Ancient paralogy in the cpDNA trnL-F region in Annonaceae: implications for plant molecular systematics

The plastid trnL-F region has proved useful in molecular phylogenetic studies addressing diverse evolutionary questions from biogeographic history to character evolution in a broad range of plant groups. An important assumption for phylogenetic reconstruction is that data used in combined analyses contain the same phylogenetic signal. The trnL-F region is often used in combined analyses of multiple chloroplast markers. These markers are assumed to contain congruent phylogenetic signal due to lack of recombination. Here we show that trnL-F sequences display a phylogenetic signal conflicting with that of other chloroplast markers in Annonaceae, and we demonstrate that this conflict results from ancient paralogy. TrnL-F copy 2 diverged from trnL-F copy 1 (as used in family-wide phylogenetic analyses) in a direct ancestor of the Annonaceae. Although this divergence dates back 88 million years or more, the exons of both copies appear to be intact. In this case, assuming that (putative) chloroplast markers contain the same phylogenetic signal results in an incorrect topology and an incorrect estimate of ages. Our study demonstrates that researchers should be cautious when interpreting gene phylogenies, irrespective of the genome from which they are presumed to have been sampled.     

Quantitative determination by real-time PCR of four vaginalLactobacillus species,Gardnerella vaginalisandAtopobium vaginaeindicates an inverse relationship betweenL. gasseriandL. iners

Background  

Most studies of the vaginal microflora have been based on culture or on qualitative molecular techniques. Here we applied existing real-time PCR formats forLactobacillus crispatus,L. gasseriandGardnerella vaginalisand developed new formats forAtopobium vaginae,L. inersandL. jenseniito obtain a quantitative non culture-based determination of these species in 71 vaginal samples from 32 pregnant and 28 non-pregnant women aged between 18 and 45 years.     

Stressor‐induced biodiversity gradients: revisiting biodiversity–ecosystem functioning relationships

Biodiversity–ecosystem functioning experiments typically inspect functioning in randomly composed communities, representing broad gradients of taxonomic richness. We tested if the resulting evenness gradients and evenness–functioning relationships reflect those found in communities facing evenness loss caused by anthropogenic stressors. To this end, we exposed marine benthic diatom communities to a series of treatments with the herbicide atrazine, and analysed the relationship between the resulting gradients of evenness and ecosystem functioning (primary production, energy content and sediment stabilization). Atrazine exposure resulted in narrower evenness gradients and steeper evenness–functioning relations than produced by the design of random community assembly. The disproportionately large decrease in functioning following atrazine treatment was related to selective atrazine effects on the species that contributed most to the ecosystem functions considered. Our findings demonstrate that the sensitivity to stress and the contribution to ecosystem functioning at the species level should be both considered to understand biodiversity and ecosystem functioning under anthropogenic stress. Synthesis Biodiversity loss affects ecosystem functioning, yet biodiversity–ecosystem functioning relations have mainly been investigated using communities with random species loss. In nature however, species are lost according to their sensitivity to environmental stress. In the present study, biodiversity loss and biodiversity–ecosystem functioning relations in randomly composed diatom communities were compared to those induced by the pesticide atrazine. Stress exposure resulted in smaller biodiversity loss but steeper decrease in functioning than in randomly composed communities, due to selective atrazine effects on the best performing species. Therefore, species‐specific sensitivity and contribution to ecosystem functioning need to be considered to predict biodiversity and ecosystem functioning under anthropogenic stress.     

Methods for large-scale production of AM fungi: past, present, and future

Many different cultivation techniques and inoculum products of the plant-beneficial arbuscular mycorrhizal (AM) fungi have been developed in the last decades. Soil- and substrate-based production techniques as well as substrate-free culture techniques (hydroponics and aeroponics) and in vitro cultivation methods have all been attempted for the large-scale production of AM fungi. In this review, we describe the principal in vivo and in vitro production methods that have been developed so far. We present the parameters that are critical for optimal production, discuss the advantages and disadvantages of the methods, and highlight their most probable sectors of application.     

Histopathological cutaneous alterations in systemic sclerosis: a clinicopathological study

Introduction  

The aims of the present study were to identify histopathological parameters which are linked to local clinical skin disease at two distinct anatomical sites in systemic sclerosis (SSc) patients with skin involvement (limited cutaneous systemic sclerosis (lcSSc) or diffuse cutaneous systemic sclerosis (dcSSc)) and to determine the sensitivity of SSc specific histological alterations, focusing on SSc patients without clinical skin involvement (limited SSc (lSSc)).     

Toward a Carbon Dioxide Neutral Industrial Park

The industrial park of Herdersbrug (Brugge, Flanders, Belgium) comprises 92 small and medium‐sized enterprises, a waste‐to‐energy incinerator, and a power plant (not included in the study) on its site. To study the carbon dioxide (CO₂) neutrality of the park, we made a park‐wide inventory for 2007 of the CO₂ emissions due to energy consumption (electricity and fossil fuel) and waste incineration, as well as an inventory of the existing renewable electricity and heat generation. The definition of CO₂ neutrality in Flanders only considers CO₂ released as a consequence of consumption or generation of electricity, not the CO₂ emitted when fossil fuel is consumed for heat generation. To further decrease or avoid CO₂ emissions, we project and evaluate measures to increase renewable energy generation. The 21 kilotons (kt) of CO₂ emitted due to electricity consumption are more than compensated by the 25 kt of CO₂ avoided by generation of renewable electricity. Herdersbrug Industrial Park is thus CO₂ neutral, according to the definition of the Flemish government. Only a small fraction (6.6%) of the CO₂ emitted as a consequence of fossil fuel consumption (heat generation) and waste incineration is compensated by existing and projected measures for renewable heat generation. Of the total CO₂ emission (149 kt) due to energy consumption (electricity + heat generation) and waste incineration on the Herdersbrug Industrial Park in 2007, 70.5% is compensated by existing and projected renewable energy generated in the park. Forty‐seven percent of the yearly avoided CO₂ corresponds to renewable energy generated from waste incineration and biomass fermentation.