Journal: PLoS ONE

Article Title: Salivary Periodontopathic Bacteria in Children and Adolescents with Down Syndrome

doi: 10.1371/journal.pone.0162988

Figure Lengend Snippet: Oligonucleotide probes, 16S rRNA (Operon Technologies ® ) marked with Cy3 fluorochrome for the identification of oral microorganisms.

Article Snippet: 16S rRNA nucleotide probes (Operon Technologies Inc., USA) were used and marked with Cy3 fluorochrome (Indo-carbocyanine) to identify oral microorganisms ( ).

Techniques: Sequencing

Journal: Cell host & microbe

Article Title: Amino acid competition shapes Acinetobacter baumannii gut carriage

doi: 10.1016/j.chom.2025.07.003

Figure Lengend Snippet: (A) α-Diversity was calculated from 16S rRNA gene sequencing at 0 and 9 DPI of A. baumannii WT and Δ astO ( n = 10; data combined from mice in and ; mean ± SD are shown; p by one-way ANOVA with Sidak’s multiple comparisons). (B) Representative image of A. baumannii WT colonization at 10 DPI in the colon, visualized by MiPACT-HCR. Scale bar is 100 μm. Red, pan-bacteria HCR; blue, DAPI; magenta, WGA-lectin; green, anti- Acinetobacter HCR. From mice in and . (C) Experimental design with germ-free mice. (D) A. baumannii CFU from fecal samples of germ-free mice ( n = 6 female and n = 4 male mice, p by two-way ANOVA with Sidak’s multiple comparisons; experiment was repeated three times with similar results). (E) L-ornithine was quantified in chow and fecal samples (chow samples are n = 3 [LOD = 1 nmol/g], fecal samples are n = 10 mice shown in , , and [LOD = 5 nmol/g], mean ± SD, p by two-way ANOVA with Fisher’s least significant difference multiple comparisons only on fecal samples). (F) Principal-component analysis of amino acids in fecal samples at 0 and 10 DPI with chow samples shown in each plot ( n = 10 mice shown in , , and , chow n = 3). Lines connect CFU of both strains enumerated from the same mouse. DPI, days post inoculation; MiPACT-HCR, microbial identification after passive CLARITY technique via hybridization chain reaction; WGA, wheat germ agglutinin; CFU, colony-forming units; LOD, approximate limit of detection; PC, principal component. See also and .

Article Snippet: Hybridization chain reaction (HCR) was performed with an Acinetobacter -specific FISH probe (Aci-16s 729) with a B4 overhang and amplified by fluorescent DNA hairpins conjugated to Alexa Fluor-488 (Molecular Instruments) and a pan-bacteria FISH probe (EUB338) with a B1 overhang amplified by fluorescent DNA hairpins conjugated to Alexa Fluor-647 (Molecular Instruments).

Techniques: Sequencing, Bacteria, Hybridization

Journal:

Article Title: Pneumolysin Detection Identifies Atypical Isolates of Streptococcus pneumoniae

doi:

Figure Lengend Snippet: Results of confirmatory tests on five isolates of S. pneumoniae with atypical colonial appearances

Article Snippet: We therefore examined further these five isolates (i) by a real-time PCR method for the pneumolysin gene which included a hybridization probe for amplicon recognition ( 4 ), (ii) by demonstrating the expression of pneumolysin in the lysed organisms using a monoclonal antibody to a recombinant pneumolysin in a Western blot technique ( 8 ), and (iii) by a commercial 16S RNA gene probe (AccuProbe; Gene-Probe Inc., San Diego, Calif.).

Techniques: Western Blot, Solubility