Chitinase and Fizz family members are a generalized feature of nematode infection with selective Upregulation of Ym1 and F10.1 by antigen-presenting cells

Ym1 and Fizz1 are secreted proteins that have been identified in a variety of Th2-mediated inflammatory settings. We originally found Ym1 and Fizz1 as highly expressed macrophage genes in a Brugia malayi infection model. Here, we show that their expression is a generalized feature of nematode infection and that they are induced at the site of infection with both the tissue nematode Litomosoides sigmodontis and the gastrointestinal nematode Nippostrongylus brasiliensis. At the sites of infection with N. brasiliensis, we also observed induction of other chitinase and Fizz family members (ChaFFs): acidic mammalian chitinase (AMCase) and Fizz2. The high expression of both Ym1 and AMCase in the lungs of infected mice suggests that abundant chitinase production is an important feature of Th2 immune responses in the lung. In addition to expression of ChaFFs in the tissues, Ym1 and Fizz1 expression was observed in the lymph nodes. Expression both in vitro and in vivo was restricted to antigen-presenting cells, with the highest expression in B cells and macrophages. ChaFFs may therefore be important effector or wound-repair molecules at the site of nematode infection, with potential regulatory roles for Ym1 and Fizz1 in the draining lymph nodes

A dedicated haem lyase is required for the maturation of a novel bacterial cytochrome c with unconventional covalent haem binding

In bacterial c-type cytochromes, the haem cofactor is covalently attached via two cysteine residues organized in a haem c-binding motif. Here, a novel octa-haem c protein, MccA, is described that contains only seven conventional haem c-binding motifs (CXXCH), in addition to several single cysteine residues and a conserved CH signature. Mass spectrometric analysis of purified MccA from Wolinella succinogenes suggests that two of the single cysteine residues are actually part of an unprecedented CX15CH sequence involved in haem c binding. Spectroscopic characterization of MccA identified an unusual high-potential haem c with a red-shifted absorption maximum, not unlike that of certain eukaryotic cytochromes c that exceptionally bind haem via only one thioether bridge. A haem lyase gene was found to be specifically required for the maturation of MccA in W. succinogenes. Equivalent haem lyase-encoding genes belonging to either the bacterial cytochrome c biogenesis system I or II are present in the vicinity of every known mccA gene suggesting a dedicated cytochrome c maturation pathway. The results necessitate reconsideration of computer-based prediction of putative haem c-binding motifs in bacterial proteomes

Vacancy-assisted domain-growth in asymmetric binary alloys: a Monte Carlo study

A Monte Carlo simulation study of the vacancy-assisted domain-growth in asymmetric binary alloys is presented. The system is modeled using a three-state ABV Hamiltonian which includes an asymmetry term, not considered in previous works. Our simulated system is a stoichiometric two-dimensional binary alloy with a single vacancy which evolves according to the vacancy-atom exchange mechanism. We obtain that, compared to the symmetric case, the ordering process slows down dramatically. Concerning the asymptotic behavior it is algebraic and characterized by the Allen-Cahn growth exponent x=1/2. The late stages of the evolution are preceded by a transient regime strongly affected by both the temperature and the degree of asymmetry of the alloy. The results are discussed and compared to those obtained for the symmetric case.Comment: 21 pages, 9 figures, accepted for publication in Phys. Rev.

Phonons and specific heat of linear dense phases of atoms physisorbed in the grooves of carbon nanotube bundles

The vibrational properties (phonons) of a one-dimensional periodic phase of atoms physisorbed in the external groove of the carbon nanotube bundle are studied. Analytical expressions for the phonon dispersion relations are derived. The derived expressions are applied to Xe, Kr and Ar adsorbates. The specific heat pertaining to dense phases of these adsorbates is calculated.Comment: 4 PS figure

