Journal: Heliyon

Article Title: Pharmacological investigation of taxifolin for its therapeutic potential in depression

doi: 10.1016/j.heliyon.2024.e30467

Figure Lengend Snippet: The best conformational pose, binding energy (kcal/mol), number of hydrogen bonds, bonding residues forming other hydrophobic interactions, of taxifolin and fluoxetine with target proteins such as peroxisome proliferator-activated receptor gamma (PPAR-γ), cyclooxygenase-2 (COX-2), Toll like receptor-4 (TLR4), c-Jun N-terminal kinase (JNK), brain-derived neurotrophic factor (BDNF), monoamine oxidase A (MAO-A), heme oxygenase-1 (HO-1), cyclooxygenase-1 (COX-1), sodium channels (NA+),Glutamate receptor (GRM2), phosphoinositide 3-kinase (PI3k), tumor necrosis factor-alpha (TNF-α), prostaglandins (PGE2), mitogen activated protein kinases (MAPK), Beta- 2 adrenergic receptor (ADRB2), Neurokinin receptor (NK-1), Procaspase activating compound (PAC-1), nuclear factor kappa B (NF-κB), nitric oxidase synthesis (iNOS), interleukin-4 (IL-4), high mobility group box 1 (HMGB1), Protein -c –fos, Beta catenin (β-Catenin), serotonin receptors (SERT), nuclear factor erythroid 2-related factor 2 (Nrf2), vasoactive intestinal peptide (VIP), Gamma-aminobutyric acid (GABA A), peptidoglycan (PG), interleukin-2 (IL-2), Dopamine receptor (D2).

Article Snippet: The ELISA kit COX-2 (CAT# PRS-30205Ra) and the ELISA kit PPAR gamma (CAT# E-EL-R0724) were supplied by Elabscience.

Techniques: Binding Assay

Journal: Heliyon

Article Title: Pharmacological investigation of taxifolin for its therapeutic potential in depression

doi: 10.1016/j.heliyon.2024.e30467

Figure Lengend Snippet: Effects of Taxifolin and Fluoxetine against (A) Peroxisomes proliferation-activated receptor-γ (PPAR-γ) and (B) Cyclooxygenase-2 (COX-2) concentration in rat's cortex tissues using enzyme linked immunosorbent assay technique (ELISA). Values expressed as mean ± SEM (n = 6). One-way ANOVA with post hoc Tukey’ s test. ### P < 0.001 vs. saline group, *P < 0.05, **P < 0.01, ***P < 0.001 vs. LPS group.

Article Snippet: The ELISA kit COX-2 (CAT# PRS-30205Ra) and the ELISA kit PPAR gamma (CAT# E-EL-R0724) were supplied by Elabscience.

Techniques: Concentration Assay, Enzyme-linked Immunosorbent Assay, Saline

Journal: Heliyon

Article Title: Pharmacological investigation of taxifolin for its therapeutic potential in depression

doi: 10.1016/j.heliyon.2024.e30467

Figure Lengend Snippet: Effects of Taxifolin and Fluoxetine against Peroxisomes proliferation-activated receptor-γ (PPAR-γ) by RT-PCR. Values expressed as mean ± SEM (n = 6). One-way ANOVA with post hoc Tukey’ s test. ### P < 0.001 vs saline group, **P < 0.01, ***P < 0.001 vs. LPS group.

Article Snippet: The ELISA kit COX-2 (CAT# PRS-30205Ra) and the ELISA kit PPAR gamma (CAT# E-EL-R0724) were supplied by Elabscience.

Techniques: Reverse Transcription Polymerase Chain Reaction, Saline

Journal: Materials Today Bio

Article Title: 4D-printed Fe3O4-PLLA scaffolds modulate osteoimmune microenvironment for oral bone repair

doi: 10.1016/j.mtbio.2025.102691

Figure Lengend Snippet: In vitro immunomodulatory properties of PLLA, Fe 3 O 4 -PLLA, CSMA/Fe 3 O 4 -PLLA, NG-CSMA/Fe 3 O 4 -PLLA scaffolds. a-b) 3 days of co-culture of RAW 264.7 with PLLA, Fe 3 O 4 -PLLA, CSMA/Fe 3 O 4 -PLLA, and NG-CSMA/Fe 3 O 4 -PLLA scaffolds, flow cytometry was performed to analyze M1, M2 markers CD86 and CD206. c) mRNA levels of TNF-α, IL-1β, Arg-1, and CD206 by qRT-PCR; d) Immunofluorescence images of M1 (iNOS) and M2 (Arg-1) macrophage markers; and e) quantitative analysis of fluorescence intensity. n = 3. (∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001).

