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  • 89
    TaKaRa polymerase chain reaction pcr buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    Polymerase Chain Reaction Pcr Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 89/100, based on 1980 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    TaKaRa polymerase chain reaction pcr buffer 10x
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    Polymerase Chain Reaction Pcr Buffer 10x, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 75 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    TaKaRa polymerase chain reaction pcr solution
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    Polymerase Chain Reaction Pcr Solution, supplied by TaKaRa, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa polymerase chain reaction pcr amplification kit
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    Polymerase Chain Reaction Pcr Amplification Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    TaKaRa polymerase chain reaction pcr buffer buffer including 2 5 mm of mg2
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    Polymerase Chain Reaction Pcr Buffer Buffer Including 2 5 Mm Of Mg2, supplied by TaKaRa, used in various techniques. Bioz Stars score: 93/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    TaKaRa 1×takara pcr buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    1×Takara Pcr Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 91/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    TaKaRa takara 5xr pcr buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    Takara 5xr Pcr Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 89/100, based on 91 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    TaKaRa 1x takara pcr buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    1x Takara Pcr Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 93/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    TaKaRa 10x takara epitaq pcr buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    10x Takara Epitaq Pcr Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    TaKaRa free pcr takara polymerase buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    Free Pcr Takara Polymerase Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 86/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    TaKaRa 1x takara extaq pcr buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    1x Takara Extaq Pcr Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    TaKaRa 1x takara hot start taq pcr buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    1x Takara Hot Start Taq Pcr Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa takara taq buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    Takara Taq Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    TaKaRa takara reaction buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    Takara Reaction Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 97/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    TaKaRa takara buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    Takara Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 88/100, based on 125 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    TaKaRa 1×takara primestar gxl buffer
    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus <t>PCR.</t> M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
    1×Takara Primestar Gxl Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus PCR. M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.

    Journal: PLoS ONE

    Article Title: Multiple Infection and Microdiversity among Helicobacter pylori Isolates in a Single Host in India

    doi: 10.1371/journal.pone.0043370

    Figure Lengend Snippet: Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus PCR. M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: Isolation, Amplification, Produced, Polymerase Chain Reaction, Marker, Positive Control, Negative Control

    PG207 showed evidence of mixed infections on the basis of obtaining either iceA1 or iceA2 alleles. M, 100 bp marker; lanes 1–10, single colonies isolated from PG207; C, positive control; N, Negative control ( E. coli DNA). (a) All the single colonies were negative for iceA1 except for lane 8. (b) All these single colonies were positive for iceA2 except for lane 8. Three different amplicon sizes were obtained in this iceA2 PCR (lanes 1, 9; lanes 2, 3, 6, 7, 10 and lanes 4, 5).

    Journal: PLoS ONE

    Article Title: Multiple Infection and Microdiversity among Helicobacter pylori Isolates in a Single Host in India

    doi: 10.1371/journal.pone.0043370

    Figure Lengend Snippet: PG207 showed evidence of mixed infections on the basis of obtaining either iceA1 or iceA2 alleles. M, 100 bp marker; lanes 1–10, single colonies isolated from PG207; C, positive control; N, Negative control ( E. coli DNA). (a) All the single colonies were negative for iceA1 except for lane 8. (b) All these single colonies were positive for iceA2 except for lane 8. Three different amplicon sizes were obtained in this iceA2 PCR (lanes 1, 9; lanes 2, 3, 6, 7, 10 and lanes 4, 5).

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: Marker, Isolation, Positive Control, Negative Control, Amplification, Polymerase Chain Reaction

    Multiplex PCR for vacA subtypes and cagA gene for PG218. M, 100 bp marker; lanes 1–10, single colonies isolated from PG218 and “P” denotes pooled DNA sample; C, Positive control (26695); N, Negative control ( E. coli DNA). All the colonies isolated from this individual were cagA + and carried vacA s1 allele. Evidence of mixed infection was detected in the vacA middle region only. Lanes 1–3 and 10 yielded amplicon specific for m1, lanes 5–9 produced amplicon specific for m2 while in lane 4, no amplicon was obtained for vacA mid-region using this specific primer set.

