The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?

The use of nucleotide and amino acid sequences allows improved understanding of the timing of evolutionary events of life on earth. Molecular estimates of divergence times are, however, controversial and are generally much more ancient than suggested by the fossil record. The limited number of genes and species explored and pervasive variations in evolutionary rates are the most likely sources of such discrepancies. Here we compared concatenated amino acid sequences of 129 proteins from 36 eukaryotes to determine the divergence times of several major clades, including animals, fungi, plants, and various protists. Due to significant variations in their evolutionary rates, and to handle the uncertainty of the fossil record, we used a Bayesian relaxed molecular clock simultaneously calibrated by six paleontological constraints. We show that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950-1,259 million years ago (Mya), animals diverged from choanoflagellates 761-957 Mya, and the debated age of the split between protostomes and deuterostomes occurred 642-761 Mya. The divergence times appeared to be robust with respect to prior assumptions and paleontological calibrations. Interestingly, these relaxed clock time estimates are much more recent than those obtained under the assumption of a global molecular clock, yet bilaterian diversification appears to be approximate to100 million years more ancient than the Cambrian boundary.

Characterisation of an amphioxus Fringe gene and the evolution of the vertebrate segmentation clock

In mouse and chick embryos, cyclic expression of lunatic fringe has an important role in the regulation of mesoderm segmentation. We have isolated a Fringe gene from the protochordate amphioxus. Amphioxus is the closest living relative of the vertebrates, and has mesoderm that is definitively segmented in a manner that is similar to, and probably homologous with, that of vertebrates. AmphiFringe is placed basal to vertebrate Fringe genes in molecular phylogenetic analyses, indicating that the duplications that formed radical-, manic- and lunatic fringe are specific to the vertebrate lineage. AmphiFringe expression was detected in the anterior neural plate of early neurulae, where it resolved into a series of segmental patches by the mid-neurulae stage. No AmphiFringe transcripts were detected in the mesoderm. Based on these observations, we propose a model depicting a successive recruitment of Fringe in the maintenance then regulation of segmentation during vertebrate evolution.

Comparative characterisation by atomic force microscopy and ellipsometry of soft and solid thin films

Ellipsometry and atomic force microscopy (AFM) were used to study the film thickness and the surface roughness of both 'soft' and solid thin films. 'Soft' polymer thin films of polystyrene and poly(styrene-ethylene/butylene-styrene) block copolymer were prepared by spin-coating onto planar silicon wafers. Ellipsometric parameters were fitted by the Cauchy approach using a two-layer model with planar boundaries between the layers. The smooth surfaces of the prepared polymer films were confirmed by AFM. There is good agreement between AFM and ellipsometry in the 80-130 nm thickness range. Semiconductor surfaces (Si) obtained by anisotropic chemical etching were investigated as an example of a randomly rough surface. To define roughness parameters by ellipsometry, the top rough layers were treated as thin films according to the Bruggeman effective medium approximation (BEMA). Surface roughness values measured by AFM and ellipsometry show the same tendency of increasing roughness with increased etching time, although AFM results depend on the used window size. The combined use of both methods appears to offer the most comprehensive route to quantitative surface roughness characterisation of solid films. Copyright (c) 2007 John Wiley & Sons, Ltd.

Cu-II acetate complexes involving N,N,O donor Schiff base ligands: Mono-atomic oxygen bridged dimers and alternating chains of the dimers and Cu-2(OAc)(4)

