Showing papers by "University College Cork published in 1997"

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

Abstract: CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.

The Behavior of Organisms

Abstract: The term & #x2018;organism & #x2018; enjoys a revered place within the vocabulary of behavior analysis, most notably perhaps within the title of Skinner’s seminal work (The Behavior of Organisms, 1938). The exact status of this term, however, is unclear. For instance, the term does not appear to be a technical one. Nevertheless, its widespread use in the behavior-analytic literature suggests that it is masquerading as such. The present paper appraises the scientific utility of the term & #x2018;organism’ within the domain of behavior analysis and discusses some possible reasons for its widespread use.

Dietary fibres: Nutritional and technological interest

Abstract: Dietary fibres are consumed from cereals, fruit and vegetables, but are also added in purified form to food preparations. Different types of dietary fibres have different structures and chemical compositions, and correspondingly are of varying nutritional and technological interest. Although many studies have confirmed the nutritional benefits of dietary fibres, the results depend on the types of dietary fibres studied or on the experimental conditions used. This article also focuses on their technological properties according to their botanical origin and physical characteristics, and discusses the main appli cations of insoluble dietary fibres in the food industry.

In vitro contracture test for diagnosis of malignant hyperthermia following the protocol of the European MH Group: Results of testing patients surviving fulminant MH and unrelated low-risk subjects

Abstract: Background: Determination of sensitivity and specificity of the in vitro contracture test (IVCT) for malignant hyperthermia (MH) susceptibility using the European MH Group (EMHG) protocol has been performed in some laboratories but only on a small sample from the combined EMHG. Thus, the purpose of the present study was to determine combined EMHG sensitivity and specificity of the test. Methods: Results of IVCT of patients with previous fulminant MH and normal, low-risk subjects (controls) were collected from 22 centresof the EMHG. IVCT was performed according to the EMHG protocol. Patients were included inthe study if the clinical crisis had a score of at least 50 points with the Clinical Grading Scale. Low-risk subjects were included provided they did not belong to a family with known MH susceptibility, they had not developed any signs of MH at previous anaesthetics, and they did not suffer from any neuromuscular disease. For inclusion of both MH patientsand low-risk subjects, at least 1 muscle bundle in the IVCT should have twitches of 10 mN(1 g) or more. For evaluation of individual tests, only muscle bundles with twitch heights of 10 mN (1 g) or more were used. Results: A total of 1502 probands had undergone IVCT because of a previous anaesthesia with symptoms and signs suggestive of MH. Of these, 119 had clinical scores of 50 and above. From these 119 MH-suspected patients and from 202 low-risk subjects, IVCT data were collected. Subsequently, 14 MH-suspected patients were excluded from further analysis for thefollowing reasons: In 3 patients, the suspected MH episode could be fully explained by diseases other than MH; in 11 MHS patients, IVCT was incomplete (n=l), data were lost (n=3), or none of the muscle bundles fulfilled twitch criteria (n=7). Of the remaining 105 MH-suspected patients, 89 were MHS, 10 MHEh, 5 MHEc, and one MHN. Thus, we observed a diagnostic sensitivity of the IVCT of 99.0% if the MHE group is considered susceptible(95% confidence interval 94.8–100.0%). Of the 202 low-risk subjects, 3 were MHS, 5 MHEh, 5 MHEc, and 189 MHN. This gives a specificity of the IVCT of 93.6% (95% confidence interval 89.2–96.5%). Conclusion: The IVCT for diagnosis of MH susceptibility in Europe has a high sensitivity and a satisfactory specificity.

The use of systems development methodologies in practice: a field study

Abstract: This paper discusses the findings of a field study of experienced systems developers which investigated the use of systems development methodologies (SDMs) in practice. Among the main findings to emerge are the following. There is a wide difference between the formalized sequence of steps and stages prescribed by a methodology and the methodology-in-action uniquely enacted for each development project. Also, there is much evidence which suggests that developers omit certain aspects of methodologies not from a position of ignorance, but from the more pragmatic basis that certain aspects are not relevant to the development environment they face. Thus, methodologies are tailored to the needs of the prevailing development environment and, being documented in a single manual often, are framed at a higher level of granularity that specifies broad activities and objectives, rather than specifying in a very detailed fashion the exact manner in which development should take place. Additionally, the findings clarify the apparently contradictory position in the literature as to whether developer experience is positively or negatively correlated with methodology use. The study would suggest that experienced developers are likely to use methodologies, albeit ones which have been heavily customized to the exigencies of the particular situation.

