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Relevant bibliographies by topics / RNA labeling

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Academic literature on the topic 'RNA labeling'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 February 2022

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Journal articles on the topic "RNA labeling"

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Igloi, Gabor L. "Nonradioactive Labeling of RNA." Analytical Biochemistry 233, no. 1 (1996): 124–29. http://dx.doi.org/10.1006/abio.1996.0016.

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Meng, Liying, Yilan Guo, Qi Tang, Rongbing Huang, Yuchen Xie, and Xing Chen. "Metabolic RNA labeling for probing RNA dynamics in bacteria." Nucleic Acids Research 48, no. 22 (2020): 12566–76. http://dx.doi.org/10.1093/nar/gkaa1111.

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Abstract Metabolic labeling of RNAs with noncanonical nucleosides that are chemically active, followed by chemoselective conjugation with imaging probes or enrichment tags, has emerged as a powerful method for studying RNA transcription and degradation in eukaryotes. However, metabolic RNA labeling is not applicable for prokaryotes, in which the complexity and distinctness of gene regulation largely remain to be explored. Here, we report 2′-deoxy-2′-azidoguanosine (AzG) as a noncanonical nucleoside compatible with metabolic labeling of bacterial RNAs. With AzG, we develop AIR-seq (azidonucleoside-incorporated RNA sequencing), which enables genome-wide analysis of transcription upon heat stress in Escherichia coli. Furthermore, AIR-seq coupled with pulse-chase labeling allows for global analysis of bacterial RNA degradation. Finally, we demonstrate that RNAs of mouse gut microbiotas can be metabolically labeled with AzG in living animals. The AzG-enabled metabolic RNA labeling should find broad applications in studying RNA biology in various bacterial species.

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Paredes, Eduardo, Molly Evans, and Subha R. Das. "RNA labeling, conjugation and ligation." Methods 54, no. 2 (2011): 251–59. http://dx.doi.org/10.1016/j.ymeth.2011.02.008.

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Baum, Dana A, and Scott K Silverman. "Deoxyribozyme-Catalyzed Labeling of RNA." Angewandte Chemie International Edition 46, no. 19 (2007): 3502–4. http://dx.doi.org/10.1002/anie.200700357.

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Baum, Dana A, and Scott K Silverman. "Deoxyribozyme-Catalyzed Labeling of RNA." Angewandte Chemie 119, no. 19 (2007): 3572–74. http://dx.doi.org/10.1002/ange.200700357.

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Nilsen, Timothy W. "Site-Specific Labeling of RNA." Cold Spring Harbor Protocols 2013, no. 3 (2013): pdb.prot072918. http://dx.doi.org/10.1101/pdb.prot072918.

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Monnot, V., C. Tora, S. Lopez, L. Menou, and A. Laayoun. "LABELING DURING CLEAVAGE (LDC), A NEW LABELING APPROACH FOR RNA." Nucleosides, Nucleotides and Nucleic Acids 20, no. 4-7 (2001): 1177–79. http://dx.doi.org/10.1081/ncn-100002514.

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Hilger, Christoph S., Michael C. Willis, Mark Wolters, and Wolfgang A. Pieken. "Tc-99m-Labeling of Modified RNA." Nucleosides and Nucleotides 18, no. 6-7 (1999): 1479–81. http://dx.doi.org/10.1080/07328319908044759.

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Koubek, Jiří, Yet-Ran Chen, Richard Ping Cheng, and Joseph Jen-Tse Huang. "Nonorthogonal tRNAcysAmberfor protein and nascent chain labeling." RNA 21, no. 9 (2015): 1672–82. http://dx.doi.org/10.1261/rna.051805.115.

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Betteridge, T., H. Liu, H. Gamper, S. Kirillov, B. S. Cooperman, and Y. M. Hou. "Fluorescent labeling of tRNAs for dynamics experiments." RNA 13, no. 9 (2007): 1594–601. http://dx.doi.org/10.1261/rna.475407.

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Dissertations / Theses on the topic "RNA labeling"

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Kosmidis, Tilemachos D. "Development of site-specific RNA labeling strategies to probe alternative RNA splicing." Thesis, University of Strathclyde, 2016. http://digitool.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=28492.

