Expert Opinion About the Pharmacoeconomic Edge of Low-Cost Dapagliflozin in Type 2 Diabetes Mellitus in Indian Clinical Settings.

Background This study aimed to understand the attitudes, beliefs, and concerns of physicians across India regarding the economic burden of diabetes and subsequently the cost-effectiveness of low-cost dapagliflozin for the management of patients with uncontrolled type 2 diabetes mellitus (T2DM) on background metformin therapy in Indian clinical settings. Method A cross-sectional questionnaire survey was conducted among physicians treating people with T2DM with or without complications. The questions covered the general aspects of affordability and adherence to diabetes medications as well as specific details of low-cost dapagliflozin and its cost-effectiveness. Results In total, 844 physicians provided a response to the survey questionnaire. The physicians who participated in the study included diabetologists, endocrinologists, cardiologists, consulting physicians, and family physicians. A majority of the physicians (53%) opined that only 10%-30% of their patients can afford the cost of newer antidiabetic medicines, while 25% of the physicians mentioned that <10% of their patients had issues related to affordability. Further, 39% of the physicians opined that 20%-40% of their patients discontinue the medicines due to high cost. Most of the physicians (95%) agreed that due to the low cost of dapagliflozin, it can be used for the primary prevention of heart failure in patients with T2DM in India. Similarly, 98% of the physicians agreed that it can be used for the treatment of heart failure in patients with or without T2DM in India. A majority of these physicians (93%) responded that switching from expensive sodium/glucose cotransporter-2 inhibitors (SGLT2i) to low-cost dapagliflozin is a long-term cost-effective management of T2DM. In total, 98% of the physicians agreed that low-cost dapagliflozin has the characteristics of an ideal SGLT2i because of its metabolic benefits, cardioprotection, nephroprotection, and potential cost-effectiveness. Conclusion This survey-based study indicates that dapagliflozin is an effective and cost-saving therapy for patients with T2DM and complications. Low-cost dapagliflozin can revolutionize the treatment of T2DM in the Indian setting.

Gla-100 Development: a Story of 'Serendipitous' Disruptive Innovation.

Ever since the discovery of insulin a century ago, relentless attempts have been made to develop insulins that closely mimic the timeaction- profile of human physiologic insulin. The early basal insulins like neutral protamine Hagedorn (NPH), were intermediate-acting, with high risk of hypoglycemia. These primary limitations led to attempts at developing improved basal insulins with a longer duration of action. After several attempts at prolonging insulin action using phenol and structural modifications of the insulin hexamer, insulin glargine was developed in 1988. The superior and unique pharmacological properties, longer duration of action, and significantly lowered risk of hypoglycemia enabled insulin glargine to be distinguished from NPH as a better basal insulin, providing holistic glycemic control. The present review highlights the circumstances that led to the search of truly basal insulins, focusing on the journey of insulin glargine 100 U/mL (Gla-100).

Comparative Evaluation of Safety and Efficacy of Glimepiride and Sitagliptin in Combination with Metformin in Patients with Type 2 Diabetes Mellitus: Indian Multicentric Randomized Trial - START Study.

