Sequence search algorithm assessment and testing toolkit (SAT)

MOTIVATION

The Sequence Search Algorithm Assessment and Testing Toolkit (SAT) aims to be a complete package for the comparison of different protein homology search algorithms. The structural classification of proteins can provide us with a clear criterion for judgment in homology detection. There have been several assessments based on structural sequences with classifications but a good deal of similar work is now being repeated with locally developed procedures and programs. The SAT will provide developers with a complete package which will save time and produce more comparable performance assessments for search algorithms. The package is complete in the sense that it provides a non-redundant large sequence resource database, a well-characterized query database of proteins domains, all the parsers and some previous results from PSI-BLAST and a hidden markov model algorithm.

RESULTS

An analysis on two different data sets was carried out using the SAT package. It compared the performance of a full protein sequence database (RSDB100) with a non-redundant representative sequence database derived from it (RSDB50). The performance measurement indicated that the full database is sub-optimal for a homology search. This result justifies the use of much smaller and faster RSDB50 than RSDB100 for the SAT.

AVAILABILITY

A web site is up. The whole packa ge is accessible via www and ftp. ftp://ftp.ebi.ac.uk/pub/contrib/jong/SAT http://cyrah.ebi.ac.uk:1111/Proj/Bio/SAT http://www.mrc-lmb.cam.ac.uk/genomes/SAT In the package, some previous assessment results produced by the package can also be found for reference.

CONTACT

jong@ebi.ac.uk

Helicobacter pylori extracts reduce gastric mucosal blood flow by a nitric oxide-independent but mast cell- and platelet-activating factor receptor-dependent pathway in rats

BACKGROUND

We have previously shown that water extracts from Helicobacter pylori reduce gastric mucosal blood flow by approximately 15%. It has also been suggested that H. pylori can inhibit endogenous nitric oxide (NO) biosynthesis. Our aim was to examine whether the reduction in blood flow induced by H. pylori is the direct consequence of an NO synthase inhibition and the possible involvement of mast cell degranulation.

METHODS

A water extract was produced from wildtype strain 88-23. The extract was applied on the exteriorized gastric corporal mucosa in inactin-anesthetized rats, after removing as much as possible of the mucus layer, during intravital microscopy. Blood flow was measured with laser-Doppler flowmetry.

RESULTS

In rats pretreated with the NO synthase inhibitor N-nitro-L-arginine there was a 19% +/- 6% reduction in blood flow 40 min after application of the extract, and a 27% +/- 9% reduction after another 20 min with saline. The reduction was abolished by concomitant pretreatment with the mast cell stabilizer ketotifen or the platelet-activating factor (PAF) receptor antagonist WEB2086.

CONCLUSION

The reduction in mucosal blood flow induced by the extract was probably mediated through an acute inflammatory response involving mast cell degranulation with consequent PAF secretion. The effect on blood flow was not the result of a decrease in vascular tone due to an inhibition of endogenous NO biosynthesis.

Coenzyme Q10 in health and disease

The literature concerning the importance of coenzyme Q10 in health and disease has been reviewed. Usual dietary intake together with normal in vivo synthesis seems to fulfil the demands for Q10 in healthy individuals. The importance of Q10 supplementation for general health has not been investigated in controlled experiments. The literature allows no firm conclusions about the significance of Q10 in physical activity. In different cardiovascular diseases, including cardiomyopathy, relatively low levels of Q10 in myocardial tissue have been reported. Positive clinical and haemodynamic effects of oral Q10 supplementation have been observed in double-blind trials, especially in chronic heart failure. These effects should be further examined. No important adverse effects have been reported from experiments using daily supplements of up to 200 mg Q10 for 6-12 months and 100 mg daily for up to 6 y.

[Changes in food habits among the population from 1995 to 1998]

In order to survey trends in food habits the Danish Nutrition Council initiated two food frequency surveys, comprising ten nutritionally important foods, in 1995 and in 1998. Participants were men and women, 15-90 yrs, from similar population samples (n = 1007 in 1995, 1024 in 1998). Participation rate was 62% in 1995 and 63% in 1998. Data were collected by telephone interview. For six of the ten foods significant changes in consumption frequencies were observed: salad/raw vegetables, rice/pasta and fish were consumed more frequently in 1998, whereas consumption of meat, potatoes and fresh fruit had become less frequent. Average frequencies differed by 4-13%. In 1998 low-fat milk had become more common, whereas whole milk was now less common. More subjects now skipped fat spreads on their bread, but more chose spreads containing butterfat. Some, but not all, of the observed changes point in the right direction compared to recommendations. The results demonstrate that food habits are currently in a dynamic process.

Sweat production and localisation of carbonic anhydrase in the equine sweat gland during exercise at two ambient temperatures

The aim of this investigation was to study sweat production during exercise at 2 ambient temperatures (20 degrees C and 35 degrees C) and the concurrent localisation of carbonic anhydrase (CA) in the sweat gland. Horses develop alkalosis during prolonged exercise and the sweat contains HCO3-. Carbonic anhydrase is therefore of interest since it catalyses the reaction CO2 + H2O<-->HCO3- + H+. Four standardbred trotters performed an exercise test. Skin biopsies were taken from the neck, and sweat rate, blood and skin temperatures were measured. There was a close relationship between sweat rate, temperatures and work intensity at 20 degrees C. Temperatures and sweat rate were higher at 35 degrees C and did not fall when the work intensity dropped. A significant decrease in the sweat gland cell area was found after exercise at 35 degrees C with an accompanying decrease of vesicles. Strong CA activity was present at the luminal cell membrane and weaker basolaterally. The staining intensity increased after exercise. We suggest that CA might be of importance for counteracting the alkalosis developed after exercise by delivering HCO3- for generation of the alkaline pH in sweat.

