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PubMed2001

A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis.

BACKGROUND: Some pathogenic bacteria are genetically very homogeneous, making strain discrimination difficult. In the last few years, tandem repeats have been increasingly recognized as markers of choice for genotyping a number of pathogens. The rapid evolution of these structures appears to contribute to the phenotypic flexibility of pathogens. The availability of whole-genome sequences has opened the way to the systematic evaluation of tandem repeats diversity and application to epidemiological studies. RESULTS: This report presents a database (http://minisatellites.u-psud.fr) of tandem repeats from publicly available bacterial genomes which facilitates the identification and selection of tandem repeats. We illustrate the use of this database by the characterization of minisatellites from two important human pathogens, Yersinia pestis and Bacillus anthracis. In order to avoid simple sequence contingency loci which may be of limited value as epidemiological markers, and to provide genotyping tools amenable to ordinary agarose gel electrophoresis, only tandem repeats with repeat units at least 9 bp long were evaluated. Yersinia pestis contains 64 such minisatellites in which the unit is repeated at least 7 times. An additional collection of 12 loci with at least 6 units, and a high internal conservation were also evaluated. Forty-nine are polymorphic among five Yersinia strains (twenty-five among three Y. pestis strains). Bacillus anthracis contains 30 comparable structures in which the unit is repeated at least 10 times. Half of these tandem repeats show polymorphism among the strains tested. CONCLUSIONS: Analysis of the currently available bacterial genome sequences classifies Bacillus anthracis and Yersinia pestis as having an average (approximately 30 per Mb) density of tandem repeat arrays longer than 100 bp when compared to the other bacterial genomes analysed to date. In both cases, testing a fraction of these sequences for polymorphism was sufficient to quickly develop a set of more than fifteen informative markers, some of which show a very high degree of polymorphism. In one instance, the polymorphism information content index reaches 0.82 with allele length covering a wide size range (600-1950 bp), and nine alleles resolved in the small number of independent Bacillus anthracis strains typed here.

Bacillus anthracis↗

PubMed1992

Sinus histiocytosis with massive lymphadenopathy.

To date, the morphological aspects of sinus histiocytosis with massive lymphadenopathy (SHML) have been fully described. The disease is characterized by an enlargement of lymph nodes in which the sinuses are dilated and infiltrated by histiocytes, often phagocytosing lymphocytes. Even if the prognosis is usually benign and not requiring therapy, several fatal cases have been reported. The etiology is still obscure and the biology is not yet completely clear. Recent immunophenotypical studies suggest that histiocytes may belong to the T-zone associated histiocyte lineage. They may be cytologically homogeneous, but can express different antigenic patterns according to their stage of differentiation. Cytogenetic and molecular aspects of the disease have only been sporadically investigated. In order to better understand the pathogenesis of SHML, which seems to be a disorder lying in between the fields of infections, immunological disease and neoplasia, it is considered very useful to systematically employ a variety of immunophenotypical, cytogenetic and molecular techniques to study the disease, particularly in cases which are clinically atypical or with a more aggressive evolution.

Antigens, CD↗

PubMed1999

[Mini-Mental State Examination:a useful method for the evaluation of the cognitive status of patients by the clinician. Consensual French version].

A PRACTICAL TOOL: Screening for cognitive deficiency has been considerably improved by the use of a standardized tool, the Mini-Mental State Examination (MMSE). The MMSE only takes a few minutes and furnishes quantitative data for comparison between patients and to follow the evolution of a given patient. AN IMPORTANT ROLE: The MMSE is particularly useful for screening for dementia and states of mental confusion. It should be used systematically for elderly subjects, not only in the neurology setting, but also in geriatrics, psychiatrics and internal medicine. INTERPRETATION: The global score gives an assessment of the subject's performance level, taking into account for age, affective status and cultural situation. The MMSE cannot alone provide the diagnosis of dementia which requires a complete neurological examination. THE CONSENSUAL FRENCH VERSION: Diverse French versions have been developed with considerable differences in scoring schemes. For this reason, the Working Group on Cognitive Evaluations (GREC) has established a consensual version of the MMSE in French.

Cognition Disorders↗

PubMedDate not supplied

The impact of accurate patient assessment on quality of care.

A nurse should be able to undertake and document a comprehensive, systematic and accurate nursing assessment of a patient. A review of the literature demonstrates a clear variation in the levels of assessment. This article examines the evolution of the nursing role and the implementation of assessment tools and looks at the potential for development within the profession.

Clinical Competence↗

PubMed1996

Factor analysis in successive hepatobiliary imaging of native and transplant livers.

