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PubMed2001

Quantifying passive and driven large-scale evolutionary trends.

I introduce a new statistical method, analysis of skewness, for quantifying large-scale evolutionary trends as a combination of both passive and driven trends. My approach is based on the skewness of subclades within a parent clade. I partition the total skewness of the parent clade into three components: (1) skewness between subclades; (2) skewness within subclades; and (3) skewness due to changes in variance among subclades. The third component corresponds to a new type of passive trend, in which overall skewness of a parent clade is due to greater variability in subclades to the right of the mean. Using this partitioning, I decompose an observed trend into two components: a driven portion and a passive portion. thus quantifying the effect of small-scale dynamics on large-scale behavior of clades. Applications are given to Miocene-Pliocene rodent size and Ordovician brachiopod muscle geometry.

Animals↗
PubMed2004

Resolving the evolutionary paradox of genetic instability: a cost-benefit analysis of DNA repair in changing environments.

Loss of genetic stability is a critical phenomenon in cancer and antibiotic resistance, and the prevailing dogma is that unstable cells survive because instability provides adaptive mutations. Challenging this view, we have argued that genetic instability arises because DNA repair may be a counterproductive strategy in mutagenic environments. This paradoxical relationship has also been confirmed by explicit experiments, but the underlying evolutionary principles remain controversial. This paper aims to clarify the issue, and presents a model that explains genetic instability from the basic perspective of molecular evolution and information processing.

Animals↗
PubMed2003

Origin and evolutionary process of the CNS elucidated by comparative genomics analysis of planarian ESTs.

Among the bilateral animals, a centralized nervous system is found in both the deuterostome and protostome. To address the question of whether the CNS was derived from a common ancestor of deuterostomes and protostomes, it is essential to know kinds of genes existed in the CNS of the putative common ancestor and to trace the evolutionary divergence of genes expressed in the CNS. To answer these questions, we took a comparative approach using different species, particularly focusing on one of the lower bilateral animals, the planarian (Platyhelminthes, Tricladida), which is known to possess a CNS. We determined the nucleotide sequence of ESTs from the head portion of planarians, obtaining 3,101 nonredundant EST clones. As a result of homology searches, we found that 116 clones had significant similarity to known genes related to the nervous system. Here, we compared these 116 planarian EST clones with all ORFs of the complete genome sequences of the human, fruit fly, and nematode, and showed that >95% of these 116 nervous system-related genes, including genes involved in brain or neural morphogenesis, were commonly shared among these organisms, thus providing evidence at the molecular level for the existence of a common ancestral CNS. Interestingly, we found that approximately 30% of planarian nervous system-related genes had homologous sequences in Arabidopsis and yeast, which do not possess a nervous system. This implies that the origin of nervous system-related genes greatly predated the emergence of the nervous system, and that these genes might have been recruited toward the nervous system.

Animals↗
PubMed2002

Molecular evolution of the equilibrative nucleoside transporter family: identification of novel family members in prokaryotes and eukaryotes.

Equilibrative nucleoside transporters (ENTs) are integral membrane proteins which enable the movement of hydrophilic nucleosides and nucleoside analogs down their concentration gradients across cell membranes. ENTs were only recently characterized at the molecular level, and little is known about the tertiary structure or distribution of these proteins in nonmammalian organisms. To identify conserved regions, residues, and motifs of ENTs that may indicate functionally important parts of the protein and to better understand the evolutionary history of this protein family, we conducted an exhaustive analysis to characterize and compare ENTs in taxonomically diverse organisms. We have identified novel ENT family members in humans, mice, fish, tunicates, slime molds, and bacteria. This greatly extends our knowledge on the distribution of the ENTs in eukaryotes, and we have identified, for the first time, family members in bacteria. The prokaryote ENTs are attractive models for future studies on transporter tertiary structure and mechanism of substrate translocation. Using sequence similarities, we have identified regions, residues, and motifs that are conserved across all family members. These areas are presumably correlated with function and therefore are important targets for future analysis. Finally, we propose an evolutionary history for the ENT family which clarifies the origin(s) of multiple isoforms in different taxa.

Amino Acid Sequence↗
PubMed2005

Partial sequence analysis of an atypical Turkish isolate provides further information on the evolutionary history of Plum pox virus (PPV).

