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  • 99
    Thermo Fisher salmon sperm dna
    Activation of <t>p53</t> by pTpT. Cultures of H1299 cells were transfected with either control vector or the p53 expression vector, treated with pTpT and processed for the electromobility shift assay as described in Materials and Methods . Lane 1, extract from cells transfected with the p53 expression vector. Lane 2, cells were transfected with the p53 expression vector and incubated with 100 μM pTpT. Lane 3, same as lane 2 but the binding reaction contained 0.1 μg mAb421. Lane 4, same as lane 3 but with a 100-fold excess (10 pmol) unlabeled wild-type p53 consensus sequence. Lane 5, same as lane 3 but with a 100-fold express (10 pmol) unlabeled mutant p53 consensus sequence. The consensus sequence <t>DNA/p53</t> complex (C.S. DNA/p53) and the supershifted complex (C.S. DNA/p53/Ab421) are indicated by arrows.
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    Millipore salmon sperm dna
    Myc and Max are associated with the Aurora-A promoter . A. Schematic representation of the potential Myc binding sites of the Aurora-A promoter. B. LS174T cells were treated or not with doxycyclin, soluble chromatin was immunoprecipitated with anti-Myc or anti-acetylated-H3 polyclonal antibodies and <t>DNA</t> samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter. <t>IgG</t> immunoprecipitations were used as controls (n = 3 +/- sd). C. HCT116 were synchronized in G1/S with hydroxyurea and released for the indicated times in growth medium complemented with 3% serum. Soluble chromatin was immunoprecipitated with anti-Myc or anti-Max antibodies and DNA samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter and quantified as compared to IgG immunoprecipitations (n = 3 +/- sd). D, E. The association of Myc and Max on the Aurora-A promoter was analyzed by a serial ChIP experiment. HCT116 were synchronized as described above, the soluble chromatin was immunoprecipitated with Myc antibodies, immune complexes were released and reimmunoprecipitated with IgG or Max antibodies. DNA samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter and analyzed by semi-quantitative PCR (D) or quantitative PCR (E, n = 3 +/- sd).
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    Millipore protein a agarose salmon sperm dna
    Myc and Max are associated with the Aurora-A promoter . A. Schematic representation of the potential Myc binding sites of the Aurora-A promoter. B. LS174T cells were treated or not with doxycyclin, soluble chromatin was immunoprecipitated with anti-Myc or anti-acetylated-H3 polyclonal antibodies and <t>DNA</t> samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter. <t>IgG</t> immunoprecipitations were used as controls (n = 3 +/- sd). C. HCT116 were synchronized in G1/S with hydroxyurea and released for the indicated times in growth medium complemented with 3% serum. Soluble chromatin was immunoprecipitated with anti-Myc or anti-Max antibodies and DNA samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter and quantified as compared to IgG immunoprecipitations (n = 3 +/- sd). D, E. The association of Myc and Max on the Aurora-A promoter was analyzed by a serial ChIP experiment. HCT116 were synchronized as described above, the soluble chromatin was immunoprecipitated with Myc antibodies, immune complexes were released and reimmunoprecipitated with IgG or Max antibodies. DNA samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter and analyzed by semi-quantitative PCR (D) or quantitative PCR (E, n = 3 +/- sd).
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    Stratagene salmon sperm dna
    Extracellular <t>DNA</t> collected from media following H. pylori growth shows degradation. (A) One percent agarose gel containing DNA samples that were isolated from growing cultures of H. pylori in the presence of sonicated salmon sperm DNA in <t>RnP</t> media at
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    ATUM salmon sperm dna
    PMA stimulates nuclear translocation and <t>DNA</t> binding of wild-type p53Val135 in S100B-REF cells. (A) Interaction of wild-type p53 with biotinylated p53-CON target DNA. Clone 6β cell nuclear extracts were prepared, and 35 S-labeled p53 was immunoprecipitated with anti-MyoD immunoglobulin G used as a control (lane 1) or wild-type-specific PAb246 (lane 2). Nuclear extracts were also incubated with <t>streptavidin-agarose</t> and biotinylated p53-CON DNA target in the absence (lane 3) or presence (lane 4) of 20 μg of nonbiotinylated p53-CON DNA used as a specific competitor. (B) PMA stimulates wild-type p53 (PAb246 + ) nuclear translocation. Clone 6β cells were not stimulated (−) or were stimulated with 15 nM PMA for 2, 5, 10, and 15 min as indicated. Wild-type p53 was immunoprecipitated with PAb246. (C) PMA stimulates wild-type p53 binding to biotinylated target DNA. Clone 6β cells were not stimulated (−) or stimulated with 15 nM PMA for 2 or 5 min as indicated. Lanes 1 to 3, nuclear extracts were incubated with biotinylated p53-CON DNA target and streptavidin (Strep.)-agarose. Lanes 4 and 5, nuclear extracts were first incubated with PAb246 and protein G-agarose; the remaining supernatants were then incubated with biotinylated p53-DNA target and streptavidin-agarose. Arrows indicate positions of 35 S-labeled p53 which bound to PAb246 or to a biotinylated DNA probe that was visualized by gel electrophoresis and autoradiography.
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    Thermo Fisher ultrapure salmon sperm dna solution
    PMA stimulates nuclear translocation and <t>DNA</t> binding of wild-type p53Val135 in S100B-REF cells. (A) Interaction of wild-type p53 with biotinylated p53-CON target DNA. Clone 6β cell nuclear extracts were prepared, and 35 S-labeled p53 was immunoprecipitated with anti-MyoD immunoglobulin G used as a control (lane 1) or wild-type-specific PAb246 (lane 2). Nuclear extracts were also incubated with <t>streptavidin-agarose</t> and biotinylated p53-CON DNA target in the absence (lane 3) or presence (lane 4) of 20 μg of nonbiotinylated p53-CON DNA used as a specific competitor. (B) PMA stimulates wild-type p53 (PAb246 + ) nuclear translocation. Clone 6β cells were not stimulated (−) or were stimulated with 15 nM PMA for 2, 5, 10, and 15 min as indicated. Wild-type p53 was immunoprecipitated with PAb246. (C) PMA stimulates wild-type p53 binding to biotinylated target DNA. Clone 6β cells were not stimulated (−) or stimulated with 15 nM PMA for 2 or 5 min as indicated. Lanes 1 to 3, nuclear extracts were incubated with biotinylated p53-CON DNA target and streptavidin (Strep.)-agarose. Lanes 4 and 5, nuclear extracts were first incubated with PAb246 and protein G-agarose; the remaining supernatants were then incubated with biotinylated p53-DNA target and streptavidin-agarose. Arrows indicate positions of 35 S-labeled p53 which bound to PAb246 or to a biotinylated DNA probe that was visualized by gel electrophoresis and autoradiography.
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    99
    Millipore salmon sperm dna protein a agarose
    HP1 loading on chromatin might depend on Sse catalytic activity. ( a , b ) An Sse mutant metaphase stained for <t>DNA</t> (DAPI) ( a ) and HP1 ( b ); the insets show a wild-type metaphase. Scale bar, 5 μm.( c – e ) Polytene chromosomes from wild-type ( c , d ) and Sse dft mutant salivary glands ( e , f ) stained with DAPI and immunostained for HOAP (red) and HP1. It is worth noting that in Sse mutant chromosomes HOAP localizes normally at telomeres, while HP1 localization is strongly reduced. Scale bar, 10 μm. ( g ) Quantification of HP1 intensity from WT and Sse dft mitotic (Mito) and Polytene (Poly) chromosomes. The intensity values, which have been measured with the Image J software, are indicated as arbitrary units. Only polytene chromosomes exhibiting a strong reduction of Hp1 staining have been considered for this analysis. ( h ) Western blot from wild type, Sse , thr and pim RNA-interferred extracts showing that loss of Sse specifically reduces HP1 level; actin is used as a loading control. ( i ) Western blotting of brain extracts from wild type, Sse mutants and Sse mutant expressing a HA-tagged catalytically inactive (C497S) Sse protein. *A nonspecific band. Quantification from three different western blottings of the HP1 levels with respect to tubulin (loading control) shows that the expression of catalytically inactive Sse fails to restore normal HP1 levels. ( j ) HP1 overexpression drastically reduces the TFs frequency in Sse mutants. Error bar indicates s.e.m. ( k ) Frequency (±s.e.m) of TFs in Sse mutant neuroblasts that overexpress Sse C497S .
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    91
    Upstate Biotechnology Inc salmon sperm dna protein a agarose
    HP1 loading on chromatin might depend on Sse catalytic activity. ( a , b ) An Sse mutant metaphase stained for <t>DNA</t> (DAPI) ( a ) and HP1 ( b ); the insets show a wild-type metaphase. Scale bar, 5 μm.( c – e ) Polytene chromosomes from wild-type ( c , d ) and Sse dft mutant salivary glands ( e , f ) stained with DAPI and immunostained for HOAP (red) and HP1. It is worth noting that in Sse mutant chromosomes HOAP localizes normally at telomeres, while HP1 localization is strongly reduced. Scale bar, 10 μm. ( g ) Quantification of HP1 intensity from WT and Sse dft mitotic (Mito) and Polytene (Poly) chromosomes. The intensity values, which have been measured with the Image J software, are indicated as arbitrary units. Only polytene chromosomes exhibiting a strong reduction of Hp1 staining have been considered for this analysis. ( h ) Western blot from wild type, Sse , thr and pim RNA-interferred extracts showing that loss of Sse specifically reduces HP1 level; actin is used as a loading control. ( i ) Western blotting of brain extracts from wild type, Sse mutants and Sse mutant expressing a HA-tagged catalytically inactive (C497S) Sse protein. *A nonspecific band. Quantification from three different western blottings of the HP1 levels with respect to tubulin (loading control) shows that the expression of catalytically inactive Sse fails to restore normal HP1 levels. ( j ) HP1 overexpression drastically reduces the TFs frequency in Sse mutants. Error bar indicates s.e.m. ( k ) Frequency (±s.e.m) of TFs in Sse mutant neuroblasts that overexpress Sse C497S .
