A Catalog of Very Isolated Galaxies from the SDSS Data Release 1

We present a new catalog of isolated galaxies obtained through an automated systematic search. These 2980 isolated galaxies were found in approximately 2099 sq deg of sky in the Sloan Digital Sky Survey Data Release 1 (SDSS DR1) photometry. The selection algorithm, implementing a variation on the criteria developed by Karachentseva in 1973, proved to be very efficient and fast. This catalog will be useful for studies of the general galaxy characteristics. Here we report on our results.Comment: 67 pages, which includes 14 figures. Accepted for publication by A

Selective incorporation of proteinaceous over nonproteinaceous cationic amino acids in model prebiotic oligomerization reactions.

Numerous long-standing questions in origins-of-life research center on the history of biopolymers. For example, how and why did nature select the polypeptide backbone and proteinaceous side chains? Depsipeptides, containing both ester and amide linkages, have been proposed as ancestors of polypeptides. In this paper, we investigate cationic depsipeptides that form under mild dry-down reactions. We compare the oligomerization of various cationic amino acids, including the cationic proteinaceous amino acids (lysine, Lys; arginine, Arg; and histidine, His), along with nonproteinaceous analogs of Lys harboring fewer methylene groups in their side chains. These analogs, which have been discussed as potential prebiotic alternatives to Lys, are ornithine, 2,4-diaminobutyric acid, and 2,3-diaminopropionic acid (Orn, Dab, and Dpr). We observe that the proteinaceous amino acids condense more extensively than these nonproteinaceous amino acids. Orn and Dab readily cyclize into lactams, while Dab and Dpr condense less efficiently. Furthermore, the proteinaceous amino acids exhibit more selective oligomerization through their α-amines relative to their side-chain groups. This selectivity results in predominantly linear depsipeptides in which the amino acids are α-amine-linked, analogous to today's proteins. These results suggest a chemical basis for the selection of Lys, Arg, and His over other cationic amino acids for incorporation into proto-proteins on the early Earth. Given that electrostatics are key elements of protein-RNA and protein-DNA interactions in extant life, we hypothesize that cationic side chains incorporated into proto-peptides, as reported in this study, served in a variety of functions with ancestral nucleic acid polymers in the early stages of life

Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder

The effects of disease mutations on protein structure and function have been extensively investigated, and many predictors of the functional impact of single amino acid substitutions are publicly available. The majority of these predictors are based on protein structure and evolutionary conservation, following the assumption that disease mutations predominantly affect folded and conserved protein regions. However, the prevalence of the intrinsically disordered proteins (IDPs) and regions (IDRs) in the human proteome together with their lack of fixed structure and low sequence conservation raise a question about the impact of disease mutations in IDRs. Here, we investigate annotated missense disease mutations and show that 21.7% of them are located within such intrinsically disordered regions. We further demonstrate that 20% of disease mutations in IDRs cause local disorder-to-order transitions, which represents a 1.7–2.7 fold increase compared to annotated polymorphisms and neutral evolutionary substitutions, respectively. Secondary structure predictions show elevated rates of transition from helices and strands into loops and vice versa in the disease mutations dataset. Disease disorder-to-order mutations also influence predicted molecular recognition features (MoRFs) more often than the control mutations. The repertoire of disorder-to-order transition mutations is limited, with five most frequent mutations (R→W, R→C, E→K, R→H, R→Q) collectively accounting for 44% of all deleterious disorder-to-order transitions. As a proof of concept, we performed accelerated molecular dynamics simulations on a deleterious disorder-to-order transition mutation of tumor protein p63 and, in agreement with our predictions, observed an increased α-helical propensity of the region harboring the mutation. Our findings highlight the importance of mutations in IDRs and refine the traditional structure-centric view of disease mutations. The results of this study offer a new perspective on the role of mutations in disease, with implications for improving predictors of the functional impact of missense mutations

Multiple prebiotic metals mediate translation.

