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Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    bionlp-st-ge-2016-test-proteins

    {"project":"bionlp-st-ge-2016-test-proteins","denotations":[{"id":"T23857","span":{"begin":2121,"end":2126},"obj":"Protein"},{"id":"T23856","span":{"begin":2074,"end":2081},"obj":"Protein"},{"id":"T23855","span":{"begin":2004,"end":2009},"obj":"Protein"},{"id":"T23854","span":{"begin":1943,"end":1946},"obj":"Protein"},{"id":"T23853","span":{"begin":1911,"end":1914},"obj":"Protein"},{"id":"T23852","span":{"begin":1884,"end":1887},"obj":"Protein"},{"id":"T23851","span":{"begin":1863,"end":1866},"obj":"Protein"},{"id":"T23850","span":{"begin":1781,"end":1787},"obj":"Protein"},{"id":"T23849","span":{"begin":1738,"end":1743},"obj":"Protein"},{"id":"T23848","span":{"begin":1562,"end":1569},"obj":"Protein"},{"id":"T23847","span":{"begin":1492,"end":1495},"obj":"Protein"},{"id":"T23846","span":{"begin":1488,"end":1491},"obj":"Protein"},{"id":"T23845","span":{"begin":1420,"end":1423},"obj":"Protein"},{"id":"T23844","span":{"begin":1388,"end":1391},"obj":"Protein"},{"id":"T23843","span":{"begin":1361,"end":1364},"obj":"Protein"},{"id":"T23842","span":{"begin":1340,"end":1343},"obj":"Protein"},{"id":"T23841","span":{"begin":1258,"end":1264},"obj":"Protein"},{"id":"T23840","span":{"begin":1232,"end":1235},"obj":"Protein"},{"id":"T23839","span":{"begin":1228,"end":1231},"obj":"Protein"},{"id":"T23838","span":{"begin":1094,"end":1099},"obj":"Protein"},{"id":"T23837","span":{"begin":1049,"end":1056},"obj":"Protein"},{"id":"T23836","span":{"begin":979,"end":984},"obj":"Protein"},{"id":"T23835","span":{"begin":942,"end":945},"obj":"Protein"},{"id":"T23834","span":{"begin":938,"end":941},"obj":"Protein"},{"id":"T23833","span":{"begin":875,"end":878},"obj":"Protein"},{"id":"T23832","span":{"begin":851,"end":854},"obj":"Protein"},{"id":"T23831","span":{"begin":712,"end":718},"obj":"Protein"},{"id":"T23830","span":{"begin":648,"end":651},"obj":"Protein"},{"id":"T23829","span":{"begin":644,"end":647},"obj":"Protein"},{"id":"T23828","span":{"begin":587,"end":592},"obj":"Protein"},{"id":"T23827","span":{"begin":503,"end":506},"obj":"Protein"},{"id":"T23826","span":{"begin":424,"end":427},"obj":"Protein"},{"id":"T23825","span":{"begin":374,"end":377},"obj":"Protein"},{"id":"T23824","span":{"begin":312,"end":315},"obj":"Protein"},{"id":"T23823","span":{"begin":284,"end":287},"obj":"Protein"},{"id":"T23822","span":{"begin":257,"end":260},"obj":"Protein"},{"id":"T23821","span":{"begin":165,"end":168},"obj":"Protein"},{"id":"T23820","span":{"begin":45,"end":48},"obj":"Protein"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"(A) Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    bionlp-st-ge-2016-uniprot