Two tridentate N,N,O donor Schiff bases, HL1 (4-(2-ethylamino-ethylimino)-pentan-2-one) and HL2 (3-(2-amino-propylimino)-1-phenyl-butan-1-one) on reaction with Cu-II acetate in presence of triethyl amine yielded two basal-apical, mono-atomic acetate oxygen-bridging dimeric copper(II) complexes, [Cu2L21(OAc)(2)] (1), [Cu2L22(OAc)(2)] (2). Whereas two other similar tridentate ligands HL3 (4-(2-amino-propylimino)-pentane-2-one) and HL3 (3-(2-amino-ethylimino)-1-phenyl-butan-1-one) under the same conditions produced a mixture of the corresponding dinners and a one-dimensional alternating chain of the dimer and copper acetate moiety, [Cu4L23(OAc)(6)](n) (3) and [Cu4L24(OAc)(6)](n) (4), formed by a very rare mu(3) bridging mode of the acetate ion. All four complexes (1-4) have been characterized by X-ray crystallography. The isotropic Hamiltonian, H = -JS(1)S(2) has been used to interpret the magnetic data. Magnetic measurements of 1 and 2 in the temperature range 2-300 K reveal a very weak antiferromagnetic coupling for both complexes U = -0.56 and -1.19 cm(-1) for 1 and 2, respectively). (C) 2008 Elsevier Ltd. All rights reserved.

Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution

Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 Angstrom. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.

A low clock frequency FFT core implementation for multiband full-rate ultra-wideband (UWB) receivers

This paper discusses the design, implementation and synthesis of an FFT module that has been specifically optimized for use in the OFDM based Multiband UWB system, although the work is generally applicable to many other OFDM based receiver systems. Previous work has detailed the requirements for the receiver FFT module within the Multiband UWB ODFM based system and this paper draws on those requirements coupled with modern digital architecture principles and low power design criteria to converge on our optimized solution particularly aimed at a low-clock rate implementation. The FFT design obtained in this paper is also applicable for implementation of the transmitter IFFT module therefore only needing one FFT module in the device for half-duplex operation. The results from this paper enable the baseband designers of the 200Mbit/sec variant of Multiband UWB systems (and indeed other OFDM based receivers) using System-on-Chip (SoC), FPGA and ASIC technology to create cost effective and low power consumer electronics product solutions biased toward the very competitive market.

Surface structure of thin asymmetric PS-b-PMMA diblock copolymers investigated by atomic force microscopy

Asymmetric poly(styrene-b-methyl methacrylate) (PS-b-PMMA) diblock copolymers of molecular weight M-n = 29,700g mol(-1) (M-PS = 9300 g mol(-1) M-PMMA = 20,100 g mol(-1), PD = 1.15, chi(PS) = 0.323, chi(PMMA) = 0.677) and M-n = 63,900 g mol(-1) (M-PS = 50,500 g mol(-1), M-PMMA = 13,400 g mol(-1), PD = 1.18, chi(PS) = 0.790, chi(PMMA) = 0.210) were prepared via reversible addition-fragmentation chain transfer (RAFT) polymerization. Atomic force microscopy (AFM) was used to investigate the surface structure of thin films, prepared by spin-coating the diblock copolymers on a silicon substrate. We show that the nanostructure of the diblock copolymer depends on the molecular weight and volume fraction of the diblock copolymers. We observed a perpendicular lamellar structure for the high molar mass sample and a hexagonal-packed cylindrical patterning for the lower molar mass one. Small-angle X-ray scattering investigation of these samples without annealing did not reveal any ordered structure. Annealing of PS-b-PMMA samples at 160 degrees C for 24 h led to a change in surface structure.

Direct visualisation of lipid bilayer cubic phases using Atomic Force Microscopy

Inverse bicontinuous cubic (Q(II)) phases are nanostructured materials formed by lipid self-assembly. We have successfully imaged thin films of hydrated Q(II) phases from two different systems using AFM. The images show periodic arrays of water channels with spacing and symmetry consistent with published SAXS data on the bulk materials.

Imaging the atomic structure of activated carbon

The precise atomic structure of activated carbon is unknown, despite its huge commercial importance in the purification of air and water. Diffraction methods have been extensively applied to the study of microporous carbons, but cannot provide an unequivocal identification of their structure. Here we show that the structure of a commercial activated carbon can be imaged directly using aberration-corrected transmission electron microscopy. Images are presented both of the as-produced carbon and of the carbon following heat treatment at 2000 degrees C. In the 2000 degrees C carbon clear evidence is found for the presence of pentagonal rings, suggesting that the carbons have a fullerene-related structure. Such a structure would help to explain the properties of activated carbon, and would also have important implications for the modelling of adsorption on microporous carbons.

