Showing papers by "Trinity College, Dublin published in 1987"

An evaluation of the molecular clock hypothesis using mammalian DNA sequences.

Abstract: A statistical analysis of extensive DNA sequence data from primates, rodents, and artiodacytls clearly indicates that no global molecular clock exists in mammals. Rates of nucleotide subsitution in rodents are estimated to be four to eight times higher than those in higher primates and two to four times higher than those in artiodactyls. There is strong evidence for lower substitution rates in apes and humans than in monkeys, supporting the hominoid slowdown hypothesis. There is also evidence for lower rates in humans than in apes, suggesting a further rate slowdown in the human lineage after the separation of humans from apes. By contrast, substitution rates are nearly equal in mouse and rat. These results suggest that differences in generation time or, more precisely, in the number of germline DNA replications per year are the primary cause of rate differences in mammals. Further, these differences are more in line with the neutral mutation hypothesis than if the rates are the same for short-and long-living mammals.

Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases.

Abstract: Codon usage data for 56 Bacillus subtilis genes show that synonymous codon usage in B. subtilis is less biased than in Escherichia coli, or in Saccharomyces cerevisiae. Nevertheless, certain genes with a high codon bias can be identified by correspondence analysis, and also by various indices of codon bias. These genes are very highly expressed, and a general trend (a decrease) in codon bias across genes seems to correspond to decreasing expression level. This, then, may be a general phenomenon in unicellular organisms. The unusually small effect of translational selection on the pattern of codon usage in lowly expressed genes in B. subtilis yields similar dinucleotide frequencies among different codon positions, and on complementary strands. These patterns could arise through selection on DNA structure, but more probably are largely determined by mutation. This prevalence of mutational bias could lead to difficulties in assessing whether open reading frames encode proteins.

On Retrieving Analogues When Solving Problems

Abstract: After criticism of the precision of previous experimental procedures for testing analogue retrieval, a new procedure that overcomes the proposed inadequacies is described. This procedure is then em...

Magnetic properties of iron-rich Fe-Sc glasses.

Abstract: Amorphous ${\mathrm{Fe}}_{\mathrm{x}}$${\mathrm{Sc}}_{100\mathrm{\ensuremath{-}}\mathrm{x}}$ alloys with x=89, 90, and 91, prepared by melt spinning, exhibit a single sharp spin-freezing transition at 100\ifmmode\pm\else\textpm\fi{}3 K to an asperomagnetic state. The average $^{57}\mathrm{Fe}$ hyperfine field at 4.2 K is 22.7 T. Magnetization curves indicate that fields in excess of 20 T would be required to achieve saturation at 4.2 K and that the iron moment extrapolated to infinite field is 1.6${\ensuremath{\mu}}_{B}$. Hysteresis is found at low temperatures. On hydrogenation, the alloys become soft collinear ferromagnets with an iron moment of 2.2${\ensuremath{\mu}}_{B}$ and a Curie point of 310 K. A magnetic phase diagram is presented that summarizes the magnetic properties of a-${\mathrm{Fe}}_{\mathrm{x}}$${\mathrm{M}}_{100\mathrm{\ensuremath{-}}\mathrm{x}}$ systems (M=Sc,Y,Zr, or Hf). The behavior when M is a IIIb element (Sc,Y) is distinct from that when it is a IVb element (Zr,Hf), suggesting that the direct iron-iron exchange is frustrated by an indirect antiferromagnetic coupling in the IIIb alloys. Both groups tend to a common limit as x\ensuremath{\rightarrow}100. .AE

The zoogeographical distribution of Chironomidae (Insecta : Diptera)

Abstract: A review of present information on the zoogeography of Chironomidae at subfamily and generic levels is given. The known distribution, including some previously unpublished records, of all recognisable genera (307) and subgenera (56) is tabulated according to zoogeographical region. The greatest number of genera is known from the Nearctic (202) followed by the Palaearctic (187), Neotropical (109), Australasian (107), Afrotropical (104) and Oriental (100). The chironomid fauna of each zoogeographical region is discussed and a comparison of the number of known species and percentage representation of each subfamily for each region is given. An account of the distribution and ecology of each of the ten subfamilies is included. To date, some 3 700 species are described representing only 30 % of the estimated world chironomid fauna. The fossil record of the group is briefly discussed and the Chironomidae are estimated to be at least 200 million years old dating back to the Triassic period.

