Domestication of Lambda Phage Genes Into a Putative Third Type of Replicative Helicase Matchmaker
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Protists and the Wild, Wild West of Gene Expression
MI70CH09-Keeling ARI 3 August 2016 18:22 ANNUAL REVIEWS Further Click here to view this article's online features: • Download figures as PPT slides • Navigate linked references • Download citations Protists and the Wild, Wild • Explore related articles • Search keywords West of Gene Expression: New Frontiers, Lawlessness, and Misfits David Roy Smith1 and Patrick J. Keeling2 1Department of Biology, University of Western Ontario, London, Ontario, Canada N6A 5B7; email: [email protected] 2Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; email: [email protected] Annu. Rev. Microbiol. 2016. 70:161–78 Keywords First published online as a Review in Advance on constructive neutral evolution, mitochondrial transcription, plastid June 17, 2016 transcription, posttranscriptional processing, RNA editing, trans-splicing The Annual Review of Microbiology is online at micro.annualreviews.org Abstract This article’s doi: The DNA double helix has been called one of life’s most elegant structures, 10.1146/annurev-micro-102215-095448 largely because of its universality, simplicity, and symmetry. The expression Annu. Rev. Microbiol. 2016.70:161-178. Downloaded from www.annualreviews.org Copyright c 2016 by Annual Reviews. Access provided by University of British Columbia on 09/24/17. For personal use only. of information encoded within DNA, however, can be far from simple or All rights reserved symmetric and is sometimes surprisingly variable, convoluted, and wantonly inefficient. Although exceptions to the rules exist in certain model systems, the true extent to which life has stretched the limits of gene expression is made clear by nonmodel systems, particularly protists (microbial eukary- otes). -
|||||||III US005478731A United States Patent (19) 11 Patent Number: 5,478,731
|||||||III US005478731A United States Patent (19) 11 Patent Number: 5,478,731 Short 45 Date of Patent: Dec. 26,9 1995 54). POLYCOS VECTORS 56 References Cited 75) Inventor: Jay M. Short, Encinitas, Calif. PUBLICATIONS (73 Assignee: Stratagene, La Jolla, Calif. Ahmed (1989), Gene 75:315-321. 21 Appl. No.: 133,179 Evans et al. (1989), Gene 79:9-20. 22) PCT Filed: Apr. 10, 1992 Primary Examiner-Mindy B. Fleisher Assistant Examiner-Philip W. Carter 86 PCT No.: PCT/US92/03012 Attorney, Agent, or Firm-Albert P. Halluin; Pennie & S371 Date: Oct. 12, 1993 Edmonds S 102(e) Date: Oct. 12, 1993 57 ABSTRACT 87, PCT Pub. No.: WO92/18632 A bacteriophage packaging site-based vector system is describe that involves cloning vectors and methods for their PCT Pub. Date: Oct. 29, 1992 use in preparing multiple copy number bacteriophage librar O ies of cloned DNA. The vector is based on a DNA segment Related U.S. Application Data that comprises a nucleotide sequence defining a bacterioph 63 abandoned.continuationin-part of ser, No. 685.215,y Apr 12, 1991, ligationage packaging means usedsite locatedto concatamerize between twofragments termining of DNA 6 having compatible ligation means. Methods for preparing a (51) Int. Cl. ............................... C12N 1/21; C12N 7/01; concatameric DNA for packaging cloned DNA segments, C12N 15/10; C12N 15/11 and for packaging the concatamers to produce a library are 52 U.S. Cl. ................ 435/914; 435/1723; 435/252.33; also described. 435/235.1; 435/252.3; 536/23.1 58) Field of Search .............................. 435/91.32, 172.3, 435/320.1,914, 252.33, 252.3, 235.1; 536/23.1 18 Claims, 1 Drawing Sheet U.S. -
Thèse Morgane Wartel
Faculté des Sciences - Aix-Marseille Université Laboratoire de Chimie Bactérienne 163 Avenue de Luminy - Case 901 31 Chemin Joseph Aiguier 13288 Marseille 13009 Marseille Thèse En vue d’obtenir le grade de Docteur d’Aix-Marseille Université Biologie, spécialité Microbiologie Présentée et soutenue publiquement par Morgane Wartel Le Mercredi 18 Décembre 2013 A novel class of bacterial motors involved in the directional transport of a sugar at the bacterial surface: The machineries of motility and sporulation in Myxococcus xanthus. Une nouvelle classe de moteurs bactériens impliqués dans le transport de macromolécules à la surface bactérienne: Les machineries de motilité et de sporulation de Myxococcus xanthus. Membres du Jury : Dr. Christophe Grangeasse Rapporteur Dr. Patrick Viollier Rapporteur Pr. Pascale Cossart Examinateur Dr. Francis-André Wollman Examinateur Dr. Tâm Mignot Directeur de Thèse Pr. Frédéric Barras Président du Jury Faculté des Sciences - Aix-Marseille Université Laboratoire de Chimie Bactérienne 163 Avenue de Luminy - Case 901 31 Chemin Joseph Aiguier 13288 Marseille 13009 Marseille Thèse En vue d’obtenir le grade de Docteur d’Aix-Marseille Université Biologie, spécialité Microbiologie Présentée et soutenue publiquement par Morgane Wartel Le Mercredi 18 Décembre 2013 A novel class of bacterial motors involved in the directional transport of a sugar at the bacterial surface: The machineries of motility and sporulation in Myxococcus xanthus. Une nouvelle classe de moteurs bactériens impliqués dans le transport de macromolécules à la surface bactérienne: Les machineries de motilité et de sporulation de Myxococcus xanthus. Membres du Jury : Dr. Christophe Grangeasse Rapporteur Dr. Patrick Viollier Rapporteur Pr. Pascale Cossart Examinateur Dr. Francis-André Wollman Examinateur Dr. -
