Bhawna Dubey | Fox Chase Cancer Center (original) (raw)

Papers by Bhawna Dubey

Research paper thumbnail of See Profile

Molecular phylogenetc analyses of genus

Research paper thumbnail of Interactive effect of TLR SNPs and exposure to sexually transmitted infections on prostate cancer risk in Jamaican men

The Prostate, 2020

Prostate cancer (PC) risk increases with African ancestry and a history of sexually transmitted i... more Prostate cancer (PC) risk increases with African ancestry and a history of sexually transmitted infections (STIs). Also, single‐nucleotide polymorphisms (SNPs) in toll‐like receptor (TLR) genes influence PC risk. This pilot study explores interactions between STIs and TLR‐related SNPs in relation to PC risk among Jamaican men.

Research paper thumbnail of Novel SERPING1 Small Deletion Mutation in an Indian Family with Autosomal Dominant Hereditary Angioedema-TypeI

Research paper thumbnail of See Profile

Molecular phylogenetc analyses of genus

Research paper thumbnail of Interactive effect of TLR SNPs and exposure to sexually transmitted infections on prostate cancer risk in Jamaican men

The Prostate, 2020

Prostate cancer (PC) risk increases with African ancestry and a history of sexually transmitted i... more Prostate cancer (PC) risk increases with African ancestry and a history of sexually transmitted infections (STIs). Also, single‐nucleotide polymorphisms (SNPs) in toll‐like receptor (TLR) genes influence PC risk. This pilot study explores interactions between STIs and TLR‐related SNPs in relation to PC risk among Jamaican men.

Research paper thumbnail of Novel SERPING1 Small Deletion Mutation in an Indian Family with Autosomal Dominant Hereditary Angioedema-TypeI

Research paper thumbnail of Development of fourteen novel microsatellite markers of Crocodylus palustris, the Indian mugger, and their cross-species transferability in ten other crocodilians

Conservation Genetics Resources, 2014

Crocodylus palustris (Indian mugger) is an endangered species with declining populations due to i... more Crocodylus palustris (Indian mugger) is an endangered species with declining populations due to illegal hunting and habitat destruction. The situation warrants conservation efforts for which understanding the genetic structure of the extant populations becomes important. Here, we describe 14 new mugger-specific microsateillte markers (Simple Sequence Repeats, SSRs), developed from SSR-enriched partial genomic DNA library and ESTs. All markers were validated using 48 population samples. In general, markers were highly polymorphic; amplified 2-12 alleles/marker with H e and H o ranging from 0.23-0.91 and 0.25-1.0, respectively. Notably, all markers except CpSSR10, also exhibited near 100 % cross-species transferability when tested on *30 samples belonging to ten related crocodilians. These microsatellite markers are thus expected to be highly useful for the population genetics and other conservation studies on Indian mugger and other crocodilians.

Research paper thumbnail of Development of fourteen novel microsatellite markers of Crocodylus palustris, the Indian mugger, and their cross-species transferability in ten other crocodilians

Conservation Genetics Resources, 2014

Crocodylus palustris (Indian mugger) is an endangered species with declining populations due to i... more Crocodylus palustris (Indian mugger) is an endangered species with declining populations due to illegal hunting and habitat destruction. The situation warrants conservation efforts for which understanding the genetic structure of the extant populations becomes important. Here, we describe 14 new mugger-specific microsateillte markers (Simple Sequence Repeats, SSRs), developed from SSR-enriched partial genomic DNA library and ESTs. All markers were validated using 48 population samples. In general, markers were highly polymorphic; amplified 2-12 alleles/marker with H e and H o ranging from 0.23-0.91 and 0.25-1.0, respectively. Notably, all markers except CpSSR10, also exhibited near 100 % cross-species transferability when tested on *30 samples belonging to ten related crocodilians. These microsatellite markers are thus expected to be highly useful for the population genetics and other conservation studies on Indian mugger and other crocodilians.

