Week 3 Lab & HW

Part 1

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

Vespers III

The paper presents a fabrication platform for making 3D-printed objects whose surfaces host living bacteria that respond to chemical signals embedded in the print material. The central idea is that a multimaterial inkjet printer can be used not just to control mechanical properties, but to spatially distribute chemical inducers throughout an object — and that bacteria coated onto the surface will “read” those signals and express proteins accordingly. The printer they used (Stratasys Objet Connex500) normally blends a rigid build resin with a sacrificial support resin to handle overhangs. The authors noticed that the support resin (SUP705) is hygroscopic — it absorbs water — which makes it useful for soaking up and slowly releasing chemical solutions like IPTG. By controlling how much support resin appears in each voxel, they could tune how much inducer gets released at any given spot on the surface. Later in the paper they go further and dissolve inducers directly into custom resin formulations loaded into the print cartridges, which lets them place two different chemical signals (IPTG and AHL) independently during a single print job. Bacteria are delivered by spraying a warm hydrogel-cell mixture onto the surface, which gels on contact. The hydrogel keeps cells alive, feeds them, and lets the inducers diffuse through from the print material below. Depending on what genetic circuits the cells carry, they produce visible outputs — blue or magenta pigment via β-galactosidase activity, or fluorescent proteins. The team also tested cells with AND and NAND logic gates, so expression only occurs where both signals are present, or where neither is. They built a computational model to predict how signals diffuse across 3D surfaces over time and how bacteria respond, which they validated against experimental results. The match was reasonable in most regions but broke down close to high-concentration signal sources, partly because some material compositions turned out to lower local pH and suppress expression — something the model didn’t account for.

Part 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.

I don’t know which direction I want to go yet for my final project. If I go the route of the emergent subtractive fabrication, I’d use the Opentrons to characterize my genetic circuit by running arabinose concentration gradients across a 96-well plate to find the induction threshold where the tphr gate reliably drives amIICP expression. I’d design and order the circuit parts through Ginkgo Nebula, and build a simple 3D printed holder to keep PET samples consistently positioned during the degradation assay. However, if I instead go with the community DNA archive, I would focus more on the software side first — writing an encoder that converts community submissions into .fasta sequences with error correction built in — and then use the Opentrons to optimize the silica encapsulation step, running a matrix of silica-to-DNA ratios to find conditions that actually hold up for long-term storage before casting the final resin tiles.

Example 1: You are creating a custom fabric, and want to deposit art onto specific parts that need to be intertwined in odd ways. You can design a 3D printed holder to attach this fabric to it, and be able to deposit bio art on top. Check out the Opentrons 3D Printing Directory. Example 2: You are using the cloud laboratory to screen an array of biosensor constructs that you design, synthesize, and express using cell-free protein synthesis. 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.

Recitation slides: 2026 Committed Listener Final Project Ideas: CRIT #1