plasmid description reference strains f nucleatum 23726 parental strain  (ATCC)


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    ATCC plasmid description reference strains f nucleatum 23726 parental strain
    Bacterial strains and plasmids used
    Plasmid Description Reference Strains F Nucleatum 23726 Parental Strain, 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 "Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum"

    Article Title: Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/aem.01665-23

    Bacterial strains and plasmids used
    Figure Legend Snippet: Bacterial strains and plasmids used

    Techniques Used: Plasmid Preparation, Isolation, Clone Assay, Expressing

    f nucleatum strain atcc 23726  (ATCC)


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    ATCC f nucleatum strain atcc 23726
    Construction and characterization of CRISPRi system in Fusobacterium nucleatum. (A) Mechanism of CRISPRi. The nuclease deficient (dCas9) binds single-guide RNA (sgRNA) to target the gene of interest via a 20-nt base-paring region. Instead of cleaving DNA, dCas9 obstructs RNA polymerase (RNAP) movement and inhibits transcription elongation, suppressing the target gene’s expression. (B) pZP4C construction blueprint for CRISPRi. pZP4C is derived from the E. coli-F. nucleatum shuttle vector pCWU6 and is aimed at ftsX. pCWU6 underwent SacI/HindIII digestion and was conjoined with two PCR fragments (Pfdx-E-dcas9 and PrpsJFP-sgRNA) through Gibson assembly, resulting in pZP4C. Within pZP4C, the dCas9’s expression is governed by Pfdx and a theophylline-responsive riboswitch E (indicated “E”), both at the transcriptional and translation stages. The sgRNA is driven by a constitutive active PrpsJ promoter from Fusobacterium periodonticum and can be replaced using the MscI and NotI restriction sites. Key features include using Pfdx-E from pREcas1 and the dCas9 and sgRNA element from pIA33, replication regions (oriFn, repA, and oriEc), and the catP, the chloramphenicol acetyltransferase gene. (C) ftsX gene suppression via CRISPRi. The wild-type F. nucleatum strain with pZP4C was cultivated in a TSPC medium under varying theophylline concentrations (0, 0.1, and 2 mM) for 22 hours. Induction of dcas9 expression by theophylline results in cells setting at the tube’s base after overnight growth, leaving a transparent supernatant characteristic similar to the ftsX deletion phenotype. (D) Western blot analysis validates ftsX silencing. Cell samples, including a wild-type control without inducer, were run on SDS-PAGE and immunoblotted. Antibodies for FtsX (α-FtsX) and FomA (α-FomA) were used, with FomA as the loading control. Molecular mass markers (in kilodaltons) are labeled on the left of the blot. (E) Silencing FtsX alters fusobacterial cell morphology. A phase-contrast microscopy recorded cell shapes in panel B. Bars, 2 µm.
    F Nucleatum Strain Atcc 23726, 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 "Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum"

