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Journal articles on the topic 'RNA hybridisation'

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Published: 4 June 2021
Last updated: 1 February 2022

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1

Dickson, M. C., H. G. Slager, E. Duffie, C. L. Mummery, and R. J. Akhurst. "RNA and protein localisations of TGF beta 2 in the early mouse embryo suggest an involvement in cardiac development." Development 117, no. 2 (February 1, 1993): 625–39. http://dx.doi.org/10.1242/dev.117.2.625.

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We have performed a detailed analysis of the localisations of RNAs for TGF beta 2 and beta 3, and of TGF beta 2 protein in mouse embryos from 6.5 to 9.5 days post coitum, using in situ hybridisation and immunohistochemistry on serial sections, and whole-mount in situ hybridisation to complete embryos. TGF beta 3 RNA was not seen in any of the tissue sections, but very low levels of the RNA were seen by whole-mount in situ hybridisation around the outflow tract of the heart at 8.5 days post coitum. TGF beta 2 RNA is expressed at high levels in all cells with the potential to differentiate into cardiomyocytes. Additionally, the foregut endoderm, juxtaposed to the heart, and the neuroepithelium at the rostral extremity of the foregut, express very high levels of TGF beta 2 RNA, between 8.5 and 9.5 days post coitum. As cardiomyogenesis proceeds, TGF beta 2 RNA levels diminishes within the myocytes, with a concomitant increase in staining for TGF beta 2 protein. TGF beta 2 protein staining of cardiomyocytes persists throughout development and in the adult, in the absence of detectable levels of the corresponding RNA. Superimposed upon this myocardial pattern of expression, there is an upregulation of TGF beta 2 RNA in the myocardium of the outflow tract and atrioventricular canal between 8.5 and 9.5 days post coitum, which returns to low levels by 11.5 days post coitum. The results are discussed in terms of a potential role of TGF beta 2 in controlling cardiomyogenesis and in inductive interactions leading to cardiac cushion tissue formation.
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2

Misra, A., S. Tripathi, and K. Misra. "Synthesis of terminally labelled RNA sequences: Fluorescence and hybridisation study of RNA-DNA duplexes." Nucleic Acids Symposium Series 1, no. 1 (November 1, 2001): 95–96. http://dx.doi.org/10.1093/nass/1.1.95.

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3

Singh, Dharam, and Mahipal Singh. "Organization of 5S ribosomal RNA genes in tea (Camellia sinensis)." Genome 44, no. 1 (February 1, 2001): 143–46. http://dx.doi.org/10.1139/g00-095.

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The 5S rRNA genes in the Camellia sinensis (L.) O. Kuntze (tea) genome are arranged as tandem repeat units of 300 and 325 bps. The 2 classes of tandem repeats were discovered by Southern hybridisation of tea genomic DNA with a 5S rRNA gene PCR product.Key words: Camellia species, 5S rDNA, multigene family, tandem repeats, spacers.
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4

Schäfer, Richard A., and Björn Voß. "RNAnue: efficient data analysis for RNA–RNA interactomics." Nucleic Acids Research 49, no. 10 (May 21, 2021): 5493–501. http://dx.doi.org/10.1093/nar/gkab340.

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Abstract RNA–RNA inter- and intramolecular interactions are fundamental for numerous biological processes. While there are reasonable approaches to map RNA secondary structures genome-wide, understanding how different RNAs interact to carry out their regulatory functions requires mapping of intermolecular base pairs. Recently, different strategies to detect RNA–RNA duplexes in living cells, so called direct duplex detection (DDD) methods, have been developed. Common to all is the Psoralen-mediated in vivo RNA crosslinking followed by RNA Proximity Ligation to join the two interacting RNA strands. Sequencing of the RNA via classical RNA-seq and subsequent specialised bioinformatic analyses the result in the prediction of inter- and intramolecular RNA–RNA interactions. Existing approaches adapt standard RNA-seq analysis pipelines, but often neglect inherent features of RNA–RNA interactions that are useful for filtering and statistical assessment. Here we present RNAnue, a general pipeline for the inference of RNA–RNA interactions from DDD experiments that takes into account hybridisation potential and statistical significance to improve prediction accuracy. We applied RNAnue to data from different DDD studies and compared our results to those of the original methods. This showed that RNAnue performs better in terms of quantity and quality of predictions.
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5

Loi, Danson S. C., Lei Yu, and Angela R. Wu. "Effective ribosomal RNA depletion for single-cell total RNA-seq by scDASH." PeerJ 9 (January 15, 2021): e10717. http://dx.doi.org/10.7717/peerj.10717.

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A decade since its invention, single-cell RNA sequencing (scRNA-seq) has become a mainstay technology for profiling transcriptional heterogeneity in individual cells. Yet, most existing scRNA-seq methods capture only polyadenylated mRNA to avoid the cost of sequencing non-messenger transcripts, such as ribosomal RNA (rRNA), that are usually not of-interest. Hence, there are not very many protocols that enable single-cell analysis of total RNA. We adapted a method called DASH (Depletion of Abundant Sequences by Hybridisation) to make it suitable for depleting rRNA sequences from single-cell total RNA-seq libraries. Our analyses show that our single-cell DASH (scDASH) method can effectively deplete rRNAs from sequencing libraries with minimal off-target non-specificity. Importantly, as a result of depleting the rRNA, the rest of the transcriptome is significantly enriched for detection.
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6

Taylor, G. R., G. I. Carter, T. J. Crow, J. A. Johnson, A. F. Fairbairn, E. K. Perry, and R. H. Perry. "Recovery and measurement of RNA in Alzheimer's disease by molecular hybridisation." Journal of Neurology, Neurosurgery & Psychiatry 50, no. 3 (March 1, 1987): 356. http://dx.doi.org/10.1136/jnnp.50.3.356.