UNLABELLED: A young male suffering from fulminant hepatic failure of unknown origin had an auxiliary partial orthotopic liver transplantation performed. The aim of the present study was to test the performance of factor analysis of medical image sequences (FAMIS) in the post-transplantation monitoring of the graft and native liver functions. METHODS: Four successive hepatobiliary studies within 63 days following transplantation using 99mTc-mebrofenin were performed (on days 13,20,34,63). The 60 one-minute dynamic series were subjected to two successive FAMIS procedures. RESULTS: For all studies, except the first, FAMIS was able to extract three factor couples (factor images and factors or curves) those of the native liver, the graft liver and the biliary region. The factors time evolution in uptake and excretion components showed the correlations between clinical status and scintigraphic results and helped interpretation of biochemical tests. CONCLUSION: The possible utility of systematic liver transplant monitoring by radionuclide hepatobiliary imaging in identification of complications requiring medical or surgical intervention in graft livers was demonstrated. Furthermore, our study showed the functional recovery potential of the native liver in patients suffering from fulminant hepatitis.

Adolescent↗

PubMed2004

Gene relics in the genome of the yeast Saccharomyces cerevisiae.

There is increasing evidence that DNA duplication is a common and ongoing process that plays a major role in molecular evolution of genomes and that a large fraction of the duplicated gene copies becomes non-functional by accumulation of deleterious mutations. In order to describe this phenomenon, we systematically searched the 6404 intergenic regions (IRs) of the genome of Saccharomyces cerevisiae for traces of coding sequences presenting degenerated but still recognizable sequence similarity with active open reading frames (5823 annotated ORFs). We detected a total of 124 anciently coding regions, or "gene relics", showing similarity to a total of 149 distinct active ORFs. This set of relics shows a continuum of sequence degeneration from those whose sequence is slightly altered compared to the functional ORF (classically defined as pseudogenes), to those that contains so many deleterious mutations, as to reach the limit of recognition. Gene relics are more concentrated in the subtelomeric regions of the chromosomes, reflecting the high plasticity of these regions. The presence of relics also revealed ancestral duplication events of chromosomal segments that were previously undetected. Some of these segments are intermingled with the more easily recognizable ancestral blocks of duplication, indicating successive duplication events. We present a compilation of all the data available, leading to a total of 278 pseudogenes in the genome of S. cerevisiae.

Chromosomes, Fungal↗

PubMed2026

Coxsackievirus A6 on the rise: epidemiology, pathogenicity, evolutionary dynamics, and antiviral strategy.

SUMMARYIn recent years, coxsackievirus A6 (CVA6) has become a predominant cause of hand, foot, and mouth disease (HFMD) worldwide, surpassing enterovirus A71 (EV-A71) and CVA16. The rise of CVA6 is of particular public health concern due to its association with atypical and severe clinical presentations, including extensive vesiculobullous eruptions and neurological complications. These diverse and often non-classical manifestations, which also occur in adults, complicate clinical diagnosis and highlight the need for enhanced molecular surveillance. Furthermore, the potential impact of enteroviral infection during pregnancy and on neonatal outcomes remains an important clinical consideration. While both structural and non-structural proteins of CVA6 are known to contribute to viral virulence, the underlying pathogenic mechanisms are not fully understood. Continuous evolution of CVA6 through genetic variation and frequent recombination has led to the emergence of distinct lineages and recombinants, posing substantial challenges to the development of effective antivirals and vaccines. To address these gaps, this review systematically examines the global epidemiology, pathogenic mechanisms, evolutionary dynamics, current diagnostic tools, and antiviral strategies for CVA6. By integrating these perspectives, this work aims to inform public health preparedness and guide future research toward mitigating outbreaks driven by emerging recombinants and novel enterovirus serotypes.

Humans↗

PubMed1987

[Mycoplasmas and pregnancy].

The pathogenic role of mycoplasms during pregnancy remains quite controverted, depending on the studies; for some it has an incidence on prematurity, delayed growth in utero and premature rupture of the membranes. The purpose of this study was, from a population of patients with term delivery, without any specific pathology, to verify the frequency of mothers carrying Mycoplasma Hominis or ureaplasma, and to determine the possible consequences on the newborn. A linear analysis of the evolution of the samples between D0 and D6 in the mother and the new born, shows that the presence of mycoplasms in the genital passages is as frequent in this non-risk population, and that the child may be contaminated about every other time; but this contamination appears to be very transient and without any consequences on the immediate neo-natal pathology. Systematic screening of genital mycoplasms in pregnant women does not permit, therefore, to select a group of exposed patients. In newborns who are contaminated, the risk of infection appears to be very low, but it would perhaps be desirable to study the long range future evolution of healthy carriers.

