@article{huang_rojas-pierce_2024, title={Rapid depletion of target proteins in plants by an inducible protein degradation system}, volume={3}, ISSN={["1532-298X"]}, url={https://doi.org/10.1093/plcell/koae072}, DOI={10.1093/plcell/koae072}, abstractNote={Abstract}, journal={PLANT CELL}, author={Huang, Linzhou and Rojas-Pierce, Marcela}, year={2024}, month={Mar} }
 @article{wang_danz_ly_rojas-pierce_2022, title={Microgravity enhances the phenotype of Arabidopsis zigzag-1 and reduces the Wortmannin-induced vacuole fusion in root cells}, volume={8}, ISSN={["2373-8065"]}, url={https://doi.org/10.1038/s41526-022-00226-3}, DOI={10.1038/s41526-022-00226-3}, abstractNote={Abstract}, number={1}, journal={NPJ MICROGRAVITY}, author={Wang, Mengying and Danz, Katherine and Ly, Vanessa and Rojas-Pierce, Marcela}, year={2022}, month={Sep} }
 @misc{aniento_medina hernandez_dagdas_rojas-pierce_russinova_2022, title={Molecular mechanisms of endomembrane trafficking in plants}, volume={34}, ISSN={["1532-298X"]}, url={https://doi.org/10.1093/plcell/koab235}, DOI={10.1093/plcell/koab235}, abstractNote={Abstract}, number={1}, journal={PLANT CELL}, publisher={Oxford University Press (OUP)}, author={Aniento, Fernando and Medina Hernandez, Victor Sanchez and Dagdas, Yasin and Rojas-Pierce, Marcela and Russinova, Eugenia}, year={2022}, month={Jan}, pages={146–173} }
 @article{ranieri_sponsel_kizer_rojas‐pierce_hernández_gatiboni_grunden_stapelmann_2021, title={Plasma agriculture: Review from the perspective of the plant and its ecosystem}, url={https://doi.org/10.1002/ppap.202000162}, DOI={10.1002/ppap.202000162}, abstractNote={Abstract}, journal={Plasma Processes and Polymers}, author={Ranieri, Pietro and Sponsel, Nicholas and Kizer, Jon and Rojas‐Pierce, Marcela and Hernández, Ricardo and Gatiboni, Luciano and Grunden, Amy and Stapelmann, Katharina}, year={2021}, month={Jan} }
 @article{cui_cao_he_zhao_wakazaki_zhuang_gao_zeng_gao_ding_et al._2019, title={A whole-cell electron tomography model of vacuole biogenesis in Arabidopsis root cells}, volume={5}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85058842555&partnerID=MN8TOARS}, DOI={10.1038/s41477-018-0328-1}, abstractNote={Plant vacuoles are dynamic organelles that play essential roles in regulating growth and development. Two distinct models of vacuole biogenesis have been proposed: separate vacuoles are formed by the fusion of endosomes, or the single interconnected vacuole is derived from the endoplasmic reticulum. These two models are based on studies of two-dimensional (2D) transmission electron microscopy and 3D confocal imaging, respectively. Here, we performed 3D electron tomography at nanometre resolution to illustrate vacuole biogenesis in Arabidopsis root cells. The whole-cell electron tomography analysis first identified unique small vacuoles (SVs; 400-1,000 nm in diameter) as nascent vacuoles in early developmental cortical cells. These SVs contained intraluminal vesicles and were mainly derived/matured from multivesicular body (MVB) fusion. The whole-cell vacuole models and statistical analysis on wild-type root cells of different vacuole developmental stages demonstrated that central vacuoles were derived from MVB-to-SV transition and subsequent fusions of SVs. Further electron tomography analysis on mutants defective in MVB formation/maturation or vacuole fusion demonstrated that central vacuole formation required functional MVBs and membrane fusion machineries.}, number={1}, journal={Nature Plants}, author={Cui, Y. and Cao, W. and He, Y. and Zhao, Q. and Wakazaki, M. and Zhuang, X. and Gao, J. and Zeng, Y. and Gao, C. and Ding, Y. and et al.}, year={2019}, pages={95–105} }