    {"project":"bionlp-st-ge-2016-uniprot","denotations":[{"id":"T24347","span":{"begin":1488,"end":1491},"obj":"http://www.uniprot.org/uniprot/P19838"},{"id":"T24346","span":{"begin":1228,"end":1231},"obj":"http://www.uniprot.org/uniprot/P19838"},{"id":"T24345","span":{"begin":938,"end":941},"obj":"http://www.uniprot.org/uniprot/P19838"},{"id":"T24344","span":{"begin":644,"end":647},"obj":"http://www.uniprot.org/uniprot/P19838"},{"id":"T24343","span":{"begin":1943,"end":1946},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24342","span":{"begin":1911,"end":1914},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24341","span":{"begin":1884,"end":1887},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24340","span":{"begin":1863,"end":1866},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24339","span":{"begin":1420,"end":1423},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24338","span":{"begin":1388,"end":1391},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24337","span":{"begin":1361,"end":1364},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24336","span":{"begin":1340,"end":1343},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24335","span":{"begin":875,"end":878},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24334","span":{"begin":851,"end":854},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24333","span":{"begin":503,"end":506},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24332","span":{"begin":424,"end":427},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24331","span":{"begin":374,"end":377},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24330","span":{"begin":312,"end":315},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24329","span":{"begin":284,"end":287},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24328","span":{"begin":257,"end":260},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24327","span":{"begin":165,"end":168},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24326","span":{"begin":45,"end":48},"obj":"http://www.uniprot.org/uniprot/P04578"},{"id":"T24325","span":{"begin":2121,"end":2126},"obj":"http://www.uniprot.org/uniprot/O94916"},{"id":"T24324","span":{"begin":2004,"end":2009},"obj":"http://www.uniprot.org/uniprot/O94916"},{"id":"T24323","span":{"begin":1738,"end":1743},"obj":"http://www.uniprot.org/uniprot/O94916"},{"id":"T24322","span":{"begin":1094,"end":1099},"obj":"http://www.uniprot.org/uniprot/O94916"},{"id":"T24321","span":{"begin":979,"end":984},"obj":"http://www.uniprot.org/uniprot/O94916"},{"id":"T24320","span":{"begin":587,"end":592},"obj":"http://www.uniprot.org/uniprot/O94916"},{"id":"T24319","span":{"begin":558,"end":563},"obj":"http://www.uniprot.org/uniprot/O94916"},{"id":"T24318","span":{"begin":334,"end":339},"obj":"http://www.uniprot.org/uniprot/O94916"},{"id":"T24317","span":{"begin":87,"end":92},"obj":"http://www.uniprot.org/uniprot/O94916"},{"id":"T24355","span":{"begin":1492,"end":1495},"obj":"http://www.uniprot.org/uniprot/P21579"},{"id":"T24354","span":{"begin":1232,"end":1235},"obj":"http://www.uniprot.org/uniprot/P21579"},{"id":"T24353","span":{"begin":942,"end":945},"obj":"http://www.uniprot.org/uniprot/P21579"},{"id":"T24352","span":{"begin":648,"end":651},"obj":"http://www.uniprot.org/uniprot/P21579"},{"id":"T24351","span":{"begin":1492,"end":1495},"obj":"http://www.uniprot.org/uniprot/Q04206"},{"id":"T24350","span":{"begin":1232,"end":1235},"obj":"http://www.uniprot.org/uniprot/Q04206"},{"id":"T24349","span":{"begin":942,"end":945},"obj":"http://www.uniprot.org/uniprot/Q04206"},{"id":"T24348","span":{"begin":648,"end":651},"obj":"http://www.uniprot.org/uniprot/Q04206"}],"namespaces":[{"prefix":"_base","uri":"http://www.uniprot.org/uniprot/"}],"text":"(A) Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    GO-BP

    {"project":"GO-BP","denotations":[{"id":"T23858","span":{"begin":807,"end":820},"obj":"http://purl.obolibrary.org/obo/GO_0006351"}],"text":"(A) Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    GO-MF

    {"project":"GO-MF","denotations":[{"id":"T23874","span":{"begin":1073,"end":1089},"obj":"http://purl.obolibrary.org/obo/GO_0051059"},{"id":"T23873","span":{"begin":2098,"end":2105},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23872","span":{"begin":1744,"end":1751},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23871","span":{"begin":1695,"end":1702},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23870","span":{"begin":1586,"end":1593},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23869","span":{"begin":1236,"end":1243},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23868","span":{"begin":1180,"end":1187},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23867","span":{"begin":1073,"end":1080},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23866","span":{"begin":685,"end":692},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23865","span":{"begin":652,"end":659},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23864","span":{"begin":593,"end":600},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23863","span":{"begin":564,"end":571},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23862","span":{"begin":340,"end":347},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23861","span":{"begin":222,"end":229},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T23860","span":{"begin":93,"end":100},"obj":"http://purl.obolibrary.org/obo/GO_0005488"}],"text":"(A) Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    sentences

