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  • 99
    Zymo Research bacterial dna
    Bacterial Dna, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 105 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher template dna
    Standard curve demonstrating the range of threshold cycle (Ct) values plotted versus genome equivalents (GE) of Brucella pinnipedialis strain B04-0821 per <t>PCR</t> reaction volume (1.5 µL of <t>DNA).</t> The regression line represents data that were in the linear range. Each point represents the mean value for triplicate runs at each dilution.
    Template Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 15134 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    ATUM template dna
    <t>PCR</t> confirms distribution of UBF on the human rDNA repeat. PCR was performed on <t>DNA</t> extracted from preimmune and α-UBF ChIP assays with primer pairs from across the human rDNA repeat. The locations of the primer pairs and gels of the resulting PCRs are shown in the appropriate position below a diagram of the human rDNA repeat. The source of DNA used in each PCR is shown below the gel.
    Template Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 94/100, based on 2248 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore template dna
    <t>PCR</t> confirms distribution of UBF on the human rDNA repeat. PCR was performed on <t>DNA</t> extracted from preimmune and α-UBF ChIP assays with primer pairs from across the human rDNA repeat. The locations of the primer pairs and gels of the resulting PCRs are shown in the appropriate position below a diagram of the human rDNA repeat. The source of DNA used in each PCR is shown below the gel.
    Template Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1527 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Bio-Rad dna template
    Adjuvant vaccination after tumor resection leads to clean RAs and reactivation of the immune system to target cancer cells (A) B16F0 tumor-bearing mice underwent R1 tumor resection, were randomized into different treatment groups, and were vaccinated with either C+I, CpG, or PBS for four weeks. (B) <t>DNA</t> from skin biopsies (*) in resection areas (RAs) showed a significant reduction in the percentage of tumor cells after four vaccination rounds with the C+I vaccine, as assessed by <t>ddPCR.</t> (C) Vaccination post-tumor resection led to a reduction of Th17 cells (CD4 + CD62L + TCR-b + (IL-2/IL-17A); CD4 + CD62L + CD44 + TCR-b + (IL-17A)) and an increased presence of TNF-α expressing myeloid cells (CD11b + CD44 + GR1 hi (TNF-a)) and IL-4 expressing CD19 + CD62L + CD44 + B-cells ( n= 8 PBS, n =10 CpG, n =10 C+I, mean±s.e.m., ANOVA with Tukey’s multiple comparison test, *p
    Dna Template, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 93/100, based on 1343 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Meridian Life Science dna template
    Accessibility of Regions of PetE to Micrococcal Nuclease. Nuclei were incubated with micrococcal nuclease for the times indicated. Control represents a reaction without added micrococcal nuclease. The amount of <t>DNA</t> sequence present at each time was determined by <t>PCR.</t> The PCR products were separated on an agarose gel, transferred onto GeneScreen Plus membrane, probed with 32 P-labeled PCR products, exposed to x-ray film, and quantified. The upstream (−800 to −449), enhancer (−444 to −177), promoter (−195 to −56), and transcribed (−103 to +504) regions of PetE were examined. For each region of PetE , PCR products obtained for each time are shown at the top, and degradation curves for two independent digestion experiments for each pea organ are shown at the bottom. The amount of DNA present at each time was normalized to that at time 0 and plotted against time to compare degradation rates in green shoots (open circles), etiolated shoots (crosses), and roots (closed squares).
    Dna Template, supplied by Meridian Life Science, used in various techniques. Bioz Stars score: 93/100, based on 934 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Pacific Biosciences dna template prep kit 2 0
    Accessibility of Regions of PetE to Micrococcal Nuclease. Nuclei were incubated with micrococcal nuclease for the times indicated. Control represents a reaction without added micrococcal nuclease. The amount of <t>DNA</t> sequence present at each time was determined by <t>PCR.</t> The PCR products were separated on an agarose gel, transferred onto GeneScreen Plus membrane, probed with 32 P-labeled PCR products, exposed to x-ray film, and quantified. The upstream (−800 to −449), enhancer (−444 to −177), promoter (−195 to −56), and transcribed (−103 to +504) regions of PetE were examined. For each region of PetE , PCR products obtained for each time are shown at the top, and degradation curves for two independent digestion experiments for each pea organ are shown at the bottom. The amount of DNA present at each time was normalized to that at time 0 and plotted against time to compare degradation rates in green shoots (open circles), etiolated shoots (crosses), and roots (closed squares).
    Dna Template Prep Kit 2 0, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 91/100, based on 838 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Stratagene dna template
    Fe-dependent transcription of the ecfIR - bfrH locus. Total RNAs were isolated from Fe-replete and Fe-stressed RB50 cultures. Oligonucleotide primer sets used in the reaction mixtures targeted a 218-bp internal region of ecfI , a 288-bp overlap region containing the 3′ end of ecfI and the 5′ end of ecfR ( ecfIR ), a 488-bp internal region ecfR , a 237-bp region overlapping ecfR , bfrH , and a 93-bp region between ecfR and bfrH ( ecfR - bfrH intergenic), a 598-bp internal region of bfrH , a 513-bp internal region of bhuR , and a 402-bp internal region of recA . Amplified <t>DNA</t> from each <t>RT-PCR</t> was resolved in a 2% agarose gel and visualized by ethidium bromide staining. Fe+, Fe-replete conditions; Fe−, Fe-stressed conditions.
    Dna Template, supplied by Stratagene, used in various techniques. Bioz Stars score: 92/100, based on 646 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    tiangen biotech co dna template
    Optimization of ARMS condition. Notes: ARMS amplifications specific for the mutation (c.C799T) were optimized by indicated different primer pairs. The genomic samples of mutant hemizygous proband <t>M001</t> (I:1) and his normal son (II:3) were used as <t>DNA</t> templates. The black and blue arrows show the position of the point mutation and nonspecific primer-dimer, respectively. I:1=M001; II:3=M002. Abbreviations: ARMS, amplification refractory mutation system; WT, wild-type primer; MT, mutant primer; C, common primer.
    Dna Template, supplied by tiangen biotech co, used in various techniques. Bioz Stars score: 93/100, based on 367 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eppendorf AG dna template
    Optimization of ARMS condition. Notes: ARMS amplifications specific for the mutation (c.C799T) were optimized by indicated different primer pairs. The genomic samples of mutant hemizygous proband <t>M001</t> (I:1) and his normal son (II:3) were used as <t>DNA</t> templates. The black and blue arrows show the position of the point mutation and nonspecific primer-dimer, respectively. I:1=M001; II:3=M002. Abbreviations: ARMS, amplification refractory mutation system; WT, wild-type primer; MT, mutant primer; C, common primer.
    Dna Template, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 94/100, based on 459 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc dna template
    Overview of <t>functional-RNA</t> array production. ( A ) The general design of the <t>DNA</t> in vitro transcription templates. From 5′ to 3′ there is: a short, biotinylated linker (to facilitate surface-immobilization of the DNA), a T7 promoter, sequence encoding the RNA of interest, a second linker (to separate the RNA of interest and the RNA aptamer) and sequence encoding an RNA aptamer (to facilitate RNA-capture). ( B ) A schematic representation of the ‘sandwich’ assembly and method used to produce the RNA array. A DNA in vitro transcription template array slide is positioned facing an RNA capture slide. Thin spacers are used to physically separate the surfaces. A solution of in vitro transcription reagents is inserted between the two surfaces and RNA transcription-capture proceeds for 90 min at 37°C to generate a functional-RNA array. This RNA array can then be used as a platform for investigating RNA-based interactions, e.g. probing with labelled binding partners.
    Dna Template, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 311 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher rna century marker templates
    Overview of <t>functional-RNA</t> array production. ( A ) The general design of the <t>DNA</t> in vitro transcription templates. From 5′ to 3′ there is: a short, biotinylated linker (to facilitate surface-immobilization of the DNA), a T7 promoter, sequence encoding the RNA of interest, a second linker (to separate the RNA of interest and the RNA aptamer) and sequence encoding an RNA aptamer (to facilitate RNA-capture). ( B ) A schematic representation of the ‘sandwich’ assembly and method used to produce the RNA array. A DNA in vitro transcription template array slide is positioned facing an RNA capture slide. Thin spacers are used to physically separate the surfaces. A solution of in vitro transcription reagents is inserted between the two surfaces and RNA transcription-capture proceeds for 90 min at 37°C to generate a functional-RNA array. This RNA array can then be used as a platform for investigating RNA-based interactions, e.g. probing with labelled binding partners.
    Rna Century Marker Templates, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa template dna
    Overview of <t>functional-RNA</t> array production. ( A ) The general design of the <t>DNA</t> in vitro transcription templates. From 5′ to 3′ there is: a short, biotinylated linker (to facilitate surface-immobilization of the DNA), a T7 promoter, sequence encoding the RNA of interest, a second linker (to separate the RNA of interest and the RNA aptamer) and sequence encoding an RNA aptamer (to facilitate RNA-capture). ( B ) A schematic representation of the ‘sandwich’ assembly and method used to produce the RNA array. A DNA in vitro transcription template array slide is positioned facing an RNA capture slide. Thin spacers are used to physically separate the surfaces. A solution of in vitro transcription reagents is inserted between the two surfaces and RNA transcription-capture proceeds for 90 min at 37°C to generate a functional-RNA array. This RNA array can then be used as a platform for investigating RNA-based interactions, e.g. probing with labelled binding partners.
    Template Dna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 5386 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    5 PRIME dna template
    Overview of <t>functional-RNA</t> array production. ( A ) The general design of the <t>DNA</t> in vitro transcription templates. From 5′ to 3′ there is: a short, biotinylated linker (to facilitate surface-immobilization of the DNA), a T7 promoter, sequence encoding the RNA of interest, a second linker (to separate the RNA of interest and the RNA aptamer) and sequence encoding an RNA aptamer (to facilitate RNA-capture). ( B ) A schematic representation of the ‘sandwich’ assembly and method used to produce the RNA array. A DNA in vitro transcription template array slide is positioned facing an RNA capture slide. Thin spacers are used to physically separate the surfaces. A solution of in vitro transcription reagents is inserted between the two surfaces and RNA transcription-capture proceeds for 90 min at 37°C to generate a functional-RNA array. This RNA array can then be used as a platform for investigating RNA-based interactions, e.g. probing with labelled binding partners.
    Dna Template, supplied by 5 PRIME, used in various techniques. Bioz Stars score: 92/100, based on 174 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bioneer Corporation dna template
    <t>PCR</t> assay for detection of bla VEB gene with product size: 600 bp. Lanes 3–17: Amplified products, Lanes 2 and 19: Positive control, Lanes 1 and 20: <t>DNA</t> ladder 100 bp, Lane 18: Negative control
    Dna Template, supplied by Bioneer Corporation, used in various techniques. Bioz Stars score: 93/100, based on 266 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Boehringer Mannheim dna template
    Restriction analysis with Rsa I of <t>DNA</t> amplified with primer pair ITS 5 and ITS 4 from P. infestans US-6 NY (lane 2), P. infestans 93-1 (lane 3), P. mirabilis 0S0016 (lane 4), P. fragariae A-8 (lane 5), P. megasperma NY 318 (lane 6), P. megasperma NY 412 (lane 7), P. sojae R1 (lane 8), P. cinnamomi 2302 (lane 9), P. cryptogea <t>PCR-1</t> (lane 10), and P. erythroseptica 4 (lane 11). Lanes 1 and 12 contain 100-bp ladders.
    Dna Template, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 92/100, based on 127 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TransGen biotech co dna template
    The effects of ChA on Akkermansia . ( A ) Comparison of the relative abundance of Akkermansia in fecal samples of DSS colitis mice analyzed by 16S rRNA gene sequencing; ( B ) A comparison of the relative abundance of Akkermansia in fecal samples of normal mice that were treated with ChA. Akkermansia was quantified with qPCR by amplifying fecal <t>DNA</t> with primers specific for Akkermansia and universal bacterial primers; ( C ) The polymerase chain reaction products were analyzed by electrophoresis in a 2% agarose gel. * p
    Dna Template, supplied by TransGen biotech co, used in various techniques. Bioz Stars score: 92/100, based on 166 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Standard curve demonstrating the range of threshold cycle (Ct) values plotted versus genome equivalents (GE) of Brucella pinnipedialis strain B04-0821 per PCR reaction volume (1.5 µL of DNA). The regression line represents data that were in the linear range. Each point represents the mean value for triplicate runs at each dilution.

