Molecular clocks in reptiles: Life history influences rate of molecular evolution

Life history has been implicated as a determinant of variation in rate of molecular evolution amongst vertebrate species because of a negative correlation between bode size and substitution rate for many Molecular data sets. Both the generality and the cause of the negative bode size trend have been debated, and the validity of key studies has been questioned (particularly concerning the failure to account for phylogenetic bias). In this study, a comparative method has been used to test for an association between a range of life-history variables-such as body size age at maturity, and clutch size-and DNA substitution rate for three genes (NADH4, cytochrome b, and c-mos). A negative relationship between body size and rate of molecular evolution was found for phylogenetically independent pairs of reptile species spanning turtles. lizards. snakes, crocodile, and tuatara. Although this Study was limited by the number of comparisons for which both sequence and lite-history data were available, the results, suggest that a negative bode size trend in rate of molecular evloution may be a general feature of reptile molecular evolution. consistent with similar studies of mammals and birds. This observation has important implications for uncovering the mechanisms of molecular evolution and warns against assuming that related lineages will share the same substitution rate (a local molecular clock) in order to date evolutionary divergences from DNA sequences.

Growth of a Bose-Einstein condensate: a detailed comparison of theory and experiment

We extend the earlier model of condensate growth of Davis et at (Davis M J, Gardiner C W and Ballagh R J 2000 Phys. Rev. A 62 063608) to include the effect of gravity in a magnetic trap. We carry out calculations to model the experiment reported by Kohl et al (Kohl M, Davis M J, Gardiner C W, Hansch T and Esslinger T 2001 Preprint cond-mat/0106642) who study the formation of a rubidium Bose-Einstein condensate for a range of evaporative cooling parameters. We find that, in the regime where our model is valid, the theoretical curves agree with all the experimental data with no fitting parameters. However, for the slowest cooling of the gas the theoretical curve deviates significantly from the experimental curves. It is possible that this discrepancy may be related to the formation of a quasicondensate.

Atom lasers, coherent states, and coherence II. Maximally robust ensembles of pure states

As discussed in the preceding paper [Wiseman and Vaccaro, preceding paper, Phys. Rev. A 65, 043605 (2002)], the stationary state of an optical or atom laser far above threshold is a mixture of coherent field states with random phase, or, equivalently, a Poissonian mixture of number states. We are interested in which, if either, of these descriptions of rho(ss) as a stationary ensemble of pure states, is more natural. In the preceding paper we concentrated upon the question of whether descriptions such as these are physically realizable (PR). In this paper we investigate another relevant aspect of these ensembles, their robustness. A robust ensemble is one for which the pure states that comprise it survive relatively unchanged for a long time under the system evolution. We determine numerically the most robust ensembles as a function of the parameters in the laser model: the self-energy chi of the bosons in the laser mode, and the excess phase noise nu. We find that these most robust ensembles are PR ensembles, or similar to PR ensembles, for all values of these parameters. In the ideal laser limit (nu=chi=0), the most robust states are coherent states. As the phase noise or phase dispersion is increased through nu or the self-interaction of the bosons chi, respectively, the most robust states become more and more amplitude squeezed. We find scaling laws for these states, and give analytical derivations for them. As the phase diffusion or dispersion becomes so large that the laser output is no longer quantum coherent, the most robust states become so squeezed that they cease to have a well-defined coherent amplitude. That is, the quantum coherence of the laser output is manifest in the most robust PR ensemble being an ensemble of states with a well-defined coherent amplitude. This lends support to our approach of regarding robust PR ensembles as the most natural description of the state of the laser mode. It also has interesting implications for atom lasers in particular, for which phase dispersion due to self-interactions is expected to be large.

