Journal: Nature Communications

Article Title: Prussian blue nanoparticles targeting multiple PANoptosome-mediated PANoptosis for myocardial ischemia-reperfusion injury therapy

doi: 10.1038/s41467-026-70012-2

Figure Lengend Snippet: A Schematic of ischemic zone (IZ), remote zone (RZ), and border zone (BZ) in human acute myocardial infarction. The heart element in the image was sourced from BioRender (Created in BioRender. xu, L. (2026) https://BioRender.com/9kka4p3 ). B UMAP visualization of cell distribution (left) and annotated cell types (right) in the control ( n = 4) versus IZ ( n = 11) groups. C Cardiomyocyte subpopulation quantification (left) and UMAP-based clustering (right) in the control and IZ groups. D , E UMAP projection ( D ) and box plots ( E ) showing PANoptosis activation across cardiac cell types. (The exact n in E = [left to right] 20, 84 cells; 17326, 3506 cells; 6231, 6969 cells; 9468, 12187 cells; 3386, 7142 cells; 3039, 2286 cells; 583, 254 cells; 531, 1138 cells). The minima, maxima, mean, median, bounds, whiskers, and percentile information were provided in the Source Data file. Exact P- values from left to right: 2.39E-265, 1.55E-300, 1.05E-35, 4.09E-05, 2.21E-06, 0.0002, 1.9E-11. F Violin plots comparing PANoptosis-related gene expression ( AIM2, ZBP1, RIPK1, Pyrin, NLRP12, NLRP3, MLKL, GSDMD, RIPK3, caspase 3, caspase 1 , and caspase 8 ) in total cells. ( n = 40706 cells [control], 33688 cells [IZ]). The minima, maxima, mean, median, bounds, whiskers, and percentile information were provided in the Source Data file. Exact P- values from left to right ( AIM2 to caspase 8 ): 0.2752, 0.0002, 0, 0.0854, 6.67E-09, 7.19E-82, 3.59E-37, 0.0709, 0.0269, 2.29E-280, 2.45E-30, 4.07E-09. G, H Cardiomyocyte-specific UMAP ( G ) and quantitative PANoptosis levels ( H ) of the control and IZ groups. (The exact n in H = [left to right] 6904 cells, 0; 5281 cells, 0; 1191, 3346 cells; 3192, 80 cells; 758, 80 cells). The minima, maxima, mean, median, bounds, whiskers, and percentile information were provided in the Source Data file. Exact P- values from left to right: 4.01E-05, 0.0021. I Proportional representation of cardiomyocyte subpopulations. J , K Heatmap depicting activation patterns of apoptosis/PANoptosis/pyroptosis/necroptosis ( J ) and PANoptosis-related genes ( K ) across cardiomyocyte subtypes. Significance: wilcox.test, a two-sided test; * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001; ns : no significant difference ( P > 0.05). Source data are provided as a Source Data file.

Article Snippet: Necrostatin-1 (HY-15760), Disulfiram (HY-B0240), Z-VAD-FMK (HY-16658B), ZBP1 (HY- P83326 ), phospho-RIPK1 (HY- P81539 ), phospho-MLKL (HY- P80468 ), cleaved caspase 1 (HY- P80622 ), cell counting kit-8 (CCK-8) assay kit (HY-K030), and cleaved caspase 8 (HY- P80624 ) were obtained from MedChemExpress, USA.

Techniques: Control, Activation Assay, Gene Expression

Journal: Nature Communications

Article Title: Prussian blue nanoparticles targeting multiple PANoptosome-mediated PANoptosis for myocardial ischemia-reperfusion injury therapy

doi: 10.1038/s41467-026-70012-2

Figure Lengend Snippet: A PCA of RNA-seq data (Sham: orange; MIRI: green; PB@PM: blue; n = 5 biologically independent replicates). B Volcano plot of differentially expressed genes (DEGs; PB@PM vs. MIRI: red/blue = up/downregulated). The Wald test of DESeq2 (DESeq(dds) default test = “Wald”) was used, which is a two-sided test. Multiple comparisons correction: the FDR (False Discovery Rate) correction of the BH (Benjamini-Hochberg) method was computed to obtain P adjustment ( P .adj.). C Venn diagram of shared DEGs between Sham-MIRI and PB@PM-MIRI comparisons. D GSVA of pathway enrichment across groups. E KEGG pathway enrichment of downregulated genes in PB@PM vs. MIRI. A one-sided hypergeometric test was used. Multiple comparisons correction: the FDR correction for the BH method was calculated to obtain P .adj. F , G GSEA networks ( F ) and protein interaction networks ( G ) for pyroptosis, apoptosis, and necroptosis. H GSEA plots showing marked downward trends of pyroptosis, apoptosis, and necroptosis in the PB@PM group compared to the MIRI group. A permutation test was used, based on weighted Kolmogorov-Smirnov-like statistics. It is a two-sided test (tests whether the enrichment scores are significantly deviated from zero, which can be positive or negative, corresponding to up- or down-regulated enrichment, respectively). Multiple comparisons correction: The FDR correction for the BH method was calculated to obtain P .adj. I Pearson correlation between pyroptosis, apoptosis, and necroptosis in the Sham (C), MIRI (I), and PB@PM (T) groups. Using psych R package, method = “spearman” function, t-test, two-sided test, and no correction for multiple comparisons. J Western blot of PANoptosis-related proteins (AIM2, ZBP1, Pyrin, ASC, FADD, Bax, Bcl-2, phosphorylated/total RIPK1/RIPK3/MLKL, cleaved/total caspase-1/3/8 and GSDMD) in ischemic myocardium (day 3; n = 5 biologically independent replicates). Source data are provided as a Source Data file.

