Conformational Transitions Accompanying Oligomerization of Yeast Alcohol Oxidase, a Peroxisomal Flavoenzyme

Alcohol oxidase (AO) is a homo-octameric flavoenzyme which catalyzes methanol oxidation in methylotrophic yeasts. AO protein is synthesized in the cytosol and subsequently sorted to peroxisomes where the active enzyme is formed. To gain further insight in the molecular mechanisms involved in AO activation, we studied spectroscopically native AO from Hansenula polymorpha and Pichia pastoris and three putative assembly intermediates. Fluorescence studies revealed that both Trp and FAD are suitable intramolecular markers of the conformation and oligomeric state of AO. A direct relationship between dissociation of AO octamers and increase in Trp fluorescence quantum yield and average fluorescence lifetime was found. The time-resolved fluorescence of the FAD cofactor showed a rapid decay component which reflects dynamic quenching due to the presence of aromatic amino acids in the FAD-binding pocket. The analysis of FAD fluorescence lifetime profiles showed a remarkable resemblance of pattern for purified AO and AO present in intact yeast cells. Native AO contains a high content of ordered secondary structure which was reduced upon FAD-removal. Dissociation of octamers into monomers resulted in a conversion of β-sheets into α-helices. Our results are explained in relation to a 3D model of AO, which was built based on the crystallographic data of the homologous enzyme glucose oxidase from Aspergillus niger. The implications of our results for the current model of the in vivo AO assembly pathway are discussed.

Theorems on gravitational time delay and related issues

Two theorems related to gravitational time delay are proven. Both theorems apply to spacetimes satisfying the null energy condition and the null generic condition. The first theorem states that if the spacetime is null geodesically complete, then given any compact set $K$, there exists another compact set $K'$ such that for any $p,q \not\in K'$, if there exists a ``fastest null geodesic'', $\gamma$, between $p$ and $q$, then $\gamma$ cannot enter $K$. As an application of this theorem, we show that if, in addition, the spacetime is globally hyperbolic with a compact Cauchy surface, then any observer at sufficiently late times cannot have a particle horizon. The second theorem states that if a timelike conformal boundary can be attached to the spacetime such that the spacetime with boundary satisfies strong causality as well as a compactness condition, then any ``fastest null geodesic'' connecting two points on the boundary must lie entirely within the boundary. It follows from this theorem that generic perturbations of anti-de Sitter spacetime always produce a time delay relative to anti-de Sitter spacetime itself.Comment: 15 pages, 1 figure. Example of gauge perturbation changed/corrected. Two footnotes added and one footnote remove

Modelling Planck-scale Lorentz violation via analogue models

Astrophysical tests of Planck-suppressed Lorentz violations had been extensively studied in recent years and very stringent constraints have been obtained within the framework of effective field theory. There are however still some unresolved theoretical issues, in particular regarding the so called "naturalness problem" - which arises when postulating that Planck-suppressed Lorentz violations arise only from operators with mass dimension greater than four in the Lagrangian. In the work presented here we shall try to address this problem by looking at a condensed-matter analogue of the Lorentz violations considered in quantum gravity phenomenology. Specifically, we investigate the class of two-component BECs subject to laser-induced transitions between the two components, and we show that this model is an example for Lorentz invariance violation due to ultraviolet physics. We shall show that such a model can be considered to be an explicit example high-energy Lorentz violations where the ``naturalness problem'' does not arise.Comment: Talk given at the Fourth Meeting on Constrained Dynamics and Quantum Gravity (QG05), Cala Gonone (Sardinia, Italy) September 12-16, 200

Area products for stationary black hole horizons

Area products for multi-horizon stationary black holes often have intriguing properties, and are often (though not always) independent of the mass of the black hole itself (depending only on various charges, angular momenta, and moduli). Such products are often formulated in terms of the areas of inner (Cauchy) horizons and outer (event) horizons, and sometimes include the effects of unphysical "virtual" horizons. But the conjectured mass-independence sometimes fails. Specifically, for the Schwarzschild-de Sitter [Kottler] black hole in (3+1) dimensions it is shown by explicit exact calculation that the product of event horizon area and cosmological horizon area is not mass independent. (Including the effect of the third "virtual" horizon does not improve the situation.) Similarly, in the Reissner-Nordstrom-anti-de Sitter black hole in (3+1) dimensions the product of inner (Cauchy) horizon area and event horizon area is calculated (perturbatively), and is shown to be not mass independent. That is, the mass-independence of the product of physical horizon areas is not generic. In spherical symmetry, whenever the quasi-local mass m(r) is a Laurent polynomial in aerial radius, r=sqrt{A/4\pi}, there are significantly more complicated mass-independent quantities, the elementary symmetric polynomials built up from the complete set of horizon radii (physical and virtual). Sometimes it is possible to eliminate the unphysical virtual horizons, constructing combinations of physical horizon areas that are mass independent, but they tend to be considerably more complicated than the simple products and related constructions currently being mooted in the literature.Comment: V1: 16 pages; V2: 9 pages (now formatted in PRD style). Minor change in title. Extra introduction, background, discussion. Several additional references; other references updated. Minor typos fixed. This version accepted for publication in PRD; V3: Minor typos fixed. Published versio