    {"project":"sentences","denotations":[{"id":"T23771","span":{"begin":2038,"end":2153},"obj":"Sentence"},{"id":"T23770","span":{"begin":1768,"end":2037},"obj":"Sentence"},{"id":"T23769","span":{"begin":1526,"end":1767},"obj":"Sentence"},{"id":"T23768","span":{"begin":1245,"end":1525},"obj":"Sentence"},{"id":"T23767","span":{"begin":1013,"end":1244},"obj":"Sentence"},{"id":"T23766","span":{"begin":699,"end":1012},"obj":"Sentence"},{"id":"T23765","span":{"begin":441,"end":698},"obj":"Sentence"},{"id":"T23764","span":{"begin":212,"end":440},"obj":"Sentence"},{"id":"T23763","span":{"begin":77,"end":211},"obj":"Sentence"},{"id":"T23762","span":{"begin":0,"end":76},"obj":"Sentence"},{"id":"T173","span":{"begin":0,"end":76},"obj":"Sentence"},{"id":"T174","span":{"begin":77,"end":211},"obj":"Sentence"},{"id":"T175","span":{"begin":212,"end":440},"obj":"Sentence"},{"id":"T176","span":{"begin":441,"end":698},"obj":"Sentence"},{"id":"T177","span":{"begin":699,"end":1012},"obj":"Sentence"},{"id":"T178","span":{"begin":1013,"end":1244},"obj":"Sentence"},{"id":"T179","span":{"begin":1245,"end":1525},"obj":"Sentence"},{"id":"T180","span":{"begin":1526,"end":1767},"obj":"Sentence"},{"id":"T181","span":{"begin":1768,"end":2037},"obj":"Sentence"},{"id":"T182","span":{"begin":2038,"end":2153},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"(A) Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    simple1

    {"project":"simple1","denotations":[{"id":"T23940","span":{"begin":1492,"end":1495},"obj":"Protein"},{"id":"T23939","span":{"begin":1488,"end":1491},"obj":"Protein"},{"id":"T23938","span":{"begin":1420,"end":1423},"obj":"Protein"},{"id":"T23937","span":{"begin":1388,"end":1391},"obj":"Protein"},{"id":"T23936","span":{"begin":1361,"end":1364},"obj":"Protein"},{"id":"T23935","span":{"begin":1340,"end":1343},"obj":"Protein"},{"id":"T23934","span":{"begin":1258,"end":1264},"obj":"Protein"},{"id":"T23933","span":{"begin":1232,"end":1235},"obj":"Protein"},{"id":"T23932","span":{"begin":1228,"end":1231},"obj":"Protein"},{"id":"T23931","span":{"begin":1094,"end":1099},"obj":"Protein"},{"id":"T23930","span":{"begin":1049,"end":1056},"obj":"Protein"},{"id":"T23929","span":{"begin":979,"end":984},"obj":"Protein"},{"id":"T23928","span":{"begin":942,"end":945},"obj":"Protein"},{"id":"T23927","span":{"begin":938,"end":941},"obj":"Protein"},{"id":"T23926","span":{"begin":875,"end":878},"obj":"Protein"},{"id":"T23925","span":{"begin":851,"end":854},"obj":"Protein"},{"id":"T23924","span":{"begin":712,"end":718},"obj":"Protein"},{"id":"T23923","span":{"begin":648,"end":651},"obj":"Protein"},{"id":"T23922","span":{"begin":644,"end":647},"obj":"Protein"},{"id":"T23921","span":{"begin":587,"end":592},"obj":"Protein"},{"id":"T23920","span":{"begin":503,"end":506},"obj":"Protein"},{"id":"T23919","span":{"begin":424,"end":427},"obj":"Protein"},{"id":"T23918","span":{"begin":374,"end":377},"obj":"Protein"},{"id":"T23917","span":{"begin":312,"end":315},"obj":"Protein"},{"id":"T23916","span":{"begin":284,"end":287},"obj":"Protein"},{"id":"T23915","span":{"begin":257,"end":260},"obj":"Protein"},{"id":"T23914","span":{"begin":165,"end":168},"obj":"Protein"},{"id":"T23913","span":{"begin":45,"end":48},"obj":"Protein"},{"id":"T23950","span":{"begin":2121,"end":2126},"obj":"Protein"},{"id":"T23949","span":{"begin":2074,"end":2081},"obj":"Protein"},{"id":"T23948","span":{"begin":2004,"end":2009},"obj":"Protein"},{"id":"T23947","span":{"begin":1943,"end":1946},"obj":"Protein"},{"id":"T23946","span":{"begin":1911,"end":1914},"obj":"Protein"},{"id":"T23945","span":{"begin":1884,"end":1887},"obj":"Protein"},{"id":"T23944","span":{"begin":1863,"end":1866},"obj":"Protein"},{"id":"T23943","span":{"begin":1781,"end":1787},"obj":"Protein"},{"id":"T23942","span":{"begin":1738,"end":1743},"obj":"Protein"},{"id":"T23941","span":{"begin":1562,"end":1569},"obj":"Protein"}],"text":"(A) Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    BioNLP16_DUT