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    Upstate Biotechnology Inc salmon sperm dna protein a agarose beads
    Meis2b protein binds the ephA8 regulatory sequence cooperatively as heterodimers with Pbx protein. (A) Nucleotide sequences of the ephA8 regulatory sites used in this study. Core recognition elements for Meis and Pbx are indicated by ^ and *, respectively, above their sequences. (B) Full-length Meis2b binds weakly to 30-bp and 44-bp probes (lanes 2 and 9 from left). Pbx2 protein does not bind the 30-bp probe (lane 4 from left) but does bind very weakly to the 44-bp probe (lane 11 from left). Meis2b and Pbx2 together form a strong cooperative complex with a 44-bp probe (lane 13 from left), but not the 30-bp probe (lane 6 from left). Mock lysate was used to normalize the levels of lysate in the reactions where one of the translated proteins was missing. (C) The binding specificities of proteins in the multimeric <t>DNA</t> complexes were tested using specific antibodies or Meis2e protein as indicated above each lane (+). SS, antibody-protein complexes resulting from supershift analyses.
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    92
    Agilent technologies salmon sperm dna
    HBM mutations do not impact <t>DNA-binding</t> by MYC:MAX complexes. ( A ) Recombinant MYC (WT, 4A, or VP16 HBM):MAX dimers used in these assays. Dimers were separated by <t>SDS-PAGE</t> alongside a BSA standard, and stained using Coomassie Brilliant Blue. ( B ) Electrophoretic mobility shift assay (EMSA) using recombinant MYC:MAX and MAX:MAX dimers incubated with a biotinylated E-box probe (5′-GCTCAGGGACCACGTGGTCGGGGATC-3′). Binding reactions were conducted with or without 100-fold excess of unlabeled specific (as above) or non-specific (5′-GCTCAGGGACCA GC TGGTCGGGGATC-3′) competitors.
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    Santa Cruz Biotechnology salmon sperm dna
    The 4ICD and STAT5A associate in vivo and bind to the endogenous β -casein promoter. (A) 4ICD is associated with STAT5A. COS-7 cells were transfected with the indicated expression plasmids and at 2 d after transfection cells were mock stimulated or stimulated with 50 ng/ml of HRG for 30 min at RT. ERBB4 and STAT5A immunoprecipitates were prepared from cell lysates, resolved by PAGE, and probed for ERBB4 and/or STAT5A by Western blot. White lines indicate that intervening lanes have been spliced out. (B) Schematic of β -casein gene indicating positions of primers for semi-quantitative PCR of distal (−4719/−4276) and proximal (−294/−1) upstream regulatory regions and a promoter region lacking STAT5A GAS binding sites (−923/−590). Gray boxes indicate positions of STAT5A GAS binding sites ( Winklehner-Jennewein et al., 1998 ). (C) Semi-quantitative PCR amplification of <t>DNA</t> bound to ERBB4 and STAT5A isolated by ChIP assay. T47D breast cancer cells were mock stimulated, stimulated with 5 μg/ml of ovine Prl, or stimulated with 50 ng/ml of HRG for 30 min at RT. PFA cross-linked chromatin was immunoprecipitated using control rabbit IgG or antibodies directed against ERBB4 and STAT5A and subjected to 35 cycles of PCR. Input chromatin was prepared from cross-linked and cleared cell lysates using standard DNA precipitation procedures and amplified by PCR as above. PCR amplified samples were resolved on a 2% agarose gel and stained with ethidium bromide.
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    Millipore protein g agarose salmon sperm dna
    The 4ICD and STAT5A associate in vivo and bind to the endogenous β -casein promoter. (A) 4ICD is associated with STAT5A. COS-7 cells were transfected with the indicated expression plasmids and at 2 d after transfection cells were mock stimulated or stimulated with 50 ng/ml of HRG for 30 min at RT. ERBB4 and STAT5A immunoprecipitates were prepared from cell lysates, resolved by PAGE, and probed for ERBB4 and/or STAT5A by Western blot. White lines indicate that intervening lanes have been spliced out. (B) Schematic of β -casein gene indicating positions of primers for semi-quantitative PCR of distal (−4719/−4276) and proximal (−294/−1) upstream regulatory regions and a promoter region lacking STAT5A GAS binding sites (−923/−590). Gray boxes indicate positions of STAT5A GAS binding sites ( Winklehner-Jennewein et al., 1998 ). (C) Semi-quantitative PCR amplification of <t>DNA</t> bound to ERBB4 and STAT5A isolated by ChIP assay. T47D breast cancer cells were mock stimulated, stimulated with 5 μg/ml of ovine Prl, or stimulated with 50 ng/ml of HRG for 30 min at RT. PFA cross-linked chromatin was immunoprecipitated using control rabbit IgG or antibodies directed against ERBB4 and STAT5A and subjected to 35 cycles of PCR. Input chromatin was prepared from cross-linked and cleared cell lysates using standard DNA precipitation procedures and amplified by PCR as above. PCR amplified samples were resolved on a 2% agarose gel and stained with ethidium bromide.
    Protein G Agarose Salmon Sperm Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 136 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eppendorf AG salmon sperm dna
    <t>DNA</t> microarray-based comparative genomics of S . Enteritidis <t>PT13.</t> Array probes represent the linear order of S . Typhimurium LT2 coding sequences from left to right, with the custom Salmonella genomic island 1 (SGI1) at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. Clusters of bacteriophage-related determinants that are divergent in S . Enteritidis compared to S . Typhimurium: A, STM893–929 (Fels-1 prophage); B, STM1005–1024 (Gifsy-2 prophage); C, STM2230–2240 (putative phage); D, STM2589–2636 (Gifsy-1 prophage); E, STM2732–2772 (Fels-2 prophage); F, STM4198–4218 (putative phage).
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    Upstate Biotechnology Inc salmon sperm dna
    <t>DNA</t> microarray-based comparative genomics of S . Enteritidis <t>PT13.</t> Array probes represent the linear order of S . Typhimurium LT2 coding sequences from left to right, with the custom Salmonella genomic island 1 (SGI1) at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. Clusters of bacteriophage-related determinants that are divergent in S . Enteritidis compared to S . Typhimurium: A, STM893–929 (Fels-1 prophage); B, STM1005–1024 (Gifsy-2 prophage); C, STM2230–2240 (putative phage); D, STM2589–2636 (Gifsy-1 prophage); E, STM2732–2772 (Fels-2 prophage); F, STM4198–4218 (putative phage).
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    Santa Cruz Biotechnology salmon sperm dna protein a agarose
    <t>DNA</t> microarray-based comparative genomics of S . Enteritidis <t>PT13.</t> Array probes represent the linear order of S . Typhimurium LT2 coding sequences from left to right, with the custom Salmonella genomic island 1 (SGI1) at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. Clusters of bacteriophage-related determinants that are divergent in S . Enteritidis compared to S . Typhimurium: A, STM893–929 (Fels-1 prophage); B, STM1005–1024 (Gifsy-2 prophage); C, STM2230–2240 (putative phage); D, STM2589–2636 (Gifsy-1 prophage); E, STM2732–2772 (Fels-2 prophage); F, STM4198–4218 (putative phage).
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    Promega salmon sperm dna
    <t>DNA</t> microarray-based comparative genomics of S . Enteritidis <t>PT13.</t> Array probes represent the linear order of S . Typhimurium LT2 coding sequences from left to right, with the custom Salmonella genomic island 1 (SGI1) at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. Clusters of bacteriophage-related determinants that are divergent in S . Enteritidis compared to S . Typhimurium: A, STM893–929 (Fels-1 prophage); B, STM1005–1024 (Gifsy-2 prophage); C, STM2230–2240 (putative phage); D, STM2589–2636 (Gifsy-1 prophage); E, STM2732–2772 (Fels-2 prophage); F, STM4198–4218 (putative phage).
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    Upstate Biotechnology Inc salmon sperm dna protein a agarose slurry
    <t>DNA</t> microarray-based comparative genomics of S . Enteritidis <t>PT13.</t> Array probes represent the linear order of S . Typhimurium LT2 coding sequences from left to right, with the custom Salmonella genomic island 1 (SGI1) at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. Clusters of bacteriophage-related determinants that are divergent in S . Enteritidis compared to S . Typhimurium: A, STM893–929 (Fels-1 prophage); B, STM1005–1024 (Gifsy-2 prophage); C, STM2230–2240 (putative phage); D, STM2589–2636 (Gifsy-1 prophage); E, STM2732–2772 (Fels-2 prophage); F, STM4198–4218 (putative phage).
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    Activation of p53 by pTpT. Cultures of H1299 cells were transfected with either control vector or the p53 expression vector, treated with pTpT and processed for the electromobility shift assay as described in Materials and Methods . Lane 1, extract from cells transfected with the p53 expression vector. Lane 2, cells were transfected with the p53 expression vector and incubated with 100 μM pTpT. Lane 3, same as lane 2 but the binding reaction contained 0.1 μg mAb421. Lane 4, same as lane 3 but with a 100-fold excess (10 pmol) unlabeled wild-type p53 consensus sequence. Lane 5, same as lane 3 but with a 100-fold express (10 pmol) unlabeled mutant p53 consensus sequence. The consensus sequence DNA/p53 complex (C.S. DNA/p53) and the supershifted complex (C.S. DNA/p53/Ab421) are indicated by arrows.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Enhancement of DNA repair in human skin cells by thymidine dinucleotides: Evidence for a p53-mediated mammalian SOS response