Methylene blue photosensitised strand cleavage of DNA: effects of dye binding and oxygen.

Abstract: It is shown that methylene blue (MB+) photosensitises DNA in either aerated or deaerated solutions, causing direct cleavage of phosphodiester bonds and rendering additional bonds labile to alkali. Evidence from unwinding and fluorimetric studies indicates that MB+ binds to DNA in at least 2 ways. Intercalation, which optimally induces helical unwinding of 24 degrees +/- 2 degrees per MB+, is markedly reduced upon neutralisation by Mg2+ of the DNA phosphates, while significant non-intercalative binding persists as shown by substantial fluorescence quenching at Mg2+ concentrations where there is little unwinding. MB+ induces photolysis at both low and high Mg2+ concentration - intercalation is apparently not required for photolysis. The quantum yield for strand breakage varies from 1-3 X 10(-7) under different conditions and is oxygen enhanced. The DNA cleavage is guanine specific. The 3' termini of the primary MB+-induced DNA photoproducts, unlike those generated by chemical sequencing retain an alkali labile adduct on the terminal phosphate.

The theory of the cohesive energies of solids

Abstract: The history of ideas concerning the cohesive energy of solids is sketched, and the recent rapid progress in this area is summarized. Reliable calculations based on first principles are now possible for a wide range of problems. This will significantly increase the predictive power of solid-state theory in the coming years.

Modeling Tetrahedrally Bonded Random Networks by Computer

Abstract: Publisher Summary The chapter presents a study on modeling of tetrahedrally bonded random networks by computer. The chapter presents an early example of such wooden balls, used in illustrating the diamond cubic structure. It offers us an appropriate introduction to the theme, because it is the first ball-and-stick model for a crystal, inspired by a notion of a preferred bonding arrangement, and one of special significance for the world today. In due course, such models became commonplace in both crystal and molecular physics. But in the subject of amorphous solids, the use of actual physical models was delayed until about 1970, and after that, many such models were built. Use was made of computers to relax and analyze models and, in a few cases, actually to construct them. Computational procedures offer great flexibility and power, once a satisfactory algorithm has been developed. The latter is, however, nontrivial. This chapter presents a review on the program of research in the development of such an algorithm for the case of tetrahedrally bonded amorphous solids, setting it in the context of previous and parallel efforts directed toward the same end. The chapter discusses several related concepts, including Guttman's method, bond transpositions, and initial randomization.

Clinical Features of Covert Toxocariasis

Abstract: The clinical features found in 14 children with toxocara ELISA titres of greater than or equal to 0.7 were compared with those found in 34 toxocara negative children. Blood eosinophils were elevated in 7 of the 14 patients and the highest eosinophilia was 14%. There was a highly significant association between hepatomegaly, cough, sleep disturbance and a raised titre (p less than 0.01). Behaviour disturbance, abdominal pain and headache were also significantly associated with a raised titre (p less than 0.05). The combination of abdominal pain, headache and cough was even more significantly associated with a high titre (p less than 0.0005) than were individual clinical features. It is suggested that in addition to the two well recognised clinical conditions of visceral larva migrans and ocular toxocariasis the clinical entity of covert toxocariasis should receive recognition. Eosinophilia may or may not be present in this condition.