    Article Title: Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/aem.01665-23

    Construction and characterization of CRISPRi system in Fusobacterium nucleatum. (A) Mechanism of CRISPRi. The nuclease deficient (dCas9) binds single-guide RNA (sgRNA) to target the gene of interest via a 20-nt base-paring region. Instead of cleaving DNA, dCas9 obstructs RNA polymerase (RNAP) movement and inhibits transcription elongation, suppressing the target gene’s expression. (B) pZP4C construction blueprint for CRISPRi. pZP4C is derived from the E. coli-F. nucleatum shuttle vector pCWU6 and is aimed at ftsX. pCWU6 underwent SacI/HindIII digestion and was conjoined with two PCR fragments (Pfdx-E-dcas9 and PrpsJFP-sgRNA) through Gibson assembly, resulting in pZP4C. Within pZP4C, the dCas9’s expression is governed by Pfdx and a theophylline-responsive riboswitch E (indicated “E”), both at the transcriptional and translation stages. The sgRNA is driven by a constitutive active PrpsJ promoter from Fusobacterium periodonticum and can be replaced using the MscI and NotI restriction sites. Key features include using Pfdx-E from pREcas1 and the dCas9 and sgRNA element from pIA33, replication regions (oriFn, repA, and oriEc), and the catP, the chloramphenicol acetyltransferase gene. (C) ftsX gene suppression via CRISPRi. The wild-type F. nucleatum strain with pZP4C was cultivated in a TSPC medium under varying theophylline concentrations (0, 0.1, and 2 mM) for 22 hours. Induction of dcas9 expression by theophylline results in cells setting at the tube’s base after overnight growth, leaving a transparent supernatant characteristic similar to the ftsX deletion phenotype. (D) Western blot analysis validates ftsX silencing. Cell samples, including a wild-type control without inducer, were run on SDS-PAGE and immunoblotted. Antibodies for FtsX (α-FtsX) and FomA (α-FomA) were used, with FomA as the loading control. Molecular mass markers (in kilodaltons) are labeled on the left of the blot. (E) Silencing FtsX alters fusobacterial cell morphology. A phase-contrast microscopy recorded cell shapes in panel B. Bars, 2 µm.
    Figure Legend Snippet: Construction and characterization of CRISPRi system in Fusobacterium nucleatum. (A) Mechanism of CRISPRi. The nuclease deficient (dCas9) binds single-guide RNA (sgRNA) to target the gene of interest via a 20-nt base-paring region. Instead of cleaving DNA, dCas9 obstructs RNA polymerase (RNAP) movement and inhibits transcription elongation, suppressing the target gene’s expression. (B) pZP4C construction blueprint for CRISPRi. pZP4C is derived from the E. coli-F. nucleatum shuttle vector pCWU6 and is aimed at ftsX. pCWU6 underwent SacI/HindIII digestion and was conjoined with two PCR fragments (Pfdx-E-dcas9 and PrpsJFP-sgRNA) through Gibson assembly, resulting in pZP4C. Within pZP4C, the dCas9’s expression is governed by Pfdx and a theophylline-responsive riboswitch E (indicated “E”), both at the transcriptional and translation stages. The sgRNA is driven by a constitutive active PrpsJ promoter from Fusobacterium periodonticum and can be replaced using the MscI and NotI restriction sites. Key features include using Pfdx-E from pREcas1 and the dCas9 and sgRNA element from pIA33, replication regions (oriFn, repA, and oriEc), and the catP, the chloramphenicol acetyltransferase gene. (C) ftsX gene suppression via CRISPRi. The wild-type F. nucleatum strain with pZP4C was cultivated in a TSPC medium under varying theophylline concentrations (0, 0.1, and 2 mM) for 22 hours. Induction of dcas9 expression by theophylline results in cells setting at the tube’s base after overnight growth, leaving a transparent supernatant characteristic similar to the ftsX deletion phenotype. (D) Western blot analysis validates ftsX silencing. Cell samples, including a wild-type control without inducer, were run on SDS-PAGE and immunoblotted. Antibodies for FtsX (α-FtsX) and FomA (α-FomA) were used, with FomA as the loading control. Molecular mass markers (in kilodaltons) are labeled on the left of the blot. (E) Silencing FtsX alters fusobacterial cell morphology. A phase-contrast microscopy recorded cell shapes in panel B. Bars, 2 µm.

    Techniques Used: Expressing, Derivative Assay, Plasmid Preparation, Western Blot, SDS Page, Labeling, Microscopy

    plasmid description reference strains f nucleatum 23726 parental strain  (ATCC)


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    ATCC plasmid description reference strains f nucleatum 23726 parental strain
    Bacterial strains and plasmids used
    Plasmid Description Reference Strains F Nucleatum 23726 Parental Strain, 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 "Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum"

    Article Title: Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/aem.01665-23

    Bacterial strains and plasmids used
    Figure Legend Snippet: Bacterial strains and plasmids used

    Techniques Used: Plasmid Preparation, Isolation, Clone Assay, Expressing

    f nucleatum atcc 25586 strains  (ATCC)


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    ATCC f nucleatum atcc 25586 strains
    F Nucleatum Atcc 25586 Strains, 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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    anaerobic strains f nucleatum atcc 25586  (ATCC)


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    ATCC anaerobic strains f nucleatum atcc 25586
    Anaerobic Strains F 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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    f nucleatum subsp fusiforme strain atcc 51190  (ATCC)


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    ATCC f nucleatum subsp fusiforme strain atcc 51190
    A) Location of subspecies-/species-specific primer sets in each Fusobacterium genome. Genes are labeled with their annotated function if available, while hypothetical proteins are unlabeled. Forward and reverse primer locations are illustrated with red arrows. Genes and primers are not drawn to scale. B) Representative example of subspecies/species primer specificity. All reactions were performed using a mixture of gDNA from the four F. <t>nucleatum</t> subspecies and F. periodonticum . A DNA ladder is shown on the left.
    F Nucleatum Subsp Fusiforme Strain Atcc 51190, 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 "The prevalence of Fusobacterium nucleatum subspecies in the oral cavity stratifies by local health status"

    Article Title: The prevalence of Fusobacterium nucleatum subspecies in the oral cavity stratifies by local health status

    Journal: bioRxiv

    doi: 10.1101/2023.10.25.563997

    A) Location of subspecies-/species-specific primer sets in each Fusobacterium genome. Genes are labeled with their annotated function if available, while hypothetical proteins are unlabeled. Forward and reverse primer locations are illustrated with red arrows. Genes and primers are not drawn to scale. B) Representative example of subspecies/species primer specificity. All reactions were performed using a mixture of gDNA from the four F. nucleatum subspecies and F. periodonticum . A DNA ladder is shown on the left.
    Figure Legend Snippet: A) Location of subspecies-/species-specific primer sets in each Fusobacterium genome. Genes are labeled with their annotated function if available, while hypothetical proteins are unlabeled. Forward and reverse primer locations are illustrated with red arrows. Genes and primers are not drawn to scale. B) Representative example of subspecies/species primer specificity. All reactions were performed using a mixture of gDNA from the four F. nucleatum subspecies and F. periodonticum . A DNA ladder is shown on the left.

