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Results for “systematic evolution”

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PubMed2005

Less is more: towards an optimal universal description of protein folds.

MOTIVATION: Identification and characterization of protein structure regularities can reveal the mechanisms governing protein structure, function and evolution. Here we focus on an intermediate level of regularity. We have developed automated methods to systematically construct a dictionary of supersecondary structures that can be used as 'protein parts' to describe fold-sized structures. RESULTS: The dictionary was constructed by aligning representative structures of all known folds, clustering similar substructures and selecting the most descriptive substructures in a minimum description length fashion. We show that the dictionary is compact and descriptive, capable of describing a substantial fraction of all known protein folds. We performed simulations using independent sets of training and testing folds. Dictionaries generated using the training set had high coverage over the folds in the testing set, suggesting that dictionary entries reflect general features of protein structures and should be capable of describing novel protein folds.

Algorithms↗

PubMedDate not supplied

Prenatal psychosocial factors and the neuroendocrine axis in human pregnancy.

OBJECTIVE: Physiological processes including neuroendocrine function have been proposed as mediators of the relationship between prenatal psychological state and pregnancy outcome; however, there are virtually no human studies that have systematically assessed such mechanisms. Neuroendocrine processes are significantly altered during pregnancy, and are characterized by the evolution of a transient neuroendocrine system, the placenta, and modifications in endocrine control mechanisms. Because these alterations have implications for neuroendocrine responsivity to exogenous conditions, the aim of the present study was to examine the cross-sectional association between prenatal psychosocial factors and stress-related neuroendocrine parameters during human pregnancy. METHOD: Fifty-four adult women with a singleton, intrauterine pregnancy were recruited before 28 weeks of gestation. Maternal antecubital venous blood samples were withdrawn at 28 weeks of gestation for bioassays of adrenocorticotropin hormone (ACTH), beta-endorphin (beta E), and cortisol. Measures of prenatal stress, social support, and personality were collected using a two-part, self-report questionnaire administered at 28 and 30 weeks of gestation. Biomedical data were obtained from the medical record. Factors known to influence neuropeptide and hormone levels during pregnancy were controlled, including gestational age, circadian variation, and obstetric risk. RESULTS: In the present sample, prenatal psychosocial stress, social support, and personality variables were associated with neuroendocrine parameters in two primary ways. First, certain psychosocial factors were significantly associated with plasma levels of ACTH, beta E, and cortisol, and second, psychosocial factors were associated with a measure of disregulation of the normal relationship between two pro-opiomelanocortin (POMC) derivatives, ACTH and beta E. Furthermore, a combination of the maternal psychosocial and sociodemographic factors during pregnancy accounted for 36% of the variance in ACTH, 22% of the variance in the ACTH-beta E disregulation index, 13% of the variance in cortisol, and 3% of the variance in beta E. CONCLUSIONS: The present findings are consistent with the premise that maternal-placental-fetal neuroendocrine parameters are significantly associated, both in magnitude and specificity, with features of maternal psychosocial functioning in pregnancy despite the systemic alterations associated with the endocrinology of pregnancy. These findings provide a basis for further investigations of the role of the neuroendocrine system as a putative mediating pathway between prenatal psychosocial factors and birth outcome, and possibly also as a mechanism linking features of the maternal psychosocial environment to fetal/infant brain development.

Adrenocorticotropic Hormone↗

PubMed2000

Non-random dispersal in the butterfly Maniola jurtina: implications for metapopulation models.

The dispersal patterns of animals are important in metapopulation ecology because they affect the dynamics and survival of populations. Theoretical models assume random dispersal but little is known in practice about the dispersal behaviour of individual animals or the strategy by which dispersers locate distant habitat patches. In the present study, we released individual meadow brown butterflies (Maniola jurtina) in a non-habitat and investigated their ability to return to a suitable habitat. The results provided three reasons for supposing that meadow brown butterflies do not seek habitat by means of random flight. First, when released within the range of their normal dispersal distances, the butterflies orientated towards suitable habitat at a higher rate than expected at random. Second, when released at larger distances from their habitat, they used a non-random, systematic, search strategy in which they flew in loops around the release point and returned periodically to it. Third, butterflies returned to a familiar habitat patch rather than a non-familiar one when given a choice. If dispersers actively orientate towards or search systematically for distant habitat, this may be problematic for existing metapopulation models, including models of the evolution of dispersal rates in metapopulations.

Animals↗

PubMed2000

Extensive duplication and reshuffling in the Arabidopsis genome.

