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  • 93
    Thermo Fisher sybr green i staining
    Effect of Cre- loxP system on the concatemer production in RCR. pUC_OriC300 (− loxP ) or pUC_OLDT (+ loxP ) (0.05 ng) was incubated in the RCR mixture at 33 °C for 3 h in the absence (0 mU) or presence (5, 15, 50, or 150 mU) of Cre recombinase. The product was analyzed by 0.5% TBE-agarose gel electrophoresis and <t>SYBR</t> <t>Green</t> I staining. The ratio of concatemers to the sum of concatemers and supercoils is shown in a graph.
    Sybr Green I Staining, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 78 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 93 stars, based on 78 article reviews
    Price from $9.99 to $1999.99
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    78
    TaKaRa sybr green i
    Specificity of RT-LAMP assay for the detection of DENV3. a Agarose gel electrophoresis analysis of the DENV3 RT-LAMP amplification product, showing the specificity of the primers. b The real-time monitoring over time for the DENV3 RT-LAMP reaction. c Visual inspection of the RT-LAMP specificity assay with <t>SYBR</t> Green I corresponding to the agarose gel electrophoresis analysis. 1, negative [ 43 ]; 2–3, DNA of HSV and EBV, respectively; 4–9, RNA of JEV, YFV and DENV1-4, respectively; M, DL1000 DNA Marker
    Sybr Green I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 78/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 78 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    sybr green i - by Bioz Stars, 2019-10
    78/100 stars
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    77
    Shanghai Generay Biotech sybr green i
    Detection of tobacco components in different tobaccocultivars. (a) LAMP method through direct visual detection with <t>SYBR</t> Green I; (b) LAMP method on 2% agarose gel electrophoresis analysis; (c) qPCR method. Lane 1 : NTC; lane 2 : PTC; lanes 3–17 : 15 tobacco samples of different cured tobacco varieties; lanes 18-19 : two fresh tobacco samples; lane M : Trans 2K DNA marker. Ct was expressed as mean Ct ± SD from 3 independent experiments with three replications.
    Sybr Green I, supplied by Shanghai Generay Biotech, used in various techniques. Bioz Stars score: 77/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sybr green i/product/Shanghai Generay Biotech
    Average 77 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    sybr green i - by Bioz Stars, 2019-10
    77/100 stars
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    77
    Beijing Solarbio Science sybr green i
    Detection of clinical samples in LAMP, CPA and IMSA assays. LAMP assay: (A) agarose gel electrophoresis of products obtained; (B) visualization of reactions performed with clinical samples (1–41) and <t>SYBR-Green</t> I under visible light; (C) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under UV light. CPA assay: (D) agarose gel electrophoresis of products obtained; (E) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under visible light; (F) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under UV light. IMSA assay: (G) agarose gel electrophoresis of products obtained; (H) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under visible light; (I) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under UV light. (J) Reverse transcription-polymerase chain reaction amplification curves for clinical samples (1–41). LAMP, loop-mediated isothermal amplification; CPA, cross-priming amplification; IMSA, isothermal multiple-self-matching-initiated amplification; M, Trans 2K plus II DNA marker; N, negative control; P, positive control (runt related transcription factor 1/runt related transcription factor 1 translocation partner 1 plasmid).
    Sybr Green I, supplied by Beijing Solarbio Science, used in various techniques. Bioz Stars score: 77/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 77 stars, based on 1 article reviews
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    77
    BioTek Instruments sybr green i
    Specificity comparison of the LAMP assay and conventional PCR. (A) LAMP products detected by 1000 × <t>SYBR</t> Green I. (B) PCR products detected by agarose gel electrophoresis stained by EB. Tube and lane 1: ddH 2 O. Tube and lane 2: the plasmid 1Ac0229 (positive control). Tubes and lanes 3–10: genomic DNA from sugarcane genotypes of a1 ( bar transgenic line from host cultivar FN15), 16k-2 ( bar transgenic line from host cultivar ROC22), FN15 ( S . spp. hybrids), ROC22 ( S . spp. hybrids), ROC10 ( S . spp. hybrids), Badila ( S. officinarum ), 82-114 ( S. spontaneum ), 57NG208 ( S. robustum ), respectively. Lane M: 100 bp DNA.
    Sybr Green I, supplied by BioTek Instruments, used in various techniques. Bioz Stars score: 77/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 77 stars, based on 1 article reviews
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    77
    Hausser Scientific sybr green i pi assay
    Exposure of spirochetal form and amoxicillin-induced round bodies of B. burgdorferi (5-day old) to different antibiotics. Log phase spirochetal form (5 day old) and amoxicillin-induced round bodies of B. burgdorferi (5-day old) were exposed to 50 μM doxycycline, cefuroxime, and ceftriaxone, respectively, for 5 days. The percentage of residual live cells ( n = 3) was determined by <t>SYBR</t> Green I/PI assay followed by fluorescence microscopy counting.
    Sybr Green I Pi Assay, supplied by Hausser Scientific, used in various techniques. Bioz Stars score: 77/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 77 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
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    Image Search Results


    Effect of Cre- loxP system on the concatemer production in RCR. pUC_OriC300 (− loxP ) or pUC_OLDT (+ loxP ) (0.05 ng) was incubated in the RCR mixture at 33 °C for 3 h in the absence (0 mU) or presence (5, 15, 50, or 150 mU) of Cre recombinase. The product was analyzed by 0.5% TBE-agarose gel electrophoresis and SYBR Green I staining. The ratio of concatemers to the sum of concatemers and supercoils is shown in a graph.

    Journal: Life

    Article Title: Efficient Arrangement of the Replication Fork Trap for In Vitro Propagation of Monomeric Circular DNA in the Chromosome-Replication Cycle Reaction

    doi: 10.3390/life8040043

    Figure Lengend Snippet: Effect of Cre- loxP system on the concatemer production in RCR. pUC_OriC300 (− loxP ) or pUC_OLDT (+ loxP ) (0.05 ng) was incubated in the RCR mixture at 33 °C for 3 h in the absence (0 mU) or presence (5, 15, 50, or 150 mU) of Cre recombinase. The product was analyzed by 0.5% TBE-agarose gel electrophoresis and SYBR Green I staining. The ratio of concatemers to the sum of concatemers and supercoils is shown in a graph.

    Article Snippet: An aliquot (2 µL) was analyzed by 0.5% or 1.0% agarose gel electrophoresis, followed by SYBR Green I staining (Molecular Probes, Eugene, USA).

    Techniques: Incubation, Agarose Gel Electrophoresis, SYBR Green Assay, Staining

    Effect of Tus on the RCR propagation of circular DNA in which the oriC-ter arrangement mimics the chromosome position. pKZter_1 (+ ter ) is a pKOZ ( −ter ) derivative containing inward-facing ter sites opposite oriC . The regions available for fork progression from the oriC cassette are indicated by dotted arrows on the circular map. pPKOZ or pKZter_1 (2.5 ng) was incubated in the RCR mixture at 30 °C for 3 h in the presence of the indicated concentrations of Tus. Aliquots (0.2 µL) were analyzed by 0.5% TBE-agarose gel electrophoresis and SYBR Green I staining. The linear DNA size marker fragments were derived from lambda phage DNA (marker).

    Journal: Life

    Article Title: Efficient Arrangement of the Replication Fork Trap for In Vitro Propagation of Monomeric Circular DNA in the Chromosome-Replication Cycle Reaction

    doi: 10.3390/life8040043

    Figure Lengend Snippet: Effect of Tus on the RCR propagation of circular DNA in which the oriC-ter arrangement mimics the chromosome position. pKZter_1 (+ ter ) is a pKOZ ( −ter ) derivative containing inward-facing ter sites opposite oriC . The regions available for fork progression from the oriC cassette are indicated by dotted arrows on the circular map. pPKOZ or pKZter_1 (2.5 ng) was incubated in the RCR mixture at 30 °C for 3 h in the presence of the indicated concentrations of Tus. Aliquots (0.2 µL) were analyzed by 0.5% TBE-agarose gel electrophoresis and SYBR Green I staining. The linear DNA size marker fragments were derived from lambda phage DNA (marker).

    Article Snippet: An aliquot (2 µL) was analyzed by 0.5% or 1.0% agarose gel electrophoresis, followed by SYBR Green I staining (Molecular Probes, Eugene, USA).

    Techniques: Incubation, Agarose Gel Electrophoresis, SYBR Green Assay, Staining, Marker, Derivative Assay

    RCR propagation of circular DNA containing ter sites on both sides of oriC . The circular maps of pCLter_1 and pCLter_2 are shown as in Figure 1 . The indicated plasmid (2.5 ng) was incubated in the RCR mixture at 30 °C for 3 h in the absence (0 nM) or presence (6, 20, or 60 nM) of Tus. The product was analyzed by 0.5% TBE-agarose gel electrophoresis and SYBR Green I staining. The ratio of concatemers to the sum of concatemers and supercoils is shown in a graph.

    Journal: Life

    Article Title: Efficient Arrangement of the Replication Fork Trap for In Vitro Propagation of Monomeric Circular DNA in the Chromosome-Replication Cycle Reaction

    doi: 10.3390/life8040043

    Figure Lengend Snippet: RCR propagation of circular DNA containing ter sites on both sides of oriC . The circular maps of pCLter_1 and pCLter_2 are shown as in Figure 1 . The indicated plasmid (2.5 ng) was incubated in the RCR mixture at 30 °C for 3 h in the absence (0 nM) or presence (6, 20, or 60 nM) of Tus. The product was analyzed by 0.5% TBE-agarose gel electrophoresis and SYBR Green I staining. The ratio of concatemers to the sum of concatemers and supercoils is shown in a graph.

    Article Snippet: An aliquot (2 µL) was analyzed by 0.5% or 1.0% agarose gel electrophoresis, followed by SYBR Green I staining (Molecular Probes, Eugene, USA).

    Techniques: Plasmid Preparation, Incubation, Agarose Gel Electrophoresis, SYBR Green Assay, Staining

    Effect of the inter -ter length on the RCR propagation in the presence of Tus. ( A ) pKZter_2–6 are pKZter_1 derivatives in which the length between the inward-facing ter sites was extended to 0.5, 1.0, 2.0, 4.0, or 10 kb. The circular maps are shown as in Figure 1 . The indicated plasmid (2.5 ng) was incubated in the RCR mixture at 30 °C for 3 h in the absence (0 nM) or presence (20 nM) of Tus. The product was analyzed by 0.5% TBE-agarose gel electrophoresis and SYBR Green I staining. The ratio of concatemers to the sum of concatemers and supercoils is shown in a graph as the average value of three repetitive experiments with standard deviation. ( B ) In pCLter30k, the regions available for fork progression were 15 kb (dotted arrows), while the inter- ter length was 0.2 kb. RCR was performed as in ( A ), except that a 1% agarose gel was used to separate large supercoiled DNAs from concatemers. Large supercoiled DNA migrates more slowly than linear DNA [ 29 ]. DNA size marker fragments were derived from lambda phage DNA (marker).

    Journal: Life

    Article Title: Efficient Arrangement of the Replication Fork Trap for In Vitro Propagation of Monomeric Circular DNA in the Chromosome-Replication Cycle Reaction

    doi: 10.3390/life8040043

    Figure Lengend Snippet: Effect of the inter -ter length on the RCR propagation in the presence of Tus. ( A ) pKZter_2–6 are pKZter_1 derivatives in which the length between the inward-facing ter sites was extended to 0.5, 1.0, 2.0, 4.0, or 10 kb. The circular maps are shown as in Figure 1 . The indicated plasmid (2.5 ng) was incubated in the RCR mixture at 30 °C for 3 h in the absence (0 nM) or presence (20 nM) of Tus. The product was analyzed by 0.5% TBE-agarose gel electrophoresis and SYBR Green I staining. The ratio of concatemers to the sum of concatemers and supercoils is shown in a graph as the average value of three repetitive experiments with standard deviation. ( B ) In pCLter30k, the regions available for fork progression were 15 kb (dotted arrows), while the inter- ter length was 0.2 kb. RCR was performed as in ( A ), except that a 1% agarose gel was used to separate large supercoiled DNAs from concatemers. Large supercoiled DNA migrates more slowly than linear DNA [ 29 ]. DNA size marker fragments were derived from lambda phage DNA (marker).

    Article Snippet: An aliquot (2 µL) was analyzed by 0.5% or 1.0% agarose gel electrophoresis, followed by SYBR Green I staining (Molecular Probes, Eugene, USA).

    Techniques: Plasmid Preparation, Incubation, Agarose Gel Electrophoresis, SYBR Green Assay, Staining, Standard Deviation, Marker, Derivative Assay

    Effect of two same direction ter sites placed opposite oriC . The circular maps of pKZter_5′ter and pKZter_3′ter are shown as in Figure 1 . The indicated plasmid (2.5 ng) was incubated in the RCR mixture at 30 °C for 3 h in the absence (0 nM) or presence (20 nM) of Tus. The product was analyzed by 0.5% TBE-agarose gel electrophoresis and SYBR Green I staining.

    Journal: Life

    Article Title: Efficient Arrangement of the Replication Fork Trap for In Vitro Propagation of Monomeric Circular DNA in the Chromosome-Replication Cycle Reaction

    doi: 10.3390/life8040043

    Figure Lengend Snippet: Effect of two same direction ter sites placed opposite oriC . The circular maps of pKZter_5′ter and pKZter_3′ter are shown as in Figure 1 . The indicated plasmid (2.5 ng) was incubated in the RCR mixture at 30 °C for 3 h in the absence (0 nM) or presence (20 nM) of Tus. The product was analyzed by 0.5% TBE-agarose gel electrophoresis and SYBR Green I staining.

    Article Snippet: An aliquot (2 µL) was analyzed by 0.5% or 1.0% agarose gel electrophoresis, followed by SYBR Green I staining (Molecular Probes, Eugene, USA).

    Techniques: Plasmid Preparation, Incubation, Agarose Gel Electrophoresis, SYBR Green Assay, Staining

    ZIKV and 18S rRNA RT-LAMP in simulated urine samples. Urine samples were spiked with either different strains of ZIKV or DENV and subjected to a ZIKV ( A ) or 18S rRNA ( B ) specific RT-LAMP reaction then visualized by addition of SYBR Green I by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane M: Low DNA Mass Marker (ThermoFisher Scientific); NTC: No template control (negative control). Relative density (RD) of the entire bands for a column relative to the DNA Mass Marker are indicated below the corresponding lane. Lanes that did not have any detectable bands over background are reported as not detectable (ND).

    Journal: Scientific Reports

    Article Title: Rapid Detection of Zika Virus in Urine Samples and Infected Mosquitos by Reverse Transcription-Loop-Mediated Isothermal Amplification

    doi: 10.1038/s41598-018-22102-5

    Figure Lengend Snippet: ZIKV and 18S rRNA RT-LAMP in simulated urine samples. Urine samples were spiked with either different strains of ZIKV or DENV and subjected to a ZIKV ( A ) or 18S rRNA ( B ) specific RT-LAMP reaction then visualized by addition of SYBR Green I by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane M: Low DNA Mass Marker (ThermoFisher Scientific); NTC: No template control (negative control). Relative density (RD) of the entire bands for a column relative to the DNA Mass Marker are indicated below the corresponding lane. Lanes that did not have any detectable bands over background are reported as not detectable (ND).

    Article Snippet: In addition, a 1:10 SYBR green I (Life Technologies) dilution was made in TAE buffer, then 2.0 μL of the SYBR dilution was added to the remaining half of the reaction.

    Techniques: SYBR Green Assay, Fluorescence, Nucleic Acid Electrophoresis, Marker, Negative Control

    ZIKV RT-LAMP sensitivity for ZIKV. Sensitivity assessment of ZIKV RT-LAMP using serial dilutions of ZIKV PCR Standard (Robert Koch Institute) from 4 × 10 5 genome copies/reaction to 1 copies/reaction as visualized by addition of SYBR Green I by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane M: Low DNA Mass Marker (ThermoFisher Scientific); NTC: No template control (negative control). Relative density (RD) of the entire bands for a column relative to the DNA Mass Marker are indicated below the corresponding lane. Lanes that did not have any detectable bands over background are reported as not detectable (ND).

    Journal: Scientific Reports

    Article Title: Rapid Detection of Zika Virus in Urine Samples and Infected Mosquitos by Reverse Transcription-Loop-Mediated Isothermal Amplification

    doi: 10.1038/s41598-018-22102-5

    Figure Lengend Snippet: ZIKV RT-LAMP sensitivity for ZIKV. Sensitivity assessment of ZIKV RT-LAMP using serial dilutions of ZIKV PCR Standard (Robert Koch Institute) from 4 × 10 5 genome copies/reaction to 1 copies/reaction as visualized by addition of SYBR Green I by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane M: Low DNA Mass Marker (ThermoFisher Scientific); NTC: No template control (negative control). Relative density (RD) of the entire bands for a column relative to the DNA Mass Marker are indicated below the corresponding lane. Lanes that did not have any detectable bands over background are reported as not detectable (ND).

    Article Snippet: In addition, a 1:10 SYBR green I (Life Technologies) dilution was made in TAE buffer, then 2.0 μL of the SYBR dilution was added to the remaining half of the reaction.

    Techniques: Polymerase Chain Reaction, SYBR Green Assay, Fluorescence, Nucleic Acid Electrophoresis, Marker, Negative Control

    ZIKV RT-LAMP specificity for ZIKV. Specificity assessment of ZIKV RT-LAMP in ZIKV or DENV infected whole cell lysates (WCL) or cell culture supernatants (SN) as visualized by the addition of SYBR Green I by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane M: Low DNA Mass Marker (ThermoFisher Scientific); NTC: No template control (negative control); + : ZIKV PCR Standard (Robert Koch Institute; positive control).

    Journal: Scientific Reports

    Article Title: Rapid Detection of Zika Virus in Urine Samples and Infected Mosquitos by Reverse Transcription-Loop-Mediated Isothermal Amplification

    doi: 10.1038/s41598-018-22102-5

    Figure Lengend Snippet: ZIKV RT-LAMP specificity for ZIKV. Specificity assessment of ZIKV RT-LAMP in ZIKV or DENV infected whole cell lysates (WCL) or cell culture supernatants (SN) as visualized by the addition of SYBR Green I by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane M: Low DNA Mass Marker (ThermoFisher Scientific); NTC: No template control (negative control); + : ZIKV PCR Standard (Robert Koch Institute; positive control).

    Article Snippet: In addition, a 1:10 SYBR green I (Life Technologies) dilution was made in TAE buffer, then 2.0 μL of the SYBR dilution was added to the remaining half of the reaction.

    Techniques: Infection, Cell Culture, SYBR Green Assay, Fluorescence, Nucleic Acid Electrophoresis, Marker, Negative Control, Polymerase Chain Reaction, Positive Control

    ZIKV and Actin detection in mosquitos. ( A ) qRT-PCR of ZIKV RNA normalized to total RNA for mock (n = 5) or ZIKV (n = 5) infected mosquitos. ( B , C ) Single mosquitos were infected with either mock, ZIKV, or DENV and subjected to a ZIKV ( B ) or Aedes aegypti Actin ( C ) specific RT-LAMP reaction then visualized by addition of SYBR Green I by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane M: Low DNA Mass Marker (ThermoFisher Scientific); NTC: No template control (negative control). Relative density (RD) of the entire bands for a column relative to the DNA Mass Marker are indicated below the corresponding lane. Lanes that did not have any detectable bands over background are reported as not detectable (ND). ( D ) Detection of ZIKV or ribosomal s17 by qRT-PCR. Data shown as mean ± standard deviation.

    Journal: Scientific Reports

    Article Title: Rapid Detection of Zika Virus in Urine Samples and Infected Mosquitos by Reverse Transcription-Loop-Mediated Isothermal Amplification

    doi: 10.1038/s41598-018-22102-5

    Figure Lengend Snippet: ZIKV and Actin detection in mosquitos. ( A ) qRT-PCR of ZIKV RNA normalized to total RNA for mock (n = 5) or ZIKV (n = 5) infected mosquitos. ( B , C ) Single mosquitos were infected with either mock, ZIKV, or DENV and subjected to a ZIKV ( B ) or Aedes aegypti Actin ( C ) specific RT-LAMP reaction then visualized by addition of SYBR Green I by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane M: Low DNA Mass Marker (ThermoFisher Scientific); NTC: No template control (negative control). Relative density (RD) of the entire bands for a column relative to the DNA Mass Marker are indicated below the corresponding lane. Lanes that did not have any detectable bands over background are reported as not detectable (ND). ( D ) Detection of ZIKV or ribosomal s17 by qRT-PCR. Data shown as mean ± standard deviation.

    Article Snippet: In addition, a 1:10 SYBR green I (Life Technologies) dilution was made in TAE buffer, then 2.0 μL of the SYBR dilution was added to the remaining half of the reaction.

