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BEI Resources dna
Dna, supplied by BEI Resources, used in various techniques. Bioz Stars score: 76/100, based on 0 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Amplification:

Article Title: Maturation of the gut microbiome and risk of asthma in childhood
Article Snippet: Paragraph title: 16S gene amplicon sequencing ... Reactions were run in a 2720 thermal cycler (Applied Biosystems®, Life Technologies, CA, USA) according to the following cycling program: 2 min of denaturation at 94 °C, followed by 30 cycles of 20 s at 94 °C (denaturing), 30 s at 56 °C (annealing), and 40 s at 68 °C (elongation), with a final extension at 68 °C for 5 min. For each plate, a negative template-free control and a positive control containing 2 µL DNA from a known bacterial mock community (1 ng/µL; HM-782D, BEI Resources, VA, USA) were included.

Article Title: Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study
Article Snippet: Amplification was performed in 96-well microtiter plates with a reaction mixture consisting of 1X AccuPrime PCR Buffer II, 0.6 U AccuPrime Taq DNA Polymerase (Invitrogen, Life technologies, CA, US), 0.5 μM primer 341F, 0.5 μM primer 806R, and 2.0 μL template DNA, resulting in a total volume of 20.0 μL for each sample. .. A negative template-free control and a positive control were applied for each plate containing 2.0 μL DNA from a known bacterial mock community (1.0 ng/μL; HM-782D, BEI Resources, VA, US).

Positive Control:

Article Title: Maturation of the gut microbiome and risk of asthma in childhood
Article Snippet: Amplification was performed in 96-well microtiter plates with a reaction mixture consisting of 1× AccuPrime PCR Buffer II, 0.6 U AccuPrime Taq DNA Polymerase (Invitrogen, Life technologies, CA, USA), 0.5 µM primer 515 F, 0.5 µM primer 806 R, and 2 µL template DNA, giving a total volume of 20 µL per sample. .. Reactions were run in a 2720 thermal cycler (Applied Biosystems®, Life Technologies, CA, USA) according to the following cycling program: 2 min of denaturation at 94 °C, followed by 30 cycles of 20 s at 94 °C (denaturing), 30 s at 56 °C (annealing), and 40 s at 68 °C (elongation), with a final extension at 68 °C for 5 min. For each plate, a negative template-free control and a positive control containing 2 µL DNA from a known bacterial mock community (1 ng/µL; HM-782D, BEI Resources, VA, USA) were included. .. The PCR products were quantified using the Quant-iT™ PicoGreen® quantification system (Life Technologies) and samples with a concentration above 6 ng/µL were diluted to ~3–6 ng/µL prior to further analysis.

Article Title: Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study
Article Snippet: The first PCR step was performed using the following program: 2 min at 94 °C (denaturation), 30 cycles of 20 s at 94 °C (denaturation), 30 s at 56 °C (annealing) and 40 s at 68 °C (elongation), and lastly 5 min at 68 °C (final extension). .. A negative template-free control and a positive control were applied for each plate containing 2.0 μL DNA from a known bacterial mock community (1.0 ng/μL; HM-782D, BEI Resources, VA, US). .. PCR products were quantified using the Quant-iT PicoGreen quantification system (Life Technologies, CA, US).

Concentration Assay:

Article Title: Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study
Article Snippet: A negative template-free control and a positive control were applied for each plate containing 2.0 μL DNA from a known bacterial mock community (1.0 ng/μL; HM-782D, BEI Resources, VA, US). .. PCR products were quantified using the Quant-iT PicoGreen quantification system (Life Technologies, CA, US).

Isolation:

Article Title: MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach
Article Snippet: Cell cultures at log phase were harvested by spinning 15-mL culture tubes at 3000 × g for 30 min, and DNA was isolated using the PowerSoil DNA kit (MoBio, Carlsbad, CA, USA) according to the manufacturer's instructions. .. An additional preparation of a mock community containing DNA of 20 bacterial species in staggered amounts was obtained from a commercial source (Catalog # HM-783D, BEI Resources, ATCC, Manassas, VA, USA).

