scholarly journals Yellow Lupine Cyclophilin Transcripts Are Highly Accumulated in the Nodule Meristem Zone

2001 ◽  
Vol 14 (12) ◽  
pp. 1384-1394 ◽  
Author(s):  
Katarzyna Nuc ◽  
Przemysław Nuc ◽  
Ryszard Słomski
Keyword(s):  
In Situ Hybridization ◽  
Genomic Dna ◽  
Root Nodules ◽  
Open Reading Frame ◽  
Intronless Gene ◽  
Reading Frame ◽  
Gene Coding ◽  
Meristem Zone ◽  
Yellow Lupine

Cyclophilin (CyP) is one of the enzymes that act as peptidylprolyl cis-trans isomerases (EC 5.2.1.8). The cDNA and an intronless gene coding for cytosolic CyP have been isolated from yellow lupine. The deduced amino acid sequence of the characterized open reading frame shows approximately 80% homology with cytosolic CyP from other organisms. Southern blots of genomic DNA indicate that there is a small family of genes for CyP-related genes in the yellow lupine genome. RNA blot analyses demonstrate that CyP genes are expressed in all plant organs. The amount of CyP transcripts is dramatically increased in root nodules. In situ hybridization experiments indicate that CyP transcripts are localized mainly in meristematic tissues, with the highest level observed in the nodule meristem zone. The promoter of the sequenced gene contains 5′ AAAGAT 3′ and AT-rich motifs that are characteristic for some nodulin promoters.

Complete sequence of rabbit kidney aminopeptidase N and mRNA localization in rabbit kidney by in situ hybridization

1993 ◽  
Vol 71 (5-6) ◽  
pp. 278-287 ◽  
Author(s):  
Xiao-Feng Yang ◽  
Pierre Emmanuel Milhiet ◽  
Florence Gaudoux ◽  
Philippe Crine ◽  
Guy Boileau
Keyword(s):  
In Situ Hybridization ◽  
Transmembrane Domain ◽  
Complete Sequence ◽  
Aminopeptidase N ◽  
Full Length ◽  
Open Reading Frame ◽  
Rabbit Kidney ◽  
Mrna Levels ◽  
Reading Frame

We have isolated and sequenced a full-length cDNA for rabbit kidney aminopeptidase N (APN). The 3-kilobase cDNA contains 12 nucleotides of the 5′ noncoding region, a 2898 nucleotide long open reading frame, and 113 nucleotides of the 3′ untranslated region. The open reading frame encodes a type II membrane protein of 966 amino acid residues composed of a 10 residue NH2-terminal cytosolic domain, a 23 residue transmembrane domain, and a large 933 residue ectodomain that contains the active site. Rabbit APN has eight potential N-glycosylation sites and seven cysteine residues, one of which is located in the transmembrane domain. Computer analysis showed that the enzymes from human, rat, and rabbit were highly conserved, except for the stalk region immediately downstream from the transmembrane domain. Using in situ hybridization techniques we showed that in rabbit kidney, APN mRNA is present in proximal tubules but not in glomeruli, which corresponds to the localization of the protein observed by immunohistochemistry. Taken together, our results strongly suggest that the expression of APN in kidney is modulated at mRNA levels and not at translational and (or) posttranslational levels.Key words: aminopeptidase N, rabbit kidney, full-length sequence, in situ hybridization.

C-banding and fluorescence in situ hybridization studies of the wheat–alien hybrid 'Agrotana'

Genome ◽  
1994 ◽  
Vol 37 (3) ◽  
pp. 477-481 ◽  
Author(s):  
Jie Xu ◽  
R. L. Conner ◽  
A. Laroche
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Genomic Dna ◽  
Chromosome Engineering ◽  
C Banding ◽  
Chinese Spring Wheat ◽  
Mother Cells ◽  
Alien Chromatin ◽  
Chromosome Segments