Polarization squeezing and continuous-variable polarization entanglement

A concept of polarization entanglement for continuous variables is introduced. For this purpose the Stokes-parameter operators and the associated Poincare sphere, which describe the quantum-optical polarization properties of light, are defined and their basic properties are reviewed. The general features of the Stokes operators are illustrated by evaluation of their means and variances for a range of simple polarization states. Some of the examples show polarization squeezing, in which the variances of one or more Stokes parameters are smaller than the coherent-state value. The main object of the paper is the application of these concepts to bright squeezed light. It is shown that a light beam formed by interference of two orthogonally polarized quadrature-squeezed beams exhibits squeezing in some of the Stokes parameters. Passage of such a primary polarization-squeezed beam through suitable optical components generates a pair of polarization-entangled light beams with the nature of a two-mode squeezed state. Implementation of these schemes using the double-fiber Sagnac interferometer provides an efficient method for the generation of bright nonclassical polarization states. The important advantage of these nonclassical polarization states for quantum communication is the possibility of experimentally determining all of the relevant conjugate variables of both squeezed and entangled fields using only linear optical elements followed by direct detection.

Current density mapping approach for design of clinical magnetic resonance imaging magnets

Novel current density mapping (CDM) schemes are developed for the design of new actively shielded, clinical magnetic resonance imaging (MRI) magnets. This is an extended inverse method in which the entire potential solution space for the superconductors has been considered, rather than single current density layers. The solution provides an insight into the required superconducting coil pattern for a desired magnet configuration. This information is then used as an initial set of parameters for the magnet structure, and a previously developed hybrid numerical optimization technique is used to obtain the final geometry of the magnet. The CDM scheme is applied to the design of compact symmetric, asymmetric, and open architecture 1.0-1.5 T MRI magnet systems of novel geometry and utility. A new symmetric 1.0-T system that is just I m in length with a full 50-cm diameter of the active, or sensitive, volume (DSV) is detailed, as well as an asymmetric system in which a 50-cm DSV begins just 14 cm from the end of the coil structure. Finally a 1.0-T open magnet system with a full 50-cm DSV is presented. These new designs provide clinically useful homogeneous regions and have appropriately restricted stray fields but, in some of the designs, the DSV is much closer to the end of the magnet system than in conventional designs. These new designs have the potential to reduce patient claustrophobia and improve physician access to patients undergoing scans. (C) 2002 Wiley Periodicals, Inc.

Molecular rates parallel diversification contrasts between carnivorous plant sister lineages

In the carnivorous plant family Lentibulariaceae, the bladderwort lineage (Utricularia and Genlisea) is substantially more species-rich and morphologically divergent than its sister lineage, the butterworts (Pinguicula). Bladderworts have a relaxed body plan that has permitted the evolution of terrestrial, epiphytic, and aquatic forms that capture prey in intricately designed suction bladders or corkscrew-shaped lobster-pot traps. In contrast, the flypaper-trapping butterworts maintain vegetative structures typical of angiosperms. We found that bladderwort genomes evolve significantly faster across seven loci (the trnL intron, the second trnL exon, the trnL-F intergenic spacer, the rps16 intron, rbcL, coxI, and 5.8S rDNA) representing all three genomic compartments. Generation time differences did not show a significant association. We relate these findings to the contested speciation rate hypothesis, which postulates a relationship between increased nucleotide substitution and increased cladogenesis. (C) 2002 The Willi Hennig Society.

Quantum correlated twin atomic beams via photodissociation of a molecular Bose-Einstein condensate

We study the process of photodissociation of a molecular Bose-Einstein condensate as a potential source of strongly correlated twin atomic beams. We show that the two beams can possess nearly perfect quantum squeezing in their relative numbers.

A molecular phylogeny of rainbow skinks (Scincidae : Carlia): taxonomic and biogeographic implications

The phylogenetic relationships amongst 29 species of Carlia and Lygisaurus were estimated using a 726-base-pair segment of the protein-coding mitochondrial ND4 gene. Results do not support the recent resurrection of the genus Lygisaurus. Although most Lygisaurus species formed a single clade, this clade is nested within Carlia and includes Carlia parrhasius. Due to this new molecular evidence, and the paucity of diagnostic morphological characters separating the genera, Lygisaurus de Vis 1884 is re-synonymised with Carlia Gray 1845. Our analysis is also inconsistent with a previous suggestion that Lygisaurus timlowi should be removed to Menetia, a genus that is distantly related relative to outgroups used here. Intraspecific variation in Carlia is, in several instances, greater than interspecific distance. The most strikingly divergent lineages are found within C. rubrigularis, which appears to be paraphyletic, with southern populations more closely related to C. rhomboidalis than to northern populations of C. rubrigularis. The two C. rubrigularis-C. rhomboidalis lineages form part of a major polytomy at an intermediate level of divergence. Lack of resolution at this level, however, does not appear to be due to saturation or loss of phylogenetic signal. Rather, the polytomy probably reflects a period of relatively rapid diversification that occurred sometime during the Miocene.