Systematic analysis of the Arabidopsis genome provides a basis for detailed studies of genome structure and evolution. Members of multigene families were mapped, and random sequence alignment was used to identify regions of extended similarity in the Arabidopsis genome. Detailed analysis showed that the number, order, and orientation of genes were conserved over large regions of the genome, revealing extensive duplication covering the majority of the known genomic sequence. Fine mapping analysis showed much rearrangement, resulting in a patchwork of duplicated regions that indicated deletion, insertion, tandem duplication, inversion, and reciprocal translocation. The implications of these observations for evolution of the Arabidopsis genome as well as their usefulness for analysis and annotation of the genomic sequence and in comparative genomics are discussed.

Arabidopsis↗

PubMedDate not supplied

[Imported tropical parasitosis in Rumania].

The frequency of intestinal parasitoses among subjects coming from warm countries is high and its range is similar to that found by other parasitologists in Europe as well as by those who made investigations in groups of individuals in various warm countries. Bearing in mind the pathogenous role--even limited--of certain parasites, their systematic detection and the treatment of every individual infested with parasites appears necessary. The hereby investigations point out the importance of a complex coproparasitologic examination and the high efficiency of some special diagnosis methods. Every laboratory must perform in rarallel several ovoscopic and larvoscopic methods of investigation in view of an accurate parasitologic diagnosis or for a prophylactic control of subjects coming from warm countries. The high frequency of ankylostomiasis raises peculiar problems related to its systematic detection and its compulsory treatment up to the parasitologic sterilization, bearing in mind the past evolution in Rumania of an underground focus, which does not exist any more, having been entirely eradicated.

Ancylostomiasis↗

PubMed2000

Phytochemistry and the systematics and ecology of Loasaceae and Gronoviaceae (Loasales).

A screening for iridoid compounds of 78 of 315 species from all major groups in Gronoviaceae and Loasaceae has been carried out. The results were compared to the systematic concepts in the family and distribution and ecology of the taxa. Iridoids are present in at least some species of all genera screened. Some simple, monomeric compounds (e.g., loganin, sweroside) are found in all major groups of the two families and represent the basic iridoid inventory. Other compounds are restricted to certain taxonomic groups: nine-carbon iridoids (e.g., deutzioside) are restricted to Mentzelia (Loasaceae subfam. Mentzelioideae), hetero-oligomeric iridoids (e.g., tricoloroside methyl ester, acerifolioside) are restricted to two small groups in Loasa (Loasa ser. Macrospermae and ser. Floribundae, Loasaceae subfam. Loasoideae), and oleosides (e.g., 10-hydroxyoleoside dimethyl ester) are restricted to the large genus Caiophora sensu Weigend). The distribution of certain iridoid compounds thus confirms some of the generic limits. Iridoid phytochemistry does not correlate with systematic entities above the generic level nor does it in any way correlate with the morphological evolution of taxa. Conversely, the amount and complexity of iridoid compounds present in taxa correlate positively with the aridity of their habitat and the extent of mammalian herbivore pressure.

Journal Article↗

PubMed2001

Silver staining of nucleolar organizer regions (NOR) in some species of Hymenoptera (bees and parasitic wasp) and Coleoptera (lady-beetle).

Adaptations of the nucleolar organizer regions (NOR) banding technique using precipitation of silver salts significantly improved the NOR characterization of some species of hymenopterans and one coleopteran. The bee Melipona marginata (2n = 18) showed one metacentric pair of chromosomes with a NOR in the pericentromeric position. The parasitic wasp Mellitobia australica (2n = 12) also showed one metacentric pair with a strongly Ag-positive NOR. The male lady-beetle Cycloneda sanguinea (2n = 18 + Xy(p)) displayed a NOR on a pair of acrocentric autosomes. In the male Euglossa sp. (a haplodiploid species) (n = 21) the NOR were multiple, and occurred in five chromosomes. In the bee Plebeia sp. 1 (2n = 34) the NOR seemed restricted to one of the homologues of a metacentric pair. The systematic advances brought out by using this technique in the context of current theories of karyotypic evolution of these taxa are described and discussed.

Animals↗

PubMedDate not supplied

[The risk of grave evolution of tuberculosis in young children (under 2 years of age)].

