Search for identical octapeptides in unrelated proteins: Structural plasticity revisited

Since proteins are dynamic in nature, they can alter their local structure in response to changes in their environment factors such as temperature, pH, phosphorylation, and binding of other small molecules. These conformational changes are extremely important for the correct folding and functioning of proteins. There are also a number of diseases associated with protein conformational change such as amyloid diseases. To stimulate research into the above factors which specify one conformation over another, different theoretical models have been proposed and tested against sequence similar distant structure protein fragments. In order to simplify the computational complexity of identifying conformational changes in proteins, various local sequence search algorithms were employed and the structural plasticity in unrelated proteins was examined by various research groups. In the present work, we revisit the mechanism of structural plasticity in unrelated proteins with increased number of structures in Protein Data Bank by comparing identical octapeptides in unrelated proteins with dictionary of protein secondary structure extracted from existing experimental data. Our goal is to bring out the influence of hydrophobic residues, hydrophilic residues, flanking residues, difference in secondary structural propensities of surrounding residues, difference in phi-psi angles and local and nonlocal interactions in identical octapeptides adopting different conformations. Also we have used surrounding hydrophobicity, environment dependent interaction energy, atomic mean force potential, structural unit contacts and difference profiles models to explore the factors which cause structural plasticity. The results discussed here may provide insights into protein folding, design and function.

Health care and equity in India

In India, despite improvements in access to health care, inequalities are related to socioeconomic status, geography, and gender, and are compounded by high out-of-pocket expenditures, with more than three-quarters of the increasing financial burden of health care being met by households. Health-care expenditures exacerbate poverty, with about 39 million additional people falling into poverty every year as a result of such expenditures. We identify key challenges for the achievement of equity in service provision, and equity in financing and financial risk protection in India. These challenges include an imbalance in resource allocation, inadequate physical access to high-quality health services and human resources for health, high out-of-pocket health expenditures, inflation in health spending, and behavioural factors that affect the demand for appropriate health care. Use of equity metrics in monitoring, assessment, and strategic planning; investment in development of a rigorous knowledge base of health-systems research; development of a refined equity-focused process of deliberative decision making in health reform; and redefinition of the specific responsibilities and accountabilities of key actors are needed to try to achieve equity in health care in India. The implementation of these principles with strengthened public health and primary-care services will help to ensure a more equitable health care for India's population.

Antidiabetic properties of Hibiscus rosa sinensis L. leaf extract fractions on nonobese diabetic (NOD) mouse

On fractionation the ethanolic extract of H. rosa sinensis leaves, 5 fractions were obtained. Of these, fraction-3 (F3) and fraction-5 (F5) were chosen for detailed investigation on non obese diabetic (NOD) mouse to study anti-diabetic properties because they were more active than others. Serum glucose, glycosylated hemoglobin, triglyceride, cholesterol, blood urea, insulin, LDL, VLDL, and HDL were estimated. Both fractions F3 and F5 on oral feeding (100 and 200 mg/kg body weight) demonstrated insulinotropic nature and protective effect in NOD mice. These fractions may contain potential oral hypoglycemic agent.

Radiation induced effects on viability and antioxidant enzymes of crustaceans from different habitats

The paper describes differential tolerance of two fresh water crustaceans Mesocyclops hyalinus and Allodiaptomus satanus to 60Co gamma radiation. Mesocyclops hyalinus is dominant species at site 1, near a Thermal Power Plant at Kolaghat East Midnapore where fly ash deposition is a regular phenomenon. Allodiaptomus satanus is dominant species at site 2 at Kolkata, Ballygung where anthroponotic activities are more pronounced. M. hyalinus is naturally exposed to more stressful situation than A. satanus as revealed by comparing the hydrological parameters of the two habitats. Experimental exposure to ionizing radiation resulted in differential changes in viability morphology and antioxidant enzyme activities in the two selected species. Survival experiments showed greater tolerance of M. hyalinus compared to A. satanus up to 8Gy (absorbed dose) after which if showed drastic fail in survival. More pronounced morphological changes were observed in A. satanus as compared to that in M. hyalinus. The pattern of changes in antioxidant enzyme activity is distinctly opposite in the two radiation exposed species. While in M. hyalinus stimulation in activity of both CAT (excepting at 10Gy absorbed dose) and SOD was observed A. satanus showed decrease in activity of both the enzymes when compared to their unirradiated counterparts.

