Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans

Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos in two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 million years ago. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 million years. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guianan shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.Fil: Gibb, Gillian C.. Universite de Montpellier; Francia. Massey Universit; Nueva ZelandaFil: Condamine, Fabien L.. University of Gothenburg; Suecia. Universite de Montpellier; Francia. University of Alberta; CanadáFil: Kuch, Melanie. McMaster University; CanadáFil: Enk, Jacob. McMaster University; CanadáFil: Moraes Barros, Nadia. Universidade Do Porto; Portugal. Universidade de Sao Paulo; BrasilFil: Superina, Mariella. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Poinar, Hendrik N.. McMaster University; CanadáFil: Delsuc, Frederic. Universite de Montpellier; Franci

KM3NeT:a large underwater neutrino telescope in the Mediterranean Sea

High energy neutrinos produced in astrophysical processes will allow for a new way of studying the universe. In order to detect the expected flux of high energy neutrinos from specific astrophysical sources, neutrino telescopes of a scale of a km^3 of water will be needed. A Northern Hemisphere detector is being proposed to be sited in a deep area of the Mediterranean Sea. This detector will provide complimentary sky coverage to the IceCube detector being built at the South Pole. The three neutrino telescope projects in the Mediterranean (ANTARES, NEMO and NESTOR) are partners in an effort to design, and build such a km^3 size neutrino telescope, the KM3NeT. The EU is funding a 3-year Design Study; the status of the Design Study is presented and some technical issues are discussed.Comment: 4 pages, 3 figures, Prepared for the 10th International Conference on Astroparticle and Underground Physics (TAUP 2007), Sendai, Japan, 11-15 Sep 200

theoretical and experimental results for Co-OEP on Ni(100)

Metal octaethylporphyrins (M-OEP), M-N4C20H4(C2H5)8, adsorbed at a metallic substrate are promising candidates to provide spin dependent electric transport. Despite these systems having been studied extensively by experiment, details of the adsorbate geometry and surface binding are still unclear. We have carried out density functional theory calculations for cobalt octaethyl porphyrin (Co-OEP) adsorbate at clean and oxygen-covered Ni(100) surfaces as well as for the free Co-OEP molecule where equilibrium structures were obtained by corresponding energy optimizations. These geometries were then used in calculations of Co-OEP carbon and nitrogen 1s core excitations yielding theoretical excitation spectra to be compared with corresponding K-edge x-ray absorption fine structure (NEXAFS) measurements. The experimental NEXAFS spectra near the carbon K-edge of Co-OEP bulk material show large intensity close to the ionization threshold and a triple-peak structure at lower energies, which can be reproduced by the calculations on free Co-OEP. The experimental nitrogen K-edge spectra of adsorbed Co-OEP layers exhibit always a double-peak structure below ionization threshold, independent of the layer thickness. The peaks are shifted slightly and their separation varies with adsorbate-substrate distance. This can be explained by hybridization of N 2p with corresponding 3d contributions of the Ni substrate in the excited final state orbitals as a result of adsorbate-substrate binding via N–Ni bond formation

Iron porphyrin molecules on Cu(001): Influence of adlayers and ligands on the magnetic properties

The structural and magnetic properties of Fe octaethylporphyrin (OEP) molecules on Cu(001) have been investigated by means of density functional theory (DFT) methods and X-ray absorption spectroscopy. The molecules have been adsorbed on the bare metal surface and on an oxygen-covered surface, which shows a $\sqrt{2}\times2\sqrt{2}R45^{\circ}$ reconstruction. In order to allow for a direct comparison between magnetic moments obtained from sum-rule analysis and DFT we calculate the dipolar term $7$, which is also important in view of the magnetic anisotropy of the molecule. The measured X-ray magnetic circular dichroism shows a strong dependence on the photon incidence angle, which we could relate to a huge value of $7$, e.g. on Cu(001) $7$ amounts to -2.07\,\mbo{} for normal incidence leading to a reduction of the effective spin moment $m_s + 7$. Calculations have also been performed to study the influence of possible ligands such as Cl and O atoms on the magnetic properties of the molecule and the interaction between molecule and surface, because the experimental spectra display a clear dependence on the ligand, which is used to stabilize the molecule in the gas phase. Both types of ligands weaken the hybridization between surface and porphyrin molecule and change the magnetic spin state of the molecule, but the changes in the X-ray absorption are clearly related to residual Cl ligands.Comment: 17 figures, full articl

