deoxynucleoside triphosphate Thermo Fisher Search Results


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  • 99
    Thermo Fisher dntp mix
    Vpx+ virus, dN and <t>dNTP</t> treatments result in minor increases in the dNTP pool of HSPCs. MDMs (A, C and E) and freshly isolated HSPCs (B, D and F) were pretreated for 2 h with Vpx+/− viruses, dNs or <t>dNTPs,</t> and cultured for 3 days before cell lysis. Quantification of dNTPs was done by a single nucleotide incorporation assay (see “Material and methods” section). Fold induction was calculated based on the absolute values of vero- vs mock-treated samples (C–F). White dots represent Vpx− virus-pretreated samples, black dots represent Vpx+ virus-pretreated samples (A–B). White bars represent dN-pretreated samples, black bars represent dNTP-pretreated samples (C–F). Data are from three donors and bars represent mean ± SEM. Statistical analysis was done using two-tailed paired t-test.
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    Thermo Fisher mgcl2
    Vpx+ virus, dN and <t>dNTP</t> treatments result in minor increases in the dNTP pool of HSPCs. MDMs (A, C and E) and freshly isolated HSPCs (B, D and F) were pretreated for 2 h with Vpx+/− viruses, dNs or <t>dNTPs,</t> and cultured for 3 days before cell lysis. Quantification of dNTPs was done by a single nucleotide incorporation assay (see “Material and methods” section). Fold induction was calculated based on the absolute values of vero- vs mock-treated samples (C–F). White dots represent Vpx− virus-pretreated samples, black dots represent Vpx+ virus-pretreated samples (A–B). White bars represent dN-pretreated samples, black bars represent dNTP-pretreated samples (C–F). Data are from three donors and bars represent mean ± SEM. Statistical analysis was done using two-tailed paired t-test.
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    Thermo Fisher taq dna polymerase
    Comparison of <t>DNA</t> sequences of rpoB genes in Rif s and Rif r M. tuberculosis isolates. The mutated nucleotides of Rif r isolates are boldfaced. ARMS primers used in this study are shown above and below the sequences. The line with the arrow shows that PCR can be performed well, whereas the line with the dot shows that the ARMS primer is refractory to extension by <t>Taq</t> DNA polymerase. Underlined letters indicate the nucleotide alterations introduced to enhance the 3′ mismatch effect. Codon numbers are assigned on the basis of alignment of the translated E. coli rpoB sequence with a portion of the translated M. tuberculosis sequence and are not the positions of the actual M. tuberculosis rpoB codons.
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    Thermo Fisher pcr buffer
    Comparison of <t>PCR</t> and Southern hybridization results for four representative V. parahaemolyticus strains. (A) <t>tdh</t> detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic
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    Thermo Fisher dithiothreitol
    Comparison of <t>PCR</t> and Southern hybridization results for four representative V. parahaemolyticus strains. (A) <t>tdh</t> detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic
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    Thermo Fisher tris hcl
    Comparison of <t>PCR</t> and Southern hybridization results for four representative V. parahaemolyticus strains. (A) <t>tdh</t> detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic
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    Thermo Fisher platinum taq polymerase
    Comparison of <t>PCR</t> and Southern hybridization results for four representative V. parahaemolyticus strains. (A) <t>tdh</t> detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic
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    Thermo Fisher superscript ii reverse transcriptase
    Comparison of <t>PCR</t> and Southern hybridization results for four representative V. parahaemolyticus strains. (A) <t>tdh</t> detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic
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    Thermo Fisher rnase inhibitor
    Comparison of <t>PCR</t> and Southern hybridization results for four representative V. parahaemolyticus strains. (A) <t>tdh</t> detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic
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    Thermo Fisher superscript iii reverse transcriptase