Article Snippet: After 3 days, cells were harvested, blocked, and stained with PE-anti-CD206 and CL647- anti -CD86 antibodies (Proteintech, China).

Techniques: In Vitro, Co-Culture Assay, Flow Cytometry, Quantitative RT-PCR, Immunofluorescence, Fluorescence

Journal: Nature chemical biology

Article Title: An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis.

doi: 10.1038/nchembio.1636

Figure Lengend Snippet: Figure 1 | Engineering and characterization of receptor-based Axl antagonists. (a) Axl’s extracellular domain consists of two Ig-like domains containing high- and low-affinity Gas6 binding sites, followed by two fibronectin type III domains. Binding of Gas6 to Axl leads to receptor dimerization and activation of downstream signaling. Axl decoy receptors sequester Gas6, preventing activation of the Axl signaling cascade. (b) Overlaid flow cytometry dot plots representing binding of yeast-displayed wild-type Axl Ig1 (red) and unsorted Axl Ig1 library (blue) to 10 nM Gas6 (y axis) and expression levels on the yeast cell surface (x axis). (c) Flow cytometry histograms of the initial Axl library and intermediate sort products compared to wild-type Axl Ig1 (gray), measuring binding to 0.5 nM Gas6 (top row) and persistent Gas6 binding after a 30-h incubation with excess competitor (bottom row). MYD1 is also included for comparison. For clarity, only the gated population of yeast expressing Axl is shown. AU, arbitrary units. (d) Binding affinities of wild-type Axl Ig1, MYD1 and Axlnb to Gas6 as determined by KinExA. (e) Binding affinities to Gas6 of every permutation of the four mutations found in MYD1. Raw KinExA data and associated error values can be found in Supplementary Figures 2 and 3.

Article Snippet: After the appropriate incubation time, reactions were flowed over MYD1 Fc–coated beads, and captured free Gas6 was probed using a 500 ng/ml solution of antiHis6 Dylight 649 antibody (Rockland Immunochemicals Inc., 200-343-382).

Techniques: Binding Assay, Activation Assay, Flow Cytometry, Expressing, Incubation, Comparison

Journal: Nature chemical biology

Article Title: An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis.

doi: 10.1038/nchembio.1636

Figure Lengend Snippet: Figure 2 | Structural basis for high-affinity binding. (a) Gas6–MYD1 co-complex showing overall architecture and 2:2 stoichiometry. (b) MYD1 Ig1 (orange) and Gas6 LG1 (gray) domains showing the location of the four mutations in MYD1 with respect to the major binding site, which lies at the interface of these two domains. (c) Analysis of the wild-type structure (PDB code 2C5D) reveals steric crowding between the side chains of T457Gas6 and V92Axl. The V92A mutation alleviates this crowding in the MYD1 co-complex and facilitates local reorganization of side chains around V92A, exemplified by R48 and Q94. This in turn creates an elongated groove on MYD1 at the binding interface that allows reorientation of T457 on Gas6. (d) Reorientation of T457 results in capping of the N terminus of helix A. The wild-type (WT, green) and MYD1 (gray) structures are overlaid for comparison. (e) Capping stabilizes helix A, as seen by B-factor analysis (Online Methods).

Article Snippet: After the appropriate incubation time, reactions were flowed over MYD1 Fc–coated beads, and captured free Gas6 was probed using a 500 ng/ml solution of antiHis6 Dylight 649 antibody (Rockland Immunochemicals Inc., 200-343-382).

