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PubMed2006

Evolutionary predictions should be based on individual-level traits.

Recent theoretical studies have analyzed the evolution of habitat specialization using either the logistic or the Ricker equation. These studies have implemented evolutionary change directly in population-level parameters such as habitat-specific intrinsic growth rates r or carrying capacities K. This approach is a shortcut to a more detailed analysis where evolutionary change is studied in underlying morphological, physiological, or behavioral traits at the level of the individual that contribute to r or K. Here we describe two pitfalls that can occur when such a shortcut is employed. First, population-level parameters that appear as independent variables in a population dynamical model might not be independent when derived from processes at the individual level. Second, patterns of covariation between individual-level traits are usually not conserved when mapped to the level of demographic parameters. Nonlinear mappings constrain the curvature of trade-offs that can sensibly be assumed at the population level. To illustrate these results, we derive a two-habitat version of the logistic and Ricker equations from individual-level processes and compare the evolutionary dynamics of habitat-specific carrying capacities with those of underlying individual-level traits contributing to the carrying capacities. Finally, we sketch how our viewpoint affects the results of earlier studies.

Animals↗
PubMed1998

Evolution of olfactomedin. Structural constraints and conservation of primary sequence motifs.

Olfactomedin is a glycosylated extracellular matrix protein originally identified at the mucociliary surface of the amphibian olfactory neuroepithelium and subsequently localized throughout the mammalian central nervous system. Although olfactomedin homologues have been identified in fish, frog, rat, mouse and human, its function is still unknown. As a first step toward elucidating the function of olfactomedin, sequences of teleost, amphibian and human homologues were compared to identify invariant, and hence, potential functionally important motifs. Previous studies revealed 33% amino acid sequence identity between rat and frog olfactomedin in their carboxyl terminal segments. Further analysis, however, reveals more extensive homologies throughout the molecule. Despite significant sequence divergence, cysteines essential for homo-polymer formation, such as the CXC motif near the amino terminus, are conserved as is the characteristic glycosylation pattern, suggesting that these posttranslational modifications are essential for function. Furthermore, alignment of a region of 53 amino acids of fish, frog, rat and human olfactomedin reveals seven invariant residues including a negatively charged cluster of aspartic and glutamic acid residues. Molecular evolutionary genetic analysis reveals an accelerated rate of nucleotide substitutions in the mammalian lineage. The evolutionary rate at the protein level, however, is constant, indicating that evolution of olfactomedin is constrained by structural limitations. Whereas considerable evolutionary divergence is evident between fish, frog and mammalian olfactomedins, olfactomedins of rat and human show 98% amino acid sequence identity. It appears that an ancestral olfactomedin gene arose before the evolution of terrestrial vertebrates and evolved independently in teleost, amphibian and mammalian lineages. The apparent evolutionary pressure toward conservation of primary structure supports the notion that olfactomedin has an important function in the mammalian nervous system.

Amino Acid Sequence↗
PubMed1995

Assignment of the bacterial agent of urinary calculus in young rats by the comparative sequence analysis of the 16S rRNA genes of corynebacteria.

Comparative 16S rRNA gene sequencing was used to assign four isolates of spontaneous urinary calculus in young laboratory rats. The phylogenetic relationships among the rat isolates and selected species of corynebacteria were also inferred. Based on the homology and evolutionary distance analysis, the 16S rRNA genes of the rat isolates were almost identical with that of Corynebacterium renale ATCC 19412. Also the results of the phylogenetic analysis showed a close relationship among the isolates and C. renale, but they were clearly different from C. pilosum, C. cystitidis, C. kutscheri and Rhodococcus equi. The results of the present study and previously published biochemical data demonstrate that the organism involving urinary infections in young rats is identified to be C. renale.

Animals↗
PubMed2001

Phylogenetic relationship and mode of evolution of yeast DNA topoisomerase II gene in the pathogenic Candida species.

