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Results for “systematic evolution”

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At least 1,153 records · Page 64Linked to original sources

PubMed1998

Footwall refrigeration along a detachment fault: implications for the thermal evolution of core complexes

Oxygen isotope compositions of epidote and quartz from chloritic breccias that underlie the detachment fault in the metamorphic core complex of the Whipple Mountains yielded quartz-epidote fractionations that range from 4.1 to 6.4 per mil and increase systematically toward the fault. These fractionations give mean temperatures that decrease from approximately 432 degrees C at 50 meters below the fault to approximately 350 degrees C at 12 meters below the fault. This extreme thermal gradient of 82 degrees C over 38 meters (2160 degrees C per kilometer) is best explained by advective heat extraction by means of circulating surface-derived fluids. Models of lithospheric extension consider only conductive cooling resulting from tectonic denudation and thus require revision to include fluid-induced fault-zone refrigeration.

Journal Article↗

PubMed2002

Evolution of the enzymes of the citric acid cycle and the glyoxylate cycle of higher plants. A case study of endosymbiotic gene transfer.

The citric acid or tricarboxylic acid cycle is a central element of higher-plant carbon metabolism which provides, among other things, electrons for oxidative phosphorylation in the inner mitochondrial membrane, intermediates for amino-acid biosynthesis, and oxaloacetate for gluconeogenesis from succinate derived from fatty acids via the glyoxylate cycle in glyoxysomes. The tricarboxylic acid cycle is a typical mitochondrial pathway and is widespread among alpha-proteobacteria, the group of eubacteria as defined under rRNA systematics from which mitochondria arose. Most of the enzymes of the tricarboxylic acid cycle are encoded in the nucleus in higher eukaryotes, and several have been previously shown to branch with their homologues from alpha-proteobacteria, indicating that the eukaryotic nuclear genes were acquired from the mitochondrial genome during the course of evolution. Here, we investigate the individual evolutionary histories of all of the enzymes of the tricarboxylic acid cycle and the glyoxylate cycle using protein maximum likelihood phylogenies, focusing on the evolutionary origin of the nuclear-encoded proteins in higher plants. The results indicate that about half of the proteins involved in this eukaryotic pathway are most similar to their alpha-proteobacterial homologues, whereas the remainder are most similar to eubacterial, but not specifically alpha-proteobacterial, homologues. A consideration of (a) the process of lateral gene transfer among free-living prokaryotes and (b) the mechanistics of endosymbiotic (symbiont-to-host) gene transfer reveals that it is unrealistic to expect all nuclear genes that were acquired from the alpha-proteobacterial ancestor of mitochondria to branch specifically with their homologues encoded in the genomes of contemporary alpha-proteobacteria. Rather, even if molecular phylogenetics were to work perfectly (which it does not), then some nuclear-encoded proteins that were acquired from the alpha-proteobacterial ancestor of mitochondria should, in phylogenetic trees, branch with homologues that are no longer found in most alpha-proteobacterial genomes, and some should reside on long branches that reveal affinity to eubacterial rather than archaebacterial homologues, but no particular affinity for any specific eubacterial donor.

Aconitate Hydratase↗

PubMed2006

Phylogeny of Cephalobina (Nematoda): molecular evidence for recurrent evolution of probolae and incongruence with traditional classifications.

Nematodes of the suborder Cephalobina include an ecologically and morphologically diverse array of species that range from soil-dwelling microbivores to parasites of vertebrates and invertebrates. Despite a long history of study, certain of these microbivores (Cephaloboidea) present some of the most intractable problems in nematode systematics; the lack of an evolutionary framework for these taxa has prevented the identification of natural groups and inhibited understanding of soil biodiversity and nematode ecology. Phylogenetic analyses of ribosomal (LSU) sequence data from 53 taxa revealed strong support for monophyly of taxa representing the Cephaloboidea, but do not support the monophyly of most genera within this superfamily. Historically these genera have primarily been recognized based on variation in labial morphology, but molecular phylogenies show the same general labial (probolae) morphotype often results from recurrent similarity, a result consistent with the phenotypic plasticity of probolae previously observed for some species in ecological time. Phylogenetic analyses of LSU rDNA also recovered strong support for some other groups of cephalobs, including taxa representing most (but not all) Panagrolaimoidea. In addition to revealing homoplasy of probolae, molecular trees also imply other unexpected patterns of character evolution or polarity, including recurrent similarity of offset spermatheca presence, and representation of complex probolae as the ancestral condition within Cephaloboidea. For Cephalobidae, molecular trees do not support traditional genera as natural groups, but it remains untested if deconstructing probolae morphotypes or other structural features into finer component characters may reveal homologies that help delimit evolutionary lineages.