Techniques: Binding Assay, Mutagenesis, Comparison

Journal: Nature chemical biology

Article Title: An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis.

doi: 10.1038/nchembio.1636

Figure Lengend Snippet: Figure 4 | MYD1 Fc inhibits Axl activation and downstream signaling in skov3.ip cells. (a) Wild- type (WT) Axl Fc and MYD1 Fc, but not Axlnb Fc, can inhibit Gas6-mediated Axl activation in vitro. (b) Inhibition of Axl activation leads to reduced levels of phosphorylated Akt and Erk1/2 and an increase in the epithelial marker e-cadherin. For full (uncut) blots, see Supplementary Figure 11.

Article Snippet: After the appropriate incubation time, reactions were flowed over MYD1 Fc–coated beads, and captured free Gas6 was probed using a 500 ng/ml solution of antiHis6 Dylight 649 antibody (Rockland Immunochemicals Inc., 200-343-382).

Techniques: Activation Assay, In Vitro, Inhibition, Marker

Journal: Nature chemical biology

Article Title: An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis.

doi: 10.1038/nchembio.1636

Figure Lengend Snippet: Figure 5 | Sequestration of Gas6 by MYD1 Fc inhibits metastasis. (a) Amount of free Gas6 in serum of mice 12 h after administration of a single dose of MYD1 Fc. (b) Kinetics of Gas6 sequestration (black) and MYD1 Fc clearance (red) following a 1 mg per kg body weight dose of MYD1 Fc. (c) Using the off-rates of the Gas6-Axl Fc interactions (Fig. 3b), dissociation of Gas6 bound to either wild-type Axl Fc (red) or MYD1 Fc (blue) is plotted over time. The in vivo clearance of the Axl decoy receptors as measured in c is overlaid in black. Two mice were analyzed for each data point in b and c. (d–f) Tumor burden in in vivo models of metastatic human ovarian cancer. The number of visible metastases in animals treated with Axlnb Fc, wild-type Axl Fc or MYD1 Fc was counted in the skov3.ip (d) and OVCAR (f) tumor models. Representative images of mice from each treatment group in the skov3.ip model are shown, and arrows indicate disease (e). In both models, animals were administered 10 mg per kg body weight of the indicated protein twice weekly. (g) Lung metastases in the 4T1 luciferase breast cancer model, as quantified by ex vivo bioluminescent imaging. Mice received intravenous injections of the indicated treatment twice weekly. (h) Representative bioluminescent images of lungs and spleens from each treatment group; scale bar, 1 cm. Error bars represent ± s.d., n = 6–12 mice per group; *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.

Article Snippet: After the appropriate incubation time, reactions were flowed over MYD1 Fc–coated beads, and captured free Gas6 was probed using a 500 ng/ml solution of antiHis6 Dylight 649 antibody (Rockland Immunochemicals Inc., 200-343-382).

Techniques: In Vivo, Luciferase, Ex Vivo, Imaging

Journal: Journal of medicinal chemistry

Article Title: A novel N-substituted valine derivative with unique PPARγ binding properties and biological activities

doi: 10.1021/acs.jmedchem.0c01555

Figure Lengend Snippet: Effect of 7j on PPARγ phosphorylation. (A) Percentage of in vitro PPARγ Ser273 phosphorylation by CDK5 in the presence of 0.1 μM of 7j or Rosi. (B) Phosphorylation of PPARγ Ser273 in 3T3-L1 adipocyte incubated for 60 minutes with 5 μM of Rosi, 7j or Roscovitine (Rsv) before TNFα stimulation (50 ng/ml; 90 minutes). Two independent experiments are shown. Phosphospecific antibodies were from Rockland or New England Peptide (NEP). Arrow heads indicate phosphorylated PPARγ and PPARγ2. (C) RT-PCR analysis of the expression levels of a selection of genes known to be regulated by CDK5-dependent phosphorylation of PPARγ. Values are means ± SD (n = 5) expressed relative to the mean of control. **p < 0.01, ***p < 0.001 vs. control (one-way ANOVA followed by Dunnett’s post hoc test).

Article Snippet: PPARγ phospho Ser273 antibodies were from Rockland (Limerick, PA, USA) or custom produced by New England Peptide (Gardner, MA, USA).

Techniques: Phospho-proteomics, In Vitro, Incubation, Reverse Transcription Polymerase Chain Reaction, Expressing, Selection, Control