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PubMed1995

Comparative and functional myology of the prehensile tail in New World monkeys.

The caudal myology of prehensile-tailed monkeys (Cebus apella, Alouatta palliata, Alouatta seniculus, Lagothrix lagotricha, and Ateles paniscus) and nonprehensile-tailed primates (Eulemur fulvus, Aotus trivirgatus, Callithrix jacchus, Pithecia pithecia, Saimiri sciureus, Macaca fascicularis, and Cercopithecus aethiops) was examined and compared in order to identify muscular differences that correlate with osteological features diagnostic of tail prehensility. In addition, electrophysiological stimulation was carried out on different segments of the intertransversarii caudae muscle of an adult spider monkey (Ateles geoffroyi) to assess their action on the prehensile tail. Several important muscular differences characterize the prehensile tail of New World monkeys compared to the nonprehensile tail of other primates. In atelines and Cebus, the mass of extensor caudae lateralis and flexor caudae longus muscles is more uniform along the tail, and their long tendons cross a small number of vertebrae before insertion. Also, prehensile-tailed monkeys, especially atelines, are characterized by well-developed flexor and intertransversarii caudae muscles compared to nonprehensile-tailed primates. Finally, Ateles possesses a bulkier abductor caudae medialis and a more cranial origin for the first segment of intertransversarii caudae than do other prehensile-tailed platyrrhines. These myological differences between nonprehensile-tailed and prehensile-tailed primates, and among prehensile-tailed monkeys, agree with published osteological and behavioral data. Caudal myological similarities and differences found in Cebus and atelines, combined with tail-use data from the literature, support the hypothesis that prehensile tails evolved in parallel in Cebus and atelines.

Animals↗
PubMed2001

Form invariance and implicit parallelism.

Holland's schema theorem (an inequality) may be viewed as an attempt to understand genetic search in terms of a coarse graining of the state space. Stephens and Waelbroeck developed that perspective, sharpening the schema theorem to an equality. Of particular interest is a "form invariance" of their equations; the form is unchanged by the degree of coarse graining. This paper establishes a similar form invariance for the more general model of Vose et al. and uses the attendant machinery as a springboard for an interpretation and discussion of implicit parallelism.

Algorithms↗
PubMed2000

Evolution of gall morphology and host-plant relationships in willow-feeding sawflies (Hymenoptera: Tenthredinidae).

There are over 200 species of nematine sawflies that induce galls on willows (Salix spp.). Most of the species are mono- or oligophagous, and they can be separated into seven or eight different groups based on the type of gall that they induce. We studied the evolution of different gall types and host plant associations by reconstructing the phylogeny of five outgroup and 31 ingroup species using DNA sequence data from the mitochondrial cytochrome b gene. Maximum-parsimony and maximum-likelihood analyses resulted in essentially the same phylogeny with high support for important branches. The results show that: (1) the galling species probably form a monophyletic group; (2) true closed galls evolved only once, via leaf folders; (3) with the possible exception of leaf rollers, all gall type groups are mono- or paraphyletic; (4) similar gall types are closer on the phylogeny than would be expected by a random process; (5) there is an apparent evolutionary trend in galling site from the leaf edge towards the more central parts of the host plant; and (6) many willow species have been colonized several times, which excludes the possibility of parallel cladogenesis between willows and the gallers; however, there are signs of restrictions in the evolution of host use. Many of the patterns in the evolutionary history of nematine gallers have also been observed in earlier studies on other insect gallers, indicating convergent evolution between the independent radiations.

Animals↗
PubMed1999

Genome evolution and the evolution of exon-shuffling--a review.

Recent studies on the genomes of protists, plants, fungi and animals confirm that the increase in genome size and gene number in different eukaryotic lineages is paralleled by a general decrease in genome compactness and an increase in the number and size of introns. It may thus be predicted that exon-shuffling has become increasingly significant with the evolution of larger, less compact genomes. To test the validity of this prediction, we have analyzed the evolutionary distribution of modular proteins that have clearly evolved by intronic recombination. The results of this analysis indicate that modular multidomain proteins produced by exon-shuffling are restricted in their evolutionary distribution. Although such proteins are present in all major groups of metazoa from sponges to chordates, there is practically no evidence for the presence of related modular proteins in other groups of eukaryotes. The biological significance of this difference in the composition of the proteomes of animals, fungi, plants and protists is best appreciated when these modular proteins are classified with respect to their biological function. The majority of these proteins can be assigned to functional categories that are inextricably linked to multicellularity of animals, and are of absolute importance in permitting animals to function in an integrated fashion: constituents of the extracellular matrix, proteases involved in tissue remodelling processes, various proteins of body fluids, membrane-associated proteins mediating cell-cell and cell-matrix interactions, membrane associated receptor proteins regulating cell cell communications, etc. Although some basic types of modular proteins seem to be shared by all major groups of metazoa, there are also groups of modular proteins that appear to be restricted to certain evolutionary lineages. In summary, the results suggest that exon-shuffling acquired major significance at the time of metazoan radiation. It is interesting to note that the rise of exon-shuffling coincides with a spectacular burst of evolutionary creativity: the Big Bang of metazoan radiation. It seems probable that modular protein evolution by exon-shuffling has contributed significantly to this accelerated evolution of metazoa, since it facilitated the rapid construction of multidomain extracellular and cell surface proteins that are indispensable for multicellularity.