The electrochemistry of gold: I the redox behaviour of the metal in aqueous media

Abstract: Gold is frequently regarded as the ideal metal for the investigation of solid electrode behaviour, which in aqueous media is often considered in very simplistic terms as being that of a metal which is highly resistant to dissolution. Gold possesses very weak chemisorbing properties and an extensive double layer region that in the presence of most pure electrolytes is often assumed to be totally free of Faradaic behaviour, and exhibits a monolayer (or Au2O3) oxide formation/removal reaction at quite positive potentials. However, recent investigations have revealed that the electrochemistry of polycrystalline gold in aqueous solution is considerably more complex. Two significantly different types of oxide deposits, monolayer (or α) and hydrous (or β), may be produced on the metal and the behaviour of the β-deposit is quite unusual. It is suggested that not only the behaviour of the β-oxide but, far more important from a practical viewpoint, the catalytic and electrocatalytic behaviour of gold (which will be discussed in more detail in Part II) may be rationalized in terms of the active state (or states) of gold. This active state (frequently present only at very low coverage) reacts in a manner that is quite different from that of stable gold. The nature of the active state of gold deserves far more attention than it has received to date.

Biological control of Pythium ultimum by Stenotrophomonas maltophilia W81 is mediated by an extracellular proteolytic activity

Abstract: Stenotrophomonas maltophilia strain W81, isolated from the rhizosphere of field-grown sugar beet, produced the extracellular enzymes chitinase and protease and inhibited the growth of the phytopathogenic fungus Pythium ultimum in vitro. The role of these lytic enzymes in the interaction between W81 and P. ultimum was investigated using Tn5 insertion mutants of W81 incapable of producing extracellular protease (W81M1), extracellular chitinase (W81M2) or the two enzymes (W81A1). Lytic enzyme activity was restored in W81A1 following introduction of a 15 kb cosmid-borne fragment of W81 genomic DNA. Incubation of P. ultimum in the presence of commercial purified protease or cell-free supernatants from cultures of wild-type W81, the chitinase-negative mutant W81M2 or the complemented derivative W81A1 (pCU800) resulted in hyphal lysis and loss of subsequent fungal growth ability once re-inoculated onto fresh plates. In contrast, commercial purified chitinase or cell-free supernatants from cultures of the protease-negative mutant WS1M1 or the chitinase- and protease-negative mutant W81A1 had no effect on integrity of the essentially chitin-free Pythium mycelium, and did not prevent subsequent growth of the fungus. In soil microcosms containing soil naturally infested by Pythium spp., strains W81, W81M2 and W81A1(pCU800) reduced the ability of Pythium spp. to colonize the seeds of sugar beet and improved plant emergence compared with the untreated control, whereas W81A1 and W21M1 failed to protect sugar beet from damping-off. Wild-type W81 and its mutant derivatives colonized the rhizosphere of sugar beet to similar extents, it was concluded that the ability of S. maltophilia W81 to protect sugar beet from Pythium -mediated damping-off was due to the production of an extracellular protease.

A transformation of respondently conditioned stimulus function in accordance with arbitrarily applicable relations

Abstract: Adult male subjects saw a sexual film clip paired with a nonsense syllable (C1). Similarly, an emotionally neutral film clip was paired with a second nonsense syllable (C3). Responses to the nonsense syllables were recorded as skin resistance responses. Subjects were also trained in a series of related conditional discriminations, using the C1 and C3 stimuli, from which the following equivalence relations were predicted; A1-B1-C1, A2-B2-C2, and A3-B3-C3. Some subjects were given matching-to-sample (equivalence) tests after the conditional discrimination training (Experiment 1), whereas others were not (Experiment 2). Subjects were tested for a transformation of eliciting functions by presenting the A1 and A3 stimuli, which were related through equivalence to C1 and C3, respectively. Five of the 6 subjects who showed significantly greater conditioned responses to C1 than to C3, also showed significantly greater skin resistance responses to A1 than to A3. Two additional subjects demonstrated a transformation of an eliciting stimulus function in accordance with five-member equivalence relations (Experiment 3), and another 5 subjects demonstrated similar effects in accordance with the relations of sameness and opposition (Experiment 4).

