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[The use of cladistic principles in the phylogeny and biogeography of the Lacerta].

The methodology used in Phylogenetics remains one of the more interesting problems in comparative biology. Among the methods used, the cladistic is the most accurate. In the present case, among the Saurians, the characters chosen appeared early and cannot be referred to any adaptation bound to an evolutive progress. We have successively considered their distribution in the classification, their polarity and one phylogenetic hypothesis based on the Hennig's concepts. Such a work leads necessarily to systematical conclusions. For instance, we note the heterogeneity of some families. Among the Iguania, the Iguanidea are polyphyletics, the north-american forms breaking up from the other very early. Among the Scincomorpha, the Lacertilia result from two parts of different origins. This research verifies some systematic cuttings in the modern classification: among the Anguimorpha, the separation between Helodermatidea and the group, Varanidea-Lanthanotidea. The characters studied show a non-random distribution in the classification and show also some consistency with the geographical distribution of the extant Saurians. Therefore, it is important to search for the most parsimonious geographical hypothesis, which is in concern with the present data on the continental drift and generally on the history of the Earth, and which strengthens the cladograms posed from the selected characters.

Animals↗

An ontological perspective on surgical procedures.

We studied terminological phrases on surgical procedures-from coding systems, controlled vocabularies, textbooks, and medical records-by an ontological point of view. A surgical procedure can be accurately described only by a set of sentences, in textbooks or surgical reports; a terminological phrase is just a short synthesis of that description. We outline three points of view actually used to construct a phrase, based on i) relevant phases and variants; ii) focus on structures, functions and pathologies; iii) evolution of information and decisions during the process of care. For each of them we discuss potential principles and mechanisms, with the aim of deriving guidelines to generate homogeneous systematic names, to organize regularities in classifications and nomenclatures, to normalize expressions in formal languages.

Medical Informatics Computing↗

[RNA world and its evolution].

The early idea of A. N. Belozersky on the precedence of RNA in the origin of life on Earth is developed. Basing on the present knowledge of functional omnipotence of RNA, the author considers three novel mechanisms that could play a critical role in the origin and evolution of the ancient RNA world: (1) the reaction of spontaneous transesterification of polyribonucleotides in aqueous media, discovered by A.B. Chetverin, which could result in elongation of primary short oligoribonucleotides and generation of sequence variants for subsequent selection; (2) compartmentation of functional RNA ensembles in the form of mixed molecular colonies on moist solid surfaces, in the absence of membranes and any other coats; (3) systematic exponential enrichment of RNA population in functionally "the best" molecules by means of alternately dissolving the colonies upon flooding and forming new ones upon drying a pool ("primordial natural SELEX").

Esterification↗

Aging effect on the phase evolution of water-based sol-gel hydroxyapatite.

In a number of recent reports on the synthesis of sol-gel hydroxyapatite, aging of the precursor solution has been found to be critical in developing an apatitic phase. Critical aging time is required to complete reaction between Ca and P molecular precursors to form a desired intermediate complex that permits a further transformation to apatite phase under appropriate thermal treatment. In this investigation, we employed a water-based sol-gel process recently developed to fabricate hydroxyapatite at relatively low temperatures. The aging effect on apatite formation was systematically studied in terms of aging time and temperature. Experimental results show that the aging time is considerably reduced as aging temperature rises. Long-term thermal aging was unfavorable for apatite formation. The optimal aging parameters for apatite formation were experimentally determined, which was further consolidated into a phase evolution map. Aging kinetic was investigated by monitoring the variation of solution pH, following the determination of an apparent activation energy, which has a value as high as 10.35 kcal/mol, for the chemical reaction occurring upon aging. Optimal solution chemistry was elucidated based on the corresponding phase evolution map.

Biocompatible Materials↗

The evolution of rhodopsins and neurotransmitter receptors.

