Lab Project


The laboratory portion of this class is concerned almost entirely with the selection, design, and execution of your own research project utilizing readily-available knockout mutants in the model plant Arabidopsis. This project can address almost any topic you choose within the broad field of plant physiology. Past project topics have included the following:

Sugar sensing & signaling, Responses to wounding, Cold sensing and acclimatization, Gravitropism, Auxin transport, Flowering time regulation, Pollen tube growth, Heavy metal tolerance & uptake, Responses to pathogens (viruses, bacteria), Plastid movement regulation, Phototropism, photomorphogenesis, Ethylene responses, Stomatal regulation, Leaf development

Explore Topics

To help you become more familiar with potential topic areas, you will begin by surveying current literature in plant physiology. At this stage, your question should be, “What do I find interesting about plants?” It could be a structure, like a flower, or it could be a process, like carbon assimilation or phototropism. If you already know of a few topics you’re interested in, great, go to one of the library’s academic databases and perform a search on your topic. If you don’t have any topics in mind, no problem, go to some of the journals listed below and just browse. The point is to find 10 or 12 articles that catch your attention and write a brief summary of the central question and findings, which you should be able to surmise from the abstract. Start with the following journals:

Create Reading Notes

When you have found an article that intrigues you, you’ll want to take some notes about it so you’ll remember what you’ve seen and can share it with the rest of the class. I have created a note-taking form for this in BishopApps. Fill in the requested information and click ‘Submit’. Do this for each article you find, ideally 10-12 at a minimum. After a period of browsing current literature for topic ideas, you will get access to the list of articles submitted by the whole class. Review the articles saved by other students in the class, looking for areas of overlap or shared interests.

Find Candidate Genes

After identifying some articles that catch your attention, you can begin to generalize that interest into a topic area within plant physiology. Your next task is to identify some genes involved in your area of interest. Given that Arabidopsis has almost 30,000 genes, this could take a while were it not for a number of useful tools that help to group and organize genes by structure, function, or process – the Gene Ontology system. You can access this tool from the Arabidopsis website ( Browse : Ontologies/Keywords. Begin by traversing the hierarchical tree of ontologies with your area of interest in mind, narrowing the field as you go. Once you have sufficiently narrowed the tree, click on the topic itself to see how many loci have been classified within that node. Clicking on the loci link with provide a list of those loci, which you can then follow to learn more about the individual genes at those loci.