Posts Tagged 'molecular biology'

Transcriptomic response to decreased pH in adult, larval and juvenile red king crab, Paralithodes camtschaticus, and interactive effects of pH and temperature on juveniles

Ocean warming and acidification are expected to influence the biology of the ecologically and economically important red king crab, Paralithodes camtschaticus. We investigated transcriptome responses of adult, larval and juvenile red king crab to assess sensitivity to reduced pH and elevated temperature. In adults, gill tissue (but not heart or cuticle) responded to reduced pH by differentially regulating many genes involved in metabolic, membrane and cuticular processes, but not ionic or acid/base regulation. In larval crabs, we found little evidence for a strong transcriptomic response to pH, but did observe large differences in the transcriptomes of newly hatched and one-week old larvae. In juvenile crabs, we found that there was a strong transcriptomic response to temperature across all pH conditions, but that only extreme low pH caused transcriptomic shifts. Most of the genes in juveniles that were differentially expressed were for cuticular and calcification processes. While inferences regarding the specific biological responses associated with changes in gene expression are likely to change as resources for red king crab genomics enabled studies continue to improve (i.e. better assemblies and annotation), our inferences about general sensitivities to temperature and pH across the life stages of red king crab are robust and unlikely to shift. Overall, our data suggest that red king crab are more sensitive to warming than acidification, and that responses to acidification at the transcriptomic level occur at different levels of pH across life stages, with juveniles being less pH sensitive than adults.

Continue reading ‘Transcriptomic response to decreased pH in adult, larval and juvenile red king crab, Paralithodes camtschaticus, and interactive effects of pH and temperature on juveniles’

Genome-wide identification, characterization of RLR genes in Yesso scallop (Patinopecten yessoensis) and functional regulations in responses to ocean acidification


• Four RLR family members were identified in Patinopecten yessoensis genome.

• Phylogenetic analysis confirmed duplication and evolutionary relationship of PyRLRs.

• Spatiotemporal expression patterns suggested the functional roles of PyRLRs.

• Constitutive and inducible divergence of PyRLRs has been arisen to the immune stress.

• The four PyRLRs showed functional differentiations in response to OA.


Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), are crucial sensors with a conserved structure in cytoplasm, inducing the production of cytokines, chemokines and host restriction factors which mediate a variety of intracellular activities to interfere with distinct PAMPs (pathogen-associated molecular patterns) for eliminating pathogens in innate immune system. Although RLR genes have been investigated in most vertebrates and some invertebrates, the systematic identification and characterization of RLR genes have not been reported in scallops. In this study, four RLR genes (PY-10413.4, PY-10413.5, PY-443.7 and PY-443.8, designated PyRLRs) were identified in Yesso scallop (Patinopecten yessoensis) through whole-genome scanning through in silico analysis, including two pairs of tandem duplicate genes located on the same scaffold (PY-10413.4 and PY-10413.5, PY-443.7 and PY-443.8, respectively). Phylogenetic and protein structural analyses were performed to determine the identities and evolutionary relationships of these genes. The expression profiles of PyRLRs were determined in all developmental stages, in healthy adult tissues, and in mantles that simulated ocean acidification (OA) exposure (pH = 6.5 and 7.5) at different time points (3, 6, 12 and 24 h). Spatiotemporal expression patterns suggested the functional roles of PyRLRs in all stages of development and growth of the scallop. Regulation expressions revealed PY-10413.4 and PY-10413.5 with one or two CARD(s) (caspase activation and recruitment domain) were up-regulated expressed at most time points, whereas PY-443.8 and PY-10413.4 without CARD were significantly down-regulated at each time points, suggesting functional differentiations in the two pairs of PyRLRs based on the structural differences in response to OA. Collectively, this study demonstrated gene duplication of RLR family genes and provide primary analysis for versatile roles in the response of the bivalve innate immune system to OA challenge.

