Journal: Cell chemical biology

Article Title: Discovery of covalent CDK14 inhibitors with pan-TAIRE family specificity

doi: 10.1016/j.chembiol.2019.02.015

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: RB , Signal Chem , Cat # R05-55G-50.

Techniques: Virus, Recombinant, Kinase Assay, Sequencing, Software

Journal: Molecular Psychiatry

Article Title: Inhibition of colony stimulating factor 1 receptor corrects maternal inflammation-induced microglial and synaptic dysfunction and behavioral abnormalities

doi: 10.1038/s41380-020-0671-2

Figure Lengend Snippet: a Gene ontology (GO) biological processes pathway analysis shows that MIA microglia increase synaptogenic functions while repopulated microglia recover homeostatic functions. Left (red): Top significantly enriched GO biological process terms increased by MIA and decreased by repopulation. Right (purple): Top significantly enriched GO biological process terms decreased by MIA and increased by repopulation. These GO findings were verified using GORILLA. b IPA of genes with differential expression in microglia between MIA versus Saline (RNA-seq data). Pathway analysis reveals MIA-induced upregulation of neuritogenic gene expression, specifically in developmental stages, based on activation z -score. Red denotes pathway activated in E17 MIA microglia. c Genes in “neuritogenesis/formation of cellular protrusions” function. Hierarchal clustering of gene sets based on relative expression values; red: high relative expression, blue: low relative expression. Cluster 1 represents genes increased in adult MIA microglia but reduced in MIA + MG-REP including Ctnnd2, Ncam2, and Ntrk2 . Cluster 2 represents genes increased in immature MIA microglia including Ncam2, Ntn, Ptn and Wnt5a . Cluster3 represents genes decreased in immature MIA microglia including Plau. In situ hybridization (ISH) and immunofluorescence of E17 Saline or MIA offspring in the cortical plate region. d mRNA of cellular protrusion/ neuritogenic genes ( Ctnnd2, Ncam2, Ntn, Ptn, and Wnt5a ) were detected by florescent-labeled antisense cRNA probes (red) but not by scramble cRNA probe (not detected: N.D.), and the sections were immunostained for IBA1 (green) and DAPI (blue). e The number of IBA1 + cells expressing the cellular protrusion/neuritogenic genes were quantified in the cortical plate region. n = (4–5/2) male mice/ litters per molecule for Saline and MIA, n = 3 for scramble control probe. * p < 0.05, ** p < 0.01, ns denotes no significance, by unpaired Student t test. Graphs indicate mean ± s.e.m. ELISA verification of selected RNA-seq molecules: CTNND2 ( f ), NCAM2 ( g ), NTRK2 ( h ), NTN ( i) , PTN ( j ) and WNT5A ( k ) in acutely isolated microglia. MIA increases protein expression of cellular protrusion/neuriotgenic molecules in microglia that were normalized via repopulation. n = (6/4, 6/3, 5/3, 6/3) female mice/litters for P60 Saline + CTRL, MIA + CTRL, Saline + MG-REP and MIA + MG-REP. CTNND2: Prenatal treatment effect, F (1,19) = 157.1, p < 0.0001, Drug effect, F (1,19) = 262.7, p < 0.0001, Interaction effect, F (1,19) = 201, p < 0.0001, NCAM2: Prenatal treatment effect, F (1,19) = 23.76, p = 0.0001, Drug effect, F (1,19) = 26.29, p < 0.0001, Interaction effect, F (1,19) = 17.63, p = 0.0005, NTRK2: Prenatal treatment effect, F (1,18) = 13.99, p = 0.0015, Drug effect, F (1,18) = 12.45, p = 0.0024, Interaction effect, F (1,18) = 0.06203, p = 0.8061, NTN: Prenatal treatment effect, F (1,19) = 0.01669, p = 0.8986, Drug effect, F (1,19) = 0.8, p = 0.3823, Interaction effect, F (1,19) = 6.121, p = 0.0230, PTN: Prenatal treatment effect, F (1,19) = 10.31, p = 0.0046, Drug effect, F (1,19) = 52.02, p < 0.0001, Interaction effect, F (1,19) = 0.002927 p = 0.9574, WNT5A: Prenatal treatment effect, F (1,19) = 5.581, p = 0.0290, Drug effect, F (1,19) = 1.550, p = 0.2282, Interaction effect, F (1,19) = 0.0834 p = 0.7799, * p < 0.05, ** p < 0.01, *** p < 0.001 and **** p < 0.0001 as determined by 2-way ANOVA (alpha = 0.05) with Tukey’s post-hoc. # p < 0.05 for main effect of MIA. Graphs indicate mean ± s.e.m.

