Pradhyumna Kumar Singh

National Botanical Research Institute - India, Lakhnau, Uttar Pradesh, India

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Publications (19)56.5 Total impact

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    ABSTRACT: Biological significance: Insects cause major loss to crop productivity through direct and indirect damages. Among them, hemipteran group of insects are major contributor of global crop yield loss. In current study, gel based proteome profile of B.tabaci (one of the major hemipteran crop insect pest) is developed and characterized, which is a gap area in field of whitefly biology. It is an important data set of future whitefly studies like insect-plant interaction, virulence of whiteflies, their control program, and discovery of new pesticides. Out of various control strategies, RNA interference offers a great potential to combat the whitefly successfully. However, the uniqueness of target genes and off target impact of the technology remains a challenge to scientific community. We used our proteome data set for the identification of B. tabaci specific gene targets for RNAi mediated control. The identified genes are critical for the life cycle of B. tabaci hence, could be proven as good molecules for making transgenic crop plant for efficient control of whiteflies in the field.
    No preview · Article · Dec 2015 · Journal of proteomics
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    ABSTRACT: Previous studies have reported that lindane, an organochlorine pesticide induces oxidative stress in rat brain that may lead to neurodegeneration. However, as the proteins involved in lindane induced neurodegeneration are yet to be identified, the present study aims to identify the proteins that may regulate lindane induced neurotoxicity. The data showed that repeated exposure of lindane (2.5mg/kg) for 21 days to adult rats significantly increased the reactive oxygen species and lipid peroxidation in different brain regions. Proteomic study revealed that lindane induces major dysregulation in the ubiquitin proteasome pathway. Alterations in the expression of molecular chaperones in brain regions and an increase in the expression of α-synuclein in substantia-nigra and corpus striatum and amyloid precursor protein (APP) in hippocampus and frontal cortex suggests the accumulation of proteins in these brain regions. Western blotting also revealed alterations in the dopaminergic and cholinergic pathways in hippocampus and substantia nigra isolated from lindane treated rats. Neurobehavioral data indicating alterations in learning and working memory, conditioned avoidance response and motor function, supports the proteomic data. The data suggests that repeated exposure of lindane to adult rats induces alterations, which are similar to that seen in neurodegenerative diseases. This article is protected by copyright. All rights reserved.
    Full-text · Article · Sep 2015 · Proteomics
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    ABSTRACT: Bryophytes are the first land plants but are scarcely studied at the molecular level. Here, we report transcriptome sequencing and functional annotation of Dumortiera hirsuta, as a representative bryophyte. Approximately 0.5 million reads with ~195 Mb data were generated by sequencing of mRNA using 454 pyrosequencer. De novo assembly of reads yielded 85,240 unigenes (12,439 contigs and 72,801 singletons). BlastX search at NCBI-NR database showed similarity of 33,662 unigenes with 10-10 e-value. A total of 23,685 unigenes were annotated at TAIR10 protein database. The annotated unigenes were further classified using the Gene Ontology. Analysis at Kyoto Encyclopedia of Genes and Genomes pathway database identified 95 pathways with significant scores, among which metabolic and biosynthesis of secondary metabolite were the major ones. Phenylpropanoid pathway was elucidated and selected genes were characterized by real time qPCR. We identified 447 transcription factors belonging to 41 families and 1594 eSSRs in 1479 unigenes. D. hirsuta unigenes showed homology across the taxa from algae to angiosperm indicating their role as the connecting link between aquatic and terrestrial plants. This could be a valuable genomic resource for molecular and evolutionary studies. Further, it sheds light for the isolation and characterization of new genes with unique functions.
