dde i Search Results


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  • 95
    New England Biolabs dde i
    Tev-mTALEN activity in HEK293T cells on an episomal target. (A) Schematic of the vectors used for co-transfection experiments. For the expression vector, the Tev-mTALEN gene is separated from the mCherry translation reporter by a T2A peptide. (B) Example of Tev-mTALEN expression vector transfection efficiency and expression in HEK293T cells, with bright field image on the left and the epifluorescent image (1-sec exposure) of the same field of view on the right. (C) Schematic of the TP15 target, with a <t>Dde</t> I restriction site and sizes of Dde I digestion products indicated. (D) Agarose gel of a representative assay in which the target region was amplified by <t>PCR</t> from total DNA isolated 48 hr after transfection, and products were digested with Dde I (+) or incubated in buffer without Dde I (−); product resistant to cleavage by Dde I, which would result from mutagenic repair after cleavage by the mTALEN, is labeled with an asterisk (*). (E) Examples of mutations in the target resulting from co-transfection with N169-T120 or D184-V152 Tev-mTALENs. The Dde I-resistant product from (C) was cloned and several clones were sequenced. Dashes indicate the length of deletions observed in individual clones relative to the wild-type sequence.
    Dde I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 246 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher restriction endonuclease dde i
    Tev-mTALEN activity in HEK293T cells on an episomal target. (A) Schematic of the vectors used for co-transfection experiments. For the expression vector, the Tev-mTALEN gene is separated from the mCherry translation reporter by a T2A peptide. (B) Example of Tev-mTALEN expression vector transfection efficiency and expression in HEK293T cells, with bright field image on the left and the epifluorescent image (1-sec exposure) of the same field of view on the right. (C) Schematic of the TP15 target, with a <t>Dde</t> I restriction site and sizes of Dde I digestion products indicated. (D) Agarose gel of a representative assay in which the target region was amplified by <t>PCR</t> from total DNA isolated 48 hr after transfection, and products were digested with Dde I (+) or incubated in buffer without Dde I (−); product resistant to cleavage by Dde I, which would result from mutagenic repair after cleavage by the mTALEN, is labeled with an asterisk (*). (E) Examples of mutations in the target resulting from co-transfection with N169-T120 or D184-V152 Tev-mTALENs. The Dde I-resistant product from (C) was cloned and several clones were sequenced. Dashes indicate the length of deletions observed in individual clones relative to the wild-type sequence.
    Restriction Endonuclease Dde I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Millipore dde i
    <t>DDE</t> activates cell signaling proteins MAPK and VASP in prostate cancer cells. LNCaP ( A ) and LAPC4 ( B ) cells were cultured in the absence of steroid for 24 h, and then either vehicle control (0.1% ethanol), 10 −10 mol/L <t>DHT,</t> or 10 −11 mol/L DDE was added. Following 40 or 120 min, cell lysates were collected and subjected to SDS-PAGE followed by immunoblotting for total ERK1/2, p-ERK1/2, or lamin B (loading control). C. LNCaP and LAPC4 cells were cultured in the absence of steroid for 24 h before treating with either 0.1% ethanol, 10 −10 mol/L DHT, or 10 −11 mol/L DDE. C. Following 10-min incubation, cells were harvested and the cell lysates were subjected to SDS-PAGE for expression analysis of phosphorylated VASP ( p-VASP ) or lamin B (loading control). Isoproterenol ( ISO )-treated lysates were used as positive control for VASP phosphorylation.
    Dde I, supplied by Millipore, used in various techniques. Bioz Stars score: 94/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    TaKaRa dde i
    Schematic representation of primer design for detection of PML-RAR α mRNA by <t>RT-LAMP</t> and cutting sites of <t>Dde</t> I restriction enzyme assay. Exon numbers of the PML gene (dark) and the RAR α gene (light) are shown. PML , promyelocytic leukemia ; RAR α, retinoic acid receptor α; RT-LAMP, reverse transcription loop-mediated isothermal amplification.
    Dde I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Promega dde i
    Diagrams representing restriction patterns of 16S rRNA gene digested with <t>Dde</t> I ( a ), Hha I ( b ) or <t>Rsa</t> I ( c ). First column in each diagram corresponds to the banding pattern for the 1 Kb ladder
    Dde I, supplied by Promega, used in various techniques. Bioz Stars score: 90/100, based on 86 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher dde i
    Fla typing of inoculation strains and strains isolated from infected chicks. The <t>flaA</t> gene was amplified by PCR and digested with either (A) Alu I or (B) Dde I. M, molecular size marker (100-bp DNA ladder); lane 1, Pen-6 inoculation strain; lanes 2 and 3, isolates from chickens colonized with the Pen-6 strain; lane 4, Kl-5133 inoculation strain; lanes 5 and 6, isolates from chickens colonized with the Kl-5133 strain; lane 7, G97-76595 inoculation strain; lanes 8 and 9, isolates from chickens colonized with the G97-76595 strain. Lane numbers refer to the same information in both panels A and B.
