Physical and Topological Properties of Circular DNA

Several types of circular DNA molecules are now known. These are classified as single-stranded rings, covalently closed duplex rings, and weakly bonded duplex rings containing an interruption in one or both strands. Single rings are exemplified by the viral DNA from φX174 bacteriophage. Duplex rings appear to exist in a twisted configuration in neutral salt solutions at room temperature. Examples of such molecules are the DNA's from the papova group of tumor viruses and certain intracellular forms of φX and λ-DNA. These DNA's have several common properties which derive from the topological requirement that the winding number in such molecules is invariant. They sediment abnormally rapidly in alkaline (denaturing) solvents because of the topological barrier to unwinding. For the same basic reason these DNA's are thermodynamically more stable than the strand separable DNA's in thermal and alkaline melting experiments. The introduction of one single strand scission has a profound effect on the properties of closed circular duplex DNA's. In neutral solutions a scission appears to generate a swivel in the complementary strand at a site in the helix opposite to the scission. The twists are then released and a slower sedimenting, weakly closed circular duplex is formed. Such circular duplexes exhibit normal melting behavior, and in alkali dissociate to form circular and linear single strands which sediment at different velocities. Weakly closed circular duplexes containing an interruption in each strand are formed by intramolecular cyclization of viral λ-DNA. A third kind of weakly closed circular duplex is formed by reannealing single strands derived from circularly permuted T2 DNA. These reconstituted duplexes again contain an interruption in each strand though not necessarily regularly spaced with respect to each other

Sequence Polymorphism in Candidate Genes for Differences in Winter Plumage between Scottish and Scandinavian Willow Grouse (Lagopus lagopus)

Background: Population variation in the degree of seasonal polymorphism is rare in birds, and the genetic basis of this phenomenon remains largely undescribed. Both sexes of Scandinavian and Scottish Willow grouse (Lagopus lagopus) display marked differences in their winter phenotypes, with Scottish grouse retaining a pigmented plumage year-round and Scandinavian Willow grouse molting to a white morph during winter. A widely studied pathway implicated in vertebrate pigmentation is the melanin system, for which functional variation has been characterised in many taxa. Methodology/Principal Findings: We sequenced coding regions from four genes involved in melanin pigmentation (DCT, MC1R, TYR and TYRP1), and an additional control involved in the melanocortin pathway (AGRP), to investigate the genetic basis of winter plumage in Lagopus. Despite the well documented role of the melanin system in animal coloration, we found no plumage-associated polymorphism or evidence for selection in a total of,2.6 kb analysed sequence. Conclusions/Significance: Our results indicate that the genetic basis of alternating between pigmented and unpigmented seasonal phenotypes is more likely explained by regulatory changes controlling the expression of these or other loci in th

Strong rules for discarding predictors in lasso-type problems

We consider rules for discarding predictors in lasso regression and related problems, for computational efficiency. El Ghaoui et al (2010) propose "SAFE" rules that guarantee that a coefficient will be zero in the solution, based on the inner products of each predictor with the outcome. In this paper we propose strong rules that are not foolproof but rarely fail in practice. These can be complemented with simple checks of the Karush- Kuhn-Tucker (KKT) conditions to provide safe rules that offer substantial speed and space savings in a variety of statistical convex optimization problems.Comment:

Crime And Poverty In Detroit: A Cross-Referential Critical Analysis Of Ideographs And Framing

This thesis examines how the relationship between crime and poverty is rhetorically constructed within the news media. To this end, I investigate the content of twelve news articles, published online, that offered coverage of crime in the city of Detroit, Michigan. I employ three methods in my criticism of these texts: ideographic analysis, critical framing analysis, and an approach that considers ideographs and framings elements to be rhetorical constructions that function together. In each phase of my analysis, I developed ideological themes from concepts emerging from the texts. I then approached my discussion of these findings from a perspective of Neo-Marxism, primarily using Gramsci\u27s (1971) critique of cultural hegemony to inform my conclusions. I ultimately argue that, through their dissemination of these representations, the news media function as a mechanism to perpetuate an ideology of classism

The InfraRed Imaging Spectrograph (IRIS) for TMT: Reflective ruled diffraction grating performance testing and discussion

We present the efficiency of near-infrared reflective ruled diffraction gratings designed for the InfraRed Imaging Spectrograph (IRIS). IRIS is a first light, integral field spectrograph and imager for the Thirty Meter Telescope (TMT) and narrow field infrared adaptive optics system (NFIRAOS). We present our experimental setup and analysis of the efficiency of selected reflective diffraction gratings. These measurements are used as a comparison sample against selected candidate Volume Phase Holographic (VPH) gratings (see Chen et al., this conference). We investigate the efficiencies of five ruled gratings designed for IRIS from two separate vendors. Three of the gratings accept a bandpass of 1.19-1.37 {\mu}m (J band) with ideal spectral resolutions of R=4000 and R=8000, groove densities of 249 and 516 lines/mm, and blaze angles of 9.86 and 20.54 degrees, respectively. The other two gratings accept a bandpass of 1.51-1.82 {\mu}m (H Band) with an ideal spectral resolution of R=4000, groove density of 141 lines/mm, and blaze angle of 9.86{\deg}. We measure the efficiencies off blaze angle for all gratings and the efficiencies between the polarization transverse magnetic (TM) and transverse electric (TE) states. The peak reflective efficiencies are 98.90 +/- 3.36% (TM) and 84.99 +/- 2.74% (TM) for the H-band R=4000 and J-band R=4000 respectively. The peak reflective efficiency for the J-band R=8000 grating is 78.78 +/- 2.54% (TE). We find that these ruled gratings do not exhibit a wide dependency on incident angle within +/-3{\deg}. Our best-manufactured gratings were found to exhibit a dependency on the polarization state of the incident beam with a ~10-20% deviation, consistent with the theoretical efficiency predictions.Comment: Proceedings of the SPIE, 9147-34