Influence of the halothane gene (HAL) on pork quality in two commercial crossbreeds

We evaluated the effect of the halothane (HAL) gene on the quality of pork in domestic pigs. Half-carcasses from two different commercial pig (Sus domestica) crossbreeds were analyzed, 46 of which were homozygous dominant (HAL(NN)) and 69 of which were heterozygous (HAL(Nn)) for the halothane gene. The measures included backfat thickness, lean meat percentage, carcass weight, pH 24 h after slaughtering, color, and drip loss; DNA was extracted from the haunch muscle. Swine with the HAL(Nn) genotype had less backfat thickness and higher lean meat percentages than swine with the HAL(NN) genotype. Yet, swine with the HAL(Nn) genotype had lower quality meat than those with the HAL(NN) swine. The pH at 24 h was lower in HAL(Nn) swine. The meat color was paler in HAL(Nn) animals, the drip loss was greater in those animals bearing the n allele, and the amount of intramuscular fat was not related to the halothane genotype. We conclude that bearers of the recessive allele of the halothane gene produce more meat, but with quality parameters that are inferior to those sought by consumers and industry.     

Indigenous arbuscular mycorrhizal fungal assemblages protect grassland host plants from pathogens

Plant roots can establish associations with neutral, beneficial and pathogenic groups of soil organisms. Although it has been recognized from the study of individual isolates that these associations are individually important for plant growth, little is known about interactions of whole assemblages of beneficial and pathogenic microorganisms associating with plants.We investigated the influence of an interaction between local arbuscular mycorrhizal (AM) fungal and pathogenic/saprobic microbial assemblages on the growth of two different plant species from semi-arid grasslands in NE Germany (Mallnow near Berlin). In a greenhouse experiment each plant species was grown for six months in either sterile soil or in sterile soil with one of three different treatments: 1) an AM fungal spore fraction isolated from field soil from Mallnow; 2) a soil pathogen/saprobe fraction consisting of a microbial community prepared with field soil from Mallnow and; 3) the combined AM fungal and pathogen/saprobe fractions. While both plant species grew significantly larger in the presence of AM fungi, they responded negatively to the pathogen/saprobe treatment. For both plant species, we found evidence of pathogen protection effects provided by the AM fungal assemblages. These results indicate that interactions between assemblages of beneficial and pathogenic microorganisms can influence the growth of host plants, but that the magnitude of these effects is plant species-specific.     

An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference

The ITS2 gene class shows a high sequence divergence among its members that have complicated its annotation and its use for reconstructing phylogenies at a higher taxonomical level (beyond species and genus). Several alignment strategies have been implemented to improve the ITS2 annotation quality and its use for phylogenetic inferences. Although, alignment based methods have been exploited to the top of its complexity to tackle both issues, no alignment-free approaches have been able to successfully address both topics. By contrast, the use of simple alignment-free classifiers, like the topological indices (TIs) containing information about the sequence and structure of ITS2, may reveal to be a useful approach for the gene prediction and for assessing the phylogenetic relationships of the ITS2 class in eukaryotes. Thus, we used the TI2BioP (Topological Indices to BioPolymers) methodology [1], [2], freely available at http://ti2biop.sourceforge.net/ to calculate two different TIs. One class was derived from the ITS2 artificial 2D structures generated from DNA strings and the other from the secondary structure inferred from RNA folding algorithms. Two alignment-free models based on Artificial Neural Networks were developed for the ITS2 class prediction using the two classes of TIs referred above. Both models showed similar performances on the training and the test sets reaching values above 95% in the overall classification. Due to the importance of the ITS2 region for fungi identification, a novel ITS2 genomic sequence was isolated from Petrakia sp. This sequence and the test set were used to comparatively evaluate the conventional classification models based on multiple sequence alignments like Hidden Markov based approaches, revealing the success of our models to identify novel ITS2 members. The isolated sequence was assessed using traditional and alignment-free based techniques applied to phylogenetic inference to complement the taxonomy of the Petrakia sp. fungal isolate.     