    Techniques Used: Labeling

    f nucleatum strain atcc 23726  (ATCC)


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    ATCC f nucleatum strain atcc 23726
    F Nucleatum Strain Atcc 23726, 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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    f nucleatum strain atcc 25586  (ATCC)


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    ATCC f nucleatum strain atcc 25586
    F Nucleatum Strain 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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    conditioned media collection f nucleatum strain atcc  (ATCC)


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    ATCC conditioned media collection f nucleatum strain atcc
    Conditioned Media Collection F Nucleatum Strain Atcc, 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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    f nucleatum strain  (ATCC)


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    ATCC f nucleatum strain
    Overall metabolic profiles of control, Fn_24hr group and Fn_48hr groups. A principal component analysis (PCA) plot for three groups was performed to visualize the overall metabolic differences and the variability within the groups. B orthogonal partial least squares discriminant analysis (OPLS-DA) plot of Fn_24hr group and control group, and C OPLS-DA of Fn_48hr group and control group were performed to further track the metabolic changes, which maximizes the variance between groups. Fn_24hr group: AMC-HN-8 cells and F. <t>nucleatum</t> were cocultured for 24hs. Fn_48hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 48hs
    F Nucleatum Strain, 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 nucleatum -triggered purine metabolic reprogramming drives tumorigenesis in head and neck carcinoma"

    Article Title: Fusobacterium nucleatum -triggered purine metabolic reprogramming drives tumorigenesis in head and neck carcinoma

    Journal: Discover. Oncology

    doi: 10.1007/s12672-023-00727-x

    Overall metabolic profiles of control, Fn_24hr group and Fn_48hr groups. A principal component analysis (PCA) plot for three groups was performed to visualize the overall metabolic differences and the variability within the groups. B orthogonal partial least squares discriminant analysis (OPLS-DA) plot of Fn_24hr group and control group, and C OPLS-DA of Fn_48hr group and control group were performed to further track the metabolic changes, which maximizes the variance between groups. Fn_24hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 24hs. Fn_48hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 48hs
    Figure Legend Snippet: Overall metabolic profiles of control, Fn_24hr group and Fn_48hr groups. A principal component analysis (PCA) plot for three groups was performed to visualize the overall metabolic differences and the variability within the groups. B orthogonal partial least squares discriminant analysis (OPLS-DA) plot of Fn_24hr group and control group, and C OPLS-DA of Fn_48hr group and control group were performed to further track the metabolic changes, which maximizes the variance between groups. Fn_24hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 24hs. Fn_48hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 48hs

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    Volcano plot showing metabolic alterations of ( A ) Fn_24hr group vs. control group and ( B ) Fn_48hr group vs. control group. Arrows point out critical metabolites related to the purine metabolic pathway. Fn_24hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 24 hs. Fn_48hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 48 hs
    Figure Legend Snippet: Volcano plot showing metabolic alterations of ( A ) Fn_24hr group vs. control group and ( B ) Fn_48hr group vs. control group. Arrows point out critical metabolites related to the purine metabolic pathway. Fn_24hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 24 hs. Fn_48hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 48 hs

    Techniques Used:

    F. nucleatum –triggered tumor progression and ROS accumulation could be reversed by uric acid: A cell proliferation measured using Cell Counting Kit-8 assay (CCK8), B invasion assay performed using transwell chambers, C migration assay performed using transwell chambers and D Intracellular ROS detection using fluorometric intracellular ROS assay kit. Left: AMC-HN-8 cells. Right: Fadu cells
    Figure Legend Snippet: F. nucleatum –triggered tumor progression and ROS accumulation could be reversed by uric acid: A cell proliferation measured using Cell Counting Kit-8 assay (CCK8), B invasion assay performed using transwell chambers, C migration assay performed using transwell chambers and D Intracellular ROS detection using fluorometric intracellular ROS assay kit. Left: AMC-HN-8 cells. Right: Fadu cells

    Techniques Used: Cell Counting, Invasion Assay, Migration, ROS Assay

    Correlation analysis of F. nucleatum abundance and uric acid level in head and neck squamous cell carcinoma (HNSCC) patients. A F. nucleatum and uric acid correlation analysis, B F. nucleatum and uric acid/creatinine correlation analysis
    Figure Legend Snippet: Correlation analysis of F. nucleatum abundance and uric acid level in head and neck squamous cell carcinoma (HNSCC) patients. A F. nucleatum and uric acid correlation analysis, B F. nucleatum and uric acid/creatinine correlation analysis

