Showing papers by "Trinity College, Dublin published in 1992"

The complete DNA sequence of yeast chromosome III.

Abstract: The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.

Potato virus X as a vector for gene expression in plants

Abstract: The suitability of potato virus X (PVX) as a gene vector in plants was tested by analysis of two viral constructs. In the first, the GUS gene of Escherichia coli was substituted for the viral coat protein gene. In the second, GUS was added into the viral genome coupled to a duplicated copy of the viral promoter for the coat protein mRNA. The viral construct with the substituted coat protein gene accumulated poorly in inoculated protoplasts and failed to spread from the site of infection in plants. These results suggest a role for the viral coat protein in key stages of the viral infection cycle and show that gene replacement constructs are not suitable for the production of PVX-based gene vector. The construct with GUS coupled to the duplicated promoter for coat protein mRNA also accumulated less well in protoplasts than the unmodified PVX, but did infect systemically and directed high level synthesis of GUS in inoculated and systemically infected tissue. Although there was some genome instability in the PVX construct, much of the viral RNA in the systemically infected tissue had retained the foreign gene insertion, especially in infected Nicotiana clevelandii plants. These data point to a general utility of PVX as a vector for unregulated gene expression in plants.

Human infection by genetically diverse SIVsm-related HIV-2 in West Africa.

Abstract: Our understanding of the biology and origins of human immunodeficiency virus type 2 (HIV-2) derives from studies of cultured isolates from urban populations experiencing epidemic infection and disease. To test the hypothesis that such isolates might represent only a subset of a larger, genetically more diverse group of viruses, we used nested polymerase chain reactions to characterize HIV-2 sequences in uncultured mononuclear blood cells of two healthy Liberian agricultural workers, from whom virus isolation was repeatedly unsuccessful, and from a culture-positive symptomatic urban dweller. Analysis of pol, env and long terminal repeat regions revealed the presence of three highly divergent HIV-2 strains, one of which (from one of the healthy subjects) was significantly more closely related to simian immunodeficiency viruses infecting sooty mangabeys and rhesus macaques (SIVSM/SIVMAC) than to any virus of human derivation. This subject also harboured multiply defective viral genotypes that resulted from hypermutation of G to A bases. Our results indicate that HIV-2, SIVSM and SIVMAC comprise a single, highly diverse group of lentiviruses which cannot be separated into distinct phylogenetic lineages according to species of origin.

Metabotropic glutamate receptors: electrophysiological properties and role in plasticity.

Abstract: Electrophysiological research on mGluRs is now very extensive, and it is clear that activation of mGluRs results in a large number of diverse cellular actions. Studies of mGluRs and on ionic channels has clearly demonstrated that mGluR activation has a widespread and potent inhibitory action on both voltage-gated Ca2+ channels and K+ channels. Inhibition of N-type Ca2+ channels, and inhibition of Ca++-dependent K+ current, IAHP, and IM being particularly prominent. Potentiation of activation of both Ca2+ and K+ channels has also been observed, although less prominently than inhibition, but mGluR-mediated activation of non-selective cationic channels is widespread. In a small number of studies, generation of an mGluR-mediated slow excitatory postsynaptic potential has been demonstrated as a consequence of the effect of mGluR activation on ion channels, such as activation of a non-selective cationic channels. Although certain mGluR-modulation of channels is a consequence of direct G-protein-linked action, for example, inhibition of Ca2+ channels, many other effects occur as a result of activation of intracellular messenger pathways, but at present, little progress has been made on the identification of the messengers. The field of study of the involvement of mGluRs in synaptic plasticity is very large. Evidence for the involvement of mGluRs in one form of LTD induction in the cerebellum and hippocampus is now particularly impressive. However, the role of mGluRs in LTP induction continues to be a source of dispute, and resolution of the question of the exact involvement of mGluRs in the induction of LTP will have to await the production of more selective ligands and of selective gene knockouts.