Continue reading ‘Genome-wide identification, characterization of RLR genes in Yesso scallop (Patinopecten yessoensis) and functional regulations in responses to ocean acidification’

Climate shapes population variation in dogwhelk predation on foundational mussels

Trait variation among populations is important for shaping ecological dynamics. In marine intertidal systems, seawater temperature, low tide emersion temperature, and pH can drive variation in traits and affect species interactions. In western North America, Nucella dogwhelks are intertidal drilling predators of the habitat-forming mussel Mytilus californianus. Nucella exhibit local adaptation, but it is not known to what extent environmental factors and genetic structure contribute to variation in prey selectivity among populations. We surveyed drilled mussels at sites across Oregon and California, USA, and used multiple regression and Mantel tests to test the effects of abiotic factors and Nucella neutral genetic relatedness on the size of mussels drilled across sites. Our results show that Nucella at sites characterized by higher and less variable temperature and pH drilled larger mussels. Warmer temperatures appear to induce faster handling time, and more stable pH conditions may prolong opportunities for active foraging by reducing exposure to repeated stressful conditions. In contrast, there was no significant effect of genetic relatedness on prey size selectivity. Our results emphasize the role of climate in shaping marine predator selectivity on a foundation species. As coastal climates change, predator traits will respond to localized environmental conditions, changing ecological interactions.

Continue reading ‘Climate shapes population variation in dogwhelk predation on foundational mussels’

Blue mussel (Genus Mytilus) transcriptome response to simulated climate change in the Gulf of Maine

The biogeochemistry of the Gulf of Maine (GOM) is rapidly changing in response to the changing climate, including rising temperatures, acidification, and declining primary productivity. These impacts are projected to worsen over the next 100 y and will apply selective pressure on populations of marine calcifiers. This study investigates the transcriptome expression response to these changes in ecologically and economically important marine calcifiers, blue mussels. Wild mussels (Mytilus edulis and Mytilus trossulus) were sampled from sites spanning the GOM and exposed to two different biogeochemical water conditions: (1) present-day conditions in the GOM and (2) simulated future conditions, which included elevated temperature, increased acidity, and decreased food supply. Patterns of gene expression were measured using RNA sequencing from 24 mussel samples and contrasted between ambient and future conditions. The net calcification rate, a trait predicted to be under climate-induced stress, was measured for each individual over a 2-wk exposure period and used as a covariate along with gene expression patterns. Generalized linear models, with and without the calcification rate, were used to identify differentially expressed transcripts between ambient and future conditions. The comparison revealed transcripts that likely comprise a core stress response characterized by the induction of molecular chaperones, genes involved in aerobic metabolism, and indicators of cellular stress. Furthermore, the model contrasts revealed transcripts that may be associated with individual variation in calcification rate and suggest possible biological processes that may have downstream effects on calcification phenotypes, such as zinc-ion binding and protein degradation. Overall, these findings contribute to the understanding of blue mussel adaptive responses to imminent climate change and suggest metabolic pathways are resilient in variable environments.

Continue reading ‘Blue mussel (Genus Mytilus) transcriptome response to simulated climate change in the Gulf of Maine’

Long-term exposure to near-future ocean acidification does not affect the expression of neurogenesis- and synaptic transmission-related genes in the olfactory bulb of European sea bass (Dicentrarchus labrax)

The decrease in ocean pH that results from the increased concentration of dissolved carbon dioxide (CO2) is likely to influence many physiological functions in organisms. It has been shown in different fish species that ocean acidification (OA) mainly affects sensory systems, including olfaction. Impairment of olfactory function may be due to a dysfunction of the GABAergic system and to an alteration of neuronal plasticity in the whole brain and particularly in olfactory bulbs. Recent studies revealed that OA-driven effects on sensory systems are partly mediated by the regulation of the expression of genes involved in neurotransmission and neuronal development. However, these studies were performed in fish exposed to acidified waters for short periods, of only a few days. In the present paper, we investigated whether such effects could be observed in adult (4-years old) European sea bass (Dicentrarchus labrax) exposed to two hypercapnic and acidified conditions (PCO2 ≈ 980 µatm; pH total = 7.7 and PCO2 ≈ 1520 µatm; pH total = 7.5) from the larval stage. In a first approach, we analyzed by qPCR the expression of five genes involved in neurogenesis (DCX) or expressed in GABAergic (Gabra3), glutamatergic (Gria1) or dopaminergic (TH and DDC) neurons in the olfactory bulbs. The tested experimental conditions did not change the expression of any of the five genes. This result would indicate that a potential disruption of the olfactory function of sea bass exposed for a long term to near-future OA, either occurs at a level other than the transcriptional one or involves other actors of the sensory function.

