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PubMed2000

Protein surface similarities: a survey of methods to describe and compare protein surfaces.

Many methods have been developed to analyse protein sequences and structures, although less work has been undertaken describing and comparing protein surfaces. Evolution can lead sequences to diverge or structures to change topology; nevertheless, surface determinants that are essential to protein function itself may be mantained. Moreover, different molecules could converge to similar functions by gaining specific surface determinants. In such cases, sequence or structure comparisons are likely to be inadequate in describing or identifying protein functions and evolutionary relationships among proteins. Surface analysis can identify function determinants that are independent of sequence or secondary structure and can therefore be a powerful tool to highlight cases of possible convergent or divergent evolution. This kind of approach can be useful for a better understanding of protein molecular and biochemical mechanisms of catalysis or interaction with a ligand, which are usually surface dependent. Protein surface comparison, when compared to sequence or structure comparison methods, is a hard computational challenge and evaluated methods allowing the comparison of protein surfaces are difficult to find. In this review, we will survey the current knowledge about protein surface similarity and the techniques to detect it.

Algorithms↗
PubMed2001

Quartet-mapping, a generalization of the likelihood-mapping procedure.

Likelihood-mapping (LM) was suggested as a method of displaying the phylogenetic content of an alignment. However, statistical properties of the method have not been studied. Here we analyze the special case of a four-species tree generated under a range of evolution models and compare the results with those of a natural extension of the likelihood-mapping approach, geometry-mapping (GM), which is based on the method of statistical geometry in sequence space. The methods are compared in their abilities to indicate the correct topology. The performance of both methods in detecting the star topology is especially explored. Our results show that LM tends to reject a star tree more often than GM. When assumptions about the evolutionary model of the maximum-likelihood reconstruction are not matched by the true process of evolution, then LM shows a tendency to favor one tree, whereas GM correctly detects the star tree except for very short outer branch lengths with a statistical significance of >0.95 for all models. LM, on the other hand, reconstructs the correct bifurcating tree with a probability of >0.95 for most branch length combinations even under models with varying substitution rates. The parameter domain for which GM recovers the true tree is much smaller. When the exterior branch lengths are larger than a (analytically derived) threshold value depending on the tree shape (rather than the evolutionary model), GM reconstructs a star tree rather than the true tree. We suggest a combined approach of LM and GM for the evaluation of starlike trees. This approach offers the possibility of testing for significant positive interior branch lengths without extensive statistical and computational efforts.

Computer Simulation↗
PubMed2026

Highly Contiguous Is Not Chromosomally Accurate: Integrated Cytogenetic and Genomic Mapping in Two Turtle Genome.

High-quality genome assemblies are essential for robust research across biological and medical fields. Assembly errors can have far-reaching consequences for downstream analyses, including gene annotation and the inference of synteny. In contrast to the rapid growth of genomic data volume, there is a notable lag in the integration of chromosome-level assemblies with cytogenetic data. We conducted the first direct genome-to-genome comparison, integrating comparative chromosome painting, the alignment of chromosome-specific probes to available genome assemblies, and synteny-based comparison of independent chromosome-level assemblies of the loggerhead sea turtle (Caretta caretta, 2n = 56) and the red-eared slider (Trachemys scripta elegans, 2n = 50). Using two independent sets of flow-sorted chromosome-specific probes in cross-species hybridizations, together with the sequencing and mapping of chromosome-derived DNA libraries, we assigned assembled scaffolds to all physical chromosomes of both species. In C. caretta, chromosomal assignments and genome-wide synteny were fully consistent with the published assembly, except for the reduced sizes of two microchromosome scaffolds, which we attribute to under-representation of repetitive DNA. In contrast, in T. s. elegans, cytogenetic validation of the assemblies revealed a false rearrangement compared to a missed one. Our results show that even highly contiguous vertebrate genome assemblies can misrepresent chromosome structure. When cytogenetic analyses reveal such inaccuracies, updated reference genomes should be generated for widely studied species to enable accurate inference of karyotype evolution and downstream comparative genomic analyses.

