Proteomic profiling of Nguni cattle liver tissue using gel and Gel-Free approaches: methodology development and potential applications

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dc.contributor.advisorBlackburn, Jonathanen_ZA
dc.contributor.advisorMancama, Den_ZA
dc.contributor.advisorStoychev, Sen_ZA
dc.contributor.authorButhelezi, Sindisiween_ZA
dc.date.accessioned2014-07-28T14:54:41Z
dc.date.available2014-07-28T14:54:41Z
dc.date.issued2013en_ZA
dc.descriptionIncludes abstract.
dc.descriptionIncludes bibliographical references.
dc.description.abstractIn South Africa, resource-poor farmers mainly depend on livestock farming for their livelihoods, with cattle production being the most important livestock sector. As a consequence of natural selection in stressful conditions, Nguni cattle have been reported to be metabolically superior to other cattle breeds under unfavourable conditions. Using proteomics, with mass spectrometry at the core of the analysis, the objective of this study was to establish a reliable set of methods for the protein profiling of Nguni cattle livers. To achieve this several alternative technologies were employed and their outcomes compared namely, two-dimensional electrophoresis, fractionation by solution phase iso-electric focusing-reversed phase chromatography (IEF-RP), offline strong cation exchange- low pH reversed phase chromatography (SCX-RP) and offline high pH reverse phase-low pH reverse phase chromatography (RP-RP). All solution based methods were coupled to a tandem mass spectrometer. Protein identification was performed using the ParagonTMAlgorithm of Protein Pilot v4.0 as well as PEAKS v6. The IEF-RP and RP-RP methods achieved similar results in terms of number of proteins identified. In addition, proteins that play a role in the urea cycle (which is believed to contribute to the Nguni cattle’s enhanced metabolic ability) were all identified with both techniques. The RP-RP method was selected as the most appropriate method for future research linked to this work and will be used in the next phase of this project, on the basis that it is easier to automate compared to the IEF-RP method. It will be used beyond the scope of this work to compare levels of expression and modification of the liver proteins and their isoforms in Nguni and Hereford cattle grown under adverse environmental conditions, in order to identify those that may contribute to enhanced liver metabolism in Nguni cattle. This will be complemented by the identification and characterisation of potential polymorphisms with in such proteins that can be used to select for this trait during breeding.en_ZA
dc.identifier.apacitationButhelezi, S. (2013). <i>Proteomic profiling of Nguni cattle liver tissue using gel and Gel-Free approaches: methodology development and potential applications</i>. (Thesis). University of Cape Town ,Faculty of Health Sciences ,Division of Medical Biochemistry. Retrieved from http://hdl.handle.net/11427/3121en_ZA
dc.identifier.chicagocitationButhelezi, Sindisiwe. <i>"Proteomic profiling of Nguni cattle liver tissue using gel and Gel-Free approaches: methodology development and potential applications."</i> Thesis., University of Cape Town ,Faculty of Health Sciences ,Division of Medical Biochemistry, 2013. http://hdl.handle.net/11427/3121en_ZA
dc.identifier.citationButhelezi, S. 2013. Proteomic profiling of Nguni cattle liver tissue using gel and Gel-Free approaches: methodology development and potential applications. University of Cape Town.en_ZA
dc.identifier.ris TY - Thesis / Dissertation AU - Buthelezi, Sindisiwe AB - In South Africa, resource-poor farmers mainly depend on livestock farming for their livelihoods, with cattle production being the most important livestock sector. As a consequence of natural selection in stressful conditions, Nguni cattle have been reported to be metabolically superior to other cattle breeds under unfavourable conditions. Using proteomics, with mass spectrometry at the core of the analysis, the objective of this study was to establish a reliable set of methods for the protein profiling of Nguni cattle livers. To achieve this several alternative technologies were employed and their outcomes compared namely, two-dimensional electrophoresis, fractionation by solution phase iso-electric focusing-reversed phase chromatography (IEF-RP), offline strong cation exchange- low pH reversed phase chromatography (SCX-RP) and offline high pH reverse phase-low pH reverse phase chromatography (RP-RP). All solution based methods were coupled to a tandem mass spectrometer. Protein identification was performed using the ParagonTMAlgorithm of Protein Pilot v4.0 as well as PEAKS v6. The IEF-RP and RP-RP methods achieved similar results in terms of number of proteins identified. In addition, proteins that play a role in the urea cycle (which is believed to contribute to the Nguni cattle’s enhanced metabolic ability) were all identified with both techniques. The RP-RP method was selected as the most appropriate method for future research linked to this work and will be used in the next phase of this project, on the basis that it is easier to automate compared to the IEF-RP method. It will be used beyond the scope of this work to compare levels of expression and modification of the liver proteins and their isoforms in Nguni and Hereford cattle grown under adverse environmental conditions, in order to identify those that may contribute to enhanced liver metabolism in Nguni cattle. This will be complemented by the identification and characterisation of potential polymorphisms with in such proteins that can be used to select for this trait during breeding. DA - 2013 DB - OpenUCT DP - University of Cape Town LK - https://open.uct.ac.za PB - University of Cape Town PY - 2013 T1 - Proteomic profiling of Nguni cattle liver tissue using gel and Gel-Free approaches: methodology development and potential applications TI - Proteomic profiling of Nguni cattle liver tissue using gel and Gel-Free approaches: methodology development and potential applications UR - http://hdl.handle.net/11427/3121 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/3121
dc.identifier.vancouvercitationButhelezi S. Proteomic profiling of Nguni cattle liver tissue using gel and Gel-Free approaches: methodology development and potential applications. [Thesis]. University of Cape Town ,Faculty of Health Sciences ,Division of Medical Biochemistry, 2013 [cited yyyy month dd]. Available from: http://hdl.handle.net/11427/3121en_ZA
dc.language.isoengen_ZA
dc.publisher.departmentDivision of Medical Biochemistryen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.subject.otherMedical Biochemistryen_ZA
dc.titleProteomic profiling of Nguni cattle liver tissue using gel and Gel-Free approaches: methodology development and potential applicationsen_ZA
dc.typeMaster Thesis
dc.type.qualificationlevelMasters
dc.type.qualificationnameMScen_ZA
uct.type.filetypeText
uct.type.publicationResearchen_ZA
uct.type.resourceThesisen_ZA
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