rdna  (New England Biolabs)


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    Structured Review

    New England Biolabs rdna
    Rdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 5 article reviews
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    92/100 stars

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    Related Articles

    Dot Blot:

    Article Title: Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring
    Article Snippet: .. rDNAs for slot blot hybridizations were amplified from environmental and reference DNAs as described above with universal primers in the presence of 5% acetamide. rDNA and E. coli rRNA (100 ng) and negative controls (300 ng; 1-kb DNA ladder [New England Biolabs], Hin dIII digested λ DNA, pBluescript KS+ ) were immobilized in triplicate on a Hybond nylon membrane (Amersham, Cleveland, Ohio) with a slot blot apparatus (Minifold II; Schleicher & Schuell, Keene, N.H.) according to the manufacturers’ instructions. .. Oligonucleotides used as probes for hybridization were UNIV-519R, ARC/EUK-1373R (5′ AGGGGCAGGGACGTATTC 3′) and BAC-924R (5′ CCGSTTGTGCGGGCCCCCG 3′).

    Polymerase Chain Reaction:

    Article Title: Isolation and Characterization of the Stress-Tolerant Candida tropicalis YHJ1 and Evaluation of Its Xylose Reductase for Xylitol Production From Acid Pre-treatment Wastewater
    Article Snippet: .. The D1/D2 domain of the 26S rDNA gene and the internal transcribed spacer (ITS) region of the rDNA were amplified via polymerase chain reaction (PCR) with Phusion® high-fidelity DNA polymerase (NEB, Ipswich, MA, USA) and appropriate primer pairs, using the isolated strain's genomic DNA as the template. .. For PCR amplification of rDNA locus genes from eukaryotic strains, the primers used in this study were as follows: NL-1 (5′-GCATATCAATAAGCGGAGGAAAAG-3′) and NL-4 (5′-GGTCCGTGTTTCAAGACGG-3′) for 26S rDNA and ITS-1 (5′-TCCGTAGGTGAACCTGCGG-3′) and ITS-4 (5′-TCCTCCGCTTATTGATATGC-3′) (Kim and Kim, ; Kim, ).

    Article Title: Host genotype-specific microbiota do not influence the susceptibility of D. magna to a bacterial pathogen
    Article Snippet: .. The first PCR amplification step involved using the primer pairs F (5′-ACACGGYCCARACTCCTAC-3′) and R (5′-TTGCWTCGAATTAAWCCAC-3′) that targets the 327–969 bp of the 16 S rDNA using Phusion High Fidelity Taq (New England Biolab, USA) with this PCR program: 98 °C for 1 min, 15 cycles of 98 °C for 10 s, 50 °C for 20 s and 72 °C for 30 s with a final extension time of 72 °C for 5 min. PCR reactions were treated with ExoSap (Fermentas, USA), to remove unincorporated nucleotides and primers. .. A second PCR reaction step was prepared using the first PCR purified product as DNA template and re-amplified with F/R primer pairs containing the Libl fusion sequence and barcodes (PFx: 5′-CCATCTCATCCCTGCGTGTCTCCGACTCAGbarcodeF primer-3′.

    Amplification:

    Article Title: Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring
    Article Snippet: .. rDNAs for slot blot hybridizations were amplified from environmental and reference DNAs as described above with universal primers in the presence of 5% acetamide. rDNA and E. coli rRNA (100 ng) and negative controls (300 ng; 1-kb DNA ladder [New England Biolabs], Hin dIII digested λ DNA, pBluescript KS+ ) were immobilized in triplicate on a Hybond nylon membrane (Amersham, Cleveland, Ohio) with a slot blot apparatus (Minifold II; Schleicher & Schuell, Keene, N.H.) according to the manufacturers’ instructions. .. Oligonucleotides used as probes for hybridization were UNIV-519R, ARC/EUK-1373R (5′ AGGGGCAGGGACGTATTC 3′) and BAC-924R (5′ CCGSTTGTGCGGGCCCCCG 3′).

