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Oligonucleotide chip assay for quantification of gamma ray-induced single strand breaks(Journal of pharmaceutical and biomedical analysis)
(Hyeon A Ki, Min Jung Kim, Sukdeb Pal, Joon Myong Song,Vol(49),Issue(2),Pages(562-566),,,Year : 2009)
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An oligonucleotide chip assay was designed for direct quantification of single strand breaks (SSBs) induced by ?-ray irradiation. The oligonucleotides used were 20-mers, which were short enough to produce only a single strand break within a single oligonucleotide. The two ends of the oligonucleotides were labeled with fluorescein and biotin, respectively. The biotinylated ends of the oligonucleotides were immobilized on a silicon wafer chip treated with (3-aminopropyl)triethoxysilane (APTES), glutaraldehyde, and avidin. The DNA fragments cleaved by ?-ray irradiation were detected by a laser-induced fluorescence (LIF) detection system. The ?-ray-induced SSBs were quantified using a calibration curve (fluorescence intensity versus ?-ray dose) without the need for complicated mathematical calculation based on gel-based separation.
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Synthesis, characterization and comparative evaluation of antivacterial activity of diverse morphological silver nanoparticles and higher-valent silver metallopharmaceuticals
(Pal Sukdeb
,,,,Year : 2009)
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No information is available
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Molecular identification of Indian crocodile species: PCR-RFLP method for forensic authentication(Journal of Forensic Sciences)
(Meganathan, P. R., Dubey, B., Haque. I
,,,1042- 1045,Year : 2009)
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South East Asian countries are known for illegal poaching and trade of crocodiles clandestinely, to be used in skin, medicinal, and cosmetic industries. Besides crocodiles being listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora, India has its Wildlife Protection Act, 1972 for conservation of crocodile species. Hitherto, lack of any rapid and reliable technique for examinations of crocodile-based crime exhibits such as skin, bones, etc. has been a major problem for an effective promulgation of law on illegal trade. DNA-based identification of species using PCR-RFLP technique for an apt identification of all the three Indian crocodile species namely, Crocodylus porosus, Crocodylus palustris and Gavialis gangeticus is presented here. A 628 bp segment of cytochrome b gene was amplified using novel primers followed by restriction digestion with three enzymes i.e., HaeIII, MboI, and MwoI, separately and in combination. The technique has produced a species-specific pattern for identifying the three crocodile species individually, which fulfills the requirement for its forensic application. It is expected that the technique will prove handy in identification of all the three Indian crocodile species and strengthen conservation efforts.
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Multiplex PCR assay for rapid identification of three endangered snake species of India. (Conservation Genetics)
(Dubey, B., Meganathan, P. R., Haque.I
,,,1861- 1864,Year : 2009)
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Species identification has been the core issue in all approaches of conservation of endangered wild life. In this regard molecular techniques for species authentication have proved indispensable. A novel multiplex PCR assay for the identification of three Indian snake species Python morulus, Ptyas mucosus, and Naja naja is successfully demonstrated using 16S rRNA gene. Three reverse primers and a common forward primer were designed to generate three different size species-specific PCR fragments. Absence of any PCR amplification in non-target species proves the specificity of the primers. These four primers were combined in a multiplex assay to enable identification of three snake species in a single reaction. The assay described here shows its utility in identifying unknown snake specimen and in case of samples yielding low quality DNA. This multiplex PCR technique using novel primers is an unprecedented approach offered for forensic identification of exhibits originating from three Indian snake species. It is expected that this endeavor will help strengthening conservation efforts for these species.
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Forensic STR profile of two endogamous populations of Madhya Pradesh, India(Legal Medicine (Tokyo))
(Dubey, B., Meganathan, P. R., Eaaswarkhanth, M., Vasulu, T. S., Haque. I.
