What Determines the Depth of BALs? Keck HIRES Observations of BALQSO 1603+300

We find that the depth and shape of the broad absorption lines (BALs) in BALQSO 1603+3002 are determined largely by the fraction of the emitting source which is covered by the BAL flow. In addition, the observed depth of the BALs is poorly correlated with their real optical depth. The implication of this result is that abundance studies based on direct extraction of column densities from the depth of the absorption troughs are unreliable. Our conclusion is based on analysis of unblended absorption features of two lines from the same ion (in this case the Si IV doublet), which allows unambiguous separation of covering factor and optical depth effects. The complex morphology of the covering factor as a function of velocity suggests that the BALs are produced by several physically separated outflows. The covering factor is ion dependent in both depth and velocity width. We also find evidence that in BALQSO 1603+3002 the flow does not cover the broad emission line region.Comment: 13 pages, 2 figures, accepted for publication in Ap

The FIRST Bright Quasar Survey. II. 60 Nights and 1200 Spectra Later

We have used the VLA FIRST survey and the APM catalog of the POSS-I plates as the basis for constructing a new radio-selected sample of optically bright quasars. This is the first radio-selected sample that is competitive in size with current optically selected quasar surveys. Using only two basic criteria, radio-optical positional coincidence and optical morphology, quasars and BL Lacs can be identified with 60% selection efficiency; the efficiency increases to 70% for objects fainter than magnitude 17. We show that a more sophisticated selection scheme can predict with better than 85% reliability which candidates will turn out to be quasars. This paper presents the second installment of the FIRST Bright Quasar Survey with a catalog of 636 quasars distributed over 2682 square degrees. The quasar sample is characterized and all spectra are displayed. The FBQS detects both radio-loud and radio-quiet quasars out to a redshift z>3. We find a large population of objects of intermediate radio-loudness; there is no evidence in our sample for a bimodal distribution of radio characteristics. The sample includes ~29 broad absorption line quasars, both high and low ionization, and a number of new objects with remarkable optical spectra.Comment: 41 pages plus 39 gifs which contain all quasar spectra. Accepted for publication in the Astrophysical Journal Supplement Serie

Helium abundance in the most metal-deficient blue compact galaxies: I Zw 18 and SBS 0335-052

We present high-quality spectroscopic observations of the two most-metal deficient blue compact galaxies known, I Zw 18 and SBS 0335-052 to determine the helium abundance. The underlying stellar absorption strongly influences the observed intensities of He I emission lines in the brightest NW component of I Zw 18, and hence this component should not be used for primordial He abundance determination. The effect of underlying stellar absorption, though present, is much smaller in the SE component. Assuming all systematic uncertainties are negligible, the He mass fraction derived in this component is Y = 0.243+/-0.007. The high signal-to-noise ratio spectrum (> 100 in the continuum) of SBS 0335-052 allows us to measure the helium mass fraction with a precision better than 2% -- 5% in nine different regions along the slit. Assuming all systematic uncertainties are negligible, the weighted mean He mass fraction in SBS 0335-052 is Y = 0.2437+/-0.0014 when the three He I 4471, 5876 and 6678 emission lines are used, and is 0.2463+/-0.0015 when the He I 4471 emission line is excluded. The weighted mean helium mass fraction in the two most metal-deficient BCGs I Zw 18 and SBS 0335-052, Y=0.2462+/-0.0015, after correction for the stellar He production results in a primordial He mass fraction Yp = 0.2452+/-0.0015. The derived Yp leads to a baryon-to-photon ratio of (4.7+/-1.0) 10^{-10}, consistent with the values derived from the primordial D and 7Li abundances, and supporting the standard big bang nucleosynthesis theory. For the most consistent set of primordial D, 4He, and 7Li abundances we derive an equivalent number of light neutrino species 3.0+/-0.3 (95% C.L.).Comment: 28 pages, 10 figures. To appear in Ap

