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  • 96
    Covaris truxtrac ffpe dna kit
    Truxtrac Ffpe Dna Kit, supplied by Covaris, used in various techniques. Bioz Stars score: 96/100, based on 67 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Valiant total dna
    Total Dna, supplied by Valiant, used in various techniques. Bioz Stars score: 99/100, based on 879 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher cdna synthesis total rna
    Cdna Synthesis Total Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 4336 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega maxwell 16 tissue dna purification kit
    Maxwell 16 Tissue Dna Purification Kit, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 1031 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher total genomic dna
    Total Genomic Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1534 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad total dna
    Total Dna, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 856 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore total genomic dna
    Total Genomic Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 602 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher total dna
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    Gentra Systems total dna
    Total Dna, supplied by Gentra Systems, used in various techniques. Bioz Stars score: 92/100, based on 278 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega total dna
    Total Dna, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 2156 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Omega Bio-tek total dna
    Phylogenetic trees of plasma HIV-1 RNA and PBMC HIV-1 <t>DNA</t> sequences from all patients included in the study. DOI: http://dx.doi.org/10.7554/eLife.18889.005
    Total Dna, supplied by Omega Bio-tek, used in various techniques. Bioz Stars score: 92/100, based on 333 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    iNtRON Biotechnology g spin total dna extraction kit
    Mechanistic study of the anti-inflammasome property of riboflavin. ( A ) LPS-primed BMDMs were treated with rotenone (Rot) with/without riboflavin (B2). The maturation and secretion of IL-1β and Casp1 were analyzed by immunoblotting and the secretion of IL-1β was analyzed by ELISA. Diphenyleneiodonium chloride (DPI) was used as a ROS scavenger. ( B ) LPS-primed BMDMs were treated with ATP in the presence of B2. The <t>cytosolic</t> release of mitochondrial <t>DNA</t> (mtDNA, cytochrome c oxygenase 1/18S rDNA) was measured by quantitative real-time PCR. ( C ) The activity of human recombinant caspase-1 (hrCasp1) in the presence of B2 was measured using a commercial kit, which is a modified luciferase assay. Briefly, hrCasp1 catalyzes Z-WEHD-aminoluciferin to aminoluciferin, a substrate of luciferase, resulting in the generation of light, which represents the activity of Casp1. Ac-YVAD-CHO (YVAD, the kit supplied) was utilized as a caspase-1 inhibitor. All immunoblot data shown are representative of at least two independent experiments. The bar graph presents the mean ± SD with at least two independent experiments.
    G Spin Total Dna Extraction Kit, supplied by iNtRON Biotechnology, used in various techniques. Bioz Stars score: 88/100, based on 142 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    iNtRON Biotechnology megaquick spin total fragment dna purification kit
    Mechanistic study of the anti-inflammasome property of riboflavin. ( A ) LPS-primed BMDMs were treated with rotenone (Rot) with/without riboflavin (B2). The maturation and secretion of IL-1β and Casp1 were analyzed by immunoblotting and the secretion of IL-1β was analyzed by ELISA. Diphenyleneiodonium chloride (DPI) was used as a ROS scavenger. ( B ) LPS-primed BMDMs were treated with ATP in the presence of B2. The <t>cytosolic</t> release of mitochondrial <t>DNA</t> (mtDNA, cytochrome c oxygenase 1/18S rDNA) was measured by quantitative real-time PCR. ( C ) The activity of human recombinant caspase-1 (hrCasp1) in the presence of B2 was measured using a commercial kit, which is a modified luciferase assay. Briefly, hrCasp1 catalyzes Z-WEHD-aminoluciferin to aminoluciferin, a substrate of luciferase, resulting in the generation of light, which represents the activity of Casp1. Ac-YVAD-CHO (YVAD, the kit supplied) was utilized as a caspase-1 inhibitor. All immunoblot data shown are representative of at least two independent experiments. The bar graph presents the mean ± SD with at least two independent experiments.
    Megaquick Spin Total Fragment Dna Purification Kit, supplied by iNtRON Biotechnology, used in various techniques. Bioz Stars score: 89/100, based on 302 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher purelink plant total dna purification kit
    Mechanistic study of the anti-inflammasome property of riboflavin. ( A ) LPS-primed BMDMs were treated with rotenone (Rot) with/without riboflavin (B2). The maturation and secretion of IL-1β and Casp1 were analyzed by immunoblotting and the secretion of IL-1β was analyzed by ELISA. Diphenyleneiodonium chloride (DPI) was used as a ROS scavenger. ( B ) LPS-primed BMDMs were treated with ATP in the presence of B2. The <t>cytosolic</t> release of mitochondrial <t>DNA</t> (mtDNA, cytochrome c oxygenase 1/18S rDNA) was measured by quantitative real-time PCR. ( C ) The activity of human recombinant caspase-1 (hrCasp1) in the presence of B2 was measured using a commercial kit, which is a modified luciferase assay. Briefly, hrCasp1 catalyzes Z-WEHD-aminoluciferin to aminoluciferin, a substrate of luciferase, resulting in the generation of light, which represents the activity of Casp1. Ac-YVAD-CHO (YVAD, the kit supplied) was utilized as a caspase-1 inhibitor. All immunoblot data shown are representative of at least two independent experiments. The bar graph presents the mean ± SD with at least two independent experiments.
