DOCSLIB.ORG

Dissertation / Doctoral Thesis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Dissertation / Doctoral Thesis DISSERTATION / DOCTORAL THESIS Titel der Dissertation /Title of the Doctoral Thesis „Proteomic studies on Chlamydomonas reinhardtii“ verfasst von / submitted by Dipl.-Biochem. Luis Recuenco-Muñoz angestrebter akademischer Grad / in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) Wien, 2017 / Vienna 2017 Studienkennzahl lt. Studienblatt / A 794 685 437 degree programme code as it appears on the student record sheet: Dissertationsgebiet lt. Studienblatt / Biologie field of study as it appears on the student record sheet: Betreut von / Supervisors: Univ.-Prof. Dr. Wolfram Weckwerth Ass.-Prof. Dipl.-Biol. Dr. Stefanie Wienkoop, Privatdoz. 2 Declaration of authorship I, Luis Recuenco-Muñoz, declare that this thesis, titled ‘Proteomic studies on Chlamydomonas reinhardtii’ and the work presented in it are my own. I confirm that: • This work was done wholly or mainly while in candidature for a research degree at this University. • Where I have consulted the published work of others, this is always clearly attributed. • Where I have quoted from the work of others, the source is always given. With the exception of such quotations, this thesis is entirely my own work. • I have acknowledged all main sources of help. • Where the thesis is based on work done by myself jointly with others, I have made clear exactly what was done by others and what I have contributed myself. Signed: Date: 3 4 Equal goes it loose (Ernst Goyke) 5 Aknowledgements • I wish to thank Prof. Dr. Wolfram Weckwerth and Dr. habil. Stefanie Wienkoop for giving me the chance to work in this utterly interesting field, tutoring and mentoring me throughout my PhD Thesis, and for all the teaching, support, advice and fun I have had both on a working and on a personal level during my whole stint in Vienna. • Very special thanks go to Dr. Luis Valledor for the extensive and intensive coaching (both in situ and in silico), the productive work and also his additional readings and corrections on my PhD-Thesis. On this last behalf I would also like to thank Dr. Thomas Nägele. • I would also like to thank Dr. Wolfgang Hoehenwarter, Dr. Alexander Seidel, Dr. Takeshi Furuhashi, Przemisław Kmiecik, Dr. Maria Angeles Castillejo, Dr. Volker Egelhofer, Dr. Gert Bachmann, Dr. David Lyon, Prof. Dr. Irene Lichtscheidl and Ella Nukarinen, whose help and/or advice have definitely made a difference for my PhD-Thesis. I would also like to thank Dr. Christian Molitor and Dr. Pierre Offre for their fruitful collaboration. • Since it has been an absolute pleasure to go to work every single day, I would like to thank the whole MoSys Department for creating such a cheerful and productive working atmo- sphere, especially Lena Fragner, Dr. Mette Hanak, Doris Dell’mour, Dr. Xiaoliang Sun, Yangfan Qiu, Dr. Vlora Mehmeti, Dr. Till Ischebeck, Manuela Leonardelli, Fernando Torralbo and Jana Klimashevskaia. I would also like to thank my good friends Torsten, Netti, Mahtin, Franzi, Natalie, Alois and Jens for their longtime personal support. • I would finally like to give the most special thanks to my parents, my sister and my brother for their inconditional support at any respect, help, encouragement, and too many other motives to be all named here. 6 List of Publications This cumulative PhD-Thesis includes the following publications: 1. Wolfgang Hoehenwarter, Yanmei Chen, Luis Recuenco-Munoz, Stefanie Wienkoop, and Wolfram Weckwerth. Functional analysis of proteins and protein species using shotgun proteomics and linear mathematics. Amino acids, 41(2):329–41, jul 2011 2. Luis Valledor, Luis Recuenco-Munoz, Stefanie Wienkoop, and Wolfram Weckwerth. The different proteomes of Chlamydomonas reinhardtii. Journal of Proteomics, 2012 