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    Millipore tris acetate
    ( A ) ChIP experiment to determine the occupancy of hras -1, hras -2 and control sequence (870 bp downstream from TSS) by <t>hnRNP</t> A1. Histograms shows the relative occupancy of hras -1 and hras -2 by hnRNP A1, RNA Pol II (positive control) and IgG (negative control). Data have been normalized by IgG signal; ( B ) EMSA of 32 P-labelled hras -1 Y and hras -2 Y in 50 mM <t>Tris-acetate</t> pH 5.5, 50 mM KCl, incubated 40 min at room temperature with increasing amounts of recombinant hnRNP A1 (0–12 μg). Lane (Δ,A1) indicates the i M incubated 40 min at room temperature, with denatured hnRNPA1 in binding buffer (see Methods); ( C ) EMSA at pH 5.5 of hras -1 Y with BSA or denatured hnRNP A1 and EMSA of hras -1 Y (m) with hnRNP A1; ss = single-stranded oligonucleotide; 1:1 and 1:2 DNA-protein complexes.
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    ( A ) ChIP experiment to determine the occupancy of hras -1, hras -2 and control sequence (870 bp downstream from TSS) by hnRNP A1. Histograms shows the relative occupancy of hras -1 and hras -2 by hnRNP A1, RNA Pol II (positive control) and IgG (negative control). Data have been normalized by IgG signal; ( B ) EMSA of 32 P-labelled hras -1 Y and hras -2 Y in 50 mM Tris-acetate pH 5.5, 50 mM KCl, incubated 40 min at room temperature with increasing amounts of recombinant hnRNP A1 (0–12 μg). Lane (Δ,A1) indicates the i M incubated 40 min at room temperature, with denatured hnRNPA1 in binding buffer (see Methods); ( C ) EMSA at pH 5.5 of hras -1 Y with BSA or denatured hnRNP A1 and EMSA of hras -1 Y (m) with hnRNP A1; ss = single-stranded oligonucleotide; 1:1 and 1:2 DNA-protein complexes.

    Journal: Scientific Reports

    Article Title: GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1

    doi: 10.1038/srep18097

    Figure Lengend Snippet: ( A ) ChIP experiment to determine the occupancy of hras -1, hras -2 and control sequence (870 bp downstream from TSS) by hnRNP A1. Histograms shows the relative occupancy of hras -1 and hras -2 by hnRNP A1, RNA Pol II (positive control) and IgG (negative control). Data have been normalized by IgG signal; ( B ) EMSA of 32 P-labelled hras -1 Y and hras -2 Y in 50 mM Tris-acetate pH 5.5, 50 mM KCl, incubated 40 min at room temperature with increasing amounts of recombinant hnRNP A1 (0–12 μg). Lane (Δ,A1) indicates the i M incubated 40 min at room temperature, with denatured hnRNPA1 in binding buffer (see Methods); ( C ) EMSA at pH 5.5 of hras -1 Y with BSA or denatured hnRNP A1 and EMSA of hras -1 Y (m) with hnRNP A1; ss = single-stranded oligonucleotide; 1:1 and 1:2 DNA-protein complexes.

    Article Snippet: Radiolabelled oligonucleotides (10 nM) were incubated for 30 min at 20 °C with increasing amounts of hnRNP A1 (0–12 μg) as specified in , in 50 mM Tris–acetate, pH 5.5, 50 mM KCl, 1 mM DTT, 8% glycerol, 1% Phosphatase Inhibitor Cocktail I (Sigma, Milan, Italy), 5 mM NaF, 1 mM Na3 VO4 , 2.5 ng/μl salmon sperm DNA (binding buffer).

    Techniques: Chromatin Immunoprecipitation, Sequencing, Positive Control, Negative Control, Incubation, Recombinant, Binding Assay

    Circular dichroism analysis of 3 μM (0.5 cm pathlength cell) hras -1 Y and hras -2 Y at pH 5.5, 50 mM Tris-acetate, 50 mM KCl, after incubation with increasing amounts of hnRNP A1 (r = 0–4). Spectra of DNA-protein complex have been subtracted of protein spectrum.