Serotonin transporter polymorphisms (SLC6A4 insertion/deletion and rs25531) do not affect the availability of 5-HTT to [11C] DASB binding in the living human brain

Studies in vitro suggest that the expression of the serotonin transporter (5-HTT) is regulated by polymorphic variation in the promoter region of the 5-HTT gene (5-HTTLPR); however, results from human brain imaging studies examining the relation between 5-HTT genotype and 5-HTT radioligand binding in vivo have been inconsistent. This inconsistency could reflect small participant numbers or the use of sub-optimal radiotracer for measuring the 5-HTT. We used positron emission tomography in conjunction with the selective 5-HTT ligand [(11)C] DASB to examine the availability of the 5-HTT in seven brain regions in 63 healthy European caucasian volunteers who were genotyped for short (S) and long (L) variants (SLC6A4 and rs25531) of the 5-HTTLPR. [(11)C] DASB binding potential was not influenced by the allelic status of participants whether classified on a biallelic or triallelic basis in any of the regions studied. Our PET findings, in a relatively large sample with a near optimal radiotracer, suggest that 5-HTTLPR polymorphic variation does not affect the availability of 5-HTT to [(11)C] DASB binding in adult human brain. The reported impact of 5-HTTLPR polymorphic variation on emotional processing and vulnerability to depression are more likely therefore to be expressed through effects exerted during neurodevelopment.

Interaction of anthraquinone dyes with lysozyme: evidences from spectroscopic and docking studies

The interaction between lysozyme and anthraquinone dyes such as Alizarin Red S, Acid blue 129 and Uniblue was studied using steady state, time resolved fluorescence measurements and docking studies. Addition of anthraquinone dyes effectively quenched the intrinsic fluorescence of lysozyme. Fluorescence quenching of lysozyme by dyes has revealed the formation of complex. The number of binding sites (n) and binding constant (K) for all the three dyes was calculated by relevant fluorescence quenching data. Based on Förster's non-radiative energy transfer theory, distance (r(0)) between the donor (lysozyme) and acceptor (dyes) as well as the critical energy transfer distance (R(0)) has also been calculated. The interaction between dyes and lysozyme occurs through static quenching mechanism as confirmed by time resolved spectroscopy. The conformational change of lysozyme has been analyzed using synchronous fluorescence measurement. Finally, docking studies revealed that specific interactions were observed with the residue of Trp 62.

Increased neural response to fear in patients recovered from depression: a 3T functional magnetic resonance imaging study

BACKGROUND

Previous imaging studies have revealed that acute major depression is characterized by altered neural responses to negative emotional stimuli. Typically, responses in limbic regions such as the amygdala are increased while activity in cortical regulatory regions such as the dorsolateral prefrontal cortex (DLPFC) is diminished. Whether these changes persist in unmedicated recovered patients is unclear.

METHOD

We used functional magnetic resonance imaging to examine neural responses to emotional faces in a facial expression-matching task in 16 unmedicated recovered depressed patients and 21 healthy controls.

RESULTS

Compared with controls, recovered depressed patients had increased responses bilaterally to fearful faces in the DLPFC and right caudate. Responses in the amygdala did not distinguish the groups.

CONCLUSIONS

Our findings indicate that clinical recovery from depression is associated with increased activity in the DLPFC to negative emotional stimuli. We suggest that this increase may reflect a compensatory cortical control mechanism with the effect of limiting emotional dysregulation in limbic regions such as the amygdala.

Variation of protein binding cavity volume and ligand volume in protein-ligand complexes

We have systematically analyzed the variation of protein binding cavity volume of 200 protein-ligand complexes belonging to eight protein families. Wide variation in protein binding cavity volume for the same protein is observed on binding different ligands. Analysis of individual protein families shows high correlation between atom-atom interactions in binding site and ligand volume. This study implies the significance of protein flexibility in docking small molecule inhibitors on the basis of protein binding cavity volume with respect to ligand volume.

Social analysis of sex imbalance in India: before and after the implementation of the Pre-Natal Diagnostic Techniques (PNDT) Act

BACKGROUND

While the issue of sex imbalance in South Asia is well recognised, less is known about its social patterning. Social patterning in the proportion of sexes was investigated among infants in India before and after the implementation of the Pre-Natal Diagnostic Techniques (PNDT) Act in 1996. The act regulates the misuse of technologies for sex determination of fetuses and subsequent selective abortion.

METHODS

Multivariable regression analysis was performed on time series data from a nationally representative sample of households with infants. The outcome was log odds of having a male infant. Household income, parental education, social caste, a variable representing periods before and after the implementation of the PNDT Act and state of residence were the main predictors of interest.

