Recent Publications from MMC Members:

2018

The Role of Diaclyglycerol Acyltransferase (DGAT) 1 and 2 in Cardiac Metabolism and Function

Glucose Promotes Cell Growth by Suppressing Branched-Chain Amino Acid Degradation

NAD(H) in Mitochondrial Energy Transduction: Implications for Health and Disease

Raising NAD in Heart Failure: Time to Translate?

2017

Metabolomics and Gene Expression Analysis Reveal Down-regulation of the Citric Acid (TCA) Cycle in Non-diabetic CKD Patients.
Hallan S, Afkarian M, Zelnick LR, Kestenbaum B, Sharma S, Saito R, Darshi M, Barding G, Raftery D, Ju W, Kretzler M, Sharma K, de Boer IH. Metabolomics and Gene Expression Analysis Reveal Down-regulation of the Citric Acid (TCA) Cycle in Non-diabetic CKD Patients. EBioMedicine. 2017 Oct 31. pii: S2352-3964(17)30426-7.doi: 10.1016/j.ebiom.2017.10.027. [Epub ahead of print] PubMed PMID: 29128444.

Plasma metabolite abundances are associated with urinary enterolactone excretion in healthy participants on controlled diets
Miles FL, Navarro SL, Schwarz Y, Gu H, Djukovic D, Randolph TW, Shojaie A, Kratz M, Hullar MAJ, Lampe PD, Neuhouser ML, Raftery D, Lampe JW. Plasma metabolite abundances are associated with urinary enterolactone excretion in healthy participants on controlled diets. Food Funct. 2017 Sep 20;8(9):3209-3218. doi: 10.1039/c7fo00684e. PubMed PMID: 28808723; PubMed Central PMCID: PMC5607107.

Activation of γ2-AMPK Suppresses Ribosome Biogenesis and Protects Against Myocardial Ischemia/Reperfusion Injury
Cao Y, Bojjireddy N, Kim M, Li T, Zhai P, Nagarajan N, Sadoshima J, Palmiter RD, Tian R. Activation of γ2-AMPK Suppresses Ribosome Biogenesis and Protects Against Myocardial Ischemia/Reperfusion Injury. Circ Res. 2017 Oct27;121(10):1182-1191. doi: 10.1161/CIRCRESAHA.117.311159. Epub 2017 Aug 23. PubMed PMID: 28835357; PubMed Central PMCID: PMC5659937.

The effects of fatty acid composition on cardiac hypertrophy and function in mouse models of diet-induced obesity.
Nguyen S, Shao D, Tomasi LC, Braun A, de Mattos ABM, Choi YS, Villet O, Roe N, Halterman CR, Tian R, Kolwicz SC Jr. The effects of fatty acid composition on cardiac hypertrophy and function in mouse models of diet-induced obesity. J Nutr Biochem. 2017 Aug;46:137-142. doi: 10.1016/j.jnutbio.2017.05.009. Epub 2017 May 25. PubMed PMID: 28605665; PubMed Central PMCID: PMC5516950.

Mitochondrial Maturation in Human Pluripotent Stem Cell Derived Cardiomyocytes
Dai DF, Danoviz ME, Wiczer B, Laflamme MA, Tian R. Mitochondrial Maturation in Human Pluripotent Stem Cell Derived Cardiomyocytes. Stem Cells Int. 2017;2017:5153625. doi: 10.1155/2017/5153625. Epub 2017 Feb 27. PubMed PMID: 28421116; PubMed Central PMCID: PMC5380852.

Metabolism in cardiomyopathy: every substrate matters
Ritterhoff J, Tian R. Metabolism in cardiomyopathy: every substrate matters. Cardiovasc Res. 2017 Mar 15;113(4):411-421. doi: 10.1093/cvr/cvx017. PubMed PMID: 28395011.

Human Retinal Pigment Epithelium Cells prefer proline as a nutrient and transport metabolic intermediates to the retinal side
Chao JR, Knight K, Engel AL, Jankowski C, Wang Y, Manson MA, Gu H, Djukovic D, Raftery D, Hurley JB, Du J. Human Retinal Pigment Epithelium Cells prefer proline as a nutrient and transport metabolic intermediates to the retinal side. J Biol Chem. 2017 Jun 14. pii: jbc.M117.788422. doi: 10.1074/jbc.M117.788422. [Epub ahead of print] PubMed PMID: 28615447.

Whole Blood Metabolomics by (1)H NMR Spectroscopy  Provides a New Opportunity To Evaluate Coenzymes and Antioxidants
Nagana Gowda GA, Raftery D. Whole Blood Metabolomics by (1)H NMR Spectroscopy  Provides a New Opportunity To Evaluate Coenzymes and Antioxidants. Anal Chem. 2017 Apr 18;89(8):4620-4627. doi:10.1021/acs.analchem.7b00171. Epub 2017 Mar 30. PubMed PMID: 28318242.

A screen for protective drugs against delayed hypoxic injury
Sun CL, Zhang H, Liu M, Wang W, Crowder CM. A screen for protective drugs against delayed hypoxic injury. PLoS One. 2017 Apr 20;12(4):e0176061. doi:10.1371/journal.pone.0176061. eCollection 2017. PubMed PMID: 28426808; PubMed Central PMCID: PMC5398677.

Parenteral and enteral nutrition in surgical critical care: Plasma metabolomics demonstrates divergent effects on nitrogen, fatty-acid, ribonucleotide, and oxidative metabolism.
Parent BA, Seaton M, Djukovic D, Gu H, Wheelock B, Navarro SL, Raftery D, O’Keefe GE. Parenteral and enteral nutrition in surgical critical care: Plasma metabolomics demonstrates divergent effects on nitrogen, fatty-acid, ribonucleotide, and oxidative metabolism. J Trauma Acute Care Surg. 2017 Apr;82(4):704-713. doi: 10.1097/TA.0000000000001381. PubMed PMID: 28129265; PubMed Central PMCID: PMC5360523.

