Long-Term Pyrene Exposure of Grass Shrimp, \u3ci\u3ePalaemonetes pugio\u3c/i\u3e, Affects Molting and Reproduction of Exposed Males and Offspring of Exposed Females

The objective of this study was to investigate the impact of long-term pyrene exposure on molting and reproduction in the model estuarine invertebrate, the grass shrimp (Palaemonetes pugio). Grass shrimp were exposed to measured concentrations of 5.1, 15.0, and 63.4 ppb (mu g/L) pyrene for 6 weeks, during which time we determined molting and survivorship. At the end of the exposure, we immediately sacrificed some of the shrimp for biomarker (CYP1A and vitellin) analyses. The remaining shrimp were used to analyze fecundity and embryo survivorship during an additional 6 weeks after termination of pyrene exposure. Male shrimp at the highest pyrene dose (63 ppb) experienced a significant delay in molting and in time until reproduction, and showed elevated ethoxycoumarin o-deethylase (ECOD) activity immediately after the 6-week exposure period. In contrast, 63 ppb pyrene did not affect these parameters in female shrimp. Females produced the same number of eggs per body weight, with high egg viability (98-100%) at all exposure levels, but with decreased survival for the offspring of the 63-ppb pyrene-exposed females. In addition, vitellin levels were elevated only in females at 63 ppb pyrene after the 6-week exposure. We hypothesize that the elevated vitellin binds pyrene and keeps it biologically unavailable to adult females, resulting in maternal transfer of pyrene to the embryos. This would account for the lack of effect of pyrene exposure on ECOD activity, molting, and reproduction in the adult females, and for reduced survival of their offspring

Beyond Affymetrix Arrays: Expanding the Set of Known Hybridization Isotherms and Observing Pre-Wash Signal Intensities

Microarray hybridization studies have attributed the nonlinearity of hybridization isotherms to probe saturation and post-hybridization washing. Both processes are thought to distort \u27true\u27 target abundance because immobilized probes are saturated with excess target and stringent washing removes loosely bound targets. Yet the paucity of studies aimed at understanding hybridization and dissociation makes it difficult to align physicochemical theory to microarray results. To fill the void, we first examined hybridization isotherms generated on different microarray platforms using a ribosomal RNA target and then investigated hybridization signals at equilibrium and after stringent wash. Hybridization signal at equilibrium was achieved by treating the microarray with isopropanol, which prevents nucleic acids from dissolving into solution. Our results suggest that (i) the shape of hybridization isotherms varied by microarray platform with some being hyperbolic or linear, and others following a power-law; (ii) at equilibrium, fluorescent signal of different probes hybridized to the same target were not similar even with excess of target and (iii) the amount of target removed by stringent washing depended upon the hybridization time, the probe sequence and the presence/absence of nonspecific targets. Possible physicochemical interpretations of the results and future studies are discussed

Generation, Analysis and Functional Annotation of Expressed Sequence Tags From the Sheepshead Minnow (\u3ci\u3eCyprinodon variegatus\u3c/i\u3e)

Background: Sheepshead minnow (Cyprinodon variegatus) are small fish capable of withstanding exposure to very low levels of dissolved oxygen, as well as extreme temperatures and salinities. It is an important model in understanding the impacts and biological response to hypoxia and co-occurring compounding stressors such as polycyclic aromatic hydrocarbons, endocrine disrupting chemicals, metals and herbicides. Here, we initiated a project to sequence and analyze over 10,000 ESTs generated from the Sheepshead minnow (Cyprinodon variegatus) as a resource for investigating stressor responses. Results: We sequenced 10,858 EST clones using a normalized cDNA library made from larval, embryonic and adult suppression subtractive hybridization-PCR (SSH) libraries. Post- sequencing processing led to 8,099 high quality sequences. Clustering analysis of these ESTs indentified 4,223 unique sequences containing 1,053 contigs and 3,170 singletons. BLASTX searches produced 1,394 significant (E-value \u3c 10(-5)) hits and further Gene Ontology (GO) analysis annotated 388 of these genes. All the EST sequences were deposited by Expressed Sequence Tags database (dbEST) in GenBank (GenBank: GE329585 to GE337683). Gene discovery and annotations are presented and discussed. This set of ESTs represents a significant proportion of the Sheepshead minnow (Cyprinodon variegatus) transcriptome, and provides a material basis for the development of microarrays useful for further gene expression studies in association with stressors such as hypoxia, cadmium, chromium and pyrene

