CYTOCHROME P450 Peroxidasefperoxygenase-DEPENDENT
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Increased Hydrogen Peroxide Concentration in the Exhaled Breath Condensate of Stable COPD Patients After Nebulized -Acetylcysteine Jacek Rysz, Robert A
Increased hydrogen peroxide concentration in the exhaled breath condensate of stable COPD patients after nebulized -acetylcysteine Jacek Rysz, Robert A. Stolarek, Rafal Luczynski, Agata Sarniak, Anna Wlodarczyk, Marek Kasielski, Dariusz Nowak To cite this version: Jacek Rysz, Robert A. Stolarek, Rafal Luczynski, Agata Sarniak, Anna Wlodarczyk, et al.. In- creased hydrogen peroxide concentration in the exhaled breath condensate of stable COPD patients after nebulized -acetylcysteine. Pulmonary Pharmacology & Therapeutics, 2007, 20 (3), pp.281. 10.1016/j.pupt.2006.03.011. hal-00499131 HAL Id: hal-00499131 https://hal.archives-ouvertes.fr/hal-00499131 Submitted on 9 Jul 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Author’s Accepted Manuscript Increased hydrogen peroxide concentration in the exhaled breath condensate of stable COPD patients after nebulized N-acetylcysteine Jacek Rysz, Robert A. Stolarek, Rafal Luczynski, Agata Sarniak,Anna Wlodarczyk, Marek Kasielski, Dariusz Nowak PII: S1094-5539(06)00045-9 DOI: doi:10.1016/j.pupt.2006.03.011 www.elsevier.com/locate/ypupt Reference: YPUPT 677 To appear in: Pulmonary Pharmacology & Therapeutics Received date: 2 January 2006 Revised date: 13 March 2006 Accepted date: 15 March 2006 Cite this article as: Jacek Rysz, Robert A. -
Next-Generation Sequencing of Representational Difference Analysis
Planta DOI 10.1007/s00425-017-2657-0 ORIGINAL ARTICLE Next-generation sequencing of representational difference analysis products for identification of genes involved in diosgenin biosynthesis in fenugreek (Trigonella foenum-graecum) 1 1 1 1 Joanna Ciura • Magdalena Szeliga • Michalina Grzesik • Mirosław Tyrka Received: 19 August 2016 / Accepted: 30 January 2017 Ó The Author(s) 2017. This article is published with open access at Springerlink.com Abstract Within the transcripts related to sterol and steroidal Main conclusion Representational difference analysis saponin biosynthesis, we discovered novel candidate of cDNA was performed and differential products were genes of diosgenin biosynthesis and validated their sequenced and annotated. Candidate genes involved in expression using quantitative RT-PCR analysis. Based on biosynthesis of diosgenin in fenugreek were identified. these findings, we supported the idea that diosgenin is Detailed mechanism of diosgenin synthesis was biosynthesized from cycloartenol via cholesterol. This is proposed. the first report on the next-generation sequencing of cDNA-RDA products. Analysis of the transcriptomes Fenugreek (Trigonella foenum-graecum L.) is a valuable enriched in low copy sequences contributed substantially medicinal and crop plant. It belongs to Fabaceae family to our understanding of the biochemical pathways of and has a unique potential to synthesize valuable steroidal steroid synthesis in fenugreek. saponins, e.g., diosgenin. Elicitation (methyl jasmonate) and precursor feeding (cholesterol and squalene) were Keywords Diosgenin Á Next-generation sequencing Á used to enhance the content of sterols and steroidal Phytosterols Á Representational difference analysis of sapogenins in in vitro grown plants for representational cDNA Á Steroidal saponins Á Transcriptome user-friendly difference analysis of cDNA (cDNA-RDA). -