Article Snippet: For the detection of NCAM2, CTNND2 and WNT5A, custom ELISA kits were developed according to the manufacturer’s instruction using anti-NCAM2 goat polyclonal antibody (0.3 μg/well Acris Antibodies GmbH, AP32136PU-N), biotinylated anti-NCAM2 goat polyclonal antibody using Antibody Biotinylation Kit (0.3 μg/ml, Pierce/Thermo Scientific, 90407), anti-CTNND2 mouse monoclonal antibody (0.3 μg/well, Santa Cruz Biotechnology, SC-81793, clone 40.1), biotinylated anti-CTNND2 rabbit antibody (1 μg/ml, Abcam, EPR17628), anti-WNT5A goat polyclonal antibody (0.3 μg/well, R&D Systems, AF645), and biotinylated anti-WNT5A antibody using Antibody Biotinylation Kit (1 μg/ml, Pierce).

Techniques: Expressing, RNA Sequencing Assay, Activation Assay, In Situ Hybridization, Immunofluorescence, Labeling, Enzyme-linked Immunosorbent Assay, Isolation

Journal: Cell reports

Article Title: Niche-mediated repair of airways is directed in an occupant-dependent manner

doi: 10.1016/j.celrep.2022.111863

Figure Lengend Snippet: (A) Schematic representation of experimental design: mice were placed on tamoxifen chow for 3 weeks starting at 8 weeks of age. After a 3 week washout period, mice were intraperitoneally (i.p.) injected with NPT at 20 weeks of age, and lungs were isolated at 3, 7, or 21 days after injury. (B) Immunostaining for club and basal cell markers Scgb1a1 and Krt5, respectively, on control, Gli1 CreERT2 ; Fgf10 f/f , Acta2 CreERT2 ; Fgf10 f/f , Lgr6 CreERT2 ; Fgf10 f/f , and Sox2 CreERT2 ; Fgfr2b f/f mice 21 days after naphthalene injury. Higher-magnification panels on the right of proximal (P) versus distal (D) parts of the airway. (C) Schematic representation of data presented in (B). (D–F) Quantification of the percentage of the airway epithelium covered by club or basal cells in control, Gli1 CreERT2 ; Fgf10 f/f , Acta2 CreERT2 ; Fgf10 f/f , Lgr6 CreERT2 ; Fgf10 f/f , and Sox2 CreERT2 ; Fgfr2b f/f mice 3, 7, and 21 days after naphthalene injury. (G–K) Relative mRNA expression of Fgf10 , Scgb1a1 , Krt5 , Tp63 , and Muc5b in control, Gli1 CreERT2 ; Fgf10 f/f , Acta2 CreERT2 ; Fgf10 f/f , Lgr6 CreERT2 ; Fgf10 f/f , and Sox2 CreERT2 ; Fgfr2b f/f mice 3, 7, and 21 days after naphthalene injury. **p < 0.01; *p < 0.05. n ≥ 6.; error bars mean ± SEM. Scale bars, 500 μm. Two-sided t test and ANOVA used to determine statistical significance.

Article Snippet: Rabbit anti-FGF10 , Acris Antibodies , Cat# AP14882PU-N; RRID: AB_1752406.

