Towards Detailed Structural Understanding of Α-ʟ-Fucosidase: Insights Through X-Ray Crystallography and Inhibitor-Binding
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A Study of the Impact of Mazie SBE I on the [Alpha]-Polyglucan Produced in Synechocystis Sp
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2007 A study of the impact of mazie SBE I on the [alpha]- polyglucan produced in Synechocystis sp. strain PCC 6803 Shayani Deborah Nesaranjani Pieris Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Plant Biology Commons Recommended Citation Pieris, Shayani Deborah Nesaranjani, "A study of the impact of mazie SBE I on the [alpha]-polyglucan produced in Synechocystis sp. strain PCC 6803" (2007). Retrospective Theses and Dissertations. 15850. https://lib.dr.iastate.edu/rtd/15850 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]. A study of the impact of mazie SBE I on the -polyglucan produced in Synechocystis sp. strain PCC 6803 by Shayani Deborah Nesaranjani Pieris A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Plant Physiology Program of Study Committee: Martin H. Spalding, Major Professor Madan K. Bhattacharyya Jay -lin Jane David J. Oliver Paul M. Scott Iowa State University Ames, Iowa 200 7 Copyright © Shayani Deborah Nesara njani Pieris , 200 7. All right s reserved. UMI Number: 3294976 UMI Microform 3294976 Copyright 2008 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. -
Characterization of Α-L-Fucosidase and Other Digestive Hydrolases From
Acta Tropica 141 (2015) 118–127 Contents lists available at ScienceDirect Acta Tropica journal homepage: www.elsevier.com/locate/actatropica Characterization of ␣-L-fucosidase and other digestive hydrolases from Biomphalaria glabrata Natalia N. Perrella a,b, Rebeca S. Cantinha c,d, Eliana Nakano c, Adriana R. Lopes a,∗ a Laboratory of Biochemistry and Biophysics—Instituto Butantan, São Paulo, Brazil b Programa de Pós Graduac¸ ão Interunidades em Biotecnologia PPIB, Universidade de São Paulo, São Paulo, SP, Brazil c Laboratory of Parasitology—Instituto Butantan, São Paulo, Brazil d Instituto de Pesquisas Energéticas e Nucleares, Universidade de São Paulo, São Paulo, SP, Brazil article info abstract Article history: Schistosoma mansoni is one of the major agents of the disease Schistosomiasis, which is one of the Received 10 February 2014 major global public health concerns. Biomphalaria glabrata is an obligate intermediate mollusc host of Received in revised form 3 July 2014 S. mansoni. Although the development of S. mansoni occurs in the snail hepatopancreas, studies that Accepted 12 August 2014 focus on this organ remain limited. In this study, we biochemically identified five distinct carbohy- Available online 16 September 2014 drases (amylase, maltase, ␣-glucosidase, trehalase, and ␣-L-fucosidase), lipases, and peptidases in the B. glabrata hepatopancreas and focused on the isolation and characterization of the activity of ␣-L- Keywords: fucosidase. The isolated ␣-L-fucosidase has a molecular mass of 141 kDa, an optimum pH of 5.8, and Hepatopancreas ␣ Enzymes is inhibited by Tris, fucose, and 1-deoxyfuconojirimycin. B. glabrata -L-fucosidase is an exoglycosidase ␣-L-Fucosidase that can hydrolyze the natural substrate fucoidan to fucose residues. -
Glycoproteomics-Based Signatures for Tumor Subtyping and Clinical Outcome Prediction of High-Grade Serous Ovarian Cancer
ARTICLE https://doi.org/10.1038/s41467-020-19976-3 OPEN Glycoproteomics-based signatures for tumor subtyping and clinical outcome prediction of high-grade serous ovarian cancer Jianbo Pan 1,2,3, Yingwei Hu1,3, Shisheng Sun 1,3, Lijun Chen1, Michael Schnaubelt1, David Clark1, ✉ Minghui Ao1, Zhen Zhang1, Daniel Chan1, Jiang Qian2 & Hui Zhang 1 1234567890():,; Inter-tumor heterogeneity is a result of genomic, transcriptional, translational, and post- translational molecular features. To investigate the roles of protein glycosylation in the heterogeneity of high-grade serous ovarian carcinoma (HGSC), we perform mass spectrometry-based glycoproteomic characterization of 119 TCGA HGSC tissues. Cluster analysis of intact glycoproteomic profiles delineates 3 major tumor clusters and 5 groups of intact glycopeptides. It also shows a strong relationship between N-glycan structures and tumor molecular subtypes, one example of which being the association