Sensitization to allergens of house-dust mite in adults with atopic dermatitis in a cold temperature region

BACKGROUND

An IgE-mediated contact reaction to airborne allergens has been suggested as one important pathogenetic mechanism in atopic dermatitis (AD). The house-dust mite (HDM) might be a common allergen involved. In Scandinavia, sensitization to HDM has been rare, probably because of the cold, dry climate. However, recent studies indicate high levels of domestic mites and HDM allergen in 15-20% of homes in central and northern Sweden.

METHODS

To evaluate the importance of the HDM in patients with AD in the Stockholm region, we screened 81 adult Stockholm residents with AD, for the prevalence and degree of sensitization to the HDM, according to specific IgE (RAST), skin prick test (SPT), and atopy patch test (APT). We also assessed the HDM exposure in their homes and correlated the results with clinical history, severity of the dermatitis, and type of residence during childhood and today.

RESULTS

The sensitization rate to HDM was high (56% according to RAST, 24% according to SPT, and 47% according to APT), and 20% of the patients were exposed to HDM allergens in their beds. Mite exposure seemed to aggravate the dermatitis in highly sensitized patients.

CONCLUSIONS

The results indicate that we have to take the HDM into account when discussing aggravating factors in adult patients with AD in the Stockholm region.

Impairment and work disability due to whiplash injury following traffic collisions. An analysis of insurance material from the Swedish Road Traffic Injury Commission

A study was set up to determine the trends in medical impairment and work disability ratings for persons affected by whiplash associated disorders (WAD) and other injuries secondary to road traffic collisions, and into the influence of age, gender, professional status, and final medical impairment rating on final work disability. A cross-sectional study was carried out of insurance files of 2,523 subjects in 1989 and 3,223 subjects in 1994 judged to have a permanent medical impairment of 10% or more and work disability due to road traffic injury. Files were obtained from the Swedish Road Traffic Injury Commission. The main outcome measures were the crude frequency and age-specific, standardized percentage of traffic injuries with a medical impairment of 10% or more for the years 1989 and 1994. Final work disability status was analysed with respect to age, gender, type of injury, degree of medical impairment, and professional status. The proportion of medical impairment due to WAD was found to have increased from 16% in 1989 to 28% in 1994, but the proportion of work disability was found to have remained the same. Age over 40 years, low professional status, and having a medical impairment judgement of 15% or more were independently associated with reduced or full work disability.

Randomized trial on protein vs carbohydrate in ad libitum fat reduced diet for the treatment of obesity

OBJECTIVE

To study the effect on weight loss in obese subjects by replacement of carbohydrate by protein in ad libitum consumed fat-reduced diets.

DESIGN

Randomized dietary intervention study over six months comparing two ad libitum fat reduced diets (30% of total energy) strictly controlled in composition: High-carbohydrate (HC, protein 12% of total energy) or high-protein (HP, protein 25% of total energy).

SETTING AND PARTICIPANTS

Subjects were 65 healthy, overweight and obese subjects (50 women, 15 men, aged 18-55 y) randomly assigned to HC (n = 25), HP (n = 25) or a control group (C, n = 15). All food was provided by self-selection in a shop at the department, and compliance to the diet composition was evaluated by urinary nitrogen excretion.

MAIN OUTCOME MEASURE

Change in body weight, body composition and blood lipids.

RESULTS

More than 90% completed the trial. Weight loss after six months was 5.1 kg in the HC group and 8.9 kg in the HP group (difference 3.7 kg, 95% confidence interval (CI)(1.3-6.2 kg) P < 0.001), and fat loss was 4.3 kg and 7.6 kg, respectively (difference 3.3 kg (1.1-5.5 kg) P < 0.0001), whereas no changes occurred in the control group. More subjects lost > 10 kg in the HP group (35%) than in the HC group (9%). The HP diet only decreased fasting plasma triglycerides and free fatty acids significantly.

CONCLUSIONS

Replacement of some dietary carbohydrate by protein in an ad libitum fat-reduced diet, improves weight loss and increases the proportion of subjects achieving a clinically relevant weight loss. More freedom to choose between protein-rich and complex carbohydrate-rich foods may allow obese subjects to choose more lean meat and dairy products, and hence improve adherence to low-fat diets in weight reduction programs.

Preferences, quantities and concerns: socio-cultural perspectives on the gendered consumption of foods

A review of the sociological research regarding the gendered features of food consumption is presented. The focus is upon differences between women and men in regard to their preferences for particular foods and types of meals, seen in relation to the cultural function of foods as symbolic markers of femininity or masculinity, assessments of the quantities of food consumed by women and men respectively, and differences between women and men in regard to concerns with food safety, health, weight reduction and fitness. Some methodological limitations of this research are discussed with particular reference to the need for interdisciplinary cooperation between sociologists and nutritionists in the design and analysis of dietary surveys. Suggestions are made in regard to future directions for sociological research in this field, with particular reference to the issue that dietary recommendations appear to focus upon increasing the consumption of foods that are markers of femininity and decreasing the consumption of foods that are markers of masculinity in Western food culture.

Nordic meals: methodological notes on a comparative survey

This article discusses some methodological aspects of the project "Eating and Modern Everyday Life. A Comparative Survey of Nordic Countries". Data were collected in April 1997 with computer assisted telephone interviews in Denmark, Finland, Norway and Sweden. Questionnaires included a record of the informant's eating on the day before the interview, attitudes related to current food discourses, socio-demographic information and a few open-ended questions. The emphasis was on social and cultural aspects of eating. One aim of this study is to investigate whether regular meals are substituted by irregular eating patterns. In order to avoid any predefined meal concepts the questionnaire therefore focused on eating events. The reconstruction of data is based on a model called the eating system. The model has three dimensions: the eating pattern (the rhythm and the number of eating events, the alternations of hot and cold eating events), the meal format (the composition of the main course, the sequence of the whole meal) and the social organization of eating (where and with whom people are eating, who did the cooking). Some preliminary results are presented suggesting that the questionnaire and the analytical model suit the purpose of studying modernization through the field of food.