Parallel gradualistic evolution of Ordovician trilobites

Abstract: There are very few high-resolution studies of the fossil record from which to assess the relative frequency of gradualistic and punctuated evolution. Here I report some of the first detailed evidence of phyletic gradualism in benthic macroinvertebrates, based on a study of ~15,000 trilobites from central Wales. Over a period of about three million years, as many as eight lineages underwent a net increase in the number of pygidial ribs, a species-diagnostic character. The end members of most lineages have previously been assigned1–3 to different species and, in one case, to different genera. In view of intermediate morphologies and temporary trend reversals, however, practical taxonomic subdivision of each lineage proved impossible. The apparent success of earlier Linnean nomenclature (with its implications of discrete species) could easily have been misinterpreted as evidence of punctuation and stasis, and it is probable that detection of many other gradualistic patterns has been hindered by ready application of binominal taxonomy to fossils.

Computer Simulation and Modelling

Abstract: Preface. Introduction an Overview. Systems. Models. Model Validation. Basic Probability and Statistics. Random Numbers and Random Variates. Discrete System Simulation. General Purpose Simulation System (GPSS). SIMSCRIPT. Simulation Experiments in Practice. Continuous System Simulation. Trends in Simulation. Index.

Ubiquitin genes as a paradigm of concerted evolution of tandem repeats

Abstract: Ubiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken,Xenopus, Drosophila, barley, and yeast have recently been determined. By analysis of these data we show that ubiquitin is evolving more slowly than any other known protein, and that this (together with its gene organization) contributes to an ideal situation for the occurrence of concerted evolution of tandem repeats. By contrast, there is little evidence of between-cluster concerted evolution. We deduce that in ubiquitin genes, concerted evolution involves both unequal crossover and gene conversion, and that the average time since two repeated units within the polyubiquitin locus most recently shared a common ancestor is approximately 38 million years (Myr) in mammals, but perhaps only 11 Myr inDrosophila. The extreme conservatism of ubiquitin evolution also allows the inference that certain synonymous serine codons differing at the first two positions were probably mutated at single steps.

The genetics and biochemistry of mercury resistance.

Abstract: (1987). The Genetics and Biochemistry of Mercury Resistance. CRC Critical Reviews in Microbiology: Vol. 15, No. 2, pp. 117-140.

Mother and Other Tongue Influence on Learner French: A Case Study.

Abstract: Recent perspectives on language transfer have highlighted the role of psychotypology and have given new life to Newmark's ignorance hypothesis. This paper examines such perspectives in the light of a body of data in French from a beginning learner of that language whose native language is English but who in addition has some knowledge of Irish, Latin, and Spanish. The fact that Spanish emerges as a privileged transfer source seems to point to a psychotypology factor, and certain distributional and contextual evidence appears to show that ignorance is in many cases triggering the transfers. However, because ignorance does not seem to explain all cases, some speculation is entered into, on the basis of clues in the data, regarding the role of memory codes in transfer.

Depressive attributional style: the role of self-esteem.

Abstract: Two studies evaluate the role of self-esteem in the depressive attributional style. In the first study, college students completed four measures of depression, four measures of self-esteem, and the Attributional Style Questionnaire (ASQ). Regression analyses revealed that across measures, self-esteem was a better predictor of attributional style for negative events than was depression. In study two, psychiatric inpatients completed a measure of self-esteem, a measure of depression, and the ASQ. In this clinical sample, self-esteem and depression were highly correlated and both predicted ASQ scores. But when variation in depth of depression and social desirability were removed statistically from the association between self-esteem and attributions for negative outcomes, there remained a significant association between self-esteem and internal, stable, and global attributions for negative outcomes. Controlling for the variation in self-esteem eliminated the relation between depression and depressive attributional style. These findings demonstrate the importance of self-esteem in depressive attributional style in both normal and clinical populations, as well as potential differences in the relations among self-esteem, depression, and attributional style in clinical versus normal samples.

A comparative study of transcutaneous electrical nerve stimulation (TENS), entonox, pethidine + promazine and lumbar epidural for pain relief in labor.

