Mutations in Long-lived Trees
Unlike animals, plants do not have a clear separation between reproductive and non-reproductive tissues, like flowers, derive from the same stem cell populations as somatic tissues. Therefore, mutations that arise during vegetative growth can be passed to a plant's offspring. This has led biologists to propose that evolution may operate differently in plants than in animals, which have important consequences for ecology, agriculture and human nutrition. However, recent advances in genomics have called these assumptions into question. In Reed Cartwright's lab, the team is developing methods to study plant somatic mutations and investigating the impact of these mutations on plant physiology and evolution.
Ciliate Mutation Rate and Genomics
Ciliates are unicellular eukaryotes with two nuclei. One nucleus, the smaller micronucleus, holds the germline chromosomes and is transcriptionally silent during vegetative growth. The other nucleus, the larger macronucleus, holds the somatic chromosomes and is responsible for cellular regulation. The macronucleus is built from the micronucleus through a complex process involving amplification and DNA editing. Ciliates have the lowest mutation rate ever measure in eukaryotes and in Reed Cartwright's lab, the team is using the species Tetrahymena thermophila to explore the evolutionary and molecular mechanisms responsible for these low mutation rates. Understanding mutation rates in ciliates can lead to potential impacts on biotech and other DNA-based industries.
Non-model and emerging-model organisms make up the majority of species important to humans; however, most genomic software is designed to work with the handful of model species that are used in laboratory research. In Reed Cartwright's lab, the team is developing new computational methods to enable researchers to study non-model and emerging-model organisms. These methods include MUTK, a robust platform for analysis of mutations, and COATI, a multiple-sequence alignment program desgiend for modern datasets.
Data Science Education
Minecraft is the bestselling video game of all time and the most popular game on YouTube. In Reed Cartwright's lab, they are developing educational materials to teach high-school and college students to analyze data using both Minecraft and R, the premier environment for statistical computing. These educational materials will be based on modern educational research and focus on participatory live coding, where learners actively follow along with an instructor programming and also participate in collaborative problem solving.