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rabbit polyclonal anti p14 arf  (Novus Biologicals)


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    Structured Review

    Novus Biologicals rabbit polyclonal anti p14 arf
    A NPM1 structural features, including the secondary structure calculated from the oligomerization domain (OD) PDB 4N8M and the nucleic acid binding domain (NBD) PDB 2LLH , using DSSP (2 o Struc.; β-strands are indicated with arrows and α-helicies are indicated with cylinders). The CIDER linear net charge per residue (LNCPR) and linear hydropathy (Hydro.) are shown for the IDR. B <t>p14</t> ARF structural features, including PSI-PRED secondary structure prediction (2 o Struc.), CIDER linear net charge per residue (LNCPR), and linear hydropathy (Hydro.). The amino acid sequence conservation (Cons.) is based on a multiple sequence alignment using MUSCLE. The bottom panel shows the Rosetta steric zipper propensity energy (R. Energy) calculated using ZipperDB. C CV-SANS curves for p14 ARF -NPM1 condensates, in 100% D 2 O buffer for full scattering intensity (NPM1 and p14 ARF detected; gray trace), in 45% D 2 O buffer where p14 ARF is contrast matched ([ 2 H]-NPM1 detected; green trace), and in 85% D 2 O buffer where [ 2 H]-NPM1 is contrast matched (p14 ARF detected; blue trace). Correlation peaks at ~200 Å and ~400 Å correspond to meso-scale organization of p14 ARF . All curves are offset for clarity. Scatter points represent the average, the error bars represent the uncertainty derived from the counting statistics of the SANS instrument, as described and cited in the Methods. D Schematic describing NPM1 with extended IDR conformations. E Schematic describing the spatial organization of p14 ARF within p14 ARF -NPM1 condensates. F 2D CC-DARR spectrum of [ 13 C, 15 N]-p14 ARF within the condensed phase. Select resonance assignments are labeled. G Secondary 13 C chemical shifts for [ 13 C, 15 N]-p14 ARF within the condensed phase. Assigned residues are highlighted in gray. The secondary structure prediction from panel B is shown for reference (2 o Struc.; top).
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    Images

    1) Product Images from "p14 ARF forms meso-scale assemblies upon phase separation with NPM1"

    Article Title: p14 ARF forms meso-scale assemblies upon phase separation with NPM1

    Journal: Nature Communications

    doi: 10.1038/s41467-024-53904-z

    A NPM1 structural features, including the secondary structure calculated from the oligomerization domain (OD) PDB 4N8M and the nucleic acid binding domain (NBD) PDB 2LLH , using DSSP (2 o Struc.; β-strands are indicated with arrows and α-helicies are indicated with cylinders). The CIDER linear net charge per residue (LNCPR) and linear hydropathy (Hydro.) are shown for the IDR. B p14 ARF structural features, including PSI-PRED secondary structure prediction (2 o Struc.), CIDER linear net charge per residue (LNCPR), and linear hydropathy (Hydro.). The amino acid sequence conservation (Cons.) is based on a multiple sequence alignment using MUSCLE. The bottom panel shows the Rosetta steric zipper propensity energy (R. Energy) calculated using ZipperDB. C CV-SANS curves for p14 ARF -NPM1 condensates, in 100% D 2 O buffer for full scattering intensity (NPM1 and p14 ARF detected; gray trace), in 45% D 2 O buffer where p14 ARF is contrast matched ([ 2 H]-NPM1 detected; green trace), and in 85% D 2 O buffer where [ 2 H]-NPM1 is contrast matched (p14 ARF detected; blue trace). Correlation peaks at ~200 Å and ~400 Å correspond to meso-scale organization of p14 ARF . All curves are offset for clarity. Scatter points represent the average, the error bars represent the uncertainty derived from the counting statistics of the SANS instrument, as described and cited in the Methods. D Schematic describing NPM1 with extended IDR conformations. E Schematic describing the spatial organization of p14 ARF within p14 ARF -NPM1 condensates. F 2D CC-DARR spectrum of [ 13 C, 15 N]-p14 ARF within the condensed phase. Select resonance assignments are labeled. G Secondary 13 C chemical shifts for [ 13 C, 15 N]-p14 ARF within the condensed phase. Assigned residues are highlighted in gray. The secondary structure prediction from panel B is shown for reference (2 o Struc.; top).
    Figure Legend Snippet: A NPM1 structural features, including the secondary structure calculated from the oligomerization domain (OD) PDB 4N8M and the nucleic acid binding domain (NBD) PDB 2LLH , using DSSP (2 o Struc.; β-strands are indicated with arrows and α-helicies are indicated with cylinders). The CIDER linear net charge per residue (LNCPR) and linear hydropathy (Hydro.) are shown for the IDR. B p14 ARF structural features, including PSI-PRED secondary structure prediction (2 o Struc.), CIDER linear net charge per residue (LNCPR), and linear hydropathy (Hydro.). The amino acid sequence conservation (Cons.) is based on a multiple sequence alignment using MUSCLE. The bottom panel shows the Rosetta steric zipper propensity energy (R. Energy) calculated using ZipperDB. C CV-SANS curves for p14 ARF -NPM1 condensates, in 100% D 2 O buffer for full scattering intensity (NPM1 and p14 ARF detected; gray trace), in 45% D 2 O buffer where p14 ARF is contrast matched ([ 2 H]-NPM1 detected; green trace), and in 85% D 2 O buffer where [ 2 H]-NPM1 is contrast matched (p14 ARF detected; blue trace). Correlation peaks at ~200 Å and ~400 Å correspond to meso-scale organization of p14 ARF . All curves are offset for clarity. Scatter points represent the average, the error bars represent the uncertainty derived from the counting statistics of the SANS instrument, as described and cited in the Methods. D Schematic describing NPM1 with extended IDR conformations. E Schematic describing the spatial organization of p14 ARF within p14 ARF -NPM1 condensates. F 2D CC-DARR spectrum of [ 13 C, 15 N]-p14 ARF within the condensed phase. Select resonance assignments are labeled. G Secondary 13 C chemical shifts for [ 13 C, 15 N]-p14 ARF within the condensed phase. Assigned residues are highlighted in gray. The secondary structure prediction from panel B is shown for reference (2 o Struc.; top).

