Sandip Das | University of Delhi (original) (raw)
Papers by Sandip Das
Physiology and molecular biology of plants : an international journal of functional plant biology, 2010
In vitro micropropagation has been achieved in medicinally important plant, Taraxacum officinale ... more In vitro micropropagation has been achieved in medicinally important plant, Taraxacum officinale collected from two different regions, Kashmir (J & K) and Garhwal (Uttarakhand). Leaf segments inoculated on MS supplemented with different combinations of Indole-3-acetic acid (IAA) and Benzyladenine (BA) produced indirect regeneration. For root induction MS fortified with Indole-3-butyric acid (IBA) was used. Taraxacum officinale collected from Garhwal responded two weeks earlier and showed shoot regeneration whereas in Kashmir population only callus proliferation occurred. Esculin content was also higher in the samples from Garhwal. The content was affected by both, the hormone concentration as well as age of the cultures. RAPD of the in vitro raised regenerants confirmed genetic stability.
Physiology and molecular biology of plants : an international journal of functional plant biology, 2011
Retrotransposons (RT) constitute a major fraction of plant genome. They are implicated in evoluti... more Retrotransposons (RT) constitute a major fraction of plant genome. They are implicated in evolution and sequence organization. These elements have been proposed to have major role in evolution and variation in genome size. The sequence information of these RT regions in terms of divergence and conservation could be utilized for determining the interrelationship among various copia retrotransposons within the genome. In order to assess the diversity of Ty1-copia group of retroelements, reverse transcriptase (RT) sequence was amplified from genomes of three medicinally important Datura species: D. innoxia, D. stramonium and D. metel using the primers derived from two conserved domains of RT region. A total of twenty one independent amplicons from RT regions were cloned, sequenced and compared. The intra-family divergence at amino acid level ranged from 4 to 52 %. Though intra-family RT sequences are conserved, no two sequences are identical. Southern blot hybridization suggested that ...
Genetics, Aug 3, 2012
Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model sp... more Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model species widely used for studying natural variation in adaptive traits such as flowering time. Although mutations in dozens of genes can affect flowering of A. thaliana in the laboratory, only a handful of such genes vary in natural populations. Chief among these are FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). Common and rare FRI mutations along with rare FLC mutations explain a large fraction of flowering time variation ...
Plant genomes are characterized by the presence of large miRNA gene families which are few in num... more Plant genomes are characterized by the presence of large miRNA gene families which are few in number.The expansion of miRNA families is thought to be driven by gene and genome duplication. Some members of these miRNA gene families are tandemly arranged and their analysis is of interest because such organisation may indicate origin through tandem duplication and also to investigate whether some such tandem clusters have similar expression patterns, and whether these are regulated through a common set of cis-regulatory elements (eg. promoters and enhancers). As a first step, we undertake a comprehensive study using micro-synteny analyses of tandemly organised miRNA families across the Brassicaceae spanning an evolutionary time scale of ca. 45 million years, among Arabidopsis, Capsella, Brassica and Thellungiella species, to address the following questions: Are most miRNA gene families present as tandem clusters? To what extent are these tandem patterns retained? To what extent can family sizes be ascribed to genome duplication? Our analysis of thirteen tandemly organised miRNA families revealed that synteny is largely conserved among Arabidopsis thaliana, A. lyrata and Capsella rubella, which form a clade spanning approximately between 6.2–9.8 my (Acarkan et al., 2000) [1]. On the other hand, comparison of sequences from these species with Brassica rapa, B. oleracea and Thellungiella halophila, which form a separate clade spanning 31 my (Franzke et al., 2011) [2] reveals many differences. The latter clade reveals several paralogous duplications that probably resulted from whole genome duplication,as well as disrupted synteny. Phylogenetic analyses of precursor sequences generally support the history inferred from synteny analysis. Synteny and phylogenetic analysis of six members of the tandemly organised miR169 family suggest that the Brassicaceae ancestral state consisted of a “dimer as a unit”which may have undergone direct local duplication to retain the transcriptional orientation followed by lineage specific changes. MiR169, to the best of our knowledge, is one of the largest tandemly organised miRNA gene family across plant kingdom and further analysis should reveal the generality of this pattern of evolution. The conserved organisation of miR395A-B-C and miR395 D-E-F as two clusters on same chromosome/scaffold across A. thaliana, B. rapa and salsuginea demonstrates retention of the large chromosomal segment across the two lineages. MiRNA family miR845 was detected only in Arabidopsis species and Thellungiella indicating a complex loss and retention history. MiR447A-B family was only found in A. thaliana indicating that it is a species-specific gene family of recent origin
Gunjan Kumari, Karuna Kusumanjali, Prem Shankar Srivastava, Sandip Das (2012)
Ya-Long Guo, Marco Todesco, Jörg Hagmann, Sandip Das, and Detlef Weigel (2012)
Physiology and molecular biology of plants : an international journal of functional plant biology, 2010
In vitro micropropagation has been achieved in medicinally important plant, Taraxacum officinale ... more In vitro micropropagation has been achieved in medicinally important plant, Taraxacum officinale collected from two different regions, Kashmir (J & K) and Garhwal (Uttarakhand). Leaf segments inoculated on MS supplemented with different combinations of Indole-3-acetic acid (IAA) and Benzyladenine (BA) produced indirect regeneration. For root induction MS fortified with Indole-3-butyric acid (IBA) was used. Taraxacum officinale collected from Garhwal responded two weeks earlier and showed shoot regeneration whereas in Kashmir population only callus proliferation occurred. Esculin content was also higher in the samples from Garhwal. The content was affected by both, the hormone concentration as well as age of the cultures. RAPD of the in vitro raised regenerants confirmed genetic stability.