RESULTS

The odds of having a male infant increased with income quartiles. Heads of household with post-secondary education had a higher odds ratio of having a male infant than those with no formal education. The odds of having a male infant did not differ between high and low caste groups, and was not associated with the educational attainment of the spouse. Punjab had a higher odds ratio of having a male infant compared with Kerala. Kerala, meanwhile, was not particularly different from the remaining Indian states. The odds of having a male infant were similar in the pre- and post-PNDT periods. In the post-PNDT period, the income gradient in the odds of having a male infant was substantially weakened.

CONCLUSION

Social analysis of the distribution of sexes among infants in India suggests that neither improvements in socioeconomic circumstances nor introducing policies that are not aligned with societal norms and preferences are likely to normalise the sex imbalance in India.

The effectiveness of national influenza vaccination policies for at-risk populations over 5 seasons in a Scottish general practice

AIM

To determine the effectiveness of serial influenza vaccination.

SCOPE

Studied in a Scottish GP population, the overall seroresponse rate increased with annual influenza vaccinations and after 5 years it increased from 45.1% to 93.3% for influenza virus A (H1) and from 48.4% to 98.3% for influenza virus A (H3). However, there was little boosting effect with further doses after becoming a seroresponder. The pre-vaccination titres were significantly higher in previous year's seroresponders compared to non-responders.

CONCLUSIONS

The policy of annual vaccination is supported by our data in order to increase the disappointing response rate after one dose. However, the lack of a boosting response with subsequent doses and the significant residual immunity after becoming a seroresponder suggests a prior serological immunity check in order to better direct the vaccine supply (in the years of no antigenic drift), to those who need it most.

Differential effects of citalopram and reboxetine on cortical Glx measured with proton MR spectroscopy

The pharmacological effects of monoamine potentiating antidepressants are likely to be expressed ultimately on cortical pyramidal neurones that use glutamate as a neurotransmitter. However, there are few data on the effects of antidepressant treatment on cortical glutamate levels in humans. The aim of the present study was to use proton magnetic resonance spectroscopy (MRS) to assess the effects of short-term administration of the selective serotonin re-uptake inhibitor, citalopram and the selective noradrenaline re-uptake inhibitor, reboxetine, on a composite measure of glutamate and glutamine (Glx) in occipital cortex in healthy volunteers using a parallel group, placebo-controlled design. We found that relative both to placebo and reboxetine, seven days treatment with citalopram significantly increased cortical Glx. Our data suggest that short-term treatment with citalopram, but not reboxetine, increases occipital Glx in healthy subjects. Further studies are needed to find out if similar effects occur in anterior brain regions and whether they reflect changes in glutamate or glutamine or both.

FOLD-RATE: prediction of protein folding rates from amino acid sequence

We have developed a web server, FOLD-RATE, for predicting the folding rates of proteins from their amino acid sequences. The relationship between amino acid properties and protein folding rates has been systematically analyzed and a statistical method based on linear regression technique has been proposed for predicting the folding rate of proteins. We found that the classification of proteins into different structural classes shows an excellent correlation between amino acid properties and folding rates of two and three-state proteins. Consequently, different regression equations have been developed for proteins belonging to all-alpha, all-beta and mixed class. We observed an excellent agreement between predicted and experimentally observed folding rates of proteins; the correlation coefficients are, 0.99, 0.97 and 0.90, respectively, for all-alpha, all-beta and mixed class proteins. The prediction server is freely available at http://psfs.cbrc.jp/fold-rate/.

A Statistical Method for Predicting Protein Unfolding Rates from Amino Acid Sequence

The prediction of protein unfolding rates from amino acid sequences is one of the most important challenges in computational biology and chemistry. The analysis on the relationship between protein unfolding rates and physical-chemical, energetic, and conformational properties of amino acid residues provides valuable information to understand and predict the unfolding rates of two- and three-state proteins. We found that the classification of proteins into different structural classes shows an excellent correlation between amino acid properties and unfolding rates of two- and three-state proteins, indicating the importance of native-state topology in determining the protein unfolding rates. We have formulated three independent linear regression equations to different structural classes of proteins for predicting their unfolding rates from amino acid sequences and obtained an excellent agreement between predicted and experimentally observed unfolding rates of proteins; the correlation coefficients are 0.999, 0.990, and 0.992, respectively, for all-alpha, all-beta, and mixed-class proteins. Further, we have derived a general equation applicable to all structural classes of proteins, which can be used for predicting the unfolding rates for proteins of an unknown structural class. We observed a correlation of 0.987 and 0.930, respectively, for back-check and jack-knife tests. These accuracy levels are better than those of other methods in the literature.

