Posts Tagged 'molecular biology'

Investigating the response of sea urchin early developmental stages to multiple stressors related to climate change

Within climate change biology, the red sea urchin Mesocentrotus franciscanus has
remained relatively overlooked despite its sizeable ecological and economic importance, particularly within the context of multi-stressor effects. I assembled and described a developmental transcriptome for M. franciscanus, providing a useful molecular resource with which to study this organism. I then examined both the physiological and molecular mechanisms that underlie the response of early developmental stage (EDS) M. franciscanus to different combinations of pH levels and temperatures that represented ecologically
relevant present and future ocean conditions. Elevated pCO2 levels decreased embryo body size, but at the prism embryo stage, warmer temperatures helped to offset this via an increase in body size. Warmer temperatures also slightly increased the thermal tolerance of prism stage embryos. Neither pCO2 nor temperature stressors affected prism metabolic rate as measured by rate of oxygen consumption. Gene expression patterns differed by developmental stage and by temperature exposure. Elevated temperatures led to an upregulation of cellular stress response genes. Under colder temperatures, the embryos
exhibited an up-regulation of epigenetic genes related to histone modifications.
There was a comparatively minimal transcriptomic response to different pCO2 levels. Examining the physiological and molecular responses of EDS M. franciscanus to multiple stressors provided much needed information regarding a species of significant ecological and economic value by examining its capacity to respond to stressors related to climate change and ocean acidification under an ecologically relevant context.

I also investigated the role of transgenerational plasticity (TGP), in which the
environmental conditions experienced by parents affect progeny phenotypes. TGP may provide a valuable mechanism by which organisms can keep pace with relatively rapid environmental change. Adult S. purpuratus were conditioned to two divergent, but ecologically relevant pH levels and temperatures throughout gametogenesis. The adults were spawned and crossed, and their progeny were raised under different pH levels to determine if maternal conditioning impacted the response of the progeny to low pH stress. I investigated maternal provisioning, a mechanism of TGP, by measuring the size, total protein content, and total lipid content of the eggs that they produced. Acclimatization of the
adult urchins to simulated upwelling conditions (combined low pH, low temperature) appeared to increase maternal provisioning of lipids to the eggs but did not affect egg size or protein content. I also investigated the physiology and gene expression of progeny responding to low pH stress, which were affected more by maternal conditioning than by offspring pH treatment. Maternal conditioning to simulated upwelling resulted in larger offspring body sizes. Additionally, I found the progeny expressed differential regulatory
patterns of genes related to epigenetic modifications, ion transport, metabolic processes and ATP production. This work showed that adult exposure to upwelling conditions can improve the resilience of EDS progeny to low pH levels.

Continue reading ‘Investigating the response of sea urchin early developmental stages to multiple stressors related to climate change’

Molecular and physiological responses to long-term carbon dioxide exposure in Atlantic salmon (Salmo salar)


• Atlantic salmon was exposed to six CO2 concentrations (5–40 mg/L) for 12 weeks followed by 6-weeks without exposure (<5 mg/L).

• Positive (pH, K+, HCO3− and PCO2) and negative (Na+, Cl−) linear relationships with CO2 exposure were observed as long as CO2 exposure persists, returning to normal levels when CO2 exposure is ended.

• Microarrays analysis of gill tissue detected 71 differentiated expressed genes that responded to CO2 and after termination of exposure 27 down-regulated genes showed compensatory up-regulation.

• The assumption that Atlantic salmon is unaffected by CO2 concentrations below the 15 mg/L threshold should be revised.


Optimal water quality is vital for the growth of Atlantic salmon aquaculture production. Recent data showed that Atlantic salmon feed intake and growth reduce linearly with increasing water carbon dioxide (CO2) concentrations, suggesting that even relatively low concentrations may impact fish performance. This study evaluated the molecular and physiological responses of Atlantic salmon (Salmo salar) to long-term CO2 exposure. For this purpose, Atlantic salmon post-smolts (N = 900; 67 ± 8 g) were exposed to six CO2 treatments (5, 12, 19, 26, 33 and 40 mg/L) for 12-weeks (RAS phase) followed by non-CO2 exposure for a (<5 mg/L) period of 6-weeks (seawaterphase). Results from blood analysis of fish exposed to CO2 for 12 weeks showed that CO2 lead to significantly higher pH, K+, HCO3− and PCO2 and lower Na+ and Cl− plasma concentrations. Whereas, haematocrit, Ca+, Mg2+, urea and glucose concentrations were similar among all CO2 treatments. After 6 weeks in the seawater phase, all the parameters that were previously altered, became similar among all CO2 treatments. Gill microarray results analysis showed 88 differentially expressed genes, resulting from the CO2 exposure. At the end of the RAS phase (week 12), fish exposed to high CO2 (40 mg/L) in comparison to fish exposed to low CO2 (5 mg/L), showed 60 down-regulated genes, including genes encoding proteins involved in immune responses, differentiation, and maintenance of tissue structure. There was no evidence for stress and metabolic changes directed to neutralization of disturbance caused with high CO2. After 6 weeks in the seawater phase, a switch of expression from down regulated to up-regulated was observed. In conclusion, the present study brings new insights on the molecular and physiological responses of Atlantic salmon post-smolts to long-term CO2 exposure. Several osmoregulation and acid-base balance parameters as well as gill gene expression levels were altered for as long as CO2 exposure persisted. Moreover, most of these parameters were linearly related with the environmental CO2 concentrations (5–40 mg/L range). The data from this study adds to recent findings that CO2 concentrations below the 15 mg/L threshold still have an impact on Atlantic salmon. This finding may be relevant for a better dimensioning and management of production systems where CO2 may accumulate in the water such as in recirculating aquaculture systems (RAS).

