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PubMed2005

Statistical behavior of complex cancer karyotypes.

Epithelial tumors commonly show complex and variable karyotypes that obscure the identification of general patterns of the karyotypic evolution. To overcome some of these problems, we previously systematically analyzed the accumulated cytogenetic data from individual tumor types by using various statistical means. In the present study, we compare previous results obtained for nine tumor types and perform several meta-analyses of data obtained from a number of epithelial tumors, including head and neck, kidney, bladder, breast, colorectal, ovarian, and lung cancer, as well as from malignant melanoma and Wilms tumor, with the specific aim of discovering common patterns of karyotypic evolution. We show that these tumors frequently develop through a hypo- or a hyperdiploid pathway and progress by an increasing number of alternative imbalances through at least two karyotypic phases, Phases I and II, and possibly through a third, Phase III. During Phase I, the karyotypes exhibited a power law distribution of both the number of changes per tumor and the frequency distribution at which bands were involved in breaks. At the transition from Phase I to Phase II/III, the observed power law distributions were lost, indicating a transition from an ordered and highly structured process to a disordered and chaotic pattern. The change in karyotypic orderliness at the transition from Phase I to Phase II/III was also shown by a drastic difference in karyotypic entropy.

Biological Evolution↗
PubMed2003

Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective.

Secondary metabolites, at least the major ones present in a plant, apparently function as defence (against herbivores, microbes, viruses or competing plants) and signal compounds (to attract pollinating or seed dispersing animals). They are thus important for the plant's survival and reproductive fitness. Secondary metabolites therefore represent adaptive characters that have been subjected to natural selection during evolution. Molecular phylogenies of the Fabaceae, Solanaceae and Lamiaceae were reconstructed and employed as a framework to map and to interpret the distribution of some major defence compounds that are typical for the respective plant families; quinolizidine alkaloids and non-protein amino acids for legumes; tropane and steroidal alkaloids for Solanaceae, and iridoids and essential oils for labiates. The distribution of the respective compounds appears to be almost mutually exclusive in the families studied, implying a strong phylogenetic and ecological component. However, on a closer look, remarkable exceptions can be observed, in that certain metabolites are absent (or present) in a given taxon, although all the neighbouring and ancestral taxa express (or do not express, respectively) the particular trait. It is argued that these patterns might reflect differential expression of the corresponding genes that have evolved earlier in plant evolution. The inconsistent secondary metabolite profiles mean that the systematic value of chemical characters becomes a matter of interpretation in the same way as traditional morphological markers. Thus, the distribution of secondary metabolites has some value for taxonomy but their occurrence apparently reflects adaptations and particular life strategies embedded in a given phylogenetic framework.

Alkaloids↗
PubMed1999

Histological adaptation of orthotopic ileal neobladder mucosa: 4-year follow-up of 30 patients.

OBJECTIVE: For 4 years we have monitored the histological evolution of ileal neobladders in a single cohort of 30 patients in order to systematically describe the histological changes occurring after surgery. The aim of the study was to evaluate the long-term evolution of many histological parameters with functional relevance as to the metabolic outcome of the reservoirs. METHODS: Ileal samples were collected during surgery and by random biopsies during cystoscopy 6, 12, 18, 24, 36 and 48 months later. At each step qualitative and quantitative assessment of the histological and cytological conditions of the samples was carried out. RESULTS: Morphological changes develop relatively early but the situation tends to level out in about 1 year. The morphological changes are topographically uneven and, although mucosal flattening becomes progressively prevalent, areas with shortened villi persist indefinitely. Goblet cells prevail over enterocytes and the secretive pattern shifts towards sialomucins. The overall replication rate decreases initially but tends to restore in 1 year. Dysplasia or atrophy were never recorded. CONCLUSIONS: The 4-year systematic follow-up revealed a typical histological adaptation pattern in the ileal neobladder without signs of dysplasia. The changes seem to be induced by the aggressive environment and develop in the time lag required for functional adaptation of the epithelium.

Adult↗
PubMed2006

Structure and evolution of the mitochondrial control region and flanking sequences in the European cave salamander Proteus anguinus.