of fucosylation with mesenchymal subtype. Further survival analysis reveals that intact glycopeptide signatures of mesenchymal subtype are associated with a poor clinical outcome of HGSC. In addition, we study the expression of mRNAs, proteins, glycosites, and intact glycopeptides, as well as the expression levels of glycosylation enzymes involved in glycoprotein biosynthesis pathways in each tumor. The results show that glycoprotein levels are mainly controlled by the expression of their individual proteins, and, furthermore, that the glycoprotein-modifying glycans cor- respond to the protein levels of glycosylation enzymes. The variation in glycan types further shows coordination to the tumor heterogeneity. Deeper understanding of the glycosylation process and glycosylation production in different subtypes of HGSC may provide important clues for precision medicine and tumor-targeted therapy. -
Rigaku Crystallography Times
Volume 12, No. 9, November 2020 WELCOME RIGAKU TOPIQ WEBINARS Rigaku has developed a series of Good day everyone. We've had a busy month and have a lot to show for it. 20-30 minute webinars that cover a First, we have almost 400 people registered for the Advanced Topics School broad range of topics in the fields on December 7-11. We still have plenty of room so you can register below. of X-ray diffraction, X-ray fluorescence and X-ray imaging. REGISTER You can register here and also watch recordings if you cannot attend live sessions. We are introducing a new hybrid counting detector this month, the HyPix-Arc 100°, which puts the unique features of the HyPix-Arc 150° into a more compact form factor. The researcher in the spotlight this month is Dr. Johan Turkenburg, the X-ray RIGAKU REAGENTS Facilities Manager at York University's Structural Biology Laboratory. This month we have a special treat, an article about Claire Jones, a deaf crystallographer who attended our first Practical Crystallography School with the assistance of her palantypist (stenographer). I hope you find her life story as inspiring as I have. Our usual sections include a few noteworthy crystallography papers, a couple of interesting videos, one about Arcimboldo and the other a TED talk about Marie Curie, and links to the Arcimboldo website and applets for teaching Rigaku Reagents has extended its Braggâs law as well as other crystallographic concepts. This month, Jeanette sales channels and is collaborating reviews Equity in Science, which as the title suggests is about diversity, with SWISSCI to provide Rigaku inclusion and representation in the scientific enterprise. -
Review Article Pullulanase: Role in Starch Hydrolysis and Potential Industrial Applications
Hindawi Publishing Corporation Enzyme Research Volume 2012, Article ID 921362, 14 pages doi:10.1155/2012/921362 Review Article Pullulanase: Role in Starch Hydrolysis and Potential Industrial Applications Siew Ling Hii,1 Joo Shun Tan,2 Tau Chuan Ling,3 and Arbakariya Bin Ariff4 1 Department of Chemical Engineering, Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, 53300 Kuala Lumpur, Malaysia 2 Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia 3 Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia 4 Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia Correspondence should be addressed to Arbakariya Bin Ariff, [email protected] Received 26 March 2012; Revised 12 June 2012; Accepted 12 June 2012 Academic Editor: Joaquim Cabral Copyright © 2012 Siew Ling Hii et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The use of pullulanase (EC 3.2.1.41) has recently been the subject of increased applications in starch-based industries especially those aimed for glucose production. Pullulanase, an important debranching enzyme, has been widely utilised to hydrolyse the α-1,6 glucosidic linkages in starch, amylopectin, pullulan, and related oligosaccharides, which enables a complete and efficient conversion of the branched polysaccharides into small fermentable sugars during saccharification process. The industrial manufacturing of glucose involves two successive enzymatic steps: liquefaction, carried out after gelatinisation by the action of α- amylase; saccharification, which results in further transformation of maltodextrins into glucose. -
Carbohydrate Anomalies in the PDB