Animals↗
PubMedDate not supplied

[The possible role of the elements of protein secondary structure in adaptation to the action of ionizing radiation].

Changes in the secondary structure of enzymes induced by gamma-rays 60Co at doses not exceeding one ionization per macromolecule were studied to elucidate a possible role of radiation-chemical processes in the evolution of proteins. The data on the comparative radioresistance of various types of secondary protein structures, alpha-helix, parallel and anti-parallel beta-structures, and beta-turn, were obtained by the method of circular dichroism. It was shown that beta-turns were resistant against radiation, alpha-helix was relatively stable, and beta-layer underwent significant changes. The importance of these structural types in the evolution of proteins is discussed. A special role of beta-turn as structural elements fixing the confirmation of macromolecules and therefore responsible for adaptation of the protein structure against a constant radiation background is proposed.

Adaptation, Physiological↗
PubMed2001

Comparison of the rates of prebiotic formation and hydrolysis of RNA under hydrothermal environments and its implications on the chemical evolution of RNA.

In order to evaluate the possibility of the RNA world hypothesis from the viewpoint of hydrothermal origin of life, parallel investigations on the formation and decomposition of RNA are indispensable under hydrothermal conditions. In this report, comparison of the rates of the template-directed formation and hydrolytic decomposition of RNA in aqueous solution at elevated to high temperatures was carried out. Furthermore, it was elucidated that these prebiotic reactions are relatively so slow compared with modern enzymatic reactions. Based on the considerations, it is predicted that RNA world would be possible at high temperatures.

Environment↗
PubMed2004

Theoretical study of the second-order nonlinear optical properties of [N]helicenes and [N]phenylenes.

The second-order nonlinear optical properties of helicenes and phenylenes have been theoretically investigated at the time-dependent Hartree-Fock level using the Austin model 1 semiempirical Hamiltonian. Both the antisymmetric isotropic component of the first hyperpolarizability (beta) and its projection on the dipole moment (beta(parallel)) have been determined for increasingly large helical systems as well as for their analogs substituted by donor/acceptor pairs. It is found that (i) in nonsubstituted helicenes and phenylenes, beta increases monotonically with the size of the system and slightly depends on the nature of the helix; (ii) the corresponding beta(parallel) is mostly determined by the radial component of the first hyperpolarizability vector; (iii) in helicenes, beta(parallel) is positive and presents quasiperiodic oscillations with the helix; (iv) in phenylenes, beta(parallel) depends upon the size of the helix and it can be either positive or negative as a result of the differences in evolution with N of the radial components of the dipole moment and first hyperpolarizability. Substituting the helicenes and phenylenes by the prototypical NH2/NO2 donor/acceptor pair provides a diversity of effects on beta and beta(parallel) that encompasses decrease, increase, and change in sign.

Journal Article↗
PubMed2001

The architecture of parallel beta-helices and related folds.

Three-dimensional structures have been determined of a large number of proteins characterized by a repetitive fold where each of the repeats (coils) supplies a strand to one or more parallel beta-sheets. Some of these proteins form superfamilies of proteins, which have probably arisen by divergent evolution from a common ancestor. The classical example is the family including four families of pectinases without obviously related primary sequences, the phage P22 tailspike endorhamnosidase, chrondroitinase B and possibly pertactin from Bordetella pertusis. These show extensive stacking of similar residues to give aliphatic, aromatic and polar stacks such as the asparagine ladder. This suggests that coils can be added or removed by duplication or deletion of the DNA corresponding to one or more coils and explains how homologous proteins can have different numbers of coils. This process can also account for the evolution of other families of proteins such as the beta-rolls, the leucine-rich repeat proteins, the hexapeptide repeat family, two separate families of beta-helical antifreeze proteins and the spiral folds. These families need not be related to each other but will share features such as relative untwisted beta-sheets, stacking of similar residues and turns between beta-strands of approximately 90 degrees often stabilized by hydrogen bonding along the direction of the parallel beta-helix.Repetitive folds present special problems in the comparison of structures but offer attractive targets for structure prediction. The stacking of similar residues on a flat parallel beta-sheet may account for the formation of amyloid with beta-strands at right-angles to the fibril axis from many unrelated peptides.

