coarse grained molecular dynamics cg md  (Molecular Dynamics Inc)

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