Journal: Emerging Infectious Diseases

Article Title: Streptococcus gallolyticus and Bacterial Endocarditis in Swine, United States, 2015–2020

doi: 10.3201/eid2801.210998

Figure Lengend Snippet: Lesions associated with swine vegetative endocarditis, United States, 2015–2020. A) Macroscopic findings of vegetative growth on the left atrioventricular heart valve leaflets. B) Histopathologic findings of inflammation characterized by necrotic leukocytes (N), fibrin (F), mineralization (M), and myriad bacterial colonization (yellow outline) along the surface of the heart valve (hematoxylin and eosin staining); original magnification ×40. Higher magnification image (inset) shows cocci bacteria in clusters and long chains; original magnification ×1,000. C) Streptococcus gallolyticus directly detected (red) on the surface of the heart valve by RNA in situ hybridization with a probe targeting the helix-hairpin helix domain–containing protein, ComEC/Rec2, and DNA pol III subunit delta genes specific to S. gallolyticus ; original magnification ×40. Higher magnification image (inset) shows the bacteria labeled by the in situ hybridization probe; original magnification ×1,000.

Article Snippet: For selected cases from which pure growth of S. gallolyticus was isolated from the heart valves, we performed bacterial biochemical analyses, sequenced 16S ribosomal RNA, and localized S. gallolyticus within lesions via RNA in situ hybridization (ISH) (RNAscope; TriStar Technology LLC, https://tristargroup.us ).

Techniques: Staining, Bacteria, RNA In Situ Hybridization, Labeling, In Situ Hybridization

Journal: Nature

Article Title: Repeated head trauma causes neuron loss and inflammation in young athletes

doi: 10.1038/s41586-025-09534-6

Figure Lengend Snippet: a . UMAP depicting excitatory neurons colored by layer subtype. b,c . Heatmap showing GO analysis of (b) excitatory layer and (c) inhibitory layer up and downregulated DEGs. n = 28 individuals. Statistics generated with GSEA and single-tailed hypergeometric test with Benjamini-Hochberg multiple hypothesis correction. d . Bar plots of excitatory neuron layer proportions by pathological group. Bar represents mean, dots represent individual samples, error bars show standard error of the mean. Statistical analysis performed by ANOVA with Bonferroni correction. Tests were two tailed. n = 28 individuals. e . UMAP showing inhibitory neurons colored by layer subtype. f . Bar plots of inhibitory neuron layer proportions by pathological group. Bar represents mean, dots represent individual samples, error bars show standard error of the mean. Statistical analysis performed by ANOVA with Bonferroni correction. Tests were two tailed. n = 28 individuals. g . Representative image showing RNAScope in situ hybridization of CUX2/LAMP5 image analysis with correct anatomical layer-wise distribution. White squares showing HALO identification of double-positive cells. Scale bar = 1 mm. h . Representative image of Nissl+ staining and neuronal masking using HALO AI. Top box is the raw image and bottom box is AI generated mask over neurons. Scale bar = 50 µm.

Article Snippet: Analysis of fluorescent RNAScope fluorescence in situ hybridization (FISH) was performed in Indica Labs HALO using the FISH v.3.2.3 algorithm or the FISH-IF v.2.2.5 algorithm.

Techniques: Generated, Two Tailed Test, RNAscope, In Situ Hybridization, Staining

Journal: Nature

Article Title: Repeated head trauma causes neuron loss and inflammation in young athletes

doi: 10.1038/s41586-025-09534-6

Figure Lengend Snippet: a , Circos plots from MultiNicheNet analysis depicting microglia as sender cells. RHI comparison with control is labelled RHI; CTE comparison with RHI is labelled CTE. n = 28 individuals. b , RNAScope in situ hybridization depicting a TGFB1 + microglia ( P2RY12 ; solid arrowheads) contacting a ITGAV + TGFBR2 + vessel ( GLUT1 ; open arrowheads). Scale bars, 10 μm. c , d , Quantification of in situ hybridization of TGFB1 + microglia ( c ) and ITGAV + TGFBR2 + vessels ( d ) in the grey matter sulcus with years of football play, colour-coded by pathological group. Each dot represents an individual donor. Statistical analysis performed by simple linear regression. The black line represents general linear model regression; the grey region shows the 95% confidence interval. The test was two-tailed. n = 19 individuals. e , Bar plot representing ITGAV + TGFBR2 + vessels with CTE status. Statistical analysis performed using a two-tailed t -test. Data are mean ± s.e.m. The test was two-tailed. n = 19 individuals. f , The proportion of TGFB1 + microglia within 25 μm of a ITGAV + TGFBR2 + vessel with CTE status. Statistical analysis performed using a two-tailed t -test. n = 19 individuals. Data are mean ± s.e.m. g , Scatter plots depicting ITGAV + TGFBR2 + vessels in the grey matter sulcus with the fraction of CUX2 + LAMP5 + neurons colour-coded by pathological group. Each dot represents an individual donor. Statistical analysis performed by simple linear regression. n = 17 individuals. The black line represents general linear model regression; the grey region shows the 95% confidence interval. The test was two-tailed.

Article Snippet: Analysis of fluorescent RNAScope fluorescence in situ hybridization (FISH) was performed in Indica Labs HALO using the FISH v.3.2.3 algorithm or the FISH-IF v.2.2.5 algorithm.

Techniques: Comparison, Control, RNAscope, In Situ Hybridization, Two Tailed Test