Journal: PLOS Pathogens

Article Title: Deciphering infected cell types, hub gene networks and cell-cell communication in infectious bronchitis virus via single-cell RNA sequencing

doi: 10.1371/journal.ppat.1012232

Figure Lengend Snippet: (a) White arrows indicate the localization of IBV N protein in AQP2-expressing collecting duct cells. Green fluorescence shows positive staining for IBV N and red fluorescence shows staining for AQP2. (b) White arrows indicate the localization of IBV N protein in CALB1-expressing distal tubule cells. Red fluorescence shows positive staining for IBV N and green fluorescence shows staining for CALB1. (c) Changes in cell communication numbers: The top network diagram shows cell clusters as nodes, with line thickness indicating changes in communication numbers. The lower heatmap details these changes, with rows representing signal-sending cells and columns indicating signal-receiving cells. The color scale reflects the inter-group differences in signal communication frequency between different cell types (number of communications in the infected group—number in control group). The bar plots at the top and right side represent the overall differences in the number of signals sent/received by specific cell clusters. (d) Changes in cell communication strength: Similar to (c), with the top network diagram displaying changes in communication strength (communication strength in the infected group—strength in the control group). In the lower heatmap, the color scale reflects the inter-group differences in signal communication strength between different cell types. The bar plots at the top and right side represent the overall differences in the strength of signals sent/received by specific cell clusters (infected group—control group). (e) Inter-group differences in the communication strength of specific signaling pathways (receptor-ligand pairs) across cell clusters. Rows represent signal pathways and columns correspond to cell clusters, with heatmap colors depicting the strength variation of signals (infect group vs. control group). Upper left triangles for signal sent and lower right triangles for signal received. The bar plot on the right side shows the overall difference in communication strength of these signaling pathways between the IBV-infected group and the control group.

Article Snippet: mouse mab calb1 , 1:200 , Boster Bio (BM0203).

Techniques: Expressing, Fluorescence, Staining, Infection, Control, Protein-Protein interactions

Journal: PLOS Pathogens

Article Title: Deciphering infected cell types, hub gene networks and cell-cell communication in infectious bronchitis virus via single-cell RNA sequencing

doi: 10.1371/journal.ppat.1012232

Figure Lengend Snippet: Antbodies and reagents used in present study.

Article Snippet: mouse mab calb1 , 1:200 , Boster Bio (BM0203).

Techniques: Blocking Assay, Immunofluorescence

Journal: The Journal of Neuroscience

Article Title: Sex-Dependent Regulation of Aromatase-Mediated Synaptic Plasticity in the Basolateral Amygdala

doi: 10.1523/JNEUROSCI.1532-16.2016

Figure Lengend Snippet: AROM expression in major subregions of rodent amygdala. A, Coronal section through anterior amygdala of an young adult mouse, immunostained for AROM using rabbit polyclonal antibodies (Yague et al., 2006). Substantial AROM expression is detectable in the MeA and CeA, in the BL and La nucleus of the BLA, and in the adjacent piriform cortex (Pir). Virtually, no AROM immunoreactivity is seen in the BM of BLA. Low levels of expression were found in the cortical amygdala (CoA). Scale bar, 250 μm. B, Western blots showing AROM protein expression in amygdala subregions CeA, BLA, and MeA of juvenile male and female rats using monoclonal antibodies against AROM (Acris). Tissue from hippocampus (Hip), cerebellum (Cer), and somatosensory cortex (Cor) was blotted for comparison. The strongest signal is found in the MeA. AROM expression levels in the CeA and BLA are comparable to levels in the hippocampus, neocortex, and cerebellum (note: a representative band for the female CeA was inserted from a different gel). C, Quantitative analysis of Western blot data, comparing AROM expression in BLA of age-matched (P20–P24) juvenile male and female rats. No difference between the sexes was evident (rel. expression of AROM: 0.46 ± 0.06 in females; 0.48 ± 0.09 in males; p = 0.88; n = 8 of each sex).

Article Snippet: Rabbit polyclonal anti-calbindin D28K antibodies (Calb; 1:2000; Merck Millipore, Billerica, MA, USA, Cat# AB1778, RRID:AB_2068336) were applied for characterization of the cultures.

