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PubMed1995

Microscopic computation in human brain evolution.

When human psychological performance is viewed in terms of cognitive modules, our species displays remarkable differences in computational power. Algorithmically simple computations are generally difficult to perform, whereas optimal routing or "Traveling Salesman" Problems (TSP) of far greater complexity are solved on an everyday basis. It is argued that even "simple" instances of TSP are not purely Euclidian problems in human computations, but involve emotional, autonomic, and cognitive constraints. They therefore require a level of parallel processing not possible in a macroscopic system to complete the algorithm within a brief period of time. A microscopic neurobiological model emphasizing the computational power of excited atoms within the neuronal membrane is presented as an alternative to classical connectionist approaches. The evolution of the system is viewed in terms of specific natural selection pressures driving satisfying computations toward global optimization. The relationship of microscopic computation to the nature of consciousness is examined, and possible mathematical models as a basis for simulation studies are briefly discussed.

Algorithms↗
PubMed2002

Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.

Enzyme-catalyzed beta-elimination of sugar uronic acids, exemplified by the degradation of plant cell wall pectins, plays an important role in a wide spectrum of biological processes ranging from the recycling of plant biomass through to pathogen virulence. The three-dimensional crystal structure of the catalytic module of a "family PL-10" polysaccharide lyase, Pel10Acm from Cellvibrio japonicus, solved at a resolution of 1.3 A, reveals a new polysaccharide lyase fold and is the first example of a polygalacturonic acid lyase that does not exhibit the "parallel beta-helix" topology. The "Michaelis" complex of an inactive mutant in association with the substrate trigalacturonate/Ca2+ reveals the catalytic machinery harnessed by this polygalacturonate lyase, which displays a stunning resemblance, presumably through convergent evolution, to the tetragalacturonic acid complex observed for a structurally unrelated polygalacturonate lyase from family PL-1. Common coordination of the -1 and +1 subsite saccharide carboxylate groups by a protein-liganded Ca2+ ion, the positioning of an arginine catalytic base in close proximity to the alpha-carbon hydrogen and numerous other conserved enzyme-substrate interactions, considered in light of mutagenesis data for both families, suggest a generic polysaccharide anti-beta-elimination mechanism.

Catalytic Domain↗
PubMed2000

The molecular evolutionary history of a winged bean alpha-chymotrypsin inhibitor and modeling of its mutations through structural analyses.

A serine protease inhibitor of the Kunitz-STI (soybean trypsin inhibitor) family, isolated from the legume seeds of winged bean, was found to inhibit chymotrypsin at a 1:2 stoichiometric ratio. When the structure was determined in our laboratory, it was found to form a characteristic beta-trefoil fold, which is also seen in other proteins from distant families and sources. The folding organization divides the protein into three approximately equal subdomains related by a pseudo-threefold axis of symmetry passing parallel to the barrel axis of the trefoil. Following the now established idea that the present-day genes originated from ancestral minigenes through evolution, the origin of the proteins having this beta-trefoil organization is scrutinized using its subdomain motif as the search probe. The results, based mainly on structural analyses, indicate the independent existence of such a motif, mimicking the unknown ancestral protein(s) that might have been distributed in nature, not only by gene duplication, but also by insertion and permutation in other folds. The understanding led to a hypothesis for the possible origin of the Kunitz-STI family. On the basis of this model of evolution, structurally hypervariable regions were located on the protein where mutations could be designed and a broad range of engineering of the protein's activity could be conceived.

Amino Acid Sequence↗
PubMed2001

Gender-associated mitochondrial DNA heteroplasmy in the venerid clam Tapes philippinarum (Mollusca Bivalvia).

This paper provides evidence of a gender-associated mitochondrial DNA (mtDNA) heteroplasmy in the clam Tapes philippinarum. The pattern of tissue distribution of the two observed mtDNA types (referred to as M and F) parallels that of the doubly uniparental inheritance system of Mytilus. The mitochondrial genetic features of the clam are related to a different rate of evolution of the M- and F-type mtDNAs. Since clams are known to be phylogenetically very distant from mussels, the present findings support the hypothesis that the mechanism producing gender-associated heteroplasmy should be considered an ancestral character in the Bivalvia.

Animals↗
PubMed2006

Evolutionary studies on an alpha-amylase gene segment in bats and other mammals.

