Two Unrelated 8-Vinyl Reductases Ensure Production of Mature Chlorophylls in Acaryochloris marina

The major photopigment of the cyanobacterium Acaryochloris marina is chlorophyll d , while its direct biosynthetic precursor, chlorophyll a , is also present in the cell. These pigments, along with the majority of chlorophylls utilized by oxygenic pho- totrophs, carry an ethyl group at the C-8 position of the molecule, having undergone reduction of a vinyl group during biosyn- thesis. Two unrelated classes of 8-vinyl reductase involved in the biosynthesis of chlorophylls are known to exist, BciA and BciB. The genome of Acaryochloris marina contains open reading frames (ORFs) encoding proteins displaying high sequence similarity to BciA or BciB, although they are annotated as genes involved in transcriptional control ( nmrA ) and methanogenesis ( frhB ), respectively. These genes were introduced into an 8-vinyl chlorophyll a -producing delta bciB strain of Synechocystis sp. strain PCC 6803, and both were shown to restore synthesis of the pigment with an ethyl group at C-8, demonstrating their activities as 8-vinyl reductases. We propose that nmrA and frhB be reassigned as bciA and bciB , respectively; transcript and proteomic analysis of Acaryochloris marina reveal that both bciA and bciB are expressed and their encoded proteins are present in the cell, possibly in order to ensure that all synthesized chlorophyll pigment carries an ethyl group at C-8. Potential reasons for the presence of two 8-vinyl reductases in this strain, which is unique for cyanobacteria, are discussed

Generation of defects and disorder from deeply quenching a liquid to form a solid

We show how deeply quenching a liquid to temperatures where it is linearly unstable and the crystal is the equilibrium phase often produces crystalline structures with defects and disorder. As the solid phase advances into the liquid phase, the modulations in the density distribution created behind the advancing solidification front do not necessarily have a wavelength that is the same as the equilibrium crystal lattice spacing. This is because in a deep enough quench the front propagation is governed by linear processes, but the crystal lattice spacing is determined by nonlinear terms. The wavelength mismatch can result in significant disorder behind the front that may or may not persist in the latter stage dynamics. We support these observations by presenting results from dynamical density functional theory calculations for simple one- and two-component two-dimensional systems of soft core particles.Comment: 25 pages, 11 figure

Fermi super-Tonks-Girardeau state for attractive Fermi gases in an optical lattice

We demonstrate that a kind of highly excited state of strongly attractive Hubbard model, named of Fermi super-Tonks-Girardeau state, can be realized in the spin-1/2 Fermi optical lattice system by a sudden switch of interaction from the strongly repulsive regime to the strongly attractive regime. In contrast to the ground state of the attractive Hubbard model, such a state is the lowest scattering state with no pairing between attractive fermions. With the aid of Bethe-ansatz method, we calculate energies of both the Fermi Tonks-Girardeau gas and the Fermi super-Tonks-Girardeau state of spin-1/2 ultracold fermions and show that both energies approach to the same limit as the strength of the interaction goes to infinity. By exactly solving the quench dynamics of the Hubbard model, we demonstrate that the Fermi super-Tonks-Girardeau state can be transferred from the initial repulsive ground state very efficiently. This allows the experimental study of properties of Fermi super-Tonks-Girardeau gas in optical lattices.Comment: 7 pages, 7 figure

Magnetic enhancement of Co0.2_{0.2}Zn0.8_{0.8}Fe2_2O4_4 spinel oxide by mechanical milling

We report the magnetic properties of mechanically milled Co$_{0.2}$Zn$_{0.8}$Fe$_2$O$_4$ spinel oxide. After 24 hours milling of the bulk sample, the XRD spectra show nanostructure with average particle size $\approx$ 20 nm. The as milled sample shows an enhancement in magnetization and ordering temperature compared to the bulk sample. If the as milled sample is annealed at different temperatures for the same duration, recrystallization process occurs and approaches to the bulk structure on increasing the annealing temperatures. The magnetization of the annealed samples first increases and then decreases. At higher annealing temperature ($\sim$ 1000$^{0}$C) the system shows two coexisting magnetic phases {\it i.e.}, spin glass state and ferrimagnetic state, similar to the as prepared bulk sample. The room temperature M\"{o}ssbauer spectra of the as milled sample, annealed at 300$^{0}$C for different durations (upto 575 hours), suggest that the observed change in magnetic behaviour is strongly related with cations redistribution between tetrahedral (A) and octahedral (O) sites in the spinel structure. Apart from the cation redistribution, we suggest that the enhancement of magnetization and ordering temperature is related with the reduction of B site spin canting and increase of strain induced anisotropic energy during mechanical milling.Comment: 14 pages LaTeX, 10 ps figure

Intragenic recombination between pseudogenes as a source of new disease specificity at a simple resistance locus