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The objective of this project was to develop a method for the labeling of RNA at specific locations using non-natural base pairs. This thesis details the efforts made towards this objective through the development of a modular synthetic platform for an expanded genetic alphabet and its evaluation using transcriptional assays. Chapter 1 introduces the structure and function of RNA, followed by a description of RNA processing events with emphasis placed on alternative RNA splicing and how aberrations in splicing can lead to disease. The concept of RNA labeling follows and examples from the literature are presented along with challenges associated with these techniques to elucidate key mechanistic splicing concepts. The concept of orthogonal base pairs is then introduced along with representative examples from the literature. The application of this concept in RNA labeling is then presented along with key examples from the literature. The limitations of these methods are highlighted followed by the specific aims behind this project. Chapter 2 presents the efforts made towards the development of a modular synthetic route for the synthesis of C-ribonucleosides, with a Heck reaction as the key step. Specifically, its application in the synthesis of the Z ribonucleoside developed by the Benner group is investigated. The chapter starts with re-introducing the Z/P pair developed by the Benner group and highlighting the reasons that placed it as our chosen base pair for RNA labeling. The synthesis of C-deoxyribonucleosides utilizing the Heck reaction is presented, followed by the challenges associated with C-ribonucleoside synthesis. The syntheses of the alkene and halide coupling partners of the proposed Heck reaction are firstly presented. Investigations on the Heck reaction are then presented, followed by investigations on the transformation of nitro group in Z to moieties suitable for further derivatization. The key outcome of this work is that a synthetic route involving the Heck reaction for the synthesis of C-ribonucleosidesis not feasible. This is due to long reaction times required to drive the Heck reaction to completion and difficulties encountered with elucidation of its stereselectivity. Furthermore, PCR experiments conducted by our collaborators within the Eperon group at the University of Leicester revealed significant misincorporation of Z opposite G. Consequently, a change in strategy towards the use of nucleotides developed by the Hirao group was made. Chapter 3 describes the development of a robust synthetic route for the synthesis of a library of C6-functionalized 2-aminopurines as potential candidates for an expanded genetic alphabet in RNA. The s/Pa pair developed by the Hirao group is re-introduced. The installation of an alkyne functionality on the guanosine scaffold via a Sonogashira reaction is described,followed by investigations of [3+2] cycloaddition reactions between the alkyne and azides or aldehyde oximes. Finally, the development of a novel Suzuki-Miyaura protocol for the direct installation of heterocyclic substituents on the guanosine scaffold is also reported. Key outcomes of this chapter are the following. A robust method was developed for the expedient synthesis of C6-functionalized s analogues. This method enabled access to various classes of analogues in three or six steps,including triazoles, isoxazoles, thiophenes and pyrazoles. Attempts to install an azide moiety to the guanosine were partly successful, but the strategy was abanonded due to reaction reproducibility issues. In addition, a C-H activation strategy was not successful on installing an oxazole moiety. Chapter 4 details the efforts towards the synthesis of nucleoside triphosphates based on the s analogues described in Chapter 3. This chapter will begin with the presentation of the most common strategies for the synthesis of nucleoside triphosphates. Initial attempts to synthesize triphosphates by global deprotection of nucleosides synthesized in Chapter 3 are next described. Attempts to install a silyl ether group in the 5’-OH are presented, followed by the installation of acetates on the 2’/3’ hydroxyls and attempts to protect the exocyclic amine on guanosine as the phenoxyacetamide. The installation of a pyrazole moiety via Suzuki-Miyauraprotocol using the corresponding boronic acid pinacol ester described in Chapter 3 is presented. The installation of an alkyne moiety is also described and the synthesis of an isoxazole analogue using this alkyne precursor will follow. The chapter will end with the presentation of the synthesis of pyrazole and isoxazole triphosphate analogues. The key outcome of this chapter is that employing different protecting groups on the 5’ and the 2’/3’ hydroxyls enabled the synthesis of pure triphosphates. Chapter 5 presents the evaluation of the nucleotide triphosphates synthesized in Chapter 4 regarding their transcriptional efficiency. Key outcome of this work are that high concentrations ( > 0.5 mM mM) are needed in order to observe significant incorporation of the analogues, compared to s, which needs 0.1 mM for efficient incorporation. At high concentration, the isoxazole moiety exhibits better incorporation efficiency compared to the pyrazole analogue. Furthermore, the addition of 0.5 mM of MnCl2 resulted in increased incorporation efficiency of the pyrazole analogue, while s and the isoxazole exhibited reduced efficiency under these conditions.

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Tomkuvienė, Miglė. "Methyltransferases as tools for sequence-specific labeling of RNA and DNA." Doctoral thesis, Lithuanian Academic Libraries Network (LABT), 2013. http://vddb.library.lt/obj/LT-eLABa-0001:E.02~2013~D_20131209_091531-59976.

