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  • hb101  (ATCC)
    93
    ATCC hb101
    FimH-mediated adhesion of T1F-UPEC to urothelial surface was a prerequisite for NF-κB activation. ( A ) Effects of different E. coli strains on RelA translocation. Wild-type mice were transurethrally instilled with PBS or that containing the following bacteria: <t>HB101</t> (a laboratory K12 strain not expressing the type 1 fimbriae); NU14-1 (a FimH deletion strain not expressing the type 1 fimbriae); NU14 (a clinical cystitis T1F-UPEC isolate which is the parental strain of NU14-1); UTI89; and CFT073 (a clinical pyelonephritis T1F-UPEC strain). Immunofluorescent staining was carried out on urinary bladders 1 h post-instillation and nuclei positively stained for RelA was counted and expressed as per 100 umbrella nuclei (see Materials and Methods for details). Note that UPEC strains expressing the type 1 fimbriae (NU14, UTI89 and CFT073), but not those non-type 1-fimbriated ones, induced significant nuclear translocation of RelA. ( B–D ) Effects of FimH-mediated adhesion of UPEC to urothelial cells on NF-κB activation. ( B ) Wild-type mice were transurethrally inoculated with the same number (10 8 cfu) of T1F-UPEC strain UTI89, or a derivative of UTI89 expressing a FimH mutant (e.g., Q133N) (*) that lacks the ability to bind the terminal mannoses; or a derivative of UTI89 with FimH deletion (∆FimH) (∆). ( C–D ) Wild-type mice were transurethrally inoculated with the same number (10 8 cfu) of T1F-UPEC strain UTI89 in the presence of 0, 0.1, 0.5 mg/ml of FimH or 0.5 mg/ml heat-inactivated (Heated) FimH ( C ), or in the presence of 0, 5 or 50 mM of D-mannose ( D ). One hour after inoculation, urinary bladders of all experimental groups ( B–D ) were processed for double-immunofluorescence staining using antibodies against E. coli and RelA. Representative images and semi-quantification of RelA-positive umbrella cell nuclei per 100 total umbrella nuclei were shown. Note that FimH mutation and deletion or addition of free FimH or D-mannose abolished UPEC-urothelial adhesion as well as NF-κB activation. Heat-inactivated FimH, however, failed to block NF-κB activation by UPEC ( C ). Scale bars: 100 μm (B–D).
    Hb101, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 45 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    ATCC e coli strain hb101
    Gene amplification of rhsA in EHEC strain EDL933. (A) Diagram of the region between loci z5013 and z5018 according to Perna et al. ( 2001 ) and according to Latif et al. ( 2014 ). The rhs gene (red) has a different C-terminal end in each genome, harboring a DNAse domain (green) in and the sequence corresponding to locus z5017 (red). (B) The 800 bp amplicon for rhsA gene (locus z5014 ) was not generated in EHEC strain EDL933 using the primer pair rhsAF-rhsA1R designed for the gene according to Perna et al. ( 2001 ). E. coli strain <t>HB101</t> was used as a positive control for these primers (rhsAF-rhsA1R), which generated an 800 bp amplicon. Whereas, when the primer pair rhsAF-rhsA2R designed based on Perna et al. ( 2001 ) and Latif et al. ( 2014 ) was used, the expected 2.6 kb fragment was not obtained, but the 875 bp was, as expected from the genome from Latif et al. ( 2014 ). By using a specific primer (rhsCR) for rhsC , a 832 bp fragment was obtained, as expected from the genome of Latif et al. ( 2014 ), while the 2.7 kb fragment from the genome of Perna et al. ( 2001 ) was not obtained neither in EHEC EDL933 nor in E. coli strain HB101. A 63°C temperature was used for (B) . The PCR products were separated in an 1.5% agarose gel and stained using ethidium bromide.
    E Coli Strain Hb101, supplied by ATCC, used in various techniques. Bioz Stars score: 88/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Irvine Scientific hb 101
