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At least 397 records · Page 22Linked to original sources
PubMed2003

The geometry of the marmot (rodentia: sciuridae) mandible: phylogeny and patterns of morphological evolution.

Marmots have a prominent role in the study of mammalian social evolution, but only recently has their systematics received the attention it deserves if sociobiological studies are to be placed in a phylogenetic context. Sciurid morphology can be used as model to test the congruence between morphological change and phylogeny because sciurid skeletal characters are considered to be inclined to convergence. However, no morphological study involving all marmot species has ever been undertaken. Geometric morphometric techniques were applied in a comparative study of the marmot mandible. The adults of all 14 living marmot species were compared, and mean mandible shape were used to investigate morphological evolution in the genus Marmota. Three major trends were observed. First, the phylogenetic signal in the variation of landmark geometry, which describes mandible morphology, seems to account for the shape differences at intermediate taxonomic levels. The subgenera Marmota and Petromarmota, recently proposed on the basis of mitochondrial cytochrome b sequence, receive support from mandible morphology. When other sciurid genera were included in the analysis, the monophyly of the genus Marmota and that of the tribe Marmotini (i.e., marmots, prairie dogs, and ground squirrels) was strengthened by the morphological data. Second, the marmotine mandible may have evolved as a mosaic of characters and does not show convergence determined by size similarities. Third, allopatric speciation in peripheral isolates may have acted as a powerful force for modeling shape. This hypothesis is strongly supported by the peculiar mandible of M. vancouverensis and, to a lesser degree, by that of M. olympus, both thought to have originated as isolated populations in Pleistocene ice-free refugia.

Adaptation, Biological↗
PubMed2000

Evolution of schistosomiasis-induced pathology after therapy and interruption of exposure to schistosomes: a review of ultrasonographic studies.

Ultrasonography (US) is suitable for diagnosing schistosomiasis-related organic pathology and is particularly useful to assess its evolution after therapy and/or interruption of exposure to the Schistosoma parasites. Evolution of pathology after treatment: Regression of hepatic abnormalities in Schistosma mansoni-infected children and adolescents has been observed already from 7 months post-therapy on. This does, however, not occur in all cases: individual differences are great ranging from spontaneous regression of pathology without treatment to persistence of pathology lasting for years after therapy even without re-infection. Intensity and duration of exposure, different parasite strains, patients' age and genetic background all influence the evolution of pathology. In communities at continuous exposure to S. mansoni infection, repeated re-treatment is required to control hepatosplenic morbidity. In Schistosoma japonicum infection, changes around the portal tree may regress, but characteristic diffuse abnormalities described as 'network pattern' abnormalities do not resolve. In Schistosoma haematobium infection bladder abnormalities and urinary tract obstruction frequently resolve after treatment. Clinically relevant pathology may resurge from 1 year after therapy on if exposure continues. Subjects with more advanced pathology before therapy, appear to be at higher risk of pathology re-appearance. Evolution of pathology after interruption of exposure to schistosomiasis: Knowledge on the evolution of pathology induced by S. mansoni is limited to some reports in emigrants and to the experience of ultrasonographists working in areas, where transmission has been partially interrupted. Due to the longevity of the parasite, infection may last for many years. Even after elimination of the parasites severe pathology may persist for long. In S. haematobium infection spontaneous healing after interruption of re-exposure may occur, but cases have been reported where urogenital lesions led to complications many years after exposure. Contrary to hepatosplenic and urinary pathology, knowlegde on the evolution of other organic abnormalities is very limited: studies on the evolution of biliary abnormalities or intestinal pathology have not been published. Genital pathology may be induced by all Schistosoma spp. Post-therapy evolution of genital schistosomiasis is largely ignored. In some European travellers partial regression of prostatic fibrosis has been described. Schistosomal adnexitis leading to infertility and/or ectopic pregnancy has been reported occurring many years after interruption of exposure. Ultrasonography (US) has never been used to study the influence of schistosomiasis on pregnancy. Concluding, current knowlegde on the evolution of pathology after treatment and/or interruption of exposure is still fragmentary. Frequently, fibrosis reverses after therapy, but advanced pathology may persist for long. Therefore, the possibility of severe clinical complications has to be taken into account, even if the infection is inactive since many years. In interventions aimed at controlling schistosomiasis-related morbidity, evolution of pathology must be monitored by US in representative patient cohorts. Further systematic US-studies are needed not only on the evolution of hepatosplenic and urinary pathology but also on that of intestinal, biliary and genital pathology induced by schistosomiasis, as well as on the influence of schistosomiasis on the outcome of pregnancy.

