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PubMed1997

Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome.

Two novel mitochondrial gene arrangements are identified in an agamid lizard and a ranid frog. Statistical tests incorporating phylogeny indicate a link between novel vertebrate mitochondrial gene orders and movement of the origin of light-strand replication. A mechanism involving errors in light-strand replication and tandem duplication of genes is proposed for rearrangement of vertebrate mitochondrial genes. A second mechanism involving small direct repeats also is identified. These mechanisms implicate gene order as a reliable phylogenetic character. Shifts in gene order define major lineages without evidence of parallelism or reversal. The loss of the origin of light-strand replication from its typical vertebrate position evolves in parallel and, therefore, is a less reliable phylogenetic character. Gene junctions also evolve in parallel. Sequencing across multigenic regions, in particular transfer RNA genes, should be a major focus of future systematic studies to locate novel gene orders and to provide a better understanding of the evolution of the vertebrate mitochondrial genome.

Amino Acid Sequence↗

PubMed2006

Dynamics of capillary condensation in aerogels.

Dynamics of capillary condensation of liquid 4He in various density silica aerogels was investigated systematically. Interfaces were clearly visible when bulk liquid was rapidly sucked into the aerogel. Time evolution of the interface positions was consistent with the Washburn model and their effective pore radii were obtained. Condensation was a single step in a dense aerogel and two steps in a low density aerogel. Crossover between the two types of condensation was observed in an intermediate density aerogel. Variety of the dynamics may be the manifestation of the fractal nature of aerogels which had a wide range of distribution of pore radii.

Journal Article↗

PubMed2002

Protein kinases and protein phosphatases in prokaryotes: a genomic perspective.

For many years, the regulation of protein structure and function by phosphorylation and dephosphorylation was considered a relatively recent invention that arose independently in each phylogenetic domain. Over time, however, incidents of apparent domain trespass involving the presence of 'eukaryotic' protein kinases or protein phosphatases in prokaryotic organisms were reported with increasing frequency. Today, genomics has provided the means to examine the phylogenetic distribution of 'eukaryotic' protein kinases and protein phosphatases in a comprehensive and systematic manner. The results of these genome searches challenge previous conceptions concerning the origins and evolution of this versatile regulatory mechanism.

Phosphoprotein Phosphatases↗

PubMedDate not supplied

Anthropoid origins and the modern symphysis.

To highlight adaptive transformations in craniomandibular form during anthropoid origins, symphyseal character states and underlying masticatory loading regimes were investigated vis-à-vis shifts in diet and body size. A study of fossil anthropoids is possible because variation in symphyseal fusion is continuous and directly proportional to the amount of symphyseal stress and because such variation can be considered a series of discrete character states each with unique functional underpinnings. Using recent systematic renderings of Eocene and Oligocene taxa as a template with which to assess character evolution, this analysis indicates when, and in which clade(s), specific masticatory features became fixed and thus diagnostic. A general trend throughout early anthropoid evolution is for descendent taxa to be progressively larger than ancestral forms. Coupled with this pattern is the tendency for larger-bodied fossil anthropoids to have ingested tougher diets variably consisting of thick-coated, unripe fruits and/or leaves. Mastication of mechanically tougher foods entails greater repetitive loading of the mandible and requires relatively larger amounts of balancing-side muscle force, thus resulting in correspondingly greater symphyseal fusion due to elevated dorsoventral shear. With a single exception, these adaptive transformations characterize the evolutionary pathway leading both to parapithecines and a catarrhine:platyrrhine clade (crown anthropoids). While the ancestor of crown anthropoids would have possessed a body size, diet and masticatory adaptations similar to parapithecines, such a common suite of features evolved independently. Moreover, the evolution of an early-fusing symphysis and associated wishboning loading regime of catarrhines and platyrrhines is unique among all anthropoids. Lastly, the apparent lack of reversals in symphyseal fusion indicates the improbability of phylogenetic hypotheses in which a relationship is proposed between 'ancestral' taxa with a greater degree of symphyseal fusion and 'descendent' anthropoids with a lesser degree of ossification.

Animals↗

PubMed2004

Will we ever understand? The undescribable diversity of the prokaryotes.