    Techniques Used: Binding Assay, Cider Assay, Residue, Sequencing, Derivative Assay, Labeling

    A A CC-DARR spectrum acquired for [ 13 C, 15 N]-p14 ARF with 20 ms DARR mixing time shows resonances for T8 in two states, including in an expanded p14 ARF conformation (top), and in a collapsed p14 ARF conformation (bottom). B A CC-DARR spectrum acquired with 400 ms DARR mixing time shows additional cross-peaks indicating intramolecular contacts between T8 and H26. C The 2D-NHHC spectrum (gray) of p14 ARF (equal mixture of [ 13 C]-p14 ARF and [ 15 N]-p14 ARF ) shows that sidechains within the p14 ARF N-terminus make intermolecular contacts within the condensed phase with NPM1. HNCA (magenta) and 2D-HNCACX (blue) spectra for [ 13 C, 15 N]-p14 ARF are shown for reference. D Schematic describing possible modes of p14 ARF intra- and intermolecular interaction.
    Figure Legend Snippet: A A CC-DARR spectrum acquired for [ 13 C, 15 N]-p14 ARF with 20 ms DARR mixing time shows resonances for T8 in two states, including in an expanded p14 ARF conformation (top), and in a collapsed p14 ARF conformation (bottom). B A CC-DARR spectrum acquired with 400 ms DARR mixing time shows additional cross-peaks indicating intramolecular contacts between T8 and H26. C The 2D-NHHC spectrum (gray) of p14 ARF (equal mixture of [ 13 C]-p14 ARF and [ 15 N]-p14 ARF ) shows that sidechains within the p14 ARF N-terminus make intermolecular contacts within the condensed phase with NPM1. HNCA (magenta) and 2D-HNCACX (blue) spectra for [ 13 C, 15 N]-p14 ARF are shown for reference. D Schematic describing possible modes of p14 ARF intra- and intermolecular interaction.

    Techniques Used:

    A The 2D 1 H- 15 N TROSY-HSQC spectrum of [ 13 C, 15 N]-NPM1 within the p14 ARF -NPM1 condensed phase displays resonances from the NPM1 IDR. B Linear net charge per residue (LNCPR) for the NPM1 IDR. Nuclear spin relaxation for [ 2 H, 15 N]-NPM1 in solution (blue scatter points) and condensed phase [ 13 C, 15 N]-NPM1 (red scatter points), including C 1 H- 15 N heteronuclear NOEs, D R 1 , and E R 2 transverse relaxation, which shows a restriction of NPM1 IDR backbone motions on the ps-ns timescale. The error bars for R 1 and R 2 transverse relaxation plots represent the standard errors from curve fitting, as described in Methods. F The contributions from exchange broadening, R ex . G 15 N-CPMG relaxation dispersion profiles for condensed [ 13 C, 15 N]-NPM1 measured at 800 MHz, including A186, T199, and A201, fit to a two-state model. Scatter points represent the decay rates, and the error bars represent the estimated systematic error, as described in Methods. H Schematic describing NPM1 IDR conformational exchange within condensates with p14 ARF .
    Figure Legend Snippet: A The 2D 1 H- 15 N TROSY-HSQC spectrum of [ 13 C, 15 N]-NPM1 within the p14 ARF -NPM1 condensed phase displays resonances from the NPM1 IDR. B Linear net charge per residue (LNCPR) for the NPM1 IDR. Nuclear spin relaxation for [ 2 H, 15 N]-NPM1 in solution (blue scatter points) and condensed phase [ 13 C, 15 N]-NPM1 (red scatter points), including C 1 H- 15 N heteronuclear NOEs, D R 1 , and E R 2 transverse relaxation, which shows a restriction of NPM1 IDR backbone motions on the ps-ns timescale. The error bars for R 1 and R 2 transverse relaxation plots represent the standard errors from curve fitting, as described in Methods. F The contributions from exchange broadening, R ex . G 15 N-CPMG relaxation dispersion profiles for condensed [ 13 C, 15 N]-NPM1 measured at 800 MHz, including A186, T199, and A201, fit to a two-state model. Scatter points represent the decay rates, and the error bars represent the estimated systematic error, as described in Methods. H Schematic describing NPM1 IDR conformational exchange within condensates with p14 ARF .

