Characterization and genomic organization of Ty1-copia group retrotransposons in rye (Secale cereale)

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 617-625 ◽  
Author(s):  
Stephen R. Pearce ◽  
Gill Harrison ◽  
Pat (J. S.) Heslop-Harrison ◽  
Andrew J. Flavell ◽  
Amar Kumar
Keyword(s):  
In Situ Hybridization ◽  
Secale Cereale ◽  
Plant Genome ◽  
Northern Analysis ◽  
Pcr Products ◽  
Slot Blot Analysis ◽  
Cereal Plants ◽  
Close Relatives ◽  
Copia Retrotransposons

The genomic organisation of the Ty1-copia retrotransposons in rye (Secale cereale) has been studied. We have used the polymerase chain reaction (PCR) to amplify sequences from a conserved domain of the reverse transcriptase gene of the Ty1-copia retrotransposons in this species. Sequence analysis of 26 of these PCR products shows them to be a highly heterogeneous population, a feature that is common in plants. Slot blot analysis shows that there are about 100 000 individual Ty1-copia retrotransposons in rye. In situ hybridization of a heterogeneous probe, representing the whole population of rye Ty1-copia retrotransposon sequences, to chromosome spreads of triticale (×Triticosecale), a rye–wheat hybrid, shows that these sequences are present throughout all the rye chromosomes but absent from the centromeric regions and, in particular, from the terminal heterochromatin. Southern analysis of oat, barley, wheat, and rye, using as a probe R9, one of the rye sequences that is closely similar to the BARE-1 element of barley, shows that close relatives of this retrotransposon subgroup are present in all these species in high copy number. Northern analysis on RNAs from seedlings shows that the BARE-1 subgroup is transcribed in all these cereal plants but in variable amounts: high in barley, moderate in wheat and rye, and extremely low in oat.Key words: retrotransposons, Secale cereale, plant genome, Ty1-copia, in situ hybridization.

Chromosomal organization of a sequence related to LTR-like elements of Ty1-copia retrotransposons in Avena species

Genome ◽  
1999 ◽  
Vol 42 (4) ◽  
pp. 706-713 ◽  
Author(s):  
Concha Linares ◽  
Antonio Serna ◽  
Araceli Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Diploid Species ◽  
D Genome ◽  
Specific Sequence ◽  
Chromosomal Organization ◽  
Intergenomic Translocations ◽  
A Genome ◽  
Slot Blot Analysis ◽  
Copia Retrotransposons

A repetitive sequence, pAs17, was isolated from Avena strigosa (As genome) and characterized. The insert was 646 bp in length and showed 54% AT content. Databank searches revealed its high homology to the long terminal repeat (LTR) sequences of the specific family of Ty1-copia retrotransposons represented by WIS2-1A and Bare. It was also found to be 70% identical to the LTR domain of the WIS2-1A retroelement of wheat and 67% identical to the Bare-1 retroelement of barley. Southern hybridizations of pAs17 to diploid (A or C genomes), tetraploid (AC genomes), and hexaploid (ACD genomes) oat species revealed that it was absent in the C diploid species. Slot-blot analysis suggested that both diploid and tetraploid oat species contained 1.3 × 104 copies, indicating that they are a component of the A-genome chromosomes. The hexaploid species contained 2.4 × 104 copies, indicating that they are a component of both A- and D-genome chromosomes. This was confirmed by fluorescent in situ hybridization analyses using pAs17, two ribosomal sequences, and a C-genome specific sequence as probes. Further, the chromosomes involved in three C-A and three C-D intergenomic translocations in Avena murphyi (AC genomes) and Avena sativa cv. Extra Klock (ACD genomes), respectively, were identified. Based on its physical distribution and Southern hybridization patterns, a parental retrotransposon represented by pAs17 appears to have been active at least once during the evolution of the A genome in species of the Avena genus.Key words: chromosomal organization, in situ hybridization, intergenomic translocations, LTR sequence, oats.

scholarly journals Ontogenetic Pattern of Thyroid Hormone Receptor Expression in the Human Testis

2000 ◽  
Vol 85 (9) ◽  
pp. 3453-3457 ◽  
Author(s):  
Emmanuele A. Jannini ◽  
Anna Crescenzi ◽  
Nadia Rucci ◽  
Emiliano Screponi ◽  
Eleonora Carosa ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Thyroid Hormone ◽  
Sertoli Cells ◽  
Pcr Amplification ◽  
Receptor Expression ◽  
Northern Analysis ◽  
Human Testis ◽  
Adult Testis ◽  
Maximal Expression

