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Results for “systematic evolution”

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PubMed1988

Do exons code for structural or functional units in proteins?

In considering the origin and evolution of proteins, the possibility that proteins evolved from exons coding for specific structure-function modules is attractive for its economy and simplicity but is not systematically supported by the available data. However, the number of correspondences between exons and units of protein structure-function that have so far been identified appears to be greater than expected by chance alone. The available data also show (i) that exons are fairly limited in size but are large enough to specify structure-function modules in proteins; (ii) that the position of introns for homologous domains in the same gene is reasonably stable, but there is also evidence for mechanisms that alter the position or existence of introns; and (iii) that it is possible that the observed relationship of exons to protein structure represents a degenerate state of an ancestral correspondence between exons and structure-function modules in proteins.

Exons↗

PubMed1999

Charles Darwin's views of classification in theory and practice.

It has long been argued that Charles Darwin was the founder of the school of "evolutionary taxonomy" of the Modern Synthesis and, accordingly, that he recognized genealogy and similarity as dual, synergistic criteria for classification. This view is based on three questionable interpretations: first, of isolated passages in the 13th chapter of the Origin of Species; second, of one phrase in a letter that Darwin wrote about the work of an author he had partly misunderstood; and third, of his taxonomic practice in the barnacle monographs, which only implicitly embody his philosophy of classification, if at all. These works, seen in fuller context and with the perspective of extensive correspondence, are consistent with the view that Darwin advocated only genealogy as the basis of classification, and that similarity was merely a tool for discovering evolutionary relationships. Darwin was neither a Mayrian taxonomist nor a cladist, and he did not approach systematic issues in the same terms that we do in the late 20th century.

Animals↗

PubMed2001

Genome size in 21 Artemisia L. species (Asteraceae, Anthemideae): systematic, evolutionary, and ecological implications.

Genome size was estimated by flow cytometry in 24 populations belonging to 22 Artemisia taxa (21 species, 1 with two subspecies), which represent the distinct subgenera, life forms, basic chromosome numbers, and ploidy levels in the genus. 2C nuclear DNA content values range from 3.5 to 25.65 pg, which represents a more than sevenfold variation. DNA content per haploid genome ranges from 1.75 to 5.76 pg. DNA amount is very well correlated with karyotype length and ploidy level. Some variations in genome size have systematic and evolutionary implications, whereas others are linked to ecological selection pressures.

Artemisia↗

PubMedDate not supplied

[Methicilline-sensitive and methicilline-resistant Staphylococcus aureus related morbidity in chronic wounds: a prospective study].

OBJECTIVE: Staphylococcus aureus is the most common bacteria responsible for cutaneous infections. Its capacity to adapt has led to the selection of methicilline-resistant strains (MRSA). These strains create specific problems in their management in dermatology (mode of contamination, treatment, added costs, increased nosocomial risks). The objective of our study was to search for morbidity of MRSA in chronic cutaneous wounds in hospital settings and assess the need of systemic antibiotic therapy. PATIENTS AND METHODS: We have conducted a one-year prospective study. All the patients hospitalized in the department with leg ulcers or foot wounds were included. Following local sampling for bacteriological examination, three groups were constituted: methicilline-sensitive patients with staphylococcus aureus (MSSA), methicilline-resistant staphylococcus aureus patients and patients in whom these bacteria were absent. Only the first two groups were compared after studying the past history, clinical description of the wound at the start of the study, results of the infectious bacteriology and of the clinical and bacteriological evolution of the wounds. RESULTS: The two groups studied were similar in number, past history, clinical aspect and therapeutic management. Only malnutrition was more frequent in patients exhibiting MRSA. There was no difference with the evolution of the wounds. CONCLUSION: Our study did not reveal any difference in the morbidity of staphylococcus aureus in the cutaneous wounds whether methicilline sensitive or resistant. Systematic antibiotherapy is not justified in the absence of signs of infection.

Adult↗

PubMed1998

Janus kinases and focal adhesion kinases play in the 4.1 band: a superfamily of band 4.1 domains important for cell structure and signal transduction.