3. Luis Valledor, Takeshi Furuhashi, Luis Recuenco-Muñoz, Stefanie Wienkoop, and Wol- fram Weckwerth. System-level network analysis of nitrogen starvation and recovery in Chlamydomonas reinhardtii reveals potential new targets for increased lipid accumula- tion. Biotechnology for biofuels, 7:171, jan 2014 4. Luis Recuenco-Muñoz, Pierre Offre, Luis Valledor, David Lyon, Wolfram Weckwerth, and Stefanie Wienkoop. Targeted quantitative analysis of a diurnal RuBisCO subunit expression and translation profile in Chlamydomonas reinhardtii introducing a novel Mass Western approach. Journal of Proteomics, 113:143–153, 2015 Any other publications quoted in this PhD-Thesis that are coauthored by me will be cited in bold letters. 7 Contents 1 Introduction 14 1.1 Proteomics...................................... 14 1.1.1 The Foundations of Proteomics....................... 14 1.1.2 Shotgun Proteomics / qualitative analysis................. 26 1.1.3 Quantitative Proteomics........................... 30 1.1.4 Different Subareas in Proteomics...................... 34 1.2 Chlamydomonas reinhardtii ............................. 35 1.2.1 History and Taxonomy............................ 35 1.2.2 Morphology.................................. 37 1.2.3 Cell cycle................................... 37 1.2.4 Genome.................................... 37 1.2.5 Relevance as a model plant......................... 39 1.2.6 Industrial applications............................ 39 1.3 Biofuel production and Chlamydomonas reinhardtii ................ 40 1.3.1 The Energy Problem............................. 40 1.3.2 Biofuels: Definition and types........................ 40 1.3.3 Biodiesel Production............................. 41 1.3.4 Growth optimization mechanisms for lipid production.......... 45 1.3.5 The Concept of Biorefinery......................... 47 2 Publications 49 2.1 Functional analysis of proteins and protein species using shotgun proteomics and linear mathematics.................................. 49 2.1.1 Declaration of authorship.......................... 49 2.1.2 Published manuscript............................ 49 2.2 The different proteomes of Chlamydomonas reinhardtii .............. 63 2.2.1 Declaration of authorship.......................... 63 2.2.2 Published manuscript............................ 63 2.3 System Level Network Analysis of Nitrogen Starvation and Recovery in Chlamy- domonas reinhardtii reveals potential new targets for increased lipid accumulation 69 2.3.1 Declaration of authorship.......................... 69 2.3.2 Published manuscript............................ 69 2.4 Targeted quantitative analysis of a diurnal RuBisCO subunit expression and translation profile in Chlamydomonas reinhardtii introducing a novel Mass West- ern approach..................................... 87 2.4.1 Declaration of authorship.......................... 87 2.4.2 Published manuscript............................ 87 8 3 Concluding Discussion 99 3.1 Consolidation of publications, delineating the preamble and comprehensive method- ology.......................................... 99 3.2 Contribution to the scientific progress....................... 101 4 Summary 104 5 Affirmation 139 9 List of Abbreviations 2DE= Two-Dimensional-Electrophoresis AAE= Acyl-ACP Esterase ACN= Acetonitrile ACP= Acyl-Carrier Protein AFAT= Algal Functional Annotation Tool AGC= Automatic Gain Control ALE= Adaptive Laboratory Evolution APEX= Absolute Protein EXpression (Profiling) AQUA= Absolute Quantification ASLs= Annotated Spectrum Libraries AspN= Endoproteinase: Flavastacin AUC= Area Under Curve BAC= Bacterial Artificial Chromosome BHT= Butylated Hydroxytoluene BLAST= Basic Local Alignment Search Tool BN-PAGE= Blue Native PolyAcrylamide Gel Electrophoresis BRI1= Brassinosteroid insensitive (mutant) 1 BSA= Bovine Serum Albumine C18= Octadecyl (reversed-phase-chromatography sorbent material) CAH= Carbonic Anhydrase CCM= Carbon Concentrating Mechanisms cDNA= Complementary DesoxyriboNucleic Acid CI= Chemical Ionisation CID= Collision-Induced Dissociation COX= CycloOxygenase CR= Chlamydomonas reinhardtii DB= Database DDA= Data Dependent Acquisition DGAT= DiacylGlycerol AcylTransferase DIA= Data Independent Acquisition DIGE= Difference Gel Electrophoresis DNA= DesoxyriboNucleic Acid DTT= DiThioThreitol EBI= European Bioinformatics Institute ECD= Electron Collision Dissociation EMPAI= Exponentially Modified Protein Abundance Index ESI= Electron-Spray-Ionization EST= Expression Sequence Tag EtOH= Ethanol FAB= Fast Atom Bombardment FAME= Fatty Acid Methyl Ester 10 FDR= False Discovery Rate FPLC= Fast Performance Liquid Chromatography FT= Fourier Transformation FTICR= Fourier Transformation Ion Cyclotrone Resonance FT-MS= Fourier Transformation Mass Spectrometry GEO= Gene Expression Omnibus GC-MS= Gas Chromatography (coupled) Mass Spectrometry GluC= Endoproteinase: Staphylococcus aureus Protease V8 GPMDB= Global Proteome Machine DataBase HA= Heteroautotrophic HCD= High-energy Collisional Dissociation HILEP= Hydroponic Isotope Labelling of Entire Plants HILIC= Hydrophilic Interaction Chromatography HPI= Human Protein Index HPLC= High Performance Liquid Chromatography HUGO= Human Genome Organization HUPO= Human Proteome Organization IC= Independent Component ICA= Independent Component Analysis ICAT= Isotope-Coded Affinity Tags ICL= Instrument Control Language IEA= International Energy Agency IFT= IntraFlagellar Transport IRMPD= Infrared multiple photon dissociation (spectroscopy) iTRAQ= Isobaric Tag for Relative and Absolute Quantification JGI= Joint Genome Institute (http://genome.jgi-psf.org/) JIPID= Japan International Protein Information Database KAAS= KEGG Automatic Annotation Server KEGG= Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg/ ) LB= Lipidic Bodies LECA= Last Eukaryotic Common Ancestor LHC= Light Harvesting
Load more

Recommended publications
  • We Wish to Share That with You By
    T HE DEPARTMENT OF BIOENGINEERING The UCSD Bioengineering Program was initiated in 1966 by Drs. Y.C. Fung, Marcos Intaglietta, and Benjamin Zweifach within the Department of Aeronautical Mechanics and Engineering Science. In August 1994 the UC Office of the President approved our request to form a Department of Bioengineering, the first in the UC System. It is wonderful that our Department is celebrating the tenth anniversary of its establishment. While an age of 10 years is young, we had a gestation period of 28 years, which are covered in this book together with the last 10 years. At this momentous occasion, I wish to express my sincere thanks to all my colleagues: faculty, research scientists, staff and students, for their wonderful work as a team in making the Department such a marvelous place to be, both scientifically and interpersonally. On behalf of the Department, I also wish to take this opportunity to thank the generous support and strong encouragement by our friends everywhere in the country and our administration at UCSD and the UC system. Our friends and colleagues are extremely precious, much more than the diamond on the cover of this book*, which is a symbol that represents the tenth anniversary. Sincerely, Shu Chien Chair, Department of Bioengineering NNIVERSARY A * The preparations for this book and the celebration on August 14, 2004, have been made TH possible by the outstanding work by the following members of UCSD central administration, Jacobs School External Relations Office, and Department of Bioengineering (listed alphabetically): 10 Kelly Briggs, Suzie Dandos, Chandra Ewell. Jennifer Griffin, Denine Hagen, Irene Jacobo, Paul Laperruque, Beth Maples, Carolyn Post-Ladd, Jeff Sanchez, and Loretta Smith.
