Relevant bibliographies by topics / RNA hybridisation

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  2. Dissertations / Theses
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  5. Conference papers

Academic literature on the topic 'RNA hybridisation'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "RNA hybridisation"

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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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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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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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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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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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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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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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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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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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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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Dissertations / Theses on the topic "RNA hybridisation"

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Hoyle, Jane Anthea. "In situ hybridisation for the detection of viral nucleic acids." Thesis, University of St Andrews, 1991. http://hdl.handle.net/10023/13924.

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The technique of in situ hybridisation was optimised for the detection of viral RNA using radioactively-labelled single-stranded DNA and RNA probes, and applied to three areas of interest. Optimum hybridisation conditions were determined in vitro using cells infected with the single-stranded negative sense RNA paramyxoviruses. Transcription of RNA probes was the most rapid and efficient method of probe labelling, since electrophoretic purification was not required and large amounts of RNA were produced. However, their use for in situ hybridisation was problematic due to RNase contamination and low sensitivity. In contrast, DNA probes produced from M13 clones and oligonucleotide probes gave consistent hybridisation results and were preferred in subsequent studies for their ease of use, stability and sensitivity. The effect of virus-host interactions on the clearance of the paramyxovirus, SV5, in a mouse model was investigated by detection of viral RNA and protein in lung sections. Immunisation with purified SV5 proteins prior to infection provided protection against infection, indicated by a reduction in the level of viral RNA and protein, due to enhanced clearance of virus by primed T cells. X-irradiation of the host prior to infection resulted in prolonged or persistent infection in which RNA was detected up to 19 days post-infection. The potential of in situ hybridisation for detection of aetiological agents was demonstrated by investigation of the presence of measles virus in two chronic human diseases. Thus, measles virus RNA was detected in brain sections from a patient with subacute sclerosing panencephalitis and in the osteoclasts of bone sections from a patient with Paget's disease of bone. In situ hybridisation was used to analyse expression of the two immediate-early genes of herpesvirus saimiri, the 52K gene and the hinG gene. Differential expression was detected by hybridisation to mRNA using oligonucleotide probes, in productively-infected cells. The 52K gene was expressed asynchronously throughout the population in agreement with immunocytochemical detection of the 52K protein. In contrast, the hinG gene was expressed synchronously, with all cells showing similar levels of hybridisation, indicating a specific control mechanism for expression of the 52K gene, which differs from that of the hinG gene in requiring or being inhibited by additional factors. This may have relevance to the mechanism of establishment of latency in this virus.
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Birchall, Philip Simon. "Multicolour fluorescence in situ hybridisation to RNA in whole-mount Caenorhabditis elegans." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296668.

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Mir, Kalim U. "Novel approaches for the analysis of nucleic acids." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362107.

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Bulman, S. R. "Testing the effect of in planta RNA silencing on Plasmodiophora brassicae infection." Lincoln University, 2006. http://hdl.handle.net/10182/1856.

