Journal: Foods

Article Title: Probiotic Potential of Weizmannia coagulans MA42, an Endospore-Forming Probiotic Bacterium Capable of Dietary Fiber Digestion

doi: 10.3390/foods15040710

Figure Lengend Snippet: Survival of W. coagulans ATCC 7050, MA42, P13, and S5 under simulated gastrointestinal conditions. Black and white arrows indicate the addition of simulated gastric juice and simulated duodenal juice, respectively.

Article Snippet: The organic acid production ability of W. coagulans MA42 and W. coagulans ATCC 7050 is presented in .

Techniques:

Journal: Foods

Article Title: Probiotic Potential of Weizmannia coagulans MA42, an Endospore-Forming Probiotic Bacterium Capable of Dietary Fiber Digestion

doi: 10.3390/foods15040710

Figure Lengend Snippet: Auto-aggregation ( A ) and cell surface hydrophobicity ( B ) of W. coagulans ATCC 7050, MA42, P13, and S5. Different letters (A–C) indicate significant differences in the values ( p < 0.05).

Article Snippet: The organic acid production ability of W. coagulans MA42 and W. coagulans ATCC 7050 is presented in .

Techniques: Cell Surface Hydrophobicity

Journal: Foods

Article Title: Probiotic Potential of Weizmannia coagulans MA42, an Endospore-Forming Probiotic Bacterium Capable of Dietary Fiber Digestion

doi: 10.3390/foods15040710

Figure Lengend Snippet: Disc diffusion assay of cell-free culture supernatants (CFCSs), obtained from W. coagulans ATCC 7050, W. coagulans MA42, W. coagulans S5, and W. coagulans P13 cultured in mMRS broth at 37 °C under static conditions for 24 h, against E. coli ATCC 25922, S. Typhimurium TISTR 292, B. cereus TISTR 747, and S. aureus TISTR 746. Control (M): uninoculated mMRS broth. Un-neutralized CFCS ( A ) and neutralized CFCS (pH 7) ( B ).

Article Snippet: The organic acid production ability of W. coagulans MA42 and W. coagulans ATCC 7050 is presented in .

Techniques: Diffusion-based Assay, Cell Culture, Control

Journal: Foods

Article Title: Probiotic Potential of Weizmannia coagulans MA42, an Endospore-Forming Probiotic Bacterium Capable of Dietary Fiber Digestion

doi: 10.3390/foods15040710

Figure Lengend Snippet: Hemolytic activity of W. coagulans ATCC 7050, MA42, P13, and S5 on blood agar at 37 °C for 48 h. Staphylococcus aureus was used as the positive control.

Article Snippet: The organic acid production ability of W. coagulans MA42 and W. coagulans ATCC 7050 is presented in .

Techniques: Activity Assay, Positive Control

Journal: Foods

Article Title: Probiotic Potential of Weizmannia coagulans MA42, an Endospore-Forming Probiotic Bacterium Capable of Dietary Fiber Digestion

doi: 10.3390/foods15040710

Figure Lengend Snippet: Viable cell count of W. coagulans MA42 and ATCC 7050 on modified MRS medium supplemented with glucose ( A ), wheat flour ( B ), oatmeal ( C ), xylan ( D ), carboxymethyl cellulose (CMC) ( E ), locust bean gum (LBG) ( F ), xanthan gum ( G ), pectin ( H ), inulin ( I ), xylo-oligosaccharides (XOS) ( J ), fructo-oligosaccharides (FOS) ( K ), and galacto-oligosaccharides (GOS) ( L ) as the sole carbon source. *, **, and *** indicate significant differences at p < 0.05, p < 0.01, and p < 0.001, respectively.

Article Snippet: The organic acid production ability of W. coagulans MA42 and W. coagulans ATCC 7050 is presented in .

