Journal: Biochimica et biophysica acta

Article Title: Role of Nhp6 and Hmo1 in SWI/SNF occupancy and nucleosome landscape at gene regulatory regions

doi: 10.1016/j.bbagrm.2017.01.002

Figure Lengend Snippet: Histone H3 occupancy is affected at gene promoters undergoing reduction of SWI/SNF occupancy upon deletion of NHP6A/B and/or deletion of HMO1. ChIP-qPCR analyses were performed to determine changes in Snf5 and H3 occupancy generated by deletion of NHP6A/B (yellow bars) or HMO1 (red bars) for selected genes listed in Table 1. The groups of genes depicted in figures A, B, C, and D are in correspondence with the groups of genes listed in Table 1. Values obtained from the qPCR reactions for all genes in wild-type and deletion mutant strains were expressed as “times over IgG” and the resulting values obtained for the deletion mutants are expressed in the graphs relative to the corresponding values obtained for the wild-type strain. Thus, the horizontal black line is representative of occupancy levels in the wild-type strain. Data in each graph correspond to an assay representative of two independent assays, each performed in triplicate. Error bars represent one standard deviation. Asterisks denote a statistically significant difference (*p < 0.05; **p < 0.01; ***p < 0.001), as deducted from the t-test. Top (figures A–D): ChIP-qPCR analysis for Snf5. Bottom (figures A–D): ChIP-qPCR analysis for histone H3. Positions given here and in the figures are relative to the translation start site. Supplementary Fig. S8 is an expanded version of figures A–D. A) Analysis for genes undergoing reduction of SWI/SNF occupancy at their promoter/TSS upon deletion of NHP6A/B, as determined by the ChIP-chip assays. Regions spanned by PCR reactions: RPS22A, −294/−200; DSE1, −97/+4; NPR3, −222/−97; PDR12, −356/−227. B) Analysis for genes undergoing reduction of SWI/SNF occupancy at their promoter/TSS upon deletion of HMO1, as determined by the ChIP-chip assays. Regions spanned by PCR reactions: MRP21, −115/−15; AAH1, −213/−119; NUP42, −348/−230; MED8, −175/−44. C) Analysis for genes undergoing reduction of SWI/SNF occupancy at their promoter/TSS in both deletion mutants, as determined by the ChIP-chip assays. Regions spanned by PCR reactions: NAT4, −162/−62; LDH1, −94/+8; VMA11, −210/−96; GEX2, −356/−223. D) Analysis for genes where deletion of neither NHP6A/B nor HMO1 affects SWI/SNF binding to the promoter/TSS, as determined by the ChIP-chip assays. Regions spanned by PCR reactions: SAG1, −101/+2; ASH1, −145/−43; GDB1, −201/−73; EFM1, −226/−115. E) ChIP-qPCR analysis of histone H3 occupancy at different stretches of the RPS22A promoter. F) ChIP-qPCR analysis of histone H3 occupancy at different stretches of the NUP42 promoter.

Article Snippet: Antibodies ChIP assays were performed using the following antibodies: anti-Snf5 (Upstate #07-320); Histone H3 antibody (Active Motif #39163); normal IgG antibody (SantaCruz #2015).

Techniques: ChIP-qPCR, Generated, Mutagenesis, Standard Deviation, ChIP-chip, Binding Assay

Journal: Virulence

Article Title: The PirB toxin protein from Vibrio parahaemolyticus induces apoptosis in hemocytes of Penaeus vannamei

doi: 10.1080/21505594.2021.1872171

Figure Lengend Snippet: Summary annotated proteins identified to interact with PirB

Article Snippet: The collected supernatant was analyzed using SDS-PAGE and Western blot, as described in subsection 2.2, with mouse anti-histone H3 antibody (1:1000, Transgen BioTech, Beijing, China), and rabbit anti-phospho histone H3 (Ser10) antibody (1:1000, Cell Signaling Technology, MA, USA).

Techniques:

Journal: Virulence

Article Title: The PirB toxin protein from Vibrio parahaemolyticus induces apoptosis in hemocytes of Penaeus vannamei

doi: 10.1080/21505594.2021.1872171

Figure Lengend Snippet: The interaction between PirB toxin protein and histones. (a) Purification of nucleosome proteins by gel filtration chromatography. (b) SDS-PAGE, Native-PAGE and Western blot analysis of purified nucleosomes. (c) Native-PAGE and Western blot analysis of the interaction between His-rPirB and nucleosome proteins. Purified nucleosomes treated with different concentrations (0.2, 0.1, and 0.05 µM) of recombinant His-rPirA or His-rPirB proteins and analyzed by Native-PAGE and Western blot using anti-histone H3 antibody

Article Snippet: The collected supernatant was analyzed using SDS-PAGE and Western blot, as described in subsection 2.2, with mouse anti-histone H3 antibody (1:1000, Transgen BioTech, Beijing, China), and rabbit anti-phospho histone H3 (Ser10) antibody (1:1000, Cell Signaling Technology, MA, USA).

