I have had a longstanding interest in metabolism and enzymology and the enterohepatic circulation of endogenous and exogenous metabolites. Because of early training in hepatobiliary diseases, this led to studies on bile acid metabolism and purification of the enzymes catalyzing their formation. A second strong area of research has been the roles of polyphenols in health and disease, with a particular emphasis on soy isoflavones. Over the past decade, I have been pursuing the basis of lens cataract formation in the lens. An overarching theme for these research areas has been the pathways of metabolism and the utilization of mass spectrometry for their study. This had led to a strong interest in metabolomics and training in this re-emerging discipline.

Sweeny, D.J., S. Barnes, G.D. Heggie, R.B. Diasio.  Metabolism of 5-fluorouracil to an N-cholyl-2 fluoro beta alanine conjugate: Previously unrecognized role for bile acids in drug conjugation.  PNAS 84: 5439-5443, 1987.

Johnson, M., S. Barnes, J. Kwakye, R.B. Diasio.  Purification of human liver cholyl CoA:amino acid N-acyltransferase.  J Biol Chem 266: 10227-10233, 1991

Falany, C.N., Xie, X, Wheeler, J.B., Wang, J., Smith, M., He, D., Barnes, S.  Molecular cloning and expression of rat liver bile acid CoA ligase. J Lipid Res, 43: 2062-2071, 2002.

Barnes, S., J.M. Geckle.  High resolution nuclear magnetic resonance spectroscopy of bile salts:  individual proton assignments for aqueous sodium cholate at 400 MHz.  J Lipid Res 23: 161-170, 1982.

Waterhous, D. V., S. Barnes, D. D. Muccio.  Nuclear Magnetic Resonance Spectroscopy of Bile Acids.  Development of two dimensional NMR methods for the elucidation of proton resonance assignments for five common bile acids, and their parent bile acid, 5 beta-cholanoic acid.  J Lipid Res 26: 1068-1078, 1985

Isom, A.I., Wilson, L., Kirk, M., Coward, L., DarleyUsmar, V.M. and Barnes, S. Modification of cytochrome c by 4 hydroxy-2 nonenal: evidence for histidine, lysine and arginine aldehyde adducts. J Amer Soc Mass Spectrom 15: 1136-1147, 2004

McClure M, DeLucas LJ, Wilson L, Ray M, Rowe S, Wu X, Dai Q, Hong JS, Sorscher EJ, Kappes JC, Barnes S. Palmitoylation and other posttranslational modifications of CFTR with relevance to gating and processing. Protein Eng Des Sel. 2012 Jan;25(1):7-14. PMCID: PMC3276306

Stella DR, Floyd KA, Grey AC, Renfrow MB, Schey KL, Barnes S. Tissue localization and solubilities of αA-crystallin and its numerous C-terminal truncation products in pre- and postcataractous ICR/f rat lenses. IOVS. 2010;51:5153-61. PMCID: PMC3066599.

Barnes S, et al. Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data.  Journal of Mass Spectrometry, 2016 July;51:461-475. 

Barnes S, et al. Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future. Journal of Mass Spectrometry, 2016 August 4;51:535-548. 

Rainey E, Wilson LS, Barnes S, Wu H. Quantitative proteomics uncovers the interaction between a virulence factor and mutanobactin synthetases in Streptococcus mutans. mSphere. 2019 Sep 25;4(5). pii: e00429-19. PMCID: PMC6763767

Larson-Casey JL, Vaid M, Gu L, Cai GQ, Ding Q, Davis D, Berryhill TF, Wilson LS, Barnes S, Neighbors JD, Hohl RJ, Surolia R, Antony VB, Carter AB. Increased post-translational modification of Rho GTPases mediates fibrosis in the absence of injury. J Clin Invest 2019 Nov 1;129(11):4962-4978. PMID: 31609245

Kirilenko B, Hagey LR, Barnes S, Falany CN, Hiller M. Evolutionary analysis of bile acid-conjugating enzymes reveals a complex duplication and reciprocal loss history. Genome Biol Evol. 2019 Nov 1;11(11):3256-3268. PMID: 31670760.

Barnes S. Overview of Experimental Methods and Study Design in Metabolomics, and Statistical and Pathway Considerations. Methods Mol Biol. 2020;2104:1-10.

Sharma NS, Vestal G, Wille K, Patel KK, Tipparaju S, Patel K, Menon S, Gaggar A, Xu X, Tousif S, Cheng F, Barnes S, Wilson LS, Lal CV, Dishaw L, Weill D, Dunning J, Hayes, Jr. D, Deshane JS, Liu R. Lung Microbiome and Metabolome Differentiates Allograft from Native Lung In Single Lung Transplant Recipients. Respir Res. 2020 May 6;21(1):104.

