Journal: Cells

Article Title: Astro-Versus Microglia-Enriched Transcriptomes from Aged Atxn2 -CAG100-Knockin Mice Suggest Underlying Pathology of RNA Processing at Ribosomes, and Possibly at U-Bodies

doi: 10.3390/cells15080699

Figure Lengend Snippet: Purity validation of isolated microglia, astrocytes, and neurons. ( A ) Expression of specific markers in the gene sequencing data of 10-month-old mice. ( B ) Viable cell counts from 3-day-old wild-type mice ( n = 3). Data are mean ± SEM. ( C ) Immunofluorescence staining of microglia with the marker IBA1, astrocytes with GFAP, and neurons with MAP2 after 5 days in culture. DAPI was used for staining the nucleus. Scale bar: 5 µM.

Article Snippet: The following Taqman assays were used: Aif1 : Mm00520165_m1, Atxn2 : Mm01199894_m1, Cd31 : Mm01242576_m1, Cldn5 : Mm00727012_s1, Dlg4 : Mm00492193_m1 Gfap : Mm01253033_m1, Kcnj8 : Mm00434620_m1, Map2 : Mm00485231_m1, Olig2 : Mm01210556_m1, Tmem119 : Mm00525305_m1, and Tbp : Mm00446973_m1.

Techniques: Biomarker Discovery, Isolation, Expressing, Sequencing, Immunofluorescence, Staining, Marker

Journal: Redox Biology

Article Title: Excessive ER-mitochondria coupling: A DRP1-driven mechanism underlying mitochondrial dysfunction and impaired autophagy in stress-induced depression-like behavior in mice

doi: 10.1016/j.redox.2026.104121

Figure Lengend Snippet: CSDS upregulates Drp1 expression in hippocampal neurons. A) Differential protein volcano map of CSDS group and Control group (n = 3 samples per group; each sample pooled from 6 hippocampi). Red: significantly upregulated (fold change >1.5); blue: significantly downregulated (fold change >1.5); gray: non-significant. B) CO-IP analysis of Drp1 protein and its ubiquitination level in hippocampus of three groups of mice. One-way ANOVA with Tukey's multiple comparisons test (Treatment, F (2, 15) = 162.8, P < 0.0001; Treatment, F (2, 15) = 12.10, P = 0.0007). Data are expressed as mean ± SEM (n = 6 mice per group). ∗∗ p < 0.01, ∗∗∗ p < 0.001 C) Representative images of Drp1 (green), MAP2 (neuron, red) and DAPI (nucleus, blue) in CA1 of two groups (left) and Pearson correlation coefficient was quantitatively analyzed (right, n = 5 mice brain slices). Scale bar: 50 μm. D) Experimental timeline of viral injection and CSDS modeling; Representative confocal Z-stack 3D reconstructed images of dendritic spines in CA1 (left) and dendritic spines was quantitatively analyzed (right, n = 5 mice brain slices). Scale bar: 2 μm. Student's t -test (P = 0.0041; P = 0.0006). Data are expressed as mean ± SEM. ∗∗ p < 0.01, ∗∗∗ p < 0.001. E) Representative images of Drp1 (green), VGLUT2 (Neuron, red) and DAPI (nucleus, blue) in hippocampal CA1 region of two groups (left) and the percentage of co-localized fluorescence was quantified (right). Scale bar: 50 μm. Two-way ANOVA with Tukey's multiple comparisons test (Interaction, F (2, 24) = 2.671, P = 0.0897). The data were expressed as mean ± SEM (n = 5 mice brain slices). ns, p > 0.05.

Article Snippet: Multiplex staining was performed using TSA-based immunofluorescence with primary antibodies: Drp1 (CST 12741S, 1:100), MAP2 (ab32454, 1:1000), GFAP (CST 12389, 1:400), IBA1 (ab178846, 1:1000), Vglut1 (CST #27181, 1:800), Vglut2 (ab216463, 1:250), OLIG2 (CST #65915, 1:400), and LAMP1 (CST 99437S, 1:100).