Amino Acid Sequence↗
PubMed2001

An error-prone T7 RNA polymerase mutant generated by directed evolution.

Viruses replicate their genomes at exceptionally high mutation rates. Their offspring evolve rapidly and therefore, are able to evade common immunological and chemical antiviral agents. In parallel, virus genomes cannot tolerate a further increase in mutation rate: Experimental evidence exists that even few additional mutations are sufficient for the extinction of a viral population. A future antiviral strategy might therefore aim at increasing the error-producing capacity of viral replication enzymes. We employed the principles of directed evolution and developed a scheme for the stringent positive selection of error-prone polymerase activity. A mutant T7 RNA polymerase with a nucleotide substitution error rate at least 20-fold greater than that of the wild-type was selected. This enzyme synthesized highly heterogeneous RNA products in vitro or in vivo and also decreased the replication efficiency of wild-type bacteriophage T7 during infection.

Bacteriophage T7↗
PubMed1994

Molecular adaptation of a leaf-eating bird: stomach lysozyme of the hoatzin.

This report describes a lysozyme expressed at high levels in the stomach of the hoatzin, the only known foregut-fermenting bird. Evolutionary comparison places it among the calcium-binding lysozymes rather than among the conventional types. Conventional lysozymes were recruited as digestive enzymes twice in the evolution of mammalian foregut fermenters, and these independently recruited lysozymes share convergent structural changes attributed to selective pressures in the stomach. Biochemical convergence and parallel amino acid replacements are observed in the hoatzin stomach lysozyme even though it has a different genetic origin from the mammalian examples and has undergone more than 300 million years of independent evolution.

Adaptation, Physiological↗
PubMed2005

Rapid miocene-pliocene dispersal and evolution of Mediterranean rajid fauna as inferred by mitochondrial gene variation.

Rajidae (colloquially known as skates and rays) experienced multiple and parallel adaptive radiations allowing high species diversity and great differences of species composition between regional faunas. Nevertheless, they show considerable conservation of bio-ecological, morphological and reproductive traits. The evolutionary history and dispersal of North-east Atlantic and Mediterranean rajid fauna were investigated throughout the sequence analysis of the control region and 16S rDNA mitochondrial genes. Molecular estimates of divergence times indicated recent origin and rapid dispersal of the present species. Compared with the ancient origin of the family (Late Cretaceous), the present species diversity arose in a relatively narrow time-window (12 Myr) from Middle Miocene to Early Pleistocene, likely by speciation processes related to dramatic geological and climatic events in the Mediterranean. Nucleotide substitution rates and phylogenetic relationships indicated Mediterranean endemic skates derived from sister species with wider distribution during Late Pliocene-Pleistocene. Skate phylogeny and systematics obtained using mitochondrial gene variation were largely consistent with those based on morpho-anatomical data.

Animals↗
PubMed1993

Differential time course and spatial expression of Fos, Jun, and Krox-24 proteins in spinal cord of rats undergoing subacute or chronic somatic inflammation.

