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  • 95
    New England Biolabs bstni
    Flow diagram of rare point-mutational analysis by CDCE/hifiPCR: natural versus ligated clamp. The copy numbers of the wild-type and of a mutant added at an initial fraction of 5 × 10 –5 are shown after each step. Restriction digestion by <t>BstNI</t> and <t>DraI</t> liberates the HPRT target-embedded fragment of 438 bp from genomic DNA. The lines in this fragment indicate the positions of the G to A transition and of the G to T transversion carried by the internal standards of the 438 bp PCR fragment and of the HPRT Munich cells, respectively. The restriction-recognition sites of AhdI, ApoI and HinfI are also indicated by the lines. The open and filled bars indicate the positions of the probes (Probe 1 and Probe 2) used for target isolation and of the PCR primers (P3 and P1), respectively.
    Bstni, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 493 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 95 stars, based on 493 article reviews
    Price from $9.99 to $1999.99
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    95/100 stars
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    93
    Thermo Fisher bstni
    DNA methylation is involved in telomere homeostasis in Arabidopsis thaliana . ( A ) Southern blot analysis showing the pattern of DNA methylation of telomeric repeats in cmt3, met1, axe1–5 (left panel), hdt4–1 and attrb2–1 mutants (right panel). DNA blots of methylation-sensitive restriction enzyme-digested gDNA probed with [TTTAGGG] 70 repeat sequences. M, <t>MspI;</t> H, HpaII; B, <t>BstNI;</t> E, EcoRII. Arrowheads represent the different signals detected by probe compared to wild-type. Small and large white bar indicate the high and low molecular weight ranges of the gDNAs, respectively, affected by restriction enzyme digestion. ( B ) Chop-PCR in subtelomeric and ITSs regions using McrBC endonuclease. 4R-300, -600, -800 and -2100 indicate the different regions on the subtelomeric regions closed to telomere in the right arm of chromosome IV. The 60S RP gene was used as a reference for quantitative comparisons. −, +; McrBC-untreated/ -treated.
    Bstni, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bstni/product/Thermo Fisher
    Average 93 stars, based on 28 article reviews
    Price from $9.99 to $1999.99
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    93/100 stars
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    93
    Thermo Fisher mvai bstni
    <t>PCR-RFLP</t> of the ITS (ca. 1,000 bp) with <t>MvaI.</t> Lanes 1 and 14, molecular size markers in base pairs; lanes 2, 3, and 16, T. interdigitale CBS 558.66, CBS 165.66, and CBS 435.73; lanes 4 and 17, clinical isolates of C. albicans ; lane 5, Epidermophyton floccosum CBS 358.93; lane 6, T. rubrum CBS 392.58 (B type); lane 7, T. rubrum CBS 289.86 (A type); lane 8, T. yaoundei CBS 730.88 (D type); lane 9, Microsporum vanbreuseghemii CBS 243.66; lanes 10 to 13, clinical isolates 1052Gr, 7112Gr, 3702Gr, and 346Gr; lane 15, T. mentagrophytes CBS 501.48; lane 18, T. rubrum CBS 100084 (A type); lanes 19 and 20, clinical isolates 817P and 5162Gr; lanes 21 to 25, DNA extracted from nails 684H2, 154Gr, 431Gr, 7962Gr, and 1024Gr.
    Mvai Bstni, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 93 stars, based on 38 article reviews
    Price from $9.99 to $1999.99
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    88
    Thermo Fisher bstni mval
    <t>PCR-RFLP</t> of the ITS (ca. 1,000 bp) with <t>MvaI.</t> Lanes 1 and 14, molecular size markers in base pairs; lanes 2, 3, and 16, T. interdigitale CBS 558.66, CBS 165.66, and CBS 435.73; lanes 4 and 17, clinical isolates of C. albicans ; lane 5, Epidermophyton floccosum CBS 358.93; lane 6, T. rubrum CBS 392.58 (B type); lane 7, T. rubrum CBS 289.86 (A type); lane 8, T. yaoundei CBS 730.88 (D type); lane 9, Microsporum vanbreuseghemii CBS 243.66; lanes 10 to 13, clinical isolates 1052Gr, 7112Gr, 3702Gr, and 346Gr; lane 15, T. mentagrophytes CBS 501.48; lane 18, T. rubrum CBS 100084 (A type); lanes 19 and 20, clinical isolates 817P and 5162Gr; lanes 21 to 25, DNA extracted from nails 684H2, 154Gr, 431Gr, 7962Gr, and 1024Gr.
