Showing papers by "Trinity College, Dublin published in 1993"

Giant energy product in nanostructured two-phase magnets.

Abstract: Exchange hardening of nanostructured two-phase systems composed of an aligned hard phase and a soft phase with high magnetization is investigated using an approach which yields analytic nucleation fields from the micromagnetic vector equation, and accounts for interactions between the soft regions. In suitable structures the nucleation field is proportional to the volume-averaged anisotropy constant. For example, a multilayer composed of alternating 2.4 nm hard-magnetic ${\mathrm{Sm}}_{2}$${\mathrm{Fe}}_{17}$${\mathrm{N}}_{3}$ layers and 9 nm ${\mathrm{Fe}}_{65}$${\mathrm{Co}}_{35}$ layers can have an energy product as high as 1 MJ/${\mathrm{m}}^{3}$ (120 MG Oe), with a rare-earth content of only 5 wt %. Giant energy products may also be achieved in suitable cellular and disordered structures.

Advances in Our Understanding of the Mechanisms of the Neurotoxicity of MPTP and Related Compounds

Abstract: The discovery that 1 -methyl4-phenyl1,2,3,6-tetrahydropyndine (MPTP), a contaminant of a synthetic pethidine analogue sold as a street drug, produced a condition resembling Parkinson’s disease has been described in detail (for reviews, see Langston, 1985; Snyder and DAmato, 1986). MPTP was shown to cause a selective destruction of nigrostriatal dopaminergic neurons in primates and some other animal species, and this stimulated a great deal ofwork on the mechanisms involved in its neurotoxic effects and their possible relationship to idiopathic Parkinson’s disease. Earlier work on the mechanism by which MPTP exerts its selective neurotoxic effects has been reviewed before, and the present account will concentrate on more recent discoveries concerning its biochemical actions and the unresolved problems that remain.

A mutation in CFTR produces different phenotypes depending on chromosomal background

Abstract: Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene but the association between mutation (genotype) and disease presentation (phenotype) is not straightforward. We have been investigating whether variants in the CFTR gene that alter splicing efficiency of exon 9 can affect the phenotype produced by a mutation. A missense mutation, R117H, which has been observed in three phenotypes, was found to occur on two chromosome backgrounds with intron 8 variants that have profoundly different effects upon splicing efficiency. A close association is shown between chromosome background of the R117H mutation and phenotype. These findings demonstrate that the genetic context in which a mutation occurs can play a significant role in determining the type of illness produced.

A 50,000-year record of climate oscillations from Florida and its temporal correlation with the heinrich events.

Abstract: Oscillations of Pinus (pine) pollen in a 50,000-year sequence from Lake Tulane, Florida, indicate that there were major vegetation shifts during the last glacial cycle. Episodes of abundant Pinus populations indicate a climate that was more wet than intervening phases dominated by Quercus (oak) and Ambrosia-type (ragweed and marsh-elder). The Pinus episodes seem to be temporally correlated with the North Atlantic Heinrich events, which were massive, periodic advances of ice streams from the eastern margin of the Laurentide Ice Sheet. Possible links between the Tulane Pinus and Heinrich events include hemispheric cooling, the influences of Mississippi meltwater on sea-surface temperatures in the Gulf of Mexico, and the effects of North Atlantic thermohaline circulation on currents in the Gulf.

Photochemical interactions of methylene blue and analogues with DNA and other biological substrates.

Abstract: The light-induced reactions of methylene blue and related phenothiazinium dyes with biological substrates are described. The properties of the excited states of the dyes, their reactions with nucleic acids and their photosensitised chemical modifications of nucleic acid bases are examined. Reports on phenothiazinium dye-induced damage to proteins, lipids, biological membranes, organelles, viruses, bacteria, mammalian cells and carcinomas are reviewed.

Semliki Forest virus expression system: production of conditionally infectious recombinant particles.

