2012 Distinguished Faculty Lecturer Talk
"Science, collaborations, alternatives and the future"
Wednesday, October 10
4:30 pm

A FREE Webinar (11/3/2011) Archive
"Targeted High Resolution LC-MSMS of Complex Proteomes"
Please register at the site to view the webcast.

Advanced Imaging Mass Spectrometry
AIMS.2013
Laboratory Course
April 16 - April 19, 2013
Vanderbilt University
Nashville, TN

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Publications


  • 2013
  • 2012
  • 2011
  • 2010
  • 2009
  • 2008
  • 2007
  • 2006
  • 2005
  • 2004
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  • 2002
  • 2001
  • 2000
  • 1999

2013

  1. Chiquito Crasto, Chandrahas Narne, Mikako Kawai, Landon Wilson and Stephen Barnes
    MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach
    Advances in Bioinformatics, vol. 2013, Article ID 527295, 10 pages, 2013. [doi: 10.1155/2013/527295]

  2. Hieu D. Hoang, Jeevan K. Prasain, Dixon Dorand, Michael A. Miller
    A Heterogeneous Mixture of F-Series Prostaglandins Promotes Sperm Guidance in the Caenorhabditis elegans Reproductive Tract
    PLoS Genet 9(1): e1003271 [doi:10.1371/journal.pgen.1003271]

  3. Jeevan K. Prasain, Alireza Arabshahi, Pam R. Taub, Scott Sweeney, Ray Moore, J. Daniel Sharer, Stephen Barnes.
    Simultaneous quantification of F2-isoprostanes and prostaglandins in human urine by liquid chromatography tandem-mass spectrometry
    Journal of Chromatography B. Volumes 913–914, 15 January 2013, Pages 161–168 [doi: 10.1016/j.jchromb.2012.12.009]








2012

  1. Prasain JK, Peng N, Rajbhandari R, Wyss JM.
    The Chinese Pueraria root extract (Pueraria lobata) ameliorates impaired glucose and lipid metabolism in obese mice.
    Phytomedicine. 2012 Nov 1. pii: S0944-7113(12)00353-4. doi: 10.1016/j.phymed.2012.09.017. [PMID: 23123226] [Epub ahead of print]

  2. He L, Kim T, Long Q, Liu J, Wang P, Zhou Y, Ding Y, Prasain J, Wood PA, Yang Q.
    Carnitine Palmitoyltransferase-1b (CPT1b) Deficiency Aggravates Pressure-Overload-Induced Cardiac Hypertrophy due to Lipotoxicity.
    Circulation. 2012 Aug 29. [Epub ahead of print] [PMID: 22932257]

  3. C. Roger White, Geeta Datta, Amanda K. W. Buck, Manjula Chaddha, Gautam Reddy, Landon Wilson, Mayakonda N. Palgunachari, Mohammad Abbasi and G. M. Anantharamaiah
    Preservation of biological function despite oxidative modifi cation of the apolipoprotein A-I mimetic peptide 4F
    J Lipid Res. Aug;53(8):1576-87 [PMID: 22589558] [DOI 10.1194/jlr.M026278]

  4. Higdon A, Landar A, Barnes S, Darley-Usmar VM.
    The Electrophile Responsive Proteome: Integrating Proteomics and Lipidomics with Cellular Function.
    Antioxidants & Redox Signaling, 2012 Feb 21 [Epub ahead of print] [PMID: 22352679]

  5. Wong WW, Taylor AA, E. Smith EO, Barnes S, Hachey DL.
    Effect of soy isoflavone supplementation on nitric oxide metabolism and blood pressure in menopausal women.
    American Journal of Clinical Nutrition. American Journal of Clinical Nutrition, 2012 Jun;95(6):1487-94. [PMID: 22552034]

  6. Li H, Cao, Z, Moore DR, Patricia L. Jackson PL, Barnes S, Lambeth JD, Thannickal VJ, Cheng G.
    Microbicidal Activity of VPO1 in Human Plasma via Generation of HOCl. Li H, Cao, Z, Moore DR, Patricia L. Jackson PL, Barnes S, Lambeth JD, Thannickal VJ, Cheng G. Microbicidal Activity of VPO1 in Human Plasma via Generation of HOCl.
    Infection and Immunity. 2012 Apr 23. [Epub ahead of print] [PMID: 22526679]

  7. Edited by: Jeevan K. Prasain
    Tandem Mass Spectrometry - Applications and Principles
    ISBN 978-953-51-0141-3, Hard cover, 794 pages
    Publisher: InTech, Free Online Book
    Publication date: February 2012

  8. McClure M, DeLucas LJ, Wilson L, Ray M, Rowe SM, Wu X, Dai Q, Hong JS, Sorscher EJ, Kappes JC, Barnes S.
    Purification of CFTR for mass spectrometry analysis: identification of palmitoylation and other post-translational modifications.
    Protein Eng Des Sel. 2012 Jan;25(1):7-14. Epub 2011 Nov 25. [PMID: 22119790] [PMCID: PMC3276306]


2011

  1. Whitehouse-Tedd KM, Cave NJ, Ugarte CE, Waldron LA, Prasain JK, Arabshahi A, Barnes S, Thomas DG.
    Dietary isoflavone absorption, excretion, and metabolism in captive cheetahs (Acinonyx jubatus).
    J Zoo Wildl Med. 2011 Dec;42(4):658-70. [PMID: 22204061] [doi:10.1638/2011-0060.1]