    Bstni Mval, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 36 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 88 stars, based on 36 article reviews
    Price from $9.99 to $1999.99
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    91
    Thermo Fisher bstni enzyme
    <t>PCR-RFLP</t> of the ITS (ca. 1,000 bp) with <t>MvaI.</t> Lanes 1 and 14, molecular size markers in base pairs; lanes 2, 3, and 16, T. interdigitale CBS 558.66, CBS 165.66, and CBS 435.73; lanes 4 and 17, clinical isolates of C. albicans ; lane 5, Epidermophyton floccosum CBS 358.93; lane 6, T. rubrum CBS 392.58 (B type); lane 7, T. rubrum CBS 289.86 (A type); lane 8, T. yaoundei CBS 730.88 (D type); lane 9, Microsporum vanbreuseghemii CBS 243.66; lanes 10 to 13, clinical isolates 1052Gr, 7112Gr, 3702Gr, and 346Gr; lane 15, T. mentagrophytes CBS 501.48; lane 18, T. rubrum CBS 100084 (A type); lanes 19 and 20, clinical isolates 817P and 5162Gr; lanes 21 to 25, DNA extracted from nails 684H2, 154Gr, 431Gr, 7962Gr, and 1024Gr.
    Bstni Enzyme, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bstni enzyme/product/Thermo Fisher
    Average 91 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    bstni enzyme - by Bioz Stars, 2020-08
    91/100 stars
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    bstni  (Roche)
    90
    Roche bstni
    <t>PCR-RFLP</t> of the ITS (ca. 1,000 bp) with <t>MvaI.</t> Lanes 1 and 14, molecular size markers in base pairs; lanes 2, 3, and 16, T. interdigitale CBS 558.66, CBS 165.66, and CBS 435.73; lanes 4 and 17, clinical isolates of C. albicans ; lane 5, Epidermophyton floccosum CBS 358.93; lane 6, T. rubrum CBS 392.58 (B type); lane 7, T. rubrum CBS 289.86 (A type); lane 8, T. yaoundei CBS 730.88 (D type); lane 9, Microsporum vanbreuseghemii CBS 243.66; lanes 10 to 13, clinical isolates 1052Gr, 7112Gr, 3702Gr, and 346Gr; lane 15, T. mentagrophytes CBS 501.48; lane 18, T. rubrum CBS 100084 (A type); lanes 19 and 20, clinical isolates 817P and 5162Gr; lanes 21 to 25, DNA extracted from nails 684H2, 154Gr, 431Gr, 7962Gr, and 1024Gr.
    Bstni, supplied by Roche, used in various techniques. Bioz Stars score: 90/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bstni/product/Roche
    Average 90 stars, based on 12 article reviews
    Price from $9.99 to $1999.99
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    93
    Thermo Fisher bstni cc↓gaa restriction enzyme
    <t>PCR-RFLP</t> of the ITS (ca. 1,000 bp) with <t>MvaI.</t> Lanes 1 and 14, molecular size markers in base pairs; lanes 2, 3, and 16, T. interdigitale CBS 558.66, CBS 165.66, and CBS 435.73; lanes 4 and 17, clinical isolates of C. albicans ; lane 5, Epidermophyton floccosum CBS 358.93; lane 6, T. rubrum CBS 392.58 (B type); lane 7, T. rubrum CBS 289.86 (A type); lane 8, T. yaoundei CBS 730.88 (D type); lane 9, Microsporum vanbreuseghemii CBS 243.66; lanes 10 to 13, clinical isolates 1052Gr, 7112Gr, 3702Gr, and 346Gr; lane 15, T. mentagrophytes CBS 501.48; lane 18, T. rubrum CBS 100084 (A type); lanes 19 and 20, clinical isolates 817P and 5162Gr; lanes 21 to 25, DNA extracted from nails 684H2, 154Gr, 431Gr, 7962Gr, and 1024Gr.
    Bstni Cc↓Gaa Restriction Enzyme, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bstni cc↓gaa restriction enzyme/product/Thermo Fisher
    Average 93 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
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    88
    New England Biolabs pbr322 dna bstni
    Genotypic variability of Candida albicans isolates from two different patients studied by MSP-PCR with the primer M13 at the time of DRS diagnosis (T0), and 6-months after diagnosis (T6m). Molecular size markers used were <t>DNA</t> Ladder (m1) and <t>pBR322</t> <t>DNA-BstNI</t> digest (m2).
    Pbr322 Dna Bstni, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 88/100, based on 45 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pbr322 dna bstni/product/New England Biolabs
    Average 88 stars, based on 45 article reviews
    Price from $9.99 to $1999.99
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    Image Search Results


