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United States Department of Agriculture

Agricultural Research Service

IVAN R. BAXTER

Computational Biologist

Lab Focus

The Baxter Lab:
The Ionomics of Crop Plants

Understanding how plants regulate element composition of tissues is critical for agriculture, the environment, and human health. Sustainably meeting the increasing food and biofuel demands of the planet will require growing crops with fewer inputs such as the primary macronutrients phosphorus (P) and potassium (K). P in fertilizer is non-renewable, too expensive for subsistence farmers, and inefficiently utilized by crops, leading to runoff and severe downstream ecological consequences. Plants comprise the major portion of the human diet, and improving their elemental nutrient content can greatly affect human health. However, efforts directed at a single element can have unforeseen deleterious effects. For example, limiting iron (Fe) or P can lead to increased accumulation of the toxic elements cadmium (Cd) and arsenic (As).
The Baxter lab is interested in understanding how plants regulate the mobilization, uptake, translocation, and storage of elements in different environments. We are focusing our efforts on the seeds of corn and soybeans, the two most commonly grown crops in the United States. The seeds are important not only as the component of the plant that gets used for food, but also as a summary tissue of many physiological processes that are important for plant growth. We also study model systems to understand basic processes and apply this knowledge to the crop plants.
The focus of our attempts to study this question is ionomics. We analyze the elemental content of 500-1000 samples per week using ICP-MS. We use this high throughput to study structured genetic populations grown in different environments. When we combine this data with cutting-edge statistical and bioinformatics methodologies, we are able to identify genes and Gene X Environment interactions which a

Bio

Ivan Baxter
Research Computational Biologist
USDA-ARS Plant Genetics Research Unit
ivan.baxter@ars.usda.gov

Assistant Member and Principal Investigator
Donald Danforth Plant Sciences Center
314-587-1438

 

 

Education

The Scripps Research Institute (TSRI), La Jolla, California
Graduate student in the laboratory of Jeffrey F. Harper, Cell Biology Department
The Scripps Research Institute (TSRI), La Jolla, California
Graduate student in the laboratory of James R. Williamson, Molecular Biology Department
Massachusetts Institute of Technology, Cambridge, Massachusetts
Graduate student in the laboratory of James R. Williamson, Department of Chemistry
Goucher College, Towson, Maryland
B.A. in Chemistry. General Honors, Honors in Chemistry
 

Employment

Research Computational Biologist, Plant Genetics Research Unit, USDA-ARS. Assistant Member and Principal Investigator, Donald Danforth Plant Science Center
Senior Research Associate, Bindley Bioscience Center, Purdue University, West Lafayette, Indiana
Postdoctoral Researcher at the Center for Phytoremediation Research and Development, Bindley Bioscience Center, Purdue University, West Lafayette, Indiana
 

Grants

The Genetic Basis of Natural Ionomic Variation, David Salt PI, National Institutes of Health, GM078536-01, 1/1/2007-12/31/2010.
Tools to Facilitate Collaboration within the Virtual Ionomics Network at ionomicshub.org to
Foster Ionomic Discovery, David Salt PI, Purdue University Cyber Center, 1/1/2009-1/1/2010

The National Association of Advanced Biofuels and Bioproducts (NAABB), Jose Olivares PI, Department of Energy, 4/1/2010-3/31/2013

 

Awards and Experience

Plant Biology Section Editor, PLoS One
Member, PLoS One Editorial Board
Inducted into Phi Beta Kappa
President, Student Government Association, Goucher College
Claasen Chemistry Scholar, Goucher College
Dean's List, Goucher College
Recipient of Dean's Scholarship, Goucher College


Lab News

For the latest Baxter lab news, please see our blog.

 

 

 

 


Publications

Peer-Reviewed Publications

    Becker A, Chao D-Y, Zhang X, Salt DE, Baxter IR. (2011) Bulk Segregant Analysis Using Single Nucleotide Polymorphism Microarrays. PLoS ONE 6(1): e15993. doi:10.1371/journal.pone.0015993
    Tian H, Baxter IR, Lahner B, Reinders A, Salt DE, and Ward JM. (2010) Arabidopsis NPCC6/NaKR1 Is a Phloem Mobile Metal Binding Protein Necessary for Phloem Function and Root Meristem Maintenance. Plant Cell  22: 3963-3979. doi:10.1105/tpc.110.080010
   

Baxter I, Brazelton J, Yu D, Huang Y, Lahner B, Nordbord M, Vitek O, Salt DE. (2010) A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1. PLoS Genetics 6(11): e1001193. doi:10.1371/journal.pgen.1001193. With accompanying perspective by Anderson JT and Mitchell-Olds T, "Beyond QTL Cloning"

    Atwell, S, Huang, YS, Vilhjalmsson, BJ, Willems, G, Horton, M, Li, Y, Meng, D, Platt, A, Tarone, AM, Hu, TT, Jiang, R, Muliyati, NW, Zhang, X, Amer, MA, Baxter, I, Brachi, B, Chory, J, Dean, C, Debieu, M, de Meaux, J, Ecker, JR, Faure, N, Kniskern, JM, Jones, JD, Michael, T, Nemri, A, Roux, F, Salt, D.E., Tang, C, Todesco, M, Traw, MB, Weigel, D, Marjoram, P, Borevitz, JO, Bergelson, J, and Nordborg, M (2010). Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465, 627–631
     
