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  • 95
    Millipore ethidium monoazide
    The frequency of intermediate/pro-inflammatory monocytes correlates with the activation of MAIT cells (A) Representative flow cytometry plots for identification of monocytes and their subsets: a, CD14 ++ CD16 − ‘classical’ monocytes; b, CD14 ++ CD16 + ‘intermediate/pro-inflammatory’ monocytes; c, CD14 + CD16 ++ ‘non-classical’ monocytes. EMA, <t>ethidium</t> <t>monoazide;</t> SSC-A, side scatter area. (B) HLA-DR expression on blood and liver monocytes of HCV-infected patients. Median and IQR are shown. (C) Linear regression analysis (non-parametric Spearman correlation) of the frequency of CD14 ++ CD16 + intermediate/pro-inflammatory monocytes and MAIT cell activation in the blood of HCV-infected patients. (D) Plasma IL-18 levels of HCV-infected patients prior to and at week 4 of antiviral therapy compared to uninfected controls. Mean and SD are shown. (E–F) HLA-DR expression of total monocytes and monocyte subsets in blood (E) and liver (F) of HCV-infected patients prior to and at week 4 of antiviral therapy. Median and IQR (E) and Mean and SD (F) are shown. Wk, week.
    Ethidium Monoazide, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 80 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher ethidium bromide
    2.3% native agarose gel in 0.5X TBE buffer, showing a representative library prep from wild-type Okazaki fragments. The gel is stained with <t>Ethidium</t> Bromide. Monosome- and disome-sized fragments with ligated sequencing-adaptors can be seen along with
    Ethidium Bromide, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 7192 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Abcam ethidium bromide uptake
    Evaluation of astrocytic GJIC permeability and hemichannel activity after OGD/R injury with Gap19 or Gap26. a For GJIC detection, we measured calcein-AM transfer between “donor cells” and “acceptor cells” with flow cytometry. Shown here is a representative flow cytometry plot of transfer after donor astrocytes were labeled with calcein-AM and cocultured with acceptor astrocytes for 4 h. Grouped dye transfer data are shown in b . OGD/R injury decreased the degree of astrocytic coupling; Gap26 further inhibited cellular coupling. c Representative images depicting <t>ethidium</t> uptake via hemichannels in the four groups. d OGD/R injury increased astrocytic ethidium uptake, while Gap19 and Gap26 achieved similar attenuation of hemichannel opening. e The supernatant ATP concentration was strongly elevated in the OGD/R group astrocytes, but Gap19 and Gap26 reversed this effect. We evaluated the statistical significance with ANOVA and Duncan’s multiple comparisons test. * p
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    85
    BioVision ethidium bromide incorporation
    Evaluation of astrocytic GJIC permeability and hemichannel activity after OGD/R injury with Gap19 or Gap26. a For GJIC detection, we measured calcein-AM transfer between “donor cells” and “acceptor cells” with flow cytometry. Shown here is a representative flow cytometry plot of transfer after donor astrocytes were labeled with calcein-AM and cocultured with acceptor astrocytes for 4 h. Grouped dye transfer data are shown in b . OGD/R injury decreased the degree of astrocytic coupling; Gap26 further inhibited cellular coupling. c Representative images depicting <t>ethidium</t> uptake via hemichannels in the four groups. d OGD/R injury increased astrocytic ethidium uptake, while Gap19 and Gap26 achieved similar attenuation of hemichannel opening. e The supernatant ATP concentration was strongly elevated in the OGD/R group astrocytes, but Gap19 and Gap26 reversed this effect. We evaluated the statistical significance with ANOVA and Duncan’s multiple comparisons test. * p
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    90
    Bio-Rad ethidium bromide
    Electrophoretic mobility gel shift assays of siRNA and dsDNA binding to DRBD fusion proteins or synthetic peptides. 1 μmol/l siRNA or dsDNA was incubated with varying concentrations of protein and their interaction measured by migration on a 6% acrylamide gel followed by staining with <t>ethidium</t> bromide. ( a , b ) Gel shift of siRNA binding to DRBD or PPS-DRBD with increasing molar ratios of protein to siRNA. ( c ) Gel shift of either siRNA or dsDNA binding to PTD-DRBD at different molar ratios. ( d ) Gel shift of 1 μmol/l siRNA interacting with synthetic peptides at either 20 or 40 μmol/l. DRBD, double-stranded RNA-binding domain; dsDNA, double-stranded DNA; PTD, protein transduction domain; siRNA, small interfering RNA.
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    96
    Amresco ethidium bromide
    Agarose gel electrophoresis of NR3C1 646 C > G fragments stained with <t>ethidium</t> bromide. Lane 1: 100 bp Ladder. Lane 2 represents unrestricted fragment, 1 band = 418 bp (experimental control: no enzyme “mock”). Lane 3 shows homozygous (GG) genotype, 1 band = 418 bp. Lane 4 shows heterozygous (GC) genotype, 3 bands = 418,263,155 bp. Lane 5 shows homozygous (CC) genotype, 2 bands = 263, 155 bp
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    96
    Promega ethidium bromide
    Inhibitors of nuclear (α) or mitochondrial (γ) DNA polymerases differentially block EdU incorporation. F11 neuroblastoma cells are incubated with or without DNA polymerase inhibitors 4 hr prior to and together with EdU for an additional 12 hr. Amplified EdU signal (EdU-OG-TSA) is compared with DNA stain (DAPI, blue) and cell morphology (DIC). ( A ) Cells incubated with EdU show both nuclear (arrowheads) and mtDNA (arrows) incorporation. ( B ) Addition of 7 μM aphidicolin (+APH) inhibits nuclear incorporation of EdU, whereas mtDNA labeling (arrows) is maintained. ( C ) The presence of 1.0 μg/ml <t>ethidium</t> bromide (+EtBr) inhibits incorporation of EdU into mtDNA but not into nuclear DNA (arrowheads). ( D ) 2′,3′-Dideoxycytidine (+ddC, 200 μM) also inhibits mtDNA but not nuclear incorporation of EdU (arrowheads). Bar = 10 μm.
    Ethidium Bromide, supplied by Promega, used in various techniques. Bioz Stars score: 96/100, based on 1335 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Carl Roth GmbH ethidium bromide
    Total RNA quality assessment on the basis of 18S and 28S rRNA . On left side, lane # 1 shows DNA ladder (0.5 kb – 7.0 kb). The <t>ethidium</t> bromide-staining pattern of intact total RNA shows clearly defined 18S and 28S ribosomal RNA bands [lane # 3–5 (GTC; fresh); lane # 6–8 (SGC; fresh sample); lane # 9–11 (GTC; frozen); and lane # 12–14 (SGC; frozen).
    Ethidium Bromide, supplied by Carl Roth GmbH, used in various techniques. Bioz Stars score: 96/100, based on 253 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Bioneer Corporation ethidium bromide
    Total RNA quality assessment on the basis of 18S and 28S rRNA . On left side, lane # 1 shows DNA ladder (0.5 kb – 7.0 kb). The <t>ethidium</t> bromide-staining pattern of intact total RNA shows clearly defined 18S and 28S ribosomal RNA bands [lane # 3–5 (GTC; fresh); lane # 6–8 (SGC; fresh sample); lane # 9–11 (GTC; frozen); and lane # 12–14 (SGC; frozen).
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    96
    Biotium ethidium bromide
    Detection of PEG-Ad5-PTEN by SDS-PAGE ( A ) and EPAP by TBE-PAGE ( B ). In Figure 3A , (A) It was stained by Coomassie Brilliant Blue; (B) It was stained by 0.1 mol/L iodine solution. Lane 1, marker; Lane 2, positive control protein of BSA; Lane 3, unmodified Ad5; Lane 4, PEG-Ad5-PTEN. In Figure 3B , it was stained by <t>ethidium</t> bromide. Lane 1, marker; Lane 2, EpDT3; Lane 3, PEG-Ad5-PTEN; Lane d 4, EPAP.
    Ethidium Bromide, supplied by Biotium, used in various techniques. Bioz Stars score: 96/100, based on 154 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Fisher Scientific ethidium bromide
    Condensation reactions demonstrating that <t>ethidium-mediated</t> oligonucleotide polymerization requires Watson–Crick base pairs. Reactions loaded in the Six Right Lanes contained various compositions of d(pCCTA) and d(pGGTA), as indicted above lanes,
    Ethidium Bromide, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 96/100, based on 424 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    FUJIFILM ethidium bromide
    The nuclear walk-on assay quantitatively and precisely measures engaged Pol II. ( A ) Steps in the nuclear walk-on assay are illustrated. ( B ) Adherent HeLa cells were transfected 48 h before isolation of nuclei with 1.5 nM NELF-A siRNA (NELF KD) or lipid reagent only (Mock). Cells were also treated 1 h before isolation with 0.1% DMSO or 1 μM flavopiridol (Flavo). Nuclear walk-ons were performed using a 6 min α- 32 P-CTP pulse in the absence or presence of 2 μg/ml α-amanitin (α-aman). After 6% Urea-PAGE, <t>ethidium</t> bromide was used to visualize nuclear RNAs. A representative gel from nuclear walk-ons performed in triplicate is shown here. ( C ) Phosphorimage to visualize radiolabeled nascent transcripts from B. ( D ) Average amanitin-sensitive Pol II nascent transcript profiles from triplicate nuclear walk-ons as represented in B and C. For each replicate, signals from each lane in the phosphorimage were normalized using quantifications of cold nuclear RNAs in the ethidium bromide stain. Then, α-amanitin-insensitive signals were subtracted from total signals. Triplicate profiles (see Supplementary Figure S1 ) were then averaged as described in the Materials and Methods. Inset: western blot of NELF-A; a nonspecific band (n.s.) indicates even loading. ( E ) PRO-Seq paired-end reads over the DDIT4 gene and upstream enhancer regions. Adherent HeLa cells were treated 1 h with either 0.1% DMSO or 1 μM flavopiridol. ( F ) Plot of sense or divergent PRO-Seq fragments lengths near Pol II promoters.
    Ethidium Bromide, supplied by FUJIFILM, used in various techniques. Bioz Stars score: 96/100, based on 708 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    BioShop ethidium bromide
    The nuclear walk-on assay quantitatively and precisely measures engaged Pol II. ( A ) Steps in the nuclear walk-on assay are illustrated. ( B ) Adherent HeLa cells were transfected 48 h before isolation of nuclei with 1.5 nM NELF-A siRNA (NELF KD) or lipid reagent only (Mock). Cells were also treated 1 h before isolation with 0.1% DMSO or 1 μM flavopiridol (Flavo). Nuclear walk-ons were performed using a 6 min α- 32 P-CTP pulse in the absence or presence of 2 μg/ml α-amanitin (α-aman). After 6% Urea-PAGE, <t>ethidium</t> bromide was used to visualize nuclear RNAs. A representative gel from nuclear walk-ons performed in triplicate is shown here. ( C ) Phosphorimage to visualize radiolabeled nascent transcripts from B. ( D ) Average amanitin-sensitive Pol II nascent transcript profiles from triplicate nuclear walk-ons as represented in B and C. For each replicate, signals from each lane in the phosphorimage were normalized using quantifications of cold nuclear RNAs in the ethidium bromide stain. Then, α-amanitin-insensitive signals were subtracted from total signals. Triplicate profiles (see Supplementary Figure S1 ) were then averaged as described in the Materials and Methods. Inset: western blot of NELF-A; a nonspecific band (n.s.) indicates even loading. ( E ) PRO-Seq paired-end reads over the DDIT4 gene and upstream enhancer regions. Adherent HeLa cells were treated 1 h with either 0.1% DMSO or 1 μM flavopiridol. ( F ) Plot of sense or divergent PRO-Seq fragments lengths near Pol II promoters.
    Ethidium Bromide, supplied by BioShop, used in various techniques. Bioz Stars score: 91/100, based on 31 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Millipore ethidium bromide
    <t>Ethidium</t> and DAPI transport mediated by QacA mutants containing cysteine substitutions at W58A second-site suppressor positions. Transport was monitored fluorimetrically from cells loaded with ethidium bromide (A and C) or DAPI (B and D) after energization.
    Ethidium Bromide, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 9205 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Beyotime ethidium bromide
    <t>Ethidium</t> and DAPI transport mediated by QacA mutants containing cysteine substitutions at W58A second-site suppressor positions. Transport was monitored fluorimetrically from cells loaded with ethidium bromide (A and C) or DAPI (B and D) after energization.
    Ethidium Bromide, supplied by Beyotime, used in various techniques. Bioz Stars score: 91/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    HiMedia Laboratories ethidium bromide
    Fluorescence emission spectra of intercalated <t>Ethidium</t> bromide and human genomic DNA incubated with increasing concentrations of TiO 2 nanoparticle at 37 °C
    Ethidium Bromide, supplied by HiMedia Laboratories, used in various techniques. Bioz Stars score: 95/100, based on 116 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Merck KGaA ethidium bromide
    Force-extension traces for the complexes of poly(dG-dC) dsDNA with the intercalants ( A ) daunomycin; ( B ) <t>ethidium</t> bromide; ( C ) YO; ( D ) YOYO.
    Ethidium Bromide, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 95/100, based on 230 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Fisher Bioreagents ethidium bromide
