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PubMed2005

Mitochondrial genomes of parasitic nematodes--progress and perspectives.

Mitochondria are subcellular organelles in which oxidative phosphorylation and other important biochemical functions take place within the cell. Within these organelles is a mitochondrial (mt) genome, which is distinct from, but cooperates with, the nuclear genome of the cell. Studying mt genomes has implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. Importantly, the mt genome is a rich source of markers for population genetic and systematic studies. To date, more than 696 mt genomes have been sequenced for a range of metazoan organisms. However, few of these are from parasitic nematodes, despite their socioeconomic importance and the need for fundamental investigations into areas such as nematode genetics, systematics and ecology. In this article, we review knowledge and recent progress in mt genomics of parasitic nematodes, summarize applications of mt gene markers to the study of population genetics, systematics, epidemiology and evolution of key nematodes, and highlight some prospects and opportunities for future research.

Animals↗
PubMed1997

Cloning and characterization of a repetitive 1.9 Kb HindIII DNA fragment from Crotalus durissus terrificus genome.

Eukaryote genomes are endowed with varying quantities of repeated DNA families. These families show different patterns of conservation among species, copy numbers, chromosomal distribution, and transcription. Characterization of repeated DNA sequences could help to understand the genome anatomy and organization or be used in molecular systematics and molecular evolution studies. We describe here a repetitive DNA sequence of the HindIII family present in the genome of the rattlesnake Crotalus durissus terrificus. In Brazil, the family Crotalus is comprised only by one species durissus, which include several subspecies. The number and distribution of these subspecies are controversial. In the present study, the genomic DNA of a female rattlesnake was digested with HindIII resulting in a strong 1.9 Kb band. A partial genomic library was constructed from the 1.9 Kb DNAs rescued from the agarose gel after HindIII digestion and ligated to the vector pGEM3Zf(+) (Promega). Analysis of 69 clones, 44 hybridized with the 1.9 Kb probe isolated from one of the clones-clone 76, indicating that the DNA isolated from this clone should represent the 1.9 Kb HindIII fragment. This 1.9 Kb HindIII DNA was completely characterized by sequencing.

Animals↗
PubMedDate not supplied

[Recombinant protein folding and production].

The biotechnology of recombinant protein production is now entering its most advanced stage, and the growth of industrial protein pharmaceuticals provides solid proof of this evolution. However, the systematic conversion of genetic information into a biologically active protein is constantly confronted by the fundamental problem of protein folding in cells, and many recombinant proteins are not produced in their native state. Instead, they aggregate into a biologically inactive state. Although this aggregation reaction has some practical advantages, in vitro renaturation of recombinant proteins, after solubilization of cellular aggregates, is still an empiric and random process. Thus, it is better to control cellular expression conditions to minimize this problem inside the cells. The most attractive approach is certainly the development of high throughput genetic screens to monitor efficient protein folding.

Bacteria↗
PubMed1992

An rbcL sequence from a Miocene Taxodium (bald cypress).

During the past decade, ancient DNAs from both animals and plants have been successfully extracted and analyzed. Recently, the age of DNA that can be recovered and sequenced was increased manyfold by the amplification and sequencing of a DNA fragment from a Magnolia fossil obtained from the Miocene Clarkia deposit (17-20 million yr old). However, the validity of this report has been questioned based on models predicting that DNA should be completely degraded after 4 million yr. We report here the successful amplification, sequencing, and analysis of a 1320-base-pair portion of the chloroplast gene rbcL from a Miocene Taxodium specimen, also from the Clarkia site. These data not only validate the earlier report of sequence data for a Magnolia species from the same site but also suggest that it may be possible to isolate and sequence DNAs routinely from the Clarkia deposit. The ability to recover and sequence DNAs of such age offers enormous research possibilities in the areas of molecular evolution, biogeography, and systematics.

Base Sequence↗
PubMed2005

Polytomies and Bayesian phylogenetic inference.

Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short branch lengths and low values for non-Bayesian measures of support such as nonparametric bootstrapping. For the four-taxon case when the true tree is the star phylogeny, Bayesian analyses become increasingly unpredictable in their preference for one of the three possible resolved tree topologies as data set size increases. This leads to the prediction that hard (or near-hard) polytomies in nature will cause unpredictable behavior in Bayesian analyses, with arbitrary resolutions of the polytomy receiving very high posterior probabilities in some cases. We present a simple solution to this problem involving a reversible-jump Markov chain Monte Carlo (MCMC) algorithm that allows exploration of all of tree space, including unresolved tree topologies with one or more polytomies. The reversible-jump MCMC approach allows prior distributions to place some weight on less-resolved tree topologies, which eliminates misleadingly high posteriors associated with arbitrary resolutions of hard polytomies. Fortunately, assigning some prior probability to polytomous tree topologies does not appear to come with a significant cost in terms of the ability to assess the level of support for edges that do exist in the true tree. Methods are discussed for applying arbitrary prior distributions to tree topologies of varying resolution, and an empirical example showing evidence of polytomies is analyzed and discussed.

Bayes Theorem↗
PubMed2004

Testing geographical pathways of speciation in a recent island radiation.

Determining the mode, or geographical context, of speciation is a critical first step to understanding the evolutionary mechanisms that cause new species to arise. In this study, we estimated phylogenetic relationships in the cerasina species group of the Hawaiian cricket genus Laupala (Orthoptera: Gryllidae) to test competing phylogeographical hypotheses and thus infer the mode of speciation. A previous phylogenetic result based on nuclear sequence data suggested that populations of L. cerasina on the Big Island of Hawaii are the result of two independent colonizations from Maui, implying parallel speciation and convergent song evolution, and contradicting systematic hypotheses based on behavioural and morphological data. We used amplified fragment length polymorphisms to investigate further the relationships among species and populations in the cerasina species group. Results of these analyses provide a robust estimate of phylogenetic relationships and support the phylogeographical history indicated by behavioural and morphological data.

Animals↗
PubMed1991

An improved photochemical model of embolic cerebral infarction in rats.

To provide further evidence that the multiple cerebral infarcts found in rats following photochemical damage to the carotid artery are caused by emboli and to eliminate the systemic hypotension and heating of the blood reported with the previous photochemical embolic stroke model (rose bengal and a green laser), I have modified the photochemical technique. Brain pathology was studied in 18 Wistar rats following carotid artery irradiation with a red laser (632 nm) at powers ranging from 100 to 800 mW/cm2 for 10 or 20 minutes following the injection of the photosensitizing dye Photofrin II. Multiple cerebral arterioles were occluded by platelet aggregates containing frequent erythrocytes and leukocytes, identical to the thrombotic material in the carotid artery but different from the platelet aggregates seen in the carotid artery and the brain in the rose bengal model. Eighty infarcts were distributed randomly throughout the brain ipsilateral to the nonocclusive carotid thrombus. Significant heating (0.5 degree C or more) of the blood occurred only with laser powers higher (1,600 mW/cm2) or laser irradiations longer (25 minutes) than those used in the improved model of embolic stroke. This model mimics one mechanism of stroke in humans and provides a means to study systematically the morphological evolution of small cerebral infarcts.

Animals↗
PubMed1996

Developmental cardiac electrophysiology recent advances in cellular physiology.

