Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution.

Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. Here, we sequenced and annotated the genome of Pocillopora damicornis, one of the most abundant and widespread corals in the world. We compared this genome, based on protein-coding gene orthology, with other publicly available coral genomes (Cnidaria, Anthozoa, Scleractinia), as well as genomes from other anthozoan groups (Actiniaria, Corallimorpharia), and two basal metazoan outgroup phlya (Porifera, Ctenophora). We found that 46.6% of P. damicornis genes had orthologs in all other scleractinians, defining a coral 'core' genome enriched in basic housekeeping functions. Of these core genes, 3.7% were unique to scleractinians and were enriched in immune functionality, suggesting an important role of the immune system in coral evolution. Genes occurring only in P. damicornis were enriched in cellular signaling and stress response pathways, and we found similar immune-related gene family expansions in each coral species, indicating that immune system diversification may be a prominent feature of scleractinian coral evolution at multiple taxonomic levels. Diversification of the immune gene repertoire may underlie scleractinian adaptations to symbiosis, pathogen interactions, and environmental stress.

Dynamic regulation of partner abundance mediates response of reef coral symbioses to environmental change.

Regulating partner abunclance may allow symmotic organisms to mediate interaction outcomes, facilitating adaptive responses to environmental change. To explore the capacity for-adaptive regulation in an ecologically important endosymbiosis, we studied the population dynamics of symbiotic algae in reef-building corals under different abiotic contexts. We found high natural variability in symbiont abundance in corals across reefs, but this variability converged to different symbiont-specific abundances when colonies were maintained under constant conditions. When conditions changed seasonally, symbiont abundance readjusted to new equilibria. We explain these patterns using an a priori model of symbiotic costs and benefits to the coral host, which shows that the observed changes in symbiont abundance are consistent with the maximization of interaction benefit under different environmental conditions. These results indicate that, while regulating symbiont abundance helps hosts sustain maximum benefit in a dynamic environment, spatiotemporal variation in abiotic factors creates a broad range of symbiont abundances (and interaction outcomes) among corals that may account for observed natural variability in performance (e.g., growth rate) and stress tolerance (e.g., bleaching susceptibility). This cost or benefit framework provides a new perspective on the dynamic regulation of reef coral symbioses and illustrates that the dependence of interaction outcomes on biotic and abiotic contexts may be important in understanding how diverse mutualisms respond to environmental change.

Investigating the causes and consequences of symbiont shuffling in a multi-partner reef coral symbiosis under environmental change.

Dynamic symbioses may critically mediate impacts of climate change on diverse organisms, with repercussions for ecosystem persistence in some cases. On coral reefs, increases in heat-tolerant symbionts after thermal bleaching can reduce coral susceptibility to future stress. However, the relevance of this adaptive response is equivocal owing to conflicting reports of symbiont stability and change. We help reconcile this conflict by showing that change in symbiont community composition (symbiont shuffling) in Orbicella faveolata depends on the disturbance severity and recovery environment. The proportion of heat-tolerant symbionts dramatically increased following severe experimental bleaching, especially in a warmer recovery environment, but tended to decrease if bleaching was less severe. These patterns can be explained by variation in symbiont performance in the changing microenvironments created by differentially bleached host tissues. Furthermore, higher proportions of heat-tolerant symbionts linearly increased bleaching resistance but reduced photochemical efficiency, suggesting that any change in community structure oppositely impacts performance and stress tolerance. Therefore, even minor symbiont shuffling can adaptively benefit corals, although fitness effects of resulting trade-offs are difficult to predict. This work helps elucidate causes and consequences of dynamism in symbiosis, which is critical to predicting responses of multi-partner symbioses such as O. faveolata to environmental change.

Geographic differences in vertical connectivity in the Caribbean coral Montastraea cavernosa despite high levels of horizontal connectivity at shallow depths.