    Gene amplification of rhsA in EHEC strain EDL933. (A) Diagram of the region between loci z5013 and z5018 according to Perna et al. ( 2001 ) and according to Latif et al. ( 2014 ). The rhs gene (red) has a different C-terminal end in each genome, harboring a DNAse domain (green) in and the sequence corresponding to locus z5017 (red). (B) The 800 bp amplicon for rhsA gene (locus z5014 ) was not generated in EHEC strain EDL933 using the primer pair rhsAF-rhsA1R designed for the gene according to Perna et al. ( 2001 ). E. coli strain <t>HB101</t> was used as a positive control for these primers (rhsAF-rhsA1R), which generated an 800 bp amplicon. Whereas, when the primer pair rhsAF-rhsA2R designed based on Perna et al. ( 2001 ) and Latif et al. ( 2014 ) was used, the expected 2.6 kb fragment was not obtained, but the 875 bp was, as expected from the genome from Latif et al. ( 2014 ). By using a specific primer (rhsCR) for rhsC , a 832 bp fragment was obtained, as expected from the genome of Latif et al. ( 2014 ), while the 2.7 kb fragment from the genome of Perna et al. ( 2001 ) was not obtained neither in EHEC EDL933 nor in E. coli strain HB101. A 63°C temperature was used for (B) . The PCR products were separated in an 1.5% agarose gel and stained using ethidium bromide.
    Hb 101, supplied by Irvine Scientific, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher hb101
    Gene amplification of rhsA in EHEC strain EDL933. (A) Diagram of the region between loci z5013 and z5018 according to Perna et al. ( 2001 ) and according to Latif et al. ( 2014 ). The rhs gene (red) has a different C-terminal end in each genome, harboring a DNAse domain (green) in and the sequence corresponding to locus z5017 (red). (B) The 800 bp amplicon for rhsA gene (locus z5014 ) was not generated in EHEC strain EDL933 using the primer pair rhsAF-rhsA1R designed for the gene according to Perna et al. ( 2001 ). E. coli strain <t>HB101</t> was used as a positive control for these primers (rhsAF-rhsA1R), which generated an 800 bp amplicon. Whereas, when the primer pair rhsAF-rhsA2R designed based on Perna et al. ( 2001 ) and Latif et al. ( 2014 ) was used, the expected 2.6 kb fragment was not obtained, but the 875 bp was, as expected from the genome from Latif et al. ( 2014 ). By using a specific primer (rhsCR) for rhsC , a 832 bp fragment was obtained, as expected from the genome of Latif et al. ( 2014 ), while the 2.7 kb fragment from the genome of Perna et al. ( 2001 ) was not obtained neither in EHEC EDL933 nor in E. coli strain HB101. A 63°C temperature was used for (B) . The PCR products were separated in an 1.5% agarose gel and stained using ethidium bromide.
    Hb101, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 61 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    FimH-mediated adhesion of T1F-UPEC to urothelial surface was a prerequisite for NF-κB activation. ( A ) Effects of different E. coli strains on RelA translocation. Wild-type mice were transurethrally instilled with PBS or that containing the following bacteria: HB101 (a laboratory K12 strain not expressing the type 1 fimbriae); NU14-1 (a FimH deletion strain not expressing the type 1 fimbriae); NU14 (a clinical cystitis T1F-UPEC isolate which is the parental strain of NU14-1); UTI89; and CFT073 (a clinical pyelonephritis T1F-UPEC strain). Immunofluorescent staining was carried out on urinary bladders 1 h post-instillation and nuclei positively stained for RelA was counted and expressed as per 100 umbrella nuclei (see Materials and Methods for details). Note that UPEC strains expressing the type 1 fimbriae (NU14, UTI89 and CFT073), but not those non-type 1-fimbriated ones, induced significant nuclear translocation of RelA. ( B–D ) Effects of FimH-mediated adhesion of UPEC to urothelial cells on NF-κB activation. ( B ) Wild-type mice were transurethrally inoculated with the same number (10 8 cfu) of T1F-UPEC strain UTI89, or a derivative of UTI89 expressing a FimH mutant (e.g., Q133N) (*) that lacks the ability to bind the terminal mannoses; or a derivative of UTI89 with FimH deletion (∆FimH) (∆). ( C–D ) Wild-type mice were transurethrally inoculated with the same number (10 8 cfu) of T1F-UPEC strain UTI89 in the presence of 0, 0.1, 0.5 mg/ml of FimH or 0.5 mg/ml heat-inactivated (Heated) FimH ( C ), or in the presence of 0, 5 or 50 mM of D-mannose ( D ). One hour after inoculation, urinary bladders of all experimental groups ( B–D ) were processed for double-immunofluorescence staining using antibodies against E. coli and RelA. Representative images and semi-quantification of RelA-positive umbrella cell nuclei per 100 total umbrella nuclei were shown. Note that FimH mutation and deletion or addition of free FimH or D-mannose abolished UPEC-urothelial adhesion as well as NF-κB activation. Heat-inactivated FimH, however, failed to block NF-κB activation by UPEC ( C ). Scale bars: 100 μm (B–D).