    {"project":"BioNLP16_DUT","denotations":[{"id":"T25141","span":{"begin":2082,"end":2090},"obj":"Protein_catabolism"},{"id":"T25140","span":{"begin":2098,"end":2105},"obj":"Binding"},{"id":"T25139","span":{"begin":1729,"end":1737},"obj":"Positive_regulation"},{"id":"T25138","span":{"begin":1744,"end":1751},"obj":"Binding"},{"id":"T25137","span":{"begin":1570,"end":1578},"obj":"Protein_catabolism"},{"id":"T25136","span":{"begin":1206,"end":1215},"obj":"Negative_regulation"},{"id":"T25135","span":{"begin":1236,"end":1243},"obj":"Binding"},{"id":"T25134","span":{"begin":1057,"end":1065},"obj":"Protein_catabolism"},{"id":"T25133","span":{"begin":1073,"end":1080},"obj":"Binding"},{"id":"T25132","span":{"begin":593,"end":600},"obj":"Binding"},{"id":"T25131","span":{"begin":577,"end":586},"obj":"Negative_regulation"},{"id":"T25130","span":{"begin":652,"end":659},"obj":"Binding"},{"id":"T25129","span":{"begin":631,"end":637},"obj":"Regulation"},{"id":"T25128","span":{"begin":2121,"end":2126},"obj":"Protein"},{"id":"T25127","span":{"begin":2074,"end":2081},"obj":"Protein"},{"id":"T25126","span":{"begin":2004,"end":2009},"obj":"Protein"},{"id":"T25125","span":{"begin":1943,"end":1946},"obj":"Protein"},{"id":"T25124","span":{"begin":1911,"end":1914},"obj":"Protein"},{"id":"T25123","span":{"begin":1884,"end":1887},"obj":"Protein"},{"id":"T25122","span":{"begin":1863,"end":1866},"obj":"Protein"},{"id":"T25121","span":{"begin":1781,"end":1787},"obj":"Protein"},{"id":"T25120","span":{"begin":1738,"end":1743},"obj":"Protein"},{"id":"T25119","span":{"begin":1562,"end":1569},"obj":"Protein"},{"id":"T25118","span":{"begin":1492,"end":1495},"obj":"Protein"},{"id":"T25117","span":{"begin":1488,"end":1491},"obj":"Protein"},{"id":"T25116","span":{"begin":1420,"end":1423},"obj":"Protein"},{"id":"T25115","span":{"begin":1388,"end":1391},"obj":"Protein"},{"id":"T25114","span":{"begin":1361,"end":1364},"obj":"Protein"},{"id":"T25113","span":{"begin":1340,"end":1343},"obj":"Protein"},{"id":"T25112","span":{"begin":1258,"end":1264},"obj":"Protein"},{"id":"T25111","span":{"begin":1232,"end":1235},"obj":"Protein"},{"id":"T25110","span":{"begin":1228,"end":1231},"obj":"Protein"},{"id":"T25109","span":{"begin":1094,"end":1099},"obj":"Protein"},{"id":"T25108","span":{"begin":1049,"end":1056},"obj":"Protein"},{