akanksha Singh - Academia.edu (original) (raw)
Papers by akanksha Singh
International Aquatic Research, 2014
The selection of most appropriate reference gene(s) is a crucial step in studies quantifying gene... more The selection of most appropriate reference gene(s) is a crucial step in studies quantifying gene expression by quantitative real-time PCR (qPCR). As a need reference gene(s) should be unaffected at transcription level by experimental conditions and/or tissue types. In this study, 11 candidate reference genes were tested in Clarias batrachus for their expression stability using the geNorm, NormFinder and BestKeeper statistical algorithms, and were compared in different tissues (brain, heart, liver, muscle, spleen and head kidney) and treatments (before and after hypoxia exposure). The results indicated that in brain, heart, liver, muscle, spleen and head kidney, respectively, 28S rRNA/TUB, 28S rRNA/TUB, RPL30/ 28S rRNA, RPL30/TUB, ELF-1A/28S rRNA and ELF-1A/TUB gene pairs were highly stable and were suitable as reference genes to study oxidative stress, while ACTB and B2M were the least stable genes in examined tissues under normoxic and/or hypoxic conditions. The observations suggested the consideration of tissue types and use of at least two reference genes, instead of one in accurate normalization of qPCR data.
Behavioural Processes, 2014
We studied sperm displacement in two members of the Drosophila bipectinata species complex i.e., ... more We studied sperm displacement in two members of the Drosophila bipectinata species complex i.e., Drosophila parabipectinata and Drosophila malerkotliana by employing mutant and wild type strains. We found a significant increase in the productivity of remated females than that of once mated ones in all the crosses of the two species. The P2' values range from 0.67 to 0.70 in D. malerkotliana and 0.52 to 0.56 in D. parabipectinata. These results were compared with that of our earlier finding in D. bipectinata belonging to the same complex. We found that though the three species exhibit differences in the degree of sperm displacement, the pattern is somewhat similar in the three species. However, as far as its genetic variability and population size maintenance is considered, D. malerkotliana and D. bipectinata (P2' is 0.60-0.67) are at the forefront. Our finding is also supported by the fact that D. parabipectinata is derived from D. bipectinata and has not diverged much since its emergence as a separate species. The differences in the pattern of sperm displacement may be attributed to differences in remating latency, duration of copulation in first mating and sperm usage pattern among the members of this complex.
Synapse, 2009
The capability of cocaine cues to generate craving in cocaine-dependent humans, even after extend... more The capability of cocaine cues to generate craving in cocaine-dependent humans, even after extended abstinence, is modeled in rats using cue reinstatement of extinguished cocaine-seeking behavior. We investigated neural activity associated with incentive motivational effects of cocaine cues using cfos mRNA and Fos protein expression as markers. Unlike preceding studies, we used responsecontingent presentation of discrete cues to elicit cocaine seeking. Rats were first trained to press a lever, resulting in cocaine reinforcement and light and tone cues. Rats then underwent extinction training, during which lever presses decreased. On the test day, rats either received responsecontingent cocaine cues or received no cues. The cues reinstated extinguished cocaine-seeking behavior on the test day. In general, cue-elicited c-fos mRNA and protein expression were similar and both were enhanced in the prefrontal cortex, ventral tegmental area (VTA), dorsal striatum and nucleus accumbens. Cues elicited more widespread Fos protein expression relative to our previous research in which cues were presented non-contingently without prior extinction training, including increases in the VTA, substantia nigra, ventral subiculum, and lateral entorhinal cortex. We also observed a correlation between cocaine-seeking behavior and Fos in the agranular insula (AgI) and basolateral amygdala (BLA). The findings suggest that connections between BLA and AgI play a role in cue-elicited incentive motivation for cocaine and that reinstatement of cocaine seeking by response-contingent cues activates a similar corticolimbic circuit as that observed with other modes of cue presentation; however, activation of midbrain and ventral hippocampal regions may be unique to reinstatement by response-contingent cues.
Molecular Ecology Resources, 2012
This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nu... more This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium da...