The band 4.1 domain was first identified in the red blood cell protein band 4.1, and subsequently in ezrin, radixin, and moesin (ERM proteins) and other proteins, including tumor suppressor merlin/schwannomin, talin, unconventional myosins VIIa and X, and protein tyrosine phosphatases. Recently, the presence of a structurally related domain has been demonstrated in the N-terminal region of two groups of tyrosine kinases: the focal adhesion kinases (FAK) and the Janus kinases (JAK). Additional proteins containing the 4.1/JEF (JAK, ERM, FAK) domain include plant kinesin-like calmodulin-binding proteins (KCBP) and a number of uncharacterized open reading frames identified by systematic DNA sequencing. Phylogenetic analysis of amino acid sequences suggests that band 4.1/JEF domains can be grouped in several families that have probably diverged early during evolution. Hydrophobic cluster analysis indicates that the band 4.1/JEF domains might consist of a duplicated module of approximately 140 residues and a central hinge region. A conserved property of the domain is its capacity to bind to the membrane-proximal region of the C-terminal cytoplasmic tail of proteins with a single transmembrane segment. Many proteins with band 4.1/JEF domains undergo regulated intra- or intermolecular homotypic interactions. Additional properties common to band 4.1/JEF domains of several proteins are binding of phosphoinositides and regulation by GTPases of the Rho family. Many proteins with band 4. 1/JEF domains are associated with the actin-based cytoskeleton and are enriched at points of contact with other cells or the extracellular matrix, from which they can exert control over cell growth. Thus, proteins with band 4.1/JEF domain are at the crossroads between cytoskeletal organization and signal transduction in multicellular organisms. Their importance is underlined by the variety of diseases that can result from their mutations.

Amino Acid Sequence↗

PubMed2004

The mitochondrial genomics of parasitic nematodes of socio-economic importance: recent progress, and implications for population genetics and systematics.

Mitochondria are subcellular organelles in which oxidative phosphorylation and other important biochemical functions take place within the cell. Within these organelles is a genome, called the mitochondrial (mt) genome, which is distinct from, but cooperates closely with the nuclear genome of the cell. Investigating mt genomes has significant implications for various fundamental research areas, including mt biochemistry and physiology, and, importantly, such genomes provide a rich source of markers for population genetic and systematic studies. While approximately 250 complete mt genome sequences have been determined for a range of metazoan organisms from various phyla, few of these represent parasitic helminths. Until 1998, only two mt genome sequences had been determined for parasitic nematodes, in spite of their socio-economic importance and the need for investigations into their population genetics, taxonomy and evolution. However, since that time, there has been some progress. The main focus of the present chapter is to review the state of knowledge of the mt genomics for parasitic nematodes, to describe recent technological improvements to mt genome sequencing, to summarize applications of mt gene markers for studying the systematics and population genetics of parasitic nematodes, and to emphasize prospects and opportunities for future research in these areas.

Animals↗

PubMed2006

Phylogenomics of several deer species revealed by comparative chromosome painting with Chinese muntjac paints.

A set of Chinese muntjac (Muntiacus reevesi) chromosome-specific paints has been hybridized onto the metaphases of sika deer (Cervus nippon, CNI, 2n = 66), red deer (Cervus elaphus, CEL, 2n = 62) and tufted deer (Elaphodus cephalophus, ECE, 2n = 47). Thirty-three homologous autosomal segments were detected in genomes of sika deer and red deer, while 31 autosomal homologous segments were delineated in genome of tufted deer. The Chinese muntjac chromosome X probe painted to the whole X chromosome, and the chromosome Y probe gave signals on the Y chromosome as well as distal region of the X chromosome of each species. Our results confirmed that exclusive Robertsonian translocations have contributed to the karyotypic evolution of sika deer and red deer. In addition to Robertsonian translocation, tandem fusions have played a more important role in the karyotypic evolution of tufted deer. Different types of chromosomal rearrangements have led to great differences in the genome organization between cervinae and muntiacinae species. Our analysis testified that six chromosomal fissions in the proposed 2n = 58 ancestral pecoran karyotype led to the formation of 2n = 70 ancestral cervid karyotype and the deer karyotypes is more derived compare with those of bovid species. Combining previous cytogenetic and molecular systematic studies, we analyzed the genome phylogeny for 11 cervid species.

Animals↗

PubMed2004

Evolution of the gall-forming plant parasitic nematodes (Tylenchida: Anguinidae) and their relationships with hosts as inferred from Internal Transcribed Spacer sequences of nuclear ribosomal DNA.

