Characterisation and physical localisation of Ty1-copia-like retrotransposons in four Alstroemeria species

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 357-367 ◽  
Author(s):  
Anja GJ Kuipers ◽  
Pat JS Heslop-Harrison ◽  
Evert Jacobsen
Keyword(s):  
In Situ Hybridisation ◽  
Amino Acid Sequences ◽  
Plant Genome ◽  
Dapi Staining ◽  
Metaphase Chromosomes ◽  
Retrotransposable Elements ◽  
Conserved Domain ◽  
Species Analysis ◽  
Hybridisation Signal

The genus Alstroemeria contains species with large genomes (2C = 36.5-78.9 pg (17 600 - 38 000 Mb) in those species with 2n = 2x = 16). We investigated the diversity and genomic and chromosomal organisation of Ty1-copia-like retrotransposons in four Alstroemeria species. Analysis of 33 PCR-amplified sequences corresponding to a conserved domain of the Ty1-copia reverse transcriptase (rt) gene showed high heterogeneity among predicted amino acid sequences; no two sequences were identical, but most fell into one of five subgroups. Levels of inter- and intra-specific heterogeneity of sequences were similar. HaeIII-digested genomic DNA of various Alstroemeria species contained distinct bands upon hybridisation with individual rt gene fragments. Hybridisation with the heterogeneous PCR pool of rt fragments (retrotransposon pool) revealed additional bands; some minor bands were characteristic of either Brazilian or Chilean species. In situ hybridisation of the retrotransposon pool from three species to metaphase chromosomes from the same species showed a dispersed distribution of the retrotransposon pool with exclusion from rDNA and other chromosomal sites.Alstroemeria pelegrina, which is without major heterochromatic sites, showed some clustering and small negative bands. The retrotransposon pool was excluded from major DAPI-staining bands in Alstroemeria aurea, but in contrast, the sites of the major tandemly repeated sequences in Alstroemeria inodora showed a hybridisation signal similar to that in the rest of the chromosomes. The data are discussed in the context of the contribution of Ty1-copia-like retrotransposons to plant genome size, their evolution, and their value for phylogenetic and biodiversity studies.Key words: Alstroemeria, in situ hybridisation, genome organisation, retrotransposable elements, Ty1-copia.

scholarly journals Human papilloma virus detection by in situ hybridisation signal amplification based on biotinylated tyramine deposition

1996 ◽  
Vol 49 (6) ◽  
pp. M340-M344 ◽  
Author(s):  
P J Poddighe ◽  
J Bulten ◽  
H M J Kerstens ◽  
J C M Robben ◽  
W J G Melchers ◽  
...  
Keyword(s):  
Human Papilloma Virus ◽  
Signal Amplification ◽  
In Situ Hybridisation ◽  
Virus Detection ◽  
Papilloma Virus ◽  
Hybridisation Signal

Nonisotopic in situ hybridization and plant genome mapping: the first 10 years

Genome ◽  
1994 ◽  
Vol 37 (5) ◽  
pp. 717-725 ◽  
Author(s):  
Jiming Jiang ◽  
Bikram S. Gill
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
Dna Sequences ◽  
Genome Mapping ◽  
Molecular Cytogenetics ◽  
Gene Families ◽  
Single Copy ◽  
Plant Genome ◽  
Metaphase Chromosomes

Nonisotopic in situ hybridization (ISH) was introduced in plants in 1985. Since then the technique has been widely used in various areas of plant genome mapping. ISH has become a routine method for physical mapping of repetitive DNA sequences and multicopy gene families. ISH patterns on somatic metaphase chromosomes using tandemly repeated sequences provide excellent physical markers for chromosome identification. Detection of low or single copy sequences were also reported. Genomic in situ hybridization (GISH) was successfully used to analyze the chromosome structure and evolution of allopolyploid species. GISH also provides a powerful technique for monitoring chromatin introgession during interspecific hybridization. A sequential chromosome banding and ISH technique was developed. The sequential technique is very useful for more precise and efficient mapping as well as cytogenetic determination of genomic affinities of individual chromosomes in allopolyploid species. A critical review is made on the present resolution of the ISH technique and the future outlook of ISH research is discussed.Key words: in situ hybridization, physical mapping, genome mapping, molecular cytogenetics.

Quantum Dot Based Duplex In Situ Hybridisation for Gene Expression Profiling.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3265-3265
Author(s):  
Eleni Tholouli ◽  
Dolores Di Vizio ◽  
Fionnuala O’Connell ◽  
Massimo Loda ◽  
David Twomey ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Myeloid Leukaemia ◽  
Semiconductor Nanocrystals ◽  
In Situ Hybridisation ◽  
Spectral Imaging ◽  
Quantitative Detection ◽  
Oligonucleotide Probes ◽  
Bone Marrow Trephine ◽  
Hybridisation Signal