    Vaginal epithelial cells are a source of S100A8 and S100A9 during infection. (A and B) S100A8 and S100A9 mRNA expression by vaginal epithelial cells. Total <t>RNA</t> was extracted from vaginal epithelial cells from estrogenized uninoculated or inoculated mice with high PMN levels or low PMN levels and reverse transcribed into cDNA. S100A8 and S100A9 mRNA expression was quantified and normalized to β-actin mRNA expression. The results are expressed as the fold increase over expression in cells from estrogenized uninoculated mice. The results are cumulative data of 3 experiments testing vaginal epithelial cells collected on day 4 postinoculation. *, P = 0.0024. SEM, standard error of the mean. (C) S100A8 and S100A9 protein production by vaginal epithelial cells. Proteins in vaginal epithelial cell lysates from estrogenized inoculated mice with high PMN levels (H) or low PMN levels (L) or estrogenized uninoculated mice (U) were separated and visualized by Western blotting with anti-S100A8 (left panel), anti-S100A9 (right panel) or β-actin (bottom panel) antibodies. Recombinant mouse S100A8 (rA8) and S100A9 (rA9) were included as positive controls. MW denotes molecular mass markers. Masses are indicated in kilodaltons on the right side of the MW lanes. Images show a representative result of <t>three</t> repeat experiments testing vaginal epithelial cells collected on day 4 postinoculation.
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    Thermo Fisher amplitaq gold dna polymerase
    Vaginal epithelial cells are a source of S100A8 and S100A9 during infection. (A and B) S100A8 and S100A9 mRNA expression by vaginal epithelial cells. Total <t>RNA</t> was extracted from vaginal epithelial cells from estrogenized uninoculated or inoculated mice with high PMN levels or low PMN levels and reverse transcribed into cDNA. S100A8 and S100A9 mRNA expression was quantified and normalized to β-actin mRNA expression. The results are expressed as the fold increase over expression in cells from estrogenized uninoculated mice. The results are cumulative data of 3 experiments testing vaginal epithelial cells collected on day 4 postinoculation. *, P = 0.0024. SEM, standard error of the mean. (C) S100A8 and S100A9 protein production by vaginal epithelial cells. Proteins in vaginal epithelial cell lysates from estrogenized inoculated mice with high PMN levels (H) or low PMN levels (L) or estrogenized uninoculated mice (U) were separated and visualized by Western blotting with anti-S100A8 (left panel), anti-S100A9 (right panel) or β-actin (bottom panel) antibodies. Recombinant mouse S100A8 (rA8) and S100A9 (rA9) were included as positive controls. MW denotes molecular mass markers. Masses are indicated in kilodaltons on the right side of the MW lanes. Images show a representative result of <t>three</t> repeat experiments testing vaginal epithelial cells collected on day 4 postinoculation.
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    Thermo Fisher moloney murine leukemia virus reverse transcriptase
    Vaginal epithelial cells are a source of S100A8 and S100A9 during infection. (A and B) S100A8 and S100A9 mRNA expression by vaginal epithelial cells. Total <t>RNA</t> was extracted from vaginal epithelial cells from estrogenized uninoculated or inoculated mice with high PMN levels or low PMN levels and reverse transcribed into cDNA. S100A8 and S100A9 mRNA expression was quantified and normalized to β-actin mRNA expression. The results are expressed as the fold increase over expression in cells from estrogenized uninoculated mice. The results are cumulative data of 3 experiments testing vaginal epithelial cells collected on day 4 postinoculation. *, P = 0.0024. SEM, standard error of the mean. (C) S100A8 and S100A9 protein production by vaginal epithelial cells. Proteins in vaginal epithelial cell lysates from estrogenized inoculated mice with high PMN levels (H) or low PMN levels (L) or estrogenized uninoculated mice (U) were separated and visualized by Western blotting with anti-S100A8 (left panel), anti-S100A9 (right panel) or β-actin (bottom panel) antibodies. Recombinant mouse S100A8 (rA8) and S100A9 (rA9) were included as positive controls. MW denotes molecular mass markers. Masses are indicated in kilodaltons on the right side of the MW lanes. Images show a representative result of <t>three</t> repeat experiments testing vaginal epithelial cells collected on day 4 postinoculation.
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    Thermo Fisher reaction buffer
    Vaginal epithelial cells are a source of S100A8 and S100A9 during infection. (A and B) S100A8 and S100A9 mRNA expression by vaginal epithelial cells. Total <t>RNA</t> was extracted from vaginal epithelial cells from estrogenized uninoculated or inoculated mice with high PMN levels or low PMN levels and reverse transcribed into cDNA. S100A8 and S100A9 mRNA expression was quantified and normalized to β-actin mRNA expression. The results are expressed as the fold increase over expression in cells from estrogenized uninoculated mice. The results are cumulative data of 3 experiments testing vaginal epithelial cells collected on day 4 postinoculation. *, P = 0.0024. SEM, standard error of the mean. (C) S100A8 and S100A9 protein production by vaginal epithelial cells. Proteins in vaginal epithelial cell lysates from estrogenized inoculated mice with high PMN levels (H) or low PMN levels (L) or estrogenized uninoculated mice (U) were separated and visualized by Western blotting with anti-S100A8 (left panel), anti-S100A9 (right panel) or β-actin (bottom panel) antibodies. Recombinant mouse S100A8 (rA8) and S100A9 (rA9) were included as positive controls. MW denotes molecular mass markers. Masses are indicated in kilodaltons on the right side of the MW lanes. Images show a representative result of <t>three</t> repeat experiments testing vaginal epithelial cells collected on day 4 postinoculation.