This communication will summarize recent estimations on prokaryotic cell numbers, technical aspects of the exploration of the hidden diversity of the as-yet-uncultured prokaryotes and their function in the environment, recognition of novel major lines of descent, elucidation of novel metabolic pathways and attempts to improve the definition of the taxon species. These are some of recent highlights that will reflect only incompletely recent advances of microbiologist and other aspects of diversity at the genomic level, including the tremendous influence of whole genome sequences on the development of DNA macro- and microarrays for rapid identification of genes and specimen, the annotation of gene sequences to gene function by proteomics and the recognition of the extent of lateral gene transfer in the evolution of the genome, hence of contemporary organisms. As an example of modern trends in systematics three new families will be described for recently described genera, namely Thermoleophilaceae, Solirubrobacteraceae and Conexibacteraceae, which are phylogenetically positioned among environmental clone sequences at the root of the class Actinobacteria.

Bacteria↗

PubMedDate not supplied

Dried blood spots collected on filter paper: an international resource for the diagnosis and genetic characterization of human immunodeficiency virus type-1.

The collection of dried blood spots (DBS) on filter paper provides a powerful approach for the development of large-scale, population-based screening programs. DBS methods are particularly valuable in developing countries and isolated rural regions where resources are limited. Large numbers of field specimens can be economically collected and shipped to centralized reference laboratories for genetic and (or) serological analysis. Alternatively, the dried blood can be stored and used as an archival resource to rapidly establish the frequency and distribution of newly recognized mutations, confirm patient identity or track the origins and emergence of newly identified pathogens. In this report, we describe how PCR-based technologies are beginning to interface with international screening programmes for the diagnosis and genetic characterization of human immunodeficiency virus type 1 (HIV-1). In particular, we review recent progress using DBS specimens to resolve the HIV-1 infection status of neonates, monitor the genetic evolution of HIV-1 during early infancy and establish a sentinel surveillance system for the systematic monitoring of HIV-1 genetic variation in Asia.

AIDS Serodiagnosis↗

PubMed2003

Iterative pass optimization of sequence data.

The problem of determining the minimum-cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete. This "tree alignment" problem has motivated the considerable effort placed in multiple sequence alignment procedures. Wheeler in 1996 proposed a heuristic method, direct optimization, to calculate cladogram costs without the intervention of multiple sequence alignment. This method, though more efficient in time and more effective in cladogram length than many alignment-based procedures, greedily optimizes nodes based on descendent information only. In their proposal of an exact multiple alignment solution, Sankoff et al. in 1976 described a heuristic procedure--the iterative improvement method--to create alignments at internal nodes by solving a series of median problems. The combination of a three-sequence direct optimization with iterative improvement and a branch-length-based cladogram cost procedure, provides an algorithm that frequently results in superior (i.e., lower) cladogram costs. This iterative pass optimization is both computation and memory intensive, but economies can be made to reduce this burden. An example in arthropod systematics is discussed.

Algorithms↗

PubMed2003

Laparoscopic radical prostatectomy: a review of techniques and results worldwide.

Laparoscopic radical prostatectomy (LRP) is currently performed in multiple centers world-wide, with several different surgical approaches and techniques utilized. A comprehensive review of the published literature worldwide on laparoscopic radical prostatectomy was performed to outline the evolution of this technique, and to review the published surgical, oncological and functional results. A systematic review of peer reviewed articles concerning laparoscopic radical prostatectomy was obtained using Medline query. LRP is being performed in multiple centers worldwide, using a variety of surgical approaches and technologies. Analysis of perioperative parameters, including surgical blood loss, operative time, complications and convalescence, demonstrates a low morbidity and shows a clear trend in improvement with increased experience. The functional results, as recorded by postoperative urinary and sexual functions, appear encouraging. The reported positive surgical margin rates decrease with more recent series. Oncological results and cancer control rates as measured by PSA recurrence and disease-free intervals are difficult to ascertain in the immature series published to date. LRP has witnessed tremendous popularity and widespread implementation in specialized centers worldwide. LRP represents a technically demanding laparoscopic procedure with a difficult learning curve, but can be performed systematically with standard techniques. The advantages include shorter convalescence and markedly lower operative blood loss, with quicker removal of the urinary catheter. Long-term functional and oncologic results are not yet available.

Global Health↗

PubMed1983

[Prolonged curarization in the newborn infant under assisted ventilation for idiopathic respiratory distress].

