Date of Award
Winter 11-16-2022
Degree Type
Thesis
Degree Name
Master of Science in Integrative Biology (MSIB)
Department
Biology
Committee Chair/First Advisor
Dr. Tsai-Tien Tseng
Major Professor
Dr. Tsai-Tien Tseng
Second Committee Member
Dr. Melanie Griffin
Third Committee Member
Dr. Thomas McElroy
Abstract
Our contemporary, comprehensive phylogenetic study spans all domains to understand the Resistance-Nodulation-Cell Division (RND) superfamily’s evolution and points of divergence. Several members of the superfamily are involved in both the acquisition and intrinsic resistance to antibiotics despite origins that are ubiquitous and ancient compared to modern-day antibiotic use (Nikaido 2018). Exhaustive searches of selected representative sequences through BLAST (Mistry et al. 2013) and HMMSearch (Camacho et al. 2009) created the most comprehensive and up-to-date dataset to establish all possible RND homologs. CD-HIT, a clustering software, was used to refine our dataset (Pearson 2013). Multiple sequence alignments like CLUSTAL (Sievers et al. 2011) and MUSCLE (Edgar 2004) were utilized. Each alignment had differing computational methods used by these programs to offer significant information about the structure and evolution of RNDs that gave collective insight. Phylogenetic trees produced from PhyML, a program based on maximum-likelihood algorithm, were our final products to characterize novel members and sub-families of the RND superfamily (Letunic & Bork, 2021). Evolutionary pathways were elucidated through highly likely clustering and branch lengths. Overall, the study provides a significant update to our understanding of the RND superfamily giving rise to previously uncharacterized members and families.
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