Techniques: Injection, Isolation, Immunostaining, Control, Expressing

Journal: Cell reports

Article Title: Niche-mediated repair of airways is directed in an occupant-dependent manner

doi: 10.1016/j.celrep.2022.111863

Figure Lengend Snippet: (A and B) Immunostaining for club and ciliated cell markers Scgb1a1 and Foxj1, respectively, on control lungs without injury or at 3 days post naphthalene injury. (C) Quantification of the number of ciliated cells per 1 mm of proximal or distal airway in non-injured lungs versus lungs 3 days after naphthalene injury. (E) Immunostaining for GFP and club cell marker Scgb1a1 on Scgb1a1 CreERT ; mTmG , Piezo2 Cre ; mTmG and Krt5 CreERT2 ; mTmG mice in which we lineage traced club cells, neuroendocrine cells, and basal cells, respectively, without injury or up to 21 days after naphthalene injury. (F and G) Quantification of the percentage of club cells that are GFP labeled in each of the lineage-tracing models represented in (C) in lung and trachea. (H) Immunostaining for Muc5b on control Gli1 CreERT2 ; Fgf10 f/f , Acta2 CreERT2 ; Fgf10 f/f , Lgr6 CreERT2 ; Fgf10 f/f , and Sox2 CreERT2 ; Fgfr2b f/f mice. **p < 0.01; *p < 0.05. n ≥ 6.; error bars mean ± SEM. Scale bars, 500 μm. Two-sided t test and ANOVA used to determine statistical significance.

Article Snippet: Rabbit anti-FGF10 , Acris Antibodies , Cat# AP14882PU-N; RRID: AB_1752406.

Techniques: Immunostaining, Control, Marker, Labeling

Journal: Cell reports

Article Title: Niche-mediated repair of airways is directed in an occupant-dependent manner

doi: 10.1016/j.celrep.2022.111863

Figure Lengend Snippet: (A and J) Immunostaining for club and basal cell markers Scgb1a1 and Krt5, respectively, on control, Gli1 CreERT2 ; Smo f/f , Gli1 CreERT2 ; Smo f/f , Fgf10 f/f , Lgr6 CreER2 ; Ctnnb1 f/f , Sox2 CreERT2 ; Shh f/f , Sox2 CreERT2 ; Shh f/f ; Fgfr2b f/f , and Sox2 CreERT2 ; Wnt7b f/f mice 21 days after naphthalene injury. (B, C, G–I, K, L, and P–R) Relative mRNA expression of Fgf10 , Scgb1a1 , Krt5 , Tp63 , and Muc5b in control, Gli1 CreERT2 ; Smo f/f , Gli1 CreERT2 ; Smo f/f , Fgf10 f/f , Lgr6 CreERT2 ; Ctnnb1 f/f , Sox2 CreERT2 ; Shh f/f , Sox2 CreERT2 ; Shh f/f ; Fgfr2b f/f , and Sox2 CreERT2 ; Wnt7b f/f mice 3, 7 and 21 days after naphthalene injury. (D–F and M–O) (D–F) Quantification of the percent of the airway epithelium covered by club or basal cells in control, Gli1 CreERT2 ; Smo f/f , Gli1 CreERT2 ; Smo f/f , Fgf10 f/f , Lgr6 CreERT2 ; Ctnnb1 f/f , Sox2 CreERT2 ; Shh f/f , Sox2 CreERT2 ; Shh f/f ; Fgfr2b f/f , and Sox2 CreERT2 ; Wnt7b f/f mice. (S) Schematic representation of data presented in (A) and (J). **p < 0.01; *p < 0.05. n ≥ 6.; error bars mean ± SEM. Scale bars, 500 μm. Two-sided t test and ANOVA used to determine statistical significance.

Article Snippet: Rabbit anti-FGF10 , Acris Antibodies , Cat# AP14882PU-N; RRID: AB_1752406.

Techniques: Immunostaining, Control, Expressing

Journal: Cell reports

Article Title: Niche-mediated repair of airways is directed in an occupant-dependent manner

doi: 10.1016/j.celrep.2022.111863

Figure Lengend Snippet: (A–I) Relative mRNA expression of Wnt7b , Bmp4 , or Shh in control, Gli1 CreERT2 ; Smo f/f , Gli1 CreERT2 ; Smo f/f , Fgf10 f/f , Gli1 CreERT2 ; Fgf10 f/f , Acta2 CreERT2 ; Fgf10 f/f , Lgr6 CreERT2 ; Fgf10 f/f , Lgr6 CreERT2 ; Ctnnb1 f/f , Sox2 CreERT2 ; Shh f/f , Sox2 CreERT2 ; Shh f/f ; Fgfr2b f/f , Sox2 CreERT2 ; Fgfr2b f/f , Sox2 CreERT2 ; Wnt7b f/f , Scgb1a1 Cre ; Shh f/f , Scgb1a1 Cre ; Shh f/f ; Fgfr2b f/f , and Scgb1a1 Cre ; Smo f/f mice 3, 7, and 21 days after naphthalene injury. **p < 0.01; *p < 0.05. n ≥ 6.; error bars mean ± SEM. Two-sided t test and ANOVA used to determine statistical significance.

