subject:(silac)

University of Manchester

1. Jarnuczak, Andrew. Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains.

Degree: 2015, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:281103

►

In the last decade omics technologies enabled detailed and system-wide analysis of complex biological samples. Genomics, transcriptomics and metabolomics all benefited tremendously from technological advances… (more)

▼

In the last decade omics technologies enabled detailed and system-wide analysis of complex biological samples. Genomics, transcriptomics and metabolomics all benefited tremendously from technological advances in their respective fields. Proteomics was revolutionised by mass spectrometry, which allowed simultaneous identification of thousands of proteins in cells, tissues and organisms. And this mainly qualitative revolution, quickly turned quantitative. This work had two main objectives. Firstly, to apply the state of the art instrumentation, data analysis and bioinformatics methods to better our understanding of basic cell biology in a model organism Saccharomyces cerevisiae. Specifically, to quantitatively describe the effects of perturbations, such as adverse environmental conditions or chaperone gene deletions, on protein abundances in the cell. Additionally, it was aimed to demonstrate and evaluate the ability of a new timeof-flight mass spectrometer to perform large-scale absolute quantification. First, it was found that yeast cells are remarkably robust to deletions of major chaperone hub proteins (Ssa1p or Ssb1p deletions). This ability was attributed to network structure and redistribution of folding workload among other related chaperones rather than simple functional redundancy. Second, to build on the first set of results, a detailed time resolved description of yeast proteome dynamics in response to heat stress was provided for the wild type and Ssb1p chaperone mutant strains. In this study, for the first time in the literature, temporal expression patterns of many hallmark heat shock proteins were elucidated. Globally, a slow and sustained proteome remodelling or ‘buffering’ was revealed in both strains. However, it was also shown that the cells knocked out for the Ssb1p chaperone respond to heat in a distinctly different manner to the wild type strain. Finally, consistent and reproducible absolute quantification of multiple yeast proteomes was demonstrated using a new commercial time-of-flight mass spectrometer with ion mobility separation capabilities. The data obtained revealed global differences in cellular protein content between various chaperone prefoldin mutants as well as differential expression of a set of proteins promising to be interesting targets for further investigations.

NA

Advisors/Committee Members: GRANT, CHRISTOPHER CM, EYERS, CLAIRE CE, SCHWARTZ, JEAN-MARC J, Grant, Christopher, Eyers, Claire, Schwartz, Jean-Marc, Hubbard, Simon.

Subjects/Keywords: quantitative proteomics; label free; SILAC; yeast

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

APA (6^th Edition):

Jarnuczak, A. (2015). Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:281103

Chicago Manual of Style (16^th Edition):

Jarnuczak, Andrew. “Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains.” 2015. Doctoral Dissertation, University of Manchester. Accessed January 19, 2021. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:281103.

MLA Handbook (7^th Edition):

Jarnuczak, Andrew. “Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains.” 2015. Web. 19 Jan 2021.

Vancouver:

Jarnuczak A. Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains. [Internet] [Doctoral dissertation]. University of Manchester; 2015. [cited 2021 Jan 19]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:281103.

Council of Science Editors:

Jarnuczak A. Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains. [Doctoral Dissertation]. University of Manchester; 2015. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:281103

University of Manchester

2. Jarnuczak, Andrew. Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains.

Degree: PhD, 2015, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometrybased-quantitative-proteomics-applied-to-the-analysis-of-saccharomyces-cerevisiae-heat-stress-response-and-chaperone-deletion-strains(c653915b-70fa-44d7-9bb7-6e7965349ff0).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764359

► In the last decade omics technologies enabled detailed and system-wide analysis of complex biological samples. Genomics, transcriptomics and metabolomics all benefited tremendously from technological advances… (more)

▼ In the last decade omics technologies enabled detailed and system-wide analysis of complex biological samples. Genomics, transcriptomics and metabolomics all benefited tremendously from technological advances in their respective fields. Proteomics was revolutionised by mass spectrometry, which allowed simultaneous identification of thousands of proteins in cells, tissues and organisms. And this mainly qualitative revolution, quickly turned quantitative. This work had two main objectives. Firstly, to apply the state of the art instrumentation, data analysis and bioinformatics methods to better our understanding of basic cell biology in a model organism Saccharomyces cerevisiae. Specifically, to quantitatively describe the effects of perturbations, such as adverse environmental conditions or chaperone gene deletions, on protein abundances in the cell. Additionally, it was aimed to demonstrate and evaluate the ability of a new timeof-flight mass spectrometer to perform large-scale absolute quantification. First, it was found that yeast cells are remarkably robust to deletions of major chaperone hub proteins (Ssa1p or Ssb1p deletions). This ability was attributed to network structure and redistribution of folding workload among other related chaperones rather than simple functional redundancy. Second, to build on the first set of results, a detailed time resolved description of yeast proteome dynamics in response to heat stress was provided for the wild type and Ssb1p chaperone mutant strains. In this study, for the first time in the literature, temporal expression patterns of many hallmark heat shock proteins were elucidated. Globally, a slow and sustained proteome remodelling or 'buffering' was revealed in both strains. However, it was also shown that the cells knocked out for the Ssb1p chaperone respond to heat in a distinctly different manner to the wild type strain. Finally, consistent and reproducible absolute quantification of multiple yeast proteomes was demonstrated using a new commercial time-of-flight mass spectrometer with ion mobility separation capabilities. The data obtained revealed global differences in cellular protein content between various chaperone prefoldin mutants as well as differential expression of a set of proteins promising to be interesting targets for further investigations.

Subjects/Keywords: quantitative proteomics; label free; SILAC; yeast

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

Jarnuczak, A. (2015). Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometrybased-quantitative-proteomics-applied-to-the-analysis-of-saccharomyces-cerevisiae-heat-stress-response-and-chaperone-deletion-strains(c653915b-70fa-44d7-9bb7-6e7965349ff0).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764359

Chicago Manual of Style (16^th Edition):

Jarnuczak, Andrew. “Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains.” 2015. Doctoral Dissertation, University of Manchester. Accessed January 19, 2021. https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometrybased-quantitative-proteomics-applied-to-the-analysis-of-saccharomyces-cerevisiae-heat-stress-response-and-chaperone-deletion-strains(c653915b-70fa-44d7-9bb7-6e7965349ff0).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764359.

MLA Handbook (7^th Edition):

Jarnuczak, Andrew. “Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains.” 2015. Web. 19 Jan 2021.

Vancouver:

Jarnuczak A. Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains. [Internet] [Doctoral dissertation]. University of Manchester; 2015. [cited 2021 Jan 19]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometrybased-quantitative-proteomics-applied-to-the-analysis-of-saccharomyces-cerevisiae-heat-stress-response-and-chaperone-deletion-strains(c653915b-70fa-44d7-9bb7-6e7965349ff0).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764359.

Council of Science Editors:

Jarnuczak A. Mass spectrometry-based quantitative proteomics applied to the analysis of Saccharomyces cerevisiae heat stress response and chaperone deletion strains. [Doctoral Dissertation]. University of Manchester; 2015. Available from: https://www.research.manchester.ac.uk/portal/en/theses/mass-spectrometrybased-quantitative-proteomics-applied-to-the-analysis-of-saccharomyces-cerevisiae-heat-stress-response-and-chaperone-deletion-strains(c653915b-70fa-44d7-9bb7-6e7965349ff0).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.764359

University of Melbourne

3. Gulati, Twishi. Exploring the involvement of E6AP in prostate cancer: a combined transcriptomic and proteomic approach.

Degree: 2017, University of Melbourne

URL: http://hdl.handle.net/11343/197703

► In Australia, one in seven men are at a risk of being diagnosed with and one in 30 men at the risk of dying from… (more)

▼ In Australia, one in seven men are at a risk of being diagnosed with and one in 30 men at the risk of dying from prostate cancer (PC) by the age of 85 [1]. Limited treatment possibilities for castration resistant prostate cancer (CRPC) highlight the need for novel therapeutics. Restoring tumour suppressors in PC by proteasomal inhibition has demonstrated promising results in clinical trials, albeit with significant side effects [2]. Developing more specific and effective treatments for PC is therefore warranted. E6-Associated Protein (E6AP) is an E3 ubiquitin ligase and a transcription cofactor. Recent work from our laboratory and colleagues has demonstrated elevated expression of E6AP in a subset of PC patients [3]. Moreover, genetic manipulations of E6AP in PC cells exposed a role of E6AP in promoting growth and survival of PC cells in vitro and in vivo experimental systems [4]. Previous work from our laboratory unravelled that E6AP mediates this impact on PC cells via tumour suppressors such as promyelocytic leukaemia protein (PML; [4]) and p27 [5]. However, the effect of E6AP on PC cells is broad and it cannot be explained fully by these two tumour suppressors. To identify additional players that mediate E6AP phenotype, we utilised a combined transcriptomic (next generation RNA sequencing) and proteomic (SILAC) approaches. We assessed changes in the total transcriptome and proteome upon E6AP knockdown in CRPC cell line, DU145. We identified 16,130 transcripts using RNA-seq and 7,209 proteins using SILAC. A total of 2,763 transcripts and 308 proteins were considered significantly altered (± 1.5-fold, p-value < 0.05). A comparison of the omics data revealed candidates were either regulated transcriptionally alone, post-transcriptionally alone, or altered at both mRNA and protein level. Pathway analyses supported the known phenotypic effect of E6AP knockdown in PC cells as well as exposed novel links of E6AP with cancer metabolism, DNA damage repair and immune response. In parallel, we explored proteins regulated by E6AP in different PC cell lines, PC3 and LNCaP in addition to DU145 cells. We identified 4,814, 4,827 and 4,819 proteins inDU145, PC3 and LNCaP cells, respectively, upon E6AP knockdown using LC/MS-MS and data-independent acquisition in combination with label-free quantitation. A total of 225, 107 and 139 proteins were considered significantly altered (± 1.5-fold, p-value < 0.05) in DU145, PC3 and LNCaP cells, respectively, following knockdown of E6AP. Metabolism was the most deregulated biological pathway in all three PC cell lines upon E6AP knockdown, substantiating the novel link between E6AP and cancer metabolism. The significantly altered proteins and biological processes in various cell lines warrant further validation and investigation. Of the top ranked candidates, clusterin was pursued further. Clusterin is a stress-induced chaperone protein that modulates apoptosis, lipid transport, DNA repair and cell migration [6]. Clusterin is commonly deregulated in cancer, including prostate…

Subjects/Keywords: E6AP; transcriptomics; SILAC; clusterin; prostate cancer

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

APA (6^th Edition):

Gulati, T. (2017). Exploring the involvement of E6AP in prostate cancer: a combined transcriptomic and proteomic approach. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/197703

Chicago Manual of Style (16^th Edition):

Gulati, Twishi. “Exploring the involvement of E6AP in prostate cancer: a combined transcriptomic and proteomic approach.” 2017. Doctoral Dissertation, University of Melbourne. Accessed January 19, 2021. http://hdl.handle.net/11343/197703.

MLA Handbook (7^th Edition):

Gulati, Twishi. “Exploring the involvement of E6AP in prostate cancer: a combined transcriptomic and proteomic approach.” 2017. Web. 19 Jan 2021.

Vancouver:

Gulati T. Exploring the involvement of E6AP in prostate cancer: a combined transcriptomic and proteomic approach. [Internet] [Doctoral dissertation]. University of Melbourne; 2017. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/11343/197703.

Council of Science Editors:

Gulati T. Exploring the involvement of E6AP in prostate cancer: a combined transcriptomic and proteomic approach. [Doctoral Dissertation]. University of Melbourne; 2017. Available from: http://hdl.handle.net/11343/197703

Virginia Tech

4. Manickam, Manisha. Differential expression profiling of proteomes of pathogenic and commensal strains of Staphylococcus aureus using SILAC.

Degree: MS, Dairy Science, 2011, Virginia Tech

URL: http://hdl.handle.net/10919/46323

► Staphylococcus aureus (S. aureus) is the etiological agent of food-borne diseases, skin infections in humans and mastitis in bovines. S. aureus is also known to… (more)

Subjects/Keywords: differential protein expression; Staphylococcus aureus; SILAC

Record Details Similar Records Cite « Share

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

APA (6^th Edition):

Manickam, M. (2011). Differential expression profiling of proteomes of pathogenic and commensal strains of Staphylococcus aureus using SILAC. (Masters Thesis). Virginia Tech. Retrieved from http://hdl.handle.net/10919/46323

Chicago Manual of Style (16^th Edition):

Manickam, Manisha. “Differential expression profiling of proteomes of pathogenic and commensal strains of Staphylococcus aureus using SILAC.” 2011. Masters Thesis, Virginia Tech. Accessed January 19, 2021. http://hdl.handle.net/10919/46323.

