Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “hybridisation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed1992

Comparative analysis of human papillomavirus detection by dot blot hybridisation and non-isotopic in situ hybridisation.

AIMS: To determine the relative diagnostic performance of non-isotopic in situ hybridisation (NISH) and a dot-blot assay for detecting human papillomavirus (HPV) on exfoliated cervical cells; and to correlate the results with cytopathological assessment. METHODS: Cervical smears and cytological samples were obtained from 122 patients during the same clinical examination and the presence of HPV sequences determined by NISH and dot-blot analysis, respectively. RESULTS: Dot-blot analysis gave an autoradiographic signal in 15 of 121 (12.4%) cases, while NISH detected viral genomes in 38 of 114 (33.3%) cases. Even in the presence of koilocytosis, where vegetative replication of the virus occurs, NISH was positive in over twice as many cases as dot-blot analysis (NISH 90%, dot-blot 40%), while in smears within normal cytological limits, where the viral copy number is likely to be considerably lower, the differences were more striking (NISH 31%, dot-blot 5%). CONCLUSIONS: These data show that NISH on cytological smears is more sensitive than a standardised dot-blot hybridisation assay for detecting HPV infection in cytological material and is therefore a more appropriate screening tool.

Cervix Uteri↗
PubMed1977

Ribonucleic acid from the higher plant Matthiola incana. Molecular weight measurements and DNA-RNA hybridisation studies.

The percentage of DNA from the crucifer Matthiola incana coding for different types of RNA was measured by filter saturation hybridisation experiments using RNA labelled in vivo. In addition, the melting curves of the various DNA - RNA hybrids formed and the buoyant densities of the DNA sequences complementary to different types of RNA were measured. 1. The RNA preparations used were 25, 18, and 5 S rRNA and 4 S RNA, purified by gel electrophoresis, and poly(A)-containing RNA purified by oligo-(dT)-cellulose chromatography. The molecular weights of the 25 S and 18 S rRNAs, calculated from the mobility in formamide-acrylamide gels relative to Escherichia coli RNA, are 1.25 - 10(6) and 0.64 - 10(6). The rRNA precursor has a molecular weight of approx. 2.1 - 10(6) and the average molecular weight of the poly(A)-containing RNA from both cotyledons and roots is 4 - 10(5). 2. The percentage of the genome, calculated on the basis of double-stranded DNA, coding for these RNAs and the estimated number of genes per haploid DNA amount are approximately 0.46% and 1100 for 25 S plus 18 S rRNA, 0.032% and 3600 for 5 S rRNA and 0.072% and 13 000 for 4 S RNA. In filter hybridisation experiments very little hybridisation of poly(A)-containing RNA was found. A rapidly-hybridising component is attributed to small amounts of contaminating rRNA. 3. M. incana DNA has a main band at 1.697 g - ml-1 in CsCl and a satellite constituting approximately 3% of the DNA, at 1.708 g - ml-1 - 25 and 18 S rRNA hybridise to DNA with a buoyant density of 1.701--2 g - ml-1. The buoyant density of 5 S DNA is slightly less at 1.700--1 g - ml-1. 4. S RNA hybridises to at least two separate regions, one within the main-band DNA and a second lighter component. None of the RNAs tested hybridised to the satellite DNA. The Tm of the DNA - RNA hybrids in 1 X SSC is 89 degrees C for 25 S rRNA, 85 degrees C for 5 S rRNA and 82 degrees C for 4 S RNA. 4. 5 and 4 S RNA preparations contain fragments which hybridise to sequences complementary to high-molecular-weight rRNA. This spurious hybridisation can be eliminated by competition with unlabelled high-molecular-weight RNA.

Base Sequence↗
PubMed1975

Influence of temperature on the detectibility and chromosomal distribution of specific DNA sequences by in situ hybridisation.

Hybridising certain AT-rich satellite complementary RNAs (cRNAs) to their homologous chromosomal DNA sequences at different temperatures of incubation results in a different dispersion of autoradiographic label throughout the karyotypes. The temperature at which most label, or cRNA-DNA hybrid formation, exists corresponds to the optimal rate temperature for the hybridisation of these same satellite cRNA-DNA hybrids as determined by RNA excess filter hybridisation. It is likely that the in situ hybridisation results can therefore be explained by the fact that there is a similar temperature-dependence on the rate of hybrid formation for both in situ and RNA excess hybridisation. This should have important implications for the designing of in situ hybridisation experiments in general.