Comparative studies of salivary glands showed that they maybe related to the adaptive radiation of bats, especially in the family Phylostomidae. In this study we have been searching for a likely relationship between different feeding habits found in bats and possible adaptive changes in a coding segment of the alpha-amylase enzyme. We have also tested some hypothesis about the phylogenetic relationship of bats and other mammals. A 663 bp segment of the alpha-amylase gene, corresponding to the exon 4 and part of the intron c, was sequenced in nine bat species. The exon 4 was also sequenced in further ten mammalian species. The phylogenetic trees generated with different methods produced the same results. When the intron c and the exon 4 were independently analyzed, they showed distinct topologies involving the bat species Sturnira lilium, different from the traditional bat phylogeny. Phylogenetic analysis of bats, primates and rodents supports the Euarchontoglires-Laurasiatheria hypothesis about the relationship among these groups. Selection tests showed that the alpha-amylase exon 4 is under strong purifying selection, probably caused by functional constraints. The conflicting bat phylogenies could not be explained by evolutionary convergence due to adaptive forces, and the different topologies may be likely due to the retention of plesiomorphic characters or the independent acquisition by evolutionary parallelism.

Amino Acid Sequence↗
PubMed1984

Modulation of enzyme activity in azaguanine-resistant V79 cells selected by chronic drug exposure.

Exposure of V79 cells to azaguanine (7-21 microM for 2-7 weeks) had little effect on growth or plating efficiency but resulted in gradual acquisition of resistance to 8-azaguanine (AZ) and 6-thioguanine (TG) and loss of ability to grow in HAT. The rate of evolution of the resistant phenotype was dependent on the concentration and duration of exposure to AZ. The increase in proportion of resistant cells was paralleled by a rise in phosphatase activity (pH optimum 7.0-7.5) expressed by intact cells and this preceded the fall in HGPRT activity. Elevated phosphatase activity and a resistant phenotype were stably expressed in clones isolated and cultured in the absence of AZ. Hypoxanthine guanine phosphoribosyl transferase (HGPRT) activity in cell extracts of three resistant clones ranged from 18 to 43% of wild-type levels but was unaltered with respect to substrate affinity and electrophoretic mobility. Mg2+-dependent activity dephosphorylated inosine 5'monophosphate (IMP), guanine 5'monophosphate (GMP), adenosine-5-monophosphate (AMP) and p-nitrophenylphosphate (PNPP) and was also elevated with respect to wild-type levels in resistant cell extracts. Purine nucleoside phosphorylase levels were similar in sensitive and resistant cell extracts. Cross-sensitivity studies with other purine analogues suggest that the elevated phosphatase activity does not contribute to the resistant phenotype. No karyotypic changes were observed in the resistant cell lines.

Animals↗
PubMed2000

Functional morphology of the gas-gland cells of the air-bladder of Oreochromis alcalicus grahami (teleostei: cichlidae): an ultrastructural study on a fish adapted to a severe, highly alkaline environment.

Oreochromis alcalicus grahami is a small cichlid fish that lives in shallow peripheral lagoons of Lake Magadi, Kenya. The internal surface of the air-bladder is highly vascularized, illustrating possible utilization as an accessory respiratory organ. The wall of the bladder consists of five distinct tissue layers. From the outer to the inner surfaces are: a squamous, undifferentiated epithelial cell; a collagen-elastic tissue space; a smooth muscle tissue band; an inner connective tissue space; and columnar gas-gland cells projecting into the lumen. The cell membrane over the perikarya of the gas-gland cells was sporadically broken. The disruptions were ascribed to possible physical damage by discharging gas-bubbles. Juxtaluminally, the gas-gland cells attached across tight junctions. The cells have highly euchromatic nuclei and conspicuously large intracytoplasmic secretory bodies. On the blood capillary facing (basal) aspect, the cell membrane of the gas-gland cells is highly amplified. The cells insert onto a smooth muscle tissue band. The morphological features and the topographical arrangement of the gas-gland cells in O. a. grahami are indicative of an operative exchange of materials between them and the underlying tissue components especially the blood capillaries. For a fish that subsists in hot, highly saline and alkaline water heavily invested by avian predators and where the partial pressure of oxygen diurnally shifts from virtual anoxia to hyperoxia, development of a versatile air-bladder for efficient buoyancy control conforms to the functional demands placed on it by a unique environment. Illustratively, instead of the gas-gland morphology in O. a. grahami resembling that in the freshwater fishes, the group from which the fish has evolved, it compares more closely to that of the marine fish. This similarity suggests amazing parallel evolutionary adaptation to biophysically corresponding aquatic milieus.

