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.

Tandem repeat DNA localizing on the proximal DAPI bands of chromosomes in Larix, Pinaceae

Genome ◽  
2002 ◽  
Vol 45 (4) ◽  
pp. 777-783 ◽  
Author(s):  
Masahiro Hizume ◽  
Fukashi Shibata ◽  
Ayako Matsumoto ◽  
Yukie Maruyama ◽  
Eiji Hayashi ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Genomic Dna ◽  
Repeat Unit ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Repeat Sequence ◽  
Proximal Region

Repetitive DNA was cloned from HindIII-digested genomic DNA of Larix leptolepis. The repetitive DNA was about 170 bp long, had an AT content of 67%, and was organized tandemly in the genome. Using fluorescence in situ hybridization and subsequent DAPI banding, the repetitive DNA was localized in DAPI bands at the proximal region of one arm of chromosomes in L. leptolepis and Larix chinensis. Southern blot hybridization to genomic DNA of seven species and five varieties probed with cloned repetitive DNA showed that the repetitive DNA family was present in a tandem organization in genomes of all Larix taxa examined. In addition to the 170-bp sequence, a 220-bp sequence belonging to the same DNA family was also present in 10 taxa. The 220-bp repeat unit was a partial duplication of the 170-bp repeat unit. The 220-bp repeat unit was more abundant in L. chinensis and Larix potaninii var. macrocarpa than in other taxa. The repetitive DNA composed 2.0–3.4% of the genome in most taxa and 0.3 and 0.5% of the genome in L. chinensis and L. potaninii var. macrocarpa, respectively. The unique distribution of the 220-bp repeat unit in Larix indicates the close relationship of these two species. In the family Pinaceae, the LPD (Larix proximal DAPI band specific repeat sequence family) family sequence is widely distributed, but their amount is very small except in the genus Larix. The abundant LPD family in Larix will occur after its speciation.Key words: AT-rich tandem repetitive DNA, fluorescence in situ hybridization, Larix, proximal DAPI band.

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.

Using genomic slot blot hybridization to assess intergeneric Saccharum x Erianthus hybrids (Andropogoneae – Saccharinae)

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 428-432 ◽  
Author(s):  
P. Besse ◽  
C. L. McIntyre ◽  
D. M. Burner ◽  
C. G. de Almeida
Keyword(s):  
Genomic Dna ◽  
Blot Hybridization ◽  
Female Parent ◽  
Saccharum Officinarum ◽  
Rapid Screening ◽  
Hybridization Technique ◽  
Slot Blot ◽  
Saccharum Species ◽  
Slot Blot Hybridization

The use of genomic slot blot hybridization enabled the differentiation of hybrids from selfs in Saccharum × Erianthus intergeneric crosses in which Saccharum was used as the female parent. Based on the genomic in situ hybridization technique, slot blots of DNA from the parents and the progeny were blocked with the Saccharum parent DNA and hybridized with the labelled male Erianthus genomic DNA. This technique allowed a rapid screening for hybrids and was sensitive enough to detect a 1/20 dilution of Erianthus in Saccharum DNA, which should enable the detection of most partial hybrids. The genomic slot blot hybridization technique was shown to be potentially useful for assessing crosses involving Saccharum species with either Old World Erianthus section Ripidium or North American Erianthus (= Saccharum) species. The effectiveness of the technique was assessed on 144 progeny of a Saccharum officinarum × Erianthus arundinaceus cross, revealing that 43% of the progeny were selfs. The importance of this test as a tool to support intergeneric breeding programs is discussed.Key words: slot blot, Erianthus, genomic DNA, Saccharum, sugarcane.

scholarly journals Papillomas and Carcinomas Associated with a Papillomavirus in European Harvest Mice (Micromys minutus)

1988 ◽  
Vol 25 (5) ◽  
pp. 356-361 ◽  
Author(s):  
J. P. Sundberg ◽  
M. K. O'Banion ◽  
A. Shima ◽  
C. Knupp ◽  
M. E. Reichmann
Keyword(s):  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Skin Lesions ◽  
Sebaceous Carcinoma ◽  
Cutaneous Lesions ◽  
Pulmonary Tumors ◽  
Papillomavirus Dna ◽  
Inverted Papillomas ◽  
Micromys Minutus