BACKGROUND AND OBJECTIVE: Modern sulfonylureas like glimepiride offer effective glycemic control with extrapancreatic benefits and good tolerability. The objective of the present study was to evaluate and compare safety and efficacy of glimepiride and sitagliptin in combination with metformin in patients with type 2 diabetes mellitus (T2DM). METHODS: In this open-label, randomized, comparative, multicenter study, a total of 305 T2DM patients who were either drug naïve or uncontrolled on metformin were randomized to glimepiride 1 or 2 mg/sustained-release metformin 1000 mg once daily (glimepiride group, n = 202) or sitagliptin 50 mg/metformin 500 mg twice daily (sitagliptin group, n = 103) for 12 weeks. Primary endpoint was change in glycosylated hemoglobin (HbA1c). Secondary endpoints were change in fasting plasma glucose (FPG), postprandial plasma glucose (PPG), body mass index (BMI) and to assess overall safety profile. RESULTS: At 12 weeks, there was a statistically significant difference in the mean HbA1c reduction in glimepiride group (0.42%) as compared to sitagliptin group (0.30%) (P = 0.001). Mean reduction in FPG and PPG was also statistically significant in the glimepiride group as compared to the sitagliptin group (P = 0.008). There was no significant difference in terms of change in BMI (0.07 ± 0.39 kg/m2 vs. 0.08 ± 0.31 kg/m2) in glimepiride and sitagliptin groups, respectively, (P = 0.644) between both the groups. The incidences of hypoglycemic events were also comparable among both the groups. CONCLUSION: In T2DM patients, glimepiride/metformin combination exhibited significant reduction in glycemic parameters as compared to sitagliptin/metformin combination. Moreover, there was no significant difference between both the groups in terms of change in BMI and incidence of hypoglycemia.

The 'straight mouse': defining anatomical axes in 3D embryo models.

A primary objective of the eMouseAtlas Project is to enable 3D spatial mapping of whole embryo gene expression data to capture complex 3D patterns for indexing, visualization, cross-comparison and analysis. For this we have developed a spatio-temporal framework based on 3D models of embryos at different stages of development coupled with an anatomical ontology. Here we introduce a method of defining coordinate axes that correspond to the anatomical or biologically relevant anterior-posterior (A-P), dorsal-ventral (D-V) and left-right (L-R) directions. These enable more sophisticated query and analysis of the data with biologically relevant associations, and provide novel data visualizations that can reveal patterns that are otherwise difficult to detect in the standard 3D coordinate space. These anatomical coordinates are defined using the concept of a 'straight mouse-embryo' within which the anatomical coordinates are Cartesian. The straight embryo model has been mapped via a complex non-linear transform onto the standard embryo model. We explore the utility of this anatomical coordinate system in elucidating the spatial relationship of spatially mapped embryonic ' Fibroblast growth factor ' gene expression patterns, and we discuss the importance of this technology in summarizing complex multimodal mouse embryo image data from gene expression and anatomy studies. Database URL: www.emouseatlas.org.

Ulcer Protective Activity of Jatropha gossypiifolia Linn. in Wistar Rats.

BACKGROUND: Several synthetic drugs are useful in the treatment of peptic ulcer, but almost of these drugs are used in prolonging time, it may cause several adverse reactions. However, the herbal medicines are more potent to the treatment and minimize the side effects. OBJECTIVE: To evaluate the methanol extract of Jatropha gossypiifolia Linn. (MEJG) for gastro protective activity against Wistar rats. MATERIALS AND METHODS: Anti-ulcer potency of MEJG (100 and 200 mg/kg, b.w.) was assessed using aspirin (200 mg/kg, p.o.) plus pylorus ligation ulcer model and the parameters studied were ulcer index (UI), gastric juice volume, pH, total acidity, and total acid output. Same extract was studied by ethanol-induced (80%, 5 mL/kg, intragastrically) ulcer model, and the UI and biochemical parameters were studied. RESULTS: The oral administration of MEJG (100 and 200 mg/kg) significantly (P < 0.001) attenuated the ulcer score and anti-secretary parameters (such as the volume of gastric content, free acidity, total acidity, and total acid output) in the aspirin plus pylorus ligation rats. The extract also significantly attenuated (P < 0.001) ulcer score in ethanol-induced ulcer model and lipid peroxidation level and significantly increased the level of glutathione peroxides, catalase, and superoxide dismutase activity. The MEJG may possess active constituents such as alkaloids, glycosides, flavonoids, and terpenes, which may play a major role in gastroprotective effect in Wistar rats. CONCLUSION: The present study provides scientific support for the anti-ulcer activities of extracts of JG and also claimed that antioxidant potential of the extracts. However, substantiates the traditional claims for the usage of this drug in the treatment of gastric ulcer. SUMMARY: The methanolic extract of jatropha gossypiifolia Linn. for gastro protective activity against aspirin plus pyloric ligation and ethanol induced ulcer models was studied in Wistar rats. JG shows significantly attenuated the ulcer score in both models. And also attenuated in anti-secretory parameters in aspirin induced ulcer model. MEJG may possess active constituents such as alkaloids, glycosides, flavonoids and terpenes, which may play a major role in gastroprotective effect in Wistar rats. Abbreviation Used: MEJG: Methanolic extract of jatropha gossypiifolia, mg: Milli gram, kg: Kilogram, b.w.: Body weight, p.o.: Per oral, UI: Ulcer index, pH: Concentration of H+ ion, mL: Milli litre, JG: Jatropha gossypiifolia,USD: United States Dollar, NSAIDs: Non steroidal anti-inflammatory drugs, v/v: Volume by volume, w/v: Weight by volume, SCMC: Sodium carboxy methyl cellulose, g: Gram, h: Hour, °C: Degree centigrade, n: Number, Rpm: Rotation per minute, Min: Minute, N: Normality, NaoH: Sodium hydroxide, mM - Millimole, TBA: Thiobarbituric acid, nmol: Nanomole, nm: Nanometer, GPx: Glutathione peroxidase, GSH: Reduced glutathione, H2O2: Hydrogen peroxide, SOD: Superoxide dismutase, ANOVA: Analysis of Variance, µmol: Micromole.