Suicide in farmers in Scotland

INTRODUCTION

Farmers and farm workers have higher than expected rates of suicide and undetermined deaths in UK studies, and some rural areas of Scotland have higher than average male suicide rates. Firearm access seems to be an influencing factor in England and Wales. Type of farming, and farming social networks may also be important. This article describes suicide and undetermined deaths in male farmers and farm workers in Scotland from 1981-1999 using anonymised, routine data.

METHOD

Deaths of men aged 15-74 years from suicide or undetermined cause were identified from anonymised Scottish death records. Farmers and farm workers were identified using occupation codes. Methods of suicide used by farmers were compared with those of the general male population of the same age. A multiple linear regression was used to examine the influence of farm type, and the proportion of farmers in the working population of an area.

RESULTS

307 male farmers or farm workers died by suicide or undetermined cause in the time period. The overall rate was 31.4/100,000 per year (95% CI 28.1-35.1). Deaths using firearms were over-represented (29% of farming deaths compared with 3.6% in the general male population). There was no significant association between the male suicide rate in an area, and the farming suicide rate. Areas with lower proportions of farmers tended to have higher rates of farming suicide and undetermined deaths. This one factor described 85% of the variance among areas.

CONCLUSION

Deaths were substantially more likely to involve firearms than suicide and undetermined deaths in the general male population. Less use of other methods did not completely compensate for this, indicating that method availability is likely to contribute to farming suicide rates. Farmers in areas where farming is less common were more likely to die by suicide, and this described most of the differences among areas. Networks and social supports may be important protective factors for farmers.

Deprivation, smoking, and quality of life in asthma

AIMS

To explore associations of deprivation and smoking, with prevalence of asthma, wheeze, and quality of life.

METHODS

Survey, using International Study of Asthma and Allergies in Childhood (ISAAC) methodology, of children aged 13-14 years attending Scottish schools previously surveyed in 1995.

RESULTS

4665/5247 (89%) pupils completed questionnaires. 3656/4665 (78.4%) had missed school for any reason in the last 12 months, 587 (12.6%) because of asthma or wheeze. Compared to children with 1-3 wheeze attacks per year, those with >12 attacks in the last year were more likely to have missed school, twice as likely to have missed physical education in the last month, to report interference with home activities, or to have visited accident and emergency departments, and three times more likely to have been hospitalised. Deprivation was not independently associated with self-reported asthma or wheeze, but was associated with school absence, either for any reason or specifically for asthma or wheeze, but not with use of services such as accident and emergency visits, doctor visits, or hospital admissions. Active smoking was associated with wheezy symptoms, and active and passive smoking with use of medical services. These associations were independent of wheeze severity, treatment taken, and other associated atopic conditions. Smoking also had an impact on school absence and home and school activities.

CONCLUSIONS

Deprivation does not affect the prevalence of asthma or wheeze. Exposure to cigarette smoke was associated with the increased use of services. Deprivation and smoking have independent adverse effects on the quality of life in subjects with asthma or wheeze.

Folding Mechanism of All‐β Globular Proteins

Elucidating the mechanism for the fast folding of proteins is a challenging task. In our earlier work, we introduced the concept of "long-range order" and related it successfully to protein folding rates. In this article, we propose a new hypothesis for the folding of two-state all-beta proteins. The mechanism is based on the formation of a hydrophobic core, propagation of beta-strands, and the establishment of hydrogen bonds. Our hypothesis has been strengthened by the observation of a folding nucleus in beta-strands and the hydrogen-bonding network between residues in beta-strands. Our insights on protein folding show an excellent agreement with experimental observations.

A(1,3)-strain mediated epimerization of 2e,3e,5e,6e-tetraarylpiperidin-4-one oximes

A series of tri- and tetraarylpiperidin-4-one oximes were synthesized from 2e,3e,6e-tri- and 2e,3e,5e,6e-tetraarylpiperidin-4-ones, respectively. In the case of the latter compounds, oximation is accompanied by epimerization at C-5 to avoid the A(1,3)-strain between the oxime OH group and the 5e-aryl ring of the initially formed oxime resulting in 2e,3e,5a,6e-tetraarylpiperidin-4-one oximes. 1H, 13C and 2D NMR spectroscopic data were employed to characterize and investigate the stereochemistry of these compounds.