    Techniques Used: Residue, Dispersion

    A p14 ARF structural features, including PSI-PRED4.0 secondary structure prediction (2 o Struc.), CIDER linear net charge per residue (LNCPR) and linear hydropathy (Hydro.). The CIDER analysis for p14 ARF ΔH1-3 is shown below. B Zoomed in regions from confocal fluorescence micrographs of NPM1-AF488 in condensates with p14 ARF (top) and p14 ARF ΔH1-3 (bottom). Scale bars = 10 µm. C Index of dispersion for NPM1 in condensates with p14 ARF (gray boxes, whiskers and trace; derived from n = 6, 6, 6, 7, 6, 6, 7, 6, 6, 6, 7 images) and p14 ARF ΔH1-3 (blue boxes and whiskers and trace, where n = 5, 4, 6, 6, 8, 6, 6, 6, 6, 6, 6 images). Whiskers extend from the box to the furthest point within 1.5x the inter-quartile range. The black arrow highlights the increased NPM1 saturation concentration, ΔC sat , upon substitution of p14 ARF hydrophobic residues to Gly/Ser spacer residues. The gray arrow highlights the reentrant phase transition, which occurs at elevated p14 ARF concentrations. D ΔG tr for NPM1 in condensates with p14 ARF (gray boxes, whiskers and trace, where n = 696, 42, 61, 159, 225, 285, 333, 276, 306, 227, 773 condensates) and p14 ARF ΔH1-3 (blue boxes, whiskers and trace, where n = 2561, 1787, 29, 31, 82, 92, 134, 153, 166, 145, 162 condensates). Whiskers extend from the box to the furthest point within 1.5x the inter-quartile range. The C sat for NPM1 increases when p14 ARF hydrophobic residues are substituted. The gray arrow highlights the destabilization of NPM1 during the reentrant phase transition. E CV-SANS curves for p14 ARF ΔH1-3-[ 2 H]-NPM1 condensates collected at 50% D 2 O, where p14 ARF ΔH1-3 is contrast matched ([ 2 H]-NPM1 detected; green trace), at 85% D 2 O where [ 2 H]-NPM1 is contrast matched (p14 ARF ΔH1-3 detected; blue trace), and p14 ARF ΔH1-3-NPM1 condensate at 100% D 2 O for full scattering intensity (NPM1 and p14 ARF ΔH1-3 detected; gray trace). All curves are offset for clarity. Scatter points represent the average, the error bars represent the uncertainty derived from the counting statistics of the SANS instrument, as described and cited in the Methods. F Schematic describing condensed NPM1 with extended IDR conformations. G Schematic describing condensed p14 ARF ΔH1-3 in an extended conformation. H FRAP of NPM1-AF488 within condensates shows that substitution of p14 ARF hydrophobic residues to Gly/Ser spacer residues restores NPM1 mobility. Scale bars = 1 µm. I FRAP recovery curves for p14 ARF -NPM1 and p14 ARF ΔH1-3-NPM1 condensates with fits, as described in Methods (statistical significance was assessed by two-sided Wilcoxon rank-sum test, n = 10 curves for each condition, the p -value is shown in the figure). J NPM1-AF488 D App values extracted from the FRAP recovery curves in panel I (statistical significance was assessed by two-sided Wilcoxon rank-sum test, n = 10 D App values for each condition, the p -value is shown in the figure).
    Figure Legend Snippet: A p14 ARF structural features, including PSI-PRED4.0 secondary structure prediction (2 o Struc.), CIDER linear net charge per residue (LNCPR) and linear hydropathy (Hydro.). The CIDER analysis for p14 ARF ΔH1-3 is shown below. B Zoomed in regions from confocal fluorescence micrographs of NPM1-AF488 in condensates with p14 ARF (top) and p14 ARF ΔH1-3 (bottom). Scale bars = 10 µm. C Index of dispersion for NPM1 in condensates with p14 ARF (gray boxes, whiskers and trace; derived from n = 6, 6, 6, 7, 6, 6, 7, 6, 6, 6, 7 images) and p14 ARF ΔH1-3 (blue boxes and whiskers and trace, where n = 5, 4, 6, 6, 8, 6, 6, 6, 6, 6, 6 images). Whiskers extend from the box to the furthest point within 1.5x the inter-quartile range. The black arrow highlights the increased NPM1 saturation concentration, ΔC sat , upon substitution of p14 ARF hydrophobic residues to Gly/Ser spacer residues. The gray arrow highlights the reentrant phase transition, which occurs at elevated p14 ARF concentrations. D ΔG tr for NPM1 in condensates with p14 ARF (gray boxes, whiskers and trace, where n = 696, 42, 61, 159, 225, 285, 333, 276, 306, 227, 773 condensates) and p14 ARF ΔH1-3 (blue boxes, whiskers and trace, where n = 2561, 1787, 29, 31, 82, 92, 134, 153, 166, 145, 162 condensates). Whiskers extend from the box to the furthest point within 1.5x the inter-quartile range. The C sat for NPM1 increases when p14 ARF hydrophobic residues are substituted. The gray arrow highlights the destabilization of NPM1 during the reentrant phase transition. E CV-SANS curves for p14 ARF ΔH1-3-[ 2 H]-NPM1 condensates collected at 50% D 2 O, where p14 ARF ΔH1-3 is contrast matched ([ 2 H]-NPM1 detected; green trace), at 85% D 2 O where [ 2 H]-NPM1 is contrast matched (p14 ARF ΔH1-3 detected; blue trace), and p14 ARF ΔH1-3-NPM1 condensate at 100% D 2 O for full scattering intensity (NPM1 and p14 ARF ΔH1-3 detected; gray trace). All curves are offset for clarity. Scatter points represent the average, the error bars represent the uncertainty derived from the counting statistics of the SANS instrument, as described and cited in the Methods. F Schematic describing condensed NPM1 with extended IDR conformations. G Schematic describing condensed p14 ARF ΔH1-3 in an extended conformation. H FRAP of NPM1-AF488 within condensates shows that substitution of p14 ARF hydrophobic residues to Gly/Ser spacer residues restores NPM1 mobility. Scale bars = 1 µm. I FRAP recovery curves for p14 ARF -NPM1 and p14 ARF ΔH1-3-NPM1 condensates with fits, as described in Methods (statistical significance was assessed by two-sided Wilcoxon rank-sum test, n = 10 curves for each condition, the p -value is shown in the figure). J NPM1-AF488 D App values extracted from the FRAP recovery curves in panel I (statistical significance was assessed by two-sided Wilcoxon rank-sum test, n = 10 D App values for each condition, the p -value is shown in the figure).

