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1.  Spectral reflectance pattern in soybean for assessing yellow mosaic disease 
Indian Journal of Virology  2013;24(2):242-249.
Remote sensing technique is useful for monitoring large crop area at a single time point, which is otherwise not possible by visual observation alone. Yellow mosaic disease (YMD) is a serious constraint in soybean production in India. However, hardly any basic information is available for monitoring YMD by remote sensing. Present study examines spectral reflectance of soybean leaves due to Mungbean yellow mosaic India virus (MYMIV) infection in order to identify YMD sensitive spectral ratio or reflectance. Spectral reflectance measurement indicated significant (p < 0.001) change in reflectance in the infected soybean canopy as compared to the healthy one. In the infected canopy, reflectance increased in visible region and decreased in near infra-red region of spectrum. Reflectance sensitivity analysis indicated wavelength ~642, ~686 and ~750 nm were sensitive to YMD infection. Whereas, in yellow leaves induced due to nitrogen deficiency, the sensitive wavelength was ~589 nm. Due to viral infection, a shift occurred in red and infra-red slope (called red edge) on the left in comparison to healthy one. Red edge shift was a good indicator to discriminate yellow mosaic as chlorophyll gets degraded due to MYMIV infection. Correlation of reflectance at 688 nm (R688) and spectral reflectance ratio at 750 and 445 nm (R750/R445) with the weighted mosaic index indicated that detection of yellow mosaic is possible based on these sensitive bands. Our study for the first time identifies the yellow mosaic sensitive band as R688 and R750/R445, which could be utilized to scan satellite data for monitoring YMD affected soybean cropping regions.
doi:10.1007/s13337-013-0161-0
PMCID: PMC3784907  PMID: 24426282
Soybean yellow mosaic; Mungbean yellow India mosaic virus; Spectral indices; Red edge; Remote sensing
2.  Lipid Profile and Correlation to Cardiac Risk Factors and Cardiovascular Function in Type 1 Adolescent Diabetics from a Developing Country 
Objective. The adverse role of dyslipidemia in predicting cardiovascular outcomes has not been elucidated extensively among type 1 diabetics in the literature. Methods. We assessed dyslipidemia and its correlation to other cardiac risk factors in adolescents with type 1 diabetes. Total thirty type 1 adolescent diabetics were evaluated for their metabolic profile, including serum lipids and echocardiography was performed. Results. The average age of the cohort was 14.3 ± 3.09 yr with disease duration of 5.35 ± 2.94 yr. The mean HbA1C was 8.01%. The mean serum cholesterol, LDL, HDL, and triglyceride were normal. Serum cholesterol was high in patients with longer disease duration (P = 0.011, r = 0.41), high systolic blood pressure (P = 0.04, r = 0.32), and elevated HbA1C > 8% (P = 0.038, r = 0.33). Higher lipid values were associated with poorer carotid artery distensibility (P > 0.05) and higher carotid artery intimomedial thickness (cIMT) (P < 0.05 for cholesterol and LDL). Hyperglycemia adversely affected ejection fractions, though serum lipids did not show any significant effect on left ventricular parameters. Conclusions. Dyslipidemia and hyperglycemia can serve as biomarkers for cardiovascular dysfunction in at-risk adolescents with type 1 diabetes. Carotid artery parameters are adjunctive tools which may be affected early in the course of macrovascular disease.
doi:10.1155/2014/513460
PMCID: PMC4036744  PMID: 24899904
3.  Rupture of single receptor-ligand bonds: A new insight into probability distribution functions 
Single molecule force spectroscopy is widely used to determine kinetic parameters of dissociation by analyzing bond rupture data obtained via applying mechanical force to cells, capsules, and beads that are attached to an intermolecular bond. The current analysis assumes that the intermolecular bond force is equal to the externally applied mechanical force. We confirm that viscous drag alone or in combination with cellular deformation resulting in viscoelasticity modulates bond force so that the instantaneous intermolecular bond force is not equivalent to the applied force. The bond force modulation leads to bond rupture time and force histograms that differ from those predicted by probability distribution functions (PDFs) using the current approach. A new methodology that accounts for bond force modulation in obtaining PDFs is presented. The predicted histograms from the new methodology are in excellent agreement with the respective histograms obtained from Monte Carlo simulation.
