reference strain f nucleatum subsp nucleatum atcc 25586  (ATCC)


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    ATCC reference strain f nucleatum subsp nucleatum atcc 25586
    Reference Strain F Nucleatum Subsp Nucleatum Atcc 25586, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    reference strain f nucleatum subsp nucleatum atcc 25586  (ATCC)


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    ATCC reference strain f nucleatum subsp nucleatum atcc 25586
    Overview of the global 5′- and 3′-end mapping results for F. <t>nucleatum</t> . ( A ) Venn diagram showing the number of detected TSSs for each RNA class. The lower panel shows TSS classification based on expression strength and genomic location. ( B ) Representation of the identified promoter motif found upstream of ~89% of pTSSs. ( C ) Length distribution and corresponding count of all 5′ UTRs associated with pTSSs. The inlet displays the consensus Shine-Dalgarno sequence associated with ~85% of 5′ UTRs and its average distance from the start codon. ( D ) Normalized coverage (by reads per million, RPM) of the dRNA-seq and term-seq libraries for the fadA mRNA. The TSS and TTS are indicated by an arrow and stem-loop symbol, respectively. ( E ) Length distribution and corresponding count of all 3′ UTRs associated with TTSs. The inlet displays a consensus sequence found within a 15 nt window upstream of the TTSs. ( F ) Display of the average GC content 100 nt upstream and 24 nt downstream of the TTS. ( G ) Normalized coverage (RPM) of the dRNA-seq and term-seq libraries for the mRNAs of C4N14_02995 and C4N14_03000. The TSS and TTSs are indicated by an arrow and stem-loop, respectively.
    Reference Strain F Nucleatum Subsp Nucleatum Atcc 25586, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Transcriptome fine-mapping in Fusobacterium nucleatum reveals FoxJ, a new σ E -dependent small RNA with unusual mRNA activation activity"

    Article Title: Transcriptome fine-mapping in Fusobacterium nucleatum reveals FoxJ, a new σ E -dependent small RNA with unusual mRNA activation activity

    Journal: mBio

    doi: 10.1128/mbio.03536-23

    Overview of the global 5′- and 3′-end mapping results for F. nucleatum . ( A ) Venn diagram showing the number of detected TSSs for each RNA class. The lower panel shows TSS classification based on expression strength and genomic location. ( B ) Representation of the identified promoter motif found upstream of ~89% of pTSSs. ( C ) Length distribution and corresponding count of all 5′ UTRs associated with pTSSs. The inlet displays the consensus Shine-Dalgarno sequence associated with ~85% of 5′ UTRs and its average distance from the start codon. ( D ) Normalized coverage (by reads per million, RPM) of the dRNA-seq and term-seq libraries for the fadA mRNA. The TSS and TTS are indicated by an arrow and stem-loop symbol, respectively. ( E ) Length distribution and corresponding count of all 3′ UTRs associated with TTSs. The inlet displays a consensus sequence found within a 15 nt window upstream of the TTSs. ( F ) Display of the average GC content 100 nt upstream and 24 nt downstream of the TTS. ( G ) Normalized coverage (RPM) of the dRNA-seq and term-seq libraries for the mRNAs of C4N14_02995 and C4N14_03000. The TSS and TTSs are indicated by an arrow and stem-loop, respectively.
    Figure Legend Snippet: Overview of the global 5′- and 3′-end mapping results for F. nucleatum . ( A ) Venn diagram showing the number of detected TSSs for each RNA class. The lower panel shows TSS classification based on expression strength and genomic location. ( B ) Representation of the identified promoter motif found upstream of ~89% of pTSSs. ( C ) Length distribution and corresponding count of all 5′ UTRs associated with pTSSs. The inlet displays the consensus Shine-Dalgarno sequence associated with ~85% of 5′ UTRs and its average distance from the start codon. ( D ) Normalized coverage (by reads per million, RPM) of the dRNA-seq and term-seq libraries for the fadA mRNA. The TSS and TTS are indicated by an arrow and stem-loop symbol, respectively. ( E ) Length distribution and corresponding count of all 3′ UTRs associated with TTSs. The inlet displays a consensus sequence found within a 15 nt window upstream of the TTSs. ( F ) Display of the average GC content 100 nt upstream and 24 nt downstream of the TTS. ( G ) Normalized coverage (RPM) of the dRNA-seq and term-seq libraries for the mRNAs of C4N14_02995 and C4N14_03000. The TSS and TTSs are indicated by an arrow and stem-loop, respectively.