    Techniques Used: Cider Assay, Residue, Fluorescence, Dispersion, Derivative Assay, Concentration Assay, Sublimation

    A Zoomed in regions from fluorescence microscopy images of live DLD-1 NPM1-G (clone B11) cells, before and after 48 h of doxycycline induced p14 ARF -iRFP expression. Scale bars = 2 µm. B Z-score analysis of NPM1-GFP and p14 ARF -iRFP levels in DLD-1 NPM1-G cells, showing that p14 ARF and NPM1 levels are anti-correlated (statistical significance was assessed by two-sided Mann–Whitney U-test, n = 2272, 122, 54 cells, p -values are shown in the figure) C FRAP curves with fits, as described in Methods, for cells sorted from the DLD-1 NPM1-G population shown in B. The curves on the left are from a cell expressing a high level of nucleolar NPM1 (clone F6; green trace) and a low level of nucleolar p14 ARF (clone F6; blue trace). The curves on the right are from a cell expressing a low level of nucleolar NPM1 (clone G2; green trace) and a high level of nucleolar p14 ARF (clone G2; blue traces). In unsorted DLD-1 NPM1-G cells, D The D App and E mobility for nucleolar NPM1-GFP and p14 ARF -iRFP (small green and blue transparent markers, respectively, n = 45 cells) are reduced as nucleolar p14 ARF -iRFP levels increase. Reductions also occur as the duration of p14 ARF -iRFP expression is extended (large opaque markers; scatter points represent the mean and error bars represent the standard deviation, where n = 20 cells). F A schematic describing the correlated reductions in p14 ARF and NPM1 dynamics and their assembly into large molecular weight complexes within the granular component (GC) of the nucleolus.
    Figure Legend Snippet: A Zoomed in regions from fluorescence microscopy images of live DLD-1 NPM1-G (clone B11) cells, before and after 48 h of doxycycline induced p14 ARF -iRFP expression. Scale bars = 2 µm. B Z-score analysis of NPM1-GFP and p14 ARF -iRFP levels in DLD-1 NPM1-G cells, showing that p14 ARF and NPM1 levels are anti-correlated (statistical significance was assessed by two-sided Mann–Whitney U-test, n = 2272, 122, 54 cells, p -values are shown in the figure) C FRAP curves with fits, as described in Methods, for cells sorted from the DLD-1 NPM1-G population shown in B. The curves on the left are from a cell expressing a high level of nucleolar NPM1 (clone F6; green trace) and a low level of nucleolar p14 ARF (clone F6; blue trace). The curves on the right are from a cell expressing a low level of nucleolar NPM1 (clone G2; green trace) and a high level of nucleolar p14 ARF (clone G2; blue traces). In unsorted DLD-1 NPM1-G cells, D The D App and E mobility for nucleolar NPM1-GFP and p14 ARF -iRFP (small green and blue transparent markers, respectively, n = 45 cells) are reduced as nucleolar p14 ARF -iRFP levels increase. Reductions also occur as the duration of p14 ARF -iRFP expression is extended (large opaque markers; scatter points represent the mean and error bars represent the standard deviation, where n = 20 cells). F A schematic describing the correlated reductions in p14 ARF and NPM1 dynamics and their assembly into large molecular weight complexes within the granular component (GC) of the nucleolus.

    Techniques Used: Fluorescence, Microscopy, Expressing, MANN-WHITNEY, Standard Deviation, Molecular Weight



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    Image Search Results


    A NPM1 structural features, including the secondary structure calculated from the oligomerization domain (OD) PDB 4N8M and the nucleic acid binding domain (NBD) PDB 2LLH , using DSSP (2 o Struc.; β-strands are indicated with arrows and α-helicies are indicated with cylinders). The CIDER linear net charge per residue (LNCPR) and linear hydropathy (Hydro.) are shown for the IDR. B p14 ARF structural features, including PSI-PRED secondary structure prediction (2 o Struc.), CIDER linear net charge per residue (LNCPR), and linear hydropathy (Hydro.). The amino acid sequence conservation (Cons.) is based on a multiple sequence alignment using MUSCLE. The bottom panel shows the Rosetta steric zipper propensity energy (R. Energy) calculated using ZipperDB. C CV-SANS curves for p14 ARF -NPM1 condensates, in 100% D 2 O buffer for full scattering intensity (NPM1 and p14 ARF detected; gray trace), in 45% D 2 O buffer where p14 ARF is contrast matched ([ 2 H]-NPM1 detected; green trace), and in 85% D 2 O buffer where [ 2 H]-NPM1 is contrast matched (p14 ARF detected; blue trace). Correlation peaks at ~200 Å and ~400 Å correspond to meso-scale organization of p14 ARF . All curves are offset for clarity. Scatter points represent the average, the error bars represent the uncertainty derived from the counting statistics of the SANS instrument, as described and cited in the Methods. D Schematic describing NPM1 with extended IDR conformations. E Schematic describing the spatial organization of p14 ARF within p14 ARF -NPM1 condensates. F 2D CC-DARR spectrum of [ 13 C, 15 N]-p14 ARF within the condensed phase. Select resonance assignments are labeled. G Secondary 13 C chemical shifts for [ 13 C, 15 N]-p14 ARF within the condensed phase. Assigned residues are highlighted in gray. The secondary structure prediction from panel B is shown for reference (2 o Struc.; top).

