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New Computational Approaches for Investigating the Impact of Mutations on the Transglucosylation Activity of Sucrose Phosphorylase Enzyme
Thesis submitted to the Université de la Réunion for award of Doctor of Philosophy in Sciences speciality in bioinformatics New computational approaches for investigating the impact of mutations on the transglucosylation activity of sucrose phosphorylase enzyme Mahesh VELUSAMY Thesis to be presented on 18th December 2018 in front of the jury composed of Mme Isabelle ANDRE, Directeur de Recherche CNRS, INSA de TOULOUSE, Rapporteur M. Manuel DAUCHEZ, Professeur, Université de Reims Champagne Ardennes, Rapporteur M. Richard DANIELLOU, Professeur, Université d'Orléans, Examinateur M. Yves-Henri SANEJOUAND, Directeur de Recherche CNRS, Université de Nantes, Examinateur Mme Irène MAFFUCCI, Maître de Conférences, Université de Technologie de Compiègne, Examinateur Mme Corinne MIRAL, Maître de Conférences HDR, Université de Nantes, Examinateur M. Frédéric CADET, Professeur, Université de La Réunion, Co-directeur de thèse M. Bernard OFFMANN, Professeur, Université de Nantes, Directeur de thèse ெ்்ந்ி ிைு்ூுத் ெ்யாம் ெ்த உதி்ு ையகு் ானகு் ஆ்ற் அிு. -ிு்ு் ுதி் அ்ப் ுுக், எனு த்ைத ேுாி, தா் க்ூி, அ்ண் ு்ு்ுமா், த்ைக பா்பா, ஆ்தா ுு்மா், ீனா, அ்ண் ்ுக், ெபிய்பா, ெபிய்மா ம்ு் உுுைணயா் இு்த அைண்ு ந்ப்கு்ு் எனு மனமா்்த ந்ி. இ்த ஆ்ி்ைக ுுைம அை3த்ு ுுுத்்காரண், எனு ஆ்ி்ைக இய்ுன் ேபராிிய் ெப்னா்் ஆஃ்ேம். ப்ேு துண்கி் நா் மனதாு், ெபாுளாதார அளிு் க்3்ி் இு்தேபாு, என்ு இ்ெனாு த்ைதயாகே இு்ு எ்ைன பா்்ு்ெகா்3ா். ுி்பாக, எனு ூ்றா் ஆ்ு இுிி், அ்்ு எ்ளோ தி்ப்3 க3ைமக் ம்ு் ிர்ிைனக் இு்தாு், அைத்ெபாு்பு்தாு, அ் என்ு ெ்த ெபாுளாதார உதி, ப்கைB்கழக பிு ம்ு் இதர ி்ாக ்ப்த்ப்3 உதிகு்ு எ்ன ைகமா்ு ெகாு்தாு் ஈ3ாகாு. -
Selective Fermentation of Potential Prebiotic Lactose-Derived Oligosaccharides By
1 Selective fermentation of potential prebiotic lactose-derived oligosaccharides by 2 probiotic bacteria 3 4 Tomás García-Cayuela, Marina Díez-Municio, Miguel Herrero, M. Carmen Martínez- 5 Cuesta, Carmen Peláez, Teresa Requena*, F. Javier Moreno 6 7 Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI 8 (UAM+CSIC), Nicolás Cabrera 9, 28049 Madrid, Spain. 9 10 * Corresponding author: Tel.: +34 91 0017900; E-mail address: [email protected] 11 1 12 Abstract 13 The growth of potential probiotic strains from the genera Lactobacillus, 14 Bifidobacterium and Streptococcus was evaluated with the novel lactose-derived 15 trisaccharides 4’-galactosyl-kojibiose and lactulosucrose and the potential prebiotics 16 lactosucrose and kojibiose. The novel oligosaccharides were synthesized from 17 equimolar sucrose:lactose and sucrose:lactulose mixtures, respectively, by the use of a 18 Leuconostoc mesenteroides dextransucrase and purified by liquid chromatography. The 19 growth of the strains using the purified carbohydrates as the sole carbon source was 20 evaluated by recording the culture optical density and calculating maximum growth 21 rates and lag phase parameters. The results revealed an apparent bifidogenic effect of 22 lactulosucrose, being also a moderate substrate for streptococci and poorlybut badly 23 utilized by lactobacilli. In addition, 4’-galactosyl-kojibiose was selectively fermented by 24 Bifidobacterium breve, which was also the only tested bifidobacterial species able to 25 ferment kojibiose. The described fermentation properties of the specific probiotic strains 26 on the lactose-derived oligosaccharides would enable the design of prebiotics with a 27 high degree of selectivity. 28 29 Keywords: Prebiotic; Lactose-derived oligosaccharides; Probiotic; Bifidobacterium; 30 Lactobacillus; Streptococcus 31 2 32 1. -
United States Patent (10) Patent No.: US 7,223,570 B2 Aga Et Al
US007223570B2 (12) United States Patent (10) Patent No.: US 7,223,570 B2 Aga et al. (45) Date of Patent: May 29, 2007 (54) BRANCHED CYCLIC TETRASACCHARIDE, 5,763,598 A 6/1998 Hamayasu et al. PROCESS FOR PRODUCING THE SAME, 5,786, 196 A * 7/1998 Cote et al. .................. 435,208 AND USE FOREIGN PATENT DOCUMENTS (75) Inventors: Hajime Aga, Okayama (JP); Takanobu f Higashiyama, Okayama (JP); Hikaru E. 1 . A1 is: Watanabe, Okayama (JP); Tomohiko JP 647s) 1, 1994 Sonoda, Okayama (JP); Michio JP 6-16705 1, 1994 Kubota, Okayama (JP) JP 6-298806 10, 1994 JP 10-25305 1, 1998 (73) Assignee: Kabushiki Kaisha Hayashibara JP 10-304882 11, 1998 Seibutsu Kagaku Kenkyujo, Okayama WO WO 01/90338 A1 11, 2001 (JP) WO WO O2/10361 A1 2/2002 WO WO O2.40659 A1 5, 2002 (*) Notice: Subject to any disclaimer, the term of this WO WO O2/O55708 A1 T 2002 patent is extended or adjusted under 35 U.S.C. 154(b) by 324 days. OTHER PUBLICATIONS (21) Appl. No.: 10/471.377 Biely, P. “Enzymic alpha-galactosylation . " Carbohyd. Res. (2001) vol. 332, pp. 299-303.* (22) PCT Filed: Mar. 8, 2002 Cote, Gregory and Biely, Peter, Enzymically produced cyclic C-1,3- linked and O-1,6-linked oligosaccharides of D-glucose, European (86). PCT No.: PCT/UPO2/O2213 Journal of Biochemistry, vol. 226, (1994), p. 641-648. Sambrook, Joseph and Russell, David, Molecular Cloning. A Labo S 371 (c)(1), ratory Manuel. 3" Edition, (Cold Spring Harbor Laboratory, New (2), (4) Date: Sep. -