The protective effects of Cyperus rotundus on behavior and cognitive function in a rat model of hypoxia injury.

CONTEXT: Hypoxia injury (HI) with its long-term neurological complications is one of the leading causes of morbidity and mortality in the world. Currently, the treatment regimens for hypoxia are aimed only at ameliorating the damage without complete cure. The need, therefore, for novel therapeutic drugs to treat HI continues. OBJECTIVE: This study investigates the protective effects of the ethanol extract of Cyperus rotundus L. (Cyperaceae) (EECR), a medicinal plant used in Ayurvedic traditional medicine against sodium nitrite-induced hypoxia in rats. MATERIALS AND METHODS: We have evaluated the protective effect of 200 and 400 mg/kg of EECR against sodium nitrite-induced hypoxia injury in rats by assessing the cognitive functions, motor, and behavioral effects of EECR treatment along with the histological changes in the brain. By comparing the protective effects of standard drugs galantamine, a reversible cholinesterase inhibitor and pyritinol, an antioxidant nootropic drug against sodium nitrite-induced hypoxia in rats, we have tested the protective ability of EECR. RESULTS: EECR at doses of 200 and 400 mg/kg was able to protect against the cognitive impairments, and the locomotor activity and muscular coordination defects, which are affected by sodium nitrite-induced hypoxia injury in rats. CONCLUSION: Based on our results, we suggest that the medicinal herb C. rotundus possesses a protective effect against sodium nitrite-induced hypoxia in rats. Further studies on these protective effects of EECR may help in designing better therapeutic regimes for hypoxia injury.

A comparative study of NONOate based NO donors: spermine NONOate is the best suited NO donor for angiogenesis.

Nitric oxide (NO) is a known modulator of angiogenesis. The NONOate subfamily of NO donors has long been used in experimental and clinical studies to promote angiogenesis. However, no studies have been conducted yet to compare the angiogenesis potential of these NO donors in respect to their pattern of NO release. We hypothesize that having different pattern of NO release, each of the NO donors in NONOate subfamily can promote key stages of angiogenesis in differential manner. To verify our hypothesis, NO donors with half life ranging from seconds to several hours and having very different pattern of NO release were selected to evaluate their efficacy in modulating angiogenesis. Endothelial tube formation using EAhy926 cells was maximally increased by Spermine NONOate (SP) treatment. SP treatment maximally induced both ex vivo and in vivo angiogenesis using egg yolk and cotton plug angiogenesis models respectively. Experiment using chick embryo partial ischemia model revealed SP as the best suited NO donor to recover ischemia driven hampered angiogenesis. The present study elaborated that differential release pattern of NO by different NO donors can modulate angiogenesis differentially and also suggested that SP have a unique pattern of NO release that best fits for angiogenesis.

