Journal: Frontiers in Aging Neuroscience

Article Title: Identification of Key Biomarkers and Pathways for Maintaining Cognitively Normal Brain Aging Based on Integrated Bioinformatics Analysis

doi: 10.3389/fnagi.2022.833402

Figure Lengend Snippet: Differentially expressed genes of healthy brain aging.

Article Snippet: The membranes were blocked for 1 h at room temperature with Blotto-Tween and incubated with primary antibody, CD44 (1:600 dilution), CD93 (1:600 dilution), and CD163 (1:600 dilution) at 4°C (all purchased from Boster Bioengineering Corporation, Wuhan, China).

Techniques:

Journal: Frontiers in Aging Neuroscience

Article Title: Identification of Key Biomarkers and Pathways for Maintaining Cognitively Normal Brain Aging Based on Integrated Bioinformatics Analysis

doi: 10.3389/fnagi.2022.833402

Figure Lengend Snippet: Detail information of 10 hub genes in the PPI network.

Article Snippet: The membranes were blocked for 1 h at room temperature with Blotto-Tween and incubated with primary antibody, CD44 (1:600 dilution), CD93 (1:600 dilution), and CD163 (1:600 dilution) at 4°C (all purchased from Boster Bioengineering Corporation, Wuhan, China).

Techniques: Activity Assay, Binding Assay, Transduction, Coagulation, Cell Surface Receptor Assay

Journal: Frontiers in Aging Neuroscience

Article Title: Identification of Key Biomarkers and Pathways for Maintaining Cognitively Normal Brain Aging Based on Integrated Bioinformatics Analysis

doi: 10.3389/fnagi.2022.833402

Figure Lengend Snippet: Cell-type expression of DEGs and differential expression of hub genes in Alzheimer’s disease. (A) Cell type gene of DEGs in brain tissue of patients with Alzheimer’s disease. (B–D) Differential expression of hub genes CD44, CD93, and CD163 in hippocampus of patients with Alzheimer’s disease.

Article Snippet: The membranes were blocked for 1 h at room temperature with Blotto-Tween and incubated with primary antibody, CD44 (1:600 dilution), CD93 (1:600 dilution), and CD163 (1:600 dilution) at 4°C (all purchased from Boster Bioengineering Corporation, Wuhan, China).

Techniques: Expressing, Quantitative Proteomics

Journal: Frontiers in Aging Neuroscience

Article Title: Identification of Key Biomarkers and Pathways for Maintaining Cognitively Normal Brain Aging Based on Integrated Bioinformatics Analysis

doi: 10.3389/fnagi.2022.833402

Figure Lengend Snippet: The expression of CD44, CD93, and CD163 in hippocampal tissue of cognitively normal aged and young mice. (A–C) The relative expression of CD44, CD93, and CD163 mRNA detected by qPCR; (D) western blot images of CD44, CD93, and CD163; (E–G) the levels of CD44, CD93, and CD163 protein detected by western blot.

Article Snippet: The membranes were blocked for 1 h at room temperature with Blotto-Tween and incubated with primary antibody, CD44 (1:600 dilution), CD93 (1:600 dilution), and CD163 (1:600 dilution) at 4°C (all purchased from Boster Bioengineering Corporation, Wuhan, China).

Techniques: Expressing, Western Blot

Journal: Frontiers in Genetics

Article Title: SYK Is Associated With Malignant Phenotype and Immune Checkpoints in Diffuse Glioma

doi: 10.3389/fgene.2022.899883

Figure Lengend Snippet: Expression pattern of SYK by single-cell sequencing analysis and the association between SYK expression and M2 macrophage infiltration. (A,B) SYK expression in the different cell types; (B–F) The correlation between SYK expression and CD163 and VSIG4 expression in the four cohorts. (G,H) The correlation between SYK expression and CD163 expression by IHC staining.

Article Snippet: Immunohistochemistry (IHC) was performed using a primary antibody against PD-L1 (Cell Signaling Technology Pathways, United States), CD163 (Proteintech, China), and SYK (Proteintech, China).

Techniques: Expressing, Sequencing, Immunohistochemistry

Journal: PLoS Pathogens

Article Title: Regulation of macrophage activity by surface receptors contained within Borrelia burgdorferi -enriched phagosomal fractions

doi: 10.1371/journal.ppat.1008163

Figure Lengend Snippet: Regulation of surface receptors by stimulation of BMMs and hMon with B . burgdorferi , as reported [ 15 ]. The transcriptomic and microarray data correspond to GEO accession number GSE103483. The proteomics data of BMM correspond to the ProteomeXchange accession number PXD008228. The last column indicates the identification of this receptors in phagosome-enriched fractions of hMACs stimulated with the spirochete. WB: immunoblotting, NP, not present.

