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GSE41159
Oryza sativa
18 Downloadable Samples
Affymetrix Rice Genome Array (rice)
Description
Leaf rate elongation is extremely sensitive to soil water status.
Publication Title
Transcriptome profiling of leaf elongation zone under drought in contrasting rice cultivars.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Oryza sativa indica group
- 17 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Rice deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify
Publication Title
Detection of genomic deletions in rice using oligonucleotide microarrays.
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 8 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
OsPSTOL1 confers phosphorus (P)-deficiency tolerance in rice through enhancement of early root growth. The larger root surface area at early stage provides the plants an advantage for nutrient uptake.
Publication Title
The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
Illumina HiSeq 2500
Description
Mutants in the imprinted PICKLE RELATED 2 gene, suppress seed abortion of fertilization independent seed class mutants and paternal excess interploidy crosses in Arabidopsis
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 12 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Leaves and panicles from recurrent parent KMR3 and a high yielding KMR3-O.rufipogon introgression line were used
Publication Title
Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice.
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 9 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
We exposed Kavya rice seedlings to different gall midge biotypes, GMB1 and GMB4M, which exhibit incompatible and compatible interactions, respectively.
Publication Title
A novel mechanism of gall midge resistance in the rice variety Kavya revealed by microarray analysis.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Epithelial cells in the intestinal mucosa maintain gut homeostasis by interacting with different types of microbiota. Proper appropriate immune responses in the intestinal epithelium are essential for the preservation of the intestinal homeostasis. In the present study, we aimed to identify genotypic and phenotypic changes in mice following oral feeding of various substances which has been shown to differentially affect intestinal homeostasis. We orally fed C57BL/6 mice for either one or seven days with one of the four substances: dextran sulfate sodium (DSS); Typhoid VI Polysaccharide vaccine (Vi vaccine); antibiotic cocktails (AB) of ampicillin, vancomycin, neomycin, and metronidazole; or(probiotics)consisting of Lactobacillus Rhamnosus R0011and L. Acidophilus R0052.While DSS and AB feeding resulted in severe gut pathology characterized by infiltration of inflammatory cells, epithelium shedding, and distortion of paneth cells. Vi vaccine and probiotics feeding resulted in phenotypic improvement of the gut health characterized by epithelial cell proliferation and increased formation of tight junctions between epithelial cells. Interestingly, microarray data showed significant increase in the expression levels of genes regulating cell proliferation and intestinal homeostasis in the gut epithelium of probiotics-and Vi vaccine-fed mice compared to DSS-or AB-fed mice. In addition, expression levels of genes regulating cell death and inflammation were significantly increased in the gut epithelium of DSS- and AB-fed mice. These results suggest that intestinal homeostasis play a pivotal role in maintaining gut health and, subsequently, in protecting host against enteric bacteria and external pathogens infection.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 21 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
In the arms race of bacterial pathogenesis, bacteria produce an array of toxins and virulence factors that disrupt host processes while hosts respond with immune countermeasures. One key virulence mediator of the ubiquitous, opportunistic, extracellular pathogen Pseudomonas aeruginosa is the iron-binding siderophore pyoverdin (PMID:10722571;PMID: 8550201). The mechanisms used by pyoverdin to acquire iron from the host remain incompletely elucidated. Here we demonstrate that mitochondria represent an important target for iron acquisition and that exposure to this toxin results in loss of mitochondrial membrane potential, altered mitochondrial dynamics, and mitophagy in both Caenorhabditis elegans and mammalian cells. We also show that animal mitophagy protects the consequences of siderophore activity, conferring resistance to pyoverdin-mediated host killing. In C. elegans, the conserved autophagic genes bec-1/BECN1 and lgg-1/LC3, and the mitophagic regulator pink-1/PINK1 are required for iron chelator-elicited mitochondrial turnover and provide protection against iron sequestration by P. aeruginosa, likely by ameliorating the mitochondrial damage. While autophagic mechanisms have been implicated in the destruction of intracellular bacteria via a process called xenophagy (PMID: 24005326), our findings represent the first report of resistance to an extracellular pathogen being conferred by authentic autophagic activity that targets host organelles.
Publication Title
A conserved mitochondrial surveillance pathway is required for defense against Pseudomonas aeruginosa.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Caenorhabditis elegans
- 9 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
Pseudomonas aeruginosa is a re-emerging opportunistic pathogen with broad antimicrobial resistance. We have previously reported that the major siderophore pyoverdine from this pathogen disrupts mitochondrial networks and induces a lethal hypoxic response in model host Caernorhabditis elegans. However, the mechanism of such cytotoxicity remained unclear. Here, we demonstrate that pyoverdine translocates into host cells, binding to host ferric iron sources. The reduction of host iron content disrupts mitochondrial function such as NADH oxidation and ATP production and activates mitophagy. This activates a specific immune response that is distinct from colonization-based pathogensis and exposure to downstream pyoverdine effector Exotoxin A. Host response to pyoverdine resembles that of a hypoxic crisis or iron chelator treatment. Furthermore, we demonstrate that pyoverdine is a crucial virulence factor in P. aerguinosa pathogenesis against cystic fibrosis patients; F508 mutation in human CFTR increases susceptibility to pyoverdine-mediated damage.
Publication Title
Pyoverdine, a siderophore from Pseudomonas aeruginosa, translocates into C. elegans, removes iron, and activates a distinct host response.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Caenorhabditis elegans
- 6 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
Pseudomonas aeruginosa is an opportunistic pathogen that causes severe health problems. Despite intensive investigation, many aspects of microbial virulence remain poorly understood. We used a high-throughput, high-content, whole-organism, phenotypic screen to identify small molecules that inhibit P. aeruginosa virulence in C. elegans. Approximately half of the hits were known antimicrobials. A large number of hits were non-antimicrobial bioactive compounds, including the cancer chemotherapeutic 5-fluorouracil. We determined that 5-fluorouracil both transiently inhibits bacterial growth and reduces pyoverdine biosynthesis. Pyoverdine is a siderophore that regulates the expression of several virulence determinants and is critical for pathogenesis in mammals. We show that 5-fluorouridine, a downstream metabolite of 5-fluorouracil, is responsible for inhibiting pyoverdine biosynthesis. We also show that 5-fluorouridine, in contrast to 5-fluorouracil, is a genuine anti-virulent compound, with no bacteriostatic or bacteriocidal activity. To our knowledge, this is the first report utilizing a whole-organism screen to identify novel compounds with antivirulent properties effective against P. aeruginosa.
Publication Title
A High-Content, Phenotypic Screen Identifies Fluorouridine as an Inhibitor of Pyoverdine Biosynthesis and Pseudomonas aeruginosa Virulence.
Sample Metadata Fields
Specimen part, Treatment
View Samples