Week 1 HW: Final Project Ideas

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For your first homework, propose and describe one idea for something you would like to biomanufacture. This could be medicine, material, food, energy, an art, design, or architectural artifact, or beyond. Draw from your own background and interests for inspiration.

The goal of this assignment is not to develop a complete or technically optimized manufacturing process. Instead, we want you to begin connecting four fundamental questions: What do you want to make? → What living system could make it? → How could automation help you make it? → What would it take to make it at a meaningful scale?

Proposing a Biomanufacturing Future: Interactive Bio-Art & Sustainable Bioplastics

1. What I want to make and why

This proposal encompasses two distinct yet complementary frontiers of biomanufacturing: interactive bio-art and environmental sustainability.

  1. “Our Inner Bloom” (Chromoprotein Dye): The objective is to biomanufacture biological dyes based on intensely colored chromoproteins. The motivation is deeply artistic and interactive: these dyes will be utilized in a 3D bio-art sculpture where human touch interacts with living biology. The project aims to produce at least 1 liter of highly concentrated, vibrant liquid dye for each targeted color.
  2. PHB Bioplastic (Polyhydroxybutyrate): The objective is to biomanufacture PHB, a 100% biodegradable and biocompatible polyester. The motivation is utilitarian and ecological: to provide a tangible, sustainable alternative to petroleum-derived plastics, mitigating the severe pollution affecting marine ecosystems. The long-term vision involves a decentralized manufacturing model empowering coastal communities in Peru.

2. The Living System

To achieve these goals, two specialized biological “chassis” will be employed:

  • For the Dye (Microbial Chassis): Escherichia coli BL21(DE3). This is an industry-standard bacterial strain specifically engineered for the high-level overexpression of recombinant proteins, utilizing the T7 promoter system.
    • Inputs: Standard liquid growth media (carbon and nitrogen sources).
    • Outputs: Intracellular accumulation of specific chromoproteins, which will subsequently be extracted and purified to form the dye.
  • For the Bioplastic (Native Microbial Chassis): Cupriavidus necator. This bacterium is renowned for its natural, robust capacity to accumulate biopolymers. The cultivation relies on a biphasic biological mechanism.
    • Inputs: First, a nutrient-rich phase for rapid biomass accumulation, followed by a nutrient-stress phase (e.g., nitrogen or phosphorus limitation).
    • Outputs: The stress triggers a biological defense mechanism, resulting in the intracellular accumulation of PHB granules, which can account for up to 80% of the cell’s dry weight.

3. Automation Strategy

Scaling these projects requires distinct automation strategies tailored to the chassis and the production stage:

  • Biofoundry and Prototyping (Opentrons OT-2): For the chromoprotein dyes, liquid handling robotics (specifically the Opentrons OT-2) will be central. This will automate repetitive pipetting, optimize media formulations, and standardize genetic transformation protocols, allowing for the rapid creation and screening of new color variants in high-throughput multi-well plates.
  • Scale-Up and Manufacturing (Cloud Lab Infrastructure): For the PHB bioplastic, automation will focus on bioprocess control via Cloud Lab infrastructure (e.g., automated bioreactor networks). This technology will provide real-time monitoring and dynamic adjustment of critical running parameters—such as pH, dissolved oxygen, and the complex biphasic feeding strategy—throughout pilot batches of up to 100 L.

4. Scale and Time Calculations

Scale Estimate

For “Our Inner Bloom” (Chromoprotein Dye)

  • Target Scale: 1 Liter of highly concentrated liquid dye per color.
  • Assumptions: A high protein concentration (10 mg/mL) is required to ensure the chromoprotein color remains intense when embedded in the sculpture’s resin. A conservative yield estimate for E. coli BL21(DE3) in shake flasks is 75 mg of purified protein per liter of culture.
  • Calculation:

    Total protein requirement: 1,000 mL * 10 mg/mL = 10,000 mg (10 grams). Required culture volume: 10,000 mg / 75 mg/L = 133.3 Liters.

  • Total Required: Approximately 133 Liters of E. coli culture per color.

For the PHB Bioplastic

  • Target Scale: Pilot-scale manufacturing (100 Liters of culture).
  • Assumptions: High-density cultivation of C. necator in a bioreactor can yield a Dry Cell Weight (gDCW) of 50 g/L. Under optimal nutrient stress, PHB accumulation reaches 80% of the gDCW.
  • Calculation:

    Total biomass per Liter = 50 g/L. PHB yield per Liter = 50 g/L * 0.80 = 40 g/L of PHB. Total production = 100 L * 40 g/L = 4,000 g (4 kg).