On the Formation Height of the SDO/HMI Fe 6173 Doppler Signal

The Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory (SDO) is designed to study oscillations and the mag- netic field in the solar photosphere. It observes the full solar disk in the Fe I absorption line at 6173\AA . We use the output of a high-resolution 3D, time- dependent, radiation-hydrodynamic simulation based on the CO5BOLD code to calculate profiles F({\lambda},x,y,t) for the Fe I 6173{\AA} line. The emerging profiles F({\lambda},x,y,t) are multiplied by a representative set of HMI filter transmission profiles R_i({\lambda},1 \leq i \leq 6) and filtergrams I_i(x,y,t;1 \leq i \leq 6) are constructed for six wavelengths. Doppler velocities V_HMI(x,y,t) are determined from these filtergrams using a simplified version of the HMI pipeline. The Doppler velocities are correlated with the original velocities in the simulated atmosphere. The cross- correlation peaks near 100 km, suggesting that the HMI Doppler velocity signal is formed rather low in the solar atmosphere. The same analysis is performed for the SOHO/MDI Ni I line at 6768\AA . The MDI Doppler signal is formed slightly higher at around 125 km. Taking into account the limited spatial resolution of the instruments, the apparent formation height of both the HMI and MDI Doppler signal increases by 40 to 50 km. We also study how uncertainties in the HMI filter-transmission profiles affect the calculated velocities.Comment: 15 pages, 11 Figure

Heavy Carriers and Non-Drude Optical Conductivity in MnSi

Optical properties of the weakly helimagnetic metal MnSi have been determined in the photon energy range from 2 meV to 4.5 eV using the combination of grazing incidence reflectance at 80 degrees (2 meV to 0.8 eV) and ellipsometry (0.8 to 4.5 eV). As the sample is cooled below 100 K the effective mass becomes strongly frequency dependent at low frequencies, while the scattering rate developes a linear frequency dependence. The complex optical conductivity can be described by the phenomenological relation \sigma(\omega,T) \propto (\Gamma(T)+i\omega)^{-1/2} used for cuprates and ruthenates.Comment: 5 pages, ReVTeX 4, 5 figures in eps forma

Cosmic distance-duality as probe of exotic physics and acceleration

In cosmology, distances based on standard candles (e.g. supernovae) and standard rulers (e.g. baryon oscillations) agree as long as three conditions are met: (1) photon number is conserved, (2) gravity is described by a metric theory with (3) photons travelling on unique null geodesics. This is the content of distance-duality (the reciprocity relation) which can be violated by exotic physics. Here we analyse the implications of the latest cosmological data sets for distance-duality. While broadly in agreement and confirming acceleration we find a 2-sigma violation caused by excess brightening of SN-Ia at z > 0.5, perhaps due to lensing magnification bias. This brightening has been interpreted as evidence for a late-time transition in the dark energy but because it is not seen in the d_A data we argue against such an interpretation. Our results do, however, rule out significant SN-Ia evolution and extinction: the "replenishing" grey-dust model with no cosmic acceleration is excluded at more than 4-sigma despite this being the best-fit to SN-Ia data alone, thereby illustrating the power of distance-duality even with current data sets.Comment: 6 pages, 4 colour figures. Version accepted as a Rapid Communication in PR

Quantum Fields in a Big Crunch/Big Bang Spacetime

We consider quantum field theory on a spacetime representing the Big Crunch/Big Bang transition postulated in the ekpyrotic or cyclic cosmologies. We show via several independent methods that an essentially unique matching rule holds connecting the incoming state, in which a single extra dimension shrinks to zero, to the outgoing state in which it re-expands at the same rate. For free fields in our construction there is no particle production from the incoming adiabatic vacuum. When interactions are included the total particle production for fixed external momentum is finite at tree level. We discuss a formal correspondence between our construction and quantum field theory on de Sitter spacetime.Comment: 30 pages, RevTex file, five postscript figure file

Domain Growth and Finite-Size-Scaling in the Kinetic Ising Model

This paper describes the application of finite-size scaling concepts to domain growth in systems with a non-conserved order parameter. A finite-size scaling ansatz for the time-dependent order parameter distribution function is proposed, and tested with extensive Monte-Carlo simulations of domain growth in the 2-D spin-flip kinetic Ising model. The scaling properties of the distribution functions serve to elucidate the configurational self-similarity that underlies the dynamic scaling picture. Moreover, it is demonstrated that the application of finite-size-scaling techniques facilitates the accurate determination of the bulk growth exponent even in the presence of strong finite-size effects, the scale and character of which are graphically exposed by the order parameter distribution function. In addition it is found that one commonly used measure of domain size--the scaled second moment of the magnetisation distribution--belies the full extent of these finite-size effects.Comment: 13 pages, Latex. Figures available on request. Rep #9401