    Techniques: Quantitative RT-PCR, Infection, SYBR Green Assay, Fluorescence, Nucleic Acid Electrophoresis, Marker, Negative Control, Standard Deviation

    RT-LAMP detection of ZIKV. ( A ) ZIKA RT-LAMP amplification of ZIKV PCR Standard (ZIKV; Robert Koch Institute) but not no template control (NTC; negative control) as visualized by addition of SYBR Green I (SYBR) by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane M: Low DNA Mass Marker (ThermoFisher Scientific). ( B ) All primers (All) are required for effective LAMP reaction. Reactions without FIP and BIP (-FIP/BIP) or FL and BL (-FL/BL) resulted in a negative RT-LAMP reaction.

    Journal: Scientific Reports

    Article Title: Rapid Detection of Zika Virus in Urine Samples and Infected Mosquitos by Reverse Transcription-Loop-Mediated Isothermal Amplification

    doi: 10.1038/s41598-018-22102-5

    Figure Lengend Snippet: RT-LAMP detection of ZIKV. ( A ) ZIKA RT-LAMP amplification of ZIKV PCR Standard (ZIKV; Robert Koch Institute) but not no template control (NTC; negative control) as visualized by addition of SYBR Green I (SYBR) by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane M: Low DNA Mass Marker (ThermoFisher Scientific). ( B ) All primers (All) are required for effective LAMP reaction. Reactions without FIP and BIP (-FIP/BIP) or FL and BL (-FL/BL) resulted in a negative RT-LAMP reaction.

    Article Snippet: In addition, a 1:10 SYBR green I (Life Technologies) dilution was made in TAE buffer, then 2.0 μL of the SYBR dilution was added to the remaining half of the reaction.

    Techniques: Amplification, Polymerase Chain Reaction, Negative Control, SYBR Green Assay, Fluorescence, Nucleic Acid Electrophoresis, Marker

    Examination of ZIKV and 18 s rRNA in human clinical samples. ( A ) ZIKV positive patient samples subjected to a ZIKV specific RT-LAMP reaction without ( A ) or with ( B ) RNA isolation then visualized by addition of SYBR Green I by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane NTC: No template control (negative control); Lane ZIKV: ZIKV PCR Standard (ZIKV; Robert Koch Institute). Relative density (RD) of the entire bands for a column relative to the DNA Mass Marker are indicated below the corresponding lane. Lanes that did not have any detectable bands over background are reported as not detectable (ND). ( C ) Detection of ZIKV or ribosomal 18 S rRNA by qRT-PCR. Data shown as mean ± standard deviation. ( D ) ZIKV specific RT-LAMP in asymptomatic control patients.

    Journal: Scientific Reports

    Article Title: Rapid Detection of Zika Virus in Urine Samples and Infected Mosquitos by Reverse Transcription-Loop-Mediated Isothermal Amplification

    doi: 10.1038/s41598-018-22102-5

    Figure Lengend Snippet: Examination of ZIKV and 18 s rRNA in human clinical samples. ( A ) ZIKV positive patient samples subjected to a ZIKV specific RT-LAMP reaction without ( A ) or with ( B ) RNA isolation then visualized by addition of SYBR Green I by eye (upper panel), green fluorescence (middle panel), or gel electrophoresis (bottom panel). Lane NTC: No template control (negative control); Lane ZIKV: ZIKV PCR Standard (ZIKV; Robert Koch Institute). Relative density (RD) of the entire bands for a column relative to the DNA Mass Marker are indicated below the corresponding lane. Lanes that did not have any detectable bands over background are reported as not detectable (ND). ( C ) Detection of ZIKV or ribosomal 18 S rRNA by qRT-PCR. Data shown as mean ± standard deviation. ( D ) ZIKV specific RT-LAMP in asymptomatic control patients.

    Article Snippet: In addition, a 1:10 SYBR green I (Life Technologies) dilution was made in TAE buffer, then 2.0 μL of the SYBR dilution was added to the remaining half of the reaction.

    Techniques: Isolation, SYBR Green Assay, Fluorescence, Nucleic Acid Electrophoresis, Negative Control, Polymerase Chain Reaction, Marker, Quantitative RT-PCR, Standard Deviation

    SYBR Green I/propidium iodide (PI) assay reveals killing of bactericidal and bacteriostatic antibiotics in 30 min. SYBR Green I/PI assay reveals killing between sensitive and resistant strains after treatment with increasing concentrations of bactericidal drugs (A) kanamycin for Staphylococcus aureus and (B) ampicillin for Escherichia coli . Upon treatment with increasing concentrations of bacteriostatic drugs (C) erythromycin for S. aureus and (D) trimethoprim for E. coli , SYBR Green I/PI assay was consistently able to distinguish sensitive and resistant strains when administered at different concentrations for both sensitive and resistant strains (Student’s t -test, * p

    Journal: Frontiers in Medicine

    Article Title: A Rapid Growth-Independent Antibiotic Resistance Detection Test by SYBR Green/Propidium Iodide Viability Assay

    doi: 10.3389/fmed.2018.00127

    Figure Lengend Snippet: SYBR Green I/propidium iodide (PI) assay reveals killing of bactericidal and bacteriostatic antibiotics in 30 min. SYBR Green I/PI assay reveals killing between sensitive and resistant strains after treatment with increasing concentrations of bactericidal drugs (A) kanamycin for Staphylococcus aureus and (B) ampicillin for Escherichia coli . Upon treatment with increasing concentrations of bacteriostatic drugs (C) erythromycin for S. aureus and (D) trimethoprim for E. coli , SYBR Green I/PI assay was consistently able to distinguish sensitive and resistant strains when administered at different concentrations for both sensitive and resistant strains (Student’s t -test, * p

    Article Snippet: SYBR Green I (10,000× stock, Invitrogen) was mixed with PI (20 mM, Sigma) in distilled H2 O.

    Techniques: SYBR Green Assay

    SYBR Green I/propidium iodide monitors the dynamics of resistant and sensitive strains during antibiotic drug exposure. A significant decrease in green/red fluorescence ratio was seen as early as 30 min between (A) sensitive Staphylococcus aureus strain Newman and resistant strain CA127 during kanamycin exposure and (B) sensitive Escherichia coli strain W3110 and resistant strain KTE181 during ampicillin exposure (twoway ANOVA, *** p

    Journal: Frontiers in Medicine

    Article Title: A Rapid Growth-Independent Antibiotic Resistance Detection Test by SYBR Green/Propidium Iodide Viability Assay

    doi: 10.3389/fmed.2018.00127

    Figure Lengend Snippet: SYBR Green I/propidium iodide monitors the dynamics of resistant and sensitive strains during antibiotic drug exposure. A significant decrease in green/red fluorescence ratio was seen as early as 30 min between (A) sensitive Staphylococcus aureus strain Newman and resistant strain CA127 during kanamycin exposure and (B) sensitive Escherichia coli strain W3110 and resistant strain KTE181 during ampicillin exposure (twoway ANOVA, *** p

    Article Snippet: SYBR Green I (10,000× stock, Invitrogen) was mixed with PI (20 mM, Sigma) in distilled H2 O.

    Techniques: SYBR Green Assay, Fluorescence

    SYBR Green I/propidium iodide (PI) stain can distinguish between R (resistant) and S (sensitive) strains of Staphylococcus aureus against various antibiotics in 30 min. Treatment with (A) gentamicin (100 µg/ml), (B) kanamycin (100 µg/ml), (C) erythromycin (400 µg/ml), and (D) ciprofloxacin (100 µg/ml) was added to various overnight S. aureus strains diluted to 1:25 (OD600 = 0.1). After incubation with antibiotics for 30 min, SYBR Green I/PI staining was performed and distinguished the strains and their respective susceptibility categories. All susceptibility results were in concordance with results from the Kirby–Bauer disk diffusion test (Student’s t -test, * p

    Journal: Frontiers in Medicine

    Article Title: A Rapid Growth-Independent Antibiotic Resistance Detection Test by SYBR Green/Propidium Iodide Viability Assay

    doi: 10.3389/fmed.2018.00127

    Figure Lengend Snippet: SYBR Green I/propidium iodide (PI) stain can distinguish between R (resistant) and S (sensitive) strains of Staphylococcus aureus against various antibiotics in 30 min. Treatment with (A) gentamicin (100 µg/ml), (B) kanamycin (100 µg/ml), (C) erythromycin (400 µg/ml), and (D) ciprofloxacin (100 µg/ml) was added to various overnight S. aureus strains diluted to 1:25 (OD600 = 0.1). After incubation with antibiotics for 30 min, SYBR Green I/PI staining was performed and distinguished the strains and their respective susceptibility categories. All susceptibility results were in concordance with results from the Kirby–Bauer disk diffusion test (Student’s t -test, * p

    Article Snippet: SYBR Green I (10,000× stock, Invitrogen) was mixed with PI (20 mM, Sigma) in distilled H2 O.

    Techniques: SYBR Green Assay, Staining, Incubation, Diffusion-based Assay

    SYBR Green I/propidium iodide (PI) stain can distinguish between R (resistant) and S (sensitive) strains of Gram-negative pathogens against various antibiotics in 30 min. Treatment with (A) ampicillin (100 µg/ml), (B) trimethoprim (50 µg/ml), and (C) streptomycin (50 µg/ml) was added to overnight cultures of Escherichia coli strains diluted to 1:25 (OD600 = 0.1). Treatment with (D) ceftriaxone (25 µg/ml) and (E) cefotaxime (50 µg/ml) was added to overnight cultures of Klebsiella pneumoniae strains diluted to 1:25 (OD600 = 0.1). After incubation with antibiotics for 30 min, SYBR Green I/PI staining was performed and distinguished their respective susceptibility categories. All susceptibility results were in concordance with results from the Kirby–Bauer disk diffusion test (Student’s t -test, * p

    Journal: Frontiers in Medicine

    Article Title: A Rapid Growth-Independent Antibiotic Resistance Detection Test by SYBR Green/Propidium Iodide Viability Assay

    doi: 10.3389/fmed.2018.00127

    Figure Lengend Snippet: SYBR Green I/propidium iodide (PI) stain can distinguish between R (resistant) and S (sensitive) strains of Gram-negative pathogens against various antibiotics in 30 min. Treatment with (A) ampicillin (100 µg/ml), (B) trimethoprim (50 µg/ml), and (C) streptomycin (50 µg/ml) was added to overnight cultures of Escherichia coli strains diluted to 1:25 (OD600 = 0.1). Treatment with (D) ceftriaxone (25 µg/ml) and (E) cefotaxime (50 µg/ml) was added to overnight cultures of Klebsiella pneumoniae strains diluted to 1:25 (OD600 = 0.1). After incubation with antibiotics for 30 min, SYBR Green I/PI staining was performed and distinguished their respective susceptibility categories. All susceptibility results were in concordance with results from the Kirby–Bauer disk diffusion test (Student’s t -test, * p

    Article Snippet: SYBR Green I (10,000× stock, Invitrogen) was mixed with PI (20 mM, Sigma) in distilled H2 O.

    Techniques: SYBR Green Assay, Staining, Incubation, Diffusion-based Assay

    Drug susceptibility testing of Mycobacterium tuberculosis against first-line tuberculosis drugs using the SYBR Green I/propidium iodide (PI) assay. (A) M. tuberculosis H37Ra and INH-resistant mutants I2, I4 (10-day old) were treated with 10, 500, and 1,000 µg/ml INH overnight (16 h). INH-resistant mutants I2 and I4 were determined to be resistant using 500 and 1,000 µg/ml INH. (B) M. tuberculosis parental strain H37Ra and pyrazinamide (PZA)-resistant mutants (P5 and P2) (20-day old) were treated with PZA (2 mg/ml) overnight (16 h). Treatment with salicylic acid (40 µg/ml) strongly increased the efficacy SYBR Green I/PI assay in detecting PZA resistance in mutants P5 and P2 compared to parental strain H37Ra (Student’s t -test, * p

    Journal: Frontiers in Medicine

    Article Title: A Rapid Growth-Independent Antibiotic Resistance Detection Test by SYBR Green/Propidium Iodide Viability Assay

    doi: 10.3389/fmed.2018.00127

    Figure Lengend Snippet: Drug susceptibility testing of Mycobacterium tuberculosis against first-line tuberculosis drugs using the SYBR Green I/propidium iodide (PI) assay. (A) M. tuberculosis H37Ra and INH-resistant mutants I2, I4 (10-day old) were treated with 10, 500, and 1,000 µg/ml INH overnight (16 h). INH-resistant mutants I2 and I4 were determined to be resistant using 500 and 1,000 µg/ml INH. (B) M. tuberculosis parental strain H37Ra and pyrazinamide (PZA)-resistant mutants (P5 and P2) (20-day old) were treated with PZA (2 mg/ml) overnight (16 h). Treatment with salicylic acid (40 µg/ml) strongly increased the efficacy SYBR Green I/PI assay in detecting PZA resistance in mutants P5 and P2 compared to parental strain H37Ra (Student’s t -test, * p

    Article Snippet: SYBR Green I (10,000× stock, Invitrogen) was mixed with PI (20 mM, Sigma) in distilled H2 O.

    Techniques: SYBR Green Assay

    A linear relationship between the percentage of live cells and the green/red fluorescence ratio from the SYBR Green I/propidium iodide (PI) viability assay for different bacterial species. Known proportions of isopropyl killed (30 min) and live (A) Staphylococcus aureus (USA300), (B) Klebsiella pneumoniae (Isolate 7), (C) Escherichia coli (W3110), (D) Acinetobacter baumannii , and (E) Mycobacterium tuberculosis (H37Ra) were stained with SYBR Green I/PI and measured using a fluorescence plate reader. A linear regression line was determined. (F) Fluorescence microscopy image showing known proportions (0, 50, and 100%) of live (i–iii) S. aureus (USA300) and (iv–vi) K. pneumoniae (isolate 7) stained with SYBR Green I/PI reveal red (dead) and green (live) ratios in concordance with the known proportions of live and killed organisms from representative Gram-positive ( S. aureus ) and Gram-negative ( K. pneumoniae ) bacteria. Data represent the means ± SEMs.

    Journal: Frontiers in Medicine

    Article Title: A Rapid Growth-Independent Antibiotic Resistance Detection Test by SYBR Green/Propidium Iodide Viability Assay

    doi: 10.3389/fmed.2018.00127

    Figure Lengend Snippet: A linear relationship between the percentage of live cells and the green/red fluorescence ratio from the SYBR Green I/propidium iodide (PI) viability assay for different bacterial species. Known proportions of isopropyl killed (30 min) and live (A) Staphylococcus aureus (USA300), (B) Klebsiella pneumoniae (Isolate 7), (C) Escherichia coli (W3110), (D) Acinetobacter baumannii , and (E) Mycobacterium tuberculosis (H37Ra) were stained with SYBR Green I/PI and measured using a fluorescence plate reader. A linear regression line was determined. (F) Fluorescence microscopy image showing known proportions (0, 50, and 100%) of live (i–iii) S. aureus (USA300) and (iv–vi) K. pneumoniae (isolate 7) stained with SYBR Green I/PI reveal red (dead) and green (live) ratios in concordance with the known proportions of live and killed organisms from representative Gram-positive ( S. aureus ) and Gram-negative ( K. pneumoniae ) bacteria. Data represent the means ± SEMs.

    Article Snippet: SYBR Green I (10,000× stock, Invitrogen) was mixed with PI (20 mM, Sigma) in distilled H2 O.

    Techniques: Fluorescence, SYBR Green Assay, Viability Assay, Staining, Microscopy

    Representative Live/Dead staining images of B. burgdorferi 7-day recovery cultures following treatment with different antimicrobial agents. Cells were stained with SYBR Green I/PI as outlined in the Material and Methods and representative images were taken at 100× magnification. Panel ( A ) Borrelia culture treated only with PBS was used as a negative control. Panel ( B ) Doxycycline (DOXY) treated, Panel ( C ) Cefoperazone (CEFO) treated, Panel ( D ) Daptomycin (DAPTO) treated and Panel ( E ) Three-antibiotic combination (D + C + D). Panels ( F – H ) Bee venom (BV) was used in increasing concentrations while Panels ( I – K ) depict melittin (M) treated cells at different concentrations. Live cells are stained with green color while dead cells are stained red. Scale bar: 100 μm.

    Journal: Antibiotics

    Article Title: Antimicrobial Activity of Bee Venom and Melittin against Borrelia burgdorferi

    doi: 10.3390/antibiotics6040031

    Figure Lengend Snippet: Representative Live/Dead staining images of B. burgdorferi 7-day recovery cultures following treatment with different antimicrobial agents. Cells were stained with SYBR Green I/PI as outlined in the Material and Methods and representative images were taken at 100× magnification. Panel ( A ) Borrelia culture treated only with PBS was used as a negative control. Panel ( B ) Doxycycline (DOXY) treated, Panel ( C ) Cefoperazone (CEFO) treated, Panel ( D ) Daptomycin (DAPTO) treated and Panel ( E ) Three-antibiotic combination (D + C + D). Panels ( F – H ) Bee venom (BV) was used in increasing concentrations while Panels ( I – K ) depict melittin (M) treated cells at different concentrations. Live cells are stained with green color while dead cells are stained red. Scale bar: 100 μm.

    Article Snippet: Staining mixture was prepared using sterile nuclease free water (Fisher, Waltham, MA, USA), SYBR Green I (10,000× stock, Invitrogen, Grand Island, NY, USA) and propidium iodide (20 mM, Thermo Scientific) before being used on B. burgdorferi samples.

    Techniques: Staining, SYBR Green Assay, Negative Control

    The effects of various antimicrobial agents on B. burgdorferi as determined by SYBR Green I/PI assay Panel ( A ) or direct counting assay Panel ( B ). Doxycycline, Cefoperazone, Daptomycin and their combination (D + C + D) as well as different concentrations of bee venom and melittin were tested on B. burgdorferi logarithmic phase (spirochetes) culture and stationary phase (persisters) cultures as well as in 7-day recovery subculture as described previously [ 6 , 7 , 8 ]. Significance against sterile PBS buffer (control vehicle) with the p value of

    Journal: Antibiotics

    Article Title: Antimicrobial Activity of Bee Venom and Melittin against Borrelia burgdorferi

    doi: 10.3390/antibiotics6040031

    Figure Lengend Snippet: The effects of various antimicrobial agents on B. burgdorferi as determined by SYBR Green I/PI assay Panel ( A ) or direct counting assay Panel ( B ). Doxycycline, Cefoperazone, Daptomycin and their combination (D + C + D) as well as different concentrations of bee venom and melittin were tested on B. burgdorferi logarithmic phase (spirochetes) culture and stationary phase (persisters) cultures as well as in 7-day recovery subculture as described previously [ 6 , 7 , 8 ]. Significance against sterile PBS buffer (control vehicle) with the p value of

    Article Snippet: Staining mixture was prepared using sterile nuclease free water (Fisher, Waltham, MA, USA), SYBR Green I (10,000× stock, Invitrogen, Grand Island, NY, USA) and propidium iodide (20 mM, Thermo Scientific) before being used on B. burgdorferi samples.

    Techniques: SYBR Green Assay

    Representative Live/Dead staining images of B. burgdorferi stationary phase persister cultures following treatment with different antimicrobial agents. Cells were stained with SYBR Green I/PI as outlined in the Methods and representative images were taken at 100× magnification. Panel ( A ) Borrelia culture treated only with PBS was used as a negative control. Panel ( B ) Doxycycline (DOXY) treated, Panel ( C ) Cefoperazone (CEFO) treated, Panel ( D ) Daptomycin (DAPTO) treated and Panel ( E ) Three-antibiotic combination (D + C + D). Panels ( F – H ) Bee venom (BV) was used in increasing concentrations while Panels ( I – K ) depicts melittin (M) treated cells. Live cells are stained with green color while dead cells are stained red. Scale bar: 100 μm.

    Journal: Antibiotics

    Article Title: Antimicrobial Activity of Bee Venom and Melittin against Borrelia burgdorferi

    doi: 10.3390/antibiotics6040031

    Figure Lengend Snippet: Representative Live/Dead staining images of B. burgdorferi stationary phase persister cultures following treatment with different antimicrobial agents. Cells were stained with SYBR Green I/PI as outlined in the Methods and representative images were taken at 100× magnification. Panel ( A ) Borrelia culture treated only with PBS was used as a negative control. Panel ( B ) Doxycycline (DOXY) treated, Panel ( C ) Cefoperazone (CEFO) treated, Panel ( D ) Daptomycin (DAPTO) treated and Panel ( E ) Three-antibiotic combination (D + C + D). Panels ( F – H ) Bee venom (BV) was used in increasing concentrations while Panels ( I – K ) depicts melittin (M) treated cells. Live cells are stained with green color while dead cells are stained red. Scale bar: 100 μm.

    Article Snippet: Staining mixture was prepared using sterile nuclease free water (Fisher, Waltham, MA, USA), SYBR Green I (10,000× stock, Invitrogen, Grand Island, NY, USA) and propidium iodide (20 mM, Thermo Scientific) before being used on B. burgdorferi samples.

    Techniques: Staining, SYBR Green Assay, Negative Control

    Representative Live/Dead staining images of B. burgdorferi log phase spirochetal cultures treated with different antimicrobial agents. Cells were stained with SYBR Green I/PI as outlined in the Methods and representative images were taken at 100× magnification. Panel ( A ) Borrelia culture treated only with PBS was used as a negative control. Panel ( B ) Doxycycline (DOXY) treated; Panel ( C ) Cefoperazone (CEFO) treated; Panel ( D ) Daptomycin (DAPTO) treated and Panel ( E ) Three-antibiotic combination (D + C + D). Panels ( F – H ) Bee venom (BV) was used in increasing concentrations while Panels ( I – K ) depicts melittin (M) treated cells. Live cells are stained with green color while dead cells are stained red. Scale bar: 100 μm.

