Reconstructing evolution of sequences subject to recombination using parsimony

The parsimony principle states that a history of a set of sequences that minimizes the amount of evolution is a good approximation to the real evolutionary history of the sequences. This principle is applied to the reconstruction of the evolution of homologous sequences where recombinations or horizontal transfer can occur. First it is demonstrated that the appropriate structure to represent the evolution of sequences with recombinations is a family of trees each describing the evolution of a segment of the sequence. Two trees for neighboring segments will differ by exactly the transfer of a subtree within the whole tree. This leads to a metric between trees based on the smallest number of such operations needed to convert one tree into the other. An algorithm is presented that calculates this metric. This metric is used to formulate a dynamic programming algorithm that finds the most parsimonious history that fits a given set of sequences. The algorithm is potentially very practical, since many groups of sequences defy analysis by methods that ignore recombinations. These methods give ambiguous or contradictory results because the sequence history cannot be described by one phylogeny, but only a family of phylogenies that each describe the history of a segment of the sequences. The generalization of the algorithm to reconstruct gene conversions and the possibility for heuristic versions of the algorithm for larger data sets are discussed.     

Molecular Fate of Heterologous Bacterial DNA in Competent BACILLUS SUBTILIS. I. Processing of B. PUMILUS and B. LICHENIFORMIS DNA in B. SUBTILIS

Competent Bacillus subtilis cells were exposed to radioactive and density labeled donor DNA extracted from B. pumilus and B. licheniformis. The DNA from these strains hybridized with B. subtilis DNA in vitro at a rate of 24% and 11%, respectively. After entry the vast majority of heterologous DNA was found at the single-strand DNA position in CsCl gradients, and was gradually degraded during incubation. Much less donor DNA than expected from the hybridization values participated in the formation of the donorrecipient complex (DRC). By subjecting the heterologous DRC to sonication and alkaline CsCl gradient centrifugation, it was established that the DRC consisted of three components: (1) recipient DNA in which breakdown products of donor DNA were incorporated through DNA synthesis, (2) recipient DNA in which donor DNA was covalently integrated and (3) recipient DNA in which the donor moiety was not covalently integrated.     

Utilization of poly-β-hydroxybutyrate in free-living cultures of Rhizobium ORS571

Abstract The effect of carbon starvation on growth and poly-β-hydroxybutyrate (PHB) utilization in oxygen-limited chemostat cultures of Rhizobium ORS571 was studied. Under oxygen-limited growth conditions PHB was not degraded. When in a nitrogen-fixing oxygen-limited culture, after stopping the medium supply, the dissolved oxygen concentration was maintained at 10 μM, a slow breakdown of PHB was observed. Addition of ammonia and air to a nitrogen-fixing oxygen-limited culture after the medium supply had been stopped, resulted in the simultaneous utilization of PHB and succinate. The possible use of the energy derived from PHB degradation in Rhizobia bacteria and bacteroids is discussed.     

Online solid phase extraction with liquid chromatography–tandem mass spectrometry to analyze remoxipride in small plasma-, brain homogenate-, and brain microdialysate samples

Remoxipride is a selective dopamine D₂ receptor antagonist, and useful as a model compound in mechanism-based pharmacological investigations. To that end, studies in small animals with serial sampling over time are needed. For these small volume samples currently no suitable analytical methods are available. We propose analytical methods for the detection of low concentrations remoxipride in small sample volumes of plasma, brain homogenate, and brain microdialysate, using online solid phase extraction with liquid chromatography–tandem mass spectrometry. Method development, optimization and validation are described in terms of calibration curves, extraction yield, lower limit of quantification (LLOQ), precision, accuracy, inter-day- and intra-day variability. The 20 μl plasma samples showed an extraction yield of 76%, with a LLOQ of 0.5 ng/ml. For 0.6 ml brain homogenate samples the extraction yield was 45%, with a LLOQ of 1.8 ng/ml. The 20 μl brain microdialysate samples, without pre-treatment, had a LLOQ of 0.25 ng/ml. The precision and accuracy were well within the acceptable 15% range. Considering the small sample volumes, the high sensitivity and good reproducibility, the analytical methods are suitable for analyzing small sample volumes with low remoxipride concentrations.     

A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given

Among the fundamental problems in molecular evolution and in the analysis of homologous sequences are alignment, phylogeny reconstruction, and the reconstruction of ancestral sequences. This paper presents a fast, combined solution to these problems. The new algorithm gives an approximation to the minimal history in terms of a distance function on sequences. The distance function on sequences is a minimal weighted path length constructed from substitutions and insertions-deletions of segments of any length. Substitutions are weighted with an arbitrary metric on the set of nucleotides or amino acids, and indels are weighted with a gap penalty function of the form gk = a + (bxk), where k is the length of the indel and a and b are two positive numbers. A novel feature is the introduction of the concept of sequence graphs and a generalization of the traditional dynamic sequence comparison algorithm to the comparison of sequence graphs. Sequence graphs ease several computational problems. They are used to represent large sets of sequences that can then be compared simultaneously. Furthermore, they allow the handling of multiple, equally good, alignments, where previous methods were forced to make arbitrary choices. A program written in C implemented this method; it was tested first on 22 5S RNA sequences.      

Temperature dependence of predation depends on the relative performance of predators and prey

The temperature dependence of predation rates is a key issue for understanding and predicting the responses of ecosystems to climate change. Using a simple mechanistic model, we demonstrate that differences in the relative performances of predator and prey can cause strong threshold effects in the temperature dependence of attack rates. Empirical data on the attack rate of northern pike (Esox lucius) feeding on brown trout (Salmo trutta) confirm this result. Attack rates fell sharply below a threshold temperature of +11°C, which corresponded to a shift in relative performance of pike and brown trout with respect to maximum attack and escape swimming speeds. The average attack speed of pike was an order of magnitude lower than the escape speed of brown trout at 5°C, but approximately equal at temperatures above 11°C. Thresholds in the temperature dependence of ecological rates can create tipping points in the responses of ecosystems to increasing temperatures. Thus, identifying thresholds is crucial when predicting future effects of climate warming.     

Free amino acids in rat ocular tissues during postnatal development

Amino acid changes in the retina, vitreous, lens, iris-ciliary body and cornea of the rat eye were determined during postnatal growth. The amino acid concentrations of the ocular tissues showed varying profiles at various developmental stages. These results suggest a different timetable for development of each ocular tissue or indicate a synthesis of specific proteins in the postnatal period. Adult amino acid levels appeared to be fully reached on the 30th day after birth at the latest. Quantitatively the greatest changes were observed in taurine concentrations, which increased in all five ocular tissues during maturation. GABA changes paralleled those of taurine in the retina, whereas in the other ocular tissues GABA changes were very low. The greatest decrease in glutamic acid and aspartic acid concentration during postnatal development was in the lens, where these amino acids probably are needed for the synthesis of the lenticular proteins, the alpha-, beta-, and gamma-crystallines.