EXPLORATION OF NUCLEIC ACID-BASED PLATFORMS FOR MICROBIAL IDENTIFICATION

Simple item page
dc.contributor.advisorDrezek, Rebekah Aen_US
dc.creatorBugga, Pallavien_US
dc.date.accessioned2020-08-21T17:20:08Zen_US
dc.date.available2021-02-01T06:01:12Zen_US
dc.date.created2020-08en_US
dc.date.issued2020-08-20en_US
dc.date.submittedAugust 2020en_US
dc.date.updated2020-08-21T17:20:08Zen_US
dc.description.abstractThe rapid and accurate identification of microbes is critical for a variety of industries, notably healthcare, bioterrorism/defense, food and agriculture, and environmental testing. Nucleic acid-based identification platforms, in particular, have introduced marked improvements in the overall specificity and sensitivity of pathogen detection. While tremendous technical progress has been made in addressing the specific demands of these various sectors, there still exists a significant unmet need for a rapid and universal microbial identification platform in the clinic. Using a set of universal, target-agnostic probes, microbial species can be readily distinguished from one another based upon the observed variability in the total number of unique hybridization events between each probe and each target genome. In this way, both the identity of the microbe and its infectious load can be determined. To that end, this work first establishes the efficacy of a specific universal-probe that builds off of existing toehold-probe technologies. Given the overly narrow thermodynamic constraints of single-mismatch protectors in traditional toehold-probes, and the inherent noisiness of standard molecular probes, we herein introduce “sloppy” or mismatch-tolerant universal toehold-probes, and validate their efficacy by demonstrating successful detection and characterization of viral subpopulations or quasi-species in patient-derived viral DNA. This work also investigates several novel schemes that utilize a set of target-agnostic universal toehold-probes to rapidly and accurately identify bacterial species with high sensitivity. These include probe-capture, endonuclease cleavage, size-exclusion chromatography, and fluorescence in situ hybridization.en_US
dc.embargo.terms2021-02-01en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationBugga, Pallavi. "EXPLORATION OF NUCLEIC ACID-BASED PLATFORMS FOR MICROBIAL IDENTIFICATION." (2020) Diss., Rice University. <a href="https://hdl.handle.net/1911/109252">https://hdl.handle.net/1911/109252</a>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/109252en_US
dc.language.isoengen_US
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.subjectBacterial Diagnosticen_US
dc.subjectBacteria Identificationen_US
dc.subjectMicrobial Detectionen_US
dc.subjectqPCRen_US
dc.subjectsmFISHen_US
dc.subjectViral Quasi-Speciesen_US
dc.subjectDNA Probesen_US
dc.subjectOligonucleotidesen_US
dc.titleEXPLORATION OF NUCLEIC ACID-BASED PLATFORMS FOR MICROBIAL IDENTIFICATIONen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentBioengineeringen_US
thesis.degree.disciplineEngineeringen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelDoctoralen_US
thesis.degree.nameDoctor of Philosophyen_US
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
BUGGA-DOCUMENT-2020.pdf
Size:
8.59 MB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 2 of 2
No Thumbnail Available
Name:
PROQUEST_LICENSE.txt
Size:
5.84 KB
Format:
Plain Text
Description:
Download
No Thumbnail Available
Name:
LICENSE.txt
Size:
2.61 KB
Format:
Plain Text
Description:
Download
Collections
Rice University Theses and Dissertations