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    ATCC plasmid description reference strains f nucleatum 23726 parental strain
    Bacterial strains and plasmids used
    Plasmid Description Reference Strains F Nucleatum 23726 Parental Strain, 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 f nucleatum strain atcc 23726
    Construction and characterization of CRISPRi system in Fusobacterium nucleatum. (A) Mechanism of CRISPRi. The nuclease deficient (dCas9) binds single-guide RNA (sgRNA) to target the gene of interest via a 20-nt base-paring region. Instead of cleaving DNA, dCas9 obstructs RNA polymerase (RNAP) movement and inhibits transcription elongation, suppressing the target gene’s expression. (B) pZP4C construction blueprint for CRISPRi. pZP4C is derived from the E. coli-F. nucleatum shuttle vector pCWU6 and is aimed at ftsX. pCWU6 underwent SacI/HindIII digestion and was conjoined with two PCR fragments (Pfdx-E-dcas9 and PrpsJFP-sgRNA) through Gibson assembly, resulting in pZP4C. Within pZP4C, the dCas9’s expression is governed by Pfdx and a theophylline-responsive riboswitch E (indicated “E”), both at the transcriptional and translation stages. The sgRNA is driven by a constitutive active PrpsJ promoter from Fusobacterium periodonticum and can be replaced using the MscI and NotI restriction sites. Key features include using Pfdx-E from pREcas1 and the dCas9 and sgRNA element from pIA33, replication regions (oriFn, repA, and oriEc), and the catP, the chloramphenicol acetyltransferase gene. (C) ftsX gene suppression via CRISPRi. The wild-type F. nucleatum strain with pZP4C was cultivated in a TSPC medium under varying theophylline concentrations (0, 0.1, and 2 mM) for 22 hours. Induction of dcas9 expression by theophylline results in cells setting at the tube’s base after overnight growth, leaving a transparent supernatant characteristic similar to the ftsX deletion phenotype. (D) Western blot analysis validates ftsX silencing. Cell samples, including a wild-type control without inducer, were run on SDS-PAGE and immunoblotted. Antibodies for FtsX (α-FtsX) and FomA (α-FomA) were used, with FomA as the loading control. Molecular mass markers (in kilodaltons) are labeled on the left of the blot. (E) Silencing FtsX alters fusobacterial cell morphology. A phase-contrast microscopy recorded cell shapes in panel B. Bars, 2 µm.
    F Nucleatum Strain Atcc 23726, 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 f nucleatum atcc 25586 strains
    Construction and characterization of CRISPRi system in Fusobacterium nucleatum. (A) Mechanism of CRISPRi. The nuclease deficient (dCas9) binds single-guide RNA (sgRNA) to target the gene of interest via a 20-nt base-paring region. Instead of cleaving DNA, dCas9 obstructs RNA polymerase (RNAP) movement and inhibits transcription elongation, suppressing the target gene’s expression. (B) pZP4C construction blueprint for CRISPRi. pZP4C is derived from the E. coli-F. nucleatum shuttle vector pCWU6 and is aimed at ftsX. pCWU6 underwent SacI/HindIII digestion and was conjoined with two PCR fragments (Pfdx-E-dcas9 and PrpsJFP-sgRNA) through Gibson assembly, resulting in pZP4C. Within pZP4C, the dCas9’s expression is governed by Pfdx and a theophylline-responsive riboswitch E (indicated “E”), both at the transcriptional and translation stages. The sgRNA is driven by a constitutive active PrpsJ promoter from Fusobacterium periodonticum and can be replaced using the MscI and NotI restriction sites. Key features include using Pfdx-E from pREcas1 and the dCas9 and sgRNA element from pIA33, replication regions (oriFn, repA, and oriEc), and the catP, the chloramphenicol acetyltransferase gene. (C) ftsX gene suppression via CRISPRi. The wild-type F. nucleatum strain with pZP4C was cultivated in a TSPC medium under varying theophylline concentrations (0, 0.1, and 2 mM) for 22 hours. Induction of dcas9 expression by theophylline results in cells setting at the tube’s base after overnight growth, leaving a transparent supernatant characteristic similar to the ftsX deletion phenotype. (D) Western blot analysis validates ftsX silencing. Cell samples, including a wild-type control without inducer, were run on SDS-PAGE and immunoblotted. Antibodies for FtsX (α-FtsX) and FomA (α-FomA) were used, with FomA as the loading control. Molecular mass markers (in kilodaltons) are labeled on the left of the blot. (E) Silencing FtsX alters fusobacterial cell morphology. A phase-contrast microscopy recorded cell shapes in panel B. Bars, 2 µm.
    F Nucleatum Atcc 25586 Strains, 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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    86
    ATCC anaerobic strains f nucleatum atcc 25586
