Journal: bioRxiv

Article Title: Coping with multiple enemies: pairwise interactions do not predict evolutionary change in complex multitrophic communities

doi: 10.1101/492132

Figure Lengend Snippet: Abundance (log-transformed, mean ± std. dev., n = 7) of the focal species B. subtilis (orange circles), competitor bacterium S. marcescens (red circles), predator P. caudatum (green circles) and B. subtilis-specific parasite phage SPP1 (purple circles) in each treatment over the duration of the experiment (Days 1-10).

Article Snippet: Our experiment consisted of seven sets of species combinations of Bacillus subtilis (NCIB3610) with (1) SPP1 phage parasite in isolation; (2) Paramecium caudatum , a generalist [ ; ; ] bacterial predator in isolation; (3) Serratia marcescens (ATCC 29632), a competitor of B. subtilis , in isolation; (4) P. caudatum and SPP1 phage; (5) S. marcescens and SPP1 phage; (6) S. marcescens and P. caudatum; and (7) S. marcescens, P. caudatum and SPP1 phage, resulting in a total of 7 experimental treatments, each replicated seven times.

Techniques: Transformation Assay

Journal: bioRxiv

Article Title: Coping with multiple enemies: pairwise interactions do not predict evolutionary change in complex multitrophic communities

doi: 10.1101/492132

Figure Lengend Snippet: The effect of community composition on B. subtilis evolution relative to the ancestral strain (solid line). a . Competitive ability of B. subtilis isolates, measured as the ratio of B. subtilis to S. marcescens (dashed line indicates a 1:1 ratio, solid line represents ancestral resistance). b . Relative resistance to parasite in B. subtilis across treatment groups. Resistance to phage SPP1 was measured as the difference in growth (optical density) of B. subtilis in the presence or absence of the ancestral phage parasite. The solid line represents the resistance of ancestral B. subtilis and the resistance of our experimental treatment isolates relative to ancestral parasite resistance. c . Growth of B. subtilis isolates in the presence of the predator P. caudatum (measured as log 10 optical density of biofilm production). Solid line indicates resistance of the ancestral B. subtilis grown in the presence of P. caudatum ). In all cases, values to the right of the solid lines indicate higher relative resistance than the ancestral strain, values to the left of the solid line indicate lower resistance relative to ancestral strain of B. subtilis .

Article Snippet: Our experiment consisted of seven sets of species combinations of Bacillus subtilis (NCIB3610) with (1) SPP1 phage parasite in isolation; (2) Paramecium caudatum , a generalist [ ; ; ] bacterial predator in isolation; (3) Serratia marcescens (ATCC 29632), a competitor of B. subtilis , in isolation; (4) P. caudatum and SPP1 phage; (5) S. marcescens and SPP1 phage; (6) S. marcescens and P. caudatum; and (7) S. marcescens, P. caudatum and SPP1 phage, resulting in a total of 7 experimental treatments, each replicated seven times.

Techniques:

Journal: Signal Transduction and Targeted Therapy

Article Title: Single-cell transcriptomic analysis reveals gut microbiota-immunotherapy synergy through modulating tumor microenvironment

doi: 10.1038/s41392-025-02226-7

Figure Lengend Snippet: Synergistic effects of gut microbiota and ICI treatment on SPP1. a Violin plots reveal Spp1 expression levels in myeloid subtypes across four groups. b Forest plot reveals the association between SPP1 gene expression levels and the prognosis of major cancer types in the TCGA dataset. c Kaplan–Meier survival curves show the correlation between SPP1 expression levels and prognosis in two immunotherapy cohorts. d Box plots indicate the levels of osteopontin measured by ELISA in the serum of mice across four groups. Each group consists of 4 mice. e Network diagram illustrates the differential interaction strength of the Spp1-related pathway between two cell types in the PW group compared to the others. f Bubble plot displays the interaction strength of the Spp1-related pathways between tumor-associated macrophages (TAMs)/NK cells and MC38 tumor cells in the PW group compared to the others. g Network diagram shows the differential interaction strength of the Spp1-related pathway between myeloid subtypes and MC38 cells in the PW group compared to the others. h Network diagram illustrates the differential interaction strength of the overall signaling between myeloid subtypes and MC38 cells in the PW group compared to the others

Article Snippet: The concentration of osteopontin (OPN) in mouse serum samples was quantified using the Mouse/Rat Osteopontin ELISA Kit (KE10046; Proteintech) with the following procedure.

Techniques: Expressing, Gene Expression, Enzyme-linked Immunosorbent Assay