(R)-2′-Benz­yloxy-5,5′,6,6′,7,7′,8,8′-octa­hydro-1,1′-binaphthyl-2-ol

The mol­ecules of the title compound, C27H28O2, exhibit axial chirality. The planes of the aromatic rings of the tetra­lin ring systems make an angle of 85.72 (11)°. The non-aromatic rings adopt distorted half-chair conformations. In one of them, two C atoms of the four-atom aliphatic chain are disordered over two sites in a 0.75 (2):0.25 (2) ratio. The substituent phenyl ring is also disordered over two positions in a 0.59 (3):0.41 (3) ratio. There are no conventional hydrogen bonds joining the mol­ecules

6β-Chloro-5α-hydr­oxy-20-oxopregnan-3β-yl acetate

The title steroid, C23H35ClO4, is a pregnane derivative prepared by ring opening of the corresponding 5α,6α-ep­oxy steroid with BiCl3. There are two symmetry-independent mol­ecules in the asymmetric unit that show no significant differences concerning bond lengths and angles. The conformation of the six-membered rings in both mol­ecules is close to a chair form, while the five-membered ring adopts an envelope conformation. All rings in both mol­ecules are trans-fused. The mol­ecules are held together by an extensive O—H⋯O hydrogen-bonding network

LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method

<p>Abstract</p> <p>Background</p> <p>Testing for selection is becoming one of the most important steps in the analysis of multilocus population genetics data sets. Existing applications are difficult to use, leaving many non-trivial, error-prone tasks to the user.</p> <p>Results</p> <p>Here we present LOSITAN, a selection detection workbench based on a well evaluated <it>F</it>_<it>st</it>-outlier detection method. LOSITAN greatly facilitates correct approximation of model parameters (e.g., genome-wide average, neutral <it>F</it>_<it>st</it>), provides data import and export functions, iterative contour smoothing and generation of graphics in a easy to use graphical user interface. LOSITAN is able to use modern multi-core processor architectures by locally parallelizing fdist, reducing computation time by half in current dual core machines and with almost linear performance gains in machines with more cores.</p> <p>Conclusion</p> <p>LOSITAN makes selection detection feasible to a much wider range of users, even for large population genomic datasets, by both providing an easy to use interface and essential functionality to complete the whole selection detection process.</p

Structural simplification compromises the potential of common insectivorous bats to provide biocontrol services against the major olive pest Prays oleae

Crop production intensification often leads to the structural simplification of production systems. This structural simplification is expected to have strong impacts on biodiversity and the provisioning of ecosystem services, but information about this topic is scarce. For instance, no information exists for Mediterranean olive (Olea europaea) groves, despite olive farming representing a significant share of the agricultural sector in some European countries. We investigated the impact of in-farm and landscape-level structural simplification on the potential of three common insectivorous bats (i.e., Pipistrellus kuhlii, P. pygmaeus and P. pipistrellus) to provide biocontrol services against one of the most harmful olive pests worldwide, the olive fruit moth Prays oleae. Bats and insect surveys were both carried out in olive groves representing increasing levels of structural simplification and during three sampling seasons (spring, summer and autumn). At grove-level, structural simplification was considered as resulting from reduced planting pattern variability (i.e., tree and row spacing) and tree features (diameter at breast height, height of the trunk and canopy area), while at landscape level was considered as resulting from reduced land-cover types. We found that the Kuhl’s pipistrelle was the most frequently recorded species in all types of olive groves and seasons. Moreover, the activity levels of pipistrelle bats as a whole significantly decreased with the structural simplification of olive groves. The abundance of P. oleae was highest at intermediate levels of structural simplification, irrespective of the season. Forest cover in the surrounding landscape had a significant positive influence on the activity levels of P. kuhlii, and a significant and negative influence on the abundance of P. oleae. Our study demonstrates that structural simplification differentially influences the activity patterns of both insectivorous bats and insect pests within olive groves. Moreover, it suggests that structural simplification may strongly compromise biocontrol services provided by bats on the major olive pest P. oleae

Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring : the need for calibration experiments

Over the last decade, steady advancements have been made in the use of DNA-based methods for detection of species in a wide range of ecosystems. This progress has culminated in molecular monitoring methods being employed for the detection of several species for enforceable management purposes of endangered, invasive, and illegally harvested species worldwide. However, the routine application of DNA-based methods to monitor whole communities (typically a metabarcoding approach) in order to assess the status of ecosystems continues to be limited. In aquatic ecosystems, the limited use is particularly true for macroinvertebrate communities. As part of the DNAqua-Net consortium, a structured discussion was initiated with the aim to identify potential molecular methods for freshwater macroinvertebrate community assessment and identify important knowledge gaps for their routine application. We focus on three complementary DNA sources that can be metabarcoded: 1) DNA from homogenised samples (bulk DNA), 2) DNA extracted from sample preservative (fixative DNA), and 3) environmental DNA (eDNA) from water or sediment. We provide a brief overview of metabarcoding macroinvertebrate communities from each DNA source and identify challenges for their application to routine monitoring. To advance the utilisation of DNA-based monitoring for macroinvertebrates, we propose an experimental design template for a series of methodological calibration tests. The template compares sources of DNA with the goal of identifying the effects of molecular processing steps on precision and accuracy. Furthermore, the same samples will be morphologically analysed, which will enable the benchmarking of molecular to traditional processing approaches. In doing so we hope to highlight pathways for the development of DNA-based methods for the monitoring of freshwater macroinvertebrates

