The haplotype distribution of two genes of citrus tristeza virus is altered after host change or aphid transmission.
Genetic variability of citrus tristeza virus (CTV) was studied using the haplotypes detected by single-strand conformation polymorphism (SSCP) analysis of genes p18 and p20 in six virus populations of two origins. The Spanish group included a CTV isolate and subisolates obtained by graft-transmission to different host species. The other included two subisolates aphid-transmitted from a single Japanese isolate. The homozygosity observed for gene p20 was always significantly higher than that expected under neutral evolution, whereas only three populations showed high homozygosity for p18, suggesting stronger host constraints for p20 than for p18. Sequential transmissions of a Spanish isolate to new host species increased the difference between its population and that of the successive subisolates for gene p18, as estimated by the F statistic. Analysis of molecular variance indicated that variation between both groups of populations was not statistically significant, whereas variations between populations of the same group or within populations were significant for both genes studied. Our data indicate that selection affects the haplotype distribution and that adaptation to a new host can be as important or more as the geographical origin. Variation of the CTV populations after host change or aphid transmission may explain in part the wide biological variability observed among CTV isolates. (+info)
Bayesian inference on biopolymer models.
MOTIVATION: Most existing bioinformatics methods are limited to making point estimates of one variable, e.g. the optimal alignment, with fixed input values for all other variables, e.g. gap penalties and scoring matrices. While the requirement to specify parameters remains one of the more vexing issues in bioinformatics, it is a reflection of a larger issue: the need to broaden the view on statistical inference in bioinformatics. RESULTS: The assignment of probabilities for all possible values of all unknown variables in a problem in the form of a posterior distribution is the goal of Bayesian inference. Here we show how this goal can be achieved for most bioinformatics methods that use dynamic programming. Specifically, a tutorial style description of a Bayesian inference procedure for segmentation of a sequence based on the heterogeneity in its composition is given. In addition, full Bayesian inference algorithms for sequence alignment are described. AVAILABILITY: Software and a set of transparencies for a tutorial describing these ideas are available at http://www.wadsworth.org/res&res/bioinfo/ (+info)
Application of distance geometry to 3D visualization of sequence relationships.
SUMMARY: We describe the application of distance geometry methods to the three-dimensional visualization of sequence relationships, with examples for mumps virus SH gene cDNA and prion protein sequences. Sequence-sequence distance measures may be obtained from either a multiple sequence alignment or from sets of pairwise alignments. AVAILABILITY: C/Perl code and HTML/VRML files from http://www.nibsc.ac.uk/dg3dseq/ (+info)
Units of measure in clinical information systems.
The authors surveyed existing standard codes for units of measures, such as ISO 2955, ANSI X3.50, and Health Level 7's ISO+. Because these standards specify only the character representation of units, the authors developed a semantic model for units based on dimensional analysis. Through this model, conversion between units and calculations with dimensioned quantities become as simple as calculating with numbers. All atomic symbols for prefixes and units are defined in one small table. Huge permutated conversion tables are not required. This method is also simple enough to be widely implementable in today's information systems. To promote the application of the method the authors provide an open-source implementation of this method in JAVA. All existing code standards for units, however, are incomplete for practical use and require substantial changes to correct their many ambiguities. The authors therefore developed a code for units that is much more complete and free from ambiguities. (+info)
Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4.
As part of the European Scientists Sequencing Arabidopsis program, a contiguous region (396607 bp) located on chromosome 4 around the APETALA2 gene was sequenced. Analysis of the sequence and comparison to public databases predicts 103 genes in this area, which represents a gene density of one gene per 3.85 kb. Almost half of the genes show no significant homology to known database entries. In addition, the first 45 kb of the contig, which covers 11 genes, is similar to a region on chromosome 2, as far as coding sequences are concerned. This observation indicates that ancient duplications of large pieces of DNA have occurred in Arabidopsis. (+info)
Validity and reliability of the Medical Outcomes Study Short Form-20 questionnaire as a measure of quality of life in elderly people living at home.
BACKGROUND: the Medical Outcomes Study Short Form-20 (SF-20) questionnaire is recommended for health-related quality of life research, but there is little information on its utility in older people. We assessed the validity, reliability and feasibility of using the SF-20 in an elderly community-dwelling population. METHODS: the SF-20 was administered to a stratified, random sample of 333 elderly subjects. FINDINGS: assessment of content validity revealed that important domains were lacking, while others appeared to be inappropriately combined. Using Spearman correlation coefficients, the SF-20 had acceptable convergent and discriminant validity. A principal components analysis provided evidence for internal consistency for some of the subscales. Evidence for test-retest reliability was good. INTERPRETATION: while the reliability and feasibility of the SF-20 appear satisfactory, concerns about validity and responsiveness should temper enthusiasm for its use with elderly people living at home. (+info)
Presenting statistical uncertainty in trends and dose-response relations.
When one estimates the effects of a polytomous exposure, it is common practice to express all effects relative to a baseline or reference level. Certain authors have challenged this practice and proposed alternatives, which we review here. One alternative, the "floating absolute risk" method, can supply useful statistics and trend graphs, but it does not yield valid confidence intervals for relative risks. All categorical methods have further shortcomings when the exposure is continuous, however. These shortcomings can be addressed by plotting or tabulating confidence limits for points on a flexible curve fitted to the uncategorized data. (+info)
The basic reproduction number for scrapie.
The basic reproduction number R0 provides a quantitative assessment of the ability of an infectious agent to invade a susceptible host population. A mathematical expression for R0 is derived based on a recently developed model for the spread of scrapie through a flock of sheep. The model incorporates sheep demography, a long and variable incubation period, genetic variation in susceptibility to scrapie, and horizontal and vertical routes of transmission. The sensitivity of R0 to a range of epidemiologically important parameters is assessed and the effects of genetic variation in susceptibility are examined. A reduction in the frequency of the susceptibility allele reduces R0 most effectively when the allele is recessive, whereas inbreeding may increase R0 when the allele is recessive, increasing the chance of an outbreak. Using this formulation, R0 is calculated for an outbreak of scrapie in a flock of Cheviot sheep. (+info)