Abstract: Analgesic effect, labor outcome, safety and consumer satisfaction were compared in 170 primigravid women; 50 using TENS initially for pain relief, 20 using entonox, 50 pethidine + promazine and 50 lumbar epidural. 88% choosing epidural related it fully effective. 90% using entonox, 96% using TENS and 54% given pethidine + promazine found partial relief. 82% of patients given TENS and 80% given pethidine + promazine required additional analgesia. This was also needed by one of the 20 patients choosing entonox. Women using entonox alone had the shortest labors and women using lumbar epidural, the longest. Operative delivery was significantly more common in women receiving lumbar epidural. No significant inter-group differences were noted in cord pH or Apgar scores. Parturients and midwives both gave high consumer satisfaction ratings to all methods--except for pethidine + promazine, whose use must therefore be questioned. The analgesic efficacy of lumbar epidural outweighs any possible side effects. Entonox appears suited to those able to cope with the earlier part of labor, drug-free. Realization of the potential of TENS requires the design of machines specifically to cope with the quality of the pain of labor.

Mutants of elongation factor Tu promote ribosomal frameshifting and nonsense readthrough.

Abstract: This is the first report of ribosomal frameshifting promoted by mutants of the elongation factor Tu (EF-Tu). EF-Tu mutants can suppress both -1 and +1 frameshift mutations. The level of nonsense readthrough is also increased at some UGA (this paper) and UAG (Hughes, 1987) sites by these mutants. Suppression occurs when a mutant tuf allele is paired with a wild-type copy of the other tuf gene but is most efficient when both tuf genes are mutant. Frameshifting mediated by the tuf alleles studied, tufA8 and tufB103, is not general; indeed most frameshift mutations are not suppressed. Several possible mechanisms by which mutant EF-Tu may cause frameshifting are discussed.

Relationship among oxidative stress, growth cycle, and sporulation in Bacillus subtilis.

Abstract: The sensitivity of Bacillus subtilis to hydrogen peroxide (oxidative stress) was found to vary with the position of the culture in the growth cycle. The most dramatic change occurred at the stationary phase, when the cells became totally resistant to 10 mM H2O2, in contrast to the loss of 3 to 4 log units of viability when treated at the early log phase. Two of the eight proteins induced by a protective concentration of H2O2 (50 muM) were also induced (in the absence of oxidative stress) on entry into the late log phase of growth. The response of five isogenic spo0 mutants (spo0B, spo0E, spo0F, spo0H, and spo0J) to oxidative stress was identical to that of the wild-type parental strain. In an isogenic spo0A strain, mid-log-phase cells were 100-fold less sensitive to 10 mM H2O2 than was the wild type. Pretreatment with 50 microM H2O2 induced little further protection, suggesting that the response is constitutive in this strain. By comparison of proteins induced by 50 microM H2O2 in the wild-type, spo0A, spo0H, and spo0J strains, four proteins were identified that may be essential for protection against lethal concentrations of H2O2. The presence of multiple copies of the spo0H gene in a spo0A background converted the stress phenotype of the spo0A mutant to that of the wild type but left the sporulation phenotype unaltered.

Clinical pharmacokinetics and endocrine disorders. Therapeutic implications.

