Ontology highlight
ABSTRACT:
PROVIDER: PRJNA994827 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25277148_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR25277149_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR25277150_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR25277151_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR25277152_subreads.fastq.gz | Fastqsanger.gz |
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Project description:We report the full transcriptome (RNA-Seq) of Vibrio fischeri ES114 in rich medium, seawater, and after venting from the Hawaiian bobtail squid Euprymna scolopes. We also report the effects of ribodepletion on low-biomass samples, down to input amount of 1ng total RNA.
2016-04-26 | GSE80607 | GEO
Project description:The marine bacterium Vibrio fischeri requires flagellar motility to undergo symbiotic initiation with its host, the Hawaiian bobtail squid Euprymna scolopes. We sought to identify the genes activated by the sigma54-dependent flagellar master regulator, FlrA, in V. fischeri, thereby determining the flagellar regulon in this model symbiont.
2013-04-05 | GSE45772 | GEO
Project description:The marine bacterium Vibrio fischeri requires flagellar motility to undergo symbiotic initiation with its host, the Hawaiian bobtail squid Euprymna scolopes. We sought to identify the genes activated by the sigma54-dependent flagellar master regulator, FlrA, in V. fischeri, thereby determining the flagellar regulon in this model symbiont. We performed microarray analysis on wild-type Vibrio fischeri ES114 and a flrA deletion mutant, DM159, grown to mid-log phase in seawater tryptone, a condition in which cells are highly motile (two biological replicates per condition).
2013-04-05 | E-GEOD-45772 | biostudies-arrayexpress
Project description:<p>Associations between animals and microbes affect not only the immediate tissues where they occur, but also the entire host. Metabolomics, the study of small biomolecules generated during metabolic processes, provides a window into how mutualistic interactions shape host biochemistry. The Hawaiian bobtail squid, Euprymna scolopes, is amenable to metabolomic studies of symbiosis because the host can be reared with or without its species-specific symbiont, Vibrio fischeri. In addition, unlike many invertebrates, the host squid has a closed circulatory system. This feature allows a direct sampling of the refined collection of metabolites circulating through the body, a focused approach that has been highly successful with mammals. Here, we show that rearing E. scolopes without its natural symbiont significantly affected one quarter of the more than 100 hemolymph metabolites defined by gas chromatography mass-spectrometry analysis. Further, as in mammals, which harbor complex consortia of bacterial symbionts, the metabolite signature oscillated on symbiont-driven daily rhythms and was dependent on the sex of the host. Thus, our results provide evidence that the population of even a single symbiont species can influence host hemolymph biochemistry as a function of symbiotic state, host sex, and circadian rhythm.</p>
2020-07-02 | MTBLS1186 | MetaboLights
Project description:The bioluminescent bacterium Vibrio fischeri forms a mutually beneficial symbiosis with the Hawaiian bobtail squid, Euprymna scolopes, in which the bacteria, housed inside a specialized light organ, produce light used by the squid in its nocturnal activities. Upon hatching, E. scolopes juveniles acquire V. fischeri from the seawater through a complex process that requires, among other factors, chemotaxis by the bacteria along a gradient of N-acetylated sugars into the crypts of the light organ, the niche in which the bacteria reside. Once inside the light organ, V. fischeri transitions into a symbiotic, sessile state in which the quorum-signaling regulator LitR induces luminescence. In this work we show that expression of litR and luminescence are repressed by a homolog of the V. cholerae virulence factor TcpP, which we have named HbtR. Further, we demonstrate that LitR represses genes involved in motility and chemotaxis into the light organ and activates genes required for exopolysaccharide production. Importance: TcpP homologs are widespread throughout the Vibrio genus; however, the only protein in this family described thus far is a V. cholerae virulence regulator. Here we show that HbtR, the TcpP homolog in V. fischeri, has both a biological role and regulatory pathway completely unlike that in V. cholerae. Through its repression of the quorum-signaling regulator LitR, HbtR affects the expression of genes important for colonization of the E. scolopes light organ. While LitR becomes activated within the crypts, and upregulates luminescence and exopolysaccharide genes and downregulates chemotaxis and motility genes, it appears that HbtR, upon expulsion of V. fischeri cells into seawater, reverses this process to aid the switch from a symbiotic to a planktonic state. The possible importance of HbtR to the survival of V. fischeri outside of its animal host may have broader implications for the ways in which bacteria transition between often vastly different environmental niches.
2020-06-03 | GSE151621 | GEO
Project description:The innate immune response is the first line of defense for all animals to not only detect invading microbes and toxins but also sense and interface with the environment. One such environment that can significantly affect innate immunity is spaceflight. In this study, we explored the impact of microgravity stress on key elements of the NFκB innate immune pathway. The symbiosis between the bobtail squid Euprymna scolopes and its beneficial symbiont Vibrio fischeri was used as a model system under a simulated microgravity environment. The expression of genes associated with the NFκB pathway was monitored over time as the symbiosis progressed. Results revealed that although the onset of the symbiosis was the major driver in the differential expression of NFκB signaling, the stress of simulated low-shear microgravity also caused a dysregulation of expression. Several genes were expressed at earlier time points suggesting that elements of the E. scolopes NFκB pathway are stress-inducible, whereas expression of other pathway components was delayed. The results provide new insights into the role of NFκB signaling in the squid-vibrio symbiosis, and how the stress of microgravity negatively impacts the host immune response. Together, these results provide a foundation to develop mitigation strategies to maintain host-microbe homeostasis during spaceflight.
2024-02-14 | GSE247559 | GEO
Project description:Transcriptome of Vibrio fischeri ES114 in rich medium, seawater, and after venting from the Hawaiian bobtail squid Euprymna scolopes
| PRJNA319479 | ENA
Project description:Coleoid cephalopods (squids, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations remains unknown. Using comparative and functional genomics in the model squid Euprymna scolopes, we reveal the unique genomic, topological, and regulatory organization of cephalopod genomes. We show that cephalopod genomes have been extensively restructured compared to other animals leading to the emergence of hundreds of tightly linked and evolutionary unique gene clusters (microsyntenies). Such novel microsyntenies correspond to topological compartments with a distinct regulatory structure and contribute to complex expression patterns. In particular, we identified a set of microsyntenies associated with cephalopod innovations (MACIs) broadly enriched in cephalopod nervous system expression. We posit that the emergence of MACIs was instrumental to cephalopod nervous system evolution and propose that microsyntenic profiling will be central to understand cephalopod innovations.
2022-03-01 | GSE157549 | GEO