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Investigation of RNA and DNA function often requires sequence-specific incorporation of various reporter and affinity probes. This can be achieved using AdoMet-dependent methyltransferases (MTases) as they can be active with synthetic AdoMet analogues equipped with transferable chains larger than the methyl group. These chains usually carry reactive groups that can be further chemically appended with required reporters. For this, azide-alkyne 1,3-cycloaddition (AAC), also called “click”, reaction is particularly attractive. This work shows that the HhaI cytosine-5 DNA MTase (variant Q82A/Y254S/N204A) catalyzes efficient sequence-specific transfer of hex-2-ynyl side chains containing terminal alkyne or azide groups from synthetic cofactor analogues to DNA. Both the enzymatic transfer and subsequent “click” coupling of a fluorophore can be performed even in cell lysates. For RNA labeling, the activity of an archaeal RNA 2‘-O-MTase C/D ribonucleoprotein complex (RNP) with synthetic cofactors was investigated. It was shown that synthetically reprogrammed guide RNA sequences can be used to direct the C/D RNP-dependent transfer of a prop-2-ynyl group to predetermined nucleotides in substrate RNAs. Followed by AAC this can be used for programmable sequence-specific labeling of a variety of RNA substrates in vitro. These new possibilities for specific labeling of nucleic acids can be adopted in biochemistry, biomedical, nanotechnology, etc. research.<br>Tiriant DNR ir RNR, neretai svarbu prijungti įvairius reporterinius ar giminingumo žymenis griežtai apibrėžtose (sekos) vietose – t.y. specifiškai. Tam galima pasitelkti fermentus metiltransferazes (MTazes). Natūraliai jos naudoja kofaktorių AdoMet, tačiau gali būti aktyvios ir su sintetiniais jo analogais, turinčiais ilgesnes nei metil- pernešamas grandines. Jei šios grandinės turi galines funkcines grupes, prie jų vėliau cheminių reakcijų pagalba galima prijungti norimus žymenis. Tam itin patogi azidų-alkinų cikloprijungimo (AAC), dar vadinama „click“, reakcija. Šiame darbe parodyta, kad DNR citozino-5 MTazė HhaI (variantas Q82A/Y254S/N204A) efektyviai katalizuoja sekai specifinę heks-2-inil- grandinių, turinčių galines alkinil- arba azido- grupes, pernašą nuo sintetinių kofaktorių ant DNR. Naudojant šią MTazės-kofaktorių sistemą bei AAC, visą specifinio DNR žymėjimo procesą galima atlikti netgi ląstelių lizate. RNR žymėjimui ištirtas archėjų RNR 2‘-O-MTazės C/D ribonukleoproteininio komplekso aktyvumas su sintetiniais kofaktoriais. Parodyta galimybė sintetiškai keičiant kreipiančiąją RNR, prop-2-inilgrupės pernašą nukreipti į norimas įvairių substratinių RNR sekos vietas ir po to AAC reakcijos pagalba prijungti fluoroforą. Taigi, sukurtas naujas molekulinis įrankis, leidžiantis be suvaržymų pasirinkti norimą pažymėti RNR seką. Šios naujos specifinio nukleorūgščių žymėjimo galimybės gali būti pritaikytos biochemijos, biomedicinos, nanotechnologijų ir kitose tyrimų srityse... [toliau žr. visą tekstą]

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Cooke, L. A. "Preparation and evaluation of novel phosphoramidites for labeling DNA and RNA." Thesis, Queen's University Belfast, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.557306.

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Phosphoramidite derivatives of a nucleoside analogue bearing photoswitchable ortho-, meta- and para azobenzene moieties were prepared and used to incorporate the azobenzene groups into DNA.8mers. The photochemical E-Z isomerisation of the azobenzene-appended 8mers was investigated by UV/vis spectroscopy and RP-HPLC. In order to investigate the stabilities of the irradiated-8mers towards thermal Z - E isomerisation, Arrhenius and Eyring parameters for the photoisomerisation were determined. The meta-isomer was found to be the most thermally stable. An initial investigation into the stability of duplexes containing a para-azobenzene-modified 8mer was carried out using melting studies. The duplex-forming activity of the oligonucleotide was modulated by the E- Z photoisomerisation of the para-azobenzene residue. A divergent methodology for the preparation of a novel structural class of photoswitchable oligonucleotide has been described. A novel anthracene methyl phosphoramidite derivative suitable for the preparation of end- labelled oligonucleotides under solid-phase directed-Arbusov conditions was prepared and its reactivity investigated. A comparison of the utility of this anthracene methyl phosphorarnidite with a related benzyl phosphorarnidite in a model reaction with the 5'-hydroxyl of support-bound decathymidylate was made. Directed Michaelis-Arbusov reactions of the putative phosphite triester intermediates with primary and secondary amines in the presence of 0.01 M iodine gave the corresponding phosphoramidate diesters in high yields. This reactivity was also demonstrated using commercially available phosphoramidites for the preparation of inter-nucleotide phosphoramidates bearing terminal primary amines. Derivatisation of these primary amine-functionalised oligomers was accomplished in solution-phase following treatment with the meta-azobenzene NHS ester.

