Dissertation Defense Schedule
Academic Excellence
Sharing original dissertation research is a principle to which the University of Delaware is deeply committed. It is the single most important assignment our graduate students undertake and upon completion is met with great pride.
We invite you to celebrate this milestone by attending their dissertation defense. Please review the upcoming dissertation defense schedule below and join us!
PROGRAM | Animal and Food Science
Integrated, scalable tools for small RNA genomics: Novel algorithms and their application to characterize germline-associated pathways in diverse species
By: Atul Kakrana Chair: Blake Meyers Co-Chair: Cathy Wu
ABSTRACT
Dissertation work focused on (1) the development of computational tools for the analysis of plant small RNAs, particularly miRNAs and their secondary siRNA products, and (2) the application of these tools to the analysis of reproductive phasiRNAs in monocots. Cells associated with the male germline, specifically in rice and maize (grasses), produce diverse and numerous “phased” 21-nt and 24-nt siRNAs. These phased siRNAs (phasiRNAs) show a striking similarity to mammalian Piwi-interacting RNAs (piRNAs) in terms of their abundance, biogenesis, and timing of accumulation. My work traces the prevalence and origins of phasiRNA pathways in monocot evolution. I will present a new set of tools to identify miRNA targets and to computationally characterize phasiRNAs, which together comprise important methods for plant sRNA field. These next generation tools efficiently scale to the increasing volume of high-throughput data and are fast, sensitive and feature-rich compared to the existing options. Using these new tools, I investigated small RNAs in the recently sequenced genome of Asparagus officinalis and two other species, each representing a distinct evolutionary time point. I demonstrate that reproductive phasiRNAs emerged at least 114 million years ago, and their presence in male germline is either not a general characteristic or it is the product of evolutionary refinement in grasses. I also show that exceptions to the canonical mechanism of biogenesis of phasiRNAs exist in monocot evolution. I conclude that plants show substantial variation in their composition and biogenesis of reproductive phasiRNAs, which have broader roles in plant germline development.
The Process
Step-by-Step
Visit our “Step-by-Step Graduation Guide” to take you through the graduation process.From formatting your Dissertation to Doctoral Hooding procedures.
Dissertation Manual
Wondering how to set up the format for your paper. Refer to the “UD Thesis/Dissertation Manual” for formatting requirements and more.
Defense Submission Form
This form must be completed two weeks in advance of a dissertation defense to meet the University of Delaware Graduate and Professional Education’s requirements.
