Journal:

Article Title: Rapid-Cycle PCR and Fluorimetry for Detection of Mycobacteria

doi: 10.1128/JCM.40.9.3364-3373.2002

Figure Lengend Snippet: Profile of 16S rRNA gene amplification and probe hybridization

Article Snippet: F2 refers to channel 2, which is used by the LightCycler's optical unit to measure signals from LightCycler Red 640 at 640 nm. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Template a and species Amplification b Melting temp (°C) of probe specific for c : Mycobacterium M. tuberculosis M. avium Mycobacteria Mycobacterium tuberculosis complex M. tuberculosis H37Rv (ATCC 25618) + 61.5 64 54 M. bovis + 61.5 64 54 M. bovis BCG Pasteur + 61.5 64 54 Nontuberculous mycobacteria M. avium (ATCC 35712) + 61.5 43.5 61 M. paratuberculosis + 61.5 43.5 61 M. intracellulare + 61.5 − 51 M. kansasii (DSMZ 44162) + 61.5 50 48 M. gastri (DSMZ 43505) + 61.5 50 48 M. abscessus (ATCC 19977) + 61.5 − − M. chelonae (ATCC 35752) + 55 − − M. celatum (ATCC 58131) + 61.5 − 44 M. farcinogenes (ATCC 35753) + 61.5 50 48 M. hämophilum (ATCC 29548) + 61.5 50 48 M. malmoense (ATCC 27046) + 61.5 − 43 M. marinum (ATCC 927) + 61.5 45 48 M. scrofulaceum (ATCC 19981) + 61.5 50 48 M. shimoidei (ATCC 27962) + 61.5 50 48 M. xenopi + 61.5 54 47 M. simiae + 61.5 50 48 M. agri (ATCC 27406) + 61.5 − 43 M. triviale (ATCC 23292) + 61.5 48 49 M. fortuitum + 61.5 45 47 M. chitae (ATCC 19627) + 61.5 51 51 M. duvalii (ATCC43910) + 61.5 43 45 M. neoaurum (ATCC 25795) + 61.5 48 53 M. phlei (ATCC 11758) + 61.5 − 44 M. rhodesiae (ATCC 27024) + 61.5 52 52 M. smegmatis + 61.5 − − M. senegalense (ATCC 33027) + 61.5 46 48 M. porcinum (ATCC 33776) + 61.5 50 51 M. gordonae (DMSZ 44160) + 61.5 − 42.5 M. szulgai (DMSZ 44166) + 61.5 51 42.0 M. genavense (DMSZ 44424) + 61.5 51 50 Nonmycobacteria Actinomycetes other than mycobacteria Nocardia farcinica (ATCC 3318) − − − − Nocardia brevicatena (ATCC 15333) − − − − Streptomyces griseus − − − − Rhodococcus equi − − − − Coryneb. pseudodiphtheriticum (ATCC 10700) + 43 44 44 Corynebacterium jeikeium + 44 44 44 Corynebacterium xerosis (ATCC 373) + − − − Gram-positive bacteria Bacillus subtilis (ATCC 6633) − − − − Bacillus cereus − − − − Staphylococcus aureus (ATCC 25923) − − − − Staphylococcus epidermidis (ATCC 12228) − − − − Streptococcus pneumoniae (ATCC 49619) − − − − Listeria monocytogenes (ATCC 19115) − − − − Enterococcus faecalis (ATCC 29212) − − − − Gram-negative bacteria Proteus mirabilis (ATCC 14153) − − − − Escherichia coli (ATCC 25922) − − − − Salmonella typhimurium (ATCC 14028) − − − − Shigella sonnei (ATCC 25930) − − − − Klebsiella pneumoniae (ATCC 10031) − − − − Pseudomonas aeruginosa (ATCC 27853) − − − − Moraxella catarrhalis (ATCC 19115) − − − − Fungi Candida albicans − − − − Candida glabrata − − − − Candida crusei − − − − Aspergillus fumigatus − − − − Fusarium − − − − Open in a separate window a Various mycobacteria or nonmycobacterial species were used as templates (2.5 mg per reaction mixture).