Techniques: Cell Characterization, Modification

Journal: Foods

Article Title: Probiotic Potential of Weizmannia coagulans MA42, an Endospore-Forming Probiotic Bacterium Capable of Dietary Fiber Digestion

doi: 10.3390/foods15040710

Figure Lengend Snippet: Enzyme activity profile of W. coagulans MA42 and W. coagulans ATCC 7050 cultivated in modified MRS medium supplemented with wheat flour ( A ), oatmeal ( B ), xylan ( C ), carboxymethyl cellulose (CMC) ( D ), locust bean gum (LBG) ( E ), xanthan gum ( F ), pectin ( G ), and inulin ( H ) as the sole carbon source at 37 °C for 48 h. * and ** indicate significant differences at p < 0.05 and p < 0.01, respectively.

Article Snippet: The organic acid production ability of W. coagulans MA42 and W. coagulans ATCC 7050 is presented in .

Techniques: Activity Assay, Modification

Journal: International Journal of Molecular Sciences

Article Title: Alpha Ketoglutarate Exerts In Vitro Anti-Osteosarcoma Effects through Inhibition of Cell Proliferation, Induction of Apoptosis via the JNK and Caspase 9-Dependent Mechanism, and Suppression of TGF-β and VEGF Production and Metastatic Potential of Cells

doi: 10.3390/ijms21249406

Figure Lengend Snippet: Effect of AKG on phosphorylation of MAP kinases and the influence of the selective JNK inhibitor (SP600125) on AKG-induced apoptosis in Saos-2 cells. The cells were incubated without or with AKG for 6 h and 24 h, and phosphorylated and total ERK1/2, JNK and p38 levels were determined with the ELISA assay. Quantification of the amounts of phosphorylated to total MAP kinases ( A – C ). The cells were treated with 50 mM AKG without or with SP600125 (5 μM) and harvested after 72 h of treatment for apoptosis analysis. The representative dot plots indicate the percentage of An − /PI + necrotic cells (Q1), An + /PI + late apoptotic cells (Q2), An − /PI − viable cells (Q3), and An + /PI − early apoptotic cells (Q4) in the AKG or/and SP600125-treated Saos-2 cell cultures ( D ). Quantification of the amounts of phosphorylated to total JKN kinase ( E ) and histogram representation of the quantitative percentage of apoptotic (early + late apoptosis) cells ( F ) in the control, SP600125, AKG, and SP600125 + AKG-treated Saos-2 cell cultures. Data are expressed as means ± SD for three independent experiments. ** p < 0.01, *** p < 0.001 in comparison to the control; one-way ANOVA test.

Article Snippet: The quantification of the intracellular levels of total and phosphorylated JNK, ERK1/2, p38, and AKT kinases and the contents of cyclin D1 and p21 proteins in the treated cells was carried out using the PathScan ® ELISA kits: Total SAPK/JNK Sandwich ELISA Kit, Phospho-SAPK/JNK (Thr183/Tyr185) Sandwich ELISA Kit, Total p44/42 MAPK (Erk1/2) Sandwich ELISA Kit, Phospho-p44/42 MAPK (Thr202/Tyr204) Sandwich ELISA Kit, Phospho-p38 MAPK (Thr180/Tyr182) Sandwich ELISA Kit, Total Cyclin D1 Sandwich ELISA Kit, Total p21 Waf1/Cip1 Sandwich ELISA Kit (Cell Signaling Technology Danvers, MA, USA), and p38 MAPK alpha ELISA Kit (Abcam, Cambridge, UK) according to the manufacturer’s instructions as described previously [ ].

Techniques: Incubation, Enzyme-linked Immunosorbent Assay

Journal: Science advances

Article Title: CDK4/6 inhibition enhances SHP2 inhibitor efficacy and is dependent upon RB function in malignant peripheral nerve sheath tumors.

doi: 10.1126/sciadv.adg8876

Figure Lengend Snippet: Fig. 4. Responses of NF1-MPNST cells to the CDK4/6i ribociclib. (A) Ten NF1-associated MPNST cell lines were treated with increasing doses of the CDK4/6i ribociclib for 5 days. Cell viability was evaluated by using the CCK-8 assay. (B) Two NF1-MPNST cell lines were treated with DMSO or 1 μM ribociclib over a time course. Signal intermediates in ERK and cell cycle pathways were assessed. (C) JH-2-002 cells were treated with DMSO or 1 μM ribociclib for 24 hours. Seventy-one phosphorylated human RTKs were evaluated using human RTK phosphorylation array C1. Signal intensity from technical duplicates was quantified using densitometry analysis and normalized to ribociclib v. DMSO, and, notably, altered RTKs are shown. (D) Cells as in Fig. 3E were treated with increasing doses of ribociclib for 5 days. Cell viability was evaluated by using the CCK-8 assay.

