Journal: Gut Microbes

Article Title: Harnessing Lactiplantibacillus plantarum EP21 and its membrane vesicles to inhibit myopia development

doi: 10.1080/19490976.2025.2534677

Figure Lengend Snippet: Lactiplantibacillus plantarum EP21 membrane vesicles containing miRNAs modify inflammation and ubiquitination pathways. (a) Ingenuity pathway analysis identified the gene networks associated with inflammation and ubiquitination pathways. (b) The levels of genes associated with ubiquitination, specifically TNF alpha induced protein 3 (TNFAIP3), TNFAIP3-interacting protein 1 (TINP1), and Tax1 binding protein 1 (TAX1BP1), were significantly elevated in RPE-1 cells following treatment with EP21 MV. NC refers to the negative control condition. (c) Total protein was extracted from the retina of eyes subjected to negative control, transforming growth factor β2 (TGF-β2), and EP21 MVs treatment, and the extent of protein ubiquitination was assessed using western blot analysis. (d) RPE-1 cells underwent treatment with tumor necrosis factor (TNF) α, transfection with miRNAs or co-treatment with TNFα and miRNAs for a duration of 24 hours. The level of protein ubiquitination was evaluated through western blotting. Poly-ub: polyubiquitinated protein; free-ub: free ubiquitin. Relative free ubiquitin expression levels were determined using image J software. Relative expression levels (below the lanes) were normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH).

Article Snippet: Original Ingenuity Pathway Analysis data have been deposited at Mendeley at [DOI: 10.17632/38wctrkx3h.1] and are publicly available as of the date of publication.

Techniques: Membrane, Ubiquitin Proteomics, Binding Assay, Negative Control, Western Blot, Transfection, Expressing, Software

Journal: Scientific Reports

Article Title: Uncovering the molecular signature of feline diffuse iris melanoma through transcriptomic analysis of disease severity

doi: 10.1038/s41598-025-09632-5

Figure Lengend Snippet: Transcriptomic analysis of feline diffuse iris melanoma (FDIM). The principal component analysis (PCA) plot grouping samples by the top 500 transcripts after variance-stabilising transformation of transcript counts ( A ). There is clear and separate clustering of the iris melanosis and late FDIM samples, with the early FDIM samples overlapping both groups, showing that early FDIM is an intermediate disease stage. Volcano plots highlight the number of significantly dysregulated transcripts between early FDIM and iris melanosis ( B i), late FDIM and iris melanosis ( C i) and between late and early FDIM ( D i). A logfold-change threshold was set at − 1.5 and 1.5 and an adjusted P-value threshold of 0.05 was used. Ingenuity pathway analysis identified cancer and organismal injury and abnormalities to be the top dysregulated disease pathways between early FDIM and iris melanosis ( B ii), late and iris melanosis ( C ii) and late and early FDIM ( D ii). The disease progression of FDIM is associated with key molecular events ( E ). Tumour initiation is associated with upregulation of STOX1, PEG3, XIAP and VIM , increasing invasive tendencies and immune cell recruitment. Progression to late FDIM is characterised by downregulation of SOX11, FOXC1 and FOXC2 , likely leading to a more dedifferentiated and plastic cellular phenotype. Significant upregulation of BIRC2 and BIRC5 leads to inhibition of apoptosis. Additionally, upregulation of BIRC5, CCL2 and HAVCR2 lead to immune-microenvironment remodelling, associated with the M2 (immunosuppressive) tumour associated macrophages as well as T-regulator (Treg) cells and inhibition of cytotoxic T-cells (CTC), aiding immune escape. Created in BioRender. Kayes, D. (2025) https://BioRender.com/m39r385 .

Article Snippet: Pathway analysis and graphical display of the data was performed using QIAGEN Ingenuity Pathway Analysis (IPA; QIAGEN Inc., https://digitalinsights.qiagen.com/IPA ) – .

Techniques: Transformation Assay, Biomarker Discovery, Inhibition