Advances in Selectable Marker Genes for Plant Transformation
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Supporting Information
Supporting Information Figure S1. The functionality of the tagged Arp6 and Swr1 was confirmed by monitoring cell growth and sensitivity to hydeoxyurea (HU). Five-fold serial dilutions of each strain were plated on YPD with or without 50 mM HU and incubated at 30°C or 37°C for 3 days. Figure S2. Localization of Arp6 and Swr1 on chromosome 3. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 3L, Tel 3R, CEN3, and the RP gene are shown under the panels. Figure S3. Localization of Arp6 and Swr1 on chromosome 4. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) in the whole chromosome region are compared. The position of Tel 4L, Tel 4R, CEN4, SWR1, and RP genes are shown under the panels. Figure S4. Localization of Arp6 and Swr1 on the region including the SWR1 gene of chromosome 4. The binding of Arp6- FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position and orientation of the SWR1 gene is shown. Figure S5. Localization of Arp6 and Swr1 on chromosome 5. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 5L, Tel 5R, CEN5, and the RP genes are shown under the panels. Figure S6. Preferential localization of Arp6 and Swr1 in the 5′ end of genes. Vertical bars represent the binding ratio of proteins in each locus. -
Nucleosome Assembly and Histone H3 Methylation During Dna Replication
NUCLEOSOME ASSEMBLY AND HISTONE H3 METHYLATION DURING DNA REPLICATION TxrwTom Rolef Ben-Shahar A thesis submitted for the degree of Ph.D. at The University of London July, 2004 Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire, EN6 3LD and University College London, Gower Street, London, WC1 6BT ProQuest Number: 10014844 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 10014844 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 ACKNOWLEDGEMENTS To begin with, I would like to acknowledge my mistakes, scientific and others. Hopefully the future will show that I have learned what I could from them. My work has been funded by Cancer Research UK and with a B’NAI BRITH scholarship, and for that I am grateful. I would like to thank Alain Verreault for his supervision, for our scientific conversations and for allowing me to make my own mistakes. My gratitude is given to Munah Abdul-Rauf for being a colleague, collaborator, friend and sister; to Michal Goldberg, Niki Hawks and to other friends and colleagues in Clare-Hall. -
WO 2014/202616 A2 24 December 2014 (24.12.2014) 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 2014/202616 A2 24 December 2014 (24.12.2014) P O P C T (51) International Patent Classification: 13 172714 1 I June 2013 (19.06.2013) EP C07K 14/37 (2006.01) 13 172724 0 I June 2013 (19.06.2013) EP 13 172685 3 I June 2013 (19.06.2013) EP (21) International Application Number: 13 172686 1 I S June 2013 (19.06.2013) EP PCT/EP2014/062737 13 172683 8 I S June 2013 (19.06.2013) EP (22) International Filing Date: 13 172672 1 I S June 2013 (19.06.2013) EP 17 June 2014 (17.06.2014) 13 172673 9 I S June 2013 (19.06.2013) EP 13 172675 4 I S June 2013 (19.06.2013) EP (25) Filing Language: English 13 172677 0 I S June 2013 (19.06.2013) EP (26) Publication Lan ua e: English 13 172681 2 I S June 2013 (19.06.2013) EP 13 172837 0 I S June 2013 (19.06.2013) EP (30) Priority Data: 13 17261 1 9 I S June 2013 (19.06.2013) EP 13 172700.0 19 June 2013 (19 .06.2013) EP 13 172784 4 I S June 2013 (19.06.2013) EP 13 172812.3 19 June 2013 (19 .06.2013) EP 13 172821 4 I S June 2013 (19.06.2013) EP 13 172758.8 19 June 2013 (19 .06.2013) EP 13 172615 0 I S June 2013 (19.06.2013) EP 13 172757.0 19 June 2013 (19 .06.2013) EP 13 172624 2 I S June 2013 (19.06.2013) EP 13 172842.0 19 June 2013 (19 .06.2013) EP 13 172680 4 I S June 2013 (19.06.2013) EP 13 172756.2 19 June 2013 (19 .06.2013) EP 13 172623 4 I S June 2013 (19.06.2013) EP 13 172759.6 -