Towards a Highly Efficient Process for the Synthesis of Kojibiose
Faculty of Bioscience Engineering Academic Year 2014 – 2015 Demonstrating the necessity of enzyme engineering: towards a highly efficient process for the synthesis of kojibiose Anoek Van Canneyt Promotor: Prof. dr. Tom Desmet Tutor: ir. Karel De Winter Mast er’s dissertation submitted in partial fulfillment of the requirements for the degree of Master of Science in Bioscience Engineering: Chemistry and Bioprocess Technology Faculty of Bioscience Engineering Academic Year 2014 – 2015 Demonstrating the necessity of enzyme engineering: towards a highly efficient process for the synthesis of kojibiose Anoek Van Canneyt Promotor: Prof. dr. Tom Desmet Tutor: ir. Karel De Winter Mast er’s dissertation submitted in partial fulfillment of the requirements for the degree of Master of Science in Bioscience Engineering: Chemistry and Bioprocess Technology IMPORTANT – PLEASE READ THIS FIRST De auteur, tutor en promotor geven de toelating deze scriptie voor consultatie beschikbaar te stellen en delen ervan de kopiëren voor persoonlijk gebruikt. Elk ander gebruik valt onder de beperking van het auteursrecht, in het bijzonder met betrekking tot de verplichting de bron te vermelden bij het aanhalen van resultaten uit deze scriptie. The author, tutor and promotor give the permission to use this thesis for consultation and to copy parts of it for personal use. Every other use is subjected to the copyright laws, more specifically the source must be extensively specified when using results from this thesis. Anoek Van Canneyt Ghent, June 2015 Promotor: Tutor: Prof. dr. Tom Desmet ir. Karel De Winter Contact person Ghent University: Prof. dr. Tom Desmet [email protected] Center for Industrial Biotechnology and Biocatalysis Coupure Links 653, 9000 Gent PREFACE “Live as if you were to die tomorrow. -
Applied Biocatalysis
k Applied Biocatalysis k k k k Applied Biocatalysis The Chemist’s Enzyme Toolbox Edited by JOHN WHITTALL k University of Manchester k Manchester UK PETER W. SUTTON Glycoscience S.L. Barcelona ES k k This edition first published 2021 © 2021 John Wiley & Sons Ltd All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by law. Advice on how to obtain permission to reuse material from this title is available at http://www.wiley.com/go/permissions. The right of John Whittall and Peter W. Sutton to be identified as the authors of the editorial material in this work hasbeen asserted in accordance with law. Registered Offices John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, USA John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK Editorial Office The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK For details of our global editorial offices, customer services, and more information about Wiley products visit usat www.wiley.com. Wiley also publishes its books in a variety of electronic formats and by print-on-demand. Some content that appears in standard print versions of this book may not be available in other formats. Limit of Liability/Disclaimer of Warranty In view of ongoing research, equipment modifications, changes in governmental regulations, and the constant flow of information relating to the use of experimental reagents, equipment, and devices, the reader is urged to review and evaluate the information provided in the package insert or instructions for each chemical, piece of equipment, reagent, or device for, among other things, any changes in the instructions or indication of usage and for added warnings and precautions. -
Cloning and Expression of the Sucrose Phosphorylase Gene in Bacillus
