Posts Tagged 'molecular biology'

Ocean acidification decreases mussel byssal attachment strength and induces molecular byssal responses

Ocean acidification (OA) is a term describing the uptake of CO2 from the atmosphere, decreasing seawater pH and altering carbonate chemistry. Mussels are an ecologically and economically important taxon that attach to solid surfaces via the byssus. To date, little is known about the effects of OA on mussel byssal attachment and the underlying molecular byssal responses. This study demonstrated that after 1 wk of exposure to acidified seawater, both mechanical properties (such as strength and extensibility) and the numbers of byssal threads produced by Mytilus coruscus were significantly reduced, leading to a 60 to 65% decrease in mussel byssal attachment strength. Real-time PCR results suggested that OA also altered the expression of genes encoding the proximal thread matrix protein (PTMP), precursor collagen proteins (preCOL-P, -NG and -D) and mussel foot proteins (mfp-1, -2, -3, -4, -5 and -6). The down-regulation of some specific byssal proteins may be one of the reasons for the weakened mechanical properties of individual byssal threads under OA conditions. In contrast, the up-regulation of some other specific byssal proteins may be adaptive responses to minimize the adverse effect of OA on byssal attachment. OA may weaken mussel byssal attachment by reducing the production and mechanical properties of byssal threads and by inducing byssal molecular responses. The weakened byssal attachment induced by OA therefore could pose a substantial threat to both mussel aquaculture and mussel-bed ecosystems.

Continue reading ‘Ocean acidification decreases mussel byssal attachment strength and induces molecular byssal responses’

Integrated regulatory and metabolic networks of the marine diatom Phaeodactylum tricornutum predict the response to rising CO2 levels

Diatoms are eukaryotic microalgae that are responsible for up to 40% of the ocean’s primary productivity. How diatoms respond to environmental perturbations such as elevated carbon concentrations in the atmosphere is currently poorly understood. We developed a transcriptional regulatory network based on various transcriptome sequencing expression libraries for different environmental responses to gain insight into the marine diatom’s metabolic and regulatory interactions and provide a comprehensive framework of responses to increasing atmospheric carbon levels. This transcriptional regulatory network was integrated with a recently published genome-scale metabolic model of Phaeodactylum tricornutum to explore the connectivity of the regulatory network and shared metabolites. The integrated regulatory and metabolic model revealed highly connected modules within carbon and nitrogen metabolism. P. tricornutum’s response to rising carbon levels was analyzed by using the recent genome-scale metabolic model with cross comparison to experimental manipulations of carbon dioxide.

IMPORTANCE: Using a systems biology approach, we studied the response of the marine diatom Phaeodactylum tricornutum to changing atmospheric carbon concentrations on an ocean-wide scale. By integrating an available genome-scale metabolic model and a newly developed transcriptional regulatory network inferred from transcriptome sequencing expression data, we demonstrate that carbon metabolism and nitrogen metabolism are strongly connected and the genes involved are coregulated in this model diatom. These tight regulatory constraints could play a major role during the adaptation of P. tricornutum to increasing carbon levels. The transcriptional regulatory network developed can be further used to study the effects of different environmental perturbations on P. tricornutum’s metabolism.

Continue reading ‘Integrated regulatory and metabolic networks of the marine diatom Phaeodactylum tricornutum predict the response to rising CO2 levels’

Linking gene expression to productivity to unravel long- and short-term responses of seagrasses exposed to CO2 in volcanic vents

Ocean acidification is a major threat for marine life but seagrasses are expected to benefit from high CO2. In situ (long-term) and transplanted (short-term) plant incubations of the seagrass Cymodocea nodosa were performed near and away the influence of volcanic CO2 vents at Vulcano Island to test the hypothesis of beneficial effects of CO2 on plant productivity. We relate, for the first time, the expression of photosynthetic, antioxidant and metal detoxification-related genes to net plant productivity (NPP). Results revealed a consistent pattern between gene expression and productivity indicating water origin as the main source of variability. However, the hypothesised beneficial effect of high CO2 around vents was not supported. We observed a consistent long- and short-term pattern of gene down-regulation and 2.5-fold NPP decrease in plants incubated in water from the vents and a generalized up-regulation and NPP increase in plants from the vent site incubated with water from the Reference site. Contrastingly, NPP of specimens experimentally exposed to a CO2 range significantly correlated with CO2 availability. The down-regulation of metal-related genes in C. nodosa leaves exposed to water from the venting site suggests that other factors than heavy metals, may be at play at Vulcano confounding the CO2 effects.

Continue reading ‘Linking gene expression to productivity to unravel long- and short-term responses of seagrasses exposed to CO2 in volcanic vents’

Ocean acidification modulates expression of genes and physiological performance of a marine diatom