    Journal: Scientific Reports

    Article Title: Dual ligand/receptor interactions activate urothelial defenses against uropathogenic E. coli

    doi: 10.1038/srep16234

    Figure Lengend Snippet: FimH-mediated adhesion of T1F-UPEC to urothelial surface was a prerequisite for NF-κB activation. ( A ) Effects of different E. coli strains on RelA translocation. Wild-type mice were transurethrally instilled with PBS or that containing the following bacteria: HB101 (a laboratory K12 strain not expressing the type 1 fimbriae); NU14-1 (a FimH deletion strain not expressing the type 1 fimbriae); NU14 (a clinical cystitis T1F-UPEC isolate which is the parental strain of NU14-1); UTI89; and CFT073 (a clinical pyelonephritis T1F-UPEC strain). Immunofluorescent staining was carried out on urinary bladders 1 h post-instillation and nuclei positively stained for RelA was counted and expressed as per 100 umbrella nuclei (see Materials and Methods for details). Note that UPEC strains expressing the type 1 fimbriae (NU14, UTI89 and CFT073), but not those non-type 1-fimbriated ones, induced significant nuclear translocation of RelA. ( B–D ) Effects of FimH-mediated adhesion of UPEC to urothelial cells on NF-κB activation. ( B ) Wild-type mice were transurethrally inoculated with the same number (10 8 cfu) of T1F-UPEC strain UTI89, or a derivative of UTI89 expressing a FimH mutant (e.g., Q133N) (*) that lacks the ability to bind the terminal mannoses; or a derivative of UTI89 with FimH deletion (∆FimH) (∆). ( C–D ) Wild-type mice were transurethrally inoculated with the same number (10 8 cfu) of T1F-UPEC strain UTI89 in the presence of 0, 0.1, 0.5 mg/ml of FimH or 0.5 mg/ml heat-inactivated (Heated) FimH ( C ), or in the presence of 0, 5 or 50 mM of D-mannose ( D ). One hour after inoculation, urinary bladders of all experimental groups ( B–D ) were processed for double-immunofluorescence staining using antibodies against E. coli and RelA. Representative images and semi-quantification of RelA-positive umbrella cell nuclei per 100 total umbrella nuclei were shown. Note that FimH mutation and deletion or addition of free FimH or D-mannose abolished UPEC-urothelial adhesion as well as NF-κB activation. Heat-inactivated FimH, however, failed to block NF-κB activation by UPEC ( C ). Scale bars: 100 μm (B–D).

