When I was child, “scientist” was the response I gave to the adults, who poll small children on career ambitions. Being a scientist meant playing with dirt and colored fluid, all day, before emerging with an Einstein-esque hair-do to proclaim facts nobody, not even teachers, knew. As I grew up, my image of a scientist became more nuanced and, well, scientific, but the idea of working in the sciences lingered in my mind. Science was the creation of wholly new knowledge explaining life, the universe, and everything else. After tasting it in my science classes, I knew I wanted more. This summer, I took a position in Professor Callahan’s plant genomics lab, ready to embark on my own Mendelian quest.
Professor Callahan’s lab is involved in the Undergraduate Phenotyping of Arabidopsis Knockouts (UnPAK) project, a collaboration between schools across the country studying genomics in the Arabidopsis thaliana plant. The Arabidopsis is a small flowering plant generally considered to be the botany equivalent of the fruit fly in genetic research. UnPAK uses a set of mutant “knockout” plants in which a single gene is disrupted and can no longer be expressed due to a T-DNA insertion. One research goal of the project is to investigate how often and which mutations result in an observable phenotypic change in fitness-related traits. The genetic basis behind how and when mutations affect fitness is not well-known and plays a key role in understanding evolution.
We have also run analyses on our UnPAK data testing the effect of differing environmental conditions on phenotypic expression. As a mean to control for unavoidable environmental differences between repeated experiments, and even between trays of plants in the same experiment, UnPAK uses a group of non-mutant plants called phytometers. This plants are from eleven different lineages, displaying a wide range of traits. For example, one phytometer plant might always be relatively short, while another is tall. By planting these phytometers amidst the mutants in each experiment, the phytometers are exposed to the same environmental variation. The mutants in each experiment are compared the phytometers when analyzing the data, in order to account for how the environment might have affected the mutant phenotype.
Due to the number of mutations and replications that must be conducted, in order to obtain sufficient data to trace genomic patterns, experiments are conducted at many different schools; the results are compiled into an UnPAK database. My additional project, this summer, involves analyzing the data amassed over several years of UnPAK experiments and looking for mutations that seem to promote increased variability for a trait. Plants with such a mutation (for example, promoting variability in plant height) would display a wide range of heights, despite having the same genotype. Previous analyses have identified several possible mutations. This summer, I will be conducting further analyses and performing additional experiments with these especially variable mutants. Since variation is the foundation on which evolution acts, increased variability could be evolutionary advantageous in some environments.
The hands-on nature of lab work: physically planting and harvesting mutant seeds, collecting tissue for genotype analysis, and measuring traits gives me a new perspective on the genetic theories that I’ve learned in class. As we observe a particularly unusual phenotype, make hypotheses, and analyze our data, my PI refers to concepts in genetics and biotechnology that I had previously understood only abstractly. There’s nothing that compares to watching biological concepts formerly taken at face value prove themselves before your very eyes. It’s really quite beautiful.