Evolutionary approach to the analysis of structure and function of gangliosides.
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Adaptation, Biological↗
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Evolutionary-based grouping of haplotypes in association analysis.
Haplotypes incorporate more information about the underlying polymorphisms than do genotypes for individual SNPs, and are considered as a more informative format of data in association analysis. To model haplotypes requires high degrees of freedom, which could decrease power and limit a model's capacity to incorporate other complex effects, such as gene-gene interactions. Even within haplotype blocks, high degrees of freedom are still a concern unless one chooses to discard rare haplotypes. To increase the efficiency and power of haplotype analysis, we adapt the evolutionary concepts of cladistic analyses and propose a grouping algorithm to cluster rare haplotypes to the corresponding ancestral haplotypes. The algorithm determines the cluster bases by preserving common haplotypes using a criterion built on the Shannon information content. Each haplotype is then assigned to its appropriate clusters probabilistically according to the cladistic relationship. Through this algorithm, we perform association analysis based on groups of haplotypes. Simulation results indicate power increases for performing tests on the haplotype clusters when compared to tests using original haplotypes or the truncated haplotype distribution.
Algorithms↗
Perceived parental efficacy: concept analysis.
AIMS: This paper describes a concept analysis carried out to remove some of the ambiguity surrounding the conceptual meaning of perceived parental efficacy and to distinguish it from related concepts such as parental confidence and parental competence. BACKGROUND: Constructing parental efficacy is a crucial step for family members after the birth of their first child. For some authors, perceived parental efficacy is a motor for adequate parental practices. Confusion about the definition and measurement of this concept has hindered both psychology and nursing practice and research. Concept delineation and concept clarification are required in order to further the development of the concept of perceived parental efficacy. METHODS: A literature search using a variety of online databases yielded 113 articles between the years 1980 and 2000. The final sample (n=60) consisted of 30 articles from two disciplines: nursing and psychology. A content analysis of the literature was done using Rodger's evolutionary concept analysis method. FINDINGS: Content analysis of the literature yielded four contributors to perceived parental efficacy: positive enactive mastery experiences, vicarious experiences, verbal persuasion and an appropriate physiological and affective state. Perceived parental efficacy can thus be defined as 'beliefs or judgements a parent holds of their capabilities to organize and execute a set of tasks related to parenting a child'. CONCLUSION: This conceptual analysis has allowed perceived parental efficacy to be distinguished from parental confidence and parental competence. Both nursing and psychology research, practice and education will benefit from a more precise and delineated concept.
Child Rearing↗
AFLP analysis of genetic polymorphism and evolutionary relationships among cultivated and wild Nicotiana species.
Amplified fragment length polymorphism (AFLP) analysis was used to determine the degree of intra- and inter-specific genetic variation in the genus Nicotiana. Forty-six lines of cultivated tobacco (Nicotiana tabacum L.) and seven wild Nicotiana species, including N. sylvestris, N. tomentosiformis, N. otophora, N. glutinosa, N. suaveolens, N. rustica, and N. longiflora, were analyzed, using at least eight different oligonucleotide primer combinations capable of detecting a minimum of 50 polymorphic bands per primer pair. The amount of genetic polymorphism present among cultivated tobacco lines (N. tabacum) was limited, as evidenced by the high degree of similarity in the AFLP profiles of cultivars collected worldwide. Six major clusters were found within cultivated tobacco that were primarily based upon geographic origin and manufacturing quality traits. A greater amount of genetic polymorphism exists among wild species of Nicotiana than among cultivated forms. Pairwise comparisons of the AFLP profiles of wild and cultivated Nicotiana species show that polymorphic bands present in N. tabacum can be found in at least one of three proposed wild progenitor species (i.e., N. sylvestris, N. tomentosiformis, and N. otophora). This observation provides additional support for these species contributing to the origin of N. tabacum.
DNA↗
Phylogenetic analysis and gene functional predictions: phylogenomics in action.
