Ashok Gopinath - Academia.edu (original) (raw)

Papers by Ashok Gopinath

PLoS ONE, 2013

Herbal remedies are increasingly being recognised in recent years as alternative medicine for a n... more Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa.

Gene Expression Patterns, 2004

Gonadotropin releasing hormone (GnRH) is a neuroendocrine decapeptide found in all vertebrate ani... more Gonadotropin releasing hormone (GnRH) is a neuroendocrine decapeptide found in all vertebrate animals. The best understood function of GnRH is its endocrine function as a releasing hormone acting on the pituitary. But GnRH also functions as a neuromodulator within the nervous system. In a given species, GnRH occurs in a variety of forms that fall into three general categories based on pattern of protein/gene expression in the brain and amino acid sequence. The salmon GnRH (sGnRH), is found in the terminal nerve, where it has a neuromodulatory function. The sGnRH form is also the hypothalamic form in many fishes, although some fishes have a species specific form in the hypothalamus. Finally, chicken-GnRH-II (cGnRH-II), the most highly conserved form, is found in the midbrain where its function remains unclear. Here we have cloned the sGnRH and cGnRH-II cDNAs from zebrafish. By conducting stage specific in situ hybridization in developing zebrafish embryos, we provide a description of the spatial and temporal expression patterns of these genes. The location of sGnRH and cGnRH-II expressing cells is in agreement with previous reports of GnRH in the brains of adult fishes. Our results provide the first developmental description of GnRH gene expression where cGnRH-II and sGnRH are initially expressed at the onset of the first day after fertilization. Unlike what has been reported in many adult fishes, we did not find sGnRH expressed in the hypothalamic population during development.

Conservation Genetics, Dec 1, 2008

Eleven polymorphic microsatellite loci were characterized for the endangered conifer Taxus yunnan... more Eleven polymorphic microsatellite loci were characterized for the endangered conifer Taxus yunnanensis. Eight loci were isolated through SSR-anchored PCR, one locus was developed by cross-species amplification tests, while the last two loci were obtained from cross-species microsatellite sequences available in GenBank. Variability of these markers was tested in 48 individuals collected from its main distribution range in Southwest China. The number of alleles per locus ranged from 2 to 9, and the observed and ...

Molecular Ecology Notes, 2001

Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. ... more Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene, 93, 125 -128. Meeker AK, Li YK, Shortle D, Stites WE (1993) A simplified protocol for isolation and characterization of ssM13 DNA templates for use in dideoxy sequencing. Biotechniques, 15, 370-372. Ostrander EA, Jong PM, Rine J, Duyk G (1992) Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proceedings of the National Academy of Sciences of the USA, 89, 3419 -3423. Rouer E (1994) Direct neutralization of alkaline-denatured plasmid DNA in sequencing protocol by the sequencing reagent itself.

Molecular Ecology Notes, 2001

The Asian subterranean termite, Coptotermes gestroi (Wasmann), is an invasive species of pest ter... more The Asian subterranean termite, Coptotermes gestroi (Wasmann), is an invasive species of pest termite. To provide tools for addressing both ecological and genetic questions concerning this pest, we developed primers for 11 microsatellite loci. When characterized using 28 individual termites, we found between 6 and 14 alleles per locus with observed heterozygosities ranging from 0.79 to 0.92. These loci were useful for analyzing the genetic structure of the population and the relationships within and among the populations.

PLoS ONE, 2013

Herbal remedies are increasingly being recognised in recent years as alternative medicine for a n... more Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa.

Gene Expression Patterns, 2004

Gonadotropin releasing hormone (GnRH) is a neuroendocrine decapeptide found in all vertebrate ani... more Gonadotropin releasing hormone (GnRH) is a neuroendocrine decapeptide found in all vertebrate animals. The best understood function of GnRH is its endocrine function as a releasing hormone acting on the pituitary. But GnRH also functions as a neuromodulator within the nervous system. In a given species, GnRH occurs in a variety of forms that fall into three general categories based on pattern of protein/gene expression in the brain and amino acid sequence. The salmon GnRH (sGnRH), is found in the terminal nerve, where it has a neuromodulatory function. The sGnRH form is also the hypothalamic form in many fishes, although some fishes have a species specific form in the hypothalamus. Finally, chicken-GnRH-II (cGnRH-II), the most highly conserved form, is found in the midbrain where its function remains unclear. Here we have cloned the sGnRH and cGnRH-II cDNAs from zebrafish. By conducting stage specific in situ hybridization in developing zebrafish embryos, we provide a description of the spatial and temporal expression patterns of these genes. The location of sGnRH and cGnRH-II expressing cells is in agreement with previous reports of GnRH in the brains of adult fishes. Our results provide the first developmental description of GnRH gene expression where cGnRH-II and sGnRH are initially expressed at the onset of the first day after fertilization. Unlike what has been reported in many adult fishes, we did not find sGnRH expressed in the hypothalamic population during development.

Conservation Genetics, Dec 1, 2008

Eleven polymorphic microsatellite loci were characterized for the endangered conifer Taxus yunnan... more Eleven polymorphic microsatellite loci were characterized for the endangered conifer Taxus yunnanensis. Eight loci were isolated through SSR-anchored PCR, one locus was developed by cross-species amplification tests, while the last two loci were obtained from cross-species microsatellite sequences available in GenBank. Variability of these markers was tested in 48 individuals collected from its main distribution range in Southwest China. The number of alleles per locus ranged from 2 to 9, and the observed and ...

Molecular Ecology Notes, 2001

Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. ... more Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene, 93, 125 -128. Meeker AK, Li YK, Shortle D, Stites WE (1993) A simplified protocol for isolation and characterization of ssM13 DNA templates for use in dideoxy sequencing. Biotechniques, 15, 370-372. Ostrander EA, Jong PM, Rine J, Duyk G (1992) Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proceedings of the National Academy of Sciences of the USA, 89, 3419 -3423. Rouer E (1994) Direct neutralization of alkaline-denatured plasmid DNA in sequencing protocol by the sequencing reagent itself.

Molecular Ecology Notes, 2001

The Asian subterranean termite, Coptotermes gestroi (Wasmann), is an invasive species of pest ter... more The Asian subterranean termite, Coptotermes gestroi (Wasmann), is an invasive species of pest termite. To provide tools for addressing both ecological and genetic questions concerning this pest, we developed primers for 11 microsatellite loci. When characterized using 28 individual termites, we found between 6 and 14 alleles per locus with observed heterozygosities ranging from 0.79 to 0.92. These loci were useful for analyzing the genetic structure of the population and the relationships within and among the populations.