subject:(proteomics)

Wesleyan University

1. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

Vancouver:

Fournier CT. The Repertoire of N-termini in the 𝘚𝘢𝘤𝘤𝘩𝘢𝘳𝘰𝘮𝘺𝘤𝘦𝘴 𝘤𝘦𝘳𝘦𝘷𝘪𝘴𝘪𝘢𝘦 Proteome: An Integrative Study. [Internet] [Doctoral dissertation]. Wesleyan University; 2013. [cited 2021 Mar 01]. 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

2. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

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 2021 Mar 01]. 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

University of Auckland

3. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. http://hdl.handle.net/2292/2565.

MLA Handbook (7^th Edition):

Atkinson, Kelly Rene LeFevre. “Proteomic biomarker discovery for preeclampsia.” 2008. Web. 01 Mar 2021.

Vancouver:

Atkinson KRL. Proteomic biomarker discovery for preeclampsia. [Internet] [Doctoral dissertation]. University of Auckland; 2008. [cited 2021 Mar 01]. 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

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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

Vancouver:

Murphy JP. Proteomics of Downstream Responses to Growth Signals in Proliferating Cells. [Internet] [Doctoral dissertation]. Dalhousie University; 2011. [cited 2021 Mar 01]. 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

5. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

Vancouver:

Uzoma IK. GLOBAL ANALYSIS OF SUMO E3 LIGASE SPECIFICITY UNCOVERS CROSSTALK-MEDIATED KINASE ACTIVATION. [Internet] [Thesis]. Johns Hopkins University; 2014. [cited 2021 Mar 01]. 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

Penn State University

6. Khanna, Mansi Rajendra. ROLE OF THE SPECTRIN BASED MEMBRANE SKELETON IN PLASMA MEMBRANE PROTEIN PRESENTATION: A PROTEOMIC APPROACH.

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/11976

► The plasma membrane (PM) and its associated proteins play an important role in determining how a cell interacts with its neighbours as well as how… (more)

▼ The plasma membrane (PM) and its associated proteins play an important role in determining how a cell interacts with its neighbours as well as how it responds to the components of, and conditions in the extracellular environment. As a reflection of this, more than 50% of the current drug targets lie at the cell surface. The amount of a protein at the cell surface is determined by its rate of delivery, internalization, recycling and degradation. All these parameters are subject to change under normal physiological adjustments, development, varying environmental influences and pathological conditions. The spectrin based membrane skeleton (SBMS) is a ubiquitous feature of all metazoan cells. This network of spectrin and associated proteins is attached directly or indirectly to plasma membrane proteins. Among the numerous functions of the SBMS, are roles in protein trafficking and turnover that determine levels of plasma membrane proteins. Regulated spectrin proteolysis, mediated by calpain, occurs under normal physiological conditions for various cellular processes, including establishment of synaptic contacts, long-term potentiation and platelet activation. Spectrin cleavage is also observed in age-related pathologies such as stroke and other ischemic events, Alzheimer’s and Parkinson’s diseases. However, little is known about the consequences of spectrin breakdown per se under these conditions. The goal of this work is to establish the fruit fly, Drosophila melanogaster as model system for some aspects of ischemic stroke, of which spectrin breakdown is a hallmark. The hypothesis being tested in this work is that disruption of the SBMS will affect the levels of many proteins at the cell surface under pathological conditions. The significance of this with respect to an ischemic stroke is that changes in levels of cell surface proteins in the event of SBMS breakdown need to be compensated for in post-stroke drug therapies and rehabilitation. In order to observe changes in the cell surface proteome under SBMS breakdown, one would first need to establish what it looks in normal conditions. Towards this, I developed a technique to isolate pure PM that employs a unique combination of density gradient centrifugation and aqueous two-phase affinity partitioning (2PAP). Density gradient centrifugation is an accepted method of fractionation on the basis of the buoyant densities of biomolecules and organelles but results in an overlap in cellular compartments due to similarities in densities. 2PAP is an established method for PM isolation in vertebrate model systems and makes use of the glycosylation pattern of PM proteins to isolate them from those in other compartments. My work demonstrates that a novel combination of both the techniques results in a robust PM preparation, which neither technique can achieve on its own. Using the new technique, 432 proteins were identified from Drosophila heads by MudPIT, of which 22% were found to be known PM residents and 34% are currently unassigned to any compartment and represent candidate… Advisors/Committee Members: Graham Hugh Thomas, Dissertation Advisor/Co-Advisor, Graham Hugh Thomas, Committee Chair/Co-Chair, Richard W Ordway, Committee Member, Hong Ma, Committee Member, Melissa Rolls, Committee Member, Bruce A Stanley, Committee Member.

