Transcriptomic profiling of Salmonella Typhimurium upon desiccation on stainless steel and subsequent rehydration
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ABSTRACT:
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74 Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
PROVIDER: GSE46763 | GEO | 2013/05/09
SECONDARY ACCESSION(S): PRJNA202291
REPOSITORIES: GEO
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Project description:Transcriptional profiles of Salmonella Typhimurium str. ST4/74 air-dried onto stainless steel for 4 h was compared to an early stationary phase (ESP) culture control. Cells that had been air-dried for 4 h were then subsequently rehydrated with water for a 30 min period, after which the transcriptional profile was compared to an ESP control. Carried out using 2 biological replicates for each sample; hybridised in a two-channel hybridization against Salmonella genomic DNA as the comparator/reference.
2013-05-09 | E-GEOD-46763 | biostudies-arrayexpress
Project description:Stainless steel biofilm
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Project description:Cronobacter sakazakii is well-known for its desiccation tolerance in the powdered infant formula (PIF) food production environment and the bacterium has been linked with high fatality rates in neonates who consume contaminated product. In this study, using deep-level RNA-sequencing, differentially expressed genes were studied in C. sakazakii ATCCTM29544 grown in simulated low-moisture environment designed to mimic the PIF production environment. Desiccation of bacteria was carried out on stainless steel coupons from which total RNA was subsequently recovered and sequenced. During 4 h of desiccation from the early stationary phase (ESP) grown culture, an approximately 3 log10 reduction was recorded for C. sakazakii viable cell count, with the largest change in viable cells occurring between desiccation hour 1 and 2 during which the culture medium was completely dried. Transcriptomic data obtained after 4 h of desiccation highlighted several highly-up regulated osmotolerance-related genes which were associated with the secondary response mechanism. These actively expressed genes mainly modulate pathways that synthetize glycine betaine and trehalose as well as the transport of these two and other compatible solutes. Understanding the activities of these genes and pathways will assist the development of technologies that mitigate the survival of C. sakazakii in the PIF production process.
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Project description:In this study we have tried to utilize the unique aspects of the T. ruralis response to desiccation and rehydration to design a strategy to identify rehydrins that are of low abundance and perhaps completely novel to the desiccated or rehydration transcriptomes. We have constructed two Subtractive Suppression Hybridization (SSH) libraries (Diatchenko et al., 1996) that are designed to enrich for differentially expressed low-abundance transcripts contained within gametophytic cells either in the slow-dried state (mRNP sequestrated rehydrin transcripts) or cells that have been rapidly dried, rehydrated and sampled at 2h of hydration (rehydrin and recovery transcripts) when the translational change in gene expression is at its peak (Oliver 1991). To achieve this aim we constructed SSH libraries using PolyA RNA isolated from the polysomal (mRNP) fractions from the slow-dried and 2h rehydrated rapid dried gametophytes selected against PolyA RNA from hydrated control gametophytes as the source for driver cDNA. Collections of cDNA clones from each library were sequenced and used to generate a small T. ruralis SSH cDNA microarray for expression profiling of both total RNA extracts for transcript accumulation assessments and polysomal RNA extracts for transcript sequestration and recruitment assessments.
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Project description:This study utilized microarray technology as an exploratory search for mechanisms of systemic effects after welding fume inhalation. In addition, the applicability of this methodological approach for determining specific exposure-induced responses was examined. C57Bl/6J mice were exposed to gas metal arc-stainless steel (GMA-SS) welding fume by inhalation for 10 days (3 hours/day) at 40 mg/m3. Microarray analysis was done on lung, blood and aorta from n=4 mice exposed to welding fume or air (control).
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Project description:RNA-seq of desiccated Cronobacter sakazakii ATCCTM29544 on stainless steel coupons
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Project description:Endothelial cell (EC)-enriched protein coding genes, such as endothelial nitric oxide synthase (eNOS), define quintessential EC-specific physiologic functions. It is not clear whether long noncoding RNAs (lncRNAs) also define cardiovascular cell-type specific phenotypes, especially in the vascular endothelium. Here, we report the existence of a set of EC-enriched lncRNAs and define a role for STEEL (spliced transcript – endothelial enriched lncRNA) in angiogenic potential, macrovascular/microvascular identity and shear stress responsiveness. STEEL is expressed from the terminus of the HOXD locus and is transcribed antisense to HOXD transcription factors. STEEL RNA increases the number and integrity of de novo perfused microvessels in an in vivo model and augments angiogenesis in vitro. The STEEL RNA is polyadenylated, nuclear-enriched and has microvascular predominance. Functionally, STEEL regulates a number of genes in diverse endothelial cells. Of interest, STEEL upregulates both eNOS and the transcription factor Kruppel-like factor 2 (KLF2), and is subject to feedback inhibition by both eNOS and shear-augmented KLF2. Mechanistically, STEEL upregulation of eNOS and KLF2 is transcriptionally mediated, in part, via interaction of chromatin-associated STEEL with the poly-ADP ribosylase, PARP1. For instance, STEEL recruits PARP1 to the KLF2 promoter. This work identifies a role for EC-enriched lncRNAs in the phenotypic adaptation of ECs to both body position and hemodynamic forces, and establishes a newer role for lncRNAs in the transcriptional regulation of EC identity.