We have determined the nucleotide sequences of about 55% of the region of the DNA topoisomerase II gene (approximately 2.3 kb) isolated from the pathogenic Candida species, C. dubliniensis, C. parapsilosis, C. tropicalis, C. krusei, C. kefyr, C. guilliermondii and C. lusitaniae. Evolutionary relationships among nine Candida species including those of C. albicans and C. glabrata were studied based on the DNA topoisomerase II gene. The nucleotide sequences of 2192 bp, which covered two catalytic domains, ATPase and cutting/resealing, were subjected to phylogenetic analysis. Sequence comparison and evolutionary analysis have revealed that the Candida species tested here are not monophyletic, and the two strains within the species C. tropicalis and C. parapsilosis are too diverse to be in a single species. A wide variety of divergence was observed among the functional domains of DNA topoisomerase II, suggesting that Candida species were in different evolutionary paths at least as regarding the DNA topoisomerase II gene. Sequence information and the observation on the species-specific manner of molecular evolution of DNA topoisomerase II in Candida will be applied to develop a method of identification and characterization of the Candida species in both natural and clinical isolates.

Candida↗
PubMed1998

Lecturer practitioner: a concept analysis.

The concept of the lecturer practitioner arose in one health authority in Britain in the late 1980s. Since its inception there, the concept has been widely adopted across the country suggesting that there is a perceived need for this role. However, there is much confusion over what a lecturer practitioner is, since each post is multifaceted, complex and unique. Rodgers' (1993) evolutionary concept analysis is used in an attempt to clarify and to identify those elements that are common to this concept. Through a review of all the available literature on this concept, the attributes, antecedents and consequences are identified and their implications discussed. Rodgers' evolutionary method is described and critiqued throughout the paper and is shown to be a suitable method for clarifying a complex concept.

Faculty, Nursing↗
PubMed1998

Spectral components of cytosolic [Ca2+] spiking in neurons.

We show here, by means of evolutionary spectral analysis and synthesis of cytosolic Ca2+ ([Ca2+]c) spiking observed at the single cell level using digital imaging fluorescence microscopy of fura-2-loaded mouse cerebellar granule cells in culture, that [Ca2+]c spiking can be resolved into evolutionary spectra of a characteristic set of frequencies. Non-delayed small spikes on top of sustained [Ca2+]c were synthesized by a main component frequency, 0.132+/-0.012 Hz, showing its maximal amplitude in phase with the start of depolarization (25 mM KCI) combined with caffeine (10 mM) application. Delayed complex responses of large [Ca2+]c spiking observed in cells from a different set of cultures were synthesized by a set of frequencies within the range 0.018-0.117 Hz. Differential frequency patterns are suggested as characteristics of the [Ca2+]c spiking responses of neurons under different conditions.

Animals↗
PubMed2000

Evolutionary history of the uterine serpins.

A bioinformatics analysis was conducted on the four members of the uterine serpin (US) family of serpins. Evolutionary analysis of the protein sequences and 86 homologous serpins by maximum parsimony and distance methods indicated that the uterine serpins proteins form a clade distinct from other serpins. Ancestral sequences were reconstructed throughout the evolutionary tree by parsimony. These suggested that some branches suffered a high ratio of nonsynonymous to synonymous mutations, suggesting episodes of adaptive evolution within the serpin family. Analysis of the sequences by neutral evolutionary distance methods suggested that the uterine serpins diverged from other serpins prior to the divergence of the mammals from other vertebrates. The porcine uterine serpins are paralogs that diverged from a single common ancestor within the Sus genus after pigs separated from other artiodactyls. The uterine serpins contain several protein kinase C and tyrosine kinase phosphorylation sites. These sites may be important for the lymphocyte-inhibitory activity of OvUS if, like other basic proteins, OvUS can cross the cell membrane of an activated lymphocyte. Internalized OvUS could serve as an alternative target to protein kinases important for the mitogenic response to antigens.

Amino Acid Sequence↗
PubMed1990

Phylogenetic placement of the Spirosomaceae.

