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).     

Graphite formation on Ni film by chemical vapor deposition

Thin film formation of graphite by chemical vapor deposition using 2-methyl-1,2′-naphthyl ketone as a starting material was carried out on Ni film substrates. On Ni films directly deposited on quartz glass, the graphite films were obtained when the Ni film thickness was above 1 000 Å and above 5 000 Å at 700 °C and 1 000 °C, respectively. Depositions on thinner Ni film substrates comprise amorphous carbon (a-C) or graphite tubes which was owing to the thermal coagulation of the Ni film into droplets. On the other hand, graphite film was obtained on the Ni film with thickness 10 Å when a-C was inserted between the Ni film and the quartz glass. The coagulation of the Ni film is considered to be avoided by inserting a-C layer.     

The computer in literary analysis: UsingTACT with students

TACT, a freeware program from the University of Toronto's Centre for Computing in the Humanities, is a highly sophisticated tool for text retrieval; although written for experienced critics and researchers, it can teach undergraduate students to read literature in new, fresh ways. Without requiring that the user become either a programmer, linguist, mathematician, or statistician,TACT introduces the literature student to the computer as a research tool. Studies of imagery and symbolism, of structural patterns, and of prosody can result from the student's careful tagging of a literary text and can yield significant insights into the work of literature. Students who use the computer as such a tool learn to read literary texts more closely and to think more clearly about literary problems.     

Ratings of Therapist Dynamic Activities and Alliance Early and Late in Psychotherapy.

The present study examines the concurrent and predictive relationships between therapist psychodynamic-interpersonal activity and therapist-rated alliance. Ratings from 45 patient and therapist dyads engaged in short term psychodynamic psychotherapy from a point early (3rd or 4th session) and late (the session at which 90% of the treatment was completed) in treatment were used. The results suggest that therapists who have positive views of the alliance early in treatment also have positive views of the alliance later in treatment. Therapists who used psychodynamic-interpersonal activities early in treatment also made use of psychodynamic-interpersonal activities later in treatment. Moreover, the use of psychodynamic-interpersonal activities early in treatment was positively related to both global and specific aspects of therapist-rated alliance late in treatment. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

On-demand Virtual Neonatal Intensive Care units supporting rural, remote and urban healthcare with Bush Babies Broadband

Premature and ill term babies born in regional Australia must be moved to another hospital with Neonatal Intensive Care Unit (NICU) facilities. Transferred pre-term and critically ill term babies have higher mortality rates and much higher rates of long term disability than similar babies born in hospitals with NICU facilities. This paper details the Bush Babies Broadband project that aims to significantly improve the quality of treatment for babies born in rural, remote as well as urban areas by providing the first on-demand virtual NICU architecture in Australia. Real-time data collected from medical monitors and ventilators attached to the baby, audiovisual streams and static physiological data such as X-ray images are transmitted to the consulting Neonatologist to gain a better picture of the patient's condition than is currently available. The key contribution of this significant research is the infrastructure providing a mechanism for Neonatologists to receive information directly from a regional hospital, thereby preventing, in some cases, the immediate need to move the baby. A key benefit of this framework is that it is available to link regional hospitals with the supporting NICU Neonatologist ‘on demand’ eliminating the need to establish permanent point to point connections. This paper further describes the application of that architecture to a specific pilot connecting the Bathurst regional hospital with Neonatologists within the NICU at Nepean Hospital, Penrith Australia.     

Sensitivity analysis of initial value problems with mixed odes and algebraic equations

An efficient method is described for sensitivity analysis of nonlinear initial value problems, which may include algebraic equations as well as ordinary differential equations.The linearity of the sensitivity equations is utilized to solve them directly via the local Jacobian of the state equations. The method is implemented with the implicit integrator DASSL and is demonstrated on a stiff industrial reaction model.     

The Witchfinder-General and the Will-o'-the-Wisp: The myth and reality of Internet control

Internet pornography, especially child pornography, has been a significant concern in British society for several years. This article seeks to examine the prevalence and impact of such material, the way public concern has developed, and media and legislative reactions to this concern. It suggests that a more rational debate of the actual and likely dangers in this sphere is necessary in order both to protect and serve the interests of justice.     

What's the use of being happy? Mood states, useful objects, and repetition priming effects.

Two experiments involving 99 undergraduate participants sought to examine the influence of mood states on encoding speed within lexical decision and pronunciation tasks. Mood states were measured naturalistically in Experiment 1 and manipulated in Experiment 2. Stimuli consisted of nouns representing useful (e.g., food) and nonuseful (e.g., lint) objects. Mood states had no implications for initial encoding speed. However, when the same words were presented a 2nd time (i.e., repeated), happy individuals displayed a tendency to encode useful words faster than nonuseful ones. Thus, mood states influenced repetition priming on the basis of stimulus valence. The authors propose that happiness sensitizes individuals to useful or rewarding objects, which in turn creates a stronger memory trace for such stimuli in the future. (PsycINFO Database Record (c) 2010 APA, all rights reserved)