scholarly journals Genome analysis of South American Elymus (Triticeae) and Leymus (Triticeae) species based on variation in repeated nucleotide sequences

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 505-520 ◽  
Author(s):  
Jorge Dubcovsky ◽  
A. R. Schlatter ◽  
M. Echaide
Keyword(s):  
Genome Analysis ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Nucleotide Sequences ◽  
South American ◽  
Restriction Fragments ◽  
Genome Constitution ◽  
Elymus Species ◽  
Hordeum Species ◽  
Species Hybridization

Variation in repeated nucleotide sequences (RNSs) at the level of entire families assayed by Southern blot hybridization is remarkably low within species and is a powerful tool for scrutinizing the origin of allopolyploid taxa. Thirty-one clones from RNSs isolated from different Triticeae genera were used to investigate the genome constitution of South American Elymus. One of these clones, pHch2, preferentially hybridized with the diploid H genome Hordeum species. Hybridization of this clone with a worldwide collection of Elymus species with known genome formulas showed that pHch2 clearly discriminates Elymus species with the H genome (StH, StHH, StStH, and StHY) from those with other genome combinations (StY, StStY, StPY, and StP). Hybridization with pHch2 indicates the presence of the H genome in all South American Elymus species except Elymus erianthus and Elymus mendocinus. Hybridization with additional clones that revealed differential restriction fragments (marker bands) for the H genome confirmed the absence of the H genome in these species. Differential restriction fragments for the Ns genome of Psathyrostachys were detected in E. erianthus and E. mendocinus and three species of Leymus. Based on genome constitution, morphology, and habitat, E. erianthus and E. mendocinus were transferred to the genus Leymus.Key words: Triticeae, Elymus, Leymus, repeated sequences.

A study of 28 Elymus species using repetitive DNA sequences

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1093-1101 ◽  
Author(s):  
Sergei Svitashev ◽  
Björn Salomon ◽  
Tomas Bryngelsson ◽  
Roland von Bothmer
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Molecular Study ◽  
Repetitive Dna Sequences ◽  
Hybridization Pattern ◽  
Specific Hybridization ◽  
Elymus Species ◽  
Hordeum Species

Four repetitive DNA sequences cloned from the barley (Hordeum vulgare) genome and common for different Triticeae species were used for a molecular study of phylogenetic relationships among 28 Elymus species. Two wild Hordeum species (H genome), two Pseudoroegneria species (S genome), Agropyron cristatum (P genome), and Australopyrum velutinum (W genome) were included as genomic representatives for the genomes that supposedly were involved in the evolution of the genus Elymus. Our results are essentially congruent with the genomic classification system. This study demonstrates that Elymus is not a monophyletic genus. Based on an analysis of Southern blot hybridization we could discriminate between SY and SH species owing to the strong specific hybridization pattern of the H genome. Hexaploid SYH species gave a hybridization pattern similar to SH species for the same reason. The results support the genomic composition of Elymus batalinii as SYP and also indicated the presence of at least one H genome in Elymus enysii with a hitherto unknown genomic constitution. Elymus erianthus had a hybridization pattern distinctly different from all other species in the investigation. Key words : Elymus, RFLP, phylogeny, repetitive DNA.

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

Genomic constitution and phylogenetic position of several New Zealand Triticeae species revealed by two single copy nuclear genes

2011 ◽  
Vol 59 (1) ◽  
pp. 1 ◽  
Author(s):  
Aimee G. Oliver ◽  
Kara Harnish ◽  
Genlou Sun
Keyword(s):  
New Zealand ◽  
North American ◽  
Diploid Species ◽  
Single Copy ◽  
Nuclear Genes ◽  
Phylogenetic Position ◽  
Genome Constitution ◽  
Elymus Species ◽  
New Zealand Flora ◽  
Hordeum Species

Three genera of Triticeae, Elymus, Stenostachys and Australopyrum, are described in the New Zealand flora. Cytological analyses suggested that five basic genomes (St, H, Y, P and W) donated by different diploid species in different combinations exist in the genera Elymus and Stenostachys, whereas Australopyrum species contain the W genome only. Morphological and cytogenetic data suggested that the genome constitution for both E. apricus and E. multiflorus is StYW. Chloroplast DNA and ITS data supported the genome constitution of these Elymus species, but the HW genome constitution was assigned to the Stenostachys species. In this study, sequences of two single copy nuclear genes, RPB2 and DMC1, were used to confirm or refute the genome constitutions of the two Stenostachys species and the two Elymus species from New Zealand, and to analyse their phylogenetic relationships with other Elymus species. Our RPB2 and DMC1 data confirmed that the genome constitution of hexaploid E. apricus is StWY, and tetraploid S. gracilis is HW. The presence of the StW genome in hexaploid E. multiflorus, and the W genome in tetraploid S. laevis is also confirmed. No obvious St genome differentiation between New Zealand and non-New Zealand species is observed. The H genomes in the S. gracilis and S. laevis are closely related to the H genome from North American species, indicating that the H genomes in these two New Zealand species might originate from North American Hordeum species.

