Induced Alterations in the Urine Metabolome in Cardiac Surgery
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Thesis Final
CHARACTERIZATION OF ADENOSINE NUCLEOSIDASE FROM ALASKA PEA SEEDS by Abdullah K. Shamsuddin A Thesis Submitted to the Faculty of the College of Graduate Studies at Middle Tennessee State University in Partial Fulfillment of the Requirements for the Degree of Master of Science in Chemistry Middle Tennessee State University August 2015 Thesis Committee: Dr. Paul C. Kline, Chair Dr. Donald A. Burden Dr. Kevin L. Bicker I dedicate this research to my parents, my sisters, and my brother. I love you all. ii" " ACKNOWLEDGEMENTS I would like to express my sincere gratitude to my advisor, Dr. Paul C. Kline, for his guidance, support, and ongoing encouragement throughout this project. I also wish to thank my committee members, Dr. Donald A. Burden and Dr. Kevin L. Bicker, for their advice and insightful comments. In addition, I would like to thank all the staff and faculty of the Department of Chemistry for their contribution to the success of this study. Lastly, I wish to thank my family and my friends, without whom none of my accomplishments would have been possible. Thank you for you endless support, concern, love, and prayer. iii" " ABSTRACT Adenosine nucleosidase was purified from Alaska pea seeds five days after germination. A 4-fold purification has been reached with a 1.3 % recovery. The subunit molecular weight of adenosine nucleosidase was determined by mass spectrometry to be 26,103 daltons. The number of subunits was 1. The Michaelis constant, Km, and the maximum velocity, V max, for adenosine were determined to be 137 ± 48 µM, and 0.34 ± 0.02 µM/min respectively. -
Nucleotide Metabolism
NUCLEOTIDE METABOLISM General Overview • Structure of Nucleotides Pentoses Purines and Pyrimidines Nucleosides Nucleotides • De Novo Purine Nucleotide Synthesis PRPP synthesis 5-Phosphoribosylamine synthesis IMP synthesis Inhibitors of purine synthesis Synthesis of AMP and GMP from IMP Synthesis of NDP and NTP from NMP • Salvage pathways for purines • Degradation of purine nucleotides • Pyrimidine synthesis Carbamoyl phosphate synthesisOrotik asit sentezi • Pirimidin nükleotitlerinin yıkımı • Ribonükleotitlerin deoksiribonükleotitlere dönüşümü Basic functions of nucleotides • They are precursors of DNA and RNA. • They are the sources of activated intermediates in lipid and protein synthesis (UDP-glucose→glycogen, S-adenosylmathionine as methyl donor) • They are structural components of coenzymes (NAD(P)+, FAD, and CoA). • They act as second messengers (cAMP, cGMP). • They play important role in carrying energy (ATP, etc). • They play regulatory roles in various pathways by activating or inhibiting key enzymes. Structures of Nucleotides • Nucleotides are composed of 1) A pentose monosaccharide (ribose or deoxyribose) 2) A nitrogenous base (purine or pyrimidine) 3) One, two or three phosphate groups. Pentoses 1.Ribose 2.Deoxyribose •Deoxyribonucleotides contain deoxyribose, while ribonucleotides contain ribose. •Ribose is produced in the pentose phosphate pathway. Ribonucleotide reductase converts ribonucleoside diphosphate deoxyribonucleotide. Nucleotide structure-Base 1.Purine 2.Pyrimidine •Adenine and guanine, which take part in the structure -
Pyrimidine Base Degradation in Cultured Murine C-1300 Neuroblastoma Cells and in Situ Tumors
Pyrimidine base degradation in cultured murine C-1300 neuroblastoma cells and in situ tumors. M Tuchman, … , M L Ramnaraine, B L Mirkin J Clin Invest. 1988;81(2):425-430. https://doi.org/10.1172/JCI113336. Research Article Dihydropyrimidine dehydrogenase (DPD), the initial, rate-limiting step in pyrimidine degradation, was studied in two cell lines of murine neuroblastoma (MNB-T1 and MNB-T2) that were derived from C-1300 MNB tumor carried in A/J mice. The MNB-T2 (low malignancy) cell line was originally derived from the in situ tumor and carried in tissue culture for more than 100 passages; the MNB-T1 (high malignancy) line consisted of a new sub-culture that was also established from the in situ MNB tumor. DPD activity was determined in cytosolic preparations of MNB utilizing high performance liquid chromatography to separate the radiolabeled substrate ([2-14C]thymine) from [2-14C]dihydrothymine. The apparent affinity of DPD for NADPH in MNB cells (Km approximately 0.08 mM) was identical to that of A/J mouse brain and liver. The DPD activity of the high malignancy (MNB-T1) cell line was 14.3% of that observed in the low malignancy (MNB-T2) line. In situ tumors formed after implantation of high malignancy (MNB-T1) cells into A/J mice had only 25.2% of the DPD activity observed in tumors derived from low malignancy (MNB-T2) cells. When MNB-T2 cells were injected into naive A/J mice, tumors developed in only 68% of animals, the tumor growth rate was slow and a mortality of 20% was observed. -
Effects of Allopurinol and Oxipurinol on Purine Synthesis in Cultured Human Cells
Effects of allopurinol and oxipurinol on purine synthesis in cultured human cells William N. Kelley, James B. Wyngaarden J Clin Invest. 1970;49(3):602-609. https://doi.org/10.1172/JCI106271. Research Article In the present study we have examined the effects of allopurinol and oxipurinol on thed e novo synthesis of purines in cultured human fibroblasts. Allopurinol inhibits de novo purine synthesis in the absence of xanthine oxidase. Inhibition at lower concentrations of the drug requires the presence of hypoxanthine-guanine phosphoribosyltransferase as it does in vivo. Although this suggests that the inhibitory effect of allopurinol at least at the lower concentrations tested is a consequence of its conversion to the ribonucleotide form in human cells, the nucleotide derivative could not be demonstrated. Several possible indirect consequences of such a conversion were also sought. There was no evidence that allopurinol was further utilized in the synthesis of nucleic acids in these cultured human cells and no effect of either allopurinol or oxipurinol on the long-term survival of human cells in vitro could be demonstrated. At higher concentrations, both allopurinol and oxipurinol inhibit the early steps ofd e novo purine synthesis in the absence of either xanthine oxidase or hypoxanthine-guanine phosphoribosyltransferase. This indicates that at higher drug concentrations, inhibition is occurring by some mechanism other than those previously postulated. Find the latest version: https://jci.me/106271/pdf Effects of Allopurinol and Oxipurinol on Purine Synthesis in Cultured Human Cells WILLIAM N. KELLEY and JAMES B. WYNGAARDEN From the Division of Metabolic and Genetic Diseases, Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina 27706 A B S TR A C T In the present study we have examined the de novo synthesis of purines in many patients. -
(10) Patent No.: US 8119385 B2
US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. -
Purine and Pyrimidine Biosynthesis
Biosynthesis of Purine & Pyrimidi ne Introduction Biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds, or joined together to form macromolecules. This process often consists of metabolic pathways. The purines are built upon a pre-existing ribose 5- phosphate. Liver is the major site for purine nucleotide synthesis. Erythrocytes, polymorphonuclear leukocytes & brain cannot produce purines. Pathways • There are Two pathways for the synthesis of nucleotides: 1. De-novo synthesis: Biochemical pathway where nucleotides are synthesized from new simple precursor molecules 2. Salvage pathway: Used to recover bases and nucleotides formed during the degradation of RNA and DNA. Step involved in purine biosynthesis (Adenine & Guanine) • Ribose-5-phosphate, of carbohydrate metabolism is the starting material for purine nucleotide synthesis. • It reacts with ATP to form phosphoribosyl pyrophosphate (PRPP). • Glutamine transfers its amide nitrogen to PRPP to replace pyrophosphate & produce 5- phosphoribosylamine. Catalysed by PRPP glutamyl amidotransferase. • This reaction is the committed. • Phosphoribosylamine reacts with glycine in the presence of ATP to form glycinamide ribosyl 5- phosphate or glycinamide ribotide (GAR).Catalyzed by synthetase. • N10-Formyl tetrahydrofolate donates the formyl group & the product formed is formylglycinamide ribosyl 5-phosphate. Catalyzed by formyltransferase. • Glutamine transfers the second amido amino group to produce formylglycinamidine ribosyl 5- phosphate. Catalyzed by synthetase. • The imidazole ring of the purine is closed in an ATP dependent reaction to yield 5- aminoimidazole ribosyl 5-phosphate. Catalyzed by synthetase. • Incorporation of CO2 (carboxylation) occurs to yield aminoimidazole carboxylate ribosyl 5- phosphate. -
NUCLEOTIDE METABOLISM Mark Rush
NUCLEOTIDE METABOLISM Mark Rush Nucleotides serve various metabolic functions. For example, they are: • Substrates (building blocks) for nucleic acid biosynthesis and repair, • The main storage form of “high energy phosphate”, • Components of many “so-called” co-enzymes (NAD, NADP, FAD, CoA), • Components of many activated metabolic intermediates (such as UDPG, SAM), • Major allosteric effectors (such as AMP, ADP, ATP, GTP), • Major second messengers (such as 3',5' cAMP), and • Precursors for the biosynthesis of a variety of important compounds (such as biopterin and histidine). Nucleotide biochemistry can be treated both as an aspect of nitrogen metabolism, along with such compounds as amino acids and porphyrins, and as an aspect of nucleic acid metabolism. When the focus is on the biosynthesis and degradation of nucleotides, in other words on their turnover, the treatment is similar to that of other nitrogenous compounds. When the focus is on the role of nucleotides in overall nucleic acid metabolism, the treatment is included in molecular biology. Both aspects will be considered here with the major emphasis directed toward relating defects in nucleotide turnover to either metabolic diseases or chemotherapy. I. Nomenclature (pages 11 and 12). II. Overall metabolic pathways (page 4). 1) PRPP synthetase. 2) Nucleoside phosphorylases. 3) Phosphoribosyl transferases. nucleotides - 1 III. Biosynthesis of purines and pyrimidines (pages 5, 6, 8). A minimum amount of time will be spent discussing these pathways in lecture. Please examine them carefully in the text and note that: 1) Purine synthesis begins at the nucleotide level, while pyrimidine synthesis does not. 2) Both syntheses are regulated at their committed steps. -
Comparing Meiothermus Ruber and Myxococcus Xanthus in the Purine Metabolism Pathway Linnea J
Augustana College Augustana Digital Commons Meiothermus ruber Genome Analysis Project Biology 2-2016 Comparing Meiothermus ruber and Myxococcus xanthus in the Purine Metabolism Pathway Linnea J. Ritchie Augustana College - Rock Island Dr. Lori Scott Augustana College, Rock Island Illinois Follow this and additional works at: http://digitalcommons.augustana.edu/biolmruber Part of the Bioinformatics Commons, Biology Commons, Genetics Commons, Genomics Commons, Molecular Biology Commons, and the Molecular Genetics Commons Recommended Citation Ritchie, Linnea J. and Scott, Dr. Lori. "Comparing Meiothermus ruber and Myxococcus xanthus in the Purine Metabolism Pathway" (2016). Meiothermus ruber Genome Analysis Project. http://digitalcommons.augustana.edu/biolmruber/7 This Student Paper is brought to you for free and open access by the Biology at Augustana Digital Commons. It has been accepted for inclusion in Meiothermus ruber Genome Analysis Project by an authorized administrator of Augustana Digital Commons. For more information, please contact [email protected]. Comparing Meiothermus ruber and Myxococcus xanthus in the Purine Metabolism Pathway Linnea Ritchie Bio-375 Molecular Genetics (Dr. Lori Scott) Background The purine metabolism pathway is an essential part of an organism’s ability to make nucleotides. It is through this pathway that adenine and guanine are made, these molecules later become the bases of nucleotides, which are a key component in DNA (Westby 1974). There are two different routes for purine synthesis: the de novo pathway and the salvage pathway (Berg 2002). During the de novo pathway the purine molecules are essentially built from scratch. While this route uses comparatively simple molecules and amino acids there is a high energy requirement which is why at times the salvage pathway is used instead. -
A Rare Bacterial RNA Motif Is Implicated in the Regulation of the Purf Gene Whose Encoded Enzyme Synthesizes Phosphoribosylamine
Downloaded from rnajournal.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press RNA (Report) RNA/2020/077313 Revised A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine Sarah N. Malkowski,1 Ruben M. Atilho,2 Etienne B. Greenlee,3 Christina E. Weinberg,3,5 Ronald R. Breaker2,3,4 1Department of Chemistry, Yale University, New Haven, Connecticut 06520-8103, USA 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA 3Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA 4Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA 5Current address: Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany Corresponding author: Ronald R. Breaker, [email protected]. KEYWORDS: aptamer; gene control; noncoding RNA; PRA; purine; ribose Downloaded from rnajournal.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Malkowski et al. and Breaker Candidate PRA Regulatory RNA ABSTRACT The Fibro-purF motif is a putative structured noncoding RNA domain that was discovered previously in species of Fibrobacter by employing comparative sequence analysis methods. An updated bioinformatics search yielded a total of only 30 unique-sequence representatives, exclusively found upstream of the purF gene that codes for the enzyme amidophosphoribosyltransferase. This enzyme synthesizes the compound 5-phospho-D- ribosylamine (PRA), which is the first committed step in purine biosynthesis. The consensus model for Fibro-purF motif RNAs includes a predicted three-stem junction that carries numerous conserved nucleotide positions within the regions joining the stems. -
Particular Metabolic Profile of Patient with Total
International Journal of Pharmaceutical Science and Health Care Issue 5, Vol. 1 (Jan-Feb. 2015) Available online on http://www.rspublication.com/ijphc/index.html ISSN 2249 – 5738 PARTICULAR METABOLIC PROFILE OF PATIENT WITH TOTAL DIHYDROPYRIMIDINE DEHYDROGENASE DEFICIENCY (DPD) Saif Eddine GAMAOUNa,b, Nissem ABDEJALLILa, Mhamed Ali HAMZAb, Saad SAGUEMa aLaboratory of Metabolic Biophysics, Professional and Applied Environmental Toxicology, Medicine faculty of Sousse, Mohamed Karoui street, Sousse 4002, Tunisia bDepartment of chemistry, sciences faculty of Monastir, Environment street, Monastir 5019, Tunisia *Author for correspondence at present address: Saif Eddine GAMAOUN Higher Institute of Technological Studies (ISET) Ksar Hellal-Hadj Ali Soua street-5070-Ksar Hellal,Tunisia Fonction : Engineer of analytical chemistry and instrumentation - Assistant teacher in ISET Ksar Hellal - Tunisia Tel.: (+216) 73 475 900 / (+216) 98 685 958 Fax: (+216) 73 475 163 E-mail: saifeddineg @ yahoo.fr ABSTRACT 5-Fluorouracil (5-FU) remains one of the most used chemotherapeutics agents in the treatment of several types of cancers. Its use could nevertheless, raise a problem of pharmacovigilance. It may engender a very grave toxicity which can be fatal at certain patient's presenting an enzymatic deficit with dihydropyrimidine dehydrogenase (DPD). The identification of the subjects at risk through the detection of a partial or total deficit before starting the treatment with 5-FU, could allow to adapt individually the prescribed dose, to optimize the therapeutic efficacy and reduce potential toxicities at expanding patients of a partial deficit to DPD. Such a screening would especially become more important when it is about a complete deficit in DPD. Such metabolic abnormality whose frequency is of the order of one per thousand, would indeed constitute a contraindication absolved from any chemotherapy with 5-FU (mortal toxicities). -
Possible Prediction of Adverse Reactions to Pyrimidine Chemotherapy from Urinary Pyrimidine Levels and a Case of Asymptomatic Adult Dihydropyrimidinuria1
Vol. 2, 1937-1 941, December 1996 Clinical Cancer Research 1937 Possible Prediction of Adverse Reactions to Pyrimidine Chemotherapy from Urinary Pyrimidine Levels and a Case of Asymptomatic Adult Dihydropyrimidinuria1 Katsuo Hayashi,2 Kiyoshi Kidouchi, INTRODUCTION Satoshi Sumi, Masashi Mizokami, Etsuro Onto, Pyrimidine chemotherapy agents such as 5-FU3 are used widely but can occasionally cause serious adverse reactions. In Kazunoni Kumada, Ryuzo Ueda, and pyrimidine metabolism, uracil and thymine are first converted to Yoshino Wada dihydropyrimidines (dihydrouracil and dihydrothymine) by Departments of Medicine [K. H., K. Ku.] and Pediatrics [K. Ki.], DPD and then are metabolized to 3-ureidopropionic acid and Nagoya City Higashi General Hospital, 2-23 Wakamizu 1-chome, 3-ureidoisobutyric acid, respectively, by dihydropyrimidinase. Chikusa-ku, Nagoya 464, Japan, and Department of Pediatrics [S. S., These compounds are converted subsequently into 3-alanine Y. W.] and Second Department of Medicine [M. M., E. 0., R. U.], Nagoya City University Medical School. Nagoya, Japan and -arninoisobutyric acid, respectively ( 1). Because about 80% of an administered dose of 5-FU is degraded by this pathway, there is a possibility of adverse reactions occurring as ABSTRACT a result of DPD or dihydrophrimidinase deficiency. The value of Deficiency of dihydropyrimidine dehydrogenase or di- measuring peripheral blood monocyte DPD activity before ad- hydropyrimidinase, enzymes that catalyze the breakdown of ministering 5-FU has been suggested in Western countries (2- pyrimidine chemotherapy agents such as 5-fluorouracil, 6), but DPD deficiency has not been reported in Japan. may cause serious adverse reactions to these agents. We Using a method that permits analysis of dihydrouracil and attempted to establish the reference range for urinary pyri- uracil in small volumes of urine, we previously screened Japa- midines in adults to detect individuals with abnormal py- nese infants for abnormalities of pyrimidine metabolism and rimidine metabolism. -
Catabolism of Xanthine and Uracil in Tumor-Bearing Rats'1
Catabolism of Xanthine and Uracil in Tumor-bearing Rats'1 CHUNGWu ANDJEREM. BAUER (Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan) SUMMARY The urinary excretion of allantoin and uric acid was greatly increased in rats bear ing Walker carcinoma 256. The increase was greater with more advanced tumor growth. A similar increase was also observed in the allantoin concentration of the plasma and liver of these rats. An increase in the RNA and DNA content and a decrease in the RNA/DNA ratio were found in the muscle of the tumor-bearing animals. Liver xan- thine oxidase activity was increased in rats bearing Walker 256 and Guerin carcinomas and NovikofT and Morris 3683 hepatomas but was unchanged in rats bearing Jensen sarcoma, Morris 5123, and Morris 3924-A hepatomas, when compared with their re spective controls fed ad libitum. Liver uracil reductase activity showed a decrease in rats bearing Morris 5123 and Morris 3924-A hepatomas but no change in rats bearing Walker carcinoma 256 and Novikoff and Morris 3683 hepatomas. These findings indi cate that the effect of different tumors on a given enzyme in the host system need not be qualitatively uniform. Finally, unlike the other hepatomas tested, Morris 5123 hepatoma was found to possess xanthine oxidase activity approaching that found in a normal liver. That the growth of a malignant tumor causes tivity has not been studied in detail in tumor-bear many disturbances in the metabolism of the host ing rats. A survey of this enzyme activity in the is well known.