Simulation of wave propagation over a submerged bar using the VOF method with a two-equation k– turbulence modeling

A two-equation k– turbulence model is used in this paper to simulate the propagation of cnoidal waves over a submerged bar, where the free surface is handled by the volume-of-fluid (VOF) method. Using a VOF partial-cell variable and a donor–acceptor method, the model is capable of treating irregular boundaries, including arbitrary bottom topography and internal obstacles, where the no-slip condition is satisfied. The model also allows the viscous sublayer to be modeled by a wall function approximation implemented in the grid nodes that are immediately adjacent to a wall boundary. The numerical model applied to the propagation of cnoidal waves over a submerged bar can produce results that are in general agreement with some laboratory measurements. Some remarks arising from the comparison between the computational and experimental results are presented.     

The vertical structure of combined wave–current flow

A simple numerical model, based on the Reynolds stress equations and k–ε turbulence closure scheme, is developed for the coastal wave and current bottom boundary layer. The current friction velocity is introduced to account for the effect of currents on waves. The implicit Crank–Nicolson finite difference method discretizes the governing equations. Vertical changing step grids with the constant ratio for two adjacent spatial steps are used together with the equal time steps in the modeling. Vertical profiles of mean current velocity and wave velocity amplitude are obtained. These modeled results are compared with the laboratory experimental data of Van Doorn [1981. Experimental investigation of near bottom velocities in water waves with and without a current. Report M1423, Delft Hydraulics Laboratory, Delft, The Netherlands; 1982. Experimenteel onderzoek naar het snelheidsveld in de turbulente bodemgrenslaag in een oscillerende stroming in een golftunnel. Report M1562, Delft Hydraulics Laboratory, Delft, The Netherlands]. It has been shown that modeled and observed (Van Doorn, T., 1981. Experimental investigation of near bottom velocities in water waves with and without a current. Report M1423, Delft Hydraulics Laboratory, Delft, The Netherlands; 1982. Experimenteel onderzoek naar het snelheidsveld in de turbulente bodemgrenslaag in een oscillerende stroming in een golftunnel. Report M1562, Delft Hydraulics Laboratory, Delft, The Netherlands) mean velocity profiles within the wave and current bottom boundary layer are in better agreement than outside. Modeled and observed (Van Doorn, T., 1981. Experimental investigation of near bottom velocities in water waves with and without a current. Report M1423, Delft Hydraulics Laboratory, Delft, The Netherlands) wave velocity amplitude profiles within the wave and current bottom boundary layer are in better agreement than outside. Modeled wave velocity amplitudes are in good agreement with the laboratory experimental data of Van Doorn [1982. Experimenteel onderzoek naar het snelheidsveld in de turbulente bodemgrenslaag in een oscillerende stroming in een golftunnel. Report M1562, Delft Hydraulics Laboratory, Delft, The Netherlands].     

σ-Coordinates hydrodynamic numerical model for coastal and ocean three-dimensional circulation

A three-dimensional finite-difference hydrodynamic model has been developed using σ-coordinate for the vertical dimension. An explicit scheme for temporal integration and a staggered grid for spatial discretization have been adopted. The model has been tested against analytical or literature cases for wind and tide induced circulation. Results are in good agreement both with analytical solutions under idealised conditions and with results from the model of Shankar et al. (1996).     

Effects of β-naphthoflavone on hepatic biotransformation and glutathione biosynthesis in largemouth bass (Micropterus salmoides)

