Journal: Journal of anatomy

Article Title: Expression of Toll-like receptor 9 in mouse and human lungs.

doi: 10.1111/joa.12039

Figure Lengend Snippet: Fig. 1 TLR9 in situ hybridization on mouse lungs. Lung sections stained using TLR9 DIG-labeled RNA show staining (arrows) in several cell types (A). Lung sections from mice stained without a specific probe (B) lacks staining in any tissue. High magnification shows staining in vascular endo- thelium (arrowhead) (C), septal (arrow) as well as alveolar macrophages (chevron) (D), and bronchial epithelium (double arrow) (E). Scale bar: 100 lm.

Article Snippet: Immuno-electron microscopy was carried out as described previously (Schneberger et al., 2009) with TLR9 antibody (1 : 50) and 20 nm gold-conjugated anti-mouse secondary antibody (1 : 100; Fitzgerald Industries International, Concord, MA, USA) for 1 h. The controls included protocols without the primary antibody and staining of sections with vWF antibody.

Techniques: In Situ Hybridization, Staining, Labeling

Journal: Journal of anatomy

Article Title: Expression of Toll-like receptor 9 in mouse and human lungs.

doi: 10.1111/joa.12039

Figure Lengend Snippet: Fig. 2 TLR9 immunohistochemistry on mouse lungs. Lung sections from mice stained with only a secondary antibody (A) lack staining in alveolar septa, whereas those stained with vWF antibody (B) shows staining in endothelium (arrowhead) alone. Lung sections stained using TLR9 antibody show staining in several tissues (arrows) (C), including bronchial epithelium (double arrow) (D), vascular endothelium (arrowhead) (E), and septal (arrow) as well as alveolar macrophages (chevron) (F). Scale bar: 100 lm.

Article Snippet: Immuno-electron microscopy was carried out as described previously (Schneberger et al., 2009) with TLR9 antibody (1 : 50) and 20 nm gold-conjugated anti-mouse secondary antibody (1 : 100; Fitzgerald Industries International, Concord, MA, USA) for 1 h. The controls included protocols without the primary antibody and staining of sections with vWF antibody.

Techniques: Immunohistochemistry, Staining

Journal: Journal of anatomy

Article Title: Expression of Toll-like receptor 9 in mouse and human lungs.

doi: 10.1111/joa.12039

Figure Lengend Snippet: Fig. 3 TLR9 staining in a mouse neutrophil. TLR9 staining (arrows) observed in mouse lung neutrophil, epithelium (arrowhead), and endothelium (chevron). N, nucleus; AS, alveolar space. Scale bar: 4 lm.

Article Snippet: Immuno-electron microscopy was carried out as described previously (Schneberger et al., 2009) with TLR9 antibody (1 : 50) and 20 nm gold-conjugated anti-mouse secondary antibody (1 : 100; Fitzgerald Industries International, Concord, MA, USA) for 1 h. The controls included protocols without the primary antibody and staining of sections with vWF antibody.

Techniques: Staining

Journal: Journal of anatomy

Article Title: Expression of Toll-like receptor 9 in mouse and human lungs.

doi: 10.1111/joa.12039

Figure Lengend Snippet: Fig. 4 TLR9 staining in a mouse type-II cell. TLR9 staining (arrows) observed in a mouse lung type-II cell. N, nucleus; AS, alveolar space; LB, lamellar bodies. Scale bar: 4 lm.

Article Snippet: Immuno-electron microscopy was carried out as described previously (Schneberger et al., 2009) with TLR9 antibody (1 : 50) and 20 nm gold-conjugated anti-mouse secondary antibody (1 : 100; Fitzgerald Industries International, Concord, MA, USA) for 1 h. The controls included protocols without the primary antibody and staining of sections with vWF antibody.

Techniques: Staining

Journal: Journal of anatomy

Article Title: Expression of Toll-like receptor 9 in mouse and human lungs.

doi: 10.1111/joa.12039

Figure Lengend Snippet: Fig. 6 Human lung TLR9 in situ RNA hybridization. Lung sections from normal (A) or COPD (B) patients stained using TLR9 DIG-labeled RNA probe show staining (arrows) in several cell types with a clear influx of TLR9 positive cells in the bronchus. Staining without a RNA probe shows lack of staining in any tissue (C). High magnification shows staining in bronchial epithelium (double arrow) (E), vascular endothelium (arrowhead) (F), and septal (arrow) as well as alveolar (chevron) macrophages (G). Scale bar: 100 lm.