'Agrotana', a wheat-alien hybrid (2n = 56), is a potential source of resistance to common root rot, stem rust, wheat streak mosaic virus, and the wheat curl mite. However, the origin of 'Agrotana', reported to be durum wheat × Agropyron trichophorum (pubescent wheatgrass), is uncertain. The objective of this investigation was to determine the chromosome constitution of 'Agrotana' using C-banding and fluorescence in situ hybridization techniques. The F1 hybrid of 'Agrotana' × 'Chinese Spring' wheat showed 7 I + 21 II in 14.9% of the pollen mother cells, evidence of the presence of the A, B, and D genomes in 'Agrotana'. The hybrid had 16 heavily C-banded chromosomes, namely 4A, and 1-7B of wheat, and a translocation that probably involved wheat chromosomes 2A and 2D. In situ hybridization using biotinylated genomic DNA of Ag. trichophorum cv. Greenleaf blocked with CS DNA failed to identify the alien chromosomes in 'Agrotana', indicating that the alien chromosomes were not likely derived from pubescent wheatgrass. In situ hybridization using labelled wheat genomic DNA blocked with 'Agrotana' DNA revealed that 'Agrotana' had 40 wheat, 14 alien, and 2 (a pair) wheat–alien translocated chromosomes. There was no homology between wheat and the alien chromosomes or chromosome segments involved in the wheat–alien recombinant. Two of the seven pairs of alien chromosomes were homoeologous to each other. The ability to identify alien chromatin in wheat using labelled wheat DNA instead of labelled alien DNA will be particularly useful in chromosome engineering of wheat germplasms having alien chromatin of unknown origin.Key words: wheat–alien hybrid, C-banding, fluorescence in situ hybridization, labelled wheat DNA as probe.

scholarly journals Rapid and efficient generation of PCR-derived riboprobe templates for in situ hybridization histochemistry.

1993 ◽  
Vol 41 (5) ◽  
pp. 773-776 ◽  
Author(s):  
J H Sitzmann ◽  
P K LeMotte
Keyword(s):  
In Situ Hybridization ◽  
Coding Region ◽  
Biopsy Material ◽  
Hybridization Histochemistry ◽  
In Situ Hybridization Histochemistry ◽  
Gene Coding ◽  
Suprabasal Cell ◽  
Cell Layers ◽  
Negative Controls

In situ hybridization histochemistry (ISH) using cRNA probes (riboprobes) has become a powerful technique for the examination of gene expression in tissue sections. The construction of plasmid templates for the synthesis of riboprobes with phage RNA polymerases is often a difficult and time-consuming step. We have therefore developed a rapid, efficient, and flexible method to generate totally artificial riboprobe templates by the polymerase chain reaction (PCR). We have made riboprobe templates using self-priming oligonucleotide primers spanning 146 BP of the 3' end of the human cytokeratin 1 (K1) gene coding region flanked by T7 and T3 promoters. These PCR-derived riboprobe templates were used to synthesize 35S-labeled anti-sense riboprobes as well as sense riboprobes as negative controls. The riboprobes were then applied in ISH to human skin sections made from routinely fixed and paraffin-embedded clinical biopsy material. Consistent with published results, we observed strong expression of K1 mRNA in the suprabasal cell layers of the epidermis but only weak to undetectable signals in the basal and cornified cell layers and in the dermis. With this experimental procedure we see no decrease in probe efficiency or quality compared to conventional methods. The use of PCR-derived riboprobe templates for ISH makes it possible to detect expression of any desired gene of known sequence rapidly and efficiently.

A rapid procedure for the isolation of C0t-1 DNA from plants

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 138-142 ◽  
Author(s):  
Michael S. Zwick ◽  
Robert E. Hanson ◽  
M. Nurul Islam-Faridi ◽  
David M. Stelly ◽  
Rod A. Wing ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Copy Number ◽  
Genomic Dna ◽  
Mammalian Species ◽  
Repetitive Dnas ◽  
Rapid Procedure ◽  
Dna Elements ◽  
Repetitive Dna Elements

In situ hybridization (ISH) for the detection of single- or low-copy sequences, particularly large DNA fragments cloned into YAC or BAC vectors, generally requires the suppression or "blocking" of highly-repetitive DNAs. C0t-1 DNA is enriched for repetitive DNA elements, high or moderate in copy number, and can therefore be used more effectively than total genomic DNA to prehybridize and competitively hybridize repetitive elements that would otherwise cause nonspecific hybridization. C0t-1 DNAs from several mammalian species are commercially available, however, none is currently available for plants to the best of our knowledge. We have developed a simple 1-day procedure to generate C0t-1 DNA without the use of specialized equipment.Key words: C0t-1 DNA, in situ hybridization, BACs, plants.