Subjects/Keywords: spectrin; proteomics

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Khanna, M. R. (2011). ROLE OF THE SPECTRIN BASED MEMBRANE SKELETON IN PLASMA MEMBRANE PROTEIN PRESENTATION: A PROTEOMIC APPROACH. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/11976

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):

Khanna, Mansi Rajendra. “ROLE OF THE SPECTRIN BASED MEMBRANE SKELETON IN PLASMA MEMBRANE PROTEIN PRESENTATION: A PROTEOMIC APPROACH.” 2011. Thesis, Penn State University. Accessed March 01, 2021. https://submit-etda.libraries.psu.edu/catalog/11976.

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

MLA Handbook (7^th Edition):

Khanna, Mansi Rajendra. “ROLE OF THE SPECTRIN BASED MEMBRANE SKELETON IN PLASMA MEMBRANE PROTEIN PRESENTATION: A PROTEOMIC APPROACH.” 2011. Web. 01 Mar 2021.

Vancouver:

Khanna MR. ROLE OF THE SPECTRIN BASED MEMBRANE SKELETON IN PLASMA MEMBRANE PROTEIN PRESENTATION: A PROTEOMIC APPROACH. [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Mar 01]. Available from: https://submit-etda.libraries.psu.edu/catalog/11976.

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

Council of Science Editors:

Khanna MR. ROLE OF THE SPECTRIN BASED MEMBRANE SKELETON IN PLASMA MEMBRANE PROTEIN PRESENTATION: A PROTEOMIC APPROACH. [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/11976

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

7. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

Vancouver:

Cao L. Quantitative Phosphoproteomic Analysis to Unravel Mast Cell and T Cell Signaling Pathways. [Internet] [Doctoral dissertation]. Brown University; 2010. [cited 2021 Mar 01]. 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/

Victoria University of Wellington

8. 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

Record Details Similar Records Cite « Share

❌

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 March 01, 2021. http://hdl.handle.net/10063/1365.

MLA Handbook (7^th Edition):

Manivannan, Bhagyashree. “Diagnostic Markers for Schistosome-Mediated Liver Disease.” 2010. Web. 01 Mar 2021.

Vancouver:

Manivannan B. Diagnostic Markers for Schistosome-Mediated Liver Disease. [Internet] [Doctoral dissertation]. Victoria University of Wellington; 2010. [cited 2021 Mar 01]. 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

9. Karuppusamy, Shanmugasundaram. Proteomic approaches to early diagnosis of Johne’s disease in dairy cows.

Degree: PhD, Department of Biomedical Sciences, 2017, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10172

► Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of paratuberculosis or Johne’s disease (JD), an infectious, chronic granulomatous enteritis of ruminants. Current diagnostic tests… (more)