    Journal: PLoS ONE

    Article Title: Multiple Infection and Microdiversity among Helicobacter pylori Isolates in a Single Host in India

    doi: 10.1371/journal.pone.0043370

    Figure Lengend Snippet: Multiplex PCR for vacA subtypes and cagA gene for PG218. M, 100 bp marker; lanes 1–10, single colonies isolated from PG218 and “P” denotes pooled DNA sample; C, Positive control (26695); N, Negative control ( E. coli DNA). All the colonies isolated from this individual were cagA + and carried vacA s1 allele. Evidence of mixed infection was detected in the vacA middle region only. Lanes 1–3 and 10 yielded amplicon specific for m1, lanes 5–9 produced amplicon specific for m2 while in lane 4, no amplicon was obtained for vacA mid-region using this specific primer set.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: Multiplex Assay, Polymerase Chain Reaction, Marker, Isolation, Positive Control, Negative Control, Infection, Amplification, Produced

    Analysis of vacA alleles by PCR and also the RFLP analysis of ∼ 3 kb fragment of vacA . M, marker; lanes 1 to 10; single colonies isolated from PG142; C, Positive control (26695); N, Negative control ( E. coli DNA). (A) Amplification of vacA s1 and m1 alleles, Lane M, 100 bp marker; all the colonies were positive for vacA s1m1. (B) Amplification of the vacA region with primer vas1F and vas GR. Lane M; 1 kb marker (Gibco BRL), Lanes 1, 3, 6, 8 and 10 failed to amplify. (C) Restriction fragment length polymorphism (RFLP) analysis of ∼3 kb fragment of vacA region using HaeIII restriction enzyme depicted microdiversity among the isolates as lane 5 showed a different digestion pattern than the rest of the colonies. Lane M, 100 bp marker.

    Journal: PLoS ONE

    Article Title: Multiple Infection and Microdiversity among Helicobacter pylori Isolates in a Single Host in India

    doi: 10.1371/journal.pone.0043370

    Figure Lengend Snippet: Analysis of vacA alleles by PCR and also the RFLP analysis of ∼ 3 kb fragment of vacA . M, marker; lanes 1 to 10; single colonies isolated from PG142; C, Positive control (26695); N, Negative control ( E. coli DNA). (A) Amplification of vacA s1 and m1 alleles, Lane M, 100 bp marker; all the colonies were positive for vacA s1m1. (B) Amplification of the vacA region with primer vas1F and vas GR. Lane M; 1 kb marker (Gibco BRL), Lanes 1, 3, 6, 8 and 10 failed to amplify. (C) Restriction fragment length polymorphism (RFLP) analysis of ∼3 kb fragment of vacA region using HaeIII restriction enzyme depicted microdiversity among the isolates as lane 5 showed a different digestion pattern than the rest of the colonies. Lane M, 100 bp marker.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: Polymerase Chain Reaction, Marker, Isolation, Positive Control, Negative Control, Amplification

    Combination of genotype and RAPD analysis for PG157 indicated multiple infections and microdiversity in a single host. M, 100 bp marker; lanes 1–10, single colonies isolated from PG157; P, pooled DNA. (a) RAPD patterns using primer 1281 showed two distinct patterns (lanes 1–8 and lanes 9–10) (b) RAPD patterns using primer 1283 also yielded two distinct patterns (lanes 1–8 and lanes 9–10) (c) Multiplex PCR for vacA alleles and cagA showed existence of s1m1 cagA + strains in lanes 1–8 and s2m2 cagA − strains in lanes 9–10. (d) Variant cagA subtypes detected on the basis of PCR for 3′ end of cagA using primers CAG1 and CAG2. This PCR assay showed existence of type A strains in lanes 4, 6–8 and existence of type B/D strains in lanes 1–3 and 5. Lanes 9–10, which were detected as cagA − , did not produce any amplicon and the pooled sample yielded amplicons for type A and type B/D strains.

