Search PubMed⌕ Search

Biomedical subjects

V Shankar

Publications and source records attributed to V Shankar.

At least 19 recordsLinked to original sources
PubMed2006

Instability and dynamics of thin viscoelastic liquid films.

The instability, rupture, and subsequent growth of holes in a thin Jeffreys-type viscoelastic film under the influence of long-range van der Waals force are investigated using both linear stability analysis and nonlinear numerical solutions. The linear stability analysis of full governing equations valid for arbitrary wave numbers shows that although fluid rheology does not influence the dominant length scale of the instability, it significantly affects the growth rate. It is shown that neglect of inertia and solvent dynamics results in a nonphysical singularity in the growth rate beyond a critical value of relaxation time. We further carry out numerical simulations of a set of long-wave, nonlinear differential equations (also derived in Rauscher et al., Eur. Phys. J. E 17, 373 (2005)) governing the evolution of the free surface. The nonlinear simulations, in their domain of validity, confirm the results of the linear analysis. Interestingly, results from nonlinear simulations further show that both for Newtonian and viscoelastic liquids, the shape and the dewetting dynamics of a hole are identical when examined in terms of a rescaled time which depends on rheological parameters. Thus, viscoelasticity of Jeffreys type merely accelerates the growth rate, without however affecting the important morphological characteristics.

Computer Simulation↗
PubMed2006

Suitability of human juvenile pancreatic islets for clinical use.

AIMS/HYPOTHESIS: The limited availability of deceased donor pancreases suitable for pancreas and islet transplantation calls for a broader utilisation of donor tissue for transplantation purposes. Young donors, representing, fortunately, a minor but significant pool of individuals, have been largely under-employed, mainly because of anatomical and functional incompatibilities with potential recipients. For islet transplantation, the isolation of pancreatic islets from young donors rarely occurs, because of technical problems. As a result of the peculiar characteristics of young donor pancreases, the standard isolation procedure does not allow efficient separation of the islets from the surrounding exocrine tissue, and favours the generation of mantled islets. Nonetheless, young donor islets offer high qualitative and clinically appealing characteristics. SUBJECTS AND METHODS: We standardised a modified methodology to obtain purified and mantle-free human islets from young donors. This method principally involves efficient delivery of isolation enzyme with reduced mechanical disruption of the pancreas combined with additional filtration steps. RESULTS: We were able to obtain purified and mantle-free human islets from donors as young as 6 months of age with good morphological and functional properties. The good qualitative characteristics of the islets, evidenced in vitro, were proven in vivo, as they were qualitatively superior to islets of older donors in transplantation studies. CONCLUSIONS/INTERPRETATION: This study justifies the utilisation of islets derived from young donors for islet transplantation.

Adolescent↗
PubMed2006

Suppression of instability in liquid flow down an inclined plane by a deformable solid layer.

The linear stability of a liquid layer flowing down an inclined plane lined with a deformable, viscoelastic solid layer is analyzed in order to determine the effect of the elastohydrodynamic coupling between the liquid flow and solid deformation on the free-surface instability in the liquid layer. The stability of this two-layer system is characterized by two qualitatively different interfacial instability modes: In the absence of the deformable solid layer, the free surface of the liquid film undergoes a long-wave instability due to fluid inertia. With the presence of the deformable solid layer, the interface between the fluid and the solid undergoes a finite-wavelength instability when the deformable solid becomes sufficiently soft. The effect of the solid layer deformability on the free-surface instability of the liquid film flow is analyzed using a long-wave asymptotic analysis. The asymptotic results show that for a fixed Reynolds number and inclination angle, the free-surface instability is completely suppressed in the long-wave limit when the nondimensional (inverse) solid elasticity parameter Gamma=Va eta/(GR)increases beyond a critical value. Here, Va is the average velocity of the liquid film flow, eta is the viscosity of the liquid, G is the shear modulus of the solid layer, and is R the thickness of the liquid layer. The predictions of the asymptotic analysis are verified and extended to finite wavelengths using a numerical solution, and this indicates that the suppression of the free-surface instability indeed continues to finite wavelength disturbances. Further increase of Gamma is found to have two consequences: first, the interface between the liquid and the deformable solid layer could become unstable at finite wavelengths; second, the free-surface interfacial mode could also become unstable at finite wavelengths due to an increase in solid layer deformability. However, our numerical results demonstrate that, for a given average velocity, there exists a sufficient window in the value of shear modulus G where both the unstable modes are absent at all wavelengths. Our study therefore suggests that soft solid layer coatings could potentially provide a passive method of suppressing free-surface instabilities in liquid film flows.