    Bacillus vector for selection of group II intron insertions. A schematic of the important vector features and selection scheme for group II intron based gene disruption. The plasmid is erythromycin resistant but kanamycin sensitve because a td group I intron interrupts its coding sequence in an antisense orientation. Transcription of the group II intron from the Ntr promoter allows self- splicing of the td intron and generates a substrate that is capable of genomic integration at pre-determined loci due to changes in sequences shown as black bars within the intron. Genomic integrants no longer have the td group I intron interrupting the kanamycin resistance gene and thus successful integrants are kanamycin resistant. For PCR verification of intron insertion, primers (shown as arrows above the genomic DNA schematic) were designed to flank the site of intron insertion in BAS4597 and BAS4553. kanamycin resistant colonies arising in Bacillus anthracis Sterne after transformation of plasmids reengineered to integrate the group II intron at BAS4597 and BAS4553 were screened by colony PCR and analyzed after electrophoresis on a 1% agarose gel in TBE buffer and visualized by staining with <t>ethidium</t> bromide. Lanes marked M have 1 Kb molecular weight markers.
    Ethidium Bromide, supplied by Fisher Bioreagents, used in various techniques. Bioz Stars score: 95/100, based on 71 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Merck & Co ethidium bromide
    Bacillus vector for selection of group II intron insertions. A schematic of the important vector features and selection scheme for group II intron based gene disruption. The plasmid is erythromycin resistant but kanamycin sensitve because a td group I intron interrupts its coding sequence in an antisense orientation. Transcription of the group II intron from the Ntr promoter allows self- splicing of the td intron and generates a substrate that is capable of genomic integration at pre-determined loci due to changes in sequences shown as black bars within the intron. Genomic integrants no longer have the td group I intron interrupting the kanamycin resistance gene and thus successful integrants are kanamycin resistant. For PCR verification of intron insertion, primers (shown as arrows above the genomic DNA schematic) were designed to flank the site of intron insertion in BAS4597 and BAS4553. kanamycin resistant colonies arising in Bacillus anthracis Sterne after transformation of plasmids reengineered to integrate the group II intron at BAS4597 and BAS4553 were screened by colony PCR and analyzed after electrophoresis on a 1% agarose gel in TBE buffer and visualized by staining with <t>ethidium</t> bromide. Lanes marked M have 1 Kb molecular weight markers.
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    91
    BBI Solutions ethidium bromide
    Bacillus vector for selection of group II intron insertions. A schematic of the important vector features and selection scheme for group II intron based gene disruption. The plasmid is erythromycin resistant but kanamycin sensitve because a td group I intron interrupts its coding sequence in an antisense orientation. Transcription of the group II intron from the Ntr promoter allows self- splicing of the td intron and generates a substrate that is capable of genomic integration at pre-determined loci due to changes in sequences shown as black bars within the intron. Genomic integrants no longer have the td group I intron interrupting the kanamycin resistance gene and thus successful integrants are kanamycin resistant. For PCR verification of intron insertion, primers (shown as arrows above the genomic DNA schematic) were designed to flank the site of intron insertion in BAS4597 and BAS4553. kanamycin resistant colonies arising in Bacillus anthracis Sterne after transformation of plasmids reengineered to integrate the group II intron at BAS4597 and BAS4553 were screened by colony PCR and analyzed after electrophoresis on a 1% agarose gel in TBE buffer and visualized by staining with <t>ethidium</t> bromide. Lanes marked M have 1 Kb molecular weight markers.
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    95
    Nacalai ethidium bromide
    Bacillus vector for selection of group II intron insertions. A schematic of the important vector features and selection scheme for group II intron based gene disruption. The plasmid is erythromycin resistant but kanamycin sensitve because a td group I intron interrupts its coding sequence in an antisense orientation. Transcription of the group II intron from the Ntr promoter allows self- splicing of the td intron and generates a substrate that is capable of genomic integration at pre-determined loci due to changes in sequences shown as black bars within the intron. Genomic integrants no longer have the td group I intron interrupting the kanamycin resistance gene and thus successful integrants are kanamycin resistant. For PCR verification of intron insertion, primers (shown as arrows above the genomic DNA schematic) were designed to flank the site of intron insertion in BAS4597 and BAS4553. kanamycin resistant colonies arising in Bacillus anthracis Sterne after transformation of plasmids reengineered to integrate the group II intron at BAS4597 and BAS4553 were screened by colony PCR and analyzed after electrophoresis on a 1% agarose gel in TBE buffer and visualized by staining with <t>ethidium</t> bromide. Lanes marked M have 1 Kb molecular weight markers.
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    TaKaRa ethidium bromide
    Bacillus vector for selection of group II intron insertions. A schematic of the important vector features and selection scheme for group II intron based gene disruption. The plasmid is erythromycin resistant but kanamycin sensitve because a td group I intron interrupts its coding sequence in an antisense orientation. Transcription of the group II intron from the Ntr promoter allows self- splicing of the td intron and generates a substrate that is capable of genomic integration at pre-determined loci due to changes in sequences shown as black bars within the intron. Genomic integrants no longer have the td group I intron interrupting the kanamycin resistance gene and thus successful integrants are kanamycin resistant. For PCR verification of intron insertion, primers (shown as arrows above the genomic DNA schematic) were designed to flank the site of intron insertion in BAS4597 and BAS4553. kanamycin resistant colonies arising in Bacillus anthracis Sterne after transformation of plasmids reengineered to integrate the group II intron at BAS4597 and BAS4553 were screened by colony PCR and analyzed after electrophoresis on a 1% agarose gel in TBE buffer and visualized by staining with <t>ethidium</t> bromide. Lanes marked M have 1 Kb molecular weight markers.
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    Teknova ethidium bromide
    Bacillus vector for selection of group II intron insertions. A schematic of the important vector features and selection scheme for group II intron based gene disruption. The plasmid is erythromycin resistant but kanamycin sensitve because a td group I intron interrupts its coding sequence in an antisense orientation. Transcription of the group II intron from the Ntr promoter allows self- splicing of the td intron and generates a substrate that is capable of genomic integration at pre-determined loci due to changes in sequences shown as black bars within the intron. Genomic integrants no longer have the td group I intron interrupting the kanamycin resistance gene and thus successful integrants are kanamycin resistant. For PCR verification of intron insertion, primers (shown as arrows above the genomic DNA schematic) were designed to flank the site of intron insertion in BAS4597 and BAS4553. kanamycin resistant colonies arising in Bacillus anthracis Sterne after transformation of plasmids reengineered to integrate the group II intron at BAS4597 and BAS4553 were screened by colony PCR and analyzed after electrophoresis on a 1% agarose gel in TBE buffer and visualized by staining with <t>ethidium</t> bromide. Lanes marked M have 1 Kb molecular weight markers.
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    96
    tiangen biotech co ethidium bromide
    Bacillus vector for selection of group II intron insertions. A schematic of the important vector features and selection scheme for group II intron based gene disruption. The plasmid is erythromycin resistant but kanamycin sensitve because a td group I intron interrupts its coding sequence in an antisense orientation. Transcription of the group II intron from the Ntr promoter allows self- splicing of the td intron and generates a substrate that is capable of genomic integration at pre-determined loci due to changes in sequences shown as black bars within the intron. Genomic integrants no longer have the td group I intron interrupting the kanamycin resistance gene and thus successful integrants are kanamycin resistant. For PCR verification of intron insertion, primers (shown as arrows above the genomic DNA schematic) were designed to flank the site of intron insertion in BAS4597 and BAS4553. kanamycin resistant colonies arising in Bacillus anthracis Sterne after transformation of plasmids reengineered to integrate the group II intron at BAS4597 and BAS4553 were screened by colony PCR and analyzed after electrophoresis on a 1% agarose gel in TBE buffer and visualized by staining with <t>ethidium</t> bromide. Lanes marked M have 1 Kb molecular weight markers.
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    92
    Roche ethidium bromide
    Expression of variants of uPAR transcripts in leukemia cells (A) KG1 or U937 cells were lysed and analyzed by Western blot with an anti-uPAR antibody; the filter was reprobed with an anti-GAPDH antibody for loading control. (B) KG1 and U937 cells were lysed in Quiazol Reagent and total RNA reversely transcribed; then, 2 μl of reversely transcribed DNA were used for PCR amplification of the region encompassing uPAR from Exon2 to the stop codon UAA (E2-UAA) or of the region encompassing uPAR from Exon2 to the whole 3’UTR (E2-3’UTR). 7 μg of PCR products and the linearized uPAR 3’UTR-PcDNA3.1, as positive control, were analyzed by electrophoresis in 1.2% agarose gel containing <t>ethidium</t> bromide, photographed under ultraviolet illumination (B, left panel), blotted to a Nylon membrane and hybridized with biotinylated 3’UTR RNA probe (B, right panel).
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    Plasmid DNA condensation by G5 PPI and its alkylcarboxylated derivatives as measured by their ability to displace DNA from its fluorescent complex with <t>ethidium</t> bromide in HBG buffer medium. The c / p ratio with highest condensation was 1.5 for unmodified
    Ethidium Bromide, supplied by CinnaGen Co, used in various techniques. Bioz Stars score: 95/100, based on 103 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Metallation of a 40-base DNA fragment following treatment with cisplatin (molar ratio 1:50) and Pd1 (molar ratios 1:100 and 1:200). The level of metal binding following interactions between the tested complexes and the DNA probe was analyzed after BamH1 treatment, electrophoretic analysis in 5% native polyacrilamide gel, and <t>ethidium</t> bromide staining. On the picture: C , unmodified DNA; CB , BamH1-digested DNA; cis , cisplatin-modified DNA; cisB , cisplatin-modified DNA (1:50) BamH1-digested; Pd , Pd1 -modified DNA; PdIB , Pd1 -modified DNA (1:100) BamH1-digested, PdIIB , Pd1 -modified DNA (1:200) BamH1-digested.
    Ethidium Bromide, supplied by Applichem, used in various techniques. Bioz Stars score: 95/100, based on 101 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Metallation of a 40-base DNA fragment following treatment with cisplatin (molar ratio 1:50) and Pd1 (molar ratios 1:100 and 1:200). The level of metal binding following interactions between the tested complexes and the DNA probe was analyzed after BamH1 treatment, electrophoretic analysis in 5% native polyacrilamide gel, and <t>ethidium</t> bromide staining. On the picture: C , unmodified DNA; CB , BamH1-digested DNA; cis , cisplatin-modified DNA; cisB , cisplatin-modified DNA (1:50) BamH1-digested; Pd , Pd1 -modified DNA; PdIB , Pd1 -modified DNA (1:100) BamH1-digested, PdIIB , Pd1 -modified DNA (1:200) BamH1-digested.
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    Metallation of a 40-base DNA fragment following treatment with cisplatin (molar ratio 1:50) and Pd1 (molar ratios 1:100 and 1:200). The level of metal binding following interactions between the tested complexes and the DNA probe was analyzed after BamH1 treatment, electrophoretic analysis in 5% native polyacrilamide gel, and <t>ethidium</t> bromide staining. On the picture: C , unmodified DNA; CB , BamH1-digested DNA; cis , cisplatin-modified DNA; cisB , cisplatin-modified DNA (1:50) BamH1-digested; Pd , Pd1 -modified DNA; PdIB , Pd1 -modified DNA (1:100) BamH1-digested, PdIIB , Pd1 -modified DNA (1:200) BamH1-digested.
    Ethidium Bromide, supplied by SERVA Electrophoresis, used in various techniques. Bioz Stars score: 91/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Metallation of a 40-base DNA fragment following treatment with cisplatin (molar ratio 1:50) and Pd1 (molar ratios 1:100 and 1:200). The level of metal binding following interactions between the tested complexes and the DNA probe was analyzed after BamH1 treatment, electrophoretic analysis in 5% native polyacrilamide gel, and <t>ethidium</t> bromide staining. On the picture: C , unmodified DNA; CB , BamH1-digested DNA; cis , cisplatin-modified DNA; cisB , cisplatin-modified DNA (1:50) BamH1-digested; Pd , Pd1 -modified DNA; PdIB , Pd1 -modified DNA (1:100) BamH1-digested, PdIIB , Pd1 -modified DNA (1:200) BamH1-digested.
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    Image Search Results