▼ Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of paratuberculosis or Johne’s disease (JD), an infectious, chronic granulomatous enteritis of ruminants. Current diagnostic tests for JD have limited sensitivity and specificity for the identification of subclinically infected animals warranting an investigation of MAP species-specific and sensitive antigens that might improve diagnostic test sensitivity and specificity. The aim of the first study was to identify antigenic proteins from the MAP cell envelope by comparing protein profiles from MAP, Mycobacterium avium subspecies hominissuis and M. smegmatis using a 2D-DIGE proteomic approach. Thirteen protein spots were selected and 15 proteins were subsequently identified by LC-MS/MS. The aim of the second study was to generate antibodies to recombinantly expressed MAP cell envelope proteins as well as to an extract of MAP total cell envelope proteins that was subsequently used to identify MAP organisms by IHC and immunomagnetic separation. Six MAP cell envelope proteins were recombinantly expressed, three of which were suitable for polyclonal antibody generation. Polyclonal antibodies generated to an extract of MAP cell envelope proteins detected MAP organisms in infected tissues using IHC and IF techniques thereby providing a more sensitive alternative to acid-fast staining of MAP in tissues for JD diagnosis. Furthermore, these antibodies were effective in immunomagnetic capture of MAP microorganisms in solution thereby providing proof-in-principle for a novel diagnostic approach. The objective of third study was to use an extract of MAP total cell envelope proteins as well as the six recombinant MAP proteins in ELISA formats to detect MAP-specific antibodies in cattle serum. The diagnostic sensitivity and specificity of the MAP envelope protein ELISA after serum absorption was 75% and 96% respectively. While ELISAs using the six recombinant protein antigens had reasonably high sensitivities, specificities were comparatively less than the commercial serum ELISA kit. The potential use of these recombinant proteins ELISAs for diagnosis of early MAP infection and control of JD requires further investigation and validation. Advisors/Committee Members: Dr. Kirby, Gordon (advisor).

Subjects/Keywords: Proteomics

10 more images…

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Karuppusamy, S. (2017). Proteomic approaches to early diagnosis of Johne’s disease in dairy cows. (Doctoral Dissertation). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10172

Chicago Manual of Style (16^th Edition):

Karuppusamy, Shanmugasundaram. “Proteomic approaches to early diagnosis of Johne’s disease in dairy cows.” 2017. Doctoral Dissertation, University of Guelph. Accessed March 01, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10172.

MLA Handbook (7^th Edition):

Karuppusamy, Shanmugasundaram. “Proteomic approaches to early diagnosis of Johne’s disease in dairy cows.” 2017. Web. 01 Mar 2021.

Vancouver:

Karuppusamy S. Proteomic approaches to early diagnosis of Johne’s disease in dairy cows. [Internet] [Doctoral dissertation]. University of Guelph; 2017. [cited 2021 Mar 01]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10172.

Council of Science Editors:

Karuppusamy S. Proteomic approaches to early diagnosis of Johne’s disease in dairy cows. [Doctoral Dissertation]. University of Guelph; 2017. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/10172

University of Manitoba

10. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

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 2021 Mar 01]. 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 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

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 2021 Mar 01]. 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

University of Helsinki

12. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. http://hdl.handle.net/10138/167646.

MLA Handbook (7^th Edition):

Cypryk, Wojciech. “Extracellular vesicles in innate immunity : Proteomic investigations.” 2016. Web. 01 Mar 2021.

Vancouver:

Cypryk W. Extracellular vesicles in innate immunity : Proteomic investigations. [Internet] [Doctoral dissertation]. University of Helsinki; 2016. [cited 2021 Mar 01]. 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 Otago

13. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

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 2021 Mar 01]. 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

14. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

Vancouver:

Couto NADs. Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach. [Internet] [Doctoral dissertation]. University of Manchester; 2011. [cited 2021 Mar 01]. 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

Vanderbilt University

15. 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://hdl.handle.net/1803/11594

► 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: Michael K. Cooper (committee member), Brian.O. Bachmann (committee member), Reid C. Thompson (committee member), Richard M. Caprioli (Committee Chair).

Subjects/Keywords: PROTEOMICS; CYCLOPAMINE; IMATINIB

Record Details Similar Records Cite « Share

❌

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

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://hdl.handle.net/1803/11594

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 March 01, 2021. http://hdl.handle.net/1803/11594.

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. 01 Mar 2021.

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 2021 Mar 01]. Available from: http://hdl.handle.net/1803/11594.

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://hdl.handle.net/1803/11594

Victoria University of Wellington

16. 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

Record Details Similar Records Cite « Share

❌

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 March 01, 2021. 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. 01 Mar 2021.

Vancouver:

Dunne JC. A Proteomic Analysis of Fibre Degradation and Assimilation by Butyrivibrio Proteoclasticus. [Internet] [Doctoral dissertation]. Victoria University of Wellington; 2010. [cited 2021 Mar 01]. 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 Colorado

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

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

URL: https://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

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Ebmeier, C. C. (2011). Targeted Proteomics and Molecular Mechanisms of Gene Activation. (Doctoral Dissertation). University of Colorado. Retrieved from https://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 March 01, 2021. https://scholar.colorado.edu/chem_gradetds/51.

