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PubMed2004

Self-affine fronts in self-affine fractures: large and small-scale structure.

The evolution and spatial structure of displacement fronts in fractures with self-affine rough walls are studied by numerical simulations. The fractures are open and the two faces are identical but shifted along their mean plane, either parallel or perpendicular to the flow. An initially flat front advected by the flow is progressively distorted into a self-affine front with a Hurst exponent equal to that of the fracture walls. The lower cutoff of the self-affine regime depends only on the aperture, while the upper cutoff grows with the lateral shift and linearly with the width of the front.

Journal Article↗

PubMed2005

Na(+)-D-glucose cotransporter in the kidney of Squalus acanthias: molecular identification and intrarenal distribution.

Using primers against conserved regions of mammalian Na(+)-d-glucose cotransporters (SGLT), a cDNA was cloned from the kidney of spiny dogfish shark (Squalus acanthias). On the basis of comparison of amino acid sequence, membrane topology, and putative glycosylation and phosphorylation sites, the cDNA could be shown to belong to the family of sglt genes. Indeed, Na(+)-dependent d-glucose uptake could be demonstrated after expression of the gene in Xenopus laevis oocytes. In a dendrogram, the SGLT from shark kidney has a high homology to the mammalian SGLT2. Computer analysis revealed that the elasmobranch protein is most similar to the mammalian proteins in the transmembrane regions and contains already all the amino acids identified to be functionally important, suggesting early conservation during evolution. Extramembraneous loops show larger variations. This holds especially for loop 13, which has been implied as a phlorizin-binding domain. Antibodies were generated and the intrarenal distribution of the SGLT was studied in cryosections. In parallel, the nephron segments were identified by lectins. Positive immunoreactions were found in the proximal tubule in the early parts PIa and PIb and the late segment PIIb. The large PIIa segment of the proximal tubule showed no reaction. In contrast to the mammalian kidney also the late distal tubule, the collecting tubule, and the collecting duct showed immunoreactivity. The molecular information confirms previous vesicle studies in which a low affinity SGLT with a low stoichiometry has been observed and supports the notion of a similarity of the shark kidney SGLT to the mammalian SGLT2. Despite its presence in the late parts of the nephron, the absence of SGLT in the major part of the proximal tubule, the relatively low affinity, and in particular the low stoichiometry might explain the lack of a T(m) for d-glucose in the shark kidney.

Amino Acid Sequence↗

PubMed2000

Automated purification of His6-tagged proteins allows exhaustive screening of libraries generated by random mutagenesis.

In the course of site-directed mutagenesis or directed evolution experiments, large numbers of protein variants are often generated. To characterize functional properties of individual mutant proteins in vitro, a rapid and reliable protein purification system is required. We have developed an automated method for the parallel purification of 96 different protein variants that takes about two hours. Using a 96-well format, the whole process can be performed automatically by a pipetting robot. Coupled with a suitable assay, again using a 96-well format, all variants can be functionally characterized within a few hours. The protein purification procedure described here is based on the interaction between His6-tagged proteins and Ni-NTA-coated microplates. Typical yields are 3-8 pmol purified protein/well, which is sufficient to analyze most enzymatic activities. Using this procedure, we have purified and characterized variants of the restriction endonuclease EcoRV, which were produced in an effort to enhance the selectivity of this enzyme. For this purpose, three amino acid residues were randomized in a region known from the co-crystal structure to be located at the protein-DNA interface. From a library of about 1200 variants, predominantly single and double mutants, more than 1000 variants were purified and characterized in parallel, which corresponds to an almost complete screening of the library.

Automation↗

PubMed1989

Contributions to psychohistory: XV. Structural characteristics as an index of mental health in Freud's, his patients' and colleagues' manifest dreams.