Candidate serum metabolite biomarkers for differentiating gastroesophageal reflux disease, Barrett’s esophagus, and high-grade dysplasia/esophageal adenocarcinoma.
Buas MF, Gu H, Djukovic D, Zhu J, Onstad L, Reid BJ, Raftery D, Vaughan TL. Candidate serum metabolite biomarkers for differentiating gastroesophageal reflux disease, Barrett’s esophagus, and high-grade dysplasia/esophageal adenocarcinoma. Metabolomics. 2017 Mar;13(3). pii: 23. doi: 10.1007/s11306-016-1154-y. Epub 2017  Jan 20. PubMed PMID: 28190989; PubMed Central PMCID: PMC5295138.

Whole Blood Metabolomics by 1H NMR Spectroscopy Provides a New Opportunity to Evaluate Coenzymes and Antioxidants
Gowda GA, Raftery D. Whole Blood Metabolomics by 1H NMR Spectroscopy Provides a New Opportunity to Evaluate Coenzymes and Antioxidants. Anal Chem. 2017 Mar 20. doi: 10.1021/acs.analchem.7b00171. [Epub ahead of print] PubMed PMID: 28318242.

A novel fission-independent role of dynamin-related protein 1 in cardiac mitochondrial respiration.
Zhang H, Wang P, Bisetto S, Yoon Y, Chen Q, Sheu SS, Wang W. A novel fission-independent role of dynamin-related protein 1 in cardiac mitochondrial respiration. Cardiovasc Res. 2017 Feb;113(2):160-170. doi: 10.1093/cvr/cvw212. Epub 2016 Oct 29. PubMed PMID: 27794519; PubMed Central PMCID: PMC5340145.

Defective Branched-Chain Amino Acid Catabolism Disrupts Glucose Metabolism and Sensitizes the Heart to Ischemia-Reperfusion Injury
Li T, Zhang Z, Kolwicz SC Jr, Abell L, Roe ND, Kim M, Zhou B, Cao Y,Ritterhoff J, Gu H, Raftery D, Sun H, Tian R. Defective Branched-Chain Amino Acid
Catabolism Disrupts Glucose Metabolism and Sensitizes the Heart to Ischemia-Reperfusion Injury. Cell Metab. 2017 Feb 7;25(2):374-385. doi:
10.1016/j.cmet.2016.11.005. PubMed PMID: 28178567; PubMed Central PMCID: PMC5301464.

Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry
Schweppe DK, Chavez JD, Lee CF, Caudal A, Kruse SE, Stuppard R, Marcinek DJ,Shadel GS, Tian R, Bruce JE. Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry. Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1732-1737. doi: 10.1073/pnas.1617220114. Epub 2017 Jan 27. PubMed PMID:28130547; PubMed Central PMCID: PMC5321032.

Dietary biomarker evaluation in a controlled feeding study in women from the Women’s Health Initiative cohort
Lampe JW, Huang Y, Neuhouser ML, Tinker LF, Song X, Schoeller DA, Kim S, Raftery D, Di C, Zheng C, Schwarz Y, Van Horn L, Thomson CA, Mossavar-Rahmani Y, Beresford SA, Prentice RL. Dietary biomarker evaluation in a controlled feeding study in women from the Women’s Health Initiative cohort. Am J Clin Nutr. 2017 Feb;105(2):466-475. doi: 10.3945/ajcn.116.144840. Epub 2016 Dec 28. PubMed PMID: 28031191.

Recent Advances in NMR-Based Metabolomics
Nagana Gowda GA, Raftery D. Recent Advances in NMR-Based Metabolomics. Anal Chem. 2017 Jan 3;89(1):490-510. doi: 10.1021/acs.analchem.6b04420. Epub 2016 Dec 2. PubMed PMID: 28105846.

Transcriptomic, proteomic, and metabolomics landscape of positional memory in the caudal fin of zebrafish
Rabinowitz JS, Robitaille AM, Wang Y, Ray CA, Thummel R, Gu H, Djukovic D, Raftery D, Berndt JD, Moon RT. Transcriptomic, proteomic, and metabolomics landscape of positional memory in the caudal fin of zebrafish. Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):E717-E726. doi: 10.1073/pnas.1620755114. Epub 2017 Jan  17. PubMed PMID: 28096348; PubMed Central PMCID: PMC5293114.

 2016

Quantitative Method to Investigate the Balance between Metabolism and Proteome Biomass: Starting from Glycine
Gu H, Carroll PA, Du J, Zhu J, Neto FC, Eisenman RN, Raftery D. Quantitative Method to Investigate the Balance between Metabolism and Proteome Biomass: Starting from Glycine. Angew Chem Int Ed Engl. 2016 Dec 12;55(50):15646-15650. doi: 10.1002/anie.201609236. Epub 2016 Nov 15. PubMed PMID: 27860107.

Preservation of myocardial fatty acid oxidation prevents diastolic dysfunction in mice subjected to angiotensin II infusion.
Choi YS, de Mattos AB, Shao D, Li T, Nabben M, Kim M, Wang W, Tian R, KolwiczSC Jr. Preservation of myocardial fatty acid oxidation prevents diastolic dysfunction in mice subjected to angiotensin II infusion. J Mol Cell Cardiol. 2016 Sep 28;100:64-71. doi: 10.1016/j.yjmcc.2016.09.001. PubMed PMID: 27693463.