    Article Snippet: Bacterial Strains and Culture The following E. coli strains were used: (1) UTI89, a type 1-fimbriated uropathogenic E. coli (T1F-UPEC) isolate from an acute cystitis patient ; (2) UTI89/Q133N, a recombinant strain engineered from the parental UTI89 strain with a point mutation converting codon 133 of FimH adhesin from Q to N, thus abolishing FimH’s ability to bind terminal mannoses; (3) UTI89/∆FimH, a recombinant strain engineered from the parental UTI89 strain with FimH adhesin deleted; (4) CFT073 (from ATCC), a T1F-UPEC strain isolated from the blood and urine of a patient with acute pyelonephritis ; (5) NU14, a T1F-UPEC strain isolated from an acute cystitis patient ; (6) NU14-1, a recombinant strain derived from NU14 with FimH adhesin deleted ; (7) HB101, a non-fimbriated, K12 laboratory E. coli strain (ATCC) ; and (8) UTI89/FimB, a derivative strain from UTI89 after transfection with a plasmid encoding the FimB gene (pACYC177/FimB), which “locks on” the type 1 fimbrial expression .

    Techniques: Activation Assay, Translocation Assay, Mouse Assay, Expressing, Staining, Mutagenesis, Double Immunofluorescence Staining, Blocking Assay

    The effect of the presence of EcoVIII RM system in recipient cells on efficiency of conjugal transfer of plasmid F. E . coli DH5α Rif [F’ ts 114 lac ::Tn 5 , Km R ] was used as donor. The following recipient bacteria were assayed: Escherichia coli HB101, Enterobacter cloacae , Klebsiella oxytoca , Citrobacter freundii , and Salmonella enteritidis that carried either pEC156-derivative pIB8 (EcoVIII R + M + , black bars) or pIB9 (EcoVIII R − M − , grey bars). Each column represents the mean value (± standard deviation) from three repeats. Statistical analysis revealed correlation between presence of a plasmid with RM system in the recipient bacteria and frequency of F plasmid conjugal transfer ( P

    Journal: PLoS ONE

    Article Title: Plasmid pEC156, a Naturally Occurring Escherichia coli Genetic Element That Carries Genes of the EcoVIII Restriction-Modification System, Is Mobilizable among Enterobacteria

    doi: 10.1371/journal.pone.0148355

    Figure Lengend Snippet: The effect of the presence of EcoVIII RM system in recipient cells on efficiency of conjugal transfer of plasmid F. E . coli DH5α Rif [F’ ts 114 lac ::Tn 5 , Km R ] was used as donor. The following recipient bacteria were assayed: Escherichia coli HB101, Enterobacter cloacae , Klebsiella oxytoca , Citrobacter freundii , and Salmonella enteritidis that carried either pEC156-derivative pIB8 (EcoVIII R + M + , black bars) or pIB9 (EcoVIII R − M − , grey bars). Each column represents the mean value (± standard deviation) from three repeats. Statistical analysis revealed correlation between presence of a plasmid with RM system in the recipient bacteria and frequency of F plasmid conjugal transfer ( P

    Article Snippet: E . coli MG1655 (wild type), E . coli HB101 (F− recA 13 rpsL 20(SmR ), Klebsiella oxytoca KPD118-BA, Citrobacter freundii NCTC 9750, Salmonella enteritidis , Enterobacter cloacae ATCC 13047 (ApR , SmR ) were obtained from the Collection of Plasmids and Microorganisms, University of Gdansk, Gdansk, Poland.

    Techniques: Plasmid Preparation, Standard Deviation

    Efficiency of natural transformation of E . coli HB101 with pEC156-derivatives pIB8A (EcoVIII R + M + ) and pIB9A (EcoVIII R − M − ). Plasmid pUC19 was used as a control. Each column represents the mean value (± standard deviation) from three repeats. Statistical significance analyzed by Student’s t test revealed lack of correlation between presence of EcoVIII RM system and efficiency of natural transformation ( P = 0.12; Student t test).

    Journal: PLoS ONE

    Article Title: Plasmid pEC156, a Naturally Occurring Escherichia coli Genetic Element That Carries Genes of the EcoVIII Restriction-Modification System, Is Mobilizable among Enterobacteria

    doi: 10.1371/journal.pone.0148355

    Figure Lengend Snippet: Efficiency of natural transformation of E . coli HB101 with pEC156-derivatives pIB8A (EcoVIII R + M + ) and pIB9A (EcoVIII R − M − ). Plasmid pUC19 was used as a control. Each column represents the mean value (± standard deviation) from three repeats. Statistical significance analyzed by Student’s t test revealed lack of correlation between presence of EcoVIII RM system and efficiency of natural transformation ( P = 0.12; Student t test).