Communication and Problematic Integration: Understanding Diverging Probability and Value, Ambiguity, Ambivalence, and Impossibility

Abstract: This essay examines the interplay of communication and the basic human need to integrate probabilistic and evaluative orientations. The analysis focuses on communication in four experiences where it is difficult to satisfy the need: diverging probability and evaluation (e.g., unlikely happiness or likely sorrow), ambiguity, ambivalence, and impossibility. The aims are to (a) present a rudimentary theory of communication and the problematic integration of probability and evaluation, and (b) establish the significance of the interplay of communication and problematic integration. In so doing, the essay offers a set of ideas that synthesizes and extends understandings of a wide range of communicative phenomena, from the mundane (commiserating on day-to-day concerns) to the momentous (debates about war and peace), from the idiosyncratic (coping styles) to the common (dynamics of attitude change), and from the intimate (parent-child relations) to the mass public (responding to natural disaster).

Topographic and Magnetic-Sensitive Scanning Tunneling Microscope Study of Magnetite

Abstract: The topographic and magnetic surface structure of a natural single crystal of magnetite (Fe304), a common mineral, has been studied from the submicrometer scale down to the atomic scale with a scanning tunneling microscope having nonmagnetic tungsten as well as ferromagnetic iron probe tips. Several different (001) crystal planes were imaged to atomic resolution with both kinds of tips. A selective imaging of the octahedrally coordinated Fe B-sites in the Fe-O planes, and even a selective imaging of the different magnetic ions Fe2+ and Fe3+, has been achieved, demonstrating for the first time that magnetic imaging can be realized at the atomic level.

Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae

Abstract: Codon usage in a sample of 28 genes from the pathogenic yeast Candida albicans has been analysed using multivariate statistical analysis. A major trend among genes, correlated with gene expression level, was identified. We have focussed on the extent and nature of divergence between C.albicans and the closely related yeast Saccharomyces cerevisiae. It was recently suggested that significant differences exist between the subsets of preferred codons in these two species [Brown et al. (1991) Nucleic Acids Res. 19, 4293]. Overall, the genes of C.albicans are more A + T-rich, reflecting the lower genomic G + C content of that species, and presumably resulting from a different pattern of mutational bias. However, in both species highly expressed genes preferentially use the same subset of 'optimal' codons. A suggestion that the low frequency of NCG codons in both yeast species results from selection against the presence of codons that are potentially highly mutable is discounted. Codon usage in C.albicans, as in other unicellular species, can be interpreted as the result of a balance between the processes of mutational bias and translational selection. Codon usage in two related Candida species, C.maltosa and C.tropicalis, is briefly discussed.

Genetic evidence that bound coagulase of Staphylococcus aureus is not clumping factor.

Abstract: Staphylococcus aureus Newman cells carry a surface receptor for fibrinogen called clumping factor. The bacteria also express coagulase, an extracellular protein that binds to prothrombin to form a complex with thrombinlike activity which coverts fibrinogen to fibrin. We have confirmed a recent report (M. K. Boden and J.-I. Flock, Infect. Immun. 57:2358-2363, 1989) that coagulase can bind to fibrinogen as well as to prothrombin and also that a fraction of coagulase is firmly attached to the cell. A mutant with a deletion in the chromosomal coa gene was isolated by allelic replacement. Allelic replacement either was directly selected by electrotransformation of S. aureus R3N4220 with a nonreplicating suicide plasmid, pCOA18, carrying the delta coa::Tcr mutation or occurred after transduction of the integrated pCOA18 plasmid. The coa mutant was completely devoid of coagulase activity but interacted both with soluble fibrinogen and with solid-phase fibrinogen with the same avidity as the parental strain. This strongly suggests that the bound form of coagulase is not clumping factor and is not responsible for the adherence of S. aureus Newman to solid-phase fibrinogen. The fibrinogen binding determinant of coagulase was located in the C terminus of the protein, by analyzing truncated fusion proteins, in contrast to the prothrombin-binding region which was located in the N terminus.

