flaa-reca-pyrh data Search Results


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  • 92
    ATCC t denticola atcc 700768
    T Denticola Atcc 700768, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    ATCC t vincentii atcc 35580
    T Vincentii Atcc 35580, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    ATCC t medium atcc 700293
    T Medium Atcc 700293, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    ATCC t denticola
    ML phylogenetic tree of oral treponeme 16S rRNA genes. The maximum clade credibility tree topology is supported by bootstrapping for 1,000 replicates (first number) and Bayesian posterior probabilities (second number) separated with a forward slash “/” symbol in percentages; only values over 40% are shown beside the branch nodes. Sequences generated in this study are in boldface type. A scale bar indicates the nucleotide changes per position. Excessively long branches were trimmed in proportion to the scale bar (indicated by “//” on the branches). The respective oral treponeme species (phylogroups) are indicated with different color shadings. The corresponding HOT numbers are also indicated as follows: T. <t>denticola</t> (HOT 584), dark blue; T. putidum (HOT 743), red; T. vincentii (HOT 029), light green; Treponema sp. IA (HOT 231), purple; Treponema sp. IB (HOT 667), light blue; and Treponema sp. IC (HOT 231), orange.
    T Denticola, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 359 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    ATCC pcr primers
    ML phylogenetic tree of oral treponeme 16S rRNA genes. The maximum clade credibility tree topology is supported by bootstrapping for 1,000 replicates (first number) and Bayesian posterior probabilities (second number) separated with a forward slash “/” symbol in percentages; only values over 40% are shown beside the branch nodes. Sequences generated in this study are in boldface type. A scale bar indicates the nucleotide changes per position. Excessively long branches were trimmed in proportion to the scale bar (indicated by “//” on the branches). The respective oral treponeme species (phylogroups) are indicated with different color shadings. The corresponding HOT numbers are also indicated as follows: T. <t>denticola</t> (HOT 584), dark blue; T. putidum (HOT 743), red; T. vincentii (HOT 029), light green; Treponema sp. IA (HOT 231), purple; Treponema sp. IB (HOT 667), light blue; and Treponema sp. IC (HOT 231), orange.
    Pcr Primers, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 261 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    ATCC vincentii la 1
    Bayesian phylogenetic trees of Treponema denticola strains based on individual 16S rRNA, flaA , recA , pyrH , ppnK , dnaN , era and radC gene datasets. The Bayesian 50% majority-rule consensus tree of 9,000 trees, following the removal of 1,000 trees as burn-in, is shown for each gene. Numbers above branches are posterior probabilities. Corresponding gene homologoues from Treponema <t>vincentii</t> <t>LA-1</t> (ATCC 33580) and Treponema pallidum subsp. pallidum SS14 were included in the phylogenetic analysis as outgroups. The radC gene is absent from the T . pallidum genome.
    Vincentii La 1, supplied by ATCC, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    ATCC ncbi genbank
    Bayesian phylogenetic trees of Treponema denticola strains based on individual 16S rRNA, flaA , recA , pyrH , ppnK , dnaN , era and radC gene datasets. The Bayesian 50% majority-rule consensus tree of 9,000 trees, following the removal of 1,000 trees as burn-in, is shown for each gene. Numbers above branches are posterior probabilities. Corresponding gene homologoues from Treponema <t>vincentii</t> <t>LA-1</t> (ATCC 33580) and Treponema pallidum subsp. pallidum SS14 were included in the phylogenetic analysis as outgroups. The radC gene is absent from the T . pallidum genome.
    Ncbi Genbank, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    ATCC t putidum strains
    ML phylogenetic tree of oral treponeme 16S rRNA genes. The maximum clade credibility tree topology is supported by bootstrapping for 1,000 replicates (first number) and Bayesian posterior probabilities (second number) separated with a forward slash “/” symbol in percentages; only values over 40% are shown beside the branch nodes. Sequences generated in this study are in boldface type. A scale bar indicates the nucleotide changes per position. Excessively long branches were trimmed in proportion to the scale bar (indicated by “//” on the branches). The respective oral treponeme species (phylogroups) are indicated with different color shadings. The corresponding HOT numbers are also indicated as follows: T. denticola (HOT 584), dark blue; T. <t>putidum</t> (HOT 743), red; T. vincentii (HOT 029), light green; Treponema sp. IA (HOT 231), purple; Treponema sp. IB (HOT 667), light blue; and Treponema sp. IC (HOT 231), orange.
    T Putidum Strains, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    ML phylogenetic tree of oral treponeme 16S rRNA genes. The maximum clade credibility tree topology is supported by bootstrapping for 1,000 replicates (first number) and Bayesian posterior probabilities (second number) separated with a forward slash “/” symbol in percentages; only values over 40% are shown beside the branch nodes. Sequences generated in this study are in boldface type. A scale bar indicates the nucleotide changes per position. Excessively long branches were trimmed in proportion to the scale bar (indicated by “//” on the branches). The respective oral treponeme species (phylogroups) are indicated with different color shadings. The corresponding HOT numbers are also indicated as follows: T. denticola (HOT 584), dark blue; T. putidum (HOT 743), red; T. vincentii (HOT 029), light green; Treponema sp. IA (HOT 231), purple; Treponema sp. IB (HOT 667), light blue; and Treponema sp. IC (HOT 231), orange.