    The frequency of intermediate/pro-inflammatory monocytes correlates with the activation of MAIT cells (A) Representative flow cytometry plots for identification of monocytes and their subsets: a, CD14 ++ CD16 − ‘classical’ monocytes; b, CD14 ++ CD16 + ‘intermediate/pro-inflammatory’ monocytes; c, CD14 + CD16 ++ ‘non-classical’ monocytes. EMA, ethidium monoazide; SSC-A, side scatter area. (B) HLA-DR expression on blood and liver monocytes of HCV-infected patients. Median and IQR are shown. (C) Linear regression analysis (non-parametric Spearman correlation) of the frequency of CD14 ++ CD16 + intermediate/pro-inflammatory monocytes and MAIT cell activation in the blood of HCV-infected patients. (D) Plasma IL-18 levels of HCV-infected patients prior to and at week 4 of antiviral therapy compared to uninfected controls. Mean and SD are shown. (E–F) HLA-DR expression of total monocytes and monocyte subsets in blood (E) and liver (F) of HCV-infected patients prior to and at week 4 of antiviral therapy. Median and IQR (E) and Mean and SD (F) are shown. Wk, week.

    Journal: Gastroenterology

    Article Title: Intra-hepatic Depletion of Mucosal Associated Invariant T cells in Hepatitis C Virus-induced Liver Inflammation

    doi: 10.1053/j.gastro.2017.07.043

    Figure Lengend Snippet: The frequency of intermediate/pro-inflammatory monocytes correlates with the activation of MAIT cells (A) Representative flow cytometry plots for identification of monocytes and their subsets: a, CD14 ++ CD16 − ‘classical’ monocytes; b, CD14 ++ CD16 + ‘intermediate/pro-inflammatory’ monocytes; c, CD14 + CD16 ++ ‘non-classical’ monocytes. EMA, ethidium monoazide; SSC-A, side scatter area. (B) HLA-DR expression on blood and liver monocytes of HCV-infected patients. Median and IQR are shown. (C) Linear regression analysis (non-parametric Spearman correlation) of the frequency of CD14 ++ CD16 + intermediate/pro-inflammatory monocytes and MAIT cell activation in the blood of HCV-infected patients. (D) Plasma IL-18 levels of HCV-infected patients prior to and at week 4 of antiviral therapy compared to uninfected controls. Mean and SD are shown. (E–F) HLA-DR expression of total monocytes and monocyte subsets in blood (E) and liver (F) of HCV-infected patients prior to and at week 4 of antiviral therapy. Median and IQR (E) and Mean and SD (F) are shown. Wk, week.

    Article Snippet: Thereafter, cytokine- or E. coli-stimulated PBMC were washed and stained with ethidium monoazide (EMA, Sigma-Aldrich), anti-TCRVα7.2-FITC, anti-CD3-AlexaFluor700, anti-CD4-APC-Cy7, anti-CD8-BV510 (Biolegend), anti-CD16-PE-Cy5, anti-CD19-PE-Cy5 (BD Bioscience), anti-CD161-APC (Miltenyi Biotec) and anti-CD14-PE-Cy5 (AbD Serotec, Raleigh, NC).

    Techniques: Activation Assay, Flow Cytometry, Cytometry, Expressing, Infection

    MAIT cells are depleted in HCV-induced liver inflammation (A) Representative flow cytometry plots for identification of MAIT cells (time gate and singlet gate are not shown). EMA, ethidium monoazide; SSC-A, side scatter area. (B) Frequency of MAIT cells in the blood of 37 HCV patients and 57 uninfected controls (left panel). Frequency of MAIT cells in the liver of 37 HCV patients and 10 uninfected controls (right panel). (C) Linear regression analysis (non-parametric Spearman correlation) of intrahepatic MAIT cell frequency and liver fibrosis (ISHAK) in chronic HCV infection. (D) Linear regression analysis (non-parametric Spearman correlation) of intrahepatic MAIT cell frequency and liver inflammation (histologic activity index) in chronic HCV infection. (E) Serum HCV RNA levels (n=37) and liver biopsy HAI score (n=28) of HCV-infected patients prior to and at week 4 of antiviral therapy. Liver biopsies of 11 patients were of insufficient size for staging and grading. (F) Frequency of MAIT cells in the liver of HCV-infected patients prior to and at week 4 of antiviral therapy compared to uninfected controls (n = 10). Frequency of MAIT cells in the blood of HCV-infected patients prior to, at week 4 of antiviral therapy and at week 24 after the end of antiviral therapy (sustained virological response, SVR) compared to uninfected controls (n = 57). Wk, week. Median and IQR are shown.

    Journal: Gastroenterology

    Article Title: Intra-hepatic Depletion of Mucosal Associated Invariant T cells in Hepatitis C Virus-induced Liver Inflammation

    doi: 10.1053/j.gastro.2017.07.043

    Figure Lengend Snippet: MAIT cells are depleted in HCV-induced liver inflammation (A) Representative flow cytometry plots for identification of MAIT cells (time gate and singlet gate are not shown). EMA, ethidium monoazide; SSC-A, side scatter area. (B) Frequency of MAIT cells in the blood of 37 HCV patients and 57 uninfected controls (left panel). Frequency of MAIT cells in the liver of 37 HCV patients and 10 uninfected controls (right panel). (C) Linear regression analysis (non-parametric Spearman correlation) of intrahepatic MAIT cell frequency and liver fibrosis (ISHAK) in chronic HCV infection. (D) Linear regression analysis (non-parametric Spearman correlation) of intrahepatic MAIT cell frequency and liver inflammation (histologic activity index) in chronic HCV infection. (E) Serum HCV RNA levels (n=37) and liver biopsy HAI score (n=28) of HCV-infected patients prior to and at week 4 of antiviral therapy. Liver biopsies of 11 patients were of insufficient size for staging and grading. (F) Frequency of MAIT cells in the liver of HCV-infected patients prior to and at week 4 of antiviral therapy compared to uninfected controls (n = 10). Frequency of MAIT cells in the blood of HCV-infected patients prior to, at week 4 of antiviral therapy and at week 24 after the end of antiviral therapy (sustained virological response, SVR) compared to uninfected controls (n = 57). Wk, week. Median and IQR are shown.

    Article Snippet: Thereafter, cytokine- or E. coli-stimulated PBMC were washed and stained with ethidium monoazide (EMA, Sigma-Aldrich), anti-TCRVα7.2-FITC, anti-CD3-AlexaFluor700, anti-CD4-APC-Cy7, anti-CD8-BV510 (Biolegend), anti-CD16-PE-Cy5, anti-CD19-PE-Cy5 (BD Bioscience), anti-CD161-APC (Miltenyi Biotec) and anti-CD14-PE-Cy5 (AbD Serotec, Raleigh, NC).

    Techniques: Flow Cytometry, Cytometry, Infection, Activity Assay

    2.3% native agarose gel in 0.5X TBE buffer, showing a representative library prep from wild-type Okazaki fragments. The gel is stained with Ethidium Bromide. Monosome- and disome-sized fragments with ligated sequencing-adaptors can be seen along with

    Journal: Methods in molecular biology (Clifton, N.J.)

    Article Title: Detection and sequencing of Okazaki fragments in S. cerevisiae

    doi: 10.1007/978-1-4939-2596-4_10

    Figure Lengend Snippet: 2.3% native agarose gel in 0.5X TBE buffer, showing a representative library prep from wild-type Okazaki fragments. The gel is stained with Ethidium Bromide. Monosome- and disome-sized fragments with ligated sequencing-adaptors can be seen along with

    Article Snippet: YPD (1% yeast extract, 2% peptone: autoclave and add filter-sterilized 40% glucose to a final concentration of 2%) 100mg/ml Doxycycline hydrochloride stock solution in DMSO (if using Dox-repressible CDC9 construct) (Fisher Scientific, Cat #BP2653-5) Shaking incubator 250ml Erlenmeyer flasks SCE: 1M sorbitol, 100mM sodium citrate, 60mM EDTA. pH to 7.0, filter-sterilize and store at 4°C Zymolyase 20T (Sunrise Science Products, N0766391) Lysis buffer: 50mM Tris-HCl pH8.0, 50mM EDTA, 100mM NaCl, 1.5% sarkosyl Proteinase K (Fisher Scientific, cat# BP1700100) Isopropanol 3M Sodium acetate, pH 5.2 Absolute ethanol STE: 100mM NaCl, 10mM Tris-HCl pH8.0, 1mM EDTA Riboshredder RNase blend (Epicentre, cat #RS12500) or RNase A (20mg/ml stock solution) TE: 10mM Tris-HCl pH8.0, 1mM EDTA (Optional) Spin-X centrifuge tubes with 0.45um cellulose acetate filter (Costar, cat#8162) Agarose, 0.5x TAE/0.5x TBE running buffer, and GelRed or ethidium bromide (Invitrogen, Cat#15585-011)

    Techniques: Agarose Gel Electrophoresis, Staining, Sequencing

    Okazaki fragment preparations resolved on 0.7% native agarose gel in 0.5X TBE buffer, stained with Ethidium bromide. Large genomic DNA can be seen above the corresponding 10kb band of 2log ladder, while contaminating RNA typically runs below 100bp as

    Journal: Methods in molecular biology (Clifton, N.J.)

