Journal: Biofilm

Article Title: Genomic insights into activated antimicrobial resistance of in situ hospital-wastewater biofilm

doi: 10.1016/j.bioflm.2026.100377

Figure Lengend Snippet: Characteristics of in situ biofilm and hospital wastewater samples. ( a ) Placement of plastic slides in hospital wastewater for in situ biofilm formation and collection of wastewater sample. ( b ) In situ biofilm samples before and after crystal-violet staining. ( c ) Fluorescent staining of in situ biofilm structure: green, red, and blue represent nucleic acids, proteins, and polysaccharides, respectively. ( d ) Comparison of contamination levels based on antimicrobial resistance between hospital wastewater and in situ biofilm. Statistical analysis using unpaired t -test; ∗∗∗p < 0.0001. DHL: deoxycholate hydrogen sulfide lactose, CTX: cefotaxime. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Article Snippet: For fluorescence staining, nucleic acid was stained with cell-permeant SYTO 9 (Thermo Fisher Scientific, Waltham, MA, USA), proteins were stained with FilmTracerTM SYPROTM Ruby Biofilm Matrix Stain (Thermo Fisher Scientific), and polysaccharides were stained with Concanavalin A conjugated to tetramethylrhodamine (Thermo Fisher Scientific).

Techniques: In Situ, Staining, Comparison

Journal: Biofilm

Article Title: Genomic insights into activated antimicrobial resistance of in situ hospital-wastewater biofilm

doi: 10.1016/j.bioflm.2026.100377

Figure Lengend Snippet: Taxonomic and functional gene profiles of in situ biofilm and hospital wastewater based on shotgun metagenomic data. Relative abundance of bacterial taxa at the order ( a ) and family ( b ) levels in in situ biofilm and hospital wastewater samples. ( c ) Distribution of genes associated with resistance to antibiotics, biocides, acids, heat, and metals, as well as virulence, shown at the metagenome-assembled genome (MAG) and contig levels for biofilm (BF) and hospital wastewater (HW). MLS: macrolide-lincosamide-streptogramin.

Article Snippet: For fluorescence staining, nucleic acid was stained with cell-permeant SYTO 9 (Thermo Fisher Scientific, Waltham, MA, USA), proteins were stained with FilmTracerTM SYPROTM Ruby Biofilm Matrix Stain (Thermo Fisher Scientific), and polysaccharides were stained with Concanavalin A conjugated to tetramethylrhodamine (Thermo Fisher Scientific).

Techniques: Functional Assay, In Situ

Journal: Biofilm

Article Title: Genomic insights into activated antimicrobial resistance of in situ hospital-wastewater biofilm

doi: 10.1016/j.bioflm.2026.100377

Figure Lengend Snippet: Network analysis of metagenome-assembled genomes, functional genes, and mobile genetic elements based on shotgun metagenomic data. Networks of metagenome-assembled genomes (MAGs) and genes related to antimicrobial resistance (AMR), biocide and metal resistance, insertion sequences (ISs), integron, and virulence are depicted for biofilm ( a ) and hospital wastewater ( b ) samples. Nodes represent individual sequences and edges indicate co-occurrence within the same MAG or contig.

Article Snippet: For fluorescence staining, nucleic acid was stained with cell-permeant SYTO 9 (Thermo Fisher Scientific, Waltham, MA, USA), proteins were stained with FilmTracerTM SYPROTM Ruby Biofilm Matrix Stain (Thermo Fisher Scientific), and polysaccharides were stained with Concanavalin A conjugated to tetramethylrhodamine (Thermo Fisher Scientific).

Techniques: Functional Assay

Journal: Biofilm

Article Title: Genomic insights into activated antimicrobial resistance of in situ hospital-wastewater biofilm

doi: 10.1016/j.bioflm.2026.100377

Figure Lengend Snippet: Differential gene expression profiles between biofilm and hospital wastewater based on metatranscriptomic data. ( a ) Number of genes with higher (Up) or lower (Down) expression in biofilm (BF) compared to hospital wastewater (HW) across all genes. ( b ) Number of genes with significantly different expression (p < 0.05) between BF and HW. ( c ) Volcano plot showing genes with significant expression differences (p < 0.05) between BF and HW, where colors describe functional categories. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Article Snippet: For fluorescence staining, nucleic acid was stained with cell-permeant SYTO 9 (Thermo Fisher Scientific, Waltham, MA, USA), proteins were stained with FilmTracerTM SYPROTM Ruby Biofilm Matrix Stain (Thermo Fisher Scientific), and polysaccharides were stained with Concanavalin A conjugated to tetramethylrhodamine (Thermo Fisher Scientific).

