The Healthcare Design Research Alliance.
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Color↗
Biomedical subjects
M J Thompson
Publications and source records attributed to M J Thompson.
Is there tissue penetration after application of topical salicylate formulations?
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Administration, Cutaneous↗
Predicting protein secondary structure with probabilistic schemata of evolutionarily derived information.
We demonstrate the applicability of our previously developed Bayesian probabilistic approach for predicting residue solvent accessibility to the problem of predicting secondary structure. Using only single-sequence data, this method achieves a three-state accuracy of 67% over a database of 473 non-homologous proteins. This approach is more amenable to inspection and less likely to overlearn specifics of a dataset than "black box" methods such as neural networks. It is also conceptually simpler and less computationally costly. We also introduce a novel method for representing and incorporating multiple-sequence alignment information within the prediction algorithm, achieving 72% accuracy over a dataset of 304 non-homologous proteins. This is accomplished by creating a statistical model of the evolutionarily derived correlations between patterns of amino acid substitution and local protein structure. This model consists of parameter vectors, termed "substitution schemata," which probabilistically encode the structure-based heterogeneity in the distributions of amino acid substitutions found in alignments of homologous proteins. The model is optimized for structure prediction by maximizing the mutual information between the set of schemata and the database of secondary structures. Unlike "expert heuristic" methods, this approach has been demonstrated to work well over large datasets. Unlike the opaque neural network algorithms, this approach is physicochemically intelligible. Moreover, the model optimization procedure, the formalism for predicting one-dimensional structural features and our previously developed method for tertiary structure recognition all share a common Bayesian probabilistic basis. This consistency starkly contrasts with the hybrid and ad hoc nature of methods that have dominated this field in recent years.
Algorithms↗
Prediction of requirement for, and outcome of, prolonged mechanical ventilation following cardiac surgery.
The prediction of requirement for, and short- and long-term outcome of, prolonged mechanical ventilation after cardiac surgery is ill-defined. The aims of this study were to isolate any predictive indices which might identify those groups of patients who may require prolonged ventilation postoperatively and to determine which factors significantly affect outcome in the prolonged-ventilation group. Following case note review of 139 consecutive cardiac surgical patients ventilated for > or = 7 days following surgery, 43 factors were recorded on each patient, including smoking, pulmonary function, chest infection, and chronic obstructive airways disease. Of 139 patients, 89 were discharged from hospital (64% survival); of these, 52 were alive at long-term follow-up (58% long-term survival). Statistical analysis identified urban residence, chronic obstructive airways disease, prolonged operation, and bypass time as significant predictors of requirement for prolonged ventilation postoperatively. On multivariate analysis five factors were predictive of increased intensive care mortality, including urban residence, inotrope days, sepsis, perioperative cerebrovascular accident and coagulopathy requiring fresh frozen plasma transfusion postoperatively. Following discharge from hospital, four factors were found to be significant predictors of increased mortality: these are impaired preoperative ejection fraction, increasing age, impaired preoperative pulmonary function, and abscence of preoperative aspirin medication. These factors should be considered in intensive care planning, long-term follow-up and importantly on clinical decision making in the individual patient.
Adult↗
Establishment and characterisation of new cell lines from human breast tumours initially established as tumour xenografts in NMRI nude mice.
Human breast cancer cell lines are required as models for use in the understanding of breast carcinoma, and for improving the ability of cell screens to detect appropriate anti-cancer agents. Four human breast cancer cell lines (MT-1, MaTu. MT-3 and MC4000) were established from human tumour xenografts grown in nude mice. All the lines were shown to be of human origin by karyotype analysis, were epithelial in morphology by both light and electron microscopy, were positive for cytokeratin 18, and were free from mycoplasma, bacterial, yeast and fungal contamination. All of the new lines were shown to be ER and PgR negative, while using the same procedures (i.e. radioligand binding and immunohistochemical staining) the positive control cell line MCF-7 was shown to be positive. MaTu had been previously reported as ER and PgR positive in vivo and it may be that this characteristic had been lost due to in vitro selection pressures. The growth rates of all the new breast cancer cell lines were similar and within the limits required for incorporation into a panel for screening anti-cancer drugs by a microtetrazolium based, colorimetric growth inhibition assay. Three of the lines (MT-1. MaTu and MC4000) were also able to grow into macroscopic colonies for use in a non-agar clonogenic assay. In addition, both MT-1 and MaTu formed spheroids and were clonogenic in soft-agar. The new lines demonstrated a wide range of sensitivities to anticancer agents commonly used in the treatment of breast cancer, and together with their corresponding xenografts are providing additional systems for the evaluation of new compounds.
Animals↗
Bioluminescent methods for determining metabolites in micro-samples of pig plasma.
