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PubMed1992

Molecular cloning and characterization of the t(2;14) translocation associated with childhood chronic lymphocytic leukemia.

Two rare cases of chronic lymphocytic leukemia (CLL) in children, patients AS and LH, have been found to be associated with a unique chromosomal translocation, t(2;14)(p13;q32). Previous studies have shown the breakpoints of this translocation to be in the gamma 2 switch region of the Ig heavy-chain locus on chromosome 14 and in an uncharacterized region of chromosome 2. We have cloned and characterized the translocation breakpoints to examine the possibility that an oncogene contributed to the pathogenesis of these cases of CLL. Sequence analysis of AS and LH breakpoints established that the chromosome 2 breakage in the two patients occurred only 38 bp apart and within a strong non-methylated CpG island. Furthermore, human probes from the region cross-hybridized to other species, indicating strong evolutionary conservation. Northern analysis using the chromosome 2 probes detected a 2.85-kb transcript in the tumor cells and in a CD5+ B-cell line. These data suggest that a potential oncogene located near the 2p13 breakpoint may have been activated by the t(2;14) translocation in these two cases of chronic lymphocytic leukemia.

Alleles↗
PubMed2002

Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover.

Comparisons between human and rodent DNA sequences are widely used for the identification of regulatory regions (phylogenetic footprinting), and the importance of such intergenomic comparisons for promoter annotation is expanding. The efficacy of such comparisons for the identification of functional regulatory elements hinges on the evolutionary dynamics of promoter sequences. Although it is widely appreciated that conservation of sequence motifs may provide a suggestion of function, it is not known as to what proportion of the functional binding sites in humans is conserved in distant species. In this report, we present an analysis of the evolutionary dynamics of transcription factor binding sites whose function had been experimentally verified in promoters of 51 human genes and compare their sequence to homologous sequences in other primate species and rodents. Our results show that there is extensive divergence within the nucleotide sequence of transcription factor binding sites. Using direct experimental data from functional studies in both human and rodents for 20 of the regulatory regions, we estimate that 32%-40% of the human functional sites are not functional in rodents. This is evidence that there is widespread turnover of transcription factor binding sites. These results have important implications for the efficacy of phylogenetic footprinting and the interpretation of the pattern of evolution in regulatory sequences.

Animals↗
PubMed2006

Association of single-nucleotide polymorphisms in the suppressor of cytokine signaling 2 (SOCS2) gene with type 2 diabetes in the Japanese.

Several previous linkage scans in type 2 diabetes (T2D) families indicated a putative susceptibility locus on chromosome 12q15-q22, while the underlying gene for T2D has not yet been identified. We performed a region-wide association analysis on 12q15-q22, using a dense set of >500 single-nucleotide polymorphisms (SNPs), in 1492 unrelated Japanese individuals enrolled in this study. We identified an association between T2D and a haplotype block spanning 13.6 kb of genomic DNA that includes the entire SOCS2 gene. Evolutionary-based haplotype analysis of haplotype-tagging SNPs followed by a "sliding window" haplotypic analysis indicated SNPs that mapped to the 5' region of the SOCS2gene to be associated with T2D with high statistical significance. The SOCS2 gene was expressed ubiquitously in human and murine tissues, including pancreatic beta-cell lines. Adenovirus-mediated expression of the SOCS2 gene in MIN6 cells or isolated rat islets significantly suppressed glucose-stimulated insulin secretion. Our data indicate that SOCS2 may play a role in susceptibility to T2D in the Japanese.

Adenoviridae↗
PubMed2006

Partnering with patients--a concept ready for action.

AIM: This paper is a report of a concept analysis of partnership within the context of a professional-patient relationship. BACKGROUND: The concept of partnership has been previously characterized as immature, with a need for further consensus and consistency. Critical attributes previously reported include relationship, power sharing and negotiation, with empowerment as the primary consequence. METHOD: Rodgers' evolutionary method of analysis for concept development was used to re-examine the concept of partnership. Historical documents and previously published conceptual papers were reviewed for context. A search of multidisciplinary literature published between 2000 and 2004 was undertaken using the keywords of 'partnership' and 'partnering', combined with nurse/professional/physician-client relationship. Attributes, uses, antecedents and consequences were inductively derived from the citations analysed (n = 62). RESULTS: Previous authors affirmed that partnership involves a process and a consistent set of eight attributes. Relationship, shared power, shared decision-making and patient autonomy are attributes that distinguish partnership from other related concepts. Most of the literature, however, consisted of expert opinion or descriptive research. Little progress has been made in applying theory, developing tools to test the process, identifying when partnerships are needed and what specific outcomes occur when they are present. CONCLUSION: Partnerships between healthcare providers and patients develop over time. They are created to support patients in having a greater voice in their care and to empower them in self-management. A descriptive model of partnership is proposed to support researchers in generating or applying existing theory to the development of research designs and tools that could test how this process actually works.

