Emission and Absorption Properties of Low-Mass Type 2 Active Galaxies with XMM-Newton

We present XMM-Newton observations of four low-redshift Seyfert galaxies selected to have low host luminosities (M_g>-20 mag) and small stellar velocity dispersions (sigma_star<45 km/s), which are among the smallest stellar velocity dispersions found in any active galaxies. These galaxies show weak or no broad optical emission lines and have likely black hole masses <10^6 M_sun. Three out of four objects were detected with >3sigma significance in ~25 ks exposures and two observations had high enough signal-to-noise ratios for rudimentary spectral analysis. We calculate hardness ratios (-0.43 to 0.01) for the three detected objects and use them to estimate photon indices in the range of Gamma=1.1-1.8. Relative to [OIII], the type 2 objects are X-ray faint in comparison with Seyfert 1 galaxies, suggesting that the central engines are obscured. We estimate the intrinsic absorption of each object under the assumption that the [OIII] emission line luminosities are correlated with the unabsorbed X-ray luminosity. The results are consistent with moderate (N_H~10^22 cm^-2) absorption over the Galactic values in three of the four objects, which might explain the non-detection of broad-line emission in optical spectra. One object in our sample, SDSS J110912.40+612346.7, is a near identical type 2 counterpart of the late-type Seyfert 1 galaxy NGC 4395. While the two objects have very similar [OIII] luminosities, the type 2 object has an X-ray/[OIII] flux ratio nearly an order of magnitude lower than NGC 4395. The most plausible explanation for this difference is absorption of the primary X-ray continuum of the type 2 object, providing an indication that obscuration-based unified models of active galaxies can apply even at the lowest luminosities seen among Seyfert nuclei, down to L_bol~10^40-10^41 erg/s.Comment: 5 figures, 3 tables, accepted for publication in Ap

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors

Three-integral multi-component dynamical models and simulations of the nuclear star cluster in NGC 4244

Adaptive optics observations of the flattened nuclear star cluster in the nearby edge-on spiral galaxy NGC 4244 using the Gemini Near-Infrared Integral Field Spectrograph (NIFS) have revealed clear rotation. Using these kinematics plus 2MASS photometry we construct a series of axisymmetric two-component particle dynamical models with our improved version of NMAGIC, a flexible Chi^2-made-to-measure code. The models consist of a nuclear cluster disc embedded within a spheroidal particle population. We find a mass for the nuclear star cluster of M=1.6^+0.5_-0.2 x 10^7 M_sun within ~42.4 pc (2"). We also explore the presence of an intermediate mass black hole and show that models with a black hole as massive as M_bh = 5.0 x 10^5 M_sun are consistent with the available data. Regardless of whether a black hole is present or not, the nuclear cluster is vertically anisotropic (beta_z < 0), as was found with earlier two-integral models. We then use the models as initial conditions for N-body simulations. These simulations show that the nuclear star cluster is stable against non-axisymmetric perturbations. We also explore the effect of the nuclear cluster accreting star clusters at various inclinations. Accretion of a star cluster with mass 13% that of the nuclear cluster is already enough to destroy the vertical anisotropy, regardless of orbital inclination.Comment: Replaced with the version accepted for publication in MNRAS. 13 pages, 10 figures, 3 table

Radiation pressure and absorption in AGN: results from a complete unbiased sample from Swift

Outward radiation pressure can exceed the inward gravitational pull on gas clouds in the neighbourhood of a luminous Active Galactic Nucleus (AGN). This creates a forbidden region for long-lived dusty clouds in the observed columnn density - Eddington fraction plane. (The Eddington fraction lambda_Edd is the ratio of the bolometric luminosity of an AGN to the Eddington limit for its black hole mass.) The Swift/BAT catalogue is the most complete hard X-ray selected sample of AGN and has 97 low redshift AGN with measured column densities N_H and inferred black hole masses. Eddington fractions for the sources have been obtained using recent bolometric corrections and the sources have been plotted on the N_H - lambda_Edd plane. Only one source lies in the forbidden region and it has a large value of N_H due to an ionized warm absorber, for which radiation pressure is reduced. The effective Eddington limit for the source population indicates that the high column density clouds in the more luminous objects lie within the inner few pc, where the central black hole provides at least half the mass. Our result shows that radiation pressure does affect the presence of gas clouds in the inner galaxy bulge. We discuss briefly how the N_H - lambda_Edd plane may evolve to higher redshift, when feedback due to radiation pressure may have been strong.Comment: 4 pages, 2 figures, MNRAS in pres