Rhodopsins share a limited number of amino acid identities with a variety of other integral membrane proteins. Most of these proteins have seven putative transmembrane segments and are likely to play a role in transmembrane signaling. We have undertaken a systematic series of comparisons of primary and secondary structure in order to clarify the functional and evolutionary significance of these sequence similarities. On the basis of consistently high similarity scores, we find that the most internally consistent definition of the rhodopsin gene family would include vertebrate rhodopsins, alpha- and beta-adrenergic receptors, M1 and M2 muscarinic acetylcholine receptors, substance K receptors, and insect rhodopsins, while excluding bacteriorhodopsin, the mass human oncogene, vertebrate and insect nicotinic acetylcholine receptors, and the yeast STE2 and STE3 peptide receptors. The rhodopsin gene family is highly diverged at the primary sequence level but has maintained a conserved secondary structure, including a previously unidentified hierarchy of transmembrane segment hydrophobicity. We have developed new computer algorithms for progressive multiple sequence alignment and the analysis of local conservation of protein domains, and we have used these algorithms to examine the phylogeny of the rhodopsin gene family and the changing domains of sequence conservation. The results show striking differences and similarities in the conserved domains in each of the three main branches of the rhodopsin gene family, and indicate that color vision arose independently in the lines of descent leading to modern humans and fruit flies.

Algorithms↗

Compensatory evolution of a precursor messenger RNA secondary structure in the Drosophila melanogaster Adh gene.

Evidence for the evolutionary maintenance of a hairpin structure possibly involved in intron processing had been found in intron 1 of the alcohol dehydrogenase gene (Adh) in diverse Drosophila species. In this study, the putative hairpin structure was evaluated systematically in Drosophila melanogaster by elimination of either side of the stem using site-directed mutagenesis. The effects of these mutations and the compensatory double mutant on intron splicing efficiency and ADH protein production were assayed in Drosophila melanogaster Schneider L2 cells and germ-line transformed adult flies. Mutations that disrupt the putative hairpin structure right upstream of the intron branch point were found to cause a significant reduction in both splicing efficiency and ADH protein production. In contrast, the compensatory double mutant that restores the putative hairpin structure was indistinguishable from the WT in both splicing efficiency and ADH level. It was also observed by mutational analysis that a more stable secondary structure (with a longer stem) in this intron decreases both splicing efficiency and ADH protein production. Implications for RNA secondary structure and intron evolution are discussed.

Alcohol Dehydrogenase↗

The phylogeny of Goussia and Choleoeimeria (Apicomplexa; Eimeriorina) and the evolution of excystation structures in coccidia.

The phylogenetic relationships of Goussia janae and Choleoeimeria sp. were analyzed using the small subunit ribosomal RNA gene (SSU rDNA). This is a first attempt to study the molecular phylogeny of coccidian genera parasitizing strictly poikilotherm hosts. The biliary Eimeria-like coccidia of reptiles classified into the genus Choleoeimeria form a sister clade to the family Eimeriidae, which confirms the separate generic status of the genus Choleoeimeria. The position of Goussia is less robustly resolved, since it forms a trichotomy with the Eimeriidae and Sarcocystidae, or alternatively constitutes the earliest branch of the coccidian lineage. Morphological similarities, namely the extracytoplasmic location of the endogenous stages, and the presence of sutures in the sporocyst wall are discussed in the context of the traditional classification of eimeriids. In contrast to the morphology-based systematics, the monophyly of Goussia and Choleoeimeria is not supported by the SSU rDNA data.

Animals↗

Comparative analysis of chloroplast genomes in ten holly (Ilex) species: insights into phylogenetics and genome evolution.