I ZW 18 -- a New Wolf-Rayet Galaxy

We report the discovery of broad Wolf-Rayet emission lines in the Multiple Mirror Telescope (MMT) spectrum of the NW component of I Zw 18, the lowest-metallicity blue compact dwarf (BCD) galaxy known. Two broad Wolf-Rayet (W-R) bumps at the wavelengths $\lambda$4650 and $\lambda$5800 are detected indicating the presence of WN and WC stars. The total numbers of WN and WC stars inferred from the luminosities of the broad He II $\lambda$4686 and C IV $\lambda$5808 lines are equal to 17(+/-)4 and 5(+/-)2, respectively. The W-R to O stars number ratio is equal to about 0.02, in satisfactory agreement with the value predicted by massive stellar evolution models with enhanced mass loss rates. The WC stars in the northwest component of I Zw 18 can be responsible for the presence of the nebular He II $\lambda$4686 emission line, however the observed intensity of this line is several times larger than model predictions, and other sources of ionizing radiation at wavelengths shorter than 228\AA are necessary.Comment: Ap.J.Lett., in pres

Inhibition of dipeptidyl peptidase IV and xanthine oxidase by amino acids and dipeptides

peer-reviewedXanthine oxidase (XO) and dipeptidyl peptidase IV (DPP-IV) inhibition by amino acids and dipeptides was studied. Trp and Trp-containing dipeptides (Arg-Trp, Trp-Val, Val-Trp, Lys-Trp and Ile-Trp) inhibited XO. Three amino acids (Met, Leu and Trp) and eight dipeptides (Phe-Leu, Trp-Val, His-Leu, Glu-Lys, Ala-Leu, Val-Ala, Ser-Leu and Gly-Leu) inhibited DPP-IV. Trp and Trp-Val were multifunctional inhibitors of XO and DPP-IV. Lineweaver and Burk analysis showed that Trp was a non-competitive inhibitor of XO and a competitive inhibitor of DPP-IV. Molecular docking with Autodock Vina was used to better understand the interaction of the peptides with the active site of the enzyme. Because of the non-competitive inhibition observed, docking of Trp-Val to the secondary binding sites of XO and DPP-IV is required. Trp-Val was predicted to be intestinally neutral (between 25% and 75% peptide remaining after 60 min simulated intestinal digestion). These results are of significance for the reduction of reactive oxygen species (ROS) and the increase of the half-life of incretins by food-derived peptides. (C) 2013 Elsevier Ltd. All rights reserved.ACCEPTEDpeer-reviewe

HST STIS Observations of PG 0946+301: the Highest Quality UV Spectrum of a BALQSO

We describe deep (40 orbits) HST/STIS observations of the BALQSO PG 0946+301 and make them available to the community. These observations are the major part of a multi-wavelength campaign on this object aimed at determining the ionization equilibrium and abundances (IEA) in broad absorption line (BAL) QSOs. We present simple template fits to the entire data set, which yield firm identifications for more than two dozen BALs from 18 ions and give lower limits for the ionic column densities. We find that the outflow's metalicity is consistent with being solar, while the abundance ratio of phosphorus to other metals is at least ten times solar. These findings are based on diagnostics that are not sensitive to saturation and partial covering effects in the BALs, which considerably weakened previous claims for enhanced metalicity. Ample evidence for these effects is seen in the spectrum. We also discuss several options for extracting tighter IEA constraints in future analyses, and present the significant temporal changes which are detected between these spectra and those taken by the HST/FOS in 1992.Comment: 32 pages, 7 figures, to appear in ApJ. See also companion paper by Arav, Korista and De Koo

Misregulation of Scm3p/HJURP Causes Chromosome Instability in Saccharomyces cerevisiae and Human Cells

