PCR Detection of Microbial Pathogens PCR Detection of Microbial ...

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Table 1 Primers for Toxin Gene Detection in Clostridium botulinum A, B, E, F and G T°C Accession Toxin Primer Sequence (5' → 3') Positions a Size (bp) of annealing number BoNT/A P478 CAGGTATTTTAAAAGACTTTTGGGG 3638-3662 M30196 BoNT/A P479 TATATACACGATCATTATTTCTAAC 3877-3901 R 263 50 BoNT/B P482 GCGAATATTTAAAAGATTTTTGGGG 3298-3322 M81186 BoNT/B P483 CTAGATATATATAATCTTCTTTTCTAA 3538-3564 R 266 50 BoNT/E P480 CAAATATTTTGAAGGATTTTTGGGG 3434-3458 X62089 BoNT/E P481 TATATACCTGATCATTCTTTCTAAC 3652-3676 R 242 50 a R indicates reverse primer. Table 2 Primers for Toxin Gene Detection in C. botulinum C and D T°C Accession Toxin Primer Sequence (5' → 3') Positions a Size (bp) of annealing number BoNT/C1-D P293 TWA TTC CMT ATA TAG GAC C 2097–2115 from bont/C1 340 X53751X54254 1917–1936 from bont/D BoNT/C1-D P294 TTT AGC TTT GAT TGC ACC TGC CTG 2413–2437 R from bont/C1 50 X53751X54254 2258–2234 R from bont/D BoNT/C1 P295 GAA GCA TTT GCA GTT A 2158–2174 199 X53781 BoNT/C1 P296T GG ATA ACC ACG TTC CCA T 2338–2357 R 50 X53781 BoNT/D P297 CAA GCA TTT GCA ACA G 1979–1995 199 X54254 BoNT/D P298 TTG ACA ACC AAT TTG ATA C 2159–2178 R X54254 a R indicates reverse primer. Clostridium PCR 139
Table 3 Primers for Toxin Gene Detection in C. perfringens Reference T°C of or accession Toxin Primer Sequence (5' —> 3') Positions a Size (bp) annealing number α PL3 AAG TTA CCT TTG CTG CAT AAT CCC 1676–1699 R 236 50 Infect. Immun. 1989, 57, 367 α PL7 ATA GAT ACT CCA TAT CAT CCT GCT 1418–1440 Enterotoxine P145 GAA AGA TCT GTA TCT ACA ACT GCT GGT CC 472–500 425 50 Ant. Leeuw. 1989 56, 181–190 Enterotoxine P146 GCT GGC TAA GAT TCT ATA TTT TTG TCC AGT 868–897 R β1 P463 CTA ATA TGT CTG TAG TTC TAA CTG CTC CTA 1127–1156 102 50 L13198 β1 P464 TAT CTA CAT TTG GGG TAT CAA AAG CTA GCC 1287–1258 R β2 P465 TTT TCT ATA TAT AAT CTT ATT TGT CTA GCA 978–948 R 277 50 L77965 β2 P466 AGT TTG TAC ATG GGA TGA TGA ACT AGC ACA 723–752 ε P497 GTC CCT TCA CAA GAT ATA CTA GTA CC 1051–1101 172 50 M80837 ε P498 CCT AGG AAA AGC TAA ATA ACT AGG 1183–1223 R ι Ia P245 GCT TTT ATT GAA AGA CCA GAA 1588–1609 642 50 X73562 ι Ia P240 CAT CTT TAA AAT CAA GAC TG 2233–2214 R ι Ib P181 GTG TGA GAA TAG CTT GTA GTT 3945–3925 R 480 50 X73562 ι Ib P187 TGA AAA TGA TCC GTT TAT ACC 3445–3465 a R indicates reverse primer. 140 Popoff
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TM Methods in Molecular Biology VOL
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4 Sachse 2. Selection of Target Seq
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Table 1 Target Sequences Used in PC
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8 Sachse Fig. 1. Structural organiz
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10 Sachse proteins (66-68), invasio
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12 Sachse Since there appears to be
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14 Sachse In the context of identif
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16 Sachse to partially compensate t
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18 Sachse nostic potential of PCR.
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20 Sachse product has to be confirm
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22 Sachse 7. van Camp, G., Fierens,
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24 Sachse 33. Rappelli, P., Are, R.
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26 Sachse 60. Furrer, B., Candrian,
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28 Sachse 89. Bloch, W. (1991) A bi
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30 Sachse
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32 Rådström et al. Fig. 1. Illust
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34 Rådström et al. immunoglobulin
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36 Rådström et al. and the captur
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Table 2 Comparison of the Performan
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40 Rådström et al. explain these
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42 Rådström et al. 5.1. Proteins
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44 Rådström et al. neous. Consequ
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46 Rådström et al. 11. Powell, H.
