An integrated nano-scale approach to profile miRNAs in limited clinical samples

Profiling miRNA expression in cells that directly contribute to human disease pathogenesis is likely to aid the discovery of novel drug targets and biomarkers. However, tissue heterogeneity and the limited amount of human diseased tissue available for research purposes present fundamental difficulties that often constrain the scope and potential of such studies. We established a flow cytometry-based method for isolating pure populations of pathogenic T cells from bronchial biopsy samples of asthma patients, and optimized a high-throughput nano-scale qRT-PCR method capable of accurately measuring 96 miRNAs in as little as 100 cells. Comparison of circulating and airway T cells from healthy and asthmatic subjects revealed asthma-associated and tissue-specific miRNA expression patterns. These results establish the feasibility and utility of investigating miRNA expression in small populations of cells involved in asthma pathogenesis, and set a precedent for application of our nano-scale approach in other human diseases. The microarray data from this study (Figure 7) has been submitted to the NCBI Gene Expression Omnibus (GEO; http://ncbi.nlm.nih.gov/geo) under accession no. GSE31030.

Genome-Wide Survey of Pseudogenes in 80 Fully Re-sequenced Arabidopsis thaliana Accessions

Pseudogenes (Ψs), including processed and non-processed Ψs, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life. However, systematic surveys of non-processed Ψs utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of Ψs within 80 fully re-sequenced Arabidopsis thaliana accessions, and 7546 genes, representing ~28% of the genomic annotated open reading frames (ORFs), were found with disruptive mutations in at least one accession. The distribution of these Ψs on chromosomes showed a significantly negative correlation between Ψs/ORFs and their local gene densities, suggesting a higher proportion of Ψs in gene desert regions, e.g. near centromeres. On the other hand, compared with the non-Ψ loci, even the intact coding sequences (CDSs) in the Ψ loci were found to have shorter CDS length, fewer exon number and lower GC content. In addition, a significant functional bias against the null hypothesis was detected in the Ψs mainly involved in responses to environmental stimuli and biotic stress as reported, suggesting that they are likely important for adaptive evolution to rapidly changing environments by pseudogenization to accumulate successive mutations.

The Appellate Body Approach to the Applicability of Article XX GATT In the Light of China - Raw Materials: A Missed Opportunity?

This article attempts to analyse and investigate the implications of the approach to the applicability of Article XX GATT adopted in the recent China – Raw Materials. Using the decision on the non-availability of Article XX defences for violations of China’s WTO-plus commitments on export duties as a backdrop, it scrutinizes the more general, ‘systemic’ approach to the applicability of Article XX exceptions developed by theWTO dispute settlement bodies, and sheds light on the implications of such approach with respect to the relationship between GATT 1994 andWTO obligations arising from different instruments of theWTOAgreement, such as new members’ accession protocols. It also suggests that an exception to this general approach could be envisaged when the fundamental environmental goals protected under Article XX b) and g) are at stake.

A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis

BACKGROUND A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The organism is described with a chemotaxonomic profile and the nearly complete genome sequence obtained through the assembly of short sequence reads. RESULTS Genome sequence analysis and characterization of respiratory quinones, fatty acids, polar lipids, and biochemical phenotype is presented here. Comparison of gene sequences revealed that the most similar species is Pelistega europaea, with BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene, and a similar GC content (~43%) as the organism isolated from the parakeet, DSM 24701 (40%). The closest full genome sequences are those of Bordetella spp. and Taylorella spp. High-throughput sequencing reads from the Illumina-Solexa platform were assembled with the Edena de novo assembler to form 195 contigs comprising the ~2 Mb genome. Genome annotation with RAST, construction of phylogenetic trees with the 16S rDNA (rrs) gene sequence and the rpoB gene, and phylogenetic placement using other highly conserved marker genes with ML Tree all suggest that the bacterial species belongs to the Alcaligenaceae family. Analysis of samples from cages with healthy parakeets suggested that the newly discovered bacterial species is not widespread in parakeet living quarters. CONCLUSIONS Classification of this organism in the current taxonomy system requires the formation of a new genus and species. We designate the new genus Basilea and the new species psittacipulmonis. The type strain of Basilea psittacipulmonis is DSM 24701 (= CIP 110308 T, 16S rDNA gene sequence Genbank accession number JX412111 and GI 406042063).

Anaplasma phagocytophilum DNA amplified from lesional skin of seropositive dogs.

