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PubMed1990

Fructose-2,6-bisphosphate in control of hepatic gluconeogenesis. From metabolites to molecular genetics.

Hormonal regulation of hepatic gluconeogenic pathway flux is brought about by phosphorylation/dephosphorylation and control of gene expression of several key regulatory enzymes. Regulation by cAMP-dependent phosphorylation occurs at the level of pyruvate kinase and 6-phosphofructo-2-kinase (6PF-1-K)/fructose-2,6-bisphosphatase (Fru-2,6-P2ase). The latter is a unique bifunctional enzyme that catalyzes both the synthesis and degradation of fructose-2,6-bisphosphate (Fru-2,6-P2), which is an activator of 6PF-1-K and an inhibitor of Fru-1,6-P2ase. The bifunctional enzyme is a homodimer whose activities are regulated by cAMP-dependent protein kinase-catalyzed phosphorylation at a single NH2-terminal seryl residue/subunit, which results in activation of the Fru-2,6-P2ase and inhibition of the PF-1-K reactions. Hormone-mediated changes in the phosphorylation state of the bifunctional enzyme are responsible for acute regulation of Fru-2,6-P2 levels. 6PF-2-K/Fru-2,6-P2ase thus provides a switching mechanism between glycolysis and gluconeogenesis in mammalian liver. Pyruvate kinase is regulated by both phosphorylation and allosteric effectors. Fru-1,6-P2, an allosteric activator, also inhibits cAMP-dependent enzyme phosphorylation, and its steady-state concentration is indirectly determined by the level of Fru-2,6-P2. Therefore, acute regulation of both pyruvate kinase and the bifunctional enzyme provide coordinated control at both the pyruvate/phosphoenolpyruvate and Fru-6-P/Fru-1,6-P2 substrate cycles. The Fru-2,6-P2 system is also subject to complex multihormonal long-term control through regulation of 6 PF-2-K/Fru-2,6-P2ase gene expression. Glucocorticoids are the major factor in turning on this gene in liver, but insulin is also a positive effector. cAMP prevents the effects of glucocorticoids and insulin. Although Fru-2,6-P2 plays a key role in the regulation of carbon flux in the gluconeogenic pathway, the regulation of this flux depends on several factors and regulation of other key enzymes whose importance varies depending on the dietary and hormonal status of the animal. Molecular cloning of the cDNA encoding PF-2-K/Fru-2,6-P2ase has elucidated its structure and permitted analysis of its evolutionary origin as well as its tissue distribution and control of its gene expression. The rat liver and skeletal muscle isoforms arose by alternative splicing of a single gene. The muscle form differs from the liver form only at the NH2-terminal and does not have a cAMP-dependent protein kinase phosphorylation site. The hepatic enzyme subunit consists of 470 amino acids.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMedDate not supplied

[Features of cytochrome P450 evolution].

It is shown that the process of mutation in the CYP2 family of the superfamily of P450 cytochromes is species-specific (man, rat, and mouse). It is also shown that, within one species (rat), different families (CYP2 and CYP11) have different mutation spectra, indicating a high specificity of the mutation process for the families of cytochrome genes. A similar specificity was demonstrated for five families (CYP1, CYP2, CYP6, CYP7, CYP11) as compared with globins and prions. The analysis of the evolutionary mutation pattern, and the pattern of pseudogenes and damaged alleles of the CYP21 family (found in patients with congenital adrenal hyperplasia) does not confirm the widely accepted hypothesis that mutations arising in pseudogenes are transduced to normal alleles of the CYP21 gene through gene conversion.

Animals↗

PubMed2000

[Genetic evolution under vaccine pressure: the Bordetella pertussis model].