Chemical methods for the characterization of proteolysis in cheese during ripening

Abstract: La proteolyse, qui est le phenomene principal et le plus complexe intervenant dans la maturation de la plupart des fromages, a ete le sujet de nombreuses etudes. Toute une gamme de techniques analytiques a ete developpee afin de permettre une meilleure comprehension de ce phenomene. Les methodes de suivi de la proteolyse peuvent etre classees en deux grands chapitres, traites dans cette revue : les techniques non specifiques, et les techniques specifiques. Les techniques non specifiques incluent la quantification de l'azote soluble dans les divers extraits, et s'interessent aussi a la liberation des groupements reactifs. Les techniques specifiques, principalement la chromatographie ou l'electrophorese, sont celles permettant de separer les peptides ou les acides amines libres. Ces diverses techniques sont souvent combinees dans la strategie de purification de la fraction azotee du fromage afin de pouvoir isoler individuellememt les peptides. Les methodes d'identification des peptides, ainsi que les differentes strategies de suivi de proteolyse dans diverses varietes de fromages sont discutees dans cette revue.

RAGA: RNA sequence alignment by genetic algorithm

Abstract: We describe a new approach for accurately aligning two homologous RNA sequences when the secondary structure of one of them is known. To do so we developed two software packages, called RAGA and PRAGA, which use a genetic algorithm approach to optimize the alignments. RAGA is mainly an extension of SAGA, an earlier package for multiple protein sequence alignment. In PRAGA several genetic algorithms run in parallel and exchange individual solutions. This method allows us to optimize an objective function that describes the quality of a RNA pairwise alignment, taking into account both primary and secondary structure, including pseudoknots. We report results obtained using PRAGA on nine test cases of pairs of eukaryotic small subunit rRNA sequence (nuclear and mitochondrial).

Isolation and identification of further peptides in the diafiltration retentate of the water-soluble fraction of Cheddar cheese

Abstract: Several peptides were isolated from the diafiltration retentate, prepared using 10 kDa membranes, of the water-soluble extract from a commercial mature Cheddar cheese and identified by amino acid sequencing and mass spectrometry. Most of the peptides were from the N-terminal half of the beta-casein, but peptides from alpha s1- and alpha s2-caseins were also identified; the extract also contained alpha-lactalbumin. Identified peptides showed the important role played by lactococcal cell envelope proteinases in the degradation of primary proteolytic products from alpha s1- and beta-caseins, produced by chymosin and plasmin respectively. Plasmin seemed to be involved in the hydrolysation of alpha s2-casein. Several phosphopeptides were identified and the action of phosphatase on these peptides was evident.

Two groups of bacteriophages infecting Streptococcus thermophilus can be distinguished on the basis of mode of packaging and genetic determinants for major structural proteins.

Abstract: A comparative study of 30 phages of Streptococcus thermophilus was performed based on DNA restriction profiles, DNA homology, structural proteins, packaging mechanisms, and host range data. All phages exhibited distinct DNA restriction profiles, with some phages displaying similarly sized restriction fragments. DNA homology was shown to be present among all 30 phages. The phages could be divided into two groups on the basis of their packaging mechanism as was derived from the appearance of submolar DNA fragments in restriction enzyme digests and the presence (cos-containing phages) or absence (pac-containing phages) of cohesive genomic extremities. Interestingly, the 19 identified cos-containing phages possessed two major structural proteins (32 and 26 kDa) in contrast to the remaining 11 pac-containing phages, which possessed three major structural proteins (41, 25, and 13 kDa). Southern hybridization demonstrated that all pac-containing phages tested contain homologs of the genes encoding the three major structural proteins of the pac-containing phage O1205, whereas all cos-containing phages tested exhibit homology to the gene specifying one of the structural components of the cos-containing phage phi 7201. Fifty-seven percent of the phages (both cos and pac containing) possessed the previously identified 2.2-kb EcoRI fragment of the temperate S. thermophilus phage Sfi18 (H. Brussow, A. Probst, M. Fremont, and J. Sidoti, Virology 200:854-857, 1994). No obvious correlation was detected between grouping based on packaging mechanism and host range data obtained with 39 industrial S. thermophilus strains.