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48 Rådström et al. 39. Katcher, H
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50 Rådström et al. 73. Nagai, M.,
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52 Hoorfar and Cook 2. FOOD-PCR: A
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54 Hoorfar and Cook Fig. 2. Practic
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56 Hoorfar and Cook Fig. 4. The str
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Table 58 3 Hoorfar and Cook Test Co
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60 Hoorfar and Cook The choosing an
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62 Hoorfar and Cook 10. Demanding L
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64 Hoorfar and Cook 15. Anon. (1995
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66 Lübeck and Hoorfar ods for the
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68 Lübeck and Hoorfar amplificatio
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70 Lübeck and Hoorfar It may be ne
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72 Lübeck and Hoorfar specificity
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74 Lübeck and Hoorfar The latter i
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76 Lübeck and Hoorfar A simple che
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78 Lübeck and Hoorfar 13. Hanai, K
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80 Lübeck and Hoorfar 43. Mitchell
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82 Lübeck and Hoorfar 70. Lawrence
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84 Lübeck and Hoorfar 98. Lantz, P
Page 85 and 86: 88 Frey Table 1 Presence of the Var
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Page 89 and 90: 92 Frey as template for PCR. In add
Page 91 and 92: 94 Frey strains, including all sero
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Page 95 and 96: 98 Ewalt and Bricker (named for the
Page 97 and 98: 100 Ewalt and Bricker 4. Ethidium b
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Page 107 and 108: 110 Englen et al. which campylobact
Page 109 and 110: 112 Englen et al. 18. Dehydrated cu
Page 111 and 112: 114 Englen et al. 3.1.3. Fecal Samp
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Page 115 and 116: 118 Englen et al. Fig. 1. Identific
Page 117 and 118: 120 Englen et al. 3. Goossens, H.,
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Page 121 and 122: 124 Sachse and Hotzel Table 1 Compa
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Page 125 and 126: 128 Sachse and Hotzel 7. Phenol: sa
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Page 141 and 142: 144 Popoff Taq reaction buffer 1X,
Page 143 and 144: 146 Popoff almost all C. perfringen
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Page 147 and 148: 150 Popoff 7. Hielm, S., Hyyttia, E
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Page 151 and 152: 154 Berri et al. 2. Materials 1. C.
Page 153 and 154: 156 Berri et al. 3.3.2. Vaginal Swa
Page 155 and 156: 158 Berri et al. Fig. 1. Trans-PCR.
Page 157 and 158: 160 Berri et al. Fig. 3. Sensitivit
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Page 161 and 162: 164 Gallien The first description o
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Page 165 and 166: 168 Gallien 2. Materials 2.1. Bacte
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Page 173 and 174: 176 Gallien 3.3. Specific Isolation
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Page 183 and 184: 186 O'Connor This chapter will desc
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190 O'Connor 4. Notes 1. In enrichi
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192 O'Connor 4. O’Sullivan, N., F
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194 Lester and LeFebvre titers (4).
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196 Lester and LeFebvre 3.1.2. Samp
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Fig. 1. Sensitivity of the PCR assa
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200 Lester and LeFebvre 5. Swart, K
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202 Skuce et al. Table 1 Significan
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204 Skuce et al. commercial kits. E
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206 Skuce et al. Fig. 1. Schematic
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208 Skuce et al. 5. Disposable ster
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210 Skuce et al. 2.5.2. Sequence An
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212 Skuce et al. 2. Carefully trans
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Table 4 Recommended PCR Amplificati
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216 Skuce et al. Fig. 3. PCR produc
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218 Skuce et al. Fig. 5. Spoligotyp
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220 Skuce et al. 14. Aranaz, A., Li
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222 Skuce et al.
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224 Khan Simultaneous detection of
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226 Khan 10. Incubate for 20 min at
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228 Khan 5. Periodically, multiplex
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230 Khan
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232 Hotzel et al. tis (2). Particul
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234 Hotzel et al. 8. Sodium dodecyl
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236 Hotzel et al. 3. Methods 3.1. D
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238 Hotzel et al. 3.1.5. Semen (see
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240 Hotzel et al. Fig. 1 Detection
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242 Hotzel et al. 4. Notes 1. The u
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244 Hotzel et al. in Mycoplasma Pro
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246 Hotzel et al.
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248 Kobisch and Frey PCR assay to d
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250 Kobisch and Frey Table 1 Oligon
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252 Kobisch and Frey 3.2.1. Prepara
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254 Kobisch and Frey First round of
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256 Kobisch and Frey References 1.
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258 Christensen et al. thrombotic m
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260 Christensen et al. Table 1 Spec
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264 Christensen et al. 3.2. Extract
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268 Christensen et al. 2. Apply fra
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270 Christensen et al. 7. To reduce
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272 Christensen et al. 24. Fisher,
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274 Christensen et al. 54. Hunt, M.
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276 Malorny and Helmuth valent meta
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278 Malorny and Helmuth 12. Apparat
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280 Malorny and Helmuth 3.3. Amplif
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282 Malorny and Helmuth Table 2 Vol
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284 Malorny and Helmuth Table 4 PCR
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286 Malorny and Helmuth 3. Wallace,
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288 Malorny and Helmuth
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290 Wastling and Mattsson is an imp
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292 Wastling and Mattsson 2. Remove
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294 Wastling and Mattsson Fig. 1. B
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296 Wastling and Mattsson time PCR
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298 Wastling and Mattsson
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300 Pozio and La Rosa Table 1 Princ
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302 Pozio and La Rosa regions; spot
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304 Pozio and La Rosa 3. Proteinase
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306 Pozio and La Rosa Table 3 PCR-R
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308 Pozio and La Rosa 2. Pepsin sho
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310 Pozio and La Rosa
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312 Knutsson and Rådström The ref
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314 Knutsson and Rådström Fig. 1.
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316 Knutsson and Rådström 2.4. El
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318 Knutsson and Rådström the swa
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320 Knutsson and Rådström Fig. 3.
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322 Knutsson and Rådström 4. Alek
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324 Knutsson and Rådström 34. Hee
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