MLA Handbook (7^th Edition):

Manickam, Manisha. “Differential expression profiling of proteomes of pathogenic and commensal strains of Staphylococcus aureus using SILAC.” 2011. Web. 19 Jan 2021.

Vancouver:

Manickam M. Differential expression profiling of proteomes of pathogenic and commensal strains of Staphylococcus aureus using SILAC. [Internet] [Masters thesis]. Virginia Tech; 2011. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10919/46323.

Council of Science Editors:

Manickam M. Differential expression profiling of proteomes of pathogenic and commensal strains of Staphylococcus aureus using SILAC. [Masters Thesis]. Virginia Tech; 2011. Available from: http://hdl.handle.net/10919/46323

Universiteit Utrecht

5. Spruijt, C.G. Readers of DNA and Histone modifications in Development.

Degree: 2015, Universiteit Utrecht

URL: http://dspace.library.uu.nl:8080/handle/1874/302486

► The development of an adult organism from a fertilized egg is accompanied by the generation of some 200 different cell types. Gene expression is highly… (more)

▼ The development of an adult organism from a fertilized egg is accompanied by the generation of some 200 different cell types. Gene expression is highly regulated, such that each cell type expresses a specific subset of genes. The genome in all these cells stays the same during cellular differentiation, which leads to the question: How does one genotype produce so many different phenotypes? Epigenetics is at least part of the answer. It is defined as DNA-sequence independent changes in gene expression and phenotype. In higher eukaryotes this is mainly achieved through methylation of DNA on cytosines and by post-translational modifications of histones. The patterns of these modifications are dynamic during development and the modifications thus help to create cell-type-specific gene expression profiles. The modifications can recruit regulatory proteins that can than exert their function at the site of recruitment. The specific binding of these so-called chromatin ‘readers’ therefore significantly contributes to the biological function of each individual epigenetic modification. In this thesis, we have studied readers for novel DNA modifications: hydroxymethylcytosine, formylcytosine and carboxylcytosine. We also identified many proteins that preferentially bind non-methylated DNA. We therefor propose that DNA methylation is a context-dependent binding signal for many proteins, whereas only a few proteins recognize the mark in a sequence-independent manner. Furthermore we found multiple tissue-specific readers for the histone modifications H3K4me3 and H3K9me3 in kidney, liver and brain. Finally this thesis focuses on one of the protein complexes that specifically recognizes DNA as well as histone modifications. The Nucleosome Remodeling and Deacetylase (NuRD) complex is a multi-subunit complex for which the biology is not fully understood. The complex is thought to repress transcription as it contains deacetylase activity. It plays an important role in development and many mutations of NuRD subunits are found in different types of cancer. We identified CDK2AP1 (also called DOC-1) as a bona fide subunit of the complex, although its role in the complex is still unclear. Since the mechanism of NuRD recruitment to target genes is largely unknown, we also focused on ZMYND8 and its zinc-finger containing interaction partners. These are probably capable of sequence-specific DNA binding. Since ZMYND8 also interacts with the NuRD complex, this could be one of the mechanisms of NuRD recruitment to promoters lacking DNA methylation. The NuRD subunit MBD2 is a reader for DNA methylation that can recruit the complex to methylated promoters. In conclusion, understanding the function and the mechanisms that underlie epigenetic regulation of gene expression is very important, because epigenetics is at the basis of every process in a cell. Studying this phenomenon will result in insights about possible intervention points in diseases such as cancer. Research into the basic working mechanisms of cells is thus very important for… Advisors/Committee Members: Timmers, H.T.M., Vermeulen, M..

Subjects/Keywords: Geneeskunde; Epigenetics; chromatin; methylcytosine; hydroxymethylcytosine; NuRD; stem cells; proteomics; SILAC; histone

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

APA (6^th Edition):

Spruijt, C. G. (2015). Readers of DNA and Histone modifications in Development. (Doctoral Dissertation). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/302486

Chicago Manual of Style (16^th Edition):

Spruijt, C G. “Readers of DNA and Histone modifications in Development.” 2015. Doctoral Dissertation, Universiteit Utrecht. Accessed January 19, 2021. http://dspace.library.uu.nl:8080/handle/1874/302486.

MLA Handbook (7^th Edition):

Spruijt, C G. “Readers of DNA and Histone modifications in Development.” 2015. Web. 19 Jan 2021.

Vancouver:

Spruijt CG. Readers of DNA and Histone modifications in Development. [Internet] [Doctoral dissertation]. Universiteit Utrecht; 2015. [cited 2021 Jan 19]. Available from: http://dspace.library.uu.nl:8080/handle/1874/302486.

Council of Science Editors:

Spruijt CG. Readers of DNA and Histone modifications in Development. [Doctoral Dissertation]. Universiteit Utrecht; 2015. Available from: http://dspace.library.uu.nl:8080/handle/1874/302486

University of Ottawa

6. Rossl, Anthony. A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast.

Degree: 2018, University of Ottawa

URL: http://hdl.handle.net/10393/38300

► Acetylation was previously thought to occur exclusively on histones, but recent high-throughput screens have identified thousands of non-histone substrates. Despite the identification of these sites,… (more)

Subjects/Keywords: Gcn5; Acetylation; Targeting; Consensus sequence; Ada3; SILAC; SAGA; Sirtuin

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

APA (6^th Edition):

Rossl, A. (2018). A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast. (Thesis). University of Ottawa. Retrieved from http://hdl.handle.net/10393/38300

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):

Rossl, Anthony. “A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast. ” 2018. Thesis, University of Ottawa. Accessed January 19, 2021. http://hdl.handle.net/10393/38300.

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

MLA Handbook (7^th Edition):

Rossl, Anthony. “A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast. ” 2018. Web. 19 Jan 2021.

Vancouver:

Rossl A. A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast. [Internet] [Thesis]. University of Ottawa; 2018. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10393/38300.

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

Council of Science Editors:

Rossl A. A Synthetic Acetylation Substrate to Study Gcn5 Targeting and Function in Yeast. [Thesis]. University of Ottawa; 2018. Available from: http://hdl.handle.net/10393/38300

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

University of Connecticut

7. Sobczynski, Alicia K. Studies on Virulence Factors of Clostridium perfringens and Necrotic Enteritis in Chickens.

Degree: MS, Pathobiology, 2011, University of Connecticut

URL: https://opencommons.uconn.edu/gs_theses/158

► Necrotic enteritis (NE) is an economically important disease of the poultry industry. It is caused by Clostridium perfringens (CP) and the pathogenesis of the… (more)

Subjects/Keywords: Necrotic Enteritis; Poultry; Alpha Toxin; Sialidase; NetB; Clostridium perfringens; Neuraminidase; SILAC

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

APA (6^th Edition):

Sobczynski, A. K. (2011). Studies on Virulence Factors of Clostridium perfringens and Necrotic Enteritis in Chickens. (Masters Thesis). University of Connecticut. Retrieved from https://opencommons.uconn.edu/gs_theses/158

Chicago Manual of Style (16^th Edition):

Sobczynski, Alicia K. “Studies on Virulence Factors of Clostridium perfringens and Necrotic Enteritis in Chickens.” 2011. Masters Thesis, University of Connecticut. Accessed January 19, 2021. https://opencommons.uconn.edu/gs_theses/158.

MLA Handbook (7^th Edition):

Sobczynski, Alicia K. “Studies on Virulence Factors of Clostridium perfringens and Necrotic Enteritis in Chickens.” 2011. Web. 19 Jan 2021.

Vancouver:

Sobczynski AK. Studies on Virulence Factors of Clostridium perfringens and Necrotic Enteritis in Chickens. [Internet] [Masters thesis]. University of Connecticut; 2011. [cited 2021 Jan 19]. Available from: https://opencommons.uconn.edu/gs_theses/158.

Council of Science Editors:

Sobczynski AK. Studies on Virulence Factors of Clostridium perfringens and Necrotic Enteritis in Chickens. [Masters Thesis]. University of Connecticut; 2011. Available from: https://opencommons.uconn.edu/gs_theses/158

University of Iowa

8. Li, Miao. Protein adducts and crosslinking by reactive metabolites of polychlorinated biphenyls (PCBs).

Degree: PhD, Human Toxicology, 2015, University of Iowa

URL: https://ir.uiowa.edu/etd/1984

► Polychlorinated biphenyls (PCBs) are the persistent environmental pollutants with the continuous concerns over adverse human health effects. As semi-volatile compounds, PCBs were found in… (more)

▼ Polychlorinated biphenyls (PCBs) are the persistent environmental pollutants with the continuous concerns over adverse human health effects. As semi-volatile compounds, PCBs were found in indoor and outdoor air. The observation of high levels of airborne PCBs in old school buildings raised the concerns of inhalation exposure and toxicity of PCBs. Lower chlorinated PCBs (LC-PCBs), major components of airborne PCBs, are subject to biotranformation. In vitro and in vivo studies revealed that reactive metabolites of LC-PCBs formed covalent adducts on DNA and proteins. The hypothesis of the project is that the reactive metabolites of LC-PCBs are able to form adducts on proteins or even protein crosslinks, and the formation of protein adducts and crosslinks causes the dysfunction of the target proteins. In addition, the objectives of the project are also to identify protein targets by PCB metabolites, which may be related to the mechanism of toxicity of LC-PCBs. The alkaline permethylation (AP) was established and optimized to identify and measure the protein adducts from LC-PCB metabolites. The AP method evidenced PCB metabolites formed protein adducts through the sulfhydryl groups and also one molecule of PCB quinoid metabolites was able to bind to more than one protein. Application of cytochrome c as the model protein revealed PCB quinoid metabolites also formed adducts on lysine and glutamic acid. The adduct formation and crosslinks caused the dysfunction of cytochrome c. In addition, the quinone protein adducts still kept the ability for redox reactions, which may lead to unexpected toxicity. The SILAC method was applied to identify the target proteins in the samples of in vitro proteome incubation. The instability of PCB quinone protein adducts was found by further reaction of quinone protein adducts. This may be the reason why cysteine-PCB quinone adducts were not frequently identified by proteomics method. The further understanding of protein adducts by reactive PCB metabolites helps to identify the target proteins, and ultimately reveal the role of protein adducts impacting on human health. Advisors/Committee Members: Ludewig, Gabriele (supervisor).

Subjects/Keywords: publicabstract; Polychlorinated Biphynels; Protein Adducts; Proteomics; Quinone; Reactive Metabolites; SILAC; Toxicology

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

APA (6^th Edition):

Li, M. (2015). Protein adducts and crosslinking by reactive metabolites of polychlorinated biphenyls (PCBs). (Doctoral Dissertation). University of Iowa. Retrieved from https://ir.uiowa.edu/etd/1984

Chicago Manual of Style (16^th Edition):

Li, Miao. “Protein adducts and crosslinking by reactive metabolites of polychlorinated biphenyls (PCBs).” 2015. Doctoral Dissertation, University of Iowa. Accessed January 19, 2021. https://ir.uiowa.edu/etd/1984.

MLA Handbook (7^th Edition):

Li, Miao. “Protein adducts and crosslinking by reactive metabolites of polychlorinated biphenyls (PCBs).” 2015. Web. 19 Jan 2021.

Vancouver:

Li M. Protein adducts and crosslinking by reactive metabolites of polychlorinated biphenyls (PCBs). [Internet] [Doctoral dissertation]. University of Iowa; 2015. [cited 2021 Jan 19]. Available from: https://ir.uiowa.edu/etd/1984.