  2. Edmonds JW, McKinney SL, Prasain JK, Miller MA.
    The gap junctional protein INX-14 functions in oocyte precursors to promote C. elegans sperm guidance.
    Dev Biol. 2011 Nov 1;359(1):47-58. Epub 2011 Aug 25. [PMID: 21889935] [PMCID: PMC3192278]

  3. Li FJ, Kubagawa Y, McCollum MK, Wilson L, Motohashi T, Bertoli LF, Barton JC, Barnes S, Davis RS, Kubagawa H.
    Enhanced levels of both membrane-bound and soluble forms of IgM Fc receptor in patients with chronic lymphocytic leukemia.
    Blood. 2011 Nov 3;118(18):4902-9. [PMID: 21908424]

  4. Buckoreelall K, Wilson L, Parker WB.
    Identification and characterization of two adenosine phosphorylase activities in Mycobacterium smegmatis.
    J Bacteriol. 2011 Oct;193(20):5668-74 [PMID: 21821769] [doi:10.1128/JB.05394-11]

  5. Frölich MA, Arabshahi A, Katholi C, Prasain J, Barnes S.
    Hemodynamic characteristics of midazolam, propofol, and dexmedetomidine in healthy volunteers. J Clin Anesth. 2011 May;23(3):218-23. [PMID: 21570617]

  6. Barnes S, Prasain J, D'Alessandro T, Arabshahi A, Botting N, Lila MA, Jackson G, Janle EM, Weaver CM.
    The metabolism and analysis of isoflavones and other dietary polyphenols in foods and biological systems.
    Food Funct. 2011 May 25;2(5):235-44. [PMID: 21779561] [DOI: 10.1039/C1FO10025D]

  7. Li F, Glinskii OV, Zhou J, Wilson LS, Barnes S, Anthony DC, Glinsky VV.
    Identification and analysis of signaling networks potentially involved in breast carcinoma metastasis to the brain.
    PLoS One. 2011;6(7):e21977. [PMID: 21779361]

  8. Anderson JT, Zeng M, Li Q, Stapley R, Moore DR 2nd, Chenna B, Fineberg N, Zmijewski J, Eltoum IE, Siegal GP, Gaggar A, Barnes S, Velu SE, Thannickal VJ, Abraham E, Patel RP, Lancaster JR Jr, Chaplin DD, Dransfield MT, Deshane JS.
    Elevated levels of NO are localized to distal airways in asthma.
    Free Radic Biol Med. 2011, 50(11):1679-88 [PMID:21419218]

  9. Floyd KA, Stella DR, Wang CC, Laurentz S, McCabe GP, Srivastava OP, Barnes S.
    Genistein and genistein-containing dietary supplements accelerate the early stages of cataractogenesis in the male ICR/f rat.
    Exp Eye Res. 2011, 92(2):120-7. [PMID: 21147102] [PMCID:PMC3034771]

  10. Rajbhandari, R, Peng, N, Moore, DR, Arabshahi, A, Wyss, JM, Barnes S, Jeevan K. Prasain JK.
    Determination of cranberry phenolic metabolites in rats by liquid chromatography-tandem mass spectrometry.
    J Agric Food Chem, 2011, 59(12):6682-8. [PMID: 21634376]

  11. Mirza S, Wilson L, Benjamin WH Jr, Novak J, Barnes S, Hollingshead SK, Briles DE.
    Serine protease PrtA from Streptococcus pneumoniae plays a role in the killing of S. pneumoniae by apolactoferrin.
    Infect Immun. 2011 79(6):2440-50. [PMID:21422179]

  12. Byer SJ, Eckert JM, Brossier NM, Clodfelder-Miller BJ, Turk AN, Carroll AJ, Kappes JC, Zinn KR, Prasain JK, Carroll SL.
    Tamoxifen inhibits malignant peripheral nerve sheath tumor growth in an estrogen receptor-independent manner.
    Neuro Oncol. 2011, 13(1):28-41. [PMID:21075781]

  13. Pressey JG, Pressey CS, Robinson G, Herring R, Wilson L, Kelly DR, Kim H.
    2D-difference gel electrophoretic proteomic analysis of a cell culture model of alveolar rhabdomyosarcoma.
    J Proteome Res. 2011, 10(2):624-36. Epub 2011 Jan 10. [PMID:21110518] [PMCID:PMC3071502]

  14. DeAngelis JT, Li Y, Mitchell N, Wilson L, Kim H, Tollefsbol TO.
    2D difference gel electrophoresis analysis of different time points during the course of neoplastic transformation of human mammary epithelial cells.
    J Proteome Res. 2011, 10(2):447-58. [PMID:21105747]

2010

  1. Edmonds JW, Prasain JK, Dorand D, Yang Y, Hoang HD, Vibbert J, Kubagawa HM, Miller MA.
    Insulin/FOXO Signaling Regulates Ovarian Prostaglandins Critical for Reproduction.
    Dev Cell. 2010 Dec 14;19(6):858-71. [PMID: 21145501]

  2. Deangelis JT, Li Y, Mitchell N, Wilson L, Kim H, Tollefsbol T.
    2D Difference Gel Electrophoresis Analysis of Different Time Points During the Course of Neoplastic Transformation of Human Mammary Epithelial Cells.
    J Proteome Res. 2010 Nov 24. [Epub ahead of print] [PMID: 21105747] [DOI: 10.1021/pr100533k]

  3. Snelgrove RJ, Jackson PL, Hardison MT, Noerager BD, Kinloch A, Gaggar A, Shastry S, Rowe SM, Shim YM, Hussell T, Blalock JE.
    A critical role for LTA4H in limiting chronic pulmonary neutrophilic inflammation.
    Science. 2010 Oct 1;330(6000):90-4. [PMID 20813919]