Adolescent↗
PubMed1991

Taxonomy, evolution and life cycles.

Three lectures were given, the first on haplodiploidy in the Oxyurida (Nematoda), the second on rodent Oxyurida and the third on the life cycle of Leishmania (Kinetoplastida, Trypanosomatidae). The oral communications and posters were divided into five subsections, covering systematics at supraspecific, specific and subspecific levels, evolution, and life cycles of parasites with hosts in both aquatic and terrestrial environments. A wide range of topics was discussed, including recent developments in the fields of genetics and cellular and molecular biology, and computer-assisted numerical taxonomy.

Animals↗
PubMed2006

Evolutionary transformations of fetal membrane characters in Eutheria with special reference to Afrotheria.

Analysis of molecular data sets has provided new insights into higher-level relationships of living Eutheria, including the recognition of Afrotheria as a novel taxon. This offers an opportunity to take a fresh look at the evolution of organ systems, including some that are little used in traditional systematics. In the present study, we attempted a reconstruction of the evolution of characters associated with placentation, the fetal membranes and the female reproductive tract. The evolutionary history of 21 characters has been traced, based on a current hypothesis of eutherian relationships, by applying the computer program MacClade. Accordingly, the analysis provides a first comprehensive interpretation of the stem species pattern of Eutheria. Of particular note, this pattern includes an endotheliochorial chorioallantoic placenta. The reconstructed pattern of Eutheria does not change in the basal nodes of the group. Thus, no character transformations occur on the stem lineages of Laurasiatheria or Euarchontoglires, and even Afrotheria has mostly plesiomorphic character conditions. However, two character transformations occur on the common stem lineage of Afrotheria and its sister taxon Xenarthra, i.e., amniogenesis by cavitation instead of folding and the precocial state of the newborn. In addition, we recognized one character transformation on the stem lineage of Afrotheria, i.e., the occurrence of a four-lobed allantoic sac. Thus, contrary to previous assertions, it is possible to identify morphological characters that could be synapomorphic for this novel taxon.

Animals↗
PubMed2002

Models of intracellular transport and evolution of the Golgi complex.

We have performed a systematic analysis of models explaining the mechanisms of the intracellular biosecretory transport. The models assessed include not only those based on one mechanism (the dissociation model (and its individual case, the vesicular model), the progression model (and its individual cases, the cisterna maturation/progression and the carrier maturation models), and the lateral diffusion model (and its individual case, the bolus model), but also combined models of transport (the percolating-vesicles model and the synthetic model), including several transport mechanisms. Most of these models are not able to explain recent data on the evolution of genes involved in intracellular transport and Golgi evolution. The carrier maturation model proposing that fusion of the large cargo domain with the distal (closer to the plasmalemma) compartment precedes fission of the domain from the proximal compartment exhibits the best performance in correlation with the available information on evolution of the biosecretory pathway.

Biological Evolution↗
PubMed2005

Molecular phylogeny, recent radiation and evolution of gross morphology of the rhubarb genus Rheum (Polygonaceae) inferred from chloroplast DNA trnL-F sequences.