Papillomaviruses, group-specific papillomavirus antigens, or extrachromosomal papillomavirus DNA were detected in cutaneous, mucocutaneous, and pulmonary tumors affecting a colony of European harvest mice (Micromys minutus). Skin lesions were classified as acanthomatous hyperplasia, epidermal inclusion cysts. squamous papillomas, inverted papillomas, trichoepitheliomas, and sebaceous carcinomas. Cutaneous horns (hyperkeratotic papillomas) were on mucocutaneous junctions of one animal. One mouse, with a cutaneous sebaceous carcinoma, had multiple pulmonary keratinaceous cysts. Papillomavirus antigens, detected by the avidin-biotin technique, were in 20 of 31 lesions tested. In contrast, by Southern blot hybridization all 28 lesions tested contained papillomavirus DNA. Papillomavirus DNA was demonstrated in two often benign cutaneous lesions by in situ hybridization.

scholarly journals Fatal Epstein-Barr virus-associated hemophagocytic syndrome

Blood ◽  
1993 ◽  
Vol 82 (11) ◽  
pp. 3259-3264 ◽  
Author(s):  
H Kikuta ◽  
Y Sakiyama ◽  
S Matsumoto ◽  
T Oh-Ishi ◽  
T Nakano ◽  
...  
Keyword(s):  
Epstein Barr Virus ◽  
Hemophagocytic Syndrome ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Barr Virus ◽  
Clonality Analysis ◽  
Serologic Evidence ◽  
Infected Cells ◽  
Epstein Barr

A virus-associated hemophagocytic syndrome is characterized by high fever, liver dysfunction, coagulation abnormalities, pancytopenia, and a benign histiocytic proliferation with prominent hemophagocytosis in bone marrow, lymph node, spleen, and liver. We describe six Japanese children with fatal Epstein-Barr virus (EBV)-associated hemophagocytic syndrome. Five of the six patients had serologic evidence of primary EBV infection at the onset of their diseases. EBV genomes were detected in all the patients by Southern blot hybridization or the polymerase chain reaction. Furthermore, clonality analysis of the EBV genome showed that EBV-infected cells proliferated monoclonally or biclonally in three examined patients. In situ hybridization study using EBV- encoded RNA 1 (EBER1) showed that EBER1 was detected in one of two examined liver tissues, which localized in hepatocytes.

Microisolation of the chicken Z chromosome and construction off microclone libraries

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 865-872 ◽  
Author(s):  
Régis Zimmer ◽  
Alon Haberfeld ◽  
Ann M. Verrinder Gibbins
Keyword(s):  
Light Microscope ◽  
Genomic Dna ◽  
Size Range ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Z Chromosome ◽  
Mitotic Metaphase ◽  
Simple Method ◽  
Dna Library ◽  
Male Chicken

A simple method was used to adapt a standard light microscope for the collection of chicken Z chromosomes from mitotic-metaphase spreads. The DNA of the collected chromosomes was enzymatically amplified using a partially degenerate primer. The resulting sequences, within a size range of 200–800 bp, were cloned to produce a Z chromosome DNA library, using blunt-end ligation into a SmaI-digested pUC18 plasmid (the SureClone system; Pharmacia, U.S.A.). The microcloning experiments produced 1250 clones; the size range of the cloned inserts was 250–800 bp, with an average of 480 bp (176 clones examined). Using male chicken genomic DNA as a probe, 10 out of 17 randomly selected clones showed strong positive signals on Southern blots, confirming the origin of the inserts as chicken DNA. In addition, the Z-chromosome origin of a selected microclone was verified in a semiquantitative Southern blot hybridization that showed positive signals with intensities that were approximately twice as strong for male (ZZ) as for female (ZW) chicken genomic DNA when the clone was used as a probe. The value of these libraries in further analysis of the chicken Z chromosome is discussed.Key words: microdissection, microcloning, chicken Z chromosome.

scholarly journals Fatal Epstein-Barr virus-associated hemophagocytic syndrome

Blood ◽  
1993 ◽  
Vol 82 (11) ◽  
pp. 3259-3264 ◽  
Author(s):  
H Kikuta ◽  
Y Sakiyama ◽  
S Matsumoto ◽  
T Oh-Ishi ◽  
T Nakano ◽  
...  
Keyword(s):  
Epstein Barr Virus ◽  
Hemophagocytic Syndrome ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Barr Virus ◽  
Clonality Analysis ◽  
Serologic Evidence ◽  
Infected Cells ◽  
Epstein Barr