    Journal: Applied and Environmental Microbiology

    Article Title: Multilocus Sequence Analysis of Phylogroup 1 and 2 Oral Treponeme Strains

    doi: 10.1128/AEM.02499-16

    Figure Lengend Snippet: ML phylogenetic tree of oral treponeme 16S rRNA genes. The maximum clade credibility tree topology is supported by bootstrapping for 1,000 replicates (first number) and Bayesian posterior probabilities (second number) separated with a forward slash “/” symbol in percentages; only values over 40% are shown beside the branch nodes. Sequences generated in this study are in boldface type. A scale bar indicates the nucleotide changes per position. Excessively long branches were trimmed in proportion to the scale bar (indicated by “//” on the branches). The respective oral treponeme species (phylogroups) are indicated with different color shadings. The corresponding HOT numbers are also indicated as follows: T. denticola (HOT 584), dark blue; T. putidum (HOT 743), red; T. vincentii (HOT 029), light green; Treponema sp. IA (HOT 231), purple; Treponema sp. IB (HOT 667), light blue; and Treponema sp. IC (HOT 231), orange.

    Article Snippet: The results from the ML phylogenetic analysis of the concatenated flaA-recA-pyrH data sets clearly separated T. putidum from T. denticola , with the T. denticola ATCC 700768 (OMZ 830) strain being a notable outlier.

    Techniques: Generated, IA

    Taxonomic resolution based on the ranges of intraspecific sequence similarity (%) for the individual 16S rRNA, flaA , recA , pyrH , ppnK , dnaN , era and radC genes, within the 20 Treponema denticola strains analyzed. The y-axis indicates the levels of nucleotide identity (%) shared between the eight individual gene sequences analyzed from each strain, with the range represented as a bar.

    Journal: BMC Microbiology

    Article Title: Multilocus sequence analysis of Treponema denticola strains of diverse origin

    doi: 10.1186/1471-2180-13-24

    Figure Lengend Snippet: Taxonomic resolution based on the ranges of intraspecific sequence similarity (%) for the individual 16S rRNA, flaA , recA , pyrH , ppnK , dnaN , era and radC genes, within the 20 Treponema denticola strains analyzed. The y-axis indicates the levels of nucleotide identity (%) shared between the eight individual gene sequences analyzed from each strain, with the range represented as a bar.

    Article Snippet: Phylogenetic analyses of T . denticola strains using individual gene sequence data Using data obtained from the NCBI GenBank, gene homologues from T . vincentii LA-1 (ATCC 35580) and T . pallidum SS14 were also included in our phylogenetic analyses for comparative purposes (see Additional file ).

    Techniques: Sequencing

    Bayesian phylogenetic trees of Treponema denticola strains based on individual 16S rRNA, flaA , recA , pyrH , ppnK , dnaN , era and radC gene datasets. The Bayesian 50% majority-rule consensus tree of 9,000 trees, following the removal of 1,000 trees as burn-in, is shown for each gene. Numbers above branches are posterior probabilities. Corresponding gene homologoues from Treponema vincentii LA-1 (ATCC 33580) and Treponema pallidum subsp. pallidum SS14 were included in the phylogenetic analysis as outgroups. The radC gene is absent from the T . pallidum genome.

    Journal: BMC Microbiology

    Article Title: Multilocus sequence analysis of Treponema denticola strains of diverse origin

    doi: 10.1186/1471-2180-13-24

    Figure Lengend Snippet: Bayesian phylogenetic trees of Treponema denticola strains based on individual 16S rRNA, flaA , recA , pyrH , ppnK , dnaN , era and radC gene datasets. The Bayesian 50% majority-rule consensus tree of 9,000 trees, following the removal of 1,000 trees as burn-in, is shown for each gene. Numbers above branches are posterior probabilities. Corresponding gene homologoues from Treponema vincentii LA-1 (ATCC 33580) and Treponema pallidum subsp. pallidum SS14 were included in the phylogenetic analysis as outgroups. The radC gene is absent from the T . pallidum genome.

