Week 1 HW: Final Project Ideas

1. What I would like to biomanufacture and why

The Product

I propose to biomanufacture Cardiovascular-Optimized Cultivated Beef, a cultivated meat product whose nutritional composition is intentionally engineered rather than simply reproducing that of conventional beef.

The goal is to produce beef with a more favorable fatty-acid profile, particularly a higher proportion of omega-3 polyunsaturated fatty acids (PUFAs), while also incorporating β-carotene as an antioxidant and potential provitamin A source.

Why Make It?

Conventional livestock production gives us some ability to influence this composition through animal genetics, breeding, and diet, but these approaches are constrained by the biology of the whole animal. Cultivated meat presents a different possibility. Instead of raising an entire animal and accepting the resulting biochemical composition of its tissues, we can potentially engineer the cells responsible for producing the meat. This creates the possibility of treating meat as a programmable biological product. My motivation is therefore to explore whether metabolic engineering can be used not only to manufacture meat without raising an entire animal, but also to design the nutritional properties of the meat itself.

Who Is the Product For?

The eventual product would be intended for consumers who want to continue eating beef while seeking a product with an intentionally modified nutritional profile. I would envision it as a food designed to offer a potentially more favorable fatty-acid composition than conventional beef.

Why Is This Interesting as a Biomanufacturing Problem?

What makes this idea particularly interesting to me is that it goes beyond simply replacing conventional meat production with cell culture and combines cultivated meat, metabolic engineering, and automated biomanufacturing. The same general approach could eventually be extended beyond fatty acids and β-carotene to engineer other nutritional, sensory, or functional properties of meat. My long-term vision is therefore a manufacturing platform in which meat is not simply grown, but biologically programmed according to the properties we want the final food to have.

2. What living system would I use?

The Manufacturing Chassis

I would use genetically engineered bovine muscle progenitor cells as the living manufacturing system.

These cells would first be expanded in culture and then differentiated into muscle cells to produce cultivated beef.

The overall process can be represented as:

Engineered bovine cells → cell Proliferation → muscle differentiation → cultivated beef

Engineering the Cells

I would introduce two main metabolic modules into the bovine cells.

The first module would contain an omega-3 desaturase such as FAT-1 from Caenorhabditis elegans. FAT-1 can convert several omega-6 fatty acids into their corresponding omega-3 fatty acids.

Conceptually:

Omega-6 PUFA → FAT-1 → corresponding omega-3 PUFA

The purpose of this modification would be to shift the fatty-acid composition of the cells toward a higher omega-3/omega-6 ratio.

FAT-1 alone would not necessarily produce large amounts of EPA or DHA. If specific long-chain omega-3 fatty acids were required, additional elongation and desaturation enzymes could be incorporated into the pathway.

β-Carotene Production

The second module would introduce a β-carotene biosynthetic pathway using enzymes such as CrtB, CrtI, and CrtY.

In simplified form:

Cellular precursors → CrtB → phytoene → CrtI → lycopene → CrtY → β-carotene

This would allow the engineered cells to synthesize β-carotene internally rather than relying entirely on β-carotene supplied through the culture medium.

The β-carotene would potentially provide both nutritional value and antioxidant activity. This is particularly relevant because increasing the amount of unsaturated fatty acids could also increase the susceptibility of the resulting meat to lipid oxidation.

Inputs and Outputs

The major inputs to the system would be engineered bovine cells and cell-culture medium containing the nutrients required for cell growth and metabolism.

The cells would use these nutrients to proliferate, produce biomass, carry out the engineered metabolic reactions, and eventually differentiate into muscle tissue.

The desired outputs would therefore be:

• Bovine muscle biomass
• An increased proportion of omega-3 PUFAs
• An increased omega-3/omega-6 ratio
• Detectable β-carotene
• A final cultivated beef product with the desired nutritional composition

At a high level:

flowchart TD
    A["Bovine Cells + Nutrients"] --> B["Cell Proliferation"]
    B --> C1["FAT-1 Pathway<br/>(Altered fatty-acid composition)"]
    B --> C2["CrtB / CrtI / CrtY Pathway<br/>(β-Carotene production)"]
    C1 --> D["Muscle Differentiation"]
    C2 --> D
    D --> E["Cardiovascular-Optimized Cultivated Beef"]

Key Biological Assumption

A major assumption is that these additional metabolic pathways can be introduced without substantially compromising the ability of the bovine cells to grow and differentiate.

The engineered pathways will require cellular resources and metabolic precursors that would otherwise be used for normal cell functions. Excessive expression could therefore create a metabolic burden, reduce growth rate, or interfere with muscle differentiation.

