DOCSLIB.ORG

(12) United States Patent (10) Patent No.: US 8,182,996 B2 Bergeron Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(12) United States Patent (10) Patent No.: US 8,182,996 B2 Bergeron Et Al USOO8182996 B2 (12) United States Patent (10) Patent No.: US 8,182,996 B2 Bergeron et al. (45) Date of Patent: May 22, 2012 (54) COMPOSITIONS AND METHODS FOR 5,523,217 A 6/1996 Lupski et al. DETECTING IKLEBSIELLA PNEUMONIAE 5,541.308 A * 7/1996 Hogan et al. ................. 536,231 5,574,145 A 1 1/1996 Barry et al. 5,595,874. A 1/1997 Hogan et al. (75) Inventors: Michel G. Bergeron, Quebec (CA); 5,599,665 A 2f1997 Barbieri et al. Maurice Boissinot, Quebec (CA); Ann 5,627,275 A 5, 1997 Ro11 Huletsky, Quebec (CA); Christian 5,652,102 A 7/1997 Fratamico et al. Ménard, Quebec (CA); Marc Ouellette, 5,708, 160 A 1/1998 Goh et al. 5,866,336 A * 2/1999 Nazarenko et al. ............... 435/6 Quebec (CA); Francois J. Picard, 5,994,066 A 1 1/1999 Bergeron et al. Quebec (CA); Paul H. Roy, Quebec 6,001,564. A 12/1999 Bergeron et al. (CA) 6,037,130 A * 3/2000 Tyagi et al. ....................... 435/6 6,582,908 B2 6/2003 Fodor et al. (73) Assignee: Geneohm Sciences Canada Inc., 6,610,836 B1* 8/2003 Breton et al. ................ 536,231 Quebec (CA) 2003. O180733 A1 9/2003 Bergeron et al. 2004/O185478 A1 9/2004 Bergeron et al. 2005, OO42606 A9 2/2005 Bergeron et al. (*) Notice: Subject to any disclaimer, the term of this 2006/026381.0 A1 11/2006 Bergeron et al. patent is extended or adjusted under 35 2007/OOO9947 A1 1/2007 Bergeron et al. U.S.C. 154(b) by 63 days. 2007/0105129 A1 5/2007 Bergeron et al. 2009/0047671 A1 2/2009 Bergeron et al. (21) Appl. No.: 11/842,141 2009.0053702 A1 2/2009 Bergeron et al. 2009.0053703 A1 2/2009 Bergeron et al. 2009.0068641 A1 3/2009 Bergeron et al. (22) Filed: Aug. 21, 2007 2010/0267012 A1 10/2010 Bergeron et al. FOREIGN PATENT DOCUMENTS (65) Prior Publication Data CA 2052822 4f1992 EP O133 288 2, 1985 US 2012/0058487 A1 Mar. 8, 2012 EP O133 671 3, 1985 EP O 272009 6, 1988 Related U.S. Application Data EP O 277 237 A1 8, 1988 EP O 297 291 B1 1, 1989 (63) Continuation of application No. 1 1/236,785, filed on EP O 337 896 10, 1989 Sep. 27, 2005, which is a continuation of application EP O 364. 255 4f1990 No. 10/089,177, filed as application No. EP O 438 115 A2 7, 1991 PCT/CAO0/01 150 on Sep. 28, 2000, now abandoned. EP O133 671 7, 1991 (Continued) (30) Foreign Application Priority Data OTHER PUBLICATIONS Sep. 28, 1999 (CA) ...................................... 2283458 Bucket al. Biotechniques, 1999, 27:528-536.* May 19, 2000 (CA) ...................................... 2307010 Christensen et al. FEMS Microbiology letters. 1998. 161: 89-96.* Abdulkoarim, F. et al., “Homologous Recombination between that of Genes of Salmonella typhirmulum, ” J. Mol. Biol. 260.506-522. (51) Int. Cl. Academic Press (1996). CI2O I/68 (2006.01) Altschal, et al. “Basic Local Alignment Search Tool.” J. Mol.Biol. CI2P 19/34 (2006.01) 215: 403-410 (1990). C7H 2L/02 (2006.01) Amann, R. et al., “B-Subunit of ATP-synthase; a Useful Marker for C7H 2L/04 (2006.01) Studying the Phylogenetic Relationship of Eubacteria.” Journal of General tollosobiotogy 134: 22I5-2821, Soddy for General (52) U.S. Cl. ...... 