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Results for “systematic evolution”

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PubMed2004

MEG study of short-term plasticity following multiple digit frequency discrimination training in humans.

We trained four right-handed male subjects to detect small changes in the frequency of 21 Hz electrical stimulation applied to digits 2+3+4 of the right hand for 4 hours. Before and after the training, we recorded magnetoencephalographic (MEG) signals when the stimulation was applied to digit 2-5 separately using a whole-head MEG system. We applied tomographic analysis to the MEG data to track the evolution of activity over the entire brain every 1.6 ms and evaluated the change for each digit before and after the training. In summary: (1) subjects improved in discrimination performance with training; (2) activations were identified in the left primary somatosensory (L-SI) and medial parietal precuneus (PCu) areas, but no systematic changes were observed in location and strength of activation of these two areas; (3) after training in L-SI, the 21 Hz spectral power increased for digits 3 and 4 over the stimulation period, while the 10 Hz spectral power increased for digit 3 around stimulus onset and offset; (4) only digit 3 showed significant change of correlation between L-SI and PCu areas around the stimulus onset and offset, coincident with the increased 10 Hz spectral power. Our results suggest that short-term plasticity is associated with changes in timing and interaction between cortical areas.

Brain Mapping↗

PubMed1989

Chloroplast-like transfer RNA genes expressed in wheat mitochondria.

In the course of a systematic survey of wheat mitochondrial tRNA genes, we have sequenced chloroplast-like serine (trnS-GGA), phenylalanine (trnF-GAA) and cysteine (trnC-GCA) tRNA genes and their flanking regions. These genes are remnants of 'promiscuous' chloroplast DNA that has been incorporated into wheat mtDNA in the course of its evolution. Each gene differs by one or a few nucleotides from the authentic chloroplast homolog previously characterized in wheat or other plants, and each could potentially encode a functional tRNA whose secondary structure shows no deviations from the generalized model. To determine whether these chloroplast-like tRNA genes are actually expressed, wheat mitochondrial tRNAs were resolved by a series of polyacrylamide gel electrophoreses, after being specifically end-labeled in vitro by 3'-CCA addition mediated by wheat tRNA nucleotidyltransferase. Subsequent direct RNA sequence analysis identified prominent tRNA species corresponding to the mitochondrial and not the chloroplast trnS, trnF and trnC genes. This analysis also revealed chloroplast-like elongator methionine, asparagine and tryptophan tRNAs. Our results suggest that at least some chloroplast-like tRNA genes in wheat mtDNA are transcribed, with transcripts undergoing processing, post-transcriptional modification and 3'-CCA addition, to produce mature tRNAs that may participate in mitochondrial protein synthesis.

Base Sequence↗

PubMed2000

The relationships of vascular plants.

Recent phylogenetic research indicates that vascular plants evolved from bryophyte-like ancestors and that this involved extensive modifications to the life cycle. These conclusions are supported by a range of systematic data, including gene sequences, as well as evidence from comparative morphology and the fossil record. Within vascular plants, there is compelling evidence for two major clades, which have been termed lycophytes (clubmosses) and euphyllophytes (seed plants, ferns, horsetails). The implications of recent phylogenetic work are discussed with reference to life cycle evolution and the interpretation of stratigraphic inconsistencies in the early fossil record of land plants. Life cycles are shown to have passed through an isomorphic phase in the early stages of vascular plant evolution. Thus, the gametophyte generation of all living vascular plants is the product of massive morphological reduction. Phylogenetic research corroborates earlier suggestions of a major representational bias in the early fossil record. Mega-fossils document a sequence of appearance of groups that is at odds with that predicted by cladogram topology. It is argued here that the pattern of appearance and diversification of plant megafossils owes more to changing geological conditions than to rapid biological diversification.

Biological Evolution↗

PubMed2005

Laparoscopic radical prostatectomy: an evolution in surgery.

