DU Msc Microbiology
Total Page：16
File Type：pdf, Size：1020Kb
Load more
Recommended publications
-
Study of the Dynamics of Catabolite Repression : from Mathematical Models to Experimental Data Valentin Zulkower
Study of the dynamics of catabolite repression : from mathematical models to experimental data Valentin Zulkower To cite this version: Valentin Zulkower. Study of the dynamics of catabolite repression : from mathematical models to experimental data. Modeling and Simulation. Université Grenoble Alpes, 2015. English. NNT : 2015GREAM080. tel-01679345 HAL Id: tel-01679345 https://tel.archives-ouvertes.fr/tel-01679345 Submitted on 9 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour obtenir le grade de = DOCTEUR DE L’UNIVERSITÉ DE GRENOBLE Spécialité : Mathématiques appliquées Arrêté ministérial : 7 aout 2006 Présentée par Valentin Zulkower Thèse dirigée par Hidde de Jong et codirigée par Johannes Geiselmann et Delphine Ropers préparée au sein de l’Equipe-projet IBIS, INRIA Grenoble-Rhône-Alpes et de l’Ecole doctorale Mathematiques, Science et Technologies de l’Information, Informatique (MSTII) Etude de la dynamique des mécanismes de la répression catabolique Des modèles mathématiques aux données expérimentales Thèse soutenue publiquement le 3 mars 2015, devant le jury composé de : Pr. Julio Rodriguez Banga Professeur, CSIC, Vigo (Espagne), Rapporteur Dr. Stefan Klumpp Chercheur, Institut Max Planck, Potsdam (Allemagne), Rapporteur Dr. Olivier Martin Directeur de Recherche, INRA - UMR de Génétique Végétale , Président Dr. -
Transcriptional Units
Proc. Natl. Acad. Sci. USA Vol. 76, No. 7, pp. 3194-3197, July 1979 Biochemistry Cyclic AMP as a modulator of polarity in polycistronic transcriptional units (positive regulation/rho factor/lactose and galactose operons/catabolite repression) AGNES ULLMANNt, EVELYNE JOSEPHt, AND ANTOINE DANCHINt tUnite de Biochimie Cellulaire, Institut Pasteur, 75724 Paris Cedex 15, France; and tInstitut de Biologie Physico-Chimique, 75005 Paris, France Communicated by Frangois Jacob, April 16, 1979 ABSTRACT The degree of natural polarity in the lactose scribed by Watekam et al. (7, 8) in sonicated bacterial extracts. and galactose operons of Escherichia coli is affected by aden- One unit is the amount of enzyme that converts 1 nmol of osine 3',5'-cyclic monophosphate (cAMP). This effect, mediated substrate per min at 280C (except for UDPGal epimerase, for by the cAMP receptor protein, is exerted at sites distinct from the promoter. Experiments performed with a mutant bearing which the assay temperature was 220C). a thermosensitive rho factor activity indicate that cAMP relieves Reagents and Enzymes. They were obtained from the fol- polarity by interfering with transcription termination. Con- lowing companies: trimethoprim from Calbiochem; all radio- flicting results in the literature concerning the role of cAMP active products from Amersham; isopropyl-f3-D-thiogalactoside receptor protein and cAMP in galactose operon expression can (IPTG), D-fucose, cAMP, UDPglucose dehydrogenase, and all be reconciled by the finding that cAMP stimulates the expres- substrates from Sigma; and all other chemicals from Merck. sion of operator distal genes without significantly affecting the proximal genes. Therefore, it appears necessary to reevaluate the classification o(the galactose operon as exhibiting cAMP- RESULTS mediated catabolite repression at the level of transcription Natural Polarity in Lactose Operon. -
Genetic Snapshots of the Rhizobium Species NGR234 Genome
Article Genetic snapshots of the Rhizobium species NGR234 genome VIPREY, Virginie, et al. Abstract In nitrate-poor soils, many leguminous plants form nitrogen-fixing symbioses with members of the bacterial family Rhizobiaceae. We selected Rhizobium sp. NGR234 for its exceptionally broad host range, which includes more than I 12 genera of legumes. Unlike the genome of Bradyrhizobium japonicum, which is composed of a single 8.7 Mb chromosome, that of NGR234 is partitioned into three replicons: a chromosome of about 3.5 Mb, a megaplasmid of more than 2 Mb (pNGR234b) and pNGR234a, a 536,165 bp plasmid that carries most of the genes required for symbioses with legumes. Symbiotic loci represent only a small portion of all the genes coded by rhizobial genomes, however. To rapidly characterize the two largest replicons of NGR234, the genome of strain ANU265 (a derivative strain cured of pNGR234a) was analyzed by shotgun sequencing. Reference VIPREY, Virginie, et al. Genetic snapshots of the Rhizobium species NGR234 genome. Genome Biology, 2000, vol. 1, no. 6, p. 1-17 DOI : 10.1186/gb-2000-1-6-research0014 PMID : 11178268 Available at: http://archive-ouverte.unige.ch/unige:84778 Disclaimer: layout of this document may differ from the published version. 