Evolution of psychoanalytic dream theory from the topographical-conflict model resulted in the relative ascendance of manifest dream content and structure. Correspondingly, Freud's emphasis on the latent dream, disguised unconscious wish-fulfillment function, was paralleled by the development of an ego problem-solving-conflict function demonstrably observable in subjects' and patients' nocturnal dreams in sleep-lab REM awakenings. This development culminated in clinical, theoretical, and operational adoption of binary opposition as a language of manifest dream structure and a corresponding definition of mental health in terms of personal problem-solving efficacy measured in a narrative as self-defined, self-advocacy-adversary statements of sequences. Process and outcome measures from initial studies of psychoanalytic patients and nonpatients' dreams evidenced concurrent validity. Use of this measure on the three types of dreams reported in Freud's seminal The Interpretation of Dreams yielded results which support the inference that Freud's dreams are significantly more healthy than those of his patients or others (mostly colleagues).

Adaptation, Psychological↗

PubMed2001

Nitric oxide: one of the more conserved and widespread signaling molecules.

After the discovery of the vasodilatory functions of nitric oxide (NO), many signaling mechanisms involving NO were identified through experiments on mammals. NO activates soluble guanylyl cyclase to induce the formation of cGMP, stimulates ADP-ribosylation of GAPDH to alter cell energy production, and combines with superoxide to generate peroxynitrite. It then became clear that NO was a major messenger molecule in mammals, involved in the regulation of blood vessel dilatation, immune function and neurotransmission in the brain and peripheral nervous system. The wide spectrum of physiological effects of NO in mammals prompted researchers to look for the presence of NO in vertebrates and invertebrates. Parallel findings on the presence of NO signaling in vertebrates and invertebrates were observed, and then NO was found to be a signaling molecule widely spread throughout the metazoan kingdom and whose functions were highly conserved during evolution. These features were extended to the entire animal kingdom after the discovery of NOS activity in protozoa, yeasts and bacteria. Recently, the involvement of NO and NOS in plant disease resistance to infection was documented and many close similarities were detected between NO-dependent signaling mechanisms involved in plants and those identified in animals. All of these results indicated that NO is one of the earliest and most widespread signaling molecules in living organisms. This short review was aimed at marshalling recent information that led to this conclusion.

Animals↗

PubMed2005

The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins.

Conservation of function is the basic tenet of protein evolution. Conservation of key electrostatic properties is a frequently employed mechanism that leads to conserved function. In a previous report, we identified several conserved electrostatic properties in four protein families and one functionally diverse enzyme superfamily. In this report, we demonstrate the evolutionary and catalytic importance of electrostatic networks in three ubiquitous metabolic enzymes: triosephosphate isomerase, enolase, and transaldolase. Evolutionary importance is demonstrated using phylogenetic motifs (sequence fragments that parallel the overall familial phylogeny). Phylogenetic motifs frequently correspond to both catalytic residues and conserved interactions that fine-tune catalytic residue pKa values. Further, in the case of triosephosphate isomerase, quantitative differences in the catalytic Glu169 pKa values parallel subfamily differentiation. Finally, phylogenetic motifs are shown to structurally cluster around the active sites of eight different TIM-barrel families. Depending upon the mechanistic requisites of each reaction catalyzed, interruptions to the canonical fold may or may not be identified as phylogenetic motifs.

Amino Acid Sequence↗

PubMed2002

Molecular evolution of nuclear genes in Cupressacea, a group of conifer trees.