MLA Handbook (7^th Edition):

Ebmeier, Christopher Carl. “Targeted Proteomics and Molecular Mechanisms of Gene Activation.” 2011. Web. 01 Mar 2021.

Vancouver:

Ebmeier CC. Targeted Proteomics and Molecular Mechanisms of Gene Activation. [Internet] [Doctoral dissertation]. University of Colorado; 2011. [cited 2021 Mar 01]. Available from: https://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: https://scholar.colorado.edu/chem_gradetds/51

University of Manchester

18. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

Vancouver:

Randles M. Proteomic analyses of kidney glomerular extracellular matrix in health and disease. [Internet] [Doctoral dissertation]. University of Manchester; 2015. [cited 2021 Mar 01]. 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

Delft University of Technology

19. Pourquié, Valérie (author). Dynamics of the transcriptome and proteome in regions of the brain differ considerably.

Degree: 2019, Delft University of Technology

URL: http://resolver.tudelft.nl/uuid:38d4d9e6-f6a2-448a-9a31-c0fc3258a301

►

Human brain research is advancing, facilitated by improved high-throughput techniques and systematically preservation of brain tissue in brain banks. Due to the complex organization and… (more)

Subjects/Keywords: Brain; Proteomics; Transcriptomics

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Pourquié, V. (. (2019). Dynamics of the transcriptome and proteome in regions of the brain differ considerably. (Masters Thesis). Delft University of Technology. Retrieved from http://resolver.tudelft.nl/uuid:38d4d9e6-f6a2-448a-9a31-c0fc3258a301

Chicago Manual of Style (16^th Edition):

Pourquié, Valérie (author). “Dynamics of the transcriptome and proteome in regions of the brain differ considerably.” 2019. Masters Thesis, Delft University of Technology. Accessed March 01, 2021. http://resolver.tudelft.nl/uuid:38d4d9e6-f6a2-448a-9a31-c0fc3258a301.

MLA Handbook (7^th Edition):

Pourquié, Valérie (author). “Dynamics of the transcriptome and proteome in regions of the brain differ considerably.” 2019. Web. 01 Mar 2021.

Vancouver:

Pourquié V(. Dynamics of the transcriptome and proteome in regions of the brain differ considerably. [Internet] [Masters thesis]. Delft University of Technology; 2019. [cited 2021 Mar 01]. Available from: http://resolver.tudelft.nl/uuid:38d4d9e6-f6a2-448a-9a31-c0fc3258a301.

Council of Science Editors:

Pourquié V(. Dynamics of the transcriptome and proteome in regions of the brain differ considerably. [Masters Thesis]. Delft University of Technology; 2019. Available from: http://resolver.tudelft.nl/uuid:38d4d9e6-f6a2-448a-9a31-c0fc3258a301

Victoria University of Wellington

20. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

Vancouver:

Hoang HD. Proteomic analysis of Saccharomyces cerevisiae grown on glucose or glycerol. [Internet] [Masters thesis]. Victoria University of Wellington; 2013. [cited 2021 Mar 01]. 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 Notre Dame

21. Katelyn Ludwig. Proteomic Analysis of Biological Systems</h1>.

Degree: Chemistry and Biochemistry, 2018, University of Notre Dame

URL: https://curate.nd.edu/show/p2676t08745

► Mass spectrometry-based proteomics have become critical for our understanding of biological systems. This technique allows for quantitative measurements of biomolecules that are altered between… (more)

Subjects/Keywords: Mass Spectrometry; Proteomics

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Ludwig, K. (2018). Proteomic Analysis of Biological Systems</h1>. (Thesis). University of Notre Dame. Retrieved from https://curate.nd.edu/show/p2676t08745

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):

Ludwig, Katelyn. “Proteomic Analysis of Biological Systems</h1>.” 2018. Thesis, University of Notre Dame. Accessed March 01, 2021. https://curate.nd.edu/show/p2676t08745.

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

MLA Handbook (7^th Edition):

Ludwig, Katelyn. “Proteomic Analysis of Biological Systems</h1>.” 2018. Web. 01 Mar 2021.