Genomic in situ hybridization to sectioned nuclei shows chromosome domains in grass hybrids

1990 ◽  
Vol 95 (3) ◽  
pp. 335-341
Author(s):  
A.R. Leitch ◽  
W. Mosgoller ◽  
T. Schwarzacher ◽  
M.D. Bennett ◽  
J.S. Heslop-Harrison
Keyword(s):  
In Situ Hybridization ◽  
Genomic Dna ◽  
Microscope Level ◽  
Hordeum Chilense ◽  
Root Tip ◽  
Interphase Nuclei ◽  
Light Microscope Level ◽  
Thin Sections ◽  
Electron Microscopes

In situ hybridization using biotinylated total genomic DNA and avidin detection systems was adapted for examination of thin-sectioned plant material in the light and electron microscopes. Root tip material was preserved prior to sectioning, so that the in vivo disposition of the chromatin was maintained. Use of total genomic DNA from Secale africanum as a probe enabled the chromatin from the two parental genomes in the grass hybrid Hordeum chilense × S. africanum to be distinguished. The biotinylated probe preferentially labelled the chromosomes of S. africanum origin. DNA-DNA hybrids were visualized at the light-microscope level by Texas Red fluorescence and at the electron-microscope level by the enzymic precipitation of DAB (diaminobenzidine) or by colloidal gold particles. The use of thin sections allowed the location of probe hybridization to be established unequivocally in both metaphase and interphase nuclei. Analysis of interphase nuclei showed that chromatin originating from the two parental genomes did not intermix but occupied distinct domains.

Identification of serum-inducible genes: different patterns of gene regulation during G0-->S and G1-->S progression

1994 ◽  
Vol 107 (1) ◽  
pp. 227-239 ◽  
Author(s):  
M. Wick ◽  
C. Burger ◽  
S. Brusselbach ◽  
F.C. Lucibello ◽  
R. Muller
Keyword(s):  
Cell Cycle Progression ◽  
Plasminogen Activator Inhibitor ◽  
Fibroblast Cell ◽  
Open Reading Frame ◽  
Proliferating Cells ◽  
Reading Frame ◽  
Gene Coding ◽  
Opposite Strand ◽  
Neutrophil Chemotactic Factor ◽  
Inducible Genes

We have identified, by differential cDNA library screening, 15 serum inducible genes in the human diploid fibroblast cell line WI-38. The genes fall into two classes that are distinguished by their dependence on protein synthesis for the induction by serum, i.e., primary and secondary genes. While 11 of these genes encode known proteins, 4 other genes have not been described to date. The former genes encode proteins of diverse functions, including the monocyte-derived neutrophil chemotactic factor (MONAP), calmodulin, tropomyosin, tenascin, collagenase, plasminogen activator inhibitor-2a, the ‘sperm-specific’ cleavage signal-1 protein, metallothionein IIa and the mitochondrial chaperonin hsp-60. Interestingly, one of the unknown genes contains a large open reading frame for a polypeptide that is highly homologous to a previously unidentified long open reading frame in the opposite strand of the gene coding for the transcription factor HTF-4. We also studied the regulation of these serum-induced genes during cell cycle progression in normally cycling WI-38 and HL-60 cells separated by counterflow elutriation as well as in serum-stimulated HL-60 cells. Our results clearly show that, in contrast to the prevailing opinion, the expression of most genes induced after mitogen stimulation is not subject to a significant regulation in normally proliferating cells. This supports the hypothesis that the progression into S from either G0 or G1 are distinct processes with specific patterns of gene expression.

