Repetitive DNA Probes Research Articles

The identification of Trypanosoma brucei subspecies using repetitive DNA sequences

We describe the use of repetitive DNA probes to characterise the relationships between different stocks of African trypanosomes representing the subspecies of Trypanosoma brucei. Probes derived from the ribosomal RNA genes (coding region and non-transcribed spacer) and another repetitive DNA sequence were used to characterise trypanosome stocks by Southern blotting. Numerical taxonomy methods applied to the resulting restriction enzyme patterns were used to derive a dendrogram depicting the relationships between the stocks examined. We show that three groups of West African human infective stocks can be distinguished: firstly, a group containing exclusively T. b. gambiense; secondly, a group which is indistinguishable from animal isolates in West Africa; and thirdly, a single stock which is indistinguishable from East African T. b. rhodesiense. In addition, we observe that T. b. rhodesiense stocks from East Africa are indistinguishable from animal isolates from the same area. Finally, we show that a group of T. b. rhodesiense stocks, isolated from a 1978 sleeping sickness outbreak in Zambia, are probably derived from a single parasite strain, and that this strain is distinct from T. b. rhodesiense parasites from Kenya and Uganda.

Use of repetitive DNA probes as physical mapping strategy inCaenorhabditis elegans

A method for linking genomic sequences cloned in yeast artificial chromosomes (YACs) has been tested using Caenorhabditis elegans as a model system. Yeast clones carrying YACs with repeated sequences were selected from a C. elegans genomic library, total DNA was digested with restriction enzymes, transferred to nylon membranes and probed with a variety of repetitive DNA probes. YAC clones that overlap share common bands with one or more repetitive DNA probes. In 159 YAC clones tested with one restriction enzyme and six probes 28 overlapping clones were detected. The advantages and limitations of this method for construction of YAC physical maps is discussed.

Cytogenetic analysis of human solid tumors by in situ hybridization with a set of 12 chromosome-specific DNA probes

We have applied fluorescent in situ hybridization (FISH) to assess the presence of numerical chromosome aberrations in fresh specimens of human solid tumors of varying histology. For this purpose, a set of 12 biotinylated chromosome-specific, repetitive alpha-satellite DNA probes (for chromosomes 1, 6, 7, 9, 10, 11, 15, 16, 17, 18, X and Y) were hybridized directly to isolated interphase nuclei. Utilizing this approach, we found numerical chromosome changes in all tumors. FISH ploidy profiles were in accordance with flow cytometric DNA histograms of these tumor cells.

Spatial topography of a pericentromeric region (1q12) in hemopoietic cells studied by in situ hybridization and confocal microscopy

A fluorescent in situ hybridization procedure with a chromosome 1-specific (1q12) repetitive satellite DNA probe was used to label the 1q12 regions of the chromosomes 1 in spherical and polymorphic hemopoietic cell nuclei. The entire procedure was performed in suspension to preserve nuclear morphology. The result was studied by three-dimensional analysis, as provided by a scanning laser confocal microscope. The 1q12 regions of chromosome 1 were measured to be closely associated with the nuclear envelope in isolated nuclei of unstimulated diploid human lymphocytes. The relative positions to each other in the periphery of these spherical nuclei could not be distinguished from a random distribution pattern. In the diploid and tetraploid polymorphic nuclei of cells of the promyelocytic leukemia cell line HL60 these pericentromeric sequences were also associated with the nuclear surface.

Three‐dimensional reconstruction of pericentromeric (1q12) DNA and ribosomal RNA sequences in HL60 cells after double‐target in situ hybridization and confocal microscopy

A fluorescent in situ hybridization procedure was applied to simultaneously label intranuclear pericentromeric (1q12) sequences of the chromosomes 1 and cytoplasmic ribosomal RNA sequences in whole cells of the promyelocytic HL60 cell line. For this purpose biotinated chromosome 1-specific (1q12) repetitive satellite DNA and 28S ribosomal ssRNA probes were used. The entire procedure was performed in suspension to preserve nuclear morphology. The result was studied by three-dimensional analysis, as provided by a scanning laser confocal microscope. The intracellular positions of both cytoplasmic rRNA and intranuclear centromere 1 DNA could easily be distinguished. This approach could be useful as a framework for the study of the 3-D localization of genes and gene transcripts.

