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A P Harrison

Publications and source records attributed to A P Harrison.

At least 19 recordsLinked to original sources
PubMed2003

The CATH database: an extended protein family resource for structural and functional genomics.

The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath_new) currently contains 34 287 domain structures classified into 1383 superfamilies and 3285 sequence families. Each structural family is expanded with domain sequence relatives recruited from GenBank using a variety of efficient sequence search protocols and reliable thresholds. This extended resource, known as the CATH-protein family database (CATH-PFDB) contains a total of 310 000 domain sequences classified into 26 812 sequence families. New sequence search protocols have been designed, based on these intermediate sequence libraries, to allow more regular updating of the classification. Further developments include the adaptation of a recently developed method for rapid structure comparison, based on secondary structure matching, for domain boundary assignment. The philosophy behind CATHEDRAL is the recognition of recurrent folds already classified in CATH. Benchmarking of CATHEDRAL, using manually validated domain assignments, demonstrated that 43% of domains boundaries could be completely automatically assigned. This is an improvement on a previous consensus approach for which only 10-20% of domains could be reliably processed in a completely automated fashion. Since domain boundary assignment is a significant bottleneck in the classification of new structures, CATHEDRAL will also help to increase the frequency of CATH updates.

Animals↗
PubMed2002

Effects of endothelin on submandibular salivary responses to parasympathetic stimulation in anaesthetized sheep.

Submandibular responses to stimulation of the parasympathetic chorda tympani nerve have been investigated in anaesthetized sheep before, during and after an intracarotid infusion of endothelin, which reduced the blood flow through the gland by 56+/-5%. Stimulation of the peripheral end of the chorda tympani nerve produced a frequency-dependent increase in the flow of submandibular saliva, and in sodium, potassium and protein output. The reduction in submandibular blood flow, which occurred in response to endothelin, was associated with a decrease in the flow of saliva at all frequencies tested amounting on average to 44+/-6% (P<0.01). The flow of saliva was linearly related to the blood flow before and after endothelin. Both parameters were also linearly related during the infusion of endothelin and the regression lines were parallel. Salivary sodium concentration was significantly increased at the lower frequencies (1 and 2 Hz). Protein output was generally reduced but the difference only achieved statistical significance during stimulation at 1 Hz (P<0.01). Thus, submandibular secretory responses to parasympathetic stimulation are significantly attenuated by reducing the blood flow through the gland in this way.

Animals↗
PubMed2001

A rapid classification protocol for the CATH Domain Database to support structural genomics.

In order to support the structural genomic initiatives, both by rapidly classifying newly determined structures and by suggesting suitable targets for structure determination, we have recently developed several new protocols for classifying structures in the CATH domain database (http://www.biochem.ucl.ac.uk/bsm/cath). These aim to increase the speed of classification of new structures using fast algorithms for structure comparison (GRATH) and to improve the sensitivity in recognising distant structural relatives by incorporating sequence information from relatives in the genomes (DomainFinder). In order to ensure the integrity of the database given the expected increase in data, the CATH Protein Family Database (CATH-PFDB), which currently includes 25,320 structural domains and a further 160,000 sequence relatives has now been installed in a relational ORACLE database. This was essential for developing more rigorous validation procedures and for allowing efficient querying of the database, particularly for genome analysis. The associated Dictionary of Homologous Superfamilies [Bray,J.E., Todd,A.E., Pearl,F.M.G., Thornton,J.M. and Orengo,C.A. (2000) Protein Eng., 13, 153-165], which provides multiple structural alignments and functional information to assist in assigning new relatives, has also been expanded recently and now includes information for 903 homologous superfamilies. In order to improve coverage of known structures, preliminary classification levels are now provided for new structures at interim stages in the classification protocol. Since a large proportion of new structures can be rapidly classified using profile-based sequence analysis [e.g. PSI-BLAST: Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Nucleic Acids Res., 25, 3389-3402], this provides preliminary classification for easily recognisable homologues, which in the latest release of CATH (version 1.7) represented nearly three-quarters of the non-identical structures.