    Reaction Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 11014 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher deoxynucleoside triphosphate
    Vaginal epithelial cells are a source of S100A8 and S100A9 during infection. (A and B) S100A8 and S100A9 mRNA expression by vaginal epithelial cells. Total <t>RNA</t> was extracted from vaginal epithelial cells from estrogenized uninoculated or inoculated mice with high PMN levels or low PMN levels and reverse transcribed into cDNA. S100A8 and S100A9 mRNA expression was quantified and normalized to β-actin mRNA expression. The results are expressed as the fold increase over expression in cells from estrogenized uninoculated mice. The results are cumulative data of 3 experiments testing vaginal epithelial cells collected on day 4 postinoculation. *, P = 0.0024. SEM, standard error of the mean. (C) S100A8 and S100A9 protein production by vaginal epithelial cells. Proteins in vaginal epithelial cell lysates from estrogenized inoculated mice with high PMN levels (H) or low PMN levels (L) or estrogenized uninoculated mice (U) were separated and visualized by Western blotting with anti-S100A8 (left panel), anti-S100A9 (right panel) or β-actin (bottom panel) antibodies. Recombinant mouse S100A8 (rA8) and S100A9 (rA9) were included as positive controls. MW denotes molecular mass markers. Masses are indicated in kilodaltons on the right side of the MW lanes. Images show a representative result of <t>three</t> repeat experiments testing vaginal epithelial cells collected on day 4 postinoculation.
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    Thermo Fisher trizol reagent
    Effect of MT1-MMP on the expression of Bst-2 in mRNA and protein levels HT1080 and MDCK cells. Cells were divided into two parts and seeded in 6-plates overnight, then transfected with plasmids as shown in figures; 48 h after transfection, ( A , B ) one part of the cells was treated with <t>TRIZOL</t> for <t>RT-PCR</t> assay and lysed with lysis buffer for western-blot assay; ( C , D ) the other part of the cells was treated with TRIZOL and harvested for qPCR as described in “Materials and Methods”.
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    Thermo Fisher first strand buffer
    Bar plots comparing gene expression changes between Arabidopsis thaliana leaves and flower buds detected by microarrays with ‘undenatured’ cDNA features, undenatured <t>oligo</t> features, and quantitative RT-PCR (QRT-PCR). Results show fold-change of expression ratios (flower buds vs. leaves; F/L) obtained from six replications in the cDNA and oligo <t>microarray</t> and 3 replications from QRT-PCR, and are grouped into four categories: (a) similar results for cDNA, oligo and QRT-PCR (b) similar for oligos and QRT-PCR, but different for cDNA (c) different for cDNA and oligos, but similar for cDNA and QRT-PCR (d) similar result for cDNA and oligo but different for QRT-PCR.
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    Thermo Fisher total rna
    clpP deficiency leads to increased sensitivity to trimethoprim. (A) Expression of dihydrofolate reductase transcript in UA159(pIB184), IBS512(pIB184), and IBS512(pIBC7). <t>RNA</t> was extracted from all three cultures and subjected to <t>cDNA</t> synthesis. Semiquantitative RT-PCR was then used to measure the levels of dihydrofolate reductase transcript in all three cultures. The expression of gyrA was included as an internal control to ensure that equal amounts of RNA were analyzed for each culture. (B) Trimethoprim-containing E strips were aseptically placed on UA159 and IBS512 lawns. The plates were incubated under microaerophilic conditions at 37°C overnight. The MICs for the two cultures were noted.
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    Thermo Fisher biotin 14 dctp
    Experimental scheme and oligonucleotide sequences. ( A ) Principle behind the joining reaction. By exposing complementary sequences, vaccinia DNA polymerase promotes duplex joint formation. ( B ) Sequences of the oligonucleotide substrates used in this paper. Homologous sequences are shown in boldface. The nucleotides shown in lower case are incorporated post-synthetically using reverse transcriptase, cidofovir diphosphate or N 4 -modified <t>biotin-14-dCTP</t> (‘x’), and dATP or dTTP. Note that the primer–template design, in FC3, FC4 and FC5, prevents extension from the other 3′ end by this fill-in reaction. The 32 P label is indicated with an asterisk (‘*’).
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    Image Search Results