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7

Loughrey, Maurice, Melanie Trivett, Stephen Lade, William Murray, Hugh Turner, and Paul Waring. "Diagnostic application of Epstein–Barr virus-encoded RNA in situ hybridisation." Pathology 36, no. 4 (August 2004): 301–8. http://dx.doi.org/10.1080/0031302042000224584.

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8

Tougianidou, D., and K. Botzenhart. "Detection of Enteroviral RNA Sequences in Different Water Samples." Water Science and Technology 27, no. 3-4 (February 1, 1993): 219–22. http://dx.doi.org/10.2166/wst.1993.0349.

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Viruses were isolated from different water samples by Sterivex-Filtration. The nucleic acids were isolated in the filter unit and purified by phenol-chloroform extraction and ethanol precipitation. Reverse transcription and polymerase chain reaction (RT/PCR) were performed with primer pairs complementary to sequences of the enteroviral 5’ noncoding region. Amplified sequences were detected by hybridisation with an oligonucleotide complementary to a part of the PCR product. The test system seems to be sensitive and specific In the detection of enteroviral RNA.
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9

Freidin, Maxim B., Dasha V. Freydina, Angeles Montero Fernandez, Alexandra Rice, Andrew G. Nicholson, and Eric Lim. "Application of RNA in situ hybridisation for identification of circulating tumour cells." Journal of Clinical Pathology 68, no. 8 (May 19, 2015): 669–70. http://dx.doi.org/10.1136/jclinpath-2015-203112.

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10

Cunningham, D. A., J. R. Pattison, and R. K. Craig. "Detection of parvovirus DNA in human serum using biotinylated RNA hybridisation probes." Journal of Virological Methods 19, no. 3-4 (March 1988): 279–88. http://dx.doi.org/10.1016/0166-0934(88)90022-5.

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11

Lacey, R. J., S. L. F. Chan, H. C. Cable, R. F. L. James, C. W. Perret, J. H. B. Scarpello, and N. G. Morgan. "Expression of α2- and β-adrenoceptor subtypes in human islets of Langerhans." Journal of Endocrinology 148, no. 3 (March 1996): 531–43. http://dx.doi.org/10.1677/joe.0.1480531.

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Abstract Sequences from cDNA molecules encoding α2-adrenoceptor subtype genes were subcloned into prokaryotic vectors and riboprobes generated to hybridise selectively with each of the human α2C2-, α2C4- and α2C10-adrenoceptor subtype mRNA species. The riboprobes were labelled with either 32P or digoxigenin and used to study the expression of α2-adrenoceptor subtypes in sections of human pancreas, in isolated human islets of Langerhans and in clonal HIT-T15 pancreatic β-cells. Using a ribonuclease protection assay protocol, expression of mRNA species encoding both α2C2 and α2C10 was demonstrated in preparations of isolated human islets of Langerhans. mRNA encoding α2C4 was also detected in human islet RNA, using reverse transcription coupled with the polymerase chain reaction. In situ hybridisation was then employed to examine the distribution of each α2-adrenoceptor subtype in sections of human pancreas. All three subtypes of α2-adrenoceptor mRNA were identified in sections of formalin-fixed, paraffinembedded human pancreas using riboprobes labelled with digoxigenin. Although some labelling of the three α2-adrenoceptor mRNA subtypes was seen in the islets, the labelling was most intense in the exocrine tissue of the pancreas for each receptor subtype. The specificity of the digoxigenin-labelled RNA probes was confirmed in several control tissues and by in situ hybridisation studies using sense probes in the pancreas. The integrity of the pancreas sections was confirmed by in situ hybridisation with an antisense riboprobe derived from human insulin cDNA. The results demonstrate that multiple α2-adrenoceptor subtypes are expressed in human pancreas. Both the exocrine and endocrine cells express more than one receptor subtype, although the islets stain less intensely than the bulk of the tissue suggesting that the islet cells may have lower levels of expression than the acinar tissue. The presence of α2-adrenoceptor subtype mRNA species in pancreatic β-cells was confirmed by Northern blotting of RNA extracted from the clonal β-cell line, HIT-T15. Transcripts encoding each of the three cloned α2-adrenoceptor subtypes were detected in HIT-T15 cells. Hybridisation of sections of human pancreas with oligodeoxynucleotide probes designed to hybridise with β2-adrenoceptor mRNA revealed expression of this species in islet β-cells but not in the exocrine tissue of the pancreas. Journal of Endocrinology (1996) 148, 531–543
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12

Tran, Nham. "Fast and Simple microRNA Northern Blots." Biochemistry Insights 2 (January 2009): BCI.S2257. http://dx.doi.org/10.4137/bci.s2257.

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RNA northern blots provide robust measurements of gene expression. The simple northern blot technique described in this report has been optimised to provide rapid, reproducible detection and analysis of mature and precursor forms of microRNAs. This protocol economises on the use of commercially available components and secondly reduces the hybridisation step to 2 hours.
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13

Morley-Bunker, Arthur, John Pearson, Margaret J. Currie, Helen Morrin, Martin R. Whitehead, Tim Eglinton, and Logan C. Walker. "Assessment of intra-tumoural colorectal cancer prognostic biomarkers using RNA in situ hybridisation." Oncotarget 10, no. 14 (February 15, 2019): 1425–39. http://dx.doi.org/10.18632/oncotarget.26675.

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14

Pöhlmann, Christopher, Irina Dieser, and Mathias Sprinzl. "A lateral flow assay for identification of Escherichia coli by ribosomal RNA hybridisation." Analyst 139, no. 5 (2014): 1063. http://dx.doi.org/10.1039/c3an02059b.

