Dem-fm.qxd 10/9/03 6:40 PM Page i The Desk Encyclopedia of Microbiology Dem-fm.qxd 10/9/03 6:40 PM Page ii Dem-fm.qxd 10/9/03 6:40 PM Page iii The Desk Encyclopedia of Microbiology Editor Moselio Schaechter Consulting Editor Joshua Lederberg Amsterdam Boston Heidelberg Paris San Diego San Francisco London New York Singapore Sydney Oxford Tokyo Dem-fm.qxd 10/9/03 6:40 PM Page iv This book is printed on acid-free paper Copyright © 2004, Elsevier Ltd All rights reserved No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means electronic, mechanical, photocopying, recording or otherwise, without the prior written permission of the publisher Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone: (ϩ44) 1865 843830, fax: (ϩ44) 1865 853333, e-mail: permissions@elsevier.co.uk You may also complete your request on-line via the Elsevier homepage (http://www.elsevier.com), by selecting ‘Customer Support’ and then ‘Obtaining Permissions’ Elsevier Academic Press 525 B Street, Suite 1900, San Diego, California 92101-4495, USA http://www.elsevier.com Elsevier Academic Press 84 Theobald’s Road, London WC1X 8RR, UK http://www.elsevier.com British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library Library of Congress Catalog Number: 2002114100 ISBN 0-12-621361-5 Printed and bound in China 03 04 05 06 07 08 Dem-fm.qxd 10/9/03 6:40 PM Page v Contents Contributors 10 11 12 13 14 x Preface xvii General websites xviii Adhesion, Bacterial Matthew A Mulvey and Scott J Hultgren Agrobacterium and plant cell transformation Peter J Christie 10 Antibiotic resistance in bacteria Julian Davies and Vera Webb 25 Antifungal agents Ana Espinel-Ingroff 47 Antisense RNAs Andrea Denise Branch 68 Antiviral agents Richard J Whitley 84 Archaea Paul Blum and Vidula Dikshit 108 Attenuation, Transcriptional Charles Yanofsky 117 Bacillus subtilis, Genetics Kevin M Devine 126 Bacteriophages Hans-Wolfgang Ackermann 135 Biocides (Nonpublic health, Nonagricultural antimicrobials) Mohammad Sondossi 147 Biofilms and biofouling Karen T Elvers and Hilary M Lappin-Scott 161 Biological warfare James A Poupard and Linda A Miller 168 Bioluminescence, Microbial J Woodland Hastings 180 v Dem-fm.qxd 10/9/03 6:40 PM Page vi vi 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 contents Bioreactors Larry E Erickson 189 Bioremediation Joseph B Hughes, C Nelson Neale, and C Herb Ward 196 Biosensors Yoko Nomura and Isao Karube 216 Cell membrane: structure and function Robert J Kadner 222 Cell Walls, Bacterial Joachim-Volker Höltje 239 Chemotaxis Jeff Stock and Sandra Da Re 251 Chromosome, Bacterial Karl Drlica and Arnold J Bendich 259 Conjugation, Bacterial Laura S Frost 271 Crystalline bacterial cell surface layers (S layers) Uwe B Sleytr and Paul Messner 286 Culture collections and their databases Mary K B Berlyn 294 Developmental processes in bacteria Yves V Brun 314 Diversity, Microbial Charles R Lovell 326 DNA repair Lawrence Grossman 340 DNA replication James A Hejna and Robb E Moses 350 DNA restriction and modification Noreen E Murray 358 DNA sequencing and genomics Brian A Dougherty 371 Ecology, Microbial Michael J Klug and David A Odelson 381 Emerging infections David L Heymann 387 Energy transduction processes: from respiration to photosynthesis Stuart J Ferguson 394 Enteropathogenic bacteria Farah K Bahrani-Mougeot and Michael S Donnenberg 403 Escherichia coli and Salmonella, Genetics K Brooks Low 415 Dem-fm.qxd 10/9/03 6:40 PM Page vii contents 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 vii Exotoxins Joseph T Barbieri 427 Extremophiles Ricardo Cavicchioli and Torsten Thomas 436 Fimbriae, Pili Matthew A Mulvey, Karen W Dodson, Gabriel E Soto, and Scott J Hultgren 454 Flagella Shin-Ichi Aizawa 470 Food-borne illnesses David W K Acheson 480 Fungal infections, Cutaneous Peter G Sohnle and David K Wagner 499 Fungal infections, Systemic Arturo Casadevall 507 Gastrointestinal microbiology T G Nagaraja 514 Genetically modified organisms: guidelines and regulations for research Sue Tolin and Anne Vidaver 526 Genomes, Mapping of Bacterial J Guespin-Michel and F Joset 536 Germ-free animal techniques Bernard S Wostmann 547 Gram-negative anaerobic pathogens Arthur O Tzianabos, Laurie E Comstock, and Dennis L Kasper 554 Gram-negative cocci, Pathogenic Emil C Gotschlich 562 Heat stress Christophe Herman and Carol A Gross 574 Horizontal transfer of genes between microorganisms Jack A Heinemann 582 Human immunodeficiency virus Luc Montagnier 591 Identification of bacteria, Computerized Trevor N Bryant 602 Industrial fermentation processes Thomas M Anderson 613 Insect’s symbiotic microorganisms A E Douglas 626 Iron metabolism Charles F Earhart 637 Lipopolysaccharides Chris Whitfield 645 Dem-fm.qxd 10/9/03 6:40 PM Page viii viii 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 contents Methanogenesis Kevin R Sowers 659 Methylotrophy J Colin Murrell and Ian R McDonald 680 Nitrogen cycle Roger Knowles 690 Nitrogen fixation L David Kuykendall, Fawzy M Hashem, Robert B Dadson, and Gerald H Elkan 702 Nodule formation in legumes Peter H Graham 715 Nutrition of microorganisms Thomas Egli 725 Oral microbiology Ian R Hamilton and George H Bowden 739 Osmotic stress Douglas H Bartlett and Mary F Roberts 754 Outer membrane, Gram-negative bacteria Mary J Osborn 767 Oxidative stress Pablo J Pomposiello and Bruce Demple 775 pH Stress Joan L Slonczewski 781 Plant pathogens George N Agrios 789 Plasmids, Bacterial Christopher M Thomas 808 Polymerase chain reaction (PCR) Carol J Palmer and Christine Paszko-Kolva 824 Prions Christine Musahl and Adriano Aguzzi 829 Protein secretion Donald B Oliver and Jorge Galan 842 Quorum sensing in gram-negative bacteria Clay Fuqua 859 Recombinant DNA, Basic procedures Judith W Zyskind 870 Sexually transmitted diseases Jane A Cecil and Thomas C Quinn 879 Skin microbiology Morton N Swartz 899 Soil microbiology Kate M Scow 914 Dem-fm.qxd 10/9/03 6:40 PM Page ix contents 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 Index ix SOS response Kevin W Winterling 927 Space flight, effects on microorganisms D L Pierson and S K Mishra 934 Sporulation Patrick J Piggot 942 Starvation, Bacterial A C Matin 951 Strain improvement Sarad Parekh 960 Sulfur cycle Piet Lens, Marcus Vallero, and Look Hulshoff Pol 974 Transcriptional regulation in prokaryotes Orna Amster-Choder 984 Transduction: host DNA transfer by bacteriophages Millicent Masters 1000 Transformation, Genetic Brian M Wilkins and Peter A Meacock 1012 Transposable elements Peter M Bennett 1025 Two-component systems Alexander J Ninfa and Mariette R Atkinson 1042 Vaccines, Bacterial Susan K Hoiseth 1053 Vaccines, Viral Ann M Arvin 1063 Viruses Sondra Schlesinger and Milton J Schlesinger 1071 Viruses, Emerging Stephen S Morse 1084 Yeasts Graeme M Walker 1102 1115 Dem-ind.qxd 10/13/03 3:39 PM Page 1136 1136 Nitrosoguanidine (NTG), 964 Nitrosomonas europaea, 695 NO2Ϫ oxidation, 695–6 nod factors, 718 definition, 702 effects on legumes, 719 nod genes, definition of, 702 Nodule formation, 693–4, 704 autoregulation, 721 cross-inoculation groups, 722 effectiveness subgroups, 722 factors affecting: environmental factors, 723 soil fertility, 722–3 in legumes, 712–13, 715–24 evolution, 716–17 introduction, 715–16 molecular basis, 718–19 nodule-specific gene expression, 719 plant defense response, 719 root-nodule bacteria, 717 mechanisms of infection: types of infection, 717 visible changes during infection, 717–18 micrographs, 720 nodulation genes, 718 nodule characteristics: shape, 719 size/number, 720–1 non-leguminous, 704, 717 root hair deformation, 717 specificity, 721–2 supernodulation, 721 Nodules, definition of, 715 Nodulins: definition, 715 expression, 719 Non-echinocandin macrocyclic lipopeptidolactones see FR-901469 North American blastomycosis, 505 Norwalk virus, 493 Nuclear localizing sequences in T-DNA, 17–18 Nuclease, definition of, 340 Nucleocapsids, 1079 Nucleoids: definition of, 259 see also Chromosomes, bacterial Nucleosomes, 266 Nucleotide sequencing: chemical defradation method, 877 dideoxynucleotide chain-termination method, 877 Nurmi concept, 524 Nus proteins, 997, 998 NusA terminator protein, 997, 998 Nutrients, definition of, 725 Nutrition, microbial, 725–38 classification: categories of organisms, 726 classes of nutrients, 726–7, 728 elements: composition of biomass, 727–8, 735 as polymeric constituents, 729 index requirements/functions, 728–32 see also specific elements limiting nutrient, 733, 736–8 requirements/functions, 727 unrestricted vs limited, 732 see also Growth media; Minimal media Nutritional categories, 726 definition, 725 Nystatin, 51–2 liposomal, 53 O-antigen, 768, 772 in LPS biosynthesis, 773 O-polymerase, 773 O-polysaccharides (O-PS), 773 biosynthesis/assembly, 651–4 ABC-transporter-dependent pathway, 653 model of synthesis, 652 synthase-dependent pathway, 653 Wzy-dependent pathway, 652–3 definition, 645 structure, 646, 650 O.3 “early” gene, 366 Occlusal, definition of, 739 Office of Biotechnology Activities (OBA) website, 528 Office of Pesticide Programs (OPP), 157, 158 Office of Pollution Prevention and Toxics website, 532 Office of Recombinant DNA Activities (ORDA), 528 2’,5’-oligo(A) synthetases, 77 Oligonucleotide tag mutagenesis, 378 Oligosaccharide, core, definition of, 645 Oligotrophs: biochemistry/physiology of adaptation, 450 definition, 436 habitats/microorganisms, 449 OmpA see Outer membrane proteins, OmpA OmpR, 764–5 Oomycetes, 333 Opacity-associated (Opa) proteins, 564 Neisseria, 4–5 pathogenic, 568–9 Neisseria gonorrhoeae, 886 Open reading frames (ORFs), 1027–8 Operation Desert Storm, 171 Operons, definition of, 415, 859 Ophthalmia neonatorum, 563, 884 Opine: catabolism, 12, 13 import, 13 production, 283 utilization, dissemination of, 283 Opportunistic infections: definition, 47, 507 fungal, 508 Oral antibodies, 743 Oral flora, 554, 555 Oral microbial ecology: factors affecting: age of host, 743–4 antimicrobial agents, 744–5 body fluids, 742–3 diet, 744, 748 habitat, 743 microbial interactions, 744 general characteristics: mineralized tissues, 740–1 saliva, 741–2 soft tissues, 741 Oral microbiology: trends, current/future, 752 see also Oral microbial ecology; Oral microflora Oral microflora: bacteria, 746 common to animals and humans, 746 in disease: control/prevention, 751–2 enamel caries, 748–50 infections outside mouth, 751 pathogenesis, 748 periodontal diseases, 750–1 root surface caries, 750 fungi, 746 interspecies comparisons, 745 normal, 745–8 dental plaque, 747–8 identification, 745, 747 soft tissues, 747 in supragingival/subgingival plaque, 749 Ordered gene library, definition of, 536 Ordered gene library/encyclopedia, 541–2 E coli K-12, 543, 545 phage , 545 Organic acids in industrial fermentation, 615 Organism clonality, 588–9 Organotrophs, 726 Origin of replication (oriC), 267 capture by replication apparatus, 269 definition, 259, 870 in E coli replication control, 351 localization/movement, 268 Origin of transfer (oriT), 272 of ColE1, 282 in G-ve bacterial conjugation, 278 Orthologous genes, 584, 585 Oseltamivir, 95 Osmolality: control, 754–5 definition, 754 increased, 756 Osmolarity, definition of, 222 Osmophile, definition of, 754 Osmoregulation model, 765–6 Osmoregulationof enteric bacteria, 764 Osmoremedial mutations, 756 Osmotaxis, 755–6 Osmotic adaptations, 755, 757 Osmotic downshift, 763–4 Osmotic pressure, 754 Osmotic stress, 754–66 compatible solutes: ␣-amino acids/derivatives, 760, 761 -amino acids/derivatives, 760, 761–2 methylamines/analogs, 762, 764 sugars/polyols, 757–60 Dem-ind.qxd 10/13/03 3:39 PM Page 1137 index general considerations, 754–6 osmosensors, 764–5 potassium ion uptake, 756–7 soil microorganisms, 920 Osmotolerance, 755 OspA protein, 1061, 1062 Otitis, external, 910 Otitis media, 910 Out exporters, 851 Outer membrane, gram-negative, 767–74 assembly, 771–4 functions: barrier function, 247, 771 host–pathogen interactions, 771 isolation of, 767–8 lipopolysaccharide biogenesis, 772–3 phospholipid export to, 774 structure: enteric paradigm, 769 zones of adhesion, 769 Outer membrane lipids: enterobacterial common antigen, 769 biosynthesis, 773 lipopolysaccharide structure, 768–9 phospholipid composition, 769 phospholipid export to, 774 Outer membrane lipoproteins, 771 murein lipoprotein, 770–1 Outer membrane proteins, 768 export, 771–2 OmpA, 278, 568, 767, 770, 772 osmoregulation, 764 pathogenic Neisseria, 564, 567–9 porins, 768 general pores, 769–70 specific channels, 770 Outer membrane stability, 654 OUTLIER program, 606, 607 Overgrowth, bacterial, 519–20 OVERMAT program, 606, 607 Oversight, definition of, 526 Oxiconazole, 55 Oxidase, definition of, 395 Oxidative phosphorylation, definition of, 395 Oxidative stress, 775–80 biological implications, 779–80 definition, 775 physiology, 777–8 reactive oxygen species, 776 responses: biochemistry, 777–8 evolutionary pressures, 780 genetics, 778–9, 780 regulation in Escherichia coli, 778 sources: aerobic metabolism, 775–6 chemical/physical agents, 776 nitric oxide, 776–7 photosynthesis, 776 in yeasts, 780 Oxidative stress-inducible proteins, 778 Oxygen: in bioluminescence, 185 in bioreactors, 191, 193 in bioremediation, 203 in denitrification, 699 exclusion strategies, 704 requirements/functions in microbes, 730 Oxygen demand, 203 Oxygen gradients in sulfur cycle, 979 Oxygen-releasing compounds, 205 H2O2, 204, 205, 206 Oxygen replenishment, 204–6 Oxygen sensitivity: diazotrophs, 692–3 in nitrogen fixers, 691, 692–3 Oxygenation in bioremediation, 205, 207–8 OxyR protein in oxidative stress, 778–9 Oxytetracycline-resistance, 28 P/O (P/2e) ratio, definition of, 395 Pac-like sites, 1006 Pac sites, 1005–6 Package, definition of, 1000 PAD1 plasmid, 280 Palindrome, definition of, 415 Pandemics, definition of, 1084 Pap pilins, 458 PapC ushers, 459, 461 PapD chaperones, 459 crystal structure, 460 PapG adhesin, 2, 458 Papillomavirus, definition of, 84 Papulocandins, 62 Paracoccidioidmycosis, 508, 512 Paracoccus denitrificans, 698 Paralogous genes, 584 Parasitism, 327 fungal, 334 Parenchyma, definition of, 789 Paromomysin, 27 Paronychia, definition of, 899 Parvovirus B19, emerging, 1091 Pasteur effect, 1108 Pasteur effect, definition of, 1102 Pasteurization and biofilms, 166 Patent depository, definition of, 294 Pathogen, definition of, 789 Pathogen elicitors, 796, 797 Pathogenesis, 1054–5 Pathogenicity: and adhesion, 902 alterations in space flight, 934 Pathogenicity islands, 263, 855 and cholera toxin, 408 definition, 403, 415–16 Pathogens: in composting, 212 cutaneous, 905 gram-negative anaerobic, 554–61 gram-positive cocci, 562–73 antigens, 565–71 capsules, 566–7 immunity, natural, 571 lipopolysaccharide, 569–71 mechanisms of infection, 564–5 outer-membrane proteins, 567–9 pili, 565–6 prevention of infection, 571–2 iron metabolism, 643–4 1137 pilus biogenesis control, 467–8 research programs, 174 S layers, 291–2 in seafood, PCR analysis of, 826 transformation, 38 PCE see Perchlorethane PCP see Pentachlorophenol PCR see Polymerase chain reaction Pedicel, definition of, 934 Pellicle, acquired, 740 Pellicle, acquired, definition of, 739 Pellicles, acquired see Conditioning films Pelvic inflammatory disease (PID), 880, 888–9 Penciclovir, 92–3 Penicillin: industrial fermentation of, 615 structure, 246 Penicillin-binding proteins (PBPs), 32, 247, 586 definition, 239 Penicilliosis, 508, 512 Penicilloyl–enzyme intermediate, 246, 247 Pentachlorophenol (PCP), 199 biodegradation, 210, 214 Peptide nucleic acid clamps, 540 Peptides: intervening, 241, 242 leader, definition of see Leader peptide signal, 235 Peptidoglycan see Murein Peptidomimetic, definition of, 84 Perchlorethane (PCE), 200 biodegradation, 203, 206, 207, 209–10 Peribacteroid membrane, definition of, 715 Periodontal pockets, 739 definition, 739 Periplasm: definition of, 239 yeast, 1106 Periplasm, definition of, 690 Periplasmic chaperones, definition of, 454 Periplasmic enzymes, 849 Periplasmic space, 240 Periplasmic space, definition of, 767 Peristalsis, 515 Peristalsis, definition of, 514 Permeable reactive barriers, 202, 208–10 Permeant acids: avoiding uptake, 784 definition, 781 measuring pH, 783 Permeant bases, definition of, 781 Peroxidases, 777 Peroxisomes, yeast, 1106 Persistence in GMOs, 527 Pertussis, 1055 Pertussis toxin secretion, 430 Pertussis vaccine, 433 Pesticide Registration Notice, 158–9 Pesticides, antimicrobial, 147–8 Petechial skin lesions, definition of, 562 pH, 781–2 in development of microbiology, 782 Dem-ind.qxd 10/13/03 3:39 PM Page 1138 1138 pH (continued) internal, measurement of: NMR of titratable phosphates, 783–4 permeant acids, radiolabeled, 783 in nodule formation, 723 range for microbial growth, 782–3 soil, 921 for yeast, 1107 pH homeostasis: alkaliphiles, 448–9 definition, 781 E coli, 782 modification of external pH, 784 permeant acids, avoiding uptake, 784 pH sensors, 782 pH stress, 781–8 applications, 786 environmental role, 786–7 genetic responses: neutralization of acid/base, 785 virulence regulators, 785–6 and organic acid stress, 784–5 Phaeohyphomycosis, 512 Phage see Bacteriophage Phage conversion, definition of see Lysogenic conversion Phage , 145, 358 cloning vectors, 874 and DNA restriction, 367 lysogenic vs lytic state, 1080 N protein, 997 ordered gene library/encyclopedia, 545 restriction, host-controlled, 360 SOS response, 928 Phage , 145 direct repeats, 1030 replication/integration, 1039 structure, 1038–9 Phage P1: DNA packaging, 1006 in gene mapping, 1010 in transduction, 1001 Phage P22: DNA packaging, 1006 in gene mapping, 1010 in transduction, 1001 Phage T1 in transduction, 1008 Phage T4 in transduction, 1008 Phage typing, 483 Pharmacokinetics, definition of, 84 Phase III, definition of, 84–5 Phase variation, definition of, 416, 454 Phenolic compound biodegradation, 199 Phenotype, definition of, 416, 808 Pheremones, 1014 definition, 1012 in Ent faecalis conjugation, 280–1 model for regulation, 1014 Phloem, definition of, 789 Phosphate (Pho) regulon, 314 Phosphatidyl ethanolamine (PE), 224, 238 Phosphatidyl glycerol (PG), 224 Phospholipids: cell membrane, 224–6, 237–8 