Occupancy modelling as a new approach to assess supranational trends using opportunistic data: a pilot study for the damselfly Calopteryx splendens

There is limited information available on changes in biodiversity at the European scale, because there is a lack of data from standardised monitoring for most species groups. However, a great number of observations made without a standardised field protocol is available in many countries for many species. Such opportunistic data offer an alternative source of information, but unfortunately such data suffer from non-standardised observation effort and geographical bias. Here we describe a new approach to compiling supranational trends using opportunistic data which adjusts for these two major imperfections. The non-standardised observation effort is dealt with by occupancy modelling, and the unequal geographical distribution of sites by a weighting procedure. The damselfly Calopteryx splendens was chosen as our test species. The data were collected from five countries (Ireland, Great Britain, the Netherlands, Belgium and France), covering the period 1990–2008. We used occupancy models to estimate the annual number of occupied 1 × 1 km sites per country. Occupancy models use presence-absence data, account for imperfect detection of species, and thereby correct for between-year variability in observation effort. The occupancy models were run per country in a Bayesian mode of inference using JAGS. The occupancy estimates per country were then aggregated to assess the supranational trend in the number of occupied 1 × 1 km². To adjust for the unequal geographical distribution of surveyed sites, we weighted the countries according to the number of sites surveyed and the range of the species per country. The distribution of C. splendens has increased significantly in the combined five countries. Our trial demonstrated that a supranational trend in distribution can be derived from opportunistic data, while adjusting for observation effort and geographical bias. This opens new perspectives for international monitoring of biodiversity.     

An evidence-based consensus for the classification of arbuscular mycorrhizal fungi (Glomeromycota)

The publication of a large number of taxon names at all levels within the arbuscular mycorrhizal fungi (Glomeromycota) has resulted in conflicting systematic schemes and generated considerable confusion among biologists working with these important plant symbionts. A group of biologists with more than a century of collective experience in the systematics of Glomeromycota examined all available molecular–phylogenetic evidence within the framework of phylogenetic hypotheses, incorporating morphological characters when they were congruent. This study is the outcome, wherein the classification of Glomeromycota is revised by rejecting some new names on the grounds that they are founded in error and by synonymizing others that, while validly published, are not evidence-based. The proposed “consensus” will provide a framework for additional original research aimed at clarifying the evolutionary history of this important group of symbiotic fungi.     

The architecture of Norway spruce ectomycorrhizae: three-dimensional models of cortical cells, fungal biomass, and interface for potential nutrient exchange

Gathering realistic data on actual fungal biomass in ectomycorrhized fine root systems is still a matter of concern. Thus far, observations on architecture of ectomycorrhizae (ECMs) have been limited to analyses of two-dimensional (2-D) images of tissue sections. This unavoidably causes stereometrical problems that lead to inadequate assumptions about actual size of cells and their arrangement within ECM's functional compartments. Based on extensive morphological investigations of field samples, we modeled the architectural components of an average-sized Norway spruce ECM. In addition to our comprehensive and detailed quantitative data on cell sizes, we studied actual shape and size, in vivo arrangement, and potential nutrient exchange area of plant cortical cells (CCs) using computer-aided three-dimensional (3-D) reconstructions based on semithin serial sections. We extrapolated a factual fungal biomass in ECMs (Hartig net (HN) included) of 1.71 t?ha^?1 FW (0.36 t?ha^?1 DW) for the top 5 cm of soil for an autochthonous, montane, optimum Norway spruce stand in the Tyrolean Alps. The corresponding potential nutrient exchange area in ECMs including main axes of ECM systems, which is defined as the sum of interfaces between plant CCs and the HN, amounts to at least 3.2?×?10⁵?m²?ha^?1. This is the first study that determines the contribution of the HN to the total fungal biomass in ECMs as well as the quantification of its contact area. Our results may stimulate future research on fungal below-ground processes and their impact on the global carbon cycle.     

Heterometallic [AgFe3S4] ferredoxin variants: synthesis, characterization, and the first crystal structure of an engineered heterometallic iron–sulfur protein