BACKGROUND AND AIMS: Rheum, a highly diversified genus with about 60 species, is mainly confined to the mountainous and desert regions of the Qinghai-Tibetan plateau and adjacent areas. This genus represents a good example of the extensive diversification of the temperate genera in the Qinghai-Tibetan plateau, in which the forces to drive diversification remain unknown. To date, the infrageneric classification of Rheum has been mainly based on morphological characters. However, it may have been subject to convergent evolution under habitat pressure, and the systematic position of some sections are unclear, especially Sect. Globulosa, which has globular inflorescences, and Sect. Nobilia, which has semi-translucent bracts. Recent palynological research has found substantial contradictions between exine patterns and the current classification of Rheum. Two specific objectives of this research were (1) to evaluate possible relationships of some ambiguous sections with a unique morphology, and (2) to examine possible occurrence of the radiative speciation with low genetic divergence across the total genus and the correlation between the extensive diversification time of Rheum and past geographical events, especially the recent large-scale uplifts of the Qinghai-Tibetan Plateau. METHODS: The chloroplast DNA trnL-F region of 29 individuals representing 26 species of Rheum, belonging to seven out of eight sections, was sequenced and compared. The phylogenetic relationships were further constructed based on the sequences obtained. KEY RESULTS: Despite the highly diversified morphology, the genetic variation in this DNA fragment is relatively low. The molecular phylogeny is highly inconsistent with gross morphology, pollen exine patterns and traditional classifications, except for identifying all samples of Sect. Palmata, three species of Sect. Spiciformia and a few species of Sect. Rheum as corresponding monophyletic groups. The monotypic Sect. Globulosa showed a tentative position within the clade comprising five species of Sect. Rheum. All of the analyses revealed the paraphyly of R. nobile and R. alexandrae, the only two species of Sect. Nobilia circumscribed by the possession of large bracts. The crude calibration of lineages based on trnL-F sequence differentiation implied an extensive diversification of Rheum within approx. 7 million years. CONCLUSIONS: Based on these results, it is suggested that the rich geological and ecological diversity caused by the recent large-scale uplifts of the Qinghai-Tibetan Plateau since the late Tertiary, coupled with the oscillating climate of the Quaternary stage, might have promoted rapid speciation in small and isolated populations, as well as allowing the fixation of unique or rare morphological characters in Rheum. Such a rapid radiation, combined with introgressive hybridization and reticulate evolution, may have caused the transfer of cpDNA haplotypes between morphologically dissimilar species, and might account for the inconsistency between morphological classification and molecular phylogeny reported here.

Biological Evolution↗
PubMed2006

Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments.

BACKGROUND: Molecular evolutionary studies of noncoding sequences rely on multiple alignments. Yet how multiple alignment accuracy varies across sequence types, tree topologies, divergences and tools, and further how this variation impacts specific inferences, remains unclear. RESULTS: Here we develop a molecular evolution simulation platform, CisEvolver, with models of background noncoding and transcription factor binding site evolution, and use simulated alignments to systematically examine multiple alignment accuracy and its impact on two key molecular evolutionary inferences: transcription factor binding site conservation and divergence estimation. We find that the accuracy of multiple alignments is determined almost exclusively by the pairwise divergence distance of the two most diverged species and that additional species have a negligible influence on alignment accuracy. Conserved transcription factor binding sites align better than surrounding noncoding DNA yet are often found to be misaligned at relatively short divergence distances, such that studies of binding site gain and loss could easily be confounded by alignment error. Divergence estimates from multiple alignments tend to be overestimated at short divergence distances but reach a tool specific divergence at which they cease to increase, leading to underestimation at long divergences. Our most striking finding was that overall alignment accuracy, binding site alignment accuracy and divergence estimation accuracy vary greatly across branches in a tree and are most accurate for terminal branches connecting sister taxa and least accurate for internal branches connecting sub-alignments. CONCLUSION: Our results suggest that variation in alignment accuracy can lead to errors in molecular evolutionary inferences that could be construed as biological variation. These findings have implications for which species to choose for analyses, what kind of errors would be expected for a given set of species and how multiple alignment tools and phylogenetic inference methods might be improved to minimize or control for alignment errors.

Binding Sites↗
PubMed2007

Self-setting properties of a beta-dicalcium silicate reinforced calcium phosphate cement.