composition, 769 index crystal structure, 226 Phosphorelay, definition of, 314 “Phosphorescence”, ocean, 185 Phosphorus: in nodule formation, 722–3 requirements/functions in microbes, 730 Phosphotransfer reaction, definition of, 1042 Phosphotransferase system, 234 Photoautotrophs, 726 in bioreactors, 192 definition, 189, 725 Photobacterium leigonathi, 182 Photobacterium luminescens, 182 Photobacterium phosphoreum, 182, 183 Photoheterotrophy, 726 definition of, 725 Photolithoautotrophs, 726 Photolyases, 343 Photophosphorylation, definition of, 395 Photoreversal, 343 Photosynthesis, 229–30 in algae, 335 in oxidative stress, 776 prokaryotic, 401 Photosynthetic bacteria, 401 Phototrophs, 914, 978 definition of, 436 PhrA protein, 944 Phthalimides, 49, 66 Phylloplane, definition of, 381 Phylogenetic analysis: bacteria, 330–1 protozoa, 336 Phylogenetic tree: Archaea, 332 methanogens, 661 bacterial, 330 methanotrophs/methylotrophs, 685 Proteobacteria, 685 universal, 109, 327–8 Phylogenetic trees, viral, 598 Phylogenic domains, 676 Phylogeny, definition of, 436, 690 Phytohemagglutinin, 497 PIBWin program, 609, 610–11 Pichia pastoris, 681 Picornavirus, definition of, 85 Picrophilus spp., 440 Piedra, white/black, 502, 503 Piezophiles see Barophiles Pig-bel, 411 Pil proteins, 464 PilC1 adhesin, 7, 464 PilE pilin subunits, 462–3, 464 Pili, 454–69 adhesins, 2–4 aggregative, 454 architecture, 454 assembly model: donor strand complementation, 460–1 outer-membrane ushers, 461 assembly pathways: chaperone pathway, alternative, 456 chaperone–usher pathway, 455, 457–61 conjugative pathway, 456, 464–6 type II secretion pathway, 456, 462–4 type III secretion pathway, 456, 467 type IV secretion pathway, 456 biogenesis regulation, 460, 467–8 bundle-forming (BFP), 409 classification, 455 conjugal, 276–8 definition, 10 structure, 276–7 conjugation, role in, 277 conjugative, 277, 464–5, 821 CS1/CS2, 461–2 definition, 403, 415, 454 dynamic nature, 468–9 ETEC, 410 F pilus assembly, 465 gram-negative bacteria, 454 gram-positive bacteria, 280 history, 455 in mating pair formation, 277 Neisseria gonorrhoeae, 886 nucleation–precipitation pathway, extracellular, 466–7 P pili, 454, 457, 458 assembly model, 459 pathogenic Neisseria, 565–6 plasmid-encoded, 821 role in disease process, 468–9 signaling function, 469 structures, 457 T pili, 20, 457, 466 thin flexible, 464–5 toxin-coregulated pilus, 408 type assembly, 462–4 model, 464 type I, 455, 458 type IV: definition, 403 in transformation, 1017 yeast, 1106 see also specific adhesins Pilin: definition, 454 subunits, 276, 277 variation, genetics of, 565–6 Pilosebaceous, definition of, 899 PilS silent genes, 463 Pimaricin, 53 Pink-pigmented facultative methylotrophs, 680 Piritetrade, 61 Pitted keratolysis, 905 Pityriasis versicolor, definition of, 499 PKR see Protein kinase, RNA-dependent Plague outbreaks, 392 Plankton, 332 Planktonic, definition of, 161 Plant cell culture, definition of, 189 Plant cell transformation: chemical signaling events, 13 crown gall disease, 11, 12 “hairy root” disease, 12 Plant pathogens, 789–807 bacteria/mollicutes, 792 classification, 798–9 Dem-ind.qxd 10/13/03 3:39 PM Page 1139 index dissemination/infection, 799 ecology, 799 epidemiology, 799–800 genetics of disease, 799 management/control, 800 morphology, 797–8 reproduction, 798 symptoms, 797 fungal-like organisms/pseudofungi, 794 fungi, 790–7 classification, 794–6 dissemination/infection, 796 ecology, 796 epidemiology, 797 genetics of disease, 796–7 life cycles, 795 management/control, 797 morphology, 791–2, 794 reproduction, 792–4, 795 introduction, 789–90 morphology, 794 nematodes, 793, 803–5 classification, 804 dissemination/infection, 804–5 ecology, 804 epidemiology, 805 management/control, 805 morphology, 803–4 reproduction, 804 parasitic green algae, 806–7 parasitic higher plants, 793, 806 protozoa, 793, 805–6 classification, 805–6 ecology/dissemination, 806 management/control, 806 morphology, 805 reproduction, 805 reproduction, 794 sizes/shapes, 791 viruses/viroids, 793 classification, 800–2 dissemination/infection, 802 ecology, 802 epidemiology, 802–3 management/control, 803 morphology, 800 replication, 800 vector-transmitted, 803 yeasts, 1113 Plants: disease symptoms, 790 functions, 790 Plaque assay, 405 Plaque, dental see specific types of plaque Plaques: amyloid, 839 definition, 829 bacteriophage, 136 definition, 1071 Plasma membrane, yeast, 1106 Plasmaviridae, 137, 138, 140, 141 Plasmids: antisense RNAs, 73 bacterial, 808–23 in bacterial conjugation, 275 bearing nodulation genes, 718 in Buchnera, 630 characteristics, 809 chromosome mobilization, 822–3 circular, 809 classification, 812 cloning vectors, 871, 873–4 conjugation systems, 272 conjugative, 271, 273, 274 antirestriction functions, 366 Bacteroides fragilis, 560 E coli/Salmonella, 418, 420, 423–4 in Ent faecalis, 280 in gram-negative bacteria, 820 in Streptomyces, 281 copy numbers: control, 816 sensing, 815 definition, 271, 403, 416, 808, 960 “dimer catastrophe”, 817 distinguishing from genes, 262 evolution, 809, 810–11 fertility inhibition (Fin), 280 gene acquisition, 822–3 history, 808–9 horizontal gene pool, 812 incompatibility, 811, 812 in industrial fermentation, 617–18 inhibitor dilution model, 816 integrating: in Bacillus subtilis, 129–30 definition, 126 genetic manipulations with, 130 integron model, 38–9 intermycelial transfer, 281 isolation of DNA, 872 linear, 809 mapping, 539 mating efficiency, 273 mating process, 272 in methanogens, 675–6, 678 mobilizable, 273, 274, 822 mobilizable, definition of, 10 mobilization, 281–2 multiple resistance, 39 in nitrogen fixation, 711–12 phages compared to, 141 phenotypes conferred by, 809, 810 replication: control of, 815–16 DNA poll-dependent replicons, 813 inhibition by antisense RNA, 71–2 iteron-activated replicons, 814–15 rolling circle replication, 813, 814 resistance determinant, 38–9 size, 809 stable inheritance, 816–19 active partitioning, 817–19 killing of plasmid-free segregants, 817 multimer resolution, 816–17 transduction, 1009 transfer: conjugative transfer, 820–2 establishment in new host, 822–3 1139 transduction, 819–20 transformation, 819 Plasmolyzed cells, definition of, 767 Pleisomonas shigelloides, 413, 491 Plumes see Groundwater plumes Pneumocandin derivatives, 64 Pneumococcal vaccines, 1057 Podoviridae, 137, 138 Point mutations, 962 Pol proteins, 595 Polarity of molecules: lipids, 224–5 phospholipids, 224–5 Polarized chromosomal transfer, definition of, 536 Polio erradication, 1069, 1070, 1082–3, 1100 Polio vaccine, 1067 Poliomylitis, 389, 390 disease development, 1081 Pollution and sulfur cycle, 981–2 Polyacrylamide gel electrophoresis (PAG), 611 Polyenes, 48, 49–53 lipid formulations, 52–3 Polymerase chain reaction (PCR), 453, 824–8 automation, 827 commercial test kits, 826–7 definition, 126, 381, 824, 870 diagnosis of infectious diseases, 825 Chlamydia, 890 future role, 826 in DNA sequencing, 375 and emerging viruses, 1085, 1089 environmental applications, 826 introduction, 824–5 microbial diversity, examination of, 327 in microbial ecology, 385 in molecular cloning, 370 and pandemic influenza, 1085–6 technology, 825 new, 827–8 tropical infectious diseases, 825–6 Polymerase, definition of, 350 Polymerases, DNA, in E coli, 351 Polymorphic transition, 470 Polymorphonuclear leukocytes (PMNs), 407 Polynuclear aromatic hydrocarbon biodegradation, 199 Polyoxin D, 65 Polyoxins/nikkomycins, 49, 65 O polysaccaride (O-PS), definition of, 645 Population, definition of, 381, 739 Population density monitoring, 859 Pore-forming toxins, 428, 434 definition, 427 Porins, 240, 768 definition, 562 expressed by barophiles, 445 general pores, 769–70 OmpF/OmpC, 770 of pathogenic Neisseria, 567 specific channels, 770 Porphyromonas spp.: oral, 747 Dem-ind.qxd 10/13/03 3:39 PM Page 1140 1140 Porphyromonas spp (continued) P gingivalis: host responses, 558 pathogenicity, 557 in periodontal disease, 751 Portal of entry, definition of, 507 Posaconazole (SCH 56592), 59–61 structure, 58 Post-translational modifications, definition of, 427 Postsegregational killing in hok/sok system, 817, 818 Posttranscriptional gene silencing, 78 definition, 68 dsRNA-induced, in worms, 80–1 RNA interference, 81–2 virus resistance, 78–80 Potassium uptake, 756–7 Poxviruses, 1077 Pradimicin A (BMY 28567), 65 Pradimicin FA-2 (BMY 28864), 65 Pradimicins/benanomycins, 49, 65 Prepilin peptidase, 463 Prepilins, definition of, 454 Preproteins: emergence/catalysis, 848 “hands-off” model of transfer, 845, 846 secretory, 843 in TAT pathway, 852 translocation, 848 Preservative, 148 Prespores, 315, 944 definition, 942 in sporulation, 943 see also Forespores Prevalence, definition of, 879, 1084 Prevotella spp.: oral, 747 pathogenicity, 558 vaginal flora, 555 Primary metabolites, definition of, 960 Primary producers, 383 Primary vaccine failure, 1068 Primordial germ cell wall (PGCW), 948 Prion diseases: drug development, 840–1 history, 837 human hereditary, 838 and immune system, 840 routes of infection, 840 transmissible spongiform encephalopathies, 