Assessing ecological impacts of shrimp and sewage effluent: Biological indicators with standard water quality analyses

Despite evidence linking shrimp farming to several cases of environmental degradation, there remains a lack of ecologically meaningful information about the impacts of effluent on receiving waters. The aim of this study was to determine the biological impact of shrimp farm effluent, and to compare and distinguish its impacts from treated sewage effluent. Analyses included standard water quality/sediment parameters, as well as biological indicators including tissue nitrogen (N) content, stable isotope ratio of nitrogen (delta N-15) and amino acid composition of inhabitant seagrasses, mangroves and macroalgae. The study area consisted of two tidal creeks, one receiving effluent from a sewage treatment plant and the other from an intensive shrimp farm. The creeks discharged into the western side of Moreton Bay, a sub-tropical coastal embayment on the east coast of Australia. Characterization of water quality revealed significant differences between the creeks, and with unimpacted eastern Moreton Bay. The sewage creek had higher concentrations of dissolved nutrients (predominantly NO3-/NO2- and PO43-, compared to NH4+ in the shrimp creek). In contrast, the shrimp creek was more turbid and had higher phytoplankton productivity. Beyond 750 m from the creek mouths, water quality parameters were indistinguishable from eastern Moreton Bay values. Biological indicators detected significant impacts up to 4 km beyond the creek mouths (reference site). Elevated plant delta N-15 values ranged from 10.4-19.6 parts per thousand at the site of sewage discharge to 2.9-4.5 parts per thousand at the reference site. The free amino acid concentration and composition of seagrass and macroalgae was used to distinguish between the uptake of sewage and shrimp derived N. Proline (seagrass) and serine (macroalgae) were high in sewage impacted plants and glutamine (seagrass) and alanine (macroalgae) were high in plants impacted by shrimp effluent. The delta N-15 isotopic signatures and free amino acid composition of inhabitant flora indicated that sewage N extended further from the creek mouths than shrimp N. The combination of physical/chemical and biological indicators used in this study was effective in distinguishing the composition and subsequent impacts of aquaculture and sewage effluent on the receiving waters. (C) 2001 Academic Press.

Quantifying stresses and support requirements in the undercut and production level drifts of block and panel caving mines

A numerical modelling strategy has been developed in order to quantify the magnitude of induced stresses at the boundaries of production level and undercut level drifts for various in situ stress environments and undercut scenarios. The results of the stress modelling were in line with qualitative experiential guidelines and a limited number of induced stress measurements documented from caving sites. A number of stress charts were developed which quantify the maximum boundary stresses in drift roofs for varying in situ stress regimes, depths and undercut scenarios. This enabled many of the experiential guidelines to be quantified and bounded. A limited number of case histories of support and support performance in cave mine drifts were compared to support recommendations using the NGI classification system, The stress charts were used to estimate the Stress Reduction Factor for this system. The back-analyses suggested that the NGI classification system might be able to give preliminary estimates of support requirements in caving mines with modifications relating to rock bolt length and the support of production level intersections. (C) 2002 Elsevier Science Ltd. All rights reserved.

Combining the analyses of introgressive hybridisation and linkage mapping to investigate the genetic architecture of population divergence in the lake whitefish (Coregonus clupeaformis, Mitchill)

Adaptation and reproductive isolation, the engines of biological diversity, are still elusive when discussing the genetic bases of speciation. Namely, the number of genes and magnitude of selection acting positively or negatively on genomic traits implicated in speciation is contentious. Here, we describe the first steps of an ongoing research program aimed at understanding the genetic bases of population divergence and reproductive isolation in the lake whitefish (Coregonus clupeaformis). A preliminary linkage map originating from a hybrid cross between dwarf and normal ecotypes is presented, whereby some of the segregating AFLP markers were found to be conserved among natural populations. Maximum-likelihood was used to estimate hybrid indices from non-diagnostic markers at 998 AFLP loci. This allowed identification of the most likely candidate loci that have been under the influence of selection during the natural hybridisation of whitefish originating from different glacial races. As some of these loci could be identified on the linkage map, the possibility that selection of traits in natural populations may eventually be correlated to specific chromosomal regions was demonstrated. The future prospects and potential of these approaches to elucidate the genetic bases of adaptation and reproductive isolation among sympatric ecotypes of lake whitefish is discussed.

Numerical investigations of flow and energy fields near a thermoacoustic couple

The flow field and the energy transport near thermoacoustic couples are simulated using a 2D full Navier-Stokes solver. The thermoacoustic couple plate is maintained at a constant temperature; plate lengths, which are short and long compared with the particle displacement lengths of the acoustic standing waves, are tested. Also investigated are the effects of plate spacing and the amplitude of the standing wave. Results are examined in the form of energy vectors, particle paths, and overall entropy generation rates. These show that a net heat-pumping effect appears only near the edges of thermoacoustic couple plates, within about a particle displacement distance from the ends. A heat-pumping effect can be seen even on the shortest plates tested when the plate spacing exceeds the thermal penetration depth. It is observed that energy dissipation near the plate increases quadratically as the plate spacing is reduced. The results also indicate that there may be a larger scale vortical motion outside the plates which disappears as the plate spacing is reduced. (C) 2002 Acoustical Society of America.