Phylogenetic relationships among gall-forming plant parasitic nematodes of the subfamily Anguininae are reconstructed by maximum parsimony and maximum likelihood analyses. Sequences of the ITS of rDNA from 53 populations and species of gall-forming nematodes and five populations of the Ditylenchus dipsaci species complex were analysed. The phylogenetic trees strongly support monophyly of the genus Anguina and show nonmonophyly for the genera Mesoanguina and Heteroanguina. Morphological and biological characters are generally congruent with the anguinid groups identified in the rDNA phylogeny. Analyses of evolution of different gall types among anguinids reveal that there are apparent evolutionary trends in gall evolution: from abnormal swelling and growth of infested plant organs toward small localised galls, and from infestation of vegetative toward generative organs. Our study demonstrates that the main anguinid groups are generally associated with host plants belonging to the same or related systematic groups. The comparison of the ITS phylogenies of anguinids parasitising Poaceae and their host grasses shows a high level of cospeciation events.

Animals↗

PubMed2026

Molecular Evolution and Expression Analysis of the ADH Gene Family in Apple Bud Mutants.

Alcohol dehydrogenase (ADH) catalyzes the reduction of aldehydes to alcohols, key precursor substrates for volatile ester biosynthesis, which determines the characteristic aroma of apple fruit. However, a comprehensive genome-wide investigation of the ADH gene family in apple has been lacking. In this study, we systematically identified ADH genes in the apple genome using integrated bioinformatics approaches, including phylogenetic analysis, synteny evaluation, promoter cis-element prediction, codon usage bias assessment, and protein interaction network modeling. Expression patterns were examined through transcriptomic data and validated by RT-qPCR analysis across different organs and among 'Red Delicious' and its four bud mutant lines. We identified 44 ADH genes, with 12 forming a prominent cluster on chromosome 1. RT-qPCR analysis revealed that MdADH20 was dramatically upregulated in the 'Red Chief' mutant (relative expression of 59.38), suggesting its pivotal role. Phylogenetic analysis revealed a close evolutionary relationship with wild strawberry. The encoded proteins were generally stable and predominantly localized to the cytoplasm. Promoter analysis showed enrichment of growth/development-related and ARE elements, while codon usage analysis identified AGA, GCU, GUU, and CUU as preferred codons. Protein interaction prediction suggested MdADH19 and MdADH20 as hub proteins. Expression profiling and RT-qPCR further identified MdADH20 as a core candidate gene, characterized by its stable and high expression, particularly in the 'Red Delicious' mutant. Its central position in the predicted protein-protein interaction network suggests a potential regulatory role in the aroma biosynthesis pathway of apple fruit. This study provides the first systematic genome-wide characterization of the apple ADH gene family, establishing a theoretical groundwork for deciphering aroma biosynthesis mechanisms and offering potential target genes for flavor improvement through bud mutation breeding strategies.

ADH gene family↗

PubMed1998

[Data interchange in blood transfusion: the impact of a new standard on the evolution of health electronic data exchange in France].

The sanitary and social data interchange within care establishments or networks is today the subject of many national or international considerations. Electronic data interchange in the health field has characteristics linked to ethical and deontological principles of care staff. Used daily, this tool contributes to the quality of care, to the optimization of patient treatment and to the organization of the system care. In the transfusion field, the standardization of messages related to the traceability of blood products in now required by the No. 2 instruction of French Blood Agency, which rules the using of national norms elaborated by the French Agency of Normalization. If the technicality is the greater part of these regulated and formalized messages, this standardization systematizes and justifies the nominative and ciphered data interchange in an open environment, opening a new dimension in the interoperability of data system between care establishments. This article analyzes the characteristics and the potential impact of this normalization on the evolution of the electronic data interchange in the health field.

Blood Transfusion↗

PubMed2006

Acetylcholinesterase genes within the Diptera: takeover and loss in true flies.

It has recently been reported that the synaptic acetylcholinesterase (AChE) in mosquitoes is encoded by the ace-1 gene, distinct and divergent from the ace-2 gene, which performs this function in Drosophila. This is an unprecedented situation within the Diptera order because both ace genes derive from an old duplication and are present in most insects and arthropods. Nevertheless, Drosophila possesses only the ace-2 gene. Thus, a secondary loss occurred during the evolution of Diptera, implying a vital function switch from one gene (ace-1) to the other (ace-2). We sampled 78 species, representing 50 families (27% of the Dipteran families) spread over all major subdivisions of the Diptera, and looked for ace-1 and ace-2 by systematic PCR screening to determine which taxonomic groups within the Diptera have this gene change. We show that this loss probably extends to all true flies (or Cyclorrhapha), a large monophyletic group of the Diptera. We also show that ace-2 plays a non-detectable role in the synaptic AChE in a lower Diptera species, suggesting that it has non-synaptic functions. A relative molecular evolution rate test showed that the intensity of purifying selection on ace-2 sequences is constant across the Diptera, irrespective of the presence or absence of ace-1, confirming the evolutionary importance of non-synaptic functions for this gene. We discuss the evolutionary scenarios for the takeover of ace-2 and the loss of ace-1, taking into account our limited knowledge of non-synaptic functions of ace genes and some specific adaptations of true flies.

