The genome strikes back: The evolutionary importance of defence against mobile elements

Increasingly, we regard the genome as a site and source of genetic conflict. This fascinating 'bottom-up' view brings up appealing connections between genome biology and whole-organism ecology, in which populations of elements compete with one another in their genomic habitat. Unlike other habitats, though, a host genome has its own evolutionary interests and is often able to defend itself against molecular parasites. Most well-studied organisms employ strategies to protect their genomes against the harmful effects of genomic parasites, including methylation, various pathways of RNA interference, and more unusual tricks such as repeat induced point-mutation (RIP). These genome defence systems are not obscure biological curiosities, but fundamentally important to the integrity and cohesion of the genome, and exert a powerful influence on genome evolution.

The coordination chemistry of 1,2,4-triazinyl bipyridines with lanthanide(III) elements - implications for the partitioning of americium(III)

It has been established that 6-(5,6-dialkyl-1,2,4-triazin-3-yl)-2,2'-bipyridines (R,hemi-BTPs) have properties which are intermediate between those of the terpyridines and the bis(1,2,4-triazin-3-yl)pyridines (BTPs). However, they resemble the terpyridines much more closely than the BTPs. It has been shown that Et, hemi-BTP when dissolved in TPH-a dodecane-like solvent-is a selective reagent for the separation of americium(III) from europium(III). Solution NMR in acetonitrile largely confirmed the crystallographic results. There was no evidence for a 1 : 3 complex cation, or for significant differences between metal(III)-N distances for the pyridine and 1,2,4-triazine rings. Intramolecular hydrogen bonding plays a crucial role in the formation of metal coordination spheres, which explains the differences between the terpyridyl, R,hemi-BTPs and the BTPs. Protonation of the R,hemi-BTPs facilitates a conformational change which is necessary for complexation.

Spatial offset of test field elements from surround elements affects the strength of motion aftereffects

Static movement aftereffects (MAEs) were measured after adaptation to vertical square-wave luminance gratings drifting horizontally within a central window in a surrounding stationary vertical grating. The relationship between the stationary test grating and the surround was manipulated by varying the alignment of the stationary stripes in the window and those in the surround, and the type of outline separating the window and the surround [no outline, black outline (invisible on black stripes), and red outline (visible throughout its length)]. Offsetting the stripes in the window significantly increased both the duration and ratings of the strength of MAEs. Manipulating the outline had no significant effect on either measure of MAE strength. In a second experiment, in which the stationary test fields alone were presented, participants judged how segregated the test field appeared from its surround. In contrast to the MAE measures, outline as well as offset contributed to judged segregation. In a third experiment, in which test-stripe offset wits systematically manipulated, segregation ratings rose with offset. However, MAE strength was greater at medium than at either small or large (180 degrees phase shift) offsets. The effects of these manipulations on the MAE are interpreted in terms of a spatial mechanism which integrates motion signals along collinear contours of the test field and surround, and so causes a reduction of motion contrast at the edges of the test field.

Quantification of boundary definition using pulsed terahertz radiation for wedged geometries

The interaction of a terahertz beam with a sample containing a material boundary across the profile of the terahertz beam produces characteristic spectroscopic detail. A full vectorial model is presented to quantify boundary definition for a series of wedged geometries. As a result of this work, using simple geometric forms, we wish to be able to extend these ideas to characterize boundaries in more irregular samples, impacting most application areas of pulsed terahertz radiation.

A new RBF neural network with boundary value constraints

We present a novel topology of the radial basis function (RBF) neural network, referred to as the boundary value constraints (BVC)-RBF, which is able to automatically satisfy a set of BVC. Unlike most existing neural networks whereby the model is identified via learning from observational data only, the proposed BVC-RBF offers a generic framework by taking into account both the deterministic prior knowledge and the stochastic data in an intelligent manner. Like a conventional RBF, the proposed BVC-RBF has a linear-in-the-parameter structure, such that it is advantageous that many of the existing algorithms for linear-in-the-parameters models are directly applicable. The BVC satisfaction properties of the proposed BVC-RBF are discussed. Finally, numerical examples based on the combined D-optimality-based orthogonal least squares algorithm are utilized to illustrate the performance of the proposed BVC-RBF for completeness.

Mixed initial-boundary value problem in particle modeling of microelectronic devices

The Boltzmann equation in presence of boundary and initial conditions, which describes the general case of carrier transport in microelectronic devices is analysed in terms of Monte Carlo theory. The classical Ensemble Monte Carlo algorithm which has been devised by merely phenomenological considerations of the initial and boundary carrier contributions is now derived in a formal way. The approach allows to suggest a set of event-biasing algorithms for statistical enhancement as an alternative of the population control technique, which is virtually the only algorithm currently used in particle simulators. The scheme of the self-consistent coupling of Boltzmann and Poisson equation is considered for the case of weighted particles. It is shown that particles survive the successive iteration steps.

Two-point boundary value problems for linear evolution equations

We study boundary value problems for a linear evolution equation with spatial derivatives of arbitrary order, on the domain 0 < x < L, 0 < t < T, with L and T positive nite constants. We present a general method for identifying well-posed problems, as well as for constructing an explicit representation of the solution of such problems. This representation has explicit x and t dependence, and it consists of an integral in the k-complex plane and of a discrete sum. As illustrative examples we solve some two-point boundary value problems for the equations iqt + qxx = 0 and qt + qxxx = 0.

The impact of genome defense on mobile elements in Microbotryum

Repeat induced point mutation (RIP), a mechanism causing hypermutation of repetitive DNA sequences in fungi, has been described as a ‘genome defense’ which functions to inactivate mobile elements and inhibit their deleterious effects on genome stability. Here we address the interactions between RIP and transposable elements in the Microbotryum violaceum species complex. Ten strains of M. violaceum, most of which belong to different species of the fungus, were all found to contain intragenomic populations of copia-like retrotransposons. Intragenomic DNA sequence variation among the copia-like elements was analyzed for evidence of RIP. Among species with RIP, there was no significant correlation between the frequency of RIP-induced mutations and inferred transposition rate based on diversity. Two strains of M. violaceum, from two different plant species but belonging to the same fungal lineage, contained copia-like elements with very low diversity, as would result from a high transposition rate, and these were also unique in showing no evidence of the hypermutation patterns indicative of the RIP genome defense. In this species, evidence of RIP was also absent from a Class II helitron-like transposable element. However, unexpectedly the absolute repetitive element load was lower than in other strains.

On a class of non-self-adjoint periodic eigenproblems with boundary and interior singularities

We prove that all the eigenvalues of a certain highly non-self-adjoint Sturm–Liouville differential operator are real. The results presented are motivated by and extend those recently found by various authors (Benilov et al. (2003) [3], Davies (2007) [7] and Weir (2008) [18]) on the stability of a model describing small oscillations of a thin layer of fluid inside a rotating cylinder.

On a class of nonselfadjoint periodic boundary value problems with discrete real spectrum

In a previous paper (J. of Differential Equations, Vol. 249 (2010), 3081-3098) we examined a family of periodic Sturm-Liouville problems with boundary and interior singularities which are highly non-self-adjoint but have only real eigenvalues. We now establish Schatten class properties of the associated resolvent operator.