Associate Professor Sara Zimmer PhD

DMED Biomedical Sciences
Medical School
Twin Cities
Project Title: 
Molecular Parasitology

These researchers explore gene expression of the mitochondria of trypanosomes. They investigate both the changes that occur in gene expression throughout the parasites' life stages which include human and insect hosts, and the mechanism whereby these changes are regulated. They are using MSI resources to store populations of non-encoded tails on 3' ends of mitochondrial mRNAs. These tails potentially play regulatory roles in RNA stability, editing, and translation. The composition and lengths of these tails appear to be transcript and life-stage specific, so the researchers sequence 100,000 to millions of these tails per each transcript to understand their characteristics. Raw reads as well as processed files are stored at MSI, and the researchers use the Galaxy platform to perform initial stages of the analysis.

The group also extensively sequences edited trypanosome mitochondrial transcriptomes and analyzes how the editing changes between strains and under different environmental conditions. They also occasionally sequence mitochondrial genomes to assess heteroplasmy, as this affects the sequence used as a reference for the RNA-seq analysis. The RNA-seq requires huge datasets since mitochondrial RNA is only a subset of total RNA.

Project Investigators

Dr. Juan Abrahante Llorns
Professor Marshall Hampton
Clara Smoniewski
Associate Professor Sara Zimmer PhD
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