    [Show full text]
  • Recent Progress in Laser Analytics
    KOLUMNE 417 CHIMIA 44 (1990) Nr.I~ (Ikzem""r) Chimia 44 (/990) 417 424 <&') Schll'ei=. Chemiker- Verhand; ISSN 0009 4293 Recent Progress in Laser Analytics Analytical methods are on their way to mass spectrometry (MS). In 1946, William penetrate the biological sciences. In this E. Stephens (University of Pennsylvania in trend, laser technology plays an important Philadelphia) described a mass spectrome- role, especially in the form of laser-desorp- ter with time dispersion, followed by the tion mass spectrometry (LD-MS). ion velocitron of A.E. Cameron and D.£. The remarkable progress made in this Eggers. These devices represented early field is nicely demonstrated by a statement forms of the time-of-flight mass spectrom- made in 1986 by Frank H. Field, a specialist eter (TOF-MS) first described by the Swiss in the mass spectrometric investigation of R. Keller in 1949. biomolecules and Professor at Rockefeller The first commercially successful TOF- University in New York. Citing Professor MS was introduced by Bendix Corpora- In dieser Kalwnne schreibl Field: 'The mass region of real interest for tion, and it was based on the design re- Prof Dr. H. M. Widmer proteins lies between 40000 and 100000 ported in 1955 by William C. Wile)' and Forse/lUng Analylik Da, and one can only speculate as to l. H. McLaren (Bendix Aviation Corpom- Ciha-Geigy AG. FO 3.2 CH 4{)()2 Basel whether such monster gaseos ions could be tion). In these early days of TOF-MS, the regelmiissig eigene Meinungsarlike/ oder liidl Giiste produced. My personal feeling is that to do ions were generated by electron impact ein.
    [Show full text]
  • Serine Proteases with Altered Sensitivity to Activity-Modulating
    (19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants.
    [Show full text]
  • ©Copyright 2015 Samuel Tabor Marionni Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling Their Structures
    ©Copyright 2015 Samuel Tabor Marionni Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling their Structures Samuel Tabor Marionni A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2015 Reading Committee: Matthew F. Bush, Chair Robert E. Synovec Dustin J. Maly James E. Bruce Program Authorized to Offer Degree: Chemistry University of Washington Abstract Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling their Structures Samuel Tabor Marionni Chair of the Supervisory Committee: Assistant Professor Matthew F. Bush Department of Chemistry Native mass spectrometry (MS) is an increasingly important structural biology technique for characterizing protein complexes. Conventional structural techniques such as X-ray crys- tallography and nuclear magnetic resonance (NMR) spectroscopy can produce very high- resolution structures, however large quantities of protein are needed, heterogeneity com- plicates structural elucidation, and higher-order complexes of biomolecules are difficult to characterize with these techniques. Native MS is rapid and requires very small amounts of sample. Though the data is not as high-resolution, information about stoichiometry, subunit topology, and ligand-binding, is readily obtained, making native MS very complementary to these techniques. When coupled with ion mobility, geometric information in the form of a collision cross section (Ω) can be obtained as well. Integrative modeling approaches are emerging that integrate gas-phase techniques — such as native MS, ion mobility, chemical cross-linking, and other forms of protein MS — with conventional solution-phase techniques and computational modeling. While conducting the research discussed in this dissertation, I used native MS to investigate two biological systems: a mammalian circadian clock protein complex and a series of engineered fusion proteins.
    [Show full text]
  • Personal and Contact Details
    CURRICULUM VITAE Carol Vivien Robinson DBE FRS FMedSci Personal and Contact Details Date of Birth 10th April 1956 Maiden Name Bradley Nationality British Contact details Department of Physical and Theoretical Chemistry University of Oxford South Parks Road Oxford OX1 3QZ Tel : +44 (0)1865 275473 E-mail : [email protected] Web : http://robinsonweb.chem.ox.ac.uk/Default.aspx Education and Appointments 2009 Professorial Fellow, Exeter College, Oxford 2009 Dr Lee’s Professor of Physical and Theoretical Chemistry, University of Oxford 2006 - 2016 Royal Society Research Professorship 2003 - 2009 Senior Research Fellow, Churchill College, University of Cambridge 2001 - 2009 Professor of Mass Spectrometry, Dept. of Chemistry, University of Cambridge 1999 - 2001 Titular Professor, University of Oxford 1998 - 2001 Research