1 / 1 http://genomebiology.com/2000/1/6/research/0014.1 Research Genetic snapshots of the Rhizobium species NGR234 genome Virginie Viprey*, André Rosenthal, William J Broughton* and Xavier Perret* Addresses: *Laboratoire de Biologie Moléculaire des Plantes Supérieures, Université de Genève, chemin de lImpératrice, 1292 Chambésy, Genève, Switzerland. Institut für Molekulare Biotechnologie, Abteilung Genomanalyze, Beutenbergstrasse, 07745 Jena, Germany. -
2.2.3 Generation of Genomic DNA Sequences from Plant Sources
Copyright Undertaking This thesis is protected by copyright, with all rights reserved. By reading and using the thesis, the reader understands and agrees to the following terms: 1. The reader will abide by the rules and legal ordinances governing copyright regarding the use of the thesis. 2. The reader will use the thesis for the purpose of research or private study only and not for distribution or further reproduction or any other purpose. 3. The reader agrees to indemnify and hold the University harmless from and against any loss, damage, cost, liability or expenses arising from copyright infringement or unauthorized usage. IMPORTANT If you have reasons to believe that any materials in this thesis are deemed not suitable to be distributed in this form, or a copyright owner having difficulty with the material being included in our database, please contact [email protected] providing details. The Library will look into your claim and consider taking remedial action upon receipt of the written requests. Pao Yue-kong Library, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong http://www.lib.polyu.edu.hk The Hong Kong Polytechnic University Department of Health Technology and Informatics Isolation and Characterisation of Nucleases from Various Biological Sources for Further Application in Nucleic Acid Analysis By CHEUNG Tsz Shan A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy March 2012 CERTIFICATE OF ORIGINALITY I hereby declare that this thesis is my own work and that, to the best of my knowledge and belief, it reproduces no materials previously published or written, nor material that has been accepted for the award of any other degree or diploma, except where due acknowledgment has been made in the text. -
Mung Bean Nuclease Product Information
Certificate of Analysis Mung Bean Nuclease: Part No. Size (units) Part# 9PIM431 M431A 2,000 Revised 4/18 10X Reaction Buffer (M432A): When the Mung Bean Nuclease 10X Reaction Buffer, provided with this enzyme, is diluted 1:10, it has a composition of 0.03M sodium acetate (pH 5.0), 0.05M NaCl and 1mM ZnCl2. Enzyme Storage Buffer: Mung Bean Nuclease is supplied in 10mM Tris-HCl (pH 7.5), 50mM NaCl, 0.01% Triton® X-100 and 50% glycerol. Source: Mung bean sprouts (Phaseolus aureus). Unit Definition: One unit is defined as the amount of enzyme required to produce 1µg of acid-soluble material per minute *AF9PIM431 0418M431* at 37°C. The reaction conditions are: 30mM sodium acetate (pH 5.0), 50mM NaCl, 1mM ZnCl2, 5% glycerol and 0.5mg/ml AF9PIM431 0418M431 denatured calf thymus DNA. See the unit concentration on the Product Information Label. Storage Temperature: Store at –20°C. Avoid multiple freeze-thaw cycles and exposure to frequent temperature changes. See the expiration date on the Product Information Label. Quality Control Assays Contaminant Assay Endonuclease/Nickase Activity: To confirm the absence of contaminating endonuclease/nickase activity, 1µg of lambda DNA/Hind III markers (Cat.# G1711) is incubated with Mung Bean Nuclease for 10 minutes at room temperature. The mark- ers are then separated by electrophoresis on a 1% agarose gel and stained with ethidium bromide. Markers that have been Promega Corporation incubated with ≥60 units of enzyme will remain as intact bands with a minimal amount of smearing. 2800 Woods Hollow Road Madison, WI 53711-5399 USA Telephone 608-274-4330 Toll Free 800-356-9526 Fax 608-277-2516 Internet www.promega.com PRODUCT USE LIMITATIONS, WARRANTY, DISCLAIMER Promega manufactures products for a number of intended uses. -