    Full-text · Article · Sep 2015 · Scientific Reports
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    ABSTRACT: Isoniazid is used either alone or in combination with other drugs for the treatment of tuberculosis. It is also used for the prevention of tuberculosis. Chronic treatment of Isoniazid may cause severe liver damage leading to acute liver failure. The mechanism through which Isoniazid causes liver damage is investigated. Isoniazid treatment generates reactive oxygen species and induces apoptosis in Hep3B cells. It induces antioxidative and apoptotic genes leading to increase in mRNA expression and protein levels in Hep3B cells. Whole genome expression analysis of Hep3B cells treated with Isoniazid has resulted in differential expression of various genes playing prime role in regulation of apoptotic, antioxidative, DNA damage, cell signaling, cell proliferation and differentiation pathways. Isoniazid increased cytosolic Nrf2 protein level while decreased nuclear Nrf2 protein level. It also decreased ERK1 phosphorylation and treatment of Hep3B cells with ERK inhibitor followed by Isoniazid resulting in increased apoptosis in these cells. Two dimensional gel electrophoresis results have also shown differential expression of various protein species including heat shock proteins, proteins playing important role in oxidative stress, DNA damage, apoptosis, cell proliferation and differentiation. Results suggest that Isoniazid induces apoptosis through oxidative stress and also prevents Nrf2 translocation into the nucleus by reducing ERK1 phosphorylation thus preventing cytoprotective effect. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.
    Full-text · Article · Aug 2015
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    ABSTRACT: An inexpensive source of industrially useful enzymes is critical for their commercial production. We have produced an industrially valuable recombinant superoxide dismutase (SOD) in tobacco chloroplasts. A gene from Withania somnifera, encoding a highly stable Cu/Zn SOD, was cloned into a chloroplast transformation vector. It expressed the SOD in tobacco chloroplasts following transformation. The transplastomic plants accumulated the recombinant SOD at up to ∼9 % of the total soluble protein in leaves. The purified chloroplast-expressed recombinant SOD had an estimated specific activity of ∼4600 U/mg. Like the native enzyme, purified recombinant enzyme, prepared from tobacco leaves, was highly stable at high temperatures and tolerated a wide pH range, SDS, ethanol and protease treatment. The results establish the potential of chloroplast transformation for commercial production of recombinant SOD in plants.
    Full-text · Article · Nov 2014 · Plant Molecular Biology Reporter
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    ABSTRACT: Cypermethrin induces the slow and progressive degeneration of the nigrostriatal dopaminergic neurons in rats. Postnatal preexposure with low doses of cypermethrin is known to enhance the susceptibility of animals upon adulthood reexposure. The study was undertaken to delineate the role of mitochondria in cypermethrin-induced neurodegeneration. Indexes of dopaminergic neurodegeneration, microglial activation, and mitochondrial dysfunction and its proteome profile were assessed in controls and cypermethrin-treated rats. Cypermethrin increased nigral dopaminergic neurodegeneration and microglial activation while reduced mitochondrial membrane potential and complex I activity. Cypermethrin attenuated striatal dopamine content and differentially regulated the expressions of the nine striatal and ten nigral proteins. Western blot analyses showed that cypermethrin also increased c-Jun N-terminal kinase (JNK), caspase-3, tumor suppressor protein (p53), tumor necrosis factor-α (TNF-α), p38 mitogen-activated protein kinase (p38 MAPK), and heme oxygenase-1 (HO-1) expressions and reduced B cell lymphoma-2 protein (Bcl-2) expression. Syndopa and minocycline rescued from cypermethrin induced augmentation in microglial activation and reductions in mitochondrial membrane potential and complex I activity, striatal dopamine content, and degeneration of nigral dopaminergic neurons. Syndopa and minocycline, respectively, modulated the expressions of four and six striatal and four and seven nigral proteins. Furthermore, they reinstated the expressions of JNK, caspase-3, Bcl-2, p53, p38 MAPK, TNF-α, and HO-1. The study demonstrates that cypermethrin induces mitochondrial dysfunction and alters mitochondrial proteome leading to oxidative stress and apoptosis, which regulate the nigrostriatal dopaminergic neurodegeneration.
