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PubMed1997

Rhodinocichla rosea is an emberizid (Aves; Passeriformes) based on mitochondrial DNA analyses.

The systematic position of the avian species Rhodinocichla rosea is unclear. Recent opinions are that it is either a mockingbird (family Mimidae) or a tanager (Thraupinae; Emberizidae). In either case, it would be an atypical member of the family. We sequenced approximately 600 bases of the mitochondrial cytochrome oxidase I (COI) gene of Rhodinocichla, several mimids, tanagers, and other passerines. We used maximum likelihood (ML), distance and parsimony approaches to analyze the sequences and concluded that Rhodinocichla belongs to the family Emberizidae. Phenotypic characteristics that suggested its relationship with mimids are the product of convergent evolution. The precise relationships of Rhodinocichla within the Emberizidae could not be resolved. Short internal branches in ML and distance trees suggested, as did earlier genetic studies, that the radiation of that family was explosive. Apparently, the extent of the tanagers as a higher taxon needs to be clarified. Our analysis of the evolutionary dynamics of avian COI suggested that its usefulness for phylogenetic studies is limited because silent positions saturate rapidly and replacement substitutions are rare. Thus, our data indicate that COI nucleotide data will be most useful in intraspecific investigations, while other data suggested its usefulness at the interordinal level.

Amino Acid Sequence↗
PubMed1998

Evolutionary Stable Strategies and Trade-Offs in Generalized Beverton and Holt Growth Models.

A generalized Beverton-Holt model is considered in which a parameter gamma characterizes the onset of density dependence. An evolutionary stable strategy analysis of this parameter, reported in Getz (1996), is developed further here, using invasion exponents and the strategy dynamics of Vincent et al. (1993). The parameter gamma is also allowed to be density dependent, and it is shown that the most successful strategies of this type are those for which gamma is large for low densities and close to its minimum for high densities. A biological interpretation is given in the context of mobile females depositing their relatively sessile young on patches of resource, namely, females should overdisperse their young on resources when adult densities are high and underdisperse them when these densities are low. Finally the per capita growth rate parameter is also allowed to depend on gamma. It is shown that this dependence provides a mechanism by which periodic or chaotic attractor dynamics could evolve towards equilibrium attractor dynamics. Copyright 1998 Academic Press.

Journal Article↗
PubMed1996

Genetic variation in neuraminidase genes of influenza A (H3N2) viruses.

Nucleotide sequences of the neuraminidase (NA) genes of 33 influenza A (H3N2) epidemic strains isolated between 1968 and 1995 were analyzed to determine their evolutionary relationships. Phylogenetic analysis using the DNA maximum-likelihood method indicates that the NA genes of recent H3N2 field strains, like their hemagglutinin genes (HA), have evolved as two distinct lineages represented by the vaccine strains. A/Beijing/353/89 and A/Beijing/32/92 for A/Shanghai/24/ 90). Furthermore, genetic reassortment of NA genes between the two lineages occurred during their circulation. Genetic reassortants, which bear an A/Beijing/32/92-like HA and an A/Beijing/353/89-like NA, have circulated worldwide and are representative of current influenza A (H3N2) epidemic strains. The mutation rate of the NA gene was found to be 2.28 x 10(-3) per nucleotide site per year with 4.2% of the mutations resulting in amino acid substitutions. Thirty-five percent of the amino acid substitutions was located in sites previously suggested to be reactive to antibody. Amino acid residues involved in NA enzyme activity have been conserved. Seven potential glycosylation sites identified in the NA of A/Hong Kong/8/68 virus were conserved by the majority of isolates, with more recently circulating viruses having an additional glycosylation site. Comparison of the rate of amino acid substitutions in the NA stalk to that of entire NA revealed high variability in this region. These findings demonstrate the importance of closely monitoring both the HA and the NA genes of influenza viruses to aid vaccine strain selection.

Amino Acid Sequence↗
PubMed1990

Localization and evolution of two human phospholipase A2 genes and two related genetic elements.