Animals↗

PubMed1998

Evolution of the vertebrate H1 histone class: evidence for the functional differentiation of the subtypes.

Histone H1 subtypes are involved in chromatin higher-order structure. The representation of the subtypes varies greatly depending on the cellular and developmental context. We have estimated the rates of nucleotide substitution for several H1 subtypes, including mammalian and amphibian H1 degree, avian H5, and mammalian H1a-e and H1t, with the aim of finding evidence for their functional differentiation. The rates of nonsynonymous substitution differ among the subtypes by almost one order of magnitude. Such a wide variation in the degree of tolerance of amino acid substitutions is consistent with the functional differentiation of the subtypes. H1 has a characteristic three-domain structure. The rate ratios among the domains of the molecule are not systematically maintained in the different subtypes. This suggests the assumption of differentiated functions by the individual domains in chromatin structure. We have estimated the average time of divergence of H1a-e and H1t paralogs as 406 +/- 80 Myr. The lack of evidence for concerted evolution of H1a-e and H1t since long before the mammalian radiation further supports the functional differentiation of the subtypes.

Animals↗

PubMed2005

Mitochondrial phylogeny reveals differential modes of chromosomal evolution in the genus Tatera (Rodentia: Gerbillinae) in Africa.

The African gerbils of the genus Tatera are widespread and abundant throughout sub-Saharan Africa. There is still today a certain controversy concerning the taxonomy of these rodents and very few attempts have been made to assess their systematic relationships. The present paper introduces findings based on the partial sequences of cytochrome b (495 bp) and the 16S rRNA (469 bp) mitochondrial genes of six (T. robusta, T. nigricauda, T. vicina, T. leucogaster, T. valida, and T. kempi) species together with two additional taxa. We also report the karyotypes of T. vicina and T. leucogaster. We propose that T. vicina should be considered as a valid species and show the monophyly of the robusta species group, with the exclusion of T. leucogaster. Our results show there is a different chromosomal evolutionary pattern within the two major lineages, which is recognizable through molecular phylogenetics. One is characterized by karyotype stability and the other by a considerable number of chromosomal rearrangements. The lineage divergence coincides with the formation of the East African Rift. The processes that led to the origin of the East African species seem to be related to the subsequent climatic changes, which caused cyclic contraction and expansion of the savannah biomes. Furthermore, geological activities that characterized East Africa during Plio-Pleistocene may also have contributed to lineage divergence.

Africa↗

PubMed2004

The developmental bases of limb reduction and body elongation in squamates.

Employing an integrative approach to investigate the evolution of morphology can yield novel perspectives not attainable from a single field of study. Studies of limb loss and body elongation in squamates (snakes and lizards) present a good example in which integrating studies of systematics and ecology with genetics and development can provide considerable new insight. In this comment we address several misunderstandings of the developmental genetic literature presented in a paper by Wiens and Slingluff (2001) to counter their criticism of previous work in these disciplines and to clarify the apparently contradictory data from different fields of study. Specifically, we comment on (1) the developmental mechanisms underlying axial regionalization, body elongation, and limb loss; (2) the utility of presacral vertebral counts versus more specific partitioning of the primary body axis; (3) the independent, modular nature of limbs and limb girdles and their utility in diagnosing genetic changes in development; and (4) the causal bases of hind limb reduction in ophidian and nonophidian squamates.

Animals↗

PubMed1998

Origin and evolution of Asian hominoid primates. Paleontological data versus molecular data.

The origin and evolution of hominoid primates (apes and man) has long been studied exclusively on the basis of available fossil remains. Indeed, a migration of African primates towards Asia at about -16 to -17 Ma might have given the lineage of Miocene Asian hominoids. This hypothesis is supported by the oldest remains of Miocene Asian hominoids dated at about -16.1 Ma. But the recent discovery of anthropoid primates in the Eocene of Asia seems to indicate that Asia was a major evolutionary and differentiation centre for anthropoid primates as early as the Eocene. In addition, Asian primates probably continued to evolve in Asia from the Eocene onward and led at least to the extant Asian hominoids (orangutans and gibbons). African and Asian extant anthropoid primates might therefore have diverged at least 36 Ma ago, and this hypothesis is also supported by the most recent data in molecular biology. Moreover, an Asiatic origin of African Paleogene propliopithecine primates is suggested. In that context, evolutionary rates might not be constant, and molecular clocks should be necessarily characteristic for each studied group of mammals. Several examples that illustrate the conflict between paleontological and molecular data are discussed. The necessity to integrate more systematically paleontological data as chronological reference points in studies in molecular phylogeny is discussed.