    Journal: Nature Communications

    Article Title: p14 ARF forms meso-scale assemblies upon phase separation with NPM1

    doi: 10.1038/s41467-024-53904-z

    Figure Lengend Snippet: A NPM1 structural features, including the secondary structure calculated from the oligomerization domain (OD) PDB 4N8M and the nucleic acid binding domain (NBD) PDB 2LLH , using DSSP (2 o Struc.; β-strands are indicated with arrows and α-helicies are indicated with cylinders). The CIDER linear net charge per residue (LNCPR) and linear hydropathy (Hydro.) are shown for the IDR. B p14 ARF structural features, including PSI-PRED secondary structure prediction (2 o Struc.), CIDER linear net charge per residue (LNCPR), and linear hydropathy (Hydro.). The amino acid sequence conservation (Cons.) is based on a multiple sequence alignment using MUSCLE. The bottom panel shows the Rosetta steric zipper propensity energy (R. Energy) calculated using ZipperDB. C CV-SANS curves for p14 ARF -NPM1 condensates, in 100% D 2 O buffer for full scattering intensity (NPM1 and p14 ARF detected; gray trace), in 45% D 2 O buffer where p14 ARF is contrast matched ([ 2 H]-NPM1 detected; green trace), and in 85% D 2 O buffer where [ 2 H]-NPM1 is contrast matched (p14 ARF detected; blue trace). Correlation peaks at ~200 Å and ~400 Å correspond to meso-scale organization of p14 ARF . All curves are offset for clarity. Scatter points represent the average, the error bars represent the uncertainty derived from the counting statistics of the SANS instrument, as described and cited in the Methods. D Schematic describing NPM1 with extended IDR conformations. E Schematic describing the spatial organization of p14 ARF within p14 ARF -NPM1 condensates. F 2D CC-DARR spectrum of [ 13 C, 15 N]-p14 ARF within the condensed phase. Select resonance assignments are labeled. G Secondary 13 C chemical shifts for [ 13 C, 15 N]-p14 ARF within the condensed phase. Assigned residues are highlighted in gray. The secondary structure prediction from panel B is shown for reference (2 o Struc.; top).

    Article Snippet: The primary antibodies were used as follows: rabbit monoclonal anti-Cyclophilin B (Cell Signaling, 43603) at 1:1500–1:2000 dilution; rabbit monoclonal anti-GAPDH (Cell Signaling, 5174) at 1:2500 dilution; mouse monoclonal anti-NPM1 (ThermoFisher Scientific, 32-5200) at 1:1000 dillution; mouse monoclonal anti-p14 Arf (Cell Signaling, 2407) at 1:1000–1:15000 dilution; mouse monoclonal anti-GAPDH (Santa Cruz, sc-47724) at 1:2500 dilution; and rabbit polyclonal anti-p14 Arf (Novus, NB200-111) at 1:2000 dilution.

    Techniques: Binding Assay, Cider Assay, Residue, Sequencing, Derivative Assay, Labeling

    A A CC-DARR spectrum acquired for [ 13 C, 15 N]-p14 ARF with 20 ms DARR mixing time shows resonances for T8 in two states, including in an expanded p14 ARF conformation (top), and in a collapsed p14 ARF conformation (bottom). B A CC-DARR spectrum acquired with 400 ms DARR mixing time shows additional cross-peaks indicating intramolecular contacts between T8 and H26. C The 2D-NHHC spectrum (gray) of p14 ARF (equal mixture of [ 13 C]-p14 ARF and [ 15 N]-p14 ARF ) shows that sidechains within the p14 ARF N-terminus make intermolecular contacts within the condensed phase with NPM1. HNCA (magenta) and 2D-HNCACX (blue) spectra for [ 13 C, 15 N]-p14 ARF are shown for reference. D Schematic describing possible modes of p14 ARF intra- and intermolecular interaction.

    Journal: Nature Communications

    Article Title: p14 ARF forms meso-scale assemblies upon phase separation with NPM1

    doi: 10.1038/s41467-024-53904-z

    Figure Lengend Snippet: A A CC-DARR spectrum acquired for [ 13 C, 15 N]-p14 ARF with 20 ms DARR mixing time shows resonances for T8 in two states, including in an expanded p14 ARF conformation (top), and in a collapsed p14 ARF conformation (bottom). B A CC-DARR spectrum acquired with 400 ms DARR mixing time shows additional cross-peaks indicating intramolecular contacts between T8 and H26. C The 2D-NHHC spectrum (gray) of p14 ARF (equal mixture of [ 13 C]-p14 ARF and [ 15 N]-p14 ARF ) shows that sidechains within the p14 ARF N-terminus make intermolecular contacts within the condensed phase with NPM1. HNCA (magenta) and 2D-HNCACX (blue) spectra for [ 13 C, 15 N]-p14 ARF are shown for reference. D Schematic describing possible modes of p14 ARF intra- and intermolecular interaction.

    Article Snippet: The primary antibodies were used as follows: rabbit monoclonal anti-Cyclophilin B (Cell Signaling, 43603) at 1:1500–1:2000 dilution; rabbit monoclonal anti-GAPDH (Cell Signaling, 5174) at 1:2500 dilution; mouse monoclonal anti-NPM1 (ThermoFisher Scientific, 32-5200) at 1:1000 dillution; mouse monoclonal anti-p14 Arf (Cell Signaling, 2407) at 1:1000–1:15000 dilution; mouse monoclonal anti-GAPDH (Santa Cruz, sc-47724) at 1:2500 dilution; and rabbit polyclonal anti-p14 Arf (Novus, NB200-111) at 1:2000 dilution.

    Techniques:

    A The 2D 1 H- 15 N TROSY-HSQC spectrum of [ 13 C, 15 N]-NPM1 within the p14 ARF -NPM1 condensed phase displays resonances from the NPM1 IDR. B Linear net charge per residue (LNCPR) for the NPM1 IDR. Nuclear spin relaxation for [ 2 H, 15 N]-NPM1 in solution (blue scatter points) and condensed phase [ 13 C, 15 N]-NPM1 (red scatter points), including C 1 H- 15 N heteronuclear NOEs, D R 1 , and E R 2 transverse relaxation, which shows a restriction of NPM1 IDR backbone motions on the ps-ns timescale. The error bars for R 1 and R 2 transverse relaxation plots represent the standard errors from curve fitting, as described in Methods. F The contributions from exchange broadening, R ex . G 15 N-CPMG relaxation dispersion profiles for condensed [ 13 C, 15 N]-NPM1 measured at 800 MHz, including A186, T199, and A201, fit to a two-state model. Scatter points represent the decay rates, and the error bars represent the estimated systematic error, as described in Methods. H Schematic describing NPM1 IDR conformational exchange within condensates with p14 ARF .