A possible genetic selective pressure related to the long-term use of vaccines has been the object of recent theoretical thought and publications. For more than thirty years, an effective vaccine has been in use against whooping cough on a wide scale basis in several countries. Thus, the Bordetella pertussis model may contribute to the analysis of an evolutionary risk linked to the vaccine. To maintain and improve the control of whooping cough, better vaccination coverage must be achieved in countries where prevalence is low. In countries where high vaccination coverage has been achieved over a long period, a trend toward the resurgence of the disease has been observed. Efforts are therefore now being directed toward primary vaccination and boosters. These two targets require new vaccines with fewer side effects. Outbreaks in highly vaccinated populations have been reported, raising the issues of vaccine efficacy, of the long-term effect of vaccines on the transmission of the disease, and of genetic selective pressure. Time trend modifications of circulating strains related to vaccination practices and vaccine types have been observed and are compatible with a selective pressure of the vaccine on related pathogens. However, evidence for a causal relation is lacking. In order to monitor and understand the various effects the vaccine may be having on the effectiveness of immunisation against whooping cough, further surveillance is needed, integrating a standardised characterisation of circulating strains and vaccines by way of a space-time sampling model.

Biological Evolution↗

PubMed2000

The complementary roles of observation and experiment: Theodosius Dobzhansky's Genetics of Natural Populations IX and XII.

Theodosius Dobzhansky has long been recognized by historians as a pioneer in the combining of the 'field natural history' and 'laboratory experimentalist' traditions in biology (Allen 1994). The following essay analyzes two papers in his well-known Genetics of Natural Populations series, GNP IX and GNP XII, which demonstrate how Dobzhansky combined field and laboratory work in the pursuit of an evolutionary question. The analysis reveals the multiple and complementary roles field observations and experiments played in his investigations. But it also identifies several interpretive problems associated with the use of intervention that limited the effectiveness of his approach. The essay argues that these problems reflect a fundamental tension between the amount of control Dobzhansky had over the circumstances of his experiments and the applicability of his results to natural populations. It concludes that this trade-off represents an important distinction between experiments in biology and most other sciences.

Animals↗

PubMed1992

The nucleotide sequence of 5S rRNA from bovine liver.

We have determined the nucleotide sequence of ribosomal 5S RNA from bovine liver. The comparison of this sequence with those from other eukaryotic sources shows that a common secondary structure model for all eukaryotic 5S rRNAs may exist. Analysis of the evolutionary conserved nucleotides in metazoan 5S rRNAs suggests that the tertiary interactions, proposed earlier for plant 5S rRNA, are also possible.

Animals↗

PubMedDate not supplied

[Highly pathogenic avian influenza virus inducing influenza pneumonia in humans].

The human disease caused by avian influenza virus in South Asia is a typical example of emerging infection resulting from transmission of a known causative agent to a new host. The first cases with a comparatively high level of lethality rates among patients were registered in 1997 and 1999. The situation is a special phenomenon in epidemiology which requires deep evolutionary and ecological analysis, as well as theoretical interpretation. With the example of avian influenza virus in Western Europe and South Asia in 2003-2004 the practical expediency of modern concepts "foci versus epidemics" and "eradication versus vaccination" is now evident.

Americas↗

PubMed1985

[Genesis of biorhythms of the cardiointervalogram in its evolutionary aspect].

Statistical characteristics and latent biorhythms of the frog, rabbit and human cardiointervalograms were studied in the volutionary aspect with the aid of ACBT-M 6000 computer. Some mechanisms of temporary organization of the heart rhythm were revealed with regard to the level of organization of biological objects. Evolutionary aspects of analysis of the heart biorhythms provide an approach to their genesis.

Adult↗

PubMed1995

Search for the FSHD gene using cDNA selection in a region spanning 100 kb on chromosome 4q35.