    Journal: Antibiotics

    Article Title: Antimicrobial Activity of Bee Venom and Melittin against Borrelia burgdorferi

    doi: 10.3390/antibiotics6040031

    Figure Lengend Snippet: Representative Live/Dead staining images of B. burgdorferi log phase spirochetal cultures treated with different antimicrobial agents. Cells were stained with SYBR Green I/PI as outlined in the Methods and representative images were taken at 100× magnification. Panel ( A ) Borrelia culture treated only with PBS was used as a negative control. Panel ( B ) Doxycycline (DOXY) treated; Panel ( C ) Cefoperazone (CEFO) treated; Panel ( D ) Daptomycin (DAPTO) treated and Panel ( E ) Three-antibiotic combination (D + C + D). Panels ( F – H ) Bee venom (BV) was used in increasing concentrations while Panels ( I – K ) depicts melittin (M) treated cells. Live cells are stained with green color while dead cells are stained red. Scale bar: 100 μm.

    Article Snippet: Staining mixture was prepared using sterile nuclease free water (Fisher, Waltham, MA, USA), SYBR Green I (10,000× stock, Invitrogen, Grand Island, NY, USA) and propidium iodide (20 mM, Thermo Scientific) before being used on B. burgdorferi samples.

    Techniques: Staining, SYBR Green Assay, Negative Control

    Representative Live/Dead images of the viability of attached Borrelia biofilms following treatment with different antimicrobial agents. Biofilms were stained with SYBR Green I and PI as outlined in the Material and Methods and representative images were taken at 100× magnification. Panel ( A ) Borrelia culture treated only with PBS was used as a negative control. Panel ( B ) Doxycycline (DOXY) treated, Panel ( C ) Cefoperazone (CEFO) treated, Panel ( D ) Daptomycin (DAPTO) treated and Panel ( E ) Three-antibiotic combination (D + C + D). Panels ( F – H ) Bee venom (BV) was used in increasing concentrations while Panels ( I – K ) depict melittin treated cells at different concentration. Live cells are stained with green color while dead cells are stained red. Scale bar: 100 μm.

    Journal: Antibiotics

    Article Title: Antimicrobial Activity of Bee Venom and Melittin against Borrelia burgdorferi

    doi: 10.3390/antibiotics6040031

    Figure Lengend Snippet: Representative Live/Dead images of the viability of attached Borrelia biofilms following treatment with different antimicrobial agents. Biofilms were stained with SYBR Green I and PI as outlined in the Material and Methods and representative images were taken at 100× magnification. Panel ( A ) Borrelia culture treated only with PBS was used as a negative control. Panel ( B ) Doxycycline (DOXY) treated, Panel ( C ) Cefoperazone (CEFO) treated, Panel ( D ) Daptomycin (DAPTO) treated and Panel ( E ) Three-antibiotic combination (D + C + D). Panels ( F – H ) Bee venom (BV) was used in increasing concentrations while Panels ( I – K ) depict melittin treated cells at different concentration. Live cells are stained with green color while dead cells are stained red. Scale bar: 100 μm.

    Article Snippet: Staining mixture was prepared using sterile nuclease free water (Fisher, Waltham, MA, USA), SYBR Green I (10,000× stock, Invitrogen, Grand Island, NY, USA) and propidium iodide (20 mM, Thermo Scientific) before being used on B. burgdorferi samples.

    Techniques: Staining, SYBR Green Assay, Negative Control, Concentration Assay

    The oligomerization domain alone is insufficient for DNA binding. ( A ) Schematic of the oligomerization domain deletion construct. Numbers represent the amino acid positions in the gp16 coding sequence. ( B ) Elution profile of the gp16 oligomerization domain deletion mutant. The void volume is indicated by an arrow. Oligomeric state of the domain was calculated from the elution volume. ( C ) The peak fraction from (B) was electrophoresed on a 4–20% gradient native polyacrylamide gel and the gel was stained with Coomassie blue for protein (lane 1) and SYBR Green I for DNA (lane 2). ( D ) In vitro DNA binding of the oligomerization domain deletion mutant. The purified protein (25–75 μM) was incubated with the 500-bp g16 DNA (5 nM) in a 12 μl reaction mixture for 15 min. Samples were then electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with SYBR Green I. The control lane 1 contained no gp16.

    Journal: Nucleic Acids Research

    Article Title: Exclusion of small terminase mediated DNA threading models for genome packaging in bacteriophage T4

    doi: 10.1093/nar/gkw184

    Figure Lengend Snippet: The oligomerization domain alone is insufficient for DNA binding. ( A ) Schematic of the oligomerization domain deletion construct. Numbers represent the amino acid positions in the gp16 coding sequence. ( B ) Elution profile of the gp16 oligomerization domain deletion mutant. The void volume is indicated by an arrow. Oligomeric state of the domain was calculated from the elution volume. ( C ) The peak fraction from (B) was electrophoresed on a 4–20% gradient native polyacrylamide gel and the gel was stained with Coomassie blue for protein (lane 1) and SYBR Green I for DNA (lane 2). ( D ) In vitro DNA binding of the oligomerization domain deletion mutant. The purified protein (25–75 μM) was incubated with the 500-bp g16 DNA (5 nM) in a 12 μl reaction mixture for 15 min. Samples were then electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with SYBR Green I. The control lane 1 contained no gp16.

    Article Snippet: The gel was stained with SYBR Green I (Life Technologies, Thermo Fisher Scientific, Inc.) for DNA and then with Coomassie blue R-250 for protein.

    Techniques: Binding Assay, Construct, Sequencing, Mutagenesis, Staining, SYBR Green Assay, In Vitro, Purification, Incubation

    gp16 binds DNA in vitro . The purified phage T4 gp16 (25–75 μM) was incubated with the substrate DNA (500-bp amplified g16 DNA) (5 nM) in a 12 μl reaction mixture for 15 min. The reaction mixture was electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with Coomassie blue for protein ( A ) and SYBR Green I for DNA ( B ). Control lanes were missing either the gp16 protein (lane 1) or the DNA (lane 5). Position of the shifted DNA band is indicated by a dashed line.

    Journal: Nucleic Acids Research

    Article Title: Exclusion of small terminase mediated DNA threading models for genome packaging in bacteriophage T4

    doi: 10.1093/nar/gkw184

    Figure Lengend Snippet: gp16 binds DNA in vitro . The purified phage T4 gp16 (25–75 μM) was incubated with the substrate DNA (500-bp amplified g16 DNA) (5 nM) in a 12 μl reaction mixture for 15 min. The reaction mixture was electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with Coomassie blue for protein ( A ) and SYBR Green I for DNA ( B ). Control lanes were missing either the gp16 protein (lane 1) or the DNA (lane 5). Position of the shifted DNA band is indicated by a dashed line.

    Article Snippet: The gel was stained with SYBR Green I (Life Technologies, Thermo Fisher Scientific, Inc.) for DNA and then with Coomassie blue R-250 for protein.

    Techniques: In Vitro, Purification, Incubation, Amplification, Staining, SYBR Green Assay

    Analysis of in vivo -bound gp16-DNA complex. (A and B) Purified gp16 from phage T4 and related phages (8 μg each) were electrophoresed on a native 4–20% gradient polyacrylamide gel. The same gel was stained with Coomassie blue for protein ( A ) and SYBR Green I for DNA ( B ). The arrow corresponds to a fragment of DNA that was dissociated from RB49 gp16 during electrophoresis (panel B, lane 3). (C and D) Most of the gp16-bound DNA is resistant to Benzonase. The purified T4 and RB49 gp16 proteins (1 mg) were treated with Benzonase (Novagen) overnight at room temperature to digest the loosely-bound DNA fragments. Benzonase was removed by passing the samples through a HiLoad 16/600 Superdex 200 size-exclusion column. The tightly bound nuclease-protected DNA was then released by digesting gp16 with Proteinase K (Thermo Scientific) at 65°C for 30 min. Samples were analyzed on a 4–20% gradient polyacrylamide gel. The gel was stained with Coomassie blue for protein ( C ) and SYBR Green I for DNA ( D ). The positions of the DNA bands released from Proteinase K digestion are marked with arrows (panel D, lanes 4 and 7).

    Journal: Nucleic Acids Research

    Article Title: Exclusion of small terminase mediated DNA threading models for genome packaging in bacteriophage T4

    doi: 10.1093/nar/gkw184

    Figure Lengend Snippet: Analysis of in vivo -bound gp16-DNA complex. (A and B) Purified gp16 from phage T4 and related phages (8 μg each) were electrophoresed on a native 4–20% gradient polyacrylamide gel. The same gel was stained with Coomassie blue for protein ( A ) and SYBR Green I for DNA ( B ). The arrow corresponds to a fragment of DNA that was dissociated from RB49 gp16 during electrophoresis (panel B, lane 3). (C and D) Most of the gp16-bound DNA is resistant to Benzonase. The purified T4 and RB49 gp16 proteins (1 mg) were treated with Benzonase (Novagen) overnight at room temperature to digest the loosely-bound DNA fragments. Benzonase was removed by passing the samples through a HiLoad 16/600 Superdex 200 size-exclusion column. The tightly bound nuclease-protected DNA was then released by digesting gp16 with Proteinase K (Thermo Scientific) at 65°C for 30 min. Samples were analyzed on a 4–20% gradient polyacrylamide gel. The gel was stained with Coomassie blue for protein ( C ) and SYBR Green I for DNA ( D ). The positions of the DNA bands released from Proteinase K digestion are marked with arrows (panel D, lanes 4 and 7).

    Article Snippet: The gel was stained with SYBR Green I (Life Technologies, Thermo Fisher Scientific, Inc.) for DNA and then with Coomassie blue R-250 for protein.

    Techniques: In Vivo, Purification, Staining, SYBR Green Assay, Electrophoresis

    Deletion of channel helix α2 did not disrupt DNA binding. ( A ) Schematic of the central domain helix α2 deletion mutants. Numbers represent the amino acid positions in the gp16 coding sequence. Deleted sequences are shown by polylines and the amino acid residues flanking the deletions are shown in blue. ( B ) Elution profiles of mutants Del-1 (magenta), Del-2 (blue) and Del-3 (green). The void volume is indicated by an arrow. The oligomeric state of the gp16 species in peak b of the mutants was calculated from the elution volume. (C and D) The peak gp16 fractions from B were electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with Coomassie blue for protein ( C ) and SYBR Green I for DNA ( D ). ‘a’ and ‘b’ correspond to the fractions from the peaks a and b of the respective mutant. ( E ) In vitro DNA binding of the deletion mutants. The purified proteins (20–60 μM) were incubated with the 500-bp g16 DNA (5 nM) in 12 μl reaction mixture for 15 min. Samples were then electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with SYBR Green I. The control lane 1 contained no gp16 and shifted bands are shown by arrows in lanes 12–16.

    Journal: Nucleic Acids Research

    Article Title: Exclusion of small terminase mediated DNA threading models for genome packaging in bacteriophage T4

    doi: 10.1093/nar/gkw184

    Figure Lengend Snippet: Deletion of channel helix α2 did not disrupt DNA binding. ( A ) Schematic of the central domain helix α2 deletion mutants. Numbers represent the amino acid positions in the gp16 coding sequence. Deleted sequences are shown by polylines and the amino acid residues flanking the deletions are shown in blue. ( B ) Elution profiles of mutants Del-1 (magenta), Del-2 (blue) and Del-3 (green). The void volume is indicated by an arrow. The oligomeric state of the gp16 species in peak b of the mutants was calculated from the elution volume. (C and D) The peak gp16 fractions from B were electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with Coomassie blue for protein ( C ) and SYBR Green I for DNA ( D ). ‘a’ and ‘b’ correspond to the fractions from the peaks a and b of the respective mutant. ( E ) In vitro DNA binding of the deletion mutants. The purified proteins (20–60 μM) were incubated with the 500-bp g16 DNA (5 nM) in 12 μl reaction mixture for 15 min. Samples were then electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with SYBR Green I. The control lane 1 contained no gp16 and shifted bands are shown by arrows in lanes 12–16.

    Article Snippet: The gel was stained with SYBR Green I (Life Technologies, Thermo Fisher Scientific, Inc.) for DNA and then with Coomassie blue R-250 for protein.

    Techniques: Binding Assay, Sequencing, Staining, SYBR Green Assay, Mutagenesis, In Vitro, Purification, Incubation

    The positively charged residues of gp16 channel are not essential for DNA binding. ( A ) Schematic of the mutations introduced into the helix α2 of T4 gp16. Numbers represent the amino acid positions in the gp16 coding sequence. Positions of the mutated residues are indicated as black bars in helix α2. ( B ) Elution profiles of WT gp16 (black) and mutants 3M (blue) and 4M (red). The void volume is indicated by an arrow. The hexamer size of gp16 species in peak b of mutant 4M was calculated from the elution volume using the column calibrated with molecular weight standards. (C and D) The peak gp16 fractions from B were electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with Coomassie blue for protein ( C ) and SYBR Green I for DNA ( D ). Lanes 4M-a and 4M-b represent the fractions from peak a and peak b of the mutant 4M. ( E ) In vitro DNA binding of gp16 mutants 3M and 4M. Proteins (20–60 μM) were incubated with the 500-bp g16 DNA (5 nM) in 12 μl reaction mixture for 15 min. Samples were then electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with SYBR Green I. The control lane 1 contained no gp16.

    Journal: Nucleic Acids Research

    Article Title: Exclusion of small terminase mediated DNA threading models for genome packaging in bacteriophage T4

    doi: 10.1093/nar/gkw184

    Figure Lengend Snippet: The positively charged residues of gp16 channel are not essential for DNA binding. ( A ) Schematic of the mutations introduced into the helix α2 of T4 gp16. Numbers represent the amino acid positions in the gp16 coding sequence. Positions of the mutated residues are indicated as black bars in helix α2. ( B ) Elution profiles of WT gp16 (black) and mutants 3M (blue) and 4M (red). The void volume is indicated by an arrow. The hexamer size of gp16 species in peak b of mutant 4M was calculated from the elution volume using the column calibrated with molecular weight standards. (C and D) The peak gp16 fractions from B were electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with Coomassie blue for protein ( C ) and SYBR Green I for DNA ( D ). Lanes 4M-a and 4M-b represent the fractions from peak a and peak b of the mutant 4M. ( E ) In vitro DNA binding of gp16 mutants 3M and 4M. Proteins (20–60 μM) were incubated with the 500-bp g16 DNA (5 nM) in 12 μl reaction mixture for 15 min. Samples were then electrophoresed on a 4–20% gradient native polyacrylamide gel and stained with SYBR Green I. The control lane 1 contained no gp16.

    Article Snippet: The gel was stained with SYBR Green I (Life Technologies, Thermo Fisher Scientific, Inc.) for DNA and then with Coomassie blue R-250 for protein.

    Techniques: Binding Assay, Sequencing, Mutagenesis, Molecular Weight, Staining, SYBR Green Assay, In Vitro, Incubation

    Growth curves of Muricauda ruestringensis (A), Desulfovibrio acrylicus (B), and Oceanospirillum sp. strain GM1 (C) obtained by determining the optical density at 436 nm (filled squares) and by fluorescence measurement after SYBR green I staining (circles).

    Journal:

    Article Title: Sensitive Determination of Microbial Growth by Nucleic Acid Staining in Aqueous Suspension

    doi: 10.1128/AEM.72.1.87-95.2006

    Figure Lengend Snippet: Growth curves of Muricauda ruestringensis (A), Desulfovibrio acrylicus (B), and Oceanospirillum sp. strain GM1 (C) obtained by determining the optical density at 436 nm (filled squares) and by fluorescence measurement after SYBR green I staining (circles).

    Article Snippet: Stock solutions of SYBR green I and II as well as of PicoGreen were purchased from Molecular Probes (Eugene, OR), subdivided into small aliquots upon receipt, and stored in 1.5-ml reaction tubes at −20°C.

    Techniques: Fluorescence, SYBR Green Assay, Staining

    Effects of different glutaric dialdehyde (circles) and formaldehyde (triangles) concentrations on fluorescence emission of SYBR green I-stained DNA. Different DNA concentrations (dotted lines, 10 ng ml −1 ; dashed lines, 100 ng ml −1 ; solid

    Journal:

    Article Title: Sensitive Determination of Microbial Growth by Nucleic Acid Staining in Aqueous Suspension

    doi: 10.1128/AEM.72.1.87-95.2006

    Figure Lengend Snippet: Effects of different glutaric dialdehyde (circles) and formaldehyde (triangles) concentrations on fluorescence emission of SYBR green I-stained DNA. Different DNA concentrations (dotted lines, 10 ng ml −1 ; dashed lines, 100 ng ml −1 ; solid

    Article Snippet: Stock solutions of SYBR green I and II as well as of PicoGreen were purchased from Molecular Probes (Eugene, OR), subdivided into small aliquots upon receipt, and stored in 1.5-ml reaction tubes at −20°C.

    Techniques: Fluorescence, SYBR Green Assay, Staining

    Quantification of washed E. coli cells at low cell densities by SYBR green I staining. Error bars represent standard deviations for eight replicates.

    Journal:

    Article Title: Sensitive Determination of Microbial Growth by Nucleic Acid Staining in Aqueous Suspension

    doi: 10.1128/AEM.72.1.87-95.2006

    Figure Lengend Snippet: Quantification of washed E. coli cells at low cell densities by SYBR green I staining. Error bars represent standard deviations for eight replicates.

    Article Snippet: Stock solutions of SYBR green I and II as well as of PicoGreen were purchased from Molecular Probes (Eugene, OR), subdivided into small aliquots upon receipt, and stored in 1.5-ml reaction tubes at −20°C.

    Techniques: SYBR Green Assay, Staining

    Interference of rRNA with SYBR green I staining of double-stranded DNA. Increasing amounts of E. coli rRNA were added to 100 ng ml −1 lambda phage DNA and stained with SYBR green I. The fluorescence was measured and is displayed as a relative increase

    Journal:

    Article Title: Sensitive Determination of Microbial Growth by Nucleic Acid Staining in Aqueous Suspension

    doi: 10.1128/AEM.72.1.87-95.2006

    Figure Lengend Snippet: Interference of rRNA with SYBR green I staining of double-stranded DNA. Increasing amounts of E. coli rRNA were added to 100 ng ml −1 lambda phage DNA and stained with SYBR green I. The fluorescence was measured and is displayed as a relative increase

    Article Snippet: Stock solutions of SYBR green I and II as well as of PicoGreen were purchased from Molecular Probes (Eugene, OR), subdivided into small aliquots upon receipt, and stored in 1.5-ml reaction tubes at −20°C.

    Techniques: SYBR Green Assay, Staining, Fluorescence

    Quantification of washed E. coli cells (open circles) and lambda phage DNA (closed circles) in a microplate assay. Samples were serially diluted, and fluorescence intensities were measured after staining with SYBR green I. Linear regression was calculated

    Journal:

    Article Title: Sensitive Determination of Microbial Growth by Nucleic Acid Staining in Aqueous Suspension

    doi: 10.1128/AEM.72.1.87-95.2006

    Figure Lengend Snippet: Quantification of washed E. coli cells (open circles) and lambda phage DNA (closed circles) in a microplate assay. Samples were serially diluted, and fluorescence intensities were measured after staining with SYBR green I. Linear regression was calculated

    Article Snippet: Stock solutions of SYBR green I and II as well as of PicoGreen were purchased from Molecular Probes (Eugene, OR), subdivided into small aliquots upon receipt, and stored in 1.5-ml reaction tubes at −20°C.

    Techniques: Fluorescence, Staining, SYBR Green Assay

    Sensitivity of the loop-mediated isothermal amplification (LAMP) assay for the detection of Clonorchis sinensis eggs in feces experimentally spiked with a known number of eggs in ten-fold serial dilutions from 10,000 eggs (lane 1) to 1 egg (lane 5). (A) Naked eye detection of LAMP products using SYBR Green I. A green color indicates a positive reaction, and an orange color indicates a negative reaction. (B) Fluorescence of LAMP products after using SYBR Green I followed by detection under UV light. (C) Agarose gel electrophoresis of LAMP products followed by ethidium bromide staining and detection under UV light. Values in the left are in base pairs. Lane 6, negative stool DNA; lane M, molecular marker.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Application of a loop-mediated isothermal amplification (LAMP) assay targeting cox1 gene for the detection of Clonorchis sinensis in human fecal samples

    doi: 10.1371/journal.pntd.0005995

    Figure Lengend Snippet: Sensitivity of the loop-mediated isothermal amplification (LAMP) assay for the detection of Clonorchis sinensis eggs in feces experimentally spiked with a known number of eggs in ten-fold serial dilutions from 10,000 eggs (lane 1) to 1 egg (lane 5). (A) Naked eye detection of LAMP products using SYBR Green I. A green color indicates a positive reaction, and an orange color indicates a negative reaction. (B) Fluorescence of LAMP products after using SYBR Green I followed by detection under UV light. (C) Agarose gel electrophoresis of LAMP products followed by ethidium bromide staining and detection under UV light. Values in the left are in base pairs. Lane 6, negative stool DNA; lane M, molecular marker.