doi:10.1016/j.colsurfb.2012.07.020
PMCID: PMC3508194  PMID: 23010061
4.  Effect of viscous drag on multiple receptor-ligand bonds rupture force 
Monte Carlo simulation of the rupture of multiple receptor-ligand bonds between two PMN cells suspended in a Newtonian fluid is performed. We demonstrate via micro-mechanical model of two cells adhered by multiple receptor-ligand bonds that viscous drag caused by relative motion of cell suspended in a Newtonian fluid modulates transmission of an applied external load to bonds. Specifically, it is demonstrated that at any time the intermolecular bond force is not equivalent to the instantaneous applied force. The difference in the instantaneous applied force and the intermolecular bond force depends on the viscosity of fluid, the size of cell, the applied loading rate, and the number of bonds at any instant of time. Viscous drag acting on cell reduces average bond rupture forces.
doi:10.1016/j.colsurfb.2012.05.028
PMCID: PMC3404210  PMID: 22766301
5.  Molecular Cloning and Nucleotide Sequence of the Gene for an Alkaline Protease from Bacillus circulans MTCC 7906 
Indian Journal of Microbiology  2012;52(4):630-637.
Bacillus circulans MTCC 7906, an extracellular alkaline protease producer was genetically characterized. B. circulans genomic DNA was isolated, oligonucleotide primers specific to alkaline protease gene of B. circulans were designed and its PCR amplification was done. The purified PCR product and pTrcHisA vector were subjected to restriction digestion with NcoI and HindIII and transformed into Escherichia coli DH5-α competent cells. The recombinant expression of alkaline protease gene studied by inducible expression and analysis by SDS-PAGE, established that the alkaline protease protein had an estimated molecular size of 46 kDa. Gene sequencing of the insert from selected recombinant clone showed it to be a 1329 bp gene encoding a protein of 442 amino acids. The sequence was blasted and aligned with known alkaline protease genes for comparison with their nucleotide and amino acid sequences. This identified major matches with three closely related subsp. of B. subtilis (B. subtilis subsp. subtilis strain 168, B. subtilis BSn5 and B. subtilis subsp. spizizenii strain W23). The insert also showed a number of substitutions (mutations) with other sp. of Bacillus which established that alkaline protease of B. circulans MTCC 7906 is a novel gene. The phylogenetic analysis of alkaline protease gene and its predicted amino acid sequences also validated that alkaline protease gene is a novel gene and the same has been accessioned in GenBank with accession number JN645176.1.
doi:10.1007/s12088-012-0297-4
PMCID: PMC3516659  PMID: 24293722
Cloning; Bacillus circulans; Alkaline protease; Sequencing; Phylogenetic analysis
6.  A Theoretical Method to determine unstressed off-rate from multiple bond force spectroscopy 
Using dynamic force spectroscopy to measure the kinetic off-rates of intermolecular bonds currently requires the isolation of single molecules. This requirement arises in part because no tractable analytic method for determining kinetic off-rates from the rupture of a large number of bonds under dynamic forces is currently available. We introduce a novel method for determining the unstressed off-rate from dynamic force spectroscopy experiments involving a large number of bonds. Using both the Bell and Dembo models we show that the unstressed off-rate calculated using the proposed method is in good agreement with the prescribed unstressed off-rate used in Monte-Carlo simulations of multiple bond dynamic force spectroscopy experiments given initial number of bonds (50–500) and loading rate 103 – 106 pN/s.
doi:10.1016/j.colsurfb.2012.02.010
PMCID: PMC3348403  PMID: 22417406
7.  Detection of Mycobacterium tuberculosis GlcB or HspX Antigens or devR DNA Impacts the Rapid Diagnosis of Tuberculous Meningitis in Children 
PLoS ONE  2012;7(9):e44630.
Background
Tuberculous meningitis (TBM) is the most common form of neurotuberculosis and the fifth most common form of extrapulmonary TB. Early diagnosis and prompt treatment are the cornerstones of effective disease management. The accurate diagnosis of TBM poses a challenge due to an extensive differential diagnosis, low bacterial load and paucity of cerebrospinal fluid (CSF) especially in children.