Re-structuring of marine communities exposed to environmental change: a global study on the interactive effects of species and functional richness

Species richness is the most commonly used but controversial biodiversity metric in studies on aspects of community stability such as structural composition or productivity. The apparent ambiguity of theoretical and experimental findings may in part be due to experimental shortcomings and/or heterogeneity of scales and methods in earlier studies. This has led to an urgent call for improved and more realistic experiments. In a series of experiments replicated at a global scale we translocated several hundred marine hard bottom communities to new environments simulating a rapid but moderate environmental change. Subsequently, we measured their rate of compositional change (re-structuring) which in the great majority of cases represented a compositional convergence towards local communities. Re-structuring is driven by mortality of community components (original species) and establishment of new species in the changed environmental context. The rate of this re-structuring was then related to various system properties. We show that availability of free substratum relates negatively while taxon richness relates positively to structural persistence (i.e., no or slow re-structuring). Thus, when faced with environmental change, taxon-rich communities retain their original composition longer than taxon-poor communities. The effect of taxon richness, however, interacts with another aspect of diversity, functional richness. Indeed, taxon richness relates positively to persistence in functionally depauperate communities, but not in functionally diverse communities. The interaction between taxonomic and functional diversity with regard to the behaviour of communities exposed to environmental stress may help understand some of the seemingly contrasting findings of past research.     

Rotifer community structure in three shallow lakes: seasonal fluctuations and explanatory factors

The present work aimed at studying the rotifer communities of three shallow eutrophic lakes in Portugal (lakes Mira, Vela and Linhos). At the time of the study, Mira and Vela faced large inputs of allochthonous nutrients, while Linhos was facing terrestrialisation, with cycles of dominance-senescence of macrophytes. The three lakes differed in terms of their abiotic features, with Linhos presenting very high nutrient levels and low pH, while Vela and Mira shared most of the characteristics. The rotifer communities of these two lakes were poorly diversified but highly abundant (max. > 2000 ind l⁻¹), with a clear dominance of eurytopic euplanktonic species (mainly Keratella cochlearis). On the other hand, Linhos presented lower abundances (<1000 ind l⁻¹) but higher species richness, mainly due to macrophyte-associated taxa, such as the littoral genera Lepadella, Testudinella and Squatinella. In all lakes, summertime represented a peak in terms of abundance and diversity. Canonical correspondence analysis (CCA) identified two main environmental gradients that shape up the rotifer assemblages: a temporal gradient, mainly related to temperature, and a eutrophy gradient, associated with nitrogenous nutrients. The latter gradient is clearly dependent on between-lake variation, due to the high nutrient levels observed in lake Linhos. Variance partitioning using CCA revealed that the largest portion (27.5%) of the total variation explained (52.1%) was attributed to the interaction between lake and environmental variables.     

Chromosomal diversification of reef fishes from genus <Emphasis Type="Italic">Centropyge</Emphasis>(Perciformes,Pomacanthidae)

The genus Centropyge is remarkable for species richness, composing a highly specialized fish group amongst members from family Pomacanthidae. However, cytogenetical reports are nearly absent in these animals. New data are provided from karyotypical studies carried out on Centropyge aurantonotus from the Brazilian coast of the Atlantic Ocean and C. ferrugatus from the Philippines Sea of the Indo-Pacific Ocean. Both species present 2n=48 but karyotypes are differentiated by fundamental number. C. aurantonotus has a great number of biarmed chromosomes (4 m + 14 sm+16 st+4 a), while C. ferrugatus presents only acrocentric chromosomes. Single nucleolar organizer regions (NORs) are located at interstitial position of an acrocentric pair in C. ferrugatus and on short arms of a subtelocentric pair in C. aurantonotus, as confirmed by fluorescent in situ hybridization (FISH) with 18S rDNA probes. Heterochromatin is distributed over NOR and centromeric regions in both species, but additional GC-rich heterochromatic blocks on short arms of up to eight chromosomal pairs can be detected in C. aurantonotus. 5S rDNA segments were located interstitially on two chromosomal pairs in C. ferrugatus and on nine pairs in C. aurantonotus, mostly equivalent to heterochromatic blocks on short arms of biarmed chromosomes. C. ferrugatus can be considered a species in which basal chromosomal features proposed for modern Teleosteans were conserved. The derived karyotype pattern of C. aurantonotus seems to be determined by pericentric inversions and heterochromatin addition which probably determined the notorious dispersion of 5S rRNA (pseudo)genes. It is demonstrated that, even within a group generally characterized by cytogenetical homogeneity as the family Pomacanthidae, diversified karyotypes can be found.     

