Similar Datasets
Project description:Rothia mucilaginosa strain:IE | isolate:IE Raw sequence reads
| PRJNA672880 | ENA
Project description:Infective endocarditis (IE) has high mortality, partly due to delayed diagnosis and treatment. Currently, no biomarker can identify IE in patients with fever and clinical picture of infection. To find putative biomarkers we analyzed serum levels of two proteins found in cardiac valves, osteoprotegerin and fibulin-1 among 689 and 696 patients on clinical suspicion of IE, respectively. In addition, proteomic analyses were performed in 24 patients with bacteremia, 12 patients with definite IE and 12 patients with excluded IE.
2020-02-26 | PXD010149 | Pride
Project description:Background—Diagnosis and pronostic assessment are challenging in infective endocarditis (IE). To investigate the host response during IE and identify potential biomarkers, we determined the circulating gene expression profile through a whole genome microarray analysis. Methods and Results—A transcriptomic case-control study was performed on blood samples from patients with native valve IE (n=39), excluded IE after an initial suspicion (n=10) at patient’s admission, and age-matched healthy controls (n=10). The whole genome microarray analysis showed that patients with IE exhibited a specific transcriptional program with a predominance of gene categories associated with cell activation, innate immune and inflammatory responses. These categories were organized in a dense network from which arose numerous subnetworks including major histocompatibily complex and natural killer cell network, type 1 interferon pathway and intracellular traffic. Quantitative real-time RT-PCR performed on a selection of highly modulated genes showed that the expression of the gene encoding S100 calcium binding protein A11 (S100A11) was significantly increased in patients with IE in comparison with controls (P<0.001) and patients with excluded IE (P<0.05). Interestingly, the upregulated expression of S100A11 gene was more pronounced in staphylococcal IE than in streptococcal IE (P<0.01). These results were confirmed by serum concentrations of the S100A11 protein. Finally, we showed that, in patients with IE, the upregulation of aquaporin-9 gene (AQP9) was significantly related to the occurrence of acute heart failure (P=0.02). Conclusions— Using transcriptional signatures of blood samples, we identified S100A11 as a potential diagnostic marker of IE. In addition, the determination of AQP9 may improve the prognostic assessment of IE.
2012-03-12 | GSE29161 | GEO
Project description:BackgroundM-bM-^@M-^TDiagnosis and pronostic assessment are challenging in infective endocarditis (IE). To investigate the host response during IE and identify potential biomarkers, we determined the circulating gene expression profile through a whole genome microarray analysis. Methods and ResultsM-bM-^@M-^TA transcriptomic case-control study was performed on blood samples from patients with native valve IE (n=39), excluded IE after an initial suspicion (n=10) at patientM-bM-^@M-^Ys admission, and age-matched healthy controls (n=10). The whole genome microarray analysis showed that patients with IE exhibited a specific transcriptional program with a predominance of gene categories associated with cell activation, innate immune and inflammatory responses. These categories were organized in a dense network from which arose numerous subnetworks including major histocompatibily complex and natural killer cell network, type 1 interferon pathway and intracellular traffic. Quantitative real-time RT-PCR performed on a selection of highly modulated genes showed that the expression of the gene encoding S100 calcium binding protein A11 (S100A11) was significantly increased in patients with IE in comparison with controls (P<0.001) and patients with excluded IE (P<0.05). Interestingly, the upregulated expression of S100A11 gene was more pronounced in staphylococcal IE than in streptococcal IE (P<0.01). These results were confirmed by serum concentrations of the S100A11 protein. Finally, we showed that, in patients with IE, the upregulation of aquaporin-9 gene (AQP9) was significantly related to the occurrence of acute heart failure (P=0.02). ConclusionsM-bM-^@M-^T Using transcriptional signatures of blood samples, we identified S100A11 as a potential diagnostic marker of IE. In addition, the determination of AQP9 may improve the prognostic assessment of IE. The transcriptomic case-control study was performed in 39 consecutive patients with native valve IE (IE group) diagnosed by a multidisciplinary team who applied the modified Duke criteria,12 10 patients admitted for a suspicion of IE but with a final excluded IE diagnosis. Ten IE patients and five controls were arbitrary selected and investigated with microarrays.
