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response of Ndrg1 depends on MTF-1\nNdrg1 was significantly downregulated in microarrays of liver transcripts from cadmium-treated Mtf1Mx-cre mice compared to similarly treated Mtf1loxP control mice (Table 1, c). Ndrg1 probably has some role in stress response since various stimuli, including hypoxia and nickel compounds, activate expression of rodent Ndrg1 and/or its human ortholog (37–40).\nThe Ndrg1 microarray results were confirmed with semiquantitative RT–PCRs (Figure 3a): for Mtf1loxP control livers, a clear increase of Ndrg1 expression was observed after cadmium exposure; in livers from Mtf1Mx-cre mice, this cadmium response was not detectable, while basal expression was similar to controls. This indicates that cadmium-induced expression of Ndrg1 depends on MTF-1.\nFive MRE core consensus sequences are located upstream of the mouse Ndrg1 transcription start (Figure 3b). Four of them are clustered (MRE1 to MRE4, −138 to −332 bp), the fifth one is located farther upstream (MRE5, −883 bp). EMSA was performed to test whether MTF-1 is interacting with some or all of the four proximal MRE sequences (Figure 3c). Separate oligonucleotides were tested for MRE1 and MRE2, whereas one oligonucleotide spanning both sequences was used for MRE3 and MRE4 (MRE3,4). No complex was seen with MRE1, but specific MTF-1 complexes were observed for both the MRE2 and MRE3,4 oligonucleotides with liver protein extract from an Mtf1loxP mouse. As expected, no bandshift was observed with protein extract from a mouse lacking MTF-1 (Mtf1Mx-cre)."}

2_test

{"project":"2_test","denotations":[{"id":"16221973-9605764-77403433","span":{"begin":394,"end":396},"obj":"9605764"},{"id":"16221973-10910041-77403433","span":{"begin":394,"end":396},"obj":"10910041"},{"id":"16221973-11059752-77403433","span":{"begin":394,"end":396},"obj":"11059752"},{"id":"16221973-15341671-77403433","span":{"begin":394,"end":396},"obj":"15341671"}],"text":"Cadmium response of Ndrg1 depends on MTF-1\nNdrg1 was significantly downregulated in microarrays of liver transcripts from cadmium-treated Mtf1Mx-cre mice compared to similarly treated Mtf1loxP control mice (Table 1, c). Ndrg1 probably has some role in stress response since various stimuli, including hypoxia and nickel compounds, activate expression of rodent Ndrg1 and/or its human ortholog (37–40).\nThe Ndrg1 microarray results were confirmed with semiquantitative RT–PCRs (Figure 3a): for Mtf1loxP control livers, a clear increase of Ndrg1 expression was observed after cadmium exposure; in livers from Mtf1Mx-cre mice, this cadmium response was not detectable, while basal expression was similar to controls. This indicates that cadmium-induced expression of Ndrg1 depends on MTF-1.\nFive MRE core consensus sequences are located upstream of the mouse Ndrg1 transcription start (Figure 3b). Four of them are clustered (MRE1 to MRE4, −138 to −332 bp), the fifth one is located farther upstream (MRE5, −883 bp). EMSA was performed to test whether MTF-1 is interacting with some or all of the four proximal MRE sequences (Figure 3c). Separate oligonucleotides were tested for MRE1 and MRE2, whereas one oligonucleotide spanning both sequences was used for MRE3 and MRE4 (MRE3,4). No complex was seen with MRE1, but specific MTF-1 complexes were observed for both the MRE2 and MRE3,4 oligonucleotides with liver protein extract from an Mtf1loxP mouse. As expected, no bandshift was observed with protein extract from a mouse lacking MTF-1 (Mtf1Mx-cre)."}

craft-ca-core-dev