A variety of techniques, such as typing with subgroup-specific monoclonal antibodies, restriction length polymorphism (RFLP) analysis or subgroup-specific RT-PCR are available for the discrimination of Plum pox virus (PPV) isolates. However, the existence of PPV isolates showing abnormal typing properties has been observed in the past [Candresse, T., Cambra, M., Dallot, S., Lanneau, M., Asensio, M., Gorris, M.T., Revers, F., Macquaire, G., Olmos, A., Boscia, D., Quiot J.B., Dunez, J., 1998. Comparison of monoclonal antibodies and polymerase chain reaction assays for the typing of isolates belonging to the D and M serotypes of Plum pox potyvirus. Phytopathology 88, 198-204.]. In an effort to understand the molecular mechanisms underlying such anomalous serological and molecular typing characteristics, partial 3' (1449 nt) and 5' (3706 nt) sequences have been determined for an atypical Turkish PPV isolate (Abricotier Turquie or Ab-Tk). The results obtained indicate that its unusual typing behaviour is caused by point mutations affecting key restriction sites and epitopes and confirm that this isolate represents a divergent member of the PPV-M subgroup. In addition, analysis of the partial Ab-Tk genomic sequences demonstrated that the 5' region of the genome of this isolate has a mosaic structure resulting from recombination event(s), shedding new light on the evolutionary history of Plum pox virus.

Antibodies, Monoclonal↗
PubMed2006

What is protocol-based care? A concept analysis.

AIM: To define protocol-based care to make this way of delivering health care amenable to theoretical and empirical studies. BACKGROUND: Although protocol-based care is associated with the evidence-based practice and standardization movements, it is an ill-defined and understood concept. METHOD: A multiphase concept analysis, inspired by an evolutionary view was used to clarify 'what is protocol-based care'. The inductive, five-phase process drew upon content analysis of policy documents and the literature, plus interviews with a purposive sample of 35 opinion leaders. RESULTS: The term was used interchangeably with protocols, pathways and guidelines in policy and guidance documents. A search of seven databases produced only 57 references to protocol-based care. The concept analysis revealed a continuum of scope and specificity and also distinguished specialist and generic applications of protocol-based care. CONCLUSIONS: Managers need to take cognizance of the significance and complexity of protocol-based care when introducing this way of working.

Clinical Protocols↗
PubMed2000

SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.

Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. A detailed computer analysis of the structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA. The endonuclease fold, whose structural prototypes are the phage lambda exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs, repair nucleases such as RecB and Vsr, restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. Within the RNase H fold a new family of predicted HJRs, which is nearly ubiquitous in bacteria, was discovered, in addition to the previously characterized RuvC family. The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and AQUIFEX: Endonuclease VII of phage T4 is shown to serve as a structural template for many nucleases, including MCR:A and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. As a result of this analysis, the principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the lambda exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This analysis resulted in the prediction of numerous previously unnoticed nucleases, some of which are likely to be new restriction enzymes.

Amino Acid Sequence↗
PubMed1999

Family-centred care: a concept analysis.

Family-centred care would seem to be a central element of children's nursing, but there is no consensus about its meaning. This paper uses a combination of Rodgers' evolutionary model of concept analysis and Schwartz-Barcott and Kim's hybrid model of concept development to facilitate a dispositional approach to analysing this concept. Data from a qualitative survey undertaken during 1994/1995 was used in conjunction with data obtained through a questionnaire, to provide the field-work element for the process of analysis. The process resulted in the identification of the antecedents and attributes of family-centred care, and the identification of a lack of clarity related to the consequences of family-centred care. Two alternative models of family-centred care emerged, both of which demonstrate strong associations with the concepts of partnership with parents, parental participation and care by parents. The paper does not conclude with any definition of family-centred care, but rather explores its usefulness in practice and considers how the concept might be operationalized. The tentative proposals for a hierarchy of family-centred care will require exploration, testing and evaluation by practitioners in the real world of children's nursing.

Humans↗
PubMed1998

Quality of life in persons with non-small cell lung cancer: a concept analysis.