Abstract: In the recently developed Semliki Forest virus (SFV) DNA expression system, recombinant RNA encoding the viral replicase, and helper RNA molecules encoding the structural proteins needed for virus assembly are cotransfected into cells. Since the helper RNA lacks the sequence needed for its packaging into nucleocapsids, only recombinant RNAs should be packaged. We have found, however, that small amounts of replication-proficient SFV particles can still be produced. Here we describe the construction of a helper variant with a mutation in the gene encoding the viral spike protein such that its product cannot undergo normal proteolytic processing to activate viral entry functions. Hence, the recombinant stock is noninfectious, but may be activated by cleavage with chymotrypsin. When recombinant virus produced with the new helper was examined in a variety of assays, including sensitive animal tests, we were unable to detect any replication-competent SFV particles. We therefore conclude that this conditional expression system meets extremely stringent biosafety requirements.

Codon usage: mutational bias, translational selection, or both?

Abstract: 7. Karimpour, I., Cutler, M., Shih, D., Smith, J. and Kleene, K. (1992) DNA Cell Hiol. 11,693-699 8. Hill, K. E., Lloyd, R. S., Yang, J. G., Read, R. and Hurk, R. F. (1991) J. Biol. Chem. 266,10050-10053 9. Burk, R. F., Lawrence, R. A. and Lane, J. M. (1980) J. Clin. Invest. 65, 1024-1031 10. Rurk, R. F., Hill, K. E., Read, R. and Rellew, T. (1991) Am. J. Physiol. 261, E26-E30 11. Yang, J. G., Morrison-Plummer, J. and Burk, R. F. (1987) J. Biol. Chem. 262,13372-1 3375 12. Read, R., Bellew, T., Yang, J. G., Hill, K. E., Palmer, I. S. and Burk, R. F. (1990) J. Biol. Chem. 265, 1789917905 13. Hill, K. E., Lloyd, R. S. and Burk, R. F. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 537-541 14. Berry, M. J., Banu, L., Chen, Y., Mandel, S. J., Kieffer, J. D., Harney, J. W. and Larsen, P. R. (1 99 1 ) Nature (London) 353,273-276 835

Mechanisms of Shaft Friction in Sand from Instrumented Pile Tests

Abstract: Comprehensive measurements of the effective stresses developed during the installation, equalization, and load testing of displacement piles in a loose to medium dense quartz sand are presented. The results shed new light on the mechanisms that control shaft friction in sand. First, it is demonstrated directly that the stresses developed at any given soil horizon depend strongly on both the distance of that horizon from the pile tip and the soil's initial state. Second, pile loading is shown to induce radial effective stress changes associated with the soil fabric set up by installation and dilation phenomena at pile‐soil interface. Thirdly, the operational angles of interface friction are found to be constant volume values that correlate well with the results from laboratory interface shear tests.

Beyond Reason: The Nature of the Ethnonational Bond

Abstract: Nationalism, as commonly encountered in the press, television news and even in most scholarly tracts, refers to an emotional attachment to one’s state or country and its political institutions – an attachment more properly termed patriotism. Nationalism, in correct usage, refers to an emotional attachment to one’s people – one’s ethnonational group. It is therefore proper to speak of an English, Scottish, or Welsh nationalism, but not of a ‘British’ nationalism, the latter being a manifestation of patriotism.

Mammalian gene evolution : nucleotide sequence divergence between mouse and rat

Abstract: As a paradigm of mammalian gene evolution, the nature and extent of DNA sequence divergence between homologous protein-coding genes from mouse and rat have been investigated. The data set examined includes 363 genes totalling 411 kilobases, making this by far the largest comparison conducted between a single pair of species. Mouse and rat genes are on average 93.4% identical in nucleotide sequence and 93.9% identical in amino acid sequence. Individual genes vary substantially in the extent of nonsynonymous nucleotide substitution, as expected from protein evolution studies; here the variation is characterized. The extent of synonymous (or silent) substitution also varies considerably among genes, though the coefficient of variation is about four times smaller than for nonsynonymous substitutions. A small number of genes mapped to the X-chromosome have a slower rate of molecular evolution than average, as predicted if molecular evolution is “male-driven.” Base composition at silent sites varies from 33% to 95% G + C in different genes; mouse and rat homologues differ on average by only 1.7% in silent-site G + C, but it is shown that this is not necessarily due to any selective constraint on their base composition. Synonymous substitution rates and silent site base composition appear to be related (genes at intermediate G + C have on average higher rates), but the relationship is not as strong as in our earlier analyses. Rates of synonymous and nonsynonymous substitution are correlated, apparently because of an excess of substitutions involving adjacent pairs of nucleotides. Several factors suggest that synonymous codon usage in rodent genes is not subject to selection.