,,,41- 44,Year : 2009)
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Genotypic polymorphism studies at 15 highly polymorphic short tandem repeat (STR) loci were carried out in two populations belonging to one caste and one tribal group of Madhya Pradesh, in central region of India. These include 110 individuals from Brahmin caste (Kanyakubj) and 89 from Gond tribe (Ojha). The 15 loci studied are: 13 CODIS STR core markers, i.e., D8S1179, D3S1358, D21S11, D7S820, CSF1PO, vWA, TPOX, D18S51, THO1, D13S317, D16S539, D5S818, FGA and 2 other loci D19S433 and D2S1338. The results show departure from the Hardy-Weinberg equilibrium with respect to two loci, viz., D3S1358 and FGA in Gond tribe and at seven loci, viz., D21S11, D19S433, TPOX, D18S51, THO1, D5S818, and FGA in Brahmin caste. Population differentiation tests between the two studied populations and with seven neighboring populations (4 tribes and 3 castes - two middle castes and one Deshasth Brahmin) revealed significant differences at several loci. The power of discrimination of the microsatellite markers used was found to be high for both the populations. The data thereof is of immense significance for forensic result interpretation and is an addition to the existing autosomal STR database on Indian population.
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Diverse genetic origin of Indian Muslims: evidence from autosomal STR loci. (Journal of Human Genetics)
(Eaaswarkhanth, M., Dubey, B., Meganathan, P. R., Ravesh, Z., Khan, F. A., Singh, L., Thangaraj, K., Haque.I
,,,340-348,Year : 2009)
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The origin and relationships of Indian Muslims is still dubious and are not yet genetically well studied. In the light of historically attested movements into Indian subcontinent during the demic expansion of Islam, the present study aims to substantiate whether it had been accompanied by any gene flow or only a cultural transformation phenomenon. An array of 13 autosomal STR markers that are common in the worldwide data sets was used to explore the genetic diversity of Indian Muslims. The austere endogamy being practiced for several generations was confirmed by the genetic demarcation of each of the six Indian Muslim communities in the phylogenetic assessments for the markers examined. The analyses were further refined by comparison with geographically closest neighboring Hindu religious groups (including several caste and tribal populations) and the populations from Middle East, East Asia and Europe. We found that some of the Muslim populations displayed high level of regional genetic affinity rather than religious affinity. Interestingly, in Dawoodi Bohras (TN and GUJ) and Iranian Shia significant genetic contribution from West Asia, especially Iran (49, 47 and 46%, respectively) was observed. This divulges the existence of Middle Eastern genetic signatures in some of the contemporary Indian Muslim populations. Our study reveals that the spread of Islamic faith in the Indian subcontinent was predominantly cultural transformation associated with minor gene flow from West Asia.
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Microsatellite diversity delineates genetic relationships of Shia and Sunni Muslim Populations of Uttar Pradesh, India(Human Biology)
(Eaaswarkhanth, M., Dubey, B., Meganathan, P. R., Noor, S., Haque.I
,,,427- 445,Year : 2009)
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In this study we characterize the genetic diversity and relationships between the Shia and Sunni Muslim populations of North India and geographically targeted neighboring and global populations. We examined a number of parameters of population genetic and forensic interest based on the allele frequencies from 15 autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D19S433, VWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818, and FGA). All the studied loci were consistent with Hardy-Weinberg equilibrium, except loci D18S51 and FGA for both Muslim populations, even after applying the Bonferroni correction. The combined power of exclusion and combined power of discrimination values for all 15 STR loci were 0.9999 and >0.99999, respectively, in both Muslim populations. Gene diversity values ranged from 0.6784 (TPOX) to 0.9027 (FGA) for Shia Muslims and from 0.7152 (CSF1PO) to 0.9120 (D18S51) for Sunni Muslims. The observed heterozygosity (H(o)) ranged from 0.5833 (D18S51) to 0.8595 (VWA) in Shia Muslims and from 0.6818 (CSF1PO) to 0.8333 (D21S11) in Sunni Muslims and was lower than the expected heterozygosity (H(e)) for 11 out of the 15 STRs typed. We analyzed the genetic affinities of the Shia and Sunni Muslim populations with their geographically closest neighboring North Indian, Middle Eastern, East Asian, and European populations using distance-based methods, including neighbor-joining trees and multidimensional scaling. In addition, we estimated the genetic contribution of the putative parental populations included in the analysis to the Shia and Sunni Muslim gene pool using admixture analysis. Although we observed a certain degree of genetic contribution from Iran to both Muslim populations, the results of the phylogenetic analyses based on autosomal STRs suggest genetic relatedness with some of the geographically closest neighboring Hindu religious populations.