    Journal: Nature Communications

    Article Title: p14 ARF forms meso-scale assemblies upon phase separation with NPM1

    doi: 10.1038/s41467-024-53904-z

    Figure Lengend Snippet: A The 2D 1 H- 15 N TROSY-HSQC spectrum of [ 13 C, 15 N]-NPM1 within the p14 ARF -NPM1 condensed phase displays resonances from the NPM1 IDR. B Linear net charge per residue (LNCPR) for the NPM1 IDR. Nuclear spin relaxation for [ 2 H, 15 N]-NPM1 in solution (blue scatter points) and condensed phase [ 13 C, 15 N]-NPM1 (red scatter points), including C 1 H- 15 N heteronuclear NOEs, D R 1 , and E R 2 transverse relaxation, which shows a restriction of NPM1 IDR backbone motions on the ps-ns timescale. The error bars for R 1 and R 2 transverse relaxation plots represent the standard errors from curve fitting, as described in Methods. F The contributions from exchange broadening, R ex . G 15 N-CPMG relaxation dispersion profiles for condensed [ 13 C, 15 N]-NPM1 measured at 800 MHz, including A186, T199, and A201, fit to a two-state model. Scatter points represent the decay rates, and the error bars represent the estimated systematic error, as described in Methods. H Schematic describing NPM1 IDR conformational exchange within condensates with p14 ARF .

    Article Snippet: The primary antibodies were used as follows: rabbit monoclonal anti-Cyclophilin B (Cell Signaling, 43603) at 1:1500–1:2000 dilution; rabbit monoclonal anti-GAPDH (Cell Signaling, 5174) at 1:2500 dilution; mouse monoclonal anti-NPM1 (ThermoFisher Scientific, 32-5200) at 1:1000 dillution; mouse monoclonal anti-p14 Arf (Cell Signaling, 2407) at 1:1000–1:15000 dilution; mouse monoclonal anti-GAPDH (Santa Cruz, sc-47724) at 1:2500 dilution; and rabbit polyclonal anti-p14 Arf (Novus, NB200-111) at 1:2000 dilution.

    Techniques: Residue, Dispersion

    A p14 ARF structural features, including PSI-PRED4.0 secondary structure prediction (2 o Struc.), CIDER linear net charge per residue (LNCPR) and linear hydropathy (Hydro.). The CIDER analysis for p14 ARF ΔH1-3 is shown below. B Zoomed in regions from confocal fluorescence micrographs of NPM1-AF488 in condensates with p14 ARF (top) and p14 ARF ΔH1-3 (bottom). Scale bars = 10 µm. C Index of dispersion for NPM1 in condensates with p14 ARF (gray boxes, whiskers and trace; derived from n = 6, 6, 6, 7, 6, 6, 7, 6, 6, 6, 7 images) and p14 ARF ΔH1-3 (blue boxes and whiskers and trace, where n = 5, 4, 6, 6, 8, 6, 6, 6, 6, 6, 6 images). Whiskers extend from the box to the furthest point within 1.5x the inter-quartile range. The black arrow highlights the increased NPM1 saturation concentration, ΔC sat , upon substitution of p14 ARF hydrophobic residues to Gly/Ser spacer residues. The gray arrow highlights the reentrant phase transition, which occurs at elevated p14 ARF concentrations. D ΔG tr for NPM1 in condensates with p14 ARF (gray boxes, whiskers and trace, where n = 696, 42, 61, 159, 225, 285, 333, 276, 306, 227, 773 condensates) and p14 ARF ΔH1-3 (blue boxes, whiskers and trace, where n = 2561, 1787, 29, 31, 82, 92, 134, 153, 166, 145, 162 condensates). Whiskers extend from the box to the furthest point within 1.5x the inter-quartile range. The C sat for NPM1 increases when p14 ARF hydrophobic residues are substituted. The gray arrow highlights the destabilization of NPM1 during the reentrant phase transition. E CV-SANS curves for p14 ARF ΔH1-3-[ 2 H]-NPM1 condensates collected at 50% D 2 O, where p14 ARF ΔH1-3 is contrast matched ([ 2 H]-NPM1 detected; green trace), at 85% D 2 O where [ 2 H]-NPM1 is contrast matched (p14 ARF ΔH1-3 detected; blue trace), and p14 ARF ΔH1-3-NPM1 condensate at 100% D 2 O for full scattering intensity (NPM1 and p14 ARF ΔH1-3 detected; gray trace). All curves are offset for clarity. Scatter points represent the average, the error bars represent the uncertainty derived from the counting statistics of the SANS instrument, as described and cited in the Methods. F Schematic describing condensed NPM1 with extended IDR conformations. G Schematic describing condensed p14 ARF ΔH1-3 in an extended conformation. H FRAP of NPM1-AF488 within condensates shows that substitution of p14 ARF hydrophobic residues to Gly/Ser spacer residues restores NPM1 mobility. Scale bars = 1 µm. I FRAP recovery curves for p14 ARF -NPM1 and p14 ARF ΔH1-3-NPM1 condensates with fits, as described in Methods (statistical significance was assessed by two-sided Wilcoxon rank-sum test, n = 10 curves for each condition, the p -value is shown in the figure). J NPM1-AF488 D App values extracted from the FRAP recovery curves in panel I (statistical significance was assessed by two-sided Wilcoxon rank-sum test, n = 10 D App values for each condition, the p -value is shown in the figure).