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15

Zhang, H. Y., G. E. Yousef, N. E. Bowles, L. C. Archard, G. F. Mann, and J. F. Mowbray. "Detection of enterovirus RNA in experimentally infected mice by molecular hybridisation: Specificity of subgenomic probes in quantitative slot blot and in situ hybridisation." Journal of Medical Virology 26, no. 4 (December 1988): 375–86. http://dx.doi.org/10.1002/jmv.1890260405.

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16

Lloyd, Andrew, Gavin Dixon, Xu Feng Huang, Phillip Ward, Stan Catts, Ian Hickie, and Denis Wakefield. "Molecular Biology and the Major Psychoses." Australian & New Zealand Journal of Psychiatry 31, no. 1 (February 1997): 12–16. http://dx.doi.org/10.3109/00048679709073794.

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Objective:To highlight the potential role of molecular biological studies in examining the expression of genes of interest in brain tissue to elucidate the pathophysiological basis of the major psychoses. Method:To review the principles underlying the available techniques for expression studies. Results:Detection of messenger RNA by in situ hybridisation and quantitation by Northern analysis are powerful tools to detect abnormalities in gene expression in brain tissue. Conclusion:The availability of simple techniques to examine the expression of RNA and protein products of individual genes, including examination at the level of individual cells, offers a clear opportunity to define the molecular basis of the major psychoses.
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17

Lavrentyeva, Elena, Kseniya Shishova, German Kagarlitsky, and Olga Zatsepina. "Localisation of RNAs and proteins in nucleolar precursor bodies of early mouse embryos." Reproduction, Fertility and Development 29, no. 3 (2017): 509. http://dx.doi.org/10.1071/rd15200.

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Early embryos of all mammalian species contain morphologically distinct but transcriptionally silent nucleoli called the nucleolar precursor bodies (NPBs), which, unlike normal nucleoli, have been poorly studied at the biochemical level. To bridge this gap, here we examined the occurrence of RNA and proteins in early mouse embryos with two fluorochromes – an RNA-binding dye pyronin Y (PY) and the protein-binding dye fluorescein-5′-isothiocyanate (FITC). The staining patterns of zygotic NPBs were then compared with those of nucleolus-like bodies (NLBs) in fully grown surrounded nucleolus (SN)-type oocytes, which are morphologically similar to NPBs. We show that both entities contain proteins, but unlike NLBs, NPBs are significantly impoverished for RNA. Detectable amounts of RNA appear on the NPB surface only after resumption of rDNA transcription and includes pre-rRNAs and 28S rRNA as evidenced by fluorescence in situ hybridisation with specific oligonucleotide probes. Immunocytochemical assays demonstrate that zygotic NPBs contain rRNA processing factors fibrillarin, nucleophosmin and nucleolin, while UBF (the RNA polymerase I transcription factor) and ribosomal proteins RPL26 and RPS10 are not detectable. Based on the results obtained and data in the contemporary literature, we suggest a scheme of NPB assembly and maturation to normal nucleoli that assumes utilisation of maternally derived nucleolar proteins but of nascent rRNAs.
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18

Ward, Rita D., Lisa M. Mendoza, Gary W. Moy, Victor D. Vacquier, and David Nishioka. "A unique expression pattern for a sperm membrane protein during sea urchin spermatogenesis." Zygote 2, no. 2 (May 1994): 159–65. http://dx.doi.org/10.1017/s096719940000191x.

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SummarySpecific mRNAs coding for a 63 kDa sperm membrane protein (63-SMP) were localised in Strongylocentrotus purpuratus testis sections using in situ hybridisation techniques. 35S-labelled antisense RNA probes transcribed from a 766 base pair fragment of the gene coding for the 63-SMP hybridised to all spermatogenic cells in the basal germinal epithelia of testicular acini, except the most peripherally located (least differentiated) spermatogonia. No hybridisation to the luminally located mature spermatozoa or somatic cells of the testis was observed. Using monoclonal antibody J17/30 and indirect immunofluorescence techniques, the 63-SMP was localised to the same subset of spermatogenic cells that contain the 63-SMP mRNA, suggesting that expression of this gene is transcriptionally controlled. In combination with previous studies on the expression of sperm histones and sperm bindin, these results show that multiple, perhaps sequential, classes of gene activity contribute to the differentiation of sea urchin sperm.
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19

Huhtamella, Sanna, Marika Leinonen, Timo Nieminen, Beatrix Fahnert, Liisa Myllykoski, Antje Breitenstein, and Peter Neubauer. "RNA-based sandwich hybridisation method for detection of lactic acid bacteria in brewery samples." Journal of Microbiological Methods 68, no. 3 (March 2007): 543–53. http://dx.doi.org/10.1016/j.mimet.2006.10.009.

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20

Kobayashi, M., T. Urata, T. Ikezoe, E. Hakoda, Y. Uemura, H. Sonobe, Y. Ohtsuki, T. Manabe, S. Miyagi, and I. Miyoshi. "Simple detection of the 5S ribosomal RNA of Pneumocystis carinii using in situ hybridisation." Journal of Clinical Pathology 49, no. 9 (September 1, 1996): 712–16. http://dx.doi.org/10.1136/jcp.49.9.712.

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21

Croner, Roland S., Berthold Lausen, Vera Schellerer, Isabel Zeittraeger, Axel Wein, Claus Schildberg, Thomas Papadopoulos, et al. "Comparability of Microarray Data between Amplified and Non Amplified RNA in Colorectal Carcinoma." Journal of Biomedicine and Biotechnology 2009 (2009): 1–9. http://dx.doi.org/10.1155/2009/837170.