    Purelink Plant Total Dna Purification Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 272 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs total dna
    Mechanistic study of the anti-inflammasome property of riboflavin. ( A ) LPS-primed BMDMs were treated with rotenone (Rot) with/without riboflavin (B2). The maturation and secretion of IL-1β and Casp1 were analyzed by immunoblotting and the secretion of IL-1β was analyzed by ELISA. Diphenyleneiodonium chloride (DPI) was used as a ROS scavenger. ( B ) LPS-primed BMDMs were treated with ATP in the presence of B2. The <t>cytosolic</t> release of mitochondrial <t>DNA</t> (mtDNA, cytochrome c oxygenase 1/18S rDNA) was measured by quantitative real-time PCR. ( C ) The activity of human recombinant caspase-1 (hrCasp1) in the presence of B2 was measured using a commercial kit, which is a modified luciferase assay. Briefly, hrCasp1 catalyzes Z-WEHD-aminoluciferin to aminoluciferin, a substrate of luciferase, resulting in the generation of light, which represents the activity of Casp1. Ac-YVAD-CHO (YVAD, the kit supplied) was utilized as a caspase-1 inhibitor. All immunoblot data shown are representative of at least two independent experiments. The bar graph presents the mean ± SD with at least two independent experiments.
    Total Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 375 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher total dna concentration
    Mechanistic study of the anti-inflammasome property of riboflavin. ( A ) LPS-primed BMDMs were treated with rotenone (Rot) with/without riboflavin (B2). The maturation and secretion of IL-1β and Casp1 were analyzed by immunoblotting and the secretion of IL-1β was analyzed by ELISA. Diphenyleneiodonium chloride (DPI) was used as a ROS scavenger. ( B ) LPS-primed BMDMs were treated with ATP in the presence of B2. The <t>cytosolic</t> release of mitochondrial <t>DNA</t> (mtDNA, cytochrome c oxygenase 1/18S rDNA) was measured by quantitative real-time PCR. ( C ) The activity of human recombinant caspase-1 (hrCasp1) in the presence of B2 was measured using a commercial kit, which is a modified luciferase assay. Briefly, hrCasp1 catalyzes Z-WEHD-aminoluciferin to aminoluciferin, a substrate of luciferase, resulting in the generation of light, which represents the activity of Casp1. Ac-YVAD-CHO (YVAD, the kit supplied) was utilized as a caspase-1 inhibitor. All immunoblot data shown are representative of at least two independent experiments. The bar graph presents the mean ± SD with at least two independent experiments.
    Total Dna Concentration, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies total dna
    Production of 2-LTR circles in infected cells. Recombinant viruses were used to infect HeLa cells, and at the indicated times, the levels of 2-LTR circles were measured by real-time <t>PCR.</t> Both a standard probe (2-LTR), which detects all 2-LTR circles, and a probe (JNCT) specific for canonical 2-LTR junctions were used. Some infected cells were treated with 1 μM raltegravir (Ral). The results for infections by wild-type (WT) SIVmac239 (A) and the A87E (B) and A87D (C) mutants are shown. The values shown represent the percentages of the maximum wild-type SIVmac239 value (823 copies/100 ng <t>DNA</t> at 24 h postinfection after raltegravir treatment). The results shown represent the averages and standard deviations derived from three independent infections.
    Total Dna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 129 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen total dna
    Production of 2-LTR circles in infected cells. Recombinant viruses were used to infect HeLa cells, and at the indicated times, the levels of 2-LTR circles were measured by real-time <t>PCR.</t> Both a standard probe (2-LTR), which detects all 2-LTR circles, and a probe (JNCT) specific for canonical 2-LTR junctions were used. Some infected cells were treated with 1 μM raltegravir (Ral). The results for infections by wild-type (WT) SIVmac239 (A) and the A87E (B) and A87D (C) mutants are shown. The values shown represent the percentages of the maximum wild-type SIVmac239 value (823 copies/100 ng <t>DNA</t> at 24 h postinfection after raltegravir treatment). The results shown represent the averages and standard deviations derived from three independent infections.
    Total Dna, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 18738 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    N/A
    RNAMATRIX is a proprietary silica based binding matrix that selectively binds RNA for purification It is in a suspension that allows for flexibility in RNA binding capacities
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    The RapidPURE RNA Plant Kit is designed to isolate and purify high quality total RNA from plant cells plant tissues and filamentous fungi in a spin filter format Special buffer
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    Image Search Results