Africa↗
PubMed2003

MrBayes 3: Bayesian phylogenetic inference under mixed models.

MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.

Algorithms↗
PubMed1996

Positive selection and sequence rearrangements generate extensive polymorphism in the gamete recognition protein bindin.

Bindin is a gamete recognition protein of sea urchins that mediates species-specific attachment of sperm to an egg-surface receptor during fertilization. Sequences of bindin from closely related urchins show fixed species-specific differences. Within species, highly polymorphic bindin alleles result from point substitution, insertion/deletion, and recombination. Since speciation, positive selection favoring allelic variants has generated diversity in bindin polypeptides. Intraspecific bindin variation can be tolerated by the egg receptor, which suggests functional parallels between this system and other flexible recognition systems, including immune recognition. These results show that polymorphism in mate recognition loci required for rapid evolution of sexual isolation can arise within natural populations.

Alleles↗
PubMed2006

Designer genes: Filling the gap in transplantation.

Accelerated evolution of the field of functional genomics has been greatly facilitated by high-throughput microarray-based gene function studies, relating to the parallel and serial expression measurements of genomes. Microarray experimentation is being applied for the study of basic research questions, drug target discovery, pharmacology, toxicogenomics, target selectivity, disease biomarker determination, development of prognostic tests, and disease subclass determination. This article will review the current applications of microarray technology in the field of organ transplantation and discuss the potential impact of this technology on transplantation medicine.

Genetic Engineering↗
PubMed2004

Endogenous morphinergic signaling and tumor growth.

The mu3 opiate receptor subtype has been characterized by various binding assays as opiate alkaloid selective (e.g. morphine) and opioid peptide (e.g. methionine enkephalin) insensitive. This opiate receptor subtype has been found on human, including cancer cell lines, and invertebrate tissues, demonstrating that it has been conserved during evolution. Furthermore, in numerous reports, this receptor is coupled to constitutive nitric oxide release. In this regard, for example, morphine immune down regulating activities parallels those actions formerly attributed to nitric oxide. We have now identified the mu3 receptor at the molecular level and sequence analysis of the isolated cDNA suggests that it is a novel, alternatively spliced variant of the mu opiate receptor gene (MOR). Furthermore, using Northern blot, reverse transcription coupled to polymerase chain reaction (RT-PCR) and sequence analysis, we have demonstrated the expression of this new mu variant in human vascular tissue, mononuclear cells, polymorphonuclear cells, and human neuroblastoma cells. The presence of this mu splice variant, adds to the growing body of evidence supporting the hypothesis that morphine is an endogenous signaling molecule in neural, immune and vascular systems. In addition to their use in the treatment of pain, opioid peptides appear to be important in the growth regulation of normal and neoplastic tissue. This review will focus on the influence of opiate alkaloids, e.g., morphine, on tumor growth, with emphasis on immuno-regulatory and antiproliferative mechanisms.

Alternative Splicing↗
PubMed1990

Chromosomal evolution and tumor progression in a myxoid liposarcoma.

A myxoid liposarcoma showed macroscopic, histologic, and cytogenetic heterogeneity. In one of three myxoid nodules and in the surrounding lipoma-like tumor tissue, the translocation t(12;16)(q13;p11), known to be specific for myxoid liposarcoma, was found as the sole chromosomal abnormality. In the other two nodules, additional rearrangements involving chromosomes 1, 12, and 16 were found. These aberrations were probably secondary to the primary t(12;16), and are cytogenetic evidence of clonal evolution. The complex chromosome aberrations were present in those tumor parts that had more malignant histology, indicating that the acquisition of secondary chromosomal aberrations parallels the histologic manifestations of tumor progression.

Chromosome Aberrations↗
PubMed2000

[Interpretations of coordination as an evaluation tool in an experimental gerontologic program].