  • Total Required: 4 kilograms of purified PHB bioplastic.

Time Estimate

  • Production Rate/Yield: 75 mg/L of protein (E. coli); 40 g/L of bioplastic (C. necator).
  • Prototyping vs. Manufacturing: Prototyping genetic variations using an Opentrons takes merely a few days at the bench scale. However, scaling manufacturing to 100L in controlled bioreactors introduces complex fluid dynamics and oxygen transfer challenges.
  • Calculation:

    E. coli divides rapidly (every 20 mins). Target biomass is reached in 1-2 days. The downstream purification for a 133 L batch is estimated to take 2-3 weeks per batch. C. necator exhibits slower metabolism and requires the dual-phase (growth + stress) process. Iterative testing to optimize a fully automated 100L pilot batch will involve long R&D cycles.

  • Total Time: Weeks per batch for the chromoprotein dye; approximately 6 months of iterative R&D to establish the automated pilot-scale process for the bioplastic.

5. Technical Unknowns and Bottlenecks

To ensure technical viability, two major bottlenecks must be addressed experimentally:

  1. In Vitro Color Stability: Chromoproteins are susceptible to thermal degradation and rapid photobleaching when extracted and exposed to ambient environments or embedded in resin.
    • Unknown: How can we stabilize these proteins long-term without compromising color intensity? This will likely require directed evolution or targeted mutagenesis to discover thermo/photo-stable variants.
  2. Green Downstream Processing (Extraction): The economical separation of intracellular PHB from the biomass without relying on aggressive, toxic solvents (like chloroform) is critical to maintaining the project’s ecological integrity.
    • Unknown: Which downstream processing method (e.g., programmed biological lysis via bacteriophages, or novel continuous secretion systems) can efficiently separate PHB at a 100L scale while maintaining low operational costs and environmental safety?

Readings from lecture 1:

  1. Asin-Garcia, E., Fawcett, J. D., Batianis, C., & Martins dos Santos, V. A. P. (2025). A snapshot of biomanufacturing and the need for enabling research infrastructure. Trends in Biotechnology, 43(5), 1000–1014. https://doi.org/10.1016/j.tibtech.2024.10.014
  2. Averesch, N. J. H., Berliner, A. J., Nangle, S. N., Zezulka, S., Vengerova, G. L., Ho, D., Casale, C. A., Lehner, B. A. E., Snyder, J. E., Clark, K. B., Dartnell, L. R., Criddle, C. S., & Arkin, A. P. (2023). Microbial biomanufacturing for space-exploration—what to take and when to make. Nature Communications, 14, 2311. https://doi.org/10.1038/s41467-023-37910-1
  3. Karim, A. S. & Jewett, M. C. (2021). “Toward sustainable, cell-free biomanufacturing.” Current Opinion in Biotechnology 69, 136–144. DOI: 10.1016/j.copbio.2020.12.012.
  4. Petzold, C. J., & Mukhopadhyay, A. (2025). From bench to biofactory: High-throughput technologies and automated workflows to accelerate biomanufacturing. Current Opinion in Biotechnology, 94, 103320. https://doi.org/10.1016/j.copbio.2025.103320
  5. Yap, W. S., Choudhury, D., & Suntornnond, R. (2023). Towards biomanufacturing of cultured meat. Trends in Biotechnology, 41(3), 292–294. https://doi.org/10.1016/j.tibtech.2023.01.014
  6. Ye, J.-W., Lin, Y.-N., Yi, X.-Q., Yu, Z.-X., Liu, X., & Chen, G.-Q. (2023). Synthetic biology of extremophiles: A new wave of biomanufacturing. Trends in Biotechnology, 41(3), 342–357. https://doi.org/10.1016/j.tibtech.2022.11.010
  7. Zhang, Y.-H. P., Sun, J., & Ma, Y. (2017). Biomanufacturing: History and perspective. Journal of Industrial Microbiology & Biotechnology, 44, 773–784. https://doi.org/10.1007/s10295-016-1863-2

AI and Prompt Citations

  • AI Used: Gemini 3.1 Pro Avanced thinking (Google)
  • Prompts Used: This proposal was generated through an iterative dialogue using the custom htbaa-course-advisor skill[cite: 2]. The interaction involved defining the biological chassis, performing Fermi calculations for yield and scale, and strategizing automation using Opentrons and Cloud Labs.*.