Molecular Biology Reports, 2012
Clarias batrachus, an Indian catfish species, is endemic to the Indian subcontinent and potential... more Clarias batrachus, an Indian catfish species, is endemic to the Indian subcontinent and potential cultivable species. The genomic resources in C. batrachus in the form of ESTs containing microsatellite repeats (EST-SSR) and single nucleotide polymorphisms (SNPs) that are associated with the expressed genes from spleen were mined. From a total of 1,937 ESTs generated, 1,698 unique sequences were obtained, out of which 221 EST-SSRs were identified and 54% could be functionally annotated by similarity searches. A total of 23 contigs containing 3 or more ESTs were found to contain 31 SNP loci, out of which 8 ESTs showed similarity to genes of known function and 1 for hypothetical protein. Nine ESTs with SSRs and/or SNPs identified in this study were reported to be associated with diseases in human and animals. These identified loci can be developed into markers in C. batrachus, which can be useful in linkage mapping, comparative genomics studies and for its genetic improvement programmes.
Molecular Biology Reports, 2011
Channa marulius (Hamilton, 1822) is a commercially important freshwater fish and a potential cand... more Channa marulius (Hamilton, 1822) is a commercially important freshwater fish and a potential candidate species for aquaculture. The present study evaluated partial Cytochrome b gene sequence of mtDNA for determining the genetic variation in wild populations of C. marulius. Genomic DNA extracted from C. marulius samples (n = 23) belonging to 3 distant rivers; Mahanadi, Teesta and Yamuna was analyzed. Sequencing of 307 bp Cytochrome b mtDNA fragment revealed the presence of 5 haplotypes with haplotype diversity value of 0.763 and nucleotide diversity value of 0.0128. Single population specific haplotype was observed in Mahanadi and Yamuna samples and 3 haplotypes in Teesta samples. The analysis of data demonstrated the suitability of partial Cytochrome b sequence in determining the genetic diversity in C. marulius population.
Journal of Biosciences, 2013
With an aim to study the mechanism of adaptation to acute hypoxic periods by hypoxia-tolerant cat... more With an aim to study the mechanism of adaptation to acute hypoxic periods by hypoxia-tolerant catfish, Clarias batrachus, the mass-specific metabolic rate (VO 2 ) along with its hematological parameters, metabolic response and antioxidant enzyme activities were studied. During progressive hypoxia, C. batrachus was found to be an oxyconformer and showed a steady decline in its aquatic oxygen consumption rate. When C. batrachus was exposed for different periods at experimental hypoxia level (0.98±0.1 mg/L, DO), hemoglobin and hematocrit concentrations were increased, along with decrease in mean cellular hemoglobin concentration, which reflected a physiological adaptation to enhance oxygen transport capacity. Significant increase in serum glucose and lactate concentration as well as lactate dehydrogenase activity was observed. Antioxidant enzymes were found to operate independently of one another, while total glutathione concentration was unaffected in any of the tissues across treatments. These observations suggested that hypoxia resulted in the development of oxidative stress and C. batrachus was able to respond through increase in the oxygen carrying capacity, metabolic depression and efficient antioxidant defense system to survive periods of acute hypoxia.
Genetica, 2014
The power of sexual selection to drive changes in the mate recognition system through divergence ... more The power of sexual selection to drive changes in the mate recognition system through divergence in sexually selected traits gives it the potential to be a potent force in speciation. To know how sexual selection can bring such type of divergence in the genus Drosophila, comparative studies based on intra-and inter-sexual selection are documented in this review. The studies provide evidence that both mate choice and male-male competition can cause selection of trait and preference which thereby leads to divergence among species. In the case of intrasexual selection, various kinds of signals play significant role in affecting the species mate recognition system and hence causing divergence between the species. However, intrasexual selection can bring the intraspecific divergence at the level of pre-and post-copulatory stage. This has been better explained through Hawaiian Drosophila which has been suggested a wonderful model system in explaining the events of speciation via sexual selection. This is due to their elaborate mating displays and some kind of ethological isolation persisting among them. Similarly, the genetic basis of sexually selected variations can provide yet another path in understanding the speciation genetics via sexual selection more closely.
