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.

Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction

The contact order is believed to be an important factor for understanding protein folding mechanisms. In our earlier work, we have shown that the long-range interactions play a vital role in protein folding. In this work, we analyzed the contribution of long-range contacts to determine the folding rate of two-state proteins. We found that the residues that are close in space and are separated by at least ten to 15 residues in sequence are important determinants of folding rates, suggesting the presence of a folding nucleus at an interval of approximately 25 residues. A novel parameter "long-range order" has been proposed to predict protein folding rates. This parameter shows as good a relationship with the folding rate of two-state proteins as contact order. Further, we examined the minimum limit of residue separation to determine the long-range contacts for different structural classes. We observed an excellent correlation between long-range order and folding rate for all classes of globular proteins. We suggest that in mixed-class proteins, a larger number of residues can serve as folding nuclei compared to all-alpha and all-beta proteins. A simple statistical method has been developed to predict the folding rates of two-state proteins using the long-range order that produces an agreement with experimental results that is better or comparable to other methods in the literature.

Clusters in alpha/beta barrel proteins: implications for protein structure, function, and folding: a graph theoretical approach

The alpha/beta barrel fold is adopted by most enzymes performing a variety of catalytic reactions, but with very low sequence similarity. In order to understand the stabilizing interactions important in maintaining the alpha/beta barrel fold, we have identified residue clusters in a dataset of 36 alpha/beta barrel proteins that have less than 10% sequence identity within themselves. A graph theoretical algorithm is used to identify backbone clusters. This approach uses the global information of the nonbonded interaction in the alpha/beta barrel fold for the clustering procedure. The nonbonded interactions are represented mathematically in the form of an adjacency matrix. On diagonalizing the adjacency matrix, clusters and cluster centers are obtained from the highest eigenvalue and its corresponding vector components. Residue clusters are identified in the strand regions forming the beta barrel and are topologically conserved in all 36 proteins studied. The residues forming the cluster in each of the alpha/beta protein are also conserved among the sequences belonging to the same family. The cluster centers are found to occur in the middle of the strands or in the C-terminal of the strands. In most cases, the residues forming the clusters are part of the active site or are located close to the active site. The folding nucleus of the alpha/beta fold is predicted based on hydrophobicity index evaluation of residues and identification of cluster centers. The predicted nucleation sites are found to occur mostly in the middle of the strands. Proteins 2001;43:103-112.

Bacteriologic and clinical efficacy of ofloxacin 0.3% versus ciprofloxacin 0.3% ophthalmic solutions in the treatment of patients with culture-positive bacterial keratitis

PURPOSE

To compare the efficacy and safety of ofloxacin 0.3% ophthalmic solution with ciprofloxacin 0.3% ophthalmic solution in patients with culture-positive bacterial keratitis.

METHODS

Patients with a microbiologic diagnosis of bacterial keratitis were included in this double-masked, parallel-group study and were randomized to treatment with either ofloxacin 0.3% or ciprofloxacin 0.3% ophthalmic solution. One drop of the study medication was instilled during the daytime according to the following schedule: every half-hour on study day 1, every hour on days 2 through 4, and every 2 hours on days 5 through 21. Healing, the primary outcome measure, was defined as complete reepithelialization, accompanied by nonprogression of stromal infiltrate for 2 days. Secondary outcome measures included signs and symptoms of infection. Patients were monitored throughout the study period for any adverse events.

RESULTS

A total of 217 patients completed the study: 112 were treated with ofloxacin and 105 were treated with ciprofloxacin. Streptococcus pneumoniae was the most commonly encountered pathogen in all patients. Complete corneal reepithelialization occurred in 85% of those treated with ofloxacin and in 77% of those treated with ciprofloxacin (p = 0.32). The average time to corneal ulcer healing was 13.7 days in those treated with ofloxacin and 14.4 days in those treated with ciprofloxacin. Both treatments were well tolerated with no patient discontinuing the study because of side effects.

CONCLUSION

Ofloxacin 0.3% and ciprofloxacin 0.3% ophthalmic solutions are effective and safe in the treatment of patients with culture-positive bacterial keratitis.