CaMKII induces permeability transition through Drp1 phosphorylation during chronic β-AR stimulation.
Xu S, Wang P, Zhang H, Gong G, Gutierrez Cortes N, Zhu W, Yoon Y, Tian R, Wang W. CaMKII induces permeability transition through Drp1 phosphorylation during chronic β-AR stimulation. Nat Commun. 2016 Oct 14;7:13189. doi:10.1038/ncomms13189. PubMed PMID: 27739424.

Real time imaging of intracellular hydrogen peroxide in pancreatic islets.
Neal A, Rountree A, Kernan K, Yserloo BV, Zhang H, Reed BJ, Osborne W, Wang W, Sweet IR. Real time imaging of intracellular hydrogen peroxide in pancreatic islets. Biochem J. 2016 Oct 11. pii: BCJ20160481. PubMed PMID: 27729543.

Mitochondrial flashes: From indicator characterization to in vivo imaging.
Wang W, Zhang H, Cheng H. Mitochondrial flashes: From indicator characterization to in vivo imaging. Methods. 2016 Jun 8. pii:S1046-2023(16)30159-1. doi: 10.1016/j.ymeth.2016.06.004. [Epub ahead of print] PubMed PMID: 27288722.

Mitochondrial Flash: Integrative Reactive Oxygen Species and pH Signals in Cell and Organelle Biology
Wang W, Gong G, Wang X, Wei-LaPierre L, Cheng H, Dirksen R, Sheu SS. Mitochondrial Flash: Integrative Reactive Oxygen Species and pH Signals in Cell and Organelle Biology. Antioxid Redox Signal. 2016 Sep 20;25(9):534-49. doi:10.1089/ars.2016.6739. PubMed PMID: 27245241; PubMed Central PMCID: PMC5035371.

Normalization of NAD+ Redox Balance as a Therapy for Heart Failure.
Lee CF, Chavez JD, Garcia-Menendez L, Choi Y, Roe ND, Chiao YA, Edgar JS, Goo YA, Goodlett DR, Bruce JE, Tian R. Normalization of NAD+ Redox Balance as a Therapy for Heart Failure. Circulation. 2016 Sep 20;134(12):883-94. doi:10.1161/CIRCULATIONAHA.116.022495. Epub 2016 Aug 3. PubMed PMID: 27489254.

Combining NMR and LC/MS Using Backward Variable Elimination: Metabolomics Analysis of Colorectal Cancer, Polyps, and Healthy Controls.
Deng L, Gu H, Zhu J, Nagana Gowda GA, Djukovic D, Chiorean EG, Raftery D. Combining NMR and LC/MS Using Backward Variable Elimination: Metabolomics Analysis of Colorectal Cancer, Polyps, and Healthy Controls. Anal Chem. 2016 Aug 16;88(16):7975-83. doi: 10.1021/acs.analchem.6b00885. Epub 2016 Aug 1. PubMed PMID: 27437783.

Dereplication of Natural Products Using GC-TOF Mass Spectrometry: Improved Metabolite Identification by Spectral Deconvolution Ratio Analysis.
Carnevale Neto F, Pilon AC, Selegato DM, Freire RT, Gu H, Raftery D, Lopes NP,Castro-Gamboa I. Dereplication of Natural Products Using GC-TOF Mass Spectrometry: Improved Metabolite Identification by Spectral Deconvolution Ratio Analysis. Front Mol Biosci. 2016 Sep 30;3:59. PubMed PMID: 27747213.

Use of Metabolomics to Trend Recovery and Therapy After Injury in Critically Ill Trauma Patients.
Parent BA, Seaton M, Sood RF, Gu H, Djukovic D, Raftery D, O’Keefe GE. Use of Metabolomics to Trend Recovery and Therapy After Injury in Critically Ill Trauma Patients. JAMA Surg. 2016 Jul 20;151(7):e160853. doi: 10.1001/jamasurg.2016.0853. Epub 2016 Jul 20. PubMed PMID: 27223119.

Pharmacometabonomic Prediction of Busulfan Clearance in Hematopoetic Cell Transplant Recipients
Navarro SL, Randolph TW, Shireman LM, Raftery D, McCune JS. Pharmacometabonomic Prediction of Busulfan Clearance in Hematopoetic Cell
Transplant Recipients. J Proteome Res. 2016 Aug 5;15(8):2802-11. doi: 10.1021/acs.jproteome.6b00370. Epub 2016 Jul 20. PubMed PMID: 27350098; PubMed
Central PMCID: PMC5025252.

Phototransduction Influences Metabolic Flux and Nucleotide Metabolism in Mouse Retina.
Du J, Rountree A, Cleghorn WM, Contreras L, Lindsay KJ, Sadilek M, Gu H, Djukovic D, Raftery D, Satrústegui J, Kanow M, Chan L, Tsang SH, Sweet IR, Hurley JB. Phototransduction Influences Metabolic Flux and Nucleotide Metabolism in Mouse Retina. J Biol Chem. 2016 Feb 26;291(9):4698-710. doi:10.1074/jbc.M115.698985. Epub 2015 Dec 16. PubMed PMID: 26677218; PubMed Central PMCID: PMC4813492.

Identification of novel candidate plasma metabolite biomarkers for distinguishing serous ovarian carcinoma and benign serous ovarian tumors.
Buas MF, Gu H, Djukovic D, Zhu J, Drescher CW, Urban N, Raftery D, Li CI. Identification of novel candidate plasma metabolite biomarkers for distinguishing serous ovarian carcinoma and benign serous ovarian tumors. Gynecol Oncol. 2016 Jan;140(1):138-44. doi: 10.1016/j.ygyno.2015.10.021. Epub 2015 Oct 30. PubMed PMID: 26521694.

Metabolomics-identified metabolites associated with body mass index and prospective weight gain among Mexican American women.
Zhao H, Shen J, Djukovic D, Daniel-MacDougall C, Gu H, Wu X, Chow WH. Metabolomics-identified metabolites associated with body mass index and
prospective weight gain among Mexican American women. Obes Sci Pract. 2016 Sep;2(3):309-317. PubMed PMID: 27708848.

