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PubMed1990

Distribution of the number of matches between nucleotide sequences.

When two strings of symbols are aligned it is important to know whether the observed number of matches is better than that expected between two independent sequences with the same frequency of symbols. When strings are of different lengths, nulls need to be inserted in order to align the sequences. One approach is to use simple approximations of sampling for replacement. We describe an algorithm for exactly determining the frequencies of given numbers of matches, sampling without replacement. This does not lead to a simple closed form expression. However, we show examples where sampling with, or without, replacement give very similar results and the simple approach may be adequate for all but the smallest cases.

Base Sequence↗
PubMed1983

Some insights into the possible development of a biosynthetic pathway and biological function for anthramycin in Streptomyces refuineus.

Using anthramycin, a potent antitumor antibiotic produced by Streptomyces refuineus, as an example, we have developed a rational model for the evolution of the capability of this microorganism to produce, tolerate and retain the genetic information needed to make this extremely potent secondary metabolite. The concepts and ideas outlined in this article have also been applied in a more general way to other antibiotics with the hope that this might stimulate research designed to test some of these concepts.

Anthramycin↗
PubMed2005

Recombination during in vitro evolution.

Recombination, the swapping of large portions of genetic information between and among parental genotypes, can be applied to in vitro evolution experiments on functional nucleic acids. Both homologous and heterologous recombination can be achieved using standard laboratory techniques. In many cases, recombination can allow for the discovery of a ribozyme or DNAzyme phenotype that would not likely be encountered by reliance on point mutations alone. In addition, recombination can often aid in the discovery of global optima in sequence space and/or lessen the number of generations it would take to reach optima. Recombination is most efficiently used in combination with point mutations and applied after the first couple of rounds of selection but before high-fitness genotypes dominate the selection. The "recombination zone" describes that region of sequence space-defined by the residues that will ultimately participate in the function of the winning nucleic acid(s)-where recombination is expected to be the most beneficial in the search for high-fitness genotypes.

Cell Nucleus↗
PubMed1998

Influence of the shape of phospholipid vesicles on the measurement of their size by photon correlation spectroscopy.

The influence of shape transformation of large unilamellar vesicles (LUV) on their size measurement by photon correlation spectroscopy (PCS) has been investigated. The experimental size of vesicles after hyperosmotic contractions of increasing intensities have been compared to the theoretical volume decrease determined by applying Boyle Van't Hoff's law. The main observation is that PCS size measurement gives overestimated values when LUV have been subjected to a volume decrease of more than 20% of their initial volume. The PCS size overestimation is related to the influence of the shape transformation of the vesicles on their diffusion coefficient (D) as shown by modelling the evolution of D of a sphere which is transformed into an ellipsoid by internal volume reduction under constant area.

Absorptiometry, Photon↗
PubMed2002

Extensive Mhc-DQB variation in humans and non-human primate species.

Non-human primates are often used in biomedical research, and the application of these animals as a model in immune-related diseases necessitates the characterisation of their MHC system. In particular, the MHC class II regions of the chimpanzee (Pan troglodytes), the rhesus macaque (Macaca mulatta)and the common marmoset (Callithrix jacchus) have been subject of molecular biological studies in recent years. In this study the emphasis was on MHC class II genes of another macaque species, Macaca fascicularis(crab eating macaque or cynomolgous monkey). The exon 2 of the Mhc-DQB gene (Mafa-DQB) was sequenced in each of a random panel of 60 non-pedigreed cynomolgous monkeys. This resulted in the detection of 23 Mafa-DQB1alleles that had not previously been published. In addition, unreported alleles were found in chimpanzees, rhesus macaques, orang-utans (Pongo pygmaeus) and stump-tailed macaques (Macaca arctoides), of which a few individuals were included in this study. Phylogenetic analyses confirm the trans-species model of evolution of the MHC-DQBlineages, in which a group of major alleles is passed on in the phylogeny, and has led to the sharing of allelic lineages by different species of non-human primates. The sharing of alleles is observed only for closely related macaque species. Furthermore, this manuscript provides an overview of all published, and whenever necessary corrected, non-human primate Mhc-DQB exon 2 alleles.

