Journal: Applied and Environmental Microbiology

Article Title: Genotyping of Giardia duodenalis Cysts by New Real-Time PCR Assays for Detection of Mixed Infections in Human Samples

doi: 10.1128/AEM.02305-09

Figure Lengend Snippet: Primers used in the study a

Article Snippet: The primers are listed in Table . table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Primer Sequence Binding site Amplicon size (bp) Melting peak (°C) TPI A forward primer 5′- TCGTCATTGCCCCTTCC GCC -3′ 116-135 77 86 TPI B sequence 5′- .T..TG....T..C... TTT -3′ TPI A reverse primer 3′- CAGT TGAGGATAGCAGCG -5′ 175-192 TPI B sequence 3′- TGTC ...AA......... -5′ TPI B forward primer 5′- GATGAACGCAAGGCCAA TAA -3′ 397-416 77 80 TPI A sequence 5′- ..C..G........... CCG -3′ TPI B reverse primer 3′- AAG AAGGAGATTGGAGAATC -5′ 454-473 TPI A sequence 3′- GGC ......C.C.....G.. -5′ GDH A forward primer 5′- CCGGCAACGTTGCCCAGT TT -3′ 710-729 180 83 GDH B sequence 5′- .T...........T.... AC -3′ GDH A reverse primer 3′- T CCGAGTTCAAGGACAAGT -5′ 871-889 GDH B sequence 3′- G .T...........G.... -5′ GDH B forward primer 5′- CGTATTGGCGTCGGCG GT -3′ 492-510 133 83 GDH A sequence 5′- ...C..C.......... CC -3′ GDH B reverse primer 3′- C TATCAGACCAGAGGCCACA -5′ 604-623 GDH A sequence 3′- T ..........G........G -5′ ORFC4 A forward primer 5′- CTGTAGACAGGGCCCAG GCC -3′ 135-154 103 85 ORFC4 B sequence 5′- ......G....AG..G. ATG -3′ ORFC4 A reverse primer 3′- ATT AAGGGCAGGGGACATCAT -5′ 217-237 ORFC4 B sequence 3′- GGC ...T.T.A.....G.... -5′ ORFC4 B forward primer 5′- ACTGTCCATTTCTATC TGAG -3′ 281-300 171 79 ORFC4 A sequence 5′- C...C........G.. ATCC -3′ ORFC4 B reverse primer 3′- AG GTGGAGGCCAATGGAATCC -5′ 431-451 ORFC4 A sequence 3′- CT ..A.....AG........A -5′ Open in a separate window a The sequence of each assemblage-specific primer is aligned over the corresponding sequence of the other assemblage.

Techniques: Sequencing, Binding Assay, Amplification

Journal: Applied and Environmental Microbiology

Article Title: Genotyping of Giardia duodenalis Cysts by New Real-Time PCR Assays for Detection of Mixed Infections in Human Samples

doi: 10.1128/AEM.02305-09

Figure Lengend Snippet: Schematic representation of the amplification curves (left), melting curves (middle), and electrophoretic separation of products (right) obtained using the gdh, orfC4, and tpi qPCR assays. In gel electrophoresis of gdh products, lane M is the 50-bp size ladder; lanes 1 and 6 show the assemblage A product (180 bp); lanes 2, 3, and 7 show the assemblage B product (133 bp); lanes 4, 5, and 8 show the presence of both assemblages A and B; and lane 9 shows the negative control. In gel electrophoresis of orfC4 products, lane M is the 50-bp size ladder; lanes 1 and 7 show the assemblage A product (103 bp); lanes 3, 4, 5, and 8 show the assemblage B product (171 bp); lanes 2, 6, and 9 show the presence of both assemblages A and B; and lane 10 shows the negative control. In gel electrophoresis of tpi amplicons, the product from assemblage A is not cut by AluI (lane 1) but is cut by HincII into two fragments of 47 bp and 31 bp (lane 2), whereas the B product is cut by AluI into two fragments of 45 bp and 32 bp (lane 3) but is not cut by HincII (lane 4).