Techniques: Amplification

Journal:

Article Title: Detection of Rifampin-Resistant Mycobacterium tuberculosis in Sputa by Nested PCR-Linked Single-Strand Conformation Polymorphism and DNA Sequencing

doi: 10.1128/JCM.39.7.2610-2617.2001

Figure Lengend Snippet: Mycobacteria and nonmycobacteria used to determine the specificity of the first-round PCR

Article Snippet: Clinical isolates were identified by conventional biochemical tests and partial 16S rDNA sequencing. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Species Type strains a No. of clinical isolates b Mycobacteria M. avium ATCC 25291 6 M. fortuitum ATCC 6841 4 M. gordonae ATCC 14470 2 M. kansasii ATCC 12478 5 M. nonchromogenicum ATCC 19530 0 M. scrofulaceum ATCC 19981 0 M. smegmatis ATCC 19420 0 M. terrae ATCC 15755 0 M. triviale ATCC 23292 0 M. vaccae ATCC 15483 0 M. chelonae ATCC 35749 3 M. gastri ATCC 15754 0 M. intracellulare ATCC 13950 8 M. malmoense ATCC 29571 0 M. phlei ATCC 11758 0 M. simiae ATCC 25275 0 M. szulgai ATCC 35799 0 M. tuberculosis ATCC 27294 20 M. ulcerans ATCC 19423 0 Nonmycobacteria Rhodococcus equi IMSNU20114 0 Rhodococcus erythropolis IMSNU20115 0 Rhodococcus rhodochrous IMSNU20349 0 Nocardia otitidiscaviarum IMSNU21221 0 Nocardia nova IMSNU21197 0 Corynebacterium diphtheriae MSNU 0 Corynebacterium glutamicum IMSNU21196 0 Neisseria meningitidis MSNU 0 Haemophilus influenzae MSNU 0 Open in a separate window a MSNU, Department of Microbiology, Seoul National University College of Medicine; IMSNU, Institute of Microbiology, Seoul National University. b Clinical isolates were identified by biochemical tests and partial 16S rDNA sequencing.

Techniques:

Journal:

Article Title: Detection of Rifampin-Resistant Mycobacterium tuberculosis in Sputa by Nested PCR-Linked Single-Strand Conformation Polymorphism and DNA Sequencing

doi: 10.1128/JCM.39.7.2610-2617.2001

Figure Lengend Snippet: Specific amplification of M. tuberculosis rpoB DNA by first-round PCR (TB1-TB2 primer set). The Southern blot shows that the PCR product (205 bp) was amplified from only M. tuberculosis by the first-round PCR. (A and B) Lanes: 1, M. tuberculosis H37Rv; 2, clinical isolate of M. tuberculosis; M, φX174/RF DNA/HaeIII digest; 3, M. avium; 4, M. fortuitum; 5, M. gastri; 6, M. gordonae; 7, M. intracellulare; 8, M. kansasii; 9; M. malmoense; 10, M. nonchromogenicum; 11, M. phlei; 12, M. scrofulaceum; 13, M. simiae; 14, M. smegmatis; 15, M. terrae. (C and D) Lanes 16, M. triviale; 17, M. vaccae; 18, M. chelonae; 19, M. szulgai; 20, M. ulcerans; 21, Rhodococcus equi; 22, Rhodococcus erythropolis; 23, Rhodococcus rhodochrous; 24, Nocardia otitidiscaviarum; 25, Nocardia nova; 26, Corynebacterium glutamicum; 27, Corynebacterium diphtheriae; 28, Neisseria meningitidis; 29, Haemophilus influenzae.

Article Snippet: Clinical isolates were identified by conventional biochemical tests and partial 16S rDNA sequencing. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Species Type strains a No. of clinical isolates b Mycobacteria M. avium ATCC 25291 6 M. fortuitum ATCC 6841 4 M. gordonae ATCC 14470 2 M. kansasii ATCC 12478 5 M. nonchromogenicum ATCC 19530 0 M. scrofulaceum ATCC 19981 0 M. smegmatis ATCC 19420 0 M. terrae ATCC 15755 0 M. triviale ATCC 23292 0 M. vaccae ATCC 15483 0 M. chelonae ATCC 35749 3 M. gastri ATCC 15754 0 M. intracellulare ATCC 13950 8 M. malmoense ATCC 29571 0 M. phlei ATCC 11758 0 M. simiae ATCC 25275 0 M. szulgai ATCC 35799 0 M. tuberculosis ATCC 27294 20 M. ulcerans ATCC 19423 0 Nonmycobacteria Rhodococcus equi IMSNU20114 0 Rhodococcus erythropolis IMSNU20115 0 Rhodococcus rhodochrous IMSNU20349 0 Nocardia otitidiscaviarum IMSNU21221 0 Nocardia nova IMSNU21197 0 Corynebacterium diphtheriae MSNU 0 Corynebacterium glutamicum IMSNU21196 0 Neisseria meningitidis MSNU 0 Haemophilus influenzae MSNU 0 Open in a separate window a MSNU, Department of Microbiology, Seoul National University College of Medicine; IMSNU, Institute of Microbiology, Seoul National University. b Clinical isolates were identified by biochemical tests and partial 16S rDNA sequencing.