Making accurate functional predictions for genes is a key step in this era of high throughput gene and genome sequencing. While most functional prediction methods are comparative in nature, many do not take advantage of the power that an evolutionary perspective provides to any comparative biology analysis. Here we review how evolutionary analysis can greatly benefit both homology-based and non-homology-based functional prediction methods. Examples that are discussed include phylogenetic determination of orthology, the use of character state reconstruction analysis of gene function, and evolutionary analysis of rates and patterns of gene evolution.
Genome↗
Analysis of the core and E1 envelope region sequences of a novel variant of hepatitis C virus obtained in Indonesia.
Hepatitis C virus (HCV) is currently classified into 6 major types, HCV-1 through -6, each of which can be further divided into a few subtypes, e.g., HCV-1a, -1b, -1c, etc., on the basis of sequence variation of the viral genome. The core and E1 envelope regions of HCV genome were amplified from sera of Indonesian patients using reverse transcription-polymerase chain reaction. Sequence analysis of both core and E1 regions followed by molecular evolutionary phylogenetic analysis identified a novel sequence variant of HCV-1 (Td-6). Antibodies in the serum from which Td-6 was isolated reacted only marginally to the core protein of HCV-J, a representative strain of HCV-1b, despite strong antibody response against a mixture of the core, NS3 and NS4 proteins of HCV-1a. The possible mechanism for the diminished reactivity of the antibodies in the serum to the core protein of HCV-J is discussed.
Amino Acid Sequence↗
Allozyme and DNA sequence data support speciation of northern and southern populations of silver catfish, Schilbe intermedius (Rüppel, 1832).
Patterns of genetic variation in Schilbe intermedius were investigated due to morphological differences and taxonomic uncertainties regarding the Southern African schilbeids. A total of three populations, two Southern populations representing the former Eutropius depressirostris and a Northern population representing S. mystus, were electrophoretically analysed to determine the extent of genetic differentiation among these populations. The Northern and Southern populations were fixed for different alleles at the G3PDH-2 protein coding locus and allozyme differentiation between populations, using the 0.95 criterion, were also encountered at the PGDH-2 locus. Genetic distance values indicate greater genetic differentiation between the Northern and Southern populations compared to the two Southern populations. DNA sequence analysis of 900-1000 nucleotides of the cytochrome b gene revealed distances of 3.2-3.5% between the Schilbe/Eutropius complex. This finding, together with ingroup and outgroup analysis of evolutionary relationships, is congruent with the results from the electrophoretic analysis of the taxa. Sufficient differentiation exist between the Northern and Southern populations to regard them as distinct species.
Animals↗
Breath-to-breath relationships between respiratory cycle variables in humans at fixed end-tidal PCO2 and PO2.
This study examined the statistical properties of breath-to-breath variations in the inspiratory and expiratory volumes and times during rest and light exercise. Sixty data sets were analyzed. Initial data and residuals after fitting time-series models were examined for 1) sustained periodicities with use of spectral analysis, 2) temporal changes in signal power with use of evolutionary spectral analysis, and 3) auto- and cross correlations with use of a portmanteau test. The major findings were as follows: 1) no sustained periodic components were detected; 2) temporal changes in signal power were normally present, but these did not affect significantly the results from time-series modeling; 3) for all variables, a simple autoregressive moving average (ARMA) AR1MA1 model generally described the autocorrelation; 4) considerable cross correlation remained between residuals from the AR1MA1 model; 5) relationships between variables could be described by using a multivariate time-series model; 6) residual fluctuations in end-tidal PCO2 had little influence; and 7) responses were broadly similar between rest and exercise, although some quantitative differences were found. The multivariate model provides a description of the structure of the interrelationships between cycle variables in a quantitative and a qualitative form.
Carbon Dioxide↗
The nucleotide sequence of 3C proteinase region of the coxsackievirus A24 variant: comparison of the isolates in Taiwan in 1985-1988.