837–40 Prions, 829–41 brain damage induction, 839 as copper-binding proteins, 830 definition, 829 GPI anchor, 830, 835 molecular biology: cellular prion protein (PrPC), 830 Prnp gene, 829–30 PrP protein, 830–1 octarepeats, 830, 838 protease resistance/sensitivity, 830 protein only hypothesis, 831–6 and mice devoid of PrP, 833 index prion strains and species barrier, 833–5 proposed conversion methods, 835–6 PrP glycosylation, 834, 835 virus and virino hypothesis, 833 yeast prions, 836–7 Probes, 543 definition, 381 Prochloraz, 56 Prodrug, definition of, 85 Proenzymes: definition, 427 exotoxins as, 430 Prokaryotes: definition of, 135, 436 osmolality, 755 Proline, 760, 761 Proline isomerases, 849 ProMED-mail, 1099 Promiscuity, definition of, 715 Promoters, 951, 987–9 definition, 984 Prophages: definition, 927 in gene mapping, 1010 in SOS response, 933 Propilins, definition of, 454 Propionibacterium spp., 905 growth suppression, 900 in hair follicles, 901 P acnes, 905 Proteases: definition, 574 selectivity, 958–9 Protective efficacy, definition of, 1063 Protein crystals, two-dimensional, definition of, 286 Protein degradation, 116 Protein engineering, 193–4, 878 definition, 189 Protein F adhesins, Protein folding: chaperones, 575–6 on export, 849 in heat stress, 574–5 for MTB secretion, 850 Protein kinase: in motility, 236 RNA-dependent (PKR), 76–7 Protein secretion/export, 842–58 ABC protein secretion pathways, 842, 853–5 bacterial pathways, 844 definition, 842 destinations of proteins, 843 general secretion pathway: chaperones/targeting factors, 845–6 definition, 842 distal steps during export, 848–9 energetics, 847–8 Escherichia coli translocon, 846–7 main terminal branch (MTB), 849–50 mechanism of translocation, 847–8 targeting signals on preproteins, 842–3, 845 terminal branches, 849–52 Sec-dependent pathway see General secretion pathway twin-arginine protein secretion pathway, 842 twin-arginine translocation (TAT) pathway, 852–3 type III protein secretion pathways, 842 chaperones, 857 export/translocation signals, 857 secretion apparatus, 855–6 substrates, 856–7 Protein synthesis/folding/turnover, 115–16 Protein translocation (secretion), 116 Proteins: antenna, 183 bending, 266, 270 of hyperthermophiles, 439–40 protection by starvation proteins, 954 Proteobacteria, definition of, 680 Proteome analysis, 752 Proteomics, definition of, 371 Proteus mirabilis, 318 Protists, symbiotic, 627–8, 633 Proton pumping/gradient, 228 Proton translocation, 395, 396 stoichiometry, 396, 397 Protonmotive force, 785 in bacteria, 397 definition, 222, 395, 781 formation, 228, 230 generation, 399, 401 linking diverse reactions, 397 in mitochondrial respiratory chain, 396–7 in secondary active transport, 233 Protoplast fusion, 968–9 Protoplast transformation, 1022 Prototrophy, 726 Protozoa: diversity, 336–7 ecological functions, 336 intestinal, 520–3 methanogenesis, 670 plant pathogens, 805–6 taxonomy, 336 Proviruses, 337 PrP knockout mice, 833 PrP protein: definition see Prions function, hypotheses on, 830–1 proteins interacting with, 831 structural properties, 831, 832 PrPC, 830 definition, 829 posttranslational processing, 830 PrPSc, 830 definition, 829 PS A: abscess induction, 557 immunity, 558 Pseudofungi, 794 Pseudohyphae, 1111 Pseudomonas spp.: biocide resistance, 158 plant diseases, 798 Dem-ind.qxd 10/13/03 3:39 PM Page 1141 index Ps aeruginosa: exotoxin, 432 folliculitis, 901, 906 lipid A, 647 multiple quorum sensors, 865 transient skin flora, 910 Ps oleovorans, 737 Pseudomurein, 241, 243 Pseudopilins, 851 Psiϩ, 836–7 Psychrophiles: biochemistry/physiology of adaptation, 443 cold shock/acclimation, 443–4 enzymes, 443 membranes, 443 definition, 108, 436 habitats/microorganisms, 441–4 artificial, 442–3 natural, 442 Psychrophilic organisms in bioremediation, 207 PTGS see Posttranscriptional gene silencing PTk-diagrams, 444 Public health: emergencies, 393 infectious disease control, 390, 392, 393 Pul exporters, 851 Pullulanase secretion, 851 Pulsed field gel electrophoresis (PFGE), definition of, 536, 540 Pycnidia, 792 Pyodermas: definition of, 899 staphylococcal, 907 streptococcal, 907–9 Pyridines, 49, 62 Pyrifenox, 62 Pyrimadine dimers: effect on transcription, 347 photoreversal, 343 Pyrimethanil, 54 Pyrimidines, synthetic, 48, 54 Pyrodinium bahamense, 185 Pyrolobus fumarii, 438 Pyrolysis-mass spectroscopy, 611 Pyrrolnitrin, 53 Quinone, definition of, 395 Quorum sensing, 163, 184, 859 dual sensors, 866 ecology/function, 867–8 gram-negative bacteria, 859–69 acyl HSL/Lux protein sensing, 861 mechanisms/generalities, 861–2 regulation, 867 in Vibrio harveyi, 866 see also Acyl HSLs Quorum sensors: gram-negative bacteria, 862 R 66905 see Saperconazole R factors, 271 R-prime, definition of, 416 R1 plasmid, 818 R751 plasmid, 811 Rabies vaccine, 1067 Radiation: mutagenic, for strain development, 963 and space flight, 936–7, 938–9 Radiation resistance in spores, 948 Radiation-resistant microorganisms biochemistry/physiology of adaptation, 451 habitats/microorganisms, 450–1 RapA in sporulation, 944 Rare-cutter endonucleases, 539–40 definition, 536 Ravuconazole (BMS-207147) (ER-30346), 60 structure, 58 Raymond process, 205 Re-emerging infections, 387 definition, 1084 facilitating factors, 390–1 Reactive arthropathy, definition of, 480 Reactive gliosis, definition of, 829 Reactive oxygen species (ROS), 776 definition, 775 RecA protein, 345 in LexA cleavage, 930–1 as SOS inducer, 929, 932, 933 in SOS mutagenesis, 931 as SOS regulator, 928 Receptors, definition of, 251 Recognet program, 609 Recognition elements in general secretion pathway, 843 Recombinant DNA: containment guidelines, 528 definition, 526 Recombinant DNA Advisory Committee (RAC), 528, 529 guidelines, 530 Recombinant DNA technology, 370 applications, 877–8 basic procedures, 870–8 in biological warfare, 175 in bioreactors, 193–4 cloning strategies: characterizing cloned gene products, 873 choosing E coli host, 872–3 direct selection by complementation, 871–2 reverse genetics, 873 screening a library, 872 cloning vectors: phage , 874 plasmids, 873–4 definition, 168, 871 in microbial ecology, 384–5 nucleotide sequencing, 877–8 restriction endonucleases, type II, 874–6 in strain improvement, 969–70 Recombination: Archaea, 114–15 bacteria, 263–4 major pathways, 264 bacterial chromosomes, 263 definition, 259, 416, 960 1141 E coli/Salmonella, 421 homologous, definition of, 1012 “illegitimate”, 18 protoplast fusion, 968–9 schematics of major classes, 421 Recombination frequency analysis, 537 Recombination pathway, definition of, 358–9 Red tides, 185, 335 Redox gradients in sulfur cycle, 979 Redox potentials: definition, 395 examples, 398 in soil, 920 Reductants in denitrification, 700 Regulatory mutants: resistant to feedback inhibition, 967 resistant to repression, 967–8 in strain improvement, 967–8 Regulatory proteins, definition of, 591 Regulons: definition, 314, 859, 927 “SOS”, 345, 346 Relaxases, 272, 275, 822 in mobilization of plasmids, 282 Relaxasomes, 821, 822 Rep proteins, 813, 814, 816 Repellent, definition of, 251 Replacement mutagenesis, 873 Replica plating, definition of, 870 Replication: definition, 350 genome, definition of, 1071 Replication, definition of, 1071 Replication forks: chromosomes, bacterial, 261, 267 definition, 259 and elongation complexes, 995 location, 267 in termination of DNA replication, 357 Replicons, 809 definition, 350 DNA poll-dependent, 813 fusion, 1041 iteron-activated, 814–15, 816 mutant, 810 Reporter fusion analyses, 378 Reporter genes, 130 definition, 927 Repression, definition of, 690 Resistance, 1029 Resistance genes see Antibiotic resistance, genes Respiration, 230 definition, 395 Respiratory chain: definition, 395 mitochondrial, 395–6 Respiratory synctial virus vaccine, 1066 Respiratory syncytial virus, 96 Respiro, definition of, 1102 Response regulator, definition of, 1042 Resting-stage cells, 449 Restriction endonucleases, 262, 360, 365, 1019 and cleavage sites, 361 in cloning, 873 Dem-ind.qxd 10/13/03 3:39 PM Page 1142 1142 Restriction endonucleases (continued) definition, 135, 659 ends generated by, 874 in strain improvement, 969–70 type II, 874–6 Restriction enzyme mapping, 876 definition, 870 Restriction enzymes, 359–60 distribution, 367 ENases, 362, 369 structures, 365 frequency of sites in DNA, 875 Restriction maps, 369–70 Resynthesis, definition of, 340 Retroviruses, emerging, 1091–2 Rev system, 594 Reverse genetics, definition of, 870 Reverse transcriptase, definition of, 591 Reverse transcriptase inhibitors, 600 Reverse transcriptase PCR, definition of, 824 Reversed electron transport, 399–400 Reversed electron transport, definition of, 395 Rhinovirus, 1077 Rhizobacteria, legume-nodulating, 710–11 Rhizobia, 693–4 current taxonomy, 710 in extreme conditions, 723 fast/slow growing, 709–10, 712 function, 715 Rhizobiophages, 713 definition, 702 Rhizobium: acid-tolerance, 716 definition, 702 nitrogen fixation, 711 rhizobiophages, 713 in symbiosis, 315, 708, 709, 710 Rhizobium–legume symbioses: history, 708–9 nitrogen fixation, 