A Monte Carlo tool for evaluating VMAT and DIMRT treatment deliveries including planar detectors.

The aim of this work is to describe and validate a new general research tool that performs Monte Carlo (MC) simulations for volumetric modulated arc therapy (VMAT) and dynamic intensity modulated radiation therapy (DIMRT), simultaneously tracking dose deposition in both the patient CT geometry and an arbitrary planar detector system. The tool is generalized to handle either entrance or exit detectors and provides the simulated dose for the individual control-points of the time-dependent VMAT and DIMRT deliveries. The MC simulation tool was developed with the EGSnrc radiation transport. For the individual control point simulation, we rotate the patient/phantom volume only (i.e. independent of the gantry and planar detector geometries) using the gantry angle in the treatment planning system (TPS) DICOM RP file such that each control point has its own unique phantom file. After MC simulation, we obtained the total dose to the phantom by summing dose contributions for all control points. Scored dose to the sensitive layer of the planar detector is available for each control point. To validate the tool, three clinical treatment plans were used including VMAT plans for a prostate case and a head-and-neck case, and a DIMRT plan for a head-and-neck case. An electronic portal imaging device operated in 'movie' mode was used with the VMAT plans delivered to cylindrical and anthropomorphic phantoms to validate the code using an exit detector. The DIMRT plan was delivered to a novel transmission detector, to validate the code using an entrance detector. The total MC 3D absolute doses in patient/phantom were compared with the TPS doses, while 2D MC doses were compared with planar detector doses for all individual control points, using the gamma evaluation test with 3%/3 mm criteria. The MC 3D absolute doses demonstrated excellent agreement with the TPS doses for all the tested plans, with about 95% of voxels having γ <1 for the plans. For planar dosimetry image comparisons, we defined an acceptable pass rate of >90% of percentage pixels with γ <1. We found that over 90% of control points in the plans passed this criterion. In general, our results indicate that the simulation tool is suitable for accurately calculating both patient/phantom doses and planar doses for VMAT dose delivery. The tool will be valuable to check performance and advance the development of in vivo planar detectors for use in measurement-based VMAT dose verification. In addition, the tool can be useful as an independent research tool for VMAT commissioning of the TPS and delivery system.

Analgesic and anti-inflammatory properties of Thespesia populnea leaf extracts.

Analgesic and anti-inflammatory activities of the aqueous and ethanol extracts of Thespesia populnea Soland. ex. Correa (Malvaceae) leaves were evaluated in animal models. Orally-administered aqueous and ethanol extracts (100, 200 and 400 mg kg⁻¹ bw) showed significant analgesic activity in chemical-, mechanical- and thermally-induced pain test models in mice. The extracts also reduced paw oedema induced by carrageenan in rats. The results obtained in this study suggest that Thespesia populnea extracts have analgesic and anti-inflammatory properties.

Evaluation of toxicological and antioxidant potential of Nardostachys jatamansi in reversing haloperidol-induced catalepsy in rats.

An aqueous root extract from Nardostachys jatamansi was investigated for its antioxidant and anticataleptic effects in the haloperidol-induced catalepsy rat model of the disease by measuring various behavioral and biochemical parameters. Catalepsy was induced by administration of haloperidol (1 mg/kg, ip) in male albino rats. A significant (P < 0.01) reduction in the cataleptic scores were observed in all the drug-treated groups as compared to the haloperidol-treated group; with maximum reduction observed in the Nardostachys jatamansi (250 and 500 mg/kg body weight) administered group. To estimate biochemical parameters: the generation of thiobarbituric acid reactive substances (TBARS); reduced glutathione (GSH) content and glutathione-dependent enzymes; catalase; and superoxide dismutase (SOD), in the brain were assessed. Haloperidol administration increased generation of TBARS and significantly reduced GSH, which were restored to near normal level with the Nardostachys jatamansi treatment. Catalase and SOD levels were also increased to normal levels, having been reduced significantly by haloperidol administration. Our findings of behavioral studies and biochemical estimations show that Nardostachys jatamansi reversed the haloperidol-induced catalepsy in rats. We conclude that the antioxidant potential has contributed to the reduction in the oxidative stress and catalepsy induced by haloperidol administration.

