Week 3 HW: Lab Automation
🤖 Week 3 Homework: Lab Automation
Find and describe a published paper utilizing automation for novel biological applications; describe automation tools for your final project.
📋 Overview
This week covers:
- Part 1: Published paper — synthetic cells via droplet-based microfluidics
- Part 2: Automation project description — gumol + ECSOD/MSC + new-Clara validation pipeline
Part 1: Published Paper — Automation for Novel Biological Applications
Paper Citation
Title: Synthetic cells and droplet-based microfluidics (review)
Journal: Small
DOI: 10.1002/smll.202400086
Year: 2024
Abstract Summary
Synthetic cells function as biological mimics of natural cells by mimicking salient features such as metabolism, response to stimuli, gene expression, direct metabolism, and high stability. Droplet-based microfluidic technology presents the opportunity for encapsulating biological functional components in uni-lamellar liposome or polymer droplets. Verified by its success in the fabrication of synthetic cells, microfluidic technology is widely replacing conventional labor-intensive, expensive, and sophisticated techniques justified by its ability to miniaturize and perform batch production operations.
Automation Tool
Droplet-based microfluidics — lab-on-chip systems that automate encapsulation, mixing, and batch production of synthetic cell constructs. Microfluidics serves as the automation platform: it replaces manual, labor-intensive methods with reproducible, tunable, high-throughput workflows.
Biological Applications
| Synthetic Cell Type | Description |
|---|---|
| Lipid vesicles (liposomes) | Uni-lamellar lipid bilayers encapsulating biological components |
| Polymer vesicles (polymersomes) | Polymer-based membranes for encapsulation |
| Coacervate microdroplets | Liquid-liquid phase separation compartments |
| Colloidosomes | Colloidal particle-stabilized droplets |
The review discusses microfluidic chip design for synthetic cell preparation, the combination of microfluidics with bottom-up synthetic biology for reproductive and tunable construction, and advances in biosensors and biomedical applications.
Novel Aspects
- Reproducible, tunable construction — Batch production from simple structures to higher hierarchical structures
- Miniaturization — Replaces conventional expensive techniques
- Integration — Design, assembly, manipulation, and analysis within lab-on-chip devices
- Biomedical relevance — Biosensors, drug delivery, therapeutic applications
Why This Paper Fits the Assignment
Microfluidics is an automation tool that achieves novel biological applications: it automates the fabrication of synthetic cells at scale, enabling research that would otherwise be labor-intensive and costly. The paper provides an overview of how this automation enables bottom-up synthetic biology and biomedical innovation.
Part 2: Automation Tools for Final Project — gumol + ECSOD + new-Clara
Project Overview
Project in development: A combined computational–experimental pipeline to study ECSOD (extracellular superoxide dismutase) overexpression from mesenchymal stem cells (MSCs) in acute radiation environments, with microfluidic validation serving as a surrogate for radiation exposure.
Pipeline Components
| Component | Role |
|---|---|
| gumol | Custom MD simulation engine in Rust for molecular dynamics in acute radiation environments |
| ECSOD / MSC | Simulated overexpression of extracellular superoxide dismutase from MSC cells (mechanism still being refined) |
| new-Clara | Microfluidic system for controlled validation runs |
| Surrogate model | Microfluidic oxidative stress used as a surrogate for radioactive conditions |
Workflow: Simulation → Validation → Correlation
Automation Tool: new-Clara Microfluidic System
new-Clara is the primary automation tool in this project. It provides:
- Controlled oxidative stress — Reproducible delivery of oxidative conditions as a surrogate for radiation
- Precision and throughput — Automated, repeatable runs instead of manual handling
- Data alignment — Outputs that can be directly compared with gumol MD results
Because radiation experiments are costly and regulated, the microfluidic oxidative environment acts as a surrogate for acute radiation, enabling validation of computational predictions under safer, more accessible conditions.
What Will Be Automated
- Microfluidic runs — new-Clara controls flow, dosing, and timing of oxidative stress
- Data collection — Automated or semi-automated readouts (e.g., fluorescence, viability) for correlation with MD
- Parameter sweeps — Systematic variation of oxidative stress levels to map dose–response and compare with simulation
Connection to Part 1 (Synthetic Cells Paper)
The synthetic cells / droplet microfluidics review supports this project by demonstrating how microfluidics enables:
- Reproducible, tunable conditions — Aligned with the need for controlled oxidative stress
- Lab-on-chip workflows — Similar to new-Clara’s role in validation
- Biosensor and biomedical applications — Relevant to ECSOD and MSC-based therapies for radiation injury
Current Status & Next Steps
- gumol — MD engine in Rust, in development
- ECSOD/MSC mechanism — Still being refined
- new-Clara — Microfluidic system for validation runs
- Surrogate design — Oxidative stress protocol as radiation surrogate
Example Pseudocode (Conceptual)
Summary
| Part | Content |
|---|---|
| Part 1 | Synthetic cells via droplet microfluidics — microfluidics as automation for reproducible, tunable biological fabrication |
| Part 2 | gumol (Rust MD) + ECSOD/MSC + new-Clara microfluidic validation — oxidative surrogate for radiation, MD–experiment correlation |
This homework does not need to be tested on the Opentrons yet; it describes the intended automation workflow for the final project.