Numerical modelling of contaminant transport in coastal aquifers

This paper employs a two-dimensional variable density flow and transport model to investigate the transport of a dense contaminant plume in an unconfined coastal aquifer. Experimental results are also presented to show the contaminant plume in a freshwater-seawater flow system. Both the numerical and experimental results suggest that the neglect of the seawater interface does not noticeably affect the horizontal migration rate of the plume before it reaches the interface. However, the contaminant will travel further seaward and part of the solute mass will exit under the sea if the higher seawater density is not included. If the seawater density is included, the contaminant will travel upwards towards the beach along the freshwater-saltwater interface as shown experimentally. Neglect of seawater density, therefore, will result in an underestimate of solute mass rate exiting around the coastline. (C) 2002 IMACS. Published by Elsevier Science B.V. All rights reserved.

Testing the applicability of molecular genetic markers to population analyses of scleratinian corals

The abundance of coral reefs worldwide is in decline, and despite the ecological importance of reefs, only a limited number of DNA markers have been identified for scleractinian coral genetic studies. This paper addresses the search for new coral molecular markers and investigates the applicability of the cytochrome c oxidase subunit I (COI), the internal transcribed spacer region 1 (ITS1), and the pocilloporin gene to the question of intraspecific variation in the scleractinian coral Pocillopora verrucosa along the southeast African coastline. The COI fragment was 710 bp long and was identical for P. verrucosa (n = 10) and P. damicornis (n = 3). Only two different ITS1 sequences were found (differing by 13 bp insertion), but more importantly, 24% of the sequences were heterogenous indicating that different multiple copies of the sequence exist. Pocilloporin is an intronless gene that was absolutely conserved throughout all P. verrucosa populations (n = 50). Thus, the three DNA regions studied appear unsuitable for the population genetic analyses of P. verrucosa.

Finite difference time domain (FDTD) method for modeling the effect of switched gradients on the human body in MRI

Numerical modeling of the eddy currents induced in the human body by the pulsed field gradients in MRI presents a difficult computational problem. It requires an efficient and accurate computational method for high spatial resolution analyses with a relatively low input frequency. In this article, a new technique is described which allows the finite difference time domain (FDTD) method to be efficiently applied over a very large frequency range, including low frequencies. This is not the case in conventional FDTD-based methods. A method of implementing streamline gradients in FDTD is presented, as well as comparative analyses which show that the correct source injection in the FDTD simulation plays a crucial rule in obtaining accurate solutions. In particular, making use of the derivative of the input source waveform is shown to provide distinct benefits in accuracy over direct source injection. In the method, no alterations to the properties of either the source or the transmission media are required. The method is essentially frequency independent and the source injection method has been verified against examples with analytical solutions. Results are presented showing the spatial distribution of gradient-induced electric fields and eddy currents in a complete body model.

Isolation and characterization of nine microsatellite loci from the Hawaiian grouper Epinephelus quernus (Serranidae) for population genetic analyses

The availability of variable genetic markers for groupers (Serranidae) has generally been limited to mitochondrial DNA. For studies of population genetic structure, more loci are usually required; particularly useful are those that are nuclear in origin such as microsatellites. Here, we isolated and characterized 9 microsatellite loci from the endemic Hawaiian grouper Epinephelus quernus using a biotin-labeled oligonucleotide-streptavidin-coated magnetic bead approach. Of the 20 repeat-containing fragments isolated, 15 had sufficient flanking region in which to design primers. Among these, 9 produced consistent polymerase chain reaction product, and 6 were highly variable. These 6 loci were all composed of dinucleotide repeats, with the number of alleles ranging from 6 to 18, and heterozygosities from 33.3% to 91.7%. The high levels of variability observed should make these markers useful for population genetic studies of E. quernus, and potentially other epinephelines.

Molecular and functional analyses of Kunjin virus infectious cDNA clones demonstrate the essential roles for NS2A in virus assembly and for a nonconservative residue in NS3 in RNA replication