    Construction and characterization of CRISPRi system in Fusobacterium nucleatum. (A) Mechanism of CRISPRi. The nuclease deficient (dCas9) binds single-guide RNA (sgRNA) to target the gene of interest via a 20-nt base-paring region. Instead of cleaving DNA, dCas9 obstructs RNA polymerase (RNAP) movement and inhibits transcription elongation, suppressing the target gene’s expression. (B) pZP4C construction blueprint for CRISPRi. pZP4C is derived from the E. coli-F. nucleatum shuttle vector pCWU6 and is aimed at ftsX. pCWU6 underwent SacI/HindIII digestion and was conjoined with two PCR fragments (Pfdx-E-dcas9 and PrpsJFP-sgRNA) through Gibson assembly, resulting in pZP4C. Within pZP4C, the dCas9’s expression is governed by Pfdx and a theophylline-responsive riboswitch E (indicated “E”), both at the transcriptional and translation stages. The sgRNA is driven by a constitutive active PrpsJ promoter from Fusobacterium periodonticum and can be replaced using the MscI and NotI restriction sites. Key features include using Pfdx-E from pREcas1 and the dCas9 and sgRNA element from pIA33, replication regions (oriFn, repA, and oriEc), and the catP, the chloramphenicol acetyltransferase gene. (C) ftsX gene suppression via CRISPRi. The wild-type F. nucleatum strain with pZP4C was cultivated in a TSPC medium under varying theophylline concentrations (0, 0.1, and 2 mM) for 22 hours. Induction of dcas9 expression by theophylline results in cells setting at the tube’s base after overnight growth, leaving a transparent supernatant characteristic similar to the ftsX deletion phenotype. (D) Western blot analysis validates ftsX silencing. Cell samples, including a wild-type control without inducer, were run on SDS-PAGE and immunoblotted. Antibodies for FtsX (α-FtsX) and FomA (α-FomA) were used, with FomA as the loading control. Molecular mass markers (in kilodaltons) are labeled on the left of the blot. (E) Silencing FtsX alters fusobacterial cell morphology. A phase-contrast microscopy recorded cell shapes in panel B. Bars, 2 µm.
    Anaerobic Strains F 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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    ATCC f nucleatum subsp fusiforme strain atcc 51190
    A) Location of subspecies-/species-specific primer sets in each Fusobacterium genome. Genes are labeled with their annotated function if available, while hypothetical proteins are unlabeled. Forward and reverse primer locations are illustrated with red arrows. Genes and primers are not drawn to scale. B) Representative example of subspecies/species primer specificity. All reactions were performed using a mixture of gDNA from the four F. <t>nucleatum</t> subspecies and F. periodonticum . A DNA ladder is shown on the left.
    F Nucleatum Subsp Fusiforme Strain Atcc 51190, 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 f nucleatum strain atcc 25586
    A) Location of subspecies-/species-specific primer sets in each Fusobacterium genome. Genes are labeled with their annotated function if available, while hypothetical proteins are unlabeled. Forward and reverse primer locations are illustrated with red arrows. Genes and primers are not drawn to scale. B) Representative example of subspecies/species primer specificity. All reactions were performed using a mixture of gDNA from the four F. <t>nucleatum</t> subspecies and F. periodonticum . A DNA ladder is shown on the left.
    F Nucleatum Strain 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
    https://www.bioz.com/result/f nucleatum strain atcc 25586/product/ATCC
    Average 86 stars, based on 1 article reviews
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    ATCC conditioned media collection f nucleatum strain atcc
    A) Location of subspecies-/species-specific primer sets in each Fusobacterium genome. Genes are labeled with their annotated function if available, while hypothetical proteins are unlabeled. Forward and reverse primer locations are illustrated with red arrows. Genes and primers are not drawn to scale. B) Representative example of subspecies/species primer specificity. All reactions were performed using a mixture of gDNA from the four F. <t>nucleatum</t> subspecies and F. periodonticum . A DNA ladder is shown on the left.
    Conditioned Media Collection F Nucleatum Strain Atcc, 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
    https://www.bioz.com/result/conditioned media collection f nucleatum strain atcc/product/ATCC
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    ATCC f nucleatum strain
    Overall metabolic profiles of control, Fn_24hr group and Fn_48hr groups. A principal component analysis (PCA) plot for three groups was performed to visualize the overall metabolic differences and the variability within the groups. B orthogonal partial least squares discriminant analysis (OPLS-DA) plot of Fn_24hr group and control group, and C OPLS-DA of Fn_48hr group and control group were performed to further track the metabolic changes, which maximizes the variance between groups. Fn_24hr group: AMC-HN-8 cells and F. <t>nucleatum</t> were cocultured for 24hs. Fn_48hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 48hs
    F Nucleatum Strain, 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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    Bacterial strains and plasmids used

