Molecular genetic analysis of phylogenetic relationships in the genus Hynobius by means of Southern blot hybridization

Genome ◽  
1992 ◽  
Vol 35 (3) ◽  
pp. 478-491 ◽  
Author(s):  
Masaki Kuro-o ◽  
Tsutomu Hikida ◽  
Sei-ichi Kohno
Keyword(s):  
Southern Blot ◽  
Repetitive Dna ◽  
Blot Hybridization ◽  
Molecular Genetic ◽  
Southern Blot Hybridization ◽  
Molecular Genetic Analysis ◽  
Manhattan Distance ◽  
Distance Analysis ◽  
Group 3 ◽  
Pond Type

Variations in repetitive DNA were examined in nine salamander species of the genera Hynobius and Onychodactylus. The data from Southern blot hybridization were processed by Manhattan distance analysis, and unrooted trees were drawn. The resulting trees suggest that the genus Hynobius can be divided into three groups: group 1 contains only H. retardatus with 40 chromosomes; group 2 contains H. kimurae, which has 58 chromosomes and is a mountain-brook type of Hynobius (this group probably contains all mountain-brook types of Hynobius with 58 chromosomes); and group 3 contains the other six pond-type species examined here, each with 56 chromosomes. Group 3 probably contains all species of Hynobius with 56 chromosomes. Furthermore, group 3 can be further separated into two groups: the first group includes H. leechii, H. tsuensis, H. nebulosus, H. nigrescens, and H. tokyoensis from Chita; and the second group includes H. tokyoensis (except the population from Chita) and H. lichenatus. According to this analysis and other information, it seems that the population from Aichi Prefecture, which belongs to H. tokyoensis, should be identified as H. nebulosus. Furthermore, it appears that the genus Onychodactylus is phylogenetically distant from Hynobius and Salamandrella.Key words: Hynobius, repetitive DNA, Southern blot hybridization, phylogenetics, neighbor-joining method.

Chromosomal Assignment of HepG2 3′-Directed Partial cDNA Sequences by Southern Blot Hybridization Using Monochromosomal Hybrid Cell Panels

Genomics ◽  
1994 ◽  
Vol 22 (1) ◽  
pp. 127-136 ◽  
Author(s):  
Atsushi Fukushima ◽  
Kousaku Okubo ◽  
Hidehiko Sugino ◽  
Naohiro Hori ◽  
Ryo Matoba ◽  
...  
Keyword(s):  
Southern Blot ◽  
Hybrid Cell ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Chromosomal Assignment ◽  
Cdna Sequences ◽  
Partial Cdna ◽  
Monochromosomal Hybrid

scholarly journals Genome analysis of HTLV-I virus in PA positive and IF negative healthy donors by southern blot hybridization.

1988 ◽  
Vol 34 (1) ◽  
pp. 50-52
Author(s):  
Chieko Suzuki ◽  
Noriko Tomita ◽  
Eiichi Uchiyama ◽  
Akio Ishii ◽  
Takeshi Nishizaki ◽  
...  
Keyword(s):  
Southern Blot ◽  
Genome Analysis ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Healthy Donors

scholarly journals Detection of “Candidatus Helicobacter suis” in Gastric Samples of Pigs by PCR: Comparison with Other Invasive Diagnostic Techniques

2000 ◽  
Vol 38 (3) ◽  
pp. 1131-1135 ◽  
Author(s):  
D. De Groote ◽  
R. Ducatelle ◽  
L. J. van Doorn ◽  
K. Tilmant ◽  
A. Verschuuren ◽  
...  
Keyword(s):  
Southern Blot ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Epidemiological Studies ◽  
Diagnostic Techniques ◽  
Diagnostic Methods ◽  
Giemsa Staining ◽  
Rapid Urease Test ◽  
Pcr Assay ◽  
Urease Test

Recently, a new 16S ribosomal DNA-based PCR assay was developed for the specific detection of “Candidatus Helicobacter suis” (former “Gastrospirillum suis”) in porcine gastric samples. In the present study, this PCR assay was compared to three other invasive diagnostic methods (rapid urease test, immunohistochemistry, histologic analysis by Giemsa staining). Antral stomach samples from 200 slaughterhouse pigs from Belgium and The Netherlands were examined. Bacterial presence was determined in 77% (154 of 200) of the samples by PCR in combination with Southern blot hybridization, 56% (111 of 200) of the samples by immunohistochemistry, 61% (122 of 200) of the samples by urease testing (20 h postinoculation [p.i.]), 36% (71 of 200) of the samples by urease testing (3 h p.i.), and 33% (65 of 200) of the samples by Giemsa staining. The intrinsic specificity of the PCR assay was assessed by Southern blot analysis with an “Candidatus H. suis”-specific probe and sequencing of PCR products. Interassay sensitivity and specificity values were assessed for each test by pairwise comparisons between tests. Agreement between tests was evaluated by calculating Cohen's kappa coefficient. From that analysis, the PCR assay was considered the most reliable benchmark. Microscopic detection of immunohistochemically labeled or Giemsa-stained “Candidatus H. suis” cells in stomach sections proved to be highly specific (100%) but relatively insensitive (72 and 42%, respectively) compared to the PCR assay. A longer incubation time of the urease test improved its sensitivity considerably (74 versus 55%) but was accompanied by a loss of specificity (72 versus 93%). In conclusion, we found the “Candidatus H. suis”-specific PCR assay to be a sensitive and reliable diagnostic method for the detection of “Candidatus H. suis” in the stomachs of pigs and could prove to be a valuable tool for further epidemiological studies both for “Candidatus H. suis”- and for “Helicobacter heilmannii” type 1-related research.

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