Monitoring frequency influences the analysis of resting behaviour in a forest carnivore

Resting sites are key structures for many mammalian species, which can affect reproduction, survival, population density, and even species persistence in human-modified landscapes. As a consequence, an increasing number of studies has estimated patterns of resting site use by mammals, as well as the processes underlying these patterns, though the impact of sampling design on such estimates remain poorly understood. Here we address this issue empirically, based on data from 21 common genets radiotracked during 28 months in Mediterranean forest landscapes. Daily radiotracking data was thinned to simulate every other day and weekly monitoring frequencies, and then used to evaluate the impact of sampling regime on estimates of resting site use. Results showed that lower monitoring frequencies were associated with major underestimates of the average number of resting sites per animal, and of site reuse rates and sharing frequency, though no effect was detected on the percentage use of resting site types. Monitoring frequency also had a major impact on estimates of environmental effects on resting site selection, with decreasing monitoring frequencies resulting in higher model uncertainty and reduced power to identify significant explanatory variables. Our results suggest that variation in monitoring frequency may have had a strong impact on intra- and interspecific differences in resting site use patterns detected in previous studies. Given the errors and uncertainties associated with low monitoring frequencies, we recommend that daily or at least every other day monitoring should be used whenever possible in studies estimating resting site use patterns by mammals

Metagenomics of the Deep Mediterranean, a Warm Bathypelagic Habitat

BACKGROUND: Metagenomics is emerging as a powerful method to study the function and physiology of the unexplored microbial biosphere, and is causing us to re-evaluate basic precepts of microbial ecology and evolution. Most marine metagenomic analyses have been nearly exclusively devoted to photic waters. METHODOLOGY/PRINCIPAL FINDINGS: We constructed a metagenomic fosmid library from 3,000 m-deep Mediterranean plankton, which is much warmer (approximately 14 degrees C) than waters of similar depth in open oceans (approximately 2 degrees C). We analyzed the library both by phylogenetic screening based on 16S rRNA gene amplification from clone pools and by sequencing both insert extremities of ca. 5,000 fosmids. Genome recruitment strategies showed that the majority of high scoring pairs corresponded to genomes from Rhizobiales within the Alphaproteobacteria, Cenarchaeum symbiosum, Planctomycetes, Acidobacteria, Chloroflexi and Gammaproteobacteria. We have found a community structure similar to that found in the aphotic zone of the Pacific. However, the similarities were significantly higher to the mesopelagic (500-700 m deep) in the Pacific than to the single 4000 m deep sample studied at this location. Metabolic genes were mostly related to catabolism, transport and degradation of complex organic molecules, in agreement with a prevalent heterotrophic lifestyle for deep-sea microbes. However, we observed a high percentage of genes encoding dehydrogenases and, among them, cox genes, suggesting that aerobic carbon monoxide oxidation may be important in the deep ocean as an additional energy source. CONCLUSIONS/SIGNIFICANCE: The comparison of metagenomic libraries from the deep Mediterranean and the Pacific ALOHA water column showed that bathypelagic Mediterranean communities resemble more mesopelagic communities in the Pacific, and suggests that, in the absence of light, temperature is a major stratifying factor in the oceanic water column, overriding pressure at least over 4000 m deep. Several chemolithotrophic metabolic pathways could supplement organic matter degradation in this most depleted habitat

Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon

Abstract Background Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited. Result We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO) terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs) and 3,073 single nucleotide polymorphisms (SNPs) in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but longer than many other dicot plants. Codon usages of melon full-length transcripts were largely similar to those of Arabidopsis coding sequences. Conclusion The collection of melon ESTs generated from full-length enriched and standard cDNA libraries is expected to play significant roles in annotating the melon genome. The ESTs and associated analysis results will be useful resources for gene discovery, functional analysis, marker-assisted breeding of melon and closely related species, comparative genomic studies and for gaining insights into gene expression patterns.This work was supported by Research Grant Award No. IS-4223-09C from BARD, the United States-Israel Binational Agricultural Research and Development Fund, and by SNC Laboratoire ASL, de Ruiter Seeds B.V., Enza Zaden B.V., Gautier Semences S.A., Nunhems B.V., Rijk Zwaan B.V., Sakata Seed Inc, Semillas Fitó S.A., Seminis Vegetable Seeds Inc, Syngenta Seeds B.V., Takii and Company Ltd, Vilmorin and Cie S.A. and Zeraim Gedera Ltd (all of them as part of the support to ICuGI). CC was supported by CNRS ERL 8196.Peer Reviewe