    Vpx+ virus, dN and dNTP treatments result in minor increases in the dNTP pool of HSPCs. MDMs (A, C and E) and freshly isolated HSPCs (B, D and F) were pretreated for 2 h with Vpx+/− viruses, dNs or dNTPs, and cultured for 3 days before cell lysis. Quantification of dNTPs was done by a single nucleotide incorporation assay (see “Material and methods” section). Fold induction was calculated based on the absolute values of vero- vs mock-treated samples (C–F). White dots represent Vpx− virus-pretreated samples, black dots represent Vpx+ virus-pretreated samples (A–B). White bars represent dN-pretreated samples, black bars represent dNTP-pretreated samples (C–F). Data are from three donors and bars represent mean ± SEM. Statistical analysis was done using two-tailed paired t-test.

    Journal: Stem cell research

    Article Title: Vpx mediated degradation of SAMHD1 has only a very limited effect on lentiviral transduction rate in ex vivo cultured HSPCs

    doi: 10.1016/j.scr.2015.06.012

    Figure Lengend Snippet: Vpx+ virus, dN and dNTP treatments result in minor increases in the dNTP pool of HSPCs. MDMs (A, C and E) and freshly isolated HSPCs (B, D and F) were pretreated for 2 h with Vpx+/− viruses, dNs or dNTPs, and cultured for 3 days before cell lysis. Quantification of dNTPs was done by a single nucleotide incorporation assay (see “Material and methods” section). Fold induction was calculated based on the absolute values of vero- vs mock-treated samples (C–F). White dots represent Vpx− virus-pretreated samples, black dots represent Vpx+ virus-pretreated samples (A–B). White bars represent dN-pretreated samples, black bars represent dNTP-pretreated samples (C–F). Data are from three donors and bars represent mean ± SEM. Statistical analysis was done using two-tailed paired t-test.

    Article Snippet: THP-1 cells transduced with lentiviral vectors encoding SAMHD1 shRNA were selected by culturing in a medium containing 0.8 μg/ml puromycin. dNs consisted of a mixture of dA (D8668), dC (D0776), dG (D0901) and dT (T1895; all from Sigma-Aldrich). dNTPs (R0192) were purchased from Fermentas (Glen Burnie, MD).

    Techniques: Isolation, Cell Culture, Lysis, Two Tailed Test

    Creating a supercoiled and fluorescent-labeled sopC-plasmid. The plasmid pBR322:: sopC is fluorescently labeled to visualize its movement over the DNA-carpeted flow cell. We have developed an efficient labeling protocol that does not require intercalating dyes and produces a negatively supercoiled plasmid. The restriction enzyme Nt.BspQ1 nicks the pBR322 backbone at a site located approximately 180° from sopC . DNA polymerase I is used with dNTPs and Alexa647-labeled dCTP to label the DNA. Ethidium Bromide promotes negative supercoiling before a final ligation reaction that covalently closes the nick. The final product is a negatively supercoiled and fluorescently labeled plasmid bearing the sopC centromere site. This protocol can be used to incorporate a variety of dyes without significant perturbation to plasmid topology.

    Journal: Methods in cell biology

    Article Title: Reconstituting ParA/ParB-mediated transport of DNA cargo

    doi: 10.1016/bs.mcb.2015.01.021

    Figure Lengend Snippet: Creating a supercoiled and fluorescent-labeled sopC-plasmid. The plasmid pBR322:: sopC is fluorescently labeled to visualize its movement over the DNA-carpeted flow cell. We have developed an efficient labeling protocol that does not require intercalating dyes and produces a negatively supercoiled plasmid. The restriction enzyme Nt.BspQ1 nicks the pBR322 backbone at a site located approximately 180° from sopC . DNA polymerase I is used with dNTPs and Alexa647-labeled dCTP to label the DNA. Ethidium Bromide promotes negative supercoiling before a final ligation reaction that covalently closes the nick. The final product is a negatively supercoiled and fluorescently labeled plasmid bearing the sopC centromere site. This protocol can be used to incorporate a variety of dyes without significant perturbation to plasmid topology.