Facioscapulohumeral muscular dystrophy (FSHD) is caused by deletions of 3.3-kb tandemly repeated units contained within a large polymorphic EcoRI fragment close to the telomere of chromosome 4q. Since the rearrangements were assumed to interfere with the structure or function of the putative FSHD gene, the gene search was focused on cosmids containing these repeat units and, in addition, cosmids spanning 75 kb of upstream sequences. cDNA selection hybridization was applied to four overlapping cosmid clones, yielding a total of 150 putative cDNA clones. These clones showed a random distribution across the cosmid contig, except for three regions which contained a much larger number of clones. Nine cDNA clones hybridized to a 2.2-kb EcoRI fragment, located 22 kb centromeric to the 3.3-kb repeated units. This 2.2-kb fragment showed evolutionary conservation, and analysis of the sequence by "GRAIL" predicted the presence of several exons. Transcripts homologous to this fragment could be identified but none of them originated from the 4q35 locus. Strikingly, most clones revealed 4-10 homologous loci, and no single copy clones could be isolated. These findings are in line with earlier observations by fluorescent in situ hybridization (FISH) showing hybridization of individual cosmid clones to multiple chromosomes. The presence of homologous regions on other chromosomes seriously complicates the cloning of the FSHD gene.

Blotting, Northern↗

PubMed1996

Microevolution and genetic affinities among six Amerindian tribes of lower Central America: comparative genetic study of serum proteins.

We evaluate the pattern of genetic variation among native Mesoamerican Amerindians by the construction of a gene frequency map that reflects the past action of evolutionary forces. The analysis is based on the theory that genes of modern human populations carry the encoded history even of humans' remote past and their early wanderings around the globe. We examined the serum proteins TF, PI, F13B and AHSG on 491 samples of 6 Mesoamerican Amerindian tribes (Guaymi, Bribri, Cabecar, Teribe, Guatuso, and Huetar) and 2 tribal mixed samples (Teribe x Guaymi and Bribri x Cabecar). We find a distinct genetic pattern in the examined tribes that clearly separates the Mesoamerican Amerindians from other living Amerindian groups. The proteins, TF, PI, and AHSG proved to be especially rich in special genetically fixed variants and polymorphisms, and F13B proved to be a powerful genetic marker to distinguish human groups. Using Nei's distance D and Mahalanobis's D2, we compared the polymorphisms and allele frequencies at the four serum protein loci to discern degrees of similarity between the samples. These data are presented in the dendrograms computed by average linkage cluster analyses and in two kinds of unrooted phylogenetic trees, neighbor-joining trees and split decompositions. Estimations are made on Hardy-Weinberg equilibrium and on genetic diversity and average heterozygosity index.

Blood Proteins↗

PubMed1998

Matrix metalloproteinases: structures, evolution, and diversification.

A comprehensive sequence alignment of 64 members of the family of matrix metalloproteinases (MMPs) for the entire sequences, and subsequently the catalytic and the hemopexin-like domains, have been performed. The 64 MMPs were selected from plants, invertebrates, and vertebrates. The analyses disclosed that as many as 23 distinct subfamilies of these proteins are known to exist. Information from the sequence alignments was correlated with structures, both crystallographic as well as computational, of the catalytic domains for the 23 representative members of the MMP family. A survey of the metal binding sites and two loops containing variable sequences of amino acids, which are important for substrate interactions, are discussed. The collective data support the proposal that the assembly of the domains into multidomain enzymes was likely to be an early evolutionary event. This was followed by diversification, perhaps in parallel among the MMPs, in a subsequent evolutionary time scale. Analysis indicates that a retrograde structure simplification may have accounted for the evolution of MMPs with simple domain constituents, such as matrilysin, from the larger and more elaborate enzymes.

Amino Acid Sequence↗

PubMed2025

A novel second-generation HIV-1 circulating recombinant form (CRF183_0107) identified among men who have sex with men in China.

OBJECTIVE: This study aimed to report a novel HIV-1 circulating recombinant form (CRF) identified among men who have sex with men (MSM) in China. DESIGN: Viral sequences were isolated from MSM patients, and the recombination and evolutionary histories of this CRF were elucidated through phylogenetic and Bayesian analyses. METHODS: Near full-length genomes (NFLGs) and partial genome sequences were amplified from RNA extracted from plasma samples of three HIV-1 seropositive MSM in Heilongjiang Province, China. Phylogenetic analysis was conducted using FastTree v2.1.9, and recombination analysis was performed using Simplot v3.5.1. The emergence time of the novel CRF was estimated by Bayesian evolutionary analysis using BEAST v1.10.4. RESULTS: Two NFLGs and two partial genome segments were successfully obtained from three MSM participants. This novel CRF was characterized by 12 mosaic gene segments, comprising 6 segments from the CRF01_AE cluster 4 and 6 segments from the CRF07_BC cluster N, and thus was designated as CRF183_0107. The estimated time of origin for the CRF01_AE and CRF07_BC components within CRF183_0107 were approximately 2009.2 and 2012.5, respectively. CONCLUSION: A novel second-generation HIV-1 recombinant, named CRF183_0107, was identified within the MSM population in China. This CRF exemplified the recombination events occurring between the CRF01_AE cluster 4 and the CRF07_BC cluster N during 2009-2012.