Flow cytometric quantification of human chromosome specific repetitive DNA sequences by single and bicolor fluorescent in situ hybridization to lymphocyte interphase nuclei

Fluorescent in situ hybridization allows for rapid and precise detection of specific nucleic acid sequences in interphase and metaphase cells. We applied fluorescent in situ hybridization to human lymphocyte interphase nuclei in suspension to determine differences in amounts of chromosome specific target sequences amongst individuals by dual beam flow cytometry. Biotinylated chromosome 1 and Y specific repetitive satellite DNA probes were used to measure chromosome 1 and Y polymorphism amongst eight healthy volunteers. The Y probe fluorescence was found to vary considerably in male volunteers (mean fluorescence 169, S.D. 35.6). It was also detectable in female volunteers (mean fluorescence 81, S.D. 10.7), because 5-10% of this repetitive sequence is located on autosomes. The Y probe fluorescence in males was correlated with the position of the Y chromosome cluster in bivariate flow karyotypes. When chromosome 1 polymorphism was studied, one person out of the group of eight appeared to be highly polymorphic, with a probe fluorescence 26% below the average. By means of fluorescent in situ hybridization on a glass slide and bivariate flow karyotyping, this 26% difference was found to be caused by a reduction of the centromere associated satellite DNA on one of the homologues of chromosome 1. The simultaneous hybridization to human lymphocyte interphase nuclei of biotinylated chromosome 1 specific repetitive DNA plus AAF-modified chromosome Y specific DNA was detected by triple beam flow cytometry. The bicolor double hybridized nuclei could be easily distinguished from the controls. When the sensitivity of this bicolor hybridization is improved, this approach could be useful for automatic detection of numerical chromosome aberrations, using one of the two probes as an internal control.

Somatic pairing of chromosome 1 centromeres in interphase nuclei of human cerebellum.

Interphase nuclei isolated from paraffin-embedded tissue of four normal brains were hybridized with biotinated repetitive DNA probes specific for the (peri)centromeric regions of chromosomes 1 and 7. Hybridization results were visualized with a peroxidase-DAB system after which the number of specific signals per nucleus was counted using bright field microscopy. Using the probe specific for chromosome 7 (p7t1), both the cerebral and the cerebellar samples showed 2 spots in 82% and 83%, respectively, of the nuclei. In situ hybridization with the chromosome 1 probe (pUC1.77) showed two spots in 69% of the cerebral nuclei. In cerebellar samples, hybridization with pUC1.77 resulted in only one large spot per nucleus in 82% of the cells. The average spot size in nuclei with one signal was about 1.6 times as large as that in nuclei with two signals. These observations suggest that the single large spot in the cerebellar cells is not the result of monosomy of chromosome 1 but that it reflects somatic pairing of the two chromosome 1 centromeres. Based on the size and the fraction of nuclei with one large spot, the small granular neuron is the most likely candidate. The difference between cerebral and cerebellar samples indicates that this somatic pairing of chromosome 1 is a cell-type-dependent phenomenon.

Molecular Characterization of Sylvatic Isolates of Trichinella spiralis

Genetic relationships of 20 Trichinella isolates from Indiana wildlife were assessed and compared to Trichinella isolated from an infected swine herd. Trichinella larvae were isolated from coyotes, mink, raccoons, and red foxes. The larvae were maintained and amplified in white mice (ICR) and wild mice (Peromyscus leucopus). Differences in phenotypic characters of sylvatic isolates in the 2 laboratory hosts included an approximately 10-30-fold increase in parasite fecundity in wild mice. DNA for each isolate was extracted from Trichinella larvae and analyzed by dot-blot hybridization using a repetitive DNA probe pBP2 that recognizes DNA sequences specific for swine Trichinella. The probe hybridized only to Trichinella from swine and a single coyote isolate. Restriction endonucleases were used to digest DNA and the resulting fragments were separated by gel electrophoresis. Based on the presence of repetitive DNA sequences in the Trichinella genome, distinctive banding patterns were seen among the isolates. Trichinella isolated from swine had a pattern distinct from all sylvatic isolates except 1 from a coyote. Because this coyote was from the same general locality as the swine Trichinella outbreak, it was concluded that the isolate represents transmission of swine trichinellosis to the wildlife population. Further analysis using the enzyme Cla I identified unique banding patterns for wild isolates, suggesting that the sylvatic group is a genetically heterogeneous complex.

Human chromosome-specific repetitive DNA probes: Targeting in situ hybridization to chromosome 17 with a 42-base-pair alphoid DNA oligomer

The pericentric region of human chromosome 17 was targeted for specific in situ hybridization of the alphoid DNA subfamily enriched on this chromosome. A recombinant DNA clone containing the entire higher order chromosome 17 alphoid repeat preferentially hybridized to the pericentric region of chromosome 17, but frequently cross-hybridized to other chromosomes under normal stringency conditions. Chromosomal specificity, after in situ hybridization to metaphase spreads and interphase nuclei, was improved by using a subclone containing predominantly monomer 1 of the higher order repeat. Further improvement was achieved by synthesizing a 42-nucleotide oligomer of a divergent region of monomer 1. Southern blot analysis confirmed the improved specificity of the shorter probes. Reducing the potential of repetitive DNA probes to cross-hybridize increases the usefulness of the probes, especially when they are used for localizing individual chromosomes in interphase nuclei.

