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PubMed1990

[Genetic and evolutionary analysis of cases of Darier's disease].

In the past 10 years the authors have observed 27 people (13 men and 14 women) suffering from Darier's disease in Somogy county. Out of these 22 cases were familiar and 5 isolated. The praevalence of dysceratosis follicularis vegetans was found 1 to 16,000 in the area. In the 3 familiar cases the dysceratotic papules of Darier's disease followed the naevus-lines, drawing out the Arnosan-triangle in the meantime. In the case of one of the nonfamiliar occurrences the Darier's diseased papules running stripelike also wrote out the naevus-lines, strictly localized to one side of the body. The stripes composed by the dysceratotic papules ran bipolarly in these cases too; heading from a point of the lumbosacral part of the median line of the back towards the navel. According to the authors the direction of the development of the epidermal elements of the skin is expressed in the early phase of embryonic life by the dysceratotic papules running bipolarly and following naevus-lines as embryological rudiments.

Adult↗
PubMed1999

Comparative analysis of evolutionary mechanisms of the hemagglutinin and three internal protein genes of influenza B virus: multiple cocirculating lineages and frequent reassortment of the NP, M, and NS genes.

Phylogenetic profiles of the genes coding for the hemagglutinin (HA) protein, nucleoprotein (NP), matrix (M) protein, and nonstructural (NS) proteins of influenza B viruses isolated from 1940 to 1998 were analyzed in a parallel manner in order to understand the evolutionary mechanisms of these viruses. Unlike human influenza A (H3N2) viruses, the evolutionary pathways of all four genes of recent influenza B viruses revealed similar patterns of genetic divergence into two major lineages. Although evolutionary rates of the HA, NP, M, and NS genes of influenza B viruses were estimated to be generally lower than those of human influenza A viruses, genes of influenza B viruses demonstrated complex phylogenetic patterns, indicating alternative mechanisms for generation of virus variability. Topologies of the evolutionary trees of each gene were determined to be quite distinct from one another, showing that these genes were evolving in an independent manner. Furthermore, variable topologies were apparently the result of frequent genetic exchange among cocirculating epidemic viruses. Evolutionary analysis done in the present study provided further evidence for cocirculation of multiple lineages as well as sequestering and reemergence of phylogenetic lineages of the internal genes. In addition, comparison of deduced amino acid sequences revealed a novel amino acid deletion in the HA1 domain of the HA protein of recent isolates from 1998 belonging to the B/Yamagata/16/88-like lineage. It thus became apparent that, despite lower evolutionary rates, influenza B viruses were able to generate genetic diversity among circulating viruses through a combination of evolutionary mechanisms involving cocirculating lineages and genetic reassortment by which new variants with distinct gene constellations emerged.

Base Sequence↗
PubMed2007

Genetic intra-tumour heterogeneity in epithelial ovarian cancer and its implications for molecular diagnosis of tumours.

Genetic analysis of solid tumours using DNA or cDNA expression microarrays may enable individualized treatment based on the profiles of genetic changes that are identified from each patient. This could result in better response to adjuvant chemotherapy and, consequently, improved clinical outcome. So far, most research studies that have tested the efficacy of such an approach have sampled only single areas of neoplastic tissue from tumours; this assumes that the genetic profile within solid tumours is homogeneous throughout. The aim of this study was to evaluate the extent of genetic intra-tumour heterogeneity (ITH) within a series of epithelial ovarian cancers. Several different regions (five to eight regions) of tumour tissue from 16 grade 3, serous epithelial ovarian cancers were analysed for genetic alterations using a combination of microsatellite analysis and single nucleotide polymorphism (SNP) analysis, in order to establish the extent of ITH. Maximum parsimony tree analysis was applied to the genetic data from each tumour to evaluate the clonal relationship between different regions within tumours. Extensive ITH was identified within all ovarian cancers using both microsatellite and SNP analysis. Evolutionary analysis of microsatellite data suggested that the origin of all tumours was monoclonal, but that subsequent clonal divergence created mixed populations of genetically distinct cells within the tumour. SNP analysis suggested that ITH was not restricted to random genetic changes, but affected genes that have an important functional role in ovarian cancer development. The frequent occurrence of ITH within epithelial ovarian cancers may have implications for the interpretation of genetic data generated from emerging technologies such as DNA and mRNA expression microarrays, and their use in the clinical management of patients with ovarian cancer. The basis of genetic ITH and the possible implications for molecular approaches to clinical diagnosis of ovarian cancers may apply to other tumour types.

Adenocarcinoma, Papillary↗
PubMed2002

The concept of self-management of type 1 diabetes in children and adolescents: an evolutionary concept analysis.

