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UNIVERSITY of CALIFORNIA, SAN DIEGO The
UNIVERSITY OF CALIFORNIA, SAN DIEGO The Transporter-Opsin-G protein-coupled receptor (TOG) Superfamily A Thesis submitted in partial satisfaction of the requirements for the degree Master of Science in Biology by Daniel Choi Yee Committee in charge: Professor Milton H. Saier Jr., Chair Professor Yunde Zhao Professor Lin Chao 2014 The Thesis of Daniel Yee is approved and it is acceptable in quality and form for publication on microfilm and electronically: _____________________________________________________________________ _____________________________________________________________________ _____________________________________________________________________ Chair University of California, San Diego 2014 iii DEDICATION This thesis is dedicated to my parents, my family, and my mentor, Dr. Saier. It is only with their help and perseverance that I have been able to complete it. iv TABLE OF CONTENTS Signature Page ............................................................................................................... iii Dedication ...................................................................................................................... iv Table of Contents ........................................................................................................... v List of Abbreviations ..................................................................................................... vi List of Supplemental Files ............................................................................................ vii List of -
Determination of Total Procyanidins in Selected Chocolate and Confectionery Products Using DMAC
SPSFAM-FLAV-11 Based from Call for Methods 12-21-2011 PAYNE ET AL.: JOURNAL OF AOAC INTERNATIONAL VOL. 93, NO. 1, 2010 89 DIETARY SUPPLEMENTS Determination of Total Procyanidins in Selected Chocolate and Confectionery Products Using DMAC MARK J. PAYNE,WILLIAM JEFFREY HURST,andDAVI D A. STUART Hershey Center for Health and Nutrition, The Hershey Co., 1025 Reese Ave, Hershey, PA 17033 BOXIN OU and ELLEN FAN Brunswick Laboratories (USA), 50 Commerce Way, Norton, MA 02766 HONGPING JI and YAN KOU Brunswick Laboratories (China), 218 Xing Hu Rd, Suzhou Industrial Park, China 215125 A simple, specific, high-throughput colorimetric which the monomers are linked through C4÷C8 or, less method based on the reaction of frequently, C4÷C6 linkages. In the less common A-type 4-dimethylaminocinnamaldehyde (DMAC) with procyanidins, the monomers are connected through C2÷O÷C7 flavan-3-ols was developed to determine total or C2÷O÷C5 linkages. Procyanidins are widely distributed in procyanidins in selected cacao-based products. plants and are found in significant quantities in foods such as Extracts of defatted samples were dispensed into a fruits, spices, tea, wine, nuts, and cocoa (1). Of the many types of 96-well plate and reacted with DMAC. The polyphenols, flavan-3-ols, flavonols, and anthocyanidins are the absorbance of the reaction products was most abundant classes found in plants (2). The interest in measured at 640 nm and compared to polyphenol antioxidants has increased dramatically due to their commercially available procyanidin B2 as a ability to scavenge free radicals and their association with a standard. -
Proanthocyanidin Metabolism, a Mini Review