We surveyed the molecular evolutionary characteristics of 11 nuclear genes from 10 conifer trees belonging to the Taxodioideae, the Cupressoideae, and the Sequoioideae. Comparisons of substitution rates among the lineages indicated that the synonymous substitution rates of the Cupressoideae lineage were higher than those of the Taxodioideae. This result parallels the pattern previously found in plastid genes. Likelihood-ratio tests showed that the nonsynonymous-synonymous rate ratio did not change significantly among lineages. In addition, after adjustments for lineage effects, the dispersion indices of synonymous and nonsynonymous substitutions were considerably reduced, and the latter was close to 1. These results indicated that the acceleration of evolutionary rates in the Cupressoideae lineage occurred in both the nuclear and plastid genomes, and that generally, this lineage effect affected synonymous and nonsynonymous substitutions similarly. We also investigated the relationship of synonymous substitution rates with the nonsynonymous substitution rate, base composition, and codon bias in each lineage. Synonymous substitution rates were positively correlated with nonsynonymous substitution rates and GC content at third codon positions, but synonymous substitution rates were not correlated with codon bias. Finally, we tested the possibility of positive selection at the protein level, using maximum likelihood models, assuming heterogeneous nonsynonymous-synonymous rate ratios among codon (amino acid) sites. Although we did not detect strong evidence of positively selected codon sites, the analysis suggested that significant variation in nonsynonymous-synonymous rate ratio exists among the sites. The most likely sites for action of positive selection were found in the ferredoxin gene, which is an important component of the apparatus for photosynthesis.

Base Sequence↗

PubMed2006

Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome.

BACKGROUND: Coordinately regulated genes often physically cluster in eukaryotic genomes, for reasons that remain unclear. RESULTS: Here we provide evidence that many S. cerevisiae genes induced by starvation and other stresses reside in non-random clusters, where transcription of these genes is repressed in the absence of stress. Most genes essential for growth or for rapid, post-transcriptional responses to stress in cycling cells map between these gene clusters. Genes that are transcriptionally induced by stresses include a large fraction of rapidly evolving paralogues of duplicated genes that arose during an ancient whole genome duplication event. Many of these rapidly evolving paralogues have acquired new or more specialized functions that are less essential for growth. The slowly evolving paralogues of these genes are less likely to be transcriptionally repressed in the absence of stress, and are frequently essential for growth or for rapid stress responses that may require constitutive expression of these genes in cycling cells. CONCLUSION: Our findings suggest that a fundamental organizing principle during evolution of the S. cerevisiae genome has been clustering of starvation and other stress-induced genes in chromosome regions that are transcriptionally repressed in the absence of stress, from which most genes essential for growth or rapid stress responses have been excluded. Chromatin-mediated repression of many stress-induced genes may have evolved since the whole genome duplication in parallel with functions for proteins encoded by these genes that are incompatible with growth. These functions likely provide fitness effects that escape detection in assays of reproductive capacity routinely employed to assess evolutionary fitness, or to identify genes that confer stress-resistance in cycling cells.

Evolution, Molecular↗

PubMed1981

Protist kinetids: structural conservatism, kinetid structure, and ancestral states.

The protist kinetid is considered a conservative indicator of phylogenetic relationship. This conclusion is supported by the apparently inverse relationship between the conservation of structure and its level in the organizational hierarchy. A comparative examination of features of protist kinetids indicates that pattern is strongly conserved; within and among flagellate taxa there is more variability in pattern than within the ciliates. It is concluded that the ancestral flagellate kinetid is a pair of orthogonally oriented kinetosomes having one striated rootlet and at least one microtubular ribbon. The ancestral kinetid of the ciliates is also a dikinetid structure, though represented by a paired set of parallel kinetosomes, probably similar to that found today in karyorelictid ciliates, presumptive descendants of the ancestral stock.

Animals↗

PubMed1999

Synexpression groups in eukaryotes.

In 1960, Jacob and Monod described the bacterial operon, a cluster of functionally interacting genes whose expression is tightly coordinated. Global expression analysis has shown that the highly coordinate expression of genes functioning in common processes is also a widespread phenomenon in eukaryotes. These sets of co-regulated genes, or 'synexpression groups', show a striking parallel to the operon, and may be a key determinant facilitating evolutionary change leading to animal diversity.

Animals↗

PubMed1972

Prokaryotic algae associated with Australian proterozoic stromatolites.

