{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/108172"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/108172","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Physical, chemical and biological controls on the origin, crystallization and dissolution of human kidney stones","abstract":"Kidney stones are mineral deposits in the renal system that afflict 1 in 11 people worldwide and the incidence and prevalence is increasing globally. Over 70% of stones are composed of calcium oxalate and other mineralogies include struvite, brushite, and apatite. Currently, stones are thought to be relatively insoluble mineral deposits that undergo few physical, chemical and biological post-depositional changes (diagenesis) such as dissolution and recrystallization. Furthermore, with the exception of struvite mineralogy, stones are generally considered sterile and microbial influences on stone formation are nil. This is in contrast to rock deposits in the natural environment, such as hot springs and coral reefs, where diagenesis and microbially-mediated mineral crystallization and dissolution processes are ubiquitous. In the current dissertation, a new multidisciplinary approach combining geology, biology, urology and microscopy (GeoBioMed) applies advanced optical microscopy techniques (e.g., brightfield, polarization, confocal and super-resolution auto-fluorescence) and geoscience concepts (e.g., Law of Superposition, paragenesis, diagenesis, microbial protein catalysis) to evaluate kidney stones in the context of renal physiology and mineral stratigraphy. Results indicate that kidney stones are composed of intricate crystalline architectures that entomb a well-preserved bacterial and fungal community during multiple repeated cycles of crystallization, dissolution and recrystallization. An estimated >80% of any given stone has been dissolved and reformed in vivo and the extensive diagenetic alteration that takes place establishes kidney stone formation as a natural continuum of mineralogical reactions events. By integrating newly developed technologies and geoscience concepts and approaches, the work from this dissertation has resulted in a new synthesis for stone pathophysiology that identifies multiple specific unexpected therapeutic targets for the prevention and treatment of kidney stone disease.","abstract_html":"Kidney stones are mineral deposits in the renal system that afflict 1 in 11 people worldwide and the incidence and prevalence is increasing globally. Over 70% of stones are composed of calcium oxalate and other mineralogies include struvite, brushite, and apatite. Currently, stones are thought to be relatively insoluble mineral deposits that undergo few physical, chemical and biological post-depositional changes (diagenesis) such as dissolution and recrystallization. Furthermore, with the exception of struvite mineralogy, stones are generally considered sterile and microbial influences on stone formation are nil. This is in contrast to rock deposits in the natural environment, such as hot springs and coral reefs, where diagenesis and microbially-mediated mineral crystallization and dissolution processes are ubiquitous. In the current dissertation, a new multidisciplinary approach combining geology, biology, urology and microscopy (GeoBioMed) applies advanced optical microscopy techniques (e.g., brightfield, polarization, confocal and super-resolution auto-fluorescence) and geoscience concepts (e.g., Law of Superposition, paragenesis, diagenesis, microbial protein catalysis) to evaluate kidney stones in the context of renal physiology and mineral stratigraphy. Results indicate that kidney stones are composed of intricate crystalline architectures that entomb a well-preserved bacterial and fungal community during multiple repeated cycles of crystallization, dissolution and recrystallization. An estimated >80% of any given stone has been dissolved and reformed in vivo and the extensive diagenetic alteration that takes place establishes kidney stone formation as a natural continuum of mineralogical reactions events. By integrating newly developed technologies and geoscience concepts and approaches, the work from this dissertation has resulted in a new synthesis for stone pathophysiology that identifies multiple specific unexpected therapeutic targets for the prevention and treatment of kidney stone disease.","abstract_has_math":false,"creators":["Saw, Jessica Jia-Wen"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Molecular & Integrative Physi","degree_department":null,"school":null,"contributors":["Fouke, Bruce W","Sweedler, Jonathan V","Nelson, Erik R","Tsai, Nien-Pei"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2020,"date_issued":"2020-08-26T23:58:44Z","date_published":"2020-08-26T23:58:44Z","updated_at":"2026-07-22T22:24:47Z","subjects":["nephrolithiasis","urolithiasis","kidney stones","microscopy","geobiology","biomineralization"],"languages":["en"],"rights":["Copyright 2020 Jessica Saw"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/108172","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Fouke, Bruce W","Sweedler, Jonathan V","Nelson, Erik R","Tsai, Nien-Pei"]},{"key":"dc:creator","label":"Author","values":["Saw, Jessica Jia-Wen"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2020-08-26T23:58:44Z","2022-08-26T23:58:55Z","2020-05-08","2020-05"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Molecular & Integrative Physi"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["nephrolithiasis","urolithiasis","kidney stones","microscopy","geobiology","biomineralization"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2020 Jessica Saw"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/108172"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Kidney