Thalidomide attenuates nitric oxide-driven angiogenesis by interacting with soluble guanylyl cyclase.

BACKGROUND AND PURPOSE: Nitric oxide (NO) promotes angiogenesis by activating endothelial cells. Thalidomide arrests angiogenesis by interacting with the NO pathway, but its putative targets are not known. Here, we have attempted to identify these targets. EXPERIMENTAL APPROACH: Cell-based angiogenesis assays (wound healing of monolayers and tube formation in ECV304, EAhy926 and bovine arterial endothelial cells), along with ex vivo and in vivo angiogenesis assays, were used to explore interactions between thalidomide and NO. We also carried out in silico homology modelling and docking studies to elucidate possible molecular interactions of thalidomide and soluble guanylyl cyclase (sGC). KEY RESULTS: Thalidomide inhibited pro-angiogenic functions in endothelial cell cultures, whereas 8-bromo-cGMP, sildenafil (a phosphodiesterase inhibitor) or a NO donor [sodium nitroprusside (SNP)] increased these functions. The inhibitory effects of thalidomide were reversed by adding 8-bromo-cGMP or sildenafil, but not by SNP. Immunoassays showed a concentration-dependent decrease of cGMP in endothelial cells with thalidomide, without affecting the expression level of sGC protein. These results suggested that thalidomide inhibited the activity of sGC. Molecular modelling and docking experiments revealed that thalidomide could interact with the catalytic domain of sGC, which would explain the inhibitory effects of thalidomide on NO-dependent angiogenesis. CONCLUSION AND IMPLICATIONS: Our results showed that thalidomide interacted with sGC, suppressing cGMP levels in endothelial cells, thus exerting its anti-angiogenic effects. These results could lead to the formulation of thalidomide-based drugs to curb angiogenesis by targeting sGC.

Cell-mediated immunity to predict cytomegalovirus disease in high-risk solid organ transplant recipients.

Late-onset cytomegalovirus (CMV) disease commonly occurs after discontinuation of antiviral prophylaxis. We determined the utility of testing CD8+ T-cell response against CMV as a predictor of late-onset CMV disease after a standard course of antiviral prophylaxis. Transplant patients at high-risk for CMV disease were enrolled. CD8+ T-cell-mediated immunity (CMI) was tested using the QuantiFERON-CMV assay at baseline, 1, 2 and 3 months posttransplant by measurement of interferon-gamma response to whole blood stimulation with a 21-peptide pool. The primary outcome was the ability of CMI testing to predict CMV disease in the first 6 months posttransplant. There were 108 evaluable patients (D+/R+ n = 39; D-/R+ n = 34; D+/R- n = 35) of whom 18 (16.7%) developed symptomatic CMV disease. At the end of prophylaxis, CMI was detectable in 38/108 (35.2%) patients (cutoff 0.1 IU/mL interferon-gamma). CMV disease occurred in 2/38 (5.3%) patients with a detectable interferon-gamma response versus 16/70 (22.9%) patients with a negative response; p = 0.038. In the subgroup of D+/R- patients, CMV disease occurred in 1/10 (10.0%) patients with a detectable interferon-gamma response (cutoff 0.1 IU/mL) versus 10/25 (40.0%) patients with a negative CMI, p = 0.12. Monitoring of CMI may be useful for predicting late-onset CMV disease.

An attempt for modeling the atmospheric transport of 3H around Kakrapar Atomic Power Station.