Acute hemorrhagic conjunctivitis caused by coxsackievirus A24 variant (CA24v) first appeared in Taiwan in October 1985, followed by two other sequential epidemics in 1986 and 1988. In order to know the evolutionary relationship of the CA24v strains isolated in Taiwan, we first determined the nucleotide sequence of the 3C proteinase (3Cpro) region of the prototype strain (EH24/70), isolated in Singapore in 1970, by molecular cloning. The nucleotide sequence of the 3Cpro region thus sequenced showed striking homology with polioviruses and coxsackievirus A21. Viral RNA of eight isolates obtained from the three epidemics was reverse transcribed, amplified by the polymerase chain reaction, and cloned into M13 phage for the production of ssDNA for nucleotide sequencing by the dideoxy chain termination method. When the number of nucleotide difference was taken as a genetic distance between isolates, all isolates showed a very similar distance from the EH24/70, the earliest isolate of CA24v, indicating that they evolved at a constant evolutionary rate. Phylogenetic analysis by the unweighted pairwise grouping method of arithmetic average (UPGMA) indicated that the six isolates collected in 1985 and 1986 were closely related, while two 1988 isolates were more distant from them. The branching time between these two groups was estimated to be May 1984, 18 months before the first recognition of the CA24v epidemic in Taiwan. This is the first report of the nucleotide sequence of CA24v genome RNA and of an evolutionary analysis of the virus using the nucleotide sequence.
3C Viral Proteases↗
Experimental determination and system level analysis of essential genes in Escherichia coli MG1655.
Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media. We identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. Functional context analysis of these data allows individual functional assignments to be refined. Evolutionary context analysis demonstrates a significant tendency of essential E. coli genes to be preserved throughout the bacterial kingdom. Projection of these data over metabolic subsystems reveals topologic modules with essential and evolutionarily preserved enzymes with reduced capacity for error tolerance.
Aerobiosis↗
Patterns of sequence conservation in presynaptic neural genes.
BACKGROUND: The neuronal synapse is a fundamental functional unit in the central nervous system of animals. Because synaptic function is evolutionarily conserved, we reasoned that functional sequences of genes and related genomic elements known to play important roles in neurotransmitter release would also be conserved. RESULTS: Evolutionary rate analysis revealed that presynaptic proteins evolve slowly, although some members of large gene families exhibit accelerated evolutionary rates relative to other family members. Comparative sequence analysis of 46 megabases spanning 150 presynaptic genes identified more than 26,000 elements that are highly conserved in eight vertebrate species, as well as a small subset of sequences (6%) that are shared among unrelated presynaptic genes. Analysis of large gene families revealed that upstream and intronic regions of closely related family members are extremely divergent. We also identified 504 exceptionally long conserved elements (> or =360 base pairs, > or =80% pair-wise identity between human and other mammals) in intergenic and intronic regions of presynaptic genes. Many of these elements form a highly stable stem-loop RNA structure and consequently are candidates for novel regulatory elements, whereas some conserved noncoding elements are shown to correlate with specific gene expression profiles. The SynapseDB online database integrates these findings and other functional genomic resources for synaptic genes. CONCLUSION: Highly conserved elements in nonprotein coding regions of 150 presynaptic genes represent sequences that may be involved in the transcriptional or post-transcriptional regulation of these genes. Furthermore, comparative sequence analysis will facilitate selection of genes and noncoding sequences for future functional studies and analysis of variation studies in neurodevelopmental and psychiatric disorders.
Animals↗
Loss of neurturin in frog--comparative genomics study of GDNF family ligand-receptor pairs.
Four different GDNF family ligand (GFL)-receptor (GFRalpha) binding pairs exist in mammals, and they all signal via the RET receptor tyrosine kinase. However, the evolution of these molecules is poorly understood. We identified orthologs of all four GFRalpha receptors and GRAL (GDNF Receptor Alpha-Like) in all vertebrate classes, and a predicted GFR-like protein in several invertebrates. In addition, Gas1 (growth arrest-specific 1), a distant member of the GFR-superfamily, is present in both vertebrates and invertebrates. Analysis of exon structures suggests a common origin of GFR-superfamily proteins and early divergence of Gas1 from the common ancestor. Bony fishes have orthologs of all four mammalian GFLs, consistent with genome duplications in early vertebrates. Surprisingly, the clawed frog and chicken have only three GFLs: synteny analysis indicates loss of neurturin in frog and of persephin in chicken. Evolutionary trace analysis and protein structure homology modeling points at GDNF as the endogenous ligand of frog GFRalpha2.