Protein folds and families: sequence and structure alignments

Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). As a result, the HSSP database not only provides aligned sequence families, but also implies secondary and tertiary structures covering 36% of all sequences in Swiss-Prot. The structure classification by Dali and the sequence families in HSSP can be browsed jointly from a web interface providing a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences. In particular, this results in a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The organization of protein structures and families provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The databases are available from http://www.embl-ebi.ac.uk/dali/

Extracts of Helicobacter pylori reduce gastric mucosal blood flow through a VacA- and CagA-independent pathway in rats

BACKGROUND

Helicobacter pylori may interfere with gastroduodenal protective mechanisms. Such effects could be due to a direct interaction with gastric epithelial cells but also to the action of a wide range of secreted and membrane-bound virulence factors. Our aim was to study the acute effects of water extracts produced from H. pylori on gastric mucosal blood flow and acid secretion and to relate them to VacA and CagA activity.

METHOD

Extracts were produced from strains 88-23 and A5, both wild type; A5VacA, an isogenic mutant lacking expression of the vacuolating cytotoxin (VacA) and the immunodominant antigen (CagA); and Escherichia coli strain ATCC-25922. Bacterial extracts were applied on the exteriorized gastric corporal mucosa in inactin-anaesthetized rats after removal of as much as possible of the mucus layer, during intravital microscopy. Blood flow was measured by means of laser-Doppler flowmetry.

RESULTS

All H. pylori extracts, including the extract from 88-23 heated to 100 degrees C for 30 min, significantly reduced blood flow by 15%-19%, whereas E. coli had no significant effect on blood flow.

CONCLUSION

A factor or a combination of factors, other than VacA and CagA released from H. pylori, might compromise the natural defence of the gastric corporal mucosa by reducing mucosal blood flow. The factor is heat-stable and lacking or less potent in E. coli.

The effect of pH on the motility of spermatozoa from chicken, turkey and quail

At 40 degrees C in a NaCl-based buffer the motility of spermatoza from chicken, turkey and quail was inhibited at pH values below 7.8, 7.2 and 7.2, respectively. At these pH values the percentage motile and velocity of spermatoza were relatively low, but the motility became vigorous when the pH was raised by 0.2 units and increased even more following further alkalinization. Spermatozoa from all three species stored motionless at pH 6.0 for 3 h could be reactivated by dilution in an alkaline solution (pH 9.0). These findings support the hypothesis that a change in the environmental pH could be implicated in the suppression and stimulation of sperm motility during oviducal sperm storage and transport.

Effectiveness of a dietary intervention strategy in general practice: effects on blood lipids, health and well-being

OBJECTIVES

To evaluate the effect of a dietary treatment programme on blood cholesterol concentration in hypercholesterolaemic patients in general practice and to analyse subjectively experienced side-effects.

DESIGN

A 1-year parallel trial comparing a new treatment programme with conventional treatment.

SETTING

General practitioners in Roskilde county, Denmark.

SUBJECTS

355 men and women, aged 20-60 years, with a persistent blood cholesterol concentration above age- and gender-specific cut-off points (265 in an intervention group and 90 in a control group).

INTERVENTION

A treatment strategy based on collaboration between doctor and dietitian using individual dietary advice and feedback from measured biological parameters.

MAIN OUTCOME MEASURES

Serum lipids, body weight, blood pressure, dietary behaviour, health parameters, quality of life parameters and acceptance by patients and general practitioners.

RESULTS

Total blood cholesterol concentration decreased by 14% (1.07 mmol l(-1), P < 0.0001) in 159 patients in the intervention group, not having any lipid altering drug during treatment, in addition to 3% from screening to start of treatment. In 65 patients in the control group, without any lipid altering drug, the reduction of cholesterol concentration was 4% (0.27 mmol l(-1), P < 0.01; intervention vs. control P < 0.001). In the intervention group overweight subjects (body mass index > 30) reduced body weight by 6% (P < 0.0001). Systolic blood pressure was reduced by 11% (P < 0.0001) and diastolic blood pressure by 10% (P < 0.0001) and 19% (P < 0.003) for intervals 90-110 mmHg and > 110 mmHg, respectively. Risk score decreased and self-assessed health, physical and psychological well-being improved.

CONCLUSIONS

The treatment strategy tested proved to be efficient, without side-effects and well accepted by patients and general practitioners. The results strongly suggest that hypercholesterolaemia can efficiently be treated non-pharmacologically in general practice.

[Despite better knowledge of pathogenesis and treatment: atopic eczema--a disease with increasing incidence in Sweden]

The past twenty years have witnessed an increasing incidence of atopic dermatitis in Western Europe. The article consists in a discussion of the pathogenesis, clinical signs and treatment of this common skin disease. Both an IgE-mediated reaction on epidermal Langerhans cells, and a physiological/biochemical defect of the skin barrier structure may be crucial factors of the multifactorial pathogenesis. Local treatment with corticosteroids and moisturisers remains the basic approach, though the development of new more specific treatments is under way. Although much remains to be learned about atopic dermatitis, today all patients can be offered effective treatment resulting in improved quality of life.

Dictionary of recurrent domains in protein structures

The rapid growth in the number of experimentally determined three-dimensional protein structures has sharpened the need for comprehensive and up-to-date surveys of known structures. Classic work on protein structure classification has made it clear that a structural survey is best carried out at the level of domains, i.e., substructures that recur in evolution as functional units in different protein contexts. We present a method for automated domain identification from protein structure atomic coordinates based on quantitative measures of compactness and, as the new element, recurrence. Compactness criteria are used to recursively divide a protein into a series of successively smaller and smaller substructures. Recurrence criteria are used to select an optimal size level of these substructures, so that many of the chosen substructures are common to different proteins at a high level of statistical significance. The joint application of these criteria automatically yields consistent domain definitions between remote homologs, a result difficult to achieve using compactness criteria alone. The method is applied to a representative set of 1,137 sequence-unique protein families covering 6,500 known structures. Clustering of the resulting set of domains (substructures) yields 594 distinct fold classes (types of substructures). The Dali Domain Dictionary (http://www.embl-ebi.ac.uk/dali/) not only provides a global structural classification, but also a comprehensive description of families of protein sequences grouped around representative proteins of known structure. The classification will be continuously updated and can serve as a basis for improving our understanding of protein evolution and function and for evolving optimal strategies to complete the map of all natural protein structures.