Concept Formation↗
PubMed2006

Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases.

MOTIVATION: According to the models of divergent molecular evolution, the evolvability of new protein function may depend on the induction of new phenotypic traits by a small number of mutations of the binding site residues. Evolutionary relationships between protein kinases are often employed to infer inhibitor binding profiles from sequence analysis. However, protein kinases binding profiles may display inhibitor selectivity within a given kinase subfamily, while exhibiting cross-activity between kinases that are phylogenetically remote from the prime target. The emerging insights into kinase function and evolution combined with a rapidly growing number of publically available crystal structures of protein kinases complexes have motivated structural bioinformatics analysis of sequence-structure relationships in determining the binding function of protein tyrosine kinases. RESULTS: In silico profiling of Imatinib mesylate and PD-173955 kinase inhibitors with protein tyrosine kinases is conducted on kinome scale by using evolutionary analysis and fingerprinting inhibitor-protein interactions with the panel of all publically available protein tyrosine kinases crystal structures. We have found that sequence plasticity of the binding site residues alone may not be sufficient to enable protein tyrosine kinases to readily evolve novel binding activities with inhibitors. While evolutionary signal derived solely from the tyrosine kinase sequence conservation can not be readily translated into the ligand binding phenotype, the proposed structural bioinformatics analysis can discriminate a functionally relevant kinase binding signal from a simple phylogenetic relationship. The results of this work reveal that protein conformational diversity is intimately linked with sequence plasticity of the binding site residues in achieving functional adaptability of protein kinases towards specific drug binding. This study offers a plausible molecular rationale to the experimental binding profiles of the studied kinase inhibitors and provides a theoretical basis for constructing functionally relevant kinase binding trees.

Amino Acid Sequence↗
PubMed2000

Evolutionary dynamics of self-incompatibility alleles in Brassica.

Self-incompatibility in Brassica entails the rejection of pollen grains that express specificities held in common with the seed parent. In Brassica, pollen specificity is encoded at the multipartite S-locus, a complex region comprising many expressed genes. A number of species within the Brassicaceae express sporophytic self-incompatibility, under which individual pollen grains bear specificities determined by one or both S-haplotypes of the pollen parent. Classical genetic and nucleotide-level analyses of the S-locus have revealed a dichotomy in sequence and function among S-haplotypes; in particular, all class I haplotypes show dominance over all class II haplotypes in determination of pollen specificity. Analysis of an evolutionary model that explicitly incorporates features of the Brassica system, including the class dichotomy, indicates that class II haplotypes may invade populations at lower rates and decline to extinction at higher rates than class I haplotypes. This analysis suggests convergence to an evolutionarily persistent state characterized by the maintenance in high frequency of a single class II haplotype together with many class I haplotypes, each in low frequency. This expectation appears to be consistent with empirical observations of high frequencies of relatively few distinct recessive haplotypes.

Alleles↗
PubMed2004

A Bayesian statistical analysis of human T-cell lymphotropic virus evolutionary rates.

HTLV is a genetically-stable retrovirus that is considered to have evolved partly in concert with human migrations. Its rate of evolution is low and therefore, difficult to estimate reliably. In the first part of this study, we provide an improved estimate of HTLV evolutionary rate using anthropological calibration of phylogenetic nodes. We investigate two different anthropological calibrations using a Bayesian method that implements a relaxed molecular clock model and can combine data from multiple genes. The analysis shows that the two calibrations are compatible. In the second part, we develop a Bayesian statistical model to combine and compare the anthropology-based estimates of evolutionary rate with a rate recently calculated using pedigree data from vertically HTLV-infected families. We compare the statistical power of the two estimates and show that the current pedigree estimate, although resulting in considerably higher evolutionary rates, is too statistically weak to warrant a re-examination of the commonly used anthropology-based estimates. Statistical uncertainty burdens HTLV rate estimates based on both anthropological calibrations and on pedigree data; the former method rests on an untested assumption, whilst that latter is affected by small sample sizes.