Quality of life, as a concept, has received increased attention in recent years. In fact, issues related to quality of life have been identified as among the top three priorities for research by the Oncology Nursing Society. Several nurse investigators have underscored the importance of quality of life research as an outcome measure to evaluate the effectiveness of nursing interventions. Given its significance in contemporary nursing practice, a clear understanding of the definition and dimensions of quality of life is essential for future development of an empirical knowledge base for practice. This article presents a concept analysis of quality of life as it relates to the health care of individuals with non-small cell lung cancer. An evolutionary method of concept analysis is used as a guide for examining the historical context of the concept, defining the concept, identifying antecedents, recognizing consequences, and distinguishing related concepts. A theoretical model of health-related quality of life is proposed on the basis of this analysis, and future directions for research in this population are discussed.

Carcinoma, Non-Small-Cell Lung↗
PubMed1999

The future of evolutionary developmental biology.

Combining fields as diverse as comparative embryology, palaeontology, molecular phylogenetics and genome analysis, the new discipline of evolutionary developmental biology aims at explaining how developmental processes and mechanisms become modified during evolution, and how these modifications produce changes in animal morphology and body plans. In the next century this should give us far greater mechanistic insight into how evolution has produced the vast diversity of living organisms, past and present.

Animals↗
PubMed2006

The endo-beta-mannanase gene families in Arabidopsis, rice, and poplar.

Mannans are widespread hemicellulosic polysaccharides in plant cell walls. Hydrolysis of the internal beta-1,4-D: -mannopyranosyl linkage in the backbone of mannans is catalyzed by endo-beta-mannanase. Plant endo-beta-mannanase has been well studied for its function in seed germination. Its involvement in other plant biological processes, however, remains poorly characterized or elusive. The completed genome sequences of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and poplar (Populus trichocarpa) provide an opportunity to conduct comparative genomic analysis of endo-beta-mannanase genes in these three species. In silico sequence analysis led to the identification of eight, nine and 11 endo-beta-mannanase genes in the genomes of Arabidopsis, rice, and poplar, respectively. Sequence comparisons revealed the conserved amino acids and motifs that are critical for the active site of endo-beta-mannanases. Intron/exon structure analysis in conjunction with phylogenetic analysis implied that both intron gain and intron loss has played roles in the evolution of endo-beta-mannanase genes. The phylogenetic analysis that included the endo-beta-mannanases from plants and other organisms implied that plant endo-beta-mannanases have an ancient evolutionary origin. Comprehensive expression analysis of all Arabidopsis and rice endo-beta-mannanase genes showed divergent expression patterns of individual genes, suggesting that the enzymes encoded by these genes, while carrying out the same biochemical reaction, are involved in diverse biological processes.

Amino Acid Sequence↗
PubMed2005

Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences.

Recently, it was proposed that alternative splicing may act as a mechanism for opening accelerated paths of evolution, by reducing negative selection pressure, but there has been little evidence so far that this mechanism could produce adaptive benefit. Here, we use metrics of very different types of selection pressures [e.g., against amino acid mutations (Ka/Ks), against mutations at synonymous sites (Ks), and for protein reading-frame preservation] to address this question by genomewide analyses of human, chimpanzee, mouse, and rat. These data show that alternative splicing relaxes Ka/Ks selection pressure up to 7-fold, but intriguingly this effect is accompanied by a strong increase in selection pressure against synonymous mutations, which propagates into the adjacent intron, and correlates strongly with the alternative splicing level observed for each exon. These effects are highly local to the alternatively spliced exon. Comparisons of these four genomes consistently show an increase in the density of amino acid mutations (Ka) in alternatively spliced exons and a decrease in the density of synonymous mutations (Ks). This selection pressure against synonymous mutations in alternatively spliced exons was accompanied in all four genomes by a striking increase in selection pressure for protein reading-frame preservation, and both increased markedly with increasing evolutionary age. Restricting our analysis to a subset of exons with strong evidence for biologically functional alternative splicing produced identical results. Thus alternative splicing apparently can create evolutionary "hotspots" within a protein sequence, and these events have evidently been selected for during mammalian evolution.

Alternative Splicing↗
PubMed2006

PhyloPat: phylogenetic pattern analysis of eukaryotic genes.