    Journal: Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc

    Article Title: Application of real-time quantitative PCR assays for detecting marine Brucella spp. in fish

    doi: 10.1177/1040638717733024

    Figure Lengend Snippet: Standard curve demonstrating the range of threshold cycle (Ct) values plotted versus genome equivalents (GE) of Brucella pinnipedialis strain B04-0821 per PCR reaction volume (1.5 µL of DNA). The regression line represents data that were in the linear range. Each point represents the mean value for triplicate runs at each dilution.

    Article Snippet: Total PCR reaction volumes were 15 µL with 4.5 µL of DNA template, 100 µM primers and probe, and a commercial master mix (TaqMan universal master mix II, Life Technologies, Carlsbad, CA).

    Techniques: Polymerase Chain Reaction

    RT progression assay determining G-quartet formation in the Sp1 binding region. Cation-dependent pausing of reverse transcription at the guanine-rich elements in the U3 region was analyzed with RNA and DNA templates. A fragment of the RNA/DNA sequence of the Sp1 binding region is shown (top) with G-rich elements (shaded). Strong pauses of the RT near G-rich elements were observed in the presence of 50 mM of KCl, but not LiCl, indicating that these elements are involved in the formation of structure, which is stabilized by potassium ions but destabilized by lithium ions. This is indicative of a G-quadruplex. The cation-independent RT pauses are likely caused by hairpin structures. DNA primer, P; DNA marker, M; KCl, K + ; LiCl, Li + .

    Journal: Biochemistry

    Article Title: U3 Region in the HIV-1 Genome Adopts a G-Quadruplex Structure in Its RNA and DNA Sequence

    doi: 10.1021/bi4016692

    Figure Lengend Snippet: RT progression assay determining G-quartet formation in the Sp1 binding region. Cation-dependent pausing of reverse transcription at the guanine-rich elements in the U3 region was analyzed with RNA and DNA templates. A fragment of the RNA/DNA sequence of the Sp1 binding region is shown (top) with G-rich elements (shaded). Strong pauses of the RT near G-rich elements were observed in the presence of 50 mM of KCl, but not LiCl, indicating that these elements are involved in the formation of structure, which is stabilized by potassium ions but destabilized by lithium ions. This is indicative of a G-quadruplex. The cation-independent RT pauses are likely caused by hairpin structures. DNA primer, P; DNA marker, M; KCl, K + ; LiCl, Li + .

    Article Snippet: Preparation of RNA Templates RNA molecules were transcribed in vitro (Ambion T7-MEGAshortscript kit; Applied Biosystems) from DNA templates amplified by PCR using Vent DNA polymerase (New England BioLabs, Inc.) and two overlapping oligomers with the sequence of the desired region.

    Techniques: Binding Assay, Sequencing, Marker

    Formation of the structure stabilized by potassium ions in the HIV-1 U3 region facilitates RT template switching during reverse transcription. (A) Reconstituted system to analyze the influence of G-rich elements on strand transfer during HIV-1 minus strand DNA synthesis in vitro . Donor and acceptor RNA templates represent two copies of the viral RNA genome; in which reverse transcription is initiated from a 32 P-labeled DNA primer annealed to the donor RNA. The acceptor RNA does not share a homology (circle) with two nucleotides at the 5′ end of the donor RNA. TP, transfer product; DE, donor extension product; and P, DNA primer. (B) A time course of strand transfer reactions performed in the presence of potassium and lithium ions. Samples were collected at 1, 5, 15, and 30 min after the reaction was initiated. Formation of a potassium-dependent structure, anticipated to be a G-quadruplex, in the RNA template paused the RT during minus strand DNA synthesis and influenced the yield of the final products. The transfer efficiency decreased about 37% in reactions with lithium ions, presumably because the templates could not form a G-quadruplex.

    Journal: Biochemistry

    Article Title: U3 Region in the HIV-1 Genome Adopts a G-Quadruplex Structure in Its RNA and DNA Sequence

    doi: 10.1021/bi4016692

    Figure Lengend Snippet: Formation of the structure stabilized by potassium ions in the HIV-1 U3 region facilitates RT template switching during reverse transcription. (A) Reconstituted system to analyze the influence of G-rich elements on strand transfer during HIV-1 minus strand DNA synthesis in vitro . Donor and acceptor RNA templates represent two copies of the viral RNA genome; in which reverse transcription is initiated from a 32 P-labeled DNA primer annealed to the donor RNA. The acceptor RNA does not share a homology (circle) with two nucleotides at the 5′ end of the donor RNA. TP, transfer product; DE, donor extension product; and P, DNA primer. (B) A time course of strand transfer reactions performed in the presence of potassium and lithium ions. Samples were collected at 1, 5, 15, and 30 min after the reaction was initiated. Formation of a potassium-dependent structure, anticipated to be a G-quadruplex, in the RNA template paused the RT during minus strand DNA synthesis and influenced the yield of the final products. The transfer efficiency decreased about 37% in reactions with lithium ions, presumably because the templates could not form a G-quadruplex.

    Article Snippet: Preparation of RNA Templates RNA molecules were transcribed in vitro (Ambion T7-MEGAshortscript kit; Applied Biosystems) from DNA templates amplified by PCR using Vent DNA polymerase (New England BioLabs, Inc.) and two overlapping oligomers with the sequence of the desired region.

    Techniques: DNA Synthesis, In Vitro, Labeling

    CD spectral analysis of the RNA and single stranded DNA with Sp1 binding sites in HIV-1. CD spectra indicate the formation of the parallel G-quadruplex for the RNA template and an antiparallel or hybrid G-quadruplex for single stranded DNA. For reference, a profile of the G-rich sequence (50% of Gs; GGGGGGAUUGUG UGGUACAGUGCAGAGA), which is unable to adopt G-quadruplex structure, is shown in gray.