We have used the evoked expression of both immediate early gene (IEG)-encoded proteins (Krox-24, c-Fos, Fos B, Jun D, Jun B, c-Jun), and dynorphin to monitor sensory processing in the spinal cords of rats undergoing subacute or chronic somatic inflammation (i.e., subcutaneous inflammation of the plantar foot and monoarthritis, respectively). Behavioral and immunocytochemical approaches were conducted in parallel up to 15 weeks postinjection in order to detect possible relationships between clinical evolution and spatiotemporal pattern of IEG-encoded protein expression. Each disease had specific characteristics both in terms of their clinical evolution and pattern of evoked protein expression. All IEG proteins were expressed in both cases. Most of the staining was observed in both the superficial layers of the dorsal horn and deep dorsal horn (laminae V-VII and X). Monoarthritis was distinguished by a high level of total protein expression. Staining was especially dense in the deep dorsal horn. More labelled cells were observed at 1-2 days and at 2 weeks postinjection, corresponding to the initiation and progressive phases of the disease, respectively. Subcutaneous inflammation was characterized by a moderate level of total IEG expression. More labelled cells were observed in the first day following injection. It is the relative degree of expression of each IEG-encoded protein with regard to the others that characterized the progression of the diseases. Early stages of the diseases coincided with the expression of all Fos and Jun proteins, while late stages showed an increase in Jun D and Fos B involvement; Krox-24 was induced mostly during the early phases and/or periods of paroxysm of the diseases. Persistent stimulation was characterized by a predominant expression in deep versus superficial layers of the dorsal horn. Evoked expression of c-Jun in motoneurons was only observed in monoarthritis. The peak of dynorphin expression was late in regard to both the induction of inflammation and period of maximal IEG-encoded protein expression. The present work indicates that the neural processing that takes place during progression of these diseases can be monitored well at the spinal cord level by using the expression of an array of IEG-encoded proteins. Study of long term evolutive diseases and especially those that evolve into chronicity can largely benefit from such an approach.

Acute Disease↗
PubMed2002

Application of molecular genetics to the diagnosis of lymphoid-rich effusions: study of 95 cases with concomitant immunophenotyping.

The cytological differentiation between reactive lymphocytosis and malignant lymphoma in serous effusions is often difficult. The present study was designed to evaluate the potential contribution of molecular genetic clonality analysis to a solution to this problem. We examined the cytological specimens of 95 consecutive patients collected during a 4-yr period, including 74 pleural, 20 peritoneal, and one pericardial fluids. Cytological diagnosis in the 95 lymphocyte-rich effusions was positive for lymphoma in 20 cases, suspicious for lymphoma in 26 cases, and negative in 49 cases. The analysis by ICC was not carried out, inconclusive, or noninterpretable in 25 cases. In five cases molecular genetic analysis was hampered by technical problems. By immunocytochemistry, eight additional cases of lymphoma were detected and lineage classification was achieved in 15 of the 20 cytologically positive effusions. PCR and Southern blot analysis were used to assess B- and T-cell clonality. Monoclonality was found in 40 (42%) of the 95 effusions analyzed. One-third of the effusions with a monoclonal B-cell gene rearrangement were detected by Southern blot analysis but not by the PCR performed in parallel. The results of molecular genetic analysis were corroborated by histological findings and/or clinical evolution in 15 cases. Our results indicate that molecular genetic analysis is a useful tool in the analysis of lymphocyte-rich serous effusions.

Adolescent↗
PubMed2004

Intratumor chromosomal heterogeneity in advanced carcinomas of the uterine cervix.

Intratumor heterogeneity in chromosomal aberrations is believed to represent a major challenge in the treatment of cancer. The aim of our work was to assess the chromosomal heterogeneity of advanced cervical carcinomas and to distinguish aberrations that had occurred at a late stage of the disease from early events. A total of 55 biopsies, sampled from 2-4 different sites within 20 tumors, were analyzed by use of comparative genomic hybridization. Heterogeneous aberrations were identified as those present in at least 1 of the biopsies and which were not seen, nor seen as a tendency, in the others of the same tumor. The homogeneous aberrations were those seen in all biopsies of the tumor. The most frequent homogeneous aberrations were gain of 3q (65%), 20q (65%) and 5p (50%), indicating that these are early events in the development of the disease. Chromosomal heterogeneity was observed in 11 tumors. The most frequent heterogeneous aberrations were loss of 4p14-q25 (60% of 10 cases with this aberration), and gain of 2p22-pter (50% of 6 cases), 11qcen-q13 (33% of 9 cases) and 8q (27% of 11 cases), suggesting that these events promote progression at a later stage. Many of the heterogeneous regions contained genes known to influence the prognosis of cervical cancer, such as 7p (EGFR), 8q (c-MYC), 11qcen-q13 (CCND1) and 17q (ERBB2). Three evolution sequences for the subpopulations in the heterogeneous tumors were identified: a serial, a parallel and a mixed sequence. In 2 tumors with a serial sequence, it was indicated that the aberrations +8 and -X had occurred after the other heterogeneous aberrations and hence were the aberrations most recently formed. Our results suggest pronounced chromosomal instability in advanced cervical carcinomas. Moreover, aggressive and treatment-resistant subpopulations may emerge at a late stage and possibly contribute to a poor prognosis of the advanced stages.

Biopsy↗
PubMed1985

Clinical usefulness of 111In-oxine-labeled autologous lymphocytes in kidney-graft rejection.