Nutrition and Aging 2 (2014) 111–116 111 DOI 10.3233/NUA-140038 IOS Press Proanthocyanidin Metabolism, a mini review Y.Y. Choy and A.L. Waterhouse∗ Viticulture and Enology, University of California, Davis, CA, USA Abstract. There is emerging evidence suggesting that consumption of beverage and food rich in polyphenol may offer protective effects against various neurodegenerative, cardiovascular diseases and cancers. Proanthocyanidins (PACs) are one of the most abundant polyphenol in human diets, but also one of the least absorbed polyphenol mostly due to their size and structure com- plexity. PACs or condensed tannins are oligomers and polymers of monomeric unit flavan-3-ol (+)-catechin or (−)-epicatechin. To date, the absorption and metabolism of PACs are still remains largely unknown. The aim of this mini review was to highlight the absorption and metabolism of PACs, their effect in the gut and sample preparation for analysis. Ultimately, the potential bioactivities derived from the interaction between PACs metabolites and the gut microbiota warrants further investigation. Keywords: Proanthocyanidins, phenolic acids, metabolism, colon 1. Introduction derived subunits. PACs that consists exclusively of (−)-epicatechin, (+)-catechin units, are known as pro- Polyphenols are among the ubiquitous constituents cyanidins because only cyanidin is released in acid, of foods of plant origins and are widely distributed and comprised the largest class of PACs, while those throughout the plant kingdom. Polyphenols can be with gallocatechin units release delphinidin. The size categorized into different groups such as flavonoids, or molecular weight of PACs can be expressed as phenolic acids, stilbenes and lignans. The flavonoids mean degree of polymerization (mDP). -
Genome-Wide Transcriptional Sequencing Identifies Novel Mutations in Metabolic Genes in Human Hepatocellular Carcinoma DAOUD M
CANCER GENOMICS & PROTEOMICS 11 : 1-12 (2014) Genome-wide Transcriptional Sequencing Identifies Novel Mutations in Metabolic Genes in Human Hepatocellular Carcinoma DAOUD M. MEERZAMAN 1,2 , CHUNHUA YAN 1, QING-RONG CHEN 1, MICHAEL N. EDMONSON 1, CARL F. SCHAEFER 1, ROBERT J. CLIFFORD 2, BARBARA K. DUNN 3, LI DONG 2, RICHARD P. FINNEY 1, CONSTANCE M. CULTRARO 2, YING HU1, ZHIHUI YANG 2, CU V. NGUYEN 1, JENNY M. KELLEY 2, SHUANG CAI 2, HONGEN ZHANG 2, JINGHUI ZHANG 1,4 , REBECCA WILSON 2, LAUREN MESSMER 2, YOUNG-HWA CHUNG 5, JEONG A. KIM 5, NEUNG HWA PARK 6, MYUNG-SOO LYU 6, IL HAN SONG 7, GEORGE KOMATSOULIS 1 and KENNETH H. BUETOW 1,2 1Center for Bioinformatics and Information Technology, National Cancer Institute, Rockville, MD, U.S.A.; 2Laboratory of Population Genetics, National Cancer Institute, National Cancer Institute, Bethesda, MD, U.S.A.; 3Basic Prevention Science Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, U.S.A; 4Department of Biotechnology/Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, U.S.A.; 5Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea; 6Department of Internal Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan, Korea; 7Department of Internal Medicine, College of Medicine, Dankook University, Cheon-An, Korea Abstract . We report on next-generation transcriptome Worldwide, liver cancer is the fifth most common cancer and sequencing results of three human hepatocellular carcinoma the third most common cause of cancer-related mortality (1). tumor/tumor-adjacent pairs. -
Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A. -
Anti-Inflammatory Activity of Sambucus Plant Bioactive
Natural Product Sciences 25(3) : 215-221 (2019) https://doi.org/10.20307/nps.2019.25.3.215 Anti-inflammatory Activity of Sambucus Plant Bioactive Compounds against TNF-α and TRAIL as Solution to Overcome Inflammation Associated Diseases: The Insight from Bioinformatics Study Wira Eka Putra1, Wa Ode Salma2, Muhaimin Rifa'i3,* 1Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, Indonesia 2Department of Nutrition, Faculty of Medicine, Halu Oleo University, Indonesia 3Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia Abstract − Inflammation is the crucial biological process of immune system which acts as body’s defense and protective response against the injuries or infection. However, the systemic inflammation devotes the adverse effects such as multiple inflammation associated diseases. One of the best ways to treat this entity is by blocking the tumor