The late 1990s witnessed an unprecedented evolution in the surgical approaches to the prostate thru the eye of the laparoscope. Initially taken with doubt, laparoscopic radical prostatectomy (LRP) has gained tremendous popularity and widespread implementation at specialized centers worldwide becoming the standard in many of them. LRP represents a technically demanding laparoscopic procedure but it can be performed systematically with standard techniques. Obvious advantages are shorter convalescence and markedly lower operative blood loss without compromise of cancer control. Long-term functional and oncological results are maturing but early reports of positive surgical margin rates and freedom from prostate-specific antigen (PSA) recurrence rates after LRP are encouraging. Early quality of life results of postoperative urinary and sexual function appear similar to those in open surgical series. The real challenge for laparoscopic surgeons entails a paradigm swift, one that breaks off from the traditional and bias impetus, and tests the instruments, procedures, techniques differences and evaluates outcomes in a prospective controlled and randomized manner. If achieved, the laparoscopic movement may give rise to a generation of forward thinking surgeons generating a wealth of clinical evidence for their patients.

Humans↗

PubMed2005

The innovation triad: an EvoDevo agenda.

This article introduces a special issue on evolutionary innovation and morphological novelty, two interrelated themes that have received a remarkable increase of attention over the past few years. We begin with a discussion of the question of whether innovation and novelty represent distinct evolutionary problems that require a distinct conceptualization. We argue that the mechanisms of innovation and their phenotypic results--novelty--can only be properly addressed if they are distinguished from the standard evolutionary themes of variation and adaptation, and we present arguments for making such a distinction. We propose that origination, the first formation of biological structures, is another distinct problem of morphological evolution, and that together with innovation and novelty it constitutes a conceptual complex we call the innovation triad. We define a problem agenda of the triad, which separates the analysis of the initiating conditions from the mechanistic realization of innovation, and we discuss the theoretical problems that arise from treating innovation as distinct from variation. Further, we categorize the empirical approaches that address themes of the innovation triad in recognizing four major strands of research: the morphology and systematics program, the gene regulation program, the epigenetic program, and the theoretical biology program. We provide examples of each program, giving priority to contributions in the present issue. In conclusion, we observe that the innovation triad is one of the defining topics of EvoDevo research and may represent its most pertinent contribution to evolutionary theory. We point out that an inclusion of developmental systems properties into evolutionary theory represents a shift of explanatory emphasis from the external factors of natural selection to the internal dynamics of developmental systems, complementing adaptation with emergence, and contingency with inherency.

Adaptation, Physiological↗

PubMed2000

Towards the minimal eukaryotic parasitic genome.

Microsporidia are well-known to infect immunocompromised patients and are also responsible for clinical syndromes in immunocompetent individuals. In recent years, evidence has been obtained in support of a very close relationship between Microsporidia and Fungi. In some species, the compaction of the genome and genes is remarkable. Thus, a systematic sequencing project has been initiated for the 2.9 Mbp genome of Encephalitozoon cuniculi, which will be useful for future comparative genomic studies.

Animals↗

PubMed2002

Genomic analysis of C-type lectins.

Many biological effects of complex carbohydrates are mediated by lectins that contain discrete carbohydrate-recognition domains. At least seven structurally distinct families of carbohydrate-recognition domains are found in lectins that are involved in intracellular trafficking, cell adhesion, cell-cell signalling, glycoprotein turnover and innate immunity. Genome-wide analysis of potential carbohydrate-binding domains is now possible. Two classes of intracellular lectins involved in glycoprotein trafficking are present in yeast, model invertebrates and vertebrates, and two other classes are present in vertebrates only. At the cell surface, calcium-dependent (C-type) lectins and galectins are found in model invertebrates and vertebrates, but not in yeast; immunoglobulin superfamily (I-type) lectins are only found in vertebrates. The evolutionary appearance of different classes of sugar-binding protein modules parallels a development towards more complex oligosaccharides that provide increased opportunities for specific recognition phenomena. An overall picture of the lectins present in humans can now be proposed. Based on our knowledge of the structures of several of the C-type carbohydrate-recognition domains, it is possible to suggest ligand-binding activity that may be associated with novel C-type lectin-like domains identified in a systematic screen of the human genome. Further analysis of the sequences of proteins containing these domains can be used as a basis for proposing potential biological functions.