    Article Snippet: Amplified LAMP products were detected by adding 1.0 μl of 1:10 diluted 10,000x concentration of SYBR Green I (Invitrogen, Carlsbad, CA, USA) to each tube.

    Techniques: Amplification, Lamp Assay, SYBR Green Assay, Fluorescence, Agarose Gel Electrophoresis, Staining, Marker

    Specificity of the loop-mediated isothermal amplification (LAMP) assay for the detection of Clonorchis sinensis genomic DNA. (A) Naked eye detection of LAMP products using SYBR Green I. A green color indicates a positive reaction, and an orange color indicates a negative reaction. (B) Fluorescence of LAMP products after using SYBR Green I followed by detection under UV light. (C) Agarose gel electrophoresis of LAMP products followed by ethidium bromide staining and detection under UV light. Values in the left are in base pairs. Lane 1, Clonorchis sinensis ; lane 2, Metagonimus yokogawai ; lane 3, Opisthorchis viverrini ; lane 4, Fasciola gigantica ; lane 5, Spirometra erinacei ; lane 6, Diphyllobothrium latum ; lane 7, Ascaris lumbricoides ; lane 8, Ascaris suum ; lane 9, Necator americanus ; lane 10, Trichuris trichiura ; lane 11, Cryptosporidium parvum ; lane 12, Entamoeba histolytica ; lane 13, Giardia lamblia ; lane 14, Escherichia coli ; lane 15, non-template control; M, molecular marker.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Application of a loop-mediated isothermal amplification (LAMP) assay targeting cox1 gene for the detection of Clonorchis sinensis in human fecal samples

    doi: 10.1371/journal.pntd.0005995

    Figure Lengend Snippet: Specificity of the loop-mediated isothermal amplification (LAMP) assay for the detection of Clonorchis sinensis genomic DNA. (A) Naked eye detection of LAMP products using SYBR Green I. A green color indicates a positive reaction, and an orange color indicates a negative reaction. (B) Fluorescence of LAMP products after using SYBR Green I followed by detection under UV light. (C) Agarose gel electrophoresis of LAMP products followed by ethidium bromide staining and detection under UV light. Values in the left are in base pairs. Lane 1, Clonorchis sinensis ; lane 2, Metagonimus yokogawai ; lane 3, Opisthorchis viverrini ; lane 4, Fasciola gigantica ; lane 5, Spirometra erinacei ; lane 6, Diphyllobothrium latum ; lane 7, Ascaris lumbricoides ; lane 8, Ascaris suum ; lane 9, Necator americanus ; lane 10, Trichuris trichiura ; lane 11, Cryptosporidium parvum ; lane 12, Entamoeba histolytica ; lane 13, Giardia lamblia ; lane 14, Escherichia coli ; lane 15, non-template control; M, molecular marker.

    Article Snippet: Amplified LAMP products were detected by adding 1.0 μl of 1:10 diluted 10,000x concentration of SYBR Green I (Invitrogen, Carlsbad, CA, USA) to each tube.

    Techniques: Amplification, Lamp Assay, SYBR Green Assay, Fluorescence, Agarose Gel Electrophoresis, Staining, Marker

    Sensitivity of the loop-mediated isothermal amplification (LAMP) assay and PCR for the detection of Clonorchis sinensis genomic DNA. Ten-fold serial dilutions starting from 1 ng of genomic DNA (lane 1) down to 1 fg (lane 7) were tested. (A) Naked eye detection of LAMP products using SYBR Green I. A green color indicates a positive reaction, and an orange color indicates a negative reaction. (B) Fluorescence of LAMP products after using SYBR Green I followed by detection under UV light. (C) Agarose gel electrophoresis of LAMP products followed by ethidium bromide staining and detection under UV light. (D) PCR with outer primers F3 and B3. Values in the left are in base pairs. Lane 8, non-template control (NTC); lane M, molecular marker.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Application of a loop-mediated isothermal amplification (LAMP) assay targeting cox1 gene for the detection of Clonorchis sinensis in human fecal samples

    doi: 10.1371/journal.pntd.0005995

    Figure Lengend Snippet: Sensitivity of the loop-mediated isothermal amplification (LAMP) assay and PCR for the detection of Clonorchis sinensis genomic DNA. Ten-fold serial dilutions starting from 1 ng of genomic DNA (lane 1) down to 1 fg (lane 7) were tested. (A) Naked eye detection of LAMP products using SYBR Green I. A green color indicates a positive reaction, and an orange color indicates a negative reaction. (B) Fluorescence of LAMP products after using SYBR Green I followed by detection under UV light. (C) Agarose gel electrophoresis of LAMP products followed by ethidium bromide staining and detection under UV light. (D) PCR with outer primers F3 and B3. Values in the left are in base pairs. Lane 8, non-template control (NTC); lane M, molecular marker.

    Article Snippet: Amplified LAMP products were detected by adding 1.0 μl of 1:10 diluted 10,000x concentration of SYBR Green I (Invitrogen, Carlsbad, CA, USA) to each tube.

    Techniques: Amplification, Lamp Assay, Polymerase Chain Reaction, SYBR Green Assay, Fluorescence, Agarose Gel Electrophoresis, Staining, Marker

    TFAM knockdown leads to reduced detachment of mt-nucleoids. ( a ) Effect of TFAM knockdown on mt-nucleoids. Knockdown of TFAM was performed in HeLa cells. mtDNAs were stained with SYBR Green I in TFAM-knockdown cells. Time after transfection of siRNAs is shown in the upper left of the images. Note that mt-nucleoid enlargement is observed from 10 h after transfection. Arrowheads indicate enlarged mt-nucleoids. Scale bar, 10 μm. ( b ) Proportion of mt-nucleoids undergoing attachment and detachment in wild-type and TFAM-knockdown HeLa cells. The significance of differences was examined by Student’s t-test (p = 0.0947). N.S., not significant. A total of 20 to 48 mt-nucleoids per cell were randomly selected and analyzed. Error bars indicate standard deviation (n cells = 6 for each condition). ( c ) Frequency of attachment and detachment per mt-nucleoid in wild-type and TFAM-knockdown HeLa cells in 2 min. The frequency was analyzed in mt-nucleoids undergoing attachment and detachment. A total of 20 to 48 mt-nucleoids per cell were randomly selected and analyzed. Error bars indicate standard deviation (n cells = 6 for each condition). The significance of differences in attachment and detachment was examined by paired t-test (WT, p = 0.1281; TFAM RNAi, p = 0.0007). N.S., not significant.

    Journal: Scientific Reports

    Article Title: Live imaging reveals the dynamics and regulation of mitochondrial nucleoids during the cell cycle in Fucci2-HeLa cells

    doi: 10.1038/s41598-017-10843-8

    Figure Lengend Snippet: TFAM knockdown leads to reduced detachment of mt-nucleoids. ( a ) Effect of TFAM knockdown on mt-nucleoids. Knockdown of TFAM was performed in HeLa cells. mtDNAs were stained with SYBR Green I in TFAM-knockdown cells. Time after transfection of siRNAs is shown in the upper left of the images. Note that mt-nucleoid enlargement is observed from 10 h after transfection. Arrowheads indicate enlarged mt-nucleoids. Scale bar, 10 μm. ( b ) Proportion of mt-nucleoids undergoing attachment and detachment in wild-type and TFAM-knockdown HeLa cells. The significance of differences was examined by Student’s t-test (p = 0.0947). N.S., not significant. A total of 20 to 48 mt-nucleoids per cell were randomly selected and analyzed. Error bars indicate standard deviation (n cells = 6 for each condition). ( c ) Frequency of attachment and detachment per mt-nucleoid in wild-type and TFAM-knockdown HeLa cells in 2 min. The frequency was analyzed in mt-nucleoids undergoing attachment and detachment. A total of 20 to 48 mt-nucleoids per cell were randomly selected and analyzed. Error bars indicate standard deviation (n cells = 6 for each condition). The significance of differences in attachment and detachment was examined by paired t-test (WT, p = 0.1281; TFAM RNAi, p = 0.0007). N.S., not significant.

    Article Snippet: Cells were plated onto an eight-well cover glass chamber (2 × 104 cells per well) and cultured at 37 °C for 24 to 36 h. SYBR Green I (Thermo Fisher Scientific, Japan) was diluted 1:10 times with dimethyl sulfoxide, and subsequently diluted with D-MEM (SYBR Green I solution) 1:30,000 times for HeLa.S-Fucci2 or 1:20,000 times for HeLa-Su9 cells.

    Techniques: Staining, SYBR Green Assay, Transfection, Standard Deviation

    mt-nucleoids undergo frequent attachment and detachment during the cell cycle. ( a ) Time-lapse series of confocal images of mt-nucleoids (green) and mitochondria (red). mtDNAs were stained with SYBR Green I in HeLa cells expressing mitochondrially targeted DsRed (HeLa-Su9 cells). Lower panels show the fluorescence intensity of SYBR Green I as heat map images. Arrowheads show each mt-nucleoid. Scale bar, 1 μm. ( b ) Proportion of mt-nucleoids undergoing attachment or detachment per cell during the cell cycle mtDNAs were stained with SYBR Green I in Fucci2 cells. A total of 20 mt-nucleoids per cell were randomly selected and analyzed. Error bars indicate standard deviation (n cells = 5 for each phase). The statistical significance of differences in attachment and detachment was examined by analysis of variance (p = 0.1005). N.S., not significant. ( c ) The frequency of attachment and detachment per mt-nucleoid for 2 min during the cell cycle. mtDNAs were stained with SYBR Green I in Fucci2 cells. mt-nucleoids undergoing attachment and detachment were analyzed for the number of attachments and detachments. A total of 20 mt-nucleoids per cell were randomly selected and analyzed. Error bars indicate standard deviation (n cells = 5 for each phase). The statistical significance of differences in attachment and detachment was examined by paired t-test (G 1 , p = 0.1739; early-middle S, p = 0.9780; late S-G 2 , p = 0.2253). N.S., not significant.

    Journal: Scientific Reports

    Article Title: Live imaging reveals the dynamics and regulation of mitochondrial nucleoids during the cell cycle in Fucci2-HeLa cells

    doi: 10.1038/s41598-017-10843-8

    Figure Lengend Snippet: mt-nucleoids undergo frequent attachment and detachment during the cell cycle. ( a ) Time-lapse series of confocal images of mt-nucleoids (green) and mitochondria (red). mtDNAs were stained with SYBR Green I in HeLa cells expressing mitochondrially targeted DsRed (HeLa-Su9 cells). Lower panels show the fluorescence intensity of SYBR Green I as heat map images. Arrowheads show each mt-nucleoid. Scale bar, 1 μm. ( b ) Proportion of mt-nucleoids undergoing attachment or detachment per cell during the cell cycle mtDNAs were stained with SYBR Green I in Fucci2 cells. A total of 20 mt-nucleoids per cell were randomly selected and analyzed. Error bars indicate standard deviation (n cells = 5 for each phase). The statistical significance of differences in attachment and detachment was examined by analysis of variance (p = 0.1005). N.S., not significant. ( c ) The frequency of attachment and detachment per mt-nucleoid for 2 min during the cell cycle. mtDNAs were stained with SYBR Green I in Fucci2 cells. mt-nucleoids undergoing attachment and detachment were analyzed for the number of attachments and detachments. A total of 20 mt-nucleoids per cell were randomly selected and analyzed. Error bars indicate standard deviation (n cells = 5 for each phase). The statistical significance of differences in attachment and detachment was examined by paired t-test (G 1 , p = 0.1739; early-middle S, p = 0.9780; late S-G 2 , p = 0.2253). N.S., not significant.

    Article Snippet: Cells were plated onto an eight-well cover glass chamber (2 × 104 cells per well) and cultured at 37 °C for 24 to 36 h. SYBR Green I (Thermo Fisher Scientific, Japan) was diluted 1:10 times with dimethyl sulfoxide, and subsequently diluted with D-MEM (SYBR Green I solution) 1:30,000 times for HeLa.S-Fucci2 or 1:20,000 times for HeLa-Su9 cells.

    Techniques: Staining, SYBR Green Assay, Expressing, Fluorescence, Standard Deviation

    Predominant increase in the number of mt-nucleoids was observed during the S phase. ( a ) The number of mt-nucleoids per cell in each cell cycle phase. SYBR Green I-stained mt-nucleoids were counted in Fucci2 cells in each phase. Error bars indicate standard deviation (Early G 1 n cells = 19, G 1 n cells = 22, Early-middle S n cells = 78, Late S-G 2 n cells = 42). ( b ) The period of time-lapse imaging for the experiment in Fig. 5c. Fucci2 cells were classified into five phases depending on the change in color of their nucleus. ( c ) Increase in the number of mt-nucleoids within 4 h during the cell cycle. We stained Fucci2 cells with 1:300,000 SYBR Green I, and performed time-lapse imaging at 4-h intervals in each cell cycle phase presented in Fig. 5b, after which we counted the mt-nucleoid number at 0 and 4 h. Error bars indicate standard deviation (n cells = 10 for each phase).

    Journal: Scientific Reports

    Article Title: Live imaging reveals the dynamics and regulation of mitochondrial nucleoids during the cell cycle in Fucci2-HeLa cells

    doi: 10.1038/s41598-017-10843-8

    Figure Lengend Snippet: Predominant increase in the number of mt-nucleoids was observed during the S phase. ( a ) The number of mt-nucleoids per cell in each cell cycle phase. SYBR Green I-stained mt-nucleoids were counted in Fucci2 cells in each phase. Error bars indicate standard deviation (Early G 1 n cells = 19, G 1 n cells = 22, Early-middle S n cells = 78, Late S-G 2 n cells = 42). ( b ) The period of time-lapse imaging for the experiment in Fig. 5c. Fucci2 cells were classified into five phases depending on the change in color of their nucleus. ( c ) Increase in the number of mt-nucleoids within 4 h during the cell cycle. We stained Fucci2 cells with 1:300,000 SYBR Green I, and performed time-lapse imaging at 4-h intervals in each cell cycle phase presented in Fig. 5b, after which we counted the mt-nucleoid number at 0 and 4 h. Error bars indicate standard deviation (n cells = 10 for each phase).

    Article Snippet: Cells were plated onto an eight-well cover glass chamber (2 × 104 cells per well) and cultured at 37 °C for 24 to 36 h. SYBR Green I (Thermo Fisher Scientific, Japan) was diluted 1:10 times with dimethyl sulfoxide, and subsequently diluted with D-MEM (SYBR Green I solution) 1:30,000 times for HeLa.S-Fucci2 or 1:20,000 times for HeLa-Su9 cells.

    Techniques: SYBR Green Assay, Staining, Standard Deviation, Imaging

    SYBR Green I can selectively visualize mt-nucleoids in Fucci2 cells. ( a ) Schematic representation of the Fucci2 cells used in this study. Average duration of each phase is shown. ( b ) Time-lapse series of typical fluorescent images during the cell cycle in Fucci2 cells. The duration of S phase was 9 h based on the experiment with EdU pulse labeling (blue bar, the detailed method is presented in the Materials and Methods section). Images showing the color of the nucleus are also presented as merged images. Scale bar, 10 μm. ( c ) Changes of staining pattern depending on the SYBR Green I concentration in normal HeLa cells. Dilutions of SYBR Green I are indicated above the images. DNAs were immunostained using anti-DNA antibodies in cells without staining of SYBR Green I (panel on the far right). Scale bars, 10 μm. ( d ) Selective visualization of mt-nucleoids in Fucci2 cells using a low concentration (1:300,000 dilution) of SYBR Green I. The color of the nucleus denoting the cell cycle phase is indicated in the upper left of each image. Scale bar, 10 μm.

    Journal: Scientific Reports

    Article Title: Live imaging reveals the dynamics and regulation of mitochondrial nucleoids during the cell cycle in Fucci2-HeLa cells

    doi: 10.1038/s41598-017-10843-8

    Figure Lengend Snippet: SYBR Green I can selectively visualize mt-nucleoids in Fucci2 cells. ( a ) Schematic representation of the Fucci2 cells used in this study. Average duration of each phase is shown. ( b ) Time-lapse series of typical fluorescent images during the cell cycle in Fucci2 cells. The duration of S phase was 9 h based on the experiment with EdU pulse labeling (blue bar, the detailed method is presented in the Materials and Methods section). Images showing the color of the nucleus are also presented as merged images. Scale bar, 10 μm. ( c ) Changes of staining pattern depending on the SYBR Green I concentration in normal HeLa cells. Dilutions of SYBR Green I are indicated above the images. DNAs were immunostained using anti-DNA antibodies in cells without staining of SYBR Green I (panel on the far right). Scale bars, 10 μm. ( d ) Selective visualization of mt-nucleoids in Fucci2 cells using a low concentration (1:300,000 dilution) of SYBR Green I. The color of the nucleus denoting the cell cycle phase is indicated in the upper left of each image. Scale bar, 10 μm.

    Article Snippet: Cells were plated onto an eight-well cover glass chamber (2 × 104 cells per well) and cultured at 37 °C for 24 to 36 h. SYBR Green I (Thermo Fisher Scientific, Japan) was diluted 1:10 times with dimethyl sulfoxide, and subsequently diluted with D-MEM (SYBR Green I solution) 1:30,000 times for HeLa.S-Fucci2 or 1:20,000 times for HeLa-Su9 cells.

    Techniques: SYBR Green Assay, Labeling, Staining, Concentration Assay

    mtDNA replication occurs throughout the cell cycle, but the activity increases during the S phase. ( a ) Visualization of mtDNA replication in Fucci2 cells during the cell cycle. Fucci2 cells were incubated with 15 μM EdU for 60 min. After fixation, the color of the nucleus of Fucci2 cells was recorded, after which we performed signal amplification of EdU (green). We also performed immunostaining of DNA using anti-DNA antibodies (magenta), because signals of SYBR Green I in mt-nucleoids disappeared after fixation. Position of the nucleus (white dotted line) and cell shape (white line) are shown in each image. Scale bar, 10 μm. ( b ) Proportion of EdU-incorporating mt-nucleoids in a cell during the cell cycle. This proportion was calculated from the number of mt-nucleoids with EdU divided by the number of mt-nucleoids immunostained with anti-DNA antibodies in a cell. Error bars indicate standard deviation (G 1, n cells = 7; early-middle S, n cells = 9; late S, n cells = 7; G 2 , n cells = 7). ( c ) Fluorescence intensity of EdU signals in each mt-nucleoid during the cell cycle. The EdU intensity in each mt-nucleoid was analyzed using Fiji software. Approximately straight lines for 0–60 min of incubation are shown in the plot area, and the r 2 value of each line is indicated in parentheses. The slopes of each approximation line are 80.31, 126.18, 141.26, and 67.53 for G 1 , early-middle S, late S, and G 2 , respectively. Error bars indicate standard deviation (n mt-nucleoid = 200 from 10 cells for each plot).

    Journal: Scientific Reports

    Article Title: Live imaging reveals the dynamics and regulation of mitochondrial nucleoids during the cell cycle in Fucci2-HeLa cells

    doi: 10.1038/s41598-017-10843-8

    Figure Lengend Snippet: mtDNA replication occurs throughout the cell cycle, but the activity increases during the S phase. ( a ) Visualization of mtDNA replication in Fucci2 cells during the cell cycle. Fucci2 cells were incubated with 15 μM EdU for 60 min. After fixation, the color of the nucleus of Fucci2 cells was recorded, after which we performed signal amplification of EdU (green). We also performed immunostaining of DNA using anti-DNA antibodies (magenta), because signals of SYBR Green I in mt-nucleoids disappeared after fixation. Position of the nucleus (white dotted line) and cell shape (white line) are shown in each image. Scale bar, 10 μm. ( b ) Proportion of EdU-incorporating mt-nucleoids in a cell during the cell cycle. This proportion was calculated from the number of mt-nucleoids with EdU divided by the number of mt-nucleoids immunostained with anti-DNA antibodies in a cell. Error bars indicate standard deviation (G 1, n cells = 7; early-middle S, n cells = 9; late S, n cells = 7; G 2 , n cells = 7). ( c ) Fluorescence intensity of EdU signals in each mt-nucleoid during the cell cycle. The EdU intensity in each mt-nucleoid was analyzed using Fiji software. Approximately straight lines for 0–60 min of incubation are shown in the plot area, and the r 2 value of each line is indicated in parentheses. The slopes of each approximation line are 80.31, 126.18, 141.26, and 67.53 for G 1 , early-middle S, late S, and G 2 , respectively. Error bars indicate standard deviation (n mt-nucleoid = 200 from 10 cells for each plot).

    Article Snippet: Cells were plated onto an eight-well cover glass chamber (2 × 104 cells per well) and cultured at 37 °C for 24 to 36 h. SYBR Green I (Thermo Fisher Scientific, Japan) was diluted 1:10 times with dimethyl sulfoxide, and subsequently diluted with D-MEM (SYBR Green I solution) 1:30,000 times for HeLa.S-Fucci2 or 1:20,000 times for HeLa-Su9 cells.