    Journal: Applied and Environmental Microbiology

    Article Title: Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum

    doi: 10.1128/aem.01665-23

    Figure Lengend Snippet: Bacterial strains and plasmids used

    Article Snippet: TABLE 2 Strain and plasmid Description Reference Strains F. nucleatum 23726 Parental strain (wild-type strain) From ATCC F. nucleatum CTI-2 Wild-type strain, isolated from human CRC samples ( 27 ) F. periodonticum 33693 Wild-type strain From ATCC F. nucleatum CW2 ∆ ftsX ; an isogenic derivative of CW1 ( 25 ) F. nucleatum BG01 ∆ radD ; an isogenic derivative of 23726 ( 39 ) F. nucleatum ZP05 WT strain 23726 containing pZP4C This study F. nucleatum ZP06 WT strain 23726 containing pZP4C( radD ) This study F. nucleatum ZP07 WT strain 23726 containing pZP4C( bamA ) This study F. nucleatum ZP07a WT strain 23726 containing pZP4C( control ) This study F. nucleatum ZP07b WT strain 23726 containing pZP4C( bamA )-P- bamA′ This study F. nucleatum ZP07c WT strain 23726 containing pZP4C( bamA )-P- skp-lpxD-glpQ This study F. nucleatum ZP07d WT strain 23726 containing pZP4C( bamA )-P- bamA′-skp-lpxD-glpQ This study F. nucleatum ZP08 WT strain 23726 containing pZP4C( ftsZ ) This study F. nucleatum ZP09 WT strain 33693 containing pZP4C( clpB Fp ) This study F. nucleatum ZP10 WT strain 33693 containing pZP4C( tnaA Fp ) This study F. nucleatum ZP11 WT strain CTI-2 containing pZP4C( tnaA CTI-2 ) This study E. coli DH5α Cloning host From NEB Plasmids pCWU6 E. coli / Fusobacterium shuttle vector, chloramphenicol /thiamphenicol resistance; cm R /thia R ( 25 ) pRECas1 The fdx promoter incorporating the riboswitch element E controls Cas9 expression ( 44 ) pIA33 P xyl::dcas9-opt P gdh ::sgRNA- rfp catP ( 67 ) pZP4C P fdx ::dcas9-opt P rpsJ FP ::sgRNA- ftsX catP This study pZP4C( radD ) P fdx ::dcas9-opt P rpsJ FP ::sgRNA- radD catP This study pZP4C- mCherry P fdx ::dcas9-opt P rpsJ FP ::P rpsJ cd :: mCherry catP This study pZP4C(control) P fdx ::dcas9-opt catP This study pZP4C( bamA ) P fdx ::dcas9-opt P rpsJ FP ::sgRNA- bamA catP This study pZP4C( bamA )-P- bamA ′ P fdx ::dcas9-opt P rpsJ FP ::sgRNA- bamA P bamA-bamA’ catP This study pZP4C( bamA )-P- skp-lpxD-glpQ P fdx ::dcas9-opt P rpsJ FP ::sgRNA- bamA P bamA-skp-lpxD-glpQ catP This study pZP4C( bamA )-P- bamA′-skp-lpxD-glpQ P fdx ::dcas9-opt P rpsJ FP ::sgRNA- bamA P bamA-bamA-skp-lpxD-glpQ catP This study pZP4C( ftsZ ) P fdx ::dcas9-opt P rpsJ FP ::sgRNA- ftsZ catP This study pZP4C( clpB Fp ) P fdx ::dcas9-opt P rpsJFP ::sgRNA- clpBFP catP This study pZP4C( tnaA Fp ) P fdx ::dcas9-opt P rpsJ FP ::sgRNA- tnaA FP catP This study pZP4C( tnaA CTI-2 ) P fdx ::dcas9-opt P rpsJ FP ::sgRNA- tnaA CTI-2 catP This study Open in a separate window Bacterial strains and plasmids used. . Plasmid and strain construction All constructed plasmids in this study are listed in .

    Techniques: Plasmid Preparation, Isolation, Clone Assay, Expressing

    Construction and characterization of CRISPRi system in Fusobacterium nucleatum. (A) Mechanism of CRISPRi. The nuclease deficient (dCas9) binds single-guide RNA (sgRNA) to target the gene of interest via a 20-nt base-paring region. Instead of cleaving DNA, dCas9 obstructs RNA polymerase (RNAP) movement and inhibits transcription elongation, suppressing the target gene’s expression. (B) pZP4C construction blueprint for CRISPRi. pZP4C is derived from the E. coli-F. nucleatum shuttle vector pCWU6 and is aimed at ftsX. pCWU6 underwent SacI/HindIII digestion and was conjoined with two PCR fragments (Pfdx-E-dcas9 and PrpsJFP-sgRNA) through Gibson assembly, resulting in pZP4C. Within pZP4C, the dCas9’s expression is governed by Pfdx and a theophylline-responsive riboswitch E (indicated “E”), both at the transcriptional and translation stages. The sgRNA is driven by a constitutive active PrpsJ promoter from Fusobacterium periodonticum and can be replaced using the MscI and NotI restriction sites. Key features include using Pfdx-E from pREcas1 and the dCas9 and sgRNA element from pIA33, replication regions (oriFn, repA, and oriEc), and the catP, the chloramphenicol acetyltransferase gene. (C) ftsX gene suppression via CRISPRi. The wild-type F. nucleatum strain with pZP4C was cultivated in a TSPC medium under varying theophylline concentrations (0, 0.1, and 2 mM) for 22 hours. Induction of dcas9 expression by theophylline results in cells setting at the tube’s base after overnight growth, leaving a transparent supernatant characteristic similar to the ftsX deletion phenotype. (D) Western blot analysis validates ftsX silencing. Cell samples, including a wild-type control without inducer, were run on SDS-PAGE and immunoblotted. Antibodies for FtsX (α-FtsX) and FomA (α-FomA) were used, with FomA as the loading control. Molecular mass markers (in kilodaltons) are labeled on the left of the blot. (E) Silencing FtsX alters fusobacterial cell morphology. A phase-contrast microscopy recorded cell shapes in panel B. Bars, 2 µm.