Henrique Pinho Oliveira
0 UNIVERSIDADE FEDERAL DO CEARÁ CENTRO DE CIÊNCIAS DEPARTAMENTO DE BIOQUÍMICA E BIOLOGIA MOLECULAR PROGRAMA DE PÓS-GRADUAÇÃO EM BIOQUÍMICA HENRIQUE PINHO OLIVEIRA PURIFICAÇÃO, CARACTERIZAÇÃO E ATIVIDADE ANTIFÚNGICA DA Mm -POX, UMA PEROXIDASE DO LÁTEX DE Marsdenia megalantha (GOYDER; MORILLO, 1994). FORTALEZA 2013 1 HENRIQUE PINHO OLVEIRA PURIFICAÇÃO, CARACTERIZAÇÃO E ATIVIDADE ANTIFÚNGICA DA Mm -POX, UMA PEROXIDASE DO LÁTEX DE Marsdenia megalantha (GOYDER; MORILLO, 1994) Tese apresentada ao Curso de Doutorado em Bioquímica do Departamento de Bioquímica e Biologia Molecular da Universidade Federal do Ceará, como parte dos requisitos para obtenção do título de Doutor em Bioquímica. Orientadora: Profa. Dra. Ilka Maria Vasconcelos FORTALEZA 2013 2 3 HENRIQUE PINHO OLIVEIRA PURIFICAÇÃO, CARACTERIZAÇÃO E ATIVIDADE ANTIFÚNGICA DA Mm -POX, UMA PEROXIDASE DO LÁTEX DE Marsdenia megalantha (GOYDER; MORILLO, 1994) Tese apresentada ao Curso de Doutorado em Bioquímica do Departamento de Bioquímica e Biologia Molecular da Universidade Federal do Ceará, como parte dos requisitos para obtenção do título de Doutor em Bioquímica. Aprovada em: ____/____/___ BANCA EXAMINADORA ________________________________________ Profa. Dra. Ilka Maria Vasconcelos Universidade Federal do Ceará (UFC) ________________________________________ Profa. Dra. Daniele de Oliveira Bezerra de Sousa Universidade Federal do Ceará (UFC) ________________________________________ Prof. Dr. Cleverson Diniz Teixeira de Freitas Universidade Federal do Ceará (UFC) ________________________________________ Prof. Dr. Renato de Azevedo Moreira Universidade de Fortaleza (UNIFOR) ________________________________________ Dr. Cleberson de Freitas Fernandes Empresa Brasileira de Pesquisa Agropecuária - Rondônia 4 À minha Mãe Selene, Ao meu Pai Régis, À minha Irmã Cristiane, Às minhas Avós Celina e Laura ( in memorian ), À minha Sherecuda Linda À todos os familiares, Dedico 5 O Mundo está mudado. -
Relating Metatranscriptomic Profiles to the Micropollutant
1 Relating Metatranscriptomic Profiles to the 2 Micropollutant Biotransformation Potential of 3 Complex Microbial Communities 4 5 Supporting Information 6 7 Stefan Achermann,1,2 Cresten B. Mansfeldt,1 Marcel Müller,1,3 David R. Johnson,1 Kathrin 8 Fenner*,1,2,4 9 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, 10 Switzerland. 2Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 11 Zürich, Switzerland. 3Institute of Atmospheric and Climate Science, ETH Zürich, 8092 12 Zürich, Switzerland. 4Department of Chemistry, University of Zürich, 8057 Zürich, 13 Switzerland. 14 *Corresponding author (email: [email protected] ) 15 S.A and C.B.M contributed equally to this work. 16 17 18 19 20 21 This supporting information (SI) is organized in 4 sections (S1-S4) with a total of 10 pages and 22 comprises 7 figures (Figure S1-S7) and 4 tables (Table S1-S4). 23 24 25 S1 26 S1 Data normalization 27 28 29 30 Figure S1. Relative fractions of gene transcripts originating from eukaryotes and bacteria. 31 32 33 Table S1. Relative standard deviation (RSD) for commonly used reference genes across all 34 samples (n=12). EC number mean fraction bacteria (%) RSD (%) RSD bacteria (%) RSD eukaryotes (%) 2.7.7.6 (RNAP) 80 16 6 nda 5.99.1.2 (DNA topoisomerase) 90 11 9 nda 5.99.1.3 (DNA gyrase) 92 16 10 nda 1.2.1.12 (GAPDH) 37 39 6 32 35 and indicates not determined. 36 37 38 39 S2 40 S2 Nitrile hydration 41 42 43 44 Figure S2: Pearson correlation coefficients r for rate constants of bromoxynil and acetamiprid with 45 gene transcripts of ECs describing nucleophilic reactions of water with nitriles. -