435/6.15:435/6.1; 435/6.11: 435/6.12: Microbiology (1988). 435/91.2:536/23.7:536/24.32:536/24.33 Anborgh, P. et al., “New Antibiotic that acts specifically on the (58) Field of Classification Search ........................ None GTP-bound form of elongation FactorTu.” The EMBO.J., vol. 10, No. See application file for complete search history. 4:779-784, IRL Press (1991). (56) References Cited (Continued) Primary Examiner — Carla Myers U.S. PATENT DOCUMENTS (74) Attorney, Agent, or Firm — Knobbe Martens Olson & 4,816,389 A 3, 1989 Sansonetti et al. Bear 5,030,556 A 7, 1991 Beaulieu et al. 5,041,372 A 8/1991 Lampel et al. (57) ABSTRACT 5,084,565 A 1/1992 Parodos et al. Four highly conserved genes, encoding translation elongation 5,089,386 A 2f1992 Stackebrandt et al. factor Tu, translation elongation factor G, the catalytic Sub 5,162,199 A 11/1992 Stern et al. unit of proton-translocating ATPase and the RecA recombi 5,232,831 A 8, 1993 Milliman et al. 5,292.874 A 3, 1994 Milliman nase, are used to generate species-specific, genus-specific, 5,298,392 A 3, 1994 Atlas et al. family-specific, group-specific and universal nucleic acid 5,334.501 A 8, 1994 Adams et al. probes and amplification primers to rapidly detect and iden 5,389,513 A 2/1995 Baquero et al. tify algal, archaeal, bacterial, fungal and parasitical patho 5,401,631 A 3, 1995 Lane et al. gens from clinical specimens for diagnosis. The detection of 5.437,978 A 8, 1995 Ubukata et al. associated antimicrobial agents resistance and toxin genes are 5,472,843. A 12/1995 Milliman 5,476,929 A 12/1995 Briles et al. also under the scope of the present invention. 5,523,205 A 6, 1996 Cossart et al. 9 Claims, 17 Drawing Sheets US 8,182,996 B2 Page 2 FOREIGN PATENT DOCUMENTS Brenner, D.J. et al., “Polynucleotide Sequence Divergence Among EP O 466 251 1, 1992 Strainsof Escherichia coli and Closely Related Organisms,” Journal EP O466 251 1, 1992 of Bacteriology, vol. 109, No. 3: 953-965, American Society for EP O 527 628 A1 2, 1993 Microbiology (1972). EP O337 896 7, 1993 Brenner, D.J. et al., “Enterobacter gergoviae sp. nov: a New Species EP O 577 523 1, 1994 ofEnterobacteriacae Found in Clinical Specimens and the Environ EP O 630973 A2 12, 1994 EP O 652291 A1 5, 1995 ment.” International Journal of Systematic Bacteriology, vol.30, No. EP O 695 803 A2 2, 1996 1: 1-6, Society for General Microbiology (1980). EP O 761815 3, 1997 Brenner D.J. et al., “Attempts to Classify Herbicola Group— EP O 786 519 7/1997 Enteroacter agglomerans Strains by Deoxyribonucleic Acid EP O 804 616 11, 1997 Hybridzation and Phenotype Tests.” International Journal of FR 2584419 A1 1, 1987 SystematicBacteriology, vol. 34, No. 1: 4-55, Society for General FR 2599743 A1 12, 1987 Microbiology (1984). FR 2636O75 3, 1990 FR 2685,334 A1 6, 1993 Brenner, D.J. et al., “Enterobacter asburiae sp. nov., a New Species FR 2686604 A1 7, 1993 Found in Clinical Specimens, and Reassignment of Erwinia dis FR 2699539 A1 6, 1994 solvens and Erwinia nimipressuralis to the Genus Enterobacter as