    Journal: PLoS ONE

    Article Title: Multiple Infection and Microdiversity among Helicobacter pylori Isolates in a Single Host in India

    doi: 10.1371/journal.pone.0043370

    Figure Lengend Snippet: Combination of genotype and RAPD analysis for PG157 indicated multiple infections and microdiversity in a single host. M, 100 bp marker; lanes 1–10, single colonies isolated from PG157; P, pooled DNA. (a) RAPD patterns using primer 1281 showed two distinct patterns (lanes 1–8 and lanes 9–10) (b) RAPD patterns using primer 1283 also yielded two distinct patterns (lanes 1–8 and lanes 9–10) (c) Multiplex PCR for vacA alleles and cagA showed existence of s1m1 cagA + strains in lanes 1–8 and s2m2 cagA − strains in lanes 9–10. (d) Variant cagA subtypes detected on the basis of PCR for 3′ end of cagA using primers CAG1 and CAG2. This PCR assay showed existence of type A strains in lanes 4, 6–8 and existence of type B/D strains in lanes 1–3 and 5. Lanes 9–10, which were detected as cagA − , did not produce any amplicon and the pooled sample yielded amplicons for type A and type B/D strains.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: Marker, Isolation, Multiplex Assay, Polymerase Chain Reaction, Variant Assay, Amplification

    Multiplex PCR for vacA subtypes, cagA and cag PAI empty site for the absence of cag PAI. M, 100 bp marker (New England Biolabs); lanes 1–10, single colonies isolated from PG207; C, 26695 for the first set (a) and AM1 ( cag PAI negative strain) for the second set (b); N, Negative control ( E. coli DNA). (a) Multiplex PCR showed this particular patient was infected by at least three different strains. Lanes 1–6 and lanes 9–10 showed existence of s2m2 cagA − strains, lane 7 showed existence of s1m1 cagA − strain and lane 8 showed existence of s1m1 cagA + strain. (b) All the single colonies, which failed to give amplicon for cagA gene, yielded ∼550 bp product for cag PAI empty site. The colony (Lane 8) that produced amplicon for cagA did not show any amplicon with primers for cag PAI empty site.

    Journal: PLoS ONE

    Article Title: Multiple Infection and Microdiversity among Helicobacter pylori Isolates in a Single Host in India

    doi: 10.1371/journal.pone.0043370

    Figure Lengend Snippet: Multiplex PCR for vacA subtypes, cagA and cag PAI empty site for the absence of cag PAI. M, 100 bp marker (New England Biolabs); lanes 1–10, single colonies isolated from PG207; C, 26695 for the first set (a) and AM1 ( cag PAI negative strain) for the second set (b); N, Negative control ( E. coli DNA). (a) Multiplex PCR showed this particular patient was infected by at least three different strains. Lanes 1–6 and lanes 9–10 showed existence of s2m2 cagA − strains, lane 7 showed existence of s1m1 cagA − strain and lane 8 showed existence of s1m1 cagA + strain. (b) All the single colonies, which failed to give amplicon for cagA gene, yielded ∼550 bp product for cag PAI empty site. The colony (Lane 8) that produced amplicon for cagA did not show any amplicon with primers for cag PAI empty site.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: Multiplex Assay, Polymerase Chain Reaction, Marker, Isolation, Negative Control, Infection, Amplification, Produced

    Variant cagA subtypes detected on the basis of PCR with primers CAG1 and CAG2 amplifying the 3′ end of the gene. M, 100 bp marker; lane 1–10, single colonies isolated from individual patient and “P” denotes pooled DNA sample; C, positive control for type A cagA (cagA types were named according to the types described by Yamaoka et al. , (1998); N, Negative control ( E. coli DNA). (a) Mixed H. pylori populations were detected by obtaining amplicons for type A and type C in PG218. (b) For PG93, mixed H. pylori populations were detected by obtaining amplicons for type A and a shorter amplicon of ∼500 bp, which could not be typed by the methodology developed by Yamaoka et al. , (1998). (c) For PG144, mixed H. p ylori populations were detected by obtaining amplicons for type A and type B/D.

