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PROVIDER: PRJNA1300354 | ENA |
REPOSITORIES: ENA
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Project description:Yilmaz2016 - Genome scale metabolic model -
Caenorhabditis elegans (iCEL1273)
This model is described in the article:
A Caenorhabditis elegans
Genome-Scale Metabolic Network Model.
Yilmaz LS, Walhout AJ.
Cell Syst 2016 May; 2(5): 297-311
Abstract:
Caenorhabditis elegans is a powerful model to study
metabolism and how it relates to nutrition, gene expression,
and life history traits. However, while numerous experimental
techniques that enable perturbation of its diet and gene
function are available, a high-quality metabolic network model
has been lacking. Here, we reconstruct an initial version of
the C. elegans metabolic network. This network model
contains 1,273 genes, 623 enzymes, and 1,985 metabolic
reactions and is referred to as iCEL1273. Using flux balance
analysis, we show that iCEL1273 is capable of representing the
conversion of bacterial biomass into C. elegans biomass
during growth and enables the predictions of gene essentiality
and other phenotypes. In addition, we demonstrate that gene
expression data can be integrated with the model by comparing
metabolic rewiring in dauer animals versus growing larvae.
iCEL1273 is available at a dedicated website
(wormflux.umassmed.edu) and will enable the unraveling of the
mechanisms by which different macro- and micronutrients
contribute to the animal's physiology.
This model is hosted on
BioModels Database
and identified by:
MODEL1604210000.
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quantitative kinetic models.
To the extent possible under law, all copyright and related or
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2016-11-03 | MODEL1604210000 | BioModels
Project description:To investigate the effect of mutant E. coli on Caenorhabditis elegans, we performed gene expression profiling of RNA-seq data from Caenorhabditis elegans fed with different E. coli mutants.
2022-09-30 | GSE214285 | GEO
Project description:We utilized a Caenorhabditis elegans (C. elegans) model of human tauopathy to investigate the role of DNA glycosylases (Ung-1 and Nth-1 knockout worms) in disease development and progression. We then performed gene expression profiling analysis using data obtained from RNA-seq of 12 different genotypes grown under normal conditions.
2024-10-23 | GSE235015 | GEO
Project description:Caenorhabditis elegans development, where different environmental or genetic stimuli can each induce larvae to switch from continuous growth to a seemingly identical dauer (dormancy) state, provides a tractable model to explore this question. To identify dauer features that differ or are invariant, we compared gene expression of dauers induced by different dauer-inducing conditions, globally and within >100 sets of curated covarying genes or “modules” enriched for functional features such as ‘protein expression’, mitochondria’, ‘germline’, etc., through gene co-expression network analyses.
2026-02-05 | GSE318477 | GEO
Project description:The oomycete Pythium oligandrum is a potential biocontrol agent to control a wide range of fungal and oomycetes-caused diseases such as Pythium myriotylum-caused rhizome rot in ginger leading to reduced yields and compromised quality. Previously, P. oligandrum has been studied for its plant growth-promoting potential by auxin production and induction of disease resistance by elicitors such as oligandrin. Volatile organic compounds (VOCs) play beneficial roles in sustainable agriculture by enhancing plant growth and resistance. We investigated the contribution of P. oligandrum-produced VOCs on plant growth and disease suppression by initially using N. benthamiana plants for screening. P. oligandrum VOCs significantly enhanced tobacco seedling and plant biomass content. Screening of the individual VOCs showed that 3-octanone and hexadecane promoted the growth of tobacco seedlings. The total VOCs from P. oligandrum also enhanced the shoot and root growth of ginger plants. Transcriptomic analysis showed a higher expression of genes related to plant growth hormones, and stress responses in the leaves of ginger plants exposed to P. oligandrum VOCs. The concentrations of plant growth hormones such as auxin, zeatin, and gibberellic acid were higher in the leaves of ginger plants exposed to P. oligandrum VOCs. In a ginger disease biocontrol assay, the VOC-exposed ginger plants infected with P. myriotylum had lower levels of disease severity. We conclude that this study contributes to understanding the growth-promoting mechanisms of P. oligandrum on ginger and tobacco, priming of ginger plants against various stress and the mechanisms of action of P. oligandrum as a biocontrol agent.
2023-06-22 | GSE235182 | GEO
Project description:Space radiations and microgravity both could cause DNA damage in cells, but the effects of microgravity on DNA damage response to space radiations are still controversial.A mRNA microarray and microRNA microarray in dauer larvae of Caenorhabditis elegans (C. elegans) that endured spaceflight environment and space radiations environment during 16.5-day Shenzhou-8 space mission was performed. The analyzation this study are further described in Gao, Y., Xu, D., Zhao, L., Zhang, M. and Sun, Y. (2015) Effects of microgravity on DNA damage response in Caenorhabditis elegans during Shenzhou-8 spaceflight. International journal of radiation biology, 91, 531-539.
2017-03-01 | GSE90872 | GEO
Project description:Space radiations and microgravity both could cause DNA damage in cells, but the effects of microgravity on DNA damage response to space radiations are still controversial. A mRNA microarray and microRNA microarray in dauer larvae of Caenorhabditis elegans (C. elegans) that endured spaceflight environment and space radiations environment during 16.5-day Shenzhou-8 space mission were performed. The analyzation this study are further described in Gao, Y., Xu, D., Zhao, L., Zhang, M. and Sun, Y. (2015) Effects of microgravity on DNA damage response in Caenorhabditis elegans during Shenzhou-8 spaceflight. International journal of radiation biology, 91, 531-539.
2017-03-01 | GSE90823 | GEO
Project description:The transcriptomes of model organisms have been defined under specific laboratory growth conditions. The standard protocol for Caenorhabditis elegans growth and maintenance is 20ºC on an Escherichia coli diet. Temperatures ranging from 15ºC to 25ºC or feeding with other species of bacteria are considered physiological lab conditions, but the effect of these conditions on the worm transcriptome have not been well characterized. Here, we compare the global patterns of gene expression for the reference Caenorhabditis elegans strain (N2) grown at 15oC, 20oC, and 25oC on two different diets, Escherichia coli and Bacillus subtilis. When C. elegans were fed E. coli and the growth temperature was increased, we observed an enhancement of defense response pathways and down-regulation of genes associated with metabolic functions. However, when C. elegans were fed B. subtilis and the growth temperature was increased, the nematodes exhibited a decrease in defense response pathways and an enhancement of expression of genes associated with metabolic functions. Our results show that C. elegans undergo significant metabolic and defense response changes when the maintenance temperature fluctuates within the physiologically accepted experimental range and that the degree of pathogenicity of the bacterial diet can further alter the worm transcriptome.
2017-11-02 | GSE101524 | GEO