Ocean Acidification (OA) is known to affect various aspects of physiological performances of diatoms, but little is known about the underlining molecular mechanisms involved. Here, we show that in the model diatom Phaeodactylum tricornutum, the expression of key genes associated with photosynthetic light harvesting as well as those encoding Rubisco, carbonic anhydrase, NADH dehydrogenase and nitrite reductase, are modulated by OA (1000 μatm, pHnbs 7.83). Growth and photosynthetic carbon fixation were enhanced by elevated CO2. OA treatment decreased the expression of β-carbonic anhydrase (β-ca), which functions in balancing intracellular carbonate chemistry and the CO2 concentrating mechanism (CCM). The expression of the genes encoding fucoxanthin chlorophyll a/c protein (lhcf type (fcp)), mitochondrial ATP synthase (mtATP), ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene (rbcl) and NADH dehydrogenase subunit 2 (ndh2), were down-regulated during the first four days (< 8 generations) after the cells were transferred from LC (cells grown under ambient air condition; 390 μatm; pHnbs 8.19) to OA conditions, with no significant difference between LC and HC treatments with the time elapsed. The expression of nitrite reductase (nir) was up-regulated by the OA treatment. Additionally, the genes for these proteins (NiR, FCP, mtATP synthase, β-CA) showed diel expression patterns. It appeared that the enhanced photosynthetic and growth rates under OA could be attributed to stimulated nitrogen assimilation, increased CO2 availability or saved energy from down-regulation of the CCM and consequently lowered cost of protein synthesis versus that of non-nitrogenous cell components.

Continue reading ‘Ocean acidification modulates expression of genes and physiological performance of a marine diatom’

KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)

Antarctic krill (Euphausia superba) is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tonnes. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem. One looming threat due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2) is ocean acidification (lowering of sea water pH by CO2 dissolving into the oceans). The genetics of Antarctic krill has long been of scientific interest for both for the analysis of population structure and analysis of functional genetics. However, the genetic resources available for the species are relatively modest. We have developed the most advanced genetic database on Euphausia superba, KrillDB, which includes comprehensive data sets of former and present transcriptome projects. In particular, we have built a de novo transcriptome assembly using more than 360 million Illumina sequence reads generated from larval krill including individuals subjected to different CO2 levels. The database gives access to: 1) the full list of assembled genes and transcripts; 2) their level of similarity to transcripts and proteins from other species; 3) the predicted protein domains contained within each transcript; 4) their predicted GO terms; 5) the level of expression of each transcript in the different larval stages and CO2 treatments. All references to external entities (sequences, domains, GO terms) are equipped with a link to the appropriate source database. Moreover, the software implements a full-text search engine that makes it possible to submit free-form queries. KrillDB represents the first large-scale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future approaches devoted to physiological and molecular study of this key species in the Southern Ocean food web.

Continue reading ‘KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)’

Plasticity and inter-population variability in physiological and life-history traits of the mussel Mytilus chilensis: A reciprocal transplant experiment

Geographically widespread species must cope with environmental differences between habitats. Information concerning geographic variations in response to climate variability is critical because many morphological, life-history and physiological traits show variation across space. Reciprocal transplant experiments have shown to be relevant to evaluate the role of phenotypic plasticity and potential local adaptation in ecophysiological responses when coping with environmental variability. In this study, we characterize through reciprocal transplant experiments the reaction norms of morphological, biochemical, physiological and life-history traits between two intertidal populations of the socioeconomically important mussel Mytilus chilensis, inhabiting contrasting local environments (estuarine vs coastal habitats). We found a gradient in phenotypic plasticity with plastic trait responses in metabolic, ingestion and clearance rates, and in HsP70 gene expression, and some traits with responses more canalized as growth and calcification rates. This emphasizes that responses not only vary across different local populations but also in different traits in M. chilensis, thus it is difficult to establish an overall trend of the responses at integrated organismal level. Moreover, the synergistic interaction of factors such as salinity and carbonate system parameters evaluated make it necessary to study the response at the population level with emphasis on benthic species important in aquaculture. Finally, field studies such as this one are useful for documenting the patterns of traits variation that occur in nature, identifying possible causes of such variation, and generating testable hypotheses for future controlled experiments.

Continue reading ‘Plasticity and inter-population variability in physiological and life-history traits of the mussel Mytilus chilensis: A reciprocal transplant experiment’

Exploring the mitochondrial response to oxidative DNA damage in octocorals (not peer-reviewed)

Mitochondrial response to oxidative stress is intricately related to cellular homeostasis due to the high susceptibility of the mitochondrial genome to oxidative damage. Octocoral mitogenomes possess a unique DNA repair gene, mtMutS, potentially capable of counteracting the effects of oxidative stress induced mtDNA damage. Despite this unique feature, the response of octocoral mitochondria to increased oxidative stress remains unexplored. Here we explore the response of the octocoral Sinularia cf. cruciata to elevated temperature and low-pH stress and its ability to reverse acute oxidative mtDNA damage caused by exogenous agents like hydrogen peroxide (H2O2). The differential transcriptional response to these climate change-related stresses was recorded for two mtDNA-encoded genes and three stress biomarkers. Only HSP70 was significantly upregulated during thermal stress whereas significant reduction in the expression levels of HSP70, GPX, and COI was observed along with an increased number of mtMutS transcripts during low-pH stress. Damage to mtDNA was evident, accompanied by changes in mtDNA copy number. Damage caused by H2O2 toxicity was reversed within 5 hours and initial mtDNA copy number apparently influenced damage reversal. Our results indicate that different stress-specific resilience strategies are used by this octocoral species and its mitochondria to reverse oxidative stress and associated mtDNA damage. These experiments provide the first account on the response of octocoral mitochondria with its unique gene repertoire among animals to different stressors and highlight its potential role in conferring resilience to the host cells during different climate change scenarios.

Continue reading ‘Exploring the mitochondrial response to oxidative DNA damage in octocorals (not peer-reviewed)’


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Ocean acidification in the IPCC AR5 WG II

OUP book