    Flow diagram of rare point-mutational analysis by CDCE/hifiPCR: natural versus ligated clamp. The copy numbers of the wild-type and of a mutant added at an initial fraction of 5 × 10 –5 are shown after each step. Restriction digestion by BstNI and DraI liberates the HPRT target-embedded fragment of 438 bp from genomic DNA. The lines in this fragment indicate the positions of the G to A transition and of the G to T transversion carried by the internal standards of the 438 bp PCR fragment and of the HPRT Munich cells, respectively. The restriction-recognition sites of AhdI, ApoI and HinfI are also indicated by the lines. The open and filled bars indicate the positions of the probes (Probe 1 and Probe 2) used for target isolation and of the PCR primers (P3 and P1), respectively.

    Journal: Nucleic Acids Research

    Article Title: Ligation of high-melting-temperature 'clamp' sequence extends the scanning range of rare point-mutational analysis by constant denaturant capillary electrophoresis (CDCE) to most of the human genome

    doi:

    Figure Lengend Snippet: Flow diagram of rare point-mutational analysis by CDCE/hifiPCR: natural versus ligated clamp. The copy numbers of the wild-type and of a mutant added at an initial fraction of 5 × 10 –5 are shown after each step. Restriction digestion by BstNI and DraI liberates the HPRT target-embedded fragment of 438 bp from genomic DNA. The lines in this fragment indicate the positions of the G to A transition and of the G to T transversion carried by the internal standards of the 438 bp PCR fragment and of the HPRT Munich cells, respectively. The restriction-recognition sites of AhdI, ApoI and HinfI are also indicated by the lines. The open and filled bars indicate the positions of the probes (Probe 1 and Probe 2) used for target isolation and of the PCR primers (P3 and P1), respectively.

    Article Snippet: Restriction digestion by BstNI and DraI (New England Biolabs, Beverly, MA) was performed with the samples of genomic DNA to liberate the HPRT target-embedded fragment of 438 bp suitable for target isolation by probe-target hybridization coupled with a biotin–streptavidin capture system ( ).

    Techniques: Flow Cytometry, Mutagenesis, Polymerase Chain Reaction, Isolation

    Genotyping results for Arg389Gly polymorphism of β1-adrenergic receptor gene. Shown is pattern of bands on ethidium bromide-stained gel electrophoresis after BstNI digestion of PCR product. Lane 1, homozygous Arg/Arg; Lane 2, heterozygous Arg/Gly; Lane 3, homozygous Gly/Gly; Lane 4, GeneRuler™ 100 bp DNA Ladder (Fermentas). The position and size of bands are indicated by arrows

    Journal: Archives of Medical Science : AMS

    Article Title: Arg389Gly ?1-adrenergic receptor polymorphism and susceptibility to syncope during tilt test

    doi: 10.5114/aoms.2014.42576

    Figure Lengend Snippet: Genotyping results for Arg389Gly polymorphism of β1-adrenergic receptor gene. Shown is pattern of bands on ethidium bromide-stained gel electrophoresis after BstNI digestion of PCR product. Lane 1, homozygous Arg/Arg; Lane 2, heterozygous Arg/Gly; Lane 3, homozygous Gly/Gly; Lane 4, GeneRuler™ 100 bp DNA Ladder (Fermentas). The position and size of bands are indicated by arrows

    Article Snippet: Final extension was performed at 72°C for 8 min. Digestion of the 221-bp PCR product with restriction enzyme BstNI (New England Biolabs, Ipswich, UK) yielded a 221-bp product for Arg/Arg genotype, three (221-, 154- and 67-bp) products for heterozygous Arg/Gly genotype and two (154- and 67-bp) products for Gly/Gly homozygotes.

