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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    95
    Millipore dde
    <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, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa 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 TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Promega dde i
    The restriction enzyme analysis on a predicted multiple infection O. tsutsugamushi strain. The DNA pattern on O. tsutsugamushi strain no. 37 undigested PCR product (1) and products after digestion with <t>Dde</t> I enzyme (2). M represents a 100 bp-DNA ladder marker.
    Dde I, supplied by Promega, used in various techniques. Bioz Stars score: 94/100, based on 86 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    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: 99/100, based on 89 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    dde i  (Roche)
    94
    Roche dde i
    Agarose gel electrophoresis of fla A typing products of Vietnamese Campylobacter isolates digested with <t>Dde</t> I (M—100 bp DNA ladder)
    Dde I, supplied by Roche, used in various techniques. Bioz Stars score: 94/100, based on 59 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Toyobo dde i
    Agarose gel electrophoresis of fla A typing products of Vietnamese Campylobacter isolates digested with <t>Dde</t> I (M—100 bp DNA ladder)
    Dde I, supplied by Toyobo, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    76
    Thermo Fisher dde i restriction enzyme
    Agarose gel electrophoresis of fla A typing products of Vietnamese Campylobacter isolates digested with <t>Dde</t> I (M—100 bp DNA ladder)
    Dde I Restriction Enzyme, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 76/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher dde i c↓tnag
    Agarose gel electrophoresis of fla A typing products of Vietnamese Campylobacter isolates digested with <t>Dde</t> I (M—100 bp DNA ladder)
    Dde I C↓Tnag, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher dde i c tnag
    Agarose gel electrophoresis of fla A typing products of Vietnamese Campylobacter isolates digested with <t>Dde</t> I (M—100 bp DNA ladder)
    Dde I C Tnag, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    75
    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: 75/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Thermo Fisher 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 Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    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: 78/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    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: 99/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    New England Biolabs restriction enzyme dde i
    Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one <t>Dde</t> I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .
    Restriction Enzyme Dde I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 27 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Promega restriction enzyme dde i
    Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one <t>Dde</t> I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .
    Restriction Enzyme Dde I, supplied by Promega, used in various techniques. Bioz Stars score: 79/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    New England Biolabs dde i restriction endonuclease
    Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one <t>Dde</t> I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .
    Dde I Restriction Endonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 80/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    Boehringer Mannheim restriction enzymes dde i
    Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one <t>Dde</t> I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .
    Restriction Enzymes Dde I, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 84/100, based on 8 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

    The restriction enzyme analysis on a predicted multiple infection O. tsutsugamushi strain. The DNA pattern on O. tsutsugamushi strain no. 37 undigested PCR product (1) and products after digestion with Dde I enzyme (2). M represents a 100 bp-DNA ladder marker.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: High Rates of Homologous Recombination in the Mite Endosymbiont and Opportunistic Human Pathogen Orientia tsutsugamushi

    doi: 10.1371/journal.pntd.0000752

    Figure Lengend Snippet: The restriction enzyme analysis on a predicted multiple infection O. tsutsugamushi strain. The DNA pattern on O. tsutsugamushi strain no. 37 undigested PCR product (1) and products after digestion with Dde I enzyme (2). M represents a 100 bp-DNA ladder marker.

    Article Snippet: PCR products of locus gpsA from 2 strains (no. 37 and 70) were digested with Dde I (Promega, USA) and Nco I (NEB, England) respectively, as recommended by the manufacturer.

    Techniques: Infection, Polymerase Chain Reaction, Marker

    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

    Agarose gel electrophoresis of fla A typing products of Vietnamese Campylobacter isolates digested with Dde I (M—100 bp DNA ladder)

    Journal: Gut Pathogens

    Article Title: Genotyping and antibiotic resistance of thermophilic Campylobacter isolated from chicken and pig meat in Vietnam

    doi: 10.1186/s13099-016-0100-x

    Figure Lengend Snippet: Agarose gel electrophoresis of fla A typing products of Vietnamese Campylobacter isolates digested with Dde I (M—100 bp DNA ladder)

    Article Snippet: The approximately 1700 bp amplicons were digested with Dde I (Roche Diagnostics GmbH) as recommended by the manufacturer.

    Techniques: Agarose Gel Electrophoresis

    (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

    Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one Dde I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .

    Journal: PLoS ONE

    Article Title: Impact of the Mitochondrial Genetic Background in Complex III Deficiency

    doi: 10.1371/journal.pone.0012801

    Figure Lengend Snippet: Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one Dde I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .

    Article Snippet: To quantify the heteroplasmy levels of the m.15533 A > G mutation, PCR-restriction fragment length polymorphism (RFLP) analysis was performed in the proband's family using the following primers: 5′-CACTATTCTCACCAGACCTC-3′ , (forward) and 5′-ACGCCTCCTAGTTTGTTAGG-3′ (reverse), and digestion with the restriction enzyme Dde I (New England Biolabs).

    Techniques: Mutagenesis, Polymerase Chain Reaction, Sequencing, Software