Abstract: Endocrine disorders are common and produce widespread changes in cellular and organ function. Alterations in the sensitivity of patients with thyroid disorders to digoxin, anticoagulants and sedatives have been recognised for many years. Many of the recently documented kinetic alterations in endocrine patients are explicable on the basis of disease-induced changes in hepatic drug metabolism, protein binding and renal function. In hyperthyroidism the rate of absorption of paracetamol, propranolol and oxazepam is increased due to increased gastrointestinal motility. The volume of distribution of propranolol and digoxin is increased and there is decreased binding of both basic and acidic drugs as a consequence of alterations in alpha 1-acid glycoprotein and albumin concentration. The rate of glucuronidation of paracetamol and oxazepam is increased in hyperthyroidism. While oxidative metabolism of antipyrine, propranolol, metoprolol and theophylline is enhanced, the clearance of a number of other agents, including diazepam, warfarin, antithyroid drugs and phenytoin, is unaltered. The systemic clearance of propranolol is enhanced as a consequence of a 50% increase in liver blood flow. The rate of elimination of a number of endogenous substances, including cortisol, thyroid hormones and insulin, also appear to be enhanced. Hyperthyroidism has a variable effect on renal function, with a possible increase in digoxin elimination, but no effect on the clearance of renally excreted beta-blockers, atenolol, sotalol and nadolol. These kinetic changes suggest that individualization and higher than normal dosage of propranolol is necessary to control hyperthyroidism, and in thyrotoxic atrial fibrillation higher doses of digoxin or additional therapy with beta-blockers, or verapamil, may be indicated. The increased sensitivity of thyrotoxic patients to warfarin suggest care with dosage and frequent monitoring of response are warranted. Less information is available concerning hypothyroidism, but there is a general trend for decreased absorption of paracetamol and propranolol. In addition, the volume of distribution of digoxin is reduced, as is renal clearance. Limited studies suggest no alteration in the glucuronidation of oxazepam, but antipyrine clearance appears to be reduced. Steady-state propranolol concentrations are elevated in hypothyroidism and there appears to be a decreased metabolism of thyroid hormones and cortisol. Preliminary information suggests the binding of propranolol is increased. Thus, in the treatment of hypothyroid patients, a lower dosage of propranolol may be required.(ABSTRACT TRUNCATED AT 400 WORDS)

Laser flash spectroscopy of methylene blue with nucleic acids

Abstract: Absorption spectra, fluorescence spectra and quantum yields, triplet state absorption spectra, yields and rates of decay have been obtained for methylene blue (MB+), MB+/CT-DNA complexes and complexes of MB+ with the synthetic polynucleotides poly[d(G-C)] and poly[d(A-T)]. Strong fluorescence quenching is observed in the complexes of the dye with CT-DNA and poly[d(G-C)] concomitant with a decrease in the triplet yield. The fluorescence and triplet yield of MB+ with poly[d(A-T)] are similar to those of the free dye. The triplet decay times are increased in all three polymer/dye complexes and show a decreased sensitivity to oxygen quenching. These results are interpreted in terms of the binding of the dye to these polymers and the implications of polymer binding on the photosensitizing properties of the dye are discussed.

Clinical growth standards for Irish children.

Abstract: A cross-sectional study, measuring height and weight, was performed on a representative sample of 3 509 Irish children aged from 5 to 19 years inclusive. Comparison with other countries showed a significantly later pubertal growth spurt than either the U.K. or the U.S. However, the final adult height and weight are similar to other countries as in the weight-for-height of children aged 5 to 9 years. The urban children are taller than the rural and the higher socio-economic groups are taller than the lower at all ages, but all achieved the same final adult height. Longitudinal tempo-conditional growth standards were constructed based on the Irish cross-sectional and menarche data together with all the available information from longitudinal studies. These charts are similar to those of the U.K., but the use of colours allows more information to be put on the charts, thus making them more suitable for clinical use.

Strouhal Numbers for Heat Exchanger Tube Arrays in Cross Flow

Abstract: The prediction of tube or acoustic resonance due to cross-flow in heat exchangers is dependent upon knowledge of the flow characteristics for a given tube array geometry. For this, a Strouhal number relating a peak frequency in the turbulence spectrum to the velocity of the flow is required. The data available in the literature for this are rather confusing and the prediction methods appear somewhat contradictory. This paper reports the results from experiments conducted to determine Strouhal numbers for eight tube array models. These results together with the data available in the literature are then compared and appropriate conclusions are drawn.