Beta-dicalcium silicate was used to reinforce the injectable calcium phosphate cement (iCPC) for the first time in this study. The influence of the content of beta-dicalcium silicate on the mechanical properties, setting time, rheological properties, injectability, phase evolution, microstructure, and biodegradability of iCPC was systematically investigated. The results demonstrated that the addition of 8 wt % beta-dicalcium silicate obviously enhanced the compressive strength of the CPC from 26.5 to 47.5 MPa, and did not significantly influence the biodegradability, setting time, injectability, phase evolution, and microstructure of the CPC. The beta-dicalcium silicate-reinforced iCPC with relatively high mechanical property should have potential prospects for the wider applications in surgery such as orthopedics, oral, and maxillofacial surgery.

Bone Cements↗
PubMed1990

The Syphaciinae (Oxyuridae, Nematoda) parasitic in rodents and lagomorpha. Numerical taxonomy. Cladistic analysis of evolution.

Two different methods are successively used for the systematic study of the Syphaciinae, a parasitic group of pin-worms specific for the Rodents and Lagomorpha. The statistical method permits to build a "phenetic classification"; the cladistic method permits to build a "phylogenetic classification". The classification finally proposed is principally found on the results of the morphological study of the parasites, but has also in view the integration of all available data concerning the biology, the biogeography and the phylogeny of the hosts.

Animals↗
PubMed2002

Microevolutionary genomics of bacteria.

The availability of multiple complete genome sequences from the same species can facilitate attempts to systematically address basic questions in genome evolution. We refer to such efforts as "microevolutionary genomics". We report the results of comparative analyses of complete intraspecific genome (and proteome) sequences from four bacterial species--Chlamydophila pneumoniae, Escherichia coli, Helicobacter pylori and Neisseria meningitidis. Comparisons of average synonymous (K(s)) and nonsynonymous (K(a)) substitution rates were used to assess the influence of various biological factors on the rate of protein evolution. For example, E. coli experiences the most intense purifying selection of the species analyzed, and this may be due to the relatively larger population size of this species. In addition, essential genes were shown to be more evolutionarily conserved than nonessential genes in E. coli and duplicated genes have higher rates of evolution than unique genes for all species studied except C. pneumoniae. Different functional categories of genes were shown to evolve at significantly different rates emphasizing the role of category-specific functional constraints in determining evolutionary rates. Finally, functionally characterized genes tend to be conserved between strains, while uncharacterized genes are over-represented among the unique, strain-specific genes. This suggests the possibility that nonessential genes are responsible for driving the evolutionary diversification between strains.

Bacteria↗
PubMed2006

The complex multidomain organization of SCO-spondin protein is highly conserved in mammals.

The multidomain organization of SCO-spondin protein is a special feature of the chordate phylum. This protein is expressed in the central nervous system (CNS) from the time a dorsal neural tube appears in the course of phylogenetical evolution. With the advance of the systematic whole genomes sequencing, we were able to determine the SCO-spondin amino acid sequence in four mammalian species using the Wise2 software. From the ClustalW alignment of bovine (Bos taurus), human (Homo sapiens), murine (Mus musculus) and rat (Rattus norvegicus) proteins, a consensus sequence for mammalian SCO-spondin was determined and further validated with the dog (Canis familiaris) SCO-spondin sequence. The analysis of this consensus sequence is consistent with a very high degree of conservation in the amino acids composition and multidomain organization of SCO-spondin in mammals. In addition, the identification of conserved domains, namely, Emilin (EMI), von Willebrand factor D (vWD), low-density lipoprotein receptor type A (LDLrA) domains, SCO repeats (SCOR), thrombospondin type 1 repeats (TSR), a coagulation factor 5/8 type C (FA5-8C) or discoidin motif and a C-terminal cystine knot (CTCK) domain, provides a greater insight into the putative function of this multidomain protein. SCO-spondin belongs to the TSR superfamily given the presence of a great number of TSR (26). A finer classification of the TSR motifs in groups 1, 2 and 3 is proposed on the basis of different cysteine patterns. Interestingly, group 2 TSR are present in a number of CNS developmental proteins including R-spondins, F-spondins and Mindins.

Animals↗
PubMed2006

Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule.