Picogreen Assay:

Article Title: Evaluation of PCR Systems for Field Screening of Bacillus anthracis
Article Snippet: We obtained DNA from BEI Resources, and for those DNA strains not available from BEI, we obtained cultures from the American Type Culture Collection (ATCC, Rockville, MD) and from Dr. Karen Hill of Los Alamos National Laboratory. .. Exclusivity DNA that was prepared on-site was isolated from freshly cultured stocks using the Qiagen DNeasy Blood and Tissue kit (Valencia, CA) as per the manufacturer's protocol.

Sequencing:

Article Title: Maturation of the gut microbiome and risk of asthma in childhood
Article Snippet: Paragraph title: 16S gene amplicon sequencing ... Reactions were run in a 2720 thermal cycler (Applied Biosystems®, Life Technologies, CA, USA) according to the following cycling program: 2 min of denaturation at 94 °C, followed by 30 cycles of 20 s at 94 °C (denaturing), 30 s at 56 °C (annealing), and 40 s at 68 °C (elongation), with a final extension at 68 °C for 5 min. For each plate, a negative template-free control and a positive control containing 2 µL DNA from a known bacterial mock community (1 ng/µL; HM-782D, BEI Resources, VA, USA) were included.

Article Title: Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study
Article Snippet: A negative template-free control and a positive control were applied for each plate containing 2.0 μL DNA from a known bacterial mock community (1.0 ng/μL; HM-782D, BEI Resources, VA, US). .. Prior to further analysis, dilution of samples with a DNA concentration of more than 6.0 ng/μL was performed to achieve a concentration of approximately 3.0–6.0 ng/μL.

Article Title: IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data
Article Snippet: Four publicly available Illumina MiSeq sequencing datasets of mock communities were used within this work. .. The DNA of the mock communities can be obtained from BEI Resources (catalog number HM-278D).

Article Title: MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach
Article Snippet: Nucleic acid quality and quantity were checked via Nanodrop 2000 and Qubit, whereafter 1 μg of DNA was used to prepare sequencing libraries. .. An additional preparation of a mock community containing DNA of 20 bacterial species in staggered amounts was obtained from a commercial source (Catalog # HM-783D, BEI Resources, ATCC, Manassas, VA, USA).

Purification:

Article Title: Maturation of the gut microbiome and risk of asthma in childhood
Article Snippet: Reactions were run in a 2720 thermal cycler (Applied Biosystems®, Life Technologies, CA, USA) according to the following cycling program: 2 min of denaturation at 94 °C, followed by 30 cycles of 20 s at 94 °C (denaturing), 30 s at 56 °C (annealing), and 40 s at 68 °C (elongation), with a final extension at 68 °C for 5 min. For each plate, a negative template-free control and a positive control containing 2 µL DNA from a known bacterial mock community (1 ng/µL; HM-782D, BEI Resources, VA, USA) were included. .. Reactions were run in a 2720 thermal cycler (Applied Biosystems®, Life Technologies, CA, USA) according to the following cycling program: 2 min of denaturation at 94 °C, followed by 30 cycles of 20 s at 94 °C (denaturing), 30 s at 56 °C (annealing), and 40 s at 68 °C (elongation), with a final extension at 68 °C for 5 min. For each plate, a negative template-free control and a positive control containing 2 µL DNA from a known bacterial mock community (1 ng/µL; HM-782D, BEI Resources, VA, USA) were included.

Article Title: The Identification and Differentiation between Burkholderia mallei and Burkholderia pseudomallei Using One Gene Pyrosequencing
Article Snippet: The B. mallei , B. pseudomallei, and 2 B. thailandensis were received from the NIH Biodefense and Emerging Infections Research Resources Repository (BEI Resources, Bethesda, MD, USA) as either live strains or purified DNA. .. Access to both isolates and DNA of both B. mallei and B. pseudomallei were limited due to restrictions on how many Tier 1 isolates and DNA can be purchased yearly from BEI Resources.