JP 06-054700 3, 1994 Enterobacter dissolvens comb, nov. and Enterobacter nimipressoalis JP 06-090798 4f1994 comb. nov.” Journal of Clinical Microbiology, vol. 23, No. 6: 114 JP 06-165681 6, 1994 120, American Society for Microbiology (1986). JP O7-O67657 3, 1995 JP O7-209294 8, 1995 Brenner, D.J., “Introduction to the Family Enterobacteriaceas, in WO WO 90,14444 11, 1990 Balows, A. et al: “The Prokaryotes, A Handbook on the Biology of WO WO91,08305 6, 1991 Bacteria: Ecophysiology, Isolation, Identification, Applications'. WO WO91f11531 8, 1991 2nd Edition, vol. III, Chapter 141, p. 2673-2695,Springer-verlag WO WO91f16454 10, 1991 (1992). WO WO91, 18926 12/1991 Brenner, D.J. Additional Genera of Enterobacteriaceae', in Balows, WO WO92fO3455 3, 1992 A. et al. “The Prokaryotes, A Handbook on the Biology of WO WO92/11273 7, 1992 WO WO92, 14488 9, 1992 Bacteria: Ecophysiology, Isolation, Identification, Applications'. 2nd WO WO93,03186 2, 1993 Edition,vol. III, Chapter 155, p. 2922-2937. Springer-Verlag (1992). WO WO93/1224.5 6, 1993 Brenner. D.J., “Calssification of Citrabacteria by DNA Hybridiza WO WO94f02645 2, 1994 tion: Designation of Citrobacter farneri sp. nov. Citrobacter WO WO94f17205 8, 1994 youngae sp. nov. Citrobacter braolai sp. nov. Citrobacter WO WO95/OO650 1, 1995 werkmaniisp. nov. Citrabactersedlakfisp. nov. and Three Unnamed WO WO95/09025 4f1995 Citrobacter Genomospecies.” International Journal of Systematic WO WO95/20055 7, 1995 WO WO 96.00298 1, 1996 Bacteriology, vol.43, No. 4645-658, Society for General Microbiol WO WO96,02648 2, 1996 ogy (1993). WO WO96,08582 3, 1996 Brenner, D.J., “Biochemical Identification of Citrobacter Species WO WO96, 18745 6, 1996 Defined by DNA Hybridization and Description of Citrobacter gil WO WO 98.2O157 5, 1998 lenil sp. nov. (Formerly Citrobacter Genomospecies 10) and WO WO99,24059 5, 1999 Citrobacter murltriae sp. nov. (Formerly Citrobacter Genomspecies WO WOOOf 14274 3, 2000 II)” Journal of Clinical Microbiology, vol. 37, No. 8: 2619-2624, WO WOO1,23604 4/2001 American Society for Microbiology (1999). WO WO 2004/055205 T 2004 Caldas, T.D. et al., “Chaperone Properties of Bacterial Elongation OTHER PUBLICATIONS FactorEF-Tu.” The Journal of Biological Chemistry, vol. 273, No. 19: Anderson, R.C., et al. (1998). “Micro Total Analysis Systems 98.” 11478-1 1482, American Society for Biochemistry and Molecular Kluwer Academic Publishers, Dordreoht, The Netherlands, pp. Biology (1998). 11-16, 221-224. Carrino, J.J., et al. (1997), “Ligation-Based Nucleic Acid Probe Belay, N. et al., “Methanogenic Bacteria from Human Dental Methods,” in Nucleic Acid Amplification Technology. Application to Plaque.” Applied and Environmental Microbiology, vol. 54, No. 2: Disease Diagnosis, Eaton Publishing, Boston, MA. pp. 61-123. 600-603, American Society for Microbiology (1988). Cha, R.S., and Thilly, W.G. (1995) “Specificity, Efficienty, and Bercovier, H. et al., “Intra- and Interspecies Relatedness of Yersinia Fidelity of PCR” in PCR Primer; A Laboratory Manual, Dieffenbach, pestis by DNA Hybridization and Its Relationship to Yersinia C.W., and Dveksler, G.S., eds.