  4. Byer SJ, Eckert JM, Brossier NM, Clodfelder-Miller BJ, Turk AN, Carroll AJ, Kappes JC, Zinn KR, Prasain JK, Carroll SL.
    Tamoxifen inhibits malignant peripheral nerve sheath tumor growth in an estrogen receptor-independent manner.
    Neuro Oncol. 2010 Nov 12. [Epub ahead of print] [PMID: 21075781]

  5. Stella DR, Floyd KA, Grey AC, Renfrow MB, Schey KL, Barnes S.
    Tissue localization and solubilities of {alpha}A-crystallin and its numerous C-terminal truncation products in pre- and post-cataractous ICR/f rat lenses.
    Invest Ophthalmol Vis Sci. 2010 Oct;51(10):5153-61. [PMID: 20435586]

  6. Raska M, Takahashi K, Czernekova L, Zachova K, Hall S, Moldoveanu Z, Elliot MC, Wilson L, Brown R, Jancova D, Barnes S, Vrbkova J, Tomana M, Smith PD, Mestecky J, Renfrow MB, Novak J.
    Glycosylation patterns of HIV-1 gp120 depend on the type of expressing cells and affect antibody recognition.
    J Biol Chem. 2010 Jul 2;285(27):20860-9. [PMID: 20439465]

2009

  1. Pyle LC, Fulton JC, Sloane PA, Backer K, Mazur M, Prasain J, Barnes S, Clancy JP, Rowe SM.
    Activation of CFTR by the Flavonoid Quercetin: Potential Use as a Biomarker of ΔF508 CFTR Rescue
    Am J Respir Cell Mol Biol. 2009 Dec 30. [PMID: 20042712]

  2. Peng N, Prasain JK, Dai Y, Moore R, Arabshahi A, Barnes S, Carlson S, Wyss JM.
    Chronic dietary kudzu isoflavones improve components of metabolic syndrome in stroke-prone spontaneously hypertensive rats.
    J Agric Food Chem. 26;57(16):7268-73, 2009. [PMID: 19938872]

  3. Prasain JK, Peng N, Dai Y, Moore R, Arabshahi A, Wilson L, Barnes S, Michael Wyss J, Kim H, Watts RL.
    Liquid chromatography tandem mass spectrometry identification of proanthocyanidins in rat plasma after oral administration of grape seed extract.
    Phytomedicine, 16(2-3):233-43, 2009. [PMID: 19095430]

  4. Prasain JK, Peng N, Moore R, Arabshahi A, Barnes S, Wyss JM.
    Tissue distribution of puerarin and its conjugated metabolites in rats assessed by liquid chromatography-tandem mass spectrometry.
    Phytomedicine, 16(1); 65-71, 2009. [PMID: 19027277]

  5. Wong WW, Lewis RD, Steinberg FM, Murray MJ, Cramer MA, Amato P, Young RL, Barnes S, Ellis KJ, Shypailo RJ, Fraley JK, Konzelmann KL, Fischer JG, Smith EO.
    Soy isoflavone supplementation and bone mineral density in menopausal women: a 2-y multicenter clinical trial.
    Am J Clin Nutr. 2009 Sep 16. Epub 2009 Sep 16. [DOI: 10.3945/ajcn.2009.28001] [PMID: 19759166]

  6. Cox KB, Liu J, Tian L, Barnes S, Yang Q, Wood PA.
    Cardiac hypertrophy in mice with long-chain acyl-CoA dehydrogenase or very long-chain acyl-CoA dehydrogenase deficiency.
    Laboratory Investigation, 2009 Sep 7. [DOI: 10.1038/labinvest.2009.86] [PMID: 19736549]

  7. Kim, Helen.
    Mass Spectrometry for non-mass spectroscopists.
    INVITED BOOK EDITORSHIP for Methods in Molecular Biology series, John Walker, ed. Humana Press., Slated for 2009.

  8. Kim, Helen.
    Proteomics and Mass Spectrometry approaches in the study of actions of dietary bioactive phytochemicals.
    INVITED BOOK EDITORSHIP for Methods in Molecular Biology series, John Walker, ed. Humana Press, slated for 2010.

2008

  1. Mullany LC, Khatry SK, Sherchand JB, LeClerq SC, Darmstadt GL, Katz J, Gauchan P, Adhikari RK, Rana A, Tielsch JM.
    A randomized controlled trial of the impact of chlorhexidine skin cleansing on bacterial colonization of hospital-born infants in Nepal.
    Pediatr Infect Dis J. 27(6):505-11, 2008. [PMID: 18449064]

  2. Prasain JK, Arabshahi A, Moore R, Barnes S, Carroll SL.
    A liquid chromatography mass spectrometry assay for determination of PD168393, a specific and irreversible inhibitor of erbB membrane tyrosine kinases, in rat serum.
    Journal of Chromatogr B. 876(2): 219-224, 2008

  3. Prasain J.K., Jones, K., Moore, D.R., Barnes, S., Leahy, M., Roderick, R., Juliana, M.M. and Grubbs, C.J.
    Effect of cranberry juice concentrate on chemically-induced urinary bladder cancers.
    Oncology Reports, 19: 1565-1570, 2008.

  4. Sarkar P, Sarkar S, Ramesh V, Kim H, Barnes S., Kulkarni A, Hall JC, Wilson BL, Thomas RL, Pellis NR, Ramesh GT.
    Proteomic Analysis of Mouse Hypothalamus under Simulated Microgravity.
    Neurochem Res. 33(11):2335-41, 2008.

