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  • 99
    New England Biolabs apali
    Probing of H-NS-DNA complexes with restriction endonucleases and DNase I footprinting. In A , B , and C , the left panels show agarose gels with digests; the right panels show the change of the relative intensity of specific restriction bands (indicated with black dotted rectangles on the left panel ) in each digestion reaction. Shown is probing with <t>BamHI-HindIII</t> ( A ), BamHI-EcoRI ( B ), and <t>ApaLI</t> ( C ). When the restriction sites are inside the inserted fragment (HindIII or EcoRI sites inside the UPPU, PUUP, or UPUP DNA) the highest protection rate is observed for the UPPU construct (steepest decay of band intensity). When the restriction sites are in the plasmid backbone (ApaLI restriction sites), the highest protection is observed for the PUUP construct and the weakest for UPPU DNA. D , DNase I footprinting of supercoiled UPPU and PUUP constructs at different H-NS concentrations (0–150 n m ). H-NS binding sites 1 and 2 are indicated on the sequencing gel image ( left panel ) by black vertical lines . H-NS induced hypersensitivity ( Position 1 ) and protection in H-NS binding site 2 ( Position 2 ) in UPPU (marked by dotted rectangles ). The graphs on the right show the relative intensity of the Position 1 and Position 2 signals at various H-NS concentrations.
    Apali, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 153 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 153 article reviews
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    92
    Thermo Fisher apali
    Amplification of isd . (A) Schematic diagram of the recombination event (RE) leading to the different numbers of fragments labelled in the Southern blot experiment. <t>ApaLI</t> restriction sites are indicated by vertical arrows. The binding site of the DIG-labelled probe is indicated by the black dash. Predicted sizes of the fragments recognized by the probe are indicated. (B) Results of the Southern blot. Chromosomal <t>DNA</t> of HKU:: tetK strains ( ΔrecA ) with different tetracycline resistance levels were digested with ApaLI and separated by electrophoresis. The DNA fragments were subsequently denatured, blotted onto a nylon membrane and hybridized with the DIG-labelled probe. Hybridization was detected using anti-DIG-Fab fragments conjugated to alkaline phosphatase. Y1, X1, W1, W2 and Z1 designate strains with different colony sizes on 8 μg/ml Tc. (C) qPCR experiment to determine the isd copy number. Known concentrations of N920143 DNA (one copy of isd ) were used to create the standard curves for isdJ and ori . Relative amounts of template ori and isdJ for each strain (all ΔrecA ) were measured. The value for ori was set to 1 and the template amount of isdJ was expressed in relation to this value, thereby giving the copy number of isdJ in the chromosome of each strain. The mean and SD of three experiments is shown.
    Apali, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 39 article reviews
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    85
    TaKaRa restriction enzyme apali
    Amplification of isd . (A) Schematic diagram of the recombination event (RE) leading to the different numbers of fragments labelled in the Southern blot experiment. <t>ApaLI</t> restriction sites are indicated by vertical arrows. The binding site of the DIG-labelled probe is indicated by the black dash. Predicted sizes of the fragments recognized by the probe are indicated. (B) Results of the Southern blot. Chromosomal <t>DNA</t> of HKU:: tetK strains ( ΔrecA ) with different tetracycline resistance levels were digested with ApaLI and separated by electrophoresis. The DNA fragments were subsequently denatured, blotted onto a nylon membrane and hybridized with the DIG-labelled probe. Hybridization was detected using anti-DIG-Fab fragments conjugated to alkaline phosphatase. Y1, X1, W1, W2 and Z1 designate strains with different colony sizes on 8 μg/ml Tc. (C) qPCR experiment to determine the isd copy number. Known concentrations of N920143 DNA (one copy of isd ) were used to create the standard curves for isdJ and ori . Relative amounts of template ori and isdJ for each strain (all ΔrecA ) were measured. The value for ori was set to 1 and the template amount of isdJ was expressed in relation to this value, thereby giving the copy number of isdJ in the chromosome of each strain. The mean and SD of three experiments is shown.
    Restriction Enzyme Apali, supplied by TaKaRa, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 85 stars, based on 7 article reviews
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    99
    TaKaRa apali
    ( A ) Pulsed field gels of S1 digested genomic DNA and Southern blot in gel hybridization with probe mcr-1 . ( B ) <t>ApaLI</t> restriction digestion profiles of mcr-1 -carrying plasmids of the three <t>transconjugants.</t>
    Apali, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 34 article reviews
    Price from $9.99 to $1999.99
    apali - by Bioz Stars, 2020-04
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    Image Search Results