Magnetic-field-induced superconductivity in layered organic molecular crystals with localized magnetic moments

l-(BETS)2FeCl4 undergoes transitions from an antiferromagnetic insulator to a metal and then to a superconductor as a magnetic field is increased. We use a Hubbard-Kondo model to clarify the role of the Fe31 magnetic ions in these phase transitions. In the high-field regime, the magnetic field acting on the electron spins is compensated by the exchange field He due to the magnetic ions. We show how He can be extracted from the observed splitting of the Shubnikov–de Haas frequencies. We predict the field range for field-induced superconductivity in other materials.

Molecular archaeology

Advances in technologies such as mass spectrometry and capillary electrophoresis have encouraged the study of ancient lipids and other ancient biomolecules. Now, microarray technology looks set to revolutionise the study of ancient DNA, perhaps with as much impact as that of PCR.

Dynamic Behavior of the Jahn-Teller distorted Cu(H2O)(6)(2+) ion in Cu2+ doped Cs-2[Zn(H2O)(6)](ZrF6)(2) and the crystal structure of the host lattice

The temperature dependence of the X- and Q-band EPR spectra of Cs-2[Zn(H2O)(6)](ZrF6)(2) containing similar to1% Cu2+ is reported. All three molecular g-values vary with temperature, and their behavior is interpreted using a model in which the potential surface of the Jahn-Teller distorted Cu(H2O)(6)(2+) ion is perturbed by an orthorhombic strain induced by interactions with the surrounding lattice. The strain parameters are significantly smaller than those reported previously for the Cu(H2O)(6)(2+) ion in similar lattices. The temperature dependence of the two higher g-values suggests that in the present compound the lattice interactions change slightly with temperature. The crystal structure of the Cs-2[Zn(H2O)(6)](ZrF6)(2) host is reported, and the geometry of the Zn(H2O)(6)(2+) ion is correlated with lattice strain parameters derived from the EPR spectrum of the guest Cu2+ complex.

From molecular complexes to zwitterions and final products. Reactions between C3O2 and amines

The formation of molecular complexes (prereactive intermediates) between C3O2 and amines (ammonia, dimethylamine, trimethylamine, and 4-(dimethylamino)pyridine) as well as the subsequent transformation of the complexes into C3O2-amine zwitterions in cryogenic matrixes (ca. 40 K) has been observed. In the case of dimethylamine, the formation of tetramethylmalonamide has also been documented. Calculations using density functional theory (B3LYP/6-31G(2d, p)) are used to assign all above species and are in excellent agreement with the IR spectra.

Crystallization of the FAD-independent acetolactate synthase of Klebsiella pneumoniae

Leucine and valine are formed in a common pathway from pyruvate in which the first intermediate is 2-acetolactate. In some bacteria, this compound also has a catabolic fate as the starting point for the butanediol fermentation. The enzyme (EC 4.1.3.18) that forms 2-acetolactate is known as either acetohydroxyacid synthase (AHAS) or acetolactate synthase (ALS), with the latter name preferred for the catabolic enzyme. A significant difference between AHAS and ALS is that the former requires FAD for catalytic activity, although the reason for this requirement is not well understood. Both enzymes require the cofactor thiamine diphosphate. Here, the crystallization and preliminary X-ray diffraction analysis of the Klebsiella pneumoniae ALS is reported. Data to 2.6 Angstrom resolution have been collected at 100 K using a rotating-anode generator and an R-AXIS IV++ detector. Crystals have unit-cell parameters a = 137.4, b = 143.9, c = 134.4 Angstrom, alpha = 90, beta = 108.4, gamma = 90degrees and belong to space group C2. Preliminary analysis indicates that there are four monomers located in each asymmetric unit.