Article Title: Evaluation of PCR Systems for Field Screening of Bacillus anthracis
Article Snippet: We obtained DNA from BEI Resources, and for those DNA strains not available from BEI, we obtained cultures from the American Type Culture Collection (ATCC, Rockville, MD) and from Dr. Karen Hill of Los Alamos National Laboratory. .. To confirm that the DNA stocks were free of PCR inhibitors, DNA from the inclusivity (2,000 GE/mL) and exclusivity (20,000 GE/mL) panel strains were analyzed by PCR in triplicate using an ABI 7500 Fast Real-Time PCR System (Life Technologies, Grand Island, NY), with primer and probe sets designed to detect the respective DNA.

Real-time Polymerase Chain Reaction:

Article Title: Evaluation of PCR Systems for Field Screening of Bacillus anthracis
Article Snippet: We obtained DNA from BEI Resources, and for those DNA strains not available from BEI, we obtained cultures from the American Type Culture Collection (ATCC, Rockville, MD) and from Dr. Karen Hill of Los Alamos National Laboratory. .. All DNA stocks were quantified using the Invitrogen Quant-iT™ PicoGreen® assay kit (Grand Island, NY), using either the lambda phage DNA provided in the kit or lambda phage DNA from New England Biolabs (Ipswitch, MA).

Modification:

Article Title: Maturation of the gut microbiome and risk of asthma in childhood
Article Snippet: In the first PCR reaction, the hypervariable V4 region of the 16S rRNA gene was amplified using the modified broad range primers 515F (5′-GTGCCAGCMGCCGCGGTAA-3′) and 806R (5′-GGACTACHVGGGTWTCTAAT-3′) – . .. Reactions were run in a 2720 thermal cycler (Applied Biosystems®, Life Technologies, CA, USA) according to the following cycling program: 2 min of denaturation at 94 °C, followed by 30 cycles of 20 s at 94 °C (denaturing), 30 s at 56 °C (annealing), and 40 s at 68 °C (elongation), with a final extension at 68 °C for 5 min. For each plate, a negative template-free control and a positive control containing 2 µL DNA from a known bacterial mock community (1 ng/µL; HM-782D, BEI Resources, VA, USA) were included.

Article Title: Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study
Article Snippet: In the first step, the V3 and V4 regions were amplified using the modified broad-range primers Uni340F (5’ – CCT AYG GGR BGC ASC AG – 3′) and Uni806R (5’ – GGA CTA CNN GGG TAT CTA AT – 3′) [ – ]. .. A negative template-free control and a positive control were applied for each plate containing 2.0 μL DNA from a known bacterial mock community (1.0 ng/μL; HM-782D, BEI Resources, VA, US).

Inhibition:

Article Title: Evaluation of PCR Systems for Field Screening of Bacillus anthracis
Article Snippet: We obtained DNA from BEI Resources, and for those DNA strains not available from BEI, we obtained cultures from the American Type Culture Collection (ATCC, Rockville, MD) and from Dr. Karen Hill of Los Alamos National Laboratory. .. To confirm that the DNA stocks were free of PCR inhibitors, DNA from the inclusivity (2,000 GE/mL) and exclusivity (20,000 GE/mL) panel strains were analyzed by PCR in triplicate using an ABI 7500 Fast Real-Time PCR System (Life Technologies, Grand Island, NY), with primer and probe sets designed to detect the respective DNA.

Selection:

Article Title: Evaluation of PCR Systems for Field Screening of Bacillus anthracis
Article Snippet: The AOAC SMPR 2010.003 was used to guide the selection of inclusivity and exclusivity Bacillus strains for DNA-based testing. (See and and for further information.) .. We obtained DNA from BEI Resources, and for those DNA strains not available from BEI, we obtained cultures from the American Type Culture Collection (ATCC, Rockville, MD) and from Dr. Karen Hill of Los Alamos National Laboratory.

