Genomic and physiological responses to strong selective pressure during late organogenesis: how natural Fundulus heteroclitus populations cope with persistent environmental pollution Superfund Site
Ontology highlight
ABSTRACT:
ORGANISM(S): Fundulus heteroclitus
PROVIDER: GSE47654 | GEO | 2013/09/30
SECONDARY ACCESSION(S): PRJNA207070
REPOSITORIES: GEO
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Project description:This study explores the synergistic effects of two model PAHs, an aryl hydrocarbon receptor (AHR) agonist (M-NM-2-naphthoflavone) and a cytochrome P4501A (CYP1A) inhibitor (M-NM-1-naphthoflavone), on gene expression in stage 31 embryos from two different population. One population (Elizabeth River population) is relatively resistant to the pollutants in its environment. A loop design (Figure 5) was used for the microarray hybridizations where each sample is hybridized to 2 arrays using both Cy3 and Cy5 labeled fluorophores (Kerr and Churchill, 2001). The loop consisted of Cy3 and Cy5 labeled embryo aRNAs from 4 biological samples and six different treatments (T1-T6: control, 1 M-NM-<g/L BNF, 50 M-NM-<g/L ANF, 100 M-NM-<g/L ANF, 1 M-NM-<g/L BNF + 50 M-NM-<g/L ANF, 1 M-NM-<g/L BNF + 100 M-NM-<g/L ANF). In total, 48 biological samples were hybridized to 24 microarrays. Each array had different combinations of biological samples, so that the most direct comparisons (i.e., 50 M-BM-5g/L ANF resistant embryo and 50 M-BM-5g/L sensitive embryo) are hybridized to the same array. The loop formed was T1SM-bM-^FM-^R T1R M-bM-^FM-^R T2SM-bM-^FM-^R T2R M-bM-^FM-^RT3SM-bM-^FM-^R T3RM-bM-^FM-^R T4SM-bM-^FM-^R T4RM-bM-^FM-^R T5SM-bM-^FM-^R T5R M-bM-^FM-^R T6SM-bM-^FM-^RT6RM-bM-^FM-^R T1SM-bM-^FM-^R T2S M-bM-^FM-^R T3S M-bM-^FM-^R T4S M-bM-^FM-^R T5S M-bM-^FM-^R T6S M-bM-^FM-^R T1S M-bM-^FM-^R T1R M-bM-^FM-^R T2R M-bM-^FM-^R T3R M-bM-^FM-^R T4R M-bM-^FM-^R T5R M-bM-^FM-^R T6R, where each arrow represents a separate hybridization (array) with the biological sample at the base of the arrow labeled with Cy3 and the biological pool at the head of the arrow labeled with Cy5. T1-6 is treatment, and S and R represent sensitive and resistant embryos.
2013-09-30 | E-GEOD-47654 | biostudies-arrayexpress
Project description:Oil spills have polluted the marine environment for decades and continue to be a major source of polycyclic aromatic hydrocarbons (PAHs) to marine ecosystems around the globe. Although the toxicity of PAHs to fish has been well studied, the combined effects of extreme abiotic factors and oil are poorly understood. Gulf of Mexico killifish Fundulus grandis larvae (< 24 hours post hatch) were exposed to varying environmental conditions (dissolved oxygen 2, 6 ppm; temperature 20, 25, 30°C; and salinity 3, 10, 30 ppt) combined with varying concentrations of high energy water accommodated fractions (HEWAF) (total PAHs 0 – ~ 125 ppb) for a total of 48 h. Larvae survival and development were negatively affected by PAHs, starting with the lowest concentration tested (~15 ppb). High temperature + hypoxia + PAHs resulted in the lowest survival with salinity having little impact on any of the endpoints tested. Expression of the hepatic detoxifying gene cyp1a was highly induced in PAH-exposed larvae, but only under normoxic conditions. A lack of cyp1a induction under hypoxia and PAH exposure could explain the enhanced toxicity observed. This work highlights the need for more studies examining the combined impact of suboptimal water quality parameters in the presence of pollution in fish early life-stages.
2019-04-18 | GSE129998 | GEO
Project description:To explore how gene expression translates to developmental phenotype in both sensitive and resistant Fundulus embryos upon POP exposure, we exposed Fundulus embryos from the Elizabeth River Superfund population and the Magotha Bay, VA clean population to Elizabeth River polluted sediment extracts and measured chemical uptake, gene expression, and altered embryo anatomy, morphology and cardiac physiology during four critical developmental stages: somitogenesis, heart beat initiation, late organogenesis, and pre-hatching.
