nucleosomes  (Worthington Biochemical)


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    Structured Review

    Worthington Biochemical nucleosomes
    Reconstitution and analysis of the nucleosomal template. (A) Schematic representation of the DNA template containing eight LexA binding sites and a 5S <t>nucleosome</t> positioning element. (B) Analysis of purified recombinant (Rec.) Xenopus octamers and hyperacetylated (Hyperac.) core histones purified from HeLa cells on SDS-polyacrylamide (15%) gel electrophoresis gel stained with Coomassie brilliant blue. (C) Partial micrococcal nuclease digestion. Nucleosomal templates were incubated with 10 mU micrococcal nuclease at 37°C for 0, 20, 40, 60, and 180 s. Reactions were stopped by adding 10 mM EGTA. DNA was phenol chloroform extracted, precipitated, and loaded onto a 1.5% agarose gel. DNA size markers are indicated on the left. An arrow indicates mononucleosomal DNA.
    Nucleosomes, supplied by Worthington Biochemical, used in various techniques. Bioz Stars score: 90/100, based on 1620 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 90 stars, based on 1620 article reviews
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    nucleosomes - by Bioz Stars, 2020-10
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    Images

    1) Product Images from "In Vitro Targeting Reveals Intrinsic Histone Tail Specificity of the Sin3/Histone Deacetylase and N-CoR/SMRT Corepressor Complexes"

    Article Title: In Vitro Targeting Reveals Intrinsic Histone Tail Specificity of the Sin3/Histone Deacetylase and N-CoR/SMRT Corepressor Complexes

    Journal: Molecular and Cellular Biology

    doi: 10.1128/MCB.24.6.2364-2372.2004

    Reconstitution and analysis of the nucleosomal template. (A) Schematic representation of the DNA template containing eight LexA binding sites and a 5S nucleosome positioning element. (B) Analysis of purified recombinant (Rec.) Xenopus octamers and hyperacetylated (Hyperac.) core histones purified from HeLa cells on SDS-polyacrylamide (15%) gel electrophoresis gel stained with Coomassie brilliant blue. (C) Partial micrococcal nuclease digestion. Nucleosomal templates were incubated with 10 mU micrococcal nuclease at 37°C for 0, 20, 40, 60, and 180 s. Reactions were stopped by adding 10 mM EGTA. DNA was phenol chloroform extracted, precipitated, and loaded onto a 1.5% agarose gel. DNA size markers are indicated on the left. An arrow indicates mononucleosomal DNA.
    Figure Legend Snippet: Reconstitution and analysis of the nucleosomal template. (A) Schematic representation of the DNA template containing eight LexA binding sites and a 5S nucleosome positioning element. (B) Analysis of purified recombinant (Rec.) Xenopus octamers and hyperacetylated (Hyperac.) core histones purified from HeLa cells on SDS-polyacrylamide (15%) gel electrophoresis gel stained with Coomassie brilliant blue. (C) Partial micrococcal nuclease digestion. Nucleosomal templates were incubated with 10 mU micrococcal nuclease at 37°C for 0, 20, 40, 60, and 180 s. Reactions were stopped by adding 10 mM EGTA. DNA was phenol chloroform extracted, precipitated, and loaded onto a 1.5% agarose gel. DNA size markers are indicated on the left. An arrow indicates mononucleosomal DNA.

    Techniques Used: Binding Assay, Purification, Recombinant, Nucleic Acid Electrophoresis, Staining, Incubation, Agarose Gel Electrophoresis

    2) Product Images from "A Microfluidic Device to Sort Cells Based on Dynamic Response to a Stimulus"

    Article Title: A Microfluidic Device to Sort Cells Based on Dynamic Response to a Stimulus

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0078261

    A microfluidic device for sorting cells based on dynamic responses. (A) Outline of the operations performed using the chip. (B) Schematic of the device. The main components are the peristaltic pump, cell trap and selection wells. The numbered circles represent points for insertion of 23 gauge needle connectors. Blue lines represent flow lines, which are located in the lower layer of the device (Figure S1 in File S1 ), while green lines are control lines, which are located in the upper layer of the device (Figure S2 in File S1 ). Cells are introduced via a flow line, and their movement is regulated by the control lines that operate the peristaltic pump and seal the cell-trap by actuating push-down valves. The stimulus is then delivered via another flow line. After this, cells are directed to one of two large wells for recovery. Flow lines for Pluronic-F127 and Ringer's buffer are used to prepare the chip. Other flow lines are available for introduction of multiple stimuli to the cell trap. (C) Different components in the system for capturing single cells and introducing stimulants (cell trap), controlling the movement of cells (peristaltic pump), and cell sorting (selector), as seen in a finished device. Scale bar represents 100 µm. (D) An operational device mounted on a microscope. The tygon tubes are used to provide control and introduce reagents.
    Figure Legend Snippet: A microfluidic device for sorting cells based on dynamic responses. (A) Outline of the operations performed using the chip. (B) Schematic of the device. The main components are the peristaltic pump, cell trap and selection wells. The numbered circles represent points for insertion of 23 gauge needle connectors. Blue lines represent flow lines, which are located in the lower layer of the device (Figure S1 in File S1 ), while green lines are control lines, which are located in the upper layer of the device (Figure S2 in File S1 ). Cells are introduced via a flow line, and their movement is regulated by the control lines that operate the peristaltic pump and seal the cell-trap by actuating push-down valves. The stimulus is then delivered via another flow line. After this, cells are directed to one of two large wells for recovery. Flow lines for Pluronic-F127 and Ringer's buffer are used to prepare the chip. Other flow lines are available for introduction of multiple stimuli to the cell trap. (C) Different components in the system for capturing single cells and introducing stimulants (cell trap), controlling the movement of cells (peristaltic pump), and cell sorting (selector), as seen in a finished device. Scale bar represents 100 µm. (D) An operational device mounted on a microscope. The tygon tubes are used to provide control and introduce reagents.

    Techniques Used: Chromatin Immunoprecipitation, Selection, Flow Cytometry, FACS, Microscopy, Introduce

    Lysine stimulation of a mixed cell population from the olfactory epithelium of TRPC2:Venus transgenic zebrafish. (A) Relative change of fluorescence intensity in cells expressing Venus, following stimulation with L-lysine. Gray lines represent the response of individual cells while the black line plots the averaged response. L-lysine was injected into the cell trap at the time indicated by the dashed line. (B) Relative fluorescence intensity change in cells with no observable Venus fluorescence, in response to L-lysine. (C) Maximum fluorescence intensity change measured for each cell after stimulation with the indicated ligand. Venus expressing cells (labeled Venus (+)) show a response to L-lysine, but not to Ringer's or GCDA. Cells that did not express Venus (labeled Venus (−)) did not respond to L-lysine or to Ringer's. For clarity, the last two columns re-plot the data for Venus-expressing cells stimulated with L-lysine, grouping the data points based on whether the maximum fluorescence change for a cell was above or below the threshold of 2.7%. (D) qRT-PCR analysis of cells in panel (C), showing relative abundance of TRPC2 and β-Actin mRNA. All Venus expressing cells expressed relatively high levels of TRPC2 . TRPC2 mRNA was detected in only two cells that did not express Venus. ND: not detected. The corresponding data for OMP, EF1α, and B2M are shown in Figures S3, S4, and S5 in File S1 . [(C): **p = 0.0005; (D): **p
    Figure Legend Snippet: Lysine stimulation of a mixed cell population from the olfactory epithelium of TRPC2:Venus transgenic zebrafish. (A) Relative change of fluorescence intensity in cells expressing Venus, following stimulation with L-lysine. Gray lines represent the response of individual cells while the black line plots the averaged response. L-lysine was injected into the cell trap at the time indicated by the dashed line. (B) Relative fluorescence intensity change in cells with no observable Venus fluorescence, in response to L-lysine. (C) Maximum fluorescence intensity change measured for each cell after stimulation with the indicated ligand. Venus expressing cells (labeled Venus (+)) show a response to L-lysine, but not to Ringer's or GCDA. Cells that did not express Venus (labeled Venus (−)) did not respond to L-lysine or to Ringer's. For clarity, the last two columns re-plot the data for Venus-expressing cells stimulated with L-lysine, grouping the data points based on whether the maximum fluorescence change for a cell was above or below the threshold of 2.7%. (D) qRT-PCR analysis of cells in panel (C), showing relative abundance of TRPC2 and β-Actin mRNA. All Venus expressing cells expressed relatively high levels of TRPC2 . TRPC2 mRNA was detected in only two cells that did not express Venus. ND: not detected. The corresponding data for OMP, EF1α, and B2M are shown in Figures S3, S4, and S5 in File S1 . [(C): **p = 0.0005; (D): **p

