Ribosomal cistrons in Bothrops neuwiedi (Serpentes) subspecies from Brazil

Genome ◽  
1995 ◽  
Vol 38 (3) ◽  
pp. 601-606 ◽  
Author(s):  
Isa Trajtengertz ◽  
M. L. Beçak ◽  
Itamar R. G. Ruiz
Keyword(s):  
Chromosomal Localization ◽  
Blot Hybridization ◽  
Intergenic Spacer ◽  
Restriction Enzymes ◽  
Southern Blot Hybridization ◽  
Banding Patterns ◽  
Ribosomal Cistrons ◽  
Pair Number ◽  
The One ◽  
Bothrops Neuwiedi

The ribosomal cistrons of six subspecies of Bothrops neuwiedi (Serpentes) were studied at both the cytogenetic and molecular levels. These subspecies populations occur in several Brazilian regions. The analysis of the nucleolar organizing region banding patterns showed variability in the chromosomal localization of rDNA cistrons. The rDNA clusters were found in two microchromosomes, in chromosome pair Number 6, or even in the one homologue of chromosome 6, and one microchromosome, according to the specimen examined but independent of the population from which it was selected. The organization of the rDNA repeat was studied by Southern blot hybridization using Xenopus laevis ribosomal DNA probes. The size of the repeat is 10.4 kilobases (kb), and the intergenic spacer (IGS), 2.6 kb long, is relatively small compared with the size of other vertebrate IGSs. Restriction mapping using the restriction enzymes EcoRI, BamHI, HindIII, and PvuII showed a highly conserved organization of the ribosomal repeats in the total genomic DNA of the subspecies studied.Key words: ribosomal cistrons, Bothrops neuwiedi, Serpentes.

scholarly journals Histologic transformation of follicular lymphoma to diffuse lymphoma represents tumor progression by a single malignant B cell.

1991 ◽  
Vol 173 (1) ◽  
pp. 197-207 ◽  
Author(s):  
A D Zelenetz ◽  
T T Chen ◽  
R Levy
Keyword(s):  
Follicular Lymphoma ◽  
B Cell ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Gene Rearrangements ◽  
Region Gene ◽  
V Region ◽  
The One ◽  
Tissue Specimens ◽  
Variable Genes

To investigate the clonal relationship between follicular lymphoma (FL) and transformed diffuse lymphoma (tDL), we examined the expression of tumor idiotype, immunoglobulin (Ig) gene rearrangements and sequence of Ig variable genes in paired tissue specimens. All 16 cases analyzed expressed surface immunoglobulin (sIg) on both the FL and the tDL, though the immunophenotype of one case of FL could not be definitively determined. In 14 of 15 cases, the surface immunophenotype was preserved; the exception was likely secondary to a class switch from IgM to IgG. In 12 of 13 cases, antiidiotypic monoclonal antibodies prepared against the FL reacted with the paired tDL. Analysis of Ig gene rearrangements in four cases by Southern blot hybridization showed evidence of clonal relationships in all cases though concordance was not seen with all probes tested (C kappa, C lambda, JH, PFL1, and PFL2). In the one case that had a discordant L chain rearrangement, sequence analysis of the L chain demonstrated a common mature B cell origin for both the FL and tDL. To determine whether tDL arose from one or more FL cells, the sequences of the H chain variable genes were analyzed. Individual clones of the V region gene of the FL showed a random distribution of changes throughout the sequence. In contrast, individual clones of the V region gene from tDL shared numerous nonrandom sequence alterations, implying a common single cell origin. In conclusion, tDL is a mature B cell and arises by transformation of a single FL cell.

scholarly journals Associations between nuclear loci and chloroplast DNA genotypes in wild barley.

Genetics ◽  
1992 ◽  
Vol 131 (1) ◽  
pp. 225-231
Author(s):  
M A Maroof ◽  
Q Zhang ◽  
D B Neale ◽  
R W Allard
Keyword(s):  
Chloroplast Dna ◽  
Linear Models ◽  
Wild Barley ◽  
Blot Hybridization ◽  
Intergenic Spacer ◽  
Southern Blot Hybridization ◽  
Gene Pools ◽  
Intergenic Spacer Region ◽  
Evolutionary Forces ◽  
Nuclear Loci

Abstract Associations among alleles at nine nuclear loci and three chloroplast DNA (cpDNA) genotypes were assessed in a sample of 247 accessions of the wild barley, Hordeum vulgare ssp. spontaneum. Alleles at two of the nine nuclear loci are marked by length variations in the intergenic spacer region of ribosomal DNA (rDNA), and those of the other seven loci are well characterized allozymes. The three chloroplast DNA (cpDNA) genotypes are marked by restriction fragment length polymorphisms resulting from three polymorphic restriction sites detected by Southern blot hybridization. The analyses were performed by dividing the nine nuclear loci into a series of two-locus subsets and constructing log-linear models to characterize associations between the subsets of two nuclear loci and the cpDNA genotypes. Statistically significant associations were detected between six of the nine nuclear loci and the cpDNA genotypes, either individually as pairwise correlations, or through interaction with another nuclear locus to form three-variate complexes. Although the sample size of the present study was inadequate for statistical evaluation of higher order interactions, the results suggest the existence of interactions in which more than two nuclear loci are involved in associations with cpDNA genotypes. The observed cytonuclear associations appear to result from interplay among a number of evolutionary forces including a mating system of predominant selfing, differentiation among gene pools of local populations, and adaptation of barley genotypes to specific environmental conditions.

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.

