Journal: Investigative ophthalmology & visual science

Article Title: Transvitreal Retinochoroidal Biopsies of Primary Uveal Melanoma Reveal an Association of Low HLA Class I and High NK Cell Abundance in Low-Risk Disease.

doi: 10.1167/iovs.66.2.24

Figure Lengend Snippet: FIGURE 6. HLA class I expression inversely associates with intratumoral NK cell percentages. (A) Bar plots showing the percentages of HLA class I–positive tumor cells (top) and the NK cells (middle) and CD8 T cells (bottom) of all immune cells per patient. (B) Box plot showing the percentage of HLA class I–positive tumor cells versus the BAP1 staining that was performed on tissue. (C) Box plot showing the percentage of HLA class I–positive tumor cells versus the risk group. (D) Kaplan–Meier plot showing the RFS of two groups of patients, separated by the median percentage of NK cells into NKhigh and NKlow groups.

Article Snippet: To identify the BRCA1 associated protein 1 (BAP1) status of tumors, a standard immunohistochemistry (IHC) staining using 1:100 anti-BAP1 (clone C-4, sc-28383; Santa Cruz Biotechnology, Dallas, TX, USA) was performed.

Techniques: Expressing, Staining

Journal: Cancers

Article Title: Analysis of TERT mRNA Levels and Clinicopathological Features in Patients with Peritoneal Mesothelioma

doi: 10.3390/cancers17020252

Figure Lengend Snippet: Histological characteristics of mesothelioma patients’ biopsies relative to BAP1, p16 and MTAP.

Article Snippet: BRCA1-associated protein 1 (BAP1) (clone C4, Santa Cruz Biotechnology, Santa Cruz, CA, USA) was classified as negative only if a complete absence of nuclear staining was observed in the presence of nuclear-positive lymphocytes.

Techniques:

Journal: Cancers

Article Title: Analysis of TERT mRNA Levels and Clinicopathological Features in Patients with Peritoneal Mesothelioma

doi: 10.3390/cancers17020252

Figure Lengend Snippet: Kaplan–Meier survival of patients with peritoneal mesothelioma. In ( A ), survival data is shown based on TERT score: patients with high TERT mRNA expression showed shorter survival times than their counterparts (violet lines); not statistically significant. In ( B ), survival data is shown based on histological type: epithelioid type (line blue), biphasic type (line red); differences are not significant. In ( C ), survival data based on mitotic index adjusted is shown: 2–4 (line red), 5–9 (line blue) or >10 (line green) mitosis expressed on 2 mm 2 ; p ≤ 0.0001. In ( D ), survival data based on sex is shown: male (line blue) and female (line red); p = 0.0152. In ( E ), survival data based on BAP1 is shown: positive (line blue) and negative (line orange); p = 0.0152. The dashed lines indicate SE.

Article Snippet: BRCA1-associated protein 1 (BAP1) (clone C4, Santa Cruz Biotechnology, Santa Cruz, CA, USA) was classified as negative only if a complete absence of nuclear staining was observed in the presence of nuclear-positive lymphocytes.

Techniques: Expressing

Journal: Cancers

Article Title: Analysis of TERT mRNA Levels and Clinicopathological Features in Patients with Peritoneal Mesothelioma

doi: 10.3390/cancers17020252

Figure Lengend Snippet: Spearman’s correlation graphs between the customized score relative to the percentage of cells containing TERT mRNA (1+–4+ on the x -axis) and the score for a series of parameters obtained from morphological and cytogenetic analyses ( y -axis). In ( A ), TERT mRNA correlation with BAP1, p16 and MTAP protein expression, and with p16 cytogenetic alterations. In ( B ), TERT mRNA correlation with histotype, atypia and inflammatory infiltrate. In ( C ), TERT mRNA correlation with asbestous exposure type and time, sex, age and survival month. In ( D ), TERT mRNA correlation with necrosis, mitotic indexes, nuclear grade and ki-67. Statistical significance was determined by linear regression analysis. Only the significant r and p -values are reported.

Article Snippet: BRCA1-associated protein 1 (BAP1) (clone C4, Santa Cruz Biotechnology, Santa Cruz, CA, USA) was classified as negative only if a complete absence of nuclear staining was observed in the presence of nuclear-positive lymphocytes.

Techniques: Expressing

Journal: Cancers

Article Title: Analysis of TERT mRNA Levels and Clinicopathological Features in Patients with Peritoneal Mesothelioma

doi: 10.3390/cancers17020252

Figure Lengend Snippet: Pathological factors predictive of peritoneal mesothelioma patient survival. Univariate analysis using log-rank test.

