Journal: Journal of AOAC International

Article Title: Validation of the 3M™ Petrifilm™ Coliform Count Plate for Enumeration of Coliforms in Bottled Water: AOAC Performance Tested Method SM 082101

doi: 10.1093/jaoacint/qsab137

Figure Lengend Snippet: Inclusivity results for 3M Petrifilm CC Plates—bottled water method

Article Snippet: 40 , Klebsiella oxytoca , ATCC 43086 , Unknown , G, G+ , NA.

Techniques:

Journal: Scientific Reports

Article Title: Single-cell analysis reveals IGF-1 potentiation of inhibition of the TGF-β/Smad pathway of fibrosis in human keratocytes in vitro

doi: 10.1038/srep34373

Figure Lengend Snippet: (a) Relative levels of Smad3 nuclearization in human keratocytes. *p < 0.001 compared to CON+; **p < 0.001 compared to CON+ and CON− (Chi 2 tests). (b) Workflow diagram of the IDEAS software. First, images of the keratocytes in focus were chosen, and then the relevant cell population was selected, excluding the nonspecific labeling. The probe similarity algorithm for co-localization of the nucleus and Smad3 was then defined. The software calculated the correlation coefficient (Similarity Dilate) of the two probes, plotted as a frequency histogram. R3, keratocytes with Similarity Dilate >1, which implies nuclearization has occurred. (c) Representative images of ketatocytes labeled for Smad3 and the nucleus, as revealed by the imaging flow cytometry (green, AlexaFluor® 488, Smad3; purple, 7AAD, nucleus). Upper panel, cytosolic Smad3; lower panel, nuclearized Smad3. CON+, positive control of 10 ng/ml TGF-β2; CON−, negative control for naïve human keratocytes. All of the following conditions also included 10 ng/ml TGF-β2: 10 ng/ml IGF-1; 5 ng/ml halofuginone (HAL); 10 ng/ml IGF-1 plus 5 ng/ml halofuginone (combo HAL); 10 nM SAHA; 10 ng/ml IGF-1 plus 10 nM SAHA (combo SAHA).

Article Snippet: The bioactives used were: 10 ng/ml, 5 ng/ml recombinant IGF-1 (R&D systems, Minneapolis, USA), 10 ng/ml, 5 ng/ml halofuginone (Santa Cruz Biotechnology, Heidelberg, Germany), and 10 nM, 5 nM SAHA (Tocris Bioscience, Bristol, UK).

Techniques: Software, Labeling, Imaging, Flow Cytometry, Positive Control, Negative Control

Journal: Scientific Reports

Article Title: Single-cell analysis reveals IGF-1 potentiation of inhibition of the TGF-β/Smad pathway of fibrosis in human keratocytes in vitro

doi: 10.1038/srep34373

Figure Lengend Snippet: As shown with imaging flow cytometry, IGF-1, SAHA and halofuginone block Smad3 translocation to the nucleus. Inhibitory Smad7 forms as a negative-feedback loop , blocking Smad3 phosphorylation and nuclearization. SAHA can also inhibit HDACs, which leads to acetylation and subsequent ubiquitination of Smad7 , resulting in higher intracellular Smad7 levels, as observed in the present study. P, phosphate group; UB, ubiquitin; HDAC, histone deacetylase.

Article Snippet: The bioactives used were: 10 ng/ml, 5 ng/ml recombinant IGF-1 (R&D systems, Minneapolis, USA), 10 ng/ml, 5 ng/ml halofuginone (Santa Cruz Biotechnology, Heidelberg, Germany), and 10 nM, 5 nM SAHA (Tocris Bioscience, Bristol, UK).

Techniques: Imaging, Flow Cytometry, Blocking Assay, Translocation Assay, Phospho-proteomics, Ubiquitin Proteomics, Histone Deacetylase Assay

Journal: bioRxiv

Article Title: Overcome Prostate Cancer Resistance to Immune Checkpoint Therapy with Ketogenic Diet-Induced Epigenetic Reprogramming