Article Snippet: CHO cells stably transfected for human Fcγ Receptor I Alpha (FcgRI, CD64) and transiently transfected for human receptors: MARCO, MSR1, SIGLEC5, CLEC4N, CLEC4D, CLEC4B1, CLEC13A, CLEC10A, Ly6E, CD24a and CD59a were generated using full open reading frames under the CMV promoter (Origene, Herford, Germany).

Techniques: Microarray, Western Blot

Journal: Diagnostics

Article Title: Increased Tissue Expression of Lectin-Like Oxidized LDL Receptor-1 (LOX-1) Is Associated with Disease Severity in Chronic Rhinosinusitis with Nasal Polyps

doi: 10.3390/diagnostics10040246

Figure Lengend Snippet: Comparison of mRNA expression in paranasal sinus mucosa from the controls, and CRSsNP and CRSwNP patients as detected by RT-PCR. ( a ) scavenger receptor class B type 1 (SR-B1) and ( b ) lectin-like oxidized LDL receptor-1 (LOX-1) mRNA levels were quantitatively normalized to the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) mRNA levels. Center lines: median values. Boxes: interquartile ranges. Error bars: overall ranges. NS: not significant.

Article Snippet: The primary antibodies used were antihuman SR-B1 rabbit polyclonal antibody (#5193; ProSci, Poway, CA, USA), antihuman LOX-1 rabbit polyclonal antibody (#11837-1-AP; Proteintech, Rosemont, IL, USA), and antihuman CD68 mouse monoclonal antibody (#M0814; Dako, Glostrup, Denmark).

Techniques: Comparison, Expressing, Reverse Transcription Polymerase Chain Reaction

Journal: Diagnostics

Article Title: Increased Tissue Expression of Lectin-Like Oxidized LDL Receptor-1 (LOX-1) Is Associated with Disease Severity in Chronic Rhinosinusitis with Nasal Polyps

doi: 10.3390/diagnostics10040246

Figure Lengend Snippet: Correlation between the severity of computed tomography (CT) findings and mRNA expression levels for ( a ) SR-B1 and ( b ) LOX-1 in sinus mucosa.

Article Snippet: The primary antibodies used were antihuman SR-B1 rabbit polyclonal antibody (#5193; ProSci, Poway, CA, USA), antihuman LOX-1 rabbit polyclonal antibody (#11837-1-AP; Proteintech, Rosemont, IL, USA), and antihuman CD68 mouse monoclonal antibody (#M0814; Dako, Glostrup, Denmark).

Techniques: Computed Tomography, Expressing

Journal: Diagnostics

Article Title: Increased Tissue Expression of Lectin-Like Oxidized LDL Receptor-1 (LOX-1) Is Associated with Disease Severity in Chronic Rhinosinusitis with Nasal Polyps

doi: 10.3390/diagnostics10040246

Figure Lengend Snippet: Representative immunohistological images showing SR-B1 ( a , b ), LOX-1 ( c , d ), and CD68 ( e , f ) expression in ethmoid sinus mucosa sampled from a CRSwNP patient. Vascular endothelial cells (arrowheads) are stained positively both for SR-B1 and LOX-1. In contrast, numerous submucosal inflammatory cells show intense positive staining for LOX-1 compared to that for SR-B1. Scale bar: 20 μm.

Article Snippet: The primary antibodies used were antihuman SR-B1 rabbit polyclonal antibody (#5193; ProSci, Poway, CA, USA), antihuman LOX-1 rabbit polyclonal antibody (#11837-1-AP; Proteintech, Rosemont, IL, USA), and antihuman CD68 mouse monoclonal antibody (#M0814; Dako, Glostrup, Denmark).

