Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1232963 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32606978_1.fastq.gz | Fastqsanger.gz | |||
| SRR32606979_1.fastq.gz | Fastqsanger.gz | |||
| SRR32606980_1.fastq.gz | Fastqsanger.gz | |||
| SRR32606981_1.fastq.gz | Fastqsanger.gz | |||
| SRR32606982_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 17 |
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Project description:Cephalopods have long been getting a lot of attention for their fascinating behavioral abilities and for the complexity of their nervous systems that set them apart from other mollusks. Because of the great evolutionary distance that separates vertebrates from mollusks, it is evident that higher cognitive features have evolved independently in this clade although they sometimes resemble cognitive functions of vertebrates. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Gaining a better understanding of the biology of various species of cephalopods can significantly improve our knowledge of how these animals evolved and better identify the mechanisms that drive the astonishing faculties of their nervous systems. In this study, we performed single-cell transcriptomics of whole heads of Loligo vulgaris pre-hatchlings. We characterized the different cell types in the head of these animals and explored the expression patterns of core cell type markers by hybridization chain reaction. We were able to thoroughly describe some major components of the squid nervous that play important roles for the maintenance, development and sensory function in the nervous system of these animals.
2022-04-07 | GSE200108 | GEO
Project description:As a vital organ to pump blood in the circulatory system, the heart has undergone gradual refinement in its structure and functional efficiency along animal evolution. The occurrence of cardiac chambers, the atrium and the ventricle, is an important event during heart evolution.The two-chambered heart, consisting of a single atrium and a single ventricle, first appeared among mollusks, prior to the evolution of multi-chambered hearts in higher vertebrates. The molecular bases driving the evolution of cardiac chambers, however, are largely unknown. In this study, we studied two common mollusks, the giant African snail (Lissachatina fulica) and scallops (Mizuhopecten yessoensis), to explore the gene profiles of atrium vs. ventricle in mollusks. By examining their heart structures, we found that the snail heart possesses a more compact muscle layer than the scallop heart. Then, RNA sequencing and differentially expressed genes (DEGs) analysis of the atrium and ventricle revealed that these two chambers are distinct in gene expression preference and functional features. Moreover, by comparing with the zebrafish heart, a typical two-chambered heart in vertebrates, mollusk ventricles share similar gene function enrichments with the zebrafish ventricle, but their atria exhibit obvious variation in functional clusters from the zebrafish atrium. Interestingly, we also found that the scallop hearts contain a high amount of collagens, which could be beneficial for heart repair after damage. Together, our work presented novel gene profiling data in the mollusk atria and ventricles, thereby providing new insights into the evolution of cardiac chambers.
2026-01-01 | GSE236112 | GEO
Project description:Biofilms are surface-adhered bacterial communities encased in an extracellular matrix composed of polysaccharides, proteins, and extracelluar (e)DNA, with eDNA being required for the formation and integrity of biofilms. Here we demonstrate that the spatial and temporal release of eDNA is regulated by BfmR, a regulator essential for Pseudomonas aeruginosa biofilm development. The expression of bfmR coincided with localized cell death and DNA release, with high eDNA concentrations localized to the outer part of microcolonies in the form of a ring and as a cap on small clusters. Additionally, eDNA release and cell lysis increased significantly following bfmR inactivation. Genome-wide transcriptional profiling indicated that bfmR was required for repression of genes associated with bacteriophage assembly and bacteriophage-mediated lysis. In order to determine which of these genes were directly regulated by BfmR, we utilized chromatin immunoprecipitation (ChIP) analysis to identify the promoter of PA0691, termed here phdA, encoding a previously undescribed homologue of the prevent-host-death (Phd) family of proteins. Lack of phdA expression coincided with impaired biofilm development, increased cell death and bacteriophage release, a phenotype comparable to ΔbfmR. Expression of phdA in ΔbfmR biofilms restored eDNA release, cell lysis, release of bacteriophages, and biofilm formation to wild type levels. Moreover, overexpression of phdA rendered P. aeruginosa resistant to lysis mediated by superinfective bacteriophage Pf4 which was only detected in biofilms. The expression of bfmR was stimulated by conditions resulting in membrane perturbation and cell lysis. Thus, we propose that BfmR regulates biofilm development by controlling bacteriophage-mediated lysis and thus, cell death and eDNA release, via PhdA.