AIM: An evolutionary concept analysis was undertaken to clarify the concept of self-management of type 1 diabetes in children and adolescents. BACKGROUND: Several problems exist in the literature on self-management of type 1 diabetes in children and adolescents. There is no uniform terminology and there is no uniform definition of the concept. Also, there is no differentiation in the literature between self-management of diabetes in children and adults. METHODS: Ninety-nine references were reviewed and analysed in the disciplines of nursing, medicine, and psychology. After separate analyses revealed no significant differences across disciplines, the analyses were combined to describe the attributes, antecedents, consequences, and surrogate and related concepts. RESULTS: The three essential attributes of the concept were identified as process, activities, and goals. Self-management of type 1 diabetes in children and adolescents is an active and proactive process; it is daily, lifelong, and flexible, and it involves shifting and shared responsibility for diabetes care tasks and decision-making between child and parent. It is a process that involves collaboration with health care providers. Self-management of type 1 diabetes in children and adolescents also consists of varied and many activities related to giving insulin, monitoring metabolic control, regulating diet and exercise, to name just a few. The concept also involves goals, which may differ from one parent/child dyad to another. A working definition of the concept is suggested. CONCLUSIONS: It is hoped that a more uniform definition of the concept will enable researchers to continue investigating antecedents and consequences of the concept in a way that allows for aggregating results.

Adolescent↗
PubMed2002

Understanding domestic violence against women: using evolutionary psychology to extend the feminist functional analysis.

Evolutionary psychologists such as Wilson and Daly (1993b) hypothesize that one goal of male-perpetrated domestic violence is control over female sexuality, including the deterrence of infidelity. According to this hypothesis, domestic violence varies with women's reproductive value or expected future reproduction, declining steeply as women age. We tested this hypothesis with a sample of 3,969 cases of male-perpetrated partner-abuse reported to a single police precinct in a large urban area over a 14-year period. Results show that (a) rates of domestic violence decrease as women age, (b) younger men are at greatest risk for perpetrating domestic violence, (c) younger, reproductive age women incur nearly 10 times the risk of domestic violence as do older, post-reproductive age women, and (d) the greater risk of domestic violence incurred by reproductive age women is not attributable solely to mateship to younger, more violent men. Discussion addresses theoretical implications of these findings and suggests a refinement of the feminist hypothesis of domestic violence against women.

Adolescent↗
PubMed1998

Association analysis in an evolutionary context: cladistic analysis of the DRD2 locus to test for association with alcoholism.

Previous studies testing the dopamine D2 receptor (DRD2) locus for association with alcoholism have produced conflicting results. Failure to screen controls for substance abuse and failure to assess alcoholics for severity have been proposed as causes for the inability of some studies to detect an association. We have reevaluated the involvement of DRD2 mutations in susceptibility to alcoholism with a cladistics-based association analysis after restricting an alcoholic sample to more severe cases. For the present study we tested 55 alcoholic probands and 80 normal controls for differences in the frequency of six haplotypes at the DRD2 locus. The haplotypes were derived from five di-allelic polymorphisms spanning all but the first exon of the DRD2 gene. A cladogram constructed from the haplotypes provided the evolutionary context for a nested statistical analysis. We found no significant evidence for association of the DRD2 haplotypes analyzed with the more severe alcoholic phenotype.

Alcoholism↗
PubMed2005

Evolutionary sequence analysis of complete eukaryote genomes.

BACKGROUND: Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence times of species. Although current methods that identify clusters of orthologous genes in complete genomes have helped to investigate gene function and gene content, they have not been optimized for evolutionary sequence analyses requiring strict orthology and complete gene matrices. Here we adopt a relatively simple and fast genome comparison approach designed to assemble orthologs for evolutionary analysis. Our approach identifies single-copy genes representing only species divergences (panorthologs) in order to minimize potential errors caused by gene duplication. We apply this approach to complete sets of proteins from published eukaryote genomes specifically for phylogeny and time estimation. RESULTS: Despite the conservative criterion used, 753 panorthologs (proteins) were identified for evolutionary analysis with four genomes, resulting in a single alignment of 287,000 amino acids. With this data set, we estimate that the divergence between deuterostomes and arthropods took place in the Precambrian, approximately 400 million years before the first appearance of animals in the fossil record. Additional analyses were performed with seven, 12, and 15 eukaryote genomes resulting in similar divergence time estimates and phylogenies. CONCLUSION: Our results with available eukaryote genomes agree with previous results using conventional methods of sequence data assembly from genomes. They show that large sequence data sets can be generated relatively quickly and efficiently for evolutionary analyses of complete genomes.

Animals↗
PubMed1995

At least four MHC class I genes are transcribed in the horse: phylogenetic analysis suggests an unusual evolutionary history for the MHC in this species.

Nineteen horse MHC class I specificities have been serologically identified previously at a single locus (ELA-A), and two other specificities appear to be coded at other loci. Biochemical studies indicate that there are at least two expressed loci. In order to establish the number of transcribed horse MHC class I genes, we made a cDNA library from a heterozygous animal (ELA-A3/A7), and screened for positive clones using a bovine class I probe. More than 200 class I clones were isolated in this way, and so far seven unique full length sequences have been identified. All of the sequences are predicted to code for surface expressed, functional molecules. The number of different sequences identified demonstrate that at least four genes are transcribed, although variations in transmembrane length (which is generally conserved in class I loci) suggest that five genes could be represented. Evolutionary analysis of these sequences (and two additional sequences known to represent different horse class I loci) reveals no firm relationships, such that the division between the different loci cannot be discerned. These results suggest an unusual evolutionary history for the horse MHC, the precise nature of which may be revealed only following further cross-species comparisons.

