{"id":"https://openalex.org/W624968345","doi":null,"title":"Nucleocapsid protein modulates the specificity of plus strand priming and recombination patterns in Human Immunodeficiency Virus","display_name":"Nucleocapsid protein modulates the specificity of plus strand priming and recombination patterns in Human Immunodeficiency Virus","publication_year":2008,"publication_date":"2008-11-30","ids":{"openalex":"https://openalex.org/W624968345","mag":"624968345"},"language":"en","primary_location":{"id":"pmh:oai:drum.lib.umd.edu:1903/8865","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1903/8865","pdf_url":"http://hdl.handle.net/1903/8865","source":{"id":"https://openalex.org/S4306401518","display_name":"University Libraries (University of Maryland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"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/1903/8865","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006399951","display_name":"Deena T. Jacob","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Deena T. Jacob","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5006399951"],"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/T10112","display_name":"HIV Research and Treatment","score":0.9473000168800354,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9473000168800354,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.04639999940991402,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12159","display_name":"T-cell and Retrovirus Studies","score":0.00139999995008111,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/polypurine-tract","display_name":"polypurine tract","score":0.9430000185966492},{"id":"https://openalex.org/keywords/reverse-transcription","display_name":"reverse transcription","score":0.906000018119812},{"id":"https://openalex.org/keywords/recombination","display_name":"recombination","score":0.6060000061988831},{"id":"https://openalex.org/keywords/helix-destabilization","display_name":"helix destabilization","score":0.796999990940094},{"id":"https://openalex.org/keywords/magnesium-ions","display_name":"magnesium ions","score":0.7369999885559082},{"id":"https://openalex.org/keywords/crossover-sites","display_name":"crossover sites","score":0.5929999947547913},{"id":"https://openalex.org/keywords/hiv-replication","display_name":"HIV replication","score":0.4000000059604645}],"concepts":[{"id":"https://openalex.org/C156719811","wikidata":"https://www.wikidata.org/wiki/Q28774","display_name":"Reverse transcriptase","level":4,"score":0.6972307562828064},{"id":"https://openalex.org/C194857396","wikidata":"https://www.wikidata.org/wiki/Q382878","display_name":"Primer extension","level":4,"score":0.628174901008606},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5977910757064819},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5876045823097229},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.5715959072113037},{"id":"https://openalex.org/C2776294106","wikidata":"https://www.wikidata.org/wiki/Q7243406","display_name":"Primer binding site","level":5,"score":0.5502394437789917},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5441750288009644},{"id":"https://openalex.org/C156695909","wikidata":"https://www.wikidata.org/wiki/Q3373825","display_name":"Recombination","level":3,"score":0.5399647951126099},{"id":"https://openalex.org/C81444415","wikidata":"https://www.wikidata.org/wiki/Q7243535","display_name":"Priming (agriculture)","level":3,"score":0.5342430472373962},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.514032244682312},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4985663890838623},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.47882941365242004},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.37239712476730347},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.278070867061615},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2650202512741089},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C100701293","wikidata":"https://www.wikidata.org/wiki/Q193838","display_name":"Germination","level":2,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:drum.lib.umd.edu:1903/8865","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1903/8865","pdf_url":"http://hdl.handle.net/1903/8865","source":{"id":"https://openalex.org/S4306401518","display_name":"University Libraries (University of Maryland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"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:624968345","doi":null,"is_oa":false,"landing_page_url":"https://drum.lib.umd.edu/bitstream/1903/8865/1/umi-umd-5899.