Ethnocentrism in the Low Countries: A comparative perspective

Contains fulltext : 3361.pdf (publisher's version ) (Open Access)New Community, continued by: Journal of ethnic and migration studies [1369-183X

Pioglitazone Prevents Capillary Rarefaction in Streptozotocin-Diabetic Rats Independently of Glucose Control and Vascular Endothelial Growth Factor Expression

Background/Aims: Reduction of capillary network density occurs early in the development of metabolic syndrome and may be relevant for the precipitation of diabetes. Agonists of the peroxisome proliferator-activated receptor (PPAR)-gamma transcription factor are vasculoprotective, but their capacity for structural preservation of the microcirculation is unclear. Methods: Male Wistar rats were rendered diabetic by streptozotocin and treated with pioglitazone in chow for up to 12 weeks. Capillary density was determined in heart and skeletal muscle after platelet endothelial cell adhesion molecule-1 (PECAM-1) immunostaining. Hallmarks of apoptosis and angiogenesis were determined. Results: Capillary density deteriorated progressively in the presence of hyperglycemia (from 971/mm(2) to 475/mm(2) in quadriceps muscle during 13 weeks). Pioglitazone did not influence plasma glucose, left ventricular weight, or body weight but nearly doubled absolute and relative capillary densities compared to untreated controls (1.2 vs. 0.6 capillaries/myocyte in heart and 1.5 vs. 0.9 capillaries/myocyte in quadriceps muscle) after 13 weeks of diabetes. No antiapoptotic or angiogenic influence of pioglitazone was detected while a reduced expression of hypoxia-inducible factor-3 alpha and PPAR coactivator-1 alpha (PGC-1 alpha) mRNA as well as vascular endothelial growth factor (VEGF) protein possibly occurred as a consequence of improved vascularization. Conclusion: Pioglitazone preserves microvascular structure in diabetes independently of improvements in glycemic control and by a mechanism unrelated to VEGF-mediated angiogenesis. Copyright (C) 2012 S. Karger AG, Base