We are investigating the effects of in vivo exposure of prototypical enzyme inducing agents on hepatic biotransformation enzyme expression in largemouth bass (Micropterus salmoides), a predatory game fish found throughout the United States and Canada. The current study targeted those genes involved in biotransformation and oxidative stress that may be regulated by Ah-receptor-dependent pathways. Exposure of bass to β-naphthoflavone (β-NF, 66 mg/kg, i.p.) elicited a 7–9-fold increase in hepatic microsomal cytochrome P4501A-dependent ethoxyresorufin O-deethylase (EROD) activities, but did not affect cytosolic GST catalytic activities toward 1-chloro-2,4-dinitrobenzene (CDNB) or 5-androstene-3,17-dione (ADI). Glutathione S-transferase A (GST-A) mRNA expression exhibited a transient, but non-significant increase following exposure to β-NF, and generally tracked the minimal changes observed in GST–CDNB activities. Expression of the mRNA encoding glutamate-cysteine ligase catalytic subunit (GCLC), the rate-limiting enzyme in glutathione (GSH) biosynthesis, was increased 1.7-fold by β-NF. Changes in GCLC mRNA expression were paralleled by increases in intracellular GSH. In summary, largemouth bass hepatic CYP1A-dependent and GSH biosynthetic pathways, and to a lesser extent GST, are responsive to exposure to β-NF.     

Non-hydrostatic pressure in σ-coordinate ocean models

Numerical ocean modelling is computationally very demanding. Traditionally, the hydrostatic approximation has been applied to reduce the computational burden. This approximation is valid in large scale studies with coarse grid resolution. With faster computers and gradually smaller grid sizes, we may expect that more studies will be performed with non-hydrostatic ocean models. In recent papers several methods for including non-hydrostatic pressure in σ-coordinate models have been suggested. In this paper the sensitivity of the non-hydrostatic pressure field, the velocity fields, and the density fields to changes in the method for computing non-hydrostatic pressure in σ-coordinate ocean models is addressed.The first test case used involves the propagation and breaking of an internal wave at an incline in a tank. The other test case concerns tidally driven flow over a sill in a stratified fjord. The results from our numerical exercises suggest that the velocity and density fields are very robust to the model choices investigated here. The differences between the model results are of the same order as the uncertainty due to the internal pressure gradient error, and they are smaller than an estimate of the uncertainty due to subgrid scale closure.     

Variability of organic δC and C/N in the Mersey Estuary, U.K. and its implications for sea-level reconstruction studies

Microfossil analysis (e.g. diatoms, foraminifera and pollen) represents the cornerstone of Holocene relative sea-level (RSL) reconstruction because their distribution in the contemporary inter-tidal zone is principally controlled by ground elevation within the tidal frame. A combination of poor microfossil preservation and a limited range in the sediment record may severely restrict the accuracy of resulting RSL reconstructions. Organic δ¹³C and C/N analysis of inter-tidal sediments have shown some potential as coastal palaeoenvironmental proxies. Here we assess their viability for reconstructing RSL change by examining patterns of organic δ¹³C and C/N values in a modern estuarine environment. δ¹³C and C/N analysis of bulk organic inter-tidal sediments and vegetation, as well as suspended and bedload organic sediments of the Mersey Estuary, U.K., demonstrate that the two main sources of organic carbon to surface saltmarsh sediments (terrestrial vegetation and tidal-derived particulate organic matter) have distinctive δ¹³C and C/N signatures. The resulting relationship between ground elevation within the tidal frame and surface sediment δ¹³C and C/N is unaffected by decompositional changes. The potential of this technique for RSL reconstruction is demonstrated by the analysis of part of an early Holocene sediment core from the Mersey Estuary. Organic δ¹³C and C/N analysis is less time consuming than microfossil analysis and is likely to provide continuous records of RSL change.     

Effects of 17β-estradiol exposure in the mussel Mytilus galloprovincialis

Mussels Mytilus galloprovincialis were exposed to different concentrations of estradiol (20, 200, and 2000 ng/l) in a semi-static regime (1-day dosing intervals) for up to 7 days in an attempt to see how mussels dealt with exogenous estrogenic compounds. Sex hormone levels were determined in whole tissue. Free-estradiol was only significantly elevated at the highest exposure dose (up to 10-fold). Most of the estradiol was in the tissues as fatty acid esters (>78%), which sharply increased in a dose-dependent manner (from 4 ng/g in controls to 258 ng/g at the high exposure group). In contrast, neither free nor esterified testosterone levels showed significant differences between control and exposure groups. The results suggest the existence of mechanisms that allow mussels to maintain their hormonal status, and the important role that fatty acid esterification may play within those mechanisms. Synthesis and conjugation rates of estradiol were further investigated by measuring the activity of P450 aromatase, and palmitoyl-CoA:estradiol acyltransferase, in digestive gland microsomal fractions. Overall, the study contributes to the better knowledge of molluscan endocrinology, and defines new mechanisms of regulation of free steroid-levels in mussels.     