    Journal: Scientific Reports

    Article Title: GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1

    doi: 10.1038/srep18097

    Figure Lengend Snippet: Circular dichroism analysis of 3 μM (0.5 cm pathlength cell) hras -1 Y and hras -2 Y at pH 5.5, 50 mM Tris-acetate, 50 mM KCl, after incubation with increasing amounts of hnRNP A1 (r = 0–4). Spectra of DNA-protein complex have been subtracted of protein spectrum.

    Article Snippet: Radiolabelled oligonucleotides (10 nM) were incubated for 30 min at 20 °C with increasing amounts of hnRNP A1 (0–12 μg) as specified in , in 50 mM Tris–acetate, pH 5.5, 50 mM KCl, 1 mM DTT, 8% glycerol, 1% Phosphatase Inhibitor Cocktail I (Sigma, Milan, Italy), 5 mM NaF, 1 mM Na3 VO4 , 2.5 ng/μl salmon sperm DNA (binding buffer).

    Techniques: Incubation

    ( A ) Sequences of the GC-rich elements located in the HRAS promoter upstream of major TSS’s; ( B,C ) Circular dichroism titrations of hras -1 Y and hras -2 Y (3 μM, 1 cm pathlength cell) in 50 mM Tris-acetate, 50 mM KCl, 40% PEG-300 and pH from 4.5 to 8; ( D ) Ellipticity (287 nm) versus pH curves for hras -1 Y and hras -2 Y in the presence and absence of PEG-300; ( E ) Determination of number of protons picked up by hras -1 Y and hras -2 Y upon folding into the i M.

    Journal: Scientific Reports

    Article Title: GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1

    doi: 10.1038/srep18097

    Figure Lengend Snippet: ( A ) Sequences of the GC-rich elements located in the HRAS promoter upstream of major TSS’s; ( B,C ) Circular dichroism titrations of hras -1 Y and hras -2 Y (3 μM, 1 cm pathlength cell) in 50 mM Tris-acetate, 50 mM KCl, 40% PEG-300 and pH from 4.5 to 8; ( D ) Ellipticity (287 nm) versus pH curves for hras -1 Y and hras -2 Y in the presence and absence of PEG-300; ( E ) Determination of number of protons picked up by hras -1 Y and hras -2 Y upon folding into the i M.

    Article Snippet: Radiolabelled oligonucleotides (10 nM) were incubated for 30 min at 20 °C with increasing amounts of hnRNP A1 (0–12 μg) as specified in , in 50 mM Tris–acetate, pH 5.5, 50 mM KCl, 1 mM DTT, 8% glycerol, 1% Phosphatase Inhibitor Cocktail I (Sigma, Milan, Italy), 5 mM NaF, 1 mM Na3 VO4 , 2.5 ng/μl salmon sperm DNA (binding buffer).

    Techniques:

    Generation and characterisation of ptxD transformants. a The pWUCA2-ptxD plasmid contains ptxD under the control of the psaA exon 1 promoter/5′UTR and rbcL 3′UTR. The trnW UCA gene immediately upstream allows translational readthrough of the two TGA stop codons in ptxD (Young and Purton 2016 ). Targeted integration of both genes into the psbH-trnE2 intergenic region of the plastome of the psbH mutant TN72 occurs via two homologous recombination events, resulting in replacement of the aadA cassette and restoration of photosynthetic function. b PCR confirmation of plastome integration using three primers per reaction. As depicted in ( a ), the original TN72 plastome yields a 0.88 kb product with primers F1 and R1, whereas the transformant plastome gives a 1.42 kb product with primers F1 and R2. The absence of a 0.88 kb band for all four transformants indicates that the plastomes are homoplasmic, as seen for the control transformant (codA). c Western blot analysis of PtxD protein accumulation in the transgenic lines. An anti-HA antibody was used to detect the HA-tagged PtxD protein (37 kDa) in crude cell lysates. The codA transformant expressing an HA-tagged cytosine deaminase protein (49 kDa) serves as a positive control, whilst a TN72 transformant generated using the empty pWUCA2 plasmid serves as a negative control. An equivalent amount of cell lysate was loaded in each lane. d Growth tests of two transformant lines and the negative control on solid Tris-acetate medium containing either phosphate or phosphite. Plates were photographed 4 days after spotting of equivalent volumes of culture onto each plate