    Article Snippet: Phylogenetic analyses of T . denticola strains using individual gene sequence data Using data obtained from the NCBI GenBank, gene homologues from T . vincentii LA-1 (ATCC 35580) and T . pallidum SS14 were also included in our phylogenetic analyses for comparative purposes (see Additional file ).

    Techniques:

    Phylogenetic trees of Treponema denticola strains based on a concatenated 7 - gene dataset ( flaA , recA , pyrH , ppnK , dnaN , era and radC ), using Maximum Likelihood and Bayesian methods. A : Maximum likelihood (ML) tree generated under the GTR + I + G substitution model, with bootstrap values shown above branches. The scale bar represents 0.015 nucleotide changes per site. Numbers beneath the breakpoints in the branches indicate the respective nucleotide changes per site that have been removed. B : Ultrametric Bayesian (BA) 50% majority-rule consensus tree of 9,000 trees following the removal of 1,000 trees as burn-in. Numbers above branches are posterior probabilities. The respective clades formed in each tree are indicated with a Roman numeral (I-VI). Corresponding gene homologoues from Treponema vincentii LA-1 (ATCC 33580) and Treponema pallidum subsp. pallidum SS14 were included in the phylogenetic analysis as outgroups.

    Journal: BMC Microbiology

    Article Title: Multilocus sequence analysis of Treponema denticola strains of diverse origin

    doi: 10.1186/1471-2180-13-24

    Figure Lengend Snippet: Phylogenetic trees of Treponema denticola strains based on a concatenated 7 - gene dataset ( flaA , recA , pyrH , ppnK , dnaN , era and radC ), using Maximum Likelihood and Bayesian methods. A : Maximum likelihood (ML) tree generated under the GTR + I + G substitution model, with bootstrap values shown above branches. The scale bar represents 0.015 nucleotide changes per site. Numbers beneath the breakpoints in the branches indicate the respective nucleotide changes per site that have been removed. B : Ultrametric Bayesian (BA) 50% majority-rule consensus tree of 9,000 trees following the removal of 1,000 trees as burn-in. Numbers above branches are posterior probabilities. The respective clades formed in each tree are indicated with a Roman numeral (I-VI). Corresponding gene homologoues from Treponema vincentii LA-1 (ATCC 33580) and Treponema pallidum subsp. pallidum SS14 were included in the phylogenetic analysis as outgroups.

    Article Snippet: Phylogenetic analyses of T . denticola strains using individual gene sequence data Using data obtained from the NCBI GenBank, gene homologues from T . vincentii LA-1 (ATCC 35580) and T . pallidum SS14 were also included in our phylogenetic analyses for comparative purposes (see Additional file ).

    Techniques: Generated

    Bayesian phylogenetic trees of Treponema denticola strains based on individual 16S rRNA, flaA , recA , pyrH , ppnK , dnaN , era and radC gene datasets. The Bayesian 50% majority-rule consensus tree of 9,000 trees, following the removal of 1,000 trees as burn-in, is shown for each gene. Numbers above branches are posterior probabilities. Corresponding gene homologoues from Treponema vincentii LA-1 (ATCC 33580) and Treponema pallidum subsp. pallidum SS14 were included in the phylogenetic analysis as outgroups. The radC gene is absent from the T . pallidum genome.

    Journal: BMC Microbiology

    Article Title: Multilocus sequence analysis of Treponema denticola strains of diverse origin

    doi: 10.1186/1471-2180-13-24

    Figure Lengend Snippet: Bayesian phylogenetic trees of Treponema denticola strains based on individual 16S rRNA, flaA , recA , pyrH , ppnK , dnaN , era and radC gene datasets. The Bayesian 50% majority-rule consensus tree of 9,000 trees, following the removal of 1,000 trees as burn-in, is shown for each gene. Numbers above branches are posterior probabilities. Corresponding gene homologoues from Treponema vincentii LA-1 (ATCC 33580) and Treponema pallidum subsp. pallidum SS14 were included in the phylogenetic analysis as outgroups. The radC gene is absent from the T . pallidum genome.