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Microarray analysis reaches increasing popularity during the investigation of prognostic gene clusters in oncology. The standardisation of technical procedures will be essential to compare various datasets produced by different research groups. In several projects the amount of available tissue is limited. In such cases the preamplification of RNA might be necessary prior to microarray hybridisation. To evaluate the comparability of microarray results generated either by amplified or non amplified RNA we isolated RNA from colorectal cancer samples (stage UICC IV) following tumour tissue enrichment by macroscopic manual dissection (CMD). One part of the RNA was directly labelled and hybridised to GeneChips (HG-U133A, Affymetrix), the other part of the RNA was amplified according to the “Eberwine” protocol and was then hybridised to the microarrays. During unsupervised hierarchical clustering the samples were divided in groups regarding the RNA pre-treatment and 5.726 differentially expressed genes were identified. Using independent microarray data of 31 amplified vs. 24 non amplified RNA samples from colon carcinomas (stage UICC III) in a set of 50 predictive genes we validated the amplification bias. In conclusion microarray data resulting from different pre-processing regarding RNA pre-amplification can not be compared within one analysis.
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22

Rigottier-Gois, Lionel, Anne-Gaëlle Bourhis, Geneviève Gramet, Violaine Rochet, and Joël Doré. "Fluorescent hybridisation combined with flow cytometry and hybridisation of total RNA to analyse the composition of microbial communities in human faeces using 16S rRNA probes." FEMS Microbiology Ecology 43, no. 2 (March 2003): 237–45. http://dx.doi.org/10.1111/j.1574-6941.2003.tb01063.x.

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23

Quennell, J. H., J. L. Stanton, and P. R. Hurst. "227. FSH receptor expression in small human ovarian follicles." Reproduction, Fertility and Development 17, no. 9 (2005): 88. http://dx.doi.org/10.1071/srb05abs227.

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Follicle-stimulating hormone (FSH) is pivotal in ovarian follicle development; the granulosa cells are the targets of FSH action in the ovary via FSH receptors. Granulosa cell growth and division mark initial follicle recruitment. The acquisition of FSH receptors on granulosa cells is regarded as a key event in hormone responsiveness and consequently follicle development. Due to the low abundance of FSH receptors and low expression of its mRNA it has been difficult to definitively characterise FSH receptor expression patterns. Here, localisation of FSH receptor in different follicle populations has been assessed with in situ hybridisation and real-time PCR of laser microdissected samples. We have used non-radioactive in situ hybridisation to investigate FSH receptor mRNA on a wide range of follicle stages. Biopsies from healthy fertile women (28–33 years) were frozen, embedded and cryosectioned at 10 µm. DIG-labelled RNA probes were designed to detect all splice variants. Hybridised probes were detected with NBT/BCIP in a colorimetric reaction. Secondly, follicles of different morphometric stages were isolated with a laser microscope. RNA extraction, reverse transcription and real-time PCR were used to confirm RNA presence and quantify relative expression. All follicle stages (from primordial to large antral) showed the presence of FSH receptor mRNA in their granulosa cells; sense controls were negative. Observations from real-time PCR indicate FSH receptor mRNA is present in all follicle stages observed and relative expression levels increase over early follicle development. These results challenge the existing doctrine that FSH receptor is absent in the smallest follicles. This suggests initial follicle recruitment may involve gonadotrophins. The use of sensitive molecular techniques will be crucial in elucidating this further.
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24

Hilton, D. A., S. Love, A. Fletcher, and J. H. Pringle. "Absence of Epstein-Barr virus RNA in multiple sclerosis as assessed by in situ hybridisation." Journal of Neurology, Neurosurgery & Psychiatry 57, no. 8 (August 1, 1994): 975–76. http://dx.doi.org/10.1136/jnnp.57.8.975.

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25

Jorgensen, Lene, Anton P. J. Middelberg, Brian K. O'Neill, and Connor J. Thomas. "Quantitation of chloramphenicol acetyl transferase (CAT) messenger RNA by filter hybridisation using a digoxigenin label." Biotechnology Techniques 10, no. 2 (February 1996): 83–88. http://dx.doi.org/10.1007/bf00765187.

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26

Zhang, Zhouwei, Donald L. Weaver, Daniel Olsen, James deKay, Zhihua Peng, Takamaru Ashikaga, and Mark F. Evans. "Long non-coding RNA chromogenic in situ hybridisation signal pattern correlation with breast tumour pathology." Journal of Clinical Pathology 69, no. 1 (August 31, 2015): 76–81. http://dx.doi.org/10.1136/jclinpath-2015-203275.

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27

Roussis, Ioannis M., Matthew Guille, Fiona A. Myers, and Garry P. Scarlett. "RNA Whole-Mount In situ Hybridisation Proximity Ligation Assay (rISH-PLA), an Assay for Detecting RNA-Protein Complexes in Intact Cells." PLOS ONE 11, no. 1 (January 29, 2016): e0147967. http://dx.doi.org/10.1371/journal.pone.0147967.

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28

Brackett, Diane G., Azfar Neyaz, Kshitij Arora, Ricard Masia, Anthony Mattia, Lawerence Zukerberg, Joseph Misdraji, et al. "Cholangiolar pattern and albumin in situ hybridisation enable a diagnosis of intrahepatic cholangiocarcinoma." Journal of Clinical Pathology 73, no. 1 (August 17, 2019): 23–29. http://dx.doi.org/10.1136/jclinpath-2019-206055.

