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Malik A.,Biomedical Informatics Center | Firoz A.,Biomedical Informatics Center | Jha V.,Biomedical Informatics Center | Sunderasan E.,Biotechnology Unit | Ahmad S.,Japan National Institute of Biomedical Innovation
Journal of Molecular Modeling | Year: 2010

Rubber trees infected with a host-specific cassiicolin toxin often experience considerable leaf fall, which in turn results in loss of crop productivity. It was recently revealed that cassiicolin-specific single-chain variable fragments (scFv) can successfully reduce the toxic effects of cassiicolin. However, the detailed mechanism of antibody action remains poorly understood. The primary sequence of the newly sequenced cassiicolin-specific scFv was highly homologous to several members of single-chain antibodies in the 14B7 family. In this study, with the aid of homology modeling, the three-dimensional structure of cassiicolinspecific scFv was elucidated, and was found to exhibit a characteristic immunoglobulin fold that mainly consists of β sheets Additionally, molecular docking between the modeled scFv antibody and the available three-dimensional crystal structure of cassiicolin toxin was also performed' The predicted structural complex and the change in accessible surface area between the toxin and the scFv antibody upon complexation reveal the potential role of certain complementarity determining region (CDR) amino acid residues in the formation of the complex These computational results suggest that mutagenesis experiments that are aimed at validating the model and improving the binding affinity of cassiicolin-specific scFv antibodies for the toxin should be performed. © Springer-Verlag 2010. Source

Ozturk M.,Ege University | Dogan Y.,Dokuz Eylul University | Sakcali M.S.,Fatih University | Doulis A.,Biotechnology Unit | Karam F.,Lebanese ARI
Journal of Environmental Biology | Year: 2010

The objective was to examine the adaptation strategies of four maquis species to drought prone environments; typical of the east Mediterranean area in degraded and healthy sites in Turkey. A comparison made between sites for Pistacia lentiscus and Quercus coccifera shows higher net daily photosynthesis in the degraded site, when compared with the healthy site; but Ceratonia siliqua and Olea oleaster exhibited no difference in their photosynthetic activity in environmentally contrasting conditions. The pattern of daily transpiration shows higher values in the degraded site in the case of P. lentiscus and Q. coccifera, while no site effect was observed for C. siliqua and O. oleaster. In the case of Q. coccifera, a behavior similar to C. siliqua was observed. A comparison made between C. siliqua and O. oleaster to observe seasonal differences in daily patterns of net photosynthesis and transpiration reveals that Q. coccifera had the highest water use efficiency (slope= 2.88; r 2= 0.61), followed by C. siliqua (slope= 2.74; r2= 0.7), P. lentiscus (slope= 2.56; r2= 0.52; and O. oleaster (slope= 2.40; r2 = 0.78). Olea oleaster and P. lentiscus performed as a drought tolerant species, being more resistant to aridity and thus indicative of the degradation state of the site. Ceratonia siliqua and Q. coccifera were found avoiding drought by adopting first a water-spending strategy, and then a water-saving strategy. © Triveni Enterprises. Source

Shekhawat M.S.,Biotechnology Laboratory | Kannan N.,Biotechnology Unit | Manokari M.,Biotechnology Laboratory
South African Journal of Botany | Year: 2015

An efficient micropropagation protocol has been developed successfully for Morinda coreia Buch.-Ham. by culturing nodal segments. The explants were washed, sterilized with HgCl2 and inoculated on semi-solid Murashige and Skoog (MS) medium containing various concentrations and combinations of plant growth regulators (PGRs). Shoot bud initiation was observed after one week and 8.6±0.32 shoots (per explant) harvested after five weeks on MS medium with 4.0mgl-1 concentration of 6-benzylaminopurine (BAP). The regenerated shoots were further multiplied on semi-solid MS medium augmented with 2.0mgl-1 BAP+1.0mgl-1 Kinetin (Kin). Maximum 24.5±0.34 shoots per explant was obtained after five weeks on this media combination. The long (4-5cm) and healthy shoots were rooted in vitro with 100% success rate on half strength MS medium+1.0mgl-1 indole-3 butyric acid (IBA). Rooting and acclimatization were achieved simultaneously by ex vitro rooting method using 200mgl-1 IBA for 5min with very good success rate (28.67±05.51 roots per shoot with 100% response). The rooted shoots were transferred to the greenhouse for acclimatization for 4-5weeks. The hardened plantlets were finally shifted to the field for further growth in the natural conditions after another five weeks. This is the first report on micropropagation of M. coreia, which can be successfully used for the large-scale multiplication and conservation of germplasm of this important medicinal plant. © 2015 South African Association of Botanists. Source