2019-05-07 | GSE130754 | GEO
Project description:Populations of the non-migratory estuarine fish Fundulus heteroclitus inhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133 F. heteroclitus from seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over three F. heteroclitus generations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction in Ne and concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade.
| S-EPMC5990737 | biostudies-literature
Project description:Fundulus heteroclitus heteroclitus RADseq reads
| PRJNA450424 | ENA
Project description:Fundulus heteroclitus raw sequence reads
| PRJNA287030 | ENA
Project description:Most studies that examine the ontogeny of lymphoid organ development in teleostean fishes use species of interest to aquaculture or genetic research and, to date, have focused strictly on marine or freshwater species. The mummichog, Fundulus heteroclitus, also known as the estuarine killifish, is a unique model for studies on developmental immunobiology, because it is euryhaline, has a high degree of thermal tolerance, and has a unique reproductive strategy. Embryonic and larval mummichogs were examined for the ontogeny of lymphoid tissue development. The first lymphoid organ to appear was the head kidney at 1 dph, followed by the spleen at 1 wph, and then the thymus at 3 wph. Rag-1 was partially cloned and sequenced and shown to be highly conserved among other vertebrate Rag-1 genes. Using QT-PCR to monitor the temporal expression of Rag-1, it was shown to reach a maximum intensity at 3 and 4 wph and then to drop to pre-2-wph levels. Overall, this study suggests that juvenile mummichogs do not possess the ability to mount T- or B-cell responses until some time after 5 wph. Even though the estuarine killifish tolerates a wide range of salinities, the developmental patterns of lymphoid tissues are similar to what has been reported for strictly marine (stenohaline) teleosts. Thus, the mummichog should be a convenient model for understanding the developmental immunobiology of most marine teleosts.
| S-EPMC2574841 | biostudies-literature
Project description:Atlantic killifish (Fundulus heteroclitus) inhabiting the Atlantic Wood Industries region of the Elizabeth River, Virginia, have passed polycyclic aromatic hydrocarbon (PAH) resistance to their offspring as evidenced by early life stage testing of developmental toxicity after exposure to specific PAHs. Our study focused on environmentally relevant PAH mixtures in the form of Elizabeth River sediment extract (ERSE). Juvenile (5 month) F1 progeny of pollution-adapted Atlantic Wood (AW) parents and of reference site (King's Creek [KC]) parents were exposed as embryos to ERSE. Liver alterations, including nonneoplastic lesions and microvesicular vacuolation, were observed in both populations. ERSE-exposed KC fish developed significantly more alterations than unexposed KC fish. Interestingly, unexposed AW killifish developed significantly more alterations than unexposed KC individuals, suggesting that AW juveniles are not fully protected from liver disease; rapid growth of juvenile fish may also be an accelerating factor for tumorigenesis. Because recent reports show hepatic tumor formation in adult AW fish, the differing responses from the 2 populations provided a way to determine whether embryo toxicity protection extends to juveniles. Future investigations will analyze older life stages of killifish to determine differences in responses related to chronic disease.
| S-EPMC4912431 | biostudies-literature
Project description:The goals of these studies are to explore the mechanisms that enable extreme physiological plasticity and that may account for evolutionary divergence of adaptive osmotic physiologies among taxa that occupy different osmotic niches. In a common-garden environment, we track physiological and genome expression responses to hypo-osmotic (freshwater) challenge during a time-course of acclimation, and contrast these responses within and between species. We seek to identify mechanisms that facilitate osmotic acclimation that are evolutionarily conserved between basal and derived physiologies, and identify mechanisms that are uniquely derived to enable the extreme osmotic plasticity exhibited by F. heteroclitus. Importantly, previous studies using a comparable experimental design have identified physiological changes and genome expression responses that are adaptive for populations of F. heteroclitus that live in fresh water. As such, this enables us to test whether mechanisms of adaptive micro-evolutionary divergence across osmotic gradients within F. heteroclitus are shared with the mechanisms that account for patterns of macro-evolutionary divergence between F. heteroclitus and F. majalis that we identify in this study. That is, are the targets of micro-evolutionary fine-tuning the same or different as the targets of macro-evolutionary divergence across osmotic boundaries? Population comparisons include between populations from Chesapeake Bay (CB), coastal Virginia (VA), and coastal Georgia (GA).
2013-04-23 | E-MTAB-1551 | biostudies-arrayexpress