Novel conopeptides of the I-superfamily occur in several clades of cone snails

The I-superfamily of conotoxins represents a new class of peptides in the venom of some Conus species. These toxins are characterized by four disulfide bridges and inhibit or modify ion channels of nerve cells. When testing venoms from 11 Conus species for a functional characterization, blocking activity on potassium channels (like Kv1.1 and Kv1.3 channels, but not Kv1.2 channels) was detected in the venom of Conus capitaneus, Conus miles, Conus vexillum and Conus virgo. Analysis at the cDNA level of these venoms using primers designed according to the amino acid sequence of a potassium channel blocking toxin (ViTx) from C. virgo confirmed the presence of structurally homologous peptides in these venoms. Moreover, peptides belonging to the I-superfamily, but with divergent amino acid sequences, were found in Conus striatus and Conus imperialis. In all cases, the sequences of the precursors' prepro-regions exhibited high conservation, whereas the sequences of the mature peptides ranged from almost identical to highly divergent between species. We then performed phylogenetic analyses of new and published mitochondrial 16S rDNA sequences representing 104 haplotypes from these and numerous other Conus species, using Bayesian, maximum-likelihood, maximum-parsimony and neighbor-joining methods of inference. Cone snails known to possess I-superfamily toxins were assigned to five different major clades in all of the resulting gene trees. Moreover, I-superfamily conopeptides were detected both in vermivorous and piscivorous species of Conus, thus demonstrating the widespread presence of such toxins in this speciose genus beyond evolutionary and ecological groups

Ferromagnetic coupling of mononuclear Fe centers in a self-assembled metal-organic network on Au(111)

The magnetic state and magnetic coupling of individual atoms in nanoscale structures relies on a delicate balance between different interactions with the atomic-scale surrounding. Using scanning tunneling microscopy, we resolve the self-assembled formation of highly ordered bilayer structures of Fe atoms and organic linker molecules (T4PT) when deposited on a Au(111) surface. The Fe atoms are encaged in a three-dimensional coordination motif by three T4PT molecules in the surface plane and an additional T4PT unit on top. Within this crystal field, the Fe atoms retain a magnetic ground state with easy-axis anisotropy, as evidenced by X-ray absorption spectroscopy and X-ray magnetic circular dichroism. The magnetization curves reveal the existence of ferromagnetic coupling between the Fe centers

Interplay between magnetic anisotropy and interlayer coupling in nanosecond magnetization reversal of spin-valve trilayers

The influence of magnetic anisotropy on nanosecond magnetization reversal in coupled FeNi/Cu/Co trilayers was studied using a photoelectron emission microscope combined with x-ray magnetic circular dicroism. In quasi-isotropic samples the reversal of the soft FeNi layer is determined by domain wall pinning that leads to the formation of small and irregular domains. In samples with uniaxial magnetic anisotropy, the domains are larger and the influence of local interlayer coupling dominates the domain structure and the reversal of the FeNi layer

Temperature-induced sign change of the magnetic interlayer coupling in Ni/Ni25Mn75/Ni trilayers on Cu3Au(001)

We investigated the magnetic interlayer coupling between two ferromagnetic (FM) Ni layers through an antiferromagnetic (AFM) Ni 25Mn75 layer and the influence of this coupling on the exchange bias phenomenon. The interlayer coupling energy of an epitaxial trilayer of 14 atomic monolayers (ML) Ni/45 ML Ni 25Mn75/16 ML Ni on Cu3Au(001) was extracted from minor-loop magnetization measurements using in-situ magneto-optical Kerr effect. The interlayer coupling changes from ferromagnetic to antiferromagnetic when the temperature is increased above 300 K. This sign change is interpreted as the result of the competition between an antiparallel Ruderman-Kittel-Kasuya-Yosida (RKKY)-type interlayer coupling, which dominates at high temperature, and a stronger direct exchange coupling across the AFM layer, which is present only below the Néel temperature of the AFM layer

Magnetic coupling of porphyrin molecules through graphene

Graphene is expected to complement todays Si-based information technology. In particular, magnetic molecules in contact with graphene constitute a tantalizing approach towards organic spin electronics because of the reduced conductivity mismatch at the interface. In such a system a bit is represented by a single molecular magnetic moment, which must be stabilized against thermal fluctuations. Here, we show in a combined experimental and theoretical study that the moments of paramagnetic Co-octaethylporphyrin (CoOEP) molecules on graphene can be aligned by a remarkable antiferromagnetic coupling to a Ni substrate underneath the graphene. This coupling is mediated via the \pi\ electronic system of graphene, while no covalent bonds between the molecule and the substrate are established.Comment: 27 pages, 12 figures, Accepted at Adv. Mate

physicochemical properties in the crystalline bulk and in thin films deposited from the gas phase

Four analogues of the spin-crossover complex [Fe(H2Bpz2)2(phen)] (H2Bpz2 = dihydrobis(pyrazolyl)borate; 2) containing functionalized 1,10-phenanthroline (phen) ligands have been prepared; i.e., [Fe(H2Bpz2)2(L)], L = 4-methyl-1,10-phenanthroline (3), 5-chloro-1,10-phenanthroline (4), 4,7-dichloro-1,10-phenanthroline (5), and 4,7-dimethyl-1,10-phenanthroline (6). The systems are investigated by magnetic susceptibility measurements and a range of spectroscopies in the solid state and in thin films obtained by physical vapour deposition (PVD). Thermal as well as light-induced SCO behaviour is observed for 3–6 in the films. By contrast, thermal SCO in the solid state occurs only for 3 and 4 but is absent for 5 and 6. These findings are discussed in the light of cooperative and intermolecular interactions