Differential modulation of xenobiotic metabolizing enzymes by vanadium during diethylnitrosamine-induced hepatocarcinogenesis in Sprague-Dawley rats

Effect of vanadium on hepatic xenobiotic biotransformation in rats exposed to diethylnitrosamine (DENA, 200 mg/kg body weight, intraperitoneally) was investigated to elucidate a possible mechanism of vanadium mediated prevention of chemical carcinogenesis. Vanadium supplementation (0.5 ppm ad libitum with drinking water), at different phases before and after DENA treatment, significantly modulated the decrease in contents of total cytochrome P-450, cytochrome b5, activity of nicotinamide adenine dinucleotide phosphate (NADPH), (reduced form) cytochrome reductase, and uridine diphospho-glucuronyl transferase (UDPGT) in microsomal fractions of whole liver, hyperplastic nodules (HNs) and non nodular surrounding parenchyma (NNSP) as induced by DENA, 20 weeks following its administration. Supplementary vanadium had also substantial influence on the activities of cytosolic enzymes, like, uridine diphospho (UDP)-glucose dehydrogenase and NAD(P)H: quinone oxidoreductase (DT-diaphorase) in the concerned tissue which were observed to be remarkably decreased as a result of DENA treatment in comparison to that of the control counterparts. However, vanadium was found to have little or no effect on the lowering ofaryl hydrocarbon hydroxylase (AHH) activity by DENA administration. On the basis of significant modulation of DENA induced alterations in cytosolic and microsomal enzyme activity it can be presumed that the chemoprotective effect of vanadium might be mediated through elevation of phase II conjugating enzymes which in turn, lead to a move and shift of metabolic profile that reduces the intracellular concentration of carcinogen derived reactive intermediates.

The madurai intraocular lens study IV: posterior capsule opacification

PURPOSE

To estimate the cumulative incidence of posterior capsule opacification 4 years after surgery in patients who participated in the Madurai Intraocular Lens Study and had extracapsular cataract extraction with posterior chamber intraocular lens implantation.

METHODS

In the Madurai Intraocular Lens Study, 1,700 patients with best-corrected visual acuity 20/120 or worse in the better eye had extracapsular cataract extraction with posterior chamber intraocular lens implantation, and 1,474 (86.7%) of these completed the 1-year follow-up examination. From this group of 1,474 pseudophakic patients, 400 were randomly selected for reexamination 4 years after the original surgery. The eye that was operated on was examined by an ophthalmologist who was involved in the 1-year follow-up examinations and posterior capsule opacification grading. A grading of I to III was used to reflect the degree of opacification. With grades II and III, posterior capsule opacification detectable with an undilated pupil was present in the central axis.

RESULTS

Three hundred twenty-seven (81.8%) of the selected population were examined between October 1997 and December 1998. Thirty-four (8.5%) were confirmed as being deceased, and 39 (9.8%) were unavailable for follow-up. The median age was 60 years, and 57.2% were women. The 4-year incidence of grade II or III posterior capsule opacification, including eyes already treated with laser capsulotomy, was 13.1% (95% confidence interval [CI], 9.7% to 17.3%). Each year of increased age was associated with a decreased risk of posterior capsule opacification (odds ratio, 0.96; 95% CI, 0.92 to 1.00). Based on best-corrected visual acuity of 20/40 or worse without co-existing pathology, the 4-year incidence of posterior capsule opacification was 13.5%.

CONCLUSION

Because patients with relatively mature cataracts routinely receive extracapsular cataract extraction with posterior chamber intraocular lens implantation instead of the traditional intracapsular extraction, the subsequent need for laser capsulotomy may be less than that anticipated, based on previous reports.

Influence of medium and long range interactions in protein folding

Protein structures are stabilized by both local and long range interactions. In this work, we analyze the residue-residue contacts and the role of medium- and long-range interactions in globular proteins belonging to different structural classes. The results show that while medium range interactions predominate in all-alpha class proteins, long-range interactions predominate in all-beta class. Based on this, we analyze the performance of several structure prediction methods in different structural classes of globular proteins and found that all the methods predict the secondary structures of all-alpha proteins more accurately than other classes. Also, we observed that the residues occurring in the range of 21-30 residues apart contributes more towards long-range contacts and about 85% of residues are involved in long-range contacts. Further, the preference of residue pairs to the folding and stability of globular proteins is discussed.

