Journal: bioRxiv

Article Title: Retinal ganglion cell input to superior colliculus encodes salient information

doi: 10.1101/2025.11.06.687035

Figure Lengend Snippet: ( a ) Retina flatmount from a mouse injected with AAV2/2-hSyn-GAP43-GCaMP6s into the vitreous of the eye. ( b ) Coronal brain section from the same mouse showing SC with fluorescent RGC axon terminals. ( c ) In vivo 2P fluorescence image of RGC boutons in sSC. ( d ) Example ΔF/F 0 traces and polar plots for 8 regions of interest (ROIs) circled in c , averaged across stimulus repeats. Dashed line: onset of drifting grating. Shaded areas: ± S.E.M. Polar plots: outer circle represents maximal ΔF/F 0 ; inner circle represents 50% of max ΔF/F 0 . ( e ) Direction-selective (DS) boutons color-coded by preferred direction. Gray boutons are visually responsive (max ΔF/F 0 > 10%) but not DS. Bars indicate the grating orientation and arrows indicate direction of motion, respectively. ( f ) Orientation-selective (OS) boutons color-coded by preferred orientation. Gray boutons are visually responsive but not OS. ( g ) DS boutons color-coded by preferred direction in 25 FOVs over 450 μm × 450 μm in sSC. B.V.: blood vessel. ( h ) gDSI distributions for DS (gray bars; 2268 boutons, median 0.43) or non-DS (hollow bars; 4742 boutons, median 0.19) boutons in the FOVs in g . p value: 8.63e-154. ( i ) Preferred direction distribution for DS boutons. ( j ) OS boutons color-coded by preferred orientation for the same FOVs shown in g . ( k ) gOSI distributions for OS (gray bars; 2374 boutons, median 0.33) or non-OS (hollow bars; 4636 boutons, median 0.22) boutons in j . p value: 9.89e-80. ( l ) Preferred orientation distribution for OS boutons.

Article Snippet: Before placing the cranial window onto the mouse, 5 μL of solution containing 2 μm diameter red fluorescent beads (Invitrogen FluoSpheres; diluted in phosphate buffered saline) were pipetted onto the surface of the SC to aid in adaptive optics correction of aberrations.

Techniques: Injection, In Vivo, Fluorescence

Journal: The EMBO Journal

Article Title: DNGR-1 signalling limits dendritic cell activation for optimal antigen cross-presentation

doi: 10.1038/s44318-025-00620-z

Figure Lengend Snippet: ( A – C ) ELISA for IFN-γ release from OT-I T E cells co-cultured with C9 KO MuTuDCs or those reconstituted with indicated receptors incubated with ( A ) DNGR-1L-OVA-coupled beads, ( B ) OVA-dead cells, or ( C ) SIINFEKL peptide. Mean ± SD from biological ( B , C ) duplicates or ( A ) triplicates are plotted. ( D , E ) Uptake of DNGR-1L-coupled beads by C9 KO MuTuDCs or those reconstituted with indicated receptors assessed by flow cytometry. ( D ) Representative plot depicting the use of post-uptake streptavidin staining to distinguish MuTuDCs that have internalised (in) biotinylated-DNGR-1L coupled beads from those attached to surface DNGR-1 (out). ( E ) Representative histogram of cells treated 20:1 with beads (left) and phagocytic index (% internalised beads x bead MFI/arbitrary unit) mean ± SD from biological duplicates (right). ( F – H ) Confocal microscopic analysis of lysenin-mCherry fusion protein-expressing C9 KO MuTuDCs or those reconstituted with indicated receptors co-cultured with α-DNGR-1 IgG-coupled or isotype IgG-coupled beads. Beads not internalised marked by α-rat IgG staining. ( F ) Violin plot quantification of internalised beads per cell per field of view ( n = 20). ( G ) Violin plot of lysenin-mCherry + phagosomes per cells in field of view (Lysenin index). ( H ) Representative images of lysenin-mCherry + phagosomes from indicated MuTuDCs, scale bar = 5 µm. ( I – K ) ELISA for IFN-γ release from OT-I T E cells co-cultured with KO/C9(I6G) or SHIP1 sufficient (guide control; gControl) or deficient KO/C9 MuTuDCs incubated with ( I ) DNGR-1L-OVA-coupled beads, ( J ) OVA-dead cells, or ( K ) SIINFEKL peptide. Mean ± SD from ( I – K ) biological duplicates or quadruplets (KO/C9 SHIP1 KO) are plotted. ( L ) Uptake of DNGR-1L-coupled beads by KO/C9 SHIP1 sufficient or deficient MuTuDCs assessed by flow cytometry. Phagocytic index plotted with mean ± SD from biological triplicates. Data are representative of two ( F – L ) or ≥ three ( A – C ) independent experiments. Data were analysed using Tukey-corrected two-way ANOVA with only significant values observed between KO/C9 and KO/C9(I6G) or KO/C7::C9 MuTuDCs plotted in ( A – C , E – G ) or between KO/C9 gControl and KO/C9(I6G) or KO/C9 SHIP1 KO MuTuDCs in ( I – K ). ( A , B , G , I , J ) **** P < 0.0001. See also Fig. . .