The mitochondrion in bloodstream forms of Trypanosoma brucei is energized by the electrogenic pumping of protons catalysed by the F1F0-ATPase

Abstract: Bloodstream forms of Trypanosoma brucei were found to maintain a significant membrane potential across their mitochondrial inner membrane (delta psi m) in addition to a plasma membrane potential (delta psi p). Significantly, the delta psi m was selectively abolished by low concentrations of specific inhibitors of the F1F0-ATPase, such as oligomycin, whereas inhibition of mitochondrial respiration with salicylhydroxamic acid was without effect. Thus, the mitochondrial membrane potential is generated and maintained exclusively by the electrogenic translocation of H+, catalysed by the mitochondrial F1F0-ATPase at the expense of ATP rather than by the mitochondrial electron-transport chain present in T. brucei. Consequently, bloodstream forms of T. brucei cannot engage in oxidative phosphorylation. The mitochondrial membrane potential generated by the mitochondrial F1F0-ATPase in intact trypanosomes was calculated after solving the two-compartment problem for the uptake of the lipophilic cation, methyltriphenylphosphonium (MePh3P+) and was shown to have a value of approximately 150 mV. When the value for the delta psi m is combined with that for the mitochondrial pH gradient (Nolan and Voorheis, 1990), the mitochondrial proton-motive force was calculated to be greater than 190 mV. It seems likely that this mitochondrial proton-motive force serves a role in the directional transport of ions and metabolites across the promitochondrial inner membrane during the bloodstream stage of the life cycle, as well as promoting the import of nuclear-encoded protein into the promitochondrion during the transformation of bloodstream forms into the next stage of the life cycle of T. brucei.

Implications of life‐history strategies for a new wrasse fishery

Abstract: The variety of life-history patterns exhibited by the five species of wrasse common in Northern Europe are reviewed. The two larger wrasse species, the ballan, Labrus bergylta Ascanius, and cuckoo, Labrus mixtus (L.), are exploited through sport angling. The three smaller species, the corkwing, Symphodus (Crenilabrus) melops (L.), rock cook, Centrolabrus exoletus (L.) and goldsinny, Ctenolabrus rupestris (L.), are being exploited by a new fishery for use as parasite cleaners of farmed salmon. The nature of salmon farming limits the wrasse fishery to a minimum size, restricted areas and the warmer months of the year. The fishery may be expected to alter population structure through selective removal of larger fish. Removal of dominant territorial males may affect social structures and removal of nest-guarding males would reduce egg survival. Quantitative models incorporating stock size and fishery requirements are now required.

Dynamics of distribution in animal communities: Theory and analysis

Abstract: Theoretical and analytical problems of the dynamics of distribution and abundance in animal communities were examined In many communities, species with low abundance and of limited spatial occurrence (ie, rare species) typically form a conspicuous peak when a frequency distribution of the number of species is constructed with respect to the proportion of sites occupied within an area of distribution Models of distribution dynamics, including a new model proposed here, were compared with a range of animal community data using a new procedure to assess single- and bi-modal patterns in frequency distributions of spatial occurrence Data reveal that single-modality with an excess of rare species occurs more frequently than bimodality Even when bimodality is detected, the mode representing wide-spread species is in the majority of cases smaller than that for rare species Thus, a new model in which the rate of local extinctions is assumed to be negatively related to patch occupancy (or population abundance) is in better agreement with observed data than earlier models Some problems of analysis, in particular model assumptions and testing, are discussed

Treatment resistance of depression after head injury: a preliminary study of amitriptyline response.

Abstract: Thirteen patients with depression following minor head injury were matched with 13 functional depressives. Both groups were indistinguishable psychopathologically. Five of the functional group had a family history of affective disorder and none of the head-injury group had such a history. Both groups were treated with amitriptyline, beginning with 100 mg daily, increasing to a maximum of 250 mg/d. There were significant differences in response between the 2 groups, with only 4 of the head-injury patients improving. Our preliminary results suggest that this condition is relatively resistant to tricyclic therapy.

