scholarly journals Comparative Analysis of Physical Maps of Four Bacillus subtilis (natto) Genomes

2004 ◽  
Vol 70 (10) ◽  
pp. 6247-6256 ◽  
Author(s):  
Dongru Qiu ◽  
Kyoko Fujita ◽  
Yuko Sakuma ◽  
Teruo Tanaka ◽  
Yoshiaki Ohashi ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Dna Sequences ◽  
Large Scale ◽  
Fragment Length Polymorphism ◽  
Genome Structure ◽  
Insertion Element ◽  
Physical Maps ◽  
Indigenous Plasmids ◽  
Bacillus Subtilis Natto ◽  
Restriction Fragment Length

ABSTRACT The complete SfiI and I-CeuI physical maps of four Bacillus subtilis (natto) strains, which were previously isolated as natto (fermented soybean) starters, were constructed to elucidate the genome structure. Not only the similarity in genome size and organization but also the microheterogeneity of the gene context was revealed. No large-scale genome rearrangements among the four strains were indicated by mapping of the genes, including 10 rRNA operons (rrn) and relevant genes required for natto production, to the loci corresponding to those of the B. subtilis strain Marburg 168. However, restriction fragment length polymorphism and the presence or absence of strain-specific DNA sequences, such as the prophages SPβ, skin element, and PBSX, as well as the insertion element IS4Bsu1, could be used to identify one of these strains as a Marburg type and the other three strains as natto types. The genome structure and gene heterogeneity were also consistent with the type of indigenous plasmids harbored by the strains.

scholarly journals Identification of Pneumococcal Serotypes by PCR–Restriction Fragment Length Polymorphism

Diagnostics ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 196 ◽  
Author(s):  
García-Suárez ◽  
González-Rodríguez ◽  
Cima-Cabal ◽  
Yuste ◽  
Vazquez ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Dna Sequences ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Pcr Rflp ◽  
Restriction Fragment Length

Streptococcus pneumoniae shows more than 90 capsular serotypes that can be distinguished by their reactivity against antisera. The main objective of this work was the development of a molecular method for serotyping without the use of antisera. A computer program containing an algorithm was used to search in a database for potentially useful enzymes for Restriction Fragment Length Polymorphism-RFLP typing, in order to maximize the discrimination between different serotypes. DNA sequences of 90 serotypes for the region between dexB and aliA genes were compiled, and a computer screening of restriction enzymes was performed. The wzg–wzh–wzd–wze region and Sse9I restriction predicted unique PCR-RFLP patterns for 39 serotypes and eight serogroups. A second restriction enzyme resolved fragment specific patterns for 25 serotypes. The method was tested with 98 serotype-unknown clinical isolates. PCR-RFLP analysis deduced correct serotypes that were confirmed by Quellung reaction for 78.5% of the isolates.

scholarly journals Identification protocol for sixArmillariaspecies from northeastern North America

2010 ◽  
Vol 40 (3) ◽  
pp. 536-548 ◽  
Author(s):  
J. A. McLaughlin ◽  
T. Hsiang
Keyword(s):  
Dna Sequences ◽  
Fragment Length Polymorphism ◽  
Intergenic Spacer ◽  
Polymorphism Analysis ◽  
Specific Primers ◽  
Northeastern North America ◽  
Armillaria Ostoyae ◽  
Armillaria Gallica ◽  
Species Specific ◽  
Restriction Fragment Length

DNA sequences (~3 kb long) extending from the intergenic spacer 1 (IGS1) region to the 18S gene were obtained for isolates of Armillaria ostoyae , Armillaria calvescens , Armillaria gallica , and Armillaria sinapina . Additional investigation of 16 A. ostoyae, 11 Armillaria gemina , 21 A. calvescens, 18 A. gallica, and 15 A. sinapina isolates produced 117 sequences spanning the 3′ end of the IGS1 through the 5S gene and into the 5′ end of the IGS2 region. Additional sequences spanning the 3′ IGS2 to 5′ 18S gene region were obtained for two A. ostoyae, three A. gemina, two A. calvescens, two A. gallica, and three A. sinapina isolates. This is the first report of complete IGS2 sequences from Armillaria spp. A species identification protocol involving species-specific primers and restriction fragment length polymorphism analysis was devised based on species-specific polymorphisms. The protocol successfully identified all 16 A. ostoyae, 11 A. gemina, three of three Armillaria mellea , 18 A. gallica, 14 of 15 A. sinapina (11/12 diploid and 3/3 haploid), and 14 of 21 A. calvescens (13/15 diploid and 1/6 haploid) isolates included in this study. To the best of our knowledge, this success rate has not been matched by other methods.