    Techniques Used: Transgenic Assay, Fluorescence, Expressing, Injection, Labeling, Quantitative RT-PCR

    Ionophore-induced calcium influx in cells extracted from zebrafish olfactory epithelium. (A) Maximum fluorescence change in individual cells after stimulation with A23187 (n = 45) or Ringer's (n = 14). The inset depicts the data for the same cells on a log scale. (*p = 0.0144, unpaired one-tailed Student's t -test). (B) Change in fluorescence intensity relative to baseline fluorescence intensity (ΔF/F 0 ) plotted over time for representative cells. The black trace indicates the averaged response. A23187 was injected into the cell trap at the indicated time (80 s), and remained in the trap. Control cells stimulated with Ringer's buffer did not exhibit a significant change in fluorescence intensity.
    Figure Legend Snippet: Ionophore-induced calcium influx in cells extracted from zebrafish olfactory epithelium. (A) Maximum fluorescence change in individual cells after stimulation with A23187 (n = 45) or Ringer's (n = 14). The inset depicts the data for the same cells on a log scale. (*p = 0.0144, unpaired one-tailed Student's t -test). (B) Change in fluorescence intensity relative to baseline fluorescence intensity (ΔF/F 0 ) plotted over time for representative cells. The black trace indicates the averaged response. A23187 was injected into the cell trap at the indicated time (80 s), and remained in the trap. Control cells stimulated with Ringer's buffer did not exhibit a significant change in fluorescence intensity.

    Techniques Used: Fluorescence, One-tailed Test, Injection

    3) Product Images from "SET Domains of Histone Methyltransferases Recognize ISWI-Remodeled Nucleosomal Species ▿"

    Article Title: SET Domains of Histone Methyltransferases Recognize ISWI-Remodeled Nucleosomal Species ▿

    Journal: Molecular and Cellular Biology

    doi: 10.1128/MCB.00775-09

    Remodeling of dinucleosomes by ISWI complexes stimulates histone methylation by SET domain proteins. (A) The SET domain of SET7 binds histones, but not nucleosomes. GST pulldown experiments were conducted with immobilized GST-SET7 polypeptides (residues
    Figure Legend Snippet: Remodeling of dinucleosomes by ISWI complexes stimulates histone methylation by SET domain proteins. (A) The SET domain of SET7 binds histones, but not nucleosomes. GST pulldown experiments were conducted with immobilized GST-SET7 polypeptides (residues

    Techniques Used: Methylation

    Analysis of ISW2 and SWI/SNF remodeled dinucleosomes. 32 P-end-labeled dinucleosomes were remodeled by ISW2 (A and B) or SWI/SNF (C and D) as described in the legend for Fig. . Remodeling was terminated by apyrase treatment, and nucleosomes
    Figure Legend Snippet: Analysis of ISW2 and SWI/SNF remodeled dinucleosomes. 32 P-end-labeled dinucleosomes were remodeled by ISW2 (A and B) or SWI/SNF (C and D) as described in the legend for Fig. . Remodeling was terminated by apyrase treatment, and nucleosomes

    Techniques Used: Labeling

    The SET domain of trithorax binds core histones and altered nucleosomal structures but not intact nucleosomes. (A) Schematic of the domain structure of trithorax. Positions of highly conserved blocks of homology with methyltransferases, a C-terminal cysteine-rich
    Figure Legend Snippet: The SET domain of trithorax binds core histones and altered nucleosomal structures but not intact nucleosomes. (A) Schematic of the domain structure of trithorax. Positions of highly conserved blocks of homology with methyltransferases, a C-terminal cysteine-rich

    Techniques Used:

    The SET domain of ALL1 does not bind remodeled mononucleosomes. (A, top) Analysis of remodeled mononucleosomes by native PAGE. Remodeling assay mixtures (50 μl) contained 1.2 μg of nucleosomes and 2.5 ng of ISWI or 5 ng of Swi-Snf complexes
    Figure Legend Snippet: The SET domain of ALL1 does not bind remodeled mononucleosomes. (A, top) Analysis of remodeled mononucleosomes by native PAGE. Remodeling assay mixtures (50 μl) contained 1.2 μg of nucleosomes and 2.5 ng of ISWI or 5 ng of Swi-Snf complexes

    Techniques Used: Clear Native PAGE

    The SET domain of ALL1 binds dinucleosomes remodeled by the ISWI class of chromatin remodeling enzymes. (A) Example of dinucleosome assembly. Dinucleosomes were reconstituted onto DNA containing two 601 minimal nucleosome positioning sequences (the orientation
    Figure Legend Snippet: The SET domain of ALL1 binds dinucleosomes remodeled by the ISWI class of chromatin remodeling enzymes. (A) Example of dinucleosome assembly. Dinucleosomes were reconstituted onto DNA containing two 601 minimal nucleosome positioning sequences (the orientation

    Techniques Used:

    4) Product Images from "Enhancement of the Influenza A Hemagglutinin (HA)-Mediated Cell-Cell Fusion and Virus Entry by the Viral Neuraminidase (NA)"

    Article Title: Enhancement of the Influenza A Hemagglutinin (HA)-Mediated Cell-Cell Fusion and Virus Entry by the Viral Neuraminidase (NA)

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0008495

    Infectivity of HA-expressing HIV-1 pseudotypes in the absence or in the presence of viral NA protein or soluble bacterial sialidase. 293-T cells were cotransfected with an env -defective HIV-1 proviral clone encoding Renilla luciferase and different ratios of a plasmid expressing the H1 protein from the H1N1 A/Paris/0650/04 virus and a plasmid encoding either the wild-type homologous N1 or a defective enzymatic variant, N1-Y406F. The HA:NA plasmid ratios (w/w) tested were: 1∶0, 1∶0.01, 1∶0.1, 1∶1, 1∶2, 1∶3 and 1∶4. Panel A: quantification of HA and NA expression in purified virions preparations by western blot. Results are representative of two independent experiments. Panel B: impact of NA activity on the production and release of pseudoparticles measured by HIV-1 p24 ELISA. Columns represent mean value of at least three independent experiments (bars represent standard errors). Panel C: infectivity of HA-expressing HIV-1 pseudotypes in the absence or in the presence of viral NA protein or soluble bacterial sialidase. Columns represent mean infectivity value of at least three independent experiments (bars represent standard errors). Panel D: infectivity of pseudoparticles expressing H1 alone, coexpressing H1 and N1 at a plasmid ratio of 1∶1, and expressing H1 alone but pretreated with neuraminidase from Clostridium perfringens prior to harvesting the virions. Columns represent mean infectivity value of at least three independent experiments (bars represent standard errors).
    Figure Legend Snippet: Infectivity of HA-expressing HIV-1 pseudotypes in the absence or in the presence of viral NA protein or soluble bacterial sialidase. 293-T cells were cotransfected with an env -defective HIV-1 proviral clone encoding Renilla luciferase and different ratios of a plasmid expressing the H1 protein from the H1N1 A/Paris/0650/04 virus and a plasmid encoding either the wild-type homologous N1 or a defective enzymatic variant, N1-Y406F. The HA:NA plasmid ratios (w/w) tested were: 1∶0, 1∶0.01, 1∶0.1, 1∶1, 1∶2, 1∶3 and 1∶4. Panel A: quantification of HA and NA expression in purified virions preparations by western blot. Results are representative of two independent experiments. Panel B: impact of NA activity on the production and release of pseudoparticles measured by HIV-1 p24 ELISA. Columns represent mean value of at least three independent experiments (bars represent standard errors). Panel C: infectivity of HA-expressing HIV-1 pseudotypes in the absence or in the presence of viral NA protein or soluble bacterial sialidase. Columns represent mean infectivity value of at least three independent experiments (bars represent standard errors). Panel D: infectivity of pseudoparticles expressing H1 alone, coexpressing H1 and N1 at a plasmid ratio of 1∶1, and expressing H1 alone but pretreated with neuraminidase from Clostridium perfringens prior to harvesting the virions. Columns represent mean infectivity value of at least three independent experiments (bars represent standard errors).