    Dde I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 89 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    dde i  (Roche)
    90
    Roche dde i
    Dendrogram based on restriction profiles of <t>fla</t> A gene digested with <t>Dde</t> I of 163 Campylobacter isolates from 5 turkey farms (FI–FV—farm 1–5)
    Dde I, supplied by Roche, used in various techniques. Bioz Stars score: 90/100, based on 59 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Toyobo dde i
    Dendrogram based on restriction profiles of <t>fla</t> A gene digested with <t>Dde</t> I of 163 Campylobacter isolates from 5 turkey farms (FI–FV—farm 1–5)
    Dde I, supplied by Toyobo, used in various techniques. Bioz Stars score: 90/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher dde i restriction enzyme
    Dendrogram based on restriction profiles of <t>fla</t> A gene digested with <t>Dde</t> I of 163 Campylobacter isolates from 5 turkey farms (FI–FV—farm 1–5)
    Dde I Restriction Enzyme, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher dde i c tnag
    Dendrogram based on restriction profiles of <t>fla</t> A gene digested with <t>Dde</t> I of 163 Campylobacter isolates from 5 turkey farms (FI–FV—farm 1–5)
    Dde I C Tnag, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher dde i c↓tnag
    Dendrogram based on restriction profiles of <t>fla</t> A gene digested with <t>Dde</t> I of 163 Campylobacter isolates from 5 turkey farms (FI–FV—farm 1–5)
    Dde I C↓Tnag, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Boehringer Mannheim dde i
    PCR-RFLP profiles generated by digestion of Fusarium histone H3 gene amplification products with <t>Dde</t> I and <t>Cfo</t> I. Electrophoresis were performed on 3% agarose gels at 3 V/cm. Lanes M, 100-bp ladder (1,500, 1,000, 900, 800, 700, 600, 500, 400, 300, 200, and 100 bp); lane A, mating population A; lane B, mating population B ( F. subglutinans associated with sugarcane); lane C, mating population C; lane D, mating population D; lane E, mating population E ( F. subglutinans associated with maize); lane F, mating population F; lane G, mating population G; lane H, F. subglutinans f. sp. pini (mating population H); lane 1, F. subglutinans from maize; lane 2, F. subglutinans from pineapple ( F. subglutinans f. sp. ananas ); lane 3, F. subglutinans from mango.
    Dde I, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 90/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Boehringer Mannheim restriction endonuclease dde i
    (A) 16S <t>PCR-RFLP</t> patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Restriction Endonuclease Dde I, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    GE Healthcare dde i
    (A) 16S <t>PCR-RFLP</t> patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Dde I, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 90/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    TaKaRa dde i enzyme
    (A) 16S <t>PCR-RFLP</t> patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Dde I Enzyme, supplied by TaKaRa, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Promega dde i enzyme
    (A) 16S <t>PCR-RFLP</t> patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Dde I Enzyme, supplied by Promega, used in various techniques. Bioz Stars score: 88/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Promega restriction enzyme dde i
    (A) 16S <t>PCR-RFLP</t> patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Restriction Enzyme Dde I, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Boehringer Mannheim restriction enzymes dde i
    (A) 16S <t>PCR-RFLP</t> patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Restriction Enzymes Dde I, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 80/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs dde i restriction endonuclease
    (A) 16S <t>PCR-RFLP</t> patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Dde I Restriction Endonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Tev-mTALEN activity in HEK293T cells on an episomal target. (A) Schematic of the vectors used for co-transfection experiments. For the expression vector, the Tev-mTALEN gene is separated from the mCherry translation reporter by a T2A peptide. (B) Example of Tev-mTALEN expression vector transfection efficiency and expression in HEK293T cells, with bright field image on the left and the epifluorescent image (1-sec exposure) of the same field of view on the right. (C) Schematic of the TP15 target, with a Dde I restriction site and sizes of Dde I digestion products indicated. (D) Agarose gel of a representative assay in which the target region was amplified by PCR from total DNA isolated 48 hr after transfection, and products were digested with Dde I (+) or incubated in buffer without Dde I (−); product resistant to cleavage by Dde I, which would result from mutagenic repair after cleavage by the mTALEN, is labeled with an asterisk (*). (E) Examples of mutations in the target resulting from co-transfection with N169-T120 or D184-V152 Tev-mTALENs. The Dde I-resistant product from (C) was cloned and several clones were sequenced. Dashes indicate the length of deletions observed in individual clones relative to the wild-type sequence.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: The I-TevI Nuclease and Linker Domains Contribute to the Specificity of Monomeric TALENs