[The sociopsychological importance of food in hospital. Evaluation of a new meal system in a children's cancer ward]

Malnutrition of patients in hospitals is a subject that is fairly well described in the medical literature, but less attention has been paid to the social significance of food in hospitals. This article describes a study of the social and psychological impact of the introduction of a new meal delivery system in a children's cancer ward. A traditional centralized meal system was replaced by a staffed local kitchen. The evaluation involved questionnaires to the children, parents and staff members; qualitative, indepth, semi-structured interviews with subgroups; observations of meals. Children, staff and parents greatly preferred the new meal system, which changed the significance of food and meals in the hospital: from an arena of conflict and problems to one with a greatly enhanced social status. The article underlines that it is important to integrate socio-psychological and nutritional aspects of food and eating if malnutrition in hospitals is to be overcome.

Localization of carbonic anhydrase in the sperm-storing regions of the turkey and quail oviduct

The localization of carbonic anhydrase in the sperm storage regions of turkey and quail was investigated using a histochemical method showing the activity of all the isozymes present. Intense carbonic anhydrase activity was found in the turkey sperm storage tubules and infundibular storage glands, whereas no activity could be detected in the quail at these sites. Both species did, however, show strong membrane-bound and cytoplasmic activity in the non-ciliated cells of the utero-vaginal surface epithelium and scattered cells of the vaginal epithelium. The enzyme catalyses the reaction CO2 + H2O <--> H+ + HCO3-, and the presence of carbonic anhydrase in these regions makes rapid changes in pH possible. It is suggested that increasing pH and/or the addition of bicarbonate stimulates sperm motility needed during transfer of the oviducal lumen. A lowering of the pH would keep the sperm quiescent during storage. The duration of sperm storage is considerably longer in the turkey than in the quail. The high quantity of carbonic anhydrase in the turkey sperm storage tubules may, thus, play a role in the duration of sperm storage.

Removing near-neighbour redundancy from large protein sequence collections

MOTIVATION

To maximize the chances of biological discovery, homology searching must use an up-to-date collection of sequences. However, the available sequence databases are growing rapidly and are partially redundant in content. This leads to increasing strain on CPU resources and decreasing density of first-hand annotation.

RESULTS

These problems are addressed by clustering closely similar sequences to yield a covering of sequence space by a representative subset of sequences. No pair of sequences in the representative set has >90% mutual sequence identity. The representative set is derived by an exhaustive search for close similarities in the sequence database in which the need for explicit sequence alignment is significantly reduced by applying deca- and pentapeptide composition filters. The algorithm was applied to the union of the Swissprot, Swissnew, Trembl, Tremblnew, Genbank, PIR, Wormpep and PDB databases. The all-against-all comparison required to generate a representative set at 90% sequence identity was accomplished in 2 days CPU time, and the removal of fragments and close similarities yielded a size reduction of 46%, from 260 000 unique sequences to 140 000 representative sequences. The practical implications are (i) faster homology searches using, for example, Fasta or Blast, and (ii) unified annotation for all sequences clustered around a representative. As tens of thousands of sequence searches are performed daily world-wide, appropriate use of the non-redundant database can lead to major savings in computer resources, without loss of efficacy.

AVAILABILITY

A regularly updated non-redundant protein sequence database (nrdb90), a server for homology searches against nrdb90, and a Perl script (nrdb90.pl) implementing the algorithm are available for academic use from http://www.embl-ebi.ac. uk/holm/nrdb90.

CONTACT

holm@embl-ebi.ac.uk

Unification of protein families

Computational biology exploits the evolutionary connectivity between proteins and protein families to predict structural and functional properties of uncharacterized gene products. In the past year, conceptual and statistical refinements have substantially improved algorithms for the detection of remote homologues. In conjunction with the rapid growth of biological databases, the global organization of proteins into sequence families, functional families and structural families has become both pertinent and feasible.

Prostaglandin E2 and aggressive factors increase the gland luminal pressure in the rat gastric mucosa in vivo

BACKGROUND & AIMS

The gastroprotective properties of prostaglandins in low concentrations are still unclear. In this study, we investigated the effects of prostaglandin E2 (PGE2), indomethacin, and intraluminally applied HCl or ethanol on intraglandular pressure, mucus thickness, acid secretion, and gastric mucosal blood flow.

METHODS

Glandular pressure and mucous gel thickness were measured with microelectrodes during intravital microscopy in thiobutabarbital sodium-anesthetized rats. Gastric blood flow was measured with laser Doppler flowmetry.

RESULTS

In pentagastrin-treated rats, glandular pressure increased significantly in response to topical (1 micrograms/mL) or intra-arterial (12 micrograms.kg-1.h-1) PGE2 from approximately 17 to 69 and 18 to 57 mm Hg, respectively, whereas blood flow, mucus thickness, and acid secretion were unaltered. Indomethacin (3 mg/kg intravenously) significantly decreased glandular pressure from approximately 20 to 11 mm Hg. Intraluminal application of 10 and 100 mmol/L HCl or 20% and 40% ethanol significantly increased glandular pressure but had no effect after indomethacin pretreatment.

CONCLUSIONS

Endogenous PGE2 is important for maintaining a high glandular pressure, and exogenous PGE2 potently increases glandular pressure at concentrations not altering blood flow, mucus thickness, or acid secretion. This suggests that high intraglandular pressures might be involved in gastroprotection.

COFFEE: an objective function for multiple sequence alignments

MOTIVATION

In order to increase the accuracy of multiple sequence alignments, we designed a new strategy for optimizing multiple sequence alignments by genetic algorithm. We named it COFFEE (Consistency based Objective Function For alignmEnt Evaluation). The COFFEE score reflects the level of consistency between a multiple sequence alignment and a library containing pairwise alignments of the same sequences.