This would need to be experimentally tested by comparing engineered and unmodified bovine cells for growth rate, viability, differentiation capacity, fatty-acid composition, β-carotene production, and lipid oxidation.

The initial objective would therefore not be to immediately produce large quantities of meat, but to identify an engineered cell line that can maintain healthy growth while producing the desired nutritional changes.

3. How would I use automation?

Automation During Development

I would use automation primarily during the development and optimization of the engineered bovine cell line.

A platform such as an Opentrons liquid-handling robot could automate cell seeding, media addition, reagent transfer, sampling, and preparation of multiple experimental conditions in parallel.

This would allow many combinations of genetic constructs, gene-expression levels, media compositions, and culture conditions to be tested simultaneously.

High-Throughput Screening

The main advantage of automation would be the ability to rapidly screen many engineered cell populations.

For example, different levels of FAT-1 expression could be tested to determine how strongly they alter the omega-3/omega-6 ratio while maintaining acceptable cell growth.

Similarly, different levels of β-carotene pathway expression could be tested to determine whether β-carotene production can be increased without creating excessive metabolic burden.

The resulting cell populations could be screened for:

• Cell growth and viability
• Differentiation efficiency
• Omega-3/omega-6 ratio
• β-carotene production
• Lipid oxidation
• Overall biomass production

Automation would make these experiments more reproducible and reduce the amount of manual laboratory work required.

Automation at Manufacturing Scale

The automation technology used during development would be different from the technology used for large-scale manufacturing.

At manufacturing scale, I would use automated stirred-tank bioreactors equipped with sensors and control systems.

These systems could continuously monitor and control parameters such as Temp, pH, DO etc

Automated sampling could also periodically collect small samples for measurements of fatty-acid composition, β-carotene concentration, cell growth, and product quality.

Ultimately, automation would allow the biological manufacturing process to move from manually optimized laboratory experiments toward a reproducible and scalable production system.

4. How much would I need to make, and how long would it take?

(a) How Much?

To define a meaningful manufacturing scale, I would target enough Cardiovascular-Optimized Cultivated Beef to supply the annual beef consumption of 10,000 people.

The USDA Economic Research Service projects U.S. beef availability at approximately 60.0 lb per person per year in 2026. I use this value as a proxy for annual beef consumption. USDA ERS

First, I convert this value to kilograms:

60.0 lb/person/year × 0.453592 kg/lb = 27.22 kg/person/year

For 10,000 people:

27.22 kg/person/year × 10,000 people = 272,200 kg/year

Therefore, my target manufacturing scale is approximately:

272,200 kg/year ≈ 272 tonnes/year

This calculation assumes that one kilogram of cultivated beef would replace one kilogram of conventional beef.

I would initially target a ground-meat-like cultivated beef product rather than a fully structured steak. This is important because current large-scale cultivated-meat models primarily describe the production of animal-cell biomass rather than fully structured whole cuts.

Production Capacity of One Reactor

To estimate the infrastructure required, I use a 2026 process model by Brenner et al. The model describes a 20,000 L stirred-tank reactor operating at a maximum cell density of approximately 5 × 10⁷ cells/mL and producing approximately 2,000 kg of biomass per 30.7-day batch. Brenner et al., 2026

The approximate number of batches that one reactor could complete per year is:

(365 days) / (30.7 days/batch) = 11.89 batches/year

Therefore, the theoretical annual output of one reactor would be:

11.89 batches/year × 2,000 kg/batch
= 23,780 kg/reactor/year

or approximately 23.8 tonnes per reactor per year.

The same model reports a maximum biomass concentration of approximately 105 g/L.

For a 20,000 L reactor:

20,000 L × 105 g/L = 2,100,000 g
= 2,100 kg

This is consistent with the model’s approximately 2,000 kg biomass output per batch.

Number of Reactors Required

The theoretical number of reactors required to produce 272,200 kg/year is:

(272,200 kg/year) / (23,780 kg/reactor/year) = 11.45

Therefore, at least:

12 reactors

would be required under ideal continuous operation.

However, real facilities would require time for cleaning, sterilization, maintenance, reactor turnaround, and potential downtime.

To account for this, I would use approximately 13 parallel 20,000 L production reactors as the practical estimate.

This gives some additional production capacity rather than designing the facility to operate at exactly 100% of its theoretical capacity.

(b) How Long Would It Take?

A single 20,000 L reactor would produce approximately 2,000 kg every 30.7 days.

