Effects of Na+ and Mg2+ on the structures of supercoiled DNAs: comparison of simulations with experiments

Recent cryo-electron microscopy (cryo-EM) results suggest that sufficient NaCl concentration (> or approximately 0.1 M) and superhelix density (> or approximately-0.05) cause circular DNAs to adopt highly extended, tightly interwound configurations, in which the strands are laterally contiguous along almost their entire length. Millimolar levels of MgCl2 reportedly act synergistically with NaCl to produce similar conformations. However, Monte Carlo simulations with purely repulsive interduplex forces failed to reproduce such structures. In the present work, solution measurements of particular physical properties were performed both to characterize the effects of Na+ and Mg2+ on DNA structure and to provide quantitative tests of Monte Carlo simulations of circular DNAs. Supercoiled p30 delta DNAs in 10 mM Tris plus 0, 0.122, and 0.1 M NaCl, and 0.1 M NaCl plus 4 mM Mg2+ were examined by static and dynamic light scattering (LS and DLS), time-resolved fluorescence polarization anisotropy (FPA) of intercalated ethidium, and circular dichroism (CD) spectroscopy. Upon addition of 0.122 M NaCl, the radius of gyration (Rg) decreased substantially, which indicates that p30 delta adopts a more compact structure. This contradicts the cryo-EM studies, where molecular extension and Rg both increase upon adding 0.1 M NaCl. In 0.1 M NaCl, the torsion constant measured by FPA is practically invariant to superhelix density, and the plateau diffusion coefficient at large scattering vector (Dplat) is likewise nearly the same at both relaxed and native superhelix densities. Such invariance is difficult to reconcile with any transition from relaxed circles to tightly interwound structures with laterally contiguous strands. Metropolis Monte Carlo simulations were performed to generate canonically distributed sets of structures, from which average Do values and scattered intensity ratios, [symbol: see text]I (zero) [symbol: see text]/[symbol: see text] l(k) [symbol: see text], were calculated. Agreement between simulations and experiments in regard to [symbol: see text] I(O) [symbol: see text] /[symbol: see text] I(k) [symbol: see text], D(zero) and the supercoiling free energy, delta Gsc (delta l), is remarkably good for the most extensively studied p30 delta samples. The simulated structures exhibit no sign of very tight interwinding with extensive lateral contacts, but instead exhibit most probable superhelix diameters of 85 to 90 A. When 4 mM Mg2+ was added to native supercoiled p30 delta in 0.1 M NaCl, Rg decreased, D(zero) increased, and the longest internal relaxation rate (1/tau 2(zero)) increased, all of which indicate a further overall contraction of the molecular envelope. The torsion constant exhibited a slight increase that is hardly statistically significant. In this case, agreement between the simulations and experiments was only semi-quantitative for most samples investigated, although the predicted contraction was exhibited by all five samples of p30 delta and one of pBR322 DNA. The simulated structures in 0.1 M NaCl plus 4 mM Mg2+ again showed no sign of extensive lateral contacts. A plausible explanation is proposed for the highly extended, tightly interwound structures seen in cryo-EM, and explicitly tested by Monte Carlo simulations of a 1000 bp circular DNA at +25 and -50 degrees C. Structures identical to those seen in cryo-EM are in fact the equilibrium structures in the simulations at -50 degrees C, and the estimated time for equilibration (2.3 x 10(-6) second) is much smaller than the estimated time for vitrification (1 x 10(-4) second).     

Influence ofAmaranthus hybridus L. allelochemics on oviposition behavior ofSpodoptera exigua andS. eridania (Lepidoptera: Noctuidae)

Common pigweed,Amaranthus hybridus L., is a favorite host of the beet army worm (BAW),Spodoptera exigua L. Chemicals extracted from homogenized pigweed with distilled water, ethanol, or dichloromethane and sprayed back on pigweed deterred oviposition by the BAW. Similarly, water extracts of frass from conspecific larvae or southern armyworm (SAW) larvae,S. eridania (Cramer), fed pigweed leaves and sprayed back on pigweed plants also deterred BAW oviposition, thus confirming that deterrence was due to plant allelochemics rather than specific compounds associated with the metabolic or excretory products of the larvae. Confirmation of the presence of oviposition-deterring chemicals in pigweed was used to explain a previously observed seasonal displacement of BAW by SAW on pigweed in the field.Mention of a commercial or proprietary product does not constitute an endorsement by the USDA.     

Patterns of DSM-III-R alcohol dependence symptom progression in a general population survey

Age of onset reports obtained retrospectively for each symptom of DSM-III-R alcohol dependence (AD) are used to study patterns of lifetime symptom progression in a large general-population survey of people in the United States. It is shown that symptom progression among a substantial majority of respondents can be summarized as movement across three clusters. Cluster A is defined by symptoms of role impairment/hazardous use (A4), use despite social, psychological or physical problems (A6), and drinking larger amounts or over a longer period of time than intended (A1). Cluster B is defined by tolerance (A7) and impaired control (A2, A3). Cluster C is defined by withdrawal (A8, A9) and giving up activities in order to drink (A5). Clusters are shown to follow a time sequence, with at least one symptom in Cluster A usually occurring first, followed by symptoms in Clusters B and C. In all, 83.4% of the symptom cluster transitions estimated from retrospective age of onset reports are consistent with this progression. Progression to AD is differentially predicted by symptom profiles reported at the age of first symptom onset, with persons reporting Cluster C symptoms most likely to progress subsequently to AD. Furthermore, profiles of AD defined by the highest symptom cluster present at AD onset are differentially predicted by prior personal and parental histories of psychopathology and, among men, are predictive of diagnosis persistence.     