    Journal: Biochemistry

    Article Title: U3 Region in the HIV-1 Genome Adopts a G-Quadruplex Structure in Its RNA and DNA Sequence

    doi: 10.1021/bi4016692

    Figure Lengend Snippet: CD spectral analysis of the RNA and single stranded DNA with Sp1 binding sites in HIV-1. CD spectra indicate the formation of the parallel G-quadruplex for the RNA template and an antiparallel or hybrid G-quadruplex for single stranded DNA. For reference, a profile of the G-rich sequence (50% of Gs; GGGGGGAUUGUG UGGUACAGUGCAGAGA), which is unable to adopt G-quadruplex structure, is shown in gray.

    Article Snippet: Preparation of RNA Templates RNA molecules were transcribed in vitro (Ambion T7-MEGAshortscript kit; Applied Biosystems) from DNA templates amplified by PCR using Vent DNA polymerase (New England BioLabs, Inc.) and two overlapping oligomers with the sequence of the desired region.

    Techniques: Binding Assay, Sequencing

    PCR confirms distribution of UBF on the human rDNA repeat. PCR was performed on DNA extracted from preimmune and α-UBF ChIP assays with primer pairs from across the human rDNA repeat. The locations of the primer pairs and gels of the resulting PCRs are shown in the appropriate position below a diagram of the human rDNA repeat. The source of DNA used in each PCR is shown below the gel.

    Journal: Molecular and Cellular Biology

    Article Title: UBF Binding In Vivo Is Not Restricted to Regulatory Sequences within the Vertebrate Ribosomal DNA Repeat

    doi: 10.1128/MCB.22.2.657-668.2002

    Figure Lengend Snippet: PCR confirms distribution of UBF on the human rDNA repeat. PCR was performed on DNA extracted from preimmune and α-UBF ChIP assays with primer pairs from across the human rDNA repeat. The locations of the primer pairs and gels of the resulting PCRs are shown in the appropriate position below a diagram of the human rDNA repeat. The source of DNA used in each PCR is shown below the gel.

    Article Snippet: PCR mixtures (each, 100 μl) contained 10 ng of template DNA, 20 pmol of each primer (T7 and SP6), and 5 U of Taq DNA polymerase in PCR buffer (see above).

    Techniques: Polymerase Chain Reaction, Chromatin Immunoprecipitation

    RNA Pol I and SL1 show a resticted distribution on the human rDNA repeat. (A) PCR was performed with DNA extracted from preimmune, α-UBF, and α-Pol I ChIP assays with primer pairs from across the human rDNA repeat. The locations of the primer pairs and gels of the resulting PCRs are shown in the appropriate position below a diagram of the human rDNA repeat. The source of DNA used in each PCR is shown below the gel. (B) PCR was performed with DNA extracted from α-Taf I 110 and α-Taf I 48 ChIP assays with primer pairs from across the human rDNA repeat. The identity of the primer pairs is shown above the appropriate gel lanes, and the identity of the antibody used in ChIP is shown alongside.

    Journal: Molecular and Cellular Biology

    Article Title: UBF Binding In Vivo Is Not Restricted to Regulatory Sequences within the Vertebrate Ribosomal DNA Repeat

    doi: 10.1128/MCB.22.2.657-668.2002

    Figure Lengend Snippet: RNA Pol I and SL1 show a resticted distribution on the human rDNA repeat. (A) PCR was performed with DNA extracted from preimmune, α-UBF, and α-Pol I ChIP assays with primer pairs from across the human rDNA repeat. The locations of the primer pairs and gels of the resulting PCRs are shown in the appropriate position below a diagram of the human rDNA repeat. The source of DNA used in each PCR is shown below the gel. (B) PCR was performed with DNA extracted from α-Taf I 110 and α-Taf I 48 ChIP assays with primer pairs from across the human rDNA repeat. The identity of the primer pairs is shown above the appropriate gel lanes, and the identity of the antibody used in ChIP is shown alongside.

    Article Snippet: PCR mixtures (each, 100 μl) contained 10 ng of template DNA, 20 pmol of each primer (T7 and SP6), and 5 U of Taq DNA polymerase in PCR buffer (see above).

    Techniques: Polymerase Chain Reaction, Chromatin Immunoprecipitation

    UBF binds to sequences across the mouse rDNA repeat. PCR was performed with DNA extracted from preimmune and α-UBF ChIP assays with primer pairs from across the mouse rDNA repeat. The locations of the primer pairs and gels of the resulting PCRs are shown in the appropriate position below a diagram of the mouse rDNA repeat. The primer pair MEn is derived from the repeated enhancer elements, depicted by the cluster of vertical lines upstream of the transcribed region. The source of DNA used in each PCR is shown below the gel.

    Journal: Molecular and Cellular Biology

    Article Title: UBF Binding In Vivo Is Not Restricted to Regulatory Sequences within the Vertebrate Ribosomal DNA Repeat

    doi: 10.1128/MCB.22.2.657-668.2002

    Figure Lengend Snippet: UBF binds to sequences across the mouse rDNA repeat. PCR was performed with DNA extracted from preimmune and α-UBF ChIP assays with primer pairs from across the mouse rDNA repeat. The locations of the primer pairs and gels of the resulting PCRs are shown in the appropriate position below a diagram of the mouse rDNA repeat. The primer pair MEn is derived from the repeated enhancer elements, depicted by the cluster of vertical lines upstream of the transcribed region. The source of DNA used in each PCR is shown below the gel.

    Article Snippet: PCR mixtures (each, 100 μl) contained 10 ng of template DNA, 20 pmol of each primer (T7 and SP6), and 5 U of Taq DNA polymerase in PCR buffer (see above).

    Techniques: Polymerase Chain Reaction, Chromatin Immunoprecipitation, Derivative Assay

    UBF binds to Xenopus and human ribosomal gene promoters in vivo. Quantitative PCR was performed using promoter-specific primers and DNA extracted from α-xUBF and preimmune ChIP assays. Gels from experiments with human and Xenopus nucleolar chromatin are shown in the top and bottom panels, respectively. See Materials and Methods for details of the ChIP assay, primers, and PCR conditions. Control PCRs were performed with the human rDNA repeat cosmid N68f1 and the Xenopus plasmid pXlr101A. The amount of cloned DNA used in control reaction mixtures (10 to 0.01 ng) is shown above each lane as appropriate. Concentrations of SDS and Triton X-100 used in immunoprecipitation washes are shown above.

    Journal: Molecular and Cellular Biology

    Article Title: UBF Binding In Vivo Is Not Restricted to Regulatory Sequences within the Vertebrate Ribosomal DNA Repeat

    doi: 10.1128/MCB.22.2.657-668.2002

    Figure Lengend Snippet: UBF binds to Xenopus and human ribosomal gene promoters in vivo. Quantitative PCR was performed using promoter-specific primers and DNA extracted from α-xUBF and preimmune ChIP assays. Gels from experiments with human and Xenopus nucleolar chromatin are shown in the top and bottom panels, respectively. See Materials and Methods for details of the ChIP assay, primers, and PCR conditions. Control PCRs were performed with the human rDNA repeat cosmid N68f1 and the Xenopus plasmid pXlr101A. The amount of cloned DNA used in control reaction mixtures (10 to 0.01 ng) is shown above each lane as appropriate. Concentrations of SDS and Triton X-100 used in immunoprecipitation washes are shown above.

    Article Snippet: PCR mixtures (each, 100 μl) contained 10 ng of template DNA, 20 pmol of each primer (T7 and SP6), and 5 U of Taq DNA polymerase in PCR buffer (see above).

    Techniques: In Vivo, Real-time Polymerase Chain Reaction, Chromatin Immunoprecipitation, Polymerase Chain Reaction, Plasmid Preparation, Clone Assay, Immunoprecipitation

    Adjuvant vaccination after tumor resection leads to clean RAs and reactivation of the immune system to target cancer cells (A) B16F0 tumor-bearing mice underwent R1 tumor resection, were randomized into different treatment groups, and were vaccinated with either C+I, CpG, or PBS for four weeks. (B) DNA from skin biopsies (*) in resection areas (RAs) showed a significant reduction in the percentage of tumor cells after four vaccination rounds with the C+I vaccine, as assessed by ddPCR. (C) Vaccination post-tumor resection led to a reduction of Th17 cells (CD4 + CD62L + TCR-b + (IL-2/IL-17A); CD4 + CD62L + CD44 + TCR-b + (IL-17A)) and an increased presence of TNF-α expressing myeloid cells (CD11b + CD44 + GR1 hi (TNF-a)) and IL-4 expressing CD19 + CD62L + CD44 + B-cells ( n= 8 PBS, n =10 CpG, n =10 C+I, mean±s.e.m., ANOVA with Tukey’s multiple comparison test, *p

    Journal: Cell stem cell

    Article Title: Autologous iPSC-based Vaccines Elicit Anti-Tumor Responses in Vivo

    doi: 10.1016/j.stem.2018.01.016

    Figure Lengend Snippet: Adjuvant vaccination after tumor resection leads to clean RAs and reactivation of the immune system to target cancer cells (A) B16F0 tumor-bearing mice underwent R1 tumor resection, were randomized into different treatment groups, and were vaccinated with either C+I, CpG, or PBS for four weeks. (B) DNA from skin biopsies (*) in resection areas (RAs) showed a significant reduction in the percentage of tumor cells after four vaccination rounds with the C+I vaccine, as assessed by ddPCR. (C) Vaccination post-tumor resection led to a reduction of Th17 cells (CD4 + CD62L + TCR-b + (IL-2/IL-17A); CD4 + CD62L + CD44 + TCR-b + (IL-17A)) and an increased presence of TNF-α expressing myeloid cells (CD11b + CD44 + GR1 hi (TNF-a)) and IL-4 expressing CD19 + CD62L + CD44 + B-cells ( n= 8 PBS, n =10 CpG, n =10 C+I, mean±s.e.m., ANOVA with Tukey’s multiple comparison test, *p

    Article Snippet: Each ddPCR reaction solution was reconstituted to a final volume of 20 μL using 40 to 50 ng of DNA template and ddPCR™ Supermix for Probes, without dUTP (BioRad).