    Phylogenetic trees of plasma HIV-1 RNA and PBMC HIV-1 DNA sequences from all patients included in the study. DOI: http://dx.doi.org/10.7554/eLife.18889.005

    Journal: eLife

    Article Title: Establishment and stability of the latent HIV-1 DNA reservoir

    doi: 10.7554/eLife.18889

    Figure Lengend Snippet: Phylogenetic trees of plasma HIV-1 RNA and PBMC HIV-1 DNA sequences from all patients included in the study. DOI: http://dx.doi.org/10.7554/eLife.18889.005

    Article Snippet: Total DNA was extracted from the PBMCs using the OMEGA E.Z.N.A Blood DNA Mini Kit (Omega Bio-Tek, Norcross, Georgia) or the QIAamp DNA Blood Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions.

    Techniques:

    Sampling times before and after start of suppressive antiretroviral therapy. For each study participant, the thick grey bar indicates the period of untreated HIV-1 replication. Circles indicate the collection times of the plasma samples used for whole genome deep sequencing of the HIV-1 RNA populations ( Zanini et al., 2015 ). Triangles and squares indicate the collection times of the PBMC samples used for p17gag deep sequencing of the HIV-1 DNA populations. All times are relative to start of therapy. DOI: http://dx.doi.org/10.7554/eLife.18889.002

    Journal: eLife

    Article Title: Establishment and stability of the latent HIV-1 DNA reservoir

    doi: 10.7554/eLife.18889

    Figure Lengend Snippet: Sampling times before and after start of suppressive antiretroviral therapy. For each study participant, the thick grey bar indicates the period of untreated HIV-1 replication. Circles indicate the collection times of the plasma samples used for whole genome deep sequencing of the HIV-1 RNA populations ( Zanini et al., 2015 ). Triangles and squares indicate the collection times of the PBMC samples used for p17gag deep sequencing of the HIV-1 DNA populations. All times are relative to start of therapy. DOI: http://dx.doi.org/10.7554/eLife.18889.002

    Article Snippet: Total DNA was extracted from the PBMCs using the OMEGA E.Z.N.A Blood DNA Mini Kit (Omega Bio-Tek, Norcross, Georgia) or the QIAamp DNA Blood Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions.

    Techniques: Sampling, Sequencing

    The distribution of plausible seeding times of reservoir HIV-1 DNA sequences for all 10 patients. For each HIV-1 DNA read obtained from the PBMCs, the plasma sample and HIV-1 RNA variant from which the read was most likely derived was determined. The plots present the distributions of these most likely origin samples across all available RNA samples. DOI: http://dx.doi.org/10.7554/eLife.18889.014

    Journal: eLife

    Article Title: Establishment and stability of the latent HIV-1 DNA reservoir

    doi: 10.7554/eLife.18889

    Figure Lengend Snippet: The distribution of plausible seeding times of reservoir HIV-1 DNA sequences for all 10 patients. For each HIV-1 DNA read obtained from the PBMCs, the plasma sample and HIV-1 RNA variant from which the read was most likely derived was determined. The plots present the distributions of these most likely origin samples across all available RNA samples. DOI: http://dx.doi.org/10.7554/eLife.18889.014

    Article Snippet: Total DNA was extracted from the PBMCs using the OMEGA E.Z.N.A Blood DNA Mini Kit (Omega Bio-Tek, Norcross, Georgia) or the QIAamp DNA Blood Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions.