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Zalma, Carre Alison. "Monitoring folding pathways for large RNAs using site-directed spin-labeling techniques." Thesis, Texas A&M University, 2005. http://hdl.handle.net/1969.1/4904.

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The function of biomolecules is very sensitive to structure. Folding in proteins and nucleic acids is a hierarchical process progressing from primary to secondary, then tertiary, and finally, quaternary structures. RNA in its folded form performs a variety of biological activities. Obtaining intramolecular distance measurements makes it possible to generate structural models along the folding pathway that may be related to the overall function of the molecule. Distances can be measured by Site-Directed Spin-Labeling (SDSL), in which nitroxyl spin-label probes are attached and observed by EPR spectroscopy. Spin-labels can provide information concerning structure and conformational changes because they are particularly sensitive to molecular motion and interspin distances. Continuous-wave EPR spectroscopy has been commonly applied to detect and monitor nitroxide spin-label probes within biological systems. A previous published SDSL study from this laboratory investigated a 10-mer RNA duplex model system with spin-label probe succinimdyl-2,2,5,5-tetramethyl-3-pyrroline-1-oxyl-carboxylate; however, an increased spin-labeling efficiency was observed with an isocyanate derivative of tetramethylpiperidyl-N-oxy (TEMPO). In this thesis, a 4-isocyano TEMPO spin-label probe replaced the previously used succinimdyl-2,2,5,5-tetramethyl-3-pyrroline-1-oxyl-carboxylate in 10-mer SDSL studies. The influence of labeling with the 4-iscocyano TEMPO spin-label in a 10-mer RNA model system was investigated with thermal denaturation, Matrix Assisted Laser Desorption Time of Flight Mass Spectrometry (MALDI-TOF-MS), Electron Paramagnetic Resonance (EPR) spectroscopy, and reverse phase high performance liquid chromatography (RP-HPLC). In the 10-mer RNA duplex model system a 4-isocyano TEMPO spin-label is individually attached to one strand and two strands are annealed to measure distances. This methodology is limited to systems in which two oligonucleotides are annealed together. To circumvent this limitation and also to explore single-strand dynamics a new methodology was implemented, double spin-labeling. Double spin-labeled single-stranded RNA was investigated as a single-strand and within a duplex via MALDI-TOF-MS, EPR spectroscopy and RP-HPLC. A double spin-labeling strategy in this work will be applicable to large complex RNAs like Group I intron of Tetrahymena thermophilia.

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Ghaem, Maghami Mohammad [Verfasser]. "Development, characterization, and application of RNA catalysts for in situ labeling of target RNA molecules / Mohammad Ghaem Maghami." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2020. http://d-nb.info/1215906196/34.

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Tserovski, Lyudmil Aleksandrov [Verfasser]. "Chemical labeling and next-generation sequencing for detection of RNA-modifications / Lyudmil Aleksandrov Tserovski." Mainz : Universitätsbibliothek Mainz, 2017. http://d-nb.info/1123042713/34.

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Driscoll, Harry. "Improving the sensitivity of aptamer-driven fluorescent protein complementation for RNA labeling and detection." Thesis, Boston University, 2013. https://hdl.handle.net/2144/21147.

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In eukaryotic cells, some mRNAs localize to distinct areas of the cell where RNA is translated and the encoded protein is specifically localized. Recent studies have suggested that even though prokaryotic cells lack internal compartmentalization, different RNAs can localize to distinct regions of the bacterial cell. Our lab is developing methods for labeling and detecting RNA with the goal of determining localization of endogenous RNAs within single cells. We currently employ an eIF4a protein-specific aptamer for RNA labeling using one of two methods. (1) Target RNA is tagged with the aptamer sequence at the 3' end and the aptamer triggers protein complementation of two fusion proteins, each containing split EGFP and split eIF4A proteins. (2) Two RNA probes, each containing a half of a split eIF4a-specific aptamer and an antisense sequence complementary to the target RNA, bind the unmodified transcript through complementary interactions. This binding brings the two fragments of the split aptamer in close proximity and allows proper folding of a split aptamer. A fluorescent signal is generated by the aptamer-driven reassociation of the fusion proteins. In this work, we investigate the sensitivity of the first method for detecting transcripts expressed from their natural chromosomal loci, and describe attempts to increase the sensitivity of the method by using multiple aptamer tagging. We also present results suggesting that the second method, combining protein complementation and split aptamer approach, provides high sensitivity enabling detection of endogenous bacterial RNAs expressed at low level.

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Hesse, Marlen. "Chemo-enzymatische Werkzeuge zur Untersuchung von nicht-codierender RNA." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät, 2017. http://dx.doi.org/10.18452/17740.