Amino Acid Sequence↗
Amantadine-resistant influenza A virus in Taiwan.
BACKGROUND AND PURPOSE: Amantadine and rimantadine have been used for treatment and prophylaxis of influenza A virus infection. We examined the amantadine susceptibility of field isolates of influenza A virus in Taiwan from 1996 to 1998 to monitor the presence of resistant strains. METHODS: Eighty-four field isolates of influenza A virus were examined for resistance to amantadine by plaque inhibition assay. Virus isolates with amantadine 50% inhibitory concentrations (IC50) greater than 0.9 microgram were chosen for sequence analysis of the M gene that is the molecular target for amantadine/rimantadine. Reverse transcription-polymerase chain reaction (RT-PCR) was used to amplify the viral RNA. RT-PCR products were examined and purified by agarose gel electrophoresis for further sequence analysis. The Genetics Computer Group Sequence Analysis Package and the neighbor-joining method listed in the Molecular Evolutionary Genetic Analysis package were used for phylogenetic analysis. RESULTS: One field strain was amantadine resistant (IC50 > 10 micrograms/mL), with a mutation (position 31, serine to asparagine) in the M2 protein. The resistant virus was isolated from a non-immunocompromised child without a history of amantadine/rimantadine treatment. None of the family members reported previous exposure to amantadine/rimantadine. CONCLUSIONS: In this series, amantadine-resistant influenza A (H1N1) virus was isolated from a non-immunocompromised Taiwanese child without a known history of exposure to this drug. Resistant field isolates were rare. Due to the increasing use of amantadine/rimantadine in Taiwan, continued surveillance for amantadine/rimantadine-resistant influenza A viruses is warranted.
Amantadine↗
A rigorous complexity analysis of the (1 + 1) evolutionary algorithm for separable functions with Boolean inputs.
Evolutionary algorithms (EAs) are heuristic randomized algorithms which, by many impressive experiments, have been proven to behave quite well for optimization problems of various kinds. In this paper a rigorous theoretical complexity analysis of the (1 + 1) evolutionary algorithm for separable functions with Boolean inputs is given. Different mutation rates are compared, and the use of the crossover operator is investigated. The main contribution is not the result that the expected run time of the (1 + 1) evolutionary algorithm is theta (n ln n) for separable functions with n variables but the methods by which this result can be proven rigorously.
Algorithms↗
Resolving tylenchid evolutionary relationships through multiple gene analysis derived from EST data.
Sequence-based phylogenetic analyses typically are based on a small number of character sets and report gene trees which may not reflect the true species tree. We employed an EST mining strategy to suppress such incongruencies, and recovered the most robust phylogeny for five species of plant-parasitic nematode (Meloidogyne arenaria, M. chitwoodi, M. hapla, M. incognita, and M. javanica), three closely related tylenchid taxa (Heterodera glycines, Globodera pallida, and G. rostochiensis) and a distant taxon, Caenorhabditis elegans. Our multiple-gene approach is based on sampling more than 80,000 publicly available tylenchid EST sequences to identify phylum-wide orthologues. Bayesian inference, minimum evolution, maximum likelihood and protein distance methods were employed for phylogenetic reconstruction and hypothesis tests were constructed to elucidate differential selective pressures across the phylogeny for each gene. Our results place M. incognita and M. javanica as sister taxa, with M. arenaria as the next closely related nematode. Significant differences in selective pressure were revealed for some genes under some hypotheses, though all but one gene are exclusively under purifying selection, indicating conservation across the orthologous groups. This EST-based multi-gene analysis is a first step towards accomplishing genome-wide coverage for tylenchid evolutionary analyses.
Animals↗
Apoptosis and change of competence limit the size of the vulva equivalence group in Pristionchus pacificus: a genetic analysis.