Article Snippet: NF1-MPNST cells were treated with DMSO, 0.3 μM TNO155, and/ or 1 μM ribociclib for 48 hours, and, then, 500 μg protein of lysates were assessed using human apoptosis antibody array (R&D Systems, #ARY009).

Techniques: CCK-8 Assay, Phospho-proteomics

Journal: Science advances

Article Title: CDK4/6 inhibition enhances SHP2 inhibitor efficacy and is dependent upon RB function in malignant peripheral nerve sheath tumors.

doi: 10.1126/sciadv.adg8876

Figure Lengend Snippet: Fig. 5. Combined inhibition of SHP2 and CDK4/6 effectively suppresses MPNST cell growth. (A) ST8814 and NF90.8 parental (Par) and trametinib-resistant (Res) lines and eight NF1-MPNST cell lines were treated with DMSO, TNO155 (0.3, 1, and 3 μM), ribociclib (1 and 3 μM), and their combination for 7 to 10 days. Direct cell counting using trypan blue exclusion assay was performed by TC20 automated cell counter. (B) Cells as in (A) were treated with drugs for 2 to 3 weeks, and colony formation was evaluated using crystal violet assay. (C) Area under the curve (AUC) is calculated on the basis of the IncuCyte cell confluence monitoring of the seven cell lines as shown, treated with DMSO, TNO155 (0.3 μM), ribociclib (1 μM), and their combination for 6 days. (D) Two NF1-MPNST cell lines were treated with DMSO, TNO155 (0.3 μM), ribociclib (1 μM), and their combination for 6 days. Cell confluence was monitored using IncuCyte imaging systems. (E) Four NF1-MPNST cell lines were treated with DMSO, 0.3 μM TNO155, and/or 1 μM ribociclib for 72 and 96 hours. ERK signaling and cell cycle regulators were evaluated using immunoblot. (F) Three NF1-MPNST cell lines transduced with shPTPN11 #818 were pretreated with vehicle or Dox (300 ng/ml) for 72 hours, followed by treatment with DMSO or 1 μM ribociclib for additional 72 hours. Cell lysates were assessed for expression of the indicated proteins.

Article Snippet: NF1-MPNST cells were treated with DMSO, 0.3 μM TNO155, and/ or 1 μM ribociclib for 48 hours, and, then, 500 μg protein of lysates were assessed using human apoptosis antibody array (R&D Systems, #ARY009).

Techniques: Inhibition, Cell Counting, Trypan Blue Exclusion Assay, Crystal Violet Assay, Imaging, Western Blot, Transduction, Expressing

Journal: Science advances

Article Title: CDK4/6 inhibition enhances SHP2 inhibitor efficacy and is dependent upon RB function in malignant peripheral nerve sheath tumors.

