Validation of the detection of Alexandrium spp using specific RNA probes tested in a microarray format: Calibration of signal using variability of RNA content with environmental conditions

The dinoflagellate genus Alexandrium contains several toxin producing species and strains, which can cause major economic losses to the shell fish industry. It is therefore important to be able to detect these toxin producers and also distinguish toxic strains from some of the morphologically identical non-toxic strains. To facilitate this DNA probes to be used in a microarray format were designed in silico or developed from existing published probes. These probes targeted either the 18S or 28S ribosomal ribonucleic acid (rRNA) gene in Alexandrium tamarense Group I, Group III and Group IV, Alexandrium ostenfeldii and Alexandrium minutum. Three strains of A. tamarense Group I, A. tamarense Group III, A. minutum and two strains of A. ostenfeldii were grown at optimal conditions and transferred into new environmental conditions changing either the light intensity, salinity, temperature or nutrient concentrations, to check if any of these environmental conditions induced changes in the cellular ribonucleic acid (RNA) concentration or growth rate. The aim of this experiment was the calibration of several species-specific probes for the quantification of the toxic Alexandrium strains. Growth rates were highly variable but only elevated or lowered salinity significantly lowered growth rate for A. tamarense Group I and Group III; differences in RNA content were not significant for the majority of the treatments. Only light intensity seemed to affect significantly the RNA content in A. tamarense Group I and Group III, but this was still within the same range as for the other treatments meaning that a back calibration from RNA to cell numbers was possible. The designed probes allow the production of quantitative information for Alexandrium species for the microarray chip

Persuasive technologies: a systematic literature review and application to PISA

Persuasive Technologies is an expansive eld that covers various research areas including engineering and social sciences. This document summarizes current and historical models of information processing, persuasion and persuasive systems design in order to place other studies in the eld within context. The Persuasive Systems Design Model is then selected as the most recent and comprehensive model in the eld, afer which a series of sample context analyses are performed using this model. The case used for these context analyses is the PISA tool. Finally, we consider the limitations and possible future work of this literature review

Quantum dynamics of Bose-Einstein condensates in tilted and driven bichromatic optical lattices

We study the dynamics of Bose-Einstein condensates in tilted and driven optical superlattices. For a bichromatic lattice, each Bloch band split up into two minibands such that the dynamics is governed by the interplay of Bloch oscillations and transitions between the bands. Thus, bichromatic potentials provide an excellent model system for the study of nonlinear Landau-Zener tunneling and allow for a variety of applications in matter wave interferometry and quantum metrology. In the present paper we investigate the coherent dynamics of an interacting Bose-Einstein condensate as well as its stability. Different mechanisms of instability are discussed, which lead to a rapid depletion of the condensate.Comment: 9 pages, 9 figures, to appear in Phys. Rev.

Simulation studies of a phenomenological model for elongated virus capsid formation

We study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to those of prolate virus capsid structures. Our simulation approach combines the traditional Monte Carlo method with a modified method of random sampling on an ellipsoidal surface and a convex hull searching algorithm. Using this approach we identify the minimum physical requirements for non-icosahedral, elongated virus capsids, such as two aberrant flock house virus (FHV) particles and the prolate prohead of bacteriophage $\phi_{29}$, and discuss the implication of our simulation results in the context of recent experimental findings. Our predicted structures may also be experimentally realized by evaporation-driven assembly of colloidal spheres

Computer literacy systematic literature review method

Although there have been many attempts to define the concept ‘computer literacy’, no consensus has been reached: many variations of the concept exist within litera-ture. The majority of papers does not explicitly define the concept at all, insteadusing an unjustified subset of elements related to computers to assess a subject’slevel of computer literacy. This can limit the generalizability of research and canlead to fallacious conclusions. This is an internal report listing the method by whichthe research was conducted

Pre-Existing Superbubbles as the Sites of Gamma-Ray Bursts

According to recent models, gamma-ray bursts apparently explode in a wide variety of ambient densities ranging from ~ 10^{-3} to 30 cm^{-3}. The lowest density environments seem, at first sight, to be incompatible with bursts in or near molecular clouds or with dense stellar winds and hence with the association of gamma-ray bursts with massive stars. We argue that low ambient density regions naturally exist in areas of active star formation as the interiors of superbubbles. The evolution of the interior bubble density as a function of time for different assumptions about the evaporative or hydrodynamical mass loading of the bubble interior is discussed. We present a number of reasons why there should exist a large range of inferred afterglow ambient densities whether gamma-ray bursts arise in massive stars or some version of compact star coalescence. We predict that many gamma-ray bursts will be identified with X-ray bright regions of galaxies, corresponding to superbubbles, rather than with blue localized regions of star formation. Massive star progenitors are expected to have their own circumstellar winds. The lack of evidence for individual stellar winds associated with the progenitor stars for the cases with afterglows in especially low density environments may imply low wind densities and hence low mass loss rates combined with high velocities. If gamma-ray bursts are associated with massive stars, this combination might be expected for compact progenitors with atmospheres dominated by carbon, oxygen or heavier elements, that is, progenitors resembling Type Ic supernovae.Comment: 14 pages, no figures, submitted to The Astrophysical Journa

Interplay between elastic fields due to gravity and a partial dislocation for a hard-sphere crystal coherently grown under gravity: driving force for defect disappearance

We previously observed that an intrinsic staking fault shrunk through a glide of a Shockley partial dislocation terminating its lower end in a hard-sphere crystal under gravity coherently grown in by Monte Carlo simulations [Mori et al., Molec. Phys. 105, 1377 (2007)]; it was an answer to a one-decade long standing question why the stacking disorder in colloidal crystals reduced under gravity [Zhu et al., Nature 387, 883 (1997)]. Here, we present an elastic energy calculation; in addition to the self-energy of the partial dislocation [Mori et al., Prog. Theor. Phys. Suppl. 178, 33 (2009)] we calculate the cross-coupling term between elastic field due to gravity and that due to a Shockley partial dislocation. The cross term is a increasing function of the linear dimension R over which the elastic field expands, showing that a driving force arises for the partial dislocation moving toward the upper boundary of a grain.Comment: 8pages, 4figures, to be published in Molecular Physic

What do emulsification failure and Bose-Einstein condensation have in common?

Ideal bosons and classical ring polymers formed via self-assembly, are known to have the same partition function, and so analogous phase transitions. In ring polymers, the analogue of Bose-Einstein condensation occurs when a ring polymer of macroscopic size appears. We show that a transition of the same general form occurs within a whole class of systems with self-assembly, and illustrate it with the emulsification failure of a microemulsion phase of water, oil and surfactant. As with Bose-Einstein condensation, the transition occurs even in the absence of interactions.Comment: 7 pages, 1 figure, typeset with EUROTeX, uses epsfi