"id":"T25107","span":{"begin":979,"end":984},"obj":"Protein"},{"id":"T25106","span":{"begin":942,"end":945},"obj":"Protein"},{"id":"T25105","span":{"begin":938,"end":941},"obj":"Protein"},{"id":"T25104","span":{"begin":875,"end":878},"obj":"Protein"},{"id":"T25103","span":{"begin":851,"end":854},"obj":"Protein"},{"id":"T25102","span":{"begin":712,"end":718},"obj":"Protein"},{"id":"T25101","span":{"begin":587,"end":592},"obj":"Protein"},{"id":"T25100","span":{"begin":648,"end":651},"obj":"Protein"},{"id":"T25099","span":{"begin":644,"end":647},"obj":"Protein"},{"id":"T25098","span":{"begin":503,"end":506},"obj":"Protein"},{"id":"T25097","span":{"begin":424,"end":427},"obj":"Protein"},{"id":"T25096","span":{"begin":374,"end":377},"obj":"Protein"},{"id":"T25095","span":{"begin":312,"end":315},"obj":"Protein"},{"id":"T25094","span":{"begin":284,"end":287},"obj":"Protein"},{"id":"T25093","span":{"begin":257,"end":260},"obj":"Protein"},{"id":"T25092","span":{"begin":165,"end":168},"obj":"Protein"},{"id":"T25091","span":{"begin":45,"end":48},"obj":"Protein"}],"relations":[{"id":"R18417","pred":"themeOf","subj":"T25099","obj":"T25130"},{"id":"R18418","pred":"themeOf","subj":"T25100","obj":"T25129"},{"id":"R18419","pred":"themeOf","subj":"T25100","obj":"T25130"},{"id":"R18420","pred":"themeOf","subj":"T25101","obj":"T25132"},{"id":"R18421","pred":"themeOf","subj":"T25108","obj":"T25134"},{"id":"R18422","pred":"themeOf","subj":"T25109","obj":"T25133"},{"id":"R18423","pred":"themeOf","subj":"T25110","obj":"T25135"},{"id":"R18424","pred":"themeOf","subj":"T25111","obj":"T25135"},{"id":"R18425","pred":"themeOf","subj":"T25119","obj":"T25137"},{"id":"R18426","pred":"themeOf","subj":"T25120","obj":"T25138"},{"id":"R18427","pred":"themeOf","subj":"T25127","obj":"T25141"},{"id":"R18428","pred":"themeOf","subj":"T25128","obj":"T25140"},{"id":"R18429","pred":"themeOf","subj":"T25130","obj":"T25129"},{"id":"R18430","pred":"themeOf","subj":"T25130","obj":"T25129"},{"id":"R18431","pred":"themeOf","subj":"T25132","obj":"T25131"},{"id":"R18432","pred":"themeOf","subj":"T25135","obj":"T25136"},{"id":"R18433","pred":"themeOf","subj":"T25135","obj":"T25136"},{"id":"R18434","pred":"themeOf","subj":"T25138","obj":"T25139"}],"text":"(A) Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    BioNLP16_Messiy