Female↗

PubMed2006

Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models.

A newly compiled data set of nearly complete sequences of the large subunit of the nuclear ribosome (LSU or 28S) sampled from 31 diverse medusozoans greatly clarifies the phylogenetic history of Cnidaria. These data have substantial power to discern among many of the competing hypotheses of relationship derived from prior work. Moreover, LSU data provide strong support at key nodes that were equivocal based on other molecular markers. Combining LSU sequences with those of the small subunit of the nuclear ribosome (SSU or 18S), we present a detailed working hypothesis of medusozoan relationships and discuss character evolution within this diverse clade. Stauromedusae, comprising the benthic, so-called stalked jellyfish, appears to be the sister group of all other medusozoans, implying that the free-swimming medusa stage, the motor nerve net, and statocysts of ecto-endodermal origin are features derived within Medusozoa. Cubozoans, which have had uncertain phylogenetic affinities since the elucidation of their life cycles, form a clade-named Acraspeda-with the scyphozoan groups Coronatae, Rhizostomeae, and Semaeostomeae. The polyps of both cubozoans and hydrozoans appear to be secondarily simplified. Hydrozoa is comprised by two well-supported clades, Trachylina and Hydroidolina. The position of Limnomedusae within Trachylina indicates that the ancestral hydrozoan had a biphasic life cycle and that the medusa was formed via an entocodon. Recently hypothesized homologies between the entocodon and bilaterian mesoderm are therefore suspect. Laingiomedusae, which has often been viewed as a close ally of the trachyline group Narcomedusae, is instead shown to be unambiguously a member of Hydroidolina. The important model organisms of the Hydra species complex are part of a clade, Aplanulata, with other hydrozoans possessing direct development not involving a ciliated planula stage. Finally, applying phylogenetic mixture models to our data proved to be of little additional value over a more traditional phylogenetic approach involving explicit hypothesis testing and bootstrap analyses under multiple optimality criteria. [18S; 28S; Cubozoa; Hydrozoa; medusa; molecular systematics; polyp; Scyphozoa; Staurozoa.].

Animals↗

PubMed2005

The evolution of reproductive systems and sex-determining mechanisms within rumex (polygonaceae) inferred from nuclear and chloroplastidial sequence data.

The genus Rumex includes hermaphroditic, polygamous, gynodioecious, monoecious, and dioecious species, with the dioecious species being represented by different sex-determining mechanisms and sex-chromosome systems. Therefore, this genus represents an exceptional case study to test several hypotheses concerning the evolution of both mating systems and the genetic control of sex determination in plants. Here, we compare nuclear intergenic transcribed spacers and chloroplast intergenic sequences of 31 species of Rumex. Our phylogenetic analysis supports a systematic classification of the genus, which differs from that currently accepted. In contrast to the current view, this new phylogeny suggests a common origin for all Eurasian and American dioecious species of Rumex, with gynodioecy as an intermediate state on the way to dioecy. Our results support the contention that sex determination based on the balance between the number of X chromosomes and the number of autosomes (X/A balance) has evolved secondarily from male-determining Y mechanisms and that multiple sex-chromosome systems, XX/XY1Y2, were derived twice from an XX/XY system. The resulting phylogeny is consistent with a classification of Rumex species according to their basic chromosome number, implying that the evolution of Rumex species might have followed a process of chromosomal reduction from x = 10 toward x = 7 through intermediate stages (x = 9 and x = 8).

Base Sequence↗

PubMed2004

Understanding protein dispensability through machine-learning analysis of high-throughput data.

MOTIVATION: Protein dispensability is fundamental to the understanding of gene function and evolution. Recent advances in generating high-throughput data such as genomic sequence data, protein-protein interaction data, gene-expression data and growth-rate data of mutants allow us to investigate protein dispensability systematically at the genome scale. RESULTS: In our studies, protein dispensability is represented as a fitness score that is measured by the growth rate of gene-deletion mutants. By the analyses of high-throughput data in yeast Saccharomyces cerevisiae, we found that a protein's dispensability had significant correlations with its evolutionary rate and duplication rate, as well as its connectivity in protein-protein interaction network and gene-expression correlation network. Neural network and support vector machine were applied to predict protein dispensability through high-throughput data. Our studies shed some lights on global characteristics of protein dispensability and evolution. AVAILABILITY: The original datasets for protein dispensability analysis and prediction, together with related scripts, are available at http://digbio.missouri.edu/~ychen/ProDispen/ CONTACT: xudong@missouri.edu.

Artificial Intelligence↗

PubMed1994

Complete primary structure of the sixth chain of human basement membrane collagen, alpha 6(IV). Isolation of the cDNAs for alpha 6(IV) and comparison with five other type IV collagen chains.