Bayes Theorem↗
PubMed1989

Concepts, analysis and the development of nursing knowledge: the evolutionary cycle.

Nursing currently evidences concern with the development and clarification of its knowledge base. As a part of this focus, attention has often been directed towards concepts and methods of clarification. Although the method of concept analysis has been employed often to provide conceptual clarity, the foundations and implications of conducting an analysis of a concept have not been well explored in nursing. In this article, the philosophical foundations of the approach to concept analysis popularized by Walker & Avant (1983) are examined. Modifications of this method are offered, along with a framework for interpreting the findings of an analysis. The result is a view of concepts and an approach to analysis that may be of use in the clarification of a variety of concepts of interest in nursing.

Humans↗
PubMed2004

Opportunity for natural selection in a Basque population and its secular trend: evolutionary implications of epidemic mortality.

Analysis of the interaction between mortality patterns and opportunity for natural selection could help to elucidate potential evolutionary implications of epidemic mortality. In this paper secular trends are studied in relation to Crow's index (It) and its components of mortality (Im) and fertility (If), using parish records for family reconstitution in a Basque population. A principal components analysis (91% of the variance accounted for) showed marked quantitative and qualitative variations of Im and If depending on the stage of demographic transition of the population analyzed: In pretransitional societies the opportunity for natural selection is determined mainly by differential prereproductive mortality, whereas in posttransitional societies selection resulting from differential fertility plays a key role. The highest values for the mortality component (range 0.81-1.26) and for the relative contribution of Im, to It (range 47.1-57.2%) were observed in periods with a high incidence of infectious diseases and when the most severe mortality crises were detected (1830-1859, 1860-1889, and 1890-1919). A differential incidence of epidemic mortality was also found at prereproductive ages (before 16 years) and at reproductive ages (16-45 years), which provides strong support for the idea of the long-term genetic consequences of mortality crises.

Adolescent↗
PubMed2000

Comparative molecular phylogeography of North American softshell turtles (Apalone): implications for regional and wide-scale historical evolutionary forces.

We use a comparative analysis of partial cytochrome b sequences to evaluate the evolutionary forces shaping wide-scale phylogeographic patterns of all three North American softshell turtles (Apalone ferox, A. mutica, and A. spinifera). The overall phylogeographic patterns are concordant with results from both extensive regional studies of southeastern species, implicating historical vicariant processes during the Pliocene and Pleistocene, and investigations of more northerly distributed species, indicating a bottleneck effect of recent dispersal into postglacial habitat. We also resolved a novel, shared genetic break between northern-western and southeastern populations within both A. mutica and A. spinifera, demonstrating the value of using widespread taxa to evaluate both regional and wider scale phylogeographic patterns. The extensive phylogenetic structure and sequence divergences within both A. mutica and A. spinifera contrast sharply with most previous studies of turtles and with the hypothesis that turtles in general have slow rates of mtDNA evolution.

Animals↗
PubMed2025

Global Evolution and Transmission Dynamics of Enterovirus D68.

Enterovirus D68 (EV-D68), a serotype of the enterovirus species D, has garnered significant attention due to outbreaks reported in 2014, 2016, and 2018. In this study, 36 Chinese EV-D68 strains were isolated, sequenced, and combined with all EV-D68 VP1 sequences from GenBank to form a data set of 1679 sequences. This data set served as the basis for phylogenetic, evolutionary dynamics, phylogeographic, and key amino acid site mutation analyses of EV-D68. Based on the VP1 region, EV-D68 is classified into four genotypes (A-D), and seven subgenotypes (B1-B3, D1-D4), with B3 and D3 being the predominant subgenotypes. Bayesian skyline plots indicated that genotypes B and D experienced multiple population expansions, aligning with reported EV-D68 outbreaks. Phylogeographic analyses of the B3 subgenotypes revealed sequences from Europe and North America clustering into a single evolutionary branch, suggesting significant transmission between these regions. Additionally, mutation analysis identified VP1-98 as a high-frequency mutation site, differing significantly between the previously prevalent A and C genotypes and the currently prevalent B and D genotypes. However, the functional implications of this mutation require further investigation. This study provides a solid theoretical basis for epidemiological research, disease surveillance, and prevention efforts related to EV-D68.

Enterovirus Infections↗
PubMed2003

Evolutionary coherence of the mammalian amygdala.