    {"project":"BioNLP16_Messiy","denotations":[{"id":"T24416","span":{"begin":648,"end":651},"obj":"Protein"},{"id":"T24415","span":{"begin":644,"end":647},"obj":"Protein"},{"id":"T24414","span":{"begin":503,"end":506},"obj":"Protein"},{"id":"T24413","span":{"begin":424,"end":427},"obj":"Protein"},{"id":"T24412","span":{"begin":374,"end":377},"obj":"Protein"},{"id":"T24411","span":{"begin":312,"end":315},"obj":"Protein"},{"id":"T24410","span":{"begin":284,"end":287},"obj":"Protein"},{"id":"T24409","span":{"begin":257,"end":260},"obj":"Protein"},{"id":"T24408","span":{"begin":165,"end":168},"obj":"Protein"},{"id":"T24407","span":{"begin":45,"end":48},"obj":"Protein"},{"id":"T24450","span":{"begin":1073,"end":1080},"obj":"Binding"},{"id":"T24449","span":{"begin":1057,"end":1065},"obj":"Protein_catabolism"},{"id":"T24448","span":{"begin":593,"end":600},"obj":"Binding"},{"id":"T24447","span":{"begin":631,"end":637},"obj":"Regulation"},{"id":"T24446","span":{"begin":652,"end":659},"obj":"Binding"},{"id":"T24445","span":{"begin":577,"end":586},"obj":"Negative_regulation"},{"id":"T24444","span":{"begin":2121,"end":2126},"obj":"Protein"},{"id":"T24443","span":{"begin":2074,"end":2081},"obj":"Protein"},{"id":"T24442","span":{"begin":2004,"end":2009},"obj":"Protein"},{"id":"T24441","span":{"begin":1943,"end":1946},"obj":"Protein"},{"id":"T24440","span":{"begin":1911,"end":1914},"obj":"Protein"},{"id":"T24439","span":{"begin":1884,"end":1887},"obj":"Protein"},{"id":"T24438","span":{"begin":1863,"end":1866},"obj":"Protein"},{"id":"T24437","span":{"begin":1781,"end":1787},"obj":"Protein"},{"id":"T24436","span":{"begin":1738,"end":1743},"obj":"Protein"},{"id":"T24435","span":{"begin":1562,"end":1569},"obj":"Protein"},{"id":"T24434","span":{"begin":1492,"end":1495},"obj":"Protein"},{"id":"T24433","span":{"begin":1488,"end":1491},"obj":"Protein"},{"id":"T24432","span":{"begin":1420,"end":1423},"obj":"Protein"},{"id":"T24431","span":{"begin":1388,"end":1391},"obj":"Protein"},{"id":"T24430","span":{"begin":1361,"end":1364},"obj":"Protein"},{"id":"T24429","span":{"begin":1340,"end":1343},"obj":"Protein"},{"id":"T24428","span":{"begin":1258,"end":1264},"obj":"Protein"},{"id":"T24427","span":{"begin":1232,"end":1235},"obj":"Protein"},{"id":"T24426","span":{"begin":1228,"end":1231},"obj":"Protein"},{"id":"T24425","span":{"begin":1094,"end":1099},"obj":"Protein"},{"id":"T24424","span":{"begin":1049,"end":1056},"obj":"Protein"},{"id":"T24423","span":{"begin":979,"end":984},"obj":"Protein"},{"id":"T24422","span":{"begin":942,"end":945},"obj":"Protein"},{"id":"T24421","span":{"begin":938,"end":941},"obj":"Protein"},{"id":"T24420","span":{"begin":875,"end":878},"obj":"Protein"},{"id":"T24419","span":{"begin":851,"end":854},"obj":"Protein"},{"id":"T24418","span":{"begin":712,"end":718},"obj":"Protein"},{"id":"T24417","span":{"begin":587,"end":592},"obj":"Protein"},{"id":"T24500","span":{"begin":2082,"end":2090},"obj":"Binding"},{"id":"T24499","span":{"begin":2098,"end":2105},"obj":"Binding"},{"id":"T24498","span":{"begin":1729,"end":1737},"obj":"Positive_regulation"},{"id":"T24497","span":{"begin":1744,"end":1751},"obj":"Binding"},{"id":"T24496","span":{"begin":1570,"end":1578},"obj":"Protein_catabolism"},{"id":"T24495","span":{"begin":1236,"end":1243},"obj":"Binding"},{"id":"T24494","span":{"begin":1206,"end":1215},"obj":"Negative_regulation"}],"relations":[{"id":"R17947","pred":"themeOf","subj":"T24415","obj":"T24446"},{"id":"R17948","pred":"themeOf","subj":"T24416","obj":"T24446"},{"id":"R17949","pred":"themeOf","subj":"T24417","obj":"T24448"},{"id":"R17950","pred":"themeOf","subj":"T24424","obj":"T24449"},{"id":"R17951","pred":"themeOf","subj":"T24425","obj":"T24450"},{"id":"R17954","pred":"themeOf","subj":"T24435","obj":"T24496"},{"id":"R17955","pred":"themeOf","subj":"T24436","obj":"T24497"},{"id":"R17956","pred":"themeOf","subj":"T24443","obj":"T24500"},{"id":"R17957","pred":"themeOf","subj":"T24444","obj":"T24499"},{"id":"R17958","pred":"themeOf","subj":"T24446","obj":"T24447"},{"id":"R17959","pred":"themeOf","subj":"T24446","obj":"T24447"},{"id":"R17960","pred":"themeOf","subj":"T24448","obj":"T24445"},{"id":"R17972","pred":"themeOf","subj":"T24497","obj":"T24498"},{"id":"R17952","pred":"themeOf","subj":"T24426","obj":"T24495"},{"id":"R17953","pred":"themeOf","subj":"T24427","obj":"T24495"},{"id":"R17970","pred":"themeOf","subj":"T24495","obj":"T24494"},{"id":"R17971","pred":"themeOf","subj":"T24495","obj":"T24494"}],"text":"(A) Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    DLUT931