Acetylcholinesterase↗

PubMed2005

Raman and IR spectroscopy of chemically processed single-walled carbon nanotubes.

IR and Raman spectroscopy has been used to study the evolution of the vibrational spectrum of bundled single-walled carbon nanotubes (SWNTs) during the purification process needed to remove metal catalyst and amorphous carbon present in arc-derived SWNT soot. We have carried out a systematic study to define the different outcomes stemming from the purification protocol (e.g., DO, DO/HCl, DO/HNO(3), H(2)O(2), H(2)O(2)/HCl), where dry oxidation (DO) or refluxing in H(2)O(2) was used in a first purification step to remove amorphous carbon. The second step involves acid reflux (HCl or HNO(3)) to remove the residual growth catalyst (Ni-Y). During strong chemical processing, it appears possible to create additional defects where carbon atoms are eliminated, the ring structure is now open, localized C=C bonds are created, and O-containing groups can be added to this defect to stabilize the structure. Evolution of SWNT skeletal disorder obtained via chemical processing was studied by Raman scattering. Higher intensity ratios of R- and G-band (I(R)/I(G)) are more typically found in SWNT materials with low D-band intensity and narrow G-band components. Using IR transmission through thin films of nanotubes, we can resolve the structure due to functional groups that were present in the starting material or added through chemical processing. After high-temperature vacuum annealing of the purified material at 1100 degrees C, IR spectroscopy shows that most of the added functional groups can be removed and that the structure that remains is assigned to the one- and two-phonon modes of SWNTs.

Journal Article↗

PubMed2000

Accommodating phylogenetic uncertainty in evolutionary studies.

Many evolutionary studies use comparisons across species to detect evidence of natural selection and to examine the rate of character evolution. Statistical analyses in these studies are usually performed by means of a species phylogeny to accommodate the effects of shared evolutionary history. The phylogeny is usually treated as known without error; this assumption is problematic because inferred phylogenies are subject to both stochastic and systematic errors. We describe methods for accommodating phylogenetic uncertainty in evolutionary studies by means of Bayesian inference. The methods are computationally intensive but general enough to be applied in most comparative evolutionary studies.

Animals↗

PubMed2006

New insights into myosin evolution and classification.

Myosins are eukaryotic actin-dependent molecular motors important for a broad range of functions like muscle contraction, vision, hearing, cell motility, and host cell invasion of apicomplexan parasites. Myosin heavy chains consist of distinct head, neck, and tail domains and have previously been categorized into 18 different classes based on phylogenetic analysis of their conserved heads. Here we describe a comprehensive phylogenetic examination of many previously unclassified myosins, with particular emphasis on sequences from apicomplexan and other chromalveolate protists including the model organism Toxoplasma, the malaria parasite Plasmodium, and the ciliate Tetrahymena. Using different phylogenetic inference methods and taking protein domain architectures, specific amino acid polymorphisms, and organismal distribution into account, we demonstrate a hitherto unrecognized common origin for ciliate and apicomplexan class XIV myosins. Our data also suggest common origins for some apicomplexan myosins and class VI, for classes II and XVIII, for classes XII and XV, and for some microsporidian myosins and class V, thereby reconciling evolutionary history and myosin structure in several cases and corroborating the common coevolution of myosin head, neck, and tail domains. Six novel myosin classes are established to accommodate sequences from chordate metazoans (class XIX), insects (class XX), kinetoplastids (class XXI), and apicomplexans and diatom algae (classes XXII, XXIII, and XXIV). These myosin (sub)classes include sequences with protein domains (FYVE, WW, UBA, ATS1-like, and WD40) previously unknown to be associated with myosin motors. Regarding the apicomplexan "myosome," we significantly update class XIV classification, propose a systematic naming convention, and discuss possible functions in these parasites.

Animals↗

PubMed2001

Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence for the monophyletic origin of toothed whales.