Gene, 2012
A normalized cDNA library from spleen of Indian catfish, Clarias batrachus, was constructed with ... more A normalized cDNA library from spleen of Indian catfish, Clarias batrachus, was constructed with a redundancy factor of 2.29. A total of 2045 clones from the library were single-pass sequenced, which generated 1937 high quality ESTs with an average read length of approximately 700 bp. Based on sequence similarities, 65 ESTs were found to be associated with immune functions, which were mainly associated with response to stress, response to chemical stimulus, cellular response to stimulus, response to external stimulus, immune response and regulation of response to stimulus. The immune-relevant gene for CD141, thrombomodulin, has been identified in Teleosts for the first time. Six EST-SSRs and three SNPs were found associated with eight immune-relevant genes. These markers associated with important immune genes would be useful for the identification of trait associated alleles for marker-assisted selection. The identification of the putative immune-related genes provides a meaningful framework to understand the Indian catfish immune system and defense mechanisms.
Fish & Shellfish Immunology, 2013
Behavioural Processes, 2013
Intra- and interspecific variations in female and male remating frequency, latency, and duration ... more Intra- and interspecific variations in female and male remating frequency, latency, and duration of copulation in first and second matings were analyzed in four species of the Drosophila bipectinata complex, employing four strains of each species i.e. D. bipectinata, D. parabipectinata, D. malerkotliana and D. pseudoananassae. Chi-square test revealed significant intraspecific variation in the number of remated females and males in D. malerkotliana and D. bipectinata, whereas D. parabipectinata showed insignificant intraspecific variations in number of remated females and males. D. pseudoananassae showed significant intraspecific variation in the number of remated females, but the frequency of remating was least. One way ANOVA depicted significant intraspecific variation in female and male remating time in D. bipectinata and D. parabipectinata. D. bipectinata took the shortest time to remate and the duration of copulation in first mating was longest. However, D. pseudoananassae exhibited the longest remating time and long duration of copulation in first mating. Results of t-test depicted that all four species exhibited shorter duration of copulation in second mating as compared to the first. Our study puts D. bipectinata and D. pseudoananassae at two extremes, and D. parabipectinata and D. malerkotliana at an intermediate position in a hierarchy of remating behaviours.
International Aquatic Research, 2014
The selection of most appropriate reference gene(s) is a crucial step in studies quantifying gene... more The selection of most appropriate reference gene(s) is a crucial step in studies quantifying gene expression by quantitative real-time PCR (qPCR). As a need reference gene(s) should be unaffected at transcription level by experimental conditions and/or tissue types. In this study, 11 candidate reference genes were tested in Clarias batrachus for their expression stability using the geNorm, NormFinder and BestKeeper statistical algorithms, and were compared in different tissues (brain, heart, liver, muscle, spleen and head kidney) and treatments (before and after hypoxia exposure). The results indicated that in brain, heart, liver, muscle, spleen and head kidney, respectively, 28S rRNA/TUB, 28S rRNA/TUB, RPL30/ 28S rRNA, RPL30/TUB, ELF-1A/28S rRNA and ELF-1A/TUB gene pairs were highly stable and were suitable as reference genes to study oxidative stress, while ACTB and B2M were the least stable genes in examined tissues under normoxic and/or hypoxic conditions. The observations suggested the consideration of tissue types and use of at least two reference genes, instead of one in accurate normalization of qPCR data.
Behavioural Processes, 2014
We studied sperm displacement in two members of the Drosophila bipectinata species complex i.e., ... more We studied sperm displacement in two members of the Drosophila bipectinata species complex i.e., Drosophila parabipectinata and Drosophila malerkotliana by employing mutant and wild type strains. We found a significant increase in the productivity of remated females than that of once mated ones in all the crosses of the two species. The P2' values range from 0.67 to 0.70 in D. malerkotliana and 0.52 to 0.56 in D. parabipectinata. These results were compared with that of our earlier finding in D. bipectinata belonging to the same complex. We found that though the three species exhibit differences in the degree of sperm displacement, the pattern is somewhat similar in the three species. However, as far as its genetic variability and population size maintenance is considered, D. malerkotliana and D. bipectinata (P2' is 0.60-0.67) are at the forefront. Our finding is also supported by the fact that D. parabipectinata is derived from D. bipectinata and has not diverged much since its emergence as a separate species. The differences in the pattern of sperm displacement may be attributed to differences in remating latency, duration of copulation in first mating and sperm usage pattern among the members of this complex.