FISH↗
PubMed1994

Effect of Mycobacterium leprae in peripheral nerve trunk on the evolution of skin lesions.

Comparative histological studies were made of a) 41 peripheral nerve lesions and the skin in the area of supply, and b) 12 peripheral nerve lesions and concurrent but unrelated skin lesions. In the first study, small, relatively early, histologically classifiable skin lesions were found in all cases, even though there were no clinical lesions. In every case the lesion was centered on a dermal nerve. In some cases disruption of the perineurium was associated with emergence of the lesion into the dermis and a small silent local reaction. It was concluded that there was a descending spread of the disease down the neural pathway to the dermis, although it was not necessarily associated with transport of bacilli. Although the first study showed a discrepancy in the classification between skin and nerve lesions in nearly 50% of the cases (as previously reported), the second study showed no discrepancies. It is suggested that discrepancies are relatively uncommon, and that those in the first study are exceptional. The probable explanation is that microreactions in the nerve trunks had caused a shift in classification, which was not yet reflected in the immature skin lesions. In the second study, the mature skin lesions had reached immunological equilibrium. Discrepancies in classification between skin and nerve lesions, as between concurrent skin lesions, are the result of reaction. Attention is drawn to the probable role of subliminal reactions in the evolution of infections.

Humans↗
PubMed1996

[Comparative genetics of representatives of the genus Yersinia and evolution of their pathogenicity].

This paper was prepared on the basis of a report presented at the first Congress of the All-Russian Society of Geneticists and Breeders (December 1994, Saratov, Russia). Analysis of published data and the authors' own investigations enabled them to propose a concept of evolution of pathogenicity within the Yersinia genus. They concluded that phenotypic features conferred by yersinia plasmids should be considered taxonomic traits.

Biological Evolution↗
PubMed2003

What works for mental health system change: evolution or revolution?

The mental health system has realized significant metamorphoses in the standards and practices of quality care for people with psychiatric disability during the past decade. Now change agents are wrestling with effective strategies that help real-world systems to adopt programs reflecting these metamorphoses. Two fundamental approaches to systems change are compared and contrasted here: evolution and revolution. First, the authors compare the different ways in which evolution and revolution might approach change in the mental health system. They do this by showing how they might influence the transformation of day treatment into supported employment programs. Then, the authors present the two approaches as naturally occurring change processes that work in tandem to affect real-world adaptations. Finally, they summarize practical strategies that change agents might adopt to realize evolution and revolution. Clearly, all stakeholder groups need to become strategic about system change so that real-world practices keep up with the ideals emerging in practice guidelines and evidence-based practice reviews.

Employment, Supported↗
PubMed1992

Evolution of the vertebrate Hox homeobox genes.

One of the most remarkable recent findings in developmental biology has been the colinear and homologous relationships shared between the Drosophila HOM-C and vertebrate Hox homeobox gene complexes. These relationships pose the question of the functional significance of colinearity and its molecular basis. While there was much initial resistance to the validity of this comparison, it now appears the Hox/HOM homology reflects a broad degree of evolutionary conservation which has reawakened interest in comparative embryology and evolution. The evolutionary conservation of protein motifs in many gene families (including those for growth factors, secreted and membrane bound signalling factors, adhesion molecules, cytoplasmic receptor kinases, nuclear receptors and transcription factors) has lead to speculation on the extent to which these homology relationships represent common developmental processes and underlying molecular mechanisms. Structural identifies in a protein may indicate the biochemical/molecular function that a protein plays in cellular and developmental processes, without reflecting a conserved role in a cascade of developmental events. However, the analysis of genes encoding transcription factors has provided evidence suggesting that there are gene complexes in arthropods and vertebrates which are true homologues and which may share common roles in the specification of regional identity along embryonic A-P axis. These genes comprise the Hox/HOM-C homeotic complexes. This review will detail some of the evidence for this proposed relationship and will speculate on the functional implications.

Amino Acid Sequence↗
PubMed2000

Structural and functional evolution of the natriuretic peptide system in vertebrates.

