Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity

BACKGROUND The Cation Diffusion Facilitator (CDF) family is a ubiquitous family of heavy metal transporters. Much interest in this family has focused on implications for human health and bioremediation. In this work a broad phylogenetic study has been undertaken which, considered in the context of the functional characteristics of some fully characterised CDF transporters, has aimed at identifying molecular determinants of substrate selectivity and at suggesting metal specificity for newly identified CDF transporters. RESULTS Representative CDF members from all three kingdoms of life (Archaea, Eubacteria, Eukaryotes) were retrieved from genomic databases. Protein sequence alignment has allowed detection of a modified signature that can be used to identify new hypothetical CDF members. Phylogenetic reconstruction has classified the majority of CDF family members into three groups, each containing characterised members that share the same specificity towards the principally-transported metal, i.e. Zn, Fe/Zn or Mn. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The function of some conserved amino acids was assessed by site-directed mutagenesis in the poplar Zn2+ transporter PtdMTP1 and compared with similar experiments performed in prokaryotic members. An essential structural role can be assigned to a widely conserved glycine residue, while aspartate and histidine residues, highly conserved in putative transmembrane domains, might be involved in metal transport. The potential role of group-conserved amino acid residues in metal specificity is discussed. CONCLUSION In the present study phylogenetic and functional analyses have allowed the identification of three major substrate-specific CDF groups. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The modified signature sequence proposed in this work can be used to identify new hypothetical CDF members

New Results from a Near-Infrared Search for Hidden Broad-Line Regions in Ultraluminous Infrared Galaxies

This paper reports the latest results from a near-infrared search for hidden broad-line regions (BLRs: FWHM >~ 2,000 km/s) in ultraluminous infrared galaxies (ULIGs). The new sample contains thirty-nine ULIGs from the 1-Jy sample selected for their lack of BLRs at optical wavelengths. The results from this new study are combined with those from our previous optical and near-infrared surveys to derive the fraction of all ULIGs with optical or near-infrared signs of genuine AGN activity (either a BLR or [Si VI] emission). Comparisons of the dereddened emission-line luminosities of the optical or obscured BLRs detected in the ULIGs of the 1-Jy sample with those of optical quasars indicate that the obscured AGN/quasar in ULIGs is the main source of energy in at least 15 -- 25% of all ULIGs in the 1-Jy sample. This fraction is 30 -- 50% among ULIGs with L_ir > 10^{12.3} L_sun. These results are compatible with those from recent mid-infrared spectroscopic surveys carried out with ISO. (abridged)Comment: 40 pages including 10 figures and 3 tables (Table 3 should be printed in landscape mode

Major Galaxy Mergers and the Growth of Supermassive Black Holes in Quasars

Despite observed strong correlations between central supermassive black holes (SMBHs) and star-formation in galactic nuclei, uncertainties exist in our understanding of their coupling. We present observations of the ratio of heavily-obscured to unobscured quasars as a function of cosmic epoch up to z~3, and show that a simple physical model describing mergers of massive, gas-rich galaxies matches these observations. In the context of this model, every obscured and unobscured quasar represent two distinct phases that result from a massive galaxy merger event. Much of the mass growth of the SMBH occurs during the heavily-obscured phase. These observations provide additional evidence for a causal link between gas-rich galaxy mergers, accretion onto the nuclear SMBH and coeval star formation.Comment: Accepted for publication in Science. Published by Science Express on March 25th. 17 pages, 5 figures, including supplemental online materia

An IRAS High Resolution Image Restoration (HIRES) Atlas of All Interacting Galaxies in the IRAS Revised Bright Galaxy Sample

We present high-resolution (30"-1') 12, 25, 60, and 100 micron images of 106 interacting galaxy systems contained in the IRAS Revised Bright Galaxy Sample (RBGS, Sanders et al. 2003), a complete sample of all galaxies having a 60 micron flux density greater than 5.24 Jy. These systems were selected to have at least two distinguishable galaxies separated by less than three average galactic diameters, and thus we have excluded very widely separated systems and very advanced mergers. The new complete survey has the same properties as the prototype survey of Surace et al. 1993. We find no increased tendency for infrared-bright galaxies to be associated with other infrared bright galaxies among the widely separated pairs studied here. We find small enhancements in far-infrared activity in multiple galaxy systems relative to RBGS non-interacting galaxies with the same blue luminosity distribution. We also find no differences in infrared activity (as measured by infrared color and luminosity) between late and early-type spiral galaxies.Comment: 49 pages, 13 figures. To appear in the Astronomical Journal. Figures have been degraded due to space considerations. A PDF version with higher quality figures is available at http://humu.ipac.caltech.edu/~jason/pubs/surace_hires.pd

Multi-Terabyte EIDE Disk Arrays running Linux RAID5

High-energy physics experiments are currently recording large amounts of data and in a few years will be recording prodigious quantities of data. New methods must be developed to handle this data and make analysis at universities possible. Grid Computing is one method; however, the data must be cached at the various Grid nodes. We examine some storage techniques that exploit recent developments in commodity hardware. Disk arrays using RAID level 5 (RAID-5) include both parity and striping. The striping improves access speed. The parity protects data in the event of a single disk failure, but not in the case of multiple disk failures. We report on tests of dual-processor Linux Software RAID-5 arrays and Hardware RAID-5 arrays using a 12-disk 3ware controller, in conjunction with 250 and 300 GB disks, for use in offline high-energy physics data analysis. The price of IDE disks is now less than $1/GB. These RAID-5 disk arrays can be scaled to sizes affordable to small institutions and used when fast random access at low cost is important.Comment: Talk from the 2004 Computing in High Energy and Nuclear Physics (CHEP04), Interlaken, Switzerland, 27th September - 1st October 2004, 4 pages, LaTeX, uses CHEP2004.cls. ID 47, Poster Session 2, Track

