Phylogenetic classification of Eudorylini (Diptera: Pipunculidae)

The phylogenetic relationships of members of Eudorylini (Diptera: Pipunculidae: Pipunculinae) were explored. Two hundred and fifty-seven species of Eudorylini from all biogeographical regions and all known genera were examined. Sixty species were included in an exemplar-based phylogeny for the tribe. Two new genera are described, Clistoabdominalis and Dasydorylas. The identity of Eudorylas Aczél, the type genus for Eudorylini, has been obscure since its inception. The genus is re-diagnosed and a proposal to stabilize the genus and tribal names is discussed. An illustrated key to the genera of Pipunculidae is presented and all Eudorylini genera are diagnosed. Numerous new generic synonyms are proposed. Moriparia nigripennis Kozánek & Kwon is preoccupied by Congomyia nigripennis Hardy when both are transferred to Claraeola, so Cla. koreana Skevington is proposed as a new name for Mo. nigripennis.

A classification of subantarctic Heard Island vegetation

The vascular and bryophyte floras of subantarctic Heard Island were classified using cluster analysis into six vegetation communities: Open Cushion Carpet, Mossy Feldmark, Wet Mixed Herbfield, Coastal Biotic Vegetation, Saltspray Vegetation, and Closed Cushion Carpet. Multidimensional scaling indicated that the vegetation communities were not well delineated but were continua. Discriminant analysis and a classification tree identified altitude, wind, peat depth, bryophyte cover and extent of bare ground, and particle size as discriminating variables. The combination of small area, glaciation, and harsh climate has resulted in reduced vegetation variety in comparison to those subantarctic islands north of the Antarctic Polar Front Zone. Some of the functional groups and vegetation communities found on warmer subantarctic islands are not present on Heard Island, notably ferns and sedges and fernbrakes and extensive mires, respectively.

Phylogeny and classification of the Digenea (Platyhelminthes : Trematoda)

Complete small subunit ribosomal RNA gene (ssrDNA) and partial (D1-D3) large subunit ribosomal RNA gene (lsrDNA) sequences were used to estimate the phylogeny of the Digenea via maximum parsimony and Bayesian inference. Here we contribute 80 new ssrDNA and 124 new lsrDNA sequences. Fully complementary data sets of the two genes were assembled from newly generated and previously published sequences and comprised 163 digenean taxa representing 77 nominal families and seven aspidogastrean outgroup taxa representing three families. Analyses were conducted on the genes independently as well as combined and separate analyses including only the higher plagiorchiidan taxa were performed using a reduced-taxon alignment including additional characters that could not be otherwise unambiguously aligned. The combined data analyses yielded the most strongly supported results and differences between the two methods of analysis were primarily in their degree of resolution. The Bayesian analysis including all taxa and characters, and incorporating a model of nucleotide substitution (general-time-reversible with among-site rate heterogeneity), was considered the best estimate of the phylogeny and was used to evaluate their classification and evolution. In broad terms, the Digenea forms a dichotomy that is split between a lineage leading to the Brachylaimoidea, Diplostomoidea and Schistosomatoidea (collectively the Diplostomida nomen novum (nom. nov.)) and the remainder of the Digenea (the Plagiorchiida), in which the Bivesiculata nom. nov. and Transversotremata nom. nov. form the two most basal lineages, followed by the Hemiurata. The remainder of the Plagiorchiida forms a large number of independent lineages leading to the crown clade Xiphidiata nom. nov. that comprises the Allocreadioidea, Gorgoderoidea, Microphalloidea and Plagiorchioidea, which are united by the presence of a penetrating stylet in their cercariae. Although a majority of families and to a lesser degree, superfamilies are supported as currently defined, the traditional divisions of the Echinostomida, Plagiorchiida and Strigeida were found to comprise non-natural assemblages. Therefore, the membership of established higher taxa are emended, new taxa erected and a revised, phylogenetically based classification proposed and discussed in light of ontogeny, morphology and taxonomic history. (C) 2003 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All rights reserved.