    Article Title: Isolation and Characterization of the Stress-Tolerant Candida tropicalis YHJ1 and Evaluation of Its Xylose Reductase for Xylitol Production From Acid Pre-treatment Wastewater
    Article Snippet: .. The D1/D2 domain of the 26S rDNA gene and the internal transcribed spacer (ITS) region of the rDNA were amplified via polymerase chain reaction (PCR) with Phusion® high-fidelity DNA polymerase (NEB, Ipswich, MA, USA) and appropriate primer pairs, using the isolated strain's genomic DNA as the template. .. For PCR amplification of rDNA locus genes from eukaryotic strains, the primers used in this study were as follows: NL-1 (5′-GCATATCAATAAGCGGAGGAAAAG-3′) and NL-4 (5′-GGTCCGTGTTTCAAGACGG-3′) for 26S rDNA and ITS-1 (5′-TCCGTAGGTGAACCTGCGG-3′) and ITS-4 (5′-TCCTCCGCTTATTGATATGC-3′) (Kim and Kim, ; Kim, ).

    Article Title: Host genotype-specific microbiota do not influence the susceptibility of D. magna to a bacterial pathogen
    Article Snippet: .. The first PCR amplification step involved using the primer pairs F (5′-ACACGGYCCARACTCCTAC-3′) and R (5′-TTGCWTCGAATTAAWCCAC-3′) that targets the 327–969 bp of the 16 S rDNA using Phusion High Fidelity Taq (New England Biolab, USA) with this PCR program: 98 °C for 1 min, 15 cycles of 98 °C for 10 s, 50 °C for 20 s and 72 °C for 30 s with a final extension time of 72 °C for 5 min. PCR reactions were treated with ExoSap (Fermentas, USA), to remove unincorporated nucleotides and primers. .. A second PCR reaction step was prepared using the first PCR purified product as DNA template and re-amplified with F/R primer pairs containing the Libl fusion sequence and barcodes (PFx: 5′-CCATCTCATCCCTGCGTGTCTCCGACTCAGbarcodeF primer-3′.

    Isolation:

    Article Title: Isolation and Characterization of the Stress-Tolerant Candida tropicalis YHJ1 and Evaluation of Its Xylose Reductase for Xylitol Production From Acid Pre-treatment Wastewater
    Article Snippet: .. The D1/D2 domain of the 26S rDNA gene and the internal transcribed spacer (ITS) region of the rDNA were amplified via polymerase chain reaction (PCR) with Phusion® high-fidelity DNA polymerase (NEB, Ipswich, MA, USA) and appropriate primer pairs, using the isolated strain's genomic DNA as the template. .. For PCR amplification of rDNA locus genes from eukaryotic strains, the primers used in this study were as follows: NL-1 (5′-GCATATCAATAAGCGGAGGAAAAG-3′) and NL-4 (5′-GGTCCGTGTTTCAAGACGG-3′) for 26S rDNA and ITS-1 (5′-TCCGTAGGTGAACCTGCGG-3′) and ITS-4 (5′-TCCTCCGCTTATTGATATGC-3′) (Kim and Kim, ; Kim, ).