    doi:

    Figure Lengend Snippet: Activation of p53 by pTpT. Cultures of H1299 cells were transfected with either control vector or the p53 expression vector, treated with pTpT and processed for the electromobility shift assay as described in Materials and Methods . Lane 1, extract from cells transfected with the p53 expression vector. Lane 2, cells were transfected with the p53 expression vector and incubated with 100 μM pTpT. Lane 3, same as lane 2 but the binding reaction contained 0.1 μg mAb421. Lane 4, same as lane 3 but with a 100-fold excess (10 pmol) unlabeled wild-type p53 consensus sequence. Lane 5, same as lane 3 but with a 100-fold express (10 pmol) unlabeled mutant p53 consensus sequence. The consensus sequence DNA/p53 complex (C.S. DNA/p53) and the supershifted complex (C.S. DNA/p53/Ab421) are indicated by arrows.

    Article Snippet: Basic binding reactions were carried out on ice for 30 min and contained approximately 20 μg of nuclear extract (corrected so that each reaction contained the same amount of p53), 1 μg salmon sperm DNA, and 0.1 pmol 32 P-labeled (GIBCO/BRL 5′ DNA terminus labeling system) wild-type consensus sequence in a final volume of 20 μl.

    Techniques: Activation Assay, Transfection, Plasmid Preparation, Expressing, Electro Mobility Shift Assay, Incubation, Binding Assay, Sequencing, Mutagenesis

    Total nuclease activity, Dnase1 and Dnase1l1-3 expression in kidneys from BALB/c and (NZBxNZW)F1 mice. Pre-proteinuric and proteinuric B/W kidneys were used, the latter divided into 2 groups; one characterized by immune complex deposits in glomerular mesangial matrix only (labeled “Mesangial deposits”), and the other with immune complex deposits in both the mesangial matrix and the capillary membranes (labeled “Capillary deposits”). ( A ) Kidney lysates (black) or sera (grey), in which total protein was measured, and protein content of the samples normalized using BCA assay (Pierce), were applied onto 1% agarose gels containing calf thymus DNA and ethidium bromide in a CaCl 2 - and MgCl 2 - containing buffer, pH 7.6, and incubated in a humidified chamber at 37°C for 24 hours. The gel was photographed under UV illumination. The radius of the non-fluorescent area surrounding each well reflected DNase activity in the sample. DNase activity is expressed as Dnase1 equivalent units, by comparison with human recombinant Dnase1. (B) Total nuclease activity in renal homogenates is shown for native samples, after addition of 5µg/mL monomeric actin and after preheating the samples to 50°C for 10 minutes prior to incubation on the gel, reflecting the results of addition and reversal of actin inhibition, respectively. The group labeled “young” represent 10 and 20 week old B/W, whereas the “Mesangial” and “Capillary” groups reflect proteinuric B/W with immune complex deposits in the mesangium and GBM, respectively. DNase activity is expressed as Dnase1 equivalent units, by comparison with human recombinant Dnase1. In panels C and D the order of samples are kidneys from normal age matched BALB/c (lanes 1–3), pre-nephritic B/W kidneys (lanes 4–6), nephritic B/W kidneys with mesangial matrix deposits only (lanes 7–9), and nephritic B/W kidneys with capillary membrane deposits (lanes 10–12). All kidney samples were analyzed for fold change of renal Dnase1 mRNA levels relative to 4 weeks old BALB/c mice (C), zymography of Dnase1 activity in 10% SDS-polyacrylamide gel of kidney lysates (D, upper part), and western blot of Dnase1 in the same samples (D, lower part). Western blotting to detect actin in the same samples demonstrated that the low Dnase1 band intensity in lanes 10–12 was not due to unequal loading of the samples on the gel. Renal mRNA expression of Dnase1l1 (TaqMan assay Mm00510102_m1), Dnase1l2 (Mm00481868_g1) and Dnase1l3 (Mm00432865_m1) was not decreased in kidneys from proteinuric mice (E).