BACKGROUND: Pooling of multi-site MRI data is often necessary when a large cohort is desired. However, different scanning platforms can introduce systematic differences which confound true effects of interest. One may reduce multi-site bias by calibrating pivotal scanning parameters, or include them as covariates to improve the data integrity. NEW METHOD: In the present study we use a source-based morphometry (SBM) model to explore scanning effects in multi-site sMRI studies and develop a data-driven correction. Specifically, independent components are extracted from the data and investigated for associations with scanning parameters to assess the influence. The identified scanning-related components can be eliminated from the original data for correction. RESULTS: A small set of SBM components captured most of the variance associated with the scanning differences. In a dataset of 1460 healthy subjects, pronounced and independent scanning effects were observed in brainstem and thalamus, associated with magnetic field strength-inversion time and RF-receiving coil. A second study with 110 schizophrenia patients and 124 healthy controls demonstrated that scanning effects can be effectively corrected with the SBM approach. COMPARISON WITH EXISTING METHOD(S): Both SBM and GLM correction appeared to effectively eliminate the scanning effects. Meanwhile, the SBM-corrected data yielded a more significant patient versus control group difference and less questionable findings. CONCLUSIONS: It is important to calibrate scanning settings and completely examine individual parameters for the control of confounding effects in multi-site sMRI studies. Both GLM and SBM correction can reduce scanning effects, though SBM's data-driven nature provides additional flexibility and is better able to handle collinear effects

AdS Wormholes

We obtain a large class of smooth Lorentzian p-brane wormholes in supergravities in various dimensions. They connect two asymptotically flat spacetimes. In cases where there is no dilaton involved in the solution, the wormhole can connect an AdS_n\times S^m in one asymptotic region to a flat spacetime in the other. We obtain explicit examples for (n,m)=(4,7), (7,4), (5,5), (3,3), (3,2). These geometries correspond to field theories with UV conformal fixed points, and they undergo decompactification in the IR region. In the case of AdS_3, we compute the central charge of the corresponding conformal field theory.Comment: 20 pages, references adde

New Einstein-Sasaki and Einstein Spaces from Kerr-de Sitter

In this paper, which is an elaboration of our results in hep-th/0504225, we construct new Einstein-Sasaki spaces L^{p,q,r_1,...,r_{n-1}} in all odd dimensions D=2n+1\ge 5. They arise by taking certain BPS limits of the Euclideanised Kerr-de Sitter metrics. This yields local Einstein-Sasaki metrics of cohomogeneity n, with toric U(1)^{n+1} principal orbits, and n real non-trivial parameters. By studying the structure of the degenerate orbits we show that for appropriate choices of the parameters, characterised by the (n+1) coprime integers (p,q,r_1,...,r_{n-1}), the local metrics extend smoothly onto complete and non-singular compact Einstein-Sasaki manifolds L^{p,q,r_1,...,r_{n-1}}. We also construct new complete and non-singular compact Einstein spaces \Lambda^{p,q,r_1,...,r_n} in D=2n+1 that are not Sasakian, by choosing parameters appropriately in the Euclideanised Kerr-de Sitter metrics when no BPS limit is taken.Comment: latex, 26 page

Gene expression time delays & Turing pattern formation systems

The incorporation of time delays can greatly affect the behaviour of partial differential equations and dynamical systems. In addition, there is evidence that time delays in gene expression due to transcription and translation play an important role in the dynamics of cellular systems. In this paper, we investigate the effects of incorporating gene expression time delays into a one-dimensional putative reaction diffusion pattern formation mechanism on both stationary domains and domains with spatially uniform exponential growth. While oscillatory behaviour is rare, we find that the time taken to initiate and stabilise patterns increases dramatically as the time delay is increased. In addition, we observe that on rapidly growing domains the time delay can induce a failure of the Turing instability which cannot be predicted by a naive linear analysis of the underlying equations about the homogeneous steady state. The dramatic lag in the induction of patterning, or even its complete absence on occasions, highlights the importance of considering explicit gene expression time delays in models for cellular reaction diffusion patterning

New supersymmetric solutions of N=2, D=5 gauged supergravity with hyperscalars

We construct new supersymmetric solutions, including AdS bubbles, in an N=2 truncation of five-dimensional N=8 gauged supergravity. This particular truncation is given by N=2 gauged supergravity coupled to two vector multiples and three incomplete hypermultiplets, and was originally investigated in the context of obtaining regular AdS bubble geometries with multiple active R-charges. We focus on cohomogeneity-one solutions corresponding to objects with two equal angular momenta and up to three independent R-charges. Curiously, we find a new set of zero and negative mass solitons asymptotic to AdS_5/Z_k, for k \ge 3, which are everywhere regular without closed timelike curves.Comment: Latex 3 times, 42 page

Large spin limits of AdS/CFT and generalized Landau-Lifshitz equations

We consider AdS_5 x S^5 string states with several large angular momenta along AdS_5 and S^5 directions which are dual to single-trace Super-Yang-Mills (SYM) operators built out of chiral combinations of scalars and covariant derivatives. In particular, we focus on the SU(3) sector (with three spins in S^5) and the SL(2) sector (with one spin in AdS_5 and one in S^5), generalizing recent work hep-th/0311203 and hep-th/0403120 on the SU(2) sector with two spins in S^5. We show that, in the large spin limit and at the leading order in the effective coupling expansion, the string sigma model equations of motion reduce to matrix Landau-Lifshitz equations. We then demonstrate that the coherent-state expectation value of the one-loop SYM dilatation operator restricted to the corresponding sector of single trace operators is also effectively described by the same equations. This implies a universal leading order equivalence between string energies and SYM anomalous dimensions, as well as a matching of integrable structures. We also discuss the more general 5-spin sector and comment on SO(6) states dual to non-chiral scalar operators