Techniques: Expressing, Staining

Journal: Communications Biology

Article Title: Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy in mice

doi: 10.1038/s42003-020-01285-6

Figure Lengend Snippet: Eight-week old, sex-matched, C57BL/6 (WT) and Msr1 deficient ( Msr1 −/− ) mice were infected with CHIKV. Quantitative RT-PCR analyses of a Msr1 , CHIKV, type I IFN, ISG mRNA ( n = 4 mice), b CHIKV loads in whole blood cells of WT and Msr1 −/− mice ( n = 8 mice per genotype). c Viremia presented as plaque-forming units (PFU) per ml serum ( n = 8 mice per genotype). d Quantitative RT-PCR analyses of CHIKV loads in the ankle joints ( n = 8 mice per genotype). e Fold changes in the footpad dimensions of infected mice over uninfected (day 0) ( n = 8 mice per experimental group). f Representative micrographs of hematoxylin and eosin staining of ankle joints at 8 days after infection. n = 5 mice per genotype. B: bone, T: tendon, M: muscle. Magnification: ×200. g Arbitrary scores of ankle joint inflammation and damage using scales of 1 to 5, with 5 representing the worst disease presentation. n = 5 mice per genotype. h Quantitative RT-PCR analyses of the cellular viral loads in bone marrow-derived macrophages (BMDM) infected with CHIKV at a multiplicity of infection (MOI) of 10, n = 4. Each dot=one mouse/biological repeat, the small horizontal line: the median of the result. The data represent two independent experiments. * p < 0.05; ** p < 0.01; *** p < 0.001 [ b – d non-parametric t -test, e , g , h Student’s t -test].

Article Snippet: The mouse anti-FLAG (Cat# TA50011) and rabbit anti-human/mouse MSR1 (Cat# TA336699) antibodies were from Origene (Rockville, MD 20850, USA); the goat anti-mouse MSR1 (Cat# AF1797), mouse ant-human MSR1 (Cat# MAB2708), mouse anti-ATG12 (Cat# MAB6807) and recombinant mouse IFN-α (Cat #:12100-1) from R&D Systems (Minneapolis, MN 55413, USA).

Techniques: Infection, Quantitative RT-PCR, Staining, Derivative Assay

Journal: Communications Biology

Article Title: Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy in mice

doi: 10.1038/s42003-020-01285-6

Figure Lengend Snippet: a Microscopic images of immunofluorescence staining for LC3B in BMDMs infected with CHIKV at a MOI of 10 for 12 h. b The mean number of LC3B-positive punctae per cell ( n = 30 cells per field × 3 fields). *p < 0.05 (two-tailed Student’s t -test). c Immunoblots of LC3B in BMDMs infected with CHIKV at a MOI of 10, following treatment without/with 20 µM of chloroquine (CQ) for 3 h. d Generation of human ATG12 −/− and MSR1 −/− trophoblasts by CRISPR-Cas9. Both anti-ATG12 and ATG5 antibodies detect the stable ATG5-ATG12 dimer, which is abolished in ATG12 −/− cells. Monomeric ATG5 is liberated and detected in ATG12 −/− cells by an anti-ATG5 antibody. e Quantitative RT-PCR analyses of intracellular CHIKV RNA in trophoblasts infected with CHIKV at a MOI of 1, n = 2 biologically independent samples, ** p < 0.01 (two-way ANOVA). f Immunoblots of LC3B in trophoblasts infected with CHIKV at a MOI of 1. g Microscopic images and quantification of DAPGreen punctae (per cell, n = 30 cells) in live trophoblasts infected with CHIKV at a MOI of 1 for 10 h. ** p < 0.01 (two-tailed Student’s t -test). h Immunoblots of LC3B in mouse feet mock-treated or infected with CHIKV for 4 days. Each lane represents one animal. The uncropped immunoblots for all figures can be found in Supplementary Fig. .

Article Snippet: The mouse anti-FLAG (Cat# TA50011) and rabbit anti-human/mouse MSR1 (Cat# TA336699) antibodies were from Origene (Rockville, MD 20850, USA); the goat anti-mouse MSR1 (Cat# AF1797), mouse ant-human MSR1 (Cat# MAB2708), mouse anti-ATG12 (Cat# MAB6807) and recombinant mouse IFN-α (Cat #:12100-1) from R&D Systems (Minneapolis, MN 55413, USA).

Techniques: Immunofluorescence, Staining, Infection, Two Tailed Test, Western Blot, CRISPR, Quantitative RT-PCR