{"project":"craft-ca-core-dev","denotations":[{"id":"T6467","span":{"begin":20,"end":25},"obj":"PR:000011059"},{"id":"T6468","span":{"begin":37,"end":42},"obj":"PR:000010717"},{"id":"T6469","span":{"begin":43,"end":48},"obj":"PR:000011059"},{"id":"T6470","span":{"begin":99,"end":104},"obj":"UBERON:0002107"},{"id":"T6471","span":{"begin":105,"end":116},"obj":"SO:0000673"},{"id":"T6472","span":{"begin":138,"end":142},"obj":"PR:000010717"},{"id":"T6473","span":{"begin":142,"end":144},"obj":"PR:000010788"},{"id":"T6474","span":{"begin":149,"end":153},"obj":"NCBITaxon:10088"},{"id":"T6475","span":{"begin":184,"end":188},"obj":"PR:000010717"},{"id":"T6476","span":{"begin":188,"end":192},"obj":"SO:0000346"},{"id":"T6477","span":{"begin":201,"end":205},"obj":"NCBITaxon:10088"},{"id":"T6478","span":{"begin":220,"end":225},"obj":"PR:000011059"},{"id":"T6479","span":{"begin":320,"end":329},"obj":"CHEBI:36357"},{"id":"T6480","span":{"begin":340,"end":350},"obj":"GO:0010467"},{"id":"T6481","span":{"begin":354,"end":360},"obj":"NCBITaxon:9989"},{"id":"T6482","span":{"begin":361,"end":366},"obj":"PR:000011059"},{"id":"T6483","span":{"begin":378,"end":383},"obj":"NCBITaxon:9606"},{"id":"T6484","span":{"begin":384,"end":392},"obj":"SO:0000855"},{"id":"T6485","span":{"begin":406,"end":411},"obj":"PR:000011059"},{"id":"T6486","span":{"begin":493,"end":497},"obj":"PR:000010717"},{"id":"T6487","span":{"begin":497,"end":501},"obj":"SO:0000346"},{"id":"T6488","span":{"begin":510,"end":516},"obj":"UBERON:0002107"},{"id":"T6489","span":{"begin":538,"end":543},"obj":"PR:000011059"},{"id":"T6490","span":{"begin":544,"end":554},"obj":"GO:0010467"},{"id":"T6491","span":{"begin":595,"end":601},"obj":"UBERON:0002107"},{"id":"T6492","span":{"begin":607,"end":611},"obj":"PR:000010717"},{"id":"T6493","span":{"begin":611,"end":613},"obj":"PR:000010788"},{"id":"T6494","span":{"begin":618,"end":622},"obj":"NCBITaxon:10088"},{"id":"T6495","span":{"begin":678,"end":688},"obj":"GO:0010467"},{"id":"T6496","span":{"begin":750,"end":760},"obj":"GO:0010467"},{"id":"T6497","span":{"begin":764,"end":769},"obj":"PR:000011059"},{"id":"T6498","span":{"begin":781,"end":786},"obj":"PR:000010717"},{"id":"T6499","span":{"begin":802,"end":811},"obj":"SO:0000993"},{"id":"T6500","span":{"begin":850,"end":855},"obj":"NCBITaxon:10088"},{"id":"T6501","span":{"begin":856,"end":861},"obj":"PR:000011059"},{"id":"T6502","span":{"begin":950,"end":952},"obj":"SO:0000028"},{"id":"T6503","span":{"begin":1009,"end":1011},"obj":"SO:0000028"},{"id":"T6504","span":{"begin":1049,"end":1054},"obj":"PR:000010717"},{"id":"T6505","span":{"begin":1284,"end":1291},"obj":"GO:0032991"},{"id":"T6506","span":{"begin":1325,"end":1330},"obj":"PR:000010717"},{"id":"T6507","span":{"begin":1331,"end":1340},"obj":"GO:0032991"},{"id":"T6508","span":{"begin":1406,"end":1411},"obj":"UBERON:0002107"},{"id":"T6509","span":{"begin":1436,"end":1440},"obj":"PR:000010717"},{"id":"T6510","span":{"begin":1440,"end":1444},"obj":"SO:0000346"},{"id":"T6511","span":{"begin":1445,"end":1450},"obj":"NCBITaxon:10088"},{"id":"T6512","span":{"begin":1519,"end":1524},"obj":"NCBITaxon:10088"},{"id":"T6513","span":{"begin":1533,"end":1538},"obj":"PR:000010717"},{"id":"T6514","span":{"begin":1540,"end":1544},"obj":"PR:000010717"},{"id":"T6515","span":{"begin":1544,"end":1546},"obj":"PR:000010788"}],"text":"Cadmium response of Ndrg1 depends on MTF-1\nNdrg1 was significantly downregulated in microarrays of liver transcripts from cadmium-treated Mtf1Mx-cre mice compared to similarly treated Mtf1loxP control mice (Table 1, c). Ndrg1 probably has some role in stress response since various stimuli, including hypoxia and nickel compounds, activate expression of rodent Ndrg1 and/or its human ortholog (37–40).\nThe Ndrg1 microarray results were confirmed with semiquantitative RT–PCRs (Figure 3a): for Mtf1loxP control livers, a clear increase of Ndrg1 expression was observed after cadmium exposure; in livers from Mtf1Mx-cre mice, this cadmium response was not detectable, while basal expression was similar to controls. This indicates that cadmium-induced expression of Ndrg1 depends on MTF-1.