North Atlantic Right Whale respiratory microbiomes
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ABSTRACT:
PROVIDER: PRJNA1273885 | ENA |
REPOSITORIES: ENA
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Project description:An 8X15k oligonucleotide microarray was developed consisting of 2334 E. glacialis probes and 2166 Tursiops truncatus probes and used to measure the transcriptome level effects of right whale kidney fibroblast cells exposed to cadmium. Cells were exposed to three concentrations of cadmium chloride (CdCl2) for three exposure times. Cells exposed to 10-6M CdCl2 for 4 hours and 24 hours showed upregulated genes involved in protection from metal toxicity, oxidative stress, protein renaturation, apoptosis inhibition, and several regulators of cellular processes. Downregulated genes represented a suite of functions including cell proliferation, transcription regulation, actin polymerization, and stress fiber synthesis. The collection of differentially expressed genes in this study support proposed mechanisms of cadmium-induced apoptosis such as mitochondrial membrane potential collapse, reactive oxygen species (ROS) influx, and cell cycle arrest. The results confirm the right whale microarray as a reproducible tool in measuring differentiated gene expression and should be a valuable asset for transcriptome analysis of other baleen whales and potential health assessment protocols.
2009-08-03 | GSE17457 | GEO
Project description:An 8X15k oligonucleotide microarray was developed consisting of 2334 E. glacialis probes and 2166 Tursiops truncatus probes and used to measure the transcriptome level effects of right whale kidney fibroblast cells exposed to cadmium. Cells were exposed to three concentrations of cadmium chloride (CdCl2) for three exposure times. Cells exposed to 10-6M CdCl2 for 4 hours and 24 hours showed upregulated genes involved in protection from metal toxicity, oxidative stress, protein renaturation, apoptosis inhibition, and several regulators of cellular processes. Downregulated genes represented a suite of functions including cell proliferation, transcription regulation, actin polymerization, and stress fiber synthesis. The collection of differentially expressed genes in this study support proposed mechanisms of cadmium-induced apoptosis such as mitochondrial membrane potential collapse, reactive oxygen species (ROS) influx, and cell cycle arrest. The results confirm the right whale microarray as a reproducible tool in measuring differentiated gene expression and should be a valuable asset for transcriptome analysis of other baleen whales and potential health assessment protocols. 35 Samples were analyzed representing 3 biological replicates for each treatment and corresponding controls except treatment 4hour_0.01uMCdCl2 had only two biological replicates due to spot intensity values. There are 3 spot replicates/probe on the array, along with Agilent control grid specific for 8X15K arrays, and 4 Karenia brevis sequences used as a negative control (K.brevis.chlorophyllA/Bbindingprotein, K.brevis.flavodoxin,K.brevis.photolyase,K.brevis.photosystemcoreprotein).
2009-08-03 | E-GEOD-17457 | biostudies-arrayexpress
Project description:Pygmy right whale Evolutionary Genomics
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Project description:Global patterns in whale shark skin microbiomes Metagenome
| PRJNA808622 | ENA
Project description:Animal movement plays a fundamental role in the ecology of migratory species, and understanding migration patterns is required for effective management. To evaluate intrinsic and environmental factors associated with probabilities of endangered North Atlantic right whales Eubalaena glacialis migrating to a wintering ground off the southeastern United States (SEUS), we applied a multistate temporary emigration capture-recapture model to 22 years of photo-identification data. Migration probabilities for juveniles were generally higher yet more variable than those for adults, and non-calving adult females were the least likely group to migrate. The highest migration probabilities for juveniles and adult males coincided with years of relatively high calving rates, following years of higher prey availability in a fall feeding ground. Right whale migration to the SEUS can be classified as condition-dependent partial migration, which includes skipped breeding partial migration for reproductive females, and is likely influenced by tradeoffs among ecological factors such as reproductive costs and foraging opportunities that vary across individuals and time. The high variability in migration reported in this study provides insight into the ecological drivers of migration but presents challenges to right whale monitoring and conservation strategies.
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Project description:This series includes 3 microarrays used to detect SWCoV1, a novel group III coronavirus in Delphinapterus leucas (Beluga whale) liver. The series includes 2 control whale livers and 1 whale liver containing SWCoV1.