    Full-text · Article · Apr 2014 · Molecular Neurobiology
  • Harpal Singh · Sameer Dixit · Praveen Chandra Verma · Pradhyumna Kumar Singh
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    ABSTRACT: Tomatoes are one of the most consumed crops in the whole world because of their versatile importance in dietary food as well as many industrial applications. They are also a rich source of secondary metabolites, such as phenolics and flavonoids. In the present study, we described a method to produce these compounds from hairy roots of tomato (THRs). Agrobacterium rhizogenes strain A4 was used to induce hairy roots in the tomato explants. The Ri T-DNA was confirmed by polymerase chain reaction amplification of the rolC gene. Biomass accumulation of hairy root lines was 1.7-3.7-fold higher compared to in vitro grown roots. Moreover, THRs efficiently produced several phenolic compounds, such as rutin, quercetin, kaempferol, gallic acid, protocatechuic acid, ferulic acid, colorogenic acid, and caffeic acid. Gallic acid [34.02 μg/g of dry weight (DW)] and rutin (20.26 μg/g of DW) were the major phenolic acid and flavonoid produced by THRs, respectively. The activities of reactive oxygen species enzymes (catalase, ascorbate peroxidase, and superoxide dismutase) were quantified. The activity of catalase in THRs was 0.97 ± 0.03 mM H2O2 min(-1) g(-1), which was 1.22-fold (0.79 ± 0.09 mM H2O2 min(-1) g(-1)) and 1.59-fold (0.61 ± 0.06 mM H2O2 min(-1) g(-1)) higher than field grown and in vitro grown roots, respectively. At 100 μL/g concentration, the phenolic compound extract caused 53.34 and 40.00% mortality against Helicoverpa armigera and Spodoptera litura, respectively, after 6 days. Surviving larvae of H. armigera and S. litura on the phenolic compound extract after 6 days showed 85.43 and 86.90% growth retardation, respectively.
    No preview · Article · Mar 2014 · Journal of Agricultural and Food Chemistry
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    ABSTRACT: Embryogenesis in cotton is a difficult task due its genome dependency. We used 3 cotton cultivars (Khandwa-2, G. Cot. 10, and BC-68-2) and Coker-312 as control for regeneration. Efficient somatic embryogenesis was induced in agronomically important Indian cotton cultivars, Khandwa-2 and G. Cot. 10. For callusing in all the cultivars, different media combinations were tried. Embryogenesis was initiated on a hormone-free MS medium (MSB). For embryo maturation and recovery excess of L-glutamine and l-asparagine were used. Khandwa-2 somatic embryos were successfully regenerated into plants. However, no plantlet was obtained in case of G. Cot. 10. Callus induction was also observed in BC-68-2 but there was no embryogenesis observed. The study indicated that the medium and genotype significantly effects embryogenesis. An efficient protocol is described here for regenerating plants via somatic embryogenesis in an elite Indian cotton cultivar Khandwa-2.
    Full-text · Article · Oct 2013 · Plant signaling & behavior
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    Harpal Singh · Sameer Dixit · Pradhyumna Kumar Singh · Praveen Chandra Verma
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    ABSTRACT: Peroxidases are the ubiquitous enzyme and reported to be present in all living genera. They catalyses reduction of peroxide and generate reactive oxygen species. In the present study we demonstrated that insect infestation induces peroxidase activity in sap and total soluble protein (TSP) of plant leaves. Three important crop plants viz. tomato, cowpea and cotton were used for this study. After infestation of chewing insect, Peroxidase activity in the sap and TSP of all the studied plants were enhanced in the range of 1.6 to 3.14 fold. Similar observations were also obtained with feeding of sap sucking insects, in which increment in peroxidase activity of sap and TSP was in the range of 1.8 to 2.53 fold. Enhanced peroxidase activity was reconfirmed by in-gel peroxidase assay. Enzyme kinetic study showed turn over efficiency of peroxidase from cotton (~101.3 min (-1) ) was almost similar to tomato (~100.8 min (-1) ) but higher than cowpea (~98.21min (-1) ). MS/MS analysis of observed band showed significant similarity with the reported peroxidases in database.
    Full-text · Article · Jul 2013 · Plant signaling & behavior
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    ABSTRACT: Background Cotton (Gossypium hirsutum L.) is a major fiber crop that is grown worldwide; it faces extensive damage from sap-sucking insects, including aphids and whiteflies. Genome-wide transcriptome analysis was performed to understand the molecular details of interaction between Gossypium hirsutum L. and sap-sucking pests, namely Aphis gossypii (Aphid) and Bemisia tabacci (Whiteflies). Roche’s GS-Titanium was used to sequence transcriptomes of cotton infested with aphids and whiteflies for 2 h and 24 h. Results A total of 100935 contigs were produced with an average length of 529 bp after an assembly in all five selected conditions. The Blastn of the non-redundant (nr) cotton EST database resulted in the identification of 580 novel contigs in the cotton plant. It should be noted that in spite of minimal physical damage caused by the sap-sucking insects, they can change the gene expression of plants in 2 h of infestation; further change in gene expression due to whiteflies is quicker than due to aphids. The impact of the whitefly 24 h after infestation was more or less similar to that of the aphid 2 h after infestation. Aphids and whiteflies affect many genes that are regulated by various phytohormones and in response to microbial infection, indicating the involvement of complex crosstalk between these pathways. The KOBAS analysis of differentially regulated transcripts in response to aphids and whiteflies indicated that both the insects induce the metabolism of amino acids biosynthesis specially in case of whiteflies infestation at later phase. Further we also observed that expression of transcript related to photosynthesis specially carbon fixation were significantly influenced by infestation of Aphids and Whiteflies. Conclusions A comparison of different transcriptomes leads to the identification of differentially and temporally regulated transcripts in response to infestation by aphids and whiteflies. Most of these differentially expressed contigs were related to genes involved in biotic, abiotic stresses and enzymatic activities related to hydrolases, transferases, and kinases. The expression of some marker genes such as the overexpressors of cationic peroxidase 3, lipoxygenase I, TGA2, and non-specific lipase, which are involved in phytohormonal-mediated plant resistance development, was suppressed after infestation by aphids and whiteflies, indicating that insects suppressed plant resistance in order to facilitate their infestation. We also concluded that cotton shares several pathways such as phagosomes, RNA transport, and amino acid metabolism with Arabidopsis in response to the infestation by aphids and whiteflies.
    Full-text · Article · Apr 2013 · BMC Genomics
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    ABSTRACT: Mitochondrial dysfunction is the foremost perpetrator of the nigrostriatal dopaminergic neurodegeneration leading to Parkinson's disease (PD). However, the roles played by majority of the mitochondrial proteins in PD pathogenesis have not yet been deciphered. Present study investigated the effects of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and combined maneb and paraquat on the mitochondrial proteome of the nigrostriatal tissues in the presence or absence of minocycline, levodopa and manganese (III) tetrakis (1-methyl-4-pyridyl) porphyrin (MnTMPyP). The differentially expressed proteins were identified and proteome profiles were correlated with the pathological and biochemical anomalies induced by MPTP and maneb and paraquat. MPTP altered the expression of twelve while combined maneb and paraquat altered the expression of fourteen proteins. Minocycline, levodopa and MnTMPyP, respectively, restored the expression of three, seven and eight proteins in MPTP and seven, eight and eight proteins in maneb- and paraquat-treated groups. Although levodopa and MnTMPyP rescued from MPTP- and maneb- and paraquat-mediated increase in the microglial activation and decrease in Mn-SOD expression and complex I activity, dopamine content and number of dopaminergic neurons, minocycline defended mainly against maneb- and paraquat-mediated alterations. The results demonstrate that MPTP and combined maneb and paraquat induce mitochondrial dysfunction and microglial activation and alter the expression of a bunch of mitochondrial proteins leading to the nigrostriatal dopaminergic neurodegeneration and minocycline, levodopa or MnTMPyP variably offset scores of such changes.
