Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only approximately 5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.

Functional significance of stiffness in adaptation of multijoint arm movements to stable and unstable dynamics.

This study compared the mechanisms of adaptation to stable and unstable dynamics from the perspective of changes in joint mechanics. Subjects were instructed to make point to point movements in force fields generated by a robotic manipulandum which interacted with the arm in either a stable or an unstable manner. After subjects adjusted to the initial disturbing effects of the force fields they were able to produce normal straight movements to the target. In the case of the stable interaction, subjects modified the joint torques in order to appropriately compensate for the force field. No change in joint torque or endpoint force was required or observed in the case of the unstable interaction. After adaptation, the endpoint stiffness of the arm was measured by applying displacements to the hand in eight different directions midway through the movements. This was compared to the stiffness measured similarly during movements in a null force field. After adaptation, the endpoint stiffness under both the stable and unstable dynamics was modified relative to the null field. Adaptation to unstable dynamics was achieved by selective modification of endpoint stiffness in the direction of the instability. To investigate whether the change in endpoint stiffness could be accounted for by change in joint torque or endpoint force, we estimated the change in stiffness on each trial based on the change in joint torque relative to the null field. For stable dynamics the change in endpoint stiffness was accurately predicted. However, for unstable dynamics the change in endpoint stiffness could not be reproduced. In fact, the predicted endpoint stiffness was similar to that in the null force field. Thus, the change in endpoint stiffness seen after adaptation to stable dynamics was directly related to changes in net joint torque necessary to compensate for the dynamics in contrast to adaptation to unstable dynamics, where a selective change in endpoint stiffness occurred without any modification of net joint torque.

An approach to functional synthesis of solutions in mechanical conceptual design. Part III: Spatial configuration

These three papers describe an approach to the synthesis of solutions to a class of mechanical design problems; these involve transmission and transformation of mechanical forces and motion, and can be described by a set of inputs and outputs. The approach involves (1) identifying a set of primary functional elements and rules of combining them, and (2) developing appropriate representations and reasoning procedures for synthesising solution concepts using these elements and their combination rules; these synthesis procedures can produce an exhaustive set of solution concepts, in terms of their topological as well as spatial configurations, to a given design problem. This paper (Part III) describes a constraint propagation procedure which, using a knowledge base of spatial information about a set of primary functional elements, can produce possible spatial configurations of solution concepts generated in Part II.

A hybrid density functional view of native vacancies in gallium nitride.

We investigated the transition energy levels of the vacancy defects in gallium nitride by means of a hybrid density functional theory approach (DFT). We show that, in contrast to predictions from a recent study on the level of purely local DFT, the inclusion of screened exchange stabilizes the triply positive charge state of the nitrogen vacancy for Fermi energies close to the valence band. On the other hand, the defect levels associated with the negative charge states of the nitrogen vacancy hybridize with the conduction band and turn out to be energetically unfavorable, except for high n-doping. For the gallium vacancy, the increased magnetic splitting between up-spin and down-spin bands due to stronger exchange interactions in sX-LDA pushes the defect levels deeper into the band gap and significantly increases the associated charge transition levels. Based on these results, we propose the ϵ(0| - 1) transition level as an alternative candidate for the yellow luminescence in GaN.