In order to clarify the chloroplast genomes and structural features of ten Ilex species and provide insights into the phylogeny and genome evolution of the genus Ilex, we conducted a comparative analysis of chloroplast genomes using bioinformatics methods. The chloroplast genomes of ten Ilex species were obtained, and their structural features and variations were compared. The results indicated that all chloroplast genomes in the genus Ilex exhibit a double-stranded circular structure, with sizes ranging from 157,356 to 158,018 bp, showing minimal differences in size. The chloroplast genomes of the ten Ilex species have a relatively conservative gene count, with a total of 134 to 135 genes, including 88 or 89 protein-coding genes, and a conserved number of 8 rRNA genes. Each chloroplast genome contains 3 to 123 SSR (Simple Sequence Repeat) sites, predominantly composed of mononucleotide and trinucleotide repeats, with no detection of pentanucleotide or hexanucleotide repeats. The variation in dispersed repeat sequences among Ilex species is minimal, with a total repeat sequence number ranging from 1 to 14, concentrated in the length range of 30 to 42 base pairs. The expansion and contraction of chloroplast genome boundaries among Ilex species are relatively stable, with only minor variations observed in individual species. Variations in non-coding regions are more pronounced than those in coding regions, with the variability in the Large Single Copy region (LSC) being the highest, while the variability in the Inverted Repeat region A (IRa) is the lowest. The divergence time among Ilex species was estimated using the MCMC-tree module, revealing the evolutionary relationships among these species, their common ancestors, and their differentiation throughout the evolutionary process. The research findings provide a valuable reference for the systematic study and molecular marker development of Ilex plants.

Genome, Chloroplast↗

Evolution of cranial blood drainage in hominids: enlarged occipital/marginal sinuses and emissary foramina.

Physiological studies of cranial blood flow in humans in reclining vs. upright postures suggest that selection for bipedalism was correlated with the establishment of epigenetic adaptations for delivering blood preferentially to the vertebral plexus of veins, depending upon momentary respiratory and postural constraints. The frequencies of vascular/osteological channels used to deliver blood to the vertebral plexus of veins were determined for samples of African pongids, various taxa of fossil hominids, and extant Homo sapiens. These channels include an enlarged occipital/marginal (O/M) sinus system, multiple hypoglossal canals, and foramina that conduct emissary veins: posterior condyloid, mastoid, occipital, and parietal. The African pongid, and therefore presumably the ancestral prebipedal hominoid, condition is characterized by low frequencies of all of these routes except multiple hypoglossal canals. The earliest known bipeds (Australopithecus afarensis) and robust australopithecines are characterized by fixation of enlarged O/M sinus systems. Robust australopithecines are also characterized by apparently low frequencies of mastoid and parietal foramina, and high frequencies of multiple hypoglossal canals and posterior condyloid foramina. In gracile australopithecines and subsequently living hominids, trends towards increased frequencies of mastoid and (later) parietal emissary foramina coincide with a trend towards decreased frequencies of an enlarged O/M sinus system and multiple hypoglossal canals. These findings suggest that selection for bipedalism initially resulted in epigenetic adaptations for routes to deliver blood to the vertebral plexus including an enlarged O/M sinus system and hypoglossal canals, but that the pressures underlying these adaptations relaxed as bipedalism became established, and other routes for delivering blood to the vertebral plexus of veins were either directly or indirectly selected for, perhaps in conjunction with a changing architecture of the skull. A systematic implication of this study is that robust australopithecines are descendants of A. afarensis rather than of A. africanus.

Animals↗

Molecular studies on two variant repeat types of the common cetacean DNA satellite of the sperm whale, and the relationship between Physeteridae (sperm whales) and Ziphiidae (beaked whales).