Perceptions and Metaperceptions of Leadership: Components, Accuracy, and Dispositional Correlates

Abstract: This research examined the components of leadership perceptions and metaperceptions in mixed-sex, problem-solving groups. A social relations analysis indicated that leadership perceptions were highly consensual. Perceivers similarly differentiated targets' leadership using similar behavioral cues and observable characteristics. Approximately 91% of the variance in perceivers' consensual judgments of targets' leadership was explained by quantity of targets' speech, quality of ideas, and friendliness. Leadership perceptions correlated reliably with targets'selfperceptions on leadership and revealed target accuracy. Also, targets knew how perceivers, in general, judged their leadership, yielding evidence of accurate metaperception. Perceptions and metaperceptions were correlated zLith target gender and endorsement of stereotypic masculine andfeminine traits. These data were consistent with a social role model which assumes that differential gnder expectancies affect behavior, perceivers'judgments of targets,...

Osmotic and growth-phase dependent regulation of the eta gene of Staphylococcus aureus: a role for DNA supercoiling.

Abstract: Transcriptional fusions were constructed between the promoter for the epidermolytic toxin A (eta) gene of Staphylococcus aureus and the luxAB and xylE reporter gene systems. The expression of the fusion products was found to be dependent upon the accessory gene regulator (agr) locus and was observed to increase significantly during the transition from the exponential to the stationary phase of growth. Furthermore the expression of the eta gene promoter was found to be osmotically regulated, with the expression levels of the eta fusions being inversely related to the osmolyte levels. The ability of environmental factors to influence DNA topology (and thence gene expression) was investigated. High osmolarity (0.7 M NaCl) resulted in an increase in the degree of negative supercoiling of plasmid DNA in the S. aureus strain 8325-4 (Agr+) but not in strain ISP546 (Agr−). Furthermore the eta promoter was strongly induced in S. aureus cultures grown in the presence of sub-inhibitory concentrations of novobiocin, a DNA gyrase inhibitor. However this induction was independent of agr, suggesting that the eta promoter is subject to both agr-dependent (osmolarity, growth phase) and -independent (DNA topology) regulatory processes.

Magnetic imaging at the atomic level

Abstract: Magnetic contrast at the atomic level has been observed for the first time in scanning tunneling microscopy experiments on a magnetite (Fe3O4(001)) surface using in-situ prepared ferromagnetic Fe tips. A periodic corrugation with a 12 A periodicity is clearly observed along the rows of FeB-sites which corresponds to the repeat period of Fe2+ and Fe3+ along these rows. This periodicity is not observed by using non-magneticW tips although the rows of FeB-sites can be resolved as well. The magnetic contrast observed with Fe tips is attributed to the different spin configurations of the magnetic ions Fe2+ and Fe3+ in Fe3O4.

Roles of selection and recombination in the evolution of type I restriction-modification systems in enterobacteria.

Abstract: Restriction-modification systems can protect bacteria against viral infection Sequences of the hsdM gene, encoding one of the three subunits of type I restriction-modification systems, have been determined for four strains of enterobacteria Comparison with the known sequences of EcoK and EcoR124 indicates that all are homologous, though they fall into three families (exemplified by EcoK, EcoA, and EcoR124), the first two of which are apparently allelic The extent of amino acid sequence identity between EcoK and EcoA is so low that the genes encoding them might be better termed pseudoalleles; this almost certainly reflects genetic exchange among highly divergent species Within the EcoK family the ratio of intra- to interspecific divergence is very high The extent of divergence between the genes from Escherichia coli K-12 and Salmonella typhimurium LT2 is similar to that for other genes with the same level of codon usage bias In contrast, intraspecific divergence (between E coli strains B and K-12) is extremely high and may reflect the action of frequency-dependent selection mediated by bacteriophages There is also evidence of lateral transfer of a short sequence between E coli and S typhimurium

