Annual Review of Microbiology 1994: Vol 48 Index

23 Pages·1994·4.4 MB·English

SUBJECT INDEX
16S rRNA sequences and, glycosomal import
263-79 as chemotherapeutic target,
phylogeny, 259-63 127-28
Abequose, 228 Actinoplanes, 273 internal targeting signals,
biosynthesis, 230 peptidoglycan, 282 124-25
Acanthamoeba castellanii Actinopolyspora, 276 peroxisomal targeting sig-
sialidase, 502 Actinosporangium, 276 nal, 122-24
3’-Acetamido-adenosine Actinosynnema, 262, 274-76 glycosomal proteins
biosynthesis, 229 Aculeacin A, 477 biosynthesis and assembly,
Acetate structure, 478 110-12
iron reduction and, 321, 331 Aculose, 227 genes encoding, 110
Shewanella putrefaciens and, Adenosine triphosphate (ATP) glycosomal targeting signals,
329 bioluminescence and, 408 2
sigma transcnption factor and, Adenoviruses, 428 glycosomes, 105-28
Adhesins, 605-7 luciferase import, 114-19
Acetobacter suboxydans Adrenodoxin, 245 membrane proteins, 125
inositol isomer oxidation and, Adriamycin metabolic functions, 109
5,11 formation genetics, 235-36 morphology and biogenesis,
N-Acetyl-D-galactosamine Adult respiratory distress syn- 107-9
parasite penetration and, 511 drome (ARDS) high-density lipoprotein-medi-
N-Acetyl-neuraminic acid, 500 Mycoplasma fermentans infec- ated lysis, 148-51
Aceuleacin A tion and, 695 potential mechanisms, 152-
glucan synthesis and, 485 Aerobacter aerogenes 55
Acholeplasma laidlawii, 699 aerobactin production, 764 human serum-mediated lysis,
Acholeplasma oculi, 699 Aerobactin, 747, 750, 764 14546
Acidothermus, 267 Aerobiosis life cycle, 109
Acidothermus cellulans, 279 manganese reduction and, 335 peroxisomal targeting signal,
Acinetobacter calcoaceticus Aerococcus viridans, 574 112-14
manganese reduction, 335 Aeromicrobium phospholipid exchange model
Acinetobacter calcoaceticus BD4 antibiotics, 280 and, 152-53
extracellular polysaccharides, Aeromicrobium erythreum, 271 pre-mRNA processing, 45-46
793 Aeromicrobium fastidiosum, 271 procyclin expression sites, 30—
Acquired immunodeficiency syn- Aeromonas salmonocida 31
drome (AIDS) surface proteins, 595-96 RNA polymerases, 40-42
causative agent, 688 African sleeping sickness, 26, sensitivity to normal human
mycoplasmas and, 687-706 106, 140-41, 144, 155, 500 serum, 143-46
opportunistic fungal infection African trypanosomes, 25-47 stage-specific antigen expres-
and, 472 antigenic variation sion, 26-27
oxidative stress and, 692-93 genetic mechanisms, 27-29 surface antigens, 26
pathophysiology, 689 apolipoprotein Al-cytotoxicity expression sites, 29-31
progression, 691-93 model and, 153-54 transcription elongation, 43-45
transmission, 690-9 | apolipoproteins and, 150-51 transcription initiation, 42-43
Acridine orange (AQ), 408 blood inoculation infectivity translational control, 46
Actinokineospora riparia, 274-76 test and, 144-45 trans-sialidase, 500-1
Actinomadura, 276-78 C-terminal microbody target- transsplicing and polyadeny|la-
Actinomadura hibisca ing signal, 112-22 tion, 45
antifungal antibiotics isolated, endocytic internal degradation variant surface glycoprotein,
489 model and, 154-55 141
Actinomyces, 270 flagellar pocket, 141-43 expression, 27, 33-36
peptidoglycan, 282 receptor-mediated endocyto- variant surface glycoprotein
Actinomycetes, 257-85 sis and, 143 genes
distribution in marine sedi- gene expression expression sites, 29-33
ments, 565 protein stability and, 46 families, 37-38
evolution time scale, 279-80 regulation, 38-47 recombination, 33-36
evolution of traits, 280-83 gencral features, 140-43 in situ activation, 31-33
novel organic molecules, 562 glycosomal assembly African trypanosomiasis, 141,
phylogenetic relationships mutational analysis, 126-27 159, 502
801
802 SUBJECT INDEX
Aglycone Amycolatopsis mediterranei, 284 protein synthesis and, 718-20
biosynthesis, 231, 237 Amycolatopsis methanolica, 274 ribosome binding and, 725-26
Agrobacterium tumefaciens Anabaena RNA-RNA pairing and, 728—
genomic distance orderings, citrate hydroxamate side- 34
636 rophore, 748 structure, 729
siderophore, 754 genomic distance orderings, AO
virulence genes, 299 633-34 See Acridine orange
Agrobactin, 754 Anaerobes AP120E, 406
Agromyces, 262 iron metabolism, 749 Apicomplexan parasites, 81-101
AIDS Anaerobic respiration extrachromosomal DNA local-
See Acquired immunodefici- iron/manganese and, 31 1-39 ization, 99-100
ency syndrome Ancylobacter aquaticus mitochondrial genome, 83-94
Albomycin, 763 haloalkane dehydrogenase, 168 organelle DNA inheritance, 98-
Alcaligenes Anguibactin, 754-55 99
biologically active substances, Animal-microbe systems putative plastid genome, 94-98