Journal: Communications Biology

Article Title: Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy in mice

doi: 10.1038/s42003-020-01285-6

Figure Lengend Snippet: a Co-immunoprecipitation (co-IP) of FLAG-tagged mouse autophagy proteins with Myc-Msr1 expressed in HEK293 cells using a mouse monoclonal anti-FLAG antibody, followed by immunoblotting (IB) with a mouse monoclonal anti-FLAG and rabbit anti-Msr1 antibody. b Co-IP of FLAG-Msr1 (mouse) with endogenous human ATG5-ATG12 complex expressed in HEK293. CHIKV infection: MOI of 1. WCE: whole-cell extract. c Co-IP of endogenous Msr1 with the Atg5-Atg12 complex from bone marrow-derived macrophages (BMDMs) following CHIKV infection at a MOI of 10 for 12 and 24 h. The IP was carried out with a rabbit anti-Msr1 antibody cross-linked to protein A/G agarose beads. Msr1 −/− cell serves as a negative control. d Immunofluorescence staining for Atg12 and Msr1 in BMDMs infected without (mock) /with CHIKV at a MOI of 10 for 12 h. Atg12 and Msr1 were stained by a mouse anti-Atg12 and rabbit anti-Msr1, followed by an Alexa Fluor-488 (green) and -594 (red)-conjugated secondary antibody respectively. The cells were counterstained for nuclei by DAPI (blue). The yellow punctae in the overlay indicate co-localizations. Magnification: ×400. e Co-IP of FLAG-MSR1 (human) or its fragment (aa1-50, 51-end) with endogenous ATG5-ATG12 complex expressed in HEK293 cells. CHIKV infection: MOI of 1 for 12 h. f Microscopic images of immunofluorescence staining for LC3B and MSR1 in trophoblasts without (mock)/infected with CHIKV at a MOI of 0.5 for 12 h. The yellow punctae in the overlay indicate co-localizations. Magnification: ×400. The uncropped immunoblots for all figures can be found in Supplementary Fig. .

Article Snippet: The mouse anti-FLAG (Cat# TA50011) and rabbit anti-human/mouse MSR1 (Cat# TA336699) antibodies were from Origene (Rockville, MD 20850, USA); the goat anti-mouse MSR1 (Cat# AF1797), mouse ant-human MSR1 (Cat# MAB2708), mouse anti-ATG12 (Cat# MAB6807) and recombinant mouse IFN-α (Cat #:12100-1) from R&D Systems (Minneapolis, MN 55413, USA).

Techniques: Immunoprecipitation, Co-Immunoprecipitation Assay, Western Blot, Infection, Derivative Assay, Negative Control, Immunofluorescence, Staining

Journal: Communications Biology

Article Title: Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy in mice

doi: 10.1038/s42003-020-01285-6

Figure Lengend Snippet: a , b Repression of CHIKV replication by MSR1 requires ATG5. Mouse primary embryonic fibroblasts were transfected with either 0.2 or 1.5 µg of empty vector (Vec) or FLAG-Msr1 (mouse) expression plasmid. Twenty-four hours later the cells were then infected with CHIKV (multiplicity of infection MOI = 0.5). a Immunoblots showing FLAG-Msr1 (mouse) and Atg5-Atg12 expression at 24 h after plasmid DNA transfection. b Quantitative RT-PCR analyses of intracellular CHIKV RNA. N = 2. c Repression of CHIKV replication by MSR1 requires ATG12. Human trophoblasts were transfected with either 0.2 µg of empty vector or a FLAG-MSR1 (human) expression plasmid. Twenty-four hours later, the cells were then infected with CHIKV MOI = 0.5 for 12 h. Intracellular CHIKV RNA was quantitated by RT-PCR. n = 3 biologically independent samples. d Generation of human ATG16L1 −/− trophoblasts by CRISPR-Cas9. The immunoblot shows ATG16L1 knockout efficiency. e Repression of CHIKV replication by MSR1 requires the FBD domain of ATG16L1. ATG16L1 −/− trophoblasts were transfected with the indicated combinations of expression plasmids (human gene) and vector (Vec) (50 ng each) respectively. After 24 h, the cells were infected with CHIKV at a MOI of 0.5 for 16 h. FL: full-length, ΔFBD: FBD domain deletion, ΔWD40: WD40 domain deletion of ATG16L1. The immunoblots show CHIKV Capsid and cellular protein expression. n = 3 biologically independent samples. The small horizontal line: the median of the result. * p < 0.05, ** p < 0.01 (Student’s t -test). The uncropped immunoblots for all figures can be found in Supplementary Fig. .

Article Snippet: The mouse anti-FLAG (Cat# TA50011) and rabbit anti-human/mouse MSR1 (Cat# TA336699) antibodies were from Origene (Rockville, MD 20850, USA); the goat anti-mouse MSR1 (Cat# AF1797), mouse ant-human MSR1 (Cat# MAB2708), mouse anti-ATG12 (Cat# MAB6807) and recombinant mouse IFN-α (Cat #:12100-1) from R&D Systems (Minneapolis, MN 55413, USA).

