Universal Microbial Diagnostics using Random DNA Probes

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dc.contributor.advisorBaraniuk, Richard G.
dc.contributor.committeeMemberKemere, Caleb T.
dc.contributor.committeeMemberDrezek, Rebekah A.
dc.creatorAghazadeh Mohandesi, Amir Ali
dc.date.accessioned2014-08-04T19:44:11Z
dc.date.available2015-05-01T05:01:02Z
dc.date.created2014-05
dc.date.issued2014-04-23
dc.date.submittedMay 2014
dc.date.updated2014-08-04T19:44:11Z
dc.description.abstractThe accurate and efficient identification of microbial organism such as viruses and bacteria has mounting importance in the fields of health care, environmental monitoring, and defense. As an example, sepsis from bacterial infection is currently the 11th leading cause of death in the United States. However, current microbial detection strategies are cost-prohibitive, time-consuming and inevitably use unique sensors that are specific to each species to be detected. In this thesis we present a novel microbial sensing platform capable of both detecting the presence and estimating the concentration of microbial organisms in an infectious sample using a small number of random DNA probes. Our Universal Microbial Diagnostics (UMD) platform leverages the theory of sparse signal recovery (compressive sensing) to stably identify the composition of a sample containing several bacteria from a potentially large library of target bacteria. We experimentally validate UMD in vitro using a set of random sloppy molecular beacons to recover pathogenic bacteria without DNA amplification. We also evaluate the average performance of UMD in silico for genus and species level identification of 38 common human pathogens. A particularly promising property of UMD for health care, environmental monitoring, and defense applications is that a fixed set of random measurement probes are universal in the sense that they can characterize novel organisms not present in the target library.
dc.embargo.terms2015-05-01
dc.format.mimetypeapplication/pdf
dc.identifier.citationAghazadeh Mohandesi, Amir Ali. "Universal Microbial Diagnostics using Random DNA Probes." (2014) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/76337">https://hdl.handle.net/1911/76337</a>.
dc.identifier.urihttps://hdl.handle.net/1911/76337
dc.language.isoeng
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.
dc.subjectCompressive sensing
dc.subjectMolecular beacons
dc.subjectPathogen
dc.subjectDiagnostics
dc.titleUniversal Microbial Diagnostics using Random DNA Probes
dc.typeThesis
dc.type.materialText
thesis.degree.departmentElectrical and Computer Engineering
thesis.degree.disciplineEngineering
thesis.degree.grantorRice University
thesis.degree.levelMasters
thesis.degree.nameMaster of Science
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