 @article{brillada_zheng_krueger_rovira-diaz_askani_schumacher_rojas-pierce_2018, title={Phosphoinositides control the localization of HOPS subunit VPS41, which together with VPS33 mediates vacuole fusion in plants}, volume={115}, ISSN={["0027-8424"]}, url={https://doi.org/10.1073/pnas.1807763115}, DOI={10.1073/pnas.1807763115}, abstractNote={Significance}, number={35}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Brillada, Carla and Zheng, Jiameng and Krueger, Falco and Rovira-Diaz, Eliezer and Askani, Jana Christin and Schumacher, Karin and Rojas-Pierce, Marcela}, year={2018}, month={Aug}, pages={EB305–EB314} }
 @article{andres_coneva_frank_tuttle_samayoa_han_kaur_zhu_fang_bowman_et al._2017, title={Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)}, volume={114}, DOI={10.1101/062612}, abstractNote={Abstract}, number={1}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Andres, R. J. and Coneva, V. and Frank, M. H. and Tuttle, J. R. and Samayoa, L. F. and Han, S. W. and Kaur, B. and Zhu, L. L. and Fang, Hui and Bowman, D. T. and et al.}, year={2017}, pages={E57–66} }
 @misc{brillada_rojas-pierce_2017, title={Vacuolar trafficking and biogenesis: a maturation in the field}, volume={40}, ISSN={["1879-0356"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85028575104&partnerID=MN8TOARS}, DOI={10.1016/j.pbi.2017.08.005}, abstractNote={The vacuole is a prominent organelle that is essential for plant viability. The vacuole size, and its role in ion homeostasis, protein degradation and storage, place significant demands for trafficking of vacuolar cargo along the endomembrane system. Recent studies indicate that sorting of vacuolar cargo initiates at the ER and Golgi, but not the trans-Golgi network/early endosome, as previously thought. Furthermore, maturation of the trans-Golgi network into pre-vacuolar compartments seems to contribute to a major route for plant vacuolar traffic that works by bulk flow and ends with membrane fusion between the pre-vacuolar compartment and the tonoplast. Here we summarize recent evidence that indicates conserved and plant-specific mechanisms involved in sorting and trafficking of proteins to this major organelle.}, journal={CURRENT OPINION IN PLANT BIOLOGY}, publisher={Elsevier BV}, author={Brillada, Carla and Rojas-Pierce, Marcela}, year={2017}, month={Dec}, pages={77–81} }
 @article{andres_coneva_frank_tuttle_samayoa_han_kaur_zhu_fang_bowman_et al._2016, title={Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)}, volume={114}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.1613593114}, DOI={10.1073/pnas.1613593114}, abstractNote={Significance}, number={1}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Andres, Ryan J. and Coneva, Viktoriya and Frank, Margaret H. and Tuttle, John R. and Samayoa, Luis Fernando and Han, Sang-Won and Kaur, Baljinder and Zhu, Linglong and Fang, Hui and Bowman, Daryl T. and et al.}, year={2016}, month={Dec}, pages={E57–E66} }
 @article{alvarez_han_toyota_brillada_zheng_gilroy_rojas-pierce_2016, title={Wortmannin-induced vacuole fusion enhances amyloplast dynamics in Arabidopsis zigzag1 hypocotyls}, volume={67}, ISSN={["1460-2431"]}, url={https://doi.org/10.1093/jxb/erw418}, DOI={10.1093/jxb/erw418}, abstractNote={Highlight The highly restricted movement of amyloplasts in graviperceptive cells of zig-1 hypocotyls is overcome by wortmannin treatment, suggesting a physical association between amyloplasts and the vacuole.}, number={22}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, publisher={Oxford University Press (OUP)}, author={Alvarez, Ashley Ann and Han, Sang Won and Toyota, Masatsugu and Brillada, Carla and Zheng, Jiameng and Gilroy, Simon and Rojas-Pierce, Marcela}, year={2016}, month={Dec}, pages={6459–6472} }