( 12 ) United States Patent
US010208322B2 (12 ) United States Patent ( 10 ) Patent No. : US 10 ,208 , 322 B2 Coelho et al. (45 ) Date of Patent: * Feb . 19, 2019 ( 54 ) IN VIVO AND IN VITRO OLEFIN ( 56 ) References Cited CYCLOPROPANATION CATALYZED BY HEME ENZYMES U . S . PATENT DOCUMENTS 3 , 965 ,204 A 6 / 1976 Lukas et al. (71 ) Applicant: California Institute of Technology , 4 , 243 ,819 A 1 / 1981 Henrick Pasadena , CA (US ) 5 ,296 , 595 A 3 / 1994 Doyle 5 , 703 , 246 A 12 / 1997 Aggarwal et al. 7 , 226 , 768 B2 6 / 2007 Farinas et al. ( 72 ) Inventors : Pedro S . Coelho , Los Angeles, CA 7 , 267 , 949 B2 9 / 2007 Richards et al . (US ) ; Eric M . Brustad , Durham , NC 7 ,625 ,642 B2 12 / 2009 Matsutani et al. (US ) ; Frances H . Arnold , La Canada , 7 ,662 , 969 B2 2 / 2010 Doyle et al. CA (US ) ; Zhan Wang , San Jose , CA 7 ,863 ,030 B2 1 / 2011 Arnold (US ) ; Jared C . Lewis , Chicago , IL 8 ,247 ,430 B2 8 / 2012 Yuan 8 , 993 , 262 B2 * 3 / 2015 Coelho . .. .. .. • * • C12P 7 /62 (US ) 435 / 119 9 ,399 , 762 B26 / 2016 Farwell et al . (73 ) Assignee : California Institute of Technology , 9 , 493 ,799 B2 * 11 /2016 Coelho .. C12P 7162 Pasadena , CA (US ) 2006 / 0030718 AL 2 / 2006 Zhang et al. 2006 / 0111347 A1 5 / 2006 Askew , Jr . et al. 2007 /0276013 AL 11 /2007 Ebbinghaus et al . ( * ) Notice : Subject to any disclaimer , the term of this 2009 /0238790 A2 9 /2009 Sommadosi et al. patent is extended or adjusted under 35 2010 / 0056806 A1 3 / 2010 Warren U . -
Geneid T-Test Q-Val Gene Symbol Gene Title GO Biological Process
Supplementary Table 2. Genes selected by FADA as the most discriminant between tumoral and normal prostate samples GO Biological Process GO Molecular Function GO Cellular Component GeneID T-test q-val Gene Symbol Gene Title Description Description Description Pathway serine-type endopeptidase inhibitor activity /// endopeptidase inhibitor serpin peptidase inhibitor, clade activity /// serine-type endopeptidase 213572_s_at -6.753 2.213E-05 SERPINB1 B (ovalbumin), member 1 --- inhibitor activity cytoplasm --- ion transport /// cellular defense response /// positive regulation of T-cell, immune regulator 1, cell proliferation /// proton plasma membrane /// integral to ATPase, H+ transporting, transport /// transport /// proton transporter activity /// hydrogen ion plasma membrane /// membrane /// 204158_s_at -5.729 8.585E-05 TCIRG1 lysosomal V0 subunit A3 transport transporter activity integral to membrane --- chemotaxis /// cell adhesion /// homophilic cell adhesion /// nervous system development /// cell differentiation /// positive roundabout, axon guidance regulation of axonogenesis /// receptor activity /// axon guidance integral to plasma membrane /// cell receptor, homolog 1 development /// nervous system receptor activity /// identical protein surface /// membrane /// integral to 213194_at -6.168 4.441E-05 ROBO1 (Drosophila) development binding /// protein binding membrane --- structural molecule activity /// nucleus /// intermediate filament /// protein binding /// microtubule cytoplasmic dynein complex /// 203411_s_at -5.297 1.636E-04 -
New Automatically Built Profiles for a Better Understanding of the Peroxidase Superfamily Evolution
University of Geneva Practical training report submitted for the Master Degree in Proteomics and Bioinformatics New automatically built profiles for a better understanding of the peroxidase superfamily evolution presented by Dominique Koua Supervisors: Dr Christophe DUNAND Dr Nicolas HULO Laboratory of Plant Physiology, Dr Christian J.A. SIGRIST University of Geneva Swiss Institute of Bioinformatics PROSITE group. Geneva, April, 18th 2008 Abstract Motivation: Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. These proteins are extremely widespread and present in almost all living organisms. An important number of haem and non-haem peroxidase sequences are annotated and classified in the peroxidase database PeroxiBase (http://peroxibase.isb-sib.ch). PeroxiBase contains about 5800 peroxidase sequences classified as haem peroxidases and non-haem peroxidases and distributed between thirteen superfamilies and fifty subfamilies, (Passardi et al., 2007). However, only a few classification tools are available for the characterisation of peroxidase sequences: InterPro motifs, PRINTS and specifically designed PROSITE profiles. However, these PROSITE profiles are very global and do not allow the differenciation between very close subfamily sequences nor do they allow the prediction of specific cellular localisations. Due to the rapid growth in the number of available sequences, there is a need for continual updates and corrections of peroxidase protein sequences as well as for new tools that facilitate acquisition and classification of existing and new sequences. Currently, the PROSITE generalised profile building manner and their usage do not allow the differentiation of sequences from subfamilies showing a high degree of similarity. -
Springer Handbook of Enzymes
Dietmar Schomburg and Ida Schomburg (Eds.) Springer Handbook of Enzymes Volume 25 Class 1 • Oxidoreductases X EC 1.9-1.13 co edited by Antje Chang Second Edition 4y Springer Index of Recommended Enzyme Names EC-No. Recommended Name Page 1.13.11.50 acetylacetone-cleaving enzyme 673 1.10.3.4 o-aminophenol oxidase 149 1.13.12.12 apo-/?-carotenoid-14',13'-dioxygenase 732 1.13.11.34 arachidonate 5-lipoxygenase 591 1.13.11.40 arachidonate 8-lipoxygenase 627 1.13.11.31 arachidonate 12-lipoxygenase 568 1.13.11.33 arachidonate 15-lipoxygenase 585 1.13.12.1 arginine 2-monooxygenase 675 1.13.11.13 ascorbate 2,3-dioxygenase 491 1.10.2.1 L-ascorbate-cytochrome-b5 reductase 79 1.10.3.3 L-ascorbate oxidase 134 1.11.1.11 L-ascorbate peroxidase 257 1.13.99.2 benzoate 1,2-dioxygenase (transferred to EC 1.14.12.10) 740 1.13.11.39 biphenyl-2,3-diol 1,2-dioxygenase 618 1.13.11.22 caffeate 3,4-dioxygenase 531 1.13.11.16 3-carboxyethylcatechol 2,3-dioxygenase 505 1.13.11.21 p-carotene 15,15'-dioxygenase (transferred to EC 1.14.99.36) 530 1.11.1.6 catalase 194 1.13.11.1 catechol 1,2-dioxygenase 382 1.13.11.2 catechol 2,3-dioxygenase 395 1.10.3.1 catechol oxidase 105 1.13.11.36 chloridazon-catechol dioxygenase 607 1.11.1.10 chloride peroxidase 245 1.13.11.49 chlorite O2-lyase 670 1.13.99.4 4-chlorophenylacetate 3,4-dioxygenase (transferred to EC 1.14.12.9) . -
Oxidative Stress Response in Lactobacillus Plantarum WCFS1: a Functional Genomics Approach