    Article Snippet: E . coli MG1655 (wild type), E . coli HB101 (F− recA 13 rpsL 20(SmR ), Klebsiella oxytoca KPD118-BA, Citrobacter freundii NCTC 9750, Salmonella enteritidis , Enterobacter cloacae ATCC 13047 (ApR , SmR ) were obtained from the Collection of Plasmids and Microorganisms, University of Gdansk, Gdansk, Poland.

    Techniques: Transformation Assay, Plasmid Preparation, Standard Deviation

    Isoelectric focusing patterns of carbapenem-resistant K. pneumoniae 1534. The gel was stained with nitrocefin, which is specific for β-lactamases. Lane 1, cell lysate prepared from the imipenem-resistant E. coli DH5α containing the bla KPC-1 gene on pBR322- catI ; lane 2, cell lysate prepared from imipenem-resistant E. coli HB101 that was transformed with K. pneumoniae 1534 DNA; lane 3, cell lysate prepared from K. pneumoniae 1534; lane 4, cell lysates prepared from strains producing SHV-2 (pI of 7.6), TEM-3 (pI of 6.3), and TEM-1 (pI of 5.4); lane 5, cell lysates prepared from strains producing TEM-1 (pI of 5.4) and SHV-4 (pI of 7.8); lane 6, cell lysates prepared from strains producing TEM-12 (pI of 5.25), TEM-10 (pI of 5.6), SHV-3 (pI of 6.8), and SHV-2 (pI of 7.6). The extra bands between pIs 6.7 and 5.4 are presumably degradation products of KPC-1 (lanes 1 to 3). The pIs of the β-lactamases were calculated by using the known pIs of TEM-12 (pI of 5.25), TEM-1 (pI of 5.4), TEM-10 (pI of 5.6), TEM-3 (pI of 6.3), SHV-3 (pI of 6.8), SHV-2 (pI of 7.6), and SHV-4 (pI of 7.8).

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Novel Carbapenem-Hydrolyzing ?-Lactamase, KPC-1, from a Carbapenem-Resistant Strain of Klebsiella pneumoniae

    doi: 10.1128/AAC.45.4.1151-1161.2001

    Figure Lengend Snippet: Isoelectric focusing patterns of carbapenem-resistant K. pneumoniae 1534. The gel was stained with nitrocefin, which is specific for β-lactamases. Lane 1, cell lysate prepared from the imipenem-resistant E. coli DH5α containing the bla KPC-1 gene on pBR322- catI ; lane 2, cell lysate prepared from imipenem-resistant E. coli HB101 that was transformed with K. pneumoniae 1534 DNA; lane 3, cell lysate prepared from K. pneumoniae 1534; lane 4, cell lysates prepared from strains producing SHV-2 (pI of 7.6), TEM-3 (pI of 6.3), and TEM-1 (pI of 5.4); lane 5, cell lysates prepared from strains producing TEM-1 (pI of 5.4) and SHV-4 (pI of 7.8); lane 6, cell lysates prepared from strains producing TEM-12 (pI of 5.25), TEM-10 (pI of 5.6), SHV-3 (pI of 6.8), and SHV-2 (pI of 7.6). The extra bands between pIs 6.7 and 5.4 are presumably degradation products of KPC-1 (lanes 1 to 3). The pIs of the β-lactamases were calculated by using the known pIs of TEM-12 (pI of 5.25), TEM-1 (pI of 5.4), TEM-10 (pI of 5.6), TEM-3 (pI of 6.3), SHV-3 (pI of 6.8), SHV-2 (pI of 7.6), and SHV-4 (pI of 7.8).

    Article Snippet: Negative controls for carbapenemase production included E. coli HB101 and K. pneumoniae ATCC 13883.

