Week 1 HW: Final Project Ideas

Important: I used ChatGPT to help me with understanding concepts, brainstorming ideas, and find relevant references

1.What would I like to biomanufacture and why?

I would like to develop an automated biomanufacturing platform for producing and optimizing a biological preservation system that could reduce the dependence of wildlife biobanks on ultra low-temperature storage.

We’ve been through a critical time for almost all kinds of wildlife in the past decades, with extinction rates becoming more and more alarming as the years pass due to habitat loss, hunting, pollution and etc. Because of that, it’s crucial for us to preserve the ecosystems and it’s species to avoid the loss of more species, and the biobank enters in this scenario as a fundamental tool on conservation efforts

Wildlife biobanks can preserve all kinds of biological materials from threatened species through cryopreservation. These genetic material collections can provide a fundamental resource in future research, population management and novel conservation efforts.

However, cryopreservation requires extremely low temperatures and specialized infrastructure, which can create logistical challenges in regions with limited access to cryogenic infrastructure.

In my project i aim to investigate a different approach: develop a biologically manufactured preservation system that could maintain cellular integrity under less extreme storage conditions through a microbial or cell-free biomanufacturing platform capable of producing the selected protective molecule.

The goal is not to replace cryogenic biobanking entirely. Instead, I would investigate if cells could be used to create a biological preservation system to extend the range of storage conditions under which wildlife-derived cells remain viable and biologically useful.

The proposed product would be a biologically manufactured preservation formulation designed to protect cells during drying and/or storage at temperatures above conventional cryogenic conditions.

One potential strategy is based on trehalose and other biological protective molecules.

Trehalose is a naturally occurring disaccharide found in many organisms that survive environmental stresses such as dehydration. It has been investigated as a cellular protectant because it can interact with cellular membranes and biomolecules during water loss.

Recent research has investigated trehalose-based approaches for preserving mammalian cells under non freezing conditions, including work with feline fibroblasts involving trehalose loading, drying, and storage above conventional cryogenic temperatures.

The proposed system would therefore investigate:

Biological production → protective molecule → formulation → cell preservation → recovery → viability assessment

The project would focus on optimizing the preservation system, rather than simply manufacturing trehalose as a commodity

2.What living system would I use?

The production component could use a microbial or cell-free biomanufacturing platform capable of producing the selected protective molecule.

The exact production organism and biological pathway would be determined during the development phase according to:

production efficiency; product stability; compatibility with the preservation formulation; scalability; cost; ease of automation.

Mammalian cells could be used to test the efficacy of this novel preservation system

The overall concept would therefore be:

Biological production system → Protective molecule → Preservation formulation → Model mammalian cells → Controlled dehydration/storage → Rehydration → Cell recovery → Viability and functional assessment

3.How would I use automation?

Automation could be used to create a system that could vary parameters such as: Concentration of the protective molecule; formulation composition; exposure time; dehydration conditions; rehydration conditions; storage temperature and storage duration to test different scenarios applied to the preservation system

The experiment could initially evaluate 96 different experimental conditions.

The workflow would follow a Design–Build–Test–Learn cycle:

DESIGN (Define preservation conditions) → BUILD (Automated preparation) → TEST (Preservation + recovery) → MEASURE (Cell viability / function) → LEARN (Computational analysis) → REDESIGN (Select improved conditions) → Repeat

This would allow the preservation system to be optimized systematically instead of relying on trial-and error experimentation

4.How much would I need to make?

For an initial calculation, i would consider a hypothetical scenario where a wildlife biobank contain 100 individuals with 10 preserved samples per individual, which would give:

100 × 10 = 1,000 samples

If each sample required a hypothetical 1 mL preservation formulation:

1,000 × 1 mL = 1,000 mL

Resulting in a total formulation of: 1 L

Then, in the initial experimental phase, 96 formulations at 1 mL each could be used:

96 × 1 mL = 96 mL per experimental round

If ten rounds were performed:

96 mL × 10 = 960 mL

The actual volume would ultimately depend on the experimental protocol and the amount of formulation required per sample.

But since i can’t be in person on the labs, i don’t know exactly how i will be putting this in practice, but i’m really excited to see how this will go on!

5.What are the main uncertainties?

Uncertainty 1 — Can cells survive non-cryogenic preservation?

The main uncertainty is if sufficient cellular integrity will be maintained when cells are subjected to dehydration and storage at temperatures above cryogenic conditions. To the system be successful it need to protect cellular structures during both water removal and rehydration.

Uncertainty 2 — How much protection can the biological product provide?

Another uncertainty is if the protective molecule will work equally well under diferent conditions. Its performance could depend on: concentration; cell type; dehydration rate; storage temperature; storage duration; rehydration protocol. Therefore, the project would need to experimentally identify the appropriate combination of parameters.

Uncertainty 3 — Will the method work for wildlife cells?

Different species and cell types can have different membrane compositions, metabolic characteristics, and sensitivities to dehydration. Therefore it’s still unknown if this preservation system will work on every specie.

Uncertainty 4 — Can preserved cells remain useful?

Another question is if whether or not the recovered cells will retain characteristics relevant to their intended application (For example, the ability to proliferate and maintain appropriate cellular characteristics). This is important since the main goal is to preserve biologically useful genetic resources.

References

Crowe, J. H. (2005). Stabilization of Dry Mammalian Cells: Lessons from Nature. Integrative and Comparative Biology, 45(5), 810–820. https://doi.org/10.1093/icb/45.5.810

Loi, P., Iuso, D., Czernik, M., Zacchini, F., & Ptak, G. (2013). Towards storage of cells and gametes in dry form. Trends in Biotechnology, 31(12), 688–695. https://doi.org/10.1016/j.tibtech.2013.09.004

Török, Z., Satpathy, G. R., Banerjee, M., Bali, R., Little, E., Novaes, R., Van Ly, H., Dwyre, D. M., Kheirolomoom, A., Tablin, F., Crowe, J. H., & Tsvetkova, N. M. (2005). Preservation of Trehalose-Loaded red blood cells by lyophilization. Cell Preservation Technology, 3(2), 96–111. https://doi.org/10.1089/cpt.2005.3.96

Wolkers, W. F., Tablin, F., & Crowe, J. H. (2002). From anhydrobiosis to freeze-drying of eukaryotic cells. Comparative Biochemistry and Physiology Part a Molecular & Integrative Physiology, 131(3), 535–543. https://doi.org/10.1016/s1095-6433(01)00505-0