575 iron uptake, 747 Apolipoprotein Al, 146-47
Alcaligenes eutrophus Anogenital cancer Trypanosoma brucei brucei
maleylacetate reductase, 183 human papillomaviruses and, and, 150-51
Alcaligenes eutrophus H850 440 Apolipoprotein Al-cytotoxicity
3,4-dioxygenase, 540 Anogenital lesions model
Alcaligenes eutrophus JMP134 human papillomaviruses and, trypanosome lysis and, 153-54
chloromuconic acid 429 Apolipoprotein All, 146
cycloisomerase, 183 Ansamycins, 280 Apolipoprotein Cl, 147
dehalogenating enzymes, 166 Antibiotic-DNA complexes Aquatic environments
Alcaligenes faecalis, 547 formation, 224 iron-uptake systems, 746
Aldolase, 111, 123 Antibiotic resistance, 346 Aquifex
Algarose Antibiotics peptidoglycan, 282
biosynthesis, 233 aminocyclitol Arachnia, 262
2-Alkanols, 786 biosynthesis, 234 Arcanobacterium haemolyticum,
2-Alkanones, 787 aminoglycoside
Altermonas biosynthesis, 239-40 Archeae
novel organic molecules, 562 antifungal, 471-91 abundance in oceans, 563
Altermonas haloplanktis deoxysugar ligands, 234-40 ARDS
novel organic molecules, 562 evolution, 280-81 See Adult respiratory distress
Altermonas ruba human immunodeficiency syndrome
novel organic molecules, 562 virus and, 689 Arginine deaminase
Alteromonas putrefaciens, 328 macrolide, 280 mycoplasmas and, 701
Alzheimer’s disease, 664 biosynthesis, 233-34 Aroclor 1221
a-Amanitin, 40 mannan-binding, 489-91 degradation, 543-44
Amastigotes, 450-51 nucleoside Aroma chemicals
American trypanosomes biosynthesis, 229 microbial biocatalysis, 777-94
glycosomes, 107 polyketide Arsenicals
Amicetose, 227 formation genetics, 235-36 trypanosomiasis and, 127
Amine oxidase, 119 Antibody-based testing Arsenite
Aminocyclitol antibiotics, 280 food-borne bacteria and, 409- transposon selection markers
biosynthesis, 234 14 and, 530
3’-Amino-3’-deoxyadenosine Antimycin, 85 Arthritis
biosynthesis, 229 Antimycin A rheumatoid
Aminoglycoside antibiotics iron reduction and, 333 Mycoplasma fermentans
biosynthesis, 239-40 manganese reduction and, 335 and, 692
8-Aminoquinolines, 85 Antisense RNA, 713-34 septic, 606
Amino sugars, 228-29 bacterial gene expression and, Arthrobacter, 261, 267-70, 279
biosynthesis, 249-50 726-28 menaquinones, 28 1
Ammonia bacteriophage development peptidoglycan, 282
histidine degradation pathway and, 723-25 Arthrobacter AD2
and, 14 binding pathways and kinetics, dehalogenating enzymes, 179
Ammonification, 315 729-34 Arthrobacter globiformis
Amphotericin B IncF and R1 plasmic conjuga- DSM3597
opportunistic fungal infection tion and, 722 eugenol biotransformation and,
and, 472 killer gene expression and, 781
Ampulariella, 273 722-23 Arthrobacter SU
Amycolatopsis plasmid replication and, 715- dehalogenating enzymes, 166,
antibiotics, 280 21 180
SUBJECT INDEX 803
Ascarylose Bacillus stearothermophilus nitrogen regulation, 17-21
biosynthesis, 228, 230, 242-49 CpG relative abundances, 625 pathogenic
Ascobolus isomerase Bacillus subtilis Sialic acids and, 501
repeat induced point muta- catechol siderophore, 749 propionic-acid, 259
tions, 620 ferulic acid deacetylase activ- Sigma transcription factor, 53-
Ascophyllum nodosum, 570 ity, 782 75
Aspergillus fumigatus genomic distance orderings, species grouping, 638
cell wall composition, 477 636 toxins
fibrinogen and, 604 histidine-degrading system, trypanosome lytic factor
LY303366 and, 483-84 15-17 and, 158-59
Aspergillus nidulans sigma transcription factor See also Marine bacteria
gene expression vegetative, 63 Bactenophage development
pH and, 454 starvation survival strategy, antisense RNA and, 723-25
Aspergillus niger, 788-90 54-55 Bacteroides, 264
fermentation of glucose, 776- Bacteria peptidoglycan, 282
77 amino acid sequences Bactometer, 407
ferulic acid biocatalysis, 783 compositional extremes, Benanomicins, 489-91
Atergatis floridus 624-26 Beneckea gazogenes
tetrodotoxin production, 568 antibiotic resistance, 346 novel organic molecules, 562
Atopobium antisense RNA control, 726-28 Benzaldehyde
peptidoglycan, 282 biogenesis of deoxysugars, microbial biocatalysis, 784—
Atopobium minutum, 265 223-50 85
ATP engineering for in situ applica- Benzene
See Adenosine triphosphate tions, 547-48 degradation, 531
ATP luminometer, 302-3 food-borne, 401-20 Benzoate
Aureobacterium flavescens JG9 antibody -based tests, 409-14 oxidative catabolism, 532
siderophore detection and, 745 isolation and identification, Benzoic acid
Aureobasidium 403 sigma transcription factor and,
2-alkanols, 786 miniaturized biochemical as- 60
Aure hs. ey P Tiesl, says, 405-6 Benzoylformate
2-alkanone production, 787 nucleic acid-based tests, conversion to benzaldehyde,
