{"id":"https://openalex.org/W2618655197","doi":null,"title":"INVESTIGATING THE PRESENCE OF MITOCHONDRIAL DNA METHYLATION, ITS ALTERATION AND ASSOCIATION WITH MITOCHONDRIAL TRANSCRIPTION AND MITOCHONDRIAL FUNCTION","display_name":"INVESTIGATING THE PRESENCE OF MITOCHONDRIAL DNA METHYLATION, ITS ALTERATION AND ASSOCIATION WITH MITOCHONDRIAL TRANSCRIPTION AND MITOCHONDRIAL FUNCTION","publication_year":2015,"publication_date":"2015-12-31","ids":{"openalex":"https://openalex.org/W2618655197","mag":"2618655197"},"language":"en","primary_location":{"id":"pmh:oai:kuscholarworks.ku.edu:1808/21927","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/1808/21927","pdf_url":"http://hdl.handle.net/1808/21927","source":{"id":"https://openalex.org/S4377196285","display_name":"KU ScholarWorks (University of Kansas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I146416000","host_organization_name":"University of Kansas","host_organization_lineage":["https://openalex.org/I146416000"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/1808/21927","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087960230","display_name":"Nairita Roy","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Nairita Roy","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5087960230"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.6855000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.6855000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10301","display_name":"Mitochondrial Function and Pathology","score":0.2712000012397766,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.004699999932199717,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/mitochondrial-dna-methylation","display_name":"mitochondrial DNA methylation","score":0.8759999871253967},{"id":"https://openalex.org/keywords/mitochondrial-transcription","display_name":"mitochondrial transcription","score":0.675000011920929},{"id":"https://openalex.org/keywords/mitochondrial-function","display_name":"mitochondrial function","score":0.7929999828338623},{"id":"https://openalex.org/keywords/mitochondrial-dysfunction","display_name":"mitochondrial dysfunction","score":0.8769999742507935},{"id":"https://openalex.org/keywords/sh-sy5y-cells","display_name":"SH-SY5Y cells","score":0.9670000076293945},{"id":"https://openalex.org/keywords/5-methylcytosine","display_name":"5-methylcytosine","score":0.7879999876022339},{"id":"https://openalex.org/keywords/12s-rrna","display_name":"12S rRNA","score":0.8420000076293945}],"concepts":[{"id":"https://openalex.org/C24586158","wikidata":"https://www.wikidata.org/wiki/Q27075","display_name":"Mitochondrial DNA","level":3,"score":0.8543270230293274},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5673505067825317},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.5578363537788391},{"id":"https://openalex.org/C28859421","wikidata":"https://www.wikidata.org/wiki/Q39572","display_name":"Mitochondrion","level":2,"score":0.47503286600112915},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4252975285053253},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.417153924703598},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41528066992759705},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3457437753677368},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33229559659957886},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15099477767944336},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.11493939161300659},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09733638167381287},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:kuscholarworks.ku.edu:1808/21927","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/1808/21927","pdf_url":"http://hdl.handle.net/1808/21927","source":{"id":"https://openalex.org/S4377196285","display_name":"KU ScholarWorks (University of Kansas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I146416000","host_organization_name":"University of Kansas","host_organization_lineage":["https://openalex.org/I146416000"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},{"id":"mag:2618655197","doi":null,"is_oa":false,"landing_page_url":"https://kuscholarworks.ku.edu/bitstream/1808/21927/1/Roy_ku_0099D_14371_DATA_1.