708–9 nodule formation, 712–13 rhizobiophages, 713 Rhizoplane, 917–18 Rhizosphere, 917 definition, 381, 914 substances released into, 919 Rho () protein, 996 Rhodobacter spaeroides chemotaxis system, 258 Rhodobacter sphaeroides photosystem, 401 Rhodococcus spp., 904 RI 331, 66 Ribavirin, 96–7 Riboflavin, adverse effects of, 96–7 Ribosomal RNA, 327, 330 Rifampicin resistance, 33 Rift valley fever (RVF), emerging, 1092 Rimantadine, 94–5 Risk Groups, 531 Ritonavir, 104–5, 106 Rmp proteins, 568 RNA-binding attenuation regulatory protein, definition of, 117 index RNA hairpin structrure: definition, 117 RNA hairpin structure, 123 in transcriptional attenuation, 119 RNA interference (RNAi), 80–2 definition, 68 RNA polymerase: catalyzing transcription, 985 multiple subunits, 985–6 transcription initiation, 986–7 RNA polymerases: definition, 659, 984 recognition by upstream sites, 988 in transcription elongation, 992–5 in transcription termination, 995, 996, 997, 998 RNA reverse-transcription viruses, 1074 “RNA silencing”, 81–2 RNA synthesis/modification/degradation archaea, 115 RNA viruses, 1072 classification, 1073–4 genetics, 1080 genome cloning, 1083 replication, 1077–8 transformation, 1081 RNAP, 347, 348 RNAs: artificial, 70, 78 definition, 68 double stranded see dsRNA see also Antisense RNAs RNase III: dsRNA, similarities to, 78 mediation of antisense RNAs, 74–5, 76 Rocio encephalitis, 1097 Ros zinc finger protein, 15 Rotavirus, 493 Rough lipopolysaccharide (R-LPS): definition, 645 in outer membrane stability, 655 structure, 646, 647 RP4 plasmid, 16 transfer, 279 Rse proteins, 581 RSF1010 mobilizable plasmid, 282 RT-PCR see Reverse transcriptase PCR Rubella virus, 76 Rudiviridae, 137, 138, 140 Rumen, definition of, 381 Rumen ecosystem, 382 definition, 514 yeasts stabilizing, 1113 Rumen of cattle: methanogenesis, 669 microbial characteristics, 515, 518 physical/chemical characteristics, 515 Rustmicin, 66 S-layer (glyco)protein glycans, 288, 289 S-layer (glyco)proteins: definition, 286 post-translational modifications, 288 structure, 289 S-layer lattices, 287–8 pores, 288 S layers, 286–93 application potential, 292 assembly, 289–90 biosynthesis, 290–1 chemical characterization, 288–9 definition, 286 functions, 291–2 genetics, 290 glycosylation, 288 isolation, 288 location/ultrastructure, 286–8 overview, 286 and pathogenicity, 291 recrystalization after isolation, 289 Saccharomyces cerevisiae definition, 1102 grown in microgravity, 940 infections, 512 life cycle, 1112 mating, 1111 Saccharopolyspora erythraea, 971 Saliva, 741–2, 743 components of, 742 Salmonella spp.: antibiotic resistance, 488 antigens, 417 and competitive exclusion, 524 detection in food, 827 discovery, 417 flagella, 471 food-borne disease, 481 food-borne disease/illness, 487–8 gene transfer between cells: conjugation, 423–4 transduction, 424–5 transformation, 425 genetics, 415–26 genome: chromosome, 418 circular genetic map, 419 copy numbers, 418 extrachromosomal elements, 418, 420 identification, 603 mutation, 421 nontyphoidal, 405–7 plasmids, 420 recombination: homologous, 421–2 site-specific, 421, 422 transpositional, 421, 422–3 S enterica, 418 S typhi, 1059 infections, 411–12 S typhimurium, 406–7 batch culture media, 734 core oligosaccharides, 649 flagellar phase variation, 423 genetic map, flagellar genes on, 475 genome, 418 histidine importer, 854 lipid A, 647, 648 lipopolysaccharide, 646 LPS structure, 769 Dem-ind.qxd 10/13/03 3:39 PM Page 1143 index lysogenic, and space flight, 939 mouse models, 411 starvation and virulence genes, 958 type III secretion machinery, 855–6 taxonomic niche, 416–18 taxonomy/serogroups, 487 typhoidal, 487 Salt tolerance: terms for range of organisms, 446 see also Halophiles Sanitizer, 148 Saperconazole (R 66905), 60 Saprophytes, 797 Saquinavir, 103–4 Sarcosine, 762 Satellites, 1075 Sbb protein, 353–4 Scale up, definition of, 613 Scanning electron microscopy (SEM), 163 SCH 39304, 59–61 SCH 51046, 59–61 SCH 56592 see Posaconazole Scintillons, 185–6 definition, 180 Scrapie, 837–8 Scromboid poisoning, 496 SDS-PAGE, 650, 770 definition, 767 SDZ 89-485, 60 Seal plague, 1097 Sec-machinery: definition, 842 recognition elements, 843 Sec proteins, 845, 846–7 Sec secretory system, 235 Secondary metabolites, definition of, 960 Secondary substrates, 197 Secretins, 851–2 Secretion signals, 235 definition, 842 Secretion systems/pathways, 235 type II, 429–30, 477 type III, 842 chaperones, 857 definition, 403, 470 export/translocation signals, 857 flagellar protein export, 477 needle complex, 856 secretion apparatus, 855–6 substrates, 856–7 Selective toxicity, definition of, 147 Selfish Operon Model, 588 Semistarvation, 951 studies, 952 Sensing, definition of, 251 Sensor kinase protein, 236 Seoul virus, 1089 Septic shock with LPS, 655, 656–7 Septum, definition of, 314 Septum formation: polar, in endospore formation, 315 Streptomyces coelicolor, 316 Sequencing gaps, 375 Sequencing, high-throughput fluorescent, 373 Sereny test, 405, 491 Serial analysis of gene expression (SAGE), 377 Serine kinases, 1052 Sessile, definition of, 161 Sewage treatment: as fermentation process, 614 of fermentation waste, 625 nitrification in, 697 Sexually transmitted diseases (STDs), 879–98 chlamydia, 887–92 definition, 879 disease burden, 880 global cost, 879–80 gonorrhea, 881–6 introduction, 879–81 major agents/diseases, 880 prevalence, 879 risk factors, 881 syphilis, 892–7 viral, 880–1 Shapiro intermediate, 1035, 1039 Shellfish poisoning, 496–7 Shiga toxin, 405, 410, 490, 492 and lipopolysaccharide, 657 Shiga toxin-producing E coli (STEC), 485–6 Shigella spp.: antibiotic resistance, 490 causing inflammatory diarrhea, 404–5 food-borne disease, 481, 490 S dysentariae: conjugation, 36 infections, 405 tetracycline resistance, 28 S flexneri actin tail formation, 405 Sialyl transferase, 570 SIDA see AIDS Siderophores, 638–40 biosynthesis, 640 defective systems, 643 definition, 637 in pathogens, 643–4 Sigma S-dependent promoters, 957–8 Sigma () factors, 132–3, 951 criss-cross regulation, 316 definition, 126, 314, 574, 942, 984 in flagellar construction, 476 in heat stress, 576–7, 580–1 regulation in E coli, 577 sigma S: biochemistry of stability, 956 in oxidative stress, 778 regulation at translational level, 956–7 role/regulation in starvation, 955–7 synthesis rates, 955–6 in sporulation, 945–6 starvation, 955 in transcription, 986 in transcription initiation, 986–7 Signal peptidase II enzymes, 848–9 Signal peptides, 235 definition, 842 in general secretion pathway, 842–3 structure, 845 Signal recognition particles (SRPs), 845, 846 1143 Signal-transduction systems, 1043 Signaling, intercellular: in fruiting-body formation, 321, 323 in neisserial infection, 564 in nodule formation, 721 in osmolyte control, 757 in protein export, 842–3, 845, 857 in septic shock, 655 Signaling molecules in biofilms, 163 Silicone and biofilms, 164–5 Sindbis virus, 1079 Single-cell protein production, 681 Sinorhizobium, 711 definition, 702 Sinorhizobium rhizobiophages, 713 Siphoviridae, 137, 138 Site-specific mutagenesis, 878 Site-specific packaging, definition of, 1000 SIV (simian immunodeficiency virus), 592, 596, 598 Skin: anatomic defences, 900–1 biochemical defenses, 900 hair follicles, 901 immunologic defenses, 900 stratum corneum, 900, 901 structural integrity, 900 Skin anatomy, normal, 501 Skin-associated lymphoid system (SALT), 501 Skin infections see Fungal infections, cutaneous Skin lesions, petechial, definition of, 562 Skin microbiology, 899–913 colonization/invasion determinants, 900–1 colonization of neonates, 903 effect of hydration, 900–1 infections: from direct contact, 912 from insect/animal bite, 913 from other body sites, 913 regional variations, 901 resident flora, 902 fungi, 906 gram-negative bacteria, 906 gram-positive bacteria, 902–5 transient flora, 906 gram-negative bacteria, 910–12 gram-positive bacteria, 906–10 Slime molds, 333 Slurry reaction systems see Bioslurry treatment Small acid-soluble proteins (SSAPs), 947, 948 Small bowel syndrome, 519 Smallpox: as biological weapon, 169 eradication, 389, 390, 1069, 1070, 1082, 1099–100 vaccination, 1064 Smooth lipopolysaccharide (S-LPS): in outer membrane stability, 655 structure, 646, 647 SnoRNAs, 70 Soda lakes/deserts, 448 Dem-ind.qxd 10/13/03 3:39 PM Page 1144 1144 Sodium pump, 232 Software for genome sequencing, 376 Soil: acid sulfate, 981 definition, 914 Soil acidity, 785 Soil food web, 924 Soil formation, 919 Soil microbiology, 914–26 emerging research areas, 926 major processes: biodegradation, 923–4 bioremediation, 923 decomposition, 923 elemental cycling, 922–3 gas exchange, 921 immobilization, 923 mineralization, 923 see also Soil microorganisms Soil microorganisms: factors affecting communities, 920–1 habitat/distribution, 916 field/landscape scale, 918 particle/aggregate scale, 917 soil profile scale, 917–18 interactions, 924–6 ammensalistic, 924–5 antagonistic, 924–5 mutualistic, 925–6 numbers/biomass, 916 overview: classification, 914–15 major groups, 915–16 Soil profile, 917–18 Soil