Techniques: Amplification, Southern Blot

Journal: Journal of Clinical Microbiology

Article Title: Novel Algorithm Identifies Species in a Polymycobacterial Sample by Fluorescence Capillary Electrophoresis-Based Single-Strand Conformation Polymorphism Analysis

doi: 10.1128/JCM.40.12.4705-4712.2002

Figure Lengend Snippet: Strains used to establish an algorithm for species identification

Article Snippet: Co., Ltd., Tokyo, Japan), or partial 16S rDNA sequencing. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Species Strain a Serovar Sequevar No. of tests run M. avium ATCC 15769 1 1 ATCC 25291 2 Mav A 5 ATCC 35718 3 1 ATCC 35767 4 Mav A 1 ATCC 35768 5 1 ATCC 35773 6 1 ATCC 35771 8 1 ATCC 35774 9 Mav D 3 ATCC 35765 10 Mav B 3 ATCC 35766 11 Mav A 1 Clinical isolates (14) 1 M. intracellulare ATCC 35762 12 Min A 5 ATCC 35769 13 1 ATCC 35761 14 Min A 1 ATCC 35848 15 Min A 1 ATCC 13950 16 Min A 1 ATCC 35763 17 Min A 1 ATCC 35770 18 MAC D 5 ATCC 35772 19 Sequevar V 5 ATCC 35764 20 Min A 1 Clinical isolates (18) 1 M. tuberculosis complex H37Rv 4 BCG Tokyo 3 Clinical isolates (12) 1 M. kansasii ATCC 12478 MKa A 6 Clinical isolates (7) 1 M. marinum ATCC 927 5 Clinical isolate (1) 5 M. scrofulaceum ATCC 19981 Mscro A 4 M. simiae ATCC 25275 Sequevar I 3 M. gordonae ATCC 14470 Mgo A 4 Clinical isolates (9) 1 M. szulgai ATCC 35799 4 M. lentiflavum Clinical isolate (1) 4 M. xenopi ATCC 19250 Mxe A 3 M. nonchronogenicum ATCC 19530 3 M. gastri ATCC 15754 3 M. terrae Clinical isolate (1) 3 M. chelonae ATCC 19237 3 Clinical isolate (1) 3 M. abscessus ATCC 19977 6 Clinical isolates (4) 2 M. smegmatis ATCC 14468 3 M. phlei ATCC 11758 Mphle A 3 M. diernhoferi ATCC 19340 3 M. fortuitum ATCC 6841 Mfo A 3 ATCC 19542 3 Clinical isolates (5) 1 Open in a separate window a The number of clinical isolates tested is shown in parentheses.

Techniques:

Journal: Journal of Clinical Microbiology

Article Title: Novel Algorithm Identifies Species in a Polymycobacterial Sample by Fluorescence Capillary Electrophoresis-Based Single-Strand Conformation Polymorphism Analysis

doi: 10.1128/JCM.40.12.4705-4712.2002

Figure Lengend Snippet: Algorithm for the identification of Mycobacterium species by FCE-RF-SSCP