Computational Biology↗
PubMed2001

Alzheimer morphology is not increased in dialysis-associated encephalopathy and long-term hemodialysis.

This study examines the role of aluminium in the etiology of Alzheimer's disease (AD). Brains taken at autopsy (n = 50) from patients with a history of long-term hemodialysis (HD) and intake of aluminium (Al)-containing drugs were examined by light microscopy. Using our modified silver stain we have been able to demonstrate and clearly discriminate between AD changes and dialysis-associated encephalopathy (DAE) on paraffin sections; evaluation was done with a 3-point scale. DAE morphology is characterized by lysosome-derived intracytoplasmic, Al-containing, pathognomonic, argyrophilic inclusions in choroid plexus epithelia, cortical glia and neurons. A statistically significant difference was found between the amounts of drug-related Al ingested and the degree of DAE-related morphological change (P < 0.001). On the other hand no apparent microscopical increase in AD morphology was found. No AD changes were seen whatsoever in patients under the age of 60, despite a history of long-term HD with ingestion of "pure" Al up to 2.5 kg. Patients over 60 years of age occasionally presented with sparse deposits of beta A4 amyloid (beta A4) and/or a low incidence of AD-type neurofibrillary tangles (NFT). In accordance with CERAD criteria these were identified as normal, age-related phenomena (P < 0.001 for beta A4; P < 0.001 for NFT). Rare, isolated cases from a group of 127 long-term hemodialyzed patients have been reported previously, who presented with intermingled, clearly distinguishable lesions of both age-related AD morphology and DAE changes. Comparison of AD morphology with an age-matched control group was not statistically significant (P > 0.6 for beta A4, P > 0.7 for NFT). In our experience, Al does not cause an increase in AD morphology, at least not in terms of bioavailable Al in drugs or as a result of long-term HD.

Adult↗
PubMed2000

Assigning genomic sequences to CATH.

We report the latest release (version 1.6) of the CATH protein domains database (http://www.biochem.ucl. ac.uk/bsm/cath ). This is a hierarchical classification of 18 577 domains into evolutionary families and structural groupings. We have identified 1028 homo-logous superfamilies in which the proteins have both structural, and sequence or functional similarity. These can be further clustered into 672 fold groups and 35 distinct architectures. Recent developments of the database include the generation of 3D templates for recognising structural relatives in each fold group, which has led to significant improvements in the speed and accuracy of updating the database and also means that less manual validation is required. We also report the establishment of the CATH-PFDB (Protein Family Database), which associates 1D sequences with the 3D homologous superfamilies. Sequences showing identifiable homology to entries in CATH have been extracted from GenBank using PSI-BLAST. A CATH-PSIBLAST server has been established, which allows you to scan a new sequence against the database. The CATH Dictionary of Homologous Superfamilies (DHS), which contains validated multiple structural alignments annotated with consensus functional information for evolutionary protein superfamilies, has been updated to include annotations associated with sequence relatives identified in GenBank. The DHS is a powerful tool for considering the variation of functional properties within a given CATH superfamily and in deciding what functional properties may be reliably inherited by a newly identified relative.

Amino Acid Sequence↗
PubMed1999

Measurement of force and both surface and deep M wave properties in isolated rat soleus muscles.

In isolated soleus muscles of 4-wk-old rats, M wave parameters were recorded with surface and deep recording electrodes and examined in relation to both twitch and tetanic force. Addition of ouabain (10(-5) M for 16 min) to isolated muscles caused an approximately 40% decrease in twitch amplitude and area (P < 0.01) that was associated with a 98% decrease in surface M wave amplitude, a 78% decrease in deep M wave amplitude (both P < 0.001), a 98% decrease in surface M wave area (P < 0.01), 48% of which occurred within 60 s of addition of ouabain (P < 0.05), and a 55% decrease in deep M wave area (P < 0.05). The decrease in twitch parameters on addition of ouabain was most closely correlated with deep M wave area (r = 0.92). Direct tetanic stimulation at a frequency of 30 Hz resulted in an initial potentiation of M waves, which was not seen at a frequency of 90 Hz. Instead, 90 Hz stimulation resulted in a prompt decrease in tetanic force that was correlated with a decrease in both deep M wave amplitude (r = 0.94; P < 0.01) and deep M wave area (r = 0.96; P < 0.01). It is concluded that simultaneous surface and deep recordings involving area and amplitude are fundamental to analysis of the effects of pharmacological agents on muscle performance and the use of M waves as predictors of muscle excitability.