remediation see under Bioremediation Soil vapor extraction (SVE), 208 Solar particle event, definition of, 934 Solfataras, 438 Solutes: compatible, 757–64 definition, 754 effect on proteins, 756 Sorbitol osmotolerance, 757, 758 Sordarins, 49, 65 SOS mutagenesis, 931 SOS regulon, 345, 346 SOS response, 927–33 in Bacillus subtilis, 932–3 definition, 126, 359, 927 E coli as paradigm, 927–8 induction, 930, 932 LexA as repressor, 928–30 in other prokaryotes, 933 regulation, 928, 933 in transformation, 1019 South American blastomycosis, 505 Southern blotting, 876 definition, 870 Southern transfer, definition of, 359 Sox proteins, 779 Space flight, effects on microbes, 934–41 antibiotic sensitivity, 937–8 bacteriophage induction, 939 genetics, 939 human–microbe interactions, 940 index radiation, 936–7, 938–9 simulated microgravity, 939–40 survival/growth, 935–7 Spacelab, 937, 939 definition, 934 Species, definition of, 326 Sphingolipid inhibitors, 66 Sphingomonas, 449, 450 Spirochaetes, motility of, 236 Spo loci, 943, 944, 945, 946 SpoϪ mutants, 943, 944 Spo proteins, 131–2, 944, 945–6, 1049 CheY regulator protein, 1051 Spo0A response regulator, 1048 Spo0F, 1047 in two-component systems, 1043, 1044, 1046 Spoilage: losses due to, 149 psychrophilic organisms, 442–3 Spongiform changes, definition of, 829 Spongiform encephalopathies see Transmissible spongiform encephalopathies SpoOA transcription regulator, 944 Sporangiospores, 792 Sporangium, definition of, 126 Spore chains, 316 Spore coat, 948 Spore dehydration, 947–8 Spore formation: Bacillus subtilis, 126–7 to escape radiation, 450 myxobacteria, 322–3 Spores: definition, 942 yeast, 1105 see also Endospores Sporocide, 148 Sporothrix schenckii, 499, 504 Sporotrichosis, 504, 508, 512 definition, 499 Sporozoa, 336 Sporulation, 942–50 Bacillus subtilis, 128, 131–2 definition, 126, 1102 different sigma factors, 945–6 division, 944–5 engulfment, 946 gene expression compartmentalization, 945–6 germination, 949–50 guide to loci, 944 initiation, 943–4 phosphorelay, 944 post-engulfment development, 947 resistances, development of, 947–9 stages, 942–3 transcription, 987 as two-compartment system, 1042–3 Sporulation mutants, 943, 944, 946, 948 SSY 726, 61 Stable transductant, definition of, 1000 Stalked bacteria, 319 Staphylococci: coagulase-negative, 902–3 coagulase-positive, 903–4 Staphylococcus spp.: adhesion, 901–2 oral, 745 St aureus: ␣-toxin, 434 antibiotic sensitivity and space flight, 937 food-borne disease, 483 food poisoning, 411 methicillin-resistant (MRSA), 32 resident flora, 903–4 toxins, 483 transient skin flora, 900, 906–7 Start point, definition of, 984 Starvation, bacterial, 951–9 appearance of cells, 952, 953 as composite stress, 952 future perspectives, 958–9 importance of, 951–2 sigma factors, 955 sigma S, 955–7 sigma S-dependent promoters, 957–8 and virulence, 958 Starvation promoters, 951 therapeutic applications, 959 Starvation proteins, 951, 952 protection of bacteria: metabolic amplification, 952–4 stress resistance, 954 Starvation sigma factors, 955 Stavudine, 100–1 Stephan Curve, 748 Sterilization: of bioreactors, 194 definition, 613 of growth media, 736 Sterilizer, chemical, 148 Sterols, 224 Stirred tank reactors, 619, 620 Stock culture collections, 294 algae/protozoa/cyanobacteria, 310–12 bacteria: Argentina, 307 Belgium, 307 Cuba, 307 France, 307 Russia, 307 specific organisms/groups, 307–8 United States, 307 comprehensive: Finland, 307 Japan, 307 Sweden, 307 United Kingdom, 306 United States, 306 databases: federations sponsoring, 294–6 links, 312 definition, 294–313 fungi: Argentina, 307 Canada, 309 Dem-ind.qxd 10/13/03 3:39 PM Page 1145 index Czech/Slovak Republics, 309 specific organisms/groups, 308–10 genetic: early, 298 microbial, 298–9 genetic vs type/germplasm, 294 national collections/consortia, 300 Australia, 305 Belarus, 304 Belgium, 302 Brazil, 306 Bulgaria, 304 Canada, 306 China, 304 Czech/Slovak Republics, 303 France, 302 Germany, 303 Hungary, 304 India, 304 Indonesia, 305 Japan, 305 Mexico, 306 The Netherlands, 302–3 New Zealand, 305–6 Poland, 303 Russia, 304 Taiwan, 305 Thailand, 305 Ukraine, 304 United Kingdom, 301–2 United States, 306 organism-specific, 300 organizations promoting, 312 tables, 301–12 type/germplasm, 296–8 Stoichiometry of ATP synthesis, 399 Strain construction, 1010 Strain improvement, 960–73 attributes of improved strains, 961–2 automated procedures, 966 engineering optimization: bioengineering, influence of, 971–2 metabolic engineering, 972 optimizing nutritional needs, 971 introduction, 961 need for, 961–2 significance/impact/benefits, 962 strategies: genetic recombination, 968–71 mutation, 962–8 Streptococci: group A, 907–8 non-group A, 908–9 Streptococcus spp.: in dental plaque, 749 oral, 740, 741, 744 Streptococcus spp.: oral: in dental plaque, 748 Streptococcus spp.: oral: identification, 747 Streptococcus spp.: oral: mutans group, 747, 748, 749 on prostheses, 751 in systemic illness, 751 Streptococcus spp.: Str iniae, 909 Str mutans: in dental caries, 748, 749 immunity, 743, 752 oral, 744 proteome analysis, 752 vaccination, 752 Str pyogenes: adhesion, 902 transient skin flora, 900, 907–9 Sttr pneumoniae: competence development, 1014–15 conjugative transposons, 36 DNA uptake, 1015–16 mismatch repair, 1018 pneumococcal vaccines, 1056–7 transformation, 1015–16 Streptogramin resistance, 30–1 Streptomyces spp.: chromosome map, 543 conjugation, 281–2 conjugative transfer, 820 identification, 603 linear chromosomes of, 261–2 plant diseases, 798 spore formation, 281 sporulation, 943 Str coelicolor: life cycle, 317 mycelium, 316–17 sporulation, 316–17 Str nodosus, 49 Str noursei, 51 Stromal keratitis, definition of, 85 Subacute bacterial endocarditis, 751 Subdivision, definition of, 326 Subgingival plaque, 741, 748 definition, 739 microflora, 749 Submarine habitats, 438 Sucrose, 758 Sulfate, 975, 976 Sulfate oxidizing bacteria, definition of, 974 Sulfate-reducing bacteria (SRB), 976–7, 979 Sulfide, 975 Sulfide oxidizing bacteria, 977, 979 Sulfobus spp., 438 bacteriophages, 140, 141 S solfaricus, 112 Sulfonamide resistance, 34, 38–9 Sulfotrehalose, 759, 760 Sulfur: amounts in components of earth, 975 requirements/functions in microbes, 730–1 in soil, 922 Sulfur cycle, 974–83 definition, 974 deposition of sulfur, 979, 981 within ecosystems, 979–81 environmental consequences, 981 1145 microbial: organic compound transformations, 979, 980 sulfate reduction, 976–7 sulfur oxidation, 977–8 planetary sulfur fluxes, 974–6 anthropogenic, 976 technological applications, 981–2 Sulfur oxidizing bacteria, 977, 979 Sulfur reducing bacteria, definition of, 974 Sulfuretum, definition of, 974 Sup35/Sup35p protein, 836–7 Superantigens, 429, 435 definition, 427 Supercoiling, 991 Superficial punctate keratopathy, definition of, 85 Superinfection, definition of, 135 Superoxide, 776, 777 Supragingival plaque, 741, 748 definition, 739 microflora, 749 Surface layers see S layers Surface plasmon resonance (SPR) detectors, 217, 220 Surfactant, definition of, 314 Survival in GMOs, 527 Swamp foot, 906 Swarm cell differentiation, 317, 318 Swarmer cells: Caulobacter crescentus, 319 Proteus mirabilis, 318 Symbiosis, 327 cyanobacteria, 707 definition, 626, 715 definition of, 703 with leguminous plants: history, 708–9 nitrogen fixation, 711–12 nodule formation, 712–13 mechanisms of infection, 707 with nodule formers, 717–19 plant defense response, 719 Symbiosis islands, 264 Symbiotic microorganisms: and insect/pest management, 634–6 in insects, 626–36 cellulose degradation by, 631–2 distribution across microbial kingdoms, 626–7 diversity, 626–9 function, 629–32 metabolic capabilities, source of, 629 nitrogen nutrition, contribution to, 629–31 sterol synthesis by, 631 transmission, transovarial, 633–4 transmission, vertical, 634, 635 vitamin synthesis by, 631 in insects’ guts, 627–8 density determinants, 632 transmission, 633 in insects’ tissues/cells, 628–9 density determinants, 632 Dem-ind.qxd 10/13/03 3:39 PM Page 1146 1146 Symport, 232–3, 397, 398 definition, 395 Symporter, definition of, 222 Syndecans, 569 Synergism: definition of, 156 gram-negative anaerobes, 556 interspecies substrate transfer, 665 Synthases, definition of, 859 Syntroph, obligate, definition of, 659 Syntropic, definition of, 381 Syphilis: clinical manifestations, 893–4 congenital, 894 diagnosis, 894–5 epidemiology, 892–3 late latent, 894, 896 latent, 893, 895 meningovascular, 894 organism/pathogenesis, 896–7 secondary, 895 transmission, 893 treatment, 895–6 T-8581, 60 T cells: in abscess formation, 557 in AIDS/HIV, 596, 599 definition, 591 T-complex, 283 T-complex transporter: architecture, 20–1 essential components, 18 type IV transporters: DNA transporters, 19 functional similarities, 19–20 toxin exporters, 18–19 T-DNA, 10, 283, 466 borders sequences, 12 definition, 10 integrity in transformed plant cells, 17–18 monocot transformation, 22 opine production, 283 plasmid conjunction, 16, 17–18 processing, 11, 12, 16–18 movement/integration, 17–18 transfer, 16–18 transfer intermediate