  5. Barnes, S., Shonsey, E.M., Eliuk, S.M., Stella, D., Mafia, K., Kim, H., Srivastava, O.P., Renfrow, M.B.
    High-resolution mass spectrometry and inactivation of protein targets during oxidant stress.
    Biochemical Society Transactions, 36(Pt 5): 1037-44, 2008.

  6. Kim, H., Cope, M., Herring, R., Robinson, G., Wilson, L., Page, G.P., Barnes, S.
    2D Difference Gel Electrophoresis of Prepubertal and Pubertal Rat Mammary Gland Proteomes.
    Journal of Proteome Research, 7(11): 4638-4650, 2008.

  7. Barnes, S., Birt, D.F., Cassileth, B.R. Cefalu, W.T., Chilton, F.H., Farnsworth, N.R., Raskin, I., van Breemen, R.B., Weaver, C.M.
    Technologies and experimental approaches in the NIH Botanical Research Centers.
    American Journal of Clinical Nutrition, 87(2): 476S-80S, 2008.

  8. Shonsey, E.M., Eliuk, S.M., Johnson, M.S., Barnes, S., Falany, C.N , Darley-Usmar, V.M. and Renfrow, M.B.
    Inactivation of human liver bile acid CoA:amino acid N-acyltransferase by the electrophilic lipid, 4-hydroxynonenal.
    Journal of Lipid Research, 49(2): 282-94, 2008.

  9. Weaver, C.M., Barnes, S.,Wyss, J.M., Kim, H., Morré, D.M., Morré, D.J., Simon, J.E., Lila, M.A., Janle, E.M., Ferruzzi, M.G..
    Botanicals for age-related diseases: from field to practice.
    American Journal of Clinical Nutrition, 87(2): 493S-7S, 2008

2006

  1. Poonam Sarkar, Shubhashish Sarkar, Vani Ramesh, Barbara E. Hayes, Renard L. Thomas, Bobby L. Wilson, Helen Kim, Stephen Barnes, Anil Kulkarni, Neal Pellis, and Govindarajan T. Ramesh
    Proteomic Analysis of Mice Hippocampus in Simulated Microgravity Environment
    Journal of Proteome Research, 5, 548-553, 2006.

  2. Barnes, S., Prasain, J.K., Wang, C-C., Moore, D.R., II.
    Applications of LC-MS in the study of the uptake, distribution, metabolism and excretion of bioactive polyphenols from dietary supplements.
    Life Sciences, Feb 2, 2006.

  3. Landar, A., Giles, N.M., Oh, J-Y., Foxwell, A., Kirk, M., Barnes, S., and Darley-Usmar, V.M.
    A sensitive method for the quantitative measurement of protein thiol modification in response to oxidative stress.
    Free Radical Biology and Medicine, 40, 459-468,, 2006.

  4. Horn-Ross, P.L., Barnes, S., Lee, V.S., Collins, C.N., Reynolds, P., Lee, M.M., Stewart, S.L., Canchola, A.J., Wilson, L., Jones, K.
    Reliability and Validity of an Assessment of Usual Phytoestrogen Consumption.
    Cancer Causes and Control, 17:85-93, 2006.

  5. Helen Kim, Jessy Deshane, Stephen Barnes, Sreelatha Meleth
    Proteomics analysis of the actions of grape seed extract in rat brain: technological and biological implications for the study of the actions of psychoactive compounds.
    Life Sciences 78: 2060-2065, 2006.

  6. Helen Kim, Shannon Eliuk, and Jessy Deshane, Stephen Barnes, Sreelatha Meleth
    Nutriproteomics Approach to Understanding Dementia-Relevant Brain Protein Changes in Response to Grape Seed Extract, a Dietary Antioxidant
    Oxidative Stress and Age-Related Neurodegeneration edited by Yuan Luo
    CRC Press, 2006, Chapter 26, ISBN: 0849337259

  7. Huang, C.M., Wang, C.C., Kawai, M., Barnes, S., and Elmets, C.A.
    Surfactant sodium lauryl sulfate enhances skin vaccination: Molecular characterization via a novel technique using ultrafiltration capillaries and mass spectrometric proteomics.
    Molecular & Cellular Proteomics 5:523-532, 2006.

  8. Hsu, H.C., Zhou, T., Kim, H., Barnes, S., Yang, P., Wu, Q., Zhou, J., Freeman, B.A., Luo, M., Mountz, J.D.
    Production of a novel class of polyreactive pathogenic autoantibodies in BXD2 mice causes glomerulonephritis and arthritis.
    Arthritis & Rheumatism 54: 343-355, 2006.

  9. Huang, C.M., Wang, C-C., Kawai, M., Barnes, S., Elmets, C.A.
    In vivo protein sampling using capillary ultrafiltration semi-permeable hollow fiber and protein identification via mass spectrometry-based proteomics.
    J Chromatogr A, 1109: 144-151, 2006.

  10. Barnes, S.
    In the postgenomic era, can high-dimensional analyses deliver the answers we're looking for?
    Journal of Nutrition 136: 2709S-2710S, 2006.

  11. Huang CM, Ananthaswamy HN, Barnes S, Ma Y, Kawai M, Elmets CA.
    Mass spectrometric proteomics profiles of in vivo tumor secretomes: Capillary ultrafiltration sampling of regressive tumor masses.
    Proteomics 6: 6107-6116, 2006.

  12. Prasain, J.K., Reppert, A., Jones, K., Moore, D.R., II, Barnes, S., and Lila, M.A.
    Identification of Isoflavone Glycosides in Pueraria lobata Cultures by Tandem Mass Spectrometry.
    Phytochemical Analysis, 18: 50-59, 2006.