    Techniques Used: Expressing, Sequencing

    Discovery of the sRNA FoxJ. ( A ) Normalized coverage (reads per million) of the dRNA-seq, term-seq, and libraries from reference (GSE192339) showing the read distribution upstream of the ylmH gene in F. nucleatum . The p. rpoE library shows the read coverage upon induction of σ E ; ctrl. is the corresponding empty vector control. The TSSs are indicated by an arrow. The sRNA FoxJ is indicated in salmon. ( B ) Genomic synteny of the sRNA FoxJ across different fusobacterial (sub)species (FNN , F. nucleatum subsp. nucleatum ; FNA , F. nucleatum subsp. animalis ; FNP, F. nucleatum subsp. polymorphum ; FNV, F. nucleatum subsp. vincentii ; FuH, Fusobacterium hwasookii ; and FuP, Fusobacterium periodonticum ). ( C ) Genomic alignment of representative strains of different fusobacterial species highlighting the strong sequence conservation of FoxJ. The TSSs of FoxJ and ylmH are indicated with an arrow. Gray boxes indicate the stop codon of der and the start codon of ylmH . A dashed line indicates putative Rho-independent terminators of FoxJ. ( D ) Northern blot detection of the sRNAs FoxJ and FoxI using RNA samples of the early (E) and mid-exponential (M) growth phase as well as the stationary phase (S). The 5S rRNA served as a loading control. Both sRNAs were detected on the same membrane, and the same 5S rRNA loading control is shown twice.
    Figure Legend Snippet: Discovery of the sRNA FoxJ. ( A ) Normalized coverage (reads per million) of the dRNA-seq, term-seq, and libraries from reference (GSE192339) showing the read distribution upstream of the ylmH gene in F. nucleatum . The p. rpoE library shows the read coverage upon induction of σ E ; ctrl. is the corresponding empty vector control. The TSSs are indicated by an arrow. The sRNA FoxJ is indicated in salmon. ( B ) Genomic synteny of the sRNA FoxJ across different fusobacterial (sub)species (FNN , F. nucleatum subsp. nucleatum ; FNA , F. nucleatum subsp. animalis ; FNP, F. nucleatum subsp. polymorphum ; FNV, F. nucleatum subsp. vincentii ; FuH, Fusobacterium hwasookii ; and FuP, Fusobacterium periodonticum ). ( C ) Genomic alignment of representative strains of different fusobacterial species highlighting the strong sequence conservation of FoxJ. The TSSs of FoxJ and ylmH are indicated with an arrow. Gray boxes indicate the stop codon of der and the start codon of ylmH . A dashed line indicates putative Rho-independent terminators of FoxJ. ( D ) Northern blot detection of the sRNAs FoxJ and FoxI using RNA samples of the early (E) and mid-exponential (M) growth phase as well as the stationary phase (S). The 5S rRNA served as a loading control. Both sRNAs were detected on the same membrane, and the same 5S rRNA loading control is shown twice.

    Techniques Used: Plasmid Preparation, Sequencing, Northern Blot, Membrane

    FoxJ as a σ E -dependent sRNA. ( A ) Genomic alignment of the promoter region for FoxJ, rpoE, and FoxI with the TSS indicated by an arrow. The conserved −10 and −35 boxes are labeled. ( B ) Northern blot detection of the sRNAs FoxJ and FoxI using RNA samples from F. nucleatum carrying either a control vector (p.ctrl.) or a vector allowing inducible expression of rpoE (p. rpoE ). Expression was either induced for 30 min with 100 ng mL −1 anhydrotetracycline (ATc) or the samples were left untreated. The 5S rRNA served as a loading control. ( C ) Detection of the FoxJ sRNA via northern blot in total RNA samples extracted from F. nucleatum subjected to the indicated stress conditions for a duration of 60 min. The 5S rRNA served as a loading control.
    Figure Legend Snippet: FoxJ as a σ E -dependent sRNA. ( A ) Genomic alignment of the promoter region for FoxJ, rpoE, and FoxI with the TSS indicated by an arrow. The conserved −10 and −35 boxes are labeled. ( B ) Northern blot detection of the sRNAs FoxJ and FoxI using RNA samples from F. nucleatum carrying either a control vector (p.ctrl.) or a vector allowing inducible expression of rpoE (p. rpoE ). Expression was either induced for 30 min with 100 ng mL −1 anhydrotetracycline (ATc) or the samples were left untreated. The 5S rRNA served as a loading control. ( C ) Detection of the FoxJ sRNA via northern blot in total RNA samples extracted from F. nucleatum subjected to the indicated stress conditions for a duration of 60 min. The 5S rRNA served as a loading control.

