The genomic diversification of grapevine clones.

BACKGROUND:Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fifteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones, Zinfandel 03. RESULTS:Though most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than in genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and because methylated cytosines often spontaneously deaminate. Of the minority of mutations that occurred in exons, larger proportions of these were putatively deleterious when they occurred in relatively few clones. CONCLUSIONS:These data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clones accumulate putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions or some mechanism by which mutations are less frequent in coding than noncoding regions of the genome

Bottom Quark Mass from Υ\Upsilon Sum Rules to O(αs3){\cal O}(\alpha_s^3)

We use the ${\cal O}(\alpha_s^3)$ approximation of the heavy-quark vacuum polarization function in the threshold region to determine the bottom quark mass from nonrelativistic $\Upsilon$ sum rules. We find very good stability and convergence of the perturbative series for the bottom quark mass in $\rm\overline{MS}$ renormalization scheme. Our final result is $\overline{m}_b(\overline{m}_b)=4.169\pm 0.008_{th}\pm 0.002_{\alpha_s}\pm 0.002_{exp}$.Comment: 23 pages, 6 figures, journal versio

Genome-wide linkage analysis of 972 bipolar pedigrees using single-nucleotide polymorphisms.

Because of the high costs associated with ascertainment of families, most linkage studies of Bipolar I disorder (BPI) have used relatively small samples. Moreover, the genetic information content reported in most studies has been less than 0.6. Although microsatellite markers spaced every 10 cM typically extract most of the genetic information content for larger multiplex families, they can be less informative for smaller pedigrees especially for affected sib pair kindreds. For these reasons we collaborated to pool family resources and carried out higher density genotyping. Approximately 1100 pedigrees of European ancestry were initially selected for study and were genotyped by the Center for Inherited Disease Research using the Illumina Linkage Panel 12 set of 6090 single-nucleotide polymorphisms. Of the ~1100 families, 972 were informative for further analyses, and mean information content was 0.86 after pruning for linkage disequilibrium. The 972 kindreds include 2284 cases of BPI disorder, 498 individuals with bipolar II disorder (BPII) and 702 subjects with recurrent major depression. Three affection status models (ASMs) were considered: ASM1 (BPI and schizoaffective disorder, BP cases (SABP) only), ASM2 (ASM1 cases plus BPII) and ASM3 (ASM2 cases plus recurrent major depression). Both parametric and non-parametric linkage methods were carried out. The strongest findings occurred at 6q21 (non-parametric pairs LOD 3.4 for rs1046943 at 119 cM) and 9q21 (non-parametric pairs logarithm of odds (LOD) 3.4 for rs722642 at 78 cM) using only BPI and schizoaffective (SA), BP cases. Both results met genome-wide significant criteria, although neither was significant after correction for multiple analyses. We also inspected parametric scores for the larger multiplex families to identify possible rare susceptibility loci. In this analysis, we observed 59 parametric LODs of 2 or greater, many of which are likely to be close to maximum possible scores. Although some linkage findings may be false positives, the results could help prioritize the search for rare variants using whole exome or genome sequencing

X-ray view of four high-luminosity Swift/BAT AGN: Unveiling obscuration and reflection with Suzaku

The Swift/BAT nine-month survey observed 153 AGN, all with ultra-hard X-ray BAT fluxes in excess of 10^-11 erg cm^-2 s^-1 and an average redshift of 0.03. Among them, four of the most luminous BAT AGN (44.73 < Log L(BAT) < 45.31) were selected as targets of Suzaku follow-up observations: J2246.0+3941 (3C 452), J0407.4+0339 (3C 105), J0318.7+6828, and J0918.5+0425. The column density, scattered/reflected emission, the properties of the Fe K line, and a possible variability are fully analyzed. For the latter, the spectral properties from Chandra, XMM-Newton and Swift/XRT public observations were compared with the present Suzaku analysis. Of our sample, 3C 452 is the only certain Compton-thick AGN candidate because of i) the high absorption and strong Compton reflection; ii) the lack of variability; iii) the "buried" nature, i.e. the low scattering fraction (<0.5%) and the extremely low relative [OIII] luminosity. In contrast 3C 105 is not reflection-dominated, despite the comparable column density, X-ray luminosity and radio morphology, but shows a strong long-term variability in flux and scattering fraction, consistent with the soft emission being scattered from a distant region (e.g., the narrow emission line region). The sample presents high (>100) X-to-[OIII] luminosity ratios, confirming the [OIII] luminosity to be affected by residual extinction in presence of mild absorption, especially for "buried" AGN such as 3C 452. Three of our targets are powerful FRII radio galaxies, making them the most luminous and absorbed AGN of the BAT Seyfert survey despite the inversely proportional N_H - L_X relation.Comment: A&A paper in press, 17 page