Outflows in Infrared-Luminous Starbursts at z < 0.5. I. Sample, NaI D Spectra, and Profile Fitting

We have conducted a spectroscopic survey of 78 starbursting infrared-luminous galaxies at redshifts up to z = 0.5. We use moderate-resolution spectroscopy of the NaI D interstellar absorption feature to directly probe the neutral phase of outflowing gas in these galaxies. Over half of our sample are ultraluminous infrared galaxies that are classified as starbursts; the rest have infrared luminosities in the range log(L_IR/L_sun) = 10.2 - 12.0. The sample selection, observations, and data reduction are described here. The absorption-line spectra of each galaxy are presented. We also discuss the theory behind absorption-line fitting in the case of a partially-covered, blended absorption doublet observed at moderate-to-high resolution, a topic neglected in the literature. A detailed analysis of these data is presented in a companion paper.Comment: 59 pages, 18 figures in AASTeX preprint style; to appear in September issue of ApJ

Gyroscopes based on nitrogen-vacancy centers in diamond

We propose solid-state gyroscopes based on ensembles of negatively charged nitrogen-vacancy (${\rm NV^-}$) centers in diamond. In one scheme, rotation of the nitrogen-vacancy symmetry axis will induce Berry phase shifts in the ${\rm NV^{-}}$ electronic ground-state coherences proportional to the solid angle subtended by the symmetry axis. We estimate sensitivity in the range of $5\times10^{-3} {\rm rad/s/\sqrt{Hz}}$ in a 1 ${\rm mm^3}$ sensor volume using a simple Ramsey sequence. Incorporating dynamical decoupling to suppress dipolar relaxation may yield sensitivity at the level of $10^{-5} {\rm rad/s/\sqrt{Hz}}$. With a modified Ramsey scheme, Berry phase shifts in the ${\rm ^{14}N}$ hyperfine sublevels would be employed. The projected sensitivity is in the range of $10^{-5} {\rm rad/s/\sqrt{Hz}}$, however the smaller gyromagnetic ratio reduces sensitivity to magnetic-field noise by several orders of magnitude. Reaching $10^{-5} {\rm rad/s/\sqrt{Hz}}$ would represent an order of magnitude improvement over other compact, solid-state gyroscope technologies.Comment: 3 figures, 5 page

Representations of the Weyl group and Wigner functions for SU(3)

Bases for SU(3) irreps are constructed on a space of three-particle tensor products of two-dimensional harmonic oscillator wave functions. The Weyl group is represented as the symmetric group of permutations of the particle coordinates of these space. Wigner functions for SU(3) are expressed as products of SU(2) Wigner functions and matrix elements of Weyl transformations. The constructions make explicit use of dual reductive pairs which are shown to be particularly relevant to problems in optics and quantum interferometry.Comment: : RevTex file, 11 pages with 2 figure

Metastability in Markov processes

We present a formalism to describe slowly decaying systems in the context of finite Markov chains obeying detailed balance. We show that phase space can be partitioned into approximately decoupled regions, in which one may introduce restricted Markov chains which are close to the original process but do not leave these regions. Within this context, we identify the conditions under which the decaying system can be considered to be in a metastable state. Furthermore, we show that such metastable states can be described in thermodynamic terms and define their free energy. This is accomplished showing that the probability distribution describing the metastable state is indeed proportional to the equilibrium distribution, as is commonly assumed. We test the formalism numerically in the case of the two-dimensional kinetic Ising model, using the Wang--Landau algorithm to show this proportionality explicitly, and confirm that the proportionality constant is as derived in the theory. Finally, we extend the formalism to situations in which a system can have several metastable states.Comment: 30 pages, 5 figures; version with one higher quality figure available at http://www.fis.unam.mx/~dsanders

Do Newton's G and Milgrom's a_0 vary with cosmological epoch ?

In the scalar tensor gravitational theories Newton's constant G_N evolves in the expanding universe. Likewise, it has been speculated that the acceleration scale a_0 in Milgrom's modified Newtonian dynamics (MOND) is tied to the scale of the cosmos, and must thus evolve. With the advent of relativistic implementations of the modified dynamics, one can address the issue of variability of the two gravitational ''constants'' with some confidence. Using TeVeS, the Tensor-Vector-Scalar gravitational theory, as an implementation of MOND, we calculate the dependence of G_N and a_0 on the TeVeS parameters and the coeval cosmological value of its scalar field, \phi_c. We find that G_N, when expressed in atomic units, is strictly nonevolving, a result fully consistent with recent empirical limits on the variation of G_N. By contrast, we find that a_0 depends on \phi_c and may thus vary with cosmological epoch. However, for the brand of TeVeS which seems most promising, a_0 variation occurs on a timescale much longer than Hubble's, and should be imperceptible back to redshift unity or even beyond it. This is consistent with emergent data on the rotation curves of disk galaxies at significants redshifts.Comment: 9 pages, RevTe