Buescher, E., Achberger, T., Amusan, I., Giannini, A., Ochsenfeld, C., Rus, A., Lahner, B., Hoekenga, O., Yakubova, E., Harper, J.F., Guerinot, M.L., Zhang, M., Salt, D.E., and Baxter, I.R. (2010). Natural genetic variation in selected populations of Arabidopsis thaliana is associated with ionomic differences. PLoS One 5, e11081.
Morrissey J, Baxter I, Lee J, Li L, Lahner B, Grotz N, Kaplan J, Salt DE, Guerinot ML (2009) The Feroportin Metal efflux proteins function in iron and cobalt homeostasis in Arabidopsis. Plant Cell, 10.1105/tpc.109.069401
Baxter I, Hosmani PS, Rus A, Lahner B, Borevitz JO, Muthukumar B, Mickelbart MV,
Schreiber L, Franke RB, Salt DE (2009) Root suberin forms an extracellular barrier that affects water relations and mineral nutrition in Arabidopsis. PLoS Genet. DOI: 10.1371/journal.pgen.1000492 Faculty of 1000 Factor: 3.0, Reccomended.
Danku J, Gumaelius L, Baxter I, Salt DE. (2008) A high-throughput method for Saccharomyces cerevisiae (yeast) ionomics. J. Anal. Atomic Spec. DOI: 10.1039/b803529f
Baxter I, Vitek O, Lahner B, Muthukumar B, Borghi M, Morrissey J, Guerinot ML, Salt DE. (2008) The leaf ionome as a multivariable system to detect a plant's physiological status. Proc. Natl. Acad. Sci. USA 105(33):12081-12086. Faculty of 1000 Factor: 6.0, Must Read.
Baxter I, Muthukumar B, Park HC, Buchner P, Lahner B, Danku J, Zhao K, Lee J, Hawkesford MJ, Guerinot ML, Salt DE. (2008) Variation in molybdenum content across broadly distributed populations of Arabidopsis thaliana is controlled by a novel mitochondrial molybdenum transporter (MOT1). PLoS Genet. 4(2):e1000004. doi: 10.1371/journal.pgen.1000004. Faculty of 1000 Factor: 6.0, Must Read.
Eltabakh MY, Ouzzani M, Aref WG, Elmagarmid AK, Laura-Silva Y, Salt DE, Baxter I. (2008) Managing biological data using bdbms. IEEE International Conference on Data Engineering.
Borevitz JO, Michael TP, Hazen SP, Morris GP, Baxter IR, Hu TT, Chen H, Werner J, Salt DE, Kay SA, Chory J, Weigel D, Nordborg M, Jones JDG, Ecker JR. (2007) Genome-wide patterns of single feature polymorphism in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 104(29):12057-12062.
Baxter I, Ouzzani M, Orcun S, Kennedy B, Jandhyala SS, Salt DE. (2007) Purdue Ionomics Information Management System (PIIMS). An integrated functional genomics platform. Plant Physiol. 143:600-611.
Rus A, Baxter I, Muthukumar B, Gustin J, Lahner B, Yakubova E, Salt DE. (2006) Natural variants of AtHKT1 enhance Na+ accumulation in two wild populations of Arabidopsis. PLoS Genet. 2(12):e210. doi: 10.1371/journal.pgen.0020210. Faculty of 1000 Factor: 4.9, Must Read.
Baxter I, Young JC, Armstrong G, Foster N, Bogenschutz N, Cordova T, Peer WA, Hazen SP, Murphy AS, Harper JF. (2005) A plasma membrane H+-ATPase is required for the formation of proanthocyanidins in the seed coat endothelium of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 102:2649-2654.
Hazen SP, Pathan MS, Sanchez A, Baxter I, Dunn M, Estes B, Chang HS, Zhu T, Kreps JA, Nguyen HT. (2005) Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array. Funct. Integr. Genomics 5(2):104-116.
Baxter I, Tchieu J, Sussman MR, Boutry MR, Palmgren MG, Gribskov M, Harper JF, Axelsen KB. (2003) Genomic comparison of P-type ATPase ion pumps in Arabidopsis and rice. Plant Physiol. 132(2):618-628.
Vitart V, Baxter I, Doerner P, Harper JF. (2001) Evidence for a role in growth and salt resistance of a plasma membrane H+-ATPase in the root endodermis. Plant J. 27:191-201.

 Hegmans A, Sabat M, Baxter I, Freisinger E, Lippert B. (1998) Synthetic ways to tris(nucleobase) complexes derived from cis-diammineplatinum(ii) and a platinum(ii) complex containing four different ligands, three of which are nucleobases. Inorg. Chem. 37(19):4921-4928.

Review Publications

     Baxter I. (2010) Ionomics: The functional genomics of elements. Brief Funct Genomics., Vol. 9 Issue 2: 149-156
Baxter I. (2009) Ionomics: Studying the Social Network of Mineral Nutrients. Current Opinon in Plant Biology, Vol. 12 Issue 3: 381-386
Guerinot, ML, Baxter I, Salt DE. (2009) From the ionome to the genome: Identifying gene networks that control the mineral content of plants. In Plant Systems Biology. Coruzzi G and Gutierrez R, eds. Wiley-Blackwell
Salt DE, Baxter I, Lahner B,. (2008) Ionomics and the study of the plant ionome. Annu. Rev. Plant Biol. 59:709-733.
Baxter IR, Borevitz JO. (2006) Mapping a plant's chemical vocabulary. Nat. Genet. 38(7):737-738.
Peer WA, Baxter IR, Richards EL, Freeman JL, Murphy AS. (2005) Phytoremediation and hyperaccumulator plants. In Molecular Biology of Metal Homeostasis and Detoxification. Topics in Current Genetics, Vol. 14, Tamas M and Martinoia E, eds. Springer, Berlin, pp. 299-340.

Last Modified: 1/30/2013