The deep reef refugia hypothesis proposes that deep reefs can act as local recruitment sources for shallow reefs following disturbance. To test this hypothesis, nine polymorphic DNA microsatellite loci were developed and used to assess vertical connectivity in 583 coral colonies of the Caribbean depth-generalist coral Montastraea cavernosa. Samples were collected from three depth zones (≤10, 15-20 and ≥25 m) at sites in Florida (within the Upper Keys, Lower Keys and Dry Tortugas), Bermuda, and the U.S. Virgin Islands. Migration rates were estimated to determine the probability of coral larval migration from shallow to deep and from deep to shallow. Finally, algal symbiont (Symbiodinium spp.) diversity and distribution were assessed in a subset of corals to test whether symbiont depth zonation might indicate limited vertical connectivity. Overall, analyses revealed significant genetic differentiation by depth in Florida, but not in Bermuda or the U.S. Virgin Islands, despite high levels of horizontal connectivity between these geographic locations at shallow depths. Within Florida, greater vertical connectivity was observed in the Dry Tortugas compared to the Lower or Upper Keys. However, at all sites, and regardless of the extent of vertical connectivity, migration occurred asymmetrically, with greater likelihood of migration from shallow to intermediate/deep habitats. Finally, most colonies hosted a single Symbiodinium type (C3), ruling out symbiont depth zonation of the dominant symbiont type as a structuring factor. Together, these findings suggest that the potential for shallow reefs to recover from deep-water refugia in M. cavernosa is location-specific, varying among and within geographic locations likely as a consequence of local hydrology.

The corrosion of depleted uranium in terrestrial and marine environments.

Depleted Uranium alloyed with titanium is used in armour penetrating munitions that have been fired in a number of conflict zones and testing ranges including the UK ranges at Kirkcudbright and Eskmeals. The study presented here evaluates the corrosion of DU alloy cylinders in soil on these two UK ranges and in the adjacent marine environment of the Solway Firth. The estimated mean initial corrosion rates and times for complete corrosion range from 0.13 to 1.9 g cm(-2) y(-1) and 2.5-48 years respectively depending on the particular physical and geochemical environment. The marine environment at the experimental site was very turbulent. This may have caused the scouring of corrosion products and given rise to a different geochemical environment from that which could be easily duplicated in laboratory experiments. The rate of mass loss was found to vary through time in one soil environment and this is hypothesised to be due to pitting increasing the surface area, followed by a build up of corrosion products inhibiting further corrosion. This indicates that early time measurements of mass loss or corrosion rate may be poor indicators of late time corrosion behaviour, potentially giving rise to incorrect estimates of time to complete corrosion. The DU alloy placed in apparently the same geochemical environment, for the same period of time, can experience very different amounts of corrosion and mass loss, indicating that even small variations in the corrosion environment can have a significant effect. These effects are more significant than other experimental errors and variations in initial surface area.

Corals from the Persian/Arabian Gulf as models for thermotolerant reef-builders: prevalence of clade C3 Symbiodinium, host fluorescence and ex situ temperature tolerance.

Corals in the Arabian/Persian Gulf endure summer temperatures of up to 36°C, making them ideal subjects to study the mechanisms underlying thermal tolerance. Unexpectedly, we found the "generalist" Symbiodinium clade C3 to be the prevalent symbiont among seven coral species from Abu Dhabi (UAE) waters. Moreover, C3 represented the only dominant symbiont type in Porites spp. from this region. The "thermotolerant" symbionts D1a and C15 were not encountered, indicating that the association with these symbionts cannot be the sole reason for the heat tolerance of Gulf corals. The association of Porites lobata with specific symbiont types (C3 vs. C15) in samples from habitats with very different temperature regimes (Abu Dhabi vs. Fiji) remained unaffected by laboratory culture. During temperature stress experiments specimens from both locations strongly downregulated green fluorescent protein (GFP)-like pigments. However, the Abu Dhabi samples were less prone to bleaching and showed lower mortality.

Differential effects of copper on three species of scleractinian corals and their algal symbionts (Symbiodinium spp.).

