Proquest Dissertations
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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. -
Embryonic Regeneration by Relocalization of the Spemann
Embryonic regeneration by relocalization of the PNAS PLUS Spemann organizer during twinning in Xenopus Yuki Moriyamaa,b,1 and Edward M. De Robertisa,b,2 aHoward Hughes Medical Institute, University of California, Los Angeles, CA 90095; and bDepartment of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662 Contributed by Edward M. De Robertis, April 3, 2018 (sent for review February 16, 2018; reviewed by Makoto Asashima, Atsushi Suzuki, and Naoto Ueno) The formation of identical twins from a single egg has fascinated side of the embryo in regularly cleaving embryos (9). The op- developmental biologists for a very long time. Previous work had posite, darker side of the embryo gives rise to the ventral (belly) shown that Xenopus blastulae bisected along the dorsal–ventral side. The displacement of egg cytoplasmic determinants along (D-V) midline (i.e., the sagittal plane) could generate twins but at microtubules toward the dorsal side triggers an early Wnt signal very low frequencies. Here, we have improved this method by (10), which is responsible for localizing the subsequent formation using an eyelash knife and changing saline solutions, reaching of the Spemann organizer signaling center in the marginal zone frequencies of twinning of 50% or more. This allowed mechanistic at the gastrula stage. The Spemann organizer is a tissue that analysis of the twinning process. We unexpectedly observed that secretes a mixture of growth factor antagonists, such as Chordin, the epidermis of the resulting twins was asymmetrically pig- Noggin, Follistatin, Cerberus, Frzb1, and Dickkopf, which are mented at the tailbud stage of regenerating tadpoles. -
Repair of Ultraviolet Irradiation Damage to a Cytoplasmic
Proc. Nat. Acad. Sci. USA Vol. 72, No. 4, pp. 1235-1239, April 1975 Repair of Ultraviolet Irradiation Damage to a Cytoplasmic Component Required for Neural Induction in the Amphibian Egg (cortex/vegetal hemisphere/gray crescent/dorsal lip/gastrulation) HAE-MOON CHUNG AND GEORGE M. MALACINSKI Department of Zoology, Indiana University, Bloomington, Ind. 47401 Communicated by Robert Briggs, January 2, 1975 ABSTRACT Localized ultraviolet irradiation of the am- In order to gain direct insight into whether an ultraviolet phibian egg destroys a cytoplasmic component that is sensitive component(s) localized in the egg cytoplasm prior required for neural induction. Destruction of that com- ponent severely diminishes the inducing capacity of the to first cleavage division is actually involved in neural dorsal lip at gastrulation, as determined by embryological induction, the following question was posed: Does regional assays. Repair of the ultraviolet lesion can be achieved by UV damage to the egg affect the subsequent inducing capacity replacing the dorsal lip of the irradiated embyro with a of the dorsal lip during gastrulation? By assaying for inducing lip from an unirradiated embryo. capacity of dorsal lips from irradiated embryos and replacing Various types of analyses have established that components the dorsal lips of irradiated embryos with normal lips it was of the amphibian egg cytoplasm influence the pattern of early possible to conclude that UV does indeed damage a localized morphogenesis (see ref. 1 for a review). One of the most component of the egg cytoplasm that is necessary for neural conveniently demonstrated, yet most incompletely under- morphogenesis. stood, cytoplasmic components in the amphibian egg is the MATERlALS AND METHODS gray crescent. -
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 -
GTPBP2 Is a Positive Regulator of TGF- Signaling, and Is Required for Embryonic Patterning in Xenopus