    Article Title: Detection and sequencing of Okazaki fragments in S. cerevisiae

    doi: 10.1007/978-1-4939-2596-4_10

    Figure Lengend Snippet: Okazaki fragment preparations resolved on 0.7% native agarose gel in 0.5X TBE buffer, stained with Ethidium bromide. Large genomic DNA can be seen above the corresponding 10kb band of 2log ladder, while contaminating RNA typically runs below 100bp as

    Article Snippet: YPD (1% yeast extract, 2% peptone: autoclave and add filter-sterilized 40% glucose to a final concentration of 2%) 100mg/ml Doxycycline hydrochloride stock solution in DMSO (if using Dox-repressible CDC9 construct) (Fisher Scientific, Cat #BP2653-5) Shaking incubator 250ml Erlenmeyer flasks SCE: 1M sorbitol, 100mM sodium citrate, 60mM EDTA. pH to 7.0, filter-sterilize and store at 4°C Zymolyase 20T (Sunrise Science Products, N0766391) Lysis buffer: 50mM Tris-HCl pH8.0, 50mM EDTA, 100mM NaCl, 1.5% sarkosyl Proteinase K (Fisher Scientific, cat# BP1700100) Isopropanol 3M Sodium acetate, pH 5.2 Absolute ethanol STE: 100mM NaCl, 10mM Tris-HCl pH8.0, 1mM EDTA Riboshredder RNase blend (Epicentre, cat #RS12500) or RNase A (20mg/ml stock solution) TE: 10mM Tris-HCl pH8.0, 1mM EDTA (Optional) Spin-X centrifuge tubes with 0.45um cellulose acetate filter (Costar, cat#8162) Agarose, 0.5x TAE/0.5x TBE running buffer, and GelRed or ethidium bromide (Invitrogen, Cat#15585-011)

    Techniques: Agarose Gel Electrophoresis, Staining

    Nested/PCR-RFLP of ( A ) Plasmodium falciparum samples, two patients from Pará State (Pf – PA) and Acre State (Pf – AC) and Pf 3D7 culture (diluted 1:100); ( B ) Plasmodium brasilianum/Plasmodium malariae , two NHPs (Pbr 2434 and Pbr 2620), two patients (Pm P3 and Pm l11) and Plasmodium brasilianum from MR4 (diluted 1:100 in water); ( C ) Negative controls of PCR: two uninfected humans (UH - 1 and 2), one uninfected NHP (UNHP), and negative control of PCR (NC - without DNA). Reactions were performed simultaneously in the same thermocycler and splited in different agarose gels. 3% Agarose gelstained with ethidium bromide. MM: 1 kb Plus Ladder. D: Digested; ND: Non Digested.

    Journal: Scientific Reports

    Article Title: An assay for the identification of Plasmodium simium infection for diagnosis of zoonotic malaria in the Brazilian Atlantic Forest

    doi: 10.1038/s41598-017-18216-x

    Figure Lengend Snippet: Nested/PCR-RFLP of ( A ) Plasmodium falciparum samples, two patients from Pará State (Pf – PA) and Acre State (Pf – AC) and Pf 3D7 culture (diluted 1:100); ( B ) Plasmodium brasilianum/Plasmodium malariae , two NHPs (Pbr 2434 and Pbr 2620), two patients (Pm P3 and Pm l11) and Plasmodium brasilianum from MR4 (diluted 1:100 in water); ( C ) Negative controls of PCR: two uninfected humans (UH - 1 and 2), one uninfected NHP (UNHP), and negative control of PCR (NC - without DNA). Reactions were performed simultaneously in the same thermocycler and splited in different agarose gels. 3% Agarose gelstained with ethidium bromide. MM: 1 kb Plus Ladder. D: Digested; ND: Non Digested.

    Article Snippet: The amplified fragments were visualized by electrophoresis on 2% agarose gels in 1x TAE buffer (40 mM Tris-acetate, 1 mM EDTA) with 5 μg/mL ethidium bromide (Invitrogen) in a horizontal system (Bio-Rad) at 100 V for 30 min. Gels were examined with a UV transilluminator (UVP - Bio-Doc System it).

    Techniques: Nested PCR, Polymerase Chain Reaction, Negative Control

    Differential diagnosis of Plasmodium simium infection by nested/PCR followed by a digestion with Hpy CH4III restriction enzyme of 9 infected human samples from Atlantic Forest in Rio de Janeiro/RJ (H2 – H9) and one from Amazon endemic region (H1) according to Additional file 1. 3% agarose gel stained with ethidium bromide. MM:1 kb Plus Ladder (ThermoFischer, Calrsbad, CA, USA). Reactions were performed simultaneously in the same thermocycler and splited in different gels.D: Digested; ND: Non Digested. PC Pv: Positive Control for P. vivax , PC Ps: positive control for P. simium . NC: Negative Control (without DNA).

    Journal: Scientific Reports

    Article Title: An assay for the identification of Plasmodium simium infection for diagnosis of zoonotic malaria in the Brazilian Atlantic Forest

    doi: 10.1038/s41598-017-18216-x

    Figure Lengend Snippet: Differential diagnosis of Plasmodium simium infection by nested/PCR followed by a digestion with Hpy CH4III restriction enzyme of 9 infected human samples from Atlantic Forest in Rio de Janeiro/RJ (H2 – H9) and one from Amazon endemic region (H1) according to Additional file 1. 3% agarose gel stained with ethidium bromide. MM:1 kb Plus Ladder (ThermoFischer, Calrsbad, CA, USA). Reactions were performed simultaneously in the same thermocycler and splited in different gels.D: Digested; ND: Non Digested. PC Pv: Positive Control for P. vivax , PC Ps: positive control for P. simium . NC: Negative Control (without DNA).

    Article Snippet: The amplified fragments were visualized by electrophoresis on 2% agarose gels in 1x TAE buffer (40 mM Tris-acetate, 1 mM EDTA) with 5 μg/mL ethidium bromide (Invitrogen) in a horizontal system (Bio-Rad) at 100 V for 30 min. Gels were examined with a UV transilluminator (UVP - Bio-Doc System it).

    Techniques: Infection, Nested PCR, Agarose Gel Electrophoresis, Staining, Positive Control, Negative Control

    Nested/PCR-RFLP of P. vivax DNA samples. 15 DNA samples from P. vivax infected individuals from different parts of Amazon: Porto Velho/Rondônia State, Brazil (PvPV/RO1 and 2), Guyana (PvGuy), Ariquemes/Rondônia State, Brazil (PvAri/RO), Venezuela (PvVen), French Guiana (PvFrGui), Novo progresso/Pará State, Brazil (PvNP/PA), Rio Pardo/Amazonas State, Brazil (PvRP/AM1, 2 and 3), Humaita/Amazonas State, Brazil (PvHu/Am1, 2, 3 and 4) and unknown city in Amazonas State, Brazil (PvAM) were used for Nested PCR amplification followed by digestion with Hpy CH4III restriction enzyme. 3% Agarose gel stained with ethidium bromide. Name tags above gels indicated the patients according to Additional file 2. Reactions were performed simultaneously in the same thermocycler and splited in different gels. MM: 1 kb Plus Ladder. D: Digested (8 μL of digestion); ND: Non Digested (the equivalent amount of PCR product used in the digestion, 6.5 μL of samples and 5 μL of controls); PC Pv: positive control of P. vivax (pool of samples from infected patient from Amazonia); PC Ps: positive control of P. simium ( Alouatta g. clamitans infected with P. simium previously sequenced 30 ); NC: negative Control.

    Journal: Scientific Reports

    Article Title: An assay for the identification of Plasmodium simium infection for diagnosis of zoonotic malaria in the Brazilian Atlantic Forest

    doi: 10.1038/s41598-017-18216-x

    Figure Lengend Snippet: Nested/PCR-RFLP of P. vivax DNA samples. 15 DNA samples from P. vivax infected individuals from different parts of Amazon: Porto Velho/Rondônia State, Brazil (PvPV/RO1 and 2), Guyana (PvGuy), Ariquemes/Rondônia State, Brazil (PvAri/RO), Venezuela (PvVen), French Guiana (PvFrGui), Novo progresso/Pará State, Brazil (PvNP/PA), Rio Pardo/Amazonas State, Brazil (PvRP/AM1, 2 and 3), Humaita/Amazonas State, Brazil (PvHu/Am1, 2, 3 and 4) and unknown city in Amazonas State, Brazil (PvAM) were used for Nested PCR amplification followed by digestion with Hpy CH4III restriction enzyme. 3% Agarose gel stained with ethidium bromide. Name tags above gels indicated the patients according to Additional file 2. Reactions were performed simultaneously in the same thermocycler and splited in different gels. MM: 1 kb Plus Ladder. D: Digested (8 μL of digestion); ND: Non Digested (the equivalent amount of PCR product used in the digestion, 6.5 μL of samples and 5 μL of controls); PC Pv: positive control of P. vivax (pool of samples from infected patient from Amazonia); PC Ps: positive control of P. simium ( Alouatta g. clamitans infected with P. simium previously sequenced 30 ); NC: negative Control.

    Article Snippet: The amplified fragments were visualized by electrophoresis on 2% agarose gels in 1x TAE buffer (40 mM Tris-acetate, 1 mM EDTA) with 5 μg/mL ethidium bromide (Invitrogen) in a horizontal system (Bio-Rad) at 100 V for 30 min. Gels were examined with a UV transilluminator (UVP - Bio-Doc System it).

    Techniques: Nested PCR, Infection, Amplification, Agarose Gel Electrophoresis, Staining, Polymerase Chain Reaction, Positive Control, Negative Control

    Differential Diagnosis of Plasmodium simium infection by nested/PCR followed by a digestion with Hpy CH4III restriction enzyme of 16 non-human primate samples: ( A ) 2 captive NHP from Rio de Janeiro/RJ ( Sapajus xanthosternos 2098; Cacajao melanocephalus 2302), one free-living Alouatta g. clamitans from Rio de Janeiro State (3636) and 6 free-living Alouatta g. clamitans from Joinville/SC, Brazil (J9, J11, J15, J20, J22, J25); ( B ) 7 Alouatta g. clamitans from CEPESBI, Indaial, SC, Brazil (Bl3, Bl6, Bl10, Bl28, Bl61, Bl64, Bl69), *Captive NHPs, all the other were free-living. More details about each sample see Additional file 1. 3% agarose gel stained with ethidium bromide. MM:1 kb Plus Ladder (ThermoFischer). Reactions were performed simultaneously in the same thermocycler and splited in different gels. PC Pv: Positive Control for P. vivax , PC Ps: positive control for P. simium . NC: Negative Control (without DNA).

    Journal: Scientific Reports

    Article Title: An assay for the identification of Plasmodium simium infection for diagnosis of zoonotic malaria in the Brazilian Atlantic Forest

    doi: 10.1038/s41598-017-18216-x

    Figure Lengend Snippet: Differential Diagnosis of Plasmodium simium infection by nested/PCR followed by a digestion with Hpy CH4III restriction enzyme of 16 non-human primate samples: ( A ) 2 captive NHP from Rio de Janeiro/RJ ( Sapajus xanthosternos 2098; Cacajao melanocephalus 2302), one free-living Alouatta g. clamitans from Rio de Janeiro State (3636) and 6 free-living Alouatta g. clamitans from Joinville/SC, Brazil (J9, J11, J15, J20, J22, J25); ( B ) 7 Alouatta g. clamitans from CEPESBI, Indaial, SC, Brazil (Bl3, Bl6, Bl10, Bl28, Bl61, Bl64, Bl69), *Captive NHPs, all the other were free-living. More details about each sample see Additional file 1. 3% agarose gel stained with ethidium bromide. MM:1 kb Plus Ladder (ThermoFischer). Reactions were performed simultaneously in the same thermocycler and splited in different gels. PC Pv: Positive Control for P. vivax , PC Ps: positive control for P. simium . NC: Negative Control (without DNA).