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. -
Global Response of Saccharomyces Cerevisiae to an Alkylating Agent
Proc. Natl. Acad. Sci. USA Vol. 96, pp. 1486–1491, February 1999 Genetics Global response of Saccharomyces cerevisiae to an alkylating agent SCOTT A. JELINSKY AND LEONA D. SAMSON* Department of Cancer Cell Biology, Division of Toxicology, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115 Edited by David Botstein, Stanford University School of Medicine, Stanford, CA, and approved December 7, 1998 (received for review September 16, 1998) ABSTRACT DNA chip technology enables simultaneous CUPr) was used in this study and was grown in 1% yeast examination of how '6,200 Saccharomyces cerevisiae gene tran- extracty2% peptoney2% glucose at 30°C. Cells were grown to a script levels, representing the entire genome, respond to envi- density of 5 3 106 cells per ml as measured by counting duplicated ronmental change. By using chips bearing oligonucleotide ar- dilutions. Cultures were split into two; MMS (0.1%) was added rays, we show that, after exposure to the alkylating agent methyl directly to one culture, and both cultures were incubated at 30°C ' methanesulfonate, 325 gene transcript levels are increased and for 1 h. Cells were pelleted and washed once in distilled H2O and '76 are decreased. Of the 21 genes that already were known to once in AE buffer (50 mM NaOAc, pH 5.2y10 mM EDTA) be induced by a DNA-damaging agent, 18 can be scored as immediately before RNA extraction. inducible in this data set, and surprisingly, most of the newly RNA Extraction. Total RNA was isolated by using a hot-phenol identified inducible genes are induced even more strongly than method (15). -
POLSKIE TOWARZYSTWO BIOCHEMICZNE Postępy Biochemii
POLSKIE TOWARZYSTWO BIOCHEMICZNE Postępy Biochemii http://rcin.org.pl WSKAZÓWKI DLA AUTORÓW Kwartalnik „Postępy Biochemii” publikuje artykuły monograficzne omawiające wąskie tematy, oraz artykuły przeglądowe referujące szersze zagadnienia z biochemii i nauk pokrewnych. Artykuły pierwszego typu winny w sposób syntetyczny omawiać wybrany temat na podstawie możliwie pełnego piśmiennictwa z kilku ostatnich lat, a artykuły drugiego typu na podstawie piśmiennictwa z ostatnich dwu lat. Objętość takich artykułów nie powinna przekraczać 25 stron maszynopisu (nie licząc ilustracji i piśmiennictwa). Kwartalnik publikuje także artykuły typu minireviews, do 10 stron maszynopisu, z dziedziny zainteresowań autora, opracowane na podstawie najnow szego piśmiennictwa, wystarczającego dla zilustrowania problemu. Ponadto kwartalnik publikuje krótkie noty, do 5 stron maszynopisu, informujące o nowych, interesujących osiągnięciach biochemii i nauk pokrewnych, oraz noty przybliżające historię badań w zakresie różnych dziedzin biochemii. Przekazanie artykułu do Redakcji jest równoznaczne z oświadczeniem, że nadesłana praca nie była i nie będzie publikowana w innym czasopiśmie, jeżeli zostanie ogłoszona w „Postępach Biochemii”. Autorzy artykułu odpowiadają za prawidłowość i ścisłość podanych informacji. Autorów obowiązuje korekta autorska. Koszty zmian tekstu w korekcie (poza poprawieniem błędów drukarskich) ponoszą autorzy. Artykuły honoruje się według obowiązujących stawek. Autorzy otrzymują bezpłatnie 25 odbitek swego artykułu; zamówienia na dodatkowe odbitki (płatne) należy zgłosić pisemnie odsyłając pracę po korekcie autorskiej. Redakcja prosi autorów o przestrzeganie następujących wskazówek: Forma maszynopisu: maszynopis pracy i wszelkie załączniki należy nadsyłać w dwu egzem plarzach. Maszynopis powinien być napisany jednostronnie, z podwójną interlinią, z marginesem ok. 4 cm po lewej i ok. 1 cm po prawej stronie; nie może zawierać więcej niż 60 znaków w jednym wierszu nie więcej niż 30 wierszy na stronie zgodnie z Normą Polską. -