necrosis factor alpha (TNF-α) and TNF-related apoptosis-inducing ligand (TRAIL) to avoid the pro- inflammation cytokines production. Thus, this study aims to evaluate the potency of Sambucus bioactive compounds as anti-inflammation through in silico approach. In order to assess that, molecular docking was performed to evaluate the interaction properties between the TNF-α or TRAIL with the ligands. The 2D structure of ligands were retrieved online via PubChem and the 3D protein modeling was done by using SWISS Model. The prediction results of the study showed that caffeic acid (-6.4 kcal/mol) and homovanillic acid (-6.6 kcal/mol) have the greatest binding affinity against the TNF-α and TRAIL respectively. This evidence suggests that caffeic acid and homovanillic acid may potent as anti-inflammatory agent against the inflammation associated diseases. -
Trimer Procyanidin Oligomers Contribute to the Protective Effects of Cinnamon Extracts on Pancreatic Β-Cells in Vitro
Acta Pharmacologica Sinica (2016) 37: 1083–1090 © 2016 CPS and SIMM All rights reserved 1671-4083/16 www.nature.com/aps Original Article Trimer procyanidin oligomers contribute to the protective effects of cinnamon extracts on pancreatic β-cells in vitro Peng SUN1, 2, #, Ting WANG1, #, Lu CHEN2, #, Bang-wei YU1, Qi JIA2, Kai-xian CHEN1, 2, Hui-min FAN3, Yi-ming LI2, *, He-yao WANG1, * 1Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; 2School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; 3Department of Cardiovascular and Thoracic Surgery, Shanghai Heart Failure Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China Aim: Cinnamon extracts rich in procyanidin oligomers have shown to improve pancreatic β-cell function in diabetic db/db mice. The aim of this study was to identify the active compounds in extracts from two species of cinnamon responsible for the pancreatic β-cell protection in vitro. Methods: Cinnamon extracts were prepared from Cinnamomum tamala (CT-E) and Cinnamomum cassia (CC-E). Six compounds procyanidin B2 (cpd1), (–)-epicatechin (cpd2), cinnamtannin B1 (cpd3), procyanidin C1 (cpd4), parameritannin A1 (cpd5) and cinnamtannin D1 (cpd6) were isolated from the extracts. INS-1 pancreatic β-cells were exposed to palmitic acid (PA) or H2O2 to induce lipotoxicity and oxidative stress. Cell viability and apoptosis as well as ROS levels were assessed. Glucose-stimulated insulin secretion was examined in PA-treated β-cells and murine islets. Results: CT-E, CC-E as well as the compounds, except cpd5, did not cause cytotoxicity in the β-cells up to the maximum dosage using in this experiment. -
Cassia Fistula Leaves; UHPLC-QTOF-MS/MS
plants Article Cassia fistula Leaves; UHPLC-QTOF-MS/MS Based Metabolite Profiling and Molecular Docking Insights to Explore Bioactives Role towards Inhibition of Pancreatic Lipase Zain Ul Aabideen 1 , Muhammad Waseem Mumtaz 1, Muhammad Tayyab Akhtar 2,* , Muhammad Asam Raza 1, Hamid Mukhtar 2 , Ahmad Irfan 3,4, Syed Ali Raza 5 , Tooba Touqeer 1, Muhammad Nadeem 1 and Nazamid Saari 6,* 1 Department of Chemistry, University of Gujrat, Gujrat 50700, Pakistan; [email protected] (Z.U.A.); [email protected] (M.W.M.); [email protected] (M.A.R.); [email protected] (T.T.); [email protected] (M.N.) 2 Institute of Industrial Biotechnology, GC University Lahore, Lahore 54000, Pakistan; [email protected] 3 Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; [email protected] 4 Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia 5 Department of Chemistry, GC University Lahore, Lahore 54000, Pakistan; [email protected] 6 Department of Food Science, University Putra Malaysia, Serdang 43400, Malaysia Citation: Aabideen, Z.U.; Mumtaz, * Correspondence: [email protected] (M.T.A.); [email protected] (N.S.) M.W.; Akhtar, M.T.; Raza, M.A.; Mukhtar, H.; Irfan, A.; Raza, S.A.; Abstract: The present work was aimed at investigating hydroethanolic leaf extracts of Cassia fistula Touqeer, T.; Nadeem, M.; Saari, N. for their antioxidant and pancreatic lipase (PL) enzyme inhibitory properties. The most active extract Cassia fistula Leaves; was selected to profile the phytoconstituents by UHPLC-QTOF-MS/MS technique. -