Polymerase Chain Reaction:

Article Title: Maturation of the gut microbiome and risk of asthma in childhood
Article Snippet: Amplification was performed in 96-well microtiter plates with a reaction mixture consisting of 1× AccuPrime PCR Buffer II, 0.6 U AccuPrime Taq DNA Polymerase (Invitrogen, Life technologies, CA, USA), 0.5 µM primer 515 F, 0.5 µM primer 806 R, and 2 µL template DNA, giving a total volume of 20 µL per sample. .. Reactions were run in a 2720 thermal cycler (Applied Biosystems®, Life Technologies, CA, USA) according to the following cycling program: 2 min of denaturation at 94 °C, followed by 30 cycles of 20 s at 94 °C (denaturing), 30 s at 56 °C (annealing), and 40 s at 68 °C (elongation), with a final extension at 68 °C for 5 min. For each plate, a negative template-free control and a positive control containing 2 µL DNA from a known bacterial mock community (1 ng/µL; HM-782D, BEI Resources, VA, USA) were included.

Article Title: Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study
Article Snippet: Paragraph title: PCR and Miseq analysis ... A negative template-free control and a positive control were applied for each plate containing 2.0 μL DNA from a known bacterial mock community (1.0 ng/μL; HM-782D, BEI Resources, VA, US).

Article Title: Evaluation of PCR Systems for Field Screening of Bacillus anthracis
Article Snippet: We obtained DNA from BEI Resources, and for those DNA strains not available from BEI, we obtained cultures from the American Type Culture Collection (ATCC, Rockville, MD) and from Dr. Karen Hill of Los Alamos National Laboratory. .. We obtained DNA from BEI Resources, and for those DNA strains not available from BEI, we obtained cultures from the American Type Culture Collection (ATCC, Rockville, MD) and from Dr. Karen Hill of Los Alamos National Laboratory.

other:

Article Title: Rapid Detection of Bacillus anthracis Bloodstream Infections by Use of a Novel Assay in the GeneXpert System
Article Snippet: Studies performed with genomic DNA (as opposed to those performed with cultures of live cells) used DNA provided by BEI Resources or were extracted directly from cell cultures by boiling the specimens at 95°C for 20 min in InstaGene matrix (Bio-Rad Laboratories, Hercules, CA).

Plasmid Preparation:

Article Title: Evaluation of PCR Systems for Field Screening of Bacillus anthracis
Article Snippet: The apparent PAK-1 strain obtained from CRP was found to be lacking the pXO2 plasmid; therefore, we obtained a PAK-1 strain from Midwest Research Institute (Kansas City, MO), which did test positive for pXO2 (see discussion below on DNA stock screening). .. We obtained DNA from BEI Resources, and for those DNA strains not available from BEI, we obtained cultures from the American Type Culture Collection (ATCC, Rockville, MD) and from Dr. Karen Hill of Los Alamos National Laboratory.