Article Snippet: Co., Ltd., Tokyo, Japan), or partial 16S rDNA sequencing. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Species Strain a Serovar Sequevar No. of tests run M. avium ATCC 15769 1 1 ATCC 25291 2 Mav A 5 ATCC 35718 3 1 ATCC 35767 4 Mav A 1 ATCC 35768 5 1 ATCC 35773 6 1 ATCC 35771 8 1 ATCC 35774 9 Mav D 3 ATCC 35765 10 Mav B 3 ATCC 35766 11 Mav A 1 Clinical isolates (14) 1 M. intracellulare ATCC 35762 12 Min A 5 ATCC 35769 13 1 ATCC 35761 14 Min A 1 ATCC 35848 15 Min A 1 ATCC 13950 16 Min A 1 ATCC 35763 17 Min A 1 ATCC 35770 18 MAC D 5 ATCC 35772 19 Sequevar V 5 ATCC 35764 20 Min A 1 Clinical isolates (18) 1 M. tuberculosis complex H37Rv 4 BCG Tokyo 3 Clinical isolates (12) 1 M. kansasii ATCC 12478 MKa A 6 Clinical isolates (7) 1 M. marinum ATCC 927 5 Clinical isolate (1) 5 M. scrofulaceum ATCC 19981 Mscro A 4 M. simiae ATCC 25275 Sequevar I 3 M. gordonae ATCC 14470 Mgo A 4 Clinical isolates (9) 1 M. szulgai ATCC 35799 4 M. lentiflavum Clinical isolate (1) 4 M. xenopi ATCC 19250 Mxe A 3 M. nonchronogenicum ATCC 19530 3 M. gastri ATCC 15754 3 M. terrae Clinical isolate (1) 3 M. chelonae ATCC 19237 3 Clinical isolate (1) 3 M. abscessus ATCC 19977 6 Clinical isolates (4) 2 M. smegmatis ATCC 14468 3 M. phlei ATCC 11758 Mphle A 3 M. diernhoferi ATCC 19340 3 M. fortuitum ATCC 6841 Mfo A 3 ATCC 19542 3 Clinical isolates (5) 1 Open in a separate window a The number of clinical isolates tested is shown in parentheses.

Techniques:

Journal: Journal of Clinical Microbiology

Article Title: Novel Algorithm Identifies Species in a Polymycobacterial Sample by Fluorescence Capillary Electrophoresis-Based Single-Strand Conformation Polymorphism Analysis

doi: 10.1128/JCM.40.12.4705-4712.2002

Figure Lengend Snippet: Identification of mycobacterial species from the SSCP patterns shown in Fig. ​ Fig.2 2 a

Article Snippet: Co., Ltd., Tokyo, Japan), or partial 16S rDNA sequencing. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Species Strain a Serovar Sequevar No. of tests run M. avium ATCC 15769 1 1 ATCC 25291 2 Mav A 5 ATCC 35718 3 1 ATCC 35767 4 Mav A 1 ATCC 35768 5 1 ATCC 35773 6 1 ATCC 35771 8 1 ATCC 35774 9 Mav D 3 ATCC 35765 10 Mav B 3 ATCC 35766 11 Mav A 1 Clinical isolates (14) 1 M. intracellulare ATCC 35762 12 Min A 5 ATCC 35769 13 1 ATCC 35761 14 Min A 1 ATCC 35848 15 Min A 1 ATCC 13950 16 Min A 1 ATCC 35763 17 Min A 1 ATCC 35770 18 MAC D 5 ATCC 35772 19 Sequevar V 5 ATCC 35764 20 Min A 1 Clinical isolates (18) 1 M. tuberculosis complex H37Rv 4 BCG Tokyo 3 Clinical isolates (12) 1 M. kansasii ATCC 12478 MKa A 6 Clinical isolates (7) 1 M. marinum ATCC 927 5 Clinical isolate (1) 5 M. scrofulaceum ATCC 19981 Mscro A 4 M. simiae ATCC 25275 Sequevar I 3 M. gordonae ATCC 14470 Mgo A 4 Clinical isolates (9) 1 M. szulgai ATCC 35799 4 M. lentiflavum Clinical isolate (1) 4 M. xenopi ATCC 19250 Mxe A 3 M. nonchronogenicum ATCC 19530 3 M. gastri ATCC 15754 3 M. terrae Clinical isolate (1) 3 M. chelonae ATCC 19237 3 Clinical isolate (1) 3 M. abscessus ATCC 19977 6 Clinical isolates (4) 2 M. smegmatis ATCC 14468 3 M. phlei ATCC 11758 Mphle A 3 M. diernhoferi ATCC 19340 3 M. fortuitum ATCC 6841 Mfo A 3 ATCC 19542 3 Clinical isolates (5) 1 Open in a separate window a The number of clinical isolates tested is shown in parentheses.

Techniques:

Journal: Standards in Genomic Sciences

Article Title: Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165 T

doi: 10.4056/sigs.3707349

Figure Lengend Snippet: Classification and general features of Mycobacterium simiae DSM44165 T [ 22 ].