Journal Article↗
PubMed2004

Instability of the interface between thin fluid films subjected to electric fields.

The effect of an externally applied electric field on the stability of the interface between two thin leaky dielectric fluid films of thickness ratio and viscosity ratio ris analyzed using a linear stability analysis in the long-wave limit. A systematic asymptotic expansion is employed in this limit to derive the coupled nonlinear differential equations describing the evolution of the position of the interface between the fluids and the interfacial free charge distribution. The linearized stability of these equations is determined and the effect of the ratio of the conductivities, dielectric constants, thicknesses, and viscosities on the wavenumber of the fastest growing mode, kmax, and the growth rate of the most unstable mode, smax, is examined in detail. Specific configurations considered in previous studies, such as a perfect dielectric-air interface, leaky dielectric-air interface, etc., emerge as limiting cases from the general formulation developed in this paper. Our results show that the viscosity ratio, mur, does not have any significant effect on kmax for the interface between perfect and leaky dielectric fluids. In marked contrast, however, mur is shown to have a significant effect on the interface between two leaky dielectrics. Increasing mur from 0.1 to 10 could decrease kmax up to a factor of 5. In general, our results show that the presence of nonzero conductivity in either one or both of the fluids has a profound influence on the length-scale characteristic of the linear instability: a reduction even by a factor of 1/50 in the length scale can be effected when compared to the interface between two perfect dielectrics. These predictions could have important implications in pattern formation applications in thin fluid films that employ electric fields. The variation of kmax and smax on the thickness ratio, beta, indicates in general that kmaxalpha(beta-apha), and smaxalpha(beta-theta), where the exponents alpha and theta (both >0) are found to depend only on the ratio of conductivities, and are largely independent of other system parameters.

Journal Article↗
PubMed2004

Nuclease Rsn from Rhizopus stolonifer: specificity and mode of action.

Nuclease Rsn from Rhizopus stolonifer catalyzes the hydrolysis of ss- and dsDNA in a ratio of approximately 2:1. Time course of 3' and 5' terminal analysis of the hydrolytic products of ss- and dsDNA showed that nuclease Rsn does not show any strict base preference and cleaves DNA in a non-specific manner. Moreover, separation of the hydrolytic products of ss- and dsDNA in the presence of Mg2+, Mn2+ or Co2+ showed the predominance of tetra-, tri-, and dinucleotides followed by mononucleotides, suggesting an endo mode of action.

Animals↗
PubMed2003

Bacterial glycoproteins: functions, biosynthesis and applications.

Although widely distributed in eukaryotic cells glycoproteins appear to be rare in prokaryotic organisms. The prevalence of the misconception that bacteria do not glycosylate their proteins has been a subject matter of discussion for a long time. Glycoconjugates that are linked to proteins or peptides, generated by the ribosomal translational mechanism have been reported only in the last two to three decades in a few prokaryotic organisms. Most studied prokaryotic glycoproteins are the S-layer glycoproteins of Archeabacteria. Apart from these, membrane-associated, surface-associated, secreted glycoproteins and exoenzymes glycoproteins are also well documented in both, Archea and Eubacteria. From the recent literature, it is now clear that prokaryotes are capable of glycosylating proteins. In general, prokaryotes are deprived of the cellular organelles required for glycosylation. In prokaryotes many different glycoprotein structures have been observed that display much more variation than that observed in eukaryotes. Besides following similar mechanisms in the process of glycosylation, prokaryotes have also been shown to use mechanisms that are different from those found in eukaryotes. The knowledge pertaining to the functional aspects of prokaryotic glycoproteins is rather scarce. This review summarizes developments and understanding relating to characteristics, synthesis, and functions of prokaryotic glycoproteins. An extensive summary of glycosylation that has been reported to occur in bacteria has also been tabulated. Various possible applications of these diverse biomolecules in biotechnology, vaccine development, pharmaceutics and diagnostics are also touched upon.