scholarly journals Genetic Analysis of Type E Botulinum Toxin-Producing Clostridium butyricum Strains

2000 ◽  
Vol 66 (11) ◽  
pp. 4992-4997 ◽  
Author(s):  
Xingmin Wang ◽  
Tsuneo Maegawa ◽  
Tadahiro Karasawa ◽  
Shunji Kozaki ◽  
Kentaro Tsukamoto ◽  
...  
Keyword(s):  
Botulinum Toxin ◽  
Southern Blot ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Nucleotide Sequences ◽  
Clostridium Butyricum ◽  
Nucleotide Sequencing ◽  
Lake Area ◽  
Chromosomal Dna ◽  
E Gene

ABSTRACT Type E botulinum toxin (BoNT/E)-producing Clostridium butyricum strains isolated from botulism cases or soil specimens in Italy and China were analyzed by using nucleotide sequencing of thebont/E gene, random amplified polymorphic DNA (RAPD) assay, pulsed-field gel electrophoresis (PFGE), and Southern blot hybridization for the bont/E gene. Nucleotide sequences of the bont/E genes of 11 Chinese isolates and of the Italian strain BL 6340 were determined. The nucleotide sequences of thebont/E genes of 11 C. butyricum isolates from China were identical. The deduced amino acid sequence of BoNT/E from the Chinese isolates showed 95.0 and 96.9% identity with those of BoNT/E from C. butyricum BL 6340 and Clostridium botulinum type E, respectively. The BoNT/E-producing C. butyricum strains were divided into the following three clusters based on the results of RAPD assay, PFGE profiles of genomic DNA digested with SmaI or XhoI, and Southern blot hybridization: strains associated with infant botulism in Italy, strains associated with food-borne botulism in China, and isolates from soil specimens of the Weishan lake area in China. A DNA probe for thebont/E gene hybridized with the nondigested chromosomal DNA of all toxigenic strains tested, indicating chromosomal localization of the bont/E gene in C. butyricum. The present results suggest that BoNT/E-producing C. butyricum is clonally distributed over a vast area.

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.

Repair and recombination of X-irradiated plasmids in Xenopus laevis oocytes

1990 ◽  
Vol 10 (11) ◽  
pp. 5849-5856
Author(s):  
S E Sweigert ◽  
D Carroll
Keyword(s):  
Homologous Recombination ◽  
Xenopus Laevis ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Coli Strain ◽  
Xenopus Laevis Oocytes ◽  
X Rays ◽  
Strand Breaks ◽  
X Ray ◽  
Dna Strand

Plasmid DNA substrates were X-irradiated and injected into the nuclei of Xenopus laevis oocytes. After incubation for 20 h, DNA was recovered from the oocytes and analyzed simultaneously for repair and for intermolecular homologous recombination by electrophoresis and bacterial transformation. Oocyte-mediated repair of DNA strand breaks was observed with both methods. Using a repair-deficient mutant Escherichia coli strain and its repair-proficient parent as hosts for the transformation assay, we also demonstrated that oocytes repaired oxidative-type DNA base damage induced by X-rays. X-irradiation of a circular DNA stimulated its potential to recombine with a homologous linear partner. Recombination products were detected directly by Southern blot hybridization and as bacterial transformant clones expressing two antibiotic resistance markers originally carried separately on the two substrates. The increase in recombination was dependent on X-ray dose. There is some suggestion that lesions other than double-strand breaks contribute to the stimulation of oocyte-mediated homologous recombination. In summary, oocytes have considerable capacity to repair X-ray-induced damage, and some X-ray lesions stimulate homologous recombination in these cells.

Tandem arrangement of tubulin genes in the protozoan parasite Leishmania enriettii

1983 ◽  
Vol 3 (6) ◽  
pp. 1070-1076
Author(s):  
S M Landfear ◽  
D McMahon-Pratt ◽  
D F Wirth
Keyword(s):  
Tandem Repeat ◽  
Blot Hybridization ◽  
Protozoan Parasite ◽  
Southern Blot Hybridization ◽  
Beta Tubulin ◽  
Developmentally Regulated ◽  
Alpha Tubulin ◽  
Tubulin Genes ◽  
Southern Blot Hybridization Analysis ◽  
Leishmania Enriettii

The arrangement of developmentally regulated alpha- and beta-tubulin genes has been studied in the parasitic protozoan Leishmania enriettii by using Southern blot hybridization analysis. The alpha-tubulin genes occur in a tandem repeat whose monomeric unit may be represented by a 2-kilobase PstI fragment. Similarly, the beta-tubulin genes probably occur in a separate tandem repeat consisting of approximately 4-kilobase units unlinked to the alpha-tubulin repeats.