Reducing horizontal diffusion errors in σ-coordinate coastal ocean models with a second-order Lagrangian-interpolation finite-difference scheme

When a steep bottom slope exists, it is well known that conventional methods for calculating horizontal diffusion in sigma-coordinate coastal ocean models causes spurious transport (e.g. salinity, temperature, and sediments) and currents. In this study, a second-order accurate finite-difference algorithm and program have been developed to reduce the spurious numerical diffusion errors. In the proposed algorithm, the finite differencing is performed in the x–z coordinate system to approximate the horizontal gradient. Each variable in the finite differential formation is calculated in the sigma-coordinate grid cells using a second-order Lagrangian interpolation polynomial. In conjunction with a stepwise bottom boundary condition, numerical experiments show that the proposed finite-difference scheme considerably reduces numerical errors compared to conventional approaches when dealing with horizontal diffusion over steep topography, which often occurs in coastal oceans and navigation channels.     

Fitting a predator–prey model to zooplankton time-series data in the Gironde estuary (France): Ecological significance of the parameters

The relationships between the seasonal fluctuations of the copepod Eurytemora affinis and the mysid Neomysis integer were studied from observed data and experimental results, using a predator–prey model in the oligo-mesohaline area of the Gironde estuary. Mean seasonal fluctuations of abundances were derived from long term data series collected from 1978 to 2003 for both species. In situ predator–prey experiments over a seasonal cycle were used to estimate the seasonal variation of the consumption rate of N. integer on E. affinis and to verify the order of magnitude of the biological parameters given by the model.Predator–prey experiments revealed a high seasonal variation in maximum consumption rates with a mean of 56 ± 9 ind. pred⁻¹ d⁻¹. Maximum consumption rates were always higher for adults than for juveniles of Neomysis integer. Recorded selectivities were higher on nauplii than on copepodids + adults of Eurytemora affinis, both for the juveniles and the adults of N. integer. Neomysis integer mainly fed on meroplanktonic larvae, when they were available in higher abundances, than E. affinis in their environment.Spring increases of abundance for Eurytemora affinis copepodids + adults seemed to be mainly controlled by temperature whereas its decreasing abundance in summer was more related to Neomysis integer predation, suggesting that summer fluctuations of E. affinis abundance are probably controlled by mysid predation at summer times. Using a Lotka–Volterra predator–prey model, the seasonal peak of abundance of the mysid N. integer was well reproduced considering a predation on copepodids + adults of E. affinis, and suggested a dependence between mysid and copepod seasonal variations. However, the seasonal peak amplitude could not be explained solely by a predation on copepodids + adults or on nauplii of the copepod. Thus, N. integer is probably dependent on the seasonal fluctuations of the copepod's abundance, complementing its diet with macrophytal detritus during periods of scarce food.     

合浦珠母贝转录因子PF-CREB3L2基因的克隆和鉴定

克隆得到了合浦珠母贝(Pinctada fucata)PF-CREB3L2蛋白的c DNA序列,其c DNA全长1 983 bp,其中开放阅读框长度为1 728 bp,编码的蛋白含有575个氨基酸残基。组织表达分布实验发现,其在合浦珠母贝内脏囊中表达量最高,在外套膜和鳃中也有大量表达,推测其广泛参与合浦珠母贝的贝壳形成等生理活动。贝壳损伤修复实验中发现,在合浦珠母贝贝壳受到损伤后,PF-CREB3L2和基质蛋白的表达量会迅速上升,且PF-CREB3L2的峰值出现更早,推测其通过影响基质蛋白转录,参与合浦珠母贝生物矿化的调控过程。PF-CREB3L2与合浦珠母贝基质蛋白表达相关性的分析发现,PF-CREB3L2与Prisilkin39、KRMP的表达量呈现显著的正相关,说明其可能特异性地调控某些基质蛋白的转录。     