Effects of Cyclic Hypoxia On Gene Expression and Reproduction In a Grass Shrimp, \u3ci\u3ePalaemonetes pugio\u3c/i\u3e

Cyclic changes in dissolved oxygen occur naturally in shallow estuarine systems, yet little is known about the adaptations and responses of estuarine organisms to cyclic hypoxia. Here we examine the responses of Palaemonetes pugio, a species of grass shrimp, to cyclic hypoxia (1.5-8 mg/l dissolved oxygen; 4.20-22.42 kPa) at both the molecular and organismal levels. We measured alterations in gene expression in hepatopancreas tissue of female grass shrimp using custom cDNA macroarrays. After short-term (3-d) exposure to cyclic hypoxia, mitochondrial manganese superoxide dismutase (MnSOD) was upregulated and 70-kd heat shock proteins (HSP70) were downregulated. After 7-d exposure, nuclear genes encoding mitochondrial proteins (ribosomal protein S2, ATP synthase, very-long-chain specific acyl-CoA dehydrogenase [VLCAD]) were downregulated, whereas mitochondrial phosphoenol pyruvate carboxykinase (PEP Cbk) was upregulated. After 14 d, vitellogenin and apolipoprotein A1 were upregulated. Taken together, these changes suggest a shift in metabolism toward gluconeogenesis and lipid export. Long-term (77-d) exposure to hypoxia showed that profiles of gene expression returned to pre-exposure levels. These molecular responses differ markedly from those induced by chronic hypoxia. At the organismal level, cyclic hypoxia reduces the number of broods and eggs a female can produce. Demographic analysis showed a lower estimated rate of population growth in grass shrimp exposed to both continuous and short-term cyclic hypoxia, suggesting population-level impacts on grass shrimp

Constructing a fish metabolic network model

We report the construction of a genome-wide fish metabolic network model, MetaFishNet, and its application to analyzing high throughput gene expression data. This model is a stepping stone to broader applications of fish systems biology, for example by guiding study design through comparison with human metabolism and the integration of multiple data types. MetaFishNet resources, including a pathway enrichment analysis tool, are accessible at http://metafishnet.appspot.com

Rationale for a New Generation of Indicators for Coastal Waters

More than half the world\u27S human population lives within 100 km of the coast, and that number is expected to increase by 25% over the next two decades. Consequently, coastal ecosystems are at serious risk. Larger coastal populations and increasing development have led to increased loading of toxic substances, nutrients and pathogens with subsequent algal blooms, hypoxia, beach closures, and damage to coastal fisheries. Recent climate change has led to the rise in sea level with loss of coastal wetlands and saltwater intrusion into coastal aquifers. Coastal resources have traditionally been monitored on a stressor-by-stressor basis such as for nutrient loading or dissolved oxygen. To fully measure the complexities of coastal systems, we must develop a new set of ecologic indicators that span the realm of biological organization from genetic markers to entire ecosystems and are broadly applicable across geographic regions while integrating stressor types. We briefly review recent developments in ecologic indicators and emphasize the need for improvements in understanding of stress-response relationships, contributions of multiple stressors, assessments over different spatial and temporal scales, and reference conditions. We provide two examples of ecologic indicators that can improve our understanding of these inherent problems: a) the use of photopigments as indicators of the interactive effects of nutrients and hydrology, and b) biological community approaches that use multiple taxa to detect effects on ecosystem structure and function. These indicators are essential to measure the condition of coastal resources, to diagnose stressors, to communicate change to the public, and ultimately to protect human health and the quality of the coastal environment

Optimizing the use of InSAR observations in data assimilation problems to estimate reservoir compaction