Techniques: Gene Expression, Expressing, Functional Assay

Journal: Biofilm

Article Title: Genomic insights into activated antimicrobial resistance of in situ hospital-wastewater biofilm

doi: 10.1016/j.bioflm.2026.100377

Figure Lengend Snippet: Maximum-likelihood phylogenetic tree of Citrobacter species, including isolates from in situ biofilm sample and publicly available genomes. The tree was constructed using core genome sequences and annotated with metadata including sequence type (ST), isolation source, country of origin, and β-lactamase gene profiles.

Article Snippet: For fluorescence staining, nucleic acid was stained with cell-permeant SYTO 9 (Thermo Fisher Scientific, Waltham, MA, USA), proteins were stained with FilmTracerTM SYPROTM Ruby Biofilm Matrix Stain (Thermo Fisher Scientific), and polysaccharides were stained with Concanavalin A conjugated to tetramethylrhodamine (Thermo Fisher Scientific).

Techniques: In Situ, Construct, Sequencing, Isolation

Journal: Military Medical Research

Article Title: The cellular response capacity (CRC) as a novel immunomonitoring approach in sepsis

doi: 10.1016/j.mmr.2026.100010

Figure Lengend Snippet: Concentration-dependent change in the humoral inflammatory response following incubation with Escherichia coli ( E. coli ) in the ex vivo whole blood model. a Absolute plasma concentrations of IL-6, IL-8, and MMP9 determined by enzyme-linked immunosorbent assay. b Normalized values and EC 50 curve fit by BuC=0% and 50 000 CFU/ml E. coli= 100%, respectively, for IL-6, IL-8, and MMP9 as indicated by EC 50 (%) on the respective Y-axis. BuC indicates buffer control after 60 min incubation; numbers on the X-axis indicate E. coli bacteria in concentrations of 2000 to 50 000 CFU/ml after 60 min incubation; LPS indicates lipopolysaccharide (LPS) 100 ng/ml after 60 min incubation. Values are shown as median and interquartile range. n =8. Statistical analysis was performed using the Kruskal-Wallis test with Dunn’s post-hoc test, comparing all shown concentrations of E. coli bacteria and 100 ng/ml LPS with BuC. P -values are indicated above the respective data points. ⁎ P <0.05, ⁎⁎ P <0.01, ⁎⁎⁎ P <0.001. CFU. Colony-forming units; IL. Interleukin; MMP9. Matrix metallopeptidase 9.

Article Snippet: For the samples of the ex vivo whole blood model, the plasma concentrations of matrix metallopeptidase 9 (MMP9, #DY911, R&D Systems, Minneapolis, USA), IL-6 (#555220, BD Biosciences, San Jose, USA), and IL-8 (#DY208, R&D Systems) were measured in citrate-anticoagulated plasma using enzyme-linked immunosorbent assay according to the respective manufacturer’s instructions.

Techniques: Concentration Assay, Incubation, Ex Vivo, Clinical Proteomics, Enzyme-linked Immunosorbent Assay, Control, Bacteria