This overview of cardiac ion channel development does not suggest any particular theme underlying the expression or regulation of all channel subtypes. Calcium and potassium channels generally exhibit increased expression in more mature hearts. However, this increase in channel number or activity as determined under voltage clamp conditions may not be translated into increased activity in vivo. Concomitant changes in other physiological factors such as local intracellular Ca2+ accumulation, increased resting membrane potential and decreased heart rate in mature heart may inhibit or augment channel activity. Na(+)-Ca2+ exchange activity appears to decrease with development, possibly reflecting its decreasing role in both systolic and diastolic Ca2+ regulation. Na+ channel activity follows a middle course, exhibiting little change in channel conductance. The reported shift in the voltage dependence of channel inactivation toward more negative membrane potentials may reflect a concomitant shift in the resting membrane potential in mature heart. However, this change is in the direction opposite to that reported for L-type Ca2+ channel inactivation, suggesting that the regulation of these channels is not modulated by a common factor such as membrane surface charge. A detailed characterization of multiple channel subtypes in mature myocardium has resulted in significant advances in models of the cardiac action potential and excitation-contraction coupling. Recently, developmental changes in ion channel physiology have been described, setting the stage for a comparable elucidation of the ontogeny of the cardiac action potential. Ca2+ and K+ channel currents generally become more prominent with development. In contrast, developmental changes in Na+ currents are less dramatic and Na(+)-Ca2+ exchange currents appear to decrease with age. These changes may, in part, be reflected by the increasingly important role of transsarcolemmal Ca2+ influx in triggering Ca2+ release from the SR in mature heart as compared to its direct role of providing Ca2+ for cell contraction in immature heart. These developmental changes in ion channel expression and function are likely to have a significant effect on the generation of the action potential in individual myocytes. Developmental changes in the characteristics of the action potential may then have a major influence on the initiation, propagation and termination of autonomic, triggered, and re-entrant arrhythmias. Progress in this area provides an essential foundation for the evolution of a systematic approach to pediatric arrhythmias comparable to that under development for mature heart [3].

Animals↗
PubMed1997

Molecular systematics of Middle American cichlid fishes and the evolution of trophic-types in 'Cichlasoma (Amphilophus)' and 'C. (Thorichthys)'.

The majority of Middle American cichlids are placed in the informal assemblage 'Cichlasoma.' The group is divided into eight sections which appear to be based primarily on trophic morphology. Although several members of 'Cichlasoma' have been used in ecomorphological, behavioral, and biogeographic studies, no phylogenetic hypotheses for the group exist. In an attempt to develop a better understanding of the phylogenetic relationships of 'cichlasomine' cichlids, we examined the evolution of the trophic specialization, substratum-sifting, in two sections, 'Cichlasoma (Thorichthys)' and 'C. (Amphilophus),' to determine whether the trait reflects common ancestry. We sequenced the complete mitochondrial cytochrome b gene for 19 cichlids representing six sections of 'Cichlasoma,' and representatives of other Neotropical Cichlidae. Additional cichlid, and noncichlid outgroup sequences were included for a total of 22 taxa. The molecular phylogeny supports the recognition of the section 'C. (Thoricthys)' as a natural group, and we place those cichlids in the genus Thorichthys. The phylogeny also depicts 'C. (Amphilophus)' as paraphyletic, with substratum-sifters and generalized predators forming separate nonsister clades. We recommend that the substratum-sifting clade of the section 'C. (Amphilophus)' be placed in the resurrected genus Astatheros. The generalized predator clade of 'C. (Amphilophus)' contains only two species, 'C. (A.) citrinellum' and 'C. (A.) labiatum,' which we place in the genus Amphilophus. The phylogenetic hypotheses generated indicate that the substratum-sifting genera Thorichthys and Amphilophus do not share a common ancestor. Reconstruction of the evolution of substratum-sifting is equivocal, requiring either the independent evolution of the trait on two separate occasions or its presence in a more inclusive clade and subsequent loss in nonsubstratum sifting species.

Americas↗
PubMed1999

Systematic changes in gene expression patterns following adaptive evolution in yeast.