Wang et al. Microb Cell Fact (2018) 17:23 https://doi.org/10.1186/s12934-017-0842-2 Microbial Cell Factories RESEARCH Open Access Cloning and expression of the sucrose phosphorylase gene in Bacillus subtilis and synthesis of kojibiose using the recombinant enzyme Miaomiao Wang1,2, Jing Wu1,2,3 and Dan Wu1,2,3* Abstract Background: Kojibiose as a prebiotic and inhibitor of α-glucosidase exhibits potential for a wide range of applica- tions in the food and medicine felds; however, large-scale separation and extraction of kojibiose from nature is dif- fcult. Sucrose phosphorylase (SPase) can be used for the production of kojibiose, and currently, SPase is only heter- ologously expressed in E. coli, making it unsuitable for use in the food industry. However, Bacillus subtilis is generally considered to be a safe organism potentially useful for SPase expression. Results: Here, for the frst time, we heterologously expressed Bifdobacterium adolescentis SPase in a food-grade B. subtilis strain. The results showed that SPase was efciently secreted into the extracellular medium in the absence of a signal peptide. After culturing the recombinant strain in a 3-L bioreactor, crude SPase yield and activity reached 7.5 g/L and 5.3 U/mL, respectively, the highest levels reported to date. The optimal reaction conditions for kojibiose synthesis catalyzed by recombinant SPase were as follows: 0.5 M sucrose, 0.5 M glucose, 0.02 Uenzyme/mgall_substrates, pH 7.0, 50 °C, and 30 h. Furthermore, the substrate-conversion rate reached 40.01%, with kojibiose accounting for 104.45 g/L and selectivity for kojibiose production at 97%. -
Reversion Reactions Catalyzed by Glucoamylases I and II From
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1986 Reversion reactions catalyzed by glucoamylases I and II from Aspergillus niger: product analysis, kinetics equilibria, and modeling Zivko Nikolov Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Chemical Engineering Commons Recommended Citation Nikolov, Zivko, "Reversion reactions catalyzed by glucoamylases I and II from Aspergillus niger: product analysis, kinetics equilibria, and modeling " (1986). Retrospective Theses and Dissertations. 8282. https://lib.dr.iastate.edu/rtd/8282 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. INFORMATION TO USERS While the most advanced technology has been used to photograph and reproduce this manuscript, the quality of the repr^uction is heavily dependent upon the quality of the material submitted. For example: • Manuscript pages may have indistinct print. In such cases, the best available copy has been filmed. • Manuscripts may not always be complete. In such cases, a note will indicate that it is not possible to obtain missing pages. • Copyrighted material may have been removed from the manuscript. In such cases, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, and charts) are photographed by sectioning the original, beginning at the upper leA-hand comer and continuing from left to right in equal sections with small overlaps. -
WO 2015/006740 A2 15 January 2015 (15.01.2015) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/006740 A2 15 January 2015 (15.01.2015) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every A61K 47/48 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (21) International Application Number: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, PCT/US20 14/046425 DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 11 July 2014 ( 11.07.2014) KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (25) Filing Language: English OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (26) Publication Language: English SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, (30) Priority Data: ZW. 61/845,279 11 July 2013 ( 11.07.2013) US (84) Designated States (unless otherwise indicated, for every (71) Applicant: ALNYLAM PHARMACEUTICALS, INC. kind of regional protection available): ARIPO (BW, GH, [US/US]; 300 Third Street, Cambridge, MA 02142 (US). GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, (72) Inventors: MANOHARAN, Muthiah; 300 Third Street, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, Cambridge, MA 02142 (US). -
Molecular Pharmacology of Honey
xperim & E en Afroz et al., Clin Exp Pharmacol 2016, 6:3 l ta a l ic P in h l DOI: 10.4172/2161-1459.1000212 a C r m f Journal of o a l c a o n l o r g u y o J ISSN: 2161-1459 Clinical and Experimental Pharmacology Review Article Open Access Molecular Pharmacology of Honey Afroz R1, Tanvir EM2, Zheng W3 and Little PJ4* 1Department of Biochemistry, Primeasia University, Banani, Dhaka 1213, Bangladesh 2Department of Biochemistry and Molecular Biology, Gono University, Savar, Dhaka 1344, Bangladesh 3Faculty of Health Sciences, University of Macau, Taipa, Macau, China 4School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, Queensland 4102, Australia *Corresponding author: Little PJ, School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, Queensland 4102, Australia, Tel: +61 33461701; E-mail: [email protected] Received date: May 11, 2016; Accepted date: May 24, 2016; Published date: May 30, 2016 Copyright: © 2016 Afroz R, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract Honey is a natural by-product from flower nectar and the aero-digestive tract of the honey bee. Honey has a complex chemical and biochemical composition including sugars, proteins, amino acids, phenolics, vitamins and minerals. Honey is a natural medicinal agent with antioxidant, anti-bacterial, antifungal, anti-malarial and anti-tumor properties. This review describes the major active ingredients in honey and their potential pharmacological effects with a description and analysis of the underlying molecular mechanism. -