Inter-residue interactions in protein folding and stability

During the process of protein folding, the amino acid residues along the polypeptide chain interact with each other in a cooperative manner to form the stable native structure. The knowledge about inter-residue interactions in protein structures is very helpful to understand the mechanism of protein folding and stability. In this review, we introduce the classification of inter-residue interactions into short, medium and long range based on a simple geometric approach. The features of these interactions in different structural classes of globular and membrane proteins, and in various folds have been delineated. The development of contact potentials and the application of inter-residue contacts for predicting the structural class and secondary structures of globular proteins, solvent accessibility, fold recognition and ab initio tertiary structure prediction have been evaluated. Further, the relationship between inter-residue contacts and protein-folding rates has been highlighted. Moreover, the importance of inter-residue interactions in protein-folding kinetics and for understanding the stability of proteins has been discussed. In essence, the information gained from the studies on inter-residue interactions provides valuable insights for understanding protein folding and de novo protein design.

Randomized double-blind clinical trial comparing topical and sub-Tenon's anaesthesia in routine cataract surgery †

BACKGROUND

Several local anaesthetic techniques are available for cataract surgery. Recently, topical anaesthesia has gained in popularity. A randomized trial was designed to compare patient discomfort and intraoperative complications following routine cataract surgery under topical or sub-Tenon's anaesthesia.

METHODS

A randomized double-blinded placebo-controlled clinical trial of 210 patients assigned to either a sub-Tenon's group (sub-Tenon's anaesthesia with placebo topical balanced salt solution, n=140) or a topical anaesthesia group (topical anaesthesia with placebo sub-Tenon's injection of balanced salt solution, n=70) was carried out. All patients underwent phacoemulsification with intraocular lens implantation. Patients in the sub-Tenon's group received a single injection (3 ml) of a combination of lidocaine 2% (2 ml) and bupivacaine 0.75% (1 ml), and four doses of topical placebo (balanced salt solution). Patients in the topical anaesthesia group received four doses of topical proxymethocaine 0.5% and a placebo sub-Tenon's injection (3 ml) of balanced salt solution. No intracameral injection of local anaesthetic was given. A 10-point visual analogue pain scale was used preoperatively and for postoperative pain assessment immediately after the operation and 30 min postoperatively. The intraoperative complications in the two groups were recorded.

RESULTS

The mean pain score immediately after surgery was 2.42 (sd 2.2) in the sub-Tenon's group and 3.44 (2.3) in the topical anaesthesia group (P=0.0043). The mean pain score 30 min after surgery was 1.24 (1.7) in the sub-Tenon's group and 2.25 (2.2) in the topical anaesthesia group (P=0.0009).

CONCLUSIONS

Patients undergoing cataract surgery under topical anaesthesia experience more postoperative discomfort than patients receiving sub-Tenon's anaesthesia. Surgery-related complications were similar in both groups.

Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins

Understanding the folding pathways of proteins is a challenging task. The Phi value approach provides a detailed understanding of transition-state structures of folded proteins. In this work, we have computed the hydrophobicity associated with each residue in the folded state of 16 two-state proteins and compared the Phi values of each mutant residue. We found that most of the residues with high Phi value coincide with local maximum in surrounding hydrophobicity, or have nearby residues that show such maximum in hydrophobicity, indicating the importance of hydrophobic interactions in the transition state. We have tested our approach to different structural classes of proteins, such as alpha-helical, SH3 domains of all-beta proteins, beta-sandwich, and alpha/beta proteins, and we observed a good agreement with experimental results. Further, we have proposed a hydrophobic contact network pattern to relate the Phi values with long-range contacts, which will be helpful to understand the transition-state structures of folded proteins. The present approach could be used to identify potential hydrophobic clusters that may form through long-range contacts during the transition state.

Childhood asthma in the Highlands of Scotland--morbidity and school absence

BACKGROUND

The prevalence of childhood asthma in Scotland is one of the highest in the world. The morbidity secondary to allergic diseases is significant in terms of costs to the nation and effects on the family including the child.

AIMS

The aims of this study were to describe the prevalence of asthma, eczema and hay fever in the Highlands of Scotland and in the Shetland Isles and to examine factors in relation to quality of life and social deprivation.

METHOD

A total population survey of 12 year old children using a parent completed questionnaire.

RESULTS

86.3% (2658/3080) returned questionnaires. Of the 2549 questionnaires analysed, 476 (18.7%) reported asthma ever, 362 (14.2%) wheeze in last 12 months, 508 (19.9%) reported hay fever ever and 555 (21.8%) reported eczema ever. Of the children reporting asthma or wheeze, 35.4% (229/647) had missed school because of asthma or wheeze, 38.0% (246/647) had missed physical education. 62.5% (354/566) of subjects with wheeze ever reported sleep disturbance. Deprivation measured by DEPCAT scores was associated with maternal smoking and bronchitis in the child but not with allergic diseases.