We studied the effects of prolonged pancuronium administration in 10 neonates under assisted ventilation for hyaline membrane disease. Pancuronium bromide was administered from the time of intubation with a load dose of 0.1 mg/kg followed by a continuous infusion of 0.03-0.07 mg/kg/h. Tolerance, especially cardiovascular, was excellent after 72 to 525 h of therapy (mean 173 h). Oxygen needs, incidence of mechanical complications and the general evolution of idiopathic respiratory distress were not significantly affected by muscle relaxation. The benefits of systematic pancuronium administration during respiratory intensive care in neonates with hyaline membrane disease appear to be of little value when considering the necessary constraints (corneal, cutaneous, vesical and tracheal supervision).

Hemodynamics↗

PubMed2004

Model selection in ecology and evolution.

Recently, researchers in several areas of ecology and evolution have begun to change the way in which they analyze data and make biological inferences. Rather than the traditional null hypothesis testing approach, they have adopted an approach called model selection, in which several competing hypotheses are simultaneously confronted with data. Model selection can be used to identify a single best model, thus lending support to one particular hypothesis, or it can be used to make inferences based on weighted support from a complete set of competing models. Model selection is widely accepted and well developed in certain fields, most notably in molecular systematics and mark-recapture analysis. However, it is now gaining support in several other areas, from molecular evolution to landscape ecology. Here, we outline the steps of model selection and highlight several ways that it is now being implemented. By adopting this approach, researchers in ecology and evolution will find a valuable alternative to traditional null hypothesis testing, especially when more than one hypothesis is plausible.

Journal Article↗

PubMed1994

Evolution of mtDNA D-loop sequences and their use in phylogenetic studies of shrews in the subgenus Otisorex (Sorex: Soricidae: Insectivora).

mtDNA D-loop sequences were examined in shrews of the genus Sorex. All specimens possessed an array of tandem repeats in which each repeat was 78 to 80 base pairs (bp) in length. Each specimen also possessed a 76-bp imperfect copy of the tandem repeats. Three observations are consistent with the tandem repeats being the product of concerted evolution: (1) the repeats are capable of forming secondary structures; (2) there was minimal sequence divergence between tandem repeats within individuals; and (3) although the tandem repeats and the imperfect repeat presumably arose due to a duplication event in an ancestor of the shrews, the imperfect repeat per se was not copied in any of the specimens observed. Interspecific homology can therefore be assumed for the imperfect repeat. Furthermore, given the apparent high rate of concerted evolution within a genome, tandem repeats in different individuals may be compared as though only a single copy were present. By including data from the imperfect repeat, the last tandem repeat, and the surrounding unique sequence cladistic and genetic distance approaches to phylogeny reconstruction indicated two sister groups within the subgenus Otisorex. One group was composed of Sorex fumeus and the S. cinereus species complex and the other group was composed of S. hoyi, S. monticolus, S. vagrans, and S. palustris. Resolution of relationships among recently evolved taxa demonstrated the usefulness of selected regions of the D-loop for molecular systematic studies.

Animals↗

PubMed1981

Karyotypic fission theory and the evolution of old world monkeys and apes.

The karyotypes of living catarrhines are correlated with the current concepts of their fossil record and systematic classification. A phylogeny, beginning at the base of the Oligocene, for those animals and their chromosome numbers is presented. Todd's (1970) theory of karyotypic fissioning is applied to this case - three fissioning events are hypothesized. A late Eocene event (the primary catarrhine fissioning) is hypothesized to underlie the diversification of the infraorder Catarrhini into its extant families, the second fissioning underlies the radiation of the pongidae/Hominidae in the Miocene and the third accounts for the high chromosome numbers (54 - 72) and the Neogene(Miocene-Pliocene-Pleistocene) radiation of members of the genus Cercopithecus. Published catarrhine chromosome data, including that for "marked" chromosomes (those with a large achromatic region that is the site for ribosomal RNA genes) are tabulated and analysed. The ancestral X chromosome is always retained in the unfissioned metacentric state. The Pongidae/Hominidae have 15 pairs of mediocentric chromosomes that survived the second fissioning whereas the other chromosomes (besides the X) are thought to be fission-derived acrocentrics. Both the detailed karyology and the trend from low to high numbers is best interpreted to support Todd's concept of adaptive radiations correlated with karyotypic fissioning in ancestral populations.