formation, 16 VirE2/VirD2, 16–18 site-specific insertion, 23 T-complex transporter, 16 tagging, 23 transfer, 12, 15, 16 transport system, 18–21 yeast/fungi, gene transfer into, 22 see also T-complex transporter T-even phages, 359 T1/2, definition of, 85 Taenia saginata, 495 Taenia solium, 495 TAK 187, 61 Taq polymerase, definition of, 824 Tar chemoreceptors, 254, 256 Target sites, definition of, 1025 Tat secretory system, 235 index Tat system, 852–3 HIV gene expression regulation, 594 TATA binding protein (TBP), 677 Tau () protein, 997 Taurine, 763 Taxon, definition of, 602 TCA cycle, definition of, 314 TCE see Trichlorethane Tectiviridae, 137, 138, 140 Teichoic acids, 240, 243 definition, 240 Teichuronic acids, 243 Temperate, definition of, 1000 Temperature: soil, 920–1 and transformation efficiency, 1020–1 Temperature-shock-inducible protein, 443 Tenofovir, 106 Terbinafine, 61 Terconazole, 59 Terminal electron acceptor process (TEAP) analysis, 918, 920 Terminal redundancy, definition of, 1000 Terminator: definition, 117 factor-dependent, definition of, 117 Terminator proteins, 357 Terminators, definition of, 984 Termite guts: cellulase in, 631–2 microbiology of, 627, 631 Termites, xylophagous, 669–70 TetA protein, 1029 Tetanus, 1055 Tetanus toxin, 433 Tetracycline resistance, 27–8 determinants, 28 gene reservoirs, 42 genes, 560 genes from producers, 40–1 mechanisms, 28 Tetrahydromethanopterin (H4MPT), 671, 672 definition, 659 Tetrodotoxin, 497 Thalassohaline brine, 445 Thermoacidophiles: definition, 781 pH range, 782 Thermophiles: definition, 108 extreme see Hyperthermophiles genomics, 678 Thermoplasma, 331 Thermoplasma volcanium, 440 Thermus aquaticus, 438 Thiabendazole, 55 Thiobacillus ferrooxidans, 441, 643 Thiobacillus spp sulfur oxidation, 977, 978 Thiocarbamates, 48, 61 Thioploca spp., 977 Thiothrix spp., 977 Thiram, 61 Thrombocytopenia: definition, 85 with ganciclovir, 91 Thymine glycol, 345 Ti plasmid, 822 conjugation, 13–14 genes, 13–15 host range studies, 584 opine catabolism, 12, 13 vir genes, 11, 282 see also T-DNA Tick-borne encephalitis vaccine, 1067 Tinea barbae, 502, 503 Tinea cruris, 502 Tinea nigra, 502 Tinea pedis, 502 Tinea unguium, 502, 503 Tinea versicolor, 502, 503 definition, 499 Tioconazole, 55 Tissue culture, 1076 Tissue engineering, definition of, 189 Tnp protein, 1029 Tobacco etch virus (TEV), 79 Tolciclate, 61 Tolnafate, 61 TonB protein, 638 Topoisomerase, definition of, 350 Toxicity: bacterial, 404, 405 selective, definition of, 147 Toxin weapons, definition of, 168 Toxins, 1053, 1054 algal, 335 cytotoxins see Cytotoxins definition, 480, 1053 detection, 482, 483, 485, 486 enteropathogenic bacteria: emetic/diarrheal, 410 inflammatory diarrhea, 405, 406, 407–8 noninflammatory diarrhea, 409, 410, 411 enterotoxins see Enterotoxins exotoxins see Exotoxins fungal, 497 natural, in food poisoning, 497–8 protozoal, 496, 497 used as pesticides, 327 see also specific toxins/toxin types Toxitolerant organisms, 451 Toxocolocical interactions, definitions of, 156 Toxoids, 433 definition, 427, 1053 as vaccines, 1054 tra genes, 283 Tra proteins, 465 in G-ve bacterial conjugation, 278–80 TraA pilin, 465 Trace elements: in growth media, 738 requirements/functions in microbes, 732 Transcongugant, definition of, 10 Transconjugant, definition of, 271 Transcription: activator proteins, 990–1 definition, 340, 984 elongation, 992 blocks to, 992–3 DNA replication, implications of, 995 Dem-ind.qxd 10/13/03 3:39 PM Page 1147 index DNA topology, implications of, 994–5 Inchworm model, 993–4 transcript cleavage, 993 transcriptional slippage, 994 on emerging bacterial DNA, 268 initiation: activation, 990–1 regulation by DNA topology changes, 991 repression, 989–90 stages, 989, 990 lac repression paradigm, 989–90 machinery, 985–7 regulation by transcriptional attenuation, 117–18 regulation in flagellar construction, 476 regulation in HIV, 594 and supercoiling, 265 termination, 995 antitermination, 997–9 auxillary factors, 997 intrinsic terminators, 995–6 rho-dependent, 996–7 Transcription antitermination, 120, 122, 124 Transcription bubble, 985, 991 Transcription factors in B subtilis, 130, 131, 132 Transcription initiation, 118–24 Transcription pause structure, definition of, 117 Transcription pausing, definition of, 117 Transcription repair coupling factor, 347–8 Transcription termination, definition of, 117 Transcription unit, definition of, 984 Transcriptional activators: Bacillus subtilis, 131 HIV, 593 Transcriptional arrests, 992 Transcriptional attenuation see Attenuation, transcriptional Transcriptional pauses, 992–3 Transcriptional regulation, 984–99 promoter recognition, 986 conserved elements, 987–8 mechanisms, 988–9 Transcriptional regulators: Bacillus subtilis, 131 in DNA restriction, 366 in heat stress, 576–7 in oxidative stress, 778 Transducers, 217 definition, 216 Transducing particles, 36, 425 formation, 1005–6 Transducing phages, 1003 specialized, creation of, 1004 Transduction, 1000–11, 1013 abortive, 1007–8 in antibiotic resistance, 36, 37 definition, 36, 416, 808, 1000–1 degradation of transduced DNA, 1007 DNA injection, 1007 in E coli/Salmonella, 424–5 generalized: basic facts, 1004–5 DNA in recipient cell, 1007–8 transducing particles, formation of, 1005–6 history, 1001 in horizontal gene transfer, 583 laboratory uses: mapping, 1009–10 mutagenesis, 1009 strain construction, 1010 in natural environment, 1010 other systems, 1008–9 overview, 1002 plasmids, 819–20 of plasmids, 1009 specialized, 425, 1001–4 by other systems, 1003 by phage , 1001, 1003 by transducing phages, 1003 specialized vs generalized, 1001, 1002 stable, 1008 Transfer gene expression, 822 Transfer intermediate, 16 definition, 10 Transfer range, definition of, 582 Transferosomes, 281 Transformation, 1012–24 in antibiotic resistance, 38 artificial systems, 1020–2 efficiency parameters, 1020 bacterial, 416 biolistic devices, 1023 definition, 359, 808, 1012, 1071 DNA binding/uptake: Bacillus subtilis, 1015–16 DNS transport across membranes, 1015 gram-negative specificity, 1016–17 Streptococcus pneumoniae, 1015–16 as DNA repair system, 1019 ecological implications, 1019–20 history/diversity of systems, 1012–13 in horizontal gene transfer, 583 integration into recipient genome homologous recombination of chromosomal genes, 1017–18 mismatch repair/DNA restriction, 1018–19 processing of plasmid DNA, 1018 sexual isolation, 1018–19 of microbial eukaryotes, 1022–3 natural, 1013 plasmids, 819 regulation of competence development, 1013–15 as scavenger system, 1020 sites of DNA entry, 1021 in strain improvement, 969 Transgenes, methylation and PTGS, 79 Transgenic mice, definition of, 829 Translocons: definition, 842 Escherichia coli, 846–7 structure, 847 proof-reading ability, 847 Transmembrane pH difference (⌬pH), 785 definition, 781 1147 Transmissible spongiform encephalopathies (TSEs): association with PrPSc, 831 definition, 829 emerging, 1092–3 Transmission, amplification of, definition, 387 Transovarial transmission, definition of, 626 Transplant recipients, 91 Transport phenomena in bioreactors, 193 Transporters: ABC, 232 ion-coupled, 232–4 function, 233–4 structure, 233 type IV, definition of, 10 Transposable elements, 38, 822, 1025–41 antisense RNAs, 73 definition, 808, 1025 general structure, 1025–6 insertion sequences, 1026, 1031 definition, 1025 gene arrangement variation, 1028 prokaryotic, 1028 IS elements: history, 1027 mechanisms of transposition, 1029–31 structure, 1027–9 long interspersed nucleotide (LINE), 1040 nomenclature, 1027 transposing bacteriophages, 1026–7 see also Transposons Transposition: consequences of: conduction, 1041 genome rearrangements, 1040–1 replicon fusion, 1041 events, 1025–6 models: circular intermediate, 1030, 1031 linear intermediate, 1030–1 one-ended, 1035–6 Transposition immunity, 1035–6 Transposons, 1026 complex/non-composite, 1026, 1027, 1032 composite, 1026, 1027 definition, 1025 prokaryotic, 1032 transposition, 1031–2 conjugative, 36, 271, 274–5 Bacteroides fragilis, 560 mobilizing DNA, 275 origin/properties, 1036 transposition, 1036 definition, 271 in E coli/Salmonella, 422 in genome mapping, 543 site-specific, 1036–8 suicide delivery systems, 1040 Tn3, 1033 Tn3/Tn3-like, 1032–3 family branches, 1033–4 mechanisms of transposition, 1035 transposition functions, 1033 Tn5, 1029 Dem-ind.qxd 10/13/03 3:39 PM Page 1148 1148 Transposons (continued) Tn7: chromosomal site of insertion, 1037 inverted repeats, 1038 mechanisms of transposition, 1037–8 transposition functions, 1037 Tn10, 1029 Tn21-like, 1034–5 Tn554, 1038 yeast transposons: transposition, 1040 Ty elements, 1039–40 types, 1039 Travel and infectious disease spread, 392 Trehalose, 756 in osmotic balance, 758, 759 Trench foot, 906 Treponema spp.: oral, 747 T pallidum, 892, 896–7 Trg chemoreceptors, 254 Triarimol, 54 Trichinella spiralis, 496 Trichlorethane (TCE), 200 biodegradation, 203, 204, 206, 214 Trichomycosis axillaris, 901 Trichuriasis, 496 Tridemorph, 62 Trifluorothymidine, 92 Trimethoprim resistance, 34 Trimethylamine-N-oxide, 