A dedicated haem lyase is required for the maturation of a novel bacterial cytochrome c with unconventional covalent haem binding

In bacterial c-type cytochromes, the haem cofactor is covalently attached via two cysteine residues organized in a haem c-binding motif. Here, a novel octa-haem c protein, MccA, is described that contains only seven conventional haem c-binding motifs (CXXCH), in addition to several single cysteine residues and a conserved CH signature. Mass spectrometric analysis of purified MccA from Wolinella succinogenes suggests that two of the single cysteine residues are actually part of an unprecedented CX15CH sequence involved in haem c binding. Spectroscopic characterization of MccA identified an unusual high-potential haem c with a red-shifted absorption maximum, not unlike that of certain eukaryotic cytochromes c that exceptionally bind haem via only one thioether bridge. A haem lyase gene was found to be specifically required for the maturation of MccA in W. succinogenes. Equivalent haem lyase-encoding genes belonging to either the bacterial cytochrome c biogenesis system I or II are present in the vicinity of every known mccA gene suggesting a dedicated cytochrome c maturation pathway. The results necessitate reconsideration of computer-based prediction of putative haem c-binding motifs in bacterial proteomes

Phylogeography, population structure and evolution of coral-eating butterflyfishes (Family Chaetodontidae, genus Chaetodon, subgenus Corallochaetodon)

Aim: This study compares the phylogeography, population structure and evolution of four butterflyfish species in the Chaetodon subgenus Corallochaetodon, with two widespread species (Indian Ocean – C. trifasciatus and Pacific Ocean – C. lunulatus), and two species that are largely restricted to the Red Sea (C. austriacus) and north-western (NW) Indian Ocean (C. melapterus). Through extensive geographical coverage of these taxa, we seek to resolve patterns of genetic diversity within and between closely related butterflyfish species in order to illuminate biogeographical and evolutionary processes. Location: Red Sea, Indian Ocean and Pacific Ocean. Methods: A total of 632 individuals from 24 locations throughout the geographical ranges of all four members of the subgenus Corallochaetodon were sequenced using a 605 bp fragment (cytochrome b) of mtDNA. In addition, 10 microsatellite loci were used to assess population structure in the two widespread species. Results: Phylogenetic reconstruction indicates that the Pacific Ocean C. lunulatus diverged from the Indian Ocean C. trifasciatus approximately 3 Ma, while C. melapterus and C. austriacus comprise a cluster of shared haplotypes derived from C. trifasciatus within the last 0.75 Myr. The Pacific C. lunulatus had significant population structure at peripheral locations on the eastern edge of its range (French Polynesia, Johnston Atoll, Hawai'i), and a strong break between two ecoregions of the Hawaiian Archipelago. The Indian Ocean C. trifasciatus showed significant structure only at the Chagos Archipelago in the central Indian Ocean, and the two range-restricted species showed no population structure but evidence of recent population expansion. Main conclusions: Patterns of endemism and genetic diversity in Corallochaetodon butterflyfishes have been shaped by (1) Plio-Pleistocene sea level changes that facilitated evolutionary divergences at biogeographical barriers between Indian and Pacific Oceans, and the Indian Ocean and Red Sea, and (2) semi-permeable oceanographic and ecological barriers working on a shorter time-scale. The evolution of range-restricted species (Red Sea and NW Indian Ocean) and isolated populations (Hawai'i) at peripheral biogeographical provinces indicates that these areas are evolutionary incubators for reef fishes

Scaling property and peculiar velocity of global monopoles

We investigate the scaling property of global monopoles in the expanding universe. By directly solving the equations of motion for scalar fields, we follow the time development of the number density of global monopoles in the radiation dominated (RD) universe and the matter dominated (MD) universe. It is confirmed that the global monopole network relaxes into the scaling regime and the number per hubble volume is a constant irrespective of the cosmic time. The number density $n(t)$ of global monopoles is given by $n(t) \simeq (0.43\pm0.07) / t^{3}$ during the RD era and $n(t) \simeq (0.25\pm0.05) / t^{3}$ during the MD era. We also examine the peculiar velocity $v$ of global monopoles. For this purpose, we establish a method to measure the peculiar velocity by use of only the local quantities of the scalar fields. It is found that $v \sim (1.0 \pm 0.3)$ during the RD era and $v \sim (0.8 \pm 0.3)$ during the MD era. By use of it, a more accurate analytic estimate for the number density of global monopoles is obtained.Comment: 17 pages, 8 figures, to appear in Phys. Rev.