    Techniques: Staining, Nucleic Acid Electrophoresis, Polymerase Chain Reaction

    PCR – RFLP analysis of FGFR4 gene G388R mutation. Lane 1, Hae III-digested pBR322 size marker; lane 2, amplification control; lane 3, wild-type control (Gly/Gly), Bst NI – digested; lane 4, heterozygote carrier (Gly/Arg), Bst NI – digested; lane 5, homozygote carrier (Arg/Arg), Bst NI – digested.

    Journal: British Journal of Cancer

    Article Title: G388R mutation of the FGFR4 gene is not relevant to breast cancer prognosis

    doi: 10.1038/sj.bjc.6601450

    Figure Lengend Snippet: PCR – RFLP analysis of FGFR4 gene G388R mutation. Lane 1, Hae III-digested pBR322 size marker; lane 2, amplification control; lane 3, wild-type control (Gly/Gly), Bst NI – digested; lane 4, heterozygote carrier (Gly/Arg), Bst NI – digested; lane 5, homozygote carrier (Arg/Arg), Bst NI – digested.

    Article Snippet: The digestion reactions contained 10 μ l of PCR product, 0.5 μ l of Bst NI (5 U; New England Biolabs, Beverly, MA, USA), 2 μ l of 10 × NEBuffer 2 (supplied with the enzyme) and 0.2 μ l bovine serum albumin (100 mg l−1 ) in a final volume of 20 μ l. These components were incubated for 60 min at 60°C.

    Techniques: Polymerase Chain Reaction, Mutagenesis, Marker, Amplification

    Establishment of  foxl2a  and  foxl2b  knockout mutant lines by TALEN. (A and B) The TALEN target sites of zebrafish (A)  foxl2a  and (B)  foxl2b . The coding and untranslated exon regions are depicted as solid and open boxes, respectively. The left and right TALEN binding sites are indicated by underlining. Cleavage sites with  Bst N I and  Bsr D I in the spacer are shown by blue color, and forward and reverse primers (F primer and R primer) are indicated in the corresponding sites. (C and D) Detection of (C)  foxl2a  and (D)  foxl2b  mutants by  Bst N I or  Bsr D I digestion. The amplified fragment sizes (bp) are shown on the right. (E and F) Sequences of different indels of TALEN-induced (E)  foxl2a  and (F)  foxl2b  mutants in F 0  embryos. A total of eight and six indels (number of embryos are indicated in each bracket) at targeted locus are shown for (E)  foxl2a  and (F)  foxl2b , and the numbers at the right-hand side indicate the number of deleted base pairs. (G) Transcription-level confirmation of  foxl2a  and  foxl2b  mutants by RT-PCR. The detected primers are shown on the left, and primer P2 is specific for the deleted sequences. The  actb1  was used as control. F, forward; R, reverse; M, marker.

    Journal: Genetics

    Article Title: Sequential, Divergent, and Cooperative Requirements of Foxl2a and Foxl2b in Ovary Development and Maintenance of Zebrafish

    doi: 10.1534/genetics.116.199133

    Figure Lengend Snippet: Establishment of foxl2a and foxl2b knockout mutant lines by TALEN. (A and B) The TALEN target sites of zebrafish (A) foxl2a and (B) foxl2b . The coding and untranslated exon regions are depicted as solid and open boxes, respectively. The left and right TALEN binding sites are indicated by underlining. Cleavage sites with Bst N I and Bsr D I in the spacer are shown by blue color, and forward and reverse primers (F primer and R primer) are indicated in the corresponding sites. (C and D) Detection of (C) foxl2a and (D) foxl2b mutants by Bst N I or Bsr D I digestion. The amplified fragment sizes (bp) are shown on the right. (E and F) Sequences of different indels of TALEN-induced (E) foxl2a and (F) foxl2b mutants in F 0 embryos. A total of eight and six indels (number of embryos are indicated in each bracket) at targeted locus are shown for (E) foxl2a and (F) foxl2b , and the numbers at the right-hand side indicate the number of deleted base pairs. (G) Transcription-level confirmation of foxl2a and foxl2b mutants by RT-PCR. The detected primers are shown on the left, and primer P2 is specific for the deleted sequences. The actb1 was used as control. F, forward; R, reverse; M, marker.