Docking Characterization and in Vitro Inhibitory Activity of Flavan-3-Ols and Dimeric Proanthocyanidins Against the Main Protease Activity of SARS-Cov-2
ORIGINAL RESEARCH published: 30 November 2020 doi: 10.3389/fpls.2020.601316 Docking Characterization and in vitro Inhibitory Activity of Flavan-3-ols and Dimeric Proanthocyanidins Against the Main Protease Activity of SARS-Cov-2 Yue Zhu and De-Yu Xie* Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States We report to use the main protease (Mpro) of SARS-Cov-2 to screen plant flavan-3-ols and proanthocyanidins. Twelve compounds, (–)-afzelechin (AF), (–)-epiafzelechin (EAF), (+)-catechin (CA), (–)-epicatechin (EC), (+)-gallocatechin (GC), (–)-epigallocatechin Edited by: (EGC), (+)-catechin-3-O-gallate (CAG), (–)-epicatechin-3-O-gallate (ECG), Guodong Wang, Chinese Academy of Sciences, China (–)-gallocatechin-3-O-gallate (GCG), (–)-epigallocatechin-3-O-gallate (EGCG), Reviewed by: procyanidin A2 (PA2), and procyanidin B2 (PB2), were selected for docking simulation. pro Hiroshi Noguchi, The resulting data predicted that all 12 metabolites could bind to M . The affinity Nihon Pharmaceutical scores of PA2 and PB2 were predicted to be −9.2, followed by ECG, GCG, EGCG, University, Japan Ericsson Coy-Barrera, and CAG, −8.3 to −8.7, and then six flavan-3-ol aglycones, −7.0 to −7.7. Docking Universidad Militar Nueva characterization predicted that these compounds bound to three or four subsites (S1, Granada, Colombia S1′, S2, and S4) in the binding pocket of Mpro via different spatial ways and various *Correspondence: De-Yu Xie formation of one to four hydrogen bonds. In vitro analysis with 10 available compounds pro [email protected] showed that CAG, ECG, GCG, EGCG, and PB2 inhibited the M activity with an IC50 value, 2.98 ± 0.21, 5.21 ± 0.5, 6.38 ± 0.5, 7.51 ± 0.21, and 75.3 ± 1.29 µM, Specialty section: respectively, while CA, EC, EGC, GC, and PA2 did not have inhibitory activities. -
USDA Database for the Proanthocyanidin Content of Selected Foods
USDA Database for the Proanthocyanidin Content of Selected Foods Release 2 Prepared by Seema Bhagwat and David Haytowitz Nutrient Data Laboratory Beltsville Human Nutrition Research Center Agricultural Research Service U.S. Department of Agriculture September 2015 Slightly Revised December 2015 U.S. Department of Agriculture Agricultural Research Service Beltsville Human Nutrition Research Center Nutrient Data Laboratory 10300 Baltimore Avenue Building 005, Room 107, BARC-West Beltsville, Maryland 20705 Tel. 301-504-0630, FAX: 301-504-0632 E-Mail: [email protected] Web site: http://www.ars.usda.gov/nutrientdata/flav Table of Contents Release History ............................................................................................................. i Suggested Citation: ....................................................................................................... i Acknowledgements ...................................................................................................... ii Documentation ................................................................................................................ 1 Changes in the update of the proanthocyanidins database ......................................... 1 Data Sources ............................................................................................................... 1 Data Management ....................................................................................................... 2 Data Quality Evaluation............................................................................................... -
UC Santa Barbara Dissertation Template
