A cluster of atypical Yersinia strains with a distinctive 16S rRNA signature

Thirty-eight bacterial isolates from raw milk samples in Queensland, Australia were identified as members of the genus Yersinia on the basis of biochemical profile, ability to hybridize with a genus-specific DNA probe, comparative 16S rDNA sequence analysis, and the presence of characteristic 16S rDNA signature nucleotides which occur in all Yersinia spp. Twenty-five of these isolates reacted with typing sera (O:22 or O:58) of Y. enterocolitica; the remainder were non-typable. None of the isolates displayed any of the phenotypic or genetic virulence-associated characteristics of Y. enterocolitica. Comparative 16S rDNA sequence analysis revealed that members of this group appear to represent a new sub-line within the genus Yersinia, most closely related to Y. frederiksenii hybridization group 2 (unnamed genomospecies 2). This finding was confirmed by DNA hybridization studies which indicated that the strains belonged to the unnamed genomospecies, Yersinia frederiksenii genomospecies 2, which is biochemically indistinguishable from Y. frederiksenii (Y. frederiksenii genomospecies 1). A 23-nucleotide 16S rDNA signature stretch which characterised these strains was identified.     

Direct and Indirect Classification in Clinical Research

We investigate if the use of a priori knowledge allows an improvement of medical decision making. We compare two frameworks of classification – direct and indirect classification – with respect to different classification errors: differential misclassification, observed misclassification and true misclassification. We analyze general behaviors of the classifiers in an artificial example and furthermore as being interested in the diagnosis of early glaucoma we adapt a simulation model of the optic nerve head. Indirect classifiers outperform direct classifiers in certain parameter situations of a Monte‐Carlo study. In summary, we demonstrate that indirect classification provides a flexible framework to improve diagnostic rules by using explicit a priori knowledge in clinical research.     

Sex-specific indicators of landscape use by servals: Consequences of living in fragmented landscapes

The conversion of wetlands and its associated habitat for farming, residential development and commercial purposes has led to many small disconnected patches of native vegetation surrounded by generally inhospitable human altered land uses. Such human interventions pose a serious threat to the survival of wetland dependent indicator species such as the serval (Leptailurus serval) in the Drakensberg Midlands of KwaZulu-Natal, South Africa. To address the effects of habitat fragmentation on serval space use we used GPS fixes of collared individuals for 100 days between May 2013 and January 2014. We tracked five females and eleven male servals with GPS-UHF collars. Fragmentation indices at the class level (wetland, forest with bushland, grassland and cropland) were measured within the collared serval's minimum convex polygon area (MCP) of home range. Serval use points and fragmentation indices were extracted to each sub-landscape unit of 2 km² falling within the MCP home range. The response of serval population to fragmentation indices was analyzed using generalized linear models at three levels: male, female and the overall population. We found that core area of wetland positively explained landscape use by servals. Effects of forest core area, forest proximity and patch richness were important for landscape use by male servals. Male and female serval use declined with increase in complex shapes of forest and grassland, wetland clumpiness for females and overall, and cropland patches for servals overall. Our results showed that wetland is a key determinant for the survival of male and female servals in fragmented landscapes therefore effective conservation of serval population demands adequate viable native habitat.     

A hybrid SOM-SVM approach for the zebrafish gene expression analysis

Microarray technology can be employed to quantitatively measure the expression of thousands of genes in a single experiment. It has become one of the main tools for global gene expression analysis in molecular biology research in recent years. The large amount of expression data generated by this technology makes the study of certain complex biological problems possible, and machine learning methods are expected to play a crucial role in the analysis process. In this paper, we present our results from integrating the self-organizing map （SOM） and the support vector machine （SVM） for the analysis of the various functions of zebrafish genes based on their expression. The most distinctive characteristic of our zebrafish gene expression is that the number of samples of different classes is imbalanced. We discuss how SOM can be used as a data-filtering tool to improve the classification performance of the SVM on this data set.     

Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and Grammitidaceae): exploring aspects of the diversification of epiphytic plants

We explore the phylogeny of the polygrammoid ferns using nucleotide sequences derived from three plastid loci for each of 98 selected species. Our analyses recovered four major monophyletic lineages: the loxogrammoids, two clades consisting of taxa restricted to the Old World, and a largely neotropical clade that also includes the pantropical Grammitidaceae. The loxogrammoid lineage diverges first and is sister to a large clade comprising the three remaining species-rich lineages. One paleotropical clade includes the drynarioid and selligueoid ferns, whereas the second paleotropical clade includes the platycerioids, lepisoroids, microsoroids, and their relatives. The grammitids nest within the neotropical clade, although the sister taxon of this circum-tropic, epiphytic group remains ambiguous. Microsorum and Polypodium, as traditionally defined, were recovered as polyphyletic. The relatively short branch lengths of the deepest clades contrast with the long branch lengths leading to the terminal groups. This suggests that the polygrammoid ferns arose through an old, rapid radiation. Our analysis also reveals that the rate of substitution in the grammitids is remarkably higher relative to other polygrammoids. Disparities in substitution rate may be correlated with one or more features characterizing grammitids, including species richness, chlorophyllous spores, and an extended gametophytic phase.     

Functional analysis and localisation of a delta-class glutathione S-transferase from Sarcoptes scabiei

The mite Sarcoptes scabiei causes sarcoptic mange, or scabies, a disease that affects both animals and humans worldwide. Our interest in S. scabiei led us to further characterise a glutathione S-transferase. This multifunctional enzyme is a target for vaccine and drug development in several parasitic diseases. The S. scabiei glutathione S-transferase open reading frame reported here is 684 nucleotides long and yields a protein with a predicted molecular mass of 26 kDa. Through phylogenetic analysis the enzyme was classified as a delta-class glutathione S-transferase, and our paper is the first to report that delta-class glutathione S-transferases occur in organisms other than insects. The recombinant S. scabiei glutathione S-transferase was expressed in Escherichia coli via three different constructs and purified for biochemical analysis. The S. scabiei glutathione S-transferase was active towards the substrate 1-chloro-2,4-dinitrobenzene, though the positioning of fusion partners influenced the kinetic activity of the enzyme. Polyclonal antibodies raised against S. scabiei glutathione S-transferase specifically localised the enzyme to the integument of the epidermis and cavities surrounding internal organs in adult parasites. However, some minor staining of parasite intestines was observed. No staining was seen in host tissues, nor could we detect any antibody response against S. scabiei glutathione S-transferase in sera from naturally S. scabiei infected dogs or pigs. Additionally, the polyclonal sera raised against recombinant S. scabiei glutathione S-transferase readily detected a protein from mites, corresponding to the predicted size of native glutathione S-transferase.