This article deals with the interpretations of coordination among actors solicited to participate in an experimental programme in the gerontological area of Lunel of the Hérault department of France. The article presents the conclusions of an evaluation report which includes two survey phases: a pre-test and a post-test survey implemented at the end of the programme with a parallel survey implemented in a control site, the Pézenas area of the Hérault department. The analysis of the initial perceptions of coordination and their evolution relies on the theory of the plurality of worlds (L. Boltanski and L. Thevenot). It aims to show that making a move toward coordination is a complex phenomenon that requires the elaboration of a common language. The material collected during this evaluation allows us to suggest that coordination questions the actors on their professional situation. It questions institutions and their internal functioning. Finally, this type of intervention brings to light the stakes in the examined field.

Aged↗
PubMed1975

[Surgical treatment of retinal detachment without drainage: apropos of 100 consecutive cases].

Recent advances in retinal detachment surgery must end in a simplification of the techniques: cryo-applications associated with a scleral buckling by one or more Lincoff sponges parallel to the equator seems to be satisfactory in almost all cases. Subretinal drainage, whatever technique used, does not seem to ameliorate significantly the evolution which depends, essentially, on the indentation and localisation quality. Furthermore, scleral perforation seemed to caused supplementary complications in an important number of cases. Analytical review of 100 consecutive cases.

Adolescent↗
PubMed1990

[Hemodynamic adaptations in proximal cerebrovascular occlusion].

In order to gain more insight into the pathophysiology of extracerebral cerebrovascular occlusion, the cerebral hemodynamic behaviour after uni- or bilateral carotid occlusion was investigated. In Wistar rats, acute occlusion of one common carotid artery leads to a moderate bilateral lowering of the resting hemispheric brain blood flow; no interhemispheric perfusion asymmetry is observed. During hypercapnia, however, a manyfold increase of the hemispheric blood flow is seen at the intact side, whereas blood flow increase at the side of the occlusion is suppressed indicating that the cerebrovascular reserve at the side of the occlusion is largely used to preserve resting hemispheric perfusion. During the days (1, 5, 15 and 30) following the occlusion, resting hemispheric blood flow is progressively restored rather rapidly (bilateral normalization on the fifth day) whereas restoration of the cerebrovascular reserve (hemispheric blood flow increase in hypercapnia) proceeds more slowly and a nearly normal hypercapnic response is reached on day thirty. Spontaneously Hypertensive Rats (SHR) show structural abnormalities of their blood vessels during the development of hypertension, leading to impaired adaptation possibilities of the cerebral vasculature after unilateral common carotid occlusion. This is indicated by the striking comparability of the compensation of hemispheric cerebral blood flow (in normo- and hypercapnia) of SH rats five days after unilateral carotid occlusion with the cerebral hemodynamic status of normotensive animals already seen 24 hours after the same occlusion. Consecutive bilateral common carotid occlusion shows that survival rate increases by increasing the interval between both occlusions. This survival relation is much more unfavorable in SH rats. The parallelism between the restoration of the measured CO2-reactivity of the blood flow in the involved hemisphere after unilateral carotid occlusion and the evolution of survival rate after consecutive bilateral carotid occlusion indicates that the response of the hemispheric circulation to CO2 offers a good estimate of true cerebrovascular reserve after cerebrovascular accidents of this kind. In cats, acute bilateral occlusion of the carotid arteries leads to a moderate decrease of resting cerebral blood flow in the anterior parts of the brain (cerebrum); the hypercapnic response of this region is, however, completely abolished. In the posterior brain regions (medulla oblongata and cerebellum) resting blood flow and its increase under hypercapnia are preserved. The experiments indicate that the relative preservation of resting cerebral blood flow in the cerebrum of the cat after acute bilateral carotid occlusion is at the expense of its complete hemodynamic reserve. Posterior brain regions are better protected in these conditions.(ABSTRACT TRUNCATED AT 400 WORDS)

Adaptation, Physiological↗
PubMed2006

Evolutionary genetics of vertebrate tissue mineralization: the origin and evolution of the secretory calcium-binding phosphoprotein family.

