SEARCH · PubMed Health

Results for “systematic evolution”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,333 records · Page 74Linked to original sources

PubMed1997

Myositis ossificans: report of seven cases in children.

The clinical features of seven children with myositis ossificans (circumscripta and progressiva) and radiographic signs of the disease are described. We recommend systematic radiological examination to seek other skeletal malformations for congenital hallux valgus in young children, for it may be the first sign of a myositis ossificans progressiva. The "zone phenomenon" observed on histology, along with differential diagnosis and evolution, is documented. The necessity of a biopsy and different forms of treatment are discussed.

Adolescent↗

PubMed2002

Evolution of ecological traits and wing morphology in Hemileuca (Saturniidae) based on a two-gene phylogeny.

We present a molecular phylogeny for the genus Hemileuca (Saturniidae), based on 624 bp of mitochondrial cytochrome oxidase I (COI) and 932 bp of the nuclear gene elongation factor 1 alpha (EF1alpha). Combined analysis of both gene sequences increased resolution and supported most of the phylogenetic relationships suggested by separate analysis of each gene. However, a maximum parsimony (MP) model for just COI sequence from one sample of most taxa produced a phylogeny incongruent with EF1alpha and combined dataset analyses under either MP or ML models. Time of year and time of day during which adult moths fly corresponded strongly with the phylogeny. Although most Hemileuca are diurnal, ancestral Hemileuca probably were nocturnal, fall-flying insects. The two-gene molecular phylogeny suggests that wing morphology is frequently homoplastic. There was no correlation between the primary larval hostplants and phylogenetic placement of taxa. No phylogenetic pattern of specialization was evident for single hostplant families across the genus. Our results suggest that phenological behavioral characters may be more conserved than the wing morphology characters that are more commonly used to infer phylogenetic relationships in Lepidoptera. Inclusion of a molecular component in the re-evaluation of systematic data is likely to alter prior assumptions of phylogenetic relationships in groups where such potentially homoplastic characters have been used.

Animals↗

PubMed1998

Unaltered cosmic spherules in a 1.4-Gyr-old sandstone from Finland.

Micrometeorites-submillimetre-sized particles derived from asteroids and comets-occur in significant quantities in deep sea sediments, and the ice sheets of Greenland and Antarctica. The most abundant micrometeorites are cosmic spherules, which contain nickel-rich spinels that were crystallized and oxidized during atmospheric entry, therefore recording the oxygen content in the uppermost atmosphere. But the use of micrometeorites for detecting past changes in the flux of incoming extraterrestrial matter, and as probes of the evolution of the atmosphere, has been hampered by the fact that most objects with depositional ages higher than 0.5 Myr show severe chemical alteration. Here we report the discovery of unaltered cosmic spherules in a 1.4-Gyr-old sandstone (red bed) from Finland. From this we infer that red beds, a common lithology in the Earth's history, may contain substantial unbiased populations of fossil micrometeorites. The study of such populations would allow systematic research on variations in the micrometeorite flux from the early Proterozoic era to recent times (a time span of about 2.5 Gyr), and could help to better constrain the time when the atmospheric oxygen content was raised to its present level.

Earth, Planet↗

PubMed2003

Constructing large-scale genetic maps using an evolutionary strategy algorithm.

This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with approximately 50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology.

Algorithms↗

PubMed2005

Evolution of insect metamorphosis: a microarray-based study of larval and adult gene expression in the ant Camponotus festinatus.

Holometabolous insects inhabit almost every terrestrial ecosystem. The evolutionary success of holometabolous insects stems partly from their developmental program, which includes discrete larval and adult stages. To gain an understanding of how development differs among holometabolous insect taxa, we used cDNA microarray technology to examine differences in gene expression between larval and adult Camponotus festinatus ants. We then compared expression patterns obtained from our study to those observed in the fruitfly Drosophila melanogaster. We found that many genes showed distinct patterns of expression between the larval and adult ant life stages, a result that was confirmed through quantitative reverse-transcriptase polymerase chain reaction. Genes involved in protein metabolism and possessing structural activity tended to be more highly expressed in larval than adult ants. In contrast, genes relatively upregulated in adults possessed a greater diversity of functions and activities. We also discovered that patterns of expression observed for homologous genes in D. melanogaster differed substantially from those observed in C. festinatus. Our results suggest that the specific molecular mechanisms involved in metamorphosis will differ substantially between insect taxa. Systematic investigation of gene expression during development of other taxa will provide additional information on how developmental pathways evolve.