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NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    bionlp-st-ge-2016-test-ihmc

    {"project":"bionlp-st-ge-2016-test-ihmc","denotations":[{"id":"T25198","span":{"begin":587,"end":600},"obj":"Binding"},{"id":"T25196","span":{"begin":334,"end":385},"obj":"Binding"},{"id":"T25195","span":{"begin":638,"end":697},"obj":"Binding"},{"id":"T25194","span":{"begin":87,"end":115},"obj":"Binding"},{"id":"T25193","span":{"begin":1174,"end":1193},"obj":"Binding"},{"id":"T25192","span":{"begin":1174,"end":1243},"obj":"Negative_regulation"},{"id":"T25191","span":{"begin":1729,"end":1766},"obj":"Positive_regulation"},{"id":"T25190","span":{"begin":551,"end":571},"obj":"Binding"},{"id":"T25189","span":{"begin":1738,"end":1751},"obj":"Binding"},{"id":"T25188","span":{"begin":1216,"end":1243},"obj":"Binding"},{"id":"T25187","span":{"begin":660,"end":697},"obj":"Entity"},{"id":"T25186","span":{"begin":1188,"end":1193},"obj":"Entity"},{"id":"T25185","span":{"begin":979,"end":984},"obj":"Protein"},{"id":"T25184","span":{"begin":1822,"end":1833},"obj":"Entity"},{"id":"T25183","span":{"begin":1299,"end":1310},"obj":"Entity"},{"id":"T25182","span":{"begin":1084,"end":1089},"obj":"Protein"},{"id":"T25181","span":{"begin":712,"end":718},"obj":"Protein"},{"id":"T25180","span":{"begin":638,"end":697},"obj":"Protein"},{"id":"T25179","span":{"begin":1049,"end":1056},"obj":"Protein"},{"id":"T25178","span":{"begin":2109,"end":2126},"obj":"Protein"},{"id":"T25177","span":{"begin":587,"end":592},"obj":"Protein"},{"id":"T25176","span":{"begin":1094,"end":1099},"obj":"Protein"},{"id":"T25175","span":{"begin":334,"end":385},"obj":"Entity"},{"id":"T25174","span":{"begin":1492,"end":1495},"obj":"Protein"},{"id":"T25173","span":{"begin":1232,"end":1235},"obj":"Protein"},{"id":"T25172","span":{"begin":77,"end":82},"obj":"Protein"},{"id":"T25170","span":{"begin":558,"end":563},"obj":"Protein"},{"id":"T25169","span":{"begin":1989,"end":2009},"obj":"Protein"},{"id":"T25168","span":{"begin":1918,"end":1925},"obj":"Protein"},{"id":"T25167","span":{"begin":638,"end":643},"obj":"Protein"},{"id":"T25166","span":{"begin":1228,"end":1235},"obj":"Protein"},{"id":"T25165","span":{"begin":1738,"end":1743},"obj":"Protein"},{"id":"T25164","span":{"begin":1466,"end":1496},"obj":"Protein"},{"id":"T25163","span":{"begin":1395,"end":1402},"obj":"Protein"},{"id":"T25162","span":{"begin":1228,"end":1235},"obj":"Protein"},{"id":"T25161","span":{"begin":572,"end":576},"obj":"Entity"},{"id":"T25160","span":{"begin":942,"end":945},"obj":"Protein"},{"id":"T25159","span":{"begin":87,"end":92},"obj":"Protein"},{"id":"T25158","span":{"begin":1488,"end":1495},"obj":"Protein"},{"id":"T25157","span":{"begin":1174,"end":1193},"obj":"Protein"},{"id":"T25156","span":{"begin":938,"end":945},"obj":"Protein"},{"id":"T25155","span":{"begin":1597,"end":1614},"obj":"Protein"},{"id":"T25154","span":{"begin":294,"end":297},"obj":"Protein"},{"id":"T25153","span":{"begin":938,"end":945},"obj":"Protein"},{"id":"T25152","span":{"begin":1781,"end":1787},"obj":"Protein"},{"id":"T25151","span":{"begin":2074,"end":2081},"obj":"Protein"},{"id":"T25150","span":{"begin":1666,"end":1707},"obj":"Entity"},{"id":"T25149","span":{"begin":1488,"end":1495},"obj":"Protein"},{"id":"T25148","span":{"begin":87,"end":115},"obj":"Entity"},{"id":"T25147","span":{"begin":1562,"end":1569},"obj":"Protein"},{"id":"T25146","span":{"begin":1258,"end":1264},"obj":"Protein"},{"id":"T25145","span":{"begin":266,"end":269},"obj":"Protein"},{"id":"T25144","span":{"begin":916,"end":946},"obj":"Protein"},{"id":"T25142","span":{"begin":212,"end":270},"obj":"Entity"}],"relations":[{"id":"R18436","pred":"causeOf","subj":"T25157","obj":"T25192"},{"id":"R18437","pred":"themeOf","subj":"T25157","obj":"T25193"},{"id":"R18438","pred":"themeOf","subj":"T25162","obj":"T25188"},{"id":"R18439","pred":"themeOf","subj":"T25165","obj":"T25189"},{"id":"R18440","pred":"themeOf","subj":"T25170","obj":"T25190"},{"id":"R18441","pred":"themeOf","subj":"T25175","obj":"T25196"},{"id":"R18442","pred":"themeOf","subj":"T25177","obj":"T25198"},{"id":"R18443","pred":"themeOf","subj":"T25180","obj":"T25195"},{"id":"R18444","pred":"themeOf","subj":"T25188","obj":"T25192"},{"id":"R18445","pred":"themeOf","subj":"T25189","obj":"T25191"}],"text":"(A) Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    bionlp-st-ge-2016-spacy-parsed