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In the late 1990s, a series of landmark publications described RNA interference (RNAi) and related RNA silencing phenomena in nematodes, plants and fungi. By manipulating RNA silencing, biologists have been able to create tools for specifically inactivating genes. In organisms from trypanosomes to insects, RNA silencing is now indispensible for studying gene function. RNA silencing has been used in a project aimed at systematically knocking out all genes in the model plant Arabidopsis thaliana. RNA silencing has a natural role in defending eukaryotic cells against virus replication. By assembling virus DNA sequences in a form that triggers RNA silencing, biologists have created plants resistant to specific viruses. In this study, we set out to test if a similar approach would protect plants against infection by the agriculturally important Brassica pathogen, Plasmodiophora brassicae. P. brassicae is an obligate intracellular biotroph, from the little studied eukaryotic supergroup, the Rhizaria. To identify the gene sequences that would be starting material for P. brassicae RNA silencing, new P. brassicae genes were gathered by cDNA cloning or genomic PCR-walking. Using suppression subtractive hybridisation (SSH) and oligo-capping cloning of full-length cDNAs, 76 new gene sequences were identified. A large proportion of the cDNAs were predicted to contain signal peptides for ER translocation. In addition to the new cDNA identified here, partial sequences for the P. brassicae actin and TPS genes were published by other researchers close to the beginning of this study. Using PCR-walking, full-length genomic DNA sequences from both genes were obtained. Later, genomic DNA sequences spanning or flanking a total of 24 P. brassicae genes were obtained. The P. brassicae genes were rich in typical eukaryotic spliceosomal introns. Transcription of P. brassicae genes also appears likely to begin from initiator elements rather than TATA-box-containing promoters. A segment of the P. brassicae actin gene was assembled in hairpin format and transformed into Arabidopsis thaliana. Observation of simultaneous knockdown of the GUS marker gene as well as detection of siRNAs indicated that the hpRNA sequences induced RNA silencing. However, inoculation of these plants with P. brassicae resulted in heavy club root infection. We were unable to detect decreases in actin gene expression in the infecting P. brassicae, at either early or late stages of infection. We conclude that, within the limits of the techniques used here, there is no evidence for induction of RNA silencing in P. brassicae by in planta produced siRNAs.
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Gage, Ewan. "The role of small RNAs in C4 photosynthesis." Thesis, University of Cambridge, 2013. https://www.repository.cam.ac.uk/handle/1810/244720.

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The C4 cycle represents a series of biochemical and anatomical modifications that are targeted to overcome the effects of photorespiration caused by the oxygenase capability of Ribulose Bisphosphate Carboxylase/Oxygenase (RuBisCO). The cycle has evolved independently in over 60 lineages, which suggests that recruitment of genes into the C4 cycle is a relatively easy process. However, the mechanisms by which the anatomy and cell-specificity of the components of the C4 cycle is achieved is poorly understood. Preliminary work in maize indicated several components of the C4 cycle may be targeted by microRNAs (miRNAs). To explore this, a library of sRNA sequences from mature leaf tissue of the model C4 species Cleome gynandra L. was generated and then searched against a list of expressed sequence tag sequences for candidate genes of the C4 cycle. To complement this, transgenic C. gynandra containing the viral p19 protein, which is capable of suppressing miRNA activity, were produced. A limited subset of the candidate C4 genes showed a high level of sRNA read alignment. In C. gynandra plants expressing p19 photosynthesis was compromised and transcripts of several genes (most notably RbcS and RCA) were upregulated. These data were complemented by examining the effect of illumination on developing C. gynandra cotyledons, and attempts to generate a hybrid between C. gynandra and the C3 C. hassleriana Chodat. RbcS also showed elevated abundance in etiolated cotyledons, although this rapidly declined after illumination. The remainder of the C4 genes profiled accumulated in etiolated tissue, but were upregulated within 6 hours of illumination. Therefore, this study has illustrated that miRNA activity may play a role in maintaining the C4 photosynthetic cycle at optimum efficiency, although it has not been possible to identify at which point(s) this regulation is applied. Secondly, RbcS appears to be subject to multiple regulatory mechanisms in C. gynandra, and it is possible that miRNAs have a role in negatively regulating expression of RbcS.
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Davey, John William. "Identification of b-catenin and other RNAs in developing thalamic axons." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/4011.