Animals↗

PubMed1996

Gene expression in a young multigene family: tissue-specific differences in the expression of the human alcohol dehydrogenase genes ADH1, ADH2, and ADH3.

Three human alcohol dehydrogenase genes, ADH1, ADH2, and ADH3, were formed by tandem duplications and have diverged in their tissue-specific and developmental expression. Their proximal promoters remain 80-84% identical in sequence, approximately the same degree of identity as at synonymous sites in the coding regions of these three genes. To understand the evolution of tissue specificity, gene expression must be studied in many different cells and tissues. A systematic comparison of their promoters reveals the effects of subtle sequence differences on the binding of nuclear proteins to their cis-acting elements. There are differences in the affinity with which some proteins are bound to altered sites including C/EBP sites, USF/MLTF sites, and the G3T site (which binds Sp1). There are also differences in the sites that are occupied, e.g. CTF/NFI-related sites. These sequence differences are reflected in differences in gene expression in three cell lines. In H4IIE-C3 hepatoma cells, the ADH1 promoter was more active than the ADH2 promoter, and the ADH3 promoter was nearly nonfunctional. In HeLa cells, both ADH1 and ADH2 promoters directed expression; again the ADH3 promoter was extremely weak. None of the three promoters had much activity in CV-1 cells. Coexpression of C/EBP alpha greatly stimulated expression of the ADH1 promoter in HeLa cells and in CV-1 cells, but only weakly stimulated expression in H4IIE-C3 cells. The stimulation of the ADH1 promoter by C/EBP alpha was comparable to that of ADH2, despite the weaker binding to the C/EBP sites that flank the TATA box in ADH1. The ADH3 promoter was not greatly stimulated by C/EBP alpha, despite good binding of C/EBP alpha. These results demonstrate that small differences in the cis-acting elements affect affinity of binding by transcription factors and the pattern of gene expression.

Alcohol Dehydrogenase↗

PubMed1998

Evolutionary characteristics of influenza B virus since its first isolation in 1940: dynamic circulation of deletion and insertion mechanism.

New antigenic variants of B/Yamagata/16/88-like lineage which appeared in the season of 1997 as a minor strain tended to predominate in the following season. Also, we could observe for the first time, three peaks of activity caused by H3N2 virus and two variants of B influenza virus. Antigenic and phylogenetic analyses revealed that B/Victoria/2/87-like variants appeared again in Japan in 1997 after a nine-year absence. Influenza B viruses evolved into three major lineages, including the earliest strain (I), B/Yamagata/16/88-like variants (II), which comprised of three sublineages (II-(i), II-(ii), II-(iii)), and B/Victoria/2/87-like variants (III). Evolution of influenza B virus hemagglutinin was apparently distinguishable from that of influenza A virus, showing a systematic mechanism of nucleotide deletion and insertion. This phenomenon was observed to be closely related to evolutionary pathways of I, II-(i), II-(ii), II-(iii) and III lineages. It was noteworthy to reveal that the nucleotide deletion and insertion mechanism of influenza B virus completed one cycle over a fifty-year period, and that a three nucleotide deletion was again observed in 1997 strains belonging to lineage II-(iii). It was evident that amino acid substitutions accompanying nucleotide insertions were highly conserved.

Antigens, Viral↗

PubMed2005

Evolution of the crystal and electronic structures of magnetic RuSr(2-x)La(x)GdCu2O8 superconductors upon La substitution.

We have investigated systematically the effects of La substitution on the chemical bonding nature and physical properties of magnetic RuSr(2-x)La(x)GdCu2O8 superconductors. X-ray diffraction and energy dispersive spectroscopic microprobe analyses reveal that a fraction of Sr ions can be successfully replaced by La ions with the contraction of unit cell volume. According to electrical resistance and dc magnetization measurements, the La substitution gives rise to a significant reduction of superconducting transition temperature (T(c)) but to an increase of magnetic ordering temperature with depressed remanent magnetization. Ru K- and Cu K-edge X-ray absorption spectroscopic results clarify that average Ru and Cu oxidation states decrease upon the La substitution. On the basis of the spectroscopic evidences presented here, we are able to attribute the T(c) reduction upon the La substitution to the depletion of the hole density in CuO2 layers and the accompanying variation of magnetic coupling behavior to the change of Ru oxidation state.

Journal Article↗

PubMed2001

The morphological evolution of galaxies.

