Anirban Chakraborty | Vidyasagar University (original) (raw)
Address: Kolkata, West Bengal, India
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Papers by Anirban Chakraborty
Journal of Applied Ichthyology, 2006
Museum fish specimens are invaluable resources for genetic studies, but extraction of high qualit... more Museum fish specimens are invaluable resources for genetic studies, but extraction of high quality DNA is often problematic. In this study, hairtail fishes of the genera Trichiurus and Lepturacanthus (family: Trichiuridae) representing a wide range of preservation histories and three different methods of preservation were analyzed for mitochondrial DNA (mtDNA) extraction, amplification and sequencing of marker genes. A total of six protocols, including a commercially available kit, were compared in this study. Amplification of conserved genes such as16S rRNA and 12S rRNA were done using polymerase chain reaction with sequence analyses using automated capillary sequencing techniques. The results show that mtDNA extraction, amplification and sequencing of conserved genes could be obtained successfully from frozen (−20°C) preserved specimens (1–5 years) and also from ethanol (95%) fixed specimens (2–5 years) but not from any of the formalin (10%) fixed specimens (3–4 years). However, specimens that have been fixed for only 7 days in buffered formalin (10% formalin with phosphate buffer containing 173 mm salt) and ethanol (95%) could yield successful mtDNA extraction, amplification and sequence information of both 16S rRNA and 12S rRNA.
Fisheries Science, 2007
Hairtail fillets are marketed as both fresh and frozen forms in retail outlets within Japan. The ... more Hairtail fillets are marketed as both fresh and frozen forms in retail outlets within Japan. The present study was undertaken to develop a rapid and reliable method for identification of the hairtail species in commercial fillets. A total of 64 fillet samples, caught from various localities within Japan and purchased from various supermarkets, were analyzed. Polymerase chain reaction (PCR) amplification of a portion of the mitochondrial DNA encoding 16S ribosomal RNA gene and subsequent restriction digestion of the amplified products, using Vspl endonuclease, generated different restriction patterns indicating two different species of hairtails in the fillet samples. The results indicated that the commercial hairtail fillets, labeled and marketed as ‘Tachiuo’ in Japan, were comprised of two species of hairtails with Trichiurus japonicus (commonly called Tachiuo) accounting for 47% and Trichiurus sp. 2 (commonly called Tenjikutachi) accounting for 53% of the analyzed samples. This simple and inexpensive PCR-restriction fragment length polymorphism analysis can be routinely applied to determine species composition of hairtails in commercial fillets.
Ichthyological Research, 2006
The mitochondrial DNA segment encoding the 16S ribosomal RNA (16S rRNA) gene sequence (ca. 600 bp... more The mitochondrial DNA segment encoding the 16S ribosomal RNA (16S rRNA) gene sequence (ca. 600 bp) was compared among Trichiurus sp. 2 (sensu Nakabo, 2002) (obtained from various areas of Japan), T. japonicus Temminck and Schlegel (collected from various localities within Japan), and true T. lepturus Linnaeus (caught off the Atlantic coast of the United States and Brazil) of the family Trichiuridae using 10, 10, and 15 specimens, respectively. Based on phylogenetic analysis using a neighbor-joining (NJ) algorithm, the haplotypes of Trichiurus sp. 2, T. japonicus, and T. lepturus indicated three distinct monophyletic lineages, being supported by 100% bootstrap values with no haplotypes overlapping or sharing among the lineages. Trichiurus sp. 2, T. japonicus, and T. lepturus are genetically different from each other, suggesting that they are three distinct species.
Human Molecular Genetics, 2008
Journal of Applied Ichthyology, 2006
Museum fish specimens are invaluable resources for genetic studies, but extraction of high qualit... more Museum fish specimens are invaluable resources for genetic studies, but extraction of high quality DNA is often problematic. In this study, hairtail fishes of the genera Trichiurus and Lepturacanthus (family: Trichiuridae) representing a wide range of preservation histories and three different methods of preservation were analyzed for mitochondrial DNA (mtDNA) extraction, amplification and sequencing of marker genes. A total of six protocols, including a commercially available kit, were compared in this study. Amplification of conserved genes such as16S rRNA and 12S rRNA were done using polymerase chain reaction with sequence analyses using automated capillary sequencing techniques. The results show that mtDNA extraction, amplification and sequencing of conserved genes could be obtained successfully from frozen (−20°C) preserved specimens (1–5 years) and also from ethanol (95%) fixed specimens (2–5 years) but not from any of the formalin (10%) fixed specimens (3–4 years). However, specimens that have been fixed for only 7 days in buffered formalin (10% formalin with phosphate buffer containing 173 mm salt) and ethanol (95%) could yield successful mtDNA extraction, amplification and sequence information of both 16S rRNA and 12S rRNA.
Fisheries Science, 2007
Hairtail fillets are marketed as both fresh and frozen forms in retail outlets within Japan. The ... more Hairtail fillets are marketed as both fresh and frozen forms in retail outlets within Japan. The present study was undertaken to develop a rapid and reliable method for identification of the hairtail species in commercial fillets. A total of 64 fillet samples, caught from various localities within Japan and purchased from various supermarkets, were analyzed. Polymerase chain reaction (PCR) amplification of a portion of the mitochondrial DNA encoding 16S ribosomal RNA gene and subsequent restriction digestion of the amplified products, using Vspl endonuclease, generated different restriction patterns indicating two different species of hairtails in the fillet samples. The results indicated that the commercial hairtail fillets, labeled and marketed as ‘Tachiuo’ in Japan, were comprised of two species of hairtails with Trichiurus japonicus (commonly called Tachiuo) accounting for 47% and Trichiurus sp. 2 (commonly called Tenjikutachi) accounting for 53% of the analyzed samples. This simple and inexpensive PCR-restriction fragment length polymorphism analysis can be routinely applied to determine species composition of hairtails in commercial fillets.
Ichthyological Research, 2006
The mitochondrial DNA segment encoding the 16S ribosomal RNA (16S rRNA) gene sequence (ca. 600 bp... more The mitochondrial DNA segment encoding the 16S ribosomal RNA (16S rRNA) gene sequence (ca. 600 bp) was compared among Trichiurus sp. 2 (sensu Nakabo, 2002) (obtained from various areas of Japan), T. japonicus Temminck and Schlegel (collected from various localities within Japan), and true T. lepturus Linnaeus (caught off the Atlantic coast of the United States and Brazil) of the family Trichiuridae using 10, 10, and 15 specimens, respectively. Based on phylogenetic analysis using a neighbor-joining (NJ) algorithm, the haplotypes of Trichiurus sp. 2, T. japonicus, and T. lepturus indicated three distinct monophyletic lineages, being supported by 100% bootstrap values with no haplotypes overlapping or sharing among the lineages. Trichiurus sp. 2, T. japonicus, and T. lepturus are genetically different from each other, suggesting that they are three distinct species.
Human Molecular Genetics, 2008