Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1080184 | ENA |
REPOSITORIES: ENA
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Project description:<p>Four species of phytoplankton representing important bloom-forming species from three globally important phyla (Bacillariophyta, Haptophyta, and Ochrophyte) were cultured in this study. These species include the cosmopolitan diatom <em>Chaetoceros affinis</em> CCMP159 (isolated from Great South Bay, NY, USA, 1958), the haptophytes<em> Chrysochromulina polylepis </em>CCMP1757 (isolated from the North Sea 1988) and <em>Gephyrocapsa oceanica</em> RCC1303 (isolated from Arachon Bay, France, Jan 1999), and the raphidophyte <em>Heterosigma akashiwo </em>strain CCMP 2393 (isolated from Rehoboth Bay, Delaware, USA). Cultures were grown under three conditions: nitrogen-stress, phosphorus-stress, and replete conditions. Intracellular metabolites were extracted from cultures and analyzed with targeted and untargeted mass spectrometry-based metabolomics methods.</p>
2024-02-28 | MTBLS1807 | MetaboLights
Project description:Royal Jelly (RJ) is a product made by honey bee workers and is required for queen differentiation and accompanying changes in queen body size, development time, lifespan and reproductive output relative to workers. Previous studies have reported similar changes in Drosophila melanogaster in response to RJ. Here, we quantified viability, development time, body size, productivity, lifespan and genome wide transcript abundance of D. melanogaster reared on standard culture medium supplemented with increasing concentrations of RJ. We found that lower concentrations of RJ do induce significant differences in body size in both sexes; higher concentrations reduce size, increase mortality, shorten lifespan and reduce productivity. Increased concentrations of RJ also consistently lengthened development time in both sexes. RJ is associated with changes in expression of 1,581 probe sets assessed using Affymetrix Drosophila 2.0 microarrays, which were enriched for genes associated with metabolism and amino acid degradation. The transcriptional changes are consistent with alterations in cellular processes to cope with excess nutrients provided by RJ, including biosynthesis and detoxification, which might contribute to accelerated senescence and reduced lifespan.
2015-08-01 | E-MTAB-3544 | biostudies-arrayexpress
Project description:modENCODE_submission_5004 This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The White Lab is aiming to map the association of all the Transcription Factors (TF) on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) utilizing an Illumina next generation sequencing platform. The data generated by ChIP-seq experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF. 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: lola-RJ-GFP; Developmental Stage: Embryo 0-12h; Genotype: PBac{y[+]-attP-3B}VK00033; Transgene: lola-RJ genomic coding region; EXPERIMENTAL FACTORS: Developmental Stage Embryo 0-12h; Target gene lola; Strain lola-RJ-GFP; Antibody GFP ab290 (target is Green Fluorescent Protein)
2013-08-11 | E-GEOD-49772 | biostudies-arrayexpress
Project description:modENCODE_submission_5005 This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The White Lab is aiming to map the association of all the Transcription Factors (TF) on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) utilizing an Illumina next generation sequencing platform. The data generated by ChIP-seq experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF. 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: lola-RJ-GFP; Developmental Stage: Embryo 12-24h; Genotype: PBac{y[+]-attP-3B}VK00033; Transgene: lola-RJ genomic coding region; EXPERIMENTAL FACTORS: Developmental Stage Embryo 12-24h; Target gene lola; Strain lola-RJ-GFP; Antibody GFP ab290 (target is Green Fluorescent Protein)
2013-08-11 | E-GEOD-49773 | biostudies-arrayexpress
Project description:MRJP-3 is an RNA binding protein that binds both double- and single-stranded RNA in vitro. To test whether i) MRJP-3 binds RNA in its natural environment, the royal jelly (RJ) and ii) to characterize its RJ RNA partners; a pull down followed by RNA-seq system was developed. MRJP-3 bound RNA was compared to total RJ RNA extracted from the same hive. To establish the system, we first incubated biotinylated MRJP-3, or biotinylated BSA in RJ and pulled the proteins out with strepavidin coated magnetic beads followed by RNA extraction and bioanalyzer profiling. MRJP-3 pull out was enriched for RNA compare to the BSA and just beads controls. The RNA population pulled down with MRJP-3 has similar profile to the total RJ RNA, further demonstrating the MRJP-3 has no affinity to a certain RNA species.