Aureomycin, 7 414-17 784-85
Axenic transformation, 458-59 physicochemical assays, B-Lactams
Azoles fungi and, 473
Candida albicans and, 488 gram-negative Bifidobacterium, 258-59, 262,
opportunistic fungal infection collagen-binding 267-68
and, 472 MSCRAMMs, 600-2 peptidoglycan, 282
Azotobacter vinelandii extracellular matrix-binding Bifidobacterium bifidum
cytidylyltransferase, 243 molecules, 590 iron transport, 745—46
genomic distance orderings, fibrinogen-binding BIT
636 MSCRAMMs, 603-4 See Blood inoculation infectiv-
siderophore production, fibronectin-binding ity test
762 MSCRAMMs, 595-96 Biocatalysis
Azurechelin, 754 iron deprivation and, 762 microbial, 773-94
gram-positive aroma chemicals and, 777—
B abundance in marine sedi- 94
ments, 567 bulk flavor chemicals and,
Babesia, 82 collagen-binding 775-77
mitochondrial DNA, 93 MSCRAMMs, 597-600 Biocatalysts
Babesia microti, 84 fibrinogen-binding environmental pollution and,
Babylonia japonica MSCRAMMs, 602-3 531-41
toxicity, 568 fibronectin-binding Biochemical assays
Bacillus, 261, 265 MSCRAMMs, 589-95 food-borne bacteria and, 405-6
citrate hydroxamate side- iron-reducing Biogeochemical metal cycles, 312
rophore, 748 bioremediation and, 329-30 Biolog Identification System, 409
iron reductase, 331 magnetite and, 327 Bioluminescence, 295-305
manganese reductase activity, iron-uptake systems, 749-59 food-borne bacteria and, 408
335-36 lactic-acid, 259 light-measuring devices and,
metal-reducing, 330 metal reduction rates, 332 302
novel organic molecules, 562 methanotrophic, 372 Bioluminescence
Bacillus cereus classes, 374 applications, 297-301
enterotoxin, 413 methane oxidation pathway, Bioremediation, 533, 544, 549
food-borne, 402 373 heavy metals and, 546
804 SUBJECT INDEX
iron-reducing bacteria and, cAMP Castor oil
329-30 sigma transcription factor and, biotransformation to y-
Bioreporter genes, 291-95 60, 66-67 decalactone, 789
characteristics, 294-95 CAMP test, 406 Catabolic plasmids
Biota Campylobacter ferulic acid metabolism and,
metal reduction and, 320 food-borne 782
Black death, 757 polymerase chain reaction Catabolite repression, 11-15
Blasticidin S assays, 417 Catalase, 117
formation, 234 Campylobacter coli in glycosomes, 108
BLASTN, 650 food-borne, 402 Mycoplasma pneumoniae in-
Blastomyces dermatitidis Campylobacter jejuni fection and, 693
cell wall composition, 477 food-borne, 402 Catalase A, 119
LY303366 and, 484 Canarose, 226 Catalase hydroperoxidase II
Blastospore, 476 Cancer katF gene and, 56
Blood inoculation infectivity test human papillomaviruses and, Catechol-2,3-dioxygenase, 539
(BIT), 144-45 428, 433, 440-41 inactivation, 535
Bloodstream Cancer chemotherapy Catenulospora, 273
African trypanosomes and, 141 opportunistic fungal infection CCCP
Boivinose, 226 and, 472 See Carbonyl! cyanide m-
Bordetella pertussis Candida chloropheny! hydrazone
integrin-binding proteins, 587 echinocandin lipopeptides and, Cell adhesion
Borrelia burgdorferi 478 extracellular matrix and, 586—
CpG relative abundances, 625 LY 303366 and, 483-84 87
genomic distance orderings, Candida albicans, 117 Cell morphology
634 azoles and, 488 sigma transcription factor and,
Bovine spongiform encephalopa cell wall composition, 476-77 71-72
thy (BSE), 655, 667 cell wall structure, 473-74 Cellulomonas, 261
Brachybacterium cilofungin and, 485 Cephalopod light organs
menaquinones, 281 fibrinogen and, 604 associations, 566
Brachybacterium faecium fibronectin and, 597 Ceratoporella nicholsoni, 571
menaquinones, 28] nikkomycins and, 488 Cerebrospinal fluid (CSF)
Bradyrhizobium japonicum polyoxin D and, 486-87 African trypanosomes and, 141
bioluminescence and, 298 pradimicins and, 490-91 Cervical cancer
Brain Candida guilliermondi human papillomaviruses and,
African trypanosomes and, 141 y-decalactone and, 789 428, 433, 440-41
Branched-chain sugars, 228-29 Candida petrophilium, 790 Chaetiacandin, 484
Brevibacterium Candida tropicalis, 117 Chagas’ disease, 106, 144, 500,
glutamic acid production and, macrocyclic musks and, 792 605
777 Carbohydrates trans-sialidase and, 515
Brevibacterium linens, 279 iron reduction and, 320 Chainia, 276
Brochothrix, 261 Carbon Chainia purpurogena
Brominated dipheny] ethers biogeochemical metal cycles novel organic molecules, 562
isolation, 568-69 and, 312 Chalcomycin, 227
Bromoacetic acid, 167 organic Chalcose, 227
Brown alga metal reduction and, 318, Chelation
gram-positive bacteria and, 322 iron, 744—45
Carbonate Chemical crosslinking
Bryostatin 1, 560, 569 iron/manganese and, 327 methane monooxygenase