Topological side-chain classification of beta-turns: Ideal motifs for peptidomimetic development

beta-turns are important topological motifs for biological recognition of proteins and peptides. Organic molecules that sample the side chain positions of beta-turns have shown broad binding capacity to multiple different receptors, for example benzodiazepines. beta-turns have traditionally been classified into various types based on the backbone dihedral angles (phi 2, psi 2, phi 3 and psi 3). Indeed, 57-68% of beta-turns are currently classified into 8 different backbone families (Type I, Type II, Type I', Type II', Type VIII, Type VIa1, Type VIa2 and Type VIb and Type IV which represents unclassified beta-turns). Although this classification of beta-turns has been useful, the resulting beta-turn types are not ideal for the design of beta-turn mimetics as they do not reflect topological features of the recognition elements, the side chains. To overcome this, we have extracted beta-turns from a data set of non-homologous and high-resolution protein crystal structures. The side chain positions, as defined by C-alpha-C-beta vectors, of these turns have been clustered using the kth nearest neighbor clustering and filtered nearest centroid sorting algorithms. Nine clusters were obtained that cluster 90% of the data, and the average intra-cluster RMSD of the four C-alpha-C-beta vectors is 0.36. The nine clusters therefore represent the topology of the side chain scaffold architecture of the vast majority of beta-turns. The mean structures of the nine clusters are useful for the development of beta-turn mimetics and as biological descriptors for focusing combinatorial chemistry towards biologically relevant topological space.

Normal and anomalous classification of category exemplars in schizophrenia

Background Schizophrenia has been associated with semantic memory impairment and previous studies report a difficulty in accessing semantic category exemplars (Moelter et al. 2005 Schizophr Res 78:209–217). The anterior temporal cortex (ATC) has been implicated in the representation of semantic knowledge (Rogers et al. 2004 Psychol Rev 111(1):205–235). We conducted a high-field (4T) fMRI study with the Category Judgment and Substitution Task (CJAST), an analogue of the Hayling test. We hypothesised that differential activation of the temporal lobe would be observed in schizophrenia patients versus controls. Methods Eight schizophrenia patients (7M : 1F) and eight matched controls performed the CJAST, involving a randomised series of 55 common nouns (from five semantic categories) across three conditions: semantic categorisation, anomalous categorisation and word reading. High-resolution 3D T1-weighted images and GE EPI with BOLD contrast and sparse temporal sampling were acquired on a 4T Bruker MedSpec system. Image processing and analyses were performed with SPM2. Results Differential activation in the left ATC was found for anomalous categorisation relative to category judgment, in patients versus controls. Conclusions We examined semantic memory deficits in schizophrenia using a novel fMRI task. Since the ATC corresponds to an area involved in accessing abstract semantic representations (Moelter et al. 2005), these results suggest schizophrenia patients utilise the same neural network as healthy controls, however it is compromised in the patients and the different ATC activity might be attributable to weakening of category-to-category associations.

The mouse secretome: functional classification of the proteins secreted into the extracellular environment

We have developed a computational strategy to identify the set of soluble proteins secreted into the extracellular environment of a cell. Within the protein sequences predominantly derived from the RIKEN representative transcript and protein set, we identified 2033 unique soluble proteins that are potentially secreted from the cell. These proteins contain a signal peptide required for entry into the secretory pathway and lack any transmembrane domains or intracellular localization signals. This class of proteins, which we have termed the mouse secretome, included >500 novel proteins and 92 proteins

Classification of perinatal deaths: Development of the Australian and New Zealand classifications

Classifications of perinatal deaths have been undertaken for surveillance of causes of death, but also for auditing individual deaths to identify suboptimal care at any level, so that preventive strategies may be implemented. This paper describes the history and development of the paired obstetric and neonatal Perinatal Society of Australia and New Zealand (PSANZ) classifications in the context of other classifications. The PSANZ Perinatal Death Classification is based on obstetric antecedent factors that initiated the sequence of events leading to the death, and was developed largely from the Aberdeen and Whitfield classifications. The PSANZ Neonatal Death Classification is based on fetal and neonatal factors associated with the death. The classifications, accessible on the PSANZ website (http://www.psanz.org), have definitions and guidelines for use, a high level of agreement between classifiers, and are now being used in nearly all Australian states and New Zealand.