditions) to bottom‑up peptide mapping, and finally to charge detection mass spectrometry (CDMS) for megadalton complexes.
Lab (Week 11) — Introduction to Cloud Laboratories
Completion status: This lab was completed virtually (contributed to the global pixel artwork, designed master mix compositions theoretically). The physical cloud lab experiment (cell-free protein synthesis with custom reagent supplements) was not performed – results pending future data return. All answers below are based on the provided protocol, slides, and scientific literature. 1. Global Artwork Contribution (Collective Artwork) What I contributed: I added a pixel to the bottom‑right plate, contributing to the DNA helix pattern. Specifically, I selected a fluorescent protein (sfGFP) and placed it at coordinate (42, 15) to form part of the letter “G” in “HTGAA”.
Lab (Week 12) — Bioproduction of Beta-Carotene and Lycopene
Completion status: This lab was completed theoretically (no physical or virtual wet lab performed). All procedures, expected results, and answers below are based on the provided protocol, scientific literature, and standard bioproduction principles. The experiment involves genetically modified E. coli with pAC-LYC (lycopene) and pAC-BETA (beta‑carotene) plasmids. Overview & Objective We work with E. coli strains carrying either pAC-LYC (lycopene pathway: CrtE, CrtI, CrtB) or pAC-BETA (adds CrtY, converting lycopene to beta‑carotene). Both plasmids confer chloramphenicol resistance. The goal is to optimise pigment production by varying temperature (30°C vs 37°C), growth media (LB, LB+fructose, 2YT, 2YT+fructose), and measuring cell density (OD600) and pigment absorbance (lycopene at 474 nm, beta‑carotene at 456 nm) after acetone extraction.
I combined these labs from these two weeks because in both cases there was no work to do on the final project Lab (Week 13) — Final Project Labwork No Lab Assignment this week. Final Project Lab time available Week 14 — Bio Design & Bio Fabrication Homework: Finish your Final Project