The European cave salamander Proteus anguinus Laurenti 1768 is one of the best-known subterranean animals, yet its evolutionary history and systematic relationships remain enigmatic. This is the first comprehensive study on molecular evolution within the taxon, using an mtDNA segment containing the control region (CR) and adjacent sequences. Two to seven tandem repeats of 24-32 bp were found in the intergenic spacer region (VNTR1), and three, four or six repeats, 59-77 bp each, in the 3' end of the CR (VNTR2). Different molecular mechanisms account for VNTR2 formation in different lineages of Proteus. The overall CR variation was lower than that of the spacer region, the 3' end of the cytb gene, or the tRNA genes. Individual genes and the concatenated non-repetitive sequences produced similar, well resolved maximum likelihood, Bayesian inference and parsimony trees. The numbers of repeat elements as well as the genealogy of the VNTR2 repeat units were mostly inconsistent with the groupings of the non-repetitive sequences. Different degrees of repeat array homogenization were detected in all major groups. Orthology was established for the first and the second VNTR2 elements of some populations. These two copies may therefore be used for analyses at the population level. The pattern of CR sequence variation points to strong genetic isolation of hydrographically separated populations. Genetic separation of the major groups of populations is incongruent with the current division into subspecies.

Animals↗
PubMed1977

[Psychology of relationships as a theoretical concept in medical psychology and psychotherapy].

The theoretical concept called "psychology of relations" (A. F. Lazursky, V. N. Myasishchev) is offered as the basis for a study of a patient's personality and psychotherapy. The author stresses ideological relationship of psychology of relations with phylosophy of dialectical materialism and I. P. Pavlov's studies about conditioned reflexes, its relationship with clinical psychoneurology, its direction to a study of the personality and adherence to primacy of consciousness over unconciousness. The perspectiveness of the evolutionally ontogenetic approach to the analysis of the system of relations and necessity to elaborate working systematizations determined by the research purpose, is stated.

Biological Evolution↗
PubMed2006

Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates.

BACKGROUND: Evolution of the deuterostome lineage was accompanied by an increase in systematic complexity especially with regard to highly specialized tissues and organs. Based on the observation of an increased number of paralogous genes in vertebrates compared with invertebrates, two entire genome duplications (2R) were proposed during the early evolution of vertebrates. Most glycolytic enzymes occur as several copies in vertebrate genomes, which are specifically expressed in certain tissues. Therefore, the glycolytic pathway is particularly suitable for testing theories of the involvement of gene/genome duplications in enzyme evolution. RESULTS: We assembled datasets from genomic databases of at least nine vertebrate species and at least three outgroups (one deuterostome and two protostomes), and used maximum likelihood and Bayesian methods to construct phylogenies of the 10 enzymes of the glycolytic pathway. Through this approach, we intended to gain insights into the vertebrate specific evolution of enzymes of the glycolytic pathway. Many of the obtained gene trees generally reflect the history of two rounds of duplication during vertebrate evolution, and were in agreement with the hypothesis of an additional duplication event within the lineage of teleost fish. The retention of paralogs differed greatly between genes, and no direct link to the multimeric structure of the active enzyme was found. CONCLUSION: The glycolytic pathway has subsequently evolved by gene duplication and divergence of each constituent enzyme with taxon-specific individual gene losses or lineage-specific duplications. The tissue-specific expression might have led to an increased retention for some genes since paralogs can subdivide the ancestral expression domain or find new functions, which are not necessarily related to the original function.

Animals↗
PubMed2001

Evolutionary history and speciation modes in the cyprinid genus Barbus.

Phylogenetic relationships and evolutionary patterns in the genus Barbus were examined through the analysis of the complete sequences of three mitochondrial genes: ATPases 8 and 6, which overlap slightly, and cytochrome b. This complex genus includes diploid as well as tetraploid and hexaploid species that are distributed throughout the Palaearctic, Ethiopian and Asiatic biogeographical regions. Given that genome duplication is an important evolutionary mechanism in eukaryotes, in the present report we attempt to describe its role in the evolution of the genus Barbus, as well as drawing systematic and phylogenetic conclusions. The phylogenetic results indicated the splitting of the current Barbus genus into five main mitochondrial lineages corresponding to (i) the genus Barbus sensu stricto (tetraploid, which is subdivided into the subgenera Barbus and Luciobarbus), (ii) the hexaploid species, (iii) the Ethiopian tetraploid species, (iv) the African diploid species, and (v) the Asian diploid species. The branching of 'foreign' genera as sister groups of some of these monophyletic assemblages (such as Aulopyge is to Barbus sensu stricto or Varicorhinus is to the hexaploid barbels) demonstrates the polyphyly of the group. Moreover, the relationships between the proposed lineages also show that genome duplication may be considered as a homoplasic character since it must have occurred over at least three independent periods and/or in three independent areas. In relation to the possible saltational evolutionary model for the polyploid species examined here, it was found that, although feasible at the nuclear level, the mitochondrial markers looked at do not appear to have undergone this type of evolution. Rather, they seem to have experienced more or less constant change through time.