Ecological impact of crayfish plague in Ireland

Abstract: Freshwater crayfish are key members of aquatic communities due to their large size and abundance. Although most commonly regarded as herbivores and detritivores, they are also selective predators. The crayfish plague fungus Aphanomyces astaci (Schikora) led to the elimination of a stock of white-clawed crayfish, Austropotamobius pallipes (Lereboullet) from Lough Lene, Co. Westmeath, in 1987. Samples taken of the flora and benthic communities of two Irish lakes, one (Lough Bane) formerly containing crayfish and the other (Lough Lene) immediately following a plague outbreak, were compared to similar samples taken a year later and ecological shifts were noted and compared to laboratory feeding results. Over time, Chara strands increased in mean length, and molluscs became more abundant.

Deletions in exon 5 of the human rhodopsin gene causing a shift in the reading frame and autosomal dominant retinitis pigmentosa.

Abstract: By screening patients with autosomal dominant retinitis pigmentosa for mutations in the rhodopsin gene, two deletions (8 bp and 1 bp) have been identified in exon 5; these deletions cause a shift in the reading frame. The predicted proteins should be radically altered with translation continuing past the normal stop signal and resulting in a rhodopsin molecule that is, respectively, 1 and 10 amino acids longer. The clinical phenotype of the patients is described and is compared with that associated with other mutations in the same region of the gene.

Lipoprotein(a) in cirrhosis.

Abstract: of these four dosing periods the subjects received concurrent treatment with placebo, ranitidine 150 mg twice a day, ranitidine 600 mg twice a day, or ranitidine 300 mg four times a day, each given simultaneously with aspirin. All subjects received each prophylactic regimen. During each treatment period the subjects were allowed to eat only at 9 am, 2 pm, 8 pm, and midnight. Half the subjects always took drugs at the same time as food. The other half always took their drugs two hours before food (at 7 am, midday, 6 pm, and 10 pm). The order in which subjects received the different treatment regimens was randomised by Latin square design. There was a washout period of nine days between each treatment regimen. Subjects were studied in the morning, approximately eight hours after the last doses had been taken. Spontaneous microbleeding was measured as previously described,4 followed by unsedated endoscopy with a paediatric endoscope, when erosions in the body, antrum, and duodenum were counted. Statistical analysis was by two way analysis of variance, with treatment and timing of dose in relation to food as the determining variables. Aspirin increased the number of gastric erosions from none at baseline to a median of 10-6 (drugs given with food) or 12 8 (drugs given before food) (figure). Ranitidine reduced the total number of gastric erosions in a dose dependent fashion when the drugs were taken two hours before food (p=0006), but had no effect when taken with food. Overall, taking drugs before food was associated with a significant reduction in mucosal injury (p=0003) in comparison to taking them with food.

Autosomal dominant retinitis pigmentosa: a novel mutation in the rhodopsin gene in the original 3q linked family.

