Transcription profiling of rice virus-susceptible and -resistant lines NIL37 and NIL22
Ontology highlight
ABSTRACT: Near-isogenic lines NIL37 and NIL22 were developed from the cross between Ilpum (recurrent parent susceptible to rice stripe virus (RSV)) and Shinkwang (donor parent resistant to RSV). NIL37 is susceptible to RSV, whereas NIL22 is resistant to RSV. In order to identify genes which are constitutively differentially expressed between NIL37 and NIL22, the gene expression in the two lines were compared at two different conditions (healthy, and RSV-inoculated). Experiment Overall Design: Total RNA was isolated from 14-day old plants of NIL37 and NIL22 at two different conditions (healthy and RSV-inoculated). The levels of gene expression in the two lines of the same condition were compared by microarray. Each experiment was repeated twice.
Project description:Near-isogenic lines TW16-1263 and TW16-1029 were developed from the cross between TN1 (recurrent parent susceptible to rice tungro spherical virus (RTSV)) and Utri Merah (donor parent resistant to RTSV). TW16-1263 is susceptible to RTSV, whereas TW16-1029 is resistant to RTSV. In order to identify genes which are constitutively differentially expressed between TW16-1263 and TW16-1029, the gene expression in the two lines were compared at three different conditions (healthy, green leafhopper (GLH)-inoculated, and RTSV-inoculated). Experiment Overall Design: Total RNA was isolated from 14-day old plants of TW16-1263 and TW16-1029 at three different conditions (healthy, GLH-inoculated, and RTSV-inoculated). The levels of gene expression in the two lines of the same condition were compared by microarray. Each experiment was repeated twice.
Project description:Near-isogenic lines TW16-4 and TW16-69 were developed from the cross between TN1 (recurrent parent susceptible to rice tungro spherical virus (RTSV)) and Utri Merah (donor parent resistant to RTSV). TW16-4 is susceptible to RTSV, whereas TW16-69 is resistant to RTSV. In order to identify genes which are constitutively differentially expressed between TW16-4 and TW16-69, the gene expression in the two lines were compared at three different conditions (healthy, green leafhopper (GLH)-inoculated, and RTSV-inoculated). Experiment Overall Design: Total RNA was isolated from 14-day old plants of TW16-4 and TW16-69 at three different conditions (healthy, GLH-inoculated, and RTSV-inoculated). The levels of gene expression in the two lines of the same condition were compared by microarray. Each experiment was repeated twice.
Project description:Near-isogenic lines NIL37 and NIL22 were developed from the cross between Ilpum (recurrent parent susceptible to rice stripe virus (RSV)) and Shinkwang (donor parent resistant to RSV). NIL37 is susceptible to RSV, whereas NIL22 is resistant to RSV. In order to identify genes which are constitutively differentially expressed between NIL37 and NIL22, the gene expression in the two lines were compared at two different conditions (healthy, and RSV-inoculated). Keywords: Constitutive differential expression
Project description:Near-isogenic lines TW16-4 and TW16-69 were developed from the cross between TN1 (recurrent parent susceptible to RTSV) and Utri Merah (donor parent resistant to RTSV). TW16-4 is susceptible to RTSV, whereas TW16-69 is resistant to RTSV based on a serolog. Experiment Overall Design: Comparison between RTSV and mock-infected rice. Biological replicates: 2 control (mock), 2 RTSV-infected, independently grown and harvested at 7 days after inoculation (DAI). Each sample was prepared using leaf tissues pooled from 5 plants grown under the same conditions.
Project description:Near-isogenic lines TW16-1263 and TW16-1029 were developed from the cross between TN1 (recurrent parent susceptible to rice tungro spherical virus (RTSV)) and Utri Merah (donor parent resistant to RTSV). TW16-1263 is susceptible to RTSV, whereas TW16-1029 is resistant to RTSV. In order to identify genes which are constitutively differentially expressed between TW16-1263 and TW16-1029, the gene expression in the two lines were compared at three different conditions (healthy, green leafhopper (GLH)-inoculated, and RTSV-inoculated). Keywords: Constitutive differential expression
Project description:Near-isogenic lines TW16-4 and TW16-69 were developed from the cross between TN1 (recurrent parent susceptible to rice tungro spherical virus (RTSV)) and Utri Merah (donor parent resistant to RTSV). TW16-4 is susceptible to RTSV, whereas TW16-69 is resistant to RTSV. In order to identify genes which are constitutively differentially expressed between TW16-4 and TW16-69, the gene expression in the two lines were compared at three different conditions (healthy, green leafhopper (GLH)-inoculated, and RTSV-inoculated). Keywords: Constitutive differential expression
Project description:Rice stripe virus (RSV) is one of the major virus diseases of rice in East Asia. Rice plants infected with RSV usually show symptoms such as chlorotic leaf stripes, weakness and senescence of leaves, and dwarfism. In order to characterize the host response to RSV infection at the gene expression level, the changes in transcriptome profiles of RSV-infected rice were monitored at three, six, nine, twelve, and fifteen days after inoculation by a rice oligomicroarray. The microarray data indicated that 1. transcription, translation and protein processing machineries were activated, 2. chloroplasts were disintegrated, and mitochondrion function was activated, 3. genes for transporters and cell wall synthesis were suppressed, and 4. the expression levels of pathogenesis-related genes were changed by RSV infection. Concurrent observation of symptom development, virus accumulation and transcriptome profiles in RSV-infected plants indicates that RSV symptoms are caused by unbalanced activities of organelles, suppression of cell elongation, and uncontrolled water transport, while translation activity of host cells may be increased in correlation with RSV propagation. Keywords: time course, virus infection, disease response Comparison between RSV- and mock-infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested; 4 time points (3, 6, 9, 12 days after inoculation (DAI)). Biological replicate: 1 control, 1 infected, independently grown and harvested; 1 time point (15 DAI). 1 sample derived from 5 plants grown under the same conditons.