    Article Snippet: After digestion with Bst N I (restriction enzyme cutting site in the spacer of foxl2a ) or Bsr D I (restriction enzyme cutting site in the spacer of foxl2b ) (New England Biolabs, Beverly, MA) respectively at 60° and 65° for 2 hr, the uncleaved DNA fragments were separated by gel electrophoresis and cloned into pMD-18T vector (Promega).

    Techniques: Knock-Out, Mutagenesis, Binding Assay, Amplification, Reverse Transcription Polymerase Chain Reaction, Marker

    TALENS-targeted frameshift deletions in Hnrnph 1 +/- mice reveal Hnrnph1 as a quantitative trait gene for MA sensitivity. (a): Left TAL effector (50,191,867–50,191,883 bp) and right TAL effector (50,191,899–50,191,915 bp) separated by the Fok I cleavage zone were used to introduce frameshift deletions in the first coding exon of Hnrnph1 (exon 4) that resulted in premature stop codons ( S8 Fig ). Founder #28 contained a 16 bp deletion and Founder #22 contained an 11 bp deletion. ( b): A PCR amplicon capturing the Fok I cleavage zone was digested with BstNI. Hnrnph1 +/+ mice contained two copies of a functional BstNI restriction site and thus, restriction digest produced a single band containing digested fragments of equal size. Hnrnph1 +/- mice were heterozygous for a deletion of the BstNI site and showed both the digested band and a larger, undigested band. Gel band lanes were cropped and re-ordered to present wild-type first (+/+) followed by B6 control, and heterozygous samples (+/-). ( c): There was a significant upregulation of total Hnrnph1 transcript levels in Hnrnph1 +/- mice as indicated by cDNA amplification using qPCR primers spanning exons 4–5 that hybridized to both genotypes (t 6 = 5.69; p = 0.0013). ( d): An upregulation of total Hnrnph1 transcript levels was also indicated by cDNA amplification using qPCR primers spanning untargeted exons 6–7 (t 6 = 8.53; p = 0.00014). (e): A significant downregulation of the Hnrnph1 +/+ transcript levels was observed in Hnrnph1 +/- mice that was indicated by cDNA amplification using primers spanning exons 4–5, one of which hybridized to the deleted Hnrnph1 +/+ sequence (t 6 = 9.45; p = 0.00091; Fig 5e). *p

    Journal: PLoS Genetics

    Article Title: Hnrnph1 Is A Quantitative Trait Gene for Methamphetamine Sensitivity

    doi: 10.1371/journal.pgen.1005713

    Figure Lengend Snippet: TALENS-targeted frameshift deletions in Hnrnph 1 +/- mice reveal Hnrnph1 as a quantitative trait gene for MA sensitivity. (a): Left TAL effector (50,191,867–50,191,883 bp) and right TAL effector (50,191,899–50,191,915 bp) separated by the Fok I cleavage zone were used to introduce frameshift deletions in the first coding exon of Hnrnph1 (exon 4) that resulted in premature stop codons ( S8 Fig ). Founder #28 contained a 16 bp deletion and Founder #22 contained an 11 bp deletion. ( b): A PCR amplicon capturing the Fok I cleavage zone was digested with BstNI. Hnrnph1 +/+ mice contained two copies of a functional BstNI restriction site and thus, restriction digest produced a single band containing digested fragments of equal size. Hnrnph1 +/- mice were heterozygous for a deletion of the BstNI site and showed both the digested band and a larger, undigested band. Gel band lanes were cropped and re-ordered to present wild-type first (+/+) followed by B6 control, and heterozygous samples (+/-). ( c): There was a significant upregulation of total Hnrnph1 transcript levels in Hnrnph1 +/- mice as indicated by cDNA amplification using qPCR primers spanning exons 4–5 that hybridized to both genotypes (t 6 = 5.69; p = 0.0013). ( d): An upregulation of total Hnrnph1 transcript levels was also indicated by cDNA amplification using qPCR primers spanning untargeted exons 6–7 (t 6 = 8.53; p = 0.00014). (e): A significant downregulation of the Hnrnph1 +/+ transcript levels was observed in Hnrnph1 +/- mice that was indicated by cDNA amplification using primers spanning exons 4–5, one of which hybridized to the deleted Hnrnph1 +/+ sequence (t 6 = 9.45; p = 0.00091; Fig 5e). *p

    Article Snippet: PCR products were treated with the BstNI restriction enzyme (New England Biolabs) or a control enzyme-free buffer solution and incubated overnight at 60°C to ensure complete digestion.

