Skip to content

Ortholog Scan Project — ispA

This capstone exercise guides you through designing and documenting a complete cloning project centered on ispA, a key enzyme in the isoprenoid biosynthesis pathway. You’ll build an ortholog expression panel in the context of plasmid pLYC72. This gene presents more complexity than previous examples—biochemical differences among orthologs can influence the outcome, making your selection and rationale especially meaningful.

Project Overview

Your goal is to follow the full cloning pipeline we've developed throughout the tutorial series. You’ll prepare a complete project folder for an experiment called lycopene34, which includes design files, construction plans, lab documents, and a short writeup.

Although this exercise is built around ispA, the tutorial doubles as a model for how to present any cloning-based project. You’re encouraged to customize or extend it depending on your interests, as long as the documentation standards are met.

Key Elements

Your lycopene34 project folder should include:

  • Construction File(s) covering all planned builds
  • Inventory, Oligos, and LabSheets
  • Annotated GenBank files
  • A Docs/ folder with a written summary (as a README.md, Word doc, or PDF)

The summary should explain:

  • What the project is about
  • The biology and context of the ispA gene
  • Why you chose your orthologs (biochemical rationale, functional hypotheses, etc.)
  • Any literature you consulted

Use this document to guide the reader through the logic and goals of your experiment.

For a reference format, see the example Docs folder from the lycopene33 project. The lycopene33 README offers only a minimal discussion of ortholog selection. A more thorough analysis will require digging into the biochemistry of ispA and understanding how functional diversity informs design.

Notes

  • Tools like BLAST, Benchling, ApE, and C6-Tools are useful for ortholog selection and design.
  • Use C6-Tools or CFS to simulate your Construction Files to catch errors.
  • This project is your chance to demonstrate what you've learned—how to plan and document a cloning experiment, how to design and simulate constructs, and how to connect biological rationale to your choices. Your submission should reflect a clear understanding of the experimental goal, how your design supports it, and the biochemical implications of your choices.

Submission

Submit a zipped copy of your completed lycopene34 project folder.

All students, regardless of project topic, are expected to document their projects in this format. The writeup should be appropriate to your specific experiment and guide the reader through your design and decisions.