 @article{han_alonso_rojas-pierce_2015, title={REGULATOR OF BULB BIOGENESIS1 (RBB1) Is Involved in Vacuole Bulb Formation in Arabidopsis}, volume={10}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84928576948&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0125621}, abstractNote={Vacuoles are dynamic compartments with constant fluctuations and transient structures such as trans-vacuolar strands and bulbs. Bulbs are highly dynamic spherical structures inside vacuoles that are formed by multiple layers of membranes and are continuous with the main tonoplast. We recently carried out a screen for mutants with abnormal trafficking to the vacuole or aberrant vacuole morphology. We characterized regulator of bulb biogenesis1-1 (rbb1-1), a mutant in Arabidopsis that contains increased numbers of bulbs when compared to the parental control. rbb1-1 mutants also contain fewer transvacuolar strands than the parental control, and we propose the hypothesis that the formation of transvacuolar strands and bulbs is functionally related. We propose that the bulbs may function transiently to accommodate membranes and proteins when transvacuolar strands fail to elongate. We show that RBB1 corresponds to a very large protein of unknown function that is specific to plants, is present in the cytosol, and may associate with cellular membranes. RBB1 is involved in the regulation of vacuole morphology and may be involved in the establishment or stability of trans-vacuolar strands and bulbs.}, number={4}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Han, Sang Won and Alonso, Jose M. and Rojas-Pierce, Marcela}, editor={Bassham, DianeEditor}, year={2015}, month={Apr}, pages={e0125621} }
 @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{zheng_han_munnik_rojas-pierce_2014, title={Multiple vacuoles inimpaired tonoplast trafficking3mutants are independent organelles}, volume={9}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84922263982&partnerID=MN8TOARS}, DOI={10.4161/psb.29783}, abstractNote={Plant vacuoles are essential and dynamic organelles, and mechanisms of vacuole biogenesis and fusion are not well characterized. We recently demonstrated that Wortmannin, an inhibitor of Phosphatidylinositol 3-Kinase (PI3K), induces the fusion of plant vacuoles both in roots of itt3/vti11 mutant alleles and in guard cells of wild type Arabidopsis and Fava bean. Here we used Fluorescence Recovery After Photobleaching (FRAP) to demonstrate that the vacuoles in itt3/vti11 are independent organelles. Furthermore, we used fluorescent protein reporters that bind specifically to Phosphatidylinositol 3-Phosphate (PtdIns(3)P) or PtdIns(4)P to show that Wortmannin treatments that induce the fusion of vti11 vacuoles result in the loss of PtdIns(3)P from cellular membranes. These results provided supporting evidence for a critical role of PtdIns(3)P in vacuole fusion in roots and guard cells.}, number={10}, journal={Plant Signaling & Behavior}, publisher={Informa UK Limited}, author={Zheng, Jiameng and Han, Sang Won and Munnik, Teun and Rojas-Pierce, Marcela}, year={2014}, month={Oct}, pages={e972113} }
 @article{rojas-pierce_whippo_davis_hangarter_springer_2014, title={PLASTID MOVEMENT IMPAIRED1 mediates ABA sensitivity during germination and implicates ABA in, light-mediated Chloroplast movements}, volume={83}, ISSN={["0981-9428"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84907306226&partnerID=MN8TOARS}, DOI={10.1016/j.plaphy.2014.07.014}, abstractNote={The plant hormone abscisic acid (ABA) controls many aspects of plant growth and development, including seed development, germination and responses to water-deficit stress. A complex ABA signaling network integrates environmental signals including water availability and light intensity and quality to fine-tune the response to a changing environment. To further define the regulatory pathways that control water-deficit and ABA responses, we carried out a gene-trap tagging screen for water-deficit-regulated genes in Arabidopsis thaliana. This screen identified PLASTID MOVEMENT IMPAIRED1 (PMI1), a gene involved in blue-light-induced chloroplast movement, as functioning in ABA-response pathways. We provide evidence that PMI1 is involved in the regulation of seed germination by ABA, acting upstream of the intersection between ABA and low-glucose signaling pathways. Furthermore, PMI1 participates in the regulation of ABA accumulation during periods of water deficit at the seedling stage. The combined phenotypes of pmi1 mutants in chloroplast movement and ABA responses indicate that ABA signaling may modulate chloroplast motility. This result was further supported by the detection of altered chloroplast movements in the ABA mutants aba1-6, aba2-1 and abi1-1.