Oxidative Stress Response in Lactobacillus plantarum WCFS: A Functional Genomics Approach L. Mariela Serrano Promotor: Prof. Dr. Willem M. de Vos Hoogleraar Microbiologie Wageningen Universiteit Co-Promotor: Dr. Eddy J. Smid Projectleider NIZO Food Research Leden van de promotiecomissie: Prof. Dr. Tjakko Abee Food Microbiology Laboratory Wageningen University, The Netherlands Dr. Philippe Gaudu INRA, Unité Bactéries Lactiques et pathogènes Jouy en Josas, France Prof. Dr. Jeroen Hugenholtz NIZO Food Research Ede, The Netherlands Prof. Dr. R. Paul Ross Moorepark Food Research Centre Cork, Ireland Dit onderzoek is utigevoerd binnen de onderzoekschool VLAG. Oxidative Stress Response in Lactobacillus plantarum WCFS1: A Functional Genomics Approach L. Mariela Serrano Proefschrift Ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, Prof. Dr. M. J. Kropff in het openbaar te verdedigen op vrijdag 18 april 2008 des ochtends om elf uur in de Aula Oxidative Stress Response in Lactobacillus plantarum WCFS1: A Functional Genomics Approach L. Mariela Serrano Ph.D. thesis Wageningen University and Research Centre, The Netherlands, 2008. With summary in dutch ISBN 978-90-8504-920-3 The road not taken Two roads diverged in a yellow wood And sorry I could not travel both And be one traveller, long I stood And looked down one as far as I could To where it bent in the undergrowth; Then took the other, as just as fair, And having perhaps the better claim, Because it was grassy and wanted wear; Though as for that the passing there Had worn them really about the same, And both that morning equally lay In leaves no step had trodden black. -
Discovery of Industrially Relevant Oxidoreductases
DISCOVERY OF INDUSTRIALLY RELEVANT OXIDOREDUCTASES Thesis Submitted for the Degree of Master of Science by Kezia Rajan, B.Sc. Supervised by Dr. Ciaran Fagan School of Biotechnology Dublin City University Ireland Dr. Andrew Dowd MBio Monaghan Ireland January 2020 Declaration I hereby certify that this material, which I now submit for assessment on the programme of study leading to the award of Master of Science, is entirely my own work, and that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge breach any law of copyright, and has not been taken from the work of others save and to the extent that such work has been cited and acknowledged within the text of my work. Signed: ID No.: 17212904 Kezia Rajan Date: 03rd January 2020 Acknowledgements I would like to thank the following: God, for sending me angels in the form of wonderful human beings over the last two years to help me with any- and everything related to my project. Dr. Ciaran Fagan and Dr. Andrew Dowd, for guiding me and always going out of their way to help me. Thank you for your patience, your advice, and thank you for constantly believing in me. I feel extremely privileged to have gotten an opportunity to work alongside both of you. Everything I’ve learnt and the passion for research that this project has sparked in me, I owe it all to you both. Although I know that words will never be enough to express my gratitude, I still want to say a huge thank you from the bottom of my heart. -
SUPPLEMENTARY MATERIAL Supplementary Table 1