Techniques: Transfection, Plasmid Preparation, Expressing, Infection, Western Blot, Quantitative RT-PCR, Reverse Transcription Polymerase Chain Reaction, CRISPR, Knock-Out

Journal: Communications Biology

Article Title: Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy in mice

doi: 10.1038/s42003-020-01285-6

Figure Lengend Snippet: a , b Co-immunoprecipitation (co-IP) of FLAG-Msr1 (mouse) with Myc-tagged CHIKV proteins expressed in HEK293 cells using a mouse anti-FLAG antibody (IP), followed by immunoblotting (IB) with a rabbit anti-FLAG and anti-Myc antibody. WCE: whole-cell extract. N.S: non-specific bands. E: CHIKV envelope, C: capsid, P: non-structural protein. c co-IP of FLAG-MSR1 (human) with Myc-nsP1 in HEK293. d Immunofluorescence staining for endogenous MSR1 and CHIKV nsP1 in trophoblasts without (mock) / infected with CHIKV at a multiplicity of infection of 0.5 for 12 h. MSR1 and nsP1 were stained by a rabbit anti-MSR1 and rat anti-nsP1, followed by an Alexa Fluor-594 (red) and -488 (green) conjugated secondary antibody respectively. The cells were counterstained for nuclei by DAPI (blue). Scale bar: 20 µM. The yellow punctae in the overlay indicate co-localizations. e Co-IP of FLAG-MSR1 fragments with endogenous nsP1 in trophoblasts infected with CHIKV (MOI = 0.5 for 12 h) using a mouse anti-FLAG antibody (IP), followed by IB with a rabbit anti-FLAG and anti-nsP1 antibody. Vec: vector. Mock: mock infection. The uncropped immunoblots for all figures can be found in Supplementary Fig. .

Article Snippet: The mouse anti-FLAG (Cat# TA50011) and rabbit anti-human/mouse MSR1 (Cat# TA336699) antibodies were from Origene (Rockville, MD 20850, USA); the goat anti-mouse MSR1 (Cat# AF1797), mouse ant-human MSR1 (Cat# MAB2708), mouse anti-ATG12 (Cat# MAB6807) and recombinant mouse IFN-α (Cat #:12100-1) from R&D Systems (Minneapolis, MN 55413, USA).

Techniques: Immunoprecipitation, Co-Immunoprecipitation Assay, Western Blot, Immunofluorescence, Staining, Infection, Plasmid Preparation

Journal: Communications Biology

Article Title: Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy in mice

doi: 10.1038/s42003-020-01285-6

Figure Lengend Snippet: a Co-immunoprecipitation (co-IP) of FLAG-Atg12 with Myc-Msr1 (mouse) proteins in the presence of nsP1 in HEK293T cells using a mouse monoclonal anti-FLAG antibody, followed by immunoblotting (IB) with a rabbit anti-FLAG or Msr1 antibody. WCE: whole-cell extract. b Co-IP of FLAG-Atg12 with Myc-nsP1 in the presence of Myc-Msr1 in HEK293T cells using a mouse monoclonal anti-FLAG antibody, followed by IB with a rabbit anti-FLAG, nsP1 or Msr1 antibody. c co-IP of FLAG-Atg12 with endogenous ns1 in trophoblasts infected with CHIKV at a multiplicity of infection (MOI) of 0.5 for 12 h using a mouse anti-FLAG antibody (IP), followed by IB with a rabbit anti-FLAG and anti-nsP1 antibody. d Immunofluorescence staining for endogenous CHIKV nsP1 and LC3 in trophoblasts infected with CHIKV at a MOI of 0.5 for 12 h. The cells were counterstained for nuclei by DAPI (blue). The arrows indicate co-localizations. e Immunoblots of Myc-tagged CHIKV proteins after rapamycin (Rapa) treatment. Myc-tagged CHIKV gene expression plasmids were transfected into HEK293T cells for 24 h. The cells were then treated with 100 nM rapamycin with/without 40 μM of chloroquine (CQ) for 24 h. f The immunoblots show P62 knockout by CRISPR-Cas9 in human trophoblasts. g Immunoblots of Myc-tagged CHIKV proteins in trophoblasts after CHIKV infection. Myc-Cap, nsP1 expression plasmids were transfected into trophoblasts for 24 h. The cells were then infected with CHIKV at a MOI of 0.5 for 12 h. The uncropped immunoblots for all figures can be found in Supplementary Fig. .

Article Snippet: The mouse anti-FLAG (Cat# TA50011) and rabbit anti-human/mouse MSR1 (Cat# TA336699) antibodies were from Origene (Rockville, MD 20850, USA); the goat anti-mouse MSR1 (Cat# AF1797), mouse ant-human MSR1 (Cat# MAB2708), mouse anti-ATG12 (Cat# MAB6807) and recombinant mouse IFN-α (Cat #:12100-1) from R&D Systems (Minneapolis, MN 55413, USA).

Techniques: Immunoprecipitation, Co-Immunoprecipitation Assay, Western Blot, Infection, Immunofluorescence, Staining, Expressing, Transfection, Knock-Out, CRISPR