Animals↗

PubMed2005

Significant expansion of exon-bordering protein domains during animal proteome evolution.

We present evidence of remarkable genome-wide mobility and evolutionary expansion for a class of protein domains whose borders locate close to the borders of their encoding exons. These exon-bordering domains are more numerous and widely distributed in the human genome than other domains. They also co-occur with more diverse domains to form a larger variety of domain architectures in human proteins. A systematic comparison of nine animal genomes from nematodes to mammals revealed that exon-bordering domains expanded faster than other protein domains in both abundance and distribution, as well as the diversity of co-occurring domains and the domain architectures of harboring proteins. Furthermore, exon-bordering domains exhibited a particularly strong preference for class 1-1 intron phase. Our findings suggest that exon-bordering domains were amplified and interchanged within a genome more often and/or more successfully than other domains during evolution, probably the result of extensive exon shuffling and gene duplication events. The diverse biological functions of these domains underscore the important role they play in the expansion and diversification of animal proteomes.

Animals↗

PubMed2026

Transcriptome mining and comparative genomics reveal 36 putative novel marafivirus species and conserved evolution of the marafibox regulatory element.

BACKGROUND: Marafiviruses are plant-infecting RNA viruses associated with several economically important crops, but their genomic diversity remains incompletely characterized. OBJECTIVE: This study aimed to identify previously unrecognized marafivirus genomes and investigate their genomic features and evolutionary relationships. METHODS: Publicly available plant transcriptome datasets were systematically mined to detect marafivirus-like sequences. Recovered genomes were analyzed using comparative sequence analysis, phylogenetic reconstruction, and genome organization characterization. RESULTS: A total of 62 marafivirus-like genomes were recovered from 33 independent sources representing diverse plant hosts. Polyprotein-based comparative and phylogenetic analyses grouped these genomes into 36 lineages likely representing novel species. All newly identified viruses clustered within the Marafivirus clade. Genome organization analysis revealed conserved polyprotein architecture and widespread presence of the marafibox promoter element. Conservation of additional open reading frames among closely related isolates aided identification of potentially functional genes. CONCLUSION: These findings substantially expand the known diversity of marafiviruses and demonstrate the effectiveness of transcriptome mining for discovering previously unrecognized plant viruses.

Phylogeny↗

PubMed2006

Molecular evolution of satellite DNA repeats and speciation of lizards of the genus Darevskia (Sauria: Lacertidae).

Satellite DNA repeats were studied in Caucasian populations of 18 rock lizard species of the genus Darevskia. Four subfamilies (Caucasian Lacerta satellites (CLsat)I-IV) were identified, which shared 70%-75% sequence similarity. The distribution of CLsat subfamilies among the species was studied. All the species could be divided into at least 3 clades, depending on the content of CLsat subfamilies in each genome: "saxicola", "rudis", and "mixta" lizards. CLsatI was found in all studied species, but in very different quantities; the "saxicola" group contained this subfamily predominantly. The "rudis" group also contained CLsatIII, and the "mixta" group carried considerable amounts of CLsatII. The highest concentrations of CLsatI and CLsatII were detected in 2 ground lizards--D. derjugini and D. praticola, respectively. D. parvula predominantly carried CLsatIII. CLsatIV was found only in the Crimean species D. lindholmi. The distribution patterns of satellite subfamilies show possible postglacial speciation within the genus Darevskia. A hybrid origin of species that possess 2 or 3 CLsat subfamilies and important clarifications to the systematics of the genus are proposed.

Animals↗

PubMed2005

A systematic review of large scale and heterogeneous gene array data in heart failure.

