subject:(proteomics)

University of Georgia

1. Jing, Li. New techniques for proteomic analysis with FTICR-MS: instrumentation, automation and application.

Degree: PhD, Chemistry, 2009, University of Georgia

URL: http://purl.galileo.usg.edu/uga_etd/jing_li_200905_phd

► Shotgun proteomics has been broadly used for high-throughput analysis of proteins in biological systems. In shotgun proteomics, proteins are digested and the resulting peptides are… (more)

▼ Shotgun proteomics has been broadly used for high-throughput analysis of proteins in biological systems. In shotgun proteomics, proteins are digested and the resulting peptides are analyzed using a combination of high performance liquid chromatography (HPLC) and mass spectrometry (MS). Our approach relies on accurate mass measurement of peptides by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). In this work, we explore and develop methodologies to improve proteomic analysis. First, we develop an algorithm to automatically identify light/heavy peptide pairs and calculate peptide relative abundance ratios in 15N metabolic labeling data. This method provides over 99% accuracy in assigning peak pair and reduces the time of data analysis from over 100 hours to tens of minutes. In the second approach, we investigate the mass accuracy for higher mass peptides by using stored waveform inverse Fourier transform (SWIFT) excitation for MALDI-FTICR mass spectrometry. Analysis of measurement errors reveals that SWIFT excitation provides smaller deviations from stepwise-external calibration and better mass accuracy than chirp excitation for a wide mass range and for widely varying ion populations. A shotgun proteomics approach is presented for simultaneous identification and quantitation of the proteins from a proteome using accurate mass measurement and nitrogen stoichiometry. We demonstrate here the utilities of 15N-metabolic labeling for protein identification when using nitrogen stoichiometry as an additional search constraint and for protein quantitation from determining the intensity ratios of light/heavy peptide pairs. The combination of stepwise-external calibration and SWIFT excitation is applied and the mass measurement accuracy (MMA) is significantly improved. Last, we describe a novel calibration method, N15Cal, which corrects the space charge induced frequency shift in FTICR-MS analysis of 15N-metabolically labeled peptides from a batch digested proteome. N15Cal utilizes the information from the mass difference between the 14N/15N peptide peak pairs to correct for space charge induced mass shifts. There is no need to include an internal calibrant or to apply ion population control. N15Cal has been successfully applied to the LC-MALDI-FTICR data of 15N-metabolic labeling proteomics. Advisors/Committee Members: Jonathan Amster.

Subjects/Keywords: Proteomics

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APA (6^th Edition):

Jing, L. (2009). New techniques for proteomic analysis with FTICR-MS: instrumentation, automation and application. (Doctoral Dissertation). University of Georgia. Retrieved from http://purl.galileo.usg.edu/uga_etd/jing_li_200905_phd

Chicago Manual of Style (16^th Edition):

Jing, Li. “New techniques for proteomic analysis with FTICR-MS: instrumentation, automation and application.” 2009. Doctoral Dissertation, University of Georgia. Accessed July 22, 2019. http://purl.galileo.usg.edu/uga_etd/jing_li_200905_phd.

MLA Handbook (7^th Edition):

Jing, Li. “New techniques for proteomic analysis with FTICR-MS: instrumentation, automation and application.” 2009. Web. 22 Jul 2019.

Vancouver:

Jing L. New techniques for proteomic analysis with FTICR-MS: instrumentation, automation and application. [Internet] [Doctoral dissertation]. University of Georgia; 2009. [cited 2019 Jul 22]. Available from: http://purl.galileo.usg.edu/uga_etd/jing_li_200905_phd.

Council of Science Editors:

Jing L. New techniques for proteomic analysis with FTICR-MS: instrumentation, automation and application. [Doctoral Dissertation]. University of Georgia; 2009. Available from: http://purl.galileo.usg.edu/uga_etd/jing_li_200905_phd

Wesleyan University

2. Fournier, Claire Theresa. The Repertoire of N-termini in the 𝘚𝘢𝘤𝘤𝘩𝘢𝘳𝘰𝘮𝘺𝘤𝘦𝘴 𝘤𝘦𝘳𝘦𝘷𝘪𝘴𝘪𝘢𝘦 Proteome: An Integrative Study.

Degree: Biology, 2013, Wesleyan University

URL: https://wesscholar.wesleyan.edu/etd_diss/20

► Within this dissertation the background theory of microwave spectroscopy is presented. This covers many of the spectral effects that may be encountered when conducting… (more)

Subjects/Keywords: Proteomics

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APA (6^th Edition):

Fournier, C. T. (2013). The Repertoire of N-termini in the 𝘚𝘢𝘤𝘤𝘩𝘢𝘳𝘰𝘮𝘺𝘤𝘦𝘴 𝘤𝘦𝘳𝘦𝘷𝘪𝘴𝘪𝘢𝘦 Proteome: An Integrative Study. (Doctoral Dissertation). Wesleyan University. Retrieved from https://wesscholar.wesleyan.edu/etd_diss/20

Chicago Manual of Style (16^th Edition):

Fournier, Claire Theresa. “The Repertoire of N-termini in the 𝘚𝘢𝘤𝘤𝘩𝘢𝘳𝘰𝘮𝘺𝘤𝘦𝘴 𝘤𝘦𝘳𝘦𝘷𝘪𝘴𝘪𝘢𝘦 Proteome: An Integrative Study.” 2013. Doctoral Dissertation, Wesleyan University. Accessed July 22, 2019. https://wesscholar.wesleyan.edu/etd_diss/20.

MLA Handbook (7^th Edition):

Fournier, Claire Theresa. “The Repertoire of N-termini in the 𝘚𝘢𝘤𝘤𝘩𝘢𝘳𝘰𝘮𝘺𝘤𝘦𝘴 𝘤𝘦𝘳𝘦𝘷𝘪𝘴𝘪𝘢𝘦 Proteome: An Integrative Study.” 2013. Web. 22 Jul 2019.

Vancouver:

Fournier CT. The Repertoire of N-termini in the 𝘚𝘢𝘤𝘤𝘩𝘢𝘳𝘰𝘮𝘺𝘤𝘦𝘴 𝘤𝘦𝘳𝘦𝘷𝘪𝘴𝘪𝘢𝘦 Proteome: An Integrative Study. [Internet] [Doctoral dissertation]. Wesleyan University; 2013. [cited 2019 Jul 22]. Available from: https://wesscholar.wesleyan.edu/etd_diss/20.

Council of Science Editors:

Fournier CT. The Repertoire of N-termini in the 𝘚𝘢𝘤𝘤𝘩𝘢𝘳𝘰𝘮𝘺𝘤𝘦𝘴 𝘤𝘦𝘳𝘦𝘷𝘪𝘴𝘪𝘢𝘦 Proteome: An Integrative Study. [Doctoral Dissertation]. Wesleyan University; 2013. Available from: https://wesscholar.wesleyan.edu/etd_diss/20

University of Tennessee – Knoxville

3. Qian, Chen. Development of MS-based proteomics approaches to examine metabolic pathways and protein:protein interactions in microbial systems.

Degree: 2017, University of Tennessee – Knoxville

URL: https://trace.tennessee.edu/utk_graddiss/4709

► The proteome is perhaps the most functional operating machinery for almost all biological processes, serving as the bridge to link the genome and phenotypes. The… (more)

▼ The proteome is perhaps the most functional operating machinery for almost all biological processes, serving as the bridge to link the genome and phenotypes. The proteome undergoes dynamic changes in terms of the abundance or interactions, responding to the environmental stimuli. Understanding this dynamic of protein alterations is the key to delineate critical biological mechanisms. Mass-spectrometry-based proteomics is a powerful tool to systematically monitor the heterogeneous alterations of the proteome, including the changes of abundance, modifications and interactions. In this dissertation, a research project was built upon current proteomics approaches to solve the issues regarding to the sample preparation and data analysis that would help propel this approach to better address certain questions in environmental microbiology and molecular biology. In the first study, we have designed an experimental method that efficiently removes humic acids prior to proteolytic peptide measurement, thus addressing one major challenge associated with soil microbiome proteome extraction and subsequent MS measurement. The second study was aimed at employing advanced proteomics approaches to better understand the microbial drivers of environmental mercury processes by using two model organisms: Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132. Our results elucidated the global proteome impacts caused by the deletion of mercury methylation essential genes hgcAB and revealed that deletion of hgcAB genes did not show significant impact on the microbial response to mercury addition. The third study focused on optimizing MS-based proteome approaches for characterizing protein-protein interactions. By coupling the rapid crosslinking procedure, affinity enrichments and high-performance MS measurements, protein-protein interaction can be captured and interrogated in a living cell by a time-resolved manner. Overall, the methods and results presented in this dissertation not only provides an enhanced sample preparation methodology for intractable samples (such as soils), but also demonstrates how this systems-biology approach can be utilized to characterize the basics of microbial physiology at a global proteome level as well as drilling down into specific proteins interactions. The optimized methods and experimental/bioinformatics techniques described in this dissertation should be broadly extendable to proteome characterization/protein interaction examination in various systems.

Subjects/Keywords: shotgun-proteomics; environmental proteomics; affinity proteomics; Biotechnology

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APA (6^th Edition):

Qian, C. (2017). Development of MS-based proteomics approaches to examine metabolic pathways and protein:protein interactions in microbial systems. (Doctoral Dissertation). University of Tennessee – Knoxville. Retrieved from https://trace.tennessee.edu/utk_graddiss/4709

Chicago Manual of Style (16^th Edition):

Qian, Chen. “Development of MS-based proteomics approaches to examine metabolic pathways and protein:protein interactions in microbial systems.” 2017. Doctoral Dissertation, University of Tennessee – Knoxville. Accessed July 22, 2019. https://trace.tennessee.edu/utk_graddiss/4709.

MLA Handbook (7^th Edition):

Qian, Chen. “Development of MS-based proteomics approaches to examine metabolic pathways and protein:protein interactions in microbial systems.” 2017. Web. 22 Jul 2019.

Vancouver:

Qian C. Development of MS-based proteomics approaches to examine metabolic pathways and protein:protein interactions in microbial systems. [Internet] [Doctoral dissertation]. University of Tennessee – Knoxville; 2017. [cited 2019 Jul 22]. Available from: https://trace.tennessee.edu/utk_graddiss/4709.

Council of Science Editors:

Qian C. Development of MS-based proteomics approaches to examine metabolic pathways and protein:protein interactions in microbial systems. [Doctoral Dissertation]. University of Tennessee – Knoxville; 2017. Available from: https://trace.tennessee.edu/utk_graddiss/4709

Dalhousie University

4. Murphy, John Patrick. Proteomics of Downstream Responses to Growth Signals in Proliferating Cells.

Degree: PhD, Department of Biology, 2011, Dalhousie University

URL: http://hdl.handle.net/10222/13498

► 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,… (more)

▼ 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. Advisors/Committee Members: Dr. Gilles Lajoie (external-examiner), Dr. Bill Pohajdak (graduate-coordinator), Dr. Patrice Cote (thesis-reader), Dr. Jonathan Blay (thesis-reader), Dr. Dev Pinto (thesis-supervisor), Not Applicable (ethics-approval), Not Applicable (manuscripts), Yes (copyright-release).

Subjects/Keywords: Proteomics; glycolysis

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APA (6^th Edition):

Murphy, J. P. (2011). Proteomics of Downstream Responses to Growth Signals in Proliferating Cells. (Doctoral Dissertation). Dalhousie University. Retrieved from http://hdl.handle.net/10222/13498

Chicago Manual of Style (16^th Edition):

Murphy, John Patrick. “Proteomics of Downstream Responses to Growth Signals in Proliferating Cells.” 2011. Doctoral Dissertation, Dalhousie University. Accessed July 22, 2019. http://hdl.handle.net/10222/13498.