Amino Acid Sequence↗
PubMed1989

Structure of the goat psi beta y beta-globin pseudogene. Analysis of goat pseudogene evolutionary patterns.

The 12-member beta-globin gene locus of the goat contains three beta(adult)-type pseudogenes, one in each of three four-gene subsets of the locus. We have determined the complete nucleotide sequence of psi beta y, the pseudogene present in the most downstream four-gene subset, which also contains the functional fetal gene, beta F. psi beta y contains, throughout its length, numerous incapacitating mutations in common with the previously sequenced goat psi beta x and psi beta z pseudogenes consistent with the model that all were descended from a common pseudogene ancestor which became defective prior to the expansion of the beta-globin locus in the goat lineage. Evolutionary analysis of the psi beta y sequence in comparison to psi beta x and psi beta z provides evidence that nucleotide substitutions were fixed in a random manner within these pseudogenes with respect to polarity, coding versus non-coding regions, and replacement sites versus silent sites. However, substitutions appear to have accumulated asymmetrically between different pseudogenes in a manner that provides evidence for partial gene conversion. Moreover, the presence of deletions in goat psi beta y, which are also observed in the cow pseudogene psi 2, but not in the cow psi 1 pseudogene, indicate that goat psi beta y and cow psi 2 are orthologous but cow psi 1 actually arose prior to the goat/cow divergence. The authentic goat orthologue to cow psi 1 temporarily existed in the goat lineage but was deleted, probably prior to the divergence of goats and sheep.

Amino Acid Sequence↗
PubMed2004

The model of cultural competence through an evolutionary concept analysis.

Becoming a culturally competent health professional is a demanding prerequisite in this multicultural society. Cultural competence is explored and abstracted as a conceptual framework through a concept analysis using the evolutionary method. Its model is constructed from a systemic, comprehensive literature review and analysis. Taking into account how cultural competence is viewed by other disciplines (medicine, psychology, education, and social work), a comprehensive definition, antecedents, and consequences of cultural competence in nursing are described and diagrammed. Additionally, two model cases and future implications are discussed. The broader American society is composed of a mosaic of discrete cultural groups existing within the context of their values and identities. Those distinct cultures affect each patient's ways of thinking and his or her perceptions on health care and health behaviors. The proposed model of cultural competence provides a theoretical guide for developing strategies to achieve culturally competent care in nursing practice and research.

Humans↗
PubMed2001

MEGA2: molecular evolutionary genetics analysis software.

UNLABELLED: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. AVAILABILITY: http://www.megasoftware.net. CONTACT: s.kumar@asu.edu

DNA↗
PubMed2003

Multichannel carotenoid deactivation in photosynthetic light harvesting as identified by an evolutionary target analysis.

A new channel of excitation energy deactivation in bacterial light harvesting was recently discovered, which leads to carotenoid triplet population on an ultrafast timescale. Here we show that this mechanism is also active in LH2 of Rhodopseudomonas acidophila through analysis of transient absorption data with an evolutionary target analysis. The algorithm offers flexible testing of kinetic network models with low a priori knowledge requirements. It applies universally to the simultaneous fitting of target state spectra and rate constants to time-wavelength-resolved data. Our best-fit model reproduces correctly the well-known cooling and decay behavior in the S(1) band, but necessitates an additional, clearly distinct singlet state that does not exchange with S(1), promotes ultrafast triplet population and participates in photosynthetic energy transfer.

Algorithms↗
PubMed2001

Structural Analysis of a Gene Cluster Encoding Two Cationic and Three Anionic Peroxidases from Rice Chromosome 4.

Sequence analysis of a rice BAC q3037(H0207F01) identified a cluster of five tandemly arranged peroxidase genes, osp1,osp2,osp3,osp4 and osp5, within a 22.5 kb region. osp4,osp5 each have three exons interrupted by two introns, while osp1,osp2 and osp3 each have two exons interrupted by a single intron. The five genes were predicted products of 338, 335, 336, 343 and 346 amino acid residues, respectively, including putative signal peptide sequence at the amino-termini. And OSP1, OSP4 and OSP5 were predicted to be anionic peroxidase, OSP2 and OSP3 are cationic. Comparative analysis and evolutionary analysis of the clustered genes and other peroxidase family members revealed that the gene cluster occurred by tandemly gene duplications(from osp5 to osp1) and that osp5,ap1 and prx7 were potential orthologies, and osp1-5, ap1 and prx7 constituted a novel evolutionary branch of class III peroxidases.

Journal Article↗
PubMed2004

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.

Databases, Genetic↗