Culturing a population of Saccharomyces cerevisiae for many generations under conditions to which it is not optimally adapted selects for fitter genetic variants. This simple experimental design provides a tractable model of adaptive evolution under natural selection. Beginning with a clonal, founding population, independently evolved strains were obtained from three independent cultures after continuous aerobic growth in glucose-limited chemostats for more than 250 generations. DNA microarrays were used to compare genome-wide patterns of gene expression in the evolved strains and the parental strain. Several hundred genes were found to have significantly altered expression in the evolved strains. Many of these genes showed similar alterations in their expression in all three evolved strains. Genes with altered expression in the three evolved strains included genes involved in glycolysis, the tricarboxylic acid cycle, oxidative phosphorylation, and metabolite transport. These results are consistent with physiological observations and indicate that increased fitness is acquired by altering regulation of central metabolism such that less glucose is fermented and more glucose is completely oxidized.

Adaptation, Physiological↗
PubMed1992

Evolution of the common cetacean highly repetitive DNA component and the systematic position of Orcaella brevirostris.

The common cetacean highly repetitive DNA component was analyzed with respect to its evolution and value for establishing phylogenetic relationships. The repeat length of the component, which is tandemly organized, is approximately 1750 bp in all cetaceans except the delphinids, in which the repeat length is approximately 1580 bp. The evolution of the component was studied after sequencing the component in different odontocetes representing the Delphinidae (delphinids), Monodontidae (narwhals), and Ziphiidae (beaked whales). The evolution of this component is very slow, and comparisons showed that sequence divergence among species corresponds closely to their generally accepted phylogenetic relationships and that the component evolves in a concerted manner. The phylogenetic information obtained in this study identified the Irrawaddy dolphin (Orcaella brevirostris) as a delphinid and did not support a close relationship of this species with the Monodontidae.

Animals↗
PubMed2006

A primate-specific acceleration in the evolution of the caspase-dependent apoptosis pathway.

Programmed cell death, or apoptosis, plays an essential role in mammalian development, especially the development of the nervous system. Here, we systematically examine the molecular evolution of the mammalian intrinsic apoptosis program. We divided the program into its several constituent pathways and examined the evolution of each pathway in diverse mammalian taxa spanning primates, rodents and carnivores. We observed that genes involved in the caspase-dependent apoptosis pathway stood out in several ways. First, these genes display an accelerated rate of protein sequence evolution in primates relative to rodents or carnivores. Secondly, this acceleration is most pronounced along the lineage leading to humans, and it is associated with signatures of positive selection. Finally, several genes in this pathway, including APAF1, CASP9 and CASP3, have been shown to be associated with dramatic defects in neuronal cell number and brain size when mutated in mice. These observations suggest the possibility that evolutionary changes in the caspase-dependent apoptosis pathway may have contributed to brain evolution in primates and humans. Our results also lend further support to the hypothesis that genes regulating brain size during development might have played a particularly important role in transforming brain size during evolution.

Animals↗
PubMed1994

The origin of vertebrate limbs.

The earliest tetrapod limbs are polydactylous, morphologically varied and do not conform to an archetypal pattern. These discoveries, combined with the unravelling of limb developmental morphogenetic and regulatory mechanisms, have prompted a re-examination of vertebrate limb evolution. The rich fossil record of vertebrate fins/limbs, although restricted to skeletal tissues, exceeds the morphological diversity of the extant biota, and a systematic approach to limb evolution produces an informative picture of evolutionary change. A composite framework of several phylogenetic hypotheses is presented incorporating living and fossil taxa, including the first report of an acanthodian metapterygium and a new reconstruction of the axial skeleton and caudal fin of Acanthostega gunnari. Although significant nodes in vertebrate phylogeny remain poorly resolved, clear patterns of morphogenetic evolution emerge: median fin origination and elaboration initially precedes that of paired fins; pectoral fins initially precede pelvic fin development; evolving patterns of fin distribution, skeletal tissue diversity and structural complexity become decoupled with increased taxonomic divergence. Transformational sequences apparent from the fish-tetrapod transition are reiterated among extant lungfishes, indicating further directions for comparative experimental research. The evolutionary diversification of vertebrate fin and limb patterns challenges a simple linkage between Hox gene conservation, expression and morphology. A phylogenetic framework is necessary in order to distinguish shared from derived characters in experimental model regulatory systems. Hox and related genomic evolution may include convergent patterns underlying functional and morphological diversification. Brachydanio is suggested as an example where tail-drive patterning demands may have converged with the regulation of highly differentiated limbs in tetrapods.