  13. Prasain, J.K., Xu, J., Kirk, M., Smith, M., Sfakianos, J., and Barnes, S.
    Differential biliary excretion of genistein metabolites following intraduodenal and intravenous infusion of genistin in female rats.
    Journal of Nutrition, 136:2975-2979, 2006.

2005

  1. Barnes, S., Prasain, J.K.
    Current Progress in the use of Traditional Medicines and Nutraceuticals.
    Current Opinions in Plant Biology, 8: 324-328, 2005.

  2. Allison, D.B., Cutter, G., Poehlman E.T., Moore, D.R. II, Barnes, S.
    Exactly which synephrine alkaloids does Citrus Aurantium (bitter orange) contain?
    International Journal of Obesity, 29:443-446, 2005.

  3. Cai, J., Zhao, Y., Glasier, J., Cullen, D., Barnes, S., Turner, C., and Weaver, C.
    Comparative effect of soy protein, soy isoflavones and 17β-estradiol on bone metabolism in adult ovariectomized rats.
    Journal of Bone and Mineral Research, 20: 828-839, 2005.

  4. Prasain JK, Moore DR, Barnes S, van Kuijk FJGM.
    Electrospray Tandem Mass Spectrometric Analysis of Carotenoids and their Oxidation Products.
    Journal of Mass Spectrometry, 40: 916-923, 2005.

  5. Hedlund, T.E., Maroni, P.D., Ferucci, P.G., Dayton, R., Barnes, S., Jones, R., Moore, D.R., Ogden, L.G., Wähälä, K., Sackett, H.M, and Gray, K.J.
    Long-term dietary habits affect soy isoflavone metabolism and accumulation in prostatic fluid in caucasian men.
    Journal of Nutrition, 135: 1400-1406, 2005.

  6. Uppala, P.T., Roy, S.K., Tousson, A., Barnes, S., Uppala, G.R., and Eastmond, D.A.
    Induction of cell proliferation, micronuclei and hyperdiploidy/polyploidy in the mammary cells of DDT- and DMBA-treated pubertal rats.
    Environmental and Molecular Mutagenesis, 46, E Pub, 2005.

  7. Chacko, B.K., Robert Chandler, R.T., Mundhekar, A., Pruitt, H.M., Kucik, D.F., Kevil, C.G., Barnes, S., Patel, R.P.
    Revealing anti-inflammatory mechanisms of soy-isoflavones by flow: modulation of leukocyte-endothelial cell interactions.
    American Journal of Physiology, 289: H908-H915, 2005.

  8. Yang, X., Wang, J., Liu, C., Grizzle, W.E., Yu, S., Zhang, S., Barnes, S., Koopman, W.J., Mountz, J.D., Kimberly, R.P., and Zhang, H-G.
    Cleavage of p53-vimentin complex enhances tumor necrosis factor-related apoptosis-inducing ligand-mediated apoptosis of rheumatoid arthritis synovial fibroblasts.
    American Journal of Pathology, 167: 705-719, 2005.

  9. Kaput, J., Ordovas, J.M., Ferguson, L., van Ommen, B, Rodriguez, R.L., Allen, L., Ames, B.N., Dawson, K., German, B., Krauss, R., Malyj, W., Archer, M.C., Barnes, S., Bartholomew, A., Birk, R., van Bladeren, P., Bradford, K.J., Brown, K.H., Caetano, R., Castle, D., Chadwick, R., Clarke, S., Clément, K., Corella. D., da Cruz, I.M., Daniel, H., Duster, T., Sven O.E. Ebbesson, S.O, Elliott, R, Fairweather-Tait, S., Felton, J., Fenech, M., Finley, J.W., Fogg-Johnson, N., Gill-Garrison, R., Gibney, M.J., Gillies, P.J., Gustafsson, J-A.,Hartman, J.L. IV, He, L., Hwang, J-K., Jang, Y., Joost, H., Junien, C., Kanter, M., Kibbe, W.A., Koletzko, B., Korf, B.R., Kornman, K., Krempin, D.W., Langin, D., Lauren, D.R., Lee, J.H., Leveille, G.A., Lin, S-J., Mathers, J., Mayne, M., McNabb, W., Milner, J.A., Morgan, P., Muller, M., Nikolsky, Y., van der Ouderaa, F., Park, T., Pensel, N., Perez-Jimenez, F., Jean-Philippe, Kaisa Poutanen, Roberts, M., Saris, W., Schuster, G., Shelling, A.N., Simopoulos, A.P., Southon, S., Tai, E.S., Towne, B, Trayhurn, P., Uauy, R., Willard J. Visek, W.J., Warden, C., Weiss, R., Wiencke, J., Winkler, J., Wolff, G.L., Zhao-Wilson, X., Zucker, J-D.
    The Case for Strategic International Alliances to Harness Nutritional Genomics for Public and Personal Health.
    British Journal of Nutrition, 94:623-632, 2005.

  10. Meezan, E., Meezan, E.M., Jones, K., Moore II, D.R., Barnes, S., and Prasain, J.K.
    Contrasting effects of the isoflavones glucosides puerarin and daidzein on glucose metabolism in mice.
    Journal of Agricultural and Food Chemistry, 53, 8760-8767, 2005.

  11. Zakharkin S.O., Kim, K., Mehta, T., Chen, L., Barnes, S., Scheirer, K.E., Parrish, R.S., Allison, D.B., and Page, G.P..
    Sources of variation in Affymetrix microarray experiments.
    BMC Bioinformatics, 6:214, 2005.