Load more

Recommended publications
  • Composition and Diversity of Endophytic Bacterial Communities in Noni (Morinda Citrifolia L.) Seeds
    International Journal of Agricultural Policy and Research Vol.2 (3), pp. 098-104, March 2014 Available online at http://www.journalissues.org/ijapr/ © 2014 Journal Issues ISSN 2350-1561 Original Research Paper Composition and diversity of endophytic bacterial communities in noni (Morinda citrifolia L.) seeds Accepted 14 February, 2014 *1Liu Yang, 1Yao Su , 2Xu The objective of this study is to investigate the endophytic bacterial Pengpeng , 1Cao Yanhua , communities in Noni (Morinda citrifolia L.) seeds. By using high-throughput 1 1 sequencing (HTS) technique, a research on the diversity of endophytic Li Jinxia , Wang bacterial communities in Noni seed samples was conducted by this paper, 3 Jiemiao , Tan Wangqiao, which were collected from four planting locations in the introduction and 1Cheng Chi cultivation base of Hainan Noni Biological Engineering Development Co., Ltd. in Sanya. A total of 268159 sequences and 2870 Operational Taxonomic Units 1 China National Research Institute (OTUs) were obtained from the seed samples, which were classified into N1, of Food and Fermentation N2, N3 and N4, through HTS by bioinformatics analysis. The results showed Industries, Beijing 100015, People’s that there was a good consistency between bacterial community structure and Republic of China distribution of dominant genus in all samples. A mount of 10 OTUs of the most 2 Beijing Geneway Technology Co., Ltd., Beijing 100010, People’s abundance associated with the four sample libraries were found to be related Republic of China. to Pelomonas sp., Ochrobactrum intermedium, Kinneretia sp., Serratia sp., 3 Hainan Noni Biological Paucibacter sp., Leptothrix sp., Inhella sp., Ewingella sp., Thiomonas sp. and Engineering Development Co., Ltd., Massilia sp..This study has laid a solid foundation for further study in Haikou 570125, People’s Republic beneficial microbes, which would help to improve the growth and efficacy of of China.
    [Show full text]
  • ABSTRACT Title of Dissertation: IDENTIFICATION, LIFE HISTORY
    ABSTRACT Title of Dissertation: IDENTIFICATION, LIFE HISTORY, AND ECOLOGY OF PERITRICH CILIATES AS EPIBIONTS ON CALANOID COPEPODS IN THE CHESAPEAKE BAY Laura Roberta Pinto Utz, Doctor of Philosophy, 2003 Dissertation Directed by: Professor Eugene B. Small Department of Biology Adjunct Professor D. Wayne Coats Department of Biology and Smithsonian Environmental Research Center Epibiotic relationships are a widespread phenomenon in marine, estuarine and freshwater environments, and include diverse epibiont organisms such as bacteria, protists, rotifers, and barnacles. Despite its wide occurrence, epibiosis is still poorly known regarding its consequences, advantages, and disadvantages for host and epibiont. Most studies performed about epibiotic communities have focused on the epibionts’ effects on host fitness, with few studies emphasizing on the epibiont itself. The present work investigates species composition, spatial and temporal fluctuations, and aspects of the life cycle and attachment preferences of Peritrich epibionts on calanoid copepods in Chesapeake Bay, USA. Two species of Peritrich ciliates (Zoothamnium intermedium Precht, 1935, and Epistylis sp.) were identified to live as epibionts on the two most abundant copepod species (Acartia tonsa and Eurytemora affinis) during spring and summer months in Chesapeake Bay. Infestation prevalence was not significantly correlated with environmental variables or phytoplankton abundance, but displayed a trend following host abundance. Investigation of the life cycle of Z. intermedium suggested that it is an obligate epibiont, being unable to attach to non-living substrates in the laboratory or in the field. Formation of free-swimming stages (telotrochs) occurs as a result of binary fission, as observed for other peritrichs, and is also triggered by death or molt of the crustacean host.
