An integrative taxonomic approach to reveal the status of the genus Pomphorhynchus Monticelli, 1905 (Acanthocephala: Pomphorhynchidae) in Austria

Species of the genus Pomphorhynchus Monticelli, 1905 (Acanthocephala: Pomphorhynchidae) are obligate endoparasites infesting mostly freshwater fish. Morphological identification is challenging due to high intraspecific variations. The use of molecular analyses enabled new insights into the diversity and revealed high cryptic presence and unknown distribution patterns for various European species. In Austria only one species, Pomphorhynchus laevis (Müller, 1776), has been reported so far. We conduct an integrative analysis of Pomphorhynchus in Austria with a combination of morphological and molecular methods. Our results revealed the presence of three species of Pomphorhynchus in Austrian waters: Pomphorhynchus laevis, Pomphorhynchus tereticollis (Rudolphi, 1809) and Pomphorhynchus bosniacus Kiskároly and Čanković, 1967. While P. bosniacus was the predominant species in the Danube, P. laevis was recorded exclusively in Styria. Pomphorhynchus tereticollis occurred mainly in rivers of Styria except for one individual found in the Danube. We document the first occurrence of P. bosniacus and P. tereticollis in Austria. We found a high intraspecific haplotype variation in P. bosniacus suggesting that the species has a longer history in Central and Western Europe. It was previously misidentified as P. laevis, which is also true for P. tereticollis. A large number of hosts examined were infected with only juvenile and cystacanth stages suggesting paratenic infections. Our study highlights the importance of using an integrative taxonomic approach in the identification of species of Pomphorhynchus.

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First evidence of Pomphorhynchus tereticollis and Pomphorhynchus bosniacus in Austria.

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Pomphorhynchus tereticollis showed a wide host range in comparison to P. bosniacus and P. laevis.

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Presentation of an integrative taxonomic approach which should prevent misidentifications in future studies.

Improvements to the APBS biomolecular solvation software suite

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK_a values, and an improved web-based visualization tool for viewing electrostatics.

Theory of Reactive Adsorption on Si(100)

Density functional calculations on cluster models of Si(100)-2xl have been used to predict reaction mechanisms and energetics for several reactive adsorption processes. Dissociative adsorption of H2, H20, BH3, and SiH4 will be described and compared to available experimental data. Based on these examples, a qualitative theory of mechanisms for dissociative adsorption of hydrides on silicon surfaces will be proposed. These reactions can largely be understood in terms of the electron density distributions in the molecule and surface dimer. On a buckled dimer, there are both electron-rich and electron-deficient sites, which have different chemical interactions with adsorbates. The role of this difference is illustrated in a novel surface Diels-Alder reaction, for which symmetric addition to an unbuckled surface dimer is allowed by orbital symmetry. This reaction creates new reactive surface sites that may be useful for subsequent chemical surface modification.

iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS)

The Adaptive Poisson-Boltzmann Solver (APBS) is a state-of-the-art suite for performing Poisson-Boltzmann electrostatic calculations on biomolecules. The iAPBS package provides a modular programmatic interface to the APBS library of electrostatic calculation routines. The iAPBS interface library can be linked with a FORTRAN or C/C++ program thus making all of the APBS functionality available from within the application. Several application modules for popular molecular dynamics simulation packages - Amber, NAMD and CHARMM are distributed with iAPBS allowing users of these packages to perform implicit solvent electrostatic calculations with APBS.

Infection patterns of Nile tilapia (Oreochromis niloticus L.) by two helminth species with contrasting life styles

The larval stages of Bolbophorus sp. (digenean) and Amirthalingamia macracantha (cestode) are frequently reported in Oreochromis niloticus in Uganda. Little, however, is known about their infection patterns. This study examined the influence of habitat type, host size, and sex and weather patterns on the parasite populations in Uganda. A total of 650 fish were collected between January and November 2008 from a reservoir, cages, fishponds and a stream. The prevalence and intensity of A. macracantha and the prevalence of Bolbophorus sp. differed across the water bodies reflecting the effect of habitat characteristics on parasite transmission. Host sex did not significantly influence the infection patterns, although female fish were slightly more parasitized than male and sexually undifferentiated individuals. The fish size was positively correlated with helminth infections demonstrating accumulation and prolonged exposure of larger (older) fish to the parasites. The metacercariae population did not vary significantly across months, while monthly A. macracantha infection fluctuated markedly. With regard to rain seasons, higher prevalence and intensity of A. macracantha were recorded in wet season. For Bolbophorus sp., only the prevalence varied with seasons, with higher prevalence recorded in the dry season than in wet season. Generally, Bolbophorus sp. responded weakly to changes in water body, host sex and size and weather patterns. Rainfall appears to be an essential cue for coracidia hatching.