Council of Science Editors:

Li M. Protein adducts and crosslinking by reactive metabolites of polychlorinated biphenyls (PCBs). [Doctoral Dissertation]. University of Iowa; 2015. Available from: https://ir.uiowa.edu/etd/1984

University of Gothenburg / Göteborgs Universitet

9. Nayakawde, Nikhil B. On tissue engineering of pig, human, and non-human primate tissues.

Degree: 2020, University of Gothenburg / Göteborgs Universitet

URL: http://hdl.handle.net/2077/63607

► Background: Demand for donor organs for transplantation has been increasing every year more than the actual supply of suitable donor organs. One of the major… (more)

▼ Background: Demand for donor organs for transplantation has been increasing every year more than the actual supply of suitable donor organs. One of the major problems associated with allogeneic transplantation includes lifelong immunosuppression. Tissue engineering and regenerative medicine is a growing field that uses knowledge of stem cell biology, developmental biology, immunology, and bioengineering to replace diseased and damaged tissues or organs. Tissue engineered (TE) hollow organs and tissues derived from natural extracellular matrix (ECM) have been used in several preclinical and clinical studies. More complex three-dimensional organs such as heart, liver, lungs, and kidney have been studied extensively both in-vitro and in-vivo in preclinical settings, but clinical experience is lacking. There is an increasing demand for understanding the composition of ECM, cell-ECM interaction in-vitro and in-vivo, and how tissue engineered organs behave immunologically after implantation. The current thesis focuses on investigation of decellularization methods for heart (porcine), esophagus (porcine, baboon, and human) and larynx (porcine); and recellularization of esophagus (porcine and human). It was also investigated during various time-points of recellularization if stem cells were able to synthesize ECM proteins, tissue specific proteins and growth factors, and if stem cells were able to differentiate into tissue-specific cells. Methods: In Paper I, a detergent based decellularization method was developed to create acellular whole porcine hearts. The cardiac ECM was then characterized for its structural and mechanical properties. In Paper III, physical and chemical methods were developed to decellularize porcine larynx. Decellularized larynx was analyzed microscopically for its ultrastructural changes and presence of cells. In Paper II, decellularization and recellularization (with human amniotic mesenchymal stem cells and epithelial cells) of porcine esophagus was carried out. In Paper IV, decellularization of pig, baboon, and human esophagus was performed as per the method described in Paper II. Paper IV studied the cell-ECM interaction during recellularization of human esophagus with human amniotic mesenchymal stem cells by using the stable isotope labeling with amino acids in cell culture (SILAC) technique. Results: Decellularization of heart, larynx, and esophagus was achieved successfully, with loss of cell nuclei, preservation of major ECM proteins such as collagen and elastin, preservation of growth factors, and maintaining three-dimensional structures of the tissues and organs. Decellularized esophagus was characterized by preservation of matrisome and non-matrisome proteins in the ECM using proteomics-bioinformatics analyses. Recellularization of pig and human esophagus was evidenced by stem cell proliferation, differentiation, and tissue specific protein synthesis by seeded stem cells. SILAC assay showed synthesis of newly produced proteins in the recellularized esophagus by seeded stem cells including…

Subjects/Keywords: Decellularization; esophagus; heart; larynx; proteomics; recellularization; SILAC; stem cells; tissue engineering

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APA (6^th Edition):

Nayakawde, N. B. (2020). On tissue engineering of pig, human, and non-human primate tissues. (Thesis). University of Gothenburg / Göteborgs Universitet. Retrieved from http://hdl.handle.net/2077/63607

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):

Nayakawde, Nikhil B. “On tissue engineering of pig, human, and non-human primate tissues.” 2020. Thesis, University of Gothenburg / Göteborgs Universitet. Accessed January 19, 2021. http://hdl.handle.net/2077/63607.

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

MLA Handbook (7^th Edition):

Nayakawde, Nikhil B. “On tissue engineering of pig, human, and non-human primate tissues.” 2020. Web. 19 Jan 2021.

Vancouver:

Nayakawde NB. On tissue engineering of pig, human, and non-human primate tissues. [Internet] [Thesis]. University of Gothenburg / Göteborgs Universitet; 2020. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/2077/63607.

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

Council of Science Editors:

Nayakawde NB. On tissue engineering of pig, human, and non-human primate tissues. [Thesis]. University of Gothenburg / Göteborgs Universitet; 2020. Available from: http://hdl.handle.net/2077/63607

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

Université de Sherbrooke

10. Del Olmo, Tomas. Caractérisation fonctionnelle de l’interactome de RAB21: RAB21 functional interactome characterisation.

Degree: 2020, Université de Sherbrooke

URL: http://hdl.handle.net/11143/17016

► Abstract: Membrane trafficking regulates vesicular transport between the different organelles of the cell as well as exchanges with the extra-cellular space. Endocytic and secretory pathways… (more)

▼ Abstract: Membrane trafficking regulates vesicular transport between the different organelles of the cell as well as exchanges with the extra-cellular space. Endocytic and secretory pathways are interconnected and form a complex network assuring cell integrity. Therefore, membrane trafficking is regulated by a large set of proteins which all act in concert to enable its proper function. RABs are considered as master regulators of trafficking. When activated, RABs recruit a wide range of effectors to mediate each steps of trafficking. Impairment of RAB activity are involved in the development of diseases such as neurodegenerative diseases and cancer. RAB21 is an endosomal RAB which regulates autophagic flux and is involved in the internalization of integrins and the EGF receptor. Despite these identified functions, only a few effectors and regulators are known for RAB21. Understanding the molecular mechanisms of action of RABs remains a major challenge to decode membrane trafficking. Indeed, identification of RABs partners with current approaches has some limitation. Here, the combination of a quantitative mass spectrometry (SILAC) approach with a proximity labeling approach (APEX2) made it possible to identify almost every RAB21 protein partners. The APEX2 approach allowed the identification of most of the known RAB21 interactors as well as potential effectors and regulators. The comparison of the relative protein enrichments obtained with RAB5, 4, 7 and 21 permitted to identify specific interactions. The SILAC approach has essentially allowed the identification of potential cargos for RAB21. Biochemical techniques validated the interactions of RAB21 with the WASH and Retromer complexes, both involved in endosomal sorting events, as well as with TMED10 which regulates the cargoes progression through secretory pathway. Subsequently, the deletion of RAB21 by CRISPR/Cas9 highlighted a role for RAB21 in maintaining the stability of the retromer complex and in regulating WASH complex activity. The deletion of RAB21 affected recycling of clathrin-independent-cargos to the plasma membrane. In addition, deletion of RAB21 decreased the stability of TMED10 and its location at Golgi. All this work allowed the characterization of new specific effectors and cargos as well as two new functions involving RAB21. This project is an example in the study of the molecular mechanisms of membrane trafficking regulation that can be used as a basis for the study of all RABs. Advisors/Committee Members: Jean, Steve (advisor).

Subjects/Keywords: RAB21; APEX2; SILAC; Rétromère; WASH; TMED10; Trafic membranaire; Membrane trafficking

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

APA (6^th Edition):

Del Olmo, T. (2020). Caractérisation fonctionnelle de l’interactome de RAB21: RAB21 functional interactome characterisation. (Doctoral Dissertation). Université de Sherbrooke. Retrieved from http://hdl.handle.net/11143/17016

Chicago Manual of Style (16^th Edition):

Del Olmo, Tomas. “Caractérisation fonctionnelle de l’interactome de RAB21: RAB21 functional interactome characterisation.” 2020. Doctoral Dissertation, Université de Sherbrooke. Accessed January 19, 2021. http://hdl.handle.net/11143/17016.

MLA Handbook (7^th Edition):

Del Olmo, Tomas. “Caractérisation fonctionnelle de l’interactome de RAB21: RAB21 functional interactome characterisation.” 2020. Web. 19 Jan 2021.

Vancouver:

Del Olmo T. Caractérisation fonctionnelle de l’interactome de RAB21: RAB21 functional interactome characterisation. [Internet] [Doctoral dissertation]. Université de Sherbrooke; 2020. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/11143/17016.

Council of Science Editors:

Del Olmo T. Caractérisation fonctionnelle de l’interactome de RAB21: RAB21 functional interactome characterisation. [Doctoral Dissertation]. Université de Sherbrooke; 2020. Available from: http://hdl.handle.net/11143/17016

Oklahoma State University

11. Voruganti, Sudhakar. Proteomics Fingerprints of Auy922 and 17-dmag Indicate Common Mechanisms of Action for Hsp90 Inhibitors.

Degree: Biochemistry & Molecular Biology, 2013, Oklahoma State University

URL: http://hdl.handle.net/11244/15159

► Title of Study: The proteomics fingerprints of AUY922 and 17-DMAG indicate common mechanisms of action for Hsp90 inhibitors. Major Field: BIOCHEMISTRY AND MOLECULAR BIOLOGY In… (more)

▼ Title of Study: The proteomics fingerprints of AUY922 and 17-DMAG indicate common mechanisms of action for Hsp90 inhibitors. Major Field: BIOCHEMISTRY AND MOLECULAR BIOLOGY In this work, we identified the proteomics fingerprint of the anti-cancer drug candidate AUY922 in Jurkat leukemia cells and compared AUY922's fingerprint to the proteomics fingerprints of flagship Hsp90 inhibitors 17–DMAG and radicicol. Protein expression changes were identified by a label-free mass spectrometry technique, spectrum counting using a bottom-up proteomics approach. We identified 30 protein expression changes that were conserved among all the three Hsp90 inhibitors. To further validate findings from spectrum counting assays and to identify more Hsp0 inhibitor-induced protein expression changes, we quantified AUY922–induced and 17-DMAG–induced protein expression changes by label–based Stable Isotope Labeling with Amino acids in Cell culture (SILAC) using a bottom-up proteomics approach. A total of 3000–4000 inhibitor-induced protein expression changes were quantified. After statistical validation, 260 protein expression changes were found to be conserved among both the Hsp90 inhibitors. The large conservation of protein expression changes between AUY922 and 17–DMAG suggested that both inhibitors work via a similar mechanism. The protein expression changes common to AUY922 and 17–DMAG identified in this study can be used as biomarkers to test bioactivity of AUY922 in clinical trials and can also be used to validate new Hsp90 N–terminal inhibitors. Additionally, they can be compared to the proteomic fingerprints of agents that bind to the C-terminal domain of Hsp90, to determine if both classes of inhibitors share similar mechanisms of action. I also demonstrated that the anti-proliferative effects of AUY922 could be enhanced in combinatorial treatments with protein folding antagonist L–azetadine–2-carboxylic acid (AZC). I further used the SILAC approach to determine the mechanism of combinatorial effects of AUY922 and AZC and showed that the combinatorial effects were largely due to AZC–mediated suppression of chaperone induction. Thus, findings from this study suggest approaches for enhancing AUY922’s activity in clinical trials by using AUY922 in combination with agents that suppress chaperone induction. Advisors/Committee Members: Hartson, Steven D. (advisor), Matts, Robert L. (committee member), Melcher, Ulrich (committee member), Deng, Junpeng (committee member), Burnap, Robert (committee member).

Subjects/Keywords: 17-dmag; auy922; hsp90 inhibitors; jurkat; proteomics; silac

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APA (6^th Edition):

Voruganti, S. (2013). Proteomics Fingerprints of Auy922 and 17-dmag Indicate Common Mechanisms of Action for Hsp90 Inhibitors. (Thesis). Oklahoma State University. Retrieved from http://hdl.handle.net/11244/15159

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):

Voruganti, Sudhakar. “Proteomics Fingerprints of Auy922 and 17-dmag Indicate Common Mechanisms of Action for Hsp90 Inhibitors.” 2013. Thesis, Oklahoma State University. Accessed January 19, 2021. http://hdl.handle.net/11244/15159.

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

MLA Handbook (7^th Edition):

Voruganti, Sudhakar. “Proteomics Fingerprints of Auy922 and 17-dmag Indicate Common Mechanisms of Action for Hsp90 Inhibitors.” 2013. Web. 19 Jan 2021.

Vancouver:

Voruganti S. Proteomics Fingerprints of Auy922 and 17-dmag Indicate Common Mechanisms of Action for Hsp90 Inhibitors. [Internet] [Thesis]. Oklahoma State University; 2013. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/11244/15159.