MLA Handbook (7^th Edition):

Murphy, John Patrick. “Proteomics of Downstream Responses to Growth Signals in Proliferating Cells.” 2011. Web. 22 Jul 2019.

Vancouver:

Murphy JP. Proteomics of Downstream Responses to Growth Signals in Proliferating Cells. [Internet] [Doctoral dissertation]. Dalhousie University; 2011. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/10222/13498.

Council of Science Editors:

Murphy JP. Proteomics of Downstream Responses to Growth Signals in Proliferating Cells. [Doctoral Dissertation]. Dalhousie University; 2011. Available from: http://hdl.handle.net/10222/13498

University of Georgia

5. Li, Chunyan. Enhancing shotgun proteomics by mass defect labeling of tryptophan, improving mass measurement accuracy and on-target digestion.

Degree: PhD, Chemistry, 2009, University of Georgia

URL: http://purl.galileo.usg.edu/uga_etd/li_chunyan_200908_phd

► Proteomics is the large-scale study of the proteins expressed in a cell, tissue and organism under a given set of physiological or environmental conditions. Mass… (more)

▼ Proteomics is the large-scale study of the proteins expressed in a cell, tissue and organism under a given set of physiological or environmental conditions. Mass spectrometry (MS) in combination with a variety of separation methods has become a primary tool for proteomic studies. Of all proteomic approaches, shotgun proteomics has gained tremendous popularity in recent years. This method involves batch proteolysis of a protein mixture, separation of peptides by high performance liquid chromatography (HPLC), and protein identification from mass spectrometric analysis of peptides. This dissertation describes three approaches to facilitate shotgun proteomic analysis by accurate mass measurement using Fourier transform ion cyclotron resonance mass spectrometry (FTICR/MS). The first approach, referred to as mass defect labeling (MDL), is based on the derivatization of tryptophan residues in protein with a reagent that alters their mass defects. We describe here the development and application of a tryptophan MDL reagent that is compatible to matrix-assisted laser desorption/ionization (MALDI). The second approach employs the stored waveform inverse Fourier transform (SWIFT) excitation to improve the mass measurement accuracy for higher mass peptides. We demonstrate that sub part-per-million (ppm) can be achieved by combining SWIFT with stepwise-external calibration. The third approach couples accurate mass measurement with nitrogen stoichiometry to improve protein identification in shotgun proteomics using HPLC-MALDI-FTICR/MS. We present here the results from identification and quantitation of the proteins in a 15N-metabolically labeled proteome sample that was obtained from Methanococcus maripaludis. The forth approach combines on-target digestion with MALDI-FTICR/MS analysis for rapid protein identification. On-target digestion of a HPLC separated proteome with MALDI-FTICR/MS analysis offers an alternative to the standard method of shotgun analysis. Advisors/Committee Members: Jonathan Amster.

Subjects/Keywords: Shotgun proteomics

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APA (6^th Edition):

Li, C. (2009). Enhancing shotgun proteomics by mass defect labeling of tryptophan, improving mass measurement accuracy and on-target digestion. (Doctoral Dissertation). University of Georgia. Retrieved from http://purl.galileo.usg.edu/uga_etd/li_chunyan_200908_phd

Chicago Manual of Style (16^th Edition):

Li, Chunyan. “Enhancing shotgun proteomics by mass defect labeling of tryptophan, improving mass measurement accuracy and on-target digestion.” 2009. Doctoral Dissertation, University of Georgia. Accessed July 22, 2019. http://purl.galileo.usg.edu/uga_etd/li_chunyan_200908_phd.

MLA Handbook (7^th Edition):

Li, Chunyan. “Enhancing shotgun proteomics by mass defect labeling of tryptophan, improving mass measurement accuracy and on-target digestion.” 2009. Web. 22 Jul 2019.

Vancouver:

Li C. Enhancing shotgun proteomics by mass defect labeling of tryptophan, improving mass measurement accuracy and on-target digestion. [Internet] [Doctoral dissertation]. University of Georgia; 2009. [cited 2019 Jul 22]. Available from: http://purl.galileo.usg.edu/uga_etd/li_chunyan_200908_phd.

Council of Science Editors:

Li C. Enhancing shotgun proteomics by mass defect labeling of tryptophan, improving mass measurement accuracy and on-target digestion. [Doctoral Dissertation]. University of Georgia; 2009. Available from: http://purl.galileo.usg.edu/uga_etd/li_chunyan_200908_phd

University of Georgia

6. Nuccio, Arthur Gayosa. The effect of search accuracy on shotgun protemoics results using a validated protein database and high resolution fragment spectra.

Degree: MS, Chemistry, 2011, University of Georgia

URL: http://purl.galileo.usg.edu/uga_etd/nuccio_arthur_g_201112_ms

► Mass spectrometry based proteomics has become one of the most powerful tools used to determine protein structure, function, and expression. The recent rapid expansion of… (more)

Subjects/Keywords: Shotgun Proteomics

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APA (6^th Edition):

Nuccio, A. G. (2011). The effect of search accuracy on shotgun protemoics results using a validated protein database and high resolution fragment spectra. (Masters Thesis). University of Georgia. Retrieved from http://purl.galileo.usg.edu/uga_etd/nuccio_arthur_g_201112_ms

Chicago Manual of Style (16^th Edition):

Nuccio, Arthur Gayosa. “The effect of search accuracy on shotgun protemoics results using a validated protein database and high resolution fragment spectra.” 2011. Masters Thesis, University of Georgia. Accessed July 22, 2019. http://purl.galileo.usg.edu/uga_etd/nuccio_arthur_g_201112_ms.

MLA Handbook (7^th Edition):

Nuccio, Arthur Gayosa. “The effect of search accuracy on shotgun protemoics results using a validated protein database and high resolution fragment spectra.” 2011. Web. 22 Jul 2019.

Vancouver:

Nuccio AG. The effect of search accuracy on shotgun protemoics results using a validated protein database and high resolution fragment spectra. [Internet] [Masters thesis]. University of Georgia; 2011. [cited 2019 Jul 22]. Available from: http://purl.galileo.usg.edu/uga_etd/nuccio_arthur_g_201112_ms.

Council of Science Editors:

Nuccio AG. The effect of search accuracy on shotgun protemoics results using a validated protein database and high resolution fragment spectra. [Masters Thesis]. University of Georgia; 2011. Available from: http://purl.galileo.usg.edu/uga_etd/nuccio_arthur_g_201112_ms

Texas A&M University

7. Niu, Lili. Escherichia coli proteomics and bioinformatics.

Degree: 2009, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-1240

► 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… (more)

Subjects/Keywords: PROTEOMICS; BIOINFORMATICS

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APA (6^th Edition):

Niu, L. (2009). Escherichia coli proteomics and bioinformatics. (Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-1240

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Niu, Lili. “Escherichia coli proteomics and bioinformatics.” 2009. Thesis, Texas A&M University. Accessed July 22, 2019. http://hdl.handle.net/1969.1/ETD-TAMU-1240.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Niu, Lili. “Escherichia coli proteomics and bioinformatics.” 2009. Web. 22 Jul 2019.

Vancouver:

Niu L. Escherichia coli proteomics and bioinformatics. [Internet] [Thesis]. Texas A&M University; 2009. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1240.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Niu L. Escherichia coli proteomics and bioinformatics. [Thesis]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1240

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Auckland

8. Atkinson, Kelly Rene LeFevre. Proteomic biomarker discovery for preeclampsia.

Degree: 2008, University of Auckland

URL: http://hdl.handle.net/2292/2565

► Preeclampsia is a serious multisystem complication of late pregnancy with adverse effects for mothers and babies. Currently this disorder is diagnosed from clinical observations occurring… (more)

▼ Preeclampsia is a serious multisystem complication of late pregnancy with adverse effects for mothers and babies. Currently this disorder is diagnosed from clinical observations occurring late in the disease process. Unknown factors in the maternal circulation, possibly released by the preeclamptic placenta, have been linked to the pathophysiological changes characteristic of the disorder. The research in this thesis used proteomic techniques to identify putative preeclampsia biomarkers from two sources: secreted from a placental cell line undergoing differentiation, and directly sampled from the serum and plasma of women with late-onset preeclampsia. The first part of this research examined the secreted proteome of a placental choriocarcinoma cell line (BeWo) undergoing forskolin-mediated differentiation. Development of serum-free culture techniques enabled analysis of these secreted proteins by two-dimensional gel electrophoresis (2DE). Statistical testing revealed the significant involvement of seven spots during this differentiation model, with VE-cadherin and matrix metalloproteinase 2 among the proteins identified. In the second part of this research, maternal serum and plasma proteins were compared from women with preeclampsia and healthy pregnant women. Serum samples were analyzed using 2DE, and plasma was subjected to difference gel electrophoresis (DIGE). Bioinformatic analysis of both datasets identified multiple spot clusters able to classify samples according to disease state. Five of these serum proteins were differentially regulated in preeclampsia, including two isoforms of apolipoprotein E whose isoform-specific expression was confirmed using western blots. Analysis of plasma from preeclamptic women identified six proteins, again including apolipoprotein E. Proteins from both studies are linked to preeclampsia pathophysiology through lipid transport, complement, and retinol transport systems. The culture methods and secreted proteomic techniques developed in this work have uncovered proteins in a placental cell line and maternal serum and plasma that are associated with preeclampsia. These methods can be extended to any system where secreted proteins are of interest. The differentially regulated proteins found in this study provide an important first step towards developing effective biomarkers for diagnosing and/or predicting preeclampsia. Advisors/Committee Members: Garth Cooper, Robyn North.

Subjects/Keywords: proteomics; pregnancy

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APA (6^th Edition):

Atkinson, K. R. L. (2008). Proteomic biomarker discovery for preeclampsia. (Doctoral Dissertation). University of Auckland. Retrieved from http://hdl.handle.net/2292/2565

Chicago Manual of Style (16^th Edition):

Atkinson, Kelly Rene LeFevre. “Proteomic biomarker discovery for preeclampsia.” 2008. Doctoral Dissertation, University of Auckland. Accessed July 22, 2019. http://hdl.handle.net/2292/2565.

MLA Handbook (7^th Edition):

Atkinson, Kelly Rene LeFevre. “Proteomic biomarker discovery for preeclampsia.” 2008. Web. 22 Jul 2019.

Vancouver:

Atkinson KRL. Proteomic biomarker discovery for preeclampsia. [Internet] [Doctoral dissertation]. University of Auckland; 2008. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/2292/2565.

Council of Science Editors:

Atkinson KRL. Proteomic biomarker discovery for preeclampsia. [Doctoral Dissertation]. University of Auckland; 2008. Available from: http://hdl.handle.net/2292/2565

9. Uzoma, Ijeoma K. GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION.

Degree: 2014, Johns Hopkins University

URL: http://jhir.library.jhu.edu/handle/1774.2/37923

► Over 100 kinases were recovered as SUMO substrates in our assays which points to a global phenomenon of kinase regulation by SUMO modification. The studies… (more)

Subjects/Keywords: Proteomics; SUMO

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APA (6^th Edition):

Uzoma, I. K. (2014). GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION. (Thesis). Johns Hopkins University. Retrieved from http://jhir.library.jhu.edu/handle/1774.2/37923

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Uzoma, Ijeoma K. “GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION.” 2014. Thesis, Johns Hopkins University. Accessed July 22, 2019. http://jhir.library.jhu.edu/handle/1774.2/37923.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Uzoma, Ijeoma K. “GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION.” 2014. Web. 22 Jul 2019.