Land-based sources of pollution have been identified as significant stressors linked to the widespread declines of coral cover in coastal reef ecosystems over the last 30 years. Metal contaminants, although noted as a concern, have not been closely monitored in these sensitive ecosystems, nor have their potential impacts on coral-algal symbioses been characterized. In this study, three species of laboratory-reared scleractinian corals, Acropora cervicornis, Pocillopora damicornis, and Montastraea faveolata each containing different algal symbionts (Symbiodinium A3, C1 and D1a, respectively) were exposed to copper (ranging from 2 to 20microg/L) for 5 weeks. At the end of the exposure period, copper had accumulated in the endosymbiotic dinoflagellate ("zooxanthellae") and animal tissue of A. cervicornis and the animal tissue of M. faveolata; however, no copper accumulation was detected in the zooxanthellae or animal tissue of P. damicornis. The three coral species exhibited significantly different sensitivities to copper, with effects occurring in A. cervicornis and P. damicornis at copper concentrations as low as 4microg/L. Copper exposure affected zooxanthellae photosynthesis in A. cervicornis and P. damicornis, and carbonic anhydrase was significantly decreased in A. cervicornis and M. faveolata. Likewise, significant decreases in skeletal growth were observed in A. cervicornis and P. damicornis after copper exposure. Based on preliminary results, no changes in Symbiodinium communities were apparent in response to increasing copper concentration. These results indicate that the relationships between physiological/toxicological endpoints and copper accumulation between coral species differ, suggesting different mechanisms of toxicity and/or susceptibility. This may be driven, in part, by differences in the algal symbiont communities of the coral species in question.

A review of the potential for radium from luminising activities to migrate in the environment.

During the first half of the twentieth century, radium, mixed with other components, was used to luminise many items, including watches, clocks, dials and meters. On many sites, and in particular MoD sites, luminised instruments and paint were disposed of by burning and burial. This paper presents a review of the potential for radium from such sites to migrate in the environment. The most likely mechanisms of migration of radium from former luminising sites in the UK are surface-water erosion and transport, and the action of animals and people. Plant uptake or rainsplash followed by cropping of the plants is another possible mechanism, but the extent of impact is uncertain. The migration of significant quantities of radium through soils or rocks, or due to landsliding or wind transport, is considered to be of minimal importance to most UK sites. A low pH, high salinity (in particular of group II metals) or reducing groundwater would need to be present for migration through soils/rocks to occur and such conditions are unlikely to be present in most shallow aquifer systems in the UK. To reduce the potential for migration to occur it is recommended that luminising wastes at ground surface are removed or covered, that controls are put in place to limit animal activity and that human entry to former luminising sites is restricted.

A possible approach to the treatment of polycystic ovarian syndrome using focused ultrasound.

A new method of treatment for infertility caused by polycystic ovarian syndrome (PCOS) using thermal lesion formation by high intensity ultrasound has been suggested. Current options for PCOS therapy and the achievements of focused ultrasound surgery technique are reviewed and discussed. A prototype of a low-cost commercial device for the treatment of PCOS has been designed and tested to prove the feasibility of the method. A transducer with curvature radius of 36 mm and aperture diameter of 36 mm, operating at 0.97 MHz, was designed and tested. It provided a maximum acoustic power output of 180 W. Well-defined tissue damage was obtained within 10 s in a pig's liver in vitro at 3 cm depth within an area 5 mm in diameter and 12 mm in length without damaging the surrounding tissue. Evaluation of the size of the lesions produced at different frequencies, sonication times and output power has been carried out by visual inspection of the colour changes in cut tissue sections. Results demonstrate that a surgical tool based on the method suggested should be feasible and warrants further investigation.

Nonlinear propagation applied to the improvement of resolution in diagnostic medical ultrasound.

Medical B-mode scanners operating under conditions typically encountered during clinical work produce ultrasonic wave fields that undergo nonlinear distortion. In general, the resulting harmonic beams are narrower and have lower sidelobe levels than the fundamental beam, making them ideal for imaging purposes. This work demonstrates the feasibility of nonlinear harmonic imaging in medical scanners using a simple broadband imaging arrangement in water. The ultrasonic system comprises a 2.25-MHz circular transducer with a diameter of 38 mm, a membrane hydrophone, also with a diameter of 38 mm, and a polymer lens with a focal length of 262 mm. These components are arranged coaxially giving an imaging geometry similar to that used in many commercial B-scanners, but with a receiver bandwidth sufficient to record the first four harmonics. A series of continuous wave and pulse-echo measurements are performed on a wire phantom to give 1-D transverse pressure profiles and 2-D B-mode images, respectively. The reflected beamwidths wn decrease as wn/W1 = 1/n0.78, where n is the harmonic number, and the reflected sidelobe levels fall off quickly with increasing n. In imaging terms, these effects correspond to a large improvement in lateral resolution and signal-to-clutter ratio for the higher harmonics.

