Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- Biological engineering application and tool
Week 2 HW: DNA Read, Write, & Edit
Benchling & In-silico Gel Art The lambda bacteriophage DNA sequence (Lambda_NEB) was imported into Benchling. Using the virtual restriction tool, simulated DNA digestion was performed with seven restriction enzymes: EcoRI, SacI, SalI, HindIII, BamHI, KpnI, and EcoRV. The results were visualized by agarose gel electrophoresis. Simulated gel electrophoresis of lambda DNA after restriction digestion with EcoRI, SacI, SalI, HindIII, BamHI, KpnI, and EcoRV
Python Script for Opentrons Artwork I made an image for Opentrons Artwork based on the eye symbol from the Plantoverse project I’m involved with. Google Colab: https://colab.research.google.com/drive/1NpGO1qk_Vl4jsJbpIHB6_8-z24hKodAW#scrollTo=pczDLwsq64mk&line=3&uniqifier=1 Concept and output Comments: POINT_SIZE = 2 was used in the code, which made printing the image difficult. It is recommended to increase the pixel size for printing.
Week 4 HW:Protein Design Part I
Protein Design I 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) The average molecular weight of an amino acid is ~100 g/mol. In 500 g of meat (if we consider all meat as amino acids) there are 5 moles, which gives 5 × 6 × 10²³ = 3 × 10²⁴ molecules. However, meat is not entirely protein: protein makes up only about 20% of the mass, i.e., 100 g of protein per 500 g of meat. After protein breakdown, this corresponds to 1 mole of amino acids, that is 6 × 10²³ molecules.
Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM The amino acid sequence of the human SOD1 protein was taken from the UniProt database (ID: P00441), and the A4V mutation was introduced. Amino acid sequence of the human SOD1 protein from UniProt (ID: P00441): MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ The A4V mutation was introduced: MVTKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Four peptides of 12 amino acids in length were generated based on the mutant SOD1 gene sequence.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
Assignment: DNA Assembly Components of the Phusion High‑Fidelity PCR Master Mix and their purposes The Phusion master mix (2×) contains: Phusion DNA polymerase – a high‑fidelity enzyme with 3′→5′ proofreading activity, minimising errors during amplification dNTPs (dATP, dTTP, dCTP, dGTP) – the building blocks for new DNA strands Optimised reaction buffer (HF or GC) – provides the correct pH and ionic conditions for the enzyme Mg²⁺ ions (MgCl₂) – an essential cofactor for polymerase activity
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) Advantages of IANNs over Boolean genetic circuits Analog computation (continuous molecular concentrations) Weighted summation of multiple inputs Nonlinear activation (sigmoid via cooperativity) More compact (one neuron replaces many logic gates) Tunable weights (promoter/RBS strength) Application: cancer biomarker detection Inputs: concentrations of miRNAs (e.g., miR‑21, miR‑155) Output: therapeutic protein or fluorescent reporter Limitations: noise, difficulty of weight tuning, latency (minutes to hours), metabolic load
Homework Part A: General and Lecturer-Specific Questions General homework questions Advantages of cell‑free protein synthesis Direct access to the reaction environment and no constraints from cell viability. Cell‑free synthesis is preferable for producing toxic proteins and for rapid screening of many variants without maintaining live cultures. Main components of a cell‑free system and their roles Cell extract (ribosomes, tRNAs, translation factors, polymerase), energy system (ATP plus regeneration), amino acids, DNA template, buffer and salts.
Week 10 HW: Advanced Imaging & Measurement Technology
Homework: Final Project What aspects of the project will be measured? The intensity of red fluorescence of E. coli bacteria carrying the P_rprA‑B0034‑mScarlet‑I‑B0015 construct after acoustic exposure will be measured. In addition, the area of fluorescent zones on the bioprinted image will be measured, and bacterial growth area as well as changes in the bioprinted image will be assessed. How will these measurements be performed? Using photography and subsequent analysis with ImageJ software, the following will be quantified:
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Collective image Part B: Cell-Free Protein Synthesis | Cell-Free Reagents Roles of components in the 20‑hour cell‑free reaction (yellow box) E. coli Lysate (BL21 (DE3) Star) – provides the cellular machinery (ribosomes, tRNAs, polymerases, translation factors) required for transcription and translation. The BL21 (DE3) strain supplies T7 RNA polymerase, enabling high‑efficiency transcription from T7 promoters. Salts/Buffer – maintain optimal pH (HEPES), ionic strength, and cofactor availability. Potassium glutamate and magnesium glutamate stabilise ribosomes and enzyme activity; potassium phosphate buffers the reaction and supplies phosphate groups.