Hoffman JM, Poonawalla A, Icyuz M, Swindell W, Wilson L, Barnes S, Sun LY. Transcriptomic and metabolomic profiling of long-lived growth hormone releasing hormone knock-out mice: Evidence for improved mitochondrial and amino acid metabolism. Aging (Albany NY). 2020 Feb 23;12(4):3473-3485.

Demirel A, Li J, Morrow C, Barnes S, Jansen J, Gower B, Kirksey K, Redden D, Yarar-Fisher C. Evaluation of a ketogenic diet for improvement of neurological recovery in individuals with acute spinal cord injury: study protocol for a randomized controlled trial. Trials. 2020 May 4;21(1):372.

Zengul AG, Demark-Wahnefried W, Barnes S, Morrow CD, Bertrand B, Berryhill TF, Frugé AD. Associations between Dietary Fiber, the Fecal Microbiota and Estrogen Metabolism in Postmenopausal Women with Breast Cancer. Nutr Cancer. 2020 Jun 26:1-10.

Ziemanski JF, Wilson L, Barnes S, Nichols KK. Saturation of cholesteryl esters produced by human meibomian gland epithelial cells after treatment with rosiglitazone. Ocul Surf. 2020 Nov 25:S1542-0124(20)30180-4.

Sharma M, Arora I, Stoll ML, Li Y, Morrow CD, Barnes S, Berryhill TF, Li S, Tollefsbol TO. Nutritional combinatorial impact on the gut microbiota and plasma short-chain fatty acids levels in the prevention of mammary cancer in Her2/neu estrogen receptor-negative transgenic mice. PLoS One. 2020 Dec 31;15(12):e0234893.

Oak ASW, Shafi R, Elsayed M, Mishra B, Bae S, Barnes S, Kashyap MP, Slominski AT, Wilson LS, Athar M, Elmets CA. Dietary table grape protects against photodamage in humans. J Am Acad Dermatol. 2021 Jan 20:S0190-9622(21)00184-5.

Curtis LM, George J, Vallon V, Barnes S, Darley-Usmar VM, Vaingankar S, Cutter GR, Gutierrez O, Seifert M, Ix J,Mehta RL, Sanders PW, Agarwal A. UAB-UCSD O’Brien Center for Acute Kidney Injury Research. Am J Physiol Renal Physiol. 2021 May 1;320(5):F870-F882.

Messina M, Mejia SB, Cassidy A, Duncan A, Kurzer M, Nagato C, Ronis M, Rowland I, Sievenpiper J, Barnes S. Neither soyfoods nor isoflavones warrant classification as endocrine disruptors: a technical review of the observational and clinical data. Critical Reviews in Food Science and Nutrition, 2021 - https://doi.org/10.1080/10408398.2021.1895054 .

Li J, Morrow C, Barnes S, Wilson L, Womack ED, McLain A, Yarar-Fisher C. Gut microbiome composition and serum metabolome profile among individuals with spinal cord injury and normal glucose tolerance or prediabetes/type 2 diabetes. Archives of Physical Medicine and Rehabilitation, Arch Phys Med Rehabil. 2021 Jun 12:S0003-9993(21)00438-X

Ziemanski JF, Wilson L, Barnes S, Nichols KK. Triacylglycerol Lipidome from Human Meibomian Gland Epithelial Cells: Description, Response to Culture Conditions, and Perspective on Function. Exp Eye Res. 2021 Apr 17;207:108573.

Chakraborti A, Graham C, Bru S, Vashi B, Umfress A, Kurup P, Vickers B, Chen A, Telange R, Berryhill TF, Van Der Pol W, Powell M, Barnes S, Morrow C, Smith D, Mukhtar S, Watts S, Kennedy G, Bibb J. High Fructose Corn Syrup-Enriched Diet Potentiates Anxio-Depressive Behavior and Alters Ventral Striatal Neuronal Signaling. Frontiers in Neuroscience, 2021 May 26;15:669410.

Khanal S, Ngo W, Nichols KK, Wilson LS, Barnes S, Nichols JJ. Human meibum and tear film derived (O-acyl)-omega-hydroxy fatty acids in meibomian gland dysfunction. Ocular Surface, 2021 Jul;21:118-128.

Khanal S, Bai Y, Ngo W, Nichols K, Wilson LS, Barnes S, Nichols JJ. Human Meibum and Tear Film (O-acyl)-Omega-Hydroxy Fatty Acids as Biomarkers of Tear Film Dynamics in Meibomian Gland Dysfunction and Dry Eye Disease. Invest Ophthalmol Vis Sci. 2021 Jul 1;62(9):13.