The effects of short- and long-term supplementation with fish oil on the incorporation of n-3 polyunsaturated fatty acids into cells of the immune system in healthy volunteers

Abstract: Eight healthy male volunteers supplemented their normal diet with 10-15 g/d of a fish oil supplement (MaxEPA) to provide 1.4-4.2 g/d of eicosapentaenoic acid (EPA; C20:5 n-3) for a period of 12 weeks. Blood samples were taken at weeks 0, 2 and 12 and the fatty acid compositions of the phospholipids of plasma, platelets, neutrophils, monocytes and T- and B-lymphocytes were determined. In all instances the level of EPA increased significantly (P < 0.05) by 2 weeks and remained so without a further increase for the ensuing 10 weeks. Beyond that, few consistent patterns in fatty acid composition were observed. Arachidonic acid (C20:4 n-6) fell significantly (P < 0.05) in plasma, platelets, neutrophils and T- and B-lymphocytes, but generally tended to do so only by week 12. Given the wide variability in the half-life of these cells (minutes for neutrophils, months for lymphocytes) it is evident that uptake of plasma EPA occurs by phospholipid exchange into preformed mature cells and does not require incorporation during cell genesis.

Monoamine oxidase inhibitors and the cheese effect.

Abstract: The behavior of inhibitors of monoamine oxidase-A (MAO-A) is considered in terms of the possibility of having an effective antidepressant that does not give rise to hypertensive interactions with dietary tyramine. Studies with punch-biopsy samples of human intestine and rat intestinal samples show MAO-A to be the predominant form of the enzyme in both species. Transport studies with everted rat intestinal preparations indicate that tyramine is extensively metabolized during transport through the intestine. Selective inhibition of MAO-A by clorgyline results in a large increase in the amount of unchanged tyramine transported, whereas selective inhibition of MAO-B with L-deprenyl (selegiline) has no significant effect. The behavior of reversible MAO-A inhibitors can significantly reduce, but not entirely eliminate, these effects on the intestinal metabolism of tyramine, but only if the inhibition is competitive in nature.

Steady-state drainage of an aqueous foam.

Abstract: The process of wetting of a monodisperse foam by the continuous addition of liquid from the top has been investigated for a cylindrical column. The velocity of the interface between dry and wet foam was found to vary as the square root of the rate of addition of liquid. Evidence of a structural transformation was found around gas fraction \ensuremath{\Phi}=0.87. It was interpreted as arising from the collapse of the four-sided faces of the (Kelvin) polyhedra which constitute the foam cells, and this was directly observed when large bubbles were used. There is a second transition at around \ensuremath{\Phi}=0.6, with the onset of bubble motion.

Oral Candida in HIV Infection and AIDS: New Perspectives/New Approaches

Abstract: Oral candidosis has become an increasingly important problem in HIV-infected individuals. At present, the small body of published literature on the characterization of the Candida strains and species found in HIV+ patients is full of confusion and contradictions. Some of these difficulties are the result of the methodological shortcomings of a number of the techniques that have been used. Examples of the problems that may be encountered on primary isolation and subculture are described and the drawbacks associated with the systems used to date for phenotyping Candidaare quoted. While molecular characterization techniques would appear to offer a reliable and objective alternative, they too have their strengths and weaknesses. An attempt is made to summarize the progress that has been made recently in the detection and identification of Candida albicansand also the non-albicans species from HIV-infected individuals. What emerges is that the commensal Candida species that inhabit the oral cavities of...

