Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo).

BACKGROUND: Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. RESULTS: In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. CONCLUSIONS: The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.

Diet, bite force and skull morphology in the generalist rodent morphotype.

For many vertebrate species, bite force plays an important functional role. Ecological characteristics of a species' niche, such as diet, are often associated with bite force. Previous evidence suggests a biomechanical trade-off between rodents specialized for gnawing, which feed mainly on seeds, and those specialized for chewing, which feed mainly on green vegetation. We tested the hypothesis that gnawers are stronger biters than chewers. We estimated bite force and measured skull and mandible shape and size in 63 genera of a major rodent radiation (the myomorph sigmodontines). Analysis of the influence of diet on bite force and morphology was made in a comparative framework. We then used phylogenetic path analysis to uncover the most probable causal relationships linking diet and bite force. Both granivores (gnawers) and herbivores (chewers) have a similar high bite force, leading us to reject the initial hypothesis. Path analysis reveals that bite force is more likely influenced by diet than the reverse causality. The absence of a trade-off between herbivores and granivores may be associated with the generalist nature of the myomorph condition seen in sigmodontine rodents. Both gnawing and chewing sigmodontines exhibit similar, intermediate phenotypes, at least compared to extreme gnawers (squirrels) and chewers (chinchillas). Only insectivorous rodents appear to be moving towards a different direction in the shape space, through some notable changes in morphology. In terms of diet, natural selection alters bite force through changes in size and shape, indicating that organisms adjust their bite force in tandem with changes in food items.

Environment-Assisted Speed-up of the Field Evolution in Cavity Quantum Electrodynamics.

We measure the quantum speed of the state evolution of the field in a weakly driven optical cavity QED system. To this end, the mode of the electromagnetic field is considered as a quantum system of interest with a preferential coupling to a tunable environment: the atoms. By controlling the environment, i.e., changing the number of atoms coupled to the optical cavity mode, an environment-assisted speed-up is realized: the quantum speed of the state repopulation in the optical cavity increases with the coupling strength between the optical cavity mode and this non-Markovian environment (the number of atoms).

Communication: The electronic structure of matter probed with a single femtosecond hard x-ray pulse.

Physical, biological, and chemical transformations are initiated by changes in the electronic configuration of the species involved. These electronic changes occur on the timescales of attoseconds (10(-18) s) to femtoseconds (10(-15) s) and drive all subsequent electronic reorganization as the system moves to a new equilibrium or quasi-equilibrium state. The ability to detect the dynamics of these electronic changes is crucial for understanding the potential energy surfaces upon which chemical and biological reactions take place. Here, we report on the determination of the electronic structure of matter using a single self-seeded femtosecond x-ray pulse from the Linac Coherent Light Source hard x-ray free electron laser. By measuring the high energy resolution off-resonant spectrum (HEROS), we were able to obtain information about the electronic density of states with a single femtosecond x-ray pulse. We show that the unoccupied electronic states of the scattering atom may be determined on a shot-to-shot basis and that the measured spectral shape is independent of the large intensity fluctuations of the incoming x-ray beam. Moreover, we demonstrate the chemical sensitivity and single-shot capability and limitations of HEROS, which enables the technique to track the electronic structural dynamics in matter on femtosecond time scales, making it an ideal probe technique for time-resolved X-ray experiments.

Two-dimensional structure from random multiparticle X-ray scattering images using cross-correlations.

Knowledge of the structure of biological macromolecules, especially in their native environment, is crucial because of the close structure-function relationship. X-ray small-angle scattering is used to determine the shape of particles in solution, but the achievable resolution is limited owing to averaging over particle orientations. In 1977, Kam proposed to obtain additional structural information from the cross-correlation of the scattering intensities. Here we develop the method in two dimensions, and give a procedure by which the single-particle diffraction pattern is extracted in a model-independent way from the correlations. We demonstrate its application to a large set of synchrotron X-ray scattering images on ensembles of identical, randomly oriented particles of 350 or 200 nm in size. The obtained 15 nm resolution in the reconstructed shape is independent of the number of scatterers. The results are discussed in view of proposed 'snapshot' scattering by molecules in the liquid phase at X-ray free-electron lasers.

Conserving large carnivores: dollars and fence.