}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, publisher={Elsevier BV}, author={Rojas-Pierce, Marcela and Whippo, Craig W. and Davis, Phillip A. and Hangarter, Roger P. and Springer, Patricia S.}, year={2014}, month={Oct}, pages={185–193} }
 @misc{rojas-pierce_2013, title={Targeting of tonoplast proteins to the vacuole}, volume={211}, ISSN={["0168-9452"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84882567439&partnerID=MN8TOARS}, DOI={10.1016/j.plantsci.2013.07.005}, abstractNote={Vacuoles are essential for plant growth and development, and are dynamic compartments that require constant deposition of integral membrane proteins. These membrane proteins carry out many critical functions of the vacuole such as transporting ions and metabolites for vacuolar storage. Understanding the mechanisms for targeting proteins to the vacuolar membrane, or tonoplast, is important for developing novel applications for biotechnology. The mechanisms to target tonoplast proteins to the vacuole are quite complex. Multiple routes, including both Golgi-dependent and Golgi-independent mechanisms, have been implicated in tonoplast protein trafficking. A few endomembrane proteins that regulate this traffic at the level of the endoplasmic reticulum, the pre-vacuolar compartment and the tonoplast are now known. Recent reports indicate that the Golgi-dependent and independent pathways may merge at the level of the pre-vacuolar compartment. Finally, the small GTP-binding protein Rab7 and the SNARE protein SYP21 have been implicated in the traffic of tonoplast proteins from the pre-vacuolar compartment to the tonoplast. With multiple cargo proteins being analyzed under a variety of experimental systems, a clearer picture for targeting mechanisms for tonoplast proteins is starting to emerge.}, journal={PLANT SCIENCE}, publisher={Elsevier BV}, author={Rojas-Pierce, Marcela}, year={2013}, month={Oct}, pages={132–136} }
 @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} }
 @article{dieck_wood_brglez_rojas-pierce_boss_2012, title={Increasing phosphatidylinositol (4,5) bisphosphate biosynthesis affects plant nuclear lipids and nuclear functions}, volume={57}, ISSN={["1873-2690"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84861821133&partnerID=MN8TOARS}, DOI={10.1016/j.plaphy.2012.05.011}, abstractNote={In order to characterize the effects of increasing phosphatidylinositol(4,5)bisphosphate (PtdIns(4,5)P2) on nuclear function, we expressed the human phosphatidylinositol (4)-phosphate 5-kinase (HsPIP5K) 1α in Nicotiana tabacum (NT) cells. The HsPIP5K-expressing (HK) cells had altered nuclear lipids and nuclear functions. HK cell nuclei had 2-fold increased PIP5K activity and increased steady state PtdIns(4,5)P2. HK nuclear lipid classes showed significant changes compared to NT (wild type) nuclear lipid classes including increased phosphatidylserine (PtdSer) and phosphatidylcholine (PtdCho) and decreased lysolipids. Lipids isolated from protoplast plasma membranes (PM) were also analyzed and compared with nuclear lipids. The lipid profiles revealed similarities and differences in the plasma membrane and nuclei from the NT and transgenic HK cell lines. A notable characteristic of nuclear lipids from both cell types is that PtdIns accounts for a higher mol% of total lipids compared to that of the protoplast PM lipids. The lipid molecular species composition of each lipid class was also analyzed for nuclei and protoplast PM samples. To determine whether expression of HsPIP5K1α affected plant nuclear functions, we compared DNA replication, histone 3 lysine 9 acetylation (H3K9ac) and phosphorylation of the retinoblastoma protein (pRb) in NT and HK cells. The HK cells had a measurable decrease in DNA replication, histone H3K9 acetylation and pRB phosphorylation.}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, publisher={Elsevier BV}, author={Dieck, Catherine B. and Wood, Austin and Brglez, Irena and Rojas-Pierce, Marcela and Boss, Wendy F.}, year={2012}, month={Aug}, pages={32–44} }