Animals↗

PubMed2004

Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: molecular epidemiology and genome evolution.

Since early March 2003, the severe acute respiratory syndrome (SARS) coronavirus (CoV) infection has claimed 346 cases and 37 deaths in Taiwan. The epidemic occurred in two stages. The first stage caused limited familial or hospital infections and lasted from early March to mid-April. All cases had clear contact histories, primarily from Guangdong or Hong Kong. The second stage resulted in a large outbreak in a municipal hospital, and quickly spread to northern and southern Taiwan from late April to mid-June. During this stage, there were some sporadic cases with untraceable contact histories. To investigate the origin and transmission route of SARS-CoV in Taiwan's epidemic, we conducted a systematic viral lineage study by sequencing the entire viral genome from ten SARS patients. SARS-CoV viruses isolated from Taiwan were found closely related to those from Guangdong and Hong Kong. In addition, all cases from the second stage belonged to the same lineage after the municipal hospital outbreak, including the patients without an apparent contact history. Analyses of these full-length sequences showed a positive selection occurring during SARS-CoV virus evolution. The mismatch distribution indicated that SARS viral genomes did not reach equilibrium and suggested a recent introduction of the viruses into human populations. The estimated genome mutation rate was approximately 0.1 per genome, demonstrating possibly one of the lowest rates among known RNA viruses.

Base Pairing↗

PubMed1990

Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI.

A new procedure for the graphic analysis of molecular dynamics (MD) simulations on proteins is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the conformational and helicoidal parameters for each structure entering the analysis via the method "Curves," developed for proteins by Sklenar, Etchebest, and Lavery (Proteins: Structure, Function Genet. 6:46-60, 1989) followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels ("dials") for each torsional parameter and "windows" on the range values assumed by the linear and angular helicoidal parameters, and is present in a form isomorphous with the primary structure per se. The complete time evolution of dynamic structure can then be depicted in a set of four composite figures. Dynamic aspects of secondary and tertiary structure are also provided. The procedure is illustrated with an analysis of a 50 psec in vacuo simulation on the 58 residue protein, bovine pancreatic trypsin inhibitor (BPTI), in the vicinity of the local minimum on the energy surface corresponding to a high resolution crystal structure. The time evolution of 272 conformational and 788 helicoidal parameters for BPTI is analyzed. A number of interesting features can be discerned in the analysis, including the dynamic range of conformational and helicoidal motions, the dynamic extent of 2 degrees structure motifs, and the calculated fluctuations in the helix axis. This approach is expected to be useful for a critical analysis of the effects of various assumptions about force field parameters, truncation of potentials, solvation, and electrostatic effects, and can thus contribute to the development of more reliable simulation protocols for proteins. Extensions of the analysis to present differential changes in conformational and helicoidal parameters is expected to be valuable in MD studies of protein complexes with substrates, inhibitors, and effectors and in determining the nature of structural changes in protein-protein interactions.

Biological Evolution↗

PubMed1999

Randomized acquisition for the suppression of systematic F1 artifacts in two-dimensional NMR spectroscopy.

2D spectra, particularly for homonuclear correlation, can show a variety of artifactual signals in the F1 domain. Common sources include carry-over of signal modulation from one transient to the next ("rapid pulsing artifacts") and systematic variations in room temperature ("parallel diagonals"). In both cases there is one very simple expedient which can greatly reduce the impact of these sources of error. Multidimensional data sets are almost invariably recorded by simply incrementing or decrementing evolution periods, largely for reasons of convenience and historical precedent. If instead the sampling of the evolution periods is carried out in random order, the perturbations responsible for the sharp F1 signals in the conventional experiment manifest themselves as t1 noise. Since the randomized acquisition redistributes coherent artifactual signals randomly in F1, the maximum artifactual signal is substantially reduced in the randomized experiment and no longer appears in the form of misleading distinct peaks.