    Journal: Nature Communications

    Article Title: p14 ARF forms meso-scale assemblies upon phase separation with NPM1

    doi: 10.1038/s41467-024-53904-z

    Figure Lengend Snippet: A p14 ARF structural features, including PSI-PRED4.0 secondary structure prediction (2 o Struc.), CIDER linear net charge per residue (LNCPR) and linear hydropathy (Hydro.). The CIDER analysis for p14 ARF ΔH1-3 is shown below. B Zoomed in regions from confocal fluorescence micrographs of NPM1-AF488 in condensates with p14 ARF (top) and p14 ARF ΔH1-3 (bottom). Scale bars = 10 µm. C Index of dispersion for NPM1 in condensates with p14 ARF (gray boxes, whiskers and trace; derived from n = 6, 6, 6, 7, 6, 6, 7, 6, 6, 6, 7 images) and p14 ARF ΔH1-3 (blue boxes and whiskers and trace, where n = 5, 4, 6, 6, 8, 6, 6, 6, 6, 6, 6 images). Whiskers extend from the box to the furthest point within 1.5x the inter-quartile range. The black arrow highlights the increased NPM1 saturation concentration, ΔC sat , upon substitution of p14 ARF hydrophobic residues to Gly/Ser spacer residues. The gray arrow highlights the reentrant phase transition, which occurs at elevated p14 ARF concentrations. D ΔG tr for NPM1 in condensates with p14 ARF (gray boxes, whiskers and trace, where n = 696, 42, 61, 159, 225, 285, 333, 276, 306, 227, 773 condensates) and p14 ARF ΔH1-3 (blue boxes, whiskers and trace, where n = 2561, 1787, 29, 31, 82, 92, 134, 153, 166, 145, 162 condensates). Whiskers extend from the box to the furthest point within 1.5x the inter-quartile range. The C sat for NPM1 increases when p14 ARF hydrophobic residues are substituted. The gray arrow highlights the destabilization of NPM1 during the reentrant phase transition. E CV-SANS curves for p14 ARF ΔH1-3-[ 2 H]-NPM1 condensates collected at 50% D 2 O, where p14 ARF ΔH1-3 is contrast matched ([ 2 H]-NPM1 detected; green trace), at 85% D 2 O where [ 2 H]-NPM1 is contrast matched (p14 ARF ΔH1-3 detected; blue trace), and p14 ARF ΔH1-3-NPM1 condensate at 100% D 2 O for full scattering intensity (NPM1 and p14 ARF ΔH1-3 detected; gray trace). All curves are offset for clarity. Scatter points represent the average, the error bars represent the uncertainty derived from the counting statistics of the SANS instrument, as described and cited in the Methods. F Schematic describing condensed NPM1 with extended IDR conformations. G Schematic describing condensed p14 ARF ΔH1-3 in an extended conformation. H FRAP of NPM1-AF488 within condensates shows that substitution of p14 ARF hydrophobic residues to Gly/Ser spacer residues restores NPM1 mobility. Scale bars = 1 µm. I FRAP recovery curves for p14 ARF -NPM1 and p14 ARF ΔH1-3-NPM1 condensates with fits, as described in Methods (statistical significance was assessed by two-sided Wilcoxon rank-sum test, n = 10 curves for each condition, the p -value is shown in the figure). J NPM1-AF488 D App values extracted from the FRAP recovery curves in panel I (statistical significance was assessed by two-sided Wilcoxon rank-sum test, n = 10 D App values for each condition, the p -value is shown in the figure).

    Article Snippet: The primary antibodies were used as follows: rabbit monoclonal anti-Cyclophilin B (Cell Signaling, 43603) at 1:1500–1:2000 dilution; rabbit monoclonal anti-GAPDH (Cell Signaling, 5174) at 1:2500 dilution; mouse monoclonal anti-NPM1 (ThermoFisher Scientific, 32-5200) at 1:1000 dillution; mouse monoclonal anti-p14 Arf (Cell Signaling, 2407) at 1:1000–1:15000 dilution; mouse monoclonal anti-GAPDH (Santa Cruz, sc-47724) at 1:2500 dilution; and rabbit polyclonal anti-p14 Arf (Novus, NB200-111) at 1:2000 dilution.

    Techniques: Cider Assay, Residue, Fluorescence, Dispersion, Derivative Assay, Concentration Assay, Sublimation

    A Zoomed in regions from fluorescence microscopy images of live DLD-1 NPM1-G (clone B11) cells, before and after 48 h of doxycycline induced p14 ARF -iRFP expression. Scale bars = 2 µm. B Z-score analysis of NPM1-GFP and p14 ARF -iRFP levels in DLD-1 NPM1-G cells, showing that p14 ARF and NPM1 levels are anti-correlated (statistical significance was assessed by two-sided Mann–Whitney U-test, n = 2272, 122, 54 cells, p -values are shown in the figure) C FRAP curves with fits, as described in Methods, for cells sorted from the DLD-1 NPM1-G population shown in B. The curves on the left are from a cell expressing a high level of nucleolar NPM1 (clone F6; green trace) and a low level of nucleolar p14 ARF (clone F6; blue trace). The curves on the right are from a cell expressing a low level of nucleolar NPM1 (clone G2; green trace) and a high level of nucleolar p14 ARF (clone G2; blue traces). In unsorted DLD-1 NPM1-G cells, D The D App and E mobility for nucleolar NPM1-GFP and p14 ARF -iRFP (small green and blue transparent markers, respectively, n = 45 cells) are reduced as nucleolar p14 ARF -iRFP levels increase. Reductions also occur as the duration of p14 ARF -iRFP expression is extended (large opaque markers; scatter points represent the mean and error bars represent the standard deviation, where n = 20 cells). F A schematic describing the correlated reductions in p14 ARF and NPM1 dynamics and their assembly into large molecular weight complexes within the granular component (GC) of the nucleolus.