Despite great interest in the role of the amygdala in animal and human behaviour, its very existence as a structurally and functionally unified brain component has been questioned, on the grounds that cell groups within it display divergent pharmacological and connectional characteristics. We argue that the question of whether particular brain nuclei constitute a valid structural and functional unit is inherently an evolutionary question, and we present a method for answering it. The method involves phylogenetic analysis of comparative data to determine whether or not separate regions of the putative brain structure show statistically correlated evolution. We find that, in three separate groups of mammals (primates and two groups of insectivores), evolutionary changes in the volumes of amygdala components are strongly correlated, even after controlling for volumetric change in a wide range of limbic and other brain structures. This allows us to reject the strong claim that the amygdala is neither a structural nor a functional unit, and demonstrates the importance of evolutionary analysis in resolving such issues in systems neuroscience.

Amygdala↗
PubMed2004

Haplotypic analyses of the IGF2-INS-TH gene cluster in relation to cardiovascular risk traits.

The IGF2-INS-TH genomic region has been implicated in various common disorders including the metabolic syndrome, type 2 diabetes and coronary heart disease (CHD). Here we present detailed haplotype analysis of 2743 males 51-62 years old in relation to body weight and composition, blood pressure (BP) and plasma triglycerides (TG). Use of the total data set was complicated by the number of loci typed, missing data, multi-allelic markers and continuous trait phenotypes. Different algorithms and subsets of the data were analysed using the programmes haplotype trend regression, haplo.score, evolutionary-based haplotype analysis package and Phase, in conjunction with SPSS. Ten haplotypes designated in frequency order *1(20.0%) to *10(3.4%) represented 89% of all haplotypes. Haplotype *5 protected against obesity. Haplotype *4 carriers exhibited elevated BP and fat mass, haplotype *6 was associated with raised plasma TG levels. Haplotype *8 also showed similar magnitude effects as *4. These cohort trait analyses and detailed haplotypic analyses enable integration with published case data. Haplotypes *4, *6 and *8 are the only INS VNTR class III-bearing haplotypes, although differing in flanking haplotype, whereas *5 displays unique features in all three genes (with significant commonality with type 1 diabetes-predisposition haplotypes). We propose that long repeat insertion in the insulin gene promoter ('class III'), reported to result in low insulin production, predisposes to the metabolic syndrome features of elevated BP, fat mass or TG level, therefore appearing more frequently in type 2 diabetic, polycystic ovary syndrome and CHD cases. The functional element(s) of *5 for weight-lowering could reside in any of the three genes.

Aged↗
PubMed2006

Tempo, mode and phylogenetic associations of relative embryo size evolution in angiosperms.

Relative embryo size (E : S, the ratio of embryo to seed) is a key trait related to germination ecology and seed plant evolution. A small, underdeveloped embryo is a primitive feature of angiosperms, which has led to the hypothesis that an evolutionary trend towards increasing E : S has occurred. Here, I examine first the tempo and mode of E : S evolution in angiosperms; then I test for phylogenetic associations of E : S with traits hypothetically related to anagenetic (germination time) and cladogenetic (number of species per family and differential speciation) change, and finally I test the existence of a directional increasing trend in E : S. The analysis of the evolutionary tempo suggests that E : S changed very fast early in evolutionary time and remained stable later, which is consistent with early radiations and fits well with the history of angiosperms consisting of rapid spread associated with great diversification rates soon after their origin. E : S evolution in angiosperms has not followed a punctuational mode of evolution but a scaled-gradualism evolution in which stasis has occurred in longer branches of the phylogeny. An evolutionary trend towards increasing E : S has not been actively driven by anagenesis nor cladogenesis, although large E : S is associated with high levels of diversification (i.e. number of species per family). This rapid ecological diversification occurring in the early radiation probably produced an increasing phenotypic variance in the E : S. Because the ancestral embryo was so small, an increase in variance might have produced a passive trend towards the only direction allowed for the ancestral embryo to evolve. Thus, a passive diffusion away from a lower bound may explain the average increase in E : S.

Biological Evolution↗
PubMedDate not supplied

Highly divergent actins from karyorelictean, heterotrich, and litostome ciliates.