A highly sensitive and simplified method for the luminometric determination of plasma metabolites has been developed. Furthermore, the technique has been automated for the Dynatech ML2250 Microtiter Plate Luminometer and can be applied to the measurement of any plasma metabolite which may be coupled to a reaction involving the reduction of NAD+. Assays are described for lactose/galactose, beta-hydroxybutyrate and D-lactate, and have been validated with plasma samples. The assays require 1-2 microliters of plasma, and are capable of detecting concentrations below 5 mumol/l. Since luminometry is based on the kinetics of the luciferase/oxidoreductase enzyme system, components of complex biological samples may interfere with the rate of the reaction; necessitating the use of internal standards for individual samples. However, the need for internal standards to account for sample to sample variation in the luminescent response, has been eliminated with the present technique.
3-Hydroxybutyric Acid↗
Cloning and characterization of two yeast genes encoding members of the CCCH class of zinc finger proteins: zinc finger-mediated impairment of cell growth.
Members of the CCCH zinc finger (Zf) protein family have in common two or more repeats of a novel Zf motif consisting of Cys and His residues in the form Cx8Cx5Cx3H [where x is a variable amino acid (aa)]. We used a degenerate polymerase chain reaction (PCR) strategy to clone members of this gene family from Saccharomyces cerevisiae. The deduced aa sequences encoded by these genes, designated CTH1 and CTH2, share 46% overall identity and 59% similarity, largely due to the two highly conserved Zf domains. We found readily detectable expression of a 1.4-kb mRNA encoding Cth1p. The 1.1-kb mRNA encoding Cth2p was barely detectable under normal growth conditions; however, disruption of CTH1 resulted in at least a threefold increase in CTH2 mRNA accumulation. No change in phenotype was detected following disruption of CTH1 and CTH2, either singly or together. In contrast, overexpression of the CTH genes or one of the related mammalian genes, tris-tetraprolin (TTP), caused delayed entry of cell cultures into exponential growth, and a decrease in final cell density. Removal of the Zf domain of Cth1p by truncation or deletion completely reversed this slow growth phenotype, indicating that it was mediated through this highly conserved structural motif.
Amino Acid Sequence↗
High-performance liquid chromatographic determination of phenol, 4-nitrophenol, beta-naphthol and a number of their glucuronide and sulphate conjugates in organ perfusate.
This paper describes a simple and more sensitive reversed-phase HPLC method for the quantification of phenol, 4-nitrophenol and beta-naphthol and some of their glucuronide and sulphate conjugates in aqueous solution and liver perfusate buffer. Methanol-water mobile phases with ion-pairing agents for each phenolic group are detailed. The assay showed good recovery, accuracy and precision and is suitable for the quantification of these phenolic compounds in liver perfusion experiments.
Animals↗
Constructing amino acid residue substitution classes maximally indicative of local protein structure.
Using an information theoretic formalism, we optimize classes of amino acid substitution to be maximally indicative of local protein structure. Our statistically-derived classes are loosely identifiable with the heuristic constructions found in previously published work. However, while these other methods provide a more rigid idealization of physicochemically constrained residue substitution, our classes provide substantially more structural information with many fewer parameters. Moreover, these substitution classes are consistent with the paradigmatic view of the sequence-to-structure relationship in globular proteins which holds that the three-dimensional architecture is predominantly determined by the arrangement of hydrophobic and polar side chains with weak constraints on the actual amino acid identities. More specific constraints are imposed on the placement of prolines, glycines, and the charged residues. These substitution classes have been used in highly accurate predictions of residue solvent accessibility. They could also be used in the identification of homologous proteins, the construction and refinement of multiple sequence alignments, and as a means of condensing and codifying the information in multiple sequence alignments for secondary structure prediction and tertiary fold recognition.
Amino Acid Sequence↗
Predicting solvent accessibility: higher accuracy using Bayesian statistics and optimized residue substitution classes.
We introduce a novel Bayesian probabilistic method for predicting the solvent accessibilities of amino acid residues in globular proteins. Using single sequence data, this method achieves prediction accuracies higher than previously published methods. Substantially improved predictions-comparable to the highest accuracies reported in the literature to date-are obtained by representing alignments of the example proteins and their homologs as strings of residue substitution classes, depending on the side chain types observed at each alignment position. These results demonstrate the applicability of this relatively simple Bayesian approach to structure prediction and illustrate the utility of the classification methodology previously developed to extract information from aligned sets of structurally related proteins.
Amino Acid Sequence↗
A pathogenetic role for TNF alpha in the syndrome of cachexia, arthritis, and autoimmunity resulting from tristetraprolin (TTP) deficiency.