Canine granulocytic anaplasmosis (CGA) is caused by the rickettsial microorganism Anaplasma phagocytophilum. CGA is typically characterized by fever, thrombocytopenia, lethargy, anorexia, arthropy, and other nonspecific clinical signs. Skin lesions have been described in naturally infected lambs and humans. The pathophysiology of CGA is not entirely clear, and the persistence of the organism after the resolution of clinical signs has been described. The aim of the study was to investigate if A. phagocytophilum can be detected in canine lesional skin biopsies from A. phagocytophilum-seropositive dogs with etiologically unclear skin lesions that improved after the treatment with doxycycline. Paraffin-embedded lesional skin biopsies were allocated into separate groups: biopsies from A. phagocytophilum-seropositive dogs responsive to treatment with doxycycline (n=12), biopsies from A. phagocytophilum-seronegative dogs (n=2), and biopsies in which skin lesions histopathologically resembled a tick bite (n=10). The serological status of the latter group was unknown. Histology of the seropositive and seronegative dog skin lesions did not indicate an etiology. DNA was extracted, and a conventional PCR for partial 16S rRNA gene was performed. Anaplasma phagocytophilum DNA was amplified from 4/12 seropositive dogs' skin biopsies. All sequences were 100% identical to the prototype A. phagocytophilum human strain (GenBank accession number U02521). Anaplasma phagocytophilum was not amplified from the 2 seronegative and 10 suspected tick bite dogs. Serum antibody titers of the PCR-positive dogs ranged from 1:200 to 1:2048. Histopathologically, a mild-to-moderate perivascular to interstitial dermatitis composed of a mixed cellular infiltrate and mild-to-moderate edema was seen in all seropositive dogs. In 8/12 seropositive dogs, vascular changes as vasculopathy, fibrinoid necrosis of the vessel walls, and leukocytoclastic changes were observed. In summary, our results support the hypothesis that the persistence of A. phagocytophilum in the skin may be causative for otherwise unexplained skin lesions in seropositive dogs.

The Jurisprudence of the World Trade Organization 2014

In 2014, the Dispute Settlement Body (DSB) of the World Trade Organization (WTO) adopted seven panel reports and six Appellate Body rulings. Two of the cases relate to anti-dumping measures. Three cases, comprising five complaints, are of particular interest and these are summarized and discussed below. China – Rare Earths further refines the relationship between protocols of accession and the general provisions of WTO agreements, in particular the exceptions of Article XX GATT. Recourse to that provision is no longer excluded but depends on a careful case-by-case analysis. While China failed to comply with the conditions for export restrictions, the case reiterates the problem of insufficiently developed disciplines on export restrictions on strategic minerals and other commodities in WTO law. EC – Seals Products is a landmark case for two reasons. Firstly, it limits the application of the Agreement on Technical Barriers to Trade (TBT Agreement) resulting henceforth in a narrow reading of technical regulations. Normative rules prescribing conditions for importation are to be dealt with under the rules of the General Agreement on Tariffs and Trade (GATT) instead. Secondly, the ruling permits recourse to public morals in justifying import restrictions essentially on the basis of process and production methods (PPMs). Meanwhile, the more detailed implications for extraterritorial application of such rules and for the concept of PPMs remain open as these key issues were not raised by the parties to the case. Peru – Agricultural Products adds to the interpretation of the Agreement on Agriculture (AoA), but most importantly, it confirms the existing segregation of WTO law and the law of free trade agreements. The case is of particular importance for Switzerland in its relations with the European Union (EU). The case raises, but does not fully answer, the question whether in a bilateral agreement, Switzerland or the EU can, as a matter of WTO law, lawfully waive their right of lodging complaints against each other under WTO law within the scope of their bilateral agreement, for example the Agreement on Agriculture where such a clause exists.

Capitalisation of Experiences of the Swiss Support to Sustainable Management of Natural Resources (SMNR) in Bulgaria

Following the collapse of the communist regime in 1989, Bulgaria has undergone dramatic political, economic and social transformations. The transition process of the past two decades was characterized by several reforms to support democratisation of the political system and the functioning of a free-market economy. Since 1992, Switzerland has been active in Bulgaria providing assistance to the transition process, with support to Sustainable Management of Natural Resources (SMNR) starting in 1995. The SMNR Capitalisation of Experiences (CapEx) took place between March and September 2007, in the context of SDC phasing out its programmes in Bulgaria by the end of 2007 due to the country’s accession to the European Union. The CapEx exercise has culminated in the identification of 17 lessons learned. In the view of the CapEx team, many of these lessons are relevant for countries that are in the process of joining the EU, facing similar democratisation challenges as Bulgaria. Overall, the Swiss SMNR projects have been effective entry points to support areas that are crucial to democratic transitions, namely participation in public goods management, decentralisation, human capacity development in research and management, and preparation for EU membership. The specificity of the Swiss support stems from an approach that combines a long-term commitment with a clear thematic focus (forestry, biodiversity conservation and organic agriculture). The multistakeholder approach and diversification of support between local, regional and national levels are also important elements that contributed to make a difference in relation to other donors supporting the Bulgarian transition. At the institutional level, there are a number of challenges where the contribution of SMNR activities was only modest, namely improving the legal framework and creating more transparency and accountability, both of which are time and resource-consuming processes. In addition, the emergence of competent and sustainable non-government organisations (NGOs) is a complex process that requires support to membership based organisations, a challenge that was hardly met in the case of SMNR. Finally, reform of government institutions involved in management of natural resources is difficult to achieve via project support only, as it requires leverage and commitment at the level of policy dialogue. At the programme management level, the CapEx team notes that corruption was not systematically addressed in SMNR projects, indicating that more attention should be given to this issue at the outset of any new project.