Article Snippet: Necrostatin-1 (HY-15760), Disulfiram (HY-B0240), Z-VAD-FMK (HY-16658B), ZBP1 (HY- P83326 ), phospho-RIPK1 (HY- P81539 ), phospho-MLKL (HY- P80468 ), cleaved caspase 1 (HY- P80622 ), cell counting kit-8 (CCK-8) assay kit (HY-K030), and cleaved caspase 8 (HY- P80624 ) were obtained from MedChemExpress, USA.

Techniques: RNA Sequencing, Western Blot

Journal: Journal of Chemical Theory and Computation

Article Title: Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern

doi: 10.1021/acs.jctc.1c00965

Figure Lengend Snippet: (A) Average force profiles of WT (red), Alpha (blue), Beta (orange), Gamma (sky blue), Epsilon (green), Kappa (pink), and Delta (gray) variants as a function of the distance between the centers of mass of RBD and ACE2. (B) Initial snapshot of WT. Residues subjected to each mutation are shown as solid sticks (N501, K417, E484, L452, and T478). RBD and ACE2 are, respectively, colored in light gray and yellow. All N-glycans, water, and ions are hidden for clarity. (C) Initial snapshot of WT with clockwise 90° rotation along the normal from (B). All N-glycans are depicted in different colors. Any other residues, water, and ions are not shown for clarity.

Article Snippet: The recombinant human ACE2 protein (GenBank accession: AF291820.1, Sino Biological 10108-H08H; Wayne, PA) was labeled with RED-NHS (second Generation) dye using the Monolith Protein Labeling Kit (NanoTemper Technologies, MO-L011, München, Germany).

Techniques: Mutagenesis

Journal: Journal of Chemical Theory and Computation

Article Title: Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern

doi: 10.1021/acs.jctc.1c00965

Figure Lengend Snippet: Two-dimensional contact maps at D = 53 Å. (A) Interacting residue pairs between RBD WT and ACE2. RBD residues subjected to mutation are shown in colored boxes at the bottom: (B) blue for Alpha, (C) orange for Beta, and (D) green for Epsilon. The contact frequency is numbered with colors from light blue to dark blue. Dark red and yellow colors on the map, respectively, represent increased and decreased interactions between RBD and ACE2 upon mutations.

Article Snippet: The recombinant human ACE2 protein (GenBank accession: AF291820.1, Sino Biological 10108-H08H; Wayne, PA) was labeled with RED-NHS (second Generation) dye using the Monolith Protein Labeling Kit (NanoTemper Technologies, MO-L011, München, Germany).

Techniques: Mutagenesis

Journal: Journal of Chemical Theory and Computation

Article Title: Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern

doi: 10.1021/acs.jctc.1c00965

Figure Lengend Snippet: (A) The average number of contacts between RBD residue 501 and ACE2. (B, C) Representative snapshots at D = 53 Å of (B) Alpha variant and (C) WT. (D) Average number of contacts between RBD residue 417 and ACE2 and (E, F) their interacting residue pairs at D = 53 Å of (E) Beta and (F) Alpha variants. (G) Average number of contacts between RBD residue 478 and ACE2 and (H, I) key interaction pairs at D = 78 Å of (H) Delta and (I) Epsilon variants. The overall color scheme is the same as in Figure , and each mutated residue in each variant is shown using the same colors (i.e., red for WT, blue for Alpha, orange for Beta, green for Epsilon, and gray for Delta). Interacting residues are depicted as solid sticks, and residues losing their interactions are shown as transparent sticks. RBD and ACE2 are presented in light gray and yellow, respectively.

Article Snippet: The recombinant human ACE2 protein (GenBank accession: AF291820.1, Sino Biological 10108-H08H; Wayne, PA) was labeled with RED-NHS (second Generation) dye using the Monolith Protein Labeling Kit (NanoTemper Technologies, MO-L011, München, Germany).

Techniques: Variant Assay

Journal: Journal of Chemical Theory and Computation

Article Title: Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern

doi: 10.1021/acs.jctc.1c00965

Figure Lengend Snippet: Binding affinities between RBD variants and ACE2 and its comparison with the simulation results. K d is obtained from microscale thermophoresis experiments. F WT / F is a ratio, where F WT and F are the respective maximum pulling force of WT and of each variant obtained from the SMD simulations.

Article Snippet: The recombinant human ACE2 protein (GenBank accession: AF291820.1, Sino Biological 10108-H08H; Wayne, PA) was labeled with RED-NHS (second Generation) dye using the Monolith Protein Labeling Kit (NanoTemper Technologies, MO-L011, München, Germany).

Techniques: Binding Assay, Microscale Thermophoresis, Variant Assay

Journal: Microbial Cell Factories

Article Title: Real-time monitoring of the sugar sensing in Saccharomyces cerevisiae indicates endogenous mechanisms for xylose signaling

doi: 10.1186/s12934-016-0580-x

Figure Lengend Snippet: Yeast strains and plasmids used in the present study

Article Snippet: E. coli DH5α containing the M3499 plasmid (Addgene plasmid #51674) was purchased from Addgene (Cambridge, MA, US).

Techniques: