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Association Analyses of Known Genetic Variants with Gene
ASSOCIATION ANALYSES OF KNOWN GENETIC VARIANTS WITH GENE EXPRESSION IN BRAIN by Viktoriya Strumba A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Bioinformatics) in The University of Michigan 2009 Doctoral Committee: Professor Margit Burmeister, Chair Professor Huda Akil Professor Brian D. Athey Assistant Professor Zhaohui S. Qin Research Statistician Thomas Blackwell To Sam and Valentina Dmitriy and Elizabeth ii ACKNOWLEDGEMENTS I would like to thank my advisor Professor Margit Burmeister, who tirelessly guided me though seemingly impassable corridors of graduate work. Throughout my thesis writing period she provided sound advice, encouragement and inspiration. Leading by example, her enthusiasm and dedication have been instrumental in my path to becoming a better scientist. I also would like to thank my co-advisor Tom Blackwell. His careful prodding always kept me on my toes and looking for answers, which taught me the depth of careful statistical analysis. His diligence and dedication have been irreplaceable in most difficult of projects. I also would like to thank my other committee members: Huda Akil, Brian Athey and Steve Qin as well as David States. You did not make it easy for me, but I thank you for believing and not giving up. Huda’s eloquence in every subject matter she explained have been particularly inspiring, while both Huda’s and Brian’s valuable advice made the completion of this dissertation possible. I would also like to thank all the members of the Burmeister lab, both past and present: Sandra Villafuerte, Kristine Ito, Cindy Schoen, Karen Majczenko, Ellen Schmidt, Randi Burns, Gang Su, Nan Xiang and Ana Progovac. -
Β-Phenylethylamines and the Isoquinoline Alkaloids
-Phenylethylamines and the isoquinoline alkaloids Kenneth W. Bentley Marrview, Tillybirloch, Midmar, Aberdeenshire, UK AB51 7PS Received (in Cambridge, UK) 28th November 2000 First published as an Advance Article on the web 7th February 2001 Covering: July 1999 to June 2000. Previous review: Nat. Prod. Rep., 2000, 17, 247. 1 Introduction 2 -Phenylethylamines 3 Isoquinolines 4 Naphthylisoquinolines 5 Benzylisoquinolines 6 Bisbenzylisoquinolines 7 Pavines and isopavines 8 Berberines and tetrahydoberberines 9 Protopines 10 Phthalide-isoquinolines 11 Other modified berberines 12 Emetine and related alkaloids 13 Benzophenanthridines 14 Aporphinoid alkaloids 14.1 Proaporphines 14.2 Aporphines 14.3 Aporphine–benzylisoquinoline dimers 14.4 Phenanthrenes 14.5 Oxoaporphines 14.6 Dioxoaporphines 14.7 Aristolochic acids and aristolactams 14.8 Oxoisoaporphines 15 Alkaloids of the morphine group 16 Colchicine and related alkaloids 17 Erythrina alkaloids 17.1 Erythrinanes 17.2 Cephalotaxine and related alkaloids 18 Other isoquinolines 19 References 1 Introduction Reviews of the occurrence of isoquinoline alkaloids in some plant species 1,2 and of recent developments in the chemistry and synthesis of alkaloids of these groups 3–6 have been published. 2 -Phenylethylamines β-Phenylethylamine, tyramine, N-methyltyramine, hordenine, mescaline, N-methylmescaline and N,N-dimethylmescaline 1, which is reported as an alkaloid for the first time, have been isolated from an unspecified species of Turbinocarpus 7 and N-trans-feruloyltyramine has been isolated from Cananga odorata.8 The N-oxides of the known alkaloid culantraramine 2 and the unknown culantraraminol 3, together with the related avicennamine 4 have been isolated as new alkaloids from Zanthoxylum avicennae.9 Three novel amides of dehydrotyr- leucine and proline respectively. -
Table 2. Significant
Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S. -
“Biosynthesis of Morphine in Mammals”
“Biosynthesis of Morphine in Mammals” D i s s e r t a t i o n zur Erlangung des akademischen Grades Doctor rerum naturalium (Dr. rer. nat.) vorgelegt der Naturwissenschaftlichen Fakultät I Biowissenschaften der Martin-Luther-Universität Halle-Wittenberg von Frau Nadja Grobe geb. am 21.08.1981 in Querfurt Gutachter /in 1. 2. 3. Halle (Saale), Table of Contents I INTRODUCTION ........................................................................................................1 II MATERIAL & METHODS ........................................................................................ 10 1 Animal Tissue ....................................................................................................... 10 2 Chemicals and Enzymes ....................................................................................... 10 3 Bacteria and Vectors ............................................................................................ 10 4 Instruments ........................................................................................................... 11 5 Synthesis ................................................................................................................ 12 5.1 Preparation of DOPAL from Epinephrine (according to DUNCAN 1975) ................. 12 5.2 Synthesis of (R)-Norlaudanosoline*HBr ................................................................. 12 5.3 Synthesis of [7D]-Salutaridinol and [7D]-epi-Salutaridinol ..................................... 13 6 Application Experiments ..................................................................................... -
Sephadex® LH-20, Isolation, and Purification of Flavonoids from Plant
molecules Review Sephadex® LH-20, Isolation, and Purification of Flavonoids from Plant Species: A Comprehensive Review Javad Mottaghipisheh 1,* and Marcello Iriti 2,* 1 Department of Pharmacognosy, Faculty of Pharmacy, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary 2 Department of Agricultural and Environmental Sciences, Milan State University, via G. Celoria 2, 20133 Milan, Italy * Correspondence: [email protected] (J.M.); [email protected] (M.I.); Tel.: +36-60702756066 (J.M.); +39-0250316766 (M.I.) Academic Editor: Francesco Cacciola Received: 20 August 2020; Accepted: 8 September 2020; Published: 10 September 2020 Abstract: Flavonoids are considered one of the most diverse phenolic compounds possessing several valuable health benefits. The present study aimed at gathering all correlated reports, in which Sephadex® LH-20 (SLH) has been utilized as the final step to isolate or purify of flavonoid derivatives among all plant families. Overall, 189 flavonoids have been documented, while the majority were identified from the Asteraceae, Moraceae, and Poaceae families. Application of SLH has led to isolate 79 flavonols, 63 flavones, and 18 flavanones. Homoisoflavanoids, and proanthocyanidins have only been isolated from the Asparagaceae and Lauraceae families, respectively, while the Asteraceae was the richest in flavones possessing 22 derivatives. Six flavones, four flavonols, three homoisoflavonoids, one flavanone, a flavanol, and an isoflavanol have been isolated as the new secondary metabolites. This technique has been able to isolate quercetin from 19 plant species, along with its 31 derivatives. Pure methanol and in combination with water, chloroform, and dichloromethane have generally been used as eluents. This comprehensive review provides significant information regarding to remarkably use of SLH in isolation and purification of flavonoids from all the plant families; thus, it might be considered an appreciable guideline for further phytochemical investigation of these compounds. -
High-Throughput Screening Studies of Inhibition of Human Carbonic Anhydrase II and Bacterial Flagella Antimicrobial Activity
Western Michigan University ScholarWorks at WMU Dissertations Graduate College 5-2010 High-Throughput Screening Studies of Inhibition of Human Carbonic Anhydrase II and Bacterial Flagella Antimicrobial Activity Albert A. Barrese III Western Michigan University Follow this and additional works at: https://scholarworks.wmich.edu/dissertations Part of the Biochemistry, Biophysics, and Structural Biology Commons, and the Biology Commons Recommended Citation Barrese, Albert A. III, "High-Throughput Screening Studies of Inhibition of Human Carbonic Anhydrase II and Bacterial Flagella Antimicrobial Activity" (2010). Dissertations. 500. https://scholarworks.wmich.edu/dissertations/500 This Dissertation-Open Access is brought to you for free and open access by the Graduate College at ScholarWorks at WMU. It has been accepted for inclusion in Dissertations by an authorized administrator of ScholarWorks at WMU. For more information, please contact [email protected]. HIGH-THROUGHPUT SCREENING STUDIES OF INHIBITION OF HUMAN CARBONIC ANHYDRASE II AND BACTERIAL FLAGELLA ANTIMICROBIAL ACTIVITY by Albert A. Barrese III A Dissertation Submitted to the Faculty of The Graduate College in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Department of Biological Sciences Advisor: Brian C. Tripp, Ph.D. Western Michigan University Kalamazoo, Michigan May 2010 UMI Number: 3410393 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMT Dissertation Publishing UMI 3410393 Copyright 2010 by ProQuest LLC. -
Quantigene Flowrna Probe Sets Currently Available
QuantiGene FlowRNA Probe Sets Currently Available Accession No. Species Symbol Gene Name Catalog No. NM_003452 Human ZNF189 zinc finger protein 189 VA1-10009 NM_000057 Human BLM Bloom syndrome VA1-10010 NM_005269 Human GLI glioma-associated oncogene homolog (zinc finger protein) VA1-10011 NM_002614 Human PDZK1 PDZ domain containing 1 VA1-10015 NM_003225 Human TFF1 Trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in) VA1-10016 NM_002276 Human KRT19 keratin 19 VA1-10022 NM_002659 Human PLAUR plasminogen activator, urokinase receptor VA1-10025 NM_017669 Human ERCC6L excision repair cross-complementing rodent repair deficiency, complementation group 6-like VA1-10029 NM_017699 Human SIDT1 SID1 transmembrane family, member 1 VA1-10032 NM_000077 Human CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) VA1-10040 NM_003150 Human STAT3 signal transducer and activator of transcripton 3 (acute-phase response factor) VA1-10046 NM_004707 Human ATG12 ATG12 autophagy related 12 homolog (S. cerevisiae) VA1-10047 NM_000737 Human CGB chorionic gonadotropin, beta polypeptide VA1-10048 NM_001017420 Human ESCO2 establishment of cohesion 1 homolog 2 (S. cerevisiae) VA1-10050 NM_197978 Human HEMGN hemogen VA1-10051 NM_001738 Human CA1 Carbonic anhydrase I VA1-10052 NM_000184 Human HBG2 Hemoglobin, gamma G VA1-10053 NM_005330 Human HBE1 Hemoglobin, epsilon 1 VA1-10054 NR_003367 Human PVT1 Pvt1 oncogene homolog (mouse) VA1-10061 NM_000454 Human SOD1 Superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (adult)) -
1 1 2 Trends in Lc-Ms and Lc-Hrms Analysis And
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Diposit Digital de la Universitat de Barcelona 1 2 3 TRENDS IN LC-MS AND LC-HRMS ANALYSIS AND CHARACTERIZATION OF 4 POLYPHENOLS IN FOOD. 5 6 Paolo Lucci1, Javier Saurina 2,3 and Oscar Núñez 2,3,4 * 7 8 9 1Department of Food Science, University of Udine, via Sondrio 2/a, 33100 Udine, Italy 10 2Department of Analytical Chemistry, University of Barcelona. Martí i Franquès, 1-11, 11 E-08028 Barcelona, Spain. 12 3 Research Institute in Food Nutrition and Food Safety, University of Barcelona, Recinte Torribera, 13 Av. Prat de la Riba 171, Edifici de Recerca (Gaudí), E-08921 Santa Coloma de Gramenet, 14 Barcelona, Spain. 15 4 Serra Húnter Fellow, Generalitat de Catalunya, Spain. 16 17 18 19 20 * Corresponding author: Oscar Núñez 21 Department of Analytical Chemistry, University of Barcelona. 22 Martí i Franquès, 1-11, E-08028 Barcelona, Spain. 23 Phone: 34-93-403-3706 24 Fax: 34-93-402-1233 25 e-mail: [email protected] 26 27 28 29 30 31 1 32 33 34 35 Contents 36 37 Abstract 38 1. Introduction 39 2. Types of polyphenols in foods 40 2.1. Phenolic acids 41 2.2. Flavonoids 42 2.3. Lignans 43 2.4. Stilbenes 44 3. Sample treatment procedures 45 4. Liquid chromatography-mass spectrometry 46 5. High resolution mass spectrometry 47 5.1. Orbitrap mass analyzer 48 5.2. Time-of-flight (TOF) mass analyzer 49 6. Chemometrics 50 6.1. -