Fellow, Wolfson College, Oxford 1995 - 2001 Royal Society University Research Fellow, University of Oxford 1991 - 1995 Postdoctoral Research Fellow, University of Oxford. Supervisor: Prof. C. M. Dobson FRS 1991 - 1991 Postgraduate Diploma in Information Technology, University of Keele 1983 - 1991 Career break: birth of three children 1982 - 1983 MRC Training Fellowship, University of Bristol Medical School 1980 - 1982 Doctor of Philosophy, University of Cambridge. Supervisor: Prof. D. H. Williams FRS 1979 - 1980 Master of Science, University of Wales. Supervisor: Prof. J. H. Beynon FRS 1976 - 1979 Graduate of the Royal Society of Chemistry, Medway College of Technology, Kent 1972 - 1976 ONC and HNC in Chemistry, Canterbury
    [Show full text]
  • 2Nd ANNUAL NORTH AMERICAN MASS SPECTROMETRY SUMMER SCHOOL
    2nd ANNUAL NORTH AMERICAN MASS SPECTROMETRY SUMMER SCHOOL JULY 21-24, 2019 | MADISON, WISCONSIN Parabola of Neon (1913) Featured on the cover is an early 20th century parabola mass spectrograph. The early mass spectrometers, pioneered by J. J. Thomson, used electric and magnetic fields to disperse ion populations on photographic plates. Depending on their masses, the ions were dispersed along parabolic lines with those of the highest energy landing in the center and those with the least extending to the outermost edges. Positive ions are imaged on the upper half of the parabola while negative ions are deflected to the bottom half. Note that Ne produces two lines in the spectrum. Francis Aston, a former Thomson student, concluded from these data that stable elements also must have isotopes. These observations won Aston the Nobel Prize in Chemistry in 1922. Grayson, M.A. Measuring Mass: From Positive Rays to Proteins. 2002. Chemical Heritage Press, Philadelphia. Welcome to the 2nd Annual North American Mass Spectrometry Summer School We are proud to assemble world-leading experts in mass spectrometry for this second annual mass spectrometry summer school. We aim for you to experience an engaging and inspiring program covering the fundamentals of mass spectrometry and how to apply this tool to study biology. Also infused in the course are several workshops aimed to promote professional development. We encourage you to actively engage in discussion during all lectures, workshops, and events. This summer school is made possible through generous funding from the National Science Foundation (Plant Genome Research Program, Grant No. 1546742), the National Institutes of Health National Center for Quantitative Biology of Complex Systems (P41 GM108538), and the Morgridge Institute for Research.
    [Show full text]
  • Focus on Proteomics in Honor of Ruedi Aebersold, 2002 Biemann Awardee
    EDITORIAL Focus on Proteomics in Honor of Ruedi Aebersold, 2002 Biemann Awardee It is a pleasure to introduce this series of articles “Trypsin Catalyzed 16O-to-18O Exchange for Compara- honouring the achievements of Ruedi Aebersold, the tive Proteomics: Tandem Mass Spectrometry Compari- 2002 recipient of the ASMS Biemann Medal. During the son using MALDI-TOF, ESI-QTOF and ESI-Ion Trap last decade enormous progress has been made in the Mass Spectrometers” by Manfred Heller, Hassan Mat- application of mass spectrometry to proteomics, an area tou, Christoph Menzel, and Xudong Yao illustrates the to which Ruedi has contributed both generally and use of alternative labeling strategies involving 16Oto specifically with his isotope labelling strategies. In his 18O, in conjunction with enzymatic digestion for iden- opening Account and Perspective, “A Mass Spectromet- tifying proteins in human plasma. Of additional interest ric Journey into Protein and Proteome Research,” Ruedi in this article is the comparison of the many different poses the interesting question ‘does technology drive mass spectrometry platforms emerging for analysing biology or is the converse the case, where the biological such data including LC MALDI MS/MS approaches. question drives the technological development?’ This of Chromatographic separation is at the heart of many course remains an open question but the accompanying successful proteomic strategies, and an alternative ap- series of articles exemplify the tremendous synergy proach is exemplified by Figeys and colleagues in their between biology and methodological development. article, “On-line Strong Cation Exchange ␮-HPLC-ESI- An important biological question prompts the first of MS/MS for Protein Identification and Process Optimi- the research articles; “Quantitative Proteomic Analysis zation.” Using a strong cation exchange micro LC of Chromatin-associated Factors” by Yuzuru Shiio, Eu- method for identification of proteins in mixtures, they gene C.
