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Mitochondrial 16S ribosomal RNA gene for forensic identification of crocodile species.(Journal of Forensic and Legal Medicine)
(Jogayya, K. N., Meganathan, P. R., Dubey, B., Haque.I
,,,334-338 ,Year : 2013)
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All crocodilians are under various threats due to over exploitation and these species have been listed in Appendix I or II of CITES. Lack of molecular techniques for the forensic identification of confiscated samples makes it difficult to enforce the law. Therefore, we herein present a molecular method developed on the basis on 16S rRNA gene of mitochondrial DNA for identification of crocodile species. We have developed a set of 16S rRNA primers for PCR based identification of crocodilian species. These novel primers amplify partial 16S rRNA sequences of six crocodile species which can be later combined to obtain a larger region (1290 bp) of 16S rRNA gene. This 16S rRNA gene could be used as an effective tool for forensic authentication of crocodiles. 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 species.
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Identification of Indian crocodiles through DNA barcodes(Journal of Forensic Sciences)
(Meganathan. P.R., Dubey, B., Jogayya, K.N., Haque. I
,,,993-998,Year : 2013)
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The biodiversity of India includes three crocodile species, Crocodylus palustris, Crocodylus porosus, and Gavialis gangeticus, whose status is threatened due to bushmeat crisis and illegal hunting. The crocodilian conservation management requires novel techniques to help forensic analysts to reveal species identity. DNA barcoding is a species identification technique, where a partial cytochrome c oxidase subunit 1 gene is used as a marker for species identification. Herein, the DNA barcoding technique is evaluated for three Indian crocodiles by analyzing an approximately 750-bp barcode region. The alignment result shows interspecific variations between sequences for discrimination of the three Indian crocodiles leading to species identification. The phylogenetic analyses also substantiate the established crocodilian relationships, which add further advantage to use this DNA barcoding approach for Indian crocodiles. This study provides preliminary evidences for the use of DNA barcoding technique in the identification of Indian crocodile species.
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Surveillance of Drinking Water Quality for Safe Water Supply—A Case Study from Shillong, India(Water Resource Manag)
(S. N. Pimpalkar, P.K. Labhasetwar,,,3321–3342,Year : 2012)
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To ascertain the quality of drinking water being supplied and maintained, it is necessary to conduct water quality surveillance for evolving suitable strategy for future planning. In the present investigation, water quality was monitored in treatment plants, service reservoirs, and at consumer ends in three seasons to assess the baseline water quality status at Shillong in Meghalaya. There are three water treatment plants at Shillong namely Umkhen, Mawlai and GSWS with design capacities of 1.5, 3.4 and 34 Million liter per day (MLD) respectively. Each treatment plant is having rapid sand filtration followed by disinfection. The study reveals that the physico-chemical parameters of water quality at consumer end meets Indian drinking water quality standards (BIS 1991) after conventional treatment followed by disinfection, whereas the bacteriological parameters for raw water sources exceed the permissible limit indicating the treatment need for drinking purposes. Throughout year the average feacal coliform contamination at service reservoir and to consumer end were found as 44 to 156 CFU/100 ml which may be attributed to the general management practices for maintenance of service reservoirs and the possibility of en route contamination.
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Change in drinking water quality from source to point of-use and storage: a case study from Guwahati, India( Environment Monitoring and Assessment)
(,,, 5343-5361,Year : 2012)
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To ascertain the quality of drinking water being supplied and maintained at Guwahati, the study was conducted on the status of water supply in city through surveillance of drinking water quality for consecutive 7 days at various treatment stages, distribution network and consumer ends. The performance of five water treatment plants (WTPs), viz. Panbazar WTP, Satpukhuri WTP, Kamakhya WTP, PHED WTP and Hegrabari WTP were assessed for summer, piost-post-monsoon and winter seasons. No significant change in raw water quality was observed on day-to-day basis. Residual chlorine was found in the range of nil to 0.2 mg/L in the treated water. During post-monsoon, winter, and summer seasons the thermotolerent TC and FC counts ranged between Nil to 168 CFU/100 ml and Nil to 84 CFU/100 ml; Nil to 3356 CFU/100 ml and Nil to 152 CFU/100 ml; and Nil to 960 CFU/100 ml and Nil to 108 CFU/100 ml respectively. There was variation in bacterial counts among the different service reservoirs and consumer ends, which may be attributed to the general management practices for maintenance of service reservoirs and the possibility of enroute contamination. Evaluation of the raw water quality indicate that the water is suitable for drinking after conventional treatment followed by disinfection. The finished water quality meets the level of standards described as per Bureau of Indian Standard specifications (BIS:10500 1991) for potability in terms of its physico-chemical characteristics.