    Techniques: Staining, Transformation Assay, Transmission Electron Microscopy

    (A) Inhibition assay with imipenem (IPM); (B) inhibition assay with meropenem (MEM). Disks: 1, lysate of K. pneumoniae 1534 (parent strain); 2, lysate of E. coli HB101/pBR322- catI ; 3, disk control with imipenem (A) or meropenem (B); 4, lysate of K. pneumoniae ATCC 13883; 5, lysate of E. coli HB101/pBR322- catI - bla KPC-1 clone.

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Novel Carbapenem-Hydrolyzing ?-Lactamase, KPC-1, from a Carbapenem-Resistant Strain of Klebsiella pneumoniae

    doi: 10.1128/AAC.45.4.1151-1161.2001

    Figure Lengend Snippet: (A) Inhibition assay with imipenem (IPM); (B) inhibition assay with meropenem (MEM). Disks: 1, lysate of K. pneumoniae 1534 (parent strain); 2, lysate of E. coli HB101/pBR322- catI ; 3, disk control with imipenem (A) or meropenem (B); 4, lysate of K. pneumoniae ATCC 13883; 5, lysate of E. coli HB101/pBR322- catI - bla KPC-1 clone.

    Article Snippet: Negative controls for carbapenemase production included E. coli HB101 and K. pneumoniae ATCC 13883.

    Techniques: Inhibition

    (A) Plasmid profiles of K. pneumoniae 1534 and an E. coli transformant on 0.85% agarose gel. Lane 1, plasmid RP4 (57-kb); lane 2, plasmid pDK9 (165-kb); lane 3, total DNA prepared from an E. coli HB101 transformant; lane 4, total DNA isolated from K. pneumoniae 1534; lane 5, plasmid R1 (97-kb). Chr., chromosomal. (B) Southern blot of the gel shown in panel A after hybridization with a 1,010-bp bla KPC-1 -specific probe. Lane 1, RP4 DNA; lane 2, pDK9 DNA; and lane 5, R1 DNA served as negative controls for the probe. DNA isolated from K. pneumoniae 1534 (lane 4) was used as a positive control. Lane 3, DNA isolated from an E. coli HB101 transformant of K. pneumoniae 1534 DNA that was imipenem resistant.

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Novel Carbapenem-Hydrolyzing ?-Lactamase, KPC-1, from a Carbapenem-Resistant Strain of Klebsiella pneumoniae

    doi: 10.1128/AAC.45.4.1151-1161.2001

    Figure Lengend Snippet: (A) Plasmid profiles of K. pneumoniae 1534 and an E. coli transformant on 0.85% agarose gel. Lane 1, plasmid RP4 (57-kb); lane 2, plasmid pDK9 (165-kb); lane 3, total DNA prepared from an E. coli HB101 transformant; lane 4, total DNA isolated from K. pneumoniae 1534; lane 5, plasmid R1 (97-kb). Chr., chromosomal. (B) Southern blot of the gel shown in panel A after hybridization with a 1,010-bp bla KPC-1 -specific probe. Lane 1, RP4 DNA; lane 2, pDK9 DNA; and lane 5, R1 DNA served as negative controls for the probe. DNA isolated from K. pneumoniae 1534 (lane 4) was used as a positive control. Lane 3, DNA isolated from an E. coli HB101 transformant of K. pneumoniae 1534 DNA that was imipenem resistant.

    Article Snippet: Negative controls for carbapenemase production included E. coli HB101 and K. pneumoniae ATCC 13883.

    Techniques: Plasmid Preparation, Agarose Gel Electrophoresis, Isolation, Southern Blot, Hybridization, Positive Control

    The chemerin-derived peptide 4 (Val 66 -Pro 85 ) strongly inhibits growth of E. coli . Chemically synthesized chemerin peptides (p1-p14) were tested against E. coli HB101 using the microtitre broth dilution assay (A) or against E. coli ATCC 25922 using radial diffusion assay (RDA) in physiological 0.15 M NaCl (B) or low salt concentration (C). Bacteria were incubated with the peptides at 100 µM. The results are expressed as the mean ± SD of three independent experiments.