    Journal: PLoS ONE

    Article Title: Renal Dnase1 Enzyme Activity and Protein Expression Is Selectively Shut Down in Murine and Human Membranoproliferative Lupus Nephritis

    doi: 10.1371/journal.pone.0012096

    Figure Lengend Snippet: Total nuclease activity, Dnase1 and Dnase1l1-3 expression in kidneys from BALB/c and (NZBxNZW)F1 mice. Pre-proteinuric and proteinuric B/W kidneys were used, the latter divided into 2 groups; one characterized by immune complex deposits in glomerular mesangial matrix only (labeled “Mesangial deposits”), and the other with immune complex deposits in both the mesangial matrix and the capillary membranes (labeled “Capillary deposits”). ( A ) Kidney lysates (black) or sera (grey), in which total protein was measured, and protein content of the samples normalized using BCA assay (Pierce), were applied onto 1% agarose gels containing calf thymus DNA and ethidium bromide in a CaCl 2 - and MgCl 2 - containing buffer, pH 7.6, and incubated in a humidified chamber at 37°C for 24 hours. The gel was photographed under UV illumination. The radius of the non-fluorescent area surrounding each well reflected DNase activity in the sample. DNase activity is expressed as Dnase1 equivalent units, by comparison with human recombinant Dnase1. (B) Total nuclease activity in renal homogenates is shown for native samples, after addition of 5µg/mL monomeric actin and after preheating the samples to 50°C for 10 minutes prior to incubation on the gel, reflecting the results of addition and reversal of actin inhibition, respectively. The group labeled “young” represent 10 and 20 week old B/W, whereas the “Mesangial” and “Capillary” groups reflect proteinuric B/W with immune complex deposits in the mesangium and GBM, respectively. DNase activity is expressed as Dnase1 equivalent units, by comparison with human recombinant Dnase1. In panels C and D the order of samples are kidneys from normal age matched BALB/c (lanes 1–3), pre-nephritic B/W kidneys (lanes 4–6), nephritic B/W kidneys with mesangial matrix deposits only (lanes 7–9), and nephritic B/W kidneys with capillary membrane deposits (lanes 10–12). All kidney samples were analyzed for fold change of renal Dnase1 mRNA levels relative to 4 weeks old BALB/c mice (C), zymography of Dnase1 activity in 10% SDS-polyacrylamide gel of kidney lysates (D, upper part), and western blot of Dnase1 in the same samples (D, lower part). Western blotting to detect actin in the same samples demonstrated that the low Dnase1 band intensity in lanes 10–12 was not due to unequal loading of the samples on the gel. Renal mRNA expression of Dnase1l1 (TaqMan assay Mm00510102_m1), Dnase1l2 (Mm00481868_g1) and Dnase1l3 (Mm00432865_m1) was not decreased in kidneys from proteinuric mice (E).

    Article Snippet: DNase zymography DNA degrading activity by Dnase1 was determined after protein separation in a 10% SDS-polyacrylamide gel containing 100µg/ml heat-denatured salmon sperm DNA (Invitrogen Corp., Carlsbad, CA) as described .

    Techniques: Activity Assay, Expressing, Mouse Assay, Labeling, BIA-KA, Incubation, Recombinant, Inhibition, Zymography, Western Blot, TaqMan Assay

    Viral protein requirements for plasmid replication. (A) Conditional lethal ts mutants. BS-C-40 cells were transfected with p716 and 24 h later were mock infected or infected with 3 PFU per cell of wild type VAC (WR) or ts mutant C ts 24, C ts 25, ts 185, or C ts 16 at permissive (31°C) and non-permissive (39.5°C) temperatures for 24 h. DNA was then isolated, digested with Dpn I and quantified by real-time PCR. (B) D4R deletion mutant. RKD4R and RK-13 cells were transfected with p716 and 24 h later were infected with 3 PFU of vD4-ZG. At 24 after infection, DNA was isolated, digested with Dpn I, and the amount of DNA quantified by real-time PCR.

    Journal: Virology Journal

    Article Title: Origin-independent plasmid replication occurs in vaccinia virus cytoplasmic factories and requires all five known poxvirus replication factors

    doi: 10.1186/1743-422X-2-23

    Figure Lengend Snippet: Viral protein requirements for plasmid replication. (A) Conditional lethal ts mutants. BS-C-40 cells were transfected with p716 and 24 h later were mock infected or infected with 3 PFU per cell of wild type VAC (WR) or ts mutant C ts 24, C ts 25, ts 185, or C ts 16 at permissive (31°C) and non-permissive (39.5°C) temperatures for 24 h. DNA was then isolated, digested with Dpn I and quantified by real-time PCR. (B) D4R deletion mutant. RKD4R and RK-13 cells were transfected with p716 and 24 h later were infected with 3 PFU of vD4-ZG. At 24 after infection, DNA was isolated, digested with Dpn I, and the amount of DNA quantified by real-time PCR.

    Article Snippet: Transfection, infection and isolation of DNA For experiments analyzed by real-time PCR, 0.1 μg of p716 DNA and 3.9 μg of salmon sperm carrier DNA were mixed with 10 μg of lipofectamine 2000 (Invitrogen) and uninfected cells were transfected according to the manufacturer's instructions.

    Techniques: Plasmid Preparation, Transfection, Infection, Mutagenesis, Isolation, Real-time Polymerase Chain Reaction

    Replication of transfected DNA in VAC-infected cells. (A) Southern blot of replicated circular plasmid and linear minichromosome. B-SC-1 cells were infected with VAC and 1 h later transfected with equal molar amounts (20 fmol) of super coiled pUC13 (sc pUC), pUC13 linearized by digestion with EcoR I (lin pUC), linear minichromosome containing pUC13 and 1.3 kbp viral telomeric sequences (lin mc). As a control, cells were mock infected and transfected with 20 fmol of linear minichromosome or 10 times that amount (200 fmol) of super coiled pUC13. At 24 h after infection or mock infection, cells were collected and total DNA extracted. Total DNA (2 μg) was digested with Dpn I subjected to agarose gel electrophoresis and analyzed by Southern blot hybridization using a 32 P-labeled pUC13 probe. Samples (0.5 fmol of lin pUC, 0.5 fmol of lin mc, 1 fmol sc pUC) of the DNA used for transfections (input DNA) were also analyzed. The positions of marker DNA (kbp) are shown on the left. (B) Real-time PCR of replicated plasmid. BS-C-1 cells were transfected with the plasmid p716 at 24 h prior to infection with VAC. At indicated hours post infection (hpi), cells were harvested and total DNA extracted. DNA was untreated or treated with Dpn I or Mbo I and analyzed by real-time PCR using primers specific to plasmid DNA. (C) Quantification of Southern blot. DNA described in panel (B) was digested with EcoR I prior to Mbo I or Dpn I treatment. The digested DNA samples were subjected to gel electrophoresis, transferred to a Nylon membrane, hybridized to a 32 P-labeled p716 probe, and the radioactivity quantified with a phosphoImager.

    Journal: Virology Journal

    Article Title: Origin-independent plasmid replication occurs in vaccinia virus cytoplasmic factories and requires all five known poxvirus replication factors

    doi: 10.1186/1743-422X-2-23

    Figure Lengend Snippet: Replication of transfected DNA in VAC-infected cells. (A) Southern blot of replicated circular plasmid and linear minichromosome. B-SC-1 cells were infected with VAC and 1 h later transfected with equal molar amounts (20 fmol) of super coiled pUC13 (sc pUC), pUC13 linearized by digestion with EcoR I (lin pUC), linear minichromosome containing pUC13 and 1.3 kbp viral telomeric sequences (lin mc). As a control, cells were mock infected and transfected with 20 fmol of linear minichromosome or 10 times that amount (200 fmol) of super coiled pUC13. At 24 h after infection or mock infection, cells were collected and total DNA extracted. Total DNA (2 μg) was digested with Dpn I subjected to agarose gel electrophoresis and analyzed by Southern blot hybridization using a 32 P-labeled pUC13 probe. Samples (0.5 fmol of lin pUC, 0.5 fmol of lin mc, 1 fmol sc pUC) of the DNA used for transfections (input DNA) were also analyzed. The positions of marker DNA (kbp) are shown on the left. (B) Real-time PCR of replicated plasmid. BS-C-1 cells were transfected with the plasmid p716 at 24 h prior to infection with VAC. At indicated hours post infection (hpi), cells were harvested and total DNA extracted. DNA was untreated or treated with Dpn I or Mbo I and analyzed by real-time PCR using primers specific to plasmid DNA. (C) Quantification of Southern blot. DNA described in panel (B) was digested with EcoR I prior to Mbo I or Dpn I treatment. The digested DNA samples were subjected to gel electrophoresis, transferred to a Nylon membrane, hybridized to a 32 P-labeled p716 probe, and the radioactivity quantified with a phosphoImager.

