{"id":{"repo_id":"unr","oai_identifier":"oai:scholarwolf.unr.edu:11714/1891"},"canonical_url":"https://search.dev.ndltd.org/etd/unr/oai:scholarwolf.unr.edu:11714/1891","repository":{"repo_id":"unr","name":"University of Nevada - Reno","base_url":"https://scholarwolf.unr.edu/server/oai/request"},"display":{"title":"Developing bioinformatic tools for phosphorylation site co-regulation and correlation: The plant Cellulose Synthase Complex as a case study","abstract":"Cellulose is the most abundant biopolymer on the planet, and this paracrystalline polysaccharide has a variety of industrial applications ranging from textiles to biofuel production. Regulation and polymerization of cellulose in plant cell walls are complex pathways consisting of many proteins with phosphorylated residues discovered through phosphoproteomic surveys. As a ubiquitous form of post-translational modification, phosphorylation by protein kinases is a crucial form of both discrete protein and whole metabolic or signaling pathway regulation. Despite the importance of protein phosphorylation, the relationships between these modifications are poorly understood at the proteomic scale. Through this work, a variety of phosphorylation site network visualization formats were developed to directly visualize the number, frequency, and sequence conservation of phosphorylation sites within a given protein or network of proteins. Further comparison of the primary sequence flanking the phosphorylated residue will help identify motifs conserved across proteins within the network, indicative of protein kinases acting on multiple targets within the pathway and playing an important regulatory role in quickly modulating different steps in the pathway in response to extra- or intra-cellular signals. Overall, this work may lead to streamlined workflows to connect tens of thousands of experimentally supported phosphorylation sites to thousands of protein kinases.","abstract_html":"Cellulose is the most abundant biopolymer on the planet, and this paracrystalline polysaccharide has a variety of industrial applications ranging from textiles to biofuel production. Regulation and polymerization of cellulose in plant cell walls are complex pathways consisting of many proteins with phosphorylated residues discovered through phosphoproteomic surveys. As a ubiquitous form of post-translational modification, phosphorylation by protein kinases is a crucial form of both discrete protein and whole metabolic or signaling pathway regulation. Despite the importance of protein phosphorylation, the relationships between these modifications are poorly understood at the proteomic scale. Through this work, a variety of phosphorylation site network visualization formats were developed to directly visualize the number, frequency, and sequence conservation of phosphorylation sites within a given protein or network of proteins. Further comparison of the primary sequence flanking the phosphorylated residue will help identify motifs conserved across proteins within the network, indicative of protein kinases acting on multiple targets within the pathway and playing an important regulatory role in quickly modulating different steps in the pathway in response to extra- or intra-cellular signals. Overall, this work may lead to streamlined workflows to connect tens of thousands of experimentally supported phosphorylation sites to thousands of protein kinases.","abstract_has_math":false,"creators":["Thomas, Joseph"],"institution":"University of Nevada, Reno","degree_name":"Biochemistry and Molecular Biology","degree_level":"Honors Thesis","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Wallace, Ian S."],"committee_chairs":[],"committee_members":[],"year":2017,"date_issued":"2017","date_published":"2017","updated_at":"2026-07-27T21:47:25Z","subjects":[],"languages":["en_US","English"],"rights":["Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 United States"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/11714/1891","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Wallace, Ian S."]},{"key":"dc:creator","label":"Author","values":["Thomas, Joseph"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2017-08-31T21:17:39Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2017-08-31T21:17:39Z"]},{"key":"dc:date.issued","label":"Date","values":["2017"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Honors Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Biochemistry and Molecular Biology"]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Nevada, Reno"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["English"]},{"key":"dc:language.iso","label":"Language (ISO)","values":["en_US"]},{"key":"dc:rights","label":"Dc Rights","values":["Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 United States"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/11714/1891"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The University of Nevada, Reno Libraries will promptly respond to removal requests related to content that violates intellectual property laws, data protections, or has been uploaded without creator consent. Takedown notices should be directed to our ScholarWolf team (scholarwolf@library.unr.edu) with information about the object, including its full URL and the nature of your complaint."]