scholarly journals Use of Long-Range Repetitive Element Polymorphism-PCR To Differentiate Bacillus anthracisStrains

2001 ◽  
Vol 67 (7) ◽  
pp. 3021-3028 ◽  
Author(s):  
Michael J. Brumlik ◽  
Urszula Szymajda ◽  
Dorota Zakowska ◽  
Xudong Liang ◽  
Rajendra J. Redkar ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Long Range ◽  
Repetitive Dna ◽  
Related Species ◽  
Molecular Level ◽  
Repetitive Element ◽  
Bacterial Genome ◽  
Chromosomal Marker ◽  
Closely Related Species ◽  
Pcr Method

ABSTRACT The genome of Bacillus anthracis is extremely monomorphic, and thus individual strains have often proven to be recalcitrant to differentiation at the molecular level. Long-range repetitive element polymorphism-PCR (LR REP-PCR) was used to differentiate various B. anthracis strains. A single PCR primer derived from a repetitive DNA element was able to amplify variable segments of a bacterial genome as large as 10 kb. We were able to characterize five genetically distinct groups by examining 105B. anthracis strains of diverse geographical origins. AllB. anthracis strains produced fingerprints comprising seven to eight bands, referred to as “skeleton” bands, while one to three “diagnostic” bands differentiated between B. anthracisstrains. LR REP-PCR fingerprints of B. anthracis strains showed very little in common with those of other closely related species such as B. cereus, B. thuringiensis, and B. mycoides, suggesting relative heterogeneity among the non-B. anthracis strains. Fingerprints from transitional non-B. anthracis strains, which possessed the B. anthracis chromosomal marker Ba813, scarcely resembled those observed for any of the five distinct B. anthracis groups that we have identified. The LR REP-PCR method described in this report provides a simple means of differentiating B. anthracisstrains.

scholarly journals PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution

2018 ◽  
Author(s):  
Sean P. Gordon ◽  
Joshua J. Levy ◽  
John P. Vogel
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Related Species ◽  
Software Package ◽  
Gc Content ◽  
Individual Species ◽  
Closely Related Species ◽  
As Species ◽  
Pooled Dna ◽  
Species Specific

AbstractExisting methods for assigning sequences to individual species from pooled DNA samples rely on differences in genome properties like GC content or sequences from related species. These approaches do not work for closely related species where gross features are indistinguishable and related genomes are lacking. We describe a method and associated software package that uses rapidly evolving repetitive DNA to circumvent these limitations. By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes without any prior knowledge. This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.

scholarly journals Quantitative analysis of mitochondrial DNAs in macaque embryos reprogrammed by rabbit oocytes

Reproduction ◽  
2004 ◽  
Vol 127 (2) ◽  
pp. 201-205 ◽  
Author(s):  
Cai-Xia Yang ◽  
Zhao-Hui Kou ◽  
Kai Wang ◽  
Yan Jiang ◽  
Wen-Wei Mao ◽  
...  
Keyword(s):  
Related Species ◽  
Nuclear Transfer ◽  
Blastocyst Stage ◽  
Cell Nuclei ◽  
Cell Stage ◽  
Closely Related Species ◽  
Copy Numbers ◽  
Mitochondrial Dnas ◽  
Morula Stage ◽  
Pcr Method

In cloned animals where somatic cell nuclei and oocytes are from the same or closely related species, the mitochondrial DNA (mtDNA) of the oocyte is dominantly inherited. However, in nuclear transfer (NT) embryos where nuclear donor and oocyte are from two distantly related species, the distribution of the mtDNA species is not known. Here we determined the levels of macaque and rabbit mtDNAs in macaque embryos reprogrammed by rabbit oocytes. Quantification using a real-time PCR method showed that both macaque and rabbit mtDNAs coexist in NT embryos at all preimplantation stages, with maternal mtDNA being dominant. Single NT embryos at the 1-cell stage immediately after fusion contained 2.6 × 104 copies of macaque mtDNA and 1.3 × 106 copies of rabbit mtDNA. Copy numbers of both mtDNA species did not change significantly from the 1-cell to the morula stages. In the single blastocyst, however, the number of rabbit mtDNA increased dramatically while macaque mtDNA decreased. The ratio of nuclear donor mtDNA to oocyte mtDNA dropped sharply from 2% at the 1-cell stage to 0.011% at the blastocyst stage. These results suggest that maternal mtDNA replicates after the morula stage.