Importance of long-range interactions in protein folding

Long-range interactions play an active role in the stability of protein molecules. In this work, we have analyzed the importance of long-range interactions in different structural classes of globular proteins in terms of residue distances. We found that 85% of residues are involved in long-range contacts. The residues occurring in the range of 4-10 residues apart contribute more towards long-range contacts in all-alpha proteins while the range is 11-20 in all-beta proteins. The hydrophobic residues Cys, Ile and Val prefer the 11-20 range and all other residues prefer the 4-10 range. The residues in all-beta proteins have an average of 3-8 long-range contacts whereas the residues in other classes have 1-4 long-range contracts. Furthermore, the preference of residue pairs to the folding and stability will be discussed.

Studies on the genotoxicity of endosulfan in bacterial systems

Endosulfan, an organochlorine pesticide, was subjected to the differential sensitivity assay in repair-deficient and repair-proficient strains of Escherichia coli K12, prophage lambda induction assay in WP2s (lambda) and mutation induction in E. coli K12. The induction of umu gene expression with endosulfan was studied also in Salmonella typhimurium TA1535/pSK1002 cells. The differential sensitivity assay revealed that the recA 13 strain was the most sensitive. Endosulfan induced prophage lambda in E. coli and umu gene expression in S. typhimurium cells; however, the extent of the effects were low. Endosulfan also induced a dose-dependent increase in forward mutations in E. coli K12 cells from ampicillin sensitivity to ampicillin resistance. Our studies indicate the genotoxic potential of endosulfan and the role of the recA gene in the repair of endosulfan-induced DNA damage.

Importance of long-range interactions in (alpha/beta)8 barrel fold

Protein structures are stabilized by both local and long-range interactions. In this work, we analyzed the importance of long-range interactions in (alpha/beta)8 barrel proteins in terms of residue distances. We found that the residues occurring in the range of 21-30 residues apart contribute more toward long-range contacts. Indeed, about 50% of successive strands in these proteins are found to occur at a sequential distance of 21-30 residues. The aromatic amino acid residues Phe, Trp, and Tyr prefer the 4-10 range and all other residues prefer the 21-30 range. Hydrophobic-hydrophobic residue pairs are the most preferred ones for long-range interactions and they may play a key role in the folding and stabilization of (alpha/beta)8 barrel proteins.

An analysis of the amino acid clustering pattern in (alpha/beta)8 barrel proteins

The (alpha/beta)8 barrel proteins, in spite of having a common fold, do not show any sequence similarity. In order to understand the factors which are responsible for maintaining the common fold, the three-dimensional structures of 36 (alpha/beta)8 barrel proteins are analyzed for the presence of identical amino acid clusters or physicochemically similar clusters. The results reveal 14 identical amino acid clusters and a large number of physicochemically similar clusters. Further analysis of the similar clusters points to the conservation of secondary structures, the presence of pairs of residues occupying topologically equivalent secondary structures, and the presence of certain key residues which may play a vital role in directing and stabilizing the (alpha/beta)8 barrel fold.

Visual functioning and quality of life outcomes among cataract operated and unoperated blind populations in Nepal

BACKGROUND

Visual acuity and vision related quality of life outcomes in cataract surgery were evaluated in a population based survey in two geographic zones in Nepal.

METHODS

Case finding was based on random sampling using a stratified cluster design with door to door enumeration of people aged > or = 45 years followed by eye examinations at village sites. All aphakics/pseudophakics, those with visual acuity less than 6/60 in either eye, and a sample of those with normal visual acuity were administered visual functioning (VF) and quality of life (QOL) questionnaires.

RESULTS

15% of the 159 cataract operated cases had presenting visual acuity > or = 6/18 in both eyes, 38% with best corrected visual acuity. 21% were still blind with presenting visual acuity < 6/60 in both eyes, 7% with best correction. On a 0-100 scale, mean VF and QOL scores were 87.2 and 93.9 respectively in normally sighted unoperated individuals, dropping to 15.6 and 29.5 for those severely blind (< 3/60). Among the cataract operated, mean VF and QOL scores were 47.5 and 55.4, respectively. VF and QOL scores correlated with vision status at statistically significant levels (p < 0.0001).