Many galaxies have taken on their familiar appearance relatively recently. In the distant Universe, galaxy morphology deviates significantly (and systematically) from that of nearby galaxies at redshifts (z) as low as 0.3. This corresponds to a time approximately 3.5 x 10(9) years in the past, which is only approximately 25% of the present age of the Universe. Beyond z = 0.5 (5 x 10(9) years in the past), spiral arms are less well developed and more chaotic, and barred spiral galaxies may become rarer. At z = 1, around 30% of the galaxy population is sufficiently peculiar that classification on Hubble's traditional "tuning fork" system is meaningless. On the other hand, some characteristics of galaxies have not changed much over time. The space density of luminous disk galaxies has not changed significantly since z = 1, indicating that although the general appearance of these galaxies has continuously changed over time, their overall numbers have been conserved.

Journal Article↗

PubMed1994

The molecular phylogeny and systematics of the actinomycetes.

Sequences of 16S ribosomal RNA have provided actinomycetologists with a phylogenetic tree that allows the investigation of the evolution of actinomycetes and also provides a basis for classification. The origin of actinomycetes and, except for bifidobacteria, the order by which the main sublines evolved, cannot yet be determined with certainty. However, calibration of rRNA sequence divergence with palaeochemical data, and previously published substitution rates of endosymbiotic bacteria, suggest that the main radiation occurred less than 1 billion years ago. Within this radiation, several phylogenetically homogeneous, but sometimes phenotypically heterogeneous, clades appear to have diverged over a short evolutionary period. The resolution of the 16S rRNA molecule appears to be insufficient to clearly determine the branching patterns between clades in this area of the phylogenetic tree. The distribution of some morphological and chemotaxonomic traits such as types of peptidoglycan, menaquinone, phospholipids, cell wall sugars, and fatty acids facilitate the phenotypic delineation of genera within each clade. At higher taxonomic levels, e.g. at the family level, phenotypic similarities are unpredictable and tend to be less conserved. With the exception of mycolic acids, most traits are polyphyletic--hence they are unreliable indicators per se of phylogenetic relationships. Nevertheless, combinations of phenotypic properties are invaluable for predicting whether a new organism is likely to be a member of an established or a novel taxon. Current knowledge about the phylogenetic structure of the actinomycetes provides not only a sound basis for future taxonomic work but also a framework for the rational exploration of their ecology and biotechnological potential.

Actinomycetales↗

PubMed1986

Genetic differentiation of Murray Valley encephalitis virus in Australia and Papua New Guinea.

The genetic relatedness of ten Murray Valley encephalitis virus (MVE) isolates from Australia has been examined by comparing HaeIII and TaqI restriction digest profiles of cDNA to virion RNA. The isolates were from the Murray Valley region of south-eastern Australia and from the Ord River region of Western Australia and spanned a period of 23 years (1951-1974). The isolates generated closely similar restriction digest profiles. The extent of similarity suggested that the level of nucleotide sequence divergence between any pair of Australian MVE isolates is probably around 1%. The genetic homogeneity of the MVE isolates contrasts with results obtained for Ross River virus, an alphavirus, using an identical methodological approach; we propose that this difference results from the important role of birds in the life cycle of MVE. Four MVE isolates from three fatal human cases showed small genetic differences one from the other. These isolates did not have a common restriction digest profile which distinguished them from strains obtained from other sources (e.g., from mosquitoes or a heron). The data do not support the view that clinical cases of MVE infection in humans are due to a particular strain of virus although this has not been rigorously excluded. The two available MVE isolates from Papua New Guinea (PNG) were from the Sepik and Port Moresby regions. They generated HaeIII and TaqI restriction digest profiles which were different both from each other and from those of the Australian type. Genetic divergence between the two PNG isolates was estimated to be approximately 6%; divergence between either of the PNG isolates and the Australian type was greater than 6%. Our data suggest that the evolution of MVE in Australia and PNG has proceeded independently and that circulating Australian MVE strains are not systematically re-seeded from regions of endemicity in PNG. Studies on the relatedness of MVE and two close antigenic relatives, Japanese encephalitis virus (JE) and Alfuy virus (ALF), showed that the genetic relatedness between any MVE isolate and JE or ALF is less than that between the most divergent of the MVE isolates, including those from Papua New Guinea.

Animals↗