Bacterial Proteins↗
PubMed2003

Comparison of disc diffusion & E test methods with agar dilution for antimicrobial susceptibility testing of Haemophilus influenzae.

BACKGROUND & OBJECTIVES: Reliable methods of detection of antimicrobial resistance are of paramount importance in the treatment and management of infections caused by Haemophilus influenzae. The objective of the present study was to compare and evaluate the performance of disc diffusion and E test (Epsilometer test) with agar dilution method for antimicrobial susceptibility testing of H. influenzae. METHODS: A total of 46 isolates of H. influenzae from various invasive sites were included as test strains. Antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion method for ampicillin, chloramphenicol, trimethoprim-sulphamethoxazole (TMP-SMZ) and cefotaxime. Minimum Inhibitory Concentration (MIC) determination was performed by E test and agar dilution for the same set of antimicrobials. All tests were performed on Haemophilus test medium (HTM). RESULTS: Disc diffusion showed a very major (2%) and minor (4%) interpretative error with TMP-SMZ and minor interpretative errors to ampicillin (13%) and chloramphenicol (24%) when compared to agar dilution method. E test produced only minor interpretative errors to chloramphenicol (7%) and TMP-SMZ (2%) and no interpretative errors with ampicillin and cefotaxime as against agar dilution. E test showed good agreement with agar dilution for each of the antimicrobial tested. INTERPRETATION & CONCLUSION: Disc diffusion test may be used as a preliminary screen for susceptibility testing of H. influenzae. E test is simple, easy to perform and a reliable method for determination of resistance in H. influenzae. However its cost and limited availability in India may limit its use. The reference agar dilution method can be used reliably in routine susceptibility testing of H. influenzae.

Agar↗
PubMed2002

Comparison of IgM capture ELISA with a commercial rapid immunochromatographic card test & IgM microwell ELISA for the detection of antibodies to dengue viruses.

BACKGROUND & OBJECTIVES: There is a need for a reliable test for the early diagnosis of dengue fever (DF), which is now active in many parts of India especially in the post monsoon months. This study evaluated two commercial tests with an assay available from a national laboratory in India to obtain information and to make a comparison among the three tests as to which will be the most suited for the detection of IgM antibodies to dengue virus. METHODS: An IgM capture ELISA (National Institute of Virology, Pune, India) was compared with two commercial tests, the PanBio Rapid Immunochromatographic Card Test (Brisbane, Australia) and the PanBio Microwell IgM ELISA for the detection of IgM antibodies to dengue virus. We tested 154 samples from individuals with febrile illnesses having DF--like symptoms. RESULTS: The NIV IgM capture ELISA (MAC-ELISA) showed a high positivity rate (38.9%) as compared to the PanBio Rapid (22.7%) and the PanBio IgM ELISA (20.7%). The true prevalence of disease, sensitivity and specificity of the three tests were estimated using 2LC latent class models using expectation-maximization (EM) algorithm. The NIV MAC-ELISA showed a high sensitivity (96%) as compared to PanBio Rapid (73%) and PanBio IgM ELISA (72%). A subset of 68 samples (of the 154 tested) were analyzed by the NIV MAC-ELISA for IgM antibodies additionally to Japanese encephalitis (JE) and West Nile (WN) of which 31 samples showed positivity to either one, two or all three flaviviruses. Out of the 8 samples which were positive for dengue IgM alone by the NIV MAC-ELISA, only 2 (25%) each were picked up by the other 2 tests. While out of 7 samples positive for IgM to all three flaviviruses IgM by the NIV MAC-ELISA, 5 (71%) were picked up by the other 2 tests. Of the 5 that were picked up by the PanBio tests, 3 had the highest absorbance values to WN by the NIV MAC-ELISA, indicating cross reactivity by PanBio tests. INTERPRETATION & CONCLUSION: The MAC-ELISA though a 3 day procedure, would be a valuable screening test for the detection of IgM to dengue in routine diagnostic laboratories because of its high sensitivity and specificity rates. The test uses specific viral antigens to detect IgM antibodies not only to dengue but also to JE and West Nile as a result of which IgM antibodies to all the 3 commonly encountered flaviviruses can be detected in a single run. It also has the advantage in that depending on the strength of the antibody units obtained to a specific flaviviral antigen, presumptive diagnosis as to which particular arboviral infection has occurred can be made in conjunction with clinical presentation.

