On quantization of singular varieties and applications to D-branes

We calculate the ring of differential operators on some singular affine varieties (intersecting stacks, a point on a singular curve or an orbifold). Our results support the proposed connection of the ring of differential operators with geometry of D-branes in (bosonic) string theory. In particular, the answer does know about the resolution of singularities in accordance with the string theory predictions.Comment: LaTeX2e, 17 pages, misprints correcte

Five Glutamic Acid Residues in the C-Terminal Domain of the ChlD Subunit Play a Major Role in Conferring Mg2+ Cooperativity upon Magnesium Chelatase

Magnesium chelatase catalyzes the first committed step in chlorophyll biosynthesis by inserting a Mg2+ ion into protoporphyrin IX in an ATP-dependent manner. The cyanobacterial (Synechocystis) and higher-plant chelatases exhibit a complex cooperative response to free magnesium, while the chelatases from Thermosynechococcus elongatus and photosynthetic bacteria do not. To investigate the basis for this cooperativity, we constructed a series of chimeric ChlD proteins using N-terminal, central, and C-terminal domains from Synechocystis and Thermosynechococcus. We show that five glutamic acid residues in the C-terminal domain play a major role in this process

The ChlD subunit links the motor and porphyrin binding subunits of magnesium chelatase

Magnesium chelatase initiates chlorophyll biosynthesis, catalysing the MgATP2- dependent insertion of a Mg2+ ion into protoporphyin IX. The catalytic core of this large enzyme complex consists of three subunits: Bch/ChlI, Bch/ChlD and Bch/ChlH (in bacteriochlorophyll and chlorophyll producing species respectively). The D and I subunits are members of the AAA+ (ATPases associated with various cellular activities) superfamily of enzymes, and they form a complex that binds to H, the site of metal ion insertion. In order to investigate the physical coupling between ChlID and ChlH in vivo and in vitro , ChlD was FLAG-tagged in the cyanobacterium Synechocystis sp. PCC 6803 and co-immunoprecipitation experiments showed interactions with both ChlI and ChlH. Co-production of recombinant ChlD and ChlH in Escherichia coli yielded a ChlDH. Quantitative analysis using microscale thermophoresis (MST) showed magnesium-dependent binding ( K d 331 ± 58 nM) between ChlD and H. The physical basis for a ChlD-H interaction was investigated using chemical crosslinking coupled with mass spectrometry (XL-MS), together with modifications that either truncate ChlD or modify single residues. We found that the C-terminal integrin I domain of ChlD governs association with ChlH, the Mg2+ dependence of which also mediates the cooperative response of the Synechocystis chelatase to magnesium. Our work, showing the interaction site between the AAA+ motor and the chelatase domain of magnesium chelatase, will be essential for understanding how free energy from the hydrolysis of ATP on the AAA+ ChlI subunit is transmitted via the bridging subunit ChlD to the active site on ChlH

Charge and Isospin Fluctuations in High Energy pp-Collisions

Charge and isospin event-by-event fluctuations in high-energy pp-collisions are predicted within the Unitary Eikonal Model, in particular the fluctuation patterns of the ratios of charged-to-charged and neutral-to-charged pions. These fluctuations are found to be sensitive to the presence of unstable resonances, such as $\rho$ and $\omega$ mesons. We predict that the charge-fluctuation observable $D_{UEM}$ should be restricted to the interval $8/3\le D_{UEM}\le 4$ depending on the $\rho /\pi$ production ratio. Also, the isospin fluctuations of the DCC-type of the ratio of neutral-to-charged pions are suppressed if pions are produced together with $\rho$ mesons.Comment: Latex, 5 pages, no figures. To appear in the proceedings of 9th Adriatic Meeting, Dubrovnik, Croatia, 4 - 14 September 2003. Added reference into reference no.

Distribution function approach to redshift space distortions. Part IV: perturbation theory applied to dark matter

We develop a perturbative approach to redshift space distortions (RSD) using the phase space distribution function approach and apply it to the dark matter redshift space power spectrum and its moments. RSD can be written as a sum over density weighted velocity moments correlators, with the lowest order being density, momentum density and stress energy density. We use standard and extended perturbation theory (PT) to determine their auto and cross correlators, comparing them to N-body simulations. We show which of the terms can be modeled well with the standard PT and which need additional terms that include higher order corrections which cannot be modeled in PT. Most of these additional terms are related to the small scale velocity dispersion effects, the so called finger of god (FoG) effects, which affect some, but not all, of the terms in this expansion, and which can be approximately modeled using a simple physically motivated ansatz such as the halo model. We point out that there are several velocity dispersions that enter into the detailed RSD analysis with very different amplitudes, which can be approximately predicted by the halo model. In contrast to previous models our approach systematically includes all of the terms at a given order in PT and provides a physical interpretation for the small scale dispersion values. We investigate RSD power spectrum as a function of \mu, the cosine of the angle between the Fourier mode and line of sight, focusing on the lowest order powers of \mu and multipole moments which dominate the observable RSD power spectrum. Overall we find considerable success in modeling many, but not all, of the terms in this expansion.Comment: 37 pages, 13 figures, published in JCA

Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency

Background & Aims: Nonalcoholic fatty liver disease affects up to 30% of the US population, but the mechanisms underlying this condition are incompletely understood. We investigated how diet standardization and choline deficiency influence the composition of the microbial community in the human gastrointestinal tract and the development of fatty liver under conditions of choline deficiency. Methods: We performed a 2-month inpatient study of 15 female subjects who were placed on well-controlled diets in which choline levels were manipulated. We used 454-FLX pyrosequencing of 16S ribosomal RNA bacterial genes to characterize microbiota in stool samples collected over the course of the study. Results: The compositions of the gastrointestinal microbial communities changed with choline levels of diets; each individual's microbiome remained distinct for the duration of the experiment, even though all subjects were fed identical diets. Variations between subjects in levels of Gammaproteobacteria and Erysipelotrichi were directly associated with changes in liver fat in each subject during choline depletion. Levels of these bacteria, change in amount of liver fat, and a single nucleotide polymorphism that affects choline were combined into a model that accurately predicted the degree to which subjects developed fatty liver on a choline-deficient diet. Conclusions: Host factors and gastrointestinal bacteria each respond to dietary choline deficiency, although the gut microbiota remains distinct in each individual. We identified bacterial biomarkers of fatty liver that result from choline deficiency, adding to the accumulating evidence that gastrointestinal microbes have a role in metabolic disorders

Dark matter halos and the anisotropy of ultra-high energy cosmic rays

Several explanations for the existence of Ultra High Energy Cosmic Rays invoke the idea that they originate from the decay of massive particles created in the reheating following inflation. It has been suggested that the decay products can explain the observed isotropic flux of cosmic rays. We have calculated the anisotropy expected for various models of the dark matter distribution and find that at present data are too sparse above $4 \times 10^{19}$ eV to discriminate between different models. However we show that with data from three years of operation of the southern section of the Pierre Auger Observatory significant progress in testing the proposals will be made.Comment: 21 pages, 6 figures (ps), Astroparticle Physics (accepted for publication

Quantum properties of the three-mode squeezed operator: triply concurrent parametric amplifiers

In this paper, we study the quantum properties of the three-mode squeezed operator. This operator is constructed from the optical parametric oscillator based on the three concurrent $\chi^{(2)}$ nonlinearities. We give a complete treatment for this operator including the symmetric and asymmetric nonlinearities cases. The action of the operator on the number and coherent states are studied in the framework of squeezing, second-order correlation function, Cauchy-Schwartz inequality and single-mode quasiprobability function. The nonclassical effects are remarkable in all these quantities. We show that the nonclassical effects generated by the asymmetric case--for certain values of the system parameters--are greater than those of the symmetric one. This reflects the important role for the asymmetry in the system. Moreover, the system can generate different types of the Schr\"odinger-cat states.Comment: 21 pages, 14 figures; comments are most welcom

The active site of magnesium chelatase

The insertion of magnesium into protoporphyrin initiates the biosynthesis of chlorophyll, the pigment that underpins photosynthesis. This reaction, catalysed by the magnesium chelatase complex, couples ATP hydrolysis by a ChlID motor complex to chelation within the ChlH subunit. We probed the structure and catalytic function of ChlH using a combination of X-ray crystallography, computational modelling, mutagenesis and enzymology. Two linked domains of ChlH in an initially open conformation of ChlH bind protoporphyrin IX, and the rearrangement of several loops envelops this substrate, forming an active site cavity. This induced fit brings an essential glutamate (E660), proposed to be the key catalytic residue for magnesium insertion, into proximity with the porphyrin. A buried solvent channel adjacent to E660 connects the exterior bulk solvent to the active site, forming a possible conduit for the delivery of magnesium or abstraction of protons

Probing the primordial power spectra with inflationary priors

We investigate constraints on power spectra of the primordial curvature and tensor perturbations with priors based on single-field slow-roll inflation models. We stochastically draw the Hubble slow-roll parameters and generate the primordial power spectra using the inflationary flow equations. Using data from recent observations of CMB and several measurements of geometrical distances in the late Universe, Bayesian parameter estimation and model selection are performed for models that have separate priors on the slow-roll parameters. The same analysis is also performed adopting the standard parameterization of the primordial power spectra. We confirmed that the scale-invariant Harrison-Zel'dovich spectrum is disfavored with increased significance from previous studies. While current observations appear to be optimally modeled with some simple models of single-field slow-roll inflation, data is not enough constraining to distinguish these models.Comment: 23 pages, 3 figures, 7 tables, accepted for publication in JCA