    doi: 10.1534/g3.114.011445

    Figure Lengend Snippet: Tev-mTALEN activity in HEK293T cells on an episomal target. (A) Schematic of the vectors used for co-transfection experiments. For the expression vector, the Tev-mTALEN gene is separated from the mCherry translation reporter by a T2A peptide. (B) Example of Tev-mTALEN expression vector transfection efficiency and expression in HEK293T cells, with bright field image on the left and the epifluorescent image (1-sec exposure) of the same field of view on the right. (C) Schematic of the TP15 target, with a Dde I restriction site and sizes of Dde I digestion products indicated. (D) Agarose gel of a representative assay in which the target region was amplified by PCR from total DNA isolated 48 hr after transfection, and products were digested with Dde I (+) or incubated in buffer without Dde I (−); product resistant to cleavage by Dde I, which would result from mutagenic repair after cleavage by the mTALEN, is labeled with an asterisk (*). (E) Examples of mutations in the target resulting from co-transfection with N169-T120 or D184-V152 Tev-mTALENs. The Dde I-resistant product from (C) was cloned and several clones were sequenced. Dashes indicate the length of deletions observed in individual clones relative to the wild-type sequence.

    Article Snippet: After gel purification, 250 ng of each PCR product was incubated with 2 U of Dde I (N.E.B.) in 1× NEBuffer 2 for 1 hr at 37°.

    Techniques: Activity Assay, Cotransfection, Expressing, Plasmid Preparation, Transfection, Size-exclusion Chromatography, Agarose Gel Electrophoresis, Amplification, Polymerase Chain Reaction, Isolation, Incubation, Labeling, Clone Assay, Sequencing

    DDE activates cell signaling proteins MAPK and VASP in prostate cancer cells. LNCaP ( A ) and LAPC4 ( B ) cells were cultured in the absence of steroid for 24 h, and then either vehicle control (0.1% ethanol), 10 −10 mol/L DHT, or 10 −11 mol/L DDE was added. Following 40 or 120 min, cell lysates were collected and subjected to SDS-PAGE followed by immunoblotting for total ERK1/2, p-ERK1/2, or lamin B (loading control). C. LNCaP and LAPC4 cells were cultured in the absence of steroid for 24 h before treating with either 0.1% ethanol, 10 −10 mol/L DHT, or 10 −11 mol/L DDE. C. Following 10-min incubation, cells were harvested and the cell lysates were subjected to SDS-PAGE for expression analysis of phosphorylated VASP ( p-VASP ) or lamin B (loading control). Isoproterenol ( ISO )-treated lysates were used as positive control for VASP phosphorylation.

