Fluorography of the colonization model (Magnification, 100×).

<p>Fluorography of the colonization model (Magnification, 100×).</p

Validation of the RNA-seq assay of selected genes with a RT-qPCR analysis.

<p>RT-qPCR data confirmed the expression trends observed in the RNA-Seq data for a number of genes in resistant strains TN4 (A) and TW4 (B) compared with parental strain T0.</p

Gene Ontology terms for DEGs grouped into functional categories.

<p>The vertical and horizontal coordinates represent the number of genes and the GO functional terms, respectively. Red, upregulated genes; green, downregulated genes. A: resistant strain TN4; B: resistant strain TW4.</p

Pathways significantly differently enriched in resistant strain TW4 and parental strain T0.

<p>Pathways significantly differently enriched in resistant strain TW4 and parental strain T0.</p

RNA-seq-based analysis of drug-resistant <i>Salmonella enterica</i> serovar Typhimurium selected <i>in vivo</i> and <i>in vitro</i>

<div><p>The aim of this study was to characterize the mechanism of fluoroquinolone (FQ) resistance in <i>Salmonella</i> Typhimurium. We established the <i>Caenorhabditis elegans</i>–<i>Salmonella</i> Typhimurium model to select for ciprofloxacin resistance in <i>Salmonella</i> Typhimurium colonizing <i>C</i>. <i>elegans</i>, generating the resistant strains TN4. Gradient doses of ciprofloxacin were used to generate the resistant strain TW4 <i>in vitro</i>. RNA sequencing was used to establish the whole-transcriptome profile of three strains of <i>Salmonella</i> Typhimurium. The gene expression patterns of resistant strains TN4 and TW4 differed from those of the parental strain. In TN4, 2,277 genes were differentially expressed (1,833 upregulated and 444 downregulated) relative to the parental strain, and in TW4, 3,464 genes were differentially expressed (3,433 upregulated and 31 downregulated). Among these differentially expressed genes, 28 were associated with drug resistance and 26 were associated with the two-component systems in the two resistant strains. Seven different pathways were significantly sffected in two strains. Efflux pump overexpression was identified as one of the main mechanisms underlying FQ resistance in the two resistant strains. TW4 differentially expressed more efflux pump genes than TN4 and most of these genes were more strongly expressed than in TN4. However, expression of the efflux pump repressor gene and the mar operon was downregulated in TN4 but not in TW4. Two-component systems are also important in drug resistance. Our findings provide an important basis for further studies of the complex network that regulate FQ resistance in <i>Salmonella</i>.</p></div

Scatterplot of the gene expression levels of the resistant and parental strains.

<p>The vertical coordinates represent the log2-transformed RPKM values for each gene in the resistant strain, and the horizontal coordinates represent the log2-transformed RPKM values for each gene in the parental strain. Green, upregulated genes; red, downregulated genes; gray, unchanged gene. A: resistant strain TN4 and parental strain T0; B: resistant strain TW4 and parental strain T0.</p

Antimicrobial susceptibility of the three strains.

<p>Antimicrobial susceptibility of the three strains.</p

DEGs related to drug resistance in the two resistant strains.

<p>DEGs related to drug resistance in the two resistant strains.</p

<b>The Investigation of the Shared Genetic Architecture between Hypothyroidism and Age at Menopause</b>

This is the supplementary data of The Investigation of the Shared Genetic Architecture between Hypothyroidism and Age at Menopause.</p

Primers used in this study.

<p>Primers used in this study.</p