BSE Carbon cycling catalytic cycle and, 388—
See Bovine spongiform en- iron/manganese and, 312-15, 90
cephalopathy 318 Chemical quench studies
BU-4794, 484 Carbon oxidation methane monooxygenase
Bubonic plague, 757 metal reduction and, 318-20 hydroxylase and, 385-86
Bugula neritina, 569 Carbonyl cyanide m- Chiral ethane
Bulk flavor chemicals chloropheny! hydrazone oxidation by methane
microbial biocatalysis, 775-77 (CCCP) monooxygenase
manganese reduction and, product distribution, 382
Cc Chiral substrate inversion
Cardiac glycosides methane monooxygenase and,
Caenorhabditis elegans biologic potency 381-83
genomes, 620 deoxysugars and, 224 Chitin synthase inhibitors, 486-89
sequence distance orderings, 2-deoxysugars, 225 Chitin synthesis
630 dideoxyhexoses, 226 inhibitors, 472
SUBJECT INDEX
Chlamydia trachomatis CJD Compound 42, 231
heparan sulfate-like See Creutzfeldt-Jakob disease Compound 43, 231-32
glycosaminoglycan, 605 Cladosporium suaveolens, 789- Compound 44, 231-33
sexual transmission of HIV-1 90 Compound 47, 233
and, 690 Clavibacter, 268 Compound 48, 233
Chlamydomonas reinhardtii Click beetle Compound 49, 236, 249
COIII gene and, 91 luciferase, 305 Compound 50, 234, 249
rRNA fragments, 88 Clomipramine Compound 51, 249
Chlamydospore, 476 Leishmania and, 455 Compound 52, 236, 249
Chloramphenicol acety! transfer- Clostridium, 265 Compound 54, 234
ase (CAT) gene, 114 peptidoglycan, 282 Compound 55, 234
Chioroacetic acid, 164 Clostridium acetobutylicum Compound 56, 237
3-Chloroacrylic acid glutamine synthetase genes Compound 57, 239, 249
dehalogenation, 180-8 | antisense RNA and, 727-28 Compound 58, 239
Chloroalkanes Clostridium botulinum Compound 62, 240, 249
metabolism neurotoxins, 412 Compound Q
oxygenases and, 182 Clostridium perfringens, 412 chemical nature, 386-87
1-Chloro-n-alkanes, 168 enterotoxin, 413 Computational DNA sequence
Chlor compound food-borne, 402 analysis, 619-SO
metabolism, 171-72 sialidase, 504 Conductance
2-Chlorobenzoate Clove oil, 780 food-bome bacteria and, 407
dehalogenation, 182 Coagulase, 603 Condylomata acuminata, 442
3-Chlorobenzoate Coated pits Condylomatous lesions
degradation, 542 flagellar pocket and, 143 human papillomaviruses and,
4-Chlorobenzoate Coated vesicles 429
dehalogenation, 180 flagellar pocket and, 143 Coniferylaldehyde, 781
4-Chlorobenzoate dehalogenase, Coconut oil, 786-87 Connective tissue
179-80 Coelenterates, 566 African trypanosomes and, 141
Chlorobenzoates ColE1 Cordycepin, 225
mineralization, 543 antisense RNA and, 716-18 biosynthesis, 229
Chlorocatechol RNA I-RNA II binding, 730— Cordycepose, 225
ortho-cleavage pathway, 542 31 Corneal transplantation
2-Chloroethylvinylether, 168 Coliphages Creutzfeldt-Jakob disease and,
Chloroflexus tetranucleotides, 627 664
peptidoglycan, 282 Colitose, 228, 230 Corynebacteriaceae, 271-73
1-Chlorohexane, 173 biosynthesis, 231 Corynebacterium, 259, 262, 268
Chloromaleylacetate Collagen-binding MSCRAMMs, chloroalkane metabolism
reductive dehalogenation, 182- 597-602 oxygenases and, 182
83 Colony hybridization method glutamic acid production, 777
Chloromuconic acid food-borne bacteria and, 415 growth on eugenol, 780
dehalogenation, 182 Complement mycolic acids, 281
3-Chloromuconic acid, 183 trans-sialidase and, 513-15 Corynebacterium amycolatum,
Chloromuconic acid isomerase, Component B 273
183 methane monooxygenase Corynebacterium diphtheriae
4-Chlorophenylacetate catalytic cycle and, 387- Fur-like genes, 763-64
dehalogenation, 182 95 Corynebacterium glutamicum,
2-Chloropropionic acid, 167. Compound 14, 226, 231 267
173-75 Compound 17, 226-27 Corynebacterium N-1074
Chiorothricin, 231 Compound 18, 227 dehalogenating enzymes, 179
Cholera toxin Compound 19, 227 Couchioplanes, 273
trypanosome lytic factor and, Compound 20, 227 peptidoglycan, 282
158 Compound 21, 227 Creutzfeldt-Jakob disease (CJD),
Chromobacterium Compound 22, 228 656, 661-63
novei organic molecules, 562 Compound 23, 228 human growth hormone ther-
Chromose C, 226 Compound 24, 228 apy and, 665-66
Chrysobactin, 748-49 Compound 25, 228 iatrogenic, 664-65
Cilofungin, 472, 477-80 Compound 26, 228 Cristispira
fungal cell wall synthesis and, Compound 27, 230 molluscs and, 566
485 Compound 28, 229 Crithidia
Citric acid Compound 29, 229-30 glycosomes, 107-8
microbial biocatalysis, 776-77 Compound 30, 243 Crithidia fasciculata
Citric acid cycle Compound 31, 243 glycosomal isozymes, 110
fatty acid oxidation and, 785 Compound 32, 243 glycosomes, 107
806 SUBJECT INDEX
Cryptococcus neoformans Dehalogenases, 164 Dictyostelium discoideum
cell wall composition, 477 4-chlorobenzoate, 179-80 gene expression
