@article{sivamani_delong_qu_2009, title={Protamine-mediated DNA coating remarkably improves bombardment transformation efficiency in plant cells}, volume={28}, ISSN={["1432-203X"]}, DOI={10.1007/s00299-008-0636-4}, abstractNote={We have developed a method by which remarkably higher efficiencies of transient and stable transformation were achieved in bombardment transformation of plants. Over fivefold increase in transient gus gene expression was achieved when rice or maize suspension cells were bombarded with gold particles coated with plasmid DNA in the presence of protamine instead of the conventional spermidine. A 3.3-fold improvement in stable transformation efficiency was also observed using rice suspension cells with the new coating approach. The coated protamine-plasmid DNA complex resisted degradation by a DNase or by rice cell extract much longer than the spermidine-plasmid DNA complex. The results from this study suggest that protamine protects plasmid DNA longer than spermidine when being delivered inside the cells, probably by forming a nano-scale complex, and thus helps improve the efficiency of particle bombardment-mediated plant transformation.}, number={2}, journal={PLANT CELL REPORTS}, author={Sivamani, Elumalai and DeLong, Robert K. and Qu, Rongda}, year={2009}, month={Feb}, pages={213–221} }
 @article{sivamani_starmer_qu_2009, title={Sequence analysis of rice rubi3 promoter gene expression cassettes for improved transgene expression}, volume={177}, ISSN={["0168-9452"]}, DOI={10.1016/j.plantsci.2009.08.006}, abstractNote={In a construct containing a GUS reporter gene driven by the 5′ regulatory elements from rubi3, expression was enhanced 4-fold when a 20-nucleotide (nt) GUS 5′ untranslated sequence was replaced with 9 nt sequences derived from rubi3′s second exon. The roles of the sequences immediately upstream from the GUS translation initiation codon, and their significance in gene expression, were investigated. Sequence analysis suggests that complementarity between sequences immediately 5′ of a translation initiation codon and the rice 17S rRNA may be responsible for the reduction in protein levels from constructs containing the GUS leader sequence. The results demonstrate an affect sequences immediately upstream from transgenic coding sequences have on expression, and when using the rubi3 5′ regulatory sequence in particular.}, number={6}, journal={PLANT SCIENCE}, author={Sivamani, Elumalai and Starmer, Joshua D. and Qu, Rongda}, year={2009}, month={Dec}, pages={549–556} }
 @article{lu_sivamani_li_qu_2008, title={Activity of the 5 ' regulatory regions of the rice polyubiquitin rubi3 gene in transgenic rice plants as analyzed by both GUS and GFP reporter genes}, volume={27}, ISSN={["1432-203X"]}, DOI={10.1007/s00299-008-0577-y}, abstractNote={Ubiquitin is an abundant protein involved in protein degradation and cell cycle control in plants and rubi3 is a polyubiquitin gene isolated from rice (Oryza sativa L.). Using both GFP and GUS as reporter genes, we analyzed the expression pattern of the rubi3 promoter as well as the effects of the rubi3 5'-UTR (5' untranslated region) intron and the 5' terminal 27 bp of the rubi3 coding sequence on the activity of the promoter in transgenic rice plants. The rubi3 promoter with the 5'-UTR intron was active in all the tissue and cell types examined and supported more constitutive expression of reporter genes than the maize Ubi-1 promoter. The rubi3 5'-UTR intron mediated enhancement on the activity of its promoter in a tissue-specific manner but did not alter its overall expression pattern. The enhancement was particularly intense in roots, pollen grains, inner tissue of ovaries, and embryos and aleurone layers in maturing seeds. The translational fusion of the first 27 bp of the rubi3 coding sequence to GUS gene further enhanced GUS expression directed by the rubi3 promoter in all the tissues examined. The rubi3 promoter should be an important addition to the arsenal of strong and constitutive promoters for monocot transformation and biotechnology.}, number={10}, journal={PLANT CELL REPORTS}, author={Lu, Jianli and Sivamani, Elumalai and Li, Xianggan and Qu, Rongda}, year={2008}, month={Oct}, pages={1587–1600} }
 @article{dong_shew_tredway_lu_sivamani_miller_qu_2008, title={Expression of the bacteriophage T4 lysozyme gene in tall fescue confers resistance to gray leaf spot and brown patch diseases}, volume={17}, ISSN={["1573-9368"]}, DOI={10.1007/s11248-007-9073-3}, abstractNote={Tall fescue (Festuca arundinacea Schreb.) is an important turf and forage grass species worldwide. Fungal diseases present a major limitation in the maintenance of tall fescue lawns, landscapes, and forage fields. Two severe fungal diseases of tall fescue are brown patch, caused by Rhizoctonia solani, and gray leaf spot, caused by Magnaporthe grisea. These diseases are often major problems of other turfgrass species as well. In efforts to obtain tall fescue plants resistant to these diseases, we introduced the bacteriophage T4 lysozyme gene into tall fescue through Agrobacterium-mediated genetic transformation. In replicated experiments under controlled environments conducive to disease development, 6 of 13 transgenic events showed high resistance to inoculation of a mixture of two M. grisea isolates from tall fescue. Three of these six resistant plants also displayed significant resistance to an R. solani isolate from tall fescue. Thus, we have demonstrated that the bacteriophage T4 lysozyme gene confers resistance to both gray leaf spot and brown patch diseases in transgenic tall fescue plants. The gene may have wide applications in engineered fungal disease resistance in various crops.}, number={1}, journal={TRANSGENIC RESEARCH}, author={Dong, Shujie and Shew, H. David and Tredway, Lane P. and Lu, Jianli and Sivamani, Elumalai and Miller, Eric S. and Qu, Rongda}, year={2008}, month={Feb}, pages={47–57} }