Short interspersed repetitive elements (SINEs) are a kind of retroposons dispersed among the eukaryotic genomes. Previously, we isolated and characterized a new SINE family, named CHR-2, members of which are distributed in the genomes of cetaceans, hippopotamuses, and ruminants. We analyzed systematically more than a hundred members of the CHR-2 SINEs, which were isolated from the genomes of cetaceans and cow, together with the additional data available in the DNA databases, and showed that these SINEs are divided into at least five distinct subfamilies that share diagnostic nucleotides and/or deletions. A hybridization analysis clearly demonstrated that, among these five subfamilies, two subfamilies, named CD and CDO, are specific to cetaceans and toothed whales, respectively. We reconstruct the evolutionary history of the CHR-2 SINEs during evolution of cetartiodactyl genomes.

Animals↗

PubMed1993

Difficulties in collecting peripheral blood stem cells in chronic myeloid leukemia related to persistence of the leukemic cell clone.

Eight chronic myeloid leukemia (CML) patients ineligible for allogeneic bone marrow transplantation (BMT) were intensively treated by a myeloablative chemotherapy identical to the treatment that we use in acute myeloid leukemia (AML). The objectives of such an intensive treatment were both to reduce the size of the leukemia stem cell mass as much as possible and subsequently to allow a better mobilization of the residual Ph-negative (Ph-) stem cells. Cytogenetic analyses were systematically performed on blood-derived stem cells collected at the hematopoietic recovery phase following post-chemotherapy aplasia. The length of aplasia did not correlate with the evolutive stage of the disease, but was negatively correlated with the total colony forming units-granulocyte macrophage (CFU-GM) amounts collected. The cytogenetic abnormality remained present in most cases in all metaphases counted in leukapheresis products. Three patients were transplanted with these leukapheresis products. One died due to sepsis before engraftment; the two others engrafted very slowly, while Ph-positive (Ph+) cells were found at post-transplant controls. These disappointing results suggest that the myeloablative chemotherapy used in this study has not resulted in satisfactory advantages for the proliferation of residual normal stem cells over the expansion of the Ph+ clone.

Adolescent↗

PubMed1991

AIDS, a social dilemma: detection of seropositives.

At present, we can observe an evolution in ideas about the detection of HIV seropositivity through a qualitative analysis of specialised literature on the ethical aspects of AIDS. In the case of this disease, systematic screening of the population does not correspond to epidemiological criteria: it is wasteful, troublesome and costly. Whether it is voluntary, and therefore biased, or compulsory, and therefore controversial, systematic screening seems an unlikely option. This situation has prompted many versions of target-group screening, which correspond to two options: systematic screening of known risk-groups, discriminatory, confidential and anonymous; target-group screening linked to particular circumstances: recognised as necessary by blood-donors and well-accepted by pregnant mothers. This method can be institutionalised and applied in the armed forces and in prisons,.... Lastly, we consider measures taken by different countries and organisations.

Acquired Immunodeficiency Syndrome↗

PubMed2000

The effect of growth temperature on the long-chain alkenes composition in the marine coccolithophorid Emiliania huxleyi.

The hydrocarbon fraction of a pure culture of Emiliania huxleyi, composed of a mixture of C31, C33, C37 and C38 polyunsaturated n-alkenes, appeared strongly dependent on the growth temperature of the alga between 8 degrees C and 25 degrees C. The total hydrocarbon content increased linearly with decreasing temperatures. C37 and C38 alkenes (which accounted for more than 90% of the total hydrocarbons) showed distinct changes in distribution compared to C31 and C33 alkenes, suggesting different biological syntheses and/or functions for these two groups of compounds. C37 and C38 alkenes and C37 methyl ketones (alkenones) all showed a trend to lower proportions of the two diunsaturated isomers and to higher proportions of the corresponding trienes with decreasing temperature. Unlike the alkenone unsaturation ratio (U37k'), ratios based on the C37 and C38 alkadi- and trienes could be linearly related to the growth temperature of E. huxleyi only between 15 degrees C and 25 degrees C. The modifications in the distribution of alkenes induced by varying temperature appeared, however, to be twice as fast as the modifications undergone by the alkenones. Although structurally and biochemically related, the distinct evolutions of alkenes and alkenones in response to changes in growth temperature might indicate that these two classes of compounds play two distinct physiological functions. The non-systematic linearity of relationships to temperature of parameters based on alkenes distribution suggested that these compounds are of limited use as paleotemperature indicator in the marine environment in contrast with the alkenones.

Alkenes↗