In the sperm whale (Physeter macrocephalus) two different repeat types (A and B) of the common cetacean DNA satellite were identified. The evolution of each group of repeats appears to be independent from that of the other. The sequence similarity between the two groups is less than the similarity between group A and repeats of the satellite in related whale species. The systematic relationship within and between the families Physeteridae (sperm whales) and Ziphiidae (beaked whales) was addressed by both sequence analysis of the satellite and comparisons with the families Delphinidae and Phocoenidae. The mysticete blue whale (Balaenoptera musculus) was used as an outgroup in the comparisons. The molecular phylogeny, when maximum-parsimony analysis and the neighbor-joining method were used, grouped together species of each family. At the family level the ziphiids grouped closet to the families Phocoenidae and Delphinidae. The similarities between the common cetacean satellite of the blue whale and the sperm whale were greater than those between the blue whale and the other odontocetes included, suggesting that the evolution of the satellite is slower in the sperm whale than in the other odontocetes.

Animals↗

[Postural strategies and falls in elderly and in parkinsonism].

OBJECTIVE: To use a posture analysis to show the evolution of postural pattern connected with falls. MATERIAL AND METHOD: It is a prospective study on two groups of 16 persons of more than 60 years. A group concerns 16 small disability off drug parkinsonian patients, a group concerns 16 healthy witnesses. All the persons benefited from a posture recording by means of a force platform and were followed during 1 year. RESULTS: Data analysis underlines three groups of persons corresponding to three postural patterns, independently of the presence of Parkinson disease. A group (n = 18) did not contain fallers, the second (n = 10 ) contained 20% of fallers, the third (n = 4) contained 100% of fallers. Differences between the groups were identified on 16 posturographic parameters. DISCUSSION: A group has a good functional value and one does not record any fall. Its characteristics, which correspond to a category of persons who compensate well for the phenomena of ageing, are found in the literature. A group has an intermediate functional value and regrets 20% of fallers. Kinetic profile reveals a tendency to the stiffness of the posture. This group is going to operate rather ankle strategies. A group has an inferior functional value and regrets 100% of fallers. Kinetic profile seems disrupted and not to be able to adapt itself in a satisfactory way to the situation otherwise than by stereotypical reactions. This group is going to operate systematically much less stabilizing hip strategies. CONCLUSION: A close determinism between physiological neuromotor ageing and Parkinson disease does exist. We showed with a prospective follow-up, the arisen of fall and showed the evolution of postural patterns related to fall. It appears as well that evolution mainly follows three stages leading from a small risk of fall gait pattern to a major risk of fall gait pattern.

Accidental Falls↗

Modularity, evolution, and the binding problem: a view from stability theory.

Any biological object, and specifically the brain, is the result of evolution. Evolution proceeds by accumulation and combination of stable intermediate states-as is well known, survival of the fittest really means survival of the stable. Simple examples abound: for instance, human emotional response involves both a fast archaic loop bypassing the cortex, and a slower cortical loop; motion control architecture in vertebrates is believed to involve combinations of simple motor primitives. However, in themselves, accumulations and combinations of stable elements have no reason to be stable. Hence the hypothesis that evolution will favor a particular form of stability, which automatically guarantees stability in combination. Such a form of stability, which we refer to as 'contraction,' can be characterized mathematically. Thus, contraction theory may help guide functional modeling of the central nervous system, and conversely it provides a systematic method to build arbitrarily complex robots out of simpler elements. Furthermore, contraction theory may shed light on the problem of perceptual unity (binding problem) by providing simple models and conditions for the overall convergence of a large number of specialized processing elements connected through networks of feedback loops.

Biological Evolution↗

Use of recombinant hirudin as antithrombotic treatment in patients with heparin-induced thrombocytopenia.