    Probing of H-NS-DNA complexes with restriction endonucleases and DNase I footprinting. In A , B , and C , the left panels show agarose gels with digests; the right panels show the change of the relative intensity of specific restriction bands (indicated with black dotted rectangles on the left panel ) in each digestion reaction. Shown is probing with BamHI-HindIII ( A ), BamHI-EcoRI ( B ), and ApaLI ( C ). When the restriction sites are inside the inserted fragment (HindIII or EcoRI sites inside the UPPU, PUUP, or UPUP DNA) the highest protection rate is observed for the UPPU construct (steepest decay of band intensity). When the restriction sites are in the plasmid backbone (ApaLI restriction sites), the highest protection is observed for the PUUP construct and the weakest for UPPU DNA. D , DNase I footprinting of supercoiled UPPU and PUUP constructs at different H-NS concentrations (0–150 n m ). H-NS binding sites 1 and 2 are indicated on the sequencing gel image ( left panel ) by black vertical lines . H-NS induced hypersensitivity ( Position 1 ) and protection in H-NS binding site 2 ( Position 2 ) in UPPU (marked by dotted rectangles ). The graphs on the right show the relative intensity of the Position 1 and Position 2 signals at various H-NS concentrations.

    Journal: The Journal of Biological Chemistry

    Article Title: Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein

    doi: 10.1074/jbc.M117.780239

    Figure Lengend Snippet: Probing of H-NS-DNA complexes with restriction endonucleases and DNase I footprinting. In A , B , and C , the left panels show agarose gels with digests; the right panels show the change of the relative intensity of specific restriction bands (indicated with black dotted rectangles on the left panel ) in each digestion reaction. Shown is probing with BamHI-HindIII ( A ), BamHI-EcoRI ( B ), and ApaLI ( C ). When the restriction sites are inside the inserted fragment (HindIII or EcoRI sites inside the UPPU, PUUP, or UPUP DNA) the highest protection rate is observed for the UPPU construct (steepest decay of band intensity). When the restriction sites are in the plasmid backbone (ApaLI restriction sites), the highest protection is observed for the PUUP construct and the weakest for UPPU DNA. D , DNase I footprinting of supercoiled UPPU and PUUP constructs at different H-NS concentrations (0–150 n m ). H-NS binding sites 1 and 2 are indicated on the sequencing gel image ( left panel ) by black vertical lines . H-NS induced hypersensitivity ( Position 1 ) and protection in H-NS binding site 2 ( Position 2 ) in UPPU (marked by dotted rectangles ). The graphs on the right show the relative intensity of the Position 1 and Position 2 signals at various H-NS concentrations.

    Article Snippet: Probing with restriction enzymes The cleavage reactions of the H-NS nucleoprotein complexes were carried out for 5 min with BamHI-EcoRI and BamHI-HindIII and for 10 min with ApaLI at 37 °C in the same standard New England BioLabs CutSmart buffer.

    Techniques: Footprinting, Construct, Plasmid Preparation, Binding Assay, Sequencing

    Amplification of isd . (A) Schematic diagram of the recombination event (RE) leading to the different numbers of fragments labelled in the Southern blot experiment. ApaLI restriction sites are indicated by vertical arrows. The binding site of the DIG-labelled probe is indicated by the black dash. Predicted sizes of the fragments recognized by the probe are indicated. (B) Results of the Southern blot. Chromosomal DNA of HKU:: tetK strains ( ΔrecA ) with different tetracycline resistance levels were digested with ApaLI and separated by electrophoresis. The DNA fragments were subsequently denatured, blotted onto a nylon membrane and hybridized with the DIG-labelled probe. Hybridization was detected using anti-DIG-Fab fragments conjugated to alkaline phosphatase. Y1, X1, W1, W2 and Z1 designate strains with different colony sizes on 8 μg/ml Tc. (C) qPCR experiment to determine the isd copy number. Known concentrations of N920143 DNA (one copy of isd ) were used to create the standard curves for isdJ and ori . Relative amounts of template ori and isdJ for each strain (all ΔrecA ) were measured. The value for ori was set to 1 and the template amount of isdJ was expressed in relation to this value, thereby giving the copy number of isdJ in the chromosome of each strain. The mean and SD of three experiments is shown.

