EXCISION OF CYCLOBUTANE DIMERS IN GENOMIC AND EPISOMAL DNA IN HUMAN CELLS

Abstract Direct determination has been made of cyclobutyl pyrimidine dimer induction and excision repair in an episomal SV40 DNA population in vivo . Maintaining SV40-transformed human (GM637) cells in confluent culture results in amplification of a mutant SV40 episome to high copy number. T4 endonuclease V was used to quantify the induction and repair of cyclobutane dimers in the SV40 episome and genomic DNA of the same cells. Differences in both parameters were observed cyclobutane dimers were induced at 1.5–2-fold greater frequency in episomal DNA and excised at a reduced rate compared to genomic DNA in the host cells.     

HOECHST 33258 DYE GENERATES DNA-PROTEIN CROSS-LINKS DURING ULTRAVIOLET LIGHT-INDUCED PHOTOLYSIS OF BROMODEOXYURIDINE IN REPLICATED AND REPAIRED DNA

Abstract— Substitution of bromodeoxyuridine for thymidine in the DNA of mammalian cells sensitizes them to a range of wavelengths of ultraviolet light. Cells are also sensitized to photochemical reactions involving dyes such as Hoechst 33258, which is used to produce differential staining of chromatids according to their bromodeoxyuridine content. Irradiation with 313 nm light of human and hamster cells containing bromodeoxyuridine in their DNA produced single-strand breaks, detectable by alkaline elution, but no DNA-protein cross-links. Irradiation with 360 nm light in the presence of Hoechst 33258 produced extensive DNA-protein cross-linkage as well as single-strand breaks. These cross-links were observed in DNA containing bromodeoxyuridine incorporated by either semiconservative or repair replication, and may provide a method for identification of proteins in close proximity to replication forks or repair sites. When the protein was removed with proteinase K, bromodeoxyuridine in repair patches after irradiation by doses of ultraviolet (254 nm) light as low as 0.26 J/m² could readily be detected. Hoechst 33258-mediated photolysis, therefore, provides a sensitive new technique for measuring repair replication after ultraviolet light irradiation.     

Gibbs ensemble simulation of nematic-isotropic coexistence in a liquid crystal mixture

The results are presented of Gibbs ensemble Monte Carlo (GEMC) simulations examining the nematic–isotropic (N–I) coexistence envelope of a liquid crystal mixture. The system studied is a 50:50 mixture of 1000 generalized Gay–Berne particles with axial ratios 2.0:1 and 2.5:1. For this system, stable N–I coexistence is observed over run lengths in excess of 5 x 10⁵ GEMC sweeps. There is unambiguous evidence of fractionation, the mole fractions of long particles in the coexisting phases typically differing by 11%. The measured coexistence envelope does not conform to the lens shape predicted by Onsager theory; qualitative finite size arguments are given in explanation of this distortion.     

The analysis of process gases: a review

 A general review of key issues involved in the analysis of process gases is presented. The reasons for such measurements – which include safety, quality, environmental and economic factors are considered. The technical issues arising from these measurements are dependent upon a variety of factors, including the overall sampling system, the type of analytical instrumentation, methods of data collection and the specified calibration protocols. The use of gas calibration cylinders as transfer standards is detailed and issues of stability and traceability to reference material discussed. Received: 1 March 2000 / Accepted: 31 March 2000     

Investigation of quasi-realistic heterotic string models with reduced Higgs spectrum

Quasi-realistic heterotic-string models in the free fermionic formulation typically contain an anomalous U(1) that leads to supersymmetry breaking. Supersymmetry is restored by imposing F- and D-flatness on the vacuum. A three generation free fermionic standard-like model which did not admit stringent F- and D-flat directions has been presented (Cleaver et al. in Phys. Rev. D 78, 046009, 2008) and it was argued that all the moduli in that model were fixed. The particular property of that model was the reduction of the untwisted Higgs spectrum by a combination of symmetric and asymmetric internal dimension boundary conditions with respect to the internal fermions associated with the compactified dimensions. This reduction occurred without the need or presence of flat directions. In this paper we extend the analysis of free fermionic models with reduced Higgs spectrum to models with the same internal space but with modified gauge groups: SO(10) or flipped SU(5) subgroup. We show that all the models studied in this paper do admit stringent flat directions. Currently, the only examples of models that do not admit stringent flat directions are the standard-like models of Cleaver et al. (Phys. Rev. D 78, 046009, 2008). We comment on the relationship between flat directions and reduced Higgs in free fermionic models as well as the possible connection between moduli stabilization and model phenomenology.     

Casimir energy and brane stability

We investigate the role of Casimir energy as a mechanism for brane stability in five-dimensional models with the fifth dimension compactified on an S¹/_Z2$S^1/{\mathbb{Z}}_2$ orbifold, which includes the Randall–Sundrum two brane model (RS1). We employ a ζ$\zeta$-function regularization technique utilizing the Schwinger proper time method and the Jacobi theta function identity to calculate the one-loop effective potential. We show that the combination of the Casimir energies of a scalar Higgs field, the three generations of Standard Model fermions and one additional massive non-SM scalar in the bulk produces a non-trivial minimum of the potential. In particular, we consider a scalar field with a coupling in the bulk to a Lorentz violating vector particle localized to the compactified dimension. Such a scalar may provide a natural means of fine tuning needed for stabilization of the brane separation. Finally, we briefly review the possibility that Casimir energy plays a role in generating the currently observed epoch of cosmological inflation by examining a simple five-dimensional anisotropic metric.     

γH2Ax: biomarker of damage or functional participant in DNA repair "all that glitters is not gold!"

The phosphorylation of H2Ax on its S139 site, γH2Ax, is important for the assembly of repair complexes at DNA double strand breaks (DSBs). The formation and functional role of γH2Ax after other kinds of DNA damage, especially UV light, where DSBs are rare, is less clear. Following UV light in the UVB and UVC ranges, complex distributions of γH2Ax can be identified, quite unlike the discrete enumerable foci seen after ionizing radiation. Several distinct distributions of γH2Ax occur: a low level nuclear-wide distribution of γH2Ax occurs during nucleotide excision repair; irregular focal distributions occur at arrested replication forks; high intensity nuclear-wide γH2Ax occurs in association with S-phase apoptosis. The intensity and distributions of γH2Ax vary according to the activity of excision repair, bypass polymerase and apoptotic caspases. The frequency of DSBs at arrested replication forks is low but highly variable in different cell types, and probably caused by enzymatic action. Despite the prominence of S139 phosphorylation following UV damage, mutation of this site has no influence on the UV damage response indicating that γH2Ax is a biomarker but not a participant in the UV-DNA damage response.     

A second order solution for the non-equilibrium flow of a relaxing gas in a plane expansion

Zusammenfassung Um eine analytische Lösung zu erhalten, welche Effekte der endlichen Entropie- und Wirbelstärkeerzeugung berücksichtigt, ist die linearisierte Theorie formell durch Einbeziehung von Grössen zweiter Ordnung erweitert worden. Anwendungen sind gegeben für den Fall einer ebenen Expansionsströmung eines harmonisch relaxierenden Gases, das sich nicht im Gleichgewicht befindet. Die Theorie zweiter Ordnung zeigt eine Verbesserung gegenüber der ersten Ordnung in der Voraussage der Zustandsgrössen entlang der Wand. Insbesondere wird eine Abschätzung der Abweichungen der asymptotischen Wandwerte des Druckes, der Temperatur usw. vom entsprechenden Gleichgewichtswert für unendliche Reaktionsgeschwindigkeiten ermöglicht.