Rice cultivar Lijiangxintuanheigu under cold stress: control vs. 8M-bM-^DM-^C treated
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
SUBMITTER: Junliang Zhao
PROVIDER: E-GEOD-58132 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Cucumber (Cucumis sativus L.) is an economically important vegetable crop distributed in over 80 countries. Downy mildew (DM) caused by the obligate oomycete Pseudoperonospora cubensis is especially destructive in cucumber production. So far, few studies on the changes in proteomes during the P. cubensis infection have been performed. Using a newly developed TMT-LC-MS/MS analysis, the proteomes of DM-resistant variety ‘ZJ’ and DM-susceptible variety ‘SDG’ under the P. cubensis infection were investigated. In total, 6400 proteins were identified, 5629 of which were quantified. The differential accumulated proteins (DAPs) exhibited various biological functions and diverse subcellular localizations. KEGG enrichment analysis showed that various metabolic pathways were significantly altered under the P. cubensis infection, such as terpenoid backbone biosynthesis, and selenocompound metabolism in ZJ, and starch and sucrose metabolism in SDG. Most of the enzymes associated with terpenoid backbone synthesis were significantly accumulated in ZJ rather than in SDG, suggesting that pathogen-induced terpenoids accumulation might play an important role in the resistance against P. cubensis infection. Furthermore, a number of pathogenesis-related proteins and heat shock proteins were identified as DAPs, suggesting that DM resistance was controlled by a complex network. Our data allowed us to identify and screen more potential proteins related to the DM resistance.
2019-11-12 | PXD010844 | Pride
Project description:Transcriptional differentiation in response to environmental stresses plays critical roles in adaptation. Mangroves are dominant in intertidal zones and form dense forest at the sea-land interface, but little is known about the impact of transcriptional phenotype on their adaptation to the saline environments. To address this issue, we prepared customized chips containing cDNA from the root cDNA library of a mangrove species, Ceriops tagal, and then monitored the time-course transcript profiles in the roots by conducting a series of microarray experiments. Five durations of salt shock with 500 mM NaCl, namely 2, 5, 10, 24 and 192 hours, were included. A total of 88 unigenes that were recognized to be up- or down-regulated by salt shock and both gene categories in relation to stresses-induced responses and transcription factor activity were over-predominant. The stresses-responsive genes were significantly overrepresented, some of which were regulated in differential manners from their homologues genes in Arabidopsis. Specific transcriptional regulations were employed by C. tagal to cope with salt shock, which could benefit the salt-tolerant lifestyle of this mangrove species and possibly contribute to establishment of adaptation to the saline environments. A reference design was used to analyze gene expression differences. Salt stressed young roots were harvested from seedlings of C. tagal at the ends of each shock duration. Young roots of unshocked seedlings were used as controls and harvested at the same time. Three biological replicates were set up for each treatment and corresponding control, respectively, each containing a pool of total RNA from 4 seedlings. Salt stressed samples were compared with the corresponding controls at each time point by co-hybridizing to the customized cDNA arrays
2013-12-31 | E-GEOD-30909 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2012-12-19 | E-GEOD-42996 | biostudies-arrayexpress
Project description:Quorum sensing (QS) is a cell density regulated communication system that bacteria use to coordinate activities, including biofilm formation, involved in colonization and pathogenesis. We have previously shown that inactivation of the QS master regulator LitR attenuates the Vibrio (Allivibrio) salmonicida strain LFI1238 in a fish model. In this work we show that LFI1238 as well as a panel of naturally occurring V. salmonicidia strains are poor biofilm producers. Inactivation of litR strongly enhances medium and temperature dependent adhesion, rugose colony morphology and biofilm formation. Chemical treatment and scanning electron microscopy of the biofilm identified an extracellular matrix consisting mainly of protein filaments and polysaccharides. Further, microarray analysis of planktonic and biofilm cells identified a number of genes regulated by LitR, and among these were homologues of the Vibrio fischeri symbiosis polysaccharide (syp) genes. Disruption of syp alleviated the different phenotypes regulated by LitR in V. salmonicida. Hence, LitR is a repressor of syp expression that is necessary for rugose colony morphology, adhesion and biofilm formation, three phenotypes of the DlitR mutant that are expressed at temperatures below 12M-BM-:C. The DlitR mutant mimics low cell density behavior suggesting that these phenotypes are important during the initial steps of colonization. Although the syp operon in V. salmonicida shows identical gene synteny to the one in the squid symbiont V. fischeri, its regulation is probably more related to vibrio polysaccharide (vps) expression in the human pathogenic Vibrio cholera which is controlled by the LitR homologue HapR. V. salmonicida wild type strain LFI1238 (control) and the isogenic DlitR mutant were grown as statical biofilm in SWT medium, at 4M-BM-0C and harvested after 72 hours. Biological replicates for each sample: 4 wild type, 4 DlitR mutant (including one dye swap), independently grown and harvested. One replicate per array.