Higher-Dimensional Bulk Wormholes and their Manifestations in Brane Worlds

There is nothing to prevent a higher-dimensional anti-de Sitter bulk spacetime from containing various other branes in addition to hosting our universe, presumed to be a positive-tension 3-brane. In particular, it could contain closed, microscopic branes that form the boundary surfaces of void bubbles and thus violate the null energy condition in the bulk. The possible existence of such micro branes can be investigated by considering the properties of the ground state of a pseudo-Wheeler-DeWitt equation describing brane quantum dynamics in minisuperspace. If they exist, a concentration of these micro branes could act as a fluid of exotic matter able to support macroscopic wormholes connecting otherwise distant regions of the bulk. Were the brane constituting our universe to expand into a region of the bulk containing such higher-dimensional macroscopic wormholes, they would likely manifest themselves in our brane as wormholes of normal dimensionality, whose spontaneous appearance and general dynamics would seem inexplicably peculiar. This encounter could also result in the formation of baby universes of a particular type.Comment: 21 pages, 1 figur

From wormhole to time machine: Comments on Hawking's Chronology Protection Conjecture

The recent interest in ``time machines'' has been largely fueled by the apparent ease with which such systems may be formed in general relativity, given relatively benign initial conditions such as the existence of traversable wormholes or of infinite cosmic strings. This rather disturbing state of affairs has led Hawking to formulate his Chronology Protection Conjecture, whereby the formation of ``time machines'' is forbidden. This paper will use several simple examples to argue that the universe appears to exhibit a ``defense in depth'' strategy in this regard. For appropriate parameter regimes Casimir effects, wormhole disruption effects, and gravitational back reaction effects all contribute to the fight against time travel. Particular attention is paid to the role of the quantum gravity cutoff. For the class of model problems considered it is shown that the gravitational back reaction becomes large before the Planck scale quantum gravity cutoff is reached, thus supporting Hawking's conjecture.Comment: 43 pages,ReV_TeX,major revision

Microsatellite genotyping of apple (Malus × domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification

A highly informative set of 16 microsatellite markers was used to fingerprint 695 apple accessions from eight Dutch collections. Among the total sample, 475 different genotypes were distinguished based on multi-locus microsatellite variation, revealing a potential redundancy within the total sample of 32%. The majority of redundancies were found between collections, rather than within collections. No single collection covered the total observed diversity well, as each collection consisted of about 50% of unique accessions. These findings reflected the fact that most collection holders focus on common Dutch varieties, as well as on region-specific diversity. Based on the diversity patterns observed, maintenance of genetic resources by a network of co-operating collection holders, rather than by collecting the total diversity in a single collection appears to be an efficient approach. Comparison of microsatellite and passport data showed that for many accessions the marker data did not provide support for the registered variety names. Verification of accessions showed that discrepancies between passport and molecular data were largely due to documentation and phenotypic determination errors. With the help of the marker data the varietal names of 45 accessions could be corrected. Microsatellite genotyping of apple appears to be an efficient tool in the management of collections and in variety identification. The development of a marker database was considered relevant as a reference instrument in variety identification and as a source of information about thus far unexplored diversity that could be of interest in the development of new apple varietie

Riemannian geometry of irrotational vortex acoustics

We consider acoustic propagation in an irrotational vortex, using the technical machinery of differential geometry to investigate the ``acoustic geometry'' that is probed by the sound waves. The acoustic space-time curvature of a constant circulation hydrodynamical vortex leads to deflection of phonons at appreciable distances from the vortex core. The scattering angle for phonon rays is shown to be quadratic in the small quantity $\Gamma/(2\pi cb)$, where $\Gamma$ is the vortex circulation, $c$ the speed of sound, and $b$ the impact parameter.Comment: 4 pages, 2 figures, RevTex4. Discussion of focal length added; to appear in Physical Review Letter

Energy conditions in f(R) gravity and Brans-Dicke theories

The equivalence between f(R) gravity and scalar-tensor theories is invoked to study the null, strong, weak and dominant energy conditions in Brans-Dicke theory. We consider the validity of the energy conditions in Brans-Dicke theory by invoking the energy conditions derived from a generic f(R) theory. The parameters involved are shown to be consistent with an accelerated expanding universe.Comment: 9 pages, 1 figure, to appear in IJMP

Lovelock Thin-Shell Wormholes

We construct the asymptotically flat charged thin-shell wormholes of Lovelock gravity in seven dimensions by cut-and-paste technique, and apply the generalized junction conditions in order to calculate the energy-momentum tensor of these wormholes on the shell. We find that for negative second order and positive third order Lovelock coefficients, there are thin-shell wormholes that respect the weak energy condition. In this case, the amount of normal matter decreases as the third order Lovelock coefficient increases. For positive second and third order Lovelock coefficients, the weak energy condition is violated and the amount of exotic matter decreases as the charge increases. Finally, we perform a linear stability analysis against a symmetry preserving perturbation, and find that the wormholes are stable provided the derivative of surface pressure density with respect to surface energy density is negative and the throat radius is chosen suitable.Comment: 13 pages, 6 figure