 @article{rojas-pierce_titapiwatanakun_sohn_fang_larive_blakeslee_cheng_cuttler_peer_murphy_et al._2008, title={Arabidopsis P-Glycoprotein19 Participates in the Inhibition of Gravitropism by Gravacin}, volume={15}, ISSN={1074-5521}, url={http://dx.doi.org/10.1016/j.chembiol.2008.01.004}, DOI={10.1016/j.chembiol.2008.01.004}, number={1}, journal={Chemistry & Biology}, publisher={Elsevier BV}, author={Rojas-Pierce, Marcela and Titapiwatanakun, Boosaree and Sohn, Eun Ju and Fang, Fang and Larive, Cynthia K. and Blakeslee, Joshua and Cheng, Yan and Cuttler, Sean and Peer, Wendy A. and Murphy, Angus S. and et al.}, year={2008}, month={Jan}, pages={87} }
 @article{zou_rojas-pierce_raikhel_pirrung_2008, title={Preparation of methyl ester precursors of biologically active agents}, volume={44}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-41849117739&partnerID=MN8TOARS}, DOI={10.2144/000112704}, abstractNote={ This method enables scientists to easily convert biologically active carboxylic acids into their methyl esters ("pro-drugs" generally having improved ability to penetrate cell membranes) using only equipment commonly found in a biology laboratory. An ion-exchange resin is used to convert the acid into its salt, which is thereby sequestered on the resin. The addition of methyl iodide converts the salt to the ester, which has no affinity for the resin and is readily eluted. Evaporation of the liquid phase provides the pure methyl ester. The preparation in good chemical yields of methyl esters of bioactive agents in excellent purity and 10–20 mg quantities can be achieved using this method. The method can be completed in 1 day. }, number={3}, journal={BioTechniques}, publisher={Informa UK (Informa Life Sciences)}, author={Zou, Yunfan and Rojas-Pierce, Marcela and Raikhel, Natasha and Pirrung, Michael}, year={2008}, month={Mar}, pages={377–384} }
 @article{rojas-pierce_titapiwatanakun_sohn_fang_larive_blakeslee_cheng_cuttler_peer_murphy_et al._2007, title={Arabidopsis P-Glycoprotein19 Participates in the Inhibition of Gravitropism by Gravacin}, volume={14}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-37149051300&partnerID=MN8TOARS}, DOI={10.1016/j.chembiol.2007.10.014}, abstractNote={ATP-binding cassette (ABC) transporters have been implicated in a multitude of biological pathways. In plants, some ABC transporters are involved in the polar transport of the plant hormone auxin and the gravitropic response. We previously identified Gravacin as a potent inhibitor of gravitropism in Arabidopsis thaliana. We demonstrate that P-glycoprotein19 (PGP19) is a target for Gravacin and participates in its inhibition of gravitropism. Gravacin inhibited the auxin transport activity of PGP19 and PGP19-PIN complexes. Furthermore, we identified E1174 as an important residue for PGP19 activity and its ability to form active transport complexes with PIN1. Gravacin is an auxin transport inhibitor that inhibits PGPs, particularly PGP19, which can be used to further dissect the role of PGP19 without the inhibition of other auxin transporters, namely PIN proteins.}, number={12}, journal={Chemistry & Biology}, publisher={Elsevier BV}, author={Rojas-Pierce, Marcela and Titapiwatanakun, Boosaree and Sohn, Eun Ju and Fang, Fang and Larive, Cynthia K. and Blakeslee, Joshua and Cheng, Yan and Cuttler, Sean and Peer, Wendy A. and Murphy, Angus S. and et al.}, year={2007}, pages={1366–1376} }