Safrole and the Versatility of a Natural Biophore Lima, L
Artigo Safrole and the Versatility of a Natural Biophore Lima, L. M.* Rev. Virtual Quim., 2015, 7 (2), 495-538. Data de publicação na Web: 31 de dezembro de 2014 http://www.uff.br/rvq Safrol e a Versatilidade de um Biofóro Natural Resumo: Safrol (1) obtido de óleos essenciais de diferentes espécies vegetais tem ampla aplicação na indústria química como precursor sintético do butóxido de piperonila, piperonal e de fármacos como a tadalafila, cinoxacina e levodopa. Do ponto vista toxicológico, é considerado uma hepatotoxina por mecanismo de bioativação metabólica conduzindo a formação de intermediários eletrofílicos, e tem sido descrito como inibidor de diferentes isoenzimas da família CYP450. A versatilidade de sua estrutura, permitindo várias transformações químicas, e a natureza biofórica de sua unidade benzodioxola ou metilenodioxifenila conferem-lhe características singulares, que o tornam atrativo material de partida para a síntese de compostos com distintas atividades farmacológicas. Exemplos selecionados de compostos bioativos, naturais e sintéticos, contendo o sistema benzodioxola serão comentados, incluindo aqueles provenientes de contribuição específica do LASSBio®. Palavras-chave: Safrol; benzodioxola; metilenodioxi; CYP450; bióforo; compostos bioativos. Abstract Safrole (1), obtained from essential oils from different plant species, has wide application in the chemical industry as a synthetic precursor of piperonyl butoxide, piperonal and drugs such as tadalafil, cinoxacin and levodopa. From the toxicological point of view, it is considered a hepatotoxin through metabolic bioactivation, leading to the formation of electrophilic metabolites, and has been described as an inhibitor of different CYP450 isoenzymes. The versatility of its structure, allowing various chemical transformations, and the biophoric nature of its benzodioxole or methylenedioxy subunit, give it unique features and make it an attractive starting material for the synthesis of compounds with different pharmacological activities. -
An Update on the Metabolic Roles of Carbonic Anhydrases in the Model Alga Chlamydomonas Reinhardtii
H OH metabolites OH Review An Update on the Metabolic Roles of Carbonic Anhydrases in the Model Alga Chlamydomonas reinhardtii Ashok Aspatwar 1,* ID , Susanna Haapanen 1 and Seppo Parkkila 1,2 1 Faculty of Medicine and Life Sciences, University of Tampere, FI-33014 Tampere, Finland; [email protected].fi (S.H.); [email protected].fi (S.P.) 2 Fimlab, Ltd., and Tampere University Hospital, FI-33520 Tampere, Finland * Correspondence: [email protected].fi; Tel.: +358-46-596-2117 Received: 11 January 2018; Accepted: 10 March 2018; Published: 13 March 2018 Abstract: Carbonic anhydrases (CAs) are metalloenzymes that are omnipresent in nature. − + CAs catalyze the basic reaction of the reversible hydration of CO2 to HCO3 and H in all living organisms. Photosynthetic organisms contain six evolutionarily different classes of CAs, which are namely: α-CAs, β-CAs, γ-CAs, δ-CAs, ζ-CAs, and θ-CAs. Many of the photosynthetic organisms contain multiple isoforms of each CA family. The model alga Chlamydomonas reinhardtii contains 15 CAs belonging to three different CA gene families. Of these 15 CAs, three belong to the α-CA gene family; nine belong to the β-CA gene family; and three belong to the γ-CA gene family. The multiple copies of the CAs in each gene family may be due to gene duplications within the particular CA gene family. The CAs of Chlamydomonas reinhardtii are localized in different subcellular compartments of this unicellular alga. The presence of a large number of CAs and their diverse subcellular localization within a single cell suggests the importance of these enzymes in the metabolic and biochemical roles they perform in this unicellular alga. -