  12. Prasain, J.K., Reppert, A., Jones, K., Moore, D.R., II, Barnes, S., and Lila, M.A.
    Identification of isoflavone glycosides in Pueraria lobata cultures by tandem mass spectrometry.
    Phytochemical Analysis, accepted for publication, 2005.

  13. Huang, C.M., Elmets, C.A., van Kampen, K.R., DeSilva, T.S., Barnes, S., Kim, H., and Tang, D.C.
    Prospective highlights of functional skin proteomics.
    Mass Spectrometry Reviews, 24, 647-660, 2005.
        This is an invited review on the application of proteomics and mass spectrometry techniques to explore the proteome of the skin in disease.

  14. Helen Kim
    New Nutrition, Proteomics, and How Both Can Enhance Studies in Cancer Prevention and Therapy.
    American Society for Nutrition J. Nutr. 135:2715-2718, November 2005.

2004

  1. Schuler, A.M., Barnes, S., Gower, B.A., and Wood, P.A.
    Dietary Phytoestrogens Increase Metabolic Resistance (Cold Tolerance) in Long-Chain Acyl-CoA Dehydrogenase-Deficient Mice
    Journal of Nutrition, 134:1028-1031, May 2004.

  2. Aparna Venkatraman, Aimee Landar, Ashley J. Davis, Laura Chamlee, Todd Sanderson, Helen Kim, Grier Page, Melissa Pompilius, Scott Ballinger, Victor Darley-Usmar, and Shannon M. Bailey.
    Modification of the Mitochondrial Proteome in Response to the Stress of Ethanol-dependent Hepatotoxicity.
    The Journal of Biological Chemistry, 279: 22092-22101,2004.

  3. Stephen Barnes and Helen Kim
    Nutriproteomics: Identifying the Molecular Targets of Nutritive and Non-nutritive Components of the Diet.
    Journal of Biochemistry and Molecular Biology, 37: 59-74, 2004.
        This review concerns how to apply proteomics and mass spectrometry to the discovery of the biologically active components of the diet.

  4. Helen Kim, PhD, Grier P. Page, PhD, and Stephen Barnes, PhD
    Proteomics and Mass Spectrometry in Nutrition Research.
    Nutrition, 20:155-165, 2004.
        This paper reviews the technologies of 2D-gel proteomics and mass spectrometry (MALDI and nanoLC-tandem mass spectrometry) as they can be applied to modern nutrition research with particular reference to experimental design. It is part of a special issue of Nutrition on nutrigenomics.

  5. Prasain, J.K., Jones, K., Brissie, N., Moore, D.R. II, Wyss, J.M., Barnes, S.
    Identification of puerarin and its metabolites in rats by liquid chromatography-tandem mass spectrometry.
    Journal of Agricultural Food Chemistry, 52: 3708-3712, 2004.
        This piece of work established a quantitative LC-MRM-MS assay for the measurement of puerarin. It was applied to studies in rats of the uptake and metabolism of this Kudzu isoflavone. It was shown that puerarin was absorbed intact and rapidly excreted in urine. It underwent minor metabolism to mono- and dihydroxylated forms as well as to daidzein and equol after 2-3 days.

  6. Foxwell, A.I., Wilson, L., Kirk, M., Coward, L., Darley-Usmar, V.M. and Barnes, S.
    Modification of cytochrome c by 4-hydroxy-2-nonenal: evidence for histidine, lysine and arginine-aldehyde adducts.
    Journal of American Society of Mass Spectrometry 15: 1136-1147, 2004.
        The reaction of cytochrome c with the reactive aldehyde 4HNE formed from oxidation of unsaturated fatty acid was studied using MALDI-TOF-MS and nanoLC-tandem mass spectrometry. Formation of up to four 4HNE adducts was discernable, three of which were fully characterized. This is the first demonstration of an arginine adduct.

  7. Prasain, J., Wang, C-C., and Barnes, S.
    Mass spectrometric methods for the determination of flavonoids in biological samples.
    Free Radical Biology and Medicine, 37: 1324-1350, 2004.
        This invited paper is an extensive review of the use of mass spectrometry for the analysis of flavonoids. It includes GC-MS, LC-MS and capillary electrophoresis-MS and MALDI-TOF, ESI, ion trap and FT-ICR techniques.

  8. Kim, H., Hall, P., Smith, M., Kirk, M., Prasain, J.K., Barnes, S., Grubbs, C.
    Chemoprevention by Grape Seed Extract and Genistein in Carcinogen-induced Mammary Cancer in Rats Is Diet Dependent.
    Journal of Nutrition, 134: 3445S-3552S, 2004.

  9. Jessy Deshane, Lisa Chaves, Kiran Varma Sarikonda, Scott Isbell, Landon Wilson, Marion Kirk, Clinton Grubbs, Stephen Barnes, Sreelatha Meleth, Helen Kim
    Proteomics Analysis of Rat Brain Protein Modulations by Grape Seed Extract.
    Journal of Agricultural Food Chemistry, 52: 7872-83, 2004.

2003

  1. Lanman, J., Lam, T., Barnes, S., Sakalian, M., Emmett, M.R., Marshall, A.G., and Prevelige, P.E., Jr.
    Identification of novel interactions in HIV-1 capsid protein assembly by high resolution mass spectrometry.
    Journal of Molecular Biology, 325:759-772, 2003.
        This piece of work concerns the folding of the capsid protein in the HIV-1 virus. A critical feature of this study was the use of high resolution FT-ICR mass spec to rapidly measure deuterium isotope enrichment in pepsin-derived capsid protein peptides.