Synapse, 2009
The capability of cocaine cues to generate craving in cocaine-dependent humans, even after extend... more The capability of cocaine cues to generate craving in cocaine-dependent humans, even after extended abstinence, is modeled in rats using cue reinstatement of extinguished cocaine-seeking behavior. We investigated neural activity associated with incentive motivational effects of cocaine cues using cfos mRNA and Fos protein expression as markers. Unlike preceding studies, we used responsecontingent presentation of discrete cues to elicit cocaine seeking. Rats were first trained to press a lever, resulting in cocaine reinforcement and light and tone cues. Rats then underwent extinction training, during which lever presses decreased. On the test day, rats either received responsecontingent cocaine cues or received no cues. The cues reinstated extinguished cocaine-seeking behavior on the test day. In general, cue-elicited c-fos mRNA and protein expression were similar and both were enhanced in the prefrontal cortex, ventral tegmental area (VTA), dorsal striatum and nucleus accumbens. Cues elicited more widespread Fos protein expression relative to our previous research in which cues were presented non-contingently without prior extinction training, including increases in the VTA, substantia nigra, ventral subiculum, and lateral entorhinal cortex. We also observed a correlation between cocaine-seeking behavior and Fos in the agranular insula (AgI) and basolateral amygdala (BLA). The findings suggest that connections between BLA and AgI play a role in cue-elicited incentive motivation for cocaine and that reinstatement of cocaine seeking by response-contingent cues activates a similar corticolimbic circuit as that observed with other modes of cue presentation; however, activation of midbrain and ventral hippocampal regions may be unique to reinstatement by response-contingent cues.
Molecular Ecology Resources, 2012
This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nu... more This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium da...
Molecular Biology Reports, 2012
Clarias batrachus, an Indian catfish species, is endemic to the Indian subcontinent and potential... more Clarias batrachus, an Indian catfish species, is endemic to the Indian subcontinent and potential cultivable species. The genomic resources in C. batrachus in the form of ESTs containing microsatellite repeats (EST-SSR) and single nucleotide polymorphisms (SNPs) that are associated with the expressed genes from spleen were mined. From a total of 1,937 ESTs generated, 1,698 unique sequences were obtained, out of which 221 EST-SSRs were identified and 54% could be functionally annotated by similarity searches. A total of 23 contigs containing 3 or more ESTs were found to contain 31 SNP loci, out of which 8 ESTs showed similarity to genes of known function and 1 for hypothetical protein. Nine ESTs with SSRs and/or SNPs identified in this study were reported to be associated with diseases in human and animals. These identified loci can be developed into markers in C. batrachus, which can be useful in linkage mapping, comparative genomics studies and for its genetic improvement programmes.
Molecular Biology Reports, 2011
Channa marulius (Hamilton, 1822) is a commercially important freshwater fish and a potential cand... more Channa marulius (Hamilton, 1822) is a commercially important freshwater fish and a potential candidate species for aquaculture. The present study evaluated partial Cytochrome b gene sequence of mtDNA for determining the genetic variation in wild populations of C. marulius. Genomic DNA extracted from C. marulius samples (n = 23) belonging to 3 distant rivers; Mahanadi, Teesta and Yamuna was analyzed. Sequencing of 307 bp Cytochrome b mtDNA fragment revealed the presence of 5 haplotypes with haplotype diversity value of 0.763 and nucleotide diversity value of 0.0128. Single population specific haplotype was observed in Mahanadi and Yamuna samples and 3 haplotypes in Teesta samples. The analysis of data demonstrated the suitability of partial Cytochrome b sequence in determining the genetic diversity in C. marulius population.
