A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA

Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to revise taxonomic concepts and to analyze environmental DNA sequences. However, clustering approaches to delineate molecular operational taxonomic units often rely on arbitrary parameter choices. Also, distance calculation is difficult for highly alignment-ambiguous sequences. Here, we applied a recently described clustering optimization method to highly divergent planktonic foraminifera SSU rDNA sequences. We determined the distance function and the clustering setting that result in the highest agreement with morphological reference data. Alignment-free distance calculation, when adapted to the use with partly non-homologous sequences caused by distinct primer pairs, outperformed multiple sequence alignment. Clustering optimization offers new perspectives for the barcoding of species diversity and for environmental sequencing. It bridges the gap between traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both genetic divergence and given species concepts

Degradation of Bradykinin by Neutral Endopeptidase (EC 3.4.24.11) in Cultured Human Endothelial Cells

Peer Reviewe

Standardisierungswettbewerb zwischen parametrisierbarer Standardsoftware und komponentenbasierten Anwendungssystemen

Standardisierungswettbewerb zwischen parametrisierbarer Standardsoftware und komponentenbasierten Anwendungssystemen / Stefan Volkert ; Bernd Reitwiesner. - In: Information age economy / Hans Ulrich Buhl ... (Hrsg.). - Heidelberg : Physica-Verl., 2001. - S. 667-68

Species Delimitation in Taxonomically Difficult Fungi: The Case of Hymenogaster

False truffles are ecologically important as mycorrhizal partners of trees and evolutionarily highly interesting as the result of a shift from epigeous mushroom-like to underground fruiting bodies. Since its first description by Vittadini in 1831, inappropriate species concepts in the highly diverse false truffle genus Hymenogaster has led to continued confusion, caused by a large variety of prevailing taxonomical opinions.In this study, we reconsidered the species delimitations in Hymenogaster based on a comprehensive collection of Central European taxa comprising more than 140 fruiting bodies from 20 years of field work. The ITS rDNA sequence dataset was subjected to phylogenetic analysis as well as clustering optimization using OPTSIL software.Among distinct species concepts from the literature used to create reference partitions for clustering optimization, the broadest concept resulted in the highest agreement with the ITS data. Our results indicate a highly variable morphology of H. citrinus and H. griseus, most likely linked to environmental influences on the phenology (maturity, habitat, soil type and growing season). In particular, taxa described in the 19(th) century frequently appear as conspecific. Conversely, H. niveus appears as species complex comprising seven cryptic species with almost identical macro- and micromorphology. H. intermedius and H. huthii are described as novel species, each of which with a distinct morphology intermediate between two species complexes. A revised taxonomy for one of the most taxonomically difficult genera of Basidiomycetes is proposed, including an updated identification key. The (semi-)automated selection among species concepts used here is of importance for the revision of taxonomically problematic organism groups in general

Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences

BACKGROUND: Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs) between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called δ value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study. RESULTS: Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. Distances based on the proportion of "matched" HSP length to average genome length were best for tree estimation. Additionally we found that using TBLASTX instead of BLASTN and, particularly, combining TBLASTX and BLASTN leads to a small but significant increase in accuracy. Other factors do not significantly affect the phylogenetic outcome. The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. δ values are found to be a reliable predictor of phylogenetic accuracy. CONCLUSION: Using the most treelike distance matrices, as judged by their δ values, distance methods are able to recover all major plant lineages, and are more in accordance with Apicomplexa organelles being derived from "green" plastids than from plastids of the "red" type. GBDP-like methods can be used to reliably infer phylogenies from different kinds of genomic data. A framework is established to further develop and improve such methods. δ values are a topology-independent tool of general use for the development and assessment of distance methods for phylogenetic inference