Parasite fauna of farmed Nile tilapia (Oreochromis niloticus) and African catfish (Clarias gariepinus) in Uganda

An intensive parasite survey was conducted in 2008 to better understand the parasite fauna occurrence, distribution and diversity in the commercial aquaculture fish species in Uganda. A total of 265 fish collected from hatcheries and grow-out systems were examined for parasites using routine parasitological techniques. The survey yielded 17 parasite species: 11 from Oreochromis niloticus and ten from Clarias gariepinus. Four parasites-Amirthalingamia macracantha, Monobothrioides sp., Zoogonoides sp. and a member of the family Amphilinidae-were recorded for the first time in the country. The parasite diversity was similar between hosts; however, O. niloticus was dominated by free-living stage-transmitted parasites in lower numbers, whereas both trophically and free-living stage-transmitted parasites were equally represented in C. gariepinus in relatively high intensities. The patterns in parasite numbers and composition in the two hosts reflect differences in fish habitat use and diet. A shift in parasite composition from monoxenous species-dominated communities in small-sized fish to heteroxenous in large fishes was recorded in both hosts. This was linked to ontogenetic feeding changes and prolonged exposure to parasites. Polyculture systems showed no effect on parasite intensity and composition. The gills were highly parasitized, mainly by protozoans and monogeneans. Generally, the occurrence and diversity of parasites in these fish species highlight the likelihood of disease outbreak in the proposed intensive aquaculture systems. This calls for raising awareness in fish health management among potential farmers, service providers and researchers.

Helminth communities of the barbel Barbus barbus from large river systems in Austria

The composition and diversity of the total and intestinal component endohelminth communities were determined in the cyprinid barbel from three study areas in two large river systems in Austria. Two sample sites in the Danube and one site in the River Drau are the only free flowing stretches of these rivers in Austria. Nine helminth species were identified, with the acanthocephalan Pomphorhynchus laevis being dominant in the Danube, with up to 100% prevalence. In the Drau, where the dominant species was the cestode Bathybothrium rectangulum, species diversity was higher than in the Danube.

Dynamics and predicted decline of Anguillicola crassus infection in European eels, Anguilla anguilla, in Neusiedler See, Austria

The eel population in Neusiedler See has been maintained by regular massive stocking since 1958. After the establishment of the National Park Neusiedler See-Seewinkel in 1993, eel stocking was prohibited and the population, together with the specific parasites of eels, was predicted to decline to extinction within 10 years. This investigation was undertaken to document the decline and extinction of the Anguillicola crassus population in eels. From 1994 to 2001, 720 eels were collected from two sites in the lake. Prevalence and abundance of A. crassus were lower in spring than in summer and autumn and larger eels harboured more parasites than smaller ones. Neither year of study nor sampling site were correlated with parasite infection levels. No significant trend in the population parameters of A. crassus was detected over the 8 years of the survey. This suggested that there had been no significant decline in the eel population. This suggestion was confirmed by investigations of the fishery, which also found evidence of regular illegal stocking. The stability of the A. crassus population over the past decade seems to reflect the lack of change in eel population density. No mass mortalities of eels occurred over the period despite the many similarities between Neusiedler See and Lake Balaton in Hungary. Differences in eel size, eel diet and the lack of large-scale insecticide use are discussed as possible explanations for the absence of eel mass mortalities in Neusiedler See.

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

Electrostatic properties of cowpea chlorotic mottle virus (CCMV) and cucumber mosaic virus (CMV) were investigated using numerical solutions to the Poisson-Boltzmann equation. Experimentally, it has been shown that CCMV particles swell in the absence of divalent cations when the pH is raised from 5 to 7. CMV, although structurally homologous, does not undergo this transition. An analysis of the calculated electrostatic potential confirms that a strong electrostatic repulsion at the calcium-binding sites in the CCMV capsid is most likely the driving force for the capsid swelling process during the release of calcium. The binding interaction between the encapsulated genome material (RNA) inside of the capsid and the inner capsid shell is weakened during the swelling transition. This probably aids in the RNA release process, but it is unlikely that the RNA is released through capsid openings due to unfavorable electrostatic interaction between the RNA and capsid inner shell residues at these openings. Calculations of the calcium binding energies show that Ca(2+) can bind both to the native and swollen forms of the CCMV virion. Favorable binding to the swollen form suggests that Ca(2+) ions can induce the capsid contraction and stabilize the native form.

Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach

Although many viruses have been crystallized and the protein capsid structures have been determined by x-ray crystallography, the nucleic acids often cannot be resolved. This is especially true for RNA viruses. The lack of information about the conformation of DNA/RNA greatly hinders our understanding of the assembly mechanism of various viruses. Here we combine a coarse-grain model and a Monte Carlo method to simulate the distribution of viral RNA inside the capsid of cowpea chlorotic mottle virus. Our results show that there is very strong interaction between the N-terminal residues of the capsid proteins, which are highly positive charged, and the viral RNA. Without these residues, the binding energy disfavors the binding of RNA by the capsid. The RNA forms a shell close to the capsid with the highest densities associated with the capsid dimers. These high-density regions are connected to each other in the shape of a continuous net of triangles. The overall icosahedral shape of the net overlaps with the capsid subunit icosahedral organization. Medium density of RNA is found under the pentamers of the capsid. These findings are consistent with experimental observations.

Long-term investigation of the composition and richness of intestinal helminth communities in the stocked population of eel, Anguilla anguilla, in Neusiedler See, Austria

Data from a long-term study of the intestinal helminth parasite community of eels, Anguilla anguilla, stocked into the shallow eutrophic Neusiedler See, Austria, were collected over an 8 year period (1994–2001). In total, 720 eels from 2 sampling sites were examined. The parasite community showed characteristics similar to those in the natural eel populations in rivers of the UK and mainland Europe: it was species poor, with only 5 species (Acanthocephalus lucii, Acanthocephalus anguillae, Raphidascaris acus, Proteocephalus macrocephalus, Bothriocephalus claviceps) comprising the component community and a maximum infracommunity richness of 4 species. Over the period, the intestinal parasite community of the sampling site in Illmitz, which was originally dominated by A. lucii, changed. As levels of A. anguillae increased to a point at which it dominated the community, diversity increased whilst dominance of a single species decreased. By contrast the community in the southern sampling site remained rather constant with a continuous high infection level of A. anguillae and low abundance of A. lucii. Both acanthocephalan species exhibited higher infection levels in larger eels and in different seasons of the year and the infection parameters were significantly different between the years of study. The significant differences in the infection levels of the 2 acanthocephalan species at the 2 sampling sites were surprising as both acanthocephalan species use the same intermediate host, Asellus aquaticus, and the sampling sites were in close proximity and were similar in terms of water quality, host size and invertebrate abundance. Differences in the fish communities of the 2 sampling sites and eel movements rather than interspecific competition are discussed as possible explanations for the differences in the parasite communities of the 2 sampling sites.

Ribosome motions modulate electrostatic properties

The electrostatic properties of the 70S ribosome of Thermus thermophilus were studied qualitatively by solving the Poisson-Boltzmann (PB) equation in aqueous solution and with physiological ionic strength. The electrostatic potential was calculated for conformations of the ribosome derived by recent normal mode analysis (Tama, F., et al. Proc Natl Acad Sci USA 2003 100, 9319-9323) of the ratchet-like reorganization that occurs during translocation (Frank, J.; Agrawal, R. K. Nature 2000 406, 318-322). To solve the PB equation, effective parameters (charges and radii), applicable to a highly charged backbone model of the ribosome, were developed. Regions of positive potential were found at the binding site of the elongation factors G and Tu, as well as where the release factors bind. Large positive potential areas are especially pronounced around the L11 and L6 proteins. The region around the L1 protein is also positively charged, supporting the idea that L1 may interact with the E-site tRNA during its release from the ribosome after translocation. Functional rearrangement of the ribosome leads to electrostatic changes which may help the translocation of the tRNAs during the elongation stage.

Observation of multipactor in an alumina-based dielectric-loaded accelerating structure

We report a new regime of single-surface multipactor that was observed during high-power testing of an 11.424-GHz alumina-based dielectric-loaded accelerating structure. Previous experimental observations of single-surface multipactor on a dielectric occurred in cases for which the rf electric field was tangential and the rf power flow was normal to the dielectric surface (such as on rf windows) and found that the fraction of power absorbed at saturation is approximately 1%, independent of the incident power. In this new regime, in which strong normal and tangential rf electric fields are present and the power flow is parallel to the surface, the fraction of power absorbed at saturation is an increasing function of the incident power, and more than half of the incident power can be absorbed. A simple model is presented to explain the experimental results.