Microarray analysis has become a widely available tool for the generation of gene expression data on a genomic scale. Since the studies with similar protocols are growing, it has become necessary to systematically revise the large body of literature to decipher the gene expression data. In this review, we analyzed and critically discussed the database presented from 14 published studies that showed the gene expression profile in heart failure (HF) using microarray as a primary tool. After comparing the diverse database from these studies, we explain the protein translational, matri-cellular, immunological and fibrosis-related mechanisms in HF. In addition to previously annotated genes, we analyzed two differentially expressed expressed sequence tags (ESTs) (KIAA0152 and Suppressor of G(Two) allele of the suppressor of kinetochore protein-1, SGT1) in HF and showed how bio-informatic analysis of ESTs can lead to the identification of novel pathways active in HF. We have also discussed the new publicly accessible tools that link the gene expression data to gene ontogeny (GO) and functionality. Finally, we have systematically revised the chromosomal localization of the genes that are specifically up-regulated in HF. We have thus spotted chromosome 1, 2, 11 and 12 as the chromosomal hotspots of HF. This methodical approach will simplify the existing concepts on the evolution and progression of HF and lead us toward the development of newer diagnostic and therapeutic tools. Although modeled to HF, this approach should be of broader scientific interest to elaborate multiple genes and complex pathways.

Cell Cycle Proteins↗

PubMed2026

Molecular Diagnostics for WHO Priority Bacterial Pathogens: A Bibliometric Mapping of Diagnostic Platforms, Resistance Markers, and Antimicrobial Resistance Research Trends.

Antimicrobial resistance (AMR) constrains effective treatment and carries implications for infection control, surveillance, and public health. The World Health Organization (WHO) priority bacterial pathogen framework has intensified the need for diagnostic innovation by redefining research priorities around organisms combining high disease burden with complex resistance profiles. Molecular diagnostics have accordingly moved beyond culture-based workflows, integrating rapid pathogen identification, resistance-marker detection, genomic surveillance, and clinical decision support. The present study conducted a bibliometric mapping of the literature on WHO priority pathogens. Rather than addressing resistance at a general level or a single pathogen or technology, it integrates priority pathogens, molecular platforms, and resistance markers within a single framework, tracing their joint thematic and temporal evolution along an explicit pathogen-platform-marker axis. Scopus-indexed articles and reviews (2000-2025) were retrieved, yielding 1746 publications after screening adapted from the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Analyses used Bibliometrix/Biblioshiny, R, and VOSviewer. The literature expanded markedly after 2018, led by China and the United States. Methicillin-resistant Staphylococcus aureus (MRSA), Mycobacterium tuberculosis, Enterococcus faecium, and the Enterobacterales-carbapenemase axis constituted the principal thematic cores, whereas conventional polymerase chain reaction (PCR)/nucleic acid amplification testing (NAAT) and whole-genome sequencing were the dominant platforms. Overall, the field has evolved from pathogen detection into an AMR-centered translational domain encompassing resistance prediction, genomic epidemiology, surveillance, and clinical decision support. Diagnostic development, stewardship, and surveillance depend on hybrid workflows coupling rapid marker-targeted assays with genome-based characterization, delivering actionable resistance within clinically meaningful timeframes, and extending coverage to underrepresented pathogens and platforms.

Humans↗

PubMed1996

Spatiotemporally exact cDNA libraries from quail embryos: a resource for studying neural crest development and neurocristopathies.

The neural crest is of fundamental importance in the developments of the head and peripheral nervous system, in the evolution of the vertebrates, and clinically because it gives rise to developmental abnormalities and neoplasms in humans. We have established a resource for studying the development of the neural crest by systematically constructing cDNA libraries from spatiotemporally exact neural crest and related cell populations. Neural crest populations were obtained from vagal and thoracic axial levels and from branchial arches, at premigratory and early and late migratory stages, at localization stages, and after differentiation into dorsal root ganglion cells, Schwann cells, sympathetic neurons, adrenal medullary cells, and melanocytes. Libraries were constructed using several methods developed to approach the issue of making representative libraries from small amounts of tissue. The fidelity and usefulness of the libraries were tested, and this revealed that they expressed a variety of sequences such as integrins, CAMs, growth factors and their receptors, protein-tyrosine kinases, and phosphatases. Differential display also revealed a unique combination of cDNA species. We then selected libraries spatiotemporally appropriate for epithelium-mesenchyme transformation and probed for TGF-beta-related sequences. As anticipated, we confirmed the presence of TGF-beta 2 and dorsalin-1 but could not detect TGF-beta 1. We also revealed new expression sites, defined by the origin of the libraries, of receptors known to be expressed elsewhere (Tsk 7l; TBRII). We anticipate that this collection of cDNA libraries will be of use in studying normal and abnormal neural crest development, by both homology searches and differential expression approaches, with spatiotemporal expression information being inherent in the initial screen.