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Nicht-codierende RNAs sind ein bedeutender Bestandteil genregulatorischer Prozesse. Ihre Fehlregulierung wird mit zellulärer Dysfunktion und der Entstehung von Krankheiten in Zusammenhang gebracht. Ziel dieser Arbeit war die Entwicklung verschiedener Testsysteme zur Untersuchung nicht codierender RNAs mit dem Schwerpunkt microRNA (miRNA), precursor miRNA (pre-miRNA) und circular RNA (circRNA). Für eine Zyklisierung und Funktionalisierung von circRNA mittels Cu-katalysierter Click-Chemie zur Identifizierung zellulärer Interaktionspartner und zugehöriger Wirkmechanismen wurden die Termini linearer RNA-Template modifiziert. Mit Hilfe enzymatischer Techniken wie Transkription und Ligation konnte in vitro die Inkorporation Azid- und Alkin-funktionalisierter Nukleotid-Bausteine am 5‘- und 3‘-Terminus gezeigt werden. Zur Untersuchung der miRNA-Reifung in cellulo wurde die pre-miRNA-134 unter Verwendung chemo-enzymatischer Methoden mit einem Fluorophor/Quencher-Paar an den Termini ausgestattet. Durch intrazelluläre Reifung der gelabelten pre-miRNA mit einhergehender Fluoreszenzfreisetzung sollte die Visualisierung und damit die Lokalisierung des miRNA-Reifungsortes innerhalb von Neuronen realisiert werden. Zudem gelang die Entwicklung eines auf branched rolling-circle amplification (BRCA) basierenden Argonaute2(Ago2)-vermittelten Spaltungsassays. Ein Enzymkomplex aus rekombinantem, humanem Ago2 und der miRNA miR 122, genannt minimal RISC, wurde dabei zur Substrat-Spaltung eingesetzt. Zur Etablierung des BRCA-basierenden Ago2-vermittelten Spaltungsassays als Screening-Tool für die Identifizierung potentieller Inhibitoren der mRNA-Spaltung wurden exemplarisch sechs Testsubstanzen aus der Gruppe der Aminoglykoside untersucht. Der BRCA-basierende Ago2-vermittelte Spaltungsassay stellte eine einfache und zuverlässige Detektionsmethode dar, der die Untersuchung einer größeren Probenzahl mit geringem Aufwand und ohne Verwendung von fluorogen gelabeltem Substrat ermöglichte.<br>Non-coding RNAs are an important factor in gene regulation in which their deregulation is associated with cellular dysfunction and disease. Here, the development of different test systems for the investigation of non-coding RNAs, namely microRNA (miRNA), precursor miRNA (pre-miRNA), and circular RNA (circRNA), was on focus. In order to circularize and functionalize circRNA with the purpose of identifying cellular interaction partners and possible mechanisms of action, 5‘- and 3‘-terminal modifications were added to a linear RNA template. This was accomplished by using azide- and alkyne-functionalized nucleotides which were incorporated by enzymatic approaches like transcription and ligation to be followed by Cu-catalyzed click chemistry for circularization. For investigating miRNA maturation in neuronal cells, pre-miR-134 was modified by chemo-enzymatic approach with fluorophore and quencher at its 5‘ and 3‘ ends, respectively. Intracellular maturation of labeled pre-miRNA would produce a fluorescent signal upon cleavage, thus enabling visualization and localization of miRNA maturation in neuronal cells. Furthermore, the development of Ago2-mediated mRNA cleavage assay based on branched rolling-circle amplification (BRCA) was accomplished. A complex of recombinant human Ago2 and miRNA miR-122, called minimal RISC, was used for substrate cleavage. To establish this assay as adequate screening method for identifying potential inhibitors of mRNA cleavage, a group of six aminoglycosides was tested. The BRCA-based Ago2-mediated cleavage assay showed to be a simple and reliable detection method and screening tool for small molecule binders with little effort and without fluorescent labeling of substrate.

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Li, Siwei. "High Throughput Automated Comparative Analysis of RNAs Using Isotope Labeling and LC-MS/MS." University of Cincinnati / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1384427990.

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Kim, Nak-Kyoon. "Metal dependent structure, dynamics, and function in RNA measured by site-directed spin labeling and EPR spectroscopy." Diss., Texas A&M University, 2005. http://hdl.handle.net/1969.1/4900.