Lattice-switch Monte Carlo

We present a Monte Carlo method for the direct evaluation of the difference between the free energies of two crystal structures. The method is built on a lattice-switch transformation that maps a configuration of one structure onto a candidate configuration of the other by `switching' one set of lattice vectors for the other, while keeping the displacements with respect to the lattice sites constant. The sampling of the displacement configurations is biased, multicanonically, to favor paths leading to `gateway' arrangements for which the Monte Carlo switch to the candidate configuration will be accepted. The configurations of both structures can then be efficiently sampled in a single process, and the difference between their free energies evaluated from their measured probabilities. We explore and exploit the method in the context of extensive studies of systems of hard spheres. We show that the efficiency of the method is controlled by the extent to which the switch conserves correlated microstructure. We also show how, microscopically, the procedure works: the system finds gateway arrangements which fulfill the sampling bias intelligently. We establish, with high precision, the differences between the free energies of the two close packed structures (fcc and hcp) in both the constant density and the constant pressure ensembles.Comment: 34 pages, 9 figures, RevTeX. To appear in Phys. Rev.

`Hath charms to soothe . . .': An exploratory study of how high-functioning adults with ASD experience music

Semi-structured interviews were conducted with 12 highfunctioning adults on the autism spectrum, in order to examine the nature of their personal experiences of music. Consistent with the literature on typically developing people’s engagement with music, the analysis showed that most participants exploit music for a wide range of purposes in the cognitive, emotional and social domains, including mood management, personal development and social inclusion. However, in contrast to typically developing people, the ASD group’s descriptions of mood states reflected a greater reliance on internally focused (arousal) rather than externally focused (emotive) language

Cosmological Evolution of Global Monopoles

We investigate the cosmological evolution of global monopoles in the radiation dominated (RD) and matter dominated (MD) universes by numerically solving field equations of scalar fields. It is shown that the global monopole network relaxes into the scaling regime, unlike the gauge monopole network. The number density of global monopoles is given by $n(t) \simeq (0.43\pm0.07) / t^{3}$ during the RD era and $n(t) \simeq (0.25\pm0.05) / t^{3}$ during the MD era. Thus, we have confirmed that density fluctuations produced by global monopoles become scale invariant and are given by $\delta \rho \sim 7.2(5.0) \sigma^{2} / t^{2}$ during the RD (MD) era, where $\sigma$ is the breaking scale of the symmetry.Comment: 6 pages, 2 figures, to appear in Phys. Rev. D (R

Crustal structure beneath western and eastern Iceland from surface waves and receiver functions

We determine the crustal structures beneath 14 broad-band seismic stations, deployed in western, eastern, central and southern Iceland, using surface wave dispersion curves and receiver functions. We implement a method to invert receiver functions using constraints obtained from genetic algorithm inversion of surface waves. Our final models satisfy both data sets. The thickness of the upper crust, as defined by the velocity horizon Vs= 3.7 km s−1, is fairly uniform at ∼6.5–9 km beneath the Tertiary intraplate areas of western and eastern Iceland, and unusually thick at 11 km beneath station HOT22 in the far south of Iceland. The depth to the base of the lower crust, as defined by the velocity horizon Vs= 4.1 km s−1 is ∼20–26 km in western Iceland and ∼27–33 km in eastern Iceland. These results agree with those of explosion profiles that detect a thinner crust beneath western Iceland than beneath eastern Iceland. An earlier report of a substantial low-velocity zone beneath the Middle Volcanic Zone in the lower crust is confirmed by a similar observation beneath an additional station there. As was found in previous receiver function studies, the most reliable feature of the results is the clear division into an upper sequence that is a few kilometres thick where velocity gradients are high, and a lower, thicker sequence where velocity gradients are low. The transition to typical mantle velocities is variable, and may range from being very gradational to being relatively sharp and clear. A clear Moho, by any definition, is rarely seen, and there is thus uncertainty in estimates of the thickness of the crust in many areas. Although a great deal of seismic data are now available constraining the structures of the crust and upper mantle beneath Iceland, their geological nature is not well understood

Dynamics of ions in the selectivity filter of the KcsA channel

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications

Lagrangian evolution of global strings

We establish a method to trace the Lagrangian evolution of extended objects consisting of a multicomponent scalar field in terms of a numerical calculation of field equations in three dimensional Eulerian meshes. We apply our method to the cosmological evolution of global strings and evaluate the energy density, peculiar velocity, Lorentz factor, formation rate of loops, and emission rate of Nambu-Goldstone (NG) bosons. We confirm the scaling behavior with a number of long strings per horizon volume smaller than the case of local strings by a factor of $\sim$ 10. The strategy and the method established here are applicable to a variety of fields in physics.Comment: 5 pages, 2 figure

Rolling Tachyon in Brane World Cosmology from Superstring Field Theory

The pressureless tachyonic matter recently found in superstring field theory has an over-abundance problem in cosmology. We argue that this problem is naturally solved in the brane inflationary scenario if almost all of the tachyon energy is drained (via its coupling to the inflaton and matter fields) to heating the universe, while the rest of the tachyon energy goes to a network of cosmic strings (lower-dimensional BPS D-branes) produced during the tachyon rolling at the end of inflation.Comment: 4 pages, one figure. This version quantifies constraints on various phenomenological models for tachyon deca