Animals↗
PubMed1998

The regulation of the Na+,K+ pump in contracting skeletal muscle.

Increased passive Na+,K+ fluxes necessitate an efficient activation of the Na+,K+ pump in working muscles to limit the rundown of the Na+,K+ chemical gradients and ensuing loss of excitability. Several studies have demonstrated an increase in Na+,K+-pump rate in working muscles, and in electrically stimulated muscles up to a 22-fold increase in active Na+,K+ transport has been observed. Excitation-induced increase in intracellular Na+ is believed to be the primary stimulus for Na+,K+ pumping in a contracting muscle. In muscles recovering from electrical stimulation, however, the activity of the pump may stay elevated even after intracellular Na+ has been reduced to below the resting level. Moreover, in rat soleus muscles 10-s stimulation at 60 Hz induced a 5-fold increase in the activity of the Na+,K+ pump although mean intracellular [Na+] was unchanged. These findings strongly suggest that a substantial part of the excitation-induced increase in Na+,K+-pump activity is caused by mechanisms other than increased intracellular [Na+]. The mechanism behind this activation is not clear, but may involve a change in the affinity of the Na+,K+ pump for intracellular Na+. In addition to intracellular [Na+], the Na+,K+ pump may be stimulated in contracting muscles by other factors such as catecholamines, calcitonin gene-related peptide (CGRP), free fatty acids and cytoskeletal links. Together, this activation may form a feed forward mechanism protecting muscles from loss of excitability during periods of contraction by increasing Na+,K+-pump activity prior to erosion of the Na+,K+ chemical gradients. During exercise of high intensity, however, intracellular [Na+] increases substantially constituting an additional stimulus for the pump.

Animals↗
PubMed1998

The Na+,K+ pump and muscle excitability.

In most types of mammalian skeletal muscles the total concentration of Na+,K+ pumps is 0.2-0.8 nmol g wet wt(-1). At rest, only around 5% of these Na+,K+ pumps are active, but during high-frequency stimulation, virtually all Na+,K+ pumps may be called into action within a few seconds. Despite this large capacity for active Na+,K+ transport, excitation often induces a net loss of K+, a net gain of Na+, depolarization and ensuing loss of excitability. In muscles exposed to high [K+]o or low [Na+]o, alone or combined, excitability is reduced. Under these conditions, hormonal or excitation-induced stimulation of the Na+,K+ pump leads to considerable force recovery. This recovery can be blocked by ouabain and seems to be the result of Na+,K+ pump induced hyperpolarization and restoration of Na+,K+ gradients. In muscles where the capacity of the Na+,K+ pump is reduced, the decline in the force developing during continuous electrical stimulation (30-90 Hz) is accelerated and the subsequent force recovery considerably delayed. The loss of endurance is significant within a few seconds after the onset of stimulation. Increased concentration of Na+ channels or open-time of Na+ channels is also associated with reduced endurance and impairment of force recovery. This indicates that during contractile activity, excitability is acutely dependent on the ratio between Na+ entry and Na+,K+ pump capacity. Contrary to previous assumptions, the Na+,K+ pump, due to rapid activation of its large transport capacity seems to play a dynamic role in the from second to second ongoing restoration and maintenance of excitability in working skeletal muscle.

Animals↗
PubMed1998

Thyroid hormone-induced upregulation of Na+ channels and Na(+)-K+ pumps: implications for contractility.