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  • 96
    BEI Resources genomic dna
    Organization of the <t>rrn</t> region in bacteria. ( A ) Hypothetical transcriptional arrangements expected for rrn and tested experimentally using 2 sets of primer pairs (see small arrows drawn in each configuration). ( B ) Agarose gel electrophoresis of PCR reactions performed under the 2 hypothetical arrangements of rrn ; lanes: (i) 1 kb ruler (Fermentas), (ii) PCR reaction from the top configuration in (A), (iii) PCR reaction from the bottom configuration in (A). The GelAnalyser Java application was used to perform the band size analysis of the 1 kb ruler standard ( C ) and the amplicons obtained from human faecal <t>DNA</t> ( D ).
    Genomic Dna, supplied by BEI Resources, used in various techniques. Bioz Stars score: 96/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/genomic dna/product/BEI Resources
    Average 96 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
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    86
    BEI Resources mtb h37rv genomic dna
    Dose–response assays with three hit compounds from the pilot HTS, suramin, doxorubicin and ellagic acid (the chemical structures are shown as insets). The assays were performed with 1.25 µM of <t>DNA,</t> 110 µM of NTP and 0.5 µM of <t>Mtb</t> DnaG.
    Mtb H37rv Genomic Dna, supplied by BEI Resources, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mtb h37rv genomic dna/product/BEI Resources
    Average 86 stars, based on 1 article reviews
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    83
    BEI Resources human microbiome project mock community dna
    Overview of experimental design. During phase I, <t>DNA</t> extraction treatments were performed on subdivided tissue, with efficiency of SSU gene amplification assessed using gel screening of PCR products. The green check mark and red X indicate that amplicons from the treatment were and were not chosen for sequencing, respectively. During phase II, well-performing PB, VG, PG, and VGl extracts were amplified and sequenced for microbial community analysis. PS PowerSoil, PP PowerPlant Pro, PB PowerBiofilm, VG UC Vortex Garnet, PG UC Powerlyzer Glass, VGl UC Vortex Glass
    Human Microbiome Project Mock Community Dna, supplied by BEI Resources, used in various techniques. Bioz Stars score: 83/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human microbiome project mock community dna/product/BEI Resources
    Average 83 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    79
    BEI Resources s mansoni dna
    A sequence of images illustrating the plasma separation process. (A) A 200 μL of blood sample spiked with S. <t>mansoni</t> <t>DNA</t> was loaded into the superhydrophobic plasma separator. (B) When the top cover was closed, the blood was sandwiched between
    S Mansoni Dna, supplied by BEI Resources, used in various techniques. Bioz Stars score: 79/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 79 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    Image Search Results


    Organization of the rrn region in bacteria. ( A ) Hypothetical transcriptional arrangements expected for rrn and tested experimentally using 2 sets of primer pairs (see small arrows drawn in each configuration). ( B ) Agarose gel electrophoresis of PCR reactions performed under the 2 hypothetical arrangements of rrn ; lanes: (i) 1 kb ruler (Fermentas), (ii) PCR reaction from the top configuration in (A), (iii) PCR reaction from the bottom configuration in (A). The GelAnalyser Java application was used to perform the band size analysis of the 1 kb ruler standard ( C ) and the amplicons obtained from human faecal DNA ( D ).

    Journal: GigaScience

    Article Title: Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

    doi: 10.1093/gigascience/gix043

    Figure Lengend Snippet: Organization of the rrn region in bacteria. ( A ) Hypothetical transcriptional arrangements expected for rrn and tested experimentally using 2 sets of primer pairs (see small arrows drawn in each configuration). ( B ) Agarose gel electrophoresis of PCR reactions performed under the 2 hypothetical arrangements of rrn ; lanes: (i) 1 kb ruler (Fermentas), (ii) PCR reaction from the top configuration in (A), (iii) PCR reaction from the bottom configuration in (A). The GelAnalyser Java application was used to perform the band size analysis of the 1 kb ruler standard ( C ) and the amplicons obtained from human faecal DNA ( D ).

    Article Snippet: We have studied the rrn of 2 mock microbial communities, composed of genomic DNA from 20 and 8 different bacterial species, obtained, respectively, from BEI Resources and ZYMO Research Corp., using the MinION™ sequencing platform in multiplex configuration.

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction

    Variability of the rrn region and its functional domains. The rrn database, compiled after parsing more than 67 000 draft and complete bacterial genomes, was assessed by clustering analysis at different levels of sequence identity: 97% (white bars), 98% (light grey bars), 99% (dark grey bars), and 100% (black bars). For comparative aims, the functional DNA sequences encoded into the rrn region were also individually studied. The normalized diversity (y-axis) resulted from calculating the number of clusters obtained for each analysis, normalized with the median sizes of the respective regions in terms of kb and referenced against the value obtained for 16S sequences clustered at 97%, the canonical threshold for species assignment.

    Journal: GigaScience

    Article Title: Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

    doi: 10.1093/gigascience/gix043

    Figure Lengend Snippet: Variability of the rrn region and its functional domains. The rrn database, compiled after parsing more than 67 000 draft and complete bacterial genomes, was assessed by clustering analysis at different levels of sequence identity: 97% (white bars), 98% (light grey bars), 99% (dark grey bars), and 100% (black bars). For comparative aims, the functional DNA sequences encoded into the rrn region were also individually studied. The normalized diversity (y-axis) resulted from calculating the number of clusters obtained for each analysis, normalized with the median sizes of the respective regions in terms of kb and referenced against the value obtained for 16S sequences clustered at 97%, the canonical threshold for species assignment.