    Journal: Nature Communications

    Article Title: p14 ARF forms meso-scale assemblies upon phase separation with NPM1

    doi: 10.1038/s41467-024-53904-z

    Figure Lengend Snippet: A Zoomed in regions from fluorescence microscopy images of live DLD-1 NPM1-G (clone B11) cells, before and after 48 h of doxycycline induced p14 ARF -iRFP expression. Scale bars = 2 µm. B Z-score analysis of NPM1-GFP and p14 ARF -iRFP levels in DLD-1 NPM1-G cells, showing that p14 ARF and NPM1 levels are anti-correlated (statistical significance was assessed by two-sided Mann–Whitney U-test, n = 2272, 122, 54 cells, p -values are shown in the figure) C FRAP curves with fits, as described in Methods, for cells sorted from the DLD-1 NPM1-G population shown in B. The curves on the left are from a cell expressing a high level of nucleolar NPM1 (clone F6; green trace) and a low level of nucleolar p14 ARF (clone F6; blue trace). The curves on the right are from a cell expressing a low level of nucleolar NPM1 (clone G2; green trace) and a high level of nucleolar p14 ARF (clone G2; blue traces). In unsorted DLD-1 NPM1-G cells, D The D App and E mobility for nucleolar NPM1-GFP and p14 ARF -iRFP (small green and blue transparent markers, respectively, n = 45 cells) are reduced as nucleolar p14 ARF -iRFP levels increase. Reductions also occur as the duration of p14 ARF -iRFP expression is extended (large opaque markers; scatter points represent the mean and error bars represent the standard deviation, where n = 20 cells). F A schematic describing the correlated reductions in p14 ARF and NPM1 dynamics and their assembly into large molecular weight complexes within the granular component (GC) of the nucleolus.

    Article Snippet: The primary antibodies were used as follows: rabbit monoclonal anti-Cyclophilin B (Cell Signaling, 43603) at 1:1500–1:2000 dilution; rabbit monoclonal anti-GAPDH (Cell Signaling, 5174) at 1:2500 dilution; mouse monoclonal anti-NPM1 (ThermoFisher Scientific, 32-5200) at 1:1000 dillution; mouse monoclonal anti-p14 Arf (Cell Signaling, 2407) at 1:1000–1:15000 dilution; mouse monoclonal anti-GAPDH (Santa Cruz, sc-47724) at 1:2500 dilution; and rabbit polyclonal anti-p14 Arf (Novus, NB200-111) at 1:2000 dilution.

    Techniques: Fluorescence, Microscopy, Expressing, MANN-WHITNEY, Standard Deviation, Molecular Weight

    Representative immunohistochemical images of p16INK4a and p14ARF. Both the nucleus and cytoplasm were stained in p16INK4a-positive neoplastic epithelium ( A ); in contrast, in the p16INK4a-negative neoplastic epithelium, the cytoplasm was unstained ( B ). In all patients, no cytoplasmic p16INK4a-positive images were observed for the non-neoplastic epithelium ( C ). The nucleus was stained in p14ARF-positive neoplastic epithelium ( D ); in contrast, in the p14ARF-negative neoplastic epithelium, the nuclei were unstained ( E ). Patients for whom the non-neoplastic epithelium stained for p14ARF in the nucleus were considered positive ( F ), and those for whom this staining was not observed were considered negative ( G ). In both neoplastic and non-neoplastic epithelium, the expression of p16INK4A in the cytoplasm and p14ARF in the nucleus (> 10%) were considered positive. p14ARF p14 alternate reading frame; p16INK4a p16 inhibitor of cyclin-dependent kinase 4A.

    Journal: Scientific Reports

    Article Title: Novel genomic alteration in superficial esophageal squamous cell neoplasms in non-smoker non-drinker females

    doi: 10.1038/s41598-021-99790-z

    Figure Lengend Snippet: Representative immunohistochemical images of p16INK4a and p14ARF. Both the nucleus and cytoplasm were stained in p16INK4a-positive neoplastic epithelium ( A ); in contrast, in the p16INK4a-negative neoplastic epithelium, the cytoplasm was unstained ( B ). In all patients, no cytoplasmic p16INK4a-positive images were observed for the non-neoplastic epithelium ( C ). The nucleus was stained in p14ARF-positive neoplastic epithelium ( D ); in contrast, in the p14ARF-negative neoplastic epithelium, the nuclei were unstained ( E ). Patients for whom the non-neoplastic epithelium stained for p14ARF in the nucleus were considered positive ( F ), and those for whom this staining was not observed were considered negative ( G ). In both neoplastic and non-neoplastic epithelium, the expression of p16INK4A in the cytoplasm and p14ARF in the nucleus (> 10%) were considered positive. p14ARF p14 alternate reading frame; p16INK4a p16 inhibitor of cyclin-dependent kinase 4A.

    Article Snippet: After blocking with 2.5% normal horse serum for 20 min at 20 °C, the sliced tissues were incubated at 4 °C overnight with an anti-human p16INK4A monoclonal antibody (1:300; EPR1473, Abcam, UK) and anti-human p14ARF polyclonal antibody (1:200; E3X6D, Cell Signaling Technology, USA).

    Techniques: Immunohistochemical staining, Staining, Expressing

    Expression levels of p14ARF and p16INK4a in neoplastic and non-neoplastic epithelium.

    Journal: Scientific Reports

    Article Title: Novel genomic alteration in superficial esophageal squamous cell neoplasms in non-smoker non-drinker females

    doi: 10.1038/s41598-021-99790-z

    Figure Lengend Snippet: Expression levels of p14ARF and p16INK4a in neoplastic and non-neoplastic epithelium.

    Article Snippet: After blocking with 2.5% normal horse serum for 20 min at 20 °C, the sliced tissues were incubated at 4 °C overnight with an anti-human p16INK4A monoclonal antibody (1:300; EPR1473, Abcam, UK) and anti-human p14ARF polyclonal antibody (1:200; E3X6D, Cell Signaling Technology, USA).

    Techniques: Expressing