    [Show full text]
  • PROTISTAS MARINOS Viviana A
    PROTISTAS MARINOS Viviana A. Alder INTRODUCCIÓN plantas y animales. Según este esquema básico, a las plantas les correspondían las características de En 1673, el editor de Philosophical Transac- ser organismos sésiles con pigmentos fotosinté- tions of the Royal Society of London recibió una ticos para la síntesis de las sustancias esenciales carta del anatomista Regnier de Graaf informan- para su metabolismo a partir de sustancias inor- do que un comerciante holandés, Antonie van gánicas (nutrición autótrofa), y de poseer células Leeuwenhoek, había “diseñado microscopios rodeadas por paredes de celulosa. En oposición muy superiores a aquéllos que hemos visto has- a las plantas, les correspondía a los animales los ta ahora”. Van Leeuwenhoek vendía lana, algo- atributos de tener motilidad activa y de carecer dón y otros materiales textiles, y se había visto tanto de pigmentos fotosintéticos (debiendo por en la necesidad de mejorar las lentes de aumento lo tanto procurarse su alimento a partir de sustan- que comúnmente usaba para contar el número cias orgánicas sintetizadas por otros organismos) de hebras y evaluar la calidad de fibras y tejidos. como de paredes celulósicas en sus células. Así fue que construyó su primer microscopio de Es a partir de los estudios de Georg Gol- lente única: simple, pequeño, pero con un poder dfuss (1782-1848) que estos diminutos organis- de magnificación de hasta 300 aumentos (¡diez mos, invisibles a ojo desnudo, comienzan a ser veces más que sus precursores!). Este magnífico clasificados como plantas primarias
    [Show full text]
  • Protist Phylogeny and the High-Level Classification of Protozoa
    Europ. J. Protistol. 39, 338–348 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/ejp Protist phylogeny and the high-level classification of Protozoa Thomas Cavalier-Smith Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK; E-mail: [email protected] Received 1 September 2003; 29 September 2003. Accepted: 29 September 2003 Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Pro- tozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eu- karyotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the an- cestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Re- taria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Cilio- phora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane).
    [Show full text]
  • Acteurs Et Mécanismes Des Bio-Transformations De L'arsenic, De
    Acteurs et mécanismes des bio-transformations de l’arsenic, de l’antimoine et du thallium pour la mise en place d’éco-technologies appliquées à la gestion d’anciens sites miniers Elia Laroche To cite this version: Elia Laroche. Acteurs et mécanismes des bio-transformations de l’arsenic, de l’antimoine et du thallium pour la mise en place d’éco-technologies appliquées à la gestion d’anciens sites miniers. Sciences de la Terre. Université Montpellier, 2019. Français. NNT : 2019MONTG048. tel-02611018 HAL Id: tel-02611018 https://tel.archives-ouvertes.fr/tel-02611018 Submitted on 18 May 2020 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 MONT PELLIER En Sciences de l’Eau École doctorale GAIA Unité de recherche Hydrosciences Montpellier UMR 5569 Unité de recherche GME (Géomicrobiologie et Monitoring Environnemental) du BRGM, Orléans Acteurs et mécanismes des bio-transformations de l’arsenic, de l’antimoine et du thallium pour la mise en place d’éco -technologies appliquées à la gestion d’anciens
    [Show full text]
  • Nanosims and Tissue Autoradiography Reveal Symbiont Carbon fixation and Organic Carbon Transfer to Giant Ciliate Host
    The ISME Journal (2018) 12:714–727 https://doi.org/10.1038/s41396-018-0069-1 ARTICLE NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate host 1 2 1 3 4 Jean-Marie Volland ● Arno Schintlmeister ● Helena Zambalos ● Siegfried Reipert ● Patricija Mozetič ● 1 4 2 1 Salvador Espada-Hinojosa ● Valentina Turk ● Michael Wagner ● Monika Bright Received: 23 February 2017 / Revised: 3 October 2017 / Accepted: 9 October 2017 / Published online: 9 February 2018 © The Author(s) 2018. This article is published with open access Abstract The giant colonial ciliate Zoothamnium niveum harbors a monolayer of the gammaproteobacteria Cand. Thiobios zoothamnicoli on its outer surface. Cultivation experiments revealed maximal growth and survival under steady flow of high oxygen and low sulfide concentrations. We aimed at directly demonstrating the sulfur-oxidizing, chemoautotrophic nature of the symbionts and at investigating putative carbon transfer from the symbiont to the ciliate host. We performed pulse-chase incubations with 14C- and 13C-labeled bicarbonate under varying environmental conditions. A combination of tissue autoradiography and nanoscale secondary ion mass spectrometry coupled with transmission electron microscopy was used to fi 1234567890();,: follow the fate of the radioactive and stable isotopes of carbon, respectively. We show that symbiont cells x substantial amounts of inorganic carbon in the presence of sulfide, but also (to a lesser degree) in the absence of sulfide by utilizing internally stored sulfur. Isotope labeling patterns point to translocation of organic carbon to the host through both release of these compounds and digestion of symbiont cells. The latter mechanism is also supported by ultracytochemical detection of acid phosphatase in lysosomes and in food vacuoles of ciliate cells.