SSStttooonnnyyy BBBrrrooooookkk UUUnnniiivvveeerrrsssiiitttyyy The official electronic file of this thesis or dissertation is maintained by the University Libraries on behalf of The Graduate School at Stony Brook University. ©©© AAAllllll RRRiiiggghhhtttsss RRReeessseeerrrvvveeeddd bbbyyy AAAuuuttthhhooorrr... GTPBP2 is a positive regulator of TGF- signaling, and is required for embryonic patterning in Xenopus. A Dissertation Presented by Arif Kirmizitas to The Graduate School in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Molecular and Cellular Biology Stony Brook University December 2008 Stony Brook University The Graduate School Arif Kirmizitas We, the dissertation committee for the above candidate for the Doctor of Philosophy degree, hereby recommend acceptance of this dissertation. Gerald H. Thomsen – Dissertation Advisor Professor, Department of Biochemistry and Cell Biology Howard I. Sirotkin – Chairperson of Defense Associate Professor, Department of Neurobiology and Behavior Nancy C. Reich Professor, Department of Molecular Genetics and Microbiology A. Wali Karzai Associate Professor, Department of Biochemistry and Cell Biology Bernadette C. Holdener Associate Professor, Department of Biochemistry and Cell Biology Daniel S. Kessler Associate Professor, Department of Cell and Developmental Biology,University of Pennsylvania School of Medicine, Philadelphia, PA This Dissertation is accepted by the Graduate School. Lawrence Martin Dean of the Graduate School ii Abstract of the Dissertation GTPBP2 is a positive regulator of TGF- signaling, and is required for embryonic patterning in Xenopus. by Arif Kirmizitas Doctor of Philosophy in Molecular and Cellular Biology Stony Brook University 2008 The Transforming Growth Factor (TGF-) superfamily of signaling proteins regulate a diverse set of biological processes, including cell proliferation, adhesion, migration, apoptosis, differentiation and embryonic pattern formation. -
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 -
The Cleavage Stage Origin of Spemann's Organizer: Analysis Of
Development 120, 1179-1189 (1994) 1179 Printed in Great Britain © The Company of Biologists Limited 1994 The cleavage stage origin of Spemann’s Organizer: analysis of the movements of blastomere clones before and during gastrulation in Xenopus Daniel V. Bauer1, Sen Huang2 and Sally A. Moody2,* 1Department of Anatomy and Cell Biology, University of Virginia 2Department of Anatomy and Neuroscience Program, The George Washington University Medical Center, 2300 I Street, NW Washington, DC 20037, USA *Author for correspondence SUMMARY Recent investigations into the roles of early regulatory the ventral animal clones extend across the entire dorsal genes, especially those resulting from mesoderm induction animal cap. These changes in the blastomere constituents or first expressed in the gastrula, reveal a need to elucidate of the animal cap during epiboly may contribute to the the developmental history of the cells in which their tran- changing capacity of the cap to respond to inductive growth scripts are expressed. Although fates both of the early blas- factors. Pregastrulation movements of clones also result in tomeres and of regions of the gastrula have been mapped, the B1 clone occupying the vegetal marginal zone to the relationship between the two sets of fate maps is not become the primary progenitor of the dorsal lip of the clear and the clonal origin of the regions of the stage 10 blastopore (Spemann’s Organizer). This report provides embryo are not known. We mapped the positions of each the fundamental descriptions of clone locations during the blastomere clone during several late blastula and early important periods of axis formation, mesoderm induction gastrula stages to show where and when these clones move. -
Competition Between Noggin and Bone Morphogenetic Protein 4
Proc. Natl. Acad. Sci. USA Vol. 92, pp. 12141-12145, December 1995 Developmental Biology Competition between noggin and bone morphogenetic protein 4 activities may regulate dorsalization during Xenopus development YAEL RE'EM KALMA*, TERESA LAMBt, AND DALE FRANK*t *Department of Biochemistry, The Rappaport Family Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel; and tDepartment of Molecular and Cellular Biology, Division of Biochemistry and Molecular Biology, 401 Barker Hall, University of California, Berkeley, CA 94720 Communicated by John Gerhart, University of California, Berkeley, CA, September 15, 1995 ABSTRACT Bone morphogenetic protein 4 (BMP-4) in- dorsalization signal (6-9), it is not clear how distinct axial borders duces ventral mesoderm but represses dorsal mesoderm for- are defined within the developing embryo. It is possible that cell mation in Xenopus embryos. We show that BMP-4 inhibits two borders are defined