Adenosine Triphosphatases↗
PubMed2006

Variation in evolutionary processes at different codon positions.

Evolutionary studies commonly model single nucleotide substitutions and assume that they occur as independent draws from a unique probability distribution across the sequence studied. This assumption is violated for protein-coding sequences, and we consider modeling approaches where codon positions (CPs) are treated as separate categories of sites because within each category the assumption is more reasonable. Such "codon-position" models have been shown to explain the evolution of codon data better than homogenous models in previous studies. This paper examines the ways in which codon-position models outperform homogeneous models and characterizes the differences in estimates of model parameters across CPs. Using the PANDIT database of multiple species DNA sequence alignments, we quantify the differences in the evolutionary processes at the 3 CPs in a systematic and comprehensive manner, characterizing previously undescribed features of protein evolution. We relate our findings to the functional constraints imposed by the genetic code, protein function, and the types of mutation that cause synonymous and nonsynonymous codon changes. The results increase our understanding of selective constraints and could be incorporated into phylogenetic analyses or gene-finding techniques in the future. The methods used are extended to an overlapping reading frame data set, and we discover that overlapping reading frames do not necessarily cause more stringent evolutionary constraints.

Base Sequence↗
PubMed1999

Brain metabolic impairment in non-cerebral and cerebral forms of X-linked adrenoleukodystrophy by proton MRS: identification of metabolic patterns by discriminant analysis.

Cerebral metabolism in six children with X-linked adrenoleukodystrophy (X-ALD) was studied using 1H magnetic resonance spectroscopy (MRS), and the status of the patients was monitored for evaluating disease progression. Spectra were abnormal even in patients with no cerebral impairment. Four different metabolic patterns were identified, and a metabolic classification of the disease was proposed, from grade 0 to grade III. The evolution of the disease toward grade II appears to be systematic, but many patients did not evolve from this grade to grade III, which is the metabolic mark of severe progressive forms. Metabolic data of X-ALD were processed using discriminant analysis, which provides a classification accuracy of 95.2%. Proton cerebral MRS together with discriminant analysis may be useful during the follow-up in X-ALD for monitoring the evolution of the disease and the effects of therapy.

Adolescent↗
PubMed2026

Unraveling evolutionary relationships in the Sida generic alliance (Malvaceae, Malvoideae): a phylogenetic and cytotaxonomic overview.

Sida (Malvaceae), the largest Malveae-Abutilinae member, has poorly defined morphological limits which overlaps with 11 phylogenetically closely related genera that comprises the "Sida generic alliance". The 12 genera are distributed in the tropics especially in Brazil where one third of its species diversity is found. Evolutionary relationships within Sida generic alliance remain unresolved due to morphological convergence, limited taxon sampling, and lack of integrative approaches including cytogenetic data. We reconstructed the phylogeny of Sida and allied genera using a multilocus dataset (nuclear ITS and seven plastid loci) including 193 species classified in 19 genera and analyzed chromosome evolution using cytogenetic data (chromosome number) for 79 species of the 19 genera. The phylogeny recovered seven clades-Abutilon, Bakeridesia, Callianthe, Gaya, and three Sida clades (I-III)-and confirmed the polyphyly of Sida, the largest genera. We detected reticulate evolution, with incongruence between nuclear and plastid topologies. Chromosome number ranged from 2n = 12 to 60 and represented synapomorphies for most clades. Ancestral character reconstruction indicated that ascending dysploidy and polyploidy predominated in karyotype evolution of Sida and allied genera. Our results reveal taxonomic incongruence in current classifications probably related to reticulate evolution. A generic-level taxonomic revision is necessary and should rely on integrated phylogenetic and karyotypic evidence. This study provides a framework for phylogenetic systematics and emphasizes the role of Brazil as a hotspot for plant genomic research.

Phylogeny↗
PubMed2004

Molecular phylogeny and character evolution in the Western Palaearctic Helicidae s.l. (Gastropoda: Stylommatophora).