Lessons from Nature: Microrna-Based Shrna Libraries
PERSPECTIVE Lessons from Nature: microRNA-based shRNA libraries methods Kenneth Chang1, Stephen J Elledge2 & Gregory J Hannon1 Loss-of-function genetics has proven essential for interrogating the functions of genes .com/nature e and for probing their roles within the complex circuitry of biological pathways. In .natur many systems, technologies allowing the use of such approaches were lacking before w the discovery of RNA interference (RNAi). We have constructed first-generation short hairpin RNA (shRNA) libraries modeled after precursor microRNAs (miRNAs) and second- http://ww generation libraries modeled after primary miRNA transcripts (the Hannon-Elledge oup libraries). These libraries were arrayed, sequence-verified, and cover a substantial portion r G of all known and predicted genes in the human and mouse genomes. Comparison of first- and second-generation libraries indicates that RNAi triggers that enter the RNAi pathway lishing through a more natural route yield more effective silencing. These large-scale resources b Pu are functionally versatile, as they can be used in transient and stable studies, and for constitutive or inducible silencing. Library cassettes can be easily shuttled into vectors Nature that contain different promoters and/or that provide different modes of viral delivery. 6 200 © RNAi is an evolutionarily conserved, sequence-specific than a decade elapsed between the discovery of the first gene-silencing mechanism that is induced by dsRNA. miRNA, Caenorhabditis elegans lin-4 (refs. 11,12) and Each dsRNA silencing trigger is processed into 21–25 bp the achievement of at least a superficial understanding dsRNAs called small interfering RNAs (siRNAs)1–3 by of the biosynthesis, processing and mode of action of Dicer, a ribonuclease III family (RNase III) enzyme4. -
Site Directed Mutagensis of Bacteriophage HK639 and Identification of Its Integration Site Madhuri Jonnalagadda Western Kentucky University
Western Kentucky University TopSCHOLAR® Masters Theses & Specialist Projects Graduate School 12-2008 Site Directed Mutagensis of Bacteriophage HK639 and Identification of Its Integration Site Madhuri Jonnalagadda Western Kentucky University Follow this and additional works at: http://digitalcommons.wku.edu/theses Part of the Cell and Developmental Biology Commons, Genetics Commons, Immunopathology Commons, and the Molecular Genetics Commons Recommended Citation Jonnalagadda, Madhuri, "Site Directed Mutagensis of Bacteriophage HK639 and Identification of Its Integration Site" (2008). Masters Theses & Specialist Projects. Paper 42. http://digitalcommons.wku.edu/theses/42 This Thesis is brought to you for free and open access by TopSCHOLAR®. It has been accepted for inclusion in Masters Theses & Specialist Projects by an authorized administrator of TopSCHOLAR®. For more information, please contact [email protected]. SITE DIRECTED MUTAGENESIS OF BACTERIOPHAGE HK639 AND IDENTIFICATION OF ITS INTEGRATION SITE A Thesis presented to The faculty of the Department of Biology Western Kentucky University Bowling Green, Kentucky. In Partial Fulfillment Of the Requirement for the Degree Master of Science By Madhuri Jonnalagadda December, 2008 Site Directed Mutagenesis of Bacteriophage HK639 and Identification of its Integration Site Date Recommended 12/4/08 Dr.Rodney A. King Director of Thesis __Dr.Jeffery Marcus Dr. Sigrid Jacobshagen _____________________________________ Dean, Graduate Studies and Research Date DEDICATION I would like to dedicate my thesis to my dear father Dr. J. Padmanabha Rao, my mother, Dr.V. Lakshmi, my sister Dr. J. Sushma for their support and encouragement. i ACKNOWLEDGEMENTS I wish to express my heartfelt gratitude to my graduate committee in the Department of Biology, Western Kentucky University. Primarily, I am thankful to my advisor, Dr. -
Genomic Signatures of Sex, Selection and Speciation in the Microbial World