Conservationists often advocate for landscape approaches to wildlife management while others argue for physical separation between protected species and human communities, but direct empirical comparisons of these alternatives are scarce. We relate African lion population densities and population trends to contrasting management practices across 42 sites in 11 countries. Lion populations in fenced reserves are significantly closer to their estimated carrying capacities than unfenced populations. Whereas fenced reserves can maintain lions at 80% of their potential densities on annual management budgets of $500 km(-2) , unfenced populations require budgets in excess of $2000 km(-2) to attain half their potential densities. Lions in fenced reserves are primarily limited by density dependence, but lions in unfenced reserves are highly sensitive to human population densities in surrounding communities, and unfenced populations are frequently subjected to density-independent factors. Nearly half the unfenced lion populations may decline to near extinction over the next 20-40 years.

Direct measurement of S-branch N2-H2 Raman linewidths using time-resolved pure rotational coherent anti-Stokes Raman spectroscopy.

S-branch N(2)-H(2) Raman linewidths have been measured in the temperature region 294-1466 K using time-resolved dual-broadband picosecond pure rotational coherent anti-Stokes Raman spectroscopy (RCARS). Data are extracted by mapping the dephasing rates of the CARS signal temporal decay. The J-dependent coherence decays are detected in the time domain by following the individual spectral lines as a function of probe delay. The linewidth data set was employed in spectral fits of N(2) RCARS spectra recorded in binary mixtures of N(2) and H(2) at calibrated temperature conditions up to 661 K using a standard nanosecond RCARS setup. In this region, the set shows a deviation of less than 2% in comparison with thermocouples. The results provide useful knowledge for the applicability of N(2) CARS thermometry on the fuel-side of H(2) diffusion flames.

Beam-induced damage on diffractive hard X-ray optics.

The issue of beam-induced damage on diffractive hard X-ray optics is addressed. For this purpose a systematic study on the radiation damage induced by a high-power X-ray beam is carried out in both ambient and inert atmospheres. Diffraction gratings fabricated by three different techniques are considered: electroplated Au gratings both with and without the polymer mold, and Ir-coated Si gratings. The beam-induced damage is monitored by X-ray diffraction and evaluated using scanning electron microscopy.

Novel opportunities for time-resolved absorption spectroscopy at the X-ray free electron laser.

Time-dependent X-ray Absorption Spectroscopy (XAS) measurements of chemical reaction dynamics have a time resolution which is limited by: (a) the speed and efficiency of the reaction initiation; (b) the duration of the X-ray pulses used for the measurement; and (c) the brightness of the X-ray source. X-Ray Free Electron Lasers (XFEL), which will deliver 20-100 fs pulses of X-rays, with a peak brightness which is 10(10) times that of a synchrotron, will alleviate limitations (b) and (c). Furthermore, by including a synchronized source of UV, visible, IR or THz pump radiation, the XFEL will contribute to the solution of limitation (a). The present article describes the XFEL operating principle and the generic design of an XFEL facility, emphasizing the features of particular interest to the XAS investigator.

Graphene on Ru(0001): a 25 x 25 supercell.

The structure of a single layer of graphene on Ru(0001) has been studied using surface x-ray diffraction. A surprising superstructure containing 1250 carbon atoms has been determined, whereby 25 x 25 graphene unit cells lie on 23 x 23 unit cells of Ru. Each supercell contains 2 x 2 crystallographically inequivalent subcells caused by corrugation. Strong intensity oscillations in the superstructure rods demonstrate that the Ru substrate is also significantly corrugated down to several monolayers and that the bonding between graphene and Ru is strong and cannot be caused by van der Waals bonds. Charge transfer from the Ru substrate to the graphene expands and weakens the C-C bonds, which helps accommodate the in-plane tensile stress. The elucidation of this superstructure provides important information in the potential application of graphene as a template for nanocluster arrays.

Structural basis for the conducting interface between LaAlO3 and SrTiO3.

The complete atomic structure of a five-monolayer film of LaAlO3 on SrTiO3 has been determined for the first time by surface x-ray diffraction in conjunction with the coherent Bragg rod analysis phase-retrieval method and further structural refinement. Cationic mixing at the interface results in dilatory distortions and the formation of metallic La(1-x)SrxTiO3. By invoking electrostatic potential minimization, the ratio of Ti{4+}/Ti{3+} across the interface was determined, from which the lattice dilation could be quantitatively explained using ionic radii considerations. The correctness of this model is supported by density functional theory calculations. Thus, the formation of a quasi-two-dimensional electron gas in this system is explained, based on structural considerations.

Surface of strontium titanate.