Predicting Drug Promiscuity Using Spherical Harmonic Surface The Open Conference Proceedings Journal, 2011, Volume 2 i SUPPLEMENTARY MATERIAL Supplementary Table 1. MDDR Target Annotations Used in the Promiscuity Predictions TARGET_KEY EXTERNAL_ID 1001 prostaglandin-endoperoxide synthase 1002 cyclooxygenase 1 1003 cyclooxygenase 2 1046 ribonucleoside-diphosphate reductase 1112 thymidylate synthase 1209 phosphoribosylglycinamide formyltransferase 1609 purine-nucleoside phosphorylase 1611 uridine phosphorylase 1637 nad adp-ribosyltransferase 1657 transferring alkyl or aryl groups, other than methyl groups 1798 thymidine kinase 1814 protein kinase 1843 1-phosphatidylinositol 4-kinase 1883 protein-tyrosine kinase 1973 nucleotidyltransferase 2018 rna-directed dna polymerase 2121 phospholipase a2 2124 acetylcholinesterase 2282 phosphoric diester hydrolase 2283 phosphodiesterase i 2309 3',5'-cyclic-nucleotide phosphodiesterase 2310 3',5'-cyclic-gmp phosphodiesterase 2316 steryl-sulfatase 2414 alpha-glucosidase 2565 adenosylhomocysteinase 2576 peptidase 25 aldehyde reductase 2613 dipeptidyl-peptidase iv 2619 peptidyl-dipeptidase a 2624 serine-type d-ala-d-ala carboxypeptidase 2659 serine endopeptidase 2663 trypsin 2664 thrombin 2665 coagulation factor xa 2672 coagulation factor viia 2695 tryptase 2742 cathepsin b 2750 cathepsin l 2765 caspase-1 2784 hiv-1 retropepsin 2811 metalloendopeptidase 2822 stromelysin 1 286 xanthine oxidase 2978 beta-lactamase 3014 adenosine deaminase ii The Open Conference Proceedings Journal, 2011, Volume 2 Pérez-Nueno -
Dalmanol Biosyntheses Require Coupling of Two Separate Polyketide Gene Clusters
Showcasing research progress from Professor Ren Xiang Tan’s As featured in: laboratories at Nanjing University & Nanjing University of Chinese Medicine, Nanjing, China. Dalmanol biosyntheses require coupling of two separate polyketide gene clusters The biosynthesis of immunosuppressants (dalmanol A and acetodalmanol A) is characterized by the coupling of two separate (naphthalene- and chromane-encoding) gene clusters under the catalysis of unspecifi c enzyme(s) that may distribute widely in the fungal kingdom. The fi nding highlights an access to the inter-cluster orchestration derived chemodiversity of microbial secondary metabolites that remain to be a reliable source of leading compounds triggering the development of See Ren Xiang Tan et al., new medicines, agrochemicals, and other tool molecules. Chem. Sci., 2019, 10, 73. rsc.li/chemical-science Registered charity number: 207890 Chemical Science View Article Online EDGE ARTICLE View Journal | View Issue Dalmanol biosyntheses require coupling of two separate polyketide gene clusters† Cite this: Chem. Sci.,2019,10,73 a a bc a a All publication charges for this article Zhen Zhen Zhou, Hong Jie Zhu, Li Ping Lin, Xuan Zhang, Hui Ming Ge, have been paid for by the Royal Society Rui Hua Jiaoa and Ren Xiang Tan *ab of Chemistry Polyketide–polyketide hybrids are unique natural products with promising bioactivity, but the hybridization processes remain poorly understood. Herein, we present that the biosynthetic pathways of two immunosuppressants, dalmanol A and acetodalmanol A, result from an unspecific monooxygenase triggered hybridization of two distinct polyketide (naphthalene and chromane) biosynthetic gene clusters. The orchestration of the functional dimorphism of the polyketide synthase (ChrA) ketoreductase (KR) domain (shortened as ChrA KR) with that of the KR partner (ChrB) in the bioassembly line increases the polyketide diversity and allows the fungal generation of plant chromanes (e.g., noreugenin) and phloroglucinols (e.g., 2,4,6-trihydroxyacetophenone).