Animals↗

PubMed1975

Duchenne muscular dystrophy and poliomyelitis. A study of dystrophic-denervated muscle.

A systematic study of dystrophy-denervation in human muscle showed minimal morphometabolic differences between dystrophic and dystrophic-denervated muscle. The only certain conclusion is that denervation influences the rhythm of evolution of the dystrophy without impressing any of the few characteristics considered at present as peculiar to denervation.

Child↗

PubMed2006

Evolution of fetal ultrasonography.

The authors wish to highlight the evolution that has occurred in fetal ultrasound in recent years. A first significant evolution lies in the increasing contribution of first trimester ultrasound for the detection of fetal anomalies. Malformations of several organs and systems have been diagnosed during the first trimester. Furthermore the systematic measurement of the fetal neck translucency has led to increasing rate of detection of aneuploidies and heart malformations. For several years now, three-dimensional (3D) and 4D ultrasound (US) have been used as a complementary tool to 2D US for the evaluation of fetal morphology. This brings an improved morphologic assessment of the fetus. Applications of the techniques are increasing, especially for the fetal face, heart and extremities. The third field where fetal US is continuously providing important information is the knowledge of the natural history of diseases. This has brought significant improvement in the postnatal management of several diseases, especially urinary tract dilatation and broncho-pulmonary malformation.

Congenital Abnormalities↗

PubMed2004

Effect of reaction media on the growth and photoluminescence of colloidal CdSe nanocrystals.

Using cadium oxide (CdO) as the Cd precursor and tri-n-octylphosphine selenide (TOPSe) as the Se source, TOP-capped and TOP/tri-n-octylphosphine oxide (TOPO)-capped CdSe nanocrystals were synthesized without the use of an acid. The synthetic approach involved the addition of a TOPSe/TOP solution into a CdO/TOP solution with or without TOPO at one temperature and subsequent growth at a lower temperature. The temporal evolution of the optical properties, namely, absorption and luminescence, of the growing nanocrystals was monitored in detail. A comprehensive examination on the control of the photoluminescence (PL) properties was performed by systematically varying the TOP/TOPO weight ratio of the reaction media. Surprisingly, a rational choice of 100% TOP or 80% TOP was found to produce "quality" nanocrystals when monitored under the present experimental conditions and growth-time scale. The term "quality" is mainly based on the sharp features and rich substructure exhibited in the absorption spectra of the growing nanocrystals, as well as the sharp features in the emission spectra with narrow full width at half-maximum (fwhm). There are two distinguishable stages of growth: an early stage (<5 min) and a later stage. TOP plays a major role in the control of a slow growth rate in the early stage, while TOPO controls slow growth in the later stage. The optical sensitivity of the growing nanocrystals when dispersed in nonpolar or polar solvents was studied, including two size-dependent parameters, namely, the solvent sensitivity (PL intensity) and nonresonant Stokes shift (NRSS). The insights gained from the present study enable a synthetic approach in which high-quality CdSe nanocrystals are achieved with high synthetic reproducibility.

Cadmium Compounds↗

PubMed2006

Improving jet distributions with effective field theory.

We obtain perturbative expressions for jet distributions using soft-collinear effective theory (SCET). By matching SCET onto QCD at high energy, tree level matrix elements and higher order virtual corrections can be reproduced in SCET. The resulting operators are then evolved to lower scales, with additional operators being populated by required threshold matchings in the effective theory. We show that the renormalization group evolution and threshold matchings reproduce the Sudakov factors and splitting functions of QCD, and that the effective theory naturally combines QCD matrix elements and parton showers. The effective theory calculation is systematically improvable and any higher order perturbative effects can be included by a well-defined procedure.

Journal Article↗

PubMed1995

Psychoanalysis and dynamical systems theory: prediction and self similarity.

The theory of dynamical systems (sometimes called chaos theory) has emerged in the past two decades as a powerful tool for understanding the evolution of complex systems. Attempts to develop psychoanalysis along the lines of nineteenth century physical science have proven unsatisfactory. The theory of dynamical systems provides another route for development. It suggests that prediction should aim at describing the overall evolution of systems and that the possibilities for such evolution are broader than classical theory suggested. It also shows that complex systems often involve structures that repeat basic features on several different levels of observation. This suggests a method for systematically exploring the overly rich data of psychoanalysis.

Ego↗