Journal:

Article Title: Loop-Mediated Isothermal Amplification for Direct Detection of Mycobacterium tuberculosis Complex, M. avium , and M. intracellulare in Sputum Samples

doi: 10.1128/JCM.41.6.2616-2622.2003

Figure Lengend Snippet: Specificity of LAMP primers for identification of mycobacterial species

Article Snippet: Genomic DNAs of M. tuberculosis H37Rv, M. tuberculosis H37Ra, Mycobacterium bovis BCG Tokyo, M. avium ATCC 15769, M. avium ATCC 25291, M. avium ATCC 35718 , M. intracellulare ATCC 13950, M. intracellulare ATCC 35847, and M. intracellulare ATCC 35762 were also extracted from Mycobacterium Growth Indicator Tube (MGIT) broth on the day when positive fluorescence was detected.

Techniques: Amplification

Journal: Journal of Clinical Microbiology

Article Title: Comparison of a Variable-Number Tandem-Repeat (VNTR) Method for Typing Mycobacterium avium with Mycobacterial Interspersed Repetitive-Unit-VNTR and IS 1245 Restriction Fragment Length Polymorphism Typing

doi: 10.1128/jcm.02373-08

Figure Lengend Snippet: FIG. 1. Dendrogram of IS1245-RFLP patterns of M. avium isolates, including 70 clinical strains and reference strains, as determined by the unweighted-pair group method using average linkages, using the different band calculation and a 1.0% position tolerance. The scale at the top shows the genetic similarity among the profiles, expressed as percentages. Faint bands were included in the comparison. MAA (M. avium subsp. avium), strain GTC00603; MAH (M. avium subsp. hominissuis), strain ATCC 19978; MAS (M. avium subsp. silvaticum), strain ATCC49884.

Article Snippet: The standard MAC strains M. avium subsp. avium (GTC00603; derived from M. avium ATCC 25291 and ATCC 35718), M. avium subsp. paratuberculosis (ATCC 19698), M. avium subsp. hominissuis (ATCC 19978), and M. avium subsp. silvaticum (ATCC 49884) were used.

Techniques: Comparison

Journal: Journal of Clinical Microbiology

Article Title: Comparison of a Variable-Number Tandem-Repeat (VNTR) Method for Typing Mycobacterium avium with Mycobacterial Interspersed Repetitive-Unit-VNTR and IS 1245 Restriction Fragment Length Polymorphism Typing

doi: 10.1128/jcm.02373-08

Figure Lengend Snippet: FIG. 2. Dendrogram and allele profiles constructed from MATR-VNTR typing results for M. avium isolates, including 70 clinical strains and reference strains. The dendrogram was created from distance matrix files by Fitch-Margoliash analysis according to MATR-VNTR markers. Allele profiles analyzed using MATR-VNTR loci from isolates showing 100% similarity are boxed. The Manhattan distance is indicated at the bottom. MAA (M. avium subsp. avium), strain GTC00603; MAH (M. avium subsp. hominissuis), strain ATCC 19978; MAS, (M. avium subsp. silvaticum) strain ATCC 49884; MAP (M. avium subsp. paratuberculosis), strain ATCC 19698.

Article Snippet: The standard MAC strains M. avium subsp. avium (GTC00603; derived from M. avium ATCC 25291 and ATCC 35718), M. avium subsp. paratuberculosis (ATCC 19698), M. avium subsp. hominissuis (ATCC 19978), and M. avium subsp. silvaticum (ATCC 49884) were used.

Techniques: Construct

Journal: Journal of Clinical Microbiology

Article Title: Comparison of a Variable-Number Tandem-Repeat (VNTR) Method for Typing Mycobacterium avium with Mycobacterial Interspersed Repetitive-Unit-VNTR and IS 1245 Restriction Fragment Length Polymorphism Typing

doi: 10.1128/jcm.02373-08

Figure Lengend Snippet: FIG. 3. Dendrogram and allele profiles constructed from MIRU-VNTR typing results for M. avium isolates, including 70 clinical strains and reference strains. The dendrogram was created from distance matrix files by Fitch-Margoliash analysis according to MIRU-VNTR markers. Allele profiles analyzed using MIRU-VNTR loci from isolates showing 100% similarity are boxed. The Manhattan distance is indicated at the bottom. MAA (M. avium subsp. avium), strain GTC00603; MAH (M. avium subsp. hominissuis), strain ATCC 19978; MAS (M. avium subsp. silvaticum), strain ATCC 49884; MAP (M. avium subsp. paratuberculosis), strain ATCC 19698.