    Techniques Used: Infection, Expressing, Luciferase, Plasmid Preparation, Variant Assay, Purification, Western Blot, Activity Assay, Enzyme-linked Immunosorbent Assay

    Schematic representations of the cell-cell fusion (panel A) and the infectivity assays (panel B). Panel A: Cell-cell fusion assay. HeLa cells seeded into 96-well plates were cotransfected with a plasmid coexpressing the HA and Tat proteins in the presence or in the absence of a vector expressing NA. Transfected cells were further co-cultured with MDCK target cells that harbor a Tat-inducible β-galactosidase reporter system (LTR- lacZ cassette). Co-culture was successively treated with TPCK-treated trypsin and with acidic medium to mediate membrane fusion. 40 hours later, cells were lysed and the β-galactosidase activity was detected using a colorimetric assay. Panel B: Infectivity assay. Subconfluent monolayer of 293-T cells were cotransfected with an env- defective HIV-1 proviral clone in which the nef gene was replaced by that encoding the Renilla luciferase and with plasmids expressing HA and/or NA. NA can also be provided in this system as exogenous and soluble NA from Clostridium perfringens . Viral supernatants were harvested, cleared, normalized by quantification of the HIV-1 p24 antigen content and further used to infect MDCK-SIAT1 target cells seeded into 96-well plates. Infected cells were incubated for 40 hours, and further lysed. Lysates were tested for luciferase activity by the addition of a specific substrate measured in a luminometer.
    Figure Legend Snippet: Schematic representations of the cell-cell fusion (panel A) and the infectivity assays (panel B). Panel A: Cell-cell fusion assay. HeLa cells seeded into 96-well plates were cotransfected with a plasmid coexpressing the HA and Tat proteins in the presence or in the absence of a vector expressing NA. Transfected cells were further co-cultured with MDCK target cells that harbor a Tat-inducible β-galactosidase reporter system (LTR- lacZ cassette). Co-culture was successively treated with TPCK-treated trypsin and with acidic medium to mediate membrane fusion. 40 hours later, cells were lysed and the β-galactosidase activity was detected using a colorimetric assay. Panel B: Infectivity assay. Subconfluent monolayer of 293-T cells were cotransfected with an env- defective HIV-1 proviral clone in which the nef gene was replaced by that encoding the Renilla luciferase and with plasmids expressing HA and/or NA. NA can also be provided in this system as exogenous and soluble NA from Clostridium perfringens . Viral supernatants were harvested, cleared, normalized by quantification of the HIV-1 p24 antigen content and further used to infect MDCK-SIAT1 target cells seeded into 96-well plates. Infected cells were incubated for 40 hours, and further lysed. Lysates were tested for luciferase activity by the addition of a specific substrate measured in a luminometer.

    Techniques Used: Infection, Cell-Cell Fusion Assay, Plasmid Preparation, Expressing, Transfection, Cell Culture, Co-Culture Assay, Activity Assay, Colorimetric Assay, Luciferase, Incubation

    5) Product Images from "Heparan Sulfate Modulates Neutrophil and Endothelial Function in Antibacterial Innate Immunity"

    Article Title: Heparan Sulfate Modulates Neutrophil and Endothelial Function in Antibacterial Innate Immunity

    Journal: Infection and Immunity

    doi: 10.1128/IAI.00545-15

    Reduced extracellular-trap (NET) formation in Hs2st-deficient neutrophils. (A) Human neutrophils were treated with 25 nM PMA for 3 h to allow NET formation, treated with heparan lyase III (5 mU/ml), fixed, and stained with mouse anti-stub heparan sulfate MAb, rabbit anti-myeloperoxidase PAb, and DAPI, followed by appropriate fluorochrome-conjugated secondary antibodies. (B) Human neutrophils were treated with 25 nM PMA for 3 h to induce NET formation and then treated with DNase I (10 U/ml) or heparan lyase I and III (5 mU/ml) for 30 min at 37°C, followed by incubation with GBS for 30 min. Surviving GBS were enumerated by serial plating. Differences between groups were calculated by unpaired t test. **, P
    Figure Legend Snippet: Reduced extracellular-trap (NET) formation in Hs2st-deficient neutrophils. (A) Human neutrophils were treated with 25 nM PMA for 3 h to allow NET formation, treated with heparan lyase III (5 mU/ml), fixed, and stained with mouse anti-stub heparan sulfate MAb, rabbit anti-myeloperoxidase PAb, and DAPI, followed by appropriate fluorochrome-conjugated secondary antibodies. (B) Human neutrophils were treated with 25 nM PMA for 3 h to induce NET formation and then treated with DNase I (10 U/ml) or heparan lyase I and III (5 mU/ml) for 30 min at 37°C, followed by incubation with GBS for 30 min. Surviving GBS were enumerated by serial plating. Differences between groups were calculated by unpaired t test. **, P

    Techniques Used: Staining, Incubation

    6) Product Images from "RNase H sequence preferences influence antisense oligonucleotide efficiency"

    Article Title: RNase H sequence preferences influence antisense oligonucleotide efficiency

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkx1073

    Sequence preferences of Escherichia coli, Homo sapiens and HIV-1 RNase H ( A ) The heatmaps display the changes in nucleotide composition at different positions for the R7 construct (left) and the R4b construct (right) after cleavage with the three different RNase H enzymes. The intensity of the red and blue color indicates the k rel of having given nucleotide at a given position fixed relative to the average hydrolysis rate of the randomized pool. The barplots below the heatmaps show the overall information content at each position and the sequence logos are based on the 1% most downregulated pentamers. Note that only the randomized parts of the probed duplexes is displayed. ( B ) Cleavage of sequences predicted to be preferred (‘P’), avoided (‘A’) and neutral (‘N’) with respect to cleavage with human RNase H1 compared to the cleavage of a reference substrate. With respect to the reference substrate, the k rel of the preferred substrate is 3.7, of the avoided is 0.26 and of the neutral it is 1.4. ( C ) The design of the dumbbell substrate mimics. The gray box indicates the region having either the preferred (‘P’) or avoided (‘A’) sequence. ( D ) The cleavage of a reference substrate in the presence of increasing concentrations of a preferred or avoided dumbbell substrate mimic.
    Figure Legend Snippet: Sequence preferences of Escherichia coli, Homo sapiens and HIV-1 RNase H ( A ) The heatmaps display the changes in nucleotide composition at different positions for the R7 construct (left) and the R4b construct (right) after cleavage with the three different RNase H enzymes. The intensity of the red and blue color indicates the k rel of having given nucleotide at a given position fixed relative to the average hydrolysis rate of the randomized pool. The barplots below the heatmaps show the overall information content at each position and the sequence logos are based on the 1% most downregulated pentamers. Note that only the randomized parts of the probed duplexes is displayed. ( B ) Cleavage of sequences predicted to be preferred (‘P’), avoided (‘A’) and neutral (‘N’) with respect to cleavage with human RNase H1 compared to the cleavage of a reference substrate. With respect to the reference substrate, the k rel of the preferred substrate is 3.7, of the avoided is 0.26 and of the neutral it is 1.4. ( C ) The design of the dumbbell substrate mimics. The gray box indicates the region having either the preferred (‘P’) or avoided (‘A’) sequence. ( D ) The cleavage of a reference substrate in the presence of increasing concentrations of a preferred or avoided dumbbell substrate mimic.

