Week 3 HW: Lab Automation

1. Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.

I came across the following paper, Brown DM, Phillips DA, Garcia DC, Arce A, Lucci T, Davies JP Jr, Mangini JT, Rhea KA, Bernhards CB, Biondo JR, Blum SM, Cole SD, Lee JA, Lee MS, McDonald ND, Wang B, Perdue DL, Bower XS, Thavarajah W, Karim AS, Lux MW, Jewett MC, Miklos AE, Lucks JB. Semiautomated Production of Cell-Free Biosensors. ACS Synth Biol. 2025 Mar 21;14(3):979-986. doi: 10.1021/acssynbio.4c00703. Epub 2025 Mar 12. PMID: 40073441., that compares the semi-automated production of cell-feee biosensors against manual production, utilizing the Opentron OT-2 liquid handler. I hope to use this and similar papers (I believe Opentron has prepared Python scripts for applications like this that I could modify as needed) as a basis for my final project.

2. 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

I would be interested in utilizing a cloud laboratory to screen biosensor constructs for biological or chemical warfare agents that I design, synthesize, and express using cell-free protein synthesis.

I did find a paper (Park Y.J., Choi S., Lee K.W., Park S.Y., Song D.Y., Yoo T.H., Kim D.M. A Cell-Free Biosensor for Multiplexed and Sensitive Detection of Biological Warfare Agents. Biosens. Bioelectron. 2024;257:116331. doi: 10.1016/j.bios.2024.116331.) in which the researchers converted detection of 16S rRNA for traditional biothreat agents into functional proteins for detection and I’d be interested to see if this could be done for other sections of genes that may allow for differentiation of wild-type pathogenic bacteria and attentuated strains.

I need to further research precisely how to work design, synthesize, and express cell-free biosensor constructs (I have no prior experience here), but taken from the example provided:

Echo transfer biosensor constructs and any required cofactors into specified wells. Bravo stamp in CPFS reagent master mix into all wells of a 96-well / 384-well plate. Multiflo dispense the CFPS lysate to all wells to start protein expression. PlateLoc seal the plate. Inheco incubate the plate at 37°C while the biosensor proteins are synthesized. XPeel remove the seal. PHERAstar measure fluorescence to compare biosensor responses.

This example does assume that I have my biosensor constructs already designed and synthesized; I would likely design this in Benchling or another online tool and then request that it be synthesized by Twist Bioscience.

As I am not physically located at MIT/Harvard, I could discuss the possibility of using the Opentron OT-2 at my local node or MIT/Harvard’s cloud lab to work on my final project, though it would require having someone follow whatever deck layout I have in mind and aliquot out my reagents to place on the deck where I have designated. I have used a couple different liquid handlers (Hamilton STAR, Biomek i7) in different labs, but have never used them as part of a cloud lab.

Ideas for a final project:

(in progress)

  1. Idea: Biothreat or chemical warfare agent cell-free biosensors a. Level 1: b. Level 2: c. Level 3:

  2. Idea: In-place/close to use production of nutrient and calorie-dense food stuffs that can be used for rations for warfighters or for space travel (could utilize yeast, bacteria, algae, etc.) a. Level 1: b. Level 2: c. Level 3:

  3. Idea: Venom-induced consumption coagulopathy (VICC): some way to impregnate cloth or gauze for wound-packing with synthetically produced venom (e.g. from certain species of snakes or catepillars) to cause localized coagulation and prevent major hemorrhaging a. Level 1: b. Level 2: c. Level 3: