Analysis of medaka cytochrome P450 3A homotropic and heterotropic cooperativity

We have previously demonstrated that medaka CYP3A is associated with metabolism of several endobiotics including steroids and bile acids. In this study, we demonstrate that medaka CYP3A catalysis exhibits unusual kinetic behaviors consistent with allosteric interaction which cannot be described by hyperbolic kinetic models. Using 7-benzyloxy-4-(trifluoromethyl)-coumarin (BFC) and nonylphenol as CYP3A substrates, we describe both homotropic and heterotropic cooperative interactions. Given the role of CYP3A in maintaining the homeostatic balance for numerous endobiotics, enzymatic activation/inhibition by endocrine disruptors (EDCs) represents a putative (non-genomic) mechanism for endocrine disruption.     

Developing a Marine Information System by Integrating Existing Ocean Models Using Object-Oriented Technology

Information systems developed for different applications within the environmental domain have common characteristics, which can potentially be abstracted for sharing and reuse of design and software modules. This article presents an approach to designing for reuse by abstracting commonalities in the design of a Marine Information System (MIS), facilitating data management in a prototype operational monitoring, forecasting, and management system for the North Atlantic and the Nordic Seas. A detailed study of the requirements and data analysis was carried out, and Object-Oriented Technology (OOT) is employed to encapsulate abstractions and to promote reuse of code and design. This article identifies the Object-Oriented Frameworks (OOFW) required to build the MIS. It also provides guidelines to environmental scientists for restructuring legacy software and employing modern programming techniques.     

Spatial patterns and environmental risks of ringnet fishing along the Kenyan coast

Ringnet fishing began in the early 20th century and is practised worldwide, mainly to target nearshore pelagic species. The method was introduced to Kenya’s coastal waters by migrant fishers from Tanzania. However, the impacts of this fishing gear remain poorly assessed. We assessed the spatial distribution of ringnet fishing effort and its possible effects on ecosystem components, such as coral reefs, marine megafauna and marine protected areas, on the south coast of Kenya. We tracked 89 ringnet fishing trips made from December 2015 to January 2016 and used spatial multicriteria analysis to determine hotspots of possible environmental risks. The results showed that habitat type and bathymetric profile influenced the spatial distribution of ringnet fishing effort. Mixed seagrass and coral habitats had the highest concentration of the effort. Most of the habitats in the study area were moderately exposed to the impacts of the ringnet fishery. The study identifies high-risk areas that require spatial measures to minimise possible environmental risks of the gear both to habitats and to endangered sea turtles.     

Steady-state analysis of undersea cables

A numerical solution and computer program developed to analyse undersea flexible cable problems is presented. The cable is subject to hydrodynamic loads from a surrounding fluid medium. The object is to determine the cable profile and tensile forces developed. The cable equations and boundary conditions result in a classical two-point boundary value problem. An iteration ‘shooting method’ is used for solution. The program has been written to analyse a class of towing and anchoring problems. However the analysis is general and applicable to most steady-state cable problems.     

Imaging of Buried Archaeological Materials: The Reflection Properties of Archaeological Wood

Effective marine archaeological site management demands detailed information on not only the spatial distribution of artefacts but also the degradation state of the materials present. Although sonar methods have frequently been used in an attempt to detect buried wooden shipwrecks they are currently unable to indicate their degradation state. To assess the sensitivity of acoustic measurements to changes in the degradation state of such material, and hence the potential for sonars to quantify degradation, laboratory measurements of compressional wave velocity, as well as bulk density for oak and pine samples, in varying states of decay, were undertaken. These data enabled the calculation of theoretical reflection coefficients for such materials buried in various marine sediments. As wood degrades, the reflection coefficients become more negative, resulting in the hypothesis that the more degraded wood becomes, the easier it should be to detect. Typical reflection coefficients of the order of −0.43 and −0.52 for the most degraded oak and pine samples in sand are predicted. Conversely, for wood exposed to seawater the predicted reflection coefficients are large and positive for undegraded material (0.35 for oak, 0.18 for pine) and decrease to zero or slightly below for the most degraded samples. This indicates that exposed timbers, when heavily degraded, can be acoustically transparent and so undetectable by acoustic methods. Corroboration of these experimental results was provided through comparison with high resolution seismic reflection data that has been acquired over two shipwrecks.     