    Article Snippet: Transfection, infection and isolation of DNA For experiments analyzed by real-time PCR, 0.1 μg of p716 DNA and 3.9 μg of salmon sperm carrier DNA were mixed with 10 μg of lipofectamine 2000 (Invitrogen) and uninfected cells were transfected according to the manufacturer's instructions.

    Techniques: Transfection, Infection, Southern Blot, Plasmid Preparation, Agarose Gel Electrophoresis, Hybridization, Labeling, Marker, Real-time Polymerase Chain Reaction, Nucleic Acid Electrophoresis, Radioactivity

    Myc and Max are associated with the Aurora-A promoter . A. Schematic representation of the potential Myc binding sites of the Aurora-A promoter. B. LS174T cells were treated or not with doxycyclin, soluble chromatin was immunoprecipitated with anti-Myc or anti-acetylated-H3 polyclonal antibodies and DNA samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter. IgG immunoprecipitations were used as controls (n = 3 +/- sd). C. HCT116 were synchronized in G1/S with hydroxyurea and released for the indicated times in growth medium complemented with 3% serum. Soluble chromatin was immunoprecipitated with anti-Myc or anti-Max antibodies and DNA samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter and quantified as compared to IgG immunoprecipitations (n = 3 +/- sd). D, E. The association of Myc and Max on the Aurora-A promoter was analyzed by a serial ChIP experiment. HCT116 were synchronized as described above, the soluble chromatin was immunoprecipitated with Myc antibodies, immune complexes were released and reimmunoprecipitated with IgG or Max antibodies. DNA samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter and analyzed by semi-quantitative PCR (D) or quantitative PCR (E, n = 3 +/- sd).

    Journal: Molecular Cancer

    Article Title: Regulation of the Aurora-A gene following topoisomerase I inhibition: implication of the Myc transcription Factor

    doi: 10.1186/1476-4598-9-205

    Figure Lengend Snippet: Myc and Max are associated with the Aurora-A promoter . A. Schematic representation of the potential Myc binding sites of the Aurora-A promoter. B. LS174T cells were treated or not with doxycyclin, soluble chromatin was immunoprecipitated with anti-Myc or anti-acetylated-H3 polyclonal antibodies and DNA samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter. IgG immunoprecipitations were used as controls (n = 3 +/- sd). C. HCT116 were synchronized in G1/S with hydroxyurea and released for the indicated times in growth medium complemented with 3% serum. Soluble chromatin was immunoprecipitated with anti-Myc or anti-Max antibodies and DNA samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter and quantified as compared to IgG immunoprecipitations (n = 3 +/- sd). D, E. The association of Myc and Max on the Aurora-A promoter was analyzed by a serial ChIP experiment. HCT116 were synchronized as described above, the soluble chromatin was immunoprecipitated with Myc antibodies, immune complexes were released and reimmunoprecipitated with IgG or Max antibodies. DNA samples were then amplified using primers that cover the -668/-400 region of the Aurora-A promoter and analyzed by semi-quantitative PCR (D) or quantitative PCR (E, n = 3 +/- sd).

    Article Snippet: Immunoprecipitation was performed overnight with specific antibodies and IgG control, and then 2 μg of sheared salmon-sperm DNA and 20 μl of proteinG-agarose coated with salmon sperm DNA (Millipore) (of 50% slurry) were further added for 1 h at 4°C.

    Techniques: Binding Assay, Immunoprecipitation, Amplification, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

    Extracellular DNA collected from media following H. pylori growth shows degradation. (A) One percent agarose gel containing DNA samples that were isolated from growing cultures of H. pylori in the presence of sonicated salmon sperm DNA in RnP media at

    Journal: Journal of Bacteriology

    Article Title: Helicobacter pylori Salvages Purines from Extracellular Host Cell DNA Utilizing the Outer Membrane-Associated Nuclease NucT

    doi: 10.1128/JB.00388-13

    Figure Lengend Snippet: Extracellular DNA collected from media following H. pylori growth shows degradation. (A) One percent agarose gel containing DNA samples that were isolated from growing cultures of H. pylori in the presence of sonicated salmon sperm DNA in RnP media at

    Article Snippet: When the salmon sperm DNA was reisolated from RnP cultures used to grow each H. pylori strain after 24 and 120 h, both the wild-type and complemented strains appeared to have degraded the DNA completely by 120 h ( , WT and comp), while DNA reisolated from the cultures containing either no bacteria (sterile) or the Δ nucT mutant appeared far less degraded ( , N/A and Δ nucT ).

    Techniques: Agarose Gel Electrophoresis, Isolation, Sonication

    H. pylori grows more rapidly in conditioned RnP media containing sonicated salmon sperm DNA. OD 600 measurements for growth assays of wild-type H. pylori strain G27 over 5 days. H. pylori was placed in RnP media containing nonsonicated salmon sperm DNA

    Journal: Journal of Bacteriology

    Article Title: Helicobacter pylori Salvages Purines from Extracellular Host Cell DNA Utilizing the Outer Membrane-Associated Nuclease NucT

    doi: 10.1128/JB.00388-13

    Figure Lengend Snippet: H. pylori grows more rapidly in conditioned RnP media containing sonicated salmon sperm DNA. OD 600 measurements for growth assays of wild-type H. pylori strain G27 over 5 days. H. pylori was placed in RnP media containing nonsonicated salmon sperm DNA

    Article Snippet: When the salmon sperm DNA was reisolated from RnP cultures used to grow each H. pylori strain after 24 and 120 h, both the wild-type and complemented strains appeared to have degraded the DNA completely by 120 h ( , WT and comp), while DNA reisolated from the cultures containing either no bacteria (sterile) or the Δ nucT mutant appeared far less degraded ( , N/A and Δ nucT ).

    Techniques: Sonication

    H. pylori can grow using DNA as its sole purine source in RnP media. OD 600 measurements (A) and CFU counts (B) for growth assays of wild-type H. pylori strain G27 in RnP media (minus purines) containing increasing concentrations of sonicated salmon sperm

    Journal: Journal of Bacteriology

    Article Title: Helicobacter pylori Salvages Purines from Extracellular Host Cell DNA Utilizing the Outer Membrane-Associated Nuclease NucT

    doi: 10.1128/JB.00388-13

    Figure Lengend Snippet: H. pylori can grow using DNA as its sole purine source in RnP media. OD 600 measurements (A) and CFU counts (B) for growth assays of wild-type H. pylori strain G27 in RnP media (minus purines) containing increasing concentrations of sonicated salmon sperm

    Article Snippet: When the salmon sperm DNA was reisolated from RnP cultures used to grow each H. pylori strain after 24 and 120 h, both the wild-type and complemented strains appeared to have degraded the DNA completely by 120 h ( , WT and comp), while DNA reisolated from the cultures containing either no bacteria (sterile) or the Δ nucT mutant appeared far less degraded ( , N/A and Δ nucT ).