doi: 10.1126/sciadv.adg8876

Figure Lengend Snippet: Fig. 6. Combination of TNO155 and ribociclib additively inhibits cell cycle and induces apoptosis. (A) Upset matrix plot derived from RNA-seq analysis, showing the overlapping numbers of significant genes (P adj < 0.05 and |fold change| > 1.5) after 24-hour treatment with 0.3 μM TNO155, 1 μM ribociclib, and their combination, and normalized to DMSO control. Rows, the sets; columns, intersections between these sets. (B and C) Heatmaps demonstrating the more potent transcriptional inhibition of mitotic prometaphase (B) and cell cycle checkpoints (C) by combined TNO155 and ribociclib relative to either single agent alone, highlighting BIRC5, PLK1, CLSPN, and CCNA2 (P adj < 0.05 marked with + and LFC). (D) Five NF1-MPNST cell lines were treated with DMSO, 0.3 μM TNO155, and/or 1 μM ribociclib for 48 hours, following overnight starvation in 0.1% FBS-containing culture medium to synchronize cells. Cells were fixed in ice cold 70% ethanol and stained with propidium iodide/ribonu- clease staining solution (Cell Signaling Technology, no. 4087) and then analyzed by flow cytometry. (E) ST8814 and JH-2-079c were treated with DMSO, 0.3 μM TNO155, and/or 1 μM ribociclib for 48 hours, and, then, protein lysates were assessed using human apoptosis antibody array (R&D Systems, no. ARY009). Signal intensity from technical duplicates was quantified by densitometry analysis using ImageJ and normalized to DMSO. Data represent means ± SEM. (F) Nine NF1-MPNST cell lines were treated as in (E), and the indicated proteins involved in apoptosis and ERK signaling were detected using immunoblot.

Article Snippet: NF1-MPNST cells were treated with DMSO, 0.3 μM TNO155, and/ or 1 μM ribociclib for 48 hours, and, then, 500 μg protein of lysates were assessed using human apoptosis antibody array (R&D Systems, #ARY009).

Techniques: Derivative Assay, RNA Sequencing, Control, Inhibition, Staining, Flow Cytometry, Ab Array, Western Blot

Journal: Science advances

Article Title: CDK4/6 inhibition enhances SHP2 inhibitor efficacy and is dependent upon RB function in malignant peripheral nerve sheath tumors.

doi: 10.1126/sciadv.adg8876

Figure Lengend Snippet: Fig. 7. The combination of TNO155 and ribociclib is active against MPNST tumor growth in vivo. (A and B) Five-to-6-week-old female NRG mice bearing six individual NF1- MPNST PDXs were treated with vehicle, ribociclib (75 mg/kg, once daily), TNO155 (7.5 mg/kg, twice daily), or their combination by oral gavage for 4 weeks. Average tumor volume of four to five mice per arm was plotted over the time course of treatment days. VS, very sensitive; PS, partially sensitive. (C) Tumors of each arm from WU-386 were harvested 4 hours after last dose of 4 weeks on drugs and fixed in 10% NBF. The Ki-67 expression was assessed using im- munohistochemistry (IHC). (D and E) Tumors of each arm from WU-225, WU-386 were harvested 4 hours after last dose, 4 weeks on drugs (D); or 24 hours after last dose, 3 days on drugs (E). The indicated proteins involved in ERK and cell cycle signaling were de- tected using immunoblot. (F) Onco- print of key driver genes in MPNST and putative others is shown. For NF1 and SUZ12, both germline (G) and somatic (S) mutations are shown. (G) Volcano plot demonstrating LFC of VS/PS as a function of −log10 (P adj). Blue dots represent 227 genes that were significantly altered (P adj < 0.05 and |LFC| > 0.585) when comparing the RNA-seq data of VS (JH-2-031, WU- 225, and JH-2-002) v. PS (WU-545, JH- 2-079c, and WU-386). (H) The mice bearing JH-2-031 were on initial treatment as in (A) for about 4 weeks and left untreated for another 4 weeks before rechallenging with the combi- nation for additional 2 weeks. (I) The mice bearing JH-2-002 as in (A) were continuously on treatment for 10 weeks. (J) Tumors of each arm from JH-2-002 and JH-2-031 were harvest- ed 4 hours after last dose of 10 weeks and fixed in 10% NBF. The Ki-67 ex- pression was assessed using IHC.

Article Snippet: NF1-MPNST cells were treated with DMSO, 0.3 μM TNO155, and/ or 1 μM ribociclib for 48 hours, and, then, 500 μg protein of lysates were assessed using human apoptosis antibody array (R&D Systems, #ARY009).

