Sub-micrometer distribution of Fe oxides and organic matter in Podzol horizons

The spatial distribution of soil constituents at the micrometer scale is of great importance to understand processes controlling the formation of micro-aggregates and the stabilization of organic carbon. Here, the spatial distribution of organic and mineral constituents in Podzol horizons is studied by concerted measurements of (i) the content of various forms of Fe, Al, Si and C determined by selective extraction in the fine earth fraction of soil (f < 2 mm); (ii) the elemental composition of the clay fraction (f < 2 um) with lateral resolution using scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDS), and with surface selectivity using X-ray photoelectron spectroscopy (XPS); (iii) the specific surface area (SSA) of fine earth and clay fractions by krypton physisorption. The SSA of the fine earth in illuvial horizons is predominantly due to finely divided Fe oxides, including goethite, characterized by an equivalent particle size of about 10 mu m. Kaolinite platelets of about 2 gm size account for a large volume proportion in the clay fraction but have a minor contribution to SSA. Fe oxides and organic matter (OM) are intimately associated. Heterogeneity at the um scale is created by local variations in the relative amounts of kaolinite and Fe-OM associations. These two kinds of physical entities are in random mixture. Moreover, variation of C/Fe atomic ratios reveals sub-mu m scale heterogeneity. The latter is due to variation in the relative proportion of organic compounds and Fe oxides, indicating that aggregation of nanoparticles, and not only mere adsorption or pore filling, plays a role in these associations. In this regard, our results highlight that OM associated with Fe protects Fe oxides against physical displacement and that part of this associated OM is oxidizable by NaOCl treatment. These findings demonstrate that the concept of OM stabilization through association with Fe must be revisited when considering the sub-mu m scale level because fine Fe oxide particles can be easily dispersed during oxidation of associated carbon. Combination of physical fractionation and microanalysis (e.g. SEM-EDS, vibrational spectroscopy) offer promising perspectives to clarify the relationship between chemical composition and sub-inn scale architecture, and to better understand soil processes

Ancient papillomavirus-host co-speciation in Felidae

The evolutionary rate of feline papillomaviruses is inferred from the phylogenetic analysis of their hosts, providing evidence for long-term virus-host co-speciatio

Earlier initiation of antiretroviral treatment coincides with an initial control of the HIV-1 sub-subtype F1 outbreak among men-having-sex-with-men in Flanders, Belgium

Human immunodeficiency virus type 1 (HIV-1) non-B subtype infections occurred in Belgium since the 1980s, mainly amongst migrants and heterosexuals, whereas subtype B predominated in men-having-sex-with-men (MSM). In the last decade, the diagnosis of F1 sub-subtype in particular has increased substantially, which prompted us to perform a detailed reconstruction of its epidemiological history. To this purpose, the Belgian AIDS Reference Laboratories collected HIV-1 pol sequences from all sub-subtype F1-infected patients for whom genotypic drug resistance testing was requested as part of routine clinical follow-up. This data was complemented with HIV-1 pol sequences from countries with a high burden of F1 infections or a potential role in the global origin of sub-subtype F1. The molecular epidemiology of the Belgian subtype F1 epidemic was investigated using Bayesian phylogenetic inference and transmission dynamics were characterized based on birth-death models. F1 sequences were retained from 297 patients diagnosed and linked to care in Belgium between 1988 and 2015. Phylogenetic inference indicated that among the 297 Belgian F1 sequences, 191 belonged to a monophyletic group that mainly contained sequences from people likely infected in Belgium (OR 26.67, 95% CI 9.59-74.15), diagnosed in Flanders (OR 7.28, 95% CI 4.23-12.53), diagnosed at a recent stage of infection (OR 7.19, 95% CI 2.88-17.95) or declared to be MSM (OR 34.8, 95% CI 16.0-75.6). Together with a Spanish clade, this Belgian clade was embedded in the genetic diversity of Brazilian subtype F1 strains and most probably emerged after one or only a few migration events from Brazil to the European continent before 2002. The origin of the Belgian outbreak was dated back to 2002 (95% higher posterior density 2000-2004) and birth-death models suggested that its extensive growth had been controlled (Re < 1) by 2012, coinciding with a time period where delay in antiretroviral treatment initiation substantially declined. In conclusion, phylogenetic reconstruction of the Belgian HIV-1 sub-subtype F1 epidemic illustrates the introduction and substantial dissemination of viral strains in a geographically restricted risk group that was most likely controlled by effective treatment as prevention.publishersversionpublishe