    Techniques: Sonication

    A deletion mutant for the external nuclease NucT exhibits growth defects when grown in RnP media with DNA as the sole purine source available. (A) OD 600 measurements indicating the growth of various H. pylori strains in RnP media supplemented with sonicated

    Journal: Journal of Bacteriology

    Article Title: Helicobacter pylori Salvages Purines from Extracellular Host Cell DNA Utilizing the Outer Membrane-Associated Nuclease NucT

    doi: 10.1128/JB.00388-13

    Figure Lengend Snippet: A deletion mutant for the external nuclease NucT exhibits growth defects when grown in RnP media with DNA as the sole purine source available. (A) OD 600 measurements indicating the growth of various H. pylori strains in RnP media supplemented with sonicated

    Article Snippet: When the salmon sperm DNA was reisolated from RnP cultures used to grow each H. pylori strain after 24 and 120 h, both the wild-type and complemented strains appeared to have degraded the DNA completely by 120 h ( , WT and comp), while DNA reisolated from the cultures containing either no bacteria (sterile) or the Δ nucT mutant appeared far less degraded ( , N/A and Δ nucT ).

    Techniques: Mutagenesis, Sonication

    PMA stimulates nuclear translocation and DNA binding of wild-type p53Val135 in S100B-REF cells. (A) Interaction of wild-type p53 with biotinylated p53-CON target DNA. Clone 6β cell nuclear extracts were prepared, and 35 S-labeled p53 was immunoprecipitated with anti-MyoD immunoglobulin G used as a control (lane 1) or wild-type-specific PAb246 (lane 2). Nuclear extracts were also incubated with streptavidin-agarose and biotinylated p53-CON DNA target in the absence (lane 3) or presence (lane 4) of 20 μg of nonbiotinylated p53-CON DNA used as a specific competitor. (B) PMA stimulates wild-type p53 (PAb246 + ) nuclear translocation. Clone 6β cells were not stimulated (−) or were stimulated with 15 nM PMA for 2, 5, 10, and 15 min as indicated. Wild-type p53 was immunoprecipitated with PAb246. (C) PMA stimulates wild-type p53 binding to biotinylated target DNA. Clone 6β cells were not stimulated (−) or stimulated with 15 nM PMA for 2 or 5 min as indicated. Lanes 1 to 3, nuclear extracts were incubated with biotinylated p53-CON DNA target and streptavidin (Strep.)-agarose. Lanes 4 and 5, nuclear extracts were first incubated with PAb246 and protein G-agarose; the remaining supernatants were then incubated with biotinylated p53-DNA target and streptavidin-agarose. Arrows indicate positions of 35 S-labeled p53 which bound to PAb246 or to a biotinylated DNA probe that was visualized by gel electrophoresis and autoradiography.

    Journal: Molecular and Cellular Biology

    Article Title: Concerted Regulation of Wild-Type p53 Nuclear Accumulation and Activation by S100B and Calcium-Dependent Protein Kinase C

    doi:

    Figure Lengend Snippet: PMA stimulates nuclear translocation and DNA binding of wild-type p53Val135 in S100B-REF cells. (A) Interaction of wild-type p53 with biotinylated p53-CON target DNA. Clone 6β cell nuclear extracts were prepared, and 35 S-labeled p53 was immunoprecipitated with anti-MyoD immunoglobulin G used as a control (lane 1) or wild-type-specific PAb246 (lane 2). Nuclear extracts were also incubated with streptavidin-agarose and biotinylated p53-CON DNA target in the absence (lane 3) or presence (lane 4) of 20 μg of nonbiotinylated p53-CON DNA used as a specific competitor. (B) PMA stimulates wild-type p53 (PAb246 + ) nuclear translocation. Clone 6β cells were not stimulated (−) or were stimulated with 15 nM PMA for 2, 5, 10, and 15 min as indicated. Wild-type p53 was immunoprecipitated with PAb246. (C) PMA stimulates wild-type p53 binding to biotinylated target DNA. Clone 6β cells were not stimulated (−) or stimulated with 15 nM PMA for 2 or 5 min as indicated. Lanes 1 to 3, nuclear extracts were incubated with biotinylated p53-CON DNA target and streptavidin (Strep.)-agarose. Lanes 4 and 5, nuclear extracts were first incubated with PAb246 and protein G-agarose; the remaining supernatants were then incubated with biotinylated p53-DNA target and streptavidin-agarose. Arrows indicate positions of 35 S-labeled p53 which bound to PAb246 or to a biotinylated DNA probe that was visualized by gel electrophoresis and autoradiography.

    Article Snippet: Nuclear extracts were incubated for 30 min with biotin-DNA probe (0.6 μg/ml), salmon sperm DNA (20 μg/ml), and streptavidin-agarose.

    Techniques: Translocation Assay, Binding Assay, Labeling, Immunoprecipitation, Incubation, Nucleic Acid Electrophoresis, Autoradiography

    HP1 loading on chromatin might depend on Sse catalytic activity. ( a , b ) An Sse mutant metaphase stained for DNA (DAPI) ( a ) and HP1 ( b ); the insets show a wild-type metaphase. Scale bar, 5 μm.( c – e ) Polytene chromosomes from wild-type ( c , d ) and Sse dft mutant salivary glands ( e , f ) stained with DAPI and immunostained for HOAP (red) and HP1. It is worth noting that in Sse mutant chromosomes HOAP localizes normally at telomeres, while HP1 localization is strongly reduced. Scale bar, 10 μm. ( g ) Quantification of HP1 intensity from WT and Sse dft mitotic (Mito) and Polytene (Poly) chromosomes. The intensity values, which have been measured with the Image J software, are indicated as arbitrary units. Only polytene chromosomes exhibiting a strong reduction of Hp1 staining have been considered for this analysis. ( h ) Western blot from wild type, Sse , thr and pim RNA-interferred extracts showing that loss of Sse specifically reduces HP1 level; actin is used as a loading control. ( i ) Western blotting of brain extracts from wild type, Sse mutants and Sse mutant expressing a HA-tagged catalytically inactive (C497S) Sse protein. *A nonspecific band. Quantification from three different western blottings of the HP1 levels with respect to tubulin (loading control) shows that the expression of catalytically inactive Sse fails to restore normal HP1 levels. ( j ) HP1 overexpression drastically reduces the TFs frequency in Sse mutants. Error bar indicates s.e.m. ( k ) Frequency (±s.e.m) of TFs in Sse mutant neuroblasts that overexpress Sse C497S .

    Journal: Nature Communications

    Article Title: A role for Separase in telomere protection

    doi: 10.1038/ncomms10405

    Figure Lengend Snippet: HP1 loading on chromatin might depend on Sse catalytic activity. ( a , b ) An Sse mutant metaphase stained for DNA (DAPI) ( a ) and HP1 ( b ); the insets show a wild-type metaphase. Scale bar, 5 μm.( c – e ) Polytene chromosomes from wild-type ( c , d ) and Sse dft mutant salivary glands ( e , f ) stained with DAPI and immunostained for HOAP (red) and HP1. It is worth noting that in Sse mutant chromosomes HOAP localizes normally at telomeres, while HP1 localization is strongly reduced. Scale bar, 10 μm. ( g ) Quantification of HP1 intensity from WT and Sse dft mitotic (Mito) and Polytene (Poly) chromosomes. The intensity values, which have been measured with the Image J software, are indicated as arbitrary units. Only polytene chromosomes exhibiting a strong reduction of Hp1 staining have been considered for this analysis. ( h ) Western blot from wild type, Sse , thr and pim RNA-interferred extracts showing that loss of Sse specifically reduces HP1 level; actin is used as a loading control. ( i ) Western blotting of brain extracts from wild type, Sse mutants and Sse mutant expressing a HA-tagged catalytically inactive (C497S) Sse protein. *A nonspecific band. Quantification from three different western blottings of the HP1 levels with respect to tubulin (loading control) shows that the expression of catalytically inactive Sse fails to restore normal HP1 levels. ( j ) HP1 overexpression drastically reduces the TFs frequency in Sse mutants. Error bar indicates s.e.m. ( k ) Frequency (±s.e.m) of TFs in Sse mutant neuroblasts that overexpress Sse C497S .