At the heart of the RNA folding problem is the number, structures, and relationships among the intermediates that populate the folding pathways of most large RNA molecules. Unique insight into the structural dynamics of these intermediates can be gleaned from the time-dependent changes in local probes of macromolecular conformation (e.g. reports on individual nucleotide solvent accessibility offered by hydroxyl radical (()OH) footprinting). Local measures distributed around a macromolecule individually illuminate the ensemble of separate changes that constitute a folding reaction. Folding pathway reconstruction from a multitude of these individual measures is daunting due to the combinatorial explosion of possible kinetic models as the number of independent local measures increases. Fortunately, clustering of time progress curves sufficiently reduces the dimensionality of the data so as to make reconstruction computationally tractable. The most likely folding topology and intermediates can then be identified by exhaustively enumerating all possible kinetic models on a super-computer grid. The folding pathways and measures of the relative flux through them were determined for Mg(2+) and Na(+)-mediated folding of the Tetrahymena thermophila group I intron using this combined experimental and computational approach. The flux during Mg(2+)-mediated folding is divided among numerous parallel pathways. In contrast, the flux during the Na(+)-mediated reaction is predominantly restricted through three pathways, one of which is without detectable passage through intermediates. Under both conditions, the folding reaction is highly parallel with no single pathway accounting for more than 50% of the molecular flux. This suggests that RNA folding is non-sequential under a variety of different experimental conditions even at the earliest stages of folding. This study provides a template for the systematic analysis of the time-evolution of RNA structure from ensembles of local measures that will illuminate the chemical and physical characteristics of each step in the process. The applicability of this analysis approach to other macromolecules is discussed.

Animals↗
PubMed2001

Estimating the need for radiotherapy for lung cancer: an evidence-based, epidemiologic approach.

BACKGROUND AND OBJECTIVES: Current estimates of the proportion of cancer patients who will require radiotherapy (RT) are based almost entirely on expert opinion. The objective of this study was to use an evidence-based approach to estimate the proportion of incident cases of lung cancer that will require RT at any point in the evolution of the illness. METHODS: A systematic review of the literature was undertaken to identify indications for RT for lung cancer, and to ascertain the level of evidence that supported each indication. An epidemiologic approach was then used to estimate the incidence of each indication for RT in a typical North American population of lung cancer patients. The effect of sampling error on the estimated appropriate rate of RT was calculated mathematically, and the effect of systematic error, was estimated by sensitivity analysis. RESULTS: It was shown that 53.6% +/- 3.3% of small-cell lung cancer (SCLC) cases develop one or more indications for RT at some point in the course of the illness, 45.4% +/- 4.3% in their initial treatment, and 8.2% +/- 1.5% later for recurrence of progression. Overall, 64.3% +/- 4.7% of non-small-cell lung cancer (NSCLC) cases require RT, 45.9% +/- 4.3% in their initial treatment, and 18.3% +/- 1.8% later in the course of the illness. The proportion of NSCLC cases that ever require RT is stage dependent; 41.0% +/- 5.5% in Stage I; 54.5% +/- 6.5% in Stage II; 83.5% +/- 10.6% in Stage III; and 65.7% +/- 7.6% in Stage IV. In total, 61.0% +/- 3.9% of all patients with lung cancer will develop one or more indications for RT at some point in the illness, 44.6% +/- 3.6% in their initial treatment, and 16.5% +/- 1.5% later for recurrence or progression. CONCLUSION: This method provides a rational starting point for the long-term planning of radiation services, and for the audit of access to RT at the population level. We now plan to extend this study to the other major cancer sites to enable us to estimate the appropriate RT treatment rate for the cancer population as a whole.

Algorithms↗
PubMed1996

Somatic microsatellite mutations as molecular tumor clocks.

Microsatellite (MS) mutations can potentially unravel the past of mutator phenotype tumors, with greater genetic diversity expected in older regions. Rapid clonal expansions of xenografts were characterized by relatively homogenous MS alleles, whereas greater diversity was observed in a colorectal cancer with the greatest variation in its adjacent adenoma. A subcutaneous lung cancer metastasis demonstrated diversity consistent with its one-month clinical duration and evidence of active mitosis during dormancy. The genetic legacy inherent to multistep tumorigenesis provides direct estimates of tumor ages, with up to thousands of cell divisions and high death rates necessary to yield the observed diversities. MS molecular tumor clocks have the unique potential to systematically reconstruct the early and occult evolution of individual human mutator phenotype tumors.