The natriuretic peptide (NP) system consists of three types of hormones [atrial NP (ANP), brain or B-type NP (BNP), and C-type NP (CNP)] and three types of receptors [NP receptor (R)-A, NPR-B, and NPR-C]. ANP and BNP are circulating hormones secreted from the heart, whereas CNP is basically a neuropeptide. NPR-A and NPR-B are membrane-bound guanylyl cyclases, whereas NPR-C is assumed to function as a clearance-type receptor. ANP, BNP, and CNP occur commonly in all tetrapods, but ventricular NP replaces BNP in teleost fish. In elasmobranchs, only CNP is found, even in the heart, suggesting that CNP is an ancestral form. A new guanylyl cyclase-uncoupled receptor named NPR-D has been identified in the eel in addition to NPR-A, -B, and -C. The NP system plays pivotal roles in cardiovascular and body fluid homeostasis. ANP is secreted in response to an increase in blood volume and acts on various organs to decrease both water and Na+, resulting in restoration of blood volume. In the eel, however, ANP is secreted in response to an increase in plasma osmolality and decreases Na+ specifically, thereby promoting seawater adaptation. Therefore, it seems that the family of NPs were originally Na(+)-extruding hormones in fishes; however, they evolved to be volume-depleting hormones promoting the excretion of both Na+ and water in tetrapods in which both are always regulated in the same direction. Vertebrates expanded their habitats from fresh water to the sea or to land during evolution. The structure and function of osmoregulatory hormones have also undergone evolution during this ecological evolution. Thus, a comparative approach to the study of the NP family affords new insights into the essential function of this osmoregulatory hormone.

Amino Acid Sequence↗
PubMed2002

Accelerated molecular evolution in halophilic crustaceans.

In contrast to the stable ionic composition of the oceans, inland waters show striking diversity, possessing salt concentrations varying from I mM to 5 M. Although species diversity is highest in fresh water, some lineages have colonized hypersaline environments where they encounter elevated levels of both ultraviolet (UV) radiation and osmotic stress. This study compares rates of evolution in halophilic and freshwater taxa for two groups of microcrustaceans, anostracans and daphniids, from Australia and North America. The results establish that halophilic species show consistent rate acceleration, involving elevated levels of both insertion/deletion events and of nucleotide substitutions. The elevated pace of molecular evolution does not appear to be linked to selection or to other agents that are known to influence the supply rate of mutations, such as UV exposure, generation length, or shifts in metabolic rate. However, variance in ionic strength, which is known to have potent effects on DNA-protein interactions as well as on the structural properties of DNA and proteins, might account for the lowered fidelity of DNA replication in life from hypersaline settings. Regardless of its cause, the consistent rate acceleration in halophiles suggests that past efforts to employ sequence divergences to date events, such as the age of asexual lineages in Artemia, have resulted in serious overestimates. More generally, the results indicate that coordinated shifts in rates of molecular evolution may occur in lineages exposed to extreme environmental conditions.

Animals↗
PubMed1979

[Echocardiographic diagnosis of obstructive myocardiopathies: study of the systolic anterior motion of the mitral valve and septal hypertrophy as compared with the hemodynamic and mechanographic findings. Evolution under medical treatment].

Characteristic echocardiographic features of hypertrophic obstructive cardiomyopathy were recorded in 24 patients, all of whom had asymmetric septal hypertrophy and systolic anterior motion of the mitral valve (SAM) at rest or after pharmacodynamic stimulation. The relationship between outflow tract obstruction and SAM was assessed by comparison with data obtained at cardiac catheterisation and external mechanography: SAM seems to be a non-specific phenomenon and may be recorded in cases of hypertrophic cardiomyopathy without obstruction during pharmacodynamic stimulation. In forms with obstruction, SAM and the severity of obstruction increase with the degree of spetal hypertrophy. The increased contractility of the left ventricular posterior wall appears to be an important factor in the mechanism of SAM which can be prevented by betablockade in moderate or labile forms. When SAM is permanent, whatever the gradient recorded, it is a sign of anatomical deformation of the left ventricle and may be an additional indication for cardiac surgery.

Adrenergic beta-Antagonists↗
PubMed1993

How are more complex brains different? One view and an agenda for comparative neurobiology.