Abstract: Retinitis Pigmentosa (RP) describes a heterogeneous group of retinopathies primarily involving photoreceptor degeneration (1). Linkage studies have enabled the localisation of disease causing genes. Two RP genes have been mapped to Xp (2). The first autosomal gene mapped to 3q, close to the gene encoding the photoreceptor cell specific pigment rhodopsin (1). Mutations within the rhodopsin gene have now been implicated in both autosomal dominant (adRP) and autosomal recessive (arRP) forms of RP (1, 3). More recently, an adRP gene has been localised to 6p, close to the gene encoding the photoreceptor protein peripherin/RDS (1). Mutations in this gene have been shown to co-segregate with the disease phenotype in a number of adRP families (4—6). Still further heterogeneity exists within adRP. It has been well established that there is an adRP locus at the pericentric region of chromosome 8 (7). There is also weak evidence for the involvement of a second adRP gene on 3q (8). We have now identified a new rhodopsin mutation in the original family (TCDM1) used to localise the first adRP gene to 3q. Using heteroduplex analysis (9), we observed that heteroduplex DNA was present in only affected individuals in DNA fragments amplified from exon 3 of the rhodopsin gene. Direct genomic sequencing revealed that this was due to a T—G base change at codon 207, which results in the substitution of a methionine residue for an arginine residue. Using an allele specific oligonucleotide based assay, we established that the disease phenotype and the mutation were co-inherited (Figure 1), with a maximum Lod score of 17.7 at zero recombination (Table la). We tested 100 normal unrelated individuals for the presence of this mutation and found that it was absent in all these controls. This finding is of particular interest in view of weak evidence suggesting the possible involvement of a second adRP locus on 3q (8). Using rhodopsin mutations in adRP families as highly polymorphic markers Inglehearn and colleagues observed 12% recombination (0 = 0.12, Z = 4.5) between the rhodopsin gene and the marker (D3S47) on 3q. They suggested that the presence of some families in which no rhodopsin mutations had been found but which showed tight linkage between adRP and D3S47 was consistent with the hypothesis that there may be a second adRP locus on 3q. Our recent identification of a rhodopsin mutation in TCDM1 must lend some doubt to the suggestion of two adRP loci on 3q, which was based on families such as this one. The clinical presentation of adRP in the TCDM1 family is of particular interest due to the uncharacteristically early onset of the disease when compared to other well documented adRP patients (10). Affected members exhibited onset of the disease within the first decade of life, diffuse funduscopic disturbances, and extinguished rod photoreceptor cell responses as assessed by ERGs. However ERG cone responses were retained until the third decade, although significantly reduced in amplitude and delayed in latency. Two colour dark adaptometry indicated a diffuse loss of rod and cone photoreceptor sensitivity with a greater involvement of rods and hence mirrored the electroretinographic findings. The mutations observed within the rhodopsin gene and implicated in human inherited retinopathies have an extremely broad clinical spectrum. We can use previously constructed models of rhodopsin to speculate on the structure/function relationships of mutant rhodopsin molecules and hence possibly gain some insights into the underlying basis of the wide clinical spectrum observed in rhodopsin linked RP. There is a considerable body of data from protein chemistry and site-directed mutagenesis which can be amalgamated to provide a crude representation of the 3-D structure of rhodopsin. Such approaches can never provide a detailed description of the conformation of the protein but they can augment our understanding of its structure and provide a model for investigating it's mechanisms of action. From such studies it is possible to speculate on the importance of the Met 207 — Arg substitution. There are two feasible scenarios. The first is that the methionine side-chain is exposed to the hydrophobic environment of the bilayer or is the interface between two transmembrane segments. Substitution by an arginine would seriously perturb folding either by destabilising the protein with a potentially charged residue to the hydrophobic phase or by a bulky polar residue at a helix-helix surface. An alignment of all rhodopsin sequences in this region indicates that Met 207 can be substituted by other hydrophobic residues and by Tyrosine (Table lb). At first sight then, one could suppose that the residue is not critical to the intersegment contacts and could therefore be exposed to lipid.

Comparative Study of Subgingival Microbiological Sampling Techniques

Abstract: The presence of specific bacteria in subgingival plaque has been used as an indicator of active periodontal disease. The technique of subgingival sampling may conjecturally influence the identification and enumeration of microorganisms reported. In this study, paper point sampling and sealer sampling are compared. Subgingival samples using both methods were taken from three surfaces in each of 12 patients at the following time points: at each of two appointments one week apart before treatment and at each of two appointments 12 and 13 weeks following treatment. Microbiological analyses were undertaken to determine the total number of colony forming units, the proportions of suspected periodontal pathogens, and the number of spirochetes using phase contrast microscopy. Significantly higher numbers of colony forming units and spirochetes were found for paper point sampling both before and after treatment. J Periodontol 1992; 63: 797–801.