Weber SM, Brossier NM, Prechtl A, Barnes S, Wilson LS, Brosius SN, Longo JF, Carroll SL R-Ras subfamily proteins elicit distinct physiologic effects and phosphoproteome alterations in neurofibromin-null MPNST cells. Cell Commun Signal. 2021 Sep 16;19(1):95.

Pak HH, Haws SA, Koller M, Green CL, Richardson NE, Yang SE, Dumas SN, Sonsalla M, Bray L, Johnson MS, Barnes S, Darley-Usmar VM, Zhang J, Denu JM, Lamming DW. Fasting Drives the Metabolic, Molecular and Geroprotective Effects of a Calorie Restricted Diet. Nat Metab. 2021 Oct;3(10):1327-1341. PMC8544824

Khanal S, Bai Y, Ngo W, Nichols KK, Wilson L, Barnes S, Nichols JJ. Human meibum and tear film derived cholesteryl and wax esters in meibomian gland dysfunction and tear film structure. Ocul Surf. 2021 Nov 11;23:12-23. PMID: 34774809

Raines NH, Cheung M, Wilson LS, Edberg J, Erdmann N, Manickas-Hill Z, Agarwal A, Barnes S, Parikh S. Acute kidney injury in COVID-19 patients alters the urinary metabolome and is associated with NAD+ biosynthetic impairment. Kidney Int Rep. 2021 Dec;6 (12):3002-3013

Ziemanski JF, Wilson L, Barnes S, Nichols KK. Prostaglandin E2 and F2α Alter Expression of Select Cholesteryl Esters and Triacylglycerols Produced by Human Meibomian Gland Epithelial Cells. Cornea. 2022 Jan 1;41(1):95-105.

Li J, Morrow C, Barnes S, Wilson L, Womack ED, McLain A, Yarar-Fisher C. Gut Microbiome Composition and Serum Metabolome Profile Among Individuals with Spinal Cord Injury and Normal Glucose Tolerance or Prediabetes/Type 2 Diabetes. Arch Phys Med Rehabil. 2022 Apr;103(4):702-710.

Newman SD, Schnakenberg Martin AM, Raymond D, Cheng H, Wilson L, Barnes S, O'Donnell BF. The relationship between cannabis use and taurine: A MRS and metabolomics study. PLoS One. 2022 Jun 2;17(6):e0269280.

Aliabadi PM, Teuber R, Jani PK, Wilson L, Enghard P, Barnes S, Chiorazzi N, Radbruch A, Melchers F, Kubagawa H. Soluble Fc Receptor for IgM in Sera From Subsets of Patients With Chronic Lymphocytic Leukemia as Determined by a New Mouse Monoclonal Antibody. Front Immunol. 2022 Jun 16;13:863895.

Foksinska A, Crowder CM, Crouse AB, Henrikson J, Byrd WE, Rosenblatt G, Patton MJ , He K, Tran-Nguyen TK , Zheng M, Ramsey SA, Amin N, Osborne J, UAB Precision Medicine Institute and Might M. The Precision Medicine Process for Treating Rare Disease Using the Artificial Intelligence Tool mediKanren. Frontiers in Artificial Intelligence (section Medicine and Public Health) DOI 10.3389/frai.2022.910216

Chehade SB, Graham CD, Chakraborti A, Vashai , Moon A, Vickers B, Berryhill TF, Van Der Pol W, Wilson LS, Powell ML, Smith DL, Jr. , Barnes S, Morrow C, Mukhtar S, Bibb JA, Kennedy GD, Watts SA. A Modified Standard American Diet (mSAD) Induces Physiological Parameters Associated With Metabolic Syndrome In C57BL/6J Mice. Frontiers in Nutrition, 9:929446, 2022

Prasain JK, Wilson LS, Grubbs C, Barnes S. Gamma-ray irradiation of rodent diets alters the urinary metabolome in chemically-induced mammary cancer in rats. Metabolites 2022 Oct 16;12(10):976..

Carson JL,Buro AW, Miller D, Pena A, Ard JD, Lampe JW, Yi N, Lefkowitz EJ, van der Pol WJ, CD, Wilson L, Barnes, S, Demark-Wahnefried, W. Rationale and study protocol for a randomized controlled feeding study to determine the structural- and functional-level effects of diet-specific interventions on the gut microbiota of Non-Hispanic Black and White adults. Contemp Clin Trials. 2022 Oct 17:106968.