Techniques: Expressing, Western Blot, Bioprocessing, Comparison

Journal: bioRxiv

Article Title: Enhanced yield and subtype identity of hPSC-derived midbrain dopamine neuron by modulation of WNT and FGF18 signaling

doi: 10.1101/2025.01.06.631400

Figure Lengend Snippet: (A) UMAP plot showing expression levels of markers of general neuronal progenitors ( VIM , NES , EDNRB , SOX9 ), cycling progenitors ( TOP2A , MKI67 , CENPF , PTTG1 ), midbrain floor progenitors ( CORIN , SHH , FOXA1 , FOXA2 , OTX2 , LMX1A , LMX1B ), dorsal diencephalic progenitors ( PAX6 , PAX3 , PAX7 ), neuroblasts ( ASCL1 , NHLH1 , NEUROD4 , NEUROD1 , NEUROG1 ), general dopamine neurons ( TH , NR4A2 , PITX3 , EN1 , DDC , SLC18A2 , SLC6A3 ), A9 mDA neurons ( ALDH1A1 , SOX6 , LMO3 ), A10 mDA neurons ( CALB1 , CALB2 ), subthalamic neurons ( IRX3 , IRX5 , PITX2 ), thalamic neurons ( LHX2 , LHX9 , LEF1 , TCF7L2 , SLC17A6 ), pretectal neurons ( MEIS2 , LHX1 , BARHL2 , TBR1 ), vLGN interneurons ( GAD1 , GAD2 , DLX1 , DLX5 , DLX6 , ARX , SLC17A6 , OTX2 , TLE4 ), red nucleus ( NKX6-1 , NKX2-2 , POU4F1 , LHX1 , LHX5 , TPH ), OMTN ( SIM1 , ISL1 , PVALB ), serotonergic neurons ( SLC6A4 ) and VLMCs ( PDGFRA , COL1A1 , COL1A2 , LUM ). (B-D) Percentage of cell types in each protocol at day 16 (B) , day 25 (C) and day 40 (D) . (E) Percentage of cells expressing EN1 , NR4A2 and TH from the scRNA-seq

Article Snippet: Mouse and chicken anti-MAP2 (1:1500, Sigma and 1:2000, Abcam), rabbit and mouse anti-TH (1:500, PelFreez and 1:1000, Immunostar), goat anti-FOXA2 (1:200, R&D), Rabbit anti-LMX1A (1:1500, Abcam), Goat anti-OTX2 (1:1000, Neuromics), rabbit and mouse anti-PAX6 (1:500, Covance and 1:200, BD-Biosciences), mouse and rabbit anti-EN1 (1:50, DSHB and 1:200 Invitrogen), goat anti-ALDH1A1 (1:250, Santa Cruz; R&D #AF5869), rabbit anti-GIRK2 (1:400, Almonte), rabbit anti-CALB1 (1:2000 Swant), and mouse anti-NURR1 (1:1500, Perseus Proteomics) were used for immuno-fluorescent staining.

Techniques: Expressing

Journal: bioRxiv

Article Title: Enhanced yield and subtype identity of hPSC-derived midbrain dopamine neuron by modulation of WNT and FGF18 signaling

doi: 10.1101/2025.01.06.631400

Figure Lengend Snippet: (A) Representative microscopy images of 1-month-old (equivalent of day 45 differentiation in vitro ) intrastriatal grafts from either Boost or Boost+ patterned progenitors (day16) on various makers, FOXA2, SC121, EN1, and ALDH1A1. Boost+ patterned neural precursors mostly maintained EN1 and ALDH1A1 expression in vivo . (B) Schematic illustration of the snRNA-seq from the grafts 1 month post implantation of the mDA neuron progenitor (day16) derived from the Boost and Boost+ method. (C) UMAP plot of 1 month grafted cells from Boost and Boost+ protocol. (D) Dotplot of canonical marker genes of midbrain progenitors, mDA neuron subtypes and off-targets (F) Percentage of mDA neurons in each protocol compared to other neuronal populations. (G) UMAP of adult midbrain dopamine neurons divided by SOX6 positive and CALB1 neurons that were selected to determine highly specific markers for A9 and A10 DA neurons, respectively. (H, I) Boxplots showing the distribution of enrichment scores for each cell type and protocol according to A9 (H) and A10 (I) mDA neurons of adult signatures. Mann-Whitney rank test and Benjamini-Hochberg correction; ∗p < 0.001.