    Journal: Molecular cancer research : MCR

    Article Title: 2,2-Bis(4-Chlorophenyl)-1,1-Dichloroethylene Stimulates Androgen Independence in Prostate Cancer Cells through Combinatorial Activation of Mutant Androgen Receptor and Mitogen-Activated Protein Kinase Pathways

    doi: 10.1158/1541-7786.MCR-07-2166

    Figure Lengend Snippet: DDE activates cell signaling proteins MAPK and VASP in prostate cancer cells. LNCaP ( A ) and LAPC4 ( B ) cells were cultured in the absence of steroid for 24 h, and then either vehicle control (0.1% ethanol), 10 −10 mol/L DHT, or 10 −11 mol/L DDE was added. Following 40 or 120 min, cell lysates were collected and subjected to SDS-PAGE followed by immunoblotting for total ERK1/2, p-ERK1/2, or lamin B (loading control). C. LNCaP and LAPC4 cells were cultured in the absence of steroid for 24 h before treating with either 0.1% ethanol, 10 −10 mol/L DHT, or 10 −11 mol/L DDE. C. Following 10-min incubation, cells were harvested and the cell lysates were subjected to SDS-PAGE for expression analysis of phosphorylated VASP ( p-VASP ) or lamin B (loading control). Isoproterenol ( ISO )-treated lysates were used as positive control for VASP phosphorylation.

    Article Snippet: DHT, DDT, DDE, resveratrol, coumestrol, and cadmium were obtained from Sigma-Aldrich.

    Techniques: Cell Culture, SDS Page, Incubation, Expressing, Positive Control

    DDE induces proliferation in AR-T877A – expressing prostate cancer cells. 22Rv1 ( A ) or LNCaP ( B ) cells were cultured in the absence of steroid for 24 h. Then, either vehicle control (0.1% ethanol), 10 −10 mol/L DHT, or increasing doses of DDE (10 −11 , 10 −8 , or 10 −5 mol/L) were added for 24 h. Cells were labeled with BrdUrd for 16 h and BrdUrd incorporation was monitored via indirect immunofluorescence. Dotted line, the level of BrdUrd incorporation in the absence of ligand (vehicle control) for each cell type was set to 1. C. LNCaP cells were cultured in the absence of steroid for 24 h before the addition of ligand [ethanol control, 10 −10 mol/L DHT, or DDE (10 −11 , 10 −8 , or 10 −5 mol/L)] for the indicated times (24, 48, 72, 96, or 120 h) with fresh ligand added every 48 h. At each time point, cells were collected and cell number and viability were determined via trypan blue exclusion. Experiments were repeated with three biological replicates, each analyzed in triplicate. *, P

    Journal: Molecular cancer research : MCR

    Article Title: 2,2-Bis(4-Chlorophenyl)-1,1-Dichloroethylene Stimulates Androgen Independence in Prostate Cancer Cells through Combinatorial Activation of Mutant Androgen Receptor and Mitogen-Activated Protein Kinase Pathways

    doi: 10.1158/1541-7786.MCR-07-2166

    Figure Lengend Snippet: DDE induces proliferation in AR-T877A – expressing prostate cancer cells. 22Rv1 ( A ) or LNCaP ( B ) cells were cultured in the absence of steroid for 24 h. Then, either vehicle control (0.1% ethanol), 10 −10 mol/L DHT, or increasing doses of DDE (10 −11 , 10 −8 , or 10 −5 mol/L) were added for 24 h. Cells were labeled with BrdUrd for 16 h and BrdUrd incorporation was monitored via indirect immunofluorescence. Dotted line, the level of BrdUrd incorporation in the absence of ligand (vehicle control) for each cell type was set to 1. C. LNCaP cells were cultured in the absence of steroid for 24 h before the addition of ligand [ethanol control, 10 −10 mol/L DHT, or DDE (10 −11 , 10 −8 , or 10 −5 mol/L)] for the indicated times (24, 48, 72, 96, or 120 h) with fresh ligand added every 48 h. At each time point, cells were collected and cell number and viability were determined via trypan blue exclusion. Experiments were repeated with three biological replicates, each analyzed in triplicate. *, P

    Article Snippet: DHT, DDT, DDE, resveratrol, coumestrol, and cadmium were obtained from Sigma-Aldrich.