doi: 10.1101/2023.08.07.552383

Figure Lengend Snippet: (A) Flow cytometry histograms of H2-K b and H2-D b for the four cell lines. (B) Volcano plot for differentially expressed genes in PPS-ICBR cells treated with 5 µM vorinostat or DMSO for 12h. Cutoff thresholds and two MHC-I genes were indicated. (C) Flow cytometry histograms of H2-K b for PPS-ICBR cells treated with 5 µM vorinostat or DMSO for 12h. (D) H3K9Ac ChIP-qPCR of the H2-K1 locus in PPS-ICBR cells treated with 5µM vorinostat or DMSO. N=3/condition. (E) Top enriched KEGG pathways for genes upregulated or downregulated by vorinostat in PPS-ICBR cells. (F) Flow cytometry plot of H2-K b and H2-D b for PPS-ICBR cells transduced with control shRNA (scScr) or Hdac1 shRNA (shHdac1). (G) Individual growth curves of PPS-ICBR tumors in mice treated with vehicle (n=20), vorinostat (n=10), ICB (anti-PD1+anti-CTLA4, n=10), or ICB+vorinostat (n=24). Complete response ratios were labeled. (H) Western blot of α-tub-K40Ac and β-actin of PPS-ICBR cells or tumors treated with vehicle or vorinostat. (I) Western blot of H3K9Ac, total H3 and β-actin of PPS-ICBR tumors treated with vehicle, vorinostat, ICB, or ICB+vorinostat. (J) Flow cytometry histograms of H2-K b for PCa cells in the dissociated PPS-ICBR tumors treated with vehicle, vorinostat, ICB, or ICB+vorinostat. (K) Quantification of CD8α IHC signals for PPS-ICBR tumors in mice treated with vehicle, vorinostat, ICB, ICB+vorinostat, or ICB+vorinostat+anti-CD8. N=7/group. (L) Growth curves of PPS-ICBR tumors in mice treated with vehicle (n=8), ICB+vorinostat+anti-CD8 (n=8), or ICB+vorinostat+isotype (n=5). Arrows indicate the dosing of anti-CD8 or isotype IgG. (M) Individual growth curves of PPS-ICBR tumors (n=6, no growth) or MC38 tumors (n=2, both grew) in C57BL/6 hosts previously cured of PPS-ICBR tumors with ICB+vorinostat treatment. In (D), (K) and (L), data represent mean ± SEM. *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001, ns, not significant; unpaired t-test for (D), Mann-Whitney test for (K), two-way ANOVA with Geisser-Greenhouse correction and Tukey’s multiple comparison test for (L).

Article Snippet: When tumors reached 50-100mm , mice were randomized to receive therapeutics, including anti-PD1 (BioLegend, 114116) and anti-CTLA4 (BioLegend, 106207) at 10mg/kg each i.p. twice a week, or vorinostat (MedChemExpress, HY-10221) at 25 mg/kg i.p. daily.

Techniques: Flow Cytometry, ChIP-qPCR, Transduction, Control, shRNA, Labeling, Western Blot, MANN-WHITNEY, Comparison

Journal: bioRxiv

Article Title: Overcome Prostate Cancer Resistance to Immune Checkpoint Therapy with Ketogenic Diet-Induced Epigenetic Reprogramming

doi: 10.1101/2023.08.07.552383

Figure Lengend Snippet: (A) Schematic of the interim cohorts of vorinostat and/or ICB treatments for CyTOF. (B) Growth curves of PPS-ICBR tumors in mice treated with vehicle (n=4), vorinostat (n=4), ICB (n=6), and ICB+vorinostat (n=8). (C) CyTOF tSNE plots showing the 14 cell clusters annotated for the 4 conditions. (D) Cell cluster percentages plotted for the 4 conditions. (E) Cell cluster densities projected on the tSNE maps for the 4 conditions. (F) Percentages of tumor-infiltrating T cell subsets in the 4 conditions. (G) Percentages of tumor-infiltrating myeloid subsets in the 4 conditions. In (B), (F) and (G), data represent mean ± SEM. *P<0.05, **P<0.01, ***P<0.001, ns, not significant; two-way ANOVA with Geisser-Greenhouse correction and Tukey’s multiple comparison test for (B), one-way ANOVA with Tukey’s multiple comparison test for (F) and (G).

Article Snippet: When tumors reached 50-100mm , mice were randomized to receive therapeutics, including anti-PD1 (BioLegend, 114116) and anti-CTLA4 (BioLegend, 106207) at 10mg/kg each i.p. twice a week, or vorinostat (MedChemExpress, HY-10221) at 25 mg/kg i.p. daily.

Techniques: Comparison

Journal: bioRxiv

Article Title: Overcome Prostate Cancer Resistance to Immune Checkpoint Therapy with Ketogenic Diet-Induced Epigenetic Reprogramming