Research paper thumbnail of A novel multiplex PCR assay for the identification of Indian crocodiles

Molecular Ecology Resources, 2010

Illegal hunting has been a major threat for the survival of wildlife fauna, including the three c... more Illegal hunting has been a major threat for the survival of wildlife fauna, including the three crocodile species that India harbours: Crocodylus palustris, Crocodylus porosus and Gavialis gangeticus. Although law prevents trade on these species, illicit hunting for trade continues to threaten the survival of these endangered species; conservation strategies therefore require a rapid molecular identification technique for Indian crocodiles. A multiplex polymerase chain reaction (PCR) assay with species-specific primers, considered as one of the most effective molecular techniques, is described herein. The primers were designed to yield species-specific sized amplicons. The assay discriminates the three Indian crocodile species unambiguously within a short time period using only simple agarose gel electrophoresis. We recommend this multiplex PCR assay to be used in the identification of Indian crocodile species.

Research paper thumbnail of Autosomal STR variations in three endogamous populations of West Bengal, India

Legal Medicine, 2008

The allele frequency distribution of 15 autosomal STR loci was determined using AmpFlSTR Identifi... more The allele frequency distribution of 15 autosomal STR loci was determined using AmpFlSTR Identifiler kit in three endogamous caste populations namely, Rajbanshi, Paliya and Dhimal from northern regions of West Bengal, India. The study includes 13 CODIS STR core markers, i.e., D8S1179, D3S1358, D21S11, D7S820, CSF1PO, vWA, TPOX, D18S51, THO1, D13S317, D16S539, D5S818, FGA and two other loci D19S433 and D2S1338. All the loci followed Hardy-Weinberg equilibrium, except loci D8S1179, vWA and FGA in Rajbanshi population, D13S317 in Paliya population and D16S539 and TPOX in Dhimal population. The allele 12 in CSF1PO in Rajbanshi population and allele nine in THO1 in Paliya as well as in Dhimal population were found to be most frequent. All the 15 STR loci studied were found to be highly polymorphic with respect to observed heterozygosity values. Population differentiation tests revealed highly significant differences at several loci suggesting the endogamous nature of studied populations. STR allele frequency data on Dhimal population presented here is a unique contribution to the existing DNA data base on Indian population. To the best of our present knowledge, hitherto Dhimal Population has not been explored genetically for generating forensic data on STR markers.

Research paper thumbnail of Molecular Evidence for the Nonmonophyly of the Asian Natricid GenusXenochrophis(Serpentes, Colubroidea) as Inferred from Mitochondrial and Nuclear Genes

Journal of Herpetology, 2012

Unresolved phylogenetic relationships within the subfamily Natricinae continue to exist, includin... more 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.

Research paper thumbnail of Forensic STR profile of two endogamous populations of Madhya Pradesh, India

Legal Medicine, 2009

Genotypic polymorphism studies at 15 highly polymorphic short tandem repeat (STR) loci were carri... more 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.

Research paper thumbnail of Inflammation polymorphisms and prostate cancer risk in Jamaican men: Role of obesity/body size

Gene

African ancestry and obesity are associated with higher risk of prostate cancer (PC). In a pilot ... more African ancestry and obesity are associated with higher risk of prostate cancer (PC). In a pilot study, we explored interactions between obesity (as measured by waist to hip ratio (WHR)) and inflammatory SNPs in relation to PC risk among Jamaican men. This study evaluated 87 chemokine and cytokine associated SNPs in obese and normal weight cases (N=109) and controls (N=102) using a Stepwise Penalized Logistic Regression approach in multivariable analyses.

Research paper thumbnail of Molecular Identification of Three Indian Snake Species Using Simple PCR–RFLP Method*

Journal of forensic …, 2010

Three endangered Indian snake species, Python molurus, Naja naja, and Xenochrophis piscator are k... more Three endangered Indian snake species, Python molurus, Naja naja, and Xenochrophis piscator are known to be significantly involved in illegal trade. Effective authentication of species is required to curb this illegal trade. In the absence of morphological features, molecular identification techniques hold promise to address the issue of species identification. We present an effective PCR-restriction fragment length polymorphism method for easy identification of the three endangered snake species, Python molurus, Naja naja, and Xenochrophis piscator. A 431-bp amplicon from cytochrome b gene was amplified using novel snake-specific primers following restriction digestion with enzymes Mbo II and Fok I. The species-specific reference fragment patterns were obtained for the target species, which enabled successful identification of even highly degraded shed skin sample confirming the utility of the technique in case of poor-quality DNA. The assay could be effectively used for forensic authentication of three Indian snake species and would help strengthen conservation efforts.