Vancouver:

Uzoma IK. GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION. [Internet] [Thesis]. Johns Hopkins University; 2014. [cited 2019 Jul 22]. Available from: http://jhir.library.jhu.edu/handle/1774.2/37923.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Uzoma IK. GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION. [Thesis]. Johns Hopkins University; 2014. Available from: http://jhir.library.jhu.edu/handle/1774.2/37923

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Hong Kong

10. Huang, Feijuan. The histidine-rich proteins in prokaryotes and their biological significance.

Degree: PhD, 2013, University of Hong Kong

URL: Huang, F. [黄飞娟]. (2013). The histidine-rich proteins in prokaryotes and their biological significance. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5223960 ; http://dx.doi.org/10.5353/th_b5223960 ; http://hdl.handle.net/10722/209759

► 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… (more)

▼ 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…

Subjects/Keywords: Prokaryotes; Proteomics

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APA (6^th Edition):

Huang, F. (2013). The histidine-rich proteins in prokaryotes and their biological significance. (Doctoral Dissertation). University of Hong Kong. Retrieved from Huang, F. [黄飞娟]. (2013). The histidine-rich proteins in prokaryotes and their biological significance. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5223960 ; http://dx.doi.org/10.5353/th_b5223960 ; http://hdl.handle.net/10722/209759

Chicago Manual of Style (16^th Edition):

Huang, Feijuan. “The histidine-rich proteins in prokaryotes and their biological significance.” 2013. Doctoral Dissertation, University of Hong Kong. Accessed July 22, 2019. Huang, F. [黄飞娟]. (2013). The histidine-rich proteins in prokaryotes and their biological significance. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5223960 ; http://dx.doi.org/10.5353/th_b5223960 ; http://hdl.handle.net/10722/209759.

MLA Handbook (7^th Edition):

Huang, Feijuan. “The histidine-rich proteins in prokaryotes and their biological significance.” 2013. Web. 22 Jul 2019.

Vancouver:

Huang F. The histidine-rich proteins in prokaryotes and their biological significance. [Internet] [Doctoral dissertation]. University of Hong Kong; 2013. [cited 2019 Jul 22]. Available from: Huang, F. [黄飞娟]. (2013). The histidine-rich proteins in prokaryotes and their biological significance. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5223960 ; http://dx.doi.org/10.5353/th_b5223960 ; http://hdl.handle.net/10722/209759.

Council of Science Editors:

Huang F. The histidine-rich proteins in prokaryotes and their biological significance. [Doctoral Dissertation]. University of Hong Kong; 2013. Available from: Huang, F. [黄飞娟]. (2013). The histidine-rich proteins in prokaryotes and their biological significance. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5223960 ; http://dx.doi.org/10.5353/th_b5223960 ; http://hdl.handle.net/10722/209759

University of Minnesota

11. Rogers, Anna. Optimization Of Mass Spectrometry-Based Proteomic Identification Of Ovarian Cancer Biomarkers From Residual Pap Test Samples.

Degree: MS, Microbiology, Immunology and Cancer Biology, 2018, University of Minnesota

URL: http://hdl.handle.net/11299/201736

► Current screening methods to detect ovarian cancer are not adequately sensitive or specific to detect early disease. In contrast, cervical cancer screening with Pap tests… (more)

Subjects/Keywords: Cancer; Proteomics

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APA (6^th Edition):

Rogers, A. (2018). Optimization Of Mass Spectrometry-Based Proteomic Identification Of Ovarian Cancer Biomarkers From Residual Pap Test Samples. (Masters Thesis). University of Minnesota. Retrieved from http://hdl.handle.net/11299/201736

Chicago Manual of Style (16^th Edition):

Rogers, Anna. “Optimization Of Mass Spectrometry-Based Proteomic Identification Of Ovarian Cancer Biomarkers From Residual Pap Test Samples.” 2018. Masters Thesis, University of Minnesota. Accessed July 22, 2019. http://hdl.handle.net/11299/201736.

MLA Handbook (7^th Edition):

Rogers, Anna. “Optimization Of Mass Spectrometry-Based Proteomic Identification Of Ovarian Cancer Biomarkers From Residual Pap Test Samples.” 2018. Web. 22 Jul 2019.

Vancouver:

Rogers A. Optimization Of Mass Spectrometry-Based Proteomic Identification Of Ovarian Cancer Biomarkers From Residual Pap Test Samples. [Internet] [Masters thesis]. University of Minnesota; 2018. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/11299/201736.

Council of Science Editors:

Rogers A. Optimization Of Mass Spectrometry-Based Proteomic Identification Of Ovarian Cancer Biomarkers From Residual Pap Test Samples. [Masters Thesis]. University of Minnesota; 2018. Available from: http://hdl.handle.net/11299/201736

Victoria University of Wellington

12. Manivannan, Bhagyashree. Diagnostic Markers for Schistosome-Mediated Liver Disease.

Degree: 2010, Victoria University of Wellington

URL: http://hdl.handle.net/10063/1365

► Chronic schistosomiasis presents with either a moderate or a severe form, termed intestinal (INT) or hepatosplenic (HS) schistosomiasis, respectively. The Schistosoma mansoni-associated hepatomegaly is estimated… (more)

▼ Chronic schistosomiasis presents with either a moderate or a severe form, termed intestinal (INT) or hepatosplenic (HS) schistosomiasis, respectively. The Schistosoma mansoni-associated hepatomegaly is estimated in 8.5 million people and ultimately results from liver granulomas induced by trapped parasitic eggs. The CBA/J mouse model replicates these two human disease forms and was used to understand the progressive pathology that leads to HS and to identify potential biomarkers. In this model 20% of infected mice spontaneously develop hypersplenomegaly syndrome (HSS) by 20 weeks of infection while the remaining 80% develop moderate splenomegaly syndrome (MSS). Using this model, we compared the liver protein patterns of control mice and mice infected for 6, 8, 12, or 20 (MSS and HSS) weeks. Two-dimensional differential in gel electrophoresis (2D-DIGE) was used to identify protein pattern variations and protein spots were identified using matrix adsorption laser desorption ionisation-time of flight (MALDI-TOF) mass spectrometry. In the first experiment, we found 124 protein spot unique changes for MSS and HSS compared to control mice of which 80 were identified and 35 changes were specific for HSS. In the second experiment, comparison between various time points with control mice revealed 76 significant protein spot changes of which 44 were identified using MALDI-TOF mass spectrometry. Importantly, we found that the abundance of liver keratin D, transferrin isoforms, collagen isoforms, hydroxyproline and Schistosoma mansoni-phosphoenolpyruvate carboxykinase increased while epoxide hydrolase isoforms, peroxiredoxin 6 and major urinary protein (MUP) isoforms decreased significantly with infection. To verify the changes in the liver 2D-DIGE analysis, candidate liver protein markers were measured in mouse serum using targeted biochemical assays. The mouse serum analysis showed MUP levels were decreased, while transferrin, connective tissue growth factor (CTGF), keratin D, hydroxyproline were increased in HSS mice compared to control mice or MSS mice supporting the liver 2D-DIGE analysis. Using targeted assays, serum samples from INT and HS patients were tested for the candidate liver protein markers: keratin D, CTGF, hydroxyproline and transferrin. The human serum analysis showed keratin D levels increased for HS compared to INT and normal sera. The CTGF levels were high in INT compared to HS and normal sera, while transferrin remained unchanged in INT and HS similar to normal sera. Additionally, in severe HS disease, serum hydroxyproline emerged as a strong indicator of fibrosis. We believe that these findings will have direct value in the development of diagnostic tools for early detection of hepatosplenic schistosomiasis in humans. Advisors/Committee Members: LaFlamme, Anne, Jordan, Bill.

Subjects/Keywords: Schistosomiasis; Proteomics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Manivannan, B. (2010). Diagnostic Markers for Schistosome-Mediated Liver Disease. (Doctoral Dissertation). Victoria University of Wellington. Retrieved from http://hdl.handle.net/10063/1365

Chicago Manual of Style (16^th Edition):

Manivannan, Bhagyashree. “Diagnostic Markers for Schistosome-Mediated Liver Disease.” 2010. Doctoral Dissertation, Victoria University of Wellington. Accessed July 22, 2019. http://hdl.handle.net/10063/1365.

MLA Handbook (7^th Edition):

Manivannan, Bhagyashree. “Diagnostic Markers for Schistosome-Mediated Liver Disease.” 2010. Web. 22 Jul 2019.

Vancouver:

Manivannan B. Diagnostic Markers for Schistosome-Mediated Liver Disease. [Internet] [Doctoral dissertation]. Victoria University of Wellington; 2010. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/10063/1365.

Council of Science Editors:

Manivannan B. Diagnostic Markers for Schistosome-Mediated Liver Disease. [Doctoral Dissertation]. Victoria University of Wellington; 2010. Available from: http://hdl.handle.net/10063/1365

13. Cao, Lulu. Quantitative Phosphoproteomic Analysis to Unravel Mast Cell and T Cell Signaling Pathways.

Degree: PhD, Chemistry, 2010, Brown University

URL: https://repository.library.brown.edu/studio/item/bdr:11036/

► Reversible protein phosphorylation plays a vital role in the regulation of cellular signaling pathways. With recent breakthrough developments in mass spectrometry-based proteomics technologies, including phosphopeptide… (more)

▼ Reversible protein phosphorylation plays a vital role in the regulation of cellular signaling pathways. With recent breakthrough developments in mass spectrometry-based proteomics technologies, including phosphopeptide enrichment and separation techniques, high-accuracy mass spectrometry and associated bioinformatics, MS-based quantitative phosphoproteomics have now gained great popularity. This technology has enabled the simultaneous identification and quantification of thousands of phosphorylation sites from entire phosphoproteomes. Mast cells play a central role in type I hypersensitivity reactions and allergic disorders such as anaphylaxis and asthma. In order to understand the molecular architecture underlying mast cell signaling, a systematic, quantitative analysis of the global tyrosine phosphorylation events triggered by activation of the mast cell receptor was performed. We have for the first time substantially characterized and quantified hundreds of tyrosine phosphorylation events in both mouse mast cell line MCP5 cells and mouse bone marrow-derived mast cells, with their temporal phosphorylation profiles providing preliminary insights into the newly discovered phosphorylation sites. However, this type of analysis does not provide enough information to make precise predictions of the placement of individual phosphorylation events within signaling pathways. Protein disruption and site-directed mutagenesis are essential to clearly define the precise biological roles of the newly discovered phosphorylation sites. To better understand the molecular mechanism underlying complex cellular signaling networks, we have also developed a hybrid quantitative approach that combines label free and SILAC quantification techniques. Label free quantification is applied to assemble high-density temporal data within a single cell type, either wide-type (WT) or mutant (Mut) cells, providing a list of phosphorylation sites that change in abundance after stimulation of a cellular receptor. SILAC quantification is then used to compare WT and Mut cells across a timecourse of receptor stimulation, providing direct information about how the newly observed phosphorylation sites respond to the mutagenesis. We have successfully applied this approach to ZAP-70 and SLP-76 deficient Jurkat T cell lines. These studies have provided great insights into the essential roles of these proteins in T cell signaling. Many hypotheses have been drawn and follow-up studies could provide directions for future investigation. Advisors/Committee Members: Salomon, Arthur (Director), Bazemore-Walker, Carthene (Reader), Peti, Wolfgang (Reader).

Subjects/Keywords: Quantitative Proteomics

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APA (6^th Edition):

Cao, L. (2010). Quantitative Phosphoproteomic Analysis to Unravel Mast Cell and T Cell Signaling Pathways. (Doctoral Dissertation). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:11036/

Chicago Manual of Style (16^th Edition):

Cao, Lulu. “Quantitative Phosphoproteomic Analysis to Unravel Mast Cell and T Cell Signaling Pathways.” 2010. Doctoral Dissertation, Brown University. Accessed July 22, 2019. https://repository.library.brown.edu/studio/item/bdr:11036/.

MLA Handbook (7^th Edition):

Cao, Lulu. “Quantitative Phosphoproteomic Analysis to Unravel Mast Cell and T Cell Signaling Pathways.” 2010. Web. 22 Jul 2019.