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

Council of Science Editors:

Voruganti S. Proteomics Fingerprints of Auy922 and 17-dmag Indicate Common Mechanisms of Action for Hsp90 Inhibitors. [Thesis]. Oklahoma State University; 2013. Available from: http://hdl.handle.net/11244/15159

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

University of Manchester

12. Hohensee, Tabea. Characterization of the focal adhesion interactome.

Degree: 2019, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318814

► It is still unknown how exactly cells respond to their extracellular matrix (ECM) and how they react to changes in it. For example a stiffer… (more)

▼ It is still unknown how exactly cells respond to their extracellular matrix (ECM) and how they react to changes in it. For example a stiffer ECM environment in breast tissue heightens the likelihood to develop breast cancer, but how theses cells detect and react to changed stiffness is not clear. In order gain a better insight into the link between ECM and the control of cell behaviour it is essential to understand the complexity of focal adhesions (FAs), the complex of proteins linking cells to the ECM and interpreting information about their extracellular environment. To identify novel regulatory components of FAs, we have used in vivo biotinylation techniques to measure changes in protein interactions by quantitative mass spectrometry. BirA is a modified bacterial enzyme capable of biotinylating proteins in close proximity while it has access to biotin. It can therefore be expressed in fusion with proteins of interest and used to identify interactions in situ. We have set out to use integrin Î±5 and focal adhesion kinase (FAK) as BirA fusions, and then stably integrated these into U2OS cells. With this approach our goal was to label proteins interacting with either integrin Î±5 or FAK, and to identify potential novel regulatory proteins. Biotin labeled proteins were purified by affinity purification and then analyzed via SILAC mass spectroscopy. The integrin and FAK interactomes thus identified were compared with those of other focal adhesion proteins studied in our lab, allowing further dissection of the network within the adhesome. To understand how these cells react to different environments, the U2OS BirA FAK cells were grown on a stiff and soft matrix. Therein a new potential role of FAK was discovered in response to ECM stiffness. Further more using the BioID approach we now identified a possibly new interactor of the adhesome, ARHGAP1. Together, these results indicate that proximity biotin labeling can be a useful tool to identify potential new transient interacting proteins in FAs. Advisors/Committee Members: GILMORE, ANDREW AP, Streuli, Charles, Gilmore, Andrew.

Subjects/Keywords: Integrin; FAK; ARHGAP1; BioID; SILAC; Focal adhesion; Interactome

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

APA (6^th Edition):

Hohensee, T. (2019). Characterization of the focal adhesion interactome. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318814

Chicago Manual of Style (16^th Edition):

Hohensee, Tabea. “Characterization of the focal adhesion interactome.” 2019. Doctoral Dissertation, University of Manchester. Accessed January 19, 2021. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318814.

MLA Handbook (7^th Edition):

Hohensee, Tabea. “Characterization of the focal adhesion interactome.” 2019. Web. 19 Jan 2021.

Vancouver:

Hohensee T. Characterization of the focal adhesion interactome. [Internet] [Doctoral dissertation]. University of Manchester; 2019. [cited 2021 Jan 19]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318814.

Council of Science Editors:

Hohensee T. Characterization of the focal adhesion interactome. [Doctoral Dissertation]. University of Manchester; 2019. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:318814

13. SWA LEE FOON HANNAH. CHARACTERIZING ROLES OF ANNEXIN-1 IN BREAST CANCER DEVELOPMENT BY MASS SPECTROMETRY - BASED QUANTITATIVE PROTEOMICS.

Degree: 2013, National University of Singapore

URL: http://scholarbank.nus.edu.sg/handle/10635/49589

Subjects/Keywords: Annexin-1; Breast Cancer Development; Quantitative Proteomics; Mass Spectrometry; SILAC; Super-SILAC

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APA (6^th Edition):

HANNAH, S. L. F. (2013). CHARACTERIZING ROLES OF ANNEXIN-1 IN BREAST CANCER DEVELOPMENT BY MASS SPECTROMETRY - BASED QUANTITATIVE PROTEOMICS. (Thesis). National University of Singapore. Retrieved from http://scholarbank.nus.edu.sg/handle/10635/49589

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):

HANNAH, SWA LEE FOON. “CHARACTERIZING ROLES OF ANNEXIN-1 IN BREAST CANCER DEVELOPMENT BY MASS SPECTROMETRY - BASED QUANTITATIVE PROTEOMICS.” 2013. Thesis, National University of Singapore. Accessed January 19, 2021. http://scholarbank.nus.edu.sg/handle/10635/49589.

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

MLA Handbook (7^th Edition):

HANNAH, SWA LEE FOON. “CHARACTERIZING ROLES OF ANNEXIN-1 IN BREAST CANCER DEVELOPMENT BY MASS SPECTROMETRY - BASED QUANTITATIVE PROTEOMICS.” 2013. Web. 19 Jan 2021.

Vancouver:

HANNAH SLF. CHARACTERIZING ROLES OF ANNEXIN-1 IN BREAST CANCER DEVELOPMENT BY MASS SPECTROMETRY - BASED QUANTITATIVE PROTEOMICS. [Internet] [Thesis]. National University of Singapore; 2013. [cited 2021 Jan 19]. Available from: http://scholarbank.nus.edu.sg/handle/10635/49589.

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

Council of Science Editors:

HANNAH SLF. CHARACTERIZING ROLES OF ANNEXIN-1 IN BREAST CANCER DEVELOPMENT BY MASS SPECTROMETRY - BASED QUANTITATIVE PROTEOMICS. [Thesis]. National University of Singapore; 2013. Available from: http://scholarbank.nus.edu.sg/handle/10635/49589

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

University of Rochester

14. Zhang, Tian. Global quantification of proteome dynamics.

Degree: PhD, 2017, University of Rochester

URL: http://hdl.handle.net/1802/32684

► Living cells continuously degrade and resynthesize their constituent proteins. The maintenance of protein homeostasis is fundamental to cell survival and function. Recent advances in mass… (more)

Subjects/Keywords: Autophagy; Long-lived proteins; Protein turnover; Quiescent cells; Selectivity of autophagy; TMT-SILAC

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

APA (6^th Edition):

Zhang, T. (2017). Global quantification of proteome dynamics. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/32684

Chicago Manual of Style (16^th Edition):

Zhang, Tian. “Global quantification of proteome dynamics.” 2017. Doctoral Dissertation, University of Rochester. Accessed January 19, 2021. http://hdl.handle.net/1802/32684.

MLA Handbook (7^th Edition):

Zhang, Tian. “Global quantification of proteome dynamics.” 2017. Web. 19 Jan 2021.

Vancouver:

Zhang T. Global quantification of proteome dynamics. [Internet] [Doctoral dissertation]. University of Rochester; 2017. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1802/32684.

Council of Science Editors:

Zhang T. Global quantification of proteome dynamics. [Doctoral Dissertation]. University of Rochester; 2017. Available from: http://hdl.handle.net/1802/32684

University of Alberta

15. Baghdasarian, Argishti. An investigation of aminoglutethimide cytotoxicity and its role in activation of cell death signaling pathways.

Degree: MS, 2013, University of Alberta

URL: https://era.library.ualberta.ca/files/w9505177q

► Aminoglutethimide (AG), a drug used for the treatment of breast and ovarian cancers, is known to cause toxicities such as agranulocytosis. To investigate its toxicity… (more)

Subjects/Keywords: Drug-induced agranulocytosis; Idiosyncratic drug reactions; HL-60 cells; Free radicals; Proteomics; Apoptosis; Aminoglutethimide; SILAC

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

APA (6^th Edition):

Baghdasarian, A. (2013). An investigation of aminoglutethimide cytotoxicity and its role in activation of cell death signaling pathways. (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/w9505177q

Chicago Manual of Style (16^th Edition):

Baghdasarian, Argishti. “An investigation of aminoglutethimide cytotoxicity and its role in activation of cell death signaling pathways.” 2013. Masters Thesis, University of Alberta. Accessed January 19, 2021. https://era.library.ualberta.ca/files/w9505177q.

MLA Handbook (7^th Edition):

Baghdasarian, Argishti. “An investigation of aminoglutethimide cytotoxicity and its role in activation of cell death signaling pathways.” 2013. Web. 19 Jan 2021.

Vancouver:

Baghdasarian A. An investigation of aminoglutethimide cytotoxicity and its role in activation of cell death signaling pathways. [Internet] [Masters thesis]. University of Alberta; 2013. [cited 2021 Jan 19]. Available from: https://era.library.ualberta.ca/files/w9505177q.

Council of Science Editors:

Baghdasarian A. An investigation of aminoglutethimide cytotoxicity and its role in activation of cell death signaling pathways. [Masters Thesis]. University of Alberta; 2013. Available from: https://era.library.ualberta.ca/files/w9505177q

Cornell University

16. Hah, Nasun. Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses.

Degree: PhD, Biochemistry, 2011, Cornell University

URL: http://hdl.handle.net/1813/33589

► Estrogens play crucial roles in regulating gene expression in physiological and disease states. Estrogens acts through estrogen receptors (ERs) and their binding sites in genomic… (more)

▼ Estrogens play crucial roles in regulating gene expression in physiological and disease states. Estrogens acts through estrogen receptors (ERs) and their binding sites in genomic DNA to modulate transcription by RNA polymerase II. Although recent gene-specific and genomic analyses have provided considerable information about of estrogen-dependent transcription, many aspects of the estrogen signaling network have not yet been elucidated. The goal of my studies was to uncover new information about the immediate and direct effects of estrogen signaling at the cell membrane, in the cytoplasm, and in the nucleus to elucidate the underlying regulatory networks. First, I investigated an ER transcriptional coregulators, SWI/SNF, an ATPdependent chromatin remodeling complex. I explored the molecular functions of the BAF57 and BAF180 subunits of SWI/SNF using a quantitative proteomic approach called SILAC (Stable Isotope Labeling by Amino Acids in Cell Culture). I found that depletion of BAF57 results in a significant depletion of BAF180 from the SWI/SNF complex without decreasing the total cellular BAF180 levels, resulting in an accumulation of cells in the G2/M phase. Knockdown of BAF57 also causes transcriptional misregulation of cell cycle-related genes involved in the late G2 checkpoint. Collectively, these studies have elucidated the role of BAF57 and BAF180 in the transcriptional control of cell proliferation. Second, I have used GRO-Seq (Global Nuclear Run-On and Massively Parallel Sequencing) to explore the immediate effects of estrogen signaling on the transcriptome of breast cancer cells. I found that estrogen directly regulates a strikingly large fraction of the transcriptome in a rapid, robust, and unexpectedly transient manner. In addition to protein coding genes, estrogen regulates the distribution and activity of all three RNA polymerases, and virtually every class of non-coding RNA that has been described to date. I also identified a large number of previously undetected estrogen-regulated intergenic transcripts, many of which are found proximal to ER[alpha] binding sites. These results provide the most comprehensive measurement of the primary and immediate estrogen effects to date. I expect that genome-wide inferences based on the direct estrogen-regulated transcriptome in combination with estrogen-regulated signaling pathway will be useful for understanding estrogen biology. Advisors/Committee Members: Kraus, William Lee (chair), Collins, Ruth N. (committee member), Lis, John T (committee member).

Subjects/Keywords: estrogen; estrogen receptor; GRO-seq; swi/snf; baf57; baf180; silac; proteomic; enhancer; edc; estrogen signaling

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APA (6^th Edition):

Hah, N. (2011). Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/33589

Chicago Manual of Style (16^th Edition):

Hah, Nasun. “Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses.” 2011. Doctoral Dissertation, Cornell University. Accessed January 19, 2021. http://hdl.handle.net/1813/33589.

MLA Handbook (7^th Edition):

Hah, Nasun. “Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses.” 2011. Web. 19 Jan 2021.

Vancouver:

Hah N. Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses. [Internet] [Doctoral dissertation]. Cornell University; 2011. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1813/33589.

Council of Science Editors:

Hah N. Signal Regulated Gene Expression: Defining The Effects Of Estrogen Signaling Through Genomic And Proteomic Analyses. [Doctoral Dissertation]. Cornell University; 2011. Available from: http://hdl.handle.net/1813/33589

University of Cambridge

17. Marino, Polly. Studies on assembly and genetic variation in mitochondrial respiratory complex I.

Degree: PhD, 2019, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/289386

► Complex I (NADH:ubiquinone oxidoreductase) couples electron transfer to proton translocation across the inner mitochondrial membrane, to drive the synthesis of ATP. Its distinctive L-shaped structure… (more)

▼ Complex I (NADH:ubiquinone oxidoreductase) couples electron transfer to proton translocation across the inner mitochondrial membrane, to drive the synthesis of ATP. Its distinctive L-shaped structure comprises 45 subunits, encoded by both the mitochondrial and nuclear genomes, which are assembled by a complicated modular pathway. Complex I genetic defects are the most common cause of mitochondrial disorders and often present in early childhood, with high mortality rates. Recent high-resolution electron cryo-microscopy structures of mammalian complex I provide a foundation for both interpreting biochemical and biomedical data and understanding the catalytic mechanism. First, this thesis explores how the flavin cofactor is inserted into the NADH-binding (N-) domain of complex I. Genetic manipulation of cultured human cells, to starve them of flavin, revealed a hierarchal impact on the mitochondrial flavoproteome. High riboflavin content in the growth media ameliorated observed phenotypes, requiring cell conditioning in low riboflavin conditions. CRISPR knockout of the putative mitochondrial flavin transporter SLC25A32 demonstrated the severe impact of decreased flavin on complexes I and II, and mass spectrometry ‘complexome’ analyses suggest that the N-domain is still assembled onto complex I in the absence of the flavin. Second, the model organism Yarrowia lipolytica was used to assess the importance of residues in the quinone-binding site of complex I. Three residues with proposed roles in binding the quinone head-group were targeted. One variant was catalytically inactive, while two retained some activity. They showed decreased ability to reduce physiologically-relevant, long chain quinones, but their ability to reduce short-chain analogues was affected less severely. The results suggest a complicated picture in which interactions between the protein and both the hydrophilic quinone head-group and hydrophobic isoprenoid chain contribute to quinone-binding affinity and catalysis. Finally, a model for human complex I, generated from a recent high-resolution structure of mouse complex I, was used to investigate whether the pathogenicity of human variants could be predicted. Structural information on variant residues, including their secondary structure, proximity to key features and surface exposure, was collated and the power of each property to predict pathogenicity investigated. The analysis was then extended to the whole structure, to identify potential pathogenic hotspots in the enzyme, inform future studies of functionally important regions in complex I, and aid the diagnosis of clinically relevant pathogenic variants.

