Journal: The EMBO Journal

Article Title: The TPR2 corepressor forms condensates with repressors to fine-tune growth and development in rice

doi: 10.1038/s44318-026-00852-7

Figure Lengend Snippet: ( A ) Volcano plot showing differentially expressed genes (DEGs) between WT and tpr2 (left, n = 2 biological replicates per group); and between COM-FL and tpr2 (right, n = 2 biological replicates per group). Differential expression analysis was performed using DESeq2 based on a negative binomial generalized linear model with Benjamini–Hochberg false discovery rate (FDR) correction for multiple testing. Genes with |log₂ (fold change)|>0.5 and adjusted p < 0.05 were considered significantly differentially expressed (red: upregulated; blue: downregulated; gray: not significant). ( B ) Venn diagram showing the overlap of downregulated DEGs in WT vs tpr2 (3987 DEGs) and COM-FL vs tpr2 (2088 DEGs). 837 DEGs were common to both comparisons. ( C ) Heatmap of 837 overlapping DEGs across WT, tpr2 , COM-FL, COM-ΔIDR1, COM-M6, and COM-M8 plants. Gene expression levels are shown as FPKM values (red, high; blue, low). ( D ) Immunoblot analysis of histone acetylation levels in WT and tpr2 seedlings. H3 acetylation was detected with anti-H3ac, anti-H3K9ac, anti-H3K14ac, anti-H3K18ac, anti-H3K23ac and anti-H3K27ac antibodies. Total H3 was used as a loading control. Experiments were independently repeated at least three times with similar results. ( E ) Immunoblot analysis of H3K9 acetylation levels in WT, tpr2 , COM-ΔIDR1, COM-M6 and COM-M8 lines. Histone extracts from WT, tpr2 , COM-ΔIDR1, COM-M6, and COM-M8 seedlings were subjected to immunoblotting using anti-acetyl-H3K9 antibody. Total H3 was used as a loading control. Experiments were independently repeated at least three times with similar results. ( F ) Density distribution of H3K9ac signals across the gene body of the 837 DEGs. Genes are grouped by genotype: tpr2 , COM-FL, COM-ΔIDR1, COM-M6, and COM-M8. TSS, transcription start site; TES, transcription end site. ( G ) Heatmap of H3K9ac CUT&Tag signals upstream and downstream of the gene body. Regions include 3000 bp upstream of TSS and 3000 bp downstream of TES. Data were representative of two independent experiments. .

Article Snippet: anti-H3ac , ABclonal , Cat#A17917.

Techniques: Quantitative Proteomics, Gene Expression, Western Blot, Control

Journal: The EMBO Journal

Article Title: The TPR2 corepressor forms condensates with repressors to fine-tune growth and development in rice

doi: 10.1038/s44318-026-00852-7

Figure Lengend Snippet: ( A ) Volcano plot showing differentially expressed genes (DEGs) between WT and tpr2 (left, n = 2 biological replicates per group); and between COM-FL and tpr2 (right, n = 2 biological replicates per group). Differential expression analysis was performed using DESeq2 based on a negative binomial generalized linear model with Benjamini–Hochberg false discovery rate (FDR) correction for multiple testing. Genes with |log₂ (fold change)|>0.5 and adjusted p < 0.05 were considered significantly differentially expressed (red: upregulated; blue: downregulated; gray: not significant). ( B ) Venn diagram showing the overlap of downregulated DEGs in WT vs tpr2 (3987 DEGs) and COM-FL vs tpr2 (2088 DEGs). 837 DEGs were common to both comparisons. ( C ) Heatmap of 837 overlapping DEGs across WT, tpr2 , COM-FL, COM-ΔIDR1, COM-M6, and COM-M8 plants. Gene expression levels are shown as FPKM values (red, high; blue, low). ( D ) Immunoblot analysis of histone acetylation levels in WT and tpr2 seedlings. H3 acetylation was detected with anti-H3ac, anti-H3K9ac, anti-H3K14ac, anti-H3K18ac, anti-H3K23ac and anti-H3K27ac antibodies. Total H3 was used as a loading control. Experiments were independently repeated at least three times with similar results. ( E ) Immunoblot analysis of H3K9 acetylation levels in WT, tpr2 , COM-ΔIDR1, COM-M6 and COM-M8 lines. Histone extracts from WT, tpr2 , COM-ΔIDR1, COM-M6, and COM-M8 seedlings were subjected to immunoblotting using anti-acetyl-H3K9 antibody. Total H3 was used as a loading control. Experiments were independently repeated at least three times with similar results. ( F ) Density distribution of H3K9ac signals across the gene body of the 837 DEGs. Genes are grouped by genotype: tpr2 , COM-FL, COM-ΔIDR1, COM-M6, and COM-M8. TSS, transcription start site; TES, transcription end site. ( G ) Heatmap of H3K9ac CUT&Tag signals upstream and downstream of the gene body. Regions include 3000 bp upstream of TSS and 3000 bp downstream of TES. Data were representative of two independent experiments. .