Comparative analysis of 16S rRNA sequences shows that the family Spirosomaceae belongs within the eubacterial phylum defined by the flavobacteria and bacteriodes. Its constituent genera, Spirosoma, Flectobacillus, and Runella form a monophyletic grouping therein. The phylogenetic assignment is based not only upon evolutionary distance analysis, but also upon sequence signatures and higher order structural synapomorphies in 16S rRNA. Another genus peripherally associated with the Spirosomaceae, Ancylobacter ("Microcyclus"), does not cluster with the flavobacteria and their relatives, but rather belongs to the alpha subdivision of the purple bacteria.

Bacteria↗
PubMed2001

Analysis of the structure and expression pattern of MRP7 (ABCC10), a new member of the MRP subfamily.

The MRP subfamily of ABC transporters currently consists of at least six members, several of which have been demonstrated to transport amphipathic anions and to confer in vitro resistance to chemotherapeutic agents. In searching the data bases we identified the product of a cDNA sequencing project that bears significant similarity to MRP subfamily transporters. In this report the predicted coding sequence, protein product and expression pattern of this cDNA, termed MRP7, are analyzed. The MRP7 cDNA sequence encodes a 1492 amino acid ABC transporter whose structural architecture resembles that of MRP1, MRP2, MRP3, and MRP6, in that its transmembrane helices are arranged in three membrane spanning domains. However, in contrast to the latter transporters, a conserved N-linked glycosylation site is not found at the N-terminus of MRP7. Comparisons of the MRP7 amino acid sequence indicated that while it is most closely related to other MRP subfamily members, its degree of relatedness is the lowest of any of the known MRP-related transporters. The integrity of the predicted MRP7 coding sequence was confirmed by the synthesis of an approximately 158 kDa protein in reticulocyte lysates programmed with the MRP7 cDNA. While MRP7 transcript was detected in a variety of tissues by RT/PCR, it was not readily detectable by RNA blot analysis, suggesting that it is expressed at low levels in these tissues. Fluorescence in situ hybridization indicated that MRP7 maps to chromosome 6p12-21, in proximity to several genes associated with glutathione conjugation and synthesis. On the basis of these findings and evolutionary cluster analysis, we conclude that MRP7 is a member of the MRP subfamily of amphipathic anion transporters.

ATP-Binding Cassette Transporters↗
PubMed2006

Influence of metabolic network structure and function on enzyme evolution.

BACKGROUND: Most studies of molecular evolution are focused on individual genes and proteins. However, understanding the design principles and evolutionary properties of molecular networks requires a system-wide perspective. In the present work we connect molecular evolution on the gene level with system properties of a cellular metabolic network. In contrast to protein interaction networks, where several previous studies investigated the molecular evolution of proteins, metabolic networks have a relatively well-defined global function. The ability to consider fluxes in a metabolic network allows us to relate the functional role of each enzyme in a network to its rate of evolution. RESULTS: Our results, based on the yeast metabolic network, demonstrate that important evolutionary processes, such as the fixation of single nucleotide mutations, gene duplications, and gene deletions, are influenced by the structure and function of the network. Specifically, central and highly connected enzymes evolve more slowly than less connected enzymes. Also, enzymes carrying high metabolic fluxes under natural biological conditions experience higher evolutionary constraints. Genes encoding enzymes with high connectivity and high metabolic flux have higher chances to retain duplicates in evolution. In contrast to protein interaction networks, highly connected enzymes are no more likely to be essential compared to less connected enzymes. CONCLUSION: The presented analysis of evolutionary constraints, gene duplication, and essentiality demonstrates that the structure and function of a metabolic network shapes the evolution of its enzymes. Our results underscore the need for systems-based approaches in studies of molecular evolution.

Amino Acid Substitution↗
PubMed2006

Genomics of the evolutionary process.

Comparative analysis of genome sequences has become the primary means by which functional elements are first identified, often preceding even the identification of their function. Although this approach capitalizes on the conservation of homologous functions, it has also been successful in identifying evolutionary novelties, including new genes and pathways. As I discuss here, the analysis of multiple alignments of sequences from species on a known phylogeny has provided rich detail about the heterogeneities in the process of genome changes. Inferences of positive selection acting on protein-encoding genes have provided clues about the role of adaptive evolution in the past. These methods also identify negatively selected genes, providing some clue to genes that are most likely to be mutable to a disease-causing state.