Subjects/Keywords: complex I; mitochondria; respiration; yarrowia; flavin; assembly; riboflavin; 143B; SILAC; complexome; transcriptomics; SLC25A32; RFK

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APA (6^th Edition):

Marino, P. (2019). Studies on assembly and genetic variation in mitochondrial respiratory complex I. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/289386

Chicago Manual of Style (16^th Edition):

Marino, Polly. “Studies on assembly and genetic variation in mitochondrial respiratory complex I.” 2019. Doctoral Dissertation, University of Cambridge. Accessed January 19, 2021. https://www.repository.cam.ac.uk/handle/1810/289386.

MLA Handbook (7^th Edition):

Marino, Polly. “Studies on assembly and genetic variation in mitochondrial respiratory complex I.” 2019. Web. 19 Jan 2021.

Vancouver:

Marino P. Studies on assembly and genetic variation in mitochondrial respiratory complex I. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Jan 19]. Available from: https://www.repository.cam.ac.uk/handle/1810/289386.

Council of Science Editors:

Marino P. Studies on assembly and genetic variation in mitochondrial respiratory complex I. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://www.repository.cam.ac.uk/handle/1810/289386

Universitat Pompeu Fabra

18. Wierer, Michael, 1982-. Role of PLK1 in steroid hormone signaling in breast cancer cells.

Degree: Departament de Ciències Experimentals i de la Salut, 2013, Universitat Pompeu Fabra

URL: http://hdl.handle.net/10803/283474

► Steroid receptors (SRs) are hormone-induced transcription factors that regulate gene expression by their concerted actions with coregulatory proteins. Performing a quantitative mass spectrometry-based interaction screen… (more)

Subjects/Keywords: PLK1; Estrogen Receptor; Progesterone Receptor; Breast cancer; Phosphorylation; Gene transcription; MLL2; Phosphoproteomics; Interactomics; SILAC; 616

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APA (6^th Edition):

Wierer, Michael, 1. (2013). Role of PLK1 in steroid hormone signaling in breast cancer cells. (Thesis). Universitat Pompeu Fabra. Retrieved from http://hdl.handle.net/10803/283474

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):

Wierer, Michael, 1982-. “Role of PLK1 in steroid hormone signaling in breast cancer cells.” 2013. Thesis, Universitat Pompeu Fabra. Accessed January 19, 2021. http://hdl.handle.net/10803/283474.

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

MLA Handbook (7^th Edition):

Wierer, Michael, 1982-. “Role of PLK1 in steroid hormone signaling in breast cancer cells.” 2013. Web. 19 Jan 2021.

Vancouver:

Wierer, Michael 1. Role of PLK1 in steroid hormone signaling in breast cancer cells. [Internet] [Thesis]. Universitat Pompeu Fabra; 2013. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10803/283474.

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

Council of Science Editors:

Wierer, Michael 1. Role of PLK1 in steroid hormone signaling in breast cancer cells. [Thesis]. Universitat Pompeu Fabra; 2013. Available from: http://hdl.handle.net/10803/283474

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

19. Patterson, Aileen. Changes to the host cell proteome induced by expression of hepatitis C virus NS3/4A open reading frames.

Degree: Medical Microbiology, 2014, University of Manitoba

URL: http://hdl.handle.net/1993/23157

► Hepatitis C virus (HCV) infects an estimated 200,000 people in Canada, and is the leading cause of liver transplants in North America. Viral infection usually… (more)

Subjects/Keywords: Proteomics; HCV; Hepatocellular carcinoma; SILAC

…pictoral representation of SILAC methodology ........ 57 Figure 12. Distribution of total and… …spectrometry ............ 58 Figure 13. Distribution of protein ratios for SILAC experiments… …63 Figure 15. Western blot analysis of candidate protein expression from SILAC experiments… …database to identify the parent protein. (B) SILAC proteins are processed the same way… …SILAC pairs, either 6 (lysine) or 10 (arginine) Th apart, are apparent…

11 more images…

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APA (6^th Edition):

Patterson, A. (2014). Changes to the host cell proteome induced by expression of hepatitis C virus NS3/4A open reading frames. (Masters Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/23157

Chicago Manual of Style (16^th Edition):

Patterson, Aileen. “Changes to the host cell proteome induced by expression of hepatitis C virus NS3/4A open reading frames.” 2014. Masters Thesis, University of Manitoba. Accessed January 19, 2021. http://hdl.handle.net/1993/23157.

MLA Handbook (7^th Edition):

Patterson, Aileen. “Changes to the host cell proteome induced by expression of hepatitis C virus NS3/4A open reading frames.” 2014. Web. 19 Jan 2021.

Vancouver:

Patterson A. Changes to the host cell proteome induced by expression of hepatitis C virus NS3/4A open reading frames. [Internet] [Masters thesis]. University of Manitoba; 2014. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1993/23157.

Council of Science Editors:

Patterson A. Changes to the host cell proteome induced by expression of hepatitis C virus NS3/4A open reading frames. [Masters Thesis]. University of Manitoba; 2014. Available from: http://hdl.handle.net/1993/23157

Freie Universität Berlin

20. Paul, Florian. Entwicklung der 'quantitative GTPase affinity purification' (qGAP) zur Identifizierung von Interaktionspartnern der Rho GTPasen.

Degree: 2015, Freie Universität Berlin

URL: http://dx.doi.org/10.17169/refubium-11349

► Rho GTPasen stellen zentrale Regulatoren des Aktin-Zytoskeletts dar. Zusätzlich können sie die Genexpression, Zellteilung und andere biologische Prozesse beeinflussen. Die klassischen Rho GTPasen sind molekulare… (more)

▼ Rho GTPasen stellen zentrale Regulatoren des Aktin-Zytoskeletts dar. Zusätzlich können sie die Genexpression, Zellteilung und andere biologische Prozesse beeinflussen. Die klassischen Rho GTPasen sind molekulare Schalter. Wenn sie GTP gebunden haben befinden sie sich im aktiven, bei Bindung von GDP im inaktiven Zustand. Der Austausch dieser beiden Nukleotide, auch GDP/GTP- Zyklus genannt, wird streng reguliert. Die vielfältigen biologischen Aktivitäten der Rho GTPasen werden durch zahlreiche Effektoren vermittelt. Trotz ihrer Wichtigkeit wurde eine systematische Untersuchung dieser Interaktionspartner noch nicht durchgeführt. In dieser Doktorarbeit sind die Entwicklung, die Validierung und die biologischen Ergebnisse einer neuen Methode zur Identifizierung von Rho GTPase Effektoren beschrieben. Diese Methode wurde von uns „quantitative GTPase affinity pull-down“ (quantitativer GTPasen Affinitäts Pulldown, qGAP) genannt. qGAP vereinigt die Affinitäts- Aufreinigung (Pulldown) mit quantitativer Massenspektrometrie. Dabei werden beide Nukleotid-Ladungszustände berücksichtigt. Zu diesem Zweck wurden rekombinante Rho GTPasen aufgereinigt und entweder mit GDP oder GTPγS geladen. Die Rho GTPasen wurden kovalent an eine Sepharose Matrix gekoppelt und für Affinitätsaufreinigung eingesetzt. Quantitative shotgun proteomics wurde verwendet, um die Menge von Proteinen zu vergleichen, die mit der GDP- und GTPγS-geladenen Form interagiert haben. Dadurch wurden Ladungs-spezifische Bindungspartner identifiziert. Zunächst wurde qGAP mit RhoA, Rac1 und Cdc42 auf zytoplasmatische Extrakte von SILAC-markierten HeLa Zellen angewendet (SILAC-qGAP). Im nächsten Schritt wurden Lysate von unmarkierten Maus Gehirnen verwendet um Interaktionspartner von RhoA, RhoB, RhoC, RhoD, Rac1 und Cdc42 zu identifizieren (LF-qGAP). In beiden Varianten von qGAP konnten Gruppe von spezifischen Interaktionspartnern klar von hunderten bis tausenden von Proteinen unterschieden werden. Durch den Vergleich mit einer Interaktionsdatenbank wurde festgestellt, dass diese spezifischen Interaktionspartner klar mit bekannten Rho Effektoren angereichert waren. Für LF-qGAP war die Sensitivität gut (50%) und die Spezifizität exzellent (97%). Falls weitere Studien zeigen, dass die neuen Interaktionspartner wahr sind, könnte die tatsächliche Sensitivität höher liegen. Eine hierarchische Clusteranalyse der biologischen Replikate ergab, dass qGAP sehr reproduzierbar war. Insgesamt wurden mit qGAP 291, größtenteils neue Interaktionspartner identifiziert. Elf von zwölf getesteten neuen Interaktionen wurden durch eine neu entwickelte, unabhängige Methode validiert. Die Bindungsdaten wurden verwendet um ein umfassendes Rho Interaktionsnetzwerk zu erstellen. Es wurde eine höhere Promiskuität zwischen Bindungspartnern gefunden als zuvor vermutet. Das Überlappen von Bindungspartnern erlaubte uns auf Ähnlichkeiten zwischen dem Netzwerk und der Stammesgeschichte der Rho-GTPasen zu folgern. Zusammenfassend zeigen die Daten, dass qGAP eine wertvolle neue Methode zum Studium der Rho… Advisors/Committee Members: [email protected] (contact), m (gender), Prof. Matthias Selbach (firstReferee), Prof. Udo Heinemann (furtherReferee).

Subjects/Keywords: Rho GTPase; mass spectrometry; SILAC; 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::572 Biochemie

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

APA (6^th Edition):

Paul, F. (2015). Entwicklung der 'quantitative GTPase affinity purification' (qGAP) zur Identifizierung von Interaktionspartnern der Rho GTPasen. (Thesis). Freie Universität Berlin. Retrieved from http://dx.doi.org/10.17169/refubium-11349

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):

Paul, Florian. “Entwicklung der 'quantitative GTPase affinity purification' (qGAP) zur Identifizierung von Interaktionspartnern der Rho GTPasen.” 2015. Thesis, Freie Universität Berlin. Accessed January 19, 2021. http://dx.doi.org/10.17169/refubium-11349.

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

MLA Handbook (7^th Edition):

Paul, Florian. “Entwicklung der 'quantitative GTPase affinity purification' (qGAP) zur Identifizierung von Interaktionspartnern der Rho GTPasen.” 2015. Web. 19 Jan 2021.

Vancouver:

Paul F. Entwicklung der 'quantitative GTPase affinity purification' (qGAP) zur Identifizierung von Interaktionspartnern der Rho GTPasen. [Internet] [Thesis]. Freie Universität Berlin; 2015. [cited 2021 Jan 19]. Available from: http://dx.doi.org/10.17169/refubium-11349.