 @article{eun_rojas-pierce_pan_carter_serrano-mislata_madueño_rojo_surpin_raikhel_2007, title={The shoot meristem identity gene TFL1 is involved in flower development and trafficking to the protein storage vacuole}, volume={104}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-36749015081&partnerID=MN8TOARS}, DOI={10.1073/pnas.0708236104}, abstractNote={
            Plants are unique in their ability to store proteins in specialized protein storage vacuoles (PSVs) within seeds and vegetative tissues. Although plants use PSV proteins during germination, before photosynthesis is fully functional, the roles of PSVs in adult vegetative tissues are not understood. Trafficking pathways to PSVs and lytic vacuoles appear to be distinct. Lytic vacuoles are analogous evolutionarily to yeast and mammalian lysosomes. However, it is unclear whether trafficking to PSVs has any analogy to pathways in yeast or mammals, nor is PSV ultrastructure known in
            Arabidopsis
            vegetative tissue. Therefore, alternative approaches are required to identify components of this pathway. Here, we show that an
            Arabidopsis thaliana
            mutant that disrupts PSV trafficking identified
            TERMINAL FLOWER 1
            (
            TFL1
            ), a shoot meristem identity gene. The
            tfl1-19/mtv5
            (for “modified traffic to the vacuole”) mutant is specifically defective in trafficking of proteins to the PSV. TFL1 localizes to endomembrane compartments and colocalizes with the putative δ-subunit of the AP-3 adapter complex. Our results suggest a developmental role for the PSV in vegetative tissues.
          }, number={47}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Eun, J.S. and Rojas-Pierce, M. and Pan, S. and Carter, C. and Serrano-Mislata, A. and Madueño, F. and Rojo, E. and Surpin, M. and Raikhel, N.V.}, year={2007}, pages={18801–18806} }
 @article{beebe_rojas-pierce_yan_blair_pedraza_muñoz_tohme_lynch_2006, title={Quantitative Trait Loci for Root Architecture Traits Correlated with Phosphorus Acquisition in Common Bean}, volume={46}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-32344439116&partnerID=MN8TOARS}, DOI={10.2135/cropsci2005.0226}, abstractNote={Low soil P availability is a primary constraint to common bean (Phaseolus vulgaris L.) production in Latin America and Africa. Substantial genotypic variation in bean adaptation to low phosphorus (LP) availability has been linked with root traits that enhance the efficiency of soil foraging. The objectives of this study were to identify quantitative trait loci (QTLs) for P accumulation and associated root architectural traits, to facilitate genetic improvement and to reveal physiological relationships. Eighty‐six F5.7 recombinant inbred lines (RILs) were developed from a cross between G19833, an Andean landrace with high total P accumulation, and DOR 364, a Mesoamerican cultivar with low total P accumulation in LP conditions. A genetic map constructed with restriction fragment length polymorphisms (RFLPs), microsatellites, and PCR‐based markers covering 1703 centimorgans (cM) total genetic distance and all eleven linkage groups (LGs) was used for QTL analysis. Seventy‐one RILs were evaluated in the field at high phosphorus (HP) and LP for P accumulation, total root length (RL), specific RL, and plant dry weight (DW), while all 86 RILs were evaluated in a hydroponic system in the greenhouse for tap, basal, total, and specific RL and plant DW. Phosphorus accumulation in the field correlated with root parameters measured in the greenhouse. A total of 26 individual QTLs were identified for P accumulation and associated root characters using composite interval mapping (CIM) analysis. Phosphorus accumulation QTLs often coincided with those for basal root development, thus, basal roots appear to be important in P acquisition. Independent QTLs were identified for basal and taproot development, and for specific RL. Distinct QTLs for greater specific RL had positive, null and negative effects on P accumulation. Our results confirm the importance of root structure for LP adaptation and highlight the need for a more detailed understanding of root architectural traits for phenotypic as well as marker‐aided selection of more P‐efficient crops.