Adaptation, Biological↗
PubMed2006

The logic of the stimulus.

This paper examines the contribution of stimulus processing to animal logics. In the classic functionalist S-O-R view of learning (and cognition), stimuli provide the raw material to which the organism applies its cognitive processes-its logic, which may be taxon-specific. Stimuli may contribute to the logic of the organism's response, and may do so in taxon-specific ways. Firstly, any non-trivial stimulus has an internal organization that may constrain or bias the way that the organism addresses it; since stimuli can only be defined relative to the organism's perceptual apparatus, and this apparatus is taxon-specific, such constraints or biases will often be taxon-specific. Secondly, the representation of a stimulus that the perceptual system builds, and the analysis it makes of this representation, may provide a model for the synthesis and analysis done at a more cognitive level. Such a model is plausible for evolutionary reasons: perceptual analysis was probably perfected before cognitive analysis in the evolutionary history of the vertebrates. Like stimulus-driven analysis, such perceptually modelled cognition may be taxon-specific because of the taxon-specificity of the perceptual apparatus. However, it may also be the case that different taxa are able to free themselves from the stimulus logic, and therefore apply a more abstract logic, to different extents. This thesis is defended with reference to two examples of cases where animals' cognitive logic seems to be isomorphic with perceptual logic, specifically in the case of pigeons' attention to global and local information in visual stimuli, and dogs' failure to comprehend means-end relationships in string-pulling tasks.

Animals↗
PubMed2001

Microevolutionary studies in nematodes: a beginning.

Comparisons between related species often allow the detailed genetic analysis of evolutionary processes. Here we advocate the use of the nematode Caenorhabditis elegans (and several other rhabditid species) as model systems for microevolutionary studies. Compared to Drosophila species, which have been a mainstay of such studies, C. elegans has a self-fertilizing mode of reproduction, a shorter life cycle and a convenient cell-level analysis of phenotypic variation. Data concerning its population genetics and ecology are still scarce, however. We review molecular, behavioral and developmental intraspecific polymorphisms for populations of C. elegans, Oscheius sp. 1 and Pristionchus pacificus. Focusing on vulval development, which has been well characterized in several species, we discuss relationships between patterns of variations: (1) for a given genotype (developmental variants), (2) after mutagenesis (mutability), (3) in different populations of the same species (polymorphisms) and (4) between closely related species. These studies have revealed that evolutionary variations between sister species affect those characters that show phenotypic developmental variants, that are mutable and that are polymorphic within species.

Animals↗
PubMed2006

Associations between milk performance traits in Holstein cows and 16 candidate SNPs identified by arrayed primer extension (APEX) microarray.

An oligonucleotide microarray-which allows for parallel genotyping of many SNPs in genes involved in cow milk protein biosynthesis-was used to identify which of the 16 candidate SNPs are associated with milk performance traits in Holstein cows. Four hundred cows were genotyped by the developed and validated microarray. Significant associations were found between four single SNPs, namely DGAT1 (acyloCoA:diacylglycerol acyltransferase), LTF (lactoferrin), CSN3 (kappa-casein), and GHR (growth hormone receptor) and with fat and protein yield and percentage. Many significant associations between combined genotypes (two SNPs) and milk performance traits were found. The associations between the combined genotypes DGAT1/LTF and DGAT1/LEPTIN analyzed traits are presented as examples. The microarray based on APEX (Arrayed Primer Extension) is a fast and reliable method for multiple SNP analysis of potential application in marker-assisted selection. After further development, the chip may prospectively be used for dairy cattle paternity analysis and evolutionary studies.

Animals↗
PubMed2000

Papio cynocephalus endogenous retrovirus among old world monkeys: evidence for coevolution and ancient cross-species transmissions.