Article Snippet: Immuno-electron microscopy was carried out as described previously (Schneberger et al., 2009) with TLR9 antibody (1 : 50) and 20 nm gold-conjugated anti-mouse secondary antibody (1 : 100; Fitzgerald Industries International, Concord, MA, USA) for 1 h. The controls included protocols without the primary antibody and staining of sections with vWF antibody.

Techniques: In Situ, Hybridization, Staining, Labeling

Journal: Journal of anatomy

Article Title: Expression of Toll-like receptor 9 in mouse and human lungs.

doi: 10.1111/joa.12039

Figure Lengend Snippet: Fig. 5 TLR9 staining in a mouse alveolar macrophage cell. TLR9 staining (arrows) observed in a mouse alveolar macrophage. N, nucleus; AS, alveolar space. Scale bar: 4 lm.

Article Snippet: Immuno-electron microscopy was carried out as described previously (Schneberger et al., 2009) with TLR9 antibody (1 : 50) and 20 nm gold-conjugated anti-mouse secondary antibody (1 : 100; Fitzgerald Industries International, Concord, MA, USA) for 1 h. The controls included protocols without the primary antibody and staining of sections with vWF antibody.

Techniques: Staining

Journal: Journal of anatomy

Article Title: Expression of Toll-like receptor 9 in mouse and human lungs.

doi: 10.1111/joa.12039

Figure Lengend Snippet: Fig. 7 Human lung TLR9 immunohistochemistry. Lung sections from human patients stained with only a secondary antibody (A) lack staining in alveolar septa, whereas those stained with vWF antibody (B) show staining in endothelium (arrowhead) alone. Lung sections stained using TLR9 antibody show staining (arrows) in several cell types in both normal (C) as well as COPD patients (D). High magnification shows staining in bron- chial epithelium (double arrow) (E), vascular endothelium (arrowhead) (F), and septal (G) as well as alveolar macrophages (chevron) (H). Scale bar: 100 lm. Field counts of control and COPD patients showed a greater density of TLR9 positive cells in those with COPD (P < 0.01).

Article Snippet: Immuno-electron microscopy was carried out as described previously (Schneberger et al., 2009) with TLR9 antibody (1 : 50) and 20 nm gold-conjugated anti-mouse secondary antibody (1 : 100; Fitzgerald Industries International, Concord, MA, USA) for 1 h. The controls included protocols without the primary antibody and staining of sections with vWF antibody.

Techniques: Immunohistochemistry, Staining, Control

Journal: Journal of anatomy

Article Title: Expression of Toll-like receptor 9 in mouse and human lungs.

doi: 10.1111/joa.12039

Figure Lengend Snippet: Fig. 8 TLR9 staining in human alveolar macrophage. TLR9 staining (arrows) observed in a human alveolar macrophage. N, nucleus; AS, alveolar space. Scale bar: 4 lm.

Article Snippet: Immuno-electron microscopy was carried out as described previously (Schneberger et al., 2009) with TLR9 antibody (1 : 50) and 20 nm gold-conjugated anti-mouse secondary antibody (1 : 100; Fitzgerald Industries International, Concord, MA, USA) for 1 h. The controls included protocols without the primary antibody and staining of sections with vWF antibody.

Techniques: Staining

Journal: Journal of anatomy

Article Title: Expression of Toll-like receptor 9 in mouse and human lungs.

doi: 10.1111/joa.12039

Figure Lengend Snippet: Fig. 9 TLR9 staining in a human type-II cell. TLR9 staining (arrows) observed in a mouse lung type-II cell. N, nucleus; AS, alveolar space. Scale bar: 4 lm.

Article Snippet: Immuno-electron microscopy was carried out as described previously (Schneberger et al., 2009) with TLR9 antibody (1 : 50) and 20 nm gold-conjugated anti-mouse secondary antibody (1 : 100; Fitzgerald Industries International, Concord, MA, USA) for 1 h. The controls included protocols without the primary antibody and staining of sections with vWF antibody.