\nFive MRE core consensus sequences are located upstream of the mouse Ndrg1 transcription start (Figure 3b). Four of them are clustered (MRE1 to MRE4, −138 to −332 bp), the fifth one is located farther upstream (MRE5, −883 bp). EMSA was performed to test whether MTF-1 is interacting with some or all of the four proximal MRE sequences (Figure 3c). Separate oligonucleotides were tested for MRE1 and MRE2, whereas one oligonucleotide spanning both sequences was used for MRE3 and MRE4 (MRE3,4). No complex was seen with MRE1, but specific MTF-1 complexes were observed for both the MRE2 and MRE3,4 oligonucleotides with liver protein extract from an Mtf1loxP mouse. As expected, no bandshift was observed with protein extract from a mouse lacking MTF-1 (Mtf1Mx-cre)."}

craft-ca-core-ex-dev

{"project":"craft-ca-core-ex-dev","denotations":[{"id":"T6516","span":{"begin":0,"end":7},"obj":"CHEBI_EXT:cadmium"},{"id":"T6517","span":{"begin":8,"end":16},"obj":"GO_EXT:reaction_or_response"},{"id":"T6518","span":{"begin":20,"end":25},"obj":"PR_EXT:000011059"},{"id":"T6519","span":{"begin":37,"end":42},"obj":"PR_EXT:000010717"},{"id":"T6520","span":{"begin":43,"end":48},"obj":"PR_EXT:000011059"},{"id":"T6521","span":{"begin":67,"end":80},"obj":"GO_EXT:negative_regulation"},{"id":"T6522","span":{"begin":99,"end":104},"obj":"UBERON:0002107"},{"id":"T6523","span":{"begin":105,"end":116},"obj":"SO_EXT:0000673"},{"id":"T6524","span":{"begin":122,"end":129},"obj":"CHEBI_EXT:cadmium"},{"id":"T6525","span":{"begin":138,"end":142},"obj":"PR_EXT:000010717"},{"id":"T6526","span":{"begin":142,"end":144},"obj":"PR_EXT:000010788"},{"id":"T6527","span":{"begin":149,"end":153},"obj":"NCBITaxon:10088"},{"id":"T6528","span":{"begin":184,"end":188},"obj":"PR_EXT:000010717"},{"id":"T6529","span":{"begin":188,"end":192},"obj":"SO_EXT:0000346"},{"id":"T6530","span":{"begin":201,"end":205},"obj":"NCBITaxon:10088"},{"id":"T6531","span":{"begin":220,"end":225},"obj":"PR_EXT:000011059"},{"id":"T6532","span":{"begin":259,"end":267},"obj":"GO_EXT:reaction_or_response"},{"id":"T6533","span":{"begin":313,"end":319},"obj":"CHEBI_EXT:nickel"},{"id":"T6534","span":{"begin":320,"end":329},"obj":"CHEBI:36357"},{"id":"T6535","span":{"begin":340,"end":350},"obj":"GO:0010467"},{"id":"T6536","span":{"begin":354,"end":360},"obj":"NCBITaxon:9989"},{"id":"T6537","span":{"begin":361,"end":366},"obj":"PR_EXT:000011059"},{"id":"T6538","span":{"begin":378,"end":383},"obj":"NCBITaxon:9606"},{"id":"T6539","span":{"begin":384,"end":392},"obj":"SO_EXT:0000855"},{"id":"T6540","span":{"begin":406,"end":411},"obj":"PR_EXT:000011059"},{"id":"T6541","span":{"begin":468,"end":470},"obj":"GO_EXT:reverse_transcription_or_reverse_transcriptase"},{"id":"T6542","span":{"begin":493,"end":497},"obj":"PR_EXT:000010717"},{"id":"T6543","span":{"begin":497,"end":501},"obj":"SO_EXT:0000346"},{"id":"T6544","span":{"begin":510,"end":516},"obj":"UBERON:0002107"},{"id":"T6545","span":{"begin":538,"end":543},"obj":"PR_EXT:000011059"},{"id":"T6546","span":{"begin":544,"end":554},"obj":"GO:0010467"},{"id":"T6547","span":{"begin":574,"end":581},"obj":"CHEBI_EXT:cadmium"},{"id":"T6548","span":{"begin":595,"end":601},"obj":"UBERON:0002107"},{"id":"T6549","span":{"begin":607,"end":611},"obj":"PR_EXT:000010717"},{"id":"T6550","span":{"begin":611,"end":613},"obj":"PR_EXT:000010788"},{"id":"T6551","span":{"begin":618,"end":622},"obj":"NCBITaxon:10088"},{"id":"T6552","span":{"begin":629,"end":636},"obj":"CHEBI_EXT:cadmium"},{"id":"T6553","span":{"begin":637,"end":645},"obj":"GO_EXT:reaction_or_response"},{"id":"T6554","span":{"begin":678,"end":688},"obj":"GO:0010467"},{"id":"T6555","span":{"begin":734,"end":741},"obj":"CHEBI_EXT:cadmium"},{"id":"T6556","span":{"begin":750,"end":760},"obj":"GO:0010467"},{"id":"