BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution

Coffee is one of the world’s most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome.     

Opportunistic feeding responses of the Yellow-legged Gull Larus michahellis to accessibility of refuse dumps

Capsule The gulls adjust their diet composition and diversity according to refuse dump accessibility.

Aims To examine the influence of the accessibility of open-air refuse dumps on the pre-laying diet of the adult Yellow-legged Gull.

Methods We studied six colonies settled on six rocky islands off the southeastern coast of France. A comparative study of the diet of breeding adults from the six colonies was made through pellet analysis (a total of 848 pellets). We determined the main foraging habitat used (refuse dumps, terrestrial habitats, marine habitat) and the number of foraging habitats used simultaneously (one, two or three), from which we deduced the mean diet diversity.

Results Refuse dumps were consistently the main foraging habitat (evidence in 53–74% of pellets) for the six colonies, even when refuse dump accessibility was low. The majority of pellets contained materials from two simultaneous foraging habitats (evidence in 50–64% of pellets). We demonstrated the influence of a gradient of refuse dump accessibility in terms of adjustment of the pre-laying adult's diet. Indeed, high refuse dump accessibility leads to a poorly diversified diet dominated by refuse. In contrast, when refuse dump accessibility is low, Yellow-legged Gulls broaden their trophic niche, with an increased exploitation of alternative foraging habitats, such as terrestrial habitats.

Conclusion These results show the species' opportunistic feeding and high adaptability, two parameters which need to be known to foresee the consequences on population dynamics, feeding and predatory behaviour of a sudden and severe food shortage, for example due to closure of open-air refuse dumps.     

Finding your mate in a seabird colony: contrasting strategies of the Guillemot Uria aalge and King Penguin Aptenodytes patagonicus

Capsule King Penguins recognize their mates by voice, but Guillemots do not need acoustic cues even though their calls show individual variation.

Aims To determine whether the structure of Guillemot calls could allow individual recognition, as with King Penguin, and whether acoustic cues are used to locate mates among a dense mass of conspecifics at a colony.

Methods Observations were made on breeding Guillemots and King Penguins. Calls made by birds returning to their mates were recorded, the signals digitized and the calls analysed. Calls were later played back to the mates of the birds concerned and the effects noted on both them and their neighbours.

Results Both Guillemots and King Penguins emitted calls on return to the breeding site which contained individual signatures and were therefore potentially usable for mate recognition. In King Penguins, auditory recognition was essential for finding a mate, whereas in Guillemots most of the arriving birds located their mate in a dense crowd of conspecifics without the help of acoustic signals. Guillemots could differentiate neighbours from strangers without auditory cues.

Conclusion Calls are essential for the successful identification of mates by King Penguins but not by Guillemots.     

MeCP2 deficiency is associated with impaired microtubule stability

Rett syndrome (RTT) is a neurodevelopmental disorder caused by MECP2 mutations. Previous studies performed on Mecp2-deficient brain showed striking changes in neuronal maturation. We recently showed that MeCP2 deficiency affects microtubule (MT) dynamics in RTT astrocytes. Here, we analyze MT stability in primary fibroblast cultures from patients with RTT syndrome and identify a significant decrease in stability compared to controls. Furthermore, we found that MT stability was reduced both in cells expressing the mutant or the wild-type allele in RTT fibroblasts, suggesting that mutated cells could damage wild-type ones through a non-cell-autonomous pathway. These results suggest that MeCP2 has a stabilizing role on MT dynamics and that its deficiency could lead to impaired MT stability that may explain in part the dendritic abnormalities observed in RTT brains.     

Pollution in mediterranean-climate rivers

This review examines information generated over the past decade on the pollution of rivers in regions with a mediterranean-type climate (med-climate). Pollution has clearly increased in the last 100 years and is correlated with the development of industry, agriculture and human population. Important efforts have been made in some med-climate countries in order to characterise the chemical status of rivers. In addition, the number of chemical substances detectable in mediterranean-climate rivers (med-rivers), as well as the limits of detection, have improved from the development of better analytical methods. New substances detected in rivers are gaining attention. We discuss available knowledge regarding real and potential effects of pollutants on the biota and ecosystems in med-rivers, taking into account natural environmental characteristics of these rivers. The extreme seasonal conditions in med-rivers add to the potential risk because these characteristics can enhance pollutant effects. Efforts and policies to prevent or reduce pollution effects on med-rivers are linked to the knowledge about pollution pressures associated with the degree of economic development. Aquatic communities in med-rivers are more sensitive to pollutants because they are exposed to strong natural and human stressors.     