    [Show full text]
  • Bakterielle Diversität in Einer Wasserbehandlungsanlage Zur Reini- Gung Saurer Grubenwässer
    Bakterielle Diversität in einer Wasserbehandlungsanlage zur Reini- gung saurer Grubenwässer E. Heinzel1, S. Hedrich1, G. Rätzel2, M. Wolf2, E. Janneck2, J. Seifert1, F. Glombitza2, M. Schlömann1 1AG Umweltmikrobiologie, IÖZ, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, [email protected], 2Fa. G.E.O.S. Ingenieurgesellschaft mbH, Gewerbepark „Schwarze Kiefern“, 09633 Halsbrücke In einer Versuchsanlage zur Gewinnung von Eisenhydroxysulfaten durch biologische Oxidation von zweiwertigem Eisen wurde die Zusammensetzung der bakteriellen Lebensgemeinschaft mit moleku- largenetischen Methoden analysiert. Die 16S rDNA-Klonbank wurde von zwei Sequenztypen, denen 68 % der Klone zugeordnet werden konnten, dominiert. Ein Sequenztyp kann phylogenetisch in die Ordnung der Nitrosomonadales eingeordnet werden, zu deren Vertretern sowohl chemo-heterotrophe Bakterien als auch autotrophe Eisen und Ammonium oxidierende Bakterien gehören. Der zweite Se- quenztyp ist ähnlich zu „Ferrimicrobium acidiphilum“, einem heterotrophen Eisenoxidierer. The microbial community of a pilot plant for the production of iron hydroxysulfates by biological oxidation of ferrous iron was studied using molecular techniques. The 16S rDNA clone library was dominated by two sequence types, to which 68 % of all clones could be assigned. One sequence type is phylogenetically classified to the order of Nitrosomonadales. Both chemoheterotrophic bacteria and autotrophic iron or ammonium oxidizing bacteria belong to this order. The second sequence type is related to “Ferrimicrobium acidiphilum”, a heterotrophic iron oxidizing bacteria. 1 Einleitung und Projektziel die biologische Oxidationskapazität zu optimie- ren. Zur Gewährleistung einer konstanten Pro- Stark eisenhaltige und saure Bergbauwässer aus duktqualität muss die Oxidation sicher be- Tagebaufolgelandschaften bedingen einen erheb- herrscht und gesteuert werden können. Dies er- lichen Sanierungsaufwand. Die konventionelle fordert die Analyse der mikrobiellen Lebens- Reinigung dieser Wässer findet durch pH- gemeinschaft.
    [Show full text]
  • Advances in Applied Microbiology, Voume 49 (Advances in Applied
    ADVANCES IN Applied Microbiology VOLUME 49 ThisPageIntentionallyLeftBlank ADVANCES IN Applied Microbiology Edited by ALLEN I. LASKIN JOAN W. BENNETT Somerset, New Jersey New Orleans, Louisiana GEOFFREY M. GADD Dundee, United Kingdom VOLUME 49 San Diego New York Boston London Sydney Tokyo Toronto This book is printed on acid-free paper. ∞ Copyright C 2001 by ACADEMIC PRESS All Rights Reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the Publisher. The appearance of the code at the bottom of the first page of a chapter in this book indicates the Publisher’s consent that copies of the chapter may be made for personal or internal use of specific clients. This consent is given on the condition, however, that the copier pay the stated per copy fee through the Copyright Clearance Center, Inc. (222 Rosewood Drive, Danvers, Massachusetts 01923), for copying beyond that permitted by Sections 107 or 108 of the U.S. Copyright Law. This consent does not extend to other kinds of copying, such as copying for general distribution, for advertising or promotional purposes, for creating new collective works, or for resale. Copy fees for pre-2000 chapters are as shown on the title pages. If no fee code appears on the title page, the copy fee is the same as for current chapters. 0065-2164/01 $35.00 Academic Press A division of Harcourt, Inc. 525 B Street, Suite 1900, San Diego, California 92101-4495, USA http://www.academicpress.com Academic Press Harcourt Place, 32 Jamestown Road, London NW1 7BY, UK http://www.academicpress.com International Standard Serial Number: 0065-2164 International Standard Book Number: 0-12-002649-X PRINTED IN THE UNITED STATES OF AMERICA 010203040506MM987654321 CONTENTS Microbial Transformations of Explosives SUSAN J.