scholarly journals Plasmid-Encoded Regulator of Extracellular Proteases in Bacillus anthracis

2005 ◽  
Vol 187 (9) ◽  
pp. 3133-3138 ◽  
Author(s):  
Arthur I. Aronson ◽  
Chris Bell ◽  
Ben Fulroth
Keyword(s):  
Bacillus Subtilis ◽  
Bacillus Thuringiensis ◽  
Bacillus Anthracis ◽  
Related Species ◽  
Protease Activity ◽  
Extracellular Proteases ◽  
Closely Related Species ◽  
Strain Transformation ◽  
Pleiotropic Regulator ◽  
Secreted Enzymes

ABSTRACT Bacillus anthracis Sterne cured of the pXO1 plasmid had enhanced secreted protease activity during the postexponential phase but no change in hemolytic or lecithinase activities. A zymogen profile revealed at least six proteases, including serine, metal, and perhaps cysteine types. There were similar amounts of protease secreted by the closely related species Bacillus cereus and Bacillus thuringiensis, but the patterns differed. Among the pXO1 plasmid-encoded proteins, there is a tetratricopeptide protein designated Cot43 that is related to the Rap proteins of Bacillus subtilis and the PlcR pleiotropic regulator of secreted enzymes and toxins in B. thuringiensis. A disruption of the cot43 gene resulted in overproduction of several proteases to a somewhat greater extent than in the plasmid-cured strain. Transformation of either of these strains with a clone of the cot43 gene resulted in the inhibition of accumulation of some of the proteases and induction of at least one. On the basis of lacZ fusions, transcription of the cot43 gene increased in late exponential cells at the time of protease accumulation. The expression of lacZ fusions to the upstream regions of two B. anthracis extracellular protease genes was greater in the strain with the disruption of cot43 than in the Sterne strain, indicating regulation at the level of transcription. In B. anthracis, a pXO1 plasmid-encoded protein directly modulates or indirectly regulates the transcription of genes for several chromosomally encoded extracellular proteases.

scholarly journals Rapid Identification of Polyhydroxyalkanoate Accumulating Members of Bacillales Using Internal Primers for phaC Gene of Bacillus megaterium

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Pramoda Kumar Nayak ◽  
Ajeet Kumar Mohanty ◽  
Teja Gaonkar ◽  
Ashwani Kumar ◽  
Saroj N. Bhosle ◽  
...  
Keyword(s):  
Bacillus Megaterium ◽  
Related Species ◽  
Rapid Identification ◽  
Rt Pcr ◽  
Closely Related Species ◽  
Banding Patterns ◽  
Phac Gene ◽  
Polyhydroxyalkanoate Synthase ◽  
Pcr Method ◽  
Respective Species

Bacillus megaterium is gaining recognition as an experimental model and biotechnologically important microorganism. Recently, descriptions of new strains of B. megaterium and closely related species isolated from diverse habitats have increased. Therefore, its identification requires several tests in combination which is usually time consuming and difficult to do. We propose using the uniqueness of the polyhydroxyalkanoate synthase C gene of B. megaterium in designing primers that amplify the 0.9 kb region of the phaC for its identification. The PCR method was optimized to amplify 0.9 kb region of phaC gene. After optimization of the PCR reaction, two methods were investigated in detail. Method I gave an amplification of a single band of 0.9 kb only in B. megaterium and was demonstrated by several strains of B. megaterium isolated from different habitats. The use of Method I did not result in the amplification of the phaC gene with other members of Bacillales. The specificity for identification of B. megaterium was confirmed using sequencing of amplicon and RT-PCR. Method II showed multiple banding patterns of nonspecific amplicons among polyhydroxyalkanoate accumulating members of Bacillales unique to the respective species. These methods are rapid and specific for the identification of polyhydroxyalkanoate accumulating B. megaterium and members of Bacillales.

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