CONCLUSION

Compared with previous studies, the prevalence of asthma was unchanged but eczema has increased in Highland adolescents. Allergic disease has a significant impact on school attendance and physical activity. Deprivation was associated with maternal smoking and bronchitis in the child but not with allergic diseases. The impact of allergic diseases in rural areas may be different from urban areas.

Characteristics associated with reported CAM use in patients attending six GP practices in the Tayside and Grampian regions of Scotland: a survey

OBJECTIVES

To study the nature of CAM use in primary care attenders, the involvement of their NHS healthcare professionals in their CAM care and differences in characteristics between CAM users and non-users.

DESIGN

Postal questionnaire for primary care attenders and analysis of practice leaflets.

SETTING

Six Scottish GP practices with a range of practice size, CAM provision within practice, deprivation and rurality.

RESULTS

Five hundred and fourteen primary care attenders described 1194 incidences of CAM use and gave details about their main therapy. 37% had contact with a practitioner, the rest mainly self-prescribed. The perceived effectiveness of CAM was high. Patients used CAM for a variety of health problems, mainly as an adjuvant to orthodox medicine rather than an alternative. The involvement of the NHS in CAM delivery was small but there is a significant role to ensure patient safety, especially regarding herb-drug interactions. Disclosure rate of CAM use was low. CAM offered options in areas where the provision in the NHS is difficult, including musculo-skeletal and mental health problems. Provision of CAM by the GP is associated with higher CAM use in primary care attenders.

CONCLUSIONS

It is recommended that healthcare professionals include patients' use of CAM in history taking and clinical decision making.

Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)8 barrel proteins

Analysis on the three dimensional structures of (alpha/beta)(8) barrel proteins provides ample light to understand the factors that are responsible for directing and maintaining their common fold. In this work, the hydrophobically enriched clusters are identified in 92% of the considered (alpha/beta)(8) barrel proteins. The residue segments with hydrophobic clusters have high thermal stability. Further, these clusters are formed and stabilized through long-range interactions. Specifically, a network of long-range contacts connects adjacent beta-strands of the (alpha/beta)(8) barrel domain and the hydrophobic clusters. The implications of hydrophobic clusters and long-range networks in providing a feasible common mechanism for the folding of (alpha/beta)(8) barrel proteins are proposed.

The Sivaganga eye survey: II. Outcomes of cataract surgery

PURPOSE

To assess the clinical outcomes of cataract surgery in rural southern India.

METHODS

Cluster sampling was used in randomly selecting a cross-sectional sample of persons 50 years of age or older for visual acuity measurement, refraction, and ocular examination in 1999. Subjects were queried as to the date and place of surgery for each cataract-operated eye. Surgical complications were noted and the principal cause of reduced vision was identified for eyes with presenting visual acuity worse than 6/18.

RESULTS

Within the cataract-operated sample of 682 persons, 13.8% had presenting visual acuity worse than 6/60 in both eyes, 25.2% better than or equal to 6/18 in both eyes, and 37.8% were bilaterally operated on. For aphakic eyes, 50.5% presented with visual acuity better than or equal to 6/18; 82.6% with best-correction. For pseudophakic eyes, the corresponding percentages were 78.0% and 94.5%. Over one-third of all eyes were pseudophakic, and nearly three-fourths had been operated on in non-governmental facilities. Uncorrected aphakia and other refractive error were the main causes of vision impairment. In multiple logistic regression modeling, poor presenting visual acuity in aphakic eyes was associated with illiteracy, rural residence, and surgery in government facilities; gender and time period of surgery were not predictors of vision outcomes. None of these variables were associated with best-corrected outcomes in aphakic eyes, nor with presenting and best-corrected outcomes in pseudophakic eyes.

CONCLUSIONS

Visual acuity outcomes in pseudophakic eyes were good. More attention must be given to needless vision impairment among the cataract-operated because of inadequate aphakic correction, especially among those operated on in government facilities, the illiterate, and those living in rural villages.

The Sivaganga eye survey: I. Blindness and cataract surgery

PURPOSE

To assess the prevalence of visual acuity impairment, blindness, and cataract surgery among older adults in rural southern India.