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Efficient removal of Brilliant Blue G (BBG) from aqueous solutions by marine Aspergillus wentii: Kinetics, equilibrium and process design(Ecological Engineering)
(Yasmin Khambhaty, Kalpana Mody,,, 74-83,Year : 2012)
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The sorption of Brilliant Blue G (BBG) by dead biomass of marine fungus Aspergillus wentii, which was chemically modified by esterification of the carboxylic acids (CB), or methylation of amine (NB), or raw biomass (RB) was studied with variation in the parameters of contact time (0–80 min), initial concentration of dye (119.3–544.8 mg/L) and solution pH (2–10). The contact time necessary to reach equilibrium was 180 min. The BBG biosorption was strictly pH dependent, and maximum uptake capacity of all three biosorbents was observed at initial pH 2. The biosorption isotherm data were fitted well to the Langmuir isotherm and the monolayer sorption capacity was found to be 384.6, 370.4 and 312.5 mg/g for CB, NB and RB, respectively. For each biosorbent-dye system, kinetic models were applied to the experimental data to examine the mechanisms of sorption and potential rate-controlling steps. The pseudo-second-order kinetic model described the biosorption kinetics accurately and the sorption process was found to be controlled by pore and surface diffusion. From the design of a single-batch biosorber it is predicted that the biosorbent, CB will require 20% less of the sorbent to treat certain volumes of wastewater containing 500 mg/L of BBG when compared with the unmodified biosorbent (RB).
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Molecular evidence for the non-monophyly of Asian natricid genus Xenochrophis (Serpentis, Colubroidea) as inferred from mitochondrial and nuclear genes.(Journal of Herpetology)
(B., Meganathan, P. R., Vidal, N., Haque.I,,, 263-268,Year : 2012)
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Unresolved phylogenetic relationships within the subfamily Natricinae continue to exist, including the position of the genus Xenochrophis. In the present study, two mitochondrial genes (cytochrome b, 12S rRNA) and one nuclear gene (c-mos) were used to infer the phylogenetic relationships among the members of Natricinae, with a special emphasis on the position of the genus Xenochrophis. Two statistical methods, Maximum Likelihood and Bayesian Inference, were used for phylogenetic reconstruction. Both the mitochondrial and nuclear datasets produced sufficiently resolved and congruent topologies. Our findings placed the genus Xenochrophis within Natricinae consistently with strong nodal support. Findings also revealed a close association between two Indian natricid snakes, Xenochrophis piscator and Xenochrophis schnurrenbergeri. However Xenochrophis vittatus, from Indonesia, does not cluster with the remaining species of Xenochrophis, suggesting a nonmonophyly of this genus. Overall Natricinae was found to be monophyletic because the two genera, Psammodynastes pulverulentus and Amplorhinus multimaculatus, are now known to be members of the Lamprophiidae. This study also finds a close relationship between the endemic species Lycognathophis seychellensis with the African natricids.
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Complete mitochondrial genome sequence of the endangered Indian snake, Python molurus molurus(Molecular Biology Reports)
(B., Meganathan, P. R., Haque.I,,,7403-7412,Year : 2012)
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This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.
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Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera(GENE)
(Meganathan. P. R., Pagan, H. J. T., McCulloch, E. S., Stevens, R.D, Ray, D.A. ,,,121-129,Year : 2012)
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Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes.
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Equilibrium modeling for biosorption of safranin onto chemically modified biomass of marine Aspergillus wentii(Water, Air, and Soil Pollution)
(Yasmin Khambhaty, Kalpana Mody and Bhavanath Jha, 679-691,,,Year : 2011)
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Safranin was used as a model reactive dye for biosorption studies onto various forms of chemically modified biomass of Aspergillus wentii. The experimental equilibrium data was analyzed by various single-, two-, three-, four-, and five-parameter isotherms to understand the biosorption process. Biosorption isotherms modeling shows that the interaction of safranin with A. wentii surface is localized monolayer sorption. Results show that in general the accuracy of models to fit experimental data improves with the degree of freedom. The interaction among adsorbed molecules is repulsive having no association between them and sorption is carried out on energetically different sites and is an endothermic process. The five-parameter Fritz–Schluender model gives the most accurate fit with high regression coefficients (0.9902–0.9941), low standard errors (0.0389–0.0758), and sum of squares error (0.0075–0.0230) values to all experimental data in comparison to other models. The results disclose that the sorption isotherm models fitted the experimental data in the order: Fritz–Schluender (five-parameter) > Langmuir > Khan > Fritz–Schluender (four-parameter) > Temkin. This systematic evaluation of the more important equilibrium isotherm models provided the general basis for making a preliminary selection of an effective model for a given application.