    Techniques: Activity Assay, Incubation, Amplification, Immunostaining, SYBR Green Assay, Standard Deviation, Fluorescence, Software

    Growth and viability in pure and mixed cultures. Species-specific cell concentrations and viability were determined over a cultivation period of 32 h by qT-RFLP and flow cytometry, respectively. Open symbols represent data from pure cultures and filled symbols from mixed culture. Left: Dynamics of log 10 -transformed species-specific cell concentrations of (A) P. aeruginosa , (C) B. cepacia , and (E) S. aureus . Right: Dynamics of relative frequencies of (B) viable and dead cells of P. aeruginosa , (D) viable and dead cells of B. cepacia and (F) viable, damaged and dead cells of S. aureus . Relative frequencies of viability subpopulations were determined based on all SYBR Green I and PI fluorescence positive events in the respective species gate. Subpopulations were defined as gated in plots shown in Figure 2 . Error bars represent standard deviation of two (*) or three biological replicates.

    Journal: BMC Microbiology

    Article Title: Species-specific viability analysis of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus in mixed culture by flow cytometry

    doi: 10.1186/1471-2180-14-56

    Figure Lengend Snippet: Growth and viability in pure and mixed cultures. Species-specific cell concentrations and viability were determined over a cultivation period of 32 h by qT-RFLP and flow cytometry, respectively. Open symbols represent data from pure cultures and filled symbols from mixed culture. Left: Dynamics of log 10 -transformed species-specific cell concentrations of (A) P. aeruginosa , (C) B. cepacia , and (E) S. aureus . Right: Dynamics of relative frequencies of (B) viable and dead cells of P. aeruginosa , (D) viable and dead cells of B. cepacia and (F) viable, damaged and dead cells of S. aureus . Relative frequencies of viability subpopulations were determined based on all SYBR Green I and PI fluorescence positive events in the respective species gate. Subpopulations were defined as gated in plots shown in Figure 2 . Error bars represent standard deviation of two (*) or three biological replicates.

    Article Snippet: For staining, working solutions of 1:100 SYBR®Green I (10,000 × concentrate in DMSO, Life Technologies, Carlsbad, CA, USA) and 1 mg/mL propidium iodide (Sigma-Aldrich, Steinheim, Germany) were prepared in ultrapure water.

    Techniques: Flow Cytometry, Cytometry, Transformation Assay, SYBR Green Assay, Fluorescence, Standard Deviation

    Species discrimination in flow cytometric viability analysis. Four-color staining was applied. Samples were incubated with 20 μg/mL WGA-CF405S, 10 μg/mL 1°Ab and 60 μg/mL R-PE conjugated 2°Ab, SYBR Green I (dilution of 5 × 10 3 ) and 5 μg/mL PI. (A) For data analysis, only events with SYBR Green I positive fluorescence (cells) were considered. The cell gate was set manually based on the signal of four-color-stained (black) and unstained cells (red) in exponential growth phase (t = 4 h) from pure culture. (B, C) Gating for species discrimination in data acquired from mixed culture samples. Gate was set manually based on WGA-CF405S fluorescence and R-PE immunofluorescence signals of four-color-stained single species from pure culture. (B) Overlaid cytometric plot of P. aeruginosa (blue), B. cepacia (red) and S. aureus (green) in exponential growth phase (t = 4 h) from pure culture. (C) Gate applied for species discrimination in mixed culture sample at time point of inoculation. For each gate region, either relative frequencies of total events or cells (in italics) are shown. Data is presented in 5% quantile contour plots.

    Journal: BMC Microbiology

    Article Title: Species-specific viability analysis of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus in mixed culture by flow cytometry

    doi: 10.1186/1471-2180-14-56

    Figure Lengend Snippet: Species discrimination in flow cytometric viability analysis. Four-color staining was applied. Samples were incubated with 20 μg/mL WGA-CF405S, 10 μg/mL 1°Ab and 60 μg/mL R-PE conjugated 2°Ab, SYBR Green I (dilution of 5 × 10 3 ) and 5 μg/mL PI. (A) For data analysis, only events with SYBR Green I positive fluorescence (cells) were considered. The cell gate was set manually based on the signal of four-color-stained (black) and unstained cells (red) in exponential growth phase (t = 4 h) from pure culture. (B, C) Gating for species discrimination in data acquired from mixed culture samples. Gate was set manually based on WGA-CF405S fluorescence and R-PE immunofluorescence signals of four-color-stained single species from pure culture. (B) Overlaid cytometric plot of P. aeruginosa (blue), B. cepacia (red) and S. aureus (green) in exponential growth phase (t = 4 h) from pure culture. (C) Gate applied for species discrimination in mixed culture sample at time point of inoculation. For each gate region, either relative frequencies of total events or cells (in italics) are shown. Data is presented in 5% quantile contour plots.

    Article Snippet: For staining, working solutions of 1:100 SYBR®Green I (10,000 × concentrate in DMSO, Life Technologies, Carlsbad, CA, USA) and 1 mg/mL propidium iodide (Sigma-Aldrich, Steinheim, Germany) were prepared in ultrapure water.

    Techniques: Flow Cytometry, Staining, Incubation, Whole Genome Amplification, SYBR Green Assay, Fluorescence, Immunofluorescence

    Viability analysis by flow cytometry. Viability was determined by membrane integrity analysis using SYBR Green I (dilution of 5 × 10 3 ) and PI (5 μg/mL). Representative pseudo color dot plots with defined gates are shown for (A) P. aeruginosa , (B) B. cepacia and (C) S. aureus in stationary growth phase (t = 12 h) from pure culture. Gates were set manually for each species based on SYBR Green I and PI fluorescence signals of isopropanol-treated (red) and untreated cells (green). For each gate region, relative frequencies of total cells are presented. Only events with positive SYBR Green I fluorescence were considered as cells (see Figure 7 ).

    Journal: BMC Microbiology

    Article Title: Species-specific viability analysis of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus in mixed culture by flow cytometry

    doi: 10.1186/1471-2180-14-56

    Figure Lengend Snippet: Viability analysis by flow cytometry. Viability was determined by membrane integrity analysis using SYBR Green I (dilution of 5 × 10 3 ) and PI (5 μg/mL). Representative pseudo color dot plots with defined gates are shown for (A) P. aeruginosa , (B) B. cepacia and (C) S. aureus in stationary growth phase (t = 12 h) from pure culture. Gates were set manually for each species based on SYBR Green I and PI fluorescence signals of isopropanol-treated (red) and untreated cells (green). For each gate region, relative frequencies of total cells are presented. Only events with positive SYBR Green I fluorescence were considered as cells (see Figure 7 ).

    Article Snippet: For staining, working solutions of 1:100 SYBR®Green I (10,000 × concentrate in DMSO, Life Technologies, Carlsbad, CA, USA) and 1 mg/mL propidium iodide (Sigma-Aldrich, Steinheim, Germany) were prepared in ultrapure water.

    Techniques: Flow Cytometry, Cytometry, SYBR Green Assay, Fluorescence

    Comparison of NaCl-P buffer and Ringer solution for viability analysis of B. cepacia and S. aureus by flow cytometry. Viability was determined by membrane integrity analysis using SYBR Green I (dilution of 5 x 10 3 ) and PI (5 μg/mL). Relative frequencies of (A) viable and dead cells of B. cepacia and (B) of viable, damaged and dead cells of S. aureus in pure culture from both exponential and stationary growth phase. Relative frequencies were determined based on all SYBR Green I and PI fluorescence positive events. Error bars represent standard deviation of three biological replicates.

    Journal: BMC Microbiology

    Article Title: Species-specific viability analysis of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus in mixed culture by flow cytometry

    doi: 10.1186/1471-2180-14-56

    Figure Lengend Snippet: Comparison of NaCl-P buffer and Ringer solution for viability analysis of B. cepacia and S. aureus by flow cytometry. Viability was determined by membrane integrity analysis using SYBR Green I (dilution of 5 x 10 3 ) and PI (5 μg/mL). Relative frequencies of (A) viable and dead cells of B. cepacia and (B) of viable, damaged and dead cells of S. aureus in pure culture from both exponential and stationary growth phase. Relative frequencies were determined based on all SYBR Green I and PI fluorescence positive events. Error bars represent standard deviation of three biological replicates.

    Article Snippet: For staining, working solutions of 1:100 SYBR®Green I (10,000 × concentrate in DMSO, Life Technologies, Carlsbad, CA, USA) and 1 mg/mL propidium iodide (Sigma-Aldrich, Steinheim, Germany) were prepared in ultrapure water.

    Techniques: Flow Cytometry, Cytometry, SYBR Green Assay, Fluorescence, Standard Deviation

    Impact of KCL on flow cytometric viability determination. Comparison of Ringer solution without and with 3 M KCl. Viability was determined by membrane integrity analysis using SYBR Green I (dilution of 5 × 10 3 ) and PI (5 μg/mL). Relative frequencies of (A) viable and dead cells of P. aeruginosa, (B) of viable and dead cells of B. cepacia and (C) of viable, damaged and dead cells of S. aureus in exponential and stationary growth phases in pure culture. Relative frequencies were determined based on all SYBR Green I and PI fluorescence positive events. Error bars represent standard deviation of three biological replicates; # indicates a statistically significant difference (p

    Journal: BMC Microbiology

    Article Title: Species-specific viability analysis of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus in mixed culture by flow cytometry

    doi: 10.1186/1471-2180-14-56

    Figure Lengend Snippet: Impact of KCL on flow cytometric viability determination. Comparison of Ringer solution without and with 3 M KCl. Viability was determined by membrane integrity analysis using SYBR Green I (dilution of 5 × 10 3 ) and PI (5 μg/mL). Relative frequencies of (A) viable and dead cells of P. aeruginosa, (B) of viable and dead cells of B. cepacia and (C) of viable, damaged and dead cells of S. aureus in exponential and stationary growth phases in pure culture. Relative frequencies were determined based on all SYBR Green I and PI fluorescence positive events. Error bars represent standard deviation of three biological replicates; # indicates a statistically significant difference (p

    Article Snippet: For staining, working solutions of 1:100 SYBR®Green I (10,000 × concentrate in DMSO, Life Technologies, Carlsbad, CA, USA) and 1 mg/mL propidium iodide (Sigma-Aldrich, Steinheim, Germany) were prepared in ultrapure water.

    Techniques: Flow Cytometry, SYBR Green Assay, Fluorescence, Standard Deviation

    Inhibition by MMV Malaria Box. SYBR Green I assay results for the MMV box screened at 10 µM. Plot of percentage of gametocytocidal activity of 400 compounds compared to pyrvinium pamoate control.

    Journal: PLoS ONE

    Article Title: Gametocytocidal Screen Identifies Novel Chemical Classes with Plasmodium falciparum Transmission Blocking Activity

    doi: 10.1371/journal.pone.0105817

    Figure Lengend Snippet: Inhibition by MMV Malaria Box. SYBR Green I assay results for the MMV box screened at 10 µM. Plot of percentage of gametocytocidal activity of 400 compounds compared to pyrvinium pamoate control.

    Article Snippet: Next 11 µl of 10x CyQUANT direct background suppressor and SYBR Green I (Life Technologies, Grand Island, NY, USA) in PBS was added to the plates and further incubated at room temperature for 2 hrs in the dark.

    Techniques: Inhibition, SYBR Green Assay, Activity Assay

    Overlap of recent screening assays for Malaria Box. Venn Diagram comparing our SYBR Green I assay (green) MMV box hits with hits from four other assays: Confocal fluorescence microscopy (red), Alamar blue early (dark blue) and late (light blue) and Luciferase (yellow) [10] , [14] – [16] .

    Journal: PLoS ONE

    Article Title: Gametocytocidal Screen Identifies Novel Chemical Classes with Plasmodium falciparum Transmission Blocking Activity

    doi: 10.1371/journal.pone.0105817

    Figure Lengend Snippet: Overlap of recent screening assays for Malaria Box. Venn Diagram comparing our SYBR Green I assay (green) MMV box hits with hits from four other assays: Confocal fluorescence microscopy (red), Alamar blue early (dark blue) and late (light blue) and Luciferase (yellow) [10] , [14] – [16] .

    Article Snippet: Next 11 µl of 10x CyQUANT direct background suppressor and SYBR Green I (Life Technologies, Grand Island, NY, USA) in PBS was added to the plates and further incubated at room temperature for 2 hrs in the dark.

    Techniques: SYBR Green Assay, Fluorescence, Microscopy, Luciferase

    SYBR Green I-Background suppressor gametocytocidal assay. (A) Giemsa stained culture before and after treatment with 10 µM pyrvinium pamoate. (B) SYBR Green I fluorescence of gametocytes, total (diamond), killed (triangle) and live gametocytes after drug treatment (total minus killed, square) with decreasing number of gametocytes per uninfected cell, diluted with 2% hematocrit RBCs in media in presence of background suppressor. (C) Z-factors calculated for each gametocyte dilution. Z factors were calculated using the equation shown, described previously for validating high throughput assays (σ = standard deviation, μ = mean, s = sample, c = control or in this case zero gametocytes) [10] . (D) SYBR Green I fluorescence of live or pyrvinium pamoate-killed gametocytes in the presence of CyQUANT background suppressor, with and without exflagellation with background well fluorescence (no parasites) subtracted out as a blank. (E) Example of assay plate SYBR Green I fluorescence in the presence of background suppressor and calculations for % inhibition. Green indicates a positive hit with high inhibition attributable to gametocyte killing and red indicates an intermediate hit, with inhibition attributable to potentially exflagellation inhibition and/or moderate gametocyte killing. (F) Overall assay setup with five steps: 1. Culture and enrich gametocytes, 2. Incubate with drug for 48 hr, 3. Add exflagellation media and incubate 30 min, 4. Add SYBR Green I and background suppressor and incubate 2 hr, 5. Read SYBR Green I fluorescence at excitation 485 nm and emission 535 nm.

    Journal: PLoS ONE

    Article Title: Gametocytocidal Screen Identifies Novel Chemical Classes with Plasmodium falciparum Transmission Blocking Activity

    doi: 10.1371/journal.pone.0105817

    Figure Lengend Snippet: SYBR Green I-Background suppressor gametocytocidal assay. (A) Giemsa stained culture before and after treatment with 10 µM pyrvinium pamoate. (B) SYBR Green I fluorescence of gametocytes, total (diamond), killed (triangle) and live gametocytes after drug treatment (total minus killed, square) with decreasing number of gametocytes per uninfected cell, diluted with 2% hematocrit RBCs in media in presence of background suppressor. (C) Z-factors calculated for each gametocyte dilution. Z factors were calculated using the equation shown, described previously for validating high throughput assays (σ = standard deviation, μ = mean, s = sample, c = control or in this case zero gametocytes) [10] . (D) SYBR Green I fluorescence of live or pyrvinium pamoate-killed gametocytes in the presence of CyQUANT background suppressor, with and without exflagellation with background well fluorescence (no parasites) subtracted out as a blank. (E) Example of assay plate SYBR Green I fluorescence in the presence of background suppressor and calculations for % inhibition. Green indicates a positive hit with high inhibition attributable to gametocyte killing and red indicates an intermediate hit, with inhibition attributable to potentially exflagellation inhibition and/or moderate gametocyte killing. (F) Overall assay setup with five steps: 1. Culture and enrich gametocytes, 2. Incubate with drug for 48 hr, 3. Add exflagellation media and incubate 30 min, 4. Add SYBR Green I and background suppressor and incubate 2 hr, 5. Read SYBR Green I fluorescence at excitation 485 nm and emission 535 nm.

    Article Snippet: Next 11 µl of 10x CyQUANT direct background suppressor and SYBR Green I (Life Technologies, Grand Island, NY, USA) in PBS was added to the plates and further incubated at room temperature for 2 hrs in the dark.

    Techniques: SYBR Green Assay, Staining, Fluorescence, High Throughput Screening Assay, Standard Deviation, CyQUANT Assay, Inhibition

    Inhibition by FDA drug library. SYBR Green I assay results for the Johns Hopkins Clinical Compound Library version 1.3 of FDA approved drugs screened at 20 µM. Plot of percentage of gametocytocidal activity of 1,584 compounds compared to clotrimazole control.

    Journal: PLoS ONE

    Article Title: Gametocytocidal Screen Identifies Novel Chemical Classes with Plasmodium falciparum Transmission Blocking Activity

    doi: 10.1371/journal.pone.0105817

    Figure Lengend Snippet: Inhibition by FDA drug library. SYBR Green I assay results for the Johns Hopkins Clinical Compound Library version 1.3 of FDA approved drugs screened at 20 µM. Plot of percentage of gametocytocidal activity of 1,584 compounds compared to clotrimazole control.

    Article Snippet: Next 11 µl of 10x CyQUANT direct background suppressor and SYBR Green I (Life Technologies, Grand Island, NY, USA) in PBS was added to the plates and further incubated at room temperature for 2 hrs in the dark.

    Techniques: Inhibition, SYBR Green Assay, Activity Assay

    Specificity assessment of LAMP assay. (A) Visual examination of LAMP products by adding SYBR Green I. (B) Agarose gel electrophoresis of amplified products. Lanes Loa, Bp, Mp, Sv, Sm, Sh, Si, Sb, Fh, Ec, As, Dd, Hd, Tt, Eg: DNA from Loa loa , Brugia pahangi, Mansonella perstans, Strongyloides venezuelensis, Schistosoma mansoni, Schistosoma haematobium, Schistosoma intercalatum, Schistosoma bovis , Fasciola hepatica , Echinostoma caproni, Anisakis simplex , Dicrocoelium dendriticum, Hymenolepis diminuta , Taenia taeniformis and Echinococcus granulosus , respectively. Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane N: negative control (no DNA template).

    Journal: PLoS ONE

    Article Title: Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa

    doi: 10.1371/journal.pone.0094664

    Figure Lengend Snippet: Specificity assessment of LAMP assay. (A) Visual examination of LAMP products by adding SYBR Green I. (B) Agarose gel electrophoresis of amplified products. Lanes Loa, Bp, Mp, Sv, Sm, Sh, Si, Sb, Fh, Ec, As, Dd, Hd, Tt, Eg: DNA from Loa loa , Brugia pahangi, Mansonella perstans, Strongyloides venezuelensis, Schistosoma mansoni, Schistosoma haematobium, Schistosoma intercalatum, Schistosoma bovis , Fasciola hepatica , Echinostoma caproni, Anisakis simplex , Dicrocoelium dendriticum, Hymenolepis diminuta , Taenia taeniformis and Echinococcus granulosus , respectively. Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane N: negative control (no DNA template).

    Article Snippet: The LAMP amplification results were also visually detected by adding 2 μL of 1∶10 diluted 10,000X concentration fluorescent dye SYBR Green I (Invitrogen) to the reaction tubes.

    Techniques: Lamp Assay, SYBR Green Assay, Agarose Gel Electrophoresis, Electrophoresis, Amplification, Molecular Weight, Marker, Negative Control

    Sensitivity assessment of the LAMP assay for Loa loa using serial dilutions of genomic DNA by the addition of SYBR Green I or by visualization on agarose gel stained with ethidium bromide. (A) Sensitivity assessment performed with a thermocycler. (B) Sensitivity assessment performed with a heating block. Lane Loa: genomic DNA from Loa loa (5 ng); lanes 10 −1 –10 −13 : 10-fold serially dilutions; lanes N, N1, N2, N3: negative controls (no DNA template). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche).

    Journal: PLoS ONE

    Article Title: Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa

    doi: 10.1371/journal.pone.0094664

    Figure Lengend Snippet: Sensitivity assessment of the LAMP assay for Loa loa using serial dilutions of genomic DNA by the addition of SYBR Green I or by visualization on agarose gel stained with ethidium bromide. (A) Sensitivity assessment performed with a thermocycler. (B) Sensitivity assessment performed with a heating block. Lane Loa: genomic DNA from Loa loa (5 ng); lanes 10 −1 –10 −13 : 10-fold serially dilutions; lanes N, N1, N2, N3: negative controls (no DNA template). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche).

    Article Snippet: The LAMP amplification results were also visually detected by adding 2 μL of 1∶10 diluted 10,000X concentration fluorescent dye SYBR Green I (Invitrogen) to the reaction tubes.

    Techniques: Lamp Assay, SYBR Green Assay, Agarose Gel Electrophoresis, Staining, Blocking Assay, Molecular Weight, Marker

    Sensitivity assessment of the LAMP assay for Loa loa performed with a heating block using simulated human blood samples spiked with serial dilutions of genomic DNA by the addition of SYBR Green I (A) or by visualization on agarose gel stained with ethidium bromide (B). Lane L1: genomic DNA from Loa loa (5 ng) as positive control; lane L2: human blood sample spiked with 5 ng of genomic DNA from Loa loa ; lanes 10 −1 –10 −12 : human blood samples spiked with 10-fold serially dilutions; lane N: negative control (no DNA template). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche).

