Structure of d(TGCGCA)(2) and a comparison with other DNA Hexamers

The X-ray crystal structure of d(TGCGCA)(2) has been determined at 120 K to a resolution of 1.3 Angstrom. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the 'pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388-11402] but with significantly different cell dimensions. The phosphate backbone exists in two equally populated discrete conformations at one nucleotide step, around phosphate 11. The structure contains two ordered cobalt hexammine molecules which have roles in stabilization of both the Z-DNA conformation of the duplex and in crystal packing. A comparison of d(TGCGCA)(2) with other Z-DNA hexamer structures available in the Nucleic Acid Database illustrates the elusive nature of crystal packing. A review of the interactions with the metal cations Na+, Mg2+ and Co3+ reveals a relatively small proportion of phosphate binding and that close contacts between metal ions are common. A prediction of the water structure is compared with the observed pattern in the reported structure

Structure of 3-[N-methyl-N-(S)-a-methylbenzyl]carbamoyl-1,2,4-trimethylpyridinium iodide

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Field Purification in the intensity-dependent Jaynes-Cummings model

We have found that, in the intensity-dependent Jaynes-Cummings model, a field initially prepared in a statistical mixture of two coherent states, $|\alpha>$ and $|-\alpha>$, evolves toward a pure state. We have also shown that an even-coherent state turns periodically a into rotated odd-coherent state during the evolution.Comment: 14 pages, RevTex, 3 figures, accepted for publication in Physics Letters

Solution-borne colloids from drip tests using actinide-doped and fully-radioactive waste glasses

Drip tests designed to replicate the synergistic interactions between waste glass, repository groundwater, water vapor, and sensitized 304L stainless steel in the potential Yucca Mountain Repository have been ongoing in our laboratory for over ten years. Results will be presented from three sets of these drip tests: two with actinide-doped glasses, and one with a fully-radioactive glass. Periodic sampling of these tests have revealed trends in actinide release behavior that are consistent with their entrainment in colloidal material when as-cast glass is reacted. Results from vapor hydrated glass show that initially the actinides are completely dissolved in solution, but as the reaction proceeds, the actinides become suspended in solution. Sequential filtering and alpha spectroscopy of colloid-bearing leachate solutions indicate that more than 80 percent of the plutonium and americium are bound to particles that are captured by a 0. 1 gm filter, while less than 10 percent of the neptunium is stopped by a 0. 1 gm filter. Analytical transmission electron microscopy has been used to examine particles from leachate solutions and to identify several actinide-bearing phases which are responsible for the majority of actinide release during glass corrosion

Scenario analysis can guide aquaculture planning to meet sustainable future production goals

Marine aquaculture holds great promise for meeting increasing demand for healthy protein that is sustainably produced, but reaching necessary production levels will be challenging. The ecosystem approach to aquaculture is a framework for sustainable aquaculture development that prioritizes multiple-stakeholder participation and spatial planning. These types of approaches have been increasingly used to help guide sustainable, persistent, and equitable aquaculture planning, but most countries have difficulties in setting or meeting longer-term development goals. Scenario analysis (SA) for future planning uses similar approaches and can complement holistic methods, such as the ecosystem approach to aquaculture framework, by providing a temporal analogue to the spatially robust design. Here we define the SA approach to planning in aquaculture, outline how SA can benefit aquaculture planning, and review how this tool is already being used. We track the use of planning tools in the 20 International Council for the Exploration of the Sea member nations, with particular attention given to Norway’s development goals to 2050. We conclude that employing a combination of an ecosystem framework with scenario analyses may help identify the scale of development aquaculture goals over time, aid in evaluating the feasibility of the desired outcomes, and highlight potential social-ecological conflicts and trade-offs that may otherwise be overlooked.Versión del editor2,27

Resonant structure of space-time of early universe

A new fully quantum method describing penetration of packet from internal well outside with its tunneling through the barrier of arbitrary shape used in problems of quantum cosmology, is presented. The method allows to determine amplitudes of wave function, penetrability $T_{\rm bar}$ and reflection $R_{\rm bar}$ relatively the barrier (accuracy of the method: $|T_{\rm bar}+R_{\rm bar}-1| < 1 \cdot 10^{-15}$), coefficient of penetration (i.e. probability of the packet to penetrate from the internal well outside with its tunneling), coefficient of oscillations (describing oscillating behavior of the packet inside the internal well). Using the method, evolution of universe in the closed Friedmann--Robertson--Walker model with quantization in presence of positive cosmological constant, radiation and component of generalize Chaplygin gas is studied. It is established (for the first time): (1) oscillating dependence of the penetrability on localization of start of the packet; (2) presence of resonant values of energy of radiation $E_{\rm rad}$, at which the coefficient of penetration increases strongly. From analysis of these results it follows: (1) necessity to introduce initial condition into both non-stationary, and stationary quantum models; (2) presence of some definite values for the scale factor $a$, where start of expansion of universe is the most probable; (3) during expansion of universe in the initial stage its radius is changed not continuously, but passes consequently through definite discrete values and tends to continuous spectrum in latter time.Comment: 18 pages, 14 figures, 4 table

The ancient evolutionary history of polyomaviruses

Author Summary: Polyomaviruses are a family of DNA-based viruses that are known to infect various terrestrial vertebrates, including humans. In this report, we describe our discovery of highly divergent polyomaviruses associated with various marine fish. Searches of public deep sequencing databases unexpectedly revealed the existence of polyomavirus-like sequences in scorpion and spider datasets. Our analysis of these new sequences suggests that polyomaviruses have slowly co-evolved with individual host animal lineages through an established mechanism known as intrahost divergence. The proposed model is similar to the mechanisms through with other DNA viruses, such as papillomaviruses, are thought to have evolved. Our analysis also suggests that distantly related polyomaviruses sometimes recombine to produce new chimeric lineages. We propose a possible taxonomic scheme that can account for these inferred ancient recombination events