Methodology/Principal Findings
We describe the utility of ELISA and qPCR for the detection of Mycobacterium tuberculosis (M. tb) proteins (GlcB, HspX, MPT51, Ag85B and PstS1) and DNA for the rapid diagnosis of TBM. CSF filtrates (n = 532) derived from children were classified as ‘Definite’ TBM (M. tb culture positive, n = 29), ‘Probable and Possible’ TBM (n = 165) and ‘Not-TBM’ including other cases of meningitis or neurological disorders (n = 338). ROC curves were generated from ELISA and qPCR data of ‘Definite’ TBM and Non-Tuberculous infectious meningitis (NTIM) samples and cut-off values were derived to provide ≥95% specificity. devR qPCR, GlcB, HspX and PstS1 ELISAs showed 100% (88;100) sensitivity and 96–97% specificity in ‘Definite’ TBM samples. The application of these cut-offs to ‘Probable and Possible’ TBM groups yielded excellent sensitivity (98%, 94;99) and specificity (98%, 96;99) for qPCR and for GlcB, HspX and MPT51 antigen ELISAs (sensitivity 92–95% and specificity 93–96%). A test combination of qPCR with GlcB and HspX ELISAs accurately detected all TBM samples at a specificity of ∼90%. Logistic regression analysis indicated that these tests significantly added value to the currently used algorithms for TBM diagnosis.
Conclusions
The detection of M. tb GlcB/HspX antigens/devR DNA in CSF is likely to improve the utility of existing algorithms for TBM diagnosis and also hasten the speed of diagnosis.
doi:10.1371/journal.pone.0044630
PMCID: PMC3440320  PMID: 22984534
9.  Turn Around Time (TAT) as a Benchmark of Laboratory Performance 
Laboratory analytical turnaround time is a reliable indicator of laboratory effectiveness. Our study aimed to evaluate laboratory analytical turnaround time in our laboratory and appraise the contribution of the different phases of analysis towards the same. The turn around time (TAT) for all the samples (both routine and emergency) for the outpatient and hospitalized patients were evaluated for one year. TAT was calculated from sample reception to report dispatch. The average TAT for the clinical biochemistry samples was 5.5 h for routine inpatient samples while the TAT for the outpatient samples was 24 h. The turnaround time for stat samples was 1 h. Pre- and Post-analytical phases were found to contribute approximately 75% to the total TAT. The TAT demonstrates the need for improvement in the pre- and post-analytical periods. We need to tread the middle path to perform optimally according to clinician expectations.
doi:10.1007/s12291-010-0056-4
PMCID: PMC2994570  PMID: 21966108
Turn around time; Pre analytical; Analytical; Post analytical; Laboratory
10.  PCR Primers for identification of high sucrose Saccharum genotypes 
The progeny of a cross between high sucrose sugarcane clone S. officinarum ‘Gungera’ and a low sucrose clone S. spontaneum ‘SES 603’ resulted in interspecific hybrids that were named as ISH-1 to ISH-29 and graded on the basis of sucrose content. Hybrids ISH-1, ISH-5, ISH-17 and ISH-23 were selected as very high sucrose (65 to 100 mg/g tissue) genotypes, whereas ISH-10, ISH-11, ISH-12 and ISH-25 were very low sucrose (2 to 25 mg/g tissue) genotypes. DNA from leaves of both the parent clones, as also the progeny hybrids, was amplified using selected primers, in order to identify markers for sucrose content. Ten specific primers were examined: primers ‘A’ and ‘B’ that detect polymorphism in promoter region of sucrose synthase-2 gene; primers AI, SS and SPS that were designed on the basis of nucleotide sequences of genes for acid invertase, sucrose synthase and sucrose phosphate synthase enzymes, respectively and primers MSSCIR43, MSSCIRI, SMC226CG, SMC1039CG and SCB07 selected for relation to sucrose accumulation process. DNA products specific to low or high sucrose clones were identified. Primer ‘A’ and AI amplified DNA products of size 230 and 500 bp, respectively only in high sucrose genotypes (‘Gungera’, ISH-1, ISH-5, ISH-17 and ISH-23), while primer SMC226CG generated a DNA product of size 920 bp only in low sucrose genotypes (‘SES 603’, ISH-10, ISH-11, ISH-12 and ISH-25). Ten random decamer primers were also examined, but their products did not show relationship to sucrose content of genotypes.
doi:10.1007/s12298-010-0002-1
PMCID: PMC3550629  PMID: 23572960
Brix; Invertase; PCR primers; Saccharum; Sugarcane; Sucrose synthas
11.  One-step purification and characterization of cellulase-free xylanase produced by alkalophilic Bacillus subtilis ash 
Brazilian Journal of Microbiology  2010;41(2):467-476.