Abstract A virus-associated hemophagocytic syndrome is characterized by high fever, liver dysfunction, coagulation abnormalities, pancytopenia, and a benign histiocytic proliferation with prominent hemophagocytosis in bone marrow, lymph node, spleen, and liver. We describe six Japanese children with fatal Epstein-Barr virus (EBV)-associated hemophagocytic syndrome. Five of the six patients had serologic evidence of primary EBV infection at the onset of their diseases. EBV genomes were detected in all the patients by Southern blot hybridization or the polymerase chain reaction. Furthermore, clonality analysis of the EBV genome showed that EBV-infected cells proliferated monoclonally or biclonally in three examined patients. In situ hybridization study using EBV- encoded RNA 1 (EBER1) showed that EBER1 was detected in one of two examined liver tissues, which localized in hepatocytes.

scholarly journals 5-Methylcytosine distribution and genome organization in triticale before and after treatment with 5-azacytidine

1999 ◽  
Vol 112 (23) ◽  
pp. 4397-4404 ◽  
Author(s):  
A. Castilho ◽  
N. Neves ◽  
M. Rufini-Castiglione ◽  
W. Viegas ◽  
J.S. Heslop-Harrison
Keyword(s):  
In Situ Hybridization ◽  
Restriction Fragment ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Restriction Enzymes ◽  
Hybrid Plant ◽  
Rrna Genes ◽  
Next Generation ◽  
Root Tips

Triticale (2n=6x=42) is a hybrid plant including rye (R) and wheat (A and B) genomes. Using genomic in situ hybridization with rye DNA as a probe, we found the chromosomes of the R genome were not intermixed with the wheat chromosomes in 85% of nuclei. After treatment of seedlings with low doses of the drug 5-azacytidine (5-AC), leading to hypomethylation of the DNA, the chromosomes became intermixed in 60% of nuclei; the next generation showed intermediate organization. These results correlate with previous data showing that expression of R-genome rRNA genes, normally suppressed, is activated by 5-AC treatment and remains partially activated in the next generation. The distribution of 5-methylcytosine (5-mC) was studied using an antibody to 5-mC. Methylation was detected along the lengths of all chromosomes; there were some chromosome regions with enhanced and reduced methylation, but these were not located at consistent positions, nor were there differences between R and wheat genome chromosomes. After 5-AC treatment, lower levels of methylation were detected. After 5-AC treatment, in situ hybridization with rye genomic DNA sometimes showed micronuclei of rye origin and multiple translocations between wheat and rye chromosomes. Genomic DNA was analysed using methylation-sensitive restriction enzymes and, as probes, two rDNA sequences, two tandemly organised DNA sequences from rye (pSc200 and pSc250), and copia and the gypsy group retrotransposon fragments from rye and wheat. DNA extracted immediately after 5-AC treatment was cut more by methylation-sensitive restriction enzymes than DNA from untreated seedlings. Each probe gave a characteristic restriction fragment pattern, but rye- and wheat-origin probes behaved similarly, indicating that hypomethylation was induced in both genomes. In DNA samples from leaves taken 13–41 days after treatment, RFLP (Restriction Fragment Length Polymorphism) patterns were indistinguishable from controls and 5-AC treatments with all probes. Surprising differences in hybridization patterns were seen between DNA from root tips and leaves with the copia-fragment probes.

scholarly journals Detection of Human Papillomavirus Type 2 Related Sequence in Oral Papilloma

1998 ◽  
Vol 16 (3) ◽  
pp. 125-130 ◽  
Author(s):  
Taihei Yamaguchi ◽  
Masanobu Shindoh ◽  
Akira Amemiya ◽  
Nobuo Inoue ◽  
Masaaki Kawamura ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Hpv Infection ◽  
Related Sequence ◽  
Copy Numbers ◽  
Labeled Probe ◽  
Virus Capsid Antigen

Oral papilloma is a benign tumourous lesion. Part of this lesion is associated with human papillomavirus (HPV) infection. We analysed the genetical and histopathological evidence for HPV type 2 infection in three oral papillomas. Southern blot hybridization showed HPV 2a sequence in one lesion. Cells of the positive specimen appeared to contain high copy numbers of the viral DNA in an episomal state.In situstaining demonstrated virus capsid antigen in koilocytotic cells and surrounding cells in the hyperplastic epithelial layer. Two other specimens contained no HPV sequences by labeled probe of full length linear HPVs 2a, 6b, 11, 16, 18, 31 and 33 DNA under low stringency hybridization conditions. These results showed the possibility that HPV 2 plays a role in oral papilloma.

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