Heterometallic [AgFe₃S₄] iron–sulfur clusters assembled in wild-type Pyrococcus furiosus ferredoxin and two variants, D14C and D14H, are characterized. The crystal structure of the [AgFe₃S₄] D14C variant shows that the silver(I) ion is indeed part of the cluster and is coordinated to the thiolate group of residue 14. Cyclic voltammetry shows one redox pair with a reduction potential of +220 mV versus the standard hydrogen electrode which is assigned to the [AgFe₃S₄]^2+/+ couple. The oxidized form of the [AgFe₃S₄] D14C variant is stable in the presence of dioxygen, whereas the oxidized forms of the [AgFe₃S₄] wild type and D14H variants convert to the [Fe₃S₄] ferredoxin form. The monovalent d ¹⁰ silver(I) ion stabilizes the [Fe₃S₄]^+/0 cluster fragment, as opposed to divalent d ¹⁰ metal ions, resulting in more than 0.4 V difference in reduction potentials between the silver(I) and, e.g., zinc(II) heterometallic [MFe₃S₄] ferredoxins. The trend in reduction potentials for the variants containing the [AgFe₃S₄] cluster is wild type ≤ D14C < D14H and shows the same trend as reported for the variants containing the [Fe₃S₄] cluster, but is different from the D14C < D14H < wild type trend reported for the [Fe₄S₄] ferredoxin. The similarity in the reduction potential trend for the variants containing the heterometallic [AgFe₃S₄] cluster and the [Fe₃S₄] cluster can be rationalized in terms of the electrostatic influence of the residue 14 side chains, rather than the dissociation constant of this residue, as is the case for [Fe₄S₄] ferredoxins. The trends in reduction potentials are in line with there being no electronic coupling between the silver(I) ion and the Fe₃S₄ fragment.     

Gene expression modulation and the molecular mechanisms involved in Nelfinavir resistance in Leishmania donovani axenic amastigotes

Drug resistance is a major public health challenge in leishmaniasis chemotherapy, particularly in the case of emerging Leishmania/HIV‐1 co‐infections. We have delineated the mechanism of cell death induced by the HIV‐1 protease inhibitor, Nelfinavir, in the Leishmania parasite. In order to further study Nelfinavir–Leishmania interactions, we selected Nelfinavir‐resistant axenic amastigotes in vitro and characterized them. RNA expression profiling analyses and comparative genomic hybridizations of closely related Leishmania species were used as a screening tool to compare Nelfinavir‐resistant and ‐sensitive parasites in order to identify candidate genes involved in drug resistance. Microarray analyses of Nelfinavir‐resistant and ‐sensitive Leishmania amastigotes suggest that parasites regulate mRNA levels either by modulating gene copy numbers through chromosome aneuploidy, or gene deletion/duplication by homologous recombination. Interestingly, supernumerary chromosomes 6 and 11 in the resistant parasites lead to upregulation of the ABC class of transporters. Transporter assays using radiolabelled Nelfinavir suggest a greater drug accumulation in the resistant parasites and in a time‐dependent manner. Furthermore, high‐resolution electron microscopy and measurements of intracellular polyphosphate levels showed an increased number of cytoplasmic vesicular compartments known as acidocalcisomes in Nelfinavir‐resistant parasites. Together these results suggest that Nelfinavir is rapidly and dramatically sequestered in drug‐induced intracellular vesicles.     

2-(1H-Pyrazol-4-yl)acetic acids as CRTh2 antagonists

High throughput screening identified the pyrazole-4-acetic acid substructure as CRTh2 receptor antagonists. Optimisation of the compounds uncovered a tight SAR but also identified some low nanomolar inhibitors.     

Inducible Arginase 1 Deficiency in Mice Leads to Hyperargininemia and Altered Amino Acid Metabolism

Arginase deficiency is a rare autosomal recessive disorder resulting from a loss of the liver arginase isoform, arginase 1 (ARG1), which is the final step in the urea cycle for detoxifying ammonia. ARG1 deficiency leads to hyperargininemia, characterized by progressive neurological impairment, persistent growth retardation and infrequent episodes of hyperammonemia. Using the Cre/loxP-directed conditional gene knockout system, we generated an inducible Arg1-deficient mouse model by crossing “floxed” Arg1 mice with CreER^T2 mice. The resulting mice (Arg-Cre) die about two weeks after tamoxifen administration regardless of the starting age of inducing the knockout. These treated mice were nearly devoid of Arg1 mRNA, protein and liver arginase activity, and exhibited symptoms of hyperammonemia. Plasma amino acid analysis revealed pronounced hyperargininemia and significant alterations in amino acid and guanidino compound metabolism, including increased citrulline and guanidinoacetic acid. Despite no alteration in ornithine levels, concentrations of other amino acids such as proline and the branched-chain amino acids were reduced. In summary, we have generated and characterized an inducible Arg1-deficient mouse model exhibiting several pathologic manifestations of hyperargininemia. This model should prove useful for exploring potential treatment options of ARG1 deficiency.     

Detection of Anorectal and Cervicovaginal Chlamydia Trachomatis Infections following Azithromycin Treatment: Prospective Cohort Study with Multiple Time-Sequential Measures of rRNA,DNA, Quantitative Load and Symptoms

Background

Determination of Chlamydia trachomatis (Ct) treatment success is hampered by current assessment methods, which involve a single post-treatment measurement only. Therefore, we evaluated Ct detection by applying multiple laboratory measures on time-sequential post-treatment samples.