A method of lymphocyte labeling with 111In-oxine was applied for the diagnosis of acute kidney-graft rejection. After the injection of labeled lymphocytes, scintigrams of the graft area, contralateral iliac fossa, and spleen were obtained. Indexes of activity were calculated. No patient without rejection (n = 3) showed lymphocyte graft deposition. Twenty-two patients with acute graft rejection and two patients with on abdominal-wall abscess over the graft area showed lymphocyte graft trapping. When acute graft rejection was present, index i (graft/contralateral iliac fossa) increased, and index c (spleen/graft) decreased. The improvement after the rejection crisis occurred parallel to the decrease in index i. Index c remained unchange regardless of rejection evolution. In summary, 111In-oxine-labeled lymphocytes may be used for the diagnosis of acute kidney-graft rejection and for evolving control.

Graft Rejection↗
PubMed2006

Four-way calibration applied to the simultaneous determination of folic acid and methotrexate in urine samples.

First-, second- and third-order calibration methods were investigated for the simultaneous determination of folic acid and methotrexate. The interest in the determination of these compounds is related to the fact that methotrexate inhibits the body's absorption of folic acid and prolonged treatment with methotrexate may lead to folic acid deficiency, and to the use of folic acid to cope with toxic side effects of methotrexate. Both analytes were converted into highly fluorescent compounds by oxidation with potassium permanganate, and the kinetics of the reaction was continuously monitored by recording the kinetics curves of fluorescence emission, the evolution with time of the emission spectra and the excitation-emission matrices (EEMs) of the samples at different reaction times. Direct determination of mixtures of both drugs in urine was accomplished on the basis of the evolution of the kinetics of EEMs by fluorescence measurements and four-way parallel-factor analysis (PARAFAC) or multiway partial least squares (N-PLS) chemometric calibration. The core consistency diagnostic (CORCONDIA) was employed to determine the correct number of factors in PARAFAC and the procedure converged to a choice of three factors, attributed to folic acid, methotrexate and to the sum of fluorescent species present in the urine.

Calibration↗
PubMed1988

Phylogenetic conservation of the benzodiazepine binding sites: pharmacological evidence.

Phylogenetic research can help to elucidate the structure of the GABA/benzodiazepine receptor complex. In this study the evolution of the beta-carboline binding site was traced to see whether it paralleled that of the benzodiazepine binding site. The ratio of [3H]ethyl-beta-carboline-3-carboxylate (beta-CCE) to [3H]flunitrazepam (FNZ) binding sites was determined in several nonmammalian species. The results further substantiate the tight link between these two binding sites. Photoaffinity labelling of the benzodiazepine receptor (BZR) has revealed phylogenetic variation of the molecular weight of the benzodiazepine binding proteins. The IC50 values for inhibition of [3H]FNZ by various compounds which are active at the central benzodiazepine receptors were determined in three phylogenetically distant species that each showed distinct subunit patterns. In these species, the respective affinities of the compounds were remarkably similar, suggesting that the binding sites for benzodiazepines are conserved in higher bony fishes and tetrapods. The conserved binding sites, in addition to recent immunological results obtained in other research groups, provide further evidence for the existence of the GABA/BZR as an isoreceptor complex.

Affinity Labels↗
PubMed1989

The structure of antiviral agents that inhibit uncoating when complexed with viral capsids.

The tertiary structure of most icosahedral viral capsid proteins consists of an eight-stranded antiparallel beta-barrel with a hydrophobic interior. In a group of picornaviruses, this hydrophobic pocket can be filled by suitable organic molecules, which stop viral uncoating after attachment and penetration into the host cell. The antiviral activity of these agents is probably due to increased rigidity of the capsid protein, thereby inhibiting disassembly. The hydrophobic pocket may be an essential functional component of the protein and may have been conserved in the evolution of many viruses from a common precursor. Since eight-stranded anti-parallel beta-barrels, with a topology as in viral capsid proteins, are not generally found in other proteins involved in cell metabolism, antiviral agents that bind in the interior of viral capsid proteins are likely to be more virus-specific and less cytotoxic. Furthermore, the greatest conservation of viral capsid proteins occurs within this pocket, whereas the least conserved part is the antigenic exterior. Thus, compounds that bind to such a pocket are likely to be effective against a broader group of serologically distinct viruses. Discovery of antiviral agents of this type depends on designing compounds that can enter and fit snugly into the hydrophobic pocket of a particular viral capsid protein.

Antiviral Agents↗