Journal of Biosciences, 2013
With an aim to study the mechanism of adaptation to acute hypoxic periods by hypoxia-tolerant cat... more With an aim to study the mechanism of adaptation to acute hypoxic periods by hypoxia-tolerant catfish, Clarias batrachus, the mass-specific metabolic rate (VO 2 ) along with its hematological parameters, metabolic response and antioxidant enzyme activities were studied. During progressive hypoxia, C. batrachus was found to be an oxyconformer and showed a steady decline in its aquatic oxygen consumption rate. When C. batrachus was exposed for different periods at experimental hypoxia level (0.98±0.1 mg/L, DO), hemoglobin and hematocrit concentrations were increased, along with decrease in mean cellular hemoglobin concentration, which reflected a physiological adaptation to enhance oxygen transport capacity. Significant increase in serum glucose and lactate concentration as well as lactate dehydrogenase activity was observed. Antioxidant enzymes were found to operate independently of one another, while total glutathione concentration was unaffected in any of the tissues across treatments. These observations suggested that hypoxia resulted in the development of oxidative stress and C. batrachus was able to respond through increase in the oxygen carrying capacity, metabolic depression and efficient antioxidant defense system to survive periods of acute hypoxia.
Genetica, 2014
The power of sexual selection to drive changes in the mate recognition system through divergence ... more The power of sexual selection to drive changes in the mate recognition system through divergence in sexually selected traits gives it the potential to be a potent force in speciation. To know how sexual selection can bring such type of divergence in the genus Drosophila, comparative studies based on intra-and inter-sexual selection are documented in this review. The studies provide evidence that both mate choice and male-male competition can cause selection of trait and preference which thereby leads to divergence among species. In the case of intrasexual selection, various kinds of signals play significant role in affecting the species mate recognition system and hence causing divergence between the species. However, intrasexual selection can bring the intraspecific divergence at the level of pre-and post-copulatory stage. This has been better explained through Hawaiian Drosophila which has been suggested a wonderful model system in explaining the events of speciation via sexual selection. This is due to their elaborate mating displays and some kind of ethological isolation persisting among them. Similarly, the genetic basis of sexually selected variations can provide yet another path in understanding the speciation genetics via sexual selection more closely.
Gene, 2012
A normalized cDNA library from spleen of Indian catfish, Clarias batrachus, was constructed with ... more A normalized cDNA library from spleen of Indian catfish, Clarias batrachus, was constructed with a redundancy factor of 2.29. A total of 2045 clones from the library were single-pass sequenced, which generated 1937 high quality ESTs with an average read length of approximately 700 bp. Based on sequence similarities, 65 ESTs were found to be associated with immune functions, which were mainly associated with response to stress, response to chemical stimulus, cellular response to stimulus, response to external stimulus, immune response and regulation of response to stimulus. The immune-relevant gene for CD141, thrombomodulin, has been identified in Teleosts for the first time. Six EST-SSRs and three SNPs were found associated with eight immune-relevant genes. These markers associated with important immune genes would be useful for the identification of trait associated alleles for marker-assisted selection. The identification of the putative immune-related genes provides a meaningful framework to understand the Indian catfish immune system and defense mechanisms.
Fish & Shellfish Immunology, 2013
Behavioural Processes, 2013
Intra- and interspecific variations in female and male remating frequency, latency, and duration ... more Intra- and interspecific variations in female and male remating frequency, latency, and duration of copulation in first and second matings were analyzed in four species of the Drosophila bipectinata complex, employing four strains of each species i.e. D. bipectinata, D. parabipectinata, D. malerkotliana and D. pseudoananassae. Chi-square test revealed significant intraspecific variation in the number of remated females and males in D. malerkotliana and D. bipectinata, whereas D. parabipectinata showed insignificant intraspecific variations in number of remated females and males. D. pseudoananassae showed significant intraspecific variation in the number of remated females, but the frequency of remating was least. One way ANOVA depicted significant intraspecific variation in female and male remating time in D. bipectinata and D. parabipectinata. D. bipectinata took the shortest time to remate and the duration of copulation in first mating was longest. However, D. pseudoananassae exhibited the longest remating time and long duration of copulation in first mating. Results of t-test depicted that all four species exhibited shorter duration of copulation in second mating as compared to the first. Our study puts D. bipectinata and D. pseudoananassae at two extremes, and D. parabipectinata and D. malerkotliana at an intermediate position in a hierarchy of remating behaviours.