Methods

A prospective cohort study was established with azithromycin-treated (1000 mg) Ct patients (44 cervicovaginal and 15 anorectal cases). Each patient provided 18 self-taken samples pre-treatment and for 8 weeks post-treatment (response: 96%; 1,016 samples). Samples were tested for 16S rRNA (TMA), bacterial load (quantitative PCR; Chlamydia plasmid DNA) and type (serovar and multilocus sequence typing). Covariates (including behavior, pre-treatment load, anatomic site, symptoms, age, and menstruation) were tested for their potential association with positivity and load at 3–8 weeks using regression analyses controlling for repeated measures.

Findings

By day 9, Ct positivity decreased to 20% and the median load to 0.3 inclusion-forming units (IFU) per ml (pre-treatment: 170 IFU/ml). Of the 35 cases who reported no sex, sex with a treated partner or safe sex with a new partner, 40% had detection, i.e. one or more positive samples from 3–8 weeks (same Ct type over time), indicating possible antimicrobial treatment failure. Cases showed intermittent positive detection and the number of positive samples was higher in anorectal cases than in cervicovaginal cases. The highest observed bacterial load between 3–8 weeks post-treatment was 313 IFU/ml, yet the majority (65%) of positive samples showed a load of ≤2 IFU/ml. Pre-treatment load was found to be associated with later load in anorectal cases.

Conclusions

A single test at 3–8 weeks post-treatment frequently misses Ct. Detection reveals intermittent low loads, with an unknown risk of later complications or transmission. These findings warrant critical re-evaluation of the clinical management of single dose azithromycin-treated Ct patients and fuel the debate on defining treatment failure. Clinicaltrials.gov Identifier: NCT01448876.     

Cenozoic climate change and diversification on the continental shelf and slope: evolution of gastropod diversity in the family Solariellidae (Trochoidea)

Recent expeditions have revealed high levels of biodiversity in the tropical deep‐sea, yet little is known about the age or origin of this biodiversity, and large‐scale molecular studies are still few in number. In this study, we had access to the largest number of solariellid gastropods ever collected for molecular studies, including many rare and unusual taxa. We used a Bayesian chronogram of these deep‐sea gastropods (1) to test the hypothesis that deep‐water communities arose onshore, (2) to determine whether Antarctica acted as a source of diversity for deep‐water communities elsewhere and (3) to determine how factors like global climate change have affected evolution on the continental slope. We show that although fossil data suggest that solariellid gastropods likely arose in a shallow, tropical environment, interpretation of the molecular data is equivocal with respect to the origin of the group. On the other hand, the molecular data clearly show that Antarctic species sampled represent a recent invasion, rather than a relictual ancestral lineage. We also show that an abrupt period of global warming during the Palaeocene Eocene Thermal Maximum (PETM) leaves no molecular record of change in diversification rate in solariellids and that the group radiated before the PETM. Conversely, there is a substantial, although not significant increase in the rate of diversification of a major clade approximately 33.7 Mya, coinciding with a period of global cooling at the Eocene–Oligocene transition. Increased nutrients made available by contemporaneous changes to erosion, ocean circulation, tectonic events and upwelling may explain increased diversification, suggesting that food availability may have been a factor limiting exploitation of deep‐sea habitats. Tectonic events that shaped diversification in reef‐associated taxa and deep‐water squat lobsters in central Indo‐West Pacific were also probably important in the evolution of solariellids during the Oligo‐Miocene.     

Evidence of gene flow between sympatric populations of the Middle East‐Asia Minor 1 and Mediterranean putative species of Bemisia tabaci

Bemisia tabaci is a complex of putative species that exhibit a strong geographical pattern. Crossing experiments have revealed various degrees of reproductive isolation between these nascent species, ranging between fertile first‐generation hybrids (F1) and no F1 at all. However, the relevance of these results under natural conditions is generally not known. The worldwide invasion of the putative species Middle East‐Asia Minor 1 (MEAM1) has caused secondary contacts between allopatric species, which in turn provide an opportunity to detect potential hybrids in nature. A total of 346 female B. tabaci were collected in 2003 and 2005 in the North East of Morocco and assigned to MEAM1 (119), Mediterranean (Med) (225) and a new putative species (2) using mitochondrial cytochrome oxidase (mtCOI) gene sequences. MEAM1 and Med individuals were characterized at seven microsatellite loci. MEAM1 and Med were found to be sympatric in 11 of 12 samples (6 fields/year). As previously reported from Spain, MEAM1 frequency decreased over time. The genetic data are consistent with a recent introduction of MEAM1. A Bayesian clustering analysis (Structure ) distinguished two groups, which were 100% consistent with the mtCOI groups. From several lines of evidence, two individuals were identified as hybrids. Assignment profiles using NewHybrids and allele composition indicated that they were not F1 hybrids. The results are discussed in relation to the secondary endosymbiont infection status determined on a sample of individuals, and the contrasting outcomes of the reported crossing experiments between MEAM1 and Med.