T6557","span":{"begin":764,"end":769},"obj":"PR_EXT:000011059"},{"id":"T6558","span":{"begin":781,"end":786},"obj":"PR_EXT:000010717"},{"id":"T6559","span":{"begin":802,"end":811},"obj":"SO:0000993"},{"id":"T6560","span":{"begin":812,"end":821},"obj":"SO_EXT:biological_sequence"},{"id":"T6561","span":{"begin":834,"end":842},"obj":"SO_EXT:sequence_upstreamness"},{"id":"T6562","span":{"begin":850,"end":855},"obj":"NCBITaxon:10088"},{"id":"T6563","span":{"begin":856,"end":861},"obj":"PR_EXT:000011059"},{"id":"T6564","span":{"begin":862,"end":881},"obj":"GO_SO_EXT:transcriptional_start_entity_or_process"},{"id":"T6565","span":{"begin":950,"end":952},"obj":"SO_EXT:0000028"},{"id":"T6566","span":{"begin":988,"end":996},"obj":"SO_EXT:sequence_upstreamness"},{"id":"T6567","span":{"begin":1009,"end":1011},"obj":"SO_EXT:0000028"},{"id":"T6568","span":{"begin":1049,"end":1054},"obj":"PR_EXT:000010717"},{"id":"T6569","span":{"begin":1112,"end":1121},"obj":"SO_EXT:biological_sequence"},{"id":"T6570","span":{"begin":1144,"end":1160},"obj":"CHEBI_SO_EXT:oligonucleotide"},{"id":"T6571","span":{"begin":1204,"end":1219},"obj":"CHEBI_SO_EXT:oligonucleotide"},{"id":"T6572","span":{"begin":1234,"end":1243},"obj":"SO_EXT:biological_sequence"},{"id":"T6573","span":{"begin":1284,"end":1291},"obj":"GO:0032991"},{"id":"T6574","span":{"begin":1325,"end":1330},"obj":"PR_EXT:000010717"},{"id":"T6575","span":{"begin":1331,"end":1340},"obj":"GO:0032991"},{"id":"T6576","span":{"begin":1384,"end":1400},"obj":"CHEBI_SO_EXT:oligonucleotide"},{"id":"T6577","span":{"begin":1406,"end":1411},"obj":"UBERON:0002107"},{"id":"T6578","span":{"begin":1412,"end":1419},"obj":"CHEBI_PR_EXT:protein"},{"id":"T6579","span":{"begin":1436,"end":1440},"obj":"PR_EXT:000010717"},{"id":"T6580","span":{"begin":1440,"end":1444},"obj":"SO_EXT:0000346"},{"id":"T6581","span":{"begin":1445,"end":1450},"obj":"NCBITaxon:10088"},{"id":"T6582","span":{"begin":1496,"end":1503},"obj":"CHEBI_PR_EXT:protein"},{"id":"T6583","span":{"begin":1519,"end":1524},"obj":"NCBITaxon:10088"},{"id":"T6584","span":{"begin":1533,"end":1538},"obj":"PR_EXT:000010717"},{"id":"T6585","span":{"begin":1540,"end":1544},"obj":"PR_EXT:000010717"},{"id":"T6586","span":{"begin":1544,"end":1546},"obj":"PR_EXT:000010788"}],"text":"Cadmium response of Ndrg1 depends on MTF-1\nNdrg1 was significantly downregulated in microarrays of liver transcripts from cadmium-treated Mtf1Mx-cre mice compared to similarly treated Mtf1loxP control mice (Table 1, c). Ndrg1 probably has some role in stress response since various stimuli, including hypoxia and nickel compounds, activate expression of rodent Ndrg1 and/or its human ortholog (37–40).\nThe Ndrg1 microarray results were confirmed with semiquantitative RT–PCRs (Figure 3a): for Mtf1loxP control livers, a clear increase of Ndrg1 expression was observed after cadmium exposure; in livers from Mtf1Mx-cre mice, this cadmium response was not detectable, while basal expression was similar to controls. This indicates that cadmium-induced expression of Ndrg1 depends on MTF-1.\nFive MRE core consensus sequences are located upstream of the mouse Ndrg1 transcription start (Figure 3b). Four of them are clustered (MRE1 to MRE4, −138 to −332 bp), the fifth one is located farther upstream (MRE5, −883 bp). EMSA was performed to test whether MTF-1 is interacting with some or all of the four proximal MRE sequences (Figure 3c). Separate oligonucleotides were tested for MRE1 and MRE2, whereas one oligonucleotide spanning both sequences was used for MRE3 and MRE4 (MRE3,4). No complex was seen with MRE1, but specific MTF-1 complexes were observed for both the MRE2 and MRE3,4 oligonucleotides with liver protein extract from an Mtf1loxP mouse. As expected, no bandshift was observed with protein extract from a mouse lacking MTF-1 (Mtf1Mx-cre)."}