Tristetraprolin (TTP) is a widely expressed potential transcription factor that contains two unusual CCCH zinc fingers and is encoded by the immediate-early response gene, Zfp-36. Mice made deficient in TTP by gene targeting appeared normal at birth, but soon manifested marked medullary and extramedullary myeloid hyperplasia associated with cachexia, erosive arthritis, dermatitis, conjunctivitis, glomerular mesangial thickening, and high titers of anti-DNA and antinuclear antibodies. Myeloid progenitors from these mice showed no increase in sensitivity to growth factors. Treatment of young TTP-deficient mice with antibodies to tumor necrosis factor alpha (TNF alpha) prevented the development of essentially all aspects of the phenotype. These results indicate a role for TTP in regulating TNF alpha synthesis, secretion, turnover, or action. TTP-deficient mice may serve as useful models of the autoimmune inflammatory state resulting from chronic effective TNF alpha excess.
Animals↗
Maintenance of villus height and crypt depth, and enhancement of disaccharide digestion and monosaccharide absorption, in piglets fed on cows' whole milk after weaning.
The aims of the present study were (a) to maintain the structure and function of the small intestine of the piglet after weaning, and (b) to compare the capacity in vivo of sucking and weaned piglets to digest oral boluses of lactose and sucrose and absorb their monosaccharide products. Piglets were fed on cows' whole milk ad libitum every 2 h for 5 d after weaning. Physiological doses of lactose plus fructose (treatment LAC+FRU) and sucrose plus galactose (treatment SUC+GAL) were administered on day 27 of lactation and on the fifth day after weaning, after which time piglets were killed. Villus height and crypt depth were maintained (P > 0.05) by feeding cows' milk after weaning. The areas under the curves (AUC) for galactose and glucose, adjusted for live weight and plasma volume, increased (P < 0.05) after weaning. Despite the enhancement of gut function after weaning, the galactose index (GalI:AUC for galactose ingested as lactose divided by the AUC for the same dose of galactose ingested as the monosaccharide) and fructose index (FruI: AUC for fructose ingested as sucrose divided by the AUC for the same dose of fructose ingested as the monosaccharide), which are indices of digestive and absorptive efficiency, both decreased after weaning. This apparent anomaly may be reconciled by increased growth, and hence surface area, of the small intestine between weaning and slaughter such that 'total' digestion and absorption most probably increased despite apparent decreases in GalI and FruI. Positive correlations (P < 0.05) between villus height and GalI are consistent with the maximum activity of lactase occurring more apically along the villus. Significant linear relationships (P < 0.05) were recorded between villus height at the proximal jejunum and adjusted AUC for galactose and glucose following treatment LAC+FRU, and between villus height at the proximal jejunum and adjusted glucose AUC following treatment SUC+GAL. These relationships suggest that maximum digestion and absorption occurs at increasing distances along the crypt:villus axis in the weaned pig.
Animals↗
Distribution of systemically administered ampicillin, benzylpenicillin, and flucloxacillin in excisional wounds in diabetic and normal rats and effects of local topical vasodilator treatment.
The present study assessed the suitability of the streptozotocin-treated diabetic rat as a model for the study of diabetes-impaired wound healing. The distribution of three antibiotics, ampicillin, benzylpenicillin, and flucloxacillin, in wound and adjacent tissue sites on the abdomens and legs of normal and diabetic rats was determined 30 min after intravenous administration of a single bolus containing 50 mg of all three antibiotics per kg of body weight. Tissue/plasma ratios showed that antibiotic tissue penetration appeared to be related to protein binding. The treatment of wound sites with vasodilators (1% solution) to increase local blood flow and antibiotic delivery to the site was then determined and appeared to be more effective with endothelium-independent sodium nitroprusside than with endothelium-dependent acetylcholine in diabetic rats. These results suggest that coadministration of topical vasodilators to wound sites in neuropathic diabetic patients undergoing antibiotic therapy for infected ulcers could increase antibiotic delivery to wound tissue sites.
Acetylcholine↗
Mental health of preschool children and their mothers in a mixed urban/rural population. I. Prevalence and ecological factors.
BACKGROUND: The prevalence rate of behaviour problems and maternal mental disturbance was estimated using a sample of 1047 families with a 3-year-old child from a mixed urban/rural area. METHOD: Parents completed the Child Behaviour Checklist, EAS Temperament Questionnaire, Weiss-Werry-Peters Activity Scale and the GHQ-30. RESULTS: The rate of behaviour problems (13.2%) was similar to that obtained in studies of urban children. The rate of maternal disturbance (27.6%) was lower than in other population samples. Few differences were found in the prevalence rates in the urban and rural areas. CONCLUSIONS: Preschool children and their parents living in non-urban areas had the same rates of problems as those in conurbations. The service needs of such families are similar regardless of locality.