    Full-text · Article · Apr 2013 · Biochimica et Biophysica Acta
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    ABSTRACT: Bacteria belonging to α-proteobacteria normally harbour multiple copies of the heat shock sigma factor (σ32 or σH or RpoH). Azospirillum brasilense, a non-photosynthetic rhizobacterium, harbours 5 copies of rpoH genes, out of which one is an rpoH2 homolog. The genes around rpoH2 locus in A. brasilense show synteny with that found in rhizobia. The rpoH2 of A. brasilense was able to complement the temperature sensitive phenotype of the E.coli rpoH mutant. Inactivation of rpoH2 in A. brasilense results in increased sensitivity to methylene blue and to triphenyl tetrazolium chrloride (TTC). Exposure of A. brasilense to TTC and the singlet oxygen generating agent, methylene blue induced the expression of rpoH2 by several fold. Comparison of the proteome of A. brasilense with its rpoH2 deletion mutant and with A. brasilense strain overexpressing rpoH2 revealed chaperone GroEL, Elongation factors (Ef-Tu and EF-G), peptidyl prolyl isomerase, peptide methionine sulfoxide reductase as the major proteins whose expression was controlled by RpoH2. Here, we show that RpoH2 sigma factor controlled photooxidative stress response in the non-photosynthetic bacterium, A. brasilense is similar to that in the photosynthetic bacterium, Rhodobacter sphaeroides but RpoH2 is not involved in the detoxification of methylglyoxal in A. brasilense.
    Full-text · Article · Sep 2012 · Microbiology
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    ABSTRACT: δ-Endotoxins produced by Bacillus thuringiensis (Bt) have been used as bio-pesticides for the control of lepidopteran insect pests. Garlic (Allium sativum L.) leaf agglutinin (ASAL), being toxic to several sap-sucking pests and some lepidopteran pests, may be a good candidate for pyramiding with δ-endotoxins in transgenic plants for enhancing the range of resistance to insect pests. Since ASAL shares the midgut receptors with Cry1Ac in Helicoverpa armigera, there is possibility of antagonism in their toxicity. Our study demonstrated that ASAL increased the toxicity of Cry1Ac against H. armigera while Cry1Ac did not alter the toxicity of ASAL against cotton aphids. The two toxins interacted and increased binding of each other to brush border membrane vesicle (BBMV) proteins and to the two important receptors, alkaline phosphatase (ALP) and aminopeptidase N (APN). The results indicated that the toxins had different binding sites on the ALP and APN but influenced mutual binding. We conclude that ASAL can be safely employed with Cry1Ac for developing transgenic crops for wider insect resistance.
    Full-text · Article · Aug 2011 · Applied Microbiology and Biotechnology
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    ABSTRACT: A gene from Withania somnifera (winter cherry), encoding a highly stable chloroplastic Cu/Zn superoxide dismutase (SOD), was cloned and expressed in Escherichia coli. The recombinant enzyme (specific activity of ~4,200 U mg−1) was purified and characterized. It retained ~90 and ~70% residual activities after 1 h at 80 and 95°C, respectively. At 95°C, thermal inactivation rate constant (K d) of the enzyme was 2.46 × 10−3 min−1 and half-life of heat inactivation was 4.68 h. The enzyme was stable against a broad pH range (2.5–11.0). It also showed a high degree of resistance to detergent, ethanol and protease digestion. This recombinant Cu/Zn SOD could therefore have useful applications.