The present study describes the one-step purification and characterization of an extracellular cellulase-free xylanase from a newly isolated alkalophilic and moderately thermophilic strain of Bacillus subtilis ASH. Xylanase was purified to homogeneity by 10.5-fold with ~43% recovery using ion-exchange chromatography through CM-Sephadex C-50. The purified enzyme revealed a single band on SDS-PAGE gel with a molecular mass of 23 kDa. It showed an optimum pH at 7.0 and was stable over the pH range 6.0-9.0. The optimum temperature for enzyme activity was 55 °C. The purified xylanase did not lose any activity up to 45 ºC, however, it retained 80% and 51% of its activity after pre-incubation at 55 ºC and 60 ºC, respectively. The enzyme obeyed Michaelis-Menton kinetics towards birch wood xylan with apparent Km 3.33 mg/ml and Vmax 100 IU/ml. The enzyme was strongly inhibited by Hg2+and Cu2+while enhanced by Co2+ and Mn2+. The purified enzyme could be stored at 4 ºC for six weeks without any loss of catalytic activity. The faster and economical purification of the cellulase-free xylanase from B. subtilis ASH by one-step procedure together with its appreciable stability at high temperature and alkaline pH makes it potentially effective for industrial applications.
doi:10.1590/S1517-838220100002000029
PMCID: PMC3768699  PMID: 24031518
Alkalophilic; Bacillus subtilis; Purification; Xylanase
12.  Comparison and Suitability of Gel Matrix for Entrapping Higher Content of Enzymes for Commercial Applications 
To check the suitability of enzyme entrapped beads for use in pharmaceutical industry, amylase enzyme was entrapped in agar/agarose, polyacrylamide gels and calcium alginate beads. Sodium alginate of 1% concentration was found to be best with respect to immobilization efficiency and calcium alginate beads so obtained were not much susceptible to breakage. When sodium alginate- amylase mixture was added from a height of about 20-30 cm. into CaCl2 solution, size of beads was large at higher alginate concentration due to the increase in the size of droplet formation before entering into CaCl2 solution. Enzyme entrapped polyacrylamide and agar/agarose gels were fragile and could not withstand repeated use whereas enzyme entrapped in large calcium alginate beads was used successfully for 50 cycles for the conversion of starch into product without much damage to the beads under stirring conditions. Amylase preparation was also mixed with urease, lysozyme and coimmobilized in large sized calcium alginate beads. These beads were used for 10 repeated cycles to check the conversion of substrates into their products by their respective enzymes and we concluded that an enzyme or mixture of two or three enzymes can be immobilized in the same large sized calcium alginate beads. This will save the additional cost of bioreactor, manpower, maintenance conditions required for the conversion of one drug into another using enzyme/s entrapped in large sized beads.
doi:10.4103/0250-474X.65010
PMCID: PMC2929782  PMID: 20838527
Agar/agarose gel; calcium alginate; entrapment; enzyme; immobilization; polyacrylamide
13.  T-cell epitope mapping of ORF2 and ORF3 proteins of human hepatitis E virus 
Journal of viral hepatitis  2007;14(4):283-292.
SUMMARY
Little data are available on cellular immune responses during infection with hepatitis E virus (HEV). We therefore mapped CD4 T-cell epitopes in open reading frame (ORF)2 and ORF3 proteins of HEV using lymphocyte proliferation assays and overlapping peptide libraries. Proliferation of peripheral blood mononuclear cells from 40 patients with acute hepatitis E and 21 healthy controls with recombinant HEV ORF2 protein or pools of overlapping HEV ORF2/ORF3 peptides was measured. HLA-DQB1 and HLA-DRB1 alleles were also determined. Mononuclear cells from patients with hepatitis E more often showed significant proliferation on stimulation with recombinant ORF2 protein than controls (32/40 vs 7/21), and had higher median (range) stimulation indices [2.6 (0.9–15.2) vs 1.3 (0.6–12.9)]. Peptide pools corresponding to amino acids 73–156, 289–372, 361–444 and 505–588 of HEV ORF2 protein were associated with significant proliferation. Individual peptides in these pools did not show a clear pattern of stimulation. HEV ORF3 peptide pools did not induce proliferative responses. Lymphocyte proliferation in response to the peptide pool corresponding to amino acids 289–372 of HEV ORF2 protein was associated with presence of HLA-DRB1 allele 010X. These data on mapping of T-cell epitopes in HEV proteins may prove useful for designing HEV vaccines and for studying the immunopathogenesis of hepatitis E.