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

Council of Science Editors:

Paul F. Entwicklung der 'quantitative GTPase affinity purification' (qGAP) zur Identifizierung von Interaktionspartnern der Rho GTPasen. [Thesis]. Freie Universität Berlin; 2015. Available from: http://dx.doi.org/10.17169/refubium-11349

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

University of Rochester

21. Hutti, Charles Richard. Role of lysosomal pathways in prion toxicity.

Degree: PhD, 2020, University of Rochester

URL: http://hdl.handle.net/1802/35929

► Prion diseases are infectious and fatal neurological disorders that afflict a number of mammalian species. In humans, these diseases have an incidence of one per… (more)

▼ Prion diseases are infectious and fatal neurological disorders that afflict a number of mammalian species. In humans, these diseases have an incidence of one per million individuals. Prion diseases are characterized by extended incubation periods before a rapid onset of neurological symptoms and decline in cognitive function. During the course of these diseases, cytotoxic aggregates of the prion protein (PrPSc) accumulate and cause the conversion of the non-toxic cellular form of the prion protein (PrPC) into additional aggregates in a self-seeding fashion. While the formation of PrPSc generally results in cell death and neurodegeneration, a few mammalian cell lines have been identified that are capable of accumulating and propagating PrPSc aggregates without succumbing to their cytotoxic effects. This thesis utilizes these cell lines as a disease model to identify cellular pathways that are impacted by the presence of PrPSc aggregates. In our first study, we investigated the effects of intracellular accumulations of PrPSc aggregates on cellular degradation pathways. Intracellular PrPSc aggregates primarily accumulate within late endosomes and lysosomes, organelles that participate in the degradation and turnover of a large subset of the proteome. Thus, intracellular accumulation of PrPSc aggregates has the potential to globally influence protein degradation kinetics within an infected cell. In order to study this phenomenon, we measured the proteome-wide effects of prion infection on protein degradation rates in N2a neuroblastoma cells by dynamic stable isotopic labeling with amino acids in cell culture (dSILAC) and bottom-up proteomics. The results of these experiments revealed that the majority of the proteome is degraded more rapidly in cells infected with PrPSc aggregates. We showed that this effect occurs concurrently with increases in the cellular activities of autophagy and some lysosomal hydrolases. The enhancement of lysosomal degradative flux may play a role in survival of N2a cells upon prion infection. In our second study, we investigated genetic factors that contribute to cellular tolerance of prion toxicity. A genome-wide CRISPR screen was performed to identify genes that have synthetically lethal interactions with PrPSc in two viable prion-infected cell lines. The screen provided a global survey of how the expression of individual genes in the genome influences cell survival in the presence of prion aggregates. The results identified members of the homotypic fusion and vacuole protein sorting (HOPS) tethering complex as key prion tolerance factors in prion-infected cell lines. The HOPS complex is responsible for facilitating vesicle fusion events with the lysosome, revealing another potentially important link between PrPSc aggregates and lysosomal pathways. In the final study, small molecule drugs that act on lysosomal degradation pathways were tested for prion clearance activities. Both STF-62247 and bafilomycin, known lysosomal inhibitors, are toxic to prion-infected…

Subjects/Keywords: Cell culture; CRISPR; Dynamic SILAC; Genome-wide CRISPR screen; Mass spectrometry; Prion

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APA (6^th Edition):

Hutti, C. R. (2020). Role of lysosomal pathways in prion toxicity. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/35929

Chicago Manual of Style (16^th Edition):

Hutti, Charles Richard. “Role of lysosomal pathways in prion toxicity.” 2020. Doctoral Dissertation, University of Rochester. Accessed January 19, 2021. http://hdl.handle.net/1802/35929.

MLA Handbook (7^th Edition):

Hutti, Charles Richard. “Role of lysosomal pathways in prion toxicity.” 2020. Web. 19 Jan 2021.

Vancouver:

Hutti CR. Role of lysosomal pathways in prion toxicity. [Internet] [Doctoral dissertation]. University of Rochester; 2020. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1802/35929.

Council of Science Editors:

Hutti CR. Role of lysosomal pathways in prion toxicity. [Doctoral Dissertation]. University of Rochester; 2020. Available from: http://hdl.handle.net/1802/35929

University of South Florida

22. Mahajan, Shikha. Protein Profiling of Adenine Nucleoside and Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-azidoadenosine Analogs as Affinity Based Protein Profiling Probes.

Degree: 2012, University of South Florida

URL: https://scholarcommons.usf.edu/etd/4139

► Identification of differential expressions of proteins in proteomic profiles of biological samples shows great potential as a valuable technique for the early diagnosis of various… (more)

▼ Identification of differential expressions of proteins in proteomic profiles of biological samples shows great potential as a valuable technique for the early diagnosis of various diseases. An important challenge in modern protein profiling approaches is to reduce the complexity of the samples by limiting the number of proteins that need to be evaluated for distinction in the expression between normal and deceased cells. In this research, an affinity based approach for the enrichment of nucleotide and nucleoside binding proteins from a complex cell proteome has been developed. To achieve this goal, new N6-biotinylated-8-azido-adenosine probes (AdoRs) have been designed and synthesized to photolabel the nucleotide and nucleoside binding proteins. These probes contain a reactive group that forms a covalent bond with the target proteins, as well as a biotin tag for affinity enrichment using avidin chromatography. Further, a mass spectrometric protein profiling approach is employed to quantitatively identify small variations in expression of nucleoside and nucleotide binding proteins in samples of interest. Mouse neuroblastoma N18TG2 cell proteome has been used as a model system for the development of the LC-MS/MS based proteomic analysis of these affinity enriched protein fractions. Upon enrichment, the photolabeled proteome exhibited an approximately four-fold abundance of nucleoside and nucleotide binding proteins over nonlabeled proteome. The approach was extended to compare the proteomic profiles of nucleotide and nucleoside binding proteins in cancerous (Hey) and non-cancerous (T-80) human ovarian cell proteome. Certain proteins that were not detected in cell lysate were also identified in labeled proteome, thereby demonstrating the strength of our approach in enriching low abundant proteins. To substantiate the qualitative analysis, we have employed the Stable Isotope Labeling in Amino Acid Cell Culture (SILAC) for the quantitative study of the protein expression in cancerous and non-cancerous human ovarian cells. A modest panel of proteins with differential expressions in these cell lines was identified, a few of which have been correlated to various forms of cancer. Vimentin, stress induced phosphoprotein-1, and heat shock protein 90 that were identified to have altered expressions in these cell lines are among some of the proteins associated with ovarian cancer.

Subjects/Keywords: ABPP; adenosine analogs; ovarian cancer; proteomics; SILAC; American Studies; Arts and Humanities; Biochemistry; Chemistry

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APA (6^th Edition):

Mahajan, S. (2012). Protein Profiling of Adenine Nucleoside and Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-azidoadenosine Analogs as Affinity Based Protein Profiling Probes. (Thesis). University of South Florida. Retrieved from https://scholarcommons.usf.edu/etd/4139

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):

Mahajan, Shikha. “Protein Profiling of Adenine Nucleoside and Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-azidoadenosine Analogs as Affinity Based Protein Profiling Probes.” 2012. Thesis, University of South Florida. Accessed January 19, 2021. https://scholarcommons.usf.edu/etd/4139.

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

MLA Handbook (7^th Edition):

Mahajan, Shikha. “Protein Profiling of Adenine Nucleoside and Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-azidoadenosine Analogs as Affinity Based Protein Profiling Probes.” 2012. Web. 19 Jan 2021.

Vancouver:

Mahajan S. Protein Profiling of Adenine Nucleoside and Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-azidoadenosine Analogs as Affinity Based Protein Profiling Probes. [Internet] [Thesis]. University of South Florida; 2012. [cited 2021 Jan 19]. Available from: https://scholarcommons.usf.edu/etd/4139.

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

Council of Science Editors:

Mahajan S. Protein Profiling of Adenine Nucleoside and Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-azidoadenosine Analogs as Affinity Based Protein Profiling Probes. [Thesis]. University of South Florida; 2012. Available from: https://scholarcommons.usf.edu/etd/4139

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

University of Cambridge

23. Marino, Polly. Studies on assembly and genetic variation in mitochondrial respiratory complex I.

Degree: PhD, 2019, University of Cambridge

URL: https://doi.org/10.17863/CAM.36634 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767729

► Complex I (NADH:ubiquinone oxidoreductase) couples electron transfer to proton translocation across the inner mitochondrial membrane, to drive the synthesis of ATP. Its distinctive L-shaped structure… (more)

▼ Complex I (NADH:ubiquinone oxidoreductase) couples electron transfer to proton translocation across the inner mitochondrial membrane, to drive the synthesis of ATP. Its distinctive L-shaped structure comprises 45 subunits, encoded by both the mitochondrial and nuclear genomes, which are assembled by a complicated modular pathway. Complex I genetic defects are the most common cause of mitochondrial disorders and often present in early childhood, with high mortality rates. Recent high-resolution electron cryo-microscopy structures of mammalian complex I provide a foundation for both interpreting biochemical and biomedical data and understanding the catalytic mechanism. First, this thesis explores how the flavin cofactor is inserted into the NADH-binding (N-) domain of complex I. Genetic manipulation of cultured human cells, to starve them of flavin, revealed a hierarchal impact on the mitochondrial flavoproteome. High riboflavin content in the growth media ameliorated observed phenotypes, requiring cell conditioning in low riboflavin conditions. CRISPR knockout of the putative mitochondrial flavin transporter SLC25A32 demonstrated the severe impact of decreased flavin on complexes I and II, and mass spectrometry 'complexome' analyses suggest that the N-domain is still assembled onto complex I in the absence of the flavin. Second, the model organism Yarrowia lipolytica was used to assess the importance of residues in the quinone-binding site of complex I. Three residues with proposed roles in binding the quinone head-group were targeted. One variant was catalytically inactive, while two retained some activity. They showed decreased ability to reduce physiologically-relevant, long chain quinones, but their ability to reduce short-chain analogues was affected less severely. The results suggest a complicated picture in which interactions between the protein and both the hydrophilic quinone head-group and hydrophobic isoprenoid chain contribute to quinone-binding affinity and catalysis. Finally, a model for human complex I, generated from a recent high-resolution structure of mouse complex I, was used to investigate whether the pathogenicity of human variants could be predicted. Structural information on variant residues, including their secondary structure, proximity to key features and surface exposure, was collated and the power of each property to predict pathogenicity investigated. The analysis was then extended to the whole structure, to identify potential pathogenic hotspots in the enzyme, inform future studies of functionally important regions in complex I, and aid the diagnosis of clinically relevant pathogenic variants.

Subjects/Keywords: complex I; mitochondria; respiration; yarrowia; flavin; assembly; riboflavin; 143B; SILAC; complexome; transcriptomics; SLC25A32; RFK

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

APA (6^th Edition):

Marino, P. (2019). Studies on assembly and genetic variation in mitochondrial respiratory complex I. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.36634 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767729

Chicago Manual of Style (16^th Edition):

Marino, Polly. “Studies on assembly and genetic variation in mitochondrial respiratory complex I.” 2019. Doctoral Dissertation, University of Cambridge. Accessed January 19, 2021. https://doi.org/10.17863/CAM.36634 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767729.

MLA Handbook (7^th Edition):

Marino, Polly. “Studies on assembly and genetic variation in mitochondrial respiratory complex I.” 2019. Web. 19 Jan 2021.

Vancouver:

Marino P. Studies on assembly and genetic variation in mitochondrial respiratory complex I. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Jan 19]. Available from: https://doi.org/10.17863/CAM.36634 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767729.

Council of Science Editors:

Marino P. Studies on assembly and genetic variation in mitochondrial respiratory complex I. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://doi.org/10.17863/CAM.36634 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767729

The Ohio State University

24. Beller, Nicole C. Selective Pulse Chase-SILAC Labeling of Three-Dimensional Multicellular Spheroids for Global Proteome Analysis.

Degree: MS, Chemistry, 2020, The Ohio State University

URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1586292839111678

► Developing accurate model systems is a major issue in cancer research. While conventional two-dimensional cell culture models are cost effective, they lack the complexity of… (more)

Subjects/Keywords: Analytical Chemistry; Biochemistry; Chemistry; pSILAC; pulse-chase SILAC; Stable Isotope Labeling; Spheroids

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APA (6^th Edition):

Beller, N. C. (2020). Selective Pulse Chase-SILAC Labeling of Three-Dimensional Multicellular Spheroids for Global Proteome Analysis. (Masters Thesis). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1586292839111678

Chicago Manual of Style (16^th Edition):

Beller, Nicole C. “Selective Pulse Chase-SILAC Labeling of Three-Dimensional Multicellular Spheroids for Global Proteome Analysis.” 2020. Masters Thesis, The Ohio State University. Accessed January 19, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu1586292839111678.

MLA Handbook (7^th Edition):

Beller, Nicole C. “Selective Pulse Chase-SILAC Labeling of Three-Dimensional Multicellular Spheroids for Global Proteome Analysis.” 2020. Web. 19 Jan 2021.

Vancouver:

Beller NC. Selective Pulse Chase-SILAC Labeling of Three-Dimensional Multicellular Spheroids for Global Proteome Analysis. [Internet] [Masters thesis]. The Ohio State University; 2020. [cited 2021 Jan 19]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1586292839111678.

