Standardized and simplified nomenclature for proteins common to all retroviruses.

We propose a revised standardized nomenclature for the proteins common to all retroviruses on the basis of biological function, enzymatic activity, and/or virion location data. (We do not discuss proteins specific for subfamilies or only some retroviruses.)     

Value of a broken umbrella: abandoned nest sites of the black stork (Ciconia nigra) host rich biodiversity

Protecting habitats for charismatic vertebrates can provide an ‘umbrella’ for less conspicuous organisms, especially when these are threatened by the same processes. However, such a conservation scheme is vulnerable to the extirpation of the focal species. We studied wider biodiversity values in long protected black stork (Ciconia nigra) nest sites, which were abandoned by the bird and thus legally subject to de-listing. In 20 abandoned nest sites in Estonia, we (i) mapped breeding birds within 600 m from the stork nest, and (ii) carried out time-limited surveys of lichens, polypore fungi, vascular plants and bryophytes in 2-ha plots. The breeding bird assemblages (64 species recorded) included 19 red-listed species, and showed no clear aggregation to the immediate surroundings of the stork nest. We recorded 740 plant and fungal species, of which 134 (18%) were of conservation concern (nationally protected, red-listed or extremely rare). Across the 2-ha plots, the numbers of the species of conservation concern varied more than three-fold (maximum 42 species), being affected notably by dead wood accumulation over time and presence of nemoral broad-leaved trees. The results demonstrate that many abandoned nest sites of the black stork have broader biodiversity significance, both due to the bird’s habitat requirements and the natural development during the protection. Expanding the umbrella function to sites abandoned by a focal species, but intact from anthropogenic degradation, can thus be a cost-effective conservation approach due to its low additional administrative burden. In most jurisdictions, the assessment procedure for such situations should be formalized, however.

     

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

Background  

Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species. These regions of macrosynteny have been very useful for locating homologous genes in different species and to guide the assembly of genome sequences. Previous analyses in the fungi have indicated that macrosynteny is rare; instead, comparisons across species show no synteny or only microsyntenic regions encompassing usually five or fewer genes. To test the hypothesis that chromosomal evolution is different in the fungi compared to other eukaryotes, synteny was compared between species of the major fungal taxa.     

Using the realized relationship matrix to disentangle confounding factors for the estimation of genetic variance components of complex traits

Background

In the analysis of complex traits, genetic effects can be confounded with non-genetic effects, especially when using full-sib families. Dominance and epistatic effects are typically confounded with additive genetic and non-genetic effects. This confounding may cause the estimated genetic variance components to be inaccurate and biased.

Methods

In this study, we constructed genetic covariance structures from whole-genome marker data, and thus used realized relationship matrices to estimate variance components in a heterogenous population of ~ 2200 mice for which four complex traits were investigated. These mice were genotyped for more than 10,000 single nucleotide polymorphisms (SNP) and the variances due to family, cage and genetic effects were estimated by models based on pedigree information only, aggregate SNP information, and model selection for specific SNP effects.

Results and conclusions

We show that the use of genome-wide SNP information can disentangle confounding factors to estimate genetic variances by separating genetic and non-genetic effects. The estimated variance components using realized relationship were more accurate and less biased, compared to those based on pedigree information only. Models that allow the selection of individual SNP in addition to fitting a relationship matrix are more efficient for traits with a significant dominance variance.     

Drosophilid Assemblages at Different Urbanization Levels in the City of Porto Alegre, State of Rio Grande do Sul, Southern Brazil

The present study analyzed the drosophilid assemblages in different levels of urbanization in the city of Porto Alegre, Rio Grande do Sul, Brazil. Collections were carried out in 2008 in three different environments: a highly urbanized area????Jardim Botanico,?? a forested area with intermediary urbanization????Parque Gabriel Knijnik,?? and in a relatively well-preserved forested area, although threatened by the urban growth????Morro Santana.?? In Jardim Botanico, 36 species belonging to four genera were found, with high abundance of exotic species as Drosophila simulans Sturtevant and Zaprionus indianus (Gupta). In Parque Gabriel Knijnik, 33 species that belonged to four genera were found, with higher abundances of native species belonging to the Drosophila tripunctata species group and Drosophila willistoni species subgroup, and lower abundance of exotic species. As for Morro Santana, 32 species and three genera were found, with higher abundances of native groups, low representativeness of exotic species, and absence of Zaprionus indianus. The analysis of the Jaccard index showed higher similarity in the species composition between samples collected in summer and autumn, and between samples collected in winter and spring. On the other hand, the Morisita index differentiated Jardim Botanico from the other two studied sites. Our results show that Morro Santana is an important area of native biodiversity, reinforcing, therefore, the inclusion of this area in the project for the creation of an ecological corridor as proposed by the Ministry of the Environment of Brazil.     