Attention Deficit Disorder with Hyperactivity↗
Mental health of preschool children and their mothers in a mixed urban/rural population. II. Family and maternal factors and child behaviour.
BACKGROUND: The extent to which certain maternal, child and family characteristics are associated in families with a 3-year-old child were examined. METHOD: A total population of families with a 3-year-old child and living in the New Forest were identified. Measures of child behaviour and the maternal GHQ-30 were obtained. RESULTS: Whereas behaviour problems were found to be significantly associated with all maternal and family factors (except social class), difficult temperament was only related to mother's recall of their own childhood as unhappy and overactivity was only significantly associated with maternal disturbance. CONCLUSIONS: The results are consistent with maternal disturbance and difficult temperament acting independently and additively to influence the development of behaviour problems in preschool children.
Child Behavior Disorders↗
Mental health of preschool children and their mothers in a mixed urban/rural population. III. Latent variable models.
BACKGROUND: There is a lack of clear and explicit models of the way various family and social influences on children's behaviour interact with factors such as temperament to produce behaviour disturbance in young children. METHOD: The following measures had been obtained on a total population sample of 1047 families with a 3-year-old child: the child's perceived cuddliness, difficult temperament, mother's unhappy childhood, maternal disturbance, social class, behaviour problems and overactivity. A latent variable analysis using the LISREL 7 program was applied to the data. RESULTS: A model that allowed the latent variables child 'temperament' and 'mother's mental state' to have separate additive effects on 'child adaptation' proved an excellent fit (goodness of fit index = 0.956). This model suggests that there is a common factor ('child adaptation') underlying behaviour problems and overactivity. Using this model 72% of child adaptation in boys could be explained. For girls however temperament and mother's mental state accounted for only 30% of the variance in child adaptation. CONCLUSION: There is a need to investigate different mechanisms for the origins of behaviour problems in preschool boys and girls.
Attention Deficit Disorder with Hyperactivity↗
Mitogens stimulate the rapid nuclear to cytosolic translocation of tristetraprolin, a potential zinc-finger transcription factor.
Tristetraprolin (TTP) is the prototype of a group of potential transcription factors that contain two or more unusual CCCH zinc fingers. TTP is encoded by the immediate-early response gene Zfp-36, which is rapidly induced in fibroblasts in response to insulin and other growth factors. Indirect evidence suggests that TTP might function as an inhibitory transcription factor. The present studies evaluated the effect of mitogens on the subcellular localization of TTP using Western blotting of cellular nuclear and cytosolic fractions. In NIH/3T3 mouse fibroblasts that constitutively express TTP, 70% of the protein was located in the nucleus of quiescent, serum-deprived cells. Immunoreactive TTP began to increase in the cytosolic compartment within 1 min of serum stimulation of the cells; this increase in cytosolic protein was essentially complete within 5 min of serum stimulation (81% of total) and was accompanied by a commensurate decrease in nuclear TTP. This translocation was complete well before the increase in TTP synthesis that occurred after serum stimulation. Similar experiments in cells expressing a mutant TTP, in which the major mitogen-activated protein kinase site (serine 220) had been mutated to alanine, revealed normal nuclear to cytosolic translocation after serum stimulation, indicating that phosphorylation of this site is not necessary for this translocation to occur. These results suggest that TTP is rapidly modified in response to mitogens so that it is rapidly released from the nucleus to the cytosol, or that proteins retaining TTP in the nucleus are modified to release it into the cytosol. Thus, TTP's proposed function as a transcription factor, possibly an inhibitory one, may be regulated in cells in part by a novel mechanism, i.e. that of rapid, mitogen-stimulated translocation out of the cellular nucleus.
3T3 Cells↗
Effect of insect-growth-disrupting amines and amides on Schistosoma mansoni in vitro.
A series of nonsteroidal alkylamines and alkylamides, which apparently inhibit phytosterol dealkylation in insects and free-living nematodes, as well as steps in the ecdysteroid biosynthetic pathway of insects, are also known to affect growth and development of animal-parasitic nematodes. The effect of these compounds on the motility, pairing, and viability of the trematode, Schistosoma mansoni, maintained in vitro was examined by incorporating the potential inhibitors into the medium employed for parasite culture. The alkylamines were more active than their amide counterparts, killing all parasites within 18 hr when tested at 25 parts per million. At lower concentrations, reductions in schistosome pairing and motility were observed. The functional group of the amine compounds influenced the schistosomicidal activity, with N-ethylamines being more effective than N,N-dimethylamines of identical carbon chain-length. Of all the compounds tested, N-ethyldodecanamine appeared to be the most promising schistosomicidal agent, killing all parasites within 22 hr at 10 parts per million and preventing parasite pairing at 3 parts per million.
Amides↗