Corporate boards and the performance of Asian firms: A meta-analysis

The prevalence of ownership concentration in Asian firms presents a challenge to the influential agency theory-based understanding of the role of corporate boards. In this paper we develop and test hypotheses about board attributes and firm performance that reflect Asian institutional conditions. We present the first meta-analysis of the relationship between board attributes and performance of Asian firms using a varied set of meta-analytical techniques on a database of 86 studies covering nine Asian countries. First, we find that board structure and composition preferences are influenced by the identity of the concentrated owner. Second, consistent with US data, we find very limited evidence of a direct relationship between board attributes and firm financial performance in the Asian context. Third, we find that the relationship between board structure and composition and firm performance is mediated by the revealed strategic preferences of Asian firms specifically by the level of R&D investment

Estudo biológico e comportamental de lagartas de Spodoptera frugiperda visando à produção de Baculovírus spodoptera

A utilização de bioinseticida a base de Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) possui potencial para o controle de Spodoptera frugiperda (Lepidoptera: Noctuidae), porém sua obtenção em larga escala depende da maximização da produção in vivo. Assim, alguns fatores biológicos e comportamentais devem ser estudados para aperfeiçoar a produção de SfMNPV com intuito de disponibilizar um bioinseticida eficiente, economicamente viável e que possa ser usado no manejo de S. frugiperda nos mais diversos sistemas agrícolas. Entre os fatores relacionados ao hospedeiro, a temperatura e a idade para inoculação do vírus são de extrema importância, pois interferem diretamente no ciclo de vida e na replicação viral. O comportamento também deve ser avaliado, para evitar condições de criação do hospedeiro que favoreçam o canibalismo e causa prejuízo na multiplicação in vivo do SfMNPV. Assim, objetivou-se determinar a melhor condição térmica para criar as lagartas e a idade ideal, para inocular e multiplicar o vírus no hospedeiro, bem como, verificar a ocorrência do comportamento canibal em lagartas de S. frugiperda. Os experimentos foram conduzidos no Laboratório de Controle Microbiano de Insetos do Núcleo de Desenvolvimento Científico e Tecnológico em Manejo Fitossanitário de Pragas e Doenças (NUDEMAFI), localizado no Centro de Ciências Agrárias da UFES, em Alegre, Espírito Santo, Brasil. A pesquisa foi desenvolvida em duas etapas, a primeira para determinar a condição térmica e a idade ideais para criar e inocular, respectivamente, o hospedeiro com o vírus, para multiplicação in vivo de SfMNPV. A segunda etapa foi para avaliar o comportamento canibal de lagartas da espécie S. frugiperda criadas a 22, 25 e 31°C, inoculadas com SfMNPV quando com idades de 10, 8 e 4 dias, respectivamente, e mantidas em diferentes densidades populacionais (5, 10, 25 e 50 lagartas por recipiente). A mortalidade diminuiu com o aumento da temperatura e da idade do hospedeiro nas temperaturas de 25, 28 e 31 °C. O aumento na taxa de canibalismo foi 12 diretamente proporcional à densidade populacional quando as lagartas foram criadas a 22 °C, inoculadas aos 10 dias de idade e 25 ºC, inoculadas aos 8 dias e atingiram 63,5 e 62,5%, respectivamente na densidade populacional de 50 lagartas. Mas, quando as lagartas foram criadas a 31ºC e inoculadas com idade de 4 dias, a densidade populacional não afetou o comportamento canibal, taxa média de 24%, inferior aos outros tratamentos com 50 lagartas por recipiente. Demonstrando que é viável para a multiplicação viral, criar lagartas a 31 °C e aos 4 dias de idade inocular o vírus, podendo a partir de então colocar até 50 lagartas por recipiente, o que reduz a mão-de-obra necessária para individualizar as lagartas e otimiza o espaço físico em uma biofábrica. Portanto, se para otimizar o processo produção viral e o serviço em uma biofábrica, é preciso maximizar a produção viral, reduzir o tempo de multiplicação do vírus e o canibalismo entre as lagartas, com ausência de contaminação da criação, a temperatura e idade ideais para criação massal de S. frugiperda e inoculação do vírus nas lagartas, respectivamente, visando produção de baculovírus em larga escala são de 31 ºC e 4 dias