    [Show full text]
  • Studies on Microbial Biodiversity of Acidophilic Heterotrophs in Acid Rock Drainage Samples of Eastern Himalaya
    Studies on microbial biodiversity of acidophilic heterotrophs in Acid Rock Drainage samples of Eastern Himalaya THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN SCIENCE (BIOTECHNOLOGY) OF THE UNIVERSITY OF NORTH BENGAL Suparna CBiiowa( Microbial Biotechnology Laboratory Department of Biotechnology University of North Bengal 2011 'lTie onfy way offindi11f1 tlie Bmits oftlie possi6(e is 6y going 6eyontf tfiem into tlie impossi6fe. -l/.rtfiur C Cfar&e Ae/CNOWI.B'DQBMBN7S This is a solemn opportunity to express my veneration to the entire magnanimous fraternity to those who directly or indirectly have contributed or associated to this work and made it possible. No words or mere accolades are big enough to express my gratitude towards, the person who stood rock solid beside me during the entire tenure of my research career, yes he is my guide, my supervisor, my guardian Dr. Ranadhir Chakraborty. His guidance, continuous inspiration and boundless optimism encouraged me to pull the worl< and give it a meaningful conclusion. Not even a part of the work would have reached its culmination without him. I owe special thanks and gratitude to my teachers Mr. T. Gopalan and Mr. Balwinder Singh Bajwa, who seeded and cultured the scientific research aptitude within me. · Right from my first day in the Department o(Biot~chnology, I had the opportunity to gain some good advice and wisdom from my teachers Dr. Shilpi Ghosh and Dr. Dipanwita Saha. I express my sincere thanks to my teachers Prof. B.N. Chakraborty, Prof. P.K. Sarkar, Prof. A.P. Das, Prof. Usha Chakraborty, Prof.
    [Show full text]
  • Exceptional Species Richness of Ciliated Protozoa in Pristine Intertidal Rock Pools
    MARINE ECOLOGY PROGRESS SERIES Vol. 335: 133–141, 2007 Published April 16 Mar Ecol Prog Ser Exceptional species richness of ciliated Protozoa in pristine intertidal rock pools Genoveva F. Esteban*, Bland J. Finlay School of Biological & Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK ABSTRACT: Marine intertidal rock pools can be found almost worldwide but little is known about the microscopic life forms they support, or the significance of regular tidal inundation. With regard to ciliated Protozoa in rock pools, little progress has been achieved since 1948, when the question was first posed as to how a community of ciliates can remain relatively constant in a rock pool that is flushed twice a day. Here we show that local ciliate species richness is very high and that it may per- sist over time. This elevated species richness can be attributed to ciliate immigration with the in- coming tide, and also to the resident ciliate community that withstands tidal flushing. A 15 cm deep intertidal rock-pool no bigger than 1 m2 on the island of St. Agnes (Scilly Islands, UK) contained at least 85 ciliate species, while a 20 cm-deep rock pool with roughly the same area on Bryher (also in the Scilly Islands) yielded 75 species. More than 20% of the global number of described marine inter- stitial ciliate species was recorded from these rock pools. We explore the paradox of a persisting com- munity assembly living in an ecosystem that is physically highly dynamic. KEY WORDS: Marine ciliates · Marine biodiversity · Intertidal rock pools Resale or republication not permitted without written consent of the publisher INTRODUCTION MATERIALS AND METHODS The question of how a community of ciliate species can Sampling sites.