Article Snippet: The standard MAC strains M. avium subsp. avium (GTC00603; derived from M. avium ATCC 25291 and ATCC 35718), M. avium subsp. paratuberculosis (ATCC 19698), M. avium subsp. hominissuis (ATCC 19978), and M. avium subsp. silvaticum (ATCC 49884) were used.

Techniques: Construct

Journal:

Article Title: Characterization of Genetic Differences between Mycobacterium avium subsp. paratuberculosis Type I and Type II Isolates

doi: 10.1128/JCM.41.11.5215-5223.2003

Figure Lengend Snippet: Strains and plasmids used in this study

Article Snippet: Other template DNA used was from two nonpigmented bovine (lanes 1 and 2), two pigmented (lanes 3 and 4), three nonpigmented ovine (lanes 5 to 7), three nonpigmented caprine (lanes 8 to 10), and one nonpigmented human (lane 11) M. avium subsp . paratuberculosis isolate as well as four M. avium subsp . avium isolates (ATCC 35712, ATCC 25291, DSM 44158, and MAA S4; lanes 12 to 15). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 3. caption a7 Genetic organization of the loci pig-RDA10, pig-RDA20, and pig-RDA30 specific for M. avium subsp . paratuberculosis type I isolates.

Techniques: TA Cloning, Plasmid Preparation, Cloning

Journal:

Article Title: Characterization of Genetic Differences between Mycobacterium avium subsp. paratuberculosis Type I and Type II Isolates

doi: 10.1128/JCM.41.11.5215-5223.2003

Figure Lengend Snippet: Primers used in this study

Article Snippet: Other template DNA used was from two nonpigmented bovine (lanes 1 and 2), two pigmented (lanes 3 and 4), three nonpigmented ovine (lanes 5 to 7), three nonpigmented caprine (lanes 8 to 10), and one nonpigmented human (lane 11) M. avium subsp . paratuberculosis isolate as well as four M. avium subsp . avium isolates (ATCC 35712, ATCC 25291, DSM 44158, and MAA S4; lanes 12 to 15). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 3. caption a7 Genetic organization of the loci pig-RDA10, pig-RDA20, and pig-RDA30 specific for M. avium subsp . paratuberculosis type I isolates.

Techniques: Sequencing

Journal:

Article Title: Characterization of Genetic Differences between Mycobacterium avium subsp. paratuberculosis Type I and Type II Isolates

doi: 10.1128/JCM.41.11.5215-5223.2003

Figure Lengend Snippet: Molecular data for the M. avium subsp. paratuberculosis subspecies- and type I-specific fragments

Article Snippet: Other template DNA used was from two nonpigmented bovine (lanes 1 and 2), two pigmented (lanes 3 and 4), three nonpigmented ovine (lanes 5 to 7), three nonpigmented caprine (lanes 8 to 10), and one nonpigmented human (lane 11) M. avium subsp . paratuberculosis isolate as well as four M. avium subsp . avium isolates (ATCC 35712, ATCC 25291, DSM 44158, and MAA S4; lanes 12 to 15). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 3. caption a7 Genetic organization of the loci pig-RDA10, pig-RDA20, and pig-RDA30 specific for M. avium subsp . paratuberculosis type I isolates.