A spatial ecosystem and populations dynamics model (SEAPODYM) – Modeling of tuna and tuna-like populations

An enhanced version of the spatial ecosystem and population dynamics model SEAPODYM is presented to describe spatial dynamics of tuna and tuna-like species in the Pacific Ocean at monthly resolution over 1° grid-boxes. The simulations are driven by a bio-physical environment predicted from a coupled ocean physical–biogeochemical model. This new version of SEAPODYM includes expanded definitions of habitat indices, movements, and natural mortality based on empirical evidences. A thermal habitat of tuna species is derived from an individual heat budget model. The feeding habitat is computed according to the accessibility of tuna predator cohorts to different vertically migrating and non-migrating micronekton (mid-trophic) functional groups. The spawning habitat is based on temperature and the coincidence of spawning fish with presence or absence of predators and food for larvae. The successful larval recruitment is linked to spawning stock biomass. Larvae drift with currents, while immature and adult tuna can move of their own volition, in addition to being advected by currents. A food requirement index is computed to adjust locally the natural mortality of cohorts based on food demand and accessibility to available forage components. Together these mechanisms induce bottom-up and top-down effects, and intra- (i.e. between cohorts) and inter-species interactions. The model is now fully operational for running multi-species, multi-fisheries simulations, and the structure of the model allows a validation from multiple data sources. An application with two tuna species showing different biological characteristics, skipjack (Katsuwonus pelamis) and bigeye (Thunnus obesus), is presented to illustrate the capacity of the model to capture many important features of spatial dynamics of these two different tuna species in the Pacific Ocean. The actual validation is presented in a companion paper describing the approach to have a rigorous mathematical parameter optimization [Senina, I., Sibert, J., Lehodey, P., 2008. Parameter estimation for basin-scale ecosystem-linked population models of large pelagic predators: application to skipjack tuna. Progress in Oceanography]. Once this evaluation and parameterization is complete, it may be possible to use the model for management of tuna stocks in the context of climate and ecosystem variability, and to investigate potential changes due to anthropogenic activities including global warming and fisheries pressures and management scenarios.     

Humic substances in estuarine soils colonized by Spartina maritima

This study characterizes humic substances (HS) from two soils colonized by Spartina maritima at different physiographical positions in estuarine environments on the north-western coast of the Iberian Peninsula: the Villaviciosa site, a stand close to the main tidal channel, and the Ortigueira site, located in the low salt marsh. Humic and fulvic acids were extracted from the soils and characterized qualitatively by the following spectroscopic techniques: Fourier transform infrared spectroscopy, fluorescence spectroscopy and solid-state ¹³C nuclear magnetic resonance.The characterized HS showed a predominance of low humified compounds with a high proportion of aliphatic components and a low degree of aromaticity. The HS composition differed substantially between sites. In the Villaviciosa soil, the large amount of nonpolar aliphatic components and the very low degree of aromaticity may indicate a significant contribution of marine organic matter and/or microbial material to the HS. However, in the HS from the Ortigueira soil, the higher proportion of polysaccharides together with the presence of lignin-derived compounds may indicate greater inputs of vascular plant material. The δ¹³C isotopic composition of the bulk soils highlights the large input of Spartina maritima debris to the Ortigueira site, whereas in the Villaviciosa site, organic contributions from this C4 vascular plant were not so evident.The results indicate that in these soils colonized by Spartina maritima, physiographical position has an important effect on the composition of soil HS and, therefore, must be considered in the study of organic matter characteristics in such estuarine environments.     