2018-10-28 | E-MTAB-6732 | biostudies-arrayexpress
Project description:We used RNA-seq to determine transcriptional profiles of whole guts or IPCs isolated from guts infected with wild type or type VI secretion system deficient Vibrio cholerae. We found significant differences between guts and progenitor cells infected wild type or type VI secretion system deficient Vibrio cholerae.
2019-08-21 | GSE136069 | GEO
Project description:One of the most important issues in the study of aging is to discover compounds with longevity-promoting activity and to unravel their underlying mechanisms. Queen honey bees are continuously fed royal jelly (RJ), and they live more than 10 times longer than hive workers, derived from the same diploid genome, which are fed it only for a short period of time during their larval stages. Therefore, RJ is likely to contain longevity-promoting agents for queens. RJ has been reported to possess diverse pharmacological properties. Furthermore, protease-treated RJ (pRJ) has additional beneficial activities. How RJ and pRJ exert these effects and which components in them play a critical role is largely unknown. The evolutionally conserved mechanisms that control lifespan have been indicated. The nematode Caenorhabditis elegans has been widely used for study of aging and longevity, due to its relatively short lifespan and well-established genetic pathways. The purpose of the present study was to elucidate whether RJ and its related substances contain the life span-extending activity in C. elegans and to obtain some insight into the active agents and their mechanisms. We found that both RJ and pRJ extended the lifespan of C. elegans. The life span-extending activity of pRJ was enriched by ODS column chromatography (pRJ-Fraction 5). pRJ-Fr. 5 extended the life span partly by acting through the FOXO transcription factor DAF-16, the activation of which is known to promote longevity in C. elegans by reducing insulin/IGF-1 signaling (IIS). pRJ-Fr. 5 induced changes in the expression of 3 genes encoding insulin-like peptides. Moreover, pRJ-Fr. 5 and reduced IIS shared some common features in terms of their effect on gene expression, such as up-regulation of dod-3 and down-regulation of dod-19, dao-4 and fkb-4. The dod-19 is a previously identified life span determinant in C. elegans, and the fkb-4 encodes a homologue of the mammalian FK506-binding protein. 10-Hydroxy-2-decenoic acid (10-HDA), which was present in high concentration in pRJ-Fr. 5, increased the lifespan independently of DAF-16 activity.These results demonstrate that RJ and its related substances extended the life span in C. elegans, suggesting that RJ may contain longevity-promoting factors common to diverse species across phyla. pRJ-Fr. 5 had higher life span-extending activity than either RJ or pRJ and extended the life span in part through the IIS-DAF-16 pathway. We provide the first evidence that 10-HDA, a defined natural product in RJ, extended organismal lifespan. It is noteworthy that 10-HDA performed its lifespan-extending function through a mechanism totally different from the IIS-DAF-16 pathway. Further search and characterization of the lifespan-extending agents in RJ and pRJ may broaden our understanding of the gene network of longevity regulation in diverse species and provide the possibility for nutraceutical interventions in the aging process.
2011-07-22 | GSE26094 | GEO
Project description:Royal jelly (RJ) is a proteinaceous secretion of the hypopharyngeal glands (HGs) in the head of honeybee workers. It is a critical food for queen bees and young larvae that decides the fate of fertilized eggs in developing into either queen bees or worker bees during the early larval stages. RJ is also widely used in humans for health promotion as agent, such as antibacterial, antioxidant, and antiaging properties. To increase RJ yields, a stock of high RJ producing honeybees (RJBs) has genetically selected from Italian honeybees (ITBs) in China since 1980s. To date, one colony of RJBs can produce more than 10 kg of RJ per year, a yield that is 10-times greater than that produced by a colony of ITBs. To elucidate the mechanism of the enforced gland performance in producing RJ in RJBs, the spatio-temporal HG proteomes of newly emerged bees, nurse bees, and forager bees, were compared between the ITBs and RJBs. Proteins in the critical pathways that are implicated in the secretory activity of RJ in HGs are validated biochemically and biologically by manipulating the NBs into extended nursing periods and the FBs to revert into NBs. This will provide a novel mechanistic insight into the HGs achieving an enhanced biological mission of producing the valuable bee-product, RJ.
2019-01-11 | PXD010898 | Pride