Antibodies, Viral↗
PubMed2001

Viscoelasticity of dilute solutions of semiflexible polymers.

We show using Brownian dynamics simulations and theory how the shear relaxation modulus G(t) of dilute solutions of relatively stiff semiflexible polymers differs qualitatively from that of rigid rods. For chains shorter than their persistence length, G(t) exhibits three time regimes: At very early times, when the longitudinal deformation is affine, G(t) approximately t(-3/4). Over a broad intermediate regime, during which the chain length relaxes, G(t) approximately t(-5/4). At long times, G(t) mimics that of rigid rods. A model of the polymer as an effectively extensible rod with a frequency dependent elastic modulus B(omega) approximately ((i)omega)(3/4) quantitatively describes G(t) throughout the first two regimes.

Journal Article↗
PubMed2001

Nucleotide sequence analysis of varicella-zoster virus glycoprotein E epitope coding regions.

Varicella-zoster virus (VZV) glycoprotein E [gE] contains 623 amino acid residues. Fifty percent of the gE gene, codons 39 to 344 that encompasses two epitope coding regions e1 and c1, was sequenced and analyzed for variation among the 30 VZV isolates. A total of eleven isolates showed variance when compared with Dumas VZV strain sequence through base substitutions, with two isolates showing an amino acid change of tryptophan to arginine outside the coding regions of the epitopes e1 and c1 that are recognized by monoclonal antibodies 4F9 and c1, respectively. The results suggest that these epitopes were stable in the various VZV isolates. Thus, VZV glycoproteins with conserved epitopes are suitable candidates for both primary and booster vaccines.

Adult↗
PubMed2001

Ribonuclease Rs from Rhizopus stolonifer: lowering of optimum temperature in the presence of urea.

RNase Rs showed an approx. 2-fold increase in its activity when incubated in the presence of 2 M urea at 37 degrees C. The increase in its activity, in the presence of urea, was comparable to the activity at its optimum temperature, i.e. 45 degrees C. Compared to the native enzyme at 37 degrees C, the K(m) and V(max) of RNase Rs at 45 degrees C and in the presence of 2 M urea at 37 degrees C showed an increase while k(cat)/K(m) decreased. Arrhenius plots in the presence and absence of urea showed a decrease in the activation energy in the presence of urea. Though there was no change in the secondary structure of the protein in the presence of urea, minor changes were observed in the tertiary structure. Hence, the increase in the activity of RNase Rs, in the presence of 2 M urea at 37 degrees C, is due to the lowering of the activation energy as a result of changes in the microenvironment of the active site.

Binding Sites↗
PubMed2001

Risk factors for post-transplant tuberculosis.