Five instances of association between distinctive stromatolites and blue-green algal nannofossils are recorded from a 100-m sequence of carbonate rocks about 1.6 x 10(9) years old, along the south side of Paradise Creek, northwestern Queensland, Australia. No eukaryotes were identified in any of these systematically limited assemblages, although they are known from rocks as old as 1.3 x 10(9) years in eastern California. Thus, eukaryotes may not have appeared until after 1.6 x 10(9) years ago (but before 1.3 x 10(9) years ago). The associations observed would also be consistent with (but do not prove) a biotic influence on stromatolite morphology. As is usual among prePaleozoic forms described, the morphology of the nannofossils is very similar to living forms, displaying marked evolutionary conservatism. Primary orientation of stromatolitic laminae and columns is not invariably convex upward, as conventionally believed, but convex away from and parallel to the initial point or surface of attachment, which may be horizontal or even downward beneath overhangs.

Australia↗

PubMed2005

The mevalonate pathway and the synthesis of juvenile hormone in insects.

The mevalonate pathway in insects has two important peculiarities, the absence of the sterol branch and the synthesis of juvenile hormone (JH), that may have influenced the mechanisms of regulation. The data available on these mechanisms indicate that cholesterol does not play a regulatory role and that JH modulates transcript levels of a number of genes of the mevalonate pathway or can influence the translatability and/or stability of the transcripts themselves. These data suggest that the mevalonate pathway in insects can best be interpreted in terms of coordinated regulation, in which regulators act in parallel to a number of enzymes, as occurs in the cholesterol-driven pathway in vertebrates.

Animals↗

PubMed2005

Evolution of resistance toward Bacillus sphaericus or a mixture of B. sphaericus+Cyt1A from Bacillus thuringiensis, in the mosquito, Culex quinquefasciatus (Diptera: Culicidae).

The 2362 strain of Bacillus sphaericus (Bs) Neide is a highly mosquitocidal bacterium used in commercial bacterial larvicides primarily to control mosquitoes of the genus Culex. Unfortunately, Bs is at high risk for selecting resistance in mosquito populations, because its binary toxin apparently only binds to a single receptor type on midgut microvilli. A potential key strategy for delaying resistance to insecticidal proteins is to use mixtures of toxins that act at different targets within the insect, especially mixtures that interact synergistically. We tested this hypothesis for delaying the phenotypic expression of resistance by exposing Culex quinquefasciatus Say larvae to Bs alone or in combination with Cyt1A from Bacillus thuringiensis subsp. israelensis. Two laboratory lines of Cx. quinquefasciatus, one sensitive to Bs and the other containing Bs resistance alleles, were subjected to intensive selection pressure for 20 generations with either Bs 2362 or a 3:1 mixture of Bs 2362+Cyt1A. At the end of the study, the sensitive line had evolved >1000-fold resistance when selected with Bs alone, whereas the parallel line selected with Bs+Cyt1A exhibited only low resistance toward this mixture (RR95, 1.4). Similar results were observed in the lines containing Bs resistance alleles. Both lines selected with Bs+Cyt1A exhibited substantial resistance to Bs in the absence of Cyt1A. Although selection with Bs+Cyt1A did not prevent the underlying evolution of resistance to Bs, these results suggest that a mixture of Bs with other endotoxins, particularly one like Bs+Cyt1A in which the components interact synergistically, will provide longer lasting and more effective mosquito control than Bs alone.

Animals↗

PubMed2006

Evolution in the treatment of metastatic colorectal carcinoma of the liver.

Metastatic colorectal cancer to the liver is associated with a uniform poor prognosis without treatment. Advances in therapy over the past decades have now allowed surgical resections of the liver to occur with a low morbidity and mortality. Improvements in chemotherapy regimes have paralleled technical improvements and now allow a new group of patients to become eligible for surgical resection. This chapter will review the recent advances in surgical and chemotherapeutic regimes in metastatic colorectal cancer to the liver.