Techniques: Staining

Journal: Cell

Article Title: Nuclear Proximity of Mtr4 with RNA exosome restricts DNA mutational asymmetry

doi: 10.1016/j.cell.2017.03.043

Figure Lengend Snippet: B cells were harvested from the spleen of an Exosc10COIN/LacZ mouse and fixed and prepared for 3D-STORM after 72 hrs of treatment with (1) stimulation cocktail and (2) 4OHT+stimulation cocktail. Reconstructed two color 3D STORM (super-Aresolution) image from a data set of 50,000 frames with Atto488 labeled AID, AlexaFluor647 labeled Mtr4 and DAPI labeled nucleus. Three dimensional views of the boxed region show spatial distribution of AID and Mtr4 molecules inside the nuclei of B cells isolated from (A) wild type cells and (D) Exosc10 knockout cells. Histogram of the distribution of interactions of AID and Mtr4 calculated in the B cell nucleus of (B) wild type & (E) Exosc10 knockout cells and in the corresponding cytoplasms (C) & (F), by using Matlab (2014b, MathWorks) software. (G) Comparison of the distribution of paired interaction of AID and Mtr4 in the nucleus versus cytoplasm by one way ANOVA (Tukey-Kramer test) method in Matlab (2014b, MathWorks) software. Comparison of the distribution of paired interaction of AID and Mtr4 were calculated in the cytoplasm versus nucleus of (H) wild type & (I) Exosc10 knockout B cells using a Student’s t-test in Matlab (2014b, MathWorks) software and P values are noted in the graph. (J) Comparison of the distribution of paired interaction of AID and Mtr4 in the nuclear center versus displaced from center versus cytoplasm by one way ANOVA (Tukey-Kramer test) method in Matlab (2014b, MathWorks) software. (K) Reconstructed two color 3D STORM (super-resolution) image with Alexa488 labeled AID, AlexaFluor647 labeled Mtr4 and DAPI labeled nucleus of wild type Exosc10 cells. Histogram of the distribution of interactions of AID and Mtr4 calculated in (L) nucleus center and (M) displaced from center of wild type cells, by using Matlab (2014b, MathWorks) software. All of the 3D STORM imaging was performed in three different B cells (from independent experiments) and repeated three or more times. 3D STORM super resolution image magnification is ×100. Scale bar: 1μm(K). Error bars indicate S.D. (P values: ** <0.01, *** <0.001)

Article Snippet: Alexa488 (Against-Goat) , Jackson Immuno Research , 805-547-008.

Techniques: Labeling, Isolation, Knock-Out, Software, Comparison, Imaging

Journal: Cell

Article Title: Nuclear Proximity of Mtr4 with RNA exosome restricts DNA mutational asymmetry

doi: 10.1016/j.cell.2017.03.043

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Alexa488 (Against-Goat) , Jackson Immuno Research , 805-547-008.

Techniques: Magnetic Beads, Recombinant, Protease Inhibitor, Modification, Electron Microscopy, Shear, Transgenic Assay, Sequencing, Subcloning, Software

Journal: Nature cancer

Article Title: ULK1 inhibition overcomes compromised antigen presentation and restores antitumor immunity in LKB1 mutant lung cancer

doi: 10.1038/s43018-021-00208-6

Figure Lengend Snippet: a . mRNA levels of antigen presentation related genes as well as conventional proteasome subunit expression from TCGA KRAS/LKB1 mutant compared with KRAS/TP53 mutant NSCLC patients. KL n=19, KP n=22 patients. (mean±sd, multiple two-tailed t test, unpaired. FDR=0.05) b . mRNA levels of immunoproteasome subunits Lmp2 / Psmb9 and Lmp7 / Psmb8 from KP and KL tumors either from genetically engineered mouse model (GEMM) (left) or cell lines (right). left, KP n=5, KL n=5 lung nodules each group. right, KP n=5, KL n=5 cell lines each group. (mean± sd, multiple two-tailed t test, unpaired. FDR=0.05). c . Immunoproteasome subunits activity changes in LKB1 mutant tumors are measured by substrates Ac-ANW-AMC, Ac-PAL-AMC and Ac-KQL-AMC cleavage. The cleavage activities Vmax were normalized with corresponding unstimulated samples and shown as fold changes. n=3 cell cultures for each group. Data shown representative one of three independent experiments. (mean±sd, multiple two-tailed t test, unpaired, two-stage step-up method of Benjamini, Krieger and Yekutieli, FDR<1%). d . Cell growth inhibition in KL and KP cells in response to autophagy inhibitors chloroquine (CQ) or ULK1 inhibitor MRT68921 (MRT). Data shown represents one of three independent experiments. n=3 cell cultures for each cell line with each treatment condition. e . Electron microscopy (EM) to visualize double-membraned autophagosome and autolysosome autophagic vacuole (AV) from KL, KL LKB1 and KL LKB1-KD cells. Top and left bottom, representative images. Data representative of 2 independent experiments. * marked AV. Lower right, quantification of AV numbers for each cell line examined. Scale bar, 500nm. For each group n=10 fields. Each dot represents quantification of one random field of EM image. (mean±sd, two-tailed t test, unpaired) f . Western blot showing autophagic flux by blocking lysosomal turnover with bafilomycin A1 (Baf A1) from KL-EV, KL-LKB1 and KL-LKB1(KD) cells. Data representative of 3 independent experiments. Blots are cropped and uncropped images can be found in Source Data.