Animals↗
PubMed2005

Shadows of culture in psychosis in south India: a methodological exploration and illustration.

Transcultural studies suggest a possible influence of culture on the course and outcome of schizophrenia. However, the notion of culture remains ill-defined in these studies; most often, hypotheses regarding protective factors seem to derive more from stereotyped visions of cultural differences than be empirically based. Explorative studies conducted in south India consider subjective experience as a key mediating variable between culture and course and outcome in schizophrenia. They explore patients and relatives experience and its evolution and aim at identifying the explicit and implicit references to culture throughout the narratives. Ethnographically oriented data collected through an open-ended Turning Point/Period Interview systematically reconstructs the perceived evolution of signs, coping, explanations, reactions and help-seeking from different perspectives. This paper examines the degree of convergence and divergence between narratives collected from a small sample of female schizophrenic patients and one of their relatives. A high degree of convergence at the level of symptoms and differences in their narrative construction are observed.

Adaptation, Psychological↗
PubMed2004

Conflicting interests: the evolution of an issue.

The systematic funding of University research has brought into relief a question of conflicting interests. The potential in funded research for conflict and the damaging effects that conflicting interests might have on civil society had been first noted by Eisenhower in the context of State-funded research. Since the 1980s, there has been greater concern with the corrosive effects of private or corporate funding on research. Initial efforts to manage the problems have focused on authorship declarations, but recent controversies with the SSRIs suggest the only way to manage the problem is by placing all clinical trial data in the public domain.

Access to Information↗
PubMed2006

Evolution of vaccination rates after the implementation of a free systematic pneumococcal vaccination in Catalonian older adults: 4-years follow-up.

BACKGROUND: The systematic vaccination with 23-valent polysaccharide pneumococcal vaccine (PPV) was introduced as a strategic objective of health for all the people over 65 in Catalonia in 1999. We analysed the evolution of the pneumococcal vaccination rates from 2000 to 2003. METHODS: We conducted a retrospective population-based study including all the individuals 65 years or older assigned to 8 Primary Care Centres (PCCs) in Tarragona (Catalonia, Spain), who figured in the administrative population databases on 31 December 2003 (n = 10,410 persons). We assessed whether every person had received PPV during the last four years (2000 to 2003) or whether they had received it before January 2000. Data sources were the computerised clinical records of the 8 participating PCCs, which included adult vaccination registries and diagnoses coded of International Classification of Diseases 9th REVIEW RESULTS: The overall vaccination uptake increased to 38.6% at the end of 2000. Global accumulated coverages increased more slowly the following years: 44.4% in 2001, 50.9% in 2002, and 53.1% at the end of 2003. Vaccine uptake varied significantly according to age (46.7% in people 65-74 years-old, 60.9% in people 75 years or more; p < 0.001) and number of diseases or risk factors (DRFs) for pneumonia (47.1% vaccinated in people without DRFs, 56.8% in patients with one DRF, and 62.2% in patients with two or more DRFs; p < 0.001). The highest coverages were observed among those patients with: diabetes (65.9%), active neoplasia (64.8%), history of stroke (63.7%), and chronic lung disease (63.5%). The lowest uptake was observed among smokers (48.7%). DISCUSSION: The pneumococcal vaccination coverage increased quickly after the introduction of the recommendation for free vaccination in all the elderly people (with and without risk factors), but two years after the improvement the coverage became stable and increased slowly.

Age Factors↗