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    New England Biolabs 5s rdna
    BRD4 has intrinsic histone acetyltransferase activity (a) HAT assays of H3 and H4 (1μg) with radiolabeled AcCoA with recombinant BRD4 (500 ng), mTAF1 (250 ng) or mock. (b) HAT assays of rHis-mBRD4 (500 μg) from insect sf9 cells, GST-hBRD4 from E.coli , Flag-hBRD4 from HeLa cells and rTAF1 with histone H3 (1μg) and acetyl CoA. Immunoblotting was with anti-AcH3, anti-H3 or anti-BRD4 antibodies. Bottom panel, silver staining as a loading control. (c) Recombinant mBRD4 from sf9 cells, hBRD4 (3.5 μg) and control Sf9 extract resolved on a denaturing gel (left panel), immunoblotted with anti-BRD4 (middle panel) or subjected to an in-gel HAT assay; acetylated H4 peptide visualized with anti-AcH4 (right hand panel). Faster mobility band in hBRD4 lane is a degradation product. (d) Histones H2A, H2B, H3, H4 (1μg) or all four (1μg each) incubated with or without 500ng BRD4 in a HAT assay followed by autoradiography or coomassie staining. (e) Mononucleosomes (equivalent to ~700bp) (10pmol) assembled on <t>5S</t> rDNA (208 bp), visualized in ethidium bromide stained gels (left panel), subjected to a HAT assay with or without recombinant p300 (500 ng) or BRD4 (500 ng) with radiolabeled AcCoA and visualized by autoradiography or coomassie staining. (f) Histone H3, H4ac and H3ac immunoblots of whole cell extracts (WCE) from HeLa cells grown 14, 16 and 18hr following transfection with 3μg hBRD4 expression plasmid or control. AU: arbitrary units. Data are representative of 3 independent experiments. Uncropped images of gels and immunoblots are shown in Supplementary Data Set 1
    5s Rdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs 16s ribosomal dna fragments
    Cultivation-independent PCR-SSCP profiles of bacterial communities isolated from rhizospheres of M. sativa (lanes 2 to 7) and C. album (lanes 8 to 13). Results from three replicate field plots are shown for each treatment. The results for plants from noninoculated field plots are shown in lanes 2 to 4 and 8 to 10. The results for plants from S. meliloti -inoculated plots are shown in lanes 5 to 7 and 11 to 13. The results for SSCP species standards, consisting of single-stranded <t>DNA</t> products obtained from PCR-amplified <t>16S</t> rRNA gene regions (including regions V4 and V5) (see Materials and Methods) of selected bacterial species (Pf, Pseudomonas fluorescens ; Bs, Bacillus subtilis ; Sm, Sinorhizobium meliloti ; Ar, Agrobacterium radiobacter ), are shown in lanes 1 and 14.
    16s Ribosomal Dna Fragments, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs mtssu rdna segment
    The <t>mtSSU</t> <t>rDNA</t> polymorphisms among 13 focal species. ( A ) Bars indicate the most common sequences of each species, bright blue, dark blue, green, and purple dots represent deletion, insertion, transition, and transversion, respectively, while the nucleotides shown in dots represent the polymorphism compared with the common sequence; lengths of sequences are drawn to scale. ( B ) Polymorphic sites between different haplotypes. Clones mean the number of clones for the corresponding haplotype found in total clones (20, 30, or 90); For F. ehrenbergii , the first two individuals and the third one might be cryptic species (i.e., they were indeed different species), so we represented them respectively; matching sites are represented by dots (.) and missing sites are marked with dashes (-); a: Coleps sp.; b: Sterkiella sp.; c: Spirostomum sp.; d: Oxytricha trifallax ; e, f: Favella ehrenbergii ; g: Epistylis sp.; h: Paramecium caudatum ; and i: Trithigmostoma sp.
    Mtssu Rdna Segment, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    New England Biolabs b pertussis 23s rdna pcr
    Screening for A2058G and A2059G mutations in B. pertussis by <t>PCR-RFLP</t> analysis. (A). Bsa I (lanes 1 to 5) or Bbs I (lanes 6 to 10) digestion of a 521-bp fragment of the <t>23S</t> <t>rDNA</t> gene of erythromycin-resistant B. pertussis clinical isolates (A228, C353, and MN2531), heterogeneous strain C352, and erythromycin-susceptible strain MN2726. The 521-bp fragment was generated by PCR amplification using primers 1907U and 2408L as described in Materials and Methods. Lanes: M, 100-bp ladder (Life Technologies); 1 and 6, B. pertussis A228; 2 and 7, B. pertussis C352; 3 and 8, B. pertussis C353; 4 and 9, B. pertussis MN2531; 5 and 10, B. pertussis MN2726. (B). Bbs I digestion of the 521-bp fragment of additional isolates of B. pertussis . Lanes: M, 100-bp ladder (Life Technologies); 1 to 7, erythromycin-susceptible clinical isolates B. pertussis MN277, MN973, MN1286, MN1699, MN1773, MN1893, and MN2726; 8, erythromycin-resistant B. pertussis isolate MN253.
    B Pertussis 23s Rdna Pcr, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    BRD4 has intrinsic histone acetyltransferase activity (a) HAT assays of H3 and H4 (1μg) with radiolabeled AcCoA with recombinant BRD4 (500 ng), mTAF1 (250 ng) or mock. (b) HAT assays of rHis-mBRD4 (500 μg) from insect sf9 cells, GST-hBRD4 from E.coli , Flag-hBRD4 from HeLa cells and rTAF1 with histone H3 (1μg) and acetyl CoA. Immunoblotting was with anti-AcH3, anti-H3 or anti-BRD4 antibodies. Bottom panel, silver staining as a loading control. (c) Recombinant mBRD4 from sf9 cells, hBRD4 (3.5 μg) and control Sf9 extract resolved on a denaturing gel (left panel), immunoblotted with anti-BRD4 (middle panel) or subjected to an in-gel HAT assay; acetylated H4 peptide visualized with anti-AcH4 (right hand panel). Faster mobility band in hBRD4 lane is a degradation product. (d) Histones H2A, H2B, H3, H4 (1μg) or all four (1μg each) incubated with or without 500ng BRD4 in a HAT assay followed by autoradiography or coomassie staining. (e) Mononucleosomes (equivalent to ~700bp) (10pmol) assembled on 5S rDNA (208 bp), visualized in ethidium bromide stained gels (left panel), subjected to a HAT assay with or without recombinant p300 (500 ng) or BRD4 (500 ng) with radiolabeled AcCoA and visualized by autoradiography or coomassie staining. (f) Histone H3, H4ac and H3ac immunoblots of whole cell extracts (WCE) from HeLa cells grown 14, 16 and 18hr following transfection with 3μg hBRD4 expression plasmid or control. AU: arbitrary units. Data are representative of 3 independent experiments. Uncropped images of gels and immunoblots are shown in Supplementary Data Set 1

