Journal: bioRxiv

Article Title: Bacterial targeting of host paraspeckles uncovers a new SFPQ-based regulation

doi: 10.64898/2026.01.11.698932

Figure Lengend Snippet: ( A ) Schematic representation of L. pneumophila LpDot1 and other eukaryotic DOT1-like proteins ( Homo sapiens [Q8TEK3], Acanthamoeba castellanii Strain C3 [FUN_002004, FUN_005565], Telotrochidium [P10K-MW-000057|gene13722], Sessilida [P10K-MW-000059|gene19854], and Astrophomene gubernaculifera [P10K-MW-000389|gene4536]). InterPro and PROSCAN were used to identify conserved motifs or domains (red: DOT1 catalytic domain with dark lines: catalytic conserved motifs; yellow: nuclear localization signal (NLS); purple: variable nuclear binding domains. ( B ) In vitro MTase assay of LpDot1 or human DOT1L recombinant proteins with calf thymus histones as substrate in the presence of 14 C-SAM as a methyl donor. Upper panel : 14 C radiography; Bottom panel amido black (AB) staining. ( C ) Crystal structure of LpDot1 (blue cartoon) with bound S-adenosyl-L-homocysteine (SAH, ball-and-stick representation) showing the conserved Class I SAM-dependent methyltransferase fold. (D) Structural superposition of LpDot1 with human DOT1L (yellow/green semi-transparent cartoon). Note the absence of critical histone-binding regions in the bacterial enzyme: a 14-residue loop and extended C-terminal α-helix (highlighted in green) essential for nucleosome binding in human DOT1L. (E) Electrostatic potential surfaces of bacterial ( left ) and human ( right ) enzymes. Dashed boxes highlight substrate-binding regions, showing highly charged features optimized for histone interactions in human DOT1L (bound SAH in ball-and-stick) versus LpDot1’s neutral profile with distinct gate loops closing the SAM-binding pocket

Article Snippet: Acanthamoeba castellanii strain C3 (ATCC 50739) trophozoites were grown at 20°C in PYG medium ass described .

Techniques: Binding Assay, In Vitro, Recombinant, Staining, Residue

Journal: iScience

Article Title: Ubiquitination and degradation of CD47 enhances macrophage phagocytosis of hemolytic erythrocytes

doi: 10.1016/j.isci.2025.114499

Figure Lengend Snippet: Erythrocyte ghosts from complement-induced hemolysis are phagocytized by macrophage (A) In vitro complement-mediated hemolysis model diagram. (B) A deep vein thrombosis mouse model diagram. (C and D) Representative images (C) of thrombi and statistical analysis (D) in deep vein thrombosis mice ( n = 6). Scale bars = 1 mm. (E) The C3 inhibitor therapy diagram of complement-induced hemolysis in mice. (F and G) Representative images (F) of thrombi and statistical analysis (G) in deep vein thrombosis mice after plasma or C3 inhibitor treatment ( n = 6). Scale bars = 1 mm. (H) Phagocytosis co-culture model diagram. (I) Representative immunofluorescence images of co-cultured RBCs and macrophages in control and hemolysis groups. The scale bar represents 20 μm in the overall image and 10 μm in the magnified images. (J) Statistical analysis of the number of RBCs around the nuclei of macrophages after co-culture ( n = 6). Data were analyzed by Student’s t test (two groups) or one-way ANOVA with Tukey’s test (multiple groups) and are expressed as mean ± SEM. ∗∗∗ p < 0.001, ∗∗ p < 0.01, ∗ p < 0.05, ns means no significance.

Article Snippet: In inhibition experiments, the C3 inhibitor (Cp40 TFA, 4 mg/kg, MedChemExpress, Cat# HY-P1717A) was administered 30 minutes prior to the experiment.

Techniques: In Vitro, Clinical Proteomics, Co-Culture Assay, Immunofluorescence, Cell Culture, Control

Journal: bioRxiv

Article Title: Consumption of processed foods impairs memory function through dietary advanced glycation end-products

doi: 10.64898/2026.01.07.698065

Figure Lengend Snippet: a , Illustration of the electrophysiology field potential recording setup. b , Ratio of field to volley from electrophysiology field potential recordings of dorsal hippocampus (HPCd) brain tissue slices in rats after 30-d early life AGE-rich diet (n=14 CTL tissue slices, n=15 AGE-rich tissue slices; 2-way repeated measures ANOVA with factors of diet group, fiber volley amplitude [repeated measure], and diet group × fiber volley interaction; P=0.04 diet group, P<0.0001 fiber volley amplitude, P=0.99 diet group × fiber volley amplitude). c , mRNA expression of complement component 3 (C3) in the HPCd (n=7 CTL, n=7 AGE-rich; unpaired two-tailed t-test, P=0.04). d , mRNA expression of complement component 5 (C5) in the HPCd (n=7 CTL, n=7 AGE-rich; unpaired two-tailed t-test, P=0.68). e , mRNA expression of C3aR in the HPCd (n=7 CTL, n=7 AGE-rich; unpaired two-tailed t-test, P=0.17). f , mRNA expression of C5aR1 in the HPCd (n=8 CTL, n=7 AGE-rich; unpaired two-tailed t-test, P=0.16). g , Structures of the peptide required for complement system receptor activation and of AGEs elevated in the heat-treated diet. h , C5aR1 pERK 1/2 signaling in response to MG-H1, CML, and CEL (smoothed lines indicate nonlinear least squares fit for each treatment). i , C5aR1 Receptor-G protein-Bioluminescence Resonance Energy Transfer (RG-BRET) assay for binding affinities between C5a and MG-H1, CML, CEL, or the C5aR1-selective antagonist avacopan (smoothed lines indicate nonlinear least squares fit for each treatment). Error bars represent standard error of the mean (SEM). *P<0.05. All n’s indicate number of rats or slices per group. Additional details about the statistical analyses for each subpanel can be found in . AGE, advanced glycation end-product; ANOVA, analysis of variance; C3, complement component 3; C3aR, receptor for complement component 3a; C5, complement component 5; C5aR1, receptor for complement component 5a; CA1, Cornu Ammonis subfield 1; CA3, Cornu Ammonis subfield 3; EC, entorhinal cortex; CEL, carboxyethyllysine; CML, carboxymethyllysine; CTL, control [diet]; HPCd, dorsal hippocampus; MG-H1, methylglyoxal-derived hydroimidazolone; pERK, phospho-extracellular signal-regulated kinase; PN, postnatal day; RG-BRET, Receptor-G protein-Bioluminescence Resonance Energy Transfer.

Article Snippet: The following Applied Biosystems probes for use with rats were used: C3 (Rn00566466_m1), C5 (Rn01436156_m1), C3aR (Rn00583199_m1), C5aR1 (Rn02134203_s1), RAGE (Rn01525753_g1), NfĸB (Rn01502266_m1), PSD-95 (Rn00571479_m1), occludin (Rn00580064_m1), claudin-1 (Rn00581740_m1), claudin-5 (Rn01753146_s1), and mucin 2 (Rn01498206_m1). qPCR was performed using Applied Biosystems TaqMan Fast Advanced Master Mix (Cat. no. 444557, ThermoFisher Scientific) and an Applied Biosystems QuantStudio 5 Real-Time PCR System (ThermoFisher Scientific).

Techniques: Expressing, Two Tailed Test, Activation Assay, Bioluminescence Resonance Energy Transfer, Binding Assay, Control, Derivative Assay