University of Groningen Genome Sequencing and Analysis Of
University of Groningen Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum van den Berg, Marco A.; Albang, Richard; Albermann, Kaj; Badger, Jonathan H.; Daran, Jean-Marc; Driessen, Arnold; Garcia-Estrada, Carlos; Fedorova, Natalie D.; Harris, Diana M.; Heijne, Wilbert H. M. Published in: Nature Biotechnology DOI: 10.1038/nbt.1498 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2008 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): van den Berg, M. A., Albang, R., Albermann, K., Badger, J. H., Daran, J-M., Driessen, A. J. M., ... Bovenberg, R. A. L. (2008). Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nature Biotechnology, 26(10), 1161-1168. DOI: 10.1038/nbt.1498 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. -
The Stress Response and Circadian Regulation of Translation
THE STRESS RESPONSE AND CIRCADIAN REGULATION OF TRANSLATION IN NEUROSPORA CRASSA A Dissertation by STEPHEN Z. CASTER Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Deborah Bell-Pedersen Committee Members, Daniel J. Ebbole Paul Hardin Matthew Sachs Terry Thomas Head of Department, Dorothy Shippen August 2016 Major Subject: Genetics Copyright 2016 Stephen Caster ABSTRACT Stress response pathways function to allow cells to adapt to changes in the environment. In Neurospora crassa, acute osmotic stress activates the conserved p38-like osmosensing mitogen-activated protein kinase (OS MAPK) pathway. When activated, the terminal MAPK, OS-2 can activate transcription factors and kinases. We show an acute osmotic stress activates OS-2, which phosphorylates and activates the conserved kinase RCK-2. RCK-2 phosphorylates and inactivates the highly conserved eukaryotic elongation factor 2 (eEF-2). To determine if this is a mechanism for translational regulation of mRNAs, I examined ribosome profiling and RNAseq data from osmotically stressed WT and Δrck-2 cultures. I found that RCK-2/eEF-2 regulate 69 constitutively expressed mRNAs at the level of translation. I also examined ribosome profiling and RNAseq data from cultures given light exposure, and found that 36 constitutively expressed mRNAs were regulated at the level of translation. In both cases, the translationally-controlled genes were enriched for metabolic processes, suggesting that rapid regulation of metabolism through translational control helps the organism overcome osmotic and light stress. The circadian clock has a profound effect on gene regulation; however, little is known about the role of the clock in controlling translation. -
All Enzymes in BRENDA™ the Comprehensive Enzyme Information System
All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA -
(12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur Et Al
US 20150240226A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur et al. (43) Pub. Date: Aug. 27, 2015 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/16 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/02 (2006.01) CI2N 9/78 (2006.01) (71) Applicant: BP Corporation North America Inc., CI2N 9/12 (2006.01) Naperville, IL (US) CI2N 9/24 (2006.01) CI2O 1/02 (2006.01) (72) Inventors: Eric J. Mathur, San Diego, CA (US); CI2N 9/42 (2006.01) Cathy Chang, San Marcos, CA (US) (52) U.S. Cl. CPC. CI2N 9/88 (2013.01); C12O 1/02 (2013.01); (21) Appl. No.: 14/630,006 CI2O I/04 (2013.01): CI2N 9/80 (2013.01); CI2N 9/241.1 (2013.01); C12N 9/0065 (22) Filed: Feb. 24, 2015 (2013.01); C12N 9/2437 (2013.01); C12N 9/14 Related U.S. Application Data (2013.01); C12N 9/16 (2013.01); C12N 9/0061 (2013.01); C12N 9/78 (2013.01); C12N 9/0071 (62) Division of application No. 13/400,365, filed on Feb. (2013.01); C12N 9/1241 (2013.01): CI2N 20, 2012, now Pat. No. 8,962,800, which is a division 9/2482 (2013.01); C07K 2/00 (2013.01); C12Y of application No. 1 1/817,403, filed on May 7, 2008, 305/01004 (2013.01); C12Y 1 1 1/01016 now Pat. No. 8,119,385, filed as application No. PCT/ (2013.01); C12Y302/01004 (2013.01); C12Y US2006/007642 on Mar. 3, 2006. -