    Article Snippet: The amplified fragments were visualized by electrophoresis on 2% agarose gels in 1x TAE buffer (40 mM Tris-acetate, 1 mM EDTA) with 5 μg/mL ethidium bromide (Invitrogen) in a horizontal system (Bio-Rad) at 100 V for 30 min. Gels were examined with a UV transilluminator (UVP - Bio-Doc System it).

    Techniques: Infection, Nested PCR, Agarose Gel Electrophoresis, Staining, Positive Control, Negative Control

    Detection limit of the Nested-PCR for a differential diagnosis of Plasmodium simium. P. simium human DNA sample were serially diluted 2-fold with a starting parasitemia of 100 parasites/µL to 1.65 parasites/µL. 2% Agarose gel stained with ethidium bromide. MM:1 kb Plus Ladder, PC: positive control, NC: negative control (without DNA).

    Journal: Scientific Reports

    Article Title: An assay for the identification of Plasmodium simium infection for diagnosis of zoonotic malaria in the Brazilian Atlantic Forest

    doi: 10.1038/s41598-017-18216-x

    Figure Lengend Snippet: Detection limit of the Nested-PCR for a differential diagnosis of Plasmodium simium. P. simium human DNA sample were serially diluted 2-fold with a starting parasitemia of 100 parasites/µL to 1.65 parasites/µL. 2% Agarose gel stained with ethidium bromide. MM:1 kb Plus Ladder, PC: positive control, NC: negative control (without DNA).

    Article Snippet: The amplified fragments were visualized by electrophoresis on 2% agarose gels in 1x TAE buffer (40 mM Tris-acetate, 1 mM EDTA) with 5 μg/mL ethidium bromide (Invitrogen) in a horizontal system (Bio-Rad) at 100 V for 30 min. Gels were examined with a UV transilluminator (UVP - Bio-Doc System it).

    Techniques: Nested PCR, Agarose Gel Electrophoresis, Staining, Positive Control, Negative Control

    Evaluation of astrocytic GJIC permeability and hemichannel activity after OGD/R injury with Gap19 or Gap26. a For GJIC detection, we measured calcein-AM transfer between “donor cells” and “acceptor cells” with flow cytometry. Shown here is a representative flow cytometry plot of transfer after donor astrocytes were labeled with calcein-AM and cocultured with acceptor astrocytes for 4 h. Grouped dye transfer data are shown in b . OGD/R injury decreased the degree of astrocytic coupling; Gap26 further inhibited cellular coupling. c Representative images depicting ethidium uptake via hemichannels in the four groups. d OGD/R injury increased astrocytic ethidium uptake, while Gap19 and Gap26 achieved similar attenuation of hemichannel opening. e The supernatant ATP concentration was strongly elevated in the OGD/R group astrocytes, but Gap19 and Gap26 reversed this effect. We evaluated the statistical significance with ANOVA and Duncan’s multiple comparisons test. * p

    Journal: Journal of Neuroinflammation

    Article Title: Roles of astrocytic connexin-43, hemichannels, and gap junctions in oxygen-glucose deprivation/reperfusion injury induced neuroinflammation and the possible regulatory mechanisms of salvianolic acid B and carbenoxolone

    doi: 10.1186/s12974-018-1127-3

    Figure Lengend Snippet: Evaluation of astrocytic GJIC permeability and hemichannel activity after OGD/R injury with Gap19 or Gap26. a For GJIC detection, we measured calcein-AM transfer between “donor cells” and “acceptor cells” with flow cytometry. Shown here is a representative flow cytometry plot of transfer after donor astrocytes were labeled with calcein-AM and cocultured with acceptor astrocytes for 4 h. Grouped dye transfer data are shown in b . OGD/R injury decreased the degree of astrocytic coupling; Gap26 further inhibited cellular coupling. c Representative images depicting ethidium uptake via hemichannels in the four groups. d OGD/R injury increased astrocytic ethidium uptake, while Gap19 and Gap26 achieved similar attenuation of hemichannel opening. e The supernatant ATP concentration was strongly elevated in the OGD/R group astrocytes, but Gap19 and Gap26 reversed this effect. We evaluated the statistical significance with ANOVA and Duncan’s multiple comparisons test. * p

    Article Snippet: Ethidium bromide uptake For dye uptake experiments, astrocytes cultured were washed and then exposed to 0.5 μM ethidium bromide (EtBr) (Abcam, Cat#ab141391) for 10 min at 37 °C.

    Techniques: Permeability, Activity Assay, Flow Cytometry, Cytometry, Labeling, Concentration Assay

    Evaluation of impact of MCM on astrocytic GJIC permeability and hemichannel activity after OGD/R injury. a For GJIC detection, we measured calcein-AM transfer between “donor cells” and “acceptor cells” with flow cytometry. Shown here is a representative flow cytometry plot of transfer after donor astrocytes were labeled with calcein-AM and co-cultured with acceptor astrocytes for 4 h. Grouped dye transfer data are shown in b . OGD/R-MCM decreased the degree of astrocytic coupling, but OGD/R-SalB-MCM increased astrocytic intercellular dye transfer. c Representative images depicting ethidium uptake via hemichannels in the four groups. d OGD/R-MCM increased astrocytic ethidium uptake, but this effect was reversed in OGD/R-SalB-MCM-treated astrocytes. e OGD/R-MCM increased ATP concentrations in the astrocytic supernatant, but this effect was reversed by OGD/R-SalB-MCM. We evaluated the statistical significance with ANOVA and Duncan’s multiple comparisons test. * p

    Journal: Journal of Neuroinflammation

    Article Title: Roles of astrocytic connexin-43, hemichannels, and gap junctions in oxygen-glucose deprivation/reperfusion injury induced neuroinflammation and the possible regulatory mechanisms of salvianolic acid B and carbenoxolone

    doi: 10.1186/s12974-018-1127-3

    Figure Lengend Snippet: Evaluation of impact of MCM on astrocytic GJIC permeability and hemichannel activity after OGD/R injury. a For GJIC detection, we measured calcein-AM transfer between “donor cells” and “acceptor cells” with flow cytometry. Shown here is a representative flow cytometry plot of transfer after donor astrocytes were labeled with calcein-AM and co-cultured with acceptor astrocytes for 4 h. Grouped dye transfer data are shown in b . OGD/R-MCM decreased the degree of astrocytic coupling, but OGD/R-SalB-MCM increased astrocytic intercellular dye transfer. c Representative images depicting ethidium uptake via hemichannels in the four groups. d OGD/R-MCM increased astrocytic ethidium uptake, but this effect was reversed in OGD/R-SalB-MCM-treated astrocytes. e OGD/R-MCM increased ATP concentrations in the astrocytic supernatant, but this effect was reversed by OGD/R-SalB-MCM. We evaluated the statistical significance with ANOVA and Duncan’s multiple comparisons test. * p

    Article Snippet: Ethidium bromide uptake For dye uptake experiments, astrocytes cultured were washed and then exposed to 0.5 μM ethidium bromide (EtBr) (Abcam, Cat#ab141391) for 10 min at 37 °C.

    Techniques: Permeability, Activity Assay, Flow Cytometry, Cytometry, Labeling, Cell Culture

    Evaluation of astrocytic GJIC permeability and hemichannel activity after OGD/R injury with SalB or CBX. a For GJIC detection, we measured calcein-AM transfer between “donor cells” and “acceptor cells” with flow cytometry. Shown here is a representative flow cytometry plot of transfer after donor astrocytes were labeled with calcein-AM and cocultured with acceptor astrocytes for 4 h. Grouped dye transfer data are shown in b . OGD/R injury decreased the degree of astrocytic coupling, but SalB reversed this effect. CBX further inhibited cellular coupling. c Representative images depicting ethidium uptake via hemichannels in the four groups. d OGD/R injury increased astrocytic ethidium uptake, but SalB and CBX achieved near-significant attenuation of this effect. e The supernatant ATP concentration was strongly elevated in the OGD/R group astrocytes, but SalB and CBX reversed this effect. We evaluated the statistical significance with ANOVA and Duncan’s multiple comparisons test. * p

    Journal: Journal of Neuroinflammation

    Article Title: Roles of astrocytic connexin-43, hemichannels, and gap junctions in oxygen-glucose deprivation/reperfusion injury induced neuroinflammation and the possible regulatory mechanisms of salvianolic acid B and carbenoxolone

    doi: 10.1186/s12974-018-1127-3

    Figure Lengend Snippet: Evaluation of astrocytic GJIC permeability and hemichannel activity after OGD/R injury with SalB or CBX. a For GJIC detection, we measured calcein-AM transfer between “donor cells” and “acceptor cells” with flow cytometry. Shown here is a representative flow cytometry plot of transfer after donor astrocytes were labeled with calcein-AM and cocultured with acceptor astrocytes for 4 h. Grouped dye transfer data are shown in b . OGD/R injury decreased the degree of astrocytic coupling, but SalB reversed this effect. CBX further inhibited cellular coupling. c Representative images depicting ethidium uptake via hemichannels in the four groups. d OGD/R injury increased astrocytic ethidium uptake, but SalB and CBX achieved near-significant attenuation of this effect. e The supernatant ATP concentration was strongly elevated in the OGD/R group astrocytes, but SalB and CBX reversed this effect. We evaluated the statistical significance with ANOVA and Duncan’s multiple comparisons test. * p

    Article Snippet: Ethidium bromide uptake For dye uptake experiments, astrocytes cultured were washed and then exposed to 0.5 μM ethidium bromide (EtBr) (Abcam, Cat#ab141391) for 10 min at 37 °C.

    Techniques: Permeability, Activity Assay, Flow Cytometry, Cytometry, Labeling, Concentration Assay

    Electrophoretic mobility gel shift assays of siRNA and dsDNA binding to DRBD fusion proteins or synthetic peptides. 1 μmol/l siRNA or dsDNA was incubated with varying concentrations of protein and their interaction measured by migration on a 6% acrylamide gel followed by staining with ethidium bromide. ( a , b ) Gel shift of siRNA binding to DRBD or PPS-DRBD with increasing molar ratios of protein to siRNA. ( c ) Gel shift of either siRNA or dsDNA binding to PTD-DRBD at different molar ratios. ( d ) Gel shift of 1 μmol/l siRNA interacting with synthetic peptides at either 20 or 40 μmol/l. DRBD, double-stranded RNA-binding domain; dsDNA, double-stranded DNA; PTD, protein transduction domain; siRNA, small interfering RNA.

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: Gene Silencing Mediated by siRNA-binding Fusion Proteins Is Attenuated by Double-stranded RNA-binding Domain Structure

    doi: 10.1038/mtna.2012.43

    Figure Lengend Snippet: Electrophoretic mobility gel shift assays of siRNA and dsDNA binding to DRBD fusion proteins or synthetic peptides. 1 μmol/l siRNA or dsDNA was incubated with varying concentrations of protein and their interaction measured by migration on a 6% acrylamide gel followed by staining with ethidium bromide. ( a , b ) Gel shift of siRNA binding to DRBD or PPS-DRBD with increasing molar ratios of protein to siRNA. ( c ) Gel shift of either siRNA or dsDNA binding to PTD-DRBD at different molar ratios. ( d ) Gel shift of 1 μmol/l siRNA interacting with synthetic peptides at either 20 or 40 μmol/l. DRBD, double-stranded RNA-binding domain; dsDNA, double-stranded DNA; PTD, protein transduction domain; siRNA, small interfering RNA.