Magnetic Resonance Spectroscopy↗

PubMed2005

Identification of 20 snoRNA-like RNAs from the primitive eukaryote, Giardia lamblia.

From a specialized cDNA library of Giardia lamblia, 20 snoRNA-like RNAs, including 16 box C/D sRNAs and four box H/ACA sRNAs, were first identified. The sRNAs were predicted to guide a total of 11 2'-O-methylation and four pseudouridylation sites on the G. lamblia rRNAs, respectively. By using primer extension assay, seven methylation sites were precisely mapped in the G. lamblia 16S rRNA, despite its high GC content. All of the sRNA genes locate on the small intergenic regions of the G. lamblia genome and seem to be independently transcribed from their own promoters. Particularly, a cluster composed of GlsR17 and GlsR18 genes is transcribed as a dicistronic precursor, implying a mechanism of endonuclease cleavage for the maturation of the two sRNAs. The systematic identification of the sRNAs in G. lamblia has provided valuable information about the characteristics of the two major families of small guide RNAs in one of the most primitive eukaryotes and would contribute to the understanding of the evolution of small non-messenger RNA genes from prokaryotes to eukaryotes.

Animals↗

PubMed2005

Analysis of the kinesin superfamily: insights into structure and function.

Kinesin superfamily proteins (KIFs) are key players or 'hub' proteins in the intracellular transport system, which is essential for cellular function and morphology. The KIF superfamily is also the first large protein family in mammals whose constituents have been completely identified and confirmed both in silico and in vivo. Numerous studies have revealed the structures and functions of individual family members; however, the relationships between members or a perspective of the whole superfamily structure until recently remained elusive. Here, we present a comprehensive summary based on a large, systematic phylogenetic analysis of the kinesin superfamily. All available sequences in public databases, including genomic information from all model organisms, were analyzed to yield the most complete phylogenetic kinesin tree thus far, comprising 14 families. This comprehensive classification builds on the recently proposed standardized nomenclature for kinesins and allows systematic analysis of the structural and functional relationships within the kinesin superfamily.

Amino Acid Sequence↗

PubMed2005

Geometries, stabilities, and electronic properties of different-sized ZrSi(n) (n=1-16) clusters: a density-functional investigation.

The ZrSi(n) (n=1-16) clusters with different spin configurations have been systematically investigated by using the density-functional approach. The total energies, equilibrium geometries, growth-pattern mechanisms, natural population analysis, etc., are discussed. The equilibrium structures of different-sized ZrSi(n) clusters can be determined by two evolution patterns. Theoretical results indicate that the most stable ZrSi(n) (n=1-7) geometries, except ZrSi3, keep the analogous frameworks as the lowest-energy or the second lowest-energy Si(n+1) clusters. However, for large ZrSi(n) (n=8-16) clusters, Zr atom obviously disturbs the framework of silicon clusters, and the localized position of the transition-metal (TM) Zr atom gradually varies from the surface insertion site to the concave site of the open silicon cage and to the encapsulated site of the sealed silicon cage. It should be mentioned that the lowest-energy sandwich-like ZrSi12 geometry is not a sealed structure and appears irregular as compared with other TM@Si12 (TM = Re,Ni). The growth patterns of ZrSi(n) (n=1-16) clusters are concerned showing the Zr-encapsulated structures as the favorable geometries. In addition, the calculated fragmentation energies of the ZrSi(n) (n=1-16) clusters manifest that the magic numbers of stabilities are 6, 8, 10, 14, and 16, and that the fullerene-like ZrSi16 is the most stable structure, which is in good agreement with the calculated atomic binding energies of ZrSi(n) (n=8-16) and with available experimental and theoretical results. Natural population analysis shows that the natural charge population of Zr atom in the most stable ZrSi(n) (n=1-16) structures exactly varies from positive to negative at the critical-sized ZrSi8 cluster; furthermore, the charge distribution around the Zr atom appears clearly covalent in character for the small- or middle-sized clusters and metallic in character for the large-sized clusters. Finally, the properties of frontier orbitals and polarizabilities of ZrSi(n) are also discussed.