Humans↗

PubMed2001

Analysis of Fc gammaRIII and IgG Fc polymorphism reveals functional and evolutionary implications of protein-protein interaction.

Fc gamma receptor III (Fc gammaRIII), a low-affinity receptor for the Fc portion of immunoglobulin G (IgG Fc), targets antigen-antibody complexes in a variety of effector cells of the immune system. We have investigated Fc gammaRIII and IgG Fc polymorphism and made comparative analysis of the functional and evolutionary implications of the interaction between these two molecules. Sequence analysis and comparison of the three-dimensional structure suggest that the C-terminal Ig domain of Fc gammaRIII is associated with the binding of IgG. The polymorphic residues of Fc gammaRIII are mainly located in the region of the C-terminal Ig domain that might be involved in IgG binding. Therefore, polymorphism and functional binding affinity seems to be related to each other as has been increasingly implicated in clinical observations. IgG Fcs, the natural ligand of Fc gammaRs, also exhibit significant polymorphism. Three regions have been identified where polymorphism frequently occurs: the putative FcR binding site, the linker region, and the intermolecular domain-domain interface of the second Ig domain. The putative Fc gammaR binding sites where polymorphic, and isotype-specific residues cluster are consistent with the regions that have been identified by mutagenesis and molecular modeling studies. The polymorphic residues of IgG Fc were mainly located in the molecular surface, which could be used in the recognition of other binding molecules. These observations suggest that polymorphic and isotype-specific residues in IgG Fc are closely related to their function and protein-protein interaction. Therefore, the colocalization of the polymorphic residues of Fc gammaRIII and IgG Fcs at their docking sites implies that the polymorphic residues would affect the IgG-Fc gammaRIII binding interactions to optimize their signaling through evolution.

Amino Acid Sequence↗

PubMed1993

Chloroplast gene sequences and the study of plant evolution.

A large body of sequence data has accumulated for the chloroplast-encoded gene ribulose-1,5-biphosphate carboxylase/oxygenase (rbcL) as the result of a cooperative effort involving many laboratories. The data span all seed plants, including most major lineages from the angiosperms, and as such they provide an unprecedented opportunity to study plant evolutionary history. The full analysis of this large data set poses many problems and opportunities for plant evolutionary biologists and for biostatisticians.

Biological Evolution↗

PubMedDate not supplied

Moving toward peace: an analysis of the concept of a good death.

One of the primary outcomes of end-of-life care should be the experience of a good death by the patient and the family. Yet there is no clear, shared understanding of what a good death is. This analysis of the concept of a good death has been guided by Rodgers' evolutionary method of concept analysis.(1) Forty-two articles were analyzed. There was the strong agreement that the concept of a good death was highly individual, changeable over time, and based on perspective and experience. Medical, nursing, and patient perspectives, as well as literature in sociology, include the following attributes of a good death, listed in order of frequency of appearance in the literature: being in control, being comfortable, sense of closure, affirmation/value of the dying person recognized, trust in care providers, recognition of impending death, beliefs and values honored, burden minimized, relationships optimized, appropriateness of death, leaving a legacy, and family care.

Attitude to Death↗

PubMed1986

Ribosomal RNA phylogenies for the vibrio-enteric group of eubacteria.