Article Snippet: Beads were washed with 1% BSA in PBS at ≥10,000× g . DNGR-1L-OVA beads were made by first incubating washed (with 1% BSA in PBS at ≥10,000× g ) 2 μm streptavidin non-fluorescent beads with 2 mg/mL ovalbumin (OVA) biotinylated using the DSB-X-biotinylation kit (Thermo Fisher Scientific) for 30 min on ice.

Techniques: Enzyme-linked Immunosorbent Assay, Cell Culture, Incubation, Flow Cytometry, Staining, Expressing, Control

Journal: bioRxiv

Article Title: Vascularized Bioengineered Kidney Using Decellularized Scaffold Recellularized with human Placenta-Derived Angiogenic stem Cells and Kidney Organoids

doi: 10.1101/2025.07.10.664023

Figure Lengend Snippet: (A), The photograph of bioengineered kidney 14 days post transplantation; (B), hPASCs promote angiogenesis: (a), Immunofluorescence of CD31 staining; (b), Statistical analysis of the density of vascular structures; (c) The immunofluorescence co-staining results of EHD3, α-SMA, and CD31 with hPASCs. (C), HE staining analysis of Glomerulus-like structure: (a), Native group; (b), DKS+hPASCs+KIO implant group. Scale bar 200 μm (up); 50 μm (down); (D), HE staining analysis of Tubule-like structure: (a), Native group; (b), DKS+hPASCs+KIO implant group. Scale bar 200 μm (up); 50 μm (down); (E), Fluorescent staining of implant: (a), The native tissue was as control; (b), Surface markers of glomerulus (NPHS1, NPHS2), collecting tube (AQP2), distal tube (NKCC2, CDH1), and proximal tube (LRP2); Scale bar 20 µm.

Article Snippet: A mixture of acrylamide and bis-acrylamide was prepared at a ratio of 5% to 0.1%, incorporating 1% fluorescent beads (0.2 μm diameter, Thermo Fisher, F8810) to create PA gels with a stiffness of 3 kPa.

Techniques: Transplantation Assay, Immunofluorescence, Staining, Control

Journal: bioRxiv

Article Title: Vascularized Bioengineered Kidney Using Decellularized Scaffold Recellularized with human Placenta-Derived Angiogenic stem Cells and Kidney Organoids

doi: 10.1101/2025.07.10.664023

Figure Lengend Snippet: (A), HE staining analysis of Glomerulus-like structure: (a), Native group; (b), DKS+hPASCs+KIO implant group. Scale bar 200 µm (up); 25 µm (down). (B), HE staining analysis of Tubule-like structure: (a), Native group; (b), DKS+hPASCs+KIO implant group.200 µm (up); 25 µm (down). (C), Fluorescent staining of implant: (a), The native tissue was as control; (b), Implant were positive for markers of glomerulus (NPHS1, NPHS2, EHD3), collecting tube (AQP2), distal tube (NKCC2, CDH1), and proximal tube (LRP2). Scale bar 20 µm. (D), ScRNA-seq analysis of implant of DKS+hPASCs+KIO using human genome: (a), Human cell types; (b), Marker genes of each cell type; (c), Specific markers. (E), The MapQuery function predicts the original cell types; (a), Vascular and immune cells were derived from hPASCs; (b), Kidney parenchymal cells originated from KIO.

Article Snippet: A mixture of acrylamide and bis-acrylamide was prepared at a ratio of 5% to 0.1%, incorporating 1% fluorescent beads (0.2 μm diameter, Thermo Fisher, F8810) to create PA gels with a stiffness of 3 kPa.

Techniques: Staining, Control, Marker, Derivative Assay