( 12 ) United States Patent
US010316323B2 (12 ) United States Patent (10 ) Patent No. : US 10 ,316 , 323 B2 South et al. ( 45 ) Date of Patent: Jun . 11, 2019 ( 54 ) MICROORGANISMS ENGINEERED TO USE OTHER PUBLICATIONS UNCONVENTIONAL SOURCES OF NITROGEN Seffernick , et al. (2001 ) , Journal J . Bacteriol. 183 ( 8 ) , 2405 - 2410 ( 2001 ) . * Boundy -Mills et al ., “ The atzB Gene of Pseudomonas sp . Strain (71 ) Applicant: Novogy , Inc. , Cambridge, MA (US ) ADP Encodes the Second Enzyme of a Novel Atrazine Degradation Pathway ,” Applied and Environmental Microbiology , 1997 , 63 ( 3 ): 916 ( 72 ) Inventors : Colin South , Lexington , MA (US ) ; 923 . Arthur J Shaw , IV , Belmont, MA (US ) Cameron et al. , “ New Family of Biuret Hydrolases Involved in S - Triazine Ring Metabolism ,” ACS Catal, 2011, 1 : 1075 - 1082. (73 ) Assignee : Novogy , Inc ., Cambridge , MA (US ) Cheng et al. , “ Allophanate Hydrolase , Not Urease , Function in Bacterial Cyanuric Acid Metabolism ,” Appl. Environ . Microb. , ( * ) Notice : Subject to any disclaimer, the term of this 2005, 71 ( 8 ) :4437 -4445 . patent is extended or adjusted under 35 Copley, “ Evolution of Efficient Pathways for Degradation of U . S . C . 154 ( b ) by 0 days . Anthropogenic Chemicals ,” Nat. Chem . Biol. , 2009, 5 ( 8 ) :559 -566 . De Souza et al ., “ The atzABC Genes encoding Atrazine Catabolism ( 21 ) Appl. No. : 15 /679 , 312 Are Located on a Self - Transmissible Plasmid in Pseudomonas sp . Strain ADP, ” Appl. Environ . Microb , 1998 , 64 (6 ) :2323 -2326 . (22 ) Filed : Aug. 17 , 2017 Dodge et al ., “ Plasmid Localization and Organization of Melamine Degradation Genes in Rhodococcus sp . Strain Mel. ” Applied and (65 ) Prior Publication Data Environmental Microbiology , 78 : 1397 - 1403 . Eaton et al . , “ Cloning and analysis of s - Triazine catabolic genes US 2018 /0051294 A1 Feb . -
Springer Handbook of Enzymes
Dietmar Schomburg Ida Schomburg (Eds.) Springer Handbook of Enzymes Alphabetical Name Index 1 23 © Springer-Verlag Berlin Heidelberg New York 2010 This work is subject to copyright. All rights reserved, whether in whole or part of the material con- cerned, specifically the right of translation, printing and reprinting, reproduction and storage in data- bases. The publisher cannot assume any legal responsibility for given data. Commercial distribution is only permitted with the publishers written consent. Springer Handbook of Enzymes, Vols. 1–39 + Supplements 1–7, Name Index 2.4.1.60 abequosyltransferase, Vol. 31, p. 468 2.7.1.157 N-acetylgalactosamine kinase, Vol. S2, p. 268 4.2.3.18 abietadiene synthase, Vol. S7,p.276 3.1.6.12 N-acetylgalactosamine-4-sulfatase, Vol. 11, p. 300 1.14.13.93 (+)-abscisic acid 8’-hydroxylase, Vol. S1, p. 602 3.1.6.4 N-acetylgalactosamine-6-sulfatase, Vol. 11, p. 267 1.2.3.14 abscisic-aldehyde oxidase, Vol. S1, p. 176 3.2.1.49 a-N-acetylgalactosaminidase, Vol. 13,p.10 1.2.1.10 acetaldehyde dehydrogenase (acetylating), Vol. 20, 3.2.1.53 b-N-acetylgalactosaminidase, Vol. 13,p.91 p. 115 2.4.99.3 a-N-acetylgalactosaminide a-2,6-sialyltransferase, 3.5.1.63 4-acetamidobutyrate deacetylase, Vol. 14,p.528 Vol. 33,p.335 3.5.1.51 4-acetamidobutyryl-CoA deacetylase, Vol. 14, 2.4.1.147 acetylgalactosaminyl-O-glycosyl-glycoprotein b- p. 482 1,3-N-acetylglucosaminyltransferase, Vol. 32, 3.5.1.29 2-(acetamidomethylene)succinate hydrolase, p. 287 Vol.