Research paper thumbnail of Molecular Evidence for the Nonmonophyly of the Asian Natricid Genus Xenochrophis (Serpentes, Colubroidea) as Inferred from Mitochondrial and Nuclear Genes

Research paper thumbnail of Development of fourteen novel microsatellite markers of Crocodylus palustris, the Indian mugger, and their cross-species transferability in ten other crocodilians

Research paper thumbnail of Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia

Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as ... more 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.

Research paper thumbnail of Identification of Indian Crocodile Species Through DNA Barcodes

The biodiversity of India includes three crocodile species, Crocodylus palustris, Crocodylus poro... more 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.

Research paper thumbnail of MOLECULAR IDENTIFICATION OF INDIAN SNAKES

Three endangered Indian snake species, Python molurus, Naja naja, and Xenochrophis piscator are k... more Three endangered Indian snake species, Python molurus, Naja naja, and Xenochrophis piscator are known to be significantly involved in illegal trade. Effective authentication of species is required to curb this illegal trade. In the absence of morphological features, molecular identification techniques hold promise to address the issue of species identification. We present an effective PCR-restriction fragment length polymorphism method for easy identification of the three endangered snake species, Python molurus, Naja naja, and Xenochrophis piscator. A 431-bp amplicon from cytochrome b gene was amplified using novel snake-specific primers following restriction digestion with enzymes Mbo II and Fok I. The species-specific reference fragment patterns were obtained for the target species, which enabled successful identification of even highly degraded shed skin sample confirming the utility of the technique in case of poor-quality DNA. The assay could be effectively used for forensic authentication of three Indian snake species and would help strengthen conservation efforts.

Research paper thumbnail of Multiplex PCR assay for rapid identification of three endangered snake species of India

Abstract Species identification has been the core issue in all approaches of conservation of enda... more Abstract 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 ...

Research paper thumbnail of See Profile

Molecular phylogenetc analyses of genus

Research paper thumbnail of Interactive effect of TLR SNPs and exposure to sexually transmitted infections on prostate cancer risk in Jamaican men

The Prostate, 2020

Prostate cancer (PC) risk increases with African ancestry and a history of sexually transmitted i... more Prostate cancer (PC) risk increases with African ancestry and a history of sexually transmitted infections (STIs). Also, single‐nucleotide polymorphisms (SNPs) in toll‐like receptor (TLR) genes influence PC risk. This pilot study explores interactions between STIs and TLR‐related SNPs in relation to PC risk among Jamaican men.

Research paper thumbnail of Novel SERPING1 Small Deletion Mutation in an Indian Family with Autosomal Dominant Hereditary Angioedema-TypeI

Research paper thumbnail of See Profile

Molecular phylogenetc analyses of genus

Research paper thumbnail of Interactive effect of TLR SNPs and exposure to sexually transmitted infections on prostate cancer risk in Jamaican men

The Prostate, 2020

Prostate cancer (PC) risk increases with African ancestry and a history of sexually transmitted i... more Prostate cancer (PC) risk increases with African ancestry and a history of sexually transmitted infections (STIs). Also, single‐nucleotide polymorphisms (SNPs) in toll‐like receptor (TLR) genes influence PC risk. This pilot study explores interactions between STIs and TLR‐related SNPs in relation to PC risk among Jamaican men.