Animals↗
PubMed1979

The effects of mercury-substitution on the hybridisation characteristics of nucleic acids.

The effect of different levels of mercury substitution on the rate and extent of hybridisation of globin mRNA with a complementary DNA (cDNA) copy has been investigated. It was found that mercuration significantly reduces both the rate of hybridisation and the extent of the reaction, but that these effects are abolished when at least stoichiometric amounts of 2-mercaptoethanol are included in the hybridisation medium. As a preliminary to using this technique to isolate specific groups of sequences after long-term hybridisations, we have investigated both the rate of demercuration of RNA and its retention on thiol-sepharose columns after extended incubation under commonly employed hybridisation conditions at 43 degrees or 60 degrees. Retention was essentially quantitative even after incubation times of 300 hours at 43 degrees, but decreased significantly after 48 hours at 60 degrees. It is concluded that thiol-sepharose chromatography offers considerable advantages over hydroxyapatite chromatography for the recovery of hybridised sequences, particularly with regard to the lower levels of non-specific binding obtained and its ability to distinguish directly between DNA-DNA and DNA-Hg RNA hybrids.

Animals↗
PubMed1975

Mouse immunoglobulin genes: studies on the reiteration frequency of light-chain genes by hybridisation procedures.

The partially purified immunoglobulin light chain messenger RNA fraction from P3K (MOPC 21) mouse myeloma tissue-culture cells has been employed in hybridisation studies. Fragments of the messenger RNA were generated by alkali hydrolysis. 6-S fragments not containing poly(A) showed the characteristic biphasic hybridisation profile seen with the intact RNA fraction. 12-S and 6-S poly(A)-containing fragments, however, showed single transitions lacking the rapidly hybridising component. Complementary DNA copies of the intact messenger RNA fraction were prepared with RNA-dependent DNA polymerase and the DNA populations fractionated on acrylamide gels. Hybridisation experiments with complementary DNA fractions up to 800 bases in length showed annealing to single (or a few) genes. A rapidly hybridising component (about 200 copies) appears in the cDNA fraction containing the largest transcripts. We conclude that the kappa constant region gene and the MOPC 21 variable region gene are present as one or a few copies in the haploid genome and that the rapidly hybridising component is not due to variable region genes.

Animals↗
PubMed1991

Detection of B19 parvovirus in human fetal tissues by in situ hybridisation.

Evidence of B19 parvovirus infection was sought by in situ hybridisation with biotinylated probes in 65 tissue samples from 32 pregnancies (fetuses, products of conception and/or placentas). Twenty-seven samples were reactive and the results were confirmed by other methods for B19 virus detection in 22 cases. The other methods used were in situ hybridisation with 3H and 35S labelled probes; dot-blot hybridisation with biotin and 32P labelled probes; polymerase chain reaction assay; negative stain and thin section electron microscopy; and radioimmunoassay for B19 antigen. The five false positive results by in situ hybridisation with biotinylated probes were considered to be due to non-specific biotin capture and were more frequent with unfixed samples than with formalin fixed material. It was concluded that while biotinylated probes offered advantages over radioactive probes for detecting B19 DNA by in situ hybridisation, positive findings should be confirmed by other methods.

Biotin↗
PubMed1991

Sensitive non-isotopic DNA hybridisation assay or immediate-early antigen detection for rapid identification of human cytomegalovirus in urine.

A sensitive non-radioactive DNA hybridisation assay employing digoxigenin-labelled probes was compared with immediate-early antigen detection and conventional virus isolation for the identification of human cytomegalovirus (HCMV) in 249 urine samples. Of 44 specimens yielding HCMV by virus isolation, more were positive by DNA hybridisation (32; 73%) than by immediate-early antigen detection (25; 52%) (P = 0.05). The specificity of the hybridisation assay in 45 apparently falsely positive specimens was supported by detection of HCMV DNA in 40 of these specimens using the polymerase chain reaction. Many urine specimens may thus contain large amounts of non-viable virus or free viral DNA. Evaluation of various protocols for the extraction and denaturation of virus DNA prior to hybridisation showed that proteinase K digestion with phenol/chloroform extraction was the most sensitive and reliable procedure. We conclude that the non-radioactive DNA hybridisation assay described is a potentially valuable routine diagnostic test.