    Techniques Used: Labeling, Northern Blot, Plasmid Preparation, Expressing

    Negative regulation of FomA expression by the sRNA FoxJ. ( A ) (Top) SDS-PAGE analysis visualized via coomassie staining. Equal amounts of OD 600 units were loaded for F. nucleatum carrying the empty control vector (p.ctrl), the FoxI- (p.FoxI), or the FoxJ-overexpressing vector (p.FoxJ). (Middle) Western blot detection of FomA using an anti-FomA antibody. (Bottom) Ponceau S staining served as a loading control for the western blot. ( B ) Secondary structure prediction of FoxJ. Conserved nucleotides (see ) are colored in red. The cytosine stretch as likely seed region and the mutations introduced in the FoxJ-M mutant sRNA are indicated. ( C ) In silico prediction of the interaction between the FoxJ sRNA and fomA mRNA using IntaRNA. The predicted FoxI binding site is highlighted in purple. ( D ) Quantification of the fluorescent signal for the indicated translational fusions with mCherry via flow cytometry. The plasmid carried either an empty expression cassette (control) or that for FoxI (FoxI) or FoxJ (FoxJ) overexpression. The data are displayed as an average and standard deviation of three biological replicates relative to the average of the control (control). Statistical testing was performed using a one-way ANOVA compared to the control group (* P ≤ 0.05; ** P ≤ 0.01; *** P ≤ 0.001; and **** P ≤ 0.0001).
    Figure Legend Snippet: Negative regulation of FomA expression by the sRNA FoxJ. ( A ) (Top) SDS-PAGE analysis visualized via coomassie staining. Equal amounts of OD 600 units were loaded for F. nucleatum carrying the empty control vector (p.ctrl), the FoxI- (p.FoxI), or the FoxJ-overexpressing vector (p.FoxJ). (Middle) Western blot detection of FomA using an anti-FomA antibody. (Bottom) Ponceau S staining served as a loading control for the western blot. ( B ) Secondary structure prediction of FoxJ. Conserved nucleotides (see ) are colored in red. The cytosine stretch as likely seed region and the mutations introduced in the FoxJ-M mutant sRNA are indicated. ( C ) In silico prediction of the interaction between the FoxJ sRNA and fomA mRNA using IntaRNA. The predicted FoxI binding site is highlighted in purple. ( D ) Quantification of the fluorescent signal for the indicated translational fusions with mCherry via flow cytometry. The plasmid carried either an empty expression cassette (control) or that for FoxI (FoxI) or FoxJ (FoxJ) overexpression. The data are displayed as an average and standard deviation of three biological replicates relative to the average of the control (control). Statistical testing was performed using a one-way ANOVA compared to the control group (* P ≤ 0.05; ** P ≤ 0.01; *** P ≤ 0.001; and **** P ≤ 0.0001).

    Techniques Used: Expressing, SDS Page, Staining, Plasmid Preparation, Western Blot, Mutagenesis, In Silico, Binding Assay, Flow Cytometry, Over Expression, Standard Deviation