Journal Article↗

PubMed1998

Phylogeny of species of Triatoma (Hemiptera: Reduviidae) based on mitochondrial DNA sequences.

DNA sequence comparisons of 12S, 16S, and COI mitochondrial DNA (mtDNA) genes were used to infer phylogenetic relationships among 8 species of Triatoma [7 belonging to the infestans complex and T. circummaculata (Stål), a member of a different complex based on morphology]. There was remarkable mtDNA similarity between T. infestans (Klug) and T. platensis Neiva that can be explained by mtDNA introgression. Evolutionary trees were constructed using Panstrongylus megistus (Burmeister) as the outgroup. This outgroup gave evidence that the root of the group would be between T. vitticeps (Stål) and the rest of the species. The placement of T. circummaculata into the middle of the infestans complex is not consistent with the morphological classification, suggesting that the current systematics of this group does not reflect phylogenetic affinities.

Animals↗

PubMed1983

The nucleotide sequences of the 5S rRNAs of four mushrooms and their use in studying the phylogenetic position of basidiomycetes among the eukaryotes.

The nucleotide sequences of the 5 S ribosomal RNAs of the mushrooms Russula cyanoxantha, Pleurotus ostreatus, Agaricus edulis, and Auricularia auricula-judae were determined. The sequences fit in a universal five-helix secondary structure model for 5 S RNA. As in most other 5 S RNAs, some helical areas contain non-standard base pairs. A clustering method was used to reconstruct an evolutionary tree from 82 eukaryotic 5 S RNA sequences. It allows to make a choice between alternative systematic classifications for basidiomycetes and reveals that the fungal kingdom is highly polyphyletic.

Base Sequence↗

PubMed1997

Blastic natural killer cell leukemia/lymphoma: a clinicopathologic study.

The classification of natural killer (NK)-cell and NK-like T-cell malignancies has undergone significant evolution in recent years. Although examples of NK-cell tumors resembling acute leukemia have been described anecdotally as blastic, blastoid, or monomorphic NK-cell leukemia/lymphoma (NKL/L), the clinical and pathologic features of these tumors have not been systematically defined. We report four patients with blastic NKL/L and describe the clinical, pathologic, and immunophenotypic findings in these cases. All patients were elderly (58-82 years) and presented with cutaneous plaques. Two patients also had adenopathy, and three patients had marrow involvement at presentation. Biopsy of cutaneous lesions showed atypical superficial and deep dermal lymphoid infiltrates. Involved lymph nodes were architecturally effaced by an interfollicular infiltrate with blastic cytologic features. In Wright-Giemsa-stained blood or marrow smears, tumor cells had finely distributed nuclear chromatin, many with nucleoli, and variable amounts of cytoplasm. In contrast to many NK and NK-like T-cell disorders, azurophilic cytoplasmic granules were absent or inconspicuous. The tumor cells were immunophenotypically distinctive. They expressed intermediate density CD45, as is characteristic of blasts; in addition, the cells were positive for HLA-DR, CD2, CD4, and the NK-associated antigen CD56. Surface CD3, cytoplasmic CD3, and CD5 were negative in all cases tested, whereas CD7 was expressed in two cases. In formalin-fixed tissue, tumor cells marked with antibodies to CD43, but not with other T- or B-lineage-related antibodies. All three cases studied for Epstein-Barr viral RNA by in situ hybridization were negative. Although treatments varied, all three patients with clinical follow-up died within months of the diagnosis. The clinical course in two patients culminated in an overtly leukemic phase. These findings suggest that blastic NKL/L represents a distinct clinicopathologic entity, characterized by cutaneous, nodal, and marrow involvement by blastic cells with immunophenotypic characteristics of true NK cells. The disease afflicts elderly patients, pursues an aggressive course, and may culminate in overt leukemia.