This is a repository copy of Carbohydrate anomalies in the PDB. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/95242/ Version: Accepted Version Article: Agirre, Jon orcid.org/0000-0002-1086-0253, Davies, Gideon orcid.org/0000-0002-7343- 776X, Wilson, Keith orcid.org/0000-0002-3581-2194 et al. (1 more author) (2015) Carbohydrate anomalies in the PDB. NATURE CHEMICAL BIOLOGY. p. 303. ISSN 1552- 4450 https://doi.org/10.1038/nchembio.1798 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ NATURE CHEMICAL BIOLOGY | CORRESPONDENCE • Carbohydrate anomalies in the PDB Jon Agirre, Gideon Davies, Keith Wilson & Kevin Cowtan York Structural Biology Laboratory, Department of Chemistry, The University of York, England. Nature Chemical Biology 11, 303 (2015) doi:10.1038/nchembio.1798 Published online 17 April 2015 Erratum (July, 2015) The importance of carbohydrates both to fundamental cellular biology and as integral parts of therapeutics (including antibodies) continues to grow. -
Postgraduate Prospectus 2013
POSTGRADUATE PROSPECTUS PROSPECTUS POSTGRADUATE 2013 2013 Postgraduate Prospectus www.york.ac.uk University contacts University of York Student Recruitment International Students’ Association Heslington and Admissions Tel: +44 (0)1904 323724 York YO10 5DD Email: [email protected] Tel: +44 (0)1904 320000 Application enquiries Website: www.yusu.org/isa Tel: +44 (0)1904 324000 Fax: +44 (0)1904 323433 Languages for All Fax: +44 (0)1904 323538 Minicom: +44 (0)1904 324283 Tel: +44 (0)1904 322493 Email: [email protected] Website: www.york.ac.uk Email: [email protected] Website: www.york.ac.uk/study/ Facebook: www.facebook.com/ Website: www.york.ac.uk/lfa universityofyork postgraduate Nursery International students Tel: +44 (0)1904 323737 The colleges Tel: +44 (0)1904 323534 Email: [email protected] Fax: +44 (0)1904 323538 Alcuin Website: www.york.ac.uk/univ/nrsry Email: [email protected] Provost: Tony Ward Website: www.york.ac.uk/study/international Registry Services Porters: +44 (0)1904 323300 Tel: +44 (0)1904 324643 College Administrator: +44 (0)1904 323313 Other information Email: [email protected] Derwent Website: www.york.ac.uk/registry-services Accommodation Office Provost: Dr Rob Aitken Tel: +44 (0)1904 322165 Student Financial Support Unit Porters: +44 (0)1904 323500 Fax: +44 (0)1904 324030 Tel: +44 (0)1904 324043 College Administrator: +44 (0)1904 323513 Email: [email protected] Fax: +44 (0)1904 324142 Goodricke Website: www.york.ac.uk/accommodation Email: [email protected] Website: www.york.ac.uk/studentmoney -
Function and Structure Studies of GH Family 31 and 97 \Alpha
110610 (RV-17) Biosci. Biotechnol. Biochem., 75 (12), 110610-1–9, 2011 Award Review Function and Structure Studies of GH Family 31 and 97 -Glycosidases Masayuki OKUYAMA Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan Online Publication, December 7, 2011 [doi:10.1271/bbb.110610] A huge number of glycoside hydrolases are classified an evolutionary relationship of proteins in the family, into the glycoside hydrolase family (GH family) based from which it is often possible to extract information on on their amino-acid sequence similarity. The glycoside function and structure.3) Classification in a GH family hydrolases acting on -glucosidic linkage are in GH has, accordingly, become indispensable for research on family 4, 13, 15, 31, 63, 97, and 122. This review deals glycoside hydrolases. Glycoside hydrolases are also mainly with findings on GH family 31 and 97 enzymes. divided into two mechanistic classes, inverting and Research on two GH family 31 enzymes is described: retaining enzymes: with inversion or net retention of clarification of the substrate recognition of Escherichia anomeric configuration during the catalytic reaction.4) coli -xylosidase, and glycosynthase derived from Schiz- The stereochemical outcome is generally conserved in a osaccharomyces pombe -glucosidase. GH family 97 is GH family. The inverting mechanism proceeds via a an aberrant GH family, containing inverting and simple single displacement. Two functional groups, retainingAdvance glycoside hydrolases. The inverting View enzyme usually carboxyl groups, act as general acid and general in GH family 97 displays significant similarity to base catalysts. The general acid catalyst donates a proton retaining -glycosidases, including GH family 97 retain- to the departure aglycon, and the general base catalyst ing -glycosidase, but the inverting enzyme has no simultaneously deprotonates the incoming water mole- catalytic nucleophile residue. -