2012-12-19 | E-GEOD-42995 | biostudies-arrayexpress
Project description:Quorum sensing (QS) is a cell density regulated communication system that bacteria use to coordinate activities, including biofilm formation, involved in colonization and pathogenesis. We have previously shown that inactivation of the QS master regulator LitR attenuates the Vibrio (Allivibrio) salmonicida strain LFI1238 in a fish model. In this work we show that LFI1238 as well as a panel of naturally occurring V. salmonicidia strains are poor biofilm producers. Inactivation of litR strongly enhances medium and temperature dependent adhesion, rugose colony morphology and biofilm formation. Chemical treatment and scanning electron microscopy of the biofilm identified an extracellular matrix consisting mainly of protein filaments and polysaccharides. Further, microarray analysis of planktonic and biofilm cells identified a number of genes regulated by LitR, and among these were homologues of the Vibrio fischeri symbiosis polysaccharide (syp) genes. Disruption of syp alleviated the different phenotypes regulated by LitR in V. salmonicida. Hence, LitR is a repressor of syp expression that is necessary for rugose colony morphology, adhesion and biofilm formation, three phenotypes of the DlitR mutant that are expressed at temperatures below 12M-BM-:C. The DlitR mutant mimics low cell density behavior suggesting that these phenotypes are important during the initial steps of colonization. Although the syp operon in V. salmonicida shows identical gene synteny to the one in the squid symbiont V. fischeri, its regulation is probably more related to vibrio polysaccharide (vps) expression in the human pathogenic Vibrio cholera which is controlled by the LitR homologue HapR. V. salmonicida wild type strain LFI1238 (control) and the isogenic DlitR deletion mutant were grown in suspension in SWT medium at 8M-BM-0C with 200 rpm and harvested at OD=0.8. Biological replicates for each sample: 4 wild type, 4 DlitR mutant (including one dye swap), independently grown and harvested. One replicate per array.
2012-12-19 | E-GEOD-42994 | biostudies-arrayexpress
Project description:The principal problem arising from prostate cancer (PCa) is its propensity to metastasize to bone. MicroRNAs (miRNAs) play a crucial role in many tumor metastases.The importance of miRNAs in bone metastasis of PCa has not been elucidated to date. We investigated whether the expression of certain miRNAs was associated with bone metastasis of PCa. We examined the miRNA expression profiles of 6 primary and 7 bone metastatic PCa samples by miRNA microarray analysis. Total RNA was taken from the specimens, low molecular weight RNA was seperate and labeled , and then hybridized to capitalbio V3.0 biochip representing about 924 microRNA.
2011-01-31 | E-GEOD-26964 | biostudies-arrayexpress
Project description:Expression changes in silkworm integuments after JH analogue (JHA) methoprene treatment. Two-condition experiments, namely JH analogue (JHA) methoprene treatment (Test) and acetone treatment (Control). Time course: 12 hours after treatment (Hat), 24 Hat, 36 Hat, and 48 Hat.
2014-06-29 | E-GEOD-53374 | biostudies-arrayexpress
Project description:Sixth generation ExiqonM-BM-. locked nucleic acid miRCURYM-bM-^DM-" LNA microarrays were used to search and validate some unidentified miRNAs that regulate EMT in head and neck cancer carcinoma. MiRNA array screening was performed to identify the differential expression of miRNAs involved in EMT in natural epithelial - mesenchymal phenotype cell line pairM-oM-<M-^HHN-4, HN-12) and in TGF-M-NM-2 induced EMT models (HN-4 TGF-M-NM-2,HN-4). HN-4 parental cell was served as the control.One M-BM-5g total RNA from sample and control was labeled with Hy5M-bM-^DM-" and Hy3M-bM-^DM-" fluorescent label, respectively, using the miRCURYM-bM-^DM-" LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
2012-06-04 | E-GEOD-38459 | biostudies-arrayexpress
Project description:Microsporidia have attracted much attention because they infect a variety of species ranging from protists to mammals, including immunocompromised patients with AIDS or cancer. Aside from the study on Nosema ceranae, few works have focused on elucidating the mechanism in host response to microsporidia infection. Nosema bombycis is a pathogen of silkworm pM-CM-)brine that causes great economic losses to the silkworm industry. Detailed understanding of the host (Bombyx mori) response to infection by N. bombycis is helpful for prevention of this disease. The 23 K silkworm genome array was used to investigate host responses (i.e., Bombyx mori) occurring at 2, 4, 6 and 8 d post-infection by Nosema bombycis.We focused on elucidating the mechanism of the host response to microsporidia infection, especially for the investigation of host immune response . The third instar molted silkworm larvae were in oral infected by Nosema bombycis. In order to known the silkworm host response to Nosema bombycis infection at different time points, samples of infected larvae (i.e., the treatment set) and uninfected larvae (i.e., the control set) were collected at 2, 4, 6 and 8 dpi for RNA extraction and array hybridization. The obtained data were usd to investigate on the interplay of the genome-wide expression profile of hosts.
2013-09-27 | E-GEOD-51247 | biostudies-arrayexpress
Project description:Hepatocellular carcinoma (HCC) is one of the most malignant and lethal cancers in the world. Its complex process of molecular pathogenesis indicates that HCC is caused by multiple etiological factors and involves multiple types of genes during its development and progression. In the current study, we performed a microarray analysis on the mRNA transcriptome of HCC (C), peri-cancerous liver (P) and normal liver (N) tissues. After integrating these results with information from the Gene Ontology and KEGG Pathway databases, we analyzed the potential interactions between different genes and constructed an interaction network, and identified the regulator, mediator and effector genes in this interaction network. Three types of tissues: 49 pairs of homogenous human primary hepatocellular carcinoma (Cancer, C) and pericancer liver tissues (Pericancer, P), 10 normal liver tissues (Normal, N). Three-condition experiment, HCC vs. Normal and Pericancer vs. Normal.
2013-03-14 | E-GEOD-45114 | biostudies-arrayexpress