    Techniques: Expressing, Cell Culture, Labeling, Immunofluorescence

    DDE uses MAPK and mutant AR pathways for induction of cell cycle progression in LNCaP cells. LNCaP cells were cultured in the absence of steroid (0.1% DMSO vehicle control; white columns ) or in the presence of 10 −6 mol/L Casodex ( CSDX; black striped columns ), 5 ×10 −6 mol/L Casodex ( black crisscrossed columns ), 10 −6 mol/L MEK inhibitor (U0126; gray columns ), or combined 10 −6 mol/L Casodex and 10 −6 mol/L U0126 ( black columns ). Following 24 h of pretreatment, cells were stimulated with vehicle control (ethanol), 10 −10 mol/L DHT, or 10 −11 mol/L DDE for 24 h and labeled with BrdUrd during the last 16 h of treatment. BrdUrd incorporation for each ligand in the absence of inhibitory challenge was set to 100%. Experiments were done in triplicate. Columns, average; bars, SD. *, P

    Journal: Molecular cancer research : MCR

    Article Title: 2,2-Bis(4-Chlorophenyl)-1,1-Dichloroethylene Stimulates Androgen Independence in Prostate Cancer Cells through Combinatorial Activation of Mutant Androgen Receptor and Mitogen-Activated Protein Kinase Pathways

    doi: 10.1158/1541-7786.MCR-07-2166

    Figure Lengend Snippet: DDE uses MAPK and mutant AR pathways for induction of cell cycle progression in LNCaP cells. LNCaP cells were cultured in the absence of steroid (0.1% DMSO vehicle control; white columns ) or in the presence of 10 −6 mol/L Casodex ( CSDX; black striped columns ), 5 ×10 −6 mol/L Casodex ( black crisscrossed columns ), 10 −6 mol/L MEK inhibitor (U0126; gray columns ), or combined 10 −6 mol/L Casodex and 10 −6 mol/L U0126 ( black columns ). Following 24 h of pretreatment, cells were stimulated with vehicle control (ethanol), 10 −10 mol/L DHT, or 10 −11 mol/L DDE for 24 h and labeled with BrdUrd during the last 16 h of treatment. BrdUrd incorporation for each ligand in the absence of inhibitory challenge was set to 100%. Experiments were done in triplicate. Columns, average; bars, SD. *, P

    Article Snippet: DHT, DDT, DDE, resveratrol, coumestrol, and cadmium were obtained from Sigma-Aldrich.

    Techniques: Mutagenesis, Cell Culture, Labeling

    DDE induces mutant AR transcriptional activity in CV1 cells. CV1 cells were transfected in the absence of androgen with plasmids encoding wtAR or mutant AR (T877A or H874Y), ARR2-luciferase reporter, along with cytomegalovirus-β-galactosidase as an internal transfection control. After transfection, the cells were treated with either ethanol ( EtOH ), DHT, or DDE for 24 h. Cells were harvested using trypsin, lysed using reporter lysis buffer, and analyzed for luciferase activity. The luciferase/β-galactosidase ratio for endogenous ligand DHT was set to 100. Experiments were done with at least three independent replicates. *, P

    Journal: Molecular cancer research : MCR

    Article Title: 2,2-Bis(4-Chlorophenyl)-1,1-Dichloroethylene Stimulates Androgen Independence in Prostate Cancer Cells through Combinatorial Activation of Mutant Androgen Receptor and Mitogen-Activated Protein Kinase Pathways

    doi: 10.1158/1541-7786.MCR-07-2166

    Figure Lengend Snippet: DDE induces mutant AR transcriptional activity in CV1 cells. CV1 cells were transfected in the absence of androgen with plasmids encoding wtAR or mutant AR (T877A or H874Y), ARR2-luciferase reporter, along with cytomegalovirus-β-galactosidase as an internal transfection control. After transfection, the cells were treated with either ethanol ( EtOH ), DHT, or DDE for 24 h. Cells were harvested using trypsin, lysed using reporter lysis buffer, and analyzed for luciferase activity. The luciferase/β-galactosidase ratio for endogenous ligand DHT was set to 100. Experiments were done with at least three independent replicates. *, P

    Article Snippet: DHT, DDT, DDE, resveratrol, coumestrol, and cadmium were obtained from Sigma-Aldrich.