Article Snippet: Mouse and chicken anti-MAP2 (1:1500, Sigma and 1:2000, Abcam), rabbit and mouse anti-TH (1:500, PelFreez and 1:1000, Immunostar), goat anti-FOXA2 (1:200, R&D), Rabbit anti-LMX1A (1:1500, Abcam), Goat anti-OTX2 (1:1000, Neuromics), rabbit and mouse anti-PAX6 (1:500, Covance and 1:200, BD-Biosciences), mouse and rabbit anti-EN1 (1:50, DSHB and 1:200 Invitrogen), goat anti-ALDH1A1 (1:250, Santa Cruz; R&D #AF5869), rabbit anti-GIRK2 (1:400, Almonte), rabbit anti-CALB1 (1:2000 Swant), and mouse anti-NURR1 (1:1500, Perseus Proteomics) were used for immuno-fluorescent staining.

Techniques: Microscopy, In Vitro, Expressing, In Vivo, Derivative Assay, Marker, MANN-WHITNEY

Journal: bioRxiv

Article Title: Enhanced yield and subtype identity of hPSC-derived midbrain dopamine neuron by modulation of WNT and FGF18 signaling

doi: 10.1101/2025.01.06.631400

Figure Lengend Snippet: (A) Schematic illustration of generation reporter line to isolate human grafted mDA cells expressing Tomato for snRNA-seq. (B) UMAP plot showing expression levels of markers of general neuronal progenitors ( VIM , NES , EDNRB , SOX9 ), cycling progenitors ( TOP2A , MKI67 , CENPF , PTTG1 ), midbrain floor progenitors ( CORIN , SHH , FOXA1 , FOXA2 , OTX2 , LMX1A , LMX1B ), dorsal diencephalic progenitors ( PAX6 , PAX3 , PAX7 ), neuroblasts ( ASCL1 , NHLH1 , NEUROD4 , NEUROD1 , NEUROG1 ), general dopamine neurons ( TH , NR4A2 , PITX3 , EN1 , DDC , SLC18A2 , SLC6A3 ), A9 mDA neurons ( ALDH1A1 , SOX6 , LMO3 ), A10 mDA neurons ( CALB1 , CALB2 ), subthalamic neurons ( IRX3 , IRX5 , PITX2 ), thalamic neurons ( LHX2 , LHX9 , LEF1 , TCF7L2 , SLC17A6 ), pretectal neurons ( MEIS2 , LHX1 , BARHL2 , TBR1 ), vLGN interneurons ( GAD1 , GAD2 , DLX1 , DLX5 , DLX6 , ARX , SLC17A6 , OTX2 , TLE4 ), red nucleus ( NKX6-1 , NKX2-2 , POU4F1 , LHX1 , LHX5 , TPH ), OMTN ( SIM1 , ISL1 , PVALB ), serotonergic neurons ( SLC6A4 ) and VLMCs ( PDGFRA , COL1A1 , COL1A2 , LUM ). (C) Abstracted graph showing the relationships between cell states. (D-I) Characterization of TH + and NR4A2 + cells from snRNA-seq in the graft. Percent of cells expressing gene markers TH, NR4A2, and EN1 separated by the Boost and Boost+ (D) . UMAP visualization of clusters of combined Boost and Boost+ cells ( E, left ) and UMAP visualization of clusters separated by Boost and Boost+ cells ( E, right ). UMAP visualization of selected gene markers highly correlated with cell types neuroblast, mDA neurons, A9 mDA neurons, and A10 mDA neurons (F). Percentage of each cluster of the NR4A2 or TH + filter by the Boost and Boost+ (G). KEGG-GO analysis of upregulated pathway in high expression of ALDH1A1 and CALB1 clusters (H). Plot showing pathways (or biological processes) enriched in the engrafted A9 mDA cells generated using the Boost (red) or Boost+ (green) protocol (I) .

Article Snippet: Mouse and chicken anti-MAP2 (1:1500, Sigma and 1:2000, Abcam), rabbit and mouse anti-TH (1:500, PelFreez and 1:1000, Immunostar), goat anti-FOXA2 (1:200, R&D), Rabbit anti-LMX1A (1:1500, Abcam), Goat anti-OTX2 (1:1000, Neuromics), rabbit and mouse anti-PAX6 (1:500, Covance and 1:200, BD-Biosciences), mouse and rabbit anti-EN1 (1:50, DSHB and 1:200 Invitrogen), goat anti-ALDH1A1 (1:250, Santa Cruz; R&D #AF5869), rabbit anti-GIRK2 (1:400, Almonte), rabbit anti-CALB1 (1:2000 Swant), and mouse anti-NURR1 (1:1500, Perseus Proteomics) were used for immuno-fluorescent staining.

Techniques: Expressing, Generated