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Molecular identification of crocodile species using novel primers for forensic analysis(Conservation Genetics)
(Meganathan, P. R., Dubey, B., Haque.I
,,,767–770,Year : 2009)
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All crocodilians are under varying degrees of threat due to over exploitation and these species have been listed in Appendix I or II of CITES. The lack of molecular techniques for the identification of confiscated samples makes it difficult to enforce the law. Conclusive forensic identification of species requires a complete gene sequence which is difficult in case of degraded samples. We have developed two novel sets of primers to amplify two partial cytochrome b gene sequences of six crocodile species i.e. Crocodylus palustris, Crocodylus porosus, Crocodylus siamensis, Crocodylus niloticus, Gavialis gangeticus and Caiman crocodilus. These partial sequences were edited to give a complete cyt b gene sequence, which can be used as an effective tool for forensic authentication of crocodile species. A phylogeny of crocodile species was reconstructed using these sequences. The described primers hold great promise in forensic identification of crocodile species, which can aid in the effective enforcement of law and conservation of these ancient species.
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GIS based Site and Structure Selection Model for Groundwater Recharge: A Hydrogeomorphic Approach(Journal of Environmental Science and Engineering)
(Ritesh Vijay R. A. Sohony ,51,4,311-314,Year : 2009)
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The groundwater in India is facing a critical situation due to over exploitation, reduction in recharge potential by change in land use and land cover and improper planning and management. A groundwater development plan needs a large volume of multidisciplinary data from various sources. A geographic information system (GIS) based hydrogeomorphic approach can provide the appropriate platform for spatial analysis of diverse data sets for decision making in groundwater recharge. The paper presents development of GIS based model to provide more accuracy in identification and suitability analysis for finding out zones and locating suitable sites with suggested structures for artificial rechar
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Development of GIS based Environmental Information System: an Indian Scenario(International Journal of Digital Earth)
(Ritesh Vijay, D R Satapathy, B. Nimje, S. Nema, S. Dhurve A. Gupta,2,4,382-392,Year : 2009)
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Ideally, scientists should be able to format, explore, analyse, and visualise data in a simple, powerful and fast application that would seamlessly integrate georeferenced data from a variety of data sources into an intuitive visualisation. The focus of an Environmental Information System is providing environmental information to decision makers, policy planners, scientists and engineers, research workers, etc. which ensures integration of data collection, collation, storage, retrieval and dissemination to all concerned. All such queries should be responded to supplying substantive information in the form of reports. The paper presents an innovative way to utilise the geographic information associated with the environmental data. The stand-alone application is the integration of using ArcObjects Environmental System Research Institute ArcGIS Engine 9.1 and VB.Net. The geographic information system (GIS)-based application, a framework of digital earth in terms of environmental information system provides a user-friendly query interface, which gives information about various environmental parameters in tabular as well as on map display. It also provides the visual interpretation to make further analysis and future decisions at multiple scales, locations and extents. The facility for modifying the map attributes and corresponding databases is integrated to update the information system. Output spatial data are produced in the form of reports using selected fields with display on map.
