PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases

The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets

In vivo synergistic interaction of liposome-coencapsulated gentamicin and ceftazidime

Antimicrobial agents may interact synergistically. But to ensure synergy in vivo, the drugs should both be present at the site of infection at sufficiently high concentrations for an adequate period of time. Coencapsulation of the drugs in a drug carrier may ensure parallel tissue distributions. Since liposomes localize preferentially at sites of infection, this mode of drug delivery could, in addition, increase drug concentrations at the focus of infection. The therapeutic efficacy of gentamicin and ceftazidime coencapsulated into liposomes was examined by monitoring survival in a rat model of an acute unilateral pneumonia caused by antibiotic-susceptible and antibiotic-resistant Klebsiella pneumoniae strains. It is shown that administration of gentamicin in combination with ceftazidime in the free form either as single dose or as 5-day treatment resulted in an additive effect on rat survival in both models. In contrast, targeted delivery of liposome-coencapsulated gentamicin and ceftazidime resulted in a synergistic interaction of the antibiotics in both models. Consequently, liposome coencapsulation of gentamicin and ceftazidime allowed both a shorter course of treatment at lower cumulative doses compared with administration of the antibiotics in the free form to obtain complete survival of rats. Liposomal coencapsulation of synergistic antibiotics may open new perspectives in the treatment of severe infections

PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases

The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets

Plant and soil microfaunal biodiversity across the borders between arable and forest ecosystems in a Mediterranean landscape

International audienceThe distribution of organisms across ecosystem borders can be indicative of trophic interactions, food-web dynamics, and the potential for recovery after disturbance. Yet relatively little is known regarding patterns and ecology of belowground organisms across borders. Our hypothesis was that incremental zonation of vegetation and soil properties at the interface between cultivated fields and forests may facilitate the recolonization of a more complex soil faunal assemblage after disturbance ceases. Vegetation, soil characteristics, and soil nematodes (indicators of disturbance) were studied at the interface between arable and natural ecosystems (oak forest and maquis shrubland) in southwestern France. Sampling was along 23-m long transects, at six positions (center and edge of grain fields, both sides of field borders, and bands of shrub and forest vegetation) at four sites. Plant functional groups changed more markedly than species richness. Total soil carbon (C) and nematode biomass were 3.5 and 6 times higher in the forest than in the center of the cultivated fields. The nematode Structure Index gradually increased from fields to forests, along with higher total and labile soil C pools, litter, root C, and root C:N, and more negative root delta N-15. Microbivore nematodes were related to labile and total soil C. Structural equation modeling indicated that nematode predators and prey were both affected by total soil C, but proximity to the forest was important for predators, whereas plant community complexity was important for prey (i.e., microbivorous nematodes). The forested borders had minor effects on zonation of nematode assemblages and soil ecosystem services within the fields, yet woody vegetation may have facilitated recolonization by plants and soil fauna after tillage ceased and probably provided benefits for production of livestock (i.e., shade and erosion reduction) that were not measured. During plant succession, litter C and N apparently decomposed slowly into active forms in the soil, creating habitats for more K-selected, larger-bodied nematodes. Due to less cultivation and higher C inputs during the past 50 years, the more homogeneous landscape may promote more complex soil food webs, but less total agrobiodiversity, compared to the mosaic of diverse ecosystems that occurred in the ancient cultural landscape of the past

PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases

The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets

Health and socioeconomic impact study of European initiatives on the prevention of work-related msds in Europe

Presented in Open Session: Surveillance and prevention policies

Social-ecological and regional adaption of agrobiodiversity management across a global set of research regions

To examine management options for biodiversity in agricultural landscapes, eight research regions were classified into social-ecological domains, using a dataset of indicators of livelihood resources, i.e., capital assets. Potential interventions for biodiversity-based agriculture were then compared among landscapes and domains. The approach combined literature review with expert judgment by researchers working in each landscape. Each landscape was described for land use, rural livelihoods and attitudes of social actors toward biodiversity and intensification of agriculture. Principal components analysis of 40 indicators of natural, human, social, financial and physical capital for the eight landscapes showed a loss of biodiversity associated with high-input agricultural intensification. High levels of natural capital (e.g. indicators of wildland biodiversity conservation and agrobiodiversity for human needs) were positively associated with indicators of human capital, including knowledge of the flora and fauna and knowledge sharing among farmers. Three social-ecological domains were identified across the eight landscapes (Tropical Agriculture-Forest Matrix, Tropical Degrading Agroecosystem, and Temperate High-Input Commodity Agriculture) using hierarchical clustering of the indicator values. Each domain shared a set of interventions for biodiversity-based agriculture and ecological intensification that could also increase food security in the impoverished landscapes. Implementation of interventions differed greatly among the landscapes, e.g. financial capital for new farming practices in the Intensive Agriculture domain vs. developing market value chains in the other domains. This exploratory study suggests that indicators of knowledge systems should receive greater emphasis in the monitoring of biodiversity and ecosystem services, and that inventories of assets at the landscape level can inform adaptive management of agrobiodiversity-based intervention