Browsing by Author "D.V. Amla"

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Computational tridimensional protein modeling of CrylAb19 toxin from Bacillus thuringiensis BtX-2
(Korean Society for Microbiolog and Biotechnology, 2012) S. Kashyap; B.D. Singh; D.V. Amla
We report the computational structural simulation of the Cry1Ab19 toxin molecule from B. thuringiensis BtX-2 based on the structure of Cry1Aa1 deduced by x-ray diffraction. Validation results showed that 93.5% of modeled residues are folded in a favorable orientation with a total energy Z-score of -8.32, and the constructed model has an RMSD of only 1.13Å. The major differences in the presented model are longer loop lengths and shortened sheet components. The overall result supports the hierarchical three-domain structural hypothesis of Cry toxins and will help in better understanding the structural variation within the Cry toxin family along with facilitating the design of domain-swapping experiments aimed at improving the toxicity of native toxins. © The Korean Society for Microbiology and Biotechnology.
High frequency multiple shoot regeneration from decapitated embryo axes of chickpea and establishment of plantlets in the open environment
(2002) R. Singh; K. Srivastava; H.K. Jaiswal; D.V. Amla; B.D. Singh
Multiple shoot regeneration from the cut plumular ends of embryo axes of chickpea (Cicer arietinum L.) was evaluated on Murashige and Skoog medium having different concentrations of thidiazuron (TDZ) (0.1 to 10.0 mg dm-3), 6-benzylaminopurine (BAP) (0.5 and 1.0 mg dm-3), kinetin (0.5 and 1.0 mg dm-3) or zeatin (2.0 and 4.0 mg dm-3). TDZ (0.2 mg dm-3) was found to be the most effective cytokinin as it produced multiple shoots in 100% of the explants from genotypes C235, ICC5166, ICC12269, ICC4951, ICC11531, BG256 and a local cultivar. Shoots were elongated on growth regulator-free medium, and rooted on growth regulator-free medium containing 1/4 MS salts + full vitamins + 3% sucrose. Plantlets formed were acclimatized for 12 15 d in MS medium with a gradual reduction in sucrose concentration and transferred into pots filled with soil and kept in the field; this resulted in more than 70% survival. The plants developed normally and produced fertile flowers and set seeds. Low temperatures, maximum 19.0°C, and minimum 8.2°C, during the first 15 d of transfer favoured survival on transfer to pots.
Homology modeling deduced 3D structure of the Cry1Ab22 toxin
(2011) S. Kashyap; B.D. Singh; D.V. Amla
δ-Endotoxin Cry1Ab22 is produced by Bacillus thuringiensis BtS2491Ab. The toxic spectrum of this protein is reported to span Lepidopteron and Dipteran. Here, we predict the theoretical structural model of newly reported Cry1Ab22 toxin by homology modeling method on the structure of the Cry1Aa toxin. Proposed model resembles the target by sharing common three dimensional, three domain structure. The main differences being located in the length of loops, absence of helixes (α7b, α10a, α10b, α11a) and presence of additional components (β21, α9b). Few of the components like α9a, α9b and α12a are positioned spatially at different locations. A better understanding of the 3D structure will be helpful in designing the domain swapping and mutagenesis experiments aimed at improving toxicity, and will lead to a deeper understanding of the common mechanism of toxins.
Homology modelling deduced 3-D structure of Bacillus thuringiensis Cry1Ab17 toxin
(Science Society of Thailand under Royal Patronage, 2010) S. Kashyap; B.D. Singh; D.V. Amla
We predict the first theoretical structural model of the newly reported Cry1Ab17 δ-endotoxin produced by Bacillus thuringiensis using homology modelling. Both Cry1Abl7 and Cry1Aa share a common structure; both contain three flexible domains that participate in the formation of a pore and determine the receptor binding specificity. The main differences between the two is in the length of loops, and in Cry1Ab17, the absence of α7b, α10a, α10b, α12a, β19, β20 and presence of additional β0 β1b, α9b components. A few of the components such as α8a, α8b, α9a, α9b, and α11a differ in their locations. A better understanding of the 3-D structure of Cry1Ab17 will be helpful in designing the domain swapping experiments to improve its insecticidal toxicity.
Mutagenesis of free and intracellular cyanophage AS-1 by ultraviolet, N-methyl-N′-nitro-N-nitrosoguanidine and acriflavine
(1979) D.V. Amla
Mutagenic actions of ultraviolet irradiation (UV), N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) and acriflavine (photodynamic) were tested in free and intracellular phage AS-1 infecting Anacystis nidulans IU625. Spontaneous and induced mutations with particular reference to host range (h) and minute plaque formation (m) were investigated. The spontaneous mutation frequencies varied from 10-9 to 10-8 and from 2 ×1 0-5 to 2 × 10-4 for h and m mutants respectively. UV was efficient in inducing h and m markers in free phage particles as well as intracellular phage; MNNG induced both markers in intracellular phage only, and acriflavine induced m mutants only in free as well as in infecting phages. UV-induced mutations in free phage were photo-reactivable by visible light. With all the mutagens used, maximal induction of both markers was observed with treatment of 2-h complexes. © 1979.
Prediction of three-dimensional structure of Cry1Ab21 toxin from bacillus thuringiensis Bt IS5056
(2011) S. Kashyap; B.D. Singh; D.V. Amla
Cry1Ab21 is a δ-endotoxin produced by Bacillus thuringiensis Bt IS5056. The toxic spectrum of this protein is reported to span Lepidopteran, Dipteran and nematodes. Here, we predict the theoretical structural model of newly reported Cry1Ab21 toxin by homology modeling on the structure of the Cry1Aa toxin (2.5Å). Cry1Ab21 resembles the Cry1Aa toxin structure by sharing a common 3D structure with three domains along with few structural deviations. The main differences being located in the length of loops, absence of α7b, α9b, β10, β11, β12 and presence of additional β0 component. Some of the components like α10a, α10b, α11a are spatially positioned at different locations. A better understanding of 3D structure will be helpful in the design of efficient biopecticides. © Society for Plant Biochemistry and Biotechnology 2011.