    Article Snippet: pBR322:: sopC plasmid (PCR template) PCR Primers for sopC DNA amplification: (Primers synthesized by IDT) 10 mM dNTPs (Life Technologies; Cat. # 18427–013) 100 mM MgSO4 (New England Biolabs, Cat. # M0254S) 2000 U/mL VENT Polymerase (New England Biolabs, Cat. # M0254S) SYBR Gold DNA Stain (Life Technologies, Cat. # S-11494) Illustra MicroSpin S-400HR columns (GE Healthcare, Cat # 27–5140-01) MyOne Streptavidin C1 Dynabeads (Life Technologies, Cat. # 65001) 20 U/μL PstI Restriction Enzyme (New England Biolabs, Cat. # R0140S) Phenol:CHCl3:Isoamyl Alcohol (UltraPure 25:24:1 v/v) Ethanol.

    Techniques: Labeling, Plasmid Preparation, Flow Cytometry, Ligation

    Comparison of DNA sequences of rpoB genes in Rif s and Rif r M. tuberculosis isolates. The mutated nucleotides of Rif r isolates are boldfaced. ARMS primers used in this study are shown above and below the sequences. The line with the arrow shows that PCR can be performed well, whereas the line with the dot shows that the ARMS primer is refractory to extension by Taq DNA polymerase. Underlined letters indicate the nucleotide alterations introduced to enhance the 3′ mismatch effect. Codon numbers are assigned on the basis of alignment of the translated E. coli rpoB sequence with a portion of the translated M. tuberculosis sequence and are not the positions of the actual M. tuberculosis rpoB codons.

    Journal: Journal of Clinical Microbiology

    Article Title: Rapid Detection of rpoB Gene Mutations in Rifampin-Resistant Mycobacterium tuberculosis Isolates in Shanghai by Using the Amplification Refractory Mutation System

    doi: 10.1128/JCM.41.3.993-997.2003

    Figure Lengend Snippet: Comparison of DNA sequences of rpoB genes in Rif s and Rif r M. tuberculosis isolates. The mutated nucleotides of Rif r isolates are boldfaced. ARMS primers used in this study are shown above and below the sequences. The line with the arrow shows that PCR can be performed well, whereas the line with the dot shows that the ARMS primer is refractory to extension by Taq DNA polymerase. Underlined letters indicate the nucleotide alterations introduced to enhance the 3′ mismatch effect. Codon numbers are assigned on the basis of alignment of the translated E. coli rpoB sequence with a portion of the translated M. tuberculosis sequence and are not the positions of the actual M. tuberculosis rpoB codons.

    Article Snippet: For each PCR, 5 μl of a supernatant containing genomic DNA as a template was added to a final volume of 50 μl containing 0.10 μM control forward primer, 0.15 μM ARMS primer, 0.20 μM common reverse primer, 50 mM KCl, 10 mM Tris-HCl (pH 8.3), 1.2 mM MgCl2 , 200 μM deoxynucleoside triphosphates, and 2.5 U of Taq DNA polymerase (MBI Fermentas, Vilnius, Lithuania).

    Techniques: Polymerase Chain Reaction, Sequencing

    Comparison of PCR and Southern hybridization results for four representative V. parahaemolyticus strains. (A) tdh detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic

    Journal: Infection and Immunity

    Article Title: Vibrio parahaemolyticus Disruption of Epithelial Cell Tight Junctions Occurs Independently of Toxin Production

    doi: 10.1128/IAI.73.3.1275-1283.2005

    Figure Lengend Snippet: Comparison of PCR and Southern hybridization results for four representative V. parahaemolyticus strains. (A) tdh detection; (B) trh detection; (C) tlh detection. Genes were detected by PCR (left panels) and Southern hybridization (right panels). Genomic

    Article Snippet: The tdh and tlh PCR mixtures (final volume, 25 μl) contained 10× PCR buffer (50 mM KCl, 10 mM Tris [pH 8.5], 0.1% gelatin, 1.5% MgCl2 ), each deoxynucleoside triphosphate (Invitrogen Life Technologies, Burlington, Ontario, Canada) at a concentration of 0.25 mM, Taq polymerase (1.25 U; New England Biolabs Ltd., Mississauga, Ontario, Canada), and nuclease-free water (Gibco).