polyoxin D and, 486 dichloromethane, 177-78 pH and, 454
pradimicins and, 490 haloacetate, 167, 172 Dicyclohexylcarbodiimide, 85
Cryptosporidium, 82 haloacid, 167-68 Didemnin B, 560
CSF 2-chloropropionic acid-spe- 2,6-Dideoxyhexose, 226-27
See Cerebrospinal fluid cific, 173-75 biosynthesis, 231-32, 249-50
Cumene hydroperoxide haloalkane, 168-73 3,6-Dideoxyhexose, 225, 227-28
methane monooxygenase and, catalytic mechanism, 169 biosynthesis, 231
380 hydrolytic, 164-77 enzymes involved, 242-49
Curli, 72 tetrachloro-p-hydroquinone re- formation
Curtobacterium, 268 ductive, 178 C-3 deoxygenation step and,
Cyanobacteria, 264 Dehalogenating enzymes, 163-87 247
abundance in oceans, 563 Dehalogenation 4,6-Dideoxyhexose, 227
iron-uptake systems, 756-57 enzyme-catalyzed, 167 biosynthesis, 249-50
Cyanobacterial symbionts, 569 reductive, 183 formation, 232-33
CyclinA 4,6-Dehydratases, 230, 243-44 Dideoxysugars, 226-28
viral E7 proteins and, 435 Dehydrochlorinase, 184 DIDS
Cyclin DI Dehydrodiconifery! alcohol, 779 See 4,4’-
Diisothiocy sa
viral E7 proteins and, 435 Dehydrodivanillic acid, 779
Cyclin E Dehydrohalogenation, 184 2,2’-disulfonic acid
viral E7 proteins and, 435 Deinococcus, 265 Dienelactone hydrolase, 171
Cyclin E2F Denitrification, 315 Difluoromethylomithine (DFMO)
viral E7 proteins and, 435 2-Deoxy-2,3-didehydro-V- trypanosomiasis and, 127
Cyclopentadecanolide, 792 acetylneuraminic acid Digitoxose, 226
Cystic fibrosis trans-sialidases and, 509 Dihydrofolate reductase (DHFR),
siderophores and, 747 Deoxyhexoses, 224-25 117
Cystodytes lobatus, 570 6-Deoxyhexoses, 225-26 Dihydroorotate dehydrogenase
Cytochrome b Deoxymulundocandin, 478 tetracycline and, 91
iron reduction and, 333 Deoxysugars, 223-50 Dihydroxyacetone phosphate
manganese reduction and, 335 biogenesis, 229-34 (DHAP), 109
Cytochrome c genetics of formation, 234-42 Dihydroxyacetone synthase, 117
iron reduction and, 333 naturally occurring, 225-29 Dihydrox ybiphenyldioxygenase,
manganese reduction and, 335 structures, 227 536, 540
Cytochrome P-450 Dermatophilaceae, 276 4,4’-Diisothiocyananostilbene-
hydrocarbon oxidation and, 372 Dermatophilus, 276 2,2’-disulfonic acid (DIDS)
structure, 536-37 Dermatophilus congolensis, 268 Leishmania donovani pro-
substituent migration and, 380 Dermatophytes mastigotes and, 457
Cytokines cell wall composition, 477 Diketopiperazines, 568
human immunodeficiency Desosamine, 249 Dimethylcyclohexane
virus and, 691 Desulfovibrio desulfuricans, 330 conformation, 11
Cytolysin, 747 Desulfuromonas acetoxidans, 1,1-Dimethylcyclopropane
Cytophaga, 264 312, 329-30 methane monooxygenase and,
Cytosylglucuronic acid DFMO 381
conversion to blasticidin S, 234 See Difluoromethylornithine 2,5-Dimethy]-4-hydroxyfuran-3-
DHAP one (DHMP), 793
D See Dihydroxyacetone phos- Dinoflagellates
phate saxitoxin isolation, 568
Dactylosporangium, 273 DHFR Dinucleotides
Daunomycin See Dihydrofolate reductase relative abundances, 622-24
formation genetics, 235-36 DHMF viral
Daunorubicin, 249 See 2,5-Dimethy!-4- extreme relative abun-
amino sugar, 234 hydrox yfuran-3-one dances, 626-27
antineoplastic activity Diaphorase, 245 Dioxygenases, 181-82
daunosamine and, 224 Dichloroacetic acid, 167 Diphtheria toxin
formation genetics, 235-36 1,2-Dichloroethane, 168 trypanosome lytic factor and,
Daunosamine, 234-36 catabolic pathway, 168 158
antineoplastic activity and, 224 Dichloromethane dehalogenase, 2,2-Dipyridyl
y-Decalactone 177-78 iron transport and, 746
microbial biocatalysis, 788-91 Dichloromuconic acid, 183 Direct epifluorescent filter tech-
DEFT 2,2-Dichloropropionic acid, 167 nique (DEFT), 408
See Direct epifluorescent fiiter Dicots Dissimilatory metal-reducing or-
technique iron deficiency and, 748 ganisms, 327-30
SUBJECT INDEX 807
Dissimilatory metal reduction, ECB Enterobacteriaceae
322-27 See Echinocandin B biochemical assays, 405-6
DNA Echinocandin B (ECB), 477-83
mitochondrial, 83-94 semisynthetic analogues, 472,
DNA hybridization 479-80 Enterobactin, 749-50, 753-54
assays structure, 478 Enterotoxins
food-borne bacteria and, Echinocandin lipopeptides staphylococcal
414-15 glucan synthesis and, 472, 477- immunoassays, 412
TetA antiporter and, 347 84 Enterotube II, 406
DNA probe-based testing modes of action, 485-86 Environmental biotechnology,
food-borne bacteria and, 414— structures, 478 527
16 Echinoderms Environmental metal cycling,
DNA:rRNA hybridization assays subcuticular bacteria and, 566 315-22
actinomycetes and, 262 ECM Environmental pollution, 525-51
DNA sequence analysis, 619-50 See Extracellular matrix biocatalysts and, 531-41