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A Hydrodynamic approach to address Yamuna riverbed development in Delhi(Canadian Journal of Civil Engineering)
(Ritesh Vijay, Aabha Sargaonkar Apurba Gupta,36,7,1155-1163,Year : 2009)
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Most critical flood problems occur in urban areas where values at risk are higher and damages tend to be heavier. In the present study, a hydrodynamic simulation of the river Yamuna has been generated under different designated flood flows to delineate the land availability under existing and modified riverbed geometry including channel dredging and riverbed dressing. Flood flows for various return periods, namely once in 10, 25, 50, and 100 years are estimated based on the past 41 years of recorded data using flood frequency analysis. The model set up considered the river stretch of 23 km from the Wazirabad barrage upstream to the Okhla barrage downstream, which includes manmade structures like bridges and barrages. Model calibration is achieved by comparing the water surface elevations with observed data at various downstream gauge stations. The land availability based on submergence scenarios under existing riverbed condition is estimated to be 1147.6, 873.1, and 762.6 ha, respectively, for 10, 50, and 100 year return flood. Various simulations are generated including channel dredging and riverbed dressing to obtain safe height and safe width for dressing the riverbed. The modified river geometry considered channel dredging in 750 to 1350 m width, and riverbed dressing for safe height and width in three levels in various sections. The land availability under this scenario is estimated to be 2197, 1129, and 545 ha for 10, 50, and 100 year return flood, respectively. It is proposed to dress the riverbed by utilizing the material obtained from channel dredging in three levels to maintain the transverse and longitudinal slope, river morphology, and river system. Developmental planning in the riverbed may include utilization of land at three levels for various purposes such as playgrounds, nursery, etc. However, it is suggested that the feasibility study of the project requires detailed engineering including slope stability prior to implementation of the riverbed development.
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Optimization of medium for the production of subtilisin from Bacillus subtilis MTCC 441
(Navaneeth, S., Bhuvanesh, S., Bhaskar, V., Vijay Kumar, P., Kandaswamy S.K.J., Anant,8,,6327-6331,Year : 2009)
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Subtilisins (E.C.3.4.21.62) are alkaline proteases that are secreted by members of the genus Bacillus. They are serine proteases that exhibit high specific activity on proteinaceous substrates, function optimally at moderate temperatures, and are stable under alkaline conditions. Thus the use of subtilisin as an enzyme additive could help in development of quality laundry detergents. In this work the subtilisin production from Bacillus subtilis (MTCC 441) was improved by altering and optimizing the media components. This alteration was brought up by process development strategy. The effect of yeast extract, casein, peptone and sodium chloride on subtilisin production was studied and were optimized using Box Behnken Design. The optimal growth conditions for B. subtilis MTCC 441 were found to 37 o C, and pH 7.5. The optimal media composition for subtilisin production was found to be yeast extract at 6.75 g/L, peptone at 4.41 g/L, sodium chloride at 6.08 g/L, casein at 10.75 g/L with glucose at 5 g/L. The predicted and observed response were 181.00 U/mg (with desirability =0.87) and 185.70 U/mg, respectively.
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Monitoring Photosensitizer Drug-induced DNA Single Strand Breaks Using Oligonucleotide Chip
(,Pages(252-252),,,Year : 2008)
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This paper describes a novel approach utilizing oligonucleotide chip for determining the photosensitizer-induced DNA single strand breaks (SSBs). Oligonucleotides chips were prepared by immobilizing fluorophore-labeled oligomers on to silicon oxide surfaces. Oligonucleotide surface coverage was determined by alkaline phosphatase (ALP) digestion method, wherein ALP (at high pH; 9.9) led to the cleavage of phosphates in the oligonucleotide backbone, releasing the fluorophore-tagged fragments back into the solution. The fluorescence maximums (measured at 520 nm) of the solutions containing those cleaved fragments were converted to molar concentrations of the fluorescein-modified oligonucleotide by interpolation from a predetermined standard linear calibration curve.