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The structure and function of RNA molecules are dependent on RNA-metal ion interactions in both diffusive and direct ways. Structural information for RNA has been obtained using various biophysical and biochemical methods. In this study, using site-directed spin labeling (SDSL) and EPR spectroscopy, distances in RNA duplexes, TAR RNA, and the hammerhead ribozyme have been measured to investigate RNA structures. Kinetic measurements have been performed in the extended hammerhead ribozyme to correlate the catalytic function with metal dependent ribozyme folding. As a basic model system for distance measurements, inter-spin distances in RNA duplexes with spin labels at various positions are measured using SDSL with continuous EPR and a Fourier deconvolution method. Divalent metal-ion dependent TAR RNA folding from bent to extended conformers is monitored by measuring inter-spin distances near the bulge region. In order to investigate a proposed loop-loop interaction in the extended hammerhead ribozyme which significantly enhances the ribozyme activity, distance measurements, dynamics studies, and kinetics measurements have been performed. We have introduced PELDOR long-distance measurements in order to investigate metal dependent folding of the hammerhead ribozyme. The dynamics of the spin labels attached to the hammerhead ribozyme with increasing mono- and divalent metal ion concentrations are monitored using CW EPR spectroscopy at room temperature. EPR data show that a loop-loop interaction occurs near the U1.6 nucleotide, and that in 0.1 M NaCl the docking occurs at submillimolar Mg2+ concentrations ([Mg2+]1/2, docking = ~ 0.7 mM). Kinetics measurements show that the hammerhead ribozyme requires high concentration of Mg2+ for the maximum cleavage activity ([Mg2+]1/2, cleavage = ~ 90 mM).

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Books on the topic "RNA labeling"

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1949-, Müller S. C., ed. Synthetic peptides as antigens. Elsevier, 1999.

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Sabharwal, Nikant, Parthiban Arumugam, and Andrew Kelion. Radionuclide ventriculography. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198759942.003.0005.

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Radionuclide ventriculography (RNV) was the first reliable non-invasive method of assessing left ventricular (LV) function, and established nuclear cardiology as a clinical discipline. The subsequent development of other imaging modalities, particularly echocardiography, has led to a sharp decline in the number of studies performed, but RNV still has a role in situations where reproducible serial assessments of LV ejection fraction are required. Equilibrium RNV (ERNV) is the most straightforward and commonly performed style of RNV, and this chapter therefore focuses on ERNV, covering blood-pool labelling, principles of electrocardiogram (ECG) gating, acquisition, processing and interpretation, and clinical value in relation to ERNV. A section on first-pass radionuclide ventriculography is also included.

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Book chapters on the topic "RNA labeling"

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Rinaldi, Arlie J., Krishna C. Suddala, and Nils G. Walter. "Native Purification and Labeling of RNA for Single Molecule Fluorescence Studies." In RNA-RNA Interactions. Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1896-6_6.

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Smolina, Irina, and Natalia Broude. "A Universal Method for Labeling Native RNA in Live Bacterial Cells." In RNA Scaffolds. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2730-2_7.

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Zhang, Xiaojun, and Peter Z. Qin. "Studying RNA Folding Using Site-Directed Spin Labeling." In Biophysics of RNA Folding. Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-4954-6_5.

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Peña, Eduardo, Manfred Heinlein, and Adrian Sambade. "In Vivo RNA Labeling Using MS2." In Methods in Molecular Biology. Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1523-1_21.

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Reginsson, Gunnar W., and Olav Schiemann. "Spin Labeling of DNA and RNA." In Encyclopedia of Biophysics. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_586.

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Igarashi, Peter. "Radioactive Labeling of DNA and RNA Probes." In Techniques in Molecular Medicine. Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/978-3-642-59811-1_9.

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Zearfoss, N. Ruth, and Sean P. Ryder. "End-Labeling Oligonucleotides with Chemical Tags After Synthesis." In Recombinant and In Vitro RNA Synthesis. Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-113-4_14.

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Rodriguez, Pedro L., and Luis Carrasco. "Biotin-Labeled Riboprobes to Study RNA-Binding Proteins." In A Laboratory Guide to Biotin-Labeling in Biomolecule Analysis. Birkhäuser Basel, 1996. http://dx.doi.org/10.1007/978-3-0348-7349-9_13.

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Warminski, Marcin, Pawel J. Sikorski, Joanna Kowalska, and Jacek Jemielity. "Applications of Phosphate Modification and Labeling to Study (m)RNA Caps." In Phosphate Labeling and Sensing in Chemical Biology. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-60357-5_8.

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Stackhouse, Thomas M., and Claude F. Meares. "Quantitative photoaffinity labeling of Escherichia coli RNA polymerase transcription complexes by nascent RNA." In Photochemical Probes in Biochemistry. Springer Netherlands, 1989. http://dx.doi.org/10.1007/978-94-009-0925-0_20.

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Conference papers on the topic "RNA labeling"

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Wagenknecht, Hans-Achim. "Postsynthetic labeling of DNA and RNA by fluorophores." In XVIth Symposium on Chemistry of Nucleic Acid Components. Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2014. http://dx.doi.org/10.1135/css201414190.