CONCLUSION

Cataract surgery outcomes, whether measured by traditional visual acuity or by patient reported VF/QOL, are at levels many would consider unacceptably low. It is apparent that in the quest to reduce cataract blindness much more attention must be given to improving surgery outcomes.

Protein secondary structure prediction in different structural classes

Information about the secondary structure of a protein can be helpful in understanding its native folded state. In previous work, it was shown that the medium-range interactions predominate in all-alpha class and the long-range interactions predominate in all-beta class proteins. Based on this, in this work the performance of several structure prediction methods in different structural classes of globular proteins was analyzed. It was found that all the methods predict the secondary structures of all-alpha proteins more accurately than other classes.

The Madurai Intraocular Lens Study. III: Visual functioning and quality of life outcomes

PURPOSE

To compare the effects of extracapsular cataract extraction with posterior chamber intraocular lens (ECCE/PC-IOL) vs intracapsular cataract extraction with aphakic glasses (ICCE-AG) on everyday visual functioning and quality of life.

METHODS

In a nonmasked randomized controlled clinical trial, 3,400 bilateral vision-impaired patients, aged 40 to 75 years, with operable cataract were randomly assigned to receive one of the two treatment options. One half in each group were randomly selected for interviewer administration of visual functioning and quality of life questionnaires before surgery and at 6 and 12 months after surgery.

RESULTS

Both ICCE-AG and ECCE/PC-IOL produced dramatic improvements in visual functioning and quality of life scores. Patients receiving ECCE/PC-IOL reported larger beneficial changes than did those receiving ICCE-AG, compatible with additional beneficial effects of a moderate magnitude for visual functioning and of a smaller beneficial magnitude for quality of life. All between-group differences were highly statistically significant (P < .00001). The additional benefits of ECCE/PC-IOL are not explained by visual acuity differences. A higher proportion of patients in the ICCE-AG group reported problems on a vision problem checklist at 6 months (more than 50%) than did patients in the ECCE/PC-IOL group (approximately 30%).

CONCLUSIONS

In this developing-country setting, ICCE-AG and ECCE/PC-IOL were associated with substantial benefits in improved everyday vision function and vision-related quality of life. Patients who received ECCE/PC-IOL reported greater benefits and fewer problems with vision than did patients who received ICCE-AG.

Influence of Medium and Long Range Interactions in (α/β)(8) Barrel Proteins

The residue-residue contacts and the role of medium and long rangeinteractions in 36 (α/β)(8) barrel proteins have beenanalysed. The influence of long range contacts in the formation ofphysico-chemically similar clusters, and the preference of amino acidresidues towards long range contacts have also been studied. Theresults reveal a nearly uniform level of medium and long rangecontacts in most of the proteins. The residues Gln and Ala havehighest medium range contacts and the residue Pro has the lowestmedium range contacts. The residue Cys has the highest long rangecontact followed by other hydrophobic residues namely Val, Ile andLeu. In the physico-chemically similar clusters identified in theseproteins, 25-40 percent residues are influenced by long rangecontacts, and the residues Cys, Ile, Val and Met are the mostpreferred ones.

Influence of medium and long range interactions in different structural classes of globular proteins

An analysis of the dependence known three dimensional structure ofglobular proteins on their residue contacts and their interactions providesmuch information about their folding and stability. In this work, we analysethe residue-residue contacts and the role of medium and long rangeinteractions in globular proteins belonging to different structural classes.The results show that while medium range interactions predominate in allalpha class proteins, long range interactions predominate in all beta class.The residues Pro and Gly are found to have lowest medium range contacts,probably due to their helix breaking tendency. The hydrophobic residues Ile,Val and Tyr have higher long range contacts, and hence may serve as goodnucleation centres. Further, the role of charged residues and disulfidebridges in these interactions are also discussed.

A long-term dose-response study of mitomycin in glaucoma filtration surgery

OBJECTIVE

To establish the long-term, dose-response relationship between the concentration of and duration of exposure to mitomycin to a decrease in intraocular pressure (IOP) and fewer complications.

