Sophie Alvarez


Area of Expertise: Plant Physiology, Weed, and Production Systems



Ph.D. PLANT BIOLOGY, University of LILLE 1 (FRANCE), 2004

Area of Focus

  • Mass Spectrometry-based Proteomics and Metabolomics

Research Interests

My research interest lies in developing and applying new proteomics and metabolomics methods using liquid-chromatography mass spectrometry to study a broad range of fields and applications, including crop breeding, plant biotechnology, food processing, biomarker discovery, toxicology and pharmacology. As the director of the Proteomics & Metabolomics facility at the Center for Biotechnology, University of Nebraska-Lincoln, I serve the scientific community in providing tools and expertise in the fields of proteomics and metabolomics, and establishing specialized methods for the analysis of proteins and a wide range of metabolites.


Book Chapters
  • Alvarez S and Naldrett MJ. Plant Structure and Specificity - Challenges and Sample Preparation Considerations for Proteomics. In: Adv Exp Med Biol. Mirzaei, H and Carrasco, M (Editors). Springer 2016, 919, 63-81
  • Alvarez S. and Hicks L.M. Survey in Plant Root Proteomics: To Know the Unknown. In: Sustainable Agriculture and New Biotechnologies. Benkeblia N (Editor). CRC Press, Boca Raton (FL), 2011, 215-256.
Research Articles
  • Westfall CS, Sherp AM, Zubieta C, Alvarez S, Schraft E, Marcellin R, Ramirez L, Jez JM. Arabidopsis thaliana GH3.5 acyl acid amido synthetase mediates metabolic crosstalk in auxin and salicylic acid homeostasis. Proc Natl Acad Sci USA., 2016, 113, 13917-13922.
  • Para A, Muhammad D, Orozco-Nunnelly DA, Memishi R, Alvarez S, Naldrett MJ, Warpeha KM. The Dehydratase ADT3 Affects ROS Homeostasis and Cotyledon Development. Plant Physiol., 2016, 172, 1045-1060.
  • Huang H, Alvarez S, Nusinow DA. Data on the identification of protein interactors with the Evening Complex and PCH1 in Arabidopsis using tandem affinity purification and mass spectrometry (TAP-MS). Data Brief, 2016, 8, 56-60.
  • Huang H, Yoo CY, Bindbeutel R, Goldsworthy J, Tielking A, Alvarez S, Naldrett MJ, Evans BS, Chen M, Nusinow DA. PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis. Elife, 2016, 5, e13292.
  • Huang H, Alvarez S, Bindbeutel R, Shen Z, Naldrett MJ, Evans BS, Briggs SP, Hicks LM, Kay SA, Nusinow DA. Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry. Mol Cell Proteomics, 2016, 15, 201-217.
  • Alvarez S, Roy Choudhury S, Sivagnanam K, Hicks LM, Pandey S. Quantitative proteomics analysis of Camelina sativa seeds overexpressing the AGG3 gene to identify the proteomic basis of increased yield and stress tolerance. Journal of Proteome Research, 2015, 14, 2606-2616.
  • Rodrigues SP, Alvarez S, Werth EG, Slade WO, Gau B, Cahoon EB, Hicks LM (2015). Multiplexing strategy for simultaneous detection of redox-, phospho and total proteome – understanding TOR regulating pathways in Chlamydomonas reinhardtii. Anal Methods, 2015, 7, 7336-7344.
  • Slade WO, Werth EG, McConnell EW, Alvarez S, Hicks LM. Quantifying reversible oxidation of protein thiols in photosynthetic organisms. J Am Soc Mass Spectrom., 2015, 26, 631-640.
  • Alvarez S., Roy Choudhury S., Pandey S. Comparative quantitative proteomics analysis of the ABA response of roots of drought-sensitive and drought-tolerant wheat varieties identifies proteomic signatures of drought adaptability. Journal of Proteome Research, 2014, 13, 1688-1701.
  • Reyes L., Eiler-McManis E., Rodrigues P.H., Chadda A.S., Wallet S.M., Bélanger M., Barrett A.G., Alvarez S., Akin D., Dunn W.A. Jr., Progulske-Fox A. Deletion of lipoprotein PG0717 in Porphyromonas gingivalis W83 reduces gingipain activity and alters trafficking in and response by host cells. PLoS One, 2013 12, 8, e74230.