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Hyunsun, Kim, Jae-Jin Choi, Minhye cho, and Heekyung Park. "Abstract 3008: PNA based microarray for cancer & stem cell related miRNAs profiling from low total RNA with on-chip labeling." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-3008.

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Darabi, Jeff. "High Performance Microfluidic-Based DNA Isolation Chip." In ASME 2013 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/sbc2013-14522.

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Magnetic separation is one of the effective ways to separate specific biological entities such as DNA/RNA, bacteria, and cells from their native environment for subsequent downstream analysis. The process involves the labeling of the desired biological entity with magnetic beads followed by separating the tagged entities via a magnetic separation device. In conventional tube-based magnetic separation, magnetically labeled biological entities are retained on the inner wall of the tube by applying an external magnet, while the supernatant is decanted off. Removing the tube from the magnetic field enables resuspension of the target entity. Although widely used, there are limitations to the conventional magnetic separation method. For example, there is a significant sample loss due to multiple sample handling, washing, and transfer. In addition, manual magnetic separation systems are labor intensive and their effectiveness is user-dependent.

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Meccariello, Angela. "RNA metabolic labeling in XX versus XX/XY embryos ofCeratitis capitataand RNAseqdifferential analysisas a tool to identify male-specific early zygotic genes." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.107782.

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Ringwelski, Beth, Vidura Jayasooriya, and Dharmakeerthi Nawarathna. "Label Free Cell Purification Following Electroporation." In 2020 Design of Medical Devices Conference. American Society of Mechanical Engineers, 2020. http://dx.doi.org/10.1115/dmd2020-9037.

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Abstract Cell transfection by electroporation is a biological assay that has been utilized to inject exogenous molecules (e.g.: RNA, DNA and protein) into live cells. Recently, electroporation has been utilized in developing cell therapy for cancer (e.g., CAR T-cell). One of the major drawbacks in current electroporation methods is the cell death during the process. These dead cells can be detrimental, if injected back to the patients. Current cell filtering methods are unable purify T-cells following electroporation, this is due to the lack of unique biomarkers that target the apoptosis and necrosis of T-cells. To address this issue, we have developed a method using dielectrophoresis and microfluidics, where no prior labeling is needed to isolate dead cells from live cells. Upon electroporation, the cell sample has to be flowed through the microfluidic chip where a selective electric field is applied through specially designed electrodes so that the dead cells are trapped on the electrodes, and the live cells are able to flow through and are collected at the end. Results after purification of the cells using our method reveal that it is possible to achieve ∼100% of purity in filtering of the live cells. This method presents a viable solution to a critical concern regarding CAR T-cell manufacturing. This paper presents an extended study of the variation of efficacy in the design with the time from the electroporation.

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Marquerie, G., A. Duperray, G. Uzan, and R. Berthier. "BIOSYNTHETIC PATHWAYS OF THE PLATELET FIBRINOGEN RECEPTOR IN HUMAN MEGAKARYOCYTES." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642954.

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Interaction between cells and between cells and extracellular matrices are critical for a number of biological processes, including organ development, cell differenciation, cell motility, and the inimune' response. These interactions are mediated by a family of adhesion receptors that recognize short sequences such as Arg-Gly-Asp (RGD). These receptors share similar structural properties. They are heterodimers composed of a and B subunits and sometime express common epitopes. This suggests that the structural and functional relationship of these receptors may result from the transcription of related genes or may arise from cell specific post-transcriptional events. Thus, analysis of the biosynthesis and processing of these receptors would provide valuable insights into the molecular mechanism which control their expression at the surface,of different cells. Platelet membrane glycoprotein (GP) IIb-IIIa is a member of this receptor family. This protein is a non covalent heterodimer composed of two distinct polypeptides, Glib which consists of two subunits Ilba and IlbB (Mr = 116 kD, Mr = 25 kD) and GPIIIa (Mr = 100 kD, reduced). GPIIb-IIIa functions at site of platelet aggregation and serves as receptor for RGD containing factors including fibrinogen, fibronectin and von Willebrand factor. We report here on the investigation of the biosynthetic pathways of this RGD receptor in human megakaryocytes. High number of megakaryocytic cells from the megakaryoblastic stage to the polyploid mature megakaryocyte were obtained from liquid culture of cryopreserved leukocyte stem cell concentrates from patients with chronic myelogenous leukemia (CML). After sorting, using a FACS IV and indirect immunofluores-cent labeling with monoclonal antibodies anti-GPIIb-IIIa, 95 % of the cells in culture were of the megakaryocytic lineage. These megakarocytes represented an excellent tool to delineate at the molecular level events associated with the biosynthesis of GPIIb-IIIa.Metabolic labeling and pulse-chase experiments indicated that GPIIb and GPIIIa are synthesized from separate mRNA and that the two subunits of GPIIb derive from a common precursor. This was further confirmed by cell-free translation of megakaryocyte mRNA and the identification of separate cDNA containing sequences coding for the pro-GPIIb and for GPIIIa. These cDNA were isolated from a Xgt11 expression library constructed with purified megakaryocyte RNA, and were used to size the messengers coding for the two polypeptides. A single mRNA species of 3.9 kB was found to encode the pro-GPIIb, whereas two different mRNA species of 2.9 kB and 4. 1 kB were identified with the GPIIIa cDNA.The newly synthesized GPIIIa associates early with the pro-GPIIb in the rough endoplasmic reticulum. Examination of the glycosylation pathways with endoglycosidase H, tunicamycin and monensin indicated that high mannose oligosaccharides are added to the GPIIIa and pro-GPIIb polypeptide backbone. The pro-GPIIb is then processed with conversion of high mannose to the complex type carbohydrate, whereas GPIIIa remains endoH sensitive. Glycosylation of pro-GPIIb-IIIa and processing of oligosaccharides are prerequisite for proteolytic maturation of pro-GPIIb and the expression of the mature complex at the surface of the cell. Thus post-translational processing of GPIIb-IIIa requires an early assembly of the complex. This may have important implications in the maturation of megakaryocyte granules and in the molecular mechanism underlying the Glanzmann thrombastenic disease.