Perera P.I.P.,Agrobiodiversity research area | Quintero M.,Agrobiodiversity research area | Dedicova B.,Biotechnology Unit | Kularatne J.D.J.S.,Decision and Policy Analysis Research Area | Ceballos H.,Agrobiodiversity research area
AoB PLANTS | Year: 2013

Background and aims: Cassava (Manihot esculenta), a major food staple in the tropics and subtropics, thrives even in environments undergoing threatening climate change. To satisfy the increasing demand for crop improvement and overcome the limitations of conventional breeding, the introduction of inbreeding techniques such as the production of doubled haploid lines via androgenesis or gynogenesis offers advantages. However, comprehensive studies on cassava flower bud biology or structural development are lacking and precise structural and biological information is a prerequisite to enhance the efficiency of these techniques. Methodology: The floral biology of three selected cassava lines was studied, focusing on morphology, phenology and pollen biology (quantity, viability and dimorphism). Histological studies were also conducted on microsporogenesis/microgametogenesis and megasporogenesis/ megagametogenesis to generate precise developmental data for these lines. Principal results: Male and female cyathia have distinct developmental phases. Pollen viability was high during immature stages of plant development; however, pollen mortality was common at later stages. Pollen trimorphism in male gametophytes towards the larger or smaller pollen size, as compared with normal size, was observed. Ten characteristic events were identified in male gametogenesis and six in female gametogenesis that were correlated with flower bud diameter. Male gametophyte diameter at different developmental stages was also determined. Conclusions: Results indicate that the three lines did not differ significantly, except regarding a few morphological aspects such as plant height, flower colour and number of male cyathia. Pollen grains were initially viable, but viability decreased drastically at later stages of growth. Abnormal meiosis or mitosis triggered pollen trimorphism. The demonstrated sequential events of reproductive development generated valuable information at the cellular level, which will help close the current information gap for cassava improvement via breeding programmes and doubled haploid plant production. © 2013 The Authors. Source

Datta S.,Indian Institute of Pulses Research | Tiwari S.,Azad University of Agriculture and Technology | Kaashyap M.,Indian Institute of Pulses Research | Gupta P.P.,Indian Institute of Pulses Research | And 3 more authors.
Crop Science | Year: 2011

Molecular markers have emerged as useful tools to assess the genetic diversity across crops. In lentil, molecular markers are limited. The objective of the study was to explore crossgenera transferability of sequence tagged microsatellite site (STMS) markers from related legumes and assess their utility in lentils. Thirty lentil (Lens culinaris Medik. subsp. culinaris) accessions were evaluated for genetic similarity analysis using cross-genera STMS markers. Thirty-nine STMS markers amplified 68 alleles with an average of 1.74 alleles per locus. Twenty lentil-specific STMS markers produced a total of 36 amplicons, of which 90% (18) markers were polymorphic. A maximum of four alleles were obtained with primers SSR13 and SSR19. Of 47 STMS markers from other legume genera, only 19 markers produced 32 scorable amplicons, and only 58% (11) of the amplified markers exhibited polymorphism. The polymorphism information content values observed with lentil specific markers ranged from 0.02 to 0.99, while for transferrable markers it ranged from 0.06 to 0.84. Maximum genetic similarity was observed between 'NDL1' and 'LH84-8' (0.942) and minimum between 'PL234' and 'Precoz' (0.709). The dendrogram based on Jaccard's similarity coefficients showed limited genetic variability among the cultivars included in the present study. A combination of lentil-specific and transferrable STMS markers was successfully used for identification of genetic similarity in lentil germplasm. © Crop Science Society of America. Source

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