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:

Article Title: Detection of Legionellae in Hospital Water Samples by Quantitative Real-Time LightCycler PCR

doi: 10.1128/AEM.67.9.3985-3993.2001

Figure Lengend Snippet: 16S rRNA primer sequences and alignment of the primer target sequences

Article Snippet: For specificity control of the 16S rRNA gene PCR, the following bacteria were used (10 pg of bacterial DNA per PCR assay each): Acinetobacter junii (ATCC 17908), Acinetobacter baumannii (ATCC 19606), Acinetobacter lwoffii (ATCC 15309), Citrobacter freundii (ATCC 8090), Citrobacter koseri (ATCC 27028), Enterobacter aerogenes (ATCC 13048), Klebsiella oxytoca (ATCC 43863), Proteus mirabilis (ATCC 29906), Proteus vulgaris (ATCC 29905), Serratia marcescens (ATCC 13880), Stenotrophomonas maltophilia (ATCC 13637), Alcaligenes faecalis, Brevundimonas vesicularis , Chryseomonas luteola , Enterobacter cloacae , Escherichia coli , Klebsiella pneumoniae , Pseudomonas aeruginosa , Pseudomonas fluorescens , Pseudomonas putida , Sphingomonas paucimobilis, Streptococcus pyogenes, Staphylococcus aureus , and Enterococcus faecium (all clinical isolates). table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Species and serogroup Strain or reference L. pneumophila 1 (Philadelphia 1) ATCC 33152 2 (Togus 1) ATCC 33154 3 (Bloomington 2) ATCC 33155 4 (Los Angeles 1) ATCC 33156 5 ATCC 33216 6 (Chicago 2) ATCC 33215 7 (Chicago 8) ATCC 33823 8 ATCC 35096 9 ATCC 35289 10 ATCC 43283 11 ATCC 43130 12 ATCC 43290 13 ATCC 43736 14 ATCC 43703 L. adelaidensis ATCC 49625 L. anisa ATCC 35292 L. birminghamensis ATCC 43702 L. bozemanii ATCC 33217 L. brunensis ATCC 43878 L. cherii ATCC 35252 L. cincinnatiensis ATCC 43753 L. dumoffii ATCC 33279 L. erythra ATCC 35303 L. feelei ATCC 35849 L. gormanii ATCC 33297 L. gratiana ATCC 49413 L. hackeliae ATCC 35250 L. israelensis ATCC 43119 L. jamestownensis ATCC 35298 L. jordanis ATCC 33623 L. lansingensis ATCC 49751 L. longbeachae ATCC 33462 L. maceachernii ATCC 35300 L. micdadei ATCC 33218 L. moravica ATCC 43877 L. oakridgensis ATCC 33761 L. parisiensis ATCC 35299 L. quinlivanii ATCC 43830 L. rubrilucens ATCC 35304 L. sainthelensis ATCC 35248 L. spiritensis ATCC 35249 L. steigerwaltii ATCC 35302 L. tucsonensis ATCC 49180 L. wadsworthii ATCC 33877 LLAP 10 1 Open in a separate window Legionella strains investigated by PCR Collection of hospital water samples.

Techniques:

Journal: PLoS ONE

Article Title: Histone Deacetylase Inhibitors Antagonize Distinct Pathways to Suppress Tumorigenesis of Embryonal Rhabdomyosarcoma

doi: 10.1371/journal.pone.0144320

Figure Lengend Snippet: (A) Western blots demonstrating hyperacetylation of histones using antibodies against acetyl-histone H3 (Lys9), acetyl-histone H3 (Lys27), acetyl-histone H4 (Lys5), and acetyl-histone H4 (Lys8). D: DMSO; S: vorinostat (SAHA); T: TSA. Each band intensity was normalized to GAPDH loading control. Relative fold increase to DMSO (vehicle) treatment is shown. (B) Analysis of cell viability by cell counts. Cell counts were performed on cells treated with DMSO, 200 nM TSA or 1 μM SAHA at day 0 and day 5. Fold change in cell counts was normalized to day 0. (C-D) Representative images of immunofluorescence (IF) against MF20 performed on RD cells treated with DMSO (C) or 200 nM TSA (D) for 3 days in 2% horse serum in DMEM. Green: MF20-positive cells. Blue: DAPI. Scale bar: 20 μm. (E) Summary of IF against MF20 in ERMS (RD, 381T and SMS-CTR) and ARMS (Rh3, Rh5 and Rh30) cell lines treated with DMSO, 200 nM TSA or 1 μM SAHA. (F) Chromatin immunoprecipitation (ChIP) assays showing differential binding of acetyl-histone H3 (Lys9) at myogenic promoters. Fold enrichment binding of MYOD1 , MYOG , and MYH4 promoter regions were determined by quantitative PCR, normalizing amplification levels to input DNA of each sample. Rabbit IgG was used as a negative control for chromatin immunoprecipitation. (G-H) Representative bright-field images from a sphere assay on RD cells treated with DMSO (G) and 200 nM TSA (H). (I) Summary of sphere assays in RD and 381T cells. Each error bar in panels (B), (E), (F) and (I) indicates standard deviation of 3 technical replicates. * indicates p < 0.05. ** indicates p < 0.01. *** indicates p < 0.001.

