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J P Bielawski

Publications and source records attributed to J P Bielawski.

9 recordsLinked to original sources
PubMed2004

The origin and evolution of geminivirus-related DNA sequences in Nicotiana.

A horizontal transmission of a geminiviral DNA sequence, into the germ line of an ancestral Nicotiana, gave rise to multiple repeats of geminivirus-related DNA, GRD, in the genome. We follow GRD evolution in Nicotiana tabacum (tobacco), an allotetraploid, and its diploid relatives, and show GRDs are derived from begomoviruses. GRDs occur in two families: the GRD5 family's ancestor integrated into the common ancestor of three diploid species, Nicotiana kawakamii, Nicotiana tomentosa and Nicotiana tomentosiformis, on homeologous group 4 chromosomes. The GRD3 family was acquired more recently on chromosome 2 in a lineage of N. tomentosiformis, the paternal ancestor of tobacco. Both GRD families include individual members that are methylated and diverged. Using relative rates of synonymous and nonsynonymous nucleotide substitutions, we tested for evidence of selection on GRD units and found none within the GRD3 and GRD5 families. However, the substitutions between GRD3 and GRD5 do show a significant excess of synonymous changes, suggesting purifying selection and hence a period of autonomous evolution between GRD3 and GRD5 integration. We observe in the GRD3 family, features of Helitrons, a major new class of putative rolling-circle replicating eukaryotic transposon, not found in the GRD5 family or geminiviruses. We speculate that the second integration event, resulting in the GRD3 family, involved a free-living geminivirus, a Helitron and perhaps also GRD5. Thus our data point towards recurrent dynamic interplay between geminivirus and plant DNA in evolution.

Base Sequence↗
PubMed2001

Substitution rates in Drosophila nuclear genes: implications for translational selection.

The relationships between synonymous and nonsynonymous substitution rates and between synonymous rate and codon usage bias are important to our understanding of the roles of mutation and selection in the evolution of Drosophila genes. Previous studies used approximate estimation methods that ignore codon bias. In this study we reexamine those relationships using maximum-likelihood methods to estimate substitution rates, which accommodate the transition/transversion rate bias and codon usage bias. We compiled a sample of homologous DNA sequences at 83 nuclear loci from Drosophila melanogaster and at least one other species of Drosophila. Our analysis was consistent with previous studies in finding that synonymous rates were positively correlated with nonsynonymous rates. Our analysis differed from previous studies, however, in that synonymous rates were unrelated to codon bias. We therefore conducted a simulation study to investigate the differences between approaches. The results suggested that failure to properly account for multiple substitutions at the same site and for biased codon usage by approximate methods can lead to an artifactual correlation between synonymous rate and codon bias. Implications of the results for translational selection are discussed.

Animals↗
PubMed2001

Positive and negative selection in the DAZ gene family.

Because a microdeletion containing the DAZ gene is the most frequently observed deletion in infertile men, the DAZ gene was considered a strong candidate for the azoospermia factor. A recent evolutionary analysis, however, suggested that DAZ was free from functional constraints and consequently played little or no role in human spermatogenesis. The major evidence for this surprising conclusion is that the nonsynonymous substitution rate is similar to the synonymous rate and to the rate in introns. In this study, we reexamined the evolution of the DAZ gene family by using maximum-likelihood methods, which accommodate variable selective pressures among sites or among branches. The results suggest that DAZ is not free from functional constraints. Most amino acids in DAZ are under strong selective constraint, while a few sites are under diversifying selection with nonsynonymous/ synonymous rate ratios (d(N)/d(S)) well above 1. As a result, the average d(N)/d(S) ratio over sites is not a sensible measure of selective pressure on the protein. Lineage-specific analysis indicated that human members of this gene family were evolving by positive Darwinian selection, although the evidence was not strong.

Amino Acid Substitution↗
PubMed2001

Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.

The selective pressure at the protein level is usually measured by the nonsynonymous/synonymous rate ratio (omega = dN/dS), with omega < 1, omega = 1, and omega > 1 indicating purifying (or negative) selection, neutral evolution, and diversifying (or positive) selection, respectively. The omega ratio is commonly calculated as an average over sites. As every functional protein has some amino acid sites under selective constraints, averaging rates across sites leads to low power to detect positive selection. Recently developed models of codon substitution allow the omega ratio to vary among sites and appear to be powerful in detecting positive selection in empirical data analysis. In this study, we used computer simulation to investigate the accuracy and power of the likelihood ratio test (LRT) in detecting positive selection at amino acid sites. The test compares two nested models: one that allows for sites under positive selection (with omega > 1), and another that does not, with the chi2 distribution used for significance testing. We found that use of the chi(2) distribution makes the test conservative, especially when the data contain very short and highly similar sequences. Nevertheless, the LRT is powerful. Although the power can be low with only 5 or 6 sequences in the data, it was nearly 100% in data sets of 17 sequences. Sequence length, sequence divergence, and the strength of positive selection also were found to affect the power of the LRT. The exact distribution assumed for the omega ratio over sites was found not to affect the effectiveness of the LRT.

