Molecular biology of Ca. Endonucleobacter
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB45543 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bathymodiolus childressi is a species of deep-sea mussels found predominantly in the Gulf of Mexico. It colonizes cold seeps such as brine pool and oil seeps. The success of these animals in such environment is thought to be due to the symbiotic association of the mussel host with several species of bacteria. The aim of this study is to understand the role of the different partners involved in the symbiotic system using various “-omics” approaches. In addition to protein identification we used the mass spectrometry data generated and submitted with this project to derive the stable carbon isotope ratios for the different members of the symbiosis using the direct Protein-SIF method. The respective isotope pattern file and SIF computation files are included with this submission.
2020-02-27 | PXD008089 | Pride
Project description:The project was designed to explore biological rhythms in the hydrothermal vent mussel Bathymodiolus azoricus. The experiment provides the first high-resolution temporal transcriptomes of an hydrothermal species, both in situ and in the laboratory. For each condition, 5 mussels were sampled every 2h 4min for 24h 48min.
2020-06-12 | E-MTAB-8451 | biostudies-arrayexpress
Project description:Genomic study of the association between 'Bathymodiolus' childressi deep sea mussel and its bacterial symbionts.
| PRJEB19882 | ENA
Project description:Transcriptomic study of the association between 'Bathymodiolus' childressi deep sea mussel and its bacterial symbionts.
| PRJEB23284 | ENA
Project description:Azotobacter vinelandii CA strain:CA Genome sequencing
| PRJNA186698 | ENA
Project description:Colonization of deep-sea hydrothermal vents by invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers of these ecosystems. Anatomical adaptations such as the establishment of specialized cells or organs have been evidenced in numerous deep-sea invertebrates. However, very few studies detailed global inter-dependencies between host and symbionts in these ecosystems. In this study, we proposed to describe, using a proteo-transcriptomic approach, the effects of symbionts on the deep-sea mussel Bathymodiolus azoricus’ molecular biology. We induced an in situ depletion of symbionts and compared the proteo-transcriptome of the gills of mussels in three conditions: symbiotic mussels (natural population), symbiont-depleted mussels and aposymbiotic mussels
2019-02-13 | GSE124699 | GEO
Project description:Transcriptome analysis of deep-sea mussel Bathymodiolus japonicus during mussel rearing
| PRJDB15847 | ENA
Project description:Carcinoma-associated mesenchymal stem cells (CA-MSCs) are critical stromal progenitor cells within the tumor microenvironment. We previously demonstrated that CA-MSCs differentially express BMP genes, promote tumor cell growth, increase cancer ‘stemness’ and chemotherapy resistance. Here we use RNA sequencing of normal omental MSCs and ovarian CA-MSCs to demonstrate CA-MSCs have global changes in gene expression. Using these expression profiles we create a unique predictive algorithm to classify CA-MSCs. Our classifier, accurately distinguishes normal omental, ovary and bone marrow MSCs from ovarian cancer CA-MSCs. Suggesting broad applicability, the model correctly classifies pancreatic and endometrial cancer CA-MSCs and distinguishes cancer associated fibroblasts (CAFs) from CA-MSCs. Using this classifier, we definitively demonstrate ovarian CA-MSCs arise from tumor mediated reprograming of local tissue MSCs. While cancer cells alone cannot induce a CA-MSC phenotype, the in vivo ovarian tumor micoenvironment (TME) can reprogram omental or ovary MSCs to protumorigenic CA-MSC (classifier score of >0.96). In vitro studies suggest that both tumor secreted factors and hypoxia are critical to induce the CA-MSC phenotype. Interestingly, while the breast cancer TME can reprogram BM MSCs into CA-MSCs, the ovarian TME cannot, demonstrating for the first time that tumor mediated CA-MSC conversion is tissue and cancer type dependent. Together these findings (1) provide a critical tool to define CA-MSCs and (2) highlight cancer cell influence on distinct normal tissues providing powerful insights into the