Animals↗

PubMed2003

Genome evolution reveals biochemical networks and functional modules.

The analysis of completely sequenced genomes uncovers an astonishing variability between species in terms of gene content and order. During genome history, the genes are frequently rear-ranged, duplicated, lost, or transferred horizontally between genomes. These events appear to be stochastic, yet they are under selective constraints resulting from the functional interactions between genes. These genomic constraints form the basis for a variety of techniques that employ systematic genome comparisons to predict functional associations among genes. The most powerful techniques to date are based on conserved gene neighborhood, gene fusion events, and common phylogenetic distributions of gene families. Here we show that these techniques, if integrated quantitatively and applied to a sufficiently large number of genomes, have reached a resolution which allows the characterization of function at a higher level than that of the individual gene: global modularity becomes detectable in a functional protein network. In Escherichia coli, the predicted modules can be bench-marked by comparison to known metabolic pathways. We found as many as 74% of the known metabolic enzymes clustering together in modules, with an average pathway specificity of at least 84%. The modules extend beyond metabolism, and have led to hundreds of reliable functional predictions both at the protein and pathway level. The results indicate that modularity in protein networks is intrinsically encoded in present-day genomes.

Amino Acids↗

PubMed2004

Evolution of the nuclear modification factors with rapidity and centrality in d + Au collisions at (sqrt)[N(S)N]=200 GeV.

We report on a study of the transverse momentum dependence of nuclear modification factors R(dAu) for charged hadrons produced in deuteron + gold collisions at sqrt[s(NN)]=200 GeV, as a function of collision centrality and of the pseudorapidity (eta=0, 1, 2.2, 3.2) of the produced hadrons. We find a significant and systematic decrease of R(dAu) with increasing rapidity. The midrapidity enhancement and the forward rapidity suppression are more pronounced in central collisions relative to peripheral collisions. These results are relevant to the study of the possible onset of gluon saturation at energies reached at BNL RHIC.

Journal Article↗

PubMedDate not supplied

[Highest level of division in classification of organisms. 2. Archaebacteria, eubacteria and eukaryotes].

In three-domain system of organic world archaebacteria are considered as the third form of life alongside with eubacteria and eukaryotes. The author gives brief characteristics of all three groups with special focus on such diagnostic attributes as: plasmatic membrane and cellular wall, flagella, protein transcription, replication, topoisomerases, transcription, translation, glycosylation, chaperons and chaperonins, proteasomes and exosomes, histones, ATP-ases. The three-domain system has been proposed by several scientists but principal ideas were put by C. Woese. The systematics according Woese should reflect contemporary level of our knowledge of organisms. In the historical plan it once had to refuse dividing the organic world into plants and animals but accept the division into prokaryotes and eukaryotes. The science however goes further and turns now to the new level of generalizations based on the molecular aspects of cellular structures and processes. From this point of view, both plants and animals are uniform. As to prokaryotes they appeared to be non-monolithic group because of essentially different transcriptional and translational mechanisms. Therefore the detachment of archaebacteria as an independent group was the important step in the development of systematics. At the same time the three-domain system of organisms is typological and requires correction according to data on phylogenetic relatedness of these groups.

Archaea↗

PubMed2003

Early loss and multiple return of the lower temporal arcade in diapsid reptiles.

