Universal Microbial Diagnostics using Random DNA Probes

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dc.contributor.advisorBaraniuk, Richard G.en_US
dc.contributor.committeeMemberKemere, Caleb T.en_US
dc.contributor.committeeMemberDrezek, Rebekah A.en_US
dc.creatorAghazadeh Mohandesi, Amir Alien_US
dc.date.accessioned2014-08-04T19:44:11Zen_US
dc.date.available2015-05-01T05:01:02Zen_US
dc.date.created2014-05en_US
dc.date.issued2014-04-23en_US
dc.date.submittedMay 2014en_US
dc.date.updated2014-08-04T19:44:11Zen_US
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.en_US
dc.embargo.terms2015-05-01en_US
dc.format.mimetypeapplication/pdfen_US
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>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/76337en_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.subjectCompressive sensingen_US
dc.subjectMolecular beaconsen_US
dc.subjectPathogenen_US
dc.subjectDiagnosticsen_US
dc.titleUniversal Microbial Diagnostics using Random DNA Probesen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentElectrical and Computer Engineeringen_US
thesis.degree.disciplineEngineeringen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelMastersen_US
thesis.degree.nameMaster of Scienceen_US
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