mechanisms underlying cancer specific metastatic niche formation. Carcinoma-associated mesenchymal stem cells (CA-MSCs) are critical stromal progenitor cells within the tumor microenvironment. We previously demonstrated that CA-MSCs differentially express BMP genes, promote tumor cell growth, increase cancer ‘stemness’ and chemotherapy resistance. Here we use RNA sequencing of normal omental MSCs and ovarian CA-MSCs to demonstrate CA-MSCs have global changes in gene expression. Using these expression profiles we create a unique predictive algorithm to classify CA-MSCs. Our classifier, accurately distinguishes normal omental, ovary and bone marrow MSCs from ovarian cancer CA-MSCs. Suggesting broad applicability, the model correctly classifies pancreatic and endometrial cancer CA-MSCs and distinguishes cancer associated fibroblasts (CAFs) from CA-MSCs. Using this classifier, we definitively demonstrate ovarian CA-MSCs arise from tumor mediated reprograming of local tissue MSCs. While cancer cells alone cannot induce a CA-MSC phenotype, the in vivo ovarian tumor micoenvironment (TME) can reprogram omental or ovary MSCs to protumorigenic CA-MSC (classifier score of >0.96). In vitro studies suggest that both tumor secreted factors and hypoxia are critical to induce the CA-MSC phenotype. Interestingly, while the breast cancer TME can reprogram BM MSCs into CA-MSCs, the ovarian TME cannot, demonstrating for the first time that tumor mediated CA-MSC conversion is tissue and cancer type dependent. Together these findings (1) provide a critical tool to define CA-MSCs and (2) highlight cancer cell influence on distinct normal tissues providing powerful insights into the mechanisms underlying cancer specific metastatic niche formation.
2018-08-17 | GSE118624 | GEO
Project description:Bathymodiolus mussels inhabiting deep-sea hydrothermal vents harbor bacterial symbionts in their gills, which support the animals’ diet. While the basic mechanisms of energy generation and CO2 fixation that drive these symbioses are largely established, details of molecular interactions between the symbiotic partners and adaptations to their respective habitats remain unknown. In this study, we therefore comparatively examined the genomes and proteomes of two Bathymodiolus hosts and their respective symbionts from different geographical locations. Two mussel species were proteomically compared: i) B. thermophilus mussel containing sulfur-oxidizing symbiont from the east pacific rise. thermophilus and ii) B. azoricus containing thiotrophic and methanotrophic symbionts from the mid-atlantic ridge. Symbionts (for both species) and host components (for B. azoricus) were selectively enriched using a multi-step centrifugation procedure. Enriched host and symbiont fractions along with unenriched gill foot tissue were subject to in-depth semi-quantitative proteomic analyses using the orbitrap and velos mass spectrometers. Proteins were quantified based on their spectral counts using the normalized spectral abundance factor (NSAF) method. We identified common strategies of metabolic interactions that provide mutual nutritional support between host and symbionts, such as the detoxification of ambient sulfide by the Bathymodiolus host, which provides a stable thiosulfate reservoir for the thiotrophic symbionts, and a putative amino acid cycling mechanism that could supply the host with symbiont-derived amino acids. A suite of genes and proteins putatively related to virulence or defense functions was particularly abundant in the B. thermophilus symbiont, compared to its symbiont relatives, and may pose a host species-specific adaptation. Our results reveal both, a high degree of integration between the symbiotic partners, and great potential to adapt to the prevailing environment, which facilitate the holobiont’s survival in its hydrothermal vent habitat.
2019-11-08 | PXD011639 | Pride
Project description:We characterized the marine natural product cortistatin A (CA) as an inhibitor of CDK8 to determine whether pharmacologic inhibition of CDK8 regulates super-enhancer function and inhibits AML proliferation. In this series, we use ChIP-seq of H3K27ac, H3K4me1, MED1, CDK8, BRD4, and RNA polymerase II (PolII) to examine enhancer occupancy and transcriptional response to CA in human cells lines.
2015-09-25 | GSE65138 | GEO