The temporal arches of diapsid reptiles have received attention for several decades. In particular, it has been observed that the lower temporal bar at the ventral margin of the cheek is frequently reduced due to the absence of a contact between jugal and quadratojugal. The loss of the arcade was formerly considered to be of high systematic value, but is now often interpreted as being autapomorphic for the respective taxon, and the presence of both arcades is generally regarded as a plesiomorphic feature. Here I show, based on a cladistic analysis as well as on further anatomical evidence, that the lower temporal arcade was lost only once in diapsid evolution, and that the presence of the arch in "higher" diapsids is secondary, which is indicated by the different ratio between jugal and quadratojugal as well as by ontogeny. This result also sheds new light on the understanding of the cheek configuration of enigmatic taxa such as ichthyosaurs and turtles.

Animals↗

PubMed2006

Regulatory objectivity and the generation and management of evidence in medicine.

The evolution of Western medicine since World War II has resulted in the emergence of new practices based on the direct interaction of biology and medicine. The post-war realignment of biology and medicine has been accompanied by the emergence of a new type of objectivity, regulatory objectivity, that is based on the systematic recourse to the collective production of evidence. Unlike forms of objectivity that emerged in earlier eras, regulatory objectivity consistently results in the production of conventions, sometimes tacit and unintentional but most often arrived at through concerted programs of action. These actions incorporate unprecedented levels of reflexivity, in the sense that biomedical practitioners in their debates and discussions take into account the conventional dimension of their endeavors. The conventions produced by regulatory objectivity create the conditions for a clinical objectivity that relies on the existence of entities and protocols produced and maintained far outside the intimate encounter between doctor and patient. By establishing endogenous forms of regulation, regulatory objectivity operates on a different plane and in a different mode from those suggested by analysts who treat all regulation as a form of rationalization imposed upon medicine from without.

Biomedical Research↗

PubMed2003

(In search of) probabilistic P systems.

The aim of this paper is to (preliminarily) discuss various ways of introducing probabilities in membrane systems. We briefly present both ideas already circulated in the literature and new proposals, trying to have a systematic overview of possibilities of associating probabilities with the ingredients of a membrane system: with (localization of) single objects, with multiplicities of objects (hence with the multisets), with the rules (depending or not on the previous applied rule), with the communication targets. For a certain mode of using the probabilities associated with the evolution rules (in string-object P systems) we obtain the computational universality.

Algorithms↗

PubMed2004

[Acute aseptic meningitis in adults. Retrospective study of 32 cases].

OBJECTIVE: The objective of this study was to analyze the characteristics of a series of acute aseptic meningitis (AAM) (defined by sterile cerebrospinal fluid (CSF) with more than 10 leucocytes per mm3 and a neutrophilic polynuclear-rich formula). We analysed the initial management, the reasons for antibiotic and/or antiviral treatment, the aetiologies, the need for lumbar puncture and the progression... METHOD: We retrospectively analyzed 32 cases of AAM (out of a total of 130 cases of meningitis) from two departments of internal medicine in Lyon, diagnosed between January 1996 and January 2003. Only the files fulfilling the AAM criteria were retained, selecting those with a minimum neutrophilic polynuclear level of 30% in the CSF. RESULTS: The mean age was 32.6 years (range: 18-75) and predominantly male patients (59%). On admission, 87% of the patients exhibited fever, but only 9% remaining so for 72 hours. Viral syndrome before admission was noted in 59% of cases, with seasonal predilection (summer: 39%, winter: 35%). The motivation for lumbar puncture (LP) was meningeal syndrome (44%), headache (94%) and vomiting (47%). The average rate of neutrophils in the CSF on admission was 63% (range: 30-96). A control LP on Day 3 was performed 16 times (50%): mean PNN rate at 18% (range: 0-80), lymphocyte rate=68% (range: 20-95). Most of the patients (77.4%) had a C reactive protein (CRP) lower than 50 mg/l on admission (range: 5-320). A cerebral scan was performed 10 times (31%) and was abnormal 2 times (multiple cerebral abscesses, possible intracranial hypertension). An antibiotic (84%) and/or antiviral (34%) treatment was initiated. The evolution on Day 3 was favourable (87.5%): no fever, regression of the meningeal syndrome, with a mean duration of hospitalisation of 8.3 days (range: 1-60). Search for Herpes simplex virus and Enterovirus was made with PCR analysis in 20 cases (62.5%): no positivity for the herpes, but 9 for the Enterovirus. The systematic blood cultures were positive only once (staphylococcal infective endocarditis with cerebral abscesses). The diagnosis of bacterial meningitis was evoked 3 times (prior antibiotic treatment). DISCUSSION: The frequency of Enterovirus AAM should encourage this type of investigation in order to withdraw the often initiated anti-infectious treatment rapidly, and hence avoid a second lumbar puncture.