stones are mineral deposits in the renal system that afflict 1 in 11 people worldwide and the incidence and prevalence is increasing globally. Over 70% of stones are composed of calcium oxalate and other mineralogies include struvite, brushite, and apatite. Currently, stones are thought to be relatively insoluble mineral deposits that undergo few physical, chemical and biological post-depositional changes (diagenesis) such as dissolution and recrystallization. Furthermore, with the exception of struvite mineralogy, stones are generally considered sterile and microbial influences on stone formation are nil. This is in contrast to rock deposits in the natural environment, such as hot springs and coral reefs, where diagenesis and microbially-mediated mineral crystallization and dissolution processes are ubiquitous. In the current dissertation, a new multidisciplinary approach combining geology, biology, urology and microscopy (GeoBioMed) applies advanced optical microscopy techniques (e.g., brightfield, polarization, confocal and super-resolution auto-fluorescence) and geoscience concepts (e.g., Law of Superposition, paragenesis, diagenesis, microbial protein catalysis) to evaluate kidney stones in the context of renal physiology and mineral stratigraphy. Results indicate that kidney stones are composed of intricate crystalline architectures that entomb a well-preserved bacterial and fungal community during multiple repeated cycles of crystallization, dissolution and recrystallization. An estimated >80% of any given stone has been dissolved and reformed in vivo and the extensive diagenetic alteration that takes place establishes kidney stone formation as a natural continuum of mineralogical reactions events. By integrating newly developed technologies and geoscience concepts and approaches, the work from this dissertation has resulted in a new synthesis for stone pathophysiology that identifies multiple specific unexpected therapeutic targets for the prevention and treatment of kidney stone disease.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2022-05-01","The student, Jessica Saw, accepted the attached license on 2020-05-07 at 17:12.","The student, Jessica Saw, submitted this Dissertation for approval on 2020-05-07 at 17:25.","This Dissertation was approved for publication on 2020-05-08 at 14:51.","DSpace SAF Submission Ingestion Package generated from Vireo submission #15283 on 2020-08-25 at 17:30:30","Made available in DSpace on 2020-08-26T23:58:44Z (GMT). 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Over 70% of stones are composed of calcium oxalate and other mineralogies include struvite, brushite, and apatite. Currently, stones are thought to be relatively insoluble mineral deposits that undergo few physical, chemical and biological post-depositional changes (diagenesis) such as dissolution and recrystallization. Furthermore, with the exception of struvite mineralogy, stones are generally considered sterile and microbial influences on stone formation are nil. This is in contrast to rock deposits in the natural environment, such as hot springs and coral reefs, where diagenesis and microbially-mediated mineral crystallization and dissolution processes are ubiquitous. In the current dissertation, a new multidisciplinary approach combining geology, biology, urology and microscopy (GeoBioMed) applies advanced optical microscopy techniques (e.g., brightfield, polarization, confocal and super-resolution auto-fluorescence) and geoscience concepts (e.g., Law of Superposition, paragenesis, diagenesis, microbial protein catalysis) to evaluate kidney stones in the context of renal physiology and mineral stratigraphy. Results indicate that kidney stones are composed of intricate crystalline architectures that entomb a well-preserved bacterial and fungal community during multiple repeated cycles of crystallization, dissolution and recrystallization. An estimated >80% of any given stone has been dissolved and reformed in vivo and the extensive diagenetic alteration that takes place establishes kidney stone formation as a natural continuum of mineralogical reactions events. By integrating newly developed technologies and geoscience concepts and approaches, the work from this dissertation has resulted in a new synthesis for stone pathophysiology that identifies multiple specific unexpected therapeutic targets for the prevention and treatment of kidney stone disease.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2022-05-01","The student, Jessica Saw, accepted the attached license on 2020-05-07 at 17:12.","The student, Jessica Saw, submitted this Dissertation for approval on 2020-05-07 at 17:25.","This Dissertation was approved for publication on 2020-05-08 at 14:51.","DSpace SAF Submission Ingestion Package generated from Vireo submission #15283 on 2020-08-25 at 17:30:30","Made available in DSpace on 2020-08-26T23:58:44Z (GMT). No. of bitstreams: 2 SAW-DISSERTATION-2020.pdf: 70560583 bytes, checksum: cc6b962ad51052051b57b43662ed29bb (MD5) LICENSE.txt: 4208 bytes, checksum: 6f66ec7bfd2beab3fffd835c36b2edf4 (MD5) Previous issue date: 2020-05-08","Embargo set by: Seth Robbins for item 115785 Lift date: 2022-08-26T23:58:55Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only"],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/108172"],"dc:language":["en"],"dc:rights":["Copyright 2020 Jessica Saw"],"dc:subject":["nephrolithiasis","urolithiasis","kidney stones","microscopy","geobiology","biomineralization"],"dc:title":["Physical, chemical and biological controls on the origin, crystallization and dissolution of human kidney stones"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Molecular & Integrative Physi"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:47Z"}