Continue reading ‘Long-term exposure to near-future ocean acidification does not affect the expression of neurogenesis- and synaptic transmission-related genes in the olfactory bulb of European sea bass (Dicentrarchus labrax)’

An integrated investigation of the effects of ocean acidification on adult abalone (Haliotis tuberculata)

Ocean acidification (OA) and its subsequent changes in seawater carbonate chemistry are threatening the survival of calcifying organisms. Due to their use of calcium carbonate to build their shells, marine molluscs are particularly vulnerable. This study investigated the effect of CO2-induced OA on adult European abalone (Haliotis tuberculata) using a multi-parameter approach. Biological (survival, growth), physiological (pHT of haemolymph, phagocytosis, metabolism, gene expression), and structural responses (shell strength, nano-indentation measurements, Scanning electron microscopy imaging of microstructure) were evaluated throughout a 5-month exposure to ambient (8.0) and low (7.7) pH conditions. During the first 2 months, the haemolymph pH was reduced, indicating that abalone do not compensate for the pH decrease of their internal fluid. Overall metabolism and immune status were not affected, suggesting that abalone maintain their vital functions when facing OA. However, after 4 months of exposure, adverse effects on shell growth, calcification, microstructure, and resistance were highlighted, whereas the haemolymph pH was compensated. Significant reduction in shell mechanical properties was revealed at pH 7.7, suggesting that OA altered the biomineral architecture leading to a more fragile shell. It is concluded that under lower pH, abalone metabolism is maintained at a cost to growth and shell integrity. This may impact both abalone ecology and aquaculture.

Continue reading ‘An integrated investigation of the effects of ocean acidification on adult abalone (Haliotis tuberculata)’

The effects of aragonite saturation state on hatchery-reared larvae of the greenshell mussel Perna canaliculus

The major cultured mussel species Perna canaliculus is now supported by hatchery production, providing the opportunity to explore and optimize environmental parameters to enhance production. Other cultured bivalve larvae have demonstrated performance that is directly correlated to the aragonite saturation state (Ωar) of their tank water, with low or undersaturated water being detrimental and artificially elevated Ωar enhancing productivity. Trials were, therefore, designed to specifically explore Ωar sensitivity in preveliger (0–2 days old, prodissoconch I = “PD1″) and veliger (2–21 days old, prodissoconch II = “PD2″) stages of P. canaliculus separately. For the PD1 experiment, commercial incubation tanks (control Ωar 1.9) were modified to target Ωar 0.5 or 0.8 by elevating pCO2, or 2.9, 4.5, and ∼7 by the addition of sodium carbonate. In the control environment, 72.8% ± 2.9% of fertilized eggs formed viable “D” veligers within two days; an increased yield of 82.6% ± 3.8% in Ωar 4.5 was found to be nonsignificant. In comparison, only 12.7% of the Ωar ∼7 and <1% of the Ωar 0.5 and 0.8 eggs attained the veliger stage, with the remaining underdeveloped or malformed. By 2 days postfertilization, reactive oxygen species were significantly elevated in the undersaturated treatments, whereas DNA damage, lipid hydroperoxides, and protein carbonyls were significantly higher in the Ωar 0.5 and ∼7 treatments. Antioxidant enzyme levels were significantly lower in these extreme treatments, whereas Ωar 4.5 larvae showed elevated superoxide dismutase, glutathione reductase, and peroxidase levels. Carry-over effects persisted when veligers were transferred to control conditions, with no net recruitment from undersaturated Ωar, 29.4% of eggs surviving to pediveliger under control conditions, compared with 33.2% following Ωar 4.5 exposure or 1.9% from Ωar ∼7. In the PD2 veliger trial, linear shell growth halved in undersaturated water, but was unaffected by elevation of Ωar. Mortality rate was consistent across all treatments, suggesting relative resilience to different Ωar. It is recommended that hatcheries trial Ωar 4–4.5 enrichment in preveliger incubation water to improve yield and minimize oxidative stress. Preveliger stages present a potential survival bottleneck, and focused research exploring sensitivity to near-future ocean acidification is, therefore, needed.

Continue reading ‘The effects of aragonite saturation state on hatchery-reared larvae of the greenshell mussel Perna canaliculus’

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Ocean acidification in the IPCC AR5 WG II

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