Heparin-induced thrombocytopenia is a rare but severe complication of heparin therapy that can result in severe venous or arterial thromboembolic events and whose treatment remains partially unanswered. Recombinant hirudin is potentially effective as an antithrombotic treatment in the management of heparin-induced thrombocytopenia, given its potent antithrombin effects without known interaction with platelets. We report the results obtained with intravenous recombinant hirudin (HBW 023) administered on a compassionate basis to patients suffering from heparin-induced thrombocytopenia. Six patients suffering from heparin-induced thrombocytopenia were submitted to intravenous recombinant hirudin (HBW 023) administered at a dose of 0.05 mg/kg/hr after an initial bolus injection of 0.07 mg/kg in the case of a venous thromboembolic event, and at a dose of 0.15 mg/kg/hr with the same initial bolus injection in the case of an arterial thromboembolic event. Whenever possible, oral anticoagulation with acenocoumarol was introduced at the same time as recombinant hirudin, which was interrupted as soon as the international normalized ratio reached 3. Clinical events, particularly thromboembolism and bleeding, were noted; activated partial thromboplastin time (aPTT), and platelet count were assessed throughout the administration of recombinant hirudin. Heparins responsible for heparin-induced thrombocytopenia were porcine sodium or calcium heparinate in four cases, nadroparin in one case, and enoxaparin in one case. Thrombocytopenia was discovered on routine systematic platelet count in two patients and after the occurrence of arterial and venous thromboembolism in two patients, respectively. After discontinuation of heparin and the onset of recombinant hirudin, clinical evolution was uneventful in all patients, with no recurrence of thromboembolism, limb amputation, or hemorrhagic complication. The aPTT ratio varied from 1.8 to 3.5 (median 2.4) throughout administration of recombinant hirudin. Platelet count rose from nadir (median value 60 x 10(9), 15 to 90) to above 100 x 10(9)/L in every patient within 3-6 days (median 5), after discontinuation of heparin. Intravenous administration of recombinant hirudin ensured safe anticoagulation in patients with heparin-induced thrombocytopenia and made it possible to wait for oral anticoagulation to become efficient and platelet count to return to normal values without occurrence or recurrence of thromboembolism.

Aged↗

Mediation of spontaneous knee osteoarthritis by progressive chondrocyte ATP depletion in Hartley guinea pigs.

OBJECTIVE: Because articular chondrocytes reside in a hypoxic milieu, anaerobic glycolysis is central in generating ATP to support chondrocyte matrix synthesis and viability, with mitochondrial oxidative phosphorylation possibly providing physiologic reserve ATP generation. Nitric oxide (NO) potently suppresses mitochondrial oxidative phosphorylation. Because enhanced cartilage NO generation occurs in osteoarthritis (OA), we systematically tested for mitochondrial dysfunction in the pathogenesis of OA. METHODS: We assessed chondrocytes for ATP depletion and for in situ changes in mitochondrial ultrastructure prior to and during the evolution of spontaneous knee OA in male Hartley guinea pigs, a model in which chondrocalcinosis also supervenes. RESULTS: Spontaneous NO release from knee cartilage samples in organ culture doubled between ages 2 months and 8 months as knee OA developed. Concomitantly, chondrocyte intracellular ATP levels declined by approximately 50%, despite a lack of mitochondrial ultrastructure abnormalities in knee chondrocytes. As ATP depletion progressed with aging in knee chondrocytes, an increased ratio of lactate to pyruvate was observed, consistent with an adaptive augmentation of glycolysis to mitochondrial dysfunction. Furthermore, we observed progressive elevation of chondrocyte ATP-scavenging nucleotide pyrophosphatase/phosphodiesterase (NPP) activity and extracellular levels of the NPP enzymatic end product inorganic pyrophosphate (PPi), which stimulate chondrocalcinosis. CONCLUSION: Profound chondrocyte ATP depletion develops in association with heightened NO generation in guinea pig knee OA. Increased NPP activity and concordant increases in extracellular PPi, which are strongly associated with human aging-associated degenerative arthropathy and directly stimulate chondrocalcinosis, may be primarily driven by chondrocyte ATP depletion. Our findings implicate a decreased mitochondrial bioenergetic reserve as a pathogenic factor in both degenerative arthropathy and chondrocalcinosis in aging.

Adenosine Triphosphate↗

Phylogenetic invariants for more general evolutionary models.

