Biomedical subjects

C Damgaard

Publications and source records attributed to C Damgaard.

5 recordsLinked to original sources

PubMed2004

Evolutionary rate variation and RNA secondary structure prediction.

Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions. In addition we obtained an alignment of the 5' HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes within a fairly large range still produce reliable predictions and conclude that using rates from a limited set of RNA sequences is valid over a broader range of sequences.

Algorithms↗

PubMed2004

Sublethal soil copper concentrations increase mortality in the earthworm Aporrectodea caliginosa during drought.

Simultaneous effects of drought and a sublethal concentration of copper on the earthworm Aporrectodea caliginosa were investigated in the laboratory. Experiments were performed with exposure to 150 mg Cu kg(-1) dry soil and different levels of drought during a 3-wk period. Soil water potentials from pF 1.5 (wet) to pF 5 (very dry) were obtained. The soil water potential resulting in 50% mortality was significantly reduced from pF 4.48 in worms not exposed to copper to pF 4.09 in copper-exposed worms, thus demonstrating synergy-like effects of drought and copper. Development of estivation cells was significantly depressed in copper-exposed worms compared to worms not exposed to copper. For all drought levels (except the highest, where 100% mortality occurred), copper-exposed earthworms with no estivation cells had more than twice as high mortality and, at severe drought exposure, also lower water content than those which had developed the estivation cells. With increasing drought level, the whole-body burden of copper increased from about 40 microg Cu g(-1) dry weight to about 90 microg Cu g(-1). When the worms were exposed to drought, the osmolality in their body fluids increased. This was due to a greater concentration of already existing solutes resulting from extensive loss of water, and not to mobilization or synthesis of additional solutes.

Animals↗

PubMed2002

Male fitness of oilseed rape (Brassica napus), weedy B. rapa and their F(1) hybrids when pollinating B. rapa seeds.

The likelihood that two species hybridise and backcross may depend strongly on environmental conditions, and possibly on competitive interactions between parents and hybrids. We studied the paternity of seeds produced by weedy Brassica rapa growing in mixtures with oilseed rape (B. napus) and their F(1) hybrids at different frequencies and densities. Paternity was determined by the presence of a transgene, morphology, and AFLP markers. In addition, observations of flower and pollen production, and published data on pollen fertilisation success, zygote survival, and seed germination, allowed us to estimate an expected paternity. The frequency and density of B. napus, B. rapa, and F(1) plants had a strong influence on flower, pollen, and seed production, and on the paternity of B. rapa seeds. Hybridisation and backcrossing mostly occurred at low densities and at high frequencies of B. napus and F(1), respectively. F(1) and backcross offspring were produced mainly by a few B. rapa mother plants. The observed hybridisation and backcrossing frequencies were much lower than expected from our compilation of fitness components. Our results show that the male fitness of B. rapa, B. napus, and F(1) hybrids is strongly influenced by their local frequencies, and that male fitness of F(1)hybrids, when pollinating B. rapa seeds, is low even when their female fitness (seed set) is high.

Brassica napus↗

PubMed2000

Fixation of advantageous alleles in partially self-fertilizing populations. The effect of different selection modes.

The expected fixation probability of an advantageous allele was examined in a partially self-fertilizing hermaphroditic plant species using the diffusion approximation. The selective advantage of the advantageous allele was assumed to be increased viability, increased fecundity, or an increase in male fitness. The mode of selection, as well as the selfing rate, the population size, and the dominance of the advantageous allele, affect the fixation probability of the allele. In general it was found that increases in selfing rate decrease the fixation probability under male sexual selection, increase fixation probability under fecundity selection, and increase when recessive and decrease when dominant under viability selection. In some cases the highest fixation probability of advantageous alleles under fecundity or under male sexual selection occurred at an intermediary selfing rate. The expected mean fixation times of the advantageous allele were also examined using the diffusion approximation.

Alleles↗

PubMed1999

Coevolution of a plant host-pathogen gene-for-gene system in a metapopulation model without cost of resistance or cost of virulence

A metapopulation model of a one-locus gene-for-gene system in a plant host and a biotrophic pathogen is described. The model allows subpopulations to go extinct, and, due to characteristic differences in life-history strategies, the plant host is assumed to be recolonized from a seed bank, whereas the pathogen is recolonized by migration. It is shown that variation in the gene-for-gene system can be maintained at a noticeable level without assuming cost of resistance or cost of virulence, if the probability of extinction depends on the host mean fitness in the subpopulation. The level of variation in the pathogen population increases with increasing extinction rate, genetic drift and fitness of the infected host, but decreases with increasing migration rate. Generally, these effects are magnified for life cycles in which selection occur before genetic drift and after migration. The metapopulation model generates positive associations between the virulence allele and the resistance allele without assuming cost of resistance or cost of virulence. Copyright 1999 Academic Press.

Journal Article↗