Vancouver:

Ludwig K. Proteomic Analysis of Biological Systems</h1>. [Internet] [Thesis]. University of Notre Dame; 2018. [cited 2021 Mar 01]. Available from: https://curate.nd.edu/show/p2676t08745.

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

Council of Science Editors:

Ludwig K. Proteomic Analysis of Biological Systems</h1>. [Thesis]. University of Notre Dame; 2018. Available from: https://curate.nd.edu/show/p2676t08745

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

University of Minnesota

22. 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

Record Details Similar Records Cite « Share

❌

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 March 01, 2021. 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. 01 Mar 2021.

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 2021 Mar 01]. 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

University of Edinburgh

23. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. http://hdl.handle.net/1842/17992.

MLA Handbook (7^th Edition):

Furlan, Cristina. “Quantitative proteomics of human chromatin.” 2013. Web. 01 Mar 2021.

Vancouver:

Furlan C. Quantitative proteomics of human chromatin. [Internet] [Doctoral dissertation]. University of Edinburgh; 2013. [cited 2021 Mar 01]. 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

24. 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

Record Details Similar Records Cite « Share

❌

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

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 March 01, 2021. 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. 01 Mar 2021.

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 2021 Mar 01]. 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 North Texas

25. Adhikari, Prem R. Proteomic Responses in the Gill of Zebrafish Following Exposure to Ibuprofen and Naproxen.

Degree: 2012, University of North Texas

URL: https://digital.library.unt.edu/ark:/67531/metadc149557/

► Non-steroidal anti-inflammatory drugs (NSAIDs) are among the most abundant environmental pharmaceutical contaminants. In this study, a proteomic analysis was conducted to identify proteins differentially expressed… (more)

Subjects/Keywords: Proteomics; NSAID; zebrafish

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Adhikari, P. R. (2012). Proteomic Responses in the Gill of Zebrafish Following Exposure to Ibuprofen and Naproxen. (Thesis). University of North Texas. Retrieved from https://digital.library.unt.edu/ark:/67531/metadc149557/

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):

Adhikari, Prem R. “Proteomic Responses in the Gill of Zebrafish Following Exposure to Ibuprofen and Naproxen.” 2012. Thesis, University of North Texas. Accessed March 01, 2021. https://digital.library.unt.edu/ark:/67531/metadc149557/.

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

MLA Handbook (7^th Edition):

Adhikari, Prem R. “Proteomic Responses in the Gill of Zebrafish Following Exposure to Ibuprofen and Naproxen.” 2012. Web. 01 Mar 2021.

Vancouver:

Adhikari PR. Proteomic Responses in the Gill of Zebrafish Following Exposure to Ibuprofen and Naproxen. [Internet] [Thesis]. University of North Texas; 2012. [cited 2021 Mar 01]. Available from: https://digital.library.unt.edu/ark:/67531/metadc149557/.

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

Council of Science Editors:

Adhikari PR. Proteomic Responses in the Gill of Zebrafish Following Exposure to Ibuprofen and Naproxen. [Thesis]. University of North Texas; 2012. Available from: https://digital.library.unt.edu/ark:/67531/metadc149557/

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

University of Texas – Austin

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

Degree: PhD, 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

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

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

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. Doctoral Dissertation, University of Texas – Austin. Accessed March 01, 2021. http://hdl.handle.net/2152/68066.

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. 01 Mar 2021.

Vancouver:

Greer, Sylvester McCarthy I. Development of ultraviolet photodissociation for high-throughput analysis of heavily modified proteins and peptides. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2018. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2152/68066.

Council of Science Editors:

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

University of California – Riverside

27. Guo, Lei. From Discovery-Based to Targeted Proteomics.

Degree: Environmental Toxicology, 2015, University of California – Riverside

URL: http://www.escholarship.org/uc/item/54b2510s

► Mass spectrometry-based proteomic approaches have become the method of choice for performing discovery-based quantitative global proteomic analysis, as well as targeted proteomics for the reproducible… (more)

