Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
At the core of the project is the development of an improved bioprinter designed for two-color bacterial printing using two strains of Escherichia coli: a non-pathogenic, non-modified strain and a genetically transformed strain carrying a plasmid encoding the expression of a color marker. This approach enables the creation of visually distinguishable bacterial images and expands both the artistic and research potential of bioprinting.
Week 2 HW: DNA read, write and edit
Part 1: Benchling & In-silico Gel Art The process of simulation of Lambda genome Restriction Enzyme Digestion in Benchling: Final result: For Gel art pattern I used KpnI, SacI and SalI Restriction Enzyme Digestion. It is a pattern of wave.
Python Script for Opentrons Artwork My Python script which draws my design using the Opentrons. I used AI for adding my color parameters. I made a drawing of Totoro - the titular forest spirit from the 1988 Studio Ghibli animated film My Neighbor Totoro written and directed by Hayao Miyazaki. On Ronan’s website:
Week 4 HW: Protein design part I
Part A. Conceptual Questions 1. 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) Assumptions: Lean meat (e.g., beef, chicken, fish) contains approximately 20% protein by weight (the remainder is water, fat, minerals, and glycogen). 500 g meat × 0.20 = 100 g of protein. Proteins are digested into individual amino acid monomers. Average molar mass of an amino acid residue ≈ 100 g/mol (as stated). Approximately 6 × 10²⁶ amino acid molecules are obtained from 500 g of meat.
Week 5 HW: Protein design part II
Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM the human SOD1 sequence (P00441): MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ the A4V mutant SOD1 sequence: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence with the known SOD1-binding peptide FLYRWLPSRRGG for comparison:
Week 6 HW: Genetic circuits part I
Assignment: DNA Assembly 1. Components of Phusion High-Fidelity PCR Master Mix and their functions The Phusion High-Fidelity PCR Master Mix typically contains: Phusion High-Fidelity DNA Polymerase A thermostable DNA polymerase with 3’→5’ exonuclease proofreading activity, which significantly reduces the error rate during DNA amplification.
Week 7 HW: Genetic circuits part II
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) 1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Intracellular Artificial Neural Networks (IANNs) provide several important advantages over traditional genetic circuits that operate using Boolean logic gates such as AND, OR, and NOT. Traditional genetic circuits typically generate binary outputs, where genes are either “ON” or “OFF.” In contrast, IANNs can process information in a continuous and weighted manner, similar to artificial neural networks used in computational machine learning.
Homework Part A: General and Lecturer-Specific Questions General homework questions 1. 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. Flexibility:
Week 10 HW: Imaging and measurement
Homework: Final Project 1. Conjugation Frequency (Quantitative HGT Efficiency) What is measured: The ratio of transconjugants to total recipient cells — the primary numerical output of the experiment. After overnight incubation on LB agar, cells are re-printed onto: Plate A (no antibiotic) → counts all recipient colonies (pink) + donor (blue) Plate B (+ ampicillin 100 µg/mL) → only AmpR transconjugants survive in recipient zones Conjugation frequency = N(blue AmpR in recipient zone) / N(total recipient on Plate A)
Week 11 HW: Bioproduction & Cloud Labs
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork I contributed a one pixel on Q3 - H1 plate with mKO2 fluorescent protein, but it was overlapped by other contributions later. My involvement in the artwork was limited to placing a single pixel, which I used primarily to familiarize myself with the interface. I also initially assumed that the canvas had a limited number of available pixels relative to the large number of course participants. Nevertheless, I found the concept of a collaborative artwork compelling, and its implementation through a great interactive website was thoughtfully designed and inspiring. Also I found the timelapse feature particularly valuable, as it effectively illustrated both the temporal evolution of the image and the conceptual development of the artwork over time.