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Kinetics, Isotherms and Thermodynamics for the biosorption of Hg(II) onto Carica papaya(Bioremediation Journal)
( Z.V.P. Murthy and B. Jha , 26-34,,,Year : 2011)
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Carica papaya, a novel sorbent, was evaluated for sorption of Hg(II) from synthetic aqueous solutions using various pseudo-second order kinetic models as well as equilibrium sorption models. Batch kinetic and equilibrium experiments were carried out for the sorption of Hg(II) onto C. papaya at pH 6.5 and solid to liquid ratio (s/l) 1.0 g L?1. The kinetic data were fitted to second order models of Sobkowsk and Czerwinski, Ritchie, Blanchard, Ho and McKay, whereas Langmuir, Freundlich, and Redlich-Peterson models were used for the equilibrium data. A comparative study on both linear and nonlinear regression showed that the Sobkowsk and Czerwinski and Ritchie's second order model were the same. Ho and McKay's pseudo-second order model fitted well to the experimental data when compared with the other second order kinetic expressions. Langmuir isotherm parameters obtained from the four Langmuir linear equations by using linear method were dissimilar, but were the same when nonlinear method was used. Additionally, various thermodynamic parameters, such as ?G 0, ?H 0, and ?S 0, were calculated. The negative values of Gibbs free energy (?G 0) and ?H 0 confirmed the intrinsic nature of biosorption process and exothermic, respectively. The negative value of ?S 0 showed the decreased randomness at the solid-solution interface during biosorption.
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Photodegradation of famotidine by integrated photocatalytic adsorbent (IPCA) and kinetic study,(Catalysis Letters)
(David Keane, Kieran Nolan, Anne Morrissey, Michael Oelgemoller , John Tobin
,300-308,,,Year : 2011)
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Integrated photocatalytic adsorbents (IPCAs) comprised of nanocrystalline titanium dioxide (TiO2) and activated carbon (AC) were prepared using an ultrasonic impregnation technique. The IPCAs were characterised by scanning electron microscopy (SEM) and Fourier-transform infrared (FT-IR) spectroscopy and were employed as catalysts for the photodegradation of famotidine-an active pharmaceutical ingredient-in aqueous solutions using illumination from a 125 W medium pressure mercury lamp. The degradation kinetics were found to follow a pseudo-first-order rate law and varying TiO2 loadings induced different increases in the apparent first-order rate constant of the process. The kinetic behaviour can be described in terms of a modified Langmuir–Hinshelwood (LH) model. The IPCA prepared using a 10% TiO2 to AC loading exhibited the highest rate constant with a K C and k r of 0.0172 L/mg and 0.237 mg/L/min, respectively. The LH model fits the experimental data and elucidates the effect of the TiO2 content of the IPCA on the degradation rate. The use of calcination (heat treatment) in IPCA preparation and its effect on photocatalytic and adsorption performance were also investigated. The present work demonstrates that the combination of TiO2 and AC results in a promising material for application in the degradation of organic pollutants.
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On the adsorption/photodegradation of Amoxicillin in aqueous solutions by an integrated photocatalytic adsorbent (IPCA): Experimental studies and kinetics analysis(Photochemical and Photobiological Sciences)
(Colin Barr, David Keane, Anne Morrissey, Kieran Nolan, Michael Oelgemoller, John Tobin,1014,,1022,Year : 2011)
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Activated carbon-supported TiO(2) nanoparticles, termed integrated photocatalytic adsorbents (IPCAs), were prepared using an ultrasonic impregnation technique and investigated for the photocatalytic degradation of amoxicillin (AMO), a ?-lactam antibiotic. The IPCAs had high adsorption affinity for AMO with the amount adsorbed proportional to the TiO(2) loading and the highest adsorption was at 10 wt% TiO(2) loading. A pseudo-second-order model was found to fit the experimental data and consistently predicted the amount of AMO adsorbed over the adsorption period. Equilibrium isotherm studies showed that the adsorption followed the Redlich-Peterson model with maximum adsorption capacity of 441.3 mg g(-1) for 10% IPCA, 23% higher than the pure activated carbon (AC). Kinetic studies on the photocatalytic degradation of AMO using non-linear regression analysis suggest that the degradation followed Langmuir-Hinshelwood (L-H) kinetics. The adsorption rate constant (K(ad)) was considerably higher than the photocatalytic rate constant (k(L-H)), indicating that the photocatalysis of AMO is the rate-determining step during the adsorption/photocatalysis process. The 10% IPCA exhibited excellent stability and reusability over four photodegradation cycles.