doi:10.1111/j.1365-2893.2006.00796.x
PMCID: PMC2441432  PMID: 17381721
cellular immune response; immunopathogenesis; lymphocytes; lymphocyte proliferation assay; peripheral blood mononuclear cells; vaccination
17.  Renal vein thrombosis in nephrotic syndrome--a prospective study and review. 
Postgraduate Medical Journal  1981;57(671):566-570.
The incidence of renal vein thrombosis (RVT) and other thrombo-embolic phenomena was evaluated in 44 unselected patients with nephrotic syndrome. Renal vein thrombosis was demonstrated by selective renal venography in 10 patients and at post-mortem in one. Extension of the thrombus from the renal veins into the inferior vena cava was seen in 3 patients. Evidence of thrombo-embolism elsewhere in the body was seen in the form of thrombophlebitis in the lower extremities in 4 patients (9.1%), pulmonary embolism in 3 (6.8%) and myocardial infarction in one (2.3%). Of the 11 patients with RVT, renal histology showed membranous glomerulonephritis in 3, minimal change nephritis in 5, membrano-proliferative in one and focal and diffuse proliferative glomerulonephritis in one patient each. The characteristics clinical findings such as gross haematuria and flank pain were noted in only 3 patients with RVT. No significant difference could be detected between the plasma fibrinogen, serum cholesterol, beta-lipoprotein, triglycerides and phospholipid concentration of those who showed RVT and the remainder in whom RVT was not demonstrated. The possible mechanisms involved in the pathogenesis of RVT in nephrotic syndrome are discussed.
Images
PMCID: PMC2426169  PMID: 7329894
18.  ROLE OF PUSHKARA GUGGULU IN THE MANAGEMENT OF ISCHAEMIC HEART DISEASE 
Ancient Science of Life  1984;4(1):9-19.
On the basis of authentic references from the literature of ayurveda and on our own observations, Puskara-Guggulu, a combination of oleoresin of C. mukul and I-recemosa, has been clinically tried on a series of ECG proved 50 patients of ischaemic heart disease. This has been administered in the dose of 6 gms per day, in three divided doses upto a period of four months. Precordial pain, discomfort and dyspnoea on effort have been controlled. Mean Serum cholesterol has been found to be decreased by 17.47%. Apart from that, marked improved in the E. C. G. pattern in 30% cases has been recorded in terms of ST-segment and T wave changes, On the whole the result was cured 10% relieved 60%, improved 20% and unchanged 10%, offering a great hope for the prevention and cure of ischaemic heart disease
PMCID: PMC3331490  PMID: 22557443
19.  Should intellectual property be disseminated by "forwarding" rejected letters without permission? 
Journal of Medical Ethics  1996;22(4):243-246.
Substantive scientific letter writing is a cost-effective mode of complementing observational and experimental research. The value of such philosophically uncommitted and unsponsored well-balanced scientific activity has been relegated. Critical letter writing entails the abilities to: maintain rational scepticism; refuse to conform in order to explain data; persist in keeping common sense centre-stage; exercise logic to evaluate the biological significance of mathematical figures, including statistics, and the ability to sustain the will to share insights regarding disease mechanisms on an ostensibly lower research platform. During peer review, innovative letter writing may share the occasionally unfortunate fate of innovative research. Rejected scientific letters do not automatically lose copyright. Periodicals with high letter loads will see some valuable contributions wasted, but that is the price for maintaining autonomy in scientific publication. The scientific community is an integrated whole that must respect the rights of authors at all levels. Unauthorised forwarding of rejected letters sets the dangerous precedent of justifying unjust means.
PMCID: PMC1377005  PMID: 8863151

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