Synthesis of novel 7-substituted pyrido[2′,3′:4,5]furo[3,2-d]pyrimidin-4-amines and their N-aryl analogues and evaluation of their inhibitory activity against Ser/Thr kinases

The efficient synthesis of 7-substituted pyrido[2′,3′:4,5]furo[3,2-d]pyrimidin-4-amines and their N-aryl analogues is described. 3,5-Dibromopyridine was converted into 3-amino-6-bromofuro[3,2-b]pyridine-2-carbonitrile intermediate which was formylated with DMFDMA. Functionalization at position 7 of the tricyclic scaffold was accomplished, before or after cyclisation step, by palladium-catalyzed Suzuki–Miyaura cross-coupling while the pyrimidin-4-amines and N-aryl counterparts were synthesized by microwave-assisted formamide degradation and Dimroth rearrangement, respectively. The final products were evaluated for their potent inhibition of a series of five Ser/Thr kinases (CDK5/p25, CK1δ/ε, CLK1, DYRK1A, GSK3α/β). Compound 35 showed the best inhibitory activity with an IC₅₀ value of 49 nM and proved to be specific to CLK1 among the panel of tested kinases.     

Determination of the binding mode and interacting amino-acids for dibasic H3 receptor antagonists

Due to its involvement in major CNS functions, the histamine H3 receptor (H3R) is the subject of intensive medicinal chemistry investigation, supported by the range of modern drug discovery tools, such as receptor modeling and ligand docking. Although the receptor models described to date share a majority of common traits, they display discrete alternatives in amino-acid conformation, rendering ligand binding modes quite different. Such variations impede structure-based drug design in the H3R field. In the present study, we used a combination of medicinal chemistry, receptor-guided and ligand-based methods to elucidate the binding mode of antagonists. The approaches converged towards a ligand orientation perpendicular to the membrane plane, bridging Glu206 of the transmembrane helix 5 to acidic amino acids of the extracellular loops. This consensus will help future structure-based drug design for H3R ligands.     

Using DNA-barcoding for sorting out protist species complexes: A case study of the Nebela tincta–collaris–bohemica group (Amoebozoa; Arcellinida,Hyalospheniidae)

Species identification by means of morphology is often problematic in protists. Nebela tincta–collaris–bohemica (Arcellinida) is a species complex of small to medium-sized (ca.100 μm) testate amoebae common in peat bogs and forest soils. The taxonomic validity of characters used to define species within this group is debated and causes confusion in studies of biogeography, and applications in palaeoecology.We examined the relationship between morphological and genetic diversity within this species complex by combined analyses of light microscopy imaging and Cytochrome Oxidase Subunit 1(COI) sequences obtained from the same individual amoeba cells. Our goals were (1) to clarify the taxonomy and the phylogenetic relationships within this group, and (2) to evaluate if individual genotypes corresponded to specific morphotypes and the extent of phenotypic plasticity.We show here that small variations in test morphology that have been often overlooked by traditional taxonomy correspond to distinct haplotypes. We therefore revise the taxonomy of the group. We redefine Nebela tincta (Leidy) Kosakyan et Lara and N. collaris (Ehrenberg 1848) Kosakyan et Gomaa, change N. tincta var. rotunda Penard to N. rotunda (Penard 1890), describe three new species: N. guttata n. sp. Kosakyan et Lara, N. pechorensis n. sp. Kosakyan et Mitchell, and N. aliciae n. sp. Mitchell et Lara.     

Characterization of the host-defense peptides from skin secretions of Merlin's clawed frog Pseudhymenochirus merlini: Insights into phylogenetic relationships among the Pipidae

The family Pipidae comprises the genera Hymenochirus, Pipa, Pseudhymenochirus, Silurana, and Xenopus but phylogenetic relationships within the family are unclear. Peptidomic analysis of norepinephrine-stimulated skin secretions from Pseudhymenochirus merlini Chabanaud, 1920, the single species within the genus Pseudhymenochirus, led to identification of 13 host-defense peptides with antimicrobial activity. Two peptides (hymenochirin-1Pa and -1Pb) show structural similarity to hymenochirin-1B from Hymenochirus boettgeri and eight peptides (hymenochirin-5Pa, -5Pb, -5Pc, -5Pd, -5Pe, -5Pf, 5Pg and -5Ph) are structurally similar to each other and to hymenochirin-5B from H. boettgeri. Two peptides differing by a single amino acid (IKIPSFFRNILKKVGKEAVSLM/I AGALKQS), termed pseudhymenochirin-1Pa and -1Pb, and pseudhymenochirin-2Pa (GIFPIFAKLLGKVIKVASSLISKGRTE) do not resemble host-defense peptides previously isolated from pipid frogs. Hymenochirin-5Pe was the most abundant peptide in the secretions and hymenochirin-1Pa the most potent against Staphylococcus aureus (MIC = 2.5 μM) and Escherichia coli (MIC = 10 μM). The data support a close phylogenetic relationship between Hymenochirus and Pseudhymenochirus that is distinct from the Xenopodinae (Xenopus + Silurana) clade with Pipa sister-group to all other extant pipids.