Journal: The ISME Journal

Article Title: Targeting Fusobacterium nucleatum through chemical modifications of host-derived transfer RNA fragments

doi: 10.1038/s41396-023-01398-w

Figure Lengend Snippet: A Incorporation of 2’-OMe phosphorothioate linkage in tsRNAs, referred to as MOD(OMe)-000794, MOD(OMe)-020498 and MOD(OMe)-scrambled RNA. B Improvement of tsRNA stability by chemical modifications in comparison to synthetic mimics of naturally occurring counterparts. Individual tsRNAs (1 nM) were incubated with Columbia broth anaerobically at 37 °C for 6 h, and intact tsRNAs were measured via quantitative real time PCR using a stem-loop method. Fold changes were normalized to the levels of naturally occurring tsRNAs, which are shown as “1” on the y axis. n = 3 technical replicates, N = 2 independent experiments. C Growth inhibition of Fn ATCC 23726 by MOD(OMe)-000794 and MOD(OMe)-020498, but not MOD(OMe)-scrambled RNA, at the nanomolar concentration ranges ( n = 3, N = 3). D Naturally occurring tsRNAs failed to inhibit Fn ATCC 23726 at indicated concentrations ( n = 3, N = 3). E Representative images showing the colony formation of Fn ATCC 23726 on agar plates after treatment with 512 nM MOD(OMe)-000794, MOD(OMe)-020498 or MOD(OMe)-scrambled RNA for 24 h. Bacteria were washed and recovered on nonselective Columbia broth sheep blood agar plates. Representative colonies are indicated by white arrows. F MOD(OMe)-000794 and MOD(OMe)-020498 at 512 nM exhibited no growth inhibition in two representative oral bacteria, a Gram-negative bacterium, Porphyromonas gingivalis ATCC 33277 ( P. gingivalis ) and a Gram-positive bacterium, Streptococcus mitis ATCC 6249 ( S. mitis ). ( n = 2, N = 2). Data were analyzed by the two-way ANOVA followed by Dunnett’s Bonferroni multiple comparison tests. ** p < 0.01, *** p < 0.001, **** p < 0.0001. Data are means ± SEM.

Article Snippet: To this end, we challenged two representative oral bacteria including Gram-negative Porphyromonas gingivalis ATCC 33277 ( Pg ), and Gram-positive Streptococcus mitis ATCC 6249 ( Sm ) (Fig. ), as well as E. coli K-12 (Fig. ) with MOD(OMe)-000794, MOD(OMe)-020498 and MOD(OMe)-scrambled RNA control.

Techniques: Incubation, Real-time Polymerase Chain Reaction, Inhibition, Concentration Assay

Journal: PLoS ONE

Article Title: Mitis Group Streptococci Express Variable Pilus Islet 2 Pili

doi: 10.1371/journal.pone.0025124

Figure Lengend Snippet: Streptococcal strains used in this study.

Article Snippet: S. mitis ATCC6249 , PI-2 , ATCC.

Techniques:

Journal: PLoS ONE

Article Title: Mitis Group Streptococci Express Variable Pilus Islet 2 Pili

doi: 10.1371/journal.pone.0025124

Figure Lengend Snippet: Type strains ( T ) and strains from genomic sequencing projects ( G ) are indicated. GenBank accession numbers: S. oralis ATCC35037: AEDW01000020; S. oralis Uo5: FR720602; S. oralis SK255: AFNM00000000; S. mitis ATCC6249: AEEN01000012; S. pneumoniae GA47901: AFGR00000000 ; S. pneumoniae TIGR4: AE005672; S. sanguinis ATCC49296: AEPO01000013; S. sanguinis ATCC10556: AFAZ00000000; S. sp. C300: ACRJ00000000. Shaded areas indicate pseudogenes (one asterisk indicates a mutation in the start codon and two asterisks indicate the position of a stop-codon).

Article Snippet: S. mitis ATCC6249 , PI-2 , ATCC.

Techniques: Genomic Sequencing, Mutagenesis

Journal: PLoS ONE

Article Title: Mitis Group Streptococci Express Variable Pilus Islet 2 Pili

doi: 10.1371/journal.pone.0025124

Figure Lengend Snippet: Western blots with cell wall extracts of the indicated strains detected with anti-PitB antiserum (A) or anti-PitA antiserum (B). Both antisera were developed against the respective S. oralis ATCC35037 proteins. The positions of the PitB and PitA monomers are indicated. (C) Electron micrographs of immmunogold-labeled S. oralis ATCC35037 (a) and S. mitis ATCC6249 (b) using anti-PitB antiserum. Scale bars 0.5 µm.

Article Snippet: S. mitis ATCC6249 , PI-2 , ATCC.

Techniques: Western Blot, Labeling

Journal: PLoS ONE

Article Title: Mitis Group Streptococci Express Variable Pilus Islet 2 Pili

doi: 10.1371/journal.pone.0025124

Figure Lengend Snippet: Phylogenetic tree constructed with the neighbor-joining method in MEGA version 5.0 based on electronic Multilocus Sequence Analysis (eMLSA) of Mitis group streptococci. Bootstrap values (%) are based on 500 replications. Strains include the strains used in this study and all Mitis group streptococci with partial or complete genomic sequence deposited at the National Center for Biotechnology Information (NCBI). Type strains are indicated (T) , and for species with >5 sequenced strains the number of additional strains with a particular pepT-hemH genotype is indicated in brackets. Strains containing a linked pepT - hemH region (blue), a PI-2-encoding pilus islet integrated in the pepT-hemH region (red) or a PI-2-unrelated insertion in the pepT-hemH region (green) are highlighted. Strains that lack a pepT-hemH region are shown in black. GenBank accession numbers are: S. oralis ATCC35037: AEDW0000000; S. sp. C300: ACRJ00000000; S. oralis Uo5: FR720602; S. sp. M143: ACRK00000000; S. sp. 73H25AP: AEEP00000000; S. oralis SK255: AFNM00000000; S. sanguinis ATCC49296: AEPO00000000; S. mitis ATCC6249: AEEN00000000; S. mitis B6: FN568063; S. mitis ATCC49456 ( = NTCT12261): AEDX00000000; S. mitis SK321: AEDT00000000; S. mitis SK564: AEDU00000000; S. mitis SK597: AEDV00000000; S. pneumoniae GA47901: AFGR00000000; S. pneumoniae TIGR4: AE005672; Streptococcus peroris ATCC700780: AEVD00000000; Streptococcus infantis ATCC70079: AEVD00000000; S. infantis ATCC1302: AEDY00000000; S. infantis SK1076: AFNN00000000; S. australis ATCC700641: AEQR00000000; S. parasanguinis 15912: CP002843; S. parasanguinis F0405: AEKM00000000; S. parasanguinis 903: AEVE00000000; S. cristatus ATCC51100: AFAZ00000000; S. sanguinis ATCC10556 ( = SK1): AFAZ00000000; S. gordonii Challis CH1: CP000725. The scale bar refers to genetic divergence as calculated by the MEGA5 software.

Article Snippet: S. mitis ATCC6249 , PI-2 , ATCC.

Techniques: Construct, Sequencing, Software