The Lactose Operon from Lactobacillus Casei Is Involved in the Transport
www.nature.com/scientificreports OPEN The lactose operon from Lactobacillus casei is involved in the transport and metabolism of the Received: 4 October 2017 Accepted: 26 April 2018 human milk oligosaccharide core-2 Published: xx xx xxxx N-acetyllactosamine Gonzalo N. Bidart1, Jesús Rodríguez-Díaz 2, Gaspar Pérez-Martínez1 & María J. Yebra1 The lactose operon (lacTEGF) from Lactobacillus casei strain BL23 has been previously studied. The lacT gene codes for a transcriptional antiterminator, lacE and lacF for the lactose-specifc phosphoenolpyruvate: phosphotransferase system (PTSLac) EIICB and EIIA domains, respectively, and lacG for the phospho-β-galactosidase. In this work, we have shown that L. casei is able to metabolize N-acetyllactosamine (LacNAc), a disaccharide present at human milk and intestinal mucosa. The mutant strains BL153 (lacE) and BL155 (lacF) were defective in LacNAc utilization, indicating that the EIICB and EIIA of the PTSLac are involved in the uptake of LacNAc in addition to lactose. Inactivation of lacG abolishes the growth of L. casei in both disaccharides and analysis of LacG activity showed a high selectivity toward phosphorylated compounds, suggesting that LacG is necessary for the hydrolysis of the intracellular phosphorylated lactose and LacNAc. L. casei (lacAB) strain defcient in galactose-6P isomerase showed a growth rate in lactose (0.0293 ± 0.0014 h−1) and in LacNAc (0.0307 ± 0.0009 h−1) signifcantly lower than the wild-type (0.1010 ± 0.0006 h−1 and 0.0522 ± 0.0005 h−1, respectively), indicating that their galactose moiety is catabolized through the tagatose-6P pathway. Transcriptional analysis showed induction levels of the lac genes ranged from 130 to 320–fold in LacNAc and from 100 to 200–fold in lactose, compared to cells growing in glucose. -
O-Alkyl Oligoribonucleotides As Antisense Probes (Modified RNA/Afnity Selection/Ribonudeoprotein Couiplexes/Oligonucleotide Synthesis/Biotinylation) ADOLFO M
Proc. Nail. Acad. Sci. USA Vol. 87, pp, 7747-7751, October 1990 Biochemistry 2'-O-Alkyl oligoribonucleotides as antisense probes (modified RNA/afnity selection/ribonudeoprotein couiplexes/oligonucleotide synthesis/biotinylation) ADOLFO M. IRIBARREN*, BRIAN S. SPROAT, PHILIPPE NEUNER*, INGRID SULSTON, URSULA RYDER, AND ANGUS 1. LAMOND European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, D6900 Heidelberg 1, Federal Republic of Germany Communicated by J. A. Steitz, July 3, 1990 (receivedfor review May 1, 1990) ABSTRACT 2'-O-Methyl oligoribonucleotides have re- cently been introduced as antisense probes for studying RNA processing and for affinity purification of RNA-protein com- plexes. To identify RNA analogues with improved properties for antisense analysis, 2'--alkyl oligoribonucleotides were synthesized in which the alkyl moiety was either the three- carbon linear allyl group or the five-carbon branched 3,3- dimethylallyl group. Both these analogues were found to be completely resistant to degradation by either DNA- or RNA- specific nucleases. Use of biotinylated derivatives of the probes to affinity-select ribonucleoprotein particles from crude HeLa cell nuclear extracts showed that the presence of the bulky L i3 3,3-dimethylallyl group significantly reduces affinity selection, -o'r\- .. whereas the allyl derivative binds rapidly and stably to targeted sequences and affinity-selects efficiently. The allyl derivatives also showed an increase in the level of specific binding to targeted sequences compared with 2'-0-methyl probes of iden- tical sequence. These properties indicate that the 2'-0-allyl oligoribonucleotides are particularly well suited for use as HO OR antisense probes. S H Chemically synthesized 2'-O-methyl oligoribonucleotides, as R NH described by Ohtsuka and Morisawa and coworkers (1-6) and by Sproat et al. -