On the difficulties of present theoretical models to predict the oxidation state of atomic Au adsorbed on regular sites of CeO2(111)

The electronic structure and oxidation state of atomic Au adsorbed on a perfect CeO2(111) surface have been investigated in detail by means of periodic density functional theory-based calculations, using the LDA+U and GGA+U potentials for a broad range of U values, complemented with calculations employing the HSE06 hybrid functional. In addition, the effects of the lattice parameter a0 and of the starting point for the geometry optimization have also been analyzed. From the present results we suggest that the oxidation state of single Au atoms on CeO2(111) predicted by LDA+U, GGA+U, and HSE06 density functional calculations is not conclusive and that the final picture strongly depends on the method chosen and on the construction of the surface model. In some cases we have been able to locate two well-defined states which are close in energy but with very different electronic structure and local geometries, one with Au fully oxidized and one with neutral Au. The energy difference between the two states is typically within the limits of the accuracy of the present exchange-correlation potentials, and therefore, a clear lowest-energy state cannot be identified. These results suggest the possibility of a dynamic distribution of Au0 and Au+ atomic species at the regular sites of the CeO2(111) surface.

Modeling the observed proton aurora and ionospheric convection responses to changes in the IMF clock angle: 2. Persistence of ionospheric convection

We apply a numerical model of time-dependent ionospheric convection to two directly driven reconnection pulses during a 15-min interval of southward IMF on 26 November 2000. The model requires an input magnetopause reconnection rate variation, which is here derived from the observed variation in the upstream IMF clock angle, q. The reconnection rate is mapped to an ionospheric merging gap, the MLT extent of which is inferred from the Doppler-shifted Lyman-a emission on newly opened field lines, as observed by the FUV instrument on the IMAGE spacecraft. The model is used to reproduce a variety of features observed during this event: SuperDARN observations of the ionospheric convection pattern and transpolar voltage; FUV observations of the growth of patches of newly opened flux; FUVand in situ observations of the location of the Open-Closed field line Boundary (OCB) and a cusp ion step. We adopt a clock angle dependence of the magnetopause reconnection electric field, mapped to the ionosphere, of the form Enosin4(q/2) and estimate the peak value, Eno, by matching observed and modeled variations of both the latitude, LOCB, of the dayside OCB (as inferred from the equatorward edge of cusp proton emissions seen by FUV) and the transpolar voltage FPC (as derived using the mapped potential technique from SuperDARN HF radar data). This analysis also yields the time constant tOCB with which the open-closed boundary relaxes back toward its equilibrium configuration. For the case studied here, we find tOCB = 9.7 ± 1.3 min, consistent with previous inferences from the observed response of ionospheric flow to southward turnings of the IMF. The analysis confirms quantitatively the concepts of ionospheric flow excitation on which the model is based and explains some otherwise anomalous features of the cusp precipitation morphology.

Modeling the observed proton aurora and ionospheric convection responses to changes in the IMF clock angle: 1. Persistence of cusp proton aurora

We employ a numerical model of cusp ion precipitation and proton aurora emission to fit variations of the peak Doppler-shifted Lyman-a intensity observed on 26 November 2000 by the SI-12 channel of the FUV instrument on the IMAGE satellite. The major features of this event appeared in response to two brief swings of the interplanetary magnetic field (IMF) toward a southward orientation. We reproduce the observed spatial distributions of this emission on newly opened field lines by combining the proton emission model with a model of the response of ionospheric convection. The simulations are based on the observed variations of the solar wind proton temperature and concentration and the interplanetary magnetic field clock angle. They also allow for the efficiency, sampling rate, integration time and spatial resolution of the FUV instrument. The good match (correlation coefficient 0.91, significant at the 98% level) between observed and modeled variations confirms the time constant (about 4 min) for the rise and decay of the proton emissions predicted by the model for southward IMF conditions. The implications for the detection of pulsed magnetopause reconnection using proton aurora are discussed for a range of interplanetary conditions.