A numerical study of the effect of drive level on the intensity loss from an ultrasonic beam.

Knowledge of the spatial distribution of intensity loss from an ultrasonic beam is vital to bioeffect predictions such as heating and streaming. A method for calculating the distribution of intensity loss over a finite-amplitude ultrasonic beam is described. The technique demonstrates that the location of peak intensity loss varies considerably with drive level for a plane circular source, as does the overall distribution of intensity loss across the beam. The effects are shown to be less pronounced but still significant for a focused source.

Impacts of invading N2-fixing Acacia species on patterns of nutrient cycling in two Cape ecosystems: evidence from soil incubation studies and 15N natural abundance values.

This study examines the impacts of woody, N2-fixing invasive Acacia spp. on the patterns of nutrient cycling in two invaded ecosystems of differing nutrient status in the Cape floristic region. Patterns of soil nutrient mineralization were measured by a field incubation method while the significance of the fixation process in altering nutrient cycling was assessed by the δ15N natural abundance technique. The results confirm earlier reports that invasion by woody shrubs results in organic matter and nutrient enrichment of surface soils of both ecosystems. However, patterns of nutrient availability (phosphorus and nitrogen) were not necessarily enhanced. In the more fertile strandveld both phosphorus and nitrogen (significant at P<0.10) showed trends towards enhanced annual mineralization rates upon invasion, while in the low nutrient fynbos system only phosphorus followed this trend. It is unclear whether this differential response is a consequence of plant- or soil-derived feedbacks on the decomposition processes in each system. The δ15N values of the soils from the invaded sites of both ecosystems indicated a strong influence of the alien species on the soil nitrogen component. However, as with other studies of natural ecosystems, the contribution of nitrogen from fixation could not be readily quantified with the δ15N natural abundance method because of problems in selecting suitable non-N2-fixing reference plants. A technique of disrupting nodule structure and function, by fumigation with O2, to obtain the δ15N value of a non-N2-fixing speciment of the study species was tried and found to overcome some of the problems associated with the lack of suitable reference plants. With this technique it was possible to detect the almost total dependence of A. saligna on N2-fixation in the fynbos soils with their low nitrogen mineralization rates. In the strandveld ecosystem with much higher soil nitrogen release rates A. cyclops was only partly dependent on fixation (about half) for its nitrogen. The nutrient enrichment of both ecosystems and trends towards enhanced rates of nutrient mineralization could have profound implications on the long-term success of alien invader clearing operations and the restoration of the indigenous flora at these sites.

Issues of human rights and HIV. Guest commentary.

PIP: The AIDS pandemic has not spread in a social and economic vacuum. Indeed, HIV and AIDS have spread in the context of widespread poverty, sexism, racism, homophobia, and heterosexism throughout most nations of the world. Globally, communities have been allowed to reject or ignore that the spread of HIV/AIDS is symptomatic of underlying social injustices. It is, however, extremely difficult to combat AIDS in the context of poverty, gay bashing, low women's status, and overt violence against HIV-seropositive individuals, notably in Russia, Mexico, and the US. It is clear even at the policy level that countries around the world are still ignorant about HIV/AIDS and violate the human rights of infected individuals. US immigration and entry restrictions against HIV-seropositive individuals is but one example of such policy. Discrimination also extends down to the fundamental need for and provision of health care to people with AIDS. These individuals are stigmatized by health care workers, discriminated against when receiving treatment, or simply denied health care services. Shapiro et al's study found that 23% of young American medical residents would not care for AIDS patients if they had a choice. The study also found that 39% of surgeons or other medical specialists have refused care to at least one of the HIV-infected patients in the respondent physicians' care. Governments must act to ensure that such discrimination is eradicated. Each country must reassess its laws which directly affect the lives of people who are most at risk, eschewing anti-gay rights initiatives and the criminalization of prostitution.^ieng

Choosing a powerful lithotriptor.