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Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    bionlp-st-ge-2016-test-tees

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Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    testone

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NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}

    test3

    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Mutations introduced into a HIV-1Lai/Bal-env infectious molecular clone. NF-κB and NFAT5 binding site mutations were introduced into the LTR of the HIV-1Lai/Bal-env-wild type (WT) infectious molecular clone. The NF-κB binding site mutants (HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, HIV-1Lai/Bal-env-κB I+II-Mut), and NFAT5 binding site mutant (HIV-1Lai/Bal-env-N5-Mut) are shown along with the HIV-1Lai/Bal-env-WT sequence. Mutations were introduced into the 3′ LTR of the HIV-1Lai/Bal-env–WT proviral sequence. (B) Specific mutation of the NFAT5 binding site abolishes NFAT5 binding to the viral LTR but does not affect NF-κB p50/p65 binding to the overlapping NF-κB binding site. Quantitative DNaseI footprinting analysis is shown using HIV-1 LTR fragments (-262 to +4 nt relative to the transcription start site) from HIV-1Lai/Bal-env-WT and HIV-1Lai/Bal-env-N5-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng), or NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of NF-κB and NFAT5 are indicated with a bars. (C) Specific disruption of the HIV-1 subtype B NF-κB binding sites effectively abrogates recombinant p50/p65 binding. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NF-κB (p50/p65) (25 ng, 100 ng, and 500 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NF-κB are indicated with a bars. (D) Specific disruption of the HIV-1 subtype B NF-κB binding site does not inhibit but enhances NFAT5 binding to this region. Quantitative DNaseI footprinting analysis is shown of nucleotides −262 to +4 from HIV-1Lai/Bal-env-WT, HIV-1Lai/Bal-env-κB I-Mut, HIV-1Lai/Bal-env-κB II-Mut, and HIV-1Lai/Bal-env-κB I+II-Mut and increasing concentrations of recombinant NFAT5 (10 ng, 50 ng, and 250 ng). The regions that are protected from DNase I cleavage by the binding of recombinant NFAT5 are indicated with a bars."}