    Journal: PLoS ONE

    Article Title: Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa

    doi: 10.1371/journal.pone.0094664

    Figure Lengend Snippet: Sensitivity assessment of the LAMP assay for Loa loa performed with a heating block using simulated human blood samples spiked with serial dilutions of genomic DNA by the addition of SYBR Green I (A) or by visualization on agarose gel stained with ethidium bromide (B). Lane L1: genomic DNA from Loa loa (5 ng) as positive control; lane L2: human blood sample spiked with 5 ng of genomic DNA from Loa loa ; lanes 10 −1 –10 −12 : human blood samples spiked with 10-fold serially dilutions; lane N: negative control (no DNA template). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche).

    Article Snippet: The LAMP amplification results were also visually detected by adding 2 μL of 1∶10 diluted 10,000X concentration fluorescent dye SYBR Green I (Invitrogen) to the reaction tubes.

    Techniques: Lamp Assay, Blocking Assay, SYBR Green Assay, Agarose Gel Electrophoresis, Staining, Positive Control, Negative Control, Molecular Weight, Marker

    LAMP detection of Loa loa genomic DNA samples. (A) By the naked eye; (B) by adding SYBR Green I; (C) on agarose gel stained with ethidium bromide. Lanes L1 and L2: Loa loa adult worm genomic DNA; lane N: no template (negative control); lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche).

    Journal: PLoS ONE

    Article Title: Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa

    doi: 10.1371/journal.pone.0094664

    Figure Lengend Snippet: LAMP detection of Loa loa genomic DNA samples. (A) By the naked eye; (B) by adding SYBR Green I; (C) on agarose gel stained with ethidium bromide. Lanes L1 and L2: Loa loa adult worm genomic DNA; lane N: no template (negative control); lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche).

    Article Snippet: The LAMP amplification results were also visually detected by adding 2 μL of 1∶10 diluted 10,000X concentration fluorescent dye SYBR Green I (Invitrogen) to the reaction tubes.

    Techniques: SYBR Green Assay, Agarose Gel Electrophoresis, Staining, Negative Control, Molecular Weight, Marker

    Effect of artesunate on the growth curve of P. falciparum (3D7) and the effect of 12 hourly renewing of artesunate during incubation. Synchronous cultures of a P. falciparum 3D7 strain were incubated for 48 hours with doubling concentrations of artesunate (A) or with a single concentration of 8 nM of artesunate for the whole time or renewed at 12 hour intervals (B and C). Figures A and B show detection of Hz (depolarizing events) while Figure C shows detection of SYBR green I fluorescence (DNA in parasites). The inhibitory effect of artesunate was already detectable after 18 hours of incubation (A). Similar to artemisinin ( Figure 4C ), the growth curve of artesunate at 4 nM showed a 6 hourly delayed growth curve from 18 to 42 hours, including a 6 hour delay in the peak, occurring at 36 hours. Interestingly, the growth curve at 8 nM seemed to show inhibition until 30 hours, when a slight increase was observed (A and B). However, renewing artesunate at 12 hourly intervals eliminates this effect (green line in B). The percentage of SYBR green I positive events remained approximately the same during the 48 hours of incubation (C). This indicates that parasites at the non-renewed 8 nM concentration showed some maturation as indicated by Hz detection but were unable to replicate. Each time point represents the mean value of triplicate samples ± one SD.

    Journal: PLoS ONE

    Article Title: A Novel Flow Cytometric Hemozoin Detection Assay for Real-Time Sensitivity Testing of Plasmodium falciparum

    doi: 10.1371/journal.pone.0061606

    Figure Lengend Snippet: Effect of artesunate on the growth curve of P. falciparum (3D7) and the effect of 12 hourly renewing of artesunate during incubation. Synchronous cultures of a P. falciparum 3D7 strain were incubated for 48 hours with doubling concentrations of artesunate (A) or with a single concentration of 8 nM of artesunate for the whole time or renewed at 12 hour intervals (B and C). Figures A and B show detection of Hz (depolarizing events) while Figure C shows detection of SYBR green I fluorescence (DNA in parasites). The inhibitory effect of artesunate was already detectable after 18 hours of incubation (A). Similar to artemisinin ( Figure 4C ), the growth curve of artesunate at 4 nM showed a 6 hourly delayed growth curve from 18 to 42 hours, including a 6 hour delay in the peak, occurring at 36 hours. Interestingly, the growth curve at 8 nM seemed to show inhibition until 30 hours, when a slight increase was observed (A and B). However, renewing artesunate at 12 hourly intervals eliminates this effect (green line in B). The percentage of SYBR green I positive events remained approximately the same during the 48 hours of incubation (C). This indicates that parasites at the non-renewed 8 nM concentration showed some maturation as indicated by Hz detection but were unable to replicate. Each time point represents the mean value of triplicate samples ± one SD.

    Article Snippet: For each measurement 5 µl of the culture (approximately 800 000 cells) was stained with the DNA-specific dye SYBR green I (Invitrogen, Carlsbad, USA) at 1×.

    Techniques: Incubation, Concentration Assay, SYBR Green Assay, Fluorescence, Inhibition

    Growth curves of Plasmodium falciparum (3D7) in culture. Flow cytometric analysis of a synchronized P. falciparum (3D7) culture (1.4% parasitemia). The percentages of depolarizing events (A) and SYBR green I positive events (B) were followed for 48 hours in uninfected (black lines in A and B) and infected red blood cells (red line in A and green line in B). Analysis of depolarizing events (Hz-containing parasitized erythrocytes) shows an increase at 18 hours, peaking at 30 hours (A). SYBR green I positive events (parasitized RBC) remain unchanged at 1.4% until 30 hours, after which a steady increase can be noted (B). Hz detection reflects parasite maturation with increasing amounts of Hz until 30 hours, while the parasitemia remains unchanged (SYBR green I positive events). After 30 hours, increasing SYBR green I positive events indicate replication and presence of immature forms, which explains the decrease observed in the depolarizing population. Each time point represents the mean value of triplicate samples ± one SD. Red blood cell lysis was excluded by absolute cell counts, which remained stable.

    Journal: PLoS ONE

    Article Title: A Novel Flow Cytometric Hemozoin Detection Assay for Real-Time Sensitivity Testing of Plasmodium falciparum

    doi: 10.1371/journal.pone.0061606

    Figure Lengend Snippet: Growth curves of Plasmodium falciparum (3D7) in culture. Flow cytometric analysis of a synchronized P. falciparum (3D7) culture (1.4% parasitemia). The percentages of depolarizing events (A) and SYBR green I positive events (B) were followed for 48 hours in uninfected (black lines in A and B) and infected red blood cells (red line in A and green line in B). Analysis of depolarizing events (Hz-containing parasitized erythrocytes) shows an increase at 18 hours, peaking at 30 hours (A). SYBR green I positive events (parasitized RBC) remain unchanged at 1.4% until 30 hours, after which a steady increase can be noted (B). Hz detection reflects parasite maturation with increasing amounts of Hz until 30 hours, while the parasitemia remains unchanged (SYBR green I positive events). After 30 hours, increasing SYBR green I positive events indicate replication and presence of immature forms, which explains the decrease observed in the depolarizing population. Each time point represents the mean value of triplicate samples ± one SD. Red blood cell lysis was excluded by absolute cell counts, which remained stable.

    Article Snippet: For each measurement 5 µl of the culture (approximately 800 000 cells) was stained with the DNA-specific dye SYBR green I (Invitrogen, Carlsbad, USA) at 1×.

    Techniques: Flow Cytometry, SYBR Green Assay, Infection, Lysis

    Gating for detection of depolarizing parasitized red blood cells in a Plasmodium falciparum culture. Flow cytometric analysis of an uninfected and a synchronized P. falciparum (3D7) infected culture (1.5% parasitemia) after 24 hours of incubation, stained with SYBR green I. Plots of forward vs. side scatter for the uninfected and infected cultures appear in Figures A and B; corresponding plots of side scatter vs. depolarized side scatter appear in Figures C and D. The gates in Figures C and D identify the depolarizing events. Figures E and F (see text) illustrate gates defining SYBR green-positive parasitized cells. The blue dots on Figure F represent the depolarizing events. Staining with the red blood cell surface marker (CD235) shows that 99.5% of events in a stained sample (red line) exhibit fluorescence above the highest level measured in an unstained control (black line), indicating that the detected events are red blood cells (G). In the SYBR green I histogram (H) of the infected culture, the overall population (black line) shows a distinct peak with a high fluorescent intensity in the third decade. This peak corresponds mainly to the gated population of depolarizing events (pink line). Because SYBR green I intensity correlates with DNA content and thus with parasite level of maturation, the depolarizing population (pink line) consists mainly (79.4%) of mature parasites. The highly red- and green-fluorescent events visible outside the SYBR green gate just to the right of its apex represent contaminating white blood cells among the donor red cells.

    Journal: PLoS ONE

    Article Title: A Novel Flow Cytometric Hemozoin Detection Assay for Real-Time Sensitivity Testing of Plasmodium falciparum

    doi: 10.1371/journal.pone.0061606

    Figure Lengend Snippet: Gating for detection of depolarizing parasitized red blood cells in a Plasmodium falciparum culture. Flow cytometric analysis of an uninfected and a synchronized P. falciparum (3D7) infected culture (1.5% parasitemia) after 24 hours of incubation, stained with SYBR green I. Plots of forward vs. side scatter for the uninfected and infected cultures appear in Figures A and B; corresponding plots of side scatter vs. depolarized side scatter appear in Figures C and D. The gates in Figures C and D identify the depolarizing events. Figures E and F (see text) illustrate gates defining SYBR green-positive parasitized cells. The blue dots on Figure F represent the depolarizing events. Staining with the red blood cell surface marker (CD235) shows that 99.5% of events in a stained sample (red line) exhibit fluorescence above the highest level measured in an unstained control (black line), indicating that the detected events are red blood cells (G). In the SYBR green I histogram (H) of the infected culture, the overall population (black line) shows a distinct peak with a high fluorescent intensity in the third decade. This peak corresponds mainly to the gated population of depolarizing events (pink line). Because SYBR green I intensity correlates with DNA content and thus with parasite level of maturation, the depolarizing population (pink line) consists mainly (79.4%) of mature parasites. The highly red- and green-fluorescent events visible outside the SYBR green gate just to the right of its apex represent contaminating white blood cells among the donor red cells.

    Article Snippet: For each measurement 5 µl of the culture (approximately 800 000 cells) was stained with the DNA-specific dye SYBR green I (Invitrogen, Carlsbad, USA) at 1×.

    Techniques: Flow Cytometry, Infection, Incubation, Staining, SYBR Green Assay, Marker, Fluorescence

    Community analysis of six digesters a – h . Column 1 : Flow cytometric measurement of the unstained samples with the respective autofluorescent subcommunities F420+. Column 2 : The total SYBR Green I stained digester communities. Column 3 : SYBR Green stained subcommunity F420+. Column 4 : the total DAPI stained digester communities. A mcrA targeted T-RFLP analysis of methanogenic archaea in the fresh samples is shown for each digester. Unidentified T-RFs are indicated in grey. The digesters were fed with a disintegrated straw, b whole plant rye silage, c corn silage, d , e chicken manure, f common duckweed, g Elodea nuttallii and h synthetic organic acids. 1,000,000 total events were recorded for unstained samples a – g while 200,000 events were recorded for unstained sample h ; 100,000 cell events were recorded in the SYBR Green I stained samples; 200,000 cell events were recorded in the DAPI stained samples. The black arrow marks the control beads (details in “ Methods ”)

    Journal: Microbial Cell Factories

    Article Title: Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence

    doi: 10.1186/s12934-017-0793-7

    Figure Lengend Snippet: Community analysis of six digesters a – h . Column 1 : Flow cytometric measurement of the unstained samples with the respective autofluorescent subcommunities F420+. Column 2 : The total SYBR Green I stained digester communities. Column 3 : SYBR Green stained subcommunity F420+. Column 4 : the total DAPI stained digester communities. A mcrA targeted T-RFLP analysis of methanogenic archaea in the fresh samples is shown for each digester. Unidentified T-RFs are indicated in grey. The digesters were fed with a disintegrated straw, b whole plant rye silage, c corn silage, d , e chicken manure, f common duckweed, g Elodea nuttallii and h synthetic organic acids. 1,000,000 total events were recorded for unstained samples a – g while 200,000 events were recorded for unstained sample h ; 100,000 cell events were recorded in the SYBR Green I stained samples; 200,000 cell events were recorded in the DAPI stained samples. The black arrow marks the control beads (details in “ Methods ”)

    Article Snippet: The staining was performed in 800-µL batches containing 5 µL sample solution, 735 µL PBS, 40 µL ethanol, and 20 µL 20× SYBR-Green I solution (ThermoFisher Scientific, Waltham, Massachusetts, USA).

    Techniques: Flow Cytometry, SYBR Green Assay, Staining

    Flow cytometric analysis of a methanogenic enrichment culture (MEC) with sort gates in black ( a unstained, b – e stained). a FSC vs. F420+. Subcommunities with high autofluorescent (MEC F420+) and low autofluorescent properties (MEC F420low) can be detected. b 3D visualization of FSC vs. F420+ vs. SYBR Green I. c FSC vs. SYBR Green I plot of the total microbial community. d F420+ vs. SYBR Green I plot used for discrimination of high (MEC F420 + S1 and MEC F420 + S2) as well as low and non-autofluorescent subcommunities (MEC F420− and MEC MF420low. e Position of subcommunities MEC F420 + S1 and MEC F420 + S2 in a FSC vs. SYBR Green I plot. The arrow marks the control beads

    Journal: Microbial Cell Factories

    Article Title: Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence

    doi: 10.1186/s12934-017-0793-7

    Figure Lengend Snippet: Flow cytometric analysis of a methanogenic enrichment culture (MEC) with sort gates in black ( a unstained, b – e stained). a FSC vs. F420+. Subcommunities with high autofluorescent (MEC F420+) and low autofluorescent properties (MEC F420low) can be detected. b 3D visualization of FSC vs. F420+ vs. SYBR Green I. c FSC vs. SYBR Green I plot of the total microbial community. d F420+ vs. SYBR Green I plot used for discrimination of high (MEC F420 + S1 and MEC F420 + S2) as well as low and non-autofluorescent subcommunities (MEC F420− and MEC MF420low. e Position of subcommunities MEC F420 + S1 and MEC F420 + S2 in a FSC vs. SYBR Green I plot. The arrow marks the control beads

    Article Snippet: The staining was performed in 800-µL batches containing 5 µL sample solution, 735 µL PBS, 40 µL ethanol, and 20 µL 20× SYBR-Green I solution (ThermoFisher Scientific, Waltham, Massachusetts, USA).

    Techniques: Flow Cytometry, Staining, SYBR Green Assay

    Influence of nucleic acid staining on F 420 fluorescence. a Unstained digester sample after 3 h as a control. b The same sample after 3 h of SYBR Green I staining. c Cell numbers of the subcommunities F420+ (white bar), F420− (light grey bar) and autofluorescence intensity (dark grey bar) of the subcommunities F420+ are indicated with the respective standard deviations. Samples were gated according to Additional file 1 : Figure S4. Values are given in Additional file 1 : S7. The arrow marks the added control beads

    Journal: Microbial Cell Factories

    Article Title: Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence

    doi: 10.1186/s12934-017-0793-7

    Figure Lengend Snippet: Influence of nucleic acid staining on F 420 fluorescence. a Unstained digester sample after 3 h as a control. b The same sample after 3 h of SYBR Green I staining. c Cell numbers of the subcommunities F420+ (white bar), F420− (light grey bar) and autofluorescence intensity (dark grey bar) of the subcommunities F420+ are indicated with the respective standard deviations. Samples were gated according to Additional file 1 : Figure S4. Values are given in Additional file 1 : S7. The arrow marks the added control beads

    Article Snippet: The staining was performed in 800-µL batches containing 5 µL sample solution, 735 µL PBS, 40 µL ethanol, and 20 µL 20× SYBR-Green I solution (ThermoFisher Scientific, Waltham, Massachusetts, USA).

    Techniques: Staining, Fluorescence, SYBR Green Assay

    Specificity of RT-LAMP assay for the detection of DENV3. a Agarose gel electrophoresis analysis of the DENV3 RT-LAMP amplification product, showing the specificity of the primers. b The real-time monitoring over time for the DENV3 RT-LAMP reaction. c Visual inspection of the RT-LAMP specificity assay with SYBR Green I corresponding to the agarose gel electrophoresis analysis. 1, negative [ 43 ]; 2–3, DNA of HSV and EBV, respectively; 4–9, RNA of JEV, YFV and DENV1-4, respectively; M, DL1000 DNA Marker

    Journal: BMC Microbiology

    Article Title: Development of reverse-transcription loop-mediated isothermal amplification assay for rapid detection and differentiation of dengue virus serotypes 1–4

    doi: 10.1186/s12866-015-0595-1

    Figure Lengend Snippet: Specificity of RT-LAMP assay for the detection of DENV3. a Agarose gel electrophoresis analysis of the DENV3 RT-LAMP amplification product, showing the specificity of the primers. b The real-time monitoring over time for the DENV3 RT-LAMP reaction. c Visual inspection of the RT-LAMP specificity assay with SYBR Green I corresponding to the agarose gel electrophoresis analysis. 1, negative [ 43 ]; 2–3, DNA of HSV and EBV, respectively; 4–9, RNA of JEV, YFV and DENV1-4, respectively; M, DL1000 DNA Marker

    Article Snippet: For naked-eye detection, 1.0 μL of 10−1 diluted SYBR Green I (Takara Bio Inc., Otsu, Japan) was dropped on the inner cover of the reaction tube to avoid the aerosol pollution, and then mixed the SYBR Green I and the reaction mixture to observe the color.

    Techniques: RT Lamp Assay, Agarose Gel Electrophoresis, Amplification, SYBR Green Assay, Marker

    Specificity of RT-LAMP assay for the detection of DENV4. a Agarose gel electrophoresis analysis of the DENV4 RT-LAMP amplification product, showing the specificity of the primers. b The real-time monitoring over time for the DENV4 RT-LAMP reaction. c Visual inspection of the RT-LAMP specificity assay with SYBR Green I corresponding to the agarose gel electrophoresis analysis. 1, negative (water); 2–3, DNA of HSV and EBV, respectively; 4–9, RNA of JEV, YFV and DENV1-4, respectively; M, DL1000 DNA Marker

    Journal: BMC Microbiology

    Article Title: Development of reverse-transcription loop-mediated isothermal amplification assay for rapid detection and differentiation of dengue virus serotypes 1–4

    doi: 10.1186/s12866-015-0595-1

    Figure Lengend Snippet: Specificity of RT-LAMP assay for the detection of DENV4. a Agarose gel electrophoresis analysis of the DENV4 RT-LAMP amplification product, showing the specificity of the primers. b The real-time monitoring over time for the DENV4 RT-LAMP reaction. c Visual inspection of the RT-LAMP specificity assay with SYBR Green I corresponding to the agarose gel electrophoresis analysis. 1, negative (water); 2–3, DNA of HSV and EBV, respectively; 4–9, RNA of JEV, YFV and DENV1-4, respectively; M, DL1000 DNA Marker

    Article Snippet: For naked-eye detection, 1.0 μL of 10−1 diluted SYBR Green I (Takara Bio Inc., Otsu, Japan) was dropped on the inner cover of the reaction tube to avoid the aerosol pollution, and then mixed the SYBR Green I and the reaction mixture to observe the color.

    Techniques: RT Lamp Assay, Agarose Gel Electrophoresis, Amplification, SYBR Green Assay, Marker

    Specificity of RT-LAMP assay for the detection of DENV2. a Agarose gel electrophoresis analysis of the DENV2 RT-LAMP amplification product, showing the specificity of the primers. b The real-time monitoring over time for the DENV2 RT-LAMP reaction. c Visual inspection of the RT-LAMP specificity assay with SYBR Green I corresponding to the agarose gel electrophoresis analysis. 1, negative (water); 2–3, DNA of HSV and EBV, respectively; 4–9, RNA of JEV, YFV and DENV1-4, respectively; M, DL1000 DNA Marker

    Journal: BMC Microbiology

    Article Title: Development of reverse-transcription loop-mediated isothermal amplification assay for rapid detection and differentiation of dengue virus serotypes 1–4

    doi: 10.1186/s12866-015-0595-1

    Figure Lengend Snippet: Specificity of RT-LAMP assay for the detection of DENV2. a Agarose gel electrophoresis analysis of the DENV2 RT-LAMP amplification product, showing the specificity of the primers. b The real-time monitoring over time for the DENV2 RT-LAMP reaction. c Visual inspection of the RT-LAMP specificity assay with SYBR Green I corresponding to the agarose gel electrophoresis analysis. 1, negative (water); 2–3, DNA of HSV and EBV, respectively; 4–9, RNA of JEV, YFV and DENV1-4, respectively; M, DL1000 DNA Marker

    Article Snippet: For naked-eye detection, 1.0 μL of 10−1 diluted SYBR Green I (Takara Bio Inc., Otsu, Japan) was dropped on the inner cover of the reaction tube to avoid the aerosol pollution, and then mixed the SYBR Green I and the reaction mixture to observe the color.