Lipid partitioning during cardiac stress.
Kolwicz SC Jr. Lipid partitioning during cardiac stress. Biochim Biophys Acta. 2016 Oct;1860(10):1472-80. doi: 10.1016/j.bbalip.2016.03.028. Epub 2016 Apr 7. PubMed PMID: 27040509.

The future of NMR-based metabolomics.
Markley JL, Brüschweiler R, Edison AS, Eghbalnia HR, Powers R, Raftery D, Wishart DS. The future of NMR-based metabolomics. Curr Opin Biotechnol. 2016 Aug 27;43:34-40. doi: 10.1016/j.copbio.2016.08.001. [Epub ahead of print] Review. PubMed PMID: 27580257.

Regulation of mitochondrial functions by protein phosphorylation and dephosphorylation
Lim S, Smith KR, Lim ST, Tian R, Lu J, Tan M. Regulation of mitochondrial functions by protein phosphorylation and dephosphorylation. Cell Biosci. 2016 Apr 14;6:25. doi: 10.1186/s13578-016-0089-3. eCollection 2016. Review. PubMed PMID: 27087918; PubMed Central PMCID: PMC4832502.

1,25-Dihydroxyvitamin D inhibits glutamine metabolism in Harvey-ras transformed MCF10A human breast epithelial cell.
Zhou X, Zheng W, Nagana Gowda GA, Raftery D, Donkin SS, Bequette B, Teegarden D.   1,25-Dihydroxyvitamin D inhibits glutamine metabolism in Harvey-ras transformed MCF10A human breast epithelial cell. J Steroid Biochem Mol Biol. 2016 May 3. pii: S0960-0760(16)30130-3. doi: 10.1016/j.jsbmb.2016.04.022. [Epub ahead of print] PubMed PMID: 27154413.

Simultaneous Analysis of Major Coenzymes of Cellular Redox Reactions and Energy Using ex Vivo (1)H NMR Spectroscopy
Nagana Gowda GA, Abell L, Lee CF, Tian R, Raftery D. Simultaneous Analysis of Major Coenzymes of Cellular Redox Reactions and Energy Using ex Vivo (1)H NMR Spectroscopy. Anal Chem. 2016 May 3;88(9):4817-24. doi:10.1021/acs.analchem.6b00442. Epub 2016 Apr 14. PubMed PMID: 27043450; PubMed Central PMCID: PMC4857157.

EGFR Signaling Enhances Aerobic Glycolysis in Triple-Negative Breast Cancer Cells to Promote Tumor Growth and Immune Escape.
Lim SO, Li CW, Xia W, Lee HH, Chang SS, Shen J, Hsu JL, Raftery D, Djukovic D, Gu H, Chang WC, Wang HL, Chen ML, Huo L, Chen CH, Wu Y, Sahin A, Hanash SM, Hortobagyi GN, Hung MC. EGFR Signaling Enhances Aerobic Glycolysis in Triple-Negative Breast Cancer Cells to Promote Tumor Growth and Immune Escape.  Cancer Res. 2016 Mar 1;76(5):1284-96. doi: 10.1158/0008-5472.CAN-15-2478. Epub 2016 Jan 12. PubMed PMID: 26759242; PubMed Central PMCID: PMC4775355.

Phototransduction Influences Metabolic Flux and Nucleotide Metabolism in Mouse Retina
Du J, Rountree A, Cleghorn WM, Contreras L, Lindsay KJ, Sadilek M, Gu H, Djukovic D, Raftery D, Satrústegui J, Kanow M, Chan L, Tsang SH, Sweet IR, Hurley
JB. Phototransduction Influences Metabolic Flux and Nucleotide Metabolism in Mouse Retina. J Biol Chem. 2016 Feb 26;291(9):4698-710. doi: 10.1074/jbc.M115.698985. Epub 2015 Dec 16. PubMed PMID: 26677218; PubMed Central  PMCID: PMC4813492.

Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis.
Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GA, Raftery D, Steinbeck C, Salek RM, Wishart DS. Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis. J Proteome Res. 2016 Feb 5;15(2):360-73. doi: 10.1021/acs.jproteome.5b00885. Epub 2016 Jan 20. PubMed PMID: 26745651;PubMed Central PMCID: PMC4865177.

Globally Optimized Targeted Mass Spectrometry: Reliable Metabolomics Analysis with Broad Coverage.
Gu H, Zhang P, Zhu J, Raftery D. Globally Optimized Targeted Mass Spectrometry: Reliable Metabolomics Analysis with Broad Coverage. Anal Chem. 2015
Dec 15;87(24):12355-62. doi: 10.1021/acs.analchem.5b03812. Epub 2015 Dec 2. PubMed PMID: 26579731.

Nicotinamide mononucleotide adenylyltransferase promotes hypoxic survival by activating the mitochondrial unfolded protein response.
Mao XR, Kaufman DM, Crowder CM. Nicotinamide mononucleotide adenylyltransferase promotes hypoxic survival by activating the mitochondrial
unfolded protein response. Cell Death Dis. 2016 Feb 25;7:e2113. doi: 10.1038/cddis.2016.5. PubMed PMID: 26913604; PubMed Central PMCID: PMC4849163.

Novel Targets for Mitochondrial Medicine.
Wang W, Karamanlidis G, Tian R. Novel targets for mitochondrial medicine. Sci Transl Med. 2016 Feb 17;8(326):326rv3. doi: 10.1126/scitranslmed.aac7410. Review. PubMed PMID: 26888432.