Techniques: Expressing, Control, Co-Immunoprecipitation Assay, Ubiquitin Proteomics, Injection, Fluorescence

Journal: bioRxiv

Article Title: A multi-omic atlas in the African turquoise killifish reveals increased glucocorticoid signaling as a hallmark of brain aging

doi: 10.64898/2026.04.09.717549

Figure Lengend Snippet: ( a ) Scheme for cell type-level analysis of the aging African turquoise killifish brain. Analyses were performed using the annotated snRNA-seq and snATAC-seq datasets. Changes in cell type proportion with aging were validated using RNAscope in-situ hybridization. ( b-c ) Annotated cell type abundances in the snRNA-seq brain atlas for the GRZ and ZMZ-1001 strains ( b ) and in the snATAC-seq brain atlas for the GRZ strain ( c ). ( d-e ) Cell type proportion change analysis with aging across sexes based on our snRNA-seq ( d ) and snATAC-seq ( e ) datasets using scProportionTest. Left-shifted cell types are more abundant in young brains and right-shifted cell types are more abundant in old brains. Data is colored according to significance, with significant changes corresponding to FDR < 5% based on scProportionTest statistics. Note consistent increases in microglia proportion with aging across comparisons. ( f ) Representative maximum z-projected images using 4-plex RNAscope for each of the GRZ conditions’ cell-type markers: apoeb in yellow , mpz in green , s100b in magenta , map2 in red and DAPI is in blue. See Extended Data Figure 5a for representative images from the ZMZ-1001 strain. Scale bars are 250mm in length. ( g ) Quantification of cell abundances in African turquoise killifish brain samples using top markers for in-situ hybridization by RNAscope. Values for each animal are reported as the average QuPath inferred values obtained across 3 Z-planes. Note that for this sample set, the middle-aged time point for GRZ corresponds to 13-week-old (rather than 10-week-old) fish. The effect of age and sex were evaluated using ANOVA for normally distributed data (GRZ astrocytes, microglia and neurons; ZMZ-1001 astrocytes, neurons, and oligodendrocytes) and non-parametric ART-ANOVA for non-normally distributed data (GRZ oligodendrocytes, ZMZ-1001 microglia). Normality of ANOVA residuals was determined using a Shapiro-Wilkes test, with p < 0.05 indicating violation of the normality assumption. Y: Young (6-7-week-old), M: middle-aged (13-week-old), O: Old (16-week-old), G: Geriatric (26-week-old). F: Female, M: Male.

Article Snippet: To develop the fluorescent signal, TSA Vivid Fluorophore 520 (Advanced Cell Diagnostics, 323272) was used to mark apoeb , TSA Vivid Fluorophore 570 (Advanced Cell Diagnostics, 323271) was used to mark mpz , Opal 620 (Akoya Biosciences, FP1495001KT) was used to mark s100b , and Opal 690 (Akoya Biosciences, FP1497001KT) was used to mark map2 .

Techniques: RNAscope, In Situ Hybridization

Journal: bioRxiv

Article Title: DNA damage drives a unique, Alzheimer’s disease-relevant senescent state in neurons