    Techniques: Mouse Assay, Expressing

    (a) ddPCR analysis of the growth of ML cultured in NK250 supplemented with human blood plasma Red, no DNase treatment; blue, DNase treated. (b) ddPCR analysis of DNase treated samples. The results of the DNase treated samples are shown on a different scale, showing an approximately two‐fold increase in ML DNA copy numbers during 150 days of culture. (c) The growth pattern of ML expressed as fold changes in cell counts compared with the start of the experiment.

    Journal: Microbiology and Immunology

    Article Title: Non‐exponential growth of Mycobacterium leprae Thai‐53 strain cultured in vitro

    doi: 10.1111/1348-0421.12454

    Figure Lengend Snippet: (a) ddPCR analysis of the growth of ML cultured in NK250 supplemented with human blood plasma Red, no DNase treatment; blue, DNase treated. (b) ddPCR analysis of DNase treated samples. The results of the DNase treated samples are shown on a different scale, showing an approximately two‐fold increase in ML DNA copy numbers during 150 days of culture. (c) The growth pattern of ML expressed as fold changes in cell counts compared with the start of the experiment.

    Article Snippet: Briefly, DNA templates were mixed with 2× QX200 ddPCR EvaGreen Supermix (Bio‐Rad) and 2 pmol of an ML‐specific primer pair (S13: 5′‐CTCCACCTCCACCGGCGAT‐3′ and S62: 5′‐GACTAGCCTGCCAAGTCG‐3′) , .

    Techniques: Cell Culture

    Effects of DNase treatment on ML‐specific DNA copy numbers in a specimen isolated on the first day of culture Treatment of the cultured specimens with DNase before DNA extraction greatly reduces the numbers of ML DNA copies detected by ddPCR analysis.

    Journal: Microbiology and Immunology

    Article Title: Non‐exponential growth of Mycobacterium leprae Thai‐53 strain cultured in vitro

    doi: 10.1111/1348-0421.12454

    Figure Lengend Snippet: Effects of DNase treatment on ML‐specific DNA copy numbers in a specimen isolated on the first day of culture Treatment of the cultured specimens with DNase before DNA extraction greatly reduces the numbers of ML DNA copies detected by ddPCR analysis.

    Article Snippet: Briefly, DNA templates were mixed with 2× QX200 ddPCR EvaGreen Supermix (Bio‐Rad) and 2 pmol of an ML‐specific primer pair (S13: 5′‐CTCCACCTCCACCGGCGAT‐3′ and S62: 5′‐GACTAGCCTGCCAAGTCG‐3′) , .

    Techniques: Isolation, Cell Culture, DNA Extraction

    Accessibility of Regions of PetE to Micrococcal Nuclease. Nuclei were incubated with micrococcal nuclease for the times indicated. Control represents a reaction without added micrococcal nuclease. The amount of DNA sequence present at each time was determined by PCR. The PCR products were separated on an agarose gel, transferred onto GeneScreen Plus membrane, probed with 32 P-labeled PCR products, exposed to x-ray film, and quantified. The upstream (−800 to −449), enhancer (−444 to −177), promoter (−195 to −56), and transcribed (−103 to +504) regions of PetE were examined. For each region of PetE , PCR products obtained for each time are shown at the top, and degradation curves for two independent digestion experiments for each pea organ are shown at the bottom. The amount of DNA present at each time was normalized to that at time 0 and plotted against time to compare degradation rates in green shoots (open circles), etiolated shoots (crosses), and roots (closed squares).

    Journal: The Plant Cell

    Article Title: Targeted Histone Acetylation and Altered Nuclease Accessibility over Short Regions of the Pea Plastocyanin Gene

    doi:

    Figure Lengend Snippet: Accessibility of Regions of PetE to Micrococcal Nuclease. Nuclei were incubated with micrococcal nuclease for the times indicated. Control represents a reaction without added micrococcal nuclease. The amount of DNA sequence present at each time was determined by PCR. The PCR products were separated on an agarose gel, transferred onto GeneScreen Plus membrane, probed with 32 P-labeled PCR products, exposed to x-ray film, and quantified. The upstream (−800 to −449), enhancer (−444 to −177), promoter (−195 to −56), and transcribed (−103 to +504) regions of PetE were examined. For each region of PetE , PCR products obtained for each time are shown at the top, and degradation curves for two independent digestion experiments for each pea organ are shown at the bottom. The amount of DNA present at each time was normalized to that at time 0 and plotted against time to compare degradation rates in green shoots (open circles), etiolated shoots (crosses), and roots (closed squares).

    Article Snippet: PCR was performed in a 50-μL reaction volume containing DNA template, 2.5 units of Taq polymerase (Bioline, UK), 5 μL of 10 × reaction buffer supplied by the manufacturer of the enzyme, 400 μM each of dATP, dTTP, dCTP, and dGTP, 1 μM of each primer, and 2 mM MgCl2 .

    Techniques: Incubation, Sequencing, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Labeling

    Acetylation States of Histone H4 Associated with Pea PetE . Nuclei isolated from green shoots, etiolated shoots, and roots were cross-linked, sonicated, and immunoprecipitated with antibodies specific for acetylated histone H4 (AcH4 AB) or nonacetylated histone H4 (nonAcH4 AB). The immunoprecipitates were analyzed for the presence of DNA with PCR. The upstream (−800 to −449), enhancer/promoter (−492 to −56), and transcribed (−103 to +504) regions of PetE were examined. The lanes labeled Total DNA contain the products of PCR performed with chromatin solution before immunoprecipitation. The immunoprecipitation step was also performed without antibody (−AB) and with nonimmune rabbit serum (Rabbit AB). Similar results were obtained for three replicates of ChIP experiments.

    Journal: The Plant Cell

    Article Title: Targeted Histone Acetylation and Altered Nuclease Accessibility over Short Regions of the Pea Plastocyanin Gene

    doi:

    Figure Lengend Snippet: Acetylation States of Histone H4 Associated with Pea PetE . Nuclei isolated from green shoots, etiolated shoots, and roots were cross-linked, sonicated, and immunoprecipitated with antibodies specific for acetylated histone H4 (AcH4 AB) or nonacetylated histone H4 (nonAcH4 AB). The immunoprecipitates were analyzed for the presence of DNA with PCR. The upstream (−800 to −449), enhancer/promoter (−492 to −56), and transcribed (−103 to +504) regions of PetE were examined. The lanes labeled Total DNA contain the products of PCR performed with chromatin solution before immunoprecipitation. The immunoprecipitation step was also performed without antibody (−AB) and with nonimmune rabbit serum (Rabbit AB). Similar results were obtained for three replicates of ChIP experiments.

    Article Snippet: PCR was performed in a 50-μL reaction volume containing DNA template, 2.5 units of Taq polymerase (Bioline, UK), 5 μL of 10 × reaction buffer supplied by the manufacturer of the enzyme, 400 μM each of dATP, dTTP, dCTP, and dGTP, 1 μM of each primer, and 2 mM MgCl2 .

    Techniques: Isolation, Sonication, Immunoprecipitation, Polymerase Chain Reaction, Labeling, Chromatin Immunoprecipitation

    Acetylation States of Histone H3 Associated with Pea PetE . Nuclei were cross-linked, sonicated, and immunoprecipitated with antibodies specific for acetylated histone H3 (AcH3 AB) or nonacetylated histone H3 (nonAcH3 AB). The immunoprecipitates were analyzed for the presence of DNA with PCR. The upstream (−800 to −449), enhancer/promoter (−492 to −56), and transcribed (−103 to +504) regions of PetE were examined. The lanes labeled Total DNA contain the products of PCR performed with chromatin solution before immunoprecipitation. The immunoprecipitation step was also performed without antibody (−AB) and with nonimmune rabbit serum (Rabbit AB). Similar results were obtained for three replicates of ChIP experiments.

    Journal: The Plant Cell

    Article Title: Targeted Histone Acetylation and Altered Nuclease Accessibility over Short Regions of the Pea Plastocyanin Gene

    doi:

    Figure Lengend Snippet: Acetylation States of Histone H3 Associated with Pea PetE . Nuclei were cross-linked, sonicated, and immunoprecipitated with antibodies specific for acetylated histone H3 (AcH3 AB) or nonacetylated histone H3 (nonAcH3 AB). The immunoprecipitates were analyzed for the presence of DNA with PCR. The upstream (−800 to −449), enhancer/promoter (−492 to −56), and transcribed (−103 to +504) regions of PetE were examined. The lanes labeled Total DNA contain the products of PCR performed with chromatin solution before immunoprecipitation. The immunoprecipitation step was also performed without antibody (−AB) and with nonimmune rabbit serum (Rabbit AB). Similar results were obtained for three replicates of ChIP experiments.