    Article Snippet: Chromatin was diluted 1:10 with 1.1% Triton X-100, 2 mM EDTA, 150 mM NaCl and 20 mM Tris-HCl pH 8.0 and precleared with a 50% salmon sperm DNA/protein A agarose slurry (Millipore).

    Techniques: Activity Assay, Mutagenesis, Staining, Software, Western Blot, Expressing, Over Expression

    Capture of DNA fragments from higher eukaryotes at fission yeast DSBs. (A) Frequency of ura4 + molecules with inserted DNA after transformation of exponentially growing wild-type (PN559), rhp51 Δ (PN2490), rad50 Δ (KT120), lig4 Δ

    Journal: Genetics

    Article Title: Capture of Extranuclear DNA at Fission Yeast Double-Strand Breaks

    doi: 10.1534/genetics.105.046144

    Figure Lengend Snippet: Capture of DNA fragments from higher eukaryotes at fission yeast DSBs. (A) Frequency of ura4 + molecules with inserted DNA after transformation of exponentially growing wild-type (PN559), rhp51 Δ (PN2490), rad50 Δ (KT120), lig4 Δ

    Article Snippet: For cotransformation experiments with salmon or human genomic DNA, cells were transformed with 2 μg ura4 + DNA and 50 μg of either sheared salmon sperm DNA (Sigma, St. Louis), or human genomic DNA extracted from 293 human embryonic kidney cells (QIAamp kit, QIAGEN, Chatsworth, CA).

    Techniques: Transformation Assay

    A new extrachromosomal DSB repair assay in S. pombe. (A) A 1747-bp PCR-amplified DNA fragment containing the S. pombe ura4 + gene was used as substrate to monitor EC DSB repair in fission yeast. Circularization of ura4 + DNA occurred with

    Journal: Genetics

    Article Title: Capture of Extranuclear DNA at Fission Yeast Double-Strand Breaks

    doi: 10.1534/genetics.105.046144

    Figure Lengend Snippet: A new extrachromosomal DSB repair assay in S. pombe. (A) A 1747-bp PCR-amplified DNA fragment containing the S. pombe ura4 + gene was used as substrate to monitor EC DSB repair in fission yeast. Circularization of ura4 + DNA occurred with

    Article Snippet: For cotransformation experiments with salmon or human genomic DNA, cells were transformed with 2 μg ura4 + DNA and 50 μg of either sheared salmon sperm DNA (Sigma, St. Louis), or human genomic DNA extracted from 293 human embryonic kidney cells (QIAamp kit, QIAGEN, Chatsworth, CA).

    Techniques: Polymerase Chain Reaction, Amplification

    MMEJ-mediated intermolecular ligation in NHEJ-deficient cells. (A) Exponentially growing cells were cotransformed with ura4 + DNA and hDNA flanked by either microhomologous (8 bp) or homologous (205 and 401 bp) sequences to 5′- and 3′-ends

    Journal: Genetics

    Article Title: Capture of Extranuclear DNA at Fission Yeast Double-Strand Breaks

    doi: 10.1534/genetics.105.046144

    Figure Lengend Snippet: MMEJ-mediated intermolecular ligation in NHEJ-deficient cells. (A) Exponentially growing cells were cotransformed with ura4 + DNA and hDNA flanked by either microhomologous (8 bp) or homologous (205 and 401 bp) sequences to 5′- and 3′-ends

    Article Snippet: For cotransformation experiments with salmon or human genomic DNA, cells were transformed with 2 μg ura4 + DNA and 50 μg of either sheared salmon sperm DNA (Sigma, St. Louis), or human genomic DNA extracted from 293 human embryonic kidney cells (QIAamp kit, QIAGEN, Chatsworth, CA).

    Techniques: Ligation, Non-Homologous End Joining

    Meis2b protein binds the ephA8 regulatory sequence cooperatively as heterodimers with Pbx protein. (A) Nucleotide sequences of the ephA8 regulatory sites used in this study. Core recognition elements for Meis and Pbx are indicated by ^ and *, respectively, above their sequences. (B) Full-length Meis2b binds weakly to 30-bp and 44-bp probes (lanes 2 and 9 from left). Pbx2 protein does not bind the 30-bp probe (lane 4 from left) but does bind very weakly to the 44-bp probe (lane 11 from left). Meis2b and Pbx2 together form a strong cooperative complex with a 44-bp probe (lane 13 from left), but not the 30-bp probe (lane 6 from left). Mock lysate was used to normalize the levels of lysate in the reactions where one of the translated proteins was missing. (C) The binding specificities of proteins in the multimeric DNA complexes were tested using specific antibodies or Meis2e protein as indicated above each lane (+). SS, antibody-protein complexes resulting from supershift analyses.

    Journal: Molecular and Cellular Biology

    Article Title: Regulation of EphA8 Gene Expression by TALE Homeobox Transcription Factors during Development of the Mesencephalon ▿

    doi: 10.1128/MCB.01429-06

    Figure Lengend Snippet: Meis2b protein binds the ephA8 regulatory sequence cooperatively as heterodimers with Pbx protein. (A) Nucleotide sequences of the ephA8 regulatory sites used in this study. Core recognition elements for Meis and Pbx are indicated by ^ and *, respectively, above their sequences. (B) Full-length Meis2b binds weakly to 30-bp and 44-bp probes (lanes 2 and 9 from left). Pbx2 protein does not bind the 30-bp probe (lane 4 from left) but does bind very weakly to the 44-bp probe (lane 11 from left). Meis2b and Pbx2 together form a strong cooperative complex with a 44-bp probe (lane 13 from left), but not the 30-bp probe (lane 6 from left). Mock lysate was used to normalize the levels of lysate in the reactions where one of the translated proteins was missing. (C) The binding specificities of proteins in the multimeric DNA complexes were tested using specific antibodies or Meis2e protein as indicated above each lane (+). SS, antibody-protein complexes resulting from supershift analyses.

    Article Snippet: The lysates were diluted 10-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, and 167 mM NaCl) and precleared with salmon sperm DNA-protein A-agarose beads (Upstate Biotechnology) at 4°C for 1 h. Following incubation with 1 μg of anti-Meis, anti-Pbx2, or anti-Pbx antibodies overnight, immune complexes were immobilized with salmon sperm DNA-protein A-agarose beads for 1 h at 4°C.

    Techniques: Sequencing, Binding Assay

    HBM mutations do not impact DNA-binding by MYC:MAX complexes. ( A ) Recombinant MYC (WT, 4A, or VP16 HBM):MAX dimers used in these assays. Dimers were separated by SDS-PAGE alongside a BSA standard, and stained using Coomassie Brilliant Blue. ( B ) Electrophoretic mobility shift assay (EMSA) using recombinant MYC:MAX and MAX:MAX dimers incubated with a biotinylated E-box probe (5′-GCTCAGGGACCACGTGGTCGGGGATC-3′). Binding reactions were conducted with or without 100-fold excess of unlabeled specific (as above) or non-specific (5′-GCTCAGGGACCA GC TGGTCGGGGATC-3′) competitors.

    Journal: bioRxiv

    Article Title: MYC regulates ribosome biogenesis and mitochondrial gene expression programs through interaction with Host Cell Factor-1

    doi: 10.1101/2020.06.22.164764

    Figure Lengend Snippet: HBM mutations do not impact DNA-binding by MYC:MAX complexes. ( A ) Recombinant MYC (WT, 4A, or VP16 HBM):MAX dimers used in these assays. Dimers were separated by SDS-PAGE alongside a BSA standard, and stained using Coomassie Brilliant Blue. ( B ) Electrophoretic mobility shift assay (EMSA) using recombinant MYC:MAX and MAX:MAX dimers incubated with a biotinylated E-box probe (5′-GCTCAGGGACCACGTGGTCGGGGATC-3′). Binding reactions were conducted with or without 100-fold excess of unlabeled specific (as above) or non-specific (5′-GCTCAGGGACCA GC TGGTCGGGGATC-3′) competitors.