Mammals are now known to contain at least two distinct classes of phospholipases A2, the progenitors of which can be seen in the venoms of snakes. Mammalian "Type I" PLA2, synthesized primarily by the pancreas, is also present in smaller amounts in other tissues including lung, spleen, and kidney. Recently, a mammalian "Type II" PLA2 has been sequenced, and shown to occur in platelets, synovial cells and fluid, cells of inflammatory peritoneal exudate, liver, intestine, kidney, and placenta. This form, referred to here as Type IIA PLA2, could play a key role in arachidonate release in both normal and pathologic inflammation. The genes encoding both forms have also been recently cloned. Here, the sites of synthesis and respective roles of the two known enzymes are discussed, along with an analysis of the evolutionary conservation of Type IIA PLA2 gene sequence. In addition, two related genetic elements containing sequences homologous to a portion of Type II PLA2 are described, which map to the same chromosome as the Type IIA PLA2 gene (chromosome 1). Either or both of these could also encode a portion of additional mammalian PLA2s.

Amino Acid Sequence↗
PubMed1993

Isolation and characterization of a cDNA encoding granule-bound starch synthase in cassava (Manihot esculenta Crantz) and its antisense expression in potato.

A tuber-specific cDNA library of cassava (Manihot esculenta Crantz) was constructed and a full-length cDNA for granule-bound starch synthase (GBSS, also known as waxy protein), the enzyme responsible for the synthesis of amylose in reserve starch, was cloned. Sequencing of the cloned cDNA showed that it has 74% identity with potato GBSS and 60-72% identity with GBSS from other plant species. The cDNA encodes a 608 amino acid protein of which 78 amino acids form a chloroplast/amyloplast transit peptide of 8.37 kDa. The mature protein has a predicted molecular mass of 58.61 kDa (530 amino acids). Comparison of the GBSS proteins of various plant species and glycogen synthase of bacteria showed extensive identity among the mature form of plant GBSS proteins, in which the monocots and dicots form two separate branches in the evolutionary tree. From analysis of the genomic DNA of allotetraploid cassava, it is shown that GBSS is a low-copy-number gene. GBSS transcript is synthesized in a number of different organs, but most abundantly in tubers. Potato plants were transformed with the cassava GBSS cDNA in antisense orientation fused between the potato GBSS promoter and the nopaline synthase terminator. The expression of the endogenous GBSS gene in these transgenic potato plants was partially or completely inhibited. Complete inhibition of GBSS activity by the cassava antisense gene resulted in absence of GBSS protein and amylose giving rise to almost complete amylose-free potato starch. This shows that also heterologous genes can be used to achieve antisense effects in other plant species.

Base Sequence↗
PubMed1992

Natural genetic engineering in evolution.

The results of molecular genetics have frequently been difficult to explain by conventional evolutionary theory. New findings about the genetic conservation of protein structure and function across very broad taxonomic boundaries, the mosaic structure of genomes and genetic loci, and the molecular mechanisms of genetic change all point to a view of evolution as involving the rearrangement of basic genetic motifs. A more detailed examination of how living cells restructure their genomes reveals a wide variety of sophisticated biochemical systems responsive to elaborate regulatory networks. In some cases, we know that cells are able to accomplish extensive genome reorganization within one or a few cell generations. The emergence of bacterial antibiotic resistance is a contemporary example of evolutionary change; molecular analysis of this phenomenon has shown that it occurs by the addition rearrangement of resistance determinants and genetic mobility systems rather than by gradual modification of pre-existing cellular genomes. In addition, bacteria and other organisms have intricate repair systems to prevent genetic change by sporadic physicochemical damage or errors of the replication machinery. In their ensemble, these results show that living cells have (and use) the biochemical apparatus to evolve by a genetic engineering process. Future research will reveal how well the regulatory systems integrate genomic change into basic life processes during evolution.

Animals↗
PubMed1988

The molecular phylogenic tree of the genus Trichinella constructed from isozyme patterns.