Techniques: In Vivo, Expressing, Western Blot, RNA Sequencing

Journal: The Journal of Physiology

Article Title: Sensitization of colonic nociceptors by TNFα is dependent on TNFR1 expression and p38 MAPK activity

doi: 10.1113/JP283170

Figure Lengend Snippet: A , representative traces illustrating the concentration‐dependent increase in the magnitude of the normalized fluorescent response to TNFα (0.03–3.0 nM) within individual neurons from respective culture dishes. B , the mean magnitude of TNFα responses per dish increased across TNFα concentrations ( P = 0.050, one‐way ANOVA with Holm–Šídák's multiple comparisons test; n = 5 dishes from N = 5 independent cultures). C , the concentration‐dependent increase in the proportion (per dish) of TNFα‐responsive DRG neurons ( P = 0.014, the Kruskal–Wallis test with Dunn's multiple comparisons test; n = 5 dishes from N = 5 independent cultures), of which the majority were also co‐sensitive to capsaicin. D , the effects of TNFα (0.1 nM) were TNFR1‐mediated as illustrated by the significant reduction in ( E ) response magnitude ( P = 0.035; P = 0.012, one‐way ANOVA with Holm–Šídák's multiple comparisons test, n = 5−6 dishes from N = 5−6 independent cultures) and ( F ) proportion of TNFα‐responsive neurons following TNFR1 inhibition with 10 μM R7050 ( P = 0.004, one‐way ANOVA with Holm–Šídák's multiple comparisons test; n = 5−6 dishes from N = 5−6 independent cultures) or genetic deletion of TNFR1 in Tnfrsf1a –/– mice in comparison with neurons from wild‐type (WT) animals ( P = 0.0001, one‐way ANOVA with Holm–Šídák's multiple comparisons test; n = 5−6 dishes from N = 5−6 independent cultures). Dotted line represents the proportion of neurons activated in ECS controls (5.54 ± 5.01%, n = 6, N = 6). [Colour figure can be viewed at wileyonlinelibrary.com ]

Article Snippet: R7050 (10 mM; DMSO), thapsigargin (1 mM; DMSO), A425619 (1 mM; DMSO) and SB203580 (10 mM; DMSO) were obtained from Tocris and stock concentrations made up as described.

Techniques: Concentration Assay, Inhibition, Comparison

Journal: Biosensors & bioelectronics

Article Title: Electrochemical As(III) whole-cell based biochip sensor.

doi: 10.1016/j.bios.2013.03.011

Figure Lengend Snippet: Fig. 1. Principle of the As(III) bioreporter. (I) The ArsR repressor protein is synthesized from the arsR gene under control of the ars promoter (Pars). (II) ArsR binds to its two binding sites on the DNA (black upright bars) and prevents expression of itself and of the reporter gene (lacZ), except for a small background. (III) When As(III) is present, ArsR loses its affinity for the binding sites on the DNA and the transcription of the arsR and lacZ genes increases, leading to the subsequent formation of beta-galactosidase (β-Gal). (IV) Finally, p-aminophenyl β-D-galactopyranoside (PAPG) diffuses through the cell membrane and is cleaved by β-Gal to form p-aminophenol (PAP) that is detected electrochemically outside the cell.

Article Snippet: 4-Aminophenyl-beta-D-galactopyranoside (PAPG, Biosynth, Thal, Switzerland), NaCl (≥ 99%, Buchs, Sigma, Switzerland), KCl (≥ 99%, om the arsR gene under control of the ars promoter (Pars). (II) ArsR binds to its two e reporter gene (lacZ), except for a small background. (III) When As(III) is present, and lacZ genes increases, leading to the subsequent formation of beta-galactosidase ell membrane and is cleaved by β-Gal to form p-aminophenol (PAP) that is detected Buchs, Sigma, Switzerland), Na2 HPO4 2H2O (Buchs, Sigma, Switzerland), KH2PO4 (Buchs, Sigma, Switzerland) and sodium pyrophosphate solution (Na4P2O7 10H2O, Buchs, Sigma, Switzerland) were used as received.

Techniques: Synthesized, Control, Binding Assay, Expressing, Membrane