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AimsThe histological distinction of intrahepatic cholangiocarcinoma (ICC) from metastatic adenocarcinoma remains a challenge. The primary goal was to evaluate the diagnostic value of morphology and albumin expression in the diagnosis of ICC.MethodsWe evaluated morphological patterns in 120 ICCs and 677 non-hepatic adenocarcinomas and performed in situ hybridisation (ISH) stain for albumin in the former cohort (retrospective cohort). We also identified 119 samples from primary and metastatic lesions, the validation cohort, in which albumin ISH was performed as part of the diagnostic workup. Targeted sequencing was performed on selected cases. We also mined existing expression profiling data including cases from The Cancer Genome Atlas (TCGA) (41 760 unique samples).ResultsIn the retrospective cohort, 45% of ICCs and <1% of non-hepatic adenocarcinomas showed a cholangiolar pattern; albumin ISH was positive in 93% of ICCs with significant intratumorous heterogeneity. In the validation cohort, 29% of ICCs showed a cholangiolar pattern and 88% expressed albumin, while all metastatic non-hepatic neoplasms were negative (n=37) (sensitivity 88% and specificity 100%). Targetable genetic alterations (IDH mutations and FGFR2 fusions) were identified in 31% of ICCs (10 of 32). An analysis of the TCGA data validated the specificity of the albumin assay.ConclusionsThe cholangiolar pattern and albumin RNA ISH distinguishes ICC from metastatic adenocarcinoma with high specificity. Given the high prevalence of targetable mutations in ICC, albumin RNA ISH is an essential component in the workup of tumours of uncertain origin. A specific diagnosis of ICC could trigger molecular testing and uncover targetable genetic alterations.
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Akhmanova, A., T. Verkerk, A. Langeveld, F. Grosveld, and N. Galjart. "Characterisation of transcriptionally active and inactive chromatin domains in neurons." Journal of Cell Science 113, no. 24 (December 15, 2000): 4463–74. http://dx.doi.org/10.1242/jcs.113.24.4463.

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The tandemly organised ribosomal DNA (rDNA) repeats are transcribed by a dedicated RNA polymerase in a specialised nuclear compartment, the nucleolus. There appears to be an intimate link between the maintenance of nucleolar structure and the presence of heterochromatic chromatin domains. This is particularly evident in many large neurons, where a single nucleolus is present, which is separated from the remainder of the nucleus by a characteristic shell of heterochromatin. Using a combined fluorescence in situ hybridisation and immunocytochemistry approach, we have analysed the molecular composition of this highly organised neuronal chromatin, to investigate its functional significance. We find that clusters of inactive, methylated rDNA repeats are present inside large neuronal nucleoli, which are often attached to the shell of heterochromatic DNA. Surprisingly, the methylated DNA-binding protein MeCP2, which is abundantly present in the centromeric and perinucleolar heterochromatin, does not associate significantly with the methylated rDNA repeats, whereas histone H1 does overlap partially with these clusters. Histone H1 also defines other, centromere-associated chromatin subdomains, together with the mammalian Polycomb group factor Eed. These data indicate that neuronal, perinucleolar heterochromatin consists of several classes of inactive DNA, that are linked to a fraction of the inactive rDNA repeats. These distinct chromatin domains may serve to regulate RNA transcription and processing efficiently and to protect rDNA repeats against unwanted silencing and/or homologous recombination events.
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Krzowska-Firych, Joanna, Hanna Fota-Markowska, Barbara Marzec-Kotarska, Roma Modrzewska, and Jacek Wojcierowski. "Inhibitory Effect of Epstein-Barr Virus Gene-Ebna1 on Human Tnfrp55 Gene Expression." Bulletin of the Veterinary Institute in Pulawy 56, no. 3 (September 1, 2012): 271–74. http://dx.doi.org/10.2478/v10213-012-0048-7.

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Abstract The aim of the study was to assess the expression of TNFRp55 mRNA and to examine if the antisense inhibition of Epstein-Barr virus (EBV) encoded EBNA1 gene product alters the expression of gene encoding TNFRp55 in lymphoblastoid cell line (LCL). The experiment was performed on LCL derived from EBV infected human peripheral blood B lymphocytes. The lymphocytes were isolated and cultured. RNA was isolated and examined according to the RNase protection assay. The hybridisation was done with HCR-4 probe. RNA was quantified by densitometry and presented in extinction units. The level of expression was calculated with TotaILab software programme. The results of the study suggest that EBV gene, responsible for the synthesis of EBNA1 protein, has an inhibitory effect on human TNFRp55 gene expression in LCL.
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Pedley, S., M. E. H. Mohamed, and P. P. C. Mertens. "Analysis of genome segments from six different isolates of bluetongue virus using RNA-RNA hybridisation: a generalised coding assignment for bluetongue viruses." Virus Research 10, no. 4 (June 1988): 381–90. http://dx.doi.org/10.1016/0168-1702(88)90078-0.

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32

He, Dan, Xue-Yuan Lou, Song-Lin He, Ya-Kai Lei, Bo-Va Lv, Zheng Wang, Yun-Bing Zheng, and Yi-Ping Liu. "Isobaric tags for relative and absolute quantitation-based quantitative proteomics analysis provides novel insights into the mechanism of cross-incompatibility between tree peony and herbaceous peony." Functional Plant Biology 46, no. 5 (2019): 417. http://dx.doi.org/10.1071/fp18163.