Prediction of downwind tritium air concentrations in the environment around Kakrapar Atomic Power Station (KAPS) was studied on the basis of Gaussian plume dispersion model. The tritium air concentration by field measurement [measured tritium air concentrations in the areas adjacent to KAPS] were compared with the theoretically calculated values (predicted) to validate the model. This approach will be useful in evaluating environmental radiological impacts due to pressurised heavy water reactors.

Preliminary evaluation of anti-pyretic and anti-ulcerogenic activities of Sida cordifolia methanolic extract.

The anti-pyretic and anti-ulcerogenic properties of methanolic extract of Sida cordifolia aerial parts (MESC) were investigated in rats. Oral dose of 500 mg/kg MESC significantly reduced pyrexia induced by TAB vaccine. MESC exhibited significant anti-ulcerogenic effect against aspirin and ethanol induced damage. Both these properties were comparable to the reference drugs.

Poster - Thurs Eve-33: Initial implementation of a novel, measurement-based IMRT QA method.

Current measurement-based QA for IMRT typically involves a composite dose delivery to a phantom. However, this approach does not allow a direct dosimetric evaluation of the delivered treatment with respect to the patient anatomy. In this work we implement a novel, measurement-based IMRT QA method which provides an accurate reconstruction of the 3D-dose distribution in the patient model. The RPC Head&Neck phantom and two clinical prostate cases have been examined to date. Step & shoot plans were developed satisfying required dose metrics. A 2D-array of dose chambers (MatriXX, IBA Dosimetry) was mounted on a linear accelerator to capture delivered fluence. The measurement data were read directly by the control software (COMPASS, IBA Dosimetry), which also provides the ability to import patient plan data from the TPS. The COMPASS software also includes a dose calculation engine and head fluence model and requires beam commissioning procedures analogous to those of a TPS. Reconstructed doses and DVHs were compared to those calculated by the TPS. The beam model in the COMPASS software was able to predict percentage depth dose and X and Y profiles for MLC-defined apertures ranging from 1×1-20×20 cm∧2 to within 1.5% (depth-dose), 2.0% (in-field profiles), and 2.5% (out-of-field profiles). Reconstructed doses in the test plans were mostly within 2% of those in the TPS. DVHs compared to <1.2%. Reconstructed doses were overlaid on CT data and contoured structures, to enable a clinically useful understanding of discrepancies as compared to the TPS plan. Research partially sponsored by IBA Dosimetry.

Comparison of the indentation and elasticity of E. coli and its spheroplasts by AFM.

Atomic force microscopy (AFM) provides a unique opportunity to study live individual bacteria at the nanometer scale. In addition to providing accurate morphological information, AFM can be exploited to investigate membrane protein localization and molecular interactions on the surface of living cells. A prerequisite for these studies is the development of robust procedures for sample preparation. While such procedures are established for intact bacteria, they are only beginning to emerge for bacterial spheroplasts. Spheroplasts are useful research models for studying mechanosensitive ion channels, membrane transport, lipopolysaccharide translocation, solute uptake, and the effects of antimicrobial agents on membranes. Furthermore, given the similarities between spheroplasts and cell wall-deficient (CWD) forms of pathogenic bacteria, spheroplast research could be relevant in biomedical research. In this paper, a new technique for immobilizing spheroplasts on mica pretreated with aminopropyltriethoxysilane (APTES) and glutaraldehyde is described. Using this mounting technique, the indentation and cell elasticity of glutaraldehyde-fixed and untreated spheroplasts of E. coli in liquid were measured. These values are compared to those of intact E. coli. Untreated spheroplasts were found to be much softer than the intact cells and the silicon nitride cantilevers used in this study.

Antiulcerogenic potential of Strychnos potatorum Linn seeds on aspirin plus pyloric ligation-induced ulcers in experimental rats.