Clinicians have no yardstick to help them choose the most efficient lithotriptor. Their leading priority is a system allowing complete disintegration of the stone with the minimum number of shocks and a low re-treatment rate. One of the prerequisites of this system is a powerful shock wave generator. "Power" is as yet ill defined in lithotripsy. Therefore clinicians' choice depends upon other factors. Acoustic output measurements were recorded on 3 commercial lithotriptors representing the 3 main shock wave generating systems. These were the Dornier MPL 9000 (standard and X-155 electrodes), the Siemens (Lithostar, Lithostar Plus and System C) and the Wolf Piezolith 2300. The shock wave measurements were correlated to the capability of the lithotriptors to disintegrate standard stone models in vitro. Two factors were identified. The pulse intensity integral in the focus and the size of the focal zone proved to be the most important factors to assess and compare the efficacy or "power" of different lithotriptors. Together they can help clinicians to identify and choose the most efficient shock wave generating systems.

The spouse's positive effect on the stroke patient's recovery.

To determine the effect of the presence of a spouse on the stroke patient's adaptation, a retrospective chart review of stroke patients who had completed rehabilitation was conducted. The convenience sample comprised 67 stroke patients of a family practice service who received rehabilitation at Pitt County Memorial Hospital Rehabilitation Center in Greenville, NC, over a 45-month period. Roy's Adaptation Model was the theoretical framework for the inquiry. The Barthel Index measured the functioning level, or adaptation, of the patients on discharge from rehabilitation. It was hypothesized that patients who had a stroke and completed a rehabilitation program would achieve a higher level of adaptation if they had a spouse than would comparable patients without a spouse. This hypothesis was supported by the findings; the average Barthel Index score on discharge was 7.5 points higher in patients who had a spouse (Wilcoxon chi-square = 4.17, p < .05). The implications for nurses are presented.

Presence of low amounts of "neuronal" antigens in cultured human skin fibroblasts.

To explore the utility of cultured skin fibroblasts in investigating diseases of the nervous system in which constituents characteristic of neurons are involved, sensitive immunochemical methods were used to test for the presence in skin fibroblasts of low amounts of proteins normally used as neuronal markers. The presence of each of the neurofilament triplet proteins and of neuron-specific enolase was demonstrated by immunoblotting and by immunocytochemistry, and of an 86-kDa synapsin-like material by immunoblotting. These observations agree with previous suggestions that readily available cultured fibroblasts may be useful in investigations of disorders in which molecules are involved which are typically associated with neurons in vivo, such as Alzheimer's disease.

Prediction of non-linear propagation in water due to diagnostic medical ultrasound equipment.

There is a well established requirement for making output measurements on medical ultrasound equipment, in particular for safety and calibration purposes. In addition there is a need for non-linear propagation models to allow predictions to be made for in vivo pressure fields of systems ranging from lithotripters to diagnostic imaging sets. In the past it has been shown that good agreement can be found between experiment and theory for transducers that behave as perfect pistons but little work has been published on comparisons for 'real' medical ultrasound systems. This paper compares experiment with theory for a medical ultrasound system operating in water. Pressure field measurements are presented for a Philips 3.5 MHz, 13 mm diameter, 'long internal focus' (LIF) transducer. The measurements were made using a membrane hydrophone in water. Initially the transducer was driven continuously with a function generator at low amplitude so that the effective aperture radius and focal length could be determined. The transducer was then driven by a Philips 'sono-Diagnost B' imaging system which produced a short finite amplitude pulse. The results are compared with a finite difference model based on the parabolic approximation to the non-linear wave equation. Reasonable agreement (typically 10-15%) is shown for spectral magnitudes although some difficulty was encountered in accurately characterizing the transducer in terms of its geometry and drive waveform.

Measurement of lithotripsy pulses through biological media.

Lithotripsy is now the method of choice for the treatment of renal calculi. The mechanism of destruction is not clearly understood, and detailed knowledge of the shock-wave characteristics at the calculus would aid understanding of the phenomenon. Current methods of measuring the pressure pulse by observing it through a water path are not well characterized, and the results may not represent the actual pressure fluctuations produced in vivo. In order to determine the actual pressure pulse experienced at the site of the calculus, measurements have been made through a variety of biological media. The results show that there are considerable differences between measurements taken through a water path and through biological media. This paper describes the pressure fluctuations in the time domain. The implications of the results for lithotripsy are discussed.