Between 1971 and 1972, 22% of all children under two years with tuberculosis presented with severe forms of the disease (meningitis, miliaria, caseous forms). In the period 1974-1975, although the number of cases in the group was reduced by half, the severe forms still represented 20,4% of the total. The risk of severe evolution of tuberculosis decreases rapidly, from 55--66% in the first months of life. to 14,2--15,5% at 1--2 years. The risk of death in children aged between 0 and 2 years with tuberculosis (all forms) was of 26,6--58,3% between 0 and 5 months but only 4,5--9,3% in the second year of life. The risk of death in young children with severe forms of tuberculosis was as high as 70--76,7% in those under the age of 6 months. The source of infection was identified in 72,4--76,4% of the severe cases. At the onset of the disease only 57,1% of the sources were known, while 42,9% were discovered later, by epidemiologic investigations. An analysis of cause for a severe evolution of tuberculosis in young children led to the conclusion that BCG vaccination should be performed systematically at birth, and that tuberculin skin test be carried out in all hospitalized children, regardless the diagnosis. They also recommend the use of anamnestic data concerning the possible existence of tuberculosis cases in the families of patients, performing of radiologic controls in young mothers etc. In the case of infants that come into a close contact at a very early age with parents, or other relatives suffering with tuberculosis, chemoprophylaxis with two associated tuberculostatics is indicated.

Age Factors↗

PubMed1985

[Intravascular bronchioloalveolar tumor or I.V.B.A.T. Apropos of a case and review of the literature].

Intravascular bronchioloalveolar tumor is a rare tumour of the lung. Having observed a case detected during systematic examination in a 44-year old woman, the authors compare the radiological, clinical, histological and evolutive signs of the disease with those reported in the 40 cases published since the first description by Dail and Liebow, in 1975.

Adenocarcinoma, Bronchiolo-Alveolar↗

PubMedDate not supplied

Non traumatic cerebellar hematomas.

Five cases of spontaneous cerebellar hematomas are reported. In four cases the diagnosis was made by computerized tomography. The clinical diagnosis being difficult, surgical treatment was often applied too late and the diagnosis sometimes never made. Systematic use of computerized tomography should allow earlier treatment of this type of lesion, the clinical evolution determining the prognosis. (Acta neurol. bels., 1980, 80, 73-79).

Adult↗

PubMed1993

[Radionecrosis of the optic chiasma. A clinical and radiological study of 3 cases].

The paper reports three cases of optic chiasmal radionecrosis due to radiotherapy of the sellar region. These three cases are compared with 34 ones found in literature. The use of M.R.I. is shown to dramatically improve diagnosis. Corticoids are useful in the treatment. The gravity of the complication, which implies visual prognosis, focuses on a strict use of radiotherapy. For benign or slowly evoluting lesions, surgery and/or regular controls by modern imaging techniques would often be more eligible than systematic earliest irradiation.

Adult↗

PubMed2005

Factors influencing the prevalence and handedness for throwing in captive chimpanzees (Pan troglodytes).

Humans throw right-handed, and it has been suggested that the neurophysiological demands of aimed throwing may have served as a precursor to the evolution of left hemisphere specialization for linguistic functions. Although there are descriptions of throwing by wild and captive chimpanzees (Pan troglodytes), systematic observations of aimed throwing and handedness have not been reported. In this article, evidence of population-level right-handedness for throwing is reported in 2 samples of captive chimpanzees. It is further reported that right-handed throwing is more pronounced than other measures of handedness in captive chimpanzees. The implications of these findings are discussed in the context of theories relating throwing to the evolution of lateralization for language functions.

Animals↗

PubMed2003

Cross-correlation tomography: measuring dark energy evolution with weak lensing.

A cross-correlation technique of lensing tomography is developed to probe dark energy in the Universe. The variation of weak shear with redshift around foreground galaxies depends only on the angular distances and is robust to the dominant systematic error in lensing. We estimate the margin-alized accuracies that deep lensing surveys with photometric redshifts can provide on the dark energy density Omega(de), the equation of state parameter w, and its evolution w('): sigma(w) approximately equal 0.01f(-1/2)(sky) and sigma(w(')) approximately equal 0.03f(-1/2)(sky), where a prior of sigma(Omega(de))=0.03 is assumed in the marginalization.

Journal Article↗

PubMed2023

Neotelomeres and Telomere-Spanning Chromosomal Arm Fusions in Cancer Genomes Revealed by Long-Read Sequencing.

Alterations in the structure and location of telomeres are key events in cancer genome evolution. However, previous genomic approaches, unable to span long telomeric repeat arrays, could not characterize the nature of these alterations. Here, we applied both long-read and short-read genome sequencing to assess telomere repeat-containing structures in cancers and cancer cell lines. Using long-read genome sequences that span telomeric repeat arrays, we defined four types of telomere repeat variations in cancer cells: neotelomeres where telomere addition heals chromosome breaks, chromosomal arm fusions spanning telomere repeats, fusions of neotelomeres, and peri-centromeric fusions with adjoined telomere and centromere repeats. Analysis of lung adenocarcinoma genome sequences identified somatic neotelomere and telomere-spanning fusion alterations. These results provide a framework for systematic study of telomeric repeat arrays in cancer genomes, that could serve as a model for understanding the somatic evolution of other repetitive genomic elements.