Strychnos potatorum (Fam: Loganiaceae) Linn seeds are useful in the treatment of gastropathy in Indian traditional system of medicine. The present study describes the antiulcerogenic potential of S. potatorum Linn seeds on aspirin plus pyloric ligation (Aspirin+PL)-induced gastric ulcer model to substantiate its folklore claim. The seed powder (SPP) and aqueous extract of the seeds (SPE) at two doses 100 and 200 mg/kg, p.o. prevented ulcer formation by decreasing acid secretory activity and increasing the mucin activity in rats. The antiulcerogenic potential was further confirmed by the histopathological studies of stomach mucosa. The results indicate that SPP and SPE exhibit antiulcerogenic activity by both antisecretory and mucoprotective actions. The mucoprotective action of SPP and SPE may be due to the presence of polysaccharides in seeds. The antiulcerogenic potential of SPP and SPE was compared with the standard antiulcer drug, ranitidine.

Tropical malabsorption.

Malabsorption is an important clinical problem both in visitors to the tropics and in native residents of tropical countries. Infections of the small intestine are the most important cause of tropical malabsorption. Protozoal infections cause malabsorption in immunocompetent hosts, but do so more commonly in the setting of immune deficiency. Helminth infections occasionally cause malabsorption or protein-losing enteropathy. Intestinal tuberculosis, chronic pancreatitis and small-bowel bacterial overgrowth are important causes of tropical malabsorption. In recent years, inflammatory bowel disease and coeliac disease have become major causes of malabsorption in the tropics. Sporadic tropical sprue is still an important cause of malabsorption in adults and in children in South Asia. Investigations to exclude specific infective, immunological or inflammatory causes are important before considering tropical sprue as a diagnosis. This article briefly reviews the management of tropical sprue and presents an algorithm for its investigation and management.

A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications.

Analysis of protein structures based on backbone structural patterns known as structural alphabets have been shown to be very useful. Among them, a set of 16 pentapeptide structural motifs known as protein blocks (PBs) has been identified and upon which backbone model of most protein structures can be built. PBs allows simplification of 3D space onto 1D space in the form of sequence of PBs. Here, for the first time, substitution probabilities of PBs in a large number of aligned homologous protein structures have been studied and are expressed as a simplified 16 x 16 substitution matrix. The matrix was validated by benchmarking how well it can align sequences of PBs rather like amino acid alignment to identify structurally equivalent regions in closely or distantly related proteins using dynamic programming approach. The alignment results obtained are very comparable to well established structure comparison methods like DALI and STAMP. Other interesting applications of the matrix have been investigated. We first show that, in variable regions between two superimposed homologous proteins, one can distinguish between local conformational differences and rigid-body displacement of a conserved motif by comparing the PBs and their substitution scores. Second, we demonstrate, with the example of aspartic proteinases, that PBs can be efficiently used to detect the lobe/domain flexibility in the multidomain proteins. Lastly, using protein kinase as an example, we identify regions of conformational variations and rigid body movements in the enzyme as it is changed to the active state from an inactive state.

Measuring cell surface elasticity on enteroaggregative Escherichia coli wild type and dispersin mutant by AFM.

Enteroaggregative Escherichia coli (EAEC) is pathogenic and produces severe diarrhea in humans. A mutant of EAEC that does not produce dispersin, a cell surface protein, is not pathogenic. It has been proposed that dispersin imparts a positive charge to the bacterial cell surface allowing the bacteria to colonize on the negatively charged intestinal mucosa. However, physical properties of the bacterial cell surface, such as rigidity, may be influenced by the presence of dispersin and may contribute to pathogenicity. Using the system developed in our laboratory for mounting and imaging bacterial cells by atomic force microscopy (AFM), in liquid, on gelatin coated mica surfaces, studies were initiated to measure cell surface elasticity. This was carried out in both wild type EAEC, that produces dispersin, and the mutant that does not produce dispersin. This was accomplished using AFM force-distance (FD) spectroscopy on the wild type and mutant grown in liquid or on solid medium. Images in liquid and in air of both the wild-type and mutant grown in liquid and on solid media are presented. This work represents an initial step in efforts to understand the pathogenic role of the dispersin protein in the wild-type bacteria.