    Techniques: TALENs, Mouse Assay, Introduce, Polymerase Chain Reaction, Amplification, Functional Assay, Produced, Real-time Polymerase Chain Reaction, Sequencing

    DNA methylation is involved in telomere homeostasis in Arabidopsis thaliana . ( A ) Southern blot analysis showing the pattern of DNA methylation of telomeric repeats in cmt3, met1, axe1–5 (left panel), hdt4–1 and attrb2–1 mutants (right panel). DNA blots of methylation-sensitive restriction enzyme-digested gDNA probed with [TTTAGGG] 70 repeat sequences. M, MspI; H, HpaII; B, BstNI; E, EcoRII. Arrowheads represent the different signals detected by probe compared to wild-type. Small and large white bar indicate the high and low molecular weight ranges of the gDNAs, respectively, affected by restriction enzyme digestion. ( B ) Chop-PCR in subtelomeric and ITSs regions using McrBC endonuclease. 4R-300, -600, -800 and -2100 indicate the different regions on the subtelomeric regions closed to telomere in the right arm of chromosome IV. The 60S RP gene was used as a reference for quantitative comparisons. −, +; McrBC-untreated/ -treated.

    Journal: Nucleic Acids Research

    Article Title: Telomere-binding protein regulates the chromosome ends through the interaction with histone deacetylases in Arabidopsis thaliana

    doi: 10.1093/nar/gkw067

    Figure Lengend Snippet: DNA methylation is involved in telomere homeostasis in Arabidopsis thaliana . ( A ) Southern blot analysis showing the pattern of DNA methylation of telomeric repeats in cmt3, met1, axe1–5 (left panel), hdt4–1 and attrb2–1 mutants (right panel). DNA blots of methylation-sensitive restriction enzyme-digested gDNA probed with [TTTAGGG] 70 repeat sequences. M, MspI; H, HpaII; B, BstNI; E, EcoRII. Arrowheads represent the different signals detected by probe compared to wild-type. Small and large white bar indicate the high and low molecular weight ranges of the gDNAs, respectively, affected by restriction enzyme digestion. ( B ) Chop-PCR in subtelomeric and ITSs regions using McrBC endonuclease. 4R-300, -600, -800 and -2100 indicate the different regions on the subtelomeric regions closed to telomere in the right arm of chromosome IV. The 60S RP gene was used as a reference for quantitative comparisons. −, +; McrBC-untreated/ -treated.

    Article Snippet: A total of 10 μg of genomic DNA was digested with the methylation sensitive restriction enzymes, 20 U of MspI, HpaII, BstNI and EcoRII (Fermentas, Thermo Scientific) and then separated by electrophoresis in a 0.8% agarose gel.

    Techniques: DNA Methylation Assay, Southern Blot, Methylation, Molecular Weight, Polymerase Chain Reaction

    PCR-RFLP of the ITS (ca. 1,000 bp) with MvaI. Lanes 1 and 14, molecular size markers in base pairs; lanes 2, 3, and 16, T. interdigitale CBS 558.66, CBS 165.66, and CBS 435.73; lanes 4 and 17, clinical isolates of C. albicans ; lane 5, Epidermophyton floccosum CBS 358.93; lane 6, T. rubrum CBS 392.58 (B type); lane 7, T. rubrum CBS 289.86 (A type); lane 8, T. yaoundei CBS 730.88 (D type); lane 9, Microsporum vanbreuseghemii CBS 243.66; lanes 10 to 13, clinical isolates 1052Gr, 7112Gr, 3702Gr, and 346Gr; lane 15, T. mentagrophytes CBS 501.48; lane 18, T. rubrum CBS 100084 (A type); lanes 19 and 20, clinical isolates 817P and 5162Gr; lanes 21 to 25, DNA extracted from nails 684H2, 154Gr, 431Gr, 7962Gr, and 1024Gr.

