On the Column Density of AGN Outflows: the Case of NGC 5548

We re-analyze the HST high resolution spectroscopic data of the intrinsic absorber in NGC 5548 and find that the C IV absorption column density is at least four times larger than previously determined. This increase arises from accounting for the kinematical nature of the absorber and from our conclusion that the outflow does not cover the narrow emission line region in this object. The improved column density determination begins to bridge the gap between the high column densities measured in the X-ray and the low ones previously inferred from the UV lines. Combined with our findings for outflows in high luminosity quasars these results suggest that traditional techniques for measuring column densities: equivalent width, curve-of-growth and Gaussian modeling, are of limited value when applied to absorption associated with AGN outflows.Comment: Published ApJ version (566, 699), including a new figure with FUSE data and a useful algebraic expression for the optical depth solutio

Accretion disk reversal and the spin-up/spin-down of accreting pulsars

We numerically investigate the hydrodynamics of accretion disk reversal and relate our findings to the observed spin-rate changes in the accreting X-ray pulsar GX~1+4. In this system, which accretes from a slow wind, the accretion disk contains two dynamically distinct regions. In the inner part viscous forces are dominant and disk evolution occurs on a viscous timescale. In the outer part dynamical mixing of material with opposite angular momentum is more important, and the externally imposed angular momentum reversal timescale governs the flow. In this outer region the disk is split into concentric rings of material with opposite senses of rotation that do not mix completely but instead remain distinct, with a clear gap between them. We thus predict that torque reversals resulting from accretion disk reversals will be accompanied by minima in accretion luminosity.Comment: 13 pages, 7 figures, accepted for publication in Ap

Chemical and Enzymatic Methods for Preparing Circular Single‐Stranded DNAs

Small circular oligonucleotides can be used for diagnostic, therapeutic, and laboratory purposes. These systems have gained considerable attention in recent years because they form unusually strong and specific complexes with RNA and DNA strands. Synthetic circular DNAs of 20 to 200 nucleotides can also serve as catalysts for amplified DNA and RNA synthesis by a rolling circle mechanism. This unit presents methods for synthesizing small circular oligonucleotides. These simple “one‐pot” procedures are carried out using short DNA splints that hold the circle together until it is chemically or enzymatically ligated.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143688/1/cpnc0502.pd

RNA major groove modifications improve siRNA stability and biological activity

RNA 5-methyl and 5-propynyl pyrimidine analogs were substituted into short interfering RNAs (siRNAs) to probe major groove steric effects in the active RNA-induced silencing complex (RISC). Synthetic RNA guide strands containing varied combinations of propynyl and methyl substitution revealed that all C-5 substitutions increased the thermal stability of siRNA duplexes containing them. Cellular gene suppression experiments using luciferase targets in HeLa cells showed that the bulky 5-propynyl modification was detrimental to RNA interference activity, despite its stabilization of the helix. Detrimental effects of this substitution were greatest at the 5′-half of the guide strand, suggesting close steric approach of proteins in the RISC complex with that end of the siRNA/mRNA duplex. However, substitutions with the smaller 5-methyl group resulted in gene silencing activities comparable to or better than that of wild-type siRNA. The major groove modifications also increased the serum stability of siRNAs

5′‐Iodination of Solid‐Phase‐Linked Oligodeoxyribonucleotides

5′‐Iodinated oligodeoxyribonucleotides readily react with 3′‐phosphorothioated DNA in the presence of a complementary template to yield a conjugate that is identical to natural DNA in every respect except that one oxygen atom in the phosphodiester backbone is replaced by a sulfur atom. The 5′‐iodo group is easily converted to a variety of other functional groups and will quickly react with thiol‐containing labels to yield stable thioether conjugates. This unit presents manual and automated procedures for converting the 5′‐hydroxyl of protected CPG–bound oligodeoxyribonucleotides to an iodo group and for releasing and purifying the products.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143744/1/cpnc0419.pd

Contrasting the UV and X-ray O VI Column Density Inferred for the Outflow in NGC 5548

We compare X-ray and UV spectroscopic observations of NGC 5548. Both data sets show O VI absorption troughs associated with the AGN outflow from this galaxy. We find that the robust lower limit on the column density of the O VI X-ray trough is seven times larger than the column density found in a study of the O VI UV troughs. This discrepancy suggests that column densities inferred for UV troughs of Seyfert outflows are often severely underestimated. We identify the physical limitations of the UV Gaussian modeling as the probable explanation of the O VI column density discrepancy. Specifically, Gaussian modeling cannot account for a velocity dependent covering fraction, and it is a poor representation for absorption associated with a dynamical outflow. Analysis techniques that use a single covering fraction value for each absorption component suffer from similar limitations. We conclude by suggesting ways to improve the UV analysis.Comment: 16 pages, 1 figure, accepted for publication in Ap

Distance to Multiple Kinematic Components of Quasar Outflows: VLT Observations of QSO 2359-1241 and SDSS J0318-0600

Using high resolution VLT spectra, we study the multi-component outflow systems of two quasars exhibiting intrinsic Fe II absorption (QSO 2359-1241 and SDSS J0318-0600). From the extracted ionic column densities and using photoionization modeling we determine the gas density, total column density, and ionization parameter for several of the components. For each object the largest column density component is also the densest, and all other components have densities of roughly 1/4 of that of the main component. We demonstrate that all the absorbers lie roughly at the same distance from the source. Further, we calculate the total kinetic luminosities and mass outflow rates of all components and show that these quantities are dominated by the main absorption component.Comment: 27 pages, 5 figure