Rapamycin transiently induces mitochondrial remodeling to reprogram energy metabolism in old hearts.
Chiao YA, Kolwicz SC, Basisty N, Gagnidze A, Zhang J, Gu H, Djukovic D, Beyer RP, Raftery D, MacCoss M, Tian R, Rabinovitch PS.
Aging (Albany NY). 2016 Feb 11. [Epub ahead of print] PMID: 26872208

The Relationship Between KLF5 and PPARα in the Heart: It’s Complicated.
Roe ND, Standage SW, Tian R. The Relationship Between KLF5 and PPARα in the Heart: It’s Complicated. Circ Res. 2016 Jan 22;118(2):193-5. doi:10.1161/CIRCRESAHA.115.308069. PubMed PMID: 26838311; PubMed Central PMCID:PMC4743553.

Ketones Step to the Plate: A Game Changer for Metabolic Remodeling in Heart Failure?
Kolwicz SC Jr, Airhart S, Tian R. Ketones Step to the Plate: A Game Changer for Metabolic Remodeling in Heart Failure? Circulation. 2016 Jan 27. pii: CIRCULATIONAHA.116.021230. [Epub ahead of print] PubMed PMID: 26819375.

2015

Glucose Transporters in Cardiac Metabolism and Hypertrophy
Shao D, Tian R. Glucose Transporters in Cardiac Metabolism and Hypertrophy. Compr Physiol. 2015 Dec 15;6(1):331-51. doi: 10.1002/cphy.c150016. PubMed PMID:26756635.

AAV6-mediated Cardiac-specific Overexpression of Ribonucleotide Reductase Enhances Myocardial Contractility.
Kolwicz SC Jr, Odom GL, Nowakowski SG, Moussavi-Harami F, Chen X, Reinecke H, Hauschka SD, Murry CE, Mahairas GG, Regnier M.
Mol Ther. 2015 Sep 21. doi: 10.1038/mt.2015.176. [Epub ahead of print] PMID: 26388461

Enhancing Cardiac Triacylglycerol Metabolism Improves Recovery From Ischemic Stress.
Kolwicz SC Jr, Liu L, Goldberg IJ, Tian R. Diabetes. 2015 Aug;64(8):2817-27. doi: 10.2337/db14-1943. Epub 2015 Apr 9. PMID: 25858561

Mitochondrial Proteostatic Collapse Leads to Hypoxic Injury.
Kaufman DM, Crowder CM. Mitochondrial Proteostatic Collapse Leads to Hypoxic Injury. Curr Biol. 2015 Aug 17;25(16):2171-6. doi: 10.1016/j.cub.2015.06.062. Epub 2015 Jul 30. PubMed PMID: 26234215.

Alpha1a-Adrenoceptor Genetic Variant Triggers Vascular Smooth Muscle Cell Hyperproliferation and Increased Contractility via EGFR Transactivation Pathway.
Gradinaru I, Babaeva E, Schwinn DA, Oganesian A. Alpha1a-Adrenoceptor Genetic Variant Triggers Vascular Smooth Muscle Cell Hyperproliferation and Increased Contractility via EGFR Transactivation Pathway. PLoS One, 10(11):e0142787,2015.

Targeted Serum Metabolite Profiling and Sequential Metabolite Ratio Analysis for Colorectal Cancer Progression Monitoring.
Zhu, J., Djukovic, D., Deng, L., Gu, H., Himmati, F., Chiorean, E.G., Raftery, D.: Targeted Serum Metabolite Profiling and Sequential Metabolite Ratio Analysis for Colorectal Cancer Progression Monitoring. Anal. Bioanal. Chem., 2015, Oct;407(26):7857-63

Night-Time Serum Tryptophan Metabolite Levels During Sleep in Patients With and Without Irritable Bowel Syndrome (IBS).
Heitkemper, M.M., Han, C.J., Jarrett, M.E., Gu, H., Djukovic, D., Shulman, R.J., Raftery, D., Cain, K.C.: Night-Time Serum Tryptophan Metabolite Levels During Sleep in Patients With and Without Irritable Bowel Syndrome (IBS). Biol. Res. Nurs., 2015, Jul 7. pii: 1099800415594251

Metabolic Signatures of Bacterial Vaginosis.
Srinivasan, S., Morgan, M., Fiedler, T., Djukovic, D., Hoffman, N., Raftery, D., Marrazzo, J., Fredricks, D.: Metabolic Signatures of Bacterial Vaginosis. mBio., 6:e00204-15. PMID:25873373, 2015

Aggression is Associated With Aerobic Glycolysis in the Honey Bee Brain.
Chandrasekaran, S., Rittschof, C.C., Djukovic, D., Gu, H., Raftery, D., Price, N.D., Robinson, G.E.: Aggression is Associated With Aerobic Glycolysis in the Honey Bee Brain. Genes, Brain and Behavior, 12:158-166, 2015.

Targeted Metabolic Profiling of Wounds in Diabetic and Nondiabetic Mice.
Sood RF, Gu H, Djukovic D, Deng L, Ga M, Muffley LA, Raftery D, Hocking AM. Targeted metabolic profiling of wounds in diabetic and nondiabetic mice. Wound Repair Regen. 2015 May;23(3):423-34. doi: 10.1111/wrr.12299. PubMed PMID:25845676.

Quantitative Detection of Nitric Oxide in Exhaled Human Breath by Extractive Electrospray Ionization Mass Spectrometry.
Pan S, Tian Y, Li M, Zhao J, Zhu L, Zhang W, Gu H, Wang H, Shi J, Fang X, Li P, Chen H. Quantitative detection of nitric oxide in exhaled human breath by extractive electrospray ionization mass spectrometry. Sci Rep. 2015 Mar 4;5:8725. doi: 10.1038/srep08725. PubMed PMID: 25735640; PubMed Central PMCID: PMC4348632.