    Journal: Nature structural & molecular biology

    Article Title: BRD4 is a Histone Acetyltransferase that Evicts Nucleosomes from Chromatin

    doi: 10.1038/nsmb.3228

    Figure Lengend Snippet: BRD4 has intrinsic histone acetyltransferase activity (a) HAT assays of H3 and H4 (1μg) with radiolabeled AcCoA with recombinant BRD4 (500 ng), mTAF1 (250 ng) or mock. (b) HAT assays of rHis-mBRD4 (500 μg) from insect sf9 cells, GST-hBRD4 from E.coli , Flag-hBRD4 from HeLa cells and rTAF1 with histone H3 (1μg) and acetyl CoA. Immunoblotting was with anti-AcH3, anti-H3 or anti-BRD4 antibodies. Bottom panel, silver staining as a loading control. (c) Recombinant mBRD4 from sf9 cells, hBRD4 (3.5 μg) and control Sf9 extract resolved on a denaturing gel (left panel), immunoblotted with anti-BRD4 (middle panel) or subjected to an in-gel HAT assay; acetylated H4 peptide visualized with anti-AcH4 (right hand panel). Faster mobility band in hBRD4 lane is a degradation product. (d) Histones H2A, H2B, H3, H4 (1μg) or all four (1μg each) incubated with or without 500ng BRD4 in a HAT assay followed by autoradiography or coomassie staining. (e) Mononucleosomes (equivalent to ~700bp) (10pmol) assembled on 5S rDNA (208 bp), visualized in ethidium bromide stained gels (left panel), subjected to a HAT assay with or without recombinant p300 (500 ng) or BRD4 (500 ng) with radiolabeled AcCoA and visualized by autoradiography or coomassie staining. (f) Histone H3, H4ac and H3ac immunoblots of whole cell extracts (WCE) from HeLa cells grown 14, 16 and 18hr following transfection with 3μg hBRD4 expression plasmid or control. AU: arbitrary units. Data are representative of 3 independent experiments. Uncropped images of gels and immunoblots are shown in Supplementary Data Set 1

    Article Snippet: Unmodified recombinant human nucleosomes were assembled on the 5S rDNA with purified human histone H2A/H2B dimers and histone H3/H4 tetramers using the EpiMark Nucleosome Assembly kit (NEB) following the manufacturer’s instructions.

    Techniques: Activity Assay, HAT Assay, Recombinant, Silver Staining, Incubation, Autoradiography, Staining, Western Blot, Transfection, Expressing, Plasmid Preparation