METHODS

Random selection of village- and urban-based clusters was used to identify a cross-sectional sample of persons 50 years of age or older from the Sivaganga district of Tamil Nadu. Subjects in 25 selected clusters were enumerated through a door-to-door survey and invited to examination sites for measurement of uncorrected, presenting, and best-corrected visual acuity and ocular examination in 1999. The principal cause was identified for eyes with presenting visual acuity worse than 6/18. Quality assurance monitoring of visual acuity measurements took place in five of the study clusters.

RESULTS

A total of 5081 persons in 3517 households were enumerated, and 4642 (91.4%) were examined. Thirty-six percent presented with visual acuity worse than 6/18 in the better eye. The prevalence of blindness, based on visual acuity worse than 6/60 in both eyes, was 6.0% (95% confidence interval [CI]: 5.1% to 6.9%) with presenting vision, and 2.5% (95% CI: 1.8% to 3.1%) with best correction. Blindness with presenting visual acuity was associated with older age and illiteracy. Cataract was the principal cause of blindness in one or both eyes in 69.4% of those presenting blind, and uncorrected aphakia and other refractive error affected 35.6% in at least one eye. The prevalence of cataract surgery was 14.7% (95% CI: 13.0% to 16.4%); low surgical coverage among the cataract blind was associated with illiteracy.

CONCLUSIONS

It appears that much has been done in the prevention of blindness in Sivaganga. Nevertheless, blindness remains an important public health problem, mainly because of cataract and refractive error. Prevention of blindness programs in the area should target these two causes, with special emphasis on the elderly and the illiterate.

Influence of medium- and long-range interactions in different folding types of globular proteins

Recognition of protein fold from amino acid sequence is a challenging task. The structure and stability of proteins from different fold are mainly dictated by inter-residue interactions. In our earlier work, we have successfully used the medium- and long-range contacts for predicting the protein folding rates, discriminating globular and membrane proteins and for distinguishing protein structural classes. In this work, we analyze the role of inter-residue interactions in commonly occurring folds of globular proteins in order to understand their folding mechanisms. In the medium-range contacts, the globin fold and four-helical bundle proteins have more contacts than that of DNA-RNA fold although they all belong to all-alpha class. In long-range contacts, only the ribonuclease fold prefers 4-10 range and the other folding types prefer the range 21-30 in alpha/beta class proteins. Further, the preferred residues and residue pairs influenced by these different folds are discussed. The information about the preference of medium- and long-range contacts exhibited by the 20 amino acid residues can be effectively used to predict the folding type of each protein.

Important amino acid properties for determining the transition state structures of two-state protein mutants

Understanding the mechanism in the folding pathways of proteins is an important problem in molecular biology. The Phi-value analysis provides insight into the transition state structures during protein folding. In this work, we have analyzed the relationship between the observed Phi values upon mutations in two-state proteins (FK506 binding protein, chymotrypsin inhibitor and src SH3 domain) and the changes in 48 various physico-chemical, energetic and conformational properties. We found that the classification of mutations based on solvent accessibility improved the correlation significantly. The relationship between conformational properties and Phi values determines the presence/absence of secondary structures in the transition state. In buried mutations, the physical properties volume, shape and flexibility, and the thermodynamic properties enthalpy, entropy and free-energy change have significant correlation with Phi. The short and medium-range non-bonded energy in partially buried mutations and average long-range contacts in exposed mutations showed a strong correlation with Phi values. Multiple regression analysis incorporating combinations of three properties from among all possible combinations of the 48 properties increased the correlation coefficient up to 0.99, by an average rise of 20% for all the data sets. Information about local sequence and structure is more important in surface mutations than those in buried mutations for explaining the transition state structures of two-state proteins. Further, the implications of our results for understanding the process of protein folding have been discussed.

Thermodynamic databases for proteins and protein-nucleic acid interactions

Thermodynamic data regarding proteins and their interactions are important for understanding the mechanisms of protein folding, protein stability, and molecular recognition. Although there are several structural databases available for proteins and their complexes with other molecules, databases for experimental thermodynamic data on protein stability and interactions are rather scarce. Thus, we have developed two electronically accessible thermodynamic databases. ProTherm, Thermodynamic Database for Proteins and Mutants, contains numerical data of several thermodynamic parameters of protein stability, experimental methods and conditions, along with structural, functional, and literature information. ProNIT, Thermodynamic Database for Protein-Nucleic Acid Interactions, contains thermodynamic data for protein-nucleic acid binding, experimental conditions, structural information of proteins, nucleic acids and the complex, and literature information. These data have been incorporated into 3DinSight, an integrated database for structure, function, and properties of biomolecules. A WWW interface allows users to search for data based on various conditions, with different display and sorting options, and to visualize molecular structures and their interactions. These thermodynamic databases, together with structural databases, help researchers gain insight into the relationship among structure, function, and thermodynamics of proteins and their interactions, and will become useful resources for studying proteins in the postgenomic era.

