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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
1

Functional proteomics in Escherichia coli

Champion, Matthew Maurice 12 April 2006 (has links)
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.
2

Escherichia coli proteomics and bioinformatics

Niu, Lili 15 May 2009 (has links)
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.
3

Proteomics of Downstream Responses to Growth Signals in Proliferating Cells

Murphy, John Patrick 19 April 2011 (has links)
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.
4

The histidine-rich proteins in prokaryotes and their biological significance

Huang, Feijuan, 黄飞娟 January 2013 (has links)
Special stretches of sequence with low complexity, highly rich in one certain residue, such as glutamine, asparagines, glutamic acid and histidine, to fulfill certain unique functions, are defined as single-residue-rich sequence (SRRs). Increasing SRRs containing proteins have recently been characterized and some of them have been indentified to be associated with immune system diseases or neuro-degenerative. A systematic and comprehensive analysis on the relationship between the occurrence of histidine-rich motifs (HRMs) and the functions of corresponding proteins have been overlooked. In this thesis, proteome sequences of 675 prokaryotes including 50 archeae proteome sequences and 625 bacteria were examined and analyzed for HRMs. The HRMs are shown to be extensively distributed in prokaryotic proteomes and the majority (62%) of them is identified to be involved in metal homeostasis. Intriguingly, HRMs are essentially absent from obligate intracellular pathogenic species such as Rickettsiales, Chlamydiae and Tenericutes but are frequently found in the proteomes of Rhizobiales and Burkholderiales, both of which habitat in soils, indicative of environmental habitat-related occurrence of HRMs. Based on the primary sequence to explore the histidine-rich proteins, the present approach could be extended to apply for searching other single-residue-rich proteins, which may shed lights on gaining a further understanding about relationship between the proteins’ sequences and their functions. A novel group of globally histidine-rich proteins was discovered, among which a histidine-rich protein, bacterioferritin-associated ferredoxin ((BFD)-like [2Fe-2S]) protein from Rhodopseudomonas Palustris BisB18 (termed as BFD shortly) was digged out. The BFD protein consists of a Fe-S cluster domain (FeSD) at the N-terminus and an extremely histidine-rich domain (HRD) at the C-terminus. The intact protein BFD as well as its histidine-rich domain (HRD) was over-expressed, purified and characterized and the effects of metal binding on BFD and HRD were examined in this work. The intact protein BFD presents as a 20 mer whereas the HRD protein exists as a monomer in solution. However, the CD spectrum of BFD showed the presence of both α-helix and β-sheet in the structure of BFD. The CD spectrum of HRD demonstrated that an extremely large portion of the structure of HRD was random coils, which indicated that the most of the α-helix and β-sheet predominately were located in the Fe-S cluster domain (FeSD) of BFD. It also indicated that HRD adopted a very flexible conformation, which was in good agreement with the results that obtained from the 2D 1H-15N HSQC spectrum of HRD. Isothermal titration calorimetry and equilibrium dialysis revealed that HRD possessed a large binding capacity to divalent metal ions (up to 9 Ni2+, 5 Zn2+ and 4 Co2+ respectively). The E. coli cells over-expressed with the HRD protein showed a significantly evaluated metal resistance to the toxic Ni and Co ions. The amounts of meals in these cells were determined to be approximate 3-5 fold higher than those in the control groups. These results of HRD taken together suggest the characteristics of common globally histidine-rich proteins. / published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy
5

Current and future trends in proteomics (SELDI-TOF) in clinical diagnosis and clinical research

Pujari, Goutam. January 2004 (has links)
published_or_final_version / Medical Sciences / Master / Master of Medical Sciences
6

Escherichia coli proteomics and bioinformatics

Niu, Lili 15 May 2009 (has links)
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.
7

New techniques for proteomics study : instrumentation, separation, and application

Wu, Si, January 2006 (has links) (PDF)
Thesis (Ph. D.)--Washington State University, December 2006. / Includes bibliographical references.
8

Current and future trends in proteomics (SELDI-TOF) in clinical diagnosis and clinical research

Pujari, Goutam. January 2004 (has links)
Thesis (M. Med. Sc.)--University of Hong Kong, 2004. / Also available in print.
9

Revealing the proteome : a machine learning approach to peptide identification /

Klammer, Aaron A. January 2008 (has links)
Thesis (Ph. D.)--University of Washington, 2008. / Vita. Includes bibliographical references (p. 89-97).
10

Protein extraction from sediment bound microbes capable of bioremediation for proteomic studies

Nicora, Carrie Diana, January 2009 (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).

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