Marine Sponges
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA431498 | ENA |
REPOSITORIES: ENA
Similar Datasets
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Project description:Viral metagenome from marine sponges Metagenome
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Project description:Polyamines, such as putrescine and spermidine, are aliphatic organic compounds with multiple amino groups. They are found ubiquitously in marine systems. However, compared with the extensive studies on the concentration and fate of other dissolved organic nitrogen compounds in seawater, such as dissolved free amino acids (DFAA), investigations of bacterially-mediated polyamine transformations have been rare. Bioinformatic analysis identified genes encoding polyamine transporters in 74 of 109 marine bacterial genomes surveyed, a surprising frequency for a class of organic nitrogen compounds not generally recognized as an important source of carbon and nitrogen for marine bacterioplankton. The genome sequence of marine model bacterium Silicibacter pomeroyi DSS-3 contains a number of genes putatively involved in polyamine use, including six four-gene ATP-binding cassette transport systems. In the present study, polyamine uptake and metabolism by S. pomeroyi was examined to confirm the role of putative polyamine-related genes, and to investigate how well current gene annotations reflect function. A comparative whole-genome microarray approach (Bürgmann et al., 2007) allowed us to identify key genes for transport and metabolism of spermidine in this bacterium, and specify candidate genes for in situ monitoring of polyamine transformations in marine bacterioplankton communities.
2008-12-31 | GSE13781 | GEO
Project description:Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments.
2016-07-06 | GSE73689 | GEO
Project description:Polyamines, such as putrescine and spermidine, are aliphatic organic compounds with multiple amino groups. They are found ubiquitously in marine systems. However, compared with the extensive studies on the concentration and fate of other dissolved organic nitrogen compounds in seawater, such as dissolved free amino acids (DFAA), investigations of bacterially-mediated polyamine transformations have been rare. Bioinformatic analysis identified genes encoding polyamine transporters in 74 of 109 marine bacterial genomes surveyed, a surprising frequency for a class of organic nitrogen compounds not generally recognized as an important source of carbon and nitrogen for marine bacterioplankton. The genome sequence of marine model bacterium Silicibacter pomeroyi DSS-3 contains a number of genes putatively involved in polyamine use, including six four-gene ATP-binding cassette transport systems. In the present study, polyamine uptake and metabolism by S. pomeroyi was examined to confirm the role of putative polyamine-related genes, and to investigate how well current gene annotations reflect function. A comparative whole-genome microarray approach (Bürgmann et al., 2007) allowed us to identify key genes for transport and metabolism of spermidine in this bacterium, and specify candidate genes for in situ monitoring of polyamine transformations in marine bacterioplankton communities. Silicibacter pomeroyi DSS-3 cells were grown in chemostat in a modified marine basal medium (MBM) containing spermidine as sole carbon and nitrogen source. Serine was used as a substrate to provide comparative data for an amino acid. After reach stable condition, total RNA were extracted, mRNA were purified and aa-aRNA were amplified and fluoresently labled before hybridize on array chips. The array design is described in Burgmann et al., 2007
2010-05-14 | E-GEOD-13781 | biostudies-arrayexpress
Project description:Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments.
2016-07-06 | GSE73690 | GEO
Project description:Marine snow plays a central role in carbon cycling. It consists of organic particles and particle-associated (PA) microbMarine snow plays a central role in carbon cycling. It consists of organic particles and particle-associated (PA) microbial communities that are embedded in a sugary matrix. Metaproteomic analysis offers the unique opportunity to gain unprecedented insight into the microbial community composition and biomolecular activity of environmental samples. In order to realize this potential for marine PA microbial communities, new methods of protein extraction must be developed. In this study, we used 1D-SDS-PAGEs and LC-MS/MS to compare the efficiency of six established protein extraction protocols for their applicability of metaproteomic analyses of the PA microbial community in the North Sea. A combination of SDS-buffer extraction and bead beating resulted in the greatest number of identified protein groups. As expected, a metagenomic database of the same environmental sample increased the number of protein identification by approximately 50%. To demonstrate the application of our established protocol, particulate bacterioplankton samples collected during spring phytoplankton bloom in 2009 near the island Helgoland, were analysed by a GeLC-MS/MS-based metaproteomic approach. Our results indicated that there are only slight differences in the taxonomical distribution between free-living (FL) and PA bacteria but that the abundance of protein groups involved in polysaccharide degradation, motility and particle specific stress (oxygen limitation, nutrient limitation, heavy metal stress) is higher in the PA fractions. ial communities that are embedded in a sugary matrix. Metaproteomic analysis offers the unique opportunity to gain unprecedented insight into the microbial community composition and biomolecular activity of environmental samples. In order to realize this potential for marine PA microbial communities, new methods of protein extraction must be developed. In this study, we used 1D-SDS-PAGEs and LC-MS/MS to compare the efficiency of six established protein extraction protocols for the their applicability of metaproteomic analyses of the PA microbial community in the North Sea. A combination of SDS-buffer extraction and bead beating resulted in the greatest number of identified protein groups. As expected, a metagenomic database of the same environmental sample increased the number of protein identification by approximately 50%. To demonstrate the application of our established protocol, particulate bacterioplankton samples collected during spring phytoplankton bloom in 2009 near the island Helgoland, were analysed by a GeLC-MS/MS-based metaproteomic approach. Our results indicated that there are only slight differences in the taxonomical distribution between free-living (FL) and PA bacteria but that the abundance of protein groups involved in polysaccharide degradation, motility and particle specific stress (oxygen limitation, nutrient limitation, heavy metal stress) is higher in the PA fractions.
2021-02-15 | PXD012699 | Pride
Project description:In the seabed, chemical defences mediate inter- and intraspecific interactions and may determine organisms’ success, shaping the diversity and function of benthic communities. Sponges represent a prominent example of chemically-defended marine organisms with great ecological success. The ecological factors controlling the production of their defensive compounds and the evolutionary forces that select for these defences remain little understood. Each sponge species produces a specific and diverse chemical arsenal with fish-deterrent, antifouling and antimicrobial properties. However, some small animals (mesograzers), mainly sea slugs, have specialized in living and feeding on sponges. Feeding on chemically-defended organisms provides a strategy to avoid predators, albeit the poor nutritional value of sponges. In order to investigate the mechanisms that control sponge chemical defence, with particular focus on the response to specialist grazers, we investigated the interaction between the sponge Aplysina aerophoba and the sea slug Tylodina perversa. Here we performed controlled experiments and collected sponge samples at different time points (3h, 1d and 6d after treatment). To further elucidate if the sponge response is specific to grazing by T. perversa, we also included a treatment in which sponges were mechanically damaged with a scalpel. We compared gene expression between treatments based on RNA-Seq data.
2022-01-30 | E-MTAB-8601 | biostudies-arrayexpress