Caenorhabditis briggsae
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| CAAC03.dat.gz | Other | |||
| CAAC03.fasta.gz | Fasta.gz | |||
| CAAC03.master.dat | Other | |||
| SRR1043066.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 235 |
Similar Datasets
Project description:An EST project for this worm is being completed
| PRJNA12867 | ENA
Project description:Gebauer2016 - Genome-scale model of
Caenorhabditis elegans metabolism (without bacteria)
This model is one of the two versions
of ElegCyc presented in the paper. It describes the metabolism of a
worm raised in a medium without bacteria.
This model is described in the article:
A Genome-Scale Database and
Reconstruction of Caenorhabditis elegans Metabolism.
Gebauer J, Gentsch C, Mansfeld J,
Schmeißer K, Waschina S, Brandes S, Klimmasch L, Zamboni N,
Zarse K, Schuster S, Ristow M, Schäuble S, Kaleta C.
Cell Syst 2016 May; 2(5): 312-322
Abstract:
We present a genome-scale model of Caenorhabditis elegans
metabolism along with the public database ElegCyc
(http://elegcyc.bioinf.uni-jena.de:1100), which represents a
reference for metabolic pathways in the worm and allows for the
visualization as well as analysis of omics datasets.
Our model reflects the metabolic peculiarities of
C. elegans that make it distinct from other higher
eukaryotes and mammals, including mice and humans. We
experimentally verify one of these peculiarities by showing
that the lifespan-extending effect of L-tryptophan
supplementation is dose dependent (hormetic). Finally, we show
the utility of our model for analyzing omics datasets through
predicting changes in amino acid concentrations after genetic
perturbations and analyzing metabolic changes during normal
aging as well as during two distinct, reactive oxygen
species (ROS)-related lifespan-extending treatments. Our
analyses reveal a notable similarity in metabolic adaptation
between distinct lifespan-extending interventions and point to
key pathways affecting lifespan in nematodes.
This model is hosted on
BioModels Database
and identified by:
MODEL1704200000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-04-20 | MODEL1704200000 | BioModels
Project description:Gebauer2016 - Genome-scale model of
Caenorhabditis elegans metabolism (with bacteria)
This model is one of the two versions
of ElegCyc presented in the paper. It describes the metabolism of a
worm raised in a medium with bacteria
This model is described in the article:
A Genome-Scale Database and
Reconstruction of Caenorhabditis elegans Metabolism.
Gebauer J, Gentsch C, Mansfeld J,
Schmeißer K, Waschina S, Brandes S, Klimmasch L, Zamboni N,
Zarse K, Schuster S, Ristow M, Schäuble S, Kaleta C.
Cell Syst 2016 May; 2(5): 312-322
Abstract:
We present a genome-scale model of Caenorhabditis elegans
metabolism along with the public database ElegCyc
(http://elegcyc.bioinf.uni-jena.de:1100), which represents a
reference for metabolic pathways in the worm and allows for the
visualization as well as analysis of omics datasets.
Our model reflects the metabolic peculiarities of
C. elegans that make it distinct from other higher
eukaryotes and mammals, including mice and humans. We
experimentally verify one of these peculiarities by showing
that the lifespan-extending effect of L-tryptophan
supplementation is dose dependent (hormetic). Finally, we show
the utility of our model for analyzing omics datasets through
predicting changes in amino acid concentrations after genetic
perturbations and analyzing metabolic changes during normal
aging as well as during two distinct, reactive oxygen
species (ROS)-related lifespan-extending treatments. Our
analyses reveal a notable similarity in metabolic adaptation
between distinct lifespan-extending interventions and point to
key pathways affecting lifespan in nematodes.
This model is hosted on
BioModels Database
and identified by:
MODEL1704200001.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-04-20 | MODEL1704200001 | BioModels
Project description:The nematode Caenorhabditis elegans (C. elegans) is often used as a model organism to study cell and developmental biology. Quantitative mass spectrometry has only recently been performed in C. elegans and, so far, most studies have been done on adult worm samples. Here we use quantitative mass spectrometry to characterise protein level changes across the four larval developmental stages (L1-L4) of C. elegans, in biological triplicate. In total, we identify 4,130 proteins and quantify 1,541 proteins that were identified across all four stages in all three biological repeats with at least 2 unique peptides per protein. Using hierarchical clustering and functional ontological analyses, we identify 21 protein groups containing proteins with similar protein profiles across the four stages, and highlight the most overrepresented biological functions in each of these protein clusters. In addition, we use the dataset to identify putative larval stage specific proteins in each individual developmental stage, as well as in the early and late developmental stages. In summary, this dataset provides a system-wide analysis of protein level changes across the four C. elegans larval developmental stages, which serves as a useful resource for the worm development research community.
2017-12-04 | PXD006676 | Pride
Project description:Cocoa protein content is a very interesting source for isolation of antioxidant bio-peptides, which can be used for the prevention of age-related diseases. We use microarrays to study the global genome expression of C. elegans fed with a peptide (13L) isolated from cocoa. Wild type strain N2 of C. elegans was fed with 1 µg/mL of 13L peptide or in Nematode Growth medium (MGM, control fed) until reach young adult stage. Worm population were age-synchronized. RNA was isolated from each populations (control and treated) using RNAasy Kit (Qiagen) and hybridizated on Affymetrix microarrays.