Article Snippet: Rabbit anti-FGF10 , Acris Antibodies , Cat# AP14882PU-N; RRID: AB_1752406.

Techniques: Expressing, Control

Journal: Cell reports

Article Title: Niche-mediated repair of airways is directed in an occupant-dependent manner

doi: 10.1016/j.celrep.2022.111863

Figure Lengend Snippet: (A) Immunostaining of human submucosal glands for Fgf10, Fgfr2b, and basal cell marker Krt5 (note the Fgf10 antibody detects Fgf10 bound to receptor). (B) Immunostaining for GFP and myoepithelial cell markers Krt5 and Acta2 on Nkx2.1 Flpo ; Acta2-Frt-STOP-Frt-Cre ERT2 ; Rosa26 mTmG mice. (C) Immunostaining for GFP and myoepithelial cell markers Krt5 and Acta2 on submucosal glands from Nkx2.1 Flpo ; Acta2-Frt-STOP-Frt-Cre ERT2 ; Rosa26 mTmG , Nkx2.1 Flpo ; Acta2-Frt-STOP-Frt-Cre ERT2 ; Rosa26 mTmG ; Fgfr2b f/f , and Nkx2.1 Flpo ; Acta2-Frt-STOP-Frt-Cre ERT2 ;Rosa26 mTmG ; Fgf10 f/f mice that were injured twice with naphthalene with a 21 day interval and were harvested 60 days after the first or 39 days after the second injury. Higher-magnification panels are found to the right. (D) Schematic representation of experimental design: mice were placed on tamoxifen chow for 3 weeks starting at 8 weeks of age. After a 3 week washout period, mice were i.p. injected with NPT at 14 weeks of age and again 3 weeks later at 17 weeks of age, and lungs were isolated 3 weeks after the second injury at 20 weeks of age. (E) Top: quantification of the percentage of basal cells that are GFP positive and therefore myoepithelial cell derived in the surface airway epithelium of the tracheas and lungs from Nkx2.1 Flpo ; Acta2-Frt-STOP-Frt-Cre ERT2 ; Rosa26 mTmG , Nkx2.1 Flpo ; Acta2-Frt-STOP-Frt-Cre ERT2 ; Rosa26 mTmG ; Fgfr2b f/f mice that were injured twice with naphthalene with a 21 day interval and were harvested 60 days after the first or 39 days after the second injury. Bottom: quantification of the percentage of the airway epithelium that is covered by basal cells in Nkx2.1 Flpo ; Acta2-Frt-STOP-Frt-Cre ERT2 ; Rosa26 mTmG , Nkx2.1 Flpo ; Acta2-Frt-STOP-Frt-Cre ERT2 ; Rosa26 mTmG ;Fgfr2b f/f mice that were injured twice with naphthalene with a 21 day interval and were harvested 60 days after the first or 39 days after the second injury. (F) Immunostaining for GFP and club and basal cell markers Scgb1a1 and Krt5, respectively, on lungs from Nkx2.1 Flpo ; Acta2-Frt-STOP-Frt-Cre ERT2 ; Rosa26 mTmG and Nkx2.1 Flpo ; Acta2-Frt-STOP-Frt-Cre ERT2 ; Rosa26 mTmG ; Fgfr2b f/f mice that were injured twice with naphthalene with a 21 day interval and were harvested 60 days after the first or 39 days after the second injury. **p < 0.01; *p < 0.05. n ≥ 6; error bars mean ± SEM. Scale bars, 200 μm. Two-sided t test and ANOVA used to determine statistical significance.

Article Snippet: Rabbit anti-FGF10 , Acris Antibodies , Cat# AP14882PU-N; RRID: AB_1752406.