Vancouver:

Cao L. Quantitative Phosphoproteomic Analysis to Unravel Mast Cell and T Cell Signaling Pathways. [Internet] [Doctoral dissertation]. Brown University; 2010. [cited 2019 Jul 22]. Available from: https://repository.library.brown.edu/studio/item/bdr:11036/.

Council of Science Editors:

Cao L. Quantitative Phosphoproteomic Analysis to Unravel Mast Cell and T Cell Signaling Pathways. [Doctoral Dissertation]. Brown University; 2010. Available from: https://repository.library.brown.edu/studio/item/bdr:11036/

University of North Texas

14. Scott, Ashley. Development of a Targeted Protein Residue Analysis Approach in Archaeology.

Degree: 2017, University of North Texas

URL: https://digital.library.unt.edu/ark:/67531/metadc1011863/

► Liquid chromatography-mass spectrometry (LC-MS) based proteomic methods have provided archaeologists with a powerful tool for the discovery and identification of proteins within artifacts. Traditionally, discovery-based… (more)

Subjects/Keywords: archaeology; proteomics

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APA (6^th Edition):

Scott, A. (2017). Development of a Targeted Protein Residue Analysis Approach in Archaeology. (Thesis). University of North Texas. Retrieved from https://digital.library.unt.edu/ark:/67531/metadc1011863/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Scott, Ashley. “Development of a Targeted Protein Residue Analysis Approach in Archaeology.” 2017. Thesis, University of North Texas. Accessed July 22, 2019. https://digital.library.unt.edu/ark:/67531/metadc1011863/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Scott, Ashley. “Development of a Targeted Protein Residue Analysis Approach in Archaeology.” 2017. Web. 22 Jul 2019.

Vancouver:

Scott A. Development of a Targeted Protein Residue Analysis Approach in Archaeology. [Internet] [Thesis]. University of North Texas; 2017. [cited 2019 Jul 22]. Available from: https://digital.library.unt.edu/ark:/67531/metadc1011863/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Scott A. Development of a Targeted Protein Residue Analysis Approach in Archaeology. [Thesis]. University of North Texas; 2017. Available from: https://digital.library.unt.edu/ark:/67531/metadc1011863/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Manitoba

15. Rahim, Md Niaz. Identification of host cellular factors that interact with Influenza A NS1 protein for viral replication.

Degree: Medical Microbiology and Infectious Diseases, 2017, University of Manitoba

URL: http://hdl.handle.net/1993/32159

► Influenza A virus (IAV) is considered one of the main threats that causes contagious respiratory disease in humans. Each year it threatens the human population… (more)

▼ Influenza A virus (IAV) is considered one of the main threats that causes contagious respiratory disease in humans. Each year it threatens the human population with epidemics and pandemics. Limited anti-Influenza drugs are available that target viral proteins. The Influenza virus can mutate rapidly and can quickly develop resistance against available drugs. Therefore, developing novel host-targeted therapeutics effective against different IAVs may be very beneficial. Influenza virus is an intracellular parasite that uses host cell system to favour its replication process and evade host cell defense system. The Influenza A viral nonstructural protein 1(NS1) is a multifunctional protein that is expressed to high levels in infected cells; thus, interacting proteins may be ideal targets for drug development. In this study nine broadly cross-reactive anti-NS1 monoclonal antibodies (mAbs) were generated, characterized and used to co-immunoprecipitate IAV NS1 and its interacting host proteins. 183 proteins were consistently identified in this NS1 interactome study. Importantly, most proteins clustered into different cellular pathways, biological processes and molecular functions, such as mRNA splicing, gene expression, processing of capped intron-containing pre-mRNA and nucleoside, nucleotide and nucleic acid metabolism. Among these, 124 proteins detected in my study represent novel NS1-interacting targets not previously identified. RNAi screening then identified 11 NS1-interacting host factors as vital for IAV replication. From RNAi screening two NS1-interacting candidates, NUMA1 and PRPF19 were chosen for further analysis. IAV production was dramatically reduced in NUMA1 knockdown (KD) cells. Although viral transcription and translation were not inhibited, transport of viral structural proteins to the cytoplasmic membrane was obstructed during maturation steps in NUMA1 KD cells. IAV maturation was also inhibited and new virion production was significantly reduced in PRPF19 KD cells. Overall, a list of novel NS1-interacting host factors were identified utilizing some broadly cross reactive anti-NS1 mAbs in my study, and 11 of them were required for IAV replication. Further research on these new proteins may discover new targets for anti-Influenza drug development. Advisors/Committee Members: Coombs, Kevin (Medical Microbiology and Infectious Diseases) (supervisor), Mai, Sabine (Physiology and Pathophysiology).

Subjects/Keywords: Influenza; Proteomics

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APA (6^th Edition):

Rahim, M. N. (2017). Identification of host cellular factors that interact with Influenza A NS1 protein for viral replication. (Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/32159

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Rahim, Md Niaz. “Identification of host cellular factors that interact with Influenza A NS1 protein for viral replication.” 2017. Thesis, University of Manitoba. Accessed July 22, 2019. http://hdl.handle.net/1993/32159.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Rahim, Md Niaz. “Identification of host cellular factors that interact with Influenza A NS1 protein for viral replication.” 2017. Web. 22 Jul 2019.

Vancouver:

Rahim MN. Identification of host cellular factors that interact with Influenza A NS1 protein for viral replication. [Internet] [Thesis]. University of Manitoba; 2017. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/1993/32159.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Rahim MN. Identification of host cellular factors that interact with Influenza A NS1 protein for viral replication. [Thesis]. University of Manitoba; 2017. Available from: http://hdl.handle.net/1993/32159

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Manitoba

16. Stein, Derek Riley. Cellular proteomic analysis of highly exposed HIV seronegative women from the Pumwani sex worker cohort in Nairobi, Kenya.

Degree: Medical Microbiology, 2014, University of Manitoba

URL: http://hdl.handle.net/1993/23959

► The HIV pandemic is well into its fourth decade and researchers have yet to develop a protective vaccine. The research presented in this thesis aims… (more)

▼ The HIV pandemic is well into its fourth decade and researchers have yet to develop a protective vaccine. The research presented in this thesis aims to identify and characterize correlates of HIV protection by studying highly exposed HIV seronegative (HESN) sex workers from Nairobi, Kenya. HESN women appear to have the natural ability to resist HIV acquisition giving the research community some hope that one-day a vaccine, microbicide or other prevention tool can be developed. Previous studies have indicated an overall immune quiescence phenotype characterized by lower immune activation in T cells and increased factors that limit HIV infection, which may play a significant role in protecting HESN women from HIV acquisition. The central hypothesis of this thesis is that quantitative shotgun proteomics of systemic and mucosal mononuclear cells from HESN women will demonstrate a proteomic profile characteristic of the immune quiescent phenotype, described by the altered expression of pathways important in immune activation, cell recruitment / migration, and proteins involved in HIV replication pathways. This hypothesis was addressed by quantifying the proteomic profile of immune cells isolated from the systemic and mucosal compartments of HESN women. In these studies HESN women were shown to have a proteomic profile representative of immune quiescence in genital tract immune cells but not systemically. Additionally, Mx2 a novel HIV restriction factor was found to be over-expressed in systemic immune cells from HESN women. These data support the role of immune quiescence in the genital tract as a potential mechanism for HIV resistance and has identified a novel HIV restriction factor that may contribute to HIV resistance in HESN women. Strategies to mimic immune quiescence at the site of HIV acquisition and regulate HIV host restriction factors such as Mx2 should be considered during future vaccine and microbicide development. Advisors/Committee Members: Ball, Blake (Medical Microbiology) Plummer, Frank (Medical Microbiology) (supervisor), Carpenter, Michael (Medical Microbiology) Yang, Xi (Medical Microbiology) Mookherjee, Neeloffer (Immunology) Foster, Leonard (University of British Columbia) (examiningcommittee).

Subjects/Keywords: HIV; Proteomics

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APA (6^th Edition):

Stein, D. R. (2014). Cellular proteomic analysis of highly exposed HIV seronegative women from the Pumwani sex worker cohort in Nairobi, Kenya. (Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/23959

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Stein, Derek Riley. “Cellular proteomic analysis of highly exposed HIV seronegative women from the Pumwani sex worker cohort in Nairobi, Kenya.” 2014. Thesis, University of Manitoba. Accessed July 22, 2019. http://hdl.handle.net/1993/23959.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Stein, Derek Riley. “Cellular proteomic analysis of highly exposed HIV seronegative women from the Pumwani sex worker cohort in Nairobi, Kenya.” 2014. Web. 22 Jul 2019.

Vancouver:

Stein DR. Cellular proteomic analysis of highly exposed HIV seronegative women from the Pumwani sex worker cohort in Nairobi, Kenya. [Internet] [Thesis]. University of Manitoba; 2014. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/1993/23959.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Stein DR. Cellular proteomic analysis of highly exposed HIV seronegative women from the Pumwani sex worker cohort in Nairobi, Kenya. [Thesis]. University of Manitoba; 2014. Available from: http://hdl.handle.net/1993/23959

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Helsinki

17. Cypryk, Wojciech. Extracellular vesicles in innate immunity : Proteomic investigations.

Degree: Department of Biosciences, Faculty of Biological and Environmental Scinces; Institute of Biotechnology, University of Helsinki, 2016, University of Helsinki

URL: http://hdl.handle.net/10138/167646

► Extracellular vesicles (EVs) are small, membranous entities secreted from most eukaryotic cells at both homeostatic and stress conditions. Carrying active biological molecules nucleic acids, lipids… (more)

▼ Extracellular vesicles (EVs) are small, membranous entities secreted from most eukaryotic cells at both homeostatic and stress conditions. Carrying active biological molecules nucleic acids, lipids and proteins EVs serve as important means of intercellular communication. In the immune system, EVs circulting in body fluids play important modulatory roles in coordination of responses. EVs are integral part of secretome all proteins secreted by cells. EVs provide means for secretion of proteins that are not trafficked through conventional, ER/Golgi-mediated mechanisms. Analysis of EV proteome provides basis for fundamental discoveries in understanding the biogenesis, secretion and delivery of these nanosized messengers to target cells. Macrophages are principal tissue-resident effector cells of innate immune system, performing surveillance of their neighborhood in search for danger. Macrophages express pattern recognition receptors (PRRs) which recognize conserved pathogen-associated molecular patterns (PAMPs) conserved range of molecules expressed by pathogens. PRRs also recognize endogeneous ligands that appear in the human body in other dangerous conditions and diseases. These are collectively called danger-associated molecular patterns (DAMPs). Recognition of PAMPs and DAMPs by PRRs triggers intracellular signaling, leading to activation of macrophage defense mechanisms. These begin with inflammation and secretion of pro-inflammatory cytokines, but many other proteins are also actively secreted by activated macrophages. Although inflammatory cytokine secretion is a well-studied process, very few studies investigating overall and EV-mediated protein secretion from human macrophages were performed. This thesis aims at broadening our understanding of EV-mediated protein secretion from human macrophages activated in response to selected innate immune activators, namely extracellular adenosine triphosphate (ATP), a potent DAMP released during cell damage; (1,3)-β-glucan, a polysaccharide component of fungal cell wall, activating dectin-1-mediated signaling and influenza A virus (IAV) - common seasonal pathogenic virus targeting lung epithelia and macrophages. Total secretome and purified EVs were analyzed using different high-throughput mass spectrometry-based methods and further explored using bioinformatic and biochemical studies. The presented results provide evidence that EV-mediated protein secretion is an integral part of responses of human macrophages to studied stimuli. Its activation is demonstrated with quantitative and comparative proteomic approaches. The secreted vesicles are characterized by a broad size range consistent with both exosomes and microvesicles, demonstrating that both types of vesicular structures are involved in protein secretion. The EVs carry distinct set of immunologically important proteins, and bioinformatic analysis suggests that the secreted EVs may exert immunomodulatory effects on recipient cells. It is shown that during IAV infection, EVs are mediators of…

Subjects/Keywords: biochemistry, immunology, proteomics; biochemistry, immunology, proteomics

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APA (6^th Edition):

Cypryk, W. (2016). Extracellular vesicles in innate immunity : Proteomic investigations. (Doctoral Dissertation). University of Helsinki. Retrieved from http://hdl.handle.net/10138/167646

Chicago Manual of Style (16^th Edition):

Cypryk, Wojciech. “Extracellular vesicles in innate immunity : Proteomic investigations.” 2016. Doctoral Dissertation, University of Helsinki. Accessed July 22, 2019. http://hdl.handle.net/10138/167646.