Comparative genomics of Dothideomycete fungi

Fungi are a diverse group of eukaryotic micro-organisms particularly suited for comparative genomics analyses. Fungi are important to industry, fundamental science and many of them are notorious pathogens of crops, thereby endangering global food supply. Dozens of fungi have been sequenced in the last decade and with the advances of the next generation sequencing, thousands of new genome sequences will become available in coming years. In this thesis I have used bioinformatics tools to study different biological and evolutionary processes in various genomes with a focus on the genomes of the Dothideomycetefungi Cladosporium fulvum, Dothistroma septosporumand Zymoseptoria tritici. Chapter 1introduces the scientific disciplines of mycology and bioinformatics from a historical perspective. It exemplifies a typical whole-genome sequence analysis of a fungal genome, and focusses in particular on structural gene annotation and detection of transposable elements. In addition it shortly reviews the microRNA pathway as known in animal and plants in the context of the putative existence of similar yet subtle different small RNA pathways in other branches of the eukaryotic tree of life. Chapter 2addresses the novel sequenced genomes of the closely related Dothideomyceteplant pathogenic fungi Cladosporium fulvumand Dothistroma septosporum. Remarkably, it revealed occurrence of a surprisingly high similarity at the protein level combined with striking differences at the DNA level, gene repertoire and gene expression. Most noticeably, the genome of C. fulvumappears to be at least twice as large, which is solely attributable to a much larger content in repetitive sequences. Chapter 3describes a novel alignment-based fungal gene prediction method (ABFGP) that is particularly suitable for plastic genomes like those of fungi. It shows excellent performance benchmarked on a dataset of 7,000 unigene-supported gene models from ten different fungi. Applicability of the method was shown by revisiting the annotations of C. fulvumand D. septosporumand of various other fungal genomes from the first-generation sequencing era. Thousands of gene models were revised in each of the gene catalogues, indeed revealing a correlation to the quality of the genome assembly, and to sequencing strategies used in the sequencing centres, highlighting different types of errors in different annotation pipelines. Chapter 4focusses on the unexpected high number of gene models that were identified by ABFGP that align nicely to informant genes, but only upon toleration of frame shifts and in-frame stop-codons. These discordances could represent sequence errors (SEs) and/or disruptive mutations (DMs) that caused these truncated and erroneous gene models. We revisited the same fungal gene catalogues as in chapter 3, confirmed SEs by resequencing and successively removed those, yielding a high-confidence and large dataset of nearly 1,000 pseudogenes caused by DMs. This dataset of fungal pseudogenes, containing genes listed as bona fide genes in current gene catalogues, does not correspond to various observations previously done on fungal pseudogenes. Moreover, the degree of pseudogenization showing up to a ten-fold variation for the lowest versus the highest affected species, is generally higher in species that reproduce asexually compared to those that in addition reproduce sexually. Chapter 5describes explorative genomics and comparative genomics analyses revealing the presence of introner-like elements (ILEs) in various Dothideomycetefungi including Zymoseptoria triticiin which they had not identified yet, although its genome sequence is already publicly available for several years. ILEs combine hallmark intron properties with the apparent capability of multiplying themselves as repetitive sequence. ILEs strongly associate with events of intron gain, thereby delivering in silico proof of their mobility. Phylogenetic analyses at the intra- and inter-species level showed that most ILEs are related and likely share common ancestry. Chapter 6provides additional evidence that ILE multiplication strongly dominates over other types of intron duplication in fungi. The observed high rate of ILE multiplication followed by rapid sequence degeneration led us to hypothesize that multiplication of ILEs has been the major cause and mechanism of intron gain in fungi, and we speculate that this could be generalized to all eukaryotes. Chapter 7describes a new strategy for miRNA hairpin prediction using statistical distributions of observed biological variation of properties (descriptors) of known miRNA hairpins. We show that the method outperforms miRNA prediction by previous, conventional methods that usually apply threshold filtering. Using this method, several novel candidate miRNAs were assigned in the genomes of Caenorhabditis elegansand two human viruses. Although this chapter is not applied on fungi, the study does provide a flexible method to find evidence for existence of a putative miRNA-like pathway in fungi. Chapter 8provides a general discussion on the advent of bioinformatics in mycological research and its implications. It highlights the necessity of a prioriplanning and integration of functional analysis and bioinformatics in order to achieve scientific excellence, and describes possible scenarios for the near future of fungal (comparative) genomics research. Moreover, it discusses the intrinsic error rate in large-scale, automatically inferred datasets and the implications of using and comparing those.</p

Interaction between M-Like Protein and Macrophage Thioredoxin Facilitates Antiphagocytosis for Streptococcus equi ssp. zooepidemicus

Streptococcus equi ssp. zooepidemicus (S. zooepidemicus, S.z) is one of the common pathogens that can cause septicemia, meningitis, and mammitis in domesticated species. M-like protein (SzP) is an important virulence factor of S. zooepidemicus and contributes to bacterial infection and antiphagocytosis. The interaction between SzP of S. zooepidemicus and porcine thioredoxin (TRX) was identified by the yeast two-hybrid and further confirmed by co-immunoprecipitation. SzP interacted with both reduced and the oxidized forms of TRX without inhibiting TRX activity. Membrane anchored SzP was able to recruit TRX to the surface, which would facilitate the antiphagocytosis of the bacteria. Further experiments revealed that TRX regulated the alternative complement pathway by inhibiting C3 convertase activity and associating with factor H (FH). TRX alone inhibited C3 cleavage and C3a production, and the inhibitory effect was additive when FH was also present. TRX inhibited C3 deposition on the bacterial surface when it was recruited by SzP. These new findings indicated that S. zooepidemicus used SzP to recruit TRX and regulated the alternative complement pathways to evade the host immune phagocytosis

Can we rate public support for democracy in a comparable way? Cross-national equivalence of democratic attitudes in the World Value Survey

In this study we examine the cross-cultural equivalence of two scales that measure attitudes toward democracy across 36 countries in the World Value Survey (WVS) 2000. We examine the equivalence of these scales in order to explore if we can meaningfully compare democratic attitudes across countries. Multiple group confirmatory factor analyses (MGCFA) is applied to answer this question. The analyses indicate that the scales may be compared but only to a certain extent and not across all the countries. We close this article by discussing the implications of the findings