Sequencing refractory regions in bird genomes are hotspots for accelerated protein evolution.

BACKGROUND: Approximately 1000 protein encoding genes common for vertebrates are still unannotated in avian genomes. Are these genes evolutionary lost or are they not yet found for technical reasons? Using genome landscapes as a tool to visualize large-scale regional effects of genome evolution, we reexamined this question. RESULTS: On basis of gene annotation in non-avian vertebrate genomes, we established a list of 15,135 common vertebrate genes. Of these, 1026 were not found in any of eight examined bird genomes. Visualizing regional genome effects by our sliding window approach showed that the majority of these "missing" genes can be clustered to 14 regions of the human reference genome. In these clusters, an additional 1517 genes (often gene fragments) were underrepresented in bird genomes. The clusters of "missing" genes coincided with regions of very high GC content, particularly in avian genomes, making them "hidden" because of incomplete sequencing. Moreover, proteins encoded by genes in these sequencing refractory regions showed signs of accelerated protein evolution. As a proof of principle for this idea we experimentally characterized the mRNA and protein products of four "hidden" bird genes that are crucial for energy homeostasis in skeletal muscle: ALDOA, ENO3, PYGM and SLC2A4. CONCLUSIONS: A least part of the "missing" genes in bird genomes can be attributed to an artifact caused by the difficulty to sequence regions with extreme GC% ("hidden" genes). Biologically, these "hidden" genes are of interest as they encode proteins that evolve more rapidly than the genome wide average. Finally we show that four of these "hidden" genes encode key proteins for energy metabolism in flight muscle.

Higher proportion of G2P[4] rotaviruses in vaccinated hospitalized cases compared with unvaccinated hospitalized cases, despite high vaccine effectiveness against heterotypic G2P[4] rotaviruses.

The overall vaccine effectiveness of the monovalent rotavirus vaccine in an observational, prospective, multicentre, hospital-based case-control study in Belgium (RotaBel) was 90%. However, rotavirus genotype and co-infecting pathogens are important parameters to take into account when assessing vaccine effectiveness. In this study we specifically investigated the effect of rotavirus genotypes and co-infecting pathogens on vaccine effectiveness of the monovalent vaccine. In addition, we also investigated the effect of co-infecting pathogens on disease severity. From February 2008 to June 2010 stool samples of rotavirus gastroenteritis cases of a random sample of 39 Belgian hospitals were collected and subsequently genotyped. Fisher's exact tests were performed to investigate the relationships between rotavirus genotype, co-infecting pathogens and disease severity. The vaccine effectiveness of a full series of the monovalent rotavirus vaccine against hospitalized rotavirus gastroenteritis caused by G1P[8] rotavirus strains was 95% (95% CI 77.5-98.7). Against G2P[4], the vaccine effectiveness was 85% (95% CI: 63.7-93.8). G4P[8]- and G3P[8]-specific vaccine effectiveness was 90% (95% CI 19.2-98.7) and 87% (95% CI -5.2 to 98.4), respectively. A post-hoc analysis showed that the genotype distribution was significantly related to the vaccination status (p <0.001), whereby G2P[4] strains were proportionally more prevalent in vaccinated cases than in unvaccinated cases. No statistical associations were found between co-infection status and vaccination status, Vesikari severity score or rotavirus genotype. The high vaccine effectiveness against the individual genotypes implies robust protection of the monovalent rotavirus vaccine against hospitalized rotavirus gastroenteritis caused by the major human rotavirus genotypes. The prevalence of G2P[4] requires continued monitoring.

Clinical and economic analysis of antimicrobial therapy of chronic obstructive pulmonary disease exacerbations.

The aim of the study was to analyse the clinical and economic indicators of the treatment of acute exacerbations of chronic obstructive pulmonary disease (COPD). The study focused specifically on antimicrobial therapy and the use of fluoroquinolones in the management of exacerbations. Data on the consumption of antibiotics to treat exacerbations in ambulatory care were derived from IMS Health. Also, an observational, retrospective analysis was carried out of patients who entered the clinical pathway for COPD exacerbations in University Hospitals Leuven. IMS Health data showed that there is a trend towards the increasing use of broad-spectrum penicillins and fluoroquinolones, and decreasing use of tetracyclines in the treatment of COPD exacerbations in ambulatory care in Belgium in the first half of the 2000s. The observational analysis enrolled 267 patients who were hospitalised between October 2000 and October 2005 to manage 359 exacerbations according to the clinical pathway. Median length of stay per exacerbation amounted to 10 days. Mean quality of life associated with an exacerbation was 74 using the Chronic Respiratory Disease Questionnaire. Median costs of hospital treatment amounted to euro5514 (third-party payer reimbursement and patient co-payment) per exacerbation. Treatment costs were driven by hospital stay (75% of total costs), diagnostic and laboratory tests (20%) and medication (5%). Antibiotics played a role in the hospital management of 75% of exacerbations. Fluoroquinolones were used to treat more severe exacerbations. Treatment of acute exacerbations of COPD imposes a significant clinical and economic burden on patients, the healthcare system and the society.

[St. Mary's Thistle: an overview]. / Le Chardon Marie: un aperçu.

St. Marys Thistle has been approved for registration as a regular medicine in Belgium. The hepatotropic properties of this plant are rather difficult to evaluate objectively. Mortality rate in case of life-threatening hepatic diseases is the most objective parameter. Legalon is the only drug registered in Belgium. It has a prescription only status. The plant Silybum marianum is a thistle and as a consequence belongs to the Compositae. There is a limited production of St.-Marys Thistle in Pajottenland, west of Brussels. The seeds are exported to Italy in order to extract silymarine, a mixture of flavonolignanes with antioxidant properties. Silymarine has been tested in living animals deliberately intoxicated with mushroom toxins, medicines, heavy metals or toxic organic solvents. Preventive as well as curative activity has been confirmed. Silymarine accumulates in the liver, which is also the target organ in therapy. Silymarine improves the prognosis after accidental ingestion of the toxic Amanita phalloides. Patients infected with hepatitis B and C might benefit from Silymarine, but more data have to be generated. Silymarine given to patients with liver damages by alcohol lowers the death toll. The drug has a general safety pattern comparable to placebo.

Antimalarial activity of Ajuga remota Benth (Labiatae) and Caesalpinia volkensii Harms (Caesalpiniaceae): in vitro confirmation of ethnopharmacological use.

Field trips to herbalists' practices in an area about 200 miles around Nairobi (Kenya) enabled us to make a list of medicinal plant species preferentially used to treat malaria. Ajuga remota and Caesalpinia volkensii were further investigated as being the most frequently used species. Aqueous decoctions, ethanol macerates, and petroleum ether, methanol and water Soxhlet extracts of these plants were further tested for their in vitro antimalarial properties in a chloroquine sensitive (FCA/20GHA) and resistant (W2) strain of Plasmodium falciparum. The activity was assessed by the parasite lactate dehydrogenase (pLDH) assay method. There was a concentration-dependent inhibition by the vegetal extracts of both plants. The IC(50) of the most active A. remota extract (ethanol macerate) was 55 and 57 microg/ml against FCA/20GHA and W2, respectively. For C. volkensii, it was the Soxhlet-water extract which was most active against FCA/20GHA with an IC(50) of 404 microg/ml while the petroleum ether extract exhibited the most activity against W2 with an IC(50) of 250 microg/ml. Further phytochemical work is being done in order to identify the active principles.