    Techniques: Polymerase Chain Reaction, Hybridization

    Vaginal epithelial cells are a source of S100A8 and S100A9 during infection. (A and B) S100A8 and S100A9 mRNA expression by vaginal epithelial cells. Total RNA was extracted from vaginal epithelial cells from estrogenized uninoculated or inoculated mice with high PMN levels or low PMN levels and reverse transcribed into cDNA. S100A8 and S100A9 mRNA expression was quantified and normalized to β-actin mRNA expression. The results are expressed as the fold increase over expression in cells from estrogenized uninoculated mice. The results are cumulative data of 3 experiments testing vaginal epithelial cells collected on day 4 postinoculation. *, P = 0.0024. SEM, standard error of the mean. (C) S100A8 and S100A9 protein production by vaginal epithelial cells. Proteins in vaginal epithelial cell lysates from estrogenized inoculated mice with high PMN levels (H) or low PMN levels (L) or estrogenized uninoculated mice (U) were separated and visualized by Western blotting with anti-S100A8 (left panel), anti-S100A9 (right panel) or β-actin (bottom panel) antibodies. Recombinant mouse S100A8 (rA8) and S100A9 (rA9) were included as positive controls. MW denotes molecular mass markers. Masses are indicated in kilodaltons on the right side of the MW lanes. Images show a representative result of three repeat experiments testing vaginal epithelial cells collected on day 4 postinoculation.

    Journal: Infection and Immunity

    Article Title: Epithelial Cell-Derived S100 Calcium-Binding Proteins as Key Mediators in the Hallmark Acute Neutrophil Response during Candida Vaginitis ▿

    doi: 10.1128/IAI.00388-10

    Figure Lengend Snippet: Vaginal epithelial cells are a source of S100A8 and S100A9 during infection. (A and B) S100A8 and S100A9 mRNA expression by vaginal epithelial cells. Total RNA was extracted from vaginal epithelial cells from estrogenized uninoculated or inoculated mice with high PMN levels or low PMN levels and reverse transcribed into cDNA. S100A8 and S100A9 mRNA expression was quantified and normalized to β-actin mRNA expression. The results are expressed as the fold increase over expression in cells from estrogenized uninoculated mice. The results are cumulative data of 3 experiments testing vaginal epithelial cells collected on day 4 postinoculation. *, P = 0.0024. SEM, standard error of the mean. (C) S100A8 and S100A9 protein production by vaginal epithelial cells. Proteins in vaginal epithelial cell lysates from estrogenized inoculated mice with high PMN levels (H) or low PMN levels (L) or estrogenized uninoculated mice (U) were separated and visualized by Western blotting with anti-S100A8 (left panel), anti-S100A9 (right panel) or β-actin (bottom panel) antibodies. Recombinant mouse S100A8 (rA8) and S100A9 (rA9) were included as positive controls. MW denotes molecular mass markers. Masses are indicated in kilodaltons on the right side of the MW lanes. Images show a representative result of three repeat experiments testing vaginal epithelial cells collected on day 4 postinoculation.

    Article Snippet: Synthesis of cDNA from 10 ng of total RNA was completed by using 20 U of SuperScript III reverse transcriptase with 5 mM dTT (Invitrogen), GeneAmp 10× PCR buffer II with 5 mM MgCl2 (Applied Biosystems, Foster City, CA), 1 mM deoxynucleoside triphosphates (GE Healthcare), and 20 U of RNasin RNase inhibitor (Promega, Madison, WI) in a total volume of 10 μl and primed with random hexamers in a 96-well thermal cycler (25°C for 10 min, 48°C for 30 min, and 95°C for 5 min).

    Techniques: Infection, Expressing, Mouse Assay, Over Expression, Western Blot, Recombinant

    Effect of MT1-MMP on the expression of Bst-2 in mRNA and protein levels HT1080 and MDCK cells. Cells were divided into two parts and seeded in 6-plates overnight, then transfected with plasmids as shown in figures; 48 h after transfection, ( A , B ) one part of the cells was treated with TRIZOL for RT-PCR assay and lysed with lysis buffer for western-blot assay; ( C , D ) the other part of the cells was treated with TRIZOL and harvested for qPCR as described in “Materials and Methods”.

    Journal: International Journal of Molecular Sciences

    Article Title: MT1-MMP Inhibits the Activity of Bst-2 via Their Cytoplasmic Domains Dependent Interaction

    doi: 10.3390/ijms17060818

    Figure Lengend Snippet: Effect of MT1-MMP on the expression of Bst-2 in mRNA and protein levels HT1080 and MDCK cells. Cells were divided into two parts and seeded in 6-plates overnight, then transfected with plasmids as shown in figures; 48 h after transfection, ( A , B ) one part of the cells was treated with TRIZOL for RT-PCR assay and lysed with lysis buffer for western-blot assay; ( C , D ) the other part of the cells was treated with TRIZOL and harvested for qPCR as described in “Materials and Methods”.