scholarly journals Construction of physical maps of Bacillus subtilis (natto) strains

2003 ◽  
Vol 3 (1) ◽  
pp. 207-208 ◽  
Author(s):  
D. Qiu ◽  
H. Oshima ◽  
Y. Ohashi ◽  
M. Itaya
Keyword(s):  
Bacillus Subtilis ◽  
Physical Maps ◽  
Bacillus Subtilis Natto

scholarly journals Genetic and Physical Maps of the Bacillus subtilis Chromosome

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1239-1244
Author(s):  
Carlo Rivolta ◽  
Marco Pagni
Keyword(s):  
Bacillus Subtilis ◽  
Nucleotide Sequence ◽  
Dna Sequences ◽  
Mapping Method ◽  
Detectable Effect ◽  
Recombination Hotspots ◽  
Physical Maps ◽  
Subtilis Chromosome ◽  
Bacillus Subtilis Chromosome ◽  
Reference Markers

Abstract Sequencing of the complete Bacillus subtilis chromosome revealed the presence of ∼4100 genes, 1000 of which were previously identified and mapped by classical genetic crosses. Comparison of these experimentally determined positions to those derived from the nucleotide sequence showed discrepancies reaching up to 24° (∼280 kb). The size of these discrepancies as a function of their position along the chromosome is not random but, apparently, reveals some periodicity. Our analyses demonstrate that the discrepancies can be accounted for by inaccurate positioning of the early reference markers with respect to which all subsequently identified loci were mapped by transduction and transformation. We conclude (i) that specific DNA sequences, such as recombination hotspots or presence of heterologous DNA, had no detectable effect on the results obtained by classical mapping, and (ii) that PBS1 transduction appears to be an accurate and unbiased mapping method in B. subtilis.

scholarly journals Stability of Insertion Sequence IS1245, a Marker for Differentiation of Mycobacterium aviumStrains

1999 ◽  
Vol 37 (2) ◽  
pp. 442-444 ◽  
Author(s):  
Jeanett Bauer ◽  
Åse Bengård Andersen
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Mycobacterium Avium ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Insertion Sequence ◽  
Fragment Length Polymorphism ◽  
Insertion Element ◽  
The Stability ◽  
Restriction Fragment Length

Recently a novel insertion element, IS1245, has been described and suggested for use as a probe in restriction fragment length polymorphism studies of Mycobacterium avium strains. An important issue in this context is the stability of the insertion element. We analyzed single colonies of M. avium cultures and found frequent small one- to two-band changes. However, following repeated in vitro passages over 1 year, similar one- to two-band changes were observed in the IS1245 patterns of only sixM. avium strains investigated.

Epidemiological relationships of Trypanosoma brucei stocks from South East Uganda: evidence for different population structures in human infective and non-human infective isolates

Parasitology ◽  
1994 ◽  
Vol 109 (1) ◽  
pp. 95-111 ◽  
Author(s):  
G. Hide ◽  
S. C. Welburn ◽  
A. Tait ◽  
I. Maudlin
Keyword(s):  
Trypanosoma Brucei ◽  
Dna Sequences ◽  
Fragment Length Polymorphism ◽  
Genetic Exchange ◽  
Repetitive Dna Sequences ◽  
Isoenzyme Analysis ◽  
Short Period ◽  
Population Structures ◽  
Isoenzyme Patterns ◽  
Restriction Fragment Length

SUMMARYThis study represents an analysis of trypanosome strains circulating within a confined location over a short period of time during a sleeping sickness epidemic in S.E. Uganda. A large number of Trypanosoma brucei isolates (88) were collected from a variety of hosts (man, cattle, pigs and tsetse) from villages within a 10 km radius and were analysed for variation in isoenzyme patterns, restriction fragment length polymorphism (RFLP) in repetitive DNA sequences and susceptibility to human serum. The human infective stocks form a clearly distinguishable population when compared with other stocks circulating in the domestic cattle reservoir. The data here support the occurrence of genetic exchange between the cattle stocks while an ‘epidemic’ population structure involving limited genetic exchange is a characteristic of the human infective stocks. Furthermore, it is shown that when both RFLP and isoenzyme analysis are carried out most stocks appear to have individual genotypes. Stocks which were formerly grouped as zymodemes are better considered as a collection of distinct individuals.

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