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.

scholarly journals Natural Hybrids of Phytophthora nicotianae and Phytophthora cactorum Demonstrated by Isozyme Analysis and Random Amplified Polymorphic DNA

1998 ◽  
Vol 88 (9) ◽  
pp. 922-929 ◽  
Author(s):  
Willem A. Man in 't Veld ◽  
Wil J. Veenbaas-Rijks ◽  
Elena Ilieva ◽  
Arthur W. A. M. de Cock ◽  
Peter J. M. Bonants ◽  
...  
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Restriction Enzymes ◽  
Phytophthora Species ◽  
Phytophthora Nicotianae ◽  
Isozyme Analysis ◽  
Maximum Temperature ◽  
Banding Patterns ◽  
The One ◽  
Species Specific ◽  
Putative Locus

Three similar isolates of Phytophthora (Phytophthora sp-h) were obtained from diseased Spathiphyllum and Primula plants. Cultural characteristics did not fit any known description of Phytophthora species. The Phytophthora sp-h isolates are papillate, are homothallic, possess 80 to 86% amphigynous antheridia, and have a maximum temperature for growth of 36.5°C. Isozyme analysis of the Phytophthora sp-h isolates revealed a three-banded pattern with malic enzyme and a three-banded pattern with malate dehydrogenase on the second putative locus. The fastest band at both enzyme loci comigrated with the single P. nicotianae band, the slowest band comigrated with the single P. cactorum (and also P. pseudotsugae) band, and one band in between was concluded to represent the heterodimeric isozyme. The random amplified polymorphic DNA patterns of the Phytophthora sp-h isolates almost exclusively consisted of bands that were also present in either P. nicotianae or P. cactorum. Southern hybridization showed that bands specific for P. nicotianae were present as comigrating bands in the Phytophthora sp-h isolates. The same was found for species-specific bands of P. cactorum. It is concluded that the three Phytophthora sp-h isolates represent interspecific hybrids, P. nicotianae being the one parent and P. cactorum the other. Analysis of mito-chondrial DNA with restriction enzymes revealed banding patterns in all the Phytophthora sp-h isolates identical with those of P. nicotianae, confirming that indeed P. nicotianae was one of the parents.

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.

Chromosomal localization and molecular characterization of three different 5S ribosomal DNA clusters in the sea urchin Paracentrotus lividus

Genome ◽  
2007 ◽  
Vol 50 (9) ◽  
pp. 867-870 ◽  
Author(s):  
Fabio Caradonna ◽  
Daniele Bellavia ◽  
Ann Maria Clemente ◽  
Giorgia Sisino ◽  
Rainer Barbieri
Keyword(s):  
Sea Urchin ◽  
Chromosomal Localization ◽  
Blot Hybridization ◽  
5S Rdna ◽  
Paracentrotus Lividus ◽  
Southern Blot Hybridization ◽  
Base Pairs ◽  
Interphase Nuclei

In this paper the chromosomal localization and molecular cloning and characterization of three 5S rDNA clusters of 700 bp (base pairs), 900 bp, and 950 bp in the sea urchin Paracentrotus lividus are reported. Southern blot hybridization demonstrated the existence of three 5S rDNA repeats of differing length in the P. lividus genome. Fluorescence in situ hybridization analysis, performed in parallel on both haploid and diploid metaphases and interphase nuclei using different 5S rDNA units as probes, localized these 5S rDNA clusters in 3 different pairs of P. lividus chromosomes. This is the first complete gene mapping not only in a sea urchin but also in the phylum of echinoderms as a whole.

Analysis of genetic polymorphisms affecting the four phospholipase C (plc) genes in Mycobacterium tuberculosis complex clinical isolates

Microbiology ◽  
2004 ◽  
Vol 150 (4) ◽  
pp. 967-978 ◽  
Author(s):  
C. Viana-Niero ◽  
P. E. de Haas ◽  
D. van Soolingen ◽  
S. C. Leão
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Phospholipase C ◽  
Genetic Polymorphisms ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Clinical Isolates ◽  
Significant Similarity ◽  
Genomic Deletions ◽  
Genes Encoding ◽  
Mycobacterium Africanum

The Mycobacterium tuberculosis genome contains four highly related genes which present significant similarity to Pseudomonas aeruginosa genes encoding phospholipase C enzymes. Three of these genes, plcA, plcB and plcC, are organized in tandem (locus plcABC). The fourth gene, plcD, is located in a different region. This study investigates variations in plcABC and plcD genes in clinical isolates of M. tuberculosis, Mycobacterium africanum and ‘Mycobacterium canettii’. Genetic polymorphisms were examined by PCR, Southern blot hybridization, sequence analysis and RT-PCR. Seven M. tuberculosis isolates contain insertions of IS6110 elements within plcA, plcC or plcD. In 19 of 25 M. tuberculosis isolates examined, genomic deletions were identified, resulting in loss of parts of genes or complete genes from the plcABC and/or plcD loci. Partial plcD deletion was observed in one M. africanum isolate. In each case, deletions were associated with the presence of a copy of the IS6110 element and in all occurrences IS6110 was transposed in the same orientation. A mechanism of deletion resulting from homologous recombination of two copies of IS6110 was recognized in a group of genetically related M. tuberculosis isolates. Five M. tuberculosis isolates presented major polymorphisms in the plcABC and plcD regions, along with loss of expression competence that affected all four plc genes. Phospholipase C is a well-known bacterial virulence factor. The precise role of phospholipase C in the pathogenicity of M. tuberculosis is unknown, but considering the potential importance that the plc genes may have in the virulence of the tubercle bacillus, the study of isolates cultured from patients with active tuberculosis bearing genetic variations affecting these genes may provide insights into the significance of phospholipase C enzymes for tuberculosis pathogenicity.

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