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:drum.lib.umd.edu:1903/8865","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1903/8865","pdf_url":"http://hdl.handle.net/1903/8865","source":{"id":"https://openalex.org/S4306401518","display_name":"University Libraries (University of Maryland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"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":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W624968345.pdf","grobid_xml":"https://content.openalex.org/works/W624968345.grobid-xml"},"referenced_works_count":120,"referenced_works":["https://openalex.org/W153121970","https://openalex.org/W201050536","https://openalex.org/W1480610066","https://openalex.org/W1493112672","https://openalex.org/W1495312602","https://openalex.org/W1501933018","https://openalex.org/W1507156025","https://openalex.org/W1508115229","https://openalex.org/W1525717886","https://openalex.org/W1634234391","https://openalex.org/W1641947900","https://openalex.org/W1668628402","https://openalex.org/W1713339284","https://openalex.org/W1738945493","https://openalex.org/W1763313231","https://openalex.org/W1788991010","https://openalex.org/W1918197787","https://openalex.org/W1930567567","https://openalex.org/W1965492323","https://openalex.org/W1967287923","https://openalex.org/W1967411577","https://openalex.org/W1968873679","https://openalex.org/W1969697850","https://openalex.org/W1970328551","https://openalex.org/W1974386629","https://openalex.org/W1976011820","https://openalex.org/W1977282539","https://openalex.org/W1977489960","https://openalex.org/W1978060081","https://openalex.org/W1979094800","https://openalex.org/W1979989142","https://openalex.org/W1981922399","https://openalex.org/W1985269862","https://openalex.org/W1986665516","https://openalex.org/W1987239216","https://openalex.org/W1988756652","https://openalex.org/W1990636994","https://openalex.org/W1990700813","https://openalex.org/W1992512034","https://openalex.org/W1993582484","https://openalex.org/W1993935694","https://openalex.org/W1994128696","https://openalex.org/W1994145517","https://openalex.org/W1996080700","https://openalex.org/W2002261956","https://openalex.org/W2009571668","https://openalex.org/W2009581957","https://openalex.org/W2011153626","https://openalex.org/W2013241878","https://openalex.org/W2015120570","https://openalex.org/W2022060139","https://openalex.org/W2023144832","https://openalex.org/W2025757251","https://openalex.org/W2026793457","https://openalex.org/W2027051533","https://openalex.org/W2029420670","https://openalex.org/W2030315713","https://openalex.org/W2030482575","https://openalex.org/W2033249095","https://openalex.org/W2033892710","https://openalex.org/W2035762783","https://openalex.org/W2037979460","https://openalex.org/W2042695720","https://openalex.org/W2046680270","https://openalex.org/W2047495166","https://openalex.org/W2048626266","https://openalex.org/W2052556060","https://openalex.org/W2057448926","https://openalex.org/W2059910556","https://openalex.org/W2060534902","https://openalex.org/W2063154356","https://openalex.org/W2063191154","https://openalex.org/W2065040389","https://openalex.org/W2065057638","https://openalex.org/W2067139969","https://openalex.org/W2067928523","https://openalex.org/W2069255902","https://openalex.org/W2070688966","https://openalex.org/W2070808858","https://openalex.org/W2077713919","https://openalex.org/W2079269647","https://openalex.org/W2082020695","https://openalex.org/W2087578826","https://openalex.org/W2091884906","https://openalex.org/W2092399994","https://openalex.org/W2094583956","https://openalex.org/W2096985241","https://openalex.org/W2097653439","https://openalex.org/W2099277378","https://openalex.org/W2100626630","https://openalex.org/W2101146285","https://openalex.org/W2103123883","https://openalex.org/W2103262528","https://openalex.org/W