▼ Mass spectrometry-based proteomic approaches have become the method of choice for performing discovery-based quantitative global proteomic analysis, as well as targeted proteomics for the reproducible analysis of a selected set of proteins. In this dissertation, we reported the application of these approaches in the profiling of global proteome with discovery-based proteomics approach, and profiling of global kinome with targeted proteomic analysis. In Chapter two, we studied hexavalent chromium [Cr(VI)]-induced alteration of proteomic landscape in human skin fibroblast cells. We utilized MS-based quantitative approach for assessing the global proteome alteration in response to Cr(VI) treatment. Here with the use of in-gel digestion and mass spectrometry analysis in data-dependant mode, we were able to quantify ~4600 unique proteins, among which around 10% exhibited significant alterations in expression levels upon a 24-h treatment with 0.5 uM Cr(VI). From these results, we revealed that Cr(VI) induced its cytotoxic effect via activating the cholesterol biosynthesis pathway. In Chapter three, we combined the filter-aided sample preparation method with LC-MS/MS analysis to reveal monomethylarsonous acid [MMA(III)]-induced alteration in the protein expression level in human skin fibroblasts. From our study, among the ~6500 quantified unique proteins, ~300 displayed significant changes in expression after exposure with 2 uM MMA(III) for 24 h. Subsequent analysis revealed the inhibition of de novo cholesterol biosynthesis upon MMA(III) treatment. In Chapter four, we applied adenosine triphosphate (ATP) affinity probe and scheduled multiple-reaction monitoring analysis for profiling global kinome in human cells in response to arsenite treatment. From the quantification of ~250 kinases, we found the expression of several kinases involved in cell cycle progression was changed significantly upon arsenite treatment. The up-regulation of cyclin-dependant kinase 1 was further verified. In Chapter five, we utilized stable isotope-labeled ATP affinity probe in conjunction with scheduled MRM analysis for profiling global kinome signatures of the radioresistant MCF-7/C6 breast cancer cells. We rigorously quantified 120 kinases, of which one third exhibited significant differences in expression levels or ATP binding affinities. Several kinases involved in cell cycle progression and DNA damage response quantified may be involved in the development of radioresistance in cancer cells.

Subjects/Keywords: Analytical chemistry; Environmental science; Discovery-based Proteomics; Environmental Toxicology; Mass Spectrometry; Quantitative Proteomics; Targeted Proteomics

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Guo, L. (2015). From Discovery-Based to Targeted Proteomics. (Thesis). University of California – Riverside. Retrieved from http://www.escholarship.org/uc/item/54b2510s

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):

Guo, Lei. “From Discovery-Based to Targeted Proteomics.” 2015. Thesis, University of California – Riverside. Accessed March 01, 2021. http://www.escholarship.org/uc/item/54b2510s.

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

MLA Handbook (7^th Edition):

Guo, Lei. “From Discovery-Based to Targeted Proteomics.” 2015. Web. 01 Mar 2021.

Vancouver:

Guo L. From Discovery-Based to Targeted Proteomics. [Internet] [Thesis]. University of California – Riverside; 2015. [cited 2021 Mar 01]. Available from: http://www.escholarship.org/uc/item/54b2510s.

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

Council of Science Editors:

Guo L. From Discovery-Based to Targeted Proteomics. [Thesis]. University of California – Riverside; 2015. Available from: http://www.escholarship.org/uc/item/54b2510s

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

Macquarie University

28. Vaibhav, Vineet. Towards breeding better oysters: a proteomic investigation of disease resistance in Sydney rock oysters.

Degree: 2017, Macquarie University

URL: http://hdl.handle.net/1959.14/1275088

►

Empirical thesis.

Chapter 1. General introduction – Chapter 2. Biomarkers of winter mortality resistance in selectively bred Sydney Rock oysters (Saccostrea glomerata) – Chapter 3.… (more)

▼

Empirical thesis.

Chapter 1. General introduction – Chapter 2. Biomarkers of winter mortality resistance in selectively bred Sydney Rock oysters (Saccostrea glomerata) – Chapter 3. Temporal comparison of Sydney rock oysters selectively bred for QX disease resistance reveals biomarkers of the disease progression response – Chapter 4. Proteomic comparison of shore caught wild oysters and disease-resistance selected Sydney rock oysters from Woolooware Bay – Chapter 5. SWATH - MS proteomic analysis of disease resistant Sydney rock oysters – Chapter 6. Conclusions and general discussion – Appendices.