RESULTS

We show that multiple sequence alignments can be optimized for their COFFEE score with the genetic algorithm package SAGA. The COFFEE function is tested on 11 test cases made of structural alignments extracted from 3D_ali. These alignments are compared to those produced using five alternative methods. Results indicate that COFFEE outperforms the other methods when the level of identity between the sequences is low. Accuracy is evaluated by comparison with the structural alignments used as references. We also show that the COFFEE score can be used as a reliability index on multiple sequence alignments. Finally, we show that given a library of structure-based pairwise sequence alignments extracted from FSSP, SAGA can produce high-quality multiple sequence alignments. The main advantage of COFFEE is its flexibility. With COFFEE, any method suitable for making pairwise alignments can be extended to making multiple alignments.

AVAILABILITY

The package is available along with the test cases through the WWW: http://www. ebi.ac.uk/cedric

CONTACT

cedric.notredame@ebi.ac.uk

Predicting protein structure using hidden Markov models

We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over 1,000 structures from the Protein Data Bank (PDB). Each CASP2 target sequence was scored against this library of HMMs. In addition, an HMM was built for each of the target sequences and all of the sequences in PDB were scored against that target model, with a good score on both methods indicating a high probability that the target sequence is homologous to the structure. The method worked well in comparison to other methods used at CASP2 for targets of moderate difficulty, where the closest structure in PDB could be aligned to the target with at least 15% residue identity.

Gastric mucosal smooth muscles may explain oscillations in glandular pressure: role of vasoactive intestinal peptide

BACKGROUND & AIMS

Oscillating (3-7 cycles/min) high pressures in gastric glands during acid secretion suggest the existence of rhythmically contracting mucosal muscles. The aim of this study was to study vasoactive intestinal peptide (VIP), an inhibitory neurotransmitter in the gastrointestinal tract, in relation to mucosal muscles, glandular pressure, and blood flow.

METHODS

Rat, dog, and human mucosae were examined immunocytochemically for smooth muscle actin and VIP. Glandular pressure was measured using microelectrodes, red blood cell velocity (V[RBC]) was measured using a cross-correlation technique, and blood flow was measured using laser Doppler flowmetry in exposed gastric mucosa of thiobutabarbital sodium-anesthetized rats.

RESULTS

Actin immunostaining showed muscle strands arising from muscularis mucosae, extending toward the gastric pits. VIP-immunoreactive nerve fibers were found in close relation to these muscles. VIP, administered intra-arterially close to the stomach (2 microg/kg bolus, followed by 10 microg x kg[-1] x h[-1]), significantly decreased glandular pressure from 18.2 +/- 1.6 to 8.9 +/- 1.6 mm Hg and almost eliminated the pressure oscillations. VIP infusion also abolished the oscillations in V(RBC) and significantly increased blood flow by approximately 35%.

CONCLUSIONS

Contracting mucosal muscles may be responsible for oscillations in glandular pressure and possibly also in V(RBC). VIP probably relaxes these muscles.

Pityrosporum orbiculare-reactive T-cell lines in atopic dermatitis patients and healthy individuals

The yeast Pityrosporum orbiculare is one of the factors that may contribute to atopic dermatitis (AD). In the present study we compared the T-cell response to P. orbiculare in 12 AD patients with specific immunoglobulin (Ig)E antibodies (Ab) in serum against P. orbiculare with that of six non-atopic healthy controls. Freshly isolated peripheral blood mononuclear cells (PBMC) were cultured for 3 days in the presence of P. orbiculare extract. The proliferative response as measured by [3H]-thymidine incorporation was significantly higher in the AD patients than in the healthy controls (P < 0.05). Furthermore, significantly higher levels of interleukin (IL)-5 (P < 0.05), as analyzed by ELISA, were produced by PBMC from the AD patients compared to the healthy controls. Pityrosporum orbiculare-reactive T-cell lines (TCL) established by P. orbiculare stimulation of PBMC for 11 days produced significantly higher levels of IL-4 and IL-5 after stimulation with anti-CD3 Ab and showed a higher IL-4/interferon (IFN)-gamma ratio (P < 0.05) in the AD patients compared to the healthy controls. The higher proliferative PBMC response to P. orbiculare and the Th2-like cytokine production by P. orbiculare-stimulated TCL from AD patients indicate that P. orbiculare may play a role in maintaining skin inflammation in AD.

Touring protein fold space with Dali/FSSP

The FSSP database and its new supplement, the Dali Domain Dictionary, present a continuously updated classification of all known 3D protein structures. The classification is derived using an automatic structure alignment program (Dali) for the all-against-all comparison of structures in the Protein Data Bank. From the resulting enumeration of structural neighbours (which form a surprisingly continuous distribution in fold space) we derive a discrete fold classification in three steps: (i) sequence-related families are covered by a representative set of protein chains; (ii) protein chains are decomposed into structural domains based on the recurrence of structural motifs; (iii) folds are defined as tight clusters of domains in fold space. The fold classification, domain definitions and test sets for sequence-structure alignment (threading) are accessible on the web at www.embl-ebi.ac.uk/dali . The web interface provides a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences leading, for example, to a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The Dali/FSSP organization of protein structures provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination.

[Efficacy and safety of dietary supplementation containing Q10]

The literature concerning the importance of Q10 for health and disease has been reviewed. Dietary intake together with normal in vivo synthesis seems to fulfil the body's demands for Q10 in younger, healthy individuals. The importance of Q10 in general well-being has not been investigated in controlled experiments. The literature allows no firm conclusions about the significance of Q10 in physical activity. In different cardiovascular diseases a positive effect of oral Q10 supplementation has been reported, especially in chronic heart failure. These effects should be further examined. No important adverse side effects have been reported from experiments using daily supplements of up to 200 mg of Q10 for six to twelve months, and 100 mg daily for up to six years.