    Journal: Applied Microbiology and Biotechnology

    Article Title: The phosphite oxidoreductase gene, ptxD as a bio-contained chloroplast marker and crop-protection tool for algal biotechnology using Chlamydomonas

    doi: 10.1007/s00253-019-10258-7

    Figure Lengend Snippet: Generation and characterisation of ptxD transformants. a The pWUCA2-ptxD plasmid contains ptxD under the control of the psaA exon 1 promoter/5′UTR and rbcL 3′UTR. The trnW UCA gene immediately upstream allows translational readthrough of the two TGA stop codons in ptxD (Young and Purton 2016 ). Targeted integration of both genes into the psbH-trnE2 intergenic region of the plastome of the psbH mutant TN72 occurs via two homologous recombination events, resulting in replacement of the aadA cassette and restoration of photosynthetic function. b PCR confirmation of plastome integration using three primers per reaction. As depicted in ( a ), the original TN72 plastome yields a 0.88 kb product with primers F1 and R1, whereas the transformant plastome gives a 1.42 kb product with primers F1 and R2. The absence of a 0.88 kb band for all four transformants indicates that the plastomes are homoplasmic, as seen for the control transformant (codA). c Western blot analysis of PtxD protein accumulation in the transgenic lines. An anti-HA antibody was used to detect the HA-tagged PtxD protein (37 kDa) in crude cell lysates. The codA transformant expressing an HA-tagged cytosine deaminase protein (49 kDa) serves as a positive control, whilst a TN72 transformant generated using the empty pWUCA2 plasmid serves as a negative control. An equivalent amount of cell lysate was loaded in each lane. d Growth tests of two transformant lines and the negative control on solid Tris-acetate medium containing either phosphate or phosphite. Plates were photographed 4 days after spotting of equivalent volumes of culture onto each plate

    Article Snippet: Direct selection for ptxD transformants was on agar plates containing Tris-acetate medium supplemented with sodium phosphite (Na2 HPO3 ·5H2 O, 04283 Sigma-Aldrich) at a final concentration of 1 mM (referred to as TA-Phi medium: Table ).

    Techniques: Plasmid Preparation, Mutagenesis, Homologous Recombination, Polymerase Chain Reaction, Western Blot, Transgenic Assay, Expressing, Positive Control, Generated, Negative Control

    Characterization of PRG4 and reduced and alkylated (R/A) PRG4. Protein stain on 3-8 % Tris-Acetate SDS-PAGE stained with SimplyBlue SafeStain ( a ) and immunoreactivity with anti-PRG4 antibody 5C11 ( b ). ** and * indicate high MW multimeric species and monomeric PRG4 species, respectively, with the former being present in the non-reduced samples and absent from the R/A PRG4

    Journal: BMC Musculoskeletal Disorders

    Article Title: Cartilage boundary lubrication synergism is mediated by hyaluronan concentration and PRG4 concentration and structure

    doi: 10.1186/s12891-015-0842-5

    Figure Lengend Snippet: Characterization of PRG4 and reduced and alkylated (R/A) PRG4. Protein stain on 3-8 % Tris-Acetate SDS-PAGE stained with SimplyBlue SafeStain ( a ) and immunoreactivity with anti-PRG4 antibody 5C11 ( b ). ** and * indicate high MW multimeric species and monomeric PRG4 species, respectively, with the former being present in the non-reduced samples and absent from the R/A PRG4

    Article Snippet: Purity of the PRG4 preparation was confirmed by 3–8 % Tris-Acetate SDS-PAGE followed by protein stain and Western blotting with anti-PRG4 antibody 5C11 (obtained from Millipore, Etobicoke, ON, Canada) [ ] with Invitrogen’s NuPAGE system.

    Techniques: Staining, SDS Page