Snow sports injuries in Scotland: a case-control study

OBJECTIVES

To examine the incidence and patterns of snow sports injuries at the three largest commercial ski areas in Scotland and to identify factors associated with injury risk.

METHODS

A prospective case-control study of all injured people at Cairngorm, Glenshee, and Nevis Range ski areas during the 1999-2000 winter season. Personal details, snow sports related variables, diagnosis, and treatment were recorded. Control data were collected at random from uninjured people at all three areas. Random counts were performed to analyse the composition of the on slope population.

RESULTS

A total of 732 injuries were recorded in 674 people. Control data were collected from 336 people. The injury rate for the study was 3.7 injuries per 1000 skier days. Alpine skiers comprised 67% of the on slope population, snowboarders 26%, skiboarders 4%, and telemark skiers 2%. Lower limb injuries and sprains were the commonest injuries in alpine skiers and skiboarders. Snowboarders sustained more injuries to the upper limb and axial areas. Skiboarders and snowboarders had a higher incidence of fractures. After adjustment for other variables, three factors were all independently associated with injury: snowboarding (odds ratio (OR) 4.07, 95% confidence interval (CI) 1.65 to 10.08), alpine skiing (OR 3.82, CI 1.6 to 9.13), and age <16 years (OR 1.9, CI 1.14 to 3.17). More than five days of experience in the current season and at least one week of experience in total had a protective effect against injury.

CONCLUSIONS

Despite a change in the composition of the alpine population at Scottish ski areas, the overall rate and pattern of injury are similar to those reported previously in comparable studies. Several factors are associated with an increased risk of injury and should be targeted in future injury prevention campaigns.

Thermodynamic database for protein-nucleic acid interactions (ProNIT)

MOTIVATION

Protein-nucleic acid interactions are fundamental to the regulation of gene expression. In order to elucidate the molecular mechanism of protein-nucleic acid recognition and analyze the gene regulation network, not only structural data but also quantitative binding data are necessary. Although there are structural databases for proteins and nucleic acids, there exists no database for their experimental binding data. Thus, we have developed a Thermodynamic Database for Protein-Nucleic Acid Interactions (ProNIT).

RESULTS

We have collected experimentally observed binding data from the literature. ProNIT contains several important thermodynamic data for protein-nucleic acid binding, such as dissociation constant (K(d)), association constant (K(a)), Gibbs free energy change (DeltaG), enthalpy change (DeltaH), heat capacity change (DeltaC(p)), experimental conditions, structural information of proteins, nucleic acids and the complex, and literature information. These data are integrated into a relational database system together with structural and functional information to provide flexible searching facilities by using combinations of various terms and parameters. A www interface allows users to search for data based on various conditions, with different display and sorting options, and to visualize molecular structures and their interactions.

AVAILABILITY

ProNIT is freely accessible at the URL http://www.rtc.riken.go.jp/jouhou/pronit/pronit.html.

Role of medium--and long-range interactions in discriminating globular and membrane proteins

The analysis of inter-residue interactions in protein structures provides considerable insight to understand their folding and stability. We have previously analyzed the role of medium- and long-range interactions in the folding of globular proteins. In this work, we study the distinct role of such interactions in the three-dimensional structures of membrane proteins. We observed a higher number of long-range contacts in the termini of transmembrane helical (TMH) segments, implying their role in the stabilization of helix-helix interactions. The transmembrane strand (TMS) proteins are having appreciably higher long-range contacts than that in all-beta class of globular proteins, indicating closer packing of the strands in TMS proteins. The residues in membrane spanning segments of TMH proteins have 1.3 times higher medium-range contacts than long-range contacts whereas that of TMS proteins have 14 times higher long-range contacts than medium-range contacts. Residue-wise analysis indicates that in TMH proteins, the residues Cys, Glu, Gly, Pro, Gln, Ser and Tyr have higher long-range contacts than medium-range contacts in contrast with all-alpha class of globular proteins. The charged residue pairs have higher medium-range contacts in all-alpha proteins, whereas hydrophobic residue pairs are dominant in TMH proteins. The information on the preference of residue pairs to form medium-range contacts has been successfully used to discriminate the TMH proteins from all-alpha proteins. The statistical significance of the results obtained from the present study has been verified using randomized structures of TMH and TMS protein templates.