The effect of genomic information on optimal contribution selection in livestock breeding programs

Background

Long-term benefits in animal breeding programs require that increases in genetic merit be balanced with the need to maintain diversity (lost due to inbreeding). This can be achieved by using optimal contribution selection. The availability of high-density DNA marker information enables the incorporation of genomic data into optimal contribution selection but this raises the question about how this information affects the balance between genetic merit and diversity.

Methods

The effect of using genomic information in optimal contribution selection was examined based on simulated and real data on dairy bulls. We compared the genetic merit of selected animals at various levels of co-ancestry restrictions when using estimated breeding values based on parent average, genomic or progeny test information. Furthermore, we estimated the proportion of variation in estimated breeding values that is due to within-family differences.

Results

Optimal selection on genomic estimated breeding values increased genetic gain. Genetic merit was further increased using genomic rather than pedigree-based measures of co-ancestry under an inbreeding restriction policy. Using genomic instead of pedigree relationships to restrict inbreeding had a significant effect only when the population consisted of many large full-sib families; with a half-sib family structure, no difference was observed. In real data from dairy bulls, optimal contribution selection based on genomic estimated breeding values allowed for additional improvements in genetic merit at low to moderate inbreeding levels. Genomic estimated breeding values were more accurate and showed more within-family variation than parent average breeding values; for genomic estimated breeding values, 30 to 40% of the variation was due to within-family differences. Finally, there was no difference between constraining inbreeding via pedigree or genomic relationships in the real data.

Conclusions

The use of genomic estimated breeding values increased genetic gain in optimal contribution selection. Genomic estimated breeding values were more accurate and showed more within-family variation, which led to higher genetic gains for the same restriction on inbreeding. Using genomic relationships to restrict inbreeding provided no additional gain, except in the case of very large full-sib families.     

A variant of Gyrodactylus mediotorus King,Marcogliese, Forest,McLaughlin and Bentzen, 2013 (Monogenea) identified from weed shiner (Notropis texanus) in Wisconsin portions of the upper Mississippi River

Systematic Parasitology - Gyrodactylus mediotorus King, Marcogliese, Forest, McLaughlin and Bentzen, 2013, previously described from the spottail shiner Notropis hudsonius (Clinton) in the St....     

Intraepithelial lymphocyte immunophenotype: a useful tool in the diagnosis of celiac disease

According to new ESPGHAN guidelines, gluten challenge is considered necessary when there is doubt about the initial diagnosis of celiac disease (CD). The main aim of this study was to quantify intraepithelial lymphocyte (IEL) immunophenotype on celiac patients on gluten-containing diet (GCD) compared to those on gluten-free diet (GFD). Another aim was to evaluate the clinical utility of IELs in the CD diagnosis, especially in selected patients on GFD where diagnostic uncertainty remains. IEL immunophenotype (TCRγδ and NK-like IELs) were studied by flow cytometry in 111 children with CD (81 children with CD on GCD and 30 celiac patients on GFD) and a control group (10 children). Duration of GFD was 5.4 ± 1.6 years. TCRγδ IELs in celiac patients receiving a GCD or GFD were significantly higher (p < 0.001) than in the control group. NK-like IELs in patients receiving a GCD or GFD were significantly lower than in the control group (p < 0.001). We observed a permanent decrease of NK-like IELs and an increment of TCRγδ IELs after following an adequate establishment and compliance of a long-term GFD in celiac patients. Recognition of IELs changes in the intestinal mucosa on celiac patients after long-term establishment of a GFD could constitute a useful tool for CD diagnosis in various situations: in which there is doubt about the initial diagnosis and repeat biopsy is necessary (avoiding the need of gluten challenges), and in those patients with symptoms/signs suggestive of CD who maintain a low gluten diet.     

Complex behaviour by coral-reef fish larvae in open-water and near-reef pelagic environments

We present the first in situ observations of the pelagic larvae of coral-reef fishes feeding, schooling and being preyed upon. In addition, we report on their behavioural interactions with adult and juvenile fishes. Observations on over 500 larvae of over 50 species (mostly from four families) near the end of their pelagic interval were made in both open water (> 1 km offshore) and near-reef environments. Nearly 10% of larvae were seen to feed in open water, but < 1% fed near the reef. Presettlement schooling was observed in five species of four families. We observed no predation upon larvae in open water except near the bottom. Near the reef, 8.5% of larvae were eaten. The main predators near and on the reef were a species of wrasse and lizardfishes. Rates of predation seem to differ among genera of pomacentrids, perhaps related to differences in behaviour when settling. When confronted with adult fishes, which happened largely near the reef, larvae reacted with a limited range of behaviours, including sheltering near the observer, swimming to the surface, slowing or stopping, or swimming offshore. The frequency of these behaviours differed among larvae of three pomacentrid genera. Interactions with reef residents, particularly pomacentrids, were common, and usually involved aggression by the resident toward settling larvae. This may act to discourage settlement during the day when such residents are active. These data show that behaviour of late larvae of coral-reef fishes is complex and can greatly influence survival and recruitment. Further, behaviour differs among taxa, showing that not only are larvae not passive, but also that a generalised behaviour of larvae does not exist.