    Article Snippet: Reverse Transcription PCR (RT-PCR) and Quantitative Real-Time PCR (qPCR) Total RNA of cells was extracted by using the Trizol reagent (Life Technologies, Inc., Burlington, ON, Canada) handled as per the manufacturer’s instructions.

    Techniques: Expressing, Transfection, Reverse Transcription Polymerase Chain Reaction, Lysis, Western Blot, Real-time Polymerase Chain Reaction

    Bar plots comparing gene expression changes between Arabidopsis thaliana leaves and flower buds detected by microarrays with ‘undenatured’ cDNA features, undenatured oligo features, and quantitative RT-PCR (QRT-PCR). Results show fold-change of expression ratios (flower buds vs. leaves; F/L) obtained from six replications in the cDNA and oligo microarray and 3 replications from QRT-PCR, and are grouped into four categories: (a) similar results for cDNA, oligo and QRT-PCR (b) similar for oligos and QRT-PCR, but different for cDNA (c) different for cDNA and oligos, but similar for cDNA and QRT-PCR (d) similar result for cDNA and oligo but different for QRT-PCR.

    Journal: Plant biotechnology journal

    Article Title: Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species

    doi: 10.1046/j.1467-7652.2003.00048.x

    Figure Lengend Snippet: Bar plots comparing gene expression changes between Arabidopsis thaliana leaves and flower buds detected by microarrays with ‘undenatured’ cDNA features, undenatured oligo features, and quantitative RT-PCR (QRT-PCR). Results show fold-change of expression ratios (flower buds vs. leaves; F/L) obtained from six replications in the cDNA and oligo microarray and 3 replications from QRT-PCR, and are grouped into four categories: (a) similar results for cDNA, oligo and QRT-PCR (b) similar for oligos and QRT-PCR, but different for cDNA (c) different for cDNA and oligos, but similar for cDNA and QRT-PCR (d) similar result for cDNA and oligo but different for QRT-PCR.

    Article Snippet: The reverse transcription reaction was carried out in a final volume of 40 μL containing 10 μg of total RNA from A. thaliana leaves and flower buds (same preparations that were used for the microarray experiments), 10 mM dithiothreitol, 500 μM deoxynucleotide triphosphates, 2 μg of oligo (dT)15 , 60 units of RNasin, and 200 units of Superscript RNase H− (Gibco BRL).

    Techniques: Expressing, Quantitative RT-PCR, Microarray

    clpP deficiency leads to increased sensitivity to trimethoprim. (A) Expression of dihydrofolate reductase transcript in UA159(pIB184), IBS512(pIB184), and IBS512(pIBC7). RNA was extracted from all three cultures and subjected to cDNA synthesis. Semiquantitative RT-PCR was then used to measure the levels of dihydrofolate reductase transcript in all three cultures. The expression of gyrA was included as an internal control to ensure that equal amounts of RNA were analyzed for each culture. (B) Trimethoprim-containing E strips were aseptically placed on UA159 and IBS512 lawns. The plates were incubated under microaerophilic conditions at 37°C overnight. The MICs for the two cultures were noted.

    Journal: Journal of Bacteriology

    Article Title: ClpP of Streptococcus mutans Differentially Regulates Expression of Genomic Islands, Mutacin Production, and Antibiotic Tolerance ▿ Differentially Regulates Expression of Genomic Islands, Mutacin Production, and Antibiotic Tolerance ▿ †

    doi: 10.1128/JB.01350-09

    Figure Lengend Snippet: clpP deficiency leads to increased sensitivity to trimethoprim. (A) Expression of dihydrofolate reductase transcript in UA159(pIB184), IBS512(pIB184), and IBS512(pIBC7). RNA was extracted from all three cultures and subjected to cDNA synthesis. Semiquantitative RT-PCR was then used to measure the levels of dihydrofolate reductase transcript in all three cultures. The expression of gyrA was included as an internal control to ensure that equal amounts of RNA were analyzed for each culture. (B) Trimethoprim-containing E strips were aseptically placed on UA159 and IBS512 lawns. The plates were incubated under microaerophilic conditions at 37°C overnight. The MICs for the two cultures were noted.

    Article Snippet: Total RNA (DNA free) was used to prepare cDNA, using Superscript II reverse transcriptase (Invitrogen).