METHODS

We performed a prospective double-masked, placebo-controlled, 1-year study evaluating the decrease in IOP and fewer complications of fornix-based trabeculectomy surgery in 300 eyes equally divided among therapy with placebo; mitomycin, 0.2 mg/ mL, applied for 2 minutes; mitomycin, 0.4 mg/mL, applied for 4 minutes; or mitomycin, 0.4 mg/mL, applied for 2 minutes. All of the eyes had vertical and horizontal cup-disc ratios greater than 0.7.

RESULTS

We observed significant treatment-related differences in IOP, with a decrease in IOP in all 3 mitomycin-treated groups for all of the times beyond 1 month. The number of eyes achieving strict IOP control and the development of cataract suggest a possible dose-response effect for concentration and time of exposure. Progressive lens opacification was the most frequent complication in 54 eyes (18.1%). The incidence of progressive lens changes markedly increased in subjects receiving 4 minutes of mitomycin therapy. Cataract formation was unrelated to IOP. Other complications were rare. Macular folds developed in 6 patients, with visual acuity returning to better than 20/40 in all but 1 patient.

CONCLUSIONS

A possible dose-response relationship seemed to exist between the concentration of and duration of exposure to mitomycin. Length of exposure seems to be more important than concentration. The benefits of additional decreases in IOP must be weighed against the potential for increases in the risk of complications.

Uveitis associated with an epidemic outbreak of leptospirosis

PURPOSE

To define uveitis associated with leptospirosis in a clinical setting.

METHODS

We present the clinical features of 73 consecutive cases of uveitis linked clinically to an outbreak of systemic leptospirosis in patients with antibodies to Leptospira species who were examined from January to September 1994.

RESULTS

In 73 patients, the pattern of ocular involvement was unilateral in 35 and bilateral in 38. Panuveitis was seen in 106 eyes (95.5%), retinal periphlebitis in 57 eyes (51.4%), and hypopyon in 14 eyes (12.6%). Anterior uveitis alone without hypopyon was observed in three eyes (2.7%), whereas vitreous inflammatory reaction alone was seen in two eyes (1.8%). Sixty of 73 patients (82.2%) or 91 of 111 eyes (82.0%) were followed up for 8 months. Final visual acuity was 6/6 (20/20) in 47 eyes (52%) and improved during treatment, although not up to 6/6, in 15 eyes (16%). Twenty-eight eyes (31%) maintained same vision, and one eye showed deterioration of vision.

CONCLUSION

Uveitis associated with leptospirosis may manifest as unilateral or bilateral uveitis, anterior uveitis, or panuveitis. The prognosis is generally good in this entity, even when the inflammation is severe. Awareness of this disease in endemic areas is important in order to differentiate it from other uveitic entities, especially in young male patients in whom other immunologic uveitides are also common.

Measurements of vision function and quality of life in patients with cataracts in southern India. Report of instrument development

OBJECTIVE

To develop and validate vision function (VF) and quality of life (QOL) instruments in patients with cataracts in the context of large volume surgery in a developing country.

MATERIALS AND METHODS

The instruments were developed using a consensus approach. One hundred patients who were undergoing cataract surgery at Aravind Eye Hospital, Madurai, India, were interviewed preoperatively and 3 and 12 months postoperatively. Standard clinical procedures were followed, including measurement of visual acuity. Between-interviewer reproducibility was measured by repeated administration of the preoperative questionnaire. Within-interviewer reproducibility was measured preoperatively in a separate study of 50 patients.

RESULTS

Preoperative scores from the VF and QOL instruments were significantly associated with visual acuity (r = 0.4). Internal reliability (Cronbach alpha) was greater than .9. Both instruments showed large changes after surgery, with effect sizes of 3 or greater for most VF scales (range, 1.8-3.7) and 1 or greater for QOL scales (range, 1.0-2.2). Changes in visual acuity after surgery were correlated with changes in the VF (r = 0.44) and QOL (r = 0.41) scale scores. Between-interviewer reproducibility was acceptable (total VF scale, Spearman r = 0.7; total QOL scale; r = 0.74). The kappa values were lower for within-interviewer reproducibility.

CONCLUSIONS

The study provided strong evidence for the validity, reproducibility, and responsiveness of the instruments, and for the feasibility of using them in the setting of a large volume of cataract surgery in a developing country.