by a combination of positive and negative signaling pathways regulating dorsal mesoderm formation, pathways which demarcate the dorsal/ventral border. the induction of dorsal mesoderm (Spemann organizer) and Bone morphogenetic protein 4 (BMP-4) is a member of the the dorsalization of ventral mesoderm. Ectopic expression of transforming growth factor ( family (11). The gene has been BMP-4 RNA reduces goosecoid and forkhead-l transcription isolated from Xenopus laevis, and ectopic expression of in vitro in whole embryos and in activin-treated animal cap explants. synthesized BMP-4 RNA in developing embryos causes de- Embryos and animal caps overexpressing BMP-4 transcribe velopmental changes which suggest that BMP-4 protein in- high levels of genes expressed in ventral mesoderm (Xbra, duces ventroposterior mesoderm. -
12) United States Patent (10
US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S. -
Supporting Document 1 Safety Assessment
Supporting document 1 Safety assessment (at Approval) – Application A1081 Food derived from Herbicide-tolerant Soybean Line SYHT0H2 Summary and Conclusions Background A genetically modified (GM) soybean line with OECD Unique Identifier SYN-0000H2-5, hereafter referred to as soybean SYHT0H2, has been developed to be tolerant to two herbicides with different modes of action, namely glufosinate-ammonium and mesotrione. Tolerance to glufosinate ammonium is achieved through expression of the enzyme phosphinothricin acetyltransferase (PAT). PAT is encoded by a pat gene obtained from the soil bacterium Streptomyces viridochromogenes. Tolerance to mesotrione is achieved through expression of the p-hydroxyphenylpyruvate dioxygenase (AvHPPD-03) protein encoded by the avhppd-03 gene from oat (Avena sativa). In conducting a safety assessment of food derived from soybean line SYHT0H2, a number of criteria have been addressed including: a characterisation of the transferred gene and its origin, function and stability in the soybean genome; the changes at the level of DNA, protein and in the whole food; compositional analyses; evaluation of intended and unintended changes; and the potential for the newly expressed proteins to be either allergenic or toxic in humans. This safety assessment report addresses only human food safety and nutritional issues of the GM line. It therefore does not address: any risks to the environment that may occur as the result of growing GM plants used in food production any risks to animals that may consume feed derived from GM plants the safety per se of food derived from the non-GM (conventional) plant. History of Use Soybean (Glycine max) is grown as a commercial crop in over 35 countries worldwide. -
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. -
Peptide Sequence
Peptide Sequence Annotation AADHDG CAS-L1 AAEAISDA M10.005-stromelysin 1 (MMP-3) AAEHDG CAS-L2 AAEYGAEA A01.009-cathepsin D AAGAMFLE M10.007-stromelysin 3 (MMP-11) AAQNASMW A06.001-nodavirus endopeptidase AASGFASP M04.003-vibriolysin ADAHDG CAS-L3 ADAPKGGG M02.006-angiotensin-converting enzyme 2 ADATDG CAS-L5 ADAVMDNP A01.009-cathepsin D ADDPDG CAS-21 ADEPDG CAS-L11 ADETDG CAS-22 ADEVDG CAS-23 ADGKKPSS S01.233-plasmin AEALERMF A01.009-cathepsin D AEEQGVTD C03.007-rhinovirus picornain 3C AETFYVDG A02.001-HIV-1 retropepsin AETWYIDG A02.007-feline immunodeficiency virus retropepsin AFAHDG CAS-L24 AFATDG CAS-25 AFDHDG CAS-L26 AFDTDG CAS-27 AFEHDG CAS-28 AFETDG CAS-29 AFGHDG CAS-30 AFGTDG CAS-31 AFQHDG CAS-32 AFQTDG CAS-33 AFSHDG CAS-L34 AFSTDG CAS-35 AFTHDG CAS-L36 AGERGFFY Insulin B-chain AGLQRGGG M14.004-carboxypeptidase N AGSHLVEA Insulin B-chain AIDIDG CAS-L37 AIDPDG CAS-38 AIDTDG CAS-39 AIDVDG CAS-L40 AIEHDG CAS-L41 AIEIDG CAS-L42 AIENDG CAS-43 AIEPDG CAS-44 AIEQDG CAS-45 AIESDG CAS-46 AIETDG CAS-47 AIEVDG CAS-48 AIFQGPID C03.007-rhinovirus picornain 3C AIGHDG CAS-49 AIGNDG CAS-L50 AIGPDG CAS-L51 AIGQDG CAS-52 AIGSDG CAS-53 AIGTDG CAS-54 AIPMSIPP M10.051-serralysin AISHDG CAS-L55 AISNDG CAS-L56 AISPDG CAS-57 AISQDG CAS-58 AISSDG CAS-59 AISTDG CAS-L60 AKQRAKRD S08.071-furin AKRQGLPV C03.007-rhinovirus picornain 3C AKRRAKRD S08.071-furin AKRRTKRD S08.071-furin ALAALAKK M11.001-gametolysin ALDIDG CAS-L61 ALDPDG CAS-62 ALDTDG CAS-63 ALDVDG CAS-L64 ALEIDG CAS-L65 ALEPDG CAS-L66 ALETDG CAS-67 ALEVDG CAS-68 ALFQGPLQ C03.001-poliovirus-type picornain