    Article Snippet: We have studied the rrn of 2 mock microbial communities, composed of genomic DNA from 20 and 8 different bacterial species, obtained, respectively, from BEI Resources and ZYMO Research Corp., using the MinION™ sequencing platform in multiplex configuration.

    Techniques: Functional Assay, Sequencing

    Dose–response assays with three hit compounds from the pilot HTS, suramin, doxorubicin and ellagic acid (the chemical structures are shown as insets). The assays were performed with 1.25 µM of DNA, 110 µM of NTP and 0.5 µM of Mtb DnaG.

    Journal: Nucleic Acids Research

    Article Title: A novel non-radioactive primase-pyrophosphatase activity assay and its application to the discovery of inhibitors of Mycobacterium tuberculosis primase DnaG

    doi: 10.1093/nar/gks1292

    Figure Lengend Snippet: Dose–response assays with three hit compounds from the pilot HTS, suramin, doxorubicin and ellagic acid (the chemical structures are shown as insets). The assays were performed with 1.25 µM of DNA, 110 µM of NTP and 0.5 µM of Mtb DnaG.

    Article Snippet: The primase gene dnaG (locus tag: Rv2343c) was amplified by polymerase chain reaction from Mtb H37Rv genomic DNA (BEI Resources, NIAID, NR-14865) by using primers (5′-AGTTAGCACATATGTCCGGCCGGATCTCCG-3′) and (5′-CCGCTCGAGTCACGCGGTGAGATCG-3′) and cloned between NdeI and XhoI sites of a modified pET19b vector , encoding an N-terminal decahistidine tag separated from the recombinant protein by a PreScission protease (GE Healthcare, Piscataway, NJ, USA) cleavage site.

    Techniques:

    Measurements of the steady-state rate of PPi release on primer synthesis by Mtb DnaG in the presence of suramin ( A and B ) and doxorubicin ( C and D ). The assays were carried out at a fixed DNA concentration of 1.25 µM as a function of concentration of NTP (A and C) and at a fixed NTP concentration of 110 µM as a function of concentration of DNA (B and D). In all panels, the data collected without inhibitor are shown as open triangles, with 1.25 µM inhibitor as open squares, 2.5 µM inhibitor as open diamonds, 5 µM inhibitor as filled circles, 10 µM inhibitor as filled squares, 20 µM inhibitor as filled diamonds and 40 µM inhibitor as filled triangles. The insets display representative Lineweaver–Burk plots of the same data.

    Journal: Nucleic Acids Research

    Article Title: A novel non-radioactive primase-pyrophosphatase activity assay and its application to the discovery of inhibitors of Mycobacterium tuberculosis primase DnaG

    doi: 10.1093/nar/gks1292

    Figure Lengend Snippet: Measurements of the steady-state rate of PPi release on primer synthesis by Mtb DnaG in the presence of suramin ( A and B ) and doxorubicin ( C and D ). The assays were carried out at a fixed DNA concentration of 1.25 µM as a function of concentration of NTP (A and C) and at a fixed NTP concentration of 110 µM as a function of concentration of DNA (B and D). In all panels, the data collected without inhibitor are shown as open triangles, with 1.25 µM inhibitor as open squares, 2.5 µM inhibitor as open diamonds, 5 µM inhibitor as filled circles, 10 µM inhibitor as filled squares, 20 µM inhibitor as filled diamonds and 40 µM inhibitor as filled triangles. The insets display representative Lineweaver–Burk plots of the same data.