    FoxJ post-transcriptionally promotes mRNA expression of terminal operon genes. Northern blot analysis of RNA samples from the mid-exponential growth phase of F. nucleatum carrying either the empty vector control (p.ctrl), the FoxJ overexpression vector (p.FoxJ), and that of the seed-region mutant (p.FoxJ-M) ( A and C ) or for samples collected from wild-type F. nucleatum , the FoxJ deletion strain (Δ foxJ ), or the FoxJ-complementation (Δ foxJ foxJ ) ( B and D ). ( A and B ) Detection of the either C4N14_00835 (top) or rpsR mRNA (bottom). RNA detected via ethidium bromide staining prior to RNA transfer served as a loading control. ( C and D ) Detection of either the C4N14_02650 (top) or C4N14_02645 mRNA (bottom). 5S rRNA served as a loading control. The asterisk marks the gene that is targeted by the northern blot probe. The quantification for the blots is shown in Fig. S9. ( E ) Schematic representation of the translational reporter system used to investigate the effect of FoxJ on targets at the end of an operon. The dashed regions of the target genes represent the target region placed into the translational fusion vector. ( F ) Quantification of the normalized fluorescent signal for the indicated translational fusions with mSc and GFP via flow cytometry. The plasmid carried either an empty expression cassette (ctrl), that for FoxJ overexpression (FoxJ), or that of the seed region mutant (FoxJ-M). The average of three biological replicates relative to that of the control (ctrl.) is displayed together with the standard deviation. Statistical testing was performed using a one-way ANOVA compared to the control group (ctrl.) (* P ≤ 0.05; ** P ≤ 0.01; *** P ≤ 0.001; and **** P ≤ 0.0001).
    Figure Legend Snippet: FoxJ post-transcriptionally promotes mRNA expression of terminal operon genes. Northern blot analysis of RNA samples from the mid-exponential growth phase of F. nucleatum carrying either the empty vector control (p.ctrl), the FoxJ overexpression vector (p.FoxJ), and that of the seed-region mutant (p.FoxJ-M) ( A and C ) or for samples collected from wild-type F. nucleatum , the FoxJ deletion strain (Δ foxJ ), or the FoxJ-complementation (Δ foxJ foxJ ) ( B and D ). ( A and B ) Detection of the either C4N14_00835 (top) or rpsR mRNA (bottom). RNA detected via ethidium bromide staining prior to RNA transfer served as a loading control. ( C and D ) Detection of either the C4N14_02650 (top) or C4N14_02645 mRNA (bottom). 5S rRNA served as a loading control. The asterisk marks the gene that is targeted by the northern blot probe. The quantification for the blots is shown in Fig. S9. ( E ) Schematic representation of the translational reporter system used to investigate the effect of FoxJ on targets at the end of an operon. The dashed regions of the target genes represent the target region placed into the translational fusion vector. ( F ) Quantification of the normalized fluorescent signal for the indicated translational fusions with mSc and GFP via flow cytometry. The plasmid carried either an empty expression cassette (ctrl), that for FoxJ overexpression (FoxJ), or that of the seed region mutant (FoxJ-M). The average of three biological replicates relative to that of the control (ctrl.) is displayed together with the standard deviation. Statistical testing was performed using a one-way ANOVA compared to the control group (ctrl.) (* P ≤ 0.05; ** P ≤ 0.01; *** P ≤ 0.001; and **** P ≤ 0.0001).

    Techniques Used: Expressing, Northern Blot, Plasmid Preparation, Over Expression, Mutagenesis, Staining, Flow Cytometry, Standard Deviation

    The expanded noncoding arm of the σ E response in F. nucleatum . ( A ) Schematic summary of the noncoding arm of the σ E -response in F. nucleatum . Upon activation of σ E , e.g., by oxygen exposure, the sigma factor drives the expression of both sRNA FoxJ and FoxI. Both sRNAs can inhibit the translation of envelope-associated proteins including several shared targets. In addition, the sRNA FoxJ is able to increase the expression of terminal genes in an operon through a yet-undefined mechanism. ( B ) Potential mechanisms through which FoxJ might positively regulate its mRNA targets. FoxJ could inhibit the binding of proteins that promote pre-mature termination of the mRNA or the activity of RNase, an enzyme that destabilizes the full-length transcript. The sRNA might also promote the transcriptional read-through by the RNA polymerase (RNAP), increasing the RNA levels of the full-length transcript. The binding of FoxJ could also increase the translation of the target mRNA, thereby enhancing the stability of the transcript.
    Figure Legend Snippet: The expanded noncoding arm of the σ E response in F. nucleatum . ( A ) Schematic summary of the noncoding arm of the σ E -response in F. nucleatum . Upon activation of σ E , e.g., by oxygen exposure, the sigma factor drives the expression of both sRNA FoxJ and FoxI. Both sRNAs can inhibit the translation of envelope-associated proteins including several shared targets. In addition, the sRNA FoxJ is able to increase the expression of terminal genes in an operon through a yet-undefined mechanism. ( B ) Potential mechanisms through which FoxJ might positively regulate its mRNA targets. FoxJ could inhibit the binding of proteins that promote pre-mature termination of the mRNA or the activity of RNase, an enzyme that destabilizes the full-length transcript. The sRNA might also promote the transcriptional read-through by the RNA polymerase (RNAP), increasing the RNA levels of the full-length transcript. The binding of FoxJ could also increase the translation of the target mRNA, thereby enhancing the stability of the transcript.