Three principal mineralized tissues are present in teeth; a highly mineralized surface layer (enamel or enameloid), body dentin, and basal bone. Similar tissues have been identified in the dermal skeleton of Paleozoic jawless vertebrates, suggesting their ancient origin. These dental tissues form on protein matrix and their mineralization is controlled by distinctive proteins. We have shown that many secretory calcium-binding phosphoproteins (SCPPs) are involved in tetrapod tissue mineralization. These SCPPs all originated from the common ancestral gene SPARCL1 (secreted protein, acidic, cysteine-rich like 1) that initially arose from SPARC. The SCPP family also includes a bird eggshell matrix protein, mammalian milk casein, and salivary proteins. The eggshell SCPP plays crucial roles in rigid eggshell production, milk SCPPs in efficient lactation and in the evolution of complex dentition, and salivary SCPPs in maintaining tooth integrity. A comparative analysis of the mammalian, avian, and amphibian genomes revealed a tandem duplication history of the SCPP genes in tetrapods. Although these tetrapod SCPP genes are fewer in teleost genomes, independent parallel duplication has created distinct SCPP genes in this lineage. These teleost SCPPs are also used for enameloid and dentin mineralization, implying essential roles of SCPPs for dental tissue mineralization in osteichthyans. However, the SCPPs used for tetrapod enamel and teleost enameloid, as well as tetrapod dentin and teleost dentin, are all different. Thus, the evolution of vertebrate mineralized tissues seems to be explained by phenogenetic drift: while mineralized tissues are retained during vertebrate evolution, the underlying genetic basis has extensively drifted.

Animals↗
PubMed2000

Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies.

Mutually catalytic sets of simple organic molecules have been suggested to be capable of self-replication and rudimentary chemical evolution. Previous models for the behavior of such sets have analyzed the global properties of short biopolymer ensembles by using graph theory and a mean field approach. In parallel, experimental studies with the autocatalytic formation of amphiphilic assemblies (e.g., lipid vesicles or micelles) demonstrated self-replication properties resembling those of living cells. Combining these approaches, we analyze here the kinetic behavior of small heterogeneous assemblies of spontaneously aggregating molecules, of the type that could form readily under prebiotic conditions. A statistical formalism for mutual rate enhancement is used to numerically simulate the detailed chemical kinetics within such assemblies. We demonstrate that a straightforward set of assumptions about kinetically enhanced recruitment of simple amphiphilic molecules, as well as about the spontaneous growth and splitting of assemblies, results in a complex population behavior. The assemblies manifest a significant degree of homeostasis, resembling the previously predicted quasi-stationary states of biopolymer ensembles (Dyson, F. J. (1982) J. Mol. Evol. 18, 344-350). Such emergent catalysis-driven, compositionally biased entities may be viewed as having rudimentary "compositional genomes." Our analysis addresses the question of how mutually catalytic metabolic networks, devoid of sequence-based biopolymers, could exhibit transfer of chemical information and might undergo selection and evolution. This computed behavior may constitute a demonstration of natural selection in populations of molecules without genetic apparatus, suggesting a pathway from random molecular assemblies to a minimal protocell.

Catalysis↗
PubMed2005

Multidimensional quantum trajectories: applications of the derivative propagation method.

In a previous publication [J. Chem. Phys. 118, 9911 (2003)], the derivative propagation method (DPM) was introduced as a novel numerical scheme for solving the quantum hydrodynamic equations of motion (QHEM) and computing the time evolution of quantum mechanical wave packets. These equations are a set of coupled, nonlinear partial differential equations governing the time evolution of the real-valued functions C and S in the complex action, S=C(r,t) + iS(r,t)/Planck's over 2pi, where Psi(r,t)=exp(S). Past numerical solutions to the QHEM were obtained via ensemble trajectory propagation, where the required first- and second-order spatial derivatives were evaluated using fitting techniques such as moving least squares. In the DPM, however, equations of motion are developed for the derivatives themselves, and a truncated set of these are integrated along quantum trajectories concurrently with the original QHEM equations for C and S. Using the DPM quantum effects can be included at various orders of approximation; no spatial fitting is involved; there is no basis set expansion; and single, uncoupled quantum trajectories can be propagated (in parallel) rather than in correlated ensembles. In this study, the DPM is extended from previous one-dimensional (1D) results to calculate transmission probabilities for 2D and 3D wave packet evolution on coupled Eckart barrier/harmonic oscillator surfaces. In the 2D problem, the DPM results are compared to standard numerical integration of the time-dependent Schrodinger equation. Also in this study, the practicality of implementing the DPM for systems with many more degrees of freedom is discussed.

Journal Article↗