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Wu, Xingyuan, Yonggang Qi, Jun Liu, and Jie Yang. "Sketchsegnet: A Rnn Model for Labeling Sketch Strokes." In 2018 IEEE 28th International Workshop on Machine Learning for Signal Processing (MLSP). IEEE, 2018. http://dx.doi.org/10.1109/mlsp.2018.8516988.

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Jagannatha, Abhyuday, and hong yu. "Structured prediction models for RNN based sequence labeling in clinical text." In Proceedings of the 2016 Conference on Empirical Methods in Natural Language Processing. Association for Computational Linguistics, 2016. http://dx.doi.org/10.18653/v1/d16-1082.

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Wang, Qingqing, and Yue Lu. "A Sequence Labeling Convolutional Network and Its Application to Handwritten String Recognition." In Twenty-Sixth International Joint Conference on Artificial Intelligence. International Joint Conferences on Artificial Intelligence Organization, 2017. http://dx.doi.org/10.24963/ijcai.2017/411.

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Handwritten string recognition has been struggling with connected patterns fiercely. Segmentation-free and over-segmentation frameworks are commonly applied to deal with this issue. For the past years, RNN combining with CTC has occupied the domain of segmentation-free handwritten string recognition, while CNN is just employed as a single character recognizer in the over-segmentation framework. The main challenges for CNN to directly recognize handwritten strings are the appropriate processing of arbitrary input string length, which implies arbitrary input image size, and reasonable design of the output layer. In this paper, we propose a sequence labeling convolutional network for the recognition of handwritten strings, in particular, the connected patterns. We properly design the structure of the network to predict how many characters present in the input images and what exactly they are at every position. Spatial pyramid pooling (SPP) is utilized with a new implementation to handle arbitrary string length. Moreover, we propose a more flexible pooling strategy called FSPP to adapt the network to the straightforward recognition of long strings better. Experiments conducted on handwritten digital strings from two benchmark datasets and our own cell-phone number dataset demonstrate the superiority of the proposed network.

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Ogura, M., N. Tanabe, M. Hamaguchi, T. Hotta та H. Saito. "BIOSYNTHESIS AND SECRETION OF β-THROMBOGLOBULIN BY A HUMAN MEGAKARYOBLASTIC CELL LINE ( MEG-01 )". У XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644618.

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β-Thromboglobulin ( βTG ) is a well known platelet specific a-granular protein, but synthesis of βTG by human megakaryocytes has not been fully proved. A human megakaryoblastic cell line ( MEG-01 ) was investigated for the presence of βJG in the culture medium and cell lysates using a specific radioimmunoassay ( RIA ). The concentration of βTG increased with time in the serum-free culture medium as well as in the cell lysates as shown in the following table.By an indirect immunofluorescent technique using a monospesific rabbit anti serum against human βTG, βTG antigen was detected in MEG-01 cells. Immunoblot analysis of culture medium revealed a single band ( mol wt 8,900 ) that is identical to the band of human plasma βTG. De novo synthesis of βTG was demonstrated by the presence of specific immunoprecipitable radioactivity in the medium after 5 h of labeling of the cells with [35S]-methionine as a 8,900 mol wt protein. These results indicate that human megakaryocytes produce βTG, The production of βTG by MEG-01 cells may be useful for the study of megakaryocyte maturation and differentiation.

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