Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards

Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics. Here, we ask whether convergent evolution of pad‐bearing lizards has followed similar evolutionary dynamics, or whether independent origins are accompanied by unique constraints and selective pressures over macroevolutionary time. We hypothesized that geckos and anoles each have unique evolutionary tempos and modes. Using performance data from 59 species, we modified Brownian motion (BM) and Ornstein–Uhlenbeck (OU) models to account for repeated origins estimated using Bayesian ancestral state reconstructions. We discovered that adhesive performance in geckos evolved in a fashion consistent with Brownian motion with a trend, whereas anoles evolved in bounded performance space consistent with more constrained evolution (an Ornstein–Uhlenbeck model). Our results suggest that convergent phenotypes can have quite distinctive evolutionary patterns, likely as a result of idiosyncratic constraints or ecological opportunities

Correlated metals and the LDA+U method

While LDA+U method is well established for strongly correlated materials with well localized orbitals, its application to weakly correlated metals is questionable. By extending the LDA Stoner approach onto LDA+U, we show that LDA+U enhances the Stoner factor, while reducing the density of states. Arguably the most important correlation effects in metals, fluctuation-induced mass renormalization and suppression of the Stoner factor, are missing from LDA+U. On the other hand, for {\it moderately} correlated metals LDA+U may be useful. With this in mind, we derive a new version of LDA+U that is consistent with the Hohenberg-Kohn theorem and can be formulated as a constrained density functional theory. We illustrate all of the above on concrete examples, including the controversial case of magnetism in FeAl.Comment: Substantial changes. In particular, examples of application of the proposed functional are adde

Electronic Structure of Transition Metals Fe, Ni and Cu in the GW Approximation

The quasiparticle band structures of 3d transition metals, ferromagnetic Fe, Ni and paramagnetic Cu, are calculated by the GW approximation. The width of occupied 3d valence band, which is overestimated in the LSDA, is in good agreement with experimental observation. However the exchange splitting and satellite in spectra are not reproduced and it is required to go beyond the GW approximation. The effects of static screening and dynamical correlation are discussed in detail in comparison with the results of the static COHSEX approximation. The dynamical screening effects are important for band width narrowing.Comment: 4 pages, 3 figure

Thermonuclear Burning Regimes and the Use of SNe Ia in Cosmology

The calculations of the light curves of thermonuclear supernovae are carried out by a method of multi-group radiation hydrodynamics. The effects of spectral lines and expansion opacity are taken into account. The predictions for UBVI fluxes are given. The values of rise time for B and V bands found in our calculations are in good agreement with the observed values. We explain why our results for the rise time have more solid physical justification than those obtained by other authors. It is shown that small variations in the chemical composition of the ejecta, produced in the explosions with different regimes of nuclear burning, can influence drastically the light curve decline in the B band and, to a lesser extent, in the V band. We argue that recent results on positive cosmological constant Lambda, found from the high redshift supernova observations, could be wrong in the case of possible variations of the preferred mode of nuclear burning in the earlier Universe.Comment: 20 pages, 5 figures, presented at the conference "Astronomy at the Eve of the New Century", Puschino, May 17-22, 1999. A few references and a table added, typos correcte

Climate Change and invasibility of the Antarctic benthos

Benthic communities living in shallow-shelf habitats in Antarctica (<100-m depth) are archaic in their structure and function. Modern predators, including fast-moving, durophagous (skeleton-crushing) bony fish, sharks, and crabs, are rare or absent; slow-moving invertebrates are the top predators; and epifaunal suspension feeders dominate many soft substratum communities. Cooling temperatures beginning in the late Eocene excluded durophagous predators, ultimately resulting in the endemic living fauna and its unique food-web structure. Although the Southern Ocean is oceanographically isolated, the barriers to biological invasion are primarily physiological rather than geographic. Cold temperatures impose limits to performance that exclude modern predators. Global warming is now removing those physiological barriers, and crabs are reinvading Antarctica. As sea temperatures continue to rise, the invasion of durophagous predators will modernize the shelf benthos and erode the indigenous character of marine life in Antarctica

Small poly-L-lysines improve cationic lipid-mediated gene transfer in vascular cells in vitro and in vivo

The potential of two small poly-L-lysines ( sPLLs), low molecular weight sPLL ( LMW-L) containing 7 - 30 lysine residues and L18 with 18 lysine repeats, to enhance the efficiency of liposome-mediated gene transfer ( GT) with cationic lipid DOCSPER {[}1,3- dioleoyloxy- 2-( N-5-carbamoyl-spermine)-propane] in vascular smooth muscle cells ( SMCs) was investigated. Dynamic light scattering was used for determination of particle size. Confocal microscopy was applied for colocalization studies of sPLLs and plasmid DNA inside cells. GT was performed in proliferating and quiescent primary porcine SMCs in vitro and in vivo in porcine femoral arteries. At low ionic strength, sPLLs formed small complexes with DNA ( 50 100 nm). At high ionic strength, large complexes ( 11 mu m) were observed without any significant differences in particle size between lipoplexes ( DOCSPER/ DNA) and lipopolyplexes ( DOCSPER/ sPLL/ DNA). Both sPLLs were colocalized with DNA inside cells 24 h after transfection, protecting DNA against degradation. DOCSPER/ sPLL/ DNA formulations enhanced GT in vitro up to 5- fold, in a porcine model using local periadventitial application up to 1.5- fold. Both sPLLs significantly increased liposome- mediated GT. Poly-L-lysine L18 was superior to LMW-L since it enabled maximal GT at a 10-fold lower concentration. Thus, sPLLs may serve as enhancers for GT applications in SMCs in vitro and in vivo using local delivery. Copyright (c) 2007 S. Karger AG, Basel