The interspecific genome structure of cultivated banana, Musa spp. revealed by genomic DNA in situ hybridization

2000 ◽  
Vol 100 (2) ◽  
pp. 177-183 ◽  
Author(s):  
A. D’Hont ◽  
A. Paget-Goy ◽  
J. Escoute ◽  
F. Carreel
Keyword(s):  
In Situ Hybridization ◽  
Genomic Dna ◽  
Genome Structure ◽  
Musa Spp

Molecular cloning, characterization, and distribution of the gerbil angiotensin II AT2 receptor

2003 ◽  
Vol 285 (6) ◽  
pp. R1373-R1383 ◽  
Author(s):  
Kwang-Lae Hoe ◽  
Ines Armando ◽  
Gustavo Baiardi ◽  
Taduru Sreenath ◽  
Ashok Kulkarni ◽  
...  
Keyword(s):  
Open Reading Frame ◽  
Late Gestation ◽  
At2 Receptor ◽  
Ang Ii ◽  
Amino Acid Residues ◽  
Receptor Ligands ◽  
Reading Frame ◽  
Receptor Mrna ◽  
Dental Papilla

We isolated a cDNA clone encoding the gerbil AT2 receptor (gAT2) gene from a gerbil adrenal gland cDNA library. The full-length cDNA contains a 1,089-bp open reading frame encoding 363 amino acid residues with 90.9, 96.1, and 95.6% identity with the human (hAT2), rat (rAT2), and mouse AT2 (mAT2) receptors, respectively. There are at least seven nonconserved amino acids in the NH2-terminal domain and in positions Val196, Val217, and Met293, important for angiotensin (ANG) II but not for CGP-42112 binding. Displacement studies in adrenal sections revealed that affinity of the gAT2 receptor was 10-20 times lower for ANG II, ANG III, and PD-123319 than was affinity of the rAT2 receptor. The affinity of each receptor remained the same for CGP-42112. When transfected into COS-7 cells, the gAT2 receptor shows affinity for ANG II that is three times lower than that shown by the hAT2 receptor, whereas affinities for ANG III and the AT2 receptor ligands CGP-42112 and PD-123319 were similar. Autoradiography in sections of the gerbil head showed higher binding in muscles, retina, skin, and molars at embryonic day 19 than at 1 wk of age. In situ hybridization and emulsion autoradiography revealed that at embryonic day 19 the gAT2 receptor mRNA was highly localized to the base of the dental papilla of maxillary and mandibular molars. Our results suggest selective growth-related functions in late gestation and early postnatal periods for the gAT2 receptor and provide an essential basis for future mutagenesis studies to further define structural requirements for agonist binding.

scholarly journals Comparison Between Integrated Genomic DNA/RNA Profiling and Fluorescence In Situ Hybridization in the Detection of MYC, BCL-2, and BCL-6 Gene Rearrangements in Large B-Cell Lymphomas

2019 ◽  
Vol 153 (3) ◽  
pp. 353-359 ◽  
Author(s):  
Daniel P Cassidy ◽  
Jennifer R Chapman ◽  
Rafael Lopez ◽  
Kyle White ◽  
Yao-Shan Fan ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
B Cell ◽  
Fluorescence In Situ Hybridization ◽  
Genomic Dna ◽  
Standard Of Care ◽  
Gene Rearrangements ◽  
B Cell Lymphomas ◽  
Rna Profiling ◽  
Large B Cell

Abstract Objectives To compare fluorescence in situ hybridization (FISH) and a commercially available sequencing assay for comprehensive genomic profiling (CGP) to determine the best approach to identify gene rearrangements (GRs) in large B-cell lymphomas (LBCLs). Methods Comparison of standard-of-care FISH assays (including a two-probe approach for MYC; break-apart and fusion probes) and an integrated genomic DNA/RNA sequencing CGP approach on a set of 69 consecutive LBCL cases. Results CGP detected GRs, including those involving MYC (1), BCL-2 (3), and BCL-6 (3), not detected by FISH. FISH detected non–IgH-MYC (4) and BCL-6 (2) GRs that were not detected by CGP. In four instances, standalone CGP or FISH testing would have missed a double-hit lymphoma. Conclusions CGP was superior to FISH in the detection of IgH-MYC rearrangements but was inferior for the detection of non–IgH-MYC rearrangements. Our study demonstrates the rationale for development of a customized approach to identify GRs in LBCLs.

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