Dissertation Defense Announcement
To:  The George Mason University Community

Candidate: Parsa Hosseini
Program:    PhD Bioinformatics & Computational Biology

Date:   Monday November 4, 2013
Time:   10:00 a.m.
Place:  George Mason University
            Prince William Campus
            Occoquan Building, Room 204
Dissertation Director: Dr. Benjamin F. Matthews
Committee Chair: Dr. Saleet Jafri
Committee members: Dr. Patrick Gillevet, Dr. James D. Willett, Dr. Ivan Ovcharenko

Title: "Quantifying the Glycine max proximal cis-regulome during pathogenesis"

The dissertation is on reserve in the Johnson Center Library, Fairfax campus.
The doctoral project will not be read at the meeting, but should be read in advance.

All members of the George Mason University community are invited to attend.

At its very essence, sequence analysis provides the ability to compare and identify patterns in biological sequences. With respect to biological systems, such patterns and their respective frequencies shed light on systematic involvement upon perception of positive or negative stress. In transcription regulation, such patterns are known as transcription factor binding sites (TFBSs) and serve as docking sites for regulatory proteins to initiate downstream transcription. With today’s transcriptomic assays capable of sequencing cDNA at unprecedented levels of granularity and resolution, we can now quantify over-representation of not only these proximal elements but also entire transcriptomes. Novel questions can now be proposed, questions that necessitate utilization of modern high-throughput sequencing platforms. Such assays can assist investigators build novel isoform models and ultimately get one step closer to filling in gaps sprinkled throughout the organismal systematic landscape. These sequencing technologies, known by many as next-generation sequencing (NGS), encompass ultrafast, parallel sequencing assays. Their name is fitting for the intent: unprecedented nucleotide resolution with a dynamic range of expression. A popular NGS assay is RNA Sequencing, or RNA-Seq for short. RNA-Seq provides the means to sequence whole-RNA without a reference library. Unlike prior hybridization-based assays such as microarrays, no probe-sets are required, making it possible to quantify exon abundance, structural variants and novel transcript isoforms.


To date, little research has been performed which uses NGS to quantify the common soybean (Glycine max) transcriptome and deduce abundance of proximal regulatory elements at various stages of pathogenesis. Over the course of four independent peer-reviewed studies, we have sequenced and quantified the soybean transcriptome upon inoculation with various pathogens. Such studies pave the way for elucidating proximal regulatory element dynamics across an infection time-course. Current results reveal a cis-regulatory signature that captures host defense regulatory dynamics as well as potentially novel transcripts involved in biotic stress response. Our results propose potentially the first high-coverage examination of the soybean cis-regulome upon inoculation with two major pathogens.