Abstract We studied the spatiotemporal distribution of thyroid hormone nuclear receptors (TRs) α1 and α2 and β messenger RNA (mRNA) levels in normal human testicular tissue during development and in adulthood. Nonpathological specimens from five aborted fetuses (17 and 23 weeks of gestation, three and two cases, respectively) and from four patients undergoing orchiectomy (18 months old and 38-, 42-, and 52-yr-old, respectively) were analyzed by Northern blot, semiquantitative RT-PCR amplification using DNA sequences or specifically designed primers for the TR isoforms, and in situ hybridization. By using PCR amplification, we found that TRα1 and TRα2 are both expressed at different levels in fetal and adult testis. At all ages TRα2 is found at higher levels. Northern analysis showed hybridization signals corresponding to the expression of TRα2 and TRα1 in a ratio that increased from 2.6 at 17 weeks of gestation to 12.0 in adulthood. In fact, the expression of TRα1 dramatically decreased throughout development, being faintly detectable in the adult testis. Expression of TRβ was not detected at any age studied. This finding was further confirmed by PCR, which did not amplify TRβ either in fetal or in adult testis mRNAs. In situ hybridization studies showed the absence of TRβ and that TRα1 and TRα2 colocalized in Sertoli cells of prepubertal testis, whereas germ and interstitial cells appeared devoid of TR mRNA signals. From these results it can be concluded that the human testis exclusively expresses TRα, which is localized in Sertoli cells, TRβ being always undetectable. Fetal and prepubertal ages represent the period of maximal expression of TRα1 and TRα2. Theα 2/α1 ratio rises dramatically after development. These results confirm a critical window for the action of thyroid hormone in human testis, in the period of maximal expression of T3 binding isoform TRα1, and may account for the macroorchidism without virilization occurring when hyposecretion of thyroid hormones occurs before puberty.

scholarly journals In situ hybridization reveals temporal and spatial changes in cellular expression of mRNA for a laminin receptor, laminin, and basement membrane (type IV) collagen in the developing kidney.

1989 ◽  
Vol 109 (3) ◽  
pp. 1351-1362 ◽  
Author(s):  
G W Laurie ◽  
S Horikoshi ◽  
P D Killen ◽  
B Segui-Real ◽  
Y Yamada
Keyword(s):  
In Situ Hybridization ◽  
Steady State ◽  
Mrna Expression ◽  
Collagen Iv ◽  
Receptor Expression ◽  
Laminin Receptor ◽  
Northern Analysis ◽  
Cellular Expression ◽  
Distal Tubules

The appearance of extracellular matrix molecules and their receptors represent key events in the differentiation of cells of the kidney. Steady-state mRNA levels for a laminin receptor, the laminin B1, B2, and A chains, and the alpha 1-chain of collagen IV (alpha 1[IV]), were examined in mouse kidneys at 16 d gestation and birth, when cell differentiation is active, and 1-3 wk after birth when this activity has subsided. Northern analysis revealed that mRNA expression of laminin receptor precedes the alpha 1(IV) and laminin B chains whereas laminin A chain mRNA expression was very low. In situ hybridization reflected this pattern and revealed the cells responsible for expression. At 16 d gestation, laminin receptor mRNA was elevated in cells of newly forming glomeruli and proximal and distal tubules of the nephrogenic zone located in the kidney cortex. These cells also expressed mRNA for alpha 1(IV) and laminin chains. At birth, mRNA expression of receptor and all chains remained high in glomeruli but was reduced in proximal and distal tubules. At 1 wk after birth, expression was located in the medulla over collecting ducts and loops of Henle. Little expression was detectable by 3 wk. These results suggest that cellular expression of steady-state mRNA for laminin receptor, laminin, and collagen IV is temporally linked, with laminin receptor expression proceeding first and thereafter subsiding.

scholarly journals Localization of urokinase-type plasminogen activator messenger RNA in the normal mouse by in situ hybridization.

1991 ◽  
Vol 39 (3) ◽  
pp. 341-349 ◽  
Author(s):  
P Kristensen ◽  
J Eriksen ◽  
K Danø
Keyword(s):  
In Situ Hybridization ◽  
Plasminogen Activator ◽  
Normal Mouse ◽  
Hybridization Signal ◽  
Mouse Tissue ◽  
Northern Analysis ◽  
Type Plasminogen Activator ◽  
Urokinase Type Plasminogen Activator ◽  
Collecting Tubules

The histological distribution of urokinase-type plasminogen activator (u-PA) mRNA was analyzed in normal mouse tissue by in situ hybridization with anti-sense RNA transcribed from three different subclones of a mouse u-PA cDNA. Hybridization signal was found over a distinct fibroblast-like cell in the lamina propria of the gastrointestinal tract, over proximal, distal, and collecting tubules of the kidney, and over the epithelium of the bladder, ductus deferens, and epididymis. No hybridization signal was found over cells of the lung, pancreas, liver, adrenal, pituitary, cerebrum, hypothalamus, cerebellum, sciatic nerve, and striated muscle, nor over endothelial cells in any tissue investigated. The lack of u-PA mRNA in lung tissue was confirmed by Northern analysis and is in contrast to the high amounts of u-PA protein found in this tissue.

Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry

Genome ◽  
2003 ◽  
Vol 46 (5) ◽  
pp. 893-905 ◽  
Author(s):  
M Kubaláková ◽  
M Valárik ◽  
J Bartoš ◽  
J Vrána ◽  
J Cíhalíková ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Physical Mapping ◽  
Secale Cereale ◽  
B Chromosomes ◽  
Addition Lines ◽  
Large Numbers ◽  
Secale Cereale L

Procedures for chromosome analysis and sorting using flow cytometry (flow cytogenetics) were developed for rye (Secale cereale L.). Suspensions of intact chromosomes were prepared by mechanical homogenization of synchronized root tips after mild fixation with formaldehyde. Histograms of relative fluorescence intensity obtained after the analysis of DAPI-stained chromosomes (flow karyotypes) were characterized and the chromosome content of the DNA peaks was determined. Chromosome 1R could be discriminated on a flow karyotype of S. cereale 'Imperial'. The remaining rye chromosomes (2R–7R) could be discriminated and sorted from individual wheat–rye addition lines. The analysis of lines with reconstructed karyotypes demonstrated a possibility of sorting translocation chromosomes. Supernumerary B chromosomes could be sorted from an experimental rye population and from S. cereale 'Adams'. Flow-sorted chromosomes were identified by fluorescence in situ hybridization (FISH) with probes for various DNA repeats. Large numbers of chromosomes of a single type sorted onto microscopic slides facilitated detection of rarely occurring chromosome variants by FISH with specific probes. PCR with chromosome-specific primers confirmed the identity of sorted fractions and indicated suitability of sorted chromosomes for physical mapping. The possibility to sort large numbers of chromosomes opens a way for the construction of large-insert chromosome-specific DNA libraries in rye.Key words: chromosome isolation, chromosome sorting, fluorescence in situ hybridization, repetitive DNA sequences, wheat-rye addition lines, B chromosomes, physical mapping.

scholarly journals In situ hybridization histochemistry localization of interleukin-3 mRNA in mouse brain

Blood ◽  
1989 ◽  
Vol 73 (1) ◽  
pp. 137-140
Author(s):  
WL Farrar ◽  
M Vinocour ◽  
JM Hill
Keyword(s):  
In Situ Hybridization ◽  
Mouse Brain ◽  
Neuronal Cell Body ◽  
Northern Analysis ◽  
Molecular Evidence ◽  
Hybridization Histochemistry ◽  
Interleukin 3 ◽  
In Situ Hybridization Histochemistry ◽  
The Brain

The hematopoietic growth factor interleukin-3 (IL-3) promotes the proliferation and maturation of pluripotent myeloid progenitor cells. In the immune system, IL-3 is synthesized by mitogen or antigen- stimulated T lymphocytes. We demonstrate the expression of IL-3 mRNA in mouse brain by in situ hybridization histochemistry and Northern blot analysis. The IL-3 mRNA is localized in discrete areas of the brain and can be found in neuronal cell body and astrocytes. Northern analysis of cerebellar RNA, compared with mRNA extracted from WEHI-3 cells, showed a single hybridization band, approximately 1.2 kb, suggesting similar processing between brain and myeloid cells. The molecular evidence and previous observations of IL-3-like biologic activity found in the brain suggest a potential role for IL-3 in the neurobiology of the CNS.

DANCE in developing and injured lung

2002 ◽  
Vol 282 (1) ◽  
pp. L75-L82 ◽  
Author(s):  
Jyh-Chang Jean ◽  
Ifeanyi Eruchalu ◽  
Yu Xia Cao ◽  
Martin Joyce-Brady
Keyword(s):  
In Situ Hybridization ◽  
Cell Biology ◽  
Exposure Period ◽  
Subtractive Hybridization ◽  
Recovery Phase ◽  
Mrna Abundance ◽  
Northern Analysis ◽  
Adult Lung ◽  
Injured Lung

We identified rat developing arteries and neural crest derivatives with multiple epidermal growth factor-like domains ( DANCE) as a developmentally regulated gene using suppression-subtractive hybridization. Northern analysis confirmed a fivefold induction of this mRNA transcript between fetal day 18 and 20 that persisted through postnatal day 17. The level was declining at postnatal day 21 and was similar in adult lung to that at fetal day 18. In adults DANCE mRNA abundance was highest in lung, kidney, and spleen, lower in heart, skeletal muscle, and brain, but absent from liver and thymus. It was abundant in pulmonary artery endothelium and a lung epithelial type 2 cell line, barely detectable in vascular smooth muscle, and absent in fibroblasts. In situ hybridization revealed a regulated pattern of expression in endothelial cells of fetal, postnatal, and adult lung. Because DANCE mRNA was inducible in systemic arteries during recovery from injury, we searched for induction in lung injured by hyperoxia. Mouse DANCE mRNA abundance was unchanged during an acute 3-day exposure period, induced threefold 5 days into the recovery phase, and returned to baseline at days 8, 11, and 14. In situ hybridization at day 5 suggested a diffuse pattern of induction. DANCE may play a role in lung endothelial cell biology during development repair after injury.

Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research

Genome ◽  
2006 ◽  
Vol 49 (9) ◽  
pp. 1057-1068 ◽  
Author(s):  
Jiming Jiang ◽  
Bikram S. Gill
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Molecular Cytogenetics ◽  
Plant Genome ◽  
Current Status ◽  
Sequence Information ◽  
Resolution Mapping

Fluorescence in situ hybridization (FISH), which allows direct mapping of DNA sequences on chromosomes, has become the most important technique in plant molecular cytogenetics research. Repetitive DNA sequence can generate unique FISH patterns on individual chromosomes for karyotyping and phylogenetic analysis. FISH on meiotic pachytene chromosomes coupled with digital imaging systems has become an efficient method to develop physical maps in plant species. FISH on extended DNA fibers provides a high-resolution mapping approach to analyze large DNA molecules and to characterize large genomic loci. FISH-based physical mapping provides a valuable complementary approach in genome sequencing and map-based cloning research. We expect that FISH will continue to play an important role in relating DNA sequence information to chromosome biology. FISH coupled with immunoassays will be increasingly used to study features of chromatin at the cytological level that control expression and regulation of genes.

Expression of Erythropoietin Receptor-Like Molecule in Xenopus laevis (xeEPOR) and the Development of Anemia by the Administration of Its Recombinant Soluble Form.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2783-2783
Author(s):  
Youichi Aizawa ◽  
Nami Nogawa ◽  
Nobuyoshi Kosaka ◽  
Yasutaka Maeda ◽  
Takafumi Watanabe ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Peripheral Blood ◽  
Cellular Proliferation ◽  
Physiological Role ◽  
Soluble Form ◽  
Northern Analysis ◽  
Binding Motif ◽  
Normal Peripheral Blood ◽  
Peripheral Erythrocyte

Abstract The regulation of hematopoiesis in non-mammalian vertebrates is poorly understood. This is partly because the structures and effects of most hematopoietic regulators have not been identified. As a first step towards studies on the key ingredient of hematopoietic regulation among phyla as well as the diversity of organisms, we have focused on amphibian hematopoiesis. In this study, a cDNA sharing the highest degree of homology with mammalian erythropoietin (EPO) receptors, named xeEPOR tentatively, was cloned from cDNA library of Xenopus immature erythrocytes. The identities of the deduced entire amino acid sequence to human and murine EPO receptors were 24% and 25%, respectively; whereas transmembrane region and motifs of WSXWS and Box1/2 domains were found in the molecule. The northern analysis revealed that two types of xeEPOR RNAs were expressed in normal peripheral blood cells. In addition, by in situ hybridization and immunostaining with monoclonal antibodies raised against the extracellular domain of xeEPOR (soluble xeEPOR), immature basophilic erythrocytes expressing xeEPOR appeared in peripheral blood of phenylhydrazine-treated adult Xenopus. The fulllength xeEPOR cDNA was introduced into murine FDC/P2 cells and the signaling for the cellular proliferation and differentiation was examined in the presence of serum derived from anemic Xenopus as a stimulator. To further understanding the contribution of the xeEPOR gene expression to primitive and definitive hematopoiesis on Xenopus development, whole mount in situ hybridization was performed. As the binding motif of GATA-1, the hematopoietic specific transcription factor, was located at −24 to −15 base upstream of the translation initiation sequence, the correlated expressions of xeEPOR and Xenopus GATA-1 on developing embryo were evaluated with RT-PCR. The xeEPOR RNA was abundantly expressed at Nieuwkoop stage 30 (blood island formation) and thereafter, and temporally followed the expression of GATA-1, suggesting that the functional expression of xeEPOR was upregulated by GATA-1 in Xenopus as reported in studies on mammalian erythropoiesis. To confirm biological functions of the molecule, soluble xeEPOR was administered into adult Xenopus by intracardiac consecutive injections. The peripheral erythrocyte counts were gradually decreased; meanwhile immature erythrocytes were emerged in the circulation, demonstrating that this molecule plays a significant physiological role in erythropoiesis in Xenopus.

Sign in / Sign up

Export Citation Format

Share Document