    Techniques: RT Lamp Assay, Agarose Gel Electrophoresis, Amplification, SYBR Green Assay, Marker

    Specificity of RT-LAMP assay for the detection of DENV1. a Agarose gel electrophoresis analysis of the DENV1 RT-LAMP amplification product, showing the specificity of the primers. b The real-time monitoring over time for the DENV1 RT-LAMP reaction. c Visual inspection of the RT-LAMP specificity assay with SYBR Green I corresponding to the agarose gel electrophoresis analysis. 1, negative [ 43 ]; 2–3, DNA of HSV and EBV, respectively; 4–9, RNA of JEV, YFV and DENV1-4, respectively; M, DL1000 DNA Marker

    Journal: BMC Microbiology

    Article Title: Development of reverse-transcription loop-mediated isothermal amplification assay for rapid detection and differentiation of dengue virus serotypes 1–4

    doi: 10.1186/s12866-015-0595-1

    Figure Lengend Snippet: Specificity of RT-LAMP assay for the detection of DENV1. a Agarose gel electrophoresis analysis of the DENV1 RT-LAMP amplification product, showing the specificity of the primers. b The real-time monitoring over time for the DENV1 RT-LAMP reaction. c Visual inspection of the RT-LAMP specificity assay with SYBR Green I corresponding to the agarose gel electrophoresis analysis. 1, negative [ 43 ]; 2–3, DNA of HSV and EBV, respectively; 4–9, RNA of JEV, YFV and DENV1-4, respectively; M, DL1000 DNA Marker

    Article Snippet: For naked-eye detection, 1.0 μL of 10−1 diluted SYBR Green I (Takara Bio Inc., Otsu, Japan) was dropped on the inner cover of the reaction tube to avoid the aerosol pollution, and then mixed the SYBR Green I and the reaction mixture to observe the color.

    Techniques: RT Lamp Assay, Agarose Gel Electrophoresis, Amplification, SYBR Green Assay, Marker

    Detection of tobacco components in different tobaccocultivars. (a) LAMP method through direct visual detection with SYBR Green I; (b) LAMP method on 2% agarose gel electrophoresis analysis; (c) qPCR method. Lane 1 : NTC; lane 2 : PTC; lanes 3–17 : 15 tobacco samples of different cured tobacco varieties; lanes 18-19 : two fresh tobacco samples; lane M : Trans 2K DNA marker. Ct was expressed as mean Ct ± SD from 3 independent experiments with three replications.

    Journal: International Journal of Analytical Chemistry

    Article Title: The Development of DNA Based Methods for the Reliable and Efficient Identification of Nicotiana tabacum in Tobacco and Its Derived Products

    doi: 10.1155/2016/4352308

    Figure Lengend Snippet: Detection of tobacco components in different tobaccocultivars. (a) LAMP method through direct visual detection with SYBR Green I; (b) LAMP method on 2% agarose gel electrophoresis analysis; (c) qPCR method. Lane 1 : NTC; lane 2 : PTC; lanes 3–17 : 15 tobacco samples of different cured tobacco varieties; lanes 18-19 : two fresh tobacco samples; lane M : Trans 2K DNA marker. Ct was expressed as mean Ct ± SD from 3 independent experiments with three replications.

    Article Snippet: The amplified LAMP products were examined either through visual inspection with 1000x SYBR Green I (Generay Biotech Co., Ltd., Shanghai, China) or on agarose gel electrophoresis (AGE) analysis.

    Techniques: SYBR Green Assay, Agarose Gel Electrophoresis, Real-time Polymerase Chain Reaction, Marker

    Practical sample detection with different practical samples. (a) LAMP method through direct visual detection with SYBR Green I; (b) LAMP method on 2% agarose gel electrophoresis analysis; (c) qPCR method. Lane 1 : NTC; lane 2 : PTC; lanes 3-4 : coriander and spinach; lanes 5-6 : burley and Oriental SAADI-6; lanes 7-8 : NT . Oriental and NT . Virginia gold; lanes 9-10 : reconstituted tobacco (no tobacco stems, no sulphate cellulose) and reconstituted tobacco (tobacco stems, with sulphate cellulose); lanes 11-12 : cigarette (Liqun and Double Happiness); lanes 13-14 : wrappers from Liqun and Marlboro, respectively; lane M : Trans 2K DNA marker. Ct was expressed as mean Ct ± SD from 3 independent experiments with three replications.

    Journal: International Journal of Analytical Chemistry

    Article Title: The Development of DNA Based Methods for the Reliable and Efficient Identification of Nicotiana tabacum in Tobacco and Its Derived Products

    doi: 10.1155/2016/4352308

    Figure Lengend Snippet: Practical sample detection with different practical samples. (a) LAMP method through direct visual detection with SYBR Green I; (b) LAMP method on 2% agarose gel electrophoresis analysis; (c) qPCR method. Lane 1 : NTC; lane 2 : PTC; lanes 3-4 : coriander and spinach; lanes 5-6 : burley and Oriental SAADI-6; lanes 7-8 : NT . Oriental and NT . Virginia gold; lanes 9-10 : reconstituted tobacco (no tobacco stems, no sulphate cellulose) and reconstituted tobacco (tobacco stems, with sulphate cellulose); lanes 11-12 : cigarette (Liqun and Double Happiness); lanes 13-14 : wrappers from Liqun and Marlboro, respectively; lane M : Trans 2K DNA marker. Ct was expressed as mean Ct ± SD from 3 independent experiments with three replications.

    Article Snippet: The amplified LAMP products were examined either through visual inspection with 1000x SYBR Green I (Generay Biotech Co., Ltd., Shanghai, China) or on agarose gel electrophoresis (AGE) analysis.

    Techniques: SYBR Green Assay, Agarose Gel Electrophoresis, Real-time Polymerase Chain Reaction, Marker

    Specificity test of UMPS gene in tobacco and nontobacco plants. (a) LAMP method through direct visual detection with SYBR Green I; (b) LAMP method on 2% agarose gel electrophoresis analysis; (c) qPCR method. Lane 1 : negative control (NTC); lane 2 : positive control (PTC); lanes 3–18 : Chinese jasmine, alfalfa, Altingia , canola, Pittosporum , Daphniphyllum , mondo grass, sapodilla, garden petunia, castor oil, indica rice, coriander, spinach, pomegranate, watermelon, and eggplant; lane M : Trans 2K DNA marker. Ct was expressed as mean Ct ± SD from 3 independent experiments with three replications.

    Journal: International Journal of Analytical Chemistry

    Article Title: The Development of DNA Based Methods for the Reliable and Efficient Identification of Nicotiana tabacum in Tobacco and Its Derived Products

    doi: 10.1155/2016/4352308

    Figure Lengend Snippet: Specificity test of UMPS gene in tobacco and nontobacco plants. (a) LAMP method through direct visual detection with SYBR Green I; (b) LAMP method on 2% agarose gel electrophoresis analysis; (c) qPCR method. Lane 1 : negative control (NTC); lane 2 : positive control (PTC); lanes 3–18 : Chinese jasmine, alfalfa, Altingia , canola, Pittosporum , Daphniphyllum , mondo grass, sapodilla, garden petunia, castor oil, indica rice, coriander, spinach, pomegranate, watermelon, and eggplant; lane M : Trans 2K DNA marker. Ct was expressed as mean Ct ± SD from 3 independent experiments with three replications.

    Article Snippet: The amplified LAMP products were examined either through visual inspection with 1000x SYBR Green I (Generay Biotech Co., Ltd., Shanghai, China) or on agarose gel electrophoresis (AGE) analysis.

    Techniques: SYBR Green Assay, Agarose Gel Electrophoresis, Real-time Polymerase Chain Reaction, Negative Control, Positive Control, Marker

    Sensitivity test of UMPS gene using serial dilutions of genomic DNA from fresh tobaccoleave samples. (a) LAMP method through direct visual detection with SYBR Green I; (b) LAMP method on 2% agarose gel electrophoresis analysis. Lane 1 : NTC; lanes 2–9 : 120, 60, 30, 15, 7.5, 3.75, 1.88, and 0.94 ng per reaction, respectively; lane M : Trans 2K DNA marker. (c) qPCR method. For standard curve, a serial dilution of DNA samples (120, 60, 30, 15, 7.5, 3.75, 1.88, 0.94, 0.47, 0.24, 0.12, and 0.06 ng) was used. The result was developed after considering 3 independent experiments with three replications.

    Journal: International Journal of Analytical Chemistry

    Article Title: The Development of DNA Based Methods for the Reliable and Efficient Identification of Nicotiana tabacum in Tobacco and Its Derived Products

    doi: 10.1155/2016/4352308

    Figure Lengend Snippet: Sensitivity test of UMPS gene using serial dilutions of genomic DNA from fresh tobaccoleave samples. (a) LAMP method through direct visual detection with SYBR Green I; (b) LAMP method on 2% agarose gel electrophoresis analysis. Lane 1 : NTC; lanes 2–9 : 120, 60, 30, 15, 7.5, 3.75, 1.88, and 0.94 ng per reaction, respectively; lane M : Trans 2K DNA marker. (c) qPCR method. For standard curve, a serial dilution of DNA samples (120, 60, 30, 15, 7.5, 3.75, 1.88, 0.94, 0.47, 0.24, 0.12, and 0.06 ng) was used. The result was developed after considering 3 independent experiments with three replications.

    Article Snippet: The amplified LAMP products were examined either through visual inspection with 1000x SYBR Green I (Generay Biotech Co., Ltd., Shanghai, China) or on agarose gel electrophoresis (AGE) analysis.

    Techniques: SYBR Green Assay, Agarose Gel Electrophoresis, Marker, Real-time Polymerase Chain Reaction, Serial Dilution

    Detection of clinical samples in LAMP, CPA and IMSA assays. LAMP assay: (A) agarose gel electrophoresis of products obtained; (B) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under visible light; (C) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under UV light. CPA assay: (D) agarose gel electrophoresis of products obtained; (E) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under visible light; (F) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under UV light. IMSA assay: (G) agarose gel electrophoresis of products obtained; (H) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under visible light; (I) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under UV light. (J) Reverse transcription-polymerase chain reaction amplification curves for clinical samples (1–41). LAMP, loop-mediated isothermal amplification; CPA, cross-priming amplification; IMSA, isothermal multiple-self-matching-initiated amplification; M, Trans 2K plus II DNA marker; N, negative control; P, positive control (runt related transcription factor 1/runt related transcription factor 1 translocation partner 1 plasmid).

    Journal: Experimental and Therapeutic Medicine

    Article Title: Development and evaluation of LAMP, CPA and IMSA methods for rapid detection of the AML1/ETO fusion gene in acute myeloid leukemia

    doi: 10.3892/etm.2018.6617

    Figure Lengend Snippet: Detection of clinical samples in LAMP, CPA and IMSA assays. LAMP assay: (A) agarose gel electrophoresis of products obtained; (B) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under visible light; (C) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under UV light. CPA assay: (D) agarose gel electrophoresis of products obtained; (E) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under visible light; (F) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under UV light. IMSA assay: (G) agarose gel electrophoresis of products obtained; (H) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under visible light; (I) visualization of reactions performed with clinical samples (1–41) and SYBR-Green I under UV light. (J) Reverse transcription-polymerase chain reaction amplification curves for clinical samples (1–41). LAMP, loop-mediated isothermal amplification; CPA, cross-priming amplification; IMSA, isothermal multiple-self-matching-initiated amplification; M, Trans 2K plus II DNA marker; N, negative control; P, positive control (runt related transcription factor 1/runt related transcription factor 1 translocation partner 1 plasmid).

    Article Snippet: The following reagents were purchased as indicated: Bst 2.0 DNA polymerase large fragment (New England Biolabs, Guangzhou Ltd., Guangzhou, China), Avian Myeloblastosis Virus Reverse Transcriptase (Promega Corporation, Madison, WI, USA), dNTPs (TransGen Biotech Co., Ltd., Beijing, China), RNAiso Plus (Takara Biotechnology Co., Ltd., Dalian, China), betaine (Sigma-Aldrich; EMD Millipore, Billerica, MA, USA), SYBR-Green I (SG I) fluorescent dye (Beijing Solarbio Science & Technology Co., Ltd., Beijing, China), PCR SuperMix (TransGen Biotech Co., Ltd.), and primers synthesized by Sangon Biotech Co., Ltd. (Shanghai, China).

    Techniques: Lamp Assay, Agarose Gel Electrophoresis, SYBR Green Assay, Reverse Transcription Polymerase Chain Reaction, Amplification, Marker, Negative Control, Positive Control, Translocation Assay, Plasmid Preparation

    Representative isothermal reaction assays of negative controls and positive samples subjected to LAMP, CPA and IMSA methods to detect the AML1 / ETO fusion gene. Reaction contents of the tubes for (A) LAMP, (B) CPA and (C) IMSA assays were subjected to agarose gel electrophoresis and UV visualization of the products. Images of reaction tubes for (D) LAMP, (E) CPA and (F) IMSA under visible light. Images of reaction tubes for (G) LAMP, (H) CPA and (I) IMSA under UV light. Images were captured following the addition of SYBR-Green I. LAMP, loop-mediated isothermal amplification; CPA, cross-priming amplification; IMSA, isothermal multiple-self-matching-initiated amplification; M, Trans 2K plus II DNA marker; 1, negative control; 2, positive detection of AML1 / ETO fusion gene. AML1 , runt related transcription factor 1; ETO , runt related transcription factor 1 translocation partner 1.

    Journal: Experimental and Therapeutic Medicine

    Article Title: Development and evaluation of LAMP, CPA and IMSA methods for rapid detection of the AML1/ETO fusion gene in acute myeloid leukemia

    doi: 10.3892/etm.2018.6617

    Figure Lengend Snippet: Representative isothermal reaction assays of negative controls and positive samples subjected to LAMP, CPA and IMSA methods to detect the AML1 / ETO fusion gene. Reaction contents of the tubes for (A) LAMP, (B) CPA and (C) IMSA assays were subjected to agarose gel electrophoresis and UV visualization of the products. Images of reaction tubes for (D) LAMP, (E) CPA and (F) IMSA under visible light. Images of reaction tubes for (G) LAMP, (H) CPA and (I) IMSA under UV light. Images were captured following the addition of SYBR-Green I. LAMP, loop-mediated isothermal amplification; CPA, cross-priming amplification; IMSA, isothermal multiple-self-matching-initiated amplification; M, Trans 2K plus II DNA marker; 1, negative control; 2, positive detection of AML1 / ETO fusion gene. AML1 , runt related transcription factor 1; ETO , runt related transcription factor 1 translocation partner 1.

    Article Snippet: The following reagents were purchased as indicated: Bst 2.0 DNA polymerase large fragment (New England Biolabs, Guangzhou Ltd., Guangzhou, China), Avian Myeloblastosis Virus Reverse Transcriptase (Promega Corporation, Madison, WI, USA), dNTPs (TransGen Biotech Co., Ltd., Beijing, China), RNAiso Plus (Takara Biotechnology Co., Ltd., Dalian, China), betaine (Sigma-Aldrich; EMD Millipore, Billerica, MA, USA), SYBR-Green I (SG I) fluorescent dye (Beijing Solarbio Science & Technology Co., Ltd., Beijing, China), PCR SuperMix (TransGen Biotech Co., Ltd.), and primers synthesized by Sangon Biotech Co., Ltd. (Shanghai, China).

    Techniques: Agarose Gel Electrophoresis, SYBR Green Assay, Amplification, Marker, Negative Control, Translocation Assay

    Specificity test for the LAMP, CPA and IMSA assays. LAMP assay: (A) Agarose gel electrophoresis of products obtained; (B) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under visible light; (C) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under UV light. CPA assay: (D) agarose gel electrophoresis of products obtained; (E) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under visible light; (F) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under UV light. IMSA assay: (G) agarose gel electrophoresis of products obtained; (H) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under visible light; (I) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under UV light. M, Trans 2K plus II DNA marker; N, negative control; LAMP, loop-mediated isothermal amplification; CPA, cross-priming amplification; IMSA, isothermal multiple-self-matching-initiated amplification; AML1 / ETO , runt related transcription factor 1/runt related transcription factor 1 translocation partner 1; 1, AML1/ETO plasmid; 2, AML1/ETO fusion gene sample; 3, chronic myelogenous leukemia (breakpoint cluster region/abelson) sample; 4, acute promyelocytic leukemia (promyelocytic leukemia/retinoic acid receptor-α) sample; 5, 11q23/mixed lineage leukemia leukemia sample; 6, acute lymphocytic leukemia/PBX homebox 1 sample; 7, healthy sample as the template.

    Journal: Experimental and Therapeutic Medicine

    Article Title: Development and evaluation of LAMP, CPA and IMSA methods for rapid detection of the AML1/ETO fusion gene in acute myeloid leukemia

    doi: 10.3892/etm.2018.6617

    Figure Lengend Snippet: Specificity test for the LAMP, CPA and IMSA assays. LAMP assay: (A) Agarose gel electrophoresis of products obtained; (B) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under visible light; (C) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under UV light. CPA assay: (D) agarose gel electrophoresis of products obtained; (E) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under visible light; (F) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under UV light. IMSA assay: (G) agarose gel electrophoresis of products obtained; (H) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under visible light; (I) visualization of reactions performed with various samples ( 1 – 7 ) and SYBR-Green I under UV light. M, Trans 2K plus II DNA marker; N, negative control; LAMP, loop-mediated isothermal amplification; CPA, cross-priming amplification; IMSA, isothermal multiple-self-matching-initiated amplification; AML1 / ETO , runt related transcription factor 1/runt related transcription factor 1 translocation partner 1; 1, AML1/ETO plasmid; 2, AML1/ETO fusion gene sample; 3, chronic myelogenous leukemia (breakpoint cluster region/abelson) sample; 4, acute promyelocytic leukemia (promyelocytic leukemia/retinoic acid receptor-α) sample; 5, 11q23/mixed lineage leukemia leukemia sample; 6, acute lymphocytic leukemia/PBX homebox 1 sample; 7, healthy sample as the template.

    Article Snippet: The following reagents were purchased as indicated: Bst 2.0 DNA polymerase large fragment (New England Biolabs, Guangzhou Ltd., Guangzhou, China), Avian Myeloblastosis Virus Reverse Transcriptase (Promega Corporation, Madison, WI, USA), dNTPs (TransGen Biotech Co., Ltd., Beijing, China), RNAiso Plus (Takara Biotechnology Co., Ltd., Dalian, China), betaine (Sigma-Aldrich; EMD Millipore, Billerica, MA, USA), SYBR-Green I (SG I) fluorescent dye (Beijing Solarbio Science & Technology Co., Ltd., Beijing, China), PCR SuperMix (TransGen Biotech Co., Ltd.), and primers synthesized by Sangon Biotech Co., Ltd. (Shanghai, China).

    Techniques: Lamp Assay, Agarose Gel Electrophoresis, SYBR Green Assay, Marker, Negative Control, Amplification, Translocation Assay, Plasmid Preparation

    Sensitivity test for the LAMP, CPA and IMSA assays. LAMP assay: (A) Agarose gel electrophoresis of the products; (B) visualization of reactions performed with serially diluted ABL1-ETO fusion gene plasmids ( 1 – 9 ) and SYBR-Green I under visible light; (C) visualization of reactions performed with various fusion gene samples ( 1 – 9 ) and SYBR-Green I under UV light. CPA assay: (D) agarose gel electrophoresis of the products; (E) visualization of reactions performed with serially diluted ABL1-ETO fusion gene plasmids ( 1 – 9 ) and SYBR-Green I under visible light; (F) visualization of reactions performed with various fusion gene samples ( 1 – 9 ) and SYBR-Green I under UV light. IMSA assay: (G) agarose gel electrophoresis of the products; (H) visualization of reactions performed with serially diluted ABL1-ETO fusion gene plasmids ( 1 – 9 ) and SYBR-Green I under visible light; (I) visualization of reactions performed with various fusion gene samples ( 1 – 9 ) and SYBR-Green I under UV light. (J) Reverse transcription-polymerase chain reaction amplification curves for samples 1–9. LAMP, loop-mediated isothermal amplification; CPA, cross-priming amplification; IMSA, isothermal multiple-self-matching-initiated amplification; M, Trans 2K plus II DNA marker; 1–9, 10 6 , 10 5 , 10 4 , 10 3 , 10 2 , 50, 25, 10, and 5 plasmid copies/tube, respectively; N, negative control.

    Journal: Experimental and Therapeutic Medicine

    Article Title: Development and evaluation of LAMP, CPA and IMSA methods for rapid detection of the AML1/ETO fusion gene in acute myeloid leukemia

    doi: 10.3892/etm.2018.6617

    Figure Lengend Snippet: Sensitivity test for the LAMP, CPA and IMSA assays. LAMP assay: (A) Agarose gel electrophoresis of the products; (B) visualization of reactions performed with serially diluted ABL1-ETO fusion gene plasmids ( 1 – 9 ) and SYBR-Green I under visible light; (C) visualization of reactions performed with various fusion gene samples ( 1 – 9 ) and SYBR-Green I under UV light. CPA assay: (D) agarose gel electrophoresis of the products; (E) visualization of reactions performed with serially diluted ABL1-ETO fusion gene plasmids ( 1 – 9 ) and SYBR-Green I under visible light; (F) visualization of reactions performed with various fusion gene samples ( 1 – 9 ) and SYBR-Green I under UV light. IMSA assay: (G) agarose gel electrophoresis of the products; (H) visualization of reactions performed with serially diluted ABL1-ETO fusion gene plasmids ( 1 – 9 ) and SYBR-Green I under visible light; (I) visualization of reactions performed with various fusion gene samples ( 1 – 9 ) and SYBR-Green I under UV light. (J) Reverse transcription-polymerase chain reaction amplification curves for samples 1–9. LAMP, loop-mediated isothermal amplification; CPA, cross-priming amplification; IMSA, isothermal multiple-self-matching-initiated amplification; M, Trans 2K plus II DNA marker; 1–9, 10 6 , 10 5 , 10 4 , 10 3 , 10 2 , 50, 25, 10, and 5 plasmid copies/tube, respectively; N, negative control.