BACKGROUND: To understand how alterations in the molecular mechanisms underlying developmental processes generate a diversity of biological forms, comparative developmental biology can be combined with genetic analysis. The formation of the nematode vulva is one tractable system for such evolutionary developmental analysis, as much is understood about its development in Caenorhabditis elegans. In Caenorhabditis, six of twelve ventral epidermal cells form the 'vulva equivalence group'; although all six cells are competent to adopt vulval cell fates in response to an inductive signal, only three of these cells are induced to form vulval tissue. RESULTS: In some species of the nematode families Rhabditidae, Neodiplogastridae and Panagrolaimidae, the number of cells in the vulva equivalence group is limited by apoptosis and decreased responsiveness to inductive signals (competence). We have initiated a genetic analysis in one of these species, Pristionchus pacificus, to understand the evolution of the specification of ventral epidermal cells that are competent to generate the vulva. A ped-4 mutation restores competence to an incompetent cell. Mutation of either of two other genes of Pristionchus cause two anterior cells that die in wild-type to survive. A ped-5 mutation causes these cells to be competent to respond to inductive signals, expanding the equivalence group. A ped-6 mutation causes these cells to form ectopic, anterior vulva-like invaginations. CONCLUSIONS: During nematode evolution, apoptosis and change of competence alter the number and potency of ventral epidermal cells. The phenotypes of Pristionchus mutants suggest that alterations in homeotic gene control of anteroposterior patterning is involved in creating this cellular diversity.
Animals↗
Genetic diversity and function in the human cytosolic sulfotransferases.
Amino-acid substitutions, which result from common nonsynonymous (NS) polymorphisms, may dramatically alter the function of the encoded protein. Gaining insight into how these substitutions alter function is a step toward acquiring predictability. In this study, we incorporated gene resequencing, functional genomics, amino-acid characterization and crystal structure analysis for the cytosolic sulfotransferases (SULTs) to attempt to gain predictability regarding the function of variant allozymes. Previously, four SULT genes were resequenced in 118 DNA samples. With additional resequencing of the remaining eight SULT family members in the same DNA samples, a total of 217 polymorphisms were revealed. Of 64 polymorphisms identified within 8785 bp of coding regions from SULT genes examined, 25 were synonymous and 39 were NS. Overall, the proportion of synonymous changes was greater than expected from a random distribution of mutations, suggesting the presence of a selective pressure against amino-acid substitutions. Functional data for common variants of five SULT genes have been previously published. These data, together with the SULT1A1 variant allozyme data presented in this paper, showed that the major mechanism by which amino acid changes altered function in a transient expression system was through decreases in immunoreactive protein rather than changes in enzyme kinetics. Additional insight with regard to mechanisms by which NS single nucleotide polymorphisms alter function was sought by analysis of evolutionary conservation, physicochemical properties of the amino-acid substitutions and crystal structure analysis. Neither individual amino-acid characteristics nor structural models were able to accurately and reliably predict the function of variant allozymes. These results suggest that common amino-acid substitutions may not dramatically alter the protein structure, but affect interactions with the cellular environment that are currently not well understood.
Amino Acid Substitution↗
Gene loss and evolutionary rates following whole-genome duplication in teleost fishes.
Teleost fishes provide the first unambiguous support for ancient whole-genome duplication in an animal lineage. Studies in yeast or plants have shown that the effects of such duplications can be mediated by a complex pattern of gene retention and changes in evolutionary pressure. To explore such patterns in fishes, we have determined by phylogenetic analysis the evolutionary origin of 675 Tetraodon duplicated genes assigned to chromosomes, using additional data from other species of actinopterygian fishes. The subset of genes, which was retained in double after the genome duplication, is enriched in development, signaling, behavior, and regulation functional categories. The evolutionary rate of duplicate fish genes appears to be determined by 3 forces: 1) fish proteins evolve faster than mammalian orthologs; 2) the genes kept in double after genome duplication represent the subset under strongest purifying selection; and 3) following duplication, there is an asymmetric acceleration of evolutionary rate in one of the paralogs. These results show that similar mechanisms are at work in fishes as in yeast or plants and provide a framework for future investigation of the consequences of duplication in fishes and other animals.
Animals↗