Article Snippet: anti-H3K18ac , ABclonal , Cat#A7257.

Techniques: Quantitative Proteomics, Gene Expression, Western Blot, Control

Journal: bioRxiv

Article Title: A designed overlapping variant immunogen pool elicits broad sarbecovirus neutralization

doi: 10.64898/2026.06.03.729821

Figure Lengend Snippet: (A) Design and execution of an immunogen efficacy experiment to test the longevity of protection against SARS-CoV-2 variants that might emerge after immunization. Mice received two doses of immunogen, and were challenged one year later with whatever SARS-CoV-2 variant was prevalent one year after the design of the immunogen. (B-F) Neutralizing titers (NT 50 ) over time (up to 1 year) against SARS-CoV-2 Wu , SARS-CoV-2 XBB, SARS-CoV-2 KP2/3 pseudotypes in mouse sera after immunization with two doses of the indicated immunogens. Graph title indicates immunogen, each line represents 1 mouse, n = 6 mice per group. Dotted line indicates the lowest sera dilution tested (1:50). (G) SARS-CoV-2 KP.3.1 lung viral loads on day 3 after infection of K18-hACE2 mice, immunized one year previously with two doses of indicated immunogen. Each symbol represents mean of measurements from the left lung and right lung of each mouse, black line = group median. Dotted line indicates limit of detection. (H) Lung viral loads (rVSV/SARS-1 RNA copies per μg total RNA) on day 3 after infection of K18-hACE2 IFNAR(-/-) mice, immunized 12 weeks prior with two doses of indicated immunogen. Each symbol represents one mouse lung, each line represents group median. Dotted line indicates limit of detection.

Article Snippet: All mouse studies were performed in compliance with the Rockefeller University Institutional Animal Care and Use Committee (IACUC) according to animal protocol 24016-H. For analysis of neutralizing antibody responses, ten-week old C57BL/6 (JAX Strain #000664) and K18-hACE2 transgenic mice expressing the human ACE [B6.

Techniques: Variant Assay, Infection

Journal: bioRxiv

Article Title: A designed overlapping variant immunogen pool elicits broad sarbecovirus neutralization

doi: 10.64898/2026.06.03.729821

Figure Lengend Snippet: (A,B) Comparison of neutralizing titers (NT 50 ) against SARS-CoV-2 variant pseudotypes in mouse sera 12 and 51 weeks post-immunization with two doses of indicated immunogen. Each symbol represents 1 mouse, lines = group mean, n = 5-6 mice per group. Dotted line indicates the lowest sera dilution tested (1:50). (C) Validation of SARS-CoV-2 challenge virus stocks, KP.3 and KP.3.1. Lung viral loads (SARS-CoV-2 RNA copies per μg total RNA) on day 3 after infection of K18-hACE2 mice. Each symbol represents 1 mouse, lines = group geometric mean, n=5 mice per group (D) Lung viral loads (rVSV/SARS-1 RNA copies per μg total lung RNA) on each of the indicated hours after infection of K18-hACE2 IFNAR(-/-) mice. Each symbol represents 1 mouse, dotted line=limit of detection.

Article Snippet: All mouse studies were performed in compliance with the Rockefeller University Institutional Animal Care and Use Committee (IACUC) according to animal protocol 24016-H. For analysis of neutralizing antibody responses, ten-week old C57BL/6 (JAX Strain #000664) and K18-hACE2 transgenic mice expressing the human ACE [B6.

Techniques: Comparison, Variant Assay, Biomarker Discovery, Virus, Infection