    [Show full text]
  • Extremophiles-Basic Concepts
    CONTENTS CONTENTS EXTREMOPHILES Extremophiles - Volume 1 No. of Pages: 396 ISBN: 978-1-905839-93-3 (eBook) ISBN: 978-1-84826-993-4 (Print Volume) Extremophiles - Volume 2 No. of Pages: 392 ISBN: 978-1-905839-94-0 (eBook) ISBN: 978-1-84826-994-1 (Print Volume) Extremophiles - Volume 3 No. of Pages: 364 ISBN: 978-1-905839-95-7 (eBook) ISBN: 978-1-84826-995-8 (Print Volume) For more information of e-book and Print Volume(s) order, please click here Or contact : [email protected] ©Encyclopedia of Life Support Systems (EOLSS) EXTREMOPHILES CONTENTS VOLUME I Extremophiles: Basic Concepts 1 Charles Gerday, Laboratory of Biochemistry, University of Liège, Belgium 1. Introduction 2. Effects of Extreme Conditions on Cellular Components 2.1. Membrane Structure 2.2. Nucleic Acids 2.2.1. Introduction 2.2.2. Desoxyribonucleic Acids 2.2.3. Ribonucleic Acids 2.3. Proteins 2.3.1. Introduction 2.3.2. Thermophilic Proteins 2.3.2.1. Enthalpically Driven Stabilization Factors: 2.3.2.2. Entropically Driven Stabilization Factors: 2.3.3. Psychrophilic Proteins 2.3.4. Halophilic Proteins 2.3.5. Piezophilic Proteins 2.3.5.1. Interaction with Other Proteins and Ligands: 2.3.5.2. Substrate Binding and Catalytic Efficiency: 2.3.6. Alkaliphilic Proteins 2.3.7. Acidophilic Proteins 3. Conclusions Extremophiles: Overview of the Biotopes 43 Michael Gross, University of London, London, UK 1. Introduction 2. Extreme Temperatures 2.1. Terrestrial Hot Springs 2.2. Hot Springs on the Ocean Floor and Black Smokers 2.3. Life at Low Temperatures 3. High Pressure 3.1.
    [Show full text]
  • Zoologica Scripta
    中国科技论文在线 http://www.paper.edu.cn Zoologica Scripta Molecular phylogeny of three ambiguous ciliate genera: Kentrophoros, Trachelolophos and Trachelotractus (Alveolata, Ciliophora) SHAN GAO,MICHAELA C. STRU¨ DER-KYPKE,KHALED A. S. AL-RASHEID,XIAOFENG LIN &WEIBO SONG Submitted: 12 May 2009 Gao, S., Stru¨der-Kypke, M.C., Al-Rasheid, K.A.S., Lin, X. & Song, W. (2010). Molecular Accepted: 31 October 2009 phylogeny of three ambiguous ciliate genera: Kentrophoros, Trachelolophos and Trachelotractus doi:10.1111/j.1463-6409.2010.00416.x (Alveolata, Ciliophora).—Zoologica Scripta, 39, 305–313. Very few molecular studies on the phylogeny of the karyorelictean ciliates have been car- ried out because data of this highly ambiguous group are extremely scarce. In the present study, we sequenced the small subunit ribosomal RNA genes of three morphospecies rep- resenting two karyorelictean genera, Kentrophoros, Trachelolophos, and one haptorid, Trache- lotractus, isolated from the South and East China Seas. The phylogenetic trees constructed using Bayesian inference, maximum likelihood, maximum parsimony and neighbor-joining methods yielded essentially similar topologies. The class Karyorelictea is depicted as a monophyletic clade, closely related to the class Heterotrichea. The generic concept of the family Trachelocercidae is confirmed by the clustering of Trachelolophos and Tracheloraphis with high bootstrap support; nevertheless, the order Loxodida is paraphyletic. The transfer of the morphotype Trachelocerca entzi Kahl, 1927 to the class Litostomatea and into the new haptorid genus Trachelotractus, as suggested by previous researchers based on morpho- logical studies, is consistently supported by our molecular analyses. In addition, the poorly known species Parduczia orbis occupies a well-supported position basal to the Geleia clade, justifying the separation of these genera from one another.
    [Show full text]