    Article Snippet: The following reagents were purchased as indicated: Bst 2.0 DNA polymerase large fragment (New England Biolabs, Guangzhou Ltd., Guangzhou, China), Avian Myeloblastosis Virus Reverse Transcriptase (Promega Corporation, Madison, WI, USA), dNTPs (TransGen Biotech Co., Ltd., Beijing, China), RNAiso Plus (Takara Biotechnology Co., Ltd., Dalian, China), betaine (Sigma-Aldrich; EMD Millipore, Billerica, MA, USA), SYBR-Green I (SG I) fluorescent dye (Beijing Solarbio Science & Technology Co., Ltd., Beijing, China), PCR SuperMix (TransGen Biotech Co., Ltd.), and primers synthesized by Sangon Biotech Co., Ltd. (Shanghai, China).

    Techniques: Lamp Assay, Agarose Gel Electrophoresis, SYBR Green Assay, Reverse Transcription Polymerase Chain Reaction, Amplification, Marker, Plasmid Preparation, Negative Control

    Specificity comparison of the LAMP assay and conventional PCR. (A) LAMP products detected by 1000 × SYBR Green I. (B) PCR products detected by agarose gel electrophoresis stained by EB. Tube and lane 1: ddH 2 O. Tube and lane 2: the plasmid 1Ac0229 (positive control). Tubes and lanes 3–10: genomic DNA from sugarcane genotypes of a1 ( bar transgenic line from host cultivar FN15), 16k-2 ( bar transgenic line from host cultivar ROC22), FN15 ( S . spp. hybrids), ROC22 ( S . spp. hybrids), ROC10 ( S . spp. hybrids), Badila ( S. officinarum ), 82-114 ( S. spontaneum ), 57NG208 ( S. robustum ), respectively. Lane M: 100 bp DNA.

    Journal: Frontiers in Plant Science

    Article Title: Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay

    doi: 10.3389/fpls.2016.00279

    Figure Lengend Snippet: Specificity comparison of the LAMP assay and conventional PCR. (A) LAMP products detected by 1000 × SYBR Green I. (B) PCR products detected by agarose gel electrophoresis stained by EB. Tube and lane 1: ddH 2 O. Tube and lane 2: the plasmid 1Ac0229 (positive control). Tubes and lanes 3–10: genomic DNA from sugarcane genotypes of a1 ( bar transgenic line from host cultivar FN15), 16k-2 ( bar transgenic line from host cultivar ROC22), FN15 ( S . spp. hybrids), ROC22 ( S . spp. hybrids), ROC10 ( S . spp. hybrids), Badila ( S. officinarum ), 82-114 ( S. spontaneum ), 57NG208 ( S. robustum ), respectively. Lane M: 100 bp DNA.

    Article Snippet: Following amplification by the LAMP method, the products were detected by the addition of 2.0 μL 1000 × SYBR Green I (Bio-tek Co., Ltd., Beijing, China) to the cap center of the tubes as reported by Zhou et al. ( ).

    Techniques: Lamp Assay, Polymerase Chain Reaction, SYBR Green Assay, Agarose Gel Electrophoresis, Staining, Plasmid Preparation, Positive Control, Transgenic Assay

    Optimization of ratios of inner vs. outer primers for the LAMP reaction of the bar transgene. (A) LAMP products detected by 1000 × SYBR Green I. (B) The amplification curves obtained in real-time LAMP based on different ratios of inner and outer primers. (A) Tubes 1, 2, 7, 8, 13, 14, 19, and 20: ddH 2 O. Tubes 3, 4, 9, 10, 15, 16, 21, and 22: FN95-1702 (negative control, CK). Tubes 5, 6, 11, 12, 17, 18, 23, and 24: the plasmid 1Ac0229. Tubes 1–6, 7–12, 13–18, and 19–24: Ratio of inner and outer primers is 2:1, 4: 1, 6: 1, and 8:1, respectively, two technical replicates. (B) Curves separately represent the ratios of inner and outer primers of 8:1, 6: 1, 4: 1, and 2:1, from left to right. The lines representing the blank and negative controls could not be observed at the bottom of this graph.

    Journal: Frontiers in Plant Science

    Article Title: Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay

    doi: 10.3389/fpls.2016.00279

    Figure Lengend Snippet: Optimization of ratios of inner vs. outer primers for the LAMP reaction of the bar transgene. (A) LAMP products detected by 1000 × SYBR Green I. (B) The amplification curves obtained in real-time LAMP based on different ratios of inner and outer primers. (A) Tubes 1, 2, 7, 8, 13, 14, 19, and 20: ddH 2 O. Tubes 3, 4, 9, 10, 15, 16, 21, and 22: FN95-1702 (negative control, CK). Tubes 5, 6, 11, 12, 17, 18, 23, and 24: the plasmid 1Ac0229. Tubes 1–6, 7–12, 13–18, and 19–24: Ratio of inner and outer primers is 2:1, 4: 1, 6: 1, and 8:1, respectively, two technical replicates. (B) Curves separately represent the ratios of inner and outer primers of 8:1, 6: 1, 4: 1, and 2:1, from left to right. The lines representing the blank and negative controls could not be observed at the bottom of this graph.

    Article Snippet: Following amplification by the LAMP method, the products were detected by the addition of 2.0 μL 1000 × SYBR Green I (Bio-tek Co., Ltd., Beijing, China) to the cap center of the tubes as reported by Zhou et al. ( ).

    Techniques: SYBR Green Assay, Amplification, Negative Control, Plasmid Preparation

    Optimization of Bst DNA polymerase concentration for the LAMP reaction of the bar transgene. (A) LAMP products detected by 1000 × SYBR Green I. (B) The amplification curves obtained in real-time LAMP based on different dosage of Bst DNA polymerase. (A) Tubes 1, 2, 7, 8, 13, 14, 19, and 20: ddH 2 O. Tubes 3, 4, 9, 10, 15, 16, 21, and 22: FN95-1702 (negative control, CK). Tubes 5, 6, 11, 12, 17, 18, 23 and 24: the plasmid 1Ac0229. Tubes 1–6, 7–12, 13–18, and 19–24: Bst DNA polymerase concentrations of 2.0, 4.0, 6.0, and 8.0 U, respectively, two repeats. (B) Curves separately represent the dosage of Bst DNA polymerase of 8.0, 6.0, 4.0, and 2.0 U, from left to right. The colored line at the very bottom indicates the blank and negative controls.

    Journal: Frontiers in Plant Science

    Article Title: Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay

    doi: 10.3389/fpls.2016.00279

    Figure Lengend Snippet: Optimization of Bst DNA polymerase concentration for the LAMP reaction of the bar transgene. (A) LAMP products detected by 1000 × SYBR Green I. (B) The amplification curves obtained in real-time LAMP based on different dosage of Bst DNA polymerase. (A) Tubes 1, 2, 7, 8, 13, 14, 19, and 20: ddH 2 O. Tubes 3, 4, 9, 10, 15, 16, 21, and 22: FN95-1702 (negative control, CK). Tubes 5, 6, 11, 12, 17, 18, 23 and 24: the plasmid 1Ac0229. Tubes 1–6, 7–12, 13–18, and 19–24: Bst DNA polymerase concentrations of 2.0, 4.0, 6.0, and 8.0 U, respectively, two repeats. (B) Curves separately represent the dosage of Bst DNA polymerase of 8.0, 6.0, 4.0, and 2.0 U, from left to right. The colored line at the very bottom indicates the blank and negative controls.

    Article Snippet: Following amplification by the LAMP method, the products were detected by the addition of 2.0 μL 1000 × SYBR Green I (Bio-tek Co., Ltd., Beijing, China) to the cap center of the tubes as reported by Zhou et al. ( ).

    Techniques: Concentration Assay, SYBR Green Assay, Amplification, Negative Control, Plasmid Preparation

    Sensitivity comparison of the LAMP assay and conventional PCR using the plasmid 1Ac0229 as templates. (A) LAMP products detected by 1000 × SYBR Green I. (B) PCR products detected by agarose gel electrophoresis stained by EB. Tube and lane 1: ddH 2 O. Tube and lane 2: FN95-1702 (negative control, CK). Tubes and lanes 3–12: plasmid 1Ac0229 copies of 1.0 × 10 9 , 1.0 × 10 8 , 1.0 × 10 7 , 1.0 × 10 6 , 1.0 × 10 5 , 1.0 × 10 4 , 1.0 × 10 3 , 1.0 × 10 2 , 1.0 × 10 1 , and 1.0 × 10 0 , respectively. Lane M: 50 bp DNA marker.

    Journal: Frontiers in Plant Science

    Article Title: Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay

    doi: 10.3389/fpls.2016.00279

    Figure Lengend Snippet: Sensitivity comparison of the LAMP assay and conventional PCR using the plasmid 1Ac0229 as templates. (A) LAMP products detected by 1000 × SYBR Green I. (B) PCR products detected by agarose gel electrophoresis stained by EB. Tube and lane 1: ddH 2 O. Tube and lane 2: FN95-1702 (negative control, CK). Tubes and lanes 3–12: plasmid 1Ac0229 copies of 1.0 × 10 9 , 1.0 × 10 8 , 1.0 × 10 7 , 1.0 × 10 6 , 1.0 × 10 5 , 1.0 × 10 4 , 1.0 × 10 3 , 1.0 × 10 2 , 1.0 × 10 1 , and 1.0 × 10 0 , respectively. Lane M: 50 bp DNA marker.

    Article Snippet: Following amplification by the LAMP method, the products were detected by the addition of 2.0 μL 1000 × SYBR Green I (Bio-tek Co., Ltd., Beijing, China) to the cap center of the tubes as reported by Zhou et al. ( ).

    Techniques: Lamp Assay, Polymerase Chain Reaction, Plasmid Preparation, SYBR Green Assay, Agarose Gel Electrophoresis, Staining, Negative Control, Marker

    LAMP and conventional PCR detection results of 100 putative bar transgenic sugarcane lines. (A) LAMP products detected by 1000 × SYBR Green I under white light. (B) PCR products detected by agarose gel electrophoresis stained by EB. Tube and lane H 2 O: ddH 2 O. Tube and lane CK: FN95-1702 (negative control). Tube and lane 1Ac: the plasmid 1Ac0229 (positive control). Tubes and Lanes 1–100: the 17 putative bar transgenic sugarcane lines in order of p1 ~ p100. Lane M: 100 bp DNA ladder.

    Journal: Frontiers in Plant Science

    Article Title: Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay

    doi: 10.3389/fpls.2016.00279

    Figure Lengend Snippet: LAMP and conventional PCR detection results of 100 putative bar transgenic sugarcane lines. (A) LAMP products detected by 1000 × SYBR Green I under white light. (B) PCR products detected by agarose gel electrophoresis stained by EB. Tube and lane H 2 O: ddH 2 O. Tube and lane CK: FN95-1702 (negative control). Tube and lane 1Ac: the plasmid 1Ac0229 (positive control). Tubes and Lanes 1–100: the 17 putative bar transgenic sugarcane lines in order of p1 ~ p100. Lane M: 100 bp DNA ladder.

    Article Snippet: Following amplification by the LAMP method, the products were detected by the addition of 2.0 μL 1000 × SYBR Green I (Bio-tek Co., Ltd., Beijing, China) to the cap center of the tubes as reported by Zhou et al. ( ).

    Techniques: Polymerase Chain Reaction, Transgenic Assay, SYBR Green Assay, Agarose Gel Electrophoresis, Staining, Negative Control, Plasmid Preparation, Positive Control

    Optimization of Mg 2+ concentration for the LAMP reaction of the bar transgene. (A) LAMP products detected by 1000 × SYBR Green I. (B) The amplification curves obtained in real-time LAMP based on different Mg 2+ concentrations. (A) : Tubes 1, 2, 7, 8, 13, 14, 19, 20, 25, and 26: ddH 2 O. Tubes 3, 4, 9, 10, 15, 16, 21, 22, 27, and 28: FN95-1702 (negative control, CK). Tubes 5, 6, 11, 12, 17, 18, 23, 24, 29, and 30: the plasmid 1Ac0229. Tubes 1–6, 7–12, 13–18, 19–24, and 25–30: Concentration of Mg 2+ is 4.75, 5.00, 5.25, 5.50, and 5.75 mM, respectively, two technical replicates. (B) Curves separately represent the Mg 2+ concentrations of 5.75, 5.5, 5.25, 5.00, and 4.75 mM, from left to right. The colored line at the very bottom indicates the blank and negative controls.

    Journal: Frontiers in Plant Science

    Article Title: Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay

    doi: 10.3389/fpls.2016.00279

    Figure Lengend Snippet: Optimization of Mg 2+ concentration for the LAMP reaction of the bar transgene. (A) LAMP products detected by 1000 × SYBR Green I. (B) The amplification curves obtained in real-time LAMP based on different Mg 2+ concentrations. (A) : Tubes 1, 2, 7, 8, 13, 14, 19, 20, 25, and 26: ddH 2 O. Tubes 3, 4, 9, 10, 15, 16, 21, 22, 27, and 28: FN95-1702 (negative control, CK). Tubes 5, 6, 11, 12, 17, 18, 23, 24, 29, and 30: the plasmid 1Ac0229. Tubes 1–6, 7–12, 13–18, 19–24, and 25–30: Concentration of Mg 2+ is 4.75, 5.00, 5.25, 5.50, and 5.75 mM, respectively, two technical replicates. (B) Curves separately represent the Mg 2+ concentrations of 5.75, 5.5, 5.25, 5.00, and 4.75 mM, from left to right. The colored line at the very bottom indicates the blank and negative controls.

    Article Snippet: Following amplification by the LAMP method, the products were detected by the addition of 2.0 μL 1000 × SYBR Green I (Bio-tek Co., Ltd., Beijing, China) to the cap center of the tubes as reported by Zhou et al. ( ).

    Techniques: Concentration Assay, SYBR Green Assay, Amplification, Negative Control, Plasmid Preparation

    Exposure of spirochetal form and amoxicillin-induced round bodies of B. burgdorferi (5-day old) to different antibiotics. Log phase spirochetal form (5 day old) and amoxicillin-induced round bodies of B. burgdorferi (5-day old) were exposed to 50 μM doxycycline, cefuroxime, and ceftriaxone, respectively, for 5 days. The percentage of residual live cells ( n = 3) was determined by SYBR Green I/PI assay followed by fluorescence microscopy counting.

    Journal: Frontiers in Microbiology

    Article Title: A Drug Combination Screen Identifies Drugs Active against Amoxicillin-Induced Round Bodies of In Vitro Borrelia burgdorferi Persisters from an FDA Drug Library

    doi: 10.3389/fmicb.2016.00743

    Figure Lengend Snippet: Exposure of spirochetal form and amoxicillin-induced round bodies of B. burgdorferi (5-day old) to different antibiotics. Log phase spirochetal form (5 day old) and amoxicillin-induced round bodies of B. burgdorferi (5-day old) were exposed to 50 μM doxycycline, cefuroxime, and ceftriaxone, respectively, for 5 days. The percentage of residual live cells ( n = 3) was determined by SYBR Green I/PI assay followed by fluorescence microscopy counting.

    Article Snippet: Cell proliferation was assessed using SYBR Green I/PI assay and bacterial counting chamber (Hausser Scientific Partnership, Horsham, PA, USA) by microscopy as described above.

    Techniques: SYBR Green Assay, Fluorescence, Microscopy

    Representative images (400 × magnification) of amoxicillin-induced round body form of B. burgdorferi treated with different antibiotics (labeled on the image). A 6- day old culture was induced with 50 μg/ml amoxicillin for 72 h and subsequently treated with the listed antibiotics (50 μM) for 7 days followed by staining with SYBR Green I/PI assay and fluorescence microscopy.

    Journal: Frontiers in Microbiology

    Article Title: A Drug Combination Screen Identifies Drugs Active against Amoxicillin-Induced Round Bodies of In Vitro Borrelia burgdorferi Persisters from an FDA Drug Library

    doi: 10.3389/fmicb.2016.00743

    Figure Lengend Snippet: Representative images (400 × magnification) of amoxicillin-induced round body form of B. burgdorferi treated with different antibiotics (labeled on the image). A 6- day old culture was induced with 50 μg/ml amoxicillin for 72 h and subsequently treated with the listed antibiotics (50 μM) for 7 days followed by staining with SYBR Green I/PI assay and fluorescence microscopy.

    Article Snippet: Cell proliferation was assessed using SYBR Green I/PI assay and bacterial counting chamber (Hausser Scientific Partnership, Horsham, PA, USA) by microscopy as described above.

    Techniques: Labeling, Staining, SYBR Green Assay, Fluorescence, Microscopy

    Effect of antibiotics alone or in combinations on stationary phase B. burgdorferi strain B31 (A) and strain 297 (B) microcolonies. Stationary phase culture of B. burgdorferi (10-day old) was treated with 10 μg/ml drugs alone or in combinations (labeled on the image) for 7 days followed by staining with SYBR Green I/PI assay and epifluorescence microscopy (200 × magnification). Green cells indicate live cells whereas red cells dead cells. Abbreviation: Dox, doxycycline; CefP, cefoperazone; Art, Artemisinin; Dap, daptomycin; CefM, cefmetazole; Scp, sulfachlorpyridazine.

    Journal: Frontiers in Microbiology

    Article Title: A Drug Combination Screen Identifies Drugs Active against Amoxicillin-Induced Round Bodies of In Vitro Borrelia burgdorferi Persisters from an FDA Drug Library

    doi: 10.3389/fmicb.2016.00743

    Figure Lengend Snippet: Effect of antibiotics alone or in combinations on stationary phase B. burgdorferi strain B31 (A) and strain 297 (B) microcolonies. Stationary phase culture of B. burgdorferi (10-day old) was treated with 10 μg/ml drugs alone or in combinations (labeled on the image) for 7 days followed by staining with SYBR Green I/PI assay and epifluorescence microscopy (200 × magnification). Green cells indicate live cells whereas red cells dead cells. Abbreviation: Dox, doxycycline; CefP, cefoperazone; Art, Artemisinin; Dap, daptomycin; CefM, cefmetazole; Scp, sulfachlorpyridazine.

    Article Snippet: Cell proliferation was assessed using SYBR Green I/PI assay and bacterial counting chamber (Hausser Scientific Partnership, Horsham, PA, USA) by microscopy as described above.

    Techniques: Labeling, Staining, SYBR Green Assay, Epifluorescence Microscopy

    Subculture of amoxicillin-induced round bodies of B. burgdorferi after treatment with different antibiotics alone or in combinations (labeled on the image). Six day old of B. burgdorferi culture was induced with 50 μg/ml amoxicillin for 72 h to form round bodies, which were then treated with single antibiotics alone or in combination. Representative images (200 × magnification) were taken with fluorescence microscopy using SYBR Green I/PI staining. Only Dox + Dap + CefP completely killed all round body B. burgdorferi persisters as shown by lack of any viable green spirochetes after 20-day subculture. Abbreviation: Dox, doxycycline; CefP, cefoperazone; Dap, daptomycin; Art: artemisinin; Scp, sulfachlorpyridazine.

    Journal: Frontiers in Microbiology

    Article Title: A Drug Combination Screen Identifies Drugs Active against Amoxicillin-Induced Round Bodies of In Vitro Borrelia burgdorferi Persisters from an FDA Drug Library

    doi: 10.3389/fmicb.2016.00743

    Figure Lengend Snippet: Subculture of amoxicillin-induced round bodies of B. burgdorferi after treatment with different antibiotics alone or in combinations (labeled on the image). Six day old of B. burgdorferi culture was induced with 50 μg/ml amoxicillin for 72 h to form round bodies, which were then treated with single antibiotics alone or in combination. Representative images (200 × magnification) were taken with fluorescence microscopy using SYBR Green I/PI staining. Only Dox + Dap + CefP completely killed all round body B. burgdorferi persisters as shown by lack of any viable green spirochetes after 20-day subculture. Abbreviation: Dox, doxycycline; CefP, cefoperazone; Dap, daptomycin; Art: artemisinin; Scp, sulfachlorpyridazine.

    Article Snippet: Cell proliferation was assessed using SYBR Green I/PI assay and bacterial counting chamber (Hausser Scientific Partnership, Horsham, PA, USA) by microscopy as described above.

    Techniques: Labeling, Fluorescence, Microscopy, SYBR Green Assay, Staining