Continue reading ‘Molecular and physiological responses to long-term carbon dioxide exposure in Atlantic salmon (Salmo salar)’

Cloning and characterization of a novel Lustrin A gene from Haliotis discus hannai


• The cysteine-rich and proline-rich domains in Lustrin A can be grouped into structural repetitive unit.

• Components of structural repetitive unit reflect the evolutionary distance.

• The expression of Lustrin A is associated with shell regeneration and innate immunity.

• Warming and acidification affected the expression pattern of Lustrin A.


Lustrin A is the first nacre protein with specific structure and amino acid residue content that was identified in abalone; since its identification, homologs have been found in several abalone species. In this study, we isolated and cloned the complete cDNA of Lustrin A from Haliotis discus hannai, which was named Hdh-Lustrin A. Hdh-Lustrin A has characteristic cysteine- and proline-rich domains, glycine- and serine-rich domains, and a whey acidic protein (WAP)-like C-terminus. The cysteine- and proline-rich domains showed internal similarity repeats that arrayed in gene coding region, and the phylogenetic tree of these repeats indicated that the similarity of structural repetitive unit components in different abalone species, reflecting their evolutionary distance. A tissue distribution analysis showed that the mRNA level of Hdh-Lustrin A has tissue-specific expression in mantle. Under lipopolysaccharide (LPS) challenge, Hdh-Lustrin A showed a significantly increase, while it showed a more complex pattern with two peaks in the process of shell regeneration. Moreover, acidification and warming raised the expression level of Hdh-Lustrin A in shell regeneration in two different manners; acidification raised the gene expression in quick response, in contrast the long run in warming treatment. Similar pattern also has been detected in immune reaction and the thermal treatments. These results suggest that the Hdh-Lustrin A is a nacre protein, which can be distinguished by its cysteine- and proline-rich domain. It involves in shell regeneration and innate immunity in abalone, and its expression pattern during shell regeneration can be disrupted by physicochemical properties of the environment.

Continue reading ‘Cloning and characterization of a novel Lustrin A gene from Haliotis discus hannai’

Alternative splicing, spatiotemporal expression of TEP family genes in Yesso scallop (Patinopecten yessoensis) and their disparity in responses to ocean acidification


• Seven PyTEP1 splices were identified in Yesso scallop transcriptome.

• Gene duplication and alternative splicing simultaneously occurred in PyTEP1.

• Spatiotemporal expressions revealed PyTEPs had functional differentiations.

• The five PyTEPs showed diverse immune response patterns to OA.

• Functional differentiations of PyTEP1 splices have been arisen to immune stress.


The complement system constitutes a highly sophisticated and powerful body defense machinery acting in the innate immunity of both vertebrates and invertebrates. As central components of the complement system, significant effects of thioester-containing protein (TEP) family members on immunity have been reported in most vertebrates and in some invertebrates, but the spatiotemporal expression and regulatory patterns of TEP family genes under environmental stress have been less widely investigated in scallops. In this study, expression profiling of TEP family members in the Yesso scallop Patinopecten yessoensis (designated PyTEPs) was performed at all developmental stages, in different healthy adult tissues, and in mantles during exposure to different levels of acidification (pH = 6.5 and 7.5) for different time points (3, 6, 12 and 24 h); this profiling was accomplished through in silico analysis of transcriptome and genome databases. Spatiotemporal expression patterns revealed that PyTEPs had specific functional differentiation in all stages of growth and development of the scallop. Expression analysis confirmed the inducible expression patterns of PyTEPs during exposure to acidification. Gene duplication and alternative splicing events simultaneously occurred in PyTEP1. Seven different cDNA variants of PyTEP1 (designated PyTEP1-A–PyTEP1-G) were identified in the scallop mantle transcriptome during acidic stress. These variants were produced by the alternative splicing of seven differentially transcribed exons (exons 18–24), which encode the highly variable central region. The responses to immune stress may have arisen through the gene duplication and alternative splicing of PyTEP1. The sequence diversity of PyTEP1 isoforms and their different expression profiles in response to ocean acidification (OA) suggested a mechanism used by scallops to differentiate and regulate PyTEP1 gene expression. Collectively, these results demonstrate the gene duplication and alternative splicing of TEP family genes and provide valuable resources for elucidating their versatile roles in bivalve innate immune responses to OA challenge.