Article Snippet: RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep (for 96 Samples, catalog number 20020595), starting from 500 ng of total RNA, with 10 cycles of PCR amplification.

Techniques: Immunopeptidomics, Expressing, Mutagenesis, Two Tailed Test, Activity Assay, Inhibition, Electron Microscopy, Western Blot, Blocking Assay

Journal:

Article Title: Global Analysis of Host Cell Gene Expression Late during Cytomegalovirus Infection Reveals Extensive Dysregulation of Cell Cycle Gene Expression and Induction of Pseudomitosis Independent of US28 Function †

doi: 10.1128/JVI.78.21.11988-12011.2004

Figure Lengend Snippet: Abnormal mitotic figures in nonnucleated CMV-infected cells. (A to M) Uninfected or CMV-infected HFs stained with an anti-γtub1 MAb (red), an FITC-conjugated MAb to the viral nuclear proteins IE1/IE2 (green) and Hoechst 44432 to detect cellular DNA (blue). (A to C) γtub1 (A) and cellular DNA (B) localization in a representative uninfected mitotic cell and A+B merged image (C); (D to I) γtub1 (D), cellular DNA (E), and IE1/IE2 (G) localization in a representative infected nonnucleated cell; phase-contrast image of the same cells (H), D+E merged image (F), and F+G+H merged image (I). (J and K) IE1/IE2 (J) and cellular DNA (K) localization in a representative infected nonnucleated cell; (L and M) IE1/IE2 (green) and γtub1 (red) localization in representative infected nonnucleated cells. Magnification, ×1,000.

Article Snippet: Cellular DNA was highlighted with Hoechst 44432 (Molecular Probes, Eugene, Oreg.).

Techniques: Infection, Staining

Journal:

Article Title: Global Analysis of Host Cell Gene Expression Late during Cytomegalovirus Infection Reveals Extensive Dysregulation of Cell Cycle Gene Expression and Induction of Pseudomitosis Independent of US28 Function †

doi: 10.1128/JVI.78.21.11988-12011.2004

Figure Lengend Snippet: Dependence of pseudomitosis on viral and cellular DNA synthesis. (A) Percentage of IE1/IE2 antigen-positive pseudomitotic cells at four different times postinfection in three independent experiments. Each bar represents the mean percentage ± the standard deviation. (B) Percentage of IE1/IE2-positive pseudomitotic cells at 72 hpi in infected HF cultures maintained in the presence of medium (•), medium plus 1 mM HU to block cellular DNA synthesis (▪), medium plus 10 mM HU to block both viral and cellular DNA synthesis (⧫), or medium plus PFA to block viral DNA synthesis (▴). Each symbol represents an independent experiment. Horizontal bars indicate mean values for all experiments.

Article Snippet: Cellular DNA was highlighted with Hoechst 44432 (Molecular Probes, Eugene, Oreg.).

Techniques: DNA Synthesis, Standard Deviation, Infection, Blocking Assay

Journal:

Article Title: Global Analysis of Host Cell Gene Expression Late during Cytomegalovirus Infection Reveals Extensive Dysregulation of Cell Cycle Gene Expression and Induction of Pseudomitosis Independent of US28 Function †

doi: 10.1128/JVI.78.21.11988-12011.2004

Figure Lengend Snippet: Progression of CMV replication cycle in pseudomitotic cells. (A to C) ppUL44 (green) and cellular DNA (red) localization in three representative infected pseudomitotic cells; (D) BrdU (green) incorporation and γtub1 (red) localization in a representative infected pseudomitotic cell; (E and F) transmission electron microscopy of a representative infected pseudomitotic cell. The rectangle in panel E shows the area magnified in panel F. Arrows indicate viral DNA encapsidation structures; arrowheads indicate events of partial or complete enclosure of capsids in vesicular structures. Ch, condensed mitotic chromosomes; Mt, mitochondria. Magnification: E, ×3,000; F, ×17,000.