    Article Snippet: The primase gene dnaG (locus tag: Rv2343c) was amplified by polymerase chain reaction from Mtb H37Rv genomic DNA (BEI Resources, NIAID, NR-14865) by using primers (5′-AGTTAGCACATATGTCCGGCCGGATCTCCG-3′) and (5′-CCGCTCGAGTCACGCGGTGAGATCG-3′) and cloned between NdeI and XhoI sites of a modified pET19b vector , encoding an N-terminal decahistidine tag separated from the recombinant protein by a PreScission protease (GE Healthcare, Piscataway, NJ, USA) cleavage site.

    Techniques: Concentration Assay

    Inhibition of Mtb DnaG activity by suramin (S) and doxorubicin (D). The assay was performed under similar optimized reaction conditions and with the same DNA template as in the HTS and visualized and quantified as described in Figure 3 .

    Journal: Nucleic Acids Research

    Article Title: A novel non-radioactive primase-pyrophosphatase activity assay and its application to the discovery of inhibitors of Mycobacterium tuberculosis primase DnaG

    doi: 10.1093/nar/gks1292

    Figure Lengend Snippet: Inhibition of Mtb DnaG activity by suramin (S) and doxorubicin (D). The assay was performed under similar optimized reaction conditions and with the same DNA template as in the HTS and visualized and quantified as described in Figure 3 .

    Article Snippet: The primase gene dnaG (locus tag: Rv2343c) was amplified by polymerase chain reaction from Mtb H37Rv genomic DNA (BEI Resources, NIAID, NR-14865) by using primers (5′-AGTTAGCACATATGTCCGGCCGGATCTCCG-3′) and (5′-CCGCTCGAGTCACGCGGTGAGATCG-3′) and cloned between NdeI and XhoI sites of a modified pET19b vector , encoding an N-terminal decahistidine tag separated from the recombinant protein by a PreScission protease (GE Healthcare, Piscataway, NJ, USA) cleavage site.

    Techniques: Inhibition, Activity Assay

    Optimization of conditions of the primase–pyrophosphatase assay. ( A ) A representative time course of the priming reaction, monitored by quantifying released PP i . ( B ) Dependence of activity of Mtb DnaG on the concentration of MnCl 2 . ( C ) Activity of Mtb DnaG as a function of the concentration of potassium glutamate. ( D ) Activity of Mtb DnaG in a variety of buffers (20 mM) at different pH in the range 6.0–9.0. The grey bars indicate the absorbance at time 0 in the reaction. ( E ) The steady-state rate of PP i release during primer synthesis by Mtb DnaG as a function of DNA concentration. The reactions were carried out for 30 min at [ Mtb DnaG] = 0.7 µM, [NTP] = 110 µM. ( F ) The steady-state rate of PP i release by Mtb DnaG as a function of NTP concentration. The reactions were carried out for 30 min at [ Mtb DnaG] = 0.7 µM, [DNA] = 1.25 µM.

    Journal: Nucleic Acids Research

    Article Title: A novel non-radioactive primase-pyrophosphatase activity assay and its application to the discovery of inhibitors of Mycobacterium tuberculosis primase DnaG

    doi: 10.1093/nar/gks1292

    Figure Lengend Snippet: Optimization of conditions of the primase–pyrophosphatase assay. ( A ) A representative time course of the priming reaction, monitored by quantifying released PP i . ( B ) Dependence of activity of Mtb DnaG on the concentration of MnCl 2 . ( C ) Activity of Mtb DnaG as a function of the concentration of potassium glutamate. ( D ) Activity of Mtb DnaG in a variety of buffers (20 mM) at different pH in the range 6.0–9.0. The grey bars indicate the absorbance at time 0 in the reaction. ( E ) The steady-state rate of PP i release during primer synthesis by Mtb DnaG as a function of DNA concentration. The reactions were carried out for 30 min at [ Mtb DnaG] = 0.7 µM, [NTP] = 110 µM. ( F ) The steady-state rate of PP i release by Mtb DnaG as a function of NTP concentration. The reactions were carried out for 30 min at [ Mtb DnaG] = 0.7 µM, [DNA] = 1.25 µM.