    BRD4 acetylation of H3K122 mediates histone eviction and nucleosome clearance a) Autoradiogram showing mononucleosomes (10 pmol) assembled in vitro with radiolabeled 5S rDNA and subjected to HAT assays for 15 and 30 minutes with or without 500ng BRD4 or TAF1 in the presence or absence of acetyl CoA or 500 μM JQ1. Free DNA resolved from mononucleosomes by electrophoresis (upper panel) . Immunoblots of identical HAT assays done in parallel with non-radiolabeled mononucleosomes, showing extent of acetylation of H3K122 and H3K9; histone H3 immunoblot served as control (lower panels) . (b) HAT assays and immunoblots as in (a) with or without BRD4, BRD4 HAT mutants or TAF1 (500ng). (c) Ethidium Bromide stained agarose gels showing native chromatin isolated from U2OS cells that was incubated in HAT assays with or without increasing amounts of BRD4 (Lane 3: 1 μg; Lane 4, 5, 6: 0.2, 0.5, 1 μg respectively; Lane 7: 1μg), Acetyl CoA and 500 μM JQ1 (lane 7) and then digested with 0.1U MNase for 3 min (left panel). Quantification of digested bands showing increased MNase digestion correlated with increasing BRD4 (right panel) . (d) Ethidium Bromide stained agarose gels showing native chromatin isolated from U2OS cells transfected with 3μg hBRD4 (BRD4 WT), hBRD4 HAT mutant (Mt BRD4) or pCMV2 vector (control) in the presence of sodium butyrate and incubated with or without 0.1U MNase for 3 min (middle panel). Quantification of digested bands from cells transfected with vector (1), BRD4 WT (2) and Mt BRD4 (3) (right panel) . Immunoblots of WCEs from the transfected cells showing H3K122ac, H3K9ac and BRD4 levels (left panel). Uncropped images of gels and immunoblots are shown in Supplementary Data Set 1

    Journal: Nature structural & molecular biology

    Article Title: BRD4 is a Histone Acetyltransferase that Evicts Nucleosomes from Chromatin

    doi: 10.1038/nsmb.3228

    Figure Lengend Snippet: BRD4 acetylation of H3K122 mediates histone eviction and nucleosome clearance a) Autoradiogram showing mononucleosomes (10 pmol) assembled in vitro with radiolabeled 5S rDNA and subjected to HAT assays for 15 and 30 minutes with or without 500ng BRD4 or TAF1 in the presence or absence of acetyl CoA or 500 μM JQ1. Free DNA resolved from mononucleosomes by electrophoresis (upper panel) . Immunoblots of identical HAT assays done in parallel with non-radiolabeled mononucleosomes, showing extent of acetylation of H3K122 and H3K9; histone H3 immunoblot served as control (lower panels) . (b) HAT assays and immunoblots as in (a) with or without BRD4, BRD4 HAT mutants or TAF1 (500ng). (c) Ethidium Bromide stained agarose gels showing native chromatin isolated from U2OS cells that was incubated in HAT assays with or without increasing amounts of BRD4 (Lane 3: 1 μg; Lane 4, 5, 6: 0.2, 0.5, 1 μg respectively; Lane 7: 1μg), Acetyl CoA and 500 μM JQ1 (lane 7) and then digested with 0.1U MNase for 3 min (left panel). Quantification of digested bands showing increased MNase digestion correlated with increasing BRD4 (right panel) . (d) Ethidium Bromide stained agarose gels showing native chromatin isolated from U2OS cells transfected with 3μg hBRD4 (BRD4 WT), hBRD4 HAT mutant (Mt BRD4) or pCMV2 vector (control) in the presence of sodium butyrate and incubated with or without 0.1U MNase for 3 min (middle panel). Quantification of digested bands from cells transfected with vector (1), BRD4 WT (2) and Mt BRD4 (3) (right panel) . Immunoblots of WCEs from the transfected cells showing H3K122ac, H3K9ac and BRD4 levels (left panel). Uncropped images of gels and immunoblots are shown in Supplementary Data Set 1

    Article Snippet: Unmodified recombinant human nucleosomes were assembled on the 5S rDNA with purified human histone H2A/H2B dimers and histone H3/H4 tetramers using the EpiMark Nucleosome Assembly kit (NEB) following the manufacturer’s instructions.

    Techniques: In Vitro, HAT Assay, Electrophoresis, Western Blot, Staining, Isolation, Incubation, Transfection, Mutagenesis, Plasmid Preparation

    Cultivation-independent PCR-SSCP profiles of bacterial communities isolated from rhizospheres of M. sativa (lanes 2 to 7) and C. album (lanes 8 to 13). Results from three replicate field plots are shown for each treatment. The results for plants from noninoculated field plots are shown in lanes 2 to 4 and 8 to 10. The results for plants from S. meliloti -inoculated plots are shown in lanes 5 to 7 and 11 to 13. The results for SSCP species standards, consisting of single-stranded DNA products obtained from PCR-amplified 16S rRNA gene regions (including regions V4 and V5) (see Materials and Methods) of selected bacterial species (Pf, Pseudomonas fluorescens ; Bs, Bacillus subtilis ; Sm, Sinorhizobium meliloti ; Ar, Agrobacterium radiobacter ), are shown in lanes 1 and 14.