    Full-text · Article · Jun 2011 · Biotechnology Letters
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    ABSTRACT: RNA interference (RNAi)-mediated gene silencing was explored for the control of sap-sucking pest Bemisia tabaci, commonly known as whitefly. dsRNAs and siRNAs were synthesized from five different genes - actin ortholog, ADP/ATP translocase, alpha-tubulin, ribosomal protein L9 (RPL9) and V-ATPase A subunit. A simplified insect bioassay method was developed for the delivery of ds/siRNA through the oral route, and efficacy was evaluated. ds/siRNA caused 29-97% mortality after 6 days of feeding. Each insect ingested nearly 150 nl of insect diet per day, which contained a maximum of 6 ng of RNA. Knocking down the expression of RPL9 and V-ATPase A caused higher mortality with LC50 11.21 and 3.08 microg/ml, respectively, as compared to other genes. Semi-quantitative PCR of the treated insects showed significant decrease in the level of RPL9 and V-ATPase A transcripts. siRNAs were found stable in the insect diet for at least 7 days at the room temperature. Phloem-specific expression of dsRNAs of RPL9 and V-ATPase A in transgenic plants for the protection against whiteflies might be an interesting application of this technology.
    Full-text · Article · Mar 2011 · Journal of Biosciences
  • Raju Madanala · Vijayta Gupta · Pradhyumna Kumar Singh · Rakesh Tuli
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    ABSTRACT: Plastid transformation vectors are used for high-level expression of industrially important recombinant proteins in plants. In the present study, new vectors for plastid transformation were developed. One of these vectors targets transgenes at a new site in the chloroplast genome. Intergenic regions of trnfM-trnG, ndhB-trnL and rrn16-trnV were selected as sites for transgene insertion. Tobacco chloroplast was successfully transformed with designed vectors, and the transplastomic plants accumulated recombinant protein as high as 5–6% of total soluble protein which remained localized in the chloroplasts. Although the vectors were designed using the plastid genome of Nicotiana tabacum, flanking regions used in two vectors show a high level of homology with chloroplast genomes of other plant species, thus it might be possible to use them for the transformation of a wider range of plant species.
    No preview · Article · Jan 2011 · Plant Biotechnology Reports
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    ABSTRACT: Allium sativum leaf agglutinin (ASAL) binds to several proteins in the midgut of Helicoverpa armigera and causes toxicity. Most of these were glycosylated. Six ASAL-binding proteins were selected for identification. PMF and MS/MS data showed their similarity with midgut aminopeptidase APN2, polycalins and alkaline phosphatase of H. armigera, cadherin-N protein (partial AGAP009726-PA) of Acyrthosiphon pisum, cytochrome P450 (CYP315A1) of Manduca sexta and alkaline phosphatase of Heliothis virescens. Some of the ASAL-binding midgut proteins were similar to the larval receptors responsible for the binding of δ-endotoxin proteins of Bacillus thuringiensis. Galanthus nivalis agglutinin also interacted with most of the ASAL-binding proteins. The ASAL showed resistance to midgut proteases and was detected in the larval hemolymph and excreta. Immunohistochemical staining revealed the presence of ASAL in the body tissue also.
    Full-text · Article · Dec 2010 · Proteomics
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    ABSTRACT: Flavonoids synthesized by the phenylpropanoid pathway participate in myriad physiological and biochemical processes in plants. Due to the diversity of secondary transformations and the complexity of the regulation of branched pathways, single gene strategies have not been very successful in enhancing the accumulation of targeted molecules. We have expressed an Arabidopsis (Arabidopsis thaliana) transcription factor, AtMYB12, in tobacco (Nicotiana tabacum), which resulted in enhanced expression of genes involved in the phenylpropanoid pathway, leading to severalfold higher accumulation of flavonols. Global gene expression and limited metabolite profiling of leaves in the transgenic lines of tobacco revealed that AtMYB12 regulated a number of pathways, leading to flux availability for the phenylpropanoid pathway in general and flavonol biosynthesis in particular. The tobacco transgenic lines developed resistance against the insect pests Spodoptera litura and Helicoverpa armigera due to enhanced accumulation of rutin. Suppression of flavonol biosynthesis by artificial microRNA reversed insect resistance of the AtMYB12-expressing tobacco plants. Our study suggests that AtMYB12 can be strategically used for developing safer insect pest-resistant transgenic plants.
    Full-text · Article · Feb 2010 · Plant physiology

  • No preview · Article · Mar 2009 · Biotechnology Journal