Adenocarcinoma↗
PubMed1999

Self-assembly of helical ribbons.

The self-assembly of helical ribbons is examined in a variety of multicomponent enantiomerically pure systems that contain a bile salt or a nonionic detergent, a phosphatidylcholine or a fatty acid, and a steroid analog of cholesterol. In almost all systems, two different pitch types of helical ribbons are observed: high pitch, with a pitch angle of 54 +/- 2 degrees, and low pitch, with a pitch angle of 11 +/- 2 degrees. Although the majority of these helices are right-handed, a small proportion of left-handed helices is observed. Additionally, a third type of helical ribbon, with a pitch angle in the range 30-47 degrees, is occasionally found. These experimental findings suggest that the helical ribbons are crystalline rather than liquid crystal in nature and also suggest that molecular chirality may not be the determining factor in helix formation. The large yields of helices produced will permit a systematic investigation of their individual kinetic evolution and their elastic moduli.

Bile Acids and Salts↗
PubMed1998

Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences.

We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction-site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the mitochondrion-encoded gene atpA, the latter of which encodes the alpha-subunit of mitochondrial ATP synthase. The plant mitochondrial genome has been little used in plant systematics, in part because nucleotide sequence evolution in enzyme-encoding genes of this genome is relatively slow. The three data sets were examined in separate and combined analyses, with a focus on patterns of congruence, homoplasy, and data decisiveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most parsimonious trees by a data set in terms of the degree to which those trees are shorter than the average length of all possible trees. Because indecisive data sets require relatively fewer additional steps than decisive ones to be optimized on nonparsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between decisiveness and character incongruence is that if incongruence is used as a criterion of noncombinability, decisive data sets, which provide robust support for relationships, are more likely to be assessed as noncombinable with other data sets than are indecisive data sets, which provide weak support for relationships. For the sampling of taxa in this study, the atpA data set has about half as many cladistically informative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least decisive of the three, exhibits the lowest levels of character incongruence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.

Adenosine Triphosphatases↗
PubMed1999

Systematic biology of gymnotiform and mormyriform electric fishes: phylogenetic relationships, molecular clocks and rates of evolution in the mitochondrial rRNA genes

The phylogenetic relationships of both African and South American electric fish orders are reviewed at their intra-ordinal level taking into consideration recent studies in which cladistic principles have been employed. Several concordant topologies emerge from the different data sets, but some unsettled issues still remain. From the studies available, a consensus topology has been suggested for the Mormyriformes and for the Gymnotiformes. Subsequently, the evolutionary relationships of these two electric fish clades are considered within each respective superorder, i.e. in relation to the other osteoglossomorph and ostariophysan orders. The inter-ordinal phylogenies are used as a framework to test the molecular clock hypothesis with two gene fragments of the mitochondrial genome. Gymnotiformes, Siluriformes and Characiformes are accumulating mutations at the same pace in relation to their respective outgroups, but for all the other combinations of sister clades tested the molecular clock can be statistically rejected. Fossil records are then surveyed and used to calibrate absolute rates of genetic differentiation for each main lineage (orders) of both osteoglossomorphs and ostariophysans. The most conserved regions (stems) of the 12S and 16S gene fragments used are evolving at an average rate of 0.123 % 10(6 )years-1 for the osteoglossomorphs and 0.137 % 10(6 )years-1 for the ostariophysans, with no significant difference between these two values. The rate of mutation in the loops, the faster-evolving segments, estimated for closely related electric fish taxa is 0.82 % 10(6 )years-1 for four Brienomyrus species and 1.01 % 10(6 )years-1 for the four eigenmanniid genera. When the entire molecule (loops + stems) is considered, the rate of mutation in both mormyriforms and gymnotiforms converges to a rounded value of 0.23 % 10(6 )years-1.

Journal Article↗