Metabolomics Method to Comprehensively Analyze Amino Acids in Different Domains.
Gu H, Du J, Carnevale Neto F, Carroll PA, Turner SJ, Chiorean EG, Eisenman RN,Raftery D. Metabolomics method to comprehensively analyze amino acids in different domains. Analyst. 2015 Apr 21;140(8):2726-34. doi: 10.1039/c4an02386b. Epub 2015 Feb 20. PubMed PMID: 25699545; PubMed Central PMCID:PMC4380628.

Deregulated Myc Requires MondoA/Mlx for Metabolic Reprogramming and Tumorigenesis.
Carroll PA, Diolaiti D, McFerrin L, Gu H, Djukovic D, Du J, Cheng PF, Anderson S, Ulrich M, Hurley JB, Raftery D, Ayer DE, Eisenman RN. Deregulated Myc requires MondoA/Mlx for metabolic reprogramming and tumorigenesis. Cancer Cell. 2015 Feb 9;27(2):271-85. doi: 10.1016/j.ccell.2014.11.024. Epub 2015 Jan 29. PubMed PMID: 25640402; PubMed Central PMCID: PMC4326605.

Fnip1 Regulates Skeletal Muscle Fiber Type Specification, Fatigue Resistance, and Susceptibility to Muscular Dystrophy.
Reyes NL, Banks GB, Tsang M, Margineantu D, Gu H, Djukovic D, Chan J, TorresM, Liggitt HD, Hirenallur-S DK, Hockenbery DM, Raftery D, Iritani BM. Fnip1 regulates skeletal muscle fiber type specification, fatigue resistance, and susceptibility to muscular dystrophy. Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):424-9. doi: 10.1073/pnas.1413021112. Epub 2014 Dec 29. PubMed PMID: 25548157; PubMed Central PMCID: PMC4299192.

The Mitochondrial Permeability Transition Pore Regulates Endothelial Bioenergetics and Angiogenesis.
Marcu R, Kotha S, Zhi Z, Qin W, Neeley CK, Wang RK, Zheng Y, Hawkins BJ. The mitochondrial permeability transition pore regulates endothelial bioenergetics and angiogenesis. Circ Res. 2015 Apr 10;116(8):1336-45. doi:10.1161/CIRCRESAHA.116.304881. Epub 2015 Feb 26. PubMed PMID: 25722455; PubMed Central PMCID: PMC4393786.

Standardizing the Experimental Conditions for using Urine in NMR-based Metabolomic Studies with a Particular Focus on Diagnostic Studies: A Review.
Emwas AH, Luchinat C, Turano P, Tenori L, Roy R, Salek RM, Ryan D, Merzaban JS, Kaddurah-Daouk R, Zeri AC, Nagana Gowda GA, Raftery D, Wang Y, Brennan L, Wishart DS. Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review. Metabolomics. 2015;11(4):872-894. Epub 2014 Nov 21. Review. PubMed PMID: 26109927; PubMed Central PMCID: PMC4475544.

Exploring Metabolic Profile Differences between Colorectal Polyp Patients and Controls Using Seemingly Unrelated Regression.
Chen C, Deng L, Wei S, Nagana Gowda GA, Gu H, Chiorean EG, Abu Zaid M, Harrison ML, Pekny JF, Loehrer PJ, Zhang D, Zhang M, Raftery D. Exploring Metabolic Profile Differences between Colorectal Polyp Patients and Controls Using Seemingly Unrelated Regression. J Proteome Res. 2015 Jun 5;14(6):2492-9. doi: 10.1021/acs.jproteome.5b00059. Epub 2015 May 13. PubMed PMID: 25919433.

Massive Glutamine Cyclization to Pyroglutamic Acid in Human Serum Discovered using NMR Spectroscopy.
Nagana Gowda GA, Gowda YN, Raftery D. Massive glutamine cyclization to pyroglutamic acid in human serum discovered using NMR spectroscopy. Anal Chem. 2015 Apr 7;87(7):3800-5. doi: 10.1021/ac504435b. Epub 2015 Mar 17. PubMed PMID: 25746059; PubMed Central PMCID: PMC4479397.

Expanding the Limits of Human Blood Metabolite Quantitation using NMR Spectroscopy.
Nagana Gowda GA, Gowda YN, Raftery D. Expanding the limits of human blood metabolite quantitation using NMR spectroscopy. Anal Chem. 2015 Jan 6;87(1):706-15. doi: 10.1021/ac503651e. Epub 2014 Dec 8. PubMed PMID: 25485990; PubMed Central PMCID: PMC4287831.

Mitochondrion as a Target for Heart Failure Therapy – Role of Protein Lysine Acetylation.
Lee CF, Tian R. Mitochondrion as a Target for Heart Failure Therapy – Role of Protein Lysine Acetylation. Circ J. 2015 Aug 4. [Epub ahead of print] PubMed PMID: 26248514.

Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks.
Ma X, Gao L, Karamanlidis G, Gao P, Lee CF, Garcia-Menendez L, Tian R, Tan K. Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks. PLoS Comput Biol. 2015 Jun 17;11(6):e1004332. doi: 10.1371/journal.pcbi.1004332. eCollection 2015 Jun. PubMed PMID: 26083688; PubMed Central PMCID: PMC4471235.

Mitochondrial Flash as a Novel Biomarker of Mitochondrial Respiration in the Heart.
Gong G, Liu X, Zhang H, Sheu SS, Wang W. Mitochondrial flash as a novel biomarker of mitochondrial respiration in the heart. Am J Physiol Heart Circ Physiol. 2015 Aug 14:ajpheart.00462.2015. doi: 10.1152/ajpheart.00462.2015. [Epub ahead of print] PubMed PMID: 26276820.