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This thesis provides evidence for the presence of multiple RNAs in the axons and growth cones of developing thalamic cells, particularly the mRNA for the cell adhesion and Wnt-signalling-related molecule b-catenin. After many decades of effort, mRNAs have been shown to be present in the axons of many different systems in recent years. Furthermore, these mRNAs have been shown to be locally translated at the growth cone, and this local translation is required for axons to turn in response to multiple guidance cues. As studies accumulate, it is becoming clear that different axonal systems contain different complements of mRNAs and have different requirements for local translation. One axonal system which has not been investigated to date is the thalamocortical tract. The nuclei of the thalamus are connected to the areas of the cortex via bundles of axons which travel from the thalamus to the cortex via the ventral telencephalon during embyronic development. These axons make a number of turns and are guided by many cues and other axonal tracts before innervating their cortical target. In this thesis, a quantitative real-time polymerase chain reaction (qRT-PCR) approach is developed to isolate multiple mRNAs from developing thalamic axons in vitro, including b-catenin mRNA, b-actin mRNA, 18S ribosomal RNA and ten other mRNAs. The method used should be suitable for use with other axonal systems and also for testing the effect of guidance cues on mRNA expression in axons. The qRT-PCR results for b-catenin, b-actin and 18S have been validated using in situ hybridisation. Analysis of in situ hybridisation results indicates that b-catenin and 18S, but not b-actin, are upregulated in the growth cone compared to the axon. As b-catenin has been shown to be involved in axon guidance via Slit and ephrin guidance cues in other axonal systems, and these guidance cues act upon thalamocortical axons, the identification of b-catenin mRNA in thalamic axons is an important step towards a full understanding of the thalamocortical system. The results presented here indicate that local protein synthesis is likely to occur in thalamic axons as it does in other axonal systems, and that local translation is likely to be important for thalamic axonal responses to guidance cues and other axonal tracts.
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Peterková, Kristýna. "Lokalizace a kvantifikace mRNA kódující trávící peptidázy motolice Fascioloides magna." Master's thesis, 2019. http://www.nusl.cz/ntk/nusl-397285.

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Trematode peptidases are important molecules responsible for biocatalysis in many basal biological processes and are crucial in host-parasite interactions. Therefore, these enzymes are intensively studied in order to characterize their biological functions and to use them as potential diagnostic or therapeutic targets. Lately, investigation of transcriptome and secretome revealed, that adult Fascioloides magna (giant liver fluke) expresses and secretes a variety of peptidases. Thus, this thesis focuses on three newly identified enzymes: cathepsin L (FmCL), cathepsin B (FmCB) and cathepsin D (FmCD). In other trematode species, these cathepsins are being linked mainly with the digestion of host blood. We applied quantitative PCR (qPCR) to investigate relative expression levels of the three enzymes among three developmental stages - egg, miracidium and adult. It was revealed that all cathepsins have the highest expression in adult flukes in comparison to eggs and miracidia. We also localized the place of transcription of FmCL, FmCB and FmCD in adult fluke using RNA in situ hybridization. All of the peptidases were detected in gastrodermis, and in addition, they were localized in the reproductive system. The latter surprising finding is suggesting that these enzymes might have multiple functions in adult F....
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Books on the topic "RNA hybridisation"

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Bysouth, James Peter Norman. Physical mapping of 45S and 5S rDNA repetitive sequences to mitotic chromosomes of Brassica species by fluorescence in situ hybridisation. Birmingham: University of Birmingham, 2003.

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Hadidi, Ahmed, Ricardo Flores, John Randles, and Joseph Semancik. Viroids. CSIRO Publishing, 2003. http://dx.doi.org/10.1071/9780643069855.

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This comprehensive volume presents indispensable and up-to-date information on viroids and viroid diseases. It provides a single source of information on the properties of viroids, the economic impact of viroid diseases, and methods for their detection and control. It examines the diseases associated with different plant species, the geographic distribution and epidemiology of viroids, diseases of possible viroid etiology, and the future applications of viroids. Viroids examines the biology of viroids, molecular characteristics, localization and movement, replication, pathogenesis, viroids and gene silencing, classification, viroid-like satellite RNAs, detection of viroids using bioamplification hosts, biological indexing, polyacrylamide gel electrophoresis, molecular hybridisation and polymerase chain reaction. The book looks at the geographical distribution and epidemiology of viroids in North America, Australasia, China, Japan, Europe, the Middle East, Africa, South America, and at the global level. It covers the control of viroids including quarantine of imported germplasm, availability of viroid-tested propagation materials, thermotherapy, tissue culture, and other conventional strategies as well as biotechnological control approaches. Special topics such as ribozyme reaction of viroids and economic advantages of viroid infection are also included. Other chapters summarise the current state of knowledge concerning viroid diseases of the crop in question and aspects of the natural history of viroids in horticulture. Among the crops covered are potato, tomato, tobacco, cucumber, pome fruits, stone fruits, avocado, citrus, grapevines, hop, chrysanthemum, coleus, columnea, and coconut palm. The four eminent editors of this watershed volume have assembled an international group of more than 70 scientists who have substantial experience with viroids and viroid diseases. They have produced a cohesive and comprehensive work that can be used by students, researchers, extension agents, and regulators. It may also be of a great value to science managers, policy makers, and industries in formulating policies and products to obtain viroid-free plants and control viroid diseases. The information on plant quarantine and certification programs will help anyone concerned with the safe movement of plant material across international boundaries or within a single country.
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Book chapters on the topic "RNA hybridisation"