MLA Handbook (7^th Edition):

Cypryk, Wojciech. “Extracellular vesicles in innate immunity : Proteomic investigations.” 2016. Web. 22 Jul 2019.

Vancouver:

Cypryk W. Extracellular vesicles in innate immunity : Proteomic investigations. [Internet] [Doctoral dissertation]. University of Helsinki; 2016. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/10138/167646.

Council of Science Editors:

Cypryk W. Extracellular vesicles in innate immunity : Proteomic investigations. [Doctoral Dissertation]. University of Helsinki; 2016. Available from: http://hdl.handle.net/10138/167646

University of Colorado

18. Ebmeier, Christopher Carl. Targeted Proteomics and Molecular Mechanisms of Gene Activation.

Degree: PhD, Chemistry & Biochemistry, 2011, University of Colorado

URL: http://scholar.colorado.edu/chem_gradetds/51

► Mass spectrometry-based proteomics is a powerful tool when combined with hypothesis driven protein purification. Regulation of protein-protein interactions is a major molecular mechanism for… (more)

▼ Mass spectrometry-based proteomics is a powerful tool when combined with hypothesis driven protein purification. Regulation of protein-protein interactions is a major molecular mechanism for gene activation. Protein purification, functional assays, and antibody-based western blots have traditionally been used to elucidate many of the most critical and perhaps universal protein-protein interactions required for gene expression, such as the assembly of the general transcription machinery. The Mediator complex is an essential part of the general transcription machinery that integrates signals from DNA-binding transcriptional activators through protein-protein interactions to regulate RNA Pol II activity. Gene activation is ultimately determined by incoming stimuli and subsequent inter-cellular signaling. How these signals are integrated in a spatial and temporal fashion for the regulation of distinct genes by activator-Mediator interactions is unclear. One proposed molecular mechanism of gene activation by the Mediator complex is through a structural shift in the complex. Mediator structural shifts may trigger new protein-protein interactions required for transcription of select genes in response to a specific stimulus. To test this, Mediator complexes were purified with and without transcriptional activators. The activation domains of the transcriptional activators SREBP-1a and VP16, which generate distinct structures upon binding Mediator, were used to affinity purify activator-bound Mediator complexes. For comparison, antibodies for the Mediator subunits MED1 and CDK8 were used to affinity purify activator-free Mediator complexes. A mass spectrometry-based proteomics platform was established to characterize the protein compositions of each Mediator complex purification. The results showed additional cofactors in the activator-bound Mediator complexes, many of which had known function related to gene expression. Selected cofactors were validated for binding Mediator with an orthogonal purification that combined the activator and antibody purifications and western blotting. Together the proteomics data predicted and the western blotting confirmed new protein-protein interactions relevant for regulation of gene expression that were activator-specific. Collectively, these targeted proteomics approaches have generated many new hypotheses and have fundamentally altered our understanding of how gene expression is regulated. Advisors/Committee Members: Dylan J. Taatjes, William Old, Natalie Ahn.

Subjects/Keywords: proteomics; transcription; Biochemistry

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APA (6^th Edition):

Ebmeier, C. C. (2011). Targeted Proteomics and Molecular Mechanisms of Gene Activation. (Doctoral Dissertation). University of Colorado. Retrieved from http://scholar.colorado.edu/chem_gradetds/51

Chicago Manual of Style (16^th Edition):

Ebmeier, Christopher Carl. “Targeted Proteomics and Molecular Mechanisms of Gene Activation.” 2011. Doctoral Dissertation, University of Colorado. Accessed July 22, 2019. http://scholar.colorado.edu/chem_gradetds/51.

MLA Handbook (7^th Edition):

Ebmeier, Christopher Carl. “Targeted Proteomics and Molecular Mechanisms of Gene Activation.” 2011. Web. 22 Jul 2019.

Vancouver:

Ebmeier CC. Targeted Proteomics and Molecular Mechanisms of Gene Activation. [Internet] [Doctoral dissertation]. University of Colorado; 2011. [cited 2019 Jul 22]. Available from: http://scholar.colorado.edu/chem_gradetds/51.

Council of Science Editors:

Ebmeier CC. Targeted Proteomics and Molecular Mechanisms of Gene Activation. [Doctoral Dissertation]. University of Colorado; 2011. Available from: http://scholar.colorado.edu/chem_gradetds/51

Victoria University of Wellington

19. Hoang, Hannah D. Proteomic analysis of Saccharomyces cerevisiae grown on glucose or glycerol.

Degree: 2013, Victoria University of Wellington

URL: http://hdl.handle.net/10063/3356

► The goal of this research was to use two-dimensional electrophoresis to examine changes in abundance of enzymes of the glycolytic pathway in the yeast Saccharomyces… (more)

▼ The goal of this research was to use two-dimensional electrophoresis to examine changes in abundance of enzymes of the glycolytic pathway in the yeast Saccharomyces cerevisiae grown on carbon sources that support either fermentation to ethanol or oxidative metabolism. Large-scale profiling of protein abundances (expression proteomics) often detects changes in protein abundance between physiological states. Such changes in enzyme abundance are often interpreted as evidence of metabolic change although most textbooks emphasise control of enzyme activities not enzyme amount. Two-dimensional difference gel electrophoresis (2DDIGE) was therefore used to examine differences in protein abundance between S. cerevisiae strain BY4741 grown on either glucose (fermentation) or glycerol. Growth on 2% glucose, but not on glycerol, was accompanied by extensive production of ethanol. Doubling times for growth were 2 h 5 min in glucose and 9 h 41 min in glycerol. Conditions for extraction and two-dimensional electrophoresis of proteins were established. One hundred and seventy nine proteins were identified by MALDI mass spectrometry of tryptic digests of protein spots excised from Coomassie stained gels. All of the enzymes for conversion of glucose to ethanol, except for the second enzyme of glycolysis phosphoglucose isomerase, were identified using twodimensional electrophoresis of 100 μg of protein from cells grown on 2% glucose. Identification of proteins excised from the DIGE gels was more challenging, partly because of the lower amount of protein. Eight of the proteins that showed statistically significant differences in abundance (≥ 2-fold, p ≤ 0.01) between glucose and glycerol were identified by mass spectrometry of proteins excised from the 2DDIGE gels, and a further 18 varying proteins were matched to proteins identified from the Coomassie stained gels. Of these total 26 identified or matched proteins, subunits of five of the enzymes for conversion of glucose to ethanol were more abundant from the fermentative cells grown on glucose. The more abundant glycolytic enzymes were phosphofructokinase 2, fructose-1,6-bisphosphate aldolase, triosephosphate isomerase and enolase, plus pyruvate decarboxylase that was required for conversion of the glycolytic product pyruvate to acetaldehyde. The alcohol dehydrogenases Adh1 and Adh4 that convert acetaldehyde to ethanol were detected but did not vary significantly between growth on glucose or glycerol. The results confirmed that in this case changes in abundance of some enzymes were consistent with the altered metabolic output. Future studies should examine whether changes in the abundance and activity of these enzymes are responsible for the differences in metabolism. Advisors/Committee Members: Jordan, Bill.

Subjects/Keywords: Yeast; Proteomics; Glycolysis

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APA (6^th Edition):

Hoang, H. D. (2013). Proteomic analysis of Saccharomyces cerevisiae grown on glucose or glycerol. (Masters Thesis). Victoria University of Wellington. Retrieved from http://hdl.handle.net/10063/3356

Chicago Manual of Style (16^th Edition):

Hoang, Hannah D. “Proteomic analysis of Saccharomyces cerevisiae grown on glucose or glycerol.” 2013. Masters Thesis, Victoria University of Wellington. Accessed July 22, 2019. http://hdl.handle.net/10063/3356.

MLA Handbook (7^th Edition):

Hoang, Hannah D. “Proteomic analysis of Saccharomyces cerevisiae grown on glucose or glycerol.” 2013. Web. 22 Jul 2019.

Vancouver:

Hoang HD. Proteomic analysis of Saccharomyces cerevisiae grown on glucose or glycerol. [Internet] [Masters thesis]. Victoria University of Wellington; 2013. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/10063/3356.

Council of Science Editors:

Hoang HD. Proteomic analysis of Saccharomyces cerevisiae grown on glucose or glycerol. [Masters Thesis]. Victoria University of Wellington; 2013. Available from: http://hdl.handle.net/10063/3356

University of Otago

20. Shi, Hongjun. Proteomic Identification and Immunological Validation of Protein Biomarkers for Early Detection and Prognosis of Colorectal Cancer .

Degree: 2012, University of Otago

URL: http://hdl.handle.net/10523/2418

► Colorectal cancer (CRC) is an important public health problem both internationally and in New Zealand. Currently available systems for early cancer detection (Faecal Occult Blood… (more)

▼ Colorectal cancer (CRC) is an important public health problem both internationally and in New Zealand. Currently available systems for early cancer detection (Faecal Occult Blood Test) and prediction of prognosis (pathological staging) are widely regarded as being imperfect, although no alternative tests are available. Identification and validation of sensitive and accurate biomarkers for the management of CRC is the goal of the work undertaken and described in the present PhD thesis. Recent developments in proteomic technologies have allowed comparison of multiple proteins from different tissues to be accomplished with good reproducibility and sensitivity. This has led to identification of many putative serological and tissue biomarkers for cancer. The vast majority of these early proteomic studies used gross tumour tissues for analysis. High intratumoural tissue heterogeneity such as differences in the amount of stroma and body fluid content within the gross tissue mass makes the crude tissue lysate less representative of the epithelial cancer cells under study and increases the technical variability. The development of laser capture microdissection (LCM) has allowed isolation of pure populations of cancer cells for analysis, significantly increasing the accuracy of quantitative tumour proteomics. In this thesis, a combined use of LCM and two-dimensional difference gel electrophoresis (2D-DIGE) in profiling CRC tissues is reported. This approach greatly improved the profiling accuracy as evidenced by a significant reduction in inter-patient variation as well as the discovery and validation of six previously unrecognised CRC–associated proteins. By performing immunohistochemistry on tumour tissue microarrays, two candidate markers — ACY1 and TUFM have been further evaluated as potential novel adverse prognostic factors for CRC. The study also developed a novel strategy to identify tumour-specific secreted proteins by incorporating secretome samples (total proteins released from cultured CRC cells) into the same 2D-DIGE analysis of the tumour tissue proteome as mentioned above. Fifteen proteins were identified to be both secreted from cancer cells and overexpressed in the tumour tissues. These tumour-specific secreted proteins have potential as specific serum/plasma markers for early cancer detection.Using an ELISA kit, developed in-house, one candidate marker — RUVBL1 was confirmed to be present in the cancer patients’ plasma at a concentration 4 fold greater on average than that found in the normal donor plasma, suggesting the potential utility of RUVBL1 as a non-invasive blood test for early detection of CRC. These results prove that the strategy used in this study is valid in discovering potentially novel biomarkers for CRC. Studies with more participants are required to confirm the clinical utility of these findings. The biological implications of these novel candidates also need to be further explored in the future. Advisors/Committee Members: Stubbs, Richard (advisor).