Localization of an autosomal dominant retinitis pigmentosa gene to chromosome 7q

Abstract: Retinitis pigmentosa is a group of clinically and genetically heterogeneous retinopathies and a significant cause of worldwide visual handicap. We have typed DNA from members of a Spanish family segregating an autosomal dominant form of retinitis pigmentosa (adRP) using a large series of simple sequence polymorphic markers. Positive two-point lod scores have been obtained with fifteen markers including D7S480 (theta max = 0.00, Zmax = 7.22). Multipoint analyses using a subset of these markers gave a lod score of 7.51 maximizing at D7S480. These data provide definitive evidence for the localisation of an adRP gene on chromosome 7q, and highlight the extensive genetic heterogeneity that exists in the autosomal dominant form of this disease.

Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure.

Abstract: The recent determination of the complete sequence of chromosome III from the yeast Saccharomyces cerevisiae allows, for the first time, the investigation of the long range primary structure of a eukaryotic chromosome. We have found that, against a background G+C level of about 35%, there are two regions (one in each chromosome arm) in which G+C values rise to over 50%. This effect is seen in silent sites within genes, but not in noncoding intergenic sequences. The variation in G+C content is not related to differential selection of synonymous codons, and probably reflects mutational biases. That the intergenic regions do not exhibit the same phenomenon is particularly interesting, and suggests that they are under substantial constraint. The yeast chromosome may be a model of the structure of the human genome, since there is evidence that it is also a mosaic of long regions of different base compositions, reflected in wide variation of G+C content at silent sites among genes. Two possible causes of this regional effect, replication timing, and recombination frequency, are discussed.

Retrieving Adaptable Cases: The Role of Adaptation Knowledge in Case Retrieval

Abstract: The retrieval of a suitable case is of crucial importance to the success of case-based reasoning. A good criterion for judging “case suitability” is how complex a case will be to adapt. However, it has proven difficult to directly calculate this measure of case “adaptability” without incurring the full cost of adaptation. This has led most researchers to exploit semantic similarity as a more tractable (albeit less accurate) answer to the question of case suitability.

Policy Watch Alcohol and Cigarette Taxes

Abstract: Increased excise taxes on cigarettes and alcohol have been suggested as a means to finance (at least partially) the Clinton administration's proposed program of health care reform. We consider the revenue potential of cigarette and alcohol tax hikes and explore the effects on consumption and related outcomes. We present estimates of the social costs and implied optimal tax rates on cigarettes and alcohol. The bulk of the evidence presented here does support higher taxes on cigarettes and alcohol.

Evolution of the recA gene and the molecular phylogeny of bacteria.

Abstract: The DNA sequences of the recA gene from 25 strains of bacteria are known. The evolution of these recA gene sequences, and of the derived RecA protein sequences, is examined, with special reference to the effect of variations in genomic G + C content. From the aligned RecA protein sequences, phylogenetic trees have been drawn using both distance matrix and maximum parsimony methods. There is a broad concordance between these trees and those derived from other data (largely 16S ribosomal RNA sequences). There is a fair degree of certainty in the relationships among the "Purple" or Proteobacteria, but the branching pattern between higher taxa within the eubacteria cannot be reliably resolved with these data.

The impact of connectives on the memory for expository texts

Abstract: Three experiments investigated the influence of connectives on memory for expository text. Subjects in Experiments 1 and 2 read and later recalled passages with either no connectives, temporal connectives (before/and then), causal connectives (which caused/which enabled), or intentional connectives (in order that/so that)

Activation of a bacterial lipase by its chaperone

Abstract: The gene lipA of Pseudomonas cepacia DSM 3959 encodes a prelipase from which a signal peptide is cleaved during secretion, producing a mature extracellular lipase. Expression of lipase in several heterologous hosts depends on the presence of another gene, limA, in cis or in trans. Lipase protein has been overproduced in Escherichia coli in the presence and absence of the lipase modulator gene limA. Therefore, limA is not required for the transcription of lipA or for the translation of the lipA mRNA. However, no lipase activity is observed in the absence of limA. limA has been overexpressed and encodes a 33-kDa protein, Lim. If lipase protein is denatured in 8 M urea and the urea is removed by dialysis, lipase activity is quantitatively recovered provided Lim protein is present during renaturation. Lip and Lim proteins form a complex precipitable either by an anti-lipase or anti-Lim antibody. The Lim protein has therefore the properties of a chaperone.