Techniques: Immunostaining, Marker, Injection, Isolation, Derivative Assay

Journal: Cell reports

Article Title: Niche-mediated repair of airways is directed in an occupant-dependent manner

doi: 10.1016/j.celrep.2022.111863

Figure Lengend Snippet: Here, we show how spatiotemporal expression of Fgf10 by two niche-maintaining cell types is primarily orchestrated by the niche’s epithelial occupants—both those that reside prior to and following injury. Prior to injury, differentiated airway epithelial cells secrete Shh to inhibit Fgf10 expression by Gli1 + peribronchial mesenchymal cells of the niche. After injury, remaining epithelial cells produce Wnt7b to induce Fgf10 expression in airway smooth muscle cells of the niche. Complete induction of Fgf10 expression in the niche requires loss of an inhibitory Shh signal from the prior epithelial occupant (club cell) as well as induction of an activating Wnt7b signal by the surviving or new epithelial occupant (ciliated and basal cells). We find that this reliance on a common activator of airway epithelial stem cells allows for the recruitment of remote stem cell populations when local populations have been destroyed or exhausted.

Article Snippet: Rabbit anti-FGF10 , Acris Antibodies , Cat# AP14882PU-N; RRID: AB_1752406.

Techniques: Expressing

Journal: Cell reports

Article Title: Niche-mediated repair of airways is directed in an occupant-dependent manner

doi: 10.1016/j.celrep.2022.111863

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Rabbit anti-FGF10 , Acris Antibodies , Cat# AP14882PU-N; RRID: AB_1752406.

Techniques: Recombinant, Plasmid Preparation, Expressing, Software

Journal: Heliyon

Article Title: Persistent immune and clotting dysfunction detected in saliva and blood plasma after COVID-19

doi: 10.1016/j.heliyon.2023.e17958

Figure Lengend Snippet: Study Design. (A) Saliva and plasma samples were collected from healthy and coronavirus disease (COVID-19) donors during the convalescent phase to investigate the viral-host axis in health versus disease. (B) The serology coupled with the global shotgun proteomic analysis of plasma and saliva samples was conducted in parallel, followed by correlation analyses to demographic factors, antibody-, and proteomic responses. (C) This study was designed to capture the inflammatory response (yellow/red dots) during the start of the convalescent phase (>20 days) after clinical symptom; antibody drawings) and investigate the correlation between biological, and demographic factors. Ultimately, our findings will be applied to discover early detection markers for the post-acute sequelae of SARS-CoV-2 infection. Total samples = 110 samples (Healthy Saliva = 13, Healthy Plasma n = 13, COVID19 Saliva n = 42, COVID19 Plasma = 42).

Article Snippet: Four different coating antigens were included; SARS-CoV-2 Spike Glycoprotein (S1) RBD, His-Tag (HEK293) (NativeAntigen, Oxfordshore, United Kingdom), SARS-CoV-2 Spike Glycoprotein (S1), His-Tag (Insect Cells) (NativeAntigen, Oxfordshore, United Kingdom), SARS-CoV-2 Spike Glycoprotein (S2), His-Tag (Insect Cells) (NativeAntigen, Oxfordshore, United Kingdom), SARS-CoV-2 Nucleoprotein, His-Tag ( E. coli ) (NativeAntigen, Oxfordshore, United Kingdom), and Human Coronavirus NL63 Spike Glycoprotein (S1) His-Tag (HEK293) (NativeAntigen, Oxfordshore, United Kingdom).

Techniques: Infection

Journal: Heliyon

Article Title: Persistent immune and clotting dysfunction detected in saliva and blood plasma after COVID-19

doi: 10.1016/j.heliyon.2023.e17958

Figure Lengend Snippet: Compartmentalized antibody responses found in saliva and plasma collaborate in response to the SARS-CoV-2 infection. (A–C) The individual area under the curve (AUC) was plotted as blue or red hollow circles (saliva or plasma, respectively). Bars and whiskers represent median and standard deviation, respectively. Mixed-effect analysis with Tukey’s multiple comparisons test was used to measure statistical significance. *p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001; ****p ≤ 0.0001. (D) Five paired immunoglobulins showing significant correlation (p < 0.05) between plasma and saliva were depicted as simple linear regression models. The individual titer of saliva was plotted by paired plasma titers. The predicted regression line and deviations were depicted as a solid and dotted lines, respectively. Functions and p-value of regression analyses were indicated next to the regression lines. Correlations of immunoglobulins specific to the SARS-CoV-2 receptor binding site (RBD) or Spike protein 1 (S1) were colored yellow and red, respectively.