BACKGROUND: Phylogenetic patterns show the presence or absence of certain genes or proteins in a set of species. They can also be used to determine sets of genes or proteins that occur only in certain evolutionary branches. Phylogenetic patterns analysis has routinely been applied to protein databases such as COG and OrthoMCL, but not upon gene databases. Here we present a tool named PhyloPat which allows the complete Ensembl gene database to be queried using phylogenetic patterns. DESCRIPTION: PhyloPat is an easy-to-use webserver, which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain evolutionary branches or even single species. We found in total 446,825 genes and 3,164,088 orthologous relationships within the EnsMart v40 database. We used a single linkage clustering algorithm to create 147,922 phylogenetic lineages, using every one of the orthologies provided by Ensembl. PhyloPat provides the possibility of querying with either binary phylogenetic patterns (created by checkboxes) or regular expressions. Specific branches of a phylogenetic tree of the 21 included species can be selected to create a branch-specific phylogenetic pattern. Users can also input a list of Ensembl or EMBL IDs to check which phylogenetic lineage any gene belongs to. The output can be saved in HTML, Excel or plain text format for further analysis. A link to the FatiGO web interface has been incorporated in the HTML output, creating easy access to functional information. Finally, lists of omnipresent, polypresent and oligopresent genes have been included. CONCLUSION: PhyloPat is the first tool to combine complete genome information with phylogenetic pattern querying. Since we used the orthologies generated by the accurate pipeline of Ensembl, the obtained phylogenetic lineages are reliable. The completeness and reliability of these phylogenetic lineages will further increase with the addition of newly found orthologous relationships within each new Ensembl release.

Algorithms↗
PubMed2005

Functional genomic analysis of the rates of protein evolution.

The evolutionary rates of proteins vary over several orders of magnitude. Recent work suggests that analysis of large data sets of evolutionary rates in conjunction with the results from high-throughput functional genomic experiments can identify the factors that cause proteins to evolve at such dramatically different rates. To this end, we estimated the evolutionary rates of >3,000 proteins in four species of the yeast genus Saccharomyces and investigated their relationship with levels of expression and protein dispensability. Each protein's dispensability was estimated by the growth rate of mutants deficient for the protein. Our analyses of these improved evolutionary and functional genomic data sets yield three main results. First, dispensability and expression have independent, significant effects on the rate of protein evolution. Second, measurements of expression levels in the laboratory can be used to filter data sets of dispensability estimates, removing variates that are unlikely to reflect real biological effects. Third, structural equation models show that although we may reasonably infer that dispensability and expression have significant effects on protein evolutionary rate, we cannot yet accurately estimate the relative strengths of these effects.

Evolution, Molecular↗
PubMed2005

Phylogenetic relationships and evolutionary traits in Ranunculus s.l. (Ranunculaceae) inferred from ITS sequence analysis.

Ranunculus is a large genus with a worldwide distribution. Phylogenetic analyses of c. 200 species of Ranunculus s.l. based on sequences of the nrITS using maximum parsimony and Bayesian inference yielded high congruence with previous cpDNA restriction site analyses, but strongly contradict previous classifications. A large core clade including Ranunculus subg. Ranunculus, subg. Batrachium, subg. Crymodes p.p., Ceratocephala, Myosurus, and Aphanostemma is separated from R. subg. Ficaria, subg. Pallasiantha, subg. Coptidium, subg. Crymodes p.p., Halerpestes, Peltocalathos, Callianthemoides, and Arcteranthis. Within the core clade, 19 clades can be described with morphological and karyological features. Several sections are not monophyletic. Parallel evolution of morphological characters in adaptation to climatic conditions may be a reason for incongruence of molecular data and morphology-based classifications. In some mountainous regions, groups of closely related species may have originated from adaptive radiation and rapid speciation. Split decomposition analysis indicated complex patterns of relationship and suggested hybridization in the apomictic R. auricomus complex, R. subg. Batrachium, and the white-flowering European alpines. The evolutionary success of the genus might be due to a combination of morphological plasticity and adaptations, hybridization and polyploidy as important factors for regional diversification, and a broad range of reproductive strategies.

DNA, Plant↗
PubMedDate not supplied

Symptom clusters: concept analysis and clinical implications for cancer nursing.