Techniques: Purification, Chromatography, SDS Page, Clear Native PAGE, Western Blot, Recombinant

Journal: Virulence

Article Title: The PirB toxin protein from Vibrio parahaemolyticus induces apoptosis in hemocytes of Penaeus vannamei

doi: 10.1080/21505594.2021.1872171

Figure Lengend Snippet: The PirB toxin protein induces dephosphorylation of histone H3 on Serine 10. Primary hemocytes were treated with His-rPirB or His-rPirA for 2 h, followed by Western blot analysis to detect total tubulin, histone H3, and phosphorylation levels of histone H3 on Serine 10

Article Snippet: The collected supernatant was analyzed using SDS-PAGE and Western blot, as described in subsection 2.2, with mouse anti-histone H3 antibody (1:1000, Transgen BioTech, Beijing, China), and rabbit anti-phospho histone H3 (Ser10) antibody (1:1000, Cell Signaling Technology, MA, USA).

Techniques: De-Phosphorylation Assay, Western Blot

Journal: Virulence

Article Title: The PirB toxin protein from Vibrio parahaemolyticus induces apoptosis in hemocytes of Penaeus vannamei

doi: 10.1080/21505594.2021.1872171

Figure Lengend Snippet: A proposed model shows that PirB induces apoptosis in shrimp hemocytes. When primary hemocytes of Penaeus vannamei are treated with the Pir proteins from Vibrio parahaemolyticus, the PirB protein enters the cytoplasm and nuclei. Once in the nucleus, the PirB protein interacts with histone proteins to dephosphorylate histone H3 and therefore induce apoptosis in hemocytes

Article Snippet: The collected supernatant was analyzed using SDS-PAGE and Western blot, as described in subsection 2.2, with mouse anti-histone H3 antibody (1:1000, Transgen BioTech, Beijing, China), and rabbit anti-phospho histone H3 (Ser10) antibody (1:1000, Cell Signaling Technology, MA, USA).

Techniques:

Journal: Scientific Reports

Article Title: Leukocyte filtration and leukocyte modulation therapy during extracorporeal cardiopulmonary resuscitation in a porcine model of prolonged cardiac arrest

doi: 10.1038/s41598-024-63522-w

Figure Lengend Snippet: Cardiac and Neuronal Histopathology ( A ) Myocardial injuries. Myofiber degeneration and myocardial hemorrhage are shown in box and whiskers plots. Sections of ventricles were stained with H&E staining. The myofiber degeneration and myocardial hemorrhage were graded from 0 to 3. The data were analyzed with Mann–Whitney test. Naïve n = 4, Control n = 8, LF n = 12, L-MOD n = 12. ( B ) Neuronal injuries in the brain. Neuronal degeneration are shown in box and whiskers plots. Brain sections were stained with cresyl violet. The neuronal degeneration scores at caudate, hippocampus, cingulate cortex, and cerebellum were graded from 0 to 4 based on the percentage of degenerated neurons. 0: 0–5%, 1: 6%-25%, 2: 26%-50%, 3: 51%-75%, and 4: 76%-100%. The data were analyzed with Mann–Whitney test. Naïve n = 8, Control n = 8, LF n = 12, L-MOD n = 12. ( C ) Neutrophil extracellular traps (NETs) in vasculatures. The colocalization of citrullinated Histone H3 in von Willebrand Factor (vWF) was detected with immunofluorescence staining. The NETs formations were quantified with Fiji Image J as percentage of citrullinated histone H3 area in von Willebrand Factor-stained vasculature. Brain: Naïve n = 8, Control n = 8, LF n = 12, L-MOD n = 12. Heart: Naïve n = 4, Control n = 8, LF n = 12, L-MOD n = 12. The data were analyzed with Mann–Whitney test. * p < 0.05 Naïve vs. Control. ( D ) Representative images of NETs immunofluorescent staining (200x) in brain tissue. The colocalization of von Willebrand Factor (Red) and citrullinated H3 (Green) was detected with immunofluorescence. DAPI counterstaining shows nuclei (blue). Top panel: NETs in Naïve group. Bottom panel: NETs in Control group.

Article Snippet: The brain or heart sections were incubated at 4 °C overnight with the following primary antibodies: mouse anti-citrullinated Histone H3 antibody (17939, Cayman Chemical, Ann Arbor, MI) and rabbit anti-von Willebrand factor antibody (NB600586, NOVUS BIOLOGICALS, Centennial, CO).

Techniques: Histopathology, Staining, MANN-WHITNEY, Control, Immunofluorescence

Journal: Scientific Reports

Article Title: Leukocyte filtration and leukocyte modulation therapy during extracorporeal cardiopulmonary resuscitation in a porcine model of prolonged cardiac arrest

doi: 10.1038/s41598-024-63522-w

Figure Lengend Snippet: NETosis Markers. ( A ) Double-Stranded DNA (dsDNA). DsDNA was measured to serve as a surrogate for NETosis. Groups were not significantly different among each other at any time point. However, there was a significant increase in dsDNA compared to baseline for all three groups at timepoints 2:38, 4:38 and the end. ( B ) Citrullinated Histone. Citrullinated Histone H3 Elisa results are graphed above. Groups were not significantly different among each other at any time point. However, there was a significant increase in citrullinated histone compared to baseline for all three groups at timepoints 0:38, 2:38, 4:38 and the end. Statistical significance was set at a p -value of < 0.05.

Article Snippet: The brain or heart sections were incubated at 4 °C overnight with the following primary antibodies: mouse anti-citrullinated Histone H3 antibody (17939, Cayman Chemical, Ann Arbor, MI) and rabbit anti-von Willebrand factor antibody (NB600586, NOVUS BIOLOGICALS, Centennial, CO).

Techniques: Enzyme-linked Immunosorbent Assay