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Interspecific hybridisation is the main method for improvement and breeding of tree peony (Paeonia ostii T.Hong &amp; J.X.Zhang), but cross-incompatibility as the major factor restricting the rapid development of interspecific hybridisation. To better understand the molecular mechanisms involved in cross-incompatibility between tree peony (Paeonia ostii cv. Fengdanbai) and herbaceous peony (Paeonia lactiflora Pall. cv. Fenyunu), a quantitative proteomic analysis using isobaric tags for relative and absolute quantitation (iTRAQ) technology was performed on the stigma 24h after pollination. Of the 2900 proteins whose levels were quantitated, 685 proteins were differentially expressed in the stigma after hybrid pollination, in contrast to self-pollination. Functional annotation analysis showed that dysregulated proteins involved in RNA degradation, the Ca signalling pathway, the phosphatidylinositol signalling system and the mitogen-activated protein kinase (MAPK) signalling pathway may have made contributions to cross-incompatibility. The downregulated expression of enolase, DnaK (Heat Shock Proteins, HSP70), GroEL (Heat Shock Proteins, HSP60), calmodulin and glyoxalase I, and the upregulated expression of adenine nucleotide translocator indicated that the energy synthesis required by pollen tube growth, the signal pathway and the metabolic pathway related to the growth polarity of the pollen tube were blocked after hybrid pollination. Eight genes were selected to confirm their expression by quantitative real-time PCR. Compared with the STRING database, a protein–protein interaction network of the chosen proteins was constructed. These results provide fundamental and important information for research into the molecular mechanisms of cross-incompatibility in peony and should facilitate interspecific hybridisation in agricultural practice.
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33

Sayyadi, Nima, Russell E. Connally, Thomas S. Lawson, Jingli Yuan, Nicolle H. Packer, and James A. Piper. "Time-Gated Luminescent In Situ Hybridization (LISH): Highly Sensitive Detection of Pathogenic Staphylococcus aureus." Molecules 24, no. 11 (May 31, 2019): 2083. http://dx.doi.org/10.3390/molecules24112083.

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We describe simple direct conjugation of a single TEGylated Europium chelate to DNA that binds to intracellular rRNA and is then detected using a homogeneous luminescent in situ hybridisation (LISH) technique. As a proof-of-principle, Staphylococcus aureus (S. aureus) was selected as a model for our study to show the ability of this probe to bind to intracellular 16S ribosomal rRNA. A highly purified Europium chelate conjugated oligonucleotide probe complementary to an rRNA sequence-specific S. aureus was prepared and found to be soluble and stable in aqueous solution. The probe was able to bind specifically to S. aureus via in situ hybridisation to differentiate S. aureus from a closely related but less pathogenic Staphylococcus species (S. epidermidis). A time-gated luminescent (TGL) microscope system was used to generate the high signal-to-noise ratio (SNR) images of the S. aureus. After excitation (365 nm, Chelate λmax = 335 nm), the long-lived (Eu3+) luminescent emission from the probe was detected without interference from natural background autofluorescence typically seen in biological samples. The luminescent images were found to have 6 times higher SNR or sensitivity compared to the fluorescent images using conventional fluorophore Alexa Fluor 488. The TEGylated Europium chelate -oligo probe stained S. aureus with mean signal intensity 3.5 times higher than the threshold level of signal from S. epidermidis (with SNR 8 times higher). A positive control probe (EUB338–BHHTEGST–Eu3+) has mean signal intensity for S. aureus and S. epidermidis equally 3.2 times higher than the threshold of signal for a negative NON-EUB338 control probe. The direct conjugation of a single Europium chelate to DNA provides simplicity and improvement over existing bovine serum albumin (BSA)/streptavidin/biotinylated DNA platforms for multi-attachment of Europium chelate per DNA and more importantly makes it feasible for hybridisation to intracellular RNA targets. This probe has great potential for highly sensitive homogeneous in situ hybridisation detection of the vast range of intracellular DNA targets.
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34

Johnson, Moira A., and Malcolm A. McCrae. "A rapid and sensitive solution hybridisation assay for the quantitative determination of specific viral RNA sequences." Journal of Virological Methods 22, no. 2-3 (December 1988): 247–54. http://dx.doi.org/10.1016/0166-0934(88)90107-3.

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35

Baker, David A., Joanne Thompson, Olalekan O. Daramola, Jane M. R. Carlton, and Geoffrey A. T. Targett. "Sexual-stage-specific RNA expression of a new Plasmodium falciparum gene detected by in situ hybridisation." Molecular and Biochemical Parasitology 72, no. 1-2 (June 1995): 193–201. http://dx.doi.org/10.1016/0166-6851(95)00073-a.

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36

Grief, C., R. Galler, L. M. C. Côrtes, and O. M. Barth. "Intracellular localisation of dengue-2 RNA in mosquito cell culture using electron microscopic in situ hybridisation." Archives of Virology 142, no. 12 (December 1997): 2347–57. http://dx.doi.org/10.1007/s007050050247.

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37

Vantarakis, A., D. Venieri, G. Komninou, and M. Papapetropoulou. "Hybridisation of F+ RNA coliphages detected in shellfish samples with oligonucleotide probes to assess the origin of microbiological pollution of shellfish." Water Science and Technology 54, no. 3 (August 1, 2006): 219–23. http://dx.doi.org/10.2166/wst.2006.472.