    Article Snippet: The gel was stained with 0.5 μg/ml ethidium bromide (Bio-Rad) and visualized using a VersaDoc 5000 MP (Bio-Rad).

    Techniques: Electrophoretic Mobility Shift Assay, Binding Assay, Incubation, Migration, Acrylamide Gel Assay, Staining, RNA Binding Assay, Transduction, Small Interfering RNA

    Agarose gel electrophoresis of NR3C1 646 C > G fragments stained with ethidium bromide. Lane 1: 100 bp Ladder. Lane 2 represents unrestricted fragment, 1 band = 418 bp (experimental control: no enzyme “mock”). Lane 3 shows homozygous (GG) genotype, 1 band = 418 bp. Lane 4 shows heterozygous (GC) genotype, 3 bands = 418,263,155 bp. Lane 5 shows homozygous (CC) genotype, 2 bands = 263, 155 bp

    Journal: Central-European Journal of Immunology

    Article Title: Influence of glucocorticoid receptor gene NR3C1 646 C > G polymorphism on glucocorticoid resistance in asthmatics: a preliminary study

    doi: 10.5114/ceji.2015.54594

    Figure Lengend Snippet: Agarose gel electrophoresis of NR3C1 646 C > G fragments stained with ethidium bromide. Lane 1: 100 bp Ladder. Lane 2 represents unrestricted fragment, 1 band = 418 bp (experimental control: no enzyme “mock”). Lane 3 shows homozygous (GG) genotype, 1 band = 418 bp. Lane 4 shows heterozygous (GC) genotype, 3 bands = 418,263,155 bp. Lane 5 shows homozygous (CC) genotype, 2 bands = 263, 155 bp

    Article Snippet: DNA analysis by gel electrophoresis Amplified product of DNA samples and restriction fragments were run on 2% agarose gel (Promega) for 30 minutes at 100 V, stained with ethidium bromide (Amresco, Germany).

    Techniques: Agarose Gel Electrophoresis, Staining

    Inhibitors of nuclear (α) or mitochondrial (γ) DNA polymerases differentially block EdU incorporation. F11 neuroblastoma cells are incubated with or without DNA polymerase inhibitors 4 hr prior to and together with EdU for an additional 12 hr. Amplified EdU signal (EdU-OG-TSA) is compared with DNA stain (DAPI, blue) and cell morphology (DIC). ( A ) Cells incubated with EdU show both nuclear (arrowheads) and mtDNA (arrows) incorporation. ( B ) Addition of 7 μM aphidicolin (+APH) inhibits nuclear incorporation of EdU, whereas mtDNA labeling (arrows) is maintained. ( C ) The presence of 1.0 μg/ml ethidium bromide (+EtBr) inhibits incorporation of EdU into mtDNA but not into nuclear DNA (arrowheads). ( D ) 2′,3′-Dideoxycytidine (+ddC, 200 μM) also inhibits mtDNA but not nuclear incorporation of EdU (arrowheads). Bar = 10 μm.

    Journal: Journal of Histochemistry and Cytochemistry

    Article Title: Mitochondrial DNA (mtDNA) Biogenesis: Visualization and Duel Incorporation of BrdU and EdU Into Newly Synthesized mtDNA In Vitro

    doi: 10.1369/jhc.2009.954701

    Figure Lengend Snippet: Inhibitors of nuclear (α) or mitochondrial (γ) DNA polymerases differentially block EdU incorporation. F11 neuroblastoma cells are incubated with or without DNA polymerase inhibitors 4 hr prior to and together with EdU for an additional 12 hr. Amplified EdU signal (EdU-OG-TSA) is compared with DNA stain (DAPI, blue) and cell morphology (DIC). ( A ) Cells incubated with EdU show both nuclear (arrowheads) and mtDNA (arrows) incorporation. ( B ) Addition of 7 μM aphidicolin (+APH) inhibits nuclear incorporation of EdU, whereas mtDNA labeling (arrows) is maintained. ( C ) The presence of 1.0 μg/ml ethidium bromide (+EtBr) inhibits incorporation of EdU into mtDNA but not into nuclear DNA (arrowheads). ( D ) 2′,3′-Dideoxycytidine (+ddC, 200 μM) also inhibits mtDNA but not nuclear incorporation of EdU (arrowheads). Bar = 10 μm.

    Article Snippet: Ethidium bromide (10 mg/ml stock; Promega, Madison, WI) at 0.5, 1.0, or 1.5 μg/ml or 2′,3′-dideoxycytidine (ddC, 10 mM stock; Sigma-Aldrich) at 50, 100, or 200 μM was added to culture media to inhibit DNA polymerase γ (mitochondrial).

    Techniques: Blocking Assay, Incubation, Amplification, Staining, Labeling

    Inhibitors of nuclear (α) or mitochondrial (γ) DNA polymerases differentially block BrdU incorporation. F11 neuroblastoma cells are incubated with BrdU for 12 hr with or without the addition of DNA polymerase inhibitors. Amplified BrdU signal [αBrdU-TSA, ( A,B in green; C,D in red)] is compared with DNA stain (DAPI, blue) and cell morphology (DIC). ( A,C ) Cells incubated with BrdU show both nuclear DNA (arrowheads) and mtDNA (arrows) incorporation. Insets ( A,B ) show magnified views of the boxed areas to illustrate the detail of the BrdU signals. ( B ) Addition of 7 μM aphidicolin (+APH) inhibits nuclear incorporation of BrdU, whereas mtDNA labeling (arrows) is maintained. ( D ) Addition of 1.0 μg/ml of ethidium bromide (+EtBr) inhibits incorporation of BrdU into mtDNA but not into nuclear DNA (arrowhead). Bar = 10 μm.

    Journal: Journal of Histochemistry and Cytochemistry

    Article Title: Mitochondrial DNA (mtDNA) Biogenesis: Visualization and Duel Incorporation of BrdU and EdU Into Newly Synthesized mtDNA In Vitro

    doi: 10.1369/jhc.2009.954701

    Figure Lengend Snippet: Inhibitors of nuclear (α) or mitochondrial (γ) DNA polymerases differentially block BrdU incorporation. F11 neuroblastoma cells are incubated with BrdU for 12 hr with or without the addition of DNA polymerase inhibitors. Amplified BrdU signal [αBrdU-TSA, ( A,B in green; C,D in red)] is compared with DNA stain (DAPI, blue) and cell morphology (DIC). ( A,C ) Cells incubated with BrdU show both nuclear DNA (arrowheads) and mtDNA (arrows) incorporation. Insets ( A,B ) show magnified views of the boxed areas to illustrate the detail of the BrdU signals. ( B ) Addition of 7 μM aphidicolin (+APH) inhibits nuclear incorporation of BrdU, whereas mtDNA labeling (arrows) is maintained. ( D ) Addition of 1.0 μg/ml of ethidium bromide (+EtBr) inhibits incorporation of BrdU into mtDNA but not into nuclear DNA (arrowhead). Bar = 10 μm.

    Article Snippet: Ethidium bromide (10 mg/ml stock; Promega, Madison, WI) at 0.5, 1.0, or 1.5 μg/ml or 2′,3′-dideoxycytidine (ddC, 10 mM stock; Sigma-Aldrich) at 50, 100, or 200 μM was added to culture media to inhibit DNA polymerase γ (mitochondrial).

    Techniques: Blocking Assay, BrdU Incorporation Assay, Incubation, Amplification, Staining, Labeling

    Total RNA quality assessment on the basis of 18S and 28S rRNA . On left side, lane # 1 shows DNA ladder (0.5 kb – 7.0 kb). The ethidium bromide-staining pattern of intact total RNA shows clearly defined 18S and 28S ribosomal RNA bands [lane # 3–5 (GTC; fresh); lane # 6–8 (SGC; fresh sample); lane # 9–11 (GTC; frozen); and lane # 12–14 (SGC; frozen).

    Journal: Diagnostic Pathology

    Article Title: Systematic comparison of RNA extraction techniques from frozen and fresh lung tissues: checkpoint towards gene expression studies

    doi: 10.1186/1746-1596-4-9

    Figure Lengend Snippet: Total RNA quality assessment on the basis of 18S and 28S rRNA . On left side, lane # 1 shows DNA ladder (0.5 kb – 7.0 kb). The ethidium bromide-staining pattern of intact total RNA shows clearly defined 18S and 28S ribosomal RNA bands [lane # 3–5 (GTC; fresh); lane # 6–8 (SGC; fresh sample); lane # 9–11 (GTC; frozen); and lane # 12–14 (SGC; frozen).

    Article Snippet: The mix was cooked until get boiled, and then 5 μl of 1% ethidium bromide (Roth, Karlsruhe, Germany) was added, mixed, and poured in to gel electrophoresis unit.

    Techniques: Staining

    Detection of PEG-Ad5-PTEN by SDS-PAGE ( A ) and EPAP by TBE-PAGE ( B ). In Figure 3A , (A) It was stained by Coomassie Brilliant Blue; (B) It was stained by 0.1 mol/L iodine solution. Lane 1, marker; Lane 2, positive control protein of BSA; Lane 3, unmodified Ad5; Lane 4, PEG-Ad5-PTEN. In Figure 3B , it was stained by ethidium bromide. Lane 1, marker; Lane 2, EpDT3; Lane 3, PEG-Ad5-PTEN; Lane d 4, EPAP.

    Journal: Oncotarget

    Article Title: Characterization of aptamer-mediated gene delivery system for liver cancer therapy

    doi: 10.18632/oncotarget.23564

    Figure Lengend Snippet: Detection of PEG-Ad5-PTEN by SDS-PAGE ( A ) and EPAP by TBE-PAGE ( B ). In Figure 3A , (A) It was stained by Coomassie Brilliant Blue; (B) It was stained by 0.1 mol/L iodine solution. Lane 1, marker; Lane 2, positive control protein of BSA; Lane 3, unmodified Ad5; Lane 4, PEG-Ad5-PTEN. In Figure 3B , it was stained by ethidium bromide. Lane 1, marker; Lane 2, EpDT3; Lane 3, PEG-Ad5-PTEN; Lane d 4, EPAP.

    Article Snippet: After 30 min for pre-electrophoresis, about 10 μg of all samples were loaded orderly on the gel and the electrophoresis was performed at a constant voltage of 80 V for 5 h. After the electrophoresis, the gels were stained with ethidium bromide (5 mg/mL, Biotium) for 10 min followed by washing 3 times with TBE buffer.

    Techniques: SDS Page, Polyacrylamide Gel Electrophoresis, Staining, Marker, Positive Control

    Condensation reactions demonstrating that ethidium-mediated oligonucleotide polymerization requires Watson–Crick base pairs. Reactions loaded in the Six Right Lanes contained various compositions of d(pCCTA) and d(pGGTA), as indicted above lanes,

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world

    doi: 10.1073/pnas.0914172107

    Figure Lengend Snippet: Condensation reactions demonstrating that ethidium-mediated oligonucleotide polymerization requires Watson–Crick base pairs. Reactions loaded in the Six Right Lanes contained various compositions of d(pCCTA) and d(pGGTA), as indicted above lanes,

    Article Snippet: Ethidium bromide (Fisher Scientific), proflavine hemisulfate (Sigma), and coralyne chloride (Sigma) were used as received. aza3 was synthesized as previously reported ( ).