Deletion of capn4 Protects the Heart Against Endotoxemic Injury by Preventing ATP Synthase Disruption and Inhibiting Mitochondrial Superoxide Generation.
Ni R, Zheng D, Wang Q, Yu Y, Chen R, Sun T, Wang W, Fan GC, Greer PA, Gardiner RB, Peng T. Deletion of capn4 Protects the Heart Against Endotoxemic Injury by Preventing ATP Synthase Disruption and Inhibiting Mitochondrial SuperoxideGeneration. Circ Heart Fail. 2015 Aug 5. pii: CIRCHEARTFAILURE.115.002383. [Epub ahead of print] PubMed PMID: 26246018.

Transient Mitochondrial Permeability Transition Mediates Excitotoxicity in Glutamate-sensitive NSC34(D) Motor Neuron-like Cells.
Liu X, Xu S, Wang P, Wang W. Transient mitochondrial permeability transition mediates excitotoxicity in glutamate-sensitive NSC34(D) motor neuron-like cells. Exp Neurol. 2015 May 27;271:122-130. doi: 10.1016/j.expneurol.2015.05.010. [Epub ahead of print] PubMed PMID: 26024861.

 

2014

Long-Term Tolerance to Factor VIII is Achieved by Administration of IL-2/IL-2mAb Complexes and Low Dosages of Factor VIII.
Liu, C.L., Ye, P., Lin, J., Djukovic, D., Miao, C.H.: Long-Term Tolerance to Factor VIII is Achieved by Administration of IL-2/IL-2mAb Complexes and Low Dosages of Factor VIII. J. Thromb. Haemost., 12:921-931, 2014.

Colorectal Cancer Detection Using Targeted Serum Metabolic Profiling.
Zhu, J., Djukovic, D., Deng, L., Gu, H., Himmati, F., Chiorean, E.G., Raftery, D.: Colorectal Cancer Detection Using Targeted Serum Metabolic Profiling. J. Proteome Res., 13:4120-4130, 2014.

Altered Proteome Turnover and Remodeling by Subacute Caloric Restriction and Rapamycin Rejuvenate the Aging Heart.
Dai, D.F., Karunadharma, P.P., Chiao, Y.A., Basisty, N., Crispin D., Hsieh, E.J., Chen, T., Gu, H., Djukovic, D., Raftery, D., Beyer, R.P., MacCoss, M.J., Rabinovitch, P.S.: Altered Proteome Turnover and Remodeling by Subacute Caloric Restriction and Rapamycin Rejuvenate the Aging Heart. Aging Cell, 13:529-539, 2014.

Statistical Analysis and Modeling of Mass Spectrometry-based Metabolomics Data.
Xi B, Gu H, Baniasadi H, Raftery D. Statistical analysis and modeling of mass spectrometry-based metabolomics data. Methods Mol Biol. 2014;1198:333-53. doi:10.1007/978-1-4939-1258-2_22. PubMed PMID: 25270940; PubMed Central PMCID:PMC4319703.

Global Metabolic Profiling using Ultra-performance Liquid Chromatography/Quadrupole Time-of-flight Mass Spectrometry
Qi Y, Song Y, Gu H, Fan G, Chai Y. Global metabolic profiling using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry. Methods Mol Biol. 2014;1198:15-27. doi:10.1007/978-1-4939-1258-2_2. PubMed PMID: 25270920.

Integrated Plasma and Urine Metabolomics Coupled with HPLC/QTOF-MS and Chemometric Analysis on Potential Biomarkers in Liver Injury and Hepatoprotective Effects of Er-Zhi-Wan.
Yao W, Gu H, Zhu J, Barding G, Cheng H, Bao B, Zhang L, Ding A, Li W.Integrated plasma and urine metabolomics coupled with HPLC/QTOF-MS and chemometric analysis on potential biomarkers in liver injury and hepatoprotectiveeffects of Er-Zhi-Wan. Anal Bioanal Chem. 2014 Nov;406(28):7367-78. doi:10.1007/s00216-014-8169-x. Epub 2014 Sep 23. PubMed PMID: 25245419.

Delayed Innocent Bystander Cell Death following Hypoxia in Caenorhabditis elegans.
Sun CL, Kim E, Crowder CM. Delayed innocent bystander cell death following hypoxia in Caenorhabditis elegans. Cell Death Differ. 2014 Apr;21(4):557-67. doi: 10.1038/cdd.2013.176. Epub 2013 Dec 6. PubMed PMID: 24317200; PubMed Central PMCID: PMC3950319.

KB-R7943, a Plasma Membrane Na(+)/Ca(2+) Exchanger Inhibitor, Blocks Opening of the Mitochondrial Permeability Transition Pore.
Wiczer BM, Marcu R, Hawkins BJ. KB-R7943, a plasma membrane Na(+)/Ca(2+) exchanger inhibitor, blocks opening of the mitochondrial permeability transition pore. Biochem Biophys Res Commun. 2014 Jan 31;444(1):44-9. doi:10.1016/j.bbrc.2014.01.009. Epub 2014 Jan 14. PubMed PMID: 24434143; PubMed Central PMCID: PMC3951502.

Mitochondrial Matrix Ca²⁺ Accumulation Regulates Cytosolic NAD⁺/NADH Metabolism, Protein Acetylation, and Sirtuin Expression.
Marcu R, Wiczer BM, Neeley CK, Hawkins BJ. Mitochondrial matrix Ca²⁺ accumulation regulates cytosolic NAD⁺/NADH metabolism, protein acetylation, and sirtuin expression. Mol Cell Biol. 2014 Aug;34(15):2890-902. doi: 10.1128/MCB.00068-14. Epub 2014 May 27. PubMed PMID: 24865966; PubMed Central PMCID: PMC4135570.