 @article{lu_sivamani_azhakanandam_samadder_li_qu_2008, title={Gene expression enhancement mediated by the 5 ' UTR intron of the rice rubi3 gene varied remarkably among tissues in transgenic rice plants}, volume={279}, ISSN={["1617-4615"]}, DOI={10.1007/s00438-008-0333-6}, abstractNote={Introns are important sequence elements that modulate the expression of genes. Using the GUS reporter gene driven by the promoter of the rice (Oryza sativa L.) polyubiquitin rubi3 gene, we investigated the effects of the 5' UTR intron of the rubi3 gene and the 5' terminal 27 bp of the rubi3 coding sequence on gene expression in stably transformed rice plants. While the intron enhanced GUS gene expression, the 27-bp fused to the GUS coding sequence further augmented GUS expression level, with both varying among different tissues. The intron elevated GUS gene expression mainly at mRNA accumulation level, but also stimulated enhancement at translational level. The enhancement on mRNA accumulation, as determined by realtime quantitative RT-PCR, varied remarkably with tissue type. The augmentation by the intron at translational level also differed by tissue type, but to a lesser extent. On the other hand, the 27-bp fusion further boosted GUS protein yield without affecting mRNA accumulation level, indicating stimulation at translation level, which was also affected by tissue type. The research revealed substantial variation in the magnitudes of intron-mediated enhancement of gene expression (IME) among tissues in rice plants and the importance of using transgenic plants for IME studies.}, number={6}, journal={MOLECULAR GENETICS AND GENOMICS}, author={Lu, Jianli and Sivamani, Elumalai and Azhakanandam, Kasi and Samadder, Partha and Li, Xianggan and Qu, Rongda}, year={2008}, month={Jun}, pages={563–572} }
 @article{dong_tredway_shew_wang_sivamani_qu_2007, title={Resistance of transgenic tall fescue to two major fungal diseases}, volume={173}, ISSN={["0168-9452"]}, DOI={10.1016/j.plantsci.2007.08.002}, abstractNote={Tall fescue (Festuca arundinacea Schreb.) is an open-pollinated, perennial, cool-season turf and forage grass species of great economic importance. The main problems of maintenance of tall fescue, and many other turfgrasses, are two severe fungal diseases: gray leaf spot caused by Magnaporthe grisea, and brown patch caused by Rhizoctonia solani. Three genes from various sources have been introduced into two elite cultivars, ‘Coronado’ and ‘Matador’, of tall fescue through Agrobacterium-mediated transformation, and conferred resistance to the diseases. Two genes, the alfalfa β-1,3-glucanase AGLU1 gene and a truncated frog dermaseptin SI gene, conferred resistance to both diseases. The rice Pi9 gene was specific against gray leaf spot. Of 15 T0 transgenic plants examined, 6 showed high levels of resistance to M. grisea, and 3 had enhanced resistance to R. solani. The resistance in most of these cases was highly significant.}, number={5}, journal={PLANT SCIENCE}, author={Dong, Shujie and Tredway, Lane P. and Shew, H. David and Wang, Guo-Liang and Sivamani, Elumalai and Qu, Rongda}, year={2007}, month={Nov}, pages={501–509} }
 @article{sivamani_qu_2006, title={Expression enhancement of a rice polyubiquitin gene promoter}, volume={60}, ISSN={["1573-5028"]}, DOI={10.1007/s11103-005-3853-z}, abstractNote={An 808 bp promoter from a rice polyubiquitin gene, rubi3, has been isolated. The rubi3 gene contained an open reading frame of 1,140 bp encoding a pentameric polyubiquitin arranged as five tandem, head-to-tail repeats of 76 aa. The 1,140 bp 5' UTR intron of the gene enhanced its promoter activity in transient expression assays by 20-fold. Translational fusion of the GUS reporter gene to the coding sequence of the ubiquitin monomer enhanced GUS enzyme activity in transient expression assays by 4.3-fold over the construct containing the original rubi3 promoter (including the 5' UTR intron) construct. The enhancing effect residing in the ubiquitin monomer coding sequence has been narrowed down to the first 9 nt coding for the first three amino acid residues of the ubiquitin protein. Mutagenesis at the third nucleotide of this 9 nt sequence still maintains the enhancing effect, but leads to translation of the native GUS protein rather than a fusion protein. The resultant 5' regulatory sequence, consisting of the rubi3 promoter, 5' UTR exon and intron, and the mutated first 9 nt coding sequence, has an activity nearly 90-fold greater than the rubi3 promoter only (without the 5' UTR intron), and 2.2-fold greater than the maize Ubi1 gene promoter (including its 5' UTR intron). The newly created expression vector is expected to enhance transgene expression in monocot plants. Considering the high conservation of the polyubiquitin gene structure in higher plants, the observed enhancement in gene expression may apply to 5' regulatory sequences of other plant polyubiquitin genes.}, number={2}, journal={PLANT MOLECULAR BIOLOGY}, author={Sivamani, E and Qu, R}, year={2006}, month={Jan}, pages={225–239} }
 @article{chen_yang_sivamani_bruneau_wang_qu_2005, title={Selective elimination of perennial ryegrass by activation of a pro-herbicide through engineering E-coli argE gene}, volume={15}, ISSN={["1572-9788"]}, DOI={10.1007/s11032-004-7243-z}, number={4}, journal={MOLECULAR BREEDING}, author={Chen, X and Yang, WQ and Sivamani, E and Bruneau, AH and Wang, BH and Qu, RD}, year={2005}, month={May}, pages={339–347} }