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Rouquette, Jacques, Karl-Henning Kalland, and Stanislav Fakan. "Visualisation of RNA by Electron Microscopic In Situ Hybridisation." In The Nucleus, 403–13. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-60327-461-6_22.

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Fleming, A. J. "Localization of RNA Transcripts in Plant Tissue by In Situ Hybridisation." In Gene Transfer to Plants, 273–85. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/978-3-642-79247-2_27.

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Giaid, A., S. J. Gibson, J. H. Steel, P. Facer, and J. M. Polak. "The use of complementary RNA probes for the identification and localisation of peptide messenger RNA in the diffuse neuroendocrine system." In In Situ Hybridisation, 43–68. Cambridge University Press, 1990. http://dx.doi.org/10.1017/cbo9780511629051.004.

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Johnson, John L. "2 DNA Reassociation and RNA Hybridisation of Bacterial Nucleic Acids." In Methods in Microbiology, 33–74. Elsevier, 1985. http://dx.doi.org/10.1016/s0580-9517(08)70471-9.

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TANIMOTO, EUGENE Y., and THOMAS L. ROST. "Non-radioactive In Situ RNA Hybridisation Using Digoxigenin and an Application for Co-localisation Studies with Radioisotopes." In Methods in Plant Biochemistry, 141–58. Elsevier, 1993. http://dx.doi.org/10.1016/b978-0-12-461020-0.50013-5.

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Ibrahim, Mohamad Mokhtar, Zulkifly Jemaat, and Abdurahman Hamid Nour. "Review on Microbial Analysis Tools in POME treatment." In Handbook of Research on Resource Management for Pollution and Waste Treatment, 220–40. IGI Global, 2020. http://dx.doi.org/10.4018/978-1-7998-0369-0.ch010.

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Palm oil mill effluent (POME) is one of the major sources of water pollution in Malaysia. POME is produced in large volumes by many palm oil mills and has acidic pH and high concentrations of COD, BOD, and suspended solids, which have adverse effect to the environment. Currently, the technology to treat POME is either physical, chemical, or biological. About 80% of palm oil mills treat their POME by using biological method. Recent studies have indicated that understanding the microbial community structure is of great importance to improve and control the biological treatment performance. Currently, the most popular molecular biology tools for microorganism community analysis are fluorescence in situ hybridisation (FISH), cloning of 16S rDNA, and denaturing gradient gel electrophoresis (DGGE). This chapter aims to review the current and ongoing treatments of POME (mainly anaerobic, aerobic, physicochemical, and membrane separation) and discuss the potential of using the molecular biology techniques in POME treatment. The importance and effectiveness of the microbiology tools are also discussed. The ability to monitor microorganisms and understand their ecology is essential to effectively control the startup and operation of biological treatment system in treating POME and eventually producing effluent of acceptable quality.
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Conference papers on the topic "RNA hybridisation"

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Králíková, Šárka, Miloš Buděšínský, Radek Liboska, Ondřej Páv, and Ivan Rosenberg. "2',5'-Linked oligo-3'-deoxynucleotide chimeras with chiral α-hydroxyphosphonate internucleotide linkage: Improvement of hybridisation selectivity toward RNA?" In XIIIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2005. http://dx.doi.org/10.1135/css200507421.

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