Week 3 HW: Lab Automation

This page tackles all homeworks of week 3.

Artistic Design Generation:

A green dinosaur on the left with a smaller red plant on the right — *My original design*

A green Brachiosaurus with a human to scale — Inspiration!
Image generated in my collab notebook is of lower quality.

A large green dinosaur in the middle with a smaller blue human on the left to scale. There is a yellow sun in the top left, a large red in the top middle, and an asteroid in the top right. The lifeforms are enjoying the blue-green horizon, unbeknownst to... — *Refined design*

Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.
The Million Molecule Challenge by Ora Biomedical aims to find the best combination-drugs for enhancing C. Elegans longevity. They developed an autonomous lab that can capture this data continuously throughout the worm’s lifespan (and the worm with the longest healthspan makes its combinatorial drug intervention win). This can be extended to larger lifeforms with novel automations.

(Post this point, I have had to use AI help extensively for my homeworks, as almost everything is brand new to me.)

Final Project Automation Strategy

For my final project investigating co-translational folding differences between wild-type and retro-proteins (GB1/Ubiquitin), precision and reproducibility are critical. Because I am testing how environmental factors (like temperature gradients and microgravity) affect folding pathways, doing this manually would introduce high pipetting variance and human error. I plan to automate the sample preparation and expression phases using the following three approaches:

1. Ginkgo Nebula (Cloud Lab) for Thermal Gradient CFPS To rigorously test my hypothesis regarding temperature-dependent final states (and simulated global warming effects), I will use the cloud lab to run a high-throughput cell-free protein synthesis (CFPS) array.

Echo Liquid Handler: Transfer specific molarities of wild-type and retro-DNA templates into a 384-well plate.
Bravo/Multiflo: Dispense the CFPS lysate and energy master mix into all wells to initiate translation.
PlateLoc: Seal the plate to prevent evaporation.
Inheco Thermocyclers: Incubate different zones of the plate at precise, distinct temperature brackets (e.g., 25°C, 30°C, 37°C, 42°C) simultaneously.
PHERAstar: Read initial baseline fluorescence/absorbance if tagged, before routing the plates to downstream purification.

2. Automated Tryptic Digestion for LC-MS/MS (Opentrons OT-2) To confirm the primary structure and sequence inversion, the proteins must be digested into peptide fragments for tandem mass spectrometry. Tryptic digestion is highly sensitive to enzyme ratios and timing.

I will script an Opentrons OT-2 protocol to automate the addition of denaturation buffers, DTT (reduction), IAA (alkylation), and Trypsin.
The robot will handle the precise micro-volume washing and desalting steps on a magnetic module before LC-MS/MS injection, ensuring my bottom-up peptide mapping is perfectly standardized.

3. Custom 3D Printed Microfluidic Holders for Microgravity For the space-based cell-free expression chambers, standard well plates cannot be used due to fluid behavior in zero gravity. I will design and 3D-print a custom hardware holder (compatible with automated liquid handler decks on Earth) that securely locks down sealed, microfluidic cell-free chips. This allows the robots to prepare the space-bound assays perfectly before they are shipped to the ISS.

UPDATE: These are my final individual project slides, which I actually presented during the Global Committed Listeners Online Spree (please comment your thoughts, or reach out if you wish to collaborate).

This visualization illustrates the core of your final project: how climate change disrupts the delicate internal energy landscapes required for proteins to fold correctly.
This detailed 3D infographic creates a narrative landscape, contrasting a stable environment with the 'Elevated Thermal Energy State' of a warming world.
Homeostatic State (Cool Zone): On the left, under a stable climate, the protein chain rolls smoothly down a clear potential energy funnel into its deep, well-defined well, labeled Native Fold (Correct). This leads to Functional Proteins and functional biology. A chart shows high correct folding probability.
Climate-Induced Impact (Warming Zone): On the right, environmental waves of fiery red and orange heat ripple through the scene, distorting the funnel. The energy wells are shallower and broader. The protein chain rolls down but gets trapped or diverted, forming tangled Misfolded Intermediates / Aggregates (Error), labeled as Biological Dysfunction. The charts show a clear shift toward error probability.
Collaboration Calls: Icons for diverse scientists and research groups (labeled with your project's context) indicate the needed global research network. The central title directly state JOIN THE RESEARCH: COLLABORATE.
This image will serve as a powerful summary and invitation for others to join you in understanding these critical climate-induced biological problems. — I am also interested in understanding how climate change-induced changes within the internal (homeostatic; thermal) energy landscape can increase the probability of protein folding errors (or even change the protein structures), which can lead to a host of other biological problems due to global warming!