    Journal: Applied and Environmental Microbiology

    Article Title: Effect of Field Inoculation with Sinorhizobium meliloti L33 on the Composition of Bacterial Communities in Rhizospheres of a Target Plant (Medicago sativa) and a Non-Target Plant (Chenopodium album)--Linking of 16S rRNA Gene-Based Single-Strand Conformation Polymorphism Community Profiles to the Diversity of Cultivated Bacteria

    doi:

    Figure Lengend Snippet: Cultivation-independent PCR-SSCP profiles of bacterial communities isolated from rhizospheres of M. sativa (lanes 2 to 7) and C. album (lanes 8 to 13). Results from three replicate field plots are shown for each treatment. The results for plants from noninoculated field plots are shown in lanes 2 to 4 and 8 to 10. The results for plants from S. meliloti -inoculated plots are shown in lanes 5 to 7 and 11 to 13. The results for SSCP species standards, consisting of single-stranded DNA products obtained from PCR-amplified 16S rRNA gene regions (including regions V4 and V5) (see Materials and Methods) of selected bacterial species (Pf, Pseudomonas fluorescens ; Bs, Bacillus subtilis ; Sm, Sinorhizobium meliloti ; Ar, Agrobacterium radiobacter ), are shown in lanes 1 and 14.

    Article Snippet: For digestion of the amplified 16S ribosomal DNA fragments, the tetranucleotide-recognizing enzymes Hha I and Hae III (New England Biolabs, Schwalbach/Taunus, Germany) were used.

    Techniques: Polymerase Chain Reaction, Isolation, Amplification

    The mtSSU rDNA polymorphisms among 13 focal species. ( A ) Bars indicate the most common sequences of each species, bright blue, dark blue, green, and purple dots represent deletion, insertion, transition, and transversion, respectively, while the nucleotides shown in dots represent the polymorphism compared with the common sequence; lengths of sequences are drawn to scale. ( B ) Polymorphic sites between different haplotypes. Clones mean the number of clones for the corresponding haplotype found in total clones (20, 30, or 90); For F. ehrenbergii , the first two individuals and the third one might be cryptic species (i.e., they were indeed different species), so we represented them respectively; matching sites are represented by dots (.) and missing sites are marked with dashes (-); a: Coleps sp.; b: Sterkiella sp.; c: Spirostomum sp.; d: Oxytricha trifallax ; e, f: Favella ehrenbergii ; g: Epistylis sp.; h: Paramecium caudatum ; and i: Trithigmostoma sp.

    Journal: Microorganisms

    Article Title: Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research

    doi: 10.3390/microorganisms8030316

    Figure Lengend Snippet: The mtSSU rDNA polymorphisms among 13 focal species. ( A ) Bars indicate the most common sequences of each species, bright blue, dark blue, green, and purple dots represent deletion, insertion, transition, and transversion, respectively, while the nucleotides shown in dots represent the polymorphism compared with the common sequence; lengths of sequences are drawn to scale. ( B ) Polymorphic sites between different haplotypes. Clones mean the number of clones for the corresponding haplotype found in total clones (20, 30, or 90); For F. ehrenbergii , the first two individuals and the third one might be cryptic species (i.e., they were indeed different species), so we represented them respectively; matching sites are represented by dots (.) and missing sites are marked with dashes (-); a: Coleps sp.; b: Sterkiella sp.; c: Spirostomum sp.; d: Oxytricha trifallax ; e, f: Favella ehrenbergii ; g: Epistylis sp.; h: Paramecium caudatum ; and i: Trithigmostoma sp.

    Article Snippet: Primers mtF (5′-TGT GCC AGC AGC CGC GGT AA-3′) and mtR (5′-CCC MTA CCR GTA CCT TGT GT-3′) were used to amplify the mtSSU rDNA segment of each species [ , ] using Q5 Hot Start High-Fidelity DNA polymerase (Cat. #M0493 L, New England Biolabs, Ipswich, MA, USA).