compositional extremes, 624-26 EEG electrode implantation biological solutions and, 527-
dinucleotide relative abun- Creutzfeldt-Jakob disease and, 28
dances, 628-30 664-65 biological treatment processes
eukaryotic distance orderings, EHEC-TEK, 411 and, 528-29
630 Eimeria, 82 expression factors and, 530-31
genomic partial ordering com- Eimeria bovis transposon cloning vectors
parisons, 631-32 mitochondrial DNA, 93 and, 529-30
genomic sequence in- Eimeria tenella Environmental reduction, 317
homogencities, 640-45 plastid DNA, 98 Enzyme-linked coagulation assay
oligonucleotide frequencies sialidase, 502 (ELCA)
and relative abundances, ELCA food-bome bacteria and, 413
628-30 See Enzyme-linked coagula- Enzyme-linked immunosorbent
prokaryotic distance orderings, tion assay assay (ELISA)
632-36 Electron acceptors food-bome bacteria and, 410-
rare and frequent oligonucleo- comparison, 316 13
tides and peptides, 636-40 Electron microscopy Epibiosis, 570
relative abundance disiance trypanosome lytic factor and, Epidermodysplasia verruciformis
measures, 628-30 148-49 (EV), 428-29, 433
score-based methods, 645-49 Electron nuclear double reso- Epifagus virginiana
viral dinucleotide extreme rela- nance (ENDOR) plastid DNA, 96-97
tive abundances, 626-27 methane monooxygenase Epimastigotes
DNA tumor viruses hydroxylase diiron clus- sialic acid, 501
host cell immortalization and, ters and, 376-77 EPR spectroscopy
434 ELISA methane monooxygenase
Doxorubicin See Enzyme-linked im- catalytic cycle and, 390
antineoplastic activity munosorbent assay Epstein-Barr virus (EBV), 434
daunosamine and, 224 Elytrosporangium, 276 lytic origin of replication, 642
formation genetics, 235-36 EMBL, 263 Erwinia
Doxycycline Endocarditis, 607 bioluminescent, 298
Mycoplasma fermentans and, Endocytic internal degradation Erwinia chrysanthemia
695 model chrysobactin, 748-49
Dr bil, 1 trypanosome lysis and, 154— Erysipelothrix, 261
genomic distance orderings, 55 Erythromycin, 249, 274
636 Endocytosis biosynthetic pathway, 236-37
nonredundant protein se- receptor-mediated Plasmodium falciparum and,
quences, 639 flagellar pocket and, 143 89
sequence distance orderings, ENDOR Erythromycin A, 236
630 Sce Electron nuclear double Escherichia
Duanosamine, 249 resonance iron reductase, 331
Dura mater grafting Endosymbiont hypothesis, 622 Escherichia coli
Creutzfeldt-Jakob disease and, Endotoxin A B-galactosidase, 12, 16
665 trypanosome lytic factor and, bioluminescent, 298
Dysidea herbacea, 569 158 collagen-binding
Endotrypanum MSCRAMM, 600-2
E trans-sialidase, 501 CTAG tetranucleotide, 625-26
Enliten test, 408 y-decalactone, 789
EBV Enterobacter DicF RNA
See Epstein-Barr virus type 3 fimbriae, 601 antisense RNA and, 727
808 SUBJECT INDEX
DNA repair mechanisms, 70— methane monooxygenase localization/induction of activ-
71 and, 380 ity, 334
epithelial cell sialic acid and, Ethylene brassylate, 792 respiration-linked, 331-32
4-Ethyltoluene, 539 Ferrioxamines, 749
ferrichrome receptor, 763 Eubacterium, 261 Ferripyochelin, 753
food-borne, 402, 404 Eugenol Ferripyoverdin, 753
DNA probe-based assays, biotransformation, 780-81 Ferrisiderophores, 331
414 Euglena gracilis Ferritin, 747
enzyme-linked immunosorb- rRNA fragments, 88 Ferulic acid metabolism, 779,
ent assays, 411-12 Eukaryotes 781-83
polymerase chain reaction ferulic acid decarboxylation FFI
assays, 417 and, 782 See Fatal familial insomnia
Fur-like genes, 763 gene expression, 454 Fibrinogen-binding
Fur protein, 763-65 Eukaryotic cells MSCRAMMs, 602-4
gene expression gene expression Fibronectin-binding
pH and, 454 DNA flexibility and, 19-20 MSCRAMMs, 589-97
genomes, 620 peroxisomes, 107 Firefly
genomic distance orderings, tet regulatory system and, 363- luciferase, 298
636 65 Flagellar pocket, 141-43
inositol metabolism, 12 Eukaryotic sequences receptor-mediated endocytosis
iron-uptake systems, 749-52 distance orderings, 630 and, 143
lacZ system, 294 EV Flavobacterium, 264
lambdoid phages, 194 See Epidermodysplasia ver- anti-tumor polysaccharide, 575
lambdoid prophage insertion ruciformis Flavobacterium ATCC33790
sites, 209 Evermicose dehalogenating enzymes, 166
nonredundant protein se- formation, 233 Flavobacterium ATCC39723
quences, 638-40 EXAFS dehalogenating enzymes, 165
O antigen genetics, 240 See X-ray absorption spectros- Flavodoxin, 756
OmpF expression copy fine structure Flavor chemicals
antisense RNA and, 726-27 Exons microbial biocatalysis, 775-77
repetitive extragenic palin- location in human B-globin role in foods, 774
dromes, 620 and growth hormone se- Fluorescence
