Molecular biomarkers and toxic consequences of impact by organic pollution in aquatic organisms

Organic contaminants are readily bioaccumulated by aquatic organisms. Exposure to and toxic effects of contaminants can be measured in terms of the biochemical responses of the organisms (i.e. molecular biomarkers). The hepatic biotransformation enzyme cytochrome P4501A (CYP1A) in vertebrates is specifically induced by organic contaminants such as aromatic hydrocarbons, PCBs and dioxins, and is involved in chemical carcinogenesis via catalysis of the covalent binding of organic contaminants to DNA (DNA-adducts). Hepatic CYP1A induction has been used extensively and successfully as a biomarker of organic contaminant exposure in fish. Fewer but equally encouraging studies in fish have used hepatic bulky, hydrophobic DNA-adducts as biomarkers of organic contaminant damage. Much less is known of the situation in marine invertebrates, but a CYPlA-like enzyme with limited inducibility and some potential for biomarker application is indicated. Stimulation of reactive oxygen species (ROS) production is another potential mechanism of organic contaminant-mediated DNA and other damage in aquatic organisms. A combination of antioxidant (enzymes, scavengers) and pro-oxidant (oxidised DNA bases, lipid peroxidation) measurements may have potential as a biomarker of organic contaminant exposure (particularly those chemicals which do not induce CYP1A) and/or oxidative stress, but more studies are required. Both CYP1A- and ROS-mediated toxicity are indicated to result in higher order deleterious effects, including cancer and other aspects of animal fitness.

On the use of combined compact scheme for numerical solution of the two-layer oceanic shallow water equations

Many types of oceanic physical phenomena have a wide range in both space and time. In general, simplified models, such as shallow water model, are used to describe these oceanic motions. The shallow water equations are widely applied in various oceanic and atmospheric extents. By using the two-layer shallow water equations, the stratification effects can be considered too. In this research, the sixth-order combined compact method is investigated and numerically implemented as a high-order method to solve the two-layer shallow water equations. The second-order centered, fourth-order compact and sixth-order super compact finite difference methods are also used to spatial differencing of the equations. The first part of the present work is devoted to accuracy assessment of the sixth-order super compact finite difference method (SCFDM) and the sixth-order combined compact finite difference method (CCFDM) for spatial differencing of the linearized two-layer shallow water equations on the Arakawa's A-E and Randall's Z numerical grids. Two general discrete dispersion relations on different numerical grids, for inertia-gravity and Rossby waves, are derived. These general relations can be used for evaluation of the performance of any desired numerical scheme. For both inertia-gravity and Rossby waves, minimum error generally occurs on Z grid using either the sixth-order SCFDM or CCFDM methods. For the Randall's Z grid, the sixth-order CCFDM exhibits a substantial improvement , for the frequency of the barotropic and baroclinic modes of the linear inertia-gravity waves of the two layer shallow water model, over the sixth-order SCFDM. For the Rossby waves, the sixth-order SCFDM shows improvement, for the barotropic and baroclinic modes, over the sixth-order CCFDM method except on Arakawa's C grid. In the second part of the present work, the sixth-order CCFDM method is used to solve the one-layer and two-layer shallow water equations in their nonlinear form. In one-layer model with periodic boundaries, the performance of the methods for mass conservation is compared. The results show high accuracy of the sixth-order CCFDM method to simulate a complex flow field. Furthermore, to evaluate the performance of the method in a non-periodic domain the sixth-order CCFDM is applied to spatial differencing of vorticity-divergence-mass representation of one-layer shallow water equations to solve a wind-driven current problem with no-slip boundary conditions. The results show good agreement with published works. Finally, the performance of different schemes for spatial differencing of two-layer shallow water equations on Z grid with periodic boundaries is investigated. Results illustrate the high accuracy of combined compact method.