  2. Aslan, M, Barnes, S., Kirk, M, Rosenfeld, S, Townes, T, Ryan, T and BA Freeman.
    Nitric oxide-dependent generation of reactive species in sickle cell disease: renal and hepatocellular actin tyrosine nitration.
    Journal of Biological Chemistry, 278: 4194-4204, 2003.
    Journal of Biological Chemistry, accepted for publication .
        In this piece of research from Dr. Bruce Freeman's laboratory and carried out by Dr. Mutay Aslan, a ombination of MALDI peptide fingerprinting and anti-nitrotyrosine antibody immunoaffinity isolation of nitrated proteins, followed by peptide sequencing using LC-MSMS, was used for the first time to identify several specific sites of actin nitration that occur in vivo.

  3. Prasain, J.K., Jones, K., Kirk, M., Wilson, L., Smith-Johnson, M., Weaver, C.M., Barnes, S.
    Profiling and Quantification of Isoflavonoids in Kudzu Dietary Supplements by High-Performance Liquid Chromatography and Electrospray Ionization Tandem Mass Spectrometry.
    Journal of Agricultural Food Chemistry, 51:4213-4218, 2003.
        This paper explored the isoflavonoid content of dietary supplements based on the root of the Kudzu, a Japanese vine that is found covering the ground and often trees in the Deep South. The key issue was the demonstration that the principal isoflavones was puerarin, a 8-C-glucoside of daidzein. It is has a unique tandem mass spectrum compared to O-linked glucosides.

  4. Prasain, J.K., Boersma, B.J., Kirk, M., Wilson, L., Patel, R., Darley-Usmar, V.M., Botting, N. and Barnes, S.
    Mass spectrometric methods for the analysis of chlorinated and nitrated isoflavonoids: a novel class of biological metabolites.
    Journal of Mass Spectrometry, 38: 764-771, 2003.
        This paper examines the tandem mass spectra of isoflavone derivatives (chlorinated and nitrated) formed by reaction with reactive oxygen species.

  5. Carballal, S., Radi, R., Kirk, M.C., Barnes, S., Freeman, B.A. and Alvarez, B.
    Sulfenic acid formation in human serum albumin by hydrogen peroxide and peroxynitrite.
    Biochemistry, 42: 9906-9914, 2003.
        This paper utilized LC-tandem mass spectrometry to identify the oxidation of a critical cysteine residue on albumin by oxidizing agents, including peroxynitrite.

  6. Boersma, B.J., D'Alessandro, T., Benton, M.R., Kirk, M., Wilson, L.S., Prasain, J., Botting, N.P., Barnes, S., Darley-Usmar, V.M. and Patel, R.P.
    Neutrophil myeloperoxidase chlorinates soy isoflavones and enhances their antioxidant properties.
    Free Radical Biology and Medicine, 35:1417-1430, 2003.
        This paper demonstrates sing LC-MS that HL-60 cells differentiated with DMSO to form neutrophil-like cells rapidly and completely convert isoflavones to their chlorinated metabolites. These metabolites have greater antioxidant properties in Cu-stimulated LDL oxidation assays.

  7. D'Alessandro, T., Prasain, J., Botting, N.P, Moore, R., Darley-Usmar, V.M., Patel, R.P., and Barnes, S.
    Polyphenols, inflammatory response, and cancer prevention: chlorination of isoflavones by human neutrophils.
    Journal of Nutrition,133:3773S-3777S, 2003.
        The principal point of this paper was the demonstration using LC-MS that freshly isolated human neutrophils when stimulated convert the isoflavone genistein to chlorinated metabolites.

  8. He, D., Barnes, S, Falany, C.N.
    Rat liver bile acid CoA:amino acid N-acyltransferase : expression, characterization, and peroxisomal localization
    Journal of Lipid Research, on line September 1, 2003.

  9. Page G.P., Edwards J.W., Barnes S., and Allison, D.B.
    A Design and Statistical Perspective on Microarray Gene Expression Studies in Nutrition: The Need for Playful Creativity and Scientific Hard-Mindedness.
    Nutrition, 19: 997-1000, 2003.

2002

  1. Sfakianos, M., Wilson, L., Sakalian, M., Falany, C.N., and Barnes, S.
    Conserved Residues in the Putative Catalytic Triad of Human Bile Acid Coenzyme A:Amino Acid N-Acyltransferase.
    Journal of Biological Chemistry, 277: 47270-47275, 2002.
        In this paper, LC-MS was used to identify and quantitate the bile acid products formed in the reaction between bile acid CoA. glycine and taurine and wild type and mutants of the hepatic enzyme, bile acid CoA:amino acid
    N-acyltransferase.

  2. Falany, C.N., Xie, X, Wheeler, J.B., Wang, J., Smith, M., He, D., and Barnes, S.
    Molecular cloning and expression of rat liver bile acid CoA ligase.
    Journal of Lipid Research, 43: 2062-2071, 2002.
         In this paper, LC-MS was used to identify and quantitate the products formed in the reaction between bile acids and the epatic enzyme, bile acid CoA ligase.

  3. Kim, H., Chaves, L., Mills, R., Oh, J-Y., DeSilva T., Coward, L., Kirk, M. and Barnes, S.
    Effects of soy on proteins implicated in dementias and other neurodegenerative conditions: the use of proteomics technology to assess protein changes.
    In: Soy and Health, 2002: Clinical Evidence and Dietetic Applications, Ed. Descheemaeker, K., Debruyne, I., Garant Publishers, Antwerp-Apeldoorn, pp 155-166, 2002.

  4. Barnes, S.
    New technologies in soy research. What can they bring?
    In: Soy and Health 2002: Clinical Evidence and Dietetic Applications, Ed. Descheemaeker, K., Debruyne, I., Garant Publishers, Antwerp-Apeldoorn, pp 39-50, 2002.

