RNA-seq analysis of blood transcriptomes from managed bottlenose dolphins in Waikoloa, Hawaii, USA
Ontology highlight
ABSTRACT:
ORGANISM(S): Tursiops truncatus
PROVIDER: GSE98627 | GEO | 2017/05/09
SECONDARY ACCESSION(S): PRJNA385773
REPOSITORIES: GEO
Similar Datasets
Project description:Four captive bottlenose dolpins housed in Kona, Hawaii, were serially sampled at approximately monthly intervals over the course of one year, in order to establish baseline information on the content and variation of the dolphin blood transcriptome.
2016-09-10 | GSE78770 | GEO
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.
2024-08-01 | PXD054283 | Pride
Project description:As apex predators, cetaceans are recognized as sentinels for the health of marine ecosystems. The ability to identify the impacts of anthropogenic contamination on the health of a species requires long term monitoring to establish baseline health parameters. This makes health measurements that can be sampled from free ranging animals highly desirable. In the current study, we investigate the utility of skin gene expression profiling to monitor the physiological, health, and contaminant exposure status in bottlenose dolphins. Remote integument biopsies were obtained from bottlenose dolphins at three locations in the northern Gulf of Mexico prior to oil exposure (May 2010) and during summer and winter of the two years (2010-2011) following their exposure to oil from the Deepwater Horizon oil spill. A bottlenose dolphin-specific oligonucleotide microarray was used to characterize the skin transcriptomes of 94 individuals from three genetically distinguishable populations in Barataria Bay, Louisiana, Chandeleur Sound, Louisiana, and Mississippi Sound, Mississippi. Location did not significantly affect the transcriptome patterns of the dolphins included in the study. In contrast, season had a profound effect on gene expression, with nearly one-third of all genes on the array differing significantly in expression between winter and the warmer seasons (p<0.01, fold-change >1.5). Gene ontology enrichment analysis revealed that processes related to cell proliferation, motility and differentiation dominated the seasonal differences in expression, which likely reflects the differences in ambient temperature to which the skin is exposed, and possibly changes in blood flow. More subtle differences were seen between spring and summer transcriptomes (1.5% differentially expressed), with two presumed oil-exposed animals presenting gene expression profiles more similar to the summer (exposed) animals than the other spring animals. Xenobiotic pathway components also showed some seasonal trends, which may reflect crosstalk between xenobiotic pathways and those regulating corticoids, hormones, and cytokines. Seasonal effects have not previously been considered in studies assessing gene expression in cetaceans, but clearly must be taken into account when applying transcriptomic analyses to investigate their exposure or health status.
2016-11-29 | GSE58471 | GEO
Project description:Common bottlenose dolphins serve as sentinels for the health of their coastal environments as they are susceptible to health impacts from anthropogenic inputs through both direct exposure and food web magnification. Remote biopsy samples have been widely used to reveal contaminant burdens in free-ranging bottlenose dolphins, but do not address the health consequences of this exposure. To gain insight into whether remote biopsies can also identify health impacts associated with contaminant burdens, we employed RNA sequencing (RNA-seq) to interrogate the transcriptomes of remote skin biopsies from 116 bottlenose dolphins from the northern Gulf of Mexico and southeastern U.S. Atlantic coasts. Gene expression was analyzed using principal component analysis, differential expression testing, and gene co-expression networks, and the results correlated to season, location, and contaminant burden. Season had a significant impact, with over 30% of genes differentially expressed between spring/summer and winter months. Geographic location exhibited lesser effects on the transcriptome, with 15% of genes differentially expressed between the northern Gulf of Mexico and the southeastern U.S. Atlantic locations. Despite a large overlap between the seasonal and geographical gene sets, the pathways altered in the observed gene expression profiles were somewhat distinct. Co-regulated gene modules and differential expression analysis both identified epidermal development and cellular architecture pathways to be expressed at lower levels in animals from the northern Gulf of Mexico. Although contaminant burdens measured were not significantly different between regions, some correlation with contaminant loads in individuals was observed among co-expressed gene modules, but these did not include classical detoxification pathways. Instead, this study identified other, possibly downstream pathways, including those involved in cellular architecture, immune response, and oxidative stress, that may prove to be contaminant responsive markers in bottlenose dolphin skin.
2016-12-06 | GSE90941 | GEO
Project description:The primary objective of the present study was to use proteomic analysis as a non-targeted approach to initially identify and classify the proteome of respiratory exudate or blow in aquarium-based bottlenose dolphins.
2022-03-03 | PXD006260 | Pride
Project description:Feeding a modified fish diet has been suggested to improve insulin sensitivity in bottlenose dolphins; however insulin sensitivity was not directly measured. Since demonstrating an improvement in insulin sensitivity is technically difficult in dolphins, we postulated that directional changes in the hormone axis: fibroblast growth factor 21 (FGF21)/Adiponectin/Ceramide (Cer), could provide further support to this hypothesis. Proteomic analysis of the serum proteins revealed few changes in serum proteins over the study period. In conclusion, changing the types of fish fed to dolphins resulted in increases in the insulin sensitizing hormone adiponectin and serum sphingosines consistent with an insulin sensitizing phenotype.
2016-04-20 | PXD003425 | Pride
Project description:To determine what can the transcriptome tell us about populations of free-ranging bottlenose dolphins, Tursiops truncatus. Keywords: health assessment
2009-02-21 | GSE10617 | GEO
Project description:To determine what can the transcriptome tell us about populations of free-ranging bottlenose dolphins, Tursiops truncatus. Keywords: health assessment A total of 151 individuals were sampled from 4 different geographic location in U.S. waters between June of 2003 and June of 2006. Of the 151 dolphins, 59 were from Charleston, 35 from Indian River Lagoon, FL, 32 from Sarasota Bay, FL and 25 from St. Josephs Bay FL. Total RNA extracted from blood leukocytes of wild dolphins was analyzed and different sets of genes were used as classifiers in a machine learning approach, Artificial Neural Networks (ANN).
2010-05-05 | E-GEOD-10617 | biostudies-arrayexpress
Project description:An Infinium microarray platform (GPL28271, Horvath MammalMethylChip40) was used to generate DNA methylation data from skin samples of Hector's and Māui dolphins.
2023-09-28 | GSE242072 | GEO