Dietary Vegetable Oils and α-Tocopherol Reduce Lipid Oxidation in Rabbit Muscle

Abstract: This experiment was conducted to study the effect of dietary vegetable oil on lipid oxidation in rabbit muscle. A control diet with no added fat and two diets with olive or sunflower oil (30 g/kg) were used. Within each treatment, one group was fed a low level of alpha-tocopheryl acetate (10 mg/kg diet), and the other a supplemental level (200 mg/kg). Rabbits were fed experimental diets from weaning (20 d) to slaughter (69 d). The supplemental level of dietary alpha-tocopheryl acetate produced higher alpha-tocopherol concentration in muscle (P < 0.006) and lower lipid oxidation (P < 0.004). Rabbits that received sunflower oil had higher concentrations of thiobarbituric acid reactive substances than rabbits that consumed olive oil (P < 0.05). Moreover, a significant effect due to fat inclusion in the diet was found. Muscles from rabbits fed diets not enriched with fat had higher susceptibility to lipid oxidation (P < 0.005) and higher concentration of (n-3) fatty acids in polar lipids (P < 0.04) than those from rabbits fed fat-enriched diets. A second experiment was conducted and confirmed the higher lipid oxidation in the muscle of rabbits fed diets not enriched with fat than in that of rabbits fed diets containing sunflower oil (28 g/kg) (P < 0.003) as well as in diets with identical digestible energy. In this experiment, alpha-tocopheryl acetate was at the lower level (10 mg/kg feed). Inclusion of oils rich in oleic (olive oil) or linoleic acid (sunflower oil) in rabbit diets reduces lipid oxidation in muscles.

Cell shrinkage and apoptosis: a role for potassium and sodium ion efflux.

Abstract: In this study we have shown that redistribution of the lipid composition of the external and internal leaflets of the PM during apoptosis results in two main alterations in the cell surface, externalisation of PS, and a looser packing of the lipid hydrophobic head groups in the external leaflet. Significantly, neither of these alterations can be directly implicated in the mechanism of apoptotic cell shrinkage, however they do have functions in other phases of the apoptotic process. Progressional studies involving morphological and flow cytometric evaluation, and DNA gel electrophoresis revealed that apoptotic cell shrinkage is associated with a decrease in [Na+]i and [K+]i which occurs after visualisation of chromatin condensation and internucleosomal DNA fragmentation, and prior to apoptotic body formation. When apoptotic cultures were supplemented with inhibitors of the Na+, K+-ATPase pump or the Ca2+-dependent K+ channel, essentially all of the respective Na+ or K+ efflux during apoptosis can be inhibited, suggesting that essentially all of the Na+ and K+ efflux can be ascribed to active pumping via the Na+, K+-ATPase pump and the Ca2+-dependent K+ channel.

Intracellular pH is a major factor in the induction of tolerance to acid and other stresses in Lactococcus lactis

Abstract: This study demonstrates that exposure of log-phase Lactococcus lactis subsp. cremoris 712 cells to mildly acid conditions induces resistance to normally lethal intensities of environmental stresses such as acid, heat, NaCl, H2O2, and ethanol. The intracellular pH (pHi) played a major role in the induction of this multistress resistance response. The pHi was dependent on the extracellular pH (pHo) and on the specific acid used to reduce the pHo. When resuspended in fresh medium, cells were able to maintain a pH gradient even at pHo values that resulted in cell death. Induction of an acid tolerance response (ATR) coincided with an increase in the ability of cells to resist change to an unfavorable pHi; nevertheless, a more favorable pHi was not the sole reason for the increased survival at acid pHo. Cells with an induced ATR survived exposure to a lethal pHo much better than did uninduced cells with a pHi identical to that of the induced cells. Survival following lethal acid shock was dependent on the pHi during induction of the ATR, and the highest survival was observed following induction at a pHi of 5.9, which was the lowest pHi at which growth occurred. Increased acid tolerance and the ability to maintain a higher pHi during lethal acid stress were not acquired if protein synthesis was inhibited by chloramphenicol during adaptation.