2018-02-28 | PXD008581 | Pride
Project description:Listeria monocytogenes (Lm) cells can attach to both cantaloupe surface and food contact surfaces and promote biofilm growth. This study was to understand the impact of cantaloupe juice on the physiology and transcriptome of Lm planktonic cells and biofilm cells grown on stainless steel coupons using confocal laser scanning microscopy (CLSM), Cryo-Scanning Electron Microscopy (Cryo-SEM) and RNA Seq technology. Lm showed a strong autoaggregation phenotype when grown in cantaloupe juice at room temperature. It is interesting to note that Lm formed significantly more biofilms on stainless steel (SS) coupons when grown in cantaloupe juice than in TSB. SEM images revealed a different attachment profile of Lm on SS coupons. In TSB, Lm cells were mainly found in scratches/groves of the metal surface, whereas, in cantaloupe juice they attached to the smooth surface as well. Interestingly, Lm planktonic and biofilm cells in cantaloupe juice showed an elongated cell shape which might be a stress-induced phenotype in cantaloupe juice. Cantaloupe juice induced a distinct transcriptional profile of biofilm and planktonic cells of Lm from TSB. Functional annotation indicated that the significantly differentially expressed genes (DEGs, Padj < 0.05, log2foldchange ≥ 1) from the comparison mainly participated in metabolism, signaling and stress response. Notably, certain pathways downregulated for planktonic cells were significantly upregulated for biofilm cells in cantaloupe juice compared to TSB, including ABC transporters, two-component system, quorum sensing, chemotaxis, and flagellar assembly. These data highlighted the interaction of Lm with food matrix (i.e., cantaloupe) and the role of food matrix on Lm survival and adaptation. These results provided the basis for future functional characterization of genes with potential roles in biofilm formation and persistence of Lm in cantaloupe juice, as well as for development of mitigation practices for Lm biofilms on produce and food contact surfaces.
2023-09-18 | GSE243459 | GEO
Project description:To determine the role of STEEL in endothelial cell (EC) gene regulation, gene expression analysis was conducted on control and STEEL siRNA-treated human dermal microvascular endothelial cells (HMVECs) and human umbilical vein endothelial cells (HUVECs). A total of 225 protein-coding genes were downregulated and 80 were upregulated when both EC types were grouped for analysis. In HMVEC alone, 544 protein-coding genes were downregulated and 218 were upregulated. In HUVEC alone, 177 protein-coding genes were downregulated and 125 were upregulated. Prominently, STEEL siRNA depletion results in the downregulation of two notable protein-coding genes, eNOS and KLF2, which are modulated in ECs subjected to continuous laminar shear stress.
2018-03-30 | GSE108262 | GEO
Project description:In this study we have tried to utilize the unique aspects of the T. ruralis response to desiccation and rehydration to design a strategy to identify rehydrins that are of low abundance and perhaps completely novel to the desiccated or rehydration transcriptomes. We have constructed two Subtractive Suppression Hybridization (SSH) libraries (Diatchenko et al., 1996) that are designed to enrich for differentially expressed low-abundance transcripts contained within gametophytic cells either in the slow-dried state (mRNP sequestrated rehydrin transcripts) or cells that have been rapidly dried, rehydrated and sampled at 2h of hydration (rehydrin and recovery transcripts) when the translational change in gene expression is at its peak (Oliver 1991). To achieve this aim we constructed SSH libraries using PolyA RNA isolated from the polysomal (mRNP) fractions from the slow-dried and 2h rehydrated rapid dried gametophytes selected against PolyA RNA from hydrated control gametophytes as the source for driver cDNA. Collections of cDNA clones from each library were sequenced and used to generate a small T. ruralis SSH cDNA microarray for expression profiling of both total RNA extracts for transcript accumulation assessments and polysomal RNA extracts for transcript sequestration and recruitment assessments. To assess the expression characteristics of the transcripts represented by the SSH contigs we established a cDNA microarray containing the inserts (PCR derived fragment) from each of the 768 individual SSH ESTs, with the exception of thirteen that failed to generate a PCR fragment. Twelve of the missing thirteen SSH EST cDNAs were replaced with PCR fragments from previously isolated T. ruralis cDNAs four of which, representing the ribosomal proteins S14, S16, L23 and L15 (Wood et al., 2000, Zeng and Wood 2000), were previously reported to be constitutively expressed and were added to serve as normalization genes. The remaining eight clones, Tr155, Tr217, Tr403, Tr416, Tr421 (described by Scott and Oliver, 1994), and TrCDPK (U82087) were added as either positive â??up-regulatedâ?? (Tr155, Tr403, Tr421), negative â??down-regulated (Tr217, Tr416), or neutral (TrCDPK) controls based on previous northern analyses. The cDNAs were printed from two 384 well plates in 12 blocks (two columns of 6) of 24 x 8 spots such that each SSH EST and controls were represented in triplicate. Each of the triplicate cDNAs was separated within the blocks to eliminate possible spatial hybridization bias. All hybridizations were duplicated as dye swaps with two separate RNA preparations, from large populations of individual gametophytes (isolated from a minimum of three separate clumps), serving as the source for the sscDNA Cy3 and Cy5 labeled probes. The RNA preparations for the Total polyA RNA were by necessity separate samples from those used to isolate Polysomal poly A RNA.
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