Today, Mg2+ is an essential cofactor with diverse structural and functional roles in life's oldest macromolecular machine, the translation system. We tested whether ancient Earth conditions (low O2, high Fe2+, and high Mn2+) can revert the ribosome to a functional ancestral state. First, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) was used to compare the effect of Mg2+, Fe2+, and Mn2+ on the tertiary structure of rRNA. Then, we used in vitro translation reactions to test whether Fe2+ or Mn2+ could mediate protein production, and quantified ribosomal metal content. We found that (i) Mg2+, Fe2+, and Mn2+ had strikingly similar effects on rRNA folding; (ii) Fe2+ and Mn2+ can replace Mg2+ as the dominant divalent cation during translation of mRNA to functional protein; and (iii) Fe and Mn associate extensively with the ribosome. Given that the translation system originated and matured when Fe2+ and Mn2+ were abundant, these findings suggest that Fe2+ and Mn2+ played a role in early ribosomal evolution

Discovery of Extreme Examples of Superclustering in Aquarius

We report the discovery of two highly extended filaments and one extremely high density knot within the region of Aquarius. The supercluster candidates were chosen via percolation analysis of the Abell and ACO catalogs and include only the richest clusters (R >= 1). The region examined is a 10x45 degree strip and is now 87% complete in cluster redshift measurements to mag_10 = 18.3. In all, we report 737 galaxy redshifts in 46 cluster fields. One of the superclusters, dubbed Aquarius, is comprised of 14 Abell/ACO clusters and extends 110h^-1Mpc in length only 7 degrees off the line-of-sight. On the near-end of the Aquarius filament, another supercluster, dubbed Aquarius-Cetus, extends for 75h^-1Mpc perpendicular to the line-of-sight. After fitting ellipsoids to both Aquarius and Aquarius-Cetus, we find axis ratios (long-to- midlength axis) of 4.3 for Aquarius and 3.0 for Aquarius-Cetus. We fit ellipsoids to all N>=5 clumps of clusters in the Abell/ACO measured-z cluster sample. The frequency of filaments with axis ratios >=3.0 (~20%) is nearly identical with that found among `superclusters' in Monte Carlo simulations of random and random- clumped clusters, however, so the rich Abell/ACO clusters have no particular tendency toward filamentation. The Aquarius filament also contains a `knot' of 6 clusters at Z ~0.11, with five of the clusters near enough togeteher to represent an apparent overdensity of 150. There are three other R >= 1 cluster density enhancements similar to this knot at lower redshifts: Corona Borealis, the Shapely Concentration, and another grouping of seven clusters in Microscopium. All four of these dense superclusters appear near the point of breaking away from the Hubble Flow, and some may now be in collapse, but there is little evidence of any being virialized.Comment: 45 pages (+ e-tables), 7 figures, AASTeX Accepted for Publication in Ap

Extra-planar gas in the spiral galaxy NGC 4559

We present 21-cm line observations of the spiral galaxy NGC 4559, made with the Westerbork Synthesis Radio Telescope. We have used them to study the HI distribution and kinematics, the relative amount and distribution of luminous and dark matter in this galaxy and, in particular, the presence of extra-planar gas. Our data do reveal the presence of such a component, in the form of a thick disk, with a mass of 5.9 x 10^8 Mo (one tenth of the total HI mass) and a mean rotation velocity 25-50 km/s lower than that of the thin disk. The extra-planar gas may be the result of galactic fountains but accretion from the IGM cannot be ruled out. With this study we confirm that lagging, thick HI layers are likely to be common in spiral galaxies.Comment: 17 pages, 10 figures. Accepted for publication in A&

Planck pre-launch status: HFI beam expectations from the optical optimisation of the focal plane

Planck is a European Space Agency (ESA) satellite, launched in May 2009, which will map the cosmic microwave background anisotropies in intensity and polarisation with unprecedented detail and sensitivity. It will also provide full-sky maps of astrophysical foregrounds. An accurate knowledge of the telescope beam patterns is an essential element for a correct analysis of the acquired astrophysical data. We present a detailed description of the optical design of the High Frequency Instrument (HFI) together with some of the optical performances measured during the calibration campaigns. We report on the evolution of the knowledge of the pre-launch HFI beam patterns when coupled to ideal telescope elements, and on their significance for the HFI data analysis procedure

Explosive Particle Dispersion in Plasma Turbulence

Particle dynamics are investigated in plasma turbulence, using self-consistent kinetic simulations, in two dimensions. In steady state, the trajectories of single protons and proton-pairs are studied, at different values of plasma "beta" (ratio between kinetic and magnetic pressure). For single-particle displacements, results are consistent with fluids and magnetic field line dynamics, where particles undergo normal diffusion for very long times, with higher "beta" being more diffusive. In an intermediate time range, with separations lying in the inertial range, particles experience an explosive dispersion in time, consistent with the Richardson prediction. These results, obtained for the first time with a self-consistent kinetic model, are relevant for astrophysical and laboratory plasmas, where turbulence is crucial for heating, mixing and acceleration processes