Purabi Mazumdar

Excess copper induced oxidative stress and response of antioxidants in rice.

To investigate the effects of copper (Cu), rice plant (Oryza sativa. L. var. MSE-9) was treated with different Cu concentrations (0, 10, 50 and 100 μM) for 5 days in hydroponic condition. Gradual decrease in shoot and root growth was observed with the increase of Cu concentration and duration of treatment where maximum inhibition was recorded in root growth. Cu was readily absorbed by the plant though the maximum accumulation was found in root than shoot. Hydrogen peroxide (H(2)O(2)) production and lipid peroxidation were found increased with the elevated Cu concentration indicating excess Cu induced oxidative stress. Antioxidant enzymes superoxide dismutase (SOD), guaiacol peroxidase (GPX) and ascorbate peroxidase (APX) and glutathione reductase (GR) were effectively generated at the elevated concentrations of Cu though catalase (CAT) did not show significant variation with respect to control. Ascorbate (ASH), glutathione (GSH) and proline contents were also increased in all the Cu treated plants compared with the control. SOD isoenzyme was greatly affected by higher concentration of Cu and it was consistent with the changes of the activity assayed in solution. The present study confirmed that excess Cu inhibits growth, induced oxidative stress by inducing ROS formation while the stimulated antioxidative system appears adaptive response of rice plant against Cu induced oxidative stress. Moreover proline accumulation in Cu stress plant seems to provide additional defense against the oxidative stress.

Efficient in vitro plant regeneration from shoot apices and gene transfer by particle bombardment in Jatropha curcas

An efficient and reproducible in vitro plant regeneration system from shoot apices was developed in Jatropha curcas. Benzylaminopurine (BAP; 2.5 μM) was most effective in inducing an average of 6.2 shoots per shoot apex. Incorporation of gibberellic acid (GA3; 0.5 μM) to basal medium was found essential for elongation of shoots. The BAP-habituated mother explants continuously produced shoots during successive subculture without any loss of morphogenic potential. The shoots rooted efficiently on half-strength MS medium. The rooted plantlets were acclimatized with more than 98 % success and the plants transferred to soil:compost in nursery showed no sign of variation compared to the seed-grown plants. The whole process of culture initiation to plant establishment was accomplished within 5–6 weeks. A genetic transformation system in J. curcas was established for the first time, using bombardment of particles coated with plasmid pBI426 with a GUS-NPT II fusion protein under the control of a double 35S cauliflower mosaic virus (CaMV) promoter. The β-glucuronidase (GUS) activity in J. curcas shoot apices was significantly affected by the gold particle size, bombardment pressure, target distance, macrocarrier travel distance, number of bombardments, and type and duration of osmotic pre-treatment. The proliferating bombarded shoot apices were screened on medium supplemented with 25 mg dm−3 kanamycin and surviving shoots were rooted on medium devoid of kanamycin. The integration of the transgene into genomic DNA of transgenic plants was confirmed by PCR and Southern blot hybridization. The transgenic plants showed insertion of single to multiple copies of the transgene.

Effect of storage parameters on stability of Jatropha-derived biodiesel

Jatropha curcas L. seeds as a raw material for biodiesel production is a rapidly growing interest over the world because of its high oil content, ecological adaptability, and excellent fuel properties. Though there is an increase in productivity of biodiesel, showing solution for future energy insecurity, there still remains some concern for commercialization due to its susceptibility to degradation during long storage. The aim of this paper is to investigate the effect of temperature and ambient condition on Jatropha biodiesel storage. An experiment was conducted for a period of 12 months, where Jatropha biodiesel stored in three groups at different temperatures (4°C, 25°C, and 35°C) and environmental conditions (exposed in dark, light, and air). At regular intervals, the samples were taken out to analyze acid value, density, kinematic viscosity, and thermogravimetric profile to monitor the quality of biodiesel. Analysis showed that acid value, density, kinematic viscosity, and the onset temperature of volatilization and distillation increases with the increase in storage time of biodiesel samples. However, Jatropha biodiesel stored at 35°C, in contact with ambient air and light showed highest degradation compared to those which were stored at 25°C and 4°C. Among all the parameters studied, high temperature and air exposure are the two most potent parameters which accelerate the degradation process. Along with that, light exposure had mild but significant effect on Jatropha biodiesel degradation over a long storage period.