  • Deng X., Weerapana E., Ulanovskaya O., Sun F., Liang H., Ji Q., Ye Y., Fu Y., Zhou L., Li J., Zhang H., Wang C., Alvarez S., Hicks L.M., Lan L., Wu M., Cravatt B.F., He C. Proteome-wide quantification and characterization of oxidation-sensitive cysteines in pathogenic bacteria. Cell Host Microbe, 2013, 13, 358-370.
  • Alvarez S., Roy Choudhury S., Hicks L.M., Pandey S. Quantitative proteomics-based analysis supports a significant role of GTG proteins in regulation of ABA response in Arabidopsis roots. Journal of Proteome Research, 2013, 1, 1487-1501.
  • Martyniuk C.J., Alvarez S. Proteome analysis of the fathead minnow (Pimephales promelas) reproductive testes. Journal of Proteomics, 2013, 79, 28-42.
  • Sun F., Ding Y., Ji Q., Liang Z., Deng X., Wong C.C., Yi C., Zhang L., Xie S., Alvarez S., Hicks L.M., Luo C., Jiang H., Lan L., He C. Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance. Proc Natl Acad Sci USA., 2012, 109, 15461-15466.
  • Martyniuk C.J., Alvarez S., Lo B.P., Elphick J.R., Marlatt V.L. Hepatic protein expression networks associated with masculinization in the female fathead minnow (Pimephales promelas). Journal of Proteome Research, 2012, 11, 4147-4161.
  • Sun F., Liang H., Kong X., Xie S., Cho H., Deng X., Ji Q., Zhang H., Alvarez S., Hicks L.M., Bae T., Luo C., Jiang H., He C. Quorum-sensing agr mediates bacterial oxidation response via an intramolecular disulfide redox switch in the response regulator AgrA. Proc Natl Acad Sci USA., 2012, 109, 9095-9100.
  • Hasnain G., Waller J.C., Alvarez S., Ravilious G.E., Jez J.M., Hanson A.D. Mutational analysis of YgfZ, a folate-dependent protein implicated in iron/sulphur cluster metabolism. FEMS Microbiology Letters, 2012, 326, 168-172.
  • Waller J.C., Ellens K.W., Hasnain G., Alvarez S., Rocca J.R., Hanson A.D. Evidence that the folate-dependent proteins YgfZ and MnmEG have opposing effects on growth and on activity of the iron-sulfur enzyme MiaB. Journal of Bacteriology, 2012, 194, 362-367.
  • Martyniuk C.J., Alvarez S., Denslow N.D. DIGE and ITRAQ as a biomarker discovery tools in aquatic toxicology. Ecotoxicology and Environmental Safety, 2012, 76, 3-10.
  • Waller J.C., Ellens K.W., Alvarez S., Loizeau K., Ravanel S., Hanson A.D. Mitochondrial and plastidial COG0354 proteins have folate2 dependent functions in iron-sulfur cluster metabolism. Journal of Experimental Botany, 2012, 63, 403-411.
  • Wang H., Wang S., Lu Y., Alvarez S., Hicks L.M., Ge X., Xia Y. Proteomic analysis of early-responsive redox-sensitive proteins in Arabidopsis. Journal of Proteome Research, 2012, 11, 412-424.
  • Wang H., Alvarez S., Hicks L.M. Comprehensive comparison of iTRAQ and label-free LC-based quantitative proteomics approaches using two Chlamydomonas reinhardtii strains of interest for biofuels engineering. Journal of Proteome Research, 2012, 11, 487-501.
  • Dalal, J.S., Stevens, Jr., S. M., Alvarez S., Munoz, N., Kempler, K.E., Dose, A.C., Burnside, B., Battelle, B-A. Mouse Class III myosins: Kinase activity and phosphorylation sites. Journal of Neurochemistry, 2011, 119, 772-784.
  • Alvarez S., Hicks L.M., Pandey S. ABA-Dependent and -independent G-Protein signaling in Arabidopsis roots revealed through an iTRAQ proteomics approach. Journal of Proteome Research, 2011, 10, 3107-3122.
  • Alvarez S., Galant A., Jez J.M., Hicks L.M. Redox-regulatory mechanisms induced by oxidative stress in Brassica juncea roots monitored by 2-DE proteomics. Proteomics, 2011, 11, 1346-1350.
  • Allam A.B., Alvarez S., Brown M.B., Reyes L. Ureaplasma parvum infection alters filamin A dynamics in host cells. BMC Infectious Diseases, 2011, 11, 101.
  • de Crécy-Lagard V., Brochier-Armanet C., Urbonavicius J., Fernandez B., Phillips G., Lyons B., Noma A., Alvarez S., Droogmans L., Armengaud J., Grosjean H. Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Molecular Biology and Evolution, 2010, 27, 2062-2077.