Presence of Human Herpesvirus 8 DNA Sequences in Renal Transplantation-Associated Pleural Kaposi Sarcoma

1999 ◽  
Vol 123 (12) ◽  
pp. 1269-1273
Author(s):  
J. Javier Gómez-Román ◽  
J. Gonzalo Ocejo-Vinyals ◽  
Pablo Sánchez-Velasco ◽  
Francisco Leyva-Cobián ◽  
J. Fernando Val-Bernal
Keyword(s):  
Kidney Transplantation ◽  
Pleural Effusion ◽  
Dna Sequences ◽  
Blot Hybridization ◽  
Human Herpesvirus ◽  
Kaposi Sarcoma ◽  
Southern Blot Hybridization ◽  
Pulmonary Involvement ◽  
Human Herpesvirus 8 ◽  
Herpesvirus 8

Abstract Objective.—To describe one case of symptomatic skin and pleural Kaposi sarcoma (KS) associated with kidney transplantation. Diagnosis was supported by morphologic study and human herpesvirus 8 (HHV-8) detection in both tissues. Pulmonary involvement was not present. Design.—The presence of HHV-8 DNA sequences was proved using polymerase chain reaction (PCR), Southern blot hybridization, and in situ hybridization. Setting.—Human herpesvirus 8 is found in most KS from patients with and without the acquired immunodeficiency syndrome. Clinically significant pulmonary infiltration by KS is diagnosed uncommonly antemortem, and pleural disease is exceptional. Patient.—A 49-year-old man who had renal transplant with immunosuppressive therapy (tacrolimus and prednisone) and developed a cutaneous KS. A pleural effusion appeared without pulmonary involvement. Both lesions disappeared when immunosuppressive drugs were suspended. Later, the pleural effusion and the cutaneous lesions reappeared. Pleural biopsy specimens showed KS infiltration. Outcome.—The patient refused treatment and was lost to follow-up. Results.—The skin and pleural biopsies showed a proliferation of spindle-shaped cells positive for CD34. The HHV-8 sequences were detected by nested PCR. No amplification was detected in uninvolved skin from the patient or in peripheral blood mononuclear cells from 10 healthy individuals used as controls. The Southern blot hybridization confirmed these results. Conclusions.—To our knowledge, this is the first report of HHV-8 in symptomatic pleural KS, which was probably associated with immunosuppression after kidney transplantation. The demonstration of HHV-8 DNA in biopsy material in the appropriate cells could be diagnostic when the morphologic setting is consistent with KS.

scholarly journals Long-Distance PCR-based Screening for Large Rearrangements of the LDL Receptor Gene in Korean Patients with Familial Hypercholesterolemia

1999 ◽  
Vol 45 (9) ◽  
pp. 1424-1430 ◽  
Author(s):  
Sung Han Kim ◽  
Ji Hyun Bae ◽  
Jae Jin Chae ◽  
Un Kyung Kim ◽  
Seong-Joon Choe ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Familial Hypercholesterolemia ◽  
Receptor Gene ◽  
Blot Hybridization ◽  
Screening Method ◽  
Ldl Receptor ◽  
Southern Blot Hybridization ◽  
Long Distance ◽  
Large Rearrangements ◽  
Long Distance Pcr

Abstract Background: The LDL receptor is a cell-surface protein that regulates plasma cholesterol by specific uptake of LDL particles from the blood circulation. Familial hypercholesterolemia (FH) results from defective catabolism of LDL, which is caused by mutations in the LDL-receptor gene. Methods: For the rapid and reliable detection of large rearrangements in the LDL-receptor gene, we established a screening method based on long-distance PCR as an alternative to Southern-blot hybridization. Using long-distance PCR, 45 unrelated Korean subjects heterozygous for FH were screened to assess the frequency and nature of major structural rearrangements in the LDL-receptor gene. Results: Two different deletion mutations, FH6 (same type as FH3 and FH311) and FH 32, were detected in four families by long-distance PCR. Detailed restriction mapping and sequence analysis showed that FH6 was a 5.71-kb deletion extending from intron 8 to intron 12 and that FH32 was a 2-kb deletion extending from intron 6 to intron 7. Sequence analysis for the breakpoints of all deletions detected in Korean FH patients showed that only the left arms of the Alu repetitive sequences were involved in the deletion event. Conclusions: The screening method based on long-distance PCR provides a powerful strategy for the detection of large rearrangements in the LDL-receptor gene and is a rapid and reliable screening alternative to Southern-blot hybridization.

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