A number of full-length cDNA clones of Kunjin virus (KUN) were previously prepared; it was shown that two of them, pAKUN and FLSDX, differed in specific infectivities of corresponding in vitro transcribed RNAs by similar to100,000-fold (A. A. Khromykh et al., J. Virol. 72:7270-7279, 1998). In this study, we analyzed a possible genetic determinant(s) of the observed differences in infectivity initially by sequencing the entire cDNAs of both clones and comparing them with the published sequence of the parental KUN strain MRM61C. We found six common amino acid residues in both cDNA clones that were different from those in the published MRM61C sequence but were similar to those in the published sequences of other flaviviruses from the same subgroup. pAKUN clone had four additional codon changes, i.e., Ile59 to Asn and Arg175 to Lys in NS2A and Tyr518 to His and Ser557 to Pro in NS3. Three of these substitutions except the previously shown marker mutation, Arg175 to Lys in NS2A, reverted to the wild-type sequence in the virus eventually recovered from pAKUN RNA-transfected BHK cells, demonstrating the functional importance of these residues in viral replication and/or viral assembly. Exchange of corresponding DNA fragments between pAKUN and FLSDX clones and site-directed mutagenesis revealed that the Tyr518-to-His mutation in NS3 was responsible for an similar to5-fold decrease in specific infectivity of transcribed RNA, while the Ile59-to-Asn mutation in NS2A completely blocked virus production. Correction of the Asn59 in pAKUN NS2A to the wild-type lie residue resulted in complete restoration of RNA infectivity. Replication of KUN replicon RNA with an Ile59-to-Asn substitution in NS2A and with a Ser557-to-Pro substitution in NS3 was not affected, while the Tyr518-to-His substitution in NS3 led to severe inhibition of RNA replication. The impaired function of the mutated NS2A in production of infectious virus was complemented in trans by the helper wild-type NS2A produced from the KUN replicon RNA. However, replicon RNA with mutated NS2A could not be packaged in trans by the KUN structural proteins. The data demonstrated essential roles for the KUN nonstructural protein NS2A in virus assembly and for NS3 in RNA replication and identified specific single-amino-acid residues involved in these functions.

Phylogenetic relationships of Hepatozoon (Haemogregarina) boigae Hepatozoon sp. Haemogregarina clelandi and Haemoproteus chelodina from Australian reptiles to other Apicomplexa based on cladistic analyses of ultrastructural and life-cycle characters

The phylogeny of representative haemozoan species of the phylum Apicomplexa was reconstructed by cladistic analyses of ultrastructural and life-cycle characteristics. The analysis incorporated 4 apicomplexans previously not included in phylogenetic reconstructions: Haemogregarina clelandi from the Brisbane River tortoise (Emydura signata), Hepatozoon sp. from the slaty grey snake (Stegonotus cucullatus), Hepatozoon (Haemogregarina) boigae from the brown tree snake (Boiga irregularis), and Haemoproteus chelodina from the saw-shelled tortoise (Elseya latisternum). There was no apparent correlation between parasite phylogeny and that of their vertebrate hosts, but there appeared to be some relationship between parasites and their intermediate hosts, suggestive of parasite/vector co-evolution.

Numerical investigation of turbulent flow around a rotating stepped cylinder for corrosion study

Direct numerical simulation has been carried out for turbulent flow set up by a rotating cylinder with two backward-facing steps axisymmetrically mounted in the circumferential direction. This flow geometry creates a qualitatively similar flow pattern as observed near, a sudden, pipe expansion or a plane backward-facing step, characterized by flow separation and reattachment. A region of intense turbulence intensity and high wall-shear-stress fluctuations is formed in,the recirculating I region downstream of the step, where high mass-transfer capacity was also experimentally observed. Since, corrosion is frequently mass-transfer., controlled, our findings, put forward this apparatus as useful tool for future corrosion research.

Numerical study of hydrogenic effective mass theory for an impurity P donor in Si in the presence of an electric field and interfaces

In this paper we examine the effects of varying several experimental parameters in the Kane quantum computer architecture: A-gate voltage, the qubit depth below the silicon oxide barrier, and the back gate depth to explore how these variables affect the electron density of the donor electron. In particular, we calculate the resonance frequency of the donor nuclei as a function of these parameters. To do this we calculated the donor electron wave function variationally using an effective-mass Hamiltonian approach, using a basis of deformed hydrogenic orbitals. This approach was then extended to include the electric-field Hamiltonian and the silicon host geometry. We found that the phosphorous donor electron wave function was very sensitive to all the experimental variables studied in our work, and thus to optimize the operation of these devices it is necessary to control all parameters varied in this paper.

Numerical simulations of wind and temperature structure within an Alpine lake basin, Lake Tekapo, New Zealand

High-resolution numerical model simulations have been used to study the local and mesoscale thermal circulations in an Alpine lake basin. The lake (87 km(2)) is situated in the Southern Alps, New Zealand and is located in a glacially excavated rock basin surrounded by mountain ranges that reach 3000 m in height. The mesoscale model used (RAMS) is a three-dimensional non-hydrostatic model with a level 2.5 turbulence closure scheme. The model demonstrates that thermal forcing at local (within the basin) and regional (coast-to-basin inflow) scales drive the observed boundary-layer airflow in the lake basin during clear anticyclonic summertime conditions. The results show that the lake can modify (perturb) both the local and regional wind systems. Following sunrise, local thermal circulations dominate, including a lake breeze component that becomes embedded within the background valley wind system. This results in a more divergent flow in the basin extending across the lake shoreline. However, a closed lake breeze circulation is neither observed nor modelled. Modelling results indicate that in the latter part of the day when the mesoscale (coast-to-basin) inflow occurs, the relatively cold pool of lake air in the basin can cause the intrusion to decouple from the surface. Measured data provide qualitative and quantitative support for the model results.