762 Triticonazole, 56 TRNA: charged, 123 definition, 117 in transcriptional attenuation, 118–19 Tropism, definition of, 1063 Trp RNA-binding attenuation protein (TRAP), 122 Tryptophan deficiency/excess, 122 Tsr chemoreceptors, 254 Tuberculosis, 389 Tubular necrosis, definition of, 85 Turgor pressure, 755 definition, 754 Two-compartment system, definition of, 126 Two-component regulatory systems, 1042–52 acetyl phosphate, role of, 1050–1 conserved motifs, 1044–5 role of, 1045–6 cross-regulation, 1051 definition, 1042 eukaryotic, 1052 overview, 1042–4 phosphoryl groups, flow of, 1050 phosphotransfer domains, 1042, 1049, 1052 enzyme activities, 1043 receiver domains, 1042, 1047–9, 1051 association with other domains, 1047 autophosphatase activity, 1048 enzyme activities, 1043 phosphorylation, 1043 response regulator, factors affecting, 1050–1 index signal transduction systems, 1049–50 transmitter domains, 1042, 1044–7, 1051 association with other domains, 1045 autophosphorylation, 1046 conserved motifs, 1044–5 enzyme activities, 1043 Type culture collections, 294 early, 296–8 Typhoid fever, 411 UK-109496 see Voriconazole Ultramicrobacteria, 450 Ultraviolet radiation, 343 UmuC/UmuD, 931 Underground storage tanks (USTs), 202 Uniport, 398 definition, 395 Universal childhood vaccination, 1100 Universal infant immunization, 1054 Universal phylogenetic tree, 109, 327–8 Unsaturated zone, definition of, 196 UR-9746, 60–1 UR-9751, 60–1 Urbanization and emerging diseases, 390 Urea, 763 Urinary tract infections, 165 Ushers, definition of, 454 UTP deficiency/excess, 120–1 UV light sensitivity in barophiles, 444 Uveitis, definition of, 85 Uvr proteins, 345 V-echinocandin see Anidulafungin Vaccination: antifungal, 512 definition, 427, 1053 for dental caries, 752 Vaccine immunology, 1067–9 Vaccine-preventable disease, 1067, 1069 Vaccine research, 177 Vaccines: bacterial, 1053–62 history, 1053–4 meningococcal, 566, 571–2 disease eradication, 1061–2 immunogenicity, 1068–9 licensed, 1054 anthrax vaccine, 1060 cholera vaccine, 1053, 1059–60 diphtheria vaccine, 1055 Haemophilus influenzae vaccine, 1056–7 Lyme disease, 1061–2 meningococcal vaccines, 1058–9 pertussis vaccine, 1055–6 plague vaccine, 1053, 1060 pneumococcal vaccines, 1057–8 tetanus vaccine, 1055 tuberculosis vaccine, 1060–1 typhoid vaccine, 1053, 1059 new approaches, 1054–5 smallpox, 1053 types, 1082 viral, 1063–70 correlates of protection, 1068 general principles, 1063–4 genetics, 1065 HIV, 601 live attenuated, 1064–6 molecular design, 1069 multivalent, 1065 non-infectious, 1065, 1066–7 public health impact, 1069–70 transport/administration, 1069 Vaccinia vaccine, 1064 Vaccinia virus, 76 Vacuolating cytotoxin, 412 Vaginal flora, 555 Valciclovir, 85 adverse effects, 88 chemistry/mechanism/activity, 87 clinical indications, 87 Valganciclovir, 91 VanA resistance, 32 Vancomycin resistance, 32 Variability and transcriptional attenuation, 117–18 Varicella infections, 87 Variolation, 1064 Vectors, definition of, 789, 1084 Vegetative cells, definition of, 942 Vegetative growth, definition of, 314 Vegetative reproduction, 1110–11 Vertical reproduction, definition of, 582 Vertical transmission, definition of, 626 Vibrio spp., 481 food-borne disease, 484–5 non-cholerae, 413 transient skin flora, 911–12 V cholerae, 408, 1059 food-borne disease, 484 toxin, 427, 428, 430 V fischeri, 182, 183, 184 LuxR proteins, 865 multiple quorum sensors, 865, 866 quorum sensing, 860–1, 862 V harveyi, 182 acyl HSLs in, 866–7 quorum sensing, 860–1 quorum sensing in, 866 V parahemolyticus, 484 V vulnificus, 484–5 Vidarabine, 93–4 toxicity, 93–4 Vif proteins, 597 vir genes, 282, 283 Vir proteins, 283 VirA/VirG signal transduction system, 14–15 Viral resistance, homology-dependent, definition of, 68 VirB proteins, 20–1 ATPases, 20–1 lipoprotein, 21 stimulation of plasmid uptake, 21 VirE2/VirD2 proteins, 16–18 Viread, 106 Virion, definition of, 135, 591, 1071 Viroids, 800–3 Virucide, 148 Dem-ind.qxd 10/13/03 3:39 PM Page 1149 1149 index Virulance (vir) genes, 11 activation, 14–15 regulation, 15 T-DNA transport, 18 Virulence: definition, 789 and starvation, 958 Virulence factors, 1054 Bacteroides fragilis, 556, 557 Bordatella pertussis, 18 H pylori, 20 Helicobacter pylori, 18 Legionella pneumophila, 19, 20 osmoregulation, 764 Porphyromonas gingivalis, 557 Prevotella spp., 558 Virulent, definition of, 1000 Virus receptors, 1076 Virus resistance in plants, homology-dependent, 78–80 Virus vectors, 1083 Viruses, 1071–83 and antisense RNAs, 75–8 budding, 1079–80 characteristics, 1071 classification, 1073–5 composition, 1073 coreceptors, 1077 “dead-end hosts”, 1082 definition, 1071 deletion mutants, 1080 diversity, 337–8 ecological functions, 337 emerging see Emerging viruses environments, 337 as gene expression vectors, 1082 genetic modification, 337 genetics, 1080 historical development, 1075–6 host–cell binding, 1076–7 interactions with host cell, 1080–1 interactions with host organism, 1081 latency, 1080–1 life-long persistent infection, 1070 lysogenic vs lytic state, 1080 mutability, 337–8 pathogenic, 337 plant pathogens, 800–3 protection against infection: disease eradication, 1082–3 vaccines, 1082 replication: assembly, 1077–80 attachment, 1076–7 definition, 1071 eclipse phase, 1077 entry/uncoating, 1077 genome expression/replication, 1077–8 routes of infection/carriers, 1081–2 satellites, 1075 in soil, 915 structure, 1071–3 supergroups, 1074 transport around host, 1082 visualization, 1072–3 Volatile fatty acids, definition of, 514 Voriconazole (UK-109496), 58–9 structure, 58–9 Vpr proteins, 597 Vpu proteins, 597 Vpx proteins, 597 W reactivation/mutagenesis, 928 Wastewater treatment, 979, 981, 982 Water: expulsion in osmotic control, 764 and soil bioactivity, 920 as solvent of life, 754 for yeast growth, 1107 Water activity, definition of, 754 Websites: culture collection databases, 294–6 genetic stock collections, 298–9 genomic resources, 376 molecular techniques, 377–8 type/germplasm culture collections, 296–8 see also chapter ends Weigle reactivation/mutagenesis, 928 Western equine encephalomyelitis (WEE), 1093, 1097 whi genes, 317 Whole genome shotgun/random sequencing, 373–5 closure phase, 373, 374–5 definition, 371 editing/annotation, 373, 375 library construction, 373, 374 random sequencing, 373, 374 strategy, 373 see also Complete genome sequence Whooping cough see Pertussis Willcox probabilities/scores, IDENT module, 605 World Health Organization International Health Regulations, 392, 393 Xanthomonas plant diseases, 798 Xenotransplantation, definition of, 1084 Xerophilic/xerotolerant organisms, 451 Xerostomia, 742 Xylem, definition of, 789 YadA adhesin, Yeast artificial chromosomes (YACs), 542 definition, 536 Yeasts, 47, 1102–14 aerobic respiration, 1109 alkaliphiles, 448 alphabetic listing of genera, 1103 anaerobic fermentation, 1109 biodiversity, 1103–4 budding, 1110 definition, 1102 carbon metabolism: carbon sources, 1107–8 sugar metabolism, 1108–9 sugar transport, 1108 cell components, 1106 cell shape, 1105 cell size, 1104 cell structure: cytology methods, 1105 general characteristics, 1104–5 subcellular architecture/function, 1105–6 characterization, 1103 classification by fermentation, 1108 definition, 1102–3 in esophagus/stomach, 517 food/beverage spoilage, 1114 in food chain, 1104 gastrointestinal, 522 genetic engineering procedures, 1113 genetics: genome/proteome projects, 1112 life cycle, 1111–12 manipulation, 1112 growth: population, 1111 vegetative reproduction, 1110–11 growth requirements: nutritional, 1107 physical, 1107 habitats, 1104 industrial commodities from, 1114 industrial/environmental significance, 1113 medical significance, 1113–14 microbial ecology, 1104 nitrogen assimilation, 1110 nitrogen metabolism: nitrogen sources, 1109 nitrogenous compound metabolism, 1110 nitrogenous compound transport, 1109–10 oxidative stress in, 780 pathogenic, 1113 as plant pathogens, 1113 psychrophilic, 442 taxonomy, 1103 transformation in, 1022–3 ultrastructure, 1106 Yellow fever, 1088 control, 1099 Yellow fever vaccines, 1066 Yersinia spp., 412 food-borne disease, 481, 489 toxins, 431, 435 type III secretion pathway, 857 Y pestis, 1060 Yops, 412 Zalcitabine, 100 Zanamivir, 95–6 Zidovudine, 98–9 Zoonosis, definition of, 1084 Zoonotic diseases, 390 emerging viruses, 1086, 1094, 1097 severity of, 1098 Zoospores, 522, 792, 807 definition, 514 Zoster, definition of, 85 Zygomycota, 333 Dem-ind.qxd 10/13/03 3:39 PM Page 1150 ...Dem-fm.qxd 10/9/03 6:40 PM Page i The Desk Encyclopedia of Microbiology Dem-fm.qxd 10/9/03 6:40 PM Page ii Dem-fm.qxd 10/9/03 6:40 PM Page iii The Desk Encyclopedia of Microbiology Editor Moselio... 6700 EV, The Netherlands Pablo J Pomposiello Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA James A Poupard Department of Automicrobial Profiling/Clinical Microbiology, ... satisfy curiosity regarding microbiological topics The Desk Encyclopedia of Microbiology is principally a synthesis from the comprehensive and multivolumed Encyclopedia of Microbiology Our intention