Genomic signatures of sex, selection and speciation in the microbial world by B. Jesse Shapiro B.Sc. Biology McGill University, 2003 M.Sc. Integrative Bioscience Oxford University, 2004 SUBMITTED TO THE PROGRAM IN COMPUTATIONAL AND SYSTEMS BIOLOGY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN COMPUTATIONAL AND SYSTEMS BIOLOGY AT THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY SEPTEMBER 2010 © 2010 Massachusetts Institute of Technology All rights reserved Signature of Author:...……………………………………………………………………………………….. Program in Computational and Systems Biology August 6, 2010 Certified by:…………………………………………………………………………………………………. Eric J. Alm Assistant Professor of Civil and Environmental Engineering and Biological Engineering Thesis Supervisor Accepted by:………………………………………………………………………………………………… Christopher B. Burge Professor of Biology and Biological Engineering Chair, Computational and Systems Biology Ph.D. Graduate Committee 1 Genomic signatures of sex, selection and speciation in the microbial world by B. Jesse Shapiro Submitted to the Program in Computational and Systems Biology on August 6, 2010 in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Computational and Systems Biology ABSTRACT Understanding the microbial world is key to understanding global biogeochemistry, human health and disease, yet this world is largely inaccessible. Microbial genomes, an increasingly accessible data source, provide an ideal entry point. The genome sequences of different microbes may be compared using the tools of population genetics to infer important genetic changes allowing them to diversify ecologically and adapt to distinct ecological niches. Yet the toolkit of population genetics was developed largely with sexual eukaryotes in mind. In this work, I assess and develop tools for inferring natural selection in microbial genomes. -
MORC1 Represses Transposable Elements in the Mouse Male Germline
ARTICLE Received 12 Sep 2014 | Accepted 7 Nov 2014 | Published 12 Dec 2014 DOI: 10.1038/ncomms6795 OPEN MORC1 represses transposable elements in the mouse male germline William A. Pastor1,*, Hume Stroud1,*,w, Kevin Nee1, Wanlu Liu1, Dubravka Pezic2, Sergei Manakov2, Serena A. Lee1, Guillaume Moissiard1, Natasha Zamudio3,De´borah Bourc’his3, Alexei A. Aravin2, Amander T. Clark1,4 & Steven E. Jacobsen1,4,5 The Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA-methylated and silent genes. MORC1-deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homologue DNMT3L. Morc1 mutants show highly localized defects in the establishment of DNA methylation at specific classes of transposons, and this is associated with failed transposon silencing at these sites. Our results identify MORC1 as an important new regulator of the epigenetic landscape of male germ cells during the period of global de novo methylation. 1 Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, 4028 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles, California 90095, USA. 2 Division of Biology and Biochemical Engineering, California Institute of Technology, 1200 E California Boulevard, Pasadena, California 91125, USA. 3 Unite´ de ge´ne´tique et biologie du de´veloppement, Instititute Curie, CNRS UMR3215, INSERM U934, Paris 75005, France. -
Genes for Degradation and Utilization of Uronic Acid-Containing Polysaccharides of a Marine Bacterium Catenovulum Sp
Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4 Go Furusawa, Nor Azura Azami and Aik-Hong Teh Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia ABSTRACT Background. Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides. Methods. To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis. Results. The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in Submitted 5 August 2020 the QB4 genome based on the CAZy database. -
The Roles of Moron Genes in the Escherichia Coli Enterobacteria Phage Phi-80
THE ROLES OF MORON GENES IN THE ESCHERICHIA COLI ENTEROBACTERIA PHAGE PHI-80 Yury V. Ivanov A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2012 Committee: Ray A. Larsen, Advisor Craig L. Zirbel Graduate Faculty Representative Vipa Phuntumart Scott O. Rogers George S. Bullerjahn © 2012 Yury Ivanov All Rights Reserved iii ABSTRACT Ray Larsen, Advisor The TonB system couples cytoplasmic membrane-derived proton motive force energy to drive ferric siderophore transport across the outer membrane of Gram-negative bacteria. While much effort has focused on this process, how energy is harnessed to provide for transport of ligands remains unknown. Several bacterial viruses (“phage”) are known to require the TonB system to irreversibly adsorb (i.e., establish infection) in the model organism Escherichia coli. One such phage is φ80, a “cousin” of the model temperate phage λ. Determining how φ80 is using the TonB system for infection should provide novel insights to the mechanisms of TonB-dependent processes. It had long been known that recombination between λ and φ80 results in a λ-like phage for whom TonB is now required; and this recombination involved the λ J gene, which encodes the tail-spike protein required for irreversible adsorption of λ to E. coli. Thus, we suspected that a φ80 homologue of the λ J gene product was responsible for the TonB dependence of φ80. While φ80 has long served as a tool for assaying TonB activity, it has not received the scrutiny afforded λ. -
