kruskal-wallis test followed by dunn's multiple comparisons test  (GraphPad Software Inc)

Journal: PLOS Genetics

Article Title: RNA cis-regulators are important for Streptococcus pneumoniae in vivo success

doi: 10.1371/journal.pgen.1011188

Figure Lengend Snippet: ( A ) Aggregated and sampled relative carrying capacity across all regulators . A randomly chosen sampled population is depicted. A total of 100 random samplings of the data were performed and the percentage of sampled populations displaying a statistically significant difference between matched control constructs (WT C ) and mutant strains is indicated (Kruskal-Wallis followed by Dunn’s test of multiple comparison, % of samplings where adj. p<0.05). Average adj. p-values and percentage of sampled populations where adj. p <0.05 reported in . (B) Sampled and aggregated relative growth rates across all regulators . (C) Sampled and aggregated mouse infection relative fitness values across the regulators examined in each in vivo environment (nasopharynx, lung, and blood) and the control conducted in vitro in rich medium. Average adj. p-values and proportion of samples where adj. p <0.05 are in . All numeric data points in .

Article Snippet: Statistical significance between the values of each mutant and the WT C was determined by comparing parameter values (doubling time = ln(2)/r, and K) from individual growth curves via a Kruskal-Wallis test followed by Dunn’s test of multiple comparisons (Graphpad version 9.5.1).

Techniques: Control, Construct, Mutagenesis, Comparison, Infection, In Vivo, In Vitro

Journal: PLOS Genetics

Article Title: RNA cis-regulators are important for Streptococcus pneumoniae in vivo success

doi: 10.1371/journal.pgen.1011188

Figure Lengend Snippet: (A) FMN biosynthesis pathway indicating the roles of different riboswitch regulated genes in the synthesis and transport of riboflavin. Pink genes are biosynthesis genes, turquoise genes are transporters, and grey genes are not riboswitch regulated. Created with BioRender. (B) Growth curves for 0178_FMN WT C and mutants in CDM +/- riboflavin shows that 0178_FMN_mOFF displays a severe growth defect in medium lacking riboflavin. (C). Growth curves for 0488_FMN WT C and mutants in CDM +/- riboflavin shows that all three 0488_FMN mutants displays a moderate defect that is riboflavin independent. (D) The SP_0178_KO strain where the promoter, regulatory region and coding region of SP_0178 have been removed shows no significant change in growth rate and carrying capacity compared to the constitutively repressed mutant 0178_FMN_mOFF at a range of riboflavin concentrations . (E) Mouse competition assays demonstrate that 0178_FMN_mOFF mutants display a statistically significant fitness defect in nasopharynx colonization, but no other environments. 0178_FMN_mLI and 0178_FMN_mON mutants do not show any significant in vivo defects. Each point represents fitness calculated from an individual mouse. (F) Mouse competition assays demonstrate that 0488_FMN_mOFF mutants display a statistically significant fitness defect in all in vivo environments. 0488_FMN_mLI and 0178_FMN_mON mutants only display a statistically significant defect in the nasopharynx. Each point represents fitness calculated from an individual mouse. Statistical significance for mouse studies assessed via Kruskal-Wallis test followed by Dunn’s test of multiple comparisons to compare each in vivo environment to the in vitro control (*adj. p<0.05, ** adj. p < .01, ***adj. p < .001). All numeric data points in .

Article Snippet: Statistical significance between the values of each mutant and the WT C was determined by comparing parameter values (doubling time = ln(2)/r, and K) from individual growth curves via a Kruskal-Wallis test followed by Dunn’s test of multiple comparisons (Graphpad version 9.5.1).

Techniques: Mutagenesis, In Vivo, In Vitro, Control

Journal: PLOS Genetics

Article Title: RNA cis-regulators are important for Streptococcus pneumoniae in vivo success

doi: 10.1371/journal.pgen.1011188

Figure Lengend Snippet: (A) PyrR regulated operons are repressed by the PyrR protein (encoded by SP_1278) bound to UMP. Figure created with Biorender. (B) Pyrimidine synthesis pathway indicating the roles of pyrR RNA regulated genes in the synthesis and transport of pyrimidines. Pink genes are biosynthesis genes, turquoise genes are transporters, and grey genes are not pyrR regulated. PyrR (SP_1278) may show both regulatory and enzymatic activity. Figure created with Biorender. (C) Growth curves for 0701_pyrR WT C and mutants in CDM +/- uracil shows that 0701_pyrR _mOFF displays a severe growth defect in medium lacking uracil that is not fully rescued in medium containing uracil. (D). Growth curves for 1286_pyrR WT C and mutants in CDM +/- uracil shows no significant growth defects. Note, that no mOFF constitutively repressed mutant was analyzed for 1286_pyrR. (E) Adding additional uracil to the medium (from 20 ug/mL to 100 ug/mL) does not alter the uracil independent growth defect observed for SP_0701_mOFF . (F) The SP_0701_KO strain where the promoter, regulatory region and coding region of SP_0701 and SP_0702 have been removed shows a more severe phenotype compared to the constitutively repressed mutant 0701_pyrR_mOFF at a range of uracil concentrations . (G) The SP_1278_KO strain where the promoter, regulatory region and regions inclusive of SP_1278 through SP_1275 were removed shows a more severe phenotype compared to the constitutively repressed mutant SP_1278_pyrR_mOFF at a range of uracil concentrations . (H) Mouse competition assays demonstrate that 0701_pyrR _mLI mutants display a statistically significant fitness defect in lung infection and the associated transition to blood. 0701_pyrR_mON and 0701_pyrR_mOFF do not show significantly decreased fitness in mouse infections. Each point represents fitness calculated from an individual mouse. (I) Mouse competition assays demonstrate that 1286_pyrR _mLI and mON mutants display a statistically significant fitness defect in most infection environments. The 1286_pyrR_mOFF mutant was not successfully constructed, and therefore could not be tested . For 1286_pyrR_mON, no colonies were recovered from the blood despite repeated attempts strongly suggesting a fitness very close to 0, but that is ultimately not quantifiable. Each point represents fitness calculated from an individual mouse. Statistical significance of in vivo defects for mouse studies assessed via Kruskal-Wallis test followed by Dunn’s test of multiple comparisons to compare each environment to the in vitro rich medium control (*adj. p<0.05, ** adj. p < .01, ***adj. p < .001). Data corresponding to growth curves and mouse infections for mutants of SP_1278 is previously published . All numeric data points in .

Article Snippet: Statistical significance between the values of each mutant and the WT C was determined by comparing parameter values (doubling time = ln(2)/r, and K) from individual growth curves via a Kruskal-Wallis test followed by Dunn’s test of multiple comparisons (Graphpad version 9.5.1).

Techniques: Activity Assay, Mutagenesis, Infection, Construct, In Vivo, In Vitro, Control