2011-06-01 | GSE28953 | GEO
Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
2024-04-14 | E-MTAB-13075 | biostudies-arrayexpress
Project description:Primary outcome(s): Development of an automatic bacterial flora evaluation program based on the indices obtained from comprehensive integrated analysis
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Project description:Assessment of Pre-Analytical Sample Handling Conditions for Comprehensive Liquid Biopsy Analysis
| PRJNA643393 | ENA
Project description:Biofilms are surface-adhered bacterial communities encased in an extracellular matrix composed of polysaccharides, proteins, and extracelluar (e)DNA, with eDNA being required for the formation and integrity of biofilms. Here we demonstrate that the spatial and temporal release of eDNA is regulated by BfmR, a regulator essential for Pseudomonas aeruginosa biofilm development. The expression of bfmR coincided with localized cell death and DNA release, with high eDNA concentrations localized to the outer part of microcolonies in the form of a ring and as a cap on small clusters. Additionally, eDNA release and cell lysis increased significantly following bfmR inactivation. Genome-wide transcriptional profiling indicated that bfmR was required for repression of genes associated with bacteriophage assembly and bacteriophage-mediated lysis. In order to determine which of these genes were directly regulated by BfmR, we utilized chromatin immunoprecipitation (ChIP) analysis to identify the promoter of PA0691, termed here phdA, encoding a previously undescribed homologue of the prevent-host-death (Phd) family of proteins. Lack of phdA expression coincided with impaired biofilm development, increased cell death and bacteriophage release, a phenotype comparable to ΔbfmR. Expression of phdA in ΔbfmR biofilms restored eDNA release, cell lysis, release of bacteriophages, and biofilm formation to wild type levels. Moreover, overexpression of phdA rendered P. aeruginosa resistant to lysis mediated by superinfective bacteriophage Pf4 which was only detected in biofilms. The expression of bfmR was stimulated by conditions resulting in membrane perturbation and cell lysis. Thus, we propose that BfmR regulates biofilm development by controlling bacteriophage-mediated lysis and thus, cell death and eDNA release, via PhdA. For biofilm growth experiments, three independent replicates of P. aeruginosa strains PAO1 and ΔbfmR were grown as biofilms in a flow-through system using a once-through continuous flow tube reactor system for biofilm sample collection and in flow cells (BioSurface Technologies) for the analysis of biofilm architecture as previously described (Sauer et al., 2002, Sauer et al., 2004, Petrova & Sauer, 2009). Cells were treated with RNAprotect (Qiagen), and total RNA was extracted using an RNeasy mini purification kit (Qiagen) per the manufacturer’s instructions. RNA quality and the presence of residual DNA were checked on an Agilent Bioanalyzer 2100 electrophoretic system pre- and post-DNase treatment. Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol. Sauer, K., A. K. Camper, G. D. Ehrlich, J. W. Costerton & D. G. Davies, (2002) Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm. J. Bacteriol. 184: 1140-1154. Sauer, K., M. C. Cullen, A. H. Rickard, L. A. H. Zeef, D. G. Davies & P. Gilbert, (2004) Characterization of nutrient-induced dispersion in Pseudomonas aeruginosa PAO1 biofilm. J. Bacteriol. 186: 7312-7326. Petrova, O. E. & K. Sauer, (2009) A novel signaling network essential for regulating Pseudomonas aeruginosa biofilm development. PLoS Pathogens 5: e1000668.
2011-06-01 | E-GEOD-28953 | biostudies-arrayexpress
Project description:<h4><strong>INTRODUCTION: </strong>Wheat (<em>Triticum aestivum</em>) it is one of the most important staple food crops worldwide and represents an important resource for human nutrition. Besides starch, proteins and micronutrients wheat grains accumulate a highly diverse set of phytochemicals.</h4><h4><strong>OBJECTIVES: </strong>This work aimed at the development and validation of an analytical workflow for comprehensive profiling of semi-polar phytochemicals in whole wheat grains.</h4><h4><strong>METHOD: </strong>Reversed-phase ultra-high performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC/ESI-QTOFMS) was used as analytical platform. For annotation of metabolites accurate mass collision-induced dissociation mass spectra were acquired and interpreted in conjunction with literature data, database queries and analyses of reference compounds.</h4><h4><strong>RESULTS: </strong>Based on reversed-phase UHPLC/ESI-QTOFMS an analytical workflow for comprehensive profiling of semi-polar phytochemicals in whole wheat grains was developed. For method development the extraction procedure and the chromatographic separation were optimized. Using whole grains of eight wheat cultivars a total of 248 metabolites were annotated and characterized by chromatographic and tandem mass spectral data. Annotated metabolites comprise hydroquinones, hydroxycinnamic acid amides, flavonoids, benzoxazinoids, lignans and other phenolics as well as numerous primary metabolites such as nucleosides, amino acids and derivatives, organic acids, saccharides and B vitamin derivatives. For method validation, recovery rates and matrix effects were determined for ten exogenous model compounds. Repeatability and linearity were assessed for 39 representative endogenous metabolites. In addition, the accuracy of relative quantification was evaluated for six exogenous model compounds.</h4><h4><strong>CONCLUSIONS: </strong>In conjunction with non-targeted and targeted data analysis strategies the developed analytical workflow was successfully applied to discern differences in the profiles of semi-polar phytochemicals accumulating in whole grains of eight wheat cultivars.</h4>
2024-05-01 | MTBLS2276 | MetaboLights
Project description:Somatic polyploidy caused by endoreplication is observed in arthropods, molluscs, and vertebrates, but is especially prominent in higher plants where it has been postulated to be essential for cell growth and fate maintenance. However, a comprehensive understanding of the physiological significance of plant endopolyploidy has remained elusive. Here, we modeled and experimentally verified a high-resolution DNA endoploidy map of the developing Arabidopsis thaliana root, revealing a remarkable spatiotemporal control of DNA endoploidy levels across tissues and a strong dependence on stress signals. Cellular and transcriptomic analysis revealed that inhibition of endoreplication onset alters the nuclear-to-cellular volume ratio and change in expression of cell wall modifying genes, correlated with the appearance of cell structural changes. Our data indicate that endopolyploidy might serve to coordinate cell expansion with structural stability, and that spatiotemporal endoreplication pattern changes may buffer for stress conditions, which may explain the widespread occurrence of the endocycle in plant species growing in extreme or variable environments.
2018-10-01 | GSE115001 | GEO