    Article Snippet: PCR was performed in a 50-μL reaction volume containing DNA template, 2.5 units of Taq polymerase (Bioline, UK), 5 μL of 10 × reaction buffer supplied by the manufacturer of the enzyme, 400 μM each of dATP, dTTP, dCTP, and dGTP, 1 μM of each primer, and 2 mM MgCl2 .

    Techniques: Sonication, Immunoprecipitation, Polymerase Chain Reaction, Labeling, Chromatin Immunoprecipitation

    Accessibility of Regions of PetE to DNaseI. Nuclei were incubated with DNaseI for the times indicated. Control represents a reaction without added DNaseI. The amount of DNA sequence present at each time was determined by PCR. The PCR products were separated on an agarose gel and stained with ethidium bromide, and the fluorescence of the bands was quantified. The upstream (−800 to −449), enhancer (−444 to −177), promoter (−195 to −56), and transcribed (−103 to +504) regions of PetE were examined. For each region of PetE , PCR products obtained for each time are shown at the top, and degradation curves for two independent digestion experiments for each pea organ are shown at the bottom. The amount of DNA present at each time was normalized to that at time 0 and plotted against time to compare degradation rates in green shoots (open circles), etiolated shoots (crosses), and roots (closed squares).

    Journal: The Plant Cell

    Article Title: Targeted Histone Acetylation and Altered Nuclease Accessibility over Short Regions of the Pea Plastocyanin Gene

    doi:

    Figure Lengend Snippet: Accessibility of Regions of PetE to DNaseI. Nuclei were incubated with DNaseI for the times indicated. Control represents a reaction without added DNaseI. The amount of DNA sequence present at each time was determined by PCR. The PCR products were separated on an agarose gel and stained with ethidium bromide, and the fluorescence of the bands was quantified. The upstream (−800 to −449), enhancer (−444 to −177), promoter (−195 to −56), and transcribed (−103 to +504) regions of PetE were examined. For each region of PetE , PCR products obtained for each time are shown at the top, and degradation curves for two independent digestion experiments for each pea organ are shown at the bottom. The amount of DNA present at each time was normalized to that at time 0 and plotted against time to compare degradation rates in green shoots (open circles), etiolated shoots (crosses), and roots (closed squares).

    Article Snippet: PCR was performed in a 50-μL reaction volume containing DNA template, 2.5 units of Taq polymerase (Bioline, UK), 5 μL of 10 × reaction buffer supplied by the manufacturer of the enzyme, 400 μM each of dATP, dTTP, dCTP, and dGTP, 1 μM of each primer, and 2 mM MgCl2 .

    Techniques: Incubation, Sequencing, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Staining, Fluorescence

    Fe-dependent transcription of the ecfIR - bfrH locus. Total RNAs were isolated from Fe-replete and Fe-stressed RB50 cultures. Oligonucleotide primer sets used in the reaction mixtures targeted a 218-bp internal region of ecfI , a 288-bp overlap region containing the 3′ end of ecfI and the 5′ end of ecfR ( ecfIR ), a 488-bp internal region ecfR , a 237-bp region overlapping ecfR , bfrH , and a 93-bp region between ecfR and bfrH ( ecfR - bfrH intergenic), a 598-bp internal region of bfrH , a 513-bp internal region of bhuR , and a 402-bp internal region of recA . Amplified DNA from each RT-PCR was resolved in a 2% agarose gel and visualized by ethidium bromide staining. Fe+, Fe-replete conditions; Fe−, Fe-stressed conditions.

    Journal: Infection and Immunity

    Article Title: Expression of BfrH, a Putative Siderophore Receptor of Bordetella bronchiseptica, Is Regulated by Iron, Fur1, and the Extracellular Function Sigma Factor EcfI ▿

    doi: 10.1128/IAI.00961-09

    Figure Lengend Snippet: Fe-dependent transcription of the ecfIR - bfrH locus. Total RNAs were isolated from Fe-replete and Fe-stressed RB50 cultures. Oligonucleotide primer sets used in the reaction mixtures targeted a 218-bp internal region of ecfI , a 288-bp overlap region containing the 3′ end of ecfI and the 5′ end of ecfR ( ecfIR ), a 488-bp internal region ecfR , a 237-bp region overlapping ecfR , bfrH , and a 93-bp region between ecfR and bfrH ( ecfR - bfrH intergenic), a 598-bp internal region of bfrH , a 513-bp internal region of bhuR , and a 402-bp internal region of recA . Amplified DNA from each RT-PCR was resolved in a 2% agarose gel and visualized by ethidium bromide staining. Fe+, Fe-replete conditions; Fe−, Fe-stressed conditions.

    Article Snippet: The amplicon was generated using pJB8.0 as a DNA template, and PCR was performed using Pfu Turbo polymerase (Stratagene) and the following parameters: 30 cycles of 95°C for 45 s, 58°C for 45 s, and 72°C for 4 min 30 s. Purified PCR products were self-ligated to produce pJB8.1.

    Techniques: Isolation, Amplification, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, Staining

    Regulation of the ecfIR-bfrH locus by fur1 . (A) Alignment of Fur1 sequence with sequence of Fur of E. coli . Amino acids within metal binding site 1 are indicated in bold and underlined, and amino acids within metal binding site 2 are denoted only in bold. (B) Fur1-dependent transcription of the ecfIR - bfrH locus. RT-PCR was performed using total RNAs obtained from Fe-replete and Fe-stressed cells, utilizing oligonucleotide primers which targeted the overlap region encompassing the 3′ end of ecfI and the 5′ end of ecfR ( ecfIR ), bfrH , bhuR , and recA . Amplified DNA from each RT-PCR was resolved in a 2% agarose gel and visualized by ethidium bromide staining. +, Fe-replete conditions; −, Fe-stressed conditions.

    Journal: Infection and Immunity

    Article Title: Expression of BfrH, a Putative Siderophore Receptor of Bordetella bronchiseptica, Is Regulated by Iron, Fur1, and the Extracellular Function Sigma Factor EcfI ▿

    doi: 10.1128/IAI.00961-09

    Figure Lengend Snippet: Regulation of the ecfIR-bfrH locus by fur1 . (A) Alignment of Fur1 sequence with sequence of Fur of E. coli . Amino acids within metal binding site 1 are indicated in bold and underlined, and amino acids within metal binding site 2 are denoted only in bold. (B) Fur1-dependent transcription of the ecfIR - bfrH locus. RT-PCR was performed using total RNAs obtained from Fe-replete and Fe-stressed cells, utilizing oligonucleotide primers which targeted the overlap region encompassing the 3′ end of ecfI and the 5′ end of ecfR ( ecfIR ), bfrH , bhuR , and recA . Amplified DNA from each RT-PCR was resolved in a 2% agarose gel and visualized by ethidium bromide staining. +, Fe-replete conditions; −, Fe-stressed conditions.

    Article Snippet: The amplicon was generated using pJB8.0 as a DNA template, and PCR was performed using Pfu Turbo polymerase (Stratagene) and the following parameters: 30 cycles of 95°C for 45 s, 58°C for 45 s, and 72°C for 4 min 30 s. Purified PCR products were self-ligated to produce pJB8.1.

    Techniques: Sequencing, Binding Assay, Reverse Transcription Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Staining

    Regulation of bfrH by EcfI. (A) Effects of overexpression of EcfI on expression of bfrH . RT-PCR was performed using total RNAs isolated from Fe-replete and Fe-stressed cells. Oligonucleotide primer sets used in the reaction mixtures targeted a 218-bp region of ecfI , a 288-bp overlap region encompassing the 3′ end of ecfI and the 5′ end of ecfR ( ecfIR ), a 237-bp region overlapping ecfR , bfrH , and a 93-bp region between ecfR and bfrH ( ecfR - bfrH intergenic), a 598-bp internal region of bfrH , a 513-bp internal region of bhuR , and a 402-bp internal region of recA . Amplified DNA from each RT-PCR was resolved in a 2% agarose gel and visualized by ethidium bromide staining. +, Fe-replete conditions; −, Fe-stressed conditions. (B) Expression of bfrH in RB50Δ ecfI . qRT-PCR was performed on total RNAs isolated from Fe-replete and Fe-stressed cells, using oligonucleotides targeting sequences within bfrH . Data are expressed as means and standard errors and were obtained by calculating the relative SQ of the respective mRNA after normalizing to the amount of recA mRNA expressed by the cell. *, statistically significantly different from Fe-stressed RB50 ( P

    Journal: Infection and Immunity

    Article Title: Expression of BfrH, a Putative Siderophore Receptor of Bordetella bronchiseptica, Is Regulated by Iron, Fur1, and the Extracellular Function Sigma Factor EcfI ▿

    doi: 10.1128/IAI.00961-09

    Figure Lengend Snippet: Regulation of bfrH by EcfI. (A) Effects of overexpression of EcfI on expression of bfrH . RT-PCR was performed using total RNAs isolated from Fe-replete and Fe-stressed cells. Oligonucleotide primer sets used in the reaction mixtures targeted a 218-bp region of ecfI , a 288-bp overlap region encompassing the 3′ end of ecfI and the 5′ end of ecfR ( ecfIR ), a 237-bp region overlapping ecfR , bfrH , and a 93-bp region between ecfR and bfrH ( ecfR - bfrH intergenic), a 598-bp internal region of bfrH , a 513-bp internal region of bhuR , and a 402-bp internal region of recA . Amplified DNA from each RT-PCR was resolved in a 2% agarose gel and visualized by ethidium bromide staining. +, Fe-replete conditions; −, Fe-stressed conditions. (B) Expression of bfrH in RB50Δ ecfI . qRT-PCR was performed on total RNAs isolated from Fe-replete and Fe-stressed cells, using oligonucleotides targeting sequences within bfrH . Data are expressed as means and standard errors and were obtained by calculating the relative SQ of the respective mRNA after normalizing to the amount of recA mRNA expressed by the cell. *, statistically significantly different from Fe-stressed RB50 ( P

    Article Snippet: The amplicon was generated using pJB8.0 as a DNA template, and PCR was performed using Pfu Turbo polymerase (Stratagene) and the following parameters: 30 cycles of 95°C for 45 s, 58°C for 45 s, and 72°C for 4 min 30 s. Purified PCR products were self-ligated to produce pJB8.1.