Do more complex brains operate on the same principles as simpler brains, merely employing more of the same; or has evolution produced new principles? A neglected research agenda is the search for relevant differences between brains of animals belonging to different major grades of complexity and cognitive capacity. More complex brains are believed to be capable of more transactions, discriminations, memory and repertoire--functional criteria of 'better' brains. While comparative cognition needs to test these expectations to verify what would be one of the major consequences of evolution, comparative neurobiology needs to discover what, in detail, by all the methods and measures of neuroanatomy, neurophysiology and neurochemistry, is different in more complex brains and which of these differences are relevant to behavioral differences. Formerly it was fashionable to deny differences in the dimension that might be called higher and lower. The criterion of complexity, defined as the number of different parts, processes, interactions and behaviors, may be a useful index of advancement. Unequivocal advancement has occurred between some major taxa, although it is not inevitable. Anatomically, it is clear that novelties have evolved and complexity is more than size or number of the same components. Physiologically, new types of cells, local and larger circuits and emergent properties of assemblies have increased the complexity of operations and organization. It needs to be reasserted that more complex brains have evolved repeatedly, both among invertebrates and among vertebrates, because similar assertions have been incorrectly labeled as 'intuitive scaling' and anthropocentric or moral statements.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1998

Evolution of disc degeneration in lumbar spine: a comparative histological study between herniated and postmortem retrieved disc specimens.

This is a prospective comparative histological study on blood supply between lumbar herniated discs and postmortem retrieved ones. The aim of this study is to observe the evolution of disc degeneration in relation to its blood supply changes. Disc vascularization is present early in life, but the nucleus pulposus becomes avascular after adolescence. Vascularization of the annulus fibrosus (AF) probably also occurs late in life in association with degenerative changes and in response to trauma. Capillary neoformation and hypervascularity in degenerated discs have also been mentioned, based on animal cases. In the present study, intervertebral lumbar disc specimens were surgically removed from 84 patients with an average age of 41 years (range 24-60 years) operated on for disc herniation. In addition, control autopsy specimens were selected from 24 cadavera with an age of 39 years (range 24th gestation week to 80 years). The material was fixed in neutral buffered formalin, and 4-microm-thick sections were stained with hematoxylin-eosin and reticulin. In addition, with use of an immunohistochemical avidin-biotin complex technique, paraffin sections were stained for Ulex europaeus agglutinin receptors (UEA-1) after binding UEA-1 to the tissue. In surgical specimens, small blood vessels were identified in 45% of the disc cases. They were of the capillary-type vessels and were intermingled with proliferating endothelial cells, fibroblasts, and few mononuclear cells. All of them were located along the edges of the surgically retrieved fibrocartilage fragments. Sometimes thin bands of fibrin were attached to them and extravasated erythrocytes were occasionally seen. In autopsy specimens, blood vessels were identified in 78% of the retrieved discs. In contrast to the edge neovascularity observed in surgical specimens, capillaries were observed at the outer layer of AF surrounded by dense hyalinized and inactive-appearing collagen. From these results it is concluded that the blood vessels in extruded tissue from every type of herniation are newly formed, possibly through metaplasia of undifferentiated mesenchymal cells. It is also possible that they are derived from blood vessels that have invaded the AF as a result of disc degeneration. The finding of detection of progressive disc degeneration in both groups after 20-25 years seems to be of special interest because disc degeneration is a process that may not be directly correlated to disc herniation in these age groups.

Adolescent↗
PubMed1977

Lloyd Morgan's theory of instinct: from Darwinism to neo-Darwinism.

Darwin's proposal of two sources of instinct--natural selection and inherited habit--fostered among late nineteenth century evolutionists a variety of conflicting notions concerning the mechanisms of evolution. The British comparative psychologist C. Lloyd Morgan was a cardinal figure in restructuring the orthodox Darwinian conception to relieve the confusion besetting it and to meet the demands of the new biology of Weismann. This paper traces the development of Morgan's ideas about instinct against the background of his philosophic assumptions and the views of instinct theorists from Darwin and Romanes to McDougall and Lorenz.

Animals↗