Techniques:

Journal:

Article Title: Characterization of Genetic Differences between Mycobacterium avium subsp. paratuberculosis Type I and Type II Isolates

doi: 10.1128/JCM.41.11.5215-5223.2003

Figure Lengend Snippet: PCR analysis of M. avium subsp. paratuberculosis isolates of different host groupings by using the internal primer pair I130A/131A and Tsp45I restriction of the PCR product RD I130. The DNA template used was derived from three nonpigmented bovine (lanes 1 to 3), three pigmented ovine (lanes 4 to 6), three nonpigmented ovine (lanes 7 to 9), three nonpigmented caprine (lanes 10 to 12), and one nonpigmented human M. avium subsp. paratuberculosis isolate (lane 13) as well as the M. avium subsp. avium ATCC 25291 isolate (lane 14). (a) The PCR with the primers I130A/I131A resulted in products of different sizes for the M. avium subsp. paratuberculosis type I and type II isolates. (b) The PCR product RD I130 of the M. avium subsp. paratuberculosis type I isolates was cut into two fragments by digestion with Tsp45I. The arrows to the left indicate the size of the corresponding PCR products.

Article Snippet: Other template DNA used was from two nonpigmented bovine (lanes 1 and 2), two pigmented (lanes 3 and 4), three nonpigmented ovine (lanes 5 to 7), three nonpigmented caprine (lanes 8 to 10), and one nonpigmented human (lane 11) M. avium subsp . paratuberculosis isolate as well as four M. avium subsp . avium isolates (ATCC 35712, ATCC 25291, DSM 44158, and MAA S4; lanes 12 to 15). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 3. caption a7 Genetic organization of the loci pig-RDA10, pig-RDA20, and pig-RDA30 specific for M. avium subsp . paratuberculosis type I isolates.

Techniques: Derivative Assay

Journal:

Article Title: Characterization of Genetic Differences between Mycobacterium avium subsp. paratuberculosis Type I and Type II Isolates

doi: 10.1128/JCM.41.11.5215-5223.2003

Figure Lengend Snippet: PCR analyses of M. avium subsp. paratuberculosis and M. avium subsp. avium isolates with the primer pair p19/p20, specific for pig-RDA10 (a); p21/p22, specific for pig-RDA20 (b); p23/p24, specific for pig-RDA30 (c); ISMav2 I/ISMav2 II, specific for M. avium subsp. paratuberculosis (d); MK5/MK6, specific for IS900 of M. avium subsp. paratuberculosis (e); and (f) MK7/MK8, specific for IS901 of M. avium subsp. avium. The template DNA used was derived from the nonpigmented type II driver strain (lane D) and the pigmented type I tester strain (lane T). Other template DNA used was from two nonpigmented bovine (lanes 1 and 2), two pigmented (lanes 3 and 4), three nonpigmented ovine (lanes 5 to 7), three nonpigmented caprine (lanes 8 to 10), and one nonpigmented human (lane 11) M. avium subsp. paratuberculosis isolate as well as four M. avium subsp. avium isolates (ATCC 35712, ATCC 25291, DSM 44158, and MAA S4; lanes 12 to 15).

Article Snippet: Other template DNA used was from two nonpigmented bovine (lanes 1 and 2), two pigmented (lanes 3 and 4), three nonpigmented ovine (lanes 5 to 7), three nonpigmented caprine (lanes 8 to 10), and one nonpigmented human (lane 11) M. avium subsp . paratuberculosis isolate as well as four M. avium subsp . avium isolates (ATCC 35712, ATCC 25291, DSM 44158, and MAA S4; lanes 12 to 15). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 3. caption a7 Genetic organization of the loci pig-RDA10, pig-RDA20, and pig-RDA30 specific for M. avium subsp . paratuberculosis type I isolates.

Techniques: Derivative Assay

Journal:

Article Title: Characterization of Genetic Differences between Mycobacterium avium subsp. paratuberculosis Type I and Type II Isolates