2008-04-15 | E-GEOD-9238 | biostudies-arrayexpress
Project description:Although small populations are expected to lose genetic diversity through genetic drift and inbreeding, a number of mechanisms exist that could minimize this genetic decline. Examples include mate choice for unrelated mates and fertilization patterns biased toward genetically dissimilar gametes. Both processes have been widely documented, but the long-term implications have received little attention. Here, we combined over 25 years of field data with high-resolution genetic data to assess the long-term impacts of biased fertilization patterns in the endangered North Atlantic right whale. Offspring have higher levels of microsatellite heterozygosity than expected from this gene pool (effect size = 0.326, P < 0.011). This pattern is not due to precopulatory mate choice for genetically dissimilar mates (P < 0.600), but instead results from postcopulatory selection for gametes that are genetically dissimilar (effect size = 0.37, P < 0.003). The long-term implication is that heterozygosity has slowly increased in calves born throughout the study period, as opposed to the slight decline that was expected. Therefore, this mechanism represents a natural means through which small populations can mitigate the loss of genetic diversity over time.
| S-EPMC3797493 | biostudies-literature
Project description:The coastal waters off the southeastern United States (SEUS) are a primary wintering ground for the endangered North Atlantic right whale (Eubalaena glacialis), used by calving females along with other adult and juvenile whales. Management actions implemented in this area for the recovery of the right whale population rely on accurate habitat characterization and the ability to predict whale distribution over time. We developed a temporally dynamic habitat model to predict wintering right whale distribution in the SEUS using a generalized additive model framework and aerial survey data from 2003/2004 through 2012/2013. We built upon previous habitat models for right whales in the SEUS and include data from new aerial surveys that extend the spatial coverage of the analysis, particularly in the northern portion of this wintering ground. We summarized whale sightings, survey effort corrected for probability of whale detection, and environmental data at a semimonthly resolution. Consistent with previous studies, sea surface temperature (SST), water depth, and survey year were significant predictors of right whale relative abundance. Additionally, distance to shore, distance to the 22°C SST isotherm, and an interaction between time of year and latitude (to account for the latitudinal migration of whales) were also selected in the analysis presented here. Predictions from the model revealed that the location of preferred habitat differs within and between years in correspondence with variation in environmental conditions. Although cow-calf pairs were rarely sighted in the company of other whales, there was minimal evidence that the preferred habitat of cow-calf pairs was different than that of whale groups without calves at the scale of this study. The results of this updated habitat model can be used to inform management decisions for a migratory species in a dynamic oceanic environment.
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Project description:Mammals with dependent young often rely on cryptic behaviour to avoid detection by potential predators. In the mysticetes, large baleen whales, young calves are known to be vulnerable to direct predation from both shark and orca predators; therefore, it is possible that mother-calf pairs may show cryptic behaviours to avoid the attention of predators. Baleen whales primarily communicate through low-frequency acoustic signals, which can travel over long ranges. In this study, we explore the potential for acoustic crypsis, a form of cryptic behaviour to avoid predator detection, in North Atlantic right whale mother-calf pairs. We predicted that mother-calf pairs would either show reduced calling rates, reduced call amplitude or a combination of these behavioural modifications when compared with other demographic groups in the same habitat. Our results show that right whale mother-calf pairs have a strong shift in repertoire usage, significantly reducing the number of higher amplitude, long-distance communication signals they produced when compared with juvenile and pregnant whales in the same habitat. These observations show that right whale mother-calf pairs rely upon acoustic crypsis, potentially to minimize the risk of acoustic eavesdropping by predators.
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Project description:The reduced genetic diversity and frequent inbreeding associated with small population size may underpin the accumulation and expression of deleterious mutations (mutation load) in some declining populations. However, demographic perturbations and inbreeding coupled with purifying selection can also purge declining populations of deleterious mutations, leading to intriguing recoveries. To better understand the links between deleterious genetic variation and population status, we assess patterns of genetic diversity, inbreeding, and mutation load across the genomes of three species of Balaenidae whale with different demographic histories and recoveries following the end of commercial whaling in the 1980s. Unlike bowhead (BH) and Southern right whales (SRW), which show signs of recent recovery, reproductive rates of the endangered North Atlantic right whale (NARW) remain lower than expected. We show that the NARW is currently marked by low genetic diversity, historical inbreeding, and a high mutation load. Still, we reveal evidence that genetic purging has reduced the frequency of highly deleterious alleles in NARW, which could increase chances of future population recovery. We also identify a suite of mutations putatively linked to congenital defects that occur at high frequencies in nulliparous NARW females but are rare in NARW with high reproductive success. These same mutations are nearly absent in BH and SRW in this study, suggesting that the purging of key variants may shape the probability of population recovery. As anthropogenic disturbances continue to reduce the sizes of many populations in nature, resolving the links between population dynamics and mutation load could become increasingly important.
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