doi: 10.1101/2023.08.07.552383

Figure Lengend Snippet: (A) Western blot of H3K9Ac and β-actin of PPS-ICBR cells treated with 5µM vorinostat, 3mM BHB and DMSO control for 12h. (B) Flow Cytometry of histograms of H2-K b for PPS-ICBR cells treated as indicated for 12h. (C) Caloric composition of SD and KD used in the study. (D) Schedule of CKD feeding. (E) Serum BHB level for C57BL/6 mice fed with SD (n=3) or CKD (n=3) for 3 cycles with BHB measured at cycle 3 day 5 and day 7. (F) Growth curves of PPS-ICBR tumors in C57BL/6 mice fed with SD (n=14) or CKD (n=10). (G) Western blot of H3K9Ac and α-tubulin for PPS-ICBR tumors from mice fed with SD or CKD. (H) Flow cytometry of H2-K b and H2-D b for PCa cells in the dissociated PPS-ICBR tumors from mice fed with SD or CKD. (I) Tumor growth curves of PPS-ICBR subcutaneous tumors in immunocompromised Batf3 -/- or Rag1 -/- C57BL/6 mice fed either a SD or CKD. ( Batf3 -/- SD N=8 CKD N=8. Rag1 -/- SD N=6 CKD N=10) (J) The rationale for Bdh1 knockout to abolish BHB from hepatic ketogenesis. (K) Western blot of Bdh1 and α-tubulin for liver tissue from wild type (WT) or Bdh1 -/- mice fed with SD, CKD, or BD. (L) Serum BHB levels from WT and Bdh1 -/- mice fed with SD or CKD (n=3∼4). (M) Volumes of PPS-ICBR tumors grown in WT mice fed with SD (n=5) or CKD (n=8) or Bdh1 -/- fed with CKD (n=6). (N) Survival curves of PPS-ICBR-bear mice treated as indicated (n=8/group). Tumor volumes at 1000mm were recorded as the endpoint. (O) Survival curves of PPS-ICBR-bear mice treated as indicated, SD (n=8), BD (n=10), SD+ICB (n=8), or BD+ICB (n=7). Tumor volumes at 1000mm were recorded as the endpoint. (P) Serum BHB levels in PPS-ICBR-bearing mice fed with SD (n=3) or BD (n=3). (Q) Flow cytometry median fluorescence intensity (MFI) of H2-K b for PCa cells in the dissociated PPS-ICBR tumors from mice treated with SD, BD, SD+ICB or BD+ICB (n=3/group). (R) Western blot of H3K9Ac, total H3 and α-tubulin for PPS-ICBR tumors from mice treated as indicated, with PPS-ICBR cells treated with 5uM vorinostat used as the control lane. In (E) (F) (I) (L) (M) (P) (Q), data represent mean ± SEM. *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001, ns, not significant; two-way ANOVA with Tukey’s multiple comparison test for (E), Mann-Whitney test for (F) (I), one-way ANOVA with Tukey’s multiple comparison test for (L) (M) (Q), log-rank test for (N) (O), unpaired t-test for (P).

Article Snippet: When tumors reached 50-100mm , mice were randomized to receive therapeutics, including anti-PD1 (BioLegend, 114116) and anti-CTLA4 (BioLegend, 106207) at 10mg/kg each i.p. twice a week, or vorinostat (MedChemExpress, HY-10221) at 25 mg/kg i.p. daily.

Techniques: Western Blot, Control, Flow Cytometry, Knock-Out, Fluorescence, Comparison, MANN-WHITNEY

Journal: Cell Reports Medicine

Article Title: Pharmacological Activation of Non-canonical NF-κB Signaling Activates Latent HIV-1 Reservoirs In Vivo

doi: 10.1016/j.xcrm.2020.100037

Figure Lengend Snippet: Ciapavir Does Not Induce Cytokine Release or T Cell Activation Human PBMCs and rCD4 + T cells from three healthy donors (n = 3) were treated with Ciapavir at the indicated concentrations, 500 nM vorinostat, 40 nM panobinostat, or combinations thereof, for 24 h. 50 ng/mL PMA and 1 μM ionomycin, or anti-CD3/CD28 antibody-coated beads, served as positive controls. (A and B) Heatmaps represent mean cytokine levels measured in the culture supernatant of PBMCs (A) or rCD4 + T cells (B) from tested donors (see Figure S2 for detailed results). (C and D) rCD4 + T cells treated as indicated were analyzed for CD69 (C) and CD25 (D) expression by flow cytometry. (E) Viability of rCD4 + T cells following treatment was assessed by measuring cellular ATP levels. Values were normalized to untreated cells from each donor. Significance was assessed with a one-way ANOVA using Dunnett’s multiple comparison correction (n = 3).

Article Snippet: Vorinostat , BioGems , Cat# 1497894.

Techniques: Activation Assay, Expressing, Flow Cytometry, Comparison

Journal: Cell Reports Medicine

Article Title: Pharmacological Activation of Non-canonical NF-κB Signaling Activates Latent HIV-1 Reservoirs In Vivo

doi: 10.1016/j.xcrm.2020.100037

Figure Lengend Snippet:

Article Snippet: Vorinostat , BioGems , Cat# 1497894.

Techniques: Virus, Modification, Recombinant, Viability Assay, Multiplex Assay, Digital PCR, Software, Cell Isolation

Journal: Phage (New Rochelle, N.y.)

Article Title: Isolation and Characterization of Klebsiella Phages for Phage Therapy

doi: 10.1089/phage.2020.0046

Figure Lengend Snippet: Details of Klebsiella Species and Strains Used in This Study

Article Snippet: Klebsiella michiganensis , 25444 , O1v1 , × , DSMZ Culture Collection , Toothbrush holder.

Techniques: Isolation