We report the first complete determination, using surface x-ray diffraction, of the surface structure of TiO2-terminated SrTiO3(001), both at room temperature in vacuum, and also hot, under typical conditions used for thin film growth. The cold structure consists of a mixture of a (1x1) relaxation and (2x1) and (2x2) reconstructions. The latter disappear over several minutes upon heating. The structures are best modeled by a TiO2-rich surface similar to that proposed by Erdman et al. [Nature (London) 419, 55 (2002).10.1038/nature01010]. Both reconstructions have been shown by density functional theory to be energetically favorable. The calculated (1x1) surface energy is higher, indicating that it may be a disordered mixture of the reconstructions. Atomic displacements are significant down to three unit cells, which may have important implications on possible surface ferroelectric phenomena in SrTiO3.

Energetic surface smoothing of complex metal-oxide thin films.

A novel energetic smoothing mechanism in the growth of complex metal-oxide thin films is reported from in situ kinetic studies of pulsed laser deposition of on , using x-ray reflectivity. Below 50% monolayer coverage, prompt insertion of energetic impinging species into small-diameter islands causes them to break up to form daughter islands. This smoothing mechanism therefore inhibits the formation of large-diameter 2D islands and the seeding of 3D growth. Above 50% coverage, islands begin to coalesce and their breakup is thereby suppressed. The energy of the incident flux is instead rechanneled into enhanced surface diffusion, which leads to an increase in the effective surface temperature of DeltaT approximately 500 K. These results have important implications on optimal conditions for nanoscale device fabrication using these materials.

X-ray diffraction method for the investigation of contacts between solid surfaces.

A coherent X-ray scattering method for investigating the formation of the contact region between two solid surfaces is presented. Diffraction of X-rays from two crossed cylindrical quartz surfaces, coated with Cr and TiO(2), revealed a total contact area of 90 +/- 10 microm. In the so-called Hertz model for two surfaces in non-adhesive contact, this value is directly related to the displacement of the surfaces and the applied external force. Values of 40 +/- 3 nm for the displacement and 24 +/- 3 mN for the force are found. The method is also useful for studying liquids in confinement.

Improved data acquisition in grazing-incidence X-ray scattering experiments using a pixel detector.

The use of an area detector in grazing-incidence X-ray experiments lends many advantages in terms of both speed and reliability. Here a discussion is given of the procedures established using the PILATUS pixel detector developed at the Swiss Light Source for optimizing data acquisition and analysis of surface diffraction data at the Materials Science beamline, especially with regard to reflectivity measurements, crystal truncation and fractional order rods, and grazing-incidence diffraction experiments.

Pancreatitis associated with valproic acid: a review of the literature.

Black box warnings for valproic acid caution clinicians of the potential for fatal hepatotoxicity and teratogenicity. Since 1979, case reports of pancreatitis induced by valproic acid have been published in the medical literature. As a result, pancreatitis was added to the black box warnings for valproic acid. We performed searches of MEDLINE and International Pharmaceutical Abstracts and found valproic acid-induced pancreatitis in 45 patients from 31 published articles. Demographics, clinical characteristics, and outcomes of these patients are summarized. Recommendations for monitoring the potential for pancreatitis to develop in patients receiving valproic acid therapy are described, as are potential mechanisms for inducement of pancreatitis by valproic acid.

The man-eaters with bad teeth.

Two cases of man-eating lions feeding on large numbers of humans (1898, 1991) are discussed. The forensic dental evidence from the lions' remains and eyewitness reports indicate all three lions had serious dental/oral pathology, which may have contributed to their selection of human food over more challenging natural animal prey.

An electrophoretic method to detect cold-induced dissociation of proteins in crude extracts of higher plants.

The phenomenon of cold denaturation has been firmly established recently in several proteins. Some multimeric enzymes from plant origins are believed to dissociate under some circumstances in the cold. To determine the presence and number of soluble, non-membrane-bound protein that undergoes cold-induced dissociation in plants, we have devised a special two-dimensional polyacrylamide gel electrophoretic method using two native gradient gels. Examination of the gel run at 0 degrees C in the second dimension showed the presence of four cold-dissociated proteins running below the diagonal and staining intensely with silver, in the extract of maize leaves. The electrophoretic method described here is expected to be a convenient way to detect cold-induced dissociation of soluble proteins in crude extracts of various tissues. It is also possible to estimate roughly the molecular weights of both the cold-dissociated subunit and the native protein from which it is derived.