    Techniques Used: Sequencing, Construct

    Functional significance of predicted HIV-1 RNase H cleavage sites. ( A ) Predicted RNase H cleavage efficiency of the HIV-1 genome, shown as log 2 (fold change) (log 2 FC). ( B ) Schematic of the HIV reverse transcription. White scissors at the black circle indicate specific areas zoomed-in in subsequent panels. ( C ) Comparison of distances (in nucleotides) between well-cleaved sites in the HIV-1 genome and in the randomized HIV-1 genomes. The red rhombi shows the observed count of distances between positions predicted to be efficiently cleaved in HIV-1 genome that fall into the indicated distance intervals. The violin plots show the density of the distributions that resulted from the same analysis, but repeated 10 000× on HIV-1 genome sequences that were randomized with preserving the local dinucleotide content; Predicted cleavage efficiency of ( D ) the sequence surrounding the 3′PPT, ( E ) of the terminal 18 nt of the tRNA-Lys3 primer and ( F ) it is reverse complement (primer binding site). ( G ) Predicted cleavage efficiency of the best-cleaved site in the terminal 18 nt of the different human tRNAs (plus CCA) and of the corresponding reverse complement. The tRNA-Lys3 is indicated in red.
    Figure Legend Snippet: Functional significance of predicted HIV-1 RNase H cleavage sites. ( A ) Predicted RNase H cleavage efficiency of the HIV-1 genome, shown as log 2 (fold change) (log 2 FC). ( B ) Schematic of the HIV reverse transcription. White scissors at the black circle indicate specific areas zoomed-in in subsequent panels. ( C ) Comparison of distances (in nucleotides) between well-cleaved sites in the HIV-1 genome and in the randomized HIV-1 genomes. The red rhombi shows the observed count of distances between positions predicted to be efficiently cleaved in HIV-1 genome that fall into the indicated distance intervals. The violin plots show the density of the distributions that resulted from the same analysis, but repeated 10 000× on HIV-1 genome sequences that were randomized with preserving the local dinucleotide content; Predicted cleavage efficiency of ( D ) the sequence surrounding the 3′PPT, ( E ) of the terminal 18 nt of the tRNA-Lys3 primer and ( F ) it is reverse complement (primer binding site). ( G ) Predicted cleavage efficiency of the best-cleaved site in the terminal 18 nt of the different human tRNAs (plus CCA) and of the corresponding reverse complement. The tRNA-Lys3 is indicated in red.

    Techniques Used: Functional Assay, Preserving, Sequencing, Binding Assay

    Refining the HIV-1 RNase H sequence preference model. ( A ) Distributions of the observed log 2 fold changes of RNA heptamers in R7 for human RNase H1 (right) and HIV-1 RNase H (left). ( B ) The observed log 2 fold changes after cleavage with HIV-1 RNase H for an efficiently cleaved hexamer (GCGCAA) located at different positions of R7. The position of the arrow indicates the cleavage site as aligned to the picture of scissors in the box and the arrow length represents the efficiency of cleavage. ( C ) Sequence logos of the best cleaved quartile of sets of heptamers predicted to have the same cleavage site. The arrows indicate the predicted cleavage site, with the length proportional to the observed cleavage efficiency.
    Figure Legend Snippet: Refining the HIV-1 RNase H sequence preference model. ( A ) Distributions of the observed log 2 fold changes of RNA heptamers in R7 for human RNase H1 (right) and HIV-1 RNase H (left). ( B ) The observed log 2 fold changes after cleavage with HIV-1 RNase H for an efficiently cleaved hexamer (GCGCAA) located at different positions of R7. The position of the arrow indicates the cleavage site as aligned to the picture of scissors in the box and the arrow length represents the efficiency of cleavage. ( C ) Sequence logos of the best cleaved quartile of sets of heptamers predicted to have the same cleavage site. The arrows indicate the predicted cleavage site, with the length proportional to the observed cleavage efficiency.

    Techniques Used: Refining, Sequencing

    7) Product Images from "Site-Specific Mapping of Sialic Acid Linkage Isomers by Ion Mobility Spectrometry"

    Article Title: Site-Specific Mapping of Sialic Acid Linkage Isomers by Ion Mobility Spectrometry

    Journal: Analytical chemistry

    doi: 10.1021/acs.analchem.6b00265

    Untargeted ATDs of glycoprotein digests. Digests of α 1AGP (top), Fetuin (middle), and Env gp140 from CHO cells (bottom) were analyzed by LC–IMS using a high cone voltage to induce glycan fragmentation in all eluting glycopeptides. The
    Figure Legend Snippet: Untargeted ATDs of glycoprotein digests. Digests of α 1AGP (top), Fetuin (middle), and Env gp140 from CHO cells (bottom) were analyzed by LC–IMS using a high cone voltage to induce glycan fragmentation in all eluting glycopeptides. The

    Techniques Used:

    8) Product Images from "RNase H sequence preferences influence antisense oligonucleotide efficiency"

    Article Title: RNase H sequence preferences influence antisense oligonucleotide efficiency

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkx1073

    Sequence preferences of Escherichia coli, Homo sapiens and HIV-1 RNase H ( A ) The heatmaps display the changes in nucleotide composition at different positions for the R7 construct (left) and the R4b construct (right) after cleavage with the three different RNase H enzymes. The intensity of the red and blue color indicates the k rel of having given nucleotide at a given position fixed relative to the average hydrolysis rate of the randomized pool. The barplots below the heatmaps show the overall information content at each position and the sequence logos are based on the 1% most downregulated pentamers. Note that only the randomized parts of the probed duplexes is displayed. ( B ) Cleavage of sequences predicted to be preferred (‘P’), avoided (‘A’) and neutral (‘N’) with respect to cleavage with human RNase H1 compared to the cleavage of a reference substrate. With respect to the reference substrate, the k rel of the preferred substrate is 3.7, of the avoided is 0.26 and of the neutral it is 1.4. ( C ) The design of the dumbbell substrate mimics. The gray box indicates the region having either the preferred (‘P’) or avoided (‘A’) sequence. ( D ) The cleavage of a reference substrate in the presence of increasing concentrations of a preferred or avoided dumbbell substrate mimic.
    Figure Legend Snippet: Sequence preferences of Escherichia coli, Homo sapiens and HIV-1 RNase H ( A ) The heatmaps display the changes in nucleotide composition at different positions for the R7 construct (left) and the R4b construct (right) after cleavage with the three different RNase H enzymes. The intensity of the red and blue color indicates the k rel of having given nucleotide at a given position fixed relative to the average hydrolysis rate of the randomized pool. The barplots below the heatmaps show the overall information content at each position and the sequence logos are based on the 1% most downregulated pentamers. Note that only the randomized parts of the probed duplexes is displayed. ( B ) Cleavage of sequences predicted to be preferred (‘P’), avoided (‘A’) and neutral (‘N’) with respect to cleavage with human RNase H1 compared to the cleavage of a reference substrate. With respect to the reference substrate, the k rel of the preferred substrate is 3.7, of the avoided is 0.26 and of the neutral it is 1.4. ( C ) The design of the dumbbell substrate mimics. The gray box indicates the region having either the preferred (‘P’) or avoided (‘A’) sequence. ( D ) The cleavage of a reference substrate in the presence of increasing concentrations of a preferred or avoided dumbbell substrate mimic.

    Techniques Used: Sequencing, Construct

    Functional significance of predicted HIV-1 RNase H cleavage sites. ( A ) Predicted RNase H cleavage efficiency of the HIV-1 genome, shown as log 2 (fold change) (log 2 FC). ( B ) Schematic of the HIV reverse transcription. White scissors at the black circle indicate specific areas zoomed-in in subsequent panels. ( C ) Comparison of distances (in nucleotides) between well-cleaved sites in the HIV-1 genome and in the randomized HIV-1 genomes. The red rhombi shows the observed count of distances between positions predicted to be efficiently cleaved in HIV-1 genome that fall into the indicated distance intervals. The violin plots show the density of the distributions that resulted from the same analysis, but repeated 10 000× on HIV-1 genome sequences that were randomized with preserving the local dinucleotide content; Predicted cleavage efficiency of ( D ) the sequence surrounding the 3′PPT, ( E ) of the terminal 18 nt of the tRNA-Lys3 primer and ( F ) it is reverse complement (primer binding site). ( G ) Predicted cleavage efficiency of the best-cleaved site in the terminal 18 nt of the different human tRNAs (plus CCA) and of the corresponding reverse complement. The tRNA-Lys3 is indicated in red.
    Figure Legend Snippet: Functional significance of predicted HIV-1 RNase H cleavage sites. ( A ) Predicted RNase H cleavage efficiency of the HIV-1 genome, shown as log 2 (fold change) (log 2 FC). ( B ) Schematic of the HIV reverse transcription. White scissors at the black circle indicate specific areas zoomed-in in subsequent panels. ( C ) Comparison of distances (in nucleotides) between well-cleaved sites in the HIV-1 genome and in the randomized HIV-1 genomes. The red rhombi shows the observed count of distances between positions predicted to be efficiently cleaved in HIV-1 genome that fall into the indicated distance intervals. The violin plots show the density of the distributions that resulted from the same analysis, but repeated 10 000× on HIV-1 genome sequences that were randomized with preserving the local dinucleotide content; Predicted cleavage efficiency of ( D ) the sequence surrounding the 3′PPT, ( E ) of the terminal 18 nt of the tRNA-Lys3 primer and ( F ) it is reverse complement (primer binding site). ( G ) Predicted cleavage efficiency of the best-cleaved site in the terminal 18 nt of the different human tRNAs (plus CCA) and of the corresponding reverse complement. The tRNA-Lys3 is indicated in red.