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences

Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 (HHV8) and human papillomavirus (HPV), we developed a rapid high-throughput-genotyping system. The method involves the alignment of a query sequence with a carefully selected set of pre-defined reference strains, followed by phylogenetic analysis of multiple overlapping segments of the alignment using a sliding window. Each segment of the query sequence is assigned the genotype and sub-genotype of the reference strain with the highest bootstrap (>70%) and bootscanning (>90%) scores. Results from all windows are combined and displayed graphically using color-coded genotypes. The new Virus-Genotyping Tools provide accurate classification of recombinant and non-recombinant viruses and are currently being assessed for their diagnostic utility. They have incorporated into several HIV drug resistance algorithms including the Stanford (http://hivdb.stanford.edu) and two European databases (http://www.umcutrecht.nl/subsite/spread-programme/ and http://www.hivrdb.org.uk/) and have been successfully used to genotype a large number of sequences in these and other databases. The tools are a PHP/JAVA web application and are freely accessible on a number of servers including

Genetic characterization of Yug Bogdanovac virus

We present pyrosequencing data and phylogenetic analysis for the full genome of Yug Bogdanovac virus (YBV), a member of the Vesicular stomatitis virus serogroup of the Rhabdoviridae isolated from a pool of Phlebotomus perfiliewi sandflies collected in Serbia in 1976. YBV shows very low nucleotide identities to other members of the Vesicular stomatitis virus serogroup and does not contain a reading frame for C&prime;/C proteins

COPD stands for complex obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) has extensively been reported as a complex disease affecting patients' health beyond the lungs with a variety of intra- and extrapulmonary components and considerable variability between individuals. This review discusses the assessment of this complexity and underlines the importance of transdisciplinary management programmes addressing the physical, emotional and social health of the individual patient.COPD management is challenging and requires advanced, sophisticated strategies meeting the patient's individual needs. Due to the heterogeneity and complexity of the disease leading to non-linear and consequently poorly predictable treatment responses, multidimensional patient profiling is crucial to identify the right COPD patient for the right treatment. Current methods are often restricted to general, well-known and commonly used assessments neglecting potentially relevant (interactions between) individual, unique "traits" to finally ensure personalised treatment. Dynamic, personalised and holistic approaches are needed to tackle this multifaceted disease and to ensure personalised medicine and value-based healthcare

Liana communities exhibit different species composition, diversity and community structure across forest types in the Congo Basin

Lianas are poorly characterized for central African forests. We quantify variation in liana composition, diversity and community structure in different forest types in the Yangambi Man and Biosphere Reserve, Democratic Republic of Congo. These attributes of liana assemblages were examined in 12 1-ha plots, randomly demarcated within regrowth forest, old growth monodominant forest, old growth mixed forest and old growth edge forest. Using a combination of multivariate and univariate community analyses, we visualize the patterns of these liana assemblage attributes and/or test for their significant differences across forest types. The combined 12 1-ha area contains 2,638 lianas (>= 2 cm diameter) representing 105 species, 49 genera and 22 families. Liana species composition differed significantly across forest types. Taxonomic diversity was higher in old growth mixed forests compared to old growth monodominant and regrowth forests. Trait diversity was higher than expected in the regrowth forest as opposed to the rest of forest types. Similarly, the regrowth forest differed from the rest of forest types in the pattern of liana species ecological traits and diameter frequency distribution. The regrowth forest was also less densely populated in lianas and had lower liana total basal area than the rest of forest types. We speculate that the mechanism of liana competitive exclusion by dominant tree species is mainly responsible for the lower liana species diversity in monodominant compared to mixed forests. We attribute variation in liana community structure between regrowth and old growth forests mostly to short development time of size hierarchies