    Journal: Journal of Clinical Microbiology

    Article Title: Forty-Eight-Hour Diagnosis of Onychomycosis with Subtyping of Trichophyton rubrum Strains

    doi: 10.1128/JCM.44.4.1419-1427.2006

    Figure Lengend Snippet: PCR-RFLP of the ITS (ca. 1,000 bp) with MvaI. Lanes 1 and 14, molecular size markers in base pairs; lanes 2, 3, and 16, T. interdigitale CBS 558.66, CBS 165.66, and CBS 435.73; lanes 4 and 17, clinical isolates of C. albicans ; lane 5, Epidermophyton floccosum CBS 358.93; lane 6, T. rubrum CBS 392.58 (B type); lane 7, T. rubrum CBS 289.86 (A type); lane 8, T. yaoundei CBS 730.88 (D type); lane 9, Microsporum vanbreuseghemii CBS 243.66; lanes 10 to 13, clinical isolates 1052Gr, 7112Gr, 3702Gr, and 346Gr; lane 15, T. mentagrophytes CBS 501.48; lane 18, T. rubrum CBS 100084 (A type); lanes 19 and 20, clinical isolates 817P and 5162Gr; lanes 21 to 25, DNA extracted from nails 684H2, 154Gr, 431Gr, 7962Gr, and 1024Gr.

    Article Snippet: Restriction enzyme analysis of the PCR products was performed using 5 U MvaI enzyme (MBI Fermentas, Amherst, NY) per sample, followed by incubation for 4 h at 37°C.

    Techniques: Polymerase Chain Reaction

    1 α ,25(OH) 2 D 3 induces dynamic looping of VDR binding regions to the TSS of the p21 gene. Schematic overview on the human p21 promoter indicating previously described VDREs ( 6 ), MvaI and Hpy81I restriction enzyme recognition sites and location of primers along with FAM-labeled probes used for quantification of the 3C products ( A ). 3C ass ays were performed with chromatin from MDA-MB453 cells that were treated for the indicated times with 10 n m 1α,25(OH) 2 D 3 ( B ). Chromatin was extracted, cross-linked, and digested with either MvaI or Hpy8I. After ligation, the DNA was extracted and analyzed by PCR with primer A in combination with primers C, D, or E for Hpy8I-digested chromatin ( left figure ) or with primers F or G for MvaI-digested chromatin ( right figure ). Re-ligated digestions of subcloned p21 promoter fragments served as positive controls. Analysis was performed by real-time quantitative PCR using a FAM-labeled probe targeting the ligation site specific for the product. PCR efficacy was normalized to positive controls. Values indicate looping as relative values compared with basal looping of region p21-2 to the TSS. Data points indicate the means of at least three independent cell treatments, and the bars represent standard deviations. A two-tailed Student's t test was performed to determine the significance of the stimulation in reference to vehicle-treated control ( * , p

    Journal: The Journal of Biological Chemistry

    Article Title: Cyclical Chromatin Looping and Transcription Factor Association on the Regulatory Regions of the p21 (CDKN1A) Gene in Response to 1?,25-Dihydroxyvitamin D3 * * S⃞

    doi: 10.1074/jbc.M808090200

    Figure Lengend Snippet: 1 α ,25(OH) 2 D 3 induces dynamic looping of VDR binding regions to the TSS of the p21 gene. Schematic overview on the human p21 promoter indicating previously described VDREs ( 6 ), MvaI and Hpy81I restriction enzyme recognition sites and location of primers along with FAM-labeled probes used for quantification of the 3C products ( A ). 3C ass ays were performed with chromatin from MDA-MB453 cells that were treated for the indicated times with 10 n m 1α,25(OH) 2 D 3 ( B ). Chromatin was extracted, cross-linked, and digested with either MvaI or Hpy8I. After ligation, the DNA was extracted and analyzed by PCR with primer A in combination with primers C, D, or E for Hpy8I-digested chromatin ( left figure ) or with primers F or G for MvaI-digested chromatin ( right figure ). Re-ligated digestions of subcloned p21 promoter fragments served as positive controls. Analysis was performed by real-time quantitative PCR using a FAM-labeled probe targeting the ligation site specific for the product. PCR efficacy was normalized to positive controls. Values indicate looping as relative values compared with basal looping of region p21-2 to the TSS. Data points indicate the means of at least three independent cell treatments, and the bars represent standard deviations. A two-tailed Student's t test was performed to determine the significance of the stimulation in reference to vehicle-treated control ( * , p

    Article Snippet: After removal of cellular debris by centrifugation, 25 μl of chromatin was diluted in 75 μl of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mm EDTA, 16.7 mm NaCl, protease inhibitors, and 16.7 mm Tris-HCl, pH 8.1) supplemented with protease inhibitors (Complete protease inhibitor mixture, Roche Applied Science), Red or Tango buffer (Fermentas, Vilnius, Lithuania) and digested overnight at 37 °C with 25 units of the restriction enzymes MvaI or Hpy8I (Fermentas), respectively.