    Techniques: Variant Assay, Derivative Assay

    Mean root-to-tip distances for plasma HIV-1 RNA sequences obtained before the start of antiretroviral therapy (ART) and PBMC HIV-1 DNA sequences obtained after the start of ART. This figure is analogous to Figure 3 in the main text. Instead of weighing each sequence by its number of reads, each sequence was counted only once. The two approaches yielded similar results. The grey cone in the upper right quadrant indicates the rate of evolution during suppressive therapy estimated by Lorenzo-Redondo et al. (2016) . DOI: http://dx.doi.org/10.7554/eLife.18889.010

    Journal: eLife

    Article Title: Establishment and stability of the latent HIV-1 DNA reservoir

    doi: 10.7554/eLife.18889

    Figure Lengend Snippet: Mean root-to-tip distances for plasma HIV-1 RNA sequences obtained before the start of antiretroviral therapy (ART) and PBMC HIV-1 DNA sequences obtained after the start of ART. This figure is analogous to Figure 3 in the main text. Instead of weighing each sequence by its number of reads, each sequence was counted only once. The two approaches yielded similar results. The grey cone in the upper right quadrant indicates the rate of evolution during suppressive therapy estimated by Lorenzo-Redondo et al. (2016) . DOI: http://dx.doi.org/10.7554/eLife.18889.010

    Article Snippet: Total DNA was extracted from the PBMCs using the OMEGA E.Z.N.A Blood DNA Mini Kit (Omega Bio-Tek, Norcross, Georgia) or the QIAamp DNA Blood Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions.

    Techniques: Sequencing

    Mean root-to-tip distances for plasma HIV-1 RNA sequences obtained before the start of ART and PBMC HIV-1 DNA sequences obtained after the start of ART. This figure is analogous to Figure 3 in the main text, but presents root-to-tip distance values for DNA sequences classified as hypermutants. The root-to-tip distances of the hypermutant HIV-1 DNA sequences were approximately 2 and 4% greater than the non-hypermutant sequences from the same samples, but the root-to-tip distances did not change over time. DOI: http://dx.doi.org/10.7554/eLife.18889.009

    Journal: eLife

    Article Title: Establishment and stability of the latent HIV-1 DNA reservoir

    doi: 10.7554/eLife.18889

    Figure Lengend Snippet: Mean root-to-tip distances for plasma HIV-1 RNA sequences obtained before the start of ART and PBMC HIV-1 DNA sequences obtained after the start of ART. This figure is analogous to Figure 3 in the main text, but presents root-to-tip distance values for DNA sequences classified as hypermutants. The root-to-tip distances of the hypermutant HIV-1 DNA sequences were approximately 2 and 4% greater than the non-hypermutant sequences from the same samples, but the root-to-tip distances did not change over time. DOI: http://dx.doi.org/10.7554/eLife.18889.009

    Article Snippet: Total DNA was extracted from the PBMCs using the OMEGA E.Z.N.A Blood DNA Mini Kit (Omega Bio-Tek, Norcross, Georgia) or the QIAamp DNA Blood Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions.

    Techniques:

    Mechanistic study of the anti-inflammasome property of riboflavin. ( A ) LPS-primed BMDMs were treated with rotenone (Rot) with/without riboflavin (B2). The maturation and secretion of IL-1β and Casp1 were analyzed by immunoblotting and the secretion of IL-1β was analyzed by ELISA. Diphenyleneiodonium chloride (DPI) was used as a ROS scavenger. ( B ) LPS-primed BMDMs were treated with ATP in the presence of B2. The cytosolic release of mitochondrial DNA (mtDNA, cytochrome c oxygenase 1/18S rDNA) was measured by quantitative real-time PCR. ( C ) The activity of human recombinant caspase-1 (hrCasp1) in the presence of B2 was measured using a commercial kit, which is a modified luciferase assay. Briefly, hrCasp1 catalyzes Z-WEHD-aminoluciferin to aminoluciferin, a substrate of luciferase, resulting in the generation of light, which represents the activity of Casp1. Ac-YVAD-CHO (YVAD, the kit supplied) was utilized as a caspase-1 inhibitor. All immunoblot data shown are representative of at least two independent experiments. The bar graph presents the mean ± SD with at least two independent experiments.

