Halichondria okadai
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB17192 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR519015_1.fastq.gz | Fastqsanger.gz | |||
| DRR519016_1.fastq.gz | Fastqsanger.gz | |||
| DRR519017_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:Halichondria okadai Transcriptome or Gene expression
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Project description:The mitogenome sequence of Sponge Halichondria okadai (Kadota, 1922) (Suberitida, Halichondriidae) was determined for the first time in this study. The circular genome is 20,722 bp in length, containing 14 protein coding genes (PCGs), two ribosomal RNAs (rRNAs), and 25 transfer RNAs (tRNAs). The nucleotide composition of mitogenome consists of 29.5% A, 14.2% C, 21.5% G, 34.7% T, showing a high content of A + T similar to the other Suberitid sponges. These results will be useful for inferring the phylogenetic relationships among the members of family Halichondriidae within the Suberitids.
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Project description:In this study, we found out the complete mitochondrial genome of Halichondria (Halichondria) sp., a common demosponge in China. This is the first complete mitochondrial report on the genus Halichondria. The mitochondrial genome of Halichondria (Halichondria) sp. is 20 746 bp in length, with 14 protein-coding genes, two rRNA genes and 25 tRNA genes. When compared with the complete mitochondrial genome of Hymeniacidon sinapium, our phylogenetic result suggested that Halichondria (Halichondria) sp. converged well according to morphological result.
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Project description:Bacteria transform nutrients and degrade organic matter, making them an essential part of healthy ecosystems. By assaying bacterial physiology within a complex system, the status of the whole ecosystem can be investigated. Proteins are the dynamic molecules that control essential bacterial physiological responses and those of every organism; characterizing an organism's proteome can therefore provide information on its interaction with the environment. Data dependen proteomic analysis (DDA) is a global approach to assay the entire proteome, but sample complexity and the stochastic nature of mass spectrometry can make it difficult to detect low abundance proteins. We explored the development of targeted proteomic (selected reaction monitoring, SRM) assays in complex ocean samples in order to detect specific bacterial proteins of interest and to assess new tools for mixed community metaproteomic exploration. A mixed community was created from a dilution series of isolated culture of bacteria (Ruegeria pomoeroyi) and phytoplankton (Thalassiosira pseudonana). Using SRM, we were able to detect bacterial peptides from the community that were undetectable with the standard DDA approach. We demonstrate benefits and drawbacks of different proteomic approaches that can be used to probe for and resolve nuances of bacterial physiological processes in complex environmental systems.
2017-02-01 | PXD004799 | Pride
Project description:Bacteria transform nutrients and degrade organic matter, making them an essential part of healthy ecosystems. By assaying bacterial physiology within a complex system, the status of the whole ecosystem can be investigated. Proteins are the dynamic molecules that control essential bacterial physiological responses and those of every organism; characterizing an organism's proteome can therefore provide information on its interaction with the environment. Data dependen proteomic analysis (DDA) is a global approach to assay the entire proteome, but sample complexity and the stochastic nature of mass spectrometry can make it difficult to detect low abundance proteins. We explored the development of targeted proteomic (selected reaction monitoring, SRM) assays in complex ocean samples in order to detect specific bacterial proteins of interest and to assess new tools for mixed community metaproteomic exploration. A mixed community was created from a dilution series of isolated culture of bacteria (Ruegeria pomoeroyi) and phytoplankton (Thalassiosira pseudonana). Using SRM, we were able to detect bacterial peptides from the community that were undetectable with the standard DDA approach. We demonstrate benefits and drawbacks of different proteomic approaches that can be used to probe for and resolve nuances of bacterial physiological processes in complex environmental systems.
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Project description:To determine whether and how warming affects the functional capacities of the active microbial communities, GeoChip 5.0 microarray was used. Briefly, four fractions of each 13C-straw sample were selected and regarded as representative for the active bacterial community if 16S rRNA genes of the corresponding 12C-straw samples at the same density fraction were close to zero.
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