UNIVERSITY OF CALIFORNIA Santa Barbara A-type Procyanidins and Their Effects on the Aggregation of Tau Prevalent in Alzheimer’s Disease A Thesis submitted in partial satisfaction of the requirements for the degree Master of Science in Biochemistry and Molecular Biology by Michael James Weingart Committee in charge: Professor John Lew, Chair Professor Rolf E. Christoffersen Professor Benjamin E. Reese January 2018 The thesis of Michael James Weingart is approved. ________________________________________ Benjamin E. Reese ________________________________________ Rolf E. Christoffersen ________________________________________ John Lew, Committee Chair January 2018 A-type Procyanidins and Their Effects on the Aggregation of Tau Prevalent in Alzheimer’s Disease Copyright © 2018 by Michael James Weingart iii Acknowledgements Thank you to Professor John Lew and Dylan Peterson for welcoming me into the lab, for giving me the opportunity to work on this project in the first place, and for teaching me pretty much everything I know about lab work. Thank you to Professors Ben Reese and Rolf Christoffersen for taking time out of their schedules to serve on my committee. And thank you to my parents for always being supportive no matter what I decided to pursue. iv Abstract A-type Procyanidins and Their Effects on the Aggregation of Tau Prevalent in Alzheimer’s Disease by Michael James Weingart Alzheimer’s disease (AD) affects over 40 million people worldwide: a number that is expected to grow to over 100 million by 2050.1 Despite this, there is a shortage of AD drugs on the market, with only five having been FDA approved, and no new ones since 2003.2 A major problem is that these drugs are merely symptomatic treatments. -
Distribution and Metabolism of Constituents and Metabolites of a Standardized Maritime Pine Bark Extract (Pycnogenol®) in Human
Distribution and metabolism of constituents and metabolites of a standardized maritime pine bark extract (Pycnogenol®) in human serum, blood cells and synovial fluid of patients with severe osteoarthritis DISSERTATION zur Erlangung des naturwissenschaftlichen Doktorgrades der Julius-Maximilians-Universität Würzburg vorgelegt von Melanie Mülek aus Aschaffenburg Würzburg 2015 Eingereicht bei der Fakultät für Chemie und Pharmazie am: ……………………............. Gutachter der schriftlichen Arbeit: 1. Gutachter ……………………............. 2. Gutachter ……………………............. Prüfer des öffentlichen Promotionskolloquiums: 1. Prüfer ……………………............. 2. Prüfer ……………………............. 3. Prüfer ……………………............. Datum des öffentlichen Promotionskolloquiums: ……………………............. Doktorurkunde ausgehändigt am: ……………………............. Die vorliegende Arbeit wurde auf Anregung und unter Anleitung von Frau Prof. Dr. Petra Högger am Lehrstuhl für Pharmazeutische Chemie des Instituts für Pharmazie und Lebensmittelchemie der Julius-Maximilians-Universität Würzburg angefertigt. PAPERS INCLUDED IN THIS THESIS This thesis is divided into five publications, which are referred to in the text by their numbers 1-5. 1 Facilitated uptake of a bioactive metabolite of maritime pine bark extract (Pycnogenol) into human erythrocytes Kurlbaum, M., Mülek, M. and Högger P. PLoS One, 2013. 8: e63197 DOI: 10.1371/journal.pone.0063197 2 Highly sensitive analysis of polyphenols and their metabolites in human blood cells using dispersive SPE extraction and LC-MS/MS Mülek, M. and Högger, P. Anal Bioanal Chem, 2015. 407: 1885-1899 DOI 10.1007/s00216-014-8451-y 3 Profiling a gut microbiota-generated catechin metabolite’s fate in human blood cells using a metabolomic approach Mülek, M., Fekete, A., Wiest, J., Holzgrabe, U., Mueller, MJ. and Högger, P. J Pharm Biomed Anal, 2015. 114: 71-81 DOI: 10.1016/j.jpba.2015.04.042 4 Development of LC-ESI/MS/MS methods for quantification of polyphenols in human plasma and serum with particular consideration of matrix effects Mülek, M.