2013-12-31 | E-GEOD-44318 | biostudies-arrayexpress
Project description:C. elegans has served as a laboratory model organism due to its ease of manipulation and the availability of both forward and reverse genetics. In recent years, efforts to study host-pathogen interactions in C. elegans have increased. For example, analysis of infections by bacteria such as Pseudomonas, Salmonella or Serratia has revealed the existence of innate immune pathways in C. elegans that are also conserved in vertebrates. To date, there has been no natural virus infection reported in C. elegans or C. briggsae. Here we describe evidence of natural virus infection in wild isolates of both C. elegans and C. briggsae. Two highly divergent but related RNA viruses in the family Nodaviridae, tentatively named Orsay nodavirus and Santeuil nodavirus, were detected and their genomes partially sequenced. Infected worm lysates passed through 0.2 um filters could be used to infect uninfected worms, which could be further passaged for many generations. Furthermore, the viruses were subject to processing by the RNAi machinery as evidenced by the detection of virally derived small RNAs. Infection of mutant worms defective in small RNA pathways yielded more robust levels of viral RNA as compared to infection of isogenic N2 reference worms. These data demonstrate that nodaviruses are natural parasites of nematodes in the wild. Further study of the interactions between these viruses and nematodes is likely to provide insight into the natural ecology of nematodes and may reveal novel innate immune mechanisms that respond to viral infection.
2011-01-01 | GSE21736 | GEO
Project description:Although most metazoan mitochondrial genomes are highly streamlined and encode little noncoding DNA outside of the "AT" region, the accumulation of mitochondrial pseudogenes and other types of noncoding DNA has been observed in a growing number of animal groups. The nematode species Caenorhabditis briggsae harbors two mitochondrial DNA (mtDNA) pseudogenes, named Psinad5-1 and Psinad5-2, presumably derived from the nad5 protein-coding gene. Here, we provide an in-depth analysis of mtDNA pseudogene evolution in C. briggsae natural isolates and related Caenorhabditis species. Mapping the observed presence and absence of the pseudogenes onto phylogenies suggests that Psinad5-1 originated in the ancestor to C. briggsae and its recently discovered outcrossing relative species Caenorhabditis sp. 5 and Caenorhabditis sp. 9. However, Psinad5-1 was not detected in Caenorhabditis sp. 9 natural isolates, suggesting a lineage-specific loss of this pseudogene in this species. Our results corroborated the previous finding that Psinad5-2 originated within C. briggsae. The observed pattern of mitochondrial pseudogene gain and loss in Caenorhabditis was inconsistent with predictions of the tandem duplication-random loss model of mitochondrial genome evolution and suggests that intralineage recombination-like mechanisms might play a major role in Caenorhabditis mtDNA evolution. Natural variation was analyzed at the pseudogenes and flanking mtDNA sequences in 141 geographically diverse C. briggsae natural isolates. Although phylogenetic analysis placed the majority of isolates into the three previously established major intraspecific clades of C. briggsae, two new and unexpected haplotypes fell outside of these conventional groupings. Psinad5-2 copy number variation was observed among C. briggsae isolates collected from the same geographic site. Patterns of nucleotide diversity were analyzed in Psinad5-1 and Psinad5-2, and confidence intervals were found to overlap values from synonymous sites in protein-coding genes, consistent with neutral expectations. Our findings provide new insights into the mode and tempo of mitochondrial genome and pseudogene evolution both within and between Caenorhabditis nematode species.
| S-EPMC2857805 | biostudies-literature
Project description:Many organisms in the nature can drive themselves into an ametabolic state known as anhydrobiosis upon extreme desiccation. The nematode C. elegans is one of them. However, the anhydrobiotic ability of the worm is limited to a special developmental stage known as the dauer. Besides, the dauer larvae must be first treated by a mild desiccation stress (preconditioning) so that they gain desiccation tolerance. In this study, we investigated the differential gene expression during preconditioning in the C. elegans dauer.
2013-08-23 | E-MEXP-3899 | biostudies-arrayexpress
Project description:The goal of this study is to identify and characterize sites in the C. elegans genome bound by the transcription factor TRA-1. TRA-1 ChIP-seq was performed in the following stages of animals in duplicate: 1) L2 stage of C. elegans wild-type N2 strain; 2) L3 stage of C. elegans wild-type N2 strain; 3) young adult stage of C. elegans glp-4(bn2) mutant; 4) young adult stage of C. elegans spe-11(hc77) mutant; 5) L3 stage of C. briggsae wild-type AF16 strain. As a negative control, TRA-1 ChIP-seq was also performed in C. elegans L3 stage with tra-1(e1834) homozygous and heterozygous mutation. Input DNA was also sequenced in each condition.
2013-11-04 | E-GEOD-48917 | biostudies-arrayexpress
Project description:The nematode Caenorhabditis briggsae is an excellent model organism for the comparative analysis of gene function and developmental mechanisms. To study the evolutionary conservation and divergence of genetic pathways mediating vulva formation, we screened for mutations in C. briggsae that cause the egg-laying defective (Egl) phenotype. Here, we report the characterization of 13 genes, including three that are orthologs of Caenorhabditis elegans unc-84 (SUN domain), lin-39 (Dfd/Scr-related homeobox), and lin-11 (LIM homeobox). Based on the morphology and cell fate changes, the mutants were placed into four different categories. Class 1 animals have normal-looking vulva and vulva-uterine connections, indicating defects in other components of the egg-laying system. Class 2 animals frequently lack some or all of the vulval precursor cells (VPCs) due to defects in the migration of P-cell nuclei into the ventral hypodermal region. Class 3 animals show inappropriate fusion of VPCs to the hypodermal syncytium, leading to a reduced number of vulval progeny. Finally, class 4 animals exhibit abnormal vulval invagination and morphology. Interestingly, we did not find mutations that affect VPC induction and fates. Our work is the first study involving the characterization of genes in C. briggsae vulva formation, and it offers a basis for future investigations of these genes in C. elegans.
| S-EPMC3516484 | biostudies-literature