Abstract Quantum dots (QDs) are fluorescent semiconductor nanocrystals (2–10-nm core diameter) possessing the unique properties of extremely high fluorescence efficiency, lack of photobleaching and long fluorescence lifetime, making them an ideal tool for bioimaging. We have developed a novel technique for in situ hybridisation (ISH) using biotinylated oligonucleotides conjugated to streptavidin coated QD, and used them in this study to label bone marrow trephine samples. 50-mer long oligonucleotide probes were conjugated to QDs prior to ISH and conjugation efficiency was demonstrated by gel electrophopresis. ISH conditions and molar ratio of QDs to probe were optimised using a polyT probe. Images were captured using a CRI Nuance spectral imaging system and signal intensity was semi-quantitated using IPLab software. Specific oligonucleotide hybridisation was demonstrated using a probe for myeloperoxidase (MPO) in 40 bone marrow sections infiltrated by acute myeloid leukaemia (AML), acute lymphoblastic leukaemia (ALL), chronic myeloid leukaemia (CML) as well as reactive bone marrow. In each case hybridisation signal was consistent with the distribution of MPO by standard immunohistochemistry - MPO was strongly expressed by myeloid blasts and absent in lymphoid blasts; in CML, most, but not all, cells were positive for MPO, in comparison to many fewer positive cells in reactive marrow. Duplex ISH was demonstrated using a probe for bcl-2 together with MPO in 5 bone marrow sections infiltrated by follicular lymphoma (FL). Strong hybridisation signal for bcl-2 was detected in all cells of the paratrabecular aggregates of FL but showed only scattered positivity in the remainder of the bone marrow. Conversely, MPO was absent in the paratrabecular aggregates and present in the myeloid cells in the remainder of the marrow. This pattern was present in both single and duplex ISH for MPO and bcl-2 in the marrow infiltrated by FL. Duplex ISH was performed both by sequential hybridisation with bcl-2 followed by MPO, and simultaneously with a mix of bcl-2 and MPO probes. As negative controls, scrambled oligonucleotide probes for the corresponding genes were used in each case and did not show hybridisation. In summary, we have developed a generic method for QD labelling and semi-quantitative detection of oligonucleotide ISH in routinely processed clinical tissue samples. Although, in this study we primarily used bone marrow trephine samples, this technique can be applied to any tissue. It has the potential to facilitate transfer of microarray-identified gene signatures to clinical research and diagnostics, whilst the ability of spectral imaging to resolve multiple signals offers the possibility of multiplexed probe detection.

Long non-coding RNA chromogenic in situ hybridisation signal pattern correlation with breast tumour pathology

2015 ◽  
Vol 69 (1) ◽  
pp. 76-81 ◽  
Author(s):  
Zhouwei Zhang ◽  
Donald L Weaver ◽  
Daniel Olsen ◽  
James deKay ◽  
Zhihua Peng ◽  
...  
Keyword(s):  
In Situ Hybridisation ◽  
Breast Tumour ◽  
Signal Pattern ◽  
Non Coding Rna ◽  
Pattern Correlation ◽  
Tumour Pathology ◽  
Hybridisation Signal ◽  
Long Non Coding Rna

Molecular cloning, characterisation and expression of two catalase genes from peach

2004 ◽  
Vol 31 (4) ◽  
pp. 349 ◽  
Author(s):  
Francesca Bagnoli ◽  
Susanna Danti ◽  
Valentina Magherini ◽  
Radiana Cozza ◽  
Anna M. Innocenti ◽  
...  
Keyword(s):  
Stress Responses ◽  
Seasonal Changes ◽  
Prunus Persica ◽  
Vascular Tissue ◽  
In Situ Hybridisation ◽  
Leaf Tissue ◽  
Amino Acid Sequences ◽  
Cdna Clones

Two cDNA clones encoding catalase (Cat1 and Cat2) from peach [Prunus persica (L.) Batsch] were identified, that show homologies to other plant catalases. The nucleotide sequences of the two coding regions showed 88% identity to each other. The amino acid sequences predicted from the two full-length clones showed the highest homology to a catalase from cotton and Nicotiana plumbaginifolia L. and included C-terminal tri-peptides typical of those used to target proteins to peroxisomes. Southern hybridisation analysis suggested the existence of two catalase genes in peach. The expression of Cat1 and Cat2 was determined in seeds, vegetative tissue, leaves during the seasonal cycle and in leaves in response to light / dark treatments. Cat1 had high levels of expression only in leaf tissue and was responsive to light and seasonal changes. Cat2 had high levels of expression in in vitro shoots and was also responsive to seasonal changes, but not to light. In situ hybridisations to leaf tissue indicated that the expression of Cat1 was localised mainly in palisade cells, while Cat2 mRNA was present in the vascular tissue. The results of the expression analysis and in situ hybridisation suggest a role for Cat1 in photorespiration and for Cat2 in stress responses.

Comparison of karyotype and rDNA-distribution in somatic chromosomes of Bowenia species (Stangeriaceae, Cycadales)

2000 ◽  
Vol 13 (1) ◽  
pp. 15 ◽  
Author(s):  
G. Kokubugata ◽  
K. Kondo ◽  
G. W. Wilson ◽  
L. M. Randall ◽  
A. van der Schans ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Ribosomal Dna ◽  
Staining Method ◽  
In Situ Hybridisation ◽  
The Other ◽  
Mitotic Metaphase ◽  
Rdna Probe ◽  
Hybridisation Signal ◽  
Orcein Staining

Somatic chromosomes at mitotic metaphase of Bowenia serrulata, B. spectabilis and B. sp. ‘Tinaroo’ is investigated by the standard aceto-orcein staining method and the fluorescent in situ hybridisation method (FISH) with ribosomal DNA (rDNA) probe. Bowenia serrulata, B. spectabilis and B. sp. ‘Tinaroo’ each have a chromosome number of 2n = 18. The karyotype of B. serrulata exhibits 10 median-centromeric chromosomes, while B. spectabilis and B. sp. ‘Tinaroo’ exhibit eight median-centromeric chromosomes. By using FISH, B. serrulata, B. spectabilis and B. sp. ‘Tinaroo’ show a hybridisation signal on the satellite of the short arm of two submedian-centromeric chromosomes. However, the other hybridisation signal pattern is different among B. serrulata, B. spectabilis and B. sp. ‘Tinaroo’.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

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