Fish macroparasites as indicators of heavy metal pollution in river sites in Austria

This paper describes two approaches to evaluate the use of fish macroparasites as bioindicators of heavy metal pollution at selected river stretches in Austria. Firstly changes in the diversity and richness of endoparasites of the cyprinid barbel, Barbus barbus (L.), were tested in relation to heavy metal contents in the aquatic system. Secondly, the bioaccumulation potential of cadmium, lead and zinc was assessed in the acanthocephalan, Pomphorhynchus laevis (Müller, 1776), and compared with that in the muscle, liver and intestine of its barbel host. The present results indicated that in order to validate the role of parasite community patterns related to heavy metal pollution, more investigations on food web dynamics, interelationships between parasites and the presence/absence of intermediate hosts will be essential. Heavy metal concentrations differed significantly between the organs of barbel and P. laevis (P=0·001) with levels up to 2860 fold in the parasite. The high level of heavy metal accumulation in P. laevis compared with that in its barbel host, suggests that despite variability in the parasite infrapopulation, host mobility and feeding behaviour, P. laevis is a most sensitive indicator of heavy metals in aquatic ecosystems.

Immunohistochemistry, ultrastructure and pathology of gills of Abramis brama from Lake Mondsee, Austria, infected with Ergasilus sieboldi (Copepoda)

Immunohistochemical, ultrastructural and pathological studies were carried out on the gills of bream Abramis brama (L.) from Lake Mondsee, Austria, that were naturally infected with Ergasilus sieboldi Nordmann, 1832. Of a total of 14 specimens of bream examined, the gills of 7 (50%) were parasitized with this copepod and the intensity of infection ranged from 1 to 23 crustaceans per host. Histopathological investigations of infected gill showed extensive tissue damage due to attachment and feeding of the crustacean. Parasites attached close to the base of filaments near the gill arch. Pressure exerted by the ectoparasite attached to the lateral margin of the gill filaments induced atrophy of the secondary lamellae. Tissue reactions included hyperplasia and mucous cell proliferation of the respiratory epithelium. Mucous cells displayed an intense immunohistochemical reactivity with the anti-nitric oxide synthase antibody. In parasitized primary and secondary lamellae, a high number of eosinophilic granular cells and rodlet cells were noticed. Rodlet cells represent an inflammatory cell type closely linked to other piscine inflammatory cells. Presence of a high number of inflammatory cells at the site of E. sieboldi attachment is related to intense host cellular reaction.

Reactivity of free radicals on hydroxylated quartz surface and its implications for pathogenicity experimental and quantum mechanical study

We studied the adsorption of hydroxyl radicals and superoxide anion radicals on a hydroxylated alpha-quartz surface using cluster and periodic slab models by means of density functional calculations. Models of two hydroxylated alpha-quartz surfaces--(0001) and (0111)--have been used in the simulations. The hydroxyl radical adsorbs readily on both surfaces. The subsurface Si-O bonds are weakened during the adsorption resulting in surface layer destabilization. This destabilization leads directly to surface disintegration in the case of *OH/(0111) adsorption. The product of the surface disintegration and reconstruction is a surface terminated by silanol groups (Si-OH) and siloxyl radicals (Si-O*). The model calculations suggest that adsorption of *OH on a hydroxylated quartz surface transforms a chemically inert, aged, silanol terminated surface to a very reactive, silicon-based radical terminated surface. The activated surface may then cause oxidative damage to the adsorbed biomaterial. The superoxide anion radical adsorbs on both surfaces, but the adsorption products are only weakly bonded to the surface. The calculated energy barrier for the O2*- activated subsurface Si-O bond dissociation is 10 kcal/mol, which is higher than for the *OH activated process (4 kcal/mol). The calculated weaker bonding to the surface and higher activation energy barrier suggest that the superoxide anion radical will be less efficient in reactivation of an aged, hydroxylated quartz surface than the hydroxyl radical. The importance of the specific geometry of the surface silicon atoms on the surface reactivity and adsorption properties is also discussed. The theoretical predictions are supported experimentally using chemiluminescence to monitor reactivation of the aged silica surface by superoxide anion radicals.

