| Start Date: | 9/21/2016 | Start Time: | 10:30 AM |
| End Date: | 9/21/2016 | End Time: | 12:30 PM |
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Event Description
BIOMED PhD Research Proposal
Title:
Microbial Characteristics of Chronic Respiratory Disease Conditions
Speaker:
Joshua P. Earl, PhD Candidate, School of Biomedical Engineering, Science and Health Systems
Advisors:
Will Dampier, PhD, Assistant Professor, Dept. of Microbiology & Immunology, and Garth Ehrlic, PhD, Professor, Dept. of Microbiology & Immunology, Otolaryngology, both in DUCoM
Abstract:
This study is primarily on how the presence of different microorganisms affect, or are affected by chronic respiratory and sinonasal disease states in human subjects. Specifically, how the composition of the sinonasal cavity bacterial microbiome changes during chronic rhinosinusitis (CRS) and how Moraxella catarrhalis (M.c.) is involved in, and evolving with another chronic disease, Otitis Media (OM). Bioinforamtic techniques are utilized to examine whole genome sequence data identifying unique genetic differences within a population that is split between two phenotypes. This is a proposal to identify these characteristics which could have profound impacts on how these diseases are treated.
Further exploration on another disease, CRS, characterizes how it is influenced by a community of different organisms. To illustrate this characterization of the microbiome with and without the disease state is required. Traditional microbiome sequencing yields poor specificity because short read sequencers can only capture a portion of the 16s ribosomal subunit gene (the gene primarily used for bacterial classification). Short sequences are significantly affected by sequencing error. Relatively few nucleotide changes are required before a read will become divergent enough from another similar read (simply by error) to be classified as a separate species (Kunin et al. 2010). To overcome these shortcomings a new pipeline (MCSMRT) was developed which combines both a new sequencing technique (using the Pacific Biosciences sequencer to acquire whole 16s gene sequence), and the Usearch suite of programs (Edgar 2010). Initial sequencing of two mock communities (combinations of multiple different known bacterial species into a single sample) illustrate the sensitivity and specificity of this method, and provide a testbed for parameter tuning. |
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Location:
New College Building, 18th Floor Conference Room, located at 245 N 15th Street (15th & Race Streets). A shuttle is available from 33rd and Market Streets. |
Audience:
Undergraduate StudentsGraduate StudentsFacultyStaff |
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