Article Snippet: The primers are listed in Table . table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Primer Sequence Binding site Amplicon size (bp) Melting peak (°C) TPI A forward primer 5′- TCGTCATTGCCCCTTCC GCC -3′ 116-135 77 86 TPI B sequence 5′- .T..TG....T..C... TTT -3′ TPI A reverse primer 3′- CAGT TGAGGATAGCAGCG -5′ 175-192 TPI B sequence 3′- TGTC ...AA......... -5′ TPI B forward primer 5′- GATGAACGCAAGGCCAA TAA -3′ 397-416 77 80 TPI A sequence 5′- ..C..G........... CCG -3′ TPI B reverse primer 3′- AAG AAGGAGATTGGAGAATC -5′ 454-473 TPI A sequence 3′- GGC ......C.C.....G.. -5′ GDH A forward primer 5′- CCGGCAACGTTGCCCAGT TT -3′ 710-729 180 83 GDH B sequence 5′- .T...........T.... AC -3′ GDH A reverse primer 3′- T CCGAGTTCAAGGACAAGT -5′ 871-889 GDH B sequence 3′- G .T...........G.... -5′ GDH B forward primer 5′- CGTATTGGCGTCGGCG GT -3′ 492-510 133 83 GDH A sequence 5′- ...C..C.......... CC -3′ GDH B reverse primer 3′- C TATCAGACCAGAGGCCACA -5′ 604-623 GDH A sequence 3′- T ..........G........G -5′ ORFC4 A forward primer 5′- CTGTAGACAGGGCCCAG GCC -3′ 135-154 103 85 ORFC4 B sequence 5′- ......G....AG..G. ATG -3′ ORFC4 A reverse primer 3′- ATT AAGGGCAGGGGACATCAT -5′ 217-237 ORFC4 B sequence 3′- GGC ...T.T.A.....G.... -5′ ORFC4 B forward primer 5′- ACTGTCCATTTCTATC TGAG -3′ 281-300 171 79 ORFC4 A sequence 5′- C...C........G.. ATCC -3′ ORFC4 B reverse primer 3′- AG GTGGAGGCCAATGGAATCC -5′ 431-451 ORFC4 A sequence 3′- CT ..A.....AG........A -5′ Open in a separate window a The sequence of each assemblage-specific primer is aligned over the corresponding sequence of the other assemblage.

Techniques: Amplification, Nucleic Acid Electrophoresis, Negative Control

Journal: Applied and Environmental Microbiology

Article Title: Genotyping of Giardia duodenalis Cysts by New Real-Time PCR Assays for Detection of Mixed Infections in Human Samples

doi: 10.1128/AEM.02305-09

Figure Lengend Snippet: Genotyping results obtained for 30 human samples at four loci using regular PCR and qPCR on genomic DNA from stools, on purified cysts, and on single cysts

Article Snippet: The primers are listed in Table . table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Primer Sequence Binding site Amplicon size (bp) Melting peak (°C) TPI A forward primer 5′- TCGTCATTGCCCCTTCC GCC -3′ 116-135 77 86 TPI B sequence 5′- .T..TG....T..C... TTT -3′ TPI A reverse primer 3′- CAGT TGAGGATAGCAGCG -5′ 175-192 TPI B sequence 3′- TGTC ...AA......... -5′ TPI B forward primer 5′- GATGAACGCAAGGCCAA TAA -3′ 397-416 77 80 TPI A sequence 5′- ..C..G........... CCG -3′ TPI B reverse primer 3′- AAG AAGGAGATTGGAGAATC -5′ 454-473 TPI A sequence 3′- GGC ......C.C.....G.. -5′ GDH A forward primer 5′- CCGGCAACGTTGCCCAGT TT -3′ 710-729 180 83 GDH B sequence 5′- .T...........T.... AC -3′ GDH A reverse primer 3′- T CCGAGTTCAAGGACAAGT -5′ 871-889 GDH B sequence 3′- G .T...........G.... -5′ GDH B forward primer 5′- CGTATTGGCGTCGGCG GT -3′ 492-510 133 83 GDH A sequence 5′- ...C..C.......... CC -3′ GDH B reverse primer 3′- C TATCAGACCAGAGGCCACA -5′ 604-623 GDH A sequence 3′- T ..........G........G -5′ ORFC4 A forward primer 5′- CTGTAGACAGGGCCCAG GCC -3′ 135-154 103 85 ORFC4 B sequence 5′- ......G....AG..G. ATG -3′ ORFC4 A reverse primer 3′- ATT AAGGGCAGGGGACATCAT -5′ 217-237 ORFC4 B sequence 3′- GGC ...T.T.A.....G.... -5′ ORFC4 B forward primer 5′- ACTGTCCATTTCTATC TGAG -3′ 281-300 171 79 ORFC4 A sequence 5′- C...C........G.. ATCC -3′ ORFC4 B reverse primer 3′- AG GTGGAGGCCAATGGAATCC -5′ 431-451 ORFC4 A sequence 3′- CT ..A.....AG........A -5′ Open in a separate window a The sequence of each assemblage-specific primer is aligned over the corresponding sequence of the other assemblage.

Techniques: Purification