We have previously observed in rat soleus muscle that endurance is a function of the ratio between the concentration of Na+ channels and Na(+)-K+ pumps [Harrison, A. P., O. B. Nielsen, and T. Clausen. Am. J. Physiol. 272 (Regulatory Integrative Comp. Physiol. 41): R1402-R1408, 1997]. In this study we explore this relationship further by comparing the changes in Na+ channel and Na(+)-K+ pump concentrations induced by injections of 3,5,3'-triiodothyronine (T3) with endurance. T3 induced upregulation of the concentration of Na+ channels and Na(+)-K+ pumps, which was associated with a progressive loss of contractile endurance. The increase in Na+ channels preceded that of the Na(+)-K+ pumps and amounted to 49 and 52% (both P < 0.01) after 48 and 72 h of T3 treatment, respectively. Concomitantly, during 90-Hz stimulation, the initial rate of force decline increased by 42 and 45% after 48 and 72 h of T3 treatment, respectively (both P < 0.001). These observations are important for an understanding of the fatigue associated with hyperthyroidism and add further support to the hypothesis that muscle endurance depends on the leak-to-pump ratio for Na+.

Age Factors↗
PubMed1997

Postnatal development and differentiation of myofibres in functionally diverse porcine skeletal muscles.

Marked changes in muscle function occur after birth, with the response being dependent on developmental stage. Therefore, postnatal cellular ontogeny of functionally distinct skeletal muscles was investigated in the pig, a large mammal born at a relatively advanced stage of development. Assessment of myofibre contractile (type I slow/type II fast) and metabolic (oxidative/glycolytic) properties at Days 0, 2, 5 and 14 revealed type-specific differences in hypertrophy and differentiation. Type I fibre proportions increased significantly in soleus and diaphragm, especially between Days 0 and 5, and rhomboideus showed a similar trend, but in longissimus there was a slight decrease during Days 0-2. Cytochrome oxidase activity was relatively high and similar among myofibres in all muscles at birth, and fibres with low activity were not detected until Day 5. In contrast with previous reports, glycolytic fibres were present in all muscles at birth; postnatal changes in alpha-glycerophosphate dehydrogenase activity were both muscle- and myofibre-specific. Hence, although myosin ATPase activity and metabolic properties of porcine myofibres are well developed at birth, they continue to mature postnatally. This suggests that postnatal muscle development can be modulated by extrinsic factors, even in mammals born at a relatively advanced stage of development.

Aging↗
PubMed1997

Role of Na(+)-K+ pump and Na+ channel concentrations in the contractility of rat soleus muscle.

The dependence of contractile performance on the leak-to-pump ratio for Na+ has been examined. In isolated rat soleus muscle the concentration of Na(+)-K+ pumps was shown to decrease with age (-57%) or K+ deficiency (-69%), whereas Na+ channel concentration remained constant. This relative increase in the ratio between Na+ channels and Na(+)-K+ pumps was associated with a markedly faster rate of force decline (58 and 97%, respectively; both P < 0.001) during stimulation at 90 Hz and reduced subsequent force recovery (-34 and -38%, respectively; both P < 0.001). Similar effects were elicited by acute inhibition of Na(+)-K+ pump activity with ouabain. Preincubation with aconitine and veratridine, resulting in a 91 and 118% increase in Na+ influx per contraction, respectively (both P < 0.05), significantly hastened the initial rate of force decline (19%; P < 0.05 for aconitine and 69%; P < 0.001 for veratridine) and slowed recovery (-59 and -86%, respectively, both P < 0.001). It is concluded that the ratio between excitation-induced Na+ influx and Na(+)-K+ pump capacity is an important determinant for endurance and rate of recovery of force in skeletal muscle.

Aconitine↗
PubMed1996

Developmental regulation of cation pumps in skeletal and cardiac muscle.