  5. Prasain, J., Wang, C-C., and Barnes, S.
    Mass spectrometry in the analysis of phytoestrogens in biological samples.
    In: Phytoestrogens and Health, Gilani, G.S. and Anderson, J.J., editors, AOCS Press, Champaign, IL, pp 147-177, 2002.

  6. Wang, C-C., Prasain, J., and Barnes, S.
    Review of the methods used in the determination of phytoestrogens.
    Journal of Chromatography, 777: 3-28, 2002.

  7. Barnes, S. and Messina, M.
    Introduction and Satellite Session at the Fourth International Symposium on the Role of Soy in Preventing and Treating Chronic Disease.
    Journal of Nutrition, 132: 545-546, 2002.

  8. Persky, V.W., Turyk, M.E., Wang, L., Freels, S., Chatterton, R., Jr, Barnes, S., Erdman, J., Jr, Sepkovic, D.W., Bradlow, H.L. and Potter.S.
    Effect of soy protein on endogenous hormones in postmenopausal women.
    American Journal of Clinical Nutrition. 75: 145-153, 2002.

  9. Brookes, P.S., Pinner, A., Ramachandran, A., Coward, L., Barnes, S., Kim, H., and Darley-Usmar, V.M.
    High throughput two-dimensional blue-native electrophoresis: A tool for functional proteomics of mitochondria and signaling complexes.
    Proteomics, 2: 969-977, 2002.
        This paper describes the effectiveness of 2-D "blue native" electrophoresis, where integral-membrane proteins are resolved as complexes in a non-denaturing first dimension electrophoresis step, then resolved in the second dimension via standard SDS-PAGE. Individual spots are identified by routine MALDI peptide fingerprinting.

  10. Patel, R.P., Boersma, B., Crawford, J.H., Hogg, N., Kirk, M., Kalyanaraman, B., Parks, D., Barnes, S. and Darley-Usmar, V.
    Antioxidant mechanisms of isoflavones in lipid systems: Paradoxical effects of peroxyl radical scavenging.
    Free Radical Biology and Medicine, 31:1570-1581, 2002.

2001

  1. Whitaker, B.D., Schmidt, W.F., Kirk, M.C. and Barnes, S.
    Novel Fatty-Acid Esters of p-Coumaryl Alcohol in Epicuticular Wax of Apple Fruit.
    Journal of Agricultural Food Chemistry, 49; 3787-3792, 2001.

  2. Boersma, B., S. Barnes, M. Kirk, C-C. Wang, M. Smith, H. Kim, J. Xu, R. Patel and V.M. Darley-Usmar.
    Soy isoflavonoids and cancer - metabolism at the target site.
    Mutation Research, 480: 121-127, 2001.

  3. Zhang, C., Eiserich, J., Reiter, C, Parks, D.A., Darley-Usmar, V., Beckman, J.S., Barnes, S., Kirk, M., and White, C.R.
    L-Arginine chlorination products inhibit endothelial nitric oxide production.
    Journal of Biological Chemistry, 276: 27159-27165, 2001.

  4. Binsack, R., Boersma, B.J., Patel,, R.P., Kirk, M.C., White, C.R., Darley-Usmar, V.M., Barnes, S., Zhou, F., and Parks, D.A..
    Enhanced antioxidant activity following chlorination of quercetin by hypochlorous acid.
    Alcoholism: Clinical and Experimental Research, 25: 434-443, 2001.

  5. Tuma, R., Coward, L. Kirk, M.C., Barnes, S., and Prevelige, P.E., Jr.
    Hydrogen-deuterium Exchange as a Probe of Folding and Assembly in Viral Capsids
    Journal of Molecular Biology, 306: 389-396, 2001.

  6. Urban, D., Irwin, W., Kirk, M., Markiewicz, M.A., Myers, R., Smith, M., Weiss, H., Grizzle, W.E. and Barnes, S.
    The effect of isolated soy protein on plasma biomarkers in elderly men with elevated serum prostate specific antigen.
    Journal of Urology 165:294-300, 2001.

2000

  1. Novak, J., Tomana, M., Kilian, M., Coward, L., Kulhavy, R., Barnes, S. and Mestecky, J.
    Heterogeneity of O-glycosylation in the hinge region of human IgA1.
    Molecular Immunology, 37: 1047-1056, 2000.

  2. Krull, R.E., Chen, P., Novak, J., Kirk, M., Barnes, S., Baker, J., Krishna, N.R. and Caufield, P.W.
    Biochemical structural analysis of the lantibiotic mutacin II.
    Journal of Biological Chemistry 275:15845-15850, 2000.

  3. Rubbo, H., Radi, R., Anselmi, D., Kirk, M., Barnes, S., Butler, J., Eiserich, J.P., and Freeman, B.A.
    Nitric Oxide Reaction with Lipid Peroxyl Radicals Spares α-Tocopherol during Lipid Peroxidation.
    Journal of Biological Chemistry 275: 10812-10818, 2000.

  4. King, L. III, S. Barnes, U. Glufke, M.E. Henz, M. Kirk, K.A. Merkler, J.C. Vederas, B.J. Wilcoz, and D.J. Merkler.
    The Enzymatic Formation of Novel Bile Acid Primary Amides.
    Archives of Biochemistry and Biophysics, 374: 107-117, 2000.

1999

  1. Boersma, B.J., Patel, R.P., Kirk, M., Darley-Usmar, V.M. and S.Barnes.
    Chlorination and Nitration of Soy Isoflavones.
    Archives of Biochemistry and Biophysics, 368: 265-275,1999.