    Article Snippet: The primase gene dnaG (locus tag: Rv2343c) was amplified by polymerase chain reaction from Mtb H37Rv genomic DNA (BEI Resources, NIAID, NR-14865) by using primers (5′-AGTTAGCACATATGTCCGGCCGGATCTCCG-3′) and (5′-CCGCTCGAGTCACGCGGTGAGATCG-3′) and cloned between NdeI and XhoI sites of a modified pET19b vector , encoding an N-terminal decahistidine tag separated from the recombinant protein by a PreScission protease (GE Healthcare, Piscataway, NJ, USA) cleavage site.

    Techniques: Activity Assay, Concentration Assay

    Overview of experimental design. During phase I, DNA extraction treatments were performed on subdivided tissue, with efficiency of SSU gene amplification assessed using gel screening of PCR products. The green check mark and red X indicate that amplicons from the treatment were and were not chosen for sequencing, respectively. During phase II, well-performing PB, VG, PG, and VGl extracts were amplified and sequenced for microbial community analysis. PS PowerSoil, PP PowerPlant Pro, PB PowerBiofilm, VG UC Vortex Garnet, PG UC Powerlyzer Glass, VGl UC Vortex Glass

    Journal: Microbiome

    Article Title: Optimization of DNA extraction for advancing coral microbiota investigations

    doi: 10.1186/s40168-017-0229-y

    Figure Lengend Snippet: Overview of experimental design. During phase I, DNA extraction treatments were performed on subdivided tissue, with efficiency of SSU gene amplification assessed using gel screening of PCR products. The green check mark and red X indicate that amplicons from the treatment were and were not chosen for sequencing, respectively. During phase II, well-performing PB, VG, PG, and VGl extracts were amplified and sequenced for microbial community analysis. PS PowerSoil, PP PowerPlant Pro, PB PowerBiofilm, VG UC Vortex Garnet, PG UC Powerlyzer Glass, VGl UC Vortex Glass

    Article Snippet: In addition, two positive DNA controls obtained from Escherichia coli (Promega) and the Human Microbiome Project mock community DNA (BEI Resources, cat # HM-276D) and a negative control (U.V. sterilized DNA-free water) were amplified, barcoded, and included in the library pool.

    Techniques: DNA Extraction, Amplification, Polymerase Chain Reaction, Sequencing

    A sequence of images illustrating the plasma separation process. (A) A 200 μL of blood sample spiked with S. mansoni DNA was loaded into the superhydrophobic plasma separator. (B) When the top cover was closed, the blood was sandwiched between

    Journal:

    Article Title: A High-Efficiency Superhydrophobic Plasma Separator

    doi: 10.1039/c5lc01235j

    Figure Lengend Snippet: A sequence of images illustrating the plasma separation process. (A) A 200 μL of blood sample spiked with S. mansoni DNA was loaded into the superhydrophobic plasma separator. (B) When the top cover was closed, the blood was sandwiched between

    Article Snippet: 200 μL of the whole blood spiked with S. mansoni DNA (obtained from the Schistosomiasis Resource Center, for distribution by BEI Resources, NIAID, NIH) was loaded into the blood well ( ).

    Techniques: Sequencing

    (A) Recovery efficiency of S. mansoni genomic DNA on our plasma separator at various concentrations. (B) Endpoint, fluorescence images of intercalating dye in three amplification chambers, target DNA amount in each chamber is 10 fg, 1 fg and 0 fg (negative

    Journal:

    Article Title: A High-Efficiency Superhydrophobic Plasma Separator

    doi: 10.1039/c5lc01235j

    Figure Lengend Snippet: (A) Recovery efficiency of S. mansoni genomic DNA on our plasma separator at various concentrations. (B) Endpoint, fluorescence images of intercalating dye in three amplification chambers, target DNA amount in each chamber is 10 fg, 1 fg and 0 fg (negative

    Article Snippet: 200 μL of the whole blood spiked with S. mansoni DNA (obtained from the Schistosomiasis Resource Center, for distribution by BEI Resources, NIAID, NIH) was loaded into the blood well ( ).

    Techniques: Fluorescence, Amplification