    Techniques: Over Expression, Expressing, Reverse Transcription Polymerase Chain Reaction, Isolation, Amplification, Agarose Gel Electrophoresis, Staining, Quantitative RT-PCR

    Optimization of ARMS condition. Notes: ARMS amplifications specific for the mutation (c.C799T) were optimized by indicated different primer pairs. The genomic samples of mutant hemizygous proband M001 (I:1) and his normal son (II:3) were used as DNA templates. The black and blue arrows show the position of the point mutation and nonspecific primer-dimer, respectively. I:1=M001; II:3=M002. Abbreviations: ARMS, amplification refractory mutation system; WT, wild-type primer; MT, mutant primer; C, common primer.

    Journal: The Application of Clinical Genetics

    Article Title: Evaluation of amplification refractory mutation system (ARMS) technique for quick and accurate prenatal gene diagnosis of CHM variant in choroideremia

    doi: 10.2147/TACG.S144383

    Figure Lengend Snippet: Optimization of ARMS condition. Notes: ARMS amplifications specific for the mutation (c.C799T) were optimized by indicated different primer pairs. The genomic samples of mutant hemizygous proband M001 (I:1) and his normal son (II:3) were used as DNA templates. The black and blue arrows show the position of the point mutation and nonspecific primer-dimer, respectively. I:1=M001; II:3=M002. Abbreviations: ARMS, amplification refractory mutation system; WT, wild-type primer; MT, mutant primer; C, common primer.

    Article Snippet: ARMS-PCR amplification PCR was performed in a 10 µL reaction volume for DNA samples M001, M002, M003, M004, M050, and M051 that comprised 1 µL DNA template (15 ng), 1 µL 3.3 µM primers, 5 µL 2X PCR Taq Master Mix (TianGen Biotech Co. Ltd., Beijing, People’s Republic of China), and 3 µL double-distilled water.

    Techniques: Mutagenesis, Amplification

    ARMS amplification by primers CHM-WT2 (WT2) and CHM-Common, and primers CHM-MT and CHM-Common. Notes: ( A ) ARMS amplification for different DNA samples. The black arrow shows the specific PCR products. ( B ) Verification of M003 by Sanger sequencing. The black arrow shows the position of the point mutation. I:1=M001; II:3=M002; II:2=M003; III:1=M004; II:1=M050; M051=Normal male control. Abbreviations: ARMS, amplification refractory mutation system; CHM, choroideremia; WT, wild-type primer; MT, mutant primer; C, common primer.

    Journal: The Application of Clinical Genetics

    Article Title: Evaluation of amplification refractory mutation system (ARMS) technique for quick and accurate prenatal gene diagnosis of CHM variant in choroideremia

    doi: 10.2147/TACG.S144383

    Figure Lengend Snippet: ARMS amplification by primers CHM-WT2 (WT2) and CHM-Common, and primers CHM-MT and CHM-Common. Notes: ( A ) ARMS amplification for different DNA samples. The black arrow shows the specific PCR products. ( B ) Verification of M003 by Sanger sequencing. The black arrow shows the position of the point mutation. I:1=M001; II:3=M002; II:2=M003; III:1=M004; II:1=M050; M051=Normal male control. Abbreviations: ARMS, amplification refractory mutation system; CHM, choroideremia; WT, wild-type primer; MT, mutant primer; C, common primer.

    Article Snippet: ARMS-PCR amplification PCR was performed in a 10 µL reaction volume for DNA samples M001, M002, M003, M004, M050, and M051 that comprised 1 µL DNA template (15 ng), 1 µL 3.3 µM primers, 5 µL 2X PCR Taq Master Mix (TianGen Biotech Co. Ltd., Beijing, People’s Republic of China), and 3 µL double-distilled water.

    Techniques: Amplification, Polymerase Chain Reaction, Sequencing, Mutagenesis

    Overview of functional-RNA array production. ( A ) The general design of the DNA in vitro transcription templates. From 5′ to 3′ there is: a short, biotinylated linker (to facilitate surface-immobilization of the DNA), a T7 promoter, sequence encoding the RNA of interest, a second linker (to separate the RNA of interest and the RNA aptamer) and sequence encoding an RNA aptamer (to facilitate RNA-capture). ( B ) A schematic representation of the ‘sandwich’ assembly and method used to produce the RNA array. A DNA in vitro transcription template array slide is positioned facing an RNA capture slide. Thin spacers are used to physically separate the surfaces. A solution of in vitro transcription reagents is inserted between the two surfaces and RNA transcription-capture proceeds for 90 min at 37°C to generate a functional-RNA array. This RNA array can then be used as a platform for investigating RNA-based interactions, e.g. probing with labelled binding partners.

    Journal: Nucleic Acids Research

    Article Title: High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions

    doi: 10.1093/nar/gky410

    Figure Lengend Snippet: Overview of functional-RNA array production. ( A ) The general design of the DNA in vitro transcription templates. From 5′ to 3′ there is: a short, biotinylated linker (to facilitate surface-immobilization of the DNA), a T7 promoter, sequence encoding the RNA of interest, a second linker (to separate the RNA of interest and the RNA aptamer) and sequence encoding an RNA aptamer (to facilitate RNA-capture). ( B ) A schematic representation of the ‘sandwich’ assembly and method used to produce the RNA array. A DNA in vitro transcription template array slide is positioned facing an RNA capture slide. Thin spacers are used to physically separate the surfaces. A solution of in vitro transcription reagents is inserted between the two surfaces and RNA transcription-capture proceeds for 90 min at 37°C to generate a functional-RNA array. This RNA array can then be used as a platform for investigating RNA-based interactions, e.g. probing with labelled binding partners.

    Article Snippet: Firstly, the physical separation of the DNA template and RNA capture surfaces simplifies the final RNA surface, relative to those in the methods based on the Illumina Next Generation Sequencing platform ( ).

    Techniques: Functional Assay, In Vitro, Sequencing, Binding Assay

    Production of a high-density MicA sa RNA array. ( A ) Preparation of a high-density DNA template array of MicA and MicA sa . (i) Schematic layout of a single 6 × 6 grid with alternating rows of MicA and MicA sa templates. (ii) A single 6 × 6 grid of a DNA template array of Alexa647-labelled MicA and MicA sa . Individual spots were separated by 750 μm. (iii) The entire DNA template array of 21 repeating 6 × 6 grids as shown in (ii). ( B ) Production of a high-density MicA sa RNA array from the DNA template array described in (A). (i) Schematic of the expected layout of a single grid of the MicA sa RNA array. (ii) A single grid of the Cy3-labelled MicA sa RNA array. (iii) The entire MicA sa RNA array of 21 repeating grids as shown in (ii). The RNA array images have been mirror imaged so that the spot positions correspond to those shown in the schematics of the DNA template array.

    Journal: Nucleic Acids Research

    Article Title: High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions

    doi: 10.1093/nar/gky410

    Figure Lengend Snippet: Production of a high-density MicA sa RNA array. ( A ) Preparation of a high-density DNA template array of MicA and MicA sa . (i) Schematic layout of a single 6 × 6 grid with alternating rows of MicA and MicA sa templates. (ii) A single 6 × 6 grid of a DNA template array of Alexa647-labelled MicA and MicA sa . Individual spots were separated by 750 μm. (iii) The entire DNA template array of 21 repeating 6 × 6 grids as shown in (ii). ( B ) Production of a high-density MicA sa RNA array from the DNA template array described in (A). (i) Schematic of the expected layout of a single grid of the MicA sa RNA array. (ii) A single grid of the Cy3-labelled MicA sa RNA array. (iii) The entire MicA sa RNA array of 21 repeating grids as shown in (ii). The RNA array images have been mirror imaged so that the spot positions correspond to those shown in the schematics of the DNA template array.

    Article Snippet: Firstly, the physical separation of the DNA template and RNA capture surfaces simplifies the final RNA surface, relative to those in the methods based on the Illumina Next Generation Sequencing platform ( ).