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Current measures for controlling the public health risks associated with bivalve molluscan shellfish consumption rely on the use of Escherichia coli to indicate the sanitary quality of shellfish harvesting areas. However, it has been demonstrated that E. coli is an inadequate indicator of the viral risk associated with shellfish. An alternative indicator, male-specific B+ coliphages, have been investigated as viral indicators of faecal contamination that may provide source-specific information for impacted environmental waters. This study compared the distribution of E. coli and F+ RNA bacteriophages in shellfish grown in harvesting areas of Greece and also examined the presence and proportions of the different subgroups of F+ RNA coliphages in shellfish. F+ RNA bacteriophages were present in shellfish at higher concentrations than E. coli. Elevated numbers of F+ RNA bacteriophages observed in the winter concur with the known increased viral risk associated with shellfish harvested at that time of year in Greece. The majority of F+ RNA coliphages detected in shellfish samples belonged to group IV which indicated the possible presence of animal faecal material in sample harvesting areas. Phages of groups II and III (human waste and human faecal material, respectively) were present at low levels. Finally, 8% of the phages hybridised were found to belong to group I. The presence of group IV showed seasonal distribution (more in winter, less in summer) whereas the other groups did not show any difference. Monitoring of F+ coliphage subgroups may indicate the presence and major sources of microbial inputs to surface waters; however, environmental effects on the relative occurrence of different groups need to be considered.
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38

Fitzpatrick, D. R., F. Denhez, P. Kondaiah, and R. J. Akhurst. "Differential expression of TGF beta isoforms in murine palatogenesis." Development 109, no. 3 (July 1, 1990): 585–95. http://dx.doi.org/10.1242/dev.109.3.585.

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We have studied the expression of genes encoding transforming growth factors (TGFs) beta 1, beta 2 and beta 3 during development of the secondary palate in the mouse from 11.5 to 15.5 days postcoitum using in situ hybridisation. The RNA detected at the earliest developmental stage is TGF beta 3, which is localised in the epithelial component of the vertical palatal shelf. This expression continues in the horizontal palatal shelf, predominantly in the medial edge epithelium, and is lost as the epithelial seam disrupts, soon after palatal shelf fusion. TGF beta 1 RNA is expressed with the same epithelial pattern as TGF beta 3, but is not detectable until the horizontal palatal shelf stage. TGF beta 2 RNA is localised to the palatal mesenchyme underlying the medial edge epithelia in the horizontal shelves and in the early postfusion palate. The temporal and spatial distribution of TGF beta 1, beta 2 and beta 3 RNAs in the developing palate, together with a knowledge of in vitro TGF beta biological activities, suggests an important role for TGF beta isoforms in this developmental process.
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39

Millan, F. A., F. Denhez, P. Kondaiah, and R. J. Akhurst. "Embryonic gene expression patterns of TGF beta 1, beta 2 and beta 3 suggest different developmental functions in vivo." Development 111, no. 1 (January 1, 1991): 131–43. http://dx.doi.org/10.1242/dev.111.1.131.

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We have compared the expression of the genes encoding transforming growth factors beta 1, beta 2 and beta 3 during mouse embryogenesis from 9.5 to 16.5 days p.c. using in situ hybridisation to cellular RNAs. Each gene has a different expression pattern, which gives some indication of possible biological function in vivo. All three genes appear to be involved in chondroossification, though each is expressed in a different cell type. Transcripts of each gene are also present in embryonic epithelia. Epithelial expression of TGF beta 1, beta 2 and beta 3 RNA is associated with regions of active morphogenesis involving epithelial-mesenchymal interactions. In addition, widespread epithelial expression of TGF beta 2 RNA can be correlated with epithelial differentiation per se. The localisation of TGF beta 2 RNA in neuronal tissue might also be correlated with differentiation. Finally both TGF beta 1 and beta 2 transcripts are seen in regions actively undergoing cardiac septation and valve formation, suggesting some interaction of these growth factors in this developmental process.
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40

Pradillon, F., A. Schmidt, J. Peplies, and N. Dubilier. "Species identification of marine invertebrate early stages by whole-larvae in situ hybridisation of 18S ribosomal RNA." Marine Ecology Progress Series 333 (March 12, 2007): 103–16. http://dx.doi.org/10.3354/meps333103.

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41

Gelmetti, Daniela, Valeria Grieco, Cesare Rossi, Lorenzo Capucci, and Antonio Lavazza. "Detection of rabbit haemorrhagic disease virus (RHDV) by in situ hybridisation with a digoxigenin labelled RNA probe." Journal of Virological Methods 72, no. 2 (June 1998): 219–26. http://dx.doi.org/10.1016/s0166-0934(98)00030-5.

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42

Baird, A., M. Wright, L. Mccarra, H. Thirstrup, A. Schønau, S. Cuffe, S. Finn, and S. Gray. "P2.09-16 Assessment of PD-L1 and CD8 Expression in Lung Cancer Using RNA in Situ Hybridisation." Journal of Thoracic Oncology 14, no. 10 (October 2019): S775. http://dx.doi.org/10.1016/j.jtho.2019.08.1665.

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43

Shahin, M., A. Gillessen, T. Pohle, C. Weber, D. Schuppan, H. Herbst, and W. Domschke. "Gastric ulcer healing in the rat: kinetics and localisation of de novo procollagen synthesis." Gut 41, no. 2 (August 1, 1997): 187–94. http://dx.doi.org/10.1136/gut.41.2.187.

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Background and aims—To gain further insight into the role of the extracellular matrix during healing of peptic ulcers, sequential changes of procollagen expression were studied over 30 days of ulcer healing.Materials and methods—Procollagens α1(I), α1(III), and α1(IV) RNA and their polypeptides were assessed in acetic acid induced rat gastric ulcers by in situ hybridisation and immunohistochemistry.Results—Three days after ulcer induction, intense hybridisation signals were obtained with all probes, with procollagen α1(I) showing the highest transcript levels. Procollagen gene expression remained elevated up to day 15, but was reduced to initial low levels on day 30. Immunohistochemical staining documented increased deposition of the three procollagen types parallel to their respective transcript levels, again with type I showing the earliest and the most prominent deposits. The highest procollagen transcript levels were found in the intact submucosa surrounding the ulcer margins, followed by the muscularis propria and the serosa, with the lamina propria exhibiting the lowest transcript levels.Conclusion—The procollagens studied are regulated differentially at the transcriptional and post-transcriptional levels. The early onset and long duration of procollagen expression as well as the involvement of all layers of the gastric wall points to their central structural and functional role in gastric ulcer healing.
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44

Chew, L.-J., V. Seah, D. Murphy, and D. Carter. "Anterior pituitary vasoactive intestinal peptide mRNA is colocalised with prolactin mRNA in hyperoestrogenised rats." Journal of Molecular Endocrinology 16, no. 3 (June 1996): 211–20. http://dx.doi.org/10.1677/jme.0.0160211.