Decision support system for the evolutionary classification of protein structures

The structures of nearly a thousand sequence-unique proteins represent only 300 different 3D shapes. Is structural resemblance between proteins with little sequence similarity the result of physical convergence to favourable folding patterns, or does it reflect a memory of common evolutionary history? Separating these two processes is important for organizing genome data in terms of protein families and for theoretical approaches to protein structure prediction by fold recognition techniques. Achieving separation requires a combination of structure, sequence and functional analysis of proteins. For this purpose, we are developing a decision support system that scans heterogeneous protein sequence and structure related databases, and collects or calculates characters indicative of common functional constraints. The criteria include sequence homology, analysis of 3D clusters of conserved residues, conservation of active sites, and keyword analysis of biological function. Even without extensive refinement, application of a combination of these criteria to a test set representing all currently known protein structures yields 87% coverage with 7% false positives, compared to 53% coverage by only 1D sequence criteria. Thus, the semiautomatic prototype system significantly enhances the efficiency of unifying families of functionally related proteins in spite of long evolutionary distances.

Elevated serum levels of soluble CD30 in patients with atopic dermatitis (AD)

The immunopathology of AD is still unclear, but evidence for an immune response polarized towards Th2 activity has been provided. The CD30 molecule belongs to the tumour necrosis factor (TNF) receptor family and is expressed on activated T cells with a sustained expression in Th2 cells. This molecule also exists in a soluble form (sCD30). Elevated serum levels of sCD30 have been found in patients with Hodgkin's disease, chronic hepatitis B infection and HIV infection. Studies were undertaken to compare the serum levels of sCD30 in patients with AD (n=49) and healthy non-atopic controls (n=94). The presence of sCD30 was analysed with ELISA. A significantly higher concentration of sCD30 was noted in AD patients, median sCD30 level 29 U/ml (range 1-708 U/ml), compared with healthy non-atopic controls (P<0.001), where the median level was 11 U/ml with a range of 1-1042 U/ml. No correlation was found between sCD30 levels and total serum IgE, or between the AD patients' SCORAD values and concentration of sCD30. sCD30 levels were also analysed in 20 AD patients, which during ketoconazole treatment had improved their clinical scores and reduced their serum IgE and eosinophil cationic protein levels. However, no significant decrease in sCD30 levels was noted after treatment. The results show that patients with AD have elevated levels of sCD30, but without correlation to total serum IgE or disease activity.

Difficulties in trying to eat healthier: descriptive analysis of perceived barriers for healthy eating

OBJECTIVE

To determine the factors which are perceived to be important barriers to healthy eating among European adults.

DESIGN

A cross sectional study in which quota-controlled, nationally-representative samples of approximately 1000 adults from each country completed a face-to-face interview-assisted questionnaire.

SETTING

The survey was conducted between October 1995 and February 1996 in the 15 member states of the European Union.

SUBJECTS

14,331 subjects (aged 15 y upwards) completed the questionnaire. Data were weighted by population size for each country and by sex, age and regional distribution within each member state.

RESULTS

The study demonstrates a great variability in the perceived barriers to healthy eating between different EU countries. Lack of time was the most frequently mentioned difficulty among EU subjects for not following nutritional advice (24% of total EU sample). This barrier was frequently reported by the younger and the higher education people. Other frequently reported barriers were giving up favourite foods (23%) and willpower (18%). Thus healthy diets do not appear to be viewed as an easy or attractive alternative to current diets. There was wide geographical variation in the number of subjects mentioning price as an important barrier to healthy eating (15% in overall EU sample) ranging from less than 10% in Germany and Italy to 23% in the UK and 24% in Luxembourg.

Definitions of 'healthy' eating: a pan-EU survey of consumer attitudes to food, nutrition and health

OBJECTIVE

To describe the perceptions of a healthy diet across Europe and to explore the socio-cultural factors that influence these perceptions.

DESIGN

A cross-sectional study in which quota-controlled, nationally-representative samples of approximately 1000 adults from each country completed a face-to-face interview-assisted questionnaire.

SETTING

The survey was conducted between October 1995 and February 1996 in the 15 member states of the European Union.

SUBJECTS

14331 subjects (aged 15 y upwards) completed the questionnaire. Data were weighted by population size for each country and by sex, age and regional distribution within each member state.

RESULTS

Responses were grouped into broad categories; overall 80% (specific country rates varied from 67-91%) of respondents mentioned either more fruit and vegetables or less fat, fatty foods, or a low fat diet, or balance and variety. The effects of age, gender and level of education were also explored: educational level appeared to have the strongest influence on perceptions of a healthy diet. Respondents who mentioned the family as a key influence on food choice, were more likely to mention eating more fruit and vegetables as part of a healthy diet. Respondents who stated that they did not have any source of information about diet were less likely to mention balance and variety or less fat or more vegetables.

CONCLUSIONS

The results of the present study suggest that many people defined healthy eating in a way which would suggest that the healthy dietary guidelines are having some impact. The results also show, however, that there may be specific groups who are missed by current national campaigns, and that any European wide campaigns to change attitudes about healthy eating need to consider the baseline perception of healthy eating reported here.

An evolutionary treasure: unification of a broad set of amidohydrolases related to urease

The recent determination of the three-dimensional structure of urease revealed striking similarities of enzyme architecture to adenosine deaminase and phosphotriesterase, evidence of a distant evolutionary relationship that had gone undetected by one-dimensional sequence comparisons. Here, based on an analysis of conservation patterns in three dimensions, we report the discovery of the same active-site architecture in an even larger set of enzymes involved primarily in nucleotide metabolism. As a consequence, we predict the three-dimensional fold and details of the active site architecture for dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases, and proteins involved in animal neuronal development. Two member families are common to archaea, eubacteria, and eukaryota. Thirteen other functions supported by the same structural motif and conserved chemical mechanism apparently represent later adaptations for different substrate specificities in different cellular contexts.