Alleles↗
PubMed2003

Analytical solution of the evolution dynamics on a multiplicative-fitness landscape.

In an infinite population the frequency distribution of individuals carrying a given number of mutations obeys a set of recursion equations, the equilibrium solution of which describes the mutation-selection balance. Although this solution is well-known in the case of a multiplicative-fitness landscape, where it is assumed that all mutations are deleterious and that each new mutation reduces the fitness of the individual by the same fraction, we are not aware of the existence of an analytical solution for the full dynamics. Using the generating function approach, we present here an explicit analytical solution for the frequency distribution recursion equations valid for all generations and initial conditions.

Alleles↗
PubMed2006

Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates.

The numbers of functional olfactory receptor (OR) genes in humans and mice are about 400 and 1,000 respectively. In both humans and mice, these genes exist as genomic clusters and are scattered over almost all chromosomes. The difference in the number of genes between the two species is apparently caused by massive inactivation of OR genes in the human lineage and a substantial increase of OR genes in the mouse lineage after the human-mouse divergence. Compared with mammals, fishes have a much smaller number of OR genes. However, the OR gene family in fishes is much more divergent than that in mammals. Fishes have many different groups of genes that are absent in mammals, suggesting that the mammalian OR gene family is characterized by the loss of many group genes that existed in the ancestor of vertebrates and the subsequent expansion of specific groups of genes. Therefore, this gene family apparently changed dynamically depending on the evolutionary lineage and evolved under the birth-and-death model of evolution. Study of the evolutionary changes of two gene families for vomeronasal receptors and two gene families for taste receptors, which are structurally similar, but remotely related to OR genes, showed that some of the gene families evolved in the same fashion as the OR gene family. It appears that the number and types of genes in chemosensory receptor gene families have evolved in response to environmental needs, but they are also affected by fortuitous factors.

Animals↗
PubMed2005

Gamma carbonic anhydrase like complex interact with plant mitochondrial complex I.

We report the identification by two hybrid screens of two novel similar proteins, called Arabidopsis thaliana gamma carbonic anhydrase like1 and 2 (AtgammaCAL1 and AtgammaCAL2), that interact specifically with putative Arabidopsis thaliana gamma Carbonic Anhydrase (AtgammaCA) proteins in plant mitochondria. The interaction region that was located in the N-terminal 150 amino acids of mature AtgammaCA and AtgammaCA like proteins represents a new interaction domain. In vitro experiments indicate that these proteins are imported into mitochondria and are associated with mitochondrial complex I as AtgammaCAs. All plant species analyzed contain both AtgammaCA and AtgammaCAL sequences indicating that these genes were conserved throughout plant evolution. Structural modeling of AtgammaCAL sequences show a deviation of functionally important active site residues with respect to gammaCAs but could form active interfaces in the interaction with AtgammaCAs. We postulate a CA complex tightly associated to plant mitochondrial complex.

Arabidopsis↗
PubMed1994

The evolutionary expansion of the Spirurida.

The possible origins of the 12 superfamilies of the Spirurida are considered, based on comparative morphology, host and geographic distributions. The available evidence suggests a complex origin of these nematodes, some families being derived from the Seuratoidea, and others from the Cosmocercoidea (Ascaridida). The spirurid radiation is an old one and seems to have occurred primarily in the Secondary or early Tertiary eras. Since then, expansion has occurred with host capture as a prominent mechanism. The Dracunculoidea Procamallanidae and Camallanidae are probably derived from the Chitwoodchabaudiidae and the Rictularioidea from the Schneidernematidae. The Seuratidae may have given rise to the Gnathostomatoidea, the Physalopteroidea, the Thelazioidea, the Habronematoidea, the Spiruroidea and the Acuarioidea. The filarioid nematodes appear to have several origins with the Diplotriaenoidea derived from the Spiruroidea, while constituents of the Aproctoidea derived from the Cystidicolinae, the Seuratoidea and the Spiruroidea. The Filarioidea are thought to have arisen from the Spiruroidea and the Thelazioidea. The evolution of tissue parasitism as a secondary phenomenon is considered in various groups.

Adaptation, Biological↗