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ABSTRACT It is well established that oestrogens can stimulate prolactin (PRL) secretion as well as the expression of the vasoactive intestinal peptide (VIP) gene whose product is also a potent PRL secretagogue. Previous evidence has supported both an autocrine and a paracrine role for pituitary VIP in PRL release in vitro; however, the cellular origin of VIP in pituitary tissue still remains poorly defined. In these studies, we have demonstrated by in situ hybridisation that VIP RNA is detected in the anterior pituitaries of chronically hyperoestrogenised rats, but not in those of untreated animals. Using a double-probe labelling procedure, VIP RNA has been shown to be present in a subpopulation of PRL-producing cells, while colocalisation of VIP and GH RNA was not observed. VIP gene expression in the rat anterior pituitary gland was characterised by the presence of two alternatively polyadenylated transcripts, 1·7 kb and 1·0 kb in size. We have generated a probe specific for the 1·7 kb transcript and double-labelling studies also showed definitive colocalisation with PRL mRNA. Our results demonstrating the presence of VIP RNA in PRL-producing cells thus suggest that VIP may play an autocrine role in PRL hypersecretion under conditions of oestrogen-induced hyperplasia.
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45

O'Flatharta, C. "Telomerase activity detected in oral lichen planus by RNA in situ hybridisation: not a marker for malignant transformation." Journal of Clinical Pathology 55, no. 8 (August 1, 2002): 602–7. http://dx.doi.org/10.1136/jcp.55.8.602.

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46

Nielsen, Poul, Henrik M. Pfundheller, and Jesper Wengel. "A novel class of conformationally restricted oligonucleotide analogues: synthesis of 2′,3′-bridged monomers and RNA-selective hybridisation." Chemical Communications, no. 9 (1997): 825–26. http://dx.doi.org/10.1039/a608231i.

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47

Fujimoto, Kenzo, Misaki Hashimoto, Nanami Watanabe, and Shigetaka Nakamura. "RNA fluorescence in situ hybridization hybridisation using photo-cross-linkable beacon probes containing pyranocarbazole in living E. coli." Bioorganic & Medicinal Chemistry Letters 29, no. 16 (August 2019): 2173–77. http://dx.doi.org/10.1016/j.bmcl.2019.06.051.

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48

Lin, Mingxuan, Peak Ling Lee, Lily Chiu, Constance Chua, Kenneth H. K. Ban, Adeline H. F. Lin, Zit Liang Chan, Tae-Hoon Chung, Benedict Yan, and Wee-Joo Chng. "Identification of novel fusion transcripts in multiple myeloma." Journal of Clinical Pathology 71, no. 8 (February 16, 2018): 708–12. http://dx.doi.org/10.1136/jclinpath-2017-204961.

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AimsMultiple myeloma (MM) is a heterogeneous disease characterised by genetically complex abnormalities. The classical mutational spectrum includes recurrent chromosomal aberrations and gene-level mutations. Recurrent translocations involving the IGH gene such as t(11;14), t(4;14) and t(14;16) are well known. However, the presence of complex genetic abnormalities raises the possibility that fusions other than the recurrent IGH translocations exist. We therefore employed a targeted RNA-sequencing panel to identify novel putative fusions in a local cohort of MM.MethodsTargeted RNA-sequencing was performed on 21 patient samples using the Illumina TruSight RNA Pan-Cancer Panel (comprising 1385 genes). Fusion calls were generated from the Illumina RNA-Sequencing Alignment software (V.1.0.0). These samples had conventional cytogenetic and fluorescence in situ hybridisation data for the common recurrent chromosomal abnormalities (t(11;14), t(4;14), t(14;16) and 17p13 deletion). The MMRF CoMMpass dataset was analysed using the TopHat-fusion pipeline.ResultsA total of 10 novel fusions were identified by the TruSight RNA Pan-Cancer Panel. Two of these fusions, HGF/CACNA2D1 and SMC3/MXI1, were validated by reverse transcription PCR and Sanger sequencing as they involve genes that may have biological relevance in MM genesis. Four of these (MAP2K4/MAP2K4P1) are likely to be spurious secondary to misalignment of reads to a pseudogene. One record of the HGF/CACNA2D1 fusion was identified from the MMRF CoMMpass dataset.ConclusionsThe identification of novel fusions offers insights into the biology of MM and might have clinical relevance. Further functional studies are required to determine the biological and clinical relevance of these novel fusions.
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Schacker, Ulrike, Hans-Peter Bermayer, Valerie Boehler, Doina Ionescu, Manuel Zapata, Hasan Grauer, and Kamal Rai. "Rapid HCV RNA detection by PCR followed by a new non-radioactive liquid hybridisation assay and comparison with RIBA." Journal of Medical Virology 46, no. 4 (August 1995): 304–9. http://dx.doi.org/10.1002/jmv.1890460403.

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50

Gorham, H., T. Sugino, J. Bolodeoku, K. Yoshida, S. Goodison, and D. Tarin. "Distribution of CD44 messenger RNA in archival paraffin wax embedded tumours and normal tissues viewed by in situ hybridisation." Molecular Pathology 49, no. 3 (June 1, 1996): M147—M150. http://dx.doi.org/10.1136/mp.49.3.m147.

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