Comparisons between the ribonucleotide sequences of 5S rRNAs of the Gram-negative eubacteria indicate that several families, namely Enterobacteriaceae, Vibrionaceae and Aeromonadaceae possess remarkably similar evolutionary histories. A study of the phylogenetic relationships among these groups, through cluster analysis and construction of evolutionary trees, suggests the existence of dissimilar rates of evolution along the several lineages. These dissimilarities are most evident in comparisons between the phylogenetic depths of the Enterobacteriaceae and Vibrionaceae. Detection of disparate rates of evolution, as well as their influence on the interpretation of the natural taxonomy of this group of bacteria, is discussed.

Aeromonas↗

PubMed1983

Species concept and taxonomic principles.

Based on the species concept of changing versus unchanging, the present work deals with the following two problems: First, why would the taxonomic system reflect evolutionary history? Second, how is this effected? Species are changing in the sense that each species has its own characteristics and there is no complete identity between any two species. On the other hand, species are unchanging and each one conserves a set of ancestral characters which allocates its taxonomic position, and this is the reason why the taxonomic system reflects evolutionary history. The taxonomic system is constructed to reflect evolutionary history mainly through the process of character analysis. Combining the viewpoints of cladistics and evolutionary systematics, the writer proposes six rules for character analysis which will provide the basis for analyzing evolutionary history.

Animals↗

PubMed2005

Evolutionary history of the greater white-toothed shrew (Crocidura russula) inferred from analysis of mtDNA, Y, and X chromosome markers.

We investigate the evolutionary history of the greater white-toothed shrew across its distribution in northern Africa and mainland Europe using sex-specific (mtDNA and Y chromosome) and biparental (X chromosome) markers. All three loci confirm a large divergence between eastern (Tunisia and Sardinia) and western (Morocco and mainland Europe) lineages, and application of a molecular clock to mtDNA divergence estimates indicates a more ancient separation (2.25 M yr ago) than described by some previous studies, supporting claims for taxonomic revision. Moroccan ancestry for the mainland European population is inconclusive from phylogenetic trees, but is supported by greater nucleotide diversity and a more ancient population expansion in Morocco than in Europe. Signatures of rapid population expansion in mtDNA, combined with low X and Y chromosome diversity, suggest a single colonization of mainland Europe by a small number of Moroccan shrews >38 K yr ago. This study illustrates that multilocus genetic analyses can facilitate the interpretation of species' evolutionary history but that phylogeographic inference using X and Y chromosomes is restricted by low levels of observed polymorphism.

Africa, Northern↗

PubMed1997

Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence.

The number of distinct functional classes of single-stranded RNAs (ssRNAs) and the number of sequences representing them are substantial and continue to increase. Organizing this data in an evolutionary context is essential, yet traditional comparative sequence analyses require that homologous sites can be identified. This prevents comparative analysis between sequences of different functional classes that share no site-to-site sequence similarity. Analysis within a single evolutionary lineage also limits evolutionary inference because shared ancestry confounds properties of molecular structure and function that are historically contingent with those that are imposed for biophysical reasons. Here, we apply a method of comparative analysis to ssRNAs that is not restricted to homologous sequences, and therefore enables comparison between distantly related or unrelated sequences, minimizing the effects of shared ancestry. This method is based on statistical similarities in nucleotide base composition among different functional classes of ssRNAs. In order to denote base composition unambiguously, we have calculated the fraction G+A and G+U content, in addition to the more commonly used fraction G+C content. These three parameters define RNA composition space, which we have visualized using interactive graphics software. We have examined the distribution of nucleotide composition from 15 distinct functional classes of ssRNAs from organisms spanning the universal phylogenetic tree and artificial ribozymes evolved in vitro. Surprisingly, these distributions are biased consistently in G+A and G+U content, both within and between functional classes, regardless of the more variable G+C content. Additionally, an analysis of the base composition of secondary structural elements indicates that paired and unpaired nucleotides, known to have different evolutionary rates, also have significantly different compositional biases. These universal compositional biases observed among ssRNAs sharing little or no sequence similarity suggest, contrary to current understanding, that base composition biases constitute a convergent adaptation among a wide variety of molecular functions.

Computer Graphics↗