Sydney Rock oysters (Saccostrea glomerata) are a native Australian oyster species present mainly along the eastern coast of New South Wales. These oysters are economically very important as they are consumed as food across Australia. Sydney Rock oysters are known in particular for their distinctive taste, making them one of the major aquaculture products of Australia. During the early 20th century, the introduction of modern farming methods resulted in rapid growth in Sydney Rock oyster production. However, during the 1970s production started to decline as a result of mass mortalities caused by different diseases such as Queensland Unknown (QX) and Winter Mortality (WM). These diseases, in addition to the changing environmental conditions such as water pollution, further diminished the production of oysters. While there has been some previous research on environmental and disease stress in oysters, the causes and impacts of different diseases on the Sydney Rock industry are relatively underexplored. This thesis makes an attempt to enhance our fundamental understanding of two diseases of Sydney Rock oysters - QX and WM - using quantitative shotgun proteomics.

Winter mortality was previously believed to be caused by a protozoan - Bonamia roughleyi, however the exact aetiology is still not clear. Whereas, QX disease is known to be caused by a paramyxean protozoan, Marteilia sydneyi, and is the major cause of the mass mortality of Sydney Rock oysters. The current mode of mitigating the impact of diseases relies on the farming of selected line of Sydney Rock oysters. The selective breeding programme of Sydney Rock oysters was established by NSW DPI using the survivors of mass mortality as a pioneering parent population. However, this mode of selection lacked the biological information of selection mechanisms and therefore it is feared that inbreeding depression might affect the future generations. Therefore, for sustainable growth of the industry it is very important to understand the biological basis of selection.

This thesis aims to understand the underlying molecular processes of better adaptability of selected lines of oysters against diseases, by identifying the proteomics differences in selected and unselected populations. Chapter 1 of this thesis deals with the proteomic investigation of oysters selected for WM. Using 2DE in association with LC-MS/MS, we identified differential proteomic expression…

Advisors/Committee Members: Macquarie University. Department of Molecular Sciences.

Subjects/Keywords: Sydney rock oyster – Diseases; Proteomics; aquaculture proteomics; oyster proteomics; Sydney rock oyster; mass spectrometry

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Vaibhav, V. (2017). Towards breeding better oysters: a proteomic investigation of disease resistance in Sydney rock oysters. (Doctoral Dissertation). Macquarie University. Retrieved from http://hdl.handle.net/1959.14/1275088

Chicago Manual of Style (16^th Edition):

Vaibhav, Vineet. “Towards breeding better oysters: a proteomic investigation of disease resistance in Sydney rock oysters.” 2017. Doctoral Dissertation, Macquarie University. Accessed March 01, 2021. http://hdl.handle.net/1959.14/1275088.

MLA Handbook (7^th Edition):

Vaibhav, Vineet. “Towards breeding better oysters: a proteomic investigation of disease resistance in Sydney rock oysters.” 2017. Web. 01 Mar 2021.

Vancouver:

Vaibhav V. Towards breeding better oysters: a proteomic investigation of disease resistance in Sydney rock oysters. [Internet] [Doctoral dissertation]. Macquarie University; 2017. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1959.14/1275088.

Council of Science Editors:

Vaibhav V. Towards breeding better oysters: a proteomic investigation of disease resistance in Sydney rock oysters. [Doctoral Dissertation]. Macquarie University; 2017. Available from: http://hdl.handle.net/1959.14/1275088

NSYSU

29. Lin, Ming-Tsung. Study on the muscle characteristics of the Swamp Eel, Monopterus albus, during Aestivation.

Degree: Master, Marine Biology, 2009, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0812109-231220

► The swamp eel, Monopterus albus, is a benthic freshwater species, inhabiting the muddy ponds, canals, and rice fields. They are highly adaptive to stressful environment… (more)

Subjects/Keywords: Monopterus albus; aestivation; proteomics

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Lin, M. (2009). Study on the muscle characteristics of the Swamp Eel, Monopterus albus, during Aestivation. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0812109-231220

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):

Lin, Ming-Tsung. “Study on the muscle characteristics of the Swamp Eel, Monopterus albus, during Aestivation.” 2009. Thesis, NSYSU. Accessed March 01, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0812109-231220.