Basement membranes were previously believed to contain five distinct type IV collagen subunits. We have recently isolated part of the cDNA for a novel type IV collagen, alpha 6(IV), and shown that COL4A6, the gene encoding this new chain, is deleted in Alport syndrome-associated leiomyomatosis (Zhou, J., Mochizuki, T., Smeets, H., Antignac, C., Laurila, P., de Paepe, A., Tryggvason, K., and Reeders, S. T. (1993) Science 261, 1167-1169). Here, we describe the entire human alpha 6(IV) cDNA and show that the gene encodes a classical type IV collagen with homology throughout its length to all the other five chains. There is a 21-residue signal peptide, a 1417-residue collagenous domain interrupted at 25 points, and a 228-residue carboxyl-terminal non-collagenous domain. When the complete primary structure of this new chain was compared with all the other known chains, it became clear that alpha 6(IV) has the most resemblance to alpha 2(IV) and alpha 4(IV). The evolution of the six chains was deduced, allowing a new classification of the type IV collagen family. The alpha 6(IV) chain is a candidate gene for X-linked Alport syndrome; knowledge of the complete structure of the chain will permit us to screen systematically for mutations in patients and to generate recombinant proteins and synthetic peptides for further study of cell-matrix interactions involving the alpha 6(IV) chain.

Amino Acid Sequence↗

PubMed2006

Testing the directionality of evolution: the case of chydorid crustaceans.

Although trends are of central interest to evolutionary biology, it is only recently that methodological advances have allowed rigorous statistical tests of putative trends in the evolution of discrete traits. Oligomerization is one such proposed trend that may have profoundly influenced evolutionary pathways in many types of animals, especially arthropods. It is a general hypothesis that repeated structures (such as appendage segments and spines) tend to evolve primarily through loss. Although largely untested, this principle of loss is commonly invoked in morphological studies of crustaceans for drawing conclusions about the systematic placements of taxa and about their phylogeny. We present a statistical evaluation of this hypothesis using a molecular phylogeny and character matrix for a family of crustaceans, the Chydoridae, analysed using maximum likelihood methods. We find that a unidirectional (loss-only) model of character evolution is a very poor fit to the data, but that there is evidence of a trend towards loss, with loss rates of structures being perhaps twice the rates of gain. Thus, our results caution against assuming loss a priori, in the absence of appropriate tests for the characters under consideration. However, oligomerization, considered as a tendency but not a rule, may indeed have had ramifications for the types of functional and ecological shifts that have been more common during evolutionary diversification.

Cladocera↗

PubMed2004

Delineation of the conserved functional properties of D1A, D1B and D1C dopamine receptor subtypes in vertebrates.

The three main subtypes of dopamine D(1) receptor (D(1A), D(1B) and D(1C)) subtypes found in most vertebrate groups were generated by two major steps of gene duplications, early in evolution. To identify the functional characteristics contributing to conservation of these paralogous D(1) receptors in vertebrates, the pharmacological and functional properties of fish (Anguilla anguilla), amphibian (Xenopus laevis) and human receptors were systematically analysed in transfected cells. The ligand-binding parameters appeared essentially similar for orthologous receptors, but differed significantly among the subtypes. The D(1A) receptors from the three species displayed low intrinsic activity and a fast rate of agonist-induced desensitization. All the orthologous D(1B) receptors exhibited a similar desensitization time-course, but with smaller amplitude of decrease than D(1A) receptors, in agreement with their higher basal activity. In contrast, D(1C) receptors, which do not exist in mammals, have low intrinsic activity and exhibit only weak, but rapid, agonist-induced desensitization, without any changes upon longer treatment with agonist. Thus, each of the three D(1) receptor subtypes are characterized by activation and desensitization properties, in a sequence-specific manner, which has been probably acquired early after gene duplications, and constrained their conservation during vertebrate evolution. These properties have been instrumental to adapt dopamine system to the physiology of the numerous neuronal networks and functions they control in the large and complex brains of vertebrates.

Animals↗

PubMed1993

The fractal geometry of evolution.

This study is aimed at showing that the fractal geometry of taxonomic systems (Burlando, 1990) reflects self-similar evolutionary pattern. Evidence is achieved by three steps: (i) examination of taxonomic data from the fossil record; (ii) examination of taxonomic data from phylogenetic systematics; (iii) comparisons among different levels of the taxonomic hierarchy. In each step, all or nearly all the examined assemblages yield frequency distributions of numbers of subtaxa within taxa which fit a hyperbolic model function, confirming the fractal pattern. The first two steps show that the pattern is not deriving from classification bias, while the third one verifies the self-similarity of evolutionary radiations. According to the first and third step, self-similar cladogenesis consists in the arising of many isolated lineages and clumps of lines, the latter consisting of isolated lines and clumps, and so on. The properties of fractals led to the hypothesis that scaling diversity emerging from taxonomy could actually encompass the species level, thus limiting the importance of species within the evolutionary context in favour of a more comprehensive view of life diversification.