X-ray afterglow detection of the short gamma-ray burst 991014

GRB 991014 is one of the shortest gamma-ray bursts detected so far with the Wide Field Cameras aboard BeppoSAX, both in gamma-rays and X-rays. The duration is 9.6 sec in 2-28 keV and 3.2 sec in 40 to 700 keV (as measured between the times when 5 and 95% of the burst photons have been accumulated). We refine the InterPlanetary Network annulus of the burst, present the detection of the X-ray afterglow of GRB 991014 within this refined annulus, and discuss X-ray and gamma-ray observations of the prompt and afterglow emission. Except for the briefness of the prompt event, no other unusual aspects were found in the prompt and afterglow observations as compared to such measurements in previous gamma-ray bursts.Comment: accepted for publication in Astrophysical Journa

Ataxia-telangiectasia Mutated (ATM)-dependent Activation of ATR Occurs through Phosphorylation of TopBP1 by ATM

ATM (ataxia-telangiectasia mutated) is necessary for activation of Chk1 by ATR (ATM and Rad3-related) in response to double-stranded DNA breaks (DSBs) but not to DNA replication stress. TopBP1 has been identified as a direct activator of ATR. We show that ATM regulates Xenopus TopBP1 by phosphorylating Ser-1131 and thereby strongly enhancing association of TopBP1 with ATR. Xenopus egg extracts containing a mutant of TopBP1 that cannot be phosphorylated on Ser-1131 are defective in the ATR-dependent phosphorylation of Chk1 in response to DSBs but not to DNA replication stress. Thus, TopBP1 is critical for the ATM-dependent activation of ATR following production of DSBs in the genome

Structure and Magnetism of Mn5Ge3 Nanoparticles

In this work, we investigated the magnetic and structural properties of isolated Mn5Ge3 nanoparticles prepared by the cluster-beam deposition technique. Particles with sizes between 7.2 and 12.6 nm were produced by varying the argon pressure and power in the cluster gun. X-ray diffraction (XRD)and selected area diffraction (SAD) measurements show that the nanoparticles crystallize in the hexagonal Mn5Si3-type crystal structure, which is also the structure of bulk Mn5Ge3. The temperature dependence of the magnetization shows that the as-made particles are ferromagnetic at room temperature and have slightly different Curie temperatures. Hysteresis-loop measurements show that the saturation magnetization of the nanoparticles increases significantly with particle size, varying from 31 kA/m to 172 kA/m when the particle size increases from 7.2 to 12.6 nm. The magnetocrystalline anisotropy constant K at 50 K, determined by fitting the high-field magnetization data to the law of approach to saturation, also increases with particle size, from 0.4 × 105 J/m3 to 2.9 × 105 J/m3 for the respective sizes. This trend is mirrored by the coercivity at 50 K, which increases from 0.04 T to 0.13 T. A possible explanation for the magnetization trend is a radial Ge concentration gradient

Reversible Superconductivity in Electrochromic Indium-Tin Oxide Films

Transparent conductive indium tin oxide (ITO) thin films, electrochemically intercalated with sodium or other cations, show tunable superconducting transitions with a maximum $T_c$ at 5 K. The transition temperature and the density of states, $D(E_F)$ (extracted from the measured Pauli susceptibility $\chi_p$ exhibit the same dome shaped behavior as a function of electron density. Optimally intercalated samples have an upper critical field $\approx 4$ T and $\Delta/{k_BT_c} \approx 2.0$. Accompanying the development of superconductivity, the films show a reversible electrochromic change from transparent to colored and are partially transparent (orange) at the peak of the superconducting dome. This reversible intercalation of alkali and alkali earth ions into thin ITO films opens diverse opportunities for tunable, optically transparent superconductors