Research paper thumbnail of Novel SERPING1 Small Deletion Mutation in an Indian Family with Autosomal Dominant Hereditary Angioedema-TypeI

Research paper thumbnail of Development of fourteen novel microsatellite markers of Crocodylus palustris, the Indian mugger, and their cross-species transferability in ten other crocodilians

Conservation Genetics Resources, 2014

Crocodylus palustris (Indian mugger) is an endangered species with declining populations due to i... more Crocodylus palustris (Indian mugger) is an endangered species with declining populations due to illegal hunting and habitat destruction. The situation warrants conservation efforts for which understanding the genetic structure of the extant populations becomes important. Here, we describe 14 new mugger-specific microsateillte markers (Simple Sequence Repeats, SSRs), developed from SSR-enriched partial genomic DNA library and ESTs. All markers were validated using 48 population samples. In general, markers were highly polymorphic; amplified 2-12 alleles/marker with H e and H o ranging from 0.23-0.91 and 0.25-1.0, respectively. Notably, all markers except CpSSR10, also exhibited near 100 % cross-species transferability when tested on *30 samples belonging to ten related crocodilians. These microsatellite markers are thus expected to be highly useful for the population genetics and other conservation studies on Indian mugger and other crocodilians.

Research paper thumbnail of Development of fourteen novel microsatellite markers of Crocodylus palustris, the Indian mugger, and their cross-species transferability in ten other crocodilians

Conservation Genetics Resources, 2014

Crocodylus palustris (Indian mugger) is an endangered species with declining populations due to i... more Crocodylus palustris (Indian mugger) is an endangered species with declining populations due to illegal hunting and habitat destruction. The situation warrants conservation efforts for which understanding the genetic structure of the extant populations becomes important. Here, we describe 14 new mugger-specific microsateillte markers (Simple Sequence Repeats, SSRs), developed from SSR-enriched partial genomic DNA library and ESTs. All markers were validated using 48 population samples. In general, markers were highly polymorphic; amplified 2-12 alleles/marker with H e and H o ranging from 0.23-0.91 and 0.25-1.0, respectively. Notably, all markers except CpSSR10, also exhibited near 100 % cross-species transferability when tested on *30 samples belonging to ten related crocodilians. These microsatellite markers are thus expected to be highly useful for the population genetics and other conservation studies on Indian mugger and other crocodilians.

Research paper thumbnail of A novel multiplex PCR assay for the identification of Indian crocodiles

Molecular Ecology Resources, 2010

Illegal hunting has been a major threat for the survival of wildlife fauna, including the three c... more Illegal hunting has been a major threat for the survival of wildlife fauna, including the three crocodile species that India harbours: Crocodylus palustris, Crocodylus porosus and Gavialis gangeticus. Although law prevents trade on these species, illicit hunting for trade continues to threaten the survival of these endangered species; conservation strategies therefore require a rapid molecular identification technique for Indian crocodiles. A multiplex polymerase chain reaction (PCR) assay with species-specific primers, considered as one of the most effective molecular techniques, is described herein. The primers were designed to yield species-specific sized amplicons. The assay discriminates the three Indian crocodile species unambiguously within a short time period using only simple agarose gel electrophoresis. We recommend this multiplex PCR assay to be used in the identification of Indian crocodile species.

Research paper thumbnail of Autosomal STR variations in three endogamous populations of West Bengal, India

Legal Medicine, 2008

The allele frequency distribution of 15 autosomal STR loci was determined using AmpFlSTR Identifi... more The allele frequency distribution of 15 autosomal STR loci was determined using AmpFlSTR Identifiler kit in three endogamous caste populations namely, Rajbanshi, Paliya and Dhimal from northern regions of West Bengal, India. The study includes 13 CODIS STR core markers, i.e., D8S1179, D3S1358, D21S11, D7S820, CSF1PO, vWA, TPOX, D18S51, THO1, D13S317, D16S539, D5S818, FGA and two other loci D19S433 and D2S1338. All the loci followed Hardy-Weinberg equilibrium, except loci D8S1179, vWA and FGA in Rajbanshi population, D13S317 in Paliya population and D16S539 and TPOX in Dhimal population. The allele 12 in CSF1PO in Rajbanshi population and allele nine in THO1 in Paliya as well as in Dhimal population were found to be most frequent. All the 15 STR loci studied were found to be highly polymorphic with respect to observed heterozygosity values. Population differentiation tests revealed highly significant differences at several loci suggesting the endogamous nature of studied populations. STR allele frequency data on Dhimal population presented here is a unique contribution to the existing DNA data base on Indian population. To the best of our present knowledge, hitherto Dhimal Population has not been explored genetically for generating forensic data on STR markers.