The Y chromosome of the mouse is decondensed in Sertoli cells.

The condensation of the Y chromosome in mouse cells was studied with two repetitive DNA probes, pY353/B and M34. Both DNA probes are specific to the Y chromosome and hybridize in situ along the whole chromosome. Due to the high resolution of the in situ hybridization technique with non-radioactive labeled DNA probes it was possible to observe the degree of condensation of the Y chromosome in the interphase cell nuclei of various somatic tissues and on testes preparations. The Sertoli cells were the only cell type in which the Y chromosome was always observed to be in a highly decondensed state. The decondensation of the Y chromosome in the Sertoli cells supports the view that the genetic activity of the Y chromosome is cell autonomous and opens the way to its molecular analysis.

Repetitive DNA probes for the detection of Babesia equi

This report describes DNA probes for the identification of Babesia equi. A genomic library of B. equi was constructed in pUC13. Several clones were identified that hybridized strongly to B. equi DNA. Clone pBE33 hybridized specifically to B. equi DNA and did not hybridize to horse DNA nor to DNA from Babesia caballi, Babesia bovis or Babesia bigemina. Two subclones of pBE33 (pSB20 and pEH21) containing B. equi repetitive sequences, could detect 0.49 ng and 0.97 ng B. equi DNA, respectively.

90 Detection of chromosomal aberrations in interphase nuclei from human primary breast tumors using in situ hybridization with chromosome-specific repetitive DNA-probes

90 Detection of chromosomal aberrations in interphase nuclei from human primary breast tumors using in situ hybridization with chromosome-specific repetitive DNA-probes

Hybridisation with a repetitive DNA probe reveals the presence of small chromosomes in Trypanosoma vivax

We have isolated and cloned a tandemly repeating element from Trypanosoma vivax for use as a species-specific DNA probe. The repeat hybridises only with DNA from T. vivax, not with DNA from other Salivarian trypanosome species ( T. brucei spp., T. congolense, T. simiae). The monomer of the repeat is approximately 180 bp long and is 64% GC rich. Hybridisation of the cloned fragment with size-fractionated large DNA molecules of 3 T. vivax stocks revealed a band in the position expected for mini-chromosomes, although these were believed absent in T. vivax. This band migrated to the 100–250 kb area of the gel at 4 different pulse frequencies and also hybridised with a telomeric repeat probe from T. brucei. The band is unlikely to be simply degraded material, since it failed to hybridise with another highly repetitive sequence from T. vivax and was consistently present in different trypanosome preparations. We conclude that T. vivax does possess mini-chromosomes, although possibly only 1 or 2 per cell.

Genetically discrete populations of Trypanosoma congolense from livestock on the Kenyan coast.

Twenty-seven stocks of Nannomonas trypanosomes isolated from livestock in 1982 on a ranch at Kilifi on the Kenyan coast were characterized by isoenzyme electrophoresis and by the abilities of the parasite's DNA to hybridize to two repetitive sequence DNA probes. All the Kilifi stocks which were examined had isoenzyme patterns which were markedly different from the 75 patterns previously described from 78 stocks of Trypanosoma congolense. On average only 15% of the enzyme bands present in the Kilifi stocks were present in those stocks of T. congolense which had previously been surveyed for isoenzymes. The DNA from all the Kilifi stocks which had been examined for isoenzymes hybridized with only the repetitive sequence probe isolated from a clone of a Kilifi stock. In contrast, the DNA from all 27 Kilifi stocks failed to hybridize with a repetitive sequence probe isolated from a clone from a different stock of T. congolense. Thus, the trypanosomes in all the Kilifi stocks examined were both phenotypically and genotypically discrete. These genetically discrete trypanosomes have also been detected in 2 stocks isolated from livestock from another location on the Kenyan coast. The results show that there is a wide range of genetic heterogeneity within the trypanosomes currently classified as T. congolense. We suggest that the limits of this genetic heterogeneity could represent incipient speciation.

In situ fluorescence hybridization of Y translocations: cytogenetic analysis using probes Y190 and Y431.

Two moderately repetitive DNA probes (Y190 and Y431) and a fluorescent in situ hybridization technique, using a biotin, avidin, anti-avidin system, were employed to investigate a group of patients with Y chromosome abnormalities. In normal male subjects, a bright fluorescent spot could be detected in cells in interphase and on the short arm of the Y chromosome in metaphase spreads. Translocations of DNA fragments of the short arm of the Y chromosome to autosomes 10, 13 and 15 were observed in five patients. In a 45,XX male subject the translocation involved one of the X chromosomes. With this in situ hybridization procedure, bright fluorescent spots were also noticed in uncultured amniotic cells and chorionic cellular elements from male fetuses, thus allowing a rapid and reproducible approach to prenatal fetal sexing.

