Week 3 HW: lab automation

Create a Python file to run on an Opentrons liquid handling robot.

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

Journal Article Cell-free biosensor with automated acoustic liquid handling for rapid and scalable characterization of cellobiohydrolases on microcrystalline cellulose Taeok Kim, Eun Jung Jeon, Kil Koang Kwon, Minji Ko, Ha-Neul Kim, Seong Keun Kim, Eugene Rha, Jonghyeok Shin, Haseong Kim, Dae-Hee Lee, Bong Hyun Sung, Soo-Jung Kim, Hyewon Lee, Seung-Goo Lee, Cell-free biosensor with automated acoustic liquid handling for rapid and scalable characterization of cellobiohydrolases on microcrystalline cellulose, Synthetic Biology, Volume 10, Issue 1, 2025, ysaf005, https://doi.org/10.1093/synbio/ysaf005

This paper talks about the high throughput screening challenges involving engineering enzymes that help in degrading cellulose in paper sludge or microplastics in sewage sludge as solid substrates are not readily accessible in cell-based biosensor systems. In the paper, a cell free cellobiose-detectable biosensor (CB-biosensor) for rapid characterization of cellobiohydrolase (CBH) activity, enabling direct detection of hydrolysis products without cellular constraints was adopted.The biosensor distinguishes between CBH subtypes (CBHI and CBHII) based on their modes of action. Echo 525 liquid handler enables precise and reproducible sample processing, with fluorescence signals from automated preparations comparable to manual experiments.Assay volumes can be reduced to just a few microlitres—impractical with manual methods. Echo 525 minimizes reagent consumption, accelerates testing, and facilitates reliable large-scale screening, advancing enzyme screening and accelerating the Design-Build-Test-Learn cycle for sustainable biomanufacturing.

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.

The final project idea which involves design of COF based biosensor with aptamer for detection of AMR genes and drug delivery, cloud laboratory can be used to automate time consuming SELEX(Systematic Evolution of Ligands by Exponential Enrichment)process for aptamer selection. this increases binding affinity,improve specificity, removing sequences that bind to non-target components. PCR/RT-PCR amplification of the bound sequences is carried out automatically to generate the pool for the next round.

Robots control the functionalization of the COF surface with various reagents(e.g., amine-functionalization). Immobilization: Automated, high-throughput liquid handling ensures consistent covalent attachment of the aptamer to the COF, ensuring uniform batch production. Robots precisely load the COF-aptamer complex with siRNA for gene silencing of AMR, ensuring consistent dosages for therapeutic applications.

Final project ideas