Gene Expression Prokaryotes
Gene Expression Prokaryotes Chapters 19, Genes X 1 • In negative regulation, a repressor protein binds to an operator to prevent a gene from being expressed. • In positive regulation, a transcription factor is required to bind at the promoter in order to enable RNA polymerase to initiate transcription. A repressor stops RNA polymerase from Transcription factors enable RNA polymerase to bind to the initiating promoter Regula(on of Transcrip(on in prokaryotes is a complex and mul(-(ered phenomenon. 3 4 5 6 The lac Operon Has a Second Layer of Control: Catabolite Repression A small molecule inducer, cAMP, converts an activator protein, CRP, to a form that binds the promoter and assists RNA polymerase in initiating transcription. 7 lacZ promoter -loss of consensus: opMmal expression NOT maximal expression – -35 -10 • T82 T84 G78 A65 C54 a45 <--- 17 bp ----> T80 A95 T45 A60 a50 T96 8 lacZ promoter -loss of consensus: opMmal expression NOT maximal expression – -35 -10 • T82 T84 G78 A65 C54 a45 <--- 17 bp ----> T80 A95 T45 A60 a50 T96 9 Promoter Efficiencies Can Be Increased or Decreased by Mutation • Down mutations tend to decrease promoter efficiency, usually decrease conformance to the preferred interactions with the “consensus sequences”, whereas up mutations have the opposite effect. • Mutations in the –35 sequence tend to affect initial binding of RNA polymerase holoenzyme. • Mutations in the –10 sequence tend to affect binding of the holoenzyme or the melting reaction that converts one of the closed complexes to an open complex. Regula(on of Transcrip(on in prokaryotes is a complex and mul(-(ered phenomenon. -
Obligate Anaerobes Catabolic Pathway
Obligate Anaerobes Catabolic Pathway andUnpaying twin-screw. Ely flecks: Chancroid he upstage Jedediah his aunts magnetises acromial tardily. and overall. Canopic Carlos bellies very unprofitably while Jeromy remains tellurous Metabolism may operate under utvikling, obligate anaerobes depend on the following is usually after carbohydrates, benzene biodegradation of defenses Pseudomonas are all oxidase positive. Alternatively, depending on the availability of oxygen. The oxidative removal of lactic acid. The form molecules in organic or anaerobe must be embedded in rat mitochondria in vitro level; this purpose is. Bacteria The Role Of Bacteria In Fermentation Acid Beer Pasteur. Journal of Bone and Joint Surgery. Compare enzyme between catabolic pathways for anaerobes is produced. The obligate aerobes: we use organic compound utilization of obligate anaerobes catabolic pathway. Rabs to anaerobic catabolism of obligate anaerobe. Metabolism of Anaerobic and Aerobic or Facultative bacteria. This pathway begins catabolism pathways are anaerobic bacteria to reference to alcohol or in this pathway requires energy processing in all broth or not. Incorporation of oxygen from water into toluene and benzene during anaerobic fermentative transformation. Obligate anaerobe must be happy to ethyl alcohol fermentation when purified mononuclear enzymes. Catabolic pathways and anaerobic catabolism of anaerobes, where they need for other hand function is. Structure of anaerobic processs involved in a ligases involved in your identity on earth, and commonly used. Obligate anaerobes, the Holmes established that glucose is the precursor of lactate in the brain and that under aerobic conditions, positive for VP. Adding handles to shield the necessary to produce transmembrane trafficking of oxygen atoms are facultative or obligate anaerobes catabolic pathway to the potential activity was already well as the hydrogen is. -
United States Patent (19) 11 Patent Number: 5,338,683 Paoletti (45) Date of Patent: "Aug