    Techniques:

    Production and screening of high-density multi-RNA arrays with single probes. ( A ) A DNA template array of MicA sa , MicA, ompA sa, hapR sa , ilvC sa , ilVE sa , hisG sa , ureA sa and MG sa templates (left: schematic of a single-field) was used to generate an eight-RNA array of MicA sa , ompA sa, hapR sa , ilvC sa , ilVE sa , hisG sa , ureA sa and MG sa that was probed with 3 μM Cy3-labelled ompA (right). ( B ) A DNA template array of MicA sa , MicA, ompA sa, hapR sa , ilvC sa , ilVE sa , hisG sa , ureA sa and MG sa templates (left: schematic of a single-field) was used to generate an eight-RNA array of MicA sa , ompA sa, hapR sa , ilvC sa , ilVE sa , hisG sa , ureA sa and MG sa that was probed with 2.5 μM Cy3-labelled Qrr1 (right). The probed array has been false-coloured red to match the key. ( C ) A DNA template array of MicA sa , Qrr1 sa , DsrA sa , RprA sa , hapR sa , ompA sa , rpoS sa and MG sa templates (left: schematic of a single-field) was used to generate an eight-RNA array of MicA sa , Qrr1 sa , DsrA sa , RprA sa , hapR sa , ompA sa , rpoS sa and MG sa that was probed with 20 μM malachite green (right). The probed array has been false-coloured cyan to match the key. DNA template arrays of repeating 4 × 5 grids (A and B) or 4 × 4 grids (C) were prepared using an automated arrayer with individual spots separated by 1250 μm. Probed RNA images have all been mirror imaged so that the spot positions correspond to those shown in the schematic of the DNA template arrays.

    Journal: Nucleic Acids Research

    Article Title: High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions

    doi: 10.1093/nar/gky410

    Figure Lengend Snippet: Production and screening of high-density multi-RNA arrays with single probes. ( A ) A DNA template array of MicA sa , MicA, ompA sa, hapR sa , ilvC sa , ilVE sa , hisG sa , ureA sa and MG sa templates (left: schematic of a single-field) was used to generate an eight-RNA array of MicA sa , ompA sa, hapR sa , ilvC sa , ilVE sa , hisG sa , ureA sa and MG sa that was probed with 3 μM Cy3-labelled ompA (right). ( B ) A DNA template array of MicA sa , MicA, ompA sa, hapR sa , ilvC sa , ilVE sa , hisG sa , ureA sa and MG sa templates (left: schematic of a single-field) was used to generate an eight-RNA array of MicA sa , ompA sa, hapR sa , ilvC sa , ilVE sa , hisG sa , ureA sa and MG sa that was probed with 2.5 μM Cy3-labelled Qrr1 (right). The probed array has been false-coloured red to match the key. ( C ) A DNA template array of MicA sa , Qrr1 sa , DsrA sa , RprA sa , hapR sa , ompA sa , rpoS sa and MG sa templates (left: schematic of a single-field) was used to generate an eight-RNA array of MicA sa , Qrr1 sa , DsrA sa , RprA sa , hapR sa , ompA sa , rpoS sa and MG sa that was probed with 20 μM malachite green (right). The probed array has been false-coloured cyan to match the key. DNA template arrays of repeating 4 × 5 grids (A and B) or 4 × 4 grids (C) were prepared using an automated arrayer with individual spots separated by 1250 μm. Probed RNA images have all been mirror imaged so that the spot positions correspond to those shown in the schematic of the DNA template arrays.

    Article Snippet: Firstly, the physical separation of the DNA template and RNA capture surfaces simplifies the final RNA surface, relative to those in the methods based on the Illumina Next Generation Sequencing platform ( ).

    Techniques:

    Production of a low-density multi-RNA array. ( A ) Generation of a Cy3-labelled MicA sa , hapR sa and MG sa RNA array (i) Schematic layout of a DNA template array of MicA, MicA sa , hapR, hapR sa , MG and MG sa. (ii) Cy3-labelled RNA array generated from the DNA template array following in vitro transcription.( B ) Probing a low-density multi-RNA array with malachite green. (i) Schematic representation of the middle row of a non-labelled RNA array generated using the DNA template array in A(i). (ii) As in B(i) following probing with malachite green. (iii) A non-labelled MicA sa , hapR sa and MG sa RNA array (i) (generated as in (A) but without labelling) probed with malachite green. The RNA array images have been mirror imaged so that the spot positions correspond to those shown in the schematics of the DNA template array.

    Journal: Nucleic Acids Research

    Article Title: High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions

    doi: 10.1093/nar/gky410

    Figure Lengend Snippet: Production of a low-density multi-RNA array. ( A ) Generation of a Cy3-labelled MicA sa , hapR sa and MG sa RNA array (i) Schematic layout of a DNA template array of MicA, MicA sa , hapR, hapR sa , MG and MG sa. (ii) Cy3-labelled RNA array generated from the DNA template array following in vitro transcription.( B ) Probing a low-density multi-RNA array with malachite green. (i) Schematic representation of the middle row of a non-labelled RNA array generated using the DNA template array in A(i). (ii) As in B(i) following probing with malachite green. (iii) A non-labelled MicA sa , hapR sa and MG sa RNA array (i) (generated as in (A) but without labelling) probed with malachite green. The RNA array images have been mirror imaged so that the spot positions correspond to those shown in the schematics of the DNA template array.

    Article Snippet: Firstly, the physical separation of the DNA template and RNA capture surfaces simplifies the final RNA surface, relative to those in the methods based on the Illumina Next Generation Sequencing platform ( ).

    Techniques: Generated, In Vitro

    Production of a low-density functional MicA sa RNA array. ( A ) Generation of a Cy3-labelled MicA sa RNA array using a DNA template array of Alexa647-labelled MicA and MicA sa . ( B ) A non-labelled MicA sa RNA array (generated as in (A) but without labelling) probed with Cy5-labelled ompA .

    Journal: Nucleic Acids Research

    Article Title: High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions

    doi: 10.1093/nar/gky410

    Figure Lengend Snippet: Production of a low-density functional MicA sa RNA array. ( A ) Generation of a Cy3-labelled MicA sa RNA array using a DNA template array of Alexa647-labelled MicA and MicA sa . ( B ) A non-labelled MicA sa RNA array (generated as in (A) but without labelling) probed with Cy5-labelled ompA .

    Article Snippet: Firstly, the physical separation of the DNA template and RNA capture surfaces simplifies the final RNA surface, relative to those in the methods based on the Illumina Next Generation Sequencing platform ( ).

    Techniques: Functional Assay, Generated

    Simultaneous screening of a high-density multi-RNA array with multiple probes. ( A ) Schematic of a DNA template array of repeating 4 × 4 grids of MicA sa , hapR sa , MG sa and ompA sa templates that was prepared using an automated arrayer with individual spots separated by 1250 μm. ( B ) The generated four-RNA array of Cy3-labelled MicA sa , hapR sa , MG sa and ompA sa . ( C ) A non-labelled MicA sa , hapR sa , MG sa and ompA sa RNA array (generated as in (B) but without labelling) probed with 3 μM Cy3-labelled Qrr1 and 20 μM malachite green. The labelled (B) and probed (C) RNA array images have been mirror imaged so that the spot positions correspond to those shown in the schematic of the DNA template array (A). ( D ) Spot profiles for the first two rows of the probed RNA array shown in ( C ). The red and green lines are the spot profile data for malachite green and Qrr1, respectively. The dashed black lines are the least-squares minimization of a function describing the sum of two co-incident Gaussian distributions (one for the main peak, and one for weak signal broadening due to diffusion of non-specifically bound probe):- \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$f\;( x ) = \mathop \sum \limits_{i = 1}^2 {a_i}\;{\rm{exp}}\left( { - \frac{{{{( {x - {\rm{\mu_i }}} )}^2}}}{{2\sigma _i^2}}}\right)$\end{document} where \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$f( x )$\end{document} is the fluorescence intensity at position x , and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${a_i},\;{\rm{\mu_i }}$\end{document} and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{\rm{\sigma }}_i}$\end{document} are the intensity, centre and standard deviation, respectively, of spot i . The FWHM for each spot was calculated as:- \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$FWHM\; = \;2\sigma \sqrt {2\ln 2}$\end{document} .

    Journal: Nucleic Acids Research

    Article Title: High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions

    doi: 10.1093/nar/gky410

    Figure Lengend Snippet: Simultaneous screening of a high-density multi-RNA array with multiple probes. ( A ) Schematic of a DNA template array of repeating 4 × 4 grids of MicA sa , hapR sa , MG sa and ompA sa templates that was prepared using an automated arrayer with individual spots separated by 1250 μm. ( B ) The generated four-RNA array of Cy3-labelled MicA sa , hapR sa , MG sa and ompA sa . ( C ) A non-labelled MicA sa , hapR sa , MG sa and ompA sa RNA array (generated as in (B) but without labelling) probed with 3 μM Cy3-labelled Qrr1 and 20 μM malachite green. The labelled (B) and probed (C) RNA array images have been mirror imaged so that the spot positions correspond to those shown in the schematic of the DNA template array (A). ( D ) Spot profiles for the first two rows of the probed RNA array shown in ( C ). The red and green lines are the spot profile data for malachite green and Qrr1, respectively. The dashed black lines are the least-squares minimization of a function describing the sum of two co-incident Gaussian distributions (one for the main peak, and one for weak signal broadening due to diffusion of non-specifically bound probe):- \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$f\;( x ) = \mathop \sum \limits_{i = 1}^2 {a_i}\;{\rm{exp}}\left( { - \frac{{{{( {x - {\rm{\mu_i }}} )}^2}}}{{2\sigma _i^2}}}\right)$\end{document} where \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$f( x )$\end{document} is the fluorescence intensity at position x , and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${a_i},\;{\rm{\mu_i }}$\end{document} and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{\rm{\sigma }}_i}$\end{document} are the intensity, centre and standard deviation, respectively, of spot i . The FWHM for each spot was calculated as:- \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$FWHM\; = \;2\sigma \sqrt {2\ln 2}$\end{document} .