    Techniques:

    Polyacrylamide gel electrophoresis analysis of reaction products of activated d(pCGTA) in the presence of varying amounts of ethidium. Ethidium concentrations are given above Lanes 1–5 . With no intercalator present ( Lane marked 0 μM

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world

    doi: 10.1073/pnas.0914172107

    Figure Lengend Snippet: Polyacrylamide gel electrophoresis analysis of reaction products of activated d(pCGTA) in the presence of varying amounts of ethidium. Ethidium concentrations are given above Lanes 1–5 . With no intercalator present ( Lane marked 0 μM

    Article Snippet: Ethidium bromide (Fisher Scientific), proflavine hemisulfate (Sigma), and coralyne chloride (Sigma) were used as received. aza3 was synthesized as previously reported ( ).

    Techniques: Polyacrylamide Gel Electrophoresis

    Acridine orange and ethidium bromide nuclear staining of HLMVECs ( A ) and HUVECs ( B ) after 24 hours of DBP-actin treatment. Cells were treated with EGM-2 growth medium, serum started, 1 μM DBP, 1 μM actin or 1 μM DBP-actin complex

    Journal: Immunobiology

    Article Title: Circulating Complexes of the Vitamin D Binding Protein with G-Actin Induce Lung Inflammation by Targeting Endothelial Cells

    doi: 10.1016/j.imbio.2013.10.001

    Figure Lengend Snippet: Acridine orange and ethidium bromide nuclear staining of HLMVECs ( A ) and HUVECs ( B ) after 24 hours of DBP-actin treatment. Cells were treated with EGM-2 growth medium, serum started, 1 μM DBP, 1 μM actin or 1 μM DBP-actin complex

    Article Snippet: Acridine orange (AO) and ethidium bromide (EB) were purchased from Fisher Scientific (Fairlawn, NJ).

    Techniques: Staining

    The nuclear walk-on assay quantitatively and precisely measures engaged Pol II. ( A ) Steps in the nuclear walk-on assay are illustrated. ( B ) Adherent HeLa cells were transfected 48 h before isolation of nuclei with 1.5 nM NELF-A siRNA (NELF KD) or lipid reagent only (Mock). Cells were also treated 1 h before isolation with 0.1% DMSO or 1 μM flavopiridol (Flavo). Nuclear walk-ons were performed using a 6 min α- 32 P-CTP pulse in the absence or presence of 2 μg/ml α-amanitin (α-aman). After 6% Urea-PAGE, ethidium bromide was used to visualize nuclear RNAs. A representative gel from nuclear walk-ons performed in triplicate is shown here. ( C ) Phosphorimage to visualize radiolabeled nascent transcripts from B. ( D ) Average amanitin-sensitive Pol II nascent transcript profiles from triplicate nuclear walk-ons as represented in B and C. For each replicate, signals from each lane in the phosphorimage were normalized using quantifications of cold nuclear RNAs in the ethidium bromide stain. Then, α-amanitin-insensitive signals were subtracted from total signals. Triplicate profiles (see Supplementary Figure S1 ) were then averaged as described in the Materials and Methods. Inset: western blot of NELF-A; a nonspecific band (n.s.) indicates even loading. ( E ) PRO-Seq paired-end reads over the DDIT4 gene and upstream enhancer regions. Adherent HeLa cells were treated 1 h with either 0.1% DMSO or 1 μM flavopiridol. ( F ) Plot of sense or divergent PRO-Seq fragments lengths near Pol II promoters.

    Journal: Nucleic Acids Research

    Article Title: Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome

    doi: 10.1093/nar/gkx724

    Figure Lengend Snippet: The nuclear walk-on assay quantitatively and precisely measures engaged Pol II. ( A ) Steps in the nuclear walk-on assay are illustrated. ( B ) Adherent HeLa cells were transfected 48 h before isolation of nuclei with 1.5 nM NELF-A siRNA (NELF KD) or lipid reagent only (Mock). Cells were also treated 1 h before isolation with 0.1% DMSO or 1 μM flavopiridol (Flavo). Nuclear walk-ons were performed using a 6 min α- 32 P-CTP pulse in the absence or presence of 2 μg/ml α-amanitin (α-aman). After 6% Urea-PAGE, ethidium bromide was used to visualize nuclear RNAs. A representative gel from nuclear walk-ons performed in triplicate is shown here. ( C ) Phosphorimage to visualize radiolabeled nascent transcripts from B. ( D ) Average amanitin-sensitive Pol II nascent transcript profiles from triplicate nuclear walk-ons as represented in B and C. For each replicate, signals from each lane in the phosphorimage were normalized using quantifications of cold nuclear RNAs in the ethidium bromide stain. Then, α-amanitin-insensitive signals were subtracted from total signals. Triplicate profiles (see Supplementary Figure S1 ) were then averaged as described in the Materials and Methods. Inset: western blot of NELF-A; a nonspecific band (n.s.) indicates even loading. ( E ) PRO-Seq paired-end reads over the DDIT4 gene and upstream enhancer regions. Adherent HeLa cells were treated 1 h with either 0.1% DMSO or 1 μM flavopiridol. ( F ) Plot of sense or divergent PRO-Seq fragments lengths near Pol II promoters.

    Article Snippet: Cold RNAs were visualized by ethidium bromide and, after gel drying, radiolabeled RNAs were visualized with a Fujifilm Typhoon FLA-7000 phosphorimager.

    Techniques: Transfection, Isolation, Polyacrylamide Gel Electrophoresis, Staining, Western Blot

    Ethidium and DAPI transport mediated by QacA mutants containing cysteine substitutions at W58A second-site suppressor positions. Transport was monitored fluorimetrically from cells loaded with ethidium bromide (A and C) or DAPI (B and D) after energization.

    Journal: Journal of Bacteriology

    Article Title: Analysis of Tryptophan Residues in the Staphylococcal Multidrug Transporter QacA Reveals Long-Distance Functional Associations of Residues on Opposite Sides of the Membrane

    doi: 10.1128/JB.01864-07

    Figure Lengend Snippet: Ethidium and DAPI transport mediated by QacA mutants containing cysteine substitutions at W58A second-site suppressor positions. Transport was monitored fluorimetrically from cells loaded with ethidium bromide (A and C) or DAPI (B and D) after energization.

    Article Snippet: Ampicillin, benzalkonium chloride, carbonyl cyanide m -chlorophenylhydrazone, chlorhexidine diacetate, dequalinium chloride, 4′,6′-diamidino-2-phenindole (DAPI), n -dodecyl-β- d -maltoside, ethidium bromide, N -ethylmaleimide (NEM), hydroxylamine hydrochloride, pentamidine isothionate, pyronin Y, and rhodamine 6G were purchased from Sigma.

    Techniques:

    Transport of the monovalent QacA substrate ethidium mediated by QacA mutants in which tryptophan has been replaced with alanine or phenylalanine. E. coli DH5α cells expressing each mutant (identified above each plot) were loaded with 15 μM

    Journal: Journal of Bacteriology

    Article Title: Analysis of Tryptophan Residues in the Staphylococcal Multidrug Transporter QacA Reveals Long-Distance Functional Associations of Residues on Opposite Sides of the Membrane

    doi: 10.1128/JB.01864-07

    Figure Lengend Snippet: Transport of the monovalent QacA substrate ethidium mediated by QacA mutants in which tryptophan has been replaced with alanine or phenylalanine. E. coli DH5α cells expressing each mutant (identified above each plot) were loaded with 15 μM

    Article Snippet: Ampicillin, benzalkonium chloride, carbonyl cyanide m -chlorophenylhydrazone, chlorhexidine diacetate, dequalinium chloride, 4′,6′-diamidino-2-phenindole (DAPI), n -dodecyl-β- d -maltoside, ethidium bromide, N -ethylmaleimide (NEM), hydroxylamine hydrochloride, pentamidine isothionate, pyronin Y, and rhodamine 6G were purchased from Sigma.

    Techniques: Expressing, Mutagenesis

    Transport mediated by W58A second-site suppressor mutants (A and B) and G400D and A403T QacA mutants (C and D). E. coli cells were loaded with either 15 μM ethidium bromide (A and C) or 8 μM DAPI (B and D), and transport was monitored

    Journal: Journal of Bacteriology

    Article Title: Analysis of Tryptophan Residues in the Staphylococcal Multidrug Transporter QacA Reveals Long-Distance Functional Associations of Residues on Opposite Sides of the Membrane

    doi: 10.1128/JB.01864-07

    Figure Lengend Snippet: Transport mediated by W58A second-site suppressor mutants (A and B) and G400D and A403T QacA mutants (C and D). E. coli cells were loaded with either 15 μM ethidium bromide (A and C) or 8 μM DAPI (B and D), and transport was monitored

    Article Snippet: Ampicillin, benzalkonium chloride, carbonyl cyanide m -chlorophenylhydrazone, chlorhexidine diacetate, dequalinium chloride, 4′,6′-diamidino-2-phenindole (DAPI), n -dodecyl-β- d -maltoside, ethidium bromide, N -ethylmaleimide (NEM), hydroxylamine hydrochloride, pentamidine isothionate, pyronin Y, and rhodamine 6G were purchased from Sigma.

    Techniques:

    DNA (1000 μ M) and ethidium bromide (50 μ M). ( a ) Absorption spectra of ethidium bromide ( dashed line ) and ethidium bromide-ct-DNA ( solid line ). ( Inset ) Enlarged region of ethidium bromide band. ( b ) Fluorescence excitation spectra with all emitted photons detected, ( c ) LD spectra of ct-DNA ( dashed line ) and ethidium bromide-ct-DNA ( solid line ), and ( d ) FDFLD spectra. All solutions prepared using a sodium cacodylate buffer (10 mM, pH 7).

    Journal: Biophysical Journal

    Article Title: Micro-Volume Couette Flow Sample Orientation for Absorbance and Fluorescence Linear Dichroism

    doi: 10.1529/biophysj.103.035022

    Figure Lengend Snippet: DNA (1000 μ M) and ethidium bromide (50 μ M). ( a ) Absorption spectra of ethidium bromide ( dashed line ) and ethidium bromide-ct-DNA ( solid line ). ( Inset ) Enlarged region of ethidium bromide band. ( b ) Fluorescence excitation spectra with all emitted photons detected, ( c ) LD spectra of ct-DNA ( dashed line ) and ethidium bromide-ct-DNA ( solid line ), and ( d ) FDFLD spectra. All solutions prepared using a sodium cacodylate buffer (10 mM, pH 7).

    Article Snippet: Aqueous solutions of ct-DNA (317 μ M, Sigma), ethidium bromide (30 μ M, Sigma) in sodium cacodylate buffer (10 mM, pH 7, Sigma), and NaCl (10 mM, Sigma) were used.

    Techniques: Fluorescence

    LD spectra of DNA (200 μ M) and different concentrations of ethidium bromide (0–50 μ M) using a sodium cacodylate buffer (10 mM, pH 7) and NaCl (10 mM).

    Journal: Biophysical Journal

    Article Title: Micro-Volume Couette Flow Sample Orientation for Absorbance and Fluorescence Linear Dichroism

    doi: 10.1529/biophysj.103.035022

    Figure Lengend Snippet: LD spectra of DNA (200 μ M) and different concentrations of ethidium bromide (0–50 μ M) using a sodium cacodylate buffer (10 mM, pH 7) and NaCl (10 mM).

    Article Snippet: Aqueous solutions of ct-DNA (317 μ M, Sigma), ethidium bromide (30 μ M, Sigma) in sodium cacodylate buffer (10 mM, pH 7, Sigma), and NaCl (10 mM, Sigma) were used.