Article Snippet: The 16S rRNA gene sequence, derived from the M. simiae strain DSM 44165 T genome sequence showed 100% sequence similarity to that of M. simiae type strain DSM 44165 T /ATCC 25275 T previously deposited in GenBank (GenBank accession: GQ153280.1) and 99% sequence similarity with M. sherrisii (GenBank accession: AY353699.1).

Techniques: Staining, Isolation

Journal: Standards in Genomic Sciences

Article Title: Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165 T

doi: 10.4056/sigs.3707349

Figure Lengend Snippet: rpo B gene sequence based phylogenetic tree highlighting the position of Mycobacterium simiae DSM 44165 relative to other type strains within the Mycobacterium genus. Phylogenetic inferences obtained using the neighbor-joining method within MEGA. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1,000 times to generate a majority consensus tree. Rhodococcus sp P14 was used as an outgroup.

Article Snippet: The 16S rRNA gene sequence, derived from the M. simiae strain DSM 44165 T genome sequence showed 100% sequence similarity to that of M. simiae type strain DSM 44165 T /ATCC 25275 T previously deposited in GenBank (GenBank accession: GQ153280.1) and 99% sequence similarity with M. sherrisii (GenBank accession: AY353699.1).

Techniques: Sequencing

Journal: Standards in Genomic Sciences

Article Title: Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165 T

doi: 10.4056/sigs.3707349

Figure Lengend Snippet: Electron microscopy graph of M. simiae DSM 44165 T

Article Snippet: The 16S rRNA gene sequence, derived from the M. simiae strain DSM 44165 T genome sequence showed 100% sequence similarity to that of M. simiae type strain DSM 44165 T /ATCC 25275 T previously deposited in GenBank (GenBank accession: GQ153280.1) and 99% sequence similarity with M. sherrisii (GenBank accession: AY353699.1).

Techniques: Electron Microscopy

Journal: Standards in Genomic Sciences

Article Title: Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165 T

doi: 10.4056/sigs.3707349

Figure Lengend Snippet: Project information

Article Snippet: The 16S rRNA gene sequence, derived from the M. simiae strain DSM 44165 T genome sequence showed 100% sequence similarity to that of M. simiae type strain DSM 44165 T /ATCC 25275 T previously deposited in GenBank (GenBank accession: GQ153280.1) and 99% sequence similarity with M. sherrisii (GenBank accession: AY353699.1).

Techniques: Sequencing

Journal: Stem Cells International

Article Title: Therapeutic Effects of Human Urine-Derived Stem Cells in a Rat Model of Cisplatin-Induced Acute Kidney Injury In Vivo and In Vitro

doi: 10.1155/2019/8035076

Figure Lengend Snippet: Multipotential differentiation of USCs. (a) SMC-differentiated cells showed an increased expression of the SMC-specific markers desmin, myosin, ASMA, and vimentin. (b) The UC-differentiated cells showed an increased expression of the UC-specific markers UP-Ia, UP-III, AE1/AE3, and CK13. NC: negative control; ASMA: alpha-smooth muscle actin; UP-Ia: uroplakin 1A; UP-III: uroplakin 3; AE1/AE3: cytokeratin, clone AE1/AE3; CK13: cytokeratin 13. Scale bar: 25 μ m.

Article Snippet: USCs were assessed for the expression of the stem cell surface markers CD31 (Cell Signaling Technology, 3528), CD34 (Proteintech, 14486-1-AP), CD45 (Cell Signaling Technology, 13917), CD44 (Abcam, ab46793), CD133 (Proteintech, 18470-1-AP), SSEA4 (Proteintech, 19497-1-AP), CD146 (Proteintech, 17564-1-AP), platelet-derived growth factor beta-receptor (PDGFRB, Proteintech, 13449-1-AP), and neural/glial antigen 2 (NG2, Abcam, ab129051), and the SMC- or UC-induced USCs were evaluated for the SMC or UC surface marker desmin (Abcam, ab32362), myosin (Proteintech, 20716-1-AP), alpha-smooth muscle actin (ASMA, Proteintech, 23660-1-AP), vimentin (Proteintech, 10366-1-AP), or uroplakin 1A (UP-Ia, Proteintech, 25275-1-AP), uroplakin 3 (UP-III, Proteintech, 15709-1-AP), cytokeratin clone AE1/AE3 (AE1/AE3, Proteintech, 18566-1-AP), and cytokeratin 13 (CK13, Proteintech, 10164-2-AP).

Techniques: Expressing, Negative Control