Journal: Frontiers in Cellular and Infection Microbiology

Article Title: A synergistic multi-omics approach: causal sepsis drivers identified in activated CD4 + T cells by single-cell RNA sequencing and Mendelian randomization

doi: 10.3389/fcimb.2026.1749207

Figure Lengend Snippet: Immune infiltration analysis. (A) Relative proportions of immune cell subpopulations in the control and sepsis groups. (B) Correlation matrix illustrating the associations between different immune cell types. Red indicates a positive correlation, and blue indicates a negative correlation; the intensity of the color and the size of the circles correspond to the strength of the correlation coefficient. (C) Comparison of immune cell abundance between the control and sepsis groups. Blue represents the control group, while yellow represents the sepsis group. (Note: These results are based on CIBERSORT deconvolution of bulk transcriptomic data). (D–G) Correlation analysis between the identified candidate genes and the infiltration levels of various immune cell types. *: p<0.05, **: P<0.01, ***: P<0.001, ns: not significant.

Article Snippet: While we partially addressed this via CIBERSORT deconvolution to explore neutrophil-related correlations, their specific contribution to the ‘Metabolism–Proteostasis–Immunity’ axis may not be fully captured at the single-cell level.

Techniques: Control, Comparison

Journal: Communications Biology

Article Title: Deep-learning deconvolution and segmentation of fluorescent membranes for high-precision bacterial cell-size profiling

doi: 10.1038/s42003-026-10303-y

Figure Lengend Snippet: a Example of deconvolution prediction with FM2FM. Top, input raw fluorescent membrane images (Raw FM 4-64); middle row, true deconvolved fluorescent membrane images (Deconvolved FM 4-64); bottom, FM2FM-predicted image. White squares mark regions zoomed in at right (Block 1 and Block 2). Diagonal dotted lines indicate profile traces in ( b ). Scale bars: full images, 10 µm; zoomed-in blocks, 5 µm. b Fluorescence profiles across the dotted lines in Block 1 (top) and Block 2 (bottom). Light blue, raw FM 4-64; orange, deconvolved FM 4-64; burgundy, FM2FM prediction. c , Structural similarity index measure (SSIM) between FM2FM predicted images and deconvolved images. The distribution of SSIM values across 74 image crops is shown. d Violin plots of cell width, length, surface area, volume, cross-sectional area, convex hull area, eccentricity and solidity calculated from deconvolved FM 4-64 images (orange) and FM2FM-predicted images (burgundy). The white dots and vertical lines within the violin plots represent the medians and standard deviations. P values from statistical comparisons between distributions (ANOVA or Kruskal test; see methods for details) are indicated in each panel. Twenty images (over 1000 cells) were processed and segmented with FMSeg. See the Methods for size calculation details.

Article Snippet: To compare model performance against the membrane deconvolution target (SoftWorx), we conducted qualitative assessments of output images' intensity profiles.

Techniques: Membrane, Blocking Assay, Fluorescence

Journal: bioRxiv

Article Title: Novel mouse reporter models for the detection of genome editing events in vivo

doi: 10.64898/2026.04.29.721708

Figure Lengend Snippet: a) Schematic of TLR-2 reporter allele structure and outcomes following editing. The allele includes two open reading frames encoding different fluorescent proteins; an upstream mVenus (green) in the +1 frame and downstream TagRFP (red) in the +3 frame linked by a P2A sequence. The mVenus cassette is interrupted by a 108 bp polylinker sequence that includes several guide target sequences and a stop codon (blue square). Thus in its native configuration, neither fluorescent protein is expressed. Following CRISPR/Cas9 editing, repair via NHEJ will result in expression of TagRFP if the frame shift results in a -2 deletion, or multiple thereof. Alternatively, HDR can be detected with the inclusion of a plasmid donor designed to repair the mVenus gap. b) Mouse embryo reporter validation workflow. Fertilized zygotes from TLR-2 reporter mice (typically male homozygous to WT female) are either microinjected or electroporated with Cas9 RNP with or without a plasmid donor for HDR. The embryos are then cultured to the blastocyst stage where the outcome can be scored by fluorescent imaging, and followed up by PCR-Sanger sequencing to confirm the identify of specific edits.

Article Snippet: Sanger sequence traces were analyzed using the ICE (Inference of CRISPR Editing) deconvolution tool from Synthego. ( https://ice.synthego.com ; Synthego Performance Analysis, ICE Analysis.

Techniques: Sequencing, CRISPR, Expressing, Plasmid Preparation, Biomarker Discovery, Cell Culture, Imaging