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Monitoring the (photo) genotoxicity of photosensitizer drugs: Direct quantitation of single-strand breaks in deoxyribonucleic acid using an oligonucleotide chip(Analytical biochemistry
)
(Min Jung Kim, Sukdeb Pal, Pravin K Naoghare, Joon Myong Song,Vol(382),Issue(1),Pages(40-47),,,Year : 2008)
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Oligonucleotide chip-based assays can be a sample-thrifty, time-saving, routine tool for evaluation of chemical-induced DNA strand breaks. This article describes a novel approach using an oligonucleotide chip to determine photosensitizer-induced DNA single-strand breaks. Surface coverage of fluorophore-labeled oligonucleotides on silicon dioxide chip surfaces was determined on alkaline phosphatase digestion. Fluorescence maxima (at 520 nm) of the solutions were converted to molar concentrations of the fluorescein-modified oligonucleotide by interpolation from a predetermined standard linear calibration curve. The photosensitizing activity of chlorpromazine and triflupromazine toward DNA single-strand breaks was then studied at different drug doses and also as a function of photoirradiation time.
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Direct Quantification of Photosensitizer Druginduced DNA Single Strand Breaks Using Oligonucleotide Chip
(KIM Min Jung, PAL Sukdeb, SONG Joon Myong,Pages(223-223),,,Year : 2008)
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Inhibition of LPS Induced iNOS, COX-2 and Cytokines Expression by Geni $ teiii" 4-0-?-L-rhainnopyranosyl-(l-2)-?-D-glucopyranoside through the NF-kB Inactivation in RAW 264.7 Cells
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Determination of Surface Coverage of Oligonucleotides Bound to Chip Surfaces by Alkaline Phosphatase Digestion
(PAL Sukdeb, KIM Min Jung, SONG Joon Myong,Pages(301-301),,,Year : 2008)
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Inhibition of LPS Induced iNOS, COX-2 and Cytokines Expression by Geni $ teiii" 4-0-?-L-rhainnopyranosyl-(l-2)-?-D-glucopyranoside through the NF-kB Inactivation in RAW 264.7 Cells
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Quantitation of ultraviolet-induced single-strand breaks using oligonucleotide chip(Analytica chimica acta
)
(Sukdeb Pal, Min Jung Kim, Jaebum Choo, Seong Ho Kang, Kyeong-Hee Lee, Joon Myong Song,Vol(622),Issue(1-2),Pages(195-200),,,Year : 2008)
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A simple, accurate and robust methodology was established for the direct quantification of ultraviolet (UV)-induced single-strand break (SSB) using oligonucleotide chip. Oligonucleotide chips were fabricated by covalently anchoring the fluorescent-labeled ssDNAs onto silicon dioxide chip surfaces. Assuming that the possibility of more than one UV-induced SSB to be generated in a small oligonucleotide is extremely low, SSB formation was investigated quantifying the endpoint probe density by fluorescence measurement upon UV irradiation. The SSB yields obtained based on the highly sensitive laser-induced fluorometric determination of fluorophore-labeled oligonucleotides were found to coincide well with that predicted from a theoretical extrapolation of the results obtained for plasmid DNAs using conventional agarose gel electrophoresis.
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Removal ofE. colifrom Water Using Surface-Modified Activated Carbon Filter Media and Its Performance over an Extended Use(Environmental Science and Technology
)
(Sukdeb Pal, J Joardar, Joon Myong Song
,Vol(42),Issue(10),Pages(3906-3906),,,Year : 2008)
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No information is available
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Parallel Applications of Integrated Circuit Bipolar Semiconductor Microchip as a Miniaturized Sample Platform and a Two-dimensional Photodetector for Optical Detection of Biomolecules
(TAK Yu Kyung, PAL Sukdeb, SONG Joon Myong,Vol(8),Pages(318-318),,,Year : 2008)
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No information is available
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Determination of Dose-depth Distribution of Proton Beam Using Resazurin Metabolism Assay
(KIM Min Jung, PAL Sukdeb, SONG Joon Myong
,Vol(8),Pages(317-317),,,Year : 2008)
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No information is available
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