Council of Science Editors:

Beller NC. Selective Pulse Chase-SILAC Labeling of Three-Dimensional Multicellular Spheroids for Global Proteome Analysis. [Masters Thesis]. The Ohio State University; 2020. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1586292839111678

25. Thorley, Matthew. Analysis of the dystrophin interactome : Analyse de l'interactome dystrophine.

Degree: Docteur es, Complexité du Vivant, 2016, Université Pierre et Marie Curie – Paris VI

URL: http://www.theses.fr/2016PA066619

►

Le but de ce projet était d'identifier de manière méthodique et standardisée les partenaires interagissant avec la protéine dystrophine dans les cellules musculaires squelettiques humaines… (more)

▼

Le but de ce projet était d'identifier de manière méthodique et standardisée les partenaires interagissant avec la protéine dystrophine dans les cellules musculaires squelettiques humaines différenciées et découvrir de nouveaux rôles de la dystrophine. Des cellules immortalisées ont été obtenue en sur-exprimant de manière stable hTERT / CDK4. Nous avons réalisé une analyse transcriptomique comparant des lignées immortalisées avec leurs populations primaires correspondantes, à l’état de prolifération et de différentiation. Nous avons constaté que l'immortalisation n'a pas d'effet mesurable sur le programme myogénique ou sur tout autre processus cellulaires, et qu'elle avait un effet protecteur contre le processus de sénescence. Les lignées de cellules musculaires humaines constituent donc de bon model in vitro pour l’étude de l’interactome de la dystrophine. Nous avons déterminé l’interactome de la dystrophine en utilisant l’approche proteomique ‘QUICK’. Nous avons identifié 18 nouveaux partenaires directs de la dystrophine, partenaires étant impliqués dans le transport vésiculaire ou étant des protéines d'adhésion. Ces résultats renforcent les données précédemment publiées suggérant un lien entre la dystrophine et le trafic vésiculaire, ainsi que dystrophine et adhesion cellulaire. Ces nouveaux partenaires ont été ajoutés à l’interactome de la dystrophine, interactome accessible sur le Web: sys-myo.rhcloud.com/dystrophin-interactome. Ce site web est dédié à être un outil facile d’utilisation permettant d’explorer et de visualiser l’interactome de la dystrophine du muscle squelettique.

The aim of this project was to systematically identify new interaction partners of the dystrophin protein within differentiated human skeletal muscle cells in order to uncover new roles in which dystrophin is involved, and to better understand how the global interactome is affected by the absence of dystrophin. hTERT/cdk4 immortalized myogenic human cell lines represent an important tool for skeletal muscle research however, disruption of the cell cycle has the potential to affect many other cellular processes to which it also linked. A transcriptome-wide analysis of healthy and diseased lines comparing immortalized lines with their parent primary populations in both differentiated and undifferentiated states testing their myogenic character by comparison with non-myogenic cells found that immortalization has no measurable effect on the myogenic cascade or on any other cellular processes, and that it was protective against the senescence. In this context the human muscle cell lines are a good in vitro model to study the dystrophin interactome. We investigated dystrophin’s interactors using the high-sensitivity proteomics ‘QUICK’ approach. We identified 18 new physical interactors of dystrophin which displayed a high proportion of vesicle transport related proteins and adhesion proteins, strengthening the link between dystrophin and these roles. The proteins determined through previously published data together with the newly…

Advisors/Committee Members: Voit, Thomas (thesis director), Butler-Browne, Gillian (thesis director), Spuler, Simone (thesis director).

Subjects/Keywords: Interactome; Dystrophine; Transcriptome; Immortalisation; Protéomique; Spectrométrie de masse; QUICK; SILAC; Interactome; Dystrophin; Proteomics; 571.6

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

APA (6^th Edition):

Thorley, M. (2016). Analysis of the dystrophin interactome : Analyse de l'interactome dystrophine. (Doctoral Dissertation). Université Pierre et Marie Curie – Paris VI. Retrieved from http://www.theses.fr/2016PA066619

Chicago Manual of Style (16^th Edition):

Thorley, Matthew. “Analysis of the dystrophin interactome : Analyse de l'interactome dystrophine.” 2016. Doctoral Dissertation, Université Pierre et Marie Curie – Paris VI. Accessed January 19, 2021. http://www.theses.fr/2016PA066619.

MLA Handbook (7^th Edition):

Thorley, Matthew. “Analysis of the dystrophin interactome : Analyse de l'interactome dystrophine.” 2016. Web. 19 Jan 2021.

Vancouver:

Thorley M. Analysis of the dystrophin interactome : Analyse de l'interactome dystrophine. [Internet] [Doctoral dissertation]. Université Pierre et Marie Curie – Paris VI; 2016. [cited 2021 Jan 19]. Available from: http://www.theses.fr/2016PA066619.

Council of Science Editors:

Thorley M. Analysis of the dystrophin interactome : Analyse de l'interactome dystrophine. [Doctoral Dissertation]. Université Pierre et Marie Curie – Paris VI; 2016. Available from: http://www.theses.fr/2016PA066619

26. M. Soldi. ESTABLISHMENT AND OPTIMIZATION OF THE CHROP APPROACH, COMBINING CHIP AND MS-BASED PROTEOMICS, FOR THE CHARACTERIZATION OF THE CHROMATOME AT DISTINCT FUNCTIONAL DOMAINS.

Degree: 2013, Università degli Studi di Milano

URL: http://hdl.handle.net/2434/219069

► Chromatin is a highly dynamic, well-structured nucleoprotein complex of DNA and proteins that controls virtually all DNA-transactions. Chromatin dynamicity is regulated at specific loci by… (more)

Subjects/Keywords: chromatin; histone post-translational modifications; epigenetics; mass spectrometry; proteomics; SILAC; histone code readers; histone variants; Settore BIO/10 - Biochimica

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

APA (6^th Edition):

Soldi, M. (2013). ESTABLISHMENT AND OPTIMIZATION OF THE CHROP APPROACH, COMBINING CHIP AND MS-BASED PROTEOMICS, FOR THE CHARACTERIZATION OF THE CHROMATOME AT DISTINCT FUNCTIONAL DOMAINS. (Thesis). Università degli Studi di Milano. Retrieved from http://hdl.handle.net/2434/219069

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):

Soldi, M.. “ESTABLISHMENT AND OPTIMIZATION OF THE CHROP APPROACH, COMBINING CHIP AND MS-BASED PROTEOMICS, FOR THE CHARACTERIZATION OF THE CHROMATOME AT DISTINCT FUNCTIONAL DOMAINS.” 2013. Thesis, Università degli Studi di Milano. Accessed January 19, 2021. http://hdl.handle.net/2434/219069.

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

MLA Handbook (7^th Edition):

Soldi, M.. “ESTABLISHMENT AND OPTIMIZATION OF THE CHROP APPROACH, COMBINING CHIP AND MS-BASED PROTEOMICS, FOR THE CHARACTERIZATION OF THE CHROMATOME AT DISTINCT FUNCTIONAL DOMAINS.” 2013. Web. 19 Jan 2021.

Vancouver:

Soldi M. ESTABLISHMENT AND OPTIMIZATION OF THE CHROP APPROACH, COMBINING CHIP AND MS-BASED PROTEOMICS, FOR THE CHARACTERIZATION OF THE CHROMATOME AT DISTINCT FUNCTIONAL DOMAINS. [Internet] [Thesis]. Università degli Studi di Milano; 2013. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/2434/219069.

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

Council of Science Editors:

Soldi M. ESTABLISHMENT AND OPTIMIZATION OF THE CHROP APPROACH, COMBINING CHIP AND MS-BASED PROTEOMICS, FOR THE CHARACTERIZATION OF THE CHROMATOME AT DISTINCT FUNCTIONAL DOMAINS. [Thesis]. Università degli Studi di Milano; 2013. Available from: http://hdl.handle.net/2434/219069

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

Erasmus University Rotterdam

27. Sap, Karen. Dynamics of Protein Ubiquitination upon Proteasome Modulation : A Quantitative Mass Spectrometry Approach.

Degree: 2018, Erasmus University Rotterdam

URL: http://hdl.handle.net/1765/110280

► markdownabstract__Scope of the Thesis__ The proteasome is a protein complex mostly known for its role in the degradation of unneeded, damaged or misfolded proteins. The… (more)

▼ markdownabstract__Scope of the Thesis__ The proteasome is a protein complex mostly known for its role in the degradation of unneeded, damaged or misfolded proteins. The proteasome plays a central role in all cells and hence a widely studied protein assembly. Malfunctioning of this protein complex has major effects on cellular processes and is known to lead to the development of a variety of diseases such as cancer and neurodegenerative disorders. The proteasome is also an important target for drug discovery; for instance, proteasome inhibitors are used for the treatment of multiple myeloma. However, not much is known about the biological mechanisms behind these treatments. In this project we monitored the cellular responses in terms of protein abundance and protein ubiquitination dynamics upon proteasome malfunctioning (Chapter 3). In order to gain more insight into the specificity and function of individual proteasome complex components, we also manipulated single proteasome subunits, i.e., the proteasome-bound deubiquitinating enzymes (DUBs) and monitored the effects on the cellular (modified) proteome (Chapter 4). The proteasome is a key player in maintaining a balance in proteostasis under both normal and abnormal cellular conditions. In order to gain further knowledge about the functioning of the proteasome under such conditions we characterized the proteasome interactome under different stress conditions, such as oxidative stress, endoplasmatic reticulum stress and proteasome inhibition (Chapter 5). Large scale quantitative mass spectrometry is the central methodology applied in all studies described in this thesis. These types of global and unbiased approaches make it possible to study the relation of a protein complex with its direct cellular protein environment. In Chapter 6 we have monitored changes in the cellular environment upon activation of ecdysone-responsive genes, in terms of global transcriptome and global proteome dynamics, as well as in terms of ecdysone-receptor interactome dynamics. As such, this work provides several clues to address the relationship between mRNA and protein abundances in Drosophila.

Subjects/Keywords: Proteasome; ubiquitin; Quantitative Mass Spectrometry; SILAC; LFQ; protein degradation

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

APA (6^th Edition):

Sap, K. (2018). Dynamics of Protein Ubiquitination upon Proteasome Modulation : A Quantitative Mass Spectrometry Approach. (Doctoral Dissertation). Erasmus University Rotterdam. Retrieved from http://hdl.handle.net/1765/110280

Chicago Manual of Style (16^th Edition):

Sap, Karen. “Dynamics of Protein Ubiquitination upon Proteasome Modulation : A Quantitative Mass Spectrometry Approach.” 2018. Doctoral Dissertation, Erasmus University Rotterdam. Accessed January 19, 2021. http://hdl.handle.net/1765/110280.

MLA Handbook (7^th Edition):

Sap, Karen. “Dynamics of Protein Ubiquitination upon Proteasome Modulation : A Quantitative Mass Spectrometry Approach.” 2018. Web. 19 Jan 2021.

Vancouver:

Sap K. Dynamics of Protein Ubiquitination upon Proteasome Modulation : A Quantitative Mass Spectrometry Approach. [Internet] [Doctoral dissertation]. Erasmus University Rotterdam; 2018. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1765/110280.

Council of Science Editors:

Sap K. Dynamics of Protein Ubiquitination upon Proteasome Modulation : A Quantitative Mass Spectrometry Approach. [Doctoral Dissertation]. Erasmus University Rotterdam; 2018. Available from: http://hdl.handle.net/1765/110280

Freie Universität Berlin

28. Kuropka, Benno. Proteomic, biochemical and biophysical investigations of phosphorylation- dependent interactions of the immune cell protein ADAP.