Article Snippet: BRCA1-associated protein 1 (BAP1) (clone C4, Santa Cruz Biotechnology, Santa Cruz, CA, USA) was classified as negative only if a complete absence of nuclear staining was observed in the presence of nuclear-positive lymphocytes.

Techniques:

Journal: bioRxiv

Article Title: Preferential binding of human BRAC1 protein with open X-like conformation of Holliday junction, a homologous recombination intermediate

doi: 10.1101/2024.08.23.609282

Figure Lengend Snippet: Auto-correlation curves of (a) HJ in buffer in presence of 0.5, 1.0, 5.0, 12.5, and 50.0 mM MgCl 2 and that of HJ-BRCA1 in presence of (b) 0.5, (c) 1.0, (d) 5.0, (e) 12.5 and (f) 50 mM MgCl 2 with varying BRCA1 concentrations. S1, S2, S3, S4, S5, S6, S7, S8, S9 and S10.

Article Snippet: Recombinant Human BRCA1 protein was purchased from Abcam, UK (ab82204).

Techniques:

Journal: bioRxiv

Article Title: Preferential binding of human BRAC1 protein with open X-like conformation of Holliday junction, a homologous recombination intermediate

doi: 10.1101/2024.08.23.609282

Figure Lengend Snippet: (a) Change in fraction of free (χ f , solid circle) and bound (χ b , open circle) HJ with BRCA1 concentration. (b) χ b vs [BRCA1] in semilog plot with the fits by . Inset, χ b vs [BRCA1] in linear scale.

Article Snippet: Recombinant Human BRCA1 protein was purchased from Abcam, UK (ab82204).

Techniques: Concentration Assay

Journal: bioRxiv

Article Title: Preferential binding of human BRAC1 protein with open X-like conformation of Holliday junction, a homologous recombination intermediate

doi: 10.1101/2024.08.23.609282

Figure Lengend Snippet: Autocorrelation curves of (a) HJ:BRCA1 = 1:24 (S1), (b)) HJ:BRCA1 = 1:20 (S2), (c) HJ:BRCA1 = 1:0.5 (S9), (d) HJ:BRCA1 = 1:0.25 (S10) with 0.5, 1.0, 5.0, 12.5 and 50 mM MgCl 2 .

Article Snippet: Recombinant Human BRCA1 protein was purchased from Abcam, UK (ab82204).

Techniques:

Journal: bioRxiv

Article Title: Preferential binding of human BRAC1 protein with open X-like conformation of Holliday junction, a homologous recombination intermediate

doi: 10.1101/2024.08.23.609282

Figure Lengend Snippet: (a) H-bonds between amino acids nitrogen bases of the junction, (b) Nucleotides at the junction (orange) directly participating in H-bonds with DBD of BRCA1.

Article Snippet: Recombinant Human BRCA1 protein was purchased from Abcam, UK (ab82204).

Techniques:

Journal: bioRxiv

Article Title: Preferential binding of human BRAC1 protein with open X-like conformation of Holliday junction, a homologous recombination intermediate

doi: 10.1101/2024.08.23.609282

Figure Lengend Snippet: Upper panel – snapshots of DBD domain of BRCA1-HJ complex at 20 ns, 50 ns, 75 ns and 100 ns, Lower panel - Change in minimum distance between DBD domain of BRCA1and HJ with time.

Article Snippet: Recombinant Human BRCA1 protein was purchased from Abcam, UK (ab82204).

Techniques:

Journal: bioRxiv

Article Title: Preferential binding of human BRAC1 protein with open X-like conformation of Holliday junction, a homologous recombination intermediate

doi: 10.1101/2024.08.23.609282

Figure Lengend Snippet: (a) Mode of interaction between DBR of BRCA1 and HJ, (b) Change in the number of H-bonds with time for all four simulations, (c) DBR binding sites on HJ and interacting residues, (d) occupancy of the interacting residues form DBR of BRCA1 protein. The amino acids found to be interacting with HJ both in docking and MD simulation are in bold and italics. The amino acid residues in light blue are places of missense changes in human BRCA1. Color code: Red: Position1, Blue: Position 2, Green: Position 3 and Orange: Position 4.

Article Snippet: Recombinant Human BRCA1 protein was purchased from Abcam, UK (ab82204).

Techniques: Binding Assay