Telomere↗

PubMed1989

Spatial variations of the 3 micron emission features within UV-excited nebulae: photochemical evolution of interstellar polycyclic aromatic hydrocarbons.

We have obtained 3 microns spectra at several positions in the Orion Bar region and in the "Red Rectangle," the nebula surrounding HD 44179. The recently discovered weak emission features at 3.40, 3.46, 3.51, and 3.57 microns (2940, 2890, 2850, and 2800 cm-1) are prominent in the Orion Bar region. The 3.40 microns and 3.51 microns features increases in intensity relative to the dominant 3.29 microns (3040 cm-1) feature when going from the ionized to the neutral zone across the Orion Bar. However, only a weak and rather broad 3.40 microns feature is present at the position of HD 44179. These spectra demonstrate that some of the 3 microns emission components vary independently of each other and in a systematic way within UV-excited nebulae. This spatial variation is discussed in terms of the UV excitation and photochemical evolution of polycyclic aromatic hydrocarbons and related molecular structures. The spatial behavior of the weak emission features can be understood qualitatively in terms of hot bands of the CH stretch and overtones and combination bands of other fundamental vibrations in simple PAHs. An explanation in terms of emission by molecular sidegroups attached to the PAHs is less straightforward, particularly in the case of the Red Rectangle and other evolved mass-losing objects. We estimate PAH sizes of 20-50 carbon atoms based on the susceptibility of PAHs to destruction by the far ultraviolet fields present in the Orion Bar and the Red Rectangle; the size range is similar to independent estimates made previously.

Astronomical Phenomena↗

PubMed2002

Red queen dynamics of protein translation.

We explore adaptive theories for the diversity of translational binding based on the genetic code viewed as a primitive mechanism of resistance. Modifying the set of codons bound by tRNA anticodon molecules or changing the specificity of binding, reduces the replication rate of translational parasites such as viruses. Increased translational efficiency of the parasite requires a high degree of specificity of host tRNAs for the parasite codons. This suggests that the genetic code might serve as the first line of defense against infection. We construct a red queen theory for translational diversity: a theory in which host-translational strategies- as defined by the degree of redundancy (a single anticodon binding many codons for a single amino acid) or degeneracy (many anticodons binding many codons for a single amino acid)-are constantly shifting through time to evade parasitism but where neither parasite nor host gain a systematic advantage.

Animals↗

PubMed2005

Weighted genome trees: refinements and applications.

There are many ways to group completed genome sequences in hierarchical patterns (trees) reflecting relationships between their genes. Such groupings help us organize biological information and bear crucially on underlying processes of genome and organismal evolution. Genome trees make use of all comparable genes but can variously weight the contributions of these genes according to similarity, congruent patterns of similarity, or prevalence among genomes. Here we explore such possible weighting strategies, in an analysis of 142 prokaryotic and 5 eukaryotic genomes. We demonstrate that alternate weighting strategies have different advantages, and we propose that each may have its specific uses in systematic or evolutionary biology. Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution.

Animals↗

PubMed2004

[Contribution of molecular phylogeny and morphometrics to the systematics of African elephants].

African elephants are conventionally classified as a single species: Loxodonta africana (Blumenbach 1797). However, the discovery in 1900 of a smaller form of the African elephant, spread throughout the equatorial belt of this land, has given rise to a debate over the relevance of a second species of elephant in Africa. The twentieth century has not provided any definite answer to this question. Actually, recent molecular analyses have sustained this issue by advocating either a division of forest elephants into a valid species, or their inclusion as a subspecies of L. africana. Our work initiated at the National Museum of Natural History of Paris provides new molecular (mitochondrial) and morphological (and morphometrical) evidence making it possible to propose a comprehensive phylogenetic hypothesis. It appears that there is no conclusive argument to keep forest elephants (cyclotis form) and savannah elephants (africana form) apart in two distinct species. A high level of mitochondrial introgression between the two forms, as well as a continuum in the morphology of the skulls of the two morphotypes rather suggests that, despite an ancient division, these two taxa freely interbreed wherever their ranges intersect. We thus adopt a conservative systematic position in considering these two forms as two subspecies, respectively: L. africana africana, the savannah elephant, and L. africana cyclotis, the forest elephant. We finally discuss the conservation topic in the light of this systematic framework.

Africa↗