    Techniques Used: Activation Assay, Expressing, Binding Assay, Activity Assay

    species strain reference f nucleatum subsp nucleatum atcc 25586 atcc f nucleatum subsp animalis thct5a4  (ATCC)


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    ATCC species strain reference f nucleatum subsp nucleatum atcc 25586 atcc f nucleatum subsp animalis thct5a4
    Species Strain Reference F Nucleatum Subsp Nucleatum Atcc 25586 Atcc F Nucleatum Subsp Animalis Thct5a4, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    reference strain f nucleatum subsp nucleatum atcc 25586  (ATCC)


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    ATCC reference strain f nucleatum subsp nucleatum atcc 25586
    Reference Strain F Nucleatum Subsp Nucleatum Atcc 25586, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    reference strain f nucleatum subsp nucleatum atcc 25586  (ATCC)


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    ATCC reference strain f nucleatum subsp nucleatum atcc 25586
    Statistics and NCBI accession numbers for FusoPortal genomes
    Reference Strain F Nucleatum Subsp Nucleatum Atcc 25586, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced Fusobacterium Genomes Improves Gene Identification and Characterization"

    Article Title: FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced Fusobacterium Genomes Improves Gene Identification and Characterization

    Journal: mSphere

    doi: 10.1128/mSphere.00228-18

    Statistics and NCBI accession numbers for FusoPortal genomes
    Figure Legend Snippet: Statistics and NCBI accession numbers for FusoPortal genomes

    Techniques Used: Sequencing

    reference strain f nucleatum subsp nucleatum atcc 25586  (ATCC)


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    ATCC reference strain f nucleatum subsp nucleatum atcc 25586
    (A) Alignment of the complete F. <t>nucleatum</t> subps. nucleatum ATCC 23726 genome with the 67 contig draft assembly (Genbank: ADVK01000000). (B) Confirmation of a 452 kb genomeic inversion in the previous F. nucleatum subps. nucleatum <t>ATCC</t> <t>25586</t> genome assembly (Genbank: GCA_000007325.1).
    Reference Strain F Nucleatum Subsp Nucleatum Atcc 25586, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Fusobacterium genomics using MinION and Illumina sequencing enables genome completion and correction"

    Article Title: Fusobacterium genomics using MinION and Illumina sequencing enables genome completion and correction

    Journal: bioRxiv

    doi: 10.1101/305573

    (A) Alignment of the complete F. nucleatum subps. nucleatum ATCC 23726 genome with the 67 contig draft assembly (Genbank: ADVK01000000). (B) Confirmation of a 452 kb genomeic inversion in the previous F. nucleatum subps. nucleatum ATCC 25586 genome assembly (Genbank: GCA_000007325.1).
    Figure Legend Snippet: (A) Alignment of the complete F. nucleatum subps. nucleatum ATCC 23726 genome with the 67 contig draft assembly (Genbank: ADVK01000000). (B) Confirmation of a 452 kb genomeic inversion in the previous F. nucleatum subps. nucleatum ATCC 25586 genome assembly (Genbank: GCA_000007325.1).

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    reference strains f nucleatum subsp nucleatum atcc 25586  (ATCC)


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    ATCC reference strains f nucleatum subsp nucleatum atcc 25586
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    ATCC species strain reference f nucleatum subsp nucleatum atcc 25586 atcc f nucleatum subsp animalis thct5a4
    Species Strain Reference F Nucleatum Subsp Nucleatum Atcc 25586 Atcc F Nucleatum Subsp Animalis Thct5a4, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATCC reference strains f nucleatum subsp nucleatum atcc 25586
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