Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Scale-up of nanocapsules for drug delivery using bacteria as ferritin manufacturers 1. Describe a biological engineering application or tool you want to develop and why. Biologics are drugs synthesized by living organisms, which have gained more notoriety throughout the years (Walsh, 2018). Cancer drugs and vaccines are some of the achievements scientists have accomplished with biotechnology. This is a novel area with increasing knowledge and endless applications. Currently, iron deficiency is one of the main global issues affecting overall health (Lee et al., 2025). This project aims to develop a drug delivery system using bacteria-made ferritin, given the popularity and extended use of these microorganisms over the years for drug manufacturing (Kulkarni, 2026).
Week 10 HW: Advanced Imaging & Measurement Technology
Please identify at least one (ideally many) aspect(s) of your project that you will measure. It could be the mass or sequence of a protein, the presence, absence, or quantity of a biomarker, etc. The main aspect to be measured is the expression and activity of the biosynthetic gene cluster (BGC). This includes: Presence and expression of BGC-associated enzymes Production of candidate metabolites Antibacterial activity against Leptospira Please describe all of the elements you would like to measure, and furthermore describe how you will perform these measurements.
Week 2 HW: DNA Read, Write, and Edit
HOMEWORK Part 1: Benchling & In-silico Gel Art Below are some screenshots from the steps followed to create a basic pattern: Step 1: The sequence is imported from the webpage to Benchling. Figures 1 and 2. Lambda DNA import process. Step 2: The digest function is shown as a test with EcoRI as the chosen restriction enzyme.
Assignment no. 1: Python Script for Opentrons Artwork The code used was the following to create a simple swirl pattenr with four different colors: from opentrons import types import math metadata = { 'author': 'Jean Colmenares', 'protocolName': 'Agar Swirl Pattern - 4 Colors', 'description': 'Swirl pattern with four colors per branch', 'source': 'HTGAA 2026 Opentrons Lab', 'apiLevel': '2.20' } TIP_RACK_DECK_SLOT = 9 COLORS_DECK_SLOT = 6 AGAR_DECK_SLOT = 5 PIPETTE_STARTING_TIP_WELL = 'A1' well_colors = { 'A1': 'Red', 'B1': 'Green', 'C1': 'Orange', 'D1': 'Blue' } def run(protocol): tips_20ul = protocol.load_labware( 'opentrons_96_tiprack_20ul', TIP_RACK_DECK_SLOT, 'Opentrons 20uL Tips' ) pipette_20ul = protocol.load_instrument( "p20_single_gen2", "right", [tips_20ul] ) temperature_module = protocol.load_module( 'temperature module gen2', COLORS_DECK_SLOT ) temperature_plate = temperature_module.load_labware( 'opentrons_96_aluminumblock_generic_pcr_strip_200ul', 'Cold Plate' ) color_plate = temperature_plate agar_plate = protocol.load_labware( 'htgaa_agar_plate', AGAR_DECK_SLOT, 'Agar Plate' ) center_location = agar_plate['A1'].top() pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL) # —————————————————————— # Helper functions # —————————————————————— def location_of_color(color_string): for well, color in well_colors.items(): if color.lower() == color_string.lower(): return color_plate[well] raise ValueError(f"No well found with color {color_string}") def dispense_and_detach(pipette, volume, location): above_location = location.move(types.Point(z=location.point.z + 5)) pipette.move_to(above_location) pipette.dispense(volume, location) pipette.move_to(above_location) # —————————————————————— # SWIRL PATTERN — BIG + FIXED COLOR PER BRANCH (P20 SAFE) # —————————————————————— DROP_VOLUME = 3 branches = 4 points_per_branch = 24 radius_start = 3 radius_step = 1.6 angle_step = math.pi/9 branch_colors = ['Red', 'Green', 'Orange', 'Blue'] for branch in range(branches): base_angle = branch * (2*math.pi/branches) color = branch_colors[branch] source = location_of_color(color) for i in range(points_per_branch): pipette_20ul.pick_up_tip() pipette_20ul.aspirate(DROP_VOLUME, source.bottom(1)) angle = base_angle + i * angle_step radius = radius_start + i * radius_step x = radius * math.cos(angle) y = radius * math.sin(angle) loc = center_location.move(types.Point(x=x, y=y, z=0)) dispense_and_detach(pipette_20ul, DROP_VOLUME, loc) pipette_20ul.drop_tip() The pattern is shown below:
Week 4 HW: Protein Design Part I
PART A: 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: 500 g of meat ~31 g of protein per 100 g of meat (British Nutrition Foundation, 2021 ) Average amino acid mass ≈ 100 g/mol Avogadro’s number = 6.022 × 10^23 molecules/mol 1. Protein content in 500 g of meat
Week 5 HW: Protein Design part II
PART A: SOD1 Binder Peptide Design The sequence for the original protein is: // sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Mutation occurs at residue 4: Alanine becomes Valine // 1UXM_1|Chains A, B, C, D, E, F, G, H, I, J, K, L|SUPEROXIDE DISMUTASE [CU-ZN]|HOMO SAPIENS (9606) ATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVS IEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Part 1: Generate Binders with PepMLM
Week 6 HW: Genetic Circuits Part I
PART 1: Protocol questions What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The mastermix contains: Phusion Hi-Fi DNA Polymerase: It is crucial for completing the amplicons generated during PCR. Deoxynucleotides: The building blocks necessary for replicating DNA fragments. Buffer including MgCl2: Prevents enzyme denaturation by maintaining pH at a fixed level. What are some factors that determine primer annealing temperature during PCR? Some factors include the primer length
Week 7 HW: Genetic Circuits Part II
PART 1: IANNs What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Describe a useful application for an IANN; include a detailed description of input/output behavior, as well as any limitations an IANN might face to achieve your goal. Below is a diagram depicting an intracellular single-layer perceptron where the X1 input is DNA encoding for the Csy4 endoribonuclease and the X2 input is DNA encoding for a fluorescent protein output whose mRNA is regulated by Csy4. Tx: transcription; Tl: translation. Draw a diagram for an intracellular multilayer perceptron where layer 1 outputs an endoribonuclease that regulates a fluorescent protein output in layer 2.
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. Main advantages (flexibility & control): Open system: You can directly add/remove components (DNA, cofactors, salts, inhibitors). Precise control: You can tune Mg²⁺, ATP, amino acids, etc. Rapid expression: No need for cloning → transformation → growth. Toxic proteins: You can express proteins that would normally kill cells.