  • Ernst L., Goodger J.Q.D., Alvarez S., Marsh E.L., Berla B., Lockhart E., Jung J., Li P., Bohnert H.J., Schachtman D.P. Sulphate as a xylem-borne chemical signal precedes the expression of ABA biosynthetic genes in maize roots. Journal of Experimental Botany, 2010, 61, 3395-3405.
  • Waller J.C., Alvarez S., Naponelli V., Lara-Nuñez A., Blaby I.K., Da Silva V., Ziemak M.J., Vickers T.J., Beverley S.M., Edison A.S., Rocca J.R., Gregory JF 3rd, de Crécy-Lagard V., Hanson A.D. A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life. Proceedings of the National Academy of Sciences U S A, 2010, 107, 10412-10417.
  • Marsh E., Alvarez S., Hicks L.M., Barbazuk W.B., Qiu W., Kovacs L., Schachtman D.. Changes in protein abundance during powdery mildew infection of leaf tissues of Cabernet Sauvignon grapevine (Vitis vinifera L.). Proteomics, 2010, 10, 2057-2064.
  • Reyes L., Alvarez S., Allam A., Reinhard M., Brown M.B. Complicated urinary tract infection is associated with uroepithelial expression of proinflammatory protein S100A8. Infection and Immunity, 2009, 77, 4265-4274.
  • Alvarez S., Zhu M., Chen S. Proteomics of Arabidopsis redox proteins in response to methyl jasmonate. Journal of Proteomics, 2009, 73, 30-40.
  • Kavazis A.N., Alvarez S., Talbert E., Lee Y., Powers S.K. Exercise training induces a cardioprotective phenotype and alterations in cardiac subsarcolemmal and intermyofibrillar mitochondrial proteins. AJP- Heart and Circulatory Physiology, 2009, 297, H144-52.
  • Martyniuk C.J., Alvarez S., McClung S., Villeneuve D.L., Ankley G.T., Denslow N.D. Quantitative proteomic profiles of androgen receptor signaling in the liver of fathead minnows (Pimephales promelas). Journal of Proteome Research, 2009, 8, 2186-2200.
  • Alvarez S., Berla B.M., Sheffield J., Cahoon R.E., Jez J.M., Hicks L.M.. Comprehensive analysis of the Brassica juncea root proteome in response to cadmium exposure by complementary proteomic approaches. Proteomics, 2009, 9, 2419–2431
  • Alvarez S., Wilson G.H., Chen S. Determination of in vivo disulfide-bonded proteins in Arabidopsis. Journal of Chromatography B, 2009, 877, 101–104.
  • Phillips G., El Yacoubi B., Lyons B., Alvarez S., Iwata-Reuyl D., de Crécy-Lagard V. The biosynthesis of the 7-deazaguanosine modified tRNA nucleosides: a new role for GTP cyclohydrolase-I. Journal of Bacteriology, 2008, 190, 7876-7884.
  • Alvarez S., He Y., Chen S. Comparative investigations of the glucosinolate-myrosinase system in Arabidopsis suspension cells and hypocotyls. Plant and Cell Physiology, 2008, 49, 324-333.
  • Alvarez S., Marsh E.L., Schroeder S.G., Schachtman D.P. Metabolomic and proteomic changes in the xylem sap of maize under drought. Plant, Cell and Environment, 2008, 31, 325-340
  • Zhu J., Alvarez S., Marsh E., Lenoble M.E., Cho I-J., Sivaguru M., Chen S., Nguyen H.T., Wu Y., Schachtman D.P., Sharp R.E. Cell wall proteome in the maize primary root elongation zone. II. Region-specific changes in water soluble and lightly ionically-bound proteins under water deficit. Plant Physiology, 2007, 145, 1533-1548.
  • Shin R., Alvarez S., Burch A., Jez J.M., Schachtman D.P. Phosphoproteomic identification of targets of the Arabidopsis SNF-like protein kinase SnRK2.8 reveals a connection to metabolic processes. Proc Natl Acad Sci USA., 2007, 104, 6460-6465.
  • Alvarez S., Goodger J.Q.D., Marsh E.L., Chen S., Asirvatham V.S., Schachtman D.P. Characterization of the maize xylem sap proteome. Journal of Proteome Research, 2006, 5: 963-972.
  • Zhu J., Chen S., Alvarez S., Asirvatham V.S., Schachtman D.P., Wu Y., Sharp R.E. Cell wall proteome in the maize primary root elongation zone. I. Extraction and identification of water-soluble and lightly ionically bound proteins. Plant Physiology, 2006, 140: 311-325.