sialic acid quences, 647-49 food-borne bacteria and, 408
complement activation and, score-based prediction, 646-47 Fluorescence spectroscopy
514 Exonuclease III methane monooxygenase
siderophore detection, 745 DNA repair and, 71 catalytic cycle and, 388—
sigma transcription factor, 58— Extracellular matrix (ECM) 90
59 cell adhesion and, 586-87 Fluoroacetic acid, 167
vegetative, 63 Fluorochromes, 408
sliding window analyses, 644 F Fluoroquinolone DR-3335
starvation survival strategy, 54— human immunodeficiency
Fatal familial insomnia (FFI), virus and, 689
tetracycline resistance proteins, 656, 661-62 Focal epithelial hyperplasia (FEH)
347 Fatty acid desaturases genetic predisposition, 433
toxins diiron clusters, 375 Food-borne bacteria, 401-20
trypanosome lytic factor Fatty acid oxidation antibody-based tests, 409-14
and, 158 citric acid cycle and, 785 isolation and identification, 403
tRNA binding, 88 peroxisomes and, 107 miniaturized biochemical as-
tryptophanase, 16 Feedback inhibition, 13 says, 405-6
virulence genes FEH nucleic acid-based tests, 414—
modulation, 72 See Focal epithelial hyperplasia 17
Escherichia coli K-12 Fermentation physicochemical assays, 406—
defective lambdoid prophages, of glucose, 776-77 9
207 of glutamic acid, 777 Food chain
Ethane Ferric citrate, 750 methanogenic, 321
oxidation by methane Ferric dicitrate, 764-65 Food poisoning, 568
monooxygenase Ferric enterochelin, 751-52 Formate
product distribution, 382 Ferrichrome, 749 iron reduction and, 331
Ethanol Ferrichrome A, 759 Shewanella putrefaciens and,
iron reduction and, 320 Ferrichrome receptor, 762 329
4-Ethylcatechol, 539 Ferric iron reduction, 331-34 FR901379, 478
Ethylene Ferric phosphate, 326 Frankia, 276
halogenated Ferric reductase Freeze quench studies
SUBJECT INDEX 809
methane monooxygenase GENMARK, 646 Sigma transcription factor and,
hydroxylase and, 384 Genomic sequences 73
Fructose compositional extremes, 621- Glycomyces, 277, 279
microbial biocatalysis, 775-76 27 Glycophorin A
Fucose, 225 distribution of close repeats sialic acid, 511
Fungal cell wall and dyads, 641-42 Gly I glyc Idehyde phos-
antibiotics and, 471-91 inhomogeneities, 640-45 phate dehydrogenase
as antifungal target, 475-77 quantile distributions of com- (gGAPDH), 111
benanomicins and, 489-91 positions, 642-45 Glycosomal import
chitin synthase inhibitors and, Geobacter metallireducens, 311- internal targeting signals, 124—
486-89 12, 329-30 25
echinocandin lipopeptides and, iron reductase activity, 332-33 peroxisomal targeting signal,
477-84 Geodermatophilus, 276 122-24
functions, 475 Gerstmann-Straussler-Scheinker Glycosomal protein import
glucan synthase inhibitors and, disease (GSS), 656, 661-64 as chemotherapeutic target,
477-86 gGAPDH 127-28
mannan-binding antibiotics See Glycosomal glyceralde- Glycosomal proteins
and, 489-91 hyde phosphate dehydro- biosynthesis and assembly,
nikkomycins and, 486-89 genase 110-12
papulacandins and, 484 Gingivitis, 603 genes encoding, 110
polyoxins and, 486-89 GK genomic organization and
pradimicins and, 489-9] See Glycerol kinase expression, 113
structure and composition, B-Globin sequences Glycosomal targeting signals,
473-75 location of exons, 647-49 112-22
Fungi Glossina, 26, 141 Glycosomes, 105-28
iron-uptake systems, 759-61 Glucan synthase inhibitors, 477- assembly
methyl ketones and, 785 86 mutational analysis, 126-27
pathogenic Glucan synthesis luciferase import, 114—19
cell wall composition, 477 inhibitors, 472 membrane proteins, 125
Fur box, 763 Glucose metabolic functions, 109
Fur protein, 763-65 aerobactin production and, 764 morphology and biogenesis,
Fusobacterium prausnitzii enzyme synthesis and, 14 107-9
ATCC27766, 270 iron reduction and, 320 Glyoxylate cycle, 107-8
isomerization by xylose Glyoxysomes, 107
G isomerase, 775-76 GMP reductase, 13
Glucose effect, 14 Gordona, 273
Gaffkya homari, 574 Glucosephosphate isomerase mycolic acids, 281
Galactose (PGI), 111 GRAIL, 646
parasite penetration and, 511 B-p-Glucosy]-hydroxy- Gram-negative bacteria
Galactose dehydrogenase, 537 methyluracil, 31 collagen-binding
B-Galactosidase, 12, 16 Glutamic acid MSCRAMMs, 600-62
GAPDH microbial biocatalysis, 777 extracellular matrix-binding
See Glyceraldehyde-3-phos- Glutamine synthetase, 17-19, 21 molecules, 590
phate dehydrogenase antisense RNA and, 727-28 fibrinogen-binding
Gardnerella vaginalis, 268 Glutathione MSCRAMMs, 603-4
Gastritis, 759 oxidative stress and, 122 fibronectin-binding
GDH T-cell immune function and, MSCRAMMs, 595-96
See Glycerol phosphate dehy- 693 iron deprivation and, 762
drogenase Glutathione peroxidase Gram-positive bacteria, 261
