Growth kinetics of <i>R. rickettsii</i> under different experimental conditions.

<p>A) Growth of <i>R. rickettsii</i> in Vero cells incubated at either 34°C or 25°C. B) Growth of <i>R. rickettsii</i> at 37°C in ISE6 and Vero cells. C) Growth of <i>R. rickettsii</i> in ISE6 cells at 22°C.</p

Genes that differentially respond early or late after shift to 4°C.

a<p>locus_tags for <i>R. rickettsii</i> Sheila Smith (CP000848) and Iowa (CP000766).</p>b<p>Comparison of gene expression levels from <i>R. rickettsii</i> grown for three days at 34°C and shifted to 4°C for 2 hrs to <i>R. rickettsii</i> grown for three days at 34°C.</p>c<p>Comparison of gene expression levels from <i>R. rickettsii</i> grown for three days at 34°C and shifted to 4°C for 24 hrs to <i>R. rickettsii</i> grown for three days at 34°C.</p>d<p>Gene fragments or predicted genes less than 10 kda.</p>e<p>No anotation in <i>R. rickettsii</i> Sheila Smith (CP000848).</p

Transcriptional differences between Vero and ISE6 cells.

a<p>locus_tag for <i>R. rickettsii</i> Sheila Smith (CP000848) and Iowa (CP000766).</p>b<p>Comparison of gene expression levels from <i>R. rickettsii</i> grown for three days at 37°C in Vero cells to <i>R. rickettsii</i> grown for eight days at 22°C in ISE6 cells.</p>c<p>Comparison of gene expression levels from <i>R. rickettsii</i> grown for three days at 37°C in Vero cell to <i>R. rickettsii</i> grown for three days at 37°C in ISE6 cells.</p>d<p>Gene fragments or predicted genes less than 10 Kda.</p

Transcriptional response of <i>R. rickettsii</i> exposed to 4°C for 24 hrs.

a<p>locus_tags for <i>R. rickettsii</i> Sheila Smith (CP000848) and Iowa (CP000766).</p>b<p>Comparison of gene expression levels from R. rickettsii grown for three days at 34°C and shifted to 4°C for 24 hrs to R. rickettsii grown for three days at 34°C.</p>c<p>No anotation in <i>R. rickettsii</i> Sheila Smith (CP000848).</p

Transcriptional response of <i>R. rickettsii</i> shifted from 34°C to 4°C to 34°C.

a<p>locus_tags for <i>R. rickettsii</i> Sheila Smith (CP000848) and Iowa (CP000766).</p>b<p>Comparison of gene expression levels from <i>R. rickettsii</i> grown for three days at 34°C and shifted to 4°C for 2 hrs to <i>R. rickettsii</i> grown for three days at 34°C.</p>c<p>Comparison of gene expression levels from <i>R. rickettsii</i> grown for three days at 34°C shifted to 4°C for 2 hrs and then back to 34°C for 2 hrs to <i>R. rickettsii</i> grown for three days at 34°C and shifted to 4°C for 2 hrs.</p>d<p>No anotation in <i>R. rickettsii</i> Sheila Smith (CP000848).</p

Transcriptional response to limiting iron conditions.

a<p>locus_tags for R. rickettsii Sheila Smith (CP000848) and Iowa (CP000766).</p>b<p>Comparison of gene expression levels from <i>R. rickettsii</i> grown for three days at 34°C and then incubated with 200 µM of deferozamine mesylate for 24 hrs to <i>R. rickettsii</i> grown for three days at 34°C.</p>c<p>Gene fragment or predicted gene less than 10 Kda.</p>d<p>No anotation in <i>R. rickettsii</i> Iowa (CP000766).</p>e<p>No anotation in <i>R. rickettsii</i> Sheila Smith (CP000848).</p

Confirmation and comparison of responses after 2 and 24 hrs at 4°C.

a<p>locus_tags for <i>R. rickettsii</i> Sheila Smith (CP000848) and Iowa (CP000766).</p>b<p>Comparison of gene expression levels from <i>R. rickettsii</i> grown for three days at 34°C and shifted to 4°C for 2 hrs to <i>R. rickettsii</i> grown for three days at 34°C.</p>c<p>Comparison of gene expression levels from <i>R. rickettsii</i> grown for three days at 34°C and shifted to 4°C for 24 hrs to <i>R. rickettsii</i> grown for three days at 34°C.</p>d<p>Gene fragments or predicted genes less than 10 kda.</p>e<p>No anotation in <i>R. rickettsii</i> Sheila Smith (CP000848).</p

Scatter plots of fold changes.

<p>A) 34°C vs 25°C. B) 34°C vs 4°C. The solid line indicates an equivalence between the two conditions, while the small dashed line indicates a two fold difference and the long-short dashed line indicates a three fold difference.</p

Sequencing, Annotation and Analysis of the Syrian Hamster (<i>Mesocricetus auratus</i>) Transcriptome

<div><p>Background</p><p>The Syrian hamster (golden hamster, <i>Mesocricetus auratus</i>) is gaining importance as a new experimental animal model for multiple pathogens, including emerging zoonotic diseases such as Ebola. Nevertheless there are currently no publicly available transcriptome reference sequences or genome for this species.</p><p>Results</p><p>A cDNA library derived from mRNA and snRNA isolated and pooled from the brains, lungs, spleens, kidneys, livers, and hearts of three adult female Syrian hamsters was sequenced. Sequence reads were assembled into 62,482 contigs and 111,796 reads remained unassembled (singletons). This combined contig/singleton dataset, designated as the Syrian hamster transcriptome, represents a total of 60,117,204 nucleotides. Our <i>Mesocricetus auratus</i> Syrian hamster transcriptome mapped to 11,648 mouse transcripts representing 9,562 distinct genes, and mapped to a similar number of transcripts and genes in the rat. We identified 214 quasi-complete transcripts based on mouse annotations. Canonical pathways involved in a broad spectrum of fundamental biological processes were significantly represented in the library. The Syrian hamster transcriptome was aligned to the current release of the Chinese hamster ovary (CHO) cell transcriptome and genome to improve the genomic annotation of this species. Finally, our Syrian hamster transcriptome was aligned against 14 other rodents, primate and laurasiatheria species to gain insights about the genetic relatedness and placement of this species.</p><p>Conclusions</p><p>This Syrian hamster transcriptome dataset significantly improves our knowledge of the Syrian hamster's transcriptome, especially towards its future use in infectious disease research. Moreover, this library is an important resource for the wider scientific community to help improve genome annotation of the Syrian hamster and other closely related species. Furthermore, these data provide the basis for development of expression microarrays that can be used in functional genomics studies.</p></div

Pie diagrams showing the alignment positions of the contigs and singletons on the mouse and rat transcript regions.

<p>(A) Pie diagram showing the distribution of alignment positions of the 41,651 contigs and singletons on the mouse transcripts regions (5′ UTR, coding region, 3′ UTR, or inter-region). (B) Pie diagram showing the distribution of alignment positions of the 26,258 contigs and singletons on the rat transcripts regions. For each species and transcript region the number and percentage of aligned sequences are indicated.</p