凡纳滨对虾水孔蛋白-4的cDNA克隆及盐度胁迫对其肝胰腺mRNA表达水平的影响

为了探索水孔蛋白(Aquaporin,AQP)在凡纳滨对虾(Litopenaeus vannamei)渗透压调节过程中作用,本研究通过RACE方法获得克隆的凡纳滨对虾AQP(命名为LvAQP4)的c DNA全长序列,并分析了盐度胁迫对其肝胰腺m RNA表达的影响。结果发现:LvAQP4 c DNA序列全长为1 048 bp,其中包括75 bp的5￠UTR,187 bp的3￠UTR和786 bp的ORF。根据ORF序列推导出LvAQP4编码261个氨基酸,预测其分子质量为27.85 k Da,等电点为8.11。推导的氨基酸序列与其他甲壳物种的AQP相似度为48.8%到97.3%。进化分析显示LvAQP4属于AQP1-like亚族、AQP4类。定量PCR(q PCR)检测到LvAQP4在不同组织中均有表达,其中鳃的表达量最高,肝胰腺、肌肉、脑和眼柄中也较高,而血淋巴、肠、胃和胸神经节中表达量则较低。在高盐(盐度40)刺激下,凡纳滨对虾的肝胰腺LvAQP4 m RNA表达量会随着时间推移而上升,到6 h达到最高,而后逐步下降。而在低盐(盐度4)刺激下,凡纳滨对虾的肝胰腺LvAQP4 m RNA表达量并无明显变化。在原代分离和培养的肝胰腺细胞中,培养液中加入额外的Na Cl会剂量依赖地提高LvAQP4 m RNA表达水平。同样,通过在培养液中额外加入蔗糖提高培养液渗透压,也会剂量依赖地提高LvAQP4 m RNA表达水平,但作用不如Na Cl明显。这些结果表明盐度与肝胰腺LvAQP4的表达量有关,LvAQP4对凡纳滨对虾的渗透压调节具有非常重要的作用。     

大黄鱼EBI3基因的克隆与表达分析

通过克隆大黄鱼(Larimichthys crocea)的EBI3(Epstein-Barr virus-induced gene 3)基因并对其进行了序列分析.大黄鱼EBI3(Lyc EBI3)基因开放阅读框长747bp,编码248个氨基酸,存在1个信号肽序列和2个FN3结构域(37~130,145~230).多序列比对发现Lyc EBI3分子与其他已知EBI3氨基酸水平一致性为27.68%~57.53%.Real-time PCR结果表明,Lyc EBI3基因在脾脏和血液中表达量最高,且溶藻弧菌(Vibrio alginolyticus)刺激后,大黄鱼头肾和脾脏中Lyc EBI3基因的转录水平会显著升高,说明Lyc EBI3基因可能参与了抑制由细菌引起的炎症反应.     

Short-term variability of fCO2 in seawater and air–sea CO2 fluxes in a coastal upwelling system (Ría de Vigo, NW Spain)

Coastal upwelling systems are regions with highly variable physical processes and very high rates of primary production and very little is known about the effect of these factors on the short-term variations of CO₂ fugacity in seawater (fCO₂^w). This paper presents the effect of short-term variability (<1 week) of upwelling–downwelling events on CO₂ fugacity in seawater (fCO₂^w), oxygen, temperature and salinity fields in the Ría de Vigo (a coastal upwelling ecosystem). The magnitude of fCO₂^w values is physically and biologically modulated and ranges from 285 μatm in July to 615 μatm in October. There is a sharp gradient in fCO₂^w between the inner and the outer zone of the Ría during almost all the sampling dates, with a landward increase in fCO₂^w.CO₂ fluxes calculated from local wind speed and air–sea fCO₂ differences indicate that the inner zone is a sink for atmospheric CO₂ in December only (−0.30 mmol m⁻² day⁻¹). The middle zone absorbs CO₂ in December and July (−0.05 and −0.27 mmol·m⁻² day⁻¹, respectively). The oceanic zone only emits CO₂ in October (0.36 mmol·m⁻² day⁻¹) and absorbs at the highest rate in December (−1.53 mmol·m⁻² day⁻¹).     