The kinetochore (centromeric DNA and associated proteins) is a key determinant for high fidelity chromosome transmission. Evolutionarily conserved Scm3p is an essential component of centromeric chromatin and is required for assembly and function of kinetochores in humans, fission yeast, and budding yeast. Overexpression of HJURP, the mammalian homolog of budding yeast Scm3p, has been observed in lung and breast cancers and is associated with poor prognosis; however, the physiological relevance of these observations is not well understood. We overexpressed SCM3 and HJURP in Saccharomyces cerevisiae and HJURP in human cells and defined domains within Scm3p that mediate its chromosome loss phenotype. Our results showed that the overexpression of SCM3 (GALSCM3) or HJURP (GALHJURP) caused chromosome loss in a wild-type yeast strain, and overexpression of HJURP led to mitotic defects in human cells. GALSCM3 resulted in reduced viability in kinetochore mutants, premature separation of sister chromatids, and reduction in Cse4p and histone H4 at centromeres. Overexpression of CSE4 or histone H4 suppressed chromosome loss and restored levels of Cse4p at centromeres in GALSCM3 strains. Using mutant alleles of scm3, we identified a domain in the N-terminus of Scm3p that mediates its interaction with CEN DNA and determined that the chromosome loss phenotype of GALSCM3 is due to centromeric association of Scm3p devoid of Cse4p/H4. Furthermore, we determined that similar to other systems the centromeric association of Scm3p is cell cycle regulated. Our results show that altered stoichiometry of Scm3p/HJURP, Cse4p, and histone H4 lead to defects in chromosome segregation. We conclude that stringent regulation of HJURP and SCM3 expression are critical for genome stability

Regulation of type 1 diabetes development and B-cell activation in nonobese diabetic mice by early life exposure to a diabetogenic environment

Microbes, including viruses, influence type 1 diabetes (T1D) development, but many such influences remain undefined. Previous work on underlying immune mechanisms has focussed on cytokines and T cells. Here, we compared two nonobese diabetic (NOD) mouse colonies, NODlow and NODhigh, differing markedly in their cumulative T1D incidence (22% vs. 90% by 30 weeks in females). NODhigh mice harbored more complex intestinal microbiota, including several pathobionts; both colonies harbored segmented filamentous bacteria (SFB), thought to suppress T1D. Young NODhigh females had increased B-cell activation in their mesenteric lymph nodes. These phenotypes were transmissible. Co-housing of NODlow with NODhigh mice after weaning did not change T1D development, but T1D incidence was increased in female offspring of co-housed NODlow mice, which were exposed to the NODhigh environment both before and after weaning. These offspring also acquired microbiota and B-cell activation approaching those of NODhigh mice. In NODlow females, the low rate of T1D was unaffected by cyclophosphamide but increased by PD-L1 blockade. Thus, environmental exposures that are innocuous later in life may promote T1D progression if acquired early during immune development, possibly by altering B-cell activation and/or PD-L1 function. Moreover, T1D suppression in NOD mice by SFB may depend on the presence of other microbial influences. The complexity of microbial immune regulation revealed in this murine model may also be relevant to the environmental regulation of human T1D

Proteomic Interrogation of Human Chromatin

Chromatin proteins provide a scaffold for DNA packaging and a basis for epigenetic regulation and genomic maintenance. Despite understanding its functional roles, mapping the chromatin proteome (i.e. the “Chromatome”) is still a continuing process. Here, we assess the biological specificity and proteomic extent of three distinct chromatin preparations by identifying proteins in selected chromatin-enriched fractions using mass spectrometry-based proteomics. These experiments allowed us to produce a chromatin catalog, including several proteins ranging from highly abundant histone proteins to less abundant members of different chromatin machinery complexes. Using a Normalized Spectral Abundance Factor approach, we quantified relative abundances of the proteins across the chromatin enriched fractions giving a glimpse into their chromosomal abundance. The large-scale data sets also allowed for the discovery of a variety of novel post-translational modifications on the identified chromatin proteins. With these comparisons, we find one of the probed methods to be qualitatively superior in specificity for chromatin proteins, but inferior in proteomic extent, evidencing a compromise that must be made between biological specificity and broadness of characterization. Additionally, we attempt to identify proteins in eu- and heterochromatin, verifying the enrichments by characterizing the post-translational modifications detected on histone proteins from these chromatin regions. In summary, our results provide insights into the value of different methods to extract chromatin-associated proteins and provide starting points to study the factors that may be involved in directing gene expression and other chromatin-related processes