Reading (For Dummies)

Genetic "Fuzzing"

One of the things I absolutely love about dating a genetic engineer is learning the crossover between our two fields. Tonight, she taught me about genetic fuzzing.

Genetic research is kind of like penetration testing. At least, as a computer security nerd, that's how I like to think of it. There's an awful lot of compiled code to look at (genes). The classically slow method of finding a portion of a gene responsible for a certain characteristic is to find a lot of examples of the organism with the trait in question, start sequencing them, and find overlaps. Bioinformatics has a lot to add, although there's is almost too much data to search through.

A researcher that she just ran into came up with one of those "Duh," ideas, though. The researcher was trying to find a way to make a certain plant drought-tolerant. A typical way to influence drought tolerance in plants is to find the genes that control their guard cells. Guard cells, if you remember from high school biology class, are on the underside of leaves, and are responsible for absorbing carbon dioxide and releasing oxygen from the plant. One of the side-effects, or "feature" of guard cells is that they release a fair amount of water. There are a few chemical modifications that can be made in the way guard cells process carbon dioxide. Naturally, implementing these changes requires knowing where and on which gene in a plant guard cells are controlled.

Laura began tackling the problem of drought tolerance by studying guard cells in undergrad. Her approach was to find the genes controlling guard cells. She looked at transgenic plants with a reporter gene (which turns blue in the presence of another chemical) randomly inserted in the genome, a method known as enhancer trap tagging. The reporter gene would mimic the expression of the adjacent gene (blue coloration in the tissue where the adjacent gene is expressed). Through screening the collection, she looked for the blue coloration in the guard cells. After finding several individuals, the adjacent gene can be determined, through gene-specific cloning, and analyzed further. It's a slow process.

The other researcher used the reverse method. Instead of finding plants that were drought tolerant, he took normal plant seeds, exposed them to a toxin that produces a high number of genetic copy errors in DNA replication (ethyl methyl sulfonate -EMS), and planted them. He let them grow up a bit, and then starved the plants of water. After a few runs, he found some plants that were surviving! Obviously they had mutations that were limiting water vapor transpiration from the guard cells. Some sequencing work could then be used to narrow it down. The gene mutation found increased drought tolerance by enhancing ABA (plant hormone: abscisic acid) sensitivity for seedling growth and stomatal closure [1]

Of course, this method doesn't work for a lot of things, like, say, animals (PETA) or humans (er...). For plant biologists, though, it's quite an interesting technique because it's almost-but-not-quite an obvious approach to finding what they're looking for...

[1] Chen Z et al. (2006) Mutations in ABO1/ELO2, a subunit of holo-Elongator, increase abscisic acid sensitivity and drought tolerance in Arabidopsis thaliana. Mol Cell Biol 26(18): 6902