Six zymograms were compared for extracts of muscle-stage larvae of the seven Trichinella isolates, using isoelectric focusing in polyacrylamide gels. The isozyme patterns of acid phosphatase among them fell into four types. T. pseudospiralis from a raccoon and the Polar strain from a polar bear formed type 1 and type 2, respectively. The Iwasaki strain from a Japanese black bear and the Yamagata strain from a raccoon dog, both from Japan, were type 3. Type 4 consisted of three remaining strains, viz. the Polish strain from a wild pig, the USA strain from a pig, and the Thai strain from a human case, all of which have similar infectivity to pigs. The isozyme patterns of esterase 1, beta-N-acetylglucosaminidase, and peptidase were similar in types 2 and 3. Those of esterase D were common to types 2-4 but not to type 1. In the zymogram of mannosephosphate isomerase, types 2-4 but not type 1 had one common band, whereas in the other bands type 2 was markedly distinguished from types 3 and 4. In the present study, the molecular phylogenic tree was constructed for the first time on the basis of our present and previous electrophoretic data by the use of cluster analysis, and the evolutionary process was considered as follows: T. pseudospiralis (type 1) and T. spiralis (the common ancestor of types 2-4) were initially separated. Next, the common ancestor of the strains from wild carnivores (types 2 and 3) and type 4 were separated. Finally, the Polar strain (type 2) and the Japanese strain (type 3) were separated.

Acetylglucosaminidase↗
PubMed1995

The phylogeny of tRNAs seems to confirm the predictions of the coevolution theory of the origin of the genetic code.

An extensive analysis of the evolutionary relationships existing between transfer RNAs, performed using parsimony algorithms, is presented. After building up an estimate of the tRNA ancestral sequences, these sequences are then compared using certain methods. The results seem to suggest that the coevolution hypothesis (Wong, J.T., 1975, Proc. Natl. Acad. Sci. USA 72, 1909-1912) that sees the genetic code as a map of the biosynthetic relationships between amino acids is further supported by these results, as compared to the hypotheses that see the physicochemical properties of amino acids as the main adaptative theme that led to the structuring of the genetic code.

Amino Acid Sequence↗
PubMed1986

Nucleotide sequences of Cyanophora paradoxa cellular and cyanelle-associated 5S ribosomal RNAs: the cyanelle as a potential intermediate in plastid evolution.

The 5S ribosomal RNAs from the cell cytoplasm and cyanelle (photosynthetic organelle) of Cyanophora paradoxa have been isolated and sequenced. The cellular and cyanelle 5S rRNAs were 119 and 118 nucleotides in length, respectively. Both RNAs exhibited typical 5S secondary structure, but the primary sequence of the cellular species was clearly eukaryotic in nature, while that of the organellar species was prokaryotelike. The primary sequence of the cyanellar 5S rRNA was most homologous to cyanobacterial 5S sequences, yet possessed secondary-structural features characteristic of higher-plant chloroplast 5S rRNAs. Both sequence comparison and structural analysis indicated an evolutionary position for cyanelle 5S rRNA intermediate between blue-green alga and chloroplast 5S rRNAs.

Animals↗
PubMed1996

CpG dinucleotides in the hMSH2 and hMLH1 genes are hotspots for HNPCC mutations.

Hereditary nonpolyposis colon cancer (HN-PCC) is an autosomally inherited predisposition to cancer that has recently been linked to defects in the human mismatch repair genes hMSH2 and hMLH1. The identification of the causative mutations in HNPCC families is desirable, since it confirms the diagnosis and allows the carrier status of unaffected relatives at risk to be determined. We report six different new mutations identified in the hMSH2 and hMLH1 genes of Russian and Moldavian HNPCC families. Three of these mutations occur in CpG dinucleotides and lead to a premature stop codon, a splicing defect or an amino-acid substitution in an evolutionary conserved residue. Analysis of a compilation of published mutations including our new data suggests that CpG dinucleotides within the coding regions of the hMSH2 and hMLH1 genes are hotspots for single base-pair substitutions.

Adaptor Proteins, Signal Transducing↗
PubMed1998

Evolution of the cytochrome c oxidase proton pump.