Subjects/Keywords: proteomics; CRC; biomarker

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APA (6^th Edition):

Shi, H. (2012). Proteomic Identification and Immunological Validation of Protein Biomarkers for Early Detection and Prognosis of Colorectal Cancer . (Doctoral Dissertation). University of Otago. Retrieved from http://hdl.handle.net/10523/2418

Chicago Manual of Style (16^th Edition):

Shi, Hongjun. “Proteomic Identification and Immunological Validation of Protein Biomarkers for Early Detection and Prognosis of Colorectal Cancer .” 2012. Doctoral Dissertation, University of Otago. Accessed July 22, 2019. http://hdl.handle.net/10523/2418.

MLA Handbook (7^th Edition):

Shi, Hongjun. “Proteomic Identification and Immunological Validation of Protein Biomarkers for Early Detection and Prognosis of Colorectal Cancer .” 2012. Web. 22 Jul 2019.

Vancouver:

Shi H. Proteomic Identification and Immunological Validation of Protein Biomarkers for Early Detection and Prognosis of Colorectal Cancer . [Internet] [Doctoral dissertation]. University of Otago; 2012. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/10523/2418.

Council of Science Editors:

Shi H. Proteomic Identification and Immunological Validation of Protein Biomarkers for Early Detection and Prognosis of Colorectal Cancer . [Doctoral Dissertation]. University of Otago; 2012. Available from: http://hdl.handle.net/10523/2418

University of Manchester

21. Randles, Michael. Proteomic analyses of kidney glomerular extracellular matrix in health and disease.

Degree: PhD, 2015, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/proteomic-analyses-of-kidney-glomerular-extracellular-matrix-in-health-and-disease(a39fe408-db06-4d80-b97b-4e0651bf7bc3).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.634958

► Glomerular filtration is a vital physiological process removing waste products from the circulation and this process occurs across the glomerular filtration barrier (GFB). The cells… (more)

▼ Glomerular filtration is a vital physiological process removing waste products from the circulation and this process occurs across the glomerular filtration barrier (GFB). The cells and extracellular matrix (ECM), which form this barrier, are exposed to forces during ultrafiltration and special adaptation is required to withstand these forces. Dysfunction in cellular adhesion machinery or ECM assembly within the GFB causes loss of selective glomerular filtration, however, the mechanisms governing these processes are poorly understood. To this end we sought to characterise the glomerular ECM and adhesion machinery using high throughput mass spectrometry (MS)-based proteomics. MS of human glomerular ECM identified a highly complex extracellular niche, revealing the potential involvement of novel ECM proteins in glomerular development and disease processes. Furthermore we identified that glomerular cells in culture had distinct ECM proteomes and interestingly, coculture experiments demonstrated that the ECM proteome was influenced by cellular crosstalk and had a closer resemblance to glomerular ECM in vivo. Protein network analyses of in vivo and in vitro ECM datasets revealed a common core of highly connected structural ECM proteins that may be important for glomerular ECM assembly. To understand how this ECM proteome altered in disease, we studied mice with mild glomerular dysfunction. Here, transcriptomic and proteomic analyses identified alterations in ECM composition and 3D electron microscopy revealed striking ultrastructural changes in glomerular ECM. MS-based proteomics was next applied to the analysis of glomerular podocyte adhesion complexes, leading to the discovery that the actin cytoskeletal regulators and trafficking machinery are recruited to adhesions sites in an ECM-ligand dependent manner. Furthermore, these differences functionally altered cell shape and adhesion strength. These same analyses were applied to podocyte cell-cell junctions, revealing an unexpected overlap of cell-ECM and cell-cell adhesion machinery. Overall, these findings demonstrate for the first time the complexity of the glomerular ECM and adhesion signalling complexes and reinforce the benefits of global, unbiased experimental approaches. In addition the results suggest that glomerular ECM composition, organisation and adhesion signalling are context dependent, and therefore, represent potential therapeutic targets.

Subjects/Keywords: 616.6; ECM; Proteomics

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APA (6^th Edition):

Randles, M. (2015). Proteomic analyses of kidney glomerular extracellular matrix in health and disease. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/proteomic-analyses-of-kidney-glomerular-extracellular-matrix-in-health-and-disease(a39fe408-db06-4d80-b97b-4e0651bf7bc3).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.634958

Chicago Manual of Style (16^th Edition):

Randles, Michael. “Proteomic analyses of kidney glomerular extracellular matrix in health and disease.” 2015. Doctoral Dissertation, University of Manchester. Accessed July 22, 2019. https://www.research.manchester.ac.uk/portal/en/theses/proteomic-analyses-of-kidney-glomerular-extracellular-matrix-in-health-and-disease(a39fe408-db06-4d80-b97b-4e0651bf7bc3).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.634958.

MLA Handbook (7^th Edition):

Randles, Michael. “Proteomic analyses of kidney glomerular extracellular matrix in health and disease.” 2015. Web. 22 Jul 2019.

Vancouver:

Randles M. Proteomic analyses of kidney glomerular extracellular matrix in health and disease. [Internet] [Doctoral dissertation]. University of Manchester; 2015. [cited 2019 Jul 22]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/proteomic-analyses-of-kidney-glomerular-extracellular-matrix-in-health-and-disease(a39fe408-db06-4d80-b97b-4e0651bf7bc3).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.634958.

Council of Science Editors:

Randles M. Proteomic analyses of kidney glomerular extracellular matrix in health and disease. [Doctoral Dissertation]. University of Manchester; 2015. Available from: https://www.research.manchester.ac.uk/portal/en/theses/proteomic-analyses-of-kidney-glomerular-extracellular-matrix-in-health-and-disease(a39fe408-db06-4d80-b97b-4e0651bf7bc3).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.634958

University of Manchester

22. Couto, Narciso Alves Da silva. Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach.

Degree: 2011, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:122515

► The main work presented in this thesis describes proteomics strategies applied to study the trafficking and turnover of glutathione reductase (Glr1) isoforms in the cytosol… (more)

▼ The main work presented in this thesis describes proteomics strategies applied to study the trafficking and turnover of glutathione reductase (Glr1) isoforms in the cytosol and mitochondria of Saccharomyces cerevisiae. Additional work was performed in order to understand mass spectrometric response factors and how they can affect peptides representation in the mass spectra. The opportunity to study two sub proteomes involved in biofilm formation of Pseudomonas aeruginosa PAO1 arose during my PhD and their analysis is also presented.Glr1 is a low abundant protein involved in the defence mechanisms against reactive oxygen species, which are sources of many diseases. Because of its biological relevance, considerable effort has been made in order to understand its functional role in the cell. This protein has been studied using biochemical strategies. In yeast, the cytosolic and mitochondrial forms of glutathione reductase are expressed by the same gene, GLR1, using alternative start codons. Translation from the first AUG codon generates the mitochondrial form incorporating a transit peptide necessary for import into the mitochondria. If the translation starts at the second AUG codon, the cytosolic counterpart is generated. Biochemical approaches show that the first AUG codon is not in favourable context and it has been suggested that leaky scanning accounts for the abundance of the cytosolic protein.The analysis of Glr1 forms by mass spectrometry was demanded because only the N-terminal region is informative about similarities and differences between cytosolic and mitochondrial forms. The protein is also of low abundance in both cytosol and mitochondrial compartments. A genetically modified strain, over-expressing this protein was, therefore, used throughout this work in order to analyse glutathione reductase in the mitochondria. This was not possible with the wild-type strain.Because the first AUG codon is now in context, the over-producing strain (MORF) yields both cytosolic and full length mitochondrial isoforms in the cytosol. Analysis of the mitochondrial protein shows that the cleavage of the pre-sequence is not specific. Three different forms of the mitochondrial N-terminal peptide were detected. Some attention was also devoted to glutathione reductase turnover in both cytosol and mitochondrial compartments using the genetically modified strain. Both N-terminal peptides generated from translation starting in the first and second AUG codon as well as mid-chain peptides from the cytosol fraction and one mid-chain peptide from the mitochondrial fraction, were used to calculate relative turnover measurements. My results illustrate that the mitochondrial protein is in faster turnover than the cytosolic counterpart. Moreover, the long and short forms observed in the cytosol also show slightly different turnover rates, the long form presenting faster turnover than the short form. Rapid turnover therefore maintains the level of glutathione reductase in the mitochondria.Despite the exquisite sensitivity of mass… Advisors/Committee Members: GASKELL, SIMON SJ, EYERS, CLAIRE CE, GORRY, PETER PA, BARBER, JILL JA, Gaskell, Simon, Gaskell, Simon, Eyers, Claire, Gorry, Peter, Barber, Jill, Barber, Jill.

Subjects/Keywords: Proteomics; Mass Spectrometry

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APA (6^th Edition):

Couto, N. A. D. s. (2011). Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:122515

Chicago Manual of Style (16^th Edition):

Couto, Narciso Alves Da silva. “Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach.” 2011. Doctoral Dissertation, University of Manchester. Accessed July 22, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:122515.

MLA Handbook (7^th Edition):

Couto, Narciso Alves Da silva. “Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach.” 2011. Web. 22 Jul 2019.

Vancouver:

Couto NADs. Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach. [Internet] [Doctoral dissertation]. University of Manchester; 2011. [cited 2019 Jul 22]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:122515.

Council of Science Editors:

Couto NADs. Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach. [Doctoral Dissertation]. University of Manchester; 2011. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:122515

University of Aberdeen

23. Causey, Dwight R. Proteomic and molecular investigations of links between growth and immune function in salmonids.

Degree: PhD, 2018, University of Aberdeen

URL: http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=240038 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767337

► The allocation of energetic resources into competing physiological systems is crucial for the survival and fitness of an organism. Maintenance of active growth and effective… (more)

▼ The allocation of energetic resources into competing physiological systems is crucial for the survival and fitness of an organism. Maintenance of active growth and effective immune function is energetically costly and therefore, trade-offs should have evolved to optimise the allocation of resources into these systems according to physiological status. While recent studies have begun to elucidate the mechanisms by which cross-talk exists between these two systems, more work is needed to characterise their interactions. A high-throughput proteomics approach was developed to investigate the molecular mechanisms underpinning fast growth and molecular cross-talk between growth and immune function. This approach revealed unique routes to fast growth in two different growth-accelerated coho salmon strains, including increased protein synthesis in fish overexpressing growth hormone (GH) through a focussed up-regulation of translation machinery. Conversely, selectively-bred fish showed more complex alterations in multiple metabolic pathways potentially underlying increased growth and domestication. Additionally, the liver proteome response of rainbow trout to a bacterial challenge unveiled host defence and immune proteins upregulated during the acute phase response (APR), along with candidate proteins involved in re-allocation of energetic resources during an immune response. Additionally, novel genetic expansions of salmonid complement C3 proteins upregulated during bacterial challenge were identified and characterised. Finally, the AMP-activated kinase (AMPK) system was investigated due to its role in managing energetic status, making it an ideal system to investigate crosstalk between growth and immunity. Novel salmonid-specific genetic expansions in AMPK subunits (α, β and γ) were demonstrated and their mRNA level expression analysed in fast-growing fish strains exposed to immune stimuli, where an increase in expression of several subunits was observed for fish overexpressing GH. However, a significant downregulation in expression of several AMPK subunit genes occurred in response to immune stimuli. Overall, this project provides insights into links between growth and immune function in salmonids, which are relevant to the aquaculture industry, where the aim is to maximise fish growth while retaining strong immunocompetence.

Subjects/Keywords: Salmonidae; Proteomics; Somatotropin

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APA (6^th Edition):

Causey, D. R. (2018). Proteomic and molecular investigations of links between growth and immune function in salmonids. (Doctoral Dissertation). University of Aberdeen. Retrieved from http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=240038 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767337

Chicago Manual of Style (16^th Edition):

Causey, Dwight R. “Proteomic and molecular investigations of links between growth and immune function in salmonids.” 2018. Doctoral Dissertation, University of Aberdeen. Accessed July 22, 2019. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=240038 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767337.