Dr. Duke's Phytochemical and Ethnobotanical Databases Chemicals Found in Papaver Somniferum
Dr. Duke's Phytochemical and Ethnobotanical Databases Chemicals found in Papaver somniferum Activities Count Chemical Plant Part Low PPM High PPM StdDev Refernce Citation 0 (+)-LAUDANIDINE Fruit -- 0 (+)-RETICULINE Fruit -- 0 (+)-RETICULINE Latex Exudate -- 0 (-)-ALPHA-NARCOTINE Inflorescence -- 0 (-)-NARCOTOLINE Inflorescence -- 0 (-)-SCOULERINE Latex Exudate -- 0 (-)-SCOULERINE Plant -- 0 10-HYDROXYCODEINE Latex Exudate -- 0 10-NONACOSANOL Latex Exudate Chemical Constituents of Oriental Herbs (3 diff. books) 0 13-OXOCRYPTOPINE Plant -- 0 16-HYDROXYTHEBAINE Plant -- 0 20-HYDROXY- Fruit 36.0 -- TRICOSANYLCYCLOHEXA NE 0 4-HYDROXY-BENZOIC- Pericarp -- ACID 0 4-METHYL-NONACOSANE Fruit 3.2 -- 0 5'-O- Plant -- DEMETHYLNARCOTINE 0 5-HYDROXY-3,7- Latex Exudate -- DIMETHOXYPHENANTHRE NE 0 6- Plant -- ACTEONLYDIHYDROSANG UINARINE 0 6-METHYL-CODEINE Plant Father Nature's Farmacy: The aggregate of all these three-letter citations. 0 6-METHYL-CODEINE Fruit -- 0 ACONITASE Latex Exudate -- 32 AESCULETIN Pericarp -- 3 ALANINE Seed 11780.0 12637.0 0.5273634907250652 -- Activities Count Chemical Plant Part Low PPM High PPM StdDev Refernce Citation 0 ALKALOIDS Latex Exudate 50000.0 250000.0 ANON. 1948-1976. The Wealth of India raw materials. Publications and Information Directorate, CSIR, New Delhi. 11 volumes. 5 ALLOCRYPTOPINE Plant Father Nature's Farmacy: The aggregate of all these three-letter citations. 15 ALPHA-LINOLENIC-ACID Seed 1400.0 5564.0 -0.22115561650586155 -- 2 ALPHA-NARCOTINE Plant Jeffery B. Harborne and H. Baxter, eds. 1983. Phytochemical Dictionary. A Handbook of Bioactive Compounds from Plants. Taylor & Frost, London. 791 pp. 17 APOMORPHINE Plant Father Nature's Farmacy: The aggregate of all these three-letter citations. 0 APOREINE Fruit -- 0 ARABINOSE Fruit ANON. -
Study on the Material Basis of Houpo Wenzhong Decoction by HPLC Fingerprint, UHPLC-ESI-LTQ-Orbitrap-MS, and Network Pharmacology
molecules Article Study on the Material Basis of Houpo Wenzhong Decoction by HPLC Fingerprint, UHPLC-ESI-LTQ-Orbitrap-MS, and Network Pharmacology Juyuan Luo 1, Gongsen Chen 1 , Donghan Liu 1, Yan Wang 1, Qi Qi 1, Haiyan Hu 1, Pengyue Li 1, Jie Bai 1,*, Shouying Du 1,*, Yang Lu 1,*, Yuming Wang 2 and Cun Liu 2 1 School of Chinese Materia Medica, Beijing University of Chinese Medicine, Yangguang South Avenue, Fangshan District, Beijing 102488, China 2 Yifan Pharmaceutical Co., Ltd., Lin’an 311300, China * Correspondence: [email protected] (J.B.); [email protected] (S.D.); [email protected] (Y.L.); Tel.: +86-010-8473-8657 (J.B.); +86-010-8473-8615 (S.D.); +86-010-5391-2123 (Y.L.) Received: 30 June 2019; Accepted: 9 July 2019; Published: 14 July 2019 Abstract: Houpo Wenzhong Decoction (HWD) as a classical prescription has been widely used for hundreds of years. However, the quality of HWDs is difficult to control because of its herb materials from different regions. It is a new idea to use HPLC fingerprints, LTQ-ESI-Orbitrap-MS, and network pharmacology in combination to screen common components (CCs) as potential quality control indicators. In this paper, the fingerprints of HWDs were established, which were used to determine HWDs compounded from different sources of traditional Chinese medicines (TCMs). Through the similarity analysis, 45 CCs were selected. UHPLC-LTQ-ESI-Orbitrap-MS was used to carry out the chemical composition analysis of HWD. Seventy-three chemical constituents were distinguished, and 30 CCs were identified. Through network pharmacology, networks of candidate CCs, diseases, and candidate targets were constructed.