Journal: Military Medical Research

Article Title: The cellular response capacity (CRC) as a novel immunomonitoring approach in sepsis

doi: 10.1016/j.mmr.2026.100010

Figure Lengend Snippet: Diagnostic performance for the detection of bacteremia, analyzing the neutrophil phenotype by determining the median fluorescence intensity (MFI) and the cellular response capacity (CRC) in comparison with traditional markers of humoral inflammation (IL-6, IL-8, MMP9). a Comparison of receiver operating characteristic (ROC) at 10,000 CFU/ml Escherichia coli ( E. coli ) with the respective 95% confidence interval (CI) and P -value, and half-maximal effective concentration (EC 50 ) as a function of the E. coli concentration. b Detailed comparison of the EC 50 as a function of the E. coli concentration. c Exemplary comparison of EC 50 curve fit after normalization as indicated by EC 50 (%) on the respective Y-axis to BuC=100% and 50 000 CFU/ml E. coli =0% for the humoral marker IL-6 (the IL-6 values were multiplied by −1 before EC 50 calculation to facilitate comparability with the CRC) and the change in neutrophil phenotype represented by CD11b CRC. BuC indicates buffer control after 60 min incubation; numbers on the X-axis of c indicate E. coli bacteria in concentrations of 2000 to 50 000 CFU/ml after 60 min incubation. Values are shown as median and interquartile range. n =8. Statistical analysis was performed using the Kruskal-Wallis test with Dunn’s post-hoc test, evaluating the EC 50 of IL-8, MMP9, the MFI, and CRC of CD10, CD11b, and CD62L in comparison to the EC 50 of IL-6. P -values are indicated above the respective data points. ⁎ P <0.05. CFU. Colony-forming units; IL. Interleukin; MMP9. Matrix metallopeptidase 9.

Article Snippet: For the samples of the ex vivo whole blood model, the plasma concentrations of matrix metallopeptidase 9 (MMP9, #DY911, R&D Systems, Minneapolis, USA), IL-6 (#555220, BD Biosciences, San Jose, USA), and IL-8 (#DY208, R&D Systems) were measured in citrate-anticoagulated plasma using enzyme-linked immunosorbent assay according to the respective manufacturer’s instructions.

Techniques: Diagnostic Assay, Fluorescence, Comparison, Concentration Assay, Marker, Control, Incubation, Bacteria

Journal: Military Medical Research

Article Title: The cellular response capacity (CRC) as a novel immunomonitoring approach in sepsis

doi: 10.1016/j.mmr.2026.100010

Figure Lengend Snippet: Clinical specifications and parameters over all time points of the sepsis cohort. a Suspected infection cause of sepsis. b Distribution of the individual score points of the Sequential Organ Failure Assessment (SOFA) score. c Total SOFA score. d-h Traditional and humoral markers of inflammation: leukocytes and neutrophil-lymphocyte ratio ( d ), C-reactive protein (CRP) and procalcitonin (PCT) ( e ), interleukin-6 (IL-6) and interleukin-8 (IL-8) ( f ), serum amyloid A (SAA) and calprotectin ( g ), matrix metallopeptidase 9 (MMP9) and myeloperoxidase (MPO) ( h ). Values are shown as median and interquartile range. n =14. CNS. Central nervous system; HV. Healthy volunteers.

Article Snippet: For the samples of the ex vivo whole blood model, the plasma concentrations of matrix metallopeptidase 9 (MMP9, #DY911, R&D Systems, Minneapolis, USA), IL-6 (#555220, BD Biosciences, San Jose, USA), and IL-8 (#DY208, R&D Systems) were measured in citrate-anticoagulated plasma using enzyme-linked immunosorbent assay according to the respective manufacturer’s instructions.

Techniques: Infection

Journal: STAR Protocols

Article Title: Protocol for isolating and culturing microglia from the adult mouse brain using a magnetic-activated cell sorting system

doi: 10.1016/j.xpro.2026.104471

Figure Lengend Snippet: Flow cytometry for MACS-isolated microglia purity (A and B) Total CD11b-positive cells from MACS columns; (C) Cell viability assessed by Zombie Red staining; (D) Infiltrating leukocytes, including neutrophils (Ly6G+) and T lymphocytes (CD3+); (E) Proportions of microglia (CD11b+CD45low) versus monocytes/border-associated macrophages (CD11b+CD45high); (F) Proportion of resting (homeostatic) microglia identified as CD11b+TMEM119+ cells.

Article Snippet: Note: We use commercial flow cytometry staining buffer from eBioscience (Cat# 00-4222-26), which is PBS-based formulation designed to prevent non-specific antibody binding and maintain cell stability during flow cytometry.

Techniques: Flow Cytometry, Isolation, Staining