doi: 10.64898/2026.04.02.716205

Figure Lengend Snippet: Protein level differences in senescence-associated markers further distinguish neuronal and fibroblast responses to DNA damage (A) Schematic of immunocytochemistry (ICC) performed after IR in healthy dermal fibroblasts and iNs from the same donors (donors: A27, A48, ID98; 3 technical replicates per donor in each condition). 0.2% FBS low serum (LS) treatment was applied to CTL and IR fibroblasts to induce quiescence 72 hours prior to collection. (B) IR iNs and IR fibroblasts were stained for p21 (top left), p16 (top right), LMNB1 (bottom left), and HMGB1 (bottom right). Mean nuclear fluorescence intensity was quantified. (C) Nuclear area of IR iNs and IR fibroblasts quantified by DAPI staining (donors: A27, A48, ID98, 18 technical replicates per donor in each condition). (D) PSD95 staining for IR iNs and IR fibroblasts, imaged by confocal microscopy, and analyzed by Imaris to detect PSD95 spots on MAP2-positive dendrites and normalize to dendrite surface area. Two donors used for PSD95 staining (donors: A27, A48; 3 technical replicates per donor in each condition; donor A48 images and quantification shown in ). Tracks on MAP2 traced in Illustrator. All iNs imaged were quantified with automatic MAP2 tracing to measure p21, p16, LMNB1, HMGB1, and DAPI only in neuronal nuclei or PSD95 only in neuronal dendrites (Supp. Fig. 5). Imaging was performed on the Harmony Operetta CLS system at 63X unless otherwise stated. Nuclear intensity quantification of images performed by the Harmony analysis system and nuclei number after IR provided in Supp. Fig. 4. Statistics were calculated using multiple unpaired t-tests using Welch’s correction with Holm–Šídák adjustment for multiple testing with alpha = 0.05. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns: not significant, nd: not detected.

Article Snippet: Cells were then incubated with primary antibodies at 4°C overnight (γH2AX, abcam, ab81299, 1:250; 1:1000; pATM, Life Technologies, MA1-2020, 1:250; p21, abcam, ab109520, 1:100; p16, abcam, ab270058, 1:50; LMNB1, abcam, ab229025, 1:1000; HMGB1, abcam, ab79823, 1:250; 53BP1, abcam, ab175933, 1:200, PSD95, Life Technologies, MA1-046, 1:300; MAP2, Novus Biologicals, NB300-213, 1:400).

Techniques: Immunocytochemistry, Staining, Fluorescence, Confocal Microscopy, Imaging

Journal: bioRxiv

Article Title: DNA damage drives a unique, Alzheimer’s disease-relevant senescent state in neurons

doi: 10.64898/2026.04.02.716205

Figure Lengend Snippet: DNA damage induces greater damage lesions and a slower DNA repair-associated response in neurons compared to fibroblasts (A) Schematic of immunocytochemistry (ICC) performed over time after IR in healthy dermal fibroblasts and iNs from the same donors (donors: A48, ID97; 3 technical replicates per donor in each condition). (B-D) iNs and fibroblasts were stained for 53BP1 (B), γH2AX (C), and pATM (D) at 0 min, 15 min, 2h, and 24h after IR with magnified images from the viewfield in the bottom right of each image. Relative fold change (right panels) was calculated from mean foci number per nucleus (middle panels). All iNs imaged were quantified with automatic MAP2 tracing to measure 53BP1, γH2AX, and pATM foci only in neuronal nuclei (Supp. Fig. 5). Imaging was performed on the Harmony Operetta CLS system at 63X. Foci quantification of images performed by the Harmony analysis system. Intensity over time without relative fold change calculations provided in Supp. Fig. 6 along with nuclei number over time after IR. Statistics were calculated by two-way ANOVA (or Mixed Model) and corrected for multiple comparisons using the Dunnett method and reporting multiplicity-adjusted p-value for each comparison with alpha = 0.05. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns: not significant, nd: not detected.

Article Snippet: Cells were then incubated with primary antibodies at 4°C overnight (γH2AX, abcam, ab81299, 1:250; 1:1000; pATM, Life Technologies, MA1-2020, 1:250; p21, abcam, ab109520, 1:100; p16, abcam, ab270058, 1:50; LMNB1, abcam, ab229025, 1:1000; HMGB1, abcam, ab79823, 1:250; 53BP1, abcam, ab175933, 1:200, PSD95, Life Technologies, MA1-046, 1:300; MAP2, Novus Biologicals, NB300-213, 1:400).

Techniques: Immunocytochemistry, Staining, Imaging, Comparison