Mutation in the γ2-subunit of AMP-activated Protein Kinase Stimulates Cardiomyocyte Proliferation and Hypertrophy Independent of Glycogen Storage.
Kim M, Hunter RW, Garcia-Menendez L, Gong G, Yang YY, Kolwicz SC Jr, Xu J, Sakamoto K, Wang W, Tian R. Mutation in the γ2-subunit of AMP-activated protein kinase stimulates cardiomyocyte proliferation and hypertrophy independent ofglycogen storage. Circ Res. 2014 Mar 14;114(6):966-75. doi:10.1161/CIRCRESAHA.114.302364. Epub 2014 Feb 6. PubMed PMID: 24503893; PubMedCentral PMCID: PMC3971100.

Promoting PGC-1α-driven Mitochondrial Biogenesis is Detrimental in Pressure-overloaded Mouse Hearts.
Karamanlidis G, Garcia-Menendez L, Kolwicz SC Jr, Lee CF, Tian R. Promoting PGC-1α-driven mitochondrial biogenesis is detrimental in pressure-overloaded mouse hearts. Am J Physiol Heart Circ Physiol. 2014 Nov 1;307(9):H1307-16. doi:10.1152/ajpheart.00280.2014. Epub 2014 Aug 29. PubMed PMID: 25172896; PubMed Central PMCID: PMC4217009.

Quantitating Metabolites in Protein Precipitated Serum using NMR Spectroscopy.
Nagana Gowda GA, Raftery D. Quantitating metabolites in protein precipitated serum using NMR spectroscopy. Anal Chem. 2014 Jun 3;86(11):5433-40. doi: 10.1021/ac5005103. Epub 2014 May 14. PubMed PMID: 24796490; PubMed Central PMCID: PMC4045325.

Alpha1a-adrenoceptor Genetic Variant induces Cardiomyoblast-to-fibroblast-like Cell Transition via Distinct Signaling Pathways.
Kleine-Brueggeney M, Gradinaru I, Babaeva E, Schwinn DA, Oganesian A. Alpha1a-adrenoceptor genetic variant induces cardiomyoblast-to-fibroblast-like cell transition via distinct signaling pathways. Cell Signal. 2014 Sep;26(9):1985-97. doi: 10.1016/j.cellsig.2014.05.007. Epub 2014 May 15. PubMed PMID: 24835978; PubMed Central PMCID: PMC4305345.

Elimination of NADPH oxidase activity promotes reductive stress and sensitizes the heart to ischemic injury.
Yu Q, Lee CF, Wang W, Karamanlidis G, Kuroda J, Matsushima S, Sadoshima J, Tian R. Elimination of NADPH oxidase activity promotes reductive stress and sensitizes the heart to ischemic injury. J Am Heart Assoc. 2014 Jan 27;3(1):e000555. doi: 10.1161/JAHA.113.000555. PubMed PMID: 24470522; PubMedCentral PMCID: PMC3959718.

Meeting highlights from the 2013 European Society of Cardiology Heart Failure Association Winter Meeting on Translational Heart Failure Research.
Hohl M, Ardehali H, Azuaje FJ, Breckenridge RA, Doehner W, Eaton P, Ehret GB,Fujita T, Gaetani R, Giacca M, Hasenfuß G, Heymans S, Leite-Moreira AF, Linke WA,Linz D, Lyon A, Mamas MA, Orešič M, Papp Z, Pedrazzini T, Piepoli M, Prosser B,Rizzuto R, Tarone G, Tian R, van Craenenbroeck E, van Rooij E, Wai T, Weiss G, Maack C. Meeting highlights from the 2013 European Society of Cardiology Heart Failure Association Winter Meeting on Translational Heart Failure Research. Eur J Heart Fail. 2014 Jan;16(1):6-14. doi: 10.1002/ejhf.10. Epub 2013 Dec 14. Review. PubMed PMID: 24453095.

Defects in the C. elegans Acyl-CoA Synthase, acs-3, and Nuclear Hormone Receptor, nhr-25, Cause Sensitivity to Distinct, but overlapping Stresses.
Ward JD, Mullaney B, Schiller BJ, He le D, Petnic SE, Couillault C, Pujol N, Bernal TU, Van Gilst MR, Ashrafi K, Ewbank JJ, Yamamoto KR. Defects in the C. elegans acyl-CoA synthase, acs-3, and nuclear hormone receptor, nhr-25, cause sensitivity to distinct, but overlapping stresses. PLoS One. 2014 Mar 20;9(3):e92552. doi: 10.1371/journal.pone.0092552. eCollection 2014. PubMed PMID:24651852; PubMed Central PMCID: PMC3961378.

Myeloid Mineralocorticoid Receptor Deficiency inhibits Aortic Constriction-induced Cardiac Hypertrophy in Mice.
Li C, Zhang YY, Frieler RA, Zheng XJ, Zhang WC, Sun XN, Yang QZ, Ma SM, Huang B, Berger S, Wang W, Wu Y, Yu Y, Duan SZ, Mortensen RM. Myeloid mineralocorticoid receptor deficiency inhibits aortic constriction-induced cardiac hypertrophy in mice. PLoS One. 2014 Oct 29;9(10):e110950. doi: 10.1371/journal.pone.0110950. eCollection 2014. PubMed PMID: 25354087; PubMed Central PMCID: PMC4212990.

Regulation of Metabolism in Individual Mitochondria during Excitation-contraction Coupling.
Gong G, Liu X, Wang W. Regulation of metabolism in individual mitochondria during excitation-contraction coupling. J Mol Cell Cardiol. 2014 Nov;76:235-46. doi: 10.1016/j.yjmcc.2014.09.012. Epub 2014 Sep 22. PubMed PMID: 25252178; PubMed Central PMCID: PMC4250349.