    Journal: Applied and Environmental Microbiology

    Article Title: Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum

    doi: 10.1128/aem.01665-23

    Figure Lengend Snippet: Construction and characterization of CRISPRi system in Fusobacterium nucleatum. (A) Mechanism of CRISPRi. The nuclease deficient (dCas9) binds single-guide RNA (sgRNA) to target the gene of interest via a 20-nt base-paring region. Instead of cleaving DNA, dCas9 obstructs RNA polymerase (RNAP) movement and inhibits transcription elongation, suppressing the target gene’s expression. (B) pZP4C construction blueprint for CRISPRi. pZP4C is derived from the E. coli-F. nucleatum shuttle vector pCWU6 and is aimed at ftsX. pCWU6 underwent SacI/HindIII digestion and was conjoined with two PCR fragments (Pfdx-E-dcas9 and PrpsJFP-sgRNA) through Gibson assembly, resulting in pZP4C. Within pZP4C, the dCas9’s expression is governed by Pfdx and a theophylline-responsive riboswitch E (indicated “E”), both at the transcriptional and translation stages. The sgRNA is driven by a constitutive active PrpsJ promoter from Fusobacterium periodonticum and can be replaced using the MscI and NotI restriction sites. Key features include using Pfdx-E from pREcas1 and the dCas9 and sgRNA element from pIA33, replication regions (oriFn, repA, and oriEc), and the catP, the chloramphenicol acetyltransferase gene. (C) ftsX gene suppression via CRISPRi. The wild-type F. nucleatum strain with pZP4C was cultivated in a TSPC medium under varying theophylline concentrations (0, 0.1, and 2 mM) for 22 hours. Induction of dcas9 expression by theophylline results in cells setting at the tube’s base after overnight growth, leaving a transparent supernatant characteristic similar to the ftsX deletion phenotype. (D) Western blot analysis validates ftsX silencing. Cell samples, including a wild-type control without inducer, were run on SDS-PAGE and immunoblotted. Antibodies for FtsX (α-FtsX) and FomA (α-FomA) were used, with FomA as the loading control. Molecular mass markers (in kilodaltons) are labeled on the left of the blot. (E) Silencing FtsX alters fusobacterial cell morphology. A phase-contrast microscopy recorded cell shapes in panel B. Bars, 2 µm.

    Article Snippet: These set it apart from the F. nucleatum strain ATCC 23726, which is sourced from the human urogenital tract.

    Techniques: Expressing, Derivative Assay, Plasmid Preparation, Western Blot, SDS Page, Labeling, Microscopy

    A) Location of subspecies-/species-specific primer sets in each Fusobacterium genome. Genes are labeled with their annotated function if available, while hypothetical proteins are unlabeled. Forward and reverse primer locations are illustrated with red arrows. Genes and primers are not drawn to scale. B) Representative example of subspecies/species primer specificity. All reactions were performed using a mixture of gDNA from the four F. nucleatum subspecies and F. periodonticum . A DNA ladder is shown on the left.

    Journal: bioRxiv

    Article Title: The prevalence of Fusobacterium nucleatum subspecies in the oral cavity stratifies by local health status

    doi: 10.1101/2023.10.25.563997

    Figure Lengend Snippet: A) Location of subspecies-/species-specific primer sets in each Fusobacterium genome. Genes are labeled with their annotated function if available, while hypothetical proteins are unlabeled. Forward and reverse primer locations are illustrated with red arrows. Genes and primers are not drawn to scale. B) Representative example of subspecies/species primer specificity. All reactions were performed using a mixture of gDNA from the four F. nucleatum subspecies and F. periodonticum . A DNA ladder is shown on the left.

    Article Snippet: The znpA and 16S V3V4 rDNA gene sequences were obtained from the following strains: F. nucleatum subsp. nucleatum ATCC 25586, F. nucleatum subsp. animalis ATCC 51191, F. nucleatum subsp. polymorphum ATCC 10953, and F. nucleatum subsp. fusiforme strain ATCC 51190.