2104422107","https://openalex.org/W2110383908","https://openalex.org/W2111750154","https://openalex.org/W2111829379","https://openalex.org/W2117623876","https://openalex.org/W2123581489","https://openalex.org/W2124409966","https://openalex.org/W2124974948","https://openalex.org/W2125421083","https://openalex.org/W2125447905","https://openalex.org/W2126301468","https://openalex.org/W2130582243","https://openalex.org/W2140537283","https://openalex.org/W2141157874","https://openalex.org/W2142753618","https://openalex.org/W2146297450","https://openalex.org/W2158977548","https://openalex.org/W2162607594","https://openalex.org/W2165627636","https://openalex.org/W2169196764","https://openalex.org/W2171305498","https://openalex.org/W2187647649","https://openalex.org/W2258770630","https://openalex.org/W2333399282","https://openalex.org/W2421085437","https://openalex.org/W3119774889","https://openalex.org/W4298363274"],"related_works":["https://openalex.org/W1985269862","https://openalex.org/W2129257592","https://openalex.org/W1970328551","https://openalex.org/W2126301468","https://openalex.org/W2105140840","https://openalex.org/W2009103687","https://openalex.org/W1979094800","https://openalex.org/W3119774889","https://openalex.org/W2103035393","https://openalex.org/W2055415154"],"abstract_inverted_index":{"Replication":[0],"in":[1,10,76,88,119,141,174,194,253],"HIV":[2,84],"(human":[3],"immunodeficiency":[4],"virus)":[5],"occurs":[6],"through":[7],"reverse":[8,189],"transcription":[9,190],"which":[11],"the":[12,32,44,50,53,57,67,71,90,98,104,128,148,159,169,200,207,227],"genomic":[13,68],"single":[14],"stranded":[15,21],"RNA":[16,69,134,236],"is":[17,47,61],"copied":[18],"into":[19,52],"double":[20],"DNA.":[22],"This":[23],"process":[24],"involves":[25],"two":[26],"priming":[27],"events":[28],"namely":[29],"those":[30],"of":[31,66,92,107,130,132,143,152,161,172,176,180,202,229],"minus":[33,45],"and":[34,100,111,154,183,224],"plus":[35,58,93,108],"strand":[36,46,59,94,109],"DNAs.":[37],"The":[38,178,260],"tRNA":[39],"primer":[40,60],"required":[41],"to":[42,157,163],"initiate":[43],"carried":[48],"by":[49,231],"virus":[51,270],"host":[54],"cell,":[55],"while":[56],"generated":[62],"from":[63],"a":[64,80,216],"region":[65],"called":[70],"polypurine":[72],"tract":[73],"(PPT).":[74],"Results":[75],"this":[77,195],"dissertation":[78],"indicate":[79],"new":[81],"role":[82],"for":[83,168],"nucleocapsid":[85],"protein":[86],"(NC)":[87],"modulating":[89],"specificity":[91],"priming.":[95],"For":[96],"HIV,":[97],"central":[99],"3\u2032":[101],"(PPTs)":[102],"are":[103,114,166],"major":[105],"sites":[106],"initiation":[110],"other":[112],"primers":[113,165],"rarely":[115],"used.":[116],"Using":[117],"reconstituted":[118],"vitro":[120],"assays,":[121],"results":[122,261],"showed":[123],"that":[124,147,263],"NC":[125,153,182,197,223,246],"greatly":[126],"reduced":[127],"efficiency":[129,201],"extension":[131,171],"non-PPT":[133,164],"primers,":[135],"but":[136],"not":[137],"PPT.":[138],"Extension":[139],"assays":[140],"presence":[142,175],"mutant":[144],"NCs":[145],"show":[146],"helix":[149],"destabilization":[150],"activity":[151],"its":[155],"ability":[156],"block":[158],"association":[160],"RT":[162,232,264],"responsible":[167],"preferential":[170],"PPT":[173],"NC.":[177],"effect":[179,218,240],"varying":[181],"Mg2+":[184,214,225],"concentrations":[185],"on":[186,219,235],"recombination":[187,203],"during":[188,233,269],"was":[191,241,249],"also":[192],"analyzed":[193],"thesis.":[196],"strongly":[198],"influences":[199],"as":[204,206],"well":[205],"location":[208],"where":[209],"crossovers":[210],"occurred.":[211],"In":[212],"contrast":[213],"had":[215],"smaller":[217],"crossover":[220],"locations.":[221],"Both":[222],"influenced":[226],"level":[228],"pausing":[230,248,265],"synthesis":[234],"templates":[237],"although":[238],"NC's":[239],"more":[242],"profound.":[243],"At":[244],"high":[245,256],"concentrations,":[247],"nearly":[250],"eliminated":[251],"even":[252],"locations":[254],"with":[255],"predicted":[257],"secondary":[258],"structure.":[259],"suggest":[262],"may":[266],"be":[267],"limited":[268],"replication.":[271]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