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:kuscholarworks.ku.edu:1808/21927","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/1808/21927","pdf_url":"http://hdl.handle.net/1808/21927","source":{"id":"https://openalex.org/S4377196285","display_name":"KU ScholarWorks (University of Kansas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I146416000","host_organization_name":"University of Kansas","host_organization_lineage":["https://openalex.org/I146416000"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},"sustainable_development_goals":[{"score":0.8371999859809875,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2618655197.pdf","grobid_xml":"https://content.openalex.org/works/W2618655197.grobid-xml"},"referenced_works_count":148,"referenced_works":["https://openalex.org/W1510431864","https://openalex.org/W1519160353","https://openalex.org/W1546375972","https://openalex.org/W1548557487","https://openalex.org/W1577875429","https://openalex.org/W1582406013","https://openalex.org/W1798313041","https://openalex.org/W1799046027","https://openalex.org/W1802480460","https://openalex.org/W1828742533","https://openalex.org/W1923994946","https://openalex.org/W1965511548","https://openalex.org/W1966618067","https://openalex.org/W1970488458","https://openalex.org/W1970508468","https://openalex.org/W1974690602","https://openalex.org/W1980360743","https://openalex.org/W1982255060","https://openalex.org/W1985706594","https://openalex.org/W1986356700","https://openalex.org/W1986635328","https://openalex.org/W1986849101","https://openalex.org/W1987793414","https://openalex.org/W1987960916","https://openalex.org/W1988540034","https://openalex.org/W1989588875","https://openalex.org/W1992477424","https://openalex.org/W1992644254","https://openalex.org/W1995706959","https://openalex.org/W1997501197","https://openalex.org/W1997992120","https://openalex.org/W1998541984","https://openalex.org/W1998974825","https://openalex.org/W2000915992","https://openalex.org/W2002322555","https://openalex.org/W2002428606","https://openalex.org/W2002973721","https://openalex.org/W2003714461","https://openalex.org/W2004215000","https://openalex.org/W2004384294","https://openalex.org/W2005185184","https://openalex.org/W2009345535","https://openalex.org/W2015638974","https://openalex.org/W2016254652","https://openalex.org/W2016387246","https://openalex.org/W2018749972","https://openalex.org/W2020089910","https://openalex.org/W2021160242","https://openalex.org/W2021172172","https://openalex.org/W2021407576","https://openalex.org/W2028418054","https://openalex.org/W2032700279","https://openalex.org/W2035257545","https://openalex.org/W2036300762","https://openalex.org/W2036566832","https://openalex.org/W2036810172","https://openalex.org/W2037749377","https://openalex.org/W2038105066","https://openalex.org/W2038843194","https://openalex.org/W2041082788","https://openalex.org/W2041959633","https://openalex.org/W2042120426","https://openalex.org/W2042450970","https://openalex.org/W2042913529","https://openalex.org/W2044088459","https://openalex.org/W2044897807","https://openalex.org/W2046069528","https://openalex.org/W2046241907","https://openalex.org/W2046464222","https://openalex.org/W2049215521","https://openalex.org/W2049547722","https://openalex.org/W2050626041","https://openalex.org/W2051691022","https://openalex.org/W2053213384","https://openalex.org/W2053621737","https://openalex.org/W2053710327","https://openalex.org/W2053870413","https://openalex.org/W2054074282","https://openalex.org/W2056004646","https://openalex.org/W2056400918","https://openalex.org/W2057506177","https://openalex.org/W2057679880","https://openalex.org/W2058567239","https://openalex.org/W2059099840","https://openalex.org/W2060446375","https://openalex.org/W2060822439","https://openalex.org/W2061574765","https://openalex.org/W2061792582","https://openalex.org/W2063389800","https://openalex.org/W2065596858","https://openalex.org/W2070471476","https://openalex.org/W2072301590","https://openalex.org/W2072595318","https://openalex.org/W2075132953","https://openalex.org/W2075172171","https://openalex.org/W2077156849","https://openalex.org/W2077359776","https://openalex.org/W2079095145","https://openalex.org/W2083127038","https://openalex.org/W2085492504","https://openalex.org/W2086088557","https://openalex.org/W2087277712","https://openalex.org/W2088977552","https://openalex.org/W2091335980","https://openalex.org/W2092992881","https://openalex