MLA Handbook (7^th Edition):

Causey, Dwight R. “Proteomic and molecular investigations of links between growth and immune function in salmonids.” 2018. Web. 22 Jul 2019.

Vancouver:

Causey DR. Proteomic and molecular investigations of links between growth and immune function in salmonids. [Internet] [Doctoral dissertation]. University of Aberdeen; 2018. [cited 2019 Jul 22]. Available from: http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=240038 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767337.

Council of Science Editors:

Causey DR. Proteomic and molecular investigations of links between growth and immune function in salmonids. [Doctoral Dissertation]. University of Aberdeen; 2018. Available from: http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=240038 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767337

University of Edinburgh

24. Furlan, Cristina. Quantitative proteomics of human chromatin.

Degree: PhD, 2013, University of Edinburgh

URL: http://hdl.handle.net/1842/17992

► The work presented in this thesis aims at unravelling human chromatin composition by quantitative proteomics to outline the functional and structural changes occurring during the… (more)

Subjects/Keywords: 572.8; chromatin; proteomics

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APA (6^th Edition):

Furlan, C. (2013). Quantitative proteomics of human chromatin. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/17992

Chicago Manual of Style (16^th Edition):

Furlan, Cristina. “Quantitative proteomics of human chromatin.” 2013. Doctoral Dissertation, University of Edinburgh. Accessed July 22, 2019. http://hdl.handle.net/1842/17992.

MLA Handbook (7^th Edition):

Furlan, Cristina. “Quantitative proteomics of human chromatin.” 2013. Web. 22 Jul 2019.

Vancouver:

Furlan C. Quantitative proteomics of human chromatin. [Internet] [Doctoral dissertation]. University of Edinburgh; 2013. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/1842/17992.

Council of Science Editors:

Furlan C. Quantitative proteomics of human chromatin. [Doctoral Dissertation]. University of Edinburgh; 2013. Available from: http://hdl.handle.net/1842/17992

25. Gilmore, Ian Richard. Quantitative proteomic analysis of the effect of 24(S),25-epoxycholesterol on SN4741 neuron cells.

Degree: PhD, 2013, Swansea University

URL: https://cronfa.swan.ac.uk/Record/cronfa42712 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.678489

► Oxysterols are oxygenated derivatives of cholesterol or its precursors. One oxysterol, 24(S),25-epoxycholesterol (24(S),25-EC), which results from a shunt in the cholesterol synthesis pathway has been… (more)

▼ Oxysterols are oxygenated derivatives of cholesterol or its precursors. One oxysterol, 24(S),25-epoxycholesterol (24(S),25-EC), which results from a shunt in the cholesterol synthesis pathway has been found at higher than expected levels in embryonic murine brain. Interestingly, the receptor that 24(5),25-EC is a ligand for, Liver X Receptor (LXR), has been implicated in neurogenesis in the ventral mid brain region of embryonic brain; an area with a high density of dopaminergic neurons. The mechanism by which LXR induces this effect is unclear. Therefore, proteomic and phosphoproteomic studies were performed using a stable isotope labelled in amino acid in cell culture (SILAC) approach in order to quantify changes in the proteome between different treatment groups in a mouse substantia nigra dopaminergic cell line (SN4741) SN4741 cells were cultured in SILAC media containing differentially isotope labelled arginine and lysine. For protein expression studies SN4741 cells were treated in serum free media with vehicle, 10muM 24(S),25-EC, or 1muM GW3965, a synthetic ligand of LXR, for 24 hours. For analysis of changes in the phosphoproteome SN4741 cells were treated in serum free media with vehicle, 10muM 24(5),25-EC, or 30muM 25- hydroxycholesterol for 6 hours. Cells were lysed and protein combined in a 1:1 ratio before trypsin digestion and peptide separation via strong cation exchange chromatography. Phosphopeptides were enriched using immobilised metal affinity chromatography (IMAC). Resulting fractions were analysed, using a data dependent LC-MS/MS method. Data was quantified using MaxQuant software in conjunction with Mascot using an IPl mouse database. In protein expression analysis known oxysterol regulated genes, via SREBP or LXR, were differentially expressed. Oxysterol treatment induced global changes in proteins involved in lipid (cholesterol, fatty acid, phospholipid, triglyceride) synthesis. LXR? protein expression increased after GW3965 and 24(5),25-EC treatment, though no change was seen on LXRp mRNA, implying that ligand binding protects LXR? from degradation. 24(S),25-EC induced changes in expression and localisation of the membrane protein caveolin-1. Also, phosphoethanolamine cytidylyltransferase and collagen type IV alpha-3-binding protein, 2 proteins involved in phospholipid synthesis, had an altered expression after 24(S),25-EC treatment suggesting a role for oxysterols in membrane homeostasis. A cytokine, macrophage colony stimulating factor, which is required for normal neuronal development and macrophage differentiation had an LXR independent increased expression after 24(S),25-EC treatment. Quantitative RT-PCR data demonstrated that proteomic changes were due to both transcriptional and post-transcriptional effects of oxysterol. In addition, studies examining changes in the mouse phosphoproteome identified a number of novel phosphorylation sites.

Subjects/Keywords: 573.8; Proteomics; Neurons

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APA (6^th Edition):

Gilmore, I. R. (2013). Quantitative proteomic analysis of the effect of 24(S),25-epoxycholesterol on SN4741 neuron cells. (Doctoral Dissertation). Swansea University. Retrieved from https://cronfa.swan.ac.uk/Record/cronfa42712 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.678489

Chicago Manual of Style (16^th Edition):

Gilmore, Ian Richard. “Quantitative proteomic analysis of the effect of 24(S),25-epoxycholesterol on SN4741 neuron cells.” 2013. Doctoral Dissertation, Swansea University. Accessed July 22, 2019. https://cronfa.swan.ac.uk/Record/cronfa42712 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.678489.

MLA Handbook (7^th Edition):

Gilmore, Ian Richard. “Quantitative proteomic analysis of the effect of 24(S),25-epoxycholesterol on SN4741 neuron cells.” 2013. Web. 22 Jul 2019.

Vancouver:

Gilmore IR. Quantitative proteomic analysis of the effect of 24(S),25-epoxycholesterol on SN4741 neuron cells. [Internet] [Doctoral dissertation]. Swansea University; 2013. [cited 2019 Jul 22]. Available from: https://cronfa.swan.ac.uk/Record/cronfa42712 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.678489.

Council of Science Editors:

Gilmore IR. Quantitative proteomic analysis of the effect of 24(S),25-epoxycholesterol on SN4741 neuron cells. [Doctoral Dissertation]. Swansea University; 2013. Available from: https://cronfa.swan.ac.uk/Record/cronfa42712 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.678489

University of Texas – Austin

26. Greer, Sylvester McCarthy, III. Development of ultraviolet photodissociation for high-throughput analysis of heavily modified proteins and peptides.

Degree: Chemistry, 2018, University of Texas – Austin

URL: http://hdl.handle.net/2152/68066

► The utility of 193 nm ultraviolet photodissociation (UVPD) is evaluated for high-throughput proteomics applications including: analysis of small peptides in a traditional bottom-up proteomics workflow,… (more)

Subjects/Keywords: Proteomics; UVPD; PTM

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APA (6^th Edition):

Greer, Sylvester McCarthy, I. (2018). Development of ultraviolet photodissociation for high-throughput analysis of heavily modified proteins and peptides. (Thesis). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/68066

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Greer, Sylvester McCarthy, III. “Development of ultraviolet photodissociation for high-throughput analysis of heavily modified proteins and peptides.” 2018. Thesis, University of Texas – Austin. Accessed July 22, 2019. http://hdl.handle.net/2152/68066.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Greer, Sylvester McCarthy, III. “Development of ultraviolet photodissociation for high-throughput analysis of heavily modified proteins and peptides.” 2018. Web. 22 Jul 2019.

Vancouver:

Greer, Sylvester McCarthy I. Development of ultraviolet photodissociation for high-throughput analysis of heavily modified proteins and peptides. [Internet] [Thesis]. University of Texas – Austin; 2018. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/2152/68066.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Greer, Sylvester McCarthy I. Development of ultraviolet photodissociation for high-throughput analysis of heavily modified proteins and peptides. [Thesis]. University of Texas – Austin; 2018. Available from: http://hdl.handle.net/2152/68066

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Vanderbilt University

27. Frappier, Sara Lynn. MALDI Imaging Mass Spectrometry for small molecule quantitation and evaluation for markers of drug response in Gliomas.

Degree: PhD, Chemistry, 2011, Vanderbilt University

URL: http://etd.library.vanderbilt.edu/available/etd-03282011-103836/ ;

► MALDI IMAGING MASS SPECTROMETRY FOR SMALL MOLECULE QUANTITATION AND EVALUATION FOR MARKERS OF DRUG RESPONSE IN GLIOMAS SARA L. FRAPPIER Dissertation under the direction of… (more)

▼ MALDI IMAGING MASS SPECTROMETRY FOR SMALL MOLECULE QUANTITATION AND EVALUATION FOR MARKERS OF DRUG RESPONSE IN GLIOMAS SARA L. FRAPPIER Dissertation under the direction of Professor Richard M. Caprioli A protocol has been developed to implement small molecule quantitation with MALDI Imaging MS directly from tissue sections. This protocol allows for MALDI based imaging technologies to correlate absolute drug concentration with pharmacological response in tissues while still maintaining spatial information in rapid, high-throughput molecularly specific experiments. The quantitation protocol has been applied to the investigation of two therapies under investigation for the treatment of Glioblastomas (brain tumors of glial cell origin) to determine the quantities of compound that reach the brain and tumor areas in mouse models. Imaging experiments performed by MALDI were able to provide the individual, label-free temporal distributions of IMAT and CYC from brain tissue sections with high sensitivity and reproducibility. Highly-accurate absolute quantities of each compound were also obtained directly from tissue sections without the need for homogenization or extraction procedures. Using the calculated drug concentrations of IMAT and CYC in conjunction with standard MALDI TOF imaging, it was possible to study the proteome affects that the drug presence had on primary brain tumor xenografts in mice. MALDI Imaging MS proved to be an invaluable tool to rapidly and reproducibly relate the tissue distribution of the IMAT and CYC to the observed pharmacological response within the same tissue sample while maintaining spatial resolution. Altered proteins were identified and can contribute to an improved understanding of the IMAT and CYC mechanisms of action as well as help gain a deeper understanding of the mechanisms involved in primary brain tumor function. Advisors/Committee Members: Richard M. Caprioli (chair), Michael K. Cooper (committee member), Brian.O. Bachmann (committee member), Reid C. Thompson (committee member).

Subjects/Keywords: PROTEOMICS; CYCLOPAMINE; IMATINIB

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APA (6^th Edition):

Frappier, S. L. (2011). MALDI Imaging Mass Spectrometry for small molecule quantitation and evaluation for markers of drug response in Gliomas. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://etd.library.vanderbilt.edu/available/etd-03282011-103836/ ;

Chicago Manual of Style (16^th Edition):

Frappier, Sara Lynn. “MALDI Imaging Mass Spectrometry for small molecule quantitation and evaluation for markers of drug response in Gliomas.” 2011. Doctoral Dissertation, Vanderbilt University. Accessed July 22, 2019. http://etd.library.vanderbilt.edu/available/etd-03282011-103836/ ;.

MLA Handbook (7^th Edition):

Frappier, Sara Lynn. “MALDI Imaging Mass Spectrometry for small molecule quantitation and evaluation for markers of drug response in Gliomas.” 2011. Web. 22 Jul 2019.

Vancouver:

Frappier SL. MALDI Imaging Mass Spectrometry for small molecule quantitation and evaluation for markers of drug response in Gliomas. [Internet] [Doctoral dissertation]. Vanderbilt University; 2011. [cited 2019 Jul 22]. Available from: http://etd.library.vanderbilt.edu/available/etd-03282011-103836/ ;.

