Journal: mBio

Article Title: Enzymatic Synthesis of Bioinformatically Predicted Microcin C-Like Compounds Encoded by Diverse Bacteria

doi: 10.1128/mBio.01059-14

Figure Lengend Snippet: In vitro adenylation of predicted MccA peptides by cognate MccB homologs. Chemically synthesized peptides corresponding to 7-amino-acid-long MccA products of E. coli (A), B. washoensis Sb944nv (B), H. pylori plasmid HPP12 (C), L. johnsonii NCC 533 (D), S. thermophilus LMD-9 (E), Y. pseudotuberculosis PB1/+ (F), full-length Synechococcus sp. CC9605 peptide (G), and peptides corresponding to the last 25 (H) and 20 (I) amino acids of Synechococcus sp. CC9605 peptide ( Table 1 ) were combined with the corresponding recombinant MccB homologs in the absence (top) and the presence (bottom) of ATP. Reaction products were analyzed by MALDI MS. Only relevant parts of the spectra are shown. Asterisks indicate peaks corresponding to adenylation reaction intermediates containing a terminal succinimide ( Fig. 1A ).

Article Snippet: The 42-amino-acid-long MccA peptide of Y. pseudotuberculosis PB1/+ was purchased from GenScript USA Inc. and was more than 85% pure.

Techniques: In Vitro, Synthesized, Plasmid Preparation, Recombinant

Journal: mBio

Article Title: Enzymatic Synthesis of Bioinformatically Predicted Microcin C-Like Compounds Encoded by Diverse Bacteria

doi: 10.1128/mBio.01059-14

Figure Lengend Snippet: Antibiotic activity of enzymatically synthesized McC-like compounds a

Article Snippet: The 42-amino-acid-long MccA peptide of Y. pseudotuberculosis PB1/+ was purchased from GenScript USA Inc. and was more than 85% pure.

Techniques: Activity Assay, Synthesized

Journal: PLoS Pathogens

Article Title: Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes involved in cell permeability and tRNA modifications

doi: 10.1371/journal.ppat.1010556

Figure Lengend Snippet: Cultures of WT Y . pseudotuberculosis were incubated in the presence or absence of 0.1μg/ml Dox and bacterial transcript levels were compared by RNA-seq. Significant changes in transcript levels were detected at 2h post-treatment by DESeq2 analysis. (A) Volcano plot of aligned genes, each dot represents one gene. Horizontal dotted line: adjusted p value of 0.05, genes above this line are considered significantly altered. X-axis: log2 fold change in transcript levels. Vertical lines mark 2-fold changes, genes outside these lines are differentially regulated more than 2-fold. Hits of interest are highlighted. (B) Table of significant hits, 2h post-treatment. Hits of interest (differentially regulated ~2-fold) are highlighted in red. Base mean values represent 4 biological replicates. Log2 fold change and fold change are shown with adjusted p-value (adjusted based on gene length). (C) qRT-PCR validation of RNA-seq results. Cultures were prepared as described above, and bacterial transcripts were detected by qRT-PCR. Log2 fold change values were calculated relative to untreated cells, horizontal dotted lines depict average values for untreated cells (0log2), and 2-fold changes. Data represents four biological replicates. Statistics: (C) Two-way ANOVA with Tukey’s multiple comparison test, comparisons made relative to untreated cells. n.s.: not significant.

Article Snippet: Experiments with Y . pseudotuberculosis were approved by the Johns Hopkins Institutional Biosafety Committee under protocol numbers P1611010206 and DN1611010106.