Article Snippet: In the differentiation assay, cells were cultured in 2% horse serum and treated with TSA or SAHA for 3 days prior to fixation and immunostaining for MF20 (1:200; R&D Systems) and DAPI (1:500; Life Technologies).

Techniques: Western Blot, Control, Immunofluorescence, Chromatin Immunoprecipitation, Binding Assay, Real-time Polymerase Chain Reaction, Amplification, Negative Control, Standard Deviation

Journal: PLoS ONE

Article Title: Histone Deacetylase Inhibitors Antagonize Distinct Pathways to Suppress Tumorigenesis of Embryonal Rhabdomyosarcoma

doi: 10.1371/journal.pone.0144320

Figure Lengend Snippet: (A-F) Scratch assays on RD cells treated with DMSO, 1 μM SAHA or 200 nM TSA. (A-C) Representative images at time of scratch (0 hr). (D-F) Representative images at 18 hours post-scratch. Scale bar = 500 μm. (G) Summary of scratch assays in RD cells, indicating % wound closure for each treatment. (H-J) Representative images post-22 hour migration from transwell assays on RD cells treated with DMSO, 1 μM SAHA or 200 nM TSA. Scale bar = 50 μm. (K) Summary of transwell assays. Each error bar in panels (G) and (K) indicates standard deviation from technical triplicates. * indicates p < 0.05.

Article Snippet: In the differentiation assay, cells were cultured in 2% horse serum and treated with TSA or SAHA for 3 days prior to fixation and immunostaining for MF20 (1:200; R&D Systems) and DAPI (1:500; Life Technologies).

Techniques: Migration, Standard Deviation

Journal: PLoS ONE

Article Title: Histone Deacetylase Inhibitors Antagonize Distinct Pathways to Suppress Tumorigenesis of Embryonal Rhabdomyosarcoma

doi: 10.1371/journal.pone.0144320

Figure Lengend Snippet: (A) Western blots demonstrating hyperacetylation of histone H3 (Lys9) and histone H4 (Lys5) in zebrafish ERMS treated with 1 μM TSA or 50 μM SAHA. GAPDH was used as loading control. The values shown represent fold change in band intensity from TSA or SAHA treatment relative to DMSO after normalizing to loading control. (B) Representative pre- and post-treatment images of zebrafish ERMS treated with DMSO (vehicle) or 1 μM TSA. Dotted line outlines the tumor in each fish. Scale bar = 2 mm. (C) Summary of tumor volume change of zebrafish Tg( myf5 :GFP; mylz2 :mCherry) ERMS treated with DMSO, 50 μM SAHA or 1 μM TSA. Overlaid images of bright field and red fluorescent channel are shown. Error bar indicates standard error of means. n = number of animals treated in each cohort. (D) Summary of quantitative Fluorescence Activated Cell Sorting analysis on ERMS treated with DMSO or 10 μM SAHA. Each pie chart shows relative proportion of each tumor cell subpopulation in an individual treated tumor. Green: myf5 :GFP + / mylz2 :mCherry − cells; yellow: myf5 :GFP + / mylz2 :mCherry + cells; red: mylz2 :mCherry + / myf5 :GFP − cells. (E) Quantitative RT-PCR analysis of myog and myod mRNA expression in ERMS treated with DMSO, 1 μM TSA or 50 μM SAHA. Each bar demonstrates an individual tumor. Each error bar indicates standard deviation of technical triplicates. (F) Annexin V analysis of ERMS tumors treated with DMSO, 50 μM SAHA, or 1μM TSA. 6 animals were analyzed per group. Each error bar indicates standard deviation. * indicates p < 0.05. ** indicates p < 0.01.

Article Snippet: In the differentiation assay, cells were cultured in 2% horse serum and treated with TSA or SAHA for 3 days prior to fixation and immunostaining for MF20 (1:200; R&D Systems) and DAPI (1:500; Life Technologies).