    Article Snippet: Firstly, the physical separation of the DNA template and RNA capture surfaces simplifies the final RNA surface, relative to those in the methods based on the Illumina Next Generation Sequencing platform ( ).

    Techniques: Generated, Diffusion-based Assay, Fluorescence, Standard Deviation

    PCR assay for detection of bla VEB gene with product size: 600 bp. Lanes 3–17: Amplified products, Lanes 2 and 19: Positive control, Lanes 1 and 20: DNA ladder 100 bp, Lane 18: Negative control

    Journal: GMS Hygiene and Infection Control

    Article Title: Prevalence of extended-spectrum beta-lactamase genes in Acinetobacter baumannii strains isolated from nosocomial infections in Tehran, Iran

    doi: 10.3205/dgkh000318

    Figure Lengend Snippet: PCR assay for detection of bla VEB gene with product size: 600 bp. Lanes 3–17: Amplified products, Lanes 2 and 19: Positive control, Lanes 1 and 20: DNA ladder 100 bp, Lane 18: Negative control

    Article Snippet: The PCR mixture contained the DNA template, Forward/Reverse primers, and master mix (Bioneer Co., Korea, Cat. number K-2016).

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

    PCR assay for detection of bla TEM gene with product size: 700 bp. Lanes 2–36: Amplified products, Lane 37: Positive control, Lanes 1 and 40: DNA ladder 100 bp, Lane 38–40: Negative control

    Journal: GMS Hygiene and Infection Control

    Article Title: Prevalence of extended-spectrum beta-lactamase genes in Acinetobacter baumannii strains isolated from nosocomial infections in Tehran, Iran

    doi: 10.3205/dgkh000318

    Figure Lengend Snippet: PCR assay for detection of bla TEM gene with product size: 700 bp. Lanes 2–36: Amplified products, Lane 37: Positive control, Lanes 1 and 40: DNA ladder 100 bp, Lane 38–40: Negative control

    Article Snippet: The PCR mixture contained the DNA template, Forward/Reverse primers, and master mix (Bioneer Co., Korea, Cat. number K-2016).

    Techniques: Polymerase Chain Reaction, Transmission Electron Microscopy, Amplification, Positive Control, Negative Control

    PCR assay for detection of bla SHV gene with product size: 700 bp. Lanes 3–18: Amplified products, Lane 2: Positive control, Lanes 1 and 20: DNA ladder 100 bp, Lane 19: Negative control

    Journal: GMS Hygiene and Infection Control

    Article Title: Prevalence of extended-spectrum beta-lactamase genes in Acinetobacter baumannii strains isolated from nosocomial infections in Tehran, Iran

    doi: 10.3205/dgkh000318

    Figure Lengend Snippet: PCR assay for detection of bla SHV gene with product size: 700 bp. Lanes 3–18: Amplified products, Lane 2: Positive control, Lanes 1 and 20: DNA ladder 100 bp, Lane 19: Negative control

    Article Snippet: The PCR mixture contained the DNA template, Forward/Reverse primers, and master mix (Bioneer Co., Korea, Cat. number K-2016).

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

    Restriction analysis with Rsa I of DNA amplified with primer pair ITS 5 and ITS 4 from P. infestans US-6 NY (lane 2), P. infestans 93-1 (lane 3), P. mirabilis 0S0016 (lane 4), P. fragariae A-8 (lane 5), P. megasperma NY 318 (lane 6), P. megasperma NY 412 (lane 7), P. sojae R1 (lane 8), P. cinnamomi 2302 (lane 9), P. cryptogea PCR-1 (lane 10), and P. erythroseptica 4 (lane 11). Lanes 1 and 12 contain 100-bp ladders.

    Journal: Applied and Environmental Microbiology

    Article Title: PCR Amplification of Ribosomal DNA for Species Identification in the Plant Pathogen Genus Phytophthora

    doi:

    Figure Lengend Snippet: Restriction analysis with Rsa I of DNA amplified with primer pair ITS 5 and ITS 4 from P. infestans US-6 NY (lane 2), P. infestans 93-1 (lane 3), P. mirabilis 0S0016 (lane 4), P. fragariae A-8 (lane 5), P. megasperma NY 318 (lane 6), P. megasperma NY 412 (lane 7), P. sojae R1 (lane 8), P. cinnamomi 2302 (lane 9), P. cryptogea PCR-1 (lane 10), and P. erythroseptica 4 (lane 11). Lanes 1 and 12 contain 100-bp ladders.

    Article Snippet: Each reaction tube contained approximately 1 μl of a 1-ng/μl DNA template, 5 μl of 10× PCR buffer (Boehringer Mannheim, Indianapolis, Ind.), 36.6 μl of sterile distilled water, 2 μl (each) of 1.25 mM deoxynucleoside triphosphates (Pharmacia Biotech, Piscataway, N.J.), 2 μl of 10 mM MgCl2 (Sigma, St. Louis, Mo.), 2 μl each of 10 μM forward and reverse primers , and 0.4 μl of Taq (5 U/μl; Boehringer Mannheim).

    Techniques: Amplification, Polymerase Chain Reaction

    Restriction analysis with Hae III of DNA amplified with ITS 5 and ITS 4 from P. palmivora P8 (lane 2), P. erythroseptica 4 (lane 3), P. cryptogea PCR-1 (lane 4), P. citrophthora M86 (lane 5), P. cinnamomi 2302 (lane 6), P. fragariae A-8 (lane 7), P. megasperma NY 412 (lane 8), P. sojae R1 (lane 9), and P. megasperma NY 318 (lane 10). Lanes 1 and 11 contain 100-bp ladders.

    Journal: Applied and Environmental Microbiology

    Article Title: PCR Amplification of Ribosomal DNA for Species Identification in the Plant Pathogen Genus Phytophthora

    doi:

    Figure Lengend Snippet: Restriction analysis with Hae III of DNA amplified with ITS 5 and ITS 4 from P. palmivora P8 (lane 2), P. erythroseptica 4 (lane 3), P. cryptogea PCR-1 (lane 4), P. citrophthora M86 (lane 5), P. cinnamomi 2302 (lane 6), P. fragariae A-8 (lane 7), P. megasperma NY 412 (lane 8), P. sojae R1 (lane 9), and P. megasperma NY 318 (lane 10). Lanes 1 and 11 contain 100-bp ladders.

    Article Snippet: Each reaction tube contained approximately 1 μl of a 1-ng/μl DNA template, 5 μl of 10× PCR buffer (Boehringer Mannheim, Indianapolis, Ind.), 36.6 μl of sterile distilled water, 2 μl (each) of 1.25 mM deoxynucleoside triphosphates (Pharmacia Biotech, Piscataway, N.J.), 2 μl of 10 mM MgCl2 (Sigma, St. Louis, Mo.), 2 μl each of 10 μM forward and reverse primers , and 0.4 μl of Taq (5 U/μl; Boehringer Mannheim).

    Techniques: Amplification, Polymerase Chain Reaction

    The effects of ChA on Akkermansia . ( A ) Comparison of the relative abundance of Akkermansia in fecal samples of DSS colitis mice analyzed by 16S rRNA gene sequencing; ( B ) A comparison of the relative abundance of Akkermansia in fecal samples of normal mice that were treated with ChA. Akkermansia was quantified with qPCR by amplifying fecal DNA with primers specific for Akkermansia and universal bacterial primers; ( C ) The polymerase chain reaction products were analyzed by electrophoresis in a 2% agarose gel. * p

    Journal: Nutrients

    Article Title: Chlorogenic Acid Ameliorates Experimental Colitis by Promoting Growth of Akkermansia in Mice

    doi: 10.3390/nu9070677

    Figure Lengend Snippet: The effects of ChA on Akkermansia . ( A ) Comparison of the relative abundance of Akkermansia in fecal samples of DSS colitis mice analyzed by 16S rRNA gene sequencing; ( B ) A comparison of the relative abundance of Akkermansia in fecal samples of normal mice that were treated with ChA. Akkermansia was quantified with qPCR by amplifying fecal DNA with primers specific for Akkermansia and universal bacterial primers; ( C ) The polymerase chain reaction products were analyzed by electrophoresis in a 2% agarose gel. * p

    Article Snippet: All polymerase chain reaction (PCR) recations contained 10 ng DNA template, TransStart FastPfu Polymerase (Transgen Biotech, Beijing, China) and forward primer and reverse primer at a final concentration of 200 nM.

    Techniques: Mouse Assay, Sequencing, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Electrophoresis, Agarose Gel Electrophoresis