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Occurrence of pharmaceutical compounds in wastewater process streams in Dublin, Ireland(Environmental Monitoring and Assessment)
(Clair Lacey, Anne Morrissey, John Tobin
,,,1049-1062.,Year : 2011)
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The aim of this work is to establish baseline levels of pharmaceuticals in three wastewater treatment plant (WWTP) streams in the greater Dublin region to assess the removal efficiency of the selected WWTPs and to investigate the existence of any seasonal variability. Twenty compounds including several classes of antibiotics, acidic and basic pharmaceuticals, and prescribed medications were selected for investigation using a combination of membrane filtration, solid phase extraction (SPE) cleanup, and liquid chromatography-electrospray ionization tandem mass spectrometry. Fourteen of the selected compounds were found in the samples. Increased effluent concentrations, compared to influent concentrations, for a number of compounds (carbamazepine, clotrimazole, propranolol, nimesulide, furosemide, mefenamic acid, diclofenac, metoprolol, and gemfibrozil) were observed. The detected concentrations were generally below toxicity levels and based on current knowledge are unlikely to pose any threat to aquatic species. Mefenamic acid concentrations detected in both Leixlip and Swords effluents may potentially exert ecotoxicological effects with maximum risk quotients (i.e., ratio of predicted exposure concentration to predicted no effect concentration) of 4.04 and 1.33, respectively.
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Treatment options for wastewater from pharmaceutical companies: a review(The International Journal of Environmental Science and Technology)
(A.M.Deegan, K.Nolan, K.Urell, M. Oelgemoeller, J.Tobin, A.Morrissey,,,649-666 ,Year : 2011)
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" In recent years, concerns about the occurrence and fate of active pharmaceutical ingredients, solvents, intermediates and raw materials that could be present in water and wastewater including pharmaceutical industry wastewater has gained increasing attention. Traditional wastewater treatment methods, such as activated sludge, are not sufficient for the complete removal of active pharmaceutical ingredients and other wastewater constituents from these waters. As a result, complementary treatment methods such as membrane filtration, reverse osmosis and activated carbon are often used in conjunction with the traditional methods for treatment of industrial wastewater. Most of the literature published to date has been on the treatment of municipal wastewater. However, there is a growing body of research that looks at the presence of active pharmaceutical ingredients in industrial wastewater, the treatment of these wastewaters and the removal rates. This article, reviews these treatment methods and includes both traditional methods and advanced oxidation processes. The paper concludes by showing that the problem of pharmaceuticals in wastewaters cannot be solved merely by adopting end of pipe measures. At source measures, such as replacement of critical chemicals, reduction in raw material consumption should continue to be pursued as the top priority"
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Novel integrated photocatalytic adsorbents (IPCAs) for degradation of pharmaceuticals from water and wastewater(EPA (European photochemistry Association) Newsletter)
( D.Keane, K. Nolan, A.Morrissey, M.Oelgemöller, J.M. Tobi,,,18-21,Year : 2011)
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The presence of pharmaceuticals and personal care products in the aquatic environment and their possible effects on living organisms has emerged as a serious environmental concern. There is an increasing need for a cost- and energy-effective clean technology for the removal and degradation of organic compounds before they find their way into ground water wells and surface waters. Photocatalysis using cheap and non-toxic TiO2 has been recently used to degrade pharmaceuticals and pesticides in water, and was found to be superior to conventional methods. However, large scale application has been hindered by problems associated with its preferential use in slurry form and the high cost of radiation of large slurry volumes. Therefore, it is proposed to combine ell-established adsorption on activated carbon with rather novel TiO2 photocatalysis. This strategy will lead to the development of TiO2-coated activated carbon materials, i.e. integrated photocatalytic adsorbents (IPCAs).
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Validation of a multiplex PCR assay for the forensic identification of Indian crocodiles. (Journal of Forensic Sciences)
(Meganathan, P. R., Dubey, B., Jogayya K. N., Haque.I
,,,1241-1244,Year : 2011)
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A dependable and efficient wildlife species identification system is essential for swift dispensation of the justice linking wildlife crimes. Development of molecular techniques is befitting the need of the time. The forensic laboratories often receive highly ill-treated samples for identification purposes, and thus, validation of any novel methodology is necessary for forensic usage. We validate a novel multiplex polymerase chain reaction assay, developed at this laboratory for the forensic identification of three Indian crocodiles, Crocodylus palustris, Crocodylus porosus, and Gavialis gangeticus, following the guidelines of Scientific Working Group on DNA Analysis Methods. The multiplex PCR was tested for its specificity, reproducibility, sensitivity, and stability. This study also includes the samples treated with various chemical substances and exposed to various environmental regimes. The result of this validation study promises this technique to be an efficient identification tool for Indian crocodiles and therefore is recommended for forensic purposes.