    Journal: Scientific Reports

    Article Title: Riboflavin, vitamin B2, attenuates NLRP3, NLRC4, AIM2, and non-canonical inflammasomes by the inhibition of caspase-1 activity

    doi: 10.1038/s41598-020-76251-7

    Figure Lengend Snippet: Mechanistic study of the anti-inflammasome property of riboflavin. ( A ) LPS-primed BMDMs were treated with rotenone (Rot) with/without riboflavin (B2). The maturation and secretion of IL-1β and Casp1 were analyzed by immunoblotting and the secretion of IL-1β was analyzed by ELISA. Diphenyleneiodonium chloride (DPI) was used as a ROS scavenger. ( B ) LPS-primed BMDMs were treated with ATP in the presence of B2. The cytosolic release of mitochondrial DNA (mtDNA, cytochrome c oxygenase 1/18S rDNA) was measured by quantitative real-time PCR. ( C ) The activity of human recombinant caspase-1 (hrCasp1) in the presence of B2 was measured using a commercial kit, which is a modified luciferase assay. Briefly, hrCasp1 catalyzes Z-WEHD-aminoluciferin to aminoluciferin, a substrate of luciferase, resulting in the generation of light, which represents the activity of Casp1. Ac-YVAD-CHO (YVAD, the kit supplied) was utilized as a caspase-1 inhibitor. All immunoblot data shown are representative of at least two independent experiments. The bar graph presents the mean ± SD with at least two independent experiments.

    Article Snippet: The cytosolic fraction was prepared by centrifugation at 15,000 rcf for 30 min at 4 °C, and the cytosolic DNA was harvested using a G-spin total DNA extraction kit (Intron Biotechnology, Gyeonggi-do, Republic of Korea) .

    Techniques: Enzyme-linked Immunosorbent Assay, Real-time Polymerase Chain Reaction, Activity Assay, Recombinant, Modification, Luciferase

    Production of 2-LTR circles in infected cells. Recombinant viruses were used to infect HeLa cells, and at the indicated times, the levels of 2-LTR circles were measured by real-time PCR. Both a standard probe (2-LTR), which detects all 2-LTR circles, and a probe (JNCT) specific for canonical 2-LTR junctions were used. Some infected cells were treated with 1 μM raltegravir (Ral). The results for infections by wild-type (WT) SIVmac239 (A) and the A87E (B) and A87D (C) mutants are shown. The values shown represent the percentages of the maximum wild-type SIVmac239 value (823 copies/100 ng DNA at 24 h postinfection after raltegravir treatment). The results shown represent the averages and standard deviations derived from three independent infections.

    Journal: Journal of Virology

    Article Title: Enhanced Autointegration in Hyperstable Simian Immunodeficiency Virus Capsid Mutants Blocked after Reverse Transcription

    doi: 10.1128/JVI.03239-12

    Figure Lengend Snippet: Production of 2-LTR circles in infected cells. Recombinant viruses were used to infect HeLa cells, and at the indicated times, the levels of 2-LTR circles were measured by real-time PCR. Both a standard probe (2-LTR), which detects all 2-LTR circles, and a probe (JNCT) specific for canonical 2-LTR junctions were used. Some infected cells were treated with 1 μM raltegravir (Ral). The results for infections by wild-type (WT) SIVmac239 (A) and the A87E (B) and A87D (C) mutants are shown. The values shown represent the percentages of the maximum wild-type SIVmac239 value (823 copies/100 ng DNA at 24 h postinfection after raltegravir treatment). The results shown represent the averages and standard deviations derived from three independent infections.

    Article Snippet: For Alu PCR, we performed a primary amplification using 100 ng total DNA, 0.2 μM each primer, and Pfu UltraII Hotstart 2× Master Mix (catalog number 600850; Agilent) in a final volume of 20 μl.

    Techniques: Infection, Recombinant, Real-time Polymerase Chain Reaction, Derivative Assay