}, number={1}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Beebe, Stephen E. and Rojas-Pierce, Marcela and Yan, Xiaolong and Blair, Matthew W. and Pedraza, Fabio and Muñoz, Fernando and Tohme, Joe and Lynch, Jonathan P.}, year={2006}, pages={413} }
 @article{surpin_rojas-pierce_carter_hicks_vasquez_raikhel_2005, title={The power of chemical genomics to study the link between endomembrane system components and the gravitropic response}, volume={102}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-16344363588&partnerID=MN8TOARS}, DOI={10.1073/pnas.0500222102}, abstractNote={
            Chemical genomics is a powerful approach to dissect processes that may be intractable using conventional genetics because of gene lethality or redundancy. Recently, a link has been established between endomembrane trafficking and gravitropism. To understand this link, we screened a library of 10,000 diverse chemicals for compounds that affected the gravitropism of
            Arabidopsis
            seedlings positively or negatively. Sixty-nine of 219 compounds from the primary screen were retested, and 34 of these were confirmed to inhibit or enhance gravitropism. Four of the 34 compounds were found to cause aberrant endomembrane morphologies. The chemicals affected gravitropism and vacuole morphology in concert in a tissue-specific manner, underscoring the link between endomembranes and gravitropism. One of the chemicals (5403629) was structurally similar to the synthetic auxin 2,4-dichlorophenoxy acetate, whereas the other three chemicals were unique in their structures. An
            in vivo
            functional assay using the reporter β-glucuronidase under the auxin-inducible DR5 promoter confirmed that the unique compounds were not auxins. Interestingly, one of the unique chemicals (5850247) appeared to decrease the responsiveness to auxin in roots, whereas another (5271050) was similar to pyocyanin, a bacterial metabolite that has been suggested to target the endomembranes of yeast. These reagents will be valuable for dissecting endomembrane trafficking and gravitropism and for cognate target identification.
          }, number={13}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Surpin, M. and Rojas-Pierce, M. and Carter, C. and Hicks, G.R. and Vasquez, J. and Raikhel, N.V.}, year={2005}, pages={4902–4907} }
 @article{rojas-pierce_springer_2003, title={Gene and enhancer traps for gene discovery.}, volume={236}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-1542548180&partnerID=MN8TOARS}, journal={Methods in molecular biology (Clifton, N.J.)}, author={Rojas-Pierce, M. and Springer, P.S.}, year={2003}, pages={221–240} }
 @article{rojas-pierce_springer, title={Gene and Enhancer Traps for Gene Discovery}, DOI={10.1385/1-59259-413-1:221}, abstractNote={Gene traps and enhancer traps provide a valuable tool for gene discovery. With this system, genes can be identified based solely on the expression pattern of an inserted reporter gene. The use of a reporter gene, such as beta-glucuoronidase (GUS), provides a very sensitive assay for the identification of tissue- and cell-type specific expression patterns. In this chapter, protocols for examining and documenting GUS reporter gene activity in individual lines are described. Methods for the amplification of sequences flanking transposant insertions and subsequent molecular and genetic characterization of individual insertions are provided.}, journal={Plant Functional Genomics}, publisher={Humana Press}, author={Rojas-Pierce, Marcela and Springer, Patricia S.}, pages={221–240} }