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Oryza sativa
18 Downloadable Samples
Affymetrix Rice Genome Array (rice)
Description
Bph6 is a gene that confers rice high resistance to its devastating pest BPH. Understanding the molecular responses of the resistant and susceptible varieties would pave the way to controlling the pest more effectively.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
NextSeq 500
Description
This study is aimed to compare the gene expression between wild type and 35S:6MYC-HARP1 in response to wounding treatment.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples
SRP094817- Zea mays
- 2 Downloadable Samples
- Illumina HiSeq 3000
Description
Transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. To test our hypothesis, we performed circRNA-Seq(RNase R treated) on B73 seedlings(third leaves of V3 stage), and uncovered 1,572 high-confidence maize circRNAs, which show distinct genomic features compared to linear transcripts. Comprehensive analyses showed that LINE1-like elements (LLE) and their reverse complementary pairs (RCPLLEs) are significantly enriched in the flanking regions of circRNAs.
Publication Title
Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize.
Sample Metadata Fields
Specimen part, Disease
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- Saccharomyces cerevisiae
- 34 Downloadable Samples
- Illumina HiSeq 2500
Description
As an ancient winning strategy of microorganisms, glucose repression mechanism has become specialized to perfection in Saccharomyces cerevisiae. The galactose (GAL) metabolism network is stringently regulated by glucose repression in yeast and has been a classic system for studying gene regulation. We show here that the population of S. cerevisiae living in fermented milks has autonomously reinstated an ancient version of the structural GAL genes through introgression. The introgressed GAL network has completely abolished the glucose repression and conversed from a strictly inducible to a constitutive system through coordinative polygenic changes in the regulatory components of the network, including transitions in the upstream repressing sequence site of GAL4 that impair Mig1p-mediated repression and loss of function of the inducer Gal3p and the repressor Gal80p. In addition, the introgressed GAL2 gene has been duplicated while the native HXT6 and HXT7 genes have been inactivated, resulting in galactose-over-glucose preference and elevated galactose utilization rate. Relying on the reverse evolution of the GAL network, the non-lactose fermenting yeast has become a dominant species co-existing with other lactose fermenting microorganisms in fermented milks. Our results also provide new clues for developing yeast strains devoid of barriers to co-utilization of different sugars.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples SRP165652- Homo sapiens
- 3 Downloadable Samples
- Ion Torrent S5
Description
This study presented the preliminary mechanistic studies of teniposide analogs for toxicity reduction
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
The differential expression of gene in bone marrow derived macrophages from Ckip-1 KO mice and WT mice.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
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