Techniques: Incubation, RNA Sequencing, Quantitative RT-PCR, Biomarker Discovery, Comparison

Journal: PLoS Pathogens

Article Title: Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes involved in cell permeability and tRNA modifications

doi: 10.1371/journal.ppat.1010556

Figure Lengend Snippet: (A) C57BL/6 mice were infected with WT Y . pseudotuberculosis , infection proceeded for 48h (hours, h), and mice were injected intraperitoneally with a single dose of 40mg/kg Dox. At the indicated timepoints spleens were harvested, and samples were enriched for bacterial RNA prior to qRT-PCR. Time: h post-treatment, 0h represents 48h post-inoculation (p.i.), the time of treatment. Log2 fold change is relative to 0h. Horizontal dotted lines depict average values for 0h (0log2), and 2-fold changes. Data represents 4 biological replicates/group. (B) Cultures of WT Y . pseudotuberculosis were incubated for 4h in the presence or absence of 1μg/ml Dox, bacterial RNA was isolated and transcripts were detected by qRT-PCR. Log2 fold change values were calculated relative to untreated cells, horizontal dotted lines depict average values for untreated cells (0log2), and 2-fold changes. Data represents four biological replicates. Statistics: ( A) Two-way ANOVA with Bonferroni’s multiple comparison test, comparisons made relative to 48h p.i./time 0h timepoint. (B) Two-way ANOVA with Tukey’s multiple comparison test, comparisons made relative to untreated cells using relative expression values. ****p < .0001, ***p < .001, **p < .01, *p < .05, n.s.: not significant.

Article Snippet: Experiments with Y . pseudotuberculosis were approved by the Johns Hopkins Institutional Biosafety Committee under protocol numbers P1611010206 and DN1611010106.

Techniques: Infection, Injection, Quantitative RT-PCR, Incubation, Isolation, Comparison, Expressing

Journal: PLoS Pathogens

Article Title: Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes involved in cell permeability and tRNA modifications

doi: 10.1371/journal.ppat.1010556

Figure Lengend Snippet: C57BL/6 mice were infected with equal numbers of WT and mutant Y . pseudotuberculosis , infection proceeded for 48h (hours, h), and mice were injected intraperitoneally with a single dose of Dox or left untreated. Spleens were harvested 24h later to quantify CFUs and microcolony areas. (A) Co-infection with Δ osmB yopE :: mCherry + WT GFP + . Total CFU/spleen for treated mice (+Dox 24h) compared to untreated mice at the same timepoint. Dots: individual mice. (B) Competitive index: CFUs of the mutant/WT in the spleen divided by the ratio of mutant/WT in the inoculum. Values above 1: mutant is more fit. Dotted line: value of 1, equal fitness. Dots: individual mice. (C) Microcolony areas were quantified for individual strains within the harvested spleens (6 untreated mice and 6 treated mice). 20–62 microcolonies were quantified in one section for untreated mice, and 1–13 microcolonies were quantified in one section for treated mice. (D) CFU/spleen of each strain in the Δ osmB + WT competition experiments. (E) Fold change in bacterial growth after 4h culture in the presence (+NO) or absence (untreated) of the NO donor compound, DETA-NONOate (2.5mM). WT, Δ osmB , and osmB + ( osmB rescued strain) are compared. Fold change relative to time 0, dotted line represents time 0 values. ( F ) Co-infection with Δ ompF yopE :: mCherry + WT GFP + . Total CFU/spleen for treated mice (+Dox 24h) compared to untreated mice at the same timepoint. Dots: individual mice. (G) Competitive index: CFUs of the mutant/WT in the spleen divided by the ratio of mutant/WT in the inoculum. Values above 1: mutant is more fit. Dotted line: value of 1, equal fitness. Dots: individual mice. (H) Microcolony areas were quantified for individual strains within the harvested spleens (4 untreated mice and 4 treated mice). 14–72 microcolonies were quantified in one section for untreated mice, and 1–7 microcolonies were quantified in one section for treated mice. (I) CFU/spleen of each strain in the Δ ompF + WT competition experiments. All mouse experiments were carried out on two independent days. Statistics: (A, B, C, F, G, H) Mann-Whitney; (E) One-way ANOVA with Tukey’s post-test; (D, I) Kruskal-Wallis one-way ANOVA with Dunn’s post-test. ****p < .0001, **p < .01, *p < .05, n.s.: not significant.

