Ralstonia solanacearum_GMI1000 and UW551_20 C and 28 C.
ABSTRACT: This SuperSeries is composed of the following subset Series: GSE33657: Expression analysis of Ralstonia solanacearum strain GMI1000 at 20°C and 28°C in rich medium (CPG) and in planta GSE33661: Expression analysis of Ralstonia solanacearum strain UW551 at 20°C and 28°C in rich medium (CPG) and in planta Refer to individual Series
Project description:Investigation of whole genome gene expression level changes in the bacterial wilt pathogen Ralstonia solanacearum, strain UW551 at 20°C and 28°C in culture and in planta. The temperatel strain UW551 can wilt and cause full-blown disease on tomato plants at 28°C as well as at 20°C. A 16 array study using total RNA recovered from the following: 8 separate cultures of Ralstonia solanacearum strain UW551 grown in rich medium-CPG (4 grown at 20°C and 4 grown at 28°C) 8 separate in planta samples of Ralstonia solanacearum strain UW551 harvested from diseased tomato plants cv. BonnyBest (4 recovered from plants grown at 20°C and 4 from plants grown at 28°C) Each array (4-plex format) measures the expression level of 4318 genes from Ralstonia solanacearum strain UW551 with 2 to 6, 40-70 mer probes per gene, with two-fold technical redundancy. The arrays also contain probes for intergenic regions with no technical replicates.
Project description:Investigation of whole genome gene expression level changes in the bacterial wilt pathogen Ralstonia solanacearum, strain GMI1000 at 20°C and 28°C in culture and in planta. The tropical strain GMI1000 cannot wilt tomato plants at 20°C although it can cause full-blown disease at 28°C. A 16 array study using total RNA recovered from the following: 8 separate cultures of Ralstonia solanacearum strain GMI1000 grown in rich medium-CPG (4 grown at 20°C and 4 grown at 28°C) 8 separate in planta samples of Ralstonia solanacearum strain GMI1000 harvested from diseased tomato plants cv. BonnyBest (4 recovered from plants grown at 20°C and 4 from plants grown at 28°C) Each array (4-plex format) measures the expression level of 5061 genes from Ralstonia solanacearum strain GMI1000 with 2 to 6, 40-70 mer probes per gene, with two-fold technical redundancy. The arrays also contain probes for intergenic regions with no technical replicates.
Project description:Investigation of whole-genome gene expression level changes in C57Bl6 Lrp5-/- mammary epithelial cells, compared to the wild-type strain. The mammary epithelial cells were isolated from numbers 4 and 5 mammary glands. The Lrp5-/- mouse strain described in this study has been further described in Lindvall C, Evans NC, Zylstra CR, Li Y, Alexander CM, Williams BO. 2006. The Wnt signaling receptor Lrp5 is required for mammary ductal stem cell activity and Wnt1-induced tumorigenesis. J Biol Chem. 2006 Nov 17;281(46):35081-7. Epub 2006 Sep 13. PMID: 16973609. Mammary epithelial cells were isolated from 6 groups of Lrp5+/+ and 3 groups of Lrp5-/- mice. The isolated RNA was submitted to the Gene Expression Center, University of Wisconsin-Madison where it was labelled with Cy3. Labelled samples were submitted to Roche Nimblegen and were hybridized to Mus musculus 1-Plex arrays that represent 42,586 mouse genes.
Project description:Whole genome expression array comparison of primary keratinocytes to retinoic acid-differentiated hES cell derivatives Cells were differentiated according to Metallo et al. Stem Cells 2008 A 3 chip study was conducted using competitive hybridization comparing pFKs to hEKs obtained in 3 independent differentiation experiments
Project description:Peyraud2016 - Metabolic reconstruction
(iRP1476) of Ralstonia solanacearum GMI1000
This model is described in the article:
A Resource Allocation
Trade-Off between Virulence and Proliferation Drives Metabolic
Versatility in the Plant Pathogen Ralstonia solanacearum.
Peyraud R, Cottret L, Marmiesse L,
Gouzy J, Genin S.
PLoS Pathog. 2016 Oct; 12(10):
Bacterial pathogenicity relies on a proficient metabolism
and there is increasing evidence that metabolic adaptation to
exploit host resources is a key property of infectious
organisms. In many cases, colonization by the pathogen also
implies an intensive multiplication and the necessity to
produce a large array of virulence factors, which may represent
a significant cost for the pathogen. We describe here the
existence of a resource allocation trade-off mechanism in the
plant pathogen R. solanacearum. We generated a genome-scale
reconstruction of the metabolic network of R. solanacearum,
together with a macromolecule network module accounting for the
production and secretion of hundreds of virulence determinants.
By using a combination of constraint-based modeling and
metabolic flux analyses, we quantified the metabolic cost for
production of exopolysaccharides, which are critical for
disease symptom production, and other virulence factors. We
demonstrated that this trade-off between virulence factor
production and bacterial proliferation is controlled by the
quorum-sensing-dependent regulatory protein PhcA. A phcA mutant
is avirulent but has a better growth rate than the wild-type
strain. Moreover, a phcA mutant has an expanded metabolic
versatility, being able to metabolize 17 substrates more than
the wild-type. Model predictions indicate that metabolic
pathways are optimally oriented towards proliferation in a phcA
mutant and we show that this enhanced metabolic versatility in
phcA mutants is to a large extent a consequence of not paying
the cost for virulence. This analysis allowed identifying
candidate metabolic substrates having a substantial impact on
bacterial growth during infection. Interestingly, the
substrates supporting well both production of virulence factors
and growth are those found in higher amount within the plant
host. These findings also provide an explanatory basis to the
well-known emergence of avirulent variants in R. solanacearum
populations in planta or in stressful environments.
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Project description:Arabidopsis plants were challenged with Ralstonia solanacearum isolate BCCF401 and expression profiles investigated during early and late wilt symptom development. Keywords: Disease state analysis A direct comparison was performed. Two replicate biological experiments were performed and two technical replicates with dye swap were included in each biological replicate.