Effect of inhibition of pentagastrin-stimulated acid secretion on gastric mucosal gland luminal pressure

We demonstrated previously that hydrochloric acid secreted from the gastric glands traverses the mucus layer in channels above the gland openings. The driving force for creation of these channels is most probably the hydrostatic pressure generated in the gastric gland lumen during stimulation of acid secretion. Here we investigated the effect of total inhibition of acid secretion on gland luminal pressure. Glandular pressure was measured in vivo with a pressure-sensitive microelectrode technique in Inactin-anaesthetized Sprague Dawley or Lewis x DA F1 rats. Glandular pressure was significantly reduced after ranitidine inhibition of acid secretion, from 17.2 +/- 2.1 mmHg during pentagastrin stimulation to 11.2 +/- 1.2 mmHg. This was also true when pentagastrin infusion was continued after inhibition of secretion with ranitidine. Omeprazole, however, did not significantly alter gland luminal pressure although it totally inhibited acid secretion. With continuation of pentagastrin infusion after omeprazole inhibition, glandular pressure increased significantly from 17.6 +/- 3.4 to 20.1 +/- 3.3 mmHg. In conclusion, total inhibition of acid secretion with ranitidine reduces but does not abolish gland luminal pressure. After omeprazole inhibition of acid secretion the gastric gland luminal pressure persisted or even increased. Since the volume secretion is lower after omeprazole administration than during pentagastrin stimulation, the outflow resistance most probably had increased after omeprazole injection. Suggestions for increased outflow resistance are narrowing in the upper part of the gland lumen by conformational changes of the cells or muscle contractions, and/or an increase in mucus secretion or viscosity.

Omeprazole induces high intraglandular pressure in the rat gastric mucosa

BACKGROUND & AIMS

In a few patients receiving high doses of omeprazole for a prolonged period, cystic changes have developed in the gastric mucosa, possibly consisting of enlarged gland lumina. To investigate this question, the luminal pressure in gastric glands was studied after omeprazole treatment in Inactin-anesthetized rats.

METHODS

The gland luminal pressure and mucus thickness were measured with microelectrodes. For pressure measurements (servo-null technique) the microelectrode was inserted into a gland at an angle of approximately 30 degrees to the mucosal surface.

RESULTS

Animals given omeprazole by gavage, 400 micromol/kg daily for 1 week, showed high gland luminal pressures (27.4 +/- 2.4 mm Hg). Similar values were found in animals given an intravenous omeprazole injection (40 micromol/kg). Much lower pressures were noted after vehicle or pentagastrin infusion. The thickness of the lower, firm mucus layer was not altered by omeprazole treatment.

CONCLUSIONS

The significantly higher gland luminal pressure after treatment with omeprazole, compared with the values during pentagastrin or vehicle infusion, cannot be explained by increased mucus thickness. The results suggest accumulation of fluid in the gland lumen caused by increased resistance to outflow from the gland. This might explain the proposed enlargement of gland lumina.

Dali/FSSP classification of three-dimensional protein folds

The FSSP database presents a continuously updated structural classification of three-dimensional protein folds. It is derived using an automatic structure comparison program (Dali) for the all-against-all comparison of over 6000 three-dimensional coordinate sets in the Protein Data Bank (PDB). Sequence-related protein families are covered by a representative set of 813 protein chains. Hierachical clustering based on structural similarities yields a fold tree that defines 253 fold classes. For each representative protein chain, there is a database entry containing structure-structure alignments with its structural neighbours in the PDB. The database is accessible online through World Wide Web browsers and by anonymous ftp (file transfer protocol). The overview of fold space and the individual data sets provide a rich source of information for the study of both divergent and convergent aspects of molecular evolution, and define useful test sets and a standard of truth for assessing the correctness of sequence-sequence or sequence-structure alignments.

[Food consumption of the population. Trends followed via telephone interviews]

This study aimed at establishing and evaluating a simple method for surveilling trends in consumption of 10 nutritionally important foods. The method is based on food frequency questions combined with questions on the previous days intake, collected through telephone interviews. Participants (461 men, 546 women, 15-60+ yrs) came from a population sample. Between 22 and 69% consumed the foods in question as frequently as prescribed by the Danish food recommendations (lowest for fish and for vegetables, highest for potatoes/rice/pasta). Characteristic sex and age differences were observed, similar to findings from traditional, quantitative food surveys in Denmark. The food frequency results were confirmed by results from the previous day's intake. Crossing of frequencies for different foods gave additional information on consumption patterns. The results indicate that this very simple method may be a useful supplement to traditional quantitative dietary surveys for surveilling trends in food consumption. The Danish Nutrition Council therefore aims at doing similar surveys every other year.

Power of one: nurses and tobacco control

OBJECTIVES

To review major events in cigarette marketing and smoking practices, and to examine courses of action that can be taken by nurses to impact public health and safety.

DATA SOURCES

Journal articles and news reports relating to the tobacco industry and tobacco regulations.

CONCLUSION

Every segment of society suffers economic and health consequences of tobacco use, yet the tobacco industry continues to successfully market and promote the use of tobacco. Successful approaches to control tobacco use can be initiated at the federal, state, or local level.

IMPLICATIONS FOR NURSING PRACTICE

Any nurse can take positive action toward tobacco control in numerous ways: by increasing awareness of the need for tobacco control; initiating personal action such as education and contacting legislators; and supporting public action through joining groups or coalitions whose efforts are directed at tobacco control.

Mapping the protein universe

The comparison of the three-dimensional shapes of protein molecules poses a complex algorithmic problem. Its solution provides biologists with computational tools to organize the rapidly growing set of thousands of known protein shapes, to identify new types of protein architecture, and to discover unexpected evolutionary relations, reaching back billions of years, between protein molecules. Protein shape comparison also improves tools for identifying gene functions in genome databases by defining the essential sequence-structure features of a protein family. Finally, an exhaustive all-on-all shape comparison provides a map of physical attractor regions in the abstract shape space of proteins, with implications for the processes of protein folding and evolution.