Differentiation of Plasmodium falciparum clones by means of a repetitive DNA probe

A recombinant DNA probe, p BRK1-14, was constructed by inserting a repetitive DNA fragment of 753 base pairs obtained from Plasmodium falciparum, isolate K1, into the EcoRI/ PstI cloning sites of p BR322. This probe could discriminate between different parasite clones derived from a single isolate by hybridization with Southern genomic blots.

Assignment of the genomic affinities of chromosomes from polyploid Elymus species added to wheat

Genomic DNAs from 10 disomic addition, substitution, or translocation chromosomes from tetraploid Elymus trachycaulus (SSHH) and 13 tetraploid Elymus ciliaris (SSYY) in Chinese Spring wheat were assayed with 18S–28S rDNA (Nor), 5S DNA, Adh, α-amylase, β-glucanase gene clones, and S-genome and H-genome repetitive DNA sequences. The rDNA from the S genome and 5S DNA from the S and H genomes, under high stringency Southern blot analysis, distinguished S-genome and H-genome loci on individual Elymus chromosomes. The single gene, or low copy gene probes (Adh and others), allowed identification of different addition lines and provided information on the gene synteny relationships of Elymus chromosomes with wheat chromosomes. The S-genome specific and H-genome repetitive DNA probes were not useful in assigning genomic affinities, due to some cross-hybridization between these genomes using these probes and (or) the occurrence of large numbers of translocations in polyploid genomes of Elymus species. However, the repetitive DNA probes provided diagnostic phenotypic markers for identification of individual Elymus addition lines. Moreover, since S- and H-genome DNA sequences were virtually absent from wheat, they were excellent markers for the detection of Elymus chromatin in wheat. The array of DNA probes should prove useful in chromosome manipulation in resistance transfer from Elymus into wheat.Key words: Triticeae, Elymus, aneuploid, DNA probe.

Conserved repetitive DNA sequences (Bkm) in normal equine males and sex-reversed females detected by in situ hybridization.

In situ hybridization with a cloned banded krait sex-specific repetitive DNA probe (Bkm) indicates a high concentration of Bkm sequences on the horse Y chromosome in both normal XY males and XY sex-reversed females. Lesser, but still significant, concentrations of Bkm sequences were mapped to horse chromosomes 3, 4, and 30.

Characterization of activated proto-oncogenes in chemically transformed Syrian hamster embryo cells.

The Syrian hamster embryo (SHE) cell transformation model has been used by many investigators to study the multistep process of neoplastic transformation induced by chemical carcinogens. In this study we have attempted to determine if activated proto-oncogenes are present in the transformed cells induced by a variety of chemical carcinogens. Twelve carcinogen-induced hamster cell lines, established by treatment of normal SHE cells with benzo[a]pyrene, diethylstilbestrol, or asbestos, were examined. One spontaneously transformed cell line (BHK-A) was also studied. Some of the cell lines were also tested for oncogene activation at the preneoplastic stage, before they acquired tumorigenic potential. DNAs from normal, preneoplastic, and neoplastic cells were tested by transfection into mouse NIH 3T3 cells, and morphologically transformed foci were scored on the contact-inhibited monolayer of 3T3 cells. The frequency of focus formation for normal SHE cell DNA was less than 0.0008 foci/microgram DNA, while approximately 40% (5 of 12) of the DNAs from carcinogen-induced, tumorigenic hamster cell lines induced foci at a frequency of greater than or equal to 0.012 foci/microgram DNA. The other seven carcinogen-induced cell lines and the BHK-A cells were negative (less than 0.002 foci/microgram DNA). When the DNAs from transformed foci induced by the five positive cell lines were retransfected into NIH 3T3 cells, the frequency of secondary foci of 3T3 cells was as much as 50-fold higher (1.34 foci/microgram DNA) than with the primary transfectants. DNAs from transformed foci or tumors derived from transformed foci were screened by Southern blot analyses with known oncogenes and with a hamster repetitive DNA probe for the presence of transfected hamster oncogenes.(ABSTRACT TRUNCATED AT 250 WORDS)

Detection of chromosome variation in interphase by in situ hybridization with repetitive DNA probes: potential applications to cytogenetic analysis and mutagenicity testing

Individual chromosomes can be identified by means of in situ hybridization with DNA probes for chromosome-specific repetitive sequences. The efficiency and sensitivity of the method are strictly dependent on the characteristics of the probes and the experimental conditions. Using three probes with different copy numbers, we demonstrated that the target chromosomes can be visualized in interphase when the homologous sequences are repeated at least 50 times.Possible applications of interphase analysis to clinical cytogenetics and mutagenicity testing are discussed.