Antigens, Viral↗
PubMed1991

Detection of Epstein-Barr virus genomes in AIDS related lymphomas: sensitivity and specificity of in situ hybridisation compared with Southern blotting.

Eighteen cases of AIDS related, non-Hodgkin's lymphomas were examined for the presence of Epstein-Barr virus (EBV) genomes using in situ hybridisation with a 35S-labelled probe. The results were compared with those obtained independently by Southern blot analysis with a 32P-labelled probe of frozen tissue from the same tumours. Technically satisfactory results were obtained with both methods in 15 lymphomas. EBV DNA was detected in seven of 15 (47%) cases by in situ hybridisation and in eight of 15 (53%) cases by Southern blotting (including all the cases positive by in situ hybridisation). The results of EBV DNA detection by the two techniques were identical in 14 of 15 (93%) cases. In situ hybridisation gave no false positive results. This study shows that the sensitivity and specificity of in situ hybridisation for the detection of EBV genomes in AIDS related lymphomas approaches that of Southern blotting, even when using routinely processed archival, paraffin wax embedded material.

Acquired Immunodeficiency Syndrome↗
PubMed1992

In situ hybridisation of albumin mRNA in normal liver and hepatocellular carcinoma with a digoxigenin labelled oligonucleotide probe.

AIMS: To study the localisation and distribution of albumin mRNA in normal liver and hepatocellular carcinoma by in situ hybridisation with an oligonucleotide probe. METHODS: A 51 base oligonucleotide was synthesised from a sequence at the 5' end of the human albumin gene and the probe was labelled at its 3' end with digoxigenin 11-dUTP. Formalin fixed, wax embedded sections of liver biopsy specimens were used to study the localisation and distribution of albumin mRNA. After in situ hybridisation the bound probe was visualised using a digoxigenin antibody conjugated with alkaline phosphatase. RESULTS: In normal liver albumin mRNA was detected in hepatocytes and no positive signal was observed in biliary epithelium, vascular endothelium, or Kupffer cells. In 75% (9/12) of the hepatocellular carcinomas studied a positive hybridisation signal was observed in tumour cells. CONCLUSIONS: Albumin mRNA can be detected in sections of formalin fixed, wax embedded liver, a digoxigenin labelled probe is ideally suited for in situ hybridisation of liver because there is no background from the detection system. The identification of albumin mRNA may be a useful marker of hepatocellular carcinoma, and the demonstration of albumin mRNA by in situ hybridisation overcomes the potential background problem associated with albumin immunohistochemistry.

Albumins↗
PubMed1992

Differential expression of growth-associated protein (GAP-43) mRNA in rat primary sensory neurons after peripheral nerve lesion: a non-radioactive in situ hybridisation study.

An alkaline phosphatase-labelled anti-sense oligodeoxynucleotide probe specific for growth-associated protein messenger RNA (GAP-43 mRNA) was used for non-radioactive in situ hybridisation histochemistry to follow relative changes in GAP-43 mRNA content in lumbar primary sensory neurons (L4-6) after unilateral ligation of the sciatic nerve. In normal dorsal root ganglia (DRG) 16% of neurons expressed GAP-43 mRNA, and these cells belonged to a sub-group of intermediate-sized (32-50 microns diameter) and large (> 50 microns) neurons. The hybridisation signal detected in these cells was weak to moderate. One day after nerve ligature a significant increase in the number of GAP-43 mRNA expressing neurons in the ipsilateral DRG was detected involving particularly the very small (12-20 microns) cells, and small cell population (20-32 microns), though the hybridisation signal was less pronounced in this latter cell group. A significant increase in the cellular content of GAP-43 mRNA was detected in both cell groups when compared to the normal DRG by 2 days after the lesion. At later times (4, 7, and 10 days postinjury) the intermediate-sized and large cell subpopulations also showed an increase in the number of GAP-43 mRNA positive neurons, followed by a significant rise in their content of GAP-43 mRNA. However, they did not reach the same intensity of hybridisation signal as seen in the small and very small neurons. All DRG neurons showed a maximum of GAP-43 mRNA expression by 10 days postsurgery. At longer times there was a slight decrease in the content of GAP-43 mRNA towards 14 days postinjury, but mRNA levels remained elevated up to 28 days after nerve ligature, the longest time point examined in this study. The different onset and levels of GAP-43 gene expression in the rat primary sensory neurons after lesion of their peripheral branch axons further characterize the different subclasses of these cells and may reflect their different involvement in the plastic changes following peripheral nerve injury.

