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.     

Numerical study of the motions and drift force of a floating OWC device

The motion and the drift force of a floating OWC (oscillating water column) wave energy device in regular waves are studied taking account of the oscillating surface-pressure due to the pressure drop across the duct of the air chamber. The potential problem inside the chamber is formulated by making use of the Green integral equation associated with the Rankine-type Green function while the outer problem with the Kelvin-type Green function. The added mass, wave damping and excitation coefficients as well as the motion and drift force of the OWC device are calculated for various values of parameter related to the pressure drop.     

A case study of a modified gravity type cage and mooring system using numerical and physical models

A modified gravity-type cage, developed by SADCO Shelf Ltd., was examined using numerical and physical models to determine if the cage and mooring system is suitable for an exposed site south of the Isles of Shoals, NH. The 3000-m/sup 3/ SADCO Shelf Submersible Fish Cage has angled stays between the upper framework and the ballasted bottom rim (in addition to net) to resist the horizontal shear deformation. The mooring system consists of three legs-each made up of a taut vertical chain and an angled rope, both leading to deadweight anchors. Normalized response amplitudes (response amplitude operators) were found for motion response in heave, surge and pitch, and load response in the anchor and bridle lines, in regular (single frequency) waves. In addition, a stochastic approach was taken to determine the motion and load transfer functions in random waves using a spectrum representative of seas at the selected site. In general, the system motion had a highly damped response, with no resonant peaks within the wave excitation range of 0.05 to 0.45 Hz. The anchor line force response was at all frequencies below 5 kN per meter of wave amplitude. The physical model tests showed consistently more conservative (larger) results compared to those for the numerical model.     

Using ocean ambient noise for array self-localization and self-synchronization

Estimates of the travel times between the elements of a bottom hydrophone array can be extracted from the time-averaged ambient noise cross-correlation function (NCF). This is confirmed using 11-min-long data blocks of ambient noise recordings that were collected in May 1995 near the southern California coast at an average depth of 21 m in the 150-700 Hz frequency range. Coherent horizontal wavefronts emerging from the time derivative of the NCF are obtained across the array's aperture and are related to the direct arrival time of the time-domain Green's function (TDGF). These coherent wavefronts are used for array element self-localization (AESL) and array element self-synchronization (AESS). The estimated array element locations are used to beamform on a towed source.     

Estuary/ocean exchange and tidal mixing in a Gulf of Maine Estuary: A Lagrangian modeling study

A Lagrangian particle method embedded within a 2-D finite element code, is used to study the transport and ocean–estuary exchange processes in the well-mixed Great Bay Estuarine System in New Hampshire, USA. The 2-D finite element model, driven by residual, semi-diurnal and diurnal tidal constituents, includes the effects of wetting and drying of estuarine mud flats through the use of a porous medium transport module. The particle method includes tidal advection, plus a random walk model in the horizontal that simulates sub-grid scale turbulent transport processes. Our approach involves instantaneous, massive [O(500,000)] particle releases that enable the quantification of ocean–estuary and inter-bay exchanges in a Markovian framework. The effects of the release time, spring–neap cycle, riverine discharge and diffusion strength on the intra-estuary and estuary–ocean exchange are also investigated.The results show a rather dynamic interaction between the ocean and the estuary with a fraction of the exiting particles being caught up in the Gulf of Maine Coastal Current and swept away. Three somewhat different estimates of estuarine residence time are calculated to provide complementary views of estuary flushing. Maps of residence time versus release location uncover a strong spatial dependency of residence time within the estuary that has very important ramifications for local water quality. Simulations with and without the turbulent random walk show that the combined effect of advective shear and turbulent diffusion is very effective at spreading particles throughout the estuary relatively quickly, even at low (1 m²/s) diffusivity. The results presented here show that a first-order Markov Chain approach has applicability and a high potential for improving our understanding of the mixing processes in estuaries.     

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.     

Direct determination of organic carbon in modern reef sediments and calcareous organisms after dissolution of carbonate

An improved method for the direct determination of organic carbon in calcareous marine sediments, organisms and particulate matter is described. Samples are dissolved in phosphoric acid to remove carbonates, purged with oxygen to remove CO₂, and the resulting acidic solution is analysed for total (dissolved and particulate) organic carbon. The method is rapid, involves minimal sample manipulation, and is both accurate (better than ± 2%) and precise (better than ± 0.2 mg organic carbon/g sediment). The method is especially suitable for modern carbonate sediments which have low levels of predominantly acid-soluble organic carbon.