BACKGROUND: Post-transplant tuberculosis (post-TxTB) occurs in 12 to 20% of patients in India and results in the death of 20 to 25% of those patients. Prospective studies on post-TxTB are few. METHODS: Renal allograft recipients were studied prospectively for 3.1 (0 to 13.9) median (range) years for incidence, manifestations, risk factors, and prognosis for post-TxTB. Kaplan-Meier analysis was used to study the survival rates. The extended Cox proportional model for time-dependent covariates was used to measure the risk factors when the hazard was nonuniform. RESULTS: Of the 1414 patients considered for inclusion, multiple-transplant subjects (N = 37) and patients who developed pre-transplant TB (pre-TxTB; N = 126) were excluded from the study. The prevalence of post-TxTB was 13.3% (N = 166). The risk of post-TxTB when on cyclosporine (CsA) therapy was 2.5 (P = 0.0311) and 1.9 (P = 0.0430) times at < or =6 and < or =12 months, respectively, compared with patients on prednisolone plus azathioprine (PRED + AZA). The risk of post-TxTB in the presence of diabetes mellitus, chronic liver disease, and other co-existing infections [including deep mycoses, cytomegalovirus (CMV), Pneumocystis carinii pneumonia (PCP), nocardia] was 2.2 (P = 0.0011), 1.7 (P = 0.0010) and 2.4 (P < 0.0001) times, respectively. Of the 166 patients with post-TxTB, 53 patients died, and of those deaths, 17 (32%) were due to post-TxTB; 11 (65%) of the 17 had co-existing infections. The factors associated with death were HLA mismatches, PRED + AZA immunosuppression, pre- and post-TxTB, diabetes mellitus, post-transplant diabetes (PTDM), and other co-existing infections. The extended Cox model for death as the outcome variable showed the following to be significant risk factors: post-TxTB> 2 years (P = 0.0036), chronic liver disease> 6 years (P = 0.0457), PTDM> 5 years (P = 0.0729), diabetes mellitus (P = 0.0091), human lymphocyte antigen match < or =1 antigen (P = 0.0134), two to three antigens (P = 0.0448), and the presence of other co-existing infections (P < 0.0001). CONCLUSIONS: Cyclosporine therapy is associated with early post-TxTB. Diabetes mellitus and chronic liver disease are risk factors for post-TxTB. The occurrence of both pre-TxTB and post-TxTB (>2 years) along with hyperglycemia, liver disease, and other co-existing infections are important risk factors for death.

Adult↗
PubMed2001

Sugar non-specific endonucleases.

Sugar non-specific endonucleases are multifunctional enzymes and are widespread in distribution. Apart from nutrition, they have also been implicated in cellular functions like replication, recombination and repair. Their ability to recognize different DNA structures has also been exploited for the determination of nucleic acid structure. Although more than 30 non-specific endonucleases have been isolated to date, very little information is available regarding their structure-function correlations except that of staphylococcal and Serratia nucleases. However, during the past few years, the primary structure, nature of the active site based on sequence homology, and the probable mechanism of action have been postulated for some of the enzymes. This review describes the purification, characteristics, biological role and applications of sugar non-specific endonucleases.

Amino Acid Sequence↗
PubMed2000

Stability of a varicella-zoster virus glycoprotein E epitope.

The epitope stability of a varicella-zoster virus (VZV) glycoprotein E (gE) was analyzed with monoclonal antibodies (mAbs) in cells infected with different passages of various VZV strains and isolates. The gE-specific mAbs recognized same antigenic sites (epitopes) in VZV isolates with various passage history. All VZV strains and virus-isolates reacted with an anti-gE monoclonal antibody by immunoprecipitation, or indirect fluorescent antibody staining test. Sera from VZV seropositive individuals reacted with a truncated VZV gE glycoprotein, designated TgpI-511. Also, human mononuclear cells (MNCs) stimulated with TgpI-511 glycoprotein were shown to produce VZV-specific antibodies in vitro. The results demonstrated the stability of these gE epitopes tested in this study in TgpI-511 and among the VZV-isolates obtained from different passages. These results also suggest that VZV glycoproteins as well as live attenuated or killed varicella vaccines containing these epitopes could be used as therapeutic booster vaccines in adults and the elderly to prevent zoster.

Adolescent↗
PubMed2000

Purification and characterization of the single-strand-specific and guanylic-acid-preferential deoxyribonuclease activity of the extracellular nuclease from Basidiobolus haptosporus.