Principles of meiotic chromosome assembly revealed in S. cerevisiae

During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we use Saccharomyces cerevisiae to explore how this elaborate three-dimensional chromosome organisation is linked to genomic sequence. As cells enter meiosis, we observe that strong cohesin-dependent grid-like Hi-C interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extrusion with growth limited by barriers, in which a heterogeneous population of expanding loops develop along the chromosome. Importantly, CTCF, the factor that imposes similar features in mammalian interphase, is absent in S. cerevisiae, suggesting alternative mechanisms of barrier formation. While grid-like interactions emerge independently of meiotic chromosome synapsis, synapsis itself generates additional compaction that matures differentially according to telomere proximity and chromosome size. Collectively, our results elucidate fundamental principles of chromosome assembly and demonstrate the essential role of cohesin within this evolutionarily conserved process

Orbital character of O 2p unoccupied states near the Fermi level in CrO2

The orbital character, orientation, and magnetic polarization of the O 2$p$ unoccupied states near the Fermi level ($E_F$) in CrO$_2$ was determined using polarization-dependent X-ray absorption spectroscopy (XAS) and X-ray magnetic circular dichroism (XMCD) from high-quality, single-crystal films. A sharp peak observed just above $E_F$ is excited only by the electric field vector ($\bf E$) normal to the tetragonal $c$-axis, characteristic of a narrow band ($\approx$ 0.7 eV bandwidth) constituted from O 2$p$ orbitals perpendicular to $c$ (O 2$p_y$) hybridized with Cr 3$d_{xz-yz}$ $t_{2g}$ states. By comparison with band-structure and configuration-interaction (CI) cluster calculations our results support a model of CrO$_2$ as a half-metallic ferromagnet with large exchange-splitting energy ($\Delta_{exch-split}$ $\approx$ 3.0 eV) and substantial correlation effects.Comment: 4 pages, 3 figures, accepted for publication in Phys. Rev. B Rapid Com

The TRAPPIST survey of southern transiting planets. I. Thirty eclipses of the ultra-short period planet WASP-43 b

We present twenty-three transit light curves and seven occultation light curves for the ultra-short period planet WASP-43 b, in addition to eight new measurements of the radial velocity of the star. Thanks to this extensive data set, we improve significantly the parameters of the system. Notably, the largely improved precision on the stellar density (2.41+-0.08 rho_sun) combined with constraining the age to be younger than a Hubble time allows us to break the degeneracy of the stellar solution mentioned in the discovery paper. The resulting stellar mass and size are 0.717+-0.025 M_sun and 0.667+-0.011 R_sun. Our deduced physical parameters for the planet are 2.034+-0.052 M_jup and 1.036+-0.019 R_jup. Taking into account its level of irradiation, the high density of the planet favors an old age and a massive core. Our deduced orbital eccentricity, 0.0035(-0.0025,+0.0060), is consistent with a fully circularized orbit. We detect the emission of the planet at 2.09 microns at better than 11-sigma, the deduced occultation depth being 1560+-140 ppm. Our detection of the occultation at 1.19 microns is marginal (790+-320 ppm) and more observations are needed to confirm it. We place a 3-sigma upper limit of 850 ppm on the depth of the occultation at ~0.9 microns. Together, these results strongly favor a poor redistribution of the heat to the night-side of the planet, and marginally favor a model with no day-side temperature inversion.Comment: 14 pages, 6 tables, 11 figures. Accepted for publication in A&

Four small puzzles that Rosetta doesn't solve

A complete macromolecule modeling package must be able to solve the simplest structure prediction problems. Despite recent successes in high resolution structure modeling and design, the Rosetta software suite fares poorly on deceptively small protein and RNA puzzles, some as small as four residues. To illustrate these problems, this manuscript presents extensive Rosetta results for four well-defined test cases: the 20-residue mini-protein Trp cage, an even smaller disulfide-stabilized conotoxin, the reactive loop of a serine protease inhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies, several lines of evidence indicate that conformational sampling is not the major bottleneck in modeling these small systems. Instead, approximations and omissions in the Rosetta all-atom energy function currently preclude discriminating experimentally observed conformations from de novo models at atomic resolution. These molecular "puzzles" should serve as useful model systems for developers wishing to make foundational improvements to this powerful modeling suite.Comment: Published in PLoS One as a manuscript for the RosettaCon 2010 Special Collectio