@article{dalal_yalamanchili_hovary_ji_rodriguez-welsh_aslett_ganapathy_grunden_sederoff_qu_et al._2015, title={A novel gateway-compatible binary vector series (PC-GW) for flexible cloning of multiple genes for genetic transformation of plants}, volume={81}, ISSN={["1095-9890"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84938634755&partnerID=MN8TOARS}, DOI={10.1016/j.plasmid.2015.06.003}, abstractNote={The rapidly advancing field of plant synthetic biology requires transforming plants with multiple genes. This has sparked a growing interest in flexible plant transformation vectors, which can be used for multi-gene transformations. We have developed a novel binary vector series, named the PC-GW series (GenBank: KP826769-KP826773), for Agrobacterium-mediated plant transformation. The PC-GW vectors use the pCAMBIA vector backbone, and contain NPTII, hpt, bar, mCherry or egfp genes as selectable markers for plant transformation. In a modified multiple cloning site (MCS) of the T-DNA region, we have placed the attR1, attR2 and ccdB sequences for rapid cloning of one to four genes by Gateway™-assisted recombination. In addition, we have introduced four meganuclease sites, and other restriction sites for multi-gene vector construction. Finally, we have placed a CaMV 35S promoter and a 35S terminator on the 5' and 3' ends of the MCS. The CaMV 35S promoter is flanked by PstI restriction sites that can be used to replace it with another promoter sequence if needed. The PC-GW vectors provide choices for selectable markers, cloning methods, and can accommodate up to eight gene constructs in a single T-DNA, thereby significantly reducing the number of transformations or crosses needed to generate multi-transgene expressing plants.}, journal={PLASMID}, author={Dalal, J. and Yalamanchili, R. and Hovary, C. La and Ji, M. and Rodriguez-Welsh, M. and Aslett, D. and Ganapathy, S. and Grunden, A. and Sederoff, Heike and Qu, R. D. and et al.}, year={2015}, month={Sep}, pages={55–62} }
 @inbook{dalal_land_vasani_he_smith_rodriguez-welsh_perera_sederoff_2015, title={Methods for RNA Profiling of Gravi-Responding Plant Tissues}, volume={1309}, ISBN={9781493926961 9781493926978}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-4939-2697-8_9}, DOI={10.1007/978-1-4939-2697-8_9}, abstractNote={Plant transcriptional responses to gravity stimulation by reorientation are among the fastest measured in any tissue or species. Upon reorientation, changes in abundance of specific mRNAs can be measured within seconds or minutes, for plastid or nuclear encoded genes, respectively. Identifying fast gravity-induced transcripts has been made possible by the development of high-throughput technology for qualitative and quantitative RNA analysis. RNA profiling has undergone further rapid development due to its enormous potential in basic sciences and medical applications. We describe here the current and most widely used methods to profile the changes in an entire transcriptome by high-throughput sequencing of RNA fractions (RNAseq) and single gene transcript analysis using real-time quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).}, booktitle={Methods in Molecular Biology}, publisher={Springer New York}, author={Dalal, Jyoti and Land, Eric and Vasani, Naresh and He, Luyan and Smith, Caroline and Rodriguez-Welsh, Maria and Perera, Imara Y. and Sederoff, Heike}, year={2015}, pages={91–117} }
 @article{zheng_han_rodriguez-welsh_rojas-pierce_2014, title={Homotypic Vacuole Fusion Requires VTI11 and Is Regulated by Phosphoinositides}, volume={7}, ISSN={["1752-9867"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84907579328&partnerID=MN8TOARS}, DOI={10.1093/mp/ssu019}, abstractNote={Most plant cells contain a large central vacuole that is essential to maintain cellular turgor. We report a new mutant allele of VTI11 that implicates the SNARE protein VTI11 in homotypic fusion of protein storage and lytic vacuoles. Fusion of the multiple vacuoles present in vti11 mutants could be induced by treatment with Wortmannin and LY294002, which are inhibitors of Phosphatidylinositol 3-Kinase (PI3K). We provide evidence that Phosphatidylinositol 3-Phosphate (PtdIns(3)P) regulates vacuole fusion in vti11 mutants, and that fusion of these vacuoles requires intact microtubules and actin filaments. Finally, we show that Wortmannin also induced the fusion of guard cell vacuoles in fava beans, where vacuoles are naturally fragmented after ABA-induced stomata closure. These results suggest a ubiquitous role of phosphoinositides in vacuole fusion, both during the development of the large central vacuole and during the dynamic vacuole remodeling that occurs as part of stomata movements.}, number={6}, journal={MOLECULAR PLANT}, publisher={Elsevier BV}, author={Zheng, Jiameng and Han, Sang Won and Rodriguez-Welsh, Maria Fernanda and Rojas-Pierce, Marcela}, year={2014}, month={Jun}, pages={1026–1040} }
 @article{rivera-serrano_rodriguez-welsh_hicks_rojas-pierce_2012, title={A Small Molecule Inhibitor Partitions Two Distinct Pathways for Trafficking of Tonoplast Intrinsic Proteins in Arabidopsis}, volume={7}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84866026793&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0044735}, abstractNote={Tonoplast intrinsic proteins (TIPs) facilitate the membrane transport of water and other small molecules across the plant vacuolar membrane, and members of this family are expressed in specific developmental stages and tissue types. Delivery of TIP proteins to the tonoplast is thought to occur by vesicle–mediated traffic from the endoplasmic reticulum to the vacuole, and at least two pathways have been proposed, one that is Golgi-dependent and another that is Golgi-independent. However, the mechanisms for trafficking of vacuolar membrane proteins to the tonoplast remain poorly understood. Here we describe a chemical genetic approach to unravel the mechanisms of TIP protein targeting to the vacuole in Arabidopsis seedlings. We show that members of the TIP family are targeted to the vacuole via at least two distinct pathways, and we characterize the bioactivity of a novel inhibitor that can differentiate between them. We demonstrate that, unlike for TIP1;1, trafficking of markers for TIP3;1 and TIP2;1 is insensitive to Brefeldin A in Arabidopsis hypocotyls. Using a chemical inhibitor that may target this BFA-insensitive pathway for membrane proteins, we show that inhibition of this pathway results in impaired root hair growth and enhanced vacuolar targeting of the auxin efflux carrier PIN2 in the dark. Our results indicate that the vacuolar targeting of PIN2 and the BFA-insensitive pathway for tonoplast proteins may be mediated in part by common mechanisms.}, number={9}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Rivera-Serrano, Efrain E. and Rodriguez-Welsh, Maria F. and Hicks, Glenn R. and Rojas-Pierce, Marcela}, editor={Damme, Els J. M.Editor}, year={2012}, month={Sep} }