Article Snippet: Experiments with Y . pseudotuberculosis were approved by the Johns Hopkins Institutional Biosafety Committee under protocol numbers P1611010206 and DN1611010106.

Techniques: Infection, Mutagenesis, Injection, MANN-WHITNEY

Journal: PLoS Pathogens

Article Title: Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes involved in cell permeability and tRNA modifications

doi: 10.1371/journal.ppat.1010556

Figure Lengend Snippet: (A) WT Y . pseudotuberculosis was grown in the presence of the indicated concentrations of chloramphenicol (Cm). Growth was measured by absorbance (A 600nm ) at the indicated timepoints (hours, h). Bacteria were grown in the presence or absence of (B) 0.0025μg/ml Cm or (C) 0.025μg/ml Cm. RNA was isolated after 2h and 4h exposure, and the indicated transcripts were detected by qRT-PCR. Fold change is relative to untreated cells (represented by a dotted line at a value of 1). Statistics: (A-C) Two-way ANOVA with Tukey’s multiple comparison test, comparisons made relative to untreated cells, comparisons between treatment conditions where indicated by brackets. In C, statistics represent treated vs. untreated comparisons for cnfy , and ompF compared to osmB , which did not change with treatment. ****p < .0001, ***p < .001, n.s.: not significant.

Article Snippet: Experiments with Y . pseudotuberculosis were approved by the Johns Hopkins Institutional Biosafety Committee under protocol numbers P1611010206 and DN1611010106.

Techniques: Bacteria, Isolation, Quantitative RT-PCR, Comparison

Journal: PLoS ONE

Article Title: Effects of urbanization on host-pathogen interactions, using Yersinia in house sparrows as a model

doi: 10.1371/journal.pone.0189509

Figure Lengend Snippet: Best models using AIC-based model selection for Y . pseudotuberculosis , Y . enterocolitica , other Yersinia species and Scaled Mass Index as respective response variables.

Article Snippet: If virulence genes were detected, Y . pseudotuberculosis isolates were serotyped at the National Reference Center Yersinia (IREC).

Techniques: Selection

Journal: PLoS ONE

Article Title: Effects of urbanization on host-pathogen interactions, using Yersinia in house sparrows as a model

doi: 10.1371/journal.pone.0189509

Figure Lengend Snippet: Variable importance after model-averaging in order to explain the presence of Y . pseudotuberculosis , Y . enterocolitica and other Yersinia species and the SMI of the host.

Article Snippet: If virulence genes were detected, Y . pseudotuberculosis isolates were serotyped at the National Reference Center Yersinia (IREC).

Techniques:

Journal: PLoS ONE

Article Title: Effects of urbanization on host-pathogen interactions, using Yersinia in house sparrows as a model

doi: 10.1371/journal.pone.0189509

Figure Lengend Snippet: Parameter estimates and standard deviation for response variables: Y . pseudotuberculosis , Y . enterocolitica , other Yersinia species and SMI (shown in Table 1 ).

Article Snippet: If virulence genes were detected, Y . pseudotuberculosis isolates were serotyped at the National Reference Center Yersinia (IREC).

Techniques: Standard Deviation

Journal: MicrobiologyOpen

Article Title: Pentaplex real‐time PCR for differential detection of Yersinia pestis and Y . pseudotuberculosis and application for testing fleas collected during plague epizootics

doi: 10.1002/mbo3.1105

Figure Lengend Snippet: Description of the genes selected for the pentaplex real‐time PCR and the validation PCR, and the primers/probes sequences

Article Snippet: All Y . pestis and Y . pseudotuberculosis DNA templates used in the study were obtained from BEI Resources or the University of Texas Medical Branch (UTMB) unless otherwise stated (Table ).

Techniques: Real-time Polymerase Chain Reaction, Biomarker Discovery, Plasmid Preparation, Control