To study the evolutionary history of Papio cynocephalus endogenous retrovirus (PcEV), we analyzed the distribution and genetic characteristics of PcEV among 17 different species of primates. The viral pol-env and long terminal repeat and untranslated region (LTR-UTR) sequences could be recovered from all Old World species of the papionin tribe, which includes baboons, macaques, geladas, and mangabeys, but not from the New World monkeys and hominoids we tested. The Old World genera Cercopithecus and Miopithecus hosted either a PcEV variant with an incomplete genome or a virus with substantial mismatches in the LTR-UTR. A complete PcEV was found in the genome of Colobus guereza-but not in Colobus badius-with a copy number of 44 to 61 per diploid genome, comparable to that seen in papionins, and with a sequence most closely related to a virus of the papionin tribe. Analysis of evolutionary distances among PcEV sequences for synonymous and nonsynonymous sites indicated that purifying selection was operational during PcEV evolution. Phylogenetic analysis suggested that possibly two subtypes of PcEV entered the germ line of a common ancestor of the papionins and subsequently coevolved with their hosts. One strain of PcEV was apparently transmitted from a papionin ancestor to an ancestor of the central African lowland C. guereza.

Animals↗
PubMed1994

Evolutionary conservation of chymotrypsinogen gene: genomic analysis and protein modeling.

Chymotrypsinogen is widely present in various animal pancreases. To study evolutionary relationship of chymotrypsinogen gene in species, we used a cDNA probe of human prechymotrypsinogen to investigate the species distribution of chymotrypsinogen gene, and designed oligodeoxynucleotide primers to investigate the genomic organization in the three domains of active sites. The genomic analyses showed that chymotrypsinogen gene is evolutionary conserved in species. On the basis of the deduced amino acid residues, a three-dimensional model for human chymotrypsinogen was further built by computer graphics. The model showed high similarity to the X-ray crystal structure of bovine chymotrypsinogen A, thus, demonstrated that the three-dimensional structure is more conserved in evolution than protein sequences.

Animals↗
PubMed1984

[The deterministic concept of human diseases].

Human disease is a complex systemic event, the theoretical analysis of which requires application of the methodological appratus of investigation. As such, the authors used the concept of Marxist-Leninist determinism. The latter is a system of universal interconnections and causative dependence of natural events, society, and human diseases in particular. Analysis of human diseases from the position of the Marxist-Leninist theory of determinism is one of the basic problems of the theory of pathology. A logical analysis of evolutionary, systemic, morphological and causative determinism is given which characterizes on the whole human diseases.

Adaptation, Physiological↗
PubMed1992

A nonstationarity test for the spectral analysis of physiological time series with an application to respiratory sinus arrhythmia.

The spectral analysis of time series requires the signal to be at least weakly stationary; i.e., the mean, (co-) variance, and spectrum of the time series should not vary from segment to segment. It is commonly assumed that psychophysiological time series are not stationary. This study introduces a nonstationarity test to the psychophysiological literature, which is derived from evolutionary spectral analysis. Basically, the test consists of a double window technique in both the time and frequency domains, leading to a two-way analysis of variance for times and frequencies. In the current study, the nonstationarity test is applied to heart rate data obtained in a typical psychophysiological setting. Heart rate and respiration were measured in four age groups under four conditions--rest, paced breathing, vigilance, and reaction time. The results indicate that only few physiological time series were completely stationary. However, for every subject, and in every condition stationary stretches could be found that were long enough to apply spectral analysis. Spectral measures (power, coherence, and phase spectra) were then compared for stationary parts of the data and the total data. This comparison indicated that nonstationarity affects all spectral measures. Most importantly, Stationarity x Task Condition x Frequency Band interactions were observed for coherence and phase spectra, and there were significant interactions with age for each of the spectral indices. These findings suggest that nonstationarity may result in biased outcomes of significance tests of the effects of task manipulations on the spectral indices of cardiac time series. Thus, it was concluded that the stationarity test should be routinely applied in the spectral analysis of physiological time series. In addition, it was suggested that the nonstationarity test has an even wider range of application that might be of interest to the psychophysiologist.

Adult↗