    Journal: PLoS ONE

    Article Title: Multiple Infection and Microdiversity among Helicobacter pylori Isolates in a Single Host in India

    doi: 10.1371/journal.pone.0043370

    Figure Lengend Snippet: Variant cagA subtypes detected on the basis of PCR with primers CAG1 and CAG2 amplifying the 3′ end of the gene. M, 100 bp marker; lane 1–10, single colonies isolated from individual patient and “P” denotes pooled DNA sample; C, positive control for type A cagA (cagA types were named according to the types described by Yamaoka et al. , (1998); N, Negative control ( E. coli DNA). (a) Mixed H. pylori populations were detected by obtaining amplicons for type A and type C in PG218. (b) For PG93, mixed H. pylori populations were detected by obtaining amplicons for type A and a shorter amplicon of ∼500 bp, which could not be typed by the methodology developed by Yamaoka et al. , (1998). (c) For PG144, mixed H. p ylori populations were detected by obtaining amplicons for type A and type B/D.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: Variant Assay, Polymerase Chain Reaction, Marker, Isolation, Positive Control, Negative Control, Amplification

    Effects of Tth MutS on standard polymerase chain reaction (PCR) amplification of an 80-bp template. ( A ) Schema tic representation of the primers and templates used in ( B , C ). Perfectly matched, GT-mismatched or unpaired T-containing primers were used; ( B ) Perfectly matched (left), GT-mismatched (middle) or unpaired T-containing (right) primers were used to amplify the perfectly matched template; ( C ) The relative amounts of the products from perfectly matched (blue), GT-mismatched (red) or unpaired T-containing (purple) primers were plotted against the Tth MutS concentration for reactions using three polymerases: LA Taq (left), KOD polymerase (middle) and A. aeolicus DnaE (right). The amounts of the products were normalized by those at 0 μM Tth MutS.

    Journal: International Journal of Molecular Sciences

    Article Title: Thermostable Mismatch-Recognizing Protein MutS Suppresses Nonspecific Amplification during Polymerase Chain Reaction (PCR)

    doi: 10.3390/ijms14036436

    Figure Lengend Snippet: Effects of Tth MutS on standard polymerase chain reaction (PCR) amplification of an 80-bp template. ( A ) Schema tic representation of the primers and templates used in ( B , C ). Perfectly matched, GT-mismatched or unpaired T-containing primers were used; ( B ) Perfectly matched (left), GT-mismatched (middle) or unpaired T-containing (right) primers were used to amplify the perfectly matched template; ( C ) The relative amounts of the products from perfectly matched (blue), GT-mismatched (red) or unpaired T-containing (purple) primers were plotted against the Tth MutS concentration for reactions using three polymerases: LA Taq (left), KOD polymerase (middle) and A. aeolicus DnaE (right). The amounts of the products were normalized by those at 0 μM Tth MutS.

    Article Snippet: PCR was performed with 0.06 units/μL LA Taq Hot-Start Version (Takara, Shiga, Japan), 0.03 units/μL KOD polymerase (Toyobo, Tokyo, Japan) or 40 nM A. aeolicus DnaE, in 1× Takara LA PCR buffer II (Takara, Shiga, Japan) containing 20 nM template DNA; 400 nM primers; 400 μM dATP, dTTP, dCTP and dGTP and various concentrations of Tth MutS or Aae MutS.

    Techniques: Polymerase Chain Reaction, Amplification, Concentration Assay