Techniques: Western Blot, Control, Fluorescence, FACS, Quantitative RT-PCR, Expressing, Standard Deviation

Journal: PLoS ONE

Article Title: Histone Deacetylase Inhibitors Antagonize Distinct Pathways to Suppress Tumorigenesis of Embryonal Rhabdomyosarcoma

doi: 10.1371/journal.pone.0144320

Figure Lengend Snippet: (A) Summary of MF20 IF of RD cells treated with two different doses of GSI-IX, PD173074, or cyclopamine. (B-C) Representative MF20 IF images of RD cells treated with DMSO (B) and 20 μM GSI-IX (C). Scale bar = 20 μm. (D) Western blot of NOTCH1 expression in RD cells treated with DMSO, 200 nM TSA, or 1 μM SAHA. Each band intensity was normalized to GAPDH loading control. Percent intensity relative to DMSO (vehicle) treatment is shown. (E) Quantitative RT-PCR analysis of NOTCH1 pathway downstream targets, HEY1 , HEY2 and HES1 in RD cells treated with DMSO, 200 nM TSA, or 1 μM SAHA. (F) ChIP assay summary showing differential binding of acetyl-histone H3 (Lys9) at the NOTCH1 promoter in RD cells treated with DMSO or 200 nM TSA. Rabbit IgG was used as a negative control for chromatin immunoprecipitation. (G) Summary of MF20 IF of control GFP-overexpressing and NICD-overexpressing RD cells treated with DMSO, 200 nM TSA or 1 μM SAHA. Error bar in each graph indicates standard deviation of technical triplicates. Brackets in each group are used to indicate comparison groups. * indicates p < 0.05. ** indicates p < 0.01.

Article Snippet: In the differentiation assay, cells were cultured in 2% horse serum and treated with TSA or SAHA for 3 days prior to fixation and immunostaining for MF20 (1:200; R&D Systems) and DAPI (1:500; Life Technologies).

Techniques: Western Blot, Expressing, Control, Quantitative RT-PCR, Binding Assay, Negative Control, Chromatin Immunoprecipitation, Standard Deviation, Comparison

Journal: PLoS ONE

Article Title: Histone Deacetylase Inhibitors Antagonize Distinct Pathways to Suppress Tumorigenesis of Embryonal Rhabdomyosarcoma

doi: 10.1371/journal.pone.0144320

Figure Lengend Snippet: Summary of (A) scratch assays and (B) transwell migration assays on RD and 381T cells with EFNB1 knockdown by two independent siRNAs. Summary of (C) scratch assays and (D) transwell migration assays performed on control GFP-overexpressing and EFNB1-overexpressing RD cell lines. (E) ChIP assays showing differential binding of acetyl-histone H3 (Lys9) on EFNB1 promoter in RD cells treated with DMSO, 200 nM TSA, or 1μM SAHA. Rabbit IgG was used as a negative control for chromatin immunoprecipitation. (F) Western blot assessing EFNB1 protein expression level in RD cells treated with DMSO, 200 nM TSA or 1 μM SAHA. Percent intensity relative to DMSO (vehicle) treatment is shown. GAPDH was used as a loading control.

Article Snippet: In the differentiation assay, cells were cultured in 2% horse serum and treated with TSA or SAHA for 3 days prior to fixation and immunostaining for MF20 (1:200; R&D Systems) and DAPI (1:500; Life Technologies).

Techniques: Migration, Knockdown, Control, Binding Assay, Negative Control, Chromatin Immunoprecipitation, Western Blot, Expressing

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

Journal: Applied Microbiology and Biotechnology

Article Title: PpEst is a novel PBAT degrading polyesterase identified by proteomic screening of Pseudomonas pseudoalcaligenes

doi: 10.1007/s00253-016-7992-8

Figure Lengend Snippet: List of esterases and lipases identified in one or more of the supernatants of cultures of P. pseudoalcaligenes grown with standard media or with the addition of cellulose, PBAT or BABuTABuBA

Article Snippet: P. pseudoalcaligenes subsp. pseudoalcaligenes (DSM 50188) was obtained from Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures in freeze-dried form.

Techniques: Polymer, Chemotaxis Assay

Journal: Applied Microbiology and Biotechnology

Article Title: PpEst is a novel PBAT degrading polyesterase identified by proteomic screening of Pseudomonas pseudoalcaligenes

doi: 10.1007/s00253-016-7992-8

Figure Lengend Snippet: Sequence similarity of PpEst from P. pseudoalcaligenes aligned to PBAT hydrolysing enzymes

Article Snippet: P. pseudoalcaligenes subsp. pseudoalcaligenes (DSM 50188) was obtained from Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures in freeze-dried form.

Techniques: Sequencing

Journal: Applied Microbiology and Biotechnology

Article Title: PpEst is a novel PBAT degrading polyesterase identified by proteomic screening of Pseudomonas pseudoalcaligenes

doi: 10.1007/s00253-016-7992-8

Figure Lengend Snippet: Model of PpEst from P. pseudoalcaligenes complexed with BABuTABuBA. a Cavity of complex model of PpEst. Leu79, Ile156, Pro113 and Pro114 as well as the loop containing Gly149 and Gly148 may widen the groove on the active site. b PpEst model in complex with BABuTABuBA as a tetrahedral intermediate where the active site groove is shown as cavity surface. The predicted catalytic triad consists of Ser10, Asp157 and His160, while the oxyanion hole encompasses Gly47 and Asn76

Article Snippet: P. pseudoalcaligenes subsp. pseudoalcaligenes (DSM 50188) was obtained from Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures in freeze-dried form.

Techniques:

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