An extracellular nuclease from Basidiobolus haptosporus (designated as nuclease Bh1) was purified to homogeneity by ammonium sulfate precipitation, heat treatment, negative adsorption on DEAE-cellulose, and chromatography on phenyl-Sepharose followed by FPLC on phenyl-Superose. The overall yield was 26%. The Mr of the purified enzyme, determined by gel filtration, was 41 000 whereas by SDS/PAGE (after deglycosylation) it was 30 000. It is a glycoprotein with a pI of 6.8. The optimum pH and temperature for DNA hydrolysis were 8. 5 and 60 degrees C, respectively. Nuclease Bh1 is a metalloprotein but has no obligate requirement for metal ions to be active, nor is its activity stimulated in the presence of metal ions. The enzyme was inhibited by Zn2+, Ag2+, Hg2+, Fe3+ and Al3+, inorganic phosphate, pyrophosphate, dithiothreitol, 2-mercaptoethanol, NaCl and KCl. It was stable to high concentrations of organic solvents and urea but susceptible to low concentrations of SDS and guanidine hydrochloride. Nuclease Bh1 is a multifunctional enzyme and its substrate specificity is in the order of ssDNA approximately 3'AMP >> RNA > dsDNA. Studies on its mode of action showed that it cleaved supercoiled pUC 18 DNA and phage M13 DNA, endonucleolytically, generating single base nicks. The enzyme hydrolyzed DNA with preferential liberation of 5'dGMP, suggesting it to be a guanylic acid preferential endoexonuclease. 5'dGMP, the end product of hydrolysis, was a competitive inhibitor of the enzyme. The absence of 5'dCMP as a hydrolytic product, coupled with the resistance of (dC)10 and deoxyribodinucleoside monophosphates having cytosine either at the 3' or the 5' end, indicates that C-linkages are resistant to cleavage by nuclease Bh1.

Amino Acid Sequence↗
PubMed1999

Extracellular nuclease from Rhizopus stolonifer: purification and characteristics of - single strand preferential - deoxyribonuclease activity.

An extracellular nuclease from Rhizopus stolonifer (designated as nuclease Rsn) was purified to homogeneity by chromatography on DEAE-cellulose followed by Blue Sepharose. The M(r) of the purified enzyme determined by native PAGE was 67¿ omitted¿000 and it is a tetramer and each protomer consists of two unidentical subunits of M(r) 21¿ omitted¿000 and 13¿ omitted¿000. It is an acidic protein with a pI of 4.2 and is not a glycoprotein. The purified enzyme showed an obligate requirement of divalent cations like Mg(2+), Mn(2+) and Co(2+) for its activity but is not a metalloprotein. The optimum pH of the enzyme was 7.0 and was not influenced by the type of metal ion used. Although, the optimum temperature of the enzyme for single stranded (ss) DNA hydrolysis in presence of all three metal ions and for double stranded (ds) DNA hydrolysis in presence of Mg(2+) was 40 degrees C, it showed higher optimum temperature (45 degrees C) for dsDNA hydrolysis in presence of Mn(2+) and Co(2+). Nuclease Rsn was inhibited by divalent cations like Zn(2+), Cu(2+) and Hg(2+), inorganic phosphate and pyrophosphate, low concentrations of SDS, guanidine hydrochloride and urea, organic solvents like dimethyl sulphoxide, dimethyl formamide and formamide but not by 3'- or 5'-mononucleotides. The studies on mode and mechanism of action showed that nuclease Rsn is an endonuclease and cleaves dsDNA through a single hit mechanism. The end products of both ssDNA and dsDNA hydrolysis were predominantly oligonucleotides ending in 3'-hydroxyl and 5'-phosphoryl termini. Moreover, the type of metal ion used did not influence the mode and mechanism of action of the enzyme.

Cations, Divalent↗
PubMed1999

Active site characterization of RNase Rs from Rhizopus stolonifer: involvement of histidine and lysine in catalysis and carboxylate in substrate binding.

Chemical modification studies on purified RNase Rs revealed the involvement of a single histidine, lysine and carboxylate residue in the catalytic activity of the enzyme. RNA could not protect the enzyme against DEP- and TNBS-mediated inactivation whereas, substrate protection was observed in case of EDAC-mediated inactivation of the enzyme. K(m) and k(cat) values of the partially inactivated enzyme samples suggested that while histidine and lysine are involved in catalysis, carboxylate is involved in substrate binding. Active site nature of RNase Rs suggests that the inability of the enzyme to readily convert 2',3'-cyclic nucleotides to 3'-mononucleotides is probably due to the absence of catalytically active second histidine residue.

Binding Sites↗