GENBANK, 210-11, 263 oxidative stress and, 122 abundance in marine sedi-
GenelD, 646 Glutathione reductase ments, 567
GeneModeler, 646 oxidative stress and, 122 collagen-binding
GeneParser, 646 Glutathione transferase, 177-78 MSCRAMMs, 597-600
Genes Glyceraldehyde-3-phosphatdee - fibrinogen-binding
score-based prediction, 646-47 hydrogenase (GAPDH), 110 MSCRAMMs, 602-3
Genetic engineering, 527, 544 Glycerol 3-phosphate fibronectin-binding
chemical mechanism of isomer- iron reduction and, 331 MSCRAMMs, 589-95
ization and, 776 Glycerol kinase (GK), 111 Gram-positive cocci, 259
Genital ulcers Glycerol phosphate dehydroge- Granaticin, 231
sexual transmission of HIV-1 nase (GDH), 111 Green alga
and, 690 a-Glycerophosphate oxidase sys- gram-positive bacteria and, 567
Genital warts tem, 109 Growth hormone sequences
genetic predisposition, 433-34 Glycogen synthesis location of exons, 647-49
810 SUBJECT INDEX
Growth hormone therapy HEC 0157 ELISA, 411 Human cytomegalovirus (HCMV)
Creutzfeldt-Jakob disease and, Helicobacter pylori lytic origin of replication, 642
665-66 siderophore production, 759 Human growth hormone therapy
GSS Hemagglutinin, 587 Creutzfeldt-Jakob disease and,
See Gerstmann-Straussler- Heme, 747 665-66
Scheinker disease as iron source, 757-58 Human immunodeficiency virus
Guaiacol, 777, 782 Hemerythrin (HIV)
Guanosine tetraphosphate diiron clusters, 375 acquired immunodeficiency
bacterial response to starvation Hemoglobin syndrome and, 688
and, 6! as iron source, 757-58 interaction with mycoplasmas,
Hemolysin, 747 689-90
H Heparan sulfate, 604—5 Human immunodeficiency virus
penetrin and, 513 (HIV) infection
Haemophilus, 268 Heparin-binding MSCRAMMs, cofactor, 690-93
Haemophilus influenzae, 347 604-5 Mycoplasma penetrans and,
genomic distance orderings, 2-Heptanone, 785-87 687-88
636 2-Hepty!-4-hydroxy-quinone-V- oxidative stress and, 692-93
heme utilization, 758 oxide (HQNO) progression, 691-93
Halimeda iron reduction and, 333 superantigens and, 691-92
gram-positive bacteria and, 567 manganese reduction and, 335 transmission, 690-91
Haloacetate dehydrogenase, 167, Herbicides Human papillomaviruses (HPV),
172 transposon selection markers 427-42
Haloacid dehalogenase, 167-68 and, 530 cellular longevity and, 441-42
2-chloropropionic acid-spe- Herpes simplex virus detection methods, 431-33
cific, 173-75 amino acid sequences, 629 distribution of infections, 429-
Haloalcohol lyase, 178-79 Herpesviruses, 428 31
Haloaikane dehalogenase, 168, amino acid sequences, 629 genital warts and, 433-34
536 genomes, 620 immortalization/transformation
catalytic mechanism, 169 Hexachlorocyclohexane and, 434-38
Haloalkanes metabolism, 184 immortalized cells
enzymatic degradation, 167 y-Hexachlorocyclohexane malignant progression, 438-
Halobacterium halobi catabolic pathway, 173 39
CpG relative abundances, 625 Hexachloroethane immune response and, 441
genomic distance orderings, 633 dehalogenation, 537 hut system, 15-17
Halobacterium salinarium Hexadecanolide, 792 autogenous regulation, 18
antisense RNA, 725 Hexokinase (HK), 111 Hydratases, 179-81
2-Halocarboxylic acids, 164-67, Hexoses, 224 Hydrocarbons
173 4-Hexuloses, 230 compound Q and, 386
Halogenated ethylenes High-density lipoproteins (HDLs) oxidation, 372-74
methane monooxygenase and, African trypanosomes and, Hydrocyanic acid, 784
380 139-59 Hydrogen
Halohydrin hydrogen halide ly- Histidase, 15, 17 iron reduction and, 321, 331
ases, 178-79 Histidine Shewanella putrefaciens and,
Halopropanols biosynthesis, 11-15 329
microbial dehalogenation, 179 Histoplasma capsulatum Hydrogenosomal enzymes, 108
Hansenula polymorpha, 117 cell wall composition, 477 Hydrogenosomes, 107-8, 114
amine oxidase, 119 LY303366 and, 483-84 Hydrogen peroxide
peroxisomal assembly mutants, HIV human immunodeficiency
126 See Human immunodeficiency virus gene expression
HCMV virus and, 693
See Human cytomegalovirus HK Hydrolytic dehalogenases, 164—
HDLs See Hexokinase 77
See High-density lipoproteins Homarus americanus, 570 4-Hydroxybenzoate, 179
Heat shock Homologous recombination 4-Hydroxy-3-methoxystyrene,
axenic transformation and, variant surface glycoprotein 782-83
458-59 genes and, 33-36 Hydroxy ph h q! i 85
Heat-shock proteins Host-encoded killer systems Hygromycin B
of Leishmania antisense RNA and, 722-23 marker genes conferring drug
molecular cloning and char- HPV resistance, 114
acterization, 459-63 See Human papillomaviruses Hyphomicrobium
Heavy metals HQNO A
bioremediation and, 546 See 2-Heptyl-4-hydroxy-qui- 177
iron/manganese and, 326 none-N-oxide Hyphomicrobium MC1