},{"key":"dc:description.abstract","label":"Abstract","values":["Cellulose is the most abundant biopolymer on the planet, and this paracrystalline polysaccharide has a variety of industrial applications ranging from textiles to biofuel production. Regulation and polymerization of cellulose in plant cell walls are complex pathways consisting of many proteins with phosphorylated residues discovered through phosphoproteomic surveys. As a ubiquitous form of post-translational modification, phosphorylation by protein kinases is a crucial form of both discrete protein and whole metabolic or signaling pathway regulation. Despite the importance of protein phosphorylation, the relationships between these modifications are poorly understood at the proteomic scale. Through this work, a variety of phosphorylation site network visualization formats were developed to directly visualize the number, frequency, and sequence conservation of phosphorylation sites within a given protein or network of proteins. Further comparison of the primary sequence flanking the phosphorylated residue will help identify motifs conserved across proteins within the network, indicative of protein kinases acting on multiple targets within the pathway and playing an important regulatory role in quickly modulating different steps in the pathway in response to extra- or intra-cellular signals. Overall, this work may lead to streamlined workflows to connect tens of thousands of experimentally supported phosphorylation sites to thousands of protein kinases."]},{"key":"dc:format","label":"Dc Format","values":["PDF"]},{"key":"dc:title","label":"Title","values":["Developing bioinformatic tools for phosphorylation site co-regulation and correlation: The plant Cellulose Synthase Complex as a case study"]}]}],"canonical_facts":{"dc:contributor.advisor":["Wallace, Ian S."],"dc:creator":["Thomas, Joseph"],"dc:date.accessioned":["2017-08-31T21:17:39Z"],"dc:date.available":["2017-08-31T21:17:39Z"],"dc:date.issued":["2017"],"dc:description":["The University of Nevada, Reno Libraries will promptly respond to removal requests related to content that violates intellectual property laws, data protections, or has been uploaded without creator consent. Takedown notices should be directed to our ScholarWolf team (scholarwolf@library.unr.edu) with information about the object, including its full URL and the nature of your complaint."],"dc:description.abstract":["Cellulose is the most abundant biopolymer on the planet, and this paracrystalline polysaccharide has a variety of industrial applications ranging from textiles to biofuel production. Regulation and polymerization of cellulose in plant cell walls are complex pathways consisting of many proteins with phosphorylated residues discovered through phosphoproteomic surveys. As a ubiquitous form of post-translational modification, phosphorylation by protein kinases is a crucial form of both discrete protein and whole metabolic or signaling pathway regulation. Despite the importance of protein phosphorylation, the relationships between these modifications are poorly understood at the proteomic scale. Through this work, a variety of phosphorylation site network visualization formats were developed to directly visualize the number, frequency, and sequence conservation of phosphorylation sites within a given protein or network of proteins. Further comparison of the primary sequence flanking the phosphorylated residue will help identify motifs conserved across proteins within the network, indicative of protein kinases acting on multiple targets within the pathway and playing an important regulatory role in quickly modulating different steps in the pathway in response to extra- or intra-cellular signals. Overall, this work may lead to streamlined workflows to connect tens of thousands of experimentally supported phosphorylation sites to thousands of protein kinases."],"dc:format":["PDF"],"dc:identifier.uri":["http://hdl.handle.net/11714/1891"],"dc:language":["English"],"dc:language.iso":["en_US"],"dc:rights":["Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 United States"],"dc:title":["Developing bioinformatic tools for phosphorylation site co-regulation and correlation: The plant Cellulose Synthase Complex as a case study"],"dc:type":["Thesis"],"thesis:degree_level":["Honors Thesis"],"thesis:degree_name":["Biochemistry and Molecular Biology"],"thesis:institution_name":["University of Nevada, Reno"]},"updated_at":"2026-07-27T21:47:25Z"}