The prenatal and early postnatal periods are critical stages during which long-term development can be affected. For example, retardation of growth during these periods is closely linked to the occurrence of adult degenerative diseases. Appropriate development of muscle is essential for numerous functions, including movement, posture, thermogenesis, breathing and maintenance of the circulation. Defects in normal muscle development could thus impair any of these functions in the neonate and may also have long-term consequences for the health of the individual. Central to normal muscle structure and function is the appropriate development not only of the sarcomeric proteins but also of the sarcolemma, transverse-tubules, sarcoplasmic reticulum and associated membrane-bound ATPases. Long-term regulation of these ATPases is by changes in their concentration, whereas short-term regulation is mediated by alterations in enzyme activity. This review focuses on changes in total concentrations of Na+, K+, and Ca(2+)-ATPases during prenatal and postnatal life, in functionally diverse muscles of mammalian species born at different stages of maturity. Both these cation pumps belong to multigene families and changes in relative abundance of their specific isoforms are also considered because they may have important consequences for contractile performance during distinct stages of development. Finally, potential regulatory mechanisms which alter markedly during normal ontogeny are discussed. These include intrinsic factors such as hormones and contractile activity, extrinsic factors such as nutrition and environmental temperature, and interactions between these variables which are known to be especially important during postnatal development.

Adenosine Triphosphatases↗
PubMed1996

Role of thyroid hormones in early postnatal development of skeletal muscle and its implications for undernutrition.

Energy intake profoundly influences many endocrine axes which in turn play a central role in development. The specific influence of a short period of mild hypothyroidism, similar to that induced by undernutrition, in regulating muscle development has been assessed in a large mammal during early postnatal life. Hypothyroidism was induced by providing methimazole and iopanoic acid in the feed of piglets between 4 and 14 d of age, and controls were pair-fed to the energy intake of their hypothyroid littermates. Thyroid status was evaluated, and myofibre differentiation and cation pump concentrations were then assessed in the following functionally distinct muscles: longissimus dorsi (l. dorsi), soleus and rhomboideus. Reductions in plasma concentrations of thyroxine (T4; 32%, P < 0.01), triiodothyronine (T3; 48%, P < 0.001), free T3 (58%, P < 0.001) and hepatic 5'-monodeiodinase (EC 1.11.1.8) activity (74%, P < 0.001) occurred with treatment. Small, although significant, increases in the proportion of type I slow-twitch oxidative fibres occurred with mild hypothyroidism, in l. dorsi (2%, P < 0.01) and soleus (7%, P < 0.01). Nuclear T3-receptor concentration in l. dorsi of hypothyroid animals compared with controls increased by 46% (P < 0.001), a response that may represent a homeostatic mechanism making muscle more sensitive to low levels of circulating thyroid hormones. Nevertheless, Na+, K(+)-ATPase (EC 3.6.1.37) concentration was reduced by 15-16% in all muscles (l. dorsi P < 0.05, soleus P < 0.001, rhomboideus P < 0.05), and Ca(2+)-ATPase (EC 3.6.1.38) concentration was significantly reduced in the two slow-twitch muscles: by 22% in rhomboideus (P < 0.001) and 23% in soleus (P < 0.05). It is concluded that during early postnatal development of large mammals a period of mild hypothyroidism, comparable with that found during undernutrition, induces changes in myofibre differentiation and a down-regulation of cation pumps in skeletal muscle. Such changes would result in slowness of movement and muscle weakness, and also reduce ATP hydrolysis with a concomitant improvement in energetic efficiency.

Animals↗
PubMed1996

Selective regulation of myofiber differentiation by energy status during postnatal development.

The role of energy status in postnatal regulation of porcine skeletal muscle development has been determined in littermate animals kept for 3-4 wk on a high (H) or low (L) energy intake (H = 2L), at a thermally neutral [26 degrees C (26H and 26L, respectively)] or low [10 degrees C (10H and 10L, respectively)] environmental temperature. A variety of skeletal muscles was assessed at 7 wk of age for changes in myofiber hypertrophy and differentiation. In contrast with findings in adult humans and rats, there was no selective preservation of type I slow-oxidative fiber size during energy restriction. However, differentiation between mature skeletal myosin heavy-chain isoforms was markedly affected by energy status, and in rhomboideus there were particularly striking effects of both nutrition and temperature: proportions of type I fibers from the four groups 26H, 26L, 10H, and 10L were 34 +/- 2, 50 +/- 4, 73 +/- 2, and 72 +/- 3 (P < 0.005 for diet at 26 degrees C; P < 0.001 for temperature). These changes may have been induced by alterations in both thyroid status and contractile activity. They support the hypothesis of a key role for rhomboideus muscle in thermoregulation and demonstrate the plasticity of skeletal muscle differentiation to environmental change during postnatal life.