A Taxonomic Framework for Emerging Groups of Ecologically
Spring S, Scheuner C, Göker M, Klenk H-P. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Frontiers in Microbiology 2015, 6, 281. Copyright: Copyright © 2015 Spring, Scheuner, Göker and Klenk. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. DOI link to article: http://dx.doi.org/10.3389/fmicb.2015.00281 Date deposited: 07/03/2016 This work is licensed under a Creative Commons Attribution 4.0 International License Newcastle University ePrints - eprint.ncl.ac.uk ORIGINAL RESEARCH published: 09 April 2015 doi: 10.3389/fmicb.2015.00281 A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data Stefan Spring 1*, Carmen Scheuner 1, Markus Göker 1 and Hans-Peter Klenk 1, 2 1 Department Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 School of Biology, Newcastle University, Newcastle upon Tyne, UK Edited by: Marcelino T. Suzuki, Sorbonne Universities (UPMC) and In recent years a large number of isolates were obtained from saline environments that are Centre National de la Recherche phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, Scientifique, France which were originally identified in seawater samples using cultivation independent Reviewed by: Fabiano Thompson, methods and are characterized by high seasonal abundances in coastal environments. -
Generalization of Genetic Code Expansion
Generalization of Genetic Code Expansion The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Stork, Devon. 2020. Generalization of Genetic Code Expansion. Doctoral dissertation, Harvard University Graduate School of Arts and Sciences. Citable link https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368951 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA HARVARD UNIVERSITY Graduate School of Arts and Sciences DISSERTATION ACCEPTANCE CERTIFICATE The undersigned, appointed by the Department of Molecular and Cellular Biology have examined a dissertation entitled Generalization of Genetic Code Expansion presented by Devon Stork candidate for the degree of Doctor of Philosophy and hereby certify that it is worthy of acceptance. Signature Richard Losick (Sep 15, 2020 15:40 EDT) Typed name: Prof. Richard Losick Vlad Denic Signatur Vlad Denic (Sep 17, 2020 14:52 EDT) Typed name: Prof. Vladimir Denic Signature Abhishek Chatterjee (Sep 23, 2020 13:28 EDT) Typed name: Prof. Abhishek Chatterjee Signature Typed name: Prof. Signature Typed name: Prof. Date: September 15, 2020 Generalization of Genetic Code Expansion A dissertation presented by Devon Stork to The Department of Molecular and Cellular Biology In partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biochemistry Harvard University Cambridge, Massachusetts September 2020 © 2020 Devon Stork All rights reserved Dissertation Advisors: Dr. -
Manual: Lambda ZAP-CMV XR Library Construction
Lambda ZAP-CMV XR Library Construction Kit INSTRUCTION MANUAL Catalog #200448 BN #200448-12 Revision A.01 For In Vitro Use Only 200448-12 LIMITED PRODUCT WARRANTY This warranty limits our liability to replacement of this product. No other warranties of any kind, express or implied, including without limitation, implied warranties of merchantability or fitness for a particular purpose, are provided by Agilent. Agilent shall have no liability for any direct, indirect, consequential, or incidental damages arising out of the use, the results of use, or the inability to use this product. ORDERING INFORMATION AND TECHNICAL SERVICES United States and Canada Agilent Technologies Stratagene Products Division 11011 North Torrey Pines Road La Jolla, CA 92037 Telephone (858) 373-6300 Order Toll Free (800) 424-5444 Technical Services (800) 894-1304 Internet [email protected] World Wide Web www.stratagene.com Europe Location Telephone Fax Technical Services Austria 0800 292 499 0800 292 496 0800 292 498 Belgium 00800 7000 7000 00800 7001 7001 00800 7400 7400 0800 15775 0800 15740 0800 15720 France 00800 7000 7000 00800 7001 7001 00800 7400 7400 0800 919 288 0800 919 287 0800 919 289 Germany 00800 7000 7000 00800 7001 7001 00800 7400 7400 0800 182 8232 0800 182 8231 0800 182 8234 Netherlands 00800 7000 7000 00800 7001 7001 00800 7400 7400 0800 023 0446 +31 (0)20 312 5700 0800 023 0448 Switzerland 00800 7000 7000 00800 7001 7001 00800 7400 7400 0800 563 080 0800 563 082 0800 563 081 United Kingdom 00800 7000 7000 00800 7001 7001 00800 7400 7400 0800 917 3282 0800 917 3283 0800 917 3281 All Other Countries Please contact your local distributor.