Comparison of the nonlocal transport characteristics of a series of one-dimensional oceanic boundary layer models

Seven one-dimensional oceanic boundary layer models are investigated to assess the possible nonlocal transport characteristics of mass and heat in the upper ocean. The dynamical models have been chosen from the diffusion and bulk types currently in use plus two modifications of the transilient type that have been used extensively for atmospheric work by Stull. The models are forced using wind speed and insolation conditions recorded during a 9-day oceanographic cruise near Bermuda in March 1993 during the decline of the spring bloom. The attenuation of sunlight in the upper ocean is calculated using a full spectral model for downwelling irradiance. The vertical heat transport characteristics are reported and compared. A series of spectral diagnostic tests (Green's function analysis, process spectra, and overall mixing lengths) reveal significant differences in the vertical transport characteristics of the models that are not observed in commonly used diagnostics such as sea surface temperature or mixed layer depth. Age spectra (or modal time since last surface contact) are calculated from Green's functions and reveal how a water mass can be cut off from the surface within a short time period. The large differences in the vertical mixing characteristics of the upper ocean boundary layer models have potential implications on the vertical distributions of short-lived chemical tracers and phytoplankton.     

The DNA de-methylating agent 5-azacytidine does not restore CYP1A induction in PCB resistant Newark Bay killifish (Fundulus heteroclitus)

Newark Bay (NB) killifish (Fundulus heteroclitus) have been chronically exposed to environmental contaminants that activate the aryl hydrocarbon receptor (AHR) and are tolerant to toxic effects and CYP1A induction provoked by AHR ligands. Resistance to CYP1A induction could be due to an epigenetic mechanism such as DNA methylation. We measured in-ovo CYP1A catalytic activity (ethoxyresorufin-O-deethylase, EROD) in NB and reference site killifish embryos aqueously exposed to various concentrations of the de-methylating agent 5-azacytidine, 5-AC (5, 50 and 500 μ(micro)M) with or without 0.2 μ(micro)g/l of the CYP1A inducer 3,3^′,4,4^′,5 pentachlorobiphenyl (IUPAC PCB126). Neither PCB126 alone, nor PCB126 plus 5-AC, induced EROD above levels in vehicle treated Newark Bay fish. In reference site fish, the same PCB126 dose provoked a 7.4-fold EROD induction relative to controls. We conclude that Newark Bay killifish are resistant to CYP1A induction by co-planar PCBs during early embryological development and our data suggests that DNA methylation does not play a critical role in resistance to CYP1A induction in this model.     

Plasma steroid levels in female flounder (Platichthys flesus) after chronic dietary exposure to single polycyclic aromatic hydrocarbons

The chronic effects of polycyclic aromatic hydrocarbons (PAHs) on ovary development, total hepatic lipids and plasma sex- and corticosteroid levels in female flounder (Platichthys flesus) were examined. Sexually mature feral female flounder were exposed via the diet to phenanthrene (0.5, 2.5 or 12.5 nmol/g food) or chrysene (0.4 nmol/g food) for 12 weeks, during the previtellogenic phase of the annual reproductive cycle. PAH exposure did not directly affect germ cell development since no structural and/or developmental differences were observed between control and exposed fish. On the contrary, all treatments resulted in altered plasma steroid levels. The most pronounced effect was the significant decrease in plasma 17β-estradiol to 19±11%, 27±7%, 63±20% and 61±12% in relation to control fish, respectively, in flounders exposed to 12.5, 2.5 or 0.5 nmol phenanthrene/g food and 0.4 nmol chrysene/g food. Impaired ovarian growth was not observed, most likely because experiments were ended before the period of vitellogenesis, even though a non-significant general decline in total hepatic lipids could be observed. Moreover, all exposed flounders, except fish fed with the highest amount of phenanthrene, showed a negative correlation between plasma 17β-estradiol and 17α-hydroxyprogesterone levels (r=−0.46). One possible explanation is that PAH action may be mediated by a specific inhibition of steroidogenic enzymes. These findings provide evidence that selected PAHs are antiestrogenic xenobiotics with the capability to impair female teleost reproductive function.     

Size increment of jumbo flying squid Dosidicus gigas mature females in Peruvian waters, 1989–2004

Changes in population structure of the jumbo flying squid Dosidicus gigas in Peruvian waters were studied based on size-at-maturity from 1989 to 2004. From 1989 to 1999, mature squid belonging to the medium-sized group prevailed, but from 2001 on, mature squids were larger. This change is not related to the changes in sea surface temperature and we hypothesized that it was caused by the population increase of mesopelagic fishes as prey.