    Techniques Used: Functional Assay, Preserving, Sequencing, Binding Assay

    Refining the HIV-1 RNase H sequence preference model. ( A ) Distributions of the observed log 2 fold changes of RNA heptamers in R7 for human RNase H1 (right) and HIV-1 RNase H (left). ( B ) The observed log 2 fold changes after cleavage with HIV-1 RNase H for an efficiently cleaved hexamer (GCGCAA) located at different positions of R7. The position of the arrow indicates the cleavage site as aligned to the picture of scissors in the box and the arrow length represents the efficiency of cleavage. ( C ) Sequence logos of the best cleaved quartile of sets of heptamers predicted to have the same cleavage site. The arrows indicate the predicted cleavage site, with the length proportional to the observed cleavage efficiency.
    Figure Legend Snippet: Refining the HIV-1 RNase H sequence preference model. ( A ) Distributions of the observed log 2 fold changes of RNA heptamers in R7 for human RNase H1 (right) and HIV-1 RNase H (left). ( B ) The observed log 2 fold changes after cleavage with HIV-1 RNase H for an efficiently cleaved hexamer (GCGCAA) located at different positions of R7. The position of the arrow indicates the cleavage site as aligned to the picture of scissors in the box and the arrow length represents the efficiency of cleavage. ( C ) Sequence logos of the best cleaved quartile of sets of heptamers predicted to have the same cleavage site. The arrows indicate the predicted cleavage site, with the length proportional to the observed cleavage efficiency.

    Techniques Used: Refining, Sequencing

    9) Product Images from "Human Immunodeficiency Virus Type 1 Protease Regulation of Tat Activity Is Essential for Efficient Reverse Transcription and Replication"

    Article Title: Human Immunodeficiency Virus Type 1 Protease Regulation of Tat Activity Is Essential for Efficient Reverse Transcription and Replication

    Journal: Journal of Virology

    doi: 10.1128/JVI.77.18.9912-9921.2003

    Tat Y47 is critical for virus replication and important for reverse transcription. (A and B) H9 or 293T cells were cotransfected with wild-type or mutant NL4.3 proviral DNAs along with a β-galactosidase reporter plasmid. The amount of CAp24 in the supernatant was measured by ELISA, normalized to the measured relative transfection efficiency, and expressed relative to the level of CAp24 made by the wild-type (WT) virus. The experiments were performed at least four times, and a representative experiment is shown for each cell line. (C) Virus stocks were obtained from the transfected 293 cells and assayed for total reverse transcriptase. NERT-PCR assays were performed using equivalent amounts of total reverse transcriptase, and the amount of minus-strand SS DNA made by each virus was expressed relative to wild-type (WT) NL4.3. (D) H9 cells were infected for 2 h with DNase I-treated virus stocks containing 100 ng of CAp24, with or without heat inactivation, and then washed thoroughly. After a further 22-h incubation, low-molecular-weight DNA was isolated from a portion of each infection and assayed for minus-strand SS DNA by the same PCR used in NERT-PCR assays. (E) The remaining cells were grown and divided every 2 or 3 days as required. A sample of the culture supernatant was saved at each cell passage, and the amount of CAp24 was measured by ELISA. A virus stock was collected from the infected cells on day 21 and used to infect naive H9 cells. The tat gene was amplified by PCR from chromosomes isolated from these cells 10 days postinfection, and the amplicon was directly sequenced.
    Figure Legend Snippet: Tat Y47 is critical for virus replication and important for reverse transcription. (A and B) H9 or 293T cells were cotransfected with wild-type or mutant NL4.3 proviral DNAs along with a β-galactosidase reporter plasmid. The amount of CAp24 in the supernatant was measured by ELISA, normalized to the measured relative transfection efficiency, and expressed relative to the level of CAp24 made by the wild-type (WT) virus. The experiments were performed at least four times, and a representative experiment is shown for each cell line. (C) Virus stocks were obtained from the transfected 293 cells and assayed for total reverse transcriptase. NERT-PCR assays were performed using equivalent amounts of total reverse transcriptase, and the amount of minus-strand SS DNA made by each virus was expressed relative to wild-type (WT) NL4.3. (D) H9 cells were infected for 2 h with DNase I-treated virus stocks containing 100 ng of CAp24, with or without heat inactivation, and then washed thoroughly. After a further 22-h incubation, low-molecular-weight DNA was isolated from a portion of each infection and assayed for minus-strand SS DNA by the same PCR used in NERT-PCR assays. (E) The remaining cells were grown and divided every 2 or 3 days as required. A sample of the culture supernatant was saved at each cell passage, and the amount of CAp24 was measured by ELISA. A virus stock was collected from the infected cells on day 21 and used to infect naive H9 cells. The tat gene was amplified by PCR from chromosomes isolated from these cells 10 days postinfection, and the amplicon was directly sequenced.

    Techniques Used: Mutagenesis, Plasmid Preparation, Enzyme-linked Immunosorbent Assay, Transfection, Polymerase Chain Reaction, Infection, Incubation, Molecular Weight, Isolation, Amplification

    10) Product Images from "Functional Domains of Tat Required for Efficient Human Immunodeficiency Virus Type 1 Reverse Transcription †"

    Article Title: Functional Domains of Tat Required for Efficient Human Immunodeficiency Virus Type 1 Reverse Transcription †

    Journal: Journal of Virology

    doi:

    NERT assay for HIV-1 wild-type and tat mutant viruses. Virus stocks for wild-type virus (lanes 1), Δ tat virus trans -complemented with wild-type tat (lanes 2), Δ tat virus (lanes 3), or Δ tat virus produced in the presence of tat mutants [E2G, D5G, E9G], P3L, P[6, 10]L, P[10, 14]L, C27S, K41A, and K/R[50-57]G (lanes 4 to 10, respectively) were analyzed for endogenous reverse transcription. Culture supernatant (200 μl) containing approximately 0.75 mU of RT activity was treated with 100 U of DNase I. Half of each reaction mixture was added to 150 μl of stop solution, incubated at 37°C for 10 min, and then boiled for 10 min (B). The remaining half of each reaction mixture was supplemented with 50 μM dNTPs and incubated at 37°C for 90 minutes before the reaction was terminated as described above. (A) PCR to detect HIV-1 negative-strand strong-stop DNA was performed on NERT reaction mixtures as described in Materials and Methods. All PCRs were performed within the linear range of the assay as determined by assays of HIV-1 DNA copy number (10, 10 2 , 10 3 , and 10 4 ).
    Figure Legend Snippet: NERT assay for HIV-1 wild-type and tat mutant viruses. Virus stocks for wild-type virus (lanes 1), Δ tat virus trans -complemented with wild-type tat (lanes 2), Δ tat virus (lanes 3), or Δ tat virus produced in the presence of tat mutants [E2G, D5G, E9G], P3L, P[6, 10]L, P[10, 14]L, C27S, K41A, and K/R[50-57]G (lanes 4 to 10, respectively) were analyzed for endogenous reverse transcription. Culture supernatant (200 μl) containing approximately 0.75 mU of RT activity was treated with 100 U of DNase I. Half of each reaction mixture was added to 150 μl of stop solution, incubated at 37°C for 10 min, and then boiled for 10 min (B). The remaining half of each reaction mixture was supplemented with 50 μM dNTPs and incubated at 37°C for 90 minutes before the reaction was terminated as described above. (A) PCR to detect HIV-1 negative-strand strong-stop DNA was performed on NERT reaction mixtures as described in Materials and Methods. All PCRs were performed within the linear range of the assay as determined by assays of HIV-1 DNA copy number (10, 10 2 , 10 3 , and 10 4 ).

    Techniques Used: Mutagenesis, Produced, Activity Assay, Incubation, Polymerase Chain Reaction

    11) Product Images from "DNase I aggravates islet β-cell apoptosis in type 2 diabetes"

    Article Title: DNase I aggravates islet β-cell apoptosis in type 2 diabetes

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5102

    DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Culture, Western Blot, Expressing, Real-time Polymerase Chain Reaction, Flow Cytometry, Cytometry, Standard Deviation

    Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.
    Figure Legend Snippet: Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.