    [Show full text]
  • Nature Milestones Mass Spectrometry October 2015
    October 2015 www.nature.com/milestones/mass-spec MILESTONES Mass Spectrometry Produced with support from: Produced by: Nature Methods, Nature, Nature Biotechnology, Nature Chemical Biology and Nature Protocols MILESTONES Mass Spectrometry MILESTONES COLLECTION 4 Timeline 5 Discovering the power of mass-to-charge (1910 ) NATURE METHODS: COMMENTARY 23 Mass spectrometry in high-throughput 6 Development of ionization methods (1929) proteomics: ready for the big time 7 Isotopes and ancient environments (1939) Tommy Nilsson, Matthias Mann, Ruedi Aebersold, John R Yates III, Amos Bairoch & John J M Bergeron 8 When a velocitron meets a reflectron (1946) 8 Spinning ion trajectories (1949) NATURE: REVIEW Fly out of the traps (1953) 9 28 The biological impact of mass-spectrometry- 10 Breaking down problems (1956) based proteomics 10 Amicable separations (1959) Benjamin F. Cravatt, Gabriel M. Simon & John R. Yates III 11 Solving the primary structure of peptides (1959) 12 A technique to carry a torch for (1961) NATURE: REVIEW 12 The pixelation of mass spectrometry (1962) 38 Metabolic phenotyping in clinical and surgical 13 Conquering carbohydrate complexity (1963) environments Jeremy K. Nicholson, Elaine Holmes, 14 Forming fragments (1966) James M. Kinross, Ara W. Darzi, Zoltan Takats & 14 Seeing the full picture of metabolism (1966) John C. Lindon 15 Electrospray makes molecular elephants fly (1968) 16 Signatures of disease (1975) 16 Reduce complexity by choosing your reactions (1978) 17 Enter the matrix (1985) 18 Dynamic protein structures (1991) 19 Protein discovery goes global (1993) 20 In pursuit of PTMs (1995) 21 Putting the pieces together (1999) CITING THE MILESTONES CONTRIBUTING JOURNALS UK/Europe/ROW (excluding Japan): The Nature Milestones: Mass Spectroscopy supplement has been published as Nature Methods, Nature, Nature Biotechnology, Nature Publishing Group, Subscriptions, a joint project between Nature Methods, Nature, Nature Biotechnology, Nature Chemical Biology and Nature Protocols.
    [Show full text]
  • Handbook of Proteolytic Enzymes Second Edition Volume 1 Aspartic and Metallo Peptidases
    Handbook of Proteolytic Enzymes Second Edition Volume 1 Aspartic and Metallo Peptidases Alan J. Barrett Neil D. Rawlings J. Fred Woessner Editor biographies xxi Contributors xxiii Preface xxxi Introduction ' Abbreviations xxxvii ASPARTIC PEPTIDASES Introduction 1 Aspartic peptidases and their clans 3 2 Catalytic pathway of aspartic peptidases 12 Clan AA Family Al 3 Pepsin A 19 4 Pepsin B 28 5 Chymosin 29 6 Cathepsin E 33 7 Gastricsin 38 8 Cathepsin D 43 9 Napsin A 52 10 Renin 54 11 Mouse submandibular renin 62 12 Memapsin 1 64 13 Memapsin 2 66 14 Plasmepsins 70 15 Plasmepsin II 73 16 Tick heme-binding aspartic proteinase 76 17 Phytepsin 77 18 Nepenthesin 85 19 Saccharopepsin 87 20 Neurosporapepsin 90 21 Acrocylindropepsin 9 1 22 Aspergillopepsin I 92 23 Penicillopepsin 99 24 Endothiapepsin 104 25 Rhizopuspepsin 108 26 Mucorpepsin 11 1 27 Polyporopepsin 113 28 Candidapepsin 115 29 Candiparapsin 120 30 Canditropsin 123 31 Syncephapepsin 125 32 Barrierpepsin 126 33 Yapsin 1 128 34 Yapsin 2 132 35 Yapsin A 133 36 Pregnancy-associated glycoproteins 135 37 Pepsin F 137 38 Rhodotorulapepsin 139 39 Cladosporopepsin 140 40 Pycnoporopepsin 141 Family A2 and others 41 Human immunodeficiency virus 1 retropepsin 144 42 Human immunodeficiency virus 2 retropepsin 154 43 Simian immunodeficiency virus retropepsin 158 44 Equine infectious anemia virus retropepsin 160 45 Rous sarcoma virus retropepsin and avian myeloblastosis virus retropepsin 163 46 Human T-cell leukemia virus type I (HTLV-I) retropepsin 166 47 Bovine leukemia virus retropepsin 169 48
    [Show full text]
  • University of Florida Thesis Or Dissertation Formatting