Article Snippet: Four different coating antigens were included; SARS-CoV-2 Spike Glycoprotein (S1) RBD, His-Tag (HEK293) (NativeAntigen, Oxfordshore, United Kingdom), SARS-CoV-2 Spike Glycoprotein (S1), His-Tag (Insect Cells) (NativeAntigen, Oxfordshore, United Kingdom), SARS-CoV-2 Spike Glycoprotein (S2), His-Tag (Insect Cells) (NativeAntigen, Oxfordshore, United Kingdom), SARS-CoV-2 Nucleoprotein, His-Tag ( E. coli ) (NativeAntigen, Oxfordshore, United Kingdom), and Human Coronavirus NL63 Spike Glycoprotein (S1) His-Tag (HEK293) (NativeAntigen, Oxfordshore, United Kingdom).

Techniques: Infection, Standard Deviation, Binding Assay

Journal: Heliyon

Article Title: Persistent immune and clotting dysfunction detected in saliva and blood plasma after COVID-19

doi: 10.1016/j.heliyon.2023.e17958

Figure Lengend Snippet: Correlation analyses suggest that proteomic alterations in convalescent saliva are associated with antibody responses specific to the receptor binding site (RBD) of SARS-CoV-2. (A–C) A significant correlation (p < 0.05) between SARS-CoV-2 RBD specific immunoglobulins and convalescent COVID-19 salivary sub-clusters was depicted as simple linear regression models. The individual titer of immunoglobulin was plotted by subcluster numbers. The predicted regression line and deviations were depicted as solid and dotted lines, respectively. Functions and p-value of regression analyses were indicated next to the regression lines. (D–H) Three differentially expressed proteins responsible for the clustering were illustrated as simple regression models as described above.

Article Snippet: Four different coating antigens were included; SARS-CoV-2 Spike Glycoprotein (S1) RBD, His-Tag (HEK293) (NativeAntigen, Oxfordshore, United Kingdom), SARS-CoV-2 Spike Glycoprotein (S1), His-Tag (Insect Cells) (NativeAntigen, Oxfordshore, United Kingdom), SARS-CoV-2 Spike Glycoprotein (S2), His-Tag (Insect Cells) (NativeAntigen, Oxfordshore, United Kingdom), SARS-CoV-2 Nucleoprotein, His-Tag ( E. coli ) (NativeAntigen, Oxfordshore, United Kingdom), and Human Coronavirus NL63 Spike Glycoprotein (S1) His-Tag (HEK293) (NativeAntigen, Oxfordshore, United Kingdom).

Techniques: Binding Assay

Journal: PLOS ONE

Article Title: Human embryonic stem cells secrete macrophage migration inhibitory factor: A novel finding

doi: 10.1371/journal.pone.0288281

Figure Lengend Snippet: A . Cells were incubated with different concentrations of MIF for 24, 48 and 72 h, and the cell viability was detected by CCK-8 assay, showing no significant difference ( P >0.05); B . Cells were incubated with different concentrations of CXCL12 for 24, 48 and 72 h, and cell viability was detected by CCK-8 assay, showing no significant difference ( P >0.05); C . Cells were incubated with different concentrations of ISO-1 for 24, 48 and 72 h, and cell viability was detected by CCK-8 assay, compared with the control group, *** P <0.001, **** P <0.0001; D . Cells were co-incubated with 96 μM ISO-1 and different concentrations of MIF simultaneously for 24, 48 and 72 h, and cell viability was detected by CCK-8 assay, compared with the control group, *** P <0.001, **** P <0.0001.

Article Snippet: The experiment was divided into control group, MIF (NBp2-35005, NOVUS, USA) group, CXCL12 (Ab259416, Abcam, U.K) group, and ISO-1 (HY-16692, MCE, USA) group.

Techniques: Incubation, CCK-8 Assay, Control