Apparatus and procedure for measuring release rates from formulations of lepidopteran semiochemicals

An apparatus was developed wherein a vacuum source was used to pull air across a controlled-release-formulation dispenser or a planchet containing a known quantity of a semiochemical and into a collector filled with a polymeric adsorbent. After a set time, the semiochemical was eluted with solvent and was quantified by gas-liquid chromatography (GLC). High percentages of known quantities of the lepidopteran semiochemicals (Z)-7-dodecen-l -ol acetate (Z7DDA), boiling point (bp) 275 ° C/1 atm, (Z)-9-tetradecen-1-ol formate (Z9TDF), bp 289 °C/1 atm, and (Z,Z)-3,13-octadecadien-1-ol acetate (ZZODDA), bp 490 °C/1 atm, were recovered. The semiochemicals did not oxidize and were recovered quantitatively from the adsorbent. The release rates of Z9TDF from a controlled-release dispenser were found to be directly proportional to the airflow rates. Release rate measurements on the Z9TDF dispensers were made for the purpose of estimating the method's precision. The method was shown to give internally consistent results by measurements on another Z9TDF formulation. The accuracy of the method is discussed.Mention of a commercial or proprietary product in this paper does not constitute an endorsement by the USDA.     

Object-Oriented Systems Development

Object-oriented design is an approach to systems development that proposes the use of system objects to build new systems and rebuild old ones. An important goal of object-oriented development is to change the nature of traditional software development from designing and writing models from scratch to building systems through the assembly of reusable software objects. This article discusses the productivity potential as well as the limitations of object-oriented systems development and makes recommendations for its use.     

Coherency Hub Design for Multisocket Sun Servers with CoolThreads Technology

CoHub, a coherency hub ASIC, provides a cost-effective way to extend a glueless two-node chip-multithreading system to a four-node system without changes to the processor. The four-node, 256-thread system achieves near-linear scaling of performance with thread count on transaction-processing workloads. Time-to-market pressure, 800-MHz operation, and a six-stage pipeline were among the constraints that shaped CoHub's design.     

Edge-Packing in Planar Graphs

Maximum G Edge-Packing (EPack _G ) is the problem of finding the maximum number of edge-disjoint isomorphic copies of a fixed guest graph G in a host graph H . This paper investigates the computational complexity of edge-packing for planar guests and planar hosts. Edge-packing is solvable in polynomial time when both G and H are trees. Edge-packing is solvable in linear time when H is outerplanar and G is either a 3-cycle or a k -star (a graph isomorphic to K _1,k ). Edge-packing is NP-complete when H is planar and G is either a cycle or a tree with edges. A strategy for developing polynomial-time approximation algorithms for planar hosts is exemplified by a linear-time approximation algorithm that finds a k -star edge-packing of size at least half the optimal. Received May 1995, and in revised form November 1995, and in final form December 1997.     

Normalizing Behavior of Unsaturated Granular Pavement Materials

One of the important components of a flexible pavement structure is granular material layers. Unsaturated granular pavement materials (UGPMs) in these layers influence stresses and strains throughout the pavement structure, and have a large effect on asphalt concrete fatigue and pavement rutting (two of the primary failure mechanisms for flexible pavements). The behavior of UGPMs is dependent on water content, but this effect has been traditionally difficult to quantify using either empirical or mechanistic methods. This paper presents a practical mechanistic framework for determining the behavior of UGPMs within the range of water contents, densities, and stress states likely to be encountered under field conditions. Both soil suction and generated pore pressures are determined and compared to confinement under typical field loading conditions. The framework utilizes a simple soil suction model that has three density-independent parameters, and can be determined using conventional triaxial equipment that is available in many pavement engineering laboratories.     

Dialdehyde Starch Hydrazones: Preparation and Properties of Cationic Dispersions

Cationic dialdehyde starch (DAS) dispersions have been prepared in water at 15% concentration by a new cooking procedure. A stable fluid form of cationic DAS, a wet- and dry-strength agent for paper, should facilitate commercial use. Cationic DAS dispersions of pH 3.0 stored in polyethylene containers at 25°C or below were unchanged after 6 months; other storage conditions were also evaluated. An unexpected benefit of the new preparative conditions was a 40% reduction of cationizing agent, betaine hydrazide hydrochloride, without loss of effectiveness. Further savings may be possible by blending cationic DAS with unmodified starch; wet- and dry-strength improvements were maintained in paper with a blend containing 33% unmodified starch and 67% cationic DAS.