    Article Snippet: The membrane was incubated overnight at 42°C with probe in hybridization buffer (50% formamide, 5X SSCPE, 5X Denhardt’s solution (Invitrogen 750018), 0.1 mg/ml salmon sperm DNA (Agilent 201190), 1% SDS, 10% Dextran solution).

    Techniques: Binding Assay, Recombinant, SDS Page, Staining, Electrophoretic Mobility Shift Assay, Incubation

    The 4ICD and STAT5A associate in vivo and bind to the endogenous β -casein promoter. (A) 4ICD is associated with STAT5A. COS-7 cells were transfected with the indicated expression plasmids and at 2 d after transfection cells were mock stimulated or stimulated with 50 ng/ml of HRG for 30 min at RT. ERBB4 and STAT5A immunoprecipitates were prepared from cell lysates, resolved by PAGE, and probed for ERBB4 and/or STAT5A by Western blot. White lines indicate that intervening lanes have been spliced out. (B) Schematic of β -casein gene indicating positions of primers for semi-quantitative PCR of distal (−4719/−4276) and proximal (−294/−1) upstream regulatory regions and a promoter region lacking STAT5A GAS binding sites (−923/−590). Gray boxes indicate positions of STAT5A GAS binding sites ( Winklehner-Jennewein et al., 1998 ). (C) Semi-quantitative PCR amplification of DNA bound to ERBB4 and STAT5A isolated by ChIP assay. T47D breast cancer cells were mock stimulated, stimulated with 5 μg/ml of ovine Prl, or stimulated with 50 ng/ml of HRG for 30 min at RT. PFA cross-linked chromatin was immunoprecipitated using control rabbit IgG or antibodies directed against ERBB4 and STAT5A and subjected to 35 cycles of PCR. Input chromatin was prepared from cross-linked and cleared cell lysates using standard DNA precipitation procedures and amplified by PCR as above. PCR amplified samples were resolved on a 2% agarose gel and stained with ethidium bromide.

    Journal: The Journal of Cell Biology

    Article Title: The ERBB4/HER4 receptor tyrosine kinase regulates gene expression by functioning as a STAT5A nuclear chaperone

    doi: 10.1083/jcb.200403155

    Figure Lengend Snippet: The 4ICD and STAT5A associate in vivo and bind to the endogenous β -casein promoter. (A) 4ICD is associated with STAT5A. COS-7 cells were transfected with the indicated expression plasmids and at 2 d after transfection cells were mock stimulated or stimulated with 50 ng/ml of HRG for 30 min at RT. ERBB4 and STAT5A immunoprecipitates were prepared from cell lysates, resolved by PAGE, and probed for ERBB4 and/or STAT5A by Western blot. White lines indicate that intervening lanes have been spliced out. (B) Schematic of β -casein gene indicating positions of primers for semi-quantitative PCR of distal (−4719/−4276) and proximal (−294/−1) upstream regulatory regions and a promoter region lacking STAT5A GAS binding sites (−923/−590). Gray boxes indicate positions of STAT5A GAS binding sites ( Winklehner-Jennewein et al., 1998 ). (C) Semi-quantitative PCR amplification of DNA bound to ERBB4 and STAT5A isolated by ChIP assay. T47D breast cancer cells were mock stimulated, stimulated with 5 μg/ml of ovine Prl, or stimulated with 50 ng/ml of HRG for 30 min at RT. PFA cross-linked chromatin was immunoprecipitated using control rabbit IgG or antibodies directed against ERBB4 and STAT5A and subjected to 35 cycles of PCR. Input chromatin was prepared from cross-linked and cleared cell lysates using standard DNA precipitation procedures and amplified by PCR as above. PCR amplified samples were resolved on a 2% agarose gel and stained with ethidium bromide.

    Article Snippet: The lysate was precleared by incubating for 2 h at 4°C with 100 μl of protein A Sepharose (Amersham Biosciences), 10 μg/ml of salmon sperm DNA, and 10 μg of rabbit IgG (Santa Cruz Biotechnology, Inc.).

    Techniques: In Vivo, Transfection, Expressing, Polyacrylamide Gel Electrophoresis, Western Blot, Real-time Polymerase Chain Reaction, Binding Assay, Amplification, Isolation, Chromatin Immunoprecipitation, Immunoprecipitation, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Staining

    DNA microarray-based comparative genomics of S . Enteritidis PT13. Array probes represent the linear order of S . Typhimurium LT2 coding sequences from left to right, with the custom Salmonella genomic island 1 (SGI1) at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. Clusters of bacteriophage-related determinants that are divergent in S . Enteritidis compared to S . Typhimurium: A, STM893–929 (Fels-1 prophage); B, STM1005–1024 (Gifsy-2 prophage); C, STM2230–2240 (putative phage); D, STM2589–2636 (Gifsy-1 prophage); E, STM2732–2772 (Fels-2 prophage); F, STM4198–4218 (putative phage).

    Journal: BMC Microbiology

    Article Title: Limited genetic diversity in Salmonella enterica Serovar Enteritidis PT13

    doi: 10.1186/1471-2180-7-87

    Figure Lengend Snippet: DNA microarray-based comparative genomics of S . Enteritidis PT13. Array probes represent the linear order of S . Typhimurium LT2 coding sequences from left to right, with the custom Salmonella genomic island 1 (SGI1) at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. Clusters of bacteriophage-related determinants that are divergent in S . Enteritidis compared to S . Typhimurium: A, STM893–929 (Fels-1 prophage); B, STM1005–1024 (Gifsy-2 prophage); C, STM2230–2240 (putative phage); D, STM2589–2636 (Gifsy-1 prophage); E, STM2732–2772 (Fels-2 prophage); F, STM4198–4218 (putative phage).

    Article Snippet: Typhimurium LT2) was combined with a Cy3 or Cy5-labeled test PT13 strain along with 20 μg of Salmon Sperm DNA and dried in a Vacufuge (Eppendorf).

    Techniques: Microarray

    Plasmid profiles for S . Enteritidis strains used in this study. Preparations were not digested with restriction endonuclease. Lanes 1–7: S . Enteritidis PT13 strains 04-6191, 04-6387, 04-7505, 05-6746, 05-0513, 05-1219 and 05-6733 respectively. Lanes 8 and 9: S . Enteritidis PT1 strains 06-1230 and 06-1751. Lanes 10 and 11: S . Enteritidis PT4 strains 06-1216 and 06-1231. Lane 12: plasmid extracted from S . Typhimurium LT2. Supercoiled DNA ladder molecular weights are to the left of lane 1. Arrow indicates a chromosomal DNA fragment.

    Journal: BMC Microbiology

    Article Title: Limited genetic diversity in Salmonella enterica Serovar Enteritidis PT13

    doi: 10.1186/1471-2180-7-87

    Figure Lengend Snippet: Plasmid profiles for S . Enteritidis strains used in this study. Preparations were not digested with restriction endonuclease. Lanes 1–7: S . Enteritidis PT13 strains 04-6191, 04-6387, 04-7505, 05-6746, 05-0513, 05-1219 and 05-6733 respectively. Lanes 8 and 9: S . Enteritidis PT1 strains 06-1230 and 06-1751. Lanes 10 and 11: S . Enteritidis PT4 strains 06-1216 and 06-1231. Lane 12: plasmid extracted from S . Typhimurium LT2. Supercoiled DNA ladder molecular weights are to the left of lane 1. Arrow indicates a chromosomal DNA fragment.

    Article Snippet: Typhimurium LT2) was combined with a Cy3 or Cy5-labeled test PT13 strain along with 20 μg of Salmon Sperm DNA and dried in a Vacufuge (Eppendorf).

    Techniques: Plasmid Preparation