    Techniques: Sequencing, Clone Assay

    The maximum likelihood (ML) tree based on mtSSU rDNA sequence alignment, highlighting the 13 species studied. Numbers near nodes represent the bootstrap values of ML and the posterior probability values of Bayesian analysis (BI). Dots (.) mean fully supported node (100/1.00) while asterisks (*) indicate the disagreement between ML and BI topologies. The scale bar corresponds to two substitutions per 100 nucleotide positions. All branches are drawn to scale.

    Journal: Microorganisms

    Article Title: Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research

    doi: 10.3390/microorganisms8030316

    Figure Lengend Snippet: The maximum likelihood (ML) tree based on mtSSU rDNA sequence alignment, highlighting the 13 species studied. Numbers near nodes represent the bootstrap values of ML and the posterior probability values of Bayesian analysis (BI). Dots (.) mean fully supported node (100/1.00) while asterisks (*) indicate the disagreement between ML and BI topologies. The scale bar corresponds to two substitutions per 100 nucleotide positions. All branches are drawn to scale.

    Article Snippet: Primers mtF (5′-TGT GCC AGC AGC CGC GGT AA-3′) and mtR (5′-CCC MTA CCR GTA CCT TGT GT-3′) were used to amplify the mtSSU rDNA segment of each species [ , ] using Q5 Hot Start High-Fidelity DNA polymerase (Cat. #M0493 L, New England Biolabs, Ipswich, MA, USA).

    Techniques: Sequencing

    Screening for A2058G and A2059G mutations in B. pertussis by PCR-RFLP analysis. (A). Bsa I (lanes 1 to 5) or Bbs I (lanes 6 to 10) digestion of a 521-bp fragment of the 23S rDNA gene of erythromycin-resistant B. pertussis clinical isolates (A228, C353, and MN2531), heterogeneous strain C352, and erythromycin-susceptible strain MN2726. The 521-bp fragment was generated by PCR amplification using primers 1907U and 2408L as described in Materials and Methods. Lanes: M, 100-bp ladder (Life Technologies); 1 and 6, B. pertussis A228; 2 and 7, B. pertussis C352; 3 and 8, B. pertussis C353; 4 and 9, B. pertussis MN2531; 5 and 10, B. pertussis MN2726. (B). Bbs I digestion of the 521-bp fragment of additional isolates of B. pertussis . Lanes: M, 100-bp ladder (Life Technologies); 1 to 7, erythromycin-susceptible clinical isolates B. pertussis MN277, MN973, MN1286, MN1699, MN1773, MN1893, and MN2726; 8, erythromycin-resistant B. pertussis isolate MN253.

    Journal: Journal of Clinical Microbiology

    Article Title: Identification of a Mutation Associated with Erythromycin Resistance in Bordetella pertussis: Implications for Surveillance of Antimicrobial Resistance

    doi: 10.1128/JCM.41.3.1167-1172.2003

    Figure Lengend Snippet: Screening for A2058G and A2059G mutations in B. pertussis by PCR-RFLP analysis. (A). Bsa I (lanes 1 to 5) or Bbs I (lanes 6 to 10) digestion of a 521-bp fragment of the 23S rDNA gene of erythromycin-resistant B. pertussis clinical isolates (A228, C353, and MN2531), heterogeneous strain C352, and erythromycin-susceptible strain MN2726. The 521-bp fragment was generated by PCR amplification using primers 1907U and 2408L as described in Materials and Methods. Lanes: M, 100-bp ladder (Life Technologies); 1 and 6, B. pertussis A228; 2 and 7, B. pertussis C352; 3 and 8, B. pertussis C353; 4 and 9, B. pertussis MN2531; 5 and 10, B. pertussis MN2726. (B). Bbs I digestion of the 521-bp fragment of additional isolates of B. pertussis . Lanes: M, 100-bp ladder (Life Technologies); 1 to 7, erythromycin-susceptible clinical isolates B. pertussis MN277, MN973, MN1286, MN1699, MN1773, MN1893, and MN2726; 8, erythromycin-resistant B. pertussis isolate MN253.

    Article Snippet: An 8-μl aliquot of the B. pertussis 23S rDNA PCR product was digested with Bsa I or Bbs I (New England Biolabs, Beverly, Mass.), and the products were resolved by electrophoresis on a 2% agarose Tris-borate-EDTA gel.

    Techniques: Polymerase Chain Reaction, Generated, Amplification