Welcome to the Methods in Modern Plant Biology course, developed by Cӑtӑlin Voiniciuc for undergraduate students at the University of Florida.
Level: Undergraduate (sophomore–senior)
Class time: 1 semester (13 weeks)
Number of students: 12
Student : robot ratio: 12:1
Content: 12 plant molecular biology labs
Protocol types: Protocol Designer, Python protocols (no coding experience required)
In 13 weeks, students complete a cloning workflow, gaining experience in lab automation, plasmid DNA methods, restriction digestion analysis, primer and experiment design, E. coli work, and more. Download the Introduction to the Course for a course overview, materials list, and additional information. You can download the full course here or individual lesson plans below.
Lab Module 1: Introduction to Automation
Students explore automation in the lab using the OT-2 and Opentrons Protocol Library and Protocol Designer.
Lab Module 2: Automating Laboratory Work with the OT-2
Students compare automated and manual tasks in the lab with a Bradford assay. This lesson plan also introduces types of protocols used with Opentrons robots.
Protocol: Pierce Bradford Protein Assay
Lab Module 3: Assembling Your Molecular Toolkit
Students manually extract plasmid DNA from bacterial cells. The OT-2 is used to perform sterile transfer of Agrobacterium reporter strains. An attached worksheet is included to prepare buffers for DNA isolation.
Protocol: LB Distribution
Lab Module 4: DNA Normalization
Students automate plasmid DNA normalization on the OT-2. In this lesson plan, students also visualize their Agrobacterium reporter strains.
Protocol: DNA Sample Normalization
Lab Module 5: Restriction Enzyme Digest
Students complete a restriction enzyme digestion on the OT-2. This lesson plan includes an online Benchling simulation and attached worksheet to guide students through the experiment.
Protocol: Restriction Enzyme Digest
Lab Module 6: Restriction Digest Analysis
Students use gel electrophoresis to analyze their restriction digestion experiment. Opentrons Protocol Designer is used to create bacterial “art” on the OT-2.
Lab Module 7: Primer Design for PCR and Cloning
Students use an attached worksheet to design primers for use in their cloning workflow. The OT-2 automates dilution of primer stocks.
Protocol: Primer Dilution
Lab Module 8: DNA Amplification with PCR
Students use the OT-2 to combine reagents, then amplify DNA for cloning.
Protocol: PCR Preparation
Lab Module 9: DNA Assembly Methods
Students use the OT-2 to prepare for modular cloning (MoClo) assembly in a “one-pot” thermocycler digestion.
Protocol: MoClo Assembly Preparation
Lab Module 10: E. coli Transformation and Recovery
Students use the OT-2 to automate sterile handling and transformation of their assembled plasmids into E. coli cells.
Include protocol library link
Protocol: E. coli Transformation and Recovery
Lab Module 11: Genotyping Bacteria with Colony PCR
Students select colonies and use the OT-2 to prepare for colony PCR.
Protocol: Colony PCR Preparation
Lab Module 12: Sanger Sequencing and Multiple Sequence Alignment
Students use the OT-2 to prepare plasmids for commercial Sanger sequencing.
Protocol: Sanger Sequencing Preparation