Council of Science Editors:

Frappier SL. MALDI Imaging Mass Spectrometry for small molecule quantitation and evaluation for markers of drug response in Gliomas. [Doctoral Dissertation]. Vanderbilt University; 2011. Available from: http://etd.library.vanderbilt.edu/available/etd-03282011-103836/ ;

Victoria University of Wellington

28. Dunne, Jonathan Craig. A Proteomic Analysis of Fibre Degradation and Assimilation by Butyrivibrio Proteoclasticus.

Degree: 2010, Victoria University of Wellington

URL: http://hdl.handle.net/10063/1654

► Butyrivibrio proteoclasticus B316T is a Gram-positive, lignocellulose degrading bacterium that is prevalent in the rumen of animals grazing pasture, and is one of only a… (more)

▼ Butyrivibrio proteoclasticus B316T is a Gram-positive, lignocellulose degrading bacterium that is prevalent in the rumen of animals grazing pasture, and is one of only a few rumen microbes known to degrade and utilise xylan in vitro. Xylan is a hemicellulose that comprises up to 45% of the polysaccharide component of ruminant forages. Often as little as 30% of the total energy content of forages is utilised by the ruminant due to poor hemicellulose degradation by the fibrolytic rumen microbes. An opportunity exists to improve forage degradation in the rumen, which is predicted to improve the productivity of forage fed ruminants. A clearer understanding of the strategies employed by fibrolytic rumen microbes to degrade and utilise lignocellulose is important in realising this goal. Almost 10% of the B. proteoclasticus genome encodes proteins involved in polysaccharide metabolism and transport, which includes 134 fibrolytic enzymes that are active upon plant fibre. Many of these are clustered into one of 36 polysaccharide utilisation loci that also contain transmembrane transporters, transcriptional regulators, environmental sensors and genes involved in further polysaccharide metabolism. Gel-based and gel-free proteomic analyses of the cytosolic, cell-associated, and secreted fractions of cells grown on xylan were used to identify proteins involved in the degradation, assimilation, and metabolism of hemicellulose. A set of 416 non-redundant proteins were identified, which included 12 extracellular and 24 cytosolic polysaccharidases, and 59 proteins involved in the uptake and further metabolism of polysaccharide degradation products, many of which were substrate-binding protein components of ATP-driven transporter systems. In cells grown on xylan, several of these proteins displayed significant protein abundance changes relative to cells grown on the monomeric sugar xylose, in a pattern that reflected the growth substrates used. A model of xylan degradation by B. proteoclasticus based on these results hypothesises that B. proteoclasticus attacks the xylan backbone and main substituent groups of hemicellulose in the extracellular space, assimilates the xylooligosaccharides and performs the final stages of degradation within the cell. These results provide insight into a xylan degrading enzyme system that has evolved to efficiently degrade and utilise hemicellulose, extend our understanding of the enzymes that are likely to play important roles in hemicellulose degradation, and support the notion that Butyrivibrio species are important contributors to rumen fibre degradation. Advisors/Committee Members: Jordan, Bill.

Subjects/Keywords: Proteomics; Rumen; Hemicellulose

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dunne, J. C. (2010). A Proteomic Analysis of Fibre Degradation and Assimilation by Butyrivibrio Proteoclasticus. (Doctoral Dissertation). Victoria University of Wellington. Retrieved from http://hdl.handle.net/10063/1654

Chicago Manual of Style (16^th Edition):

Dunne, Jonathan Craig. “A Proteomic Analysis of Fibre Degradation and Assimilation by Butyrivibrio Proteoclasticus.” 2010. Doctoral Dissertation, Victoria University of Wellington. Accessed July 22, 2019. http://hdl.handle.net/10063/1654.

MLA Handbook (7^th Edition):

Dunne, Jonathan Craig. “A Proteomic Analysis of Fibre Degradation and Assimilation by Butyrivibrio Proteoclasticus.” 2010. Web. 22 Jul 2019.

Vancouver:

Dunne JC. A Proteomic Analysis of Fibre Degradation and Assimilation by Butyrivibrio Proteoclasticus. [Internet] [Doctoral dissertation]. Victoria University of Wellington; 2010. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/10063/1654.

Council of Science Editors:

Dunne JC. A Proteomic Analysis of Fibre Degradation and Assimilation by Butyrivibrio Proteoclasticus. [Doctoral Dissertation]. Victoria University of Wellington; 2010. Available from: http://hdl.handle.net/10063/1654

University of Minnesota

29. Van Riper, Susan Kaye. The importance of being proportional: a paradigm shift for intensity-based label free relative quantification in mass spectrometry proteomics.

Degree: PhD, Biomedical Informatics and Computational Biology, 2013, University of Minnesota

URL: http://purl.umn.edu/154674

► Biological variation not only provides insight into the molecular machinery of disease progression, but accurately informs clinicians about a patient's health status, both current and… (more)

▼ Biological variation not only provides insight into the molecular machinery of disease progression, but accurately informs clinicians about a patient's health status, both current and future. Researchers discover biological variation by conducting large scale comparative studies aimed at detecting differences in the molecular makeup (biomarkers) of samples in different states. Ideally suited for biomarkers are proteins because their cellular composition (proteome) and their degraded parts, endogenous peptides (peptidome), change in response to their environment and disease progression. For comparative proteomic studies, researchers commonly employ high performance liquid chromatography, coupled with electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) and labeled quantification. However, intensity-based label free relative quantification (iLFRQ) is more desirable than labeled quantification because iLFRQ is more cost effective and does not limit the number of samples in a study. Unfortunately, iLFRQ for proteins, and especially peptides, is challenging. Here, I highlight three challenges. 1) I contend that the current relative abundance paradigm is ill-suited to detect biological variation using iLFRQ. 2) HPLC-ESI-MS/ MS analyses produce poorly repeatable and reproducible results, and current normalization methods fail to mitigate localized extraneous variability (complex variability in measurements) from transient stochastic events occurring during an HPLC-ESI-MS/MS run. 3) Current software frameworks report protein level quantification rather than peptide level quantification. To overcome these challenges, I offer three contributions. 1) I propose to use the proportionality paradigm for iLFRQ instead of the relative abundance paradigm. 2) Proximity-based Intensity Normalization (PIN), an embodiment of the proportionality paradigm, normalizes a peptide's signal intensity by constructing its temporal neighborhood and computing its relative proportion within that neighborhood. 3) RIPPER, a new software framework that reports normalized peptide signal intensities rather than protein intensities. Evaluation results demonstrate that PIN dominates current normalization methods in reducing systematic bias and complex variability. Furthermore, RIPPER/PIN finds statistically significant biological variation which is now falsely reported or missed. I expect the proportionality paradigm for iLFRQ, embodied in PIN, and implemented in RIPPER, to change the way researchers analyze HPLC-ESI-MS/MS experimental data. The upshot will, I expect, will be reproducibility and repeatability improved, and otherwise falsely reported or missed, statistically significant biological variation discovered.

Subjects/Keywords: Normalization; Proteomics; Quantification

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Van Riper, S. K. (2013). The importance of being proportional: a paradigm shift for intensity-based label free relative quantification in mass spectrometry proteomics. (Doctoral Dissertation). University of Minnesota. Retrieved from http://purl.umn.edu/154674

Chicago Manual of Style (16^th Edition):

Van Riper, Susan Kaye. “The importance of being proportional: a paradigm shift for intensity-based label free relative quantification in mass spectrometry proteomics.” 2013. Doctoral Dissertation, University of Minnesota. Accessed July 22, 2019. http://purl.umn.edu/154674.

MLA Handbook (7^th Edition):

Van Riper, Susan Kaye. “The importance of being proportional: a paradigm shift for intensity-based label free relative quantification in mass spectrometry proteomics.” 2013. Web. 22 Jul 2019.

Vancouver:

Van Riper SK. The importance of being proportional: a paradigm shift for intensity-based label free relative quantification in mass spectrometry proteomics. [Internet] [Doctoral dissertation]. University of Minnesota; 2013. [cited 2019 Jul 22]. Available from: http://purl.umn.edu/154674.

Council of Science Editors:

Van Riper SK. The importance of being proportional: a paradigm shift for intensity-based label free relative quantification in mass spectrometry proteomics. [Doctoral Dissertation]. University of Minnesota; 2013. Available from: http://purl.umn.edu/154674

Australian National University

30. de Jong, Femke. Analysis of protoplasts and somatic embryogenesis in Medicago truncatula .

Degree: 2011, Australian National University

URL: http://hdl.handle.net/1885/7161

► This thesis examined protoplast proliferation and somatic embryogenesis, by comparing a highly with a poorly embryogenic Medicago truncatula line through microscopic, proteomic and in situ… (more)

▼ This thesis examined protoplast proliferation and somatic embryogenesis, by comparing a highly with a poorly embryogenic Medicago truncatula line through microscopic, proteomic and in situ hybridization analysis. Proteome analysis of M. truncatula was used to identify proteins involved in protoplast proliferation and the initiation of somatic embryogenesis. Furthermore, an in situ hybridization study was done to compare the expression of genes known to be involved in zygotic embryogenesis with the expression during somatic embryogenesis. A large number of proteins were up-, and down-regulated during the first 5 days of protoplast culture indicating that cellular reorganization took place. An up-regUlation of PR 1 O-like proteins and flavonoid synthesis proteins and a down-regulation of energy metabolism proteins were observed, indicating an initiation of a stress response. The observed stress response in protoplasts was down-regulated before the first cell divisions at 5-7 d. A stress-inducing bioassay on protoplasts showed that the ability of protoplasts to overcome stress and to proliferate under stress conditions depended on the level of stress and density of the protoplast culture, whereby more stress or a lower culture density resulted in higher levels of cell death. Proteomic analysis of the initiation of somatic embryogenesis showed that similar metabolic pathways were involved in the initiation of somatic embryogenesis and protoplast proliferation. By using a highly embryogenic (2HA) line, and a poorly embryogenic (A 17) line of M. truncatu!a, it was shown that particular proteins were specifically accumulated during the initiation of somatic embryogenesis. A high accumulation of a peroxidase was observed only in At7 tissue at the time of initiation of somatic embryogenesis and might be the reason why the initiation of somatic embryogenesis is inhibited in A 17 tissue. The specific accumulation of flavonoid synthesis proteins might also indicate that flavonoids are involved during the initiation of somatic embryogenesis. In situ hybridization with probes to genes known to be involved in zygotic embryogenesis, showed that M. truncatula somatic and Arabidopsis thaliana zygotic embryogenesis both followed similar developmental pathways. However, a few genes showed distinct patterns of gene expression in M. truncatula somatic embryos.

Subjects/Keywords: protoplast proliferation; proteomics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

de Jong, F. (2011). Analysis of protoplasts and somatic embryogenesis in Medicago truncatula . (Thesis). Australian National University. Retrieved from http://hdl.handle.net/1885/7161

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

de Jong, Femke. “Analysis of protoplasts and somatic embryogenesis in Medicago truncatula .” 2011. Thesis, Australian National University. Accessed July 22, 2019. http://hdl.handle.net/1885/7161.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

de Jong, Femke. “Analysis of protoplasts and somatic embryogenesis in Medicago truncatula .” 2011. Web. 22 Jul 2019.

Vancouver:

de Jong F. Analysis of protoplasts and somatic embryogenesis in Medicago truncatula . [Internet] [Thesis]. Australian National University; 2011. [cited 2019 Jul 22]. Available from: http://hdl.handle.net/1885/7161.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

de Jong F. Analysis of protoplasts and somatic embryogenesis in Medicago truncatula . [Thesis]. Australian National University; 2011. Available from: http://hdl.handle.net/1885/7161

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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Open Access Theses and Dissertations