    Techniques: Labeling

    Overall metabolic profiles of control, Fn_24hr group and Fn_48hr groups. A principal component analysis (PCA) plot for three groups was performed to visualize the overall metabolic differences and the variability within the groups. B orthogonal partial least squares discriminant analysis (OPLS-DA) plot of Fn_24hr group and control group, and C OPLS-DA of Fn_48hr group and control group were performed to further track the metabolic changes, which maximizes the variance between groups. Fn_24hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 24hs. Fn_48hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 48hs

    Journal: Discover. Oncology

    Article Title: Fusobacterium nucleatum -triggered purine metabolic reprogramming drives tumorigenesis in head and neck carcinoma

    doi: 10.1007/s12672-023-00727-x

    Figure Lengend Snippet: Overall metabolic profiles of control, Fn_24hr group and Fn_48hr groups. A principal component analysis (PCA) plot for three groups was performed to visualize the overall metabolic differences and the variability within the groups. B orthogonal partial least squares discriminant analysis (OPLS-DA) plot of Fn_24hr group and control group, and C OPLS-DA of Fn_48hr group and control group were performed to further track the metabolic changes, which maximizes the variance between groups. Fn_24hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 24hs. Fn_48hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 48hs

    Article Snippet: The F. nucleatum strain was purchased from the American Type Culture Collection (ATCC 25586, Virginia, USA) and was maintained overnight at 37 °C under anaerobic conditions on Columbia blood agar supplemented with five mg/mL hemin, 5% defibrinated sheep blood, and one mg/mL vitamin K1.

    Techniques:

    Volcano plot showing metabolic alterations of ( A ) Fn_24hr group vs. control group and ( B ) Fn_48hr group vs. control group. Arrows point out critical metabolites related to the purine metabolic pathway. Fn_24hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 24 hs. Fn_48hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 48 hs

    Journal: Discover. Oncology

    Article Title: Fusobacterium nucleatum -triggered purine metabolic reprogramming drives tumorigenesis in head and neck carcinoma

    doi: 10.1007/s12672-023-00727-x

    Figure Lengend Snippet: Volcano plot showing metabolic alterations of ( A ) Fn_24hr group vs. control group and ( B ) Fn_48hr group vs. control group. Arrows point out critical metabolites related to the purine metabolic pathway. Fn_24hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 24 hs. Fn_48hr group: AMC-HN-8 cells and F. nucleatum were cocultured for 48 hs

    Article Snippet: The F. nucleatum strain was purchased from the American Type Culture Collection (ATCC 25586, Virginia, USA) and was maintained overnight at 37 °C under anaerobic conditions on Columbia blood agar supplemented with five mg/mL hemin, 5% defibrinated sheep blood, and one mg/mL vitamin K1.

    Techniques:

    F. nucleatum –triggered tumor progression and ROS accumulation could be reversed by uric acid: A cell proliferation measured using Cell Counting Kit-8 assay (CCK8), B invasion assay performed using transwell chambers, C migration assay performed using transwell chambers and D Intracellular ROS detection using fluorometric intracellular ROS assay kit. Left: AMC-HN-8 cells. Right: Fadu cells

    Journal: Discover. Oncology

    Article Title: Fusobacterium nucleatum -triggered purine metabolic reprogramming drives tumorigenesis in head and neck carcinoma

    doi: 10.1007/s12672-023-00727-x

    Figure Lengend Snippet: F. nucleatum –triggered tumor progression and ROS accumulation could be reversed by uric acid: A cell proliferation measured using Cell Counting Kit-8 assay (CCK8), B invasion assay performed using transwell chambers, C migration assay performed using transwell chambers and D Intracellular ROS detection using fluorometric intracellular ROS assay kit. Left: AMC-HN-8 cells. Right: Fadu cells

    Article Snippet: The F. nucleatum strain was purchased from the American Type Culture Collection (ATCC 25586, Virginia, USA) and was maintained overnight at 37 °C under anaerobic conditions on Columbia blood agar supplemented with five mg/mL hemin, 5% defibrinated sheep blood, and one mg/mL vitamin K1.

    Techniques: Cell Counting, Invasion Assay, Migration, ROS Assay

    Correlation analysis of F. nucleatum abundance and uric acid level in head and neck squamous cell carcinoma (HNSCC) patients. A F. nucleatum and uric acid correlation analysis, B F. nucleatum and uric acid/creatinine correlation analysis

    Journal: Discover. Oncology

    Article Title: Fusobacterium nucleatum -triggered purine metabolic reprogramming drives tumorigenesis in head and neck carcinoma

    doi: 10.1007/s12672-023-00727-x

    Figure Lengend Snippet: Correlation analysis of F. nucleatum abundance and uric acid level in head and neck squamous cell carcinoma (HNSCC) patients. A F. nucleatum and uric acid correlation analysis, B F. nucleatum and uric acid/creatinine correlation analysis

    Article Snippet: The F. nucleatum strain was purchased from the American Type Culture Collection (ATCC 25586, Virginia, USA) and was maintained overnight at 37 °C under anaerobic conditions on Columbia blood agar supplemented with five mg/mL hemin, 5% defibrinated sheep blood, and one mg/mL vitamin K1.

    Techniques: