Biomedical subjects

S I Wright

Publications and source records attributed to S I Wright.

9 recordsLinked to original sources

PubMed2005

Analysis of local orientation gradients in deformed single crystals.

Grain fragmentation and local orientation gradients in deformed single crystals are characterized using electron backscatter diffraction (EBSD) to obtain statistically reliable information. Interrogation of the dislocation substructure is accomplished by extracting information gleaned from small point-to-point misorientations as measured by EBSD. Along with an estimate of the geometrically necessary dislocation (GND) content, the point-to-point deviation from an average grain orientation is described by an orientation difference vector defined in Rodrigues space. Mapping of parameters such as GND, and divergence and gradient fields created from analysis of the difference vectors provide an alternative approach to obtain quantitative information and images from EBSD data.

Journal Article↗

PubMed2004

Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana.

BACKGROUND: Rates of recombination can vary among genomic regions in eukaryotes, and this is believed to have major effects on their genome organization in terms of base composition, DNA repeat density, intron size, evolutionary rates and gene order. In highly self-fertilizing species such as Arabidopsis thaliana, however, heterozygosity is expected to be strongly reduced and recombination will be much less effective, so that its influence on genome organization should be greatly reduced. RESULTS: Here we investigated theoretically the joint effects of recombination and self-fertilization on base composition, and tested the predictions with genomic data from the complete A. thaliana genome. We show that, in this species, both codon-usage bias and GC content do not correlate with the local rates of crossing over, in agreement with our theoretical results. CONCLUSIONS: We conclude that levels of inbreeding modulate the effect of recombination on base composition, and possibly other genomic features (for example, transposable element dynamics). We argue that inbreeding should be considered when interpreting patterns of molecular evolution.

Arabidopsis↗

PubMed2004

Phase differentiation via combined EBSD and XEDS.

Electron backscatter diffraction (EBSD) and orientation imaging microscopy have become established techniques for analysing the crystallographic microstructure of single and multiphase materials. In certain instances, however, it can be difficult and/or time intensive to differentiate phases within a material by crystallography alone. Traditionally a list of candidate phases is specified prior to data collection. The crystallographic information extracted from the diffraction patterns is then compared with the crystallographic information from these candidate phases, and a best-fit match is determined. Problems may arise when two phases have similar crystal structures. The phase differentiation process can be improved by collecting chemical information through X-ray energy-dispersive spectroscopy (XEDS) simultaneously with the crystallographic information through EBSD and then using the chemical information to pre-filter the crystallographic phase candidates. This technique improves both the overall speed of the data collection and the accuracy of the final characterization. Examples of this process and the limitations involved will be presented and discussed.

Copper↗

PubMed2002

Extracting twins from orientation imaging microscopy scan data.

Automated electron backscatter diffraction or orientation imaging microscopy (OIM) provides spatially specific measurements of crystallographic orientation. These measurements are typically collected on regular grids. By inspecting the misorientation between neighbouring measurements on the grid, potential twin boundaries can be identified. If the misorientation is within some given tolerance of a specified twin misorientation, the boundary separating the two measurements may be identified as a potential twin boundary. In addition, for a coherent twin, the twinning planes must be coincident with the grain boundary plane. As OIM scans are inherently two-dimensional, the scan data provide only limited information on the boundary plane. Thus, it is not possible to ascertain definitively whether the twinning planes are coincident with the boundary plane. Nonetheless, the alignment of the surface traces of the twinning planes with the trace of the boundary provides a partial indication of coincidence. An automated approach has been developed that allows data concerning both twin criterion to be extracted from OIM scans. Application of the methodology to deformed zirconium suggests that the twinning planes remain coherent during deformation. The methodology was also used to improve grain size distributions measured by OIM. These results more closely match those obtained by conventional metallography.

Journal Article↗

PubMed2001

Breeding systems and genome evolution.

The profound effects of inbreeding and other non-recombining breeding systems on genetic variability and molecular evolution are now beginning to be understood. Theoretical models predict how such populations are expected to differ from outcrossed populations, and DNA sequence data are being collected and used to test the predictions.

Animals↗

PubMed2001

Population dynamics of an Ac-like transposable element in self- and cross-pollinating arabidopsis.

Theoretical models predict that the mating system should be an important factor driving the dynamics of transposable elements in natural populations due to differences in selective pressure on both element and host. We used a PCR-based approach to examine the abundance and levels of insertion polymorphism of Ac-III, a recently identified Ac-like transposon family, in natural populations of the selfing plant Arabidopsis thaliana and its close outcrossing relative, Arabidopsis lyrata. Although several insertions appeared to be ancient and shared between species, there is strong evidence for recent activity of this element family in both species. Sequences of the regions flanking insertions indicate that all Ac-III transposons segregating in natural populations are in noncoding regions and provide no evidence for local transposition events. Transposon display analysis suggests the presence of slightly higher numbers of insertion sites per individual but fewer total polymorphic insertions in the self-pollinating A. thaliana than A. lyrata. Element insertions appear to be segregating at significantly lower frequencies in A. lyrata than A. thaliana, which is consistent with a reduction in transposition rate, reduction in effective population size, or reduced efficacy of natural selection against element insertions in selfing populations.

Arabidopsis↗

PubMed2000

Mutator-like elements in Arabidopsis thaliana. Structure, diversity and evolution.

While genome-wide surveys of abundance and diversity of mobile elements have been conducted for some class I transposable element families, little is known about the nature of class II transposable elements on this scale. In this report, we present the results from analysis of the sequence and structural diversity of Mutator-like elements (MULEs) in the genome of Arabidopsis thaliana (Columbia). Sequence similarity searches and subsequent characterization suggest that MULEs exhibit extreme structure, sequence, and size heterogeneity. Multiple alignments at the nucleotide and amino acid levels reveal conserved, potentially transposition-related sequence motifs. While many MULEs share common structural features to Mu elements in maize, some groups lack characteristic long terminal inverted repeats. High sequence similarity and phylogenetic analyses based on nucleotide sequence alignments indicate that many of these elements with diverse structural features may remain transpositionally competent and that multiple MULE lineages may have been evolving independently over long time scales. Finally, there is evidence that MULEs are capable of the acquisition of host DNA segments, which may have implications for adaptive evolution, both at the element and host levels.

Amino Acid Motifs↗

PubMed1999

Transposon dynamics and the breeding system.

The selfish DNA hypothesis predicts that natural selection is responsible for preventing the unregulated build up of transposable elements in organismal genomes. Accordingly, between-species differences in the strength and effectiveness of selection against transposons should be important in driving the evolution of transposon activity and abundance. We used a modeling approach to investigate how the rate of self-fertilization influences the population dynamics of transposable elements. Contrasting effects of the breeding system were observed under selection based on transposon disruption of gene function versus selection based on element-mediated ectopic exchange. This suggests that the comparison of TE copy number in organisms with different breeding systems may provide a test of the relative importance of these forces in regulating transposon multiplication. The effects of breeding system also interacted with population size, particularly when there was no element excision. The strength and effectiveness of selection against transposons was reflected not only in their equilibrium abundance, but also in the per-site element frequency of individual insertions and the coefficient of variation in copy number. These results are discussed in relation to evidence on transposon abundance available from the literature, and suggestions for future data collection.

Breeding↗

PubMed1980

Differential feedback used by speech and language clinicians.

Differential feedback used by speech and language clinicians in schools was investigated and described. Eleven clinicians were tape-recorded during three consecutive treatment sessions with groups of second-or third-grade articulation-defective children. Recordings were analyzed according to feedback category, frequency, and consistency of administration. Results indicated restricted repertoires of applied categorical items and extreme variability in frequency and consistency of utilization.

Biofeedback, Psychology↗