Research paper thumbnail of Molecular Evidence for the Nonmonophyly of the Asian Natricid GenusXenochrophis(Serpentes, Colubroidea) as Inferred from Mitochondrial and Nuclear Genes

Journal of Herpetology, 2012

Unresolved phylogenetic relationships within the subfamily Natricinae continue to exist, includin... more 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.

Research paper thumbnail of Forensic STR profile of two endogamous populations of Madhya Pradesh, India

Legal Medicine, 2009

Genotypic polymorphism studies at 15 highly polymorphic short tandem repeat (STR) loci were carri... more 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.

Research paper thumbnail of Inflammation polymorphisms and prostate cancer risk in Jamaican men: Role of obesity/body size

Gene

African ancestry and obesity are associated with higher risk of prostate cancer (PC). In a pilot ... more African ancestry and obesity are associated with higher risk of prostate cancer (PC). In a pilot study, we explored interactions between obesity (as measured by waist to hip ratio (WHR)) and inflammatory SNPs in relation to PC risk among Jamaican men. This study evaluated 87 chemokine and cytokine associated SNPs in obese and normal weight cases (N=109) and controls (N=102) using a Stepwise Penalized Logistic Regression approach in multivariable analyses.

Research paper thumbnail of Molecular Identification of Three Indian Snake Species Using Simple PCR–RFLP Method*

Journal of forensic …, 2010

Three endangered Indian snake species, Python molurus, Naja naja, and Xenochrophis piscator are k... more Three endangered Indian snake species, Python molurus, Naja naja, and Xenochrophis piscator are known to be significantly involved in illegal trade. Effective authentication of species is required to curb this illegal trade. In the absence of morphological features, molecular identification techniques hold promise to address the issue of species identification. We present an effective PCR-restriction fragment length polymorphism method for easy identification of the three endangered snake species, Python molurus, Naja naja, and Xenochrophis piscator. A 431-bp amplicon from cytochrome b gene was amplified using novel snake-specific primers following restriction digestion with enzymes Mbo II and Fok I. The species-specific reference fragment patterns were obtained for the target species, which enabled successful identification of even highly degraded shed skin sample confirming the utility of the technique in case of poor-quality DNA. The assay could be effectively used for forensic authentication of three Indian snake species and would help strengthen conservation efforts.

Research paper thumbnail of Molecular Evidence for the Nonmonophyly of the Asian Natricid Genus Xenochrophis (Serpentes, Colubroidea) as Inferred from Mitochondrial and Nuclear Genes

Research paper thumbnail of Development of fourteen novel microsatellite markers of Crocodylus palustris, the Indian mugger, and their cross-species transferability in ten other crocodilians

Research paper thumbnail of Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia

Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as ... more 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.

Research paper thumbnail of Identification of Indian Crocodile Species Through DNA Barcodes

The biodiversity of India includes three crocodile species, Crocodylus palustris, Crocodylus poro... more 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.

Research paper thumbnail of MOLECULAR IDENTIFICATION OF INDIAN SNAKES

Three endangered Indian snake species, Python molurus, Naja naja, and Xenochrophis piscator are k... more Three endangered Indian snake species, Python molurus, Naja naja, and Xenochrophis piscator are known to be significantly involved in illegal trade. Effective authentication of species is required to curb this illegal trade. In the absence of morphological features, molecular identification techniques hold promise to address the issue of species identification. We present an effective PCR-restriction fragment length polymorphism method for easy identification of the three endangered snake species, Python molurus, Naja naja, and Xenochrophis piscator. A 431-bp amplicon from cytochrome b gene was amplified using novel snake-specific primers following restriction digestion with enzymes Mbo II and Fok I. The species-specific reference fragment patterns were obtained for the target species, which enabled successful identification of even highly degraded shed skin sample confirming the utility of the technique in case of poor-quality DNA. The assay could be effectively used for forensic authentication of three Indian snake species and would help strengthen conservation efforts.

Research paper thumbnail of Multiplex PCR assay for rapid identification of three endangered snake species of India

Abstract Species identification has been the core issue in all approaches of conservation of enda... more Abstract 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 ...