Project description:Whirling disease, caused by the pathogen Myxobolus cerebralis, afflicts several salmonid species. Rainbow trout are particularly susceptible and suffer high mortality rates. The disease is persistent and spreading in hatcheries and natural waters of several countries, including the U.S., and the economic losses associated with whirling disease have been extremely large. In this study, gene expression profiling was conducted for resistant and susceptible rainbow trout strains following pathogen exposure with the primary objective of identifying specific genes associated with whirling disease resistance. Several genes were significantly up-regulated in skin following pathogen exposure for both the resistant Hofer and susceptible Trout Lodge rainbow trout strains. For both strains, response to infection appears to be associated with the interferon system. Metallothionein is differentially expressed between the resistant and susceptible strains and is a good candidate for future studies due to its diverse functional roles in inflammation and immune response. The present study has provided the first examination into the genetic basis underlying rainbow trout’s immune response and resistance to the whirling disease pathogen. The identified genes have allowed us to gain initial insight into the molecular mechanisms associated with a salmonid host’s immune response and resistance to whirling disease infection. Keywords: Disease state comparison. 1st comparison: exposed vs control. 2nd comparison: resistant vs susceptible strains Resistant (Hofer) and susceptible (Trout Lodge) rainbow trout strains were exposed to 2,000 triactinomyxons (whirling disease pathogen) per fish. Unexposed controls for each strain were treated identically to exposed other than their lack of pathogen exposure. After twenty-four hours, caudal fin tissue was collected for RNA extraction. Amplified RNA was competitively hybridized (exposed versus control) for each strain. Four biological replicates were used for each experimental condition and a balanced block design was incorporated.
Project description:Defects in DNA damage responses may underlie genetic instability and malignant progression in melanoma. Cultures of normal human melanocytes (NHMs) and melanoma lines were analyzed to determine whether global patterns of gene expression could predict the efficacy of DNA damage cell cycle checkpoints that arrest growth and suppress genetic instability. NHMs displayed effective G1 and G2 checkpoint responses to ionizing radiation-induced DNA damage. A majority of melanoma cell lines (11/16) displayed significant quantitative defects in one or both checkpoints. Melanomas with B-RAF mutations as a class displayed a significant defect in DNA damage G2 checkpoint function. In contrast the epithelial-like subtype of melanomas with wildtype N-RAS and B-RAF alleles displayed an effective G2 checkpoint but a significant defect in G1 checkpoint function. RNA expression profiling revealed that melanoma lines with defects in the DNA damage G1 checkpoint displayed reduced expression of p53 transcriptional targets, such as CDKN1A and DDB2, and enhanced expression of proliferation-associated genes, such as CDC7 and GEMININ. A Bayesian analysis tool was more accurate than significance analysis of microarrays for predicting checkpoint function using a leave-one-out method. The results suggest that defects in DNA damage checkpoints may be recognized in melanomas through analysis of gene expression. Experiment Overall Design: Normal human melanocyte and melanoma cell lines w/wo mutations in B-raf or N-ras were treated with 1.5 Gy IR irridiartion for G1 and G2 checkpoint determination. RNA was isolated from exponentially growing cultures and applied for microarray hybridizaton with Agilent 44 K (G4112A) array.
Project description:We observed the expression profile of the total mRNA of wild-type Thermus thermophilus HB8 strain grown in a rich (TR) medium at 45oC compared with that of 70oC. Experiment Overall Design: wild-type T. thermophilus HB8 strains were each pre-cultured at 70oC for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (0.3 ml) were inoculated into 0.15 liter of the same medium and then cultivated at 70oC. At the Abs600=0.8 (0min), cold medium was added and the temperature were shifted down to 45oC. Cells were collected at 0min and 30min after temperature shift, and then crude RNA was extracted. In order to compare mRNA expression in thewild-type cell between 45oC and 70oC, the expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample in this website.