    Article Snippet: Homologues of the flaA , recA , pyrH , ppnK , dnaN , era and radC genes are present in T . vincentii LA-1.

    Techniques:

    Phylogenetic trees of Treponema denticola strains based on a concatenated 7 - gene dataset ( flaA , recA , pyrH , ppnK , dnaN , era and radC ), using Maximum Likelihood and Bayesian methods. A : Maximum likelihood (ML) tree generated under the GTR + I + G substitution model, with bootstrap values shown above branches. The scale bar represents 0.015 nucleotide changes per site. Numbers beneath the breakpoints in the branches indicate the respective nucleotide changes per site that have been removed. B : Ultrametric Bayesian (BA) 50% majority-rule consensus tree of 9,000 trees following the removal of 1,000 trees as burn-in. Numbers above branches are posterior probabilities. The respective clades formed in each tree are indicated with a Roman numeral (I-VI). Corresponding gene homologoues from Treponema vincentii LA-1 (ATCC 33580) and Treponema pallidum subsp. pallidum SS14 were included in the phylogenetic analysis as outgroups.

    Journal: BMC Microbiology

    Article Title: Multilocus sequence analysis of Treponema denticola strains of diverse origin

    doi: 10.1186/1471-2180-13-24

    Figure Lengend Snippet: Phylogenetic trees of Treponema denticola strains based on a concatenated 7 - gene dataset ( flaA , recA , pyrH , ppnK , dnaN , era and radC ), using Maximum Likelihood and Bayesian methods. A : Maximum likelihood (ML) tree generated under the GTR + I + G substitution model, with bootstrap values shown above branches. The scale bar represents 0.015 nucleotide changes per site. Numbers beneath the breakpoints in the branches indicate the respective nucleotide changes per site that have been removed. B : Ultrametric Bayesian (BA) 50% majority-rule consensus tree of 9,000 trees following the removal of 1,000 trees as burn-in. Numbers above branches are posterior probabilities. The respective clades formed in each tree are indicated with a Roman numeral (I-VI). Corresponding gene homologoues from Treponema vincentii LA-1 (ATCC 33580) and Treponema pallidum subsp. pallidum SS14 were included in the phylogenetic analysis as outgroups.

    Article Snippet: Homologues of the flaA , recA , pyrH , ppnK , dnaN , era and radC genes are present in T . vincentii LA-1.

    Techniques: Generated

    ML phylogenetic tree of oral treponeme 16S rRNA genes. The maximum clade credibility tree topology is supported by bootstrapping for 1,000 replicates (first number) and Bayesian posterior probabilities (second number) separated with a forward slash “/” symbol in percentages; only values over 40% are shown beside the branch nodes. Sequences generated in this study are in boldface type. A scale bar indicates the nucleotide changes per position. Excessively long branches were trimmed in proportion to the scale bar (indicated by “//” on the branches). The respective oral treponeme species (phylogroups) are indicated with different color shadings. The corresponding HOT numbers are also indicated as follows: T. denticola (HOT 584), dark blue; T. putidum (HOT 743), red; T. vincentii (HOT 029), light green; Treponema sp. IA (HOT 231), purple; Treponema sp. IB (HOT 667), light blue; and Treponema sp. IC (HOT 231), orange.

    Journal: Applied and Environmental Microbiology

    Article Title: Multilocus Sequence Analysis of Phylogroup 1 and 2 Oral Treponeme Strains

    doi: 10.1128/AEM.02499-16

    Figure Lengend Snippet: ML phylogenetic tree of oral treponeme 16S rRNA genes. The maximum clade credibility tree topology is supported by bootstrapping for 1,000 replicates (first number) and Bayesian posterior probabilities (second number) separated with a forward slash “/” symbol in percentages; only values over 40% are shown beside the branch nodes. Sequences generated in this study are in boldface type. A scale bar indicates the nucleotide changes per position. Excessively long branches were trimmed in proportion to the scale bar (indicated by “//” on the branches). The respective oral treponeme species (phylogroups) are indicated with different color shadings. The corresponding HOT numbers are also indicated as follows: T. denticola (HOT 584), dark blue; T. putidum (HOT 743), red; T. vincentii (HOT 029), light green; Treponema sp. IA (HOT 231), purple; Treponema sp. IB (HOT 667), light blue; and Treponema sp. IC (HOT 231), orange.

    Article Snippet: This is consistent with a previous report ( ) which stated that this strain had a notably different phenotype from the other T. denticola and T. putidum strains analyzed.

    Techniques: Generated, IA