Crude extracts of bacterially-expressed dsRNA protect orchid plants against Cymbidium mosaic virus during transplantation from in vitro culture

Summary Cymbidium mosaic virus (CymMV) is one of the most prevalent viruses infecting and causing damage to orchids. As tissue culture methods are widely used for commercial orchid production, CymMV infection commonly occurs during transplantation and pruning, so the protection of plants during these stages would be of value to the industry. Double-stranded RNA (dsRNA) has been shown to mediate gene silencing via mRNA degradation and the inactivation of both endogenous and virally-expressed genes in plants. In this study, crude bacterial extracts were prepared from an RNase-deficient strain of Escherichia coli, HT115 (DE3), that expressed sense or anti-sense RNA corresponding to the CymMV coat protein gene (CP). A mixture of sense and anti-sense CP RNAs were used to produce dsRNA. Exogenous sense or anti-sense RNA introduced into the leaves of Brassolaeliocattleya hybrida by mechanical inoculation reduced the symptoms of CymMV infection and reduced expression of the CymMV CP RNA in virus-infected plants three-fold (with sense ssRNA) and over seven-fold (with anti-sense ssRNA) compared to the levels in virus-infected control plants with no ssRNA treatment. Most orchid plants infected with CymMV and treated with CymMV CP dsRNA, showed no symptoms of CymMV infection. The levels of expression of the CymMV CP gene in CymMV CP dsRNA-treated plants were 40-fold lower than in virus-infected control plants and similar to the CP RNA levels detected by quantitative RT-PCR in uninfected control orchid plants. These results demonstrate that the application of a crude extract of bacterially-expressed ssRNA or dsRNA corresponding to the CymMV CP gene was able to reduce viral symptoms and levels of CymMV CP RNA in infected orchids. This approach could provide a relatively low-cost method to protect orchid plants during commercial transplantation from tissue culture.

Jatropha ( Jatropha curcas L.)

The seed oil of Jatropha (Jatropha curcas L.) as a source of biodiesel fuel is gaining worldwide importance. Commercial-scale exploration of Jatropha has not succeeded due to low and unstable seed yield in semiarid lands unsuitable for the food production and infestation to diseases. Genetic engineering is promising to improve various agronomic traits in Jatropha and to understand the molecular functions of key Jatropha genes for molecular breeding. We describe a protocol routinely followed in our laboratory for stable and efficient Agrobacterium tumefaciens-mediated transformation of Jatropha using cotyledonary leaf as explants. The 4-day-old explants are infected with Agrobacterium tumefaciens strain EHA105 harboring pBI121 plant binary vector, which contains nptII as plant selectable marker and gus as reporter. The putative transformed plants are selected on kanamycin, and stable integration of transgene(s) is confirmed by histochemical GUS assay, polymerase chain reaction, and Southern hybridization.

QCM Coupled Resonating Systems Under Vacuum: Sensitivity and Characteristics

We present the underlying physics in the resonance frequency characteristics of a bare quartz crystal microbalance (QCM) and a QCM-micro pillar based coupled resonator sensor (QCM-CRS) when they were subjected to pressure changes in a vacuum chamber. The QCMs experienced an increase in resonance frequency with decrease in pressure due to an inverse mass loading effect introduced on the QCM surface. However, when the pressure (below atmospheric pressure) dominated the mass loading, the resonance frequency of QCMs decreased. A sensitivity increase of 11 times to the pressure changes was observed for the case of QCM-CRS made of resonating micropillars attached around the central region of the electrode. In addition, the resonance frequency shift was linear for pressure changes between 31 and 71 kPa, demonstrating the possibility of employing the QCM-CRS as a vacuum detector element. The proposed sensor element is envisioned to have wide industrial applications ranging from detecting vacuum in chambers used in coating systems to crack detection in closed chambers.

Codon usage and codon pair patterns in non-grass monocot genomes

Background and AimsnStudies on codon usage in monocots have focused on grasses, and observed patterns of this taxon were generalized to all monocot species. Here, non-grass monocot species were analysed to investigate the differences between grass and non-grass monocots.nnnMethodsnFirst, studies of codon usage in monocots were reviewed. The current information was then extended regarding codon usage, as well as codon-pair context bias, using four completely sequenced non-grass monocot genomes (Musa acuminata, Musa balbisiana, Phoenix dactylifera and Spirodela polyrhiza) for which comparable transcriptome datasets are available. Measurements were taken regarding relative synonymous codon usage, effective number of codons, derived optimal codon and GC content and then the relationships investigated to infer the underlying evolutionary forces.nnnKey ResultsnThe research identified optimal codons, rare codons and preferred codon-pair context in the non-grass monocot species studied. In contrast to the bimodal distribution of GC3 (GC content in third codon position) in grasses, non-grass monocots showed a unimodal distribution. Disproportionate use of G and C (and of A and T) in two- and four-codon amino acids detected in the analysis rules out the mutational bias hypothesis as an explanation of genomic variation in GC content. There was found to be a positive relationship between CAI (codon adaptation index; predicts the level of expression of a gene) and GC3. In addition, a strong correlation was observed between coding and genomic GC content and negative correlation of GC3 with gene length, indicating a strong impact of GC-biased gene conversion (gBGC) in shaping codon usage and nucleotide composition in non-grass monocots.nnnConclusionnOptimal codons in these non-grass monocots show a preference for G/C in the third codon position. These results support the concept that codon usage and nucleotide composition in non-grass monocots are mainly driven by gBGC.