13- and 14-membered macrocyclic ligands containing methylcarboxylate or methylphosphonate pendant arms: chemical and biological evaluation of their (153)Sm and (166)Ho complexes as potential agents for therapy or bone pain palliation

The stability constants of La(3+), Sm(3+) and Ho(3+) complexes with 13- and 14-membered macrocycles having methylcarboxylate (trita and teta) or methylphosphonate (tritp and tetp) arms were determined. All the ligands were labelled with (153)Sm and (166)Ho in order to evaluate the effect of the macrocyclic cavity size and type of appended arms on their in vitro and in vivo behaviour. The radiolabelling efficiency was found to be higher than 98% for all the complexes, except for those of tetp. All radiocomplexes studied are hydrophilic with an overall negative charge and low plasmatic protein binding. Good in vitro stability in physiological media and human serum was found for all complexes, except the (153)Sm/(166)Ho-teta, which are unstable in phosphate buffer (pH 7.4). In vitro hydroxyapatite (HA) adsorption studies indicated that (153)Sm/(166)Ho-tritp complexes bind to HA having the (166)Ho complex the highest degree of adsorption (>80%, 10 mg). Biodistribution studies in mice demonstrated that (153)Sm/(166)Ho-trita complexes have a fast tissue clearance with more than 95% of the injected activity excreted after 2 h, value that is comparable to the corresponding dota complexes. In contrast, the (153)Sm-teta complex has a significantly lower total excretion. (153)Sm/(166)Ho-tritp complexes are retained by the bone, particularly (166)Ho-tritp that has 5-6% (% I.D./g) bone uptake and also a high rate of total excretion. Thus, these studies support the potential interest of (153)Sm/(166)Ho-trita complexes for therapy when conjugated to a biomolecule and the potential usefulness of the (166)Ho-tritp complex in bone pain palliation.     

The effect of metal diffusion and supply limitations on conditional stability constants determined for durum wheat roots

Conditional stability constants (log K), and binding site densities (Γ_max) for dissolved metals and biota are important input parameters for the Biotic Ligand Model. However, determination of these binding parameters is likely to be influenced by solution kinetics because roots have a large metal-binding capacity and can accumulate metals rapidly. The aim of this study was to determine if the rate of free metal ion diffusion to the root surface, and amount of metal in the bulk solution, is sufficient to accommodate the maximum root–metal accumulation capacity. The extent to which these kinetic limitations affect the magnitude of log K and Γ_max values was also assessed. Seven day old hydroponically grown durum wheat (Triticum turgidum L. var durum, cv ‘Arcola’) were exposed to solutions with p{Cu²⁺}s ranging from 10.54 to 2.26 (~20 °C, pH = 6.0, ionic strength = 0.03 M). Exposure solutions were prepared with and without the metal buffer nitrilotriacetic acid (NTA) so that the total amount of metal in the exposure solution, and net flux of metal to the root, could be varied. The results demonstrate that NTA enhances Cu accumulation at exposure p{Cu²⁺}s between 10 and 6. Comparison of the diffusive flux to the root with the metal flux into the root, for (−NTA) and (+NTA) Cu exposures, showed that the flux of the un-buffered free metal ion to the root was not large enough to accommodate the maximum Cu binding capacity between 10 and 6 p{Cu²⁺} in solution. The total amount of Cu in solution may have limited uptake for exposure p{Cu²⁺}s of 10.01 and 9.01, but the background concentrations of Cu in the control plants prevented definitive conclusions from being made within this exposure range. Similar results were found for Mn and Ni. For Cd, which had lower background concentrations in the roots, the amount of metal in solution did not limit uptake until a p{Cd²⁺} of 10.01. Limiting the supply of Cu²⁺ to the root (i.e. low {Cu²⁺}s with no NTA) caused only a moderate bias in Γ_max values, but suppressed the log K value by 3.44 log units. The log K values for Cd, Mn and Ni, in the absence of NTA, were more similar than expected, which suggests that the kinetics of free ion re-supply to the root surface limited metal uptake, as it did for Cu. Section Editor: T. B. Kinraide