Project description:Two introgression strains (ZZY10307 and ZZY10330) of C. briggsae onto the X chromosome of C. nigoni results in male sterility. In order to determine the cause, we sequenced the mRNAs from young adult males from these two strains, and compared to fertile males of the two parent species (AF16 and JU1421). Two wild-type female samples were also included as platform QC.
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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the public domain worldwide. Please refer to
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Project description:Infection of Pseudomonas donghuensis HYS strain and its fur deletion mutant in Caenorhabditis elegans was conducted to assess changes in the expression profile of Caenorhabditis elegans, and potential core virulence factors were identified by measuring the gene expression levels of the HYS colonizing the nematode's intestine. Preliminary studies indicate that P. donghuensis HYS exhibits significant toxicity towards Caenorhabditis elegans, yet the underlying mechanisms of this pronounced toxicity remain unclear. Previous work identified several virulence factors contributing to the toxicity of HYS through detection and functional validation; however, the molecular mechanisms responsible for its strong toxicity have not been elucidated. Therefore, we aim to analyze the mechanisms underlying HYS's pronounced toxicity by examining the responses of infected Caenorhabditis elegans. The Ferric uptake regulator (Fur) is responsible for maintaining iron homeostasis in Gram-negative bacteria, and given that HYS possesses a greater iron uptake capacity than other common species in the same genus, such as Pseudomonas aeruginosa, we hypothesize that Fur may play a critical role in the strong toxicity exhibited by HYS. Consequently, we infected Caenorhabditis elegans with both HYS and its fur deletion mutant and analyzed the changes in the expression profile of Caenorhabditis elegans. We observed a significant reduction in toxicity following the deletion of fur, indicating that Fur regulates core virulence factors. To identify these core virulence factors, we conducted transcriptomic sequencing of the pathogenic bacteria under various conditions and performed a screening for virulence factors.