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Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia. (GENE)
(Meganathan, P. R., Dubey, B., Batzer, M. A., Ray, D. A., Haque.I,,,35-41,Year : 2011)
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Crocodylus is the largest genus within the Order Crocodylia consisting of eleven species. This paper reports the complete mitochondrial genome sequences of three Crocodylus species, Crocodylus moreletii, Crocodylus johnstoni and Crocodylus palustris, and compares the newly obtained mitochondrial DNA sequences with other crocodilians, available in the public databases. The mitochondrial genomes of C. moreletii, C. johnstoni and C. palustris are 16,827 bp, 16,851 bp and 16,852 bp in length, respectively. These mitochondrial genomes consist of 13 protein coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding region. The mitochondrial genomes of all the Crocodylus species, studied herein show identical characteristics in terms of nucleotide composition and codon usage, suggestive of the existence of analogous evolutionary patterns within the genus, Crocodylus. The synonymous and non-synonymous substitution rates for all the protein coding genes of Crocodylus were observed in between 0.001 and 0.275 which reveal the prevalence of purifying selection in these genes. The phylogenetic analyses based on complete mitochondrial DNA data substantiate the previously established crocodilian phylogeny. This study provides a better understanding of the crocodilian mitochondrial genome and the data described herein will prove useful for future studies concerning crocodilian mitochondrial genome evolution.
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DNA mini-barcoding: an approach for forensic identification of some endangered Indian snake species(Forensic Science International: Genetics)
(Dubey, B., Meganathan, P. R., Haque. I
,,,181-184,Year : 2011)
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Illegal trade of snake skin and uncontrolled hunting have instigated the extermination of many endangered snake species. Efforts to check illegal trade are often impeded due to lack of proper species identification methods. Hence, conservation strategies demand for authentic and quick identification techniques to trace the origin of the seized samples. This study employs DNA mini-barcoding as a method to identify some endangered snake species of India. We have designed two sets of novel primers for targeting regions within the mitochondrial Cytochrome Oxidase I gene to produce 175 bp and 245 bp amplicons. 175 bp fragment was amplified in all 11 snake species studied while the 245 bp amplicon was obtained in 10 species. DNA mini-barcodes recovered from these amplicons enabled the identification of snake species by retrieving the sequences available in public databases. The similarity scores ranging from 98 to 100% (98% taken as threshold value for species identification) signify the consistency of these mini-barcodes in snake species identification. Moreover, the results of the validation study confirm the effectiveness of the technique in forensic perspective, where the diagnostic morphological features of the seized sample are often missing.
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Surveillance of drinking water quality for safe water supply ? A case study from Shillong India(Water Resources Management)
(G.K. Khadse , M. Kalita , S. N. Pimpalkar ,P. K. Labhsetwar,25,,3321–3342,Year : 2011)
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No information is available
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Drinking water quality monitoring and surveillance for safe water supply in Gangtok, India(Environment Monitoring and Assessment)
(G. K. Khadse, M. Kalita, S.N. Pimpalkar, P. K. Labhsetwar,78,,401–414,Year : 2011)
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To ascertain the quality of drinking water being supplied, water quality monitoring and surveillance was conducted in Gangtok city at various treatment stages, service reservoirs, distribution network, public standposts, and households. No significant change in raw water quality was observed on day-to-day basis. Residual chlorine was found in the range of nil to 0.2 mg/l in the sump water/finished water. Throughout the year (i.e., during summer, winter, and monsoon seasons), the total coliform and fecal coliform counts were ranged from nil to 7 CFU/100 ml and nil to 3 CFU/100 ml, respectively, in sump water of Selep and VIP complex water treatment plant; however, at consumer end, those were observed as nil to 210 CFU/100 ml and nil to 90 CFU/100 ml,respectively. These variations in bacterial counts among the different service reservoirs and consumer ends may be attributed to the general management practices for maintenance of service reservoirs and the possibility of enroute contamination. Evaluation of the raw water quality indicates that the water is suitable for drinking after conventional treatment followed by disinfection. The finished water quality meets the level of standards described as per Bureau of Indian Standard specifications (BIS:10500 1991) for potability in terms of its physicochemical characteristics.
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