Alkaline Phosphatase↗
PubMed1992

Epstein Barr virus (EBV) encoded small RNAs: targets for detection by in situ hybridisation with oligonucleotide probes.

AIMS: To develop a rapid, sensitive, and specific non-isotopic in situ hybridisation (NISH) procedure for the detection of Epstein-Barr virus in formalin fixed, paraffin wax embedded tissues. METHODS: Two low molecular weight RNAs, designated EBER-1 and EBER-2 (Epstein-Barr encoded RNA), were used: cells latently infected with EBV secrete large amounts of EBERs. The method uses digoxigenin labelled anti-sense oligonucleotides, corresponding to sequences in EBER-1 and EBER-2. RESULTS: The use of these probes, in conjunction with high temperature microwave denaturation, ensured that the technique was considerably more sensitive than other in situ hybridisation techniques for detecting EBV. Furthermore, the hybridisation signal was morphologically distinct in that only the nucleus and not the nucleolus give a positive signal. No cross-hybridisation was observed with cells infected with other lymphotropic herpes viruses. CONCLUSION: The sensitivity, simplicity, and rapidity of this technique make it ideal for diagnostic use, and for studies investigating the role of this virus in neoplastic disease.

Cell Line↗
PubMed1992

In situ hybridisation: principles and applications.

In situ hybridisation (ISH) is based on the complementary pairing of labelled DNA or RNA probes with normal or abnormal nucleic acid sequences in intact chromosomes, cells or tissue sections. Compared with other molecular biology techniques applicable to anatomical pathology, ISH enjoys better rapport with histopathologists because of its similarity to immunohistochemistry. It has the unique advantage over other molecular biology techniques--largely based on probe hybridisation with nucleic acid extracted from homogenised tissue samples--of allowing localisation and visualisation of target nucleic acid sequences within morphologically identifiable cells or cellular structures. Probes for ISH may bear radioactive or non-radioactive labels. Isotopic probes (3H, 32P, 35S, 125I) are generally more sensitive than non-isotopic ones but are less stable, require longer processing times and stringent disposal methods. Numerous non-isotopic labels have been used; of these biotin and digoxigenin are the reporters of choice. Optimised non-isotopic systems of equivalent sensitivity to those which use radioactive-labelled probes have been described. In ISH, finding the optimal balance between good morphological preservation of cells and strong hybridisation signals is crucial. Tissue fixation and retention of cytoskeletal structures, unfortunately, impede diffusion of probes into tissues. ISH sensitivity is also influenced by inherent properties of the probe and hybridisation conditions. Although ISH is largely a research tool, it is already making strong inroads into diagnostic histopathology. It has been applied for the detection of various infective agents particularly CMV, HPV, HIV, JC virus, B19 parvovirus, HSV-1, EBV, HBV, hepatitis delta virus, Chlamydia trachomatis, salmonella and mycoplasma in tissue sections.(ABSTRACT TRUNCATED AT 250 WORDS)

Humans↗
PubMed1992

Carrier detection of deletions in female relatives of X-linked disorders by non-isotopic in situ hybridisation.

Recent studies suggest that a non-isotopic in situ hybridisation (NISH) approach can be successfully employed to investigate the carrier status of female relatives in families of selected patients with Duchenne muscular dystrophy (DMD) or Hunter syndrome, whose diseases are due to a specific X chromosome deletion. Whilst the majority of metaphase spreads from normal females show specific hybridisation signals on both X chromosomes when tested with either dystrophin or Hunter gene-derived probes, only one X chromosome in each metaphase spread will show the relevant hybridisation complex in female carriers of deletions involving the dystrophin or Hunter gene. Thus, the NISH method can be a valuable diagnostic tool for the detection of the carrier status of female relatives of patients with X chromosome deletions.

Chromosome Deletion↗
PubMed1991

Coxsackie virus B4 infection of the mouse pancreas: I. Detection of virus-specific RNA in the pancreas by in situ hybridisation.