Animals↗
PubMed1994

Nutritional regulation of growth hormone receptor gene expression.

The role of energy intake in regulating growth hormone receptor (GHR) gene expression has been assessed in young growing pigs living at thermal neutrality (26 degrees C) for a 4-wk period. To determine the importance of altering metabolic demand while maintaining food intake constant, littermates were also studied in a cold environment (10 degrees C). Results were tissue-specific: the level of GHR mRNA per unit total RNA in liver was greater on high than low (high = 2 x low) food intake (P < 0.001), whereas in muscle it was elevated on the low compared with the high intake diet (P < 0.02) and also at 10 degrees C compared with 26 degrees C (P < 0.04). When results for GHR mRNA were expressed per unit weight of tissue, only the effects of diet on liver and temperature on muscle remained significant. The changes in hepatic GHR mRNA may have been driven in part by nutritionally induced changes in thyroid status, because both plasma 3,5,3'-triiodothyronine concentration and liver 5'-deiodinase activity were greater on the high than the low intake diet (P < 0.001). Levels of liver GHR mRNA probably had a direct influence on growth of the animals, as they were positively correlated with plasma IGF-I and growth rate (P < 0.001), whereas muscle GHR mRNA may have had a metabolic role when energy supplies were limited.

Animal Nutritional Physiological Phenomena↗
PubMed1994

Roles of skeletal muscle morphology and activity in determining Na(+)-K(+)-ATPase concentration in young pigs.

It has been demonstrated previously that the Na(+)-K(+)-adenosinetriphosphatase (Na(+)-K(+)-ATPase) concentration (total concentration of [3H]ouabain-binding sites = maximal [3H]ouabain-binding capacity, Bmax) in longissimus dorsi muscle is higher in young pigs living in a cold than in a warm environment, with the effect being even greater in those on a low rather than a high energy intake in the cold. The importance of thyroid status, myofiber type and size, and muscular activity in determining the concentration of Na(+)-K(+)-ATPase has therefore been assessed in longissimus dorsi, semitendinosus, and soleus muscles from 8-wk-old littermate pigs, which had been living 35 or 10 degrees C on either a high or a low energy intake for 3-4 wk. Changes in neither plasma thyroid hormone concentrations nor myofiber type could account for the greater Bmax at 10 vs. 35 degrees C observed in all three muscles; instead, it was possibly related to the greater muscular activity associated with shivering in the cold. More than 50% of the increase in Bmax on the low compared with the high intake in the cold could be attributed to the smaller fiber size and hence greater membrane area in animals on the low intake, and it is concluded that membrane surface area must be assessed in studies of membrane-bound enzymes.

Animals↗
PubMed1992

Evolutionary relationships among sulfur- and iron-oxidizing eubacteria.

Some 37 reverse transcriptase, partial 16S rRNA sequences from sulfur- and/or iron-oxidizing eubacteria, including sequences from species of the genera Thiobacillus, Thiothrix, Thiomicrospira, Acidophilium, "Leptospirillum," Thiovulum, and Chlorobium, have been determined. In addition, 16S sequences from a number of unnamed sulfur- and/or iron-oxidizing bacteria from hydrothermal vent sites, from invertebrate-bacterial endosymbioses, and from various mineral recovery operations also have been determined. The majority of sequences place their bacterial donors in one or another of the subdivisions of the Proteobacteria. However, three unnamed facultatively thermophilic iron-oxidizing isolates, Alv, BC, and TH3, are affiliated with the gram-positive division. One H2S-oxidizer, from the genus Thiovulum, is affiliated with Campylobacter, Wolinella, and other genera in what appears to be a new subdivision of the Proteobacteria. Three "Leptospirillum"-helical vibrioid isolates, BU-1, LfLa, and Z-2, exhibit no clear phylum level affiliation at all, other than their strong relationship to each other. A picture is emerging of an evolutionary widespread capacity for sulfur and/or iron oxidation among the eubacteria.

Bacteria↗