In this study, we present a molecular phylogeny for the west Palaearctic Helicidae sensu lato based on sequence data from two mitochondrial (COI, 16S rDNA) and two nuclear (ITS-1, 18S rDNA) genes. Maximum likelihood analysis and Bayesian inference revealed well supported monophyletic clades partly conflicting traditional classifications. Based on these results, we propose the following system. The Western Palaearctic Helicidae s.l. consist of two families, Helicidae and Hygromiidae. Within the Helicidae, three well supported subfamilies can be recognised: the Helicinae, Ariantinae, and Helicodontinae. The Hygromiidae consist of three clades: the Hygromiinae, the Helicellinae, and a yet unnamed clade comprising the genera Sphincterochila and Cochlicella. We then used the phylogeny to study the evolution of anatomical, and ecological characters traditionally used for systematic classification. In the Helicidae s.l., two independent evolutionary transitions to life in xeric environments occurred, which allowed the occupation of new niches with a subsequent radiation of the Helicellinae-Cochlicella/Sphincterochila clade and the Helicinae. Whereas, the multiplication of the Glandulae mucosae is a synapomorphy of the Hygromiidae, the lovedart sac apparatus is present in all groups and thus, the trait cannot provide a synapomorphy for either families or subfamilies. Additionally, we evaluated the use of structural molecular genetic characters for taxonomic assessment. The presence of an unique loop region of the 16S rDNA gene and a short tandem repeat in the ITS-1 region provide independent evidence for the monophyly of these major two groups, and can be used for preliminary classification.

Animals↗
PubMed1996

Structure optimization of an artificial neural filter detecting membrane-spanning amino acid sequences.

An artificial neural network has been developed for the recognition and prediction of transmembrane regions in the amino acid sequences of human integral membrane proteins. It provides an additional prediction method besides the common hydrophobicity analysis by statistical means. Membrane/nonmembrane transition regions are predicted with 92% accuracy in both training and independent test data. The method used for the development of the neural filter is the algorithm of structure evolution. It subjects both the architecture and parameters of the system to a systematical optimization process and carries out local search in the respective structure and parameter spaces. The training technique of incomplete induction as part of the structure evolution provides for a comparatively general solution of the problem that is described by input-output relations only. Seven physiochemical side-chain properties were used to encode the amino acid sequences. It was found that geometric parameters like side-chain volume, bulkiness, or surface area are of minor importance. The properties polarity, refractivity, and hydrophobicity, however, turned out to support feature extraction. It is concluded that membrane transition regions in proteins are encoded in sequences as a characteristic feature based on the respective side-chain properties. The method of structure evolution is described in detail for this particular application and suggestions for further development of amino acid sequence filters are made.

Algorithms↗
PubMed2002

A ceratopsian dinosaur from China and the early evolution of Ceratopsia.

Ceratopsians (horned dinosaurs) represent one of the last and the most diverse radiations of non-avian dinosaurs. Although recent systematic work unanimously supports a basal division of Ceratopsia into parrot-like psittacosaurids and frilled neoceratopsians, the early evolution of the group remains poorly understood, mainly owing to its incomplete early fossil record. Here we describe a primitive ceratopsian from China. Cladistic analysis posits this new species as the most basal neoceratopsian. This new taxon demonstrates that some neoceratopsian characters evolved in a more incremental fashion than previously known and also implies mosaic evolution of characters early in ceratopsian history.

Animals↗
PubMed2006

Cross-species analysis of biological networks by Bayesian alignment.

Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by alignment, which maps bona fide functional relationships between genes in different organisms. Network alignment is based on a scoring function measuring mutual similarities between networks, taking into account their interaction patterns as well as sequence similarities between their nodes. High-scoring alignments and optimal alignment parameters are inferred by a systematic Bayesian analysis. We apply this method to analyze the evolution of coexpression networks between humans and mice. We find evidence for significant conservation of gene expression clusters and give network-based predictions of gene function. We discuss examples where cross-species functional relationships between genes do not concur with sequence similarity.

Algorithms↗
PubMed1998

[Reconstruction of possible paths of the origin and morphological evolution of bacteriophages].

The problem of the origin and evolution of viruses and, in particular, the origin and evolution of bacteriophages is of considerable interest. However, so far, this problem has not been solved with quantitative methods of molecular systematics. In the present study, an attempt to reconstruct the possible paths of appearance and evolution of bacteriophages based on their structural features and morphogenesis, as well as general characteristics of their life cycles and genome organization, was carried out. A scheme describing phylogeny of the main bacteriophage groups and evolution of their life cycles is suggested. Existence of two independently evaluating types of morphogenesis ("budding outward" and "budding inward") is postulated.

Bacteriophages↗