The superfamily of quinol and cytochrome c terminal oxidase complexes is related by a homologous subunit containing six positionally conserved histidines that ligate a low-spin heme and a heme-copper dioxygen activating and reduction center. On the basis of the structural similarities of these enzymes, it has been postulated that all members of this superfamily catalyze proton translocation by similar mechanisms and that the CuA center found in most cytochrome c oxidase complexes serves merely as an electron conduit shuttling electrons from ferrocytochrome c into the hydrophobic core of the enzyme. The recent characterization of cytochrome c oxidase complexes and structurally similar cytochrome c:nitric oxide oxidoreductase complexes without CuA centers has strengthened this view. However, recent experimental evidence has shown that there are two ubiquinone(ol) binding sites on the Escherichia coli cytochrome bo3 complex in dynamic equilibrium with the ubiquinone(ol) pool, thereby strengthening the argument for a Q(H2)-loop mechanism of proton translocation [Musser SM et al. (1997) Biochemistry 36:894-902]. In addition, a number of reports suggest that a Q(H2)-loop or another alternate proton translocation mechanism distinct from the mitochondrial aa3-type proton pump functions in Sulfolobus acidocaldarius terminal oxidase complexes. The possibility that a primitive quinol oxidase complex evolved to yield two separate complexes, the cytochrome bc1 and cytochrome c oxidase complexes, is explored here. This idea is the basis for an evolutionary tree constructed using the notion that respiratory complexity and efficiency progressively increased throughout the evolutionary process. The analysis suggests that oxygenic respiration is quite an old process and, in fact, predates nitrogenic respiration as well as reaction-center photosynthesis.

Electron Transport Complex IV↗
PubMed1998

Accelerated evolution of cytochrome b in simian primates: adaptive evolution in concert with other mitochondrial proteins?

We have sequenced the cytochrome b gene of Horsfield's tarsier, Tarsius bancanus, to complete a data set of sequences for this gene from representatives of each primate infraorder. These primate cytochrome b sequences were combined with those from representatives of three other mammalian orders (cat, whale, and rat) in an analysis of relative evolutionary rates. The nonsynonymous nucleotide substitution rate of the cytochrome b gene has increased approximately twofold along lineages leading to simian primates compared to that of the tarsier and other primate and nonprimate mammalian species. However, the rate of transversional substitutions at fourfold degenerate sites has remained uniform among all lineages. This increase in the evolutionary rate of cytochrome b is similar in character and magnitude to that described previously for the cytochrome c oxidase subunit II gene. We propose that the evolutionary rate increase observed for cytochrome b and cytochrome c oxidase subunit II may underlie an episode of coadaptive evolution of these two proteins in the mitochondria of simian primates.

Adaptation, Physiological↗
PubMed1998

Astroglial interlaminar processes in the cerebral cortex of prosimians and Old World monkeys.

Previous observations have shown that astrocytes with interlaminar processes are present in the cerebral cortex of humans and New and Old World monkeys, but not in the rodent. The present report furthers the analysis of possible evolutionary aspects regarding the expression of such astroglial features. A comparison between young and adult Microcebus murinus, a prosimian, and Old World monkeys (Macaca mulatta and Papio hamadryas) is presented. Brain samples were processed for glial fibrillary acidic protein (GFAP), vimentin, MAP2 and SMI 311 immunocytochemistry, using different procedures. The cerebral cortex of adult Microcebus showed the presence of long astroglial processes, albeit reduced in number and length with respect to those observed in Old World monkeys. Macaca and Papio showed dense packing of such processes extending in most cortical regions to a depth of approximately 700 micrometers. Based on double immunolabelling for GFAP and MAP 2 antigens, the location and extent of these processes was shown to overlap with areas traversed by bundles and individual apical dendrites. Aged Old World specimens depicted an increased thickness of terminal portions of interlaminar processes, with increased morphological alterations. Comparisons made between the average thickness of the "brush" composed of interlaminar processes and the thickness of lamina I among the species analyzed disclosed an absence of relationship between them. This suggests that interlaminar processes do not represent cellular adaptations to the increase in thickness in superficial cortical laminae, but rather to some other evolutionary pressure. Since astroglial interlaminar processes are already present in a prosimian, although in a comparatively reduced manner, it is suggested that such processes underwent an early expression within the primate order, with increasing presence in more recent primate species.

Animals↗
PubMed2006

High-resolution comparative chromosome painting in the Arizona collared peccary (Pecari tajacu, Tayassuidae): a comparison with the karyotype of pig and sheep.

