Characterization of the Opisthorchis viverrini genome

1991 ◽  
Vol 65 (1) ◽  
pp. 51-54 ◽  
Author(s):  
R. Sermswan ◽  
S. Mongkolsuk ◽  
S. Sirisinha
Keyword(s):  
Southern Blot ◽  
Genomic Dna ◽  
Blot Hybridization ◽  
Restriction Enzymes ◽  
Southern Blot Hybridization ◽  
Fasciola Gigantica ◽  
Opisthorchis Viverrini ◽  
Repeated Dna ◽  
Dna Elements

ABSTRACTThe methylations of trematode genomic DNA were analyzed using restriction enzymes and Southern blot hybridization. Restriction enzymes MspI, HpaII, HhaI were used to probe CpG methylation while MboI, Sau3A, DpnI were used for A methylation. The results revealed that Opisthorchis viverrini, Fasciola gigantica and Gigantocotyle siamensis had neither CpG nor A methylations. The presence of highly repeated DNA elements was also demonstrated in O. viverrini genomic DNA.

Centromeric tandem repeat from the chaffinch genome: Isolation and molecular characterization

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 96-103 ◽  
Author(s):  
A F Saifitdinova ◽  
S E Derjusheva ◽  
A G Malykh ◽  
V G Zhurov ◽  
T F Andreeva ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Blot Hybridization ◽  
Restriction Enzymes ◽  
Southern Blot Hybridization ◽  
Repeated Sequence ◽  
Centromeric Heterochromatin ◽  
Specific Primers ◽  
Fringilla Coelebs ◽  
New Family

A new family of avian centromeric satellites is described. The highly repeated sequence, designated FCP (Fringilla coelebs PstI element), was cloned from the 500-bp PstI digest fraction of the chaffinch (Fringilla coelebs L.) genomic DNA, sequenced, and characterized. The FCP repeat was found to have 505–506 bp length of monomer, 57% content of GC, to compose about 0.9% of the chaffinch genome, and to be highly methylated. Results of Southern-blot hybridization of cloned FCP element onto genomic DNA digested with different restriction enzymes, and sequencing directly from total genomic DNA using FCP-specific primers and ThermoFidelase enzyme (Fidelity Systems Inc.) were in agreement with a tandem arrangement of this repeat in the chaffinch genome. Five positions of single-nucleotide polymorphism (SNP) were found in the FCP monomers using direct genomic sequencing. Fluorescence in situ hybridization (FISH) with FCP probe and primed in situ labelling (PRINS) with FCP specific primers showed that the FCP elements occupy pericentric regions of all chaffinch chromosomes. On chromosome spreads, the fluorescent signals were also observed in the intercentromeric connectives between nonhomologous chromosomes. The results suggest that the centromeric FCP repeat is responsible for chromosome ordering during mitosis in chaffinch.Key words: satellite DNA, centromeric heterochromatin, Fringilla coelebs.

A Contigs Strategy of Southern Blot Hybridization: Screening for DNase I Hypersensitive Sites in the 200 Kb Region 5′ to the B-Globin Locus LCR.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1219-1219
Author(s):  
Ping Xiang ◽  
Hemei Han ◽  
Xiangdong Fang ◽  
George Stamatoyannopoulos ◽  
Qiliang Li
Keyword(s):  
Southern Blot ◽  
Dna Sequences ◽  
Globin Gene ◽  
Blot Hybridization ◽  
Restriction Enzymes ◽  
Southern Blot Hybridization ◽  
Dnase I ◽  
Screening Process ◽  
Dnase I Hypersensitive Sites ◽  
Hypersensitive Sites

Abstract Formation of DNase I hypersensitive sites is an indication of local disruption of chromatin conformation. It has been documented that HS sites are frequently associated with functional DNA sequences, such as, promoters, enhancers, and insulators. While Southern blot hybridization is the standard method to detect HS sites, this procedure is time-consuming and labor intensive. To improve the efficiency of HS detection through Southern blot hybridization, we designed a contigs strategy of Southern blot hybridization and test it in the 200 kb region 5′ to the LCR in the b-globin locus. Based on the human genome sequence we made physical maps of seven 6-bp-cut restriction enzymes in the 200 kb region. From the map we selected continuous contigs of 10 to 15 kb fragment; and designed hybridization probes for the 5′ and 3′ ends of each fragment (some probes can be used in two neighboring fragments). The screening was performed on erythroid (K562) and non-erythroid (Jurkat) cell lines. We found about 40 HS sites within the region. The major sites were either erythroid specific (for instance, HSs at −66 kb, −142 kb, and −236 kb, the cap site of the e-globin gene is +1), or non-erythroid specific (for instances, HSs at −111 kb, −164 kb, and −205 kb). These HS sites will be investigated for enhancer, promoter, and insulator function using transient and stable transfection studies. Due to the limited number of enzyme required and the fact that each blot could be used several times, this strategy can greatly expedite the screening process for presence of DNase I hypersensitive sites. Estimated efficiency of this screening approach is about 0.5 to1 Mb per person per year.