    Journal: PLoS Genetics

    Article Title: Competing for Iron: Duplication and Amplification of the isd Locus in Staphylococcus lugdunensis HKU09-01 Provides a Competitive Advantage to Overcome Nutritional Limitation

    doi: 10.1371/journal.pgen.1006246

    Figure Lengend Snippet: Amplification of isd . (A) Schematic diagram of the recombination event (RE) leading to the different numbers of fragments labelled in the Southern blot experiment. ApaLI restriction sites are indicated by vertical arrows. The binding site of the DIG-labelled probe is indicated by the black dash. Predicted sizes of the fragments recognized by the probe are indicated. (B) Results of the Southern blot. Chromosomal DNA of HKU:: tetK strains ( ΔrecA ) with different tetracycline resistance levels were digested with ApaLI and separated by electrophoresis. The DNA fragments were subsequently denatured, blotted onto a nylon membrane and hybridized with the DIG-labelled probe. Hybridization was detected using anti-DIG-Fab fragments conjugated to alkaline phosphatase. Y1, X1, W1, W2 and Z1 designate strains with different colony sizes on 8 μg/ml Tc. (C) qPCR experiment to determine the isd copy number. Known concentrations of N920143 DNA (one copy of isd ) were used to create the standard curves for isdJ and ori . Relative amounts of template ori and isdJ for each strain (all ΔrecA ) were measured. The value for ori was set to 1 and the template amount of isdJ was expressed in relation to this value, thereby giving the copy number of isdJ in the chromosome of each strain. The mean and SD of three experiments is shown.

    Article Snippet: Genomic DNA (3 μg) was cleaved for 18 h using ApaLI (Fermentas) and separated by electrophoresis through a 0.8% agarose gel (40 V for 22 h).

    Techniques: Amplification, Southern Blot, Binding Assay, Electrophoresis, Hybridization, Real-time Polymerase Chain Reaction

    Duplication of isd in HKU09-01. (A) Schematic diagram of the ApaLI restriction sites in the single region of N920143 and the duplication in HKU09-01. Restriction sites are indicated by vertical arrows. The binding site of the DIG-labelled probe is indicated by the black dash. Predicted sizes of the fragments recognized by the probe are indicated. Primer binding sites and amplification direction (F and R) for the rapid screening for the duplication are indicated by horizontal filled arrows. (B) Results of the Southern blot. Chromosomal DNA of S . lugdunensis strains N920143 and HKU09-01 were digested with ApaLI and separated by electrophoresis. The DNA fragments were subsequently denatured, blotted onto a nylon membrane and hybridized with the DIG-labelled probe. Hybridization was detected using anti-DIG-Fab fragments conjugated to alkaline phosphatase. (C) HKU09-01 (wild-type and Δ recA mutant) cultures were plated out and 22 colonies were screened for the presence of the duplication using primer F/R indicated in A. The frequency of loss of the duplication of seven independent cultures is shown.

    Journal: PLoS Genetics

    Article Title: Competing for Iron: Duplication and Amplification of the isd Locus in Staphylococcus lugdunensis HKU09-01 Provides a Competitive Advantage to Overcome Nutritional Limitation

    doi: 10.1371/journal.pgen.1006246

    Figure Lengend Snippet: Duplication of isd in HKU09-01. (A) Schematic diagram of the ApaLI restriction sites in the single region of N920143 and the duplication in HKU09-01. Restriction sites are indicated by vertical arrows. The binding site of the DIG-labelled probe is indicated by the black dash. Predicted sizes of the fragments recognized by the probe are indicated. Primer binding sites and amplification direction (F and R) for the rapid screening for the duplication are indicated by horizontal filled arrows. (B) Results of the Southern blot. Chromosomal DNA of S . lugdunensis strains N920143 and HKU09-01 were digested with ApaLI and separated by electrophoresis. The DNA fragments were subsequently denatured, blotted onto a nylon membrane and hybridized with the DIG-labelled probe. Hybridization was detected using anti-DIG-Fab fragments conjugated to alkaline phosphatase. (C) HKU09-01 (wild-type and Δ recA mutant) cultures were plated out and 22 colonies were screened for the presence of the duplication using primer F/R indicated in A. The frequency of loss of the duplication of seven independent cultures is shown.

    Article Snippet: Genomic DNA (3 μg) was cleaved for 18 h using ApaLI (Fermentas) and separated by electrophoresis through a 0.8% agarose gel (40 V for 22 h).

    Techniques: Binding Assay, Amplification, Southern Blot, Electrophoresis, Hybridization, Mutagenesis

    ( A ) Pulsed field gels of S1 digested genomic DNA and Southern blot in gel hybridization with probe mcr-1 . ( B ) ApaLI restriction digestion profiles of mcr-1 -carrying plasmids of the three transconjugants.

    Journal: Scientific Reports

    Article Title: Clonal spread of mcr-1 in PMQR-carrying ST34 Salmonella isolates from animals in China

    doi: 10.1038/srep38511

    Figure Lengend Snippet: ( A ) Pulsed field gels of S1 digested genomic DNA and Southern blot in gel hybridization with probe mcr-1 . ( B ) ApaLI restriction digestion profiles of mcr-1 -carrying plasmids of the three transconjugants.

    Article Snippet: Transconjugants containing one plasmid were extracted and analyzed by RFLP using ApaLI (TaKaRa, Dalian, China) digestion.

    Techniques: Southern Blot, Hybridization