Degree: 2015, Freie Universität Berlin

URL: http://dx.doi.org/10.17169/refubium-9508

► T cells play a major role in cell-mediated immunity. Their ability to initiate an immune response depends on their capability to change their adhesive and… (more)

▼ T cells play a major role in cell-mediated immunity. Their ability to initiate an immune response depends on their capability to change their adhesive and migratory properties in response to an extracellular stimulus. Signal transduction from activated receptors to adhesion molecules known as integrins is mediated by a receptor-proximal signalling complex that contains the adapter protein ADAP as a central constituent. Upon stimulation, ADAP is phosphorylated on several tyrosine residues, which then serve as docking sites for SH2-domain containing proteins like the adapters SLP76 and NCK, as well as the tyrosine kinase FYN. In this study, ADAP was phosphorylated by FYN kinase in vitro in order to undertake a comprehensive analysis of tyrosine- phosphorylation sites by mass spectrometry. The tyrosine residues 462 and 571 were among the most heavily phosphorylated positions, yet, prior to this study, no interaction partners were known for these positions. Interestingly, ADAP-Y571 was also identified by independent phosphoproteomic studies. Using SILAC-based pulldown experiments with short synthetic peptide baits in combination with quantitative mass spectrometry, several novel potential interaction partners were identified. Since ADAP-Y571 is located at the border of the ADAP-hSH3N-domain, additional pulldown experiments were performed using recombinant and in vitro-phosphorylated protein constructs as baits. Surprisingly, the tyrosine kinase ZAP70 could be reproducibly identified as a specific interaction partner of Y571-phosphorylated ADAP-hSH3N-domain, but not in the context of the unstructured peptide sequence. NMR spectroscopy and MST measurements were used to confirm a direct and phosphorylation-dependent interaction between the phosphorylated hSH3N-domain of ADAP and the N-terminal SH2-domain of ZAP70 (KD = 2,3 μM). In functional assays with Jurkat T cells, ADAP-Y571 was shown to selectively affect chemokine-mediated migration and actin polymerisation, while no influence was observed for adhesion and conjugate formation with antigen presenting cells. In contrast, the depletion of full-length ADAP led to impaired adhesion and migration. Therefore, ADAP-Y571 was identified as a critical determinant for distinguishing the different functionalities of ADAP. In classical AP-MS methods, the identification of low-abundance interaction partners is often hampered by dominant peptide signals of the bait protein in the analyte solution. To overcome this inherent problem, an efficient and robust method for covalent and site-specific immobilization of synthetic peptides or recombinantly expressed proteins was developed using the transpeptidase sortase A. Subsequently, this new “sortase approach” was successfully utilized for investigating phosphorylation-dependent peptide-protein interactions of ADAP and PRS-mediated protein-protein interactions of the CD2BP2-GYF-domain. Advisors/Committee Members: m (gender), Dr. Eberhard Krause (firstReferee), Prof. Dr. Christian Freund (furtherReferee).

Subjects/Keywords: adap; tyrosine phosphorylation; t cell signalling; proteomics; SILAC; 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::572 Biochemie

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

APA (6^th Edition):

Kuropka, B. (2015). Proteomic, biochemical and biophysical investigations of phosphorylation- dependent interactions of the immune cell protein ADAP. (Thesis). Freie Universität Berlin. Retrieved from http://dx.doi.org/10.17169/refubium-9508

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):

Kuropka, Benno. “Proteomic, biochemical and biophysical investigations of phosphorylation- dependent interactions of the immune cell protein ADAP.” 2015. Thesis, Freie Universität Berlin. Accessed January 19, 2021. http://dx.doi.org/10.17169/refubium-9508.

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

MLA Handbook (7^th Edition):

Kuropka, Benno. “Proteomic, biochemical and biophysical investigations of phosphorylation- dependent interactions of the immune cell protein ADAP.” 2015. Web. 19 Jan 2021.

Vancouver:

Kuropka B. Proteomic, biochemical and biophysical investigations of phosphorylation- dependent interactions of the immune cell protein ADAP. [Internet] [Thesis]. Freie Universität Berlin; 2015. [cited 2021 Jan 19]. Available from: http://dx.doi.org/10.17169/refubium-9508.

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

Council of Science Editors:

Kuropka B. Proteomic, biochemical and biophysical investigations of phosphorylation- dependent interactions of the immune cell protein ADAP. [Thesis]. Freie Universität Berlin; 2015. Available from: http://dx.doi.org/10.17169/refubium-9508

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

University of Manitoba

29. Berard, Alicia. Global quantitative host proteomic assay of infected cells highlight virus specific protein changes and identify a novel role for secretogranin ii protein in virus infections.

Degree: Medical Microbiology, 2012, University of Manitoba

URL: http://hdl.handle.net/1993/30717

► Viruses are obligate parasites that use the host cellular machinery to produce progeny virions. The host responds to this invading pathogen by induction of the… (more)

▼ Viruses are obligate parasites that use the host cellular machinery to produce progeny virions. The host responds to this invading pathogen by induction of the immune system; however, the virus employs a variety of strategies to overcome these attacks. The complexity of the virus-host interaction is of great interest to researchers with aims to both characterize the relationship and target steps of the viral life cycle to hinder infection. Many targeted tactics employ single protein analysis; however, approaches that examine the whole set of virus/host interactions are available. Transcriptional alterations within host cells have been determined for many virus- host interactions by micro-array techniques; however little is known about the effects on cellular proteins. This study uses a quantitative mass spectrometric-based method, SILAC, to study differences in a host cell's proteome with infection by a virus. Mammalian reoviruses and herpes simplex viruses are prototypical viruses commonly studied to determine virus life cycle and interactions with hosts. Using three strains of reoviruses and one HSV1 strain, cells were infected to identify differentially regulated proteins at different times. Thousands of proteins were identified for each virus type, some up or down regulated after infection. Biological functions and network analyses were performed using online networking tools. These pathway analyses indicated numerous processes including cell death and inflammatory response are affected by T1L reovirus infection. Comparing reovirus strains revealed a greater overall proteomic change in host function when infected with the more pathogenic T3DC strain. For the HSV infection, host proteins altered during the different immediate early, earlyand late phases of infection helped characterize the host-virus interaction parallel to the virus life cycle. Overall, my study has characterized proteomic changes in different virus infection systems, identifying numerous novel cellular functional pathways and specific proteins altered during virus infections, specifically the secretogranin II protein that had opposite types of regulation in reoviruses and HSV and was examined for its effects on virus replication. Further studies on the novel proteomic characteristics may provide greater understanding to the complex virus-host interactome, leading to possible antiviral targets. Advisors/Committee Members: Severini, Alberto (Medical Microbiology) Coombs, Kevin (Medical Microbiology) (supervisor), Wilkins, John (Biochemistry & Medical Genetics) Feldmann, Heinz (Medical Microbiology).

Subjects/Keywords: SILAC; Reovirus; Herpes simplex virus 1; Proteomics; Host-virus relationship; Cell biology; Mass spectrometry; Systems biology

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

APA (6^th Edition):

Berard, A. (2012). Global quantitative host proteomic assay of infected cells highlight virus specific protein changes and identify a novel role for secretogranin ii protein in virus infections. (Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/30717

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):

Berard, Alicia. “Global quantitative host proteomic assay of infected cells highlight virus specific protein changes and identify a novel role for secretogranin ii protein in virus infections.” 2012. Thesis, University of Manitoba. Accessed January 19, 2021. http://hdl.handle.net/1993/30717.

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

MLA Handbook (7^th Edition):

Berard, Alicia. “Global quantitative host proteomic assay of infected cells highlight virus specific protein changes and identify a novel role for secretogranin ii protein in virus infections.” 2012. Web. 19 Jan 2021.

Vancouver:

Berard A. Global quantitative host proteomic assay of infected cells highlight virus specific protein changes and identify a novel role for secretogranin ii protein in virus infections. [Internet] [Thesis]. University of Manitoba; 2012. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1993/30717.

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

Council of Science Editors:

Berard A. Global quantitative host proteomic assay of infected cells highlight virus specific protein changes and identify a novel role for secretogranin ii protein in virus infections. [Thesis]. University of Manitoba; 2012. Available from: http://hdl.handle.net/1993/30717

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

Freie Universität Berlin

30. Thorley, Matthew. Analyse der Dystrophin-Interaktivität.

Degree: 2017, Freie Universität Berlin

URL: http://dx.doi.org/10.17169/refubium-13898

► Ziel dieses Projektes war die systematische Aufdeckung neuer Interaktionspartner des Dystrophin-Proteins in differenzierten Skelettmuskelzellen, um neue Funktionen von Dystrophin zu identifizieren und ein eingehenderes Verständnis… (more)

▼ Ziel dieses Projektes war die systematische Aufdeckung neuer Interaktionspartner des Dystrophin-Proteins in differenzierten Skelettmuskelzellen, um neue Funktionen von Dystrophin zu identifizieren und ein eingehenderes Verständnis darüber zu erlangen, welche Auswirkungen das Fehlen von Dystrophin auf das Interaktom insgesamt hat. Eine umfassendere Kenntnis der Wechselspieler und Funktionen von Dystrophin ist entscheidend für ein besseres Verständnis des Krankheitsgeschehens bei Patienten mit Muskeldystrophie vom Typ Duchenne oder Becker und anderer Krankheiten, bei denen Dystrophin oder Dystrophin-assoziierte Proteine beeinträchtigt sind, und wird zur Entwicklung und Erforschung von Therapien beitragen, die auf eine Wiederherstellung fehlender bzw. gestörter fundamentaler Interaktionen und Signalwege abzielen. Zunächst wurde eine Recherche in der vorhandenen Fachliteratur und in Bioinformatik-Ressourcen durchgeführt und als Grundlage für ein Online-Interaktom der physischen Wechselspieler von Dystrophin verwendet. Anschließend wurden mithilfe der in der Proteomik gängigen SILAC- Technik neue Interaktionspartner identifiziert und dieser Bioinformatik- Ressource hinzugefügt. Um im Sinne einer Maximierung der Empfindlichkeit hohe Proteinmengen zu erhalten, benötigten wir eine große Anzahl von Zellen, was nur durch Verwendung immortalisierter Zelllinien möglich war. Immortalisierte myogene Humanzelllinien vom Typ hTERT/cdk4 sind ein wichtiges Hilfsmittel in der Skelettmuskelforschung, allerdings könnten durch die Unterbrechung des Zellzyklus zahlreiche andere zelluläre Prozesse beeinflusst sein, mit denen der Zellzyklus verknüpft ist. Wir führten eine Transkriptom-weite Analyse gesunder Zelllinien und krankheitsspezifischer Zelllinien durch, indem wir immortalisierte Zelllinien mit ihren Primärzell-Elternpopulationen sowohl im differenzierten als auch im undifferenzierten Zustand verglichen, um ihren myogenen Charakter durch Vergleich mit nicht-myogenen Zellen zu prüfen. Bestimmte Zelllinien wurden außerdem im Hinblick auf Aneuploidie und chromosomale Rearrangements überprüft. Wir stellten fest, dass Immortalisierung keine messbaren Auswirkungen auf die myogene Signalkaskase oder auf andere zelluläre Prozesse hatte und dass sie vor den systemischen Auswirkungen von Seneszenz, die nach einer großen Zahl von Teilungen von Primärzellen zu beobachten sind, schützte. Nachdem wir unsere Zelllinien validiert hatten, untersuchten wir Dystrophin-Wechselspieler im Rahmen eines hochempfindlichen Proteomik-Ansatzes mit Knockdown, Isotopenmarkierung von Aminosäuren (SILAC), Knockdown der Dystrophin-Expression, Immunpräzipitation und Massenspektrometrie. Dies ermöglichte eine zuverlässige Identifizierung von Dystrophin-Wechselspielern unter Eliminierung der Präzipitation der zahlreichen falschpositiven Proteine infolge einer unspezifischen Bindung an die Beads und den Antikörper. Wir identifizierten 18 neue physische Wechselspieler von Dystrophin, darunter anteilsmäßig viele Proteine, die am Vesikeltransport beteiligt sind, sowie… Advisors/Committee Members: m (gender), Prof. Simone Spuler (firstReferee), Prof. Sigmar Stricker (furtherReferee).

Subjects/Keywords: Dystrophin; interactome; immortalisation; hTERT; CDK4; transcriptome; proteomics; mass spectrometry; QUICK; SILAC; 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::572 Biochemie

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

APA (6^th Edition):

Thorley, M. (2017). Analyse der Dystrophin-Interaktivität. (Thesis). Freie Universität Berlin. Retrieved from http://dx.doi.org/10.17169/refubium-13898

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):

Thorley, Matthew. “Analyse der Dystrophin-Interaktivität.” 2017. Thesis, Freie Universität Berlin. Accessed January 19, 2021. http://dx.doi.org/10.17169/refubium-13898.

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

MLA Handbook (7^th Edition):

Thorley, Matthew. “Analyse der Dystrophin-Interaktivität.” 2017. Web. 19 Jan 2021.

Vancouver:

Thorley M. Analyse der Dystrophin-Interaktivität. [Internet] [Thesis]. Freie Universität Berlin; 2017. [cited 2021 Jan 19]. Available from: http://dx.doi.org/10.17169/refubium-13898.

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

Council of Science Editors:

Thorley M. Analyse der Dystrophin-Interaktivität. [Thesis]. Freie Universität Berlin; 2017. Available from: http://dx.doi.org/10.17169/refubium-13898

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

Open Access Theses and Dissertations