2012-03-12 | E-GEOD-29161 | biostudies-arrayexpress
Project description:The goal of the present study was to determine whether loss of the insulin receptor alters the molecular landscape of the intestinal mucosa, using intestinal-epithelial insulin receptor knockout (IE-irKO) mice and both genetic (IRfl/fl and Villin-cre) controls. Quantitative proteomic analysis by Liquid Chromatography Mass Spectrometry (LC-MS) was deployed on jejunal and colonic mucosa from mice fed a chow- or Western diet (WD). Jejunal mucosa from IE-irKO mice demonstrated alterations in all intestinal cell linages, Paneth, goblet, absorptive and enteroendocrine cells, whereas only goblet and absorptive cells were affected in the colon. There was also a significant effect of the WD on the gut proteome. A significant reduction was detected in Paneth cell proteins with anti-microbial activity, including lysozyme C-1, angiogenin-4, cryptdin-related sequence1C-3 and -2, a-defensin 17 and intelectin-1a. The key protein expressed by goblet cells, mucin-2, was also reduced in the IE-irKO mice. Proteins involved in lipid metabolism, including aldose reductase-related protein 1, 15-hydroxyprostaglandin dehydrogenase [NAD(+)], apolipoprotein A-II and pyruvate dehydrogenase kinase isozyme 4, were increased in the mucosa of WD-fed IE-irKO mice as compared to controls. In contrast, expression of the nutrient-responsive gut hormones, glucose-dependent insulinotropic polypeptide and neurotensin, was reduced in the jejunal mucosa of IE-irKO mice, and there was a reduction in proteins of the P-type ATPases and the solute carrier-transporter family in the colon of WD-fed IE-irKO mice. In conclusion, IE-irKO mice display a distinct molecular phenotype, suggesting a biological role of insulin and its receptor in determining differentiated cell-specificity in the intestinal epithelium.
2017-08-18 | PXD005932 | Pride
Project description:Larkinella sp. IE-0392 Genome sequencing
| PRJNA793357 | ENA
Project description:Salivary glands produce saliva and play essential roles in digestion and oral health. Pluripotent stem cell-derived (PSC) organoids provide a powerful platform for studying salivary gland development and developing new regenerative therapy. The previous protocol of PSC-derived salivary gland organoids required complicated manufacturing processes, which hampered the organoids for basic research and clinical application.Here, by mimicking the regulatory mechanism of developing salivary glands, we reported the differentiation of induced embryonic salivary glands (iE-SGs) from mouse embryonic stem cells by step-wise treatment of retinoic acid and FGF10. We showed that the iE-SGs recapitulated early morphogenetic events, including the thickening and invagination of the salivary gland placode, and then formed initial buds. The iE-SGs also differentiated into developing ducts structures and could develop to striated and excretory ducts when transplanted in vivo. RNA- seq revealed that iE-SGs had gene expression profiles similar to mouse embryonic SMGs. Thus, our study provided an easy and safe method to generate iE-SGs and offered possibilities for studying events during salivary gland morphogenesis in vitro
2022-08-03 | GSE198489 | GEO
Project description:Tan2012 - Antibiotic Treatment, Inoculum Effect
The efficacy of many antibiotics decreases with increasing bacterial density, a phenomenon called the ‘inoculum effect’ (IE). This study reveals that, for ribosome-targeting antibiotics, IE is due to bistable inhibition of bacterial growth, which reduces the efficacy of certain treatment frequencies.
This model is described in the article:
The inoculum effect and band-pass bacterial response to periodic antibiotic treatment.
Tan C, Phillip Smith R, Srimani JK, Riccione KA, Prasada S, Kuehn M, You L.
Mol Syst Biol. 2012 Oct 9; 8:617
Abstract:
The inoculum effect (IE) refers to the decreasing efficacy of an antibiotic with increasing bacterial density. It represents a unique strategy of antibiotic tolerance and it can complicate design of effective antibiotic treatment of bacterial infections. To gain insight into this phenomenon, we have analyzed responses of a lab strain of Escherichia coli to antibiotics that target the ribosome. We show that the IE can be explained by bistable inhibition of bacterial growth. A critical requirement for this bistability is sufficiently fast degradation of ribosomes, which can result from antibiotic-induced heat-shock response. Furthermore, antibiotics that elicit the IE can lead to 'band-pass' response of bacterial growth to periodic antibiotic treatment: the treatment efficacy drastically diminishes at intermediate frequencies of treatment. Our proposed mechanism for the IE may be generally applicable to other bacterial species treated with antibiotics targeting the ribosomes.
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and identified by: MODEL1208300000
.
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.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
2012-11-01 | BIOMD0000000425 | BioModels
Project description:Degeneration of the RPE leads to severe vision loss in, so far incurable, diseases such as age-related macular degeneration and some forms of retinitis pigmentosa. A promising future replacement therapy may be autologous iris epithelial cell transdifferentiation into RPE in vitro and, subsequently, transplantation. In this study we compared the gene expression profiles of the iris epithelium (IE) and the RPE.We compared the gene expression profiles of RPE and IE.
2017-08-02 | GSE81058 | GEO