    Techniques:

    Fluorescence emission spectra of intercalated Ethidium bromide and human genomic DNA incubated with increasing concentrations of TiO 2 nanoparticle at 37 °C

    Journal: Cytotechnology

    Article Title: Titanium dioxide nanoparticles: an in vitro study of DNA binding, chromosome aberration assay, and comet assay

    doi: 10.1007/s10616-016-0054-3

    Figure Lengend Snippet: Fluorescence emission spectra of intercalated Ethidium bromide and human genomic DNA incubated with increasing concentrations of TiO 2 nanoparticle at 37 °C

    Article Snippet: Complete growth medium; RPMI-1640 HiKaryoXL™ -AL165A; low melting point agarose, agarose, sodium chloride, sodium EDTA, Trizma base, 1% Triton X-100, DMSO, EDTA and Ethidium bromide, were purchased from Himedia (Mumbai, India).

    Techniques: Fluorescence, Incubation

    6MP induced damage to plasmid DNA in presence of light. Agarose gel electrophoresis pattern of ethidium bromide stained pBR322 DNA after the treatment with 6MP in presence of white light. Lane ‘ A ’ depicts the ‘Control’ which contain only plasmid DNA. The concentrations of 6MP in lanes ‘ B–F ’ was 100, 200, 300, 400 and 500 μM respectively. Arrows indicating OC and SC on the right represent the open circular and supercoiled forms of plasmid DNA.

    Journal: PLoS ONE

    Article Title: Interaction of 6 Mercaptopurine with Calf Thymus DNA - Deciphering the Binding Mode and Photoinduced DNA Damage

    doi: 10.1371/journal.pone.0093913

    Figure Lengend Snippet: 6MP induced damage to plasmid DNA in presence of light. Agarose gel electrophoresis pattern of ethidium bromide stained pBR322 DNA after the treatment with 6MP in presence of white light. Lane ‘ A ’ depicts the ‘Control’ which contain only plasmid DNA. The concentrations of 6MP in lanes ‘ B–F ’ was 100, 200, 300, 400 and 500 μM respectively. Arrows indicating OC and SC on the right represent the open circular and supercoiled forms of plasmid DNA.

    Article Snippet: Ethidium bromide (EB) was purchased from Himedia, India.

    Techniques: Plasmid Preparation, Agarose Gel Electrophoresis, Staining

    Force-extension traces for the complexes of poly(dG-dC) dsDNA with the intercalants ( A ) daunomycin; ( B ) ethidium bromide; ( C ) YO; ( D ) YOYO.

    Journal: Biophysical Journal

    Article Title: Identification of Binding Mechanisms in Single Molecule-DNA Complexes

    doi:

    Figure Lengend Snippet: Force-extension traces for the complexes of poly(dG-dC) dsDNA with the intercalants ( A ) daunomycin; ( B ) ethidium bromide; ( C ) YO; ( D ) YOYO.

    Article Snippet: The DNA-binding agents daunomycin (Sigma), ethidium bromide (Merck, Darmstadt, Germany), distamycin A (Sigma), YO (Molecular Probes, Eugene, OR), YOYO (Molecular Probes), Ac-(Leu-Ala-Arg-Leu)3 -NH-linker and Ac-(Aib-Leu-Arg)4 -NH-linker were added to 10 μ l of the DNA solution in a concentration of 150 μ M, corresponding to a 1:10 ratio of agent molecules per base pair.

    Techniques:

    Bacillus vector for selection of group II intron insertions. A schematic of the important vector features and selection scheme for group II intron based gene disruption. The plasmid is erythromycin resistant but kanamycin sensitve because a td group I intron interrupts its coding sequence in an antisense orientation. Transcription of the group II intron from the Ntr promoter allows self- splicing of the td intron and generates a substrate that is capable of genomic integration at pre-determined loci due to changes in sequences shown as black bars within the intron. Genomic integrants no longer have the td group I intron interrupting the kanamycin resistance gene and thus successful integrants are kanamycin resistant. For PCR verification of intron insertion, primers (shown as arrows above the genomic DNA schematic) were designed to flank the site of intron insertion in BAS4597 and BAS4553. kanamycin resistant colonies arising in Bacillus anthracis Sterne after transformation of plasmids reengineered to integrate the group II intron at BAS4597 and BAS4553 were screened by colony PCR and analyzed after electrophoresis on a 1% agarose gel in TBE buffer and visualized by staining with ethidium bromide. Lanes marked M have 1 Kb molecular weight markers.

    Journal: BMC Biotechnology

    Article Title: Rapid targeted gene disruption in Bacillus anthracis

    doi: 10.1186/1472-6750-13-72

    Figure Lengend Snippet: Bacillus vector for selection of group II intron insertions. A schematic of the important vector features and selection scheme for group II intron based gene disruption. The plasmid is erythromycin resistant but kanamycin sensitve because a td group I intron interrupts its coding sequence in an antisense orientation. Transcription of the group II intron from the Ntr promoter allows self- splicing of the td intron and generates a substrate that is capable of genomic integration at pre-determined loci due to changes in sequences shown as black bars within the intron. Genomic integrants no longer have the td group I intron interrupting the kanamycin resistance gene and thus successful integrants are kanamycin resistant. For PCR verification of intron insertion, primers (shown as arrows above the genomic DNA schematic) were designed to flank the site of intron insertion in BAS4597 and BAS4553. kanamycin resistant colonies arising in Bacillus anthracis Sterne after transformation of plasmids reengineered to integrate the group II intron at BAS4597 and BAS4553 were screened by colony PCR and analyzed after electrophoresis on a 1% agarose gel in TBE buffer and visualized by staining with ethidium bromide. Lanes marked M have 1 Kb molecular weight markers.

    Article Snippet: The following cycling conditions were used: initial denaturation at 94°C for 30 sec, followed by 30 cycles of denaturation at 94°C for 30 sec, annealing at 60°C for 45 sec and extension at 65°C for 3 min, with a final extension at 65°C for 10 min. Products were visualized using 1% ethidium bromide (Fisher Bioreagents) on a 1% agarose gel.

    Techniques: Plasmid Preparation, Selection, Sequencing, Polymerase Chain Reaction, Transformation Assay, Electrophoresis, Agarose Gel Electrophoresis, Staining, Molecular Weight

    Expression of variants of uPAR transcripts in leukemia cells (A) KG1 or U937 cells were lysed and analyzed by Western blot with an anti-uPAR antibody; the filter was reprobed with an anti-GAPDH antibody for loading control. (B) KG1 and U937 cells were lysed in Quiazol Reagent and total RNA reversely transcribed; then, 2 μl of reversely transcribed DNA were used for PCR amplification of the region encompassing uPAR from Exon2 to the stop codon UAA (E2-UAA) or of the region encompassing uPAR from Exon2 to the whole 3’UTR (E2-3’UTR). 7 μg of PCR products and the linearized uPAR 3’UTR-PcDNA3.1, as positive control, were analyzed by electrophoresis in 1.2% agarose gel containing ethidium bromide, photographed under ultraviolet illumination (B, left panel), blotted to a Nylon membrane and hybridized with biotinylated 3’UTR RNA probe (B, right panel).

    Journal: Oncotarget

    Article Title: A novel oncogenic role for urokinase receptor in leukemia cells: molecular sponge for oncosuppressor microRNAs

    doi: 10.18632/oncotarget.25597

    Figure Lengend Snippet: Expression of variants of uPAR transcripts in leukemia cells (A) KG1 or U937 cells were lysed and analyzed by Western blot with an anti-uPAR antibody; the filter was reprobed with an anti-GAPDH antibody for loading control. (B) KG1 and U937 cells were lysed in Quiazol Reagent and total RNA reversely transcribed; then, 2 μl of reversely transcribed DNA were used for PCR amplification of the region encompassing uPAR from Exon2 to the stop codon UAA (E2-UAA) or of the region encompassing uPAR from Exon2 to the whole 3’UTR (E2-3’UTR). 7 μg of PCR products and the linearized uPAR 3’UTR-PcDNA3.1, as positive control, were analyzed by electrophoresis in 1.2% agarose gel containing ethidium bromide, photographed under ultraviolet illumination (B, left panel), blotted to a Nylon membrane and hybridized with biotinylated 3’UTR RNA probe (B, right panel).

    Article Snippet: 7μg of PCR products (see RT-PCR paragraph) were electrophoresed in 1.2% agarose gel containing ethidium bromide and photographed under ultraviolet illumination; then, the gel was incubated in 0.5 M NaOH, 1.5 M NaCl for DNA denaturation, neutralized and blotted to a Nylon membrane (Roche).

    Techniques: Expressing, Western Blot, Polymerase Chain Reaction, Amplification, Positive Control, Electrophoresis, Agarose Gel Electrophoresis

    Plasmid DNA condensation by G5 PPI and its alkylcarboxylated derivatives as measured by their ability to displace DNA from its fluorescent complex with ethidium bromide in HBG buffer medium. The c / p ratio with highest condensation was 1.5 for unmodified

    Journal: AAPS PharmSciTech

    Article Title: Preparation of Effective and Safe Gene Carriers by Grafting Alkyl Chains to Generation 5 Polypropyleneimine

    doi: 10.1208/s12249-015-0284-2

    Figure Lengend Snippet: Plasmid DNA condensation by G5 PPI and its alkylcarboxylated derivatives as measured by their ability to displace DNA from its fluorescent complex with ethidium bromide in HBG buffer medium. The c / p ratio with highest condensation was 1.5 for unmodified

    Article Snippet: Ethidium bromide was supplied by CinnaGen (Tehran, Iran).

    Techniques: Plasmid Preparation

    Metallation of a 40-base DNA fragment following treatment with cisplatin (molar ratio 1:50) and Pd1 (molar ratios 1:100 and 1:200). The level of metal binding following interactions between the tested complexes and the DNA probe was analyzed after BamH1 treatment, electrophoretic analysis in 5% native polyacrilamide gel, and ethidium bromide staining. On the picture: C , unmodified DNA; CB , BamH1-digested DNA; cis , cisplatin-modified DNA; cisB , cisplatin-modified DNA (1:50) BamH1-digested; Pd , Pd1 -modified DNA; PdIB , Pd1 -modified DNA (1:100) BamH1-digested, PdIIB , Pd1 -modified DNA (1:200) BamH1-digested.

    Journal: International Journal of Molecular Sciences

    Article Title: Cellular Pharmacology of Palladinum(III) Hematoporphyrin IX Complexes: Solution Stability, Antineoplastic and Apoptogenic Activity, DNA Binding, and Processing of DNA-Adducts

    doi: 10.3390/ijms19082451

    Figure Lengend Snippet: Metallation of a 40-base DNA fragment following treatment with cisplatin (molar ratio 1:50) and Pd1 (molar ratios 1:100 and 1:200). The level of metal binding following interactions between the tested complexes and the DNA probe was analyzed after BamH1 treatment, electrophoretic analysis in 5% native polyacrilamide gel, and ethidium bromide staining. On the picture: C , unmodified DNA; CB , BamH1-digested DNA; cis , cisplatin-modified DNA; cisB , cisplatin-modified DNA (1:50) BamH1-digested; Pd , Pd1 -modified DNA; PdIB , Pd1 -modified DNA (1:100) BamH1-digested, PdIIB , Pd1 -modified DNA (1:200) BamH1-digested.

    Article Snippet: Agarose, ethanol, DMSO, formic acid, 2-propanol, methanol, EDTA, ethidium bromide, sodium chloride, Tris hydrochloride, Triton® X-100, l -glutamine were purchased from AppliChem GmbH, Darmstadt, Germany.

    Techniques: Binding Assay, Staining, Modification