Radio-frequency measurements of coherent transition and cherenkov radiation: implications for high-energy neutrino detection

We report on measurements of (11-18)-cm wavelength radio emission from interactions of 15.2 MeV pulsed electron bunches at the Argonne Wakefield Accelerator. The electrons were observed both in a configuration where they produced primarily transition radiation from an aluminum foil, and in a configuration designed for the electrons to produce Cherenkov radiation in a silica sand target. Our aim was to emulate the large electron excess expected to develop during an electromagnetic cascade initiated by an ultrahigh-energy particle. Such charge asymmetries are predicted to produce strong coherent radio pulses, which are the basis for several experiments to detect high-energy neutrinos from the showers they induce in Antarctic ice and in the lunar regolith. We detected coherent emission which we attribute both to transition and possibly Cherenkov radiation at different levels depending on the experimental conditions. We discuss implications for experiments relying on radio emission for detection of electromagnetic cascades produced by ultrahigh-energy neutrinos.

CuZn Superoxide Dismutase Geometry Optimization, Energetics, and Redox Potential Calculations by Density Functional and Electrostatic Methods

The structures, energetics, and orbital- and charge-dependent properties of copper zinc superoxide dismutase (CuZnSOD) have been studied using density functional and electrostatic methods. The CuZnSOD was represented with a model consisting of copper and zinc sites connected by a bridging histidine ligand. In addition to the bridge, three histidine ligands and one water molecule were bonded to the Cu ion in the copper site as first-shell ligands. Two histidine ligands and an aspartate were coordinated to the zinc ion in the zinc site. Full optimization of the model was performed using different functionals, both local and nonlocal. Geometrical parameters calculated with the nonlocal functionals agree well with the experimental X-ray data. In our calculated results, the His61 Nepsilon-Cu bond in the active site breaks during the reduction and protonation, consistent with a number of X-ray structures and with EXAFS and NMR evidence. The reduction potential and pK(a) of the coupled electron/proton reaction catalyzed by CuZnSOD were determined using different models for the extended environment-from an electrostatic representation of continuum solvent, to the full protein/solvent environment using a Poisson-Boltzmann method. The predicted redox potential and pK(a) values determined using the model with the full protein/solvent environment are in excellent agreement with experiment. Inclusion of the full protein environment is essential for an accurate description of the redox process. Although the zinc ion does not play a direct redox role in the dismutation, its electronic contribution is very important for the catalytic mechanism.

Density Functional and Electrostatic Calculations of Manganese Superoxide Dismutase Active Site Complexes in Protein Environments

Density functional and electrostatic methods have been applied to calculate active site geometries and the redox potential of manganese superoxide dismutase (MnSOD). The initial active site clusters were built up by including only first-shell side chain ligands and then augmented by second-shell ligands. The density functional optimized Mn-ligand bond lengths for the reduced complexes in general compared fairly well with protein crystallography data; however, large deviations for calculated Mn-OH distances were found for the oxidized active site clusters. Our calculations suggest that this deviation can be attributed to the redox heterogeneity of the oxidized protein in X-ray crystallography studies. The redox potential was calculated by treating the protein environment and the solvent bulk by a semimacroscopic electrostatic model. The protein structures were taken from the Thermus thermophilus enzyme. The calculated coupled redox potentials converge toward experimental values with increasing size of the active site cluster models, and the final calculated value was +0.06 V, compared to experimental values of +0.26 V determined for Bacillus stearothermophilus and +0.31 V in Escherichia coli enzymes. Using an energy decomposition scheme, the effects of the second-shell ligands and the protein and reaction fields have been analyzed.

Endoparasitic helminths of the European eel, Anguilla anguilla, from four disconnected meanders from the rivers Leie and Scheldt in western Flanders, Belgium

The endoparasitic helminth communities of the European eel, Anguilla anguilla (L.), were investigated in four meanders, cut off from the rivers Leie and Scheldt in western Flanders, Belgium. Six species of helminths (2 cestodes, 2 nematodes and 2 acanthocephalans) were found. The dominant parasite species was the nematode Anguillicola crassus (Kuwahara, Niimi et Itagaki, 1974) infecting 79% of the eel population with intensities up to 112 specimens per fish. At two localities no acanthocephalans could be found, whereas these parasites were very common at the other sites. The prevalence, mean intensity, intensity and abundance, their correlation to the body length, and the frequency distributions were analysed. The site selection of parasites is in relation to food composition and feeding habits of eels, physiological and structural differences in the intestine and possible interspecific competition were discussed.