Genome-Wide Regulatory Network Mapping of miRNA and Transcription Factors in Banana Roots

MicroRNA (miRNA) are important regulators of gene expression. Plant miRNA have been reported both to target and to be regulated by transcription factors, however, genomic distribution of miRNA, transcription factor targets for miRNA, transcription factor binding sites (TFBS) of miRNA promoters and their regulatory networks have not been systematically mapped in banana. In this study, genome-wide annotation of miRNA in the most recently published banana genome sequence was used to predict miRNA promoter regions and to map TFBS of miRNA genes. A total of 183 mature miRNAs, comprising 144 orthologous miRNA and 39 Musa-specific miRNA were predicted. Following this, banana root degradome data was used to confirm miRNA targets and the transcription factor targets were placed into a predicted network together with their targeting miRNA using cytoscape. Gene ontology of the 20 transcription factors among the predicted miRNA targets, showed predominance for auxin-activated signalling and developmental processes. Profiling of TFBS motifs across miRNA promoter regions showed that binding site motifs for TCP, AP2/ERF, GATA, NF-YB, DOF, B3, bZIP, trihelix, ZF-HD, bHLH and Dehydrin transcription factor families are abundant in the Musa acuminata genome. Finally, we propose a regulatory network for the miRNA families miR156, miR164, miR166, miR171, miR319, miR396, miR528, mac-miR-new14 and mac-miR-new20 and their respective transcription factor targets.

Ectopic expression of a Musa acuminata root hair defective 3 (MaRHD3) in Arabidopsis enhances drought tolerance

Genetic improvement is an important approach for crop improvement towards yield stability in stress-prone areas. Functional analysis of candidate stress response genes can provide key information to allow the selection and modification of improved crop varieties. In this study, the constitutive expression of a banana cDNA, MaRHD3 in Arabidopsis improved the ability of transgenic lines to adapt to drought conditions. Transgenic Arabidopsis plants expressing MaRHD3 had roots with enhanced branching and more root hairs when challenged with drought stress. The MaRHD3 plants had higher biomass accumulation, higher relative water content, higher chlorophyll content and an increase in activity of reactive oxygen species (ROS) scavenging enzymes; SOD, CAT, GR, POD and APX with reduced water loss rates compared to control plants. The analysis of oxidative damage indicated lower cell membrane damage in transgenic lines compared to control plants. These findings, together with data from higher expression of ABF-3 and higher ABA content of drought-stressed transgenic MaRHD3 expressing plants, support the involvement of the ABA signal pathway and ROS scavenging enzyme systems in MaRHD3 mediated drought tolerance.

Genome-wide Analysis of the CCCH Zinc-Finger Gene Family in Banana (Musa acuminata): An Insight Into Motif and Gene Structure Arrangement, Evolution and Salt Stress Responses

The CCCH zinc finger proteins contain a signature motif comprising of three cysteine and one histidine residues. Increasing evidence suggests that members of this large family regulate the transcription of genes that participate in plant growth and development as well as responses to environmental stresses including salt stress in plants. However, little is known about this gene family in banana (Musa acuminata), a tropical crop that is globally consumed and is highly sensitive to salt stress conditions. Here, we present the genome-wide identification of the CCCH Zinc-Finger (CCCH-ZF) gene family in banana. We identified 89 CCCH-ZFP (MaZFP) genes and evaluated their phylogenetic relationships. Our analysis showed that this gene family encodes proteins with variable lengths and highly conserved motif structures. Distribution mapping of this gene family revealed that MaZFP genes are unevenly dispersed on the 11 chromosomes with segmental duplication in 15 gene pairs, suggesting an important contribution of duplication in expansion of this gene family in banana. Expression analysis of four selected MaZFP genes in leaf and root tissues of banana showed temporal and spatial expression in response to salt stress conditions with high transcript accumulation in root tissue. The highest level of transcript was measured for MaZFP88 in root tissues sampled 24xa0h after treatment with 100xa0mM NaCl. The analysis presented here provides a valuable reference for future functional studies of MaZFP genes with the potential for use in developing salt-tolerant banana varieties.