    Techniques Used: Immunohistochemistry, Staining

    DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Counting, Expressing, Western Blot, Real-time Polymerase Chain Reaction, TUNEL Assay, Flow Cytometry, Cytometry, Standard Deviation

    DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P
    Figure Legend Snippet: DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P

    Techniques Used: Activity Assay, Standard Deviation

    12) Product Images from "DNase I aggravates islet β-cell apoptosis in type 2 diabetes"

    Article Title: DNase I aggravates islet β-cell apoptosis in type 2 diabetes

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5102

    DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Culture, Western Blot, Expressing, Real-time Polymerase Chain Reaction, Flow Cytometry, Cytometry, Standard Deviation

    Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.
    Figure Legend Snippet: Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.

    Techniques Used: Immunohistochemistry, Staining

    DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Counting, Expressing, Western Blot, Real-time Polymerase Chain Reaction, TUNEL Assay, Flow Cytometry, Cytometry, Standard Deviation

    DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P
    Figure Legend Snippet: DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P

    Techniques Used: Activity Assay, Standard Deviation

    13) Product Images from "Human CHD2 Is a Chromatin Assembly ATPase Regulated by Its Chromo- and DNA-binding Domains"

    Article Title: Human CHD2 Is a Chromatin Assembly ATPase Regulated by Its Chromo- and DNA-binding Domains

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M114.609156

    WT CHD2 is a chromatin-stimulated ATPase. A , top , the WT human CHD2 protein contains a central SNF2-like ATPase domain (Core) that is flanked by tandem CDs and a putative DBD. Bottom , a partial alignment of human CHD2 (hCHD2), yeast CHD1 ( yCHD1 ), and Drosophila ISWI ( dISWI ) highlights the conserved DE X H sequence of the Walker B box. We used site-directed mutagenesis to clone a mutant version of CHD2 (Mut) that contains a two-amino acid alanine substitution of the Asp-617 and Glu-618 residues. B , WT and Mut CHD2 were purified from baculovirus-infected cells and analyzed by SDS-PAGE and Coomassie staining. C , a representative radiometric ATPase assay used to measure the ability of CHD2 to hydrolyze ATP over time. ATPase reactions with WT CHD2 alone (Basal) or containing DNA or chromatin were incubated for 0, 0.5, 1, 5, 15, 30, 60, or 90 min, stopped by the addition of EDTA, and resolved by TLC on PEI-cellulose plates. The positions of the ATP and released phosphate on the TLC plate are indicated. D , quantification of the ATPase assays with WT CHD2 stimulated by chromatin, DNA, or core histones. E , quantification of the radiometric ATPase assays using purified WT or Mut CHD2 protein in the presence or absence of chromatin. The fraction of ATP hydrolyzed was calculated and the values shown are mean and S.D.; n = 3.
    Figure Legend Snippet: WT CHD2 is a chromatin-stimulated ATPase. A , top , the WT human CHD2 protein contains a central SNF2-like ATPase domain (Core) that is flanked by tandem CDs and a putative DBD. Bottom , a partial alignment of human CHD2 (hCHD2), yeast CHD1 ( yCHD1 ), and Drosophila ISWI ( dISWI ) highlights the conserved DE X H sequence of the Walker B box. We used site-directed mutagenesis to clone a mutant version of CHD2 (Mut) that contains a two-amino acid alanine substitution of the Asp-617 and Glu-618 residues. B , WT and Mut CHD2 were purified from baculovirus-infected cells and analyzed by SDS-PAGE and Coomassie staining. C , a representative radiometric ATPase assay used to measure the ability of CHD2 to hydrolyze ATP over time. ATPase reactions with WT CHD2 alone (Basal) or containing DNA or chromatin were incubated for 0, 0.5, 1, 5, 15, 30, 60, or 90 min, stopped by the addition of EDTA, and resolved by TLC on PEI-cellulose plates. The positions of the ATP and released phosphate on the TLC plate are indicated. D , quantification of the ATPase assays with WT CHD2 stimulated by chromatin, DNA, or core histones. E , quantification of the radiometric ATPase assays using purified WT or Mut CHD2 protein in the presence or absence of chromatin. The fraction of ATP hydrolyzed was calculated and the values shown are mean and S.D.; n = 3.

    Techniques Used: Sequencing, Mutagenesis, Purification, Infection, SDS Page, Staining, ATPase Assay, Incubation, Thin Layer Chromatography

    14) Product Images from "DNase I aggravates islet β-cell apoptosis in type 2 diabetes"

    Article Title: DNase I aggravates islet β-cell apoptosis in type 2 diabetes

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5102

    DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Culture, Western Blot, Expressing, Real-time Polymerase Chain Reaction, Flow Cytometry, Cytometry, Standard Deviation

    Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.
    Figure Legend Snippet: Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.

    Techniques Used: Immunohistochemistry, Staining

    DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Counting, Expressing, Western Blot, Real-time Polymerase Chain Reaction, TUNEL Assay, Flow Cytometry, Cytometry, Standard Deviation

    DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P
    Figure Legend Snippet: DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P

    Techniques Used: Activity Assay, Standard Deviation

    15) Product Images from "DNase I aggravates islet β-cell apoptosis in type 2 diabetes"

    Article Title: DNase I aggravates islet β-cell apoptosis in type 2 diabetes

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5102

    DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Culture, Western Blot, Expressing, Real-time Polymerase Chain Reaction, Flow Cytometry, Cytometry, Standard Deviation

    Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.
    Figure Legend Snippet: Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.

    Techniques Used: Immunohistochemistry, Staining

    DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Counting, Expressing, Western Blot, Real-time Polymerase Chain Reaction, TUNEL Assay, Flow Cytometry, Cytometry, Standard Deviation

    DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P
    Figure Legend Snippet: DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P

    Techniques Used: Activity Assay, Standard Deviation

    16) Product Images from "DNase I aggravates islet β-cell apoptosis in type 2 diabetes"

    Article Title: DNase I aggravates islet β-cell apoptosis in type 2 diabetes

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5102

    DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Culture, Western Blot, Expressing, Real-time Polymerase Chain Reaction, Flow Cytometry, Cytometry, Standard Deviation

    Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.
    Figure Legend Snippet: Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.

    Techniques Used: Immunohistochemistry, Staining

    DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Counting, Expressing, Western Blot, Real-time Polymerase Chain Reaction, TUNEL Assay, Flow Cytometry, Cytometry, Standard Deviation

    DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P
    Figure Legend Snippet: DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P

    Techniques Used: Activity Assay, Standard Deviation

    17) Product Images from "DNase I aggravates islet β-cell apoptosis in type 2 diabetes"

    Article Title: DNase I aggravates islet β-cell apoptosis in type 2 diabetes

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5102

    DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Culture, Western Blot, Expressing, Real-time Polymerase Chain Reaction, Flow Cytometry, Cytometry, Standard Deviation

    Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.
    Figure Legend Snippet: Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.

    Techniques Used: Immunohistochemistry, Staining

    DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Counting, Expressing, Western Blot, Real-time Polymerase Chain Reaction, TUNEL Assay, Flow Cytometry, Cytometry, Standard Deviation

    DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P
    Figure Legend Snippet: DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P

    Techniques Used: Activity Assay, Standard Deviation

    18) Product Images from "Isolation, Characterization, and Molecular Cloning of a Protein (Abp2) That Binds to a Schizosaccharomyces pombe Origin of Replication (ars3002)"

    Article Title: Isolation, Characterization, and Molecular Cloning of a Protein (Abp2) That Binds to a Schizosaccharomyces pombe Origin of Replication (ars3002)

    Journal: Molecular and Cellular Biology

    doi:

    DNase I footprint of the MMACS dimer complexed with Abp2. Increasing amounts of purified Abp2 were incubated with 5 fmol of labeled MMACS dimer and then treated with DNase I as described in Materials and Methods. A control reaction with no Abp2 protein is shown in lane 4. The sequence of the labeled DNA strand of the MMACS dimer used in the footprinting assay is shown. Thick and medium lines indicate a perfect match or one base mismatch, respectively, to the S. pombe ARS consensus sequence. The hatched boxes indicate the DNA regions protected by Abp2 binding. The perfect matches to the S. pombe ARS consensus sequence are indicated; they span nt 13 to 23 and nt 44 to 54. The position marked at nt 32 indicates the beginning of the second MMACS monomer.
    Figure Legend Snippet: DNase I footprint of the MMACS dimer complexed with Abp2. Increasing amounts of purified Abp2 were incubated with 5 fmol of labeled MMACS dimer and then treated with DNase I as described in Materials and Methods. A control reaction with no Abp2 protein is shown in lane 4. The sequence of the labeled DNA strand of the MMACS dimer used in the footprinting assay is shown. Thick and medium lines indicate a perfect match or one base mismatch, respectively, to the S. pombe ARS consensus sequence. The hatched boxes indicate the DNA regions protected by Abp2 binding. The perfect matches to the S. pombe ARS consensus sequence are indicated; they span nt 13 to 23 and nt 44 to 54. The position marked at nt 32 indicates the beginning of the second MMACS monomer.