scholarly journals Differences in Virulence and Genomic Features of Strains of ‘Candidatus Phytoplasma mali’, the Apple Proliferation Agent

2007 ◽  
Vol 97 (8) ◽  
pp. 964-970 ◽  
Author(s):  
Erich Seemüller ◽  
Bernd Schneider
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Blot Hybridization ◽  
Pcr Amplification ◽  
Restriction Enzymes ◽  
Southern Blot Hybridization ◽  
Apple Proliferation ◽  
Candidatus Phytoplasma Mali ◽  
Polymerase Chain

Root and shoot samples from 24 symptomatic or nonsymptomatic apple trees infected with ‘Candidatus Phytoplasma mali’ were collected at different locations in Germany and France and used to inoculate rootstock M11 top grafted with cv. Golden Delicious. Inoculated trees were monitored over a 12-year period for apple proliferation (AP) symptoms and categorized as not or slightly, moderately, or severely affected. Based on symptomatology, the phytoplasma strains were defined as being avirulent to mildly, moderately, or highly virulent. Determination of phytoplasma titers by quantitative polymerase chain reaction (PCR) with DNA from roots revealed similar phytoplasma concentrations in all virulence groups. Molecular characterization of the strains by differential PCR amplification with five sets of primers resulted in 13 profiles. Six strains that were maintained in periwinkle and tobacco were molecularly characterized in more detail. The genome sizes of these strains as determined by pulsed-field gel electrophoresis using yeast chromosomes as size references ranged between 640 and 680 kb. Cleavage of the chromosome with the rare cutting restriction enzymes ApaI, BamHI, BssHII, MluI, and SmaI resulted in macro fragment patterns distinctly different in all strains. Similar results were obtained by Southern blot hybridization with three probes derived from strain AT. Differential PCR amplification at an annealing temperature of 52°C using eight primer pairs derived from strain AT revealed heterogeneity of target sequences among all strains. Based on these results, there is considerable variability in virulence and genomic traits in ‘Ca. P. mali’. However, correlations between molecular markers and virulence or phytoplasma titer could not be identified.

scholarly journals Characterization of the bla KPC-2 and bla KPC-3 genes and the novel bla KPC-15 gene in Klebsiella pneumoniae

2014 ◽  
Vol 63 (7) ◽  
pp. 981-987 ◽  
Author(s):  
Dongguo Wang ◽  
Wei Hou ◽  
Jiayu Chen ◽  
Yonghua Mou ◽  
Linjun Yang ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Gene Mapping ◽  
Southern Blot ◽  
Blot Hybridization ◽  
Carbapenem Resistance ◽  
Southern Blot Hybridization ◽  
The Novel ◽  
Plasmid Analysis ◽  
High Level

Three Klebsiella pneumoniae isolates exhibiting high-level resistance to carbapenem were analysed by PCR, PFGE, gene mapping, plasmid conjugation and Southern blot hybridization using a bla KPC probe. In addition to the frequently reported bla KPC-2 and bla KPC-3 genes, a novel bla KPC-15 gene was identified in one of the isolates. The results of plasmid analysis and Southern blot hybridization revealed that the three bla KPC genes were located on transferable plasmids exhibiting three different patterns. The patterns A, B and C were observed in the genetic makeup of each individual plasmid, and all three structures contained ISKpn6-like and ISKpn8 transposons. The results of the gene mapping and hybridization experiments performed with the bla KPC probe demonstrated that the plasmids harboured the three genes at approximately the 85.0, 54.0 and 73.0 kb positions. The study concluded that carbapenem resistance in the three isolates was primarily due to the production of carbapenem-hydrolysing β-lactamase.

Characterization of Listeria monocytogenes isolates by Southern blot hybridization

1990 ◽  
Vol 24 (3-4) ◽  
pp. 341-353 ◽  
Author(s):  
Irene V. Wesley ◽  
Ronald D. Wesley ◽  
Judy Heisick ◽  
Fannie Harrell ◽  
Dean Wagner
Keyword(s):  
Listeria Monocytogenes ◽  
Southern Blot ◽  
Blot Hybridization ◽  
Southern Blot Hybridization
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