    CHARACTERIZATION OF Mycoplasma alligatoris IMMUNODOMINANT ANTIGENS By NIORA J. FABIAN A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2010 1 © 2010 Niora J. Fabian 2 To N.N., E.N., S.N., A.N., and my entire family 3 ACKNOWLEDGMENTS I thank my main advisor, Dr. Daniel Brown, and my committee members for their support and education. I would also like to thank Kevin Kroll for his kind advice with Western blotting optimization and Mengmeng Zhu for her recommendations with IEF and 2DGE equipment. Finally, I would like to thank Diane Duke and Linda Green of the ICBR Hybridoma Lab, and Carolyn Diaz and Dr. Sixue Chen of the ICBR Proteomics Core. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS ...................................................................................................... 4 LIST OF TABLES ................................................................................................................ 7 LIST OF FIGURES .............................................................................................................. 8 ABSTRACT.......................................................................................................................... 9 CHAPTER 1 INTRODUCTION ........................................................................................................ 11 Discovery and Characterization of M. alligatoris ....................................................... 11 Mycoplasmosis
    [Show full text]
  • February 2016
    NEWS AND VIEWS Correspondence to: Gavin E. Reid; e-mail: [email protected] February 2016 Announcements For more information and online registration for any of the conferences listed below, please visit www.asms.org/conferences. 64th ASMS Annual Conference June 5 - 9, 2016 San Antonio, TX www.asms.org/conferences/annual- conference February 5 - Abstract submission deadline April 30 - Advance conference and short course OHIWWRULJKW Professor Simon Gaskell, Professor Perdita Barran and registration deadline Professor Graham Cooks (Purdue University) at the Gaskell symposium dinner held at the Museum of Science and Industry, Manchester, UK. University of Manchester in 2004, he served as Associate Vice The Gaskell Symposium – President for Research, and WKHQ as Vice President IRU 5HVHDUFK IURP WR +H MRLQHG 4XHHQ 0DU\ A Celebration of Mass University of London in October 2009. Spectrometry ,Q D VFLHQWL¿F FDUHHU VSDQQLQJ \HDUV 3URIHVVRU *DVNHOO¶V research involved the development and application of state- A two day meeting was held December 14th and 15th at the University of-the-art mass spectrometry and related analytical techniques, of Manchester, UK, to celebrate the career of Professor Simon ZLWKDSSOLFDWLRQVLQWKHELRPHGLFDOVFLHQFHV+HLVSDUWLFXODUO\ J. Gaskell, President and Principal, and Professor of Biological recognized for his work in developing, along with Professor Vicki Chemistry, at Queen Mary College of London. Organized by Wysocki (Ohio State University), the concept of the ‘mobile Professor Perdita Barran (Chair of Mass
    [Show full text]
  • Proquest Dissertations
    REGULATION OF THE BMP SIGNALLING PATHWAY BY BMPl-RELATED METALLOPROTEASES FIONA CLAIRE WARDLE A Thesis Submitted for the Degree of Doctor of Philosophy at the University of London 1998 Department of Anatomy and Developmental Biology University College, London. ProQuest Number: 10016134 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. uest. ProQuest 10016134 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 ABSTRACT Bone Morphogenetic Proteins (BMPs) 2-8 are members of the TGFp superfamily of secreted signalling molecules. During embryonic development BMPs are involved in many processes including cell fate determination, morphogenesis, growth and programmed cell death, all of which are essential for normal development. BMP activity may be regulated in variety of ways. Of particular interest is the finding that three Xenopus proteins. Noggin, Chordin and Follistatin are able to bind BMP4 and prevent it activating its receptor (Piccolo et al., 1996; Zimmerman et al., 1996; Fainsod et al., 1997). Inhibition by Chordin can be alleviated by Xolloid, a BMP 1-related metalloprotease that cleaves Chordin (Piccolo et al., 1997). Similarly, in the Drosophila embryo Dpp, a BMP2/4 homologue, is inhibited by the Chordin homologue, Sog, but activated by Tolloid, a BMP 1-related metalloprotease (Marqués et al., 1997).
    [Show full text]