    Journal: PLoS ONE

    Article Title: Chemerin Is an Antimicrobial Agent in Human Epidermis

    doi: 10.1371/journal.pone.0058709

    Figure Lengend Snippet: The chemerin-derived peptide 4 (Val 66 -Pro 85 ) strongly inhibits growth of E. coli . Chemically synthesized chemerin peptides (p1-p14) were tested against E. coli HB101 using the microtitre broth dilution assay (A) or against E. coli ATCC 25922 using radial diffusion assay (RDA) in physiological 0.15 M NaCl (B) or low salt concentration (C). Bacteria were incubated with the peptides at 100 µM. The results are expressed as the mean ± SD of three independent experiments.

    Article Snippet: The selected chemerin-derived peptides (100 µM) were tested for antibacterial activity against E. coli strains HB101 and ATCC 25922 using the MBD and RDA assays, respectively.

    Techniques: Derivative Assay, Synthesized, Dilution Assay, Diffusion-based Assay, Concentration Assay, Incubation

    Gene amplification of rhsA in EHEC strain EDL933. (A) Diagram of the region between loci z5013 and z5018 according to Perna et al. ( 2001 ) and according to Latif et al. ( 2014 ). The rhs gene (red) has a different C-terminal end in each genome, harboring a DNAse domain (green) in and the sequence corresponding to locus z5017 (red). (B) The 800 bp amplicon for rhsA gene (locus z5014 ) was not generated in EHEC strain EDL933 using the primer pair rhsAF-rhsA1R designed for the gene according to Perna et al. ( 2001 ). E. coli strain HB101 was used as a positive control for these primers (rhsAF-rhsA1R), which generated an 800 bp amplicon. Whereas, when the primer pair rhsAF-rhsA2R designed based on Perna et al. ( 2001 ) and Latif et al. ( 2014 ) was used, the expected 2.6 kb fragment was not obtained, but the 875 bp was, as expected from the genome from Latif et al. ( 2014 ). By using a specific primer (rhsCR) for rhsC , a 832 bp fragment was obtained, as expected from the genome of Latif et al. ( 2014 ), while the 2.7 kb fragment from the genome of Perna et al. ( 2001 ) was not obtained neither in EHEC EDL933 nor in E. coli strain HB101. A 63°C temperature was used for (B) . The PCR products were separated in an 1.5% agarose gel and stained using ethidium bromide.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: In silico Analyses of Core Proteins and Putative Effector and Immunity Proteins for T6SS in Enterohemorrhagic E. coli

    doi: 10.3389/fcimb.2020.00195

    Figure Lengend Snippet: Gene amplification of rhsA in EHEC strain EDL933. (A) Diagram of the region between loci z5013 and z5018 according to Perna et al. ( 2001 ) and according to Latif et al. ( 2014 ). The rhs gene (red) has a different C-terminal end in each genome, harboring a DNAse domain (green) in and the sequence corresponding to locus z5017 (red). (B) The 800 bp amplicon for rhsA gene (locus z5014 ) was not generated in EHEC strain EDL933 using the primer pair rhsAF-rhsA1R designed for the gene according to Perna et al. ( 2001 ). E. coli strain HB101 was used as a positive control for these primers (rhsAF-rhsA1R), which generated an 800 bp amplicon. Whereas, when the primer pair rhsAF-rhsA2R designed based on Perna et al. ( 2001 ) and Latif et al. ( 2014 ) was used, the expected 2.6 kb fragment was not obtained, but the 875 bp was, as expected from the genome from Latif et al. ( 2014 ). By using a specific primer (rhsCR) for rhsC , a 832 bp fragment was obtained, as expected from the genome of Latif et al. ( 2014 ), while the 2.7 kb fragment from the genome of Perna et al. ( 2001 ) was not obtained neither in EHEC EDL933 nor in E. coli strain HB101. A 63°C temperature was used for (B) . The PCR products were separated in an 1.5% agarose gel and stained using ethidium bromide.

    Article Snippet: E. coli strain HB101 was obtained from ATCC 33694.

    Techniques: Amplification, Sequencing, Generated, Positive Control, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Staining