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Updike, M. Scott
Thesis (Ph. D.)--Ohio State University, 2007. Title from first page of PDF file. Includes bibliographical references (p. 107-128).
Klammer, Aaron A.
Thesis (Ph. D.)--University of Washington, 2008. Vita. Includes bibliographical references (p. 89-97).
The development of analytical techniques for the detection and characterization of biomolecules a dissertationBlack, Terrence M. 2008 (has links)
Thesis (Ph. D.)--Northeastern University, 2008. Title from title page (viewed Mar. 24, 2009). Graduate School of Arts and Sciences, Dept. of Chemistry and Chemical Biology. Includes bibliographical references (p. 173-176).
Nicora, Carrie Diana
(has links) (PDF)
Thesis (M.S. in environmental science)--Washington State University, August 2009. Title from PDF title page (viewed on Aug. 7, 2009). "School of Earth and Environmental Sciences." Includes bibliographical references (p. 85-94).
Murphy, John Patrick
19 April 2011
Some of the most profound changes elicited by cell growth stimuli influence dramatic rewiring of metabolism. Intriguingly, rapidly dividing cells with aberrant growth factor signalling, such as cancer cells, tend to rely on glycolysis to generate an adequate supply of building blocks required for cell proliferation and invasion. In this study, we observed that in response to stimulation with insulin-like growth factor 1 (IGF-1), MCF-7 breast adenocarcinoma cells show increased levels of the key glycolysis proteins pyruvate kinase M2 and lactate dehydrogenase A. We then developed targeted multiple reaction monitoring (MRM) mass spectrometry assays to conduct quantitative analysis of glycolysis proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs), the latter implicated in pyruvate kinase splicing and many other aspects of cell proliferation. Application of the glycolysis MRM assay to examine IGF-1 stimulated MCF-7 cells revealed increased levels of all sequential proteins from phosphoglycerate mutase 1 to lactate dehydrogenase A in the glycolysis pathway. An extension of this study to cell lines of varying invasiveness, suggest a relation between glycolysis and metastasis. The clinical applicability of glycolysis MRM assay was also shown by its successful application to lung cancer biopsy analysis. Success with the targeted analysis of glycolysis proteins led to a similar approach for the hnRNP family. Our results showed evidence that a poorly characterized hnRNP (A/B) may be regulated by the c-Myc transcription factor but does not evidently influence pyruvate kinase splicing. Our approach using MRM to examine small subsets of proteins downstream of cellular growth signals is relatively novel. Our results demonstrate the potential for such targeted MS strategies because of their high selectivity and multiplexing capabilities. Further, the findings from our analyses provide novel insights into the downstream changes elicited by growth signals such as IGF-1 and c-Myc.
Thesis (M. Med. Sc.)--University of Hong Kong, 2004. Also available in print.
A lot of things happen to proteins when Escherichia coli cells enter stationary phase, such as protein amount, post-translational modifications, conformation changes, and component of protein complex. Proteomics, which study the whole component of proteins, can be used to study the products of the genome and the physiology of Escherichia coli cells at different conditions. By comparing proteome from different growth phases, such as exponential and stationary phase, a lot of proteins with changes can be identified at the same time, which provides a pilot for further studies of mechanism. Current global proteomic studies have identified about 27% of the annotated proteins of E. coli, most of which are predicted to be abundance proteins. Subproteomics, the study of specific subsets of the proteome, can be used to study specific functional classes of proteins and low abundance proteins. In this dissertation, using non-denatured anion exchange column with 2D SDS-PAGE and tandem mass spectrometry, difference of E. coli cells between exponential and stationary phase were studied for whole soluble proteome. Also, using heparin column and mass spectrometry with tandem mass spectrometry, heparin-binding proteins were identified and analyzed for exponential growth and stationary phases. To manage and display the data generated by proteomics, a web-based database has been constructed for experiments in E. coli proteomics (EEP), which includes NonDeLC, Heparome, AIX/2D PAGE and other proteomic studies.
(has links) (PDF)
Thesis (Ph. D.)--Washington State University, December 2006. Includes bibliographical references.
Champion, Matthew Maurice
Cells respond to their environment with programmed changes in gene expression. Cataloging these changes at the protein level is key towards understanding the physiology of an organism. Multi-subunit and multi-protein complexes are also important and pathogenic and physiologic processes. In order to identify expressed proteins and potential protein complexes, we utilized a combination of non-denaturing chromatography and peptide mass fingerprinting. This approach allows us to identify the components of protein mixtures, as well as information lost in traditional proteomics, such as subunit associations. Applying this methodology to cells at both mid-exponential and stationary phase growth conditions, we identified several thousand proteins from each cell-state of E. coli corresponding to hundreds of unique gene products. The copurification of proteins when fractionated at varying pHs could suggest the components of higher order complexes. This non-denaturing proteomic approach should provide physiological data unavailable by other means. The components of several known cellular complexes were also evident in this analysis. To characterize proteins associated with nucleic acid binding, we also performed proteome analysis on log and stationary phase cells grown in LB separated over heparin chromatography at neutral pH, which enriches for these proteins. The complete analysis of these identifications is discussed.
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