.org/W2093319492","https://openalex.org/W2095861466","https://openalex.org/W2098992864","https://openalex.org/W2105909048","https://openalex.org/W2106592077","https://openalex.org/W2107600848","https://openalex.org/W2109291482","https://openalex.org/W2112299930","https://openalex.org/W2119278281","https://openalex.org/W2119417280","https://openalex.org/W2121594663","https://openalex.org/W2122118508","https://openalex.org/W2126514078","https://openalex.org/W2127192982","https://openalex.org/W2134857136","https://openalex.org/W2135792486","https://openalex.org/W2139122477","https://openalex.org/W2139235231","https://openalex.org/W2139300390","https://openalex.org/W2140410657","https://openalex.org/W2140751228","https://openalex.org/W2142188572","https://openalex.org/W2144458575","https://openalex.org/W2146502895","https://openalex.org/W2146545991","https://openalex.org/W2147713812","https://openalex.org/W2149126458","https://openalex.org/W2149206894","https://openalex.org/W2150095915","https://openalex.org/W2150708667","https://openalex.org/W2154129077","https://openalex.org/W2155453721","https://openalex.org/W2157890202","https://openalex.org/W2159036201","https://openalex.org/W2159788913","https://openalex.org/W2160209396","https://openalex.org/W2163291903","https://openalex.org/W2165505691","https://openalex.org/W2184618836","https://openalex.org/W2202722181","https://openalex.org/W2315512556","https://openalex.org/W2326023299","https://openalex.org/W4242239767"],"related_works":["https://openalex.org/W4414475832","https://openalex.org/W2964899170","https://openalex.org/W197276276","https://openalex.org/W2971428127","https://openalex.org/W7208490784","https://openalex.org/W2591582018","https://openalex.org/W2801861490","https://openalex.org/W6999984937","https://openalex.org/W4413439637","https://openalex.org/W3044819207"],"abstract_inverted_index":{"Mitochondrial":[0],"proteins":[1],"are":[2,20,140],"encoded":[3],"by":[4,210,235,378,401,411,459,494,533,736],"both":[5],"the":[6,45,55,62,171,189,516,566,582,599,619,630,644,665,670,771],"nuclear":[7,34,225,312],"and":[8,19,90,122,137,147,149,182,204,222,242,250,260,356,381,393,403,447,450,474,497,500,508,541,553,576,615,634,662,689,713,739,742,748,763],"mitochondrial":[9,17,29,92,145,162,276,391,394,476,509,523,572,620,639,687,746,749,761],"genome":[10],"(mtDNA).":[11],"Thus,":[12,342,480,676],"alterations":[13,607],"in":[14,22,37,68,74,85,126,144,157,176,196,257,263,271,294,320,326,339,352,363,420,425,437,505,521,559,581,598,610,643,664,669,685,694,697,717,759,765,774],"mtDNA":[15,49,65,69,83,89,98,120,132,153,174,272,295,303,319,328,353,373,384,397,426,440,467,485,506,520,666,680,690,711,727,758,766],"affect":[16],"function":[18,93],"involved":[21],"a":[23,75,116,158,201,258,336,345,591,682,706,754],"plethora":[24],"of":[25,33,48,61,77,82,88,110,173,191,220,231,237,248,289,302,308,311,318,324,360,406,435,444,457,466,471,519,538,594,627,629,657,720,757,770],"diseases":[26],"associated":[27,142,160,502,744],"with":[28,161,315,503,745],"dysfunction.":[30,163],"Although":[31,618,650],"role":[32,81,424,518,684,756],"DNA":[35,221,226,232,241,283,313,362,460,554,652],"methylation":[36,50,70,84,99,121,133,154,175,192,268,284,290,325,351,374,385,398,405,427,461,486,653,663,691,712,715,728,767],"regulating":[38,86],"gene":[39],"expression":[40],"is":[41,113,155,416,428,487,492,501,692,729,734,743],"fairly":[42],"well":[43],"understood,":[44],"very":[46],"existence":[47],"has":[51,104,386],"been":[52,72,106],"debated":[53],"for":[54,240,335],"past":[56],"four":[57],"decades.":[58],"In":[59,164,185,367,511,700],"spite":[60],"controversies":[63],"revolving":[64],"methylation,":[66,441,468],"differences":[67],"have":[71,681],"reported":[73,358,431],"number":[76],"pathological":[78],"conditions.":[79],"However,":[80,605],"transcription":[87,146,392,443,470,507,747],"consequently,":[91],"remains":[94],"unexplored.":[95],"Besides,":[96],"whether":[97,382],"can":[100,134,375],"be":[101,135,376],"altered":[102,136,156,377,383,475,693],"experimentally":[103],"not":[105,623],"investigated.":[107],"The":[108],"goal":[109],"this":[111,702],"dissertation":[112,703],"to":[114,118,169,187,281,348,418,545,565,708],"establish":[115],"method":[117,207,347,707],"quantitate":[119],"evaluate":[123],"its":[124,423],"presence":[125,172,190,359],"SH-SY5Y":[127