Ontology highlight
ABSTRACT:
PROVIDER: PRJNA902934 | ENA |
REPOSITORIES: ENA
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Project description:Mastacembelus armatus (zig-zag eel) genome assembly, fMasArm1
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Project description:Sequential hermaphroditism, whereby the sex of one individual changes during its development, has been described in many fish species. Yet, the genetic regulation of this dynamic process of sexual differentiation is not well understood. Here, we report the characterization of sequential hermaphroditism in an aquacultural fish, the zig-zag eel (Mastacembelus armatus), based on 4 years of artificial breeding. All M. armatus individuals initially developed as females, with approximately half of them then becoming males after going through an intersex phase.
2021-05-25 | GSE175406 | GEO
Project description:Mastacembelus armatus (zig-zag eel) genome assembly, fMasArm1.2, alternate haplotype
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Project description:The zig-zag model of host-pathogen interaction describes the relative strength of defense response across a spectrum of pathogen-induced plant phenotypes. A stronger defense response results in increased resistance. Here, we investigate the strength of pathogen virulence during disease and place these findings in the context of the zig-zag model. Xanthomonas vasicola pv. holcicola (Xvh) causes sorghum bacterial leaf streak. Despite being widespread, this disease has not been described in detail at the molecular level. We divided diverse sorghum genotypes into three groups based on disease symptoms: water-soaked lesions, red lesions, and resistance. Bacterial growth assays confirmed that these three phenotypes represent a range of resistance and susceptibility. To simultaneously reveal defense and virulence responses across the spectrum of disease phenotypes, we performed dual RNA-seq on Xvh-infected sorghum. Consistent with the zig-zag model, the expression of plant defense-related genes was strongest in the resistance interaction. Surprisingly, bacterial virulence genes related to the type III secretion system (T3SS) and type III effectors (T3Es) were also most highly expressed in the resistance interaction. This expression pattern was observed at multiple time points within the sorghum-Xvh pathosystem. Further, a similar expression pattern was observed in Arabidopsis infected with Pseudomonas syringae for effector-triggered immunity via AvrRps4 but not AvrRpt2. Specific metabolites were able to repress the Xvh virulence response in vitro and in planta suggesting a possible signaling mechanism. Taken together, these findings reveal multiple permutations of the continually evolving host-pathogen arms race from the perspective of host defense and pathogen virulence responses.
2019-12-14 | GSE142035 | GEO
Project description:Pritchard2014 - plant-microbe
interaction
This
model is an abstraction of a generic interaction between microbes,
and a plant host. The reactions are generally intended to be
representative of processes, not specific molecular mechanisms
(except where indicated, eg. for activation of receptors). The
model is intended to be of a similar level of abstraction as the
Zig-Zag model proposed in Jones and Dangl (2006) [PMID:
17108957
],
but
to represent a dynamic system. Jones and Dangl (2006) model is
used here to illustrate the advantages of dynamic representations
of systems over expository models such as the Zig-Zag
model.
This model is described in the article:
The zigzag model of
plant-microbe interactions: is it time to move on?
Pritchard L, Birch PR.
Mol. Plant Pathol. 2014 Dec; 15(9):
865-870
Abstract:
This model is hosted on
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and identified by:
BIOMD0000000563.
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quantitative kinetic models.
To the extent possible under law, all copyright and related or
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2024-09-02 | BIOMD0000000563 | BioModels
Project description:modENCODE_submission_3376 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP83(official name : OP83 genotype : unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZAG-1::EGFP fusion protein is expressed in the correct zag-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZAG-1 transcription factor. made_by : R Waterston ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene zag-1; Strain OP83(official name : OP83 genotype : unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZAG-1::EGFP fusion protein is expressed in the correct zag-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZAG-1 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius
2011-05-24 | E-GEOD-29476 | biostudies-arrayexpress
Project description:modENCODE_submission_3220 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP83(official name : OP83 genotype : unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZAG-1::EGFP fusion protein is expressed in the correct zag-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZAG-1 transcription factor. made_by : R Waterston ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene zag-1; Strain OP83(official name : OP83 genotype : unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZAG-1::EGFP fusion protein is expressed in the correct zag-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZAG-1 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius
2011-05-24 | E-GEOD-29466 | biostudies-arrayexpress