doi: 10.1128/JCM.41.11.5215-5223.2003

Figure Lengend Snippet: Genetic organization of the loci pig-RDA10, pig-RDA20, and pig-RDA30 specific for M. avium subsp. paratuberculosis type I isolates. The numbers given in the maps relate to the positions on the M. avium subsp. avium (TIGR strain 104, contig 3294) and M. avium subsp. paratuberculosis (UMN strain K-10, contig 16) genomes. (a) pig-RDA10 locus. The sequence identified is also present in the 16K locus present in M. avium subsp. avium (top) and M. avium subsp. paratuberculosis type I (middle) but is absent from M. avium subsp. paratuberculosis type II (bottom). The 16K locus is flanked by a 0.9-Mbp sequence (designated A) present in M. avium subsp. avium and partially present in M. avium subsp. paratuberculosis but is oriented in the opposite direction (indicated by an arrow). These sequences are bounded by regions (designated B, C, and D) which are interrupted by IS900 locus 15 in both M. avium subsp. paratuberculosis type I and type II isolates. A putative organization of the locus in M. avium subsp. paratuberculosis type I strains is depicted in the middle map. (b) pig-RDA20 locus. The sequence identified is also present in the 197K locus specific for M. avium subsp. avium (top). In M. avium subsp. paratuberculosis the same flanking regions embrace the 19Klocus specific for M. avium subsp. paratuberculosis (middle). The probable organization of the locus in M. avium subsp. paratuberculosis type I strains is depicted in the bottom map. (c) pig-RDA30 locus. The sequence identified is also present in the 27K locus specific for M. avium subsp. avium (top) flanked by a transposase (designated 1K) and containing an additional truncated 1K region. In M. avium subsp. paratuberculosis the 27K locus is missing (middle). The probable organization of the locus in M. avium subsp. paratuberculosis type I strains is depicted in the bottom map. The arrows are numbered to indicate the positions of the primers used (Table ​(Table44).

Article Snippet: Other template DNA used was from two nonpigmented bovine (lanes 1 and 2), two pigmented (lanes 3 and 4), three nonpigmented ovine (lanes 5 to 7), three nonpigmented caprine (lanes 8 to 10), and one nonpigmented human (lane 11) M. avium subsp . paratuberculosis isolate as well as four M. avium subsp . avium isolates (ATCC 35712, ATCC 25291, DSM 44158, and MAA S4; lanes 12 to 15). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 3. caption a7 Genetic organization of the loci pig-RDA10, pig-RDA20, and pig-RDA30 specific for M. avium subsp . paratuberculosis type I isolates.

Techniques: Sequencing

Journal:

Article Title: Characterization of Genetic Differences between Mycobacterium avium subsp. paratuberculosis Type I and Type II Isolates

doi: 10.1128/JCM.41.11.5215-5223.2003

Figure Lengend Snippet: Primers for the PCR analyses of the M. avium subsp. avium 16K locus and the M. avium subsp. paratuberculosis C locus

Article Snippet: Other template DNA used was from two nonpigmented bovine (lanes 1 and 2), two pigmented (lanes 3 and 4), three nonpigmented ovine (lanes 5 to 7), three nonpigmented caprine (lanes 8 to 10), and one nonpigmented human (lane 11) M. avium subsp . paratuberculosis isolate as well as four M. avium subsp . avium isolates (ATCC 35712, ATCC 25291, DSM 44158, and MAA S4; lanes 12 to 15). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 3. caption a7 Genetic organization of the loci pig-RDA10, pig-RDA20, and pig-RDA30 specific for M. avium subsp . paratuberculosis type I isolates.

Techniques: Sequencing

Journal:

Article Title: Characterization of Genetic Differences between Mycobacterium avium subsp. paratuberculosis Type I and Type II Isolates

doi: 10.1128/JCM.41.11.5215-5223.2003

Figure Lengend Snippet: Primers for the PCR analyses of the M. avium subsp. avium 197K locus and the M. avium subsp. paratuberculosis 19K locus

Article Snippet: Other template DNA used was from two nonpigmented bovine (lanes 1 and 2), two pigmented (lanes 3 and 4), three nonpigmented ovine (lanes 5 to 7), three nonpigmented caprine (lanes 8 to 10), and one nonpigmented human (lane 11) M. avium subsp . paratuberculosis isolate as well as four M. avium subsp . avium isolates (ATCC 35712, ATCC 25291, DSM 44158, and MAA S4; lanes 12 to 15). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 3. caption a7 Genetic organization of the loci pig-RDA10, pig-RDA20, and pig-RDA30 specific for M. avium subsp . paratuberculosis type I isolates.

Techniques: Sequencing