    Techniques Used: Purification, Incubation, Labeling, Sequencing, Footprinting, Binding Assay

    19) Product Images from "A Genetically Engineered Waterfowl Influenza Virus with a Deletion in the Stalk of the Neuraminidase Has Increased Virulence for Chickens ▿"

    Article Title: A Genetically Engineered Waterfowl Influenza Virus with a Deletion in the Stalk of the Neuraminidase Has Increased Virulence for Chickens ▿

    Journal: Journal of Virology

    doi: 10.1128/JVI.01581-09

    Efficiency of production of MZ and MZ-delNA pseudoparticles from DF1 cells. DF1 cells were transfected with plasmids allowing the expression of the indicated combinations of proteins. They were incubated for 24 h at 37°C in complete medium, in complete medium supplemented with 1 μM zanamivir, or in complete medium supplemented with 60 mU/ml of exogenous Clostridium perfringens neuraminidase. The efficiency of production of VPP was monitored by measuring the amounts of HIV-1 p24 protein in the cell supernatants by ELISA. The results are expressed as the ratio to the amount of p24 protein measured in the supernatants of cells expressing the MZ-HA protein alone in the absence of zanamivir and of exogenous Clostridium perfringens neuraminidase and are the means + standard variations from four independent experiments.
    Figure Legend Snippet: Efficiency of production of MZ and MZ-delNA pseudoparticles from DF1 cells. DF1 cells were transfected with plasmids allowing the expression of the indicated combinations of proteins. They were incubated for 24 h at 37°C in complete medium, in complete medium supplemented with 1 μM zanamivir, or in complete medium supplemented with 60 mU/ml of exogenous Clostridium perfringens neuraminidase. The efficiency of production of VPP was monitored by measuring the amounts of HIV-1 p24 protein in the cell supernatants by ELISA. The results are expressed as the ratio to the amount of p24 protein measured in the supernatants of cells expressing the MZ-HA protein alone in the absence of zanamivir and of exogenous Clostridium perfringens neuraminidase and are the means + standard variations from four independent experiments.

    Techniques Used: Transfection, Expressing, Incubation, Enzyme-linked Immunosorbent Assay

    20) Product Images from "DNase I aggravates islet β-cell apoptosis in type 2 diabetes"

    Article Title: DNase I aggravates islet β-cell apoptosis in type 2 diabetes

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5102

    DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Culture, Western Blot, Expressing, Real-time Polymerase Chain Reaction, Flow Cytometry, Cytometry, Standard Deviation

    Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.
    Figure Legend Snippet: Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.

    Techniques Used: Immunohistochemistry, Staining

    DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Counting, Expressing, Western Blot, Real-time Polymerase Chain Reaction, TUNEL Assay, Flow Cytometry, Cytometry, Standard Deviation

    DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P
    Figure Legend Snippet: DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P

    Techniques Used: Activity Assay, Standard Deviation

    21) Product Images from "DNase I aggravates islet β-cell apoptosis in type 2 diabetes"

    Article Title: DNase I aggravates islet β-cell apoptosis in type 2 diabetes

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5102

    DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Culture, Western Blot, Expressing, Real-time Polymerase Chain Reaction, Flow Cytometry, Cytometry, Standard Deviation

    Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.
    Figure Legend Snippet: Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.

    Techniques Used: Immunohistochemistry, Staining

    DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Counting, Expressing, Western Blot, Real-time Polymerase Chain Reaction, TUNEL Assay, Flow Cytometry, Cytometry, Standard Deviation

    DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P
    Figure Legend Snippet: DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P

    Techniques Used: Activity Assay, Standard Deviation

    22) Product Images from "DNase I aggravates islet β-cell apoptosis in type 2 diabetes"

    Article Title: DNase I aggravates islet β-cell apoptosis in type 2 diabetes

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5102

    DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Culture, Western Blot, Expressing, Real-time Polymerase Chain Reaction, Flow Cytometry, Cytometry, Standard Deviation

    Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.
    Figure Legend Snippet: Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.

    Techniques Used: Immunohistochemistry, Staining

    DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Counting, Expressing, Western Blot, Real-time Polymerase Chain Reaction, TUNEL Assay, Flow Cytometry, Cytometry, Standard Deviation

    DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P
    Figure Legend Snippet: DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P

    Techniques Used: Activity Assay, Standard Deviation

    23) Product Images from "DNase I aggravates islet β-cell apoptosis in type 2 diabetes"

    Article Title: DNase I aggravates islet β-cell apoptosis in type 2 diabetes

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5102

    DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I knockdown can reduce the apoptosis of cells cultured with high glucose. (A) Knockdown efficiency examined by western blotting. Expression of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Apoptotic rate examined by flow cytometry [(a), normal; (b), high glucose; and (c), siRNA group]. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Culture, Western Blot, Expressing, Real-time Polymerase Chain Reaction, Flow Cytometry, Cytometry, Standard Deviation

    Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.
    Figure Legend Snippet: Immunohistochemistry of the human pancreas. Pancreatic tissues from patients with pancreatic cancer, with or without type 2 diabetes were stained with insulin, glucagon, and DNase I. (A) Insulin, (B) glucagon and (C) DNase I staining of tissues from patients without type 2 diabetes. (D) Insulin, (E) glucagon and (F) DNase I staining of tissues from patients with type 2 diabetes. DNase I, deoxyribonuclease I.

    Techniques Used: Immunohistochemistry, Staining

    DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P
    Figure Legend Snippet: DNase I combined with high glucose induced cell apoptosis. (A) Cell viability assessed by the Cell Counting Kit-8 assay. The expression levels of DNase I, Bcl-2 and caspase-3 in the three groups were examined by (B) western blotting and (C) reverse transcription-quantitative polymerase chain reaction. (D) Cell apoptosis results from (a) the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and (b) flow cytometry. Data are expressed as the mean ± standard deviation from three independent experiments. * P

    Techniques Used: Cell Counting, Expressing, Western Blot, Real-time Polymerase Chain Reaction, TUNEL Assay, Flow Cytometry, Cytometry, Standard Deviation

    DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P
    Figure Legend Snippet: DNase I activity in human serum. (A) DNase I activity in human serum. (B) The correlation of DNase I activity with calcium. (C) DNase I activity Spearman correlation coefficient. All data are presented as the mean ± standard deviation. *** P

    Techniques Used: Activity Assay, Standard Deviation

    24) Product Images from "Functional Domains of Tat Required for Efficient Human Immunodeficiency Virus Type 1 Reverse Transcription †"

    Article Title: Functional Domains of Tat Required for Efficient Human Immunodeficiency Virus Type 1 Reverse Transcription †

    Journal: Journal of Virology

    doi:

    NERT assay for HIV-1 wild-type and tat mutant viruses. Virus stocks for wild-type virus (lanes 1), Δ tat virus trans -complemented with wild-type tat (lanes 2), Δ tat virus (lanes 3), or Δ tat virus produced in the presence of tat mutants [E2G, D5G, E9G], P3L, P[6, 10]L, P[10, 14]L, C27S, K41A, and K/R[50-57]G (lanes 4 to 10, respectively) were analyzed for endogenous reverse transcription. Culture supernatant (200 μl) containing approximately 0.75 mU of RT activity was treated with 100 U of DNase I. Half of each reaction mixture was added to 150 μl of stop solution, incubated at 37°C for 10 min, and then boiled for 10 min (B). The remaining half of each reaction mixture was supplemented with 50 μM dNTPs and incubated at 37°C for 90 minutes before the reaction was terminated as described above. (A) PCR to detect HIV-1 negative-strand strong-stop DNA was performed on NERT reaction mixtures as described in Materials and Methods. All PCRs were performed within the linear range of the assay as determined by assays of HIV-1 DNA copy number (10, 10 2 , 10 3 , and 10 4 ).
    Figure Legend Snippet: NERT assay for HIV-1 wild-type and tat mutant viruses. Virus stocks for wild-type virus (lanes 1), Δ tat virus trans -complemented with wild-type tat (lanes 2), Δ tat virus (lanes 3), or Δ tat virus produced in the presence of tat mutants [E2G, D5G, E9G], P3L, P[6, 10]L, P[10, 14]L, C27S, K41A, and K/R[50-57]G (lanes 4 to 10, respectively) were analyzed for endogenous reverse transcription. Culture supernatant (200 μl) containing approximately 0.75 mU of RT activity was treated with 100 U of DNase I. Half of each reaction mixture was added to 150 μl of stop solution, incubated at 37°C for 10 min, and then boiled for 10 min (B). The remaining half of each reaction mixture was supplemented with 50 μM dNTPs and incubated at 37°C for 90 minutes before the reaction was terminated as described above. (A) PCR to detect HIV-1 negative-strand strong-stop DNA was performed on NERT reaction mixtures as described in Materials and Methods. All PCRs were performed within the linear range of the assay as determined by assays of HIV-1 DNA copy number (10, 10 2 , 10 3 , and 10 4 ).

