Ontology highlight
ABSTRACT:
PROVIDER: PRJNA642909 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12112869_1.fastq.gz | Fastqsanger.gz | |||
| SRR12112869_2.fastq.gz | Fastqsanger.gz | |||
| SRR12112870_1.fastq.gz | Fastqsanger.gz | |||
| SRR12112870_2.fastq.gz | Fastqsanger.gz | |||
| SRR12112871_1.fastq.gz | Fastqsanger.gz |
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Project description:Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments, indicating some difference in ecology and/or physiology of the AOA assemblage. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature was the main factor that correlated with the differences between the AOA communities from the Arabian Sea and those from the ETSP. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role than did geography in shaping the AOA community composition.
2013-06-20 | GSE46851 | GEO
Project description:Collected in the Bay of Bengal, at Point Calimare
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Project description:Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments, indicating some difference in ecology and/or physiology of the AOA assemblage. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature was the main factor that correlated with the differences between the AOA communities from the Arabian Sea and those from the ETSP. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role than did geography in shaping the AOA community composition. Two-color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
2013-06-20 | E-GEOD-46851 | biostudies-arrayexpress
Project description:Urinary proteins provide valuable insights into renal health, with implications spanning human and domestic animal veterinary medical research. However, the field of marine mammal medicine lacks comprehensive studies on urine protein composition. This research aimed to fill this gap by 1) selecting an optimal search strategy that yields the highest number of protein families in the bottlenose dolphin urine based on post-translational modifications (PTMs), 2) describing the urine proteome of wild bottlenose dolphins (Tursiops truncatus) in the Gulf of the Mexico, USA, considering sex (females vs. males), site (Barataria Bay, LA vs. Sarasota Bay, FL), and comparing with California sea lions (Zalophus californianus). Ten urine samples (Barataria Bay, LA: N= 6; Sarasota Bay, FL: N=4) collected during 2023 catch-and-release heath assessment were proteolytically digested and analyzed using an UltiMate 3000 Nano LC and Fusion Lumos Orbitrap mass spectrometer. A 2-step search strategy, incorporating dehydroalanine formation and semi-trypsin on the list of unassigned spectra, significantly increased the number of identified protein families by an average of 6.2% compared to the 1-step strategy (P < 0.001, t = -8.32). The top 30 proteins in bottlenose dolphin urine were ranked according to an exponentially modified protein abundance index for comparison based on sex, site, and species. There were no significant differences in urine proteins between sexes or sites (padj > 0.05), although there was sperm contribution in two of the male bottlenose dolphin urine samples. Two putative antimicrobial proteins (cathelicidin and lysozyme) were identified and found to be abundant in bottlenose dolphin urine, similar to California sea lions. The study also identified 27 potential markers of acute kidney injury and 12 regulators of kidney stone formation. This study established a reference database of urinary proteins from bottlenose dolphins, aiding future research in monitoring and evaluating renal health in marine mammals.
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Project description:Total RNA was purified from keratinocytes isolated from FFPE arsenic-induced skin lesion samples collected from individuals exposed to high concentrations of arsenic exceeding 50 ppb in drinking water in Murshidibad district of West Bengal, India.
2018-06-01 | GSE102892 | GEO
Project description:Arabian Sea coastal cores
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