,177,197,264,327,365,438,458,547],"neuroblastoma":[128,178],"cells;":[129],"examine":[130],"if":[131,138,152,372],"there":[139,589],"any":[141,387],"changes":[143,504,773],"function;":[148],"further,":[150],"determine":[151],"model":[159],"Chapter":[165,368],"II,":[166],"we":[167,199,343,370,481,514,677],"aimed":[168],"investigate":[170,188],"cells":[179],"at":[180,193],"global":[181,194,350,710],"site-specific":[183,404],"levels.":[184,285],"order":[186],"levels":[195,465,496,626,656,716,738],"mtDNA,":[198],"established":[200,344,705,725,753],"direct,":[202],"sensitive":[203],"highly":[205],"specific":[206,337],"using":[208,243,332,354,525],"HPLC-ESI-MS/MS":[209,402],"addressing":[211],"limitations":[212],"such":[213],"as":[214,252,768],"differential":[215],"or":[216],"incomplete":[217],"enzymatic":[218,229],"digestion":[219,230,239],"also,":[223,357],"potential":[224],"contamination.":[227],"Differential":[228],"was":[233,255,269,279,304,329,399,409,590,622],"addressed":[234],"incorporation":[236],"one-step":[238],"oligonucleotides":[244],"harboring":[245],"known":[246,417],"amounts":[247],"dC":[249],"5m-dC":[251,254],"calibrators.":[253],"detected":[256],"linear":[259],"proportional":[261],"manner":[262,696],"mtDNA.":[265,775],"Around":[266],"3%":[267],"found":[270,482,609,678],"obtained":[273,296],"from":[274,297,536,569,585,602,647,673],"crude":[275],"isolates,":[277],"which":[278,491,733],"comparable":[280],"whole-cell":[282],"Interestingly,":[286,588],"similar":[287],"percentages":[288],"were":[291,531,557,579,608,641,667],"observed":[292],"even":[293],"gradient-purified":[298,321],"mitochondria.":[299,322,366],"Further,":[300,751],"purity":[301],"characterized,":[305],"indicating":[306],"elimination":[307],"99.95":[309],"%":[310],"contamination":[314],"115":[316],"fold-enrichment":[317],"Presence":[323],"further":[330],"substantiated":[331],"methylation-specific":[333,412],"PCR":[334,413],"site":[338],"12S":[340,407],"rRNA.":[341],"direct":[346,517,683,755],"quantify":[349],"HPLC-MS/MS":[355],"methylated":[361],"purified":[364],"III,":[369],"investigated":[371,515],"experimental":[379],"interventions":[380],"concomitant":[388],"effects":[389],"on":[390],"function.":[395,510,750],"Global":[396],"assessed":[400],"rRNA":[408],"studied":[410],"assay.":[414],"DNMT1":[415,436,495,658,737],"localize":[419],"mitochondria":[421,535,719],"but":[422],"unknown.":[429],"We":[430],"that":[432,483,484,530,637,679,726],"transient":[433],"over-expression":[434],"increased":[439,469],"decreased":[442],"mtDNA-encoded":[445,472,631],"genes":[446,473,633,636],"reduced":[448,464,580],"total":[449,651],"basal-mitochondrial":[451],"oxygen":[452,477,573],"consumption":[453,478,574],"rates.":[454],"Likewise,":[455],"treatment":[456,499,741],"inhibitor":[462],"(5-aza-dC)":[463],"rate.":[479],"an":[488,730],"alterable":[489,731],"phenomenon,":[490,732],"affected":[493,735],"5-aza-dC":[498,740],"chapter":[512],"IV,":[513],"aging-associated":[522],"dysfunction":[524,688,762],"cytoplasmic":[526,562],"hybrid":[527],"cell":[528],"lines":[529],"created":[532,646],"transferring":[534],"platelets":[537],"healthy":[539],"young":[540,570],"aged":[542,586,603,648,674],"human":[543],"subjects":[544],"mtDNA-depleted":[546],"\u03c10cells.":[548],"Bioenergetic":[549],"fluxes,":[550],"their":[551],"regulators":[552],"methylation-associated":[555],"parameters":[556,575],"characterized":[558,721],"these":[560],"resulting":[561],"hybrids.":[563],"Relative":[564],"cybrids":[567,583,600,645,671],"generated":[568,601,672],"donors,":[571],"COX":[577],"activity":[578,597],"made":[584],"subjects.":[587,604,649,675],"compensatory":[592],"increase":[593],"Complex":[595],"I":[596],"no":[606],"ATP":[611],"levels,":[612],"redox":[613],"states":[614],"glycolysis":[616],"fluxes.":[617],"mass":[621],"different,":[624],"mRNA":[625,661],"some":[628],"OXPHOS":[632],"nuclear-encoded":[635],"promote":[638],"biogenesis":[640],"induced":[642],"remained":[654],"unaltered,":[655],"protein,":[659],"mtDNMT1":[660],"higher":[668],"age-associated":[686,760],"age-dependent":[695,772],"cybrid":[698],"model.":[699],"summary,":[701],"work":[704],"detect":[709],"quantified":[714],"isolated":[718],"purity.":[722],"Also,":[723],"it":[724,752],"alteration":[764],"one":[769]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2017-06-05T00:00:00"}