    Techniques Used: Mutagenesis, Produced, Activity Assay, Incubation, Polymerase Chain Reaction

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    Article Title: Extracellular traps are associated with human and mouse neutrophil and macrophage mediated killing of larval Strongyloides stercoralis
    Article Snippet: .. Treatment with DNase I eliminated the presence of released DNA, but did not block killing of the larvae by mouse neutrophils and macrophages in vitro. .. This observation suggests that in contrast to human neutrophils and macrophages, mouse cells do not require ET formation in vitro to kill the worms.

    Blocking Assay:

    Article Title: Extracellular traps are associated with human and mouse neutrophil and macrophage mediated killing of larval Strongyloides stercoralis
    Article Snippet: .. Treatment with DNase I eliminated the presence of released DNA, but did not block killing of the larvae by mouse neutrophils and macrophages in vitro. .. This observation suggests that in contrast to human neutrophils and macrophages, mouse cells do not require ET formation in vitro to kill the worms.

    Produced:

    Article Title: Novel High-Throughput Deoxyribonuclease 1 Assay
    Article Snippet: .. The percentage of DNase I activity was calculated using Equation 1: DNase\u00a0I\u00a0activity (%) =\u00a0 (mean\u00a0velocity\u00a0of\u00a0a\u00a0compound/mean\u00a0velocity\u00a0of\u00a0DMSO)\u00a0\u00d7\u00a0100 (1) In similar assays, recombinant murine EndoG (produced in-house) was used at a concentration of 0.14 μM in 0.1 mM MgCl2 , 10 mM Tris-HCl, pH 7.4; and DNase II (Worthington, Lakewood, NJ) (3.32 nM) was tested in 100 mM sodium citrate buffer, pH 5.0. .. For evaluation of the quality of the assay, Z’ values were calculated using Equation 2: Z\u2019 =\u00a01\u00a0\u2212\u00a0(3SDC +\u00a03SDB )/(MC \u00a0\u2212\u00a0MB ) (2) where M = mean value; SD = standard deviation; C = control; and B = background.

    Concentration Assay:

    Article Title: Interactions of NBU1 IntN1 and Orf2x Proteins with Attachment Site DNA
    Article Snippet: .. DNase I (Worthington) diluted in DNase I dilution buffer (2.5 mM MgCl2 , 0.5 mM CaCl2 , 10 mM Tris-HCl, pH 7.6, 0.1 mg/ml BSA) to a final concentration of 0.0625 μg/ml was incubated with reaction mixtures for 1 min. ..

    Article Title: Novel High-Throughput Deoxyribonuclease 1 Assay
    Article Snippet: .. The percentage of DNase I activity was calculated using Equation 1: DNase\u00a0I\u00a0activity (%) =\u00a0 (mean\u00a0velocity\u00a0of\u00a0a\u00a0compound/mean\u00a0velocity\u00a0of\u00a0DMSO)\u00a0\u00d7\u00a0100 (1) In similar assays, recombinant murine EndoG (produced in-house) was used at a concentration of 0.14 μM in 0.1 mM MgCl2 , 10 mM Tris-HCl, pH 7.4; and DNase II (Worthington, Lakewood, NJ) (3.32 nM) was tested in 100 mM sodium citrate buffer, pH 5.0. .. For evaluation of the quality of the assay, Z’ values were calculated using Equation 2: Z\u2019 =\u00a01\u00a0\u2212\u00a0(3SDC +\u00a03SDB )/(MC \u00a0\u2212\u00a0MB ) (2) where M = mean value; SD = standard deviation; C = control; and B = background.

    Incubation:

    Article Title: Epigenetic Control of Cell Cycle-Dependent Histone Gene Expression Is a Principal Component of the Abbreviated Pluripotent Cell Cycle
    Article Snippet: .. Nuclei were then resuspended in RSB buffer supplemented with 1 mM CaCl2 and incubated with increasing concentrations of DNase I (DPRF; Worthington Biochemical Corporation, Lakewood, NJ) for 10 min at room temperature with gentle agitation. ..

    Article Title: Interactions of NBU1 IntN1 and Orf2x Proteins with Attachment Site DNA
    Article Snippet: .. DNase I (Worthington) diluted in DNase I dilution buffer (2.5 mM MgCl2 , 0.5 mM CaCl2 , 10 mM Tris-HCl, pH 7.6, 0.1 mg/ml BSA) to a final concentration of 0.0625 μg/ml was incubated with reaction mixtures for 1 min. ..

    other:

    Article Title: Interactions of NBU1 IntN1 and Orf2x Proteins with Attachment Site DNA
    Article Snippet: The region is dA+dT rich, and protection seen from positions +126 to +129 is subtle because DNase I does not cleave DNA efficiently in this region.

    Article Title: Identification of Viral Peptide Fragments for Vaccine Development
    Article Snippet: In the random digestion step, the use of DNase I in the presence of MnCl2 is critical as this protocol will generate DNA fragments of relatively uniform sizes, which facilitates the reassembly step ( 17 , also see Note ).

    Activity Assay:

    Article Title: Novel High-Throughput Deoxyribonuclease 1 Assay
    Article Snippet: .. The percentage of DNase I activity was calculated using Equation 1: DNase\u00a0I\u00a0activity (%) =\u00a0 (mean\u00a0velocity\u00a0of\u00a0a\u00a0compound/mean\u00a0velocity\u00a0of\u00a0DMSO)\u00a0\u00d7\u00a0100 (1) In similar assays, recombinant murine EndoG (produced in-house) was used at a concentration of 0.14 μM in 0.1 mM MgCl2 , 10 mM Tris-HCl, pH 7.4; and DNase II (Worthington, Lakewood, NJ) (3.32 nM) was tested in 100 mM sodium citrate buffer, pH 5.0. .. For evaluation of the quality of the assay, Z’ values were calculated using Equation 2: Z\u2019 =\u00a01\u00a0\u2212\u00a0(3SDC +\u00a03SDB )/(MC \u00a0\u2212\u00a0MB ) (2) where M = mean value; SD = standard deviation; C = control; and B = background.

    Expressing:

    Article Title: Epigenetic Control of Cell Cycle-Dependent Histone Gene Expression Is a Principal Component of the Abbreviated Pluripotent Cell Cycle
    Article Snippet: .. Analysis of nuclease sensitivity ( ) of the genomic histone HIST2H4 locus to DNase I reveals changes in chromatin structure that accompany increased histone gene expression in hES cells. ..

    Recombinant:

    Article Title: Novel High-Throughput Deoxyribonuclease 1 Assay
    Article Snippet: .. The percentage of DNase I activity was calculated using Equation 1: DNase\u00a0I\u00a0activity (%) =\u00a0 (mean\u00a0velocity\u00a0of\u00a0a\u00a0compound/mean\u00a0velocity\u00a0of\u00a0DMSO)\u00a0\u00d7\u00a0100 (1) In similar assays, recombinant murine EndoG (produced in-house) was used at a concentration of 0.14 μM in 0.1 mM MgCl2 , 10 mM Tris-HCl, pH 7.4; and DNase II (Worthington, Lakewood, NJ) (3.32 nM) was tested in 100 mM sodium citrate buffer, pH 5.0. .. For evaluation of the quality of the assay, Z’ values were calculated using Equation 2: Z\u2019 =\u00a01\u00a0\u2212\u00a0(3SDC +\u00a03SDB )/(MC \u00a0\u2212\u00a0MB ) (2) where M = mean value; SD = standard deviation; C = control; and B = background.

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