    Techniques: Mutagenesis, Activity Assay, Transfection, Luciferase, Lysis

    Schematic representation of primer design for detection of PML-RAR α mRNA by RT-LAMP and cutting sites of Dde I restriction enzyme assay. Exon numbers of the PML gene (dark) and the RAR α gene (light) are shown. PML , promyelocytic leukemia ; RAR α, retinoic acid receptor α; RT-LAMP, reverse transcription loop-mediated isothermal amplification.

    Journal: Yonago Acta Medica

    Article Title: Development of Reverse Transcription Loop-Mediated Isothermal Amplification for Simple and Rapid Detection of Promyelocytic Leukemia–Retinoic Acid Receptor α mRNA

    doi:

    Figure Lengend Snippet: Schematic representation of primer design for detection of PML-RAR α mRNA by RT-LAMP and cutting sites of Dde I restriction enzyme assay. Exon numbers of the PML gene (dark) and the RAR α gene (light) are shown. PML , promyelocytic leukemia ; RAR α, retinoic acid receptor α; RT-LAMP, reverse transcription loop-mediated isothermal amplification.

    Article Snippet: The specificity of LAMP was confirmed by restriction enzyme digestion using Dde I (Takara Bio, Otsu, Japan) under the following conditions: 5 μL LAMP product was mixed with 2 μL of 10 × K buffer (Takara Bio), 1 μL Dde I, with distilled water added to obtain a final volume of 20 μL, followed by incubation at 37 °C for 120 min. Dde I was inactivated at 70 °C for 15 min and the digestion products (10-μL aliquots) were mixed with loading buffer (Nippon Gene, Toyama, Japan) and separated by 1.5% agarose gel electrophoresis (100 V, 35 min) with 0.005% ethidium bromide using a Mupid mini gel electrophoresis system (Advance, Tokyo, Japan), with 5 μL Gene Ladder 100 (Nippon Gene) used as a molecular size marker.

    Techniques: Enzymatic Assay, Amplification

    Dde I restriction enzyme digestion of RT-LAMP products. Products of bcr1, bcr2, and bcr3 plasmid DNA amplification were incubated with (+) or without (−) Dde I at 37 °C for 120 min, followed by deactivation at 70 °C for 15 min and separation by 1.5% agarose gel electrophoresis (100 V, 35 min). The amounts of bcr1, bcr2 and bcr3 plasmid DNAs were 8.8, 7.8, and 8.0 × 10 6 copies/tube, respectively. The expected sizes of digested RT-LAMP products are the followings: 468 bp, about 234 bp (stem and loop structure) and 83 bp for bcr1; 232 bp, about 116 bp (stem and loop structure) and 83 bp for bcr2; and 139 bp and 121 bp (merged in Figure) for bcr3. DW, distilled water (negative control); M, 100-bp ladder size marker; neg RNA, IVS-0035 RNA (negative control); RT-LAMP, reverse transcription loop-mediated isothermal amplification.

    Journal: Yonago Acta Medica

    Article Title: Development of Reverse Transcription Loop-Mediated Isothermal Amplification for Simple and Rapid Detection of Promyelocytic Leukemia–Retinoic Acid Receptor α mRNA

    doi:

    Figure Lengend Snippet: Dde I restriction enzyme digestion of RT-LAMP products. Products of bcr1, bcr2, and bcr3 plasmid DNA amplification were incubated with (+) or without (−) Dde I at 37 °C for 120 min, followed by deactivation at 70 °C for 15 min and separation by 1.5% agarose gel electrophoresis (100 V, 35 min). The amounts of bcr1, bcr2 and bcr3 plasmid DNAs were 8.8, 7.8, and 8.0 × 10 6 copies/tube, respectively. The expected sizes of digested RT-LAMP products are the followings: 468 bp, about 234 bp (stem and loop structure) and 83 bp for bcr1; 232 bp, about 116 bp (stem and loop structure) and 83 bp for bcr2; and 139 bp and 121 bp (merged in Figure) for bcr3. DW, distilled water (negative control); M, 100-bp ladder size marker; neg RNA, IVS-0035 RNA (negative control); RT-LAMP, reverse transcription loop-mediated isothermal amplification.