Antineoplastic Agents↗

PubMed2003

Constructing large-scale genetic maps using an evolutionary strategy algorithm.

This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with approximately 50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology.

Algorithms↗

PubMed1996

A network theory of ageing: the interactions of defective mitochondria, aberrant proteins, free radicals and scavengers in the ageing process.

Evolution theory indicates that ageing is caused by progressive accumulation of defects, since the evolutionary optimal level of maintenance is always below the minimum required for indefinite survival. Evolutionary theories also suggest that multiple processes are operating in parallel, but unfortunately they make no predictions about specific mechanisms. To understand and evaluate the many different mechanistic theories of ageing which have been proposed, it is therefore important to understand and study the network of maintenance processes which control cellular homeostasis. In this paper we describe a Network Theory of Ageing which integrates the contributions of defective mitochondria, aberrant proteins, and free radicals to the ageing process, and which includes the protective effects of antioxidant enzymes and proteolytic scavengers. The model simulations not only confirm and explain many experimental, age related findings like an increase in the fraction of inactive proteins, a significant rise in protein half-life, an increase in the amount of damaged mitochondria, and a drop in the energy generation per mitochondrion, but they also show interactions between the different theories which could not have been observed without the network approach. In some simulations, for example, the mechanism of the final breakdown seems to be a consequence of the cooperation of mitochondrial and cytoplasmic reactions, the mitochondria being responsible for a long term, gradual change which eventually triggers a short lived cytoplasmic error loop.

Aging↗

PubMed2004

Alpha event-related desynchronization preceding a go/no-go task: a high-resolution EEG study.

The authors delineated the time evolution of alpha event-related desynchronization over human frontal, parietal, and primary sensorimotor areas during the expectancy of a go/no-go task. The main issue under investigation was whether anticipatory processes impinged upon cortical areas in sequential or parallel mode. Compared with the control condition, in the experimental condition there was an Alpha 1 desynchronization over the central midline, an Alpha 2 desynchronization increasing over primary sensorimotor areas, and an Alpha 3 desynchronization increasing in parallel over bilateral primary sensorimotor areas. These processes had different temporal features. Results disclose an anticipatory activity of central midline areas and primary sensorimotor areas in both parallel and sequential modes. This reflects an adaptive, energy-consuming strategy rather than an economic waiting for the go stimulus.

Adult↗

PubMed2006

Molecular systematics, phylogeny and ecology of anisakid nematodes of the genus Anisakis Dujardin, 1845: an update.

Advances in the taxonomy and ecological aspects concerning geographical distribution and hosts of the so far genetically recognised nine taxa of the nematodes belonging to genus Anisakis (i.e. A. pegreffii, A. simplex s.s., A. simplex C, A. typica, A. ziphidarum, Anisakis sp., A. physeteris, A. brevispiculata and A. paggiae) are here summarized. Genetic differentiation and phylogenetic relationships inferred from allozyme (20 enzyme-loci) and mitochondrial (sequences of cox-2 gene) markers, are revised and compared. The two genetic analyses are congruent in depicting their phylogenetic relationships. Two main clusters are showed to exist in the obtained trees, one encompassing the species A. pegreffii, A. simplex s.s., A. simplex C, A. typica, A. ziphidarum and Anisakis sp.; while, the second including A. physeteris, A. brevispiculata and A. paggiae. The existence of two clades is also supported by their morphological differentiation in adult and larval morphology. Comparison of phylogenetic relationships among Anisakis spp. with those currently available for their cetacean definitive hosts suggests parallelism between host and parasite phylogenetic tree topologies. Preliminary data for reconstruction of a possible co-evolutionary scenario between cetacean hosts and their Anisakis endoparasites suggests that cospeciation and host-switching events may have accompanied the evolution of this group of parasites. Finally, genetic/molecular markers for the identification of the so far genetically recognized taxa of Anisakis at any life-stage and both sexes were given also in relation to human anisakiosis is discussed.

Animals↗