WO 2015/017866 Al 5 February 2015 (05.02.2015) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/017866 Al 5 February 2015 (05.02.2015) P O P C T (51) International Patent Classification: Gregory, B. [US/US]; C/o 83 Cambridge Parkway, Cam C12N 15/63 (2006.01) C40B 40/06 (2006.01) bridge, MA 02142 (US). C12N 15/87 (2006.01) (74) Agents: ALTIERI, Stephen, L. et al; Bingham Mc- (21) International Application Number: cutchen LLP, 2020 K Street, NW, Washington, DC 20006- PCT/US20 14/049649 1806 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 4 August 2014 (04.08.2014) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (25) Filing Language: English BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (26) Publication Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/861,805 2 August 2013 (02.08.2013) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/883,13 1 26 September 2013 (26.09.2013) US OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 61/935,265 3 February 2014 (03.02.2014) US SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, 61/938,933 12 February 2014 (12.02.2014) US TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, (71) Applicant: ENEVOLV, INC. -
Structure Determination of Derivatized Disaccharides by Tandem Mass Spectrometry and Molecular Modeling
Louisiana State University LSU Digital Commons LSU Historical Dissertations and Theses Graduate School 2000 Structure Determination of Derivatized Disaccharides by Tandem Mass Spectrometry and Molecular Modeling. Sanford Louis Mendonca Louisiana State University and Agricultural & Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_disstheses Recommended Citation Mendonca, Sanford Louis, "Structure Determination of Derivatized Disaccharides by Tandem Mass Spectrometry and Molecular Modeling." (2000). LSU Historical Dissertations and Theses. 7378. https://digitalcommons.lsu.edu/gradschool_disstheses/7378 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Historical Dissertations and Theses by an authorized administrator of LSU Digital Commons. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy subm itted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. -
HPAE-PAD Determination of Carbohydrates in Honey to Evaluate Samples for Quality and Adulteration
APPLICATION NOTE No. 1158 HPAE-PAD determination of carbohydrates in honey to evaluate samples for quality and adulteration Manali Aggrawal and Jeffrey Rohrer, Sunnyvale, CA, USA Key words Dionex CarboPac PA210-4 µm column, food adulteration, sugar syrup, honey sugars authenticity Introduction Honey is a complex mixture of sugars produced in nature by honeybees. It consists mainly of sugars but also contains small amounts of proteins (enzymes), amino acids, organic acids, carotenoids, vitamins, minerals, and aromatic substances. The sugar composition of honey is mainly dependent on its floral source and differs in various honeys. It is also affected by climate, processing, and have shown that the amount of sucrose can be used to storage conditions.1 Fructose and glucose are the major differentiate the adulteration of honey samples by sugar components and account for 85–95% of the honeybee syrups.5, 6 High levels of sucrose may indicate a variety honey sugars. Their concentrations of fructose and of adulterations, such as adding cheap sweeteners, like glucose, as well as their ratios are useful parameters for cane sugar or refined beet sugar, during early harvest. Due the classification of monofloral honeys.2 The remaining to these factors, various regulations require a minimum carbohydrates are a mixture of at least 11 disaccharides, amount of reducing sugars and a maximum amount of 11 trisaccharides, and several larger oligosaccharides.3 sucrose among other honey quality parameters. The Minor honey sugars may be useful for the determination of Codex Alimentarius Committee on Sugars (2001) specified floral origin and may act as a “fingerprint” for a sample’s a maximum value of 5 g of sucrose in 100 g of floral floral source.4 Besides the reducing sugars (glucose honey (Codex Standard for Honey, 2001).7 Therefore, and fructose), the amount of sucrose is a very important carbohydrate analysis is important as a honey quality indicator for evaluating honey quality.