Black Holes in the Early Universe

The existence of massive black holes was postulated in the sixties, when the first quasars were discovered. In the late nineties their reality was proven beyond doubt, in the Milky way and a handful nearby galaxies. Since then, enormous theoretical and observational efforts have been made to understand the astrophysics of massive black holes. We have discovered that some of the most massive black holes known, weighing billions of solar masses, powered luminous quasars within the first billion years of the Universe. The first massive black holes must therefore have formed around the time the first stars and galaxies formed. Dynamical evidence also indicates that black holes with masses of millions to billions of solar masses ordinarily dwell in the centers of today's galaxies. Massive black holes populate galaxy centers today, and shone as quasars in the past; the quiescent black holes that we detect now in nearby bulges are the dormant remnants of this fiery past. In this review we report on basic, but critical, questions regarding the cosmological significance of massive black holes. What physical mechanisms lead to the formation of the first massive black holes? How massive were the initial massive black hole seeds? When and where did they form? How is the growth of black holes linked to that of their host galaxy? Answers to most of these questions are work in progress, in the spirit of these Reports on Progress in Physics.Comment: Reports on Progress in Physics, in pres

The FaceBase Consortium: A comprehensive program to facilitate craniofacial research

The FaceBase Consortium consists of ten interlinked research and technology projects whose goal is to generate craniofacial research data and technology for use by the research community through a central data management and integrated bioinformatics hub. Funded by the National Institute of Dental and Craniofacial Research (NIDCR) and currently focused on studying the development of the middle region of the face, the Consortium will produce comprehensive datasets of global gene expression patterns, regulatory elements and sequencing; will generate anatomical and molecular atlases; will provide human normative facial data and other phenotypes; conduct follow up studies of a completed genome-wide association study; generate independent data on the genetics of craniofacial development, build repositories of animal models and of human samples and data for community access and analysis; and will develop software tools and animal models for analyzing and functionally testing and integrating these data. The FaceBase website (http://www.facebase.org) will serve as a web home for these efforts, providing interactive tools for exploring these datasets, together with discussion forums and other services to support and foster collaboration within the craniofacial research community

Rare Variants Found in Clinical Gene Panels Illuminate the Genetic and Allelic Architecture of Orofacial Clefting

PURPOSE: Orofacial clefts (OFCs) are common birth defects including cleft lip, cleft lip and palate, and cleft palate. OFCs have heterogeneous etiologies, complicating clinical diagnostics because it is not always apparent if the cause is Mendelian, environmental, or multifactorial. Sequencing is not currently performed for isolated or sporadic OFCs; therefore, we estimated the diagnostic yield for 418 genes in 841 cases and 294 controls. METHODS: We evaluated 418 genes using genome sequencing and curated variants to assess their pathogenicity using American College of Medical Genetics criteria. RESULTS: 9.04% of cases and 1.02% of controls had likely pathogenic variants (P \u3c .0001), which was almost exclusively driven by heterozygous variants in autosomal genes. Cleft palate (17.6%) and cleft lip and palate (9.09%) cases had the highest yield, whereas cleft lip cases had a 2.80% yield. Out of 39 genes with likely pathogenic variants, 9 genes, including CTNND1 and IRF6, accounted for more than half of the yield (4.64% of cases). Most variants (61.8%) were variants of uncertain significance , occurring more frequently in cases (P = .004), but no individual gene showed a significant excess of variants of uncertain significance. CONCLUSION: These results underscore the etiological heterogeneity of OFCs and suggest sequencing could reduce the diagnostic gap in OFCs

International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci.

The risk of posttraumatic stress disorder (PTSD) following trauma is heritable, but robust common variants have yet to be identified. In a multi-ethnic cohort including over 30,000 PTSD cases and 170,000 controls we conduct a genome-wide association study of PTSD. We demonstrate SNP-based heritability estimates of 5-20%, varying by sex. Three genome-wide significant loci are identified, 2 in European and 1 in African-ancestry analyses. Analyses stratified by sex implicate 3 additional loci in men. Along with other novel genes and non-coding RNAs, a Parkinson's disease gene involved in dopamine regulation, PARK2, is associated with PTSD. Finally, we demonstrate that polygenic risk for PTSD is significantly predictive of re-experiencing symptoms in the Million Veteran Program dataset, although specific loci did not replicate. These results demonstrate the role of genetic variation in the biology of risk for PTSD and highlight the necessity of conducting sex-stratified analyses and expanding GWAS beyond European ancestry populations

Trio-Based GWAS Identifies Novel Associations and Subtype-Specific Risk Factors for Cleft Palate

Cleft palate (CP) is one of the most common craniofacial birth defects; however, there are relatively few established genetic risk factors associated with its occurrence despite high heritability. Historically, CP has been studied as a single phenotype, although it manifests across a spectrum of defects involving the hard and/or soft palate. We performed a genome-wide association study using transmission disequilibrium tests of 435 case-parent trios to evaluate broad risks for any cleft palate (ACP) (n = 435), and subtype-specific risks for any cleft soft palate (CSP), (n = 259) and any cleft hard palate (CHP) (n = 125). We identified a single genome-wide significant locus at 9q33.3 (lead SNP rs7035976, p = 4.24 × 1