Week 3 HW: Lab Automation

Post-Lab Questions

Find and describe a published paper that utilises the Opentrons or an automation tool to achieve novel biological applications. Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode, Python scripts, 3D printed holders, a plan for how to use Ginkgo Nebula, and more. You may reference this week’s recitation slide deck for lab automation details. While your description/project idea doesn’t need to be set in stone, we would like to see core details of what you would automate. This is due at the start of lecture and does not need to be tested on the Opentrons yet.

PUBLICATION:

The publication Semiautomated Production of Cell-Free Biosensors, published by the American Chemical Society (ACS Publications), explores the assembly of cell-free biosensors through liquid handling robotics versus manual methods commonly used in lab-scale development. The process is a combination where, “both manual and semiautomated reaction assembly approaches using the Opentrons OT-2 liquid handling platform on two different cell-free gene expression assay systems that constitutively produce colourimetric (LacZ) or fluorescent (GFP) signals,(Brown).” The deigned protocols demonstrate that they perform close to expected detection outcomes, in a more controlled environment, (Brown).

IDEA:

In my final project, I intend to use automated fabrication tools to create 3d printed templates, moulds, and matrices within the fabric, as well automating the liquid handling in the textile. Through automation, I will construct a textile embedded with patterned cavities designed to host distinct bacterial-sensing environments. The fabric’s automated structure serves as the fixed framework, while the bacteria and their metabolic activity constitute the variable component. As microbial signals interact with each cavity, dynamic changes in colour and pattern emerge, allowing the fabric to visually reflect microbial activity and ecological variation across its surface.

To do this, the following steps are needed.

Opentron OT-2 liquid handling and 3d Printed textile: First, I need to design the 3D mould for the hydrogel fabric textile, which will consist of a cavity matrix that will host the cell-free biosensors. I also need to 3d print a holder to lay the textile flat and dispense to OT-2 coordinates.
Bioprinting hydrogel: Next, I need to print the hydrogel containing the pattern cavities designed and corresponding to the OT-2 dispense coordinates. This can be done by bioprinting or mould casting the hydrogel into shape/texture.
Opentrol OT-2 despensing: The Opentron OT-2 will despense the DNA mixture and CFE into the bioprinted hydrogel cavities and coordinates. This will ensure accurate volume, distribution, and reproducibility across various textile matrices.
Sealing of textile hydrogel: The textile hydrogel will be sealed with a semipermeable layer that allows skin metabolites to permeate into the cavities and activate cell-free biosensors to reveal patterns.

PROJECT PROPOSALS: https://docs.google.com/presentation/d/19T22uOQz9aTvnzh426tri4xrg-ZoG1ksy6I5bswGHaw/edit?usp=sharing

RESOURCES:

Brown, D.M., Phillips, D.A., Garcia, D.C., Arce, A., Lucci, T.J., Davies, J.P., Mangini, J.T., Rhea, K.A., Bernhards, C.B., Biondo, J.R., Blum, S.M., Cole, S.D., Lee, J.A., McDonald, N.D., Wang, B., Perdue, D.L., Bower, X.S., Thavarajah, W., Karim, A.S., Lux, M.W., Jewett, M.C., Miklos, A.E. & Lucks, J.B., 2025. Semiautomated production of cell-free biosensors. ACS Synthetic Biology, 14(3), pp.979–986. doi:10.1021/acssynbio.4c00703.

Chowdhury, M.-U.-S., Roy, S., Kumar, A., Kakadiya, D., Deshpande, G. G., Aryal, K. P., Leung, H. & Pandey, R., 2025. Development of a conductive fabric-based wearable patch for multiplexed measurement of sweat glucose and sweat secretion. Preprint. Research Square.. https://www.researchgate.net/publication/393943187_Development_of_a_Conductive_Fabric-based_Wearable_Patch_for_Multiplexed_Measurement_of_Sweat_Glucose_and_Sweat_secretion

Horland, R., Lindner, G., Wagner, I., Atac, B., Hoffmann, S., Gruchow, M., Sonntag, F., Klotzbach, U., Lauster, R. & Marx, U., 2011. Human hair follicle equivalents in vitro for transplantation and chip-based substance testing. BMC Proceedings, 5(Suppl 8), p.O7.https://pmc.ncbi.nlm.nih.gov/articles/PMC3284944/?utm_

SOL – Seed Of Life, 2018. 3D Printed Wearables Bio-Engineered with Bacteria That Can Embed Living Matter, 8 June 2018. Psychedelic Clothing & Visionary Art blog. https://www.psytshirt.com/blog/psychedelic-fashion-clothing-trippy-t-shirt-seed-of-life-3D-Printed-Wearables.html?srsltid=AfmBOoptLpo7rSj0967utQ-LieopClYKuq6HHlT0tg63bBcr-ivp7RZO