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Incubation

    Detection and characterization of rapsyn RNA. a , RT-PCR of total RNA from muscle ( lane 1 ) and SCG ( lane 2 ), using rapsyn-specific primers. A band of the predicted size of 609 nt was readily amplified from both samples but was more abundant in muscle than in SCG. A band of 450 nt was also detected in both samples but was a larger fraction of the total product in SCG. b , RT-PCR of poly(A + ) RNA from muscle ( lane 1 ), PC12 cells ( lane 2 ), and brain ( lane 3 ) using a second set of rapsyn-specific primers designed to amplify a 768 nt segment. Low levels of rapsyn RNA were detected in the brain sample, and relatively high levels were detected in PC12 cells. As in a , a band ∼150 nt smaller than the predicted band was also amplified. c , Part of the sequence of the 450 nt band from a , lane 2 ( bottom line ), aligned with sequence of full-length rapsyn ( top line ). The shorter band encodes a protein that lacks a 53-amino acid segment. d , The short form of rapsyn is likely to be generated from an alternatively spliced mRNA that lacks exon 3. Top . Bottom , The alternatively spliced RNA that encodes the short form.

    Journal: The Journal of Neuroscience

    Article Title: Rapsyn Clusters Neuronal Acetylcholine Receptors But Is Inessential for Formation of an Interneuronal Cholinergic Synapse

    doi: 10.1523/JNEUROSCI.18-11-04166.1998

    Figure Lengend Snippet: Detection and characterization of rapsyn RNA. a , RT-PCR of total RNA from muscle ( lane 1 ) and SCG ( lane 2 ), using rapsyn-specific primers. A band of the predicted size of 609 nt was readily amplified from both samples but was more abundant in muscle than in SCG. A band of 450 nt was also detected in both samples but was a larger fraction of the total product in SCG. b , RT-PCR of poly(A + ) RNA from muscle ( lane 1 ), PC12 cells ( lane 2 ), and brain ( lane 3 ) using a second set of rapsyn-specific primers designed to amplify a 768 nt segment. Low levels of rapsyn RNA were detected in the brain sample, and relatively high levels were detected in PC12 cells. As in a , a band ∼150 nt smaller than the predicted band was also amplified. c , Part of the sequence of the 450 nt band from a , lane 2 ( bottom line ), aligned with sequence of full-length rapsyn ( top line ). The shorter band encodes a protein that lacks a 53-amino acid segment. d , The short form of rapsyn is likely to be generated from an alternatively spliced mRNA that lacks exon 3. Top . Bottom , The alternatively spliced RNA that encodes the short form.

    Article Snippet: The 50 μl PCR mixture contained 5 μl of first-strand cDNA from total RNA (or 1 μl if synthesized from mRNA), 0.2 m m deoxynucleotide triphosphates, 10 m m Tris-HCl, pH 8.3, 50 m m KCl, 1.5 m m MgCl2 , a 0.1 μ m concentration of each primer, and 1.25 U of Taq polymerase (Life Technologies, Gaithersburg, MD).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Amplification, Sequencing, Generated

    Experimental scheme and oligonucleotide sequences. ( A ) Principle behind the joining reaction. By exposing complementary sequences, vaccinia DNA polymerase promotes duplex joint formation. ( B ) Sequences of the oligonucleotide substrates used in this paper. Homologous sequences are shown in boldface. The nucleotides shown in lower case are incorporated post-synthetically using reverse transcriptase, cidofovir diphosphate or N 4 -modified biotin-14-dCTP (‘x’), and dATP or dTTP. Note that the primer–template design, in FC3, FC4 and FC5, prevents extension from the other 3′ end by this fill-in reaction. The 32 P label is indicated with an asterisk (‘*’).

    Journal: Nucleic Acids Research

    Article Title: Duplex strand joining reactions catalyzed by vaccinia virus DNA polymerase

    doi: 10.1093/nar/gkl1015

    Figure Lengend Snippet: Experimental scheme and oligonucleotide sequences. ( A ) Principle behind the joining reaction. By exposing complementary sequences, vaccinia DNA polymerase promotes duplex joint formation. ( B ) Sequences of the oligonucleotide substrates used in this paper. Homologous sequences are shown in boldface. The nucleotides shown in lower case are incorporated post-synthetically using reverse transcriptase, cidofovir diphosphate or N 4 -modified biotin-14-dCTP (‘x’), and dATP or dTTP. Note that the primer–template design, in FC3, FC4 and FC5, prevents extension from the other 3′ end by this fill-in reaction. The 32 P label is indicated with an asterisk (‘*’).

    Article Snippet: Biotinylated oligonucleotides were prepared in the same way except we substituted 40 μM N4 -modified biotin-14-dCTP (Invitrogen) for cidofovir diphosphate.

    Techniques: Modification