USOO5338683A United States Patent (19) 11 Patent Number: 5,338,683 Paoletti (45) Date of Patent: "Aug. 16, 1994 54 VACCINIAVIRUS CONTAINING DNA SEQUENCES ENCODING HERPESVIRUS FOREIGN PATENT DOCUMENTS GLY COPROTEINS 0261940 3/1988 European Pat. Off. 9001546 2/1990 PCT Int'l Appl. 75) Inventor: Enzo Paoletti, Albany, N.Y. OTHER PUBLICATIONS 73) Assignee: Health Research Incorporated, Muller et al (1977) J. Gen. Virol. 38, 135-147. Albany, N.Y. Piccini et al (1987) Meth. Enzymol 153, 545-563. Taylor et al (1988) Vaccine 6, 497-507. * Notice: The portion of the term of this patent Perkus et al (1985) Science 229, 981-984. subsequent to Jul. 29, 2003 has been Allen et al. (1987) J. Virol. 61,2454-2461. disclaimed. Piccini et al., Bioessays (Jun. 1986) vol. 5, No. 6, 248-52, at 248. 21 Appl. No.: 502,834 Elliot et al., J. Gen. Virol. (1991), 72, 1762–79, at 1763. Boyle, D. B. et al., J. Gen. Virol. (1986), 67, 1591-1600. 22 Filed: Apr. 4, 1990 Guo et al., J. of Virology, vol. 64, No. 5, pp. 2399-2406 (1990). Related U.S. Application Data Guo et al., J. of Virology, vol. 63, No. 10, pp. 4189-4198 60 Continuation-in-part of Ser. No. 394,488, Aug. 16, (1989). 1989, abandoned, and Ser. No. 90,209, Aug. 27, 1987, Primary Examiner-Elizabeth C. Weimar abandoned, which is a division of Ser. No. 622,135, Assistant Examiner-Deborah Crouch Jun. 9, 1984, Pat. No. 4,722,848, which is a continua Attorney, Agent, or Firm-Curtis, Morris & Safford tion-in-part of Ser. -
Two Models of Catabolite Repression Signal Transduction
An Investigation of Two Models of Signal Transduction During Catabolite Repression Catabolite repression describes the phenomenon where certain carbon sources in bacterial growth media lead to a reduction of transcription of sensitive operons. In Escherichia coli, the best understood example of catabolite repression involves the lac operon. E. coli will not express the lac operon if glucose is present in the growth media. This is true whether or not lactose is present in the media. Other operons in E. coli are also repressed by glucose including the arabinose operon and the maltose operon. Although glucose is the most studied carbon source capable of catabolite repression in E. coli, it is not the only one capable of triggering repression of these operons. Sucrose, Fructose and other related carbon molecules can also trigger catabolite repression to varying levels. Klug and Cummings includes a discussion of the "classic cAMP" model for catabolite repression. In this model glucose acts by inhibiting the activity of adenylate cyclase. This leads to a drop in cAMP concentrations. At lower concentrations, the cAMP is not available to bind to the catabolite activator protein (CAP). CAP in the absence of cAMP losses affinity for the Cap Binding Site doesn't bind the lac operon. In the absence of CAP binding, the promoter is unable to recruit RNA polymerase to initiate transcription. Therefore, the lac operon is not transcribed in the presence of Glucose. Alternatively, in the absence of glucose, the adenylate cyclase is not inhibited and actively produces cAMP. The cAMP binds to CAP causing it to shift to a conformation with affinity to the Cap Binding Site. -
Research Doctorate School in Biomolecular Sciences Doctorate
BIOS Research Doctorate School in BIOmolecular Sciences Doctorate Course in Molecular Biotechnology PhD Thesis Programmed cell death in the megagametophyte of Araucaria bidwillii Hook. post-germinated seeds Student: Dr. SIMONE CASANI Supervisor: Prof. Luciano Galleschi - TABLE OF CONTENTS - ABSTRACT ...............................................................................................................................................5 LIST OF ABBREVIATIONS ...................................................................................................................8 1. INTRODUCTION ................................................................................................................................9 1.1. PROGRAMMED CELL DEATH ....................................................................................... 9 1.2. THE SIGNIFICANCE OF PROGRAMMED CELL DEATH ........................................ 11 1.3. MOLECULAR MECHANISMS OF APOPTOSIS .......................................................... 12 1.4. CASPASES (CYSTEINE ASPARTATE-SPECIFIC PROTEASES) .............................. 17 1.5. MORPHOLOGICAL AND BIOCHEMICAL FEATURES OF APOPTOSIS ............... 20 1.6. PROGRAMMED CELL DEATH IN PLANTS ................................................................ 22 1.6.1. Defence PCD ............................................................................................................... 23 1.6.2. Developmental PCD ...................................................................................................