Continue reading ‘Alternative splicing, spatiotemporal expression of TEP family genes in Yesso scallop (Patinopecten yessoensis) and their disparity in responses to ocean acidification’

Combined effects of ocean acidification and crude oil pollution on tissue damage and lipid metabolism in embryo–larval development of marine medaka (Oryzias melastigma)

Ocean acidification (OA) and crude oil pollution have been highlighted as some of the most pervasive anthropogenic influences on the ocean.In marine teleosts, early life-history stages are particularly vulnerable to disturbance by CO2-driven acidification as they lack pH-mediated intracellular regulation. Embryos exposed to trace levels of crude oil constituents dissolved in water exhibit a common syndrome of developmental abnormalities. So far, little is known about the combined effects of OA and crude oil on the early life history of marine fish. Eggs and larvae of the marine medaka (Oryzias melastigma) were treated with CO2 (1080 μatm atmospheric CO2), the water-soluble fraction (WSF) of crude oil (500 μg/L) and a CO2 (1080 μatm atmospheric CO2)/WSF (500 μg/L) mixture within 4 h after oviposition. Isolated and combined OA/WSF had no detectable effect on embryonic duration, egg survival rate and size at hatching. Histopathological anomalies of tissue and lipid metabolic disorder were significant when CO2 or WSF was given alone at 30 days of age. Combination of CO2 and WSF enhanced their toxicity compared to their separate administration. Since the early life-history stage of marine fish is thought to be impacted more heavily by increasing CO2 partial pressure (pCO2) levels and crude oil pollution, OA and crude oil pollution have the potential to act as an additional source of natural mortality.

Continue reading ‘Combined effects of ocean acidification and crude oil pollution on tissue damage and lipid metabolism in embryo–larval development of marine medaka (Oryzias melastigma)’

Ocean acidification and warming effects on the physiology, skeletal properties, and microbiome of the purple-hinge rock scallop


• Is the physiology of Crassadoma gigantea affected by warming and acidification?

• Warming and acidification reduced shell strength & increased total lipid content.

• Exposed scallops reorganized fatty acids to sustain metabolic functions.

• Treatments lead to differences in microbiome community composition.

• This was the first multi-stressor experiment on Crassadoma gigantea.

• This was the first multi-stressors experiment to define a core microbiome in a bivalve.


Ocean acidification and increased ocean temperature from elevated atmospheric carbon dioxide can significantly influence the physiology, growth and survival of marine organisms. Despite increasing research efforts, there are still many gaps in our knowledge of how these stressors interact to affect economically and ecologically important species. This project is the first to explore the physiological effects of high pCO2 and temperature on the acclimation potential of the purple-hinge rock scallop (Crassadoma gigantea), a widely distributed marine bivalve, important reef builder, and potential aquaculture product. Scallops were exposed to two pCO2 (365 and 1050 μatm) and temperature (14 and 21.5 °C) conditions in a two-factor experimental design. Simultaneous exposure to high temperature and high pCO2 reduced shell strength, decreased outer shell density and increased total lipid content. Despite identical diets, scallops exposed to high pCO2 had higher content of saturated fatty acids, and lower content of polyunsaturated fatty acids suggesting reorganization of fatty acid chains to sustain basic metabolic functions under high pCO2. Metagenomic sequencing of prokaryotes in scallop tissue revealed treatment differences in community composition between treatments and in the presence of genes associated with microbial cell regulation, signaling, and pigmentation. Results from this research highlight the complexity of physiological responses for calcifying species under global change related stress and provide the first insights for understanding the response of a bivalve’s microbiome under multiple stressors.

Continue reading ‘Ocean acidification and warming effects on the physiology, skeletal properties, and microbiome of the purple-hinge rock scallop’

Present and future adaptation of marine species assemblages: DNA-based insights into climate change from studies of physiology, genomics, and evolution

Marine species live in a dynamic physical and biological environment that demands frequent physiological adjustment and can result in strong natural selection or shifts in species ranges. We illustrate the patterns and processes of adaptation to environmental change with genetic-based examples that range from a focus on single proteins to whole genomes to whole communities. This work shows how single amino acid changes adapt proteins to function at different temperatures. It shows how acidification impacts expression of proteins in energy pathways in adults and exerts natural selection on many genes in larvae. Whole genome surveys along coastlines are now possible, and they reveal unexpected patterns of genetic differentiation even in highly dispersive species. Genetic surveys of over 70 species along the North American west coast show high levels of genetic diversity and genetic structure clustered at headlands and capes known to mark species range boundaries. Finally, new surveys of DNA variation in whole communities show promise for rapid monitoring that can augment and complement traditional dive surveys. Overall, dynamics in the physical environment have a strong effect on organism physiology, which results in diverse patterns of population growth and persistence, as well as of species range and evolutionary capacity. The high level of adaptive genetic variation shown here suggests an ability for marine populations to adapt in the face of climate change, but many questions remain about how fast, complete, and effective this evolution will be.

Continue reading ‘Present and future adaptation of marine species assemblages: DNA-based insights into climate change from studies of physiology, genomics, and evolution’

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Ocean acidification in the IPCC AR5 WG II

OUP book