Aged↗

PubMed2004

Iron isotope fractionation and the oxygen fugacity of the mantle.

The oxygen fugacity of the mantle exerts a fundamental influence on mantle melting, volatile speciation, and the development of the atmosphere. However, its evolution through time is poorly understood. Changes in mantle oxidation state should be reflected in the Fe3+/Fe2+ of mantle minerals, and hence in stable iron isotope fractionation. Here it is shown that there are substantial (1.7 per mil) systematic variations in the iron isotope compositions (delta57/54Fe) of mantle spinels. Spinel delta57/54Fe values correlate with relative oxygen fugacity, Fe3+/sigmaFe, and chromium number, and provide a proxy of changes in mantle oxidation state, melting, and volatile recycling.

Journal Article↗

PubMed1991

[Quantitative analysis of the teleost brain: evolutionary and adaptive characteristics of encephalization. III. Multivariate analysis of the cephalic index].

A multivariate analysis of 9 brain indices from 83 teleost species showed a marked opposition between the non-olfactory telencephalon (and diencephalon) and the medulla oblongata (phylogenetic characters) and between the olfactory bulbs and the optic tectum (adaptive characters). Results of three different classifying algorithms allowed determination of 6 stable groupings and 9 intermediate ones, some with systematic importance and some purely adaptive. For this reason brain organization criteria must be used with precaution for systematic purposes. Nevertheless, the position of Brotula multibarbata showed that this fish is an evolved acanthopterygian.

Adaptation, Physiological↗

PubMed1991

[Coronary disease in patient following heart transplantation].

Coronary artery disease is a common and particularly severe complication of cardiac transplantation because it may cause progressive destruction of the graft by acute or chronic ischemia. The ischemia is usually silent because of cardiac denervation. Cardiac failure related to graft dysfunction, asymptomatic infarction on the ECG, or sudden death, are sometimes the only signs of severe coronary disease. The prevalence of coronary lesions has been evaluated by coronary angiography at nearly 25% at 2 years and 50% at 5 years. The distribution and morphology of the lesions are characteristic: diffuse concentric, irregular and occlusive, predominantly distal stenoses, without a distal and usually without a collateral circulation. The histological features are variable: the association of medial necrosis, severe endothelial lesions and intense parietal inflammation are suggestive of acute arteriolitis, often present during acute rejection, may be related to a common pathological process. Diffuse obliterative arteriolar lesions with concentric proliferation of medial smooth muscle are the usual appearances in transplant patients who have died or been retransplanted. There is no non-invasive diagnostic method sufficiently sensitive of specific which justifies the practice of many groups of systematic annual coronary angiography in transplanted patients. The pathogenesis is poorly understood and probably multifactorial: disorders of lipid metabolism, immunological factors, the atherogenic role of Cytomegalovirus infection. The absence of an identifiable risk factor makes preventive measures difficult. The evolutive risk justifies retransplantation in selected patients, the results of which are less satisfactory but which reduces the risk of acute coronary events and sudden death.(ABSTRACT TRUNCATED AT 250 WORDS)

Coronary Angiography↗

PubMed1977

A chromosome survey of five species of Cassidinae (Coleoptera: Chrysomelidae).

Chromosome numbers and sex-determining mechanisms of five species of Cassida beetles from different Spanish sources are given. C. deflorata Suffr. and C. flaveola Thunb. show a 8(11) + Xyp formula, C. vibex L. 9(11) + Xyp, and C. margaritacea Schall. and C. viridis L., 14(11) + Xyp. These chromosomal findings are in agreement with the current morphological systematics of Cassida. The karyotypes of C. deflorata, C. vibex and C. viridis are constituted by metacentric chromosomes mostly, but there are clear differences in the total complement lengths between the three species. The possible tendencies in the chromosomal evolution of Cassidinae beetles are also discussed assuming a primitive karyotype of 18 chromosomes.

Animals↗