Adaptation, Biological↗
PubMed2000

Rates of nucleotide substitution and mammalian nuclear gene evolution. Approximate and maximum-likelihood methods lead to different conclusions.

Rates and patterns of synonymous and nonsynonymous substitutions have important implications for the origin and maintenance of mammalian isochores and the effectiveness of selection at synonymous sites. Previous studies of mammalian nuclear genes largely employed approximate methods to estimate rates of nonsynonymous and synonymous substitutions. Because these methods did not account for major features of DNA sequence evolution such as transition/transversion rate bias and unequal codon usage, they might not have produced reliable results. To evaluate the impact of the estimation method, we analyzed a sample of 82 nuclear genes from the mammalian orders Artiodactyla, Primates, and Rodentia using both approximate and maximum-likelihood methods. Maximum-likelihood analysis indicated that synonymous substitution rates were positively correlated with GC content at the third codon positions, but independent of nonsynonymous substitution rates. Approximate methods, however, indicated that synonymous substitution rates were independent of GC content at the third codon positions, but were positively correlated with nonsynonymous rates. Failure to properly account for transition/transversion rate bias and unequal codon usage appears to have caused substantial biases in approximate estimates of substitution rates.

Animals↗
PubMed1997

Randomly amplified polymorphic DNA (RAPD) analysis of Atlantic Coast striped bass.

Atlantic Coast striped bass exhibit exceptionally low levels of genetic variation. The ability of the randomly amplified polymorphic DNA (RAPD) method to uncover genetic variation in this highly conserved species was investigated. Sufficient levels of variation were detected to allow a population genetic analysis of the four migratory populations of Atlantic Coast striped bass. Lynch's analogue of Wright's FST (F'ST) suggests that Atlantic Coast striped bass are genetically subdivided (F'ST for pooled Atlantic samples = 0.44). Significant heterogeneity was detected in the frequencies of 32 per cent of surveyed RAPD markers. A modification of Slatkin's conditional average frequency method suggests that gene flow is present among the sampled Atlantic Coast striped bass. Results of the RAPD analysis suggest that gene flow is sufficient to prevent fixation of alternate genetic markers, but not sufficient to prevent the development of significant divergence in frequencies of these markers.

Animals↗
PubMed1996

Optimization and visualization of molecular diversity of combinatorial libraries.

One of the major goals of rational design of combinatorial libraries is to design libraries with maximum diversity to enhance the potential of finding active compounds in the initial rounds of high-throughput screening programs. We present strategies to visualize and optimize the structural diversity of sets of molecules, which can be either potential substituents to be attached at specific positions of the library scaffold, or entire molecules corresponding to enumerated libraries. The selection of highly diverse subsets of molecules from the library is based on the stochastic optimization of 'Diversity' functions using a single-point-mutation Monte Carlo technique. The Diversity functions are defined in terms of the distances among molecules in multidimensional property space resulting from the calculation of 2D and 3D molecular descriptors. Several Diversity functions, including an implementation of D-Optimal design, are applied to select diverse subsets and the results are compared. The diversity of the selected subsets of molecules is visualized by embedding the intermolecular distances, defined by the molecules in multidimensional property space, into a three-dimensional space.

Amino Acids↗
PubMed1995

Reproducible amplification of RAPD markers from vertebrate DNA.

Randomly amplified polymorphic DNA (RAPD) is a modification of PCR that uses short, randomly generated primers to amplify genomic DNA. Generally, many bands of mixed intensity (i.e., strong, faint, fuzzy or sharp) are generated with each primer. Mixed-intensity bands are inherent with the RAPD technique because (i) the target DNAs are undefined, (ii) one or more copies of the target DNA may exist per genome and (iii) the percentage of hybridization of primer to target may vary. The problem of mixed-intensity band exacerbates the well-known sensitivity of PCRs to reagent and template concentrations, pH and other reaction parameters. These complications have discouraged many investigators from using RAPD. Our goal was to optimize the RAPD amplification conditions for vertebrate DNA. We present the optimized protocol along with an experimental strategy for obtaining reproducible, interpretable RAPD banding patterns in vertebrates.

Animals↗