OUR EXPERIENCE WITH DIAGNOSTIC AND THERAPEUTIC CHOLEDOCHOSCOPY

Flexible choledochoscope was used in 16 patients undergoing common bile duct (CBD) exploration for suspected stones. Stones were found in the CBD in 4 patients in whom introperative cholangiogram was normal. T-tube cholangiogram done between the 10th and 14th postoperative days was normal in all 16 patients. None of the patients had symptoms suggestive of retained stones during follow-up ranging from 6 to 19 months. We feel that the use of choledochoscopy in patients undergoing CBD exploration will help reduce the incidence of retained stones.

Analysis of the amino acid sequences of plant Bowman-Birk inhibitors

Plant seeds contain a large number of protease inhibitors of animal, fungal, and bacterial origin. One of the well-studied families of these inhibitors is the Bowman-Birk family(BBI). The BBIs from dicotyledonous seeds are 8K, double-headed proteins. In contrast, the 8K inhibitors from monocotyledonous seeds are single headed. Monocots also have a 16K, double-headed inhibitor. We have determined the primary structure of a Bowman-Birk inhibitor from a dicot, horsegram, by sequential edman analysis of the intact protein and peptides derived from enzymatic and chemical cleavage. The 76-residue-long inhibitor is very similar to that of Macrotyloma axillare. An analysis of this inhibitor along with 26 other Bowman-Birk inhibitor domains (MW 8K) available in the SWISSPROT databank revealed that the proteins from monocots and dicots belong to related but distinct families. Inhibitors from monocots show larger variation in sequence. Sequence comparison shows that a crucial disulphide which connects the amino and carboxy termini of the active site loop is lost in monocots. The loss of a reactive site in monocots seems to be correlated to this. However, it appears that this disulphide is not absolutely essential for retention of inhibitory function. Our analysis suggests that gene duplication leading to a 16K inhibitor in monocots has occurred, probably after the divergence of monocots and dicots, and also after the loss of second reactive site in monocots.

Preparation and biological evaluation of radiolabelled antibodies with selected carbohydrate modifications

Two carbohydrates, N-acetylgalactosamine (GalNAc) and galactose-beta-1,3-GalNAc have been attached to human IgG (hIgG) by a novel linking reagent, hexafluoroglutaric acid dimethyl ester. Fluorine-19 NMR signals were used for the determination of the conjugation ratio. A third carbohydrate, sialic acid, was conjugated via reductive amination and the conjugation ratio determined by a resorcinol assay. The biological behaviour of these radioiodinated antibodies with carbohydrate modifications in normal mice indicates an enhanced liver uptake at 15 min post-injection with an associated change in circulating blood levels occurs for the galactose-based hIgG preparations. However, no significant differences in the biodistribution were observed for the sialic acid conjugate. These studies confirm the potential of carbohydrate-antibody conjugation for modifying the behaviour of antibodies in immunoscintigraphy and radioimmunotherapy.

Blockers of platelet-derived growth factor-activated nonselective cation channel inhibit cell proliferation

In serum-deprived G(o)-arrested cells, the addition of serum or growth factors initiates a cascade of events that culminates in DNA synthesis and mitosis. Recently, we showed that in mouse L-M(TK-) fibroblasts a 28-pS nonselective cation channel (NS channel) becomes quiescent at G(o) arrest and rapidly active within seconds of platelet-derived growth factor (PDGF) or serum addition, placing this response very early in the postreceptor signaling cascade. However, lack of specific channel blockers hindered determination of whether channel activation was necessary for mitogenesis. Derivatives of N-phenylanthranilic acid (DCA) have been reported to block a pancreatic nonselective channel. Therefore, using single-channel analysis, we examined the effect of these agents on the L-M(TK-) NS channel. Flufenamic acid and mefenamic acid rapidly produced reversible channel block with an inhibitory constant (Ki) approximately 10 microM. Furthermore, the component of the macroscopic K+ efflux shown to be mediated by the NS channel was blocked with a similar Ki value. DCA effects on cell proliferation were tested by measuring cloning efficiency and growth rate. Both were inhibited over the range of concentration that affected channel activity, and a 50% inhibitory dose of 50-100 microM was determined. This observation further substantiates the hypothesis that NS channel activation forms a necessary component in the transduction of the mitogenic signal from the PDGF receptor.