If only one reactor were available, the number of batches required to produce the full annual target would be:

(272,200 kg) / (2,000 kg/batch) = 136.1 batches

The corresponding production time would be:

136.1 batches × 30.7 days/batch
= 4,178 days

or approximately:

11.4 years

This demonstrates why a single large reactor would not be sufficient for the proposed scale.

Instead, multiple reactors would operate in parallel. With approximately 13 reactors, production could be distributed across the reactors so that different batches are continuously entering, growing, harvesting, and undergoing downstream processing.

Under the simplified assumptions, this would provide enough capacity to produce approximately 272 tonnes of cultivated beef per year, corresponding to the annual beef consumption of 10,000 people.

Important Assumptions and Limitations

Several assumptions are required for this back-of-the-envelope calculation.

1. Reactor performance: I assume that the engineered bovine cells can eventually achieve performance comparable to the cells represented in the published 20,000 L process model.

2. Batch productivity: I use approximately 2,000 kg of biomass per 30.7-day batch as the primary manufacturing benchmark.

3. Downtime: The theoretical calculation assumes continuous operation, while the practical estimate of 13 reactors provides some additional capacity for cleaning, maintenance, and other downtime.

4. Engineered-cell performance: The most important assumption is that introducing the FAT-1 and β-carotene pathways does not substantially reduce cell growth, viability, or differentiation efficiency.

The published process model itself does not represent every step required to manufacture a commercial steak. In particular, differentiation, tissue maturation, and structured tissue formation introduce additional engineering challenges.

This scale also illustrates why automation is important. Producing hundreds of tonnes of engineered cultivated meat would require automated monitoring, feeding, sampling, quality control, and coordination across many parallel bioreactors rather than relying on manual operation.

Sources:

Brenner et al. (2026) — Decoding cultured meat manufacturing: a full process model to identify scale-up bottlenecks.
This is the primary source for the 20,000 L reactor, 105 g/L biomass concentration, ~2,000 kg/batch, and 30.7-day production cycle.
https://www.frontiersin.org/journals/nutrition/articles/10.3389/fnut.2026.1844185/full USDA Economic Research Service (2026) — Projected 60.0 lb/person/year beef availability.
https://ers.usda.gov/data-products/charts-of-note/114196 Risner et al. (2019) — Independent cultivated-meat bioprocess calculation estimating approximately $2.9 \times 10^{11}$ (2.9 × 10¹¹) muscle cells per kg of wet cultivated meat, useful as a sanity check on the enormous cell numbers involved.
https://www.frontiersin.org/journals/sustainable-food-systems/articles/10.3389/fsufs.2019.00044/full

5. What don’t I know yet?

There are several important technical uncertainties that would need to be resolved before this concept could become a practical manufacturing process.

1. Will the genetic modifications interfere with cell growth?

The biggest unknown is how introducing the FAT-1 and β-carotene pathways will affect bovine cell growth and differentiation.

These pathways will consume cellular resources, metabolic precursors, and energy. This could create a metabolic burden and cause the cells to grow more slowly or differentiate less efficiently.

I would compare engineered and unmodified cells for growth rate, viability, and differentiation efficiency.

2. Will the pathways produce enough of the desired molecules?

FAT-1 may shift the omega-6/omega-3 balance, but it may not produce high levels of specific long-chain omega-3 fatty acids such as EPA or DHA on its own.

Similarly, introducing CrtB, CrtI, and CrtY does not guarantee that enough β-carotene will accumulate.

I would therefore measure the omega-3/omega-6 ratio, individual fatty acids, β-carotene concentration, and lipid oxidation to determine whether the engineering produces the intended nutritional profile.

3. Will the system work at manufacturing scale?

Performance in a small culture vessel may not translate directly to a large bioreactor.

Large-scale cultivation introduces challenges such as oxygen transfer, nutrient gradients, mixing, pH control, and waste accumulation.

The engineered cells would therefore need to be tested progressively from small cultures to larger bioreactors while monitoring their growth and metabolic performance.

4. Will the product remain stable?

Increasing unsaturated fatty acids could make the final product more susceptible to lipid oxidation.

Although β-carotene is intended to provide antioxidant protection, I do not yet know whether the amount produced would be sufficient.

This would need to be tested during processing, storage, and cooking.

The Biggest Questions

The three most important questions are:

1. Can the engineered pathways improve the nutritional profile without reducing cell growth or differentiation?
2. Can the engineered cells maintain their performance during large-scale cultivation?
3. Can the final high-PUFA product remain stable against lipid oxidation?

The first major experiment would therefore compare engineered and unmodified bovine cells under identical conditions.

If the engineered cells maintain similar growth and differentiation while producing more omega-3 PUFAs and β-carotene, the concept would have a strong foundation for further scale-up.