P

PAI see pathogenicity island PAIs 95 ff.

- Shigella flexneri 92

- see also pathogenicity island Paracoccidioides brasiliensis 396 ff.

- EST sequencing project 397 parasites

- Cryptosporidium 417, 423

- Eimeria 417, 423

- Giardia 417

- insect vector genetics 436

- Leishmania 417

- new drug discovery 433

- Plasmodium 417, 423

- post-genome analyses 433

- Theileria 417, 423

- Toxoplasma 417, 423

- Trichomonas 417

- Trypanosoma 417

pathogenicity island 13, 92, 156, 162, 286

- regions of difference (RDs) 177 ff. pathway analysis 6

- elementary mode 14 peusodene 117 ff. phage 177 ff. phages 287

phase variation 158 plasmid 86, 99, 177 ff. Plasmodium 423 ff.

- drug and vaccine development 435 ff.

- gene expression analysis 434

- genome sequence 423

- microarray 434

- P. aeruginosa 450

- P. chabaudi 426

- P. falciparum 423

- proteomics 434 ff Plasmodium falciparum

- antigenic variation 426

- LCCL-domain 426

- linear chromosomes 424

- linear mitochondrial genome 424

- multidomain adhesive molecules 426

- plastid-like genome 424

- surface protein 424 ff. Pneumocystis

- genome sequence 401

- major surface glycoproteins 401

- MSG genes 401

- MSG-related proteins (MSTgenes) 401

- Pneumocystisjirovecii 401 polymerase chain reaction 484 population equilibrium 375 postgenomic era 487 primary fungal pathogens 390

- dermatophytes 390

- dimorphic fungi 390 primer design

- genome PRIDE 24

- PrimeArray 24

- Primer 3 24 progressive alignment 374 progressive sequence alignment 374

- CHROMAS 374

- CLUSTAL W 374

- DDBJ 374

- EMBOSS 374

- FASTA 374

- SEQ-CONVERT 374 prophage 86,89 prophage attachment site 165 protein secretion 62 proteomics 43 ff.

- color coding 49

- dual channel imaging 47

- first-level proteomics 65

- proteome signature 51 ff.

- second-level proteomics 65

- starvation proteins 47

- stress proteins 47

- vegetative proteome 46, 56 protozoans 417

- apicomplexa 422 ff.

- apicoplast 424

- endosymbiosis 424

- genome analysis 418 ff.

- horizontal gene transfer 421

- organelle-encoded genes 422

- phylogenetic studies 420 pseudogene 89, 115 Pseudomonas aeruginosa 76, 448

q quasispecies 374, 379 ff., 381, 382, 383 r random mutagenesis 73,74 RD see regions of difference rearrangement 118, 156, 161, 163 recombination 161 regulon 47 ff.

- virulence 63 repetitive element 158 resistance 14 ff., 125, 194 ff. reverse genetics 70

reverse vaccinology 247, 533 ff.

- group B streptococcus 538 Rhizobiales 281

RNA virus 371,379,381 RNAi see RNA interference RTq-PCR 36

Saccaromyces cerevisiae 73 ff. Salmonella

- csrA 112

- lipopolysaccharides 113 ff.

- S. arizonae 109

- S. enterica 109

- S. diarizonae 109

- S. houtenae 109

- S. enterica serotype Gallinarum 118

- S. enterica serotype Paratyphi A 115 ff.

- S. enterica serotype Typhimurium 110

- S. enterica serotypes Typhi 115 ff.

- S. pathogenicity system 111 ff.

- S. signature genes 110 ff. Salmonella typhimurium 71,449

- C. neoformans 449

- hypersensitivity 449

- innate immune response 449

- P. aeroginosa 449

- Serratia marcescens 449

- Staphylococcus aureus 449

- Yersinia pestis 449

SaPi see Staphylococcus aureus pathogenicity island

SCC see staphylococcal cassette chromosome

SCCmec 190 ff.

- see also staphylococcal cassette chromosome mec sequence annotation

- BLAST 17

sequence annotation tools

- aptamers 4

- Genepredict 4

- Genescan 4

- Orpheus 4

- Prophet 4

- riboswitch 4

- RNA analyzer 4

- UTRscan 4

- Vienna package 4 sequence space

- mutant cloud 380

Serratica marcescens, Listeria monocytogenes 450

serial analysis of gene expression (SAGE) 433

serotype conversion 89

SERPA see serological proteome analysis

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