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

MLA Handbook (7^th Edition):

Lin, Ming-Tsung. “Study on the muscle characteristics of the Swamp Eel, Monopterus albus, during Aestivation.” 2009. Web. 01 Mar 2021.

Vancouver:

Lin M. Study on the muscle characteristics of the Swamp Eel, Monopterus albus, during Aestivation. [Internet] [Thesis]. NSYSU; 2009. [cited 2021 Mar 01]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0812109-231220.

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

Council of Science Editors:

Lin M. Study on the muscle characteristics of the Swamp Eel, Monopterus albus, during Aestivation. [Thesis]. NSYSU; 2009. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0812109-231220

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

Oregon State University

30. Sowell, Sarah M. Proteomic analyses of marine bacteria.

Degree: PhD, Molecular and Cellular Biology, 2008, Oregon State University

URL: http://hdl.handle.net/1957/9321

► Proteins are the metabolic machines of the cell and as such, the study of proteins could illuminate the dominant biological activities that are occurring within… (more)

▼ Proteins are the metabolic machines of the cell and as such, the study of proteins could illuminate the dominant biological activities that are occurring within cells and reveal how an organism interacts with its environment. Here, we used proteomic techniques to study the abundant marine bacterium SAR11 both as an isolate and in the context of microbial communities. An accurate mass and time tag library was built to allow quantitative comparison of exponentially growing and stationary phase proteomes of the cultured SAR11 strain Candidatus Pelagibacter ubique HTCC1062. Significant increases in stationary-phase proteins that mitigate oxidative damage; OsmC and thioredoxin reductase were detected. In addition, molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, and regulatory proteins were also up-regulated in stationary phase. The up-regulation of this suite of proteins suggests a system by which Cand. P. ubique cells protect themselves against external stressors when nutrients are scarce without devoting significant resources to proteome remodeling. A mechanism for a global stationary-phase response was not identified. Metaproteomics is the study of all of the proteins expressed by a microbial community at a given point in time. Metaproteomic analyses were applied to mixed marine microbial communities collected from both oligotrophic and nutrient replete environments. Abundant proteins from SAR11, Prochlorococcus, and Synechococcus cells from the microbial community in the oligotrophic Sargasso Sea were identified using a novel technique for binning organism-specific metagenomic sequences. The SAR11 metaproteome was dominated by periplasmic substrate-binding proteins, specifically for phosphate, amino acids, phosphonate, and polyamines. A large-scale search on an unfiltered database with post-search BLAST annotations allowed for identification of proteins from SAR11 and other dominant bacterioplankton within the microbial community from the nutrient-replete Oregon coast. Here, the SAR11 metaproteome was also dominated by periplasmic substrate-binding proteins, but key substrates were amino acids, taurine, mannitol, and polyamines, suggesting that these substrates may become limiting before phosphorus when nutrients are freely available. The abundance of transport proteins suggests a means by which these cells remain competitive in the microbial community and play a key role in global nutrient cycling. Advisors/Committee Members: Giovannoni, Stephen (advisor), Beckman, Joe (committee member).

Subjects/Keywords: Proteomics; Marine bacteria – Composition

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Sowell, S. M. (2008). Proteomic analyses of marine bacteria. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/9321

Chicago Manual of Style (16^th Edition):

Sowell, Sarah M. “Proteomic analyses of marine bacteria.” 2008. Doctoral Dissertation, Oregon State University. Accessed March 01, 2021. http://hdl.handle.net/1957/9321.

MLA Handbook (7^th Edition):

Sowell, Sarah M. “Proteomic analyses of marine bacteria.” 2008. Web. 01 Mar 2021.

Vancouver:

Sowell SM. Proteomic analyses of marine bacteria. [Internet] [Doctoral dissertation]. Oregon State University; 2008. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1957/9321.

Council of Science Editors:

Sowell SM. Proteomic analyses of marine bacteria. [Doctoral Dissertation]. Oregon State University; 2008. Available from: http://hdl.handle.net/1957/9321

		in
And / Or
		in
And / Or
		in
And / Or
		in

Open Access Theses and Dissertations