Article Snippet: Cellular DNA was highlighted with Hoechst 44432 (Molecular Probes, Eugene, Oreg.).

Techniques: Infection, Transmission Assay, Electron Microscopy

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARMC10 regulates mitochondrial dynamics and affects mitochondrial function via the Wnt/β‐catenin signalling pathway involved in ischaemic stroke

doi: 10.1111/jcmm.18449

Figure Lengend Snippet: Changes of mitochondrial dynamics and function in clinical samples and OGD models (* p < 0.05, ** p < 0.01, *** p < 0.001). (A) The mitochondrial morphology of PBMCs was compared between IS group and control group with LSCM (Mitotracker Red was used for mitochondrial staining).(B) Comparison of mitochondrial morphology between control group and OGD/R group (Mitotracker Red was used for mitochondrial staining). (C) The changes of mitochondrial ultrastructure after OGD/R treatment were observed by electron microscopy. (D) After OGD/R, flow cytometry was used to detect the level of ROS and apoptosis, ATP detection with Microplate Luminometer.

Article Snippet: Apoptosis was evaluated using the Annexin V‐FITC/PI Apoptosis Detection kit(Beyotime Biotechnology, China).Collected cells and washed with PBS, and resuspended in 500 μL binding buffer.

Techniques: Control, Staining, Comparison, Electron Microscopy, Flow Cytometry

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARMC10 regulates mitochondrial dynamics and affects mitochondrial function via the Wnt/β‐catenin signalling pathway involved in ischaemic stroke

doi: 10.1111/jcmm.18449

Figure Lengend Snippet: ARMC10 affects mitochondrial function and Neuronal apoptosis (* p < 0.05, ** p < 0.01, *** p < 0.001). (A) Flow cytometry detect the effect of ARMC10 expression on mitochondrial function. (B) Western blot detect the effect of ARMC10 expression on apoptosis proteins. (C) Flow cytometry was used to detect the effect of ARMC10 expression on cell apoptosis.

Article Snippet: Apoptosis was evaluated using the Annexin V‐FITC/PI Apoptosis Detection kit(Beyotime Biotechnology, China).Collected cells and washed with PBS, and resuspended in 500 μL binding buffer.

Techniques: Flow Cytometry, Expressing, Western Blot

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARMC10 regulates mitochondrial dynamics and affects mitochondrial function via the Wnt/β‐catenin signalling pathway involved in ischaemic stroke

doi: 10.1111/jcmm.18449

Figure Lengend Snippet: Agonist and inhibitor affect mitochondrial function and neuronal apoptosis by targeting Wnt/β‐Catenin signal pathway (* p < 0.05, ** p < 0.01, *** p < 0.001). (A) Western blot detected protein expression levels of key molecules in Wnt/β‐catenin signalling pathway. (B) Western blot was used to detect the expression of downstream target genes of Wnt/β‐catenin signalling pathway. (C) FCM was used to detect effects of LiCl (20 mM) and XAV‐939 (10 μM) on mitochondrial function. (D) Western blot was used to detect the effect of ARMC10 expression on apoptosis proteins.

Article Snippet: Apoptosis was evaluated using the Annexin V‐FITC/PI Apoptosis Detection kit(Beyotime Biotechnology, China).Collected cells and washed with PBS, and resuspended in 500 μL binding buffer.

Techniques: Western Blot, Expressing

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARMC10 regulates mitochondrial dynamics and affects mitochondrial function via the Wnt/β‐catenin signalling pathway involved in ischaemic stroke

doi: 10.1111/jcmm.18449

Figure Lengend Snippet: In OGD/R model, ARMC10 regulates Wnt/β‐Catenin signalling pathway affecting mitochondrial function and neuronal apoptosis (* p < 0.05, ** p < 0.01, *** p < 0.001). (A) The key molecules of Wnt/β‐catenin signalling pathway were detected by western blot. (B) FCM was used to detect the function of different groups of mitochondria. (C) Expression of apoptosis‐related proteins under different conditions. (A and C shares the same batch of GAPDH bands in their WB results)

Article Snippet: Apoptosis was evaluated using the Annexin V‐FITC/PI Apoptosis Detection kit(Beyotime Biotechnology, China).Collected cells and washed with PBS, and resuspended in 500 μL binding buffer.

Techniques: Western Blot, Expressing