    Article Snippet: The specificity of LAMP was confirmed by restriction enzyme digestion using Dde I (Takara Bio, Otsu, Japan) under the following conditions: 5 μL LAMP product was mixed with 2 μL of 10 × K buffer (Takara Bio), 1 μL Dde I, with distilled water added to obtain a final volume of 20 μL, followed by incubation at 37 °C for 120 min. Dde I was inactivated at 70 °C for 15 min and the digestion products (10-μL aliquots) were mixed with loading buffer (Nippon Gene, Toyama, Japan) and separated by 1.5% agarose gel electrophoresis (100 V, 35 min) with 0.005% ethidium bromide using a Mupid mini gel electrophoresis system (Advance, Tokyo, Japan), with 5 μL Gene Ladder 100 (Nippon Gene) used as a molecular size marker.

    Techniques: Plasmid Preparation, Amplification, Incubation, Agarose Gel Electrophoresis, Negative Control, Marker

    Diagrams representing restriction patterns of 16S rRNA gene digested with Dde I ( a ), Hha I ( b ) or Rsa I ( c ). First column in each diagram corresponds to the banding pattern for the 1 Kb ladder

    Journal: Microbial ecology

    Article Title: Characterization of the Bacterial Diversity in Indo-West Pacific Loliginid and Sepiolid Squid Light Organs

    doi: 10.1007/s00248-012-0099-6

    Figure Lengend Snippet: Diagrams representing restriction patterns of 16S rRNA gene digested with Dde I ( a ), Hha I ( b ) or Rsa I ( c ). First column in each diagram corresponds to the banding pattern for the 1 Kb ladder

    Article Snippet: RFLP analysis was completed as described by Urakawa et al. [ , ] using three restriction endonucleases: Rsa I (5′GTAC3′), Hha I (5′GCGC3′) and Dde I (5′CTNAG3′; Promega Corporation, Madison, WI).

    Techniques:

    Fla typing of inoculation strains and strains isolated from infected chicks. The flaA gene was amplified by PCR and digested with either (A) Alu I or (B) Dde I. M, molecular size marker (100-bp DNA ladder); lane 1, Pen-6 inoculation strain; lanes 2 and 3, isolates from chickens colonized with the Pen-6 strain; lane 4, Kl-5133 inoculation strain; lanes 5 and 6, isolates from chickens colonized with the Kl-5133 strain; lane 7, G97-76595 inoculation strain; lanes 8 and 9, isolates from chickens colonized with the G97-76595 strain. Lane numbers refer to the same information in both panels A and B.

    Journal: Applied and Environmental Microbiology

    Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks

    doi: 10.1128/AEM.67.5.2388-2392.2001

    Figure Lengend Snippet: Fla typing of inoculation strains and strains isolated from infected chicks. The flaA gene was amplified by PCR and digested with either (A) Alu I or (B) Dde I. M, molecular size marker (100-bp DNA ladder); lane 1, Pen-6 inoculation strain; lanes 2 and 3, isolates from chickens colonized with the Pen-6 strain; lane 4, Kl-5133 inoculation strain; lanes 5 and 6, isolates from chickens colonized with the Kl-5133 strain; lane 7, G97-76595 inoculation strain; lanes 8 and 9, isolates from chickens colonized with the G97-76595 strain. Lane numbers refer to the same information in both panels A and B.

    Article Snippet: Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker.

    Techniques: Isolation, Infection, Amplification, Polymerase Chain Reaction, Marker

    Dendrogram based on restriction profiles of fla A gene digested with Dde I of 163 Campylobacter isolates from 5 turkey farms (FI–FV—farm 1–5)

    Journal: Gut Pathogens

    Article Title: Prevalence, genotyping and risk factors of thermophilic Campylobacter spreading in organic turkey farms in Germany

    doi: 10.1186/s13099-016-0108-2

    Figure Lengend Snippet: Dendrogram based on restriction profiles of fla A gene digested with Dde I of 163 Campylobacter isolates from 5 turkey farms (FI–FV—farm 1–5)

    Article Snippet: The fla A amplicon was digested for 18 h at 37 °C with Dde I (Roche Diagnostics GmbH).