Animals↗

PubMed2002

Evolution of insular Pacific Pittosporum (Pittosporaceae): origin of the Hawaiian radiation.

We investigated the origin of Hawaiian Pittosporum and their relationship to other South Pacific Pittosporum species using internal transcribed spacer sequences of nuclear ribosomal DNA. We performed both maximum-parsimony and maximum-likelihood analyses, which produced congruent results. Sequence divergence was 0.0% between Hawaiian members of Pittosporum. These taxa formed a strongly supported clade, suggesting a single colonization event followed by phyletic radiation. Sister to the Hawaiian clade were two South Pacific species, P. yunckeri from Tonga and P. rhytidocarpum from Fiji. This result presents convincing evidence for a South Pacific origin of Hawaiian Pittosporum. Our results also identify a monophyletic group comprising three species representing the Fijian Province and East Polynesia, two introductions onto New Caledonia, and at least one (but possibly two) introduction(s) onto New Zealand. Whether the New Zealand taxa form a monophyletic group is unclear from these data. Previous morphologically based hypotheses, however, suggest the presence of four different lineages occupying New Zealand. The nonmonophyly of the New Caledonian species was not surprising based on the extent of their morphological diversity. Although this latter result is not strongly supported, these species are morphologically complex and are currently the subject of taxonomic revision and molecular systematic analyses.

Base Sequence↗

PubMed2006

[Influence of the size and the localization of metastases in melanoma sentinel lymph nodes on the results of lymphadenectomy].

AIM: Thirty-five cases of lymphadenectomy carried out in the context of positive sentinel lymph node for malignant melanoma have been reviewed to assess the prognostic value of certain metastatic charachteristics. We have checked wether the type (macro or micrometastasis) and localisation (subcapsular or intraparenchymal) in the sentinel lymph node had predictive value for the lymphadenectomy outcome and evolution of the case. MATERIAL AND METHODS: The retrospective study relates to 35 cases (with an average 2 years history) taken from a total of 87 sentinel lymph node protocols; average age 46.5 years, Breslow 2.5 mm with an history of 25 months. RESULTS: Among the 35 positive sentinel lymph nodes we have 19 cases (54.2%) of micrometastasis. Among the 35 lymphadenectomy 5 cases (14.28%) turned out positive, 3 of which concerned micrometastatic sentinel lymph nodes. In our cohort the micrometastatic nature of sentinel lymph nodes did not have statistically significant impact upon the lymphadenectomy result but showed more favourable short-term evolution with 68.42% metastatic free evolution as against 43.75% in case of initial macrometastasis. The subcapsular localisation of micrometastasis equally represents a factor of improved prognosis (69.2% of metastatic free evolution against of 30.8% in the case of intraparenchymal localistion). CONCLUSION: Unfortunately, none of the studied criteria justifies a modification of our present clinical attitude whereby a systematic lymphadenectomy in cases of positive sentinel lymph nodes is performed, whatever the type or localisation of the relevant metastases.

Adult↗

PubMed2002

What role for radiosurgery in mesial temporal lobe epilepsy.

SUMMARY: The Gamma Knife radiosurgery is a neurosurgical approach having now demonstrated well its efficiency, its low morbidity and its comfort in the treatment of numerous neurosurgical disorders. These advantages of this type of intervention make it a method of great interest in functional neurosurgery and quite particularly in surgery of epilepsy. French experience is a pioneer one in this domain. Since for several years the positive evolution of the epilepsy associated with brain lesions had been noticed after radiosurgical Gamma Knife treatment, the use of this approach in surgery of epilepsy has been systematically evaluated since 1993. Data are today available concerning the surgical treatment of the epilepsies originating in the temporomesial area without space-occupying process, epilepsies associated to hypothalamic hamartomas and epilepsies associated with cavernous angiomas or low grade gliomas. The quality of the epileptological result obtained in these various indications associated with a very reduced morbidity lets assume that the Gamma Knife radiosurgery could indeed have tomorrow a place within the sample group of surgical approaches dedicated to the treatment of severe epilepsies. However, a larger number of treated patients and a more prolonged follow-up remains necessary to assess this approach in a more definitive way.

Epilepsy, Temporal Lobe↗