Physiology and molecular biology of plants : an international journal of functional plant biology, 2011
Retrotransposons (RT) constitute a major fraction of plant genome. They are implicated in evoluti... more Retrotransposons (RT) constitute a major fraction of plant genome. They are implicated in evolution and sequence organization. These elements have been proposed to have major role in evolution and variation in genome size. The sequence information of these RT regions in terms of divergence and conservation could be utilized for determining the interrelationship among various copia retrotransposons within the genome. In order to assess the diversity of Ty1-copia group of retroelements, reverse transcriptase (RT) sequence was amplified from genomes of three medicinally important Datura species: D. innoxia, D. stramonium and D. metel using the primers derived from two conserved domains of RT region. A total of twenty one independent amplicons from RT regions were cloned, sequenced and compared. The intra-family divergence at amino acid level ranged from 4 to 52 %. Though intra-family RT sequences are conserved, no two sequences are identical. Southern blot hybridization suggested that ...
Genetics, Aug 3, 2012
Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model sp... more Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model species widely used for studying natural variation in adaptive traits such as flowering time. Although mutations in dozens of genes can affect flowering of A. thaliana in the laboratory, only a handful of such genes vary in natural populations. Chief among these are FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). Common and rare FRI mutations along with rare FLC mutations explain a large fraction of flowering time variation ...
Plant genomes are characterized by the presence of large miRNA gene families which are few in num... more Plant genomes are characterized by the presence of large miRNA gene families which are few in number.The expansion of miRNA families is thought to be driven by gene and genome duplication. Some members of these miRNA gene families are tandemly arranged and their analysis is of interest because such organisation may indicate origin through tandem duplication and also to investigate whether some such tandem clusters have similar expression patterns, and whether these are regulated through a common set of cis-regulatory elements (eg. promoters and enhancers). As a first step, we undertake a comprehensive study using micro-synteny analyses of tandemly organised miRNA families across the Brassicaceae spanning an evolutionary time scale of ca. 45 million years, among Arabidopsis, Capsella, Brassica and Thellungiella species, to address the following questions: Are most miRNA gene families present as tandem clusters? To what extent are these tandem patterns retained? To what extent can family sizes be ascribed to genome duplication? Our analysis of thirteen tandemly organised miRNA families revealed that synteny is largely conserved among Arabidopsis thaliana, A. lyrata and Capsella rubella, which form a clade spanning approximately between 6.2–9.8 my (Acarkan et al., 2000) [1]. On the other hand, comparison of sequences from these species with Brassica rapa, B. oleracea and Thellungiella halophila, which form a separate clade spanning 31 my (Franzke et al., 2011) [2] reveals many differences. The latter clade reveals several paralogous duplications that probably resulted from whole genome duplication,as well as disrupted synteny. Phylogenetic analyses of precursor sequences generally support the history inferred from synteny analysis. Synteny and phylogenetic analysis of six members of the tandemly organised miR169 family suggest that the Brassicaceae ancestral state consisted of a “dimer as a unit”which may have undergone direct local duplication to retain the transcriptional orientation followed by lineage specific changes. MiR169, to the best of our knowledge, is one of the largest tandemly organised miRNA gene family across plant kingdom and further analysis should reveal the generality of this pattern of evolution. The conserved organisation of miR395A-B-C and miR395 D-E-F as two clusters on same chromosome/scaffold across A. thaliana, B. rapa and salsuginea demonstrates retention of the large chromosomal segment across the two lineages. MiRNA family miR845 was detected only in Arabidopsis species and Thellungiella indicating a complex loss and retention history. MiR447A-B family was only found in A. thaliana indicating that it is a species-specific gene family of recent origin
Gunjan Kumari, Karuna Kusumanjali, Prem Shankar Srivastava, Sandip Das (2012)
Ya-Long Guo, Marco Todesco, Jörg Hagmann, Sandip Das, and Detlef Weigel (2012)