The pathology of Coxsackie virus B4 (CVB4) infection in a murine model was investigated by in situ hybridisation using a biotinylated cDNA probe derived from CVB4. During the acute phase of infection virus RNA sequences were detected in the exocrine pancreas of 60% of mice infected with a pancreotropic variant of CVB4. A positive hybridisation signal was observed in other organs in some animals including the heart and liver of 1 mouse 28 days after infection. The cellular distribution of virus RNA sequences corresponded well with the histological findings in most tissues. Possible causes for failure of hybridisation in some infected pancreases are discussed in conjunction with potential application of the technique in human pancreas biopsy samples.

Animals↗
PubMed1992

Detection of cytomegalovirus-infected cells by flow cytometry and fluorescence in suspension hybridisation (FLASH) using DNA probes labeled with biotin by polymerase chain reaction.

A biotin-labeled DNA probe specific for the immediate early gene of the cytomegalovirus (CMV) strain AD 169 was generated with the polymerase chain reaction. Nucleic acid hybridisation was carried out with CMV-infected T-lymphoblastoid cells (MOLT-4) after 4 hr to 6 days of culture. Biotin molecules were made visible with streptavidin coupled with fluorescein. The fluorescence signal of the hybridised probe was measured by flow cytometry in the cell suspension. The number of CMV-positive cells was 7% at 4 hr, 8% after 28 hr, 18% after 2 days, 26% after 3 days, 91% after 4 days, 97% after 5 days, and 98% after 6 days. The first detection of CMV antigen (pp65) was possible with immunoenzymatic labeling by day 4, whereas CMV-DNA was detected by PCR after 4 hr. CMV-specific RNA could be detected in a similar way. The analysis of mononuclear peripheral blood leukocytes in a patient with active CMV infection showed 14.7% CMV DNA-positive cells at day 1 and 7% at day 8, as compared to 0.9% and 0.0% cells which were positive for CMV antigen (pp65) by immunoenzymatic labeling at day 1 and day 8, respectively. We conclude that flow cytometry and fluorescence in suspension hybridisation (FLASH) offers a new tool for analysing exactly and quantifying large numbers of cells for specific DNA or RNA and may be useful for other laboratory and clinical applications.

Antigens, Viral↗
PubMed1977

Isoelectric focusing and hybridisation experiments on creatine kinase (EC 2.7.3.2).

In the case of increased creatine kinase levels, the MM isozyme in human serum can often be subdivided by electrophoresis into three isozymes: MM1, MM2 and MM3. This paper presents the results of hybridisation experiments, which prove the existence of two different M-subunits. The MM isozyme fractions used in the hybridisation experiments were isolated by isoelectric focusing of human sera. The experiments were completed by hybridisation of mixtures of BB and MM isozymes, leading to the formation of two MB isozymes.

Creatine Kinase↗
PubMed1992

Detection of mycobacterial rRNA in sarcoidosis with liquid-phase hybridisation.

Because sarcoidosis resembles tuberculosis clinically and histologically, it has been suggested that mycobacteria might have a role in the pathogenesis of the disorder. Mycobacteria have not been found in sarcoid tissues by conventional culture techniques, so we have used a liquid-phase hybridisation method to see whether we could detect mycobacterial rRNA in such tissues. RNA was extracted from five sarcoid and five normal spleens. Extracts were assayed by liquid-phase DNA/RNA hybridisation with a DNA probe specific for the rRNA of the Mycobacterium tuberculosis complex. Hybridisation obtained with the sarcoid spleens, from which mycobacteria were neither seen on microscopy nor cultured with standard methods, was 4.8 times higher than that with normal spleens (p less than 0.001). Our demonstration of mycobacterial nucleic-acid components in sarcoid splenic tissues supports the notion that mycobacteria play a part in the cause of sarcoidosis.

DNA Probes↗
PubMed1991

Detection of human papillomavirus DNA in cancer of the urinary bladder by in situ hybridisation.

The association of the human papillomavirus (HPV) with cancer of the urinary bladder was assessed by in situ hybridisation using probes selective for HPV types 6/11 and 16/18 DNA. No hybridisation signal was detected with the type 6/11 probe on 100 formalin-fixed, paraffin-embedded bladder tumours sampled. However, when the same samples were hybridised with the HPV type 16/18 DNA probe, 11 of 66 (16.6%) papillary and 1 of 10 (10%) solid transitional cell carcinomas gave positive signals. These results suggest the involvement of HPV in cancer of the bladder, although the frequency of multiple HPV types in these tumours is uncertain.

Carcinoma, Transitional Cell↗