Consumers' views on food quality. A qualitative interview study

The study investigated the themes consumers discuss when describing their everyday considerations about food quality. Twenty Copenhagen families with young children were interviewed open-endedly concerning daily food-related practices and thoughts, making particular use of narrative descriptions of specific meals. Respondents expressed both positive and negative opinions about a broad variety of processed and unprocessed foods. Positive opinions about food quality related mainly to personal criteria such as taste or convenience. Negative comments mainly related to how foods were processed or distributed. The study suggests that concerns about food safety are integrated in everyday concepts of food quality, and that consumers individually develop strategies to deal with this. However, feelings of uncertainty, helplessness and self reproach were frequently reported. The results suggest that choices of foods often reflect compromises in everyday life rather than the consumers' preferences.

Localisation of carbonic anhydrase in the sperm storing regions of the domestic hen oviduct

In the female bird sperm is stored in a quiescent mode, but full motility is needed for successful fertilisation. Regulation of sperm motility is thus of vital interest and the pH is a factor of importance. For this reason the localisation of carbonic anhydrase in the vagina, uterovaginal junction and infundibulum was studied with a histochemical method. Carbonic anhydrase catalyses the reaction CO2 + H2O <--> H+ + HCO3- and is known to take significant part in acid-base regulation in the body. The enzyme was found in all regions with the highest activity, both cytoplasmic and membrane-bound, in the non-ciliated cells of the uterovaginal surface epithelium. Intense membrane-bound activity was also found in the infundibular grooves and glands with slightly less in the sperm storage tubules and vaginal epithelium. Occasionally cytoplasmic and nuclear staining was seen. Changes in pH affect sperm motility and our results provide the first evidence for cellular mechanisms that makes rapid changes of the pH possible in these regions. Judging from the distribution of carbonic anhydrase we suggest two possible functions: (1) increasing pH and/or adding bicarbonate ions to stimulate sperm motility needed for the transfer to the storage sites and at fertilisation, and (2) a lowering of the pH in the sperm storage sites to keep the sperm quiescent during storage.

Multidisciplinary intensive treatment for chronic low back pain: a randomized, prospective study

BACKGROUND

Americans with low back pain have been helped to return to work by multidisciplinary intensive treatment programs. Whether this treatment method will succeed in countries with a more generous social welfare system, where the incentive to return to work might be less, is not proven.

OBJECTIVES

To evaluate a Danish program of functional restoration combined with behavioral support.

METHODS

Patients who had experienced at least 6 months of disabling low back pain were randomly assigned to either a 3-week intensive treatment program (n = 55) or an untreated control group (n = 51).

RESULTS

Of the 106 patients randomized, 94 (89%) returned for a 4-month follow-up visit. At that time, 29 (64%) of the 45 treated patients were able to work, compared with 14 of 49 (29%) in the control group. The treated patients had used fewer days of sick leave (P < .02), had contacted health care. professionals fewer times (P < .001), and had lower pain and disability scores.

CONCLUSIONS

Although such programs are expensive, they can reduce pension expenditures, sick leave days, health care contacts, and pain.

The FSSP database: fold classification based on structure-structure alignment of proteins

The FSSP database presents a continuously updated classification of 3-D protein folds based on an all-against-all comparison of structures currently in the Protein Data Bank (PDB) [Bernstein et al. (1977) J. Mol. Biol., 112, 535- 542]. The database currently contains an extended structural family for each of 600 representative protein chains which have <25% mutual sequence identity. The results of the exhaustive pairwise structure comparisons are reported in the form of a fold tree generated by hierarchical clustering and as a series of structurally representative sets of folds at varying levels of uniqueness. For each query structure from the representative set, there is a database entry containing structure-structure alignments with its structural neighbours in the representative set and its sequence homologs in the PDB. All alignments are based purely on the 3-D co-ordinates of the proteins and are derived by an automatic structure comparison program (Dali). The FSSP database is accessible electronically on the World Wide Web and by anonymous ftp.

Psychiatric diagnoses and sexual victimization in women with chronic pelvic pain

The authors evaluated 100 women scheduled for diagnostic laparoscopy (50 for chronic pain, 50 for tubal ligation or infertility evaluation) using structured psychiatric, family history, and sexual trauma interviews. Laparoscopy reports were blindly rated by a gynecologist. Compared with the nonpain group, the women with chronic pelvic pain had significantly higher current and lifetime rates of psychiatric disorders, as well as childhood and adult sexual victimization. They reported significantly higher mean numbers of somatization symptoms, but no significant differences in objective laparoscopic findings. Psychiatric disorders and sexual victimization are common in women with chronic pelvic pain and should be considered in the evaluation and treatment of these patients.

Mucus and alkali secretion in the rat duodenum: effects of indomethacin, N omega-nitro-L-arginine, and luminal acid

BACKGROUND & AIMS

Duodenal mucus and bicarbonate secretion appear to play an essential role in the protection of the duodenum. The aim of this study was to examine duodenal bicarbonate and mucus secretion and the effects of cyclooxygenase inhibition, nitric oxide synthase inhibition, and luminal acid.

METHODS

Duodenal mucus gel thickness was measured using microelectrodes during intravital microscopy in anesthetized rats. Bicarbonate secretion was measured using back-titration.

RESULTS

A continuous layer of mucus with a mean thickness of 284 +/- 11 microns (n = 35) and a mean alkaline secretion of 0.18 +/- 0.01 mumol.cm-2.min-1 were found in untreated animals. Indomethacin decreased both mucus and bicarbonate secretion by about 35%. NO synthase inhibition with N omega-nitro-L-arginine reduced mucus secretion by about 21% but increased bicarbonate secretion by 39%. Exposure of the mucosal surface to 10 mmol/L HCI increased mucus secretion by 44% and bicarbonate secretion by 22%.

CONCLUSIONS

The duodenal mucus layer is continuous. It can be easily removed, and new secretion can be followed. Duodenal mucus secretion is strongly stimulated by luminal acid and endogenous prostanoids and less markedly by NO, whereas bicarbonate secretion is stimulated by acid and endogenous prostanoids and inhibited by endogenous NO.