Partitioning of polycyclic aromatic hydrocarbons between water and particles compared to bioaccumulation in mussels: a harbour case

Water and particles from three sites located in Halifax Harbour, near and further away from combined municipal sewage effluents (CMSE) were analysed for parental and alkylated polycyclic aromatic hydrocarbons (par and alkPAH). Bioavailability of PAH was compared for inter-tidal mussels collected at the same sites in April and November. The PAH fingerprint determined over 9 sampling times covering a period of 19 months differed more between phases (water and particles) and seasons, than between sites. In the spring, more alkPAH associated with diesel and gasoline were detected in the soluble phase, along with more bioaccumulation of alkPAH in inter-tidal mussels. A broader number of parPAH were detected in mussels collected in the fall. The mean sum of dissolved alkPAH concentrations was higher in water at the site closer to raw CMSE than at the other two sites and particles of that site. However, lowest bioconcentration factors (BCF) were determined in mussels of this more contaminated site. Similar biota-particle accumulation factors (BPAF) were determined for parPAH in mussels from the three sites, all lower than the BCF of alkPAH. The study indicates that sewage treatment plants will reduce the amount of parPAH especially larger than fluoranthene and pyrene from being deposited in the harbour; that alk naphthalenes and fluorenes present in water will continue to be discharged; that the disturbance of sediments can make particle-bound PAH available to mussels.     

Multi-decadal synthesis of benthic–pelagic coupling in the western arctic: Role of cross-shelf advective processes

Using geographic information systems (GIS) software and geostatistical techniques, we utilized three decades of water-column chlorophyll a data to examine the relative importance of autochthonous versus allochthonous sources of reduced carbon to benthic communities that occur from the northern Bering to the eastern Beaufort Sea shelf. Spatial trend analyses revealed areas of high benthic biomass (>300 g m⁻²) and chlorophyll (>150 mg m⁻²) on both the southern and northern Chukchi shelf; both areas are known as depositional centers for reduced organic matter that originates on the Bering Sea shelf and is advected northward in Anadyr and Bering shelf water masses. We found a significant correlation between biomass and chlorophyll a in the Chukchi Sea, reflective of the strong benthic–pelagic coupling in a system that is utilized heavily by benthic-feeding marine mammals. In contrast, there was no significant correlation between biomass and chlorophyll in the Beaufort Sea, which by comparison, is considerably less productive (biomass and chlorophyll, <75 g m⁻² and <50 mg m⁻², respectively). One notable exception is an area of relatively high biomass (50–100 g m⁻²) and chlorophyll (80 mg m⁻²) near Barter Island in the eastern Beaufort Sea. Compared to other adjacent areas in the Beaufort Sea, the chlorophyll values in the vicinity of Barter Island were considerably higher and likely reflect a long-hypothesized upwelling in that area and close coupling between the benthos and autochthonous production. In the Bering Sea, a drop in benthic biomass in 1994 compared with previous measurements (1974–1993) may support earlier observations that document a decline in biomass that began between the 1980s and 1990s in the Chirikov Basin and south of St. Lawrence Island. The results of this study indicate that the benthos is an excellent long-term indicator of both local and physical advective processes. In addition, this work provides further evidence that secondary production on arctic shelves can be significantly augmented by reduced carbon advected from highly productive adjacent shelves.     

Fluxes and sources of suspended organic matter in an estuarine turbidity maximum region during low discharge conditions

Water column concentrations of total suspended solids (TSS), particulate organic carbon (POC) and particulate nitrogen (PN) were measured at three different depths in four different locations bracketing the estuarine turbidity maximum (ETM) along the main channel of a temperate riverine estuary (Winyah Bay, South Carolina, USA). Measurements were carried out over full tidal cycle (over 24 h). Salinity, temperature, current magnitude and direction were also monitored at the same time throughout the water column. Tidally averaged net fluxes of salt, TSS, POC and PN were calculated by combining the current measurements with the concentration data. Under the extreme low river discharge conditions that characterized the study period, net landward fluxes of salt were measured in the lower part of the study area, suggesting that the landward transport through the main channel of the estuary was probably balanced by export out through the sides. In contrast, the net fluxes of salt in the upper reaches of the study area were near zero, indicating a closed salt balance in this part of the estuary. In contrast to salt, the net fluxes of TSS, POC and PN in the deeper parts of the water column were consistently landward at all four sites in Winyah Bay indicating the non-conservative behavior of particulate components and their active transport up the estuary in the region around the ETM.The carbon contents (%POC), carbon:nitrogen ratios (org[C:N]a) and stable carbon isotopic compositions (δ¹³C_POC) of the suspended particles varied significantly with depth, location and tidal stage. Tidally averaged compositions showed a significant increase up the estuary in the %POC and org[C:N]a values of suspended particles consistent with the preferential landward transport of carbon-rich particles with higher vascular plant debris content. The combination of tidal resuspension and flood-dominated flow appeared to be responsible for the hydrodynamic sorting of particles along the estuary that resulted in denser, organic-poor particles being transported landward less efficiently. The elemental and isotopic compositions indicated that vascular C₃ plants and estuarine algae were the major sources of the particulate organic matter of all the samples, without any significant contributions from salt marsh C₄ vegetation (Spartina alterniflora) and/or marine phytoplankton.