An invariant Q of a tree T under a k-state Markov model, where a generalized time parameter is identified with the E edges of T, allows us to recognize whether data on N observed species (usually, N DNA sequences, one from each species) can be associated with the N leaves of T in the sense of having been generated on T rather than on any other N-leaf tree. The form of the generalized time parameter is a positive determinant matrix in some semigroup S of Markov matrices. The invariance is with respect to the choice of the set of E matrices in S, one associated with each of the E edges of T. The parametric form of S represents a model of the evolutionary process. In this paper, we apply a general method of finding invariants of a parametrized functional form to find low-degree polynomial invariants for different models. Quadratic invariants are obtained for the Kimura two-parameter model, for a model allowing evolutionary dependence between positions in the sequences and for an asymmetric model that allows for A + T versus G + C asymmetries in DNA base composition. Those invariants are found for trees (unrooted in case of the Kimura model and rooted for the others) with N = 3 or N = 4 terminal vertices. We also find cubic invariants for a ten-parameter model with k = 4 states, for rooted trees with N = 4. In each case, we use implicit function theory to predict the number of algebraically independent invariants and then use this prediction to guide a systematic search for algebraic dependence within the set of invariants produced by our method.

Animals↗

Coevolutionary chase in two-species systems with applications to mimicry.

We study a general dynamical model describing coevolution of two haploid populations with two alleles at a single locus under weak linear symmetric frequency-dependent selection. A novel and more realistic element of our modeling approach is that both species are allowed to evolve. We analyse conditions for "evolutionary chase" between two phenotypically similar species in which one species evolves to decrease its resemblance with the other species while this other species evolves to increase its resemblance with the first species. We apply our results to a series of simple population genetics models describing classical Müllerian and Batesian mimicries as well as intermediate cases. We show that one of the most important factors influencing the plausibility of non-equilibrium dynamics in systems of mimicry is the relationship between the strength of between-species and within-species interactions. This indicates that this relationship should be the focus of both experimental and theoretical work. Our results suggest that systematic studies of frequencies of different mimicry morphs through time may be very useful.

Animals↗

Phylogeny of ips DeGeer species (Coleoptera: scolytidae) inferred from mitochondrial cytochrome oxidase I DNA sequence.

We used 766 bp of DNA sequence data from the mitochondrial cytochrome oxidase I gene to reconstruct a phylogeny for 39 of 43 Ips species, many of which are economically important bark beetles. The phylogeny was reconstructed using equally weighted and weighted parsimony. In both analyses, peripheral clades were well supported while internal clades were poorly supported. Phylogenetic analysis of translated amino acids produced a poorly resolved tree that was discordant with trees reconstructed with nucleotide sequence data. Two main conclusions are drawn about the monophyly of Ips and traditional systematic groups within Ips. First, Ips is monophyletic only when I. mannsfeldi, I. nobilis, and the concinnus and latidens species groups are excluded. The latidens group, I. mannsfeldi, and I. nobilis form a monophyletic group with 3 Orthotomicus species, while the concinnus group has a more basal position. Second, the majority of the species groups in the current classification for Ips are not monophyletic. European Ips species do not form a monophyletic group, contrary to common usage, and are dispersed on the phylogenetic tree among North American species. These results indicate that a formal systematic revision of Ips is needed.

Animals↗

The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise.

Phylogenetic trees based on gene repertoires are remarkably similar to the current consensus of life history. Yet it has been argued that shared gene content is unreliable for phylogenetic reconstruction because of convergence in gene content due to horizontal gene transfer and parallel gene loss. Here we test this argument, by filtering out as noise those orthologous groups that have an inconsistent phylogenetic distribution, using two independent methods. The resulting phylogenies do indeed contain small but significant improvements. More importantly, we find that the majority of orthologous groups contain some phylogenetic signal and that the resulting phylogeny is the only detectable signal present in the gene distribution across genomes. Horizontal gene transfer or parallel gene loss does not cause systematic biases in the gene content tree.

Computational Biology↗