Hydrocarbon production may cause subsidence as a result of the pressure reduction in the gas-producing layer and reservoir compaction. To analyze the process of subsidence and estimate reservoir parameters, we use a particle method to assimilate Interferometric synthetic-aperture radar (InSAR) observations of surface deformation with a conceptual model of reservoir. As example, we use an analytical model of the Groningen gas reservoir based on a geometry representing the compartmentalized structure of the subsurface at the reservoir depth. The efficacy of the particle method becomes less when the degree of freedom is large compared to the ensemble size. This degree of freedom, in turn, varies because of spatial correlation in the observed field. The resolution of the InSAR data and the number of observations affect the performance of the particle method. In this study, we quantify the information in a Sentinel-1 SAR dataset using the concept of Shannon entropy from information theory. We investigate how to best capture the level of detail in model resolved by the InSAR data while maximizing their information content for a data assimilation use. We show that incorrect representation of the existing correlations leads to weight collapse when the number of observation increases, unless the ensemble size growths. However, simulations of mutual information show that we could optimize data reduction by choosing an adequate mesh given the spatial correlation in the observed subsidence. Our approach provides a means to achieve a better information use from available InSAR data reducing weight collapse without additional computational cost

Getting into the water with the Ecosystem Services Approach: The DESSIN ESS evaluation framework

Driven by Europe's pressing need to overcome its water quality and water scarcity challenges, the speed of innovation in the water sector is outpacing that of science. The methodologies available to assess the impact of innovative solutions to water-related challenges remain limited and highly theoretical, which sets boundaries on their application and usefulness to water practitioners. This hampers the uptake of new technologies and innovative management practices, thus foregoing potential gains in resource efficiency and nature protection, as well as wider benefits to society and the economy. To address this gap, the DESSIN project developed a framework to evaluate the changes in ecosystem services (ESS) associated with technical or management solutions implemented at the water body, sub-catchment or catchment level. The framework was developed with a specific focus on freshwater ecosystems to allow for a more detailed exploration of practical implementation issues. Its development, testing and validation was carried out by conducting ESS evaluations in three different urban case study settings. The framework builds upon existing classification systems for ESS (CICES and FEGS-CS) and incorporates the DPSIR adaptive management scheme as its main structural element. This enables compatibility with other international initiatives on ESS assessments and establishes a direct link to the EU Water Framework Directive, respectively. This work furthers research on practical implementation of the Ecosystem Services Approach, while pushing the discussion on how to promote more informed decision-making and support innovation uptake to address Europe's current water-related challenges

Biochemical Defense Mechanisms Against Copper-Induced Oxidative Damage in the Blue Crab, \u3ci\u3eCallinectes sapidus\u3c/i\u3e

The blue crab (Callinectes sapidus) has a very dynamic copper metabolism associated with the biosynthesis and degradation of its respiratory pigment hemocyanin. In this study we report on the cellular defense mechanisms used by the crab to protect itself from copper toxicity. Short-term copper-exposure studies, conducted by incubating hepatopancreas tissue explants in copper-containing medium, show that copper taken up by the cells during the first 60 min combines with low-molecular-weight copper complex(es), which include Cu(I)–glutathione. Thereafter, copper binds to newly synthesized metallothionein (MT), with a concomitant decrease in Cu(I)–glutathione. Copper does not displace zinc from the endogenous ZnMT pool. Long-term exposure by means of copper-rich diets results in the synthesis of two MT isoforms in the hepatopancreas: CuMT-I and CuMT-II (D. Schlenk and M. Brouwer, 1991,Aquat. Toxicol.20, 25–34). Transfer of copper from Cu(I)–glutathione to apoMT-I and apoMT-II can be accomplishedin vitro.Cu(I) binding by the two isoforms is very different. Cu(I) binds to apoMT-I in a strictly cooperative manner. No partially filled Cu(I)–thiolate clusters appear to be present. In contrast, the Cu(I)–thiolate clusters in MT-II are formed only after more than four Cu(I) ions are bound. Long-term copper exposure leads to increased activity of two antioxidant enzymes: glutathione peroxidase and manganese superoxide dismutase (SOD). No CuZnSOD is found. Activities of catalase and glutathione reductase and the intracellular levels of glutathione are unaffected by copper. The defense mechanisms are not entirely sufficient for preventing copper-induced oxidative damage. Levels of oxidized lipids are significantly higher in copper-exposed crabs, but oxidized protein levels are nearly the same