Acute Disease↗

PubMed2003

Cytogenetic studies in patients on imatinib.

With the introduction of imatinib (Gleevec) (formerly STI571) for the treatment of chronic myeloid leukemia (CML), the various diagnostic methods used to monitor patients must be re-evaluated. Conventional cytogenetics has been the established method for follow-up of patients treated with interferon-alpha (IFN-alpha), and the prognostic value of major and complete cytogenetic remission was demonstrated in a number of studies. In patients on imatinib, these endpoints will likely remain valid, although longer observation is required. Cytogenetic remission as a time-dependent variable may aid risk stratification early on. Clonal evolution, ie, the presence of cytogenetic abnormalities in addition to the Philadelphia (Ph) chromosome, may provide important prognostic information as to the likely response to imatinib in all phases of CML but must be interpreted within the context of other disease characteristics. In some patients, clonal evolution is related to imatinib resistance. Information regarding the impact of specific types of additional cytogenetic abnormalities is still limited. Surprisingly, nonrandom karyotypic abnormalities have also been noted in the Ph-negative cells of some patients in cytogenetic remission. This is a novel phenomenon whose causality and prognostic implications require thorough and systematic evaluation.

Benzamides↗

PubMed1997

Is the Felsenstein zone a fly trap?

Although long-branch attraction, the incorrect grouping of long lineages in a phylogeny because of systematic error, has been identified as a potential source of error in phylogenetic analysis for almost two decades, no empirical examples of the phenomenon exist. Here, I outline several criteria for identifying long-branch attraction and apply these criteria to 18S ribosomal DNA (rDNA) sequence data for 13 insects. Parsimony and minimum evolution with p distances group the two longest branches together (those leading to Strepsiptera and Diptera). Simulation studies show that the long branches are long enough to attract. When a tree is assumed in which Strepsiptera and Diptera are separated and many data sets are simulated for that tree (using the parameter estimates for that tree for the original data), parsimony analysis of the simulated data consistently groups Strepsiptera and Diptera. Analyses of the 18S rDNA sequences using methods that are less sensitive to the problem of long-branch attraction estimate trees in which the long branches are separate.

Animals↗

PubMed2002

Fokker-Planck equation for bistable potential in the optimized expansion.

The optimized expansion is used to formulate a systematic approximation scheme to the probability distribution of a stochastic system. The first-order approximation for the one-dimensional system driven by noise in an anharmonic potential is shown to agree well with the exact solution of the Fokker-Planck equation. Even for a bistable system the whole period of evolution to equilibrium is correctly described at various noise intensities.

Journal Article↗

PubMedDate not supplied

Using social marketing to develop and test tailored health messages.

OBJECTIVE: To advance and promote procedures to evaluate tailored health messages based on the 4 Ps of social marketing (SM). METHOD: Three studies are presented for heuristic purposes to show the evolution and application of a "research plan" to 3 phases of SM research that address the 4 Ps. RESULTS: Qualitative and quantitative methods provide useful information to develop messages and to evaluate message efficacy for public health campaigns, to recruit participants to interventions, and/or to influence program adherence and participant retention. CONCLUSIONS: Formal, systematic research methods offer a viable means to evaluate the potential of SM constructs.

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