    Techniques: Binding Assay, Labeling, Multiple Displacement Amplification, Ligation, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Two Tailed Test

    Effect of cofactor silencing on chromatin looping VDRE containing regions to the TSS of the p21 gene. MDA-MB453 cells were transfected for 24 h with siRNA oligonucleotides against HDAC4, MED1 , or LSD1 and subsequently stimulated with 10 n m 1α,25(OH) 2 D 3 for the indicated times. Chromatin was extracted, cross-linked, and digested with either Hpy8I ( upper and center graphs representing regions p21-1 and p21-2 , respectively) or MvaI ( lower graph representing region p21-3 ). After ligation, the DNA was extracted and analyzed by PCR with primers and FAM-labeled probes as indicated in Fig. 3 . Values indicate looping as percentage to that in untreated cells transfected with non-targeting siRNA from indicated region to the p21 TSS. Data points indicate the means of at least three independent cell treatments, and the bars represent standard deviations. A two-tailed Student's t test was performed to determine the significance of the effects of the specific siRNAs in reference to control siRNA ( * , p

    Journal: The Journal of Biological Chemistry

    Article Title: Cyclical Chromatin Looping and Transcription Factor Association on the Regulatory Regions of the p21 (CDKN1A) Gene in Response to 1?,25-Dihydroxyvitamin D3 * * S⃞

    doi: 10.1074/jbc.M808090200

    Figure Lengend Snippet: Effect of cofactor silencing on chromatin looping VDRE containing regions to the TSS of the p21 gene. MDA-MB453 cells were transfected for 24 h with siRNA oligonucleotides against HDAC4, MED1 , or LSD1 and subsequently stimulated with 10 n m 1α,25(OH) 2 D 3 for the indicated times. Chromatin was extracted, cross-linked, and digested with either Hpy8I ( upper and center graphs representing regions p21-1 and p21-2 , respectively) or MvaI ( lower graph representing region p21-3 ). After ligation, the DNA was extracted and analyzed by PCR with primers and FAM-labeled probes as indicated in Fig. 3 . Values indicate looping as percentage to that in untreated cells transfected with non-targeting siRNA from indicated region to the p21 TSS. Data points indicate the means of at least three independent cell treatments, and the bars represent standard deviations. A two-tailed Student's t test was performed to determine the significance of the effects of the specific siRNAs in reference to control siRNA ( * , p

    Article Snippet: After removal of cellular debris by centrifugation, 25 μl of chromatin was diluted in 75 μl of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mm EDTA, 16.7 mm NaCl, protease inhibitors, and 16.7 mm Tris-HCl, pH 8.1) supplemented with protease inhibitors (Complete protease inhibitor mixture, Roche Applied Science), Red or Tango buffer (Fermentas, Vilnius, Lithuania) and digested overnight at 37 °C with 25 units of the restriction enzymes MvaI or Hpy8I (Fermentas), respectively.

    Techniques: Multiple Displacement Amplification, Transfection, Ligation, Polymerase Chain Reaction, Labeling, Two Tailed Test

    Genotypic variability of Candida albicans isolates from two different patients studied by MSP-PCR with the primer M13 at the time of DRS diagnosis (T0), and 6-months after diagnosis (T6m). Molecular size markers used were DNA Ladder (m1) and pBR322 DNA-BstNI digest (m2).

    Journal: The Open Dentistry Journal

    Article Title: Effect of Denture-Related Stomatitis Fluconazole Treatment on Oral Candida albicans Susceptibility Profile and Genotypic Variability

    doi: 10.2174/1874210601509010046

    Figure Lengend Snippet: Genotypic variability of Candida albicans isolates from two different patients studied by MSP-PCR with the primer M13 at the time of DRS diagnosis (T0), and 6-months after diagnosis (T6m). Molecular size markers used were DNA Ladder (m1) and pBR322 DNA-BstNI digest (m2).

    Article Snippet: DNA Ladder and pBR322 DNA-BstNI digest (New England Biolabs, Beverly, Mass.) were used as molecular size standards.

    Techniques: Polymerase Chain Reaction