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.     

Thermal Characterizations of Inorganic and Organometallic Polymers

This review emphasizes the breadth of metallic and metallic-like polymers evaluated as to thermal properties. Techniques usefully applied to particular systems are noted with the aim of suggesting their application to other systems.     

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.     

Low-lying energy levels of the FeH molecule

Multireference configuration interaction (MRCI) and complete active space second-order perturbation theory (CASPT2) calculations are performed on Fe₂ and Fe^? ₂. Although it is not possible to definitively identify the ground states of Fe₂ and Fe^? ₂, the calculations suggest that the ground state of Fe^? ₂ in ⁸Σ^? _u derived from 3d¹³4σ² _g4σ² _u and that the states observed in photodetachment are the ⁹Σ^? _g and ⁷Σ^? _g states with a 3d¹³4σ² _g4σ¹ _u occupation, but that the ground state of Fe₂ is ⁷Δ_u(3d¹⁴4σ² _g) and is not observed in the photo-detachment spectra.     

Data Formats for Elementary Gas Phase Kinetics,Part 1: Unique Representations of Species at the Molecular Level

Standardized electronic formats for data are needed to efficiently and transparently communicate the results of scientific studies. A format for the unique identification of chemical species is a requirement in the field of chemistry, and the IUPAC International Chemical Identifier (InChI) has been widely adopted for this purpose. The InChI identifier has proved to be very useful. The InChI identifier, however, is currently insufficient to uniquely specify some types of molecular entities at a detailed molecular level needed to fully characterize their chemical nature, to differentiate between chemically distinct conformers, to uniquely identify structures used in quantum chemical calculations, and to completely describe elementary chemical reactions. To address this limitation, we propose an augmented form of InChI, denoted as InChI–ER, which contains additional optional layers that allow the unique and unambiguous identification of molecules at a detailed molecular level. The new layers proposed herein are optional extensions of the existing InChI formalism and, like all other InChI layers, would not interfere with InChI identifiers currently in use. The focus of the present work is the better specification of required molecular entities such as rotational conformations, ring conformations, and electronic states. In companion articles, we propose additional reaction layers using an extended InChI format that will enable the unique identification of elementary chemical reactions, including specification of associated transition states, specification of the changes in bonds that occur during reaction, and classification of reaction types.     

OPTIMAL FISH HARVESTING FOR A POPULATION MODELED BY A NONLINEAR PARABOLIC PARTIAL DIFFERENTIAL EQUATION

As the human population continues to grow, there is a need for better management of our natural resources in order for our planet to be able to produce enough to sustain us. One important resource we must consider is marine fish populations. We use the tool of optimal control to investigate harvesting strategies for maximizing yield of a fish population in a heterogeneous, finite domain. We determine whether these solutions include no‐take marine reserves as part of the optimal solution. The fishery stock is modeled using a nonlinear, parabolic partial differential equation with logistic growth, movement by diffusion and advection, and with Robin boundary conditions. The objective for the problem is to find the harvest rate that maximizes the discounted yield. Optimal harvesting strategies are found numerically.     

Entropy-driven formation of the gyroid cubic phase

We show, by computer simulation, that tapered or pear-shaped particles, interacting through purely repulsive interactions, can freely self-assemble to form the three-dimensionally periodic, gyroid cubic phase. The Ia3d gyroid cubic phase is formed by these particles on both compression of an isotropic configuration and expansion of a smectic A bilayer arrangement. For the latter case, it is possible to identify the steps by which the topological transformation from nonintersecting planes to fully interpenetrating, periodic networks takes place.