The purpose of this article is to analyze the concept of symptom clusters and to discuss its application to cancer nursing to promote communication and enhance scientific knowledge. Rodgers' evolutionary method of concept analysis served as the framework for reviewing literature from psychology/psychiatry, general medicine, and nursing. Attributes of symptom clusters were relationships of symptoms and relationships of clusters, concurrence, underlying dimensions, stability, and common etiology. The major antecedent was the presence of 2 or more symptoms. Consequences were poorer physical health status, interference with activities of daily living, emotional distress, and increased financial burden. A symptom cluster is defined as consisting of 2 or more symptoms that are related to each other and that occur together. Symptom clusters are composed of stable groups of symptoms, are relatively independent of other clusters, and may reveal specific underlying dimensions of symptoms. Relationships among symptoms within a cluster should be stronger than relationships among symptoms across different clusters. Symptoms in a cluster may or may not share the same etiology. Symptom should be broadened to include both subjective (self-reported) symptoms and objective (observed) signs. Implications for researchers include the need to use a clear definition, determine the optimal methods of identifying etiology and nature of symptom clusters in various populations, assess the clinical utility of symptom clusters, and test interventions. Implications for practitioners include the need to comprehensively assess symptoms over the entire cancer trajectory, select interventions that target single and multiple symptoms, and evaluate outcomes that include quality of life and economic variables.

Fatigue↗
PubMed2004

Genome SEGE: a database for 'intronless' genes in eukaryotic genomes.

BACKGROUND: A number of completely sequenced eukaryotic genome data are available in the public domain. Eukaryotic genes are either 'intron containing' or 'intronless'. Eukaryotic 'intronless' genes are interesting datasets for comparative genomics and evolutionary studies. The SEGE database containing a collection of eukaryotic single exon genes is available. However, SEGE is derived using GenBank. The redundant, incomplete and heterogeneous qualities of GenBank data are a bottleneck for biological investigation in comparative genomics and evolutionary studies. Such studies often require representative gene sets from each genome and this is possible only by deriving specific datasets from completely sequenced genome data. Thus Genome SEGE, a database for 'intronless' genes in completely sequenced eukaryotic genomes, has been constructed. AVAILABILITY: http://sege.ntu.edu.sg/wester/intronless DESCRIPTION: Eukaryotic 'intronless' genes are extracted from nine completely sequenced genomes (four of which are unicellular and five of which are multi-cellular). The complete dataset is available for download. Data subsets are also available for 'intronless' pseudo-genes. The database provides information on the distribution of 'intronless' genes in different genomes together with their length distributions in each genome. Additionally, the search tool provides pre-computed PROSITE motifs for each sequence in the database with appropriate hyperlinks to InterPro. A search facility is also available through the web server. CONCLUSIONS: The unique features that distinguish Genome SEGE from SEGE is the service providing representative 'intronless' datasets for completely sequenced genomes. 'Intronless' gene sets available in this database will be of use for subsequent bio-computational analysis in comparative genomics and evolutionary studies. Such analysis may help to revisit the original genome data for re-examination and re-annotation.

Databases, Genetic↗
PubMed1994

Structural analysis of the rat homologue of CD1. Evidence for evolutionary conservation of the CD1D class and widespread transcription by rat cells.

The cDNA encoding the rat homologue of CD1 was isolated and the complete nucleotide sequence was determined. It contained an open reading frame of 1008 bp that was capable of encoding a polypeptide with 336 amino acids composed of hydrophobic leader and transmembrane sequences, three extracellular domains, and 5' and 3' untranslated sequences. Comparison of the amino acid sequence of rat CD1 with those of other species revealed that it showed the highest similarity to mouse CD1, which belongs to the CD1D class of the CD1 system and is distinct from the classic CD1 class including CD1a, CD1b, and CD1c expressed primarily on human thymocytes and some dendritic cells. Widespread transcription of rat CD1 was readily detected by Northern blot analysis in nonlymphoid organs, including the liver, kidney, and heart, as well as in lymphoid organs, including the thymus, lymph node, and spleen. Intestinal expression was also demonstrated by the more sensitive reverse transcription-PCR method. Immunoprecipitation with a rabbit anti-rat CD1 Ab showed that rat CD1 was expressed on the cell surface as a beta 2-microglobulin-associated heterodimer. Southern blot analysis of inbred rat strains suggested that rat CD1 shows limited polymorphism and that only one CD1 gene is detectable in the F344 rat genome. These results provide evidence for the conservation of CD1D class through mammalian evolution and an apparent lack of the classic CD1 class genes in rodents. Functional similarity of rodent CD1 is implied.

Amino Acid Sequence↗