Monoclonal antibodies and synthetic tumor-associated glycoconjugates in the study of the expression of Thomsen-Friedenreich-like and Tn-like antigens on human cancers

Synthetic carbohydrate haptens, which are conjugated to carrier human serum albumin molecules [synthetic tumor-associated glycoconjugates (S-TAGs)], were used to immunize mice for monoclonal antibody (MoAb) production. Two of the S-TAGs were composed of haptens related to the Thomsen-Friedenreich (TF) antigen, and their structures are beta Gal(1----3)-beta GalNAc (TF-beta) and beta Gal(1----3) alpha GalNAc (TF-alpha) (Gal = galactose; GaNAc = N-acetylgalactosamine). The third S-TAG was made up of Tn hapten groups of the structure alpha GalNAc-O-serine. MoAbs specific for TF-alpha and Tn were able to be generated. All MoAbs generated against TF-beta cross-reacted with TF-alpha but not with Tn. None of the TF-alpha-specific MoAbs reacted with human carcinomas, whereas several TF-beta and Tn MoAbs were found to react with most human lung, colon, and breast carcinomas. It is believed that this is the first report of the use of synthetic carbohydrate cancer antigens for the production of anticancer MoAbs.

Pattern of neutral and phospholipids in the semen of normospermic, oligospermic and azoospermic men

Total lipid concentration was elevated in the seminal plasma of oligo- and azoospermic men. The total cholesterol content was comparatively more in the seminal plasma of azoospermic men than in that of normo- and oligospermic men. In general, infertility was associated with increased seminal concentrations for most of the neutral lipid classes. However, total phospholipids and most of the phospholipid classes were diminished in the seminal plasma of oligo- and azoospermic men and in the spermatozoa of oligospermic men. We suggest that there is a positive correlation between seminal phospholipids and fertility and a negative correlation between seminal neutral lipids and fertility.

A molecular approach to immunoscintigraphy: a study of the T-antigen conformation on the surface of tumors

The role of glycoconjugates in tumor cell differentiation has been well documented. We have examined the expression of the two anomers of the Thomsen-Friedenreich antigen on the surface of human, canine and murine tumor cell membranes both in vitro and in vivo. This has been accomplished through the synthesis of the disaccharide terminal residues in both alpha and beta configuration. Both entities were used to generate murine monoclonal antibodies which recognized the carbohydrate determinants. The determination of fine specificities of these antibodies was effected by means of cellular uptake, immunohistopathology and immunoscintigraphy. Examination of pathological specimens of human and canine tumor tissue indicated that the expressed antigen was in the beta configuration. More than 89% of all human carcinomas tested expressed the antigen in the above anomeric form. The combination of synthetic antigens and monoclonal antibodies raised specifically against them provide us with invaluable tools for the study of tumor marker expression in humans and their respective animal tumor models.

T cell recognition of a tumor-associated glycoprotein and its synthetic carbohydrate epitopes: stimulation of anticancer T cell immunity in vivo

The Thomsen, Friedenreich (TF) and Tn carbohydrate antigens are expressed on the vast majority of human adenocarcinomas and are associated with aggressive behavior of certain tumors. TF and Tn antigens are also expressed on certain murine cancer cell lines including TA3-Ha, a highly lethal, transplantable mammary adenocarcinoma. TF and Tn cancer-associated carbohydrate haptens were synthesized, conjugated to protein carriers and used to demonstrate that delayed-type hypersensitivity (DTH) effector T cells can specifically recognize and respond to carbohydrate determinants on the TA3-Ha tumor-associated glycoprotein, epiglycanin. The effector cells were shown to have the helper DTH phenotype (Lyt1+, Lyt2-, Thy1+) and it was demonstrated that they respond to specific carbohydrate determinants in an MHC-restricted fashion. These experiments provide the rationale for the use of synthetic tumor-associated glycoconjugates (S-TAGs) to stimulate anticancer T cell immunity. In support of this hypothesis, it was shown that preimmunization with the appropriate S-TAGs could provide a degree of protection against a subsequent tumor transplant and that antitumor effector Lyt1+, Lyt2- T cells could be generated in vitro using the appropriate S-TAGs as antigens.