We used chromosome painting with chromosome-specific probes derived from domestic sheep and pig for a high-resolution cytogenetic comparison with the karyotype of collared peccary (Pecari tajacu sonoriensis). A reorganization of the karyotype involving at least 62-66 conserved segments were observed between the sheep and collared peccary. This is an extremely high number compared with other members of the same mammalian order (Cetartiodactyla). The comparison between pig and collared peccary, both belonging to the Suiformes, however, revealed various changes in the gross organization of both karyotypes that may have already occurred in a common ancestor of both species suggesting a monophyletic origin of Suidae/Tayassuidae. The sheep probes, however, also revealed several rearrangements between the two Suidae/Tayassuidae, indicating that these probes represent a useful tool for a more detailed analysis of the evolutionary history of Suiformes. Our sample of the collared peccary from North America (Arizona, USA) showed distinct differences to those already described from South America. The chromosome painting results defined a complex translocation that involves chromosomes including about one-quarter of the entire collared peccary karyotype. This considerable rearrangement indicates subspecies or even species status of both peccary populations, as it should present a significant barrier for their hybridization.

Animals↗
PubMed1994

A mutation data matrix for transmembrane proteins.

The widely used Mutation Data Matrix (MDM), is an amino acid comparison matrix calculated from a study of the exchange probabilities (or odds) derived from an analysis of the evolutionary changes seen in groups of very similar proteins. In this work, a mutation data matrix is calculated for membrane spanning segments. This new mutation data matrix is found to be very different from matrices calculated from general sequence sets which are biased towards water-soluble globular proteins, and the differences are discussed in the context of specific structural requirements of membrane spanning segments. This new matrix will help improve the accuracy of integral membrane protein sequence alignments, and could also be of use in the rational design of site directed mutagenesis experiments for this class of proteins.

Amino Acid Sequence↗
PubMed1984

Simian virus 40 illegitimate recombination occurs near short direct repeats.

We have analysed nucleotide sequences at the junction between simian virus 40 (SV40) and cellular DNA in the Fisher rat transformed line tsA30-N2. This line contains a single insertion of one complete SV40 genome with a terminal duplication of 267 nucleotides, the recombination sites being located at nucleotides 439 and 705 in the late region of SV40. These two positions are located within short direct repeats in the virus genome. In order to test the significance of such repeats with respect to illegitimate recombination events, we analysed two series of published sequences of SV40 recombination sites: the first one consists of eight SV40 insertion endpoints derived from four SV40-transformed cell lines; the second one consists of 18 junction points from SV40 evolutionary variants. Our analysis demonstrates that in both cases, recombination preferentially takes place near short direct repeats in the virus genome. A model involving a "slipped mispairing" mechanism is proposed in order to account for this finding.

Animals↗
PubMed1990

The use of information theory to analyze genomic changes in neoplasia.

How the cell maintains and uses its heritable information may be a critical factor in neoplasia. For example, neoplastic development is thought to depend upon the interplay between random genomic instability and nonrandom selective forces. Information theory provides a means to analyze these processes. One may quantitate not only the amount and lability of information contained within a segment of genetic code, but also the genotypic heterogeneity and the degree of selection affecting a population of cells. In addition, it is theoretically possible to monitor genetic information as it is processed by cells during replication, transcription, and translation. These parameters could permit a detailed analysis of the evolutionary changes hypothesized to underlie neoplastic development.

Animals↗
PubMed1996

Identification of a 5' truncated non-LTR-retrotransposon, YAKPs1, from the variegated cutworm, Peridroma saucia, using PCR.

Retrotransposable elements encode for several polypeptides that contain a number of conserved amino acid motifs, especially in the region encoding reverse transcriptase. We have used these motifs to design primers for the PCR amplification of retrotransposon DNA. These primers have allowed us to isolate a retroposon, or LINE (long interspersed nuclear element), from the pest insect, Peridroma saucia. DNA sequence analysis of this element, YAKPs1, demonstrated a high degree of homology to a number of retroposons from Drosophila melanogaster, in particular the Fw and Doc elements with homologies of up to 69%. Determination of the complete sequence of the YAKPs1 element will enable a detailed analysis of its evolutionary relatedness to other elements as well as a greater insight into its mode of action.

Amino Acid Sequence↗