We have cloned, sequenced, and characterized cDNA of actins from five ciliate species of three different classes of the phylum Ciliophora: Karyorelictea (Loxodes striatus), Heterotrichea (Blepharisma japonicum, Blepharisma musculus), and Litostomatea (Didinium nasutum, Dileptus margaritifer). Loxodes striatus uses UGA as the stop codon and has numerous in-frame UAA and UAG, which are translated into glutamine. The other four species use UAA as the stop codon and have no in-frame UAG nor UGA. The putative amino acid sequences of the newly determined actin genes were found to be highly divergent as expected from previous findings of other ciliate actins. These sequences were also highly divergent from other ciliate actins, indicating that actin genes are highly diverse even within the phylum Ciliophora. Phylogenetic analysis showed high evolutionary rate of ciliate actins. Our results suggest that the evolutionary rate was accelerated because of the differences in molecular interactions.

Actins↗
PubMed1986

Primary structure of the reaction center from Rhodopseudomonas sphaeroides.

The reaction center is a pigment-protein complex that mediates the initial photochemical steps of photosynthesis. The amino-terminal sequences of the L, M, and H subunits and the nucleotide and derived amino acid sequences of the L and M structural genes from Rhodopseudomonas sphaeroides have previously been determined. We report here the sequence of the H subunit, completing the primary structure determination of the reaction center from R. sphaeroides. The nucleotide sequence of the gene encoding the H subunit was determined by the dideoxy method after subcloning fragments into single-stranded M13 phage vectors. This information was used to derive the amino acid sequence of the corresponding polypeptide. The termini of the primary structure of the H subunit were established by means of the amino and carboxy terminal sequences of the polypeptide. The data showed that the H subunit is composed of 260 residues, corresponding to a molecular weight of 28,003. A molecular weight of 100,858 for the reaction center was calculated from the primary structures of the subunits and the cofactors. Examination of the genes encoding the reaction center shows that the codon usage is strongly biased towards codons ending in G and C. Hydropathy analysis of the H subunit sequence reveals one stretch of hydrophobic residues near the amino terminus; the L and M subunits contain five such stretches. From a comparison of the sequences of homologous proteins found in bacterial reaction centers and photosystem II of plants, an evolutionary tree was constructed. The analysis of evolutionary relationships showed that the L and M subunits of reaction centers and the D1 and D2 proteins of photosystem II are descended from a common ancestor, and that the rate of change in these proteins was much higher in the first billion years after the divergence of the reaction center and photosystem II than in the subsequent billion years represented by the divergence of the species containing these proteins.

Amino Acid Sequence↗
PubMed1995

Evolutionary history of the ligand-gated ion-channel superfamily of receptors.

The fast-acting ligand-gated ion channels (LGICs) constitute a group that encompasses nicotinic ACh, 5-HT3, GABAA and glycine receptors. Undoubtedly, they all share a common evolutionary ancestor, and the group can therefore be considered to be a gene superfamily. Because the members of the superfamily are all receptors, it is reasonable to suppose that their common ancestor must also have been some type of receptor, and because the receptors are made of similar subunits, the ancestor was probably homo-oligomeric. Although we failed to find a group of proteins that are related evolutionarily to this superfamily, the analysis of the evolutionary relationships within the superfamily is possible and can give rise to information about the evolution of the structure and function of present-day receptors and indeed of the nervous system itself.

Animals↗
PubMed2005

Cloning and sequence analysis of the beta2-microglobulin transcript from flounder, Paralichthys olivaceous.

Beta2-microglobulin (beta2M) is a protein found free-form in the serum or on the cell surface non-covalently associated with the alpha-chain of the class I major histocompatibility (MHC-I) complex. The full-length cDNA containing beta2M was cloned from flounder, Paralichthys olivaceous. The transcript consists of 1610 nucleotides (nts), including an open reading frame (ORF) of 384 nts encoding a polypeptide of 128 amino acids. The amino acid sequence of beta2M in flounder is 59, 57, 56, and 48% conserved in catfish, rainbow trout, zebrafish, and humans, respectively. Genomic Southern hybridization suggested the presence of a single copy of beta2M in the flounder genome, and reverse transcription-polymerase chain reaction (RT-PCR) and Northern blot analysis detected the beta2M transcript in the head kidney, spleen, body kidney, liver, and muscle tissues of the flounder. PCR amplification and sequence analysis revealed the lack of an intron in the beta2M gene. The phylogenetic analysis confirmed the evolutionary diversion of the beta2M protein among warm-blooded vertebrates and fish, and the separation between freshwater and seawater fish.

Amino Acid Sequence↗