Queryor: a Comprehensive Web Platform for Genetic Variant Analysis
Bertoldi et al. BMC Bioinformatics (2017) 18:225 DOI 10.1186/s12859-017-1654-4 SOFTWARE Open Access QueryOR: a comprehensive web platform for genetic variant analysis and prioritization Loris Bertoldi1, Claudio Forcato1, Nicola Vitulo1,5, Giovanni Birolo1, Fabio De Pascale1, Erika Feltrin1, Riccardo Schiavon2, Franca Anglani3, Susanna Negrisolo4, Alessandra Zanetti4, Francesca D’Avanzo4, Rosella Tomanin4, Georgine Faulkner2, Alessandro Vezzi2 and Giorgio Valle1,2* Abstract Background: Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results: Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions: QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
Carbohydrate Active Enzymes in Medicine and Biotechnology
19–21 AUGUST 2015 University of St Andrews, UK A joint Biochemical Society/ DEADLINES Royal Society of Chemistry Focused Meeting Abstract submission: Carbohydrate Active 15 JUNE 2015 Earlybird registration: Enzymes in Medicine 17 JULY 2015 and Biotechnology Organizers: Tracey Gloster Rob Field Gideon Davies Jerry Turnbull Overview: Carbohydrate active enzymes are vital in an Image kindly supplied by Tracey Gloster, University of St Andrews, UK Andrews, of St University Gloster, Tracey Image kindly supplied by abundance of cellular processes. These enzymes catalyse biologically important reactions and malfunction of these is often implicated in diseases. Fundamental to carbohydrate manipulation is gaining an understanding of such enzymes from a mechanistic, bioengineering, structural, functional, and biological viewpoint. Topics: * Insights into carbohydrate active enzymes in medicine * Use of carbohydrate active enzymes in biotechnology * Understanding mechanism and structure of carbohydrate active enzymes * Exploiting carbohydrate active enzymes in biosynthesis For a full programme please visit: www.biochemistry.org Sponsored by: 19–21 AUGUST 2015 University of St Andrews, UK A joint Biochemical Society/ Royal Society of Chemistry Focused Meeting DEADLINES Abstract submission: Carbohydrate Active 15 JUNE 2015 Enzymes in Medicine Earlybird registration: and Biotechnology 17 JULY 2015 Researching? Oral communication slots available. Award Lecture Studying? Apply for a student Sabine Flitsch – RSC Interdisciplinary Prize 2014 bursary online. -
Information Quarterly Protein Crystallograpby
DARESBURY LABORATORY INFORMATION QUARTERLY for PROTEIN CRYSTALLOGRAPBY An Informal Newsletter associated with Collaborative Computational Project No,4 on Protein Crystallography Number 21 OCTOBER 1987 Contents Editorial 1 Beta-lactoglobulin: a transport protein 3 (Stephen Yewdall, Leeds) Electron density maps from Laue photographs of protein crystals 5 (Janos Hajdu et al., Oxford) Crystal structure determination using intensity data from Laue 11 photographs (Jennifer Glucas et al., Liverpool) Hardware changes at Birkbeck 17 (F. Hayes, Birkbeck) Measurement of oscillation photographs collected on the SRS: 19 recent practical experience (Peter Brick et al., Imper'i'al College) A computer-controlled syringe system for crystallisation 21 screening (Jan White et al., Sh~ffield) Some UK crystallography JANET addresses 25 (Andrew Lyall, Bristol) Editor: Sue Bailey Science and Engineering Research Council, Daresbury Laboratory, Daresbury, Warrington WA4 4AD, England. EDITORIAL Thanks are due to the contributersto this edition of the newsletter and to Peter Brick for organising the colleotion of contributions. A copy of toe papers in this newsletter have been sent to Keith Wilson for inclusion in the EACeM (European Association for Crystallography of Biological Macromolecules) newsletter. I would like to _take this opportunity to give ad'ITance publicity for a meeting to be organised by the CCP4 and Daresbury Laboratory. The meeting will take place on the 5-6 of Februaury 1_988 and will be entitled 'Improving Protein Phases'. Practical applications of ~olvent flattening, density averaging, direct methods etc. will be covered. A notice announcing the meetin~ is to be circulat,ed in the near future. Sue Bailey 8th October 1987 " 1 , S-LACTOGLOBULIN; a transport protein.