    Techniques:

    PCR-RFLP profiles generated by digestion of Fusarium histone H3 gene amplification products with Dde I and Cfo I. Electrophoresis were performed on 3% agarose gels at 3 V/cm. Lanes M, 100-bp ladder (1,500, 1,000, 900, 800, 700, 600, 500, 400, 300, 200, and 100 bp); lane A, mating population A; lane B, mating population B ( F. subglutinans associated with sugarcane); lane C, mating population C; lane D, mating population D; lane E, mating population E ( F. subglutinans associated with maize); lane F, mating population F; lane G, mating population G; lane H, F. subglutinans f. sp. pini (mating population H); lane 1, F. subglutinans from maize; lane 2, F. subglutinans from pineapple ( F. subglutinans f. sp. ananas ); lane 3, F. subglutinans from mango.

    Journal: Applied and Environmental Microbiology

    Article Title: Differentiation of Fusarium subglutinans f. sp. pini by Histone Gene Sequence Data

    doi:

    Figure Lengend Snippet: PCR-RFLP profiles generated by digestion of Fusarium histone H3 gene amplification products with Dde I and Cfo I. Electrophoresis were performed on 3% agarose gels at 3 V/cm. Lanes M, 100-bp ladder (1,500, 1,000, 900, 800, 700, 600, 500, 400, 300, 200, and 100 bp); lane A, mating population A; lane B, mating population B ( F. subglutinans associated with sugarcane); lane C, mating population C; lane D, mating population D; lane E, mating population E ( F. subglutinans associated with maize); lane F, mating population F; lane G, mating population G; lane H, F. subglutinans f. sp. pini (mating population H); lane 1, F. subglutinans from maize; lane 2, F. subglutinans from pineapple ( F. subglutinans f. sp. ananas ); lane 3, F. subglutinans from mango.

    Article Snippet: Amplified DNA was digested with two restriction enzymes, Cfo I and Dde I (Boehringer Mannheim South Africa Pty.

    Techniques: Polymerase Chain Reaction, Generated, Amplification, Electrophoresis

    Restriction maps of the histone H3 genes from the different isolates of Fusarium , generated with restriction enzymes Dde I and Cfo I. The Fusarium introns are indicated as boxes, and the exons are indicated as horizontal lines. Bold letters refer to the G. fujikuroi mating populations. An arrow indicates a Cfo I restriction site, and a vertical line indicates a Dde I restriction site. Exon and fragment sizes are indicated in base pairs.

    Journal: Applied and Environmental Microbiology

    Article Title: Differentiation of Fusarium subglutinans f. sp. pini by Histone Gene Sequence Data

    doi:

    Figure Lengend Snippet: Restriction maps of the histone H3 genes from the different isolates of Fusarium , generated with restriction enzymes Dde I and Cfo I. The Fusarium introns are indicated as boxes, and the exons are indicated as horizontal lines. Bold letters refer to the G. fujikuroi mating populations. An arrow indicates a Cfo I restriction site, and a vertical line indicates a Dde I restriction site. Exon and fragment sizes are indicated in base pairs.

    Article Snippet: Amplified DNA was digested with two restriction enzymes, Cfo I and Dde I (Boehringer Mannheim South Africa Pty.

    Techniques: Generated

    (A) 16S PCR-RFLP patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.

    Journal: Journal of Clinical Microbiology

    Article Title: Rapid Identification of Campylobacter, Arcobacter, and Helicobacter Isolates by PCR-Restriction Fragment Length Polymorphism Analysis of the 16S rRNA Gene

